Params: --no-stderr --filter 430 20 RF00010.cm @div1_4.list 1 specfile data/RF00010.filterspec Build: release Host: salal ----specfile: hmm data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,72,r-AG-U_-C,71,r-AG_-CU,117,r-AG-CU-_,144,r-AGU-C-_,163,r-AGU-C-_,162,l-AG_-CU,203,r-ACGU-_,202,l-ACGU-_,229,r-A_-GU-C,228,l-AG_-CU,262,l-AU-C-G-_,261,r-CGU-A_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,55,r-AGU-C_,72,r-AG-U_-C,71,r-AG_-CU,70,l-CU_-AG,117,r-AG-CU-_,116,r-AG-CU-_,144,r-AGU-C-_,143,r-AU-C-G-_,163,r-AGU-C-_,162,l-A-C-G-U-_,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,229,r-A_-GU-C,228,l-AG-C-U-_,262,r-AC-GU-_,261,r-CGU-A_,260,r-AG-CU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,55,r-AGU-C_,54,l-AGU-C_,72,r-AU-C-G-_,71,r-AG_-CU,70,l-CU_-AG,69,r-ACU-G_,117,r-AG-CU-_,116,r-ACU-G_,115,l-ACU-G_,144,r-AGU-C-_,143,r-AU-C-G-_,140,r-AGU_-C,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,229,r-AG-C-U-_,228,l-AG-C-U-_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,259,r-AG-CU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,55,r-AGU-C_,54,l-AGU-C_,53,l-AGU_-C,72,r-AU-C-G-_,71,r-AG_-CU,70,l-CU_-AG,69,r-ACU-G_,67,l-AC_-GU,117,r-AG-CU-_,116,r-AG-CU-_,115,l-ACU-G_,113,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-AG-C-U-_,161,r-CU_-AG,157,l-CU_-AG,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,178,l-ACGU-_,229,r-AG-C-U-_,228,l-AG-C-U-_,225,l-ACU-G_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,55,r-A_-GU-C,54,l-AGU-C_,53,l-AGU_-C,72,r-AU-C-G-_,71,l-A_-CU-G,70,l-CU_-AG,69,r-ACU-G_,67,l-AC_-GU,117,r-AG-CU-_,116,r-AG-CU-_,115,l-AG-CU-_,113,r-ACU_-G,144,r-AGU-C-_,143,l-AG-CU-_,142,l-ACG-U_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,157,l-CU_-AG,156,r-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,177,l-AGU-C-_,229,r-AG-C-U-_,228,l-AG-C-U-_,225,r-AG-CU-_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,255,l-ACGU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-C-U-_,56,l-ACU_-G,55,r-A_-GU-C,54,r-CU_-A-G,53,l-AGU_-C,72,r-AU-C-G-_,71,l-A_-CU-G,70,l-CU_-AG,69,r-ACU-G_,67,r-A_-CU-G,117,r-AG-CU-_,116,r-AG-CU-_,115,l-ACU-G_,114,r-ACG-U_,113,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,142,l-ACG-U_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,157,l-CU_-AG,156,r-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,178,l-ACGU-_,176,l-CGU-A_,229,r-AG-C-U-_,228,l-AG-C-U-_,225,r-AG-CU-_,224,l-A_-GU-C,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,255,l-ACGU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-C-U-_,56,l-ACU_-G,55,r-A_-GU-C,54,r-CU_-A-G,53,l-AGU_-C,72,r-AU-C-G-_,71,l-A_-CU-G,70,l-A_-CU-G,69,r-ACU-G_,67,r-A_-CU-G,117,r-AG-CU-_,116,r-AG-CU-_,115,l-AG-CU-_,113,r-ACU_-G,112,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,142,l-ACG-U_,141,r-ACU-G_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-AG-C-U-_,161,r-CU_-AG,157,l-CU_-AG,156,r-ACU_-G,154,l-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,177,l-AGU-C-_,176,l-CGU-A_,229,r-A_-GU-C,228,l-AG-C-U-_,227,r-AG-CU-_,225,r-AG-CU-_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,258,r-AGU-C_,255,l-ACGU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,222,61/sub,53,202/sub,67,162/sub,202,102/sub,175,430 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-C-U-_,56,l-ACU-G-_,55,r-A-C-G-U-_,54,r-CU_-A-G,53,l-AU_-C-G,72,r-AU-C-G-_,71,r-AU-C-G-_,70,l-A_-CU-G,69,r-A_-CU-G,67,r-U_-A-C-G,117,r-AG-CU-_,116,r-AG-CU-_,115,l-AG-CU-_,114,r-ACG-U_,113,r-ACU_-G,112,r-ACU_-G,108,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,142,l-ACU-G-_,141,r-ACU-G_,140,r-AGU-C-_,139,l-ACU_-G,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,159,l-AGU-C_,157,l-CU-A-G-_,156,r-ACU_-G,154,l-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,191,r-AGU-C_,178,l-ACGU-_,177,l-AGU-C-_,176,l-CGU-A_,229,r-AG-C-U-_,228,l-AG-C-U-_,227,r-AG-CU-_,225,r-AG-CU-_,224,l-A_-GU-C,223,r-ACU-G_,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,258,l-AG-CU-_,256,r-ACGU-_,255,l-ACGU-_ ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu Exploded HMM has 2282 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,72,r-AG-U_-C/remember-nuc,71,r-AG_-CU/remember-nuc,117,r-AG-CU-_/remember-nuc,144,r-AGU-C-_/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-AG_-CU/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,229,r-A_-GU-C/remember-nuc,228,l-AG_-CU/remember-nuc,262,l-AU-C-G-_/remember-nuc,261,r-CGU-A_ Exploded HMM has 4158 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-AGU-C_/remember-nuc,72,r-AG-U_-C/remember-nuc,71,r-AG_-CU/remember-nuc,70,l-CU_-AG/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,229,r-A_-GU-C/remember-nuc,228,l-AG-C-U-_/remember-nuc,262,r-AC-GU-_/remember-nuc,261,r-CGU-A_/remember-nuc,260,r-AG-CU-_ Exploded HMM has 7377 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-AGU-C_/remember-nuc,54,l-AGU-C_/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,r-AG_-CU/remember-nuc,70,l-CU_-AG/remember-nuc,69,r-ACU-G_/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-ACU-G_/remember-nuc,115,l-ACU-G_/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,140,r-AGU_-C/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,224,l-AG_-CU/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,259,r-AG-CU-_ Exploded HMM has 14893 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-AGU-C_/remember-nuc,54,l-AGU-C_/remember-nuc,53,l-AGU_-C/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,r-AG_-CU/remember-nuc,70,l-CU_-AG/remember-nuc,69,r-ACU-G_/remember-nuc,67,l-AC_-GU/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-ACU-G_/remember-nuc,113,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,140,r-AGU_-C/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-AG-C-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,157,l-CU_-AG/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,178,l-ACGU-_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,225,l-ACU-G_/remember-nuc,224,l-AG_-CU/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_ Exploded HMM has 24152 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-A_-GU-C/remember-nuc,54,l-AGU-C_/remember-nuc,53,l-AGU_-C/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,l-A_-CU-G/remember-nuc,70,l-CU_-AG/remember-nuc,69,r-ACU-G_/remember-nuc,67,l-AC_-GU/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-AG-CU-_/remember-nuc,113,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,l-AG-CU-_/remember-nuc,142,l-ACG-U_/remember-nuc,140,r-AGU_-C/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,157,l-CU_-AG/remember-nuc,156,r-ACU_-G/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,177,l-AGU-C-_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,225,r-AG-CU-_/remember-nuc,224,l-AG_-CU/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_/remember-nuc,255,l-ACGU-_ Exploded HMM has 31974 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-C-U-_/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-A_-GU-C/remember-nuc,54,r-CU_-A-G/remember-nuc,53,l-AGU_-C/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,l-A_-CU-G/remember-nuc,70,l-CU_-AG/remember-nuc,69,r-ACU-G_/remember-nuc,67,r-A_-CU-G/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-ACU-G_/remember-nuc,114,r-ACG-U_/remember-nuc,113,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,142,l-ACG-U_/remember-nuc,140,r-AGU_-C/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,157,l-CU_-AG/remember-nuc,156,r-ACU_-G/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,178,l-ACGU-_/remember-nuc,176,l-CGU-A_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,225,r-AG-CU-_/remember-nuc,224,l-A_-GU-C/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_/remember-nuc,255,l-ACGU-_ Exploded HMM has 49384 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-C-U-_/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-A_-GU-C/remember-nuc,54,r-CU_-A-G/remember-nuc,53,l-AGU_-C/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,l-A_-CU-G/remember-nuc,70,l-A_-CU-G/remember-nuc,69,r-ACU-G_/remember-nuc,67,r-A_-CU-G/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-AG-CU-_/remember-nuc,113,r-ACU_-G/remember-nuc,112,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,142,l-ACG-U_/remember-nuc,141,r-ACU-G_/remember-nuc,140,r-AGU_-C/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-AG-C-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,157,l-CU_-AG/remember-nuc,156,r-ACU_-G/remember-nuc,154,l-ACU_-G/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,177,l-AGU-C-_/remember-nuc,176,l-CGU-A_/remember-nuc,229,r-A_-GU-C/remember-nuc,228,l-AG-C-U-_/remember-nuc,227,r-AG-CU-_/remember-nuc,225,r-AG-CU-_/remember-nuc,224,l-AG_-CU/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_/remember-nuc,258,r-AGU-C_/remember-nuc,255,l-ACGU-_ ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,222,61/sub,53,202/sub,67,162/sub,202,102/sub,175,430 Exploded HMM has 168364 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-C-U-_/remember-nuc,56,l-ACU-G-_/remember-nuc,55,r-A-C-G-U-_/remember-nuc,54,r-CU_-A-G/remember-nuc,53,l-AU_-C-G/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,r-AU-C-G-_/remember-nuc,70,l-A_-CU-G/remember-nuc,69,r-A_-CU-G/remember-nuc,67,r-U_-A-C-G/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-AG-CU-_/remember-nuc,114,r-ACG-U_/remember-nuc,113,r-ACU_-G/remember-nuc,112,r-ACU_-G/remember-nuc,108,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,142,l-ACU-G-_/remember-nuc,141,r-ACU-G_/remember-nuc,140,r-AGU-C-_/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,159,l-AGU-C_/remember-nuc,157,l-CU-A-G-_/remember-nuc,156,r-ACU_-G/remember-nuc,154,l-ACU_-G/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,191,r-AGU-C_/remember-nuc,178,l-ACGU-_/remember-nuc,177,l-AGU-C-_/remember-nuc,176,l-CGU-A_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,227,r-AG-CU-_/remember-nuc,225,r-AG-CU-_/remember-nuc,224,l-A_-GU-C/remember-nuc,223,r-ACU-G_/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_/remember-nuc,258,l-AG-CU-_/remember-nuc,256,r-ACGU-_/remember-nuc,255,l-ACGU-_ ----cmFile: RF00010.cm (global) ----fastaFile: hum03.dat.fasta.gz ----fastaFile: hum10.dat.fasta.gz ----fastaFile: hum11.dat.fasta.gz ----fastaFile: hum12.dat.fasta.gz ----fastaFile: hum13.dat.fasta.gz ----fastaFile: hum20.dat.fasta.gz ----fastaFile: hum21.dat.fasta.gz ----fastaFile: hum22.dat.fasta.gz ----fastaFile: hum23.dat.fasta.gz ----fastaFile: hum24.dat.fasta.gz ----fastaFile: hum25.dat.fasta.gz ----fastaFile: hum26.dat.fasta.gz Found 0 hits. done 3.97572e+009 nucs (frac lets thru so far=7.12576e-007, 2d-fracLetsThru=3.93215e-007). Filter report: done 3.97572e+009 nucs (frac lets thru so far=0.363064, 2d-fracLetsThru=0.270402). Filter report: done 1.44344e+009 nucs (frac lets thru so far=0.18248, 2d-fracLetsThru=0.147697). Filter report: done 2.63398e+008 nucs (frac lets thru so far=0.263143, 2d-fracLetsThru=0.24688). Filter report: done 6.93115e+007 nucs (frac lets thru so far=0.225676, 2d-fracLetsThru=0.21929). Filter report: done 1.5642e+007 nucs (frac lets thru so far=0.179991, 2d-fracLetsThru=0.176665). Filter report: done 2.81542e+006 nucs (frac lets thru so far=0.282704, 2d-fracLetsThru=0.279322). Filter report: done 795929 nucs (frac lets thru so far=0.361536, 2d-fracLetsThru=0.361025). Filter report: done 287757 nucs (frac lets thru so far=0.34535, 2d-fracLetsThru=0.348958). Filter report: done 99377 nucs (frac lets thru so far=0.0886926, 2d-fracLetsThru=0.0856595). Filter report: done 8814 nucs (frac lets thru so far=0.32142, 2d-fracLetsThru=0.341507). FULL: done 3.97572e+009 nucs (frac lets thru so far=7.12576e-007, 2d-fracLetsThru=3.93215e-007). CPU time: 561528.88u 155:58:48.88 Elapsed: 155:58:49 Params: --no-stderr --filter 430 20 RF00010.cm @div2_4.list 1 specfile data/RF00010.filterspec Build: release Host: cress ----specfile: hmm data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,72,r-AG-U_-C,71,r-AG_-CU,117,r-AG-CU-_,144,r-AGU-C-_,163,r-AGU-C-_,162,l-AG_-CU,203,r-ACGU-_,202,l-ACGU-_,229,r-A_-GU-C,228,l-AG_-CU,262,l-AU-C-G-_,261,r-CGU-A_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,55,r-AGU-C_,72,r-AG-U_-C,71,r-AG_-CU,70,l-CU_-AG,117,r-AG-CU-_,116,r-AG-CU-_,144,r-AGU-C-_,143,r-AU-C-G-_,163,r-AGU-C-_,162,l-A-C-G-U-_,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,229,r-A_-GU-C,228,l-AG-C-U-_,262,r-AC-GU-_,261,r-CGU-A_,260,r-AG-CU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,55,r-AGU-C_,54,l-AGU-C_,72,r-AU-C-G-_,71,r-AG_-CU,70,l-CU_-AG,69,r-ACU-G_,117,r-AG-CU-_,116,r-ACU-G_,115,l-ACU-G_,144,r-AGU-C-_,143,r-AU-C-G-_,140,r-AGU_-C,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,229,r-AG-C-U-_,228,l-AG-C-U-_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,259,r-AG-CU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,55,r-AGU-C_,54,l-AGU-C_,53,l-AGU_-C,72,r-AU-C-G-_,71,r-AG_-CU,70,l-CU_-AG,69,r-ACU-G_,67,l-AC_-GU,117,r-AG-CU-_,116,r-AG-CU-_,115,l-ACU-G_,113,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-AG-C-U-_,161,r-CU_-AG,157,l-CU_-AG,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,178,l-ACGU-_,229,r-AG-C-U-_,228,l-AG-C-U-_,225,l-ACU-G_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,55,r-A_-GU-C,54,l-AGU-C_,53,l-AGU_-C,72,r-AU-C-G-_,71,l-A_-CU-G,70,l-CU_-AG,69,r-ACU-G_,67,l-AC_-GU,117,r-AG-CU-_,116,r-AG-CU-_,115,l-AG-CU-_,113,r-ACU_-G,144,r-AGU-C-_,143,l-AG-CU-_,142,l-ACG-U_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,157,l-CU_-AG,156,r-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,177,l-AGU-C-_,229,r-AG-C-U-_,228,l-AG-C-U-_,225,r-AG-CU-_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,255,l-ACGU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-C-U-_,56,l-ACU_-G,55,r-A_-GU-C,54,r-CU_-A-G,53,l-AGU_-C,72,r-AU-C-G-_,71,l-A_-CU-G,70,l-CU_-AG,69,r-ACU-G_,67,r-A_-CU-G,117,r-AG-CU-_,116,r-AG-CU-_,115,l-ACU-G_,114,r-ACG-U_,113,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,142,l-ACG-U_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,157,l-CU_-AG,156,r-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,178,l-ACGU-_,176,l-CGU-A_,229,r-AG-C-U-_,228,l-AG-C-U-_,225,r-AG-CU-_,224,l-A_-GU-C,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,255,l-ACGU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-C-U-_,56,l-ACU_-G,55,r-A_-GU-C,54,r-CU_-A-G,53,l-AGU_-C,72,r-AU-C-G-_,71,l-A_-CU-G,70,l-A_-CU-G,69,r-ACU-G_,67,r-A_-CU-G,117,r-AG-CU-_,116,r-AG-CU-_,115,l-AG-CU-_,113,r-ACU_-G,112,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,142,l-ACG-U_,141,r-ACU-G_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-AG-C-U-_,161,r-CU_-AG,157,l-CU_-AG,156,r-ACU_-G,154,l-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,177,l-AGU-C-_,176,l-CGU-A_,229,r-A_-GU-C,228,l-AG-C-U-_,227,r-AG-CU-_,225,r-AG-CU-_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,258,r-AGU-C_,255,l-ACGU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,222,61/sub,53,202/sub,67,162/sub,202,102/sub,175,430 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-C-U-_,56,l-ACU-G-_,55,r-A-C-G-U-_,54,r-CU_-A-G,53,l-AU_-C-G,72,r-AU-C-G-_,71,r-AU-C-G-_,70,l-A_-CU-G,69,r-A_-CU-G,67,r-U_-A-C-G,117,r-AG-CU-_,116,r-AG-CU-_,115,l-AG-CU-_,114,r-ACG-U_,113,r-ACU_-G,112,r-ACU_-G,108,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,142,l-ACU-G-_,141,r-ACU-G_,140,r-AGU-C-_,139,l-ACU_-G,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,159,l-AGU-C_,157,l-CU-A-G-_,156,r-ACU_-G,154,l-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,191,r-AGU-C_,178,l-ACGU-_,177,l-AGU-C-_,176,l-CGU-A_,229,r-AG-C-U-_,228,l-AG-C-U-_,227,r-AG-CU-_,225,r-AG-CU-_,224,l-A_-GU-C,223,r-ACU-G_,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,258,l-AG-CU-_,256,r-ACGU-_,255,l-ACGU-_ ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu Exploded HMM has 2282 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,72,r-AG-U_-C/remember-nuc,71,r-AG_-CU/remember-nuc,117,r-AG-CU-_/remember-nuc,144,r-AGU-C-_/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-AG_-CU/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,229,r-A_-GU-C/remember-nuc,228,l-AG_-CU/remember-nuc,262,l-AU-C-G-_/remember-nuc,261,r-CGU-A_ Exploded HMM has 4158 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-AGU-C_/remember-nuc,72,r-AG-U_-C/remember-nuc,71,r-AG_-CU/remember-nuc,70,l-CU_-AG/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,229,r-A_-GU-C/remember-nuc,228,l-AG-C-U-_/remember-nuc,262,r-AC-GU-_/remember-nuc,261,r-CGU-A_/remember-nuc,260,r-AG-CU-_ Exploded HMM has 7377 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-AGU-C_/remember-nuc,54,l-AGU-C_/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,r-AG_-CU/remember-nuc,70,l-CU_-AG/remember-nuc,69,r-ACU-G_/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-ACU-G_/remember-nuc,115,l-ACU-G_/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,140,r-AGU_-C/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,224,l-AG_-CU/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,259,r-AG-CU-_ Exploded HMM has 14893 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-AGU-C_/remember-nuc,54,l-AGU-C_/remember-nuc,53,l-AGU_-C/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,r-AG_-CU/remember-nuc,70,l-CU_-AG/remember-nuc,69,r-ACU-G_/remember-nuc,67,l-AC_-GU/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-ACU-G_/remember-nuc,113,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,140,r-AGU_-C/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-AG-C-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,157,l-CU_-AG/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,178,l-ACGU-_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,225,l-ACU-G_/remember-nuc,224,l-AG_-CU/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_ Exploded HMM has 24152 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-A_-GU-C/remember-nuc,54,l-AGU-C_/remember-nuc,53,l-AGU_-C/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,l-A_-CU-G/remember-nuc,70,l-CU_-AG/remember-nuc,69,r-ACU-G_/remember-nuc,67,l-AC_-GU/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-AG-CU-_/remember-nuc,113,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,l-AG-CU-_/remember-nuc,142,l-ACG-U_/remember-nuc,140,r-AGU_-C/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,157,l-CU_-AG/remember-nuc,156,r-ACU_-G/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,177,l-AGU-C-_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,225,r-AG-CU-_/remember-nuc,224,l-AG_-CU/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_/remember-nuc,255,l-ACGU-_ Exploded HMM has 31974 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-C-U-_/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-A_-GU-C/remember-nuc,54,r-CU_-A-G/remember-nuc,53,l-AGU_-C/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,l-A_-CU-G/remember-nuc,70,l-CU_-AG/remember-nuc,69,r-ACU-G_/remember-nuc,67,r-A_-CU-G/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-ACU-G_/remember-nuc,114,r-ACG-U_/remember-nuc,113,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,142,l-ACG-U_/remember-nuc,140,r-AGU_-C/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,157,l-CU_-AG/remember-nuc,156,r-ACU_-G/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,178,l-ACGU-_/remember-nuc,176,l-CGU-A_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,225,r-AG-CU-_/remember-nuc,224,l-A_-GU-C/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_/remember-nuc,255,l-ACGU-_ Exploded HMM has 49384 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-C-U-_/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-A_-GU-C/remember-nuc,54,r-CU_-A-G/remember-nuc,53,l-AGU_-C/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,l-A_-CU-G/remember-nuc,70,l-A_-CU-G/remember-nuc,69,r-ACU-G_/remember-nuc,67,r-A_-CU-G/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-AG-CU-_/remember-nuc,113,r-ACU_-G/remember-nuc,112,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,142,l-ACG-U_/remember-nuc,141,r-ACU-G_/remember-nuc,140,r-AGU_-C/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-AG-C-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,157,l-CU_-AG/remember-nuc,156,r-ACU_-G/remember-nuc,154,l-ACU_-G/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,177,l-AGU-C-_/remember-nuc,176,l-CGU-A_/remember-nuc,229,r-A_-GU-C/remember-nuc,228,l-AG-C-U-_/remember-nuc,227,r-AG-CU-_/remember-nuc,225,r-AG-CU-_/remember-nuc,224,l-AG_-CU/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_/remember-nuc,258,r-AGU-C_/remember-nuc,255,l-ACGU-_ ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,222,61/sub,53,202/sub,67,162/sub,202,102/sub,175,430 Exploded HMM has 168364 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-C-U-_/remember-nuc,56,l-ACU-G-_/remember-nuc,55,r-A-C-G-U-_/remember-nuc,54,r-CU_-A-G/remember-nuc,53,l-AU_-C-G/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,r-AU-C-G-_/remember-nuc,70,l-A_-CU-G/remember-nuc,69,r-A_-CU-G/remember-nuc,67,r-U_-A-C-G/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-AG-CU-_/remember-nuc,114,r-ACG-U_/remember-nuc,113,r-ACU_-G/remember-nuc,112,r-ACU_-G/remember-nuc,108,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,142,l-ACU-G-_/remember-nuc,141,r-ACU-G_/remember-nuc,140,r-AGU-C-_/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,159,l-AGU-C_/remember-nuc,157,l-CU-A-G-_/remember-nuc,156,r-ACU_-G/remember-nuc,154,l-ACU_-G/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,191,r-AGU-C_/remember-nuc,178,l-ACGU-_/remember-nuc,177,l-AGU-C-_/remember-nuc,176,l-CGU-A_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,227,r-AG-CU-_/remember-nuc,225,r-AG-CU-_/remember-nuc,224,l-A_-GU-C/remember-nuc,223,r-ACU-G_/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_/remember-nuc,258,l-AG-CU-_/remember-nuc,256,r-ACGU-_/remember-nuc,255,l-ACGU-_ ----cmFile: RF00010.cm (global) ----fastaFile: hum01.dat.fasta.gz ----fastaFile: hum02.dat.fasta.gz ----fastaFile: hum04.dat.fasta.gz ----fastaFile: hum05.dat.fasta.gz ----fastaFile: hum06.dat.fasta.gz ----fastaFile: hum07.dat.fasta.gz ----fastaFile: hum08.dat.fasta.gz ----fastaFile: hum09.dat.fasta.gz ----fastaFile: hum14.dat.fasta.gz ----fastaFile: hum15.dat.fasta.gz ----fastaFile: hum16.dat.fasta.gz ----fastaFile: hum17.dat.fasta.gz ----fastaFile: hum18.dat.fasta.gz ----fastaFile: hum19.dat.fasta.gz Found 0 hits. done 4.02417e+009 nucs (frac lets thru so far=1.07997e-006, 2d-fracLetsThru=5.54642e-007). Filter report: done 4.02417e+009 nucs (frac lets thru so far=0.376275, 2d-fracLetsThru=0.28132). Filter report: done 1.5142e+009 nucs (frac lets thru so far=0.185373, 2d-fracLetsThru=0.149631). Filter report: done 2.80692e+008 nucs (frac lets thru so far=0.262469, 2d-fracLetsThru=0.245642). Filter report: done 7.36729e+007 nucs (frac lets thru so far=0.224437, 2d-fracLetsThru=0.217445). Filter report: done 1.65349e+007 nucs (frac lets thru so far=0.180783, 2d-fracLetsThru=0.177689). Filter report: done 2.98923e+006 nucs (frac lets thru so far=0.285805, 2d-fracLetsThru=0.283525). Filter report: done 854337 nucs (frac lets thru so far=0.355032, 2d-fracLetsThru=0.35529). Filter report: done 303317 nucs (frac lets thru so far=0.35782, 2d-fracLetsThru=0.361452). Filter report: done 108533 nucs (frac lets thru so far=0.0762717, 2d-fracLetsThru=0.0802436). Filter report: done 8278 nucs (frac lets thru so far=0.525006, 2d-fracLetsThru=0.475166). FULL: done 4.02417e+009 nucs (frac lets thru so far=1.07997e-006, 2d-fracLetsThru=5.54642e-007). CPU time: 579618.14u 161:00:18.14 Elapsed: 161:00:18 Params: ./cmzasha --no-stderr --filter 430 20 Rfam/cm/RF00010.cm @/projects/bio/zasha/seqs/embl_release76/div3_4.list 1 specfile data/RF00010.filterspec Build: release Host: xmen.cs.washington.edu pid: 13508 ----specfile: hmm data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,72,r-AG-U_-C,71,r-AG_-CU,117,r-AG-CU-_,144,r-AGU-C-_,163,r-AGU-C-_,162,l-AG_-CU,203,r-ACGU-_,202,l-ACGU-_,229,r-A_-GU-C,228,l-AG_-CU,262,l-AU-C-G-_,261,r-CGU-A_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,55,r-AGU-C_,72,r-AG-U_-C,71,r-AG_-CU,70,l-CU_-AG,117,r-AG-CU-_,116,r-AG-CU-_,144,r-AGU-C-_,143,r-AU-C-G-_,163,r-AGU-C-_,162,l-A-C-G-U-_,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,229,r-A_-GU-C,228,l-AG-C-U-_,262,r-AC-GU-_,261,r-CGU-A_,260,r-AG-CU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,55,r-AGU-C_,54,l-AGU-C_,72,r-AU-C-G-_,71,r-AG_-CU,70,l-CU_-AG,69,r-ACU-G_,117,r-AG-CU-_,116,r-ACU-G_,115,l-ACU-G_,144,r-AGU-C-_,143,r-AU-C-G-_,140,r-AGU_-C,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,229,r-AG-C-U-_,228,l-AG-C-U-_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,259,r-AG-CU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,55,r-AGU-C_,54,l-AGU-C_,53,l-AGU_-C,72,r-AU-C-G-_,71,r-AG_-CU,70,l-CU_-AG,69,r-ACU-G_,67,l-AC_-GU,117,r-AG-CU-_,116,r-AG-CU-_,115,l-ACU-G_,113,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-AG-C-U-_,161,r-CU_-AG,157,l-CU_-AG,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,178,l-ACGU-_,229,r-AG-C-U-_,228,l-AG-C-U-_,225,l-ACU-G_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-U_-C,56,l-ACU_-G,55,r-A_-GU-C,54,l-AGU-C_,53,l-AGU_-C,72,r-AU-C-G-_,71,l-A_-CU-G,70,l-CU_-AG,69,r-ACU-G_,67,l-AC_-GU,117,r-AG-CU-_,116,r-AG-CU-_,115,l-AG-CU-_,113,r-ACU_-G,144,r-AGU-C-_,143,l-AG-CU-_,142,l-ACG-U_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,157,l-CU_-AG,156,r-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,177,l-AGU-C-_,229,r-AG-C-U-_,228,l-AG-C-U-_,225,r-AG-CU-_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,255,l-ACGU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-C-U-_,56,l-ACU_-G,55,r-A_-GU-C,54,r-CU_-A-G,53,l-AGU_-C,72,r-AU-C-G-_,71,l-A_-CU-G,70,l-CU_-AG,69,r-ACU-G_,67,r-A_-CU-G,117,r-AG-CU-_,116,r-AG-CU-_,115,l-ACU-G_,114,r-ACG-U_,113,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,142,l-ACG-U_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,157,l-CU_-AG,156,r-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,178,l-ACGU-_,176,l-CGU-A_,229,r-AG-C-U-_,228,l-AG-C-U-_,225,r-AG-CU-_,224,l-A_-GU-C,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,255,l-ACGU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-C-U-_,56,l-ACU_-G,55,r-A_-GU-C,54,r-CU_-A-G,53,l-AGU_-C,72,r-AU-C-G-_,71,l-A_-CU-G,70,l-A_-CU-G,69,r-ACU-G_,67,r-A_-CU-G,117,r-AG-CU-_,116,r-AG-CU-_,115,l-AG-CU-_,113,r-ACU_-G,112,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,142,l-ACG-U_,141,r-ACU-G_,140,r-AGU_-C,139,l-ACU_-G,163,r-AGU-C-_,162,l-AG-C-U-_,161,r-CU_-AG,157,l-CU_-AG,156,r-ACU_-G,154,l-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,177,l-AGU-C-_,176,l-CGU-A_,229,r-A_-GU-C,228,l-AG-C-U-_,227,r-AG-CU-_,225,r-AG-CU-_,224,l-AG_-CU,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,258,r-AGU-C_,255,l-ACGU-_ 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,222,61/sub,53,202/sub,67,162/sub,202,102/sub,175,430 2struct-str data/TryAllCm_5.0/RF00010_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,57,r-AG-C-U-_,56,l-ACU-G-_,55,r-A-C-G-U-_,54,r-CU_-A-G,53,l-AU_-C-G,72,r-AU-C-G-_,71,r-AU-C-G-_,70,l-A_-CU-G,69,r-A_-CU-G,67,r-U_-A-C-G,117,r-AG-CU-_,116,r-AG-CU-_,115,l-AG-CU-_,114,r-ACG-U_,113,r-ACU_-G,112,r-ACU_-G,108,r-ACU_-G,144,r-AGU-C-_,143,r-AU-C-G-_,142,l-ACU-G-_,141,r-ACU-G_,140,r-AGU-C-_,139,l-ACU_-G,163,r-AGU-C-_,162,l-A-C-G-U-_,161,r-CU_-AG,159,l-AGU-C_,157,l-CU-A-G-_,156,r-ACU_-G,154,l-ACU_-G,203,r-ACGU-_,202,l-ACGU-_,197,r-ACGU-_,196,l-ACGU-_,191,r-AGU-C_,178,l-ACGU-_,177,l-AGU-C-_,176,l-CGU-A_,229,r-AG-C-U-_,228,l-AG-C-U-_,227,r-AG-CU-_,225,r-AG-CU-_,224,l-A_-GU-C,223,r-ACU-G_,262,r-AC-GU-_,261,l-AG-CU-_,260,r-AG-CU-_,259,r-AG-CU-_,258,l-AG-CU-_,256,r-ACGU-_,255,l-ACGU-_ ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu Exploded HMM has 2282 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,72,r-AG-U_-C/remember-nuc,71,r-AG_-CU/remember-nuc,117,r-AG-CU-_/remember-nuc,144,r-AGU-C-_/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-AG_-CU/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,229,r-A_-GU-C/remember-nuc,228,l-AG_-CU/remember-nuc,262,l-AU-C-G-_/remember-nuc,261,r-CGU-A_ Exploded HMM has 4158 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-AGU-C_/remember-nuc,72,r-AG-U_-C/remember-nuc,71,r-AG_-CU/remember-nuc,70,l-CU_-AG/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,229,r-A_-GU-C/remember-nuc,228,l-AG-C-U-_/remember-nuc,262,r-AC-GU-_/remember-nuc,261,r-CGU-A_/remember-nuc,260,r-AG-CU-_ Exploded HMM has 7377 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-AGU-C_/remember-nuc,54,l-AGU-C_/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,r-AG_-CU/remember-nuc,70,l-CU_-AG/remember-nuc,69,r-ACU-G_/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-ACU-G_/remember-nuc,115,l-ACU-G_/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,140,r-AGU_-C/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,224,l-AG_-CU/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,259,r-AG-CU-_ Exploded HMM has 14893 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-AGU-C_/remember-nuc,54,l-AGU-C_/remember-nuc,53,l-AGU_-C/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,r-AG_-CU/remember-nuc,70,l-CU_-AG/remember-nuc,69,r-ACU-G_/remember-nuc,67,l-AC_-GU/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-ACU-G_/remember-nuc,113,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,140,r-AGU_-C/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-AG-C-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,157,l-CU_-AG/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,178,l-ACGU-_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,225,l-ACU-G_/remember-nuc,224,l-AG_-CU/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_ Exploded HMM has 24152 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-U_-C/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-A_-GU-C/remember-nuc,54,l-AGU-C_/remember-nuc,53,l-AGU_-C/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,l-A_-CU-G/remember-nuc,70,l-CU_-AG/remember-nuc,69,r-ACU-G_/remember-nuc,67,l-AC_-GU/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-AG-CU-_/remember-nuc,113,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,l-AG-CU-_/remember-nuc,142,l-ACG-U_/remember-nuc,140,r-AGU_-C/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,157,l-CU_-AG/remember-nuc,156,r-ACU_-G/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,177,l-AGU-C-_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,225,r-AG-CU-_/remember-nuc,224,l-AG_-CU/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_/remember-nuc,255,l-ACGU-_ Exploded HMM has 31974 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-C-U-_/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-A_-GU-C/remember-nuc,54,r-CU_-A-G/remember-nuc,53,l-AGU_-C/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,l-A_-CU-G/remember-nuc,70,l-CU_-AG/remember-nuc,69,r-ACU-G_/remember-nuc,67,r-A_-CU-G/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-ACU-G_/remember-nuc,114,r-ACG-U_/remember-nuc,113,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,142,l-ACG-U_/remember-nuc,140,r-AGU_-C/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,157,l-CU_-AG/remember-nuc,156,r-ACU_-G/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,178,l-ACGU-_/remember-nuc,176,l-CGU-A_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,225,r-AG-CU-_/remember-nuc,224,l-A_-GU-C/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_/remember-nuc,255,l-ACGU-_ Exploded HMM has 49384 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-C-U-_/remember-nuc,56,l-ACU_-G/remember-nuc,55,r-A_-GU-C/remember-nuc,54,r-CU_-A-G/remember-nuc,53,l-AGU_-C/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,l-A_-CU-G/remember-nuc,70,l-A_-CU-G/remember-nuc,69,r-ACU-G_/remember-nuc,67,r-A_-CU-G/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-AG-CU-_/remember-nuc,113,r-ACU_-G/remember-nuc,112,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,142,l-ACG-U_/remember-nuc,141,r-ACU-G_/remember-nuc,140,r-AGU_-C/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-AG-C-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,157,l-CU_-AG/remember-nuc,156,r-ACU_-G/remember-nuc,154,l-ACU_-G/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,177,l-AGU-C-_/remember-nuc,176,l-CGU-A_/remember-nuc,229,r-A_-GU-C/remember-nuc,228,l-AG-C-U-_/remember-nuc,227,r-AG-CU-_/remember-nuc,225,r-AG-CU-_/remember-nuc,224,l-AG_-CU/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_/remember-nuc,258,r-AGU-C_/remember-nuc,255,l-ACGU-_ ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,222,61/sub,53,202/sub,67,162/sub,202,102/sub,175,430 Exploded HMM has 168364 states ----hmm-from-cmFileName: Rfam/cm/RF00010.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00010.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,57,r-AG-C-U-_/remember-nuc,56,l-ACU-G-_/remember-nuc,55,r-A-C-G-U-_/remember-nuc,54,r-CU_-A-G/remember-nuc,53,l-AU_-C-G/remember-nuc,72,r-AU-C-G-_/remember-nuc,71,r-AU-C-G-_/remember-nuc,70,l-A_-CU-G/remember-nuc,69,r-A_-CU-G/remember-nuc,67,r-U_-A-C-G/remember-nuc,117,r-AG-CU-_/remember-nuc,116,r-AG-CU-_/remember-nuc,115,l-AG-CU-_/remember-nuc,114,r-ACG-U_/remember-nuc,113,r-ACU_-G/remember-nuc,112,r-ACU_-G/remember-nuc,108,r-ACU_-G/remember-nuc,144,r-AGU-C-_/remember-nuc,143,r-AU-C-G-_/remember-nuc,142,l-ACU-G-_/remember-nuc,141,r-ACU-G_/remember-nuc,140,r-AGU-C-_/remember-nuc,139,l-ACU_-G/remember-nuc,163,r-AGU-C-_/remember-nuc,162,l-A-C-G-U-_/remember-nuc,161,r-CU_-AG/remember-nuc,159,l-AGU-C_/remember-nuc,157,l-CU-A-G-_/remember-nuc,156,r-ACU_-G/remember-nuc,154,l-ACU_-G/remember-nuc,203,r-ACGU-_/remember-nuc,202,l-ACGU-_/remember-nuc,197,r-ACGU-_/remember-nuc,196,l-ACGU-_/remember-nuc,191,r-AGU-C_/remember-nuc,178,l-ACGU-_/remember-nuc,177,l-AGU-C-_/remember-nuc,176,l-CGU-A_/remember-nuc,229,r-AG-C-U-_/remember-nuc,228,l-AG-C-U-_/remember-nuc,227,r-AG-CU-_/remember-nuc,225,r-AG-CU-_/remember-nuc,224,l-A_-GU-C/remember-nuc,223,r-ACU-G_/remember-nuc,262,r-AC-GU-_/remember-nuc,261,l-AG-CU-_/remember-nuc,260,r-AG-CU-_/remember-nuc,259,r-AG-CU-_/remember-nuc,258,l-AG-CU-_/remember-nuc,256,r-ACGU-_/remember-nuc,255,l-ACGU-_ ----cmFile: Rfam/cm/RF00010.cm (global) ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #7009,sp|AB046578.1|AB046578 Treponema medium flagellar gene region (flgE to Tp0494 gene), complete cds. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGACUCCUUCGGAAAUGAUGCCGGUUAACGGCCGGGCGCUUGUAUUGUAAAAUGCAGGCGACAGACAGCGCAACAGAAAAUAAACCGCCGGUAAAACGGUAAGGGUGAAAAGGCGGGGUAAGAGCCCACCGCGCUUCCGGUAACGGGGUGGCAGUGCAAGCCUCAUCAGGAGCAAAAUUGAAUAGUAAAGGAUAUCCGAUCAGGGCAAGACGGUGAUCGAAGCCUUUCCGGAAUCGCAUCAGGCCGAUUGUUAUCGUAAGCUCGCCGAAGCAAUCCUUGCGAG hit 0 : 15267 15560 (fwd) 162.55 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<......___ 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGgg......GcG 54 GAGGAAAGUCCGG CUCC + GG A:G:UGC:GG:UAACG:CC:G:CG:: G++ 15267 GAGGAAAGUCCGGACUCCUUCGGAAAUGAUGCCGGUUAACGGCCGGGCGCUuguauuGUA 15326 _......>>>>->((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>> 55 A......ccCgAgGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGG 108 A ::CGA::GA AG::C:ACAGAAAA A+ACCGCC: U A+ :GG 15327 AaaugcaGGCGACAGACAGCGCAACAGAAAAUAAACCGCCGG-----UAAA-----ACGG 15376 >-->>,,,,,,,<<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->,,)))- 109 UAAGGGUGAAAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGCAcGGUA 168 UAAGGGUGAAAAGG:G:GGUAAGAGC:C:CCGC C: CCGGU+ACGG :G GGCA :G:A 15377 UAAGGGUGAAAAGGCGGGGUAAGAGCCCACCGCGCUUCCGGUAACGG-GGUGGCAGUGCA 15435 -))))]]]]]]]]],,,<<<<------<<<<<-<<.............--<<________ 169 AACCCCACCcGGAGCAAGaCCAAAUAGGgaagCgu.............AugGgGcGGCCC 215 A:CC:CA:C:GGAGCAA:A+ AAUAG::AAG +U A+:: G +G +C 15436 AGCCUCAUCAGGAGCAAAAUUGAAUAGUAAAGGAUauccgaucagggcAAGACGGUGAUC 15495 >>-->>>>>>>----->>>>,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,, 216 GccCcgcuucCGGGUAGGuCGCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUC 275 :: C CUU:: GG A U:GC U AG+ +C GAU+ 15496 GAAGC-CUUUCCGGAA--UCGCAUCAGG----------------CC----------GAUU 15526 ,,,,,<<<<<<<<<.............>>>>>>>>>::::::::::::::::: 276 GcCCAcccccgccg.............cggcgggggcgACAGAACCCGGCUUA 315 G+ :C::::: :::::G: 15527 GUU--AUCGUAAGCucgccgaagcaauCCUUGCGAG----------------- 15560 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #7189,sp|AB047584.1|AB047584 Vibrio parahaemolyticus rnpB, ORF1, ORF2 genes, partial cds. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGGCUUCAUAGAGCAAGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUACGACAAGUGCAGCAGAGAGAAGACCGCCGAUGGCCCGCAAGGGAACAGGUAAGGGUGAAAGGGUGCGGUAAGAGCGCACCGGACGACUAGUAAUAGUUCGUAGCAGGGUAAACUCCACCUGAAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAAGGAGGCGGGUAGGUUGCUCGAGCCAGUGAGUGAUUGCUGGCCUAGACGAAUGGCUACCGCCGCGCAAGCGGAACAGAACCCGGCUUA hit 1 : 547 856 (fwd) 338.99 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCU:CA+AG+GCA:GGUGC::GGUAACGCC::G::GG:GC+A:CC:A 547 GAGGAAAGUCCGGGCUUCAUAGAGCAAGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUA 606 >((---(((((,,,,,,,,,,,,<<<<<..<<<<__________>>.>>>>>-->>,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCC..uggcCggUUagggGgc.caGGUAAGGGUGA 117 :G: AAGUGC: CAGA+A+ AGACCGCC UG CC+ +A+ GGG CAGGUAAGGGUGA 607 CGACAAGUGCAGCAGAGAGAAGACCGCCgaUGGCCC-GCAA-GGGAaCAGGUAAGGGUGA 664 ,,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))--))))]]] 118 AAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUAAACCCCAC 176 AA GGUGCGGUAAGAGCGCACCG :C::C::GU+A::G ::G: GCA :GUAAAC:CCAC 665 AAGGGUGCGGUAAGAGCGCACCGGACGACUAGUAAUAGuUCGUAGCAGGGUAAACUCCAC 724 ]]]]]],,,<<<<------<<<<<-<<--<<________>>-->.>>>>>>----->>>> 177 CcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc.gcuucCGGGUAGGuC 235 C:G:AGCAA:ACCAAAUAGG::::C: AU:G G++GC+CG: :::::CGGGUAGGU: 725 CUGAAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAaGGAGGCGGGUAGGUU 784 ,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>> 236 GCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcgg 295 GCU GAG:C:G:+:G++A:+:C:G:CCUAGA GAAUG++++CC :CC:C G: 785 GCUCGAGCCAGUGAGUGAUUGCUGGCCUAGACGAAUGGCUACC--GCCGCGC----AAGC 838 >>>::::::::::::::::: 296 gggcgACAGAACCCGGCUUA 315 GG: ACAGAACCCGGCUUA 839 GGA--ACAGAACCCGGCUUA 856 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #7190,sp|AB047585.1|AB047585 Vibrio proteolyticus rnpB, ORF1, ORF2, ORF3, ORF4 genes, partial and complete cds. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGGCUCCAUAGAGCAGGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUACGACAAGUGCAGCAGAGAGAAGACCGCCGAUGGCCCGUAAGGGAUCAGGUAAGGGUGAAAGGGUGCGGUAAGAGCGCACCGGACGACUGGCAACAGUUCGUUGCAAGGUAAACUCCACCCGGAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAAGGAGGCGGGUAGGUUGCUUGAGCCAGUGAGCGAUUGCUGGCCUAGACGAAUGGCUACUGCCGCGCAAGCGGAACAGAACCCGGCUUA hit 2 : 518 827 (fwd) 350.41 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCUCCA+AG+GCAGGGUGC::GGUAACGCC::G::GG:GC+A:CC:A 518 GAGGAAAGUCCGGGCUCCAUAGAGCAGGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUA 577 >((---(((((,,,,,,,,,,,,<<<<<..<<<<__________>.>>>>>>-->>,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCC..uggcCggUUagggGg.ccaGGUAAGGGUGA 117 :G: AAGUGC: CAGA+A+ AGACCGCC UG:CC+GU AG GG :CAGGUAAGGGUGA 578 CGACAAGUGCAGCAGAGAGAAGACCGCCgaUGGCCCGUAAG--GGaUCAGGUAAGGGUGA 635 ,,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))--))))]]] 118 AAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUAAACCCCAC 176 AA GGUGCGGUAAGAGCGCACCG :C::C:GG++AC:G ::G: GCA+:GUAAAC:CCAC 636 AAGGGUGCGGUAAGAGCGCACCGGACGACUGGCAACAGuUCGUUGCAAGGUAAACUCCAC 695 ]]]]]],,,<<<<------<<<<<-<<--<<________>>-->.>>>>>>----->>>> 177 CcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc.gcuucCGGGUAGGuC 235 CCGGAGCAA:ACCAAAUAGG::::C: AU:G G++GC+CG: :::::CGGGUAGGU: 696 CCGGAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAaGGAGGCGGGUAGGUU 755 ,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>> 236 GCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcgg 295 GCUUGAG:C:G:+:GC+A:+:C:G:CCUAGA GAAUG++++C :CC:C G: 756 GCUUGAGCCAGUGAGCGAUUGCUGGCCUAGACGAAUGGCUACU--GCCGCGC----AAGC 809 >>>::::::::::::::::: 296 gggcgACAGAACCCGGCUUA 315 GG: ACAGAACCCGGCUUA 810 GGA--ACAGAACCCGGCUUA 827 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #7191,sp|AB047586.1|AB047586 Vibrio alginolyticus rnpB, ORF1, ORF2 genes, partial cds. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGGCUUCAUAGAGCAAGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUACGACAAGUGCAGCAGAGAGAAGACCGCCGAUGGCCCGUAAGGGUACAGGUAAGGGUGAAAGGGUGCGGUAAGAGCGCACCGGACGACUAGCAAUAGUUCGUAGCAGGGUAAACUCCACCUGAAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAAGGAGGCGGGUAGGUUGCUCGAGCCAGUGAGUGAUUGCUGGCCUAGACGAAUGGCUACCGCCGCGCAAGCGGAACAGAACCCGGCUUA hit 3 : 475 784 (fwd) 344.08 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCU:CA+AG+GCA:GGUGC::GGUAACGCC::G::GG:GC+A:CC:A 475 GAGGAAAGUCCGGGCUUCAUAGAGCAAGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUA 534 >((---(((((,,,,,,,,,,,,<<<<<..<<<<__________>>.>>>>>-->>,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCC..uggcCggUUagggGgc.caGGUAAGGGUGA 117 :G: AAGUGC: CAGA+A+ AGACCGCC UG:CC+GU AG GG: CAGGUAAGGGUGA 535 CGACAAGUGCAGCAGAGAGAAGACCGCCgaUGGCCCGUAAG--GGUaCAGGUAAGGGUGA 592 ,,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))--))))]]] 118 AAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUAAACCCCAC 176 AA GGUGCGGUAAGAGCGCACCG :C::C::G++A::G ::G: GCA :GUAAAC:CCAC 593 AAGGGUGCGGUAAGAGCGCACCGGACGACUAGCAAUAGuUCGUAGCAGGGUAAACUCCAC 652 ]]]]]],,,<<<<------<<<<<-<<--<<________>>-->.>>>>>>----->>>> 177 CcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc.gcuucCGGGUAGGuC 235 C:G:AGCAA:ACCAAAUAGG::::C: AU:G G++GC+CG: :::::CGGGUAGGU: 653 CUGAAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAaGGAGGCGGGUAGGUU 712 ,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>> 236 GCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcgg 295 GCU GAG:C:G:+:G++A:+:C:G:CCUAGA GAAUG++++CC :CC:C G: 713 GCUCGAGCCAGUGAGUGAUUGCUGGCCUAGACGAAUGGCUACC--GCCGCGC----AAGC 766 >>>::::::::::::::::: 296 gggcgACAGAACCCGGCUUA 315 GG: ACAGAACCCGGCUUA 767 GGA--ACAGAACCCGGCUUA 784 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #7192,sp|AB047587.1|AB047587 Vibrio natriegens rnpB, ORF1, ORF2 genes, partial cds. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGGCUUCAUAGAGCAAGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUACGACAAGUGCAGCAGAGAGAAGACCGCCGAUGGCCCGUAAGGGAUCAGGUAAGGGUGAAAGGGUGCGGUAAGAGCGCACCGGGCGACUAGUAAUAGUUCGUAGCAGGGUAAACUCCACCUGAAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAAGGAGGCGGGUAGGUUGCUCGAGCCAGUGAGUGAUUGCUGGCCUAGACGAAUGGCUACCGCCGCGCAAGCGGAACAGAACCCGGCUUA hit 4 : 548 857 (fwd) 341.67 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCU:CA+AG+GCA:GGUGC::GGUAACGCC::G::GG:GC+A:CC:A 548 GAGGAAAGUCCGGGCUUCAUAGAGCAAGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUA 607 >((---(((((,,,,,,,,,,,,<<<<<..<<<<__________>.>>>>>>-->>,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCC..uggcCggUUagggGg.ccaGGUAAGGGUGA 117 :G: AAGUGC: CAGA+A+ AGACCGCC UG:CC+GU AG GG :CAGGUAAGGGUGA 608 CGACAAGUGCAGCAGAGAGAAGACCGCCgaUGGCCCGUAAG--GGaUCAGGUAAGGGUGA 665 ,,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))--))))]]] 118 AAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUAAACCCCAC 176 AA GGUGCGGUAAGAGCGCACCG C::C::GU+A::G ::G GCA :GUAAAC:CCAC 666 AAGGGUGCGGUAAGAGCGCACCGGGCGACUAGUAAUAGuUCGUAGCAGGGUAAACUCCAC 725 ]]]]]],,,<<<<------<<<<<-<<--<<________>>-->.>>>>>>----->>>> 177 CcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc.gcuucCGGGUAGGuC 235 C:G:AGCAA:ACCAAAUAGG::::C: AU:G G++GC+CG: :::::CGGGUAGGU: 726 CUGAAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAaGGAGGCGGGUAGGUU 785 ,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>> 236 GCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcgg 295 GCU GAG:C:G:+:G++A:+:C:G:CCUAGA GAAUG++++CC :CC:C G: 786 GCUCGAGCCAGUGAGUGAUUGCUGGCCUAGACGAAUGGCUACC--GCCGCGC----AAGC 839 >>>::::::::::::::::: 296 gggcgACAGAACCCGGCUUA 315 GG: ACAGAACCCGGCUUA 840 GGA--ACAGAACCCGGCUUA 857 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #7193,sp|AB047588.1|AB047588 Vibrio harveyi rnpB, ORF1, ORF2 genes, partial cds. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGGCUUCAUAGAGCAAGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUACGACAAGUGCAGCAGAGAGAAGACCGCCGAUGGCCUUAGGGCACAGGUAAGGGUGAAAGGGUGCGGUAAGAGCGCACCGGACGACUAGUAAUAGUUCGUAGCAGGGUAAACUCCACCUGAAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAAGGAGGCGGGUAGGUUGCUCGAGCCAGUGAGUGAUUGCUGGCCUAGACGAAUGGCUACCGCCGCGCAAGCGGAACAGAACCCGGCUUA hit 5 : 737 1044 (fwd) 346.87 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCU:CA+AG+GCA:GGUGC::GGUAACGCC::G::GG:GC+A:CC:A 737 GAGGAAAGUCCGGGCUUCAUAGAGCAAGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUA 796 >((---(((((,,,,,,,,,,,,<<<<<..<<<<__________>>.>>>>>-->>,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCC..uggcCggUUagggGgc.caGGUAAGGGUGA 117 :G: AAGUGC: CAGA+A+ AGACCGCC UGGCC UUAG GGC CAGGUAAGGGUGA 797 CGACAAGUGCAGCAGAGAGAAGACCGCCgaUGGCC--UUAG--GGCaCAGGUAAGGGUGA 852 ,,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))--))))]]] 118 AAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUAAACCCCAC 176 AA GGUGCGGUAAGAGCGCACCG :C::C::GU+A::G ::G: GCA :GUAAAC:CCAC 853 AAGGGUGCGGUAAGAGCGCACCGGACGACUAGUAAUAGuUCGUAGCAGGGUAAACUCCAC 912 ]]]]]],,,<<<<------<<<<<-<<--<<________>>-->.>>>>>>----->>>> 177 CcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc.gcuucCGGGUAGGuC 235 C:G:AGCAA:ACCAAAUAGG::::C: AU:G G++GC+CG: :::::CGGGUAGGU: 913 CUGAAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAaGGAGGCGGGUAGGUU 972 ,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>> 236 GCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcgg 295 GCU GAG:C:G:+:G++A:+:C:G:CCUAGA GAAUG++++CC :CC:C G: 973 GCUCGAGCCAGUGAGUGAUUGCUGGCCUAGACGAAUGGCUACC--GCCGCGC----AAGC 1026 >>>::::::::::::::::: 296 gggcgACAGAACCCGGCUUA 315 GG: ACAGAACCCGGCUUA 1027 GGA--ACAGAACCCGGCUUA 1044 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #7194,sp|AB047589.1|AB047589 Vibrio carchariae rnpB, ORF1, ORF2 genes, partial cds. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGGCUUCAUAGAGCAAGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUACGACAAGUGCAGCAGAGAGAAGACCGCCGAUGGCCUUAGGGCACAGGUAAGGGUGAAAGGGUGCGGUAAGAGCGCACCGGACGACUAGUAAUAGUUCGUAGCAGGGUAAACUCCACCUGAAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAAGGAGGCGGGUAGGUUGCUCGAGCCAGUGAGUGAUUGCUGGCCUAGACGAAUGGCUACCGCCGCGCAAGCGGAACAGAACCCGGCUUA hit 6 : 712 1019 (fwd) 346.87 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCU:CA+AG+GCA:GGUGC::GGUAACGCC::G::GG:GC+A:CC:A 712 GAGGAAAGUCCGGGCUUCAUAGAGCAAGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUA 771 >((---(((((,,,,,,,,,,,,<<<<<..<<<<__________>>.>>>>>-->>,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCC..uggcCggUUagggGgc.caGGUAAGGGUGA 117 :G: AAGUGC: CAGA+A+ AGACCGCC UGGCC UUAG GGC CAGGUAAGGGUGA 772 CGACAAGUGCAGCAGAGAGAAGACCGCCgaUGGCC--UUAG--GGCaCAGGUAAGGGUGA 827 ,,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))--))))]]] 118 AAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUAAACCCCAC 176 AA GGUGCGGUAAGAGCGCACCG :C::C::GU+A::G ::G: GCA :GUAAAC:CCAC 828 AAGGGUGCGGUAAGAGCGCACCGGACGACUAGUAAUAGuUCGUAGCAGGGUAAACUCCAC 887 ]]]]]],,,<<<<------<<<<<-<<--<<________>>-->.>>>>>>----->>>> 177 CcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc.gcuucCGGGUAGGuC 235 C:G:AGCAA:ACCAAAUAGG::::C: AU:G G++GC+CG: :::::CGGGUAGGU: 888 CUGAAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAaGGAGGCGGGUAGGUU 947 ,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>> 236 GCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcgg 295 GCU GAG:C:G:+:G++A:+:C:G:CCUAGA GAAUG++++CC :CC:C G: 948 GCUCGAGCCAGUGAGUGAUUGCUGGCCUAGACGAAUGGCUACC--GCCGCGC----AAGC 1001 >>>::::::::::::::::: 296 gggcgACAGAACCCGGCUUA 315 GG: ACAGAACCCGGCUUA 1002 GGA--ACAGAACCCGGCUUA 1019 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #7195,sp|AB047590.1|AB047590 Vibrio campbellii rnpB, ORF1, ORF2 genes, partial cds. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGGCUUCAUAGAGCAAGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUACGACAAGUGCAGCAGAGAGAAGACCGCCGAUGGCCCUAGGGCACAGGUAAGGGUGAAAGGGUGCGGUAAGAGCGCACCGGACGACUAGUAAUAGUUCGUAGCAGGGUAAACUCCACCUGAAGCAAGACCAAAUAGGCCUUCACAUUGCGUUGCUCGCGUAAGGAGGCGGGUAGGUUGCUCGAGCCAGUGAGUGAUUGCUGGCCUAGACGAAUGGCUACCGCCGCGCAAGCGGAACAGAACCCGGCUUA hit 7 : 897 1204 (fwd) 342.32 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCU:CA+AG+GCA:GGUGC::GGUAACGCC::G::GG:GC+A:CC:A 897 GAGGAAAGUCCGGGCUUCAUAGAGCAAGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUA 956 >((---(((((,,,,,,,,,,,,<<<<<..<<<<__________>>.>>>>>-->>,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCC..uggcCggUUagggGgc.caGGUAAGGGUGA 117 :G: AAGUGC: CAGA+A+ AGACCGCC UGGCC UAG GGC CAGGUAAGGGUGA 957 CGACAAGUGCAGCAGAGAGAAGACCGCCgaUGGCC--CUAG--GGCaCAGGUAAGGGUGA 1012 ,,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))--))))]]] 118 AAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUAAACCCCAC 176 AA GGUGCGGUAAGAGCGCACCG :C::C::GU+A::G ::G: GCA :GUAAAC:CCAC 1013 AAGGGUGCGGUAAGAGCGCACCGGACGACUAGUAAUAGuUCGUAGCAGGGUAAACUCCAC 1072 ]]]]]],,,<<<<------<<<<<-<<--<<________>>-->.>>>>>>----->>>> 177 CcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc.gcuucCGGGUAGGuC 235 C:G:AGCAA:ACCAAAUAGG::: C: AU:G G++GC+CG: : :::CGGGUAGGU: 1073 CUGAAGCAAGACCAAAUAGGCCUUCACAUUGCGUUGCUCGCGUAaGGAGGCGGGUAGGUU 1132 ,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>> 236 GCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcgg 295 GCU GAG:C:G:+:G++A:+:C:G:CCUAGA GAAUG++++CC :CC:C G: 1133 GCUCGAGCCAGUGAGUGAUUGCUGGCCUAGACGAAUGGCUACC--GCCGCGC----AAGC 1186 >>>::::::::::::::::: 296 gggcgACAGAACCCGGCUUA 315 GG: ACAGAACCCGGCUUA 1187 GGA--ACAGAACCCGGCUUA 1204 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #7196,sp|AB047591.1|AB047591 Vibrio pelagius rnpB, ORF1, ORF2 genes, partial cds. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGGCUCCAUAGAGCAGGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCCACGACAAGUGCAGCAGAGAGAAGACCGCCGAUGGCCUCAUUUCUUCGGAAGGGGCACAGGUAAGGGUGAAAGGGUGCGGUAAGAGCGCACCGGACGGCUAGCAAUAGUCCGUUGCAGGGUAAACUCCACCCGGAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAAGGAGGCGGGUAGGUUGCUUGAGCCAGUGAGCGAUUGCUGGCCUAGACGAAUGGCUACUACCGCGCAAGCGGAACAGAACCCGGCUUA hit 8 : 397 716 (fwd) 346.46 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCUCCA+AG+GCAGGGUGC::GGUAACGCC::G::GG:GC+A:CC:A 397 GAGGAAAGUCCGGGCUCCAUAGAGCAGGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCCA 456 >((---(((((,,,,,,,,,,,,<<<<<..<<<<___.....____...___>>.>>>>> 61 gGGAAAGUGCCACAGAAAaCAgACCGCC..uggcCgg.....UUag...ggGgc.caGGU 109 :G: AAGUGC: CAGA+A+ AGACCGCC UGGCC + UU+G GGGGC CAGGU 457 CGACAAGUGCAGCAGAGAGAAGACCGCCgaUGGCCUCauuucUUCGgaaGGGGCaCAGGU 516 -->>,,,,,,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))- 110 AAGGGUGAAAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUA 168 AAGGGUGAAA GGUGCGGUAAGAGCGCACCG :C::C::G++A::G ::G: GCA :GUA 517 AAGGGUGAAAGGGUGCGGUAAGAGCGCACCGGACGGCUAGCAAUAGuCCGUUGCAGGGUA 576 -))))]]]]]]]]],,,<<<<------<<<<<-<<--<<________>>-->.>>>>>>- 169 AACCCCACCcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc.gcuucCG 227 AAC:CCACCCGGAGCAA:ACCAAAUAGG::::C: AU:G G++GC+CG: :::::CG 577 AACUCCACCCGGAGCAAGACCAAAUAGGCCUCCACAUUGCGUUGCUCGCGUAaGGAGGCG 636 ---->>>>,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<< 228 GGUAGGuCGCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgc 287 GGUAGGU:GCUUGAG:C:G:+:GC+A:+:C:G:CCUAGA GAAUG++++C +CC:C 637 GGUAGGUUGCUUGAGCCAGUGAGCGAUUGCUGGCCUAGACGAAUGGCUACU--ACCGCGC 694 <<>>>>>>>>>::::::::::::::::: 288 cgcggcgggggcgACAGAACCCGGCUUA 315 G:GG+ ACAGAACCCGGCUUA 695 ----AAGCGGA--ACAGAACCCGGCUUA 716 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #9273,sp|AB063522.2|AB063522 Wigglesworthia brevipalpis DNA, complete genome, section 2/2. ----isReversed: 1 ----hitSequence: GAGGAAAGUCCGGGCCCUAAAGAGCAAGAUGCCAGGUAAUUCCUGGGAGGAGUGAUCCUACGACUAGUGCAACAGAAAAAAAACCGCCACUUUUGUUGGUAAGGGUGAAAAGGUGCGAUAAGAGCGUACCGCAAUUUAUGGUAACAUAAUUGGCAGUGUAAACUCCAUCUAGGGCAAGGCCAAAUAAAAGCUUGAUUGCUCGUCUUUAAGCUUUGGUAGGCUGCAAGAAUAAAUAUGUGAAUGUUUAUCUAGAUAAAUGAUUGUCCAAGACAGAACCCGGCUUA hit 9 : 174552 174269 (rev) 276.20 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGC:C:A AG+GCA:G:UGC::GGUAA CC::G::GG:G+GA:CC:A 174623 GAGGAAAGUCCGGGCCCUAAAGAGCAAGAUGCCAGGUAAUUCCUGGGAGGAGUGAUCCUA 174682 >((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>>>-->>,,,,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGGUAAGGGUGAAAa 120 :G: AGUGC:ACAGAAAA A+ACCGCC: UU G :GGUAAGGGUGAAAA 174683 CGACUAGUGCAACAGAAAAAAAACCGCCAC-----UUUU--G--UUGGUAAGGGUGAAAA 174733 <<<<<<_______>>>>>><<<<.<<<<<____>>>>>>>>->,,)))--))))]]]]]] 121 GGUGcGGUAAGAGCgCACCGCgc.ccccGGUGACgggggcGGCAcGGUAAACCCCACCcG 179 GGU:CG UAAGAGCG:ACCGC:: ::::GGU+AC::::::GGCA :GUAAAC:CCA:C:: 174734 GGUGCGAUAAGAGCGUACCGCAAuUUAUGGUAACAUAAUUGGCAGUGUAAACUCCAUCUA 174793 ]]],,,<<<<------<<<<<-<<--<<________.>>-->>>>>>>----->>>>,,, 180 GAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCC.GccCcgcuucCGGGUAGGuCGCU 238 G:GCAA::CCAAAUA ::::: U G ++GC+C C+ + ::::: GGUAGG::GC 174794 GGGCAAGGCCAAAUAAAAGCU----U--GAUUGCUCgUCUUUAAGCUUUGGUAGGCUGCA 174847 ,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>>>>> 239 uGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcggggg 298 +GA::::::::G++A::::::::CUAGAU+AAUGAU+G+CCA 174848 AGAAUAAAUAUGUGAAUGUUUAUCUAGAUAAAUGAUUGUCCA------------------ 174889 ::::::::::::::::: 299 cgACAGAACCCGGCUUA 315 +GACAGAACCCGGCUUA 174890 AGACAGAACCCGGCUUA 174906 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #16804,sp|AE000573.1|AE000573 Helicobacter pylori 26695 section 51 of 134 of the complete genome. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGGCUACAUUAGACAAAAUUCCAUCUAACGGAUGGCUAGCGCAAGCUAAGGGAAAGUGCCACAGAAAGCAAACCGCCUUUUAAGGUAAGGGUGAAAGGGUGGGGUAAGAGCCCACCARAGCUAAAGCAAUUUAGCUUGUUUGGGCAAACCCAAUUUGUAGCAAGAAGCGCAUGGUAAGUCUAAAUUGAUACACGCUUCGCUUGAGGAAUAUUGCAAAAUAUUUCCCAGAUAAAUGGCCAUCCAUUGACAGAACCCGGCUUA hit 10 : 3672 3943 (fwd) 255.20 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCU:CA+ G CA:::U:C::::UAACG::::GC::G:GC+A:C::A 3672 GAGGAAAGUCCGGGCUACAUUAGACAAAAUUCCAUCUAACGGAUGGCUAGCGCAAGCUAA 3731 >((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>>>-->>,,,,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGGUAAGGGUGAAAa 120 GGGAAAGU:CCACAGAAA+CA+ACCGCCU UU + AGGUAAGGGUGAAA 3732 GGGAAAGUGCCACAGAAAGCAAACCGCCU------UUUA------AGGUAAGGGUGAAAG 3779 <<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->..,,)))--))))]]]]] 121 GGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGC..AcGGUAAACCCCACCc 178 GGUG:GGUAAGAGC:CACC: ::C::::G++A::::G:: G: GG:AAACCC:A::: 3780 GGUGGGGUAAGAGCCCACCARAGCUAAAGCAAUUUAGCUUGUuu-GGGCAAACCCAAUUU 3838 ]]]],,,<<<<------<<<<<-<<--<<________>>-->....>>>>>>----->>> 179 GGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc....gcuucCGGGUAGGu 234 G:AGCAAGA :::GC: U: G C+ :+ + :C::: U 3839 GUAGCAAGA---------AGCGCA--UGGUAAGUCUAAAUUGauacACGCU--------U 3879 >,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<...>> 235 CGCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccg...cg 291 CGCUUGAGG::::::GCAA::::::UCC+AGAU+AAUG++C++CCA 3880 CGCUUGAGGAAUAUUGCAAAAUAUUUCCCAGAUAAAUGGCCAUCCA---------uug-- 3928 >>>>>>>::::::::::::::::: 292 gcgggggcgACAGAACCCGGCUUA 315 ACAGAACCCGGCUUA 3929 ---------ACAGAACCCGGCUUA 3943 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17385,sp|AE001171.1|AE001171 Borrelia burgdorferi B31 (section 57 of 70) of the complete genome. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGAGCUCCAAUAAGAACAUAAUGCUAGGUAAUGCCUAGGGGUUUUAAACCUAAGAAAGUGUCGCAGAAAAUUACCGCCGUAAAAGGUAAGGGUGAAAAGGUGAGGUAAGAGCUCACCGCUUAUUUAGCAAUAAAUACAGGCAAGAUAAACCUCAUUAGGAGCAAGAUCAAGUAUGUAAGCACCCUUUGUUCUUGAGGACAUGCUUACGGGUAGAUCGCACGAUUUUUUUAGCGAUAAAAAAAUAAGAGAGAUGAUGGCAUAGUACAGAACUCGGCUUA hit 11 : 8232 8519 (fwd) 248.51 bits ::::::::::::::[[[[---..-----[[[[[<<<<<_____>>>>><<<<<____>>> 1 GAGGAAAGUCCGGGCUCCACA..GGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccC 58 GAGGAAAGUCCG GCUCCA G+ CA:::UGCU:GGUAA GCC:AG+:G : ++A: C 8232 GAGGAAAGUCCGAGCUCCAAUaaGAACAUAAUGCUAGGUAAUGCCUAGGGGUUUUAAACC 8291 >->((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>>>-->>,,,,, 59 gAgGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGGUAAGGGUGAA 118 :A :GAAAGUG:C CAGAAAA ACCGCC U A+ GGUAAGGGUGAA 8292 UA-AGAAAGUGUCGCAGAAAAUU-ACCGCCG------UAAA------AGGUAAGGGUGAA 8337 ,,<<<<<<_______>>>>>><<<<<<<<<____>>>>>>.>>->,,)))--))))]]]] 119 AaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACggggg.cGGCAcGGUAAACCCCACC 177 AAGGUG:GGUAAGAGC:CACCGC:::::::G++A:::::: :GGCA+G:UAAACC:CA:: 8338 AAGGUGAGGUAAGAGCUCACCGCUUAUUUAGCAAUAAAUAcAGGCAAGAUAAACCUCAUU 8397 ]]]]],,,<<<<------<<<<<-<<--<<________>>-->.....>>>>>>-----> 178 cGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc.....gcuucCGGGUAG 232 :GGAGCAAGA:CAA+UA G:AAGC: : ++G +C:+ + :CUU:CGGGUAG 8398 AGGAGCAAGAUCAAGUAUGUAAGCA--C-CCUUUGUUCUUGAGgacauGCUUACGGGUAG 8454 >>>,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>> 233 GuCGCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcgg 292 :UCGC GA::::::::GC+A:::::::: AGA+++AUGAU GC A 8455 AUCGCACGAUUUUUUUAGCGAUAAAAAAAUAAGAGAGAUGAUGGCAUA------------ 8502 >>>>>>::::::::::::::::: 293 cgggggcgACAGAACCCGGCUUA 315 ACAGAAC CGGCUUA 8503 ------GUACAGAACUCGGCUUA 8519 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17440,sp|AE001226.1|AE001226 Treponema pallidum section 42 of 87 of the complete genome. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGACUCCUUCGGAAAUGAUGCUAGUUAAUUACUAGGCAGCGGCUCUCUGCAGUGCCGCUGACAGCAAGCGCCACAGAAAAUAUACCGCCUUUGGGUAAGGGUGAAAGGGCGAGGUAAGAGCUCACCGCGUUUUGGCGACAAAACGGCACGGCAAGCCUCAUCAGGAGCAAGAUCGAGCAGCAAAGGAUAUUCCGAUCCUGUUUUGCGGGUUGAUUGCAUAAAUUUAUAUAGCGAUAUAUAAAGUGAGACAGAUGAUUAUCCUUGACAGAAUCCGGCUUA hit 12 : 44 333 (fwd) 241.51 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<........_ 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGgg........G 52 GAGGAAAGUCCGG CUCC + GG A:G:UGCU:G:UAA :C:AG:C:G: G 44 GAGGAAAGUCCGGACUCCUUCGGAAAUGAUGCUAGUUAAUUACUAGGCAGCggcucucuG 103 ___....>>>>->((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>> 53 cGA....ccCgAgGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGG 108 C+ :C:GA::G AAG::CCACAGAAAA A ACCGCC UU G GG 104 CAGugccGCUGACAGCAAGCGCCACAGAAAAUAUACCGCC-------UUUG-------GG 149 >-->>,,,,,,,<<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->,,)))- 109 UAAGGGUGAAAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGCAcGGUA 168 UAAGGGUGAAA GG:G:GGUAAGAGC:C:CCGCG::::: G+GA :::::CGGCACGG:A 150 UAAGGGUGAAAGGGCGAGGUAAGAGCUCACCGCGUUUUG-GCGA-CAAAACGGCACGGCA 207 -))))]]]]]]]]],,,<<<<------<<<<<-<<--<<________>>-->..>>>>>> 169 AACCCCACCcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc..gcuucC 226 A:CC:CA:C:GGAGCAA:A:C A G:A: : + GG + CCG +CC : :U:C 208 AGCCUCAUCAGGAGCAAGAUCGA----GCAGC-A--AAGGAUAUUCCGAUCCugUUUUGC 260 ----->>>>,,.,,,,<<<<<<<<____>>>>>>>>,,.,,,,,,,,,,,,,,,,,<<<< 227 GGGUAGGuCGC.UuGAGgCggccGGCAACggccGuCCu.AGAUgAAUGAUCGcCCAcccc 284 GGGU G:U:GC U+ A::::::::GC+A:::::::: U AGA ++AUGAU+++CC 261 GGGUUGAUUGCaUAAAUUUAUAUAGCGAUAUAUAAAGUgAGACAGAUGAUUAUCCU---- 316 <<<<<>>>>>>>>>::::::::::::::::: 285 cgccgcggcgggggcgACAGAACCCGGCUUA 315 GACAGAA CCGGCUUA 317 --------------UGACAGAAUCCGGCUUA 333 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17525,sp|AE001313.1|AE001313 Chlamydia trachomatis section 40 of 87 of the complete genome. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGACUUUAUAAGAAAAGAUGCUGGAGAAAUUCCAGGGGCCGUAAGGCUACGGAAAGUGCAACAGAAAACACUCCGCUAUAAAUUGUAUAAUUUAUAGACAGGCUGAAAAAUCUUACUUUAGGAGUAAGAGCUGCUAGGGAGACCUAGCAGACUUGUAAACCCCAUCUGAAGCAAGAGAAAAAGUUAUUUGUUUCUGCAAACAACCUUUCUAACGAAAGGCACAGGCUUUUUCAUAAUCGCUUGAGGAGUACAGUAAUGUGCUCCCUAGAUGAAUGGUUGCCCGCAAGCAAGAACUUCCGUUCGUGCUUGUCGACAGAAUCCGGCUUA hit 13 : 3344 3681 (fwd) 221.60 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGG CU::A+A G A:G:UGCUGG: AA :CCAG::G::G++A::C:A 3344 GAGGAAAGUCCGGACUUUAUAAGAAAAGAUGCUGGAGAAAUUCCAGGGGCCGUAAGGCUA 3403 >((---(((((,,,,,,,,,,,,<<<<<<<<<___..._______>>>>>>>-->>,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCCuggcCgg...UUagggGgccaGGUAAGGGUGA 117 :GGAAAGUGC:ACAGAAAACA CC:C::::: U A :::::G: AGG UGA 3404 CGGAAAGUGCAACAGAAAACACUCCGCUAUAAAUUguaUAAU---UUAUAGACAGGCUGA 3460 ,,,.<<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->,,)))--))))]]] 118 AAa.GGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGCAcGGUAAACCCCAC 176 AAA : U:: U AG ::A :GC::C:::GG GAC:::G::G C :GUAAACCCCA: 3461 AAAaUCUUACUUUAGGAGUAAGAGCUGCUAGGGAGACCUAGCAGAC-UUGUAAACCCCAU 3519 ]]]]]],,,<<<<------<<<<<-<<..........................--<<___ 177 CcGGAGCAAGaCCAAAUAGGgaagCgu..........................AugGgGc 210 C:::AGCAAGA G:AA: G+ A+ 3520 CUGAAGCAAGA--------GAAAAAGUuauuuguuucugcaaacaaccuuucuAACGAAA 3571 _____>>-->>>>>>>----->>>>,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,, 211 GGCCCGccCcgcuucCGGGUAGGuCGCUuGAGgCggccGGCAACggccGuCCuAGAUgAA 270 GGC C C+ :UU:C UA UCGCUUGAG+:G::C:G+AA:G::C:+CCUAGAUGAA 3572 GGCACAGGCU-UUUUC--AUA-AUCGCUUGAGGAGUACAGUAAUGUGCUCCCUAGAUGAA 3627 ,,,,,,,,,,<<<<<<<<<............>>>>>>>.>>::::::::::::::::: 271 UGAUCGcCCAcccccgccg............cggcggg.ggcgACAGAACCCGGCUUA 315 UG+U+GCC C:C::GC:: ::GC::G :G ACAGAA CCGGCUUA 3628 UGGUUGCC--CGCAAGCAAgaacuuccguucGUGCUUGuCG--ACAGAAUCCGGCUUA 3681 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17621,sp|AE001486.1|AE001486 Helicobacter pylori, strain J99 section 47 of 132 of the complete genome. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGGCUACAUUAGACAAAAUUCCAUCUAACGGAUGGCUAGCGCAAGCUAAGGGAAAGUGCCACAGAAAGCAAACCGCCUUUUUAAGGUAAGGGUGAAAGGGUGGGGUAAGAGCCCACCAAAGCUAAAGCGAUUUAGCUUGUUUGGGCAAACCCAAUUUGUAGCAAGAAGCGCAUGGUAAGUCUAAAUUA hit 14 : 11579 11777 (fwd) 116.04 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCU:CA+ G CA:::U:C::::UAACG::::GC::G:GC+A:C::A 11579 GAGGAAAGUCCGGGCUACAUUAGACAAAAUUCCAUCUAACGGAUGGCUAGCGCAAGCUAA 11638 >((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>>>-->>,,,,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGGUAAGGGUGAAAa 120 GGGAAAGU:CCACAGAAA+CA+ACCGCCU: UU :AGGUAAGGGUGAAA 11639 GGGAAAGUGCCACAGAAAGCAAACCGCCUU-----UUU------AAGGUAAGGGUGAAAG 11687 <<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->..,,)))--))))]]]]] 121 GGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGC..AcGGUAAACCCCACCc 178 GGUG:GGUAAGAGC:CACC::::C::::G+GA::::G:::G: GG:AAACCC:A::: 11688 GGUGGGGUAAGAGCCCACCAAAGCUAAAGCGAUUUAGCUUGUuu-GGGCAAACCCAAUUU 11746 ]]]],,,<<<<------<<<<<-<<--<<________>>-->>>>>>>----->>>>,,, 179 GGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCcgcuucCGGGUAGGuCGCU 238 G:AGCAAG + + + CGC 11747 GUAGCAAG---------------A--A--------------G--------------CGCA 11761 ,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>>>>> 239 uGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcggggg 298 UG G+AA G+C A 11762 UG---------GUAA----------------------GUCUA------------------ 11772 ::::::::::::::::: 299 cgACAGAACCCGGCUUA 315 ++ UUA 11773 AA------------UUA 11777 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17769,sp|AE001637.1|AE001637 Chlamydia pneumoniae section 53 of 103 of the complete genome. ----isReversed: 0 ----hitSequence: GAGGAAAGUCUGGACUUCAUAAGAGAAGAUACUGGAGAAAUUCCAGGGGCCGUAAGGCUACGGAAAGUGCAACAGAAAACACUCCGCUAUAAAAUUUAUUUUAUAGACAGGCUGAAAAUUCCUACUUUAGGAGUAGGAGCCAUUAAGGUGACUUAAUAGGCAUGCAAACCCUAUCUGAAGCAAGAGAAAAAAGCUUUUUGUGUCUGCAAAUGUGAGAGGAAUUCCUCCCAUAGGCUUUUUCGAAAUCGCUUGAGGGAUCUAGUAAUAGCUCCCCUAGAUGAAUGGUUGCCCUUAGGAUAGUUCGCAAGAGCUAUCUUAUAGACAGAAUCCAGCUUA hit 15 : 6521 6856 (fwd) 208.28 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUC GG CU:CA+A G A:G:U:CUGG: AA :CCAG::G::G++A::C:A 6521 GAGGAAAGUCUGGACUUCAUAAGAGAAGAUACUGGAGAAAUUCCAGGGGCCGUAAGGCUA 6580 >((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>>>-->>,,,,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGGUAAGGGUGAAAa 120 :GGAAAGU:C:ACAGAAAACA CC:C::::: UU + :::::G: AGG UGAAAA 6581 CGGAAAGUGCAACAGAAAACACUCCGCUAUAAAA-UUUA-UUUUAUAGACAGGCUGAAAA 6638 .<<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->,,)))--))))]]]]]] 121 .GGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGCAcGGUAAACCCCACCcG 179 : ::: U AG ::: :GC :::::GGUGAC::::: GGC +:G:AAACCC:A:C:G 6639 uUCCUACUUUAGGAGUAGGAGCCAUUAAGGUGACUUAAUAGGC-AUGCAAACCCUAUCUG 6697 ]]],,,<<<<------<<<<<-<<....................--<<________>>-- 180 GAGCAAGaCCAAAUAGGgaagCgu....................AugGgGcGGCCCGccC 219 :AGCAAGA AA ::AAGC:: +G ++ C+C C 6698 AAGCAAGA--GAA---AAAAGCUUuuugugucugcaaaugugag-AGGAAUUCCUCCCAU 6751 >.>>>>>>----->>>>,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,, 220 c.gcuucCGGGUAGGuCGCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcC 278 : :CUU:: G A UCGCUUGAG+:: C::G+AA::G ::+CCUAGAUGAAUG+U+GCC 6752 AgGCUUUUUCGAA-AUCGCUUGAGGGAUCUAGUAAUAGCUCCCCUAGAUGAAUGGUUGCC 6810 ,,<<<<<<<<<............>>>>>>>.>>::::::::::::::::: 279 CAcccccgccg............cggcggg.ggcgACAGAACCCGGCUUA 315 C::: G::: :::C :: :G ACAGAA CC GCUUA 6811 --CUUAGGAUAguucgcaagagcUAUCUUAuAG--ACAGAAUCCAGCUUA 6856 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17875,sp|AE001744.1|AE001744 Thermotoga maritima section 56 of 136 of the complete genome. ----isReversed: 0 ----hitSequence: GGACAGGGCCAUAGAGAAGAAGACCGCCCGUUGAGGGCAAGGGUGGAACGGUGGGGUAAGAGCCCACCAGCGUCGGGGCAACCCGGCGGCUUGGCAACCCCCACCUGGAGCAAGGCCAAGCAGGGGGUUGGGUCGCUCCCCCUAUUCCCCCGGGUUGGCCGCUUGAGGUGUGCGGUAACGCACACCCCAGAUUGAUGACCGCCCACGACAGAAUCCGGCUUA hit 16 : 1 222 (fwd) 140.56 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 - ------------------------------------------------------------ - >((---(((((,,,,,,,,,,,.,<<<<<<<<<__________>>>>>>>-->>,,,,,, 61 gGGAAAGUGCCACAGAAAaCAg.ACCGCCuggcCggUUagggGgccaGGUAAGGGUGAAA 119 GGA AG::CCA AGA+AA A+ ACC:CC: U G :GG:AAGGGUG AA 1 -GGACAGGGCCAUAGAGAAGAAgACCGCCC------GUUG--A---GGGCAAGGGUGGAA 48 ,<<<<<<_______>>>>>>.<<<<<<<<<____>>>>>>>>->.,,)))--))))]]]] 120 aGGUGcGGUAAGAGCgCACC.GCgcccccGGUGACgggggcGGC.AcGGUAAACCCCACC 177 +GGUG:GGUAAGAGC:CACC GCG:C::: G++A :::G:CGGC GG:AA:CCCCACC 49 CGGUGGGGUAAGAGCCCACCaGCGUCGGG-GCAA-CCCGGCGGCu-UGGCAACCCCCACC 105 ]]]]],,,<<<<------<<<<<-<<--<<________>>-->..>>>>>>----->>>> 178 cGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc..gcuucCGGGUAGGuC 235 +GGAGCAAG:CCAA+ AGGG:: U GG+ GC+C CCC+ ::CCGGGU GG:C 106 UGGAGCAAGGCCAAGCAGGGGGU----U-GGGUCGCUCCCCCUauUCCCCCGGGUUGGCC 160 ,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>> 236 GCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcgg 295 GCUUGAG+:G::CGG+AACG::C:+CC+AGAU +AUGA+CGCCCA 161 GCUUGAGGUGUGCGGUAACGCACACCCCAGAUUGAUGACCGCCCA--------------- 205 >>>::::::::::::::::: 296 gggcgACAGAACCCGGCUUA 315 CGACAGAA CCGGCUUA 206 ---CGACAGAAUCCGGCUUA 222 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18038,sp|AE001942.1|AE001942 Deinococcus radiodurans R1 section 79 of 229 of the complete chromosome 1. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGGCACCGCAGGGCAAGGAUGCCAGCUAACGGCUGGUCGGCGAGCCGAGCGUCCGCCUGAGUGCCGCAAGCAGGCGGAAAGCGGCGAAGUCGAAGGACAGUGCCACAGAAACCAGACCGCCACCCCACACAGGCCCCGGCGCGGGCGCGGGUGGUCAGGGUGAAACGGUGCGGUAAGAGCGCACCAGGUUCCCGGGAGACCGGGAGCGUCUGGUCAACCCCAUCCGGUGCAAGACCCGACAGUGCGGCGAGGGCGGCCCGCCCGUUUGAGCCGCCAGGAUGGUCGCUUGAGGCGUCCUGGCAACAGGCGUCCCAGACAGAUGAUCAGGCUGCCCCAGGGCCAACCCUCUGGGGCAGACAGAACCCGGCUUA hit 17 : 5548 5929 (fwd) 309.37 bits ::::::::::::::[[[[-------.-[[[[[<<<<<_____>>>>><<<<<........ 1 GAGGAAAGUCCGGGCUCCACAGGGC.AgGGUGCUGGgUAACGcCCAGccGgg........ 51 GAGGAAAGUCCGGGC:CC CAGGGC AGG:UGC::G:UAACG:C::G:CG : 5548 GAGGAAAGUCCGGGCACCGCAGGGCaAGGAUGCCAGCUAACGGCUGGUCGGCgagccgag 5607 ..................................____.>>>>->((---(((((,,,,, 52 ..................................GcGA.ccCgAgGGAAAGUGCCACAGA 76 GCGA : CGA:GGA AGUGCCACAGA 5608 cguccgccugagugccgcaagcaggcggaaagcgGCGAaGUCGAAGGACAGUGCCACAGA 5667 ,,,,,,,<<<<<<<<<___......____.......___>>>>>>>-->>,,,,,,,<<< 77 AAaCAgACCGCCuggcCgg......UUag.......ggGgccaGGUAAGGGUGAAAaGGU 123 AA CAGACCGCC:::CC + ++G +G G:::GGU AGGGUGAAA+GGU 5668 AACCAGACCGCCACCCCACacaggcCCCGgcgcgggCGCGGGUGGUCAGGGUGAAACGGU 5727 <<<_______>>>>>>.<<<<<<<<<____>>>>>>>>->.,,)))--))))]]]]]]]] 124 GcGGUAAGAGCgCACC.GCgcccccGGUGACgggggcGGC.AcGGUAAACCCCACCcGGA 181 GCGGUAAGAGCGCACC + :CCC:GG GAC:GGG: +G GGU AACCCCA:CCGG: 5728 GCGGUAAGAGCGCACCaGGUUCCCGGGAGACCGGGAGCGUc-UGGUCAACCCCAUCCGGU 5786 ],,,<<<<------<<<<<-<<--<<________>>-->.....>>>>>>----->>>>, 182 GCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc.....gcuucCGGGUAGGuCG 236 GCAAGACC A AG:G::GCG + GGGCGGCCCGCCC+ GC::C: GG GGUCG 5787 GCAAGACCCGACAGUGCGGCG--A-GGGCGGCCCGCCCGuuugaGCCGCCAGGAUGGUCG 5843 ,,,,,<<<<<.<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<...... 237 CUuGAGgCgg.ccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccg...... 289 CUUGAGGCG: C:GGCAAC:G:CGUCC+AGA ++AUGAUC+ C::CC:C:G 5844 CUUGAGGCGUcCUGGCAACAGGCGUCCCAGACAGAUGAUCAGG--CUGCCCCAGggccaa 5901 ....>>>>>>>>>::::::::::::::::: 290 ....cggcgggggcgACAGAACCCGGCUUA 315 C:G:GG::G ACAGAACCCGGCUUA 5902 cccuCUGGGGCAG--ACAGAACCCGGCUUA 5929 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18266,sp|AE002183.2|AE002183 Chlamydophila pneumoniae AR39, section 18 of 94 of the complete genome. ----isReversed: 1 ----hitSequence: GAGGAAAGUCUGGACUUCAUAAGAGAAGAUACUGGAGAAAUUCCAGGGGCCGUAAGGCUACGGAAAGUGCAACAGAAAACACUCCGCUAUAAAAUUUAUUUUAUAGACAGGCUGAAAAUUCCUACUUUAGGAGUAGGAGCCAUUAAGGUGACUUAAUAGGCAUGCAAACCCUAUCUGAAGCAAGAGAAAAAAGCUUUUUGUGUCUGCAAAUGUGAGAGGAAUUCCUCCCAUAGGCUUUUUCGAAAUCGCUUGAGGGAUCUAGUAAUAGCUCCCCUAGAUGAAUGGUUGCCCUUAGGAUAGUUCGCAAGAGCUAUCUUAUAGACAGAAUCCAGCUUA hit 18 : 10452 10117 (rev) 208.28 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUC GG CU:CA+A G A:G:U:CUGG: AA :CCAG::G::G++A::C:A 1021 GAGGAAAGUCUGGACUUCAUAAGAGAAGAUACUGGAGAAAUUCCAGGGGCCGUAAGGCUA 1080 >((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>>>-->>,,,,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGGUAAGGGUGAAAa 120 :GGAAAGU:C:ACAGAAAACA CC:C::::: UU + :::::G: AGG UGAAAA 1081 CGGAAAGUGCAACAGAAAACACUCCGCUAUAAAA-UUUA-UUUUAUAGACAGGCUGAAAA 1138 .<<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->,,)))--))))]]]]]] 121 .GGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGCAcGGUAAACCCCACCcG 179 : ::: U AG ::: :GC :::::GGUGAC::::: GGC +:G:AAACCC:A:C:G 1139 uUCCUACUUUAGGAGUAGGAGCCAUUAAGGUGACUUAAUAGGC-AUGCAAACCCUAUCUG 1197 ]]],,,<<<<------<<<<<-<<....................--<<________>>-- 180 GAGCAAGaCCAAAUAGGgaagCgu....................AugGgGcGGCCCGccC 219 :AGCAAGA AA ::AAGC:: +G ++ C+C C 1198 AAGCAAGA--GAA---AAAAGCUUuuugugucugcaaaugugag-AGGAAUUCCUCCCAU 1251 >.>>>>>>----->>>>,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,, 220 c.gcuucCGGGUAGGuCGCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcC 278 : :CUU:: G A UCGCUUGAG+:: C::G+AA::G ::+CCUAGAUGAAUG+U+GCC 1252 AgGCUUUUUCGAA-AUCGCUUGAGGGAUCUAGUAAUAGCUCCCCUAGAUGAAUGGUUGCC 1310 ,,<<<<<<<<<............>>>>>>>.>>::::::::::::::::: 279 CAcccccgccg............cggcggg.ggcgACAGAACCCGGCUUA 315 C::: G::: :::C :: :G ACAGAA CC GCUUA 1311 --CUUAGGAUAguucgcaagagcUAUCUUAuAG--ACAGAAUCCAGCUUA 1356 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18406,sp|AE002336.2|AE002336 Chlamydia muridarum section 64 of 85 of the complete genome. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGACUUCGUAAGAAAAGAUGCUGGAGAAAUUCCAGGGGCCGUAAGGCUACGGAAAGUGCAACAGAAAACAUUCCGCUAUAAAUGAUAUCAUUUAUAGACAGGCUGAAAAAUCCUACUUUAGGAGUAGGAGCUGCUAGGGAGACCUGGUAGACUUGUAAACCCCAUCUGAAGCAAGAGAAAAAGUUAUUUGUCUCUGCAAAAUCCUUUCUAAUGAAAGGCAUAAACUUUUUCAUAAUCGCUUGAGGAGUACAGUAAUGUGCUCCCUAGAUGAAUGGUUGCCCACAAGUAAGAAUUUCUUAUUCGUACUUGUUGACAGAAUCCGGCUUA hit 19 : 7270 7607 (fwd) 219.02 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGG CU:C +A G A:G:UGCUGG: AA :CCAG::G::G++A::C:A 7270 GAGGAAAGUCCGGACUUCGUAAGAAAAGAUGCUGGAGAAAUUCCAGGGGCCGUAAGGCUA 7329 >((---(((((,,,,,,,,,,,,<<<<<<<<<___..._______>>>>>>>-->>,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCCuggcCgg...UUagggGgccaGGUAAGGGUGA 117 :GGAAAGUGC:ACAGAAAACA CC:C::::: G U+A :::::G: AGG UGA 7330 CGGAAAGUGCAACAGAAAACAUUCCGCUAUAAAUGauaUCAU---UUAUAGACAGGCUGA 7386 ,,,.<<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->,,)))--))))]]] 118 AAa.GGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGCAcGGUAAACCCCAC 176 AAA : ::: U AG ::: :GC: C ::GG GAC:: G :G C :GUAAACCCCA: 7387 AAAaUCCUACUUUAGGAGUAGGAGCUGCUAGGGAGACCUGGUAGAC-UUGUAAACCCCAU 7445 ]]]]]],,,<<<<------<<<<<-<<--<<________......>>-->.......... 177 CcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCC......GccCc.......... 220 C:G:AGCAAGA G:AA: + U: +G C+C +:CC+ 7446 CUGAAGCAAGA--------GAAAAAGU-UA-UUUGUCUCugcaaaAUCCUuucuaaugaa 7495 ..........>>>>>>----->>>>,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,, 221 ..........gcuucCGGGUAGGuCGCUuGAGgCggccGGCAACggccGuCCuAGAUgAA 270 :UU:C UA UCGCUUGAG+:G::C:G+AA:G::C:+CCUAGAUGAA 7496 aggcauaaacUUUUUC--AUA-AUCGCUUGAGGAGUACAGUAAUGUGCUCCCUAGAUGAA 7552 ,,,,,,,,,,<<<<<<<<<.............>>>>>>>.>>::::::::::::::::: 271 UGAUCGcCCAcccccgccg.............cggcggg.ggcgACAGAACCCGGCUUA 315 UG+U+GCC C C::G::: :::C::G G ACAGAA CCGGCUUA 7553 UGGUUGCC--CACAAGUAAgaauuucuuauucGUACUUGuUG--ACAGAAUCCGGCUUA 7607 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18631,sp|AE002562.1|AE002562 Neisseria meningitidis serogroup B strain MC58 section 204 of 206 of the complete genome. ----isReversed: 1 ----hitSequence: GAGGAAAGUCCGGGCUCCGCAGGGUAGAAUGCCGGUUAACGGCCGGGCGCGGUAACGCGACGGAAAGUGGAACAGAAAGCAAAACCGCCGAUGGCUGCUUUGGCAGCACAGGUAAGGGUGAAAAGGUGCGGUAAGGGCGCACCGCGCAUUUGGUAACAAUAUGCGGCAGGCCAAACCCCAUUCGGAGCAAGACCAAACAGAACGCAAUGACGCUGCCCGCCGAGCGUUCGGGUAGGUUGCUUGAGCAUACCGGUAACGGUAUGCCUAGAGGAAUGACUGUCCGAGACAGAACCCGGCUUA hit 20 : 2999 2700 (rev) 348.40 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCUCC CAGGG AG::UGC:GG:UAACG:CC:G:CG:GG++AC:CGA 6833 GAGGAAAGUCCGGGCUCCGCAGGGUAGAAUGCCGGUUAACGGCCGGGCGCGGUAACGCGA 6892 >((---(((((,,,,,,,,,,,.,<<<<<..<<<<__________>>.>>>>>-->>,,, 61 gGGAAAGUGCCACAGAAAaCAg.ACCGCC..uggcCggUUagggGgc.caGGUAAGGGUG 116 :GGAAAGU: :ACAGAAA+CA+ ACCGCC UGGC G+UU GG+ GC CAGGUAAGGGUG 6893 CGGAAAGUGGAACAGAAAGCAAaACCGCCgaUGGCUGCUUUGGCAGCaCAGGUAAGGGUG 6952 ,,,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))--))))]] 117 AAAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUAAACCCCA 175 AAAAGGUGCGGUAAG GCGCACCGCGC::::GGU+AC:: ::GCGGCA : :AAACCCCA 6953 AAAAGGUGCGGUAAGGGCGCACCGCGCAUUUGGUAACAAuAUGCGGCAGGCCAAACCCCA 7012 ]]]]]]],,,<<<<------<<<<<-<<--<<________>>-->>>>>>>----->>>> 176 CCcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCcgcuucCGGGUAGGuC 235 ::CGGAGCAA:ACCAAA G:A:GC:: UG: GC+GCCC:CC ::C:U:CGGGUAGGU: 7013 UUCGGAGCAAGACCAAA-CAGAACGCAA-UGACGCUGCCCGCCGAGCGUUCGGGUAGGUU 7070 ,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>> 236 GCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcgg 295 GCUUGAG::::CCGG+AACGG::::CCUAGA+GAAUGA++G+CC 7071 GCUUGAGCAUACCGGUAACGGUAUGCCUAGAGGAAUGACUGUCCG--------------- 7115 >>>::::::::::::::::: 296 gggcgACAGAACCCGGCUUA 315 +GACAGAACCCGGCUUA 7116 ---AGACAGAACCCGGCUUA 7132 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18724,sp|AE003942.1|AE003942 Xylella fastidiosa 9a5c, section 88 of 229 of the complete genome. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGGGCUCCAUAGGGCAAGGUGCCAGGUAACACCUGGGCGGCGUGAGUCGACGGAAAGUGCAACAGAAAGAUACCGCCAAUAUUCCUUUCUAGGAUUCGGUAAGGGUGAAAUGGUGCGGUAAGAGCGCACCGCGAGUUCGGUAACGGACCGGCACGGCAAACCCCACCUGGAGCAAGACCAAAUAGGGAUCCUAUGGUGUGGCCCGCGCUGGAUCCGGGUAGGUUGCUUGAGCACCGUGGUGACGCGGUGCCUAGAUGAAUGGCUGUUCAUGACAGAACCCGGCUUA hit 21 : 8757 9052 (fwd) 349.79 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCUCCA+AGGGCA:GGUGC::GGUAAC CC::G:CG :G+GA: CGA 8757 GAGGAAAGUCCGGGCUCCAUAGGGCAAGGUGCCAGGUAACACCUGGGCGGCGUGAGUCGA 8816 >((---(((((,,,,,,,,,,,,<<<<<...<<<<__________>>>>.>>>-->>,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCC...uggcCggUUagggGgcca.GGUAAGGGUG 116 :GGAAAGU:C:ACAGAAA+ ACCGCC : :CC U+ + GG: : GGUAAGGGUG 8817 CGGAAAGUGCAACAGAAAGAU-ACCGCCaauAUUCCUUUCUA--GGAUUcGGUAAGGGUG 8873 ,,,,<<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->,,)))--))))]]] 117 AAAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGCAcGGUAAACCCCAC 176 AAA GGUGCGGUAAGAGCGCACCGCG+:::CGGU+ACG::: CGGCAC:G:AAACCCCAC 8874 AAAUGGUGCGGUAAGAGCGCACCGCGAGUUCGGUAACGGAC-CGGCACGGCAAACCCCAC 8932 ]]]]]],,,<<<<------<<<<<-<<--<<________>>-->>>>>>>----->>>>, 177 CcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCcgcuucCGGGUAGGuCG 236 C:GGAGCAA:ACCAAAUAGGGA::C:: UGG G+GGCCCGC C::::UCCGGGUAGGU:G 8933 CUGGAGCAAGACCAAAUAGGGAUCCUA-UGGUGUGGCCCGCGCUGGAUCCGGGUAGGUUG 8991 ,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>>> 237 CUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcggg 296 CUUGAG::::: GG++AC :::::CCUAGAUGAAUG+++G+ CA 8992 CUUGAGCACCGUGGUGACGCGGUGCCUAGAUGAAUGGCUGUUCA---------------- 9035 >>::::::::::::::::: 297 ggcgACAGAACCCGGCUUA 315 GACAGAACCCGGCUUA 9036 --UGACAGAACCCGGCUUA 9052 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #19084,sp|AE004311.1|AE004311 Vibrio cholerae chromosome I, section 219 of 251 of the complete chromosome. ----isReversed: 1 ----hitSequence: GAGGAAAGUCCGGGCUCCAUAGAGCAGGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUACGACAAGUGCAACAGAGAGCAAACCGCCGAUGGCCUCUCCUUCGGGAUGGGAUCAGGUAAGGGUGAAAGGGUGCGGUAAGAGCGCACCGUGCGACUGGCAACAGUUCGUAGCAGGGUAAACUCCACCCGGAGCAAGACCAAAUAGGCCUCCACAUAGCGUUGCUCGCGUUAGGAGGCGGGUAGGUUGCUUGAGCCA hit 22 : 262 7 (rev) 261.10 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCUCCA+AG+GCAGGGUGC::GGUAACGCC::G::GG:GC+A:CC:A 14059 GAGGAAAGUCCGGGCUCCAUAGAGCAGGGUGCCAGGUAACGCCUGGGGGGCGCAAGCCUA 14118 >((---(((((,,,,,,,,,,,,<<<<<..<<<<___...____...___>.>>>>>>-- 61 gGGAAAGUGCCACAGAAAaCAgACCGCC..uggcCgg...UUag...ggGg.ccaGGUAA 111 :G: AAGUGC:ACAGA+A+CA+ACCGCC UG:CC + UU+G +GGG :CAGGUAA 14119 CGACAAGUGCAACAGAGAGCAAACCGCCgaUGGCCUCuccUUCGggaUGGGaUCAGGUAA 14178 >>,,,,,,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))--) 112 GGGUGAAAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUAAA 170 GGGUGAAA GGUGCGGUAAGAGCGCACCG: C::C:GG++AC:G ::G :GCA :GUAAA 14179 GGGUGAAAGGGUGCGGUAAGAGCGCACCGUGCGACUGGCAACAGuUCGUAGCAGGGUAAA 14238 )))]]]]]]]]],,,<<<<------<<<<<-<<--<<________>>-->.>>>>>>--- 171 CCCCACCcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCc.gcuucCGGG 229 C:CCACCCGGAGCAA:ACCAAAUAGG::::C::AU:G G++GC+CG: : :::::CGGG 14239 CUCCACCCGGAGCAAGACCAAAUAGGCCUCCACAUAGCGUUGCUCGCGUUaGGAGGCGGG 14298 -->>>>,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<< 230 UAGGuCGCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccg 289 UAGGU:GCUUGA CCA 14299 UAGGUUGCUUGA-----------------------------------GCCA--------- 14314 >>>>>>>>>::::::::::::::::: 290 cggcgggggcgACAGAACCCGGCUUA 315 - -------------------------- - ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #19627,sp|AE004857.1|AE004857 Pseudomonas aeruginosa PAO1, section 418 of 529 of the complete genome. ----isReversed: 1 ----hitSequence: GAGGAAAGUCCGGGCUCCAUAGGGCAGAGUGCCAGGUAACGCCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAGAAAAUAACCGCCUAAGCGCAACAGCGCCGGUAAGGGUGAAAAGGUGCGGUAAGAGCGCACCGCACGGCUGGCAACAGUGCGUGGCUAGGUAAACCCCACUCGGAGCAAGACCAAAUAGGAAUCCAUUGGCGCGGCCCGCGUUGGAUUCGGGUAGGUCGCUUGAGGCGUACAGUGAUGUGCGUCCCAGAGGAAUGGCUGUCCUCGACAGAACCCGGCUUA hit 23 : 302 9 (rev) 372.94 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCUCCA+AGGGCAG:GUGC::GGUAACGCC::G::GG:GCGA:CC:A 10647 GAGGAAAGUCCGGGCUCCAUAGGGCAGAGUGCCAGGUAACGCCUGGGAGGCGCGAGCCUA 10706 >((---(((((,,,,,,,,,,,,<<<<<..<<<<__________>>>>>>>-->>,,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCC..uggcCggUUagggGgccaGGUAAGGGUGAA 118 :GGAAAGUGCCACAGAAAA A ACCGCC G::C +AG ::C GGUAAGGGUGAA 10707 CGGAAAGUGCCACAGAAAAUA-ACCGCCuaAGCGCA-ACAG---CGCCGGUAAGGGUGAA 10761 ,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->.,,)))--))))]]] 119 AaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGC.AcGGUAAACCCCAC 176 AAGGUGCGGUAAGAGCGCACCGC:C: C:GG++AC:G :G:GGC +GGUAAACCCCAC 10762 AAGGUGCGGUAAGAGCGCACCGCACGGCUGGCAACAGuGCGUGGCu-AGGUAAACCCCAC 10820 ]]]]]],,,<<<<------<<<<<-<<--<<________>>-->>>>>>>----->>>>, 177 CcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCcgcuucCGGGUAGGuCG 236 :CGGAGCAAGACCAAAUAGG:A::C:+ UGG GCGGCCCGC +:::U:CGGGUAGGUCG 10821 UCGGAGCAAGACCAAAUAGGAAUCCAU-UGGCGCGGCCCGCGUUGGAUUCGGGUAGGUCG 10879 ,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>>> 237 CUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcggg 296 CUUGAGGCG::C:G++A:G::CGUCC+AGA+GAAUG+++G+CC 10880 CUUGAGGCGUACAGUGAUGUGCGUCCCAGAGGAAUGGCUGUCCU---------------- 10923 >>::::::::::::::::: 297 ggcgACAGAACCCGGCUUA 315 CGACAGAACCCGGCUUA 10924 --CGACAGAACCCGGCUUA 10940 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #20305,sp|AE005541.1|AE005541 Escherichia coli O157:H7 EDL933 genome, contig 3 of 3, section 160 of 290. ----isReversed: 1 ----hitSequence: GAGGAAAGUCCGGGCUCCAUAGGGCAGGGUGCCAGGUAACGCCUGGGGGGGAAACCCACGACCAGUGCAACAGAGAGCAAACCGCCGAUGGCCCGCGCAAGCGGGAUCAGGUAAGGGUGAAAGGGUGCGGUAAGAGCGCACCGCGCGGCUGGUAACAGUCCGUGGCACGGUAAACUCCACCCGGAGCAAGGCCAAAUAGGGGUUCAUAAGGUACGGCCCGUACUGAACCCGGGUAGGCUGCUUGAGCCAGUGAGCGAUUGCUGGCCUAGAUGAAUGACUGUCCACGACAGAACCCGGCUUA hit 24 : 4091 3791 (rev) 360.58 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCUCCA+AGGGCAGGGUGC::GGUAACGCC::G::GG G +A CC:A 6426 GAGGAAAGUCCGGGCUCCAUAGGGCAGGGUGCCAGGUAACGCCUGGGGGG-GAAA-CCCA 6483 >((---(((((,,,,,,,,,,,,<<<<<..<<<<___.._______>.>>>>>>-->>,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCC..uggcCgg..UUagggGg.ccaGGUAAGGGU 115 :G: AGUGC:ACAGA+A+CA+ACCGCC UG:CC+G AG+GGG :CAGGUAAGGGU 6484 CGACCAGUGCAACAGAGAGCAAACCGCCgaUGGCCCGcgCAAGCGGGaUCAGGUAAGGGU 6543 ,,,,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))--))))] 116 GAAAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUAAACCCC 174 GAAA GGUGCGGUAAGAGCGCACCGC C::C:GGU+AC:G ::G GGCAC:GUAAAC:CC 6544 GAAAGGGUGCGGUAAGAGCGCACCGCGCGGCUGGUAACAGuCCGUGGCACGGUAAACUCC 6603 ]]]]]]]],,,<<<<------<<<<<-<<--<<________>>-->>>>>>>----->>> 175 ACCcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCcgcuucCGGGUAGGu 234 ACCCGGAGCAA::CCAAAUAGGG:::C:+A+:G CGGCCCG: C+::::CCGGGUAGG: 6604 ACCCGGAGCAAGGCCAAAUAGGGGUUCAUAAGGUACGGCCCGUACUGAACCCGGGUAGGC 6663 >,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>> 235 CGCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcg 294 :GCUUGAG:C:G:+:GC+A:+:C:G:CCUAGAUGAAUGA++G+CCA 6664 UGCUUGAGCCAGUGAGCGAUUGCUGGCCUAGAUGAAUGACUGUCCA-------------- 6709 >>>>::::::::::::::::: 295 ggggcgACAGAACCCGGCUUA 315 CGACAGAACCCGGCUUA 6710 ----CGACAGAACCCGGCUUA 6726 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #20686,sp|AE005925.1|AE005925 Caulobacter crescentus CB15 section 251 of 359 of the complete genome. ----isReversed: 1 ----hitSequence: GAGGAAAGUCCGGGCUCCACGGUGACAAGGCGGUGGGUAACGCCCACCGGGAGCGAUCCCAGGGAUAGCGCCACAGAAAGCAAACCUCCUCCCUACGGGGCGGGAAGGGUGAAAGGGUGGGGUAAGAGCCCACCGCGGACCUGGUGACAGGGACGGCAUGGCAAGCCCCGCCUGGAGCAAGACCGAAUAGGGAUCCCGCGUCGGCCUCGCGCCGACUAGGCCGUCACUGGCUGAGAGGAUCCGGGUAGGUCGCGAGAGCCGUCCAGCAAUGGCCGGCCUAGAGGAAUGAUCGUCGCCGUCUCCCUGUCUUCGGAUGGGCGGGGCGGAACAGA hit 25 : 332 1 (rev) 313.66 bits ::::::::::::::[[[[---.-----[[[[[<<<<<_____>>>>><<<<<____>>>> 1 GAGGAAAGUCCGGGCUCCACA.GGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCg 59 GAGGAAAGUCCGGGCUCCAC G CA:GG:G:UGGGUAACGCCCA:C:GG:GCGA:CC: 11023 GAGGAAAGUCCGGGCUCCACGgUGACAAGGCGGUGGGUAACGCCCACCGGGAGCGAUCCC 11082 ->((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>>>-->>,,,,,, 60 AgGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGGUAAGGGUGAAA 119 AGGGA AG::CCACAGAAA+CA+ACC CC ::C U +G G:: GG AAGGGUGAAA 11083 AGGGAUAGCGCCACAGAAAGCAAACCUCCUCCC---UACG---GGGCGGGAAGGGUGAAA 11136 ,<<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->,,)))--))))]]]]]] 120 aGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGCAcGGUAAACCCCACCcG 179 GGUG:GGUAAGAGC:CACCGCG :CC:GGUGAC:GG: CGGCA GG:AA:CCCC:CC:G 11137 GGGUGGGGUAAGAGCCCACCGCGGACCUGGUGACAGGGACGGCAUGGCAAGCCCCGCCUG 11196 ]]],,,<<<<------<<<<<-.<<.................--<<________..>>-- 180 GAGCAAGaCCAAAUAGGgaagC.gu.................AugGgGcGGCCC..GccC 219 GAGCAAGACC AAUAGGGA::C G U:GG CG C C G:+ 11197 GAGCAAGACCGAAUAGGGAUCCcGCgucggccucgcgccgac-UAGGCCGUCACugGCUG 11255 >..>>>>>>----->>>>,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,, 220 c..gcuucCGGGUAGGuCGCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGc 277 G::UCCGGGUAGGUCGC +GAG:CG CC:GCAA:GG CG:CCUAGA+GAAUGAUCG+ 11256 AgaGGAUCCGGGUAGGUCGCGAGAGCCGUCCAGCAAUGGCCGGCCUAGAGGAAUGAUCGU 11315 ,,,<<<<<<<<<...............>>>>>>>>>::::::::::::::::: 278 CCAcccccgccg...............cggcgggggcgACAGAACCCGGCUUA 315 C :CC::::C G::::GG: ACAGA 11316 C--GCCGUCUCCcugucuucggaugggCGGGGCGGA--ACAGA---------- 11354 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #20849,sp|AE006088.1|AE006088 Pasteurella multocida PM70 section 55 of 204 of the complete genome. ----isReversed: 0 ----hitSequence: CGCCUGGGAGGCGCGAGCCUACGACAAGUGCAACAGAGAGCAGACCGCCAGUUUCGGCUGGUAAGGGUGAAAGGGUGCGGUAAGAGCGCACCGCAUGGCUGGCAACAGUACAUGGCAGGGUAAACUCCACUCGUAGCAAGACCAAAUAGGAAUCCAAUGAGUGGCCCGCUCAGGAUUCGGGUAGGUUGCUUGAGCGUAUGUGCGAAUGUACGCCUAGAGGAAUGAUUGUCCGCGACAGAACUCGGCUUA hit 26 : 2 250 (fwd) 228.16 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 C GC: + :G::GG:GCGA:CC:A 2 -----------------C------------GCC--------U--GGGAGGCGCGAGCCUA 22 >((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>>>-->>,,,,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGGUAAGGGUGAAAa 120 :G: AAGUGC:ACAGA+A+CAGACCGCC:G UU+G C:GGUAAGGGUGAAA 23 CGACAAGUGCAACAGAGAGCAGACCGCCAGU----UUCG----GCUGGUAAGGGUGAAAG 74 <<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))--))))]]]]]] 121 GGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUAAACCCCACCcG 179 GGUGCGGUAAGAGCGCACCGC::: C:GG++AC:G :::GGCA :GUAAAC:CCAC+CG 75 GGUGCGGUAAGAGCGCACCGCAUGGCUGGCAACAGuACAUGGCAGGGUAAACUCCACUCG 134 ]]],,,<<<<------<<<<<-<<--<<________>>-->>>>>>>----->>>>,,,, 180 GAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCcgcuucCGGGUAGGuCGCUu 239 AGCAA:ACCAAAUAGG:A::C:: U G G+GGCCCGC+C::::U:CGGGUAGGU:GCUU 135 UAGCAAGACCAAAUAGGAAUCCAA-U-GAGUGGCCCGCUCAGGAUUCGGGUAGGUUGCUU 192 ,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>>>>>: 240 GAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcgggggc 299 GAG:::::+:GC+A:+:::::CCUAGA+GAAUGAU+G+CC C 193 GAGCGUAUGUGCGAAUGUACGCCUAGAGGAAUGAUUGUCCG------------------C 234 :::::::::::::::: 300 gACAGAACCCGGCUUA 315 GACAGAAC CGGCUUA 235 GACAGAACUCGGCUUA 250 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #21820,sp|AE007073.1|AE007073 Mycobacterium tuberculosis CDC1551, section 159 of 280 of the complete genome. ----isReversed: 1 ----hitSequence: GAGGAAAGUCCGGACUUCACAGAGCAGGGUGAUUGCUAACGGCAAUCCGAGGUGACUCGCGGGAAAGUGCCACAGAAAACAGACCGCCAUCCUCGUGGUGGCAAGGGUGAAACGGUGCGGUAAGAGCGCACCAGCAUUCCGGGUGACCGGGGUGGCUAGGCAAACCCCACCCGAAGCAAGGCCAAGAAGGCCGCACCGAAAGUGCGGCCGCGCAGGCGCUUGAGGGUUGCUCGCCCGAGCCUGCGGGUAGGCCGCUCGAGGCACCCGGUAACGGUGUGUCCAGAUGGAUGGUCGCCGCCGUGCCGCCGUUAGCUUGGCUGUGGCGGCGCGGAACAGAAUCCGGCUUA hit 27 : 13226 12880 (rev) 347.02 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGG CU:CACAG+GCAGGGUG:U:G:UAACG:C:A:CCG:GG+GAC:CG 4939 GAGGAAAGUCCGGACUUCACAGAGCAGGGUGAUUGCUAACGGCAAUCCGAGGUGACUCGC 4998 >((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>>>-->>,,,,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGGUAAGGGUGAAAa 120 GGGAAAGU:CCACAGAAAACAGACC:CC::: U+G :::GG:AAGGGUGAAA+ 4999 GGGAAAGUGCCACAGAAAACAGACCGCCAUC----CUCG--U-GGUGGCAAGGGUGAAAC 5051 <<<<<<_______>>>>>>.<<<<<<<<<____>>>>>>>>->.,,)))--))))]]]]] 121 GGUGcGGUAAGAGCgCACC.GCgcccccGGUGACgggggcGGC.AcGGUAAACCCCACCc 178 GGUGCGGUAAGAGCGCACC GC:::CC:GGUGAC:GG:::GGC +GG:AAACCCCACCC 5052 GGUGCGGUAAGAGCGCACCaGCAUUCCGGGUGACCGGGGUGGCu-AGGCAAACCCCACCC 5110 ]]]],,,<<<<----......................--<<<<<-<<--.<<________ 179 GGAGCAAGaCCAAAU......................AGGgaagCguAu.gGgGcGGCCC 215 G:AGCAAG:CCAA+ G:A:GCG:+U :GGG++GC+C 5111 GAAGCAAGGCCAAGAaggccgcaccgaaagugcggccGCGCAGGCGCUUgAGGGUUGCUC 5170 >>-->.>>>>>>----->>>>,,,,,,<<<<<<<<____>>>.>>>>>,,,,,,,,,,,, 216 GccCc.gcuucCGGGUAGGuCGCUuGAGgCggccGGCAACgg.ccGuCCuAGAUgAAUGA 273 G:CC: GC:U:CGGGUAGG:CGCU GAGGC::CCGG+AACGG ::GUC +AGAUG+AUG+ 5171 GCCCGaGCCUGCGGGUAGGCCGCUCGAGGCACCCGGUAACGGuGUGUC-CAGAUGGAUGG 5229 ,,,,,,,<<<<<<<<<..................>>>>>>>>>::::::::::::::::: 274 UCGcCCAcccccgccg..................cggcgggggcgACAGAACCCGGCUUA 315 UCGCC :CC::GCCG CGGC::GG: ACAGAA CCGGCUUA 5230 UCGCC--GCCGUGCCGccguuagcuuggcuguggCGGCGCGGA--ACAGAAUCCGGCUUA 5285 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22386,sp|AE007642.1|AE007642 Clostridium acetobutylicum ATCC824 section 130 of 356 of the complete genome. ----isReversed: 0 ----hitSequence: GAGGAAAGUCCGAGCUCCAUAGGGCAGGGUGCCGGGUAACUCCCGGUCAAGGCGACUUGAAGGAAAGUGCAACAGAGAUAUACCGCCAUUUUAUAAUGGUAAGGGUGGAAAGGCGAGGUAAGAGCUCACCAGCGCAUUGGCGACUUUGCGGCUAUGUAAACCCCAUCUGGAGCAAGAUCAAAUAGGGAAGCGUUUUGGAGUGGCCCGCUCUGCUUCCGGGUAGCAUCGCUUGAAUCUUAUGGUAACAUAAGGUCUAGAUAGAUGAUUGUCGAAUACAGAACUCGGCUUA hit 28 : 7963 8251 (fwd) 326.04 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCG GCUCCA+AGGGCA:G UGC:GGGUAAC CCC:G:C::GGCGAC::GA 7963 GAGGAAAGUCCGAGCUCCAUAGGGCAGGGUGCCGGGUAACUCCCGGUCAAGGCGACUUGA 8022 >((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>>>-->>,,,,,,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGGUAAGGGUGAAAa 120 :GGAAAGUGC:ACAGA+A ACCGCC::: UUA :::GGUAAGGGUG AAA 8023 AGGAAAGUGCAACAGAGAUAU-ACCGCCAUU----UUAU----AAUGGUAAGGGUGGAAA 8073 <<<<<<_______>>>>>>.<<<<<<<<<____>>>>>>>>->.,,)))--))))]]]]] 121 GGUGcGGUAAGAGCgCACC.GCgcccccGGUGACgggggcGGC.AcGGUAAACCCCACCc 178 GG:G:GGUAAGAGC:C:CC GCGC: : G+GA : :GCGGC +:GUAAACCCCA C: 8074 GGCGAGGUAAGAGCUCACCaGCGCAUUG-GCGA-CUUUGCGGCu-AUGUAAACCCCAUCU 8130 ]]]],,,<<<<------<<<<<-<<--.<<________>>-->>>>>>>----->.>>>, 179 GGAGCAAGaCCAAAUAGGgaagCguAu.gGgGcGGCCCGccCcgcuucCGGGUAG.GuCG 236 GGAGCAAGA:CAAAUAGGGAAGCG++U GG G+GGCCCGC+C+GCUUCCGGGUAG :UCG 8131 GGAGCAAGAUCAAAUAGGGAAGCGUUUuGGAGUGGCCCGCUCUGCUUCCGGGUAGcAUCG 8190 ,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>>>> 237 CUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcggg 296 CUUGA: C::::GG+AAC::::G :CUAGAU++AUGAU+G+C A 8191 CUUGAAUCUUAUGGUAACAUAAGGUCUAGAUAGAUGAUUGUCGA---------------- 8234 >>::::::::::::::::: 297 ggcgACAGAACCCGGCUUA 315 + ACAGAAC CGGCUUA 8235 --AUACAGAACUCGGCUUA 8251 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22867,sp|AE008127.1|AE008127 Agrobacterium tumefaciens str. C58 circular chromosome, section 185 of 254 of the complete sequence. ----isReversed: 1 ----hitSequence: GAGGAAAGUCCGGGCUCCACGGAAAUACGGUGCCGGAUAACGUCCGGCGGGGGCGACCCCAGGGAAAGUGCCACAGAGAGCAAACCGCCAUGCCUUGCAUGGUAAGGGUGAAAGGGUGGGGUAAGAGCCCACCGCGCCGCUGGUGACAGUGGUGGCAAGGUAAACCCCACCGGGAGCAAGACCGAAUAGGGAUGACACGGGGCGGGCGAAAGCCUGUUCACAGCCGGUUUCCGGGCCCGUCAUCCGGGUGGGUUGCGAGAGGCGGCAUGCAAAUGCCGUCCCAGAUGAAUGGCUGCCACGUUCCGGGUCAAACCGGGGCCAUACAGAACCCGGCUUA hit 29 : 4448 4112 (rev) 346.50 bits ::::::::::::::[[[[-------.-[[[[[<<<<<_____>>>>><<<<<____>>>> 1 GAGGAAAGUCCGGGCUCCACAGGGC.AgGGUGCUGGgUAACGcCCAGccGggGcGAccCg 59 GAGGAAAGUCCGGGCUCCAC G+ A:GGUGC:GG:UAACG:CC:GC:GGGGCGACCC: 7268 GAGGAAAGUCCGGGCUCCACGGAAAuACGGUGCCGGAUAACGUCCGGCGGGGGCGACCCC 7327 ->((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>>>-->>,,,,,, 60 AgGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGGUAAGGGUGAAA 119 AGGGAAAGUGCCACAGA+A+CA+ACCGCC::GC U GC::GGUAAGGGUGAAA 7328 AGGGAAAGUGCCACAGAGAGCAAACCGCCAUGC---CUU----GCAUGGUAAGGGUGAAA 7380 ,<<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->,,)))--))))]]]]]] 120 aGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGCAcGGUAAACCCCACCcG 179 GGUG:GGUAAGAGC:CACCGC CC C:GGUGAC:G GG GGCA+GGUAAACCCCACC:G 7381 GGGUGGGGUAAGAGCCCACCGCGCCGCUGGUGACAGUGGUGGCAAGGUAAACCCCACCGG 7440 ]]],,,<<<<------<<<<<-<<.......................--<<________. 180 GAGCAAGaCCAAAUAGGgaagCgu.......................AugGgGcGGCCC. 215 GAGCAA:ACC AAUAGGGA:G :: A :G G +C 7441 GAGCAAGACCGAAUAGGGAUG-ACacggggcgggcgaaagccuguucACAGCCGGUUUCc 7499 ..>>-->>>>>>>----->>>>,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,, 216 ..GccCcgcuucCGGGUAGGuCGCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGA 273 G:CC::C:UCCGGGU GGU:GC +GAGGCGGC::GCAA::GCCGUCC+AGAUGAAUG+ 7500 ggGCCCGUCAUCCGGGUGGGUUGCGAGAGGCGGCAUGCAAAUGCCGUCCCAGAUGAAUGG 7559 ,,,,,,,<<<<<<<<<......>>>>>>>.>>::::::::::::::::: 274 UCGcCCAcccccgccg......cggcggg.ggcgACAGAACCCGGCUUA 315 ++GCC : ::::C:G C:G:::: : ACAGAACCCGGCUUA 7560 CUGCC--ACGUUCCGGgucaaaCCGGGGCcAU--ACAGAACCCGGCUUA 7604 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23373,sp|AE008634.1|AE008634 Rickettsia conorii Malish 7, section 66 of 114 of the complete genome. ----isReversed: 1 ----hitSequence: GAGGAAAGUCCGGACUCUAUAGAGGUAUGGUGCCGGUUAACCUCCGGCAGAGUAUUAUUACUUUAGGGACAGUACCACAGAAAAUACACCGCCAAGUAUGAAUACGAAGAUCCUUCAAAAAGAGCUAGGAGUUCACAAGACGAGGAACGGAGCGUAUACUUAAUACGUGAGUACCGUAGUACUUGUGAAAUGACGCAGCCAAUUUUUGCAGUUGAUCGAGUAUUUUUGGUAAGGGUGAAAAGGUACGGUAAGAGCGUACCGGUAAGUUGGUAACAAAUUACGCAUGGUAAACCCCACCAAGAGCAAGAUCAAAUAGGCGUUACAGAACUUAUCAAGUUCCCGGGUUAUCUCUAGCCGGCUUGUAAUGCGGGUAGAUCGCUUGAGGUAAACGGUAACGUUUAUCCUAGAUAAAUAACUGCAAU hit 30 : 6846 6425 (rev) 214.47 bits ::::::::::::::[[[[-------.-[[[[[<<<<<_____>>>>><<<<<.____... 1 GAGGAAAGUCCGGGCUCCACAGGGC.AgGGUGCUGGgUAACGcCCAGccGgg.GcGA... 55 GAGGAAAGUCCGG CUC:A+AG+G A:GGUGC:GG UAAC CC:GC:+:G + A 3590 GAGGAAAGUCCGGACUCUAUAGAGGuAUGGUGCCGGUUAACCUCCGGCAGAGuAUUAuua 3649 >>>>->((---(((((,,,,,,,,,,,,<<<<<<<<<_______................ 56 ccCgAgGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUag................ 99 C:+:AGGGA AGU:CCACAGAAAA A ACCGCC::: U G 3650 CUUUAGGGACAGUACCACAGAAAAUACACCGCCAAG----UAUGaauacgaagauccuuc 3705 ............................................................ - ............................................................ - 3706 aaaaagagcuaggaguucacaagacgaggaacggagcguauacuuaauacgugaguaccg 3765 .............................................___>>>>>>>-->>, 100 .............................................ggGgccaGGUAAGGG 114 :::GGUAAGGG 3766 uaguacuugugaaaugacgcagccaauuuuugcaguugaucgaguAUU-UUUGGUAAGGG 3824 ,,,,,,<<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->,,)))--))))] 115 UGAAAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGCAcGGUAAACCCC 174 UGAAAAGGU:CGGUAAGAGCG:ACCG+::: ::GGU+AC:: :::+GCA GG:AAACCCC 3825 UGAAAAGGUACGGUAAGAGCGUACCGGUAAGUUGGUAACAAAUUACGCAUGGUAAACCCC 3884 ]]]]]]]],,,<<<<------<<<<<-<<.....................--<<______ 175 ACCcGGAGCAAGaCCAAAUAGGgaagCgu.....................AugGgGcGGC 213 ACC::GAGCAAGA:CAAAUAGG:::: :: +U:: C+ 3885 ACCAAGAGCAAGAUCAAAUAGGCGUU-ACagaacuuaucaaguucccgggUUAUCUCUAG 3943 __>>-->.>>>>>>----->>>>,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,, 214 CCGccCc.gcuucCGGGUAGGuCGCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUG 272 CC::C : :::::CGGGUAG:UCGCUUGAGG::::CGG+AACG::::UCCUAGAU+AAU 3944 CCGGCUUgUAAUGCGGGUAGAUCGCUUGAGGUAAACGGUAACGUUUAUCCUAGAUAAAUA 4003 ,,,,,,,,<<<<<<<<<>>>>>>>>>::::::::::::::::: 273 AUCGcCCAcccccgccgcggcgggggcgACAGAACCCGGCUUA 315 A++GC 4004 ACUGCAAU----------------------------------- 4011 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23574,sp|AE008849.1|AE008849 Salmonella typhimurium LT2, section 153 of 220 of the complete genome. ----isReversed: 1 ----hitSequence: GAGGAAAGUCCGGGCUCCAUAGGGCAGGGUGCCAGGUAACGCCUGGGGGGGAAACCCACGACCAGUGCAACAGAGAGCAAACCGCCGAUGGCCCACGUAAGUGGGAUCAGGUAAGGGUGAAAGGGUGCGGUAAGAGCGCACCGCGCGGCUGGUAACAGUCCGUGGCACGGUAAACUCCACCCGGAGCAAGGCCAAAUAGGGGUUCAUAAGGUACGGCCCGUACUGAACCCGGGUAGGCUGCUUGAGCCAGUGAGCGAUUGCUGGCCUAGAUGAAUGACUGUCCACGACAGAACCCGGCUUA hit 31 : 15608 15308 (rev) 361.00 bits ::::::::::::::[[[[--------[[[[[<<<<<_____>>>>><<<<<____>>>>- 1 GAGGAAAGUCCGGGCUCCACAGGGCAgGGUGCUGGgUAACGcCCAGccGggGcGAccCgA 60 GAGGAAAGUCCGGGCUCCA+AGGGCAGGGUGC::GGUAACGCC::G::GG G +A CC:A 5271 GAGGAAAGUCCGGGCUCCAUAGGGCAGGGUGCCAGGUAACGCCUGGGGGG-GAAA-CCCA 5328 >((---(((((,,,,,,,,,,,,<<<<<..<<<<___.._______>.>>>>>>-->>,, 61 gGGAAAGUGCCACAGAAAaCAgACCGCC..uggcCgg..UUagggGg.ccaGGUAAGGGU 115 :G: AGUGC:ACAGA+A+CA+ACCGCC UG:CC+ U AG+GGG :CAGGUAAGGGU 5329 CGACCAGUGCAACAGAGAGCAAACCGCCgaUGGCCCAcgUAAGUGGGaUCAGGUAAGGGU 5388 ,,,,,<<<<<<_______>>>>>><<<<<<<<<____>>>.>>>>>->,,)))--))))] 116 GAAAaGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgg.gggcGGCAcGGUAAACCCC 174 GAAA GGUGCGGUAAGAGCGCACCGC C::C:GGU+AC:G ::G GGCAC:GUAAAC:CC 5389 GAAAGGGUGCGGUAAGAGCGCACCGCGCGGCUGGUAACAGuCCGUGGCACGGUAAACUCC 5448 ]]]]]]]],,,<<<<------<<<<<-<<--<<________>>-->>>>>>>----->>> 175 ACCcGGAGCAAGaCCAAAUAGGgaagCguAugGgGcGGCCCGccCcgcuucCGGGUAGGu 234 ACCCGGAGCAA::CCAAAUAGGG:::C:+A+:G CGGCCCG: C+::::CCGGGUAGG: 5449 ACCCGGAGCAAGGCCAAAUAGGGGUUCAUAAGGUACGGCCCGUACUGAACCCGGGUAGGC 5508 >,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,,,,,,<<<<<<<<<>>>>> 235 CGCUuGAGgCggccGGCAACggccGuCCuAGAUgAAUGAUCGcCCAcccccgccgcggcg 294 :GCUUGAG:C:G:+:GC+A:+:C:G:CCUAGAUGAAUGA++G+CCA 5509 UGCUUGAGCCAGUGAGCGAUUGCUGGCCUAGAUGAAUGACUGUCCA-------------- 5554 >>>>::::::::::::::::: 295 ggggcgACAGAACCCGGCUUA 315 CGACAGAACCCGGCUUA 5555 ----CGACAGAACCCGGCUUA 5571 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23882,sp|AE009161.1|AE009161 Agrobacterium tumefaciens strain C58 circular chromosome, section 187 of 256 of the complete sequence. ----isReversed: 1 ----hitSequence: GAGGAAAGUCCGGGCUCCACGGAAAUACGGUGCCGGAUAACGUCCGGCGGGGGCGACCCCAGGGAAAGUGCCACAGAGAGCAAACCGCCAUGCCUUGCAUGGUAAGGGUGAAAGGGUGGGGUAAGAGCCCACCGCGCCGCUGGUGACAGUGGUGGCAAGGUAAACCCCACCGGGAGCAAGACCGAAUAGGGAUGACACGGGGCGGGCGAAAGCCUGUUCACAGCCGGUUUCCGGGCCCGUCAUCCGGGUGGGUUGCGAGAGGCGGCAUGCAAAUGCCGUCCCAGAUGAAUGGCUGCCACGUUCCGGGUCAAACCGGGGCCAUACAGAACCCGGCUUA hit 32 : 4540 4204 (rev) 346.50 bits ::::::::::::::[[[[-------.-[[[[[<<<<<_____>>>>><<<<<____>>>> 1 GAGGAAAGUCCGGGCUCCACAGGGC.AgGGUGCUGGgUAACGcCCAGccGggGcGAccCg 59 GAGGAAAGUCCGGGCUCCAC G+ A:GGUGC:GG:UAACG:CC:GC:GGGGCGACCC: 7268 GAGGAAAGUCCGGGCUCCACGGAAAuACGGUGCCGGAUAACGUCCGGCGGGGGCGACCCC 7327 ->((---(((((,,,,,,,,,,,,<<<<<<<<<__________>>>>>>>-->>,,,,,, 60 AgGGAAAGUGCCACAGAAAaCAgACCGCCuggcCggUUagggGgccaGGUAAGGGUGAAA 119 AGGGAAAGUGCCACAGA+A+CA+ACCGCC::GC U GC::GGUAAGGGUGAAA 7328 AGGGAAAGUGCCACAGAGAGCAAACCGCCAUGC---CUU----GCAUGGUAAGGGUGAAA 7380 ,<<<<<<_______>>>>>><<<<<<<<<____>>>>>>>>->,,)))--))))]]]]]] 120 aGGUGcGGUAAGAGCgCACCGCgcccccGGUGACgggggcGGCAcGGUAAACCCCACCcG 179 GGUG:GGUAAGAGC:CACCGC CC C:GGUGAC:G GG GGCA+GGUAAACCCCACC:G 7381 GGGUGGGGUAAGAGCCCACCGCGCCGCUGGUGACAGUGGUGGCAAGGUAAACCCCACCGG 7440 ]]],,,<<<<------<<<<<-<<.......................--<<________. 180 GAGCAAGaCCAAAUAGGgaagCgu.......................AugGgGcGGCCC. 215 GAGCAA:ACC AAUAGGGA:G :: A :G G +C 7441 GAGCAAGACCGAAUAGG