Origin IGS: gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggagcgaacaggatgttcgctgatttaatcttacgatgttttagacgtaagtctaaaactcgaaagctaaaaaatgtacaggatgtacattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgcaaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctttgcaaagggaaaagattattaagaaaaaccgcaggtttgtcttaatgacaatccatgcctctaacttaggggagatttttaagaggggagctaaaaaatgtacatcctgtacattttttagctttcgagttttagacttacgtctaaaacatcgtaagattaaatcagcgaacatcctgttcgctccccctcttaaatggcgttttgaaaagatgaggggttataggggagaagaaaaacttttgctccatcaaaagtttgtcctctccc Mask Tandem Repeat Region ================================================ gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggagcgaacaggatgttcgctgatttaatcttacgatgttttagacgtaagtctaaaactcgaaagctaaaaaatgtacaggatgtacattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgcaaag Find is-nt database================================================ Query_seq: TDE0969:TDE0970|TDE0969:TDE0970:hypothetical protein:hypothetical protein:->->:994636..994908 273 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggagcgaacaggatgttcgctgatttaatcttacgatgttttagacgtaagtctaaaactcgaaagctaaaaaatgtacaggatgtacattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgcaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0969:TDE0970|TDE0969:TDE0970:hypothetical protein:hypothetical protein:->->:994636..994908 273 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggagcgaacaggatgttcgctgatttaatcttacgatgttttagacgtaagtctaaaactcgaaagctaaaaaatgtacaggatgtacattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgcaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0969:TDE0970|TDE0969:TDE0970:hypothetical protein:hypothetical protein:->->:994636..994908 273 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggagcgaacaggatgttcgctgatttaatcttacgatgttttagacgtaagtctaaaactcgaaagctaaaaaatgtacaggatgtacattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgcaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggagcgaacaggatgttcgctgatttaatcttacgatgttttagacgtaagtctaaaactcgaaagctaaaaaatgtacaggatgtacattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgcaaag Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 57 End: 272 ........................................................ M F S K R H L R G G A N R M F A D L I L R C F R R K S K T R K L K N V Q D V H F L A P L L K I S P K L E A W I V I K T N . Protein_Len: 60 Strand: - Start: 2 End: 271 . L I N A S K I K R H K L R L D L V R F S F F T C S T C K K A G R K F I E G L N S A H I T M L V F R R N K K I I K E R Q M .. gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggagcgaacaggatgttcgctgatttaatcttacgatgttttagacgtaagtctaaaactcgaaagctaaaaaatgtacaggatgtacattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgcaaag Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggagcgaacaggatgttcgctgatttaatcttacgatgttttagacgtaagtctaaaactcgaaagctaaaaaatgtacaggatgtacattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgcaaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 78 HP_score: -10.9 Tail_Score: -3.02568 Start: 87 End: 103 Full_Region: CATTTAAGAGGGGGA GCGAACA GGA TGTTCGC TGATTTAATCTTACG ......................................................................................GCGAACAGGATGTTCGC.......................................................................................................................................................................... TransTerm Strand: - Conf: 77 HP_score: -8.2 Tail_Score: -4.19953 Start: 142 End: 188 Full_Region: aggggagatttttaa gaggggagctaaaaaatgtaca tcc tgtacattttttagctttcgag ttttagacttacgtc .............................................................................................................................................gaggggagctaaaaaatgtacatcctgtacattttttagctttcgag..................................................................................... TransTerm Strand: + Conf: 78 HP_score: -10.8 Tail_Score: -3.05343 Start: 144 End: 186 Full_Region: CGTAAGTCTAAAACT CGAAAGCTAAAAAATGTACA GGA TGTACATTTTTTAGCTCCCC TCTTAAAAATCTCCC ...............................................................................................................................................CGAAAGCTAAAAAATGTACAGGATGTACATTTTTTAGCTCCCC....................................................................................... TransTerm Strand: - Conf: 100 HP_score: -18.1 Tail_Score: -3.76413 Start: 149 End: 181 Full_Region: atttttaagagggga gctaaaaaatgtaca tcc tgtacattttttagc tttcgagttttagac ....................................................................................................................................................gctaaaaaatgtacatcctgtacattttttagc............................................................................................ TransTerm Strand: + Conf: 86 HP_score: -7.2 Tail_Score: -5.09225 Start: 158 End: 172 Full_Region: TCGAAAGCTAAAAAA TGTACA GGA TGTACA TTTTTTAGCTCCCCT .............................................................................................................................................................TGTACAGGATGTACA..................................................................................................... TransTerm Strand: - Conf: 90 HP_score: -7.2 Tail_Score: -5.22039 Start: 158 End: 172 Full_Region: aggggagctaaaaaa tgtaca tcc tgtaca ttttttagctttcga .............................................................................................................................................................tgtacatcctgtaca..................................................................................................... TransTerm Strand: + Conf: 70 HP_score: -7.9 Tail_Score: -3.78026 Start: 223 End: 255 Full_Region: TAGAGGCATGGATTG TCATTAAGACAAACC TGC GGTTTTTCTTAATAA TCTTTTCCCTTTGCA ..............................................................................................................................................................................................................................TCATTAAGACAAACCTGCGGTTTTTCTTAATAA.................. TransTerm Strand: + Conf: 72 HP_score: -9.6 Tail_Score: -2.96755 Start: 226 End: 252 Full_Region: AGGCATGGATTGTCA TTAAGACAAACC TGC GGTTTTTCTTAA TAATCTTTTCCCTTT .................................................................................................................................................................................................................................TTAAGACAAACCTGCGGTTTTTCTTAA..................... Find igs database================================================ Query_seq: TDE0969:TDE0970|TDE0969:TDE0970:hypothetical protein:hypothetical protein:->->:994636..994908 273 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggagcgaacaggatgttcgctgatttaatcttacgatgttttagacgtaagtctaaaactcgaaagctaaaaaatgtacaggatgtacattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgcaaag Intra-Species Hit: Count: 5 Min: 1 Max: 273 Len: 273 Subject: NC_002967_TDE0969_TDE0970|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[994636,994908]|273 HSP 1 e-value: 1.0E-153 bit: 541.0 Len: 273 Query Start:1 Query End:273 Subject Strand: POSITIVE Subject Start: 1 Subject End: 273 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggagcgaacaggatgttcgctgatttaatcttacgatgttttagacgtaagtctaaaactcgaaagctaaaaaatgtacaggatgtacattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgcaaag gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggagcgaacaggatgttcgctgatttaatcttacgatgttttagacgtaagtctaaaactcgaaagctaaaaaatgtacaggatgtacattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgcaaag Subject: NC_002967_TDE0722_TDE0723|lipoprotein, putative:hypothetical protein|POSITIVE:POSITIVE|[759925,760443]|519 HSP 1 e-value: 4.0E-45 bit: 182.0 Len: 100 Query Start:170 Query End:269 Subject Strand: POSITIVE Subject Start: 86 Subject End: 185 .........................................................................................................................................................................acattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgc.... .........................................................................................................................................................................acattttttagctcccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgc.... HSP 2 e-value: 2.0E-40 bit: 167.0 Len: 84 Query Start:1 Query End:84 Subject Strand: POSITIVE Subject Start: 1 Subject End: 84 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg............................................................................................................................................................................................. gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg............................................................................................................................................................................................. Subject: NC_002967_TDE0724_TDE0725|hypothetical protein:exopolysaccharide biosynthesis protein|POSITIVE:POSITIVE|[763298,763604]|307 HSP 1 e-value: 2.0E-41 bit: 170.0 Len: 86 Query Start:1 Query End:86 Subject Strand: POSITIVE Subject Start: 1 Subject End: 86 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggga........................................................................................................................................................................................... gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggga........................................................................................................................................................................................... HSP 2 e-value: 9.0E-37 bit: 155.0 Len: 93 Query Start:170 Query End:262 Subject Strand: POSITIVE Subject Start: 87 Subject End: 180 .........................................................................................................................................................................acattttttagctcccc-tcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttc........... .........................................................................................................................................................................acattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttc........... Subject: NC_002967_TDE0715_TDE0716|hypothetical protein:CAAX amino terminal protease family protein|POSITIVE:POSITIVE|[750611,750967]|357 HSP 1 e-value: 2.0E-40 bit: 167.0 Len: 100 Query Start:170 Query End:269 Subject Strand: POSITIVE Subject Start: 86 Subject End: 185 .........................................................................................................................................................................acattttttagctcccctcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctttgc.... .........................................................................................................................................................................acattttttagctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgc.... HSP 2 e-value: 4.0E-36 bit: 153.0 Len: 77 Query Start:8 Query End:84 Subject Strand: POSITIVE Subject Start: 8 Subject End: 84 .......gacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg............................................................................................................................................................................................. .......gacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg............................................................................................................................................................................................. Subject: NC_002967_TDE0723_TDE0724|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[761722,761992]|271 HSP 1 e-value: 1.0E-29 bit: 131.0 Len: 97 Query Start:170 Query End:266 Subject Strand: POSITIVE Subject Start: 67 Subject End: 163 .........................................................................................................................................................................acattttttagctcccc-tcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctt....... .........................................................................................................................................................................acattttttagctccccctcttaaaaatctcccctaagtta-aggtgtggattatcattaagacaaacctacggtttttcttaataatcttttccctt....... HSP 2 e-value: 2.0E-28 bit: 127.0 Len: 64 Query Start:21 Query End:84 Subject Strand: POSITIVE Subject Start: 1 Subject End: 64 ....................tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg............................................................................................................................................................................................. ....................tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg............................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAGAGGACAAACUUUUGAUGGAGCAAAAGUUUUUCUUCUCCCCUAUAACCCCUCAUCUUUUCAAAACGCCAUUUAAGAGGGGGAGCGAACAGGAUGUUCGCUGAUUUAAUCUUACGAUGUUUUAGACGUAAGUCUAAAACUCGAAAGCUAAAAAAUGUACAGGAUGUACAUUUUUUAGCUCCCCUCUUAAAAAUCUCCCCUAAGUUAGAGGCAUGGAUUGUCAUUAAGACAAACCUGCGGUUUUUCUUAAUAAUCUUUUCCCUUUGCAAAG (((((((((.(((((((((......))))))))).)))))))))..............((((.((((..(((.(((((((((((.(((((((.....)))))))............(((.(((((((((....))))))))))))..(((((((((((((((.....))))))))))))))))))))))))))..(((..(....)..))))))..(((..(..(((((((.(((((...))))).)))))))...)...))).)))).)))) (-104.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUGCAAAGGGAAAAGAUUAUUAAGAAAAACCGCAGGUUUGUCUUAAUGACAAUCCAUGCCUCUAACUUAGGGGAGAUUUUUAAGAGGGGAGCUAAAAAAUGUACAUCCUGUACAUUUUUUAGCUUUCGAGUUUUAGACUUACGUCUAAAACAUCGUAAGAUUAAAUCAGCGAACAUCCUGUUCGCUCCCCCUCUUAAAUGGCGUUUUGAAAAGAUGAGGGGUUAUAGGGGAGAAGAAAAACUUUUGCUCCAUCAAAAGUUUGUCCUCUCCC ((((.(((((.(......(((((((((.(((((...))))).)))))))))....((((.((((((...))))))......((((((((((.((((((((((((((.....))))))))))))))...((((((((((((....))))))))).)))............(((((((.....))))))).))))))))))))))).))))).))))..............((((((.((.(((((((((......))))))))).)).)))))) (-98.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 582 170 121 151 102 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 522 170 121 227 178 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 474 181 141 46 6 NC_002967:TDE1934|5end_hypothetical_protein_1952614..1952844_POSITIVE 464 170 121 174 125 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 436 71 34 213 170 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 421 89 41 205 160 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 393 79 34 226 179 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 384 46 1 60 15 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 384 46 1 182 137 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 370 89 41 210 169 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 367 73 31 180 137 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 345 86 41 118 76 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 337 84 41 102 62 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 334 63 22 220 182 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 326 129 81 124 69 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 326 49 1 170 126 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 320 147 112 211 178 NC_002967:TDE1936|5end_hypothetical_protein_1953086..1953316_POSITIVE 320 147 112 119 86 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 320 182 141 223 185 NC_002967:TDE1933|5end_hypothetical_protein_1952611..1952841_NEGATIVE 315 190 141 192 143 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 522 170 121 75 26 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 494 170 121 76 27 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 476 181 141 88 48 NC_002967:TDE0834|3end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854291..854441_NEGATIVE 471 47 1 93 47 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 471 47 1 93 47 NC_002967:TDE0724|3end_hypothetical_protein_763237..763387_POSITIVE 471 47 1 93 47 NC_002967:TDE0722|3end_lipoprotein,_putative_759864..760014_POSITIVE 468 46 1 51 7 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 453 189 141 92 46 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 449 47 1 113 67 NC_002967:TDE0723|3end_hypothetical_protein_761661..761811_POSITIVE 427 160 112 134 89 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 422 90 43 120 72 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 402 47 1 93 47 NC_002967:TDE0715|3end_hypothetical_protein_750550..750700_POSITIVE 383 150 101 52 3 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 383 45 1 83 43 NC_002967:TDE2420|3end_DNA-directed_RNA_polymerase_beta'_subunit_2444960..2445110_NEGATIVE 369 45 1 82 41 NC_002967:TDE0665|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_699792..699942_NEGATIVE 361 187 142 46 1 NC_002967:TDE0975|3end_hypothetical_protein_999879..1000029_POSITIVE 359 50 1 143 95 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 349 90 44 120 72 NC_002967:TDE1569|3end_hypothetical_protein_1619975..1620125_POSITIVE 334 63 22 133 95 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 331 140 91 95 44 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE