Origin IGS: agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagctttaattaaagaaataacagtcctttccaaaaagagattgaaaaatttgtaatgcttaaccaggaacagcttcctaattaagcattactactacaccaggtttaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaaacctggtgtagtagtaatgcttaattaggaagctgttcctggttaagcattacaaatttttcaatctctttttggaaaggactgttatttctttaattaaagctatatcaacgttttttagcttcataagtttagctgtttatttcttagtttcataaaaacctttataccataatatttgtaggaattatttgaaaaaaatagtaaattagaaaaatatttttataaattggattaaactaaaaatttgataacaatgcgggttcttagaggcgcagcccataagcggaattttggagaaaggaggggttataggggagggtaacaaccaacgcagtttcaaggtcaaacacctttcttccgaaaaagggtcttagcctcgaagct Mask Tandem Repeat Region ================================================ agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagctttaattaaagaaataacagtcctttccaaaaagagattgaaaaatttgtaatgcttaaccaggaacagcttcctaattaagcattactactacaccaggtttaa Find is-nt database================================================ Query_seq: TDE1982:TDE1983|TDE1982:TDE1983:hypothetical protein:hypothetical protein:<-<-:1993075..1993465 391 agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagctttaattaaagaaataacagtcctttccaaaaagagattgaaaaatttgtaatgcttaaccaggaacagcttcctaattaagcattactactacaccaggtttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1982:TDE1983|TDE1982:TDE1983:hypothetical protein:hypothetical protein:<-<-:1993075..1993465 391 agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagctttaattaaagaaataacagtcctttccaaaaagagattgaaaaatttgtaatgcttaaccaggaacagcttcctaattaagcattactactacaccaggtttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1982:TDE1983|TDE1982:TDE1983:hypothetical protein:hypothetical protein:<-<-:1993075..1993465 391 agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagctttaattaaagaaataacagtcctttccaaaaagagattgaaaaatttgtaatgcttaaccaggaacagcttcctaattaagcattactactacaccaggtttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagctttaattaaagaaataacagtcctttccaaaaagagattgaaaaatttgtaatgcttaaccaggaacagcttcctaattaagcattactactacaccaggtttaa Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 39 End: 176 ...................................... M T L K L R W L L P S P I T P P F S K I P L M G C A S K N P H C Y Q I F S L I Q F I K I F F ....................................................................................................................................................................................................................... Protein_Len: 44 Strand: - Start: 233 End: 364 ........................................................................................................................................................................................................................................ S V L F Y V A L S I F S F F T S I A K I L S I V T R E L F L N F F K Y H K V L F L K R M ........................... Protein_Len: 31 Strand: - Start: 14 End: 106 ............. S G K E S S L H K V K F S R Q N N G E G I V G G K E L I G S M ............................................................................................................................................................................................................................................................................................. agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagctttaattaaagaaataacagtcctttccaaaaagagattgaaaaatttgtaatgcttaaccaggaacagcttcctaattaagcattactactacaccaggtttaa 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================================================ agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagctttaattaaagaaataacagtcctttccaaaaagagattgaaaaatttgtaatgcttaaccaggaacagcttcctaattaagcattactactacaccaggtttaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.7 Tail_Score: -4.75356 Start: 332 End: 377 Full_Region: ttaaacctggtgta gtagtaatgcttaattaggaa gctg ttcctggttaagcattacaaa tttttcaatctcttt ...........................................................................................................................................................................................................................................................................................................................................gtagtaatgcttaattaggaagctgttcctggttaagcattacaaa.............. Find igs database================================================ Query_seq: TDE1982:TDE1983|TDE1982:TDE1983:hypothetical protein:hypothetical protein:<-<-:1993075..1993465 391 agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagctttaattaaagaaataacagtcctttccaaaaagagattgaaaaatttgtaatgcttaaccaggaacagcttcctaattaagcattactactacaccaggtttaa Intra-Species Hit: Count: 2 Min: 1 Max: 391 Len: 391 Subject: NC_002967_TDE1982_TDE1983|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1993075,1993465]|391 HSP 1 e-value: 1.0E-103 bit: 375.0 Len: 189 Query Start:203 Query End:391 Subject Strand: POSITIVE Subject Start: 203 Subject End: 391 ..........................................................................................................................................................................................................cctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagctttaattaaagaaataacagtcctttccaaaaagagattgaaaaatttgtaatgcttaaccaggaacagcttcctaattaagcattactactacaccaggtttaa ..........................................................................................................................................................................................................cctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagctttaattaaagaaataacagtcctttccaaaaagagattgaaaaatttgtaatgcttaaccaggaacagcttcctaattaagcattactactacaccaggtttaa HSP 2 e-value: 2.0E-72 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatc............................................................................................................................................................................................................................................................. agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatc............................................................................................................................................................................................................................................................. Subject: NC_002967_TDE2312_TDE2313|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[2349110,2349595]|486 HSP 1 e-value: 8.0E-63 bit: 242.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 72 Subject End: 209 agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatc............................................................................................................................................................................................................................................................. agcttcaaggctaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatc............................................................................................................................................................................................................................................................. HSP 2 e-value: 3.0E-28 bit: 127.0 Len: 84 Query Start:203 Query End:286 Subject Strand: POSITIVE Subject Start: 274 Subject End: 357 ..........................................................................................................................................................................................................cctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagc......................................................................................................... ..........................................................................................................................................................................................................cctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagc......................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUUCGAGGCUAAGACCCUUUUUCGGAAGAAAGGUGUUUGACCUUGAAACUGCGUUGGUUGUUACCCUCCCCUAUAACCCCUCCUUUCUCCAAAAUUCCGCUUAUGGGCUGCGCCUCUAAGAACCCGCAUUGUUAUCAAAUUUUUAGUUUAAUCCAAUUUAUAAAAAUAUUUUUCUAAUUUACUAUUUUUUUCAAAUAAUUCCUACAAAUAUUAUGGUAUAAAGGUUUUUAUGAAACUAAGAAAUAAACAGCUAAACUUAUGAAGCUAAAAAACGUUGAUAUAGCUUUAAUUAAAGAAAUAACAGUCCUUUCCAAAAAGAGAUUGAAAAAUUUGUAAUGCUUAACCAGGAACAGCUUCCUAAUUAAGCAUUACUACUACACCAGGUUUAA ......(((((..((.(((.....(((((((((((.((((.......))))......((((((...........))))))...))))))).......)))).....)))))..)))))...(((((.((.....((((((.((((((((((.......(((((((((((.(((........((((((...........................)))))).))).)))))))))))..((((...............))))..))))))))))...))))))..)).................(((((((((....)))).)))))........(((((((((((..(((((....)))))..)))))))))))..........))))).. (-78.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAACCUGGUGUAGUAGUAAUGCUUAAUUAGGAAGCUGUUCCUGGUUAAGCAUUACAAAUUUUUCAAUCUCUUUUUGGAAAGGACUGUUAUUUCUUUAAUUAAAGCUAUAUCAACGUUUUUUAGCUUCAUAAGUUUAGCUGUUUAUUUCUUAGUUUCAUAAAAACCUUUAUACCAUAAUAUUUGUAGGAAUUAUUUGAAAAAAAUAGUAAAUUAGAAAAAUAUUUUUAUAAAUUGGAUUAAACUAAAAAUUUGAUAACAAUGCGGGUUCUUAGAGGCGCAGCCCAUAAGCGGAAUUUUGGAGAAAGGAGGGGUUAUAGGGGAGGGUAACAACCAACGCAGUUUCAAGGUCAAACACCUUUCUUCCGAAAAAGGGUCUUAGCCUCGAAGCU ..((((.(((((((((.((((((((((((((((((....))))))))))))))))))...((((((((.......))))))))......................)))))))))..))))...((((((...((((((.((((((.((((.((((((((((((..................))))).)))))))...)))).))))))))))))..................((..((((........))))..)).................(((((...((((.....((((.......(((((((.((.(((((........)))))..))......((((.......)))).))))))))))).....))))....))))))))))) (-93.28) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1038 130 81 221 172 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 617 110 67 220 177 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 611 90 42 189 143 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 533 110 66 229 185 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 478 127 81 215 167 NC_002967:TDE2142|5end_methyl-accepting_chemotaxis_protein_2175769..2175999_POSITIVE 463 88 43 80 37 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 424 100 53 205 154 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 417 127 82 192 135 NC_002967:TDE0619|5end_methyl-accepting_chemotaxis_protein_650318..650548_POSITIVE 412 88 43 96 49 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 412 88 43 75 28 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 412 88 43 197 150 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 408 119 71 194 149 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 373 128 84 210 164 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 370 26 1 230 205 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 361 117 79 50 6 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 341 50 2 108 52 NC_002967:TDE1027|5end_ribonuclease_III_1057562..1057792_POSITIVE 334 88 43 47 8 NC_002967:TDE2310|5end_hypothetical_protein_2348042..2348272_POSITIVE 333 117 71 208 164 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 329 218 171 228 181 NC_002967:TDE2687|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_2728254..2728484_NEGATIVE 328 218 171 174 127 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 534 300 251 51 2 NC_002967:TDE2195|3end_RNA_pseudouridylate_synthase_family_protein_2231911..2232061_POSITIVE 515 90 42 90 43 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 491 300 252 51 3 NC_002967:TDE2437|3end_cyclic_nucleotide_binding_domain_protein_2467418..2467568_NEGATIVE 478 300 251 51 2 NC_002967:TDE2136|3end_hypothetical_protein_2165390..2165540_NEGATIVE 415 148 101 48 2 NC_002967:TDE2098|3end_hypothetical_protein_2124951..2125101_NEGATIVE 386 110 62 78 34 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 372 48 1 86 39 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 362 265 237 29 1 NC_002967:TDE1978|3end_hypothetical_protein_1991501..1991651_NEGATIVE 357 140 96 80 24 NC_002967:TDE1981|3end_hypothetical_protein_1992437..1992587_POSITIVE 352 72 38 82 47 NC_002967:TDE0862|3end_hypothetical_protein_884126..884276_POSITIVE 350 75 31 88 45 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE 349 70 31 61 21 NC_002967:TDE2135|3end_hypothetical_protein_2165418..2165568_POSITIVE 341 50 2 84 28 NC_002967:TDE1026|3end_acyl_carrier_protein_1057618..1057768_POSITIVE 338 86 66 150 131 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 333 117 71 76 32 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 328 129 81 127 67 NC_002967:TDE1157|3end_phage_terminase,_large_subunit,_putative_1192040..1192190_NEGATIVE 327 42 2 65 15 NC_002967:TDE1911|3end_hypothetical_protein_1928943..1929093_NEGATIVE 326 75 34 88 49 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 325 150 102 151 110 NC_002967:TDE0859|3end_hypothetical_protein_881106..881256_POSITIVE 318 136 91 71 27 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE