Origin IGS: aaagctgatggagatggggggaattgaacccccgtcccgaaaagggaatcagaagcgtctacaggcttatcggtgcgaggtggttgtagggatccggtagcagcaccgaaagcgtcgaatccttagtgtaaaaaaagtcccttttaacgtttacacgccgctaaaaagcaagccccgattggcgtcggaatcatgccccgctcggagcagtgcaaagcagattccgcgattatgcagctaaggcgtaatcgaaactgtcgttattttcggcagttatagtgtttgccgaatcaggagatcggcactccgcctgcagcttaagcctccgtctttccggtcgaaaccggaacatccccaagctgtaaatagattactatatttatattaaatttatatgaaaaagtcaagaatatagaaaactaaaatcgaaacattata .........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 tataatgtttcgattttagttttctatattcttgactttttcatataaatttaatataaatatagtaatctatttacagcttggggatgttccggtttcgaccggaaagacggaggcttaagctgcaggcggagtgccgatctcctgattcggcaaacactataactgccgaaaataacgacagtttcgattacgccttagctgcataatcgcggaatctgctttgcactgctccgagcggggcatgattccgacgccaatcggggcttgctttttagcggcgtgtaaacgttaaaagggactttttttacactaaggattcgacgctttcggtgctgctaccggatccctacaaccacctcgcaccgataagcctgtagacgcttctgattcccttttcgggacgggggttcaattccccccatctccatcagcttt Mask Tandem Repeat Region ================================================ aaagctgatggagatggggggaattgaacccccgtcccgaaaagggaatcagaagcgtctacaggcttatcggtgcgaggtggttgtagggatccggtagcagcaccgaaagcgtcgaatccttagtgtaaaaaaagtcccttttaacgtttacacgccgctaaaaagcaagccccgattggcgtcggaatcatgccccgctcggagcagtgcaaagcagattccgcgattatgcagctaaggcgtaatcgaaactgtcgttattttcggcagttatagtgtttgccgaatcaggagatcggcactccgcctgcagcttaagcctccgtctttccggtcgaaaccggaacatccccaagctgtaaatagattactatatttatattaaatttatatgaaaaagtcaagaatatagaaaactaaaatcgaaacattata Find is-nt database================================================ Query_seq: TDE0210:TDE0211|TDE0210:TDE0211:cob(I)yrinic acid a,c-diamide adenosyltransferase:ABC transporter, permease protein, cysTW family:-><-:246207..246644 438 aaagctgatggagatggggggaattgaacccccgtcccgaaaagggaatcagaagcgtctacaggcttatcggtgcgaggtggttgtagggatccggtagcagcaccgaaagcgtcgaatccttagtgtaaaaaaagtcccttttaacgtttacacgccgctaaaaagcaagccccgattggcgtcggaatcatgccccgctcggagcagtgcaaagcagattccgcgattatgcagctaaggcgtaatcgaaactgtcgttattttcggcagttatagtgtttgccgaatcaggagatcggcactccgcctgcagcttaagcctccgtctttccggtcgaaaccggaacatccccaagctgtaaatagattactatatttatattaaatttatatgaaaaagtcaagaatatagaaaactaaaatcgaaacattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0210:TDE0211|TDE0210:TDE0211:cob(I)yrinic acid a,c-diamide adenosyltransferase:ABC transporter, permease protein, cysTW family:-><-:246207..246644 438 aaagctgatggagatggggggaattgaacccccgtcccgaaaagggaatcagaagcgtctacaggcttatcggtgcgaggtggttgtagggatccggtagcagcaccgaaagcgtcgaatccttagtgtaaaaaaagtcccttttaacgtttacacgccgctaaaaagcaagccccgattggcgtcggaatcatgccccgctcggagcagtgcaaagcagattccgcgattatgcagctaaggcgtaatcgaaactgtcgttattttcggcagttatagtgtttgccgaatcaggagatcggcactccgcctgcagcttaagcctccgtctttccggtcgaaaccggaacatccccaagctgtaaatagattactatatttatattaaatttatatgaaaaagtcaagaatatagaaaactaaaatcgaaacattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0210:TDE0211|TDE0210:TDE0211:cob(I)yrinic acid a,c-diamide adenosyltransferase:ABC transporter, permease protein, cysTW family:-><-:246207..246644 438 aaagctgatggagatggggggaattgaacccccgtcccgaaaagggaatcagaagcgtctacaggcttatcggtgcgaggtggttgtagggatccggtagcagcaccgaaagcgtcgaatccttagtgtaaaaaaagtcccttttaacgtttacacgccgctaaaaagcaagccccgattggcgtcggaatcatgccccgctcggagcagtgcaaagcagattccgcgattatgcagctaaggcgtaatcgaaactgtcgttattttcggcagttatagtgtttgccgaatcaggagatcggcactccgcctgcagcttaagcctccgtctttccggtcgaaaccggaacatccccaagctgtaaatagattactatatttatattaaatttatatgaaaaagtcaagaatatagaaaactaaaatcgaaacattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagctgatggagatggggggaattgaacccccgtcccgaaaagggaatcagaagcgtctacaggcttatcggtgcgaggtggttgtagggatccggtagcagcaccgaaagcgtcgaatccttagtgtaaaaaaagtcccttttaacgtttacacgccgctaaaaagcaagccccgattggcgtcggaatcatgccccgctcggagcagtgcaaagcagattccgcgattatgcagctaaggcgtaatcgaaactgtcgttattttcggcagttatagtgtttgccgaatcaggagatcggcactccgcctgcagcttaagcctccgtctttccggtcgaaaccggaacatccccaagctgtaaatagattactatatttatattaaatttatatgaaaaagtcaagaatatagaaaactaaaatcgaaacattata Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 5 End: 97 .... M M E M G G I E P P S R K G N Q K R L Q A Y R C E V V V G I R ..................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 40 Strand: + Start: 119 End: 238 ...................................................................................................................... M L S V K K V P F N V Y T P L K S K P R L A S E S C P A R S S A K Q I P R L C S ........................................................................................................................................................................................................ Protein_Len: 33 Strand: + Start: 178 End: 276 ................................................................................................................................................................................. M G V G I M P R S E Q C K A D S A I M Q L R R N R N C R Y F R Q L .................................................................................................................................................................. Protein_Len: 36 Strand: + Start: 255 End: 362 .............................................................................................................................................................................................................................................................. M S L F S A V I V F A E S G D R H S A C S L S L R L S G R N R N I P K L ............................................................................ Protein_Len: 46 Strand: + Start: 248 End: 385 ....................................................................................................................................................................................................................................................... M E T V V I F G S Y S V C R I R R S A L R L Q L K P P S F R S K P E H P Q A V N R L L Y L Y ..................................................... Protein_Len: 31 Strand: - Start: 321 End: 413 ................................................................................................................................................................................................................................................................................................................................ A E T K G T S V P V D G L Q L Y I V I N I N F K Y S F T L F M ......................... Protein_Len: 45 Strand: - Start: 233 End: 367 ........................................................................................................................................................................................................................................ A A L A Y D F S D N N E A T I T N A S D P S R C E A Q L K L R R R E P R F R F M G L S Y M ....................................................................... aaagctgatggagatggggggaattgaacccccgtcccgaaaagggaatcagaagcgtctacaggcttatcggtgcgaggtggttgtagggatccggtagcagcaccgaaagcgtcgaatccttagtgtaaaaaaagtcccttttaacgtttacacgccgctaaaaagcaagccccgattggcgtcggaatcatgccccgctcggagcagtgcaaagcagattccgcgattatgcagctaaggcgtaatcgaaactgtcgttattttcggcagttatagtgtttgccgaatcaggagatcggcactccgcctgcagcttaagcctccgtctttccggtcgaaaccggaacatccccaagctgtaaatagattactatatttatattaaatttatatgaaaaagtcaagaatatagaaaactaaaatcgaaacattata Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 379 End: 408 ..........................................................................................................................................................................................................................................................................................................................................................................................CTTGACTTTTTCATATAAATTTAATATAAA.............................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 373 End: 402 ....................................................................................................................................................................................................................................................................................................................................................................................TTTTTCATATAAATTTAATATAAATATAGT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagctgatggagatggggggaattgaacccccgtcccgaaaagggaatcagaagcgtctacaggcttatcggtgcgaggtggttgtagggatccggtagcagcaccgaaagcgtcgaatccttagtgtaaaaaaagtcccttttaacgtttacacgccgctaaaaagcaagccccgattggcgtcggaatcatgccccgctcggagcagtgcaaagcagattccgcgattatgcagctaaggcgtaatcgaaactgtcgttattttcggcagttatagtgtttgccgaatcaggagatcggcactccgcctgcagcttaagcctccgtctttccggtcgaaaccggaacatccccaagctgtaaatagattactatatttatattaaatttatatgaaaaagtcaagaatatagaaaactaaaatcgaaacattata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0210:TDE0211|TDE0210:TDE0211:cob(I)yrinic acid a,c-diamide adenosyltransferase:ABC transporter, permease protein, cysTW family:-><-:246207..246644 438 aaagctgatggagatggggggaattgaacccccgtcccgaaaagggaatcagaagcgtctacaggcttatcggtgcgaggtggttgtagggatccggtagcagcaccgaaagcgtcgaatccttagtgtaaaaaaagtcccttttaacgtttacacgccgctaaaaagcaagccccgattggcgtcggaatcatgccccgctcggagcagtgcaaagcagattccgcgattatgcagctaaggcgtaatcgaaactgtcgttattttcggcagttatagtgtttgccgaatcaggagatcggcactccgcctgcagcttaagcctccgtctttccggtcgaaaccggaacatccccaagctgtaaatagattactatatttatattaaatttatatgaaaaagtcaagaatatagaaaactaaaatcgaaacattata Intra-Species Hit: Count: 1 Min: 1 Max: 438 Len: 438 Subject: NC_002967_TDE0210_TDE0211|cob(I)yrinic acid a,c-diamide adenosyltransferase:ABC transporter, permease protein, cysTW family|POSITIVE:NEGATIVE|[246207,246644]|438 HSP 1 e-value: 0.0 bit: 827.0 Len: 438 Query Start:1 Query End:438 Subject Strand: POSITIVE Subject Start: 1 Subject End: 438 aaagctgatggagatggggggaattgaacccccgtcccgaaaagggaatcagaagcgtctacaggcttatcggtgcgaggtggttgtagggatccggtagcagcaccgaaagcgtcgaatccttagtgtnnnnnnngtcccttttaacgtttacacgccgctaaaaagcaagccccgattggcgtcggaatcatgccccgctcggagcagtgcaaagcagattccgcgattatgcagctaaggcgtaatcgaaactgtcgttattttcggcagttatagtgtttgccgaatcaggagatcggcactccgcctgcagcttaagcctccgtctttccggtcgaaaccggaacatccccaagctgtaaatagattactatatttatattaaatttatatgaaaaagtcaagaatatagaaaactaaaatcgaaacattata aaagctgatggagatggggggaattgaacccccgtcccgaaaagggaatcagaagcgtctacaggcttatcggtgcgaggtggttgtagggatccggtagcagcaccgaaagcgtcgaatccttagtgtaaaaaaagtcccttttaacgtttacacgccgctaaaaagcaagccccgattggcgtcggaatcatgccccgctcggagcagtgcaaagcagattccgcgattatgcagctaaggcgtaatcgaaactgtcgttattttcggcagttatagtgtttgccgaatcaggagatcggcactccgcctgcagcttaagcctccgtctttccggtcgaaaccggaacatccccaagctgtaaatagattactatatttatattaaatttatatgaaaaagtcaagaatatagaaaactaaaatcgaaacattata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGCUGAUGGAGAUGGGGGGAAUUGAACCCCCGUCCCGAAAAGGGAAUCAGAAGCGUCUACAGGCUUAUCGGUGCGAGGUGGUUGUAGGGAUCCGGUAGCAGCACCGAAAGCGUCGAAUCCUUAGUGUAAAAAAAGUCCCUUUUAACGUUUACACGCCGCUAAAAAGCAAGCCCCGAUUGGCGUCGGAAUCAUGCCCCGCUCGGAGCAGUGCAAAGCAGAUUCCGCGAUUAUGCAGCUAAGGCGUAAUCGAAACUGUCGUUAUUUUCGGCAGUUAUAGUGUUUGCCGAAUCAGGAGAUCGGCACUCCGCCUGCAGCUUAAGCCUCCGUCUUUCCGGUCGAAACCGGAACAUCCCCAAGCUGUAAAUAGAUUACUAUAUUUAUAUUAAAUUUAUAUGAAAAAGUCAAGAAUAUAGAAAACUAAAAUCGAAACAUUAUA ..((((..(((.((((((((........)))))))))))....((((.....((((........))))...(..(.(((((((((((((((((.((((((..((((.....(((((.((((....(((((((....((........)).)))))))...(((....))).......)))))))))(((((((.(((...((.(......).))...))))))))))(((((((((.......))))))))).((((((((.......))))))))...)))))))))).))).((((.......)))).)))))))))...))))))..).(((((((....)))))))..))))..)))).....(((.((.((((((((..........................)))))))).)).)))................ (-136.77) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAUGUUUCGAUUUUAGUUUUCUAUAUUCUUGACUUUUUCAUAUAAAUUUAAUAUAAAUAUAGUAAUCUAUUUACAGCUUGGGGAUGUUCCGGUUUCGACCGGAAAGACGGAGGCUUAAGCUGCAGGCGGAGUGCCGAUCUCCUGAUUCGGCAAACACUAUAACUGCCGAAAAUAACGACAGUUUCGAUUACGCCUUAGCUGCAUAAUCGCGGAAUCUGCUUUGCACUGCUCCGAGCGGGGCAUGAUUCCGACGCCAAUCGGGGCUUGCUUUUUAGCGGCGUGUAAACGUUAAAAGGGACUUUUUUUACACUAAGGAUUCGACGCUUUCGGUGCUGCUACCGGAUCCCUACAACCACCUCGCACCGAUAAGCCUGUAGACGCUUCUGAUUCCCUUUUCGGGACGGGGGUUCAAUUCCCCCCAUCUCCAUCAGCUUU ......(((..((...(((....)))...))..)))............................((((.....)))).((((((((((((((((((....)))))))...(((((((.....((((((((.(((((.(((..((((..(((((((...........))))))).........(((..(((((..((....))........(((((((((((((((((.(......).)))))))).))))))).))..)))))..)))..((((((((((.........))))))))))................)))).))).)))))(((((((.......((..........)).....)))))))...))))))))..)))))))..((((.....)))).(((((.......)))))))))))))..)))... (-138.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 412 346 301 165 108 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 406 340 292 73 13 NC_002967:TDE0924|5end_ABC_transporter,_ATP-binding/permease_protein_947634..947864_NEGATIVE 401 110 62 76 22 NC_002967:TDE1679|5end_ATP_synthase_subunit_K_1731049..1731279_NEGATIVE 400 57 15 156 106 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 396 116 71 70 28 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 393 337 307 143 113 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 392 349 305 117 73 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 391 120 71 228 182 NC_002967:TDE2329|5end_hypothetical_protein_2366493..2366723_NEGATIVE 389 330 282 84 41 NC_002967:TDE2706|5end_hypothetical_protein_2753793..2754023_NEGATIVE 387 238 193 228 191 NC_002967:TDE2056|5end_outer_membrane_hemin-binding_protein_A_2085070..2085300_NEGATIVE 387 58 15 188 136 NC_002967:TDE0863|5end_MgtC_family_protein_884526..884756_POSITIVE 385 361 321 107 65 NC_002967:TDE1459|5end_hypothetical_protein_1508707..1508937_NEGATIVE 383 330 281 228 183 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 383 340 300 62 8 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 379 360 311 229 179 NC_002967:TDE1143|5end_hypothetical_protein_1181834..1182064_NEGATIVE 378 109 64 192 148 NC_002967:TDE2261|5end_hypothetical_protein_2298013..2298243_NEGATIVE 375 327 281 109 50 NC_002967:TDE0544|5end_hypothetical_protein_583854..584084_POSITIVE 374 45 4 207 167 NC_002967:TDE2583|5end_hypothetical_protein_2616322..2616552_POSITIVE 374 220 173 191 135 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 373 345 307 38 1 NC_002967:TDE2644|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2683651..2683881_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 459 96 56 50 4 NC_002967:TDE1739|3end_femAB_family_protein_1792657..1792807_POSITIVE 417 337 291 140 81 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 416 190 149 49 6 NC_002967:TDE1277|3end_Fe-hydrogenase_large_subunit_family_protein_1312242..1312392_POSITIVE 387 238 193 140 103 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 386 109 61 137 79 NC_002967:TDE2739|3end_hypothetical_protein_2795169..2795319_POSITIVE 385 361 321 107 65 NC_002967:TDE1460|3end_hypothetical_protein_1508707..1508857_NEGATIVE 376 345 305 41 1 NC_002967:TDE2643|3end_oxidoreductase,_FAD-dependent_2683734..2683884_POSITIVE 374 220 173 104 48 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 372 209 170 151 97 NC_002967:TDE2434|3end_polysaccharide_deacetylase_family_protein_2463300..2463450_NEGATIVE 367 337 298 151 112 NC_002967:TDE0857|3end_lipoprotein,_putative_879598..879748_POSITIVE 367 349 303 112 59 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 364 200 158 134 85 NC_002967:TDE2182|3end_hypothetical_protein_2213035..2213185_NEGATIVE 361 328 281 75 18 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 360 239 192 136 81 NC_002967:TDE0616|3end_hypothetical_protein_650079..650229_POSITIVE 358 219 172 78 36 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 356 340 292 139 85 NC_002967:TDE1105|3end_ribosome-binding_factor_A_1137801..1137951_NEGATIVE 356 90 44 134 82 NC_002967:TDE0742|3end_hypothetical_protein_778450..778600_NEGATIVE 355 327 286 135 102 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 355 218 171 62 13 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 355 339 292 126 58 NC_002967:TDE0362|3end_bacterial_Ig-like_domain_protein_407501..407651_NEGATIVE