Origin IGS: taaaccgcaggaaaagggtcgagggttttattcaaaacccacaaccttttttagagaatacgataacggcaatttactgaacaggcagaatggtgggaatgccacgaacacggttaaacacagaatgcagtgcattcgttttcaagcagaaaaatgctttatgtgtaaacggcctattgggtagcattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatcgggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaagaaataacgaaaagaggacttttatatgaacagaaacaacagaaagactgcccgatggcagcaacaggagaagaaagaacagcgg .........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 ccgctgttctttcttctcctgttgctgccatcgggcagtctttctgttgtttctgttcatataaaagtcctcttttcgttatttcttaatttctgatggctgaccgatgagaacggagtgattacggtctaacctcccgataattaaacgaggagagcaagcgcagtttgtgggtacaaactgacgtcttgcaatgctacccaataggccgtttacacataaagcatttttctgcttgaaaacgaatgcactgcattctgtgtttaaccgtgttcgtggcattcccaccattctgcctgttcagtaaattgccgttatcgtattctctaaaaaaggttgtgggttttgaataaaaccctcgacccttttcctgcggttta Mask Tandem Repeat Region ================================================ taaaccgcaggaaaagggtcgagggttttattcaaaacccacaaccttttttagagaatacgataacggcaatttactgaacaggcagaatggtgggaatgccacgaacacggttaaacacagaatgcagtgcattcgttttcaagcagaaaaatgctttatgtgtaaacggcctattgggtagcattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatcgggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaagaaataacgaaaagaggacttttatatgaacagaaacaacagaaagactgcccgatggcagcaacaggagaagaaagaacagcgg Find is-nt database================================================ Query_seq: PI0745:PI0746|PI0745:PI0746:conserved hypothetical protein:hypothetical protein:->->:675731..676110 380 taaaccgcaggaaaagggtcgagggttttattcaaaacccacaaccttttttagagaatacgataacggcaatttactgaacaggcagaatggtgggaatgccacgaacacggttaaacacagaatgcagtgcattcgttttcaagcagaaaaatgctttatgtgtaaacggcctattgggtagcattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatcgggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaagaaataacgaaaagaggacttttatatgaacagaaacaacagaaagactgcccgatggcagcaacaggagaagaaagaacagcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0745:PI0746|PI0745:PI0746:conserved hypothetical protein:hypothetical protein:->->:675731..676110 380 taaaccgcaggaaaagggtcgagggttttattcaaaacccacaaccttttttagagaatacgataacggcaatttactgaacaggcagaatggtgggaatgccacgaacacggttaaacacagaatgcagtgcattcgttttcaagcagaaaaatgctttatgtgtaaacggcctattgggtagcattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatcgggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaagaaataacgaaaagaggacttttatatgaacagaaacaacagaaagactgcccgatggcagcaacaggagaagaaagaacagcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0745:PI0746|PI0745:PI0746:conserved hypothetical protein:hypothetical protein:->->:675731..676110 380 taaaccgcaggaaaagggtcgagggttttattcaaaacccacaaccttttttagagaatacgataacggcaatttactgaacaggcagaatggtgggaatgccacgaacacggttaaacacagaatgcagtgcattcgttttcaagcagaaaaatgctttatgtgtaaacggcctattgggtagcattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatcgggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaagaaataacgaaaagaggacttttatatgaacagaaacaacagaaagactgcccgatggcagcaacaggagaagaaagaacagcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaccgcaggaaaagggtcgagggttttattcaaaacccacaaccttttttagagaatacgataacggcaatttactgaacaggcagaatggtgggaatgccacgaacacggttaaacacagaatgcagtgcattcgttttcaagcagaaaaatgctttatgtgtaaacggcctattgggtagcattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatcgggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaagaaataacgaaaagaggacttttatatgaacagaaacaacagaaagactgcccgatggcagcaacaggagaagaaagaacagcgg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 77 End: 181 ............................................................................ M N R Q N G G N A T N T V K H R M Q C I R F Q A E K C F M C K R P I G ....................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 90 End: 299 ......................................................................................... M V G M P R T R L N T E C S A F V F K Q K N A L C V N G L L G S I A R R Q F V P T N C A C S P R L I I G R L D R N H S V ................................................................................. Protein_Len: 30 Strand: - Start: 288 End: 377 ............................................................................................................................................................................................................................................................................................... F N L F L S F L V K I H V S V V S L S G S P L L L L L F F M ... Protein_Len: 37 Strand: - Start: 77 End: 187 ............................................................................ Q V P L I T P I G R V R N F V S H L A N T K L C F F A K H T F P R N P L M ................................................................................................................................................................................................. Protein_Len: 35 Strand: - Start: 31 End: 135 .............................. E F G V V K K L S Y S L P L K S F L C F P P F A V F V T L C L I C H M ..................................................................................................................................................................................................................................................... taaaccgcaggaaaagggtcgagggttttattcaaaacccacaaccttttttagagaatacgataacggcaatttactgaacaggcagaatggtgggaatgccacgaacacggttaaacacagaatgcagtgcattcgttttcaagcagaaaaatgctttatgtgtaaacggcctattgggtagcattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatcgggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaagaaataacgaaaagaggacttttatatgaacagaaacaacagaaagactgcccgatggcagcaacaggagaagaaagaacagcgg 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================================================ taaaccgcaggaaaagggtcgagggttttattcaaaacccacaaccttttttagagaatacgataacggcaatttactgaacaggcagaatggtgggaatgccacgaacacggttaaacacagaatgcagtgcattcgttttcaagcagaaaaatgctttatgtgtaaacggcctattgggtagcattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatcgggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaagaaataacgaaaagaggacttttatatgaacagaaacaacagaaagactgcccgatggcagcaacaggagaagaaagaacagcgg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 84 HP_score: -11.5 Tail_Score: -3.16936 Start: 17 End: 46 Full_Region: gtattctctaaaaaa ggttgtgggtttt gaat aaaaccctcgacc cttttcctgcggttt ................ggttgtgggttttgaataaaaccctcgacc.............................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 79 HP_score: -10.7 Tail_Score: -2.90456 Start: 189 End: 224 Full_Region: CTATTGGGTAGCATT GCAAGACGTCAGTTTGT ACCC ACAAACTGCGCTTGC TCTCCTCGTTTAATT ............................................................................................................................................................................................GCAAGACGTCAGTTTGTACCCACAAACTGCGCTTGC............................................................................................................................................................ Find igs database================================================ Query_seq: PI0745:PI0746|PI0745:PI0746:conserved hypothetical protein:hypothetical protein:->->:675731..676110 380 taaaccgcaggaaaagggtcgagggttttattcaaaacccacaaccttttttagagaatacgataacggcaatttactgaacaggcagaatggtgggaatgccacgaacacggttaaacacagaatgcagtgcattcgttttcaagcagaaaaatgctttatgtgtaaacggcctattgggtagcattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatcgggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaagaaataacgaaaagaggacttttatatgaacagaaacaacagaaagactgcccgatggcagcaacaggagaagaaagaacagcgg Intra-Species Hit: Count: 3 Min: 1 Max: 380 Len: 380 Subject: pint_PI0745_PI0746|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[675731,676110]|380 HSP 1 e-value: 0.0 bit: 753.0 Len: 380 Query Start:1 Query End:380 Subject Strand: POSITIVE Subject Start: 1 Subject End: 380 taaaccgcaggaaaagggtcgagggttttattcaaaacccacaaccttttttagagaatacgataacggcaatttactgaacaggcagaatggtgggaatgccacgaacacggttaaacacagaatgcagtgcattcgttttcaagcagaaaaatgctttatgtgtaaacggcctattgggtagcattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatcgggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaagaaataacgaaaagaggacttttatatgaacagaaacaacagaaagactgcccgatggcagcaacaggagaagaaagaacagcgg taaaccgcaggaaaagggtcgagggttttattcaaaacccacaaccttttttagagaatacgataacggcaatttactgaacaggcagaatggtgggaatgccacgaacacggttaaacacagaatgcagtgcattcgttttcaagcagaaaaatgctttatgtgtaaacggcctattgggtagcattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatcgggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaagaaataacgaaaagaggacttttatatgaacagaaacaacagaaagactgcccgatggcagcaacaggagaagaaagaacagcgg Subject: pint_PI0375_PI0376|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[346143,346556]|414 HSP 1 e-value: 8.0E-35 bit: 149.0 Len: 145 Query Start:185 Query End:329 Subject Strand: NEGATIVE Subject Start: 52 Subject End: 206 ........................................................................................................................................................................................cattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatc-gggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaag---------aaataacgaaaagaggacttttatatgaacaga................................................... ........................................................................................................................................................................................cattgcaagacgtcagtttgtacccacaaactgcgcttgctcccctcgttcggttatcggggagattagaccgtaatcactccgttctcatcggtcagcgttcggaaattaagcaagattgaaaacaaagaaaagaggacttttatatgaacaga................................................... Subject: pint_PI1543_PI1544|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1463342,1463646]|305 HSP 1 e-value: 3.0E-31 bit: 137.0 Len: 120 Query Start:180 Query End:299 Subject Strand: NEGATIVE Subject Start: 42 Subject End: 162 ...................................................................................................................................................................................ggtagcattgcaagacgtcagtttgtacccacaaactgcgcttgctctcctcgtttaattatc-gggaggttagaccgtaatcactccgttctcatcggtcagccatcagaaattaagaaa................................................................................. ...................................................................................................................................................................................ggtagcattgcaagacgtcagtttgtacccacaaactgctcttgctcccctcgttcgattgtcggggagataagaccgtaatcactccgttctcatcggtcagtattcaggaattaagaaa................................................................................. Inter-species Hit: Count: 1 Min: 180 Max: 281 Len: 102 Subject: tfor_TF1631_TF1632|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1743594,1743999]|406 HSP 1 e-value: 2.0E-23 bit: 111.0 Len: 102 Query Start:180 Query End:281 Subject Strand: NEGATIVE Subject Start: 125 Subject End: 228 ...................................................................................................................................................................................ggtagcattgcaagacgtcagtttgtacccacaaactgcgctt-gctctcctcgtttaattatcggg-aggttagaccgtaatcactccgttctcatcggtcag................................................................................................... ...................................................................................................................................................................................ggtagcattgcaagacgtcagtttgtacccacaaactgcgcccagctcccctcgttagattgtcggggagataagaccgtaatcactccgttctcatcggtcag................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUAGCAUUGCAAGACGUCAGUUUGUACCCACAAACUGCGCUUGCUCUCCUCGUUUAAUUAUCGGGAGGUUAGACCGUAAUCACUCCGUUCUCAUCGGUCAG .........(((((.((.((((((((....))))))))))))))).(((((.((......)).)))))....(((((..................))))).. (-31.37) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGACCGAUGAGAACGGAGUGAUUACGGUCUAACCUCCCGAUAAUUAAACGAGGAGAGCAAGCGCAGUUUGUGGGUACAAACUGACGUCUUGCAAUGCUACC ..(((((.(((..((...))..))))))))....((((((.........)).)))).(((((((((((((((....)))))))).)).)))))......... (-32.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 78 36 228 186 pint:PI1567|5end_hypothetical_protein_1489229..1489459_POSITIVE 325 69 27 224 185 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 325 69 27 57 18 pint:PI0196|5end_hypothetical_protein_188435..188665_POSITIVE 319 45 4 127 81 pint:PI0906|5end_hypothetical_protein_835653..835883_POSITIVE 319 89 41 96 52 pint:PI0011|5end_conserved_hypothetical_protein_12142..12372_POSITIVE 318 69 21 214 170 pint:PI1767|5end_fructokinase,_pfkB_family_1694285..1694515_POSITIVE 316 76 36 223 180 pint:PI2005|5end_potassium_uptake_protein_1962950..1963180_POSITIVE 315 71 36 163 124 pint:PI0428|5end_hypothetical_protein_393080..393310_POSITIVE 293 96 63 174 142 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 288 75 36 213 172 pint:PI1382|5end_hypothetical_protein_1303608..1303838_POSITIVE 287 41 1 113 77 pint:PI0434|5end_possible_beta-lactamase_405692..405922_POSITIVE 284 44 1 89 43 pint:PI1911|5end_ribosomal_protein_S20_1855904..1856134_POSITIVE 282 43 5 185 144 pint:PI1870|5end_hypothetical_protein_1815302..1815532_POSITIVE 282 45 1 202 153 pint:PI0581|5end_conserved_hypothetical_protein_525055..525285_POSITIVE 282 43 5 212 171 pint:PI0159|5end_hypothetical_protein_151273..151503_POSITIVE 282 43 5 124 83 pint:PI0157|5end_hypothetical_protein_151185..151415_POSITIVE 281 43 1 102 55 pint:PI0851|5end_hypothetical_protein_784310..784540_POSITIVE 281 43 1 229 182 pint:PI0842|5end_5-formyltetrahydrofolate_cyclo-ligase_775533..775763_POSITIVE 281 43 1 102 55 pint:PI0841|5end_hypothetical_protein_775406..775636_POSITIVE 278 50 9 65 14 pint:PI0259|5end_conserved_protein_found_in_conjugation,_TraI_252355..252585_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 537 100 72 29 1 pint:PI1543|3end_hypothetical_protein_1463281..1463431_POSITIVE 327 78 36 143 101 pint:PI1566|3end_predicted_TPR-repeat-containing_protein_1489224..1489374_POSITIVE 326 46 2 109 64 pint:PI1818|3end_hypothetical_protein_1757270..1757420_POSITIVE 315 71 36 91 52 pint:PI0427|3end_conserved_hypothetical_protein_393088..393238_POSITIVE 302 75 31 63 5 pint:PI1723|3end_conserved_hypothetical_protein_1642133..1642283_POSITIVE 301 47 1 118 70 pint:PI0721|3end_hypothetical_protein_654982..655132_POSITIVE 300 42 1 138 93 pint:PI0615|3end_hydrolase,_haloacid_dehalogenase-like_family_565386..565536_POSITIVE 284 44 1 70 24 pint:PI1910|3end_hypothetical_protein_1855965..1856115_POSITIVE 280 90 44 100 43 pint:PI0225|3end_conserved_hypothetical_protein_222759..222909_POSITIVE 273 50 6 106 56 pint:PI0026|3end_two-component_system_response_regulator_30537..30687_POSITIVE 270 77 38 135 84 pint:PI0624|3end_hypothetical_protein_574471..574621_POSITIVE 269 46 5 56 19 pint:PI1630|3end_hypothetical_protein_1552494..1552644_POSITIVE 265 69 23 118 71 pint:PI0243|3end_hypothetical_protein_240738..240888_POSITIVE 263 55 11 63 21 pint:PI1458|3end_dihydroneopterin_aldolase_1381626..1381776_POSITIVE 263 88 41 62 15 pint:PI0247|3end_conjugative_transposon_protein,_TraA_246232..246382_POSITIVE 261 48 7 69 19 pint:PI1848|3end_hypothetical_protein_1795015..1795165_POSITIVE 259 77 37 57 22 pint:PI1815|3end_polyphosphate-selective_porin_O_1754510..1754660_POSITIVE 259 47 1 59 13 pint:PI0028|3end_aminopeptidase_32727..32877_POSITIVE 257 49 1 74 12 pint:PI0262|3end_conserved_hypothetical_protein_255094..255244_POSITIVE 256 67 21 82 45 pint:PI0573|3end_aminopeptidase_C_(bleomycin_hydrolase)_519219..519369_POSITIVE