Origin IGS: taataggggctcatagatgtcaggaaggtgataaatgataccccctataatgggtgtgtgttgctcgtagtaaagttccaagcacacagatgctacccttgatatattcgtttctcttgaacatactgatggctccagcatcgcgaaaggagttacagtaatagcaatactgatgcaaccattggatggtttctctttcatattcttcgaattagttatgttttcttgttttatctccttattggtttcaatttttgatgatacctgaatgggaataacgagctatatttcttcaagaagaatcctgcttgattaaaagacaaaaaactacgaaggtatttttatttgtcttaaacaaaaagaggtcgtgccaaatagacacgacctctttgtatttcaagtcttataaaactctttatta .........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 taataaagagttttataagacttgaaatacaaagaggtcgtgtctatttggcacgacctctttttgtttaagacaaataaaaataccttcgtagttttttgtcttttaatcaagcaggattcttcttgaagaaatatagctcgttattcccattcaggtatcatcaaaaattgaaaccaataaggagataaaacaagaaaacataactaattcgaagaatatgaaagagaaaccatccaatggttgcatcagtattgctattactgtaactcctttcgcgatgctggagccatcagtatgttcaagagaaacgaatatatcaagggtagcatctgtgtgcttggaactttactacgagcaacacacacccattatagggggtatcatttatcaccttcctgacatctatgagcccctatta Mask Tandem Repeat Region ================================================ taataggggctcatagatgtcaggaaggtgataaatgataccccctataatgggtgtgtgttgctcgtagtaaagttccaagcacacagatgctacccttgatatattcgtttctcttgaacatactgatggctccagcatcgcgaaaggagttacagtaatagcaatactgatgcaaccattggatggtttctctttcatattcttcgaattagttatgttttcttgttttatctccttattggtttcaatttttgatgatacctgaatgggaataacgagctatatttcttcaagaagaatcctgcttgattaaaagacaaaaaactacgaaggtatttttatttgtcttaaacaaaaagaggtcgtgccaaatagacacgacctctttgtatttcaagtcttataaaactctttatta Find is-nt database================================================ Query_seq: PI1715:PI1717|PI1715:PI1717:conserved hypothetical protein; possible DNA-binding protein, histone-like family:major outer membrane protein:->->:1632385..1632805 421 taataggggctcatagatgtcaggaaggtgataaatgataccccctataatgggtgtgtgttgctcgtagtaaagttccaagcacacagatgctacccttgatatattcgtttctcttgaacatactgatggctccagcatcgcgaaaggagttacagtaatagcaatactgatgcaaccattggatggtttctctttcatattcttcgaattagttatgttttcttgttttatctccttattggtttcaatttttgatgatacctgaatgggaataacgagctatatttcttcaagaagaatcctgcttgattaaaagacaaaaaactacgaaggtatttttatttgtcttaaacaaaaagaggtcgtgccaaatagacacgacctctttgtatttcaagtcttataaaactctttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1715:PI1717|PI1715:PI1717:conserved hypothetical protein; possible DNA-binding protein, histone-like family:major outer membrane protein:->->:1632385..1632805 421 taataggggctcatagatgtcaggaaggtgataaatgataccccctataatgggtgtgtgttgctcgtagtaaagttccaagcacacagatgctacccttgatatattcgtttctcttgaacatactgatggctccagcatcgcgaaaggagttacagtaatagcaatactgatgcaaccattggatggtttctctttcatattcttcgaattagttatgttttcttgttttatctccttattggtttcaatttttgatgatacctgaatgggaataacgagctatatttcttcaagaagaatcctgcttgattaaaagacaaaaaactacgaaggtatttttatttgtcttaaacaaaaagaggtcgtgccaaatagacacgacctctttgtatttcaagtcttataaaactctttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1715:PI1717|PI1715:PI1717:conserved hypothetical protein; possible DNA-binding protein, histone-like family:major outer membrane protein:->->:1632385..1632805 421 taataggggctcatagatgtcaggaaggtgataaatgataccccctataatgggtgtgtgttgctcgtagtaaagttccaagcacacagatgctacccttgatatattcgtttctcttgaacatactgatggctccagcatcgcgaaaggagttacagtaatagcaatactgatgcaaccattggatggtttctctttcatattcttcgaattagttatgttttcttgttttatctccttattggtttcaatttttgatgatacctgaatgggaataacgagctatatttcttcaagaagaatcctgcttgattaaaagacaaaaaactacgaaggtatttttatttgtcttaaacaaaaagaggtcgtgccaaatagacacgacctctttgtatttcaagtcttataaaactctttatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taataggggctcatagatgtcaggaaggtgataaatgataccccctataatgggtgtgtgttgctcgtagtaaagttccaagcacacagatgctacccttgatatattcgtttctcttgaacatactgatggctccagcatcgcgaaaggagttacagtaatagcaatactgatgcaaccattggatggtttctctttcatattcttcgaattagttatgttttcttgttttatctccttattggtttcaatttttgatgatacctgaatgggaataacgagctatatttcttcaagaagaatcctgcttgattaaaagacaaaaaactacgaaggtatttttatttgtcttaaacaaaaagaggtcgtgccaaatagacacgacctctttgtatttcaagtcttataaaactctttatta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 54 End: 158 ..................................................... M C V A R S K V P S T Q M L P L I Y S F L L N I L M A P A S R K E L Q ....................................................................................................................................................................................................................................................................... Protein_Len: 54 Strand: + Start: 104 End: 265 ....................................................................................................... M F V S L E H T D G S S I A K G V T V I A I L M Q P L D G F S F I F F E L V M F S C F I S L L V S I F D D T ............................................................................................................................................................ Protein_Len: 45 Strand: + Start: 285 End: 419 ............................................................................................................................................................................................................................................................................................ M F L Q E E S C L I K R Q K T T K V F L F V L N K K R S C Q I D T T S L Y F K S Y K T L Y .. Protein_Len: 35 Strand: - Start: 296 End: 400 ....................................................................................................................................................................................................................................................................................................... S S D Q K I L L C F V V F T N K N T K F L F L D H W I S V V E K Y K M ..................... Protein_Len: 30 Strand: - Start: 234 End: 323 ......................................................................................................................................................................................................................................... R R I P K L K Q H Y R F P F L S S Y K K L F F G A Q N F S M .................................................................................................. Protein_Len: 55 Strand: - Start: 23 End: 187 ...................... S P S L H Y G R Y H T H T A R L L T G L V C I S G K I Y E N R K F M S I A G A D R F S N C Y Y C Y Q H L W Q M .......................................................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 276 R S I N T E R S C V S P E L M A F P T V T I A I S I C G N S P K E K M N K S N T I N E Q K I E K N T E I K S S V Q I P M ................................................................................................................................................. taataggggctcatagatgtcaggaaggtgataaatgataccccctataatgggtgtgtgttgctcgtagtaaagttccaagcacacagatgctacccttgatatattcgtttctcttgaacatactgatggctccagcatcgcgaaaggagttacagtaatagcaatactgatgcaaccattggatggtttctctttcatattcttcgaattagttatgttttcttgttttatctccttattggtttcaatttttgatgatacctgaatgggaataacgagctatatttcttcaagaagaatcctgcttgattaaaagacaaaaaactacgaaggtatttttatttgtcttaaacaaaaagaggtcgtgccaaatagacacgacctctttgtatttcaagtcttataaaactctttatta 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: 81 Start: 98 End: 127 .................................................................................................CTTGATATATTCGTTTCTCTTGAACATACT...................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taataggggctcatagatgtcaggaaggtgataaatgataccccctataatgggtgtgtgttgctcgtagtaaagttccaagcacacagatgctacccttgatatattcgtttctcttgaacatactgatggctccagcatcgcgaaaggagttacagtaatagcaatactgatgcaaccattggatggtttctctttcatattcttcgaattagttatgttttcttgttttatctccttattggtttcaatttttgatgatacctgaatgggaataacgagctatatttcttcaagaagaatcctgcttgattaaaagacaaaaaactacgaaggtatttttatttgtcttaaacaaaaagaggtcgtgccaaatagacacgacctctttgtatttcaagtcttataaaactctttatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -5.4 Tail_Score: -4.39414 Start: 179 End: 189 Full_Region: GCAATACTGATGCAA CCAT TGG ATGG TTTCTCTTTCATATT ..................................................................................................................................................................................CCATTGGATGG........................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -14.5 Tail_Score: -5.27335 Start: 362 End: 388 Full_Region: gacttgaaatacaaa gaggtcgtgtc tattt ggcacgacctc tttttgtttaagaca .........................................................................................................................................................................................................................................................................................................................................................................gaggtcgtgtctatttggcacgacctc................................. Find igs database================================================ Query_seq: PI1715:PI1717|PI1715:PI1717:conserved hypothetical protein; possible DNA-binding protein, histone-like family:major outer membrane protein:->->:1632385..1632805 421 taataggggctcatagatgtcaggaaggtgataaatgataccccctataatgggtgtgtgttgctcgtagtaaagttccaagcacacagatgctacccttgatatattcgtttctcttgaacatactgatggctccagcatcgcgaaaggagttacagtaatagcaatactgatgcaaccattggatggtttctctttcatattcttcgaattagttatgttttcttgttttatctccttattggtttcaatttttgatgatacctgaatgggaataacgagctatatttcttcaagaagaatcctgcttgattaaaagacaaaaaactacgaaggtatttttatttgtcttaaacaaaaagaggtcgtgccaaatagacacgacctctttgtatttcaagtcttataaaactctttatta Intra-Species Hit: Count: 1 Min: 1 Max: 421 Len: 421 Subject: pint_PI1715_PI1717|conserved hypothetical protein; possible DNA-binding protein, histone-like family:major outer membrane protein|POSITIVE:POSITIVE|[1632385,1632805]|421 HSP 1 e-value: 0.0 bit: 835.0 Len: 421 Query Start:1 Query End:421 Subject Strand: POSITIVE Subject Start: 1 Subject End: 421 taataggggctcatagatgtcaggaaggtgataaatgataccccctataatgggtgtgtgttgctcgtagtaaagttccaagcacacagatgctacccttgatatattcgtttctcttgaacatactgatggctccagcatcgcgaaaggagttacagtaatagcaatactgatgcaaccattggatggtttctctttcatattcttcgaattagttatgttttcttgttttatctccttattggtttcaatttttgatgatacctgaatgggaataacgagctatatttcttcaagaagaatcctgcttgattaaaagacaaaaaactacgaaggtatttttatttgtcttaaacaaaaagaggtcgtgccaaatagacacgacctctttgtatttcaagtcttataaaactctttatta taataggggctcatagatgtcaggaaggtgataaatgataccccctataatgggtgtgtgttgctcgtagtaaagttccaagcacacagatgctacccttgatatattcgtttctcttgaacatactgatggctccagcatcgcgaaaggagttacagtaatagcaatactgatgcaaccattggatggtttctctttcatattcttcgaattagttatgttttcttgttttatctccttattggtttcaatttttgatgatacctgaatgggaataacgagctatatttcttcaagaagaatcctgcttgattaaaagacaaaaaactacgaaggtatttttatttgtcttaaacaaaaagaggtcgtgccaaatagacacgacctctttgtatttcaagtcttataaaactctttatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAGGGGCUCAUAGAUGUCAGGAAGGUGAUAAAUGAUACCCCCUAUAAUGGGUGUGUGUUGCUCGUAGUAAAGUUCCAAGCACACAGAUGCUACCCUUGAUAUAUUCGUUUCUCUUGAACAUACUGAUGGCUCCAGCAUCGCGAAAGGAGUUACAGUAAUAGCAAUACUGAUGCAACCAUUGGAUGGUUUCUCUUUCAUAUUCUUCGAAUUAGUUAUGUUUUCUUGUUUUAUCUCCUUAUUGGUUUCAAUUUUUGAUGAUACCUGAAUGGGAAUAACGAGCUAUAUUUCUUCAAGAAGAAUCCUGCUUGAUUAAAAGACAAAAAACUACGAAGGUAUUUUUAUUUGUCUUAAACAAAAAGAGGUCGUGCCAAAUAGACACGACCUCUUUGUAUUUCAAGUCUUAUAAAACUCUUUAUUA ..(((((((.((((...(((((......))))).))))...))))))).((((.(((((((((((.........((((..((((......))))......((.....)).........)))).(((((.(((((((.((...))....))))))))))))..))))))))....))).))))((((.(((((.........(((((((.....((..((((...((((((...((((.((...(((.(((........))).)))..)).))))..))))))..))))..))....)))))))...((((((....(((((((((((.(((....))).)))..))))))))......((((((((((((.(.....).)))))))))))).....))))))......))))).))))... (-109.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAAGAGUUUUAUAAGACUUGAAAUACAAAGAGGUCGUGUCUAUUUGGCACGACCUCUUUUUGUUUAAGACAAAUAAAAAUACCUUCGUAGUUUUUUGUCUUUUAAUCAAGCAGGAUUCUUCUUGAAGAAAUAUAGCUCGUUAUUCCCAUUCAGGUAUCAUCAAAAAUUGAAACCAAUAAGGAGAUAAAACAAGAAAACAUAACUAAUUCGAAGAAUAUGAAAGAGAAACCAUCCAAUGGUUGCAUCAGUAUUGCUAUUACUGUAACUCCUUUCGCGAUGCUGGAGCCAUCAGUAUGUUCAAGAGAAACGAAUAUAUCAAGGGUAGCAUCUGUGUGCUUGGAACUUUACUACGAGCAACACACACCCAUUAUAGGGGGUAUCAUUUAUCACCUUCCUGACAUCUAUGAGCCCCUAUUA .(((((.(((((.(((....(((((((((.((((((((((((((.....)))))))))))))).)))).((((((((.((...(((....))).)).))))))))....)))))(((((....))))).....))).))))).)))))........(((.(((........))).)))...((((((.........................................(.((((((...)))))).)..(((((.......)))))...))))))....((((((...(((....((((((((.........))))))))....))))))))).(((((((((...........))))).)))).........(((((((...((((...(((......))).....)))).))))))).. (-107.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 669 69 21 160 112 pint:PI1749|5end_conserved_hypothetical_protein_1671039..1671269_POSITIVE 342 146 108 98 58 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 322 90 51 63 24 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 317 190 148 72 29 pint:PI0388|5end_integrase_354927..355157_POSITIVE 313 69 22 71 26 pint:PI1939|5end_hypothetical_protein_1896428..1896658_POSITIVE 310 121 81 108 63 pint:PI0370|5end_conserved_hypothetical_protein_340453..340683_POSITIVE 306 156 111 132 77 pint:PI0558|5end_probable_transcriptional_regulator,_TetR_family_507036..507266_POSITIVE 301 99 51 222 176 pint:PI0266|5end_DNA_primase_(bacterial_type)_257931..258161_POSITIVE 296 176 137 108 61 pint:PI1381|5end_conserved_hypothetical_protein_1303060..1303290_POSITIVE 292 64 21 60 16 pint:PI0259|5end_conserved_protein_found_in_conjugation,_TraI_252355..252585_POSITIVE 292 83 41 181 126 pint:PI0122|5end_outer_membrane_protein,_ompH_family_113319..113549_POSITIVE 290 98 53 134 64 pint:PI0489|5end_probable_cardiolipin_synthetase_447610..447840_POSITIVE 289 84 43 103 67 pint:PI2174|5end_hypothetical_protein_2114245..2114475_POSITIVE 286 90 43 96 49 pint:PI1328|5end_conserved_hypothetical_protein_1246197..1246427_POSITIVE 286 93 61 158 130 pint:PI1157|5end_hypothetical_protein_1081704..1081934_POSITIVE 286 96 52 48 8 pint:PI0175|5end_succinyl-CoA_synthetase_beta_subunit_167023..167253_POSITIVE 282 96 52 159 107 pint:PI0785|5end_hypothetical_protein_723744..723974_POSITIVE 282 150 108 192 145 pint:PI0264|5end_transfer_region-related_protein,_TraN_256494..256724_POSITIVE 281 190 141 208 154 pint:PI0376|5end_conserved_hypothetical_protein_346417..346647_POSITIVE 281 177 132 224 168 pint:PI0025|5end_two_component_system_sensor_histidine_kinase_28682..28912_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 150 105 137 82 pint:PI0721|3end_hypothetical_protein_654982..655132_POSITIVE 330 64 22 89 48 pint:PI1440|3end_conserved_hypothetical_protein_1363009..1363159_POSITIVE 322 90 51 58 19 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 286 89 50 45 11 pint:PI1647|3end_hypothetical_protein_1562531..1562681_POSITIVE 286 90 43 85 38 pint:PI1327|3end_conserved_hypothetical_protein_1246266..1246416_POSITIVE 286 89 50 45 11 pint:PI0353|3end_hypothetical_protein_325337..325487_POSITIVE 284 140 95 131 92 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 283 190 141 73 10 pint:PI1884|3end_conserved_hypothetical_protein_1827457..1827607_POSITIVE 280 99 51 151 106 pint:PI0361|3end_hypothetical_protein_333426..333576_POSITIVE 279 67 21 90 50 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 274 91 59 58 23 pint:PI2105|3end_hypothetical_protein_2059586..2059736_POSITIVE 274 98 51 99 57 pint:PI0747|3end_possible_mobilization_protein_676702..676852_POSITIVE 272 106 62 132 92 pint:PI1343|3end_conserved_hypothetical_protein_1258539..1258689_POSITIVE 271 189 141 94 44 pint:PI1546|3end_mobilizable_transposon,_excision_protein_1465099..1465249_POSITIVE 271 399 353 74 23 pint:PI0694|3end_Na+/dicarboxylate_or_sulfate_symporter_631177..631327_POSITIVE 268 107 62 67 14 pint:PI1010|3end_conserved_hypothetical_protein_932195..932345_POSITIVE 268 94 51 147 107 pint:PI0314|3end_conserved_hypothetical_protein_296678..296828_POSITIVE 265 191 158 142 110 pint:PI2064|3end_conserved_hypothetical_protein;_possible_type_I_restriction-modification_system,_S_subunit_2026991..2027141_POSITIVE 265 39 5 70 33 pint:PI0830|3end_conserved_hypothetical_protein_768206..768356_POSITIVE 263 395 357 57 13 pint:PI0488|3end_conserved_hypothetical_protein_447537..447687_POSITIVE