Origin IGS: tttctcttgcttcatacgctttgatgttttgtgacaaaattaccaaattcaaagcgttcctcacttatgcagaagactgccgaccgaagcaacagccacacgagcgaaaataattcagttaccgaacattactccatcgttacctatcccaaaatcaggtagtgctttggtaactgaacttctgcctaaatctgcatattcctgccctttttgaaaagagtacttctatgcaaatcgttccgtttctcccacattatcagttagttttcgccaacttcgattttgcttcattttctgtgattagttaccgtgcaaaacagccgcttttgtaacgcaaaacaataggttttacaaagttttgataatgaactggttacacaaaataatctgtttgaaaatttctttacagttttattgctttatttccaactatgaaacaaaaagtaaaacagataagaagacaccctgaaaaacaaagcgagcaccttgaaaacaagatgctcgcttttatttgaatgctttattgtttta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaacaataaagcattcaaataaaagcgagcatcttgttttcaaggtgctcgctttgtttttcagggtgtcttcttatctgttttactttttgtttcatagttggaaataaagcaataaaactgtaaagaaattttcaaacagattattttgtgtaaccagttcattatcaaaactttgtaaaacctattgttttgcgttacaaaagcggctgttttgcacggtaactaatcacagaaaatgaagcaaaatcgaagttggcgaaaactaactgataatgtgggagaaacggaacgatttgcatagaagtactcttttcaaaaagggcaggaatatgcagatttaggcagaagttcagttaccaaagcactacctgattttgggataggtaacgatggagtaatgttcggtaactgaattattttcgctcgtgtggctgttgcttcggtcggcagtcttctgcataagtgaggaacgctttgaatttggtaattttgtcacaaaacatcaaagcgtatgaagcaagagaaa Mask Tandem Repeat Region ================================================ tttctcttgcttcatacgctttgatgttttgtgacaaaattaccaaattcaaagcgttcctcacttatgcagaagactgccgaccgaagcaacagccacacgagcgaaaataattcagttaccgaacattactccatcgttacctatcccaaaatcaggtagtgctttggtaactgaacttctgcctaaatctgcatattcctgccctttttgaaaagagtacttctatgcaaatcgttccgtttctcccacattatcagttagttttcgccaacttcgattttgcttcattttctgtgattagttaccgtgcaaaacagccgcttttgtaacgcaaaacaataggttttacaaagttttgataatgaactggttacacaaaataatctgtttgaaaatttctttacagttttattgctttatttccaactatgaaacaaaaagtaaaacagataagaagacaccctgaaaaacaaagcgagcaccttgaaaacaagatgctcgcttttatttgaatgctttattgtttta Find is-nt database================================================ Query_seq: PI1560:PI1561|PI1560:PI1561:integrase:conserved hypothetical protein; possible lipoprotein:->->:1478326..1478856 531 tttctcttgcttcatacgctttgatgttttgtgacaaaattaccaaattcaaagcgttcctcacttatgcagaagactgccgaccgaagcaacagccacacgagcgaaaataattcagttaccgaacattactccatcgttacctatcccaaaatcaggtagtgctttggtaactgaacttctgcctaaatctgcatattcctgccctttttgaaaagagtacttctatgcaaatcgttccgtttctcccacattatcagttagttttcgccaacttcgattttgcttcattttctgtgattagttaccgtgcaaaacagccgcttttgtaacgcaaaacaataggttttacaaagttttgataatgaactggttacacaaaataatctgtttgaaaatttctttacagttttattgctttatttccaactatgaaacaaaaagtaaaacagataagaagacaccctgaaaaacaaagcgagcaccttgaaaacaagatgctcgcttttatttgaatgctttattgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1560:PI1561|PI1560:PI1561:integrase:conserved hypothetical protein; possible lipoprotein:->->:1478326..1478856 531 tttctcttgcttcatacgctttgatgttttgtgacaaaattaccaaattcaaagcgttcctcacttatgcagaagactgccgaccgaagcaacagccacacgagcgaaaataattcagttaccgaacattactccatcgttacctatcccaaaatcaggtagtgctttggtaactgaacttctgcctaaatctgcatattcctgccctttttgaaaagagtacttctatgcaaatcgttccgtttctcccacattatcagttagttttcgccaacttcgattttgcttcattttctgtgattagttaccgtgcaaaacagccgcttttgtaacgcaaaacaataggttttacaaagttttgataatgaactggttacacaaaataatctgtttgaaaatttctttacagttttattgctttatttccaactatgaaacaaaaagtaaaacagataagaagacaccctgaaaaacaaagcgagcaccttgaaaacaagatgctcgcttttatttgaatgctttattgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1560:PI1561|PI1560:PI1561:integrase:conserved hypothetical protein; possible lipoprotein:->->:1478326..1478856 531 tttctcttgcttcatacgctttgatgttttgtgacaaaattaccaaattcaaagcgttcctcacttatgcagaagactgccgaccgaagcaacagccacacgagcgaaaataattcagttaccgaacattactccatcgttacctatcccaaaatcaggtagtgctttggtaactgaacttctgcctaaatctgcatattcctgccctttttgaaaagagtacttctatgcaaatcgttccgtttctcccacattatcagttagttttcgccaacttcgattttgcttcattttctgtgattagttaccgtgcaaaacagccgcttttgtaacgcaaaacaataggttttacaaagttttgataatgaactggttacacaaaataatctgtttgaaaatttctttacagttttattgctttatttccaactatgaaacaaaaagtaaaacagataagaagacaccctgaaaaacaaagcgagcaccttgaaaacaagatgctcgcttttatttgaatgctttattgtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctcttgcttcatacgctttgatgttttgtgacaaaattaccaaattcaaagcgttcctcacttatgcagaagactgccgaccgaagcaacagccacacgagcgaaaataattcagttaccgaacattactccatcgttacctatcccaaaatcaggtagtgctttggtaactgaacttctgcctaaatctgcatattcctgccctttttgaaaagagtacttctatgcaaatcgttccgtttctcccacattatcagttagttttcgccaacttcgattttgcttcattttctgtgattagttaccgtgcaaaacagccgcttttgtaacgcaaaacaataggttttacaaagttttgataatgaactggttacacaaaataatctgtttgaaaatttctttacagttttattgctttatttccaactatgaaacaaaaagtaaaacagataagaagacaccctgaaaaacaaagcgagcaccttgaaaacaagatgctcgcttttatttgaatgctttattgtttta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 21 End: 110 .................... M M F C D K I T K F K A F L T Y A E D C R P K Q Q P H E R K ..................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 43 Strand: + Start: 31 End: 159 .............................. M T K L P N S K R S S L M Q K T A D R S N S H T S E N N S V T E H Y S I V T Y P K I R .................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 55 Strand: + Start: 47 End: 211 .............................................. M Q S V P H L C R R L P T E A T A T R A K I I Q L P N I T P S L P I P K S G S A L V T E L L P K S A Y S C P F ................................................................................................................................................................................................................................................................................................................................ Protein_Len: 52 Strand: + Start: 174 End: 329 ............................................................................................................................................................................. M N F C L N L H I P A L F E K S T S M Q I V P F L P H Y Q L V F A N F D F A S F S V I S Y R A K Q P L L .......................................................................................................................................................................................................... Protein_Len: 36 Strand: + Start: 359 End: 466 ...................................................................................................................................................................................................................................................................................................................................................................... M I M N W L H K I I C L K I S L Q F Y C F I S N Y E T K S K T D K K T P ................................................................. Protein_Len: 33 Strand: + Start: 414 End: 512 ............................................................................................................................................................................................................................................................................................................................................................................................................................. M A L F P T M K Q K V K Q I R R H P E K Q S E H L E N K M L A F I ................... Protein_Len: 34 Strand: - Start: 423 End: 524 ...................................................................................................................................................................................................................................................................................................................................................................................................................................... K W S H F L F Y F L Y S S V R F F L A L V K F V L H E S K N S H K M ....... Protein_Len: 37 Strand: - Start: 407 End: 517 ...................................................................................................................................................................................................................................................................................................................................................................................................................... L K I A K N G V I F C F T F C I L L C G S F C L S C R S F L I S A K I Q M .............. tttctcttgcttcatacgctttgatgttttgtgacaaaattaccaaattcaaagcgttcctcacttatgcagaagactgccgaccgaagcaacagccacacgagcgaaaataattcagttaccgaacattactccatcgttacctatcccaaaatcaggtagtgctttggtaactgaacttctgcctaaatctgcatattcctgccctttttgaaaagagtacttctatgcaaatcgttccgtttctcccacattatcagttagttttcgccaacttcgattttgcttcattttctgtgattagttaccgtgcaaaacagccgcttttgtaacgcaaaacaataggttttacaaagttttgataatgaactggttacacaaaataatctgtttgaaaatttctttacagttttattgctttatttccaactatgaaacaaaaagtaaaacagataagaagacaccctgaaaaacaaagcgagcaccttgaaaacaagatgctcgcttttatttgaatgctttattgtttta 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: 358 End: 387 .....................................................................................................................................................................................................................................................................................................................................................................TTTGATAATGAACTGGTTACACAAAATAAT................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttctcttgcttcatacgctttgatgttttgtgacaaaattaccaaattcaaagcgttcctcacttatgcagaagactgccgaccgaagcaacagccacacgagcgaaaataattcagttaccgaacattactccatcgttacctatcccaaaatcaggtagtgctttggtaactgaacttctgcctaaatctgcatattcctgccctttttgaaaagagtacttctatgcaaatcgttccgtttctcccacattatcagttagttttcgccaacttcgattttgcttcattttctgtgattagttaccgtgcaaaacagccgcttttgtaacgcaaaacaataggttttacaaagttttgataatgaactggttacacaaaataatctgtttgaaaatttctttacagttttattgctttatttccaactatgaaacaaaaagtaaaacagataagaagacaccctgaaaaacaaagcgagcaccttgaaaacaagatgctcgcttttatttgaatgctttattgtttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.2 Tail_Score: -4.9138 Start: 478 End: 505 Full_Region: ACCCTGAAAAACAAA GCGAGCACCTTG AAAA CAAGATGCTCGC TTTTATTTGAATGCT .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCGAGCACCTTGAAAACAAGATGCTCGC.......................... Find igs database================================================ Query_seq: PI1560:PI1561|PI1560:PI1561:integrase:conserved hypothetical protein; possible lipoprotein:->->:1478326..1478856 531 tttctcttgcttcatacgctttgatgttttgtgacaaaattaccaaattcaaagcgttcctcacttatgcagaagactgccgaccgaagcaacagccacacgagcgaaaataattcagttaccgaacattactccatcgttacctatcccaaaatcaggtagtgctttggtaactgaacttctgcctaaatctgcatattcctgccctttttgaaaagagtacttctatgcaaatcgttccgtttctcccacattatcagttagttttcgccaacttcgattttgcttcattttctgtgattagttaccgtgcaaaacagccgcttttgtaacgcaaaacaataggttttacaaagttttgataatgaactggttacacaaaataatctgtttgaaaatttctttacagttttattgctttatttccaactatgaaacaaaaagtaaaacagataagaagacaccctgaaaaacaaagcgagcaccttgaaaacaagatgctcgcttttatttgaatgctttattgtttta Intra-Species Hit: Count: 2 Min: 1 Max: 531 Len: 531 Subject: pint_PI1560_PI1561|integrase:conserved hypothetical protein; possible lipoprotein|POSITIVE:POSITIVE|[1478326,1478856]|531 HSP 1 e-value: 0.0 bit: 1053.0 Len: 531 Query Start:1 Query End:531 Subject Strand: POSITIVE Subject Start: 1 Subject End: 531 tttctcttgcttcatacgctttgatgttttgtgacaaaattaccaaattcaaagcgttcctcacttatgcagaagactgccgaccgaagcaacagccacacgagcgaaaataattcagttaccgaacattactccatcgttacctatcccaaaatcaggtagtgctttggtaactgaacttctgcctaaatctgcatattcctgccctttttgaaaagagtacttctatgcaaatcgttccgtttctcccacattatcagttagttttcgccaacttcgattttgcttcattttctgtgattagttaccgtgcaaaacagccgcttttgtaacgcaaaacaataggttttacaaagttttgataatgaactggttacacaaaataatctgtttgaaaatttctttacagttttattgctttatttccaactatgaaacaaaaagtaaaacagataagaagacaccctgaaaaacaaagcgagcaccttgaaaacaagatgctcgcttttatttgaatgctttattgtttta tttctcttgcttcatacgctttgatgttttgtgacaaaattaccaaattcaaagcgttcctcacttatgcagaagactgccgaccgaagcaacagccacacgagcgaaaataattcagttaccgaacattactccatcgttacctatcccaaaatcaggtagtgctttggtaactgaacttctgcctaaatctgcatattcctgccctttttgaaaagagtacttctatgcaaatcgttccgtttctcccacattatcagttagttttcgccaacttcgattttgcttcattttctgtgattagttaccgtgcaaaacagccgcttttgtaacgcaaaacaataggttttacaaagttttgataatgaactggttacacaaaataatctgtttgaaaatttctttacagttttattgctttatttccaactatgaaacaaaaagtaaaacagataagaagacaccctgaaaaacaaagcgagcaccttgaaaacaagatgctcgcttttatttgaatgctttattgtttta Subject: pint_PI0725_PI0726|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[658994,659181]|188 HSP 1 e-value: 2.0E-11 bit: 71.9 Len: 148 Query Start:168 Query End:315 Subject Strand: NEGATIVE Subject Start: 33 Subject End: 180 .......................................................................................................................................................................tggtaactgaacttctgcctaaatctgcatattcctgccctttttgaaaagagtacttctatgcaaatcgttccgtttctcccacattatcagttagttttcgccaacttcgattttgcttcattttctgtgattagttaccgtgcaa........................................................................................................................................................................................................................ .......................................................................................................................................................................tggtaactgaacttctgcctaagtctgcatatttctgccctttacaaatagagcagtattatgcaaatcagagcatttcctcctcattatcagttagtttacactaatttcgatatttctccattttcgttgattagttacagtgcaa........................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCUUGCUUCAUACGCUUUGAUGUUUUGUGACAAAAUUACCAAAUUCAAAGCGUUCCUCACUUAUGCAGAAGACUGCCGACCGAAGCAACAGCCACACGAGCGAAAAUAAUUCAGUUACCGAACAUUACUCCAUCGUUACCUAUCCCAAAAUCAGGUAGUGCUUUGGUAACUGAACUUCUGCCUAAAUCUGCAUAUUCCUGCCCUUUUUGAAAAGAGUACUUCUAUGCAAAUCGUUCCGUUUCUCCCACAUUAUCAGUUAGUUUUCGCCAACUUCGAUUUUGCUUCAUUUUCUGUGAUUAGUUACCGUGCAAAACAGCCGCUUUUGUAACGCAAAACAAUAGGUUUUACAAAGUUUUGAUAAUGAACUGGUUACACAAAAUAAUCUGUUUGAAAAUUUCUUUACAGUUUUAUUGCUUUAUUUCCAACUAUGAAACAAAAAGUAAAACAGAUAAGAAGACACCCUGAAAAACAAAGCGAGCACCUUGAAAACAAGAUGCUCGCUUUUAUUUGAAUGCUUUAUUGUUUUA ...((.(((((((..(((((((((.((((.((((.....)))).)))))))))))))...........((((....)))).....))))))).))......((((((......((((((((((((((((((((........................))))))).)))))))))))))..............((((((....(((.((((....)))).)))....))))))..))))))...........((((.((((...((((((....................(((((.(((((((((((......((((((((((....((((........))))..)))).......))))))......))))))))))).))))).((((((((........((((...(((((((................)))))))..))))..))))))))..))))))...)))).....((((((((((.((((....)))).))))))))))......))))............. (-128.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACAAUAAAGCAUUCAAAUAAAAGCGAGCAUCUUGUUUUCAAGGUGCUCGCUUUGUUUUUCAGGGUGUCUUCUUAUCUGUUUUACUUUUUGUUUCAUAGUUGGAAAUAAAGCAAUAAAACUGUAAAGAAAUUUUCAAACAGAUUAUUUUGUGUAACCAGUUCAUUAUCAAAACUUUGUAAAACCUAUUGUUUUGCGUUACAAAAGCGGCUGUUUUGCACGGUAACUAAUCACAGAAAAUGAAGCAAAAUCGAAGUUGGCGAAAACUAACUGAUAAUGUGGGAGAAACGGAACGAUUUGCAUAGAAGUACUCUUUUCAAAAAGGGCAGGAAUAUGCAGAUUUAGGCAGAAGUUCAGUUACCAAAGCACUACCUGAUUUUGGGAUAGGUAACGAUGGAGUAAUGUUCGGUAACUGAAUUAUUUUCGCUCGUGUGGCUGUUGCUUCGGUCGGCAGUCUUCUGCAUAAGUGAGGAACGCUUUGAAUUUGGUAAUUUUGUCACAAAACAUCAAAGCGUAUGAAGCAAGAGAAA (((((((((((((((((((((..(((((((((((((((....)))))))))))))))...)))..))))).))..)))).))))))).((((((((((((((((.((................((.(((((...((((...(((((..((((((....(((...(((((((...(((.((((((((...(((((((........)))))))..)))))))).)))..............................((((((......)))))))))))))))).....))))))..)))))....))))...))))).)).....(((((((.(((.(((((((((((...((((((((((((...((.((((((......))).))))).((......)).......)))))))))))).((((((((..((((((((((((....).))))))))....)))..))))))))..)).)))))))))))).)))))))........))..))).)))))))))))))... (-149.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 886 120 71 52 3 pint:PI0726|5end_hypothetical_protein_659042..659272_POSITIVE 724 350 305 99 54 pint:PI2153|5end_hypothetical_protein_2099392..2099622_POSITIVE 724 350 305 56 11 pint:PI1905|5end_hypothetical_protein_1847628..1847858_POSITIVE 724 350 305 71 26 pint:PI0061|5end_hypothetical_protein_60500..60730_POSITIVE 724 350 305 71 26 pint:PI0004|5end_hypothetical_protein_6199..6429_POSITIVE 672 350 305 60 15 pint:PI0099|5end_hypothetical_protein_95530..95760_POSITIVE 665 360 311 109 60 pint:PI1076|5end_hypothetical_protein_998893..999123_POSITIVE 660 350 305 99 54 pint:PI1601|5end_hypothetical_protein_1530282..1530512_POSITIVE 653 350 305 99 54 pint:PI1346|5end_hypothetical_protein_1260814..1261044_POSITIVE 653 350 305 60 15 pint:PI1339|5end_hypothetical_protein_1256671..1256901_POSITIVE 653 350 305 87 42 pint:PI1129|5end_hypothetical_protein_1055377..1055607_POSITIVE 653 350 305 225 180 pint:PI0788|5end_3-methyladenine_DNA_glycosylase_(DNA-3-methyladenine_glycosylase_I)_726152..726382_POSITIVE 653 350 305 230 185 pint:PI0771|5end_conserved_hypothetical_protein_706524..706754_POSITIVE 653 350 305 60 15 pint:PI0104|5end_hypothetical_protein_99105..99335_POSITIVE 653 350 305 148 103 pint:PI0055|5end_hypothetical_protein_54815..55045_POSITIVE 653 350 305 60 15 pint:PI0053|5end_hypothetical_protein_54727..54957_POSITIVE 652 350 305 60 15 pint:PI1057|5end_hypothetical_protein_977286..977516_POSITIVE 649 350 305 82 37 pint:PI1528|5end_hypothetical_protein_1449685..1449915_POSITIVE 624 350 305 99 54 pint:PI1567|5end_hypothetical_protein_1489229..1489459_POSITIVE 618 350 305 99 54 pint:PI2002|5end_hypothetical_protein_1960662..1960892_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 724 350 305 141 96 pint:PI1141|3end_hypothetical_protein_1069713..1069863_POSITIVE 724 350 305 54 9 pint:PI0688|3end_hypothetical_protein_625750..625900_POSITIVE 724 350 305 48 3 pint:PI0669|3end_hypothetical_protein_611147..611297_POSITIVE 695 350 305 141 96 pint:PI0759|3end_hypothetical_protein_693998..694148_POSITIVE 687 88 41 151 104 pint:PI0726|3end_hypothetical_protein_659253..659403_POSITIVE 653 350 305 54 9 pint:PI0186|3end_hypothetical_protein_178003..178153_POSITIVE 653 350 305 82 37 pint:PI0054|3end_hypothetical_protein_54829..54979_POSITIVE 581 350 305 50 5 pint:PI1051|3end_hypothetical_protein_970228..970378_POSITIVE 579 350 305 82 37 pint:PI0996|3end_hypothetical_protein_920660..920810_POSITIVE 500 354 317 38 1 pint:PI1813|3end_hypothetical_protein_1753086..1753236_POSITIVE 415 346 305 151 110 pint:PI1356|3end_hypothetical_protein_1273340..1273490_POSITIVE 403 380 334 57 11 pint:PI2143|3end_DNA_mismatch_repair_protein_2091974..2092124_POSITIVE 362 350 310 142 96 pint:PI0819|3end_hypothetical_protein_759919..760069_POSITIVE 360 368 322 52 6 pint:PI1391|3end_hypothetical_protein_1311694..1311844_POSITIVE 355 106 64 60 14 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 352 340 309 149 117 pint:PI0158|3end_hypothetical_protein_151298..151448_POSITIVE 343 335 311 143 119 pint:PI1521|3end_hypothetical_protein_1441461..1441611_POSITIVE 343 335 311 52 28 pint:PI1520|3end_hypothetical_protein_1441370..1441520_POSITIVE 339 315 276 58 19 pint:PI0725|3end_hypothetical_protein_658933..659083_POSITIVE 334 98 51 47 10 pint:PI1864|3end_chromate_transport_protein_1811009..1811159_POSITIVE