Origin IGS: aaacttataggtaagcagttatcctcctacttgttctaagtatttgtgtcgtttttgcgaaacgtagacgaattatttacgtgtaaataaatatttttctacacgtaaataataatttccatacacgtaaataaatatttctttacgtgtaagtaattctgcggggaaaagaaaattcagggctaacttattgctgccgtttagtttaagtagtattctgtaattgttgtaacaattcctattctgtaggtttgtaaaggatttttttgtttttatcgagaaagaatattgtctttttaacagcatcttaaaataaatttattatttttgcattgtgtttctttggaaacaacaatgttttatttgctcaataccctaacaatcaccatacgagaaagagcaaaacaattgttattgagacctgtgctatacggttgcaggctttcctatatacagttgtggcttgtggtaaaccgtgaggcgtatgacgaaagcttatgctttgtctatcggcaaaggaaaatcggaactattaaacttaattcagataaag .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctttatctgaattaagtttaatagttccgattttcctttgccgatagacaaagcataagctttcgtcatacgcctcacggtttaccacaagccacaactgtatataggaaagcctgcaaccgtatagcacaggtctcaataacaattgttttgctctttctcgtatggtgattgttagggtattgagcaaataaaacattgttgtttccaaagaaacacaatgcaaaaataataaatttattttaagatgctgttaaaaagacaatattctttctcgataaaaacaaaaaaatcctttacaaacctacagaataggaattgttacaacaattacagaatactacttaaactaaacggcagcaataagttagccctgaattttcttttccccgcagaattacttacacgtaaagaaatatttatttacgtgtatggaaattattatttacgtgtagaaaaatatttatttacacgtaaataattcgtctacgtttcgcaaaaacgacacaaatacttagaacaagtaggaggataactgcttacctataagttt Mask Tandem Repeat Region ================================================ aaacttataggtaagcagttatcctcctacttgttctaagtatttgtgtcgtttttgcgaaacgtagacgaattatttacgtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctttacgtgtaagtaattctgcggggaaaagaaaattcagggctaacttattgctgccgtttagtttaagtagtattctgtaattgttgtaacaattcctattctgtaggtttgtaaaggatttttttgtttttatcgagaaagaatattgtctttttaacagcatcttaaaataaatttattatttttgcattgtgtttctttggaaacaacaatgttttatttgctcaataccctaacaatcaccatacgagaaagagcaaaacaattgttattgagacctgtgctatacggttgcaggctttcctatatacagttgtggcttgtggtaaaccgtgaggcgtatgacgaaagcttatgctttgtctatcggcaaaggaaaatcggaactattaaacttaattcagataaag Find is-nt database================================================ Query_seq: PI0491:PI0492|PI0491:PI0492:hypothetical protein:hypothetical protein:->->:451288..451840 553 aaacttataggtaagcagttatcctcctacttgttctaagtatttgtgtcgtttttgcgaaacgtagacgaattatttacgtgtaaataaatatttttctacacgtaaataataatttccatacacgtaaataaatatttctttacgtgtaagtaattctgcggggaaaagaaaattcagggctaacttattgctgccgtttagtttaagtagtattctgtaattgttgtaacaattcctattctgtaggtttgtaaaggatttttttgtttttatcgagaaagaatattgtctttttaacagcatcttaaaataaatttattatttttgcattgtgtttctttggaaacaacaatgttttatttgctcaataccctaacaatcaccatacgagaaagagcaaaacaattgttattgagacctgtgctatacggttgcaggctttcctatatacagttgtggcttgtggtaaaccgtgaggcgtatgacgaaagcttatgctttgtctatcggcaaaggaaaatcggaactattaaacttaattcagataaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0491:PI0492|PI0491:PI0492:hypothetical protein:hypothetical protein:->->:451288..451840 553 aaacttataggtaagcagttatcctcctacttgttctaagtatttgtgtcgtttttgcgaaacgtagacgaattatttacgtgtaaataaatatttttctacacgtaaataataatttccatacacgtaaataaatatttctttacgtgtaagtaattctgcggggaaaagaaaattcagggctaacttattgctgccgtttagtttaagtagtattctgtaattgttgtaacaattcctattctgtaggtttgtaaaggatttttttgtttttatcgagaaagaatattgtctttttaacagcatcttaaaataaatttattatttttgcattgtgtttctttggaaacaacaatgttttatttgctcaataccctaacaatcaccatacgagaaagagcaaaacaattgttattgagacctgtgctatacggttgcaggctttcctatatacagttgtggcttgtggtaaaccgtgaggcgtatgacgaaagcttatgctttgtctatcggcaaaggaaaatcggaactattaaacttaattcagataaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0491:PI0492|PI0491:PI0492:hypothetical protein:hypothetical protein:->->:451288..451840 553 aaacttataggtaagcagttatcctcctacttgttctaagtatttgtgtcgtttttgcgaaacgtagacgaattatttacgtgtaaataaatatttttctacacgtaaataataatttccatacacgtaaataaatatttctttacgtgtaagtaattctgcggggaaaagaaaattcagggctaacttattgctgccgtttagtttaagtagtattctgtaattgttgtaacaattcctattctgtaggtttgtaaaggatttttttgtttttatcgagaaagaatattgtctttttaacagcatcttaaaataaatttattatttttgcattgtgtttctttggaaacaacaatgttttatttgctcaataccctaacaatcaccatacgagaaagagcaaaacaattgttattgagacctgtgctatacggttgcaggctttcctatatacagttgtggcttgtggtaaaccgtgaggcgtatgacgaaagcttatgctttgtctatcggcaaaggaaaatcggaactattaaacttaattcagataaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacttataggtaagcagttatcctcctacttgttctaagtatttgtgtcgtttttgcgaaacgtagacgaattatttacgtgtaaataaatatttttctacacgtaaataataatttccatacacgtaaataaatatttctttacgtgtaagtaattctgcggggaaaagaaaattcagggctaacttattgctgccgtttagtttaagtagtattctgtaattgttgtaacaattcctattctgtaggtttgtaaaggatttttttgtttttatcgagaaagaatattgtctttttaacagcatcttaaaataaatttattatttttgcattgtgtttctttggaaacaacaatgttttatttgctcaataccctaacaatcaccatacgagaaagagcaaaacaattgttattgagacctgtgctatacggttgcaggctttcctatatacagttgtggcttgtggtaaaccgtgaggcgtatgacgaaagcttatgctttgtctatcggcaaaggaaaatcggaactattaaacttaattcagataaag Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 131 End: 220 .................................................................................................................................. M N I S L R V S N S A G K R K F R A N L L L P F S L S S I L ............................................................................................................................................................................................................................................................................................................................................. Protein_Len: 52 Strand: + Start: 321 End: 476 ................................................................................................................................................................................................................................................................................................................................ M I F A L C F F G N N N V L F A Q Y P N N H H T R K S K T I V I E T C A I R L Q A F L Y T V V A C G K P ............................................................................. Protein_Len: 60 Strand: + Start: 313 End: 552 ........................................................................................................................................................................................................................................................................................................................ M N L L F L H C V S L E T T M F Y L L N T L T I T I R E R A K Q L L L R P V L Y G C R L S Y I Q L W L V V N R E A Y D E . Protein_Len: 38 Strand: - Start: 386 End: 499 ................................................................................................................................................................................................................................................................................................................................................................................................. W V L F L L V I T I S V Q A I R N C A K R Y V T T A Q P L G H P T H R F S M ...................................................... Protein_Len: 60 Strand: - Start: 76 End: 318 ........................................................................... E K R T L L E A P F L F N L A L K N S G N L K L L I R Y N N Y C N R N Q L N T F S K K T K I S F S Y Q R K L L M K F Y M ........................................................................................................................................................................................................................................... aaacttataggtaagcagttatcctcctacttgttctaagtatttgtgtcgtttttgcgaaacgtagacgaattatttacgtgtaaataaatatttttctacacgtaaataataatttccatacacgtaaataaatatttctttacgtgtaagtaattctgcggggaaaagaaaattcagggctaacttattgctgccgtttagtttaagtagtattctgtaattgttgtaacaattcctattctgtaggtttgtaaaggatttttttgtttttatcgagaaagaatattgtctttttaacagcatcttaaaataaatttattatttttgcattgtgtttctttggaaacaacaatgttttatttgctcaataccctaacaatcaccatacgagaaagagcaaaacaattgttattgagacctgtgctatacggttgcaggctttcctatatacagttgtggcttgtggtaaaccgtgaggcgtatgacgaaagcttatgctttgtctatcggcaaaggaaaatcggaactattaaacttaattcagataaag 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: 83 Start: 296 End: 325 .......................................................................................................................................................................................................................................................................................................TTTAACAGCATCTTAAAATAAATTTATTAT.................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaacttataggtaagcagttatcctcctacttgttctaagtatttgtgtcgtttttgcgaaacgtagacgaattatttacgtgtaaataaatatttttctacacgtaaataataatttccatacacgtaaataaatatttctttacgtgtaagtaattctgcggggaaaagaaaattcagggctaacttattgctgccgtttagtttaagtagtattctgtaattgttgtaacaattcctattctgtaggtttgtaaaggatttttttgtttttatcgagaaagaatattgtctttttaacagcatcttaaaataaatttattatttttgcattgtgtttctttggaaacaacaatgttttatttgctcaataccctaacaatcaccatacgagaaagagcaaaacaattgttattgagacctgtgctatacggttgcaggctttcctatatacagttgtggcttgtggtaaaccgtgaggcgtatgacgaaagcttatgctttgtctatcggcaaaggaaaatcggaactattaaacttaattcagataaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 75 HP_score: -9.6 Tail_Score: -2.94144 Start: 73 End: 112 Full_Region: CGAAACGTAGACGAA TTATTTACGTGTAAATAA ATAT TTTTCTACACGTAAATAA TAATTTCCATACACG ........................................................................TTATTTACGTGTAAATAAATATTTTTCTACACGTAAATAA......................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 89 HP_score: -11.8 Tail_Score: -3.31196 Start: 73 End: 112 Full_Region: cgtgtatggaaatta ttatttacgtgtagaaaa atat ttatttacacgtaaataa ttcgtctacgtttcg ........................................................................ttatttacgtgtagaaaaatatttatttacacgtaaataa......................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 89 HP_score: -7.5 Tail_Score: -4.9448 Start: 331 End: 357 Full_Region: AATTTATTATTTTTG CATTGTGTTTC TTTG GAAACAACAATG TTTTATTTGCTCAAT ..........................................................................................................................................................................................................................................................................................................................................CATTGTGTTTCTTTGGAAACAACAATG.................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0491:PI0492|PI0491:PI0492:hypothetical protein:hypothetical protein:->->:451288..451840 553 aaacttataggtaagcagttatcctcctacttgttctaagtatttgtgtcgtttttgcgaaacgtagacgaattatttacgtgtaaataaatatttttctacacgtaaataataatttccatacacgtaaataaatatttctttacgtgtaagtaattctgcggggaaaagaaaattcagggctaacttattgctgccgtttagtttaagtagtattctgtaattgttgtaacaattcctattctgtaggtttgtaaaggatttttttgtttttatcgagaaagaatattgtctttttaacagcatcttaaaataaatttattatttttgcattgtgtttctttggaaacaacaatgttttatttgctcaataccctaacaatcaccatacgagaaagagcaaaacaattgttattgagacctgtgctatacggttgcaggctttcctatatacagttgtggcttgtggtaaaccgtgaggcgtatgacgaaagcttatgctttgtctatcggcaaaggaaaatcggaactattaaacttaattcagataaag Intra-Species Hit: Count: 1 Min: 1 Max: 553 Len: 553 Subject: pint_PI0491_PI0492|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[451288,451840]|553 HSP 1 e-value: 1.0E-156 bit: 553.0 Len: 279 Query Start:275 Query End:553 Subject Strand: POSITIVE Subject Start: 275 Subject End: 553 ..................................................................................................................................................................................................................................................................................atcgagaaagaatattgtctttttaacagcatcttaaaataaatttattatttttgcattgtgtttctttggaaacaacaatgttttatttgctcaataccctaacaatcaccatacgagaaagagcaaaacaattgttattgagacctgtgctatacggttgcaggctttcctatatacagttgtggcttgtggtaaaccgtgaggcgtatgacgaaagcttatgctttgtctatcggcaaaggaaaatcggaactattaaacttaattcagataaag ..................................................................................................................................................................................................................................................................................atcgagaaagaatattgtctttttaacagcatcttaaaataaatttattatttttgcattgtgtttctttggaaacaacaatgttttatttgctcaataccctaacaatcaccatacgagaaagagcaaaacaattgttattgagacctgtgctatacggttgcaggctttcctatatacagttgtggcttgtggtaaaccgtgaggcgtatgacgaaagcttatgctttgtctatcggcaaaggaaaatcggaactattaaacttaattcagataaag HSP 2 e-value: 1.0E-145 bit: 517.0 Len: 261 Query Start:1 Query End:261 Subject Strand: POSITIVE Subject Start: 1 Subject End: 261 aaacttataggtaagcagttatcctcctacttgttctaagtatttgtgtcgtttttgcgaaacgtagacgaattatttacgtgtaaataaatatttttctacacgtaaataataatttccatacacgtaaataaatatttctttacgtgtaagtaattctgcggggaaaagaaaattcagggctaacttattgctgccgtttagtttaagtagtattctgtaattgttgtaacaattcctattctgtaggtttgtaaagga.................................................................................................................................................................................................................................................................................................... aaacttataggtaagcagttatcctcctacttgttctaagtatttgtgtcgtttttgcgaaacgtagacgaattatttacgtgtaaataaatatttttctacacgtaaataataatttccatacacgtaaataaatatttctttacgtgtaagtaattctgcggggaaaagaaaattcagggctaacttattgctgccgtttagtttaagtagtattctgtaattgttgtaacaattcctattctgtaggtttgtaaagga.................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUUAUAGGUAAGCAGUUAUCCUCCUACUUGUUCUAAGUAUUUGUGUCGUUUUUGCGAAACGUAGACGAAUUAUUUACGUGUAAAUAAAUAUUUUUCUACACGUAAAUAAUAAUUUCCAUACACGUAAAUAAAUAUUUCUUUACGUGUAAGUAAUUCUGCGGGGAAAAGAAAAUUCAGGGCUAACUUAUUGCUGCCGUUUAGUUUAAGUAGUAUUCUGUAAUUGUUGUAACAAUUCCUAUUCUGUAGGUUUGUAAAGGAUUUUUUUGUUUUUAUCGAGAAAGAAUAUUGUCUUUUUAACAGCAUCUUAAAAUAAAUUUAUUAUUUUUGCAUUGUGUUUCUUUGGAAACAACAAUGUUUUAUUUGCUCAAUACCCUAACAAUCACCAUACGAGAAAGAGCAAAACAAUUGUUAUUGAGACCUGUGCUAUACGGUUGCAGGCUUUCCUAUAUACAGUUGUGGCUUGUGGUAAACCGUGAGGCGUAUGACGAAAGCUUAUGCUUUGUCUAUCGGCAAAGGAAAAUCGGAACUAUUAAACUUAAUUCAGAUAAAG .((((((((((.((((.((((.(((........((((...........((((....))))..((((((...((((((((((((((..............))))))))))))))........((((((((((.((....)).))))))))))......))))))......))))......))).))))....(((.(((((.((((...((.((((((((....(((.....((((..(((((...))))).)))).((((((......))))))..)))...))))))))(((((..((((((......(((((((.....))))))).((((((((((((....))))).)))))))....(((((((............................)))))))....))))))..)))))))..)))).))))).))).)))).))))))...))))..(((((((.(((..((....))..))).))..)))))..(.(((((((....))))))).)..(((.(((.((.......)).))).))).... (-132.47) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAUCUGAAUUAAGUUUAAUAGUUCCGAUUUUCCUUUGCCGAUAGACAAAGCAUAAGCUUUCGUCAUACGCCUCACGGUUUACCACAAGCCACAACUGUAUAUAGGAAAGCCUGCAACCGUAUAGCACAGGUCUCAAUAACAAUUGUUUUGCUCUUUCUCGUAUGGUGAUUGUUAGGGUAUUGAGCAAAUAAAACAUUGUUGUUUCCAAAGAAACACAAUGCAAAAAUAAUAAAUUUAUUUUAAGAUGCUGUUAAAAAGACAAUAUUCUUUCUCGAUAAAAACAAAAAAAUCCUUUACAAACCUACAGAAUAGGAAUUGUUACAACAAUUACAGAAUACUACUUAAACUAAACGGCAGCAAUAAGUUAGCCCUGAAUUUUCUUUUCCCCGCAGAAUUACUUACACGUAAAGAAAUAUUUAUUUACGUGUAUGGAAAUUAUUAUUUACGUGUAGAAAAAUAUUUAUUUACACGUAAAUAAUUCGUCUACGUUUCGCAAAAACGACACAAAUACUUAGAACAAGUAGGAGGAUAACUGCUUACCUAUAAGUUU .....((((((((..(((((((((((((..(((((((.(((.(...((((((((....))))).)))...........(((((.....)))))....).)))...))))))).........(((.((((...((.......))...)))).)))...((((.(((.(((..((((.(((((....((((.......((((((.(((((....)))))))))))..(((((((.....)))))))....)))).....(((((......)))))..................)))))..))))))))))))))..)))))))))).))))))).)))).....(((((........((((((.....))).)))..................((((.....(.((((((((((..........)))))))))).)......((((((((((((((((.((....)).))))))))))))))))((.(((..((.(((......))).))...(((((.....)))))))).))...)))).......))))).. (-116.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 652 159 111 167 119 pint:PI0130|5end_hypothetical_protein_122032..122262_POSITIVE 550 110 67 231 188 pint:PI0599|5end_hypothetical_protein_547376..547606_POSITIVE 545 150 101 203 154 pint:PI0115|5end_hypothetical_protein_108062..108292_POSITIVE 545 150 101 189 140 pint:PI0111|5end_hypothetical_protein_108048..108278_POSITIVE 545 150 101 154 105 pint:PI0112|5end_hypothetical_protein_108013..108243_POSITIVE 485 108 62 138 87 pint:PI1462|5end_hypothetical_protein_1385094..1385324_POSITIVE 479 110 64 96 49 pint:PI1450|5end_hypothetical_protein_1372683..1372913_POSITIVE 468 108 61 211 164 pint:PI0173|5end_hypothetical_protein_165305..165535_POSITIVE 450 150 101 148 99 pint:PI0619|5end_hypothetical_protein_569364..569594_POSITIVE 374 166 122 154 104 pint:PI0312|5end_hypothetical_protein_294591..294821_POSITIVE 371 166 122 167 123 pint:PI0983|5end_hypothetical_protein_909750..909980_POSITIVE 359 516 474 97 52 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 355 99 51 231 173 pint:PI1776|5end_probable_peptidase_of_the_M22_family_(inactive?_chaperone?))_1708623..1708853_POSITIVE 353 87 49 186 151 pint:PI0702|5end_conserved_hypothetical_protein;_possible_tetracenomycin_C_synthesis_protein_homolog_638640..638870_POSITIVE 352 477 432 49 7 pint:PI0324|5end_conserved_hypothetical_protein_303735..303965_POSITIVE 347 67 21 192 145 pint:PI0380|5end_conserved_hypothetical_protein_350162..350392_POSITIVE 345 520 476 210 159 pint:PI1486|5end_alginate_O-acetylation_protein_1405507..1405737_POSITIVE 342 520 476 56 5 pint:PI2144|5end_hypothetical_protein_2091954..2092184_POSITIVE 335 500 451 154 94 pint:PI0891|5end_transketolase_820912..821142_POSITIVE 334 491 454 75 39 pint:PI1145|5end_50S_ribosomal_protein_L35_1072520..1072750_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 652 159 111 57 9 pint:PI0598|3end_hypothetical_protein_547233..547383_POSITIVE 468 108 61 64 17 pint:PI0172|3end_ISPg3-related_transposase_165238..165388_POSITIVE 446 113 72 42 1 pint:PI1461|3end_conserved_hypothetical_protein_1385073..1385223_POSITIVE 368 160 115 48 3 pint:PI0808|3end_ISPg3-related_transposase_746457..746607_POSITIVE 359 516 474 107 62 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 352 477 432 46 4 pint:PI0322|3end_hypothetical_protein_303812..303962_POSITIVE 338 108 62 97 51 pint:PI2105|3end_hypothetical_protein_2059586..2059736_POSITIVE 335 500 451 93 33 pint:PI0890|3end_ribose_5-phosphate_isomerase_B_820931..821081_POSITIVE 333 520 476 124 73 pint:PI1356|3end_hypothetical_protein_1273340..1273490_POSITIVE 328 204 161 140 99 pint:PI0171|3end_hypothetical_protein_164085..164235_POSITIVE 328 204 161 91 50 pint:PI0169|3end_hypothetical_protein_164036..164186_POSITIVE 314 113 72 73 32 pint:PI0533|3end_ABC_transporter,_permease_protein_488421..488571_POSITIVE 305 520 475 128 87 pint:PI2011|3end_hypothetical_protein_1970730..1970880_POSITIVE 303 514 475 111 71 pint:PI1136|3end_conserved_hypothetical_protein_1062541..1062691_POSITIVE 302 477 433 74 19 pint:PI1647|3end_hypothetical_protein_1562531..1562681_POSITIVE 302 477 433 74 19 pint:PI0353|3end_hypothetical_protein_325337..325487_POSITIVE 300 112 72 50 10 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 298 527 487 135 94 pint:PI0034|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_37833..37983_POSITIVE 295 468 424 145 99 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 293 160 119 146 112 pint:PI2082|3end_hypothetical_protein_2040263..2040413_POSITIVE