Origin IGS: taaggacataccagccagctcttagcgaagacttacggtgggcatactgtctgccttcacaaccctaccttatatattatggtgttcagcaagactgtaaccgatgcgctcttagagaaaatcaggaacggtaattctatgacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgtcatagaattaccgttcctgattttctctaagagcgcatcggttacagtcttgctgaacaccataatatataaggtagggttgtgaaggcagacagtatgcccaccgtaagtcttcgctaagagctggctggtatgtcctta Mask Tandem Repeat Region ================================================ taaggacataccagccagctcttagcgaagacttacggtgggcatactgtctgccttcacaaccctaccttatatattatggtgttcagcaagactgtaaccgatgcgctcttagagaaaatcaggaacggtaattctatgacg Find is-nt database================================================ Query_seq: PI1738:PI1739|PI1738:PI1739:FKBP-type peptidyl-prolyl cis-trans isomerase:Na+-driven multidrug efflux pump, MATE efflux family protein:->->:1660173..1660316 144 taaggacataccagccagctcttagcgaagacttacggtgggcatactgtctgccttcacaaccctaccttatatattatggtgttcagcaagactgtaaccgatgcgctcttagagaaaatcaggaacggtaattctatgacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1738:PI1739|PI1738:PI1739:FKBP-type peptidyl-prolyl cis-trans isomerase:Na+-driven multidrug efflux pump, MATE efflux family protein:->->:1660173..1660316 144 taaggacataccagccagctcttagcgaagacttacggtgggcatactgtctgccttcacaaccctaccttatatattatggtgttcagcaagactgtaaccgatgcgctcttagagaaaatcaggaacggtaattctatgacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1738:PI1739|PI1738:PI1739:FKBP-type peptidyl-prolyl cis-trans isomerase:Na+-driven multidrug efflux pump, MATE efflux family protein:->->:1660173..1660316 144 taaggacataccagccagctcttagcgaagacttacggtgggcatactgtctgccttcacaaccctaccttatatattatggtgttcagcaagactgtaaccgatgcgctcttagagaaaatcaggaacggtaattctatgacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaggacataccagccagctcttagcgaagacttacggtgggcatactgtctgccttcacaaccctaccttatatattatggtgttcagcaagactgtaaccgatgcgctcttagagaaaatcaggaacggtaattctatgacg Predict ORF larger than 30AA ================================================ taaggacataccagccagctcttagcgaagacttacggtgggcatactgtctgccttcacaaccctaccttatatattatggtgttcagcaagactgtaaccgatgcgctcttagagaaaatcaggaacggtaattctatgacg 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================================================ taaggacataccagccagctcttagcgaagacttacggtgggcatactgtctgccttcacaaccctaccttatatattatggtgttcagcaagactgtaaccgatgcgctcttagagaaaatcaggaacggtaattctatgacg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1738:PI1739|PI1738:PI1739:FKBP-type peptidyl-prolyl cis-trans isomerase:Na+-driven multidrug efflux pump, MATE efflux family protein:->->:1660173..1660316 144 taaggacataccagccagctcttagcgaagacttacggtgggcatactgtctgccttcacaaccctaccttatatattatggtgttcagcaagactgtaaccgatgcgctcttagagaaaatcaggaacggtaattctatgacg Intra-Species Hit: Count: 1 Min: 1 Max: 144 Len: 144 Subject: pint_PI1738_PI1739|FKBP-type peptidyl-prolyl cis-trans isomerase:Na+-driven multidrug efflux pump, MATE efflux family protein|POSITIVE:POSITIVE|[1660173,1660316]|144 HSP 1 e-value: 2.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 taaggacataccagccagctcttagcgaagacttacggtgggcatactgtctgccttcacaaccctaccttatatattatggtgttcagcaagactgtaaccgatgcgctcttagagaaaatcaggaacggtaattctatgacg taaggacataccagccagctcttagcgaagacttacggtgggcatactgtctgccttcacaaccctaccttatatattatggtgttcagcaagactgtaaccgatgcgctcttagagaaaatcaggaacggtaattctatgacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGACAUACCAGCCAGCUCUUAGCGAAGACUUACGGUGGGCAUACUGUCUGCCUUCACAACCCUACCUUAUAUAUUAUGGUGUUCAGCAAGACUGUAACCGAUGCGCUCUUAGAGAAAAUCAGGAACGGUAAUUCUAUGACG ...(((..((((...(((.((((.((..........((..(((.....)))..))..........((((.((.....)).))))....)))))))))...(((((...(((...)))...))).))...))))..)))...... (-31.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUCAUAGAAUUACCGUUCCUGAUUUUCUCUAAGAGCGCAUCGGUUACAGUCUUGCUGAACACCAUAAUAUAUAAGGUAGGGUUGUGAAGGCAGACAGUAUGCCCACCGUAAGUCUUCGCUAAGAGCUGGCUGGUAUGUCCUUA .((((..((((....)))).))))......((((..((.((((((..((((((((((..................))))))...((((((((..((.((......)).))..)))))))).....)))))))))).))..)))) (-30.47) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 59 11 103 54 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 360 59 17 74 29 pint:PI1778|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1710009..1710239_POSITIVE 353 59 11 221 157 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 329 44 6 47 3 pint:PI0144|5end_conserved_hypothetical_protein_135420..135650_POSITIVE 317 63 24 85 47 pint:PI0668|5end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610216..610446_POSITIVE 314 119 75 111 67 pint:PI1383|5end_biopolymer_transport_protein_tolQ_related_1304121..1304351_POSITIVE 314 57 11 203 141 pint:PI0753|5end_hypothetical_protein_683391..683621_POSITIVE 312 61 24 200 164 pint:PI0735|5end_ABC_transporter,_ATP-binding_/_permease_668793..669023_POSITIVE 312 60 12 91 35 pint:PI0729|5end_integrase_661428..661658_POSITIVE 310 57 12 195 140 pint:PI0719|5end_conserved_hypothetical_protein_653043..653273_POSITIVE 307 66 36 64 36 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 302 99 51 88 27 pint:PI0576|5end_helicase,_UvrD/Rep_520226..520456_POSITIVE 298 54 11 77 17 pint:PI1736|5end_topoisomerase_IV,_subunit_A_1654254..1654484_POSITIVE 298 45 6 192 154 pint:PI0937|5end_hypothetical_protein_869235..869465_POSITIVE 297 56 11 220 173 pint:PI0246|5end_conserved_hypothetical_protein_244166..244396_POSITIVE 294 43 2 200 157 pint:PI0641|5end_conserved_hypothetical_protein_583791..584021_POSITIVE 294 70 25 156 105 pint:PI0331|5end_hypothetical_protein_311656..311886_POSITIVE 293 57 13 196 157 pint:PI0767|5end_possible_TonB-dependent_receptor_701915..702145_POSITIVE 293 50 2 113 65 pint:PI0519|5end_5'-nucleotidase/2',3'-cyclic_phosphodiesterase_477953..478183_POSITIVE 292 60 13 208 153 pint:PI0529|5end_hypothetical_protein_483026..483256_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 59 17 66 21 pint:PI1777|3end_conserved_hypothetical_protein_1710081..1710231_POSITIVE 314 119 75 47 3 pint:PI1382|3end_hypothetical_protein_1304137..1304287_POSITIVE 313 67 25 118 76 pint:PI1007|3end_conserved_hypothetical_protein_928571..928721_POSITIVE 312 61 24 87 51 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 312 60 12 91 35 pint:PI0728|3end_integrase_661508..661658_POSITIVE 308 130 81 143 102 pint:PI0375|3end_hypothetical_protein_346082..346232_POSITIVE 303 60 11 122 74 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 298 54 11 66 6 pint:PI1735|3end_conserved_hypothetical_protein_1654323..1654473_POSITIVE 295 54 12 125 81 pint:PI1723|3end_conserved_hypothetical_protein_1642133..1642283_POSITIVE 294 58 14 105 68 pint:PI1947|3end_hypothetical_protein_1902865..1903015_POSITIVE 294 43 2 150 107 pint:PI0640|3end_conserved_hypothetical_protein_583821..583971_POSITIVE 291 68 23 52 16 pint:PI1049|3end_hypothetical_protein_967341..967491_POSITIVE 290 99 55 131 91 pint:PI1611|3end_aspartate-semialdehyde_dehydrogenase_1539189..1539339_POSITIVE 287 59 11 138 82 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE 287 108 62 79 27 pint:PI1733|3end_hypothetical_protein_1652437..1652587_POSITIVE 284 55 13 109 61 pint:PI2041|3end_conserved_hypothetical_protein_1994660..1994810_POSITIVE 281 60 11 141 97 pint:PI0247|3end_conjugative_transposon_protein,_TraA_246232..246382_POSITIVE 281 55 13 61 21 pint:PI0159|3end_hypothetical_protein_152120..152270_POSITIVE 280 65 25 62 17 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 279 55 14 127 68 pint:PI1493|3end_conserved_hypothetical_protein_1412818..1412968_POSITIVE