Origin IGS: taagttttaggagttaaaccactacctttgtttgctaccagctttgatgtatcaacgcatcgaagttctctgaaacaagcagcataggtattggttcaactccttttctttacgaaaaaccactatgataaacgaatgtaaattttactactaatctaataaagattggttaagttgccttttttatttgttaaatacgaataaagaaaactgacaaattagcacatttacattttttgggtctatatttgcacttggttttgcatcgagacggtaaataaagaacaactgcctcaagataacaaagacctttaacacaggtttaccagctgacaaattgtcatttaacgcattagaattataaaaacaacaatattaatttaataagataaagagatt .........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 aatctctttatcttattaaattaatattgttgtttttataattctaatgcgttaaatgacaatttgtcagctggtaaacctgtgttaaaggtctttgttatcttgaggcagttgttctttatttaccgtctcgatgcaaaaccaagtgcaaatatagacccaaaaaatgtaaatgtgctaatttgtcagttttctttattcgtatttaacaaataaaaaaggcaacttaaccaatctttattagattagtagtaaaatttacattcgtttatcatagtggtttttcgtaaagaaaaggagttgaaccaatacctatgctgcttgtttcagagaacttcgatgcgttgatacatcaaagctggtagcaaacaaaggtagtggtttaactcctaaaactta Mask Tandem Repeat Region ================================================ taagttttaggagttaaaccactacctttgtttgctaccagctttgatgtatcaacgcatcgaagttctctgaaacaagcagcataggtattggttcaactccttttctttacgaaaaaccactatgataaacgaatgtaaattttactactaatctaataaagattggttaagttgccttttttatttgttaaatacgaataaagaaaactgacaaattagcacatttacattttttgggtctatatttgcacttggttttgcatcgagacggtaaataaagaacaactgcctcaagataacaaagacctttaacacaggtttaccagctgacaaattgtcatttaacgcattagaattataaaaacaacaatattaatttaataagataaagagatt Find is-nt database================================================ Query_seq: PI1575:PI1576|PI1575:PI1576:LemA protein:serine protease precursor:->->:1501913..1502311 399 taagttttaggagttaaaccactacctttgtttgctaccagctttgatgtatcaacgcatcgaagttctctgaaacaagcagcataggtattggttcaactccttttctttacgaaaaaccactatgataaacgaatgtaaattttactactaatctaataaagattggttaagttgccttttttatttgttaaatacgaataaagaaaactgacaaattagcacatttacattttttgggtctatatttgcacttggttttgcatcgagacggtaaataaagaacaactgcctcaagataacaaagacctttaacacaggtttaccagctgacaaattgtcatttaacgcattagaattataaaaacaacaatattaatttaataagataaagagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1575:PI1576|PI1575:PI1576:LemA protein:serine protease precursor:->->:1501913..1502311 399 taagttttaggagttaaaccactacctttgtttgctaccagctttgatgtatcaacgcatcgaagttctctgaaacaagcagcataggtattggttcaactccttttctttacgaaaaaccactatgataaacgaatgtaaattttactactaatctaataaagattggttaagttgccttttttatttgttaaatacgaataaagaaaactgacaaattagcacatttacattttttgggtctatatttgcacttggttttgcatcgagacggtaaataaagaacaactgcctcaagataacaaagacctttaacacaggtttaccagctgacaaattgtcatttaacgcattagaattataaaaacaacaatattaatttaataagataaagagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1575:PI1576|PI1575:PI1576:LemA protein:serine protease precursor:->->:1501913..1502311 399 taagttttaggagttaaaccactacctttgtttgctaccagctttgatgtatcaacgcatcgaagttctctgaaacaagcagcataggtattggttcaactccttttctttacgaaaaaccactatgataaacgaatgtaaattttactactaatctaataaagattggttaagttgccttttttatttgttaaatacgaataaagaaaactgacaaattagcacatttacattttttgggtctatatttgcacttggttttgcatcgagacggtaaataaagaacaactgcctcaagataacaaagacctttaacacaggtttaccagctgacaaattgtcatttaacgcattagaattataaaaacaacaatattaatttaataagataaagagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagttttaggagttaaaccactacctttgtttgctaccagctttgatgtatcaacgcatcgaagttctctgaaacaagcagcataggtattggttcaactccttttctttacgaaaaaccactatgataaacgaatgtaaattttactactaatctaataaagattggttaagttgccttttttatttgttaaatacgaataaagaaaactgacaaattagcacatttacattttttgggtctatatttgcacttggttttgcatcgagacggtaaataaagaacaactgcctcaagataacaaagacctttaacacaggtttaccagctgacaaattgtcatttaacgcattagaattataaaaacaacaatattaatttaataagataaagagatt Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: - Start: 187 End: 336 .......................................................................................................................................................................................... K N F V F L S F Q C I L V N V N K P D I N A S P K A D L R Y I F F L Q R L I V F V K L V P K G A S M ............................................................... taagttttaggagttaaaccactacctttgtttgctaccagctttgatgtatcaacgcatcgaagttctctgaaacaagcagcataggtattggttcaactccttttctttacgaaaaaccactatgataaacgaatgtaaattttactactaatctaataaagattggttaagttgccttttttatttgttaaatacgaataaagaaaactgacaaattagcacatttacattttttgggtctatatttgcacttggttttgcatcgagacggtaaataaagaacaactgcctcaagataacaaagacctttaacacaggtttaccagctgacaaattgtcatttaacgcattagaattataaaaacaacaatattaatttaataagataaagagatt 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================================================ taagttttaggagttaaaccactacctttgtttgctaccagctttgatgtatcaacgcatcgaagttctctgaaacaagcagcataggtattggttcaactccttttctttacgaaaaaccactatgataaacgaatgtaaattttactactaatctaataaagattggttaagttgccttttttatttgttaaatacgaataaagaaaactgacaaattagcacatttacattttttgggtctatatttgcacttggttttgcatcgagacggtaaataaagaacaactgcctcaagataacaaagacctttaacacaggtttaccagctgacaaattgtcatttaacgcattagaattataaaaacaacaatattaatttaataagataaagagatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -3.9 Tail_Score: -3.24122 Start: 151 End: 169 Full_Region: ATGTAAATTTTACTA CTAATCT AATAA AGATTGG TTAAGTTGCCTTTTT ......................................................................................................................................................CTAATCTAATAAAGATTGG...................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI1575:PI1576|PI1575:PI1576:LemA protein:serine protease precursor:->->:1501913..1502311 399 taagttttaggagttaaaccactacctttgtttgctaccagctttgatgtatcaacgcatcgaagttctctgaaacaagcagcataggtattggttcaactccttttctttacgaaaaaccactatgataaacgaatgtaaattttactactaatctaataaagattggttaagttgccttttttatttgttaaatacgaataaagaaaactgacaaattagcacatttacattttttgggtctatatttgcacttggttttgcatcgagacggtaaataaagaacaactgcctcaagataacaaagacctttaacacaggtttaccagctgacaaattgtcatttaacgcattagaattataaaaacaacaatattaatttaataagataaagagatt Intra-Species Hit: Count: 1 Min: 1 Max: 399 Len: 399 Subject: pint_PI1575_PI1576|LemA protein:serine protease precursor|POSITIVE:POSITIVE|[1501913,1502311]|399 HSP 1 e-value: 0.0 bit: 791.0 Len: 399 Query Start:1 Query End:399 Subject Strand: POSITIVE Subject Start: 1 Subject End: 399 taagttttaggagttaaaccactacctttgtttgctaccagctttgatgtatcaacgcatcgaagttctctgaaacaagcagcataggtattggttcaactccttttctttacgaaaaaccactatgataaacgaatgtaaattttactactaatctaataaagattggttaagttgccttttttatttgttaaatacgaataaagaaaactgacaaattagcacatttacattttttgggtctatatttgcacttggttttgcatcgagacggtaaataaagaacaactgcctcaagataacaaagacctttaacacaggtttaccagctgacaaattgtcatttaacgcattagaattataaaaacaacaatattaatttaataagataaagagatt taagttttaggagttaaaccactacctttgtttgctaccagctttgatgtatcaacgcatcgaagttctctgaaacaagcagcataggtattggttcaactccttttctttacgaaaaaccactatgataaacgaatgtaaattttactactaatctaataaagattggttaagttgccttttttatttgttaaatacgaataaagaaaactgacaaattagcacatttacattttttgggtctatatttgcacttggttttgcatcgagacggtaaataaagaacaactgcctcaagataacaaagacctttaacacaggtttaccagctgacaaattgtcatttaacgcattagaattataaaaacaacaatattaatttaataagataaagagatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUUUUAGGAGUUAAACCACUACCUUUGUUUGCUACCAGCUUUGAUGUAUCAACGCAUCGAAGUUCUCUGAAACAAGCAGCAUAGGUAUUGGUUCAACUCCUUUUCUUUACGAAAAACCACUAUGAUAAACGAAUGUAAAUUUUACUACUAAUCUAAUAAAGAUUGGUUAAGUUGCCUUUUUUAUUUGUUAAAUACGAAUAAAGAAAACUGACAAAUUAGCACAUUUACAUUUUUUGGGUCUAUAUUUGCACUUGGUUUUGCAUCGAGACGGUAAAUAAAGAACAACUGCCUCAAGAUAACAAAGACCUUUAACACAGGUUUACCAGCUGACAAAUUGUCAUUUAACGCAUUAGAAUUAUAAAAACAACAAUAUUAAUUUAAUAAGAUAAAGAGAUU ........(((((((.(((((.(((((.((((.(((..((((((((((((......)))))))))....))).....))))))).))))).))))).)))))))((((((((...........((((((.....(((((.(((((....((((((((.....)))))))).)))))...((((((((((((.....))))))))))))...((((((.(((((...........((((((((((.(((((((.((((((.....))))))...))))))).)))........)))))))......((((((.......))))))....)))))....))))))......)))))...))))))..........(((((...)))))...)))))))).. (-93.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUCUUUAUCUUAUUAAAUUAAUAUUGUUGUUUUUAUAAUUCUAAUGCGUUAAAUGACAAUUUGUCAGCUGGUAAACCUGUGUUAAAGGUCUUUGUUAUCUUGAGGCAGUUGUUCUUUAUUUACCGUCUCGAUGCAAAACCAAGUGCAAAUAUAGACCCAAAAAAUGUAAAUGUGCUAAUUUGUCAGUUUUCUUUAUUCGUAUUUAACAAAUAAAAAAGGCAACUUAACCAAUCUUUAUUAGAUUAGUAGUAAAAUUUACAUUCGUUUAUCAUAGUGGUUUUUCGUAAAGAAAAGGAGUUGAACCAAUACCUAUGCUGCUUGUUUCAGAGAACUUCGAUGCGUUGAUACAUCAAAGCUGGUAGCAAACAAAGGUAGUGGUUUAACUCCUAAAACUUA ....(((((((......((((((..(((((..(((.....((....)).....)))..)))))........((((((((..........(((((.((((...(((((((.((............)).))))))).(((........))).)))).))))).....(((((((((.(((((........(((((.((((((.((.....)).)))))).))))).........(((((.....)))))..)))))..))))))))).))))))))...))))))...)))))))..(((((((((((((.(((((.(((((((.((((..((.....((((....))))....)).)))).))))))).....))))).)))))))))))))........ (-91.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 299 251 71 15 pint:PI1032|5end_methylmalonyl-CoA_decarboxylase,_alpha_subunit_948463..948693_POSITIVE 294 296 251 77 32 pint:PI1923|5end_conserved_hypothetical_protein_1865560..1865790_POSITIVE 286 268 222 132 82 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 277 88 46 97 60 pint:PI0954|5end_hypothetical_protein_885567..885797_POSITIVE 276 79 33 65 19 pint:PI1977|5end_hypothetical_protein_1933268..1933498_POSITIVE 275 80 32 90 47 pint:PI0872|5end_hypothetical_protein_807371..807601_POSITIVE 272 276 232 195 144 pint:PI0713|5end_hypothetical_protein_650294..650524_POSITIVE 272 273 231 194 156 pint:PI0431|5end_Xaa-Pro_aminopeptidase_403064..403294_POSITIVE 266 95 56 227 188 pint:PI1886|5end_cell_division_protein_1827633..1827863_POSITIVE 262 70 22 120 65 pint:PI0334|5end_hypothetical_protein_313234..313464_POSITIVE 261 284 250 42 4 pint:PI0694|5end_Na+/dicarboxylate_or_sulfate_symporter_629745..629975_POSITIVE 257 43 10 192 159 pint:PI1263|5end_probable_integrase_1184502..1184732_POSITIVE 256 62 25 205 165 pint:PI1735|5end_conserved_hypothetical_protein_1653428..1653658_POSITIVE 256 280 231 230 169 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 256 280 231 63 2 pint:PI0196|5end_hypothetical_protein_188435..188665_POSITIVE 255 293 251 225 170 pint:PI1744|5end_chromosome_partitioning_protein_1665635..1665865_POSITIVE 255 53 12 116 77 pint:PI1104|5end_GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-redu_ctase_1027749..1027979_POSITIVE 253 89 41 201 144 pint:PI2028|5end_shikimate_kinase_1982162..1982392_POSITIVE 253 322 286 229 191 pint:PI1772|5end_pullulanase_1702257..1702487_POSITIVE 252 80 32 84 36 pint:PI2148|5end_ribonuclease_III_2094505..2094735_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 272 238 68 27 pint:PI1378|3end_GTP-binding_protein_lepA_1301651..1301801_POSITIVE 286 268 222 136 86 pint:PI0354|3end_hypothetical_protein_326241..326391_POSITIVE 276 79 33 71 25 pint:PI1976|3end_hypothetical_protein_1933354..1933504_POSITIVE 272 273 231 151 113 pint:PI0430|3end_periplasmic_protease;_MdsD_protein_403101..403251_POSITIVE 265 269 221 147 80 pint:PI0985|3end_aspartyl-tRNA_synthetase_911912..912062_POSITIVE 261 99 53 127 81 pint:PI1723|3end_conserved_hypothetical_protein_1642133..1642283_POSITIVE 260 50 9 127 83 pint:PI2099|3end_D-alanyl-D-alanine_dipeptidase_2053277..2053427_POSITIVE 257 220 174 131 75 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE 256 88 50 121 78 pint:PI0778|3end_hypothetical_protein_714885..715035_POSITIVE 253 89 41 89 32 pint:PI2027|3end_arginine_decarboxylase_1982130..1982280_POSITIVE 249 266 221 41 7 pint:PI0070|3end_conserved_hypothetical_protein_70108..70258_POSITIVE 248 70 25 108 64 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 248 275 234 150 95 pint:PI0263|3end_conjugative_transposon_protein,_TraM_256412..256562_POSITIVE 244 111 72 60 21 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 244 104 61 82 45 pint:PI1575|3end_LemA_protein_1501852..1502002_POSITIVE 243 280 241 147 106 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 243 87 41 50 2 pint:PI0290|3end_conserved_hypothetical_protein_274131..274281_POSITIVE 240 126 81 55 17 pint:PI1049|3end_hypothetical_protein_967341..967491_POSITIVE 240 99 58 76 29 pint:PI1000|3end_conserved_hypothetical_protein_923672..923822_POSITIVE 239 46 7 93 46 pint:PI1187|3end_conserved_hypothetical_protein_1107245..1107395_POSITIVE