Origin IGS: atcggtggtgaacccaaactcgtatttttgttcagccactttccttacatactcattgctattattttctgacatttactttttacctttttattaggcggttgaatcaatgaaaagcaaattccaacatctgcctttcattcttcttacgccaccttatacataatatattatatgcagacaaagattgtgccgatattcttttccgtaacatttgttaccaaaatacaaaccgcctcgcttttcctatggaaatgagaggcggtttggcacatatctta .........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 taagatatgtgccaaaccgcctctcatttccataggaaaagcgaggcggtttgtattttggtaacaaatgttacggaaaagaatatcggcacaatctttgtctgcatataatatattatgtataaggtggcgtaagaagaatgaaaggcagatgttggaatttgcttttcattgattcaaccgcctaataaaaaggtaaaaagtaaatgtcagaaaataatagcaatgagtatgtaaggaaagtggctgaacaaaaatacgagtttgggttcaccaccgat Mask Tandem Repeat Region ================================================ atcggtggtgaacccaaactcgtatttttgttcagccactttccttacatactcattgctattattttctgacatttactttttacctttttattaggcggttgaatcaatgaaaagcaaattccaacatctgcctttcattcttcttacgccaccttatacataatatattatatgcagacaaagattgtgccgatattcttttccgtaacatttgttaccaaaatacaaaccgcctcgcttttcctatggaaatgagaggcggtttggcacatatctta Find is-nt database================================================ Query_seq: PI1953:PI1954|PI1953:PI1954:possible ABC-type permease:translation initiation factor IF-2:->->:1908643..1908923 281 atcggtggtgaacccaaactcgtatttttgttcagccactttccttacatactcattgctattattttctgacatttactttttacctttttattaggcggttgaatcaatgaaaagcaaattccaacatctgcctttcattcttcttacgccaccttatacataatatattatatgcagacaaagattgtgccgatattcttttccgtaacatttgttaccaaaatacaaaccgcctcgcttttcctatggaaatgagaggcggtttggcacatatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1953:PI1954|PI1953:PI1954:possible ABC-type permease:translation initiation factor IF-2:->->:1908643..1908923 281 atcggtggtgaacccaaactcgtatttttgttcagccactttccttacatactcattgctattattttctgacatttactttttacctttttattaggcggttgaatcaatgaaaagcaaattccaacatctgcctttcattcttcttacgccaccttatacataatatattatatgcagacaaagattgtgccgatattcttttccgtaacatttgttaccaaaatacaaaccgcctcgcttttcctatggaaatgagaggcggtttggcacatatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1953:PI1954|PI1953:PI1954:possible ABC-type permease:translation initiation factor IF-2:->->:1908643..1908923 281 atcggtggtgaacccaaactcgtatttttgttcagccactttccttacatactcattgctattattttctgacatttactttttacctttttattaggcggttgaatcaatgaaaagcaaattccaacatctgcctttcattcttcttacgccaccttatacataatatattatatgcagacaaagattgtgccgatattcttttccgtaacatttgttaccaaaatacaaaccgcctcgcttttcctatggaaatgagaggcggtttggcacatatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcggtggtgaacccaaactcgtatttttgttcagccactttccttacatactcattgctattattttctgacatttactttttacctttttattaggcggttgaatcaatgaaaagcaaattccaacatctgcctttcattcttcttacgccaccttatacataatatattatatgcagacaaagattgtgccgatattcttttccgtaacatttgttaccaaaatacaaaccgcctcgcttttcctatggaaatgagaggcggtttggcacatatctta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 5 End: 94 .... M V N P N S Y F C S A T F L T Y S L L L F S D I Y F L P F Y ........................................................................................................................................................................................... Protein_Len: 50 Strand: + Start: 106 End: 255 ......................................................................................................... M N E K Q I P T S A F H S S Y A T L Y I I Y Y M Q T K I V P I F F S V T F V T K I Q T A S L F L W K .......................... Protein_Len: 51 Strand: + Start: 129 End: 281 ................................................................................................................................ M C L S F F L R H L I H N I L Y A D K D C A D I L F R N I C Y Q N T N R L A F P M E M R G G L A H I L Protein_Len: 34 Strand: - Start: 174 End: 275 ............................................................................................................................................................................. I C V F I T G I N K E T V N T V L I C V A E S K R H F H S A T Q C M ...... Protein_Len: 35 Strand: - Start: 110 End: 214 ............................................................................................................. H F A F E L M Q R E N K K R W R I C L I N Y A S L S Q A S I R K R L M ................................................................... atcggtggtgaacccaaactcgtatttttgttcagccactttccttacatactcattgctattattttctgacatttactttttacctttttattaggcggttgaatcaatgaaaagcaaattccaacatctgcctttcattcttcttacgccaccttatacataatatattatatgcagacaaagattgtgccgatattcttttccgtaacatttgttaccaaaatacaaaccgcctcgcttttcctatggaaatgagaggcggtttggcacatatctta 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================================================ atcggtggtgaacccaaactcgtatttttgttcagccactttccttacatactcattgctattattttctgacatttactttttacctttttattaggcggttgaatcaatgaaaagcaaattccaacatctgcctttcattcttcttacgccaccttatacataatatattatatgcagacaaagattgtgccgatattcttttccgtaacatttgttaccaaaatacaaaccgcctcgcttttcctatggaaatgagaggcggtttggcacatatctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -2.2 Tail_Score: -3.9461 Start: 111 End: 140 Full_Region: AGGCGGTTGAATCAA TGAAAAGCAAAT TCCAAC ATCTGCCTTTCA TTCTTCTTACGCCAC ..............................................................................................................TGAAAAGCAAATTCCAACATCTGCCTTTCA............................................................................................................................................. TransTerm Strand: - Conf: 62 HP_score: -6.6 Tail_Score: -3.33815 Start: 111 End: 140 Full_Region: gtggcgtaagaagaa tgaaaggcagat gttgga atttgcttttca ttgattcaaccgcct ..............................................................................................................tgaaaggcagatgttggaatttgcttttca............................................................................................................................................. TransTerm Strand: - Conf: 59 HP_score: -2.0 Tail_Score: -4.4959 Start: 117 End: 134 Full_Region: taagaagaatgaaag gcagat gttgga atttgc ttttcattgattcaa ....................................................................................................................gcagatgttggaatttgc................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -16.3 Tail_Score: -3.57387 Start: 233 End: 265 Full_Region: TTACCAAAATACAAA CCGCCTCGCTTTTCC TAT GGAAATGAGAGGCGG TTTGGCACATATCTT ........................................................................................................................................................................................................................................CCGCCTCGCTTTTCCTATGGAAATGAGAGGCGG................ Find igs database================================================ Query_seq: PI1953:PI1954|PI1953:PI1954:possible ABC-type permease:translation initiation factor IF-2:->->:1908643..1908923 281 atcggtggtgaacccaaactcgtatttttgttcagccactttccttacatactcattgctattattttctgacatttactttttacctttttattaggcggttgaatcaatgaaaagcaaattccaacatctgcctttcattcttcttacgccaccttatacataatatattatatgcagacaaagattgtgccgatattcttttccgtaacatttgttaccaaaatacaaaccgcctcgcttttcctatggaaatgagaggcggtttggcacatatctta Intra-Species Hit: Count: 1 Min: 1 Max: 281 Len: 281 Subject: pint_PI1953_PI1954|possible ABC-type permease:translation initiation factor IF-2|POSITIVE:POSITIVE|[1908643,1908923]|281 HSP 1 e-value: 1.0E-158 bit: 557.0 Len: 281 Query Start:1 Query End:281 Subject Strand: POSITIVE Subject Start: 1 Subject End: 281 atcggtggtgaacccaaactcgtatttttgttcagccactttccttacatactcattgctattattttctgacatttactttttacctttttattaggcggttgaatcaatgaaaagcaaattccaacatctgcctttcattcttcttacgccaccttatacataatatattatatgcagacaaagattgtgccgatattcttttccgtaacatttgttaccaaaatacaaaccgcctcgcttttcctatggaaatgagaggcggtttggcacatatctta atcggtggtgaacccaaactcgtatttttgttcagccactttccttacatactcattgctattattttctgacatttactttttacctttttattaggcggttgaatcaatgaaaagcaaattccaacatctgcctttcattcttcttacgccaccttatacataatatattatatgcagacaaagattgtgccgatattcttttccgtaacatttgttaccaaaatacaaaccgcctcgcttttcctatggaaatgagaggcggtttggcacatatctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGGUGGUGAACCCAAACUCGUAUUUUUGUUCAGCCACUUUCCUUACAUACUCAUUGCUAUUAUUUUCUGACAUUUACUUUUUACCUUUUUAUUAGGCGGUUGAAUCAAUGAAAAGCAAAUUCCAACAUCUGCCUUUCAUUCUUCUUACGCCACCUUAUACAUAAUAUAUUAUAUGCAGACAAAGAUUGUGCCGAUAUUCUUUUCCGUAACAUUUGUUACCAAAAUACAAACCGCCUCGCUUUUCCUAUGGAAAUGAGAGGCGGUUUGGCACAUAUCUUA ...((((((((((..(((......)))..))))).)))))...........................((((.(((.((..................((((...(((..(((((((.(((.((......)).))).))))))).)))...))))....((((.....)))).)).)))))))..(((((((((((.............(((((....)))))........((((((((((...(((((...)))))...)))))))))))))))).))))). (-70.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAUAUGUGCCAAACCGCCUCUCAUUUCCAUAGGAAAAGCGAGGCGGUUUGUAUUUUGGUAACAAAUGUUACGGAAAAGAAUAUCGGCACAAUCUUUGUCUGCAUAUAAUAUAUUAUGUAUAAGGUGGCGUAAGAAGAAUGAAAGGCAGAUGUUGGAAUUUGCUUUUCAUUGAUUCAACCGCCUAAUAAAAAGGUAAAAAGUAAAUGUCAGAAAAUAAUAGCAAUGAGUAUGUAAGGAAAGUGGCUGAACAAAAAUACGAGUUUGGGUUCACCACCGAU .(((((.((((((.(((((((((.(.(((((...))))).).)))))))))....((((.(((((....))))).))))........)))))))))))....(((((((.((.((((((........((((((..(((.((((((((((((((......))))))))))))))..)))....((((.......)))).........))))))....))))))...))..)))))))......((((.(((((..((((....))))..))))))))).... (-86.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 37 1 61 17 pint:PI0097|5end_aspartate_aminotransferase_93235..93465_POSITIVE 317 271 233 167 135 pint:PI1230|5end_probable_metallo-beta-lactamase_family_protein_1151840..1152070_POSITIVE 315 270 233 52 16 pint:PI1588|5end_DNA_polymerase_III,_epsilon_chain_1516302..1516532_POSITIVE 305 268 231 136 106 pint:PI1726|5end_ATP-dependent_DNA_helicase_1643402..1643632_POSITIVE 305 272 235 152 121 pint:PI0916|5end_hypothetical_protein_845617..845847_POSITIVE 304 279 233 71 29 pint:PI2137|5end_RNA_methylase_SpoU_family_2083173..2083403_POSITIVE 297 278 234 177 134 pint:PI0092|5end_regulatory_protein_RecX_89080..89310_POSITIVE 296 272 237 67 34 pint:PI1690|5end_transcription_regulator;_possible_Fe2+/Zn2+_uptake_regulation_proteins_1604984..1605214_POSITIVE 295 272 233 96 47 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 294 269 234 208 167 pint:PI0269|5end_conserved_hypothetical_protein_259835..260065_POSITIVE 286 42 1 49 14 pint:PI1082|5end_polypeptide_deformylase_1001282..1001512_POSITIVE 286 49 3 207 160 pint:PI0953|5end_hypothetical_protein_885119..885349_POSITIVE 285 266 229 119 85 pint:PI1664|5end_conserved_hypothetical_protein_1577285..1577515_POSITIVE 285 266 229 119 85 pint:PI0370|5end_conserved_hypothetical_protein_340453..340683_POSITIVE 284 140 96 175 120 pint:PI1669|5end_hypothetical_protein_1581257..1581487_POSITIVE 284 48 1 73 27 pint:PI0797|5end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735016..735246_POSITIVE 283 273 235 118 76 pint:PI0938|5end_hypothetical_protein_869345..869575_POSITIVE 283 159 112 145 83 pint:PI0387|5end_hypothetical_protein_354631..354861_POSITIVE 282 49 3 79 30 pint:PI1710|5end_ABC-type_permease_component_1626644..1626874_POSITIVE 282 272 234 134 82 pint:PI1439|5end_hypothetical_protein_1360009..1360239_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 37 1 51 7 pint:PI0096|3end_glycerol-3-phosphate_cytidylyltransferase_93305..93455_POSITIVE 316 274 234 98 60 pint:PI1941|3end_outer_membrane_receptor;_ragA_protein_1900619..1900769_POSITIVE 306 280 232 137 85 pint:PI0068|3end_arginine_repressor_67019..67169_POSITIVE 305 152 116 138 102 pint:PI1548|3end_conserved_hypothetical_protein_1466886..1467036_POSITIVE 304 279 233 71 29 pint:PI2135|3end_conserved_hypothetical_protein_2083253..2083403_POSITIVE 294 269 234 83 42 pint:PI0268|3end_lysozyme-related_protein_259790..259940_POSITIVE 285 266 229 101 67 pint:PI1663|3end_hypothetical_protein_1577347..1577497_POSITIVE 283 159 112 74 12 pint:PI0386|3end_integrase_354640..354790_POSITIVE 281 272 232 151 110 pint:PI0900|3end_signal_recognition_particle_protein_831092..831242_POSITIVE 281 280 233 95 51 pint:PI0728|3end_integrase_661508..661658_POSITIVE 278 270 221 150 98 pint:PI0844|3end_cytidine/deoxycytidylate_deaminase_(dCMP_deaminase)_778316..778466_POSITIVE 274 264 233 150 114 pint:PI0669|3end_hypothetical_protein_611147..611297_POSITIVE 270 104 61 59 22 pint:PI0978|3end_hypothetical_protein_905114..905264_POSITIVE 267 42 2 48 13 pint:PI0253|3end_conjugative_transposon_protein,_TraD_248973..249123_POSITIVE 266 266 233 36 6 pint:PI1766|3end_sugar_transporter,_possible_glucose/galactose_transporter_1694350..1694500_POSITIVE 265 272 237 61 16 pint:PI0787|3end_glycosyltransferase_725793..725943_POSITIVE 264 270 222 84 35 pint:PI2028|3end_shikimate_kinase_1982802..1982952_POSITIVE 264 246 202 114 75 pint:PI0368|3end_hypothetical_protein_339985..340135_POSITIVE 263 275 232 117 77 pint:PI1065|3end_hypothetical_protein_983650..983800_POSITIVE 262 279 232 111 73 pint:PI1644|3end_hypothetical_protein_1561030..1561180_POSITIVE