Origin IGS: taagtagtttgtttacaccttatatataatagggaaggtttggcacggcaagaatggttttagggtcgtggcaaaccaatagcgtaaaagagaaaggaagtacttctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagaagtacttcctttctcttttacgctattggtttgccacgaccctaaaaccattcttgccgtgccaaaccttccctattatatataaggtgtaaacaaactactta Mask Tandem Repeat Region ================================================ taagtagtttgtttacaccttatatataatagggaaggtttggcacggcaagaatggttttagggtcgtggcaaaccaatagcgtaaaagagaaaggaagtacttctta Find is-nt database================================================ Query_seq: PI0538:PI0540|PI0538:PI0540:transcriptional regulator:conserved hypothetical protein:->->:492986..493094 109 taagtagtttgtttacaccttatatataatagggaaggtttggcacggcaagaatggttttagggtcgtggcaaaccaatagcgtaaaagagaaaggaagtacttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0538:PI0540|PI0538:PI0540:transcriptional regulator:conserved hypothetical protein:->->:492986..493094 109 taagtagtttgtttacaccttatatataatagggaaggtttggcacggcaagaatggttttagggtcgtggcaaaccaatagcgtaaaagagaaaggaagtacttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0538:PI0540|PI0538:PI0540:transcriptional regulator:conserved hypothetical protein:->->:492986..493094 109 taagtagtttgtttacaccttatatataatagggaaggtttggcacggcaagaatggttttagggtcgtggcaaaccaatagcgtaaaagagaaaggaagtacttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtagtttgtttacaccttatatataatagggaaggtttggcacggcaagaatggttttagggtcgtggcaaaccaatagcgtaaaagagaaaggaagtacttctta Predict ORF larger than 30AA ================================================ taagtagtttgtttacaccttatatataatagggaaggtttggcacggcaagaatggttttagggtcgtggcaaaccaatagcgtaaaagagaaaggaagtacttctta 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================================================ taagtagtttgtttacaccttatatataatagggaaggtttggcacggcaagaatggttttagggtcgtggcaaaccaatagcgtaaaagagaaaggaagtacttctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0538:PI0540|PI0538:PI0540:transcriptional regulator:conserved hypothetical protein:->->:492986..493094 109 taagtagtttgtttacaccttatatataatagggaaggtttggcacggcaagaatggttttagggtcgtggcaaaccaatagcgtaaaagagaaaggaagtacttctta Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: pint_PI0538_PI0540|transcriptional regulator:conserved hypothetical protein|POSITIVE:POSITIVE|[492986,493094]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 taagtagtttgtttacaccttatatataatagggaaggtttggcacggcaagaatggttttagggtcgtggcaaaccaatagcgtaaaagagaaaggaagtacttctta taagtagtttgtttacaccttatatataatagggaaggtttggcacggcaagaatggttttagggtcgtggcaaaccaatagcgtaaaagagaaaggaagtacttctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUAGUUUGUUUACACCUUAUAUAUAAUAGGGAAGGUUUGGCACGGCAAGAAUGGUUUUAGGGUCGUGGCAAACCAAUAGCGUAAAAGAGAAAGGAAGUACUUCUUA .(((((.(((.(((...((((((.....))))))..((((((.((((((...((.....))...)))))).))))))...............))).))).))))).... (-32.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAGUACUUCCUUUCUCUUUUACGCUAUUGGUUUGCCACGACCCUAAAACCAUUCUUGCCGUGCCAAACCUUCCCUAUUAUAUAUAAGGUGUAAACAAACUACUUA ..(((((.......)))))..((((((((...((((((.((((...................)))).)))))).....(((.....))).))))))))........... (-16.61) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 69 21 172 123 pint:PI1426|5end_flavodoxin_1344881..1345111_POSITIVE 323 78 36 171 130 pint:PI1295|5end_hypothetical_protein_1208636..1208866_POSITIVE 318 84 42 80 27 pint:PI2040|5end_conserved_hypothetical_protein;_possible_transporter_1993068..1993298_POSITIVE 313 71 31 208 171 pint:PI0274|5end_conserved_hypothetical_protein_262856..263086_POSITIVE 307 72 31 207 175 pint:PI1889|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-(pentape_ptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1831411..1831641_POSITIVE 301 78 31 179 139 pint:PI0178|5end_2-oxoglutarate_synthase,_subunit_korA_169524..169754_POSITIVE 300 78 32 231 184 pint:PI0795|5end_hypothetical_protein_730964..731194_POSITIVE 298 86 48 34 1 pint:PI1305|5end_conserved_hypothetical_protein_1216854..1217084_POSITIVE 296 78 41 111 72 pint:PI0703|5end_hypothetical_protein_639655..639885_POSITIVE 295 85 41 63 4 pint:PI0427|5end_conserved_hypothetical_protein_391140..391370_POSITIVE 289 100 51 117 72 pint:PI1579|5end_penicillin-binding_protein_2_1505713..1505943_POSITIVE 288 65 29 124 81 pint:PI1543|5end_hypothetical_protein_1462773..1463003_POSITIVE 287 71 31 42 4 pint:PI0668|5end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610216..610446_POSITIVE 286 71 44 168 141 pint:PI0805|5end_conserved_hypothetical_protein_742729..742959_POSITIVE 286 89 41 107 57 pint:PI0765|5end_conserved_hypothetical_protein;_possible_surface_protein_699753..699983_POSITIVE 284 100 51 60 7 pint:PI0185|5end_conserved_hypothetical_protein_176992..177222_POSITIVE 282 78 36 223 182 pint:PI1303|5end_ISPg3-related_transposase_1215135..1215365_POSITIVE 282 73 31 193 154 pint:PI0646|5end_hypothetical_protein_586583..586813_POSITIVE 280 82 41 53 15 pint:PI1429|5end_L-aspartate_oxidase_1347650..1347880_POSITIVE 278 88 43 83 39 pint:PI0943|5end_conserved_hypothetical_protein_875153..875383_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 69 29 139 98 pint:PI1999|3end_hypothetical_protein_1956668..1956818_POSITIVE 340 69 21 60 11 pint:PI1425|3end_conserved_hypothetical_protein_1344849..1344999_POSITIVE 324 73 37 123 95 pint:PI0981|3end_outer_membrane_protein,_TonB_dependent_receptor_909390..909540_POSITIVE 306 72 31 64 13 pint:PI0273|3end_hypothetical_protein_263284..263434_POSITIVE 289 100 51 64 19 pint:PI1578|3end_rod_shape-determining_protein_1505740..1505890_POSITIVE 289 80 31 127 84 pint:PI0286|3end_ISPg3-related_transposase_272065..272215_POSITIVE 288 65 29 137 94 pint:PI1542|3end_mobilization_protein_1462866..1463016_POSITIVE 286 71 44 149 122 pint:PI0804|3end_conserved_hypothetical_protein;_possible_membrane_protein_742790..742940_POSITIVE 286 72 31 51 7 pint:PI0403|3end_probable_integrase_371125..371275_POSITIVE 283 85 41 143 92 pint:PI0846|3end_transcription_regulator,_CRP_family_781009..781159_POSITIVE 282 73 31 99 60 pint:PI0644|3end_dnaJ_protein_586569..586719_POSITIVE 278 76 31 130 85 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE 278 88 43 99 55 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 275 78 31 97 28 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 272 78 31 122 81 pint:PI1029|3end_seryl-tRNA_synthetase_947205..947355_POSITIVE 270 74 31 102 44 pint:PI2107|3end_hypothetical_protein_2060023..2060173_POSITIVE 268 69 29 57 11 pint:PI1183|3end_conserved_hypothetical_protein_1105847..1105997_POSITIVE 267 68 23 148 98 pint:PI1754|3end_conserved_hypothetical_protein_1682010..1682160_POSITIVE 265 72 32 107 62 pint:PI0221|3end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_217796..217946_POSITIVE 261 100 51 149 106 pint:PI1884|3end_conserved_hypothetical_protein_1827457..1827607_POSITIVE