Origin IGS: tgatacacttttctctttcaccgatatcaacctacgacataactacaaaagatataaaattgtgatagaaagaaagttagaatgtagttagagaaaaacaagcattacaaccctatgactacattctacttttcttctttacgtaccttcacatgttatttttattttgagtatagtcatttcatgtattaaaatggagtca .........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 tgactccattttaatacatgaaatgactatactcaaaataaaaataacatgtgaaggtacgtaaagaagaaaagtagaatgtagtcatagggttgtaatgcttgtttttctctaactacattctaactttctttctatcacaattttatatcttttgtagttatgtcgtaggttgatatcggtgaaagagaaaagtgtatca Mask Tandem Repeat Region ================================================ tgatacacttttctctttcaccgatatcaacctacgacataactacaaaagatataaaattgtgatagaaagaaagttagaatgtagttagagaaaaacaagcattacaaccctatgactacattctacttttcttctttacgtaccttcacatgttatttttattttgagtatagtcatttcatgtattaaaatggagtca Find is-nt database================================================ Query_seq: PI0730:PI0731|PI0730:PI0731:hypothetical protein:conserved hypothetical protein:->->:662227..662428 202 tgatacacttttctctttcaccgatatcaacctacgacataactacaaaagatataaaattgtgatagaaagaaagttagaatgtagttagagaaaaacaagcattacaaccctatgactacattctacttttcttctttacgtaccttcacatgttatttttattttgagtatagtcatttcatgtattaaaatggagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0730:PI0731|PI0730:PI0731:hypothetical protein:conserved hypothetical protein:->->:662227..662428 202 tgatacacttttctctttcaccgatatcaacctacgacataactacaaaagatataaaattgtgatagaaagaaagttagaatgtagttagagaaaaacaagcattacaaccctatgactacattctacttttcttctttacgtaccttcacatgttatttttattttgagtatagtcatttcatgtattaaaatggagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0730:PI0731|PI0730:PI0731:hypothetical protein:conserved hypothetical protein:->->:662227..662428 202 tgatacacttttctctttcaccgatatcaacctacgacataactacaaaagatataaaattgtgatagaaagaaagttagaatgtagttagagaaaaacaagcattacaaccctatgactacattctacttttcttctttacgtaccttcacatgttatttttattttgagtatagtcatttcatgtattaaaatggagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatacacttttctctttcaccgatatcaacctacgacataactacaaaagatataaaattgtgatagaaagaaagttagaatgtagttagagaaaaacaagcattacaaccctatgactacattctacttttcttctttacgtaccttcacatgttatttttattttgagtatagtcatttcatgtattaaaatggagtca Predict ORF larger than 30AA ================================================ tgatacacttttctctttcaccgatatcaacctacgacataactacaaaagatataaaattgtgatagaaagaaagttagaatgtagttagagaaaaacaagcattacaaccctatgactacattctacttttcttctttacgtaccttcacatgttatttttattttgagtatagtcatttcatgtattaaaatggagtca 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: 166 End: 195 .....................................................................................................................................................................TTTGAGTATAGTCATTTCATGTATTAAAAT....... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgatacacttttctctttcaccgatatcaacctacgacataactacaaaagatataaaattgtgatagaaagaaagttagaatgtagttagagaaaaacaagcattacaaccctatgactacattctacttttcttctttacgtaccttcacatgttatttttattttgagtatagtcatttcatgtattaaaatggagtca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0730:PI0731|PI0730:PI0731:hypothetical protein:conserved hypothetical protein:->->:662227..662428 202 tgatacacttttctctttcaccgatatcaacctacgacataactacaaaagatataaaattgtgatagaaagaaagttagaatgtagttagagaaaaacaagcattacaaccctatgactacattctacttttcttctttacgtaccttcacatgttatttttattttgagtatagtcatttcatgtattaaaatggagtca Intra-Species Hit: Count: 1 Min: 1 Max: 202 Len: 202 Subject: pint_PI0730_PI0731|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[662227,662428]|202 HSP 1 e-value: 1.0E-111 bit: 400.0 Len: 202 Query Start:1 Query End:202 Subject Strand: POSITIVE Subject Start: 1 Subject End: 202 tgatacacttttctctttcaccgatatcaacctacgacataactacaaaagatataaaattgtgatagaaagaaagttagaatgtagttagagaaaaacaagcattacaaccctatgactacattctacttttcttctttacgtaccttcacatgttatttttattttgagtatagtcatttcatgtattaaaatggagtca tgatacacttttctctttcaccgatatcaacctacgacataactacaaaagatataaaattgtgatagaaagaaagttagaatgtagttagagaaaaacaagcattacaaccctatgactacattctacttttcttctttacgtaccttcacatgttatttttattttgagtatagtcatttcatgtattaaaatggagtca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUACACUUUUCUCUUUCACCGAUAUCAACCUACGACAUAACUACAAAAGAUAUAAAAUUGUGAUAGAAAGAAAGUUAGAAUGUAGUUAGAGAAAAACAAGCAUUACAACCCUAUGACUACAUUCUACUUUUCUUCUUUACGUACCUUCACAUGUUAUUUUUAUUUUGAGUAUAGUCAUUUCAUGUAUUAAAAUGGAGUCA (((((((...............(....).......(((...(((.(((((...((((...(((((.((((..(((((.((((((((((((.((...................)).)))))))))))))))))..))))..........)))))..)))).....))))))))...)))......)))))))........... (-39.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACUCCAUUUUAAUACAUGAAAUGACUAUACUCAAAAUAAAAAUAACAUGUGAAGGUACGUAAAGAAGAAAAGUAGAAUGUAGUCAUAGGGUUGUAAUGCUUGUUUUUCUCUAACUACAUUCUAACUUUCUUUCUAUCACAAUUUUAUAUCUUUUGUAGUUAUGUCGUAGGUUGAUAUCGGUGAAAGAGAAAAGUGUAUCA ......(((((((.....)))))))..((((((................(((((.((........(((((((..(((((((((((..(((((....(((....)))...))))))))))))))))..))))))))).)))))........(((((..(....((((((.....))))))..)..)))))....))))))... (-43.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 487 48 1 139 92 pint:PI0385|5end_hypothetical_protein_353968..354198_POSITIVE 327 156 111 40 2 pint:PI0576|5end_helicase,_UvrD/Rep_520226..520456_POSITIVE 315 47 1 145 100 pint:PI1559|5end_hypothetical_protein_1476506..1476736_POSITIVE 274 199 158 160 122 pint:PI1651|5end_hypothetical_protein_1563845..1564075_POSITIVE 273 95 60 142 108 pint:PI1408|5end_glucose-1-phosphate_thymidylyltransferase_1329055..1329285_POSITIVE 268 187 141 156 99 pint:PI1612|5end_hypothetical_protein_1539167..1539397_POSITIVE 249 139 92 134 82 pint:PI0387|5end_hypothetical_protein_354631..354861_POSITIVE 242 158 113 142 89 pint:PI0192|5end_conserved_hypothetical_protein_182131..182361_POSITIVE 226 173 133 86 36 pint:PI0916|5end_hypothetical_protein_845617..845847_POSITIVE 223 33 6 172 144 pint:PI0729|5end_integrase_661428..661658_POSITIVE 221 140 91 189 130 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 220 123 83 129 82 pint:PI1019|5end_hypothetical_protein_938228..938458_POSITIVE 220 128 81 206 157 pint:PI0525|5end_transcriptional_regulator,_Arac_family_481332..481562_POSITIVE 217 197 156 162 120 pint:PI0356|5end_hypothetical_protein_326642..326872_POSITIVE 213 154 129 207 179 pint:PI1463|5end_fumarate_hydratase,_class_I_1385349..1385579_POSITIVE 208 87 48 224 180 pint:PI0905|5end_hypothetical_protein_834399..834629_POSITIVE 203 178 140 171 123 pint:PI1928|5end_conserved_hypothetical_protein_1871996..1872226_POSITIVE 202 39 16 213 189 pint:PI0125|5end_undecaprenyl_pyrophosphate_synthase_117106..117336_POSITIVE 199 150 102 148 97 pint:PI2084|5end_hypothetical_protein_2040387..2040617_POSITIVE 199 150 102 85 34 pint:PI2083|5end_hypothetical_protein_2040324..2040554_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 199 158 136 98 pint:PI1650|3end_N-acetylmuramoyl-L-alanine_amidase_1563901..1564051_POSITIVE 273 95 60 123 89 pint:PI1407|3end_conserved_hypothetical_protein_1329116..1329266_POSITIVE 268 187 141 98 41 pint:PI1611|3end_aspartate-semialdehyde_dehydrogenase_1539189..1539339_POSITIVE 249 139 92 63 11 pint:PI0386|3end_integrase_354640..354790_POSITIVE 220 123 83 102 55 pint:PI1591|3end_ISPg3-related_transposase_1519723..1519873_POSITIVE 220 123 83 102 55 pint:PI1018|3end_ISPg3-related_transposase,_N-terminal_region_938281..938431_POSITIVE 217 197 156 138 96 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 210 150 101 114 64 pint:PI0444|3end_50S_ribosomal_protein_L7/L12_413390..413540_POSITIVE 210 150 101 83 33 pint:PI0445|3end_conserved_hypothetical_protein_413359..413509_POSITIVE 209 149 101 131 84 pint:PI1527|3end_immunoreactive_46_kDa_antigen_PG99_1449520..1449670_POSITIVE 205 159 111 126 73 pint:PI1182|3end_hypothetical_protein_1104371..1104521_POSITIVE 203 178 140 141 93 pint:PI1927|3end_hypothetical_protein_1872046..1872196_POSITIVE 201 47 7 127 90 pint:PI1090|3end_tRNA_uracil_5-methyltransferase_1015780..1015930_POSITIVE 198 172 141 121 83 pint:PI1007|3end_conserved_hypothetical_protein_928571..928721_POSITIVE 196 140 91 115 77 pint:PI0749|3end_hypothetical_protein_677469..677619_POSITIVE 194 147 101 148 92 pint:PI1386|3end_sugar_phosphate_isomerase_1308031..1308181_POSITIVE 194 150 102 54 13 pint:PI0096|3end_glycerol-3-phosphate_cytidylyltransferase_93305..93455_POSITIVE 189 135 100 89 58 pint:PI1455|3end_hypothetical_protein_1378963..1379113_POSITIVE 186 146 110 111 74 pint:PI0962|3end_phosphoglycerate_mutase_892702..892852_POSITIVE 184 76 31 76 20 pint:PI1170|3end_possible_response_regulator_1091398..1091548_POSITIVE