Origin IGS: tgctatgaagttcttacctgttttaattgtttctactgttttcataatgctatttgtttatttgttataagagttgttattattcttgttttgataatgcaaagatattgtgtttcaaaagtttatgcaagtaggcacgcaaatgtaagccagttacttagaggtaagtaatattgaaagtgagcgagttaagtgttttacttttagcactgtttaacaataaaaaaacaactgctcaacttataatagttacttttgtacagtaatatcgttttaaaactctattagct .........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 agctaatagagttttaaaacgatattactgtacaaaagtaactattataagttgagcagttgtttttttattgttaaacagtgctaaaagtaaaacacttaactcgctcactttcaatattacttacctctaagtaactggcttacatttgcgtgcctacttgcataaacttttgaaacacaatatctttgcattatcaaaacaagaataataacaactcttataacaaataaacaaatagcattatgaaaacagtagaaacaattaaaacaggtaagaacttcatagca Mask Tandem Repeat Region ================================================ tgctatgaagttcttacctgttttaattgtttctactgttttcataatgctatttgtttatttgttataagagttgttattattcttgttttgataatgcaaagatattgtgtttcaaaagtttatgcaagtaggcacgcaaatgtaagccagttacttagaggtaagtaatattgaaagtgagcgagttaagtgttttacttttagcactgtttaacaataaaaaaacaactgctcaacttataatagttacttttgtacagtaatatcgttttaaaactctattagct Find is-nt database================================================ Query_seq: PI1589:PI1590|PI1589:PI1590:conserved hypothetical protein:transcriptional regulator:->->:1517903..1518192 290 tgctatgaagttcttacctgttttaattgtttctactgttttcataatgctatttgtttatttgttataagagttgttattattcttgttttgataatgcaaagatattgtgtttcaaaagtttatgcaagtaggcacgcaaatgtaagccagttacttagaggtaagtaatattgaaagtgagcgagttaagtgttttacttttagcactgtttaacaataaaaaaacaactgctcaacttataatagttacttttgtacagtaatatcgttttaaaactctattagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1589:PI1590|PI1589:PI1590:conserved hypothetical protein:transcriptional regulator:->->:1517903..1518192 290 tgctatgaagttcttacctgttttaattgtttctactgttttcataatgctatttgtttatttgttataagagttgttattattcttgttttgataatgcaaagatattgtgtttcaaaagtttatgcaagtaggcacgcaaatgtaagccagttacttagaggtaagtaatattgaaagtgagcgagttaagtgttttacttttagcactgtttaacaataaaaaaacaactgctcaacttataatagttacttttgtacagtaatatcgttttaaaactctattagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1589:PI1590|PI1589:PI1590:conserved hypothetical protein:transcriptional regulator:->->:1517903..1518192 290 tgctatgaagttcttacctgttttaattgtttctactgttttcataatgctatttgtttatttgttataagagttgttattattcttgttttgataatgcaaagatattgtgtttcaaaagtttatgcaagtaggcacgcaaatgtaagccagttacttagaggtaagtaatattgaaagtgagcgagttaagtgttttacttttagcactgtttaacaataaaaaaacaactgctcaacttataatagttacttttgtacagtaatatcgttttaaaactctattagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgctatgaagttcttacctgttttaattgtttctactgttttcataatgctatttgtttatttgttataagagttgttattattcttgttttgataatgcaaagatattgtgtttcaaaagtttatgcaagtaggcacgcaaatgtaagccagttacttagaggtaagtaatattgaaagtgagcgagttaagtgttttacttttagcactgtttaacaataaaaaaacaactgctcaacttataatagttacttttgtacagtaatatcgttttaaaactctattagct Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 52 End: 168 ................................................... M C L F V I R V V I I L V L I M Q R Y C V S K V Y A S R H A N V S Q L L R G K .......................................................................................................................... Protein_Len: 31 Strand: + Start: 171 End: 263 .......................................................................................................................................................................... M L K V S E L S V L L L A L F N N K K T T A Q L I I V T F V Q ........................... tgctatgaagttcttacctgttttaattgtttctactgttttcataatgctatttgtttatttgttataagagttgttattattcttgttttgataatgcaaagatattgtgtttcaaaagtttatgcaagtaggcacgcaaatgtaagccagttacttagaggtaagtaatattgaaagtgagcgagttaagtgttttacttttagcactgtttaacaataaaaaaacaactgctcaacttataatagttacttttgtacagtaatatcgttttaaaactctattagct 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================================================ tgctatgaagttcttacctgttttaattgtttctactgttttcataatgctatttgtttatttgttataagagttgttattattcttgttttgataatgcaaagatattgtgtttcaaaagtttatgcaagtaggcacgcaaatgtaagccagttacttagaggtaagtaatattgaaagtgagcgagttaagtgttttacttttagcactgtttaacaataaaaaaacaactgctcaacttataatagttacttttgtacagtaatatcgttttaaaactctattagct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1589:PI1590|PI1589:PI1590:conserved hypothetical protein:transcriptional regulator:->->:1517903..1518192 290 tgctatgaagttcttacctgttttaattgtttctactgttttcataatgctatttgtttatttgttataagagttgttattattcttgttttgataatgcaaagatattgtgtttcaaaagtttatgcaagtaggcacgcaaatgtaagccagttacttagaggtaagtaatattgaaagtgagcgagttaagtgttttacttttagcactgtttaacaataaaaaaacaactgctcaacttataatagttacttttgtacagtaatatcgttttaaaactctattagct Intra-Species Hit: Count: 1 Min: 1 Max: 290 Len: 290 Subject: pint_PI1589_PI1590|conserved hypothetical protein:transcriptional regulator|POSITIVE:POSITIVE|[1517903,1518192]|290 HSP 1 e-value: 1.0E-150 bit: 533.0 Len: 290 Query Start:1 Query End:290 Subject Strand: POSITIVE Subject Start: 1 Subject End: 290 tgctatgaagttcttacctgttttaattgtttctactgttttcataatgctatttgtttatttgttataagagttgttattattcttgttttgataatgcaaagatattgtgtttcaaaagtttatgcaagtaggcacgcaaatgtaagccagttacttagaggtaagtaatattgaaagtgagcgagttaagtgttttacttttagcactgtttaacaatnnnnnnncaactgctcaacttataatagttacttttgtacagtaatatcgttttaaaactctattagct tgctatgaagttcttacctgttttaattgtttctactgttttcataatgctatttgtttatttgttataagagttgttattattcttgttttgataatgcaaagatattgtgtttcaaaagtttatgcaagtaggcacgcaaatgtaagccagttacttagaggtaagtaatattgaaagtgagcgagttaagtgttttacttttagcactgtttaacaataaaaaaacaactgctcaacttataatagttacttttgtacagtaatatcgttttaaaactctattagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUAUGAAGUUCUUACCUGUUUUAAUUGUUUCUACUGUUUUCAUAAUGCUAUUUGUUUAUUUGUUAUAAGAGUUGUUAUUAUUCUUGUUUUGAUAAUGCAAAGAUAUUGUGUUUCAAAAGUUUAUGCAAGUAGGCACGCAAAUGUAAGCCAGUUACUUAGAGGUAAGUAAUAUUGAAAGUGAGCGAGUUAAGUGUUUUACUUUUAGCACUGUUUAACAAUAAAAAAACAACUGCUCAACUUAUAAUAGUUACUUUUGUACAGUAAUAUCGUUUUAAAACUCUAUUAGCU .((((((.(((((((((((.(..((((((........((((.(((..(((....(((((((((((.((((((((.......))))))))(((((.(((((((.....)))))))))))).......))))))))))).))).))).))))))))))...).)))))))...(((((.((((((((.((((.((((((........)))))).((((....)))).....)))))))).)))).)))))((((((.......))))))..........)))).)).)))). (-58.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUAAUAGAGUUUUAAAACGAUAUUACUGUACAAAAGUAACUAUUAUAAGUUGAGCAGUUGUUUUUUUAUUGUUAAACAGUGCUAAAAGUAAAACACUUAACUCGCUCACUUUCAAUAUUACUUACCUCUAAGUAACUGGCUUACAUUUGCGUGCCUACUUGCAUAAACUUUUGAAACACAAUAUCUUUGCAUUAUCAAAACAAGAAUAAUAACAACUCUUAUAACAAAUAAACAAAUAGCAUUAUGAAAACAGUAGAAACAAUUAAAACAGGUAAGAACUUCAUAGCA .((((...(((((((....................((((((.((((..((((.(((((((((...(((((((.(((........))).)))))))....))))).))))))))..))))))))))((((.(((((.....))))).......((..(((((..(((((..((((((((..(((.....)))..)).)))))).((((...........)))).....................))))).....)))))..)).........)))).)))))))..)))). (-44.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 218 171 79 23 pint:PI0591|5end_adenylosuccinate_lyase_538595..538825_POSITIVE 277 169 126 215 171 pint:PI0627|5end_conserved_hypothetical_protein_575618..575848_POSITIVE 272 200 152 106 52 pint:PI1571|5end_surface_antigen_BspA_1494765..1494995_POSITIVE 271 189 143 169 131 pint:PI1199|5end_possible_acetyltransferase_1115139..1115369_POSITIVE 266 170 129 60 5 pint:PI1406|5end_tyrosine-protein_kinase_1326536..1326766_POSITIVE 266 166 126 140 98 pint:PI1042|5end_hypothetical_protein_961452..961682_POSITIVE 266 166 124 99 51 pint:PI0992|5end_RNA_polymerase_sigma-70_factor_916456..916686_POSITIVE 263 168 121 79 15 pint:PI0136|5end_surface_antigen_BspA_127105..127335_POSITIVE 261 165 121 205 157 pint:PI1822|5end_ABC_transporter,_ATP-binding_/_permease_1761452..1761682_POSITIVE 252 219 179 78 32 pint:PI1525|5end_CDP-diacylglycerol--serine_O-phosphatidyltransferase_1446758..1446988_POSITIVE 246 51 12 97 58 pint:PI1701|5end_sensor_histidine_kinase_1619312..1619542_POSITIVE 244 179 133 211 162 pint:PI0909|5end_possible_mutT/NUDIX_family_protein_837526..837756_POSITIVE 244 50 1 164 107 pint:PI0463|5end_50S_ribosomal_protein_L2_434158..434388_POSITIVE 243 166 127 208 162 pint:PI1083|5end_TPR-repeat-containing_protein_1001975..1002205_POSITIVE 242 111 71 69 26 pint:PI1390|5end_hypothetical_protein_1311154..1311384_POSITIVE 240 165 128 136 97 pint:PI2077|5end_hypothetical_protein_2035892..2036122_POSITIVE 239 166 126 83 35 pint:PI1812|5end_possible_alpha-amylase_1750759..1750989_POSITIVE 234 158 134 31 1 pint:PI1432|5end_DNA_methylase_1353011..1353241_POSITIVE 233 167 126 50 13 pint:PI1729|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase,_trigger_factor_1648416..1648646_POSITIVE 233 170 121 187 132 pint:PI0980|5end_conserved_hypothetical_protein_905703..905933_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 168 121 151 87 pint:PI0135|3end_internalin-related_protein_127257..127407_POSITIVE 259 150 101 63 15 pint:PI1510|3end_cell_division_protein_1429274..1429424_POSITIVE 256 170 125 76 35 pint:PI0058|3end_conserved_hypothetical_protein_57044..57194_POSITIVE 249 139 98 92 49 pint:PI1730|3end_hypothetical_protein_1650367..1650517_POSITIVE 246 170 126 117 71 pint:PI1440|3end_conserved_hypothetical_protein_1363009..1363159_POSITIVE 243 166 127 75 29 pint:PI1082|3end_polypeptide_deformylase_1001922..1002072_POSITIVE 240 187 149 149 118 pint:PI2092|3end_hypothetical_protein_2049406..2049556_POSITIVE 234 216 175 90 50 pint:PI2123|3end_adenine_phosphoribosyltransferase_2072324..2072474_POSITIVE 234 150 108 151 91 pint:PI0637|3end_hypothetical_protein_582397..582547_POSITIVE 233 170 121 82 27 pint:PI0979|3end_transcriptional_regulator,_tetR_family_905678..905828_POSITIVE 230 41 3 74 30 pint:PI1549|3end_conserved_hypothetical_protein_1467382..1467532_POSITIVE 229 170 126 143 100 pint:PI1230|3end_probable_metallo-beta-lactamase_family_protein_1152729..1152879_POSITIVE 228 100 51 107 57 pint:PI0773|3end_D-3-phosphoglycerate_dehydrogenase_709492..709642_POSITIVE 226 150 108 80 20 pint:PI0567|3end_hypothetical_protein_513055..513205_POSITIVE 225 143 108 151 96 pint:PI0638|3end_hypothetical_protein_582402..582552_POSITIVE 225 170 126 109 52 pint:PI0117|3end_ribonuclease_HI_111314..111464_POSITIVE 224 166 127 39 5 pint:PI1031|3end_hypothetical_protein_948507..948657_POSITIVE 224 215 181 130 92 pint:PI0312|3end_hypothetical_protein_294940..295090_POSITIVE 222 167 125 68 25 pint:PI1821|3end_possible_thioredoxin_family_protein_1761517..1761667_POSITIVE 221 127 81 75 28 pint:PI1388|3end_transcriptional_regulator,_LuxR_family_1310024..1310174_POSITIVE