Origin IGS: tagtggtgtaatcgcatagtaaaacgattcttctatcaatttatttacgtgtaaataaatatttttctacacgtaaataataatttctttacacgtaaataaatatttctcaaagttctgataattcagaaatcagcctctcaggcacatcaaaagctattttttaaggagaggttttatttctatttttatgtatgagcagtcgatttagggaacggcaactttataatcatcatcttttcacctaattatatataaggtgaaagggcggaaatttgtgtgtttcatattattattgtacttttgtaccctaaaagattaaataaaaagaaataaag .........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 ctttatttctttttatttaatcttttagggtacaaaagtacaataataatatgaaacacacaaatttccgccctttcaccttatatataattaggtgaaaagatgatgattataaagttgccgttccctaaatcgactgctcatacataaaaatagaaataaaacctctccttaaaaaatagcttttgatgtgcctgagaggctgatttctgaattatcagaactttgagaaatatttatttacgtgtaaagaaattattatttacgtgtagaaaaatatttatttacacgtaaataaattgatagaagaatcgttttactatgcgattacaccacta Mask Tandem Repeat Region ================================================ tagtggtgtaatcgcatagtaaaacgattcttctatcaatttatttacgtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncaaagttctgataattcagaaatcagcctctcaggcacatcaaaagctattttttaaggagaggttttatttctatttttatgtatgagcagtcgatttagggaacggcaactttataatcatcatcttttcacctaattatatataaggtgaaagggcggaaatttgtgtgtttcatattattattgtacttttgtaccctaaaagattaaataaaaagaaataaag Find is-nt database================================================ Query_seq: PI0797:PI0798|PI0797:PI0798:tRNA pseudouridine synthase A (pseudouridylate synthase):malonyl CoA-acyl carrier protein transacylase:->->:735813..736150 338 tagtggtgtaatcgcatagtaaaacgattcttctatcaatttatttacgtgtaaataaatatttttctacacgtaaataataatttctttacacgtaaataaatatttctcaaagttctgataattcagaaatcagcctctcaggcacatcaaaagctattttttaaggagaggttttatttctatttttatgtatgagcagtcgatttagggaacggcaactttataatcatcatcttttcacctaattatatataaggtgaaagggcggaaatttgtgtgtttcatattattattgtacttttgtaccctaaaagattaaataaaaagaaataaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0797:PI0798|PI0797:PI0798:tRNA pseudouridine synthase A (pseudouridylate synthase):malonyl CoA-acyl carrier protein transacylase:->->:735813..736150 338 tagtggtgtaatcgcatagtaaaacgattcttctatcaatttatttacgtgtaaataaatatttttctacacgtaaataataatttctttacacgtaaataaatatttctcaaagttctgataattcagaaatcagcctctcaggcacatcaaaagctattttttaaggagaggttttatttctatttttatgtatgagcagtcgatttagggaacggcaactttataatcatcatcttttcacctaattatatataaggtgaaagggcggaaatttgtgtgtttcatattattattgtacttttgtaccctaaaagattaaataaaaagaaataaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0797:PI0798|PI0797:PI0798:tRNA pseudouridine synthase A (pseudouridylate synthase):malonyl CoA-acyl carrier protein transacylase:->->:735813..736150 338 tagtggtgtaatcgcatagtaaaacgattcttctatcaatttatttacgtgtaaataaatatttttctacacgtaaataataatttctttacacgtaaataaatatttctcaaagttctgataattcagaaatcagcctctcaggcacatcaaaagctattttttaaggagaggttttatttctatttttatgtatgagcagtcgatttagggaacggcaactttataatcatcatcttttcacctaattatatataaggtgaaagggcggaaatttgtgtgtttcatattattattgtacttttgtaccctaaaagattaaataaaaagaaataaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtggtgtaatcgcatagtaaaacgattcttctatcaatttatttacgtgtaaataaatatttttctacacgtaaataataatttctttacacgtaaataaatatttctcaaagttctgataattcagaaatcagcctctcaggcacatcaaaagctattttttaaggagaggttttatttctatttttatgtatgagcagtcgatttagggaacggcaactttataatcatcatcttttcacctaattatatataaggtgaaagggcggaaatttgtgtgtttcatattattattgtacttttgtaccctaaaagattaaataaaaagaaataaag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 103 End: 195 ...................................................................................................... M F L K V L I I Q K S A S Q A H Q K L F F K E R F Y F Y F Y V ............................................................................................................................................... tagtggtgtaatcgcatagtaaaacgattcttctatcaatttatttacgtgtaaataaatatttttctacacgtaaataataatttctttacacgtaaataaatatttctcaaagttctgataattcagaaatcagcctctcaggcacatcaaaagctattttttaaggagaggttttatttctatttttatgtatgagcagtcgatttagggaacggcaactttataatcatcatcttttcacctaattatatataaggtgaaagggcggaaatttgtgtgtttcatattattattgtacttttgtaccctaaaagattaaataaaaagaaataaag 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================================================ tagtggtgtaatcgcatagtaaaacgattcttctatcaatttatttacgtgtaaataaatatttttctacacgtaaataataatttctttacacgtaaataaatatttctcaaagttctgataattcagaaatcagcctctcaggcacatcaaaagctattttttaaggagaggttttatttctatttttatgtatgagcagtcgatttagggaacggcaactttataatcatcatcttttcacctaattatatataaggtgaaagggcggaaatttgtgtgtttcatattattattgtacttttgtaccctaaaagattaaataaaaagaaataaag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -8.3 Tail_Score: -3.14564 Start: 40 End: 81 Full_Region: acgtgtaaagaaatt attatttacgtgtagaaaa atat ttatttacacgtaaataaa ttgatagaagaatcg .......................................attatttacgtgtagaaaaatatttatttacacgtaaataaa................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 79 HP_score: -9.6 Tail_Score: -3.18452 Start: 41 End: 80 Full_Region: GATTCTTCTATCAAT TTATTTACGTGTAAATAA ATAT TTTTCTACACGTAAATAA TAATTTCTTTACACG ........................................TTATTTACGTGTAAATAAATATTTTTCTACACGTAAATAA.................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 73 HP_score: -9.1 Tail_Score: -2.56596 Start: 44 End: 77 Full_Region: gtaaagaaattatta tttacgtgtagaaaa atat ttatttacacgtaaa taaattgatagaaga ...........................................tttacgtgtagaaaaatatttatttacacgtaaa..................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0797:PI0798|PI0797:PI0798:tRNA pseudouridine synthase A (pseudouridylate synthase):malonyl CoA-acyl carrier protein transacylase:->->:735813..736150 338 tagtggtgtaatcgcatagtaaaacgattcttctatcaatttatttacgtgtaaataaatatttttctacacgtaaataataatttctttacacgtaaataaatatttctcaaagttctgataattcagaaatcagcctctcaggcacatcaaaagctattttttaaggagaggttttatttctatttttatgtatgagcagtcgatttagggaacggcaactttataatcatcatcttttcacctaattatatataaggtgaaagggcggaaatttgtgtgtttcatattattattgtacttttgtaccctaaaagattaaataaaaagaaataaag Intra-Species Hit: Count: 1 Min: 1 Max: 338 Len: 338 Subject: pint_PI0797_PI0798|tRNA pseudouridine synthase A (pseudouridylate synthase):malonyl CoA-acyl carrier protein transacylase|POSITIVE:POSITIVE|[735813,736150]|338 HSP 1 e-value: 0.0 bit: 670.0 Len: 338 Query Start:1 Query End:338 Subject Strand: POSITIVE Subject Start: 1 Subject End: 338 tagtggtgtaatcgcatagtaaaacgattcttctatcaatttatttacgtgtaaataaatatttttctacacgtaaataataatttctttacacgtaaataaatatttctcaaagttctgataattcagaaatcagcctctcaggcacatcaaaagctattttttaaggagaggttttatttctatttttatgtatgagcagtcgatttagggaacggcaactttataatcatcatcttttcacctaattatatataaggtgaaagggcggaaatttgtgtgtttcatattattattgtacttttgtaccctaaaagattaaataaaaagaaataaag tagtggtgtaatcgcatagtaaaacgattcttctatcaatttatttacgtgtaaataaatatttttctacacgtaaataataatttctttacacgtaaataaatatttctcaaagttctgataattcagaaatcagcctctcaggcacatcaaaagctattttttaaggagaggttttatttctatttttatgtatgagcagtcgatttagggaacggcaactttataatcatcatcttttcacctaattatatataaggtgaaagggcggaaatttgtgtgtttcatattattattgtacttttgtaccctaaaagattaaataaaaagaaataaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUGGUGUAAUCGCAUAGUAAAACGAUUCUUCUAUCAAUUUAUUUACGUGUAAAUAAAUAUUUUUCUACACGUAAAUAAUAAUUUCUUUACACGUAAAUAAAUAUUUCUCAAAGUUCUGAUAAUUCAGAAAUCAGCCUCUCAGGCACAUCAAAAGCUAUUUUUUAAGGAGAGGUUUUAUUUCUAUUUUUAUGUAUGAGCAGUCGAUUUAGGGAACGGCAACUUUAUAAUCAUCAUCUUUUCACCUAAUUAUAUAUAAGGUGAAAGGGCGGAAAUUUGUGUGUUUCAUAUUAUUAUUGUACUUUUGUACCCUAAAAGAUUAAAUAAAAAGAAAUAAAG ..(((((...)))))..((((((((..(((((((....(((((((((((((((((.(((((((...............))).)))).)))))))))))))))))...........((((((....))))))....(((.....)))....................)))))))))))))))..(((((((...(((....((((..(((((((....((((...((((((.....(((((((((((.((.....)).)))))))))))..(((((......)))))........))))))...)))).))))))).))))..)))...)))))))... (-74.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAUUUCUUUUUAUUUAAUCUUUUAGGGUACAAAAGUACAAUAAUAAUAUGAAACACACAAAUUUCCGCCCUUUCACCUUAUAUAUAAUUAGGUGAAAAGAUGAUGAUUAUAAAGUUGCCGUUCCCUAAAUCGACUGCUCAUACAUAAAAAUAGAAAUAAAACCUCUCCUUAAAAAAUAGCUUUUGAUGUGCCUGAGAGGCUGAUUUCUGAAUUAUCAGAACUUUGAGAAAUAUUUAUUUACGUGUAAAGAAAUUAUUAUUUACGUGUAGAAAAAUAUUUAUUUACACGUAAAUAAAUUGAUAGAAGAAUCGUUUUACUAUGCGAUUACACCACUA .(((((((((((((((.((....(((((((.((....((...(((....)))...)).....((((..((.(.((((((((...........)))))))).).))..))))...........)).)))))))..((....)).)).))))))..)))))))))...((((.........((((((((.(......).))))))))..((((((....))))))....))))...(((((((((((((((((.((((.....((((....)))).....)))).))))))))))))))))).........((((((........))))))......... (-66.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 569 110 61 195 146 pint:PI0115|5end_hypothetical_protein_108062..108292_POSITIVE 569 110 61 181 132 pint:PI0111|5end_hypothetical_protein_108048..108278_POSITIVE 569 110 61 146 97 pint:PI0112|5end_hypothetical_protein_108013..108243_POSITIVE 490 110 62 150 102 pint:PI0130|5end_hypothetical_protein_122032..122262_POSITIVE 457 78 37 231 190 pint:PI0599|5end_hypothetical_protein_547376..547606_POSITIVE 439 99 51 151 103 pint:PI0619|5end_hypothetical_protein_569364..569594_POSITIVE 433 81 41 143 103 pint:PI1462|5end_hypothetical_protein_1385094..1385324_POSITIVE 428 76 41 211 176 pint:PI0173|5end_hypothetical_protein_165305..165535_POSITIVE 368 89 41 108 59 pint:PI1450|5end_hypothetical_protein_1372683..1372913_POSITIVE 355 77 44 113 80 pint:PI0312|5end_hypothetical_protein_294591..294821_POSITIVE 316 284 242 186 143 pint:PI0792|5end_conserved_hypothetical_protein_729068..729298_POSITIVE 316 284 242 71 28 pint:PI0790|5end_hypothetical_protein_728953..729183_POSITIVE 313 77 44 228 195 pint:PI1674|5end_hypothetical_protein_1587829..1588059_POSITIVE 313 77 44 117 84 pint:PI1673|5end_hypothetical_protein_1587718..1587948_POSITIVE 301 81 41 165 125 pint:PI0648|5end_hypothetical_protein_589448..589678_POSITIVE 289 108 68 119 79 pint:PI0983|5end_hypothetical_protein_909750..909980_POSITIVE 286 176 135 73 27 pint:PI1986|5end_hypothetical_protein_1940863..1941093_POSITIVE 284 122 83 225 185 pint:PI0750|5end_zinc_protease_677746..677976_POSITIVE 282 220 173 83 29 pint:PI1509|5end_conserved_hypothetical_protein_1428103..1428333_POSITIVE 280 69 32 231 194 pint:PI0114|5end_hypothetical_protein_108139..108369_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 433 81 41 42 2 pint:PI1461|3end_conserved_hypothetical_protein_1385073..1385223_POSITIVE 428 76 41 64 29 pint:PI0172|3end_ISPg3-related_transposase_165238..165388_POSITIVE 406 110 71 40 1 pint:PI0598|3end_hypothetical_protein_547233..547383_POSITIVE 316 284 242 147 104 pint:PI0791|3end_conserved_hypothetical_protein_729109..729259_POSITIVE 301 81 41 73 33 pint:PI0533|3end_ABC_transporter,_permease_protein_488421..488571_POSITIVE 299 90 41 111 62 pint:PI2105|3end_hypothetical_protein_2059586..2059736_POSITIVE 287 80 41 50 11 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 282 220 173 80 26 pint:PI1508|3end_undecaprenol_kinase_1428180..1428330_POSITIVE 278 110 69 48 11 pint:PI0808|3end_ISPg3-related_transposase_746457..746607_POSITIVE 276 200 156 83 37 pint:PI2135|3end_conserved_hypothetical_protein_2083253..2083403_POSITIVE 275 208 162 145 86 pint:PI1209|3end_phosphate_starvation-inducible_protein,_phoH_family_1128995..1129145_POSITIVE 268 232 198 124 87 pint:PI1582|3end_cell_shape-determining_protein_1510457..1510607_POSITIVE 258 75 39 45 9 pint:PI0701|3end_hypothetical_protein_638537..638687_POSITIVE 249 175 132 114 66 pint:PI1546|3end_mobilizable_transposon,_excision_protein_1465099..1465249_POSITIVE 248 216 171 151 104 pint:PI2123|3end_adenine_phosphoribosyltransferase_2072324..2072474_POSITIVE 247 307 262 142 101 pint:PI0698|3end_conserved_hypothetical_protein_636711..636861_POSITIVE 245 280 233 122 73 pint:PI0657|3end_conserved_hypothetical_protein_602167..602317_POSITIVE 243 306 261 123 63 pint:PI1329|3end_dTDP-glucose_4,6-dehydratase_1247954..1248104_POSITIVE 239 325 285 74 35 pint:PI1134|3end_ABC_transporter,_ATP-binding_protein_1062073..1062223_POSITIVE 239 75 39 100 64 pint:PI0725|3end_hypothetical_protein_658933..659083_POSITIVE