Origin IGS: acggatgtcagttnnnnnttaattaattaannnnnatccgccagtttacactagcagatatccgtcactgctctgttttcacgactacatgccctggagcagcacacaacggcacctagctcatacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgtatgagctaggtgccgttgtgtgctgctccagggcatgtagtcgtgaaaacagagcagtgacggatatctgctagtgtaaactggcggatnnnnnttaattaattaannnnnaactgacatccgt Mask Tandem Repeat Region ================================================ acggatgtcagttnnnnnttaattaattaannnnnatccgccagtttacactagcagatatccgtcactgctctgttttcacgactacatgccctggagcagcacacaacggcacctagctcatacg Find is-nt database================================================ Query_seq: SMT_1786:SMT_1787|SMT_1786:SMT_1787:phenylalanyl-tRNA synthetase beta chain:phosphoribosylformylglycinamidine synthase:<-<-:1763631..1763757 127 acggatgtcagttnnnnnttaattaattaannnnnatccgccagtttacactagcagatatccgtcactgctctgttttcacgactacatgccctggagcagcacacaacggcacctagctcatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1786:SMT_1787|SMT_1786:SMT_1787:phenylalanyl-tRNA synthetase beta chain:phosphoribosylformylglycinamidine synthase:<-<-:1763631..1763757 127 acggatgtcagttnnnnnttaattaattaannnnnatccgccagtttacactagcagatatccgtcactgctctgttttcacgactacatgccctggagcagcacacaacggcacctagctcatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1786:SMT_1787|SMT_1786:SMT_1787:phenylalanyl-tRNA synthetase beta chain:phosphoribosylformylglycinamidine synthase:<-<-:1763631..1763757 127 acggatgtcagttnnnnnttaattaattaannnnnatccgccagtttacactagcagatatccgtcactgctctgttttcacgactacatgccctggagcagcacacaacggcacctagctcatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acggatgtcagttnnnnnttaattaattaannnnnatccgccagtttacactagcagatatccgtcactgctctgttttcacgactacatgccctggagcagcacacaacggcacctagctcatacg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 26 End: 127 ......................... M X X X P P V Y T S R Y P S L L C F H D Y M P W S S T Q R H L A H T acggatgtcagttnnnnnttaattaattaannnnnatccgccagtttacactagcagatatccgtcactgctctgttttcacgactacatgccctggagcagcacacaacggcacctagctcatacg 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================================================ acggatgtcagttnnnnnttaattaattaannnnnatccgccagtttacactagcagatatccgtcactgctctgttttcacgactacatgccctggagcagcacacaacggcacctagctcatacg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1786:SMT_1787|SMT_1786:SMT_1787:phenylalanyl-tRNA synthetase beta chain:phosphoribosylformylglycinamidine synthase:<-<-:1763631..1763757 127 acggatgtcagttnnnnnttaattaattaannnnnatccgccagtttacactagcagatatccgtcactgctctgttttcacgactacatgccctggagcagcacacaacggcacctagctcatacg Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: smit_SMT_1786_SMT_1787|phenylalanyl-tRNA synthetase beta chain:phosphoribosylformylglycinamidine synthase|NEGATIVE:NEGATIVE|[1763631,1763757]|127 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 acggatgtcagttnnnnnttaattaattaannnnnatccgccagtttacactagcagatatccgtcactgctctgttttcacgactacatgccctggagcagcacacaacggcacctagctcatacg acggatgtcagttnnnnnttaattaattaannnnnatccgccagtttacactagcagatatccgtcactgctctgttttcacgactacatgccctggagcagcacacaacggcacctagctcatacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGGAUGUCAGUUNNNNNUUAAUUAAUUAANNNNNAUCCGCCAGUUUACACUAGCAGAUAUCCGUCACUGCUCUGUUUUCACGACUACAUGCCCUGGAGCAGCACACAACGGCACCUAGCUCAUACG (((((((((..........(((....)))..........((.(((....))).)).)))))))))..(((((((.....................)))))))........(((.....)))...... (-23.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUAUGAGCUAGGUGCCGUUGUGUGCUGCUCCAGGGCAUGUAGUCGUGAAAACAGAGCAGUGACGGAUAUCUGCUAGUGUAAACUGGCGGAUNNNNNUUAAUUAAUUAANNNNNAACUGACAUCCGU ((.(((.........(((((....(((((((.....((((....))))......))))))))))))..((((((((((....))))))))))............................))).)). (-34.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1056 120 71 211 162 smit:SMT_1786|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763540..1763770_NEGATIVE 315 120 73 40 1 smit:SMT_807|5end_hypothetical_protein_predicted_by_Glimmer/Critica_716815..717045_NEGATIVE 309 100 52 72 11 smit:SMT_1630|5end_hypothetical_protein_1617291..1617521_POSITIVE 309 100 52 72 11 smit:SMT_1241|5end_hypothetical_protein_1201040..1201270_POSITIVE 309 74 39 202 162 smit:SMT_534|5end_hypothetical_protein_predicted_by_Glimmer/Critica_453571..453801_POSITIVE 309 74 39 202 162 smit:SMT_531|5end_hypothetical_protein_predicted_by_Glimmer/Critica_452672..452902_POSITIVE 309 74 39 202 162 smit:SMT_527|5end_hypothetical_protein_predicted_by_Glimmer/Critica_451502..451732_POSITIVE 309 74 39 202 162 smit:SMT_511|5end_hypothetical_protein_predicted_by_Glimmer/Critica_439391..439621_POSITIVE 308 98 56 99 65 smit:SMT_1709|5end_aminopeptidase_P_1695450..1695680_NEGATIVE 305 100 51 225 177 smit:SMT_1543|5end_diphosphomevalonate_decarboxylase_1528024..1528254_NEGATIVE 301 107 61 146 87 smit:SMT_1697|5end_hypothetical_protein_1678846..1679076_POSITIVE 301 120 71 200 147 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 301 117 71 226 180 smit:SMT_142|5end_hypothetical_protein_95088..95318_NEGATIVE 300 96 51 55 1 smit:SMT_1731|5end_K06442_putative_hemolysin_1715643..1715873_POSITIVE 299 120 71 89 40 smit:SMT_1259|5end_hypothetical_protein_1225139..1225369_POSITIVE 295 120 75 58 14 smit:SMT_147|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_97406..97636_POSITIVE 295 120 75 58 14 smit:SMT_119|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_70457..70687_POSITIVE 291 98 51 230 171 smit:SMT_755|5end_shikimate_5-dehydrogenase_659917..660147_NEGATIVE 290 120 73 87 29 smit:SMT_1959|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1892585..1892815_POSITIVE 289 79 42 77 44 smit:SMT_1590|5end_DNA-entry_nuclease_1578565..1578795_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 110 61 147 95 smit:SMT_1025|3end_hypothetical_protein_959550..959700_NEGATIVE 315 120 73 147 108 smit:SMT_807|3end_hypothetical_protein_predicted_by_Glimmer/Critica_716708..716858_NEGATIVE 309 74 39 88 48 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 309 74 39 88 48 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 309 74 39 88 48 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 309 74 39 88 48 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE 301 107 61 144 85 smit:SMT_1696|3end_hypothetical_protein_1678924..1679074_POSITIVE 300 96 51 62 8 smit:SMT_1730|3end_geranyltranstransferase_1715730..1715880_POSITIVE 296 70 37 145 115 smit:SMT_137|3end_hypothetical_protein_88137..88287_NEGATIVE 293 71 38 77 38 smit:SMT_1925|3end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_1867458..1867608_POSITIVE 293 71 38 85 46 smit:SMT_1557|3end_hypothetical_protein_1543650..1543800_POSITIVE 289 79 42 38 5 smit:SMT_1589|3end_hypothetical_protein_1578606..1578756_POSITIVE 286 103 61 147 103 smit:SMT_1290|3end_autolysin_1253753..1253903_POSITIVE 284 103 61 148 98 smit:SMT_340|3end_chaperone_protein_280566..280716_POSITIVE 279 99 51 64 12 smit:SMT_1958|3end_tryptophan_synthase,_beta_subunit_1892052..1892202_POSITIVE 278 117 71 146 103 smit:SMT_1219|3end_hypothetical_protein_1180398..1180548_POSITIVE 276 83 41 52 22 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 275 111 72 145 103 smit:SMT_186|3end_50S_ribosomal_protein_L18_123059..123209_POSITIVE 272 93 51 75 35 smit:SMT_1682|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_1666373..1666523_POSITIVE 272 80 37 150 107 smit:SMT_1493|3end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1479494..1479644_POSITIVE