Origin IGS: gtgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt .........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 aacccctttacaaatctagccattcatggtaaaatggattttgtgtgaaatatcagcaggaaagcatgaagctcgtcaacaggtgtcttatgataagtaaccttggctgtttaggcgaagggcatctgcacgaatcagggctttctaagtgactatttccaccgaaatattatttatatcaggagggcattcac Mask Tandem Repeat Region ================================================ gtgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt Find is-nt database================================================ Query_seq: SMT_1661:SMT_1662|SMT_1661:SMT_1662:K02986 small subunit ribosomal protein S4:histidine protein kinase:<-<-:1651201..1651394 194 gtgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1661:SMT_1662|SMT_1661:SMT_1662:K02986 small subunit ribosomal protein S4:histidine protein kinase:<-<-:1651201..1651394 194 gtgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1661:SMT_1662|SMT_1661:SMT_1662:K02986 small subunit ribosomal protein S4:histidine protein kinase:<-<-:1651201..1651394 194 gtgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 46 End: 150 ............................................. K S L G S E H L H G E G L C G L N S I M L C R N V L K M S E Q Q Y K M ............................................ gtgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt 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: 89 Start: 160 End: 189 ...............................................................................................................................................................CTTTACAAATCTAGCCATTCATGGTAAAAT..... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1661:SMT_1662|SMT_1661:SMT_1662:K02986 small subunit ribosomal protein S4:histidine protein kinase:<-<-:1651201..1651394 194 gtgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: smit_SMT_1661_SMT_1662|K02986 small subunit ribosomal protein S4:histidine protein kinase|NEGATIVE:NEGATIVE|[1651201,1651394]|194 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 gtgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt gtgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt Inter-species Hit: Count: 3 Min: 2 Max: 194 Len: 193 Subject: NC_008533_SPD_0082_SPD_0083|sensor histidine kinase:ribosomal protein S4|POSITIVE:POSITIVE|[85586,85779]|194 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 193 Query Start:2 Query End:194 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 193 .tgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt .tgaatgtcctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttgtcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatctattctaccatgaatagctggatttgtaaaggggtt Subject: NC_003098_spr0077_spr0078|Histidine kinase:30S ribosomal protein S4|POSITIVE:POSITIVE|[85586,85779]|194 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 193 Query Start:2 Query End:194 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 193 .tgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt .tgaatgtcctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttgtcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatctattctaccatgaatagctggatttgtaaaggggtt Subject: NC_003028_SP_0084_SP_0085|sensor histidine kinase:30S ribosomal protein S4|POSITIVE:POSITIVE|[90786,90979]|194 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 193 Query Start:2 Query End:194 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 193 .tgaatgccctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttatcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatccattttaccatgaatggctagatttgtaaaggggtt .tgaatgtcctcctgatataaataatatttcggtggaaatagtcacttagaaagccctgattcgtgcagatgcccttcgcctaaacagccaaggttacttgtcataagacacctgttgacgagcttcatgctttcctgctgatatttcacacaaaatctattctaccatgaatagctggatttgtaaaggggtt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUGCCCUCCUGAUAUAAAUAAUAUUUCGGUGGAAAUAGUCACUUAGAAAGCCCUGAUUCGUGCAGAUGCCCUUCGCCUAAACAGCCAAGGUUACUUAUCAUAAGACACCUGUUGACGAGCUUCAUGCUUUCCUGCUGAUAUUUCACACAAAAUCCAUUUUACCAUGAAUGGCUAGAUUUGUAAAGGGGUU ........(((((..(((((((.........(((((((((.(((.(..((((((..((((((((((((....((((.((.......)).))))...((((...))))....))))..)))))..))).))))))..).))))))))).))).....((((((......))))))....))))))).))))).. (-44.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCCCUUUACAAAUCUAGCCAUUCAUGGUAAAAUGGAUUUUGUGUGAAAUAUCAGCAGGAAAGCAUGAAGCUCGUCAACAGGUGUCUUAUGAUAAGUAACCUUGGCUGUUUAGGCGAAGGGCAUCUGCACGAAUCAGGGCUUUCUAAGUGACUAUUUCCACCGAAAUAUUAUUUAUAUCAGGAGGGCAUUCA ..................(((.(((.(((((((((((((((((((.(((((((((...(((((((.(((...((((...(((((((..............((((.(((.....))).))))))))))).)))).)))..)))))))...))).)))))))).)))))).)))))).))))).))))))..... (-53.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1016 90 41 182 133 smit:SMT_1661|5end_K02986_small_subunit_ribosomal_protein_S4_1651110..1651340_NEGATIVE 328 97 52 52 11 smit:SMT_825|5end_aspartate_aminotransferase_749594..749824_NEGATIVE 316 145 113 180 153 smit:SMT_1873|5end_K02006_cobalt_transport_system_ATP-binding_protein_1831936..1832166_POSITIVE 316 70 29 48 3 smit:SMT_1570|5end_hypothetical_protein_1563504..1563734_NEGATIVE 309 140 97 63 17 smit:SMT_1785|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763277..1763507_NEGATIVE 302 96 51 172 127 smit:SMT_835|5end_polypeptide_deformylase_777549..777779_NEGATIVE 296 139 92 205 147 smit:SMT_1346|5end_tellurite_resistance_protein_TehB_1324703..1324933_NEGATIVE 286 117 71 66 20 smit:SMT_2153|5end_putative_cell_division_protein_2026905..2027135_POSITIVE 286 117 71 66 20 smit:SMT_2139|5end_cell_division_protein_FtsZ_2017083..2017313_POSITIVE 286 117 71 66 20 smit:SMT_2137|5end_cell_division_protein_FtsZ_2015797..2016027_POSITIVE 286 117 71 66 20 smit:SMT_2129|5end_cell_division_protein_FtsZ_2010090..2010320_POSITIVE 286 117 71 66 20 smit:SMT_1548|5end_cell_division_protein_FtsZ_1532384..1532614_POSITIVE 282 99 51 69 3 smit:SMT_764|5end_alanyl-tRNA_synthetase_672113..672343_NEGATIVE 280 94 51 167 129 smit:SMT_1151|5end_histidyl-tRNA_synthetase_1096168..1096398_NEGATIVE 279 130 88 89 52 smit:SMT_1786|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763540..1763770_NEGATIVE 279 99 52 209 142 smit:SMT_555|5end_K09015_Fe-S_cluster_assembly_protein_SufD_472271..472501_POSITIVE 277 138 102 52 11 smit:SMT_1704|5end_D-alanine-D-alanine_ligase_1687431..1687661_POSITIVE 276 99 54 144 77 smit:SMT_1915|5end_pyridoxine_biosynthesis_protein_1860329..1860559_POSITIVE 275 110 63 195 155 smit:SMT_568|5end_hypothetical_protein_485674..485904_POSITIVE 274 129 110 62 39 smit:SMT_1483|5end_GTP-binding_protein_1463676..1463906_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 97 52 55 14 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 309 140 97 105 59 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 302 96 51 57 12 smit:SMT_836|3end_cell_surface_protein_precursor_777664..777814_NEGATIVE 286 117 71 48 2 smit:SMT_2152|3end_cell_division_protein_2026967..2027117_POSITIVE 286 117 71 48 2 smit:SMT_2138|3end_cell_division_protein_FtsA_2017145..2017295_POSITIVE 286 117 71 48 2 smit:SMT_2136|3end_cell_division_protein_FtsA_2015859..2016009_POSITIVE 286 117 71 48 2 smit:SMT_2128|3end_cell_division_protein_FtsA_2010152..2010302_POSITIVE 286 117 71 48 2 smit:SMT_1547|3end_cell_division_protein_FtsA_1532446..1532596_POSITIVE 269 96 55 72 19 smit:SMT_1532|3end_hypothetical_protein_1515994..1516144_NEGATIVE 268 141 106 64 31 smit:SMT_174|3end_30S_ribosomal_protein_S19_117792..117942_POSITIVE 267 96 54 139 78 smit:SMT_1704|3end_D-alanine-D-alanine_ligase_1688554..1688704_POSITIVE 267 185 141 81 37 smit:SMT_239|3end_hypothetical_protein_177788..177938_POSITIVE 264 80 31 113 54 smit:SMT_1371|3end_hypothetical_protein_1350579..1350729_NEGATIVE 263 49 8 102 55 smit:SMT_493|3end_K01996_branched-chain_amino_acid_transport_system_ATP-binding_protein_427927..428077_POSITIVE 260 105 61 130 87 smit:SMT_1255|3end_cell_division_protein_FtsH_1220987..1221137_NEGATIVE 258 139 96 79 36 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 257 80 33 53 13 smit:SMT_1044|3end_chaperonin_GroEL_(HSP60_family)_986038..986188_NEGATIVE 257 75 31 85 42 smit:SMT_540|3end_DNA_gyrase,_B_subunit_457157..457307_POSITIVE 256 92 53 52 9 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 255 80 31 142 77 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE