Origin IGS: cttaagacctttctattttagaagtacaatttattataacataaaatggtaatgagagaaaaggagatgcttaaataacttcatgtgacgctaattgtcaaaaccttggagcacatttacctcacgtaccagcttacaggcggagtgtttgatgattgataatgaagaataagattatacaataaaaaaacacctataatatttagaaaaaatatcatctaaatctcc .........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 ggagatttagatgatattttttctaaatattataggtgtttttttattgtataatcttattcttcattatcaatcatcaaacactccgcctgtaagctggtacgtgaggtaaatgtgctccaaggttttgacaattagcgtcacatgaagttatttaagcatctccttttctctcattaccattttatgttataataaattgtacttctaaaatagaaaggtcttaag Mask Tandem Repeat Region ================================================ cttaagacctttctattttagaagtacaatttattataacataaaatggtaatgagagaaaaggagatgcttaaataacttcatgtgacgctaattgtcaaaaccttggagcacatttacctcacgtaccagcttacaggcggagtgtttgatgattgataatgaagaataagattatacaataaaaaaacacctataatatttagaaaaaatatcatctaaatctcc Find is-nt database================================================ Query_seq: SMT_728:SMT_729|SMT_728:SMT_729:hypothetical protein:K07707 two-component system, AgrA family, response regulator AgrA:<-<-:634439..634666 228 cttaagacctttctattttagaagtacaatttattataacataaaatggtaatgagagaaaaggagatgcttaaataacttcatgtgacgctaattgtcaaaaccttggagcacatttacctcacgtaccagcttacaggcggagtgtttgatgattgataatgaagaataagattatacaataaaaaaacacctataatatttagaaaaaatatcatctaaatctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_728:SMT_729|SMT_728:SMT_729:hypothetical protein:K07707 two-component system, AgrA family, response regulator AgrA:<-<-:634439..634666 228 cttaagacctttctattttagaagtacaatttattataacataaaatggtaatgagagaaaaggagatgcttaaataacttcatgtgacgctaattgtcaaaaccttggagcacatttacctcacgtaccagcttacaggcggagtgtttgatgattgataatgaagaataagattatacaataaaaaaacacctataatatttagaaaaaatatcatctaaatctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_728:SMT_729|SMT_728:SMT_729:hypothetical protein:K07707 two-component system, AgrA family, response regulator AgrA:<-<-:634439..634666 228 cttaagacctttctattttagaagtacaatttattataacataaaatggtaatgagagaaaaggagatgcttaaataacttcatgtgacgctaattgtcaaaaccttggagcacatttacctcacgtaccagcttacaggcggagtgtttgatgattgataatgaagaataagattatacaataaaaaaacacctataatatttagaaaaaatatcatctaaatctcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttaagacctttctattttagaagtacaatttattataacataaaatggtaatgagagaaaaggagatgcttaaataacttcatgtgacgctaattgtcaaaaccttggagcacatttacctcacgtaccagcttacaggcggagtgtttgatgattgataatgaagaataagattatacaataaaaaaacacctataatatttagaaaaaatatcatctaaatctcc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 120 End: 218 ....................................................................................................................... R V Y W S V P P T N S S Q Y H L I L N Y L L F V G I I N L F F I M .......... cttaagacctttctattttagaagtacaatttattataacataaaatggtaatgagagaaaaggagatgcttaaataacttcatgtgacgctaattgtcaaaaccttggagcacatttacctcacgtaccagcttacaggcggagtgtttgatgattgataatgaagaataagattatacaataaaaaaacacctataatatttagaaaaaatatcatctaaatctcc 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: 84 Start: 33 End: 62 ................................TTTTCTCTCATTACCATTTTATGTTATAAT...................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttaagacctttctattttagaagtacaatttattataacataaaatggtaatgagagaaaaggagatgcttaaataacttcatgtgacgctaattgtcaaaaccttggagcacatttacctcacgtaccagcttacaggcggagtgtttgatgattgataatgaagaataagattatacaataaaaaaacacctataatatttagaaaaaatatcatctaaatctcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_728:SMT_729|SMT_728:SMT_729:hypothetical protein:K07707 two-component system, AgrA family, response regulator AgrA:<-<-:634439..634666 228 cttaagacctttctattttagaagtacaatttattataacataaaatggtaatgagagaaaaggagatgcttaaataacttcatgtgacgctaattgtcaaaaccttggagcacatttacctcacgtaccagcttacaggcggagtgtttgatgattgataatgaagaataagattatacaataaaaaaacacctataatatttagaaaaaatatcatctaaatctcc Intra-Species Hit: Count: 1 Min: 1 Max: 228 Len: 228 Subject: smit_SMT_728_SMT_729|hypothetical protein:K07707 two-component system, AgrA family, response regulator AgrA|NEGATIVE:NEGATIVE|[634439,634666]|228 HSP 1 e-value: 1.0E-114 bit: 410.0 Len: 228 Query Start:1 Query End:228 Subject Strand: POSITIVE Subject Start: 1 Subject End: 228 cttaagacctttctattttagaagtacaatttattataacataaaatggtaatgagagaaaaggagatgcttaaataacttcatgtgacgctaattgtcaaaaccttggagcacatttacctcacgtaccagcttacaggcggagtgtttgatgattgataatgaagaataagattatacaatnnnnnnncacctataatatttagaaaaaatatcatctaaatctcc cttaagacctttctattttagaagtacaatttattataacataaaatggtaatgagagaaaaggagatgcttaaataacttcatgtgacgctaattgtcaaaaccttggagcacatttacctcacgtaccagcttacaggcggagtgtttgatgattgataatgaagaataagattatacaataaaaaaacacctataatatttagaaaaaatatcatctaaatctcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAAGACCUUUCUAUUUUAGAAGUACAAUUUAUUAUAACAUAAAAUGGUAAUGAGAGAAAAGGAGAUGCUUAAAUAACUUCAUGUGACGCUAAUUGUCAAAACCUUGGAGCACAUUUACCUCACGUACCAGCUUACAGGCGGAGUGUUUGAUGAUUGAUAAUGAAGAAUAAGAUUAUACAAUAAAAAAACACCUAUAAUAUUUAGAAAAAAUAUCAUCUAAAUCUCC ((((..(((.(((((...)))))......(((((......)))))..)))..))))......((((((...(((((..(((((..(((((.....)))))......)))))...)))))..((.....((.(((....))))).((((((....(((((((((..........))))).))))....))))))............))...............)))))) (-33.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAGAUUUAGAUGAUAUUUUUUCUAAAUAUUAUAGGUGUUUUUUUAUUGUAUAAUCUUAUUCUUCAUUAUCAAUCAUCAAACACUCCGCCUGUAAGCUGGUACGUGAGGUAAAUGUGCUCCAAGGUUUUGACAAUUAGCGUCACAUGAAGUUAUUUAAGCAUCUCCUUUUCUCUCAUUACCAUUUUAUGUUAUAAUAAAUUGUACUUCUAAAAUAGAAAGGUCUUAAG .(((((((..(((((((((.....))))))))).(((((((..(.((((.(((((..........))))))))).)..)))))))....((((.....(((((....(((((.((.(....((((...((.....((((.((....)).))))......))...))))....).)))))))..(((((......)))))..)))))......))))..)))))))... (-37.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 913 130 81 221 172 smit:SMT_728|5end_hypothetical_protein_634348..634578_NEGATIVE 450 220 179 93 52 smit:SMT_809|5end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_719745..719975_NEGATIVE 320 148 102 70 24 smit:SMT_999|5end_hypothetical_protein_predicted_by_Glimmer/Critica_941642..941872_NEGATIVE 313 147 104 46 3 smit:SMT_935|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_887326..887556_POSITIVE 308 164 125 83 31 smit:SMT_1404|5end_lipoate-protein_ligase_A_1380967..1381197_POSITIVE 298 159 112 142 87 smit:SMT_2023|5end_tryptophan_synthase,_alpha_subunit_1939315..1939545_POSITIVE 298 159 112 142 87 smit:SMT_1818|5end_tryptophan_synthase,_alpha_subunit_1792190..1792420_POSITIVE 280 141 104 230 183 smit:SMT_1786|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763540..1763770_NEGATIVE 278 152 114 39 1 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 274 168 137 39 1 smit:SMT_1620|5end_hypothetical_protein_1607240..1607470_NEGATIVE 272 158 127 81 55 smit:SMT_1504|5end_topology_modulation_protein_1487204..1487434_POSITIVE 270 158 111 137 88 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 270 164 124 226 192 smit:SMT_1675|5end_adenylosuccinate_synthetase_1661147..1661377_NEGATIVE 268 148 110 66 17 smit:SMT_635|5end_ribonucleoside-diphosphate_reductase_alpha_chain_540658..540888_POSITIVE 265 133 91 67 28 smit:SMT_281|5end_glycosyl_transferase,_group_1_223551..223781_POSITIVE 263 150 108 212 173 smit:SMT_1425|5end_hypothetical_protein_1410805..1411035_NEGATIVE 261 148 104 152 113 smit:SMT_1299|5end_MutT/NUDIX_family_protein_1261719..1261949_POSITIVE 261 154 116 131 95 smit:SMT_688|5end_carbamoyl-phosphate_synthase_small_chain_600655..600885_NEGATIVE 261 146 105 67 23 smit:SMT_644|5end_O-acetylhomoserine_(thiol)-lyase_549871..550101_NEGATIVE 257 148 104 206 157 smit:SMT_1887|5end_LicC_protein_1841445..1841675_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 147 104 109 55 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 272 158 127 28 2 smit:SMT_1503|3end_SSU_ribosomal_protein_S20P_1487231..1487381_POSITIVE 265 133 91 64 25 smit:SMT_280|3end_polysaccharide_biosynthesis_protein/putative_rhamnosyl_transferase_223628..223778_POSITIVE 261 148 104 150 111 smit:SMT_1298|3end_K03811_nicotinamide_mononucleotide_transporter_1261797..1261947_POSITIVE 261 154 116 81 45 smit:SMT_689|3end_aspartate_carbamoyltransferase_600705..600855_NEGATIVE 255 157 111 59 9 smit:SMT_404|3end_hypothetical_protein_334029..334179_POSITIVE 248 178 131 72 22 smit:SMT_492|3end_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_427217..427367_POSITIVE 247 154 125 33 4 smit:SMT_1970|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1903032..1903182_POSITIVE 247 154 125 55 26 smit:SMT_1954|3end_6-phospho-beta-glucosidase_1888831..1888981_POSITIVE 247 140 91 62 2 smit:SMT_1523|3end_ferrochelatase_1503390..1503540_NEGATIVE 245 148 108 151 114 smit:SMT_1426|3end_K03095_SprT-like_protein_1410864..1411014_NEGATIVE 242 150 102 79 29 smit:SMT_929|3end_hypothetical_protein_883202..883352_NEGATIVE 239 126 83 147 100 smit:SMT_1704|3end_D-alanine-D-alanine_ligase_1688554..1688704_POSITIVE 237 150 110 77 24 smit:SMT_381|3end_hypothetical_protein_317437..317587_POSITIVE 237 150 110 77 24 smit:SMT_371|3end_hypothetical_protein_305906..306056_POSITIVE 234 145 106 66 20 smit:SMT_1302|3end_hypothetical_protein_1264649..1264799_POSITIVE 233 150 103 143 103 smit:SMT_1061|3end_hypothetical_protein_999915..1000065_POSITIVE 231 168 122 88 36 smit:SMT_1216|3end_hypothetical_protein_1175969..1176119_POSITIVE 230 150 101 117 62 smit:SMT_1333|3end_glycosyltransferase_1307592..1307742_NEGATIVE 230 144 103 137 95 smit:SMT_490|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_425493..425643_POSITIVE