Origin IGS: attttttagtaaaaaatatttacaaagttcggaatttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttttgatgcccaaaagtgaggtttat .........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 ataaacctcacttttgggcatcaaaaaagagcccattattttacagcaataggccctcagagtaagacttctctaaaatctagactttaaagagtttcaagtatttctgcgtcttcgtcacctcacgggatgacattaaaaacctttgcttgtgatagtatagcagaaattccgaactttgtaaatattttttactaaaaaat Mask Tandem Repeat Region ================================================ attttttagtaaaaaatatttacaaagttcggaatttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttttgatgcccaaaagtgaggtttat Find is-nt database================================================ Query_seq: SMT_697:SMT_698|SMT_697:SMT_698:glucose-inhibited division protein B:uracil permease:->->:608343..608545 203 attttttagtaaaaaatatttacaaagttcggaatttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttttgatgcccaaaagtgaggtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_697:SMT_698|SMT_697:SMT_698:glucose-inhibited division protein B:uracil permease:->->:608343..608545 203 attttttagtaaaaaatatttacaaagttcggaatttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttttgatgcccaaaagtgaggtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_697:SMT_698|SMT_697:SMT_698:glucose-inhibited division protein B:uracil permease:->->:608343..608545 203 attttttagtaaaaaatatttacaaagttcggaatttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttttgatgcccaaaagtgaggtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttttagtaaaaaatatttacaaagttcggaatttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttttgatgcccaaaagtgaggtttat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 9 End: 101 ........ Y F I N V F N P I E A I S D C A F T K L T M G H P S S S A S M ...................................................................................................... attttttagtaaaaaatatttacaaagttcggaatttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttttgatgcccaaaagtgaggtttat 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: 87 Start: 18 End: 47 .................ATTTACAAAGTTCGGAATTTCTGCTATACT............................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attttttagtaaaaaatatttacaaagttcggaatttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttttgatgcccaaaagtgaggtttat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -3.4 Tail_Score: -5.14563 Start: 148 End: 175 Full_Region: GAAGTCTTACTCTGA GGGCCTATTGCT GTAA AATAATGGGCTC TTTTTTGATGCCCAA ...................................................................................................................................................GGGCCTATTGCTGTAAAATAATGGGCTC............................ Find igs database================================================ Query_seq: SMT_697:SMT_698|SMT_697:SMT_698:glucose-inhibited division protein B:uracil permease:->->:608343..608545 203 attttttagtaaaaaatatttacaaagttcggaatttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttttgatgcccaaaagtgaggtttat Intra-Species Hit: Count: 1 Min: 1 Max: 203 Len: 203 Subject: smit_SMT_697_SMT_698|glucose-inhibited division protein B:uracil permease|POSITIVE:POSITIVE|[608343,608545]|203 HSP 1 e-value: 1.0E-111 bit: 402.0 Len: 203 Query Start:1 Query End:203 Subject Strand: POSITIVE Subject Start: 1 Subject End: 203 attttttagtaaaaaatatttacaaagttcggaatttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttttgatgcccaaaagtgaggtttat attttttagtaaaaaatatttacaaagttcggaatttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttttgatgcccaaaagtgaggtttat Inter-species Hit: Count: 3 Min: 35 Max: 203 Len: 169 Subject: NC_008533_SPD_1140_SPD_1141|methyltransferase GidB:uracil-xanthine permease|POSITIVE:POSITIVE|[1174446,1174796]|351 HSP 1 e-value: 3.0E-79 bit: 295.0 Len: 169 Query Start:35 Query End:203 Subject Strand: POSITIVE Subject Start: 183 Subject End: 351 ..................................tttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttttgatgcccaaaagtgaggtttat ..................................tttctgctatactatcctaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcaaaaatatttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaataatgggctcttttctgatgcccaaaagtgaggtttat Subject: NC_003098_spr1164_spr1165|glucose-inhibited division protein B:Uracil permease|POSITIVE:POSITIVE|[1166915,1167229]|315 HSP 1 e-value: 4.0E-60 bit: 232.0 Len: 133 Query Start:35 Query End:167 Subject Strand: POSITIVE Subject Start: 183 Subject End: 315 ..................................tttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaata.................................... ..................................tttctgctatactatcctaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcaaaaatatttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaata.................................... Subject: NC_003028_SP_1285_SP_1286|glucose-inhibited division protein B:uracil permease|POSITIVE:POSITIVE|[1220200,1220465]|266 HSP 1 e-value: 5.0E-53 bit: 208.0 Len: 133 Query Start:35 Query End:167 Subject Strand: POSITIVE Subject Start: 134 Subject End: 266 ..................................tttctgctatactatcacaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatacttgaaactctttaaagtctagattttagagaagtcttactctgagggcctattgctgtaaaata.................................... ..................................tttctgctatactatcctaagcaaaggtttttaatgtcatcccgtgaggtgacgaagacgcagaaatatttaaaactctttaaaatctaaattttaaagaagtcttactctgagggcctattgctgtaaaata.................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUGCUAUACUAUCACAAGCAAAGGUUUUUAAUGUCAUCCCGUGAGGUGACGAAGACGCAGAAAUACUUGAAACUCUUUAAAGUCUAGAUUUUAGAGAAGUCUUACUCUGAGGGCCUAUUGCUGUAAAAUAAUGGGCUCUUUUUUGAUGCCCAAAAGUGAGGUUUAU .......((.(((.((((.((((((((((((((..((((..((....)))))).(((((.(((......)))....((((((((((....)))))))))).)))))....))))))))).))))).........(((((((......)).)))))...))))))).)). (-47.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAACCUCACUUUUGGGCAUCAAAAAAGAGCCCAUUAUUUUACAGCAAUAGGCCCUCAGAGUAAGACUUCUCUAAAAUCUAGACUUUAAAGAGUUUCAAGUAUUUCUGCGUCUUCGUCACCUCACGGGAUGACAUUAAAAACCUUUGCUUGUGAUAGUAUAGCAGAAA .......((((...(((((.((......))))))).........(((((.(((..(.(((((....((((((((..((........))..))))....))))..))))).).....((((((.....)).))))........)))))))).)))).............. (-33.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 69 25 54 2 smit:SMT_1620|5end_hypothetical_protein_1607240..1607470_NEGATIVE 279 60 26 217 180 smit:SMT_544|5end_aminoglycoside_6-adenylyltransferase_460292..460522_POSITIVE 275 60 12 59 13 smit:SMT_1217|5end_hypothetical_protein_1176603..1176833_NEGATIVE 272 129 87 147 104 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 267 119 72 218 167 smit:SMT_1978|5end_hypothetical_protein_1909566..1909796_NEGATIVE 261 47 3 93 42 smit:SMT_1891|5end_putative_dihydrolipoamide_S-acetyltransferase_1844373..1844603_POSITIVE 261 47 3 93 42 smit:SMT_1402|5end_pyruvate_dehydrogenase_E2_component_(dihydrolipoamide_acetyltransferase)_1378115..1378345_POSITIVE 259 60 12 200 142 smit:SMT_488|5end_dCMP_deaminase_422956..423186_POSITIVE 257 127 85 141 103 smit:SMT_1897|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1848858..1849088_NEGATIVE 257 125 90 36 2 smit:SMT_1059|5end_NAD(P)H-flavin_oxidoreductase_997379..997609_POSITIVE 256 150 108 86 48 smit:SMT_548|5end_K02035_peptide/nickel_transport_system_substrate-binding_protein_464992..465222_POSITIVE 254 63 36 136 107 smit:SMT_215|5end_leucyl-tRNA_synthetase_147045..147275_POSITIVE 252 128 83 214 163 smit:SMT_225|5end_pullulanase_163529..163759_NEGATIVE 251 50 1 113 65 smit:SMT_1255|5end_cell_division_protein_FtsH_1221811..1222041_NEGATIVE 249 127 82 181 137 smit:SMT_1128|5end_surface_antigen_1063140..1063370_NEGATIVE 245 117 78 112 66 smit:SMT_2035|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1947167..1947397_POSITIVE 245 80 34 192 139 smit:SMT_915|5end_sucrose_operon_repressor_867574..867804_POSITIVE 244 150 109 219 177 smit:SMT_1857|5end_hypothetical_protein_1820931..1821161_POSITIVE 244 150 109 219 177 smit:SMT_834|5end_hypothetical_protein_777112..777342_NEGATIVE 243 63 21 209 170 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 69 36 38 1 smit:SMT_1621|3end_K09134_hypothetical_protein_1607256..1607406_NEGATIVE 257 127 85 122 84 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 257 125 90 39 5 smit:SMT_1058|3end_primosomal_protein_DnaI_997462..997612_POSITIVE 256 150 108 63 25 smit:SMT_547|3end_branched-chain_amino_acid_aminotransferase_465049..465199_POSITIVE 254 63 36 77 48 smit:SMT_214|3end_leucyl-tRNA_synthetase_147066..147216_POSITIVE 251 50 1 69 21 smit:SMT_1256|3end_ketol-acid_reductoisomerase_1221855..1222005_NEGATIVE 251 148 108 144 102 smit:SMT_1040|3end_K03565_regulatory_protein_983542..983692_POSITIVE 245 117 78 122 76 smit:SMT_2034|3end_hydrolase,_haloacid_dehalogenase-like_family_1947257..1947407_POSITIVE 243 63 21 48 9 smit:SMT_1487|3end_hypothetical_protein_1467076..1467226_POSITIVE 242 118 76 124 78 smit:SMT_1192|3end_phosphoribosylaminoimidazolecarboxamide_formyltransferase_/_IMP_cyclohydrolase_1149859..1150009_NEGATIVE 241 120 71 139 86 smit:SMT_1303|3end_tRNA-dihydrouridine_synthase_1264676..1264826_NEGATIVE 240 47 4 82 11 smit:SMT_1864|3end_integral_membrane_protein_1827172..1827322_POSITIVE 239 130 84 126 83 smit:SMT_1330|3end_hypothetical_protein_1305852..1306002_NEGATIVE 238 60 12 89 33 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE 237 117 77 140 102 smit:SMT_153|3end_sensor_histidine_kinase,_putative_101960..102110_POSITIVE 236 88 44 89 32 smit:SMT_345|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_284803..284953_POSITIVE 232 125 85 67 34 smit:SMT_1453|3end_K07335_basic_membrane_protein_A_and_related_proteins_1436355..1436505_NEGATIVE 228 62 23 142 96 smit:SMT_335|3end_glutamine_synthetase_275179..275329_POSITIVE 226 144 108 69 35 smit:SMT_1738|3end_peptidyl-prolyl_cis-trans_isomerase_1721341..1721491_POSITIVE 226 154 111 63 23 smit:SMT_167|3end_acetyltransferase,_GNAT_family_113757..113907_POSITIVE