Origin IGS: gattttctccttttagtgaaaaaagttaacaaacaataaaatcctattaaaaatattgtatcatagtaatataaaaagtaaaaaagaaagctaaaataagtttggtgtaattttaatatggggttaatgagtactatgatgtagctagaaaaggggtggaaaaatgtttaaaaataaggaactttttcgagtagtcatgatatttgtgataggaattatcctaattttaatgacacccgtcttatttaaagttatgatggacctattttcaaaataaataggcttctgttttaggcagaggtgtgaatcaggaggttaagcg .........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 cgcttaacctcctgattcacacctctgcctaaaacagaagcctatttattttgaaaataggtccatcataactttaaataagacgggtgtcattaaaattaggataattcctatcacaaatatcatgactactcgaaaaagttccttatttttaaacatttttccaccccttttctagctacatcatagtactcattaaccccatattaaaattacaccaaacttattttagctttcttttttactttttatattactatgatacaatatttttaataggattttattgtttgttaacttttttcactaaaaggagaaaatc Mask Tandem Repeat Region ================================================ gattttctccttttagtgaaaaaagttaacaaacaataaaatcctattaaaaatattgtatcatagtaatataaaaagtaaaaaagaaagctaaaataagtttggtgtaattttaatatggggttaatgagtactatgatgtagctagaaaaggggtggaaaaatgtttaaaaataaggaactttttcgagtagtcatgatatttgtgataggaattatcctaattttaatgacacccgtcttatttaaagttatgatggacctattttcaaaataaataggcttctgttttaggcagaggtgtgaatcaggaggttaagcg Find is-nt database================================================ Query_seq: SMT_135:SMT_136|SMT_135:SMT_136:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:<-->:87132..87453 322 gattttctccttttagtgaaaaaagttaacaaacaataaaatcctattaaaaatattgtatcatagtaatataaaaagtaaaaaagaaagctaaaataagtttggtgtaattttaatatggggttaatgagtactatgatgtagctagaaaaggggtggaaaaatgtttaaaaataaggaactttttcgagtagtcatgatatttgtgataggaattatcctaattttaatgacacccgtcttatttaaagttatgatggacctattttcaaaataaataggcttctgttttaggcagaggtgtgaatcaggaggttaagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_135:SMT_136|SMT_135:SMT_136:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:<-->:87132..87453 322 gattttctccttttagtgaaaaaagttaacaaacaataaaatcctattaaaaatattgtatcatagtaatataaaaagtaaaaaagaaagctaaaataagtttggtgtaattttaatatggggttaatgagtactatgatgtagctagaaaaggggtggaaaaatgtttaaaaataaggaactttttcgagtagtcatgatatttgtgataggaattatcctaattttaatgacacccgtcttatttaaagttatgatggacctattttcaaaataaataggcttctgttttaggcagaggtgtgaatcaggaggttaagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_135:SMT_136|SMT_135:SMT_136:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:<-->:87132..87453 322 gattttctccttttagtgaaaaaagttaacaaacaataaaatcctattaaaaatattgtatcatagtaatataaaaagtaaaaaagaaagctaaaataagtttggtgtaattttaatatggggttaatgagtactatgatgtagctagaaaaggggtggaaaaatgtttaaaaataaggaactttttcgagtagtcatgatatttgtgataggaattatcctaattttaatgacacccgtcttatttaaagttatgatggacctattttcaaaataaataggcttctgttttaggcagaggtgtgaatcaggaggttaagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattttctccttttagtgaaaaaagttaacaaacaataaaatcctattaaaaatattgtatcatagtaatataaaaagtaaaaaagaaagctaaaataagtttggtgtaattttaatatggggttaatgagtactatgatgtagctagaaaaggggtggaaaaatgtttaaaaataaggaactttttcgagtagtcatgatatttgtgataggaattatcctaattttaatgacacccgtcttatttaaagttatgatggacctattttcaaaataaataggcttctgttttaggcagaggtgtgaatcaggaggttaagcg Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 164 End: 274 ................................................................................................................................................................... M F K N K E L F R V V M I F V I G I I L I L M T P V L F K V M M D L F S K ................................................ Protein_Len: 44 Strand: - Start: 148 End: 279 ................................................................................................................................................... F L P P F I N L F L S S K R T T M I N T I P I I R I K I V G T K N L T I I S R N E F Y M ........................................... Protein_Len: 46 Strand: - Start: 3 End: 140 .. K R R K T F F T L L C Y F G I L F I T D Y Y Y L F Y F L F S F Y T Q H L K L I P N I L V I M ...................................................................................................................................................................................... gattttctccttttagtgaaaaaagttaacaaacaataaaatcctattaaaaatattgtatcatagtaatataaaaagtaaaaaagaaagctaaaataagtttggtgtaattttaatatggggttaatgagtactatgatgtagctagaaaaggggtggaaaaatgtttaaaaataaggaactttttcgagtagtcatgatatttgtgataggaattatcctaattttaatgacacccgtcttatttaaagttatgatggacctattttcaaaataaataggcttctgttttaggcagaggtgtgaatcaggaggttaagcg 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: 229 End: 258 ....................................................................................................................................................................................................................................AATGACACCCGTCTTATTTAAAGTTATGAT................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gattttctccttttagtgaaaaaagttaacaaacaataaaatcctattaaaaatattgtatcatagtaatataaaaagtaaaaaagaaagctaaaataagtttggtgtaattttaatatggggttaatgagtactatgatgtagctagaaaaggggtggaaaaatgtttaaaaataaggaactttttcgagtagtcatgatatttgtgataggaattatcctaattttaatgacacccgtcttatttaaagttatgatggacctattttcaaaataaataggcttctgttttaggcagaggtgtgaatcaggaggttaagcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_135:SMT_136|SMT_135:SMT_136:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:<-->:87132..87453 322 gattttctccttttagtgaaaaaagttaacaaacaataaaatcctattaaaaatattgtatcatagtaatataaaaagtaaaaaagaaagctaaaataagtttggtgtaattttaatatggggttaatgagtactatgatgtagctagaaaaggggtggaaaaatgtttaaaaataaggaactttttcgagtagtcatgatatttgtgataggaattatcctaattttaatgacacccgtcttatttaaagttatgatggacctattttcaaaataaataggcttctgttttaggcagaggtgtgaatcaggaggttaagcg Intra-Species Hit: Count: 1 Min: 101 Max: 322 Len: 222 Subject: smit_SMT_135_SMT_136|hypothetical protein:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:POSITIVE|[87132,87453]|322 HSP 1 e-value: 1.0E-122 bit: 440.0 Len: 222 Query Start:101 Query End:322 Subject Strand: POSITIVE Subject Start: 101 Subject End: 322 ....................................................................................................tttggtgtaattttaatatggggttaatgagtactatgatgtagctagaaaaggggtggaaaaatgtttaaaaataaggaactttttcgagtagtcatgatatttgtgataggaattatcctaattttaatgacacccgtcttatttaaagttatgatggacctattttcaaaataaataggcttctgttttaggcagaggtgtgaatcaggaggttaagcg ....................................................................................................tttggtgtaattttaatatggggttaatgagtactatgatgtagctagaaaaggggtggaaaaatgtttaaaaataaggaactttttcgagtagtcatgatatttgtgataggaattatcctaattttaatgacacccgtcttatttaaagttatgatggacctattttcaaaataaataggcttctgttttaggcagaggtgtgaatcaggaggttaagcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGGUGUAAUUUUAAUAUGGGGUUAAUGAGUACUAUGAUGUAGCUAGAAAAGGGGUGGAAAAAUGUUUAAAAAUAAGGAACUUUUUCGAGUAGUCAUGAUAUUUGUGAUAGGAAUUAUCCUAAUUUUAAUGACACCCGUCUUAUUUAAAGUUAUGAUGGACCUAUUUUCAAAAUAAAUAGGCUUCUGUUUUAGGCAGAGGUGUGAAUCAGGAGGUUAAGCG ......((((((((((.((((((((((..((((.((((((...(((.(((((((...........................))))))).))).)))))).))))..)..(((((....))))).......)))).))))).....))))))))))......(((((((.......)))))))((((((.((((.((....)).)))).))))))........ (-50.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCUUAACCUCCUGAUUCACACCUCUGCCUAAAACAGAAGCCUAUUUAUUUUGAAAAUAGGUCCAUCAUAACUUUAAAUAAGACGGGUGUCAUUAAAAUUAGGAUAAUUCCUAUCACAAAUAUCAUGACUACUCGAAAAAGUUCCUUAUUUUUAAACAUUUUUCCACCCCUUUUCUAGCUACAUCAUAGUACUCAUUAACCCCAUAUUAAAAUUACACCAAA ((((((.................((((.......)))).((((((((.......))))))))................)))).))(((((.(((.....(((((....)))))...........((((.((((.(((((((((...........))).)))))).....((.....)).........)))).))))..............))).)))))... (-28.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 570 40 1 231 192 smit:SMT_135|5end_hypothetical_protein_87041..87271_NEGATIVE 277 216 180 63 20 smit:SMT_435|5end_orotate_phosphoribosyltransferase_376842..377072_POSITIVE 275 210 180 219 190 smit:SMT_153|5end_sensor_histidine_kinase,_putative_101443..101673_POSITIVE 260 216 183 68 37 smit:SMT_1678|5end_inorganic_pyrophosphatase_1662126..1662356_POSITIVE 260 216 181 108 77 smit:SMT_541|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457842..458072_NEGATIVE 257 188 141 197 139 smit:SMT_1992|5end_carboxynorspermidine_decarboxylase_1919207..1919437_NEGATIVE 257 188 141 197 139 smit:SMT_1415|5end_carboxynorspermidine_decarboxylase_1399570..1399800_NEGATIVE 253 217 182 80 40 smit:SMT_635|5end_ribonucleoside-diphosphate_reductase_alpha_chain_540658..540888_POSITIVE 252 219 177 204 152 smit:SMT_1120|5end_hypothetical_protein_1057063..1057293_NEGATIVE 249 56 17 183 142 smit:SMT_516|5end_hypothetical_protein_442847..443077_NEGATIVE 246 217 180 210 175 smit:SMT_1546|5end_hypothetical_protein_1530068..1530298_POSITIVE 243 219 181 75 24 smit:SMT_2135|5end_dipeptidase_2015053..2015283_NEGATIVE 242 66 22 166 125 smit:SMT_2142|5end_hypothetical_protein_predicted_by_Glimmer/Critica_2019999..2020229_POSITIVE 242 220 178 224 179 smit:SMT_1843|5end_transposase,_TnpA_1808100..1808330_POSITIVE 242 220 178 224 179 smit:SMT_1238|5end_transposase,_TnpA_1198738..1198968_POSITIVE 241 217 177 166 130 smit:SMT_452|5end_phosphomethylpyrimidine_kinase_390568..390798_NEGATIVE 236 220 183 68 28 smit:SMT_639|5end_6-phospho-beta-galactosidase_544885..545115_NEGATIVE 234 215 178 229 185 smit:SMT_760|5end_K01990_ABC-2_type_transport_system_ATP-binding_protein_666442..666672_NEGATIVE 233 216 181 113 71 smit:SMT_1255|5end_cell_division_protein_FtsH_1221811..1222041_NEGATIVE 232 220 181 43 5 smit:SMT_1470|5end_K06188_aquaporin_Z_1452560..1452790_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 210 178 55 18 smit:SMT_635|3end_ribonucleoside-diphosphate_reductase_alpha_chain_541043..541193_POSITIVE 237 80 38 134 94 smit:SMT_1950|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_1885069..1885219_POSITIVE 233 216 181 69 27 smit:SMT_1256|3end_ketol-acid_reductoisomerase_1221855..1222005_NEGATIVE 231 202 181 102 81 smit:SMT_1460|3end_K02038_phosphate_transport_system_permease_protein_1442393..1442543_POSITIVE 231 211 180 79 38 smit:SMT_843|3end_hypothetical_protein_789264..789414_NEGATIVE 230 215 178 117 83 smit:SMT_599|3end_glucosamine-1-phosphate_N-acetyltransferase_/_UDP-N-acetylglucosamine_pyrophosphorylase_516377..516527_POSITIVE 227 57 32 89 60 smit:SMT_1662|3end_histidine_protein_kinase_1651305..1651455_NEGATIVE 224 59 11 130 78 smit:SMT_778|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_687834..687984_POSITIVE 221 195 152 53 5 smit:SMT_1811|3end_hypothetical_protein_1786366..1786516_POSITIVE 221 200 151 143 94 smit:SMT_1022|3end_glycine_betaine_transport_ATP-binding_protein_957992..958142_NEGATIVE 220 72 40 76 43 smit:SMT_1371|3end_hypothetical_protein_1350579..1350729_NEGATIVE 219 204 163 139 96 smit:SMT_1737|3end_peptidyl-prolyl_cis-trans_isomerase_1720598..1720748_POSITIVE 218 143 102 54 1 smit:SMT_1859|3end_serine_protease_1822050..1822200_NEGATIVE 218 143 102 54 1 smit:SMT_1660|3end_serine_protease_1649852..1650002_NEGATIVE 218 143 102 54 1 smit:SMT_87|3end_serine_protease_18908..19058_POSITIVE 217 69 23 91 39 smit:SMT_838|3end_cation_efflux_family_protein_784203..784353_POSITIVE 216 213 174 148 113 smit:SMT_1902|3end_proton-translocating_NADH-quinone_oxidoreductase,_chain_L_1852028..1852178_NEGATIVE 216 80 31 57 16 smit:SMT_756|3end_3-dehydroquinate_dehydratase_659907..660057_NEGATIVE 216 60 22 134 102 smit:SMT_621|3end_K03346_replication_initiation_and_membrane_attachment_protein_529059..529209_POSITIVE 216 60 22 46 14 smit:SMT_620|3end_hypothetical_protein_predicted_by_Glimmer/Critica_528971..529121_POSITIVE