Origin IGS: tgttcccctttctcttctcttaaaaataacttgttactatcataccattttttcaaaatttttcaagagaaaagaagaaattttctgaattttctattttaacgtttatttatgaatgttatttttgtttttattaaaaagataccgatttcatttactaaaaaagaaaaaagaactgatttctcagttcttcattaatcttattccacactaaataggtatgggtaaactggttgttggccttggtgaatctctacctcaacatcttnnnnnttaattaattaannnnnataagcgcaaccacgcggttgaagtgagtttt .........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 aaaactcacttcaaccgcgtggttgcgcttatnnnnnttaattaattaannnnnaagatgttgaggtagagattcaccaaggccaacaaccagtttacccatacctatttagtgtggaataagattaatgaagaactgagaaatcagttcttttttcttttttagtaaatgaaatcggtatctttttaataaaaacaaaaataacattcataaataaacgttaaaatagaaaattcagaaaatttcttcttttctcttgaaaaattttgaaaaaatggtatgatagtaacaagttatttttaagagaagagaaaggggaaca Mask Tandem Repeat Region ================================================ tgttcccctttctcttctcttaaaaataacttgttactatcataccattttttcaaaatttttcaagagaaaagaagaaattttctgaattttctattttaacgtttatttatgaatgttatttttgtttttattaaaaagataccgatttcatttactaaaaaagaaaaaagaactgatttctcagttcttcattaatcttattccacactaaataggtatgggtaaactggttgttggccttggtgaatctctacctcaacatcttnnnnnttaattaattaannnnnataagcgcaaccacgcggttgaagtgagtttt Find is-nt database================================================ Query_seq: SMT_1258:SMT_1259|SMT_1258:SMT_1259:acetolactate synthase large subunit:hypothetical protein:<-->:1224957..1225278 322 tgttcccctttctcttctcttaaaaataacttgttactatcataccattttttcaaaatttttcaagagaaaagaagaaattttctgaattttctattttaacgtttatttatgaatgttatttttgtttttattaaaaagataccgatttcatttactaaaaaagaaaaaagaactgatttctcagttcttcattaatcttattccacactaaataggtatgggtaaactggttgttggccttggtgaatctctacctcaacatcttnnnnnttaattaattaannnnnataagcgcaaccacgcggttgaagtgagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1258:SMT_1259|SMT_1258:SMT_1259:acetolactate synthase large subunit:hypothetical protein:<-->:1224957..1225278 322 tgttcccctttctcttctcttaaaaataacttgttactatcataccattttttcaaaatttttcaagagaaaagaagaaattttctgaattttctattttaacgtttatttatgaatgttatttttgtttttattaaaaagataccgatttcatttactaaaaaagaaaaaagaactgatttctcagttcttcattaatcttattccacactaaataggtatgggtaaactggttgttggccttggtgaatctctacctcaacatcttnnnnnttaattaattaannnnnataagcgcaaccacgcggttgaagtgagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1258:SMT_1259|SMT_1258:SMT_1259:acetolactate synthase large subunit:hypothetical protein:<-->:1224957..1225278 322 tgttcccctttctcttctcttaaaaataacttgttactatcataccattttttcaaaatttttcaagagaaaagaagaaattttctgaattttctattttaacgtttatttatgaatgttatttttgtttttattaaaaagataccgatttcatttactaaaaaagaaaaaagaactgatttctcagttcttcattaatcttattccacactaaataggtatgggtaaactggttgttggccttggtgaatctctacctcaacatcttnnnnnttaattaattaannnnnataagcgcaaccacgcggttgaagtgagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttcccctttctcttctcttaaaaataacttgttactatcataccattttttcaaaatttttcaagagaaaagaagaaattttctgaattttctattttaacgtttatttatgaatgttatttttgtttttattaaaaagataccgatttcatttactaaaaaagaaaaaagaactgatttctcagttcttcattaatcttattccacactaaataggtatgggtaaactggttgttggccttggtgaatctctacctcaacatcttnnnnnttaattaattaannnnnataagcgcaaccacgcggttgaagtgagtttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 39 End: 134 ...................................... M I P F F Q N F S R E K K K F S E F S I L T F I Y E C Y F C F Y ............................................................................................................................................................................................ Protein_Len: 32 Strand: + Start: 116 End: 211 ................................................................................................................... M L F L F L L K R Y R F H L L K K K K E L I S Q F F I N L I P H ............................................................................................................... tgttcccctttctcttctcttaaaaataacttgttactatcataccattttttcaaaatttttcaagagaaaagaagaaattttctgaattttctattttaacgtttatttatgaatgttatttttgtttttattaaaaagataccgatttcatttactaaaaaagaaaaaagaactgatttctcagttcttcattaatcttattccacactaaataggtatgggtaaactggttgttggccttggtgaatctctacctcaacatcttnnnnnttaattaattaannnnnataagcgcaaccacgcggttgaagtgagtttt 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================================================ tgttcccctttctcttctcttaaaaataacttgttactatcataccattttttcaaaatttttcaagagaaaagaagaaattttctgaattttctattttaacgtttatttatgaatgttatttttgtttttattaaaaagataccgatttcatttactaaaaaagaaaaaagaactgatttctcagttcttcattaatcttattccacactaaataggtatgggtaaactggttgttggccttggtgaatctctacctcaacatcttnnnnnttaattaattaannnnnataagcgcaaccacgcggttgaagtgagtttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 81 HP_score: -3.1 Tail_Score: -5.74684 Start: 100 End: 121 Full_Region: CTGAATTTTCTATTT TAACGTTTA TTTA TGAATGTTA TTTTTGTTTTTATTA ...................................................................................................TAACGTTTATTTATGAATGTTA......................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -8.5 Tail_Score: -6.04324 Start: 173 End: 190 Full_Region: aataagattaatgaa gaactga gaaa tcagttc ttttttcttttttag ............................................................................................................................................................................gaactgagaaatcagttc.................................................................................................................................... Find igs database================================================ Query_seq: SMT_1258:SMT_1259|SMT_1258:SMT_1259:acetolactate synthase large subunit:hypothetical protein:<-->:1224957..1225278 322 tgttcccctttctcttctcttaaaaataacttgttactatcataccattttttcaaaatttttcaagagaaaagaagaaattttctgaattttctattttaacgtttatttatgaatgttatttttgtttttattaaaaagataccgatttcatttactaaaaaagaaaaaagaactgatttctcagttcttcattaatcttattccacactaaataggtatgggtaaactggttgttggccttggtgaatctctacctcaacatcttnnnnnttaattaattaannnnnataagcgcaaccacgcggttgaagtgagtttt Intra-Species Hit: Count: 1 Min: 1 Max: 322 Len: 322 Subject: smit_SMT_1258_SMT_1259|acetolactate synthase large subunit:hypothetical protein|NEGATIVE:POSITIVE|[1224957,1225278]|322 HSP 1 e-value: 1.0E-61 bit: 238.0 Len: 150 Query Start:173 Query End:322 Subject Strand: POSITIVE Subject Start: 173 Subject End: 322 ............................................................................................................................................................................gaactgatttctcagttcttcattaatcttattccacactaaataggtatgggtaaactggttgttggccttggtgaatctctacctcaacatcttnnnnnttaattaattaannnnnataagcgcaaccacgcggttgaagtgagtttt ............................................................................................................................................................................gaactgatttctcagttcttcattaatcttattccacactaaataggtatgggtaaactggttgttggccttggtgaatctctacctcaacatcttnnnnnttaattaattaannnnnataagcgcaaccacgcggttgaagtgagtttt HSP 2 e-value: 1.0E-17 bit: 91.7 Len: 46 Query Start:1 Query End:46 Subject Strand: POSITIVE Subject Start: 1 Subject End: 46 tgttcccctttctcttctcttaaaaataacttgttactatcatacc.................................................................................................................................................................................................................................................................................... tgttcccctttctcttctcttaaaaataacttgttactatcatacc.................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCCCCUUUCUCUUCUCUUAAAAAUAACUUGUUACUAUCAUACCAUUUUUUCAAAAUUUUUCAAGAGAAAAGAAGAAAUUUUCUGAAUUUUCUAUUUUAACGUUUAUUUAUGAAUGUUAUUUUUGUUUUUAUUAAAAAGAUACCGAUUUCAUUUACUAAAAAAGAAAAAAGAACUGAUUUCUCAGUUCUUCAUUAAUCUUAUUCCACACUAAAUAGGUAUGGGUAAACUGGUUGUUGGCCUUGGUGAAUCUCUACCUCAACAUCUUNNNNNUUAAUUAAUUAANNNNNAUAAGCGCAACCACGCGGUUGAAGUGAGUUUU ..............(((.((....(((((((..(((((..((((((............((((((...((((((..(((.....)))...)))))).............((((((((((..(((..(((((((.....)))))))..)))..)))))).))))...)))))).(((((((....)))))))...........................)))))))))))...)))))))......)).))).(((.((.(((((...........(((....)))..........(((......))).))))).))))).... (-55.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACUCACUUCAACCGCGUGGUUGCGCUUAUNNNNNUUAAUUAAUUAANNNNNAAGAUGUUGAGGUAGAGAUUCACCAAGGCCAACAACCAGUUUACCCAUACCUAUUUAGUGUGGAAUAAGAUUAAUGAAGAACUGAGAAAUCAGUUCUUUUUUCUUUUUUAGUAAAUGAAAUCGGUAUCUUUUUAAUAAAAACAAAAAUAACAUUCAUAAAUAAACGUUAAAAUAGAAAAUUCAGAAAAUUUCUUCUUUUCUCUUGAAAAAUUUUGAAAAAAUGGUAUGAUAGUAACAAGUUAUUUUUAAGAGAAGAGAAAGGGGAACA ....(((((((((((.((((....))))..........(((....)))...........)))))))).)))....(((..((.......)).((((((((((((.......))))))...((((.....((((((((((....))))))))))..)))).....))))))......))).((((((((((.............................))))))).)))............(..((((((((((((((((((..((((....................))))...))))))))))))))).)))..).... (-63.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 760 50 1 141 92 smit:SMT_1258|5end_acetolactate_synthase_large_subunit_1224866..1225096_NEGATIVE 317 253 214 41 9 smit:SMT_1990|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1917565..1917795_POSITIVE 303 262 224 72 41 smit:SMT_1085|5end_sensor_histidine_kinase_(homolog_to_HK11_Spn)_1022267..1022497_NEGATIVE 291 260 211 132 77 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 287 266 229 100 56 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 264 268 222 184 133 smit:SMT_233|5end_hypothetical_protein_172656..172886_POSITIVE 259 205 175 73 45 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 259 205 175 73 45 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 258 262 222 221 174 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 253 249 203 68 21 smit:SMT_1747|5end_anthranilate_synthase_component_I_1726279..1726509_POSITIVE 253 268 222 162 120 smit:SMT_1057|5end_replicative_DNA_helicase_995316..995546_POSITIVE 249 250 204 76 30 smit:SMT_817|5end_aminotransferase_728699..728929_NEGATIVE 248 249 203 75 25 smit:SMT_1666|5end_hypothetical_protein_1657467..1657697_NEGATIVE 246 259 211 72 16 smit:SMT_1457|5end_16S_rRNA_m(2)G_1207_methyltransferase_1440209..1440439_NEGATIVE 245 267 221 68 17 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 243 47 7 96 45 smit:SMT_1104|5end_K06346_spoIIIJ-associated_protein_1046784..1047014_NEGATIVE 240 262 229 59 8 smit:SMT_1783|5end_peptide_methionine_sulfoxide_reductase_1759756..1759986_POSITIVE 240 256 217 43 10 smit:SMT_680|5end_choline_transport_protein_589962..590192_NEGATIVE 238 268 222 223 181 smit:SMT_1410|5end_exonuclease_RexA_1392182..1392412_NEGATIVE 237 22 1 118 97 smit:SMT_1075|5end_hypothetical_protein_1013473..1013703_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 253 214 73 41 smit:SMT_1990|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1917677..1917827_POSITIVE 283 244 204 146 95 smit:SMT_397|3end_NAD(+)_synthetase_327423..327573_POSITIVE 282 255 215 142 93 smit:SMT_1224|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1187900..1188050_NEGATIVE 270 250 205 146 98 smit:SMT_2042|3end_K04077_chaperonin_GroEL_(Hsp60)_1952960..1953110_NEGATIVE 266 89 42 126 80 smit:SMT_1775|3end_K07478_putative_ATPase_1751315..1751465_NEGATIVE 266 268 237 44 6 smit:SMT_1450|3end_K02057_simple_sugar_transport_system_permease_protein_1432666..1432816_NEGATIVE 261 227 182 84 23 smit:SMT_1667|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1657439..1657589_NEGATIVE 251 247 205 140 106 smit:SMT_942|3end_hypothetical_protein_893528..893678_NEGATIVE 249 250 204 68 22 smit:SMT_818|3end_cystathionine_gamma-synthase_728707..728857_NEGATIVE 248 250 208 141 105 smit:SMT_1431|3end_K08986_putative_membrane_protein_1416654..1416804_POSITIVE 247 258 218 63 25 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 243 47 7 78 27 smit:SMT_1105|3end_K03217_preprotein_translocase_YidC_subunit_1046802..1046952_NEGATIVE 240 256 217 53 20 smit:SMT_681|3end_choline_kinase_589952..590102_NEGATIVE 237 256 217 44 10 smit:SMT_792|3end_hypothetical_protein_predicted_by_Glimmer/Critica_702458..702608_NEGATIVE 236 268 232 144 103 smit:SMT_1690|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1673370..1673520_NEGATIVE 230 85 54 70 34 smit:SMT_1018|3end_hypothetical_protein_predicted_by_Glimmer/Critica_954739..954889_POSITIVE 228 261 224 85 41 smit:SMT_2014|3end_tryptophan_synthase_beta_chain_1932727..1932877_POSITIVE 225 253 216 86 32 smit:SMT_1379|3end_thymidylate_kinase_1356800..1356950_NEGATIVE 224 246 203 81 26 smit:SMT_477|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_414232..414382_NEGATIVE 221 217 180 146 106 smit:SMT_1189|3end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1146663..1146813_NEGATIVE