Origin IGS: ttctattccttatttttttataattgccttagatggtggggacgtaagcaaacctccggtttcattgcttatttttgagccttatatctcaaaaatcccctgtcatgtaacaaactaaataatttgttacatgacttacaccacagcggcaatcatttctttaactcgctgagctcggataggagctgagctaaatcatatattttagtatcaattaatgaatcagaaaaaattctt .........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 aagaattttttctgattcattaattgatactaaaatatatgatttagctcagctcctatccgagctcagcgagttaaagaaatgattgccgctgtggtgtaagtcatgtaacaaattatttagtttgttacatgacaggggatttttgagatataaggctcaaaaataagcaatgaaaccggaggtttgcttacgtccccaccatctaaggcaattataaaaaaataaggaatagaa Mask Tandem Repeat Region ================================================ ttctattccttatttttttataattgccttagatggtggggacgtaagcaaacctccggtttcattgcttatttttgagccttatatctcaaaaatcccctgtcatgtaacaaactaaataatttgttacatgacttacaccacagcggcaatcatttctttaactcgctgagctcggataggagctgagctaaatcatatattttagtatcaattaatgaatcagaaaaaattctt Find is-nt database================================================ Query_seq: SSA_1409:SSA_1410|SSA_1409:SSA_1410:DTDP-glucose-4,6-dehydratase, putative:DTDP-4-keto-6-deoxyglucose-3,5-epimerase, putative:<-<-:1422346..1422582 237 ttctattccttatttttttataattgccttagatggtggggacgtaagcaaacctccggtttcattgcttatttttgagccttatatctcaaaaatcccctgtcatgtaacaaactaaataatttgttacatgacttacaccacagcggcaatcatttctttaactcgctgagctcggataggagctgagctaaatcatatattttagtatcaattaatgaatcagaaaaaattctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1409:SSA_1410|SSA_1409:SSA_1410:DTDP-glucose-4,6-dehydratase, putative:DTDP-4-keto-6-deoxyglucose-3,5-epimerase, putative:<-<-:1422346..1422582 237 ttctattccttatttttttataattgccttagatggtggggacgtaagcaaacctccggtttcattgcttatttttgagccttatatctcaaaaatcccctgtcatgtaacaaactaaataatttgttacatgacttacaccacagcggcaatcatttctttaactcgctgagctcggataggagctgagctaaatcatatattttagtatcaattaatgaatcagaaaaaattctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1409:SSA_1410|SSA_1409:SSA_1410:DTDP-glucose-4,6-dehydratase, putative:DTDP-4-keto-6-deoxyglucose-3,5-epimerase, putative:<-<-:1422346..1422582 237 ttctattccttatttttttataattgccttagatggtggggacgtaagcaaacctccggtttcattgcttatttttgagccttatatctcaaaaatcccctgtcatgtaacaaactaaataatttgttacatgacttacaccacagcggcaatcatttctttaactcgctgagctcggataggagctgagctaaatcatatattttagtatcaattaatgaatcagaaaaaattctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctattccttatttttttataattgccttagatggtggggacgtaagcaaacctccggtttcattgcttatttttgagccttatatctcaaaaatcccctgtcatgtaacaaactaaataatttgttacatgacttacaccacagcggcaatcatttctttaactcgctgagctcggataggagctgagctaaatcatatattttagtatcaattaatgaatcagaaaaaattctt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 5 End: 115 .... M P Y F F I I A L D G G D V S K P P V S L L I F E P Y I S K I P C H V T N .......................................................................................................................... ttctattccttatttttttataattgccttagatggtggggacgtaagcaaacctccggtttcattgcttatttttgagccttatatctcaaaaatcccctgtcatgtaacaaactaaataatttgttacatgacttacaccacagcggcaatcatttctttaactcgctgagctcggataggagctgagctaaatcatatattttagtatcaattaatgaatcagaaaaaattctt 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: 82 Start: 202 End: 231 .........................................................................................................................................................................................................TTTTTCTGATTCATTAATTGATACTAAAAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttctattccttatttttttataattgccttagatggtggggacgtaagcaaacctccggtttcattgcttatttttgagccttatatctcaaaaatcccctgtcatgtaacaaactaaataatttgttacatgacttacaccacagcggcaatcatttctttaactcgctgagctcggataggagctgagctaaatcatatattttagtatcaattaatgaatcagaaaaaattctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1409:SSA_1410|SSA_1409:SSA_1410:DTDP-glucose-4,6-dehydratase, putative:DTDP-4-keto-6-deoxyglucose-3,5-epimerase, putative:<-<-:1422346..1422582 237 ttctattccttatttttttataattgccttagatggtggggacgtaagcaaacctccggtttcattgcttatttttgagccttatatctcaaaaatcccctgtcatgtaacaaactaaataatttgttacatgacttacaccacagcggcaatcatttctttaactcgctgagctcggataggagctgagctaaatcatatattttagtatcaattaatgaatcagaaaaaattctt Intra-Species Hit: Count: 1 Min: 20 Max: 237 Len: 218 Subject: NC_009009_SSA_1409_SSA_1410|DTDP-glucose-4,6-dehydratase, putative:DTDP-4-keto-6-deoxyglucose-3,5-epimerase, putative|NEGATIVE:NEGATIVE|[1422346,1422582]|237 HSP 1 e-value: 1.0E-120 bit: 432.0 Len: 218 Query Start:20 Query End:237 Subject Strand: POSITIVE Subject Start: 20 Subject End: 237 ...................ataattgccttagatggtggggacgtaagcaaacctccggtttcattgcttatttttgagccttatatctcaaaaatcccctgtcatgtaacaaactaaataatttgttacatgacttacaccacagcggcaatcatttctttaactcgctgagctcggataggagctgagctaaatcatatattttagtatcaattaatgaatcagaaaaaattctt ...................ataattgccttagatggtggggacgtaagcaaacctccggtttcattgcttatttttgagccttatatctcaaaaatcccctgtcatgtaacaaactaaataatttgttacatgacttacaccacagcggcaatcatttctttaactcgctgagctcggataggagctgagctaaatcatatattttagtatcaattaatgaatcagaaaaaattctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUUGCCUUAGAUGGUGGGGACGUAAGCAAACCUCCGGUUUCAUUGCUUAUUUUUGAGCCUUAUAUCUCAAAAAUCCCCUGUCAUGUAACAAACUAAAUAAUUUGUUACAUGACUUACACCACAGCGGCAAUCAUUUCUUUAACUCGCUGAGCUCGGAUAGGAGCUGAGCUAAAUCAUAUAUUUUAGUAUCAAUUAAUGAAUCAGAAAAAAUUCUU ...((((((...(.(((((((((.(((((((((((...)))....))))))))(((((((........))))))).))))).(((((((((((((........)))))))))))))....)))))...))))))..(((((.......(((.(((((......))))).)))...................(((.....)))...)))))........ (-61.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAUUUUUUCUGAUUCAUUAAUUGAUACUAAAAUAUAUGAUUUAGCUCAGCUCCUAUCCGAGCUCAGCGAGUUAAAGAAAUGAUUGCCGCUGUGGUGUAAGUCAUGUAACAAAUUAUUUAGUUUGUUACAUGACAGGGGAUUUUUGAGAUAUAAGGCUCAAAAAUAAGCAAUGAAACCGGAGGUUUGCUUACGUCCCCACCAUCUAAGGCAAUUAU ..(((((......))))).....................((((((.(((.(((((......))))).))))))))).....(((((((((...(((((....(((((((((((((((....))))))))))))))).(((((((((((((........))))))).(((((((....(((...)))))))))).)))))))))))....))))))))) (-71.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 949 50 1 160 111 NC_009009:SSA_1409|5end_DTDP-glucose-4,6-dehydratase,_putative_1422255..1422485_NEGATIVE 464 60 12 173 127 NC_009009:SSA_0039|5end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_45833..46063_POSITIVE 388 163 121 165 117 NC_009009:SSA_0111|5end_30S_ribosomal_protein_S19,_putative_110672..110902_POSITIVE 344 174 133 217 169 NC_009009:SSA_2384|5end_Acetyltransferase,_GNAT_family,_putative_1465896..1466126_NEGATIVE 332 180 136 51 6 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 327 170 122 142 86 NC_009009:SSA_1973|5end_Histidine_kinase,_putative_1969507..1969737_NEGATIVE 327 80 33 108 50 NC_009009:SSA_0789|5end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772451..772681_POSITIVE 323 51 12 180 152 NC_009009:SSA_1398|5end_Membrane_protein,_hemolysin_III-like,_putative_1410881..1411111_POSITIVE 315 172 133 132 87 NC_009009:SSA_1444|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1447267..1447497_NEGATIVE 312 166 122 227 177 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 310 169 148 146 125 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 308 174 138 51 20 NC_009009:SSA_0370|5end_Acetyltransferase,_GNAT_family,_putative_360382..360612_NEGATIVE 305 50 4 63 12 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 305 59 11 82 23 NC_009009:SSA_1596|5end_hypothetical_protein_1603034..1603264_NEGATIVE 304 59 12 205 153 NC_009009:SSA_1841|5end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1835822..1836052_NEGATIVE 303 60 17 62 8 NC_009009:SSA_1784|5end_Glutamate_racemase,_putative_1769897..1770127_NEGATIVE 297 48 5 212 168 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 294 151 121 74 45 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 293 50 9 210 161 NC_009009:SSA_0653|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_636390..636620_POSITIVE 292 169 122 56 13 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 163 121 79 31 NC_009009:SSA_0110|3end_50S_ribosomal_protein_L2,_putative_110666..110816_POSITIVE 332 180 136 54 9 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE 327 170 122 137 81 NC_009009:SSA_1974|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1969512..1969662_NEGATIVE 327 80 33 100 42 NC_009009:SSA_0788|3end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_772523..772673_POSITIVE 315 172 133 97 52 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 310 169 148 143 122 NC_009009:SSA_0824|3end_DNA_primase_(bacterial_type),_putative_803941..804091_POSITIVE 295 165 121 140 89 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 294 151 121 60 31 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 293 170 126 142 97 NC_009009:SSA_1126|3end_Thiamine_biosynthesis_lipoprotein,_putative_1150587..1150737_NEGATIVE 292 169 122 69 26 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 288 179 134 143 91 NC_009009:SSA_0967|3end_hypothetical_protein_976620..976770_POSITIVE 284 55 17 118 63 NC_009009:SSA_1093|3end_ATP-dependent_Clp_protease_ATP-binding_subunit_clpX,_putative_1111645..1111795_POSITIVE 280 179 148 112 75 NC_009009:SSA_2081|3end_hypothetical_protein_2085490..2085640_POSITIVE 277 172 137 56 16 NC_009009:SSA_0097|3end_Multi_antimicrobial_extrusion_(MATE)_family_transporter,_putative_99505..99655_POSITIVE 273 159 112 110 58 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 272 70 24 86 35 NC_009009:SSA_2176|3end_hypothetical_protein_2174269..2174419_NEGATIVE 268 175 134 144 95 NC_009009:SSA_1597|3end_hypothetical_protein_1603267..1603417_NEGATIVE 267 38 6 136 102 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 266 170 121 89 30 NC_009009:SSA_1244|3end_hypothetical_protein_1268465..1268615_NEGATIVE 264 80 32 62 18 NC_009009:SSA_1949|3end_AliA_protein,_putative_1942403..1942553_NEGATIVE