Origin IGS: ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaattaaatagagacttcctccatcttctcacgtcctnnnnn .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 nnnnnaggacgtgagaagatggaggaagtctctatttaattaktctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa Mask Tandem Repeat Region ================================================ ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaattaaatagagacttcctccatcttctcacgtcctnnnnn Find is-nt database================================================ Query_seq: SMT_2061:SMT_2062|SMT_2061:SMT_2062:K02011 iron(III) transport system permease protein:phosphoglycerate mutase:-><-:1970863..1971002 140 ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaattaaatagagacttcctccatcttctcacgtcctnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2061:SMT_2062|SMT_2061:SMT_2062:K02011 iron(III) transport system permease protein:phosphoglycerate mutase:-><-:1970863..1971002 140 ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaattaaatagagacttcctccatcttctcacgtcctnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2061:SMT_2062|SMT_2061:SMT_2062:K02011 iron(III) transport system permease protein:phosphoglycerate mutase:-><-:1970863..1971002 140 ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaattaaatagagacttcctccatcttctcacgtcctnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaattaaatagagacttcctccatcttctcacgtcctnnnnn Predict ORF larger than 30AA ================================================ ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaattaaatagagacttcctccatcttctcacgtcctnnnnn 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================================================ ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaattaaatagagacttcctccatcttctcacgtcctnnnnn Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 93 HP_score: -8.9 Tail_Score: -4.72272 Start: 17 End: 40 Full_Region: caaaataagaaaaaa cagccgaag taatcc tttcggctg tttttgatggggaaa ................cagccgaagtaatcctttcggctg.................................................................................................... Find igs database================================================ Query_seq: SMT_2061:SMT_2062|SMT_2061:SMT_2062:K02011 iron(III) transport system permease protein:phosphoglycerate mutase:-><-:1970863..1971002 140 ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaattaaatagagacttcctccatcttctcacgtcctnnnnn Intra-Species Hit: Count: 3 Min: 1 Max: 135 Len: 135 Subject: smit_SMT_2061_SMT_2062|K02011 iron(III) transport system permease protein:phosphoglycerate mutase|POSITIVE:NEGATIVE|[1970863,1971002]|140 HSP 1 e-value: 3.0E-70 bit: 265.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaattaaatagagacttcctccatcttctcacgtcct..... ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaattaaatagagacttcctccatcttctcacgtcct..... Subject: smit_SMT_1993_SMT_1994|hypothetical protein:phosphoglycerate mutase|NEGATIVE:NEGATIVE|[1919891,1920147]|257 HSP 1 e-value: 7.0E-50 bit: 197.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 157 Subject End: 257 ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaa....................................... ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa....................................... Subject: smit_SMT_201_SMT_202|phosphoglycerate mutase:K02011 iron(III) transport system permease protein|POSITIVE:NEGATIVE|[132162,132262]|101 HSP 1 e-value: 7.0E-50 bit: 197.0 Len: 101 Query Start:1 Query End:101 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 101 ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagamtaa....................................... ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa....................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCCCCAUCAAAAACAGCCGAAAGGAUUACUUCGGCUGUUUUUUCUUAUUUUGAUAUUCCUACUAGAUUCCUAGUUCAUUGCAAGCAAGUCUAGAMUAAUUAAAUAGAGACUUCCUCCAUCUUCUCACGUCCU ...........(((((((((((((.(.....)))))))))))))).........(((.......(((((((.((.((.....)).))..)))))))............((((............))))..))).. (-27.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGACGUGAGAAGAUGGAGGAAGUCUCUAUUUAAUUAKUCUAGACUUGCUUGCAAUGAACUAGGAAUCUAGUAGGAAUAUCAAAAUAAGAAAAAACAGCCGAAGUAAUCCUUUCGGCUGUUUUUGAUGGGGAAAA ....(....)..(((((((.((((((...............)))))).))).......(((((....))))).....)))).........((((((((((((((......))))))))))))))........... (-32.36) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 63 25 201 163 smit:SMT_309|5end_acyl-carrier-protein_S-malonyltransferase_250406..250636_POSITIVE 269 97 52 94 49 smit:SMT_1179|5end_aldose_1-epimerase_1137854..1138084_NEGATIVE 263 37 7 132 105 smit:SMT_1681|5end_D-alanine-activating_enzyme_1664184..1664414_POSITIVE 263 76 33 114 61 smit:SMT_600|5end_ADP-ribose_pyrophosphatase_516307..516537_POSITIVE 259 38 8 178 149 smit:SMT_221|5end_prolyl-tRNA_synthetase_153019..153249_POSITIVE 255 49 6 104 62 smit:SMT_920|5end_serine/threonine_protein_kinase_874501..874731_NEGATIVE 251 94 54 149 108 smit:SMT_1857|5end_hypothetical_protein_1820931..1821161_POSITIVE 251 42 7 59 20 smit:SMT_1254|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1220882..1221112_NEGATIVE 251 94 54 149 108 smit:SMT_834|5end_hypothetical_protein_777112..777342_NEGATIVE 250 42 7 47 15 smit:SMT_297|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_238547..238777_POSITIVE 247 72 32 111 77 smit:SMT_1276|5end_rod_shape-determining_protein_MreD_1239412..1239642_POSITIVE 246 50 8 217 178 smit:SMT_786|5end_hypothetical_protein_697964..698194_NEGATIVE 242 130 83 54 9 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 240 45 1 185 128 smit:SMT_816|5end_SWF/SNF_family_helicase_727440..727670_NEGATIVE 239 96 55 58 14 smit:SMT_1611|5end_K05896_segregation_and_condensation_protein_A_1599305..1599535_POSITIVE 239 96 55 58 14 smit:SMT_1034|5end_K05896_segregation_and_condensation_protein_A_977307..977537_NEGATIVE 237 97 52 64 11 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 232 49 1 181 130 smit:SMT_845|5end_hypothetical_protein_791868..792098_NEGATIVE 232 40 7 36 9 smit:SMT_619|5end_riboflavin_kinase_/_FMN_adenylyltransferase_527812..528042_POSITIVE 231 79 33 149 99 smit:SMT_973|5end_signal_transduction_histidine_kinase_922177..922407_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 788 80 31 69 20 smit:SMT_1994|3end_phosphoglycerate_mutase_1920058..1920208_NEGATIVE 788 80 31 69 20 smit:SMT_201|3end_phosphoglycerate_mutase_132101..132251_POSITIVE 315 45 12 79 46 smit:SMT_2061|3end_K02011_iron(III)_transport_system_permease_protein_1970802..1970952_POSITIVE 315 45 12 79 46 smit:SMT_202|3end_K02011_iron(III)_transport_system_permease_protein_132173..132323_NEGATIVE 263 37 7 41 14 smit:SMT_1680|3end_hypothetical_protein_1664173..1664323_POSITIVE 263 76 33 104 51 smit:SMT_599|3end_glucosamine-1-phosphate_N-acetyltransferase_/_UDP-N-acetylglucosamine_pyrophosphorylase_516377..516527_POSITIVE 255 49 6 107 65 smit:SMT_921|3end_putative_PP2C_protein_phosphatase_874498..874648_NEGATIVE 251 94 54 137 96 smit:SMT_1856|3end_polypeptide_deformylase_1820999..1821149_POSITIVE 251 94 54 137 96 smit:SMT_835|3end_polypeptide_deformylase_777124..777274_NEGATIVE 247 72 32 111 77 smit:SMT_1275|3end_rod_shape-determining_protein_MreC_1239492..1239642_POSITIVE 246 50 8 93 54 smit:SMT_787|3end_K02440_glycerol_uptake_facilitator_protein_698088..698238_NEGATIVE 240 45 1 92 35 smit:SMT_817|3end_aminotransferase_727533..727683_NEGATIVE 239 96 55 58 14 smit:SMT_1610|3end_tyrosine_recombinase_1599385..1599535_POSITIVE 237 97 52 67 14 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 235 78 32 124 77 smit:SMT_1019|3end_K03295_cation_efflux_system_protein,_CDF_family_954782..954932_NEGATIVE 235 54 12 97 56 smit:SMT_142|3end_hypothetical_protein_93409..93559_NEGATIVE 234 50 10 77 32 smit:SMT_320|3end_alcohol_dehydrogenase,_zinc-containing_259241..259391_NEGATIVE 228 69 24 112 60 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE 228 69 24 112 60 smit:SMT_1320|3end_transcriptional_regulator,_MarR_family_1290754..1290904_POSITIVE 228 43 3 83 48 smit:SMT_877|3end_hypothetical_protein_823558..823708_NEGATIVE