Origin IGS: ttttttacctctgacctctattataataaaaaaatggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttcttacctcattattttaataatctacagtctatgatagcgcttttcagatttttatgcaagcgtttgcctaatctttttgattccttttttaactccatagtttcctaacttccatttttttattataatagaggtcagaggtaaaaaa Mask Tandem Repeat Region ================================================ ttttttacctctgacctctattataataaaaaaatggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag Find is-nt database================================================ Query_seq: SMT_272:SMT_273|SMT_272:SMT_273:hypothetical protein:glucan 1,6-alpha-glucosidase:<-->:213406..213557 152 ttttttacctctgacctctattataataaaaaaatggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_272:SMT_273|SMT_272:SMT_273:hypothetical protein:glucan 1,6-alpha-glucosidase:<-->:213406..213557 152 ttttttacctctgacctctattataataaaaaaatggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_272:SMT_273|SMT_272:SMT_273:hypothetical protein:glucan 1,6-alpha-glucosidase:<-->:213406..213557 152 ttttttacctctgacctctattataataaaaaaatggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttttacctctgacctctattataataaaaaaatggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag Predict ORF larger than 30AA ================================================ ttttttacctctgacctctattataataaaaaaatggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag 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: 85 Start: 20 End: 49 ...................GTTTCCTAACTTCCATTTTTTTATTATAAT....................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 89 End: 118 ........................................................................................CTTGCATAAAAATCTGAAAAGCGCTATCAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttttacctctgacctctattataataaaaaaatggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_272:SMT_273|SMT_272:SMT_273:hypothetical protein:glucan 1,6-alpha-glucosidase:<-->:213406..213557 152 ttttttacctctgacctctattataataaaaaaatggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: smit_SMT_272_SMT_273|hypothetical protein:glucan 1,6-alpha-glucosidase|NEGATIVE:POSITIVE|[213406, 213557]|152 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 ttttttacctctgacctctattataatnnnnnnntggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag ttttttacctctgacctctattataataaaaaaatggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag Inter-species Hit: Count: 3 Min: 1 Max: 152 Len: 152 Subject: NC_008533_SPD_0310_SPD_0311|hypothetical protein:glucan 1,6-alpha-glucosidase|NEGATIVE:POSITIVE|[310564, 310715]|152 HSP 1 e-value: 6.0E-52 bit: 204.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 ttttttacctctgacctctattataatnnnnnnntggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag ttttttacctctgacctctattataataaaaaattggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcacaaaattttaaaaagtgctatcatagactatagattatgaaaataatgaggtaagaag Subject: NC_003098_spr0309_spr0310|hypothetical protein:Alpha, 1-6-glucosidase|NEGATIVE:POSITIVE|[310515,310666]|152 HSP 1 e-value: 6.0E-52 bit: 204.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 ttttttacctctgacctctattataatnnnnnnntggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaagaag ttttttacctctgacctctattataataaaaaattggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcacaaaattttaaaaagtgctatcatagactatagattatgaaaataatgaggtaagaag Subject: NC_003028_SP_0341_SP_0342|hypothetical protein:glucan 1,6-alpha-glucosidase|NEGATIVE:POSITIVE|[315186, 315337]|152 HSP 1 e-value: 7.0E-33 bit: 141.0 Len: 148 Query Start:1 Query End:148 Subject Strand: POSITIVE Subject Start: 1 Subject End: 148 ttttttacctctgacctctattataatnnnnnnntggaagttaggaaactatggagttaaaaaaggaatcaaaaagattaggcaaacgcttgcataaaaatctgaaaagcgctatcatagactgtagattattaaaataatgaggtaa.... ttttttacctctggactctattataataaaaaattggaagttaggaaactacggagctaaaaaagaaattaaaaagattaagcaaacgcttgcacaaaattttaaaaagtgctatcatagactatagattatgaaaataatgaggtaa.... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUACCUCUGACCUCUAUUAUAAUAAAAAAAUGGAAGUUAGGAAACUAUGGAGUUAAAAAAGGAAUCAAAAAGAUUAGGCAAACGCUUGCAUAAAAAUCUGAAAAGCGCUAUCAUAGACUGUAGAUUAUUAAAAUAAUGAGGUAAGAAG .((((((((((((((.((((((..........)))))).)))))....(((((((((.........((((.....))))..((((....)))).................))).))))))......................))))))))). (-27.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUUACCUCAUUAUUUUAAUAAUCUACAGUCUAUGAUAGCGCUUUUCAGAUUUUUAUGCAAGCGUUUGCCUAAUCUUUUUGAUUCCUUUUUUAACUCCAUAGUUUCCUAACUUCCAUUUUUUUAUUAUAAUAGAGGUCAGAGGUAAAAAA (((((.((((((((((..(((........((((((((..(((((((..((........)).))))))).....((((.....)))).............))))).......))).........)))..))))).))))).)))))....... (-25.44) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 860 130 81 221 172 smit:SMT_272|5end_hypothetical_protein_213315..213545_NEGATIVE 273 112 74 217 178 smit:SMT_2122|5end_cell_surface_protein_precursor_2008116..2008346_NEGATIVE 258 124 100 197 170 smit:SMT_1867|5end_peptide_chain_release_factor_1_1828218..1828448_NEGATIVE 243 127 81 184 143 smit:SMT_953|5end_hypothetical_protein_901576..901806_NEGATIVE 238 125 82 214 166 smit:SMT_1534|5end_signal_peptidase_I_1517218..1517448_POSITIVE 232 131 102 197 168 smit:SMT_1994|5end_phosphoglycerate_mutase_1920501..1920731_NEGATIVE 230 133 91 227 187 smit:SMT_1593|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1581417..1581647_POSITIVE 228 128 84 180 135 smit:SMT_1647|5end_3-isopropylmalate_dehydratase_small_subunit_1633403..1633633_POSITIVE 228 125 81 172 117 smit:SMT_748|5end_prephenate_dehydratase_653498..653728_NEGATIVE 227 74 33 178 130 smit:SMT_1544|5end_mevalonate_kinase_1528884..1529114_NEGATIVE 224 125 88 195 156 smit:SMT_1528|5end_K03310_alanine_or_glycine:cation_symporter,_AGCS_family_1512667..1512897_NEGATIVE 224 130 81 165 127 smit:SMT_174|5end_30S_ribosomal_protein_S19_117431..117661_POSITIVE 214 130 81 105 40 smit:SMT_2131|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2011665..2011895_POSITIVE 213 94 56 44 6 smit:SMT_1878|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836577..1836807_NEGATIVE 212 132 92 73 28 smit:SMT_1866|5end_extramembranal_protein_1827290..1827520_POSITIVE 212 132 92 73 28 smit:SMT_1313|5end_extramembranal_protein_1277274..1277504_POSITIVE 208 92 52 59 14 smit:SMT_1589|5end_hypothetical_protein_1578332..1578562_POSITIVE 206 94 63 36 7 smit:SMT_591|5end_K02029_polar_amino_acid_transport_system_permease_protein_508108..508338_POSITIVE 204 117 80 72 35 smit:SMT_879|5end_hypothetical_protein_826989..827219_NEGATIVE 204 48 1 149 92 smit:SMT_411|5end_thymidylate_synthase_355496..355726_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 127 81 83 42 smit:SMT_954|3end_cation-transporting_ATPase,_E1-E2_family_901677..901827_NEGATIVE 232 115 77 51 17 smit:SMT_1191|3end_phosphoribosylamine--glycine_ligase_1148475..1148625_NEGATIVE 224 125 88 86 47 smit:SMT_1529|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1512776..1512926_NEGATIVE 224 130 81 61 23 smit:SMT_173|3end_50S_ribosomal_protein_L2_117407..117557_POSITIVE 223 70 32 143 109 smit:SMT_1220|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1180509..1180659_NEGATIVE 213 94 56 54 16 smit:SMT_1879|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836567..1836717_NEGATIVE 212 132 92 80 35 smit:SMT_1865|3end_D-alanyl_carrier_protein_1827377..1827527_POSITIVE 212 132 92 80 35 smit:SMT_1312|3end_D-alanyl_carrier_protein_1277361..1277511_POSITIVE 208 92 52 72 27 smit:SMT_1588|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1578425..1578575_POSITIVE 199 45 8 76 43 smit:SMT_1094|3end_membrane_carboxypeptidase_(penicillin-binding_protein)_1034141..1034291_NEGATIVE 198 118 88 147 122 smit:SMT_885|3end_single-stranded-DNA-specific_exonuclease_RecJ_832340..832490_NEGATIVE 198 119 79 65 19 smit:SMT_609|3end_laminin-binding_surface_protein_521731..521881_POSITIVE 195 150 102 52 2 smit:SMT_148|3end_glycoprotein_endopeptidase_98601..98751_POSITIVE 194 50 10 83 44 smit:SMT_1376|3end_tetrapyrrole_(corrin/porphyrin)_methylase_family_protein_1354675..1354825_NEGATIVE 192 106 76 151 120 smit:SMT_488|3end_dCMP_deaminase_423416..423566_POSITIVE 190 120 75 48 7 smit:SMT_1776|3end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_1751892..1752042_NEGATIVE 190 130 81 66 28 smit:SMT_1735|3end_K03596_GTP-binding_protein_LepA_1719549..1719699_POSITIVE 190 73 34 57 17 smit:SMT_544|3end_aminoglycoside_6-adenylyltransferase_461190..461340_POSITIVE 190 48 7 50 1 smit:SMT_410|3end_glucokinase_355477..355627_POSITIVE 189 132 99 149 112 smit:SMT_592|3end_amino_acid_ABC_transporter,_ATP-binding_protein_509468..509618_POSITIVE