Origin IGS: aatcgcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatagcgaatttctctaacttctgtcttttgtttttcttttctttctatgatacaatggaaaaaatgaattcaaaaggagtttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaaactccttttgaattcattttttccattgtatcatagaaagaaaagaaaaacaaaagacagaagttagagaaattcgctatgttggcgtttacttattaatggataaatgataaaataaacttgataaaaatatcacaaggaagcgatt Mask Tandem Repeat Region ================================================ aatcgcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatagcgaatttctctaacttctgtcttttgtttttcttttctttctatgatacaatggaaaaaatgaattcaaaaggagtttttt Find is-nt database================================================ Query_seq: SMT_1523:SMT_1524|SMT_1523:SMT_1524:ferrochelatase:peptidase T:<-->:1504551..1504703 153 aatcgcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatagcgaatttctctaacttctgtcttttgtttttcttttctttctatgatacaatggaaaaaatgaattcaaaaggagtttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1523:SMT_1524|SMT_1523:SMT_1524:ferrochelatase:peptidase T:<-->:1504551..1504703 153 aatcgcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatagcgaatttctctaacttctgtcttttgtttttcttttctttctatgatacaatggaaaaaatgaattcaaaaggagtttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1523:SMT_1524|SMT_1523:SMT_1524:ferrochelatase:peptidase T:<-->:1504551..1504703 153 aatcgcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatagcgaatttctctaacttctgtcttttgtttttcttttctttctatgatacaatggaaaaaatgaattcaaaaggagtttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatcgcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatagcgaatttctctaacttctgtcttttgtttttcttttctttctatgatacaatggaaaaaatgaattcaaaaggagtttttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 42 End: 137 ......................................... K D M L L Y V G V Y R I E R V E T K Q K E K R E I I C H F F H M ................ aatcgcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatagcgaatttctctaacttctgtcttttgtttttcttttctttctatgatacaatggaaaaaatgaattcaaaaggagtttttt 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: 33 End: 62 ................................GTTTACTTATTAATGGATAAATGATAAAAT........................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 95 End: 124 ..............................................................................................TTTGTTTTTCTTTTCTTTCTATGATACAAT............................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 115 End: 144 ..................................................................................................................CTTTTGAATTCATTTTTTCCATTGTATCAT......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatcgcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatagcgaatttctctaacttctgtcttttgtttttcttttctttctatgatacaatggaaaaaatgaattcaaaaggagtttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1523:SMT_1524|SMT_1523:SMT_1524:ferrochelatase:peptidase T:<-->:1504551..1504703 153 aatcgcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatagcgaatttctctaacttctgtcttttgtttttcttttctttctatgatacaatggaaaaaatgaattcaaaaggagtttttt Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: smit_SMT_1523_SMT_1524|ferrochelatase:peptidase T|NEGATIVE:POSITIVE|[1504551,1504703]|153 HSP 1 e-value: 8.0E-36 bit: 151.0 Len: 76 Query Start:1 Query End:76 Subject Strand: POSITIVE Subject Start: 1 Subject End: 76 aatcgcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatagcgaa............................................................................. aatcgcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatagcgaa............................................................................. HSP 2 e-value: 9.0E-14 bit: 77.8 Len: 39 Query Start:115 Query End:153 Subject Strand: POSITIVE Subject Start: 115 Subject End: 153 ..................................................................................................................atgatacaatggaaaaaatgaattcaaaaggagtttttt ..................................................................................................................atgatacaatggaaaaaatgaattcaaaaggagtttttt Inter-species Hit: Count: 3 Min: 5 Max: 153 Len: 149 Subject: NC_008533_SPD_0894_SPD_0895|peptidase T:ferrochelatase|NEGATIVE:POSITIVE|[909483,909636]|154 HSP 1 e-value: 1.0E-16 bit: 87.7 Len: 68 Query Start:5 Query End:72 Subject Strand: NEGATIVE Subject Start: 83 Subject End: 150 ....gcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatag................................................................................. ....gcttccttgtgatgtttttatcaagtttattttatcattaattcatcgataagtaaacgctaacatag................................................................................. HSP 2 e-value: 2.0E-11 bit: 69.9 Len: 39 Query Start:115 Query End:153 Subject Strand: NEGATIVE Subject Start: 2 Subject End: 40 ..................................................................................................................atgatacaatggaaaaaatgaattcaaaaggagtttttt ..................................................................................................................atgatacaatggaaaaaataaattcaaaaggagtttttt Subject: NC_003098_spr0913_spr0914|peptidase T:Ferrochelatase|NEGATIVE:POSITIVE|[901952,902105]|154 HSP 1 e-value: 1.0E-16 bit: 87.7 Len: 68 Query Start:5 Query End:72 Subject Strand: NEGATIVE Subject Start: 83 Subject End: 150 ....gcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgccaacatag................................................................................. ....gcttccttgtgatgtttttatcaagtttattttatcattaattcatcgataagtaaacgctaacatag................................................................................. HSP 2 e-value: 2.0E-11 bit: 69.9 Len: 39 Query Start:115 Query End:153 Subject Strand: NEGATIVE Subject Start: 2 Subject End: 40 ..................................................................................................................atgatacaatggaaaaaatgaattcaaaaggagtttttt ..................................................................................................................atgatacaatggaaaaaataaattcaaaaggagtttttt Subject: NC_003028_SP_1008_SP_1009|peptidase T:ferrochelatase|NEGATIVE:POSITIVE|[953695,953848]|154 HSP 1 e-value: 2.0E-14 bit: 79.8 Len: 60 Query Start:5 Query End:64 Subject Strand: NEGATIVE Subject Start: 91 Subject End: 150 ....gcttccttgtgatatttttatcaagtttattttatcatttatccattaataagtaaacgc......................................................................................... ....gcttccttgtgatgtttttatcaagtttattttatcattaattcatcgataagtaaacgc......................................................................................... HSP 2 e-value: 2.0E-11 bit: 69.9 Len: 39 Query Start:115 Query End:153 Subject Strand: NEGATIVE Subject Start: 2 Subject End: 40 ..................................................................................................................atgatacaatggaaaaaatgaattcaaaaggagtttttt ..................................................................................................................atgatacaatggaaaaaataaattcaaaaggagtttttt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUCCUUGUGAUAUUUUUAUCAAGUUUAUUUUAUCAUUUAUCCAUUAAUAAGUAAACGCCAACAUAGCGAAUUUCUCUAACUUCUGUCUUUUGUUUUUCUUUUCUUUCUAUGAUACAAUGGAAAAAAUGAAUUCAAAAGGAGUUUUUU (((...(((.((((....))))..((((((((..................))))))))..)))...)))..........(((((((....((((...(((.(((.(((((((......)))))))))).)))..))))))))))).... (-22.67) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAACUCCUUUUGAAUUCAUUUUUUCCAUUGUAUCAUAGAAAGAAAAGAAAAACAAAAGACAGAAGUUAGAGAAAUUCGCUAUGUUGGCGUUUACUUAUUAAUGGAUAAAUGAUAAAAUAAACUUGAUAAAAAUAUCACAAGGAAGC .......(((((......((((((..(((((((...........................(((....))).(((.((..((((.....)))).)).)))..))))))).))))))...........(((((....))))).)))))... (-21.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 816 90 41 185 136 smit:SMT_1523|5end_ferrochelatase_1504460..1504690_NEGATIVE 290 109 69 206 164 smit:SMT_895|5end_cysteinyl-tRNA_synthetase_843037..843267_NEGATIVE 261 109 64 74 28 smit:SMT_2150|5end_threonyl-tRNA_synthetase_2024673..2024903_POSITIVE 261 109 64 74 28 smit:SMT_2146|5end_threonyl-tRNA_synthetase_2022048..2022278_POSITIVE 253 95 58 217 173 smit:SMT_1719|5end_DNA_mismatch_repair_protein_1706842..1707072_NEGATIVE 243 50 2 122 64 smit:SMT_1318|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1283511..1283741_POSITIVE 243 96 64 175 138 smit:SMT_380|5end_hypothetical_protein_316376..316606_POSITIVE 243 96 64 175 138 smit:SMT_371|5end_hypothetical_protein_305248..305478_POSITIVE 242 110 63 135 88 smit:SMT_1137|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1079267..1079497_NEGATIVE 241 46 1 157 113 smit:SMT_397|5end_NAD(+)_synthetase_326519..326749_POSITIVE 241 98 59 206 158 smit:SMT_308|5end_trans-2-enoyl-ACP_reductase_II_249439..249669_POSITIVE 235 58 12 128 90 smit:SMT_1498|5end_transcriptional_regulator,_LytR_family_1481958..1482188_POSITIVE 227 104 61 229 180 smit:SMT_730|5end_hypothetical_protein_638387..638617_NEGATIVE 226 99 58 147 104 smit:SMT_378|5end_hypothetical_protein_predicted_by_Glimmer/Critica_315884..316114_POSITIVE 222 87 58 185 159 smit:SMT_1021|5end_K05846_osmoprotectant_transport_system_permease_protein_957999..958229_NEGATIVE 219 100 55 114 84 smit:SMT_1093|5end_K03073_preprotein_translocase_SecE_subunit_1033926..1034156_NEGATIVE 217 100 58 124 83 smit:SMT_1636|5end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1622568..1622798_POSITIVE 215 70 24 50 5 smit:SMT_1226|5end_ribosomal_protein_S9_1188737..1188967_POSITIVE 215 99 57 56 8 smit:SMT_1004|5end_thioredoxin_945430..945660_POSITIVE 214 110 68 120 57 smit:SMT_495|5end_bacterial_peptide_chain_release_factor_2_(RF-2)_429038..429268_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 104 67 91 53 smit:SMT_1412|3end_hypothetical_protein_1396411..1396561_POSITIVE 290 109 69 124 82 smit:SMT_896|3end_hypothetical_protein_843119..843269_NEGATIVE 261 109 64 55 9 smit:SMT_2149|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2024734..2024884_POSITIVE 251 103 67 70 32 smit:SMT_184|3end_30S_ribosomal_protein_S8_121891..122041_POSITIVE 243 50 2 118 60 smit:SMT_1317|3end_glycosyltransferase_1283587..1283737_POSITIVE 242 110 63 133 86 smit:SMT_1138|3end_hypothetical_protein_1079269..1079419_NEGATIVE 241 98 59 88 40 smit:SMT_307|3end_K02078_acyl_carrier_protein_249401..249551_POSITIVE 235 58 12 120 82 smit:SMT_1497|3end_acetyltransferase,_GNAT_family_1482030..1482180_POSITIVE 229 33 1 150 116 smit:SMT_396|3end_putative_nicotinate_phosphoribosyltransferase_326602..326752_POSITIVE 219 115 72 144 93 smit:SMT_1554|3end_isoleucyl-tRNA_synthetase_1539912..1540062_POSITIVE 217 100 58 112 71 smit:SMT_1635|3end_putative_N-acetyldiaminopimelate_deacetylase_1622636..1622786_POSITIVE 216 79 31 58 1 smit:SMT_1441|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1424887..1425037_NEGATIVE 214 101 64 128 96 smit:SMT_414|3end_K03665_GTP-binding_protein_HflX_358872..359022_POSITIVE 211 79 34 104 62 smit:SMT_1657|3end_glutamine-binding_protein_/_glutamine_transport_system_permease_protein_GlnP_1645912..1646062_NEGATIVE 211 122 86 68 22 smit:SMT_1153|3end_alpha-mannosidase_1097383..1097533_NEGATIVE 210 93 56 134 105 smit:SMT_2023|3end_tryptophan_synthase,_alpha_subunit_1939997..1940147_POSITIVE 208 38 1 65 26 smit:SMT_1662|3end_histidine_protein_kinase_1651305..1651455_NEGATIVE 208 124 83 50 7 smit:SMT_858|3end_triosephosphate_isomerase_802525..802675_NEGATIVE 208 93 61 90 51 smit:SMT_695|3end_heat_shock_protein_HtpX_605984..606134_NEGATIVE 208 110 68 109 70 smit:SMT_522|3end_K02003_447500..447650_POSITIVE