Origin IGS: tttattttacctcattcattattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaagatttttttagaataaaacctagtcactttcaaactctcttaacagctataaaataaagaaaaagagtatacaatttgtaggctcttttctcattttacatc .........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 gatgtaaaatgagaaaagagcctacaaattgtatactctttttctttattttatagctgttaagagagtttgaaagtgactaggttttattctaaaaaaatcttaaattatcagtctattgcaacttttctcatgtgagtcatttggcttgctattggttttccttagtagtatactaaggtagtaatcattaagaagtggttacaaataataatgaatgaggtaaaataaa Mask Tandem Repeat Region ================================================ tttattttacctcattcattattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaagatttttttagaataaaacctagtcactttcaaactctcttaacagctataaaataaagaaaaagagtatacaatttgtaggctcttttctcattttacatc Find is-nt database================================================ Query_seq: SMT_856:SMT_857|SMT_856:SMT_857:peroxide resistance protein,non-heme iron-containing ferritin:endo-beta-N-acetylglucosaminidase:<-<-:800739..800970 232 tttattttacctcattcattattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaagatttttttagaataaaacctagtcactttcaaactctcttaacagctataaaataaagaaaaagagtatacaatttgtaggctcttttctcattttacatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_856:SMT_857|SMT_856:SMT_857:peroxide resistance protein,non-heme iron-containing ferritin:endo-beta-N-acetylglucosaminidase:<-<-:800739..800970 232 tttattttacctcattcattattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaagatttttttagaataaaacctagtcactttcaaactctcttaacagctataaaataaagaaaaagagtatacaatttgtaggctcttttctcattttacatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_856:SMT_857|SMT_856:SMT_857:peroxide resistance protein,non-heme iron-containing ferritin:endo-beta-N-acetylglucosaminidase:<-<-:800739..800970 232 tttattttacctcattcattattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaagatttttttagaataaaacctagtcactttcaaactctcttaacagctataaaataaagaaaaagagtatacaatttgtaggctcttttctcattttacatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttattttacctcattcattattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaagatttttttagaataaaacctagtcactttcaaactctcttaacagctataaaataaagaaaaagagtatacaatttgtaggctcttttctcattttacatc Predict ORF larger than 30AA ================================================ tttattttacctcattcattattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaagatttttttagaataaaacctagtcactttcaaactctcttaacagctataaaataaagaaaaagagtatacaatttgtaggctcttttctcattttacatc 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: 83 Start: 56 End: 85 .......................................................CTTGCTATTGGTTTTCCTTAGTAGTATACT................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 4 End: 33 ...GGTTACAAATAATAATGAATGAGGTAAAAT....................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttattttacctcattcattattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaagatttttttagaataaaacctagtcactttcaaactctcttaacagctataaaataaagaaaaagagtatacaatttgtaggctcttttctcattttacatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_856:SMT_857|SMT_856:SMT_857:peroxide resistance protein,non-heme iron-containing ferritin:endo-beta-N-acetylglucosaminidase:<-<-:800739..800970 232 tttattttacctcattcattattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaagatttttttagaataaaacctagtcactttcaaactctcttaacagctataaaataaagaaaaagagtatacaatttgtaggctcttttctcattttacatc Intra-Species Hit: Count: 1 Min: 1 Max: 232 Len: 232 Subject: smit_SMT_856_SMT_857|peroxide resistance protein,non-heme iron-containing ferritin:endo-beta-N- acetylglucosaminidase|NEGATIVE:NEGATIVE|[800739, 800970]|232 HSP 1 e-value: 1.0E-116 bit: 418.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 tttattttacctcattcattattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaagannnnnnnagaataaaacctagtcactttcaaactctcttaacagctataaaataaagaaaaagagtatacaatttgtaggctcttttctcattttacatc tttattttacctcattcattattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaagatttttttagaataaaacctagtcactttcaaactctcttaacagctataaaataaagaaaaagagtatacaatttgtaggctcttttctcattttacatc Inter-species Hit: Count: 3 Min: 6 Max: 132 Len: 127 Subject: NC_008533_SPD_1402_SPD_1403|non-heme iron-containing ferritin:1,4-beta-N-acetylmuramidase, putative|NEGATIVE:NEGATIVE|[1421547,1422041]|495 HSP 1 e-value: 2.0E-49 bit: 196.0 Len: 127 Query Start:6 Query End:132 Subject Strand: POSITIVE Subject Start: 5 Subject End: 131 .....tttacctcattcattattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaaga.................................................................................................... .....tttacctcattcattattttttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagaaaaagaacttatatgagaaaagttgcaatagactgataatttaaga.................................................................................................... Subject: NC_003028_SP_1572_SP_1573|non-heme iron-containing ferritin:lysozyme|NEGATIVE:NEGATIVE|[1478590, 1479066]|477 HSP 1 e-value: 2.0E-43 bit: 176.0 Len: 113 Query Start:20 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 ...................tattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaaga.................................................................................................... ...................tattttttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagacaaagaacttatatgagaaaagttgcaatagactgataatttaaga.................................................................................................... Subject: NC_003098_spr1430_spr1431|DNA binding protein starved cells-like peroxide resistance protein:1, 4-beta-N-acetylmuramidase|NEGATIVE:NEGATIVE|[1414034, 1414510]|477 HSP 1 e-value: 5.0E-41 bit: 168.0 Len: 113 Query Start:20 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 ...................tattatttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagccaaatgactcacatgagaaaagttgcaatagactgataatttaaga.................................................................................................... ...................tattttttgtaaccacttcttaatgattactaccttagtatactactaaggaaaaccaatagcaagaaaaagaacttatatgagaaaagttgcaatagactgataatttaaga.................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACCUCAUUCAUUAUUAUUUGUAACCACUUCUUAAUGAUUACUACCUUAGUAUACUACUAAGGAAAACCAAUAGCAAGCCAAAUGACUCACAUGAGAAAAGUUGCAAUAGACUGAUAAUUUAAGA ............(((((((.(((((((...((((((.((.......((((((((...)))))))).........((((.......)).))..))))))))..))))))).....)))))))...... (-19.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUAAAUUAUCAGUCUAUUGCAACUUUUCUCAUGUGAGUCAUUUGGCUUGCUAUUGGUUUUCCUUAGUAGUAUACUAAGGUAGUAAUCAUUAAGAAGUGGUUACAAAUAAUAAUGAAUGAGGUAAA .......................(((((..(((((..((((....))))..)..........((((((((...))))))))..(((((((((....)))))))))........))))..)))))... (-28.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 840 100 51 196 147 smit:SMT_856|5end_peroxide_resistance_protein,non-heme_iron-containing_ferritin_800648..800878_NEGATIVE 295 99 51 206 144 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 247 56 14 132 85 smit:SMT_1384|5end_glutaredoxin_1362227..1362457_NEGATIVE 241 99 51 221 182 smit:SMT_324|5end_K02029_polar_amino_acid_transport_system_permease_protein_262070..262300_NEGATIVE 240 104 63 210 163 smit:SMT_1719|5end_DNA_mismatch_repair_protein_1706842..1707072_NEGATIVE 239 60 21 79 37 smit:SMT_1588|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1577062..1577292_POSITIVE 238 50 1 163 109 smit:SMT_721|5end_Tn5252,_relaxase_628754..628984_NEGATIVE 216 120 73 66 21 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 216 117 75 231 179 smit:SMT_150|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_98787..99017_POSITIVE 213 101 62 182 149 smit:SMT_434|5end_orotidine_5'-phosphate_decarboxylase_376107..376337_POSITIVE 211 82 63 100 79 smit:SMT_712|5end_alcohol_dehydrogenase,_zinc-containing_620381..620611_NEGATIVE 209 82 41 193 142 smit:SMT_623|5end_50S_ribosomal_protein_L21_529412..529642_POSITIVE 208 50 5 128 80 smit:SMT_1870|5end_K07566_putative_translation_factor_1829819..1830049_NEGATIVE 208 109 65 154 115 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 207 110 75 79 38 smit:SMT_1021|5end_K05846_osmoprotectant_transport_system_permease_protein_957999..958229_NEGATIVE 204 108 62 119 78 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 204 66 26 115 77 smit:SMT_1393|5end_hypothetical_protein_1369106..1369336_POSITIVE 204 49 20 103 81 smit:SMT_338|5end_heat-inducible_transcription_repressor_HrcA_276825..277055_POSITIVE 203 109 61 202 154 smit:SMT_1567|5end_transketolase,_N-terminal_subunit_1559268..1559498_POSITIVE 202 98 71 49 23 smit:SMT_741|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_645618..645848_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 99 51 44 5 smit:SMT_325|3end_K02029_polar_amino_acid_transport_system_permease_protein_262247..262397_NEGATIVE 240 119 75 151 97 smit:SMT_149|3end_hypothetical_protein_predicted_by_Glimmer/Critica_98785..98935_POSITIVE 239 60 21 55 13 smit:SMT_1587|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1577118..1577268_POSITIVE 216 120 73 79 34 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 209 82 41 142 91 smit:SMT_622|3end_methionine_aminopeptidase_529441..529591_POSITIVE 208 50 5 144 96 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 207 110 75 86 45 smit:SMT_1022|3end_glycine_betaine_transport_ATP-binding_protein_957992..958142_NEGATIVE 206 82 43 75 38 smit:SMT_1682|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_1666373..1666523_POSITIVE 204 66 26 115 77 smit:SMT_1392|3end_dihydroxyacetone_kinase_1369186..1369336_POSITIVE 201 109 74 138 92 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 199 116 75 55 24 smit:SMT_1322|3end_K02075_zinc/manganese_transport_system_permease_protein_1292257..1292407_POSITIVE 196 83 46 40 1 smit:SMT_2067|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1974216..1974366_POSITIVE 195 103 63 136 81 smit:SMT_1857|3end_hypothetical_protein_1821145..1821295_POSITIVE 193 114 82 38 3 smit:SMT_1897|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1848766..1848916_NEGATIVE 193 101 62 145 108 smit:SMT_330|3end_membrane-associated_phospholipid_phosphatase_266187..266337_POSITIVE 191 52 21 70 32 smit:SMT_1251|3end_hypothetical_protein_1211329..1211479_NEGATIVE 187 49 13 69 26 smit:SMT_2050|3end_K03712_MarR_family_transcriptional_regulator_1959539..1959689_NEGATIVE 187 90 43 136 87 smit:SMT_1259|3end_hypothetical_protein_1225578..1225728_POSITIVE 187 119 76 138 104 smit:SMT_1121|3end_hypothetical_protein_1057105..1057255_NEGATIVE 182 96 51 109 59 smit:SMT_1900|3end_K03710_GntR_family_transcriptional_regulator_1850620..1850770_POSITIVE