Origin IGS: aaaattcaaaatcagaagaggtttggtattccagcctctttttgacttctgctatcattttataataaagatgttgatcgttccataacctaatctttcattttacagacgaatcttacatttttgtaagattgtaaattttagctatttcagcttcatttgatattcctttgaaatatccatcaagaaattccaaaaattatgaaaaacaatctttttattacttattatatgcgaaaaggagcctgaaatgaaatctcagactcctttttct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaaaaaggagtctgagatttcatttcaggctccttttcgcatataataagtaataaaaagattgtttttcataatttttggaatttcttgatggatatttcaaaggaatatcaaatgaagctgaaatagctaaaatttacaatcttacaaaaatgtaagattcgtctgtaaaatgaaagattaggttatggaacgatcaacatctttattataaaatgatagcagaagtcaaaaagaggctggaataccaaacctcttctgattttgaatttt Mask Tandem Repeat Region ================================================ aaaattcaaaatcagaagaggtttggtattccagcctctttttgacttctgctatcattttataataaagatgttgatcgttccataacctaatctttcattttacagacgaatcttacatttttgtaagattgtaaattttagctatttcagcttcatttgatattcctttgaaatatccatcaagaaattccaaaaattatgaaaaacaatctttttattacttattatatgcgaaaaggagcctgaaatgaaatctcagactcctttttct Find is-nt database================================================ Query_seq: SSA_1533:SSA_1535|SSA_1533:SSA_1535:Glutathione reductase, putative:hypothetical protein:-><-:1542273..1542546 274 aaaattcaaaatcagaagaggtttggtattccagcctctttttgacttctgctatcattttataataaagatgttgatcgttccataacctaatctttcattttacagacgaatcttacatttttgtaagattgtaaattttagctatttcagcttcatttgatattcctttgaaatatccatcaagaaattccaaaaattatgaaaaacaatctttttattacttattatatgcgaaaaggagcctgaaatgaaatctcagactcctttttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1533:SSA_1535|SSA_1533:SSA_1535:Glutathione reductase, putative:hypothetical protein:-><-:1542273..1542546 274 aaaattcaaaatcagaagaggtttggtattccagcctctttttgacttctgctatcattttataataaagatgttgatcgttccataacctaatctttcattttacagacgaatcttacatttttgtaagattgtaaattttagctatttcagcttcatttgatattcctttgaaatatccatcaagaaattccaaaaattatgaaaaacaatctttttattacttattatatgcgaaaaggagcctgaaatgaaatctcagactcctttttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1533:SSA_1535|SSA_1533:SSA_1535:Glutathione reductase, putative:hypothetical protein:-><-:1542273..1542546 274 aaaattcaaaatcagaagaggtttggtattccagcctctttttgacttctgctatcattttataataaagatgttgatcgttccataacctaatctttcattttacagacgaatcttacatttttgtaagattgtaaattttagctatttcagcttcatttgatattcctttgaaatatccatcaagaaattccaaaaattatgaaaaacaatctttttattacttattatatgcgaaaaggagcctgaaatgaaatctcagactcctttttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaattcaaaatcagaagaggtttggtattccagcctctttttgacttctgctatcattttataataaagatgttgatcgttccataacctaatctttcattttacagacgaatcttacatttttgtaagattgtaaattttagctatttcagcttcatttgatattcctttgaaatatccatcaagaaattccaaaaattatgaaaaacaatctttttattacttattatatgcgaaaaggagcctgaaatgaaatctcagactcctttttct Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 138 End: 251 ......................................................................................................................................... M L A I S A S F D I P L K Y P S R N S K N Y E K Q S F Y Y L L Y A K R S L K ....................... Protein_Len: 35 Strand: - Start: 148 End: 252 ................................................................................................................................................... K L K M Q Y E K S I D M L F N W F N H F V I K K N S I I H S F S G S M ...................... Protein_Len: 31 Strand: - Start: 2 End: 94 . F E F D S S T Q Y E L R K K V E A I M K Y Y L H Q D N W L R M .................................................................................................................................................................................... aaaattcaaaatcagaagaggtttggtattccagcctctttttgacttctgctatcattttataataaagatgttgatcgttccataacctaatctttcattttacagacgaatcttacatttttgtaagattgtaaattttagctatttcagcttcatttgatattcctttgaaatatccatcaagaaattccaaaaattatgaaaaacaatctttttattacttattatatgcgaaaaggagcctgaaatgaaatctcagactcctttttct 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: 227 End: 256 ..................................................................................................................................................................................................................................TTTCATTTCAGGCTCCTTTTCGCATATAAT.................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaattcaaaatcagaagaggtttggtattccagcctctttttgacttctgctatcattttataataaagatgttgatcgttccataacctaatctttcattttacagacgaatcttacatttttgtaagattgtaaattttagctatttcagcttcatttgatattcctttgaaatatccatcaagaaattccaaaaattatgaaaaacaatctttttattacttattatatgcgaaaaggagcctgaaatgaaatctcagactcctttttct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1533:SSA_1535|SSA_1533:SSA_1535:Glutathione reductase, putative:hypothetical protein:-><-:1542273..1542546 274 aaaattcaaaatcagaagaggtttggtattccagcctctttttgacttctgctatcattttataataaagatgttgatcgttccataacctaatctttcattttacagacgaatcttacatttttgtaagattgtaaattttagctatttcagcttcatttgatattcctttgaaatatccatcaagaaattccaaaaattatgaaaaacaatctttttattacttattatatgcgaaaaggagcctgaaatgaaatctcagactcctttttct Intra-Species Hit: Count: 1 Min: 1 Max: 274 Len: 274 Subject: NC_009009_SSA_1533_SSA_1535|Glutathione reductase, putative:hypothetical protein|POSITIVE:NEGATIVE|[1542273,1542546]|274 HSP 1 e-value: 1.0E-153 bit: 543.0 Len: 274 Query Start:1 Query End:274 Subject Strand: POSITIVE Subject Start: 1 Subject End: 274 aaaattcaaaatcagaagaggtttggtattccagcctctttttgacttctgctatcattttataataaagatgttgatcgttccataacctaatctttcattttacagacgaatcttacatttttgtaagattgtaaattttagctatttcagcttcatttgatattcctttgaaatatccatcaagaaattccaaaaattatgaaaaacaatctttttattacttattatatgcgaaaaggagcctgaaatgaaatctcagactcctttttct aaaattcaaaatcagaagaggtttggtattccagcctctttttgacttctgctatcattttataataaagatgttgatcgttccataacctaatctttcattttacagacgaatcttacatttttgtaagattgtaaattttagctatttcagcttcatttgatattcctttgaaatatccatcaagaaattccaaaaattatgaaaaacaatctttttattacttattatatgcgaaaaggagcctgaaatgaaatctcagactcctttttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUCAAAAUCAGAAGAGGUUUGGUAUUCCAGCCUCUUUUUGACUUCUGCUAUCAUUUUAUAAUAAAGAUGUUGAUCGUUCCAUAACCUAAUCUUUCAUUUUACAGACGAAUCUUACAUUUUUGUAAGAUUGUAAAUUUUAGCUAUUUCAGCUUCAUUUGAUAUUCCUUUGAAAUAUCCAUCAAGAAAUUCCAAAAAUUAUGAAAAACAAUCUUUUUAUUACUUAUUAUAUGCGAAAAGGAGCCUGAAAUGAAAUCUCAGACUCCUUUUUCU ...........((((((((((((.((....)))))))).)))))).................(((((((((.((((....((.(((((.............((((((.....((((((((....))))))))))))))....((((.....))))...((((..(((..(((((........))))).)))..))))..))))).))..)))).)))))))))............(((((((((.((((.........)))).))))))))).. (-53.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAAAGGAGUCUGAGAUUUCAUUUCAGGCUCCUUUUCGCAUAUAAUAAGUAAUAAAAAGAUUGUUUUUCAUAAUUUUUGGAAUUUCUUGAUGGAUAUUUCAAAGGAAUAUCAAAUGAAGCUGAAAUAGCUAAAAUUUACAAUCUUACAAAAAUGUAAGAUUCGUCUGUAAAAUGAAAGAUUAGGUUAUGGAACGAUCAACAUCUUUAUUAUAAAAUGAUAGCAGAAGUCAAAAAGAGGCUGGAAUACCAAACCUCUUCUGAUUUUGAAUUUU ...((((((((((((((((...)))))))))))))))).((.(((.....((((((((..((((((..((((((((((......((((......(((((((.....)))))))......(((((...)))))....((((((((((((((....)))))))).....))))))..))))....))))))))))))))))......))))))))......))))).(((((((..((((((.(((....)))..)))))).)))))))....... (-70.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 443 127 81 197 151 NC_009009:SSA_1660|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1657580..1657810_NEGATIVE 389 58 11 61 9 NC_009009:SSA_1299|5end_Maltose/maltodextrin_ABC_transport_system,_putative_1316629..1316859_POSITIVE 329 127 83 193 148 NC_009009:SSA_1682|5end_hypothetical_protein_1676885..1677115_NEGATIVE 310 135 93 141 98 NC_009009:SSA_1656|5end_Nisin_resistance_protein,_putative_1652890..1653120_NEGATIVE 310 57 11 116 72 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 285 57 11 132 72 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 284 53 19 193 154 NC_009009:SSA_1893|5end_N-acetylglucosamine-6-phosphate_deacetylase,_putative_1890572..1890802_NEGATIVE 282 185 141 196 152 NC_009009:SSA_1279|5end_Oxidoreductase,_putative_1300832..1301062_NEGATIVE 282 49 5 108 54 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 280 60 18 169 129 NC_009009:SSA_1260|5end_Phosphopentomutase,_putative_1286963..1287193_NEGATIVE 279 60 11 93 44 NC_009009:SSA_1541|5end_Peptidase,_U32_family,_putative_1546600..1546830_NEGATIVE 279 59 11 171 108 NC_009009:SSA_1420|5end_Homoserine_O-succinyltransferase,_putative_1430625..1430855_NEGATIVE 278 59 17 159 121 NC_009009:SSA_2006|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme,_putative_2007215..2007445_NEGATIVE 273 79 31 41 1 NC_009009:SSA_0283|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIB_component,_putative_274559..274789_POSITIVE 267 127 83 117 73 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 267 57 21 63 31 NC_009009:SSA_0781|5end_Mannose-6-phosphate_isomerase,_putative_765373..765603_POSITIVE 266 57 13 81 26 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 262 269 228 141 88 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 260 188 144 95 56 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 260 60 14 207 136 NC_009009:SSA_0151|5end_hypothetical_protein_145354..145584_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 130 83 78 31 NC_009009:SSA_1682|3end_hypothetical_protein_1676130..1676280_NEGATIVE 356 50 1 108 50 NC_009009:SSA_0798|3end_ABC_transporter_membrane-spanning_permease-macrolide_efflux,_putative_781724..781874_POSITIVE 319 47 6 135 101 NC_009009:SSA_1573|3end_hypothetical_protein_1576054..1576204_NEGATIVE 310 135 93 69 26 NC_009009:SSA_1657|3end_hypothetical_protein_1652962..1653112_NEGATIVE 290 270 233 86 47 NC_009009:SSA_0688|3end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_672132..672282_POSITIVE 282 49 5 97 43 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 269 127 85 44 1 NC_009009:SSA_1683|3end_NrdI_protein,_putative_1677034..1677184_NEGATIVE 267 50 4 151 97 NC_009009:SSA_0454|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_456050..456200_NEGATIVE 266 57 13 84 29 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE 262 269 228 88 35 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 259 57 19 52 4 NC_009009:SSA_2117|3end_DNA_recombination_protein_RmuC,_putative_2118556..2118706_NEGATIVE 256 55 13 86 48 NC_009009:SSA_2108|3end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2111457..2111607_NEGATIVE 255 53 16 83 39 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 252 43 14 56 33 NC_009009:SSA_2170|3end_hypothetical_protein_2169557..2169707_NEGATIVE 252 53 12 143 102 NC_009009:SSA_1365|3end_FmtA-like_protein,_putative_1381352..1381502_NEGATIVE 250 246 214 69 36 NC_009009:SSA_1482|3end_Pullulanase,_putative_1486949..1487099_NEGATIVE 246 48 1 116 64 NC_009009:SSA_0989|3end_Conserved_protein,_possible_transcriptional_regulator_(sigma-70,_region_4),_putative_991816..991966_POSITIVE 244 54 11 131 90 NC_009009:SSA_1140|3end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1169207..1169357_POSITIVE 244 55 13 87 36 NC_009009:SSA_0157|3end_hypothetical_protein_153877..154027_POSITIVE 241 53 12 100 58 NC_009009:SSA_1729|3end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1714539..1714689_NEGATIVE