Origin IGS: cttgcatcctcgctgaactttctatcattagtataacaaaaatcgctgcaagaatacagtgtctaagcctttctttgatgtttagattttcttcattcgcttgtaatcgttttgcgattattatataatcaaagcgtacgatttaaaaaataaaaagtaaaaattctttagctagtttacagaaaatttggcttgctttttacttttttgcaaaaggagaatcctatt .........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 aataggattctccttttgcaaaaaagtaaaaagcaagccaaattttctgtaaactagctaaagaatttttactttttattttttaaatcgtacgctttgattatataataatcgcaaaacgattacaagcgaatgaagaaaatctaaacatcaaagaaaggcttagacactgtattcttgcagcgatttttgttatactaatgatagaaagttcagcgaggatgcaag Mask Tandem Repeat Region ================================================ cttgcatcctcgctgaactttctatcattagtataacaaaaatcgctgcaagaatacagtgtctaagcctttctttgatgtttagattttcttcattcgcttgtaatcgttttgcgattattatataatcaaagcgtacgatttaaaaaataaaaagtaaaaattctttagctagtttacagaaaatttggcttgctttttacttttttgcaaaaggagaatcctatt Find is-nt database================================================ Query_seq: SSA_0256:SSA_0257|SSA_0256:SSA_0257:Metalloregulator ScaR (Fe/Mn-dependent transcriptional repressor), putative:N-acetylmuramidase/lysin, putative:<-->:248790..249017 228 cttgcatcctcgctgaactttctatcattagtataacaaaaatcgctgcaagaatacagtgtctaagcctttctttgatgtttagattttcttcattcgcttgtaatcgttttgcgattattatataatcaaagcgtacgatttaaaaaataaaaagtaaaaattctttagctagtttacagaaaatttggcttgctttttacttttttgcaaaaggagaatcctatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0256:SSA_0257|SSA_0256:SSA_0257:Metalloregulator ScaR (Fe/Mn-dependent transcriptional repressor), putative:N-acetylmuramidase/lysin, putative:<-->:248790..249017 228 cttgcatcctcgctgaactttctatcattagtataacaaaaatcgctgcaagaatacagtgtctaagcctttctttgatgtttagattttcttcattcgcttgtaatcgttttgcgattattatataatcaaagcgtacgatttaaaaaataaaaagtaaaaattctttagctagtttacagaaaatttggcttgctttttacttttttgcaaaaggagaatcctatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0256:SSA_0257|SSA_0256:SSA_0257:Metalloregulator ScaR (Fe/Mn-dependent transcriptional repressor), putative:N-acetylmuramidase/lysin, putative:<-->:248790..249017 228 cttgcatcctcgctgaactttctatcattagtataacaaaaatcgctgcaagaatacagtgtctaagcctttctttgatgtttagattttcttcattcgcttgtaatcgttttgcgattattatataatcaaagcgtacgatttaaaaaataaaaagtaaaaattctttagctagtttacagaaaatttggcttgctttttacttttttgcaaaaggagaatcctatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttgcatcctcgctgaactttctatcattagtataacaaaaatcgctgcaagaatacagtgtctaagcctttctttgatgtttagattttcttcattcgcttgtaatcgttttgcgattattatataatcaaagcgtacgatttaaaaaataaaaagtaaaaattctttagctagtttacagaaaatttggcttgctttttacttttttgcaaaaggagaatcctatt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 6 End: 125 ..... M L A E L S I I S I T K I A A R I Q C L S L S L M F R F S S F A C N R F A I I I ....................................................................................................... Protein_Len: 47 Strand: - Start: 2 End: 142 . Q M R A S S E I M L I V F I A A L I C H R L R E K I N L N E E N A Q L R K A I I I Y D F R V M ...................................................................................... cttgcatcctcgctgaactttctatcattagtataacaaaaatcgctgcaagaatacagtgtctaagcctttctttgatgtttagattttcttcattcgcttgtaatcgttttgcgattattatataatcaaagcgtacgatttaaaaaataaaaagtaaaaattctttagctagtttacagaaaatttggcttgctttttacttttttgcaaaaggagaatcctatt 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: 100 End: 129 ...................................................................................................CTTGTAATCGTTTTGCGATTATTATATAAT................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 120 End: 149 .......................................................................................................................TTTTTAAATCGTACGCTTTGATTATATAAT............................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttgcatcctcgctgaactttctatcattagtataacaaaaatcgctgcaagaatacagtgtctaagcctttctttgatgtttagattttcttcattcgcttgtaatcgttttgcgattattatataatcaaagcgtacgatttaaaaaataaaaagtaaaaattctttagctagtttacagaaaatttggcttgctttttacttttttgcaaaaggagaatcctatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0256:SSA_0257|SSA_0256:SSA_0257:Metalloregulator ScaR (Fe/Mn-dependent transcriptional repressor), putative:N-acetylmuramidase/lysin, putative:<-->:248790..249017 228 cttgcatcctcgctgaactttctatcattagtataacaaaaatcgctgcaagaatacagtgtctaagcctttctttgatgtttagattttcttcattcgcttgtaatcgttttgcgattattatataatcaaagcgtacgatttaaaaaataaaaagtaaaaattctttagctagtttacagaaaatttggcttgctttttacttttttgcaaaaggagaatcctatt Intra-Species Hit: Count: 1 Min: 1 Max: 196 Len: 196 Subject: NC_009009_SSA_0256_SSA_0257|Metalloregulator ScaR (Fe/Mn-dependent transcriptional repressor), putative:N-acetylmuramidase/lysin, putative|NEGATIVE:POSITIVE|[248790,249017]|228 HSP 1 e-value: 3.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 cttgcatcctcgctgaactttctatcattagtataacaaaaatcgctgcaagaatacagtgtctaagcctttctttgatgtttagattttcttcattcgcttgtaatcgttttgcgattattatataatcaaagcgtacgattt.................................................................................... cttgcatcctcgctgaactttctatcattagtataacaaaaatcgctgcaagaatacagtgtctaagcctttctttgatgtttagattttcttcattcgcttgtaatcgttttgcgattattatataatcaaagcgtacgattt.................................................................................... HSP 2 e-value: 6.0E-10 bit: 65.9 Len: 33 Query Start:164 Query End:196 Subject Strand: POSITIVE Subject Start: 164 Subject End: 196 ...................................................................................................................................................................ttctttagctagtttacagaaaatttggcttgc................................ ...................................................................................................................................................................ttctttagctagtttacagaaaatttggcttgc................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGCAUCCUCGCUGAACUUUCUAUCAUUAGUAUAACAAAAAUCGCUGCAAGAAUACAGUGUCUAAGCCUUUCUUUGAUGUUUAGAUUUUCUUCAUUCGCUUGUAAUCGUUUUGCGAUUAUUAUAUAAUCAAAGCGUACGAUUUAAAAAAUAAAAAGUAAAAAUUCUUUAGCUAGUUUACAGAAAAUUUGGCUUGC ...........((..((.(((((...((((((.......((((((.(((..((((..((.((((((((.((.....)).))))))))...))..))))....(((((((.....)))))))..............))))))))).........((((........)))).))))))....))))).))..)).... (-37.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAGCCAAAUUUUCUGUAAACUAGCUAAAGAAUUUUUACUUUUUAUUUUUUAAAUCGUACGCUUUGAUUAUAUAAUAAUCGCAAAACGAUUACAAGCGAAUGAAGAAAAUCUAAACAUCAAAGAAAGGCUUAGACACUGUAUUCUUGCAGCGAUUUUUGUUAUACUAAUGAUAGAAAGUUCAGCGAGGAUGCAAG ..(((((....(((((..........((((((((...........))))))))..((((.(((((.(.........((((((.....)))))))))))).))))..................))))))))))......(((((((((((.....((((((((((....)))))))))).....))))))))))).. (-40.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 860 50 1 141 92 NC_009009:SSA_0256|5end_Metalloregulator_ScaR_(Fe/Mn-dependent_transcriptional_repressor),_putative_248699..248929_NEGATIVE 304 50 1 143 85 NC_009009:SSA_0448|5end_Excinuclease_ATPase_subunit_A,_putative_446480..446710_POSITIVE 282 99 56 182 134 NC_009009:SSA_2222|5end_Tyrosine-protein_kinase_Wze,_putative_2223997..2224227_NEGATIVE 274 49 4 140 98 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 271 50 5 229 188 NC_009009:SSA_2279|5end_hypothetical_protein_2281910..2282140_NEGATIVE 263 110 63 81 39 NC_009009:SSA_1152|5end_Protein_chain_release_factor_A,_putative_1180759..1180989_POSITIVE 260 76 32 86 35 NC_009009:SSA_1644|5end_hypothetical_protein_1645617..1645847_NEGATIVE 257 80 36 71 33 NC_009009:SSA_2381|5end_DegP_protein,_putative_2386298..2386528_POSITIVE 252 89 42 74 26 NC_009009:SSA_0522|5end_Ethanolamine_utilization_protein,_putative_521067..521297_POSITIVE 251 81 41 112 64 NC_009009:SSA_1411|5end_Glucose-1-phosphate_thymidylytransferase,_putative_1423960..1424190_NEGATIVE 250 118 72 54 3 NC_009009:SSA_0148|5end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_142257..142487_POSITIVE 249 100 58 38 3 NC_009009:SSA_0922|5end_hypothetical_protein_932950..933180_NEGATIVE 247 100 58 222 182 NC_009009:SSA_1250|5end_Conserved_uncharacterized_protein,_putative_1274512..1274742_NEGATIVE 245 50 1 67 13 NC_009009:SSA_0932|5end_hypothetical_protein_941453..941683_POSITIVE 245 97 66 103 62 NC_009009:SSA_0103|5end_Integral_membrane_protein,_putative_105490..105720_NEGATIVE 243 109 62 71 18 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 242 73 40 44 15 NC_009009:SSA_0049|5end_Dihydroxyacetone_kinase_(Dak1),_putative_53612..53842_POSITIVE 239 100 59 46 4 NC_009009:SSA_0199|5end_GTP_cyclohydrolase_I,_putative_198276..198506_POSITIVE 238 48 7 135 95 NC_009009:SSA_1851|5end_Guanylate_kinase,_putative_1846682..1846912_NEGATIVE 235 50 1 129 85 NC_009009:SSA_1719|5end_Conserved_uncharacterized_protein_1706793..1707023_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 80 36 142 102 NC_009009:SSA_1094|3end_GTP-binding_protein,_putative_1112243..1112393_POSITIVE 274 49 4 150 108 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 268 49 4 70 26 NC_009009:SSA_2329|3end_hypothetical_protein_2333169..2333319_POSITIVE 263 110 63 44 2 NC_009009:SSA_1151|3end_Thymidine_kinase,_putative_1180802..1180952_POSITIVE 260 76 32 102 51 NC_009009:SSA_1645|3end_hypothetical_protein_1645601..1645751_NEGATIVE 252 89 42 58 10 NC_009009:SSA_0521|3end_Ethanolamine_utilization_protein_EutL,_putative_521131..521281_POSITIVE 251 81 41 78 30 NC_009009:SSA_1412|3end_hypothetical_protein_1423994..1424144_NEGATIVE 239 100 59 65 23 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 238 49 6 149 114 NC_009009:SSA_2327|3end_hypothetical_protein_2331400..2331550_POSITIVE 235 50 1 126 82 NC_009009:SSA_1720|3end_Initiation-control_protein,_putative_1706796..1706946_NEGATIVE 235 79 37 88 56 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 234 97 61 80 44 NC_009009:SSA_2040|3end_ABC_transporter_ATP-binding_protein-multiple_sugar_transport,_putative_2044568..2044718_NEGATIVE 233 109 65 117 70 NC_009009:SSA_1930|3end_Acetyl-CoA_carboxylase_alpha_subunit,_putative_1917777..1917927_NEGATIVE 232 102 62 47 10 NC_009009:SSA_1576|3end_Catabolite_control_protein_A,_putative_1579177..1579327_NEGATIVE 230 82 42 66 31 NC_009009:SSA_0836|3end_SecA-like_protein,_putative_823969..824119_POSITIVE 230 95 51 121 72 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 229 33 4 145 119 NC_009009:SSA_0770|3end_Ribonucleoside-diphosphate_reductase,_putative_749252..749402_NEGATIVE 228 87 42 96 50 NC_009009:SSA_1563|3end_Metal-dependent_hydrolase,_beta-lactamase_superfamily_I,_putative_1566456..1566606_NEGATIVE 224 90 46 91 40 NC_009009:SSA_2146|3end_Metallo-beta-lactamase,_putative_2146732..2146882_NEGATIVE 223 49 6 142 93 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE