Origin IGS: gacttccctttccagttgagaatttcagaataaatttcttttttcttgtttctctaacattgactatctttgactaatattataccggaaaagtctctattttgaaagaaaaagggatgactgaaaggtctgataattcaaactagtgaaaaagctttgtcaggcttatgtaacctcttgctttttgcttttaaagcgttataatataggtggaaatccacaaggaaaagacagacagaaactcctgcctgccaactatcatctaaacaaggaggataatcca .........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 tggattatcctccttgtttagatgatagttggcaggcaggagtttctgtctgtcttttccttgtggatttccacctatattataacgctttaaaagcaaaaagcaagaggttacataagcctgacaaagctttttcactagtttgaattatcagacctttcagtcatccctttttctttcaaaatagagacttttccggtataatattagtcaaagatagtcaatgttagagaaacaagaaaaaagaaatttattctgaaattctcaactggaaagggaagtc Mask Tandem Repeat Region ================================================ gacttccctttccagttgagaatttcagaataaatttcttttttcttgtttctctaacattgactatctttgactaatattataccggaaaagtctctattttgaaagaaaaagggatgactgaaaggtctgataattcaaactagtgaaaaagctttgtcaggcttatgtaacctcttgctttttgcttttaaagcgttataatataggtggaaatccacaaggaaaagacagacagaaactcctgcctgccaactatcatctaaacaaggaggataatcca Find is-nt database================================================ Query_seq: SSA_2200:SSA_2201|SSA_2200:SSA_2201:Firmicutes transcriptional repressor of class III stress genes (CtsR), putative:hypothetical protein:<-->:2201664..2201946 283 gacttccctttccagttgagaatttcagaataaatttcttttttcttgtttctctaacattgactatctttgactaatattataccggaaaagtctctattttgaaagaaaaagggatgactgaaaggtctgataattcaaactagtgaaaaagctttgtcaggcttatgtaacctcttgctttttgcttttaaagcgttataatataggtggaaatccacaaggaaaagacagacagaaactcctgcctgccaactatcatctaaacaaggaggataatcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2200:SSA_2201|SSA_2200:SSA_2201:Firmicutes transcriptional repressor of class III stress genes (CtsR), putative:hypothetical protein:<-->:2201664..2201946 283 gacttccctttccagttgagaatttcagaataaatttcttttttcttgtttctctaacattgactatctttgactaatattataccggaaaagtctctattttgaaagaaaaagggatgactgaaaggtctgataattcaaactagtgaaaaagctttgtcaggcttatgtaacctcttgctttttgcttttaaagcgttataatataggtggaaatccacaaggaaaagacagacagaaactcctgcctgccaactatcatctaaacaaggaggataatcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2200:SSA_2201|SSA_2200:SSA_2201:Firmicutes transcriptional repressor of class III stress genes (CtsR), putative:hypothetical protein:<-->:2201664..2201946 283 gacttccctttccagttgagaatttcagaataaatttcttttttcttgtttctctaacattgactatctttgactaatattataccggaaaagtctctattttgaaagaaaaagggatgactgaaaggtctgataattcaaactagtgaaaaagctttgtcaggcttatgtaacctcttgctttttgcttttaaagcgttataatataggtggaaatccacaaggaaaagacagacagaaactcctgcctgccaactatcatctaaacaaggaggataatcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacttccctttccagttgagaatttcagaataaatttcttttttcttgtttctctaacattgactatctttgactaatattataccggaaaagtctctattttgaaagaaaaagggatgactgaaaggtctgataattcaaactagtgaaaaagctttgtcaggcttatgtaacctcttgctttttgcttttaaagcgttataatataggtggaaatccacaaggaaaagacagacagaaactcctgcctgccaactatcatctaaacaaggaggataatcca Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 146 End: 283 ................................................................................................................................................. M K K L C Q A Y V T S C F L L L K R Y N I G G N P Q G K D R Q K L L P A N Y H L N K E D N P gacttccctttccagttgagaatttcagaataaatttcttttttcttgtttctctaacattgactatctttgactaatattataccggaaaagtctctattttgaaagaaaaagggatgactgaaaggtctgataattcaaactagtgaaaaagctttgtcaggcttatgtaacctcttgctttttgcttttaaagcgttataatataggtggaaatccacaaggaaaagacagacagaaactcctgcctgccaactatcatctaaacaaggaggataatcca 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: 87 Start: 79 End: 108 ..............................................................................CTTTCAAAATAGAGACTTTTCCGGTATAAT............................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacttccctttccagttgagaatttcagaataaatttcttttttcttgtttctctaacattgactatctttgactaatattataccggaaaagtctctattttgaaagaaaaagggatgactgaaaggtctgataattcaaactagtgaaaaagctttgtcaggcttatgtaacctcttgctttttgcttttaaagcgttataatataggtggaaatccacaaggaaaagacagacagaaactcctgcctgccaactatcatctaaacaaggaggataatcca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2200:SSA_2201|SSA_2200:SSA_2201:Firmicutes transcriptional repressor of class III stress genes (CtsR), putative:hypothetical protein:<-->:2201664..2201946 283 gacttccctttccagttgagaatttcagaataaatttcttttttcttgtttctctaacattgactatctttgactaatattataccggaaaagtctctattttgaaagaaaaagggatgactgaaaggtctgataattcaaactagtgaaaaagctttgtcaggcttatgtaacctcttgctttttgcttttaaagcgttataatataggtggaaatccacaaggaaaagacagacagaaactcctgcctgccaactatcatctaaacaaggaggataatcca Intra-Species Hit: Count: 1 Min: 1 Max: 283 Len: 283 Subject: NC_009009_SSA_2200_SSA_2201|Firmicutes transcriptional repressor of class III stress genes (CtsR), putative:hypothetical protein|NEGATIVE:POSITIVE|[2201664,2201946]|283 HSP 1 e-value: 1.0E-159 bit: 561.0 Len: 283 Query Start:1 Query End:283 Subject Strand: POSITIVE Subject Start: 1 Subject End: 283 gacttccctttccagttgagaatttcagaataaatttcttttttcttgtttctctaacattgactatctttgactaatattataccggaaaagtctctattttgaaagaaaaagggatgactgaaaggtctgataattcaaactagtgaaaaagctttgtcaggcttatgtaacctcttgctttttgcttttaaagcgttataatataggtggaaatccacaaggaaaagacagacagaaactcctgcctgccaactatcatctaaacaaggaggataatcca gacttccctttccagttgagaatttcagaataaatttcttttttcttgtttctctaacattgactatctttgactaatattataccggaaaagtctctattttgaaagaaaaagggatgactgaaaggtctgataattcaaactagtgaaaaagctttgtcaggcttatgtaacctcttgctttttgcttttaaagcgttataatataggtggaaatccacaaggaaaagacagacagaaactcctgcctgccaactatcatctaaacaaggaggataatcca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUUCCCUUUCCAGUUGAGAAUUUCAGAAUAAAUUUCUUUUUUCUUGUUUCUCUAACAUUGACUAUCUUUGACUAAUAUUAUACCGGAAAAGUCUCUAUUUUGAAAGAAAAAGGGAUGACUGAAAGGUCUGAUAAUUCAAACUAGUGAAAAAGCUUUGUCAGGCUUAUGUAACCUCUUGCUUUUUGCUUUUAAAGCGUUAUAAUAUAGGUGGAAAUCCACAAGGAAAAGACAGACAGAAACUCCUGCCUGCCAACUAUCAUCUAAACAAGGAGGAUAAUCCA ..(((((.(((((.((((((((....((((.(((....))).))))...))))).)))..................((((((((..((....((((((.((((....)))).)))))).......(((((((((((((((......))))......)))))))))))......))....(((((........)))))..))))))))..((((....))))..))))).(.(((.(((......))).))).).................)))))........ (-61.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGAUUAUCCUCCUUGUUUAGAUGAUAGUUGGCAGGCAGGAGUUUCUGUCUGUCUUUUCCUUGUGGAUUUCCACCUAUAUUAUAACGCUUUAAAAGCAAAAAGCAAGAGGUUACAUAAGCCUGACAAAGCUUUUUCACUAGUUUGAAUUAUCAGACCUUUCAGUCAUCCCUUUUUCUUUCAAAAUAGAGACUUUUCCGGUAUAAUAUUAGUCAAAGAUAGUCAAUGUUAGAGAAACAAGAAAAAAGAAAUUUAUUCUGAAAUUCUCAACUGGAAAGGGAAGUC .((.((((((((.((((((..((((((...((((((((((....))))))))))........((((....))))...))))))...(((.....)))...))))))))))....)))).)).(((...............((((((....))))))..........((((..(((((........)))))..((((((((.(((((((.(.(.......).))))))))(((((...((((.(((....))).))))....))))).)))))))))))).))) (-67.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 817 130 81 221 172 NC_009009:SSA_2200|5end_Firmicutes_transcriptional_repressor_of_class_III_stress_genes_(CtsR),_putative_2201573..2201803_NEGATIVE 313 260 211 185 129 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 295 260 211 179 121 NC_009009:SSA_0650|5end_GTP-binding_protein_TypA/BipA,_putative_632548..632778_POSITIVE 284 220 173 198 147 NC_009009:SSA_2371|5end_Zn-dependent_peptidase,_putative_2373681..2373911_NEGATIVE 282 176 142 102 69 NC_009009:SSA_1810|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1795396..1795626_NEGATIVE 280 189 148 84 30 NC_009009:SSA_0228|5end_hypothetical_protein_223363..223593_POSITIVE 278 192 151 211 167 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 265 260 211 194 150 NC_009009:SSA_0050|5end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_54612..54842_POSITIVE 264 272 232 153 114 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 260 276 240 124 85 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 260 188 151 230 193 NC_009009:SSA_1747|5end_hypothetical_protein_1733450..1733680_NEGATIVE 259 190 148 145 116 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 259 182 147 131 92 NC_009009:SSA_1264|5end_hypothetical_protein_1290042..1290272_NEGATIVE 259 190 141 193 147 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 259 188 141 158 112 NC_009009:SSA_0583|5end_Nucleotidyltransferase,_putative_574505..574735_POSITIVE 258 252 212 55 18 NC_009009:SSA_1121|5end_Cytochrome_C-type_biogenesis_protein,_putative_1147149..1147379_POSITIVE 257 218 173 107 63 NC_009009:SSA_0939|5end_Inositol_monophosphatase_(Mg++_dependent),_putative_946810..947040_POSITIVE 256 265 222 72 36 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 254 209 161 83 40 NC_009009:SSA_1859|5end_Penicillin-binding_protein-like_factor_A/_recombinase,_putative_1853704..1853934_POSITIVE 254 197 151 225 166 NC_009009:SSA_0064|5end_hypothetical_protein_66330..66560_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 210 161 113 65 NC_009009:SSA_2052|3end_Thioredoxin,_putative_2057193..2057343_NEGATIVE 297 275 242 63 22 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE 296 198 151 148 100 NC_009009:SSA_1748|3end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1733543..1733693_NEGATIVE 282 176 142 92 59 NC_009009:SSA_1811|3end_6-phosphogluconate_dehydrogenase,_putative_1795406..1795556_NEGATIVE 261 258 215 43 6 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 261 166 121 138 103 NC_009009:SSA_0149|3end_hypothetical_protein_143833..143983_POSITIVE 259 190 148 108 79 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 257 254 212 96 46 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE 256 167 123 78 37 NC_009009:SSA_0683|3end_DNA-binding_protein_HU,_putative_664739..664889_POSITIVE 255 250 217 50 16 NC_009009:SSA_0143|3end_Conserved_uncharacterized_protein_137880..138030_POSITIVE 252 90 41 89 37 NC_009009:SSA_2246|3end_Competence-damage_protein,_putative_2241168..2241318_NEGATIVE 252 200 153 88 34 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 251 165 126 108 62 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 250 270 242 57 25 NC_009009:SSA_2177|3end_hypothetical_protein_2175232..2175382_NEGATIVE 250 189 151 151 110 NC_009009:SSA_2123|3end_Dimethyladenosine_transferase,_putative_2127664..2127814_NEGATIVE 250 200 152 56 2 NC_009009:SSA_0554|3end_hypothetical_protein_549692..549842_POSITIVE 245 259 218 57 2 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 245 177 141 147 110 NC_009009:SSA_0582|3end_Methylase,_putative_574583..574733_POSITIVE 241 214 175 98 60 NC_009009:SSA_2283|3end_Conserved_uncharacterized_protein_2285537..2285687_NEGATIVE 240 275 231 60 28 NC_009009:SSA_2096|3end_ATP-dependent_protease,_ATP-binding_subunit,_putative_2099557..2099707_NEGATIVE