Origin IGS: tcgcatagtaaagataaaaactttagatgtttcaagcatctaaagttttttcattatttatttgcagcttagcttttctttattcaggtttcgatttttttgtcctttctttttgatgtgatataatgggcttaaataaatgggaaaggagcaagtct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agacttgctcctttcccatttatttaagcccattatatcacatcaaaaagaaaggacaaaaaaatcgaaacctgaataaagaaaagctaagctgcaaataaataatgaaaaaactttagatgcttgaaacatctaaagtttttatctttactatgcga Mask Tandem Repeat Region ================================================ tcgcatagtaaagataaaaactttagatgtttcaagcatctaaagttttttcattatttatttgcagcttagcttttctttattcaggtttcgatttttttgtcctttctttttgatgtgatataatgggcttaaataaatgggaaaggagcaagtct Find is-nt database================================================ Query_seq: SSA_0593:SSA_0594|SSA_0593:SSA_0594:Rhodanese-like sulfurtransferase, putative:Transcriptional regulator, AraC family, putative:->->:585612..585769 158 tcgcatagtaaagataaaaactttagatgtttcaagcatctaaagttttttcattatttatttgcagcttagcttttctttattcaggtttcgatttttttgtcctttctttttgatgtgatataatgggcttaaataaatgggaaaggagcaagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0593:SSA_0594|SSA_0593:SSA_0594:Rhodanese-like sulfurtransferase, putative:Transcriptional regulator, AraC family, putative:->->:585612..585769 158 tcgcatagtaaagataaaaactttagatgtttcaagcatctaaagttttttcattatttatttgcagcttagcttttctttattcaggtttcgatttttttgtcctttctttttgatgtgatataatgggcttaaataaatgggaaaggagcaagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0593:SSA_0594|SSA_0593:SSA_0594:Rhodanese-like sulfurtransferase, putative:Transcriptional regulator, AraC family, putative:->->:585612..585769 158 tcgcatagtaaagataaaaactttagatgtttcaagcatctaaagttttttcattatttatttgcagcttagcttttctttattcaggtttcgatttttttgtcctttctttttgatgtgatataatgggcttaaataaatgggaaaggagcaagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcgcatagtaaagataaaaactttagatgtttcaagcatctaaagttttttcattatttatttgcagcttagcttttctttattcaggtttcgatttttttgtcctttctttttgatgtgatataatgggcttaaataaatgggaaaggagcaagtct Predict ORF larger than 30AA ================================================ tcgcatagtaaagataaaaactttagatgtttcaagcatctaaagttttttcattatttatttgcagcttagcttttctttattcaggtttcgatttttttgtcctttctttttgatgtgatataatgggcttaaataaatgggaaaggagcaagtct Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcgcatagtaaagataaaaactttagatgtttcaagcatctaaagttttttcattatttatttgcagcttagcttttctttattcaggtttcgatttttttgtcctttctttttgatgtgatataatgggcttaaataaatgggaaaggagcaagtct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -8.7 Tail_Score: -5.22289 Start: 21 End: 45 Full_Region: taaataatgaaaaaa ctttagatgct tga aacatctaaag tttttatctttacta ....................ctttagatgcttgaaacatctaaag................................................................................................................. Find igs database================================================ Query_seq: SSA_0593:SSA_0594|SSA_0593:SSA_0594:Rhodanese-like sulfurtransferase, putative:Transcriptional regulator, AraC family, putative:->->:585612..585769 158 tcgcatagtaaagataaaaactttagatgtttcaagcatctaaagttttttcattatttatttgcagcttagcttttctttattcaggtttcgatttttttgtcctttctttttgatgtgatataatgggcttaaataaatgggaaaggagcaagtct Intra-Species Hit: Count: 1 Min: 1 Max: 158 Len: 158 Subject: NC_009009_SSA_0593_SSA_0594|Rhodanese-like sulfurtransferase, putative:Transcriptional regulator, AraC family, putative|POSITIVE:POSITIVE|[585612,585769]|158 HSP 1 e-value: 1.0E-19 bit: 97.6 Len: 49 Query Start:110 Query End:158 Subject Strand: POSITIVE Subject Start: 110 Subject End: 158 .............................................................................................................tttttgatgtgatataatgggcttaaataaatgggaaaggagcaagtct .............................................................................................................tttttgatgtgatataatgggcttaaataaatgggaaaggagcaagtct HSP 2 e-value: 3.0E-17 bit: 89.7 Len: 45 Query Start:1 Query End:45 Subject Strand: POSITIVE Subject Start: 1 Subject End: 45 tcgcatagtaaagataaaaactttagatgtttcaagcatctaaag................................................................................................................. tcgcatagtaaagataaaaactttagatgtttcaagcatctaaag................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGCAUAGUAAAGAUAAAAACUUUAGAUGUUUCAAGCAUCUAAAGUUUUUUCAUUAUUUAUUUGCAGCUUAGCUUUUCUUUAUUCAGGUUUCGAUUUUUUUGUCCUUUCUUUUUGAUGUGAUAUAAUGGGCUUAAAUAAAUGGGAAAGGAGCAAGUCU ..(((.(((((.((.(((((((((((((((.....))))))))))))))))).)))))....))).((((..((((((((((((.((((..(.(((....((((...((.....))...)))).))).))))).)))))..)))))))))))...... (-38.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGACUUGCUCCUUUCCCAUUUAUUUAAGCCCAUUAUAUCACAUCAAAAAGAAAGGACAAAAAAAUCGAAACCUGAAUAAAGAAAAGCUAAGCUGCAAAUAAAUAAUGAAAAAACUUUAGAUGCUUGAAACAUCUAAAGUUUUUAUCUUUACUAUGCGA ....(((.(((((((..................................)))))))))).................((((((...((......)).............((((((((((((((.......)))))))))))))).))))))........ (-26.88) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 106 61 94 31 NC_009009:SSA_2226|5end_Organic_radical_activating_chaperone,_putative_2227756..2227986_NEGATIVE 275 129 84 117 67 NC_009009:SSA_2329|5end_hypothetical_protein_2332262..2332492_POSITIVE 270 108 65 119 65 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 268 108 64 184 145 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 255 118 76 123 77 NC_009009:SSA_0601|5end_Phosphorylase,_Pnp/Udp_family,_putative_589147..589377_POSITIVE 254 108 66 43 9 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 253 79 35 210 158 NC_009009:SSA_0910|5end_ABC-type_multidrug_transporter,_ATPase_component,_putative_921356..921586_POSITIVE 252 100 56 122 86 NC_009009:SSA_0044|5end_hypothetical_protein_49041..49271_POSITIVE 244 110 61 114 58 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 244 108 65 111 62 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 244 105 63 135 96 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 243 150 101 212 174 NC_009009:SSA_0099|5end_hypothetical_protein_100619..100849_NEGATIVE 242 119 72 112 68 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 241 114 72 65 28 NC_009009:SSA_2357|5end_50S_ribosomal_protein_L9,_putative_2358437..2358667_NEGATIVE 238 87 43 228 185 NC_009009:SSA_2241|5end_Conserved_uncharacterized_protein_2237943..2238173_NEGATIVE 238 94 56 219 185 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 238 109 64 55 13 NC_009009:SSA_0246|5end_Conserved_uncharacterized_protein_239703..239933_POSITIVE 237 76 40 217 168 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 236 120 84 119 81 NC_009009:SSA_1625|5end_Lactoylglutathione_lyase,_putative_1626963..1627193_NEGATIVE 235 150 103 223 174 NC_009009:SSA_1325|5end_Ketoacyl_reductase_hetN,_putative_1342343..1342573_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 50 3 75 26 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 298 106 61 134 71 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 275 129 84 84 34 NC_009009:SSA_2328|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_2332309..2332459_POSITIVE 268 108 64 99 60 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 254 108 66 56 22 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 252 100 56 109 73 NC_009009:SSA_0043|3end_hypothetical_protein_49108..49258_POSITIVE 251 96 54 71 26 NC_009009:SSA_1479|3end_Transposase,_putative_1483889..1484039_POSITIVE 247 104 61 99 52 NC_009009:SSA_1501|3end_Cytidylate_kinase,_putative_1505095..1505245_NEGATIVE 245 115 86 48 17 NC_009009:SSA_0688|3end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_672132..672282_POSITIVE 244 108 65 99 50 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 244 105 63 133 94 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 242 119 72 119 75 NC_009009:SSA_0709|3end_hypothetical_protein_695632..695782_NEGATIVE 241 114 72 68 31 NC_009009:SSA_2358|3end_hypothetical_protein_2358434..2358584_NEGATIVE 240 106 63 118 73 NC_009009:SSA_0343|3end_DNA-damage-inducible_protein_P,_putative_338669..338819_POSITIVE 238 87 43 50 7 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 238 110 63 133 74 NC_009009:SSA_1554|3end_hypothetical_protein_1556847..1556997_POSITIVE 238 94 56 134 100 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 233 107 68 44 7 NC_009009:SSA_0199|3end_GTP_cyclohydrolase_I,_putative_198910..199060_POSITIVE 225 109 61 85 32 NC_009009:SSA_2065|3end_hypothetical_protein_2065051..2065201_NEGATIVE 225 89 47 100 44 NC_009009:SSA_0895|3end_ATP-binding_cassette_transporter-like_protein,_putative_887763..887913_POSITIVE