Origin IGS: tcccttcgcagttacaacataaccaaaacttccactcttttcttttttagtgaatcaaacactcttaattagttgattttttcacaaacttcctataaaatagaattagaaaggttgtgatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatcacaacctttctaattctattttataggaagtttgtgaaaaaatcaactaattaagagtgtttgattcactaaaaaagaaaagagtggaagttttggttatgttgtaactgcgaaggga Mask Tandem Repeat Region ================================================ tcccttcgcagttacaacataaccaaaacttccactcttttcttttttagtgaatcaaacactcttaattagttgattttttcacaaacttcctataaaatagaattagaaaggttgtgatttt Find is-nt database================================================ Query_seq: SSA_1215:SSA_1216|SSA_1215:SSA_1216:hypothetical protein:AT-rich DNA-binding protein, possible redox-sensing transcriptional repressor, putative:->->:1238308..1238431 124 tcccttcgcagttacaacataaccaaaacttccactcttttcttttttagtgaatcaaacactcttaattagttgattttttcacaaacttcctataaaatagaattagaaaggttgtgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1215:SSA_1216|SSA_1215:SSA_1216:hypothetical protein:AT-rich DNA-binding protein, possible redox-sensing transcriptional repressor, putative:->->:1238308..1238431 124 tcccttcgcagttacaacataaccaaaacttccactcttttcttttttagtgaatcaaacactcttaattagttgattttttcacaaacttcctataaaatagaattagaaaggttgtgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1215:SSA_1216|SSA_1215:SSA_1216:hypothetical protein:AT-rich DNA-binding protein, possible redox-sensing transcriptional repressor, putative:->->:1238308..1238431 124 tcccttcgcagttacaacataaccaaaacttccactcttttcttttttagtgaatcaaacactcttaattagttgattttttcacaaacttcctataaaatagaattagaaaggttgtgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcccttcgcagttacaacataaccaaaacttccactcttttcttttttagtgaatcaaacactcttaattagttgattttttcacaaacttcctataaaatagaattagaaaggttgtgatttt Predict ORF larger than 30AA ================================================ tcccttcgcagttacaacataaccaaaacttccactcttttcttttttagtgaatcaaacactcttaattagttgattttttcacaaacttcctataaaatagaattagaaaggttgtgatttt 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: 86 Start: 72 End: 101 .......................................................................GTTGATTTTTTCACAAACTTCCTATAAAAT....................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcccttcgcagttacaacataaccaaaacttccactcttttcttttttagtgaatcaaacactcttaattagttgattttttcacaaacttcctataaaatagaattagaaaggttgtgatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1215:SSA_1216|SSA_1215:SSA_1216:hypothetical protein:AT-rich DNA-binding protein, possible redox-sensing transcriptional repressor, putative:->->:1238308..1238431 124 tcccttcgcagttacaacataaccaaaacttccactcttttcttttttagtgaatcaaacactcttaattagttgattttttcacaaacttcctataaaatagaattagaaaggttgtgatttt Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_009009_SSA_1215_SSA_1216|hypothetical protein:AT-rich DNA-binding protein, possible redox-sensing transcriptional repressor, putative|POSITIVE:POSITIVE|[1238308,1238431]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 tcccttcgcagttacaacataaccaaaacttccactcttttcttttttagtgaatcaaacactcttaattagttgattttttcacaaacttcctataaaatagaattagaaaggttgtgatttt tcccttcgcagttacaacataaccaaaacttccactcttttcttttttagtgaatcaaacactcttaattagttgattttttcacaaacttcctataaaatagaattagaaaggttgtgatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCUUCGCAGUUACAACAUAACCAAAACUUCCACUCUUUUCUUUUUUAGUGAAUCAAACACUCUUAAUUAGUUGAUUUUUUCACAAACUUCCUAUAAAAUAGAAUUAGAAAGGUUGUGAUUUU .................(((((((.........................(((((..((.((..((.....)).)).))..))))).......((((...)))).........)))))))..... (-14.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCACAACCUUUCUAAUUCUAUUUUAUAGGAAGUUUGUGAAAAAAUCAACUAAUUAAGAGUGUUUGAUUCACUAAAAAAGAAAAGAGUGGAAGUUUUGGUUAUGUUGUAACUGCGAAGGGA ....((((((.(((((((...........))))))).))))))......(((((((((((((.(......((((((............))))))).))))))))).)))).............. (-22.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 230 59 15 77 29 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 228 48 3 185 123 NC_009009:SSA_1891|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888991..1889221_NEGATIVE 228 40 6 178 141 NC_009009:SSA_1754|5end_hypothetical_protein_1743478..1743708_NEGATIVE 228 45 1 117 65 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 224 66 30 141 105 NC_009009:SSA_0156|5end_ATPase_with_chaperone_activity,_ATP-binding_subunit,_putative_151326..151556_POSITIVE 217 117 71 138 93 NC_009009:SSA_1322|5end_Glycosyl_transferase,_putative_1339819..1340049_NEGATIVE 213 50 8 51 7 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 212 66 21 134 71 NC_009009:SSA_0270|5end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_262873..263103_POSITIVE 211 44 4 175 127 NC_009009:SSA_2023|5end_Fructan_beta-fructosidase_precursor,_putative_2028826..2029056_NEGATIVE 210 33 1 221 185 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 210 34 3 219 190 NC_009009:SSA_0416|5end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase,_putative_411890..412120_POSITIVE 208 49 1 116 78 NC_009009:SSA_2374|5end_Inosine-5'-monophosphate_dehydrogenase,_putative_2377015..2377245_NEGATIVE 203 99 54 167 125 NC_009009:SSA_0146|5end_DNA_repair_ATPase,_putative_139686..139916_POSITIVE 202 45 8 62 16 NC_009009:SSA_0635|5end_Indole-3-glycerol_phosphate_synthase,_putative_624388..624618_POSITIVE 200 109 70 132 91 NC_009009:SSA_1844|5end_hypothetical_protein_1838183..1838413_NEGATIVE 199 66 29 231 184 NC_009009:SSA_1139|5end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1166823..1167053_POSITIVE 198 38 1 38 9 NC_009009:SSA_1655|5end_hypothetical_protein_1651816..1652046_NEGATIVE 198 49 22 105 74 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 198 35 3 195 167 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 198 66 22 103 53 NC_009009:SSA_0244|5end_hypothetical_protein_238698..238928_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 228 48 3 108 46 NC_009009:SSA_1892|3end_hypothetical_protein_1889068..1889218_NEGATIVE 224 66 30 141 105 NC_009009:SSA_0155|3end_hypothetical_protein_151406..151556_POSITIVE 216 45 1 145 102 NC_009009:SSA_2354|3end_hypothetical_protein_2355605..2355755_NEGATIVE 214 70 28 128 84 NC_009009:SSA_1312|3end_RADC-like_protein,_putative_1328737..1328887_NEGATIVE 213 50 8 79 35 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 212 66 21 128 65 NC_009009:SSA_0269|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262947..263097_POSITIVE 202 45 8 65 19 NC_009009:SSA_0634|3end_Anthranilate_phosphoribosyltransferase,_putative_624471..624621_POSITIVE 202 38 1 151 119 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 198 49 22 57 26 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 193 75 32 149 96 NC_009009:SSA_2215|3end_Oligosaccharide_repeat_unit_polymerase_Wzy,_putative_2215832..2215982_NEGATIVE 191 33 4 103 83 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 190 42 1 92 53 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 190 80 31 107 49 NC_009009:SSA_0233|3end_Permease,_putative_228179..228329_POSITIVE 189 44 6 92 54 NC_009009:SSA_2004|3end_Zinc_metalloprotease_zmpB_precursor,_putative_1999216..1999366_NEGATIVE 188 44 6 69 18 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 184 96 59 91 47 NC_009009:SSA_0520|3end_Ethanolamine_ammonia-lyase_light_chain,_putative_520462..520612_POSITIVE 184 48 8 80 37 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE 183 48 1 120 64 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 182 75 31 117 53 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 182 78 33 81 41 NC_009009:SSA_0459|3end_hypothetical_protein_462513..462663_POSITIVE