Origin IGS: tcttttcctcactttctatttttgaatgaacagtttaaaatattcattcaaaatcttctaaaaaataattcactttatctgattaagttcctttccatttccgaatcacaagacataacccatcacctcctttgtttatgaatgaataatttttttaattcattcatgtctacttctaagaaaaggaatttcct .........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 aggaaattccttttcttagaagtagacatgaatgaattaaaaaaattattcattcataaacaaaggaggtgatgggttatgtcttgtgattcggaaatggaaaggaacttaatcagataaagtgaattattttttagaagattttgaatgaatattttaaactgttcattcaaaaatagaaagtgaggaaaaga Mask Tandem Repeat Region ================================================ tcttttcctcactttctatttttgaatgaacagtttaaaatattcattcaaaatcttctaaaaaataattcactttatctgattaagttcctttccatttccgaatcacaagacataacccatcacctcctttgtttatgaatgaataatttttttaattcattcatgtctacttctaagaaaaggaatttcct Find is-nt database================================================ Query_seq: SSA_1669:SSA_1670|SSA_1669:SSA_1670:hypothetical protein:Transcriptional regulator, TetR/AcrR family, putative:<-<-:1668533..1668726 194 tcttttcctcactttctatttttgaatgaacagtttaaaatattcattcaaaatcttctaaaaaataattcactttatctgattaagttcctttccatttccgaatcacaagacataacccatcacctcctttgtttatgaatgaataatttttttaattcattcatgtctacttctaagaaaaggaatttcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1669:SSA_1670|SSA_1669:SSA_1670:hypothetical protein:Transcriptional regulator, TetR/AcrR family, putative:<-<-:1668533..1668726 194 tcttttcctcactttctatttttgaatgaacagtttaaaatattcattcaaaatcttctaaaaaataattcactttatctgattaagttcctttccatttccgaatcacaagacataacccatcacctcctttgtttatgaatgaataatttttttaattcattcatgtctacttctaagaaaaggaatttcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1669:SSA_1670|SSA_1669:SSA_1670:hypothetical protein:Transcriptional regulator, TetR/AcrR family, putative:<-<-:1668533..1668726 194 tcttttcctcactttctatttttgaatgaacagtttaaaatattcattcaaaatcttctaaaaaataattcactttatctgattaagttcctttccatttccgaatcacaagacataacccatcacctcctttgtttatgaatgaataatttttttaattcattcatgtctacttctaagaaaaggaatttcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttttcctcactttctatttttgaatgaacagtttaaaatattcattcaaaatcttctaaaaaataattcactttatctgattaagttcctttccatttccgaatcacaagacataacccatcacctcctttgtttatgaatgaataatttttttaattcattcatgtctacttctaagaaaaggaatttcct Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 22 End: 138 ..................... M N E Q F K I F I Q N L L K N N S L Y L I K F L S I S E S Q D I T H H L L C L ........................................................ tcttttcctcactttctatttttgaatgaacagtttaaaatattcattcaaaatcttctaaaaaataattcactttatctgattaagttcctttccatttccgaatcacaagacataacccatcacctcctttgtttatgaatgaataatttttttaattcattcatgtctacttctaagaaaaggaatttcct 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: 12 End: 41 ...........CTTTCTATTTTTGAATGAACAGTTTAAAAT......................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcttttcctcactttctatttttgaatgaacagtttaaaatattcattcaaaatcttctaaaaaataattcactttatctgattaagttcctttccatttccgaatcacaagacataacccatcacctcctttgtttatgaatgaataatttttttaattcattcatgtctacttctaagaaaaggaatttcct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 50 HP_score: -4.3 Tail_Score: -3.03474 Start: 139 End: 166 Full_Region: CACCTCCTTTGTTTA TGAATGAATAA TTTTTT TAATTCATTCA TGTCTACTTCTAAGA ..........................................................................................................................................TGAATGAATAATTTTTTTAATTCATTCA............................ Find igs database================================================ Query_seq: SSA_1669:SSA_1670|SSA_1669:SSA_1670:hypothetical protein:Transcriptional regulator, TetR/AcrR family, putative:<-<-:1668533..1668726 194 tcttttcctcactttctatttttgaatgaacagtttaaaatattcattcaaaatcttctaaaaaataattcactttatctgattaagttcctttccatttccgaatcacaagacataacccatcacctcctttgtttatgaatgaataatttttttaattcattcatgtctacttctaagaaaaggaatttcct Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: NC_009009_SSA_1669_SSA_1670|hypothetical protein:Transcriptional regulator, TetR/AcrR family, putative|NEGATIVE:NEGATIVE|[1668533,1668726]|194 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 tcttttcctcactttctatttttgaatgaacagtttaaaatattcattcaaaatcttctaaaaaataattcactttatctgattaagttcctttccatttccgaatcacaagacataacccatcacctcctttgtttatgaatgaataannnnnnnaattcattcatgtctacttctaagaaaaggaatttcct tcttttcctcactttctatttttgaatgaacagtttaaaatattcattcaaaatcttctaaaaaataattcactttatctgattaagttcctttccatttccgaatcacaagacataacccatcacctcctttgtttatgaatgaataatttttttaattcattcatgtctacttctaagaaaaggaatttcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUUCCUCACUUUCUAUUUUUGAAUGAACAGUUUAAAAUAUUCAUUCAAAAUCUUCUAAAAAAUAAUUCACUUUAUCUGAUUAAGUUCCUUUCCAUUUCCGAAUCACAAGACAUAACCCAUCACCUCCUUUGUUUAUGAAUGAAUAAUUUUUUUAAUUCAUUCAUGUCUACUUCUAAGAAAAGGAAUUUCCU ...................(((((((((((.(........).)))))))))))...............................((((((((((.(...............((((.................))))(((((((((((..........)))))))))))...........).))))))))))... (-26.73) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAAAUUCCUUUUCUUAGAAGUAGACAUGAAUGAAUUAAAAAAAUUAUUCAUUCAUAAACAAAGGAGGUGAUGGGUUAUGUCUUGUGAUUCGGAAAUGGAAAGGAACUUAAUCAGAUAAAGUGAAUUAUUUUUUAGAAGAUUUUGAAUGAAUAUUUUAAACUGUUCAUUCAAAAAUAGAAAGUGAGGAAAAGA ......(((((((((...(((......((((((((((..........))))))))))...((.((((.((((....)))).)))).)).)))......)))))))))...................((((((((((.....(((((((((((((........))))))))))))).))))))))))........ (-42.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 882 130 81 221 172 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 283 140 91 118 71 NC_009009:SSA_1080|5end_Transcriptional_repressor_of_the_fructose_operon,_DeoR_family,_putative_1097538..1097768_POSITIVE 257 137 95 104 63 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 255 113 80 74 37 NC_009009:SSA_2085|5end_Glyoxylate_reductase,_NADH-dependent,_putative_2090404..2090634_NEGATIVE 248 120 72 56 2 NC_009009:SSA_0540|5end_Glycerol_uptake_facilitator_protein,_putative_534955..535185_POSITIVE 247 104 79 75 47 NC_009009:SSA_0272|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_266023..266253_POSITIVE 242 123 90 222 192 NC_009009:SSA_1353|5end_hypothetical_protein_1368519..1368749_NEGATIVE 238 130 82 89 32 NC_009009:SSA_2145|5end_Tributyrin_esterase,_putative_2146658..2146888_NEGATIVE 235 130 87 227 187 NC_009009:SSA_1035|5end_Pyrimidine_nucleoside_phosphorylase,_putative_1050174..1050404_POSITIVE 235 129 85 105 62 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 229 120 71 129 85 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 228 148 101 189 135 NC_009009:SSA_2023|5end_Fructan_beta-fructosidase_precursor,_putative_2028826..2029056_NEGATIVE 227 130 84 196 146 NC_009009:SSA_0567|5end_Isochorismitase_family_protein,_putative_560805..561035_POSITIVE 223 130 92 46 1 NC_009009:SSA_1786|5end_Conserved_uncharacterized_protein_1770244..1770474_NEGATIVE 223 128 85 164 99 NC_009009:SSA_1647|5end_hypothetical_protein_1647169..1647399_NEGATIVE 223 127 81 105 59 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 222 157 111 134 86 NC_009009:SSA_2336|5end_Transcriptional_regulator,_PadR_family,_putative_2338367..2338597_POSITIVE 220 109 73 188 154 NC_009009:SSA_1424|5end_Hydrolase,_putative_1434479..1434709_NEGATIVE 218 127 99 176 146 NC_009009:SSA_0494|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_494407..494637_POSITIVE 215 130 81 201 153 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 137 95 113 72 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 255 113 80 81 44 NC_009009:SSA_2086|3end_hypothetical_protein_2090397..2090547_NEGATIVE 247 104 79 65 37 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 236 150 102 147 101 NC_009009:SSA_0682|3end_Conserved_uncharacterized_protein_664351..664501_POSITIVE 229 120 71 129 85 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 223 127 81 133 87 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 216 130 87 150 119 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 215 129 84 123 74 NC_009009:SSA_0589|3end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_582207..582357_POSITIVE 214 130 81 142 80 NC_009009:SSA_2353|3end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2354550..2354700_NEGATIVE 213 126 86 106 55 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 212 133 93 108 53 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 212 156 113 86 46 NC_009009:SSA_0652|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase,_putative_636468..636618_POSITIVE 212 120 71 148 99 NC_009009:SSA_0346|3end_hypothetical_protein_340322..340472_POSITIVE 212 137 96 46 7 NC_009009:SSA_0195|3end_hypothetical_protein_195831..195981_POSITIVE 210 130 90 103 59 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 209 190 150 63 17 NC_009009:SSA_1099|3end_Calcium_binding_hemolysin-like_protein,_putative_1119874..1120024_POSITIVE 208 128 81 151 89 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 207 140 91 100 51 NC_009009:SSA_0528|3end_Conserved_uncharacterized_protein_526010..526160_POSITIVE 205 125 86 104 58 NC_009009:SSA_0199|3end_GTP_cyclohydrolase_I,_putative_198910..199060_POSITIVE 205 139 91 86 26 NC_009009:SSA_0061|3end_Tagatose_1,6-diphosphate_aldolase,_putative_63787..63937_POSITIVE