Origin IGS: ttcagctccattcccgacccgatttcaaatcagccgttttgttttattcttaaataatttgatattcaaattatacacaacttatattttatcataaaatataaaagaaaggaaataaaaaatgggaaaaattagatggtcttcaaatttgaagtgtgaaagtaataatttggataaaaatagtataaaaacagcgtttgaataattttcagaattttgttataatttttaaaataagataggagaacca .........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 tggttctcctatcttattttaaaaattataacaaaattctgaaaattattcaaacgctgtttttatactatttttatccaaattattactttcacacttcaaatttgaagaccatctaatttttcccattttttatttcctttcttttatattttatgataaaatataagttgtgtataatttgaatatcaaattatttaagaataaaacaaaacggctgatttgaaatcgggtcgggaatggagctgaa Mask Tandem Repeat Region ================================================ ttcagctccattcccgacccgatttcaaatcagccgttttgttttattcttaaataatttgatattcaaattatacacaacttatattttatcataaaatataaaagaaaggaaataaaaaatgggaaaaattagatggtcttcaaatttgaagtgtgaaagtaataatttggataaaaatagtataaaaacagcgtttgaataattttcagaattttgttataatttttaaaataagataggagaacca Find is-nt database================================================ Query_seq: SSA_1942:SSA_1943|SSA_1942:SSA_1943:Enoyl-CoA hydratase/carnithine racemase, putative:Aspartate kinase, putative:<-->:1928587..1928836 250 ttcagctccattcccgacccgatttcaaatcagccgttttgttttattcttaaataatttgatattcaaattatacacaacttatattttatcataaaatataaaagaaaggaaataaaaaatgggaaaaattagatggtcttcaaatttgaagtgtgaaagtaataatttggataaaaatagtataaaaacagcgtttgaataattttcagaattttgttataatttttaaaataagataggagaacca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1942:SSA_1943|SSA_1942:SSA_1943:Enoyl-CoA hydratase/carnithine racemase, putative:Aspartate kinase, putative:<-->:1928587..1928836 250 ttcagctccattcccgacccgatttcaaatcagccgttttgttttattcttaaataatttgatattcaaattatacacaacttatattttatcataaaatataaaagaaaggaaataaaaaatgggaaaaattagatggtcttcaaatttgaagtgtgaaagtaataatttggataaaaatagtataaaaacagcgtttgaataattttcagaattttgttataatttttaaaataagataggagaacca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1942:SSA_1943|SSA_1942:SSA_1943:Enoyl-CoA hydratase/carnithine racemase, putative:Aspartate kinase, putative:<-->:1928587..1928836 250 ttcagctccattcccgacccgatttcaaatcagccgttttgttttattcttaaataatttgatattcaaattatacacaacttatattttatcataaaatataaaagaaaggaaataaaaaatgggaaaaattagatggtcttcaaatttgaagtgtgaaagtaataatttggataaaaatagtataaaaacagcgtttgaataattttcagaattttgttataatttttaaaataagataggagaacca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcagctccattcccgacccgatttcaaatcagccgttttgttttattcttaaataatttgatattcaaattatacacaacttatattttatcataaaatataaaagaaaggaaataaaaaatgggaaaaattagatggtcttcaaatttgaagtgtgaaagtaataatttggataaaaatagtataaaaacagcgtttgaataattttcagaattttgttataatttttaaaataagataggagaacca Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 85 End: 186 .................................................................................... I K D Y F I F S L F Y F I P F I L H D E F K F H S L L L K S L F L M ................................................................ ttcagctccattcccgacccgatttcaaatcagccgttttgttttattcttaaataatttgatattcaaattatacacaacttatattttatcataaaatataaaagaaaggaaataaaaaatgggaaaaattagatggtcttcaaatttgaagtgtgaaagtaataatttggataaaaatagtataaaaacagcgtttgaataattttcagaattttgttataatttttaaaataagataggagaacca 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: 90 Start: 197 End: 226 ....................................................................................................................................................................................................TTTGAATAATTTTCAGAATTTTGTTATAAT........................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 70 End: 99 .....................................................................TTTTATGATAAAATATAAGTTGTGTATAAT....................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 206 End: 235 .............................................................................................................................................................................................................TTTTCAGAATTTTGTTATAATTTTTAAAAT............... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcagctccattcccgacccgatttcaaatcagccgttttgttttattcttaaataatttgatattcaaattatacacaacttatattttatcataaaatataaaagaaaggaaataaaaaatgggaaaaattagatggtcttcaaatttgaagtgtgaaagtaataatttggataaaaatagtataaaaacagcgtttgaataattttcagaattttgttataatttttaaaataagataggagaacca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -7.6 Tail_Score: -3.57144 Start: 55 End: 73 Full_Region: aatataagttgtgta taatttga ata tcaaatta tttaagaataaaaca ......................................................taatttgaatatcaaatta................................................................................................................................................................................. Find igs database================================================ Query_seq: SSA_1942:SSA_1943|SSA_1942:SSA_1943:Enoyl-CoA hydratase/carnithine racemase, putative:Aspartate kinase, putative:<-->:1928587..1928836 250 ttcagctccattcccgacccgatttcaaatcagccgttttgttttattcttaaataatttgatattcaaattatacacaacttatattttatcataaaatataaaagaaaggaaataaaaaatgggaaaaattagatggtcttcaaatttgaagtgtgaaagtaataatttggataaaaatagtataaaaacagcgtttgaataattttcagaattttgttataatttttaaaataagataggagaacca Intra-Species Hit: Count: 1 Min: 1 Max: 250 Len: 250 Subject: NC_009009_SSA_1942_SSA_1943|Enoyl-CoA hydratase/carnithine racemase, putative:Aspartate kinase, putative|NEGATIVE:POSITIVE|[1928587,1928836]|250 HSP 1 e-value: 1.0E-60 bit: 234.0 Len: 118 Query Start:133 Query End:250 Subject Strand: POSITIVE Subject Start: 133 Subject End: 250 ....................................................................................................................................tagatggtcttcaaatttgaagtgtgaaagtaataatttggataaaaatagtataaaaacagcgtttgaataattttcagaattttgttataatttttaaaataagataggagaacca ....................................................................................................................................tagatggtcttcaaatttgaagtgtgaaagtaataatttggataaaaatagtataaaaacagcgtttgaataattttcagaattttgttataatttttaaaataagataggagaacca HSP 2 e-value: 1.0E-45 bit: 184.0 Len: 93 Query Start:1 Query End:93 Subject Strand: POSITIVE Subject Start: 1 Subject End: 93 ttcagctccattcccgacccgatttcaaatcagccgttttgttttattcttaaataatttgatattcaaattatacacaacttatattttatc............................................................................................................................................................. ttcagctccattcccgacccgatttcaaatcagccgttttgttttattcttaaataatttgatattcaaattatacacaacttatattttatc............................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAGCUCCAUUCCCGACCCGAUUUCAAAUCAGCCGUUUUGUUUUAUUCUUAAAUAAUUUGAUAUUCAAAUUAUACACAACUUAUAUUUUAUCAUAAAAUAUAAAAGAAAGGAAAUAAAAAAUGGGAAAAAUUAGAUGGUCUUCAAAUUUGAAGUGUGAAAGUAAUAAUUUGGAUAAAAAUAGUAUAAAAACAGCGUUUGAAUAAUUUUCAGAAUUUUGUUAUAAUUUUUAAAAUAAGAUAGGAGAACCA .....((((.((((((....(((.....))).....(((((((((.(((((..((((((((.....))))))))........(((((((((...))))))))).)))))..)))))))))..))))))..........(((((...(((..((.(((.......))).))..)))..............(((((..((((((.....))))))...)))))..............))))).))))..... (-41.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGUUCUCCUAUCUUAUUUUAAAAAUUAUAACAAAAUUCUGAAAAUUAUUCAAACGCUGUUUUUAUACUAUUUUUAUCCAAAUUAUUACUUUCACACUUCAAAUUUGAAGACCAUCUAAUUUUUCCCAUUUUUUAUUUCCUUUCUUUUAUAUUUUAUGAUAAAAUAUAAGUUGUGUAUAAUUUGAAUAUCAAAUUAUUUAAGAAUAAAACAAAACGGCUGAUUUGAAAUCGGGUCGGGAAUGGAGCUGAA .(((((((((((((.((((((((................((((.....))))...((((((((.....((((((((................(((.(((((....)))))...................................(((((((((((...)))))))))))..))).((((((((.....)))))))).))))))))....))))))))...)))))))).)))).))))...)))))... (-42.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 893 50 1 141 92 NC_009009:SSA_1942|5end_Enoyl-CoA_hydratase/carnithine_racemase,_putative_1928496..1928726_NEGATIVE 326 47 4 91 39 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 303 45 4 195 152 NC_009009:SSA_1511|5end_Glycosyltransferase,_putative_1516697..1516927_NEGATIVE 297 41 3 143 83 NC_009009:SSA_1342|5end_Carbamoyl-phosphate_synthase_small_chain,_putative_1361017..1361247_NEGATIVE 290 50 4 78 39 NC_009009:SSA_1432|5end_HflX_GTPase,_putative_1439901..1440131_NEGATIVE 287 36 1 191 150 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 277 50 1 100 44 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 277 50 1 72 19 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 266 40 1 182 138 NC_009009:SSA_1804|5end_NADPH-flavin_oxidoreductase,_putative_1788668..1788898_NEGATIVE 266 41 4 43 2 NC_009009:SSA_1261|5end_Ribose-5-phosphate_isomerase_A,_putative_1287654..1287884_NEGATIVE 264 50 5 215 159 NC_009009:SSA_1817|5end_Conserved_uncharacterized_protein_1805595..1805825_NEGATIVE 262 49 1 59 13 NC_009009:SSA_1982|5end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975873..1976103_NEGATIVE 260 39 4 93 60 NC_009009:SSA_0975|5end_2-isopropylmalate_synthase,_putative_980971..981201_POSITIVE 256 37 2 215 178 NC_009009:SSA_0773|5end_PTS_enzyme_I,_putative_752603..752833_POSITIVE 254 50 3 184 129 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 254 50 1 100 47 NC_009009:SSA_0077|5end_Oxidoreductase,_putative_80738..80968_POSITIVE 253 40 5 227 189 NC_009009:SSA_0017|5end_Cell_shape_determining_protein_MreC,_putative_22811..23041_POSITIVE 252 49 4 106 45 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 250 37 2 221 185 NC_009009:SSA_1306|5end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324910..1325140_NEGATIVE 248 43 1 129 87 NC_009009:SSA_0882|5end_Phosphoserine_phosphatase,_putative_876903..877133_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 41 3 118 58 NC_009009:SSA_1343|3end_Aspartate_carbamoyltransferase,_putative_1361042..1361192_NEGATIVE 290 50 4 46 7 NC_009009:SSA_1433|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1439933..1440083_NEGATIVE 287 36 1 145 104 NC_009009:SSA_0346|3end_hypothetical_protein_340322..340472_POSITIVE 258 37 8 28 2 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 252 49 4 96 35 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 249 40 5 142 99 NC_009009:SSA_1818|3end_Very_short_patch_repair_endonuclease,_putative_1805655..1805805_NEGATIVE 248 43 1 95 53 NC_009009:SSA_0881|3end_Lipoprotein,_putative_876949..877099_POSITIVE 246 41 4 141 88 NC_009009:SSA_1353|3end_hypothetical_protein_1367974..1368124_NEGATIVE 246 42 6 131 86 NC_009009:SSA_0353|3end_Conserved_uncharacterized_protein_346310..346460_POSITIVE 243 39 3 151 111 NC_009009:SSA_2327|3end_hypothetical_protein_2331400..2331550_POSITIVE 241 50 1 85 27 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 240 21 1 56 31 NC_009009:SSA_1512|3end_hypothetical_protein_1516701..1516851_NEGATIVE 237 39 2 83 53 NC_009009:SSA_0460|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_463146..463296_POSITIVE 232 44 1 151 103 NC_009009:SSA_0214|3end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210690..210840_POSITIVE 231 47 4 81 21 NC_009009:SSA_1248|3end_hypothetical_protein_1272355..1272505_NEGATIVE 229 50 1 137 69 NC_009009:SSA_2228|3end_Acetyltransferase_(GNAT)_family,_putative_2228271..2228421_NEGATIVE 228 50 1 142 85 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE 226 50 1 132 82 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 225 57 11 111 71 NC_009009:SSA_0915|3end_hypothetical_protein_928014..928164_POSITIVE 223 38 4 101 55 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE