Origin IGS: acctttacatcagttctttggagctggtgttttttggtatttgaaagaagctataatcataggaatagaaaaagcctacttcaagtgaagcgggctttttaaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcttaaaaagcccgcttcacttgaagtaggctttttctattcctatgattatagcttctttcaaataccaaaaaacaccagctccaaagaactgatgtaaaggt Mask Tandem Repeat Region ================================================ acctttacatcagttctttggagctggtgttttttggtatttgaaagaagctataatcataggaatagaaaaagcctacttcaagtgaagcgggctttttaaga Find is-nt database================================================ Query_seq: SSA_1041:SSA_1042|SSA_1041:SSA_1042:Sugar ABC transporter, permease protein, putative:Xylanase/chitin deacetylase, putative:-><-:1057495..1057598 104 acctttacatcagttctttggagctggtgttttttggtatttgaaagaagctataatcataggaatagaaaaagcctacttcaagtgaagcgggctttttaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1041:SSA_1042|SSA_1041:SSA_1042:Sugar ABC transporter, permease protein, putative:Xylanase/chitin deacetylase, putative:-><-:1057495..1057598 104 acctttacatcagttctttggagctggtgttttttggtatttgaaagaagctataatcataggaatagaaaaagcctacttcaagtgaagcgggctttttaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1041:SSA_1042|SSA_1041:SSA_1042:Sugar ABC transporter, permease protein, putative:Xylanase/chitin deacetylase, putative:-><-:1057495..1057598 104 acctttacatcagttctttggagctggtgttttttggtatttgaaagaagctataatcataggaatagaaaaagcctacttcaagtgaagcgggctttttaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acctttacatcagttctttggagctggtgttttttggtatttgaaagaagctataatcataggaatagaaaaagcctacttcaagtgaagcgggctttttaaga Predict ORF larger than 30AA ================================================ acctttacatcagttctttggagctggtgttttttggtatttgaaagaagctataatcataggaatagaaaaagcctacttcaagtgaagcgggctttttaaga 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: 83 Start: 56 End: 85 .......................................................CTTGAAGTAGGCTTTTTCTATTCCTATGAT................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acctttacatcagttctttggagctggtgttttttggtatttgaaagaagctataatcataggaatagaaaaagcctacttcaagtgaagcgggctttttaaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1041:SSA_1042|SSA_1041:SSA_1042:Sugar ABC transporter, permease protein, putative:Xylanase/chitin deacetylase, putative:-><-:1057495..1057598 104 acctttacatcagttctttggagctggtgttttttggtatttgaaagaagctataatcataggaatagaaaaagcctacttcaagtgaagcgggctttttaaga Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_009009_SSA_1041_SSA_1042|Sugar ABC transporter, permease protein, putative:Xylanase/chitin deacetylase, putative|POSITIVE:NEGATIVE|[1057495,1057598]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 acctttacatcagttctttggagctggtgttttttggtatttgaaagaagctataatcataggaatagaaaaagcctacttcaagtgaagcgggctttttaaga acctttacatcagttctttggagctggtgttttttggtatttgaaagaagctataatcataggaatagaaaaagcctacttcaagtgaagcgggctttttaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUUUACAUCAGUUCUUUGGAGCUGGUGUUUUUUGGUAUUUGAAAGAAGCUAUAAUCAUAGGAAUAGAAAAAGCCUACUUCAAGUGAAGCGGGCUUUUUAAGA .(((..((((((((((....))))))))))....((((.(((....))))))).......))).....((((((((..((((....))))..)))))))).... (-33.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUAAAAAGCCCGCUUCACUUGAAGUAGGCUUUUUCUAUUCCUAUGAUUAUAGCUUCUUUCAAAUACCAAAAAACACCAGCUCCAAAGAACUGAUGUAAAGGU ....((((((((..((((....))))..)))))))).....(((.(((............)))...........(((.(((.((....)).))).)))..))). (-21.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 80 34 65 21 NC_009009:SSA_1515|5end_hypothetical_protein_1522129..1522359_NEGATIVE 265 77 33 193 147 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 257 38 3 141 100 NC_009009:SSA_1074|5end_Pyrroline-5-carboxylate_reductase,_putative_1092151..1092381_POSITIVE 253 95 71 149 121 NC_009009:SSA_1368|5end_hypothetical_protein_1384077..1384307_NEGATIVE 253 97 57 194 158 NC_009009:SSA_0095|5end_Threonine_synthase,_putative_96555..96785_POSITIVE 250 47 6 55 8 NC_009009:SSA_2222|5end_Tyrosine-protein_kinase_Wze,_putative_2223997..2224227_NEGATIVE 250 82 43 152 107 NC_009009:SSA_1914|5end_hypothetical_protein_1905195..1905425_NEGATIVE 249 59 11 57 5 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 248 100 72 198 167 NC_009009:SSA_1470|5end_3-dehydroquinate_dehydratase,_putative_1476984..1477214_NEGATIVE 247 99 67 113 76 NC_009009:SSA_0432|5end_Formate--tetrahydrofolate_ligase,_putative_434991..435221_NEGATIVE 246 29 2 31 2 NC_009009:SSA_1325|5end_Ketoacyl_reductase_hetN,_putative_1342343..1342573_NEGATIVE 245 100 58 228 187 NC_009009:SSA_0229|5end_hypothetical_protein_223535..223765_POSITIVE 245 100 58 56 15 NC_009009:SSA_0228|5end_hypothetical_protein_223363..223593_POSITIVE 234 29 1 127 101 NC_009009:SSA_1843|5end_Histidine_kinase,_putative_1837491..1837721_NEGATIVE 232 36 10 179 147 NC_009009:SSA_2374|5end_Inosine-5'-monophosphate_dehydrogenase,_putative_2377015..2377245_NEGATIVE 231 38 2 52 22 NC_009009:SSA_2061|5end_Peptide_deformylase,_putative_2062547..2062777_POSITIVE 230 100 60 214 155 NC_009009:SSA_0939|5end_Inositol_monophosphatase_(Mg++_dependent),_putative_946810..947040_POSITIVE 229 100 56 228 194 NC_009009:SSA_1189|5end_GTP-binding_protein,_putative_1217657..1217887_NEGATIVE 229 46 2 131 96 NC_009009:SSA_0467|5end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_470588..470818_POSITIVE 227 96 61 222 179 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 100 62 61 26 NC_009009:SSA_0429|3end_Histidine_ammonia-lyase,_putative_429701..429851_NEGATIVE 289 97 52 55 13 NC_009009:SSA_2052|3end_Thioredoxin,_putative_2057193..2057343_NEGATIVE 282 97 65 73 42 NC_009009:SSA_0144|3end_Transcriptional_regulator,_TetR_family,_putative_137993..138143_NEGATIVE 273 96 60 105 66 NC_009009:SSA_1548|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_1551119..1551269_NEGATIVE 267 80 34 65 21 NC_009009:SSA_1516|3end_Cell-wall_biogenesis_glycosyltransferase,_putative_1522129..1522279_NEGATIVE 257 38 3 138 97 NC_009009:SSA_1073|3end_Gamma-glutamyl_phosphate_reductase,_putative_1092228..1092378_POSITIVE 253 95 71 84 56 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE 253 97 57 81 45 NC_009009:SSA_0094|3end_Cell_wall_metabolism,_LysM_type_protein,_putative_96522..96672_POSITIVE 250 82 43 71 26 NC_009009:SSA_1915|3end_hypothetical_protein_1905276..1905426_NEGATIVE 247 99 67 76 39 NC_009009:SSA_0433|3end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435028..435178_NEGATIVE 246 44 1 104 53 NC_009009:SSA_1041|3end_Sugar_ABC_transporter,_permease_protein,_putative_1057434..1057584_POSITIVE 242 94 55 57 1 NC_009009:SSA_1549|3end_hypothetical_protein_1551816..1551966_NEGATIVE 238 38 10 150 122 NC_009009:SSA_1339|3end_Pneumococcal_histidine_triad_protein_D_precursor,_putative_1351879..1352029_NEGATIVE 236 43 2 44 8 NC_009009:SSA_1532|3end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1539460..1539610_NEGATIVE 236 100 58 70 36 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 235 98 53 122 65 NC_009009:SSA_1341|3end_Carbamoyl-phosphate_synthase_large_chain,_putative_1356648..1356798_NEGATIVE 234 94 57 61 15 NC_009009:SSA_2094|3end_Conserved_uncharacterized_protein_2097990..2098140_NEGATIVE 234 29 1 130 104 NC_009009:SSA_1844|3end_hypothetical_protein_1837488..1837638_NEGATIVE 229 100 56 86 52 NC_009009:SSA_1190|3end_Conserved_uncharacterized_protein_1217799..1217949_NEGATIVE 229 46 2 131 96 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE