Origin IGS: ctcagaacgacagctcaagtctcaaagactgctgtcgttttttattgtcataaaataggaaatttccagtcgtttcctcttaataaagcctatattttatgatataatgatttgataa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttatcaaatcattatatcataaaatataggctttattaagaggaaacgactggaaatttcctattttatgacaataaaaaacgacagcagtctttgagacttgagctgtcgttctgag Mask Tandem Repeat Region ================================================ ctcagaacgacagctcaagtctcaaagactgctgtcgttttttattgtcataaaataggaaatttccagtcgtttcctcttaataaagcctatattttatgatataatgatttgataa Find is-nt database================================================ Query_seq: SSA_1525:SSA_1526|SSA_1525:SSA_1526:Lyzozyme M1 (1,4-beta-N-acetylmuramidase), putative:hypothetical protein:->->:1533744..1533861 118 ctcagaacgacagctcaagtctcaaagactgctgtcgttttttattgtcataaaataggaaatttccagtcgtttcctcttaataaagcctatattttatgatataatgatttgataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1525:SSA_1526|SSA_1525:SSA_1526:Lyzozyme M1 (1,4-beta-N-acetylmuramidase), putative:hypothetical protein:->->:1533744..1533861 118 ctcagaacgacagctcaagtctcaaagactgctgtcgttttttattgtcataaaataggaaatttccagtcgtttcctcttaataaagcctatattttatgatataatgatttgataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1525:SSA_1526|SSA_1525:SSA_1526:Lyzozyme M1 (1,4-beta-N-acetylmuramidase), putative:hypothetical protein:->->:1533744..1533861 118 ctcagaacgacagctcaagtctcaaagactgctgtcgttttttattgtcataaaataggaaatttccagtcgtttcctcttaataaagcctatattttatgatataatgatttgataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcagaacgacagctcaagtctcaaagactgctgtcgttttttattgtcataaaataggaaatttccagtcgtttcctcttaataaagcctatattttatgatataatgatttgataa Predict ORF larger than 30AA ================================================ ctcagaacgacagctcaagtctcaaagactgctgtcgttttttattgtcataaaataggaaatttccagtcgtttcctcttaataaagcctatattttatgatataatgatttgataa 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: 79 End: 108 ..............................................................................CTTAATAAAGCCTATATTTTATGATATAAT.......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctcagaacgacagctcaagtctcaaagactgctgtcgttttttattgtcataaaataggaaatttccagtcgtttcctcttaataaagcctatattttatgatataatgatttgataa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1525:SSA_1526|SSA_1525:SSA_1526:Lyzozyme M1 (1,4-beta-N-acetylmuramidase), putative:hypothetical protein:->->:1533744..1533861 118 ctcagaacgacagctcaagtctcaaagactgctgtcgttttttattgtcataaaataggaaatttccagtcgtttcctcttaataaagcctatattttatgatataatgatttgataa Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_009009_SSA_1525_SSA_1526|Lyzozyme M1 (1,4-beta-N-acetylmuramidase), putative:hypothetical protein|POSITIVE:POSITIVE|[1533744,1533861]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 ctcagaacgacagctcaagtctcaaagactgctgtcgttttttattgtcataaaataggaaatttccagtcgtttcctcttaataaagcctatattttatgatataatgatttgataa ctcagaacgacagctcaagtctcaaagactgctgtcgttttttattgtcataaaataggaaatttccagtcgtttcctcttaataaagcctatattttatgatataatgatttgataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAGAACGACAGCUCAAGUCUCAAAGACUGCUGUCGUUUUUUAUUGUCAUAAAAUAGGAAAUUUCCAGUCGUUUCCUCUUAAUAAAGCCUAUAUUUUAUGAUAUAAUGAUUUGAUAA ...(((((((((((...((((.....)))))))))))))))....((((((((((((((((((........)))))).(((....)))....)))))))))))).............. (-31.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUCAAAUCAUUAUAUCAUAAAAUAUAGGCUUUAUUAAGAGGAAACGACUGGAAAUUUCCUAUUUUAUGACAAUAAAAAACGACAGCAGUCUUUGAGACUUGAGCUGUCGUUCUGAG ...(((..........(((((((..(((((........((.(....)..))........))))))))))))........(((((((((((((.....))))...))))))))).))). (-28.59) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 39 1 171 130 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 267 41 1 229 184 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 260 50 1 84 37 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 256 39 9 41 5 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 255 35 3 63 16 NC_009009:SSA_1055|5end_Conserved_uncharacterized_protein_1070899..1071129_POSITIVE 254 42 2 200 156 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 253 78 31 117 60 NC_009009:SSA_0510|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_508523..508753_POSITIVE 250 49 4 208 165 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 249 80 31 102 53 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 249 60 17 46 9 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 248 76 34 219 172 NC_009009:SSA_1693|5end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1686811..1687041_NEGATIVE 246 49 4 76 39 NC_009009:SSA_2155|5end_hypothetical_protein_2156102..2156332_NEGATIVE 245 49 1 206 148 NC_009009:SSA_0546|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_540852..541082_POSITIVE 243 41 1 143 100 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 243 38 11 30 2 NC_009009:SSA_0901|5end_Alpha-acetolactate_decarboxylase,_putative_892447..892677_POSITIVE 242 40 1 151 114 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 241 50 4 169 122 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 240 49 2 67 18 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 239 50 1 68 11 NC_009009:SSA_1937|5end_Malonyl-CoA:ACP_transacylase,_putative_1924771..1925001_NEGATIVE 238 50 11 51 2 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 398 47 4 96 50 NC_009009:SSA_1525|3end_Lyzozyme_M1_(1,4-beta-N-acetylmuramidase),_putative_1533683..1533833_POSITIVE 302 39 1 53 12 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 280 40 1 77 32 NC_009009:SSA_1061|3end_50S_ribosomal_protein_L21,_putative_1077986..1078136_POSITIVE 263 43 1 107 62 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 255 35 3 57 10 NC_009009:SSA_1054|3end_CBS_domain_protein,_putative_1070973..1071123_POSITIVE 253 48 4 83 45 NC_009009:SSA_2135|3end_Transcriptional_repressor,_DeoR_family_(possibly_truncated),_putative_2137474..2137624_POSITIVE 250 39 12 35 7 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 250 49 4 95 52 NC_009009:SSA_0748|3end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_730635..730785_POSITIVE 249 60 17 46 9 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 244 44 3 77 46 NC_009009:SSA_0739|3end_Carbamate_kinase,_putative_722114..722264_POSITIVE 243 49 1 101 55 NC_009009:SSA_1253|3end_hypothetical_protein_1280976..1281126_NEGATIVE 243 41 1 131 88 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 240 49 2 74 25 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 239 50 1 75 18 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 237 49 2 77 27 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 236 98 59 105 62 NC_009009:SSA_1847|3end_RRNA_methyltransferase_RsmB,_putative_1840937..1841087_NEGATIVE 235 43 4 122 71 NC_009009:SSA_2068|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_2070931..2071081_NEGATIVE 234 50 1 85 26 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 233 92 52 104 51 NC_009009:SSA_1207|3end_Phosphate_acetyltransferase,_putative_1231297..1231447_NEGATIVE 232 53 13 121 81 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE