Origin IGS: cttgtcctctattctattatcctaactattataccaaaaaattgaccatcctgcttaccctcaaatctaagaagcagaaaagcgagccagagactcgcttcttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caagaagcgagtctctggctcgcttttctgcttcttagatttgagggtaagcaggatggtcaattttttggtataatagttaggataatagaatagaggacaag Mask Tandem Repeat Region ================================================ cttgtcctctattctattatcctaactattataccaaaaaattgaccatcctgcttaccctcaaatctaagaagcagaaaagcgagccagagactcgcttcttg Find is-nt database================================================ Query_seq: SSA_1869:SSA_1870|SSA_1869:SSA_1870:ATP-dependent RNA helicase, putative:Phospho-N-acetylmuramoyl-pentapeptide- transferase, putative:<-<-:1865586..1865689 104 cttgtcctctattctattatcctaactattataccaaaaaattgaccatcctgcttaccctcaaatctaagaagcagaaaagcgagccagagactcgcttcttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1869:SSA_1870|SSA_1869:SSA_1870:ATP-dependent RNA helicase, putative:Phospho-N-acetylmuramoyl-pentapeptide- transferase, putative:<-<-:1865586..1865689 104 cttgtcctctattctattatcctaactattataccaaaaaattgaccatcctgcttaccctcaaatctaagaagcagaaaagcgagccagagactcgcttcttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1869:SSA_1870|SSA_1869:SSA_1870:ATP-dependent RNA helicase, putative:Phospho-N-acetylmuramoyl-pentapeptide- transferase, putative:<-<-:1865586..1865689 104 cttgtcctctattctattatcctaactattataccaaaaaattgaccatcctgcttaccctcaaatctaagaagcagaaaagcgagccagagactcgcttcttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttgtcctctattctattatcctaactattataccaaaaaattgaccatcctgcttaccctcaaatctaagaagcagaaaagcgagccagagactcgcttcttg Predict ORF larger than 30AA ================================================ cttgtcctctattctattatcctaactattataccaaaaaattgaccatcctgcttaccctcaaatctaagaagcagaaaagcgagccagagactcgcttcttg Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttgtcctctattctattatcctaactattataccaaaaaattgaccatcctgcttaccctcaaatctaagaagcagaaaagcgagccagagactcgcttcttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1869:SSA_1870|SSA_1869:SSA_1870:ATP-dependent RNA helicase, putative:Phospho-N-acetylmuramoyl-pentapeptide- transferase, putative:<-<-:1865586..1865689 104 cttgtcctctattctattatcctaactattataccaaaaaattgaccatcctgcttaccctcaaatctaagaagcagaaaagcgagccagagactcgcttcttg Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_009009_SSA_1869_SSA_1870|ATP-dependent RNA helicase, putative:Phospho-N-acetylmuramoyl-pentapeptide- transferase, putative|NEGATIVE:NEGATIVE|[1865586,1865689]|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 cttgtcctctattctattatcctaactattataccaaaaaattgaccatcctgcttaccctcaaatctaagaagcagaaaagcgagccagagactcgcttcttg cttgtcctctattctattatcctaactattataccaaaaaattgaccatcctgcttaccctcaaatctaagaagcagaaaagcgagccagagactcgcttcttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGUCCUCUAUUCUAUUAUCCUAACUAUUAUACCAAAAAAUUGACCAUCCUGCUUACCCUCAAAUCUAAGAAGCAGAAAAGCGAGCCAGAGACUCGCUUCUUG ..................................................((((((...............))))))..(((((((.......))))))).... (-14.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGAAGCGAGUCUCUGGCUCGCUUUUCUGCUUCUUAGAUUUGAGGGUAAGCAGGAUGGUCAAUUUUUUGGUAUAAUAGUUAGGAUAAUAGAAUAGAGGACAAG ..((((((((((.....))))))))))(((((((((........))).))))))....(((....(((((.(((..(....)..))).))))).....)))... (-25.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 976 100 51 191 142 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 382 89 41 56 1 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 377 90 46 179 133 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 369 100 62 45 5 NC_009009:SSA_0215|5end_Periplasmic_sugar-binding_protein_(ribose_porter),_putative_210891..211121_POSITIVE 301 98 70 40 13 NC_009009:SSA_0639|5end_hypothetical_protein_627906..628136_NEGATIVE 300 100 51 230 178 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 292 98 51 183 127 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 290 100 61 231 188 NC_009009:SSA_0409|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_405605..405835_NEGATIVE 284 89 48 36 2 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 283 100 74 131 105 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 279 98 51 52 1 NC_009009:SSA_1694|5end_PTS_system,_lactose-specific_IIA_component,_putative_1687128..1687358_NEGATIVE 277 48 1 149 94 NC_009009:SSA_0356|5end_Dipeptidase,_putative_349259..349489_POSITIVE 274 87 46 67 35 NC_009009:SSA_1267|5end_crcB-like_protein_2,_putative_1291347..1291577_NEGATIVE 273 98 63 179 135 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 272 99 51 219 179 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 269 100 59 63 18 NC_009009:SSA_1930|5end_Acetyl-CoA_carboxylase_alpha_subunit,_putative_1918547..1918777_NEGATIVE 269 98 51 208 160 NC_009009:SSA_1665|5end_hypothetical_protein_1665353..1665583_NEGATIVE 268 99 53 51 19 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 267 98 52 159 112 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 267 89 46 42 5 NC_009009:SSA_1382|5end_hypothetical_protein_1400270..1400500_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 100 51 86 43 NC_009009:SSA_1030|3end_Transcriptional_regulator,_TetR_family,_putative_1047749..1047899_POSITIVE 290 100 61 86 43 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 283 100 74 66 40 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 277 48 1 70 15 NC_009009:SSA_0355|3end_DNA_mismatch_repair_protein,_putative_349260..349410_POSITIVE 274 87 46 67 35 NC_009009:SSA_1268|3end_Chorismate_mutase/prephenate_dehydratase,_putative_1291347..1291497_NEGATIVE 269 100 59 66 21 NC_009009:SSA_1931|3end_Acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta,_putative_1918544..1918694_NEGATIVE 268 99 53 58 26 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 267 98 52 74 27 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 261 97 51 63 21 NC_009009:SSA_2135|3end_Transcriptional_repressor,_DeoR_family_(possibly_truncated),_putative_2137474..2137624_POSITIVE 261 99 71 80 47 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 258 90 53 55 12 NC_009009:SSA_1051|3end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1066808..1066958_POSITIVE 254 83 46 151 113 NC_009009:SSA_2335|3end_D-Ala-teichoic_acid_biosynthesis_protein,_putative_2338027..2338177_NEGATIVE 254 90 46 55 5 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 253 49 1 72 11 NC_009009:SSA_2177|3end_hypothetical_protein_2175232..2175382_NEGATIVE 250 90 46 62 3 NC_009009:SSA_1796|3end_Transcription_elongation_factor_GreA,_putative_1777825..1777975_NEGATIVE 248 89 46 124 86 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 245 93 66 46 19 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 244 95 52 130 94 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 243 99 53 73 26 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 242 88 46 47 15 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE