Origin IGS: atctctacctcatacacttctagtcctactattatactaaaaaatcccccgtatttcaaaaaatagctagtattgctctgaaaatggaagttgcaagaaaaaagctctcagaaaattccgagagcttattatttcactacatgagatagtcaaggaaacattaaaatttcccctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaggggaaattttaatgtttccttgactatctcatgtagtgaaataataagctctcggaattttctgagagcttttttcttgcaacttccattttcagagcaatactagctattttttgaaatacgggggattttttagtataatagtaggactagaagtgtatgaggtagagat Mask Tandem Repeat Region ================================================ atctctacctcatacacttctagtcctactattatactaaaaaatcccccgtatttcaaaaaatagctagtattgctctgaaaatggaagttgcaagaaaaaagctctcagaaaattccgagagcttattatttcactacatgagatagtcaaggaaacattaaaatttcccctt Find is-nt database================================================ Query_seq: SSA_1958:SSA_1959|SSA_1958:SSA_1959:Adapter protein mecA, putative:Undecaprenyl-diphosphatase, putative:<-<-:1955504..1955678 175 atctctacctcatacacttctagtcctactattatactaaaaaatcccccgtatttcaaaaaatagctagtattgctctgaaaatggaagttgcaagaaaaaagctctcagaaaattccgagagcttattatttcactacatgagatagtcaaggaaacattaaaatttcccctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1958:SSA_1959|SSA_1958:SSA_1959:Adapter protein mecA, putative:Undecaprenyl-diphosphatase, putative:<-<-:1955504..1955678 175 atctctacctcatacacttctagtcctactattatactaaaaaatcccccgtatttcaaaaaatagctagtattgctctgaaaatggaagttgcaagaaaaaagctctcagaaaattccgagagcttattatttcactacatgagatagtcaaggaaacattaaaatttcccctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1958:SSA_1959|SSA_1958:SSA_1959:Adapter protein mecA, putative:Undecaprenyl-diphosphatase, putative:<-<-:1955504..1955678 175 atctctacctcatacacttctagtcctactattatactaaaaaatcccccgtatttcaaaaaatagctagtattgctctgaaaatggaagttgcaagaaaaaagctctcagaaaattccgagagcttattatttcactacatgagatagtcaaggaaacattaaaatttcccctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atctctacctcatacacttctagtcctactattatactaaaaaatcccccgtatttcaaaaaatagctagtattgctctgaaaatggaagttgcaagaaaaaagctctcagaaaattccgagagcttattatttcactacatgagatagtcaaggaaacattaaaatttcccctt Predict ORF larger than 30AA ================================================ atctctacctcatacacttctagtcctactattatactaaaaaatcccccgtatttcaaaaaatagctagtattgctctgaaaatggaagttgcaagaaaaaagctctcagaaaattccgagagcttattatttcactacatgagatagtcaaggaaacattaaaatttcccctt 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: 91 Start: 31 End: 60 ..............................TTTGAAATACGGGGGATTTTTTAGTATAAT................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atctctacctcatacacttctagtcctactattatactaaaaaatcccccgtatttcaaaaaatagctagtattgctctgaaaatggaagttgcaagaaaaaagctctcagaaaattccgagagcttattatttcactacatgagatagtcaaggaaacattaaaatttcccctt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.9 Tail_Score: -5.45652 Start: 104 End: 125 Full_Region: gtagtgaaataataa gctctcgga attt tctgagagc ttttttcttgcaact .......................................................................................................gctctcggaattttctgagagc.................................................. Find igs database================================================ Query_seq: SSA_1958:SSA_1959|SSA_1958:SSA_1959:Adapter protein mecA, putative:Undecaprenyl-diphosphatase, putative:<-<-:1955504..1955678 175 atctctacctcatacacttctagtcctactattatactaaaaaatcccccgtatttcaaaaaatagctagtattgctctgaaaatggaagttgcaagaaaaaagctctcagaaaattccgagagcttattatttcactacatgagatagtcaaggaaacattaaaatttcccctt Intra-Species Hit: Count: 1 Min: 1 Max: 175 Len: 175 Subject: NC_009009_SSA_1958_SSA_1959|Adapter protein mecA, putative:Undecaprenyl-diphosphatase, putative|NEGATIVE:NEGATIVE|[1955504,1955678]|175 HSP 1 e-value: 8.0E-95 bit: 347.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 atctctacctcatacacttctagtcctactattatactaaaaaatcccccgtatttcaaaaaatagctagtattgctctgaaaatggaagttgcaagaaaaaagctctcagaaaattccgagagcttattatttcactacatgagatagtcaaggaaacattaaaatttcccctt atctctacctcatacacttctagtcctactattatactaaaaaatcccccgtatttcaaaaaatagctagtattgctctgaaaatggaagttgcaagaaaaaagctctcagaaaattccgagagcttattatttcactacatgagatagtcaaggaaacattaaaatttcccctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUCUACCUCAUACACUUCUAGUCCUACUAUUAUACUAAAAAAUCCCCCGUAUUUCAAAAAAUAGCUAGUAUUGCUCUGAAAAUGGAAGUUGCAAGAAAAAAGCUCUCAGAAAAUUCCGAGAGCUUAUUAUUUCACUACAUGAGAUAGUCAAGGAAACAUUAAAAUUUCCCCUU ....(((.(((((..(((((((...........((((((............................))))))...........))))))).....((((.((((((((.((....)).))))))))....)))).....))))).)))....(((((........))))).... (-31.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGGGAAAUUUUAAUGUUUCCUUGACUAUCUCAUGUAGUGAAAUAAUAAGCUCUCGGAAUUUUCUGAGAGCUUUUUUCUUGCAACUUCCAUUUUCAGAGCAAUACUAGCUAUUUUUUGAAAUACGGGGGAUUUUUUAGUAUAAUAGUAGGACUAGAAGUGUAUGAGGUAGAGAU ..((((((((......))))))))..(((((((((((((.((((....(((((((((((....))))))))))).))))))))..(((((..((((((((.((((.....))))))))))))...)))))..((((((((.((....))..))))))))...))))))))).... (-53.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 839 50 1 141 92 NC_009009:SSA_1958|5end_Adapter_protein_mecA,_putative_1955413..1955643_NEGATIVE 311 106 63 77 30 NC_009009:SSA_1536|5end_Biotin_synthase,_putative_1543609..1543839_POSITIVE 309 48 4 159 112 NC_009009:SSA_0281|5end_hypothetical_protein_273404..273634_POSITIVE 272 49 1 142 90 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 254 108 63 191 144 NC_009009:SSA_2204|5end_hypothetical_protein_2204663..2204893_POSITIVE 254 119 75 61 17 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 254 134 91 225 173 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 251 125 89 211 176 NC_009009:SSA_1928|5end_Acyl-CoA_dehydrogenase,_putative_1917010..1917240_NEGATIVE 247 145 103 94 35 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 241 49 2 148 100 NC_009009:SSA_0005|5end_GTP-binding_protein,_putative_3821..4051_POSITIVE 239 157 115 192 149 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 238 110 67 223 181 NC_009009:SSA_1500|5end_Translation_initiation_factor_IF-3,_putative_1504921..1505151_NEGATIVE 237 38 2 135 93 NC_009009:SSA_0623|5end_hypothetical_protein_614512..614742_POSITIVE 236 123 84 53 15 NC_009009:SSA_0424|5end_Exopolysaccharide_biosynthesis_protein,_putative_422233..422463_NEGATIVE 234 119 79 176 136 NC_009009:SSA_2375|5end_Tryptophanyl-tRNA_synthetase,_putative_2378246..2378476_NEGATIVE 231 125 84 59 6 NC_009009:SSA_0181|5end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_184902..185132_POSITIVE 230 128 85 69 19 NC_009009:SSA_2060|5end_Arabinose_efflux_permease,_putative_2062403..2062633_NEGATIVE 230 158 113 187 126 NC_009009:SSA_0225|5end_10_kDa_chaperonin_218642..218872_POSITIVE 226 90 46 187 147 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 225 31 1 119 92 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 155 115 119 77 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 285 110 66 65 19 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE 267 109 64 66 13 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 259 48 7 45 1 NC_009009:SSA_0279|3end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_273370..273520_POSITIVE 254 126 84 73 27 NC_009009:SSA_0868|3end_hypothetical_protein_860675..860825_NEGATIVE 238 110 67 49 7 NC_009009:SSA_1501|3end_Cytidylate_kinase,_putative_1505095..1505245_NEGATIVE 236 123 84 56 18 NC_009009:SSA_0425|3end_Glycosyltransferase,_putative_422230..422380_NEGATIVE 231 148 101 61 8 NC_009009:SSA_0304|3end_Bacterial_cell_wall_degradation_(CHAP/LysM_domains),_putative_301888..302038_POSITIVE 231 125 84 66 13 NC_009009:SSA_0180|3end_hypothetical_protein_184989..185139_POSITIVE 225 31 1 122 95 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 224 126 83 137 96 NC_009009:SSA_0867|3end_hypothetical_protein_860711..860861_POSITIVE 220 136 100 74 36 NC_009009:SSA_2107|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2109295..2109445_NEGATIVE 220 130 90 87 37 NC_009009:SSA_0694|3end_Mutator_protein,_putative_678421..678571_POSITIVE 219 90 47 139 102 NC_009009:SSA_1005|3end_Sugar_ABC_transporter,_permease_protein,_putative_1006941..1007091_POSITIVE 218 127 81 67 6 NC_009009:SSA_1053|3end_Pyruvate_phosphate_dikinase,_putative_1067447..1067597_NEGATIVE 217 49 8 61 17 NC_009009:SSA_1889|3end_Conserved_uncharacterized_protein_1886283..1886433_NEGATIVE 217 50 3 138 84 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 217 83 45 133 82 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 214 59 22 57 12 NC_009009:SSA_0190|3end_hypothetical_protein_191905..192055_POSITIVE 213 31 1 118 80 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE