Origin IGS: agtaaaaatatcctttcttctttgacaactattatagaagattcagaggcaaaaacaagggcttttcagtaagtggtattaaccatcaggtatccggtaagaaaacgatggtcagttgcataaaaaaacaagcgtcaatgttcattgacacttgttttctgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacagaaaacaagtgtcaatgaacattgacgcttgtttttttatgcaactgaccatcgttttcttaccggatacctgatggttaataccacttactgaaaagcccttgtttttgcctctgaatcttctataatagttgtcaaagaagaaaggatatttttact Mask Tandem Repeat Region ================================================ agtaaaaatatcctttcttctttgacaactattatagaagattcagaggcaaaaacaagggcttttcagtaagtggtattaaccatcaggtatccggtaagaaaacgatggtcagttgcataaaaaaacaagcgtcaatgttcattgacacttgttttctgtt Find is-nt database================================================ Query_seq: SSA_1662:SSA_1663|SSA_1662:SSA_1663:NADH-dependent oxidoreductase, putative:Collagen-binding protein A:<-<-:1659513..1659675 163 agtaaaaatatcctttcttctttgacaactattatagaagattcagaggcaaaaacaagggcttttcagtaagtggtattaaccatcaggtatccggtaagaaaacgatggtcagttgcataaaaaaacaagcgtcaatgttcattgacacttgttttctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1662:SSA_1663|SSA_1662:SSA_1663:NADH-dependent oxidoreductase, putative:Collagen-binding protein A:<-<-:1659513..1659675 163 agtaaaaatatcctttcttctttgacaactattatagaagattcagaggcaaaaacaagggcttttcagtaagtggtattaaccatcaggtatccggtaagaaaacgatggtcagttgcataaaaaaacaagcgtcaatgttcattgacacttgttttctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1662:SSA_1663|SSA_1662:SSA_1663:NADH-dependent oxidoreductase, putative:Collagen-binding protein A:<-<-:1659513..1659675 163 agtaaaaatatcctttcttctttgacaactattatagaagattcagaggcaaaaacaagggcttttcagtaagtggtattaaccatcaggtatccggtaagaaaacgatggtcagttgcataaaaaaacaagcgtcaatgttcattgacacttgttttctgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtaaaaatatcctttcttctttgacaactattatagaagattcagaggcaaaaacaagggcttttcagtaagtggtattaaccatcaggtatccggtaagaaaacgatggtcagttgcataaaaaaacaagcgtcaatgttcattgacacttgttttctgtt Predict ORF larger than 30AA ================================================ agtaaaaatatcctttcttctttgacaactattatagaagattcagaggcaaaaacaagggcttttcagtaagtggtattaaccatcaggtatccggtaagaaaacgatggtcagttgcataaaaaaacaagcgtcaatgttcattgacacttgttttctgtt 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================================================ agtaaaaatatcctttcttctttgacaactattatagaagattcagaggcaaaaacaagggcttttcagtaagtggtattaaccatcaggtatccggtaagaaaacgatggtcagttgcataaaaaaacaagcgtcaatgttcattgacacttgttttctgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1662:SSA_1663|SSA_1662:SSA_1663:NADH-dependent oxidoreductase, putative:Collagen-binding protein A:<-<-:1659513..1659675 163 agtaaaaatatcctttcttctttgacaactattatagaagattcagaggcaaaaacaagggcttttcagtaagtggtattaaccatcaggtatccggtaagaaaacgatggtcagttgcataaaaaaacaagcgtcaatgttcattgacacttgttttctgtt Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: NC_009009_SSA_1662_SSA_1663|NADH-dependent oxidoreductase, putative:Collagen-binding protein A|NEGATIVE:NEGATIVE|[1659513,1659675]|163 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 agtaaaaatatcctttcttctttgacaactattatagaagattcagaggcaaaaacaagggcttttcagtaagtggtattaaccatcaggtatccggtaagaaaacgatggtcagttgcatnnnnnnncaagcgtcaatgttcattgacacttgttttctgtt agtaaaaatatcctttcttctttgacaactattatagaagattcagaggcaaaaacaagggcttttcagtaagtggtattaaccatcaggtatccggtaagaaaacgatggtcagttgcataaaaaaacaagcgtcaatgttcattgacacttgttttctgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAAAAAUAUCCUUUCUUCUUUGACAACUAUUAUAGAAGAUUCAGAGGCAAAAACAAGGGCUUUUCAGUAAGUGGUAUUAACCAUCAGGUAUCCGGUAAGAAAACGAUGGUCAGUUGCAUAAAAAAACAAGCGUCAAUGUUCAUUGACACUUGUUUUCUGUU .((((.(((((((((((((((.(((......))).))))))...((((((..........))))))....))).)))))).((((((.(...((......))...)))))))...)))).....((((((((.((((((....)))))).))))))))..... (-34.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGAAAACAAGUGUCAAUGAACAUUGACGCUUGUUUUUUUAUGCAACUGACCAUCGUUUUCUUACCGGAUACCUGAUGGUUAAUACCACUUACUGAAAAGCCCUUGUUUUUGCCUCUGAAUCUUCUAUAAUAGUUGUCAAAGAAGAAAGGAUAUUUUUACU ...(((((((((((((((((....)))))))))))))))))........(((((((((...(((....)))....)))))))))...........((((((..((((.(((((((..(((............)))..).))))))...))))...)))))).. (-39.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 899 120 71 211 162 NC_009009:SSA_1662|5end_NADH-dependent_oxidoreductase,_putative_1659422..1659652_NEGATIVE 368 76 31 168 123 NC_009009:SSA_1664|5end_Phosphatidylethanolamine_N-methyltransferase,_putative_1665189..1665419_NEGATIVE 324 78 31 169 120 NC_009009:SSA_1982|5end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975873..1976103_NEGATIVE 296 67 21 218 172 NC_009009:SSA_0614|5end_Transporter,_putative_607974..608204_NEGATIVE 285 84 42 65 18 NC_009009:SSA_1375|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1394827..1395057_NEGATIVE 275 100 56 210 154 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 268 122 81 62 19 NC_009009:SSA_0418|5end_AraC-type_DNA-binding_domain-containing_protein,_putative_415256..415486_POSITIVE 266 75 36 72 24 NC_009009:SSA_0841|5end_hypothetical_protein_826935..827165_POSITIVE 260 98 58 73 33 NC_009009:SSA_1133|5end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159397..1159627_POSITIVE 257 99 55 197 145 NC_009009:SSA_0925|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_934749..934979_POSITIVE 257 120 81 44 1 NC_009009:SSA_0415|5end_Permease,_putative_410568..410798_POSITIVE 256 90 44 93 49 NC_009009:SSA_1317|5end_hypothetical_protein_1333544..1333774_NEGATIVE 256 69 28 130 95 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 254 120 72 80 34 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 247 89 44 67 23 NC_009009:SSA_0231|5end_Conserved_uncharacterized_protein_225713..225943_POSITIVE 246 115 72 177 131 NC_009009:SSA_1946|5end_Oligopeptide_transport_system_permease_protein,_putative_1938624..1938854_NEGATIVE 245 150 105 169 122 NC_009009:SSA_0033|5end_Phosphoribosylglycinamide_(GAR)_formyltransferase,_putative_38957..39187_POSITIVE 244 86 43 41 4 NC_009009:SSA_2167|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2167371..2167601_NEGATIVE 243 114 72 56 5 NC_009009:SSA_1727|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713420..1713650_NEGATIVE 242 120 73 206 152 NC_009009:SSA_1061|5end_50S_ribosomal_protein_L21,_putative_1077592..1077822_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 76 31 135 90 NC_009009:SSA_1665|3end_hypothetical_protein_1665222..1665372_NEGATIVE 266 75 36 70 22 NC_009009:SSA_0839|3end_hypothetical_protein_827013..827163_POSITIVE 260 98 58 73 33 NC_009009:SSA_1132|3end_TatC,_sec-independent_protein_translocase,_putative_1159477..1159627_POSITIVE 254 120 72 78 32 NC_009009:SSA_0463|3end_Cobyrinic_acid_A,C-diamide_synthase,_putative_468303..468453_POSITIVE 248 78 44 110 71 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 243 114 72 52 1 NC_009009:SSA_1728|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713424..1713574_NEGATIVE 241 121 87 146 102 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 238 88 47 148 106 NC_009009:SSA_0859|3end_Triosephosphate_isomerase,_putative_847485..847635_POSITIVE 238 99 57 140 97 NC_009009:SSA_0599|3end_hypothetical_protein_589007..589157_POSITIVE 237 98 55 141 99 NC_009009:SSA_2103|3end_hypothetical_protein_2106500..2106650_NEGATIVE 235 90 49 58 17 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 232 119 72 62 9 NC_009009:SSA_1308|3end_hypothetical_protein_1326267..1326417_NEGATIVE 230 49 7 97 51 NC_009009:SSA_2006|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme,_putative_2006583..2006733_NEGATIVE 230 75 35 82 39 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE 228 113 82 129 98 NC_009009:SSA_1313|3end_hypothetical_protein_1329715..1329865_NEGATIVE 227 110 62 54 6 NC_009009:SSA_0848|3end_Pyruvate_kinase_I,_fructose-stimulated,_putative_836024..836174_POSITIVE 227 98 58 91 34 NC_009009:SSA_0730|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_715167..715317_POSITIVE 226 98 62 141 98 NC_009009:SSA_1559|3end_Conserved_uncharacterized_protein_1560862..1561012_NEGATIVE 226 97 58 147 113 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 226 60 11 121 68 NC_009009:SSA_0725|3end_hypothetical_protein_710812..710962_POSITIVE