Origin IGS: aattcaaaggttttaagagttttctcttaaagcctttttgcatggttttccatttgaaaaaacggagcaatcgtgttagaatagacctagtaatttttaaaggatagaggtgttatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gataacacctctatcctttaaaaattactaggtctattctaacacgattgctccgttttttcaaatggaaaaccatgcaaaaaggctttaagagaaaactcttaaaacctttgaatt Mask Tandem Repeat Region ================================================ aattcaaaggttttaagagttttctcttaaagcctttttgcatggttttccatttgaaaaaacggagcaatcgtgttagaatagacctagtaatttttaaaggatagaggtgttatc Find is-nt database================================================ Query_seq: SSA_0805:SSA_0806|SSA_0805:SSA_0806:Collagen-binding surface protein, putative:hypothetical protein:->->:789293..789409 117 aattcaaaggttttaagagttttctcttaaagcctttttgcatggttttccatttgaaaaaacggagcaatcgtgttagaatagacctagtaatttttaaaggatagaggtgttatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0805:SSA_0806|SSA_0805:SSA_0806:Collagen-binding surface protein, putative:hypothetical protein:->->:789293..789409 117 aattcaaaggttttaagagttttctcttaaagcctttttgcatggttttccatttgaaaaaacggagcaatcgtgttagaatagacctagtaatttttaaaggatagaggtgttatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0805:SSA_0806|SSA_0805:SSA_0806:Collagen-binding surface protein, putative:hypothetical protein:->->:789293..789409 117 aattcaaaggttttaagagttttctcttaaagcctttttgcatggttttccatttgaaaaaacggagcaatcgtgttagaatagacctagtaatttttaaaggatagaggtgttatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattcaaaggttttaagagttttctcttaaagcctttttgcatggttttccatttgaaaaaacggagcaatcgtgttagaatagacctagtaatttttaaaggatagaggtgttatc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 2 End: 94 . N L P K L L K R K F G K Q M T K W K F F R L L R T L I S R T M ....................... aattcaaaggttttaagagttttctcttaaagcctttttgcatggttttccatttgaaaaaacggagcaatcgtgttagaatagacctagtaatttttaaaggatagaggtgttatc 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: 88 Start: 53 End: 82 ....................................................TTTGAAAAAACGGAGCAATCGTGTTAGAAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattcaaaggttttaagagttttctcttaaagcctttttgcatggttttccatttgaaaaaacggagcaatcgtgttagaatagacctagtaatttttaaaggatagaggtgttatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0805:SSA_0806|SSA_0805:SSA_0806:Collagen-binding surface protein, putative:hypothetical protein:->->:789293..789409 117 aattcaaaggttttaagagttttctcttaaagcctttttgcatggttttccatttgaaaaaacggagcaatcgtgttagaatagacctagtaatttttaaaggatagaggtgttatc Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_009009_SSA_0805_SSA_0806|Collagen-binding surface protein, putative:hypothetical protein|POSITIVE:POSITIVE|[789293,789409]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 aattcaaaggttttaagagttttctcttaaagcctttttgcatggttttccatttgaaaaaacggagcaatcgtgttagaatagacctagtaatttttaaaggatagaggtgttatc aattcaaaggttttaagagttttctcttaaagcctttttgcatggttttccatttgaaaaaacggagcaatcgtgttagaatagacctagtaatttttaaaggatagaggtgttatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCAAAGGUUUUAAGAGUUUUCUCUUAAAGCCUUUUUGCAUGGUUUUCCAUUUGAAAAAACGGAGCAAUCGUGUUAGAAUAGACCUAGUAAUUUUUAAAGGAUAGAGGUGUUAUC .((((.(((((((((((((....)))))))))))))...((((((((((((.(((....))).)))).))))))))..))))..((((....((((.....))))..))))...... (-33.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAACACCUCUAUCCUUUAAAAAUUACUAGGUCUAUUCUAACACGAUUGCUCCGUUUUUUCAAAUGGAAAACCAUGCAAAAAGGCUUUAAGAGAAAACUCUUAAAACCUUUGAAUU ((((.......))))...............(((....((......))....(((((((....)))))))..)))......(((((.((((((((....)))))))).)))))..... (-19.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 50 1 98 60 NC_009009:SSA_1047|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_1061860..1062090_POSITIVE 283 77 31 61 6 NC_009009:SSA_2080|5end_hypothetical_protein_2085341..2085571_NEGATIVE 266 77 31 94 59 NC_009009:SSA_2381|5end_DegP_protein,_putative_2386298..2386528_POSITIVE 264 50 2 196 156 NC_009009:SSA_0249|5end_hypothetical_protein_241751..241981_POSITIVE 256 52 24 227 191 NC_009009:SSA_2090|5end_Hexulose-6-phosphate_synthase,_putative_2095038..2095268_NEGATIVE 255 50 4 194 152 NC_009009:SSA_1842|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_HTH_DNA-binding_domains),_putative_1836494..1836724_NEGATIVE 255 90 41 73 16 NC_009009:SSA_1038|5end_Lipoprotein,_putative_1052579..1052809_POSITIVE 252 48 5 212 161 NC_009009:SSA_0841|5end_hypothetical_protein_826935..827165_POSITIVE 247 70 22 228 173 NC_009009:SSA_0938|5end_hypothetical_protein_946587..946817_POSITIVE 245 58 16 81 42 NC_009009:SSA_0746|5end_Glucosamine-6-phosphate_deaminase,_putative_727078..727308_POSITIVE 233 52 19 52 13 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 233 73 31 209 171 NC_009009:SSA_0431|5end_hypothetical_protein_433275..433505_NEGATIVE 232 70 21 174 120 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 231 53 16 226 191 NC_009009:SSA_2253|5end_3-Methyladenine_DNA_glycosylase_I,_constitutive,_putative_2249424..2249654_NEGATIVE 231 60 16 192 140 NC_009009:SSA_1293|5end_hypothetical_protein_1312249..1312479_NEGATIVE 231 74 31 122 78 NC_009009:SSA_0292|5end_Transcriptional_regulator,_AraC_family_(arabinose_operon_control),_putative_286208..286438_POSITIVE 230 56 11 135 86 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 230 108 62 194 139 NC_009009:SSA_0122|5end_50S_ribosomal_protein_L6,_putative_115427..115657_POSITIVE 230 59 16 109 59 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 229 50 3 195 144 NC_009009:SSA_0177|5end_DNA-directed_RNA_polymerase_I,_beta_chain_(160_kDa_subunit),_putative_178405..178635_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 37 6 85 54 NC_009009:SSA_0805|3end_Collagen-binding_surface_protein,_putative_789232..789382_POSITIVE 261 73 31 75 34 NC_009009:SSA_1521|3end_Phosphoenolpyruvate_carboxylase,_putative_1527837..1527987_NEGATIVE 258 77 34 51 3 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 253 109 64 109 64 NC_009009:SSA_1683|3end_NrdI_protein,_putative_1677034..1677184_NEGATIVE 243 110 71 87 54 NC_009009:SSA_1217|3end_Conserved_uncharacterized_protein_1239736..1239886_POSITIVE 241 50 6 144 94 NC_009009:SSA_1869|3end_ATP-dependent_RNA_helicase,_putative_1864152..1864302_NEGATIVE 240 71 31 55 14 NC_009009:SSA_0685|3end_hypothetical_protein_669432..669582_POSITIVE 231 74 31 103 59 NC_009009:SSA_0291|3end_Oxidoreductase,_putative_286269..286419_POSITIVE 230 56 11 120 71 NC_009009:SSA_0434|3end_Glutamate_formiminotransferase,_putative_435669..435819_NEGATIVE 230 108 62 129 74 NC_009009:SSA_0121|3end_hypothetical_protein_115442..115592_POSITIVE 230 59 16 63 13 NC_009009:SSA_0079|3end_ROK_family_protein,_putative_83819..83969_POSITIVE 228 110 63 148 98 NC_009009:SSA_1444|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1446644..1446794_NEGATIVE 226 70 24 52 9 NC_009009:SSA_2316|3end_General_secretory_pathway_protein_F,_putative_2317116..2317266_NEGATIVE 221 80 31 113 55 NC_009009:SSA_1701|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1691299..1691449_NEGATIVE 221 51 11 88 30 NC_009009:SSA_1439|3end_hypothetical_protein_1443624..1443774_NEGATIVE 219 79 40 137 101 NC_009009:SSA_1016|3end_Phosphoenolpyruvate_synthase,_putative_1022165..1022315_POSITIVE 217 45 1 115 62 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE 216 110 61 89 37 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 216 69 22 79 41 NC_009009:SSA_1090|3end_Glucokinase,_putative_1108610..1108760_POSITIVE 214 78 31 122 68 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE