Origin IGS: taatgaaggtcgagacaagtgtcttggcctttttgcttattaattgttgttttaatcgcaaatagcttatccttatcaaatcatcaaaatccgctcagagagcatgaagtatctgagtgagaaaaactcttcttgaaagcctttacaagtttaaaaagaatcggtataataaatacagaaaacgtttgcatagatgttctctataagaaaaaataaaggagttttctgttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaacagaaaactcctttattttttcttatagagaacatctatgcaaacgttttctgtatttattataccgattctttttaaacttgtaaaggctttcaagaagagtttttctcactcagatacttcatgctctctgagcggattttgatgatttgataaggataagctatttgcgattaaaacaacaattaataagcaaaaaggccaagacacttgtctcgaccttcatta Mask Tandem Repeat Region ================================================ taatgaaggtcgagacaagtgtcttggcctttttgcttattaattgttgttttaatcgcaaatagcttatccttatcaaatcatcaaaatccgctcagagagcatgaagtatctgagtgagaaaaactcttcttgaaagcctttacaagtttaaaaagaatcggtataataaatacagaaaacgtttgcatagatgttctctataagaaaaaataaaggagttttctgttt Find is-nt database================================================ Query_seq: SSA_0452:SSA_0453|SSA_0452:SSA_0453:Nitrogen utilization substance protein B, putative:Type II secretory pathway, pullulanase PulA glycosidase, putative:->->:452121..452351 231 taatgaaggtcgagacaagtgtcttggcctttttgcttattaattgttgttttaatcgcaaatagcttatccttatcaaatcatcaaaatccgctcagagagcatgaagtatctgagtgagaaaaactcttcttgaaagcctttacaagtttaaaaagaatcggtataataaatacagaaaacgtttgcatagatgttctctataagaaaaaataaaggagttttctgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0452:SSA_0453|SSA_0452:SSA_0453:Nitrogen utilization substance protein B, putative:Type II secretory pathway, pullulanase PulA glycosidase, putative:->->:452121..452351 231 taatgaaggtcgagacaagtgtcttggcctttttgcttattaattgttgttttaatcgcaaatagcttatccttatcaaatcatcaaaatccgctcagagagcatgaagtatctgagtgagaaaaactcttcttgaaagcctttacaagtttaaaaagaatcggtataataaatacagaaaacgtttgcatagatgttctctataagaaaaaataaaggagttttctgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0452:SSA_0453|SSA_0452:SSA_0453:Nitrogen utilization substance protein B, putative:Type II secretory pathway, pullulanase PulA glycosidase, putative:->->:452121..452351 231 taatgaaggtcgagacaagtgtcttggcctttttgcttattaattgttgttttaatcgcaaatagcttatccttatcaaatcatcaaaatccgctcagagagcatgaagtatctgagtgagaaaaactcttcttgaaagcctttacaagtttaaaaagaatcggtataataaatacagaaaacgtttgcatagatgttctctataagaaaaaataaaggagttttctgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatgaaggtcgagacaagtgtcttggcctttttgcttattaattgttgttttaatcgcaaatagcttatccttatcaaatcatcaaaatccgctcagagagcatgaagtatctgagtgagaaaaactcttcttgaaagcctttacaagtttaaaaagaatcggtataataaatacagaaaacgtttgcatagatgttctctataagaaaaaataaaggagttttctgttt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 19 End: 117 .................. M S W P F C L L I V V L I A N S L S L S N H Q N P L R E H E V S E .................................................................................................................. Protein_Len: 35 Strand: - Start: 87 End: 191 ...................................................................................... F G S L S C S T D S H S F S K K F A K V L K F L I P I I F V S F T Q M ........................................ taatgaaggtcgagacaagtgtcttggcctttttgcttattaattgttgttttaatcgcaaatagcttatccttatcaaatcatcaaaatccgctcagagagcatgaagtatctgagtgagaaaaactcttcttgaaagcctttacaagtttaaaaagaatcggtataataaatacagaaaacgtttgcatagatgttctctataagaaaaaataaaggagttttctgttt 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: 141 End: 170 ............................................................................................................................................CTTTACAAGTTTAAAAAGAATCGGTATAAT............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatgaaggtcgagacaagtgtcttggcctttttgcttattaattgttgttttaatcgcaaatagcttatccttatcaaatcatcaaaatccgctcagagagcatgaagtatctgagtgagaaaaactcttcttgaaagcctttacaagtttaaaaagaatcggtataataaatacagaaaacgtttgcatagatgttctctataagaaaaaataaaggagttttctgttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0452:SSA_0453|SSA_0452:SSA_0453:Nitrogen utilization substance protein B, putative:Type II secretory pathway, pullulanase PulA glycosidase, putative:->->:452121..452351 231 taatgaaggtcgagacaagtgtcttggcctttttgcttattaattgttgttttaatcgcaaatagcttatccttatcaaatcatcaaaatccgctcagagagcatgaagtatctgagtgagaaaaactcttcttgaaagcctttacaagtttaaaaagaatcggtataataaatacagaaaacgtttgcatagatgttctctataagaaaaaataaaggagttttctgttt Intra-Species Hit: Count: 1 Min: 1 Max: 231 Len: 231 Subject: NC_009009_SSA_0452_SSA_0453|Nitrogen utilization substance protein B, putative:Type II secretory pathway, pullulanase PulA glycosidase, putative|POSITIVE:POSITIVE|[452121,452351]|231 HSP 1 e-value: 1.0E-128 bit: 458.0 Len: 231 Query Start:1 Query End:231 Subject Strand: POSITIVE Subject Start: 1 Subject End: 231 taatgaaggtcgagacaagtgtcttggcctttttgcttattaattgttgttttaatcgcaaatagcttatccttatcaaatcatcaaaatccgctcagagagcatgaagtatctgagtgagaaaaactcttcttgaaagcctttacaagtttaaaaagaatcggtataataaatacagaaaacgtttgcatagatgttctctataagaaaaaataaaggagttttctgttt taatgaaggtcgagacaagtgtcttggcctttttgcttattaattgttgttttaatcgcaaatagcttatccttatcaaatcatcaaaatccgctcagagagcatgaagtatctgagtgagaaaaactcttcttgaaagcctttacaagtttaaaaagaatcggtataataaatacagaaaacgtttgcatagatgttctctataagaaaaaataaaggagttttctgttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAAGGUCGAGACAAGUGUCUUGGCCUUUUUGCUUAUUAAUUGUUGUUUUAAUCGCAAAUAGCUUAUCCUUAUCAAAUCAUCAAAAUCCGCUCAGAGAGCAUGAAGUAUCUGAGUGAGAAAAACUCUUCUUGAAAGCCUUUACAAGUUUAAAAAGAAUCGGUAUAAUAAAUACAGAAAACGUUUGCAUAGAUGUUCUCUAUAAGAAAAAAUAAAGGAGUUUUCUGUUU ....((((((((((((....))))))))))))((((..(((((........))))).)))).....((((((.................((((((((((..((.....)).)))))))).)).......(((((..((((........))))...)))))..)).)))).....(((((((((.(((..(((((.....)))))..)))...........))))))))).. (-50.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACAGAAAACUCCUUUAUUUUUUCUUAUAGAGAACAUCUAUGCAAACGUUUUCUGUAUUUAUUAUACCGAUUCUUUUUAAACUUGUAAAGGCUUUCAAGAAGAGUUUUUCUCACUCAGAUACUUCAUGCUCUCUGAGCGGAUUUUGAUGAUUUGAUAAGGAUAAGCUAUUUGCGAUUAAAACAACAAUUAAUAAGCAAAAAGGCCAAGACACUUGUCUCGACCUUCAUUA ..(((((((((..((((((........))))))..((....)).....))))))))).(((((((..........((((((..((((((((((((((.....(((.....)))..((((((...((((((((...))))).....)))..))))))....)).))))).))))))))))))).......)))))))....((((.(.((((....)))).).))))..... (-42.43) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 59 11 198 141 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 329 38 7 141 111 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 267 93 55 209 159 NC_009009:SSA_0741|5end_Acetylornithine_deacetylase/Succinyl-diaminopimelate_desuccinylase,_putative_723773..724003_POSITIVE 266 140 91 66 16 NC_009009:SSA_0856|5end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_843210..843440_POSITIVE 258 114 71 86 40 NC_009009:SSA_0308|5end_hypothetical_protein_304385..304615_POSITIVE 257 110 61 79 32 NC_009009:SSA_0459|5end_hypothetical_protein_462098..462328_POSITIVE 252 103 70 134 103 NC_009009:SSA_0222|5end_PTS_system,_mannose-specific_IID_component,_putative_217217..217447_POSITIVE 250 110 65 133 86 NC_009009:SSA_0654|5end_Cell_division_protein_DivIB,_putative_637457..637687_POSITIVE 248 117 93 231 207 NC_009009:SSA_1964|5end_conserved_uncharacterized_protein_1961211..1961441_NEGATIVE 248 68 23 148 93 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 247 67 21 115 73 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 246 103 65 77 29 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 245 110 63 154 101 NC_009009:SSA_1422|5end_hypothetical_protein_1431555..1431785_NEGATIVE 245 59 11 225 168 NC_009009:SSA_1127|5end_H2O-forming_NADH_dehydrogenase,_putative_1151731..1151961_POSITIVE 245 50 8 71 29 NC_009009:SSA_0412|5end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_408163..408393_NEGATIVE 244 95 58 165 125 NC_009009:SSA_0373|5end_Dihydroorotate_dehydrogenase,_putative_362062..362292_POSITIVE 242 136 91 75 38 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 241 129 86 221 182 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 241 100 56 182 131 NC_009009:SSA_0785|5end_Proton-translocating_ATPase,_F1_sector,_delta_subunit,_putative_768044..768274_POSITIVE 241 36 8 42 11 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 34 7 75 47 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 336 126 88 52 6 NC_009009:SSA_1326|3end_Peptidase_T,_putative_1343735..1343885_POSITIVE 329 38 7 88 58 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 311 34 3 38 7 NC_009009:SSA_0266|3end_ORFB,_transposon_ISSsa1_260822..260972_POSITIVE 309 48 1 95 49 NC_009009:SSA_0452|3end_Nitrogen_utilization_substance_protein_B,_putative_452060..452210_POSITIVE 299 34 5 42 14 NC_009009:SSA_1590|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1593342..1593492_POSITIVE 283 118 72 83 25 NC_009009:SSA_0406|3end_hypothetical_protein_402196..402346_NEGATIVE 280 132 93 135 98 NC_009009:SSA_1965|3end_Stomatin/prohibitin-like_membrane_protease_subunits,_putative_1961320..1961470_NEGATIVE 273 35 6 78 47 NC_009009:SSA_2265|3end_Maltodextrin_phosphorylase,_putative_2261936..2262086_NEGATIVE 273 32 4 92 58 NC_009009:SSA_0267|3end_ROK_family_protein,_putative_260873..261023_NEGATIVE 262 107 62 81 37 NC_009009:SSA_1041|3end_Sugar_ABC_transporter,_permease_protein,_putative_1057434..1057584_POSITIVE 252 103 70 132 101 NC_009009:SSA_0221|3end_PTS_system,_mannose-specific_IIC_component,_putative_217295..217445_POSITIVE 250 41 5 85 50 NC_009009:SSA_1591|3end_Dipeptidase,_putative_1593403..1593553_NEGATIVE 250 110 65 136 89 NC_009009:SSA_0653|3end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_637540..637690_POSITIVE 250 41 4 95 54 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 249 41 6 95 57 NC_009009:SSA_0844|3end_hypothetical_protein_828491..828641_NEGATIVE 248 68 23 126 71 NC_009009:SSA_0895|3end_ATP-binding_cassette_transporter-like_protein,_putative_887763..887913_POSITIVE 245 110 63 148 95 NC_009009:SSA_1423|3end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1431561..1431711_NEGATIVE 245 104 89 62 47 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 242 48 1 95 44 NC_009009:SSA_2344|3end_hypothetical_protein_2346766..2346916_POSITIVE