Origin IGS: aaattaagtatataataagcccttgtggaaagtaacccctttagggaaatgagacggtttttagagcttttttatactctttagatttgtgttatacattatcataaaaaacgattaatttttatacactaattttacgataggttctaaaatatattaagggaacaatttaaaaatagcgagtgccagtggtaaagcacgcaagaaactattgctgtaaattttttataacaaattgagtatgaatggcatttgaaaatcgatacactaagatagaaaactgtatatcaagaaaatgtaaacgtttttgacagtggaatagagctatagtaaactgtgggtaagaagtcaactggaaaggaggaacctgt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acaggttcctcctttccagttgacttcttacccacagtttactatagctctattccactgtcaaaaacgtttacattttcttgatatacagttttctatcttagtgtatcgattttcaaatgccattcatactcaatttgttataaaaaatttacagcaatagtttcttgcgtgctttaccactggcactcgctatttttaaattgttcccttaatatattttagaacctatcgtaaaattagtgtataaaaattaatcgttttttatgataatgtataacacaaatctaaagagtataaaaaagctctaaaaaccgtctcatttccctaaaggggttactttccacaagggcttattatatacttaattt Mask Tandem Repeat Region ================================================ aaattaagtatataataagcccttgtggaaagtaacccctttagggaaatgagacggtttttagagcttttttatactctttagatttgtgttatacattatcataaaaaacgattaatttttatacactaattttacgataggttctaaaatatattaagggaacaatttaaaaatagcgagtgccagtggtaaagcacgcaagaaactattgctgtaaattttttataacaaattgagtatgaatggcatttgaaaatcgatacactaagatagaaaactgtatatcaagaaaatgtaaacgtttttgacagtggaatagagctatagtaaactgtgggtaagaagtcaactggaaaggaggaacctgt Find is-nt database================================================ Query_seq: SSA_1145:SSA_1146|SSA_1145:SSA_1146:hypothetical protein:Phosphotransferase system cellobiose-specific component IIA, putative:<-->:1176222..1176592 371 aaattaagtatataataagcccttgtggaaagtaacccctttagggaaatgagacggtttttagagcttttttatactctttagatttgtgttatacattatcataaaaaacgattaatttttatacactaattttacgataggttctaaaatatattaagggaacaatttaaaaatagcgagtgccagtggtaaagcacgcaagaaactattgctgtaaattttttataacaaattgagtatgaatggcatttgaaaatcgatacactaagatagaaaactgtatatcaagaaaatgtaaacgtttttgacagtggaatagagctatagtaaactgtgggtaagaagtcaactggaaaggaggaacctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1145:SSA_1146|SSA_1145:SSA_1146:hypothetical protein:Phosphotransferase system cellobiose-specific component IIA, putative:<-->:1176222..1176592 371 aaattaagtatataataagcccttgtggaaagtaacccctttagggaaatgagacggtttttagagcttttttatactctttagatttgtgttatacattatcataaaaaacgattaatttttatacactaattttacgataggttctaaaatatattaagggaacaatttaaaaatagcgagtgccagtggtaaagcacgcaagaaactattgctgtaaattttttataacaaattgagtatgaatggcatttgaaaatcgatacactaagatagaaaactgtatatcaagaaaatgtaaacgtttttgacagtggaatagagctatagtaaactgtgggtaagaagtcaactggaaaggaggaacctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1145:SSA_1146|SSA_1145:SSA_1146:hypothetical protein:Phosphotransferase system cellobiose-specific component IIA, putative:<-->:1176222..1176592 371 aaattaagtatataataagcccttgtggaaagtaacccctttagggaaatgagacggtttttagagcttttttatactctttagatttgtgttatacattatcataaaaaacgattaatttttatacactaattttacgataggttctaaaatatattaagggaacaatttaaaaatagcgagtgccagtggtaaagcacgcaagaaactattgctgtaaattttttataacaaattgagtatgaatggcatttgaaaatcgatacactaagatagaaaactgtatatcaagaaaatgtaaacgtttttgacagtggaatagagctatagtaaactgtgggtaagaagtcaactggaaaggaggaacctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattaagtatataataagcccttgtggaaagtaacccctttagggaaatgagacggtttttagagcttttttatactctttagatttgtgttatacattatcataaaaaacgattaatttttatacactaattttacgataggttctaaaatatattaagggaacaatttaaaaatagcgagtgccagtggtaaagcacgcaagaaactattgctgtaaattttttataacaaattgagtatgaatggcatttgaaaatcgatacactaagatagaaaactgtatatcaagaaaatgtaaacgtttttgacagtggaatagagctatagtaaactgtgggtaagaagtcaactggaaaggaggaacctgt Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: - Start: 212 End: 352 ................................................................................................................................................................................................................... Q Q L N K I V F Q T H I A N S F R Y V L I S F Q I D L F H L R K Q C H F L A I T F Q P Y S T M ................... Protein_Len: 37 Strand: - Start: 150 End: 260 ..................................................................................................................................................... F I N L S C N L F L S H W H Y L V C S V I A T F K K Y C I S Y S H C K F M ............................................................................................................... aaattaagtatataataagcccttgtggaaagtaacccctttagggaaatgagacggtttttagagcttttttatactctttagatttgtgttatacattatcataaaaaacgattaatttttatacactaattttacgataggttctaaaatatattaagggaacaatttaaaaatagcgagtgccagtggtaaagcacgcaagaaactattgctgtaaattttttataacaaattgagtatgaatggcatttgaaaatcgatacactaagatagaaaactgtatatcaagaaaatgtaaacgtttttgacagtggaatagagctatagtaaactgtgggtaagaagtcaactggaaaggaggaacctgt 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: 83 Start: 132 End: 161 ...................................................................................................................................CTTAATATATTTTAGAACCTATCGTAAAAT.................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 307 End: 336 ..................................................................................................................................................................................................................................................................................................................TTTGACAGTGGAATAGAGCTATAGTAAACT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaattaagtatataataagcccttgtggaaagtaacccctttagggaaatgagacggtttttagagcttttttatactctttagatttgtgttatacattatcataaaaaacgattaatttttatacactaattttacgataggttctaaaatatattaagggaacaatttaaaaatagcgagtgccagtggtaaagcacgcaagaaactattgctgtaaattttttataacaaattgagtatgaatggcatttgaaaatcgatacactaagatagaaaactgtatatcaagaaaatgtaaacgtttttgacagtggaatagagctatagtaaactgtgggtaagaagtcaactggaaaggaggaacctgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1145:SSA_1146|SSA_1145:SSA_1146:hypothetical protein:Phosphotransferase system cellobiose-specific component IIA, putative:<-->:1176222..1176592 371 aaattaagtatataataagcccttgtggaaagtaacccctttagggaaatgagacggtttttagagcttttttatactctttagatttgtgttatacattatcataaaaaacgattaatttttatacactaattttacgataggttctaaaatatattaagggaacaatttaaaaatagcgagtgccagtggtaaagcacgcaagaaactattgctgtaaattttttataacaaattgagtatgaatggcatttgaaaatcgatacactaagatagaaaactgtatatcaagaaaatgtaaacgtttttgacagtggaatagagctatagtaaactgtgggtaagaagtcaactggaaaggaggaacctgt Intra-Species Hit: Count: 1 Min: 1 Max: 371 Len: 371 Subject: NC_009009_SSA_1145_SSA_1146|hypothetical protein:Phosphotransferase system cellobiose-specific component IIA, putative|NEGATIVE:POSITIVE|[1176222,1176592]|371 HSP 1 e-value: 0.0 bit: 735.0 Len: 371 Query Start:1 Query End:371 Subject Strand: POSITIVE Subject Start: 1 Subject End: 371 aaattaagtatataataagcccttgtggaaagtaacccctttagggaaatgagacggtttttagagcttttttatactctttagatttgtgttatacattatcataaaaaacgattaatttttatacactaattttacgataggttctaaaatatattaagggaacaatttaaaaatagcgagtgccagtggtaaagcacgcaagaaactattgctgtaaattttttataacaaattgagtatgaatggcatttgaaaatcgatacactaagatagaaaactgtatatcaagaaaatgtaaacgtttttgacagtggaatagagctatagtaaactgtgggtaagaagtcaactggaaaggaggaacctgt aaattaagtatataataagcccttgtggaaagtaacccctttagggaaatgagacggtttttagagcttttttatactctttagatttgtgttatacattatcataaaaaacgattaatttttatacactaattttacgataggttctaaaatatattaagggaacaatttaaaaatagcgagtgccagtggtaaagcacgcaagaaactattgctgtaaattttttataacaaattgagtatgaatggcatttgaaaatcgatacactaagatagaaaactgtatatcaagaaaatgtaaacgtttttgacagtggaatagagctatagtaaactgtgggtaagaagtcaactggaaaggaggaacctgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUAAGUAUAUAAUAAGCCCUUGUGGAAAGUAACCCCUUUAGGGAAAUGAGACGGUUUUUAGAGCUUUUUUAUACUCUUUAGAUUUGUGUUAUACAUUAUCAUAAAAAACGAUUAAUUUUUAUACACUAAUUUUACGAUAGGUUCUAAAAUAUAUUAAGGGAACAAUUUAAAAAUAGCGAGUGCCAGUGGUAAAGCACGCAAGAAACUAUUGCUGUAAAUUUUUUAUAACAAAUUGAGUAUGAAUGGCAUUUGAAAAUCGAUACACUAAGAUAGAAAACUGUAUAUCAAGAAAAUGUAAACGUUUUUGACAGUGGAAUAGAGCUAUAGUAAACUGUGGGUAAGAAGUCAACUGGAAAGGAGGAACCUGU .......(((((((.....((((...((.........))...))))........((((((((((((((..(((((((((....(((((((.............(((((((........)))))))........(((((.....(((((.............)))))............((...((((...))))..))..((((.......)))).))))).........)))))))))))))))).))).)))))))))))...................)))))))..............(.(((((..((((.((....(.((((((....)))))).)......)).))))..))))).)....... (-69.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGGUUCCUCCUUUCCAGUUGACUUCUUACCCACAGUUUACUAUAGCUCUAUUCCACUGUCAAAAACGUUUACAUUUUCUUGAUAUACAGUUUUCUAUCUUAGUGUAUCGAUUUUCAAAUGCCAUUCAUACUCAAUUUGUUAUAAAAAAUUUACAGCAAUAGUUUCUUGCGUGCUUUACCACUGGCACUCGCUAUUUUUAAAUUGUUCCCUUAAUAUAUUUUAGAACCUAUCGUAAAAUUAGUGUAUAAAAAUUAAUCGUUUUUUAUGAUAAUGUAUAACACAAAUCUAAAGAGUAUAAAAAAGCUCUAAAAACCGUCUCAUUUCCCUAAAGGGGUUACUUUCCACAAGGGCUUAUUAUAUACUUAAUUU ..((((((.........((....))........((((((((..(((((.(((((...((((.(((...............(((((((((((........))..)))))))))....(((((..............)))))..........))))))).)))))........(((((........)))))..)))))...)))))))).................))))))............(((((((...((((.((((.....)))))))).))).)))).........(((((((((.(((((((...............((((....))))............))))))).)).)))))))..... (-59.27) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 885 70 21 161 112 NC_009009:SSA_1145|5end_hypothetical_protein_1176131..1176361_NEGATIVE 285 45 21 32 1 NC_009009:SSA_1360|5end_Arginine/histidine_ABC_transporter,_ATPase_component,_putative_1376350..1376580_POSITIVE 285 88 41 228 189 NC_009009:SSA_0398|5end_hypothetical_protein_396452..396682_NEGATIVE 283 218 174 159 118 NC_009009:SSA_1197|5end_DNA_alkylation_repair_enzyme,_putative_1222699..1222929_NEGATIVE 283 357 315 53 12 NC_009009:SSA_0813|5end_Thioredoxin_reductase,_putative_795406..795636_NEGATIVE 267 218 179 95 64 NC_009009:SSA_1258|5end_Purine_nucleoside_phosphorylase,_family_1,_putative_1284652..1284882_NEGATIVE 264 355 312 67 23 NC_009009:SSA_1750|5end_Extracellular_nuclease,_putative_1737922..1738152_NEGATIVE 262 100 52 120 65 NC_009009:SSA_1348|5end_hypothetical_protein_1365355..1365585_POSITIVE 254 348 310 70 29 NC_009009:SSA_1536|5end_Biotin_synthase,_putative_1543609..1543839_POSITIVE 253 370 321 63 14 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 248 369 323 184 130 NC_009009:SSA_1365|5end_FmtA-like_protein,_putative_1382299..1382529_NEGATIVE 247 209 181 39 7 NC_009009:SSA_0820|5end_Ribosomal_protein_S21,_putative_801249..801479_POSITIVE 245 69 31 181 136 NC_009009:SSA_0790|5end_hypothetical_protein_773047..773277_POSITIVE 245 359 313 216 172 NC_009009:SSA_0728|5end_Protease,_putative_713688..713918_POSITIVE 244 355 312 223 182 NC_009009:SSA_1588|5end_Conserved_ABC-type_antimicrobial_permease-like_protein,_putative_1591905..1592135_NEGATIVE 243 68 23 119 72 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 243 70 27 163 126 NC_009009:SSA_0781|5end_Mannose-6-phosphate_isomerase,_putative_765373..765603_POSITIVE 242 207 161 78 37 NC_009009:SSA_1411|5end_Glucose-1-phosphate_thymidylytransferase,_putative_1423960..1424190_NEGATIVE 241 370 323 180 133 NC_009009:SSA_0729|5end_hypothetical_protein_714397..714627_POSITIVE 241 216 181 192 159 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 45 21 32 1 NC_009009:SSA_1359|3end_Arginine/histidine_ABC_transporter,_permease_component,_putative_1376430..1376580_POSITIVE 274 70 22 72 17 NC_009009:SSA_0429|3end_Histidine_ammonia-lyase,_putative_429701..429851_NEGATIVE 270 370 321 105 50 NC_009009:SSA_0727|3end_Metal-dependent_membrane_protease,_putative_713639..713789_POSITIVE 268 368 335 50 14 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 265 59 15 142 93 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 255 58 17 135 102 NC_009009:SSA_1861|3end_Aminopeptidase_C,_putative_1856568..1856718_NEGATIVE 253 370 323 67 1 NC_009009:SSA_0908|3end_ABC-type_uncharacterized_transport_system,_periplasmic_component,_putative_920787..920937_POSITIVE 243 70 27 38 1 NC_009009:SSA_0780|3end_Acid_phosphatase_(PAP2_family),_putative_765328..765478_POSITIVE 242 207 161 44 3 NC_009009:SSA_1412|3end_hypothetical_protein_1423994..1424144_NEGATIVE 241 365 324 107 58 NC_009009:SSA_1479|3end_Transposase,_putative_1483889..1484039_POSITIVE 239 70 22 60 1 NC_009009:SSA_0817|3end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_799375..799525_POSITIVE 239 62 22 78 35 NC_009009:SSA_0433|3end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435028..435178_NEGATIVE 236 58 12 64 13 NC_009009:SSA_1054|3end_CBS_domain_protein,_putative_1070973..1071123_POSITIVE 232 370 321 98 40 NC_009009:SSA_1685|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1678390..1678540_NEGATIVE 231 229 184 91 44 NC_009009:SSA_1268|3end_Chorismate_mutase/prephenate_dehydratase,_putative_1291347..1291497_NEGATIVE 230 218 180 82 38 NC_009009:SSA_2046|3end_Uridine_phosphorylase,_putative_2048957..2049107_NEGATIVE 228 95 63 45 4 NC_009009:SSA_0456|3end_Phosphotransferase_system_IIC_components,_glucose/maltose/N-acetylglucosamine-specific,_putative_460585..460735_POSITIVE 223 215 173 85 39 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 223 67 21 126 74 NC_009009:SSA_0939|3end_Inositol_monophosphatase_(Mg++_dependent),_putative_947705..947855_POSITIVE 221 204 176 87 61 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE