Origin IGS: tttgtcacctcgttatttttcctctacgccttttcatttttacttaatgcaaacgtttgcgtcgacttgattataacctatttttttttttagtgcaaggggtttttgagatttttttcaatttattggttaatagatataatgctcttttaggactctcctacagccccaattatttgccgtttttctcttcttgcaagcgttctctttttgtgttaaaatgttcttacaaacagaaaacgtttgcgtttactgagaaactgctttatacttgtctcttcaaccataatagttaggcaatatcacttgttttgatagccattttgggcataggtttgcatgactcatagaaagcaagtgcttctactactagatttaaaatagttgatgttatagaaaggatttccagcaaatgcaggcctttaggaggttttt .........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 aaaaacctcctaaaggcctgcatttgctggaaatcctttctataacatcaactattttaaatctagtagtagaagcacttgctttctatgagtcatgcaaacctatgcccaaaatggctatcaaaacaagtgatattgcctaactattatggttgaagagacaagtataaagcagtttctcagtaaacgcaaacgttttctgtttgtaagaacattttaacacaaaaagagaacgcttgcaagaagagaaaaacggcaaataattggggctgtaggagagtcctaaaagagcattatatctattaaccaataaattgaaaaaaatctcaaaaaccccttgcactaaaaaaaaaaataggttataatcaagtcgacgcaaacgtttgcattaagtaaaaatgaaaaggcgtagaggaaaaataacgaggtgacaaa Mask Tandem Repeat Region ================================================ tttgtcacctcgttatttttcctctacgccttttcatttttacttaatgcaaacgtttgcgtcgacttgattataacctatttttttttttagtgcaaggggtttttgagatttttttcaatttattggttaatagatataatgctcttttaggactctcctacagccccaattatttgccgtttttctcttcttgcaagcgttctctttttgtgttaaaatgttcttacaaacagaaaacgtttgcgtttactgagaaactgctttatacttgtctcttcaaccataatagttaggcaatatcacttgttttgatagccattttgggcataggtttgcatgactcatagaaagcaagtgcttctactactagatttaaaatagttgatgttatagaaaggatttccagcaaatgcaggcctttaggaggttttt Find is-nt database================================================ Query_seq: SSA_2266:SSA_2267|SSA_2266:SSA_2267:4-alpha-glucanotransferase, putative:Lactose operon transcriptional repressor, LacI family, putative:<-->:2265832..2266266 435 tttgtcacctcgttatttttcctctacgccttttcatttttacttaatgcaaacgtttgcgtcgacttgattataacctatttttttttttagtgcaaggggtttttgagatttttttcaatttattggttaatagatataatgctcttttaggactctcctacagccccaattatttgccgtttttctcttcttgcaagcgttctctttttgtgttaaaatgttcttacaaacagaaaacgtttgcgtttactgagaaactgctttatacttgtctcttcaaccataatagttaggcaatatcacttgttttgatagccattttgggcataggtttgcatgactcatagaaagcaagtgcttctactactagatttaaaatagttgatgttatagaaaggatttccagcaaatgcaggcctttaggaggttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2266:SSA_2267|SSA_2266:SSA_2267:4-alpha-glucanotransferase, putative:Lactose operon transcriptional repressor, LacI family, putative:<-->:2265832..2266266 435 tttgtcacctcgttatttttcctctacgccttttcatttttacttaatgcaaacgtttgcgtcgacttgattataacctatttttttttttagtgcaaggggtttttgagatttttttcaatttattggttaatagatataatgctcttttaggactctcctacagccccaattatttgccgtttttctcttcttgcaagcgttctctttttgtgttaaaatgttcttacaaacagaaaacgtttgcgtttactgagaaactgctttatacttgtctcttcaaccataatagttaggcaatatcacttgttttgatagccattttgggcataggtttgcatgactcatagaaagcaagtgcttctactactagatttaaaatagttgatgttatagaaaggatttccagcaaatgcaggcctttaggaggttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2266:SSA_2267|SSA_2266:SSA_2267:4-alpha-glucanotransferase, putative:Lactose operon transcriptional repressor, LacI family, putative:<-->:2265832..2266266 435 tttgtcacctcgttatttttcctctacgccttttcatttttacttaatgcaaacgtttgcgtcgacttgattataacctatttttttttttagtgcaaggggtttttgagatttttttcaatttattggttaatagatataatgctcttttaggactctcctacagccccaattatttgccgtttttctcttcttgcaagcgttctctttttgtgttaaaatgttcttacaaacagaaaacgtttgcgtttactgagaaactgctttatacttgtctcttcaaccataatagttaggcaatatcacttgttttgatagccattttgggcataggtttgcatgactcatagaaagcaagtgcttctactactagatttaaaatagttgatgttatagaaaggatttccagcaaatgcaggcctttaggaggttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgtcacctcgttatttttcctctacgccttttcatttttacttaatgcaaacgtttgcgtcgacttgattataacctatttttttttttagtgcaaggggtttttgagatttttttcaatttattggttaatagatataatgctcttttaggactctcctacagccccaattatttgccgtttttctcttcttgcaagcgttctctttttgtgttaaaatgttcttacaaacagaaaacgtttgcgtttactgagaaactgctttatacttgtctcttcaaccataatagttaggcaatatcacttgttttgatagccattttgggcataggtttgcatgactcatagaaagcaagtgcttctactactagatttaaaatagttgatgttatagaaaggatttccagcaaatgcaggcctttaggaggttttt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 57 End: 293 ........................................................ M R R L D Y N L F F F L V Q G V F E I F F N L L V N R Y N A L L G L S Y S P N Y L P F F S S C K R S L F V L K C S Y K Q .............................................................................................................................................. Protein_Len: 41 Strand: - Start: 296 End: 418 ....................................................................................................................................................................................................................................................................................................... A I D S T K I A M K P M P K C S E Y F A L A E V V L N L I T S T I S L I E L L H M ................. Protein_Len: 30 Strand: - Start: 133 End: 222 .................................................................................................................................... Y I Y H E K L V R R C G W N N A T K R K K C A N E K Q T L M ..................................................................................................................................................................................................................... tttgtcacctcgttatttttcctctacgccttttcatttttacttaatgcaaacgtttgcgtcgacttgattataacctatttttttttttagtgcaaggggtttttgagatttttttcaatttattggttaatagatataatgctcttttaggactctcctacagccccaattatttgccgtttttctcttcttgcaagcgttctctttttgtgttaaaatgttcttacaaacagaaaacgtttgcgtttactgagaaactgctttatacttgtctcttcaaccataatagttaggcaatatcacttgttttgatagccattttgggcataggtttgcatgactcatagaaagcaagtgcttctactactagatttaaaatagttgatgttatagaaaggatttccagcaaatgcaggcctttaggaggttttt 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: 86 Start: 70 End: 99 .....................................................................CTTGCACTAAAAAAAAAAATAGGTTATAAT................................................................................................................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 114 End: 143 .................................................................................................................TTTTTCAATTTATTGGTTAATAGATATAAT.................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 193 End: 222 ................................................................................................................................................................................................CTTGCAAGCGTTCTCTTTTTGTGTTAAAAT..................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgtcacctcgttatttttcctctacgccttttcatttttacttaatgcaaacgtttgcgtcgacttgattataacctatttttttttttagtgcaaggggtttttgagatttttttcaatttattggttaatagatataatgctcttttaggactctcctacagccccaattatttgccgtttttctcttcttgcaagcgttctctttttgtgttaaaatgttcttacaaacagaaaacgtttgcgtttactgagaaactgctttatacttgtctcttcaaccataatagttaggcaatatcacttgttttgatagccattttgggcataggtttgcatgactcatagaaagcaagtgcttctactactagatttaaaatagttgatgttatagaaaggatttccagcaaatgcaggcctttaggaggttttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -7.3 Tail_Score: -3.8709 Start: 234 End: 255 Full_Region: tataaagcagtttct cagtaaacg caaa cgttttctg tttgtaagaacattt .........................................................................................................................................................................................................................................cagtaaacgcaaacgttttctg.................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_2266:SSA_2267|SSA_2266:SSA_2267:4-alpha-glucanotransferase, putative:Lactose operon transcriptional repressor, LacI family, putative:<-->:2265832..2266266 435 tttgtcacctcgttatttttcctctacgccttttcatttttacttaatgcaaacgtttgcgtcgacttgattataacctatttttttttttagtgcaaggggtttttgagatttttttcaatttattggttaatagatataatgctcttttaggactctcctacagccccaattatttgccgtttttctcttcttgcaagcgttctctttttgtgttaaaatgttcttacaaacagaaaacgtttgcgtttactgagaaactgctttatacttgtctcttcaaccataatagttaggcaatatcacttgttttgatagccattttgggcataggtttgcatgactcatagaaagcaagtgcttctactactagatttaaaatagttgatgttatagaaaggatttccagcaaatgcaggcctttaggaggttttt Intra-Species Hit: Count: 1 Min: 1 Max: 435 Len: 435 Subject: NC_009009_SSA_2266_SSA_2267|4-alpha-glucanotransferase, putative:Lactose operon transcriptional repressor, LacI family, putative|NEGATIVE:POSITIVE|[2265832,2266266]|435 HSP 1 e-value: 1.0E-179 bit: 628.0 Len: 317 Query Start:119 Query End:435 Subject Strand: POSITIVE Subject Start: 119 Subject End: 435 ......................................................................................................................caatttattggttaatagatataatgctcttttaggactctcctacagccccaattatttgccgtttttctcttcttgcaagcgttctctttttgtgttaaaatgttcttacaaacagaaaacgtttgcgtttactgagaaactgctttatacttgtctcttcaaccataatagttaggcaatatcacttgttttgatagccattttgggcataggtttgcatgactcatagaaagcaagtgcttctactactagatttaaaatagttgatgttatagaaaggatttccagcaaatgcaggcctttaggaggttttt ......................................................................................................................caatttattggttaatagatataatgctcttttaggactctcctacagccccaattatttgccgtttttctcttcttgcaagcgttctctttttgtgttaaaatgttcttacaaacagaaaacgtttgcgtttactgagaaactgctttatacttgtctcttcaaccataatagttaggcaatatcacttgttttgatagccattttgggcataggtttgcatgactcatagaaagcaagtgcttctactactagatttaaaatagttgatgttatagaaaggatttccagcaaatgcaggcctttaggaggttttt HSP 2 e-value: 1.0E-37 bit: 159.0 Len: 80 Query Start:1 Query End:80 Subject Strand: POSITIVE Subject Start: 1 Subject End: 80 tttgtcacctcgttatttttcctctacgccttttcatttttacttaatgcaaacgtttgcgtcgacttgattataaccta................................................................................................................................................................................................................................................................................................................................................................... tttgtcacctcgttatttttcctctacgccttttcatttttacttaatgcaaacgtttgcgtcgacttgattataaccta................................................................................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUCACCUCGUUAUUUUUCCUCUACGCCUUUUCAUUUUUACUUAAUGCAAACGUUUGCGUCGACUUGAUUAUAACCUAUUUUUUUUUUUAGUGCAAGGGGUUUUUGAGAUUUUUUUCAAUUUAUUGGUUAAUAGAUAUAAUGCUCUUUUAGGACUCUCCUACAGCCCCAAUUAUUUGCCGUUUUUCUCUUCUUGCAAGCGUUCUCUUUUUGUGUUAAAAUGUUCUUACAAACAGAAAACGUUUGCGUUUACUGAGAAACUGCUUUAUACUUGUCUCUUCAACCAUAAUAGUUAGGCAAUAUCACUUGUUUUGAUAGCCAUUUUGGGCAUAGGUUUGCAUGACUCAUAGAAAGCAAGUGCUUCUACUACUAGAUUUAAAAUAGUUGAUGUUAUAGAAAGGAUUUCCAGCAAAUGCAGGCCUUUAGGAGGUUUUU .................((((((..(.((((...((((.......))))....(((((((..........((((((((((((((....(((((((...((((((.((((((....)))))).............................((((.....)))).))))))......(((((...((((((....((((((((((.(((.((((((............)))))).))).))))))))))......))))))..(((((((..(((......)))..)))).)))..)))))...((((((((((....(((......)))...((((.....)))).....)))))))))).......)))))))...))))))).....)))))))...((....)).))))))).)))).)..))))))..... (-97.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACCUCCUAAAGGCCUGCAUUUGCUGGAAAUCCUUUCUAUAACAUCAACUAUUUUAAAUCUAGUAGUAGAAGCACUUGCUUUCUAUGAGUCAUGCAAACCUAUGCCCAAAAUGGCUAUCAAAACAAGUGAUAUUGCCUAACUAUUAUGGUUGAAGAGACAAGUAUAAAGCAGUUUCUCAGUAAACGCAAACGUUUUCUGUUUGUAAGAACAUUUUAACACAAAAAGAGAACGCUUGCAAGAAGAGAAAAACGGCAAAUAAUUGGGGCUGUAGGAGAGUCCUAAAAGAGCAUUAUAUCUAUUAACCAAUAAAUUGAAAAAAAUCUCAAAAACCCCUUGCACUAAAAAAAAAAAUAGGUUAUAAUCAAGUCGACGCAAACGUUUGCAUUAAGUAAAAAUGAAAAGGCGUAGAGGAAAAAUAACGAGGUGACAAA .......((((..(.((((.((((((((((((((.((((.(((..(.((((((((..((......((((((....((((((.(((.....(((((((((......))).....))))))...))).)))))).)))))).....))..)))))))).)......))).))))..))))).)))))...(((((((((((((.((((((((....((((........)))).....)))))))).)))))....((((......((((((((.......))))))))....(.((((((((((((..........((((........)))).......((......))......)))))).)))))))..))))......))))))))..........))))...)))).)..))))..........(....)... (-91.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 863 70 21 161 112 NC_009009:SSA_2266|5end_4-alpha-glucanotransferase,_putative_2265741..2265971_NEGATIVE 368 205 161 49 6 NC_009009:SSA_0728|5end_Protease,_putative_713688..713918_POSITIVE 336 339 291 214 164 NC_009009:SSA_1217|5end_Conserved_uncharacterized_protein_1238964..1239194_POSITIVE 322 345 303 75 39 NC_009009:SSA_1394|5end_hypothetical_protein_1409048..1409278_NEGATIVE 320 195 153 103 64 NC_009009:SSA_2176|5end_hypothetical_protein_2175159..2175389_NEGATIVE 312 349 305 68 30 NC_009009:SSA_0579|5end_Hydrolase,_HAD_superfamily,_putative_572220..572450_POSITIVE 310 368 321 183 133 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 303 210 166 135 94 NC_009009:SSA_0638|5end_Tryptophan_synthase_alpha_chain,_putative_626935..627165_POSITIVE 300 344 307 47 1 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 299 377 338 56 7 NC_009009:SSA_1079|5end_hypothetical_protein_1096385..1096615_POSITIVE 294 430 384 219 173 NC_009009:SSA_0571|5end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B,_putative_565381..565611_POSITIVE 293 345 309 193 161 NC_009009:SSA_1657|5end_hypothetical_protein_1653231..1653461_NEGATIVE 289 430 382 75 16 NC_009009:SSA_2056|5end_Cinnamoyl_ester_hydrolase,_putative_2058587..2058817_POSITIVE 289 219 178 227 184 NC_009009:SSA_1250|5end_Conserved_uncharacterized_protein,_putative_1274512..1274742_NEGATIVE 289 210 161 63 4 NC_009009:SSA_1035|5end_Pyrimidine_nucleoside_phosphorylase,_putative_1050174..1050404_POSITIVE 287 424 388 168 126 NC_009009:SSA_0605|5end_Methyltransferase_gidB,_putative_593707..593937_NEGATIVE 284 348 302 229 187 NC_009009:SSA_1581|5end_Metal-binding_ABC_transporter_(probably_hemin),_putative_1583662..1583892_POSITIVE 284 198 156 137 98 NC_009009:SSA_1543|5end_hypothetical_protein_1547835..1548065_POSITIVE 283 190 142 101 39 NC_009009:SSA_1306|5end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324910..1325140_NEGATIVE 283 190 144 220 163 NC_009009:SSA_0216|5end_Histidine_kinase,_putative_211877..212107_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 345 303 78 42 NC_009009:SSA_1395|3end_hypothetical_protein_1409045..1409195_NEGATIVE 312 349 305 71 33 NC_009009:SSA_0578|3end_Nicotinate-nucleotide_adenylyltransferase,_putative_572303..572453_POSITIVE 309 190 141 141 104 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 303 210 166 142 101 NC_009009:SSA_0637|3end_Tryptophan_synthase_beta_chain,_putative_627022..627172_POSITIVE 293 345 309 150 118 NC_009009:SSA_1658|3end_Cationic_amino_acid_transporter,_putative_1653274..1653424_NEGATIVE 289 210 161 61 2 NC_009009:SSA_1034|3end_Conserved_uncharacterized_protein_1050252..1050402_POSITIVE 287 424 388 86 44 NC_009009:SSA_0606|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_593789..593939_NEGATIVE 284 347 303 151 98 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 283 190 142 90 28 NC_009009:SSA_1307|3end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1324921..1325071_NEGATIVE 282 238 196 54 17 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 278 195 155 92 46 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 278 202 166 46 1 NC_009009:SSA_0056|3end_Phosphotransferase_system_sugar-specific_EIID_component,_putative_60830..60980_POSITIVE 277 205 165 123 84 NC_009009:SSA_0536|3end_B12-dependent_diol_dehydratase_small_subunit,_putative_531937..532087_POSITIVE 276 208 161 59 2 NC_009009:SSA_2316|3end_General_secretory_pathway_protein_F,_putative_2317116..2317266_NEGATIVE 276 363 325 70 28 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 269 350 306 56 15 NC_009009:SSA_1258|3end_Purine_nucleoside_phosphorylase,_family_1,_putative_1283858..1284008_NEGATIVE 268 338 292 55 10 NC_009009:SSA_1432|3end_HflX_GTPase,_putative_1438663..1438813_NEGATIVE 267 62 21 139 99 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 265 189 143 132 76 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 264 209 167 129 87 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE