Origin IGS: caaaaaaggattttcgaatcctttttttgatgtctccttaaataaatagaaccttgtggacaaatttgataacccattgttatttgtttgtttaacagatttagctcagtttcaaccagcagagatttttttgtaaacctaataaaattttggaaaaagatagtatgataaaaaagcgattgacaggttaagttattttttgttatactgacaatgatactatataaagataactgacgtttttttgaaaagtaatatttcaatcacctgatgcgattaaataaaaggttctgttgataatctattttcctaactcttttattctctttgttttttcgattatctatcataaaaacgagatggcatccaaggccgagattcttacttgccatatatagtattataccaacaaattatataaggagtaaa .........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 tttactccttatataatttgttggtataatactatatatggcaagtaagaatctcggccttggatgccatctcgtttttatgatagataatcgaaaaaacaaagagaataaaagagttaggaaaatagattatcaacagaaccttttatttaatcgcatcaggtgattgaaatattacttttcaaaaaaacgtcagttatctttatatagtatcattgtcagtataacaaaaaataacttaacctgtcaatcgcttttttatcatactatctttttccaaaattttattaggtttacaaaaaaatctctgctggttgaaactgagctaaatctgttaaacaaacaaataacaatgggttatcaaatttgtccacaaggttctatttatttaaggagacatcaaaaaaaggattcgaaaatccttttttg Mask Tandem Repeat Region ================================================ caaaaaaggattttcgaatcctttttttgatgtctccttaaataaatagaaccttgtggacaaatttgataacccattgttatttgtttgtttaacagatttagctcagtttcaaccagcagagatttttttgtaaacctaataaaattttggaaaaagatagtatgataaaaaagcgattgacaggttaagttattttttgttatactgacaatgatactatataaagataactgacgtttttttgaaaagtaatatttcaatcacctgatgcgattaaataaaaggttctgttgataatctattttcctaactcttttattctctttgttttttcgattatctatcataaaaacgagatggcatccaaggccgagattcttacttgccatatatagtattataccaacaaattatataaggagtaaa Find is-nt database================================================ Query_seq: SSA_1098:SSA_1099|SSA_1098:SSA_1099:Formate-nitrate transporter, putative:Calcium binding hemolysin-like protein, putative:->->:1115072..1115500 429 caaaaaaggattttcgaatcctttttttgatgtctccttaaataaatagaaccttgtggacaaatttgataacccattgttatttgtttgtttaacagatttagctcagtttcaaccagcagagatttttttgtaaacctaataaaattttggaaaaagatagtatgataaaaaagcgattgacaggttaagttattttttgttatactgacaatgatactatataaagataactgacgtttttttgaaaagtaatatttcaatcacctgatgcgattaaataaaaggttctgttgataatctattttcctaactcttttattctctttgttttttcgattatctatcataaaaacgagatggcatccaaggccgagattcttacttgccatatatagtattataccaacaaattatataaggagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1098:SSA_1099|SSA_1098:SSA_1099:Formate-nitrate transporter, putative:Calcium binding hemolysin-like protein, putative:->->:1115072..1115500 429 caaaaaaggattttcgaatcctttttttgatgtctccttaaataaatagaaccttgtggacaaatttgataacccattgttatttgtttgtttaacagatttagctcagtttcaaccagcagagatttttttgtaaacctaataaaattttggaaaaagatagtatgataaaaaagcgattgacaggttaagttattttttgttatactgacaatgatactatataaagataactgacgtttttttgaaaagtaatatttcaatcacctgatgcgattaaataaaaggttctgttgataatctattttcctaactcttttattctctttgttttttcgattatctatcataaaaacgagatggcatccaaggccgagattcttacttgccatatatagtattataccaacaaattatataaggagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1098:SSA_1099|SSA_1098:SSA_1099:Formate-nitrate transporter, putative:Calcium binding hemolysin-like protein, putative:->->:1115072..1115500 429 caaaaaaggattttcgaatcctttttttgatgtctccttaaataaatagaaccttgtggacaaatttgataacccattgttatttgtttgtttaacagatttagctcagtttcaaccagcagagatttttttgtaaacctaataaaattttggaaaaagatagtatgataaaaaagcgattgacaggttaagttattttttgttatactgacaatgatactatataaagataactgacgtttttttgaaaagtaatatttcaatcacctgatgcgattaaataaaaggttctgttgataatctattttcctaactcttttattctctttgttttttcgattatctatcataaaaacgagatggcatccaaggccgagattcttacttgccatatatagtattataccaacaaattatataaggagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaaaaaggattttcgaatcctttttttgatgtctccttaaataaatagaaccttgtggacaaatttgataacccattgttatttgtttgtttaacagatttagctcagtttcaaccagcagagatttttttgtaaacctaataaaattttggaaaaagatagtatgataaaaaagcgattgacaggttaagttattttttgttatactgacaatgatactatataaagataactgacgtttttttgaaaagtaatatttcaatcacctgatgcgattaaataaaaggttctgttgataatctattttcctaactcttttattctctttgttttttcgattatctatcataaaaacgagatggcatccaaggccgagattcttacttgccatatatagtattataccaacaaattatataaggagtaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 76 End: 165 ........................................................................... M V I C L F N R F S S V S T S R D F F V N L I K F W K K I V ........................................................................................................................................................................................................................................................................ Protein_Len: 35 Strand: + Start: 291 End: 395 .................................................................................................................................................................................................................................................................................................. M L I I Y F P N S F I L F V F S I I Y H K N E M A S K A E I L T C H I .................................. Protein_Len: 42 Strand: + Start: 304 End: 429 ............................................................................................................................................................................................................................................................................................................... M F L T L L F S L F F R L S I I K T R W H P R P R F L L A I Y S I I P T N Y I R S K Protein_Len: 46 Strand: - Start: 267 End: 404 .......................................................................................................................................................................................................................................................................... R I R N F L L N Q Q Y D I K R V R K N E K N K R N D I M F V L H C G L G L N K S A M Y L I M ......................... Protein_Len: 60 Strand: - Start: 3 End: 263 .. Q K N L L N L E T E V L L S K K T F R I F N Q F F I T H Y F L S Q C T L N N K T I S V I I S Y L S L Q R K K S F Y Y K M ...................................................................................................................................................................... caaaaaaggattttcgaatcctttttttgatgtctccttaaataaatagaaccttgtggacaaatttgataacccattgttatttgtttgtttaacagatttagctcagtttcaaccagcagagatttttttgtaaacctaataaaattttggaaaaagatagtatgataaaaaagcgattgacaggttaagttattttttgttatactgacaatgatactatataaagataactgacgtttttttgaaaagtaatatttcaatcacctgatgcgattaaataaaaggttctgttgataatctattttcctaactcttttattctctttgttttttcgattatctatcataaaaacgagatggcatccaaggccgagattcttacttgccatatatagtattataccaacaaattatataaggagtaaa 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: 82 Start: 400 End: 429 ...............................................................................................................................................................................................................................................................................................................................................................................................................TTTACTCCTTATATAATTTGTTGGTATAAT Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caaaaaaggattttcgaatcctttttttgatgtctccttaaataaatagaaccttgtggacaaatttgataacccattgttatttgtttgtttaacagatttagctcagtttcaaccagcagagatttttttgtaaacctaataaaattttggaaaaagatagtatgataaaaaagcgattgacaggttaagttattttttgttatactgacaatgatactatataaagataactgacgtttttttgaaaagtaatatttcaatcacctgatgcgattaaataaaaggttctgttgataatctattttcctaactcttttattctctttgttttttcgattatctatcataaaaacgagatggcatccaaggccgagattcttacttgccatatatagtattataccaacaaattatataaggagtaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 44 HP_score: -3.5 Tail_Score: -2.64333 Start: 259 End: 281 Full_Region: caacagaacctttta tttaatcgc atcag gtgattgaa atattacttttcaaa ..................................................................................................................................................................................................................................................................tttaatcgcatcaggtgattgaa.................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1098:SSA_1099|SSA_1098:SSA_1099:Formate-nitrate transporter, putative:Calcium binding hemolysin-like protein, putative:->->:1115072..1115500 429 caaaaaaggattttcgaatcctttttttgatgtctccttaaataaatagaaccttgtggacaaatttgataacccattgttatttgtttgtttaacagatttagctcagtttcaaccagcagagatttttttgtaaacctaataaaattttggaaaaagatagtatgataaaaaagcgattgacaggttaagttattttttgttatactgacaatgatactatataaagataactgacgtttttttgaaaagtaatatttcaatcacctgatgcgattaaataaaaggttctgttgataatctattttcctaactcttttattctctttgttttttcgattatctatcataaaaacgagatggcatccaaggccgagattcttacttgccatatatagtattataccaacaaattatataaggagtaaa Intra-Species Hit: Count: 1 Min: 1 Max: 429 Len: 429 Subject: NC_009009_SSA_1098_SSA_1099|Formate-nitrate transporter, putative:Calcium binding hemolysin-like protein, putative|POSITIVE:POSITIVE|[1115072,1115500]|429 HSP 1 e-value: 0.0 bit: 726.0 Len: 429 Query Start:1 Query End:429 Subject Strand: POSITIVE Subject Start: 1 Subject End: 429 caaaaaaggattttcgaatccnnnnnnngatgtctccttaaataaatagaaccttgtggacaaatttgataacccattgttatttgtttgtttaacagatttagctcagtttcaaccagcagagannnnnnngtaaacctaataaaattttggaaaaagatagtatgataaaaaagcgattgacaggttaagttattttttgttatactgacaatgatactatataaagataactgacgnnnnnnngaaaagtaatatttcaatcacctgatgcgattaaataaaaggttctgttgataatctattttcctaactcttttattctctttgttttttcgattatctatcataaaaacgagatggcatccaaggccgagattcttacttgccatatatagtattataccaacaaattatataaggagtaaa caaaaaaggattttcgaatcctttttttgatgtctccttaaataaatagaaccttgtggacaaatttgataacccattgttatttgtttgtttaacagatttagctcagtttcaaccagcagagatttttttgtaaacctaataaaattttggaaaaagatagtatgataaaaaagcgattgacaggttaagttattttttgttatactgacaatgatactatataaagataactgacgtttttttgaaaagtaatatttcaatcacctgatgcgattaaataaaaggttctgttgataatctattttcctaactcttttattctctttgttttttcgattatctatcataaaaacgagatggcatccaaggccgagattcttacttgccatatatagtattataccaacaaattatataaggagtaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAAAAGGAUUUUCGAAUCCUUUUUUUGAUGUCUCCUUAAAUAAAUAGAACCUUGUGGACAAAUUUGAUAACCCAUUGUUAUUUGUUUGUUUAACAGAUUUAGCUCAGUUUCAACCAGCAGAGAUUUUUUUGUAAACCUAAUAAAAUUUUGGAAAAAGAUAGUAUGAUAAAAAAGCGAUUGACAGGUUAAGUUAUUUUUUGUUAUACUGACAAUGAUACUAUAUAAAGAUAACUGACGUUUUUUUGAAAAGUAAUAUUUCAAUCACCUGAUGCGAUUAAAUAAAAGGUUCUGUUGAUAAUCUAUUUUCCUAACUCUUUUAUUCUCUUUGUUUUUUCGAUUAUCUAUCAUAAAAACGAGAUGGCAUCCAAGGCCGAGAUUCUUACUUGCCAUAUAUAGUAUUAUACCAACAAAUUAUAUAAGGAGUAAA .(((((((((((....)))))))))))......(((((((.((((.(((.......(((((((((..((((((.....)))))).)))))))))(((((.....(((.(((......))).))).....)))))....)))........((((.......(((((((((((((((....((((....))))....)))))))))))))))...(((((((((((((((((.(((....))).))))...((((((.(((((.....((((((((.(((.(((((((((((..(..((((...))))..)..))).))))))))....((((((((..(((.....)))..))))))))))).)))))..)))..)))))..))))))....))))))))))))).))))....)))).))))))).... (-93.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACUCCUUAUAUAAUUUGUUGGUAUAAUACUAUAUAUGGCAAGUAAGAAUCUCGGCCUUGGAUGCCAUCUCGUUUUUAUGAUAGAUAAUCGAAAAAACAAAGAGAAUAAAAGAGUUAGGAAAAUAGAUUAUCAACAGAACCUUUUAUUUAAUCGCAUCAGGUGAUUGAAAUAUUACUUUUCAAAAAAACGUCAGUUAUCUUUAUAUAGUAUCAUUGUCAGUAUAACAAAAAAUAACUUAACCUGUCAAUCGCUUUUUUAUCAUACUAUCUUUUUCCAAAAUUUUAUUAGGUUUACAAAAAAAUCUCUGCUGGUUGAAACUGAGCUAAAUCUGUUAAACAAACAAAUAACAAUGGGUUAUCAAAUUUGUCCACAAGGUUCUAUUUAUUUAAGGAGACAUCAAAAAAAGGAUUCGAAAAUCCUUUUUUG ....(((((((.((((((..(((.....(((((((((((((.((((((...((...((((..(((((......((((((.((((.....)))).)))))).....(((((((((.(((..(...............)..))))))))))))....)))))))))....))....)))))).)))....(((....))).....))))))))))..((((..((.(((((.....((.((((.....((((((((..................(((....))).......((((((......))))))..)).))))))...)))).))....))))).))..))))....)))..)))))).((((....((....))....))))...)))))))......(((((((((((....))))))))))). (-77.46) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 392 359 91 47 NC_009009:SSA_0739|5end_Carbamate_kinase,_putative_721087..721317_POSITIVE 294 399 357 56 1 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 277 408 368 169 126 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 276 375 337 63 19 NC_009009:SSA_0696|5end_hypothetical_protein_679154..679384_POSITIVE 274 389 350 166 118 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 273 379 334 76 29 NC_009009:SSA_0081|5end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_85071..85301_NEGATIVE 268 303 265 126 91 NC_009009:SSA_2382|5end_Chromosome_partitioning_protein_ParB_or_transcriptional_regulator_Spo0J,_putative_2387516..2387746_POSITIVE 268 391 358 181 136 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 267 409 361 66 13 NC_009009:SSA_1377|5end_Asparaginyl-tRNA_synthetase,_putative_1397614..1397844_NEGATIVE 266 399 361 98 60 NC_009009:SSA_0706|5end_RNA_helicase,_putative_691363..691593_POSITIVE 260 337 291 196 141 NC_009009:SSA_1655|5end_hypothetical_protein_1651816..1652046_NEGATIVE 260 402 362 69 26 NC_009009:SSA_0588|5end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_579800..580030_POSITIVE 257 43 7 66 33 NC_009009:SSA_0286|5end_Transaldolase-like_protein,_putative_278814..279044_POSITIVE 256 391 356 65 24 NC_009009:SSA_0833|5end_Accessory_secretory_protein_Asp1,_putative_817940..818170_POSITIVE 256 400 360 231 192 NC_009009:SSA_0462|5end_ABC-type_multidrug_transport_system_(phospholipid,_LPS,_lipid_A_and_drug_exporter),_ATPase_and_permease_components,_putative_464815..465045_POSITIVE 253 390 348 59 16 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 252 390 356 74 25 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 250 116 71 230 182 NC_009009:SSA_1932|5end_Biotin_carboxylase,_putative_1920874..1921104_NEGATIVE 249 375 333 129 85 NC_009009:SSA_1668|5end_NrdI_protein,_putative_1668091..1668321_NEGATIVE 248 390 344 200 146 NC_009009:SSA_1322|5end_Glycosyl_transferase,_putative_1339819..1340049_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 390 343 53 11 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 274 389 350 71 23 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 268 303 265 80 45 NC_009009:SSA_2381|3end_DegP_protein,_putative_2387550..2387700_POSITIVE 260 337 291 132 77 NC_009009:SSA_1656|3end_Nisin_resistance_protein,_putative_1651880..1652030_NEGATIVE 257 43 7 51 18 NC_009009:SSA_0285|3end_Formate_acetyltransferase_3,_putative_278879..279029_POSITIVE 256 391 356 56 15 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 253 390 348 86 43 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 250 393 356 151 109 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 250 392 351 75 38 NC_009009:SSA_0378|3end_TRZ/ATZ_family_hydrolase,_putative_368627..368777_POSITIVE 249 375 333 125 81 NC_009009:SSA_1669|3end_hypothetical_protein_1668095..1668245_NEGATIVE 244 378 331 50 8 NC_009009:SSA_1207|3end_Phosphate_acetyltransferase,_putative_1231297..1231447_NEGATIVE 242 120 75 109 56 NC_009009:SSA_1353|3end_hypothetical_protein_1367974..1368124_NEGATIVE 242 398 356 45 1 NC_009009:SSA_1087|3end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1106472..1106622_POSITIVE 242 399 361 43 1 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 241 394 358 140 93 NC_009009:SSA_0855|3end_O-acetylhomoserine_sulfhydrylase,_putative_843192..843342_POSITIVE 239 401 362 51 15 NC_009009:SSA_0830|3end_Glycosyltransferase,_putative_815734..815884_POSITIVE 237 135 97 70 29 NC_009009:SSA_1166|3end_hypothetical_protein_1192350..1192500_POSITIVE 236 118 71 108 60 NC_009009:SSA_1696|3end_Tagatose_1,6-diphosphate_aldolase_2,_putative_1688207..1688357_NEGATIVE 236 408 368 151 112 NC_009009:SSA_0283|3end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIB_component,_putative_274950..275100_POSITIVE 235 391 357 51 17 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE