Origin IGS: ttacatccaatacaaaagtattgtacttgcttctatgagtaacctttacattattcttggttaatgtaataatctgattaatttcaatgccttttttaggtgctaacaatatctctcccgttacgtataacagttctttattaatggaataagcaggaagaatatcgacgacacttggcagctttcgtatttcgtgtaaagaaagcgcttcggagttgacaacttccgtataattttccaaacggtcagtagagtgtattttgctgtttctttgcaaagcgcttcttgtctgatgcgacgatacggatgacgataattttacaacaaacttgttttcgacctcggttaaaaactgtttttttcctgccgaccaataatagttctgctgtccggacaggtgtgctccggctgtaaatagcagaagcaaaatgataatattctttttcatgatggatttatttttta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaaataaatccatcatgaaaaagaatattatcattttgcttctgctatttacagccggagcacacctgtccggacagcagaactattattggtcggcaggaaaaaaacagtttttaaccgaggtcgaaaacaagtttgttgtaaaattatcgtcatccgtatcgtcgcatcagacaagaagcgctttgcaaagaaacagcaaaatacactctactgaccgtttggaaaattatacggaagttgtcaactccgaagcgctttctttacacgaaatacgaaagctgccaagtgtcgtcgatattcttcctgcttattccattaataaagaactgttatacgtaacgggagagatattgttagcacctaaaaaaggcattgaaattaatcagattattacattaaccaagaataatgtaaaggttactcatagaagcaagtacaatacttttgtattggatgtaa Mask Tandem Repeat Region ================================================ ttacatccaatacaaaagtattgtacttgcttctatgagtaacctttacattattcttggttaatgtaataatctgattaatttcaatgccttttttaggtgctaacaatatctctcccgttacgtataacagttctttattaatggaataagcaggaagaatatcgacgacacttggcagctttcgtatttcgtgtaaagaaagcgcttcggagttgacaacttccgtataattttccaaacggtcagtagagtgtattttgctgtttctttgcaaagcgcttcttgtctgatgcgacgatacggatgacgataattttacaacaaacttgttttcgacctcggttaaaaactgtttttttcctgccgaccaataatagttctgctgtccggacaggtgtgctccggctgtaaatagcagaagcaaaatgataatattctttttcatgatggatttatttttta Find is-nt database================================================ Query_seq: TF0347:TF0348|TF0347:TF0348:possible serine protease:hypothetical protein:->->:369605..370069 465 ttacatccaatacaaaagtattgtacttgcttctatgagtaacctttacattattcttggttaatgtaataatctgattaatttcaatgccttttttaggtgctaacaatatctctcccgttacgtataacagttctttattaatggaataagcaggaagaatatcgacgacacttggcagctttcgtatttcgtgtaaagaaagcgcttcggagttgacaacttccgtataattttccaaacggtcagtagagtgtattttgctgtttctttgcaaagcgcttcttgtctgatgcgacgatacggatgacgataattttacaacaaacttgttttcgacctcggttaaaaactgtttttttcctgccgaccaataatagttctgctgtccggacaggtgtgctccggctgtaaatagcagaagcaaaatgataatattctttttcatgatggatttatttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0347:TF0348|TF0347:TF0348:possible serine protease:hypothetical protein:->->:369605..370069 465 ttacatccaatacaaaagtattgtacttgcttctatgagtaacctttacattattcttggttaatgtaataatctgattaatttcaatgccttttttaggtgctaacaatatctctcccgttacgtataacagttctttattaatggaataagcaggaagaatatcgacgacacttggcagctttcgtatttcgtgtaaagaaagcgcttcggagttgacaacttccgtataattttccaaacggtcagtagagtgtattttgctgtttctttgcaaagcgcttcttgtctgatgcgacgatacggatgacgataattttacaacaaacttgttttcgacctcggttaaaaactgtttttttcctgccgaccaataatagttctgctgtccggacaggtgtgctccggctgtaaatagcagaagcaaaatgataatattctttttcatgatggatttatttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0347:TF0348|TF0347:TF0348:possible serine protease:hypothetical protein:->->:369605..370069 465 ttacatccaatacaaaagtattgtacttgcttctatgagtaacctttacattattcttggttaatgtaataatctgattaatttcaatgccttttttaggtgctaacaatatctctcccgttacgtataacagttctttattaatggaataagcaggaagaatatcgacgacacttggcagctttcgtatttcgtgtaaagaaagcgcttcggagttgacaacttccgtataattttccaaacggtcagtagagtgtattttgctgtttctttgcaaagcgcttcttgtctgatgcgacgatacggatgacgataattttacaacaaacttgttttcgacctcggttaaaaactgtttttttcctgccgaccaataatagttctgctgtccggacaggtgtgctccggctgtaaatagcagaagcaaaatgataatattctttttcatgatggatttatttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttacatccaatacaaaagtattgtacttgcttctatgagtaacctttacattattcttggttaatgtaataatctgattaatttcaatgccttttttaggtgctaacaatatctctcccgttacgtataacagttctttattaatggaataagcaggaagaatatcgacgacacttggcagctttcgtatttcgtgtaaagaaagcgcttcggagttgacaacttccgtataattttccaaacggtcagtagagtgtattttgctgtttctttgcaaagcgcttcttgtctgatgcgacgatacggatgacgataattttacaacaaacttgttttcgacctcggttaaaaactgtttttttcctgccgaccaataatagttctgctgtccggacaggtgtgctccggctgtaaatagcagaagcaaaatgataatattctttttcatgatggatttatttttta Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 286 End: 411 ............................................................................................................................................................................................................................................................................................. M S D A T I R M T I I L Q Q T C F R P R L K T V F F L P T N N S S A V R T G V L R L ...................................................... Protein_Len: 30 Strand: - Start: 349 End: 438 ............................................................................................................................................................................................................................................................................................................................................................ F S N K E Q R G I I T R S D P C T H E P Q L Y C F C F S L M ........................... Protein_Len: 60 Strand: - Start: 249 End: 455 ........................................................................................................................................................................................................................................................ F R K K D S A V I R I V I I K C C V Q K R G R N F V T K K R G V L L L E A T R V P T S R S Y I A S A F H Y Y E K E H H M .......... Protein_Len: 57 Strand: - Start: 124 End: 294 ........................................................................................................................... T Y C N K I L P I L L F F I S S V Q C S E Y K T Y L F R K P T S L K R I I K W V T L L T Y K A T E K C L A E Q R M ........................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 2 End: 451 . Q L A S R T Q H S S V S S S L K V V F K N E V E T L F Q K K G A S W Y Y N Q Q G S L H A G A T F L L L L I I I N K K M M .............. ttacatccaatacaaaagtattgtacttgcttctatgagtaacctttacattattcttggttaatgtaataatctgattaatttcaatgccttttttaggtgctaacaatatctctcccgttacgtataacagttctttattaatggaataagcaggaagaatatcgacgacacttggcagctttcgtatttcgtgtaaagaaagcgcttcggagttgacaacttccgtataattttccaaacggtcagtagagtgtattttgctgtttctttgcaaagcgcttcttgtctgatgcgacgatacggatgacgataattttacaacaaacttgttttcgacctcggttaaaaactgtttttttcctgccgaccaataatagttctgctgtccggacaggtgtgctccggctgtaaatagcagaagcaaaatgataatattctttttcatgatggatttatttttta 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: 44 End: 73 ...........................................CTTTACATTATTCTTGGTTAATGTAATAAT........................................................................................................................................................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttacatccaatacaaaagtattgtacttgcttctatgagtaacctttacattattcttggttaatgtaataatctgattaatttcaatgccttttttaggtgctaacaatatctctcccgttacgtataacagttctttattaatggaataagcaggaagaatatcgacgacacttggcagctttcgtatttcgtgtaaagaaagcgcttcggagttgacaacttccgtataattttccaaacggtcagtagagtgtattttgctgtttctttgcaaagcgcttcttgtctgatgcgacgatacggatgacgataattttacaacaaacttgttttcgacctcggttaaaaactgtttttttcctgccgaccaataatagttctgctgtccggacaggtgtgctccggctgtaaatagcagaagcaaaatgataatattctttttcatgatggatttatttttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 41 HP_score: -2.6 Tail_Score: -2.72052 Start: 46 End: 69 Full_Region: TTCTATGAGTAACCT TTACATTA TTCTTGGT TAATGTAA TAATCTGATTAATTT .............................................TTACATTATTCTTGGTTAATGTAA............................................................................................................................................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 83 HP_score: -4.1 Tail_Score: -5.52384 Start: 343 End: 355 Full_Region: ACTTGTTTTCGACCT CGGTT AAA AACTG TTTTTTTCCTGCCGA ......................................................................................................................................................................................................................................................................................................................................................CGGTTAAAAACTG.............................................................................................................. Find igs database================================================ Query_seq: TF0347:TF0348|TF0347:TF0348:possible serine protease:hypothetical protein:->->:369605..370069 465 ttacatccaatacaaaagtattgtacttgcttctatgagtaacctttacattattcttggttaatgtaataatctgattaatttcaatgccttttttaggtgctaacaatatctctcccgttacgtataacagttctttattaatggaataagcaggaagaatatcgacgacacttggcagctttcgtatttcgtgtaaagaaagcgcttcggagttgacaacttccgtataattttccaaacggtcagtagagtgtattttgctgtttctttgcaaagcgcttcttgtctgatgcgacgatacggatgacgataattttacaacaaacttgttttcgacctcggttaaaaactgtttttttcctgccgaccaataatagttctgctgtccggacaggtgtgctccggctgtaaatagcagaagcaaaatgataatattctttttcatgatggatttatttttta Intra-Species Hit: Count: 1 Min: 1 Max: 465 Len: 465 Subject: tfor_TF0347_TF0348|possible serine protease:hypothetical protein|POSITIVE:POSITIVE|[369605,370069]|465 HSP 1 e-value: 0.0 bit: 880.0 Len: 465 Query Start:1 Query End:465 Subject Strand: POSITIVE Subject Start: 1 Subject End: 465 ttacatccaatacaaaagtattgtacttgcttctatgagtaacctttacattattcttggttaatgtaataatctgattaatttcaatgccttttttaggtgctaacaatatctctcccgttacgtataacagttctttattaatggaataagcaggaagaatatcgacgacacttggcagctttcgtatttcgtgtaaagaaagcgcttcggagttgacaacttccgtataattttccaaacggtcagtagagtgtattttgctgtttctttgcaaagcgcttcttgtctgatgcgacgatacggatgacgataattttacaacaaacttgttttcgacctcggttaaaaactgnnnnnnncctgccgaccaataatagttctgctgtccggacaggtgtgctccggctgtaaatagcagaagcaaaatgataatattctttttcatgatggatttatttttta ttacatccaatacaaaagtattgtacttgcttctatgagtaacctttacattattcttggttaatgtaataatctgattaatttcaatgccttttttaggtgctaacaatatctctcccgttacgtataacagttctttattaatggaataagcaggaagaatatcgacgacacttggcagctttcgtatttcgtgtaaagaaagcgcttcggagttgacaacttccgtataattttccaaacggtcagtagagtgtattttgctgtttctttgcaaagcgcttcttgtctgatgcgacgatacggatgacgataattttacaacaaacttgttttcgacctcggttaaaaactgtttttttcctgccgaccaataatagttctgctgtccggacaggtgtgctccggctgtaaatagcagaagcaaaatgataatattctttttcatgatggatttatttttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACAUCCAAUACAAAAGUAUUGUACUUGCUUCUAUGAGUAACCUUUACAUUAUUCUUGGUUAAUGUAAUAAUCUGAUUAAUUUCAAUGCCUUUUUUAGGUGCUAACAAUAUCUCUCCCGUUACGUAUAACAGUUCUUUAUUAAUGGAAUAAGCAGGAAGAAUAUCGACGACACUUGGCAGCUUUCGUAUUUCGUGUAAAGAAAGCGCUUCGGAGUUGACAACUUCCGUAUAAUUUUCCAAACGGUCAGUAGAGUGUAUUUUGCUGUUUCUUUGCAAAGCGCUUCUUGUCUGAUGCGACGAUACGGAUGACGAUAAUUUUACAACAAACUUGUUUUCGACCUCGGUUAAAAACUGUUUUUUUCCUGCCGACCAAUAAUAGUUCUGCUGUCCGGACAGGUGUGCUCCGGCUGUAAAUAGCAGAAGCAAAAUGAUAAUAUUCUUUUUCAUGAUGGAUUUAUUUUUUA ...((((.........((((((((..(((((((...(((((((((((((((((........))))))))...((((............((((.....))))............................(((((...((((((.(((.....(((((((((.(((((.((((.((.(((.((((((.(((.....)))..)))))))))..)).))))......(((((((...(((.((((..(.((((((((....)))))))).)..)))).))).(((.((......)).)))...)))))))...)))))..........((((..(((((..((....))..))))).)))))))))))))...))).))))))....))))).)))).)))).)))))..((((....)))).)))))))....)))))))).........))))............. (-110.67) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAAUAAAUCCAUCAUGAAAAAGAAUAUUAUCAUUUUGCUUCUGCUAUUUACAGCCGGAGCACACCUGUCCGGACAGCAGAACUAUUAUUGGUCGGCAGGAAAAAAACAGUUUUUAACCGAGGUCGAAAACAAGUUUGUUGUAAAAUUAUCGUCAUCCGUAUCGUCGCAUCAGACAAGAAGCGCUUUGCAAAGAAACAGCAAAAUACACUCUACUGACCGUUUGGAAAAUUAUACGGAAGUUGUCAACUCCGAAGCGCUUUCUUUACACGAAAUACGAAAGCUGCCAAGUGUCGUCGAUAUUCUUCCUGCUUAUUCCAUUAAUAAAGAACUGUUAUACGUAACGGGAGAGAUAUUGUUAGCACCUAAAAAAGGCAUUGAAAUUAAUCAGAUUAUUACAUUAACCAAGAAUAAUGUAAAGGUUACUCAUAGAAGCAAGUACAAUACUUUUGUAUUGGAUGUAA .............((((....................((((((((((((.((((((((..((((...((((.(((..(((...........)))..))))))).........(((((..((....))..)))))..))))))))))))....((((....(((...(((......)))..(((((((((((.......(((((......((......)).((((.(((....))).))))..)))))......)))))))))))......)))....)))).))).(((..((((...((((((..((((((.((((.....(((((......)))))...))))))))))..))))))...))))........)))..............(((..((((((((........))))))))..)))......)))))))))..((((((....))))))))))... (-106.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 478 409 361 56 6 tfor:TF1589|5end_surface_antigen_BspA_1703189..1703419_POSITIVE 469 426 382 61 9 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 442 408 361 63 6 tfor:TF1591|5end_surface_antigen_BspA_1706387..1706617_POSITIVE 410 425 381 222 177 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 386 409 364 200 157 tfor:TF0982|5end_conserved_hypothetical_protein_1038633..1038863_POSITIVE 371 426 381 57 6 tfor:TF1794|5end_possible_glucose-1-phosphatase_1934453..1934683_POSITIVE 367 408 366 208 169 tfor:TF1831|5end_conserved_hypothetical_protein_1980365..1980595_POSITIVE 366 219 173 202 160 tfor:TF0181|5end_ATP-dependent_DNA_helicase_192408..192638_POSITIVE 364 406 361 50 7 tfor:TF0677|5end_ATP-binding_protein,_Mrp/Nbp35_family,_involved_in_chromosome_partitioning_719799..720029_POSITIVE 363 218 171 176 122 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 363 306 263 210 163 tfor:TF0302|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_328641..328871_POSITIVE 361 408 364 43 1 tfor:TF0421|5end_alpha-L-fucosidase_436021..436251_POSITIVE 358 410 362 83 27 tfor:TF2879|5end_tRNA_(guanine-N-1)-methyltransferase_3068254..3068484_POSITIVE 355 274 243 224 193 tfor:TF0430|5end_hypothetical_protein_452163..452393_POSITIVE 351 410 361 86 14 tfor:TF2331|5end_conserved_hypothetical_protein_2491073..2491303_POSITIVE 351 411 381 34 1 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 349 428 385 183 138 tfor:TF1910|5end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase_2064001..2064231_POSITIVE 348 219 171 86 26 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 348 425 381 57 14 tfor:TF0287|5end_peptidase,_M23_family_315810..316040_POSITIVE 346 405 361 102 63 tfor:TF0024|5end_conserved_hypothetical_protein;_possible_ATPase_20191..20421_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 407 361 109 51 tfor:TF1301|3end_hypothetical_protein_1383487..1383637_POSITIVE 348 219 171 81 21 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 348 289 244 56 11 tfor:TF0337|3end_hypothetical_protein_360711..360861_POSITIVE 346 405 361 64 25 tfor:TF0023|3end_possible_response_element_in_two_component_regulation_20233..20383_POSITIVE 345 300 252 66 3 tfor:TF2755|3end_hypothetical_protein_2941053..2941203_POSITIVE 345 209 164 53 5 tfor:TF1925|3end_hypothetical_protein_2075101..2075251_POSITIVE 345 425 385 81 47 tfor:TF0247|3end_conserved_hypothetical_protein_278348..278498_POSITIVE 343 425 381 102 52 tfor:TF1775|3end_oxidoreductase,_Gfo/Idh/MocA_family_1914618..1914768_POSITIVE 341 407 378 44 14 tfor:TF1821|3end_cation_efflux_system_protein_1967645..1967795_POSITIVE 335 247 201 102 42 tfor:TF1730|3end_diaminopimelate_decarboxylase_1855907..1856057_POSITIVE 333 409 364 140 82 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 329 426 383 44 1 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 327 423 385 110 65 tfor:TF1476|3end_outer_membrane_protein_P49_1571203..1571353_POSITIVE 326 187 144 145 103 tfor:TF2735|3end_hypothetical_protein_2917928..2918078_POSITIVE 326 310 262 61 16 tfor:TF0037|3end_sialic_acid-specific_9-O-acetylesterase_39991..40141_POSITIVE 325 425 387 76 42 tfor:TF2332|3end_signal_peptidase_I_2492613..2492763_POSITIVE 324 409 384 147 120 tfor:TF0994|3end_maltose_O-acetyltransferase_1049782..1049932_POSITIVE 323 256 211 89 25 tfor:TF1084|3end_transposase_1153788..1153938_POSITIVE 322 305 263 128 82 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 317 409 362 54 5 tfor:TF2759|3end_xylose_repressor,_ROK_family_2944853..2945003_POSITIVE