Origin IGS: taatcatgcggtcagtcttgttttataagaaaaggcaaatataattataaaggaagcattcaacagttgtattaagcttgttggctttcttgatattcagcatctatctgaaaagataggtgcttttattgtgttcaacctcttttgtttaatcttgccgaatctctgccgatgcgtgtggaaaataagaatatttttcggtgaaagtatctgttcctatttgttgaagcgatattcttgggtggtttgaaaagaaagatgaagtacaaaaaagaaatgtgggacttaaatgtcccacacttcttctgtttgctctttgccttctgcaaagccatcgcttatcgtaccattatcaataggcacctttatattttgtctgagtctgccaatggcatttgtatttctactggtagggtttgtatcagaggtttagtgtatgttttttgttttactttcattgcttta .........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 taaagcaatgaaagtaaaacaaaaaacatacactaaacctctgatacaaaccctaccagtagaaatacaaatgccattggcagactcagacaaaatataaaggtgcctattgataatggtacgataagcgatggctttgcagaaggcaaagagcaaacagaagaagtgtgggacatttaagtcccacatttcttttttgtacttcatctttcttttcaaaccacccaagaatatcgcttcaacaaataggaacagatactttcaccgaaaaatattcttattttccacacgcatcggcagagattcggcaagattaaacaaaagaggttgaacacaataaaagcacctatcttttcagatagatgctgaatatcaagaaagccaacaagcttaatacaactgttgaatgcttcctttataattatatttgccttttcttataaaacaagactgaccgcatgatta Mask Tandem Repeat Region ================================================ taatcatgcggtcagtcttgttttataagaaaaggcaaatataattataaaggaagcattcaacagttgtattaagcttgttggctttcttgatattcagcatctatctgaaaagataggtgcttttattgtgttcaacctcttttgtttaatcttgccgaatctctgccgatgcgtgtggaaaataagaatatttttcggtgaaagtatctgttcctatttgttgaagcgatattcttgggtggtttgaaaagaaagatgaagtacaaaaaagaaatgtgggacttaaatgtcccacacttcttctgtttgctctttgccttctgcaaagccatcgcttatcgtaccattatcaataggcacctttatattttgtctgagtctgccaatggcatttgtatttctactggtagggtttgtatcagaggtttagtgtatgttttttgttttactttcattgcttta Find is-nt database================================================ Query_seq: PI0492:PI0493|PI0492:PI0493:hypothetical protein:surface antigen BspA:->->:452519..452983 465 taatcatgcggtcagtcttgttttataagaaaaggcaaatataattataaaggaagcattcaacagttgtattaagcttgttggctttcttgatattcagcatctatctgaaaagataggtgcttttattgtgttcaacctcttttgtttaatcttgccgaatctctgccgatgcgtgtggaaaataagaatatttttcggtgaaagtatctgttcctatttgttgaagcgatattcttgggtggtttgaaaagaaagatgaagtacaaaaaagaaatgtgggacttaaatgtcccacacttcttctgtttgctctttgccttctgcaaagccatcgcttatcgtaccattatcaataggcacctttatattttgtctgagtctgccaatggcatttgtatttctactggtagggtttgtatcagaggtttagtgtatgttttttgttttactttcattgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0492:PI0493|PI0492:PI0493:hypothetical protein:surface antigen BspA:->->:452519..452983 465 taatcatgcggtcagtcttgttttataagaaaaggcaaatataattataaaggaagcattcaacagttgtattaagcttgttggctttcttgatattcagcatctatctgaaaagataggtgcttttattgtgttcaacctcttttgtttaatcttgccgaatctctgccgatgcgtgtggaaaataagaatatttttcggtgaaagtatctgttcctatttgttgaagcgatattcttgggtggtttgaaaagaaagatgaagtacaaaaaagaaatgtgggacttaaatgtcccacacttcttctgtttgctctttgccttctgcaaagccatcgcttatcgtaccattatcaataggcacctttatattttgtctgagtctgccaatggcatttgtatttctactggtagggtttgtatcagaggtttagtgtatgttttttgttttactttcattgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0492:PI0493|PI0492:PI0493:hypothetical protein:surface antigen BspA:->->:452519..452983 465 taatcatgcggtcagtcttgttttataagaaaaggcaaatataattataaaggaagcattcaacagttgtattaagcttgttggctttcttgatattcagcatctatctgaaaagataggtgcttttattgtgttcaacctcttttgtttaatcttgccgaatctctgccgatgcgtgtggaaaataagaatatttttcggtgaaagtatctgttcctatttgttgaagcgatattcttgggtggtttgaaaagaaagatgaagtacaaaaaagaaatgtgggacttaaatgtcccacacttcttctgtttgctctttgccttctgcaaagccatcgcttatcgtaccattatcaataggcacctttatattttgtctgagtctgccaatggcatttgtatttctactggtagggtttgtatcagaggtttagtgtatgttttttgttttactttcattgcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatcatgcggtcagtcttgttttataagaaaaggcaaatataattataaaggaagcattcaacagttgtattaagcttgttggctttcttgatattcagcatctatctgaaaagataggtgcttttattgtgttcaacctcttttgtttaatcttgccgaatctctgccgatgcgtgtggaaaataagaatatttttcggtgaaagtatctgttcctatttgttgaagcgatattcttgggtggtttgaaaagaaagatgaagtacaaaaaagaaatgtgggacttaaatgtcccacacttcttctgtttgctctttgccttctgcaaagccatcgcttatcgtaccattatcaataggcacctttatattttgtctgagtctgccaatggcatttgtatttctactggtagggtttgtatcagaggtttagtgtatgttttttgttttactttcattgcttta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 41 End: 247 ........................................ M I I K E A F N S C I K L V G F L D I Q H L S E K I G A F I V F N L F C L I L P N L C R C V W K I R I F F G E S I C S Y .......................................................................................................................................................................................................................... Protein_Len: 41 Strand: + Start: 234 End: 356 ......................................................................................................................................................................................................................................... M L G W F E K K D E V Q K R N V G L K C P T L L L F A L C L L Q S H R L S Y H Y Q ............................................................................................................. Protein_Len: 47 Strand: + Start: 290 End: 430 ................................................................................................................................................................................................................................................................................................. M S H T S S V C S L P S A K P S L I V P L S I G T F I F C L S L P M A F V F L L V G F V S E V ................................... Protein_Len: 60 Strand: + Start: 211 End: 465 .................................................................................................................................................................................................................. M F L F V E A I F L G G L K R K M K Y K K E M W D L N V P H F F C L L F A F C K A I A Y R T I I N R H L Y I L S E S A N Protein_Len: 30 Strand: - Start: 369 End: 458 ................................................................................................................................................................................................................................................................................................................................................................................ I K D S D A L P M Q I E V P L T Q I L P K T Y T K Q K V K M ....... Protein_Len: 34 Strand: - Start: 289 End: 390 ................................................................................................................................................................................................................................................................................................ I D W V E E T Q E K G E A F G D S I T G N D I P V K I N Q R L R G M ........................................................................... Protein_Len: 49 Strand: - Start: 152 End: 298 ....................................................................................................................................................... D Q R I E A S A H P F Y S Y K E T F T D T G I Q Q L S I R P H N S F F S S T C F L F T P S L H G M ....................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 138 End: 335 ......................................................................................................................................... A S D R G I R T S F L F I K R H F Y R N R N T S A I N K P P K F L F I F Y L F S I H S K F T G C K K Q K S K A K Q L A M .................................................................................................................................. Protein_Len: 37 Strand: - Start: 100 End: 210 ................................................................................................... C R D S F I P A K I T N L R K Q K I K G F R Q R H T H F I L I N K P S L M ............................................................................................................................................................................................................................................................... Protein_Len: 30 Strand: - Start: 7 End: 96 ...... A T L R T K Y S F A F I I I F S A N L L Q I L S T P K R S M ................................................................................................................................................................................................................................................................................................................................................................................. taatcatgcggtcagtcttgttttataagaaaaggcaaatataattataaaggaagcattcaacagttgtattaagcttgttggctttcttgatattcagcatctatctgaaaagataggtgcttttattgtgttcaacctcttttgtttaatcttgccgaatctctgccgatgcgtgtggaaaataagaatatttttcggtgaaagtatctgttcctatttgttgaagcgatattcttgggtggtttgaaaagaaagatgaagtacaaaaaagaaatgtgggacttaaatgtcccacacttcttctgtttgctctttgccttctgcaaagccatcgcttatcgtaccattatcaataggcacctttatattttgtctgagtctgccaatggcatttgtatttctactggtagggtttgtatcagaggtttagtgtatgttttttgttttactttcattgcttta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatcatgcggtcagtcttgttttataagaaaaggcaaatataattataaaggaagcattcaacagttgtattaagcttgttggctttcttgatattcagcatctatctgaaaagataggtgcttttattgtgttcaacctcttttgtttaatcttgccgaatctctgccgatgcgtgtggaaaataagaatatttttcggtgaaagtatctgttcctatttgttgaagcgatattcttgggtggtttgaaaagaaagatgaagtacaaaaaagaaatgtgggacttaaatgtcccacacttcttctgtttgctctttgccttctgcaaagccatcgcttatcgtaccattatcaataggcacctttatattttgtctgagtctgccaatggcatttgtatttctactggtagggtttgtatcagaggtttagtgtatgttttttgttttactttcattgcttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.4 Tail_Score: -4.90381 Start: 100 End: 123 Full_Region: CTTTCTTGATATTCA GCATCTATCT GAAA AGATAGGTGC TTTTATTGTGTTCAA ...................................................................................................GCATCTATCTGAAAAGATAGGTGC...................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 89 HP_score: -10.8 Tail_Score: -3.90949 Start: 274 End: 303 Full_Region: ATGAAGTACAAAAAA GAAATGTGGGAC TTAAAT GTCCCACACTTC TTCTGTTTGCTCTTT .................................................................................................................................................................................................................................................................................GAAATGTGGGACTTAAATGTCCCACACTTC.................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -13.0 Tail_Score: -5.38249 Start: 274 End: 303 Full_Region: aaagagcaaacagaa gaagtgtgggac atttaa gtcccacatttc ttttttgtacttcat .................................................................................................................................................................................................................................................................................gaagtgtgggacatttaagtcccacatttc.................................................................................................................................................................. TransTerm Strand: + Conf: 70 HP_score: -6.7 Tail_Score: -4.05193 Start: 277 End: 300 Full_Region: AAGTACAAAAAAGAA ATGTGGGAC TTAAAT GTCCCACAC TTCTTCTGTTTGCTC ....................................................................................................................................................................................................................................................................................ATGTGGGACTTAAATGTCCCACAC..................................................................................................................................................................... TransTerm Strand: + Conf: 76 HP_score: -6.8 Tail_Score: -4.41609 Start: 384 End: 394 Full_Region: TATTTTGTCTGAGTC TGCC AAT GGCA TTTGTATTTCTACTG ...............................................................................................................................................................................................................................................................................................................................................................................................TGCCAATGGCA....................................................................... Find igs database================================================ Query_seq: PI0492:PI0493|PI0492:PI0493:hypothetical protein:surface antigen BspA:->->:452519..452983 465 taatcatgcggtcagtcttgttttataagaaaaggcaaatataattataaaggaagcattcaacagttgtattaagcttgttggctttcttgatattcagcatctatctgaaaagataggtgcttttattgtgttcaacctcttttgtttaatcttgccgaatctctgccgatgcgtgtggaaaataagaatatttttcggtgaaagtatctgttcctatttgttgaagcgatattcttgggtggtttgaaaagaaagatgaagtacaaaaaagaaatgtgggacttaaatgtcccacacttcttctgtttgctctttgccttctgcaaagccatcgcttatcgtaccattatcaataggcacctttatattttgtctgagtctgccaatggcatttgtatttctactggtagggtttgtatcagaggtttagtgtatgttttttgttttactttcattgcttta Intra-Species Hit: Count: 1 Min: 1 Max: 465 Len: 465 Subject: pint_PI0492_PI0493|hypothetical protein:surface antigen BspA|POSITIVE:POSITIVE|[452519,452983]|465 HSP 1 e-value: 0.0 bit: 922.0 Len: 465 Query Start:1 Query End:465 Subject Strand: POSITIVE Subject Start: 1 Subject End: 465 taatcatgcggtcagtcttgttttataagaaaaggcaaatataattataaaggaagcattcaacagttgtattaagcttgttggctttcttgatattcagcatctatctgaaaagataggtgcttttattgtgttcaacctcttttgtttaatcttgccgaatctctgccgatgcgtgtggaaaataagaatatttttcggtgaaagtatctgttcctatttgttgaagcgatattcttgggtggtttgaaaagaaagatgaagtacaaaaaagaaatgtgggacttaaatgtcccacacttcttctgtttgctctttgccttctgcaaagccatcgcttatcgtaccattatcaataggcacctttatattttgtctgagtctgccaatggcatttgtatttctactggtagggtttgtatcagaggtttagtgtatgttttttgttttactttcattgcttta taatcatgcggtcagtcttgttttataagaaaaggcaaatataattataaaggaagcattcaacagttgtattaagcttgttggctttcttgatattcagcatctatctgaaaagataggtgcttttattgtgttcaacctcttttgtttaatcttgccgaatctctgccgatgcgtgtggaaaataagaatatttttcggtgaaagtatctgttcctatttgttgaagcgatattcttgggtggtttgaaaagaaagatgaagtacaaaaaagaaatgtgggacttaaatgtcccacacttcttctgtttgctctttgccttctgcaaagccatcgcttatcgtaccattatcaataggcacctttatattttgtctgagtctgccaatggcatttgtatttctactggtagggtttgtatcagaggtttagtgtatgttttttgttttactttcattgcttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCAUGCGGUCAGUCUUGUUUUAUAAGAAAAGGCAAAUAUAAUUAUAAAGGAAGCAUUCAACAGUUGUAUUAAGCUUGUUGGCUUUCUUGAUAUUCAGCAUCUAUCUGAAAAGAUAGGUGCUUUUAUUGUGUUCAACCUCUUUUGUUUAAUCUUGCCGAAUCUCUGCCGAUGCGUGUGGAAAAUAAGAAUAUUUUUCGGUGAAAGUAUCUGUUCCUAUUUGUUGAAGCGAUAUUCUUGGGUGGUUUGAAAAGAAAGAUGAAGUACAAAAAAGAAAUGUGGGACUUAAAUGUCCCACACUUCUUCUGUUUGCUCUUUGCCUUCUGCAAAGCCAUCGCUUAUCGUACCAUUAUCAAUAGGCACCUUUAUAUUUUGUCUGAGUCUGCCAAUGGCAUUUGUAUUUCUACUGGUAGGGUUUGUAUCAGAGGUUUAGUGUAUGUUUUUUGUUUUACUUUCAUUGCUUUA .......(((((.((....((...((((((((..((((((((((((((.((((((((...((((((((......))).))))))))))))).)))...(((((((((((....)))))))))))...)))))))).(((((((..((...(((((((((........((....))..((((((((((((.......(((((..(((((((..((.((((((...((..((((((.....(((((((((....((((.(..((((..((((.(((((.((((((((......)))))))).)))))...))))..))))..)))))...)))))))).).))))))..)).....)))))).))....)))))))..)))))...(((...))).))))).))))))).)))))))))..))..)))))))...)))...))))))))...)).)).))))).... (-130.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGCAAUGAAAGUAAAACAAAAAACAUACACUAAACCUCUGAUACAAACCCUACCAGUAGAAAUACAAAUGCCAUUGGCAGACUCAGACAAAAUAUAAAGGUGCCUAUUGAUAAUGGUACGAUAAGCGAUGGCUUUGCAGAAGGCAAAGAGCAAACAGAAGAAGUGUGGGACAUUUAAGUCCCACAUUUCUUUUUUGUACUUCAUCUUUCUUUUCAAACCACCCAAGAAUAUCGCUUCAACAAAUAGGAACAGAUACUUUCACCGAAAAAUAUUCUUAUUUUCCACACGCAUCGGCAGAGAUUCGGCAAGAUUAAACAAAAGAGGUUGAACACAAUAAAAGCACCUAUCUUUUCAGAUAGAUGCUGAAUAUCAAGAAAGCCAACAAGCUUAAUACAACUGUUGAAUGCUUCCUUUAUAAUUAUAUUUGCCUUUUCUUAUAAAACAAGACUGACCGCAUGAUUA ....((..((((((((.......................(((((..............(((....)))...((((...))))...)))))............((.((((((.....(((..(((((..(..(((.((((.((((((..(((.(((((..(((((((((((((((......)))))))))))))))))))).)))...))))))...))))))).....)..)))))..)))...)))))).))...))))))))..(.((((((....)))))).)....))..((((((......((((((..(((.....(((((..(....(((((..((((.((((((....)))))).))))...........((((......))))........)))))....)..)))))....)))..))))))...((((.......))))))).)))........ (-107.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 344 310 69 21 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 376 346 312 180 140 pint:PI1813|5end_hypothetical_protein_1752878..1753108_POSITIVE 357 376 332 201 143 pint:PI1404|5end_hypothetical_protein_1324903..1325133_POSITIVE 344 348 302 204 136 pint:PI0141|5end_glutamine_amidotransferase_involved_in_pyridoxine_biosynthesis_132710..132940_POSITIVE 339 347 302 163 110 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 337 340 291 217 154 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 336 345 312 60 26 pint:PI1694|5end_hypothetical_protein_1609717..1609947_POSITIVE 331 377 336 55 13 pint:PI1021|5end_conserved_hypothetical_protein;_possible_methyltransferase_938985..939215_POSITIVE 326 339 291 99 44 pint:PI0564|5end_hypothetical_protein_511537..511767_POSITIVE 320 345 312 60 26 pint:PI1829|5end_hypothetical_protein_1769255..1769485_POSITIVE 320 365 324 213 169 pint:PI1413|5end_hypothetical_protein_1333727..1333957_POSITIVE 319 349 303 104 49 pint:PI1705|5end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_1621781..1622011_POSITIVE 318 344 303 40 2 pint:PI0514|5end_possible_cell_filamentation_protein_472408..472638_POSITIVE 318 354 311 164 112 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 315 367 321 56 11 pint:PI0507|5end_transcriptional_regulator_466255..466485_POSITIVE 312 182 145 47 1 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 312 339 295 181 123 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 310 365 322 104 57 pint:PI1876|5end_possible_flagellar_motor_protein,_OmpA_family_1819082..1819312_POSITIVE 310 348 303 204 148 pint:PI0029|5end_glutamine_amidotransferase_(GMP_synthase_(glutamine-hydrolyzing))_32593..32823_POSITIVE 308 349 303 75 14 pint:PI0962|5end_phosphoglycerate_mutase_892101..892331_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 346 312 76 36 pint:PI1812|3end_possible_alpha-amylase_1752854..1753004_POSITIVE 344 348 302 138 70 pint:PI0139|3end_pyridoxine_biosynthesis_protein_132724..132874_POSITIVE 326 339 291 139 84 pint:PI0565|3end_hypothetical_protein_511657..511807_POSITIVE 317 342 304 137 103 pint:PI0121|3end_outer_membrane_protein,_ompH_family_113208..113358_POSITIVE 310 365 322 48 1 pint:PI1875|3end_hypothetical_protein_1819106..1819256_POSITIVE 309 340 295 142 105 pint:PI0642|3end_thioredoxin_family_protein_585582..585732_POSITIVE 309 308 261 67 17 pint:PI0282|3end_hypothetical_protein_266826..266976_POSITIVE 305 171 139 121 83 pint:PI1622|3end_hypothetical_protein_1547230..1547380_POSITIVE 300 346 312 117 85 pint:PI0560|3end_hypothetical_protein_508910..509060_POSITIVE 299 345 312 43 9 pint:PI0996|3end_hypothetical_protein_920660..920810_POSITIVE 299 345 312 102 68 pint:PI0759|3end_hypothetical_protein_693998..694148_POSITIVE 299 345 312 142 108 pint:PI0689|3end_hypothetical_protein_625877..626027_POSITIVE 299 345 312 142 108 pint:PI0670|3end_hypothetical_protein_611280..611430_POSITIVE 299 345 312 142 108 pint:PI0061|3end_hypothetical_protein_60690..60840_POSITIVE 297 340 291 151 100 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 294 181 155 37 13 pint:PI0816|3end_glycogen_debranching_enzyme_756920..757070_POSITIVE 290 393 359 134 94 pint:PI2147|3end_GTP-binding_protein_2094407..2094557_POSITIVE 290 345 312 102 68 pint:PI1141|3end_hypothetical_protein_1069713..1069863_POSITIVE 290 345 312 43 9 pint:PI0054|3end_hypothetical_protein_54829..54979_POSITIVE 286 313 278 150 112 pint:PI2098|3end_hypothetical_protein_2052473..2052623_POSITIVE