Origin IGS: tgaagagtgaaaaacgaaaagtgaagagtgaaaaacgaaaaacgaagagtgaaaagtgaagagtgaaaagtgaagagtagtcaacagtaattaatgttgtcaatgtaggggcgaaccttgtgttcgccctttttttgtgtggcgtcgggtttatccgaacgcaaatttcgcaaataggcgcgaatggacgcaaatattaacccgacgggactattttgtgatttttgaaactattaaatgtctgactaatatatttttgtcaaaataaaaataacgtta .........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 taacgttatttttattttgacaaaaatatattagtcagacatttaatagtttcaaaaatcacaaaatagtcccgtcgggttaatatttgcgtccattcgcgcctatttgcgaaatttgcgttcggataaacccgacgccacacaaaaaaagggcgaacacaaggttcgcccctacattgacaacattaattactgttgactactcttcacttttcactcttcacttttcactcttcgtttttcgtttttcactcttcacttttcgtttttcactcttca Mask Tandem Repeat Region ================================================ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtcaacagtaattaatgttgtcaatgtaggggcgaaccttgtgttcgccctttttttgtgtggcgtcgggtttatccgaacgcaaatttcgcaaataggcgcgaatggacgcaaatattaacccgacgggactattttgtgatttttgaaactattaaatgtctgactaatatatttttgtcaaaataaaaataacgtta Find is-nt database================================================ Query_seq: TF1843:TF1844|TF1843:TF1844:surface antigen BspA:hypothetical protein:->->:1996250..1996528 279 tgaagagtgaaaaacgaaaagtgaagagtgaaaaacgaaaaacgaagagtgaaaagtgaagagtgaaaagtgaagagtagtcaacagtaattaatgttgtcaatgtaggggcgaaccttgtgttcgccctttttttgtgtggcgtcgggtttatccgaacgcaaatttcgcaaataggcgcgaatggacgcaaatattaacccgacgggactattttgtgatttttgaaactattaaatgtctgactaatatatttttgtcaaaataaaaataacgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1843:TF1844|TF1843:TF1844:surface antigen BspA:hypothetical protein:->->:1996250..1996528 279 tgaagagtgaaaaacgaaaagtgaagagtgaaaaacgaaaaacgaagagtgaaaagtgaagagtgaaaagtgaagagtagtcaacagtaattaatgttgtcaatgtaggggcgaaccttgtgttcgccctttttttgtgtggcgtcgggtttatccgaacgcaaatttcgcaaataggcgcgaatggacgcaaatattaacccgacgggactattttgtgatttttgaaactattaaatgtctgactaatatatttttgtcaaaataaaaataacgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1843:TF1844|TF1843:TF1844:surface antigen BspA:hypothetical protein:->->:1996250..1996528 279 tgaagagtgaaaaacgaaaagtgaagagtgaaaaacgaaaaacgaagagtgaaaagtgaagagtgaaaagtgaagagtagtcaacagtaattaatgttgtcaatgtaggggcgaaccttgtgttcgccctttttttgtgtggcgtcgggtttatccgaacgcaaatttcgcaaataggcgcgaatggacgcaaatattaacccgacgggactattttgtgatttttgaaactattaaatgtctgactaatatatttttgtcaaaataaaaataacgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaagagtgaaaaacgaaaagtgaagagtgaaaaacgaaaaacgaagagtgaaaagtgaagagtgaaaagtgaagagtagtcaacagtaattaatgttgtcaatgtaggggcgaaccttgtgttcgccctttttttgtgtggcgtcgggtttatccgaacgcaaatttcgcaaataggcgcgaatggacgcaaatattaacccgacgggactattttgtgatttttgaaactattaaatgtctgactaatatatttttgtcaaaataaaaataacgtta Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 90 End: 197 ......................................................................................... M N V V N V G A N L V F A L F L C G V G F I R T Q I S Q I G A N G R K Y .................................................................................. Protein_Len: 43 Strand: + Start: 137 End: 265 ........................................................................................................................................ M W R R V Y P N A N F A N R R E W T Q I L T R R D Y F V I F E T I K C L T N I F L S K .............. Protein_Len: 38 Strand: - Start: 84 End: 197 ................................................................................... C Y N I N D I Y P R V K H E G K K Q T A D P K D S R L N R L Y A R I S A F M .................................................................................. Protein_Len: 60 Strand: - Start: 2 End: 193 . R F T F L S F R F V F L S F H L T F L S S Y D V T I L T T L T P A F R T N A R K K H P T P N I R V C I E C I P A F P R M ...................................................................................... tgaagagtgaaaaacgaaaagtgaagagtgaaaaacgaaaaacgaagagtgaaaagtgaagagtgaaaagtgaagagtagtcaacagtaattaatgttgtcaatgtaggggcgaaccttgtgttcgccctttttttgtgtggcgtcgggtttatccgaacgcaaatttcgcaaataggcgcgaatggacgcaaatattaacccgacgggactattttgtgatttttgaaactattaaatgtctgactaatatatttttgtcaaaataaaaataacgtta 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================================================ tgaagagtgaaaaacgaaaagtgaagagtgaaaaacgaaaaacgaagagtgaaaagtgaagagtgaaaagtgaagagtagtcaacagtaattaatgttgtcaatgtaggggcgaaccttgtgttcgccctttttttgtgtggcgtcgggtttatccgaacgcaaatttcgcaaataggcgcgaatggacgcaaatattaacccgacgggactattttgtgatttttgaaactattaaatgtctgactaatatatttttgtcaaaataaaaataacgtta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 67 HP_score: -9.1 Tail_Score: -2.52795 Start: 108 End: 130 Full_Region: acgccacacaaaaaa agggcgaac acaag gttcgcccc tacattgacaacatt ...........................................................................................................agggcgaacacaaggttcgcccc..................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -12.6 Tail_Score: -5.71712 Start: 109 End: 129 Full_Region: ATGTTGTCAATGTAG GGGCGAAC CTTGT GTTCGCCC TTTTTTTGTGTGGCG ............................................................................................................GGGCGAACCTTGTGTTCGCCC...................................................................................................................................................... Find igs database================================================ Query_seq: TF1843:TF1844|TF1843:TF1844:surface antigen BspA:hypothetical protein:->->:1996250..1996528 279 tgaagagtgaaaaacgaaaagtgaagagtgaaaaacgaaaaacgaagagtgaaaagtgaagagtgaaaagtgaagagtagtcaacagtaattaatgttgtcaatgtaggggcgaaccttgtgttcgccctttttttgtgtggcgtcgggtttatccgaacgcaaatttcgcaaataggcgcgaatggacgcaaatattaacccgacgggactattttgtgatttttgaaactattaaatgtctgactaatatatttttgtcaaaataaaaataacgtta Intra-Species Hit: Count: 1 Min: 79 Max: 279 Len: 201 Subject: tfor_TF1843_TF1844|surface antigen BspA:hypothetical protein|POSITIVE:POSITIVE|[1996250,1996528]|279 HSP 1 e-value: 1.0E-97 bit: 357.0 Len: 201 Query Start:79 Query End:279 Subject Strand: POSITIVE Subject Start: 79 Subject End: 279 ..............................................................................agtcaacagtaattaatgttgtcaatgtaggggcgaaccttgtgttcgcccnnnnnnngtgtggcgtcgggtttatccgaacgcaaatttcgcaaataggcgcgaatggacgcaaatattaacccgacgggactattttgtgatttttgaaactattaaatgtctgactaatatatttttgtcaaaataaaaataacgtta ..............................................................................agtcaacagtaattaatgttgtcaatgtaggggcgaaccttgtgttcgccctttttttgtgtggcgtcgggtttatccgaacgcaaatttcgcaaataggcgcgaatggacgcaaatattaacccgacgggactattttgtgatttttgaaactattaaatgtctgactaatatatttttgtcaaaataaaaataacgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCAACAGUAAUUAAUGUUGUCAAUGUAGGGGCGAACCUUGUGUUCGCCCUUUUUUUGUGUGGCGUCGGGUUUAUCCGAACGCAAAUUUCGCAAAUAGGCGCGAAUGGACGCAAAUAUUAACCCGACGGGACUAUUUUGUGAUUUUUGAAACUAUUAAAUGUCUGACUAAUAUAUUUUUGUCAAAAUAAAAAUAACGUUA ((((((((....((((((...((((...((((((((((.....))))))))))..(((((((.((((((((....)))).))))....(((((........)))))...)))))))......(((...)))...............))))...)))))).))).)))))....(((((((((....)))))))))...... (-53.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGUUAUUUUUAUUUUGACAAAAAUAUAUUAGUCAGACAUUUAAUAGUUUCAAAAAUCACAAAAUAGUCCCGUCGGGUUAAUAUUUGCGUCCAUUCGCGCCUAUUUGCGAAAUUUGCGUUCGGAUAAACCCGACGCCACACAAAAAAAGGGCGAACACAAGGUUCGCCCCUACAUUGACAACAUUAAUUACUGUUGACU ....((((.........))))...........((((((....(((((.(((((((.............((..(((((((((.((....((((...((((((......))))))....))))....)).)))))))))..)).........((((((((.....)))))))).....)))).))))))))......)))))) (-53.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 912 50 1 156 107 tfor:TF2998|5end_surface_antigen_BspA_3211811..3212041_POSITIVE 843 80 31 168 118 tfor:TF1580|5end_conserved_hypothetical_protein;_possible_fibronectin_domain_containing_protein_1687187..1687417_POSITIVE 716 118 76 88 47 tfor:TF0018|5end_hypothetical_protein_11250..11480_POSITIVE 598 53 11 228 186 tfor:TF2994|5end_hypothetical_protein_3210605..3210835_POSITIVE 585 118 71 93 51 tfor:TF1579|5end_hypothetical_protein_1686889..1687119_POSITIVE 536 50 5 231 188 tfor:TF0471|5end_conserved_hypothetical_protein_487516..487746_POSITIVE 521 113 77 212 177 tfor:TF2996|5end_hypothetical_protein_3210802..3211032_POSITIVE 485 51 24 224 196 tfor:TF1169|5end_lipoprotein_ABC_transporter,_permease_component_1249136..1249366_POSITIVE 469 69 22 105 64 tfor:TF2172|5end_hypothetical_protein_2345822..2346052_POSITIVE 469 69 22 99 58 tfor:TF2173|5end_hypothetical_protein_2345816..2346046_POSITIVE 469 69 22 99 58 tfor:TF2171|5end_hypothetical_protein_2345485..2345715_POSITIVE 469 69 22 99 58 tfor:TF2166|5end_hypothetical_protein_2342115..2342345_POSITIVE 448 51 22 87 58 tfor:TF0366|5end_hypothetical_protein_383564..383794_POSITIVE 448 51 22 87 58 tfor:TF0362|5end_hypothetical_protein_379952..380182_POSITIVE 448 51 22 87 58 tfor:TF0346|5end_hypothetical_protein_367048..367278_POSITIVE 427 79 31 85 46 tfor:TF1577|5end_hypothetical_protein_1685960..1686190_POSITIVE 424 50 1 179 137 tfor:TF1170|5end_conserved_hypothetical_protein_1251862..1252092_POSITIVE 424 50 1 167 125 tfor:TF1171|5end_ABC_transporter,_ATP-binding_protein_1251850..1252080_POSITIVE 420 114 78 173 138 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 409 110 61 179 137 tfor:TF2467|5end_3-dehydroquinate_dehydratase_II_2645827..2646057_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 749 118 73 142 98 tfor:TF0018|3end_hypothetical_protein_12091..12241_POSITIVE 691 110 61 60 13 tfor:TF2996|3end_hypothetical_protein_3211121..3211271_POSITIVE 638 118 74 99 56 tfor:TF1761|3end_hypothetical_protein_1899579..1899729_POSITIVE 628 80 31 128 79 tfor:TF1716|3end_hypothetical_protein_1837710..1837860_POSITIVE 564 56 24 151 118 tfor:TF1579|3end_hypothetical_protein_1687274..1687424_POSITIVE 547 69 21 136 77 tfor:TF2346|3end_hypothetical_protein_2509973..2510123_POSITIVE 506 69 24 112 72 tfor:TF1168|3end_hypothetical_protein_1249092..1249242_POSITIVE 495 51 15 126 83 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 485 101 66 151 112 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE 473 117 76 88 37 tfor:TF2166|3end_hypothetical_protein_2342362..2342512_POSITIVE 473 117 76 88 37 tfor:TF0366|3end_hypothetical_protein_383811..383961_POSITIVE 473 117 76 88 37 tfor:TF0362|3end_hypothetical_protein_380199..380349_POSITIVE 469 48 5 151 110 tfor:TF0470|3end_hypothetical_protein_487518..487668_POSITIVE 452 115 76 86 37 tfor:TF2173|3end_hypothetical_protein_2346063..2346213_POSITIVE 420 114 76 144 109 tfor:TF2172|3end_hypothetical_protein_2346135..2346285_POSITIVE 420 114 78 36 1 tfor:TF2013|3end_polysaccharide_deacetylase_2169341..2169491_POSITIVE 400 110 62 46 7 tfor:TF2693|3end_possible_aminotransferase_2869720..2869870_POSITIVE 390 68 31 45 1 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 377 80 32 96 49 tfor:TF0960|3end_beta-galactosidase_1010506..1010656_POSITIVE 376 106 66 147 99 tfor:TF1576|3end_hypothetical_protein_1686135..1686285_POSITIVE