Origin IGS: taaagacagtctcgccttgtgtggattgcccccccctccggcacacttgccggagggatataaagaatattcatcgctgacactctgaatgaaagggaaggagaattacgaattacgagaagagtagtcaatgtaggggcggacctctgtgttcgcctgtcataacgccaatatgaatatcccccctgcccccctttaaaagggagaatgcagagctgatggctgactgatgagaaccgaacgctgaataacaattaattaaatatattatattcacattttaattcaaattatc .........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 gataatttgaattaaaatgtgaatataatatatttaattaattgttattcagcgttcggttctcatcagtcagccatcagctctgcattctcccttttaaaggggggcaggggggatattcatattggcgttatgacaggcgaacacagaggtccgcccctacattgactactcttctcgtaattcgtaattctccttccctttcattcagagtgtcagcgatgaatattctttatatccctccggcaagtgtgccggaggggggggcaatccacacaaggcgagactgtcttta Mask Tandem Repeat Region ================================================ taaagacagtctcgccttgtgtggattgcccccccctccggcacacttgccggagggatataaagaatattcatcgctgacactctgaatgaaagggaaggagaattacgaattacgagaagagtagtcaatgtaggggcggacctctgtgttcgcctgtcataacgccaatatgaatatcccccctgcccccctttaaaagggagaatgcagagctgatggctgactgatgagaaccgaacgctgaataacaattaattaaatatattatattcacattttaattcaaattatc Find is-nt database================================================ Query_seq: TF0535:TF0536|TF0535:TF0536:surface antigen BspA:conserved hypothetical protein:->->:561762..562056 295 taaagacagtctcgccttgtgtggattgcccccccctccggcacacttgccggagggatataaagaatattcatcgctgacactctgaatgaaagggaaggagaattacgaattacgagaagagtagtcaatgtaggggcggacctctgtgttcgcctgtcataacgccaatatgaatatcccccctgcccccctttaaaagggagaatgcagagctgatggctgactgatgagaaccgaacgctgaataacaattaattaaatatattatattcacattttaattcaaattatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0535:TF0536|TF0535:TF0536:surface antigen BspA:conserved hypothetical protein:->->:561762..562056 295 taaagacagtctcgccttgtgtggattgcccccccctccggcacacttgccggagggatataaagaatattcatcgctgacactctgaatgaaagggaaggagaattacgaattacgagaagagtagtcaatgtaggggcggacctctgtgttcgcctgtcataacgccaatatgaatatcccccctgcccccctttaaaagggagaatgcagagctgatggctgactgatgagaaccgaacgctgaataacaattaattaaatatattatattcacattttaattcaaattatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0535:TF0536|TF0535:TF0536:surface antigen BspA:conserved hypothetical protein:->->:561762..562056 295 taaagacagtctcgccttgtgtggattgcccccccctccggcacacttgccggagggatataaagaatattcatcgctgacactctgaatgaaagggaaggagaattacgaattacgagaagagtagtcaatgtaggggcggacctctgtgttcgcctgtcataacgccaatatgaatatcccccctgcccccctttaaaagggagaatgcagagctgatggctgactgatgagaaccgaacgctgaataacaattaattaaatatattatattcacattttaattcaaattatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagacagtctcgccttgtgtggattgcccccccctccggcacacttgccggagggatataaagaatattcatcgctgacactctgaatgaaagggaaggagaattacgaattacgagaagagtagtcaatgtaggggcggacctctgtgttcgcctgtcataacgccaatatgaatatcccccctgcccccctttaaaagggagaatgcagagctgatggctgactgatgagaaccgaacgctgaataacaattaattaaatatattatattcacattttaattcaaattatc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 67 End: 162 .................................................................. M F I A D T L N E R E G E L R I T R R V V N V G A D L C V R L S ..................................................................................................................................... Protein_Len: 49 Strand: - Start: 131 End: 277 .................................................................................................................................. H L P P G R H E G T M V G I H I D G R G G K L L S F A S S I A S Q H S G F A S Y C N I L Y I I N M .................. Protein_Len: 60 Strand: - Start: 3 End: 254 .. A S V R F S L S P S N R I V L L T T L T P A S R Q T R R D Y R W Y S Y G G Q G G K F P L I C L Q H S V S S F R V S F L M ......................................... Protein_Len: 30 Strand: - Start: 1 End: 90 L S L R A K H P N G G G G A C K G S P Y L S Y E D S V S Q M ............................................................................................................................................................................................................. taaagacagtctcgccttgtgtggattgcccccccctccggcacacttgccggagggatataaagaatattcatcgctgacactctgaatgaaagggaaggagaattacgaattacgagaagagtagtcaatgtaggggcggacctctgtgttcgcctgtcataacgccaatatgaatatcccccctgcccccctttaaaagggagaatgcagagctgatggctgactgatgagaaccgaacgctgaataacaattaattaaatatattatattcacattttaattcaaattatc 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================================================ taaagacagtctcgccttgtgtggattgcccccccctccggcacacttgccggagggatataaagaatattcatcgctgacactctgaatgaaagggaaggagaattacgaattacgagaagagtagtcaatgtaggggcggacctctgtgttcgcctgtcataacgccaatatgaatatcccccctgcccccctttaaaagggagaatgcagagctgatggctgactgatgagaaccgaacgctgaataacaattaattaaatatattatattcacattttaattcaaattatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 56 HP_score: -7.1 Tail_Score: -2.78463 Start: 138 End: 157 Full_Region: AGTAGTCAATGTAGG GGCGGAC CTCTGT GTTCGCC TGTCATAACGCCAAT .........................................................................................................................................GGCGGACCTCTGTGTTCGCC.......................................................................................................................................... Find igs database================================================ Query_seq: TF0535:TF0536|TF0535:TF0536:surface antigen BspA:conserved hypothetical protein:->->:561762..562056 295 taaagacagtctcgccttgtgtggattgcccccccctccggcacacttgccggagggatataaagaatattcatcgctgacactctgaatgaaagggaaggagaattacgaattacgagaagagtagtcaatgtaggggcggacctctgtgttcgcctgtcataacgccaatatgaatatcccccctgcccccctttaaaagggagaatgcagagctgatggctgactgatgagaaccgaacgctgaataacaattaattaaatatattatattcacattttaattcaaattatc Intra-Species Hit: Count: 1 Min: 1 Max: 295 Len: 295 Subject: tfor_TF0535_TF0536|surface antigen BspA:conserved hypothetical protein|POSITIVE:POSITIVE|[561762,562056]|295 HSP 1 e-value: 3.0E-83 bit: 309.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 taaagacagtctcgccttgtgtggattgnnnnnnnntccggcacacttgccggagggatataaagaatattcatcgctgacactctgaatgaaagggaaggagaattacgaattacgagaagagtagtcaatgtaggggcggacctctgtgttcgcctgtcataacgccaatatgaatat................................................................................................................... taaagacagtctcgccttgtgtggattgcccccccctccggcacacttgccggagggatataaagaatattcatcgctgacactctgaatgaaagggaaggagaattacgaattacgagaagagtagtcaatgtaggggcggacctctgtgttcgcctgtcataacgccaatatgaatat................................................................................................................... HSP 2 e-value: 2.0E-50 bit: 200.0 Len: 101 Query Start:195 Query End:295 Subject Strand: POSITIVE Subject Start: 195 Subject End: 295 ..................................................................................................................................................................................................tttaaaagggagaatgcagagctgatggctgactgatgagaaccgaacgctgaataacaattaattaaatatattatattcacattttaattcaaattatc ..................................................................................................................................................................................................tttaaaagggagaatgcagagctgatggctgactgatgagaaccgaacgctgaataacaattaattaaatatattatattcacattttaattcaaattatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGACAGUCUCGCCUUGUGUGGAUUGCCCCCCCCUCCGGCACACUUGCCGGAGGGAUAUAAAGAAUAUUCAUCGCUGACACUCUGAAUGAAAGGGAAGGAGAAUUACGAAUUACGAGAAGAGUAGUCAAUGUAGGGGCGGACCUCUGUGUUCGCCUGUCAUAACGCCAAUAUGAAUAUCCCCCCUGCCCCCCUUUAAAAGGGAGAAUGCAGAGCUGAUGGCUGACUGAUGAGAACCGAACGCUGAAUAACAAUUAAUUAAAUAUAUUAUAUUCACAUUUUAAUUCAAAUUAUC ......(((((..(((.........(((((((.((((((((((....)))))))))).......((.(((((.((.......((((...(....)....)))).....((.....)).)).))))).))......)))))))..((((((((((.....(((((.......)))))...............((((.....)))).)))))))))).....))).)))))....(((..(((...((((((.....((((.......))))))))))...)))..)))........ (-77.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAAUUUGAAUUAAAAUGUGAAUAUAAUAUAUUUAAUUAAUUGUUAUUCAGCGUUCGGUUCUCAUCAGUCAGCCAUCAGCUCUGCAUUCUCCCUUUUAAAGGGGGGCAGGGGGGAUAUUCAUAUUGGCGUUAUGACAGGCGAACACAGAGGUCCGCCCCUACAUUGACUACUCUUCUCGUAAUUCGUAAUUCUCCUUCCCUUUCAUUCAGAGUGUCAGCGAUGAAUAUUCUUUAUAUCCCUCCGGCAAGUGUGCCGGAGGGGGGGGCAAUCCACACAAGGCGAGACUGUCUUUA ........((((..((...((((((((((.((......)))))).))))))...))..))))....(((((.(((.....((((((...((((((.....)))))))))))).((((.........((.(((((((...((((....(((((((............)))..))))..))))...)))))))...)).((((........(((((((((....)).)))))))......((((((((((....)))))))))).))))..))))......)))..)))))...... (-85.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 843 180 131 115 66 tfor:TF2172|5end_hypothetical_protein_2345822..2346052_POSITIVE 843 180 131 109 60 tfor:TF2173|5end_hypothetical_protein_2345816..2346046_POSITIVE 843 180 131 109 60 tfor:TF2171|5end_hypothetical_protein_2345485..2345715_POSITIVE 843 180 131 109 60 tfor:TF2166|5end_hypothetical_protein_2342115..2342345_POSITIVE 767 180 131 109 60 tfor:TF0366|5end_hypothetical_protein_383564..383794_POSITIVE 767 180 131 109 60 tfor:TF0362|5end_hypothetical_protein_379952..380182_POSITIVE 767 180 131 109 60 tfor:TF0346|5end_hypothetical_protein_367048..367278_POSITIVE 719 187 144 210 166 tfor:TF1170|5end_conserved_hypothetical_protein_1251862..1252092_POSITIVE 719 187 144 198 154 tfor:TF1171|5end_ABC_transporter,_ATP-binding_protein_1251850..1252080_POSITIVE 707 165 121 231 187 tfor:TF1169|5end_lipoprotein_ABC_transporter,_permease_component_1249136..1249366_POSITIVE 703 169 121 98 50 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 572 157 116 138 87 tfor:TF1580|5end_conserved_hypothetical_protein;_possible_fibronectin_domain_containing_protein_1687187..1687417_POSITIVE 542 157 127 156 127 tfor:TF2998|5end_surface_antigen_BspA_3211811..3212041_POSITIVE 471 157 124 231 199 tfor:TF0471|5end_conserved_hypothetical_protein_487516..487746_POSITIVE 461 216 175 217 180 tfor:TF0685|5end_hypothetical_protein_730852..731082_POSITIVE 460 157 127 225 197 tfor:TF2994|5end_hypothetical_protein_3210605..3210835_POSITIVE 450 233 192 101 61 tfor:TF1167|5end_hypothetical_protein_1248559..1248789_POSITIVE 447 90 49 192 151 tfor:TF1578|5end_hypothetical_protein_1686187..1686417_POSITIVE 423 98 51 184 133 tfor:TF1585|5end_hypothetical_protein_1690369..1690599_POSITIVE 423 98 51 60 9 tfor:TF1584|5end_hypothetical_protein_1690245..1690475_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 838 180 131 122 73 tfor:TF1168|3end_hypothetical_protein_1249092..1249242_POSITIVE 763 190 141 54 5 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 703 229 181 69 21 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 688 229 182 53 6 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 638 228 182 60 12 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 572 157 116 145 94 tfor:TF1579|3end_hypothetical_protein_1687274..1687424_POSITIVE 482 161 123 105 65 tfor:TF1716|3end_hypothetical_protein_1837710..1837860_POSITIVE 471 168 127 143 98 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 453 230 188 66 2 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 450 233 192 65 25 tfor:TF1166|3end_ABC_transporter,_permease_component_1248603..1248753_POSITIVE 447 90 49 60 19 tfor:TF1576|3end_hypothetical_protein_1686135..1686285_POSITIVE 423 98 51 82 31 tfor:TF1583|3end_conserved_hypothetical_protein;_possible_endonuclease_1690223..1690373_POSITIVE 408 57 34 57 34 tfor:TF0535|3end_surface_antigen_BspA_561701..561851_POSITIVE 405 169 127 121 77 tfor:TF2346|3end_hypothetical_protein_2509973..2510123_POSITIVE 404 155 124 151 121 tfor:TF0470|3end_hypothetical_protein_487518..487668_POSITIVE 399 57 11 127 85 tfor:TF2893|3end_conserved_hypothetical_protein;_possible_phosphoesterase_3082039..3082189_POSITIVE 391 246 205 135 90 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 386 104 62 44 5 tfor:TF1591|3end_surface_antigen_BspA_1708266..1708416_POSITIVE 376 54 11 56 12 tfor:TF0214|3end_DNA_recombination_and_repair_protein,_RecN_241571..241721_POSITIVE 374 179 131 60 8 tfor:TF2312|3end_conserved_hypothetical_protein;_possible_glycosyl_transferase_2472522..2472672_POSITIVE