Origin IGS: gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaatggttaatggttatgccgggttatccga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcggataacccggcataaccattaaccattaatttatcattcagagcgaagcgatgaatctcttttccgttacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttcacacgccttcgcgacgc Mask Tandem Repeat Region ================================================ gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaatggttaatggttatgccgggttatccga Find is-nt database================================================ Query_seq: TF1659:TF1660|TF1659:TF1660:hypothetical protein:hypothetical protein:->->:1775270..1775408 139 gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaatggttaatggttatgccgggttatccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1659:TF1660|TF1659:TF1660:hypothetical protein:hypothetical protein:->->:1775270..1775408 139 gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaatggttaatggttatgccgggttatccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1659:TF1660|TF1659:TF1660:hypothetical protein:hypothetical protein:->->:1775270..1775408 139 gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaatggttaatggttatgccgggttatccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaatggttaatggttatgccgggttatccga Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 33 End: 137 ................................ M T F G L L L G Q A K S N G K E I H R F A L N D K L M V N G Y A G L S .. Protein_Len: 36 Strand: - Start: 1 End: 108 R R S P T H L A R L R S R Q T V K P D L W F Y R F L S E D S R E S H Y M ............................... gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaatggttaatggttatgccgggttatccga 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================================================ gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaatggttaatggttatgccgggttatccga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1659:TF1660|TF1659:TF1660:hypothetical protein:hypothetical protein:->->:1775270..1775408 139 gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaatggttaatggttatgccgggttatccga Intra-Species Hit: Count: 8 Min: 1 Max: 139 Len: 139 Subject: tfor_TF1659_TF1660|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1775270,1775408]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaatggttaatggttatgccgggttatccga gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaatggttaatggttatgccgggttatccga Subject: tfor_TF1187_TF1188|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1269933,1270295]|363 HSP 1 e-value: 9.0E-54 bit: 210.0 Len: 121 Query Start:4 Query End:124 Subject Strand: POSITIVE Subject Start: 4 Subject End: 125 ...tcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgctt-cgctctgaatgataaattaatggttaatggtta............... ...tcgcgaaggcgtgtgaagcgcacgaagccttgaccttttggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttacgctctgaatgacaaattaatggttaatggtta............... Subject: tfor_TF0685_TF0686|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[731193,732338]|1146 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 119 Query Start:1 Query End:119 Subject Strand: NEGATIVE Subject Start: 165 Subject End: 283 gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaatggttaat.................... gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttactttttggtcaagccaaaagtgacaaaaaagagattcttcgcttcgctctgaatgacaaattaatggttaat.................... HSP 2 e-value: 1.0E-12 bit: 73.8 Len: 49 Query Start:76 Query End:124 Subject Strand: NEGATIVE Subject Start: 537 Subject End: 585 ...........................................................................aagagattcatcgcttcgctctgaatgataaattaatggttaatggtta............... ...........................................................................aagagattcatcgcttcgctctgaatgacaaattaatggtcaattgtta............... Subject: tfor_TF2500_TF2501|ABC transporter, ATP-binding protein:DNA mismatch repair protein|POSITIVE:POSITIVE|[2675363,2676419]|1057 HSP 1 e-value: 7.0E-36 bit: 151.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 644 Subject End: 762 gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgctt-cgctctgaatgataaattaatggttaat.................... gcgtcgcgaaggcgtgtgaagcgcacgaagccttgaccttttggttacttttgggtcaagccaaaagtgacag-aaggagattcttcgcttacgctctgaatgacatattaatggttaat.................... Subject: tfor_TF2922_TF2923|surface antigen BspA:hypothetical protein|POSITIVE:POSITIVE|[3121599,3122307]|709 HSP 1 e-value: 2.0E-33 bit: 143.0 Len: 76 Query Start:1 Query End:76 Subject Strand: NEGATIVE Subject Start: 151 Subject End: 226 gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaa............................................................... gcgtcgcgaaggcgtgtgaagcgcacgaagccttgaccttttggttacttttgggtcaagccaaaagtaacggaaa............................................................... HSP 2 e-value: 3.0E-13 bit: 75.8 Len: 46 Query Start:74 Query End:119 Subject Strand: NEGATIVE Subject Start: 573 Subject End: 618 .........................................................................aaaagagattcatcgcttcgctctgaatgataaattaatggttaat.................... .........................................................................aaaagagattcatcgcttcgcgctgaatgacaaattaatggttaat.................... HSP 3 e-value: 8.0E-11 bit: 67.9 Len: 53 Query Start:75 Query End:127 Subject Strand: NEGATIVE Subject Start: 400 Subject End: 453 ..........................................................................aaagagattcatcgctt-cgctctgaatgataaattaatggttaatggttatgc............ ..........................................................................aaagagattcttcgcttacgctctgaatgacaaattaatggttaattgttatgc............ HSP 4 e-value: 5.0E-6 bit: 52.0 Len: 30 Query Start:110 Query End:139 Subject Strand: NEGATIVE Subject Start: 539 Subject End: 568 .............................................................................................................aatggttaatggttatgccgggttatccga .............................................................................................................aatggttaattgttatgccgggttatccga Subject: tfor_TF2920_TF2921|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3117231,3118637]|1407 HSP 1 e-value: 3.0E-32 bit: 139.0 Len: 74 Query Start:3 Query End:76 Subject Strand: NEGATIVE Subject Start: 207 Subject End: 280 ..gtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaa............................................................... ..gtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacagaaa............................................................... HSP 2 e-value: 2.0E-8 bit: 60.0 Len: 45 Query Start:75 Query End:119 Subject Strand: NEGATIVE Subject Start: 398 Subject End: 443 ..........................................................................aaagagattcatcgctt-cgctctgaatgataaattaatggttaat.................... ..........................................................................aaagagattcttcgcttacgctctgaatgacaaattaatggttaat.................... Subject: tfor_TF2745_TF2746|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2928008,2928135]|128 HSP 1 e-value: 2.0E-30 bit: 133.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 19 Subject End: 128 gcgtcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagagattcatcgcttcgctctgaatgataaattaa............................ gcgtcacgagggcgtgcgaagcgcacgaagccttgatcttttggttacttttgggtcaagccaaaagtgacag-aaagagattcttcgcttcgctctgaatgacaaattaa............................ Subject: tfor_TF2914_TF2915|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3109704,3110561]|858 HSP 1 e-value: 2.0E-24 bit: 113.0 Len: 77 Query Start:4 Query End:80 Subject Strand: NEGATIVE Subject Start: 9 Subject End: 85 ...tcgcgaaggcgtgtgaagcgcacgaagccttgacctttgggttacttttgggtcaagccaaaagtaacggaaaagag........................................................... ...tcgcgaaggcgtgtgaagagcacgaagccttgactttttggttacttttgggtcaagccaaaagtgacagaaaagag........................................................... HSP 2 e-value: 3.0E-10 bit: 65.9 Len: 41 Query Start:79 Query End:119 Subject Strand: NEGATIVE Subject Start: 204 Subject End: 244 ..............................................................................agattcatcgcttcgctctgaatgataaattaatggttaat.................... ..............................................................................agattcttcgcttcgctctgaatgacaaattaatggttaat.................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGUCGCGAAGGCGUGUGAAGCGCACGAAGCCUUGACCUUUGGGUUACUUUUGGGUCAAGCCAAAAGUAACGGAAAAGAGAUUCAUCGCUUCGCUCUGAAUGAUAAAUUAAUGGUUAAUGGUUAUGCCGGGUUAUCCGA (((((((....)))......)))).((((((..((((((((..(((((((((((......)))))))))))...)))).)..)))..))))))........(((((.....((((..........))))..)))))... (-40.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGGAUAACCCGGCAUAACCAUUAACCAUUAAUUUAUCAUUCAGAGCGAAGCGAUGAAUCUCUUUUCCGUUACUUUUGGCUUGACCCAAAAGUAACCCAAAGGUCAAGGCUUCGUGCGCUUCACACGCCUUCGCGACGC ((((.....))))..................................(((((((((((((((((((..(((((((((((......)))))))))))..)))))...))).))))).))))))...(((....))).... (-35.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1075 50 1 141 92 tfor:TF2997|5end_hypothetical_protein_3211408..3211638_POSITIVE 1021 50 1 115 66 tfor:TF2996|5end_hypothetical_protein_3210802..3211032_POSITIVE 1021 50 1 125 76 tfor:TF1588|5end_hypothetical_protein_1702268..1702498_POSITIVE 999 50 1 141 92 tfor:TF1578|5end_hypothetical_protein_1686187..1686417_POSITIVE 999 50 1 54 5 tfor:TF0685|5end_hypothetical_protein_730852..731082_POSITIVE 870 60 13 84 37 tfor:TF0469|5end_hypothetical_protein_486960..487190_POSITIVE 870 60 13 53 6 tfor:TF0468|5end_hypothetical_protein_486929..487159_POSITIVE 857 60 11 135 83 tfor:TF1168|5end_hypothetical_protein_1248755..1248985_POSITIVE 696 119 71 142 95 tfor:TF2653|5end_hypothetical_protein_2822093..2822323_POSITIVE 680 119 72 228 181 tfor:TF2923|5end_hypothetical_protein_3122168..3122398_POSITIVE 637 90 43 43 3 tfor:TF2921|5end_hypothetical_protein_3118498..3118728_POSITIVE 633 119 72 104 57 tfor:TF2994|5end_hypothetical_protein_3210605..3210835_POSITIVE 586 119 72 223 177 tfor:TF2669|5end_possible_Fe-S_oxidoreductase_2842971..2843201_POSITIVE 586 119 72 186 140 tfor:TF2668|5end_hypothetical_protein_2842471..2842701_POSITIVE 586 119 72 110 64 tfor:TF2667|5end_hypothetical_protein_2842395..2842625_POSITIVE 586 119 72 186 140 tfor:TF2665|5end_hypothetical_protein_2841973..2842203_POSITIVE 578 109 67 104 62 tfor:TF0470|5end_hypothetical_protein_487253..487483_POSITIVE 542 120 72 211 157 tfor:TF1579|5end_hypothetical_protein_1686889..1687119_POSITIVE 525 108 71 45 3 tfor:TF0018|5end_hypothetical_protein_11250..11480_POSITIVE 521 105 72 177 140 tfor:TF1585|5end_hypothetical_protein_1690369..1690599_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1021 50 1 82 33 tfor:TF2994|3end_hypothetical_protein_3210849..3210999_POSITIVE 999 50 1 108 59 tfor:TF1577|3end_hypothetical_protein_1686234..1686384_POSITIVE 863 100 51 72 23 tfor:TF2639|3end_hypothetical_protein_2809333..2809483_POSITIVE 858 60 11 139 90 tfor:TF2668|3end_hypothetical_protein_2842733..2842883_POSITIVE 858 60 11 111 62 tfor:TF2667|3end_hypothetical_protein_2842705..2842855_POSITIVE 858 60 11 111 62 tfor:TF2665|3end_hypothetical_protein_2842235..2842385_POSITIVE 858 60 11 139 90 tfor:TF2666|3end_hypothetical_protein_2842263..2842413_POSITIVE 858 60 11 111 62 tfor:TF2664|3end_hypothetical_protein_2841730..2841880_POSITIVE 782 60 11 62 13 tfor:TF2914|3end_hypothetical_protein_3109643..3109793_POSITIVE 710 100 51 59 10 tfor:TF1576|3end_hypothetical_protein_1686135..1686285_POSITIVE 696 119 71 91 44 tfor:TF2652|3end_hypothetical_protein_2822122..2822272_POSITIVE 667 119 72 57 9 tfor:TF1578|3end_hypothetical_protein_1686416..1686566_POSITIVE 656 79 38 41 1 tfor:TF2998|3end_surface_antigen_BspA_3215151..3215301_POSITIVE 652 119 72 78 27 tfor:TF2997|3end_hypothetical_protein_3211664..3211814_POSITIVE 521 105 72 75 38 tfor:TF1583|3end_conserved_hypothetical_protein;_possible_endonuclease_1690223..1690373_POSITIVE 517 105 72 110 73 tfor:TF1582|3end_hypothetical_protein_1690506..1690656_POSITIVE 458 44 1 141 97 tfor:TF0684|3end_conserved_hypothetical_protein_730564..730714_POSITIVE 443 107 72 35 1 tfor:TF1591|3end_surface_antigen_BspA_1708266..1708416_POSITIVE 438 99 53 151 107 tfor:TF0017|3end_hypothetical_protein_11231..11381_POSITIVE 432 107 79 29 1 tfor:TF1589|3end_surface_antigen_BspA_1705746..1705896_POSITIVE