Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: NTFQ01008664.1 Kokia drynarioides strain JFW-HI SEQ_123346, whole genome shotgun sequence Parameters: 2 7 7 80 10 50 1000 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 1000 Length: 53888 ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34 Warning! 31 characters in sequence are not A, C, G, or T Found at i:4331 original size:22 final size:21 Alignment explanation
Indices: 4307--4346 Score: 80 Period size: 21 Copynumber: 1.9 Consensus size: 21 4297 TTAACGTAGT 4307 TTTTCTATATTTTCCATTTAG 1 TTTTCTATATTTTCCATTTAG 4328 TTTTCTATATTTTCCATTT 1 TTTTCTATATTTTCCATTT 4347 GTCAAAACTA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.17, C:0.15, G:0.03, T:0.65 Consensus pattern (21 bp): TTTTCTATATTTTCCATTTAG Found at i:15867 original size:12 final size:12 Alignment explanation
Indices: 15810--15899 Score: 55 Period size: 12 Copynumber: 7.8 Consensus size: 12 15800 ATAACATCTA 15810 AACAACAAAAAT 1 AACAACAAAAAT * 15822 AACAATC-AAAAC 1 AACAA-CAAAAAT * ** 15834 AGCAGTAAAAAT 1 AACAACAAAAAT * * 15846 AATAA-TAAAAT 1 AACAACAAAAAT 15857 AACAAC--AAA- 1 AACAACAAAAAT 15866 AACAACAAAAAT 1 AACAACAAAAAT * * 15878 AGCAACAAAACT 1 AACAACAAAAAT * 15890 AACAGCAAAA 1 AACAACAAAA 15900 CAACACCAAA Statistics Matches: 58, Mismatches: 14, Indels: 12 0.69 0.17 0.14 Matches are distributed among these distances: 9 6 0.10 10 3 0.05 11 12 0.21 12 36 0.62 13 1 0.02 ACGTcount: A:0.69, C:0.17, G:0.04, T:0.10 Consensus pattern (12 bp): AACAACAAAAAT Found at i:15959 original size:19 final size:20 Alignment explanation
Indices: 15937--15990 Score: 67 Period size: 19 Copynumber: 2.8 Consensus size: 20 15927 TCAAAACGCA * 15937 ACCAAAATAGTAAAAA-AAT 1 ACCAAAATAGTAAAAATAAC * 15956 ACCAAAACAGTAAAAAATAAC 1 ACCAAAATAGT-AAAAATAAC 15977 ACCAAAATAG-AAAA 1 ACCAAAATAGTAAAA 15991 GAAAAAAAAA Statistics Matches: 30, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 19 14 0.47 20 5 0.17 21 11 0.37 ACGTcount: A:0.69, C:0.15, G:0.06, T:0.11 Consensus pattern (20 bp): ACCAAAATAGTAAAAATAAC Found at i:15972 original size:21 final size:21 Alignment explanation
Indices: 15948--15997 Score: 55 Period size: 21 Copynumber: 2.3 Consensus size: 21 15938 CCAAAATAGT * * 15948 AAAAAAATACCAAAACAGTAA 1 AAAAAAACACCAAAACAGAAA * * 15969 AAAATAACACCAAAATAGAAA 1 AAAAAAACACCAAAACAGAAA 15990 AGAAAAAA 1 A-AAAAAA 15998 AAAACATCAA Statistics Matches: 23, Mismatches: 5, Indels: 1 0.79 0.17 0.03 Matches are distributed among these distances: 21 18 0.78 22 5 0.22 ACGTcount: A:0.74, C:0.12, G:0.06, T:0.08 Consensus pattern (21 bp): AAAAAAACACCAAAACAGAAA Found at i:20247 original size:2 final size:2 Alignment explanation
Indices: 20240--20266 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 20230 TTCTTTAAAT 20240 TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA T 20267 GAGGAATGAT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:39564 original size:2 final size:2 Alignment explanation
Indices: 39507--39546 Score: 71 Period size: 2 Copynumber: 20.0 Consensus size: 2 39497 CTTCACAAAC * 39507 AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 39547 CGAAAAAGAA Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 36 1.00 ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:39674 original size:5 final size:5 Alignment explanation
Indices: 39664--39689 Score: 52 Period size: 5 Copynumber: 5.2 Consensus size: 5 39654 CTCTTTCCAA 39664 GCCAT GCCAT GCCAT GCCAT GCCAT G 1 GCCAT GCCAT GCCAT GCCAT GCCAT G 39690 TTGAAGAAAA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 21 1.00 ACGTcount: A:0.19, C:0.38, G:0.23, T:0.19 Consensus pattern (5 bp): GCCAT Found at i:40951 original size:14 final size:13 Alignment explanation
Indices: 40926--40959 Score: 59 Period size: 14 Copynumber: 2.5 Consensus size: 13 40916 GTTTATTTCA 40926 CTGAAAATGATTT 1 CTGAAAATGATTT 40939 CTGAAACATGATTT 1 CTGAAA-ATGATTT 40953 CTGAAAA 1 CTGAAAA 40960 ATTATTTATT Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 13 7 0.35 14 13 0.65 ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32 Consensus pattern (13 bp): CTGAAAATGATTT Found at i:40966 original size:14 final size:14 Alignment explanation
Indices: 40929--40966 Score: 58 Period size: 14 Copynumber: 2.7 Consensus size: 14 40919 TATTTCACTG 40929 AAAATGATTTCTGA 1 AAAATGATTTCTGA * 40943 AACATGATTTCTGA 1 AAAATGATTTCTGA * 40957 AAAATTATTT 1 AAAATGATTT 40967 ATTTTTTGAA Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 14 21 1.00 ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39 Consensus pattern (14 bp): AAAATGATTTCTGA Found at i:43728 original size:23 final size:23 Alignment explanation
Indices: 43684--43729 Score: 56 Period size: 23 Copynumber: 2.0 Consensus size: 23 43674 AAAATTTTCA * ** 43684 AAAATTGAAAACAAAAGTCTTTT 1 AAAATTGAAAAAAAAAAACTTTT * 43707 AAAATTTAAAAAAAAAAACTTTT 1 AAAATTGAAAAAAAAAAACTTTT 43730 TTTAATTTTT Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 23 19 1.00 ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30 Consensus pattern (23 bp): AAAATTGAAAAAAAAAAACTTTT Found at i:43991 original size:22 final size:22 Alignment explanation
Indices: 43935--43991 Score: 64 Period size: 22 Copynumber: 2.6 Consensus size: 22 43925 TTGCATCAAA * 43935 AAAAATAAATATGATCAAAATC 1 AAAAATAAATATTATCAAAATC * * 43957 TATAATAAA-ATTATTCAAAAT- 1 AAAAATAAATATTA-TCAAAATC 43978 AAAAATAAATATTA 1 AAAAATAAATATTA 43992 ATTAAATTAC Statistics Matches: 28, Mismatches: 5, Indels: 4 0.76 0.14 0.11 Matches are distributed among these distances: 21 10 0.36 22 18 0.64 ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30 Consensus pattern (22 bp): AAAAATAAATATTATCAAAATC Found at i:45015 original size:63 final size:64 Alignment explanation
Indices: 44947--45075 Score: 215 Period size: 63 Copynumber: 2.0 Consensus size: 64 44937 AAACCTAAAT * 44947 ATTATGATTTTTATCGGATGTCATTTTAGTTAACGAGT-CACAATTTTATTTTTTTCTCTTGAA 1 ATTATGATTTTTATCGGATGTCATTTTAGTTAACGAGTCCACAATTTTATTTTTCTCTCTTGAA ** * 45010 ATTATGATTTTTATTTGATGTCATTTTAGTTAGCGAGTCCACAATTTTATTTTTCTCTCTTGAA 1 ATTATGATTTTTATCGGATGTCATTTTAGTTAACGAGTCCACAATTTTATTTTTCTCTCTTGAA 45074 AT 1 AT 45076 ATGTTTAATT Statistics Matches: 61, Mismatches: 4, Indels: 1 0.92 0.06 0.02 Matches are distributed among these distances: 63 35 0.57 64 26 0.43 ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51 Consensus pattern (64 bp): ATTATGATTTTTATCGGATGTCATTTTAGTTAACGAGTCCACAATTTTATTTTTCTCTCTTGAA Found at i:49768 original size:21 final size:23 Alignment explanation
Indices: 49717--49768 Score: 65 Period size: 24 Copynumber: 2.3 Consensus size: 23 49707 AGAGAGTTAA 49717 ATTTAATAAAATAGTATGGATGTGT 1 ATTTAATAAAATAGTAT-G-TGTGT 49742 -TTTAATAAAATA-TAT-TGTGT 1 ATTTAATAAAATAGTATGTGTGT 49762 ATTTAAT 1 ATTTAAT 49769 TCCGTAGCTG Statistics Matches: 26, Mismatches: 0, Indels: 6 0.81 0.00 0.19 Matches are distributed among these distances: 20 5 0.19 21 6 0.23 23 3 0.12 24 12 0.46 ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46 Consensus pattern (23 bp): ATTTAATAAAATAGTATGTGTGT Done.