Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001118.1 Kokia drynarioides strain JFW-HI SEQ_112400, 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: 34131
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:2856 original size:2 final size:2
Alignment explanation
Indices: 2834--2886 Score: 78
Period size: 2 Copynumber: 28.5 Consensus size: 2
2824 AACACTTTAA
2834 AT AT A- AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2873 AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT A
2887 ATCTTAACAA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 4 0.09
2 43 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24905 original size:15 final size:15
Alignment explanation
Indices: 24864--24906 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
24854 TTTTAAATTA
24864 ATTTTTAATATTTTTT
1 ATTTTTAATA-TTTTT
24880 ATTTATT--TATTTTT
1 ATTT-TTAATATTTTT
24894 ATTTTTAATATTT
1 ATTTTTAATATTT
24907 AATTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 7 0.29
16 4 0.17
17 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTAATATTTTT
Found at i:27127 original size:43 final size:43
Alignment explanation
Indices: 27059--27213 Score: 195
Period size: 43 Copynumber: 3.6 Consensus size: 43
27049 TTGCTAATGA
* * * * *
27059 TAAAGATCATGTTCTTTAACGGCGCTTCTACTACAAACGCCGT
1 TAAAGACCATGTTCTTTAGCGGCGCTTCTCCCACAAACGCCGC
** *
27102 TAAAGACCATGTTCTTTAGTTGCGCTTCTCCCAAAAACGCCGC
1 TAAAGACCATGTTCTTTAGCGGCGCTTCTCCCACAAACGCCGC
*
27145 TAAAGACCATGTTCTTTAGCGGCGCTTCTCCCACAAACGCTGC
1 TAAAGACCATGTTCTTTAGCGGCGCTTCTCCCACAAACGCCGC
* **
27188 TAATGACC-TGACCTTTAGCGGCGCTT
1 TAAAGACCATGTTCTTTAGCGGCGCTT
27214 GGGGGAGCGC
Statistics
Matches: 97, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 16 0.16
43 81 0.84
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (43 bp):
TAAAGACCATGTTCTTTAGCGGCGCTTCTCCCACAAACGCCGC
Found at i:27283 original size:41 final size:40
Alignment explanation
Indices: 27186--27394 Score: 298
Period size: 41 Copynumber: 5.2 Consensus size: 40
27176 CACAAACGCT
27186 GCTAATGACCTGACCTTTAGCGGCGCTTGGGGG--AGCGC
1 GCTAATGACCTGACCTTTAGCGGCGCTTGGGGGAAAGCGC
*
27224 TGCTAATGACCTGACCTTTAGTGGCGCTTGGGGGAAAGCGTC
1 -GCTAATGACCTGACCTTTAGCGGCGCTTGGGGGAAAGCG-C
* *
27266 GGTAATGACCTGACCTTTAGCGGTGCTT-GGGGAAAGCGCC
1 GCTAATGACCTGACCTTTAGCGGCGCTTGGGGGAAAGCG-C
* * *
27306 GCTAATGAACTGACCTTTAGTGGCGCTTGGTGGAAAGCGC
1 GCTAATGACCTGACCTTTAGCGGCGCTTGGGGGAAAGCGC
27346 AGCTAATGACCTGACCTTTAGCGGCGCTTGGGGGAAAGCGCC
1 -GCTAATGACCTGACCTTTAGCGGCGCTTGGGGGAAAGCG-C
27388 GCTAATG
1 GCTAATG
27395 CTTTACCTTT
Statistics
Matches: 151, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
39 32 0.21
40 36 0.24
41 81 0.54
42 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (40 bp):
GCTAATGACCTGACCTTTAGCGGCGCTTGGGGGAAAGCGC
Found at i:27319 original size:81 final size:81
Alignment explanation
Indices: 27186--27394 Score: 332
Period size: 81 Copynumber: 2.6 Consensus size: 81
27176 CACAAACGCT
* * *
27186 GCTAATGACCTGACCTTTAGCGGCGCTTGGGG-GAGCGCTGCTAATGACCTGACCTTTAGTGGCG
1 GCTAATGACCTGACCTTTAGCGGCGCTTGGGGAAAGCGCCGCTAATGAACTGACCTTTAGTGGCG
27250 CTTGGGGGAAAGCGTC-
66 CTTGGGGGAAAGCG-CA
* *
27266 GGTAATGACCTGACCTTTAGCGGTGCTTGGGGAAAGCGCCGCTAATGAACTGACCTTTAGTGGCG
1 GCTAATGACCTGACCTTTAGCGGCGCTTGGGGAAAGCGCCGCTAATGAACTGACCTTTAGTGGCG
*
27331 CTTGGTGGAAAGCGCA
66 CTTGGGGGAAAGCGCA
27347 GCTAATGACCTGACCTTTAGCGGCGCTTGGGGGAAAGCGCCGCTAATG
1 GCTAATGACCTGACCTTTAGCGGCGCTT-GGGGAAAGCGCCGCTAATG
27395 CTTTACCTTT
Statistics
Matches: 118, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
80 31 0.26
81 68 0.58
82 19 0.16
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (81 bp):
GCTAATGACCTGACCTTTAGCGGCGCTTGGGGAAAGCGCCGCTAATGAACTGACCTTTAGTGGCG
CTTGGGGGAAAGCGCA
Found at i:27981 original size:8 final size:8
Alignment explanation
Indices: 27968--27993 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
27958 TAATATTAAC
27968 TTATAATT
1 TTATAATT
27976 TTATAATT
1 TTATAATT
27984 TTATAATT
1 TTATAATT
27992 TT
1 TT
27994 GTTGTCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTATAATT
Done.