Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005761.1 Kokia drynarioides strain JFW-HI SEQ_120020, 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: 4731
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Found at i:637 original size:23 final size:23
Alignment explanation
Indices: 515--685 Score: 134
Period size: 23 Copynumber: 7.3 Consensus size: 23
505 ACACTAGCGC
*
515 GCCCTCT-ATTTAGCACGTTT-CGT
1 GCCCTCTGA-TTAGCAC-TTTGTGT
* *
538 GCTCTCT-ATTCAGCACTGTGTGT
1 GCCCTCTGATT-AGCACTTTGTGT
* * *
561 GCTCTCTGTTTAGCACTGTGTGT
1 GCCCTCTGATTAGCACTTTGTGT
** * *
584 GCTTTTTGTTTAGCA-TGTTGTGT
1 GCCCTCTGATTAGCACT-TTGTGT
*
607 GCCCTCTGATCAGCACTTTGTGT
1 GCCCTCTGATTAGCACTTTGTGT
**
630 GCCCTCTGTTATTAGCACTTCATGT
1 GCCCTCTG--ATTAGCACTTTGTGT
*
655 GCCTTCTGATTAGCACTTTGTGT
1 GCCCTCTGATTAGCACTTTGTGT
678 GCCCTCTG
1 GCCCTCTG
686 TTACCCAGCA
Statistics
Matches: 122, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.04
23 95 0.78
24 3 0.02
25 19 0.16
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.42
Consensus pattern (23 bp):
GCCCTCTGATTAGCACTTTGTGT
Found at i:645 original size:48 final size:48
Alignment explanation
Indices: 604--708 Score: 158
Period size: 48 Copynumber: 2.2 Consensus size: 48
594 TAGCATGTTG
604 TGTGCCCTCTGATCAGCACTTTGTGTGCCCTCTGTTATTAGCACTTCA
1 TGTGCCCTCTGATCAGCACTTTGTGTGCCCTCTGTTATTAGCACTTCA
* * **
652 TGTGCCTTCTGATTAGCACTTTGTGTGCCCTCTGTTACCCAGCACTT-A
1 TGTGCCCTCTGATCAGCACTTTGTGTGCCCTCTGTTA-TTAGCACTTCA
700 TGTGCCCTC
1 TGTGCCCTC
709 GGTTAAGTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 44 0.86
49 7 0.14
ACGTcount: A:0.13, C:0.30, G:0.19, T:0.37
Consensus pattern (48 bp):
TGTGCCCTCTGATCAGCACTTTGTGTGCCCTCTGTTATTAGCACTTCA
Found at i:668 original size:71 final size:69
Alignment explanation
Indices: 547--685 Score: 174
Period size: 71 Copynumber: 2.0 Consensus size: 69
537 TGCTCTCTAT
* * * * *
547 TCAGCACTGTGTGTGCTCTCTGTTTAGCACTGTGTGTGCTTTTTGTTTAGCA-TGTTGTGTGCCC
1 TCAGCACTGTGTGTGCCCTCTGTTTAGCACTGTATGTGCCTTCTGATTAGCACT-TTGTGTGCCC
611 TCTGA
65 TCTGA
*
616 TCAGCACTTTGTGTGCCCTCTGTTATTAGCACT-TCATGTGCCTTCTGATTAGCACTTTGTGTGC
1 TCAGCACTGTGTGTGCCCTCTG-T-TTAGCACTGT-ATGTGCCTTCTGATTAGCACTTTGTGTGC
680 CCTCTG
63 CCTCTG
686 TTACCCAGCA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
69 20 0.33
70 2 0.03
71 37 0.62
72 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.42
Consensus pattern (69 bp):
TCAGCACTGTGTGTGCCCTCTGTTTAGCACTGTATGTGCCTTCTGATTAGCACTTTGTGTGCCCT
CTGA
Found at i:706 original size:25 final size:24
Alignment explanation
Indices: 604--713 Score: 93
Period size: 25 Copynumber: 4.6 Consensus size: 24
594 TAGCATGTTG
* *
604 TGTGCCCTCTGAT-CAGCACTTTG
1 TGTGCCCTCTGTTACAGCACTTTA
* *
627 TGTGCCCTCTGTTATTAGCACTTCA
1 TGTGCCCTCTGTTA-CAGCACTTTA
* *
652 TGTGCCTTCTGATT--AGCACTTTG
1 TGTGCCCTCTG-TTACAGCACTTTA
675 TGTGCCCTCTGTTACCCAGCAC-TTA
1 TGTGCCCTCTGTTA--CAGCACTTTA
*
700 TGTGCCCTCGGTTA
1 TGTGCCCTCTGTTA
714 AGTACTTCGG
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
22 2 0.03
23 29 0.41
25 32 0.46
26 7 0.10
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.37
Consensus pattern (24 bp):
TGTGCCCTCTGTTACAGCACTTTA
Found at i:1091 original size:82 final size:82
Alignment explanation
Indices: 991--1154 Score: 285
Period size: 82 Copynumber: 2.0 Consensus size: 82
981 GATGAAAATG
* *
991 TAAAATCTACCATTGAGGTAAGTTGCG-ATATGAGAATTAATGTGTGTTGTGGTGACATTAAGGT
1 TAAAATCTACCATTGAGGTAAGTTG-GAATATGAGAATGAATGTGTGATGTGGTGACATTAAGGT
1055 AAGTTAAATGTTACATGC
65 AAGTTAAATGTTACATGC
*
1073 TAAAATCTACCATTGAGGTAAGTTGGAATATGAGAATGAATGTGTGATGTGGTGGCATTAAGGTA
1 TAAAATCTACCATTGAGGTAAGTTGGAATATGAGAATGAATGTGTGATGTGGTGACATTAAGGTA
1138 AGTTAAATGTTACATGC
66 AGTTAAATGTTACATGC
1155 AAGAAAGGTT
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
81 1 0.01
82 77 0.99
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.33
Consensus pattern (82 bp):
TAAAATCTACCATTGAGGTAAGTTGGAATATGAGAATGAATGTGTGATGTGGTGACATTAAGGTA
AGTTAAATGTTACATGC
Found at i:2849 original size:24 final size:24
Alignment explanation
Indices: 2802--2851 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
2792 GTACTGGAGC
* *
2802 TACTGATGCTATTACAGCAAGTGT
1 TACTGATGCTACTACAACAAGTGT
* *
2826 TACTGATGCTACTATAACATGTGT
1 TACTGATGCTACTACAACAAGTGT
2850 TA
1 TA
2852 GTACTAGTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (24 bp):
TACTGATGCTACTACAACAAGTGT
Done.