Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007406.1 Corchorus capsularis cultivar CVL-1 contig07427, 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: 21014
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1304 original size:10 final size:10
Alignment explanation
Indices: 1289--1314 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1279 GAAGACTCTA
1289 GAATTTTCTG
1 GAATTTTCTG
1299 GAATTTTCTG
1 GAATTTTCTG
1309 GAATTT
1 GAATTT
1315 GGCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:2336 original size:40 final size:40
Alignment explanation
Indices: 2242--2351 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
2232 ACCAATTTTA
* * *
2242 TTATTTTCCAAAAGTCTTCTCTTGGATTT--TTAAAGCCT
1 TTATTTTCCAAAAGTCTTCTCTTGGATTTGCTAAAAACAT
*
2280 TTATTTTCCAAAAGTCTTCTTTTGGATTTGCTAAAAACAT
1 TTATTTTCCAAAAGTCTTCTCTTGGATTTGCTAAAAACAT
* *
2320 TTATTTTCCAACAGTCTTCTCTTGGAATTGCT
1 TTATTTTCCAAAAGTCTTCTCTTGGATTTGCT
2352 TAAATTGAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
38 28 0.44
40 35 0.56
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.46
Consensus pattern (40 bp):
TTATTTTCCAAAAGTCTTCTCTTGGATTTGCTAAAAACAT
Found at i:3696 original size:10 final size:10
Alignment explanation
Indices: 3681--3713 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3671 ATTCATATAA
3681 AAACACACAC
1 AAACACACAC
3691 AAACACACAC
1 AAACACACAC
*
3701 ACACACACAC
1 AAACACACAC
3711 AAA
1 AAA
3714 TTATTTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.61, C:0.39, G:0.00, T:0.00
Consensus pattern (10 bp):
AAACACACAC
Found at i:4605 original size:2 final size:2
Alignment explanation
Indices: 4600--4630 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4590 GAGTTCTTTC
4600 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4631 CTGTATTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6360 original size:22 final size:22
Alignment explanation
Indices: 6334--6388 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
6324 TTGTAAAAGC
*
6334 TTGAAACCTTGGGGTTTTAAAA
1 TTGAAACCTTGGGGTTTCAAAA
6356 TTGAAACCTTGGGGTTTCAAAA
1 TTGAAACCTTGGGGTTTCAAAA
6378 TTGAAACCTTG
1 TTGAAACCTTG
6389 CTGCTCATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.35
Consensus pattern (22 bp):
TTGAAACCTTGGGGTTTCAAAA
Found at i:7643 original size:26 final size:28
Alignment explanation
Indices: 7614--7665 Score: 90
Period size: 26 Copynumber: 1.9 Consensus size: 28
7604 AAGTAGACTT
7614 AAAATGACCAAAATG-CCCCT-GGTGCC
1 AAAATGACCAAAATGTCCCCTAGGTGCC
7640 AAAATGACCAAAATGTCCCCTAGGTG
1 AAAATGACCAAAATGTCCCCTAGGTG
7666 ACCCTAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 15 0.62
27 5 0.21
28 4 0.17
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (28 bp):
AAAATGACCAAAATGTCCCCTAGGTGCC
Found at i:13849 original size:22 final size:22
Alignment explanation
Indices: 13806--13849 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
13796 TTAAGGGGGT
* *
13806 AATAAATATTTTTAATCTTTGA
1 AATAAATATTTTCAATCATTGA
13828 AATAAATATTTTCCAA-CATTGA
1 AATAAATATTTT-CAATCATTGA
13850 GTAGCTCCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (22 bp):
AATAAATATTTTCAATCATTGA
Found at i:17834 original size:13 final size:13
Alignment explanation
Indices: 17818--17890 Score: 51
Period size: 13 Copynumber: 5.3 Consensus size: 13
17808 TAACTAATTC
17818 TATATATTTAATG
1 TATATATTTAATG
17831 TATATATTTAAATTG
1 TATATATTT-AA-TG
*
17846 TTAAATTATGTTATAT-
1 -TATA-TAT-TTA-ATG
* *
17862 TATACATTTAATA
1 TATATATTTAATG
17875 TATATATTT-ATG
1 TATATATTTAATG
17887 TATA
1 TATA
17891 CATCAGTTAC
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
12 8 0.17
13 20 0.42
14 4 0.08
15 5 0.10
16 3 0.06
17 5 0.10
18 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.53
Consensus pattern (13 bp):
TATATATTTAATG
Found at i:18215 original size:19 final size:18
Alignment explanation
Indices: 18191--18226 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18181 TGAAGATTTC
18191 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
18210 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
18227 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:19522 original size:15 final size:16
Alignment explanation
Indices: 19502--19535 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19492 GATTGTTGTC
*
19502 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
19517 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
19533 TTA
1 TTA
19536 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Done.