Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010365.1 Corchorus capsularis cultivar CVL-1 contig10386, 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: 22506
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:4451 original size:11 final size:11
Alignment explanation
Indices: 4416--4457 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
4406 ATTATACAAT
4416 TATATATAAAA
1 TATATATAAAA
* **
4427 TATATTTATGA
1 TATATATAAAA
4438 TATATATAAAA
1 TATATATAAAA
4449 TATATATAA
1 TATATATAA
4458 TAGATTATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
TATATATAAAA
Found at i:4705 original size:36 final size:36
Alignment explanation
Indices: 4654--4726 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
4644 GACAATGCCC
**
4654 TTTTCATGTGTTGGACGTGAGTCACGTAATGACACA
1 TTTTCATGTAATGGACGTGAGTCACGTAATGACACA
*
4690 TTTTCATGTAATGGACGTGAGTCACTTAATGACACA
1 TTTTCATGTAATGGACGTGAGTCACGTAATGACACA
4726 T
1 T
4727 GACTAACGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.34
Consensus pattern (36 bp):
TTTTCATGTAATGGACGTGAGTCACGTAATGACACA
Found at i:10446 original size:53 final size:53
Alignment explanation
Indices: 10365--10520 Score: 230
Period size: 53 Copynumber: 3.0 Consensus size: 53
10355 CGCACCTGGT
*
10365 TACGGTGGATGAGTCTCTAAACAAGGGCAGCTGCGTACGCAATGTCTCGAACC
1 TACGGTGGATGAGTCTCTAAACAGGGGCAGCTGCGTACGCAATGTCTCGAACC
10418 TACGGTGGATGAGTCTCTAAACAGGGGCAGCTGCGTACGCAATGTCTCGAACC
1 TACGGTGGATGAGTCTCTAAACAGGGGCAGCTGCGTACGCAATGTCTCGAACC
** ** *
10471 T---GT-CTTGAGTCTCCCAACAGGGGCAGCTGCATACGCAATGTCTCGAACC
1 TACGGTGGATGAGTCTCTAAACAGGGGCAGCTGCGTACGCAATGTCTCGAACC
10520 T
1 T
10521 GTCTTGATTA
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
49 42 0.43
50 2 0.02
53 53 0.55
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (53 bp):
TACGGTGGATGAGTCTCTAAACAGGGGCAGCTGCGTACGCAATGTCTCGAACC
Found at i:10499 original size:49 final size:49
Alignment explanation
Indices: 10374--10527 Score: 218
Period size: 49 Copynumber: 3.1 Consensus size: 49
10364 TTACGGTGGA
* **
10374 TGAGTCTCTAAACAAGGGCAGCTGCGTACGCAATGTCTCGAACCTACGGTGGA
1 TGAGTCTCTAAACAGGGGCAGCTGCGTACGCAATGTCTCGAACCT---GT-CT
10427 TGAGTCTCTAAACAGGGGCAGCTGCGTACGCAATGTCTCGAACCTGTCT
1 TGAGTCTCTAAACAGGGGCAGCTGCGTACGCAATGTCTCGAACCTGTCT
** *
10476 TGAGTCTCCCAACAGGGGCAGCTGCATACGCAATGTCTCGAACCTGTCT
1 TGAGTCTCTAAACAGGGGCAGCTGCGTACGCAATGTCTCGAACCTGTCT
10525 TGA
1 TGA
10528 TTAATTAAGA
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
49 49 0.52
50 2 0.02
53 44 0.46
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.23
Consensus pattern (49 bp):
TGAGTCTCTAAACAGGGGCAGCTGCGTACGCAATGTCTCGAACCTGTCT
Found at i:10548 original size:18 final size:18
Alignment explanation
Indices: 10525--10590 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 18
10515 GAACCTGTCT
10525 TGATTAATTAAGAAATGA
1 TGATTAATTAAGAAATGA
* * *
10543 TGATTATATAATACGAACCTGTCT
1 TGATTA-AT--TAAGAA-ATG--A
10567 TGATTAATTAAGAAATGA
1 TGATTAATTAAGAAATGA
10585 TGATTA
1 TGATTA
10591 TAAAGAGCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 12 0.33
19 2 0.06
20 2 0.06
21 10 0.28
22 2 0.06
23 2 0.06
24 6 0.17
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (18 bp):
TGATTAATTAAGAAATGA
Found at i:10800 original size:26 final size:26
Alignment explanation
Indices: 10763--10814 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
10753 GTTTTATTTG
* *
10763 AGTTTTTTTTTAGTCGGTTT-GAGTC
1 AGTTTTTCTTTAGTCAGTTTCGAGTC
10788 AGTTTGTTCTTTAGTCAGTTTCGAGTC
1 AGTTT-TTCTTTAGTCAGTTTCGAGTC
10815 TAGTCTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 13 0.57
27 5 0.22
ACGTcount: A:0.13, C:0.12, G:0.23, T:0.52
Consensus pattern (26 bp):
AGTTTTTCTTTAGTCAGTTTCGAGTC
Found at i:11006 original size:13 final size:13
Alignment explanation
Indices: 10988--11012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10978 CGTTGATCAA
10988 AGCTTTTTGTTTT
1 AGCTTTTTGTTTT
11001 AGCTTTTTGTTT
1 AGCTTTTTGTTT
11013 GGAAGAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.68
Consensus pattern (13 bp):
AGCTTTTTGTTTT
Found at i:16006 original size:5 final size:5
Alignment explanation
Indices: 15996--16026 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
15986 TAAGGTGTAA
*
15996 TCGAG TCGAG TCGAG TCGAG TCGAG TTGAG T
1 TCGAG TCGAG TCGAG TCGAG TCGAG TCGAG T
16027 AATAAACTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.19, C:0.16, G:0.39, T:0.26
Consensus pattern (5 bp):
TCGAG
Found at i:18578 original size:2 final size:2
Alignment explanation
Indices: 18535--18561 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18525 TAATTAATTC
18535 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
18562 GTTGCAGGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21260 original size:16 final size:16
Alignment explanation
Indices: 21241--21274 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21231 TTTTTTATTA
* *
21241 ATTTATGTATTTATAT
1 ATTTATGAATTAATAT
21257 ATTTATGAATTAATAT
1 ATTTATGAATTAATAT
21273 AT
1 AT
21275 ATTTTAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
ATTTATGAATTAATAT
Found at i:22409 original size:2 final size:2
Alignment explanation
Indices: 22402--22430 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
22392 GTATGAGTAC
22402 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22431 ATTATGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.