Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006426.1 Corchorus capsularis cultivar CVL-1 contig06447, 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: 38782
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:3510 original size:10 final size:10
Alignment explanation
Indices: 3495--3520 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3485 ACTCCTCCCT
3495 TGCACAGCCC
1 TGCACAGCCC
3505 TGCACAGCCC
1 TGCACAGCCC
3515 TGCACA
1 TGCACA
3521 TGAGGTCTTC
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:0.46, G:0.19, T:0.12
Consensus pattern (10 bp):
TGCACAGCCC
Found at i:4594 original size:17 final size:17
Alignment explanation
Indices: 4569--4601 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4559 ATCTTTCTCA
4569 TTCTCCATATTCTCTTC
1 TTCTCCATATTCTCTTC
*
4586 TTCTTCATATTCTCTT
1 TTCTCCATATTCTCTT
4602 GTCTTTTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.30, G:0.00, T:0.58
Consensus pattern (17 bp):
TTCTCCATATTCTCTTC
Found at i:10026 original size:15 final size:16
Alignment explanation
Indices: 9989--10108 Score: 118
Period size: 16 Copynumber: 7.6 Consensus size: 16
9979 CAGACAGTTT
9989 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
10005 TTTCGGGTCA-TCTGGG
1 TTTCGGGTCATTC-GGG
*
10021 -TTCGGGTTATTCGGG
1 TTTCGGGTCATTCGGG
10036 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
*** *
10052 TTTTTAGTCATTTGGG
1 TTTCGGGTCATTCGGG
*
10068 TCTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
* * * **
10084 TTCCGAGTCCTTTAGG
1 TTTCGGGTCATTCGGG
10100 TTTCGGGTC
1 TTTCGGGTC
10109 TACCAGGTCT
Statistics
Matches: 82, Mismatches: 19, Indels: 6
0.77 0.18 0.06
Matches are distributed among these distances:
15 13 0.16
16 69 0.84
ACGTcount: A:0.07, C:0.18, G:0.34, T:0.40
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:10049 original size:47 final size:48
Alignment explanation
Indices: 9989--10108 Score: 143
Period size: 48 Copynumber: 2.5 Consensus size: 48
9979 CAGACAGTTT
*
9989 TTTCGGGTCATTCGGGTTTCGGGTCATCTGGGT-TCGGGTTATTCGGG
1 TTTCGGGTCATTCGGGTTTCGGGTCATCTGGGTCTCGGGTCATTCGGG
*** *
10036 TTTCGGGTCATTCGGGTTTTTAGTCATTTGGGTCTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGGTTTCGGGTCATCTGGGTCTCGGGTCATTCGGG
* * * **
10084 TTCCGAGTCCTTTAGGTTTCGGGTC
1 TTTCGGGTCATTCGGGTTTCGGGTC
10109 TACCAGGTCT
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
47 29 0.49
48 30 0.51
ACGTcount: A:0.07, C:0.18, G:0.34, T:0.40
Consensus pattern (48 bp):
TTTCGGGTCATTCGGGTTTCGGGTCATCTGGGTCTCGGGTCATTCGGG
Found at i:10053 original size:31 final size:31
Alignment explanation
Indices: 9990--10086 Score: 115
Period size: 31 Copynumber: 3.1 Consensus size: 31
9980 AGACAGTTTT
9990 TTCGGGTCATTCGGGTTTCGGGTCA-TCTGGG
1 TTCGGGTCATTCGGGTTTCGGGTCATTC-GGG
*
10021 TTCGGGTTATTCGGGTTTCGGGTCATTCGGG
1 TTCGGGTCATTCGGGTTTCGGGTCATTCGGG
*** * *
10052 TTTTTAGTCATTTGGGTCTCGGGTCATTCGGG
1 -TTCGGGTCATTCGGGTTTCGGGTCATTCGGG
10084 TTC
1 TTC
10087 CGAGTCCTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
31 29 0.52
32 27 0.48
ACGTcount: A:0.07, C:0.18, G:0.35, T:0.40
Consensus pattern (31 bp):
TTCGGGTCATTCGGGTTTCGGGTCATTCGGG
Found at i:10995 original size:16 final size:15
Alignment explanation
Indices: 10976--11097 Score: 109
Period size: 16 Copynumber: 7.7 Consensus size: 15
10966 GGTTATTCAT
10976 GTTTCGGGTCATACGG
1 GTTTCGGGTCAT-CGG
*
10992 GTTTTGGGTCATCTGG
1 GTTTCGGGTCATC-GG
*
11008 GTTACGGGTCATTCGG
1 GTTTCGGGTCA-TCGG
* *
11024 CTCTCGGGTCATCTGG
1 GTTTCGGGTCATC-GG
*
11040 GTTGCGGGTCATTCGG
1 GTTTCGGGTCA-TCGG
*
11056 GTCTCGGGTCATCTGG
1 GTTTCGGGTCATC-GG
*
11072 GTTGCGGGTCATTCGG
1 GTTTCGGGTCA-TCGG
*
11088 GTCTCGGGTC
1 GTTTCGGGTC
11098 GGGCAGGTTC
Statistics
Matches: 85, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
15 5 0.06
16 74 0.87
17 6 0.07
ACGTcount: A:0.07, C:0.21, G:0.39, T:0.33
Consensus pattern (15 bp):
GTTTCGGGTCATCGG
Found at i:11016 original size:32 final size:32
Alignment explanation
Indices: 10980--11097 Score: 191
Period size: 32 Copynumber: 3.7 Consensus size: 32
10970 ATTCATGTTT
* * * *
10980 CGGGTCATACGGGTTTTGGGTCATCTGGGTTA
1 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTG
*
11012 CGGGTCATTCGGCTCTCGGGTCATCTGGGTTG
1 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTG
11044 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTG
1 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTG
11076 CGGGTCATTCGGGTCTCGGGTC
1 CGGGTCATTCGGGTCTCGGGTC
11098 GGGCAGGTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 80 1.00
ACGTcount: A:0.08, C:0.22, G:0.39, T:0.31
Consensus pattern (32 bp):
CGGGTCATTCGGGTCTCGGGTCATCTGGGTTG
Found at i:18945 original size:15 final size:16
Alignment explanation
Indices: 18913--18946 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
18903 AAAGAAGAAT
*
18913 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
18929 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
18944 TAA
1 TAA
18947 GACAACAATC
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:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:20262 original size:19 final size:18
Alignment explanation
Indices: 20229--20264 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20219 TTGAAATAAT
20229 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
20247 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
20265 GAAATCTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:27994 original size:15 final size:16
Alignment explanation
Indices: 27962--27995 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27952 AAAGAAGAAT
*
27962 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
27978 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
27993 TAA
1 TAA
27996 GACAACAATC
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:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:29311 original size:19 final size:18
Alignment explanation
Indices: 29278--29313 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29268 TTGAAATAAT
29278 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
29296 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
29314 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:29515 original size:20 final size:21
Alignment explanation
Indices: 29477--29515 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
29467 TAGAAAATAA
*
29477 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
29498 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
29516 ATAGCCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:30207 original size:23 final size:25
Alignment explanation
Indices: 30176--30224 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
30166 ACCTTTATCA
* *
30176 TTTATATTTTTCG-TTATTTTTCTT
1 TTTATATTTTTAGTTTAGTTTTCTT
30200 TTTA-ATTTTTAGTTTAGTTTTCTT
1 TTTATATTTTTAGTTTAGTTTTCTT
30224 T
1 T
30225 ACTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.73
Consensus pattern (25 bp):
TTTATATTTTTAGTTTAGTTTTCTT
Found at i:33600 original size:20 final size:21
Alignment explanation
Indices: 33563--33602 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33553 CCGATCCTAG
*
33563 CTGGGCCCCCATGCCGCAAGC
1 CTGGGCACCCATGCCGCAAGC
33584 CTGGGCACCCA-GCCGCAAG
1 CTGGGCACCCATGCCGCAAG
33603 GGCCTGTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.45, G:0.30, T:0.07
Consensus pattern (21 bp):
CTGGGCACCCATGCCGCAAGC
Done.