Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010601.1 Corchorus capsularis cultivar CVL-1 contig10622, 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: 60957
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2369 original size:12 final size:12
Alignment explanation
Indices: 2352--2376 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2342 ATCCTACAAC
2352 TTCCCCCTAGTT
1 TTCCCCCTAGTT
2364 TTCCCCCTAGTT
1 TTCCCCCTAGTT
2376 T
1 T
2377 ACAAAAGAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.40, G:0.08, T:0.44
Consensus pattern (12 bp):
TTCCCCCTAGTT
Found at i:2713 original size:21 final size:21
Alignment explanation
Indices: 2648--2727 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
2638 CATGAGGAAA
* *
2648 AATCAAAATTTCATGGTTTAGT
1 AATCAAAATTTCATAGTGT-GT
** * * *
2670 TTTCAAATTTTCATAGGGGGT
1 AATCAAAATTTCATAGTGTGT
2691 AATCAAAATTTCATAGTGTGT
1 AATCAAAATTTCATAGTGTGT
*
2712 AAATGAAAA-TTCATAG
1 -AATCAAAATTTCATAG
2728 GTATAAGGTT
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
21 25 0.57
22 19 0.43
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (21 bp):
AATCAAAATTTCATAGTGTGT
Found at i:2805 original size:45 final size:45
Alignment explanation
Indices: 2754--2848 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 45
2744 ATTTCATAAC
2754 TATCAAAAAATCATAGGGAA-G-TTATCAAAATTTTATAGAGAGATT
1 TATCAAAAAATCATA-GGAAGGTTTATCAAAATTTTATAGAGAGA-T
** * * *
2799 TATCAAAATTTTATAGGAAGGTTTGTCAAAATTTTATAGTGAGAT
1 TATCAAAAAATCATAGGAAGGTTTATCAAAATTTTATAGAGAGAT
2844 TATCA
1 TATCA
2849 CAATTTCATA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
44 4 0.09
45 19 0.44
46 20 0.47
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (45 bp):
TATCAAAAAATCATAGGAAGGTTTATCAAAATTTTATAGAGAGAT
Found at i:2877 original size:22 final size:22
Alignment explanation
Indices: 2775--3212 Score: 124
Period size: 22 Copynumber: 19.7 Consensus size: 22
2765 CATAGGGAAG
* * *
2775 TTATCAAAATTTTATAGAGAGA
1 TTATCAAAATTTCATAGTGTGA
* * *
2797 TTTATCAAAATTTTATAG-GAAGGT
1 -TTATCAAAATTTCATAGTG--TGA
* * *
2821 TTGTCAAAATTTTATAGTGAGA
1 TTATCAAAATTTCATAGTGTGA
*
2843 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
*
2865 TTATCAAAATTTCA-CGATGTGA
1 TTATCAAAATTTCATAG-TGTGA
* * * * *
2887 TTATTAACATTTTATAGGGAGA
1 TTATCAAAATTTCATAGTGTGA
* * * *
2909 TTCTTAAAATTTCACAGTGTGC
1 TTATCAAAATTTCATAGTGTGA
*
2931 TTA-CAAACATTTCACA-TG-GA
1 TTATCAAA-ATTTCATAGTGTGA
**
2951 GGTTATTGAAATTTCATAGTGTGGTTA
1 --TTATCAAAATTTCATAGTGT-G--A
* ** *
2978 TGATCAAAATTTCATAGTAAGG
1 TTATCAAAATTTCATAGTGTGA
* * * * *
3000 TTTTCAAAATTCCATAGGGAGG
1 TTATCAAAATTTCATAGTGTGA
* * ** *
3022 TTAACAAAATTTCATGGAATGG
1 TTATCAAAATTTCATAGTGTGA
* * * *
3044 TTCTCGAAATTCCATAATGTCG-
1 TTATCAAAATTTCATAGTGT-GA
* * *
3066 TTACCAAAATTTCATAG-GAAGG
1 TTATCAAAATTTCATAGTG-TGA
*
3088 TTATCAAATTTTCATA-TG-GA
1 TTATCAAAATTTCATAGTGTGA
* *
3108 GGTTATCAAAATTTTAATAGTGTAA
1 --TTATCAAAA-TTTCATAGTGTGA
* * * * *
3133 TTATCATAATGTCACAGGGAGA
1 TTATCAAAATTTCATAGTGTGA
* * *
3155 TTACCACAATTTCATA-TATGA
1 TTATCAAAATTTCATAGTGTGA
* ** * *
3176 ATAT-TTAATTGCATAATGTGA
1 TTATCAAAATTTCATAGTGTGA
3197 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
3213 TGAATATTTA
Statistics
Matches: 298, Mismatches: 92, Indels: 51
0.68 0.21 0.12
Matches are distributed among these distances:
20 10 0.03
21 19 0.06
22 193 0.65
23 53 0.18
24 5 0.02
25 17 0.06
27 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:3054 original size:44 final size:43
Alignment explanation
Indices: 2982--3121 Score: 138
Period size: 44 Copynumber: 3.2 Consensus size: 43
2972 TGGTTATGAT
* * *
2982 CAAAATTTCATAGTAAGGTTTTCAAAATTCCATAGGGAGGTTAA
1 CAAAATTTCATAGGAAGGTTATC-AAATTCCATAAGGAGGTTAA
* * ** *
3026 CAAAATTTCAT-GGAATGGTTCTCGAAATTCCATAATGTCGTTAC
1 CAAAATTTCATAGGAA-GGTTATC-AAATTCCATAAGGAGGTTAA
* * *
3070 CAAAATTTCATAGGAAGGTTATCAAATTTTCATATGGAGGTTAT
1 CAAAATTTCATAGGAAGGTTATCAAA-TTCCATAAGGAGGTTAA
3114 CAAAATTT
1 CAAAATTT
3122 TAATAGTGTA
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
43 6 0.08
44 68 0.87
45 4 0.05
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (43 bp):
CAAAATTTCATAGGAAGGTTATCAAATTCCATAAGGAGGTTAA
Found at i:13474 original size:30 final size:31
Alignment explanation
Indices: 13439--13501 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
13429 TATGCTAAAT
*
13439 ACACAAACAAATAAATTACAAAG-GAAACTC
1 ACACAAACAAATAAATTACAAAGAAAAACTC
13469 ACACAAACAAATAAATTACAAAGAAAAACTC
1 ACACAAACAAATAAATTACAAAGAAAAACTC
13500 AC
1 AC
13502 GTAGCGTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.62, C:0.21, G:0.05, T:0.13
Consensus pattern (31 bp):
ACACAAACAAATAAATTACAAAGAAAAACTC
Found at i:16234 original size:31 final size:31
Alignment explanation
Indices: 16140--16241 Score: 109
Period size: 29 Copynumber: 3.3 Consensus size: 31
16130 AAATACCTAA
*
16140 TTAGTCCCTGTACTATTGAAAAAAAGATCAAT
1 TTAGTCCCTCTACTATTG-AAAAAAGATCAAT
* * * ***
16172 TTAGTCCTTCCATTA-TGAAATCTG-TCAAT
1 TTAGTCCCTCTACTATTGAAAAAAGATCAAT
*
16201 TTAGTCCCTCTACTATTGAAAAGAGATCAAT
1 TTAGTCCCTCTACTATTGAAAAAAGATCAAT
16232 TTAGTCCCTC
1 TTAGTCCCTC
16242 CATGAAACCG
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
29 17 0.31
30 10 0.18
31 17 0.31
32 11 0.20
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (31 bp):
TTAGTCCCTCTACTATTGAAAAAAGATCAAT
Found at i:20375 original size:2 final size:2
Alignment explanation
Indices: 20368--20403 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20358 CTCGCAATTA
20368 AT AT AT AT AT AT 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
20404 TTGTTTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21691 original size:2 final size:2
Alignment explanation
Indices: 21684--21709 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21674 ATTCAATTTC
21684 AT 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
21710 TGAGAGGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30892 original size:2 final size:2
Alignment explanation
Indices: 30887--30919 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30877 CAAGTAATCA
30887 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
30920 TCTTCTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:30935 original size:12 final size:11
Alignment explanation
Indices: 30919--30953 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
30909 TCTCTCTCTC
30919 TTCTTCTTTCT
1 TTCTTCTTTCT
30930 TCTCTTCTTTCT
1 T-TCTTCTTTCT
30942 TTCTTTCTTTCT
1 TTC-TTCTTTCT
30954 AGTTTTAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 19 0.86
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
TTCTTCTTTCT
Found at i:30935 original size:15 final size:16
Alignment explanation
Indices: 30915--30950 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
30905 TCTCTCTCTC
30915 TCTCTTC-TTCTTTCT
1 TCTCTTCTTTCTTTCT
30930 TCTCTTCTTTCTTTCT
1 TCTCTTCTTTCTTTCT
30946 T-TCTT
1 TCTCTT
30951 TCTAGTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TCTCTTCTTTCTTTCT
Found at i:42806 original size:61 final size:61
Alignment explanation
Indices: 42711--42839 Score: 240
Period size: 61 Copynumber: 2.1 Consensus size: 61
42701 AACGATATTG
*
42711 TTTATGTGAACGAGTTAGCAATAACATTTAATCTTAATAAATGTTTCAACAAAGTTGGGCA
1 TTTATGTGAACGAGTTAGCAATAACATTTAATCTTAAAAAATGTTTCAACAAAGTTGGGCA
*
42772 TTTATGTGAACGAGTTAGCAATAACATTTAATCTTAAAAAATGTTTTAACAAAGTTGGGCA
1 TTTATGTGAACGAGTTAGCAATAACATTTAATCTTAAAAAATGTTTCAACAAAGTTGGGCA
42833 TTTATGT
1 TTTATGT
42840 TTGAGTTCTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (61 bp):
TTTATGTGAACGAGTTAGCAATAACATTTAATCTTAAAAAATGTTTCAACAAAGTTGGGCA
Found at i:46649 original size:14 final size:14
Alignment explanation
Indices: 46611--46641 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
46601 CCACAACAAT
46611 AGAAGAAAAGAAAA
1 AGAAGAAAAGAAAA
46625 AGAAGAAAAGAAAA
1 AGAAGAAAAGAAAA
46639 AGA
1 AGA
46642 GAAGAAGACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AGAAGAAAAGAAAA
Found at i:48399 original size:32 final size:30
Alignment explanation
Indices: 48335--48391 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
48325 CTAAGTTTTT
*
48335 TTTTTTTTTTTCGCCATCATATAGGTGAAG
1 TTTTTTTTTTTCGCCAACATATAGGTGAAG
*
48365 TTTTTTTTTTTGGCCAACATATAGGTG
1 TTTTTTTTTTTCGCCAACATATAGGTG
48392 CTAAGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.51
Consensus pattern (30 bp):
TTTTTTTTTTTCGCCAACATATAGGTGAAG
Found at i:49507 original size:32 final size:33
Alignment explanation
Indices: 49471--49534 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
49461 ACGATTACAG
* *
49471 CTGCTGCTTTTTTACTTTTG-CCCCATTTTGCA
1 CTGCTGCTTTTTGACTTTCGCCCCCATTTTGCA
49503 CTGCTGCTTTTTGACTTTCGCCCCCATTTTGC
1 CTGCTGCTTTTTGACTTTCGCCCCCATTTTGC
49535 GCCTTAATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.08, C:0.31, G:0.14, T:0.47
Consensus pattern (33 bp):
CTGCTGCTTTTTGACTTTCGCCCCCATTTTGCA
Found at i:51978 original size:24 final size:24
Alignment explanation
Indices: 51944--51995 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
51934 GATAAATAAA
51944 CATGAGCAGAAGAATTTGGAAGAG
1 CATGAGCAGAAGAATTTGGAAGAG
*
51968 CATGAGTAGAAGAATTTGGAAGAG
1 CATGAGCAGAAGAATTTGGAAGAG
51992 CATG
1 CATG
51996 GCCCTGAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.33, T:0.19
Consensus pattern (24 bp):
CATGAGCAGAAGAATTTGGAAGAG
Found at i:56182 original size:12 final size:12
Alignment explanation
Indices: 56165--56189 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56155 GACAGATGAA
56165 CTTTCTTTTTCC
1 CTTTCTTTTTCC
56177 CTTTCTTTTTCC
1 CTTTCTTTTTCC
56189 C
1 C
56190 GTCGGAGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (12 bp):
CTTTCTTTTTCC
Found at i:57308 original size:24 final size:24
Alignment explanation
Indices: 57273--57378 Score: 113
Period size: 24 Copynumber: 4.4 Consensus size: 24
57263 TTAGTTTGGT
* *
57273 GGTGCCGATGCATCACCAGAGGGC
1 GGTGCCGGTGCATCATCAGAGGGC
**
57297 GGTGCCGGTGCATCATTGGAGGGC
1 GGTGCCGGTGCATCATCAGAGGGC
** *
57321 GGTGCCGGTGCATCATCAGCTGGT
1 GGTGCCGGTGCATCATCAGAGGGC
* * * *
57345 GGTGCCGGTGTAGCATCAGATGGT
1 GGTGCCGGTGCATCATCAGAGGGC
57369 GGTGCCGGTG
1 GGTGCCGGTG
57379 TAGCATCGGA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.14, C:0.23, G:0.42, T:0.21
Consensus pattern (24 bp):
GGTGCCGGTGCATCATCAGAGGGC
Found at i:57379 original size:24 final size:24
Alignment explanation
Indices: 57321--57390 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
57311 ATTGGAGGGC
* * *
57321 GGTGCCGGTGCATCATCAGCTGGT
1 GGTGCCGGTGTAGCATCAGATGGT
57345 GGTGCCGGTGTAGCATCAGATGGT
1 GGTGCCGGTGTAGCATCAGATGGT
*
57369 GGTGCCGGTGTAGCATCGGATG
1 GGTGCCGGTGTAGCATCAGATG
57391 AACAATGGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.14, C:0.20, G:0.41, T:0.24
Consensus pattern (24 bp):
GGTGCCGGTGTAGCATCAGATGGT
Found at i:58583 original size:33 final size:33
Alignment explanation
Indices: 58539--58602 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
58529 TCACCAAAGA
58539 TTCTCCCTCATTTGTCTCGCAACATCAACTATC
1 TTCTCCCTCATTTGTCTCGCAACATCAACTATC
*
58572 TTCTCCTTCATTTGTCTCGCAACATCAACTA
1 TTCTCCCTCATTTGTCTCGCAACATCAACTA
58603 AATCTCAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.34, G:0.06, T:0.38
Consensus pattern (33 bp):
TTCTCCCTCATTTGTCTCGCAACATCAACTATC
Found at i:58930 original size:76 final size:77
Alignment explanation
Indices: 58759--58941 Score: 314
Period size: 76 Copynumber: 2.4 Consensus size: 77
58749 CATTACAGAT
* * *
58759 ATAATGATATTATTTATAATCCTTTTCAAAGGTATAAACATCTTTCACAAAAAAAAAAAAAGTAT
1 ATAATGATCTTGTTTATAACCCTTTTCAAAGGTATAAACATCTTTCACAAAAAAAAAAAAAGTAT
58824 AAACATCTTCCA
66 AAACATCTTCCA
* *
58836 ATAATGATCTTGTTTATAACCCTTTTCAAAGGTATAAACATCTTTCAC-CAAAAAAAAAAGGTAT
1 ATAATGATCTTGTTTATAACCCTTTTCAAAGGTATAAACATCTTTCACAAAAAAAAAAAAAGTAT
58900 AAACATCTTCCA
66 AAACATCTTCCA
58912 ATAATGATCTTGTTTATAACCCTTTTCAAA
1 ATAATGATCTTGTTTATAACCCTTTTCAAA
58942 ACGGATCGAC
Statistics
Matches: 101, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
76 56 0.55
77 45 0.45
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (77 bp):
ATAATGATCTTGTTTATAACCCTTTTCAAAGGTATAAACATCTTTCACAAAAAAAAAAAAAGTAT
AAACATCTTCCA
Done.