Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012997.1 Corchorus capsularis cultivar CVL-1 contig13018, 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: 76132
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:9336 original size:12 final size:13
Alignment explanation
Indices: 9314--9344 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
9304 TTAATACAGG
9314 TATCGAACGGATA
1 TATCGAACGGATA
9327 TATC-AACGGATA
1 TATCGAACGGATA
9339 TATCGA
1 TATCGA
9345 GGTATCGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (13 bp):
TATCGAACGGATA
Found at i:10417 original size:3 final size:3
Alignment explanation
Indices: 10409--10438 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
10399 TCATTTCCCC
10409 CAT CAT CAT CAT CAT CAT CAT CAT CA- CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
10439 TTCCGTGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
CAT
Found at i:18924 original size:14 final size:14
Alignment explanation
Indices: 18905--18935 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
18895 TTCACTAAAT
18905 TCATATTTTCACCC
1 TCATATTTTCACCC
18919 TCATATTTTCACCC
1 TCATATTTTCACCC
18933 TCA
1 TCA
18936 ATCTTAATTA
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:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (14 bp):
TCATATTTTCACCC
Found at i:19045 original size:8 final size:7
Alignment explanation
Indices: 19029--19058 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
19019 ATCAGTTCAA
*
19029 GGGTTTG
1 GGGTTTT
19036 GGGTTTT
1 GGGTTTT
19043 GGGTTTT
1 GGGTTTT
19050 GGGTTTT
1 GGGTTTT
19057 GG
1 GG
19059 CTATGGTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (7 bp):
GGGTTTT
Found at i:24358 original size:161 final size:161
Alignment explanation
Indices: 24093--24416 Score: 648
Period size: 161 Copynumber: 2.0 Consensus size: 161
24083 TAAAATTAAG
24093 AATACAGCAAATAGTAATCATTTTTTAGATGTACCCTTCTTTAAAAGAGAGAATGAGATGAATAT
1 AATACAGCAAATAGTAATCATTTTTTAGATGTACCCTTCTTTAAAAGAGAGAATGAGATGAATAT
24158 TTAAGTAAAGTGAAAAATATGAGCGAAAGATTAAGGTTAATTGTTCATTTGAAGACTTAACGTTT
66 TTAAGTAAAGTGAAAAATATGAGCGAAAGATTAAGGTTAATTGTTCATTTGAAGACTTAACGTTT
24223 GCAAAAATGTTAAATCTATGGCCTATTGTTC
131 GCAAAAATGTTAAATCTATGGCCTATTGTTC
24254 AATACAGCAAATAGTAATCATTTTTTAGATGTACCCTTCTTTAAAAGAGAGAATGAGATGAATAT
1 AATACAGCAAATAGTAATCATTTTTTAGATGTACCCTTCTTTAAAAGAGAGAATGAGATGAATAT
24319 TTAAGTAAAGTGAAAAATATGAGCGAAAGATTAAGGTTAATTGTTCATTTGAAGACTTAACGTTT
66 TTAAGTAAAGTGAAAAATATGAGCGAAAGATTAAGGTTAATTGTTCATTTGAAGACTTAACGTTT
24384 GCAAAAATGTTAAATCTATGGCCTATTGTTC
131 GCAAAAATGTTAAATCTATGGCCTATTGTTC
24415 AA
1 AA
24417 AAAAGCTCAA
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
161 163 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (161 bp):
AATACAGCAAATAGTAATCATTTTTTAGATGTACCCTTCTTTAAAAGAGAGAATGAGATGAATAT
TTAAGTAAAGTGAAAAATATGAGCGAAAGATTAAGGTTAATTGTTCATTTGAAGACTTAACGTTT
GCAAAAATGTTAAATCTATGGCCTATTGTTC
Found at i:27609 original size:55 final size:56
Alignment explanation
Indices: 27524--27639 Score: 207
Period size: 55 Copynumber: 2.1 Consensus size: 56
27514 GAAGTAGACA
*
27524 GGCCCGGTTCTTCTCCCAACAAGTGGTATCAGAGCCTGGTTAGACTCGACCGGTGT
1 GGCCCGGTTCCTCTCCCAACAAGTGGTATCAGAGCCTGGTTAGACTCGACCGGTGT
*
27580 GGCCCGGTTCCTCT-CCAACAAGTGGTATCAGAGCCTGGTTAGACTCGATCGGTGT
1 GGCCCGGTTCCTCTCCCAACAAGTGGTATCAGAGCCTGGTTAGACTCGACCGGTGT
27635 GGCCC
1 GGCCC
27640 ATGAGCACAG
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
55 45 0.78
56 13 0.22
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.24
Consensus pattern (56 bp):
GGCCCGGTTCCTCTCCCAACAAGTGGTATCAGAGCCTGGTTAGACTCGACCGGTGT
Found at i:28867 original size:27 final size:28
Alignment explanation
Indices: 28812--28875 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
28802 GTGACAAACG
* * * *
28812 AATGATTAAAAACTTGAAAG-CAATTTT
1 AATGAATAAAAACTTGAAAGAAAAATTA
28839 AATGGAATAAAAA-TTGAAAGAAAAATTA
1 AAT-GAATAAAAACTTGAAAGAAAAATTA
28867 AATGAATAA
1 AATGAATAA
28876 GAATAAATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.58, C:0.03, G:0.12, T:0.27
Consensus pattern (28 bp):
AATGAATAAAAACTTGAAAGAAAAATTA
Found at i:29221 original size:13 final size:13
Alignment explanation
Indices: 29205--29229 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29195 TAACCATTCC
29205 CTTTAGATTTTAT
1 CTTTAGATTTTAT
29218 CTTTAGATTTTA
1 CTTTAGATTTTA
29230 ATCATCAATA
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:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (13 bp):
CTTTAGATTTTAT
Found at i:33006 original size:60 final size:60
Alignment explanation
Indices: 32932--33058 Score: 182
Period size: 60 Copynumber: 2.1 Consensus size: 60
32922 CTAATTGCTT
* * * * * *
32932 AAATAAGGATCTAATGTTTGCCAAAATGCTCATATAAGGGTCTGATCTTTTAATTTGTCA
1 AAATAAGAACCTAATGTTTGCCAAAATGCTCAAATAAGGATCCGATCTTTTAATTTGACA
* *
32992 AAATAAGAACCTAATGTTTGCCAAAATTCTCAAATAAGGATCCGATCTTTTAATTTGACC
1 AAATAAGAACCTAATGTTTGCCAAAATGCTCAAATAAGGATCCGATCTTTTAATTTGACA
33052 AAATAAG
1 AAATAAG
33059 GGCTCAACAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (60 bp):
AAATAAGAACCTAATGTTTGCCAAAATGCTCAAATAAGGATCCGATCTTTTAATTTGACA
Found at i:35686 original size:32 final size:32
Alignment explanation
Indices: 35641--35731 Score: 137
Period size: 32 Copynumber: 2.8 Consensus size: 32
35631 CATATATGAG
*
35641 ATTTAAAAAGGTGGGAACACCATTAATCATGC
1 ATTTAAAATGGTGGGAACACCATTAATCATGC
* *
35673 ATTTAAAATGGTGGAAATACCATTAATCATGC
1 ATTTAAAATGGTGGGAACACCATTAATCATGC
* *
35705 ATTTAAATTGATGGGAACACCATTAAT
1 ATTTAAAATGGTGGGAACACCATTAAT
35732 TGAAGTTAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (32 bp):
ATTTAAAATGGTGGGAACACCATTAATCATGC
Found at i:36302 original size:16 final size:16
Alignment explanation
Indices: 36281--36314 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
36271 ATTATTAATG
36281 AACTTAATTTAACATT
1 AACTTAATTTAACATT
36297 AACTTAATTTAACATT
1 AACTTAATTTAACATT
36313 AA
1 AA
36315 GAGCACATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
AACTTAATTTAACATT
Found at i:38027 original size:11 final size:11
Alignment explanation
Indices: 38011--38053 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
38001 TATACTATAT
38011 CTAATTAATAG
1 CTAATTAATAG
*
38022 CTAATTAATAT
1 CTAATTAATAG
38033 CTAATTAATAG
1 CTAATTAATAG
*
38044 TTAATTAATA
1 CTAATTAATA
38054 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:38032 original size:22 final size:22
Alignment explanation
Indices: 38007--38053 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
37997 CCATTATACT
38007 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
38029 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
38051 ATA
1 ATA
38054 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:39985 original size:1 final size:1
Alignment explanation
Indices: 39979--40003 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
39969 GTGTGTGTGG
39979 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
40004 CAGCAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:57281 original size:59 final size:60
Alignment explanation
Indices: 57144--57299 Score: 190
Period size: 59 Copynumber: 2.6 Consensus size: 60
57134 CTAATTGCTG
* ** ** * *
57144 AAATAAGGGCCTAACGTTTTACAAAATACTCAAATAAGGGCATGATCTTTTAATTTGGCC
1 AAATAAGGGCTTAACGTTTGCCAAAATACTCAAATAAGGGCACCATCTTTGAATTTAGCC
* * * *
57204 AAATAAGAG-TCTAACGTTTGCCAAAATGCTCAAATAAGGGC-CCCTCTTTGAATTTAGCT
1 AAATAAGGGCT-TAACGTTTGCCAAAATACTCAAATAAGGGCACCATCTTTGAATTTAGCC
57263 AAATAAGGGCTTAACGTTTGCCAAAATACTCAAATAA
1 AAATAAGGGCTTAACGTTTGCCAAAATACTCAAATAA
57300 ATGTCTGTCT
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
59 45 0.56
60 36 0.44
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (60 bp):
AAATAAGGGCTTAACGTTTGCCAAAATACTCAAATAAGGGCACCATCTTTGAATTTAGCC
Found at i:64261 original size:24 final size:25
Alignment explanation
Indices: 64228--64278 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
64218 TTACCATTTT
64228 TTTACTTTATTCATTAAATTCTTAA
1 TTTACTTTATTCATTAAATTCTTAA
** *
64253 TTTA-TTTATTTTTTAAATTTTTAA
1 TTTACTTTATTCATTAAATTCTTAA
64277 TT
1 TT
64279 GTACACGTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTACTTTATTCATTAAATTCTTAA
Found at i:64383 original size:31 final size:29
Alignment explanation
Indices: 64348--64413 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
64338 CGTCCAAAAT
64348 TATCC-TTATTTGACCTTTCTGGGTAACGTTA
1 TATCCTTTA-TTGACCTTT-T-GGTAACGTTA
* *
64379 TATCCTTTATTGACGTTTTTGTAACGTTA
1 TATCCTTTATTGACCTTTTGGTAACGTTA
64408 TATCCT
1 TATCCT
64414 GAATTGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 15 0.47
30 1 0.03
31 13 0.41
32 3 0.09
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (29 bp):
TATCCTTTATTGACCTTTTGGTAACGTTA
Found at i:64419 original size:29 final size:28
Alignment explanation
Indices: 64370--64459 Score: 83
Period size: 31 Copynumber: 3.0 Consensus size: 28
64360 ACCTTTCTGG
**
64370 GTAACGTTATATCCTTTATTGACGTTTTT-
1 GTAACGTTATATCCTGAATTGA--TTTTTA
64399 GTAACGTTATATCCTGAATTGATTTTTCA
1 GTAACGTTATATCCTGAATTGATTTTT-A
* *
64428 GGCAAACGTTATATCCTGAATTGGTTATTTA
1 -G-TAACGTTATATCCTGAATTGATT-TTTA
64459 G
1 G
64460 CCTATATAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
27 5 0.10
29 20 0.38
30 2 0.04
31 22 0.42
32 3 0.06
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (28 bp):
GTAACGTTATATCCTGAATTGATTTTTA
Found at i:64726 original size:16 final size:17
Alignment explanation
Indices: 64705--64739 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
64695 GTTAATTTGG
64705 TTTTTTG-TTTTTGTTT
1 TTTTTTGTTTTTTGTTT
64721 TTTTTTGTTTTTTGTTT
1 TTTTTTGTTTTTTGTTT
64738 TT
1 TT
64740 GCAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (17 bp):
TTTTTTGTTTTTTGTTT
Found at i:65439 original size:31 final size:31
Alignment explanation
Indices: 65400--65566 Score: 190
Period size: 31 Copynumber: 5.4 Consensus size: 31
65390 TCCTTTTATG
**
65400 CACGTGGCATGCCACGTGTCACTTTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * **
65431 CATGTGGCATGACACGTGTCACTTTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * * *
65462 CAGGTGGCGTGACATGTGTCACTTTTTTGGTA
1 CACGTGGCATGCCACGTGTCAC-TTTTTGGTA
* * *
65494 CACGTAGCGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* *
65525 CACGTGGCGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
65556 CACGTGGCATG
1 CACGTGGCATG
65567 TCATGTCGGA
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
31 97 0.80
32 24 0.20
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.32
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:65563 original size:94 final size:94
Alignment explanation
Indices: 65400--65572 Score: 220
Period size: 94 Copynumber: 1.8 Consensus size: 94
65390 TCCTTTTATG
* * * * *
65400 CACGTGGCATGCCACGTGTCACTTTTTGAAACATGTGGCATGACACGTGTCACTTTTTGAAACAG
1 CACGTAGCATGCCACATGTCACTTTTTGAAACACGTGGCATGACACATGTCACTTTTTGAAACAC
*
65465 GTGGCGTGACATGTGTCACTTTTTTGGTA
66 GTGGCATGACATGTGTCACTTTTTTGGTA
* ** * * **
65494 CACGTAGCGTGCCACATGTCACTTTTTGGTACACGTGGCGTGCCACATGTCACTTTTTGGTACAC
1 CACGTAGCATGCCACATGTCACTTTTTGAAACACGTGGCATGACACATGTCACTTTTTGAAACAC
*
65559 GTGGCATGTCATGT
66 GTGGCATGACATGT
65573 CGGACACCGT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
94 65 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (94 bp):
CACGTAGCATGCCACATGTCACTTTTTGAAACACGTGGCATGACACATGTCACTTTTTGAAACAC
GTGGCATGACATGTGTCACTTTTTTGGTA
Found at i:68775 original size:2 final size:2
Alignment explanation
Indices: 68768--68803 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
68758 AGGATTTAAA
68768 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
68804 CTCTAAACAA
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:72479 original size:33 final size:33
Alignment explanation
Indices: 72437--72538 Score: 113
Period size: 33 Copynumber: 3.1 Consensus size: 33
72427 TTTTACACTG
* *
72437 AGCCTCCCCACTA-GGACGGTTCAGCCACGGCGA
1 AGCCTCCCCACTAGGGA-GGCTCAACCACGGCGA
*
72470 AGCCTCCCCACTAGGGAGGCTCAACCACGGCGG
1 AGCCTCCCCACTAGGGAGGCTCAACCACGGCGA
*
72503 AGCCTCCCCACTGGGGCA-GCTTC-ACCACGGC-A
1 AGCCTCCCCACTAGGG-AGGC-TCAACCACGGCGA
72535 AGCC
1 AGCC
72539 GCCCTCATGG
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
32 4 0.07
33 51 0.84
34 6 0.10
ACGTcount: A:0.21, C:0.41, G:0.27, T:0.11
Consensus pattern (33 bp):
AGCCTCCCCACTAGGGAGGCTCAACCACGGCGA
Found at i:72557 original size:32 final size:32
Alignment explanation
Indices: 72514--72619 Score: 142
Period size: 32 Copynumber: 3.3 Consensus size: 32
72504 GCCTCCCCAC
* *
72514 TGGGGCAGCTTCACCACGGCAAGCCGCCCTCA
1 TGGGGCGGCTTCACCACGGCAGGCCGCCCTCA
*
72546 TGGGGCGGCTTCACCACGGCAGGCCGCCCTTA
1 TGGGGCGGCTTCACCACGGCAGGCCGCCCTCA
** *
72578 TGGGGCGGCTTTGCCACGGCAGGCCGCCC-CGG
1 TGGGGCGGCTTCACCACGGCAGGCCGCCCTC-A
72610 TGGGGCGGCT
1 TGGGGCGGCT
72620 AGACCAAACT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.11, C:0.37, G:0.38, T:0.14
Consensus pattern (32 bp):
TGGGGCGGCTTCACCACGGCAGGCCGCCCTCA
Done.