Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019287.1 Corchorus olitorius cultivar O-4 contig19320, 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: 70484
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:3076 original size:21 final size:21
Alignment explanation
Indices: 3051--3104 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
3041 CGGCCATTCA
*
3051 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCTAAGC
*
3072 CCGTGCCACCACCGGCTATGC
1 CCGTGCCACCACCGGCTAAGC
3093 CCGTGCCACCAC
1 CCGTGCCACCAC
3105 AATTCAGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.48, G:0.22, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGGCTAAGC
Found at i:3480 original size:15 final size:14
Alignment explanation
Indices: 3460--3489 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3450 ATCTTTTTAA
3460 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
3475 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
3489 T
1 T
3490 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:6378 original size:15 final size:15
Alignment explanation
Indices: 6348--6389 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
6338 TTACTCTGCT
6348 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
6364 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
6379 TTGCTTTCTGT
1 TTGTTTTCTGT
6390 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:13406 original size:25 final size:25
Alignment explanation
Indices: 13372--13445 Score: 121
Period size: 25 Copynumber: 3.0 Consensus size: 25
13362 TGTTGGTTTG
*
13372 TAGATACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
13397 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
**
13422 TAGAGATAGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
13446 GATTATTGGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.36, C:0.18, G:0.31, T:0.15
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:14349 original size:25 final size:25
Alignment explanation
Indices: 14315--14388 Score: 148
Period size: 25 Copynumber: 3.0 Consensus size: 25
14305 TGTTGGTTTG
14315 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
14340 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
14365 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
14389 GATTGTTAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.32, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:15321 original size:30 final size:30
Alignment explanation
Indices: 15285--15384 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
15275 TACAAACTCA
15285 GGGGGCAAAGTGGCATAATTTAAAGTTTTT
1 GGGGGCAAAGTGGCATAATTTAAAGTTTTT
** * **
15315 GGGGGCAACCTGATC-TAAATTTGCAAAG-TTCA
1 GGGGGCAAAGTG-GCAT-AATTT--AAAGTTTTT
*
15347 GGGGGCCAAGTGGCATAATTTAAAGTTTTT
1 GGGGGCAAAGTGGCATAATTTAAAGTTTTT
15377 GGGGGCAA
1 GGGGGCAA
15385 CCTGACCTAA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
29 4 0.08
30 20 0.38
31 12 0.23
32 12 0.23
33 4 0.08
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.28
Consensus pattern (30 bp):
GGGGGCAAAGTGGCATAATTTAAAGTTTTT
Found at i:15352 original size:32 final size:32
Alignment explanation
Indices: 15315--15416 Score: 104
Period size: 32 Copynumber: 3.2 Consensus size: 32
15305 TAAAGTTTTT
*
15315 GGGGGCAACCTGATCTAAATTTGCAAAGTTCA
1 GGGGGCAACCTGACCTAAATTTGCAAAGTTCA
* * * **
15347 GGGGGCCAA-GTGGCAT-AATTT--AAAGTTTTT
1 GGGGG-CAACCTGACCTAAATTTGCAAAG-TTCA
15377 GGGGGCAACCTGACCTAAATTTGCAAAGTTCA
1 GGGGGCAACCTGACCTAAATTTGCAAAGTTCA
15409 GGGGGCAA
1 GGGGGCAA
15417 AAGGACTATT
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
29 7 0.13
30 11 0.21
31 10 0.19
32 18 0.34
33 7 0.13
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (32 bp):
GGGGGCAACCTGACCTAAATTTGCAAAGTTCA
Found at i:15359 original size:62 final size:62
Alignment explanation
Indices: 15282--15417 Score: 254
Period size: 62 Copynumber: 2.2 Consensus size: 62
15272 TTTTACAAAC
*
15282 TCAGGGGGCAAAGTGGCATAATTTAAAGTTTTTGGGGGCAACCTGATCTAAATTTGCAAAGT
1 TCAGGGGGCAAAGTGGCATAATTTAAAGTTTTTGGGGGCAACCTGACCTAAATTTGCAAAGT
*
15344 TCAGGGGGCCAAGTGGCATAATTTAAAGTTTTTGGGGGCAACCTGACCTAAATTTGCAAAGT
1 TCAGGGGGCAAAGTGGCATAATTTAAAGTTTTTGGGGGCAACCTGACCTAAATTTGCAAAGT
15406 TCAGGGGGCAAA
1 TCAGGGGGCAAA
15418 AGGACTATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (62 bp):
TCAGGGGGCAAAGTGGCATAATTTAAAGTTTTTGGGGGCAACCTGACCTAAATTTGCAAAGT
Found at i:15405 original size:33 final size:33
Alignment explanation
Indices: 15306--15406 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
15296 GGCATAATTT
*
15306 AAAGTTTTTGGGGGCAACCTGATCTAAATTTGC
1 AAAGTTTTTGGGGGCAACCTGACCTAAATTTGC
** * * *
15339 AAAG-TTCAGGGGGCCAA-GTGGCAT-AATTT--
1 AAAGTTTTTGGGGG-CAACCTGACCTAAATTTGC
15368 AAAGTTTTTGGGGGCAACCTGACCTAAATTTGC
1 AAAGTTTTTGGGGGCAACCTGACCTAAATTTGC
15401 AAAGTT
1 AAAGTT
15407 CAGGGGGCAA
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
29 7 0.14
30 11 0.22
31 10 0.20
32 10 0.20
33 13 0.25
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (33 bp):
AAAGTTTTTGGGGGCAACCTGACCTAAATTTGC
Found at i:17144 original size:16 final size:17
Alignment explanation
Indices: 17112--17153 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
17102 TGAGGTCAAA
*
17112 CCTAAACCC-GCCTGAC
1 CCTAAACCCAGCCAGAC
17128 CCTAAACCCAG-CAGAC
1 CCTAAACCCAGCCAGAC
*
17144 CCTAGACCCA
1 CCTAAACCCA
17154 AATGACCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 22 0.96
17 1 0.04
ACGTcount: A:0.31, C:0.48, G:0.12, T:0.10
Consensus pattern (17 bp):
CCTAAACCCAGCCAGAC
Found at i:18972 original size:18 final size:18
Alignment explanation
Indices: 18946--18981 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18936 CAGATAAACT
*
18946 ATCTCCTTGGTTTTGTGA
1 ATCTCCTTGGTTTGGTGA
*
18964 ATCTTCTTGGTTTGGTGA
1 ATCTCCTTGGTTTGGTGA
18982 GGAGTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.50
Consensus pattern (18 bp):
ATCTCCTTGGTTTGGTGA
Found at i:19346 original size:27 final size:30
Alignment explanation
Indices: 19185--19384 Score: 272
Period size: 30 Copynumber: 6.9 Consensus size: 30
19175 AATCTCCAAA
* *
19185 TGACACCAGAAGTTGTCATGATCTTGCAAA
1 TGACACCAGAAGTTGTCATGATCTTACAAT
19215 TGACACCAGAAGTTGTCATGATCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
19245 TGACACCAGAAGTTGTCATGATCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* *
19275 TGACACCAGAAGTTGTCAAGGGTCTTACAAT
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
*
19306 TG--ACCAGAAGTTGTCAT-A-ATTA-AAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
*
19331 TGACACCAGAAGTTGTCAT-A-ATT-CAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
*
19358 TGACACCAGAAGTTGTCATGATTTTAC
1 TGACACCAGAAGTTGTCATGATCTTAC
19385 CTTTCAAATT
Statistics
Matches: 155, Mismatches: 8, Indels: 14
0.88 0.05 0.08
Matches are distributed among these distances:
25 5 0.03
26 3 0.02
27 41 0.26
28 2 0.01
29 15 0.10
30 76 0.49
31 13 0.08
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTACAAT
Found at i:19546 original size:16 final size:16
Alignment explanation
Indices: 19525--19560 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
19515 AAATTCTGTC
*
19525 TAAGGAGTATGGATTT
1 TAAGGAGTATGGACTT
19541 TAAGGAGTATGGACTT
1 TAAGGAGTATGGACTT
19557 TAAG
1 TAAG
19561 TGAGACCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (16 bp):
TAAGGAGTATGGACTT
Found at i:23940 original size:13 final size:15
Alignment explanation
Indices: 23924--23955 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23914 AATATATTTG
23924 AAATAA-TAA-ATAT
1 AAATAAGTAATATAT
23937 AAATAAGTAATATAT
1 AAATAAGTAATATAT
23952 AAAT
1 AAAT
23956 CTAAATGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 3 0.18
15 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAATAAGTAATATAT
Found at i:25713 original size:2 final size:2
Alignment explanation
Indices: 25706--25737 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25696 GAAGAGTGAG
25706 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
25738 GTTGAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26624 original size:7 final size:7
Alignment explanation
Indices: 26612--26637 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
26602 CTATTCCAGG
26612 TTGGTAA
1 TTGGTAA
26619 TTGGTAA
1 TTGGTAA
26626 TTGGTAA
1 TTGGTAA
26633 TTGGT
1 TTGGT
26638 TGGTTTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (7 bp):
TTGGTAA
Found at i:29561 original size:21 final size:21
Alignment explanation
Indices: 29521--29560 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29511 GTGAGTATAA
*
29521 TGGTAGTTTTCTTTTTAAAAT
1 TGGTAGTTTTCTTTTAAAAAT
29542 TGGTAGTTTT-TTTTAAAAA
1 TGGTAGTTTTCTTTTAAAAA
29561 AATATATATA
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:0.28, C:0.03, G:0.15, T:0.55
Consensus pattern (21 bp):
TGGTAGTTTTCTTTTAAAAAT
Found at i:40358 original size:16 final size:16
Alignment explanation
Indices: 40337--40369 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40327 GCGGCAAACA
40337 ATCCTCCCAAGTTCTT
1 ATCCTCCCAAGTTCTT
40353 ATCCTCCCAAGTTCTT
1 ATCCTCCCAAGTTCTT
40369 A
1 A
40370 AGTTCTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATCCTCCCAAGTTCTT
Found at i:57897 original size:19 final size:19
Alignment explanation
Indices: 57875--57916 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
57865 TTATGTGGAA
*
57875 ATAAACATGGATGCAAATG
1 ATAAACATGGATCCAAATG
*
57894 ATAAATATGGATCCAAATG
1 ATAAACATGGATCCAAATG
57913 ATAA
1 ATAA
57917 TTTCTTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.24
Consensus pattern (19 bp):
ATAAACATGGATCCAAATG
Found at i:58306 original size:19 final size:20
Alignment explanation
Indices: 58265--58306 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
58255 ACCCGTACCC
* * *
58265 TTCTTCCTTCTCTTCTTCTT
1 TTCTTCCTTCACTTCTCCAT
58285 TTCTT-CTTCACTTCTCCAT
1 TTCTTCCTTCACTTCTCCAT
58304 TTC
1 TTC
58307 CTTTCTCTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.05, C:0.36, G:0.00, T:0.60
Consensus pattern (20 bp):
TTCTTCCTTCACTTCTCCAT
Found at i:66138 original size:11 final size:11
Alignment explanation
Indices: 66122--66146 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
66112 AACAAAAATC
66122 CTAAAAATGAA
1 CTAAAAATGAA
66133 CTAAAAATGAA
1 CTAAAAATGAA
66144 CTA
1 CTA
66147 TGGATTGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.12, G:0.08, T:0.20
Consensus pattern (11 bp):
CTAAAAATGAA
Done.