Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013244.1 Corchorus olitorius cultivar O-4 contig13277, 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: 59731
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:6630 original size:1 final size:1
Alignment explanation
Indices: 6624--6653 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
6614 GTTAGTTAGG
6624 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6654 CAATTCTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9659 original size:6 final size:6
Alignment explanation
Indices: 9591--9658 Score: 127
Period size: 6 Copynumber: 11.3 Consensus size: 6
9581 CAAGGATAGA
9591 GACAGG GACAGG GACAGG GACAGG GACAGG GACAGG GACAGG GACAGG
1 GACAGG GACAGG GACAGG GACAGG GACAGG GACAGG GACAGG GACAGG
*
9639 GACAGG GACAGG GATAGG GA
1 GACAGG GACAGG GACAGG GA
9659 TCGTTATCGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.34, C:0.15, G:0.50, T:0.01
Consensus pattern (6 bp):
GACAGG
Found at i:13911 original size:1 final size:1
Alignment explanation
Indices: 13905--13935 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
13895 TGTTTACCAG
13905 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13936 CAGCATACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16043 original size:18 final size:20
Alignment explanation
Indices: 16020--16063 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
16010 GAAAATAAAT
16020 AAAAAAG-GTTTAAA-GAAA
1 AAAAAAGTGTTTAAATGAAA
*
16038 AAAAAAGTTTTTAAATGAAA
1 AAAAAAGTGTTTAAATGAAA
16058 AAAAAA
1 AAAAAA
16064 ATCGGAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 6 0.26
20 10 0.43
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.20
Consensus pattern (20 bp):
AAAAAAGTGTTTAAATGAAA
Found at i:17262 original size:14 final size:14
Alignment explanation
Indices: 17243--17275 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
17233 AATGGCTTTT
17243 TTTAAAAAAAAAAA
1 TTTAAAAAAAAAAA
*
17257 TTTAAAGAAAAAAA
1 TTTAAAAAAAAAAA
17271 TTTAA
1 TTTAA
17276 TAATTGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
TTTAAAAAAAAAAA
Found at i:17407 original size:23 final size:23
Alignment explanation
Indices: 17374--17420 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
17364 GTAAGGTTTG
*
17374 ATCCTACAATGACACAACACGAT
1 ATCCTAAAATGACACAACACGAT
17397 ATCCTAAAATGACACAACACGAT
1 ATCCTAAAATGACACAACACGAT
17420 A
1 A
17421 ACGTTTGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.28, G:0.09, T:0.17
Consensus pattern (23 bp):
ATCCTAAAATGACACAACACGAT
Found at i:21164 original size:13 final size:12
Alignment explanation
Indices: 21132--21165 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
21122 AGGATCAAGC
21132 AAAAAAAA-AAA
1 AAAAAAAAGAAA
21143 AAAAAAAAGAAA
1 AAAAAAAAGAAA
21155 AAAACAAAAGA
1 AAAA-AAAAGA
21166 TGTATTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.38
12 7 0.33
13 6 0.29
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:23703 original size:73 final size:73
Alignment explanation
Indices: 23584--23730 Score: 267
Period size: 73 Copynumber: 2.0 Consensus size: 73
23574 ATGTGCTTTG
* * *
23584 CAAACTAAATTCATTTGAGAAATCAACAGCATATGAACATATTGTGTAGTACATGCAGTTTACAC
1 CAAACTAAATTCATTTCAGAAATCAACAGCATATGAACAAATTGTGTAGCACATGCAGTTTACAC
23649 CTTAAACA
66 CTTAAACA
23657 CAAACTAAATTCATTTCAGAAATCAACAGCATATGAACAAATTGTGTAGCACATGCAGTTTACAC
1 CAAACTAAATTCATTTCAGAAATCAACAGCATATGAACAAATTGTGTAGCACATGCAGTTTACAC
23722 CTTAAACA
66 CTTAAACA
23730 C
1 C
23731 TACTTAAGAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (73 bp):
CAAACTAAATTCATTTCAGAAATCAACAGCATATGAACAAATTGTGTAGCACATGCAGTTTACAC
CTTAAACA
Found at i:24678 original size:1 final size:1
Alignment explanation
Indices: 24672--24703 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
24662 GCTGTTTGAA
24672 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
24704 AAAAAAAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:33169 original size:1 final size:1
Alignment explanation
Indices: 33163--33193 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
33153 CAAATTTCGG
33163 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33194 CCCGCATGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:33266 original size:3 final size:3
Alignment explanation
Indices: 33258--33283 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33248 TATAACATAT
33258 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
33284 CAAGAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:33387 original size:27 final size:25
Alignment explanation
Indices: 33352--33414 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
33342 AGAACATTAA
*
33352 GAAAATATAATTTTCATTCATAAAAAT
1 GAAATTATAATTTTC-TTCAT-AAAAT
* *
33379 GAAATTATATCTTTTCTTCATAACAT
1 GAAATTATA-ATTTTCTTCATAAAAT
33405 -AAATTATAAT
1 GAAATTATAAT
33415 AGATTGAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 1 0.03
25 8 0.26
26 4 0.13
27 13 0.42
28 5 0.16
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (25 bp):
GAAATTATAATTTTCTTCATAAAAT
Found at i:37184 original size:21 final size:21
Alignment explanation
Indices: 37160--37223 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
37150 CTAAAAACAG
* *
37160 GACAAGTCCTATCAAGGACTT
1 GACAACTCCTACCAAGGACTT
* *
37181 GACAACTCCTGCCCAGGACTT
1 GACAACTCCTACCAAGGACTT
* *
37202 GACAACTCCTGCCCAGGACTT
1 GACAACTCCTACCAAGGACTT
37223 G
1 G
37224 GTCTGTTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (21 bp):
GACAACTCCTACCAAGGACTT
Found at i:37280 original size:21 final size:21
Alignment explanation
Indices: 37254--37315 Score: 115
Period size: 21 Copynumber: 3.0 Consensus size: 21
37244 AAAATCAGAG
37254 CAACTCCTGCCCAGGACTTGA
1 CAACTCCTGCCCAGGACTTGA
*
37275 CAACTCCTGCCCAAGACTTGA
1 CAACTCCTGCCCAGGACTTGA
37296 CAACTCCTGCCCAGGACTTG
1 CAACTCCTGCCCAGGACTTG
37316 GTCTGTTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.24, C:0.39, G:0.18, T:0.19
Consensus pattern (21 bp):
CAACTCCTGCCCAGGACTTGA
Found at i:37332 original size:92 final size:91
Alignment explanation
Indices: 37174--37386 Score: 354
Period size: 92 Copynumber: 2.3 Consensus size: 91
37164 AGTCCTATCA
*
37174 AGGACTTGACAACTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACG
1 AGGACTTGACAACTCCTGCCCAAGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACG
*
37239 GAAGAAAAATCAGAGCAACTCCTGCCC
66 GAAG-AAAATCAGAACAACTCCTGCCC
*
37266 AGGACTTGACAACTCCTGCCCAAGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAATACG
1 AGGACTTGACAACTCCTGCCCAAGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACG
* * *
37331 GAAGAAATTCAGAACAAGTCCTGTCC
66 GAAGAAAATCAGAACAACTCCTGCCC
37357 AGGACTTGGACAACTCCTGCCCAAGACTTG
1 AGGACTT-GACAACTCCTGCCCAAGACTTG
37387 TTGCGGGAAA
Statistics
Matches: 114, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
91 25 0.22
92 89 0.78
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (91 bp):
AGGACTTGACAACTCCTGCCCAAGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACG
GAAGAAAATCAGAACAACTCCTGCCC
Found at i:37374 original size:22 final size:22
Alignment explanation
Indices: 37344--37386 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
37334 GAAATTCAGA
* * *
37344 ACAAGTCCTGTCCAGGACTTGG
1 ACAACTCCTGCCCAAGACTTGG
37366 ACAACTCCTGCCCAAGACTTG
1 ACAACTCCTGCCCAAGACTTG
37387 TTGCGGGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCCAAGACTTGG
Found at i:41424 original size:18 final size:19
Alignment explanation
Indices: 41401--41440 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
41391 TTCTTGAGAT
41401 AATTCTTCA-ATGATCTTC
1 AATTCTTCACATGATCTTC
*
41419 AATTCTTCACATTATCTTC
1 AATTCTTCACATGATCTTC
41438 AAT
1 AAT
41441 AAGTCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCACATGATCTTC
Found at i:43073 original size:11 final size:11
Alignment explanation
Indices: 43057--43081 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43047 AAGCCCCCTT
43057 GTCATCTTCAA
1 GTCATCTTCAA
43068 GTCATCTTCAA
1 GTCATCTTCAA
43079 GTC
1 GTC
43082 CATGATAAGT
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:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (11 bp):
GTCATCTTCAA
Found at i:43175 original size:18 final size:19
Alignment explanation
Indices: 43141--43178 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
43131 ATCAATCGTT
*
43141 ATCTCCATGGTCTCCATGC
1 ATCTCCATGGCCTCCATGC
43160 ATCTCCAT-GCCTCCATGC
1 ATCTCCATGGCCTCCATGC
43178 A
1 A
43179 ACCCATGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29
Consensus pattern (19 bp):
ATCTCCATGGCCTCCATGC
Found at i:44067 original size:14 final size:14
Alignment explanation
Indices: 44048--44074 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44038 TGCAAAAGTC
44048 AATTTTTTTTTTCG
1 AATTTTTTTTTTCG
44062 AATTTTTTTTTTC
1 AATTTTTTTTTTC
44075 AAAATTTGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (14 bp):
AATTTTTTTTTTCG
Found at i:47704 original size:6 final size:6
Alignment explanation
Indices: 47693--47717 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
47683 CAAATCAAAT
47693 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
47718 TCAAACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:50167 original size:22 final size:21
Alignment explanation
Indices: 50115--50168 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
50105 TGCTTCTTGT
50115 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
50136 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
50155 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
50169 CACAAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:53342 original size:6 final size:6
Alignment explanation
Indices: 53331--53371 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
53321 CAAATCAAAT
*
53331 AGAAAA AGAAAA AGAAAA AGAAAA AG-AAA AGAAAA ATAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
53372 CATAATCTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:53354 original size:11 final size:11
Alignment explanation
Indices: 53334--53371 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
53324 ATCAAATAGA
53334 AAAAGAAAAAG
1 AAAAGAAAAAG
53345 AAAAAGAAAAAG
1 -AAAAGAAAAAG
*
53357 AAAAGAAAAAT
1 AAAAGAAAAAG
53368 AAAA
1 AAAA
53372 CATAATCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:53354 original size:18 final size:17
Alignment explanation
Indices: 53331--53371 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
53321 CAAATCAAAT
53331 AGAAAAAGAAAAAGAAAA
1 AGAAAAAG-AAAAGAAAA
53349 AGAAAAAGAAAAGAAAA
1 AGAAAAAGAAAAGAAAA
*
53366 ATAAAA
1 AGAAAA
53372 CATAATCTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (17 bp):
AGAAAAAGAAAAGAAAA
Found at i:54938 original size:19 final size:18
Alignment explanation
Indices: 54905--54940 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
54895 TTGAGATAAT
54905 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
54923 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
54941 TATGTCTTCA
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:57997 original size:16 final size:17
Alignment explanation
Indices: 57955--57997 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
57945 TCTCTTTTAA
57955 TTTTCTGATTTTTGACT
1 TTTTCTGATTTTTGACT
57972 TTTT-TGATTTTT-ACCT
1 TTTTCTGATTTTTGA-CT
57988 TTTTCT-ATTT
1 TTTTCTGATTT
57998 CTAAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.04
16 18 0.75
17 5 0.21
ACGTcount: A:0.12, C:0.12, G:0.07, T:0.70
Consensus pattern (17 bp):
TTTTCTGATTTTTGACT
Done.