Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020680.1 Corchorus olitorius cultivar O-4 contig20713, 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: 20855
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2690 original size:316 final size:316
Alignment explanation
Indices: 2117--2733 Score: 1171
Period size: 316 Copynumber: 2.0 Consensus size: 316
2107 TTCGAATTCG
2117 ACAACTATGACATGTAACAATGTCAGCGTAAAAGCAAATTTACTATTAATAGGCAAATTTACTAT
1 ACAACTATGACATGTAACAATGTCAGCGTAAAAGCAAATTTACTATTAATAGGCAAATTTACTAT
* *
2182 TAAGAGAGTGAAAATTACCGAAATACCCTTAATAGGCACATTTACTATTTTGTCCCGAAAAGCGC
66 TAAGAGAGTGAAAATTACCGAAATACCCTTAATAGGCAAATTTACTATTTTGCCCCGAAAAGCGC
*
2247 GATACAAATAATTAAACTTTAAGATCGTATATTCGGGATTGGAAAGCTACCGTAGAGACCCTTTT
131 GATACAAATAATTAAACTTTAAGATCGTATATTCAGGATTGGAAAGCTACCGTAGAGACCCTTTT
* *
2312 GGGTAAAATTATTGTGCTGCCATCGACCTATCAACATTACCATTATGCCCTTTAGTCATCAAATT
196 GGGTAAAATTACTGTGCTACCATCGACCTATCAACATTACCATTATGCCCTTTAGTCATCAAATT
2377 TACTAAAGTACCCCTAAGGGTGGAAATGAGAGAATTCATTTGTCATAGTAGGGTCA
261 TACTAAAGTACCCCTAAGGGTGGAAATGAGAGAATTCATTTGTCATAGTAGGGTCA
2433 ACAACTATGACATGTAACAATGTCAGCGTAAAAGCAAATTTACTATTAATAGGCAAATTTACTAT
1 ACAACTATGACATGTAACAATGTCAGCGTAAAAGCAAATTTACTATTAATAGGCAAATTTACTAT
*
2498 TAAGAGAGTGAAAATTACCGAAATACCCTTAATAGGCAAATTTACTATTTTGCCCCGAAAAGCGT
66 TAAGAGAGTGAAAATTACCGAAATACCCTTAATAGGCAAATTTACTATTTTGCCCCGAAAAGCGC
2563 GATACAAATAATTAAACTTTAAGATCGTATATTCAGGATTGGAAAGCTACCGTAGAGACCCTTTT
131 GATACAAATAATTAAACTTTAAGATCGTATATTCAGGATTGGAAAGCTACCGTAGAGACCCTTTT
*
2628 GGGTAAAATTACTGTGCTACCCTCGACCTATCAACATTACCATTATGCCCTTTAGTCATCAAATT
196 GGGTAAAATTACTGTGCTACCATCGACCTATCAACATTACCATTATGCCCTTTAGTCATCAAATT
2693 TACTAAAGTACCCCTAAGGGTGGAAATGAGAGAATTCATTT
261 TACTAAAGTACCCCTAAGGGTGGAAATGAGAGAATTCATTT
2734 ATATCACTCA
Statistics
Matches: 294, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
316 294 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (316 bp):
ACAACTATGACATGTAACAATGTCAGCGTAAAAGCAAATTTACTATTAATAGGCAAATTTACTAT
TAAGAGAGTGAAAATTACCGAAATACCCTTAATAGGCAAATTTACTATTTTGCCCCGAAAAGCGC
GATACAAATAATTAAACTTTAAGATCGTATATTCAGGATTGGAAAGCTACCGTAGAGACCCTTTT
GGGTAAAATTACTGTGCTACCATCGACCTATCAACATTACCATTATGCCCTTTAGTCATCAAATT
TACTAAAGTACCCCTAAGGGTGGAAATGAGAGAATTCATTTGTCATAGTAGGGTCA
Found at i:3355 original size:13 final size:12
Alignment explanation
Indices: 3337--3379 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
3327 TTTATTACTA
3337 TTTTATTAAATTG
1 TTTTA-TAAATTG
*
3350 TTTTATAAATGG
1 TTTTATAAATTG
3362 TTTTTAATAAATTG
1 -TTTT-ATAAATTG
3376 TTTT
1 TTTT
3380 TGGTGCATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 6 0.23
13 13 0.50
14 7 0.27
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.60
Consensus pattern (12 bp):
TTTTATAAATTG
Found at i:3373 original size:14 final size:14
Alignment explanation
Indices: 3337--3380 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
3327 TTTATTACTA
*
3337 TTTTATTAAATTG-
1 TTTTAATAAATTGT
*
3350 TTTT-ATAAATGGT
1 TTTTAATAAATTGT
3363 TTTTAATAAATTGT
1 TTTTAATAAATTGT
3377 TTTT
1 TTTT
3381 GGTGCATGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
14 12 0.46
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (14 bp):
TTTTAATAAATTGT
Found at i:8229 original size:12 final size:12
Alignment explanation
Indices: 8212--8243 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
8202 CGTTATAAAG
8212 AAAAAAATTATT
1 AAAAAAATTATT
*
8224 AAAAAATTTATT
1 AAAAAAATTATT
8236 AAAAAAAT
1 AAAAAAAT
8244 CACGTTACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAAAAATTATT
Found at i:9795 original size:28 final size:28
Alignment explanation
Indices: 9755--9810 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
9745 TGAACTCAAC
9755 CTCGCTGGGCCATTGTAACCCTAACAAT
1 CTCGCTGGGCCATTGTAACCCTAACAAT
9783 CTCGCTGGGCCATTGTAACCCTAACAAT
1 CTCGCTGGGCCATTGTAACCCTAACAAT
9811 GGGGGCTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (28 bp):
CTCGCTGGGCCATTGTAACCCTAACAAT
Found at i:17635 original size:34 final size:34
Alignment explanation
Indices: 17590--17660 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
17580 TATTAAAAAG
17590 TACATACTCTTGTAAAACTTTTGAATCGCTATTA
1 TACATACTCTTGTAAAACTTTTGAATCGCTATTA
* *
17624 TACATATTCTTGTAAAATTTTTGAATCGCTATTA
1 TACATACTCTTGTAAAACTTTTGAATCGCTATTA
17658 TAC
1 TAC
17661 CCTTATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.44
Consensus pattern (34 bp):
TACATACTCTTGTAAAACTTTTGAATCGCTATTA
Found at i:18794 original size:21 final size:22
Alignment explanation
Indices: 18770--18810 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18760 GAGTATAATA
*
18770 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
18791 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
18811 CAAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:19961 original size:79 final size:79
Alignment explanation
Indices: 19873--20032 Score: 320
Period size: 79 Copynumber: 2.0 Consensus size: 79
19863 TTTTGATAAC
19873 AATTTTTATATGTTTCCTTTTTCTTTTTAGGTAATTATATGCCCAGTTATTGTCTGTCTTTATAG
1 AATTTTTATATGTTTCCTTTTTCTTTTTAGGTAATTATATGCCCAGTTATTGTCTGTCTTTATAG
19938 TTGCTTTAGACGTG
66 TTGCTTTAGACGTG
19952 AATTTTTATATGTTTCCTTTTTCTTTTTAGGTAATTATATGCCCAGTTATTGTCTGTCTTTATAG
1 AATTTTTATATGTTTCCTTTTTCTTTTTAGGTAATTATATGCCCAGTTATTGTCTGTCTTTATAG
20017 TTGCTTTAGACGTG
66 TTGCTTTAGACGTG
20031 AA
1 AA
20033 CGGTTAGCCA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.53
Consensus pattern (79 bp):
AATTTTTATATGTTTCCTTTTTCTTTTTAGGTAATTATATGCCCAGTTATTGTCTGTCTTTATAG
TTGCTTTAGACGTG
Done.