Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011116.1 Corchorus olitorius cultivar O-4 contig11149, 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: 20584
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:1757 original size:19 final size:20
Alignment explanation
Indices: 1716--1758 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1706 AGGACTAAAT
*
1716 ATTTTTTTTCATCTTAAATA
1 ATTTTTTTTCATCTTAAACA
1736 ATTTTTTTT-AT-TTAAAACA
1 ATTTTTTTTCATCTT-AAACA
1755 ATTT
1 ATTT
1759 AAAATACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 10 0.48
20 9 0.43
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTTTTCATCTTAAACA
Found at i:2245 original size:101 final size:101
Alignment explanation
Indices: 2113--2309 Score: 297
Period size: 103 Copynumber: 1.9 Consensus size: 101
2103 GTTTTTATAG
* * * * *
2113 CTATTTTATTTTTACCATTTACTATTTTAATTGAAAAACTT-ATATATTAGAATTTTTTAAATAT
1 CTATTTTATTTTTACAATTTACTATTTTAATTAAAAAAATTAATATATAAGAATTTTTTAAAAAT
**
2177 ATTTCTGAAATGACATTGTATAAACTTTTATAGTAA
66 ATTTCTGAAAAAACATTGTATAAACTTTTATAGTAA
2213 CTATTTTATTTTTACAATTTTACTATTTTAATTAAAAAAATTAGATATATAAGAATTTTTTAAAA
1 CTATTTTATTTTTACAA-TTTACTATTTTAATTAAAAAAATTA-ATATATAAGAATTTTTTAAAA
*
2278 ATATTTCTTAAAAAACATTGTATAAACTTTTA
64 ATATTTCTGAAAAAACATTGTATAAACTTTTA
2310 CAGGTTTATT
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
100 16 0.19
101 22 0.26
103 48 0.56
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (101 bp):
CTATTTTATTTTTACAATTTACTATTTTAATTAAAAAAATTAATATATAAGAATTTTTTAAAAAT
ATTTCTGAAAAAACATTGTATAAACTTTTATAGTAA
Found at i:4651 original size:2 final size:2
Alignment explanation
Indices: 4611--4635 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4601 TCTCTCTCTC
4611 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4636 TCCCAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9569 original size:16 final size:16
Alignment explanation
Indices: 9548--9580 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
9538 CCTACTGCTA
9548 GTTGGATTGGATGAGC
1 GTTGGATTGGATGAGC
9564 GTTGGATTGGATGAGC
1 GTTGGATTGGATGAGC
9580 G
1 G
9581 ATCTCTCTGC
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:0.18, C:0.06, G:0.45, T:0.30
Consensus pattern (16 bp):
GTTGGATTGGATGAGC
Found at i:9642 original size:11 final size:11
Alignment explanation
Indices: 9626--9651 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9616 GAGTTTATCA
9626 ATTTCATTGAG
1 ATTTCATTGAG
9637 ATTTCATTGAG
1 ATTTCATTGAG
9648 ATTT
1 ATTT
9652 GATTTGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (11 bp):
ATTTCATTGAG
Found at i:10171 original size:27 final size:27
Alignment explanation
Indices: 10148--10208 Score: 104
Period size: 27 Copynumber: 2.2 Consensus size: 27
10138 TTGCTGGTGA
10148 CCTGGAATCTCTGGGGTGACCTGGAAT
1 CCTGGAATCTCTGGGGTGACCTGGAAT
*
10175 CTTGGAATCTCTGGGGTGACCTGGAAT
1 CCTGGAATCTCTGGGGTGACCTGGAAT
10202 CTCTGGA
1 C-CTGGA
10209 GGGATTGCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.18, C:0.21, G:0.33, T:0.28
Consensus pattern (27 bp):
CCTGGAATCTCTGGGGTGACCTGGAAT
Found at i:10765 original size:19 final size:19
Alignment explanation
Indices: 10733--10791 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
10723 GTGAAAATTT
10733 TCATTACACTCAAA-AATGA
1 TCATTACAC-CAAATAATGA
* *
10752 TATATTACACCAAATAAAGA
1 T-CATTACACCAAATAATGA
10772 TCATTACACCAAATAATGA
1 TCATTACACCAAATAATGA
10791 T
1 T
10792 TACTTTCCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 22 0.65
20 12 0.35
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (19 bp):
TCATTACACCAAATAATGA
Found at i:13352 original size:82 final size:82
Alignment explanation
Indices: 13254--13417 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
13244 CTTTAATTAT
13254 AATATTGAGAGCTAATTATTGCTTAAATCATGTTTAATTAACTAATTAATGTCTTTAATTTCTCA
1 AATATTGAGAGCTAATTATTGCTTAAATCATGTTTAATTAACTAATTAATGTCTTTAATTTCTCA
13319 TCAATTATACTTTTTCA
66 TCAATTATACTTTTTCA
13336 AATATTGAGAGCTAATTATTGCTTAAATCATGTTTAATTAACTAATTAATGTCTTTAATTTCTCA
1 AATATTGAGAGCTAATTATTGCTTAAATCATGTTTAATTAACTAATTAATGTCTTTAATTTCTCA
13401 TCAATTATACTTTTTCA
66 TCAATTATACTTTTTCA
13418 TGTGGCTGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46
Consensus pattern (82 bp):
AATATTGAGAGCTAATTATTGCTTAAATCATGTTTAATTAACTAATTAATGTCTTTAATTTCTCA
TCAATTATACTTTTTCA
Found at i:16140 original size:102 final size:102
Alignment explanation
Indices: 16012--16303 Score: 482
Period size: 99 Copynumber: 2.9 Consensus size: 102
16002 AAGCTGAAGA
* *
16012 TGATCCAAATAACAAAGGTGTAAATGATCCAGAGTTTGGTGCTTATGGATATGATTATGAATATA
1 TGATCCAAATAACGAAGGTGTAAATGACCCAGAGTTTGGTGCTTATGGATATGATTATGAATATA
* *
16077 AAGATTCATCAAAAGAATCTAGAGGAGGCCGTGATAG
66 AAGATTCAGCAAAAGAATCTAGAGGAGGCCATGATAG
*
16114 TGATCCAAATAACGAAGGTGTAAATGACCCGGAGTTTGGTGCTTATGGATATGATTATGAATATA
1 TGATCCAAATAACGAAGGTGTAAATGACCCAGAGTTTGGTGCTTATGGATATGATTATGAATATA
*
16179 AAGATTCAGCAAAAGAATCT--A-GAGGTCATGATAG
66 AAGATTCAGCAAAAGAATCTAGAGGAGGCCATGATAG
*
16213 TGATCCAAATAATGAAGGTGTAAATGACCCAGAGTTTGGTGCTTATGGATATGATTATGAATATA
1 TGATCCAAATAACGAAGGTGTAAATGACCCAGAGTTTGGTGCTTATGGATATGATTATGAATATA
* *
16278 AAGATTCAGCAAAAGGACCTAGAGGA
66 AAGATTCAGCAAAAGAATCTAGAGGA
16304 ACTGCTCCAA
Statistics
Matches: 177, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
99 92 0.52
100 1 0.01
101 1 0.01
102 83 0.47
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (102 bp):
TGATCCAAATAACGAAGGTGTAAATGACCCAGAGTTTGGTGCTTATGGATATGATTATGAATATA
AAGATTCAGCAAAAGAATCTAGAGGAGGCCATGATAG
Found at i:18649 original size:15 final size:16
Alignment explanation
Indices: 18629--18658 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18619 GGTAAACTTC
18629 ATTATATGAA-AAATT
1 ATTATATGAATAAATT
18644 ATTATATGAATAAAT
1 ATTATATGAATAAAT
18659 ACTAAATCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTATATGAATAAATT
Found at i:19785 original size:131 final size:126
Alignment explanation
Indices: 19612--19844 Score: 342
Period size: 131 Copynumber: 1.8 Consensus size: 126
19602 CTAATAGATC
* *
19612 TAAGTTTTCTAATTAAATTAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATTTAAT
1 TAAGTTTTCTAATTAAAATAATAAAATGATAAAAATAAAATAGGTATAAGGATATTAG-----AT
19677 TAGAAATAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAATATTCTAGCATA
61 T-GAAATAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAATATTCTAGCATA
19742 TA
125 TA
* * * *
19744 TAAGTTTT-TAATTAAAATAATAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATTGAAT
1 TAAGTTTTCTAATTAAAATAATAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATTGAAA
*
19808 TAAAATAGAGTTTTTAGTTGGGTAAAACTATAAAAGT
66 TAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
19845 TTAAACAATG
Statistics
Matches: 94, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
125 39 0.41
126 3 0.03
131 44 0.47
132 8 0.09
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.36
Consensus pattern (126 bp):
TAAGTTTTCTAATTAAAATAATAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATTGAAA
TAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAATATTCTAGCATATA
Done.