Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024522.1 Corchorus olitorius cultivar O-4 contig24555, 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: 12633
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:1742 original size:11 final size:13
Alignment explanation
Indices: 1715--1746 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
1705 AAAACCATTT
1715 ATAAAACATATTA
1 ATAAAACATATTA
1728 ATAAAACA-A-TA
1 ATAAAACATATTA
1739 ATAAAACA
1 ATAAAACA
1747 GTTCCTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAAAACATATTA
Found at i:3474 original size:21 final size:22
Alignment explanation
Indices: 3449--3490 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3439 CGTTAAATCT
3449 CTTATTATTATAAT-TATTAAA
1 CTTATTATTATAATATATTAAA
*
3470 CTTATTATTATTATATATTAA
1 CTTATTATTATAATATATTAA
3491 TATTAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
CTTATTATTATAATATATTAAA
Found at i:4726 original size:93 final size:92
Alignment explanation
Indices: 4610--4780 Score: 272
Period size: 94 Copynumber: 1.8 Consensus size: 92
4600 TTTTTTTGGG
** *
4610 AAAAAGGGAGTCATTAATTCAGTATTATTTCAATA-ATTATTTTGGGTGAGTGAAAATATTAATT
1 AAAAAGGGAGTCATTAATTCAGTATTATCCCAATATATTATTTTGGGTGAATGAAAATATTAATT
*
4674 ATACCCAACCAATTAAAAACCTTGAAT
66 ACACCCAACCAATTAAAAACCTTGAAT
4701 AAAAATGGAGAGTCATTAATTCAGTATTATCCCAATATATTATTTTGGGTGAATGAAAATATTAA
1 AAAAA-GG-GAGTCATTAATTCAGTATTATCCCAATATATTATTTTGGGTGAATGAAAATATTAA
*
4766 TTGCACCCAACCAAT
64 TTACACCCAACCAAT
4781 CAACTTTGGA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
91 5 0.07
92 2 0.03
93 26 0.36
94 39 0.54
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (92 bp):
AAAAAGGGAGTCATTAATTCAGTATTATCCCAATATATTATTTTGGGTGAATGAAAATATTAATT
ACACCCAACCAATTAAAAACCTTGAAT
Found at i:6507 original size:21 final size:22
Alignment explanation
Indices: 6483--6524 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
6473 AATTAAATCT
6483 CTTATTATTATAAT-TATTAAA
1 CTTATTATTATAATATATTAAA
*
6504 CTTATTATTATTATATATTAA
1 CTTATTATTATAATATATTAA
6525 TATTAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
CTTATTATTATAATATATTAAA
Found at i:7500 original size:71 final size:70
Alignment explanation
Indices: 7374--7509 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 70
7364 TAAAATAACC
* *
7374 TTTTTAATTTTAAAAGTATAGTATTCCTTTAAAGGGTAAACATGTTATTTCATTTTGATTAATTA
1 TTTTTAATTTTAAAAGTATAGTATTCCTTTAAAGGATAAACATGTTATTTCATTTT-AATAATTA
7439 ATTATG
65 ATTATG
* * *
7445 TTTTTAATTTTAGAAGTTTAGTATTCCTTTAAAGGATAAACATG-TATTTTTATTTTAATAATTA
1 TTTTTAATTTTAAAAGTATAGTATTCCTTTAAAGGATAAACATGTTA-TTTCATTTTAATAATTA
7509 A
65 A
7510 AATTTCTAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
70 10 0.17
71 49 0.83
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (70 bp):
TTTTTAATTTTAAAAGTATAGTATTCCTTTAAAGGATAAACATGTTATTTCATTTTAATAATTAA
TTATG
Found at i:9117 original size:35 final size:35
Alignment explanation
Indices: 9072--9139 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
9062 TTTTGAGTCA
9072 TTTGTTTGCTGCAGCAGTGAGAAGATATCGTGACG
1 TTTGTTTGCTGCAGCAGTGAGAAGATATCGTGACG
9107 TTTGTTTGCTGCAGCAGTGAGAAGATATCGTGA
1 TTTGTTTGCTGCAGCAGTGAGAAGATATCGTGA
9140 GAAATACTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.32
Consensus pattern (35 bp):
TTTGTTTGCTGCAGCAGTGAGAAGATATCGTGACG
Found at i:11534 original size:183 final size:183
Alignment explanation
Indices: 11226--11594 Score: 729
Period size: 183 Copynumber: 2.0 Consensus size: 183
11216 TTTTTATAGA
*
11226 GAAAAGGCGACGGGGGCAGATAAAACACATGTAAAAGTGATGCCTTTGCTCTTTAAAAACACTTG
1 GAAAAGGCGACGGGGGCAGATAAAACACATGTAAAAGTGAAGCCTTTGCTCTTTAAAAACACTTG
11291 TTGTACATTTTACAGCATAATGCAAGTGTTGTTAAAGGCCTTAATTGGTGTAGTGTGTTGATCGA
66 TTGTACATTTTACAGCATAATGCAAGTGTTGTTAAAGGCCTTAATTGGTGTAGTGTGTTGATCGA
11356 ATTCCACTTTTAAGTTTTAATCTAACCTTTATTAAAGACTAAGCAAAGACTAG
131 ATTCCACTTTTAAGTTTTAATCTAACCTTTATTAAAGACTAAGCAAAGACTAG
11409 GAAAAGGCGACGGGGGCAGATAAAACACATGTAAAAGTGAAGCCTTTGCTCTTTAAAAACACTTG
1 GAAAAGGCGACGGGGGCAGATAAAACACATGTAAAAGTGAAGCCTTTGCTCTTTAAAAACACTTG
11474 TTGTACATTTTACAGCATAATGCAAGTGTTGTTAAAGGCCTTAATTGGTGTAGTGTGTTGATCGA
66 TTGTACATTTTACAGCATAATGCAAGTGTTGTTAAAGGCCTTAATTGGTGTAGTGTGTTGATCGA
11539 ATTCCACTTTTAAGTTTTAATCTAACCTTTATTAAAGACTAAGCAAAGACTAG
131 ATTCCACTTTTAAGTTTTAATCTAACCTTTATTAAAGACTAAGCAAAGACTAG
11592 GAA
1 GAA
11595 GTCAAACACA
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 185 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (183 bp):
GAAAAGGCGACGGGGGCAGATAAAACACATGTAAAAGTGAAGCCTTTGCTCTTTAAAAACACTTG
TTGTACATTTTACAGCATAATGCAAGTGTTGTTAAAGGCCTTAATTGGTGTAGTGTGTTGATCGA
ATTCCACTTTTAAGTTTTAATCTAACCTTTATTAAAGACTAAGCAAAGACTAG
Found at i:11944 original size:93 final size:92
Alignment explanation
Indices: 11828--11998 Score: 272
Period size: 94 Copynumber: 1.8 Consensus size: 92
11818 TTTTTTTGGG
** *
11828 AAAAAGGGAGTCATTAATTCAGTATTATTTCAATA-ATTATTTTGGGTGAGTGAAAATATTAATT
1 AAAAAGGGAGTCATTAATTCAGTATTATCCCAATATATTATTTTGGGTGAATGAAAATATTAATT
*
11892 ATACCCAACCAATTAAAAACCTTGAAT
66 ACACCCAACCAATTAAAAACCTTGAAT
11919 AAAAATGGAGAGTCATTAATTCAGTATTATCCCAATATATTATTTTGGGTGAATGAAAATATTAA
1 AAAAA-GG-GAGTCATTAATTCAGTATTATCCCAATATATTATTTTGGGTGAATGAAAATATTAA
*
11984 TTGCACCCAACCAAT
64 TTACACCCAACCAAT
11999 CAACTTTGGA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
91 5 0.07
92 2 0.03
93 26 0.36
94 39 0.54
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (92 bp):
AAAAAGGGAGTCATTAATTCAGTATTATCCCAATATATTATTTTGGGTGAATGAAAATATTAATT
ACACCCAACCAATTAAAAACCTTGAAT
Done.