Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022116.1 Corchorus olitorius cultivar O-4 contig22149, 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: 20459
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:2740 original size:18 final size:19
Alignment explanation
Indices: 2714--2752 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2704 AAAACATTCA
* *
2714 TTTTGATATTTTTG-TATT
1 TTTTAATATTTGTGTTATT
2732 TTTTAATATTTGTGTTATT
1 TTTTAATATTTGTGTTATT
2751 TT
1 TT
2753 ATTTAGGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (19 bp):
TTTTAATATTTGTGTTATT
Found at i:6128 original size:26 final size:27
Alignment explanation
Indices: 6099--6152 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
6089 TTGAGAGGAG
6099 TCAA-CATTTTTTTTTTTGTAATTTTT
1 TCAATCATTTTTTTTTTTGTAATTTTT
**
6125 TCAATTTTTTTTTTTTTTTGTAATTTTT
1 TCAA-TCATTTTTTTTTTTGTAATTTTT
6153 CTGAAACTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
28 20 0.83
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.74
Consensus pattern (27 bp):
TCAATCATTTTTTTTTTTGTAATTTTT
Found at i:6430 original size:39 final size:39
Alignment explanation
Indices: 6385--6466 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 39
6375 ATAATGAGAC
*
6385 TAAGTGAAATGTAAGCACAAAATAAGACTAAATGAAATA
1 TAAGTGAAATGTAAGAACAAAATAAGACTAAATGAAATA
* * *
6424 TAAGTGAAATGTAAGAATAAAATGAGACTAAATGAAATG
1 TAAGTGAAATGTAAGAACAAAATAAGACTAAATGAAATA
6463 TAAG
1 TAAG
6467 AACAAAGGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.22
Consensus pattern (39 bp):
TAAGTGAAATGTAAGAACAAAATAAGACTAAATGAAATA
Found at i:6438 original size:28 final size:28
Alignment explanation
Indices: 6414--6468 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
6404 AAATAAGACT
6414 AAATGA-AATATAAGTGAAATGTAAGAATA
1 AAATGAGAATA-AA-TGAAATGTAAGAATA
*
6443 AAATGAGACTAAATGAAATGTAAGAA
1 AAATGAGAATAAATGAAATGTAAGAA
6469 CAAAGGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 13 0.54
29 8 0.33
30 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.18, T:0.22
Consensus pattern (28 bp):
AAATGAGAATAAATGAAATGTAAGAATA
Found at i:6534 original size:33 final size:33
Alignment explanation
Indices: 6485--6548 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
6475 AAATACTATA
* *
6485 TTAATGTGACTAGAATGGAACAAAAACATTTCC
1 TTAACGTGACTAGAATGAAACAAAAACATTTCC
*
6518 TTAACGTGATTAGAATGAAACAAAAACATTT
1 TTAACGTGACTAGAATGAAACAAAAACATTT
6549 TTAGCTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.28
Consensus pattern (33 bp):
TTAACGTGACTAGAATGAAACAAAAACATTTCC
Found at i:7037 original size:20 final size:20
Alignment explanation
Indices: 7012--7071 Score: 120
Period size: 20 Copynumber: 3.0 Consensus size: 20
7002 AATTACAAAC
7012 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
7032 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
7052 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
7072 TTGAACCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAACTCACATTCCGTGAGAG
Found at i:9627 original size:1 final size:1
Alignment explanation
Indices: 9623--9649 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
9613 AGGATTTTAG
9623 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
9650 CAAACCGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9884 original size:2 final size:2
Alignment explanation
Indices: 9877--9905 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9867 ACAAAACATA
9877 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9906 AAGATAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10306 original size:29 final size:30
Alignment explanation
Indices: 10232--10336 Score: 99
Period size: 31 Copynumber: 3.5 Consensus size: 30
10222 GGCTAAATAT
* *
10232 CCAATTTGGGCCTAAACCTTTCACGGTCTGC-
1 CCAAATTGGGCCTAAACCTTTCAC--TCAGCA
*
10263 TCAAATTGGGCCTAAACCTTT-ACTCAGCA
1 CCAAATTGGGCCTAAACCTTTCACTCAGCA
* **
10292 CCAAATTGGGCCTAAACCTATTTGA-TGGGCA
1 CCAAATTGGGCCTAAACC--TTTCACTCAGCA
10323 CCAAATTGGGCCTA
1 CCAAATTGGGCCTA
10337 TTTTTTACGG
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
28 4 0.06
29 17 0.27
30 2 0.03
31 40 0.62
32 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.27
Consensus pattern (30 bp):
CCAAATTGGGCCTAAACCTTTCACTCAGCA
Found at i:14633 original size:45 final size:45
Alignment explanation
Indices: 14569--14767 Score: 263
Period size: 45 Copynumber: 4.4 Consensus size: 45
14559 TCACTGTTAT
* * * *** *
14569 ACCCATCCAGATTTTCACCCCCATTATTGGCTCTAACTCCCTCAA
1 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCATCAA
* * *
14614 ACCCATCAAGATTTTCACCCTCATTCTCCTCTCTAACTCTATCAA
1 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCATCAA
14659 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCATCAA
1 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCATCAA
* ***
14704 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCCTGTT
1 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCATCAA
*
14749 CCCCATCCACATTTTCACC
1 ACCCATCCACATTTTCACC
14768 TTCTGCAACA
Statistics
Matches: 138, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 138 1.00
ACGTcount: A:0.23, C:0.43, G:0.03, T:0.32
Consensus pattern (45 bp):
ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCATCAA
Found at i:14993 original size:15 final size:15
Alignment explanation
Indices: 14975--15003 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
14965 AACATCAAAA
14975 ACATTATCAGTGGTG
1 ACATTATCAGTGGTG
14990 ACATTATCAGTGGT
1 ACATTATCAGTGGT
15004 CACAGTGGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (15 bp):
ACATTATCAGTGGTG
Found at i:16533 original size:20 final size:20
Alignment explanation
Indices: 16504--16572 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
16494 AGACTTTATG
*
16504 ACGTGTCCTCTGATAATTCC
1 ACGTGGCCTCTGATAATTCC
*
16524 ACGTGGCCTCTCATAATTCC
1 ACGTGGCCTCTGATAATTCC
16544 ACGTGGCCTCTGATAATTCC
1 ACGTGGCCTCTGATAATTCC
16564 ACGTGGCCT
1 ACGTGGCCT
16573 ATATTCACGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.30
Consensus pattern (20 bp):
ACGTGGCCTCTGATAATTCC
Found at i:16666 original size:31 final size:29
Alignment explanation
Indices: 16631--16699 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
16621 CAAAAATAGG
16631 CCCAATTTGGTGCCCATCAAATAGGTTTAGA
1 CCCAATTTGGTGCCCA-CAAA-AGGTTTAGA
** **
16662 CCCAATTTGGTGCTGAGGAAAGGTTTAGA
1 CCCAATTTGGTGCCCACAAAAGGTTTAGA
16691 CCCAATTTG
1 CCCAATTTG
16700 AGCAGACCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
30 2 0.06
31 14 0.41
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (29 bp):
CCCAATTTGGTGCCCACAAAAGGTTTAGA
Found at i:16717 original size:31 final size:29
Alignment explanation
Indices: 16653--16726 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
16643 CCCATCAAAT
* *
16653 AGGTTTAGACCCAATTTGGTGCTGAGGAA
1 AGGTTTAGACCCAATTTGGAGCAGAGGAA
16682 AGGTTTAGACCCAATTT-GAGCAGACCGTGAA
1 AGGTTTAGACCCAATTTGGAGCAGA--G-GAA
*
16713 AGGTTTAGGCCCAA
1 AGGTTTAGACCCAA
16727 ATTCGACATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 5 0.13
29 17 0.44
30 1 0.03
31 16 0.41
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (29 bp):
AGGTTTAGACCCAATTTGGAGCAGAGGAA
Found at i:18410 original size:30 final size:30
Alignment explanation
Indices: 18374--18572 Score: 389
Period size: 30 Copynumber: 6.6 Consensus size: 30
18364 ACTCTCTAAA
18374 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
18404 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
18434 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
18464 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
18494 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
18524 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
18554 TGACACAAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
18573 ATGCACTATT
Statistics
Matches: 168, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 168 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Done.