Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021386.1 Corchorus olitorius cultivar O-4 contig21419, 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: 24485
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:4741 original size:20 final size:20
Alignment explanation
Indices: 4689--4746 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
4679 AGGGAGATTA
*
4689 ACAAAATCTCACAGAAAGGTT
1 ACAAAAT-TCATAGAAAGGTT
* *
4710 ATCAAAAATCATAGGAAGGTT
1 A-CAAAATTCATAGAAAGGTT
4731 ACAAAATTCATAGAAA
1 ACAAAATTCATAGAAA
4747 AGTTTATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 13 0.42
21 13 0.42
22 5 0.16
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.21
Consensus pattern (20 bp):
ACAAAATTCATAGAAAGGTT
Found at i:4841 original size:22 final size:22
Alignment explanation
Indices: 4794--4874 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
4784 CTTATGGAGT
* * *
4794 TTATCACAATTTTATAGG-TAA
1 TTATCAAAATTTCATAGGATGA
*
4815 TTATCAAAATTTCATATGG-TGG
1 TTATCAAAATTTCATA-GGATGA
* *
4837 TTATCAACATTTAATAGGATGA
1 TTATCAAAATTTCATAGGATGA
4859 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
4875 AAAATATCCA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 16 0.33
22 33 0.67
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGATGA
Found at i:4939 original size:2 final size:2
Alignment explanation
Indices: 4932--4968 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4922 GCTAAAACTA
4932 AT AT AT AT 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 AT AT AT AT A
4969 GGAATAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5527 original size:21 final size:21
Alignment explanation
Indices: 5501--5544 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5491 GAATACTTAT
5501 AACTTTCCCATTTATTTATAA
1 AACTTTCCCATTTATTTATAA
5522 AACTTTCCCATTTATTTATAA
1 AACTTTCCCATTTATTTATAA
5543 AA
1 AA
5545 GAGTTTCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (21 bp):
AACTTTCCCATTTATTTATAA
Found at i:5681 original size:30 final size:32
Alignment explanation
Indices: 5645--5705 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 32
5635 CCTCCCTAAA
5645 AAATTCAAAAGG-TGTTGCCAAA-AAAAAAAC
1 AAATTCAAAAGGTTGTTGCCAAAGAAAAAAAC
*
5675 AAATTCAAAAGGTTGTTGTCAAAGAAAAAAA
1 AAATTCAAAAGGTTGTTGCCAAAGAAAAAAA
5706 ATCAAAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 12 0.43
31 9 0.32
32 7 0.25
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (32 bp):
AAATTCAAAAGGTTGTTGCCAAAGAAAAAAAC
Found at i:5711 original size:28 final size:29
Alignment explanation
Indices: 5642--5715 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 29
5632 TTGCCTCCCT
*
5642 AAAAAATTCAAAAGG-TGTTGCCAAAAAA
1 AAAAAAATCAAAAGGTTGTTGCCAAAAAA
* *
5670 AAAACAAATTCAAAAGGTTGTTGTC-AAAGA
1 AAAA-AAA-TCAAAAGGTTGTTGCCAAAAAA
5700 AAAAAAATCAAAAGGT
1 AAAAAAATCAAAAGGT
5716 AAAATCTGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.32
29 5 0.12
30 16 0.40
31 6 0.15
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.19
Consensus pattern (29 bp):
AAAAAAATCAAAAGGTTGTTGCCAAAAAA
Found at i:8386 original size:7 final size:7
Alignment explanation
Indices: 8376--8401 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
8366 TCTTTTGAAA
8376 TTTATAC
1 TTTATAC
8383 TTTATAC
1 TTTATAC
8390 TTTATAC
1 TTTATAC
8397 TTTAT
1 TTTAT
8402 TTTATCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTATAC
Found at i:17902 original size:21 final size:22
Alignment explanation
Indices: 17873--17913 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17863 CCAAATTTTC
17873 TTTAATTTT-CTTATTTTCCTA
1 TTTAATTTTACTTATTTTCCTA
* *
17894 TTTATTTTTATTTATTTTCC
1 TTTAATTTTACTTATTTTCC
17914 CTTTCCCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTAATTTTACTTATTTTCCTA
Found at i:17932 original size:6 final size:6
Alignment explanation
Indices: 17925--18026 Score: 118
Period size: 6 Copynumber: 16.8 Consensus size: 6
17915 TTTCCCTTTC
* *
17925 CTTTTC CTTTTT CTTTTT CTTTTT CTTTTC CTTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
* * *
17973 CTTTTT CTTTTT CTTTCTT -TCTTT CTTTCTT CCTTCTT CTTCTT CTTTTT
1 CTTTTT CTTTTT CTTT-TT CTTTTT CTTT-TT -CTTTTT CTTTTT CTTTTT
18023 -TTTT
1 CTTTT
18027 GACTTGGGCC
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
5 6 0.07
6 70 0.82
7 6 0.07
8 3 0.04
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
CTTTTT
Found at i:18115 original size:29 final size:29
Alignment explanation
Indices: 18045--18122 Score: 138
Period size: 29 Copynumber: 2.7 Consensus size: 29
18035 CCTGGTGGCA
*
18045 TGCCAGGCCCGCATGTGGCCCGCGCGGCC
1 TGCCAGGCCCGCGTGTGGCCCGCGCGGCC
18074 TGCCAGGCCCGCGTGTGGCCCGCGCGGCC
1 TGCCAGGCCCGCGTGTGGCCCGCGCGGCC
*
18103 TGCCAGGCCCGCGCGTGGCC
1 TGCCAGGCCCGCGTGTGGCC
18123 TGCCACACGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.05, C:0.45, G:0.40, T:0.10
Consensus pattern (29 bp):
TGCCAGGCCCGCGTGTGGCCCGCGCGGCC
Found at i:20140 original size:22 final size:22
Alignment explanation
Indices: 20109--20155 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
20099 AAGAAGGTTA
*
20109 TACCAATCTTCTTATTCAAGGT
1 TACCAATCTTCTTATTCAAGAT
*
20131 TACCATTCTTCTTATTCAAGAT
1 TACCAATCTTCTTATTCAAGAT
20153 TAC
1 TAC
20156 TAAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (22 bp):
TACCAATCTTCTTATTCAAGAT
Found at i:22746 original size:23 final size:23
Alignment explanation
Indices: 22720--22763 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
22710 TTCTCTTGAT
22720 TGACTAAATAGAAGCAAAAAATA
1 TGACTAAATAGAAGCAAAAAATA
*
22743 TGACTAAATTGAAGCAAAAAA
1 TGACTAAATAGAAGCAAAAAA
22764 AGTAGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.18
Consensus pattern (23 bp):
TGACTAAATAGAAGCAAAAAATA
Found at i:24061 original size:2 final size:2
Alignment explanation
Indices: 24054--24087 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
24044 AACACAATAC
24054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24088 TTCTAACTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.