Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012236.1 Corchorus olitorius cultivar O-4 contig12269, 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: 25341
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Found at i:4538 original size:4 final size:4
Alignment explanation
Indices: 4510--4566 Score: 84
Period size: 4 Copynumber: 15.0 Consensus size: 4
4500 TAGAATTGGA
*
4510 AAAG AAA- AAA- AAAG AAA- AAAA AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
4555 AAAG AAAG AAAG
1 AAAG AAAG AAAG
4567 GTTAACACAT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
3 9 0.18
4 41 0.82
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:7654 original size:26 final size:25
Alignment explanation
Indices: 7596--7654 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 25
7586 ACATAACCAC
*
7596 CATAAACTACCCTCCTAGAAAACAG
1 CATAAACTACCCTCCTAAAAAACAG
7621 CAATTAAACTACCCTCCTAAAAAACAG
1 C-A-TAAACTACCCTCCTAAAAAACAG
7648 TCATAAA
1 -CATAAA
7655 ATTATTCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.17
27 23 0.77
28 1 0.03
ACGTcount: A:0.47, C:0.29, G:0.05, T:0.19
Consensus pattern (25 bp):
CATAAACTACCCTCCTAAAAAACAG
Found at i:9302 original size:21 final size:21
Alignment explanation
Indices: 9276--9316 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
9266 TACCTGTCTA
9276 ATTGACTCAAGGACACTTCTG
1 ATTGACTCAAGGACACTTCTG
*
9297 ATTGACTTAAGGACACTTCT
1 ATTGACTCAAGGACACTTCT
9317 TTTATTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (21 bp):
ATTGACTCAAGGACACTTCTG
Found at i:9433 original size:3 final size:3
Alignment explanation
Indices: 9425--9456 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
9415 GCATCCAATT
9425 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
9457 GGAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:11855 original size:1 final size:1
Alignment explanation
Indices: 11849--11873 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
11839 AGTAAAATTT
11849 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
11874 CTCATAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13087 original size:20 final size:22
Alignment explanation
Indices: 13062--13110 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 22
13052 AGCTTATTTT
13062 CCGTTAAT-AAATTACTTAAC-
1 CCGTTAATCAAATTACTTAACA
13082 CCGTT-ATCAAATTACTTAACA
1 CCGTTAATCAAATTACTTAACA
13103 CCGTTAAT
1 CCGTTAAT
13111 TTTACCTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.08
20 17 0.65
21 5 0.19
22 2 0.08
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (22 bp):
CCGTTAATCAAATTACTTAACA
Found at i:13645 original size:42 final size:43
Alignment explanation
Indices: 13594--13687 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
13584 AGTGCATTAC
*
13594 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
*
13635 CTCATATTCTAGTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
13680 CTAATATT
1 CTAATATT
13688 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 3 0.07
42 6 0.13
45 37 0.80
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:15735 original size:21 final size:20
Alignment explanation
Indices: 15709--15749 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
15699 GCATCTTAGG
15709 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTT-AAAC
*
15730 CAACTCTGATGAGCTTAAAC
1 CAACTCCGATGAGCTTAAAC
15750 TTCTTCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (20 bp):
CAACTCCGATGAGCTTAAAC
Found at i:17633 original size:33 final size:31
Alignment explanation
Indices: 17560--17705 Score: 123
Period size: 33 Copynumber: 4.5 Consensus size: 31
17550 GCTATGATCA
** *
17560 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
17592 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
17625 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
** * *
17658 ACTCAAATTAGGTTTAGTATT-ATCGCAAACAAC
1 AC-CAAAACAGATTT-GT-TTCATCACAAACAAC
*
17691 ATCTAAAACAGATTT
1 A-CCAAAACAGATTT
17706 AGAATTACTC
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
32 7 0.07
33 79 0.84
34 8 0.09
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Found at i:20190 original size:21 final size:21
Alignment explanation
Indices: 20164--20205 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20154 GCATCTTAGG
20164 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
*
20185 CAACTCTGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
20206 TTCTTCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Done.