Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014339.1 Corchorus capsularis cultivar CVL-1 contig14360, 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: 35784
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:891 original size:21 final size:21
Alignment explanation
Indices: 852--904 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
842 GTGCTTAGGC
852 ATGGCCGGGTCATGCGATGGTG
1 ATGGCCGGG-CATGCGATGGTG
*
874 ATGGCCGGGCATGTGATGGTG
1 ATGGCCGGGCATGCGATGGTG
*
895 AGGGCCGGGC
1 ATGGCCGGGC
905 TTGTAGCTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.13, C:0.19, G:0.49, T:0.19
Consensus pattern (21 bp):
ATGGCCGGGCATGCGATGGTG
Found at i:14288 original size:21 final size:21
Alignment explanation
Indices: 14262--14307 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
14252 ACCCCTGCGA
14262 TGGCGCGACTACTCCATGCTT
1 TGGCGCGACTACTCCATGCTT
* * *
14283 TGGCGCGGCTTCTCCATGTTT
1 TGGCGCGACTACTCCATGCTT
14304 TGGC
1 TGGC
14308 CGATCATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.30, G:0.28, T:0.33
Consensus pattern (21 bp):
TGGCGCGACTACTCCATGCTT
Found at i:19557 original size:21 final size:21
Alignment explanation
Indices: 19533--19580 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
19523 GTTCATGGAC
19533 CCATGCGATGGCGCGGCTACT
1 CCATGCGATGGCGCGGCTACT
** *
19554 CCATGCTTTGGCGCGGCTTCT
1 CCATGCGATGGCGCGGCTACT
19575 CCATGC
1 CCATGC
19581 TTTGGCCGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.35, G:0.29, T:0.25
Consensus pattern (21 bp):
CCATGCGATGGCGCGGCTACT
Found at i:19581 original size:21 final size:21
Alignment explanation
Indices: 19541--19586 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
19531 ACCCATGCGA
19541 TGGCGCGGCTACTCCATGCTT
1 TGGCGCGGCTACTCCATGCTT
*
19562 TGGCGCGGCTTCTCCATGCTT
1 TGGCGCGGCTACTCCATGCTT
19583 TGGC
1 TGGC
19587 CGGTCATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.07, C:0.33, G:0.30, T:0.30
Consensus pattern (21 bp):
TGGCGCGGCTACTCCATGCTT
Found at i:19905 original size:19 final size:18
Alignment explanation
Indices: 19881--19917 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
19871 AAGTTCGTGT
19881 TTTGAAGATAATTTGAAGA
1 TTTGAAGATAA-TTGAAGA
*
19900 TTTGAAGATCATTGAAGA
1 TTTGAAGATAATTGAAGA
19918 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (18 bp):
TTTGAAGATAATTGAAGA
Found at i:21270 original size:6 final size:6
Alignment explanation
Indices: 21259--21289 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
21249 TCTATTCTGC
21259 TTAGAT TTAGAT TTAGAT TTAGAT TTA-AT TT
1 TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TT
21290 GCTTTGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (6 bp):
TTAGAT
Found at i:25503 original size:21 final size:22
Alignment explanation
Indices: 25460--25503 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
25450 GAAGAGAGTT
*
25460 TAAAATTAAATCTAGCAAACAA
1 TAAAATTAAATCTAACAAACAA
25482 TAAAATT-AA-CTAACATAACAA
1 TAAAATTAAATCTAACA-AACAA
25503 T
1 T
25504 CAAGAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 8 0.40
22 7 0.35
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (22 bp):
TAAAATTAAATCTAACAAACAA
Found at i:33085 original size:53 final size:53
Alignment explanation
Indices: 32993--33145 Score: 191
Period size: 53 Copynumber: 2.9 Consensus size: 53
32983 AATTGCAAGT
* * * * *
32993 ACTATAAACAAAAGATTTTGGTGAAACATTGATCAATTCACCAAGTACTATAA
1 ACTAGAAACAAAAGACTTTGATGAAACATTGTTCCATTCACCAAGTACTATAA
* * *
33046 ACTAGATAGAAAAGACTTTGATGAAATATTGTTCCATTCACCATA-TACTATAA
1 ACTAGAAACAAAAGACTTTGATGAAACATTGTTCCATTCACCA-AGTACTATAA
* * *
33099 ACTATAAACAGAAGACTTTGTTGAAACATTGTTCCATTCACCAAGTA
1 ACTAGAAACAAAAGACTTTGATGAAACATTGTTCCATTCACCAAGTA
33146 ATAATATATA
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
52 1 0.01
53 82 0.98
54 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (53 bp):
ACTAGAAACAAAAGACTTTGATGAAACATTGTTCCATTCACCAAGTACTATAA
Found at i:35692 original size:21 final size:22
Alignment explanation
Indices: 35667--35714 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
35657 CTCACTAAGT
*
35667 TTGATTTGAAT-TTGAAAAC-C
1 TTGATTTAAATCTTGAAAACTC
35687 TCTGA-TTAAATCTTGAAAACTC
1 T-TGATTTAAATCTTGAAAACTC
35709 TTGATT
1 TTGATT
35715 ACCAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
20 6 0.26
21 14 0.61
22 3 0.13
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (22 bp):
TTGATTTAAATCTTGAAAACTC
Done.