Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006707.1 Corchorus capsularis cultivar CVL-1 contig06728, 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: 28082
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:1372 original size:21 final size:20
Alignment explanation
Indices: 1342--1394 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1332 ACTAGCGCTG
*
1342 GGCGCCCATGTGGTATGCTT
1 GGCGCCCATGTGGTATGCCT
*
1362 GGCGCCCCATGTGGTTTGCCT
1 GGCG-CCCATGTGGTATGCCT
*
1383 CGCGACCCATGT
1 GGCG-CCCATGT
1395 ACTCCAGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.09, C:0.32, G:0.32, T:0.26
Consensus pattern (20 bp):
GGCGCCCATGTGGTATGCCT
Found at i:7676 original size:12 final size:13
Alignment explanation
Indices: 7653--7677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7643 GAAAATAGTG
7653 AAAATTCAAAAAA
1 AAAATTCAAAAAA
7666 AAAATTCAAAAA
1 AAAATTCAAAAA
7678 CGTTTGCGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATTCAAAAAA
Found at i:10597 original size:102 final size:102
Alignment explanation
Indices: 10421--10626 Score: 412
Period size: 102 Copynumber: 2.0 Consensus size: 102
10411 CCTTGGCAGC
10421 ACCTATTACAAGTGTGATGAAGAAGAATGCACCATTCAAATGGGGTCCAGAACAACAAGACGCAT
1 ACCTATTACAAGTGTGATGAAGAAGAATGCACCATTCAAATGGGGTCCAGAACAACAAGACGCAT
10486 TTGAGACATTAAAGACTAAGCTTACTAATGCTTCTTT
66 TTGAGACATTAAAGACTAAGCTTACTAATGCTTCTTT
10523 ACCTATTACAAGTGTGATGAAGAAGAATGCACCATTCAAATGGGGTCCAGAACAACAAGACGCAT
1 ACCTATTACAAGTGTGATGAAGAAGAATGCACCATTCAAATGGGGTCCAGAACAACAAGACGCAT
10588 TTGAGACATTAAAGACTAAGCTTACTAATGCTTCTTT
66 TTGAGACATTAAAGACTAAGCTTACTAATGCTTCTTT
10625 AC
1 AC
10627 TTGTGTTACC
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 104 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (102 bp):
ACCTATTACAAGTGTGATGAAGAAGAATGCACCATTCAAATGGGGTCCAGAACAACAAGACGCAT
TTGAGACATTAAAGACTAAGCTTACTAATGCTTCTTT
Found at i:14662 original size:11 final size:10
Alignment explanation
Indices: 14644--14677 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
14634 GAAGTTCGTG
14644 TTTTGAAGAT
1 TTTTGAAGAT
14654 TTCTTGAAGAT
1 TT-TTGAAGAT
14665 ATTTTGAAGAT
1 -TTTTGAAGAT
14676 TT
1 TT
14678 GAAGCCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:16394 original size:34 final size:32
Alignment explanation
Indices: 16319--16397 Score: 86
Period size: 35 Copynumber: 2.4 Consensus size: 32
16309 ATTAATCTGC
* * *
16319 TCTAAAAAAAACGTTTTTGTTTTTCCGTTTTT
1 TCTAAAAAAAAAGTTTTTGTTTTTCAGATTTT
* *
16351 TCTCTAAAAAAAAGTTTTTCCTTTTTTCAGATTTT
1 TCT-AAAAAAAAAGTTTTT--GTTTTTCAGATTTT
16386 TCTAAAAAAAAA
1 TCTAAAAAAAAA
16398 AAAGTTTGCG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
32 3 0.08
33 13 0.34
34 8 0.21
35 14 0.37
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (32 bp):
TCTAAAAAAAAAGTTTTTGTTTTTCAGATTTT
Found at i:19853 original size:23 final size:21
Alignment explanation
Indices: 19827--19877 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
19817 GTCATCCGCG
* *
19827 CCATGCCCGGCCTTGTCCGTGC
1 CCATGCCCGGCCATGCCCG-GC
*
19849 ACCATGTCCGGCCATGCCCGGC
1 -CCATGCCCGGCCATGCCCGGC
19871 CCATGCC
1 CCATGCC
19878 AGACCATCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 6 0.25
22 2 0.08
23 16 0.67
ACGTcount: A:0.10, C:0.47, G:0.25, T:0.18
Consensus pattern (21 bp):
CCATGCCCGGCCATGCCCGGC
Found at i:21781 original size:11 final size:11
Alignment explanation
Indices: 21765--21798 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
21755 GAAGTTCGTG
21765 TTTTGAAGATT
1 TTTTGAAGATT
*
21776 TTTTGAAGATA
1 TTTTGAAGATT
21787 TTTTGAAGATT
1 TTTTGAAGATT
21798 T
1 T
21799 GAAGACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (11 bp):
TTTTGAAGATT
Found at i:22954 original size:27 final size:27
Alignment explanation
Indices: 22920--22998 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
22910 ATTAGGTTCG
* * *
22920 CCCAAGGGTATTTTGGGTCATTTTTGTA
1 CCCAGGGGCATTTT-GGTCATTTTTGCA
22948 CCCAGGGGCATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
* *
22975 CTCAGGGGCATTTTAGTCATTTTT
1 CCCAGGGGCATTTTGGTCATTTTT
22999 AGGTTCACCT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 34 0.74
28 12 0.26
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (27 bp):
CCCAGGGGCATTTTGGTCATTTTTGCA
Found at i:23684 original size:16 final size:16
Alignment explanation
Indices: 23663--23696 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23653 ATTTGGACCT
23663 TGCAAAGAAAAAGAAA
1 TGCAAAGAAAAAGAAA
* *
23679 TGCAAAGCACAAGAAA
1 TGCAAAGAAAAAGAAA
23695 TG
1 TG
23697 TTCCCCAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.12, G:0.21, T:0.09
Consensus pattern (16 bp):
TGCAAAGAAAAAGAAA
Done.