Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011969.1 Corchorus capsularis cultivar CVL-1 contig11990, 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: 24490
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:59 original size:20 final size:21
Alignment explanation
Indices: 20--65 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
10 AAATATTATA
*
20 TTTATCCTATAATGGATAGTT
1 TTTATCCTAAAATGGATAGTT
*
41 TTTAT-CTAAAATGGGTAGTT
1 TTTATCCTAAAATGGATAGTT
61 TTTAT
1 TTTAT
66 TTTATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (21 bp):
TTTATCCTAAAATGGATAGTT
Found at i:7964 original size:14 final size:14
Alignment explanation
Indices: 7942--7975 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
7932 ATTTCCATAT
* *
7942 ATGCTAAATTGCTA
1 ATGCCAAATTGCCA
7956 ATGCCAAATTGCCA
1 ATGCCAAATTGCCA
7970 ATGCCA
1 ATGCCA
7976 TCTTATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (14 bp):
ATGCCAAATTGCCA
Found at i:10132 original size:6 final size:6
Alignment explanation
Indices: 10121--10162 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
10111 TATCACCTCA
10121 TCATAT TCATAT TCATAT TCATAT TCATAT TCATAT TCATAT
1 TCATAT TCATAT TCATAT TCATAT TCATAT TCATAT TCATAT
10163 ATACGAGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATAT
Found at i:13484 original size:7 final size:7
Alignment explanation
Indices: 13474--13508 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
13464 CCGACCCTTC
13474 CTTTCTA
1 CTTTCTA
13481 CTTTCTA
1 CTTTCTA
13488 CTTTCTA
1 CTTTCTA
13495 CTTTCTA
1 CTTTCTA
13502 CTTTCTA
1 CTTTCTA
13509 TATATATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (7 bp):
CTTTCTA
Found at i:14773 original size:7 final size:7
Alignment explanation
Indices: 14761--14790 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
14751 AATTATTATG
14761 TATGAAA
1 TATGAAA
14768 TATGAAA
1 TATGAAA
14775 TATGAAA
1 TATGAAA
14782 TATGAAA
1 TATGAAA
14789 TA
1 TA
14791 CTACTAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (7 bp):
TATGAAA
Found at i:14912 original size:6 final size:6
Alignment explanation
Indices: 14903--14929 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
14893 ATTGATACCC
14903 ATTGAG ATTGAG ATTGAG ATTGAG ATT
1 ATTGAG ATTGAG ATTGAG ATTGAG ATT
14930 CAACCTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (6 bp):
ATTGAG
Found at i:15229 original size:2 final size:2
Alignment explanation
Indices: 15222--15255 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15212 ATTCCGATGC
15222 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
15256 TAAAAGACAA
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
Found at i:20124 original size:33 final size:34
Alignment explanation
Indices: 20087--20152 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
20077 TAGGGATTGG
20087 AAGAG-TACAATTGATGGATGTGAGCCCCATAGA
1 AAGAGATACAATTGATGGATGTGAGCCCCATAGA
*
20120 AAGAGTATACAATTGATGTATGTGAGCCCCATA
1 AAGAG-ATACAATTGATGGATGTGAGCCCCATA
20153 CATACCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
35 25 0.83
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (34 bp):
AAGAGATACAATTGATGGATGTGAGCCCCATAGA
Found at i:20991 original size:2 final size:2
Alignment explanation
Indices: 20984--21008 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20974 CACCTTAACC
20984 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21009 GAAGGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21784 original size:1 final size:1
Alignment explanation
Indices: 21778--21807 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
21768 CGAGATATTT
21778 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21808 GCCAAGCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22983 original size:21 final size:22
Alignment explanation
Indices: 22957--23001 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
22947 GAGATGTGGA
22957 TTGCTAAAC-ACAGTCCCATTT
1 TTGCTAAACTACAGTCCCATTT
** *
22978 TTGCTATTCTACCGTCCCATTT
1 TTGCTAAACTACAGTCCCATTT
23000 TT
1 TT
23002 CGACGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.20, C:0.29, G:0.09, T:0.42
Consensus pattern (22 bp):
TTGCTAAACTACAGTCCCATTT
Found at i:23457 original size:33 final size:33
Alignment explanation
Indices: 23420--23516 Score: 119
Period size: 33 Copynumber: 2.9 Consensus size: 33
23410 GGCGGCTGAG
23420 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
1 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
* *
23453 CCATGGCCAGGCCG-CCTCCCTGGGGCGGCCCTA
1 CCATGGCCAAGCCGCCCT-CCTGGGGCGGCACTA
*
23486 CCATGG--ATAGACCGCCCCCCTGGGGCGGCAC
1 CCATGGCCA-AG-CCGCCCTCCTGGGGCGGCAC
23517 CGGTACTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
31 1 0.02
32 4 0.07
33 48 0.87
34 2 0.04
ACGTcount: A:0.13, C:0.43, G:0.32, T:0.11
Consensus pattern (33 bp):
CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
Found at i:23628 original size:33 final size:33
Alignment explanation
Indices: 23556--23644 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
23546 AAAAAGCCTT
* * * *
23556 GCCGCCCTAGTGGGGCGGCT-AGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCATGGCAGA
23588 GCCGTCCTAGTGGGGAGGCTCCGCCATGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCATGGCAGA
*
23621 GCTGTCCTAGTGGGGAGGCTCCGC
1 GCCGTCCTAGTGGGGAGGCTCCGC
23645 GTGACTAAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 18 0.35
33 33 0.65
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (33 bp):
GCCGTCCTAGTGGGGAGGCTCCGCCATGGCAGA
Done.