Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013541.1 Corchorus capsularis cultivar CVL-1 contig13562, 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: 29157
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4892 original size:31 final size:31
Alignment explanation
Indices: 4854--5023 Score: 173
Period size: 31 Copynumber: 5.4 Consensus size: 31
4844 AGTGTCCGAC
*
4854 GTGGCACGCCACATGTACCCAAAAGTGACAT
1 GTGGCACGCCACATGTACCAAAAAGTGACAT
* *
4885 GTGGCACGCCACGTGTACTAAAAAGTGACAT
1 GTGGCACGCCACATGTACCAAAAAGTGACAT
*
4916 GTGGCACGCCACATGTACAAAAAAGTCGTGCCACAT
1 GTGGCACGCCACATGTACCAAAAA---GTG--ACAT
*
4952 GT--CACGCCACGTGTACCAAAAAGTGACAT
1 GTGGCACGCCACATGTACCAAAAAGTGACAT
* ** * * *
4981 GTGGCATGCCACATGTTTCAAAAAATGGCAC
1 GTGGCACGCCACATGTACCAAAAAGTGACAT
*
5012 GTGGCATGCCAC
1 GTGGCACGCCAC
5024 GTGCACAAAA
Statistics
Matches: 118, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
29 6 0.05
31 85 0.72
34 21 0.18
36 6 0.05
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (31 bp):
GTGGCACGCCACATGTACCAAAAAGTGACAT
Found at i:5023 original size:96 final size:96
Alignment explanation
Indices: 4858--5033 Score: 237
Period size: 96 Copynumber: 1.8 Consensus size: 96
4848 TCCGACGTGG
* * * *
4858 CACGCCACATGTACCCAAAAGTGACATGTGGCACGCCACGTGTACTAAAAAGTGACATGTGGCAC
1 CACGCCACATGTACCAAAAAGTGACATGTGGCACGCCACATGTACTAAAAAATGACACGTGGCAC
*
4923 GCCACATGTACAAAAAAGTCGTGCCACATGT
66 GCCACATGCACAAAAAAGTCGTGCCACATGT
* * * *
4954 CACGCCACGTGTACCAAAAAGTGACATGTGGCATGCCACATGT-TTCAAAAAATGGCACGTGGCA
1 CACGCCACATGTACCAAAAAGTGACATGTGGCACGCCACATGTACT-AAAAAATGACACGTGGCA
* *
5018 TGCCACGTGCACAAAA
65 CGCCACATGCACAAAA
5034 GGATACGTGC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 1 0.01
96 67 0.99
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.18
Consensus pattern (96 bp):
CACGCCACATGTACCAAAAAGTGACATGTGGCACGCCACATGTACTAAAAAATGACACGTGGCAC
GCCACATGCACAAAAAAGTCGTGCCACATGT
Found at i:7926 original size:3 final size:3
Alignment explanation
Indices: 7918--7943 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7908 AAAATGCAAA
7918 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
7944 GGGTGATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:12011 original size:6 final size:6
Alignment explanation
Indices: 11991--12031 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
11981 CAGAGCGCAG
*
11991 CAAAAA C-AAAG CAAAAA C-AAAA CAAAAA CAAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA C-AAAAA CAAAAA
12032 AACAGAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 9 0.30
6 15 0.50
7 6 0.20
ACGTcount: A:0.80, C:0.17, G:0.02, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:12023 original size:11 final size:11
Alignment explanation
Indices: 11991--12040 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
11981 CAGAGCGCAG
*
11991 CAAAAACAAAG
1 CAAAAACAAAA
12002 CAAAAACAAAA
1 CAAAAACAAAA
12013 CAAAAACAAAA
1 CAAAAACAAAA
12024 -AACAAA-AAAA
1 CAA-AAACAAAA
*
12034 CAGAAAC
1 CAAAAAC
12041 GATGCCAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.26
11 25 0.74
ACGTcount: A:0.78, C:0.18, G:0.04, T:0.00
Consensus pattern (11 bp):
CAAAAACAAAA
Found at i:17937 original size:42 final size:42
Alignment explanation
Indices: 17878--17960 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
17868 TTTTATATAC
17878 TCAAATGAGTATATGGGTGTTTTGTTTAGCCAATAATGATAA
1 TCAAATGAGTATATGGGTGTTTTGTTTAGCCAATAATGATAA
*
17920 TCAAATGAGTTTATGGGTGTTTTGTTTAGCCAATAATGATA
1 TCAAATGAGTATATGGGTGTTTTGTTTAGCCAATAATGATA
17961 GAGTATTTCG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (42 bp):
TCAAATGAGTATATGGGTGTTTTGTTTAGCCAATAATGATAA
Found at i:18533 original size:16 final size:16
Alignment explanation
Indices: 18512--18546 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
18502 ATATCAGTAC
*
18512 TTTTTTTCT-TGACTT
1 TTTTTTTCTCTAACTT
18527 TTTTTTTCTCTAACTT
1 TTTTTTTCTCTAACTT
18543 TTTT
1 TTTT
18547 ATGTTGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.09, C:0.14, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTTTCTCTAACTT
Found at i:25893 original size:2 final size:2
Alignment explanation
Indices: 25886--25917 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25876 GTTATTCTGA
25886 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
25918 CAAATCCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28101 original size:31 final size:31
Alignment explanation
Indices: 28064--28128 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
28054 TTGAGTTATC
*
28064 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAAATCTTGGATGTTTG
*
28095 AGTCTCCAGATCTTTAAATTTTGGATGTTTG
1 AGTCTCCAGATCTTTAAATCTTGGATGTTTG
28126 AGT
1 AGT
28129 TAGTTCAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.43
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAAATCTTGGATGTTTG
Done.