Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006717.1 Corchorus capsularis cultivar CVL-1 contig06738, 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: 31497
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Found at i:748 original size:14 final size:14
Alignment explanation
Indices: 721--766 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
711 AATGAAAAAA
721 TATC-CCTTTTCTC
1 TATCTCCTTTTCTC
734 TATCT-CTTGTTCTC
1 TATCTCCTT-TTCTC
* *
748 TCTCTCCTTTTTTC
1 TATCTCCTTTTCTC
762 TATCT
1 TATCT
767 TTTCCCTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 7 0.26
14 17 0.63
15 3 0.11
ACGTcount: A:0.07, C:0.33, G:0.02, T:0.59
Consensus pattern (14 bp):
TATCTCCTTTTCTC
Found at i:5434 original size:28 final size:28
Alignment explanation
Indices: 5402--5458 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
5392 TTCACCGGAA
5402 AGGCCATCATTTCTTCTCACCTTCCTTC
1 AGGCCATCATTTCTTCTCACCTTCCTTC
*
5430 AGGCCATCCTTTCTTCTCACCTTCCTTC
1 AGGCCATCATTTCTTCTCACCTTCCTTC
5458 A
1 A
5459 CCTCCACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.40, G:0.07, T:0.39
Consensus pattern (28 bp):
AGGCCATCATTTCTTCTCACCTTCCTTC
Found at i:17701 original size:24 final size:24
Alignment explanation
Indices: 17674--17720 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
17664 GTTTAACGAC
*
17674 GACTCTGTTCATATATGTTCTGAA
1 GACTCTGTTCACATATGTTCTGAA
* *
17698 GACTCTGTTGACATGTGTTCTGA
1 GACTCTGTTCACATATGTTCTGA
17721 GTGTTGTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (24 bp):
GACTCTGTTCACATATGTTCTGAA
Found at i:18084 original size:2 final size:2
Alignment explanation
Indices: 18077--18104 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18067 CTAATCAAAC
18077 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
18105 GTCTTGTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19020 original size:33 final size:33
Alignment explanation
Indices: 18978--19045 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
18968 TATCAGCAAG
18978 AGAAATTCCCCATTCACAAAGGCGTGCATGAGT
1 AGAAATTCCCCATTCACAAAGGCGTGCATGAGT
19011 AGAAATTCCCCATTCACAAAGGCGTGCATGAGT
1 AGAAATTCCCCATTCACAAAGGCGTGCATGAGT
19044 AG
1 AG
19046 GCAATCTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.21
Consensus pattern (33 bp):
AGAAATTCCCCATTCACAAAGGCGTGCATGAGT
Found at i:22442 original size:17 final size:17
Alignment explanation
Indices: 22410--22450 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
22400 AGATTTTATA
*
22410 TACTAG-CTAGTACTAG
1 TACTAGACTACTACTAG
22426 TACTAGACTACTACTAG
1 TACTAGACTACTACTAG
*
22443 TACCAGAC
1 TACTAGAC
22451 ATTTTTCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (17 bp):
TACTAGACTACTACTAG
Found at i:23456 original size:30 final size:30
Alignment explanation
Indices: 23422--23479 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
23412 AGGCTTATTG
* *
23422 AAGGGTTGGATTCTTTTTGTCCAAAAAAGA
1 AAGGGTTAGATTCTGTTTGTCCAAAAAAGA
23452 AAGGGTTAGATTCTGTTTGTCCAAAAAA
1 AAGGGTTAGATTCTGTTTGTCCAAAAAA
23480 AACAAAGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.33
Consensus pattern (30 bp):
AAGGGTTAGATTCTGTTTGTCCAAAAAAGA
Found at i:23487 original size:32 final size:30
Alignment explanation
Indices: 23422--23492 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
23412 AGGCTTATTG
* * *
23422 AAGGGTTGGATTCTTTTTGTCCAAAAAAGA
1 AAGGGTTAGATTCTGTTTGTCCAAAAAACA
23452 AAGGGTTAGATTCTGTTTGTCCAAAAAAAACA
1 AAGGGTTAGATTCTGTTTGTCC--AAAAAACA
23484 AAGGGTTAG
1 AAGGGTTAG
23493 GTTGGGAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 20 0.56
32 16 0.44
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.30
Consensus pattern (30 bp):
AAGGGTTAGATTCTGTTTGTCCAAAAAACA
Found at i:26855 original size:34 final size:34
Alignment explanation
Indices: 26812--26879 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
26802 ATATAGGGCA
26812 GAGCAAGGATACTACTGCTGAGGACATTGATGAC
1 GAGCAAGGATACTACTGCTGAGGACATTGATGAC
26846 GAGCAAGGATACTACTGCTGAGGACATTGATGAC
1 GAGCAAGGATACTACTGCTGAGGACATTGATGAC
26880 CAGGTTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (34 bp):
GAGCAAGGATACTACTGCTGAGGACATTGATGAC
Done.