Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011362.1 Corchorus capsularis cultivar CVL-1 contig11383, 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: 29286
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:5708 original size:21 final size:21
Alignment explanation
Indices: 5684--5732 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5674 CAGCTGGGGG
* * *
5684 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
5705 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
5726 CCCATGT
1 CCCATGT
5733 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:6542 original size:24 final size:24
Alignment explanation
Indices: 6490--6536 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
6480 TGAAGCACTT
6490 GCGT-TGAGCTTGGAGAAGTTCGG
1 GCGTGTGAGCTTGGAGAAGTTCGG
6513 GCGTGTGAGCTTGGTA-AAGTTCGG
1 GCGTGTGAGCTTGG-AGAAGTTCGG
6537 TTGTGTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.18
24 17 0.77
25 1 0.05
ACGTcount: A:0.17, C:0.13, G:0.43, T:0.28
Consensus pattern (24 bp):
GCGTGTGAGCTTGGAGAAGTTCGG
Found at i:17578 original size:22 final size:21
Alignment explanation
Indices: 17543--17597 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
17533 TTCCGTTTTT
*
17543 TTCTAATAAAAAAAATTGCGAT
1 TTCTAA-AAAAAAAATTGCGAA
17565 TTACTAAAAAAAAAATTGCGAA
1 TT-CTAAAAAAAAAATTGCGAA
17587 TT-TAAAAAAAA
1 TTCTAAAAAAAA
17598 TTAGGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 9 0.29
22 18 0.58
23 4 0.13
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.27
Consensus pattern (21 bp):
TTCTAAAAAAAAAATTGCGAA
Found at i:21119 original size:42 final size:42
Alignment explanation
Indices: 21072--21166 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
21062 GCTAAGCCTT
*
21072 ATCCGCGCACCATGCCCAGCCAAGCCCGGCCCATGCCACGCC
1 ATCCGCGCACCATGCCCAGCCAAGCCCGACCCATGCCACGCC
* *
21114 ATCCGCGCACCATGCTCAGCCATGCCCGACCCATGCCACGCC
1 ATCCGCGCACCATGCCCAGCCAAGCCCGACCCATGCCACGCC
*
21156 ATCCACGCACC
1 ATCCGCGCACC
21167 CAACCAAGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.20, C:0.52, G:0.19, T:0.09
Consensus pattern (42 bp):
ATCCGCGCACCATGCCCAGCCAAGCCCGACCCATGCCACGCC
Found at i:21156 original size:21 final size:20
Alignment explanation
Indices: 21081--21157 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 20
21071 TATCCGCGCA
*
21081 CCATGCC-CAGCCAAGCCCGGC
1 CCATGCCAC-GCCATGCCC-GC
21102 CCATGCCACGCCAT-CCGCGC
1 CCATGCCACGCCATGCC-CGC
21122 ACCATGCTCA-GCCATGCCCGAC
1 -CCATGC-CACGCCATGCCCG-C
21144 CCATGCCACGCCAT
1 CCATGCCACGCCAT
21158 CCACGCACCC
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
20 6 0.12
21 36 0.75
22 6 0.12
ACGTcount: A:0.19, C:0.51, G:0.19, T:0.10
Consensus pattern (20 bp):
CCATGCCACGCCATGCCCGC
Found at i:25969 original size:5 final size:5
Alignment explanation
Indices: 25959--25983 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25949 TCAAGTTTTT
25959 AAAGG AAAGG AAAGG AAAGG AAAGG
1 AAAGG AAAGG AAAGG AAAGG AAAGG
25984 GGAGGGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
AAAGG
Done.