Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016267.1 Corchorus capsularis cultivar CVL-1 contig16288, 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: 17408
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:972 original size:32 final size:32
Alignment explanation
Indices: 936--1031 Score: 138
Period size: 32 Copynumber: 2.9 Consensus size: 32
926 ATTTGGTGAC
**
936 CTCACCAGGTGAGTATTGTACTGGGTGAGTAT
1 CTCACCAGGTGAGTATTGTACCAGGTGAGTAT
968 CTCACCAGGTGAGTATTGTACCAGGTGAGTAT
1 CTCACCAGGTGAGTATTGTACCAGGTGAGTAT
* *
1000 TTGTACCAGGTGAGTATTTGTACCAGGTGAGT
1 CT-CACCAGGTGAGTA-TTGTACCAGGTGAGT
1032 GTTTGTACAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
32 31 0.53
33 12 0.21
34 15 0.26
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (32 bp):
CTCACCAGGTGAGTATTGTACCAGGTGAGTAT
Found at i:1005 original size:17 final size:17
Alignment explanation
Indices: 939--1049 Score: 147
Period size: 17 Copynumber: 6.7 Consensus size: 17
929 TGGTGACCTC
939 ACCAGGTGAGTA-TTGT
1 ACCAGGTGAGTATTTGT
** * *
955 ACTGGGTGAGTATCT-C
1 ACCAGGTGAGTATTTGT
971 ACCAGGTGAGTA-TTGT
1 ACCAGGTGAGTATTTGT
987 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
1004 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
*
1021 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
*
1038 ACAAGGTGAGTA
1 ACCAGGTGAGTA
1050 GGGTAGGAAC
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
15 1 0.01
16 32 0.40
17 48 0.59
ACGTcount: A:0.24, C:0.13, G:0.32, T:0.32
Consensus pattern (17 bp):
ACCAGGTGAGTATTTGT
Found at i:8909 original size:18 final size:18
Alignment explanation
Indices: 8882--8920 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
8872 GAAAACTCTA
*
8882 ATAAAATTAAATTTCTTT
1 ATAAAATTAAATTTATTT
*
8900 ATAAATTTAAATTTATTT
1 ATAAAATTAAATTTATTT
8918 ATA
1 ATA
8921 GTATTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAAAATTAAATTTATTT
Found at i:9224 original size:1 final size:1
Alignment explanation
Indices: 9218--9256 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
9208 AACTGATCGG
9218 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9257 ATAAATTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:14357 original size:16 final size:15
Alignment explanation
Indices: 14336--14459 Score: 70
Period size: 16 Copynumber: 7.6 Consensus size: 15
14326 CCCAATACAG
14336 ATACTCACCTGGTGCA
1 ATACTCACCTGGTG-A
*
14352 ATACTCATCTGGTGA
1 ATACTCACCTGGTGA
** *
14367 GATACTCACCCAGTACA
1 -ATACTCACCTGGT-GA
14384 ATACTCACCTGCTGGTGA
1 ATACTCA-C--CTGGTGA
** *
14402 GATACTCACCCAGTACA
1 -ATACTCACCTGGT-GA
*
14419 ATACTCA-CTCGGTTTA
1 ATACTCACCT-GG-TGA
14435 ATACTCACCTGGTGA
1 ATACTCACCTGGTGA
14450 GATACTCACC
1 -ATACTCACC
14460 CGCACTCACC
Statistics
Matches: 82, Mismatches: 15, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
15 4 0.05
16 60 0.73
17 6 0.07
18 2 0.02
19 10 0.12
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (15 bp):
ATACTCACCTGGTGA
Found at i:14406 original size:35 final size:33
Alignment explanation
Indices: 14334--14428 Score: 138
Period size: 35 Copynumber: 2.8 Consensus size: 33
14324 CACCCAATAC
** *
14334 AGATACTCACCTGGTGCAATACTCA-TCTGGTG
1 AGATACTCACCCAGTACAATACTCACTCTGGTG
14366 AGATACTCACCCAGTACAATACTCACCTGCTGGTG
1 AGATACTCACCCAGTACAATACTCA-CT-CTGGTG
14401 AGATACTCACCCAGTACAATACTCACTC
1 AGATACTCACCCAGTACAATACTCACTC
14429 GGTTTAATAC
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
32 22 0.39
33 1 0.02
34 3 0.05
35 31 0.54
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (33 bp):
AGATACTCACCCAGTACAATACTCACTCTGGTG
Found at i:14989 original size:2 final size:2
Alignment explanation
Indices: 14982--15015 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
14972 ATATTCTTAT
14982 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15016 GCTTAACAAG
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):
TA
Found at i:16785 original size:18 final size:18
Alignment explanation
Indices: 16759--16794 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16749 CTTATGAAAT
* *
16759 TCCATAAAATTTTCAAAA
1 TCCAAAAAATCTTCAAAA
16777 TCCAAAAAATCTTCAAAA
1 TCCAAAAAATCTTCAAAA
16795 AACATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (18 bp):
TCCAAAAAATCTTCAAAA
Done.