Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010528.1 Corchorus capsularis cultivar CVL-1 contig10549, 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: 7097
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Found at i:1024 original size:27 final size:28
Alignment explanation
Indices: 947--1026 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 28
937 AGTAAGGGCA
947 CTGCAAGAATGTAGGACCTATAAGCATT
1 CTGCAAGAATGTAGGACCTATAAGCATT
* * * * *
975 CTACCA-CA-GGA-GA--TATAAACATT
1 CTGCAAGAATGTAGGACCTATAAGCATT
998 -TGCAAGAATGTAGGACCTATAAGCATT
1 CTGCAAGAATGTAGGACCTATAAGCATT
1025 CT
1 CT
1027 ACCACAGGAT
Statistics
Matches: 36, Mismatches: 10, Indels: 12
0.62 0.17 0.21
Matches are distributed among these distances:
22 3 0.08
23 10 0.28
24 2 0.06
25 4 0.11
26 2 0.06
27 10 0.28
28 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (28 bp):
CTGCAAGAATGTAGGACCTATAAGCATT
Found at i:5836 original size:17 final size:17
Alignment explanation
Indices: 5772--5883 Score: 147
Period size: 17 Copynumber: 6.7 Consensus size: 17
5762 TGGTGACCTC
*
5772 ACCAGGTGAATA-TTGT
1 ACCAGGTGAGTATTTGT
** *
5788 ACTGGGTGAGTA-TTGC
1 ACCAGGTGAGTATTTGT
*
5804 ACTAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
* *
5821 ACCAGATGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
5838 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
5855 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
5872 ACCAGGTGAGTA
1 ACCAGGTGAGTA
5884 GGGTAGGAAC
Statistics
Matches: 84, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
16 23 0.27
17 61 0.73
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.33
Consensus pattern (17 bp):
ACCAGGTGAGTATTTGT
Found at i:6878 original size:30 final size:29
Alignment explanation
Indices: 6844--7027 Score: 96
Period size: 27 Copynumber: 6.5 Consensus size: 29
6834 GGAATTGGTT
*
6844 CTCCCCTGGTGCGTGGCACTAGGGGAGTCC
1 CTCCCCTGGTGCG-CGCACTAGGGGAGTCC
* * **
6874 CT-CCCTTG-GCGCGCACTGGGGGAGTGT
1 CTCCCCTGGTGCGCGCACTAGGGGAGTCC
* * **
6901 CTCCCCTGGTGCCACGCACTTGGGGAGTGT
1 CTCCCCTGGTG-CGCGCACTAGGGGAGTCC
* * * **
6931 CTCCCAT--TGTGCGCACTTGGGGAGTGT
1 CTCCCCTGGTGCGCGCACTAGGGGAGTCC
* *
6958 CTCCCCTTGTGCGC-C-CT-GGGGAG-CAT
1 CTCCCCTGGTGCGCGCACTAGGGGAGTC-C
* * **
6984 CTCCCCTGGTGGTGCGCACTTGGGGAGTGT
1 CTCCCCTGGT-GCGCGCACTAGGGGAGTCC
7014 CTCCCCTGGTGCGC
1 CTCCCCTGGTGCGC
7028 CTCACCTGGG
Statistics
Matches: 125, Mismatches: 18, Indels: 23
0.75 0.11 0.14
Matches are distributed among these distances:
26 16 0.13
27 41 0.33
28 12 0.10
29 15 0.12
30 41 0.33
ACGTcount: A:0.08, C:0.33, G:0.35, T:0.24
Consensus pattern (29 bp):
CTCCCCTGGTGCGCGCACTAGGGGAGTCC
Found at i:6935 original size:57 final size:56
Alignment explanation
Indices: 6843--7081 Score: 218
Period size: 57 Copynumber: 4.2 Consensus size: 56
6833 GGGAATTGGT
** * ** *
6843 TCTCCCCTGGTGCGTGGCACTAGGGGAGTCCCTCCCTTGGCGCGCACTGGGGGAGTG
1 TCTCCCCTGGTGC-CCGCACTTGGGGAGTGTCTCCCTTGGTGCGCACTGGGGGAGTG
*
6900 TCTCCCCTGGTGCCACGCACTTGGGGAGTGTCTCCCATT-GTGCGCACTTGGGGAGTG
1 TCTCCCCTGGTGCC-CGCACTTGGGGAGTGTCTCCC-TTGGTGCGCACTGGGGGAGTG
* * ** *
6957 TCTCCCCTTGTG--CGC-CCTGGGGAGCATCTCCCCTGGTGGTGCGCACTTGGGGAGTG
1 TCTCCCCTGGTGCCCGCACTTGGGGAGTGTCT-CCCT--TGGTGCGCACTGGGGGAGTG
* * * *
7013 TCTCCCCTGGTGCGCCTCACCTGGGGGATTGACTCCCTTGGTGCGC-CTGGGGGAGTG
1 TCTCCCCTGGTGC-CCGCA-CTTGGGGAGTGTCTCCCTTGGTGCGCACTGGGGGAGTG
*
7070 TCTCCCTTGGTG
1 TCTCCCCTGGTG
7082 ACTTTTTTTT
Statistics
Matches: 150, Mismatches: 21, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
53 12 0.08
54 6 0.04
55 1 0.01
56 29 0.19
57 78 0.52
58 10 0.07
59 2 0.01
60 4 0.03
61 8 0.05
ACGTcount: A:0.08, C:0.31, G:0.36, T:0.25
Consensus pattern (56 bp):
TCTCCCCTGGTGCCCGCACTTGGGGAGTGTCTCCCTTGGTGCGCACTGGGGGAGTG
Found at i:7038 original size:30 final size:29
Alignment explanation
Indices: 6843--7081 Score: 158
Period size: 30 Copynumber: 8.4 Consensus size: 29
6833 GGGAATTGGT
** * *
6843 TCTCCCCTGGTGCGTGGCACTAGGGGAGTC
1 TCTCCCCTGGTGCG-CCCACTTGGGGAGTG
* * * *
6873 CCT-CCCTTG-GCGCGCACTGGGGGAGTG
1 TCTCCCCTGGTGCGCCCACTTGGGGAGTG
6900 TCTCCCCTGGTGC-CACGCACTTGGGGAGTG
1 TCTCCCCTGGTGCGC-C-CACTTGGGGAGTG
* *
6930 TCTCCCATTGTGCG--CACTTGGGGAGTG
1 TCTCCCCTGGTGCGCCCACTTGGGGAGTG
* **
6957 TCTCCCCTTGTGCG-CC-C-TGGGGAGCA
1 TCTCCCCTGGTGCGCCCACTTGGGGAGTG
* *
6983 TCTCCCCTGGTGGTGCGCACTTGGGGAGTG
1 TCTCCCCTGGT-GCGCCCACTTGGGGAGTG
* *
7013 TCTCCCCTGGTGCGCCTCACCTGGGGGATTG
1 TCTCCCCTGGTGCGCC-CA-CTTGGGGAGTG
* * *
7044 ACTCCCTTGGTGCG--C-CTGGGGGAGTG
1 TCTCCCCTGGTGCGCCCACTTGGGGAGTG
*
7070 TCTCCCTTGGTG
1 TCTCCCCTGGTG
7082 ACTTTTTTTT
Statistics
Matches: 170, Mismatches: 27, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
26 38 0.22
27 43 0.25
28 12 0.07
29 11 0.06
30 45 0.26
31 21 0.12
ACGTcount: A:0.08, C:0.31, G:0.36, T:0.25
Consensus pattern (29 bp):
TCTCCCCTGGTGCGCCCACTTGGGGAGTG
Done.