Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006881.1 Corchorus capsularis cultivar CVL-1 contig06902, 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: 22717
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:4146 original size:33 final size:33
Alignment explanation
Indices: 4109--4215 Score: 144
Period size: 33 Copynumber: 3.2 Consensus size: 33
4099 CGCCTAGCGA
* *
4109 TGGCCGGTTG-TGGCCGGACATGTCCATGTCGCG
1 TGGCCGG-TGATGGCCGGACATCTCCAAGTCGCG
*
4142 TGGCCGGTGATGGCCGGGCATCTCCAAGTCGCG
1 TGGCCGGTGATGGCCGGACATCTCCAAGTCGCG
* * *
4175 TGGCCGGTGTTGGCCGGACTTCTCCAAGTCGCA
1 TGGCCGGTGATGGCCGGACATCTCCAAGTCGCG
4208 TGGCCGGT
1 TGGCCGGT
4216 CACTAGTGCT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 2 0.03
33 64 0.97
ACGTcount: A:0.10, C:0.29, G:0.38, T:0.22
Consensus pattern (33 bp):
TGGCCGGTGATGGCCGGACATCTCCAAGTCGCG
Found at i:6867 original size:33 final size:33
Alignment explanation
Indices: 6827--6964 Score: 163
Period size: 33 Copynumber: 4.2 Consensus size: 33
6817 CACTTGTGAA
* *
6827 CGGCCATGCGACTTGGAGATGCCC-GCGCAACAC
1 CGGCCATGCGACATGGACATGCCCGGC-CAACAC
* * *
6860 CGGCCATGCGACTTGGAGATGCCCGGCCATCAC
1 CGGCCATGCGACATGGACATGCCCGGCCAACAC
* * *
6893 CGGCCACGCGACATGGCCATGCCCGGCCATCAC
1 CGGCCATGCGACATGGACATGCCCGGCCAACAC
*
6926 CGGCCATGCGACATGGCCATGCCCGGCC-ACAAC
1 CGGCCATGCGACATGGACATGCCCGGCCAAC-AC
6959 CGGCCA
1 CGGCCA
6965 CATGACTCGG
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 93 0.97
34 2 0.02
ACGTcount: A:0.20, C:0.41, G:0.29, T:0.11
Consensus pattern (33 bp):
CGGCCATGCGACATGGACATGCCCGGCCAACAC
Found at i:6961 original size:10 final size:10
Alignment explanation
Indices: 6948--6999 Score: 61
Period size: 10 Copynumber: 4.9 Consensus size: 10
6938 ATGGCCATGC
6948 CCGGCCACAA
1 CCGGCCACAA
6958 CCGGCCACATGA
1 CCGGCCACA--A
6970 CTCGGCCA-AA
1 C-CGGCCACAA
6980 CCCGGCCACAA
1 -CCGGCCACAA
6991 CCGGCCACA
1 CCGGCCACA
7000 TGATCCTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
10 25 0.68
11 3 0.08
12 3 0.08
13 6 0.16
ACGTcount: A:0.27, C:0.48, G:0.21, T:0.04
Consensus pattern (10 bp):
CCGGCCACAA
Found at i:6977 original size:33 final size:33
Alignment explanation
Indices: 6878--6999 Score: 142
Period size: 33 Copynumber: 3.7 Consensus size: 33
6868 CGACTTGGAG
*
6878 ATGCCCGGCCATCACCGGCCACGCGACATGGCC
1 ATGCCCGGCCATCACCGGCCACACGACATGGCC
**
6911 ATGCCCGGCCATCACCGGCCATGCGACATGGCC
1 ATGCCCGGCCATCACCGGCCACACGACATGGCC
*
6944 ATGCCCGGCCA-CAACCGGCCACATGAC-TCGGCC
1 ATGCCCGGCCATC-ACCGGCCACACGACAT-GGCC
**
6977 AAACCCGGCCA-CAACCGGCCACA
1 ATGCCCGGCCATC-ACCGGCCACA
7000 TGATCCTTTA
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 2 0.02
33 79 0.98
ACGTcount: A:0.22, C:0.45, G:0.25, T:0.08
Consensus pattern (33 bp):
ATGCCCGGCCATCACCGGCCACACGACATGGCC
Found at i:6977 original size:66 final size:65
Alignment explanation
Indices: 6856--6997 Score: 171
Period size: 66 Copynumber: 2.2 Consensus size: 65
6846 TGCCCGCGCA
* * * **
6856 ACACCGGCCATGCGACTTGGAGATGCCCGGCCATCACCGGCCACGCGACATGGCCATGCCCGGCC
1 ACACCGGCCATGCGACATGGACATGCCCGGCCATCACCGGCCACACGACATGGCCAAACCCGGCC
* *
6921 ATCACCGGCCATGCGACATGGCCATGCCCGGCCA-CAACCGGCCACATGAC-TCGGCCAAACCCG
1 A-CACCGGCCATGCGACATGGACATGCCCGGCCATC-ACCGGCCACACGACAT-GGCCAAACCCG
6984 GCC
63 GCC
6987 ACAACCGGCCA
1 AC-ACCGGCCA
6998 CATGATCCTT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
65 4 0.06
66 62 0.94
ACGTcount: A:0.22, C:0.43, G:0.26, T:0.09
Consensus pattern (65 bp):
ACACCGGCCATGCGACATGGACATGCCCGGCCATCACCGGCCACACGACATGGCCAAACCCGGCC
Found at i:10332 original size:19 final size:18
Alignment explanation
Indices: 10300--10336 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
10290 TTGAATTAAT
*
10300 TCTTCAAATGTCTTCAAA
1 TCTTCAAATATCTTCAAA
10318 TCTTCAAAATATCTTCAAA
1 TCTTC-AAATATCTTCAAA
10337 CACGAACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (18 bp):
TCTTCAAATATCTTCAAA
Found at i:15751 original size:2 final size:2
Alignment explanation
Indices: 15746--15776 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
15736 TAAAAAATGG
15746 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15777 ACATATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.