Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012911.1 Corchorus capsularis cultivar CVL-1 contig12932, 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: 31914
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:7282 original size:30 final size:30
Alignment explanation
Indices: 7248--7308 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
7238 ACAAGTTGTG
* *
7248 CCATTTGATTCTTAAGGTTTGTGAGTTCTC
1 CCATTTGATTCTTAAGGCTTGTGAGCTCTC
* * *
7278 CCATTTTATTCTTGATGCTTGTGAGCTCTC
1 CCATTTGATTCTTAAGGCTTGTGAGCTCTC
7308 C
1 C
7309 ATCATATCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (30 bp):
CCATTTGATTCTTAAGGCTTGTGAGCTCTC
Found at i:12469 original size:214 final size:216
Alignment explanation
Indices: 12078--12507 Score: 837
Period size: 214 Copynumber: 2.0 Consensus size: 216
12068 CATGTTTGCA
12078 TTTTTCATTGAAAAAGTTATTAGAAAGTTATAGATGGATAGAATTATTCGTGCAGCTAATTAGAA
1 TTTTTCATTGAAAAAGTTATTAGAAAGTTATAGATGGATAGAATTATTCGTGCAGCTAATTAGAA
*
12143 CTAATAGAATATAATAAAGGTTTCTTGGTTTTTTACATGCTAATTAACTTGAGTGGGGAATCAGA
66 CTAATAGAATATAATAAAGGTTTCTTGGCTTTTTACATGCTAATTAACTTGAGTGGGGAATCAGA
12208 TACTAGTAGTAATTTCTAGTTGTTACTTACAATAAAATTAATTAATATGTTTGTTGAGTTAGGAA
131 TACTAGTAGTAATTTCTAGTTGTTACTTACAATAAAATTAATTAATATGTTTGTTGAGTTAGGAA
12273 GCTTGTATTAATATATAATTC
196 GCTTGTATTAATATATAATTC
12294 TTTTTCATTGAAAAAGTTATTAGAAAGTTATAGATGGATAGAATTATTCGTGCAGCTAATTAGAA
1 TTTTTCATTGAAAAAGTTATTAGAAAGTTATAGATGGATAGAATTATTCGTGCAGCTAATTAGAA
12359 CTAATAGAATATAATAAA-GTTTCTT-GCTTTTTACATGCTAATTAACTTGAGTGGGGAATCAGA
66 CTAATAGAATATAATAAAGGTTTCTTGGCTTTTTACATGCTAATTAACTTGAGTGGGGAATCAGA
12422 TACTAGTAGTAATTTCTAGTTGTTACTTACAATAAAATTAATTAATATGTTTGTTGAGTTAGGAA
131 TACTAGTAGTAATTTCTAGTTGTTACTTACAATAAAATTAATTAATATGTTTGTTGAGTTAGGAA
12487 GCTTGTATTAATATATAATTC
196 GCTTGTATTAATATATAATTC
12508 CAGCATTTAA
Statistics
Matches: 213, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
214 123 0.58
215 7 0.03
216 83 0.39
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.40
Consensus pattern (216 bp):
TTTTTCATTGAAAAAGTTATTAGAAAGTTATAGATGGATAGAATTATTCGTGCAGCTAATTAGAA
CTAATAGAATATAATAAAGGTTTCTTGGCTTTTTACATGCTAATTAACTTGAGTGGGGAATCAGA
TACTAGTAGTAATTTCTAGTTGTTACTTACAATAAAATTAATTAATATGTTTGTTGAGTTAGGAA
GCTTGTATTAATATATAATTC
Found at i:14582 original size:13 final size:13
Alignment explanation
Indices: 14552--14582 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
14542 TCTACAGCTA
*
14552 TTTTCAAAAGCAC
1 TTTTTAAAAGCAC
14565 TTTTTAAAAGCAC
1 TTTTTAAAAGCAC
14578 TTTTT
1 TTTTT
14583 GCAAACCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTTAAAAGCAC
Found at i:27516 original size:92 final size:92
Alignment explanation
Indices: 27359--27597 Score: 469
Period size: 92 Copynumber: 2.6 Consensus size: 92
27349 GAAAAATAAT
*
27359 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGATATTGTCTCCAATAATGCAAAGCTGACTCAT
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
27424 TGGATGAAGAGAAAGCCAAATTATGAA
66 TGGATGAAGAGAAAGCCAAATTATGAA
27451 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
27516 TGGATGAAGAGAAAGCCAAATTATGAA
66 TGGATGAAGAGAAAGCCAAATTATGAA
27543 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAA
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAA
27598 TAGTACAAAG
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 146 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (92 bp):
GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
TGGATGAAGAGAAAGCCAAATTATGAA
Found at i:31863 original size:3 final size:3
Alignment explanation
Indices: 31857--31909 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
31847 AAAAACTTTA
* *
31857 AAG AAG AAG AAG AAG AAG AA- AA- AAG AAA AAG AAA AAG AAAG AA-
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG
31900 AAG AA- AAG AA
1 AAG AAG AAG AA
31910 AAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 8 0.19
3 31 0.74
4 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:31888 original size:16 final size:16
Alignment explanation
Indices: 31863--31913 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
31853 TTTAAAGAAG
*
31863 AAGAAGAAGAAGAAAA
1 AAGAAAAAGAAGAAAA
31879 AAGAAAAAGAA-AAAGA
1 AAGAAAAAGAAGAAA-A
*
31895 AAGAAAAGAAAAGAAAA
1 AAGAAAA-AGAAGAAAA
31912 AA
1 AA
31914 A
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 3 0.10
16 18 0.60
17 6 0.20
18 3 0.10
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAGAAAA
Found at i:31888 original size:22 final size:21
Alignment explanation
Indices: 31856--31912 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
31846 AAAAAACTTT
* *
31856 AAAGAAGAAGAAGAAGAAGAAA
1 AAAGAAAAAGAAAAAGAA-AAA
*
31878 AAAGAAAAAGAAAAAGAAAGA
1 AAAGAAAAAGAAAAAGAAAAA
31899 AAAG-AAAAGAAAAA
1 AAAGAAAAAGAAAAA
31913 AA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 10 0.31
21 6 0.19
22 16 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAGAAAAAGAAAAA
Done.