Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023405.1 Corchorus olitorius cultivar O-4 contig23438, 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: 33958
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:2092 original size:15 final size:16
Alignment explanation
Indices: 2072--2103 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2062 ATAAACAATG
2072 CCCCCCCCTC-CCCCC
1 CCCCCCCCTCACCCCC
2087 CCCCCCCCTCACCCCC
1 CCCCCCCCTCACCCCC
2103 C
1 C
2104 AAAGCTTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.03, C:0.91, G:0.00, T:0.06
Consensus pattern (16 bp):
CCCCCCCCTCACCCCC
Found at i:12963 original size:11 final size:11
Alignment explanation
Indices: 12939--12973 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12929 TAAAACTTAG
*
12939 AAAAGTAAATA
1 AAAAGTAAAGA
*
12950 AAAAGAAAAGA
1 AAAAGTAAAGA
12961 AAAAGTAAAGA
1 AAAAGTAAAGA
12972 AA
1 AA
12974 GTAAACCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (11 bp):
AAAAGTAAAGA
Found at i:15750 original size:13 final size:13
Alignment explanation
Indices: 15732--15760 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
15722 TTGTTAAACT
15732 TGTAGGCATAAGC
1 TGTAGGCATAAGC
15745 TGTAGGCATAAGC
1 TGTAGGCATAAGC
15758 TGT
1 TGT
15761 CTCTTCTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (13 bp):
TGTAGGCATAAGC
Found at i:20220 original size:24 final size:24
Alignment explanation
Indices: 20193--20267 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
20183 ATTTTGAAGA
20193 TTCTGATATAAATTGTGAATATAT
1 TTCTGATATAAATTGTGAATATAT
* ** * *
20217 TTCTGATTTTCATTTTG-A-AGA-
1 TTCTGATATAAATTGTGAATATAT
20238 TTCTGATATAAATTGTGAATATAT
1 TTCTGATATAAATTGTGAATATAT
20262 TTCTGA
1 TTCTGA
20268 ATATTATATA
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
21 13 0.34
22 3 0.08
23 3 0.08
24 19 0.50
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (24 bp):
TTCTGATATAAATTGTGAATATAT
Found at i:20233 original size:45 final size:45
Alignment explanation
Indices: 20178--20267 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
20168 TTGAATTAAT
20178 TTTTCATTTTGAAGATTCTGATATAAATTGTGAATATATTTCTGA
1 TTTTCATTTTGAAGATTCTGATATAAATTGTGAATATATTTCTGA
20223 TTTTCATTTTGAAGATTCTGATATAAATTGTGAATATATTTCTGA
1 TTTTCATTTTGAAGATTCTGATATAAATTGTGAATATATTTCTGA
20268 ATATTATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (45 bp):
TTTTCATTTTGAAGATTCTGATATAAATTGTGAATATATTTCTGA
Found at i:20243 original size:21 final size:21
Alignment explanation
Indices: 20178--20244 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
20168 TTGAATTAAT
20178 TTTTCATTTTGAAGATTCTGA
1 TTTTCATTTTGAAGATTCTGA
* ** * *
20199 TATAAATTGTGAATATATTTCTGA
1 TTTTCATTTTG-A-AGA-TTCTGA
20223 TTTTCATTTTGAAGATTCTGA
1 TTTTCATTTTGAAGATTCTGA
20244 T
1 T
20245 ATAAATTGTG
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
21 14 0.42
22 3 0.09
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.51
Consensus pattern (21 bp):
TTTTCATTTTGAAGATTCTGA
Found at i:20256 original size:21 final size:21
Alignment explanation
Indices: 20187--20256 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
20177 TTTTTCATTT
20187 TGAAGATTCTGATATAAATTG
1 TGAAGATTCTGATATAAATTG
* * ** *
20208 TGAATATATTTCTGATTTTCATTT
1 TG-A-AGA-TTCTGATATAAATTG
20232 TGAAGATTCTGATATAAATTG
1 TGAAGATTCTGATATAAATTG
20253 TGAA
1 TGAA
20257 TATATTTCTG
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
21 17 0.47
22 3 0.08
23 3 0.08
24 13 0.36
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (21 bp):
TGAAGATTCTGATATAAATTG
Found at i:26412 original size:19 final size:18
Alignment explanation
Indices: 26388--26423 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
26378 TGAAGATTTA
26388 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
26407 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
26424 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:27056 original size:18 final size:19
Alignment explanation
Indices: 27028--27063 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
27018 CTCTTCTTCT
27028 TTTTCTCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
27047 TTTT-TCTTCTAGTTTTA
1 TTTTCTCTTCTAGTTTTA
27064 CGGCTAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.11, C:0.14, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTTCTCTTCTAGTTTTAG
Found at i:30743 original size:29 final size:30
Alignment explanation
Indices: 30706--30765 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
30696 AATTCTTTCC
* *
30706 TCTTGAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA
30735 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA
30766 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAATAGTCTTCAAA
Found at i:32661 original size:21 final size:21
Alignment explanation
Indices: 32635--32694 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
32625 GGAATGGTGA
32635 TGGCACGGGCATGGCCGATGG
1 TGGCACGGGCATGGCCGATGG
* ** *
32656 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATGGCCGATGG
*
32677 TGGCACGGTGAATGGCCG
1 TGGCACGG-GCATGGCCG
32695 GTTGTGGCTT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.17
Consensus pattern (21 bp):
TGGCACGGGCATGGCCGATGG
Found at i:32921 original size:21 final size:21
Alignment explanation
Indices: 32897--32937 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
32887 GCATTTGGCT
* *
32897 CGGATGGCGCGGAAGAAGGCG
1 CGGATGACGCAGAAGAAGGCG
*
32918 CGGATGACGCAGAGGAAGGC
1 CGGATGACGCAGAAGAAGGC
32938 ACGGCTAGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.20, G:0.49, T:0.05
Consensus pattern (21 bp):
CGGATGACGCAGAAGAAGGCG
Done.