Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020811.1 Corchorus olitorius cultivar O-4 contig20844, 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: 67369
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3919 original size:21 final size:19
Alignment explanation
Indices: 3894--3951 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
3884 GCTGCTCTAA
3894 TAATCTCATATGTACAGTACC
1 TAATCTCATATGTACAGT--C
* * *
3915 TAATCTAATTTGTACAGTG
1 TAATCTCATATGTACAGTC
*
3934 TAATATCATATGTACAGT
1 TAATCTCATATGTACAGT
3952 TGCTAAACAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATCTCATATGTACAGTC
Found at i:4815 original size:14 final size:12
Alignment explanation
Indices: 4777--4810 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4767 GTGATTTAGG
*
4777 AAAAATAAAGAA
1 AAAAAAAAAGAA
*
4789 CAAAAAAAAGAA
1 AAAAAAAAAGAA
4801 AAAAAAAAAG
1 AAAAAAAAAG
4811 CGAAAGAAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.85, C:0.03, G:0.09, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:8843 original size:5 final size:6
Alignment explanation
Indices: 8820--8850 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
8810 GTAATATCTG
8820 GAAACAA GAAAAA GAAAAA GAAAAA GAAAAA
1 GAAA-AA GAAAAA GAAAAA GAAAAA GAAAAA
8851 TCCATGCACG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:14957 original size:14 final size:14
Alignment explanation
Indices: 14938--14965 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14928 TTCTATCGAA
14938 TCCAATCTCTGCTG
1 TCCAATCTCTGCTG
14952 TCCAATCTCTGCTG
1 TCCAATCTCTGCTG
14966 GGCCTTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.36, G:0.14, T:0.36
Consensus pattern (14 bp):
TCCAATCTCTGCTG
Found at i:16025 original size:41 final size:43
Alignment explanation
Indices: 15944--16031 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 43
15934 ACAGGATTAT
15944 TTTGTCACTTAAATTTGTAAAGACTTATTTTATTTTGAAGTA-
1 TTTGTCACTTAAATTTGTAAAGACTTATTTTATTTTGAAGTAG
*
15986 TTTGTCACTTGAATTTGTAAAGA-TTATTTTATTTTGAAGTAG
1 TTTGTCACTTAAATTTGTAAAGACTTATTTTATTTTGAAGTAG
16028 TTTG
1 TTTG
16032 AGTTATATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 18 0.41
42 26 0.59
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (43 bp):
TTTGTCACTTAAATTTGTAAAGACTTATTTTATTTTGAAGTAG
Found at i:22450 original size:66 final size:65
Alignment explanation
Indices: 22369--22498 Score: 199
Period size: 66 Copynumber: 2.0 Consensus size: 65
22359 TCCAAAATTA
** *
22369 ATCTGAGACGTGAAAAGTTGAATCTCTTTAAT-AAATATACATTTGAATAATTGGAATTTTATTT
1 ATCTGAGACGTGAAAAGTTGAATCTCTAAAATGAAA-ATACATTTGAATAATCGGAA-TTTATTT
22433 AG
64 AG
*
22435 ATCTGAGACGTGAAAAGTTGAATCTCTAAAATGAAAATGCATTTGAATAATCGGAATTTATTTA
1 ATCTGAGACGTGAAAAGTTGAATCTCTAAAATGAAAATACATTTGAATAATCGGAATTTATTTA
22499 AATTCCTGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
65 8 0.14
66 48 0.81
67 3 0.05
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.36
Consensus pattern (65 bp):
ATCTGAGACGTGAAAAGTTGAATCTCTAAAATGAAAATACATTTGAATAATCGGAATTTATTTAG
Found at i:25387 original size:17 final size:17
Alignment explanation
Indices: 25365--25402 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
25355 TTTTGGGATC
*
25365 AAACGGAGTTTAAGTGT
1 AAACGGAGCTTAAGTGT
25382 AAACGGAGCTTAAGTGT
1 AAACGGAGCTTAAGTGT
25399 AAAC
1 AAAC
25403 TCCGTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (17 bp):
AAACGGAGCTTAAGTGT
Found at i:26673 original size:26 final size:25
Alignment explanation
Indices: 26640--26689 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
26630 AAATTACAAG
26640 GAAAAAAGAAAAAGAAAAAGAAAGT
1 GAAAAAAGAAAAAGAAAAAGAAAGT
* *
26665 GAAAGAAAGAAAAAGTAGAAGAAAG
1 GAAA-AAAGAAAAAGAAAAAGAAAG
26690 GAGGATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (25 bp):
GAAAAAAGAAAAAGAAAAAGAAAGT
Found at i:29289 original size:29 final size:29
Alignment explanation
Indices: 29229--29291 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
29219 ACGTGGCATC
* **
29229 CCAAAATTGAAATTCAGGGGTTAAAATGT
1 CCAAAATTGAAATTCAGGGGATAAAACAT
*
29258 CCAAAATTGAAATTCATGGGATAAAACAT
1 CCAAAATTGAAATTCAGGGGATAAAACAT
29287 CCAAA
1 CCAAA
29292 CACTGCAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (29 bp):
CCAAAATTGAAATTCAGGGGATAAAACAT
Found at i:40574 original size:43 final size:43
Alignment explanation
Indices: 40527--40612 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
40517 GAGTAAGTGG
*
40527 TTCTAAACATACATAAGCAGTAGATCAAGCATTGTTATAGAAC
1 TTCTAAACATACATAAGCAGGAGATCAAGCATTGTTATAGAAC
*
40570 TTCTAAACATACATAAGCAGGAGATCGAGCATTGTTATAGAAC
1 TTCTAAACATACATAAGCAGGAGATCAAGCATTGTTATAGAAC
40613 AGAACAGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (43 bp):
TTCTAAACATACATAAGCAGGAGATCAAGCATTGTTATAGAAC
Found at i:46176 original size:29 final size:29
Alignment explanation
Indices: 46141--46200 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
46131 AAAATTCCAG
*
46141 TGGGCTGAGTTCTGGATCCAAGTCCAATA
1 TGGGCTGAGTTATGGATCCAAGTCCAATA
46170 TGGGCTGAGTTATGGATCCAAGTCCAATA
1 TGGGCTGAGTTATGGATCCAAGTCCAATA
46199 TG
1 TG
46201 TTGGACCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (29 bp):
TGGGCTGAGTTATGGATCCAAGTCCAATA
Found at i:51025 original size:143 final size:143
Alignment explanation
Indices: 50768--51053 Score: 563
Period size: 143 Copynumber: 2.0 Consensus size: 143
50758 AAACCAAAAA
50768 AAAAATGATCAAAAGTGATTGAAAATGAAGCAGGAAAGGAAGGAAGAGTTGCTTCCTTTGTGCTT
1 AAAAATGATCAAAAGTGATTGAAAATGAAGCAGGAAAGGAAGGAAGAGTTGCTTCCTTTGTGCTT
50833 TGCTTGGCTGGTTTTGTTTTATATGTATCAGTTTGCAGAGTTTGGAGCAGACGCTAAACCAAGTA
66 TGCTTGGCTGGTTTTGTTTTATATGTATCAGTTTGCAGAGTTTGGAGCAGACGCTAAACCAAGTA
50898 TGGGCAGCCAGGC
131 TGGGCAGCCAGGC
50911 AAAAATGATCAAAAGTGATTGAAAATGAAGCAGGAAAGGAAGGAAGAGTTGCTTCCTTTGTGCTT
1 AAAAATGATCAAAAGTGATTGAAAATGAAGCAGGAAAGGAAGGAAGAGTTGCTTCCTTTGTGCTT
*
50976 TGCTTGGTTGGTTTTGTTTTATATGTATCAGTTTGCAGAGTTTGGAGCAGACGCTAAACCAAGTA
66 TGCTTGGCTGGTTTTGTTTTATATGTATCAGTTTGCAGAGTTTGGAGCAGACGCTAAACCAAGTA
51041 TGGGCAGCCAGGC
131 TGGGCAGCCAGGC
51054 TGGCCCTTAT
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 142 1.00
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (143 bp):
AAAAATGATCAAAAGTGATTGAAAATGAAGCAGGAAAGGAAGGAAGAGTTGCTTCCTTTGTGCTT
TGCTTGGCTGGTTTTGTTTTATATGTATCAGTTTGCAGAGTTTGGAGCAGACGCTAAACCAAGTA
TGGGCAGCCAGGC
Found at i:67339 original size:2 final size:2
Alignment explanation
Indices: 67332--67367 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
67322 TACCATTAGC
67332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67368 GT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.