Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013412.1 Corchorus olitorius cultivar O-4 contig13445, 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: 53450
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:1652 original size:60 final size:60
Alignment explanation
Indices: 1540--1686 Score: 152
Period size: 60 Copynumber: 2.4 Consensus size: 60
1530 ACACCAGGGT
* * *
1540 CTTATTTGAGCATTTTCAGTTGCAAACATTAGAGCCCTATTTAACCAGATTAAAA-ATATGAGCC
1 CTTATTTGAGCATTTTCA----CATACATTAGAGCCATATTTAACCAAATTAAAAGA-ATGAGCC
* * * *
1604 CTTATTTGAGCATTTTCACATATATTAGGGCCATATTTAACCAAATTAAAAGAATGGGCT
1 CTTATTTGAGCATTTTCACATACATTAGAGCCATATTTAACCAAATTAAAAGAATGAGCC
* * *
1664 TTTATTTGAGTATTTTCGCATAC
1 CTTATTTGAGCATTTTCACATAC
1687 GCTAGGACCC
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
60 52 0.73
61 1 0.01
64 18 0.25
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (60 bp):
CTTATTTGAGCATTTTCACATACATTAGAGCCATATTTAACCAAATTAAAAGAATGAGCC
Found at i:6561 original size:17 final size:18
Alignment explanation
Indices: 6530--6564 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6520 AATTTTACCC
6530 AAAAAAAAAATTAAAAAT
1 AAAAAAAAAATTAAAAAT
*
6548 AAAAATAAAA-TAAAAAT
1 AAAAAAAAAATTAAAAAT
6565 GGAATGTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAAAAAAATTAAAAAT
Found at i:15241 original size:6 final size:6
Alignment explanation
Indices: 15230--15262 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
15220 TTAAATAGCC
*
15230 ATATCT ATATCT AAATCT ATATCT ATA-CT ATAT
1 ATATCT ATATCT ATATCT ATATCT ATATCT ATAT
15263 ATAAAAGTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.45
Consensus pattern (6 bp):
ATATCT
Found at i:18528 original size:16 final size:16
Alignment explanation
Indices: 18507--18541 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
18497 TCTGAATGGA
*
18507 AACAGTAATTCTCAGG
1 AACAGTAATTCCCAGG
18523 AACAGTAATTCCCAGG
1 AACAGTAATTCCCAGG
18539 AAC
1 AAC
18542 GAGATCTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (16 bp):
AACAGTAATTCCCAGG
Found at i:29515 original size:31 final size:31
Alignment explanation
Indices: 29480--29559 Score: 101
Period size: 30 Copynumber: 2.6 Consensus size: 31
29470 AATTCGTTCT
* *
29480 AAAAAATCAATCATATTCTTTTTTTTAAGT-G
1 AAAAAATCAATCATATTC-TTTTTATAAGTAA
* *
29511 AAAAAATAAATCATATTC-TTTTATGAGTAA
1 AAAAAATCAATCATATTCTTTTTATAAGTAA
29541 AAAAAATCAATCATATTCT
1 AAAAAATCAATCATATTCT
29560 ATTACAACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.19
30 17 0.40
31 17 0.40
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (31 bp):
AAAAAATCAATCATATTCTTTTTATAAGTAA
Found at i:29574 original size:30 final size:30
Alignment explanation
Indices: 29511--29574 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
29501 TTTTTAAGTG
* ** *
29511 AAAAAATAAATCATATTCTTTTATGAGTAA
1 AAAAAATAAATCATATTCTATTACAACTAA
* *
29541 AAAAAATCAATCATATTCTATTACAACTTA
1 AAAAAATAAATCATATTCTATTACAACTAA
29571 AAAA
1 AAAA
29575 CCATGAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAAAATAAATCATATTCTATTACAACTAA
Found at i:30747 original size:11 final size:11
Alignment explanation
Indices: 30731--30761 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
30721 TCTATTTTTT
30731 GTTTTTGTTTC
1 GTTTTTGTTTC
*
30742 GTTTTTGTTTT
1 GTTTTTGTTTC
30753 GTTTTTGTT
1 GTTTTTGTT
30762 GCGCTGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.19, T:0.77
Consensus pattern (11 bp):
GTTTTTGTTTC
Found at i:31633 original size:13 final size:13
Alignment explanation
Indices: 31615--31646 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
31605 AATTATCCCA
31615 AACAAAGAAAAAT
1 AACAAAGAAAAAT
*
31628 AACAAAGTAAAAT
1 AACAAAGAAAAAT
31641 AACAAA
1 AACAAA
31647 TTTAAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.75, C:0.09, G:0.06, T:0.09
Consensus pattern (13 bp):
AACAAAGAAAAAT
Found at i:31662 original size:15 final size:14
Alignment explanation
Indices: 31623--31664 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
31613 CAAACAAAGA
*
31623 AAAATAACAAA-GT
1 AAAATAACAAATTT
31636 AAAATAACAAATTT
1 AAAATAACAAATTT
*
31650 AAACATAATAAATTT
1 AAA-ATAACAAATTT
31665 TAATCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.44
14 4 0.16
15 10 0.40
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.26
Consensus pattern (14 bp):
AAAATAACAAATTT
Found at i:31728 original size:12 final size:12
Alignment explanation
Indices: 31711--31741 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
31701 TTATTAAACC
31711 CGACCCGGAGAG
1 CGACCCGGAGAG
31723 CGACCCGGAGAG
1 CGACCCGGAGAG
31735 CGACCCG
1 CGACCCG
31742 TTCAAGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.39, G:0.39, T:0.00
Consensus pattern (12 bp):
CGACCCGGAGAG
Found at i:36966 original size:27 final size:27
Alignment explanation
Indices: 36936--37057 Score: 163
Period size: 27 Copynumber: 4.5 Consensus size: 27
36926 AGTGTATTTA
* **
36936 AAATGATCAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTGGACATGC
*
36963 AAATGACCAAAATGCCCCTGGGCATGC
1 AAATGACCAAAATGCCCCTGGACATGC
* **
36990 AAATGACCAAAATGACCCTGGATGTGC
1 AAATGACCAAAATGCCCCTGGACATGC
*
37017 AAAACGACCAAAATGCCCCTGGACATGC
1 -AAATGACCAAAATGCCCCTGGACATGC
37045 AAATGACCAAAAT
1 AAATGACCAAAAT
37058 AAGTAAATAG
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
27 58 0.72
28 23 0.28
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGACATGC
Found at i:37049 original size:55 final size:54
Alignment explanation
Indices: 36936--37057 Score: 199
Period size: 55 Copynumber: 2.2 Consensus size: 54
36926 AGTGTATTTA
* * * *
36936 AAATGATCAAAATGCCCCTGGATGTGCAAATGACCAAAATGCCCCTGGGCATGC
1 AAATGACCAAAATGACCCTGGATGTGCAAACGACCAAAATGCCCCTGGACATGC
36990 AAATGACCAAAATGACCCTGGATGTGCAAAACGACCAAAATGCCCCTGGACATGC
1 AAATGACCAAAATGACCCTGGATGTGC-AAACGACCAAAATGCCCCTGGACATGC
37045 AAATGACCAAAAT
1 AAATGACCAAAAT
37058 AAGTAAATAG
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
54 25 0.40
55 38 0.60
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (54 bp):
AAATGACCAAAATGACCCTGGATGTGCAAACGACCAAAATGCCCCTGGACATGC
Found at i:38692 original size:13 final size:13
Alignment explanation
Indices: 38674--38698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38664 TATGCTTGAG
38674 GCCTCTGTTTTGC
1 GCCTCTGTTTTGC
38687 GCCTCTGTTTTG
1 GCCTCTGTTTTG
38699 TCATGACTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.28, G:0.24, T:0.48
Consensus pattern (13 bp):
GCCTCTGTTTTGC
Found at i:40975 original size:15 final size:15
Alignment explanation
Indices: 40955--40984 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40945 TTGCGTTCAT
*
40955 ACTGTAATTTTGTAA
1 ACTGTAATTTCGTAA
40970 ACTGTAATTTCGTAA
1 ACTGTAATTTCGTAA
40985 GAAAACCGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (15 bp):
ACTGTAATTTCGTAA
Found at i:42903 original size:40 final size:41
Alignment explanation
Indices: 42858--42942 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 41
42848 GCATTCCTCC
* * *
42858 ATTTTTAAATG-ATATTTAAGAAT-TTATTTTTAAAGTATTT
1 ATTTTTAAA-GAATATTTAAGAATGTAATATTTAAAGGATTT
*
42898 ATTTTTGAAGAATATTTAAGAATGTAATATTTAAAGGATTT
1 ATTTTTAAAGAATATTTAAGAATGTAATATTTAAAGGATTT
42939 ATTT
1 ATTT
42943 CCGAATGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
39 1 0.03
40 20 0.51
41 18 0.46
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.51
Consensus pattern (41 bp):
ATTTTTAAAGAATATTTAAGAATGTAATATTTAAAGGATTT
Found at i:51201 original size:2 final size:2
Alignment explanation
Indices: 51194--51222 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
51184 TAATATTTAG
51194 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51223 CTACCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53414 original size:3 final size:3
Alignment explanation
Indices: 53406--53441 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
53396 TTCACATGAT
*
53406 TTC TTC TTC TTC TTC TTC TTC TTC TTAT TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TT
53442 TTTTTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 28 0.93
4 2 0.07
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Done.