Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008149.1 Corchorus capsularis cultivar CVL-1 contig08170, 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: 86288
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:13635 original size:82 final size:80
Alignment explanation
Indices: 13397--13637 Score: 338
Period size: 81 Copynumber: 3.0 Consensus size: 80
13387 CCACATGGCC
*
13397 AAAGAATAGGAATCGAAGAAGAAATTGGATTGTCGTTTGATGAAAAGTTTTTGAAATTAGGGTTT
1 AAAG-ATAGGAATCGAAGAAGAAATTGGATTCTCGTTTGATGAAAAGTTTTTGAAATTAGGGTTT
*
13462 TGGCGTAAGAGGGTTT
65 TGGCGGAAGAGGGTTT
* *
13478 AAAGATAGGAATCGAAGAAAGAAATTGGATTCTCGATTGATGAAGAGTTTTTGAAATTAGGGTTT
1 AAAGATAGGAATCGAAG-AAGAAATTGGATTCTCGTTTGATGAAAAGTTTTTGAAATTAGGGTTT
*
13543 TGGCTGAAGAGGGTTT
65 TGGCGGAAGAGGGTTT
* * * ** * *
13559 AAAGATAGGAATCGACGAAGAATTTGGATTTTATTTTGATAAAAAAAGTTGTTGAAATTAGGGTT
1 AAAGATAGGAATCGAAGAAGAAATTGGATTCTCGTTTGAT--GAAAAGTTTTTGAAATTAGGGTT
13624 TTGGCGGAAGAGGG
64 TTGGCGGAAGAGGG
13638 ATCTTGGTTC
Statistics
Matches: 142, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
80 31 0.22
81 78 0.55
82 33 0.23
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.31
Consensus pattern (80 bp):
AAAGATAGGAATCGAAGAAGAAATTGGATTCTCGTTTGATGAAAAGTTTTTGAAATTAGGGTTTT
GGCGGAAGAGGGTTT
Found at i:15526 original size:7 final size:7
Alignment explanation
Indices: 15516--15553 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
15506 TAAAAAGCAA
15516 AAAAAAG
1 AAAAAAG
15523 AAAAAAG
1 AAAAAAG
15530 -AAAAAG
1 AAAAAAG
15536 AAAAAAG
1 AAAAAAG
15543 AAAGAAAG
1 AAA-AAAG
15551 AAA
1 AAA
15554 GAATAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:15535 original size:13 final size:13
Alignment explanation
Indices: 15517--15545 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
15507 AAAAAGCAAA
15517 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
15530 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
15543 AAA
1 AAA
15546 GAAAGAAAGA
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:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:15546 original size:17 final size:16
Alignment explanation
Indices: 15507--15549 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
15497 AGCACCCTAT
15507 AAAAAGCAAAAAAAAGA
1 AAAAAG-AAAAAAAAGA
15524 AAAAAGAAAAAGAAA-A
1 AAAAAGAAAAA-AAAGA
15540 AAGAAAGAAA
1 AA-AAAGAAA
15550 GAAAGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGA
Found at i:16038 original size:33 final size:33
Alignment explanation
Indices: 15996--16063 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
15986 AACAGCAAAA
15996 TTATTGACTCCTCGGAGTACATTCACACGACAT
1 TTATTGACTCCTCGGAGTACATTCACACGACAT
16029 TTATTGACTCCTCGGAGTACATTCACACGACAT
1 TTATTGACTCCTCGGAGTACATTCACACGACAT
16062 TT
1 TT
16064 TAATTCACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (33 bp):
TTATTGACTCCTCGGAGTACATTCACACGACAT
Found at i:17828 original size:30 final size:30
Alignment explanation
Indices: 17792--17853 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
17782 CCATCAATAA
17792 ATTCAAAACCGTAAAGGAAGTTCATAGTTC
1 ATTCAAAACCGTAAAGGAAGTTCATAGTTC
17822 ATTCAAAACCGTAAAGGAAGTTCATAGTTC
1 ATTCAAAACCGTAAAGGAAGTTCATAGTTC
17852 AT
1 AT
17854 ACATAATCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (30 bp):
ATTCAAAACCGTAAAGGAAGTTCATAGTTC
Found at i:19695 original size:13 final size:12
Alignment explanation
Indices: 19672--19714 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
19662 TTAATACAGG
19672 TATCGACGGATA
1 TATCGACGGATA
19684 TATCGAACGGATA
1 TATCG-ACGGATA
19697 TATCGACGGATA
1 TATCGACGGATA
19709 TATCGA
1 TATCGA
19715 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:25889 original size:56 final size:56
Alignment explanation
Indices: 25804--25916 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
25794 TATACGGTGG
* *
25804 ATCATCAAAGTTTCAAAAGGAAATGGGATTTCTTCTTGCAGTTACCAGAATTTCAC
1 ATCATCAAAGTTTCAAAAGGAAATGGGATTTCTTCATGCAATTACCAGAATTTCAC
*
25860 ATCATCAAAGTTTCAAAAGGAAGTGGGATTTCTTCATGCAATTACCAGAATTTCAC
1 ATCATCAAAGTTTCAAAAGGAAATGGGATTTCTTCATGCAATTACCAGAATTTCAC
25916 A
1 A
25917 ATAAACACAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (56 bp):
ATCATCAAAGTTTCAAAAGGAAATGGGATTTCTTCATGCAATTACCAGAATTTCAC
Found at i:37163 original size:19 final size:19
Alignment explanation
Indices: 37139--37178 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
37129 CTAATAATCA
37139 AACTCTCAAACAAAAAGGC
1 AACTCTCAAACAAAAAGGC
37158 AACTCTCAAACAAAAAGGC
1 AACTCTCAAACAAAAAGGC
37177 AA
1 AA
37179 AGATGGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.25, G:0.10, T:0.10
Consensus pattern (19 bp):
AACTCTCAAACAAAAAGGC
Found at i:40872 original size:1 final size:1
Alignment explanation
Indices: 40866--40890 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
40856 GAAGATGAAG
40866 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
40891 GCTAAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:47631 original size:40 final size:40
Alignment explanation
Indices: 47576--47655 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
47566 TGAAACTGAT
* *
47576 TGATTTGGGATGAATAAGACTTGAAAATACCTTGGTTAAA
1 TGATTTGGGATGAATAAGACTTAAAAATACCTTGCTTAAA
*
47616 TGATTTGGGATGAATAGGACTTAAAAATACCTTGCTTAAA
1 TGATTTGGGATGAATAAGACTTAAAAATACCTTGCTTAAA
47656 AAAATATATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.33
Consensus pattern (40 bp):
TGATTTGGGATGAATAAGACTTAAAAATACCTTGCTTAAA
Found at i:50469 original size:35 final size:35
Alignment explanation
Indices: 50423--50492 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
50413 ATTGCCGAAG
*
50423 TAAGATTACACCTTGTAAAAACAAGGGTGATGAAA
1 TAAGATTACACCTTGCAAAAACAAGGGTGATGAAA
50458 TAAGATTACACCTTGCAAAAACAAGGGTGATGAAA
1 TAAGATTACACCTTGCAAAAACAAGGGTGATGAAA
50493 AATAAAAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (35 bp):
TAAGATTACACCTTGCAAAAACAAGGGTGATGAAA
Found at i:69947 original size:31 final size:31
Alignment explanation
Indices: 69876--69947 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
69866 GTTCATTAGC
*
69876 TTTTAATTTGTTTAATCTAAGACTTGCATTT
1 TTTTAATTTGTTTAATCTAAGACTTGAATTT
** * * *
69907 TGATGATTTGTTTAATTTAATACTT-AATTT
1 TTTTAATTTGTTTAATCTAAGACTTGAATTT
69937 GTTTTAATTTG
1 -TTTTAATTTG
69948 CTACAATTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (31 bp):
TTTTAATTTGTTTAATCTAAGACTTGAATTT
Found at i:72302 original size:15 final size:15
Alignment explanation
Indices: 72282--72311 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
72272 TTCCACACGT
72282 ACCGGAACCGGTTGA
1 ACCGGAACCGGTTGA
72297 ACCGGAACCGGTTGA
1 ACCGGAACCGGTTGA
72312 CATACCCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.13
Consensus pattern (15 bp):
ACCGGAACCGGTTGA
Found at i:79483 original size:21 final size:21
Alignment explanation
Indices: 79458--79497 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
79448 GTTGTAGAGA
79458 AAAGCAATTG-CGTAGAAGTCT
1 AAAGCAATTGTCG-AGAAGTCT
79479 AAAGCAATTGTCGAGAAGT
1 AAAGCAATTGTCGAGAAGT
79498 GTTGAGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (21 bp):
AAAGCAATTGTCGAGAAGTCT
Done.