Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014932.1 Corchorus olitorius cultivar O-4 contig14965, 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: 50423
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Found at i:7869 original size:90 final size:90
Alignment explanation
Indices: 7712--7887 Score: 298
Period size: 90 Copynumber: 2.0 Consensus size: 90
7702 ACCAGCAGAT
* ** *
7712 AAAGTTGCCACAAGGTCTCGTGAAAGAAGAGTTCTATAATTAAATAACATGAAAACGGAATACAA
1 AAAGTTGCCACAAGGTCTCGTGAAAGAAGAGTTCTATAAGTAAATAACATGAAAACAAAATAAAA
7777 TAAAATGCTTTTGTTGTGTTTTTCC
66 TAAAATGCTTTTGTTGTGTTTTTCC
* *
7802 AAAGTTGCCACAAGGTCTCGTGAAAGAAGATTTCTATAAGTAAATAACATGACAACAAAATAAAA
1 AAAGTTGCCACAAGGTCTCGTGAAAGAAGAGTTCTATAAGTAAATAACATGAAAACAAAATAAAA
7867 TAAAATGCTTTTGTTGTGTTT
66 TAAAATGCTTTTGTTGTGTTT
7888 AGACTTTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (90 bp):
AAAGTTGCCACAAGGTCTCGTGAAAGAAGAGTTCTATAAGTAAATAACATGAAAACAAAATAAAA
TAAAATGCTTTTGTTGTGTTTTTCC
Found at i:11067 original size:2 final size:2
Alignment explanation
Indices: 11062--11093 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11052 TGCGCGCGCG
11062 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
11094 AAAGAAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:16062 original size:71 final size:71
Alignment explanation
Indices: 15954--16101 Score: 289
Period size: 71 Copynumber: 2.1 Consensus size: 71
15944 CAAAATAAGC
15954 AATC-AACAGATGGGTTTATTAAGTAACAATACCTGCAGTACCCATTCATTATAAACAAAACCTA
1 AATCAAACAGATGGGTTTATTAAGTAACAATACCTGCAGTACCCATTCATTATAAACAAAACCTA
16018 AATAAT
66 AATAAT
16024 AATCAAACAGATGGGTTTATTAAGTAACAATACCTGCAGTACCCATTCATTATAAACAAAACCTA
1 AATCAAACAGATGGGTTTATTAAGTAACAATACCTGCAGTACCCATTCATTATAAACAAAACCTA
16089 AATAAT
66 AATAAT
16095 AATCAAA
1 AATCAAA
16102 GTTTTTAGCA
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 4 0.05
71 73 0.95
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.26
Consensus pattern (71 bp):
AATCAAACAGATGGGTTTATTAAGTAACAATACCTGCAGTACCCATTCATTATAAACAAAACCTA
AATAAT
Found at i:16389 original size:77 final size:77
Alignment explanation
Indices: 16303--16456 Score: 254
Period size: 77 Copynumber: 2.0 Consensus size: 77
16293 AAGCCAAAGG
* *
16303 AACAAATGATCAAGAAGCACGGAAAAAGCAACCAACAATAATTAAGATATATGGAGAACGAAATT
1 AACAAATGATCAAGAAGCACAGAAAAAACAACCAACAATAATTAAGATATATGGAGAACGAAATT
16368 GGTTTAGCAGAC
66 GGTTTAGCAGAC
* * * *
16380 AACAAATGATCAAGATGCACATAAAAAACAACCAACAATATTTAAGATATATGGAGAACGAGATT
1 AACAAATGATCAAGAAGCACAGAAAAAACAACCAACAATAATTAAGATATATGGAGAACGAAATT
16445 GGTTTAGCAGAC
66 GGTTTAGCAGAC
16457 CTTCTAATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (77 bp):
AACAAATGATCAAGAAGCACAGAAAAAACAACCAACAATAATTAAGATATATGGAGAACGAAATT
GGTTTAGCAGAC
Found at i:21149 original size:18 final size:18
Alignment explanation
Indices: 21126--21161 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21116 TAATCGAAGA
21126 AACACGAGCTTTGTAGTT
1 AACACGAGCTTTGTAGTT
21144 AACACGAGCTTTGTAGTT
1 AACACGAGCTTTGTAGTT
21162 TCTGGGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (18 bp):
AACACGAGCTTTGTAGTT
Found at i:21982 original size:15 final size:15
Alignment explanation
Indices: 21962--21993 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
21952 TTTAAAATTC
21962 ATTGCAACTTGATTT
1 ATTGCAACTTGATTT
21977 ATTGCAACTTGATTT
1 ATTGCAACTTGATTT
21992 AT
1 AT
21994 GGATTAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (15 bp):
ATTGCAACTTGATTT
Found at i:25138 original size:16 final size:16
Alignment explanation
Indices: 25117--25147 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
25107 AAGGCAAAGA
25117 ACCAATGGGACTTCAG
1 ACCAATGGGACTTCAG
25133 ACCAATGGGACTTCA
1 ACCAATGGGACTTCA
25148 TGTACAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (16 bp):
ACCAATGGGACTTCAG
Found at i:25433 original size:16 final size:17
Alignment explanation
Indices: 25407--25452 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
25397 ATTATTAACC
25407 TTAATTAAATTTTA-TAA
1 TTAA-TAAATTTTATTAA
**
25424 TTAATAAATTAAATTAA
1 TTAATAAATTTTATTAA
25441 -TAATAAATTTTA
1 TTAATAAATTTTA
25453 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATAAATTTTATTAA
Found at i:33110 original size:21 final size:21
Alignment explanation
Indices: 33069--33110 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
33059 AGCCGCCTTT
**
33069 TCTCGCTCTTCTCGTCTCTGA
1 TCTCGCTCTTCTCGTAACTGA
33090 TCTCGCTCTTCATC-TAACTGA
1 TCTCGCTCTTC-TCGTAACTGA
33111 ATCTTAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.12, C:0.36, G:0.12, T:0.40
Consensus pattern (21 bp):
TCTCGCTCTTCTCGTAACTGA
Found at i:37226 original size:7 final size:7
Alignment explanation
Indices: 37214--37243 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
37204 TATTTAGGCT
37214 AAAGAAA
1 AAAGAAA
37221 AAAGAAA
1 AAAGAAA
37228 AAAGAAA
1 AAAGAAA
37235 AAAGAAA
1 AAAGAAA
37242 AA
1 AA
37244 GGGAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Done.