Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024523.1 Corchorus olitorius cultivar O-4 contig24556, 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: 17695
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:234 original size:22 final size:21
Alignment explanation
Indices: 182--235 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
172 TGCTTCTTGA
182 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
203 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
222 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
236 CATGAGCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:1673 original size:18 final size:19
Alignment explanation
Indices: 1650--1686 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1640 CTCTTCTATC
1650 ATGAAAAC-ACTTCTTTTT
1 ATGAAAACAACTTCTTTTT
*
1668 ATGAAAACAATTTCTTTTT
1 ATGAAAACAACTTCTTTTT
1687 TATAATTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (19 bp):
ATGAAAACAACTTCTTTTT
Found at i:6456 original size:18 final size:19
Alignment explanation
Indices: 6430--6469 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
6420 AAGTGCAAAT
*
6430 CAAATAGAAAAAGAAAA-A
1 CAAAAAGAAAAAGAAAACA
*
6448 CAAAAAGAAAAATAAAACA
1 CAAAAAGAAAAAGAAAACA
6467 CAA
1 CAA
6470 TCTCCCCGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.78, C:0.10, G:0.07, T:0.05
Consensus pattern (19 bp):
CAAAAAGAAAAAGAAAACA
Found at i:9973 original size:14 final size:14
Alignment explanation
Indices: 9954--9985 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
9944 AACTTCAGAA
9954 TTCAGAATCCATAT
1 TTCAGAATCCATAT
9968 TTCAGAATCCATAT
1 TTCAGAATCCATAT
9982 TTCA
1 TTCA
9986 AAACAGTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (14 bp):
TTCAGAATCCATAT
Found at i:11853 original size:20 final size:20
Alignment explanation
Indices: 11824--11881 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
11814 TTTGATTAAT
* *
11824 ATATATATATATATTTAGAA
1 ATATAAATATATATTTAAAA
*
11844 ATATAAATATAATATATAAAA
1 ATATAAATAT-ATATTTAAAA
*
11865 ACTAT-ATTATATATTTA
1 A-TATAAATATATATTTA
11882 TATAAAATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 15 0.48
21 13 0.42
22 3 0.10
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
ATATAAATATATATTTAAAA
Found at i:12387 original size:20 final size:20
Alignment explanation
Indices: 12349--12387 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12339 TATTGACATT
12349 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
12369 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
12388 AAATAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:14653 original size:11 final size:11
Alignment explanation
Indices: 14632--14665 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
14622 TTTGACCTTT
14632 AATTATAAAAAA
1 AATT-TAAAAAA
14644 AATTTAAAAAA
1 AATTTAAAAAA
14655 AA-TTAAAAAA
1 AATTTAAAAAA
14665 A
1 A
14666 TTATGTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 9 0.41
12 4 0.18
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AATTTAAAAAA
Found at i:15831 original size:96 final size:91
Alignment explanation
Indices: 15661--15833 Score: 247
Period size: 96 Copynumber: 1.8 Consensus size: 91
15651 TTTTTTTGGG
* *
15661 AAAAAGGGAGTCATTAATTCAGTATTATTTCAATAATTATTTTGGGTGAGTGAAAATATTAATTA
1 AAAAAGGGAGTCATTAATTCAGTATTATTCCAATAATTATTTTGGGTGAATGAAAATATTAATTA
* *
15726 TACCTAACCAATTAAAAACCTTGAAT
66 CACCCAACCAATTAAAAACCTTGAAT
15752 AAAAATGGAGAGTCATTAATTCAGTATTATTCCAATATATATTATTTTGGGTGAATGAAAATATT
1 AAAAA-GG-GAGTCATTAATTCAGTATTATTCC-A-ATA-ATTATTTTGGGTGAATGAAAATATT
* *
15817 TATTGCACCCAACCAAT
61 AATTACACCCAACCAAT
15834 CAACTTTGGA
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
91 5 0.07
92 2 0.03
93 23 0.32
94 1 0.01
95 3 0.04
96 37 0.52
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (91 bp):
AAAAAGGGAGTCATTAATTCAGTATTATTCCAATAATTATTTTGGGTGAATGAAAATATTAATTA
CACCCAACCAATTAAAAACCTTGAAT
Done.