Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021359.1 Corchorus olitorius cultivar O-4 contig21392, 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: 17289
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3179 original size:51 final size:50
Alignment explanation
Indices: 3078--3180 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
3068 GTTCTTCATA
** *
3078 TTTTTCTTGTTTAGATCTTGTCTCAGGACACCCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
* * * *
3128 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTATTCGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
3179 TT
1 TT
3181 CTCTTTCAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 4 0.09
51 39 0.89
52 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
Found at i:4372 original size:2 final size:2
Alignment explanation
Indices: 4365--4399 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4355 GTAGAGATTC
4365 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4400 GATTGTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4563 original size:25 final size:25
Alignment explanation
Indices: 4535--4585 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
4525 AATTTTTATT
4535 TTTAAGGGTTAATAAATGATATCTC
1 TTTAAGGGTTAATAAATGATATCTC
4560 TTTAAGGGTTAATAAATGATATCTC
1 TTTAAGGGTTAATAAATGATATCTC
4585 T
1 T
4586 GCTCTCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (25 bp):
TTTAAGGGTTAATAAATGATATCTC
Found at i:5262 original size:25 final size:24
Alignment explanation
Indices: 5234--5295 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
5224 GTGGATTGTA
*
5234 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
5259 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
5283 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
5296 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:9472 original size:38 final size:37
Alignment explanation
Indices: 9430--9510 Score: 117
Period size: 38 Copynumber: 2.2 Consensus size: 37
9420 CCAGTGCGCT
* * * *
9430 GGCCCAGCGTGCCAGGCCAGGCGCGCGGGCCTGCAAGC
1 GGCCCAGCGCGCCAGGCCAAGCACGCGGGCCAGC-AGC
9468 GGCCCAGCGCGCCAGGCCAAGCACGCGGGCCAGCAGC
1 GGCCCAGCGCGCCAGGCCAAGCACGCGGGCCAGCAGC
9505 GGCCCA
1 GGCCCA
9511 AGCGAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 9 0.23
38 30 0.77
ACGTcount: A:0.16, C:0.42, G:0.40, T:0.02
Consensus pattern (37 bp):
GGCCCAGCGCGCCAGGCCAAGCACGCGGGCCAGCAGC
Found at i:9625 original size:4 final size:4
Alignment explanation
Indices: 9609--9638 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
9599 GCCCAAATTG
9609 AAAT AAA- AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
9639 AGGGAAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:13202 original size:2 final size:2
Alignment explanation
Indices: 13195--13225 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13185 TCCAAACCAA
13195 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13226 AAGGTGCTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13679 original size:14 final size:14
Alignment explanation
Indices: 13660--13694 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
13650 GGCGACGAAG
13660 ATGGAGGAGAAGAA
1 ATGGAGGAGAAGAA
13674 ATGGAGGAGAAGAA
1 ATGGAGGAGAAGAA
13688 ATCGGAG
1 AT-GGAG
13695 AGTTGTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.46, C:0.03, G:0.43, T:0.09
Consensus pattern (14 bp):
ATGGAGGAGAAGAA
Done.