Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012635.1 Corchorus olitorius cultivar O-4 contig12668, 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: 20007
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1517 original size:13 final size:13
Alignment explanation
Indices: 1499--1525 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1489 CCAAATGGAA
1499 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
1512 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
1525 T
1 T
1526 TTAGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:4954 original size:11 final size:11
Alignment explanation
Indices: 4925--4954 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4915 ACGAACATGC
*
4925 TCGTTTAGTGT
1 TCGTTTATTGT
4936 TCGTTTATTGT
1 TCGTTTATTGT
4947 TCGTTTAT
1 TCGTTTAT
4955 AGCTCGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.60
Consensus pattern (11 bp):
TCGTTTATTGT
Found at i:6587 original size:31 final size:31
Alignment explanation
Indices: 6552--6614 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
6542 TTATTTCAAA
* *
6552 TAATATTTAAAAT-TTTATTAGAAATATTTAT
1 TAATATATAAAATAATTATTA-AAATATTTAT
**
6583 TAATATATGCAATAATTATTAAAATATTTAT
1 TAATATATAAAATAATTATTAAAATATTTAT
6614 T
1 T
6615 TAATGTAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (31 bp):
TAATATATAAAATAATTATTAAAATATTTAT
Found at i:10047 original size:36 final size:36
Alignment explanation
Indices: 10000--10072 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
9990 TTATGTGTGA
10000 TTTTAGGTCTTGAAGAGAAGAAAAGTGGAAACATGT
1 TTTTAGGTCTTGAAGAGAAGAAAAGTGGAAACATGT
10036 TTTTAGGTCTTGAAGAGAAGAAAAGTGGAAACATGT
1 TTTTAGGTCTTGAAGAGAAGAAAAGTGGAAACATGT
10072 T
1 T
10073 GTTTTTCACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.29
Consensus pattern (36 bp):
TTTTAGGTCTTGAAGAGAAGAAAAGTGGAAACATGT
Found at i:10617 original size:11 final size:11
Alignment explanation
Indices: 10601--10625 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10591 CATCTTTTAG
10601 TTTTCTCTAGT
1 TTTTCTCTAGT
10612 TTTTCTCTAGT
1 TTTTCTCTAGT
10623 TTT
1 TTT
10626 AGAAGAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTCTCTAGT
Found at i:14902 original size:13 final size:13
Alignment explanation
Indices: 14884--14909 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14874 TACTTAGTCG
14884 AACTTCTTCTTCT
1 AACTTCTTCTTCT
14897 AACTTCTTCTTCT
1 AACTTCTTCTTCT
14910 TTTTCCTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (13 bp):
AACTTCTTCTTCT
Found at i:17472 original size:16 final size:15
Alignment explanation
Indices: 17434--17475 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
17424 ACAGAGGTTG
17434 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
17449 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
17464 ACTAGAAAACAA
1 AC-AGAAAACAA
17476 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.