Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019799.1 Corchorus olitorius cultivar O-4 contig19832, 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: 32115
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:680 original size:13 final size:13
Alignment explanation
Indices: 662--687 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
652 ATTAGTGTCA
662 AATGTGTTATAAT
1 AATGTGTTATAAT
675 AATGTGTTATAAT
1 AATGTGTTATAAT
688 TCATTATTAT
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:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
AATGTGTTATAAT
Found at i:3150 original size:25 final size:25
Alignment explanation
Indices: 3114--3166 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
3104 TACTATTATT
3114 TTACTTTACAAAATTACCTCTTCAA
1 TTACTTTACAAAATTACCTCTTCAA
* *
3139 TTACTTTGCAAAATTAGCTCTTCAA
1 TTACTTTACAAAATTACCTCTTCAA
3164 TTA
1 TTA
3167 TAAGATCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.42
Consensus pattern (25 bp):
TTACTTTACAAAATTACCTCTTCAA
Found at i:14328 original size:2 final size:2
Alignment explanation
Indices: 14321--14347 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14311 AGAAACTTTG
14321 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 T
14348 GAGAGGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15568 original size:18 final size:17
Alignment explanation
Indices: 15543--15583 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
15533 GTGGGTATAC
*
15543 TTGTTTATACTTGTTAT
1 TTGTTTATACCTGTTAT
15560 TTAGTTTATACCTGTTAT
1 TT-GTTTATACCTGTTAT
15578 TTGTTT
1 TTGTTT
15584 TGCAAGTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.63
Consensus pattern (17 bp):
TTGTTTATACCTGTTAT
Found at i:15696 original size:41 final size:41
Alignment explanation
Indices: 15637--15729 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
15627 TCATCATAAT
15637 ATATCCTTCAAAAATAAATCCTTTAAAAAATACATTCTTAA
1 ATATCCTTCAAAAATAAATCCTTTAAAAAATACATTCTTAA
* **
15678 ATATCCTTCAAAATTAAATCCTTTAAAAAATTTATTCTTAA
1 ATATCCTTCAAAAATAAATCCTTTAAAAAATACATTCTTAA
15719 ATATCCTTCAA
1 ATATCCTTCAA
15730 CAATGGAGGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (41 bp):
ATATCCTTCAAAAATAAATCCTTTAAAAAATACATTCTTAA
Found at i:21714 original size:29 final size:29
Alignment explanation
Indices: 21673--21735 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
21663 GAAGACTGCA
21673 AGAG-TCTGTAAAATATTTGCAGATCGGG
1 AGAGATCTGTAAAATATTTGCAGATCGGG
21701 AGAGATCTGTAAAATATTTGCAGATCGGG
1 AGAGATCTGTAAAATATTTGCAGATCGGG
21730 AGAGAT
1 AGAGAT
21736 GAGAGAGCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.35, C:0.10, G:0.29, T:0.27
Consensus pattern (29 bp):
AGAGATCTGTAAAATATTTGCAGATCGGG
Found at i:22419 original size:23 final size:23
Alignment explanation
Indices: 22393--22440 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
22383 TTGAACAAAC
22393 CTCTCAAATAAACCAAACAGTTT
1 CTCTCAAATAAACCAAACAGTTT
*
22416 CTCTCAAATAAACCAAACGGTTT
1 CTCTCAAATAAACCAAACAGTTT
22439 CT
1 CT
22441 ATTAGTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.27, G:0.06, T:0.27
Consensus pattern (23 bp):
CTCTCAAATAAACCAAACAGTTT
Found at i:23426 original size:8 final size:9
Alignment explanation
Indices: 23390--23427 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
23380 CCCAAATTAC
23390 TTATGGAAA
1 TTATGGAAA
*
23399 TTAAGGAAA
1 TTATGGAAA
23408 TTATGGAAA
1 TTATGGAAA
23417 TTAT-GAAA
1 TTATGGAAA
23425 TTA
1 TTA
23428 AATGAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Found at i:24783 original size:49 final size:47
Alignment explanation
Indices: 24706--24846 Score: 160
Period size: 49 Copynumber: 2.9 Consensus size: 47
24696 CAAGCAATCC
* *
24706 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT
* * *
24754 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT
* *
24803 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
24847 TTGGCACGCT
Statistics
Matches: 79, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
47 15 0.19
48 22 0.28
49 35 0.44
50 7 0.09
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (47 bp):
TTTAATTTTCATTGCACTTTTTCTCAATTTTTATACAAAATTGAACT
Done.