Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2981
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: 28418
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:6096 original size:29 final size:29
Alignment explanation
Indices: 6034--6100 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
6024 AATCAACCAT
6034 GCACACTTAGTGCCATGCACTTTAAACTC
1 GCACACTTAGTGCCATGCACTTTAAACTC
* **
6063 ACACACTTAGTGCCATGCA-TTTCAAGTTC
1 GCACACTTAGTGCCATGCACTTT-AAACTC
6092 GCACACTTA
1 GCACACTTA
6101 CCTTTTTCCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.28
Consensus pattern (29 bp):
GCACACTTAGTGCCATGCACTTTAAACTC
Found at i:6240 original size:28 final size:29
Alignment explanation
Indices: 6204--6281 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
6194 CTTAATAATC
6204 AACCGCGCACACTTAGTGCCATGTAC-TTA
1 AACC-CGCACACTTAGTGCCATGTACATTA
*
6233 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-A-TTA
6262 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
6282 ATCTCATGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 5 0.12
27 1 0.02
28 13 0.31
29 22 0.52
30 1 0.02
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGTACATTA
Found at i:10564 original size:15 final size:15
Alignment explanation
Indices: 10544--10600 Score: 105
Period size: 15 Copynumber: 3.7 Consensus size: 15
10534 GATATCAAGT
10544 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
10559 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
10574 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
10589 TGAAAAAGAAAA
1 TGAAAAA-AAAA
10601 AAAAGCTAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
15 37 0.90
16 4 0.10
ACGTcount: A:0.63, C:0.05, G:0.14, T:0.18
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:19283 original size:15 final size:15
Alignment explanation
Indices: 19263--19317 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
19253 ACTCTCCTCA
*
19263 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
19278 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
19293 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
19307 TTCTTTT-TCTC
1 TTCTTTTCTCTC
19318 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:21362 original size:17 final size:17
Alignment explanation
Indices: 21328--21362 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21318 AATCACTTCT
*
21328 TTTTTTTTAATTCCGAA
1 TTTTTTTTAATACCGAA
*
21345 TTTTTTTTAATACTGAA
1 TTTTTTTTAATACCGAA
21362 T
1 T
21363 ACACAAAGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTTTTTAATACCGAA
Found at i:21409 original size:10 final size:10
Alignment explanation
Indices: 21394--21431 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
21384 AATACAAACT
*
21394 TTTTTTTTTA
1 TTTTTTTTAA
21404 TTTTTTTTCAA
1 TTTTTTTT-AA
21415 TTTTTTTTAA
1 TTTTTTTTAA
21425 TTTTTTT
1 TTTTTTT
21432 ACAATCTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:21409 original size:11 final size:11
Alignment explanation
Indices: 21393--21431 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
21383 GAATACAAAC
*
21393 TTTTTTTTTTA
1 TTTTTTTTTAA
*
21404 TTTTTTTTCAA
1 TTTTTTTTTAA
21415 -TTTTTTTTAA
1 TTTTTTTTTAA
21425 TTTTTTT
1 TTTTTTT
21432 ACAATCTCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:21420 original size:21 final size:21
Alignment explanation
Indices: 21394--21436 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
21384 AATACAAACT
* *
21394 TTTTTTTTTATTTTTTTTCAA
1 TTTTTTTTAATTTTTTTACAA
21415 TTTTTTTTAATTTTTTTACAA
1 TTTTTTTTAATTTTTTTACAA
21436 T
1 T
21437 CTCGTAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTTTTAATTTTTTTACAA
Found at i:23648 original size:20 final size:20
Alignment explanation
Indices: 23625--23671 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
23615 GGGTTAAGAT
*
23625 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
23645 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
23665 TGAGCTG
1 TGAGCTG
23672 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:24807 original size:52 final size:52
Alignment explanation
Indices: 24693--24793 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
24683 TAAGGAAACG
* *
24693 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
24745 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
24794 TATGTGCATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Done.