Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5662.1
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: 19645
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8254 original size:27 final size:26
Alignment explanation
Indices: 8196--8257 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
8186 GACTGTATAC
*
8196 AATTTTTTTCGTTTCAATTTTTTTGA
1 AATTTTTTTCGTTTCAATTTTTTTCA
** **
8222 TTTTTTTTTCGATTTCTTTTTTTTTCA
1 AATTTTTTTCG-TTTCAATTTTTTTCA
8249 AATTTTTTT
1 AATTTTTTT
8258 TCACGAATCT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.73
Consensus pattern (26 bp):
AATTTTTTTCGTTTCAATTTTTTTCA
Found at i:11100 original size:30 final size:30
Alignment explanation
Indices: 11066--11162 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
11056 AGCTCACTCC
11066 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
11096 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
11126 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
11156 TAGCTCA
1 TAGCTCA
11163 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:13374 original size:37 final size:37
Alignment explanation
Indices: 13323--13393 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
13313 CATTCTTGTA
13323 AAGAGAAAACAAAG-AAAAGAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAAAG-AAAGAAAAAGAAAAAGC
*
13360 AAGAGAAGAA-AAAGAAAAAGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAAAGAAAGAAAAAGAAAA
13394 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 24 0.77
38 7 0.23
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.01
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAAAGAAAGAAAAAGAAAAAGC
Found at i:13381 original size:15 final size:16
Alignment explanation
Indices: 13322--13393 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
13312 ACATTCTTGT
*
13322 AAAGAGAAAACAAAG-A
1 AAAGA-AAAAGAAAGAA
*
13338 AAAGAAAAGAAAAAGAA
1 AAAGAAAA-AGAAAGAA
* *
13355 AAAGCAAGAG-AAGAA
1 AAAGAAAAAGAAAGAA
*
13370 AAAGAAAAAGAAATAA
1 AAAGAAAAAGAAAGAA
13386 AAAGAAAA
1 AAAGAAAA
13394 GAGAGGCAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
15 16 0.35
16 23 0.50
17 7 0.15
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (16 bp):
AAAGAAAAAGAAAGAA
Found at i:13393 original size:6 final size:6
Alignment explanation
Indices: 13333--13382 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
13323 AAGAGAAAAC
13333 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
13382 A
1 A
13383 TAAAAAGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 9 0.22
6 23 0.56
7 3 0.07
8 3 0.07
9 3 0.07
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:13395 original size:21 final size:21
Alignment explanation
Indices: 13333--13393 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
13323 AAGAGAAAAC
13333 AAAGAAAAGAAAAGAAAAAGAA
1 AAAGAAAA-AAAAGAAAAAGAA
* * *
13355 AAAGCAAGAGAAGAAAAAGAA
1 AAAGAAAAAAAAGAAAAAGAA
13376 AAAGAAATAAAAAGAAAA
1 AAAGAAA-AAAAAGAAAA
13394 GAGAGGCAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAGAAAAAAAAGAAAAAGAA
Found at i:13475 original size:11 final size:12
Alignment explanation
Indices: 13443--13473 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
13433 TTGAGAGAAC
13443 TTGAAAAAGCCT
1 TTGAAAAAGCCT
13455 TTGAAAAAGCCT
1 TTGAAAAAGCCT
13467 TTGAAAA
1 TTGAAAA
13474 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:15688 original size:30 final size:30
Alignment explanation
Indices: 15654--15750 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
15644 AGCTCACTCC
15654 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
15684 TAGCTCAACTTCAGCTTAAGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
15714 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
15744 TAGCTCA
1 TAGCTCA
15751 TTTCAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:19411 original size:12 final size:12
Alignment explanation
Indices: 19394--19448 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
19384 ACGATATTGT
19394 AAAAAAAA-TC-
1 AAAAAAAATTCA
*
19404 AAAAAAAATTGA
1 AAAAAAAATTCA
* *
19416 AAGAAAAATTTGA
1 AA-AAAAAATTCA
19429 AAAAAAAATTCA
1 AAAAAAAATTCA
19441 AAAAAAAA
1 AAAAAAAA
19449 GAGTTTGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 8 0.21
11 1 0.03
12 18 0.47
13 11 0.29
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:19422 original size:13 final size:12
Alignment explanation
Indices: 19404--19448 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
19394 AAAAAAAATC
19404 AAAAAAAATTGA
1 AAAAAAAATTGA
*
19416 AAGAAAAATTTGA
1 AA-AAAAAATTGA
*
19429 AAAAAAAATTCA
1 AAAAAAAATTGA
19441 AAAAAAAA
1 AAAAAAAA
19449 GAGTTTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTGA
Done.