Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold524
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: 28188
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:556 original size:30 final size:31
Alignment explanation
Indices: 522--618 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
512 AGCTCACTCC
*
522 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
552 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
582 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
612 TAGCTCA
1 TAGCTCA
619 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:3173 original size:15 final size:14
Alignment explanation
Indices: 3142--3180 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
3132 AAGAGAAAAT
3142 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
3158 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
3173 AAAGAAAA
1 AAAGAAAA
3181 CGAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 4 0.18
17 5 0.23
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:3278 original size:11 final size:12
Alignment explanation
Indices: 3246--3276 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3236 TTGAGAGAAC
*
3246 TTGAAAAAACCT
1 TTGAAAAAGCCT
3258 TTGAAAAAGCCT
1 TTGAAAAAGCCT
3270 TTGAAAA
1 TTGAAAA
3277 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:3287 original size:12 final size:12
Alignment explanation
Indices: 3279--3303 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3269 TTTGAAAAGC
3279 AAAAAGAAAATG
1 AAAAAGAAAATG
3291 AAAAAGAAAATG
1 AAAAAGAAAATG
3303 A
1 A
3304 GATTGAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:3313 original size:29 final size:31
Alignment explanation
Indices: 3279--3359 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 31
3269 TTTGAAAAGC
* *
3279 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAACGAAAAAGAAATATGAGAGTG
* *
3309 -AAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAACGAAAAAGAAATATGAGAGTG
* *
3338 AAAAAGAAGAGGAAAAAGAAAT
1 AAAAAGAAAACGAAAAAGAAAT
3360 TGAAACAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
28 8 0.20
29 16 0.39
30 8 0.20
31 9 0.22
ACGTcount: A:0.64, C:0.01, G:0.23, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAACGAAAAAGAAATATGAGAGTG
Found at i:3345 original size:28 final size:28
Alignment explanation
Indices: 3292--3345 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3282 AAGAAAATGA
*
3292 AAAAGAAAATGAGATTGAAAAGAGAACG
1 AAAAGAAAATGAGAGTGAAAAGAGAACG
*
3320 AAAAGAAATTTGAGAGTGAAAA-AGAA
1 AAAAGAAA-ATGAGAGTGAAAAGAGAA
3346 GAGGAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.61, C:0.02, G:0.24, T:0.13
Consensus pattern (28 bp):
AAAAGAAAATGAGAGTGAAAAGAGAACG
Found at i:4971 original size:28 final size:29
Alignment explanation
Indices: 4906--4961 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
4896 GATTCAAAGA
*
4906 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
4935 TGGGTTTATGGATATAAAGTTT-TGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
4962 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:9560 original size:28 final size:28
Alignment explanation
Indices: 9528--9583 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
9518 GATTCAAAGA
*
9528 TGGGTTTATGGATATGAAGTTTATGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
*
9556 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
9584 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (28 bp):
TGGGTTTATGGATATAAAGTTTATGTAG
Found at i:11725 original size:30 final size:31
Alignment explanation
Indices: 11691--11787 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
11681 AGCTCACTCC
*
11691 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
11721 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
11751 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
11781 TAGCTCA
1 TAGCTCA
11788 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:14347 original size:16 final size:16
Alignment explanation
Indices: 14328--14369 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
14318 AAGAGAAAAT
14328 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
*
14344 AAAGAAAACG-AAATAA
1 AAAGAAAA-GAAAAGAA
*
14360 AAAGGAAAGA
1 AAAGAAAAGA
14370 GAGGCAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.02
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:14431 original size:11 final size:12
Alignment explanation
Indices: 14417--14446 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
14407 TTGAGAGAAC
14417 TTGAAAAA-CCT
1 TTGAAAAAGCCT
14428 TTGAAAAAGCCT
1 TTGAAAAAGCCT
14440 TTGAAAA
1 TTGAAAA
14447 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:14457 original size:12 final size:12
Alignment explanation
Indices: 14449--14473 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14439 TTTGAAAAGC
14449 AAAAAGAAAATG
1 AAAAAGAAAATG
14461 AAAAAGAAAATG
1 AAAAAGAAAATG
14473 A
1 A
14474 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:14470 original size:18 final size:18
Alignment explanation
Indices: 14443--14486 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
14433 AAAGCCTTTG
14443 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
14462 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
14480 AAAAGAA
1 AAAAGAA
14487 CGAAAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:14502 original size:28 final size:27
Alignment explanation
Indices: 14462--14514 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
14452 AAGAAAATGA
*
14462 AAAAGAAAATGAGATTGAAAAAGAACG
1 AAAAGAAAATGAGAGTGAAAAAGAACG
*
14489 AAAAGAAATTTGAGAGTGAAAAAGAA
1 AAAAGAAA-ATGAGAGTGAAAAAGAA
14515 GAGGAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.62, C:0.02, G:0.23, T:0.13
Consensus pattern (27 bp):
AAAAGAAAATGAGAGTGAAAAAGAACG
Found at i:16140 original size:28 final size:29
Alignment explanation
Indices: 16075--16130 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
16065 GATTCAAAGA
*
16075 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
16104 TGGGTTTATGGATATAAAGTTT-TGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
16131 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:20732 original size:26 final size:27
Alignment explanation
Indices: 20703--20754 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
20693 ATTCAAAGAT
*
20703 GGTTTA-GATATGAAGTTTATGTAGTG
1 GGTTTAGGATATAAAGTTTATGTAGTG
*
20729 GGTTTATGGATATAAAGTTTTTGTAG
1 GGTTTA-GGATATAAAGTTTATGTAG
20755 GTTTGGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
28 16 0.73
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (27 bp):
GGTTTAGGATATAAAGTTTATGTAGTG
Found at i:22888 original size:30 final size:31
Alignment explanation
Indices: 22854--22950 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
22844 AGCTCACTCC
*
22854 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
22884 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
22914 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
22944 TAGCTCA
1 TAGCTCA
22951 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:27565 original size:30 final size:30
Alignment explanation
Indices: 27480--27576 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
27470 TAAACTAAAA
* *
27480 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
27510 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
27540 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
27569 ATGAGCTA
1 -TGAGCTA
27577 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Done.