Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1619
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: 27534
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:351 original size:5 final size:5
Alignment explanation
Indices: 341--398 Score: 50
Period size: 5 Copynumber: 12.0 Consensus size: 5
331 AAAGAGAAAC
* * * *
341 AAAGA AAAGA AAAAA AAAGA AAAG- CAAGA GAAG- AAAGA AATGA AATA-A
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA-AGA
389 AAAGA AAAGA
1 AAAGA AAAGA
399 GAGGCAAGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
4 7 0.17
5 35 0.83
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:359 original size:15 final size:15
Alignment explanation
Indices: 331--398 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
321 ACATTCTTGT
* *
331 AAAGAGAAACAAAGA
1 AAAGAAAAAAAAAGA
346 AAAGAAAAAAAAAGA
1 AAAGAAAAAAAAAGA
*
361 AAAGCAAGAGAAGAAAGA
1 AAAG-AA-A-AAAAAAGA
* *
379 AATGAAATAAAAAGA
1 AAAGAAAAAAAAAGA
394 AAAGA
1 AAAGA
399 GAGGCAAGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
15 27 0.63
16 3 0.07
17 3 0.07
18 10 0.23
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (15 bp):
AAAGAAAAAAAAAGA
Found at i:380 original size:33 final size:34
Alignment explanation
Indices: 332--397 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
322 CATTCTTGTA
332 AAGAGAAACAAAGAAAAGAAAAAAAAAGAAAAGC
1 AAGAGAAACAAAGAAAAGAAAAAAAAAGAAAAGC
* * *
366 AAGAG-AAGAAAGAAATGAAATAAAAAGAAAAG
1 AAGAGAAACAAAGAAAAGAAAAAAAAAGAAAAG
398 AGAGGCAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 24 0.83
34 5 0.17
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.03
Consensus pattern (34 bp):
AAGAGAAACAAAGAAAAGAAAAAAAAAGAAAAGC
Found at i:1924 original size:21 final size:23
Alignment explanation
Indices: 1900--1942 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
1890 TTTGGAAATT
1900 ATTTATACTTTG-A-TGTGATGG
1 ATTTATACTTTGAATTGTGATGG
* *
1921 ATTTTTTCTTTGAATTGTGATG
1 ATTTATACTTTGAATTGTGATG
1943 ATGTGATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (23 bp):
ATTTATACTTTGAATTGTGATGG
Found at i:2633 original size:30 final size:30
Alignment explanation
Indices: 2599--2695 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
2589 AGCTCACTCC
2599 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
2629 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
2659 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
2689 TAGCTCA
1 TAGCTCA
2696 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:4356 original size:1 final size:1
Alignment explanation
Indices: 4350--4419 Score: 68
Period size: 1 Copynumber: 70.0 Consensus size: 1
4340 TATTGTATTG
* *** ** * *
4350 AAAAAAAAAAAAAAAGAAAAAAAATTGAAAAAAAAATCAAAAAAAAAAAAAAAAAAGAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4415 AAAAA
1 AAAAA
4420 GTGAAAAGTC
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.89, C:0.01, G:0.06, T:0.04
Consensus pattern (1 bp):
A
Found at i:4384 original size:27 final size:28
Alignment explanation
Indices: 4346--4402 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
4336 TTACTATTGT
*
4346 ATTGAAAAAAAAA-AAAAAAGAAAAAAA
1 ATTGAAAAAAAAACAAAAAAAAAAAAAA
4373 ATTGAAAAAAAAATCAAAAAAAAAAAAAA
1 ATTGAAAAAAAAA-CAAAAAAAAAAAAAA
4402 A
1 A
4403 AAAGAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 13 0.48
29 14 0.52
ACGTcount: A:0.84, C:0.02, G:0.05, T:0.09
Consensus pattern (28 bp):
ATTGAAAAAAAAACAAAAAAAAAAAAAA
Found at i:4426 original size:11 final size:11
Alignment explanation
Indices: 4350--4420 Score: 83
Period size: 11 Copynumber: 6.5 Consensus size: 11
4340 TATTGTATTG
4350 AAAAA-AAAAA
1 AAAAAGAAAAA
4360 AAAAAGAAAAA
1 AAAAAGAAAAA
**
4371 AAATTGAAAAA
1 AAAAAGAAAAA
**
4382 AAAATCAAAAA
1 AAAAAGAAAAA
4393 AAAAA-AAAAA
1 AAAAAGAAAAA
4403 AAAGAAGAAAAA
1 AAA-AAGAAAAA
4415 AAAAAG
1 AAAAAG
4421 TGAAAAGTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
10 13 0.25
11 32 0.60
12 8 0.15
ACGTcount: A:0.87, C:0.01, G:0.07, T:0.04
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:5347 original size:37 final size:37
Alignment explanation
Indices: 5296--5366 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
5286 CATTCTTGTA
5296 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
5333 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
5367 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:5366 original size:6 final size:6
Alignment explanation
Indices: 5306--5355 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
5296 AAGAGAAAAC
*
5306 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
5355 A
1 A
5356 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:5448 original size:11 final size:12
Alignment explanation
Indices: 5416--5446 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
5406 TTGAGAGAAC
5416 TTGAAAAAGCCT
1 TTGAAAAAGCCT
5428 TTGAAAAAGCCT
1 TTGAAAAAGCCT
5440 TTGAAAA
1 TTGAAAA
5447 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:7659 original size:30 final size:30
Alignment explanation
Indices: 7625--7721 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
7615 AGCTCACTCC
7625 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
7655 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
7685 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
7715 TAGCTCA
1 TAGCTCA
7722 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:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:9391 original size:1 final size:1
Alignment explanation
Indices: 9385--9455 Score: 61
Period size: 1 Copynumber: 71.0 Consensus size: 1
9375 ATTGTAATTG
*** ** *** *
9385 AAAAAAAAAAAAAAAAAAAAAAAATTGAAAAAAAAATCAAAAAAAAATTCAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9450 AAAAAA
1 AAAAAA
9456 GTGAAAAGTC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.87, C:0.03, G:0.03, T:0.07
Consensus pattern (1 bp):
A
Found at i:9419 original size:23 final size:23
Alignment explanation
Indices: 9389--9462 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
9379 TAATTGAAAA
9389 AAAAAAAAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAAAAAAATTG
** *
9412 AAAAAAAAATCAAAAAAAAATTC
1 AAAAAAAAAAAAAAAAAAAATTG
*
9435 AAAAAAAAAGAAAAAAAAAAAGTG
1 AAAAAAAAA-AAAAAAAAAAATTG
9459 AAAA
1 AAAA
9463 GTCTTGTGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 29 0.67
24 14 0.33
ACGTcount: A:0.84, C:0.03, G:0.05, T:0.08
Consensus pattern (23 bp):
AAAAAAAAAAAAAAAAAAAATTG
Found at i:9462 original size:12 final size:12
Alignment explanation
Indices: 9400--9462 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
9390 AAAAAAAAAA
* *
9400 AAAAAAAAATTG
1 AAAAAAAAAGTC
9412 AAAAAAAAA-TC
1 AAAAAAAAAGTC
*
9423 AAAAAAAAATTC
1 AAAAAAAAAGTC
**
9435 AAAAAAAAAGAA
1 AAAAAAAAAGTC
*
9447 AAAAAAAAAGTG
1 AAAAAAAAAGTC
9459 AAAA
1 AAAA
9463 GTCTTGTGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
11 10 0.23
12 34 0.77
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.10
Consensus pattern (12 bp):
AAAAAAAAAGTC
Found at i:10382 original size:37 final size:37
Alignment explanation
Indices: 10331--10401 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
10321 CATTCTTGTA
10331 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
10368 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
10402 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:10401 original size:6 final size:6
Alignment explanation
Indices: 10341--10390 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
10331 AAGAGAAAAC
*
10341 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
10390 A
1 A
10391 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:12679 original size:30 final size:30
Alignment explanation
Indices: 12645--12740 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
12635 AGCTCACTCC
12645 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
12675 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
*
12705 CAGCTCAACTTTAGCTCACGAGCTAAA-CT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
12734 TAGCTCA
1 TAGCTCA
12741 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
29 9 0.18
30 42 0.82
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:16106 original size:40 final size:40
Alignment explanation
Indices: 16051--16304 Score: 298
Period size: 40 Copynumber: 6.4 Consensus size: 40
16041 TGATAACCGG
* * * *
16051 GCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TCTGA
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCGA
16091 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGA
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGA
* *
16131 GCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGA
* * *
16171 GCTAAGTCCCGAAGGCATTTGTTCGAGTTGCTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGA
* * *
16211 GCTAAGCCCCGAAGGCATTGGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGA
* * ***
16251 GCTATGTCCTGAAGGCATTCAAGCGAG-TAGCTATATCCG-
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGA
* *
16290 GTTAAATCCCGAAGG
1 GCTAAGTCCCGAAGG
16305 TACTTGGCTT
Statistics
Matches: 189, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
39 14 0.07
40 175 0.93
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGA
Found at i:16260 original size:120 final size:120
Alignment explanation
Indices: 16047--16304 Score: 335
Period size: 120 Copynumber: 2.2 Consensus size: 120
16037 TGGATGATAA
* * * *
16047 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCTGAGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGAGCTAAGCCCCGAAGGCATTGG
***
16112 TGCGAGTTACTATATCCGAGCTAAGTCCTGAAGGCATTTGTGCGAGTTA-CTATAT
66 TGCGAGTTACTATATCCGAGCTAAGTCCTGAAGGCATTCAAGCGAG-TAGCTATAT
** *
16167 CCGGGCTAAGTCCCGAAGGCATTTGTTCGAGTTG-CTA-TATCCGGGCTAAGCCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAG-TGACTAGT-TCCGAGCTAAGCCCCGAAGGCATT
* *
16230 GGTGCGAGTTACTATATCCGGGCTATGTCCTGAAGGCATTCAAGCGAGTAGCTATAT
64 GGTGCGAGTTACTATATCCGAGCTAAGTCCTGAAGGCATTCAAGCGAGTAGCTATAT
* *
16287 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
16305 TACTTGGCTT
Statistics
Matches: 121, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
119 17 0.14
120 102 0.84
121 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (120 bp):
CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGAGCTAAGCCCCGAAGGCATTGG
TGCGAGTTACTATATCCGAGCTAAGTCCTGAAGGCATTCAAGCGAGTAGCTATAT
Found at i:22224 original size:20 final size:19
Alignment explanation
Indices: 22201--22265 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
22191 AAGCTCAAAC
22201 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
22221 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
22241 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
22261 GAGCT
1 GAGCT
22266 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:26925 original size:20 final size:19
Alignment explanation
Indices: 26902--26966 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
26892 AAGCTCAAAC
26902 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
26922 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
26942 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
26962 GAGCT
1 GAGCT
26967 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Done.