Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1316
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: 42017
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:2219 original size:20 final size:20
Alignment explanation
Indices: 2194--2241 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2184 TAATTAATTT
*
2194 TAAATAAAAATTTTATTAAA
1 TAAATAAAAATTTAATTAAA
*
2214 TAAATAATAATTTAATTAAA
1 TAAATAAAAATTTAATTAAA
*
2234 TTAATAAA
1 TAAATAAA
2242 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATAAAAATTTAATTAAA
Found at i:2240 original size:17 final size:17
Alignment explanation
Indices: 2209--2272 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
2199 AAAAATTTTA
*
2209 TTAAATAAA-TAATAAT
1 TTAATTAAATTAATAAT
*
2225 TTAATTAAATTAATAAA
1 TTAATTAAATTAATAAT
* *
2242 TTAA-AAAATATCATAGAT
1 TTAATTAAAT-TAATA-AT
*
2260 TTAATTCAATTAA
1 TTAATTAAATTAA
2273 AATCAAATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
16 12 0.33
17 14 0.39
18 7 0.19
19 3 0.08
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (17 bp):
TTAATTAAATTAATAAT
Found at i:2271 original size:35 final size:33
Alignment explanation
Indices: 2208--2272 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
2198 TAAAAATTTT
2208 ATTAAATAAATAATAATTTAATTAAATTAATAA
1 ATTAAATAAATAATAATTTAATTAAATTAATAA
*
2241 ATTAAA-AAATATCATAGATTTAATTCAATTAA
1 ATTAAATAAATA--ATA-ATTTAATTAAATTAA
2273 AATCAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 5 0.18
33 6 0.21
34 3 0.11
35 14 0.50
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (33 bp):
ATTAAATAAATAATAATTTAATTAAATTAATAA
Found at i:3054 original size:5 final size:5
Alignment explanation
Indices: 3037--3111 Score: 52
Period size: 5 Copynumber: 15.0 Consensus size: 5
3027 AGATTAAACT
3037 TTTAA TTTAAA TTTAA TTT-- TTTAA TTT-A TTTGAA TTTAAA TTTAAA
1 TTTAA TTT-AA TTTAA TTTAA TTTAA TTTAA TTT-AA TTT-AA TTT-AA
* *
3083 TATTAA --TAA TTCAA ATTAA TTTAA TTTAA
1 T-TTAA TTTAA TTTAA TTTAA TTTAA TTTAA
3112 ACTTAAACAT
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
3 6 0.11
4 4 0.07
5 25 0.44
6 20 0.35
7 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (5 bp):
TTTAA
Found at i:5346 original size:10 final size:10
Alignment explanation
Indices: 5331--5355 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5321 TTTGAAAATA
5331 TAGCCGTTAC
1 TAGCCGTTAC
5341 TAGCCGTTAC
1 TAGCCGTTAC
5351 TAGCC
1 TAGCC
5356 AATGTATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.28
Consensus pattern (10 bp):
TAGCCGTTAC
Found at i:5396 original size:13 final size:13
Alignment explanation
Indices: 5378--5403 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5368 CATTTTTGGG
5378 ATGTATCGATACA
1 ATGTATCGATACA
5391 ATGTATCGATACA
1 ATGTATCGATACA
5404 TATTTGTGTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5398 original size:34 final size:33
Alignment explanation
Indices: 5355--5424 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 33
5345 CGTTACTAGC
*
5355 CAATGTATCGATACATTTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTTGGG-TGTATCGATA
*
5389 CAATGTATCGATACATATTTGTGTGTATCGATA
1 CAATGTATCGATACATATTTGGGTGTATCGATA
5422 CAA
1 CAA
5425 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 13 0.38
34 21 0.62
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATATTTGGGTGTATCGATA
Found at i:10258 original size:52 final size:52
Alignment explanation
Indices: 10188--10308 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
10178 GAAAATTTAT
*
10188 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* *
10240 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
10292 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
10309 AAGATTGGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:10321 original size:52 final size:52
Alignment explanation
Indices: 10188--10328 Score: 194
Period size: 52 Copynumber: 2.7 Consensus size: 52
10178 GAAAATTTAT
* *
10188 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACAATTATTAGTGTATCGATACATCTGGGCAAATTTGC
* * *
10240 TTGCATGTATCGATAC-ATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACAATTAT-TAGTGTATCGATACATCTGGGCAAATTTGC
** *
10292 CTGCATGTATCGATACAAAGATTGGTGTATCGATACA
1 CTGCATGTATCGATACAATTATTAGTGTATCGATACA
10329 ATGTATCGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
51 2 0.03
52 72 0.95
53 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACAATTATTAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:10335 original size:13 final size:13
Alignment explanation
Indices: 10317--10341 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10307 CAAAGATTGG
10317 TGTATCGATACAA
1 TGTATCGATACAA
10330 TGTATCGATACA
1 TGTATCGATACA
10342 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:10354 original size:21 final size:21
Alignment explanation
Indices: 10328--10407 Score: 160
Period size: 21 Copynumber: 3.8 Consensus size: 21
10318 GTATCGATAC
10328 AATGTATCGATACATTTGAGT
1 AATGTATCGATACATTTGAGT
10349 AATGTATCGATACATTTGAGT
1 AATGTATCGATACATTTGAGT
10370 AATGTATCGATACATTTGAGT
1 AATGTATCGATACATTTGAGT
10391 AATGTATCGATACATTT
1 AATGTATCGATACATTT
10408 CTTTGGCAGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (21 bp):
AATGTATCGATACATTTGAGT
Found at i:10465 original size:13 final size:13
Alignment explanation
Indices: 10447--10471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10437 CAAAAAAATA
10447 TGTATCGATACAT
1 TGTATCGATACAT
10460 TGTATCGATACA
1 TGTATCGATACA
10472 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10467 original size:33 final size:33
Alignment explanation
Indices: 10425--10491 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
10415 AGTAGCTTAA
10425 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
10458 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
10491 A
1 A
10492 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:11335 original size:67 final size:68
Alignment explanation
Indices: 11213--11339 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 68
11203 ATTGGGTTTT
* * * *
11213 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGACCAACAATATTGGACTTAAAGATGAAGATG
11278 AGA
66 AGA
* * ** *
11281 AAAG-TGATAAAGATGCCAATATGTTGATTCACGACCAACGCTATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGACCAACAATATTGGACTTAAAGATGA
11340 GAAAAAGGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
67 46 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGACCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:11431 original size:49 final size:44
Alignment explanation
Indices: 11342--11576 Score: 267
Period size: 49 Copynumber: 5.1 Consensus size: 44
11332 AAAGATGAGA
* *
11342 AAAAGGATGTCAATGTGCTGATTCAAGGCCTGCTACATTGGACTT
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
* *
11387 AAAGAAGAAGTTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 -AA-AAG--G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
11436 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
11479 AAAGAAGAAGTTGCCAATATGCTGATTCAAGGCCAGCTATATTAGACTT
1 -AA-AAG--G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
* *
11528 -AAAGGTGCCAATGTACTGATTCAAGGCCAGCTACATTGGGCTT
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
11571 AGAAGG
1 AAAAGG
11577 GTTGCCATCG
Statistics
Matches: 163, Mismatches: 16, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
43 69 0.42
44 6 0.04
45 1 0.01
46 11 0.07
47 5 0.03
48 1 0.01
49 70 0.43
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (44 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:11459 original size:43 final size:45
Alignment explanation
Indices: 11352--11583 Score: 283
Period size: 43 Copynumber: 5.0 Consensus size: 45
11342 AAAAGGATGT
*
11352 CAATGTGCTGATTCAAGGCCTGCTACATTGGACTTAAAGAAGAAGTTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTT--AGAAG--GTTGC
* *
11401 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-AAGG-TGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAGAAGGTTGC
11444 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTT--AGAAG--GTTGC
* * *
11493 CAATATGCTGATTCAAGGCCAGCTATATTAGACTTA-AAGG-TGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAGAAGGTTGC
* *
11536 CAATGTACTGATTCAAGGCCAGCTACATTGGGCTTAGAAGGGTTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAGAA-GGTTGC
11582 CA
1 CA
11584 TCGACTTGTG
Statistics
Matches: 161, Mismatches: 13, Indels: 21
0.83 0.07 0.11
Matches are distributed among these distances:
43 70 0.43
44 4 0.02
45 3 0.02
46 14 0.09
47 2 0.01
48 1 0.01
49 67 0.42
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (45 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAGAAGGTTGC
Found at i:11509 original size:92 final size:92
Alignment explanation
Indices: 11343--11571 Score: 404
Period size: 92 Copynumber: 2.5 Consensus size: 92
11333 AAGATGAGAA
* *
11343 AAAGGATGTCAATGTGCTGATTCAAGGCCTGCTACATTGGACTTAAAGAAGAAGTTGCCAATATG
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTTGCCAATATG
*
11408 CTGATTCAAGGCCAGCTATATTGGACTT
65 CTGATTCAAGGCCAGCTATATTAGACTT
11436 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTTGCCAATATGC
11501 TGATTCAAGGCCAGCTATATTAGACTT
66 TGATTCAAGGCCAGCTATATTAGACTT
* *
11528 AAAGGTGCCAATGTACTGATTCAAGGCCAGCTACATTGGGCTTA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
11572 GAAGGGTTGC
Statistics
Matches: 131, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
92 126 0.96
93 5 0.04
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTTGCCAATATGC
TGATTCAAGGCCAGCTATATTAGACTT
Found at i:11609 original size:33 final size:33
Alignment explanation
Indices: 11571--11642 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
11561 CATTGGGCTT
*
11571 AGAAGGGTTGCCATCGACTTGTGAGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGAGGGCTTTAG
*
11604 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGAGGGCTTTAG
*
11637 AAAAGG
1 AGAAGG
11643 TGAAAGATGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.24, C:0.15, G:0.36, T:0.25
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGAGGGCTTTAG
Found at i:11730 original size:36 final size:35
Alignment explanation
Indices: 11625--11980 Score: 376
Period size: 34 Copynumber: 10.3 Consensus size: 35
11615 CACCGACTTG
** *
11625 TGTGGGCTTTAGAAAAGGTGAAAGA-TGCCACGAAGT
1 TGTGGGCTTT--AAAAGGAAAAAGAGTGCCACGGAGT
* * *
11661 TGTGGAC-TTAAAAAGAACAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
11694 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTTAAAA-GGAAAAAGAGTGCCACGGAGT
11730 TGTGGGCTTTGAAAA-G---AAGA-TGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
* * *
11761 TGTGGAC-TTAGAAGGAAAAAGAGGGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
** * *
11795 TGTGGATTTTAAAAAGAAAAAG-GTACCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
11829 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAAT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
11863 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
* * *
11900 TGTGGGCTTTAAAAAGAAATAG-GTTGCCACGGAAT
1 TGTGGGCTTTAAAAGGAAAAAGAG-TGCCACGGAGT
*
11935 TGTGGGCTTTAAAAGGGAAAAAAAGTGCCACGGAGT
1 TGTGGGCTTTAAAA-GGAAAAAGAGTGCCACGGAGT
11971 TGTGGGCTTT
1 TGTGGGCTTT
11981 GAGACAAAAT
Statistics
Matches: 271, Mismatches: 32, Indels: 34
0.80 0.09 0.10
Matches are distributed among these distances:
29 3 0.01
30 3 0.01
31 16 0.06
32 4 0.01
33 28 0.10
34 73 0.27
35 55 0.20
36 63 0.23
37 26 0.10
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.21
Consensus pattern (35 bp):
TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
Found at i:11909 original size:71 final size:71
Alignment explanation
Indices: 11625--11980 Score: 366
Period size: 71 Copynumber: 5.1 Consensus size: 71
11615 CACCGACTTG
** * * *
11625 TGTGGGCTTTAGAAAAGGTGAAAGA-TGCCAC-GAAGTTGTGGAC-TT-AAAAAGAACAAG-GTG
1 TGTGGGCTTTA-AAAA-GAAAAAGAGTGCCACGGAA-TTGTGGGCTTTGAAAAGGAAAAAGAGTG
11685 CCACGGAGT
63 CCACGGAGT
* * *
11694 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAA-G---AAGA-TGCC
1 TGTGGGCTTTAAAA-AGAAAAAGAGTGCCACGGAATTGTGGGCTTTGAAAAGGAAAAAGAGTGCC
11754 ACGGAGT
65 ACGGAGT
* * * * * * * * *
11761 TGTGGAC-TTAGAAGGAAAAAGAGGGCCACGGAGTTGT-GGATTTTAAAAAGAAAAAG-GTACCA
1 TGTGGGCTTTAAAAAGAAAAAGAGTGCCACGGAATTGTGGGCTTTGAAAAGGAAAAAGAGTGCCA
11823 CGGAGT
66 CGGAGT
11829 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAATTGTGGGCTTTGAAAAGGGAAAAAGAGTGCC
1 TGTGGGCTTTAAAAAGAAAAAGAGTGCCACGGAATTGTGGGCTTTGAAAA-GGAAAAAGAGTGCC
11893 ACGGAGT
65 ACGGAGT
* *
11900 TGTGGGCTTTAAAAAGAAATAG-GTTGCCACGGAATTGTGGGCTTT-AAAAGGGAAAAAAAGTGC
1 TGTGGGCTTTAAAAAGAAAAAGAG-TGCCACGGAATTGTGGGCTTTGAAAA-GGAAAAAGAGTGC
11963 CACGGAGT
64 CACGGAGT
11971 TGTGGGCTTT
1 TGTGGGCTTT
11981 GAGACAAAAT
Statistics
Matches: 248, Mismatches: 23, Indels: 30
0.82 0.08 0.10
Matches are distributed among these distances:
64 9 0.04
65 23 0.09
66 5 0.02
67 20 0.08
68 41 0.17
69 45 0.18
70 12 0.05
71 72 0.29
72 21 0.08
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.21
Consensus pattern (71 bp):
TGTGGGCTTTAAAAAGAAAAAGAGTGCCACGGAATTGTGGGCTTTGAAAAGGAAAAAGAGTGCCA
CGGAGT
Found at i:12011 original size:30 final size:31
Alignment explanation
Indices: 11960--12072 Score: 140
Period size: 31 Copynumber: 3.7 Consensus size: 31
11950 GGAAAAAAAG
* * *
11960 TGCCACGGAGTTGTGGGCTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAGA-AGAGAA
*
11990 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAA
* * *
12021 TACCACTAAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAA
12052 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
12073 AAAAAGGTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
29 1 0.01
30 23 0.32
31 49 0.67
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.27
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGAA
Found at i:12033 original size:31 final size:31
Alignment explanation
Indices: 11992--12072 Score: 144
Period size: 31 Copynumber: 2.6 Consensus size: 31
11982 AGACAAAATG
11992 CCACTGAGTCGTGGACTTTGAGAAGAGATTA
1 CCACTGAGTCGTGGACTTTGAGAAGAGATTA
* *
12023 CCACTAAGTCGTGGACTTTGAGAAGAGATTG
1 CCACTGAGTCGTGGACTTTGAGAAGAGATTA
12054 CCACTGAGTCGTGGACTTT
1 CCACTGAGTCGTGGACTTT
12073 AAAAAGGTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (31 bp):
CCACTGAGTCGTGGACTTTGAGAAGAGATTA
Found at i:13042 original size:11 final size:11
Alignment explanation
Indices: 13026--13060 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
13016 TTTTTCCTTC
13026 TTTTGTTTTTT
1 TTTTGTTTTTT
*
13037 TTTTGTTTGTT
1 TTTTGTTTTTT
*
13048 TGTTGTTTTTT
1 TTTTGTTTTTT
13059 TT
1 TT
13061 GTGTGGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:20349 original size:52 final size:52
Alignment explanation
Indices: 20279--20399 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
20269 GAAAATTTAT
*
20279 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* *
20331 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
20383 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
20400 AAGATTGGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:20412 original size:52 final size:52
Alignment explanation
Indices: 20279--20419 Score: 194
Period size: 52 Copynumber: 2.7 Consensus size: 52
20269 GAAAATTTAT
* *
20279 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACAATTATTAGTGTATCGATACATCTGGGCAAATTTGC
* * *
20331 TTGCATGTATCGATAC-ATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACAATTAT-TAGTGTATCGATACATCTGGGCAAATTTGC
** *
20383 CTGCATGTATCGATACAAAGATTGGTGTATCGATACA
1 CTGCATGTATCGATACAATTATTAGTGTATCGATACA
20420 ATGTATCGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
51 2 0.03
52 72 0.95
53 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACAATTATTAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:20426 original size:13 final size:13
Alignment explanation
Indices: 20408--20432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20398 CAAAGATTGG
20408 TGTATCGATACAA
1 TGTATCGATACAA
20421 TGTATCGATACA
1 TGTATCGATACA
20433 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:20514 original size:13 final size:13
Alignment explanation
Indices: 20496--20520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20486 CAAAAAAATA
20496 TGTATCGATACAT
1 TGTATCGATACAT
20509 TGTATCGATACA
1 TGTATCGATACA
20521 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:20516 original size:33 final size:33
Alignment explanation
Indices: 20474--20540 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
20464 AGTAGCTTAA
20474 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
20507 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
20540 A
1 A
20541 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:21215 original size:21 final size:20
Alignment explanation
Indices: 21186--21228 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
21176 TGTGAGTGTG
*
21186 GGGGCTGCCCAGTTGCGACCT
1 GGGGCTG-CCAGTCGCGACCT
* *
21207 GGGGTTGCCGGTCGCGACCT
1 GGGGCTGCCAGTCGCGACCT
21227 GG
1 GG
21229 TGAGTGCTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.07, C:0.30, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGGCTGCCAGTCGCGACCT
Found at i:21888 original size:8 final size:8
Alignment explanation
Indices: 21870--21900 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
21860 TTTTCAACAT
21870 CAAACATCA
1 CAAA-ATCA
21879 CAAAATCA
1 CAAAATCA
21887 CAAAATCA
1 CAAAATCA
21895 CAAAAT
1 CAAAAT
21901 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:27891 original size:33 final size:33
Alignment explanation
Indices: 27828--27896 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
27818 CGTTACAAGC
*
27828 CAATGTATCGATACATTTTGGGATGGATCGATA
1 CAATGTATCGATACATTATGGGATGGATCGATA
* *
27861 CAATGTATCGATACATATAT-GTATGTATCGATA
1 CAATGTATCGATACAT-TATGGGATGGATCGATA
27894 CAA
1 CAA
27897 ACAGTTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACATTATGGGATGGATCGATA
Found at i:30481 original size:2 final size:2
Alignment explanation
Indices: 30474--30509 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
30464 ATCCGTATGC
30474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30510 TACATAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30856 original size:1 final size:1
Alignment explanation
Indices: 30821--30846 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
30811 TATTTGTTTT
30821 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
30847 TGGACGGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:32344 original size:15 final size:15
Alignment explanation
Indices: 32310--32357 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
32300 TATTTTTTAT
32310 TATAATATATAATAAAA
1 TATAA-ATATAAT-AAA
*
32327 TATAAATTTAATAAA
1 TATAAATATAATAAA
*
32342 TATTAATATAA-AAA
1 TATAAATATAATAAA
32356 TA
1 TA
32358 ATTTTTCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 5 0.18
15 12 0.43
16 6 0.21
17 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TATAAATATAATAAA
Found at i:32356 original size:23 final size:23
Alignment explanation
Indices: 32312--32356 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
32302 TTTTTTATTA
* *
32312 TAATATATAATAAAATATAAATT
1 TAATAAATAATAAAATAAAAATT
* *
32335 TAATAAATATTAATATAAAAAT
1 TAATAAATAATAAAATAAAAAT
32357 AATTTTTCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TAATAAATAATAAAATAAAAATT
Found at i:34303 original size:2 final size:2
Alignment explanation
Indices: 34296--34430 Score: 112
Period size: 2 Copynumber: 77.5 Consensus size: 2
34286 TTTCAATTAT
34296 TA TA TA TA TA -A TA TA TA TA T- TA -A TA -A TA -A TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
34332 TA TA TA TA TA T- TA TA TA TG T- TA TA TA TA T- TA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34370 TA T- TA T- TA TA TA -A TA TA TA -A TA TA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34406 T- TA TA TA T- TA TA T- TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34431 TTATTATCAT
Statistics
Matches: 111, Mismatches: 2, Indels: 40
0.73 0.01 0.26
Matches are distributed among these distances:
1 20 0.18
2 91 0.82
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (2 bp):
TA
Found at i:34347 original size:36 final size:37
Alignment explanation
Indices: 34291--34437 Score: 171
Period size: 36 Copynumber: 4.0 Consensus size: 37
34281 ATTATTTTCA
* *
34291 ATTATTATATATATAATATATATATTAATA-ATAATAT
1 ATTA-TATATATATATTATATATATTAATATATATTAT
*
34328 ATTATATATATATATTATATATGTT-ATATATATTAT
1 ATTATATATATATATTATATATATTAATATATATTAT
34364 ATT-T-TATAT-TATTATATAATATATAATATATATTAT
1 ATTATATATATATATTATAT-ATAT-TAATATATATTAT
*
34400 ATTATAT-TATATATTATATTATATTATATATTTATTAT
1 ATTATATATATATATTATA-TATATTA-ATATATATTAT
34438 CATATTAGTT
Statistics
Matches: 96, Mismatches: 5, Indels: 17
0.81 0.04 0.14
Matches are distributed among these distances:
33 8 0.08
34 8 0.08
35 5 0.05
36 42 0.44
37 10 0.10
38 22 0.23
39 1 0.01
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
ATTATATATATATATTATATATATTAATATATATTAT
Found at i:34430 original size:7 final size:7
Alignment explanation
Indices: 34293--34444 Score: 106
Period size: 7 Copynumber: 21.7 Consensus size: 7
34283 TATTTTCAAT
34293 TATTATA
1 TATTATA
34300 TA-TATA
1 TATTATA
34306 -ATATATA
1 TAT-TATA
34313 TATTA-A
1 TATTATA
*
34319 TAATAATA
1 T-ATTATA
34327 TATTATA
1 TATTATA
34334 TA-TATA
1 TATTATA
34340 TATTATA
1 TATTATA
*
34347 TA-TGT-
1 TATTATA
34352 TA-TATA
1 TATTATA
34358 TATTATA
1 TATTATA
*
34365 TTTTATA
1 TATTATA
34372 TTATTATA
1 -TATTATA
*
34380 TAATATA
1 TATTATA
*
34387 TAATATA
1 TATTATA
34394 TA-T-TA
1 TATTATA
34399 TATTATA
1 TATTATA
34406 TTATATATTA
1 -TAT-TA-TA
34416 TATTATA
1 TATTATA
*
34423 TTATATATT
1 -TAT-TATA
34432 TATTATCA
1 TATTAT-A
34440 TATTA
1 TATTA
34445 GTTTTGCTTT
Statistics
Matches: 119, Mismatches: 9, Indels: 33
0.74 0.06 0.20
Matches are distributed among these distances:
5 9 0.08
6 18 0.15
7 56 0.47
8 26 0.22
9 8 0.07
10 2 0.02
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (7 bp):
TATTATA
Found at i:34442 original size:12 final size:12
Alignment explanation
Indices: 34293--34444 Score: 122
Period size: 12 Copynumber: 12.4 Consensus size: 12
34283 TATTTTCAAT
34293 TATTATATATATAA
1 TATTATAT-TAT-A
34307 TATATATATTAATAA
1 TAT-TATATT-AT-A
*
34322 TAATATATTATA
1 TATTATATTATA
34334 TATATATATTATA
1 TAT-TATATTATA
34347 TATGT-TA-TATA
1 TAT-TATATTATA
*
34358 TATTATATTTTA
1 TATTATATTATA
34370 TA-T-TATTATA
1 TATTATATTATA
*
34380 TAATATATAATATA
1 T-AT-TATATTATA
34394 TATTATA-T-TA
1 TATTATATTATA
34404 TATTATA-TATTA
1 TATTATATTA-TA
34416 TATTATATTATA
1 TATTATATTATA
34428 TATT-TATTATCA
1 TATTATATTAT-A
34440 TATTA
1 TATTA
34445 GTTTTGCTTT
Statistics
Matches: 118, Mismatches: 6, Indels: 29
0.77 0.04 0.19
Matches are distributed among these distances:
10 18 0.15
11 18 0.15
12 34 0.29
13 20 0.17
14 17 0.14
15 11 0.09
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (12 bp):
TATTATATTATA
Found at i:34467 original size:17 final size:19
Alignment explanation
Indices: 34445--34479 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
34435 TATCATATTA
34445 GTTTTGC-TT-TTTTTTTT
1 GTTTTGCATTATTTTTTTT
34462 GTTTTGCATTATTTTTTT
1 GTTTTGCATTATTTTTTT
34480 CGTTAAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.06, C:0.06, G:0.11, T:0.77
Consensus pattern (19 bp):
GTTTTGCATTATTTTTTTT
Found at i:34478 original size:18 final size:17
Alignment explanation
Indices: 34445--34479 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
34435 TATCATATTA
*
34445 GTTTTGCTTTTTTTTTT
1 GTTTTGCTTATTTTTTT
34462 GTTTTGCATTATTTTTTT
1 GTTTTGC-TTATTTTTTT
34480 CGTTAAGCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.06, C:0.06, G:0.11, T:0.77
Consensus pattern (17 bp):
GTTTTGCTTATTTTTTT
Found at i:37856 original size:20 final size:19
Alignment explanation
Indices: 37831--37900 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
37821 TTTTACCTAG
37831 ATGTATCGATACAGTTTTCA
1 ATGTATCGATACA-TTTTCA
* *
37851 ATGTATCGATACATGTATGA
1 ATGTATCGATACAT-TTTCA
*
37871 ATTTATCGATA-ATTTTTCA
1 ATGTATCGATACA-TTTTCA
*
37890 ATGTATTGATA
1 ATGTATCGATA
37901 TATTCTATCT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 14 0.34
20 27 0.66
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Done.