Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 192 of 199
Found at i:55902812 original size:21 final size:21
Alignment explanation
Indices: 55902786--55902825 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55902776 ACTTGTATGT
* *
55902786 ATTTTTATTTTTATTTTTACA
1 ATTTTTATATATATTTTTACA
55902807 ATTTTTATATATATTTTTA
1 ATTTTTATATATATTTTTA
55902826 TACATATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTTATATATATTTTTACA
Found at i:55902822 original size:12 final size:12
Alignment explanation
Indices: 55902807--55902859 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
55902797 TATTTTTACA
55902807 ATTTTTATATAT
1 ATTTTTATATAT
*
55902819 ATTTTTATACAT
1 ATTTTTATATAT
**
55902831 ATTCATATATAT
1 ATTTTTATATAT
* *
55902843 ATATATATATAT
1 ATTTTTATATAT
*
55902855 CTTTT
1 ATTTT
55902860 ACTTTTTATA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTTTATATAT
Found at i:55906628 original size:28 final size:28
Alignment explanation
Indices: 55906587--55906665 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 28
55906577 CTGAATCTCG
* * **
55906587 AACCTCGAACCTCGAACCTTGAATTATA
1 AACCTCAAATCTCGAACCTTGAACCATA
* * * *
55906615 AATCTTAAATCTCGAATCTTGAACCCTA
1 AACCTCAAATCTCGAACCTTGAACCATA
55906643 AACCTCAAATC-CGAACCTTGAAC
1 AACCTCAAATCTCGAACCTTGAAC
55906666 TCCGAATACT
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
27 11 0.28
28 29 0.73
ACGTcount: A:0.37, C:0.29, G:0.09, T:0.25
Consensus pattern (28 bp):
AACCTCAAATCTCGAACCTTGAACCATA
Found at i:55907427 original size:37 final size:36
Alignment explanation
Indices: 55907355--55907459 Score: 128
Period size: 37 Copynumber: 2.9 Consensus size: 36
55907345 TTTCTTTTTT
* *
55907355 TTTTA-AAACACGAATTTTTTTTAAATACA--AGAA
1 TTTTAGAAACACGAATTTTTTTTAAAAACACGAAAA
55907388 TTTTAGAAACACGAATTTTTTTTAAAAAACACGAAAA
1 TTTTAGAAACACGAATTTTTTTT-AAAAACACGAAAA
*
55907425 TTTT-GAAACACGAGATTTTTTTTTGAAAACACGAA
1 TTTTAGAAACACGA-A-TTTTTTTTAAAAACACGAA
55907460 TTTTCCTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
33 5 0.08
34 17 0.27
35 6 0.10
36 9 0.14
37 18 0.29
38 8 0.13
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (36 bp):
TTTTAGAAACACGAATTTTTTTTAAAAACACGAAAA
Found at i:55907450 original size:20 final size:20
Alignment explanation
Indices: 55907425--55907479 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
55907415 AACACGAAAA
*
55907425 TTTTGAAACACGAGATTTT-T
1 TTTTGAAACACGA-ATTTTCC
55907445 TTTTGAAAACACGAATTTTCC
1 TTTTG-AAACACGAATTTTCC
*
55907466 TTTTGAAGCACGAA
1 TTTTGAAACACGAA
55907480 AATTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTTGAAACACGAATTTTCC
Found at i:55907456 original size:21 final size:21
Alignment explanation
Indices: 55907425--55907472 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
55907415 AACACGAAAA
*
55907425 TTTTG-AAACACGAGATTTT-T
1 TTTTGAAAACACGA-ATTTTCC
55907445 TTTTGAAAACACGAATTTTCC
1 TTTTGAAAACACGAATTTTCC
55907466 TTTTGAA
1 TTTTGAA
55907473 GCACGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (21 bp):
TTTTGAAAACACGAATTTTCC
Found at i:55907463 original size:57 final size:57
Alignment explanation
Indices: 55907394--55907513 Score: 145
Period size: 58 Copynumber: 2.1 Consensus size: 57
55907384 AGAATTTTAG
* * * *
55907394 AAACACGAATTTT-TTTTAAAAAACACGAAAA-TTTTGAAACACGAGATTTTTTTTTGA
1 AAACACGAATTTTCTTTT--AAAACACGAAAATTTTTAAAACACAAAATTTGTTTTTGA
* *
55907451 AAACACGAATTTTCCTTTTGAAGCACGAAAATTTTTAAAACACAAAATTTGTTTTTGA
1 AAACACGAATTTT-CTTTTAAAACACGAAAATTTTTAAAACACAAAATTTGTTTTTGA
55907509 AAACA
1 AAACA
55907514 TAAAAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
57 23 0.43
58 27 0.50
59 4 0.07
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (57 bp):
AAACACGAATTTTCTTTTAAAACACGAAAATTTTTAAAACACAAAATTTGTTTTTGA
Found at i:55907522 original size:22 final size:20
Alignment explanation
Indices: 55907482--55907522 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
55907472 AGCACGAAAA
*
55907482 TTTTTAAAACACAAAATTTG
1 TTTTTAAAACAAAAAATTTG
55907502 TTTTTGAAAACATAAAAATTT
1 TTTTT-AAAACA-AAAAATTT
55907523 TGATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (20 bp):
TTTTTAAAACAAAAAATTTG
Found at i:55907603 original size:18 final size:18
Alignment explanation
Indices: 55907549--55907852 Score: 171
Period size: 18 Copynumber: 16.8 Consensus size: 18
55907539 ATGAGGGTTT
*
55907549 TTTTTG-AAACACAAAAA
1 TTTTTGAAAACACGAAAA
* **
55907566 TTTATG-AAACACGGTCAA
1 TTTTTGAAAACAC-GAAAA
*
55907584 TTTTTGAAAACACAAAAA
1 TTTTTGAAAACACGAAAA
* * *
55907602 TTTTTGAAAGAC-GGGAAT
1 TTTTTGAAA-ACACGAAAA
55907620 TTTTTGAAAACACTG-AAA
1 TTTTTGAAAACAC-GAAAA
*
55907638 TTTATG-AAACACGGAAAA
1 TTTTTGAAAACAC-GAAAA
*
55907656 TTTTTTTTGAAAACAAGAAAA
1 ---TTTTTGAAAACACGAAAA
* **
55907677 TTTTTG-AAATACGGGAA
1 TTTTTGAAAACACGAAAA
*
55907694 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
*
55907712 TTTTTG-AAACACTG-GAA
1 TTTTTGAAAACAC-GAAAA
* *
55907729 -TGTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
* *
55907746 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGAAAA
**
55907763 TTTTTGAAAACACGAATTT
1 TTTTTGAAAACACGAA-AA
* * *
55907782 TTTTTTAAAACACGGAAG
1 TTTTTGAAAACACGAAAA
* **
55907800 TTTTTGAAACACAAGAATTTT
1 TTTTTGAAA-ACACGAA--AA
*
55907821 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
55907839 TTTTTG-AAACACGA
1 TTTTTGAAAACACGA
55907853 TTTTTTTTAG
Statistics
Matches: 214, Mismatches: 53, Indels: 40
0.70 0.17 0.13
Matches are distributed among these distances:
16 5 0.02
17 69 0.32
18 83 0.39
19 28 0.13
20 6 0.03
21 18 0.08
22 5 0.02
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:55907621 original size:35 final size:35
Alignment explanation
Indices: 55907549--55907821 Score: 232
Period size: 36 Copynumber: 7.7 Consensus size: 35
55907539 ATGAGGGTTT
* *
55907549 TTTTTG-AAACACAAAAATTTATGAAACACGGTCAA
1 TTTTTGAAAACACAAAAATTTTTGAAACACGG-GAA
*
55907584 TTTTTGAAAACACAAAAATTTTTGAAAGACGGGAA
1 TTTTTGAAAACACAAAAATTTTTGAAACACGGGAA
** * *
55907619 TTTTTTGAAAACACTGAAATTTATGAAACACGGAAAA
1 -TTTTTGAAAACACAAAAATTTTTGAAACACGG-GAA
*
55907656 TTTTTTTTGAAAACA-AGAAAATTTTTGAAATACGGGAA
1 ---TTTTTGAAAACACA-AAAATTTTTGAAACACGGGAA
** *
55907694 TTTTTGAAAACATGAAAATTTTTGAAACACTGGAA
1 TTTTTGAAAACACAAAAATTTTTGAAACACGGGAA
* * * * *
55907729 -TGTTGAAAACACGAAGATTTTTGAAACATGAGAA
1 TTTTTGAAAACACAAAAATTTTTGAAACACGGGAA
*** *
55907763 TTTTTGAAAACACGAATTTTTTTTTAAAACAC-GGAA
1 TTTTTGAAAACAC-AA-AAATTTTTGAAACACGGGAA
*
55907799 GTTTTTG-AAACACAAGAATTTTT
1 -TTTTTGAAAACACAAAAATTTTT
55907822 TTTTAAAAAC
Statistics
Matches: 194, Mismatches: 33, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
34 33 0.17
35 52 0.27
36 61 0.31
37 18 0.09
38 2 0.01
39 28 0.14
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.33
Consensus pattern (35 bp):
TTTTTGAAAACACAAAAATTTTTGAAACACGGGAA
Found at i:55907827 original size:38 final size:37
Alignment explanation
Indices: 55907746--55907850 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 37
55907736 AACACGAAGA
* * *
55907746 TTTTTGAAACATGAGAATTTTTGAAA-ACACGAATTTT
1 TTTTTAAAACACG-GAATTTTTGAAACACAAGAATTTT
55907783 TTTTTAAAACACGGAAGTTTTTGAAACACAAGAATTTT
1 TTTTTAAAACACGGAA-TTTTTGAAACACAAGAATTTT
*
55907821 TTTTTAAAAACACGAAAATTTTTGAAACAC
1 TTTTT-AAAACACG-GAATTTTTGAAACAC
55907851 GATTTTTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
36 3 0.05
37 20 0.33
38 15 0.25
39 20 0.33
40 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (37 bp):
TTTTTAAAACACGGAATTTTTGAAACACAAGAATTTT
Found at i:55907848 original size:17 final size:17
Alignment explanation
Indices: 55907549--55907852 Score: 157
Period size: 17 Copynumber: 16.8 Consensus size: 17
55907539 ATGAGGGTTT
*
55907549 TTTTTGAAACACAAAAA
1 TTTTTGAAACACGAAAA
* **
55907566 TTTATGAAACACGGTCAA
1 TTTTTGAAACAC-GAAAA
*
55907584 TTTTTGAAAACACAAAAA
1 TTTTTG-AAACACGAAAA
* * *
55907602 TTTTTGAAAGACGGGAAT
1 TTTTTGAAACAC-GAAAA
55907620 TTTTTGAAAACACTG-AAA
1 TTTTTG-AAACAC-GAAAA
*
55907638 TTTATGAAACACGGAAAA
1 TTTTTGAAACAC-GAAAA
*
55907656 TTTTTTTTGAAAACAAGAAAA
1 ---TTTTTG-AAACACGAAAA
* **
55907677 TTTTTGAAATACGGGAA
1 TTTTTGAAACACGAAAA
*
55907694 TTTTTGAAAACATGAAAA
1 TTTTTG-AAACACGAAAA
*
55907712 TTTTTGAAACACTG-GAA
1 TTTTTGAAACAC-GAAAA
* *
55907729 -TGTTGAAAACACGAAGA
1 TTTTTG-AAACACGAAAA
* *
55907746 TTTTTGAAACATGAGAA
1 TTTTTGAAACACGAAAA
**
55907763 TTTTTGAAAACACGAATTTT
1 TTTTTG-AAACACGAA--AA
* * *
55907783 TTTTTAAAACACGGAAG
1 TTTTTGAAACACGAAAA
55907800 TTTTTGAAACAC-AAGAA
1 TTTTTGAAACACGAA-AA
*
55907817 TTTTTTTTTAAAAACACGAAAA
1 ----TTTTT-GAAACACGAAAA
55907839 TTTTTGAAACACGA
1 TTTTTGAAACACGA
55907853 TTTTTTTTAG
Statistics
Matches: 214, Mismatches: 49, Indels: 48
0.69 0.16 0.15
Matches are distributed among these distances:
16 6 0.03
17 84 0.39
18 69 0.32
19 20 0.09
20 5 0.02
21 15 0.07
22 13 0.06
23 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:55907860 original size:39 final size:36
Alignment explanation
Indices: 55907746--55907860 Score: 142
Period size: 39 Copynumber: 3.1 Consensus size: 36
55907736 AACACGAAGA
* * *
55907746 TTTTTGAAACATGAGAATTTTTGAAAACACGAATTTT
1 TTTTTAAAACACGAAAATTTTTG-AAACACGAATTTT
* *
55907783 TTTTTAAAACACGGAAGTTTTTGAAACACAAGAATTTT
1 TTTTTAAAACACGAAAATTTTTGAAACAC--GAATTTT
55907821 TTTTTAAAAACACGAAAATTTTTGAAACACG-ATTTT
1 TTTTT-AAAACACGAAAATTTTTGAAACACGAATTTT
55907857 TTTT
1 TTTT
55907861 AGAAGTACCG
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
36 15 0.22
37 19 0.28
38 12 0.18
39 22 0.32
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (36 bp):
TTTTTAAAACACGAAAATTTTTGAAACACGAATTTT
Found at i:55908571 original size:4 final size:4
Alignment explanation
Indices: 55908564--55908620 Score: 53
Period size: 4 Copynumber: 13.8 Consensus size: 4
55908554 TTTTTTTTCC
* * *
55908564 CTTT CTTT CTTCCC CTTT CTTTT CTTT CTTT ATTT CTTT -TTT CTTC CTTT
1 CTTT CTTT CTT--T CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
55908614 CTTT CTT
1 CTTT CTT
55908621 CCCCGATCAG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
3 3 0.07
4 33 0.77
5 4 0.09
6 3 0.07
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:55908605 original size:19 final size:19
Alignment explanation
Indices: 55908583--55908620 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55908573 TTCCCCTTTC
*
55908583 TTTTCTTTCTTTATTTCTT
1 TTTTCTTCCTTTATTTCTT
*
55908602 TTTTCTTCCTTTCTTTCTT
1 TTTTCTTCCTTTATTTCTT
55908621 CCCCGATCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTTCCTTTATTTCTT
Found at i:55908775 original size:28 final size:28
Alignment explanation
Indices: 55908724--55908785 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
55908714 CCCCCTTTTT
**
55908724 CTTTTTTATTCTTTGCTCTTTTTTCTTC
1 CTTTTTTATTCTTTGCTCGCTTTTCTTC
* * * *
55908752 TTTTTTTCTTTTTTGCTCGCTTTTTTTC
1 CTTTTTTATTCTTTGCTCGCTTTTCTTC
55908780 CTTTTT
1 CTTTTT
55908786 CTTGCCTCTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.74
Consensus pattern (28 bp):
CTTTTTTATTCTTTGCTCGCTTTTCTTC
Found at i:55909184 original size:29 final size:29
Alignment explanation
Indices: 55909151--55909303 Score: 98
Period size: 30 Copynumber: 5.2 Consensus size: 29
55909141 GCAAAAATGA
*
55909151 AATTTTAGGAAAATATAGGGCTAAAGTGT
1 AATTTTAGAAAAATATAGGGCTAAAGTGT
* *
55909180 AATTTATAG-AAAGTTTAGGGGCCT-AAGTGT
1 AATTT-TAGAAAAATATA-GGG-CTAAAGTGT
* * *
55909210 AA-TTTA-CAAAATATTAGGGGTCAAGATGT
1 AATTTTAGAAAAATA-TAGGGCTAAAG-TGT
* * *
55909239 AATTTTTGAAAAATTTAGAGGCTAAAATGT
1 AATTTTAGAAAAATATAG-GGCTAAAGTGT
* * * *
55909269 AATTTTTGAAAAATTCTGGGGCTAAAATGT
1 AATTTTAGAAAAA-TATAGGGCTAAAGTGT
55909299 AATTT
1 AATTT
55909304 ATTTTTTGTA
Statistics
Matches: 100, Mismatches: 13, Indels: 21
0.75 0.10 0.16
Matches are distributed among these distances:
27 1 0.01
28 12 0.12
29 20 0.20
30 52 0.52
31 15 0.15
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (29 bp):
AATTTTAGAAAAATATAGGGCTAAAGTGT
Found at i:55909256 original size:59 final size:57
Alignment explanation
Indices: 55909160--55909273 Score: 124
Period size: 59 Copynumber: 2.0 Consensus size: 57
55909150 AAATTTTAGG
* * *
55909160 AAAATATAGGGCTAAAGTGTAATTTATAGAAAGTTTAGGGGCCT-AAGTGTAATTTAC
1 AAAATATAGGGCTAAAGTGTAATTTATAGAAAATTTAGAGG-CTAAAATGTAATTTAC
* * *
55909217 AAAATATTAGGGGTCAAGATGTAATTT-TTGAAAAATTTAGAGGCTAAAATGTAATTT
1 AAAATA-TAGGGCTAAAG-TGTAATTTATAG-AAAATTTAGAGGCTAAAATGTAATTT
55909274 TTGAAAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
57 6 0.13
58 13 0.28
59 28 0.60
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (57 bp):
AAAATATAGGGCTAAAGTGTAATTTATAGAAAATTTAGAGGCTAAAATGTAATTTAC
Found at i:55909271 original size:30 final size:30
Alignment explanation
Indices: 55909235--55909303 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
55909225 AGGGGTCAAG
55909235 ATGTAATTTTTGAAAAATT-TAGAGGCTAAA
1 ATGTAATTTTTGAAAAATTCT-GAGGCTAAA
*
55909265 ATGTAATTTTTGAAAAATTCTGGGGCTAAA
1 ATGTAATTTTTGAAAAATTCTGAGGCTAAA
55909295 ATGTAATTT
1 ATGTAATTT
55909304 ATTTTTTGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
30 36 0.97
31 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (30 bp):
ATGTAATTTTTGAAAAATTCTGAGGCTAAA
Found at i:55911503 original size:55 final size:56
Alignment explanation
Indices: 55911411--55911522 Score: 181
Period size: 55 Copynumber: 2.0 Consensus size: 56
55911401 GTAAGGTTCC
* * * *
55911411 AAATCTATAATTCTAATTATTTTATGAGTTCATAATCCAAATATGTTATGTGAAAA
1 AAATCTATAATTCTAAGTAATTTATGAATTCACAATCCAAATATGTTATGTGAAAA
55911467 AAAT-TATAATTCTAAGTAATTTATGAATTCACAATCCAAATATGTTATGTGAAAA
1 AAATCTATAATTCTAAGTAATTTATGAATTCACAATCCAAATATGTTATGTGAAAA
55911522 A
1 A
55911523 GAAAACAACA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
55 48 0.92
56 4 0.08
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (56 bp):
AAATCTATAATTCTAAGTAATTTATGAATTCACAATCCAAATATGTTATGTGAAAA
Found at i:55913631 original size:17 final size:16
Alignment explanation
Indices: 55913611--55913660 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
55913601 GGAAGAGCCA
55913611 TTATTGAGGAACAACTC
1 TTATTGA-GAACAACTC
*
55913628 TTATTTAGAACAACCTC
1 TTATTGAGAACAA-CTC
*
55913645 TACATTGAGAACAACT
1 T-TATTGAGAACAACT
55913661 ATGTTGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 6 0.21
17 12 0.43
18 10 0.36
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (16 bp):
TTATTGAGAACAACTC
Found at i:55913657 original size:18 final size:17
Alignment explanation
Indices: 55913613--55913659 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
55913603 AAGAGCCATT
*
55913613 ATTGAGGAACAA-CTCTT
1 ATTGA-GAACAACCTCTC
*
55913630 ATTTAGAACAACCTCTAC
1 ATTGAGAACAACCTCT-C
55913648 ATTGAGAACAAC
1 ATTGAGAACAAC
55913660 TATGTTGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 6 0.24
17 8 0.32
18 11 0.44
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (17 bp):
ATTGAGAACAACCTCTC
Found at i:55914310 original size:12 final size:12
Alignment explanation
Indices: 55914279--55914310 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
55914269 CAGATTTGCA
55914279 TTTCTTT-TTAT
1 TTTCTTTATTAT
55914290 TTT-TTTATTAT
1 TTTCTTTATTAT
55914301 TTTCTTTATT
1 TTTCTTTATT
55914311 TTGTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.16
11 10 0.53
12 6 0.32
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTCTTTATTAT
Found at i:55919303 original size:8 final size:8
Alignment explanation
Indices: 55919290--55919328 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
55919280 AAAAGAGAAG
55919290 AAAAAAAT
1 AAAAAAAT
55919298 AAAAAAAT
1 AAAAAAAT
*
55919306 CAAAAAAT
1 AAAAAAAT
*
55919314 CAAAAAA-
1 AAAAAAAT
55919321 AAAAAAAT
1 AAAAAAAT
55919329 CAATCAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:55919348 original size:23 final size:23
Alignment explanation
Indices: 55919291--55919340 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
55919281 AAAGAGAAGA
55919291 AAAAAATAAAAAAATCAAAAAATC
1 AAAAAA-AAAAAAATCAAAAAATC
**
55919315 AAAAAAAAAAAAATCAATCAATC
1 AAAAAAAAAAAAATCAAAAAATC
55919338 AAA
1 AAA
55919341 GCCAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (23 bp):
AAAAAAAAAAAAATCAAAAAATC
Found at i:55921605 original size:43 final size:42
Alignment explanation
Indices: 55921557--55921695 Score: 102
Period size: 43 Copynumber: 3.2 Consensus size: 42
55921547 AAAATAAAGC
55921557 CTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGAT
1 CTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAA-CAGAT
* * *** * * ** * *
55921600 CTTGCCTTC-CTGCGTTAACAGCAAAGCAGATCGAA-AACAAAGC
1 CTTGCCTTCATTG-GTT-GCAGTGGAGCTGGTTAAAGAACAGA-T
*
55921643 CTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGACAAAAGAT
1 CTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAG--AACAGAT
55921687 CTTGCCTTC
1 CTTGCCTTC
55921696 CTGCATTGAC
Statistics
Matches: 66, Mismatches: 23, Indels: 13
0.65 0.23 0.13
Matches are distributed among these distances:
42 15 0.23
43 26 0.39
44 21 0.32
45 4 0.06
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (42 bp):
CTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAACAGAT
Found at i:55921735 original size:44 final size:44
Alignment explanation
Indices: 55921600--55921900 Score: 138
Period size: 44 Copynumber: 6.9 Consensus size: 44
55921590 AGAAGCAGAT
* * * * *
55921600 CTTGCCTTCCTGCGTTAACAGCAAAGCAGATCGAAA-ACA-AAGC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTC-AAAGACACAAAC
* * * * * * * *
55921643 CTTGCCTTCATTG-GTTG-CAGTGGAGCTGGTTAAAGACAAAAGAT
1 CTTGCCTTC-CTGCATTGACAGCGAAGCAGGTCAAAGACACAA-AC
*
55921687 CTTGCCTTCCTGCATTGACGGCGAAGCAGGTCAAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAAC
** * * * * *
55921731 CTTGCC-TCTCTCGGTTGTGA-TG-G-AGCTGGTTAAAGACAAAAGAT
1 CTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCAAAGACACAA-AC
*
55921775 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAAC
* ** * * ** * *
55921819 CTTGCCTCCCTCGGTTGTGA-TG-G-AGCTGGTTGAAGACAACAGAT
1 CTTGCCTTCCT-GCAT-TGACAGCGAAGCAGGTCAAAGAC-ACAAAC
* *
55921863 CTTGCCTTCTTGCATTGACAGCGAAGCAGGTCGAAGAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGAC
55921901 GAACCTTACC
Statistics
Matches: 189, Mismatches: 49, Indels: 38
0.68 0.18 0.14
Matches are distributed among these distances:
41 3 0.02
42 17 0.09
43 51 0.27
44 60 0.32
45 52 0.28
46 6 0.03
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (44 bp):
CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAAC
Found at i:55921764 original size:88 final size:88
Alignment explanation
Indices: 55921577--55921922 Score: 454
Period size: 88 Copynumber: 4.0 Consensus size: 88
55921567 TTGGTTGCAG
** * * * *
55921577 TGGAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCAAAGCAGATCGAAA-ACA-
1 TGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTC-AAAGACAC
* * *
55921639 AAGCCTTGCCT-TCATTGGTTG-CA
65 AAACCTTGCCTCTC-TCGGTTGTGA
*
55921662 GTGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACGGCGAAGCAGGTCAAAGACAC
1 -TGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACAC
55921727 AAACCTTGCCTCTCTCGGTTGTGA
65 AAACCTTGCCTCTCTCGGTTGTGA
*
55921751 TGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACA
1 TGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACA
*
55921816 AACCTTGCCTCCCTCGGTTGTGA
66 AACCTTGCCTCTCTCGGTTGTGA
* * * * *
55921839 TGGAGCTGGTTGAAGACAACAGATCTTGCCTTCTTGCATTGACAGCGAAGCAGGTCGAAG--ACG
1 TGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACA
*
55921902 AACCTTACCTCTCTCGGTTGT
66 AACCTTGCCTCTCTCGGTTGT
55921923 AGTGAAGCTG
Statistics
Matches: 236, Mismatches: 19, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
86 40 0.17
87 35 0.15
88 158 0.67
89 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (88 bp):
TGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACA
AACCTTGCCTCTCTCGGTTGTGA
Found at i:55921768 original size:43 final size:43
Alignment explanation
Indices: 55921719--55921856 Score: 120
Period size: 43 Copynumber: 3.2 Consensus size: 43
55921709 GAAGCAGGTC
55921719 AAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
1 AAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
* * ** * * *
55921762 AAAGACAAAAGATCTTGCCT-TC-CTGCAT-TGACAGCGAAGCAGGTC
1 AAAGACACAA-ACCTTGCCTCTCTC-GGTTGTGA-TG-G-AGCTGGTT
* *
55921807 GAAGACACAAACCTTGCCTCCCTCGGTTGTGATGGAGCTGGTT
1 AAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
*
55921850 GAAGACA
1 AAAGACA
55921857 ACAGATCTTG
Statistics
Matches: 71, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
42 4 0.06
43 27 0.38
44 18 0.25
45 18 0.25
46 4 0.06
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (43 bp):
AAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
Found at i:55922051 original size:44 final size:44
Alignment explanation
Indices: 55921947--55922381 Score: 211
Period size: 44 Copynumber: 9.8 Consensus size: 44
55921937 AAGAATTTTA
* * * * * *
55921947 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGACATA-
1 GATCTTATCTCTCTGAAGTTACAGTGGAGCAGATT-AAAATAAAG
* * *
55921991 -ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAG
1 GATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
* * * **
55922034 GATCTTATCTCTCTGAAGTTACAGTAGAGCAGA-TCACA-CCAG
1 GATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
** **
55922076 G-TCTTATCT-TCCTGATA-TTACAGTGGAGCAGAGGAAGAATTTCA-
1 GATCTTATCTCT-CTGA-AGTTACAGTGGAGCAGATTAA-AA-TAAAG
* * * *
55922120 GATCTTATCTCCCTG-AGATATCAGCGGAGCAGATTGAAGAT--AG
1 GATCTTATCTCTCTGAAGTTA-CAGTGGAGCAGATT-AAAATAAAG
* * * *
55922163 TAATCCTATCTCCCTG-AGATTACAGTGGAGCGGATTAAAATAAAG
1 -GATCTTATCTCTCTGAAG-TTACAGTGGAGCAGATTAAAATAAAG
* *
55922208 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATTACATCAGATTGAAGCCAG
1 GATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTA-A--A-A-T-AA---AG
* **
55922261 AGATC-T-TCTCTCTG-AGATTACAGTGGAGTAGATTTAAGCT--AG
1 -GATCTTATCTCTCTGAAG-TTACAGTGGAGCAGA-TTAAAATAAAG
* * ** *
55922303 TAATCCTATCTCTCTGAAGTTACAGTGGAGTGGATTAAAATAAAA
1 -GATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
* *
55922348 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
1 GATCTTATCTCTCTGAAGTTACAGTGGAGCAGAT
55922382 CACATCACAT
Statistics
Matches: 304, Mismatches: 51, Indels: 72
0.71 0.12 0.17
Matches are distributed among these distances:
40 1 0.00
41 26 0.09
42 16 0.05
43 45 0.15
44 138 0.45
45 35 0.12
46 2 0.01
47 1 0.00
48 2 0.01
49 1 0.00
50 2 0.01
51 2 0.01
52 23 0.08
53 6 0.02
54 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (44 bp):
GATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
Found at i:55922339 original size:140 final size:140
Alignment explanation
Indices: 55922127--55922441 Score: 431
Period size: 140 Copynumber: 2.2 Consensus size: 140
55922117 TCAGATCTTA
55922127 TCTCCCTGAGATATCAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGA
1 TCTCCCTGAGATATCAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGA
* * *
55922192 GCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATTACATCAGATTGAAG
66 GCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCACATTGAAG
55922257 CCAGAGATCT
131 CCAGAGATCT
* * * * * *
55922267 TCTCTCTGAGAT-TACAGTGGAGTAGATTTAAGCTAGTAATCCTATCTCTCTGA-AGTTACAGTG
1 TCTCCCTGAGATAT-CAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGA-TTACAGTG
*
55922330 GAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCACATTGA
64 GAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCACATTGA
55922395 AGCCAGTA-ATTCT
129 AGCCAG-AGA-TCT
* * **
55922408 ATCTCCCTG-GATAGCAGTGGAATAGATTGAAGAT
1 -TCTCCCTGAGATATCAGCGGAGCAGATTGAAGAT
55922442 TGTAGATCTT
Statistics
Matches: 154, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
139 2 0.01
140 121 0.79
141 24 0.16
142 7 0.05
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (140 bp):
TCTCCCTGAGATATCAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGA
GCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCACATTGAAG
CCAGAGATCT
Found at i:55923845 original size:3 final size:3
Alignment explanation
Indices: 55923837--55923897 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
55923827 ACAAATTTCA
55923837 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55923885 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
55923898 TCCCTTTCAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:55924705 original size:110 final size:112
Alignment explanation
Indices: 55924487--55924705 Score: 354
Period size: 110 Copynumber: 2.0 Consensus size: 112
55924477 GTTATGCATA
* *
55924487 TTAATATCCTTAAAAAATATATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAAC
1 TTAATATCCTTAAAAAATATATTTCAAAATAAGACAATGTTTTGCATTTGGAAATTCGAGAAAAC
55924552 ATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGC
66 ATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGC
* * *
55924599 TTAATATCCTTTTAAAAA-AT-TTT-AAAATAAGACAATGTTTTGTATTTGGAAATTTGAGAAAA
1 TTAATATCC-TTAAAAAATATATTTCAAAATAAGACAATGTTTTGCATTTGGAAATTCGAGAAAA
*
55924661 CATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTTAACCAAAT
65 CATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAAT
55924706 TGTCAGATAT
Statistics
Matches: 100, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
110 79 0.79
111 3 0.03
112 11 0.11
113 7 0.07
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (112 bp):
TTAATATCCTTAAAAAATATATTTCAAAATAAGACAATGTTTTGCATTTGGAAATTCGAGAAAAC
ATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGC
Found at i:55924749 original size:110 final size:108
Alignment explanation
Indices: 55924507--55924730 Score: 290
Period size: 110 Copynumber: 2.1 Consensus size: 108
55924497 TAAAAAATAT
* * * **
55924507 ATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
1 ATTTTAAAACAAGACAATGTTTTGTATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
* *
55924572 TCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAA
66 TCGATTTTTCTCGTTCAACCAAATGGCTCAATATCCTCTT--AAA
* *
55924617 ATTTTAAAATAAGACAATGTTTTGTATTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGGGTG
1 ATTTTAAAACAAGACAATGTTTTGTATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
* * * *
55924682 TCGATTTTTCTCGTTTAACCAAATTG-TCAGATATTCTCTT-GA
66 TCGATTTTTCTCGTTCAACCAAATGGCTCA-ATATCCTCTTAAA
55924724 ATTTTAA
1 ATTTTAA
55924731 TCCATGCCAT
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
107 8 0.08
109 2 0.02
110 92 0.90
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (108 bp):
ATTTTAAAACAAGACAATGTTTTGTATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
TCGATTTTTCTCGTTCAACCAAATGGCTCAATATCCTCTTAAA
Found at i:55929383 original size:17 final size:17
Alignment explanation
Indices: 55929357--55929390 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55929347 ACGGAAATGA
* *
55929357 TTTGTTAGATTCTAAAT
1 TTTGTAAGATTCCAAAT
55929374 TTTGTAAGATTCCAAAT
1 TTTGTAAGATTCCAAAT
55929391 CTATGATTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (17 bp):
TTTGTAAGATTCCAAAT
Found at i:55932658 original size:3 final size:3
Alignment explanation
Indices: 55932629--55932683 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
55932619 TTTACTCCTC
55932629 ATT ATT A-T ATT A-T ATT AATGT -TT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT -AT-T ATT ATT ATT ATT ATT ATT ATT ATT
55932673 ATT ATT ATT AT
1 ATT ATT ATT AT
55932684 CATCATATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 5 0.11
3 39 0.83
4 2 0.04
5 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:55936581 original size:12 final size:12
Alignment explanation
Indices: 55936564--55936593 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
55936554 GTGGTTGAGT
55936564 ATTCAAAACAAA
1 ATTCAAAACAAA
55936576 ATTCAAAACAAA
1 ATTCAAAACAAA
55936588 A-TCAAA
1 ATTCAAA
55936594 CTTTGCAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (12 bp):
ATTCAAAACAAA
Found at i:55937548 original size:5 final size:5
Alignment explanation
Indices: 55937538--55937565 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
55937528 GTGAGCATTC
55937538 AATCG AATCG AATCG AATCG AATCG AAT
1 AATCG AATCG AATCG AATCG AATCG AAT
55937566 AAAAATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (5 bp):
AATCG
Found at i:55938609 original size:9 final size:9
Alignment explanation
Indices: 55938595--55938631 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55938585 TATAGTTTGA
55938595 TATTCGAAT
1 TATTCGAAT
55938604 TATTCGAAT
1 TATTCGAAT
* *
55938613 TATTTGAGT
1 TATTCGAAT
55938622 TATTCGAAT
1 TATTCGAAT
55938631 T
1 T
55938632 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55941344 original size:17 final size:17
Alignment explanation
Indices: 55941324--55941361 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
55941314 TTTGATTATA
55941324 AAATATGA-AAAATGTAT
1 AAATATGATAAAA-GTAT
*
55941341 AAATATTATAAAAGTAT
1 AAATATGATAAAAGTAT
55941358 AAAT
1 AAAT
55941362 GTACATACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (17 bp):
AAATATGATAAAAGTAT
Found at i:55941512 original size:3 final size:3
Alignment explanation
Indices: 55941504--55941552 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
55941494 ATATGTAAGT
* *
55941504 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55941552 A
1 A
55941553 AGTCATAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55941562 original size:14 final size:15
Alignment explanation
Indices: 55941504--55941562 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
55941494 ATATGTAAGT
* *
55941504 ATAATAATAATAATA
1 ATAATAGTAATAGTA
* *
55941519 ATAATAATAATAATA
1 ATAATAGTAATAGTA
55941534 ATAATAGTAATAGTA
1 ATAATAGTAATAGTA
*
55941549 ATAA-AGTCATAGTA
1 ATAATAGTAATAGTA
55941563 TAACATAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 9 0.22
15 32 0.78
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (15 bp):
ATAATAGTAATAGTA
Found at i:55943195 original size:45 final size:44
Alignment explanation
Indices: 55943063--55943252 Score: 254
Period size: 44 Copynumber: 4.3 Consensus size: 44
55943053 ATAAGACTTG
* * * *
55943063 TATCTTCGATCTACTTCACGCTAATAAATGAAGACAAGACCTGC
1 TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
55943107 TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
1 TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
* * * * ***
55943151 TTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC
1 TATCTTTGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGC
*
55943196 TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGT
1 TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
*
55943240 TTTCTTTGATCTA
1 TATCTTTGATCTA
55943253 TTCCACTGCC
Statistics
Matches: 125, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
44 88 0.70
45 37 0.30
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (44 bp):
TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
Found at i:55943434 original size:132 final size:132
Alignment explanation
Indices: 55943248--55943859 Score: 1023
Period size: 132 Copynumber: 4.6 Consensus size: 132
55943238 GTTTTCTTTG
* *
55943248 ATCTATTCCACTGCCGA-CCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTCA
1 ATCTATTCCACTG-CTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCA
* * *
55943312 GGGAGGTAAAATCTACCATCTTCGATCTACTCCACTACTG-TCTGGGGAGATAAGATCTGTAATC
65 GGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCT-TAGGGAGATAAGATCTGTAATC
55943376 TTCA
129 TTCA
55943380 ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAG
1 ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAG
* *
55943445 GGAGGTAAAATCCACCATCTTTGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
66 GGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
55943510 CA
131 CA
55943512 ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAG
1 ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAG
* * *
55943577 GGAGGTAAAATCCACCATCTTTGATTTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATCTT
66 GGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
55943642 CA
131 CA
* *
55943644 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTTAG
1 ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAG
*
55943709 GGAGGTAAAATCTACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGAA-CT
66 GGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT-AATCT
*
55943773 TTA
130 TCA
* *
55943776 ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAACCTTAG
1 ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAG
*
55943841 GGAGGTAAAATCCGCCATC
66 GGAGGTAAAATCCACCATC
55943860 AACCTGCTCC
Statistics
Matches: 458, Mismatches: 19, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
131 2 0.00
132 453 0.99
133 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
ATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAG
GGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
CA
Found at i:55943729 original size:88 final size:88
Alignment explanation
Indices: 55943373--55943759 Score: 222
Period size: 88 Copynumber: 4.4 Consensus size: 88
55943363 AAGATCTGTA
* *
55943373 ATCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACTGT
1 ATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAGAATCTACTGGCTTCAATGTACTCCACTGT
* *
55943437 AACCTCAGGGAGGTAAAATCCACC
66 -ACCTCAGGGAGATAAAATCTACC
** * * * ** * * *
55943461 ATCTTTGATTTGCTCCACTACTGCTTAGGGAGATA-AGATCTGTAAT--CTTCAATCTATTCCAC
1 ATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAGA-ATC--TACTGGCTTCAATGTACTCCAC
* *
55943523 TGCTACC-CAGGGAGATAGAAT-TACT
63 TG-TACCTCAGGGAGATAAAATCTACC
** * * * * * *** ** * *
55943548 GGCTTCAATGTACTCCACTG-TAACCTCAGGGAGGTAAAATCCACCATCTTTGATTTGCTCCAC-
1 ATCTTCAATCTACTCCACTGCT-GCC-CAGGGAGATAGAATCTACTGGCTTCAATGTACTCCACT
* *
55943611 -TACTGCTTAGGGAGATAAGATATGTA--
64 GTAC--CTCAGGGAGATAA-A-ATCTACC
*
55943637 ATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACTGT
1 ATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAGAATCTACTGGCTTCAATGTACTCCACTGT
* *
55943701 AACCTTAGGGAGGTAAAATCTACC
66 -ACCTCAGGGAGATAAAATCTACC
* * * **
55943725 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATA
1 ATCTTCAATCTACTCCACTGCTGCCCAGGGAGATA
55943760 AGATCTGTGA
Statistics
Matches: 217, Mismatches: 60, Indels: 44
0.68 0.19 0.14
Matches are distributed among these distances:
85 3 0.01
86 6 0.03
87 33 0.15
88 124 0.57
89 40 0.18
90 6 0.03
91 5 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (88 bp):
ATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAGAATCTACTGGCTTCAATGTACTCCACTGT
ACCTCAGGGAGATAAAATCTACC
Found at i:55943947 original size:45 final size:45
Alignment explanation
Indices: 55943896--55944036 Score: 132
Period size: 45 Copynumber: 3.2 Consensus size: 45
55943886 GTAAGGCTGG
55943896 TATCTTTAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGC
1 TATCTTTAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGC
* * * * * **
55943941 TATCTTTAA-CTTGCTCCACCG-CAACT-AAGGGAGGCAAGGCTT--
1 TATCTTTAATC-TGCTTCGCTGTCAA-TGTAGGAAGGCAAGATTTGC
* *
55943983 TAT-TTTCGATCTGCTTCGCTGTCGATGTAGGAAGGCAAGATTTGC
1 TATCTTT-AATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGC
55944028 TATCTTTAA
1 TATCTTTAA
55944037 CTTGCTCCAC
Statistics
Matches: 70, Mismatches: 17, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
41 3 0.04
42 12 0.17
43 15 0.21
44 16 0.23
45 21 0.30
46 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (45 bp):
TATCTTTAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGC
Found at i:55944016 original size:87 final size:87
Alignment explanation
Indices: 55943904--55944072 Score: 311
Period size: 87 Copynumber: 1.9 Consensus size: 87
55943894 GGTATCTTTA
55943904 ATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGCTATCTTTAACTTGCTCCACCGCAACTAA
1 ATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGCTATCTTTAACTTGCTCCACCGCAACTAA
55943969 GGGAGGCAAGGCTTTATTTTCG
66 GGGAGGCAAGGCTTTATTTTCG
* * *
55943991 ATCTGCTTCGCTGTCGATGTAGGAAGGCAAGATTTGCTATCTTTAACTTGCTCCACTGCAACTGA
1 ATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGCTATCTTTAACTTGCTCCACCGCAACTAA
55944056 GGGAGGCAAGGCTTTAT
66 GGGAGGCAAGGCTTTAT
55944073 AATTTCACTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 79 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (87 bp):
ATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATTTGCTATCTTTAACTTGCTCCACCGCAACTAA
GGGAGGCAAGGCTTTATTTTCG
Found at i:55950106 original size:17 final size:17
Alignment explanation
Indices: 55950086--55950123 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
55950076 TTTGATTATA
55950086 AAATATGA-AAAATGTAT
1 AAATATGATAAAA-GTAT
*
55950103 AAATATTATAAAAGTAT
1 AAATATGATAAAAGTAT
55950120 AAAT
1 AAAT
55950124 GTACATACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (17 bp):
AAATATGATAAAAGTAT
Found at i:55950270 original size:3 final size:3
Alignment explanation
Indices: 55950262--55950313 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
55950252 ATATGTAAGT
*
55950262 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55950310 ATA A
1 ATA A
55950314 AGTCATAGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55951473 original size:16 final size:16
Alignment explanation
Indices: 55951448--55951478 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55951438 TAAATAAAAA
55951448 ACATAGATATATATAC
1 ACATAGATATATATAC
*
55951464 ACATATATATATATA
1 ACATAGATATATATA
55951479 AATATAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (16 bp):
ACATAGATATATATAC
Found at i:55951562 original size:27 final size:29
Alignment explanation
Indices: 55951494--55951562 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 29
55951484 AAAAATATTC
55951494 ATTAAAAAAATATATACATGTACATATATAA
1 ATTAAAAAAATATATACA-GTA-ATATATAA
*
55951525 A-GAAAATAAATATATACA-T-ATATATAA
1 ATTAAAA-AAATATATACAGTAATATATAA
55951552 ATTAAAAAAAT
1 ATTAAAAAAAT
55951563 TAATTACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 13 0.38
28 4 0.12
29 1 0.03
30 4 0.12
31 12 0.35
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.30
Consensus pattern (29 bp):
ATTAAAAAAATATATACAGTAATATATAA
Found at i:55951562 original size:31 final size:31
Alignment explanation
Indices: 55951497--55951562 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
55951487 AATATTCATT
* *
55951497 AAAA-AAATATATACATGTACATATATAAAG
1 AAAATAAATATATACATATACATAAATAAAG
*
55951527 AAAATAAATATATACATATATATAAATTAAA-
1 AAAATAAATATATACATATACATAAA-TAAAG
55951558 AAAAT
1 AAAAT
55951563 TAATTACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 4 0.13
31 23 0.74
32 4 0.13
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.29
Consensus pattern (31 bp):
AAAATAAATATATACATATACATAAATAAAG
Found at i:55953733 original size:50 final size:50
Alignment explanation
Indices: 55953618--55953861 Score: 281
Period size: 50 Copynumber: 4.7 Consensus size: 50
55953608 GATAATAACA
* ** * *
55953618 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
55953669 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ** *
55953719 TGCCAACGCCATGTCCCAGACATGGTCTTACATAAGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
55953769 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-CGG
*
55953824 ATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
55953862 TCACTTTACC
Statistics
Matches: 162, Mismatches: 25, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
50 90 0.56
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 34 0.21
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:55953798 original size:100 final size:105
Alignment explanation
Indices: 55953617--55953854 Score: 324
Period size: 100 Copynumber: 2.3 Consensus size: 105
55953607 TGATAATAAC
** ** * *
55953617 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATAAGATCCTCTCATCTCGGTGCCCATGCCATG
* *
55953682 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
66 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
55953719 -TGCCAACGCCATGTCCCAGACATGGTCTTACATAAGA-CCTCTCGTCTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATAAGATCCTCTCATCTCGGTGCCCATGCCATG
55953782 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
*
55953824 ATGCCAATGCCATGTCCCAGACATGGTCTTA
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTA
55953855 TATGGGATCA
Statistics
Matches: 119, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
100 50 0.42
101 34 0.29
103 3 0.03
104 1 0.01
105 2 0.02
106 29 0.24
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (105 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATAAGATCCTCTCATCTCGGTGCCCATGCCATG
TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:55953982 original size:13 final size:13
Alignment explanation
Indices: 55953961--55953991 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
55953951 GCTTAGATCA
*
55953961 TCATCAAATAAAT
1 TCATAAAATAAAT
55953974 TCATAAAATAAAT
1 TCATAAAATAAAT
55953987 TCATA
1 TCATA
55953992 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:55954238 original size:30 final size:30
Alignment explanation
Indices: 55954204--55954261 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
55954194 CCTTGACTCT
*
55954204 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
55954234 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
55954262 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:55956035 original size:43 final size:43
Alignment explanation
Indices: 55955890--55956050 Score: 159
Period size: 43 Copynumber: 3.8 Consensus size: 43
55955880 CTTTCTTGAG
* * *
55955890 TCTGCTCCACTGCAAATTCAG-GAAGATAAGACCTAATAC---AA
1 TCTGCTCCACTGCAACTTCAGAG-AGATAAGA-TTACTACTTTAA
* * * *
55955931 TCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TACTACTTTAA
* * *
55955975 TCCGCTCCACTGCAACTTCAGAGAGATAGGATTACTGCTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATTACTACTTTAA
* *
55956018 TCTGCTCCACTGTAACTTCAGGGAGATAAGATT
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATT
55956051 CGCCATATTA
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
41 30 0.31
42 1 0.01
43 37 0.38
44 30 0.31
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGATTACTACTTTAA
Found at i:55957234 original size:25 final size:26
Alignment explanation
Indices: 55957206--55957254 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
55957196 GTGTCTTGAA
55957206 AAGAA-AAAGGTATT-CAAGAACAACG
1 AAGAATAAA-GTATTGCAAGAACAACG
55957231 AAGAATAAAGTATTGCAAGAACAA
1 AAGAATAAAGTATTGCAAGAACAA
55957255 ACAAATTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.14
Consensus pattern (26 bp):
AAGAATAAAGTATTGCAAGAACAACG
Found at i:55970099 original size:25 final size:25
Alignment explanation
Indices: 55970065--55970113 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
55970055 GGAATAAAAC
55970065 TGTATTATTATTGTAATTATATTTT
1 TGTATTATTATTGTAATTATATTTT
*
55970090 TGTATTATTATTGTCATTATATTT
1 TGTATTATTATTGTAATTATATTT
55970114 CTATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (25 bp):
TGTATTATTATTGTAATTATATTTT
Found at i:55970122 original size:25 final size:25
Alignment explanation
Indices: 55970067--55970123 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
55970057 AATAAAACTG
* *
55970067 TATTATTATTGTAATTATATTTTTG
1 TATTATTATTGTAATTATATTTCTA
*
55970092 TATTATTATTGTCATTATATTTCTA
1 TATTATTATTGTAATTATATTTCTA
*
55970117 TTTTATT
1 TATTATT
55970124 TATTTATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.26, C:0.04, G:0.05, T:0.65
Consensus pattern (25 bp):
TATTATTATTGTAATTATATTTCTA
Found at i:55970170 original size:3 final size:3
Alignment explanation
Indices: 55970162--55970264 Score: 88
Period size: 3 Copynumber: 35.0 Consensus size: 3
55970152 TCTTTTAACC
*
55970162 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTG TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * * * * *
55970208 TTA AAA TTA TAA TATA TTA TTA TCA GTA TTA TAA AT- TTA TTA TGTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
55970254 TTA TTA -TA TTA
1 TTA TTA TTA TTA
55970265 AGTTTCTTCA
Statistics
Matches: 80, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
2 7 0.09
3 68 0.85
4 5 0.06
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:55970281 original size:25 final size:23
Alignment explanation
Indices: 55970252--55970302 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
55970242 ATTTATTATG
* *
55970252 TATTATTATATTAAGTTTCTTCATA
1 TATTAATAT-TTAA-TTTCGTCATA
55970277 TATTAATATTTAATTTCGTCATA
1 TATTAATATTTAATTTCGTCATA
55970300 TAT
1 TAT
55970303 CGTCTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.50
24 4 0.17
25 8 0.33
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (23 bp):
TATTAATATTTAATTTCGTCATA
Found at i:55970462 original size:49 final size:47
Alignment explanation
Indices: 55970361--55970465 Score: 128
Period size: 47 Copynumber: 2.3 Consensus size: 47
55970351 TTTTATAATT
*
55970361 CATACGTACATACATTTTTTATATATATTTTATAACTTAAAACTATA
1 CATACATACATACATTTTTTATATATATTTTATAACTTAAAACTATA
* * *
55970408 TATACATACATATATTCTTTT-TATATATTTTATAGTCTTAAAA-TATA
1 CATACATACATACATT-TTTTATATATATTTTATA-ACTTAAAACTATA
55970455 C--ACATACATAC
1 CATACATACATAC
55970466 TTACATATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
45 9 0.18
47 30 0.60
48 11 0.22
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (47 bp):
CATACATACATACATTTTTTATATATATTTTATAACTTAAAACTATA
Found at i:55970558 original size:4 final size:4
Alignment explanation
Indices: 55970549--55970575 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
55970539 TTTTTATAAT
55970549 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
55970576 TTCATTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:55972816 original size:6 final size:6
Alignment explanation
Indices: 55972799--55972828 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
55972789 TCTTCACTAT
*
55972799 TCACCA TTACCA TCACCA TCACCA TCACCA
1 TCACCA TCACCA TCACCA TCACCA TCACCA
55972829 ACAAAAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (6 bp):
TCACCA
Found at i:55977752 original size:13 final size:13
Alignment explanation
Indices: 55977736--55977761 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55977726 GCTAGGTTTT
55977736 GAGGAAGAAGAAG
1 GAGGAAGAAGAAG
55977749 GAGGAAGAAGAAG
1 GAGGAAGAAGAAG
55977762 AAGAAAGAAA
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:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (13 bp):
GAGGAAGAAGAAG
Found at i:55977769 original size:13 final size:13
Alignment explanation
Indices: 55977740--55977782 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
55977730 GGTTTTGAGG
* *
55977740 AAGAAGAAGGAGG
1 AAGAAGAAGAAGA
55977753 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
*
55977766 AAGAA-AAGAAAA
1 AAGAAGAAGAAGA
55977778 AAGAA
1 AAGAA
55977783 AAAAACGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:55977781 original size:16 final size:16
Alignment explanation
Indices: 55977762--55977801 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
55977752 GAAGAAGAAG
55977762 AAGAAAGAAAA-GAAAA
1 AAGAAA-AAAACGAAAA
55977778 AAGAAAAAAACGAAAA
1 AAGAAAAAAACGAAAA
*
55977794 AATAAAAA
1 AAGAAAAA
55977802 TAATAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (16 bp):
AAGAAAAAAACGAAAA
Found at i:55977977 original size:21 final size:23
Alignment explanation
Indices: 55977927--55977980 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
55977917 AATCCAGCGT
* *
55977927 AGGCCCAGTGCAGCAGCAGGCTCC
1 AGGCCCAGCGCAGCAGCAAGC-CC
55977951 AGGCCCAGCGCAGCAGCAAG-CC
1 AGGCCCAGCGCAGCAGCAAGCCC
55977973 A-GCCCAGC
1 AGGCCCAGC
55977981 AGGCCCACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 7 0.25
22 3 0.11
24 18 0.64
ACGTcount: A:0.24, C:0.41, G:0.31, T:0.04
Consensus pattern (23 bp):
AGGCCCAGCGCAGCAGCAAGCCC
Found at i:55978041 original size:11 final size:10
Alignment explanation
Indices: 55978023--55978072 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 10
55978013 AGCCCAACAG
55978023 AAAAAAGAAA
1 AAAAAAGAAA
55978033 AAGAAAAGAAA
1 AA-AAAAGAAA
* *
55978044 AGGAAAGGAAA
1 A-AAAAAGAAA
55978055 AAAGAAAGAAA
1 AAA-AAAGAAA
55978066 AAAAAAG
1 AAAAAAG
55978073 GGCCCAAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 7 0.21
11 26 0.79
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:55978072 original size:22 final size:22
Alignment explanation
Indices: 55978023--55978073 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
55978013 AGCCCAACAG
55978023 AAAAAA-GAAAAAGAAAAGAAA
1 AAAAAAGGAAAAAGAAAAGAAA
**
55978044 AGGAAAGGAAAAA-AGAAAGAAA
1 AAAAAAGGAAAAAGA-AAAGAAA
55978066 AAAAAAGG
1 AAAAAAGG
55978074 GCCCAAGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (22 bp):
AAAAAAGGAAAAAGAAAAGAAA
Found at i:55978620 original size:19 final size:19
Alignment explanation
Indices: 55978596--55978887 Score: 123
Period size: 19 Copynumber: 15.6 Consensus size: 19
55978586 AAAATTCCCG
55978596 TGTTTT-AAAAAATATTCA
1 TGTTTTCAAAAAATATTCA
* *
55978614 TGTTTTTTAAAAAA-ATTCC
1 TG-TTTTCAAAAAATATTCA
* *
55978633 CGTGTTTCAAAAAATATTCG
1 TGT-TTTCAAAAAATATTCA
*
55978653 TGTTTTCAAAAAAAATTC-
1 TGTTTTCAAAAAATATTCA
55978671 TCGTGTTTCAAAAAATATTCA
1 T-GT-TTTCAAAAAATATTCA
* *
55978692 TGTTTTCAAAAAAAATTCC
1 TGTTTTCAAAAAATATTCA
* * *
55978711 CGTGTTTC-AAAAATTTTCG
1 TGT-TTTCAAAAAATATTCA
* * *
55978730 TGTTTTC-AGAAAT-TCCCG
1 TGTTTTCAAAAAATAT-TCA
* **
55978748 TGTTTT--AAAAATTTTTG
1 TGTTTTCAAAAAATATTCA
*
55978765 TGTTTTCAAAAAAT-TTCCC
1 TGTTTTCAAAAAATATT-CA
*
55978784 T-TGTTTC-AAAAAT-TTCCG
1 TGT-TTTCAAAAAATATT-CA
* *
55978802 TGTTTTCAAAAAAAATTTCG
1 TGTTTTCAAAAAATA-TTCA
55978822 TG-TTTCAAAAAAT-TCTCA
1 TGTTTTCAAAAAATAT-TCA
* * *
55978840 T-ATTTC-AAAAATTTTCG
1 TGTTTTCAAAAAATATTCA
* *
55978857 CGTTTTCAAAAATTATT-A
1 TGTTTTCAAAAAATATTCA
55978875 TTGTGTTTCAAAA
1 -TGT-TTTCAAAA
55978888 TTCTCGTGTT
Statistics
Matches: 217, Mismatches: 32, Indels: 48
0.73 0.11 0.16
Matches are distributed among these distances:
17 22 0.10
18 52 0.24
19 96 0.44
20 44 0.20
21 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.42
Consensus pattern (19 bp):
TGTTTTCAAAAAATATTCA
Found at i:55978850 original size:37 final size:38
Alignment explanation
Indices: 55978585--55978835 Score: 298
Period size: 39 Copynumber: 6.7 Consensus size: 38
55978575 TTCTTGTTTC
* * **
55978585 AAAAATTCCCGTGTTTTAAAAAATATTCATGTTTTTTAA
1 AAAAATTCCCGTGTTTCAAAAAAT-TTCGTGTTTTCAAA
55978624 AAAAATTCCCGTGTTTCAAAAAATATTCGTGTTTTCAAA
1 AAAAATTCCCGTGTTTCAAAAAAT-TTCGTGTTTTCAAA
* *
55978663 AAAAATTCTCGTGTTTCAAAAAATATTCATGTTTTCAAA
1 AAAAATTCCCGTGTTTCAAAAAAT-TTCGTGTTTTCAAA
*
55978702 AAAAATTCCCGTGTTTCAAAAATTTTCGTGTTTTC---
1 AAAAATTCCCGTGTTTCAAAAAATTTCGTGTTTTCAAA
* * * *
55978737 AGAAATTCCCGTGTTTTAAAAATTTTTGTGTTTTC-AA
1 AAAAATTCCCGTGTTTCAAAAAATTTCGTGTTTTCAAA
* *
55978774 AAAATTTCCCTTGTTTC-AAAAATTTCCGTGTTTTCAAA
1 AAAAATTCCCGTGTTTCAAAAAATTT-CGTGTTTTCAAA
*
55978812 AAAAATT-TCGTGTTTCAAAAAATT
1 AAAAATTCCCGTGTTTCAAAAAATT
55978836 CTCATATTTC
Statistics
Matches: 186, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
35 32 0.17
36 7 0.04
37 28 0.15
38 25 0.13
39 94 0.51
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (38 bp):
AAAAATTCCCGTGTTTCAAAAAATTTCGTGTTTTCAAA
Found at i:55978863 original size:18 final size:18
Alignment explanation
Indices: 55978581--55978904 Score: 162
Period size: 18 Copynumber: 17.5 Consensus size: 18
55978571 AAAATTCTTG
**
55978581 TTTCAAAAATTCCCGTGT
1 TTTCAAAAATTTTCGTGT
* * *
55978599 TTTAAAAAATATTCATGTTT
1 TTTCAAAAATTTTC--GTGT
* **
55978619 TTTAAAAAAATTCCCGTG-
1 TTT-CAAAAATTTTCGTGT
*
55978637 TTTCAAAAAATATTCGTGT
1 TTTC-AAAAATTTTCGTGT
*
55978656 TTTCAAAAAAAATTCTCGTG-
1 TTTC---AAAAATTTTCGTGT
* *
55978676 TTTCAAAAAATATTCATGT
1 TTTC-AAAAATTTTCGTGT
**
55978695 TTTCAAAAAAAATTCCCGTG-
1 TTTC---AAAAATTTTCGTGT
55978715 TTTCAAAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
* **
55978733 TTTCAGAAATTCCCGTGT
1 TTTCAAAAATTTTCGTGT
*
55978751 TTT-AAAAATTTTTGTGT
1 TTTCAAAAATTTTCGTGT
* *
55978768 TTTCAAAAAATTTCCCT-T
1 TTTC-AAAAATTTTCGTGT
*
55978786 GTTTCAAAAATTTCCGTGT
1 -TTTCAAAAATTTTCGTGT
*
55978805 TTTCAAAAAAAATTTCGTG-
1 TTTC--AAAAATTTTCGTGT
* * *
55978824 TTTCAAAAAATTCTCAT-A
1 TTTC-AAAAATTTTCGTGT
*
55978842 TTTCAAAAATTTTCGCGT
1 TTTCAAAAATTTTCGTGT
**
55978860 TTTCAAAAATTATTATTGT
1 TTTCAAAAATT-TTCGTGT
*
55978879 GTTTC-AAAATTCTCGTGT
1 -TTTCAAAAATTTTCGTGT
55978897 TTT-AAAAA
1 TTTCAAAAA
55978905 AAATCATGCT
Statistics
Matches: 234, Mismatches: 50, Indels: 45
0.71 0.15 0.14
Matches are distributed among these distances:
17 40 0.17
18 97 0.41
19 38 0.16
20 29 0.12
21 30 0.13
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:55986285 original size:46 final size:45
Alignment explanation
Indices: 55986218--55986543 Score: 368
Period size: 46 Copynumber: 7.6 Consensus size: 45
55986208 TTTGAGTACT
* *
55986218 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
55986264 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
55986300 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
55986346 TCTGATCAAGTGAAAAAGTGATAAGT-G-A---TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* * *
55986382 TCTGATTAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
55986428 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
55986474 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
55986519 TCTGATC-AG-GGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
55986544 ATCATACGTA
Statistics
Matches: 243, Mismatches: 17, Indels: 43
0.80 0.06 0.14
Matches are distributed among these distances:
36 59 0.24
37 2 0.01
38 2 0.01
40 4 0.02
42 4 0.02
43 13 0.05
44 4 0.02
45 23 0.09
46 132 0.54
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:55986295 original size:36 final size:36
Alignment explanation
Indices: 55986254--55986408 Score: 166
Period size: 36 Copynumber: 4.0 Consensus size: 36
55986244 GGTAGCTTTA
55986254 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
55986290 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
55986335 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * * *
55986372 GATATACTTATCTGATTAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
55986408 G
1 G
55986409 TTAGCCTTAG
Statistics
Matches: 101, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
36 63 0.62
37 2 0.02
40 2 0.02
42 2 0.02
45 2 0.02
46 30 0.30
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:55986355 original size:82 final size:82
Alignment explanation
Indices: 55986218--55986543 Score: 433
Period size: 82 Copynumber: 3.9 Consensus size: 82
55986208 TTTGAGTACT
*
55986218 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
55986283 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
55986300 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
55986365 GATAAGTGATATACTTA
66 GATAAGTGCTACACTTA
* * * * *
55986382 TCTGATTAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
55986447 GATAAGTGGTAGCCTTAGCTACACTTA
66 GAT-A-----AG---T-GCTACACTTA
* * * *
55986474 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATC-AG-GGACAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
55986536 GATAAGTG
66 GATAAGTG
55986544 ATCATACGTA
Statistics
Matches: 218, Mismatches: 16, Indels: 23
0.85 0.06 0.09
Matches are distributed among these distances:
79 1 0.00
80 1 0.00
82 142 0.65
83 3 0.01
88 3 0.01
89 8 0.04
90 2 0.01
91 20 0.09
92 38 0.17
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:55986536 original size:128 final size:126
Alignment explanation
Indices: 55986218--55986543 Score: 383
Period size: 128 Copynumber: 2.6 Consensus size: 126
55986208 TTTGAGTACT
* * *
55986218 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAG-GGAAAAGT
*
55986283 GATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
64 GATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* * * * ** * *
55986346 TCTGATCAAGTGAAAAAGTGATAAGTGATATACTTATCT-GA-TTAAGTGA-CAAAGTGATAAGT
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTA-GCTTAGCTACACTTATCTGATC-AAGGGAAAAGT
* * *
55986408 G-TTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACT
64 GATAAG---T-GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACT
55986472 TA
125 TA
* * *
55986474 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-AGGGACAAGTGA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGGGAAAAGTGA
55986538 TAAGTG
66 TAAGTG
55986544 ATCATACGTA
Statistics
Matches: 162, Mismatches: 26, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
124 3 0.02
125 8 0.05
126 10 0.06
127 7 0.04
128 123 0.76
129 10 0.06
130 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (126 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGGGAAAAGTGA
TAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:55988790 original size:80 final size:81
Alignment explanation
Indices: 55988607--55988912 Score: 372
Period size: 80 Copynumber: 3.8 Consensus size: 81
55988597 TTTTTTTTTT
* * * * *
55988607 AAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTTGGGCACACGCCGAGGTATTTC--TT-AAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
***
55988669 TTCTGTTTTT-TTCAA
66 TTCTGTTTTTCAAAAA
*
55988684 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAAC-CATGCCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
55988748 TTCTGTTTTTCAAAAA
66 TTCTGTTTTTCAAAAA
* *
55988764 AAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTTGGAC-CATGCCGAGGTATTTCTTTTAAAT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
*
55988828 TTCTATTTTTCCAAAAAATCAA
66 TTCTGTTTTT-C---AAA--AA
***
55988850 CAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATAATGAGGTATTTCTTTTA
1 -AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTA
55988913 CATTAATCAA
Statistics
Matches: 199, Mismatches: 18, Indels: 13
0.87 0.08 0.06
Matches are distributed among these distances:
76 15 0.08
77 35 0.18
78 2 0.01
79 13 0.07
80 72 0.36
81 1 0.01
84 3 0.02
86 2 0.01
87 38 0.19
88 18 0.09
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (81 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAAT
TTCTGTTTTTCAAAAA
Found at i:55989230 original size:30 final size:30
Alignment explanation
Indices: 55989123--55989219 Score: 140
Period size: 30 Copynumber: 3.2 Consensus size: 30
55989113 TTGTGTTAAA
* *
55989123 AAAATTGCATTTTAACCCTTAAACTTTTTC
1 AAAATTACATTTTAACCCTTAAACTTTCTC
* *
55989153 AAAATTACATTTTAACCCCTAAACTTTCTT
1 AAAATTACATTTTAACCCTTAAACTTTCTC
* *
55989183 AAAATTACATTTTGACCCTTGAACTTTCTC
1 AAAATTACATTTTAACCCTTAAACTTTCTC
55989213 AAAATTA
1 AAAATTA
55989220 TCTTTTGACC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTTAAACTTTCTC
Found at i:55989231 original size:60 final size:60
Alignment explanation
Indices: 55989123--55989260 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
55989113 TTGTGTTAAA
* * *
55989123 AAAATTGCATTTTAACCCTTAAACTTTTTCAAAATTACATTTTAACCCCTAAACTTTCTT-
1 AAAATTACATTTTGACCCTTAAACTTTCTCAAAATTACATTTTAACCCC-AAACTTTCTTC
* * ** *
55989183 AAAATTACATTTTGACCCTTGAACTTTCTCAAAATTATC-TTTTGACCCCAATTTTTTTTC
1 AAAATTACATTTTGACCCTTAAACTTTCTCAAAATTA-CATTTTAACCCCAAACTTTCTTC
*
55989243 AAAATTACGTTTTGACCC
1 AAAATTACATTTTGACCC
55989261 CAAAATTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 7 0.10
60 59 0.88
61 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (60 bp):
AAAATTACATTTTGACCCTTAAACTTTCTCAAAATTACATTTTAACCCCAAACTTTCTTC
Found at i:55989270 original size:30 final size:30
Alignment explanation
Indices: 55989123--55989270 Score: 120
Period size: 30 Copynumber: 4.9 Consensus size: 30
55989113 TTGTGTTAAA
* * ** *
55989123 AAAATTGCATTTTAACCCTTAAACTTTTTC
1 AAAATTACATTTTGACCCCAAAATTTTTTC
* * *
55989153 AAAATTACATTTTAACCCCTAAACTTTCTT-
1 AAAATTACATTTTGACCCC-AAAATTTTTTC
*** * *
55989183 AAAATTACATTTTGACCCTTGAACTTTCTC
1 AAAATTACATTTTGACCCCAAAATTTTTTC
**
55989213 AAAATTATC-TTTTGACCCCAATTTTTTTTC
1 AAAATTA-CATTTTGACCCCAAAATTTTTTC
*
55989243 AAAATTACGTTTTGACCCCAAAATTTTT
1 AAAATTACATTTTGACCCCAAAATTTTT
55989271 ACTACGCTTA
Statistics
Matches: 91, Mismatches: 23, Indels: 8
0.75 0.19 0.07
Matches are distributed among these distances:
29 5 0.05
30 79 0.87
31 7 0.08
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAATTTTTTC
Found at i:55989626 original size:3 final size:3
Alignment explanation
Indices: 55989618--55989673 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
55989608 TTTGAGGAGA
*
55989618 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
55989666 AAG AAG AA
1 AAG AAG AA
55989674 ATGAAAAATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:55990521 original size:39 final size:38
Alignment explanation
Indices: 55990478--55990727 Score: 203
Period size: 39 Copynumber: 6.7 Consensus size: 38
55990468 CGATACGTCC
* * *
55990478 TTAAAAAAAATCGCTTGTTTCAAAAAATATTCATGTTTT
1 TTAAAAAAATTC-CGTGTTTCAAAAAATATTCGTGTTTT
55990517 TTAAAAAAATTCCAGTGTTTCAAAAAATATTCGTG-TTT
1 TTAAAAAAATTCC-GTGTTTCAAAAAATATTCGTGTTTT
* * *
55990555 TCAAAAAAACTCCCGTGTTTCAAAAAATATTCGTTTTTT
1 TTAAAAAAA-TTCCGTGTTTCAAAAAATATTCGTGTTTT
* * * *
55990594 TTTAAAAATTTCTCGTGTTTC-AAAAATTTTTGTG-TTT
1 TTAAAAAAATTC-CGTGTTTCAAAAAATATTCGTGTTTT
* * *
55990631 TCAAAAAAATTCCCGTGTTTC-AAAAAT-TTCAT-TATT
1 TTAAAAAAATT-CCGTGTTTCAAAAAATATTCGTGTTTT
* * * * *
55990667 TTCAAAAATTTTCGTGTTTC-AAAAA-ATTC-TCTTAT
1 TTAAAAAAATTCCGTGTTTCAAAAAATATTCGTGTTTT
* * *
55990702 TTCAAAAATTTCCGTGTTTTAAAAAA
1 TTAAAAAAATTCCGTGTTTCAAAAAA
55990728 ATTATTATTG
Statistics
Matches: 175, Mismatches: 27, Indels: 21
0.78 0.12 0.09
Matches are distributed among these distances:
34 1 0.01
35 36 0.21
36 18 0.10
37 25 0.14
38 45 0.26
39 50 0.29
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (38 bp):
TTAAAAAAATTCCGTGTTTCAAAAAATATTCGTGTTTT
Found at i:55990522 original size:20 final size:20
Alignment explanation
Indices: 55990495--55990674 Score: 89
Period size: 19 Copynumber: 9.4 Consensus size: 20
55990485 AAATCGCTTG
55990495 TTTCAAAAAATATTCATGTT
1 TTTCAAAAAATATTCATGTT
* *
55990515 TTTTAAAAAA-ATTCCA-GTG
1 TTTCAAAAAATATT-CATGTT
*
55990534 TTTCAAAAAATATTCGTG-T
1 TTTCAAAAAATATTCATGTT
* ** *
55990553 TTTCAAAAAA-ACTCCCGTG
1 TTTCAAAAAATATTCATGTT
* *
55990572 TTTCAAAAAATATTCGTTTT
1 TTTCAAAAAATATTCATGTT
** *
55990592 TTTTTAAAAAT-TTC-TCGTG
1 TTTCAAAAAATATTCAT-GTT
*
55990611 TTTC-AAAAAT-TT-TTGTGT
1 TTTCAAAAAATATTCATGT-T
** *
55990629 TTTCAAAAAA-ATTCCCGTG
1 TTTCAAAAAATATTCATGTT
55990648 TTTC-AAAAAT-TTCAT-TAT
1 TTTCAAAAAATATTCATGT-T
55990666 TTTCAAAAA
1 TTTCAAAAA
55990675 TTTTCGTGTT
Statistics
Matches: 120, Mismatches: 26, Indels: 29
0.69 0.15 0.17
Matches are distributed among these distances:
17 3 0.03
18 30 0.25
19 57 0.47
20 30 0.25
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.43
Consensus pattern (20 bp):
TTTCAAAAAATATTCATGTT
Found at i:55990620 original size:18 final size:18
Alignment explanation
Indices: 55990597--55990726 Score: 124
Period size: 18 Copynumber: 7.3 Consensus size: 18
55990587 GTTTTTTTTT
55990597 AAAAATTTCTCGTGTTTC
1 AAAAATTTCTCGTGTTTC
*
55990615 AAAAATTT-TTGTGTTTTC
1 AAAAATTTCTCGTG-TTTC
* *
55990633 AAAAAAATTCCCGTGTTTC
1 -AAAAATTTCTCGTGTTTC
**
55990652 AAAAATTTCATTAT-TTTC
1 AAAAATTTC-TCGTGTTTC
55990670 AAAAATTT-TCGTGTTTC
1 AAAAATTTCTCGTGTTTC
* * *
55990687 AAAAAATTCTCTTATTTC
1 AAAAATTTCTCGTGTTTC
*
55990705 AAAAATTTC-CGTGTTTT
1 AAAAATTTCTCGTGTTTC
55990722 AAAAA
1 AAAAA
55990727 AATTATTATT
Statistics
Matches: 89, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
16 2 0.02
17 25 0.28
18 47 0.53
19 12 0.13
20 3 0.03
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (18 bp):
AAAAATTTCTCGTGTTTC
Found at i:55990683 original size:35 final size:35
Alignment explanation
Indices: 55990567--55990726 Score: 162
Period size: 35 Copynumber: 4.4 Consensus size: 35
55990557 AAAAAAACTC
* *
55990567 CCGTGTTTCAAAAAATATTCGTTTTTTTTTAAAAATTT
1 CCGTGTTTC-AAAAAT-TTC-TTTATTTTCAAAAATTT
* *
55990605 CTCGTGTTTCAAAAATTT-TTGTGTTTTCAAAAAAATTC
1 C-CGTGTTTCAAAAATTTCTT-TATTTTC--AAAAATTT
*
55990643 CCGTGTTTCAAAAATTTCATTATTTTCAAAAATTT
1 CCGTGTTTCAAAAATTTCTTTATTTTCAAAAATTT
* *
55990678 TCGTGTTTCAAAAAATTCTCTTA-TTTCAAAAATTT
1 CCGTGTTTCAAAAATTTCT-TTATTTTCAAAAATTT
*
55990713 CCGTGTTTTAAAAA
1 CCGTGTTTCAAAAA
55990727 AATTATTATT
Statistics
Matches: 105, Mismatches: 11, Indels: 15
0.80 0.08 0.11
Matches are distributed among these distances:
35 49 0.47
36 8 0.08
37 24 0.23
38 16 0.15
39 8 0.08
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (35 bp):
CCGTGTTTCAAAAATTTCTTTATTTTCAAAAATTT
Found at i:55990727 original size:35 final size:36
Alignment explanation
Indices: 55990493--55990736 Score: 133
Period size: 38 Copynumber: 6.6 Consensus size: 36
55990483 AAAAATCGCT
* * * *
55990493 TGTTTCAAAAAATATTCATGTTTTTTAAAAAAATTCCAG
1 TGTTTTAAAAAAT-TTCAT-TATTTTCAAAAATTTCC-G
* * * * *
55990532 TGTTTCAAAAAATATTC-GTGTTTTCAAAAAAACTCCCG
1 TGTTTTAAAAAAT-TTCATTATTTTC--AAAAATTTCCG
* * * *
55990570 TGTTTCAAAAAATATTCGTTTTTTTTTAAAAATTTCTCG
1 TGTTTTAAAAAAT-TTC-ATTATTTTCAAAAATTTC-CG
* * * *
55990609 TG-TTTCAAAAATTT-TTGTGTTTTCAAAAAAATTCCCG
1 TGTTTTAAAAAATTTCAT-TATTTTC--AAAAATTTCCG
* *
55990646 TG-TTTCAAAAATTTCATTATTTTCAAAAATTTTCG
1 TGTTTTAAAAAATTTCATTATTTTCAAAAATTTCCG
*
55990681 TGTTTCAAAAAATTCTC-TTA-TTTCAAAAATTTCCG
1 TGTTTTAAAAAATT-TCATTATTTTCAAAAATTTCCG
*
55990716 TGTTTTAAAAAAATT-ATTATT
1 TGTTTTAAAAAATTTCATTATT
55990737 GTGCTTCAAA
Statistics
Matches: 168, Mismatches: 24, Indels: 30
0.76 0.11 0.14
Matches are distributed among these distances:
34 4 0.02
35 40 0.24
36 17 0.10
37 31 0.18
38 42 0.25
39 29 0.17
40 5 0.03
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (36 bp):
TGTTTTAAAAAATTTCATTATTTTCAAAAATTTCCG
Found at i:55990730 original size:19 final size:18
Alignment explanation
Indices: 55990515--55990727 Score: 98
Period size: 18 Copynumber: 11.6 Consensus size: 18
55990505 TATTCATGTT
*
55990515 TTTTAAAAAAATTCCAGTG
1 TTTTAAAAAATTTCC-GTG
*
55990534 TTTCAAAAAATATT-CGTG
1 TTTTAAAAAAT-TTCCGTG
* *
55990552 TTTTCAAAAAAACTCCCGTG
1 TTTT--AAAAAATTTCCGTG
* *
55990572 TTTCAAAAAATATT-CGTTTT
1 TTTTAAAAAAT-TTCCG--TG
*
55990592 TTTTTAAAAATTTCTCGTG
1 TTTTAAAAAATTTC-CGTG
* **
55990611 -TTTCAAAAATTTTTGTG
1 TTTTAAAAAATTTCCGTG
*
55990628 TTTTCAAAAAAATTCCCGTG
1 TTTT--AAAAAATTTCCGTG
* ** *
55990648 -TTTCAAAAATTTCATTA
1 TTTTAAAAAATTTCCGTG
* *
55990665 TTTTCAAAAATTTTCGTG
1 TTTTAAAAAATTTCCGTG
*
55990683 TTTCAAAAAA-TTCTC-T-
1 TTTTAAAAAATTTC-CGTG
*
55990699 TATTTCAAAAATTTCCGTG
1 T-TTTAAAAAATTTCCGTG
55990718 TTTTAAAAAA
1 TTTTAAAAAA
55990728 ATTATTATTG
Statistics
Matches: 142, Mismatches: 34, Indels: 37
0.67 0.16 0.17
Matches are distributed among these distances:
16 1 0.01
17 23 0.16
18 62 0.44
19 19 0.13
20 35 0.25
21 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (18 bp):
TTTTAAAAAATTTCCGTG
Found at i:55991227 original size:27 final size:26
Alignment explanation
Indices: 55991148--55991300 Score: 108
Period size: 26 Copynumber: 5.7 Consensus size: 26
55991138 AATTTTAAGC
* * * *
55991148 AATTTAAAATAAACATTACATAAAAT
1 AATTTAAAATAAATAATATATAAAAA
* * * *
55991174 AGTTTAAAAGAAATGATATGTAAAAAA
1 AATTTAAAATAAATAATATAT-AAAAA
*
55991201 AATCTAAAATAAATAATATATATAAAA
1 AATTTAAAATAAATAATATATA-AAAA
* * * **
55991228 CAGTTTAAGATAAAATAATATAGAAAGT
1 -AATTTAAAAT-AAATAATATATAAAAA
* * *
55991256 AATTCAAAATAAATAATATATGAAAC
1 AATTTAAAATAAATAATATATAAAAA
*
55991282 AATTTAAAATAGATAATAT
1 AATTTAAAATAAATAATAT
55991301 CAAACAGCTT
Statistics
Matches: 95, Mismatches: 28, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
26 44 0.46
27 31 0.33
28 9 0.09
29 11 0.12
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (26 bp):
AATTTAAAATAAATAATATATAAAAA
Found at i:55996685 original size:23 final size:23
Alignment explanation
Indices: 55996654--55996704 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
55996644 TTAATAAGAT
55996654 TATTATTAAATATAA-T-TTTTTAA
1 TATTATT-AATATAAGTATTTTT-A
*
55996677 TATTTTTAATATAAGTATTTTTA
1 TATTATTAATATAAGTATTTTTA
55996700 TATTA
1 TATTA
55996705 AATCATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 7 0.29
23 12 0.50
24 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TATTATTAATATAAGTATTTTTA
Found at i:55998672 original size:29 final size:29
Alignment explanation
Indices: 55998561--55998665 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
55998551 TCGTTTTTTT
* *
55998561 AATTATATTTTAACCCCTCAACTTTTTAA
1 AATTGTATTTTAACCCCTAAACTTTTTAA
* *
55998590 AATTGTA-TTTGACCCCTAAAATTTTTAAA
1 AATTGTATTTTAACCCCTAAACTTTTT-AA
* * * *
55998619 AATTGCATTTTGACCCTTAAACTTTTTTA
1 AATTGTATTTTAACCCCTAAACTTTTTAA
*
55998648 AATTTTATTTTAACCCCT
1 AATTGTATTTTAACCCCT
55998666 GGACTTTCTT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
28 16 0.26
29 29 0.47
30 17 0.27
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (29 bp):
AATTGTATTTTAACCCCTAAACTTTTTAA
Found at i:55998952 original size:20 final size:20
Alignment explanation
Indices: 55998929--55998988 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 20
55998919 AAAAACTTGC
55998929 GAAAAAGAGAAAAAGAAGAG
1 GAAAAAGAGAAAAAGAAGAG
*
55998949 GAAAAAAGAGAGAAAG-AGAG
1 G-AAAAAGAGAAAAAGAAGAG
* *
55998969 GAGAAAG-G-AGAAGAAGAG
1 GAAAAAGAGAAAAAGAAGAG
55998987 GA
1 GA
55998989 GAGGGTCCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 3 0.09
18 7 0.21
19 5 0.15
20 6 0.18
21 13 0.38
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (20 bp):
GAAAAAGAGAAAAAGAAGAG
Found at i:55998954 original size:21 final size:21
Alignment explanation
Indices: 55998930--55998985 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
55998920 AAAACTTGCG
55998930 AAAAAGAGAAAAAGAAGAGGA
1 AAAAAGAGAAAAAGAAGAGGA
*
55998951 AAAAAGAGAGAAAG-AGAGGA
1 AAAAAGAGAAAAAGAAGAGGA
* * *
55998971 GAAAGGAGAAGAAGA
1 AAAAAGAGAAAAAGA
55998986 GGAGAGGGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AAAAAGAGAAAAAGAAGAGGA
Found at i:55998979 original size:18 final size:19
Alignment explanation
Indices: 55998941--55998990 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
55998931 AAAAGAGAAA
*
55998941 AAGAAGAGGAAAAAAGAGAG
1 AAGAAGAGG-AGAAAGAGAG
55998961 AA-AGAGAGGAGAAAG-GAG
1 AAGA-AGAGGAGAAAGAGAG
55998979 AAGAAGAGGAGA
1 AAGAAGAGGAGA
55998991 GGGTCCTACG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 13 0.48
19 7 0.26
20 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (19 bp):
AAGAAGAGGAGAAAGAGAG
Found at i:55999382 original size:11 final size:10
Alignment explanation
Indices: 55999365--55999407 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
55999355 AGTAGAGAAA
55999365 AAAGAAAAAG
1 AAAGAAAAAG
55999375 AGAAGAAAAAAG
1 A-AAG-AAAAAG
55999387 AAAAGAAAAAG
1 -AAAGAAAAAG
*
55999398 AAAAAAAAAG
1 AAAGAAAAAG
55999408 GGGTTTCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 10 0.34
11 9 0.31
12 9 0.31
13 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:55999383 original size:18 final size:18
Alignment explanation
Indices: 55999360--55999403 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
55999350 GGCCCAGTAG
*
55999360 AGAAAAAAGAAAA-AGAGA
1 AGAAAAAAGAAAAGA-AAA
55999378 AGAAAAAAGAAAAGAAAA
1 AGAAAAAAGAAAAGAAAA
55999396 AGAAAAAA
1 AGAAAAAA
55999404 AAAGGGGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AGAAAAAAGAAAAGAAAA
Found at i:55999392 original size:23 final size:21
Alignment explanation
Indices: 55999364--55999407 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 21
55999354 CAGTAGAGAA
55999364 AAAAGAAAAAGAGAAGAAAAAAG
1 AAAAGAAAAAGA-AA-AAAAAAG
55999387 AAAAGAAAAAGAAAAAAAAAG
1 AAAAGAAAAAGAAAAAAAAAG
55999408 GGGTTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.33
22 2 0.10
23 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAGAAAAAAAAAG
Found at i:55999575 original size:17 final size:18
Alignment explanation
Indices: 55999549--55999589 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
55999539 ATTTTTTTGT
55999549 ATTTATATTTTTAATTTA
1 ATTTATATTTTTAATTTA
*
55999567 ATTTA-ATTTTTATTTTA
1 ATTTATATTTTTAATTTA
*
55999584 TTTTAT
1 ATTTAT
55999590 TTAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTATATTTTTAATTTA
Found at i:55999598 original size:25 final size:30
Alignment explanation
Indices: 55999543--55999601 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 30
55999533 TTATGCATTT
*
55999543 TTTTGTATTTATATTTTTAATTTAATTTAA
1 TTTTGTATTTATATTTTTAATTTAATATAA
55999573 TTTT-TATTT-TA-TTTT-ATTTAA-ATAA
1 TTTTGTATTTATATTTTTAATTTAATATAA
55999598 TTTT
1 TTTT
55999602 AATAAATAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 7 0.25
26 6 0.21
27 4 0.14
28 2 0.07
29 5 0.18
30 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (30 bp):
TTTTGTATTTATATTTTTAATTTAATATAA
Found at i:55999821 original size:38 final size:38
Alignment explanation
Indices: 55999720--55999822 Score: 102
Period size: 38 Copynumber: 2.7 Consensus size: 38
55999710 ATCAAAAAAA
* * * *
55999720 TTCAAAAAAAATTCGTGTTTTCAAAAAAATTCTTGAGT
1 TTCAGAAAATATTCGTGTTTTAAAAAAAATTCTCGAGT
* ** *
55999758 TTC-G-AAATTTTCGTGTCTTTAAAAAATTTTTCTCGTGT
1 TTCAGAAAATATTCGTGT-TTTAAAAAA-AATTCTCGAGT
55999796 TTCAGAAAATATTCGTGTTTTAAAAAA
1 TTCAGAAAATATTCGTGTTTTAAAAAA
55999823 TAAGGCAACG
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
36 10 0.19
37 8 0.15
38 13 0.25
39 10 0.19
40 11 0.21
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.42
Consensus pattern (38 bp):
TTCAGAAAATATTCGTGTTTTAAAAAAAATTCTCGAGT
Found at i:55999822 original size:18 final size:18
Alignment explanation
Indices: 55999723--55999824 Score: 55
Period size: 18 Copynumber: 5.4 Consensus size: 18
55999713 AAAAAAATTC
*
55999723 AAAAAAAATTCGTGTTTT
1 AAAAAATATTCGTGTTTT
* *
55999741 CAAAAAA-ATTCTTGAGTTT
1 -AAAAAATATTCGTG-TTTT
** *
55999760 -CGAAATTTTCGTGTCTTT
1 AAAAAATATTCGTGT-TTT
* *
55999778 AAAAAATTTTTCTCGTGTTTC
1 AAAAAA--TAT-TCGTGTTTT
*
55999799 AGAAAATATTCGTGTTTT
1 AAAAAATATTCGTGTTTT
55999817 AAAAAATA
1 AAAAAATA
55999825 AGGCAACGAA
Statistics
Matches: 62, Mismatches: 14, Indels: 15
0.68 0.15 0.16
Matches are distributed among these distances:
17 3 0.05
18 29 0.47
19 14 0.23
21 10 0.16
22 6 0.10
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (18 bp):
AAAAAATATTCGTGTTTT
Found at i:55999953 original size:18 final size:18
Alignment explanation
Indices: 55999930--56000172 Score: 252
Period size: 17 Copynumber: 13.9 Consensus size: 18
55999920 AAAAGAATCG
*
55999930 AAAATTTTCATGTTTTCA
1 AAAATTTTCGTGTTTTCA
*
55999948 AAAATTCTCGTGTTTT-A
1 AAAATTTTCGTGTTTTCA
*
55999965 AAAATTTCCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
55999983 AAAATTTTCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
56000000 AAAATTTTTGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
* * *
56000018 ACAATTCTCGTGTTTTAAA
1 AAAATTTTCGTGTTTT-CA
* *
56000037 AAAATTTTGGTGTTTTGA
1 AAAATTTTCGTGTTTTCA
*
56000055 CAAAATTCTCGTG-TTTCA
1 -AAAATTTTCGTGTTTTCA
*
56000073 AAAATTATCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
56000090 AAAA-TTTCGTGTTTTTA
1 AAAATTTTCGTGTTTTCA
*
56000107 AAAA-TAT-GTGTTTTCA
1 AAAATTTTCGTGTTTTCA
* *
56000123 AAAATTCTCGTATTTTCA
1 AAAATTTTCGTGTTTTCA
*
56000141 AAAATTCTCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
56000158 AAAACTTTCGT-TTTT
1 AAAATTTTCGTGTTTT
56000173 TTTATTTTTC
Statistics
Matches: 190, Mismatches: 27, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
16 18 0.09
17 80 0.42
18 68 0.36
19 24 0.13
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (18 bp):
AAAATTTTCGTGTTTTCA
Found at i:55999979 original size:35 final size:35
Alignment explanation
Indices: 55999930--56000161 Score: 267
Period size: 35 Copynumber: 6.6 Consensus size: 35
55999920 AAAAGAATCG
*
55999930 AAAATTTTCATGTTTTCAAAAATTCTCGTGTTTTA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTA
* * *
55999965 AAAATTTCCGTGTTTTCAAAAATTTTCGTGTTTCA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTA
* *
56000000 AAAATTTTTGTGTTTTCAACAATTCTCGTGTTTTAAA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT--A
* * *
56000037 AAAATTTTGGTGTTTTGACAAAATTCTCGTGTTTCA
1 AAAATTTTCGTGTTTTCA-AAAATTCTCGTGTTTTA
*
56000073 AAAATTATCGTG-TTTCAAAAATT-TCGTGTTTTTA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTG-TTTTA
* *
56000107 AAAA-TAT-GTGTTTTCAAAAATTCTCGTATTTTCA
1 AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTT-A
*
56000141 AAAATTCTCGTG-TTTCAAAAA
1 AAAATTTTCGTGTTTTCAAAAA
56000162 CTTTCGTTTT
Statistics
Matches: 169, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
32 3 0.02
33 23 0.14
34 23 0.14
35 75 0.44
36 14 0.08
37 17 0.10
38 14 0.08
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (35 bp):
AAAATTTTCGTGTTTTCAAAAATTCTCGTGTTTTA
Found at i:56003169 original size:23 final size:23
Alignment explanation
Indices: 56003143--56003188 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
56003133 TGAGCAAGGT
56003143 AAACAAATTATTCAAAATTTCAA
1 AAACAAATTATTCAAAATTTCAA
*
56003166 AAACAAGTTATTCAAAATTTCAA
1 AAACAAATTATTCAAAATTTCAA
56003189 CTCGAGATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (23 bp):
AAACAAATTATTCAAAATTTCAA
Found at i:56003467 original size:19 final size:20
Alignment explanation
Indices: 56003426--56003467 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
56003416 TTGGTTGCAT
* *
56003426 TTTTTTGGAGTCTTGTACTC
1 TTTTTTGGAGCCTTGCACTC
*
56003446 TTTTTTGGTGCCTTGCAC-C
1 TTTTTTGGAGCCTTGCACTC
56003465 TTT
1 TTT
56003468 ATTAATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.07, C:0.19, G:0.19, T:0.55
Consensus pattern (20 bp):
TTTTTTGGAGCCTTGCACTC
Found at i:56007216 original size:2 final size:2
Alignment explanation
Indices: 56007209--56007235 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56007199 AGATAAATAA
56007209 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
56007236 ACTTAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56010248 original size:20 final size:20
Alignment explanation
Indices: 56010223--56010262 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
56010213 GGCATTTATA
56010223 CAATTC-ACATATACAACATT
1 CAATTCAACATATA-AACATT
56010243 CAATTCAAACATATAAACAT
1 CAATTC-AACATATAAACAT
56010263 ACACAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (20 bp):
CAATTCAACATATAAACATT
Found at i:56013649 original size:36 final size:37
Alignment explanation
Indices: 56013568--56013649 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 37
56013558 TACTTCATGC
* * *
56013568 TAATTTTTTTTATTTTTTATATTATTTTTTTGAATTT
1 TAATTTATTTTATTTTTTATAATATTTTTATGAATTT
* *
56013605 TGAGTTATTTTATTTTTTA-AATATTTTTAT-AATTAT
1 TAATTTATTTTATTTTTTATAATATTTTTATGAATT-T
56013641 TAATTTATT
1 TAATTTATT
56013650 GTTGGCGTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
35 4 0.11
36 17 0.46
37 16 0.43
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (37 bp):
TAATTTATTTTATTTTTTATAATATTTTTATGAATTT
Found at i:56019005 original size:6 final size:6
Alignment explanation
Indices: 56018989--56019041 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
56018979 CTGTGAGTTA
* *
56018989 CTGTT- CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CAGTTG CTGCTG
1 CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG CTGTTG
56019036 CTGTTG
1 CTGTTG
56019042 ATGCAACTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
5 5 0.12
6 38 0.88
ACGTcount: A:0.02, C:0.19, G:0.32, T:0.47
Consensus pattern (6 bp):
CTGTTG
Found at i:56019685 original size:30 final size:30
Alignment explanation
Indices: 56019649--56019706 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
56019639 ATCACATTAT
* *
56019649 TTAGATTCCAAATATACAAGTAATATGAAC
1 TTAGATTCCAAATAAACAAGTAAAATGAAC
*
56019679 TTAGATTCCAAATAAATAAGTAAAATGA
1 TTAGATTCCAAATAAACAAGTAAAATGA
56019707 CCCGAGTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (30 bp):
TTAGATTCCAAATAAACAAGTAAAATGAAC
Found at i:56020751 original size:27 final size:27
Alignment explanation
Indices: 56020721--56020880 Score: 158
Period size: 27 Copynumber: 5.8 Consensus size: 27
56020711 TGCTGTGGTG
*
56020721 GCTGCTGCTGCTGTTGCTGTTGTTGCT
1 GCTGCTGCTGCTGTTGCTGTTGCTGCT
* * * *
56020748 GCTGTTGTTGCTGTTGCTGTTGTTGTTGTT
1 GCTGCTGCTGCTGTTGC---TGTTGCTGCT
* * *
56020778 GTTGCTGTTGCTGTTGCTGTTGCTGTT
1 GCTGCTGCTGCTGTTGCTGTTGCTGCT
*
56020805 GCTGCTGTTGCTGTTGCTGTTGCTGCT
1 GCTGCTGCTGCTGTTGCTGTTGCTGCT
* * *
56020832 GCTGTTGCTGCTGCTGTTGTTGCTGCT
1 GCTGCTGCTGCTGTTGCTGTTGCTGCT
* * *
56020859 GTTGTTGCTGCTGTTGTTGTTG
1 GCTGCTGCTGCTGTTGCTGTTG
56020881 TTGGGCATGC
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
27 92 0.79
30 24 0.21
ACGTcount: A:0.00, C:0.17, G:0.34, T:0.49
Consensus pattern (27 bp):
GCTGCTGCTGCTGTTGCTGTTGCTGCT
Found at i:56020875 original size:12 final size:12
Alignment explanation
Indices: 56020710--56020877 Score: 183
Period size: 12 Copynumber: 14.0 Consensus size: 12
56020700 CCTGCTGGGA
* *
56020710 CTGCTGTGGTGG
1 CTGCTGTTGTTG
* *
56020722 CTGCTGCTGCTG
1 CTGCTGTTGTTG
*
56020734 TTGCTGTTGTTG
1 CTGCTGTTGTTG
56020746 CTGCTGTTGTTG
1 CTGCTGTTGTTG
* *
56020758 CTGTTGCTGTTG
1 CTGCTGTTGTTG
* *
56020770 TTGTTGTTGTTG
1 CTGCTGTTGTTG
* *
56020782 CTGTTGCTGTTG
1 CTGCTGTTGTTG
* *
56020794 CTGTTGCTGTTG
1 CTGCTGTTGTTG
*
56020806 CTGCTGTTGCTG
1 CTGCTGTTGTTG
* *
56020818 TTGCTGTTGCTG
1 CTGCTGTTGTTG
*
56020830 CTGCTGTTGCTG
1 CTGCTGTTGTTG
56020842 CTGCTGTTGTTG
1 CTGCTGTTGTTG
56020854 CTGCTGTTGTTG
1 CTGCTGTTGTTG
56020866 CTGCTGTTGTTG
1 CTGCTGTTGTTG
56020878 TTGTTGGGCA
Statistics
Matches: 136, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 136 1.00
ACGTcount: A:0.00, C:0.17, G:0.35, T:0.48
Consensus pattern (12 bp):
CTGCTGTTGTTG
Found at i:56020881 original size:6 final size:6
Alignment explanation
Indices: 56020732--56020883 Score: 97
Period size: 6 Copynumber: 25.3 Consensus size: 6
56020722 CTGCTGCTGC
* * * * *
56020732 TGTTGC TGTTGT TGCTGC TGTTGT TGCTGT TGCTGT TGTTGT TGTTGT
1 TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT
* * * * * * * * *
56020780 TGCTGT TGCTGT TGCTGT TGCTGT TGCTGC TGTTGC TGTTGC TGTTGC
1 TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT
* * * * * * * * *
56020828 TGCTGC TGTTGC TGCTGC TGTTGT TGCTGC TGTTGT TGCTGC TGTTGT
1 TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT TGTTGT
56020876 TGTTGT TG
1 TGTTGT TG
56020884 GGCATGCCTC
Statistics
Matches: 123, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 123 1.00
ACGTcount: A:0.00, C:0.15, G:0.34, T:0.51
Consensus pattern (6 bp):
TGTTGT
Found at i:56020983 original size:12 final size:12
Alignment explanation
Indices: 56020921--56020984 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
56020911 CATCTGCAGT
56020921 TGTTGCTGCTGC
1 TGTTGCTGCTGC
* *
56020933 TGTTGCTGTTGA
1 TGTTGCTGCTGC
* *
56020945 TGTTGAGGCTGTTGA
1 TGTT---GCTGCTGC
*
56020960 GGTTGCTGCTGC
1 TGTTGCTGCTGC
56020972 TGTTGCTGCTGC
1 TGTTGCTGCTGC
56020984 T
1 T
56020985 CCCGTGCTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
12 32 0.74
15 11 0.26
ACGTcount: A:0.05, C:0.17, G:0.36, T:0.42
Consensus pattern (12 bp):
TGTTGCTGCTGC
Found at i:56022944 original size:1 final size:1
Alignment explanation
Indices: 56022940--56022984 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
56022930 TTTTGAGAGC
* * * *
56022940 TTTTTTTTTCTTTTTCTTTTTCTTTTTTTTCTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
56022985 GGTGTATGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:56022984 original size:15 final size:15
Alignment explanation
Indices: 56022939--56022984 Score: 74
Period size: 15 Copynumber: 3.0 Consensus size: 15
56022929 TTTTTGAGAG
56022939 CTTTTTTTTTCTTTTT
1 CTTTTTTTTT-TTTTT
*
56022955 CTTTTTCTTTTTTTT
1 CTTTTTTTTTTTTTT
56022970 CTTTTTTTTTTTTTT
1 CTTTTTTTTTTTTTT
56022985 GGTGTATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
CTTTTTTTTTTTTTT
Found at i:56026707 original size:31 final size:31
Alignment explanation
Indices: 56026667--56026789 Score: 101
Period size: 31 Copynumber: 4.0 Consensus size: 31
56026657 TTAAAATGAG
*
56026667 TATAATTGAATCAAC-ATTAAAGTTTCATGTA
1 TATAATTGAA-CAACAATCAAAGTTTCATGTA
* * *
56026698 TATATTTGAACCACAATCAAAGTTTCATGTG
1 TATAATTGAACAACAATCAAAGTTTCATGTA
* * * *
56026729 CACAATTGCACCA-AATCAAAG-TTCATGTA
1 TATAATTGAACAACAATCAAAGTTTCATGTA
* * *
56026758 TCTAATTGCACATTCAATCAAAG-TTCATGTA
1 TATAATTGAACA-ACAATCAAAGTTTCATGTA
56026789 T
1 T
56026790 CATTTTGAGA
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
29 15 0.20
30 11 0.15
31 49 0.65
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (31 bp):
TATAATTGAACAACAATCAAAGTTTCATGTA
Found at i:56033622 original size:19 final size:18
Alignment explanation
Indices: 56033574--56033612 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
56033564 ATTTTACAAC
*
56033574 AAATTTAATTGTTATAAT
1 AAATTTAATTATTATAAT
56033592 AAATTTAATTATTATAAT
1 AAATTTAATTATTATAAT
56033610 AAA
1 AAA
56033613 ATGTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AAATTTAATTATTATAAT
Found at i:56036798 original size:17 final size:17
Alignment explanation
Indices: 56036776--56036808 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56036766 GCATAATTTA
*
56036776 AAATAAATATTTTAAAG
1 AAATAAATATTGTAAAG
56036793 AAATAAATATTGTAAA
1 AAATAAATATTGTAAA
56036809 AATATTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
AAATAAATATTGTAAAG
Done.