Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008355.1 Hibiscus syriacus cultivar Beakdansim tig00111092_pilon, whole genome shotgun sequence
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: 983659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:535640 original size:23 final size:23
Alignment explanation
Indices: 535571--535647 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
535561 TTTATTTATT
*
535571 TATTTATTTATTTATTTTGGACT
1 TATTTATTTATTTATTTTGGACA
*
535594 TATTTGTTTATTTA-TTT---CA
1 TATTTATTTATTTATTTTGGACA
*
535613 AATTTATTTATTTATTTTGGACA
1 TATTTATTTATTTATTTTGGACA
535636 TATTTATTTATT
1 TATTTATTTATT
535648 CAACACGAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
19 13 0.29
20 3 0.07
22 3 0.07
23 26 0.58
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (23 bp):
TATTTATTTATTTATTTTGGACA
Found at i:535647 original size:4 final size:4
Alignment explanation
Indices: 535552--535629 Score: 77
Period size: 4 Copynumber: 19.0 Consensus size: 4
535542 TTTATTTCAA
* ** *
535552 ATTT ATTT GTTT ATTT ATTT ATTT ATTT ATTT ATTT -TGG ACTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
*
535599 GTTT ATTT ATTT CAAATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ---ATTT ATTT ATTT ATTT
535630 TGGACATATT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
3 1 0.02
4 55 0.92
7 4 0.07
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:535692 original size:12 final size:12
Alignment explanation
Indices: 535675--535699 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
535665 TTTATTTCAA
535675 ATTTATTTGTTT
1 ATTTATTTGTTT
535687 ATTTATTTGTTT
1 ATTTATTTGTTT
535699 A
1 A
535700 GAGATTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (12 bp):
ATTTATTTGTTT
Found at i:537950 original size:18 final size:17
Alignment explanation
Indices: 537927--537971 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
537917 TAAAAATTTG
537927 TTTAAATTATTAATCAAC
1 TTTAAATTATTAAT-AAC
**
537945 TTTAAATTATTAATTTC
1 TTTAAATTATTAATAAC
537962 TTTAAATTAT
1 TTTAAATTAT
537972 CCTTGAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAATTATTAATAAC
Found at i:537966 original size:17 final size:17
Alignment explanation
Indices: 537921--537971 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
537911 AGTTTTTAAA
*
537921 AATTTGTTTAAATTATT
1 AATTTCTTTAAATTATT
**
537938 AATCAACTTTAAATTATT
1 AAT-TTCTTTAAATTATT
537956 AATTTCTTTAAATTAT
1 AATTTCTTTAAATTAT
537972 CCTTGAACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTCTTTAAATTATT
Found at i:545748 original size:17 final size:17
Alignment explanation
Indices: 545722--545768 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
545712 TTTTAGTTAA
545722 TTTA-ATTTTTAAATAT
1 TTTATATTTTTAAATAT
*
545738 TTCT-TATTTTTAGATAT
1 TT-TATATTTTTAAATAT
545755 TTTATATTTTTAAA
1 TTTATATTTTTAAA
545769 ATTAGATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.12
17 23 0.88
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTATATTTTTAAATAT
Found at i:550693 original size:23 final size:23
Alignment explanation
Indices: 550613--550677 Score: 103
Period size: 24 Copynumber: 2.8 Consensus size: 23
550603 TGTGACATGT
550613 TCTATACCTTTATGACACGTTTA
1 TCTATACCTTTATGACACGTTTA
*
550636 TCTATACCTTTTATGATACGTTTA
1 TCTATACC-TTTATGACACGTTTA
*
550660 TCTATGCCTTTATGACAC
1 TCTATACCTTTATGACAC
550678 TTTTTTCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 17 0.45
24 21 0.55
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.45
Consensus pattern (23 bp):
TCTATACCTTTATGACACGTTTA
Found at i:552686 original size:43 final size:43
Alignment explanation
Indices: 552638--552735 Score: 196
Period size: 43 Copynumber: 2.3 Consensus size: 43
552628 TAAAAACCCT
552638 AAATCATACCCTTTAGATTTTTAAACCCAAACCTTAAACTCAC
1 AAATCATACCCTTTAGATTTTTAAACCCAAACCTTAAACTCAC
552681 AAATCATACCCTTTAGATTTTTAAACCCAAACCTTAAACTCAC
1 AAATCATACCCTTTAGATTTTTAAACCCAAACCTTAAACTCAC
552724 AAATCATACCCT
1 AAATCATACCCT
552736 AAACCTATCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.40, C:0.29, G:0.02, T:0.30
Consensus pattern (43 bp):
AAATCATACCCTTTAGATTTTTAAACCCAAACCTTAAACTCAC
Found at i:552763 original size:12 final size:11
Alignment explanation
Indices: 552736--552770 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
552726 ATCATACCCT
552736 AAACCTATCAG
1 AAACCTATCAG
552747 AAACCTATCATG
1 AAACCTATCA-G
552759 AAACCTATCAG
1 AAACCTATCAG
552770 A
1 A
552771 TTGACGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.46, C:0.26, G:0.09, T:0.20
Consensus pattern (11 bp):
AAACCTATCAG
Found at i:565995 original size:14 final size:14
Alignment explanation
Indices: 565976--566002 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
565966 TACATTTTCA
565976 TTCTTCATTCTTTG
1 TTCTTCATTCTTTG
565990 TTCTTCATTCTTT
1 TTCTTCATTCTTT
566003 ACATTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.04, T:0.67
Consensus pattern (14 bp):
TTCTTCATTCTTTG
Found at i:569506 original size:9 final size:8
Alignment explanation
Indices: 569482--569590 Score: 97
Period size: 8 Copynumber: 14.0 Consensus size: 8
569472 AAAGAGAATG
569482 AATGAAAA
1 AATGAAAA
569490 AATGAAAA
1 AATGAAAA
*
569498 AGTG-AAA
1 AATGAAAA
569505 AA-GAAAA
1 AATGAAAA
*
569512 AATAAAAA
1 AATGAAAA
*
569520 AATGAAAT
1 AATGAAAA
569528 AATGAAAA
1 AATGAAAA
569536 AA--AAGAGA
1 AATGAA-A-A
569544 AA--AAAA
1 AATGAAAA
*
569550 GA-GAAAAA
1 AATG-AAAA
569558 AATGAAAAA
1 AATG-AAAA
569567 AATGAAAA
1 AATGAAAA
569575 AATGAAAA
1 AATGAAAA
569583 AATGAAAA
1 AATGAAAA
569591 GAAAAAAGAA
Statistics
Matches: 86, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
6 5 0.06
7 11 0.13
8 60 0.70
9 10 0.12
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (8 bp):
AATGAAAA
Found at i:569522 original size:30 final size:28
Alignment explanation
Indices: 569486--569603 Score: 111
Period size: 30 Copynumber: 4.1 Consensus size: 28
569476 AGAATGAATG
*
569486 AAAAAATGAAAAAGTGAAAAAGAAAAAATA
1 AAAAAATGAAAAA-TG-AAAAGAAAAAAGA
*
569516 AAAAAATGAAATAATGAAAA-AAAAGAGA
1 AAAAAATGAAA-AATGAAAAGAAAAAAGA
*
569544 AAAAAA-GAGAAAA--AAATGAAAAAA-A
1 AAAAAATGA-AAAATGAAAAGAAAAAAGA
569569 TGAAAAAATGAAAAAATGAAAAGAAAAAAGA
1 --AAAAAATG-AAAAATGAAAAGAAAAAAGA
569600 AAAA
1 AAAA
569604 GGAGGGTTCG
Statistics
Matches: 73, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
25 4 0.05
26 5 0.07
27 10 0.14
28 19 0.26
29 9 0.12
30 23 0.32
31 3 0.04
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (28 bp):
AAAAAATGAAAAATGAAAAGAAAAAAGA
Found at i:569524 original size:38 final size:38
Alignment explanation
Indices: 569482--569603 Score: 120
Period size: 38 Copynumber: 3.0 Consensus size: 38
569472 AAAGAGAATG
569482 AATGAAAAAATGAAAAAGTGAAAAAGAAAAAATAAAAA
1 AATGAAAAAATGAAAAAGTGAAAAAGAAAAAATAAAAA
* *
569520 AATGAAATAATGAAAAAAAAGAGAAAAAAAGAGAAAAAAATGAAAAA
1 AATGAAAAAATG---AAAAAGTG---AAAA-AG-AAAAAAT-AAAAA
* *
569567 AATGAAAAAATGAAAAAATG-AAAAGAAAAAAGAAAAA
1 AATGAAAAAATGAAAAAGTGAAAAAGAAAAAATAAAAA
569604 GGAGGGTTCG
Statistics
Matches: 69, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
37 5 0.07
38 17 0.25
39 2 0.03
40 3 0.04
41 7 0.10
44 10 0.14
45 2 0.03
46 7 0.10
47 16 0.23
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (38 bp):
AATGAAAAAATGAAAAAGTGAAAAAGAAAAAATAAAAA
Found at i:569548 original size:10 final size:10
Alignment explanation
Indices: 569533--569568 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
569523 GAAATAATGA
569533 AAAAAAAGAG
1 AAAAAAAGAG
569543 AAAAAAAGAG
1 AAAAAAAGAG
*
569553 AAAAAAA-TG
1 AAAAAAAGAG
569562 AAAAAAA
1 AAAAAAA
569569 TGAAAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:569596 original size:6 final size:7
Alignment explanation
Indices: 569502--569603 Score: 50
Period size: 8 Copynumber: 13.6 Consensus size: 7
569492 TGAAAAAGTG
569502 AAAAAGA
1 AAAAAGA
*
569509 AAAAATAA
1 AAAAA-GA
569517 AAAAATGA
1 AAAAA-GA
*
569525 AATAATGA
1 AA-AAAGA
569533 AAAAA-A
1 AAAAAGA
569539 AGAGAAA-A
1 A-A-AAAGA
*
569547 AAAGAGAA
1 AAAAAG-A
569555 AAAAATGAA
1 AAAAA-G-A
569564 AAAAATGA
1 AAAAA-GA
569572 AAAAATGA
1 AAAAA-GA
569580 AAAAATG-
1 AAAAA-GA
569587 -AAAAGA
1 AAAAAGA
569593 AAAAAGA
1 AAAAAGA
569600 AAAA
1 AAAA
569604 GGAGGGTTCG
Statistics
Matches: 80, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
5 1 0.01
6 8 0.10
7 19 0.24
8 40 0.50
9 12 0.15
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (7 bp):
AAAAAGA
Found at i:569603 original size:8 final size:8
Alignment explanation
Indices: 569502--569604 Score: 57
Period size: 9 Copynumber: 11.8 Consensus size: 8
569492 TGAAAAAGTG
569502 AAAAAGAA
1 AAAAAGAA
569510 AAAATA-AA
1 AAAA-AGAA
*
569518 AAAATGAA
1 AAAAAGAA
569526 ATAATGAA-AA
1 A-AA--AAGAA
569536 AAAAGAGAAA
1 AAAA-AG-AA
569546 AAAAGAGAA
1 AAAA-AGAA
569555 AAAAATGAA
1 AAAAA-GAA
569564 AAAAATGAA
1 AAAAA-GAA
*
569573 AAAATGAA
1 AAAAAGAA
*
569581 AAAATGAA
1 AAAAAGAA
*
569589 AAGAAAAAA
1 AA-AAAGAA
569598 GAAAAAG
1 -AAAAAG
569605 GAGGGTTCGT
Statistics
Matches: 78, Mismatches: 6, Indels: 21
0.74 0.06 0.20
Matches are distributed among these distances:
7 1 0.01
8 28 0.36
9 34 0.44
10 14 0.18
11 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.08
Consensus pattern (8 bp):
AAAAAGAA
Found at i:571220 original size:105 final size:105
Alignment explanation
Indices: 570513--571202 Score: 1200
Period size: 105 Copynumber: 6.6 Consensus size: 105
570503 TCAACAACAA
570513 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
570578 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
570618 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
*
570683 CATAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
570723 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
570788 CCTAAAGGAGAAGGTTCGTAATGAGAAGAACTTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
570828 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
570893 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
* *
570933 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
**
570998 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGTATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
* * *
571038 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* * * * *
571103 CTTAAAAGAGAAGGTTTGTAATGAGAATAGCATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
* * ** *
571143 TCAAATTCACCCCAGAAGGAGGTGAATCGACATTTCCAGAAGAGTTCATAATGAGAAGAA
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAA
571203 ATCATCCGAC
Statistics
Matches: 564, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 564 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (105 bp):
TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
Found at i:584345 original size:14 final size:14
Alignment explanation
Indices: 584326--584352 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
584316 TACATTTTCA
584326 TTCTTCATTCTTTG
1 TTCTTCATTCTTTG
584340 TTCTTCATTCTTT
1 TTCTTCATTCTTT
584353 ACATTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.04, T:0.67
Consensus pattern (14 bp):
TTCTTCATTCTTTG
Found at i:587854 original size:9 final size:8
Alignment explanation
Indices: 587830--587937 Score: 97
Period size: 8 Copynumber: 14.0 Consensus size: 8
587820 AAAGAGAATG
587830 AATGAAAA
1 AATGAAAA
587838 AATGAAAA
1 AATGAAAA
*
587846 AGTG-AAA
1 AATGAAAA
587853 AA-GAAAA
1 AATGAAAA
*
587860 AATAAAAA
1 AATGAAAA
587868 AATGAAAA
1 AATGAAAA
587876 AATGAAAA
1 AATGAAAA
587884 AA--AAGAGA
1 AATGAA-A-A
587892 AA--AAAA
1 AATGAAAA
*
587898 GA-GAAAAA
1 AATG-AAAA
587906 AATGAAAAA
1 AATG-AAAA
587915 AATG-AAA
1 AATGAAAA
587922 AATGAAAA
1 AATGAAAA
587930 AATGAAAA
1 AATGAAAA
587938 GAAAAAGAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 16
0.80 0.06 0.15
Matches are distributed among these distances:
6 5 0.06
7 18 0.21
8 53 0.62
9 10 0.12
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (8 bp):
AATGAAAA
Found at i:587870 original size:30 final size:30
Alignment explanation
Indices: 587834--587949 Score: 109
Period size: 30 Copynumber: 3.9 Consensus size: 30
587824 AGAATGAATG
*
587834 AAAAAATGAAAAAGTGAAAAAGAAAAAATA
1 AAAAAATGAAAAAATGAAAAAGAAAAAATA
587864 AAAAAATGAAAAAATGAAAAA-AAAGAGAA-A
1 AAAAAATGAAAAAATGAAAAAGAAA-A-AATA
* * *
587894 AAAAGA-GAAAAAAATGAAAAAAATGAAAAATG
1 AAAAAATG-AAAAAATGAAAAAGA--AAAAATA
587926 AAAAAATG--AAAA-GAAAAAGAAAAA
1 AAAAAATGAAAAAATGAAAAAGAAAAA
587950 GGAGGGTTCG
Statistics
Matches: 73, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
27 4 0.05
29 11 0.15
30 44 0.60
31 5 0.07
32 6 0.08
33 3 0.04
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (30 bp):
AAAAAATGAAAAAATGAAAAAGAAAAAATA
Found at i:587872 original size:38 final size:36
Alignment explanation
Indices: 587814--587943 Score: 136
Period size: 38 Copynumber: 3.4 Consensus size: 36
587804 ACTATGCTTG
**
587814 AAAAAAAAAGAGAATGAATGAAAAAATGAAAAAGTGAA
1 AAAAAAAAAGA-AAAAAATGAAAAAATGAAAAA-TGAA
* *
587852 AAAGAAAAAATAAAAAAATGAAAAAATGAAAAA-AAA
1 AAA-AAAAAAGAAAAAAATGAAAAAATGAAAAATGAA
587888 GAGAAAAAAAGAGAAAAAAATGAAAAAAATGAAAAATGAA
1 -A-AAAAAAA-AGAAAAAAATG-AAAAAATGAAAAATGAA
*
587928 AAAATGAAAAGAAAAA
1 AAAA-AAAAAGAAAAA
587944 GAAAAAGGAG
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
36 2 0.03
37 6 0.08
38 44 0.56
39 24 0.31
40 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (36 bp):
AAAAAAAAAGAAAAAAATGAAAAAATGAAAAATGAA
Found at i:587876 original size:10 final size:10
Alignment explanation
Indices: 587863--587923 Score: 69
Period size: 10 Copynumber: 6.4 Consensus size: 10
587853 AAGAAAAAAT
587863 AAAAAAATG-
1 AAAAAAATGA
587872 -AAAAAATGA
1 AAAAAAATGA
587881 AAAAAAA-GA
1 AAAAAAATGA
587890 GAAAAAAA-GA
1 -AAAAAAATGA
587900 GAAAAAAATG-
1 -AAAAAAATGA
587910 AAAAAAATGA
1 AAAAAAATGA
587920 AAAA
1 AAAA
587924 TGAAAAAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.17
9 11 0.23
10 27 0.57
11 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:589566 original size:105 final size:105
Alignment explanation
Indices: 588859--589548 Score: 1200
Period size: 105 Copynumber: 6.6 Consensus size: 105
588849 TCAACAACAA
588859 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
588924 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
588964 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
*
589029 CATAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
589069 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
589134 CCTAAAGGAGAAGGTTCGTAATGAGAAGAACTTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
589174 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
589239 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
* *
589279 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
**
589344 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGTATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
* * *
589384 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* * * * *
589449 CTTAAAAGAGAAGGTTTGTAATGAGAATAGCATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
* * ** *
589489 TCAAATTCACCCCAGAAGGAGGTGAATCGACATTTCCAGAAGAGTTCATAATGAGAAGAA
1 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAA
589549 ATCATCCGAC
Statistics
Matches: 564, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 564 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (105 bp):
TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
Found at i:597221 original size:21 final size:20
Alignment explanation
Indices: 597176--597221 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
597166 GGTCATCCAA
*
597176 ATTTTTAAACCTCAGATCGG
1 ATTTTTAAACCTCAGACCGG
597196 ATTTTTAAACC-CTAGACCGG
1 ATTTTTAAACCTC-AGACCGG
597216 ATTTTT
1 ATTTTT
597222 TTCGGATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (20 bp):
ATTTTTAAACCTCAGACCGG
Found at i:598168 original size:22 final size:21
Alignment explanation
Indices: 598141--598209 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
598131 TTATTATCTT
598141 AATTCTATATATTATTCCCTTG
1 AATTCTATATA-TATTCCCTTG
* *
598163 AATTCT-TTTCCATAAT--CTT-
1 AATTCTATAT--ATATTCCCTTG
598182 AATTCTATATACTATTCCCTTG
1 AATTCTATATA-TATTCCCTTG
598204 AATTCT
1 AATTCT
598210 TTTTAAATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
18 1 0.03
19 9 0.25
20 5 0.14
21 5 0.14
22 15 0.42
23 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.03, T:0.49
Consensus pattern (21 bp):
AATTCTATATATATTCCCTTG
Found at i:598950 original size:13 final size:14
Alignment explanation
Indices: 598934--598965 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
598924 AATAAAAAAC
598934 AAAAGAAAAAA-GA
1 AAAAGAAAAAAGGA
598947 AAAAGAAAAAAGGA
1 AAAAGAAAAAAGGA
598961 AAAAG
1 AAAAG
598966 GTTAAAGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAGGA
Found at i:599104 original size:28 final size:28
Alignment explanation
Indices: 599073--599129 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
599063 CGATGCGTGA
599073 AGTATAATGTAATTAAAACAAAATAGGT
1 AGTATAATGTAATTAAAACAAAATAGGT
*
599101 AGTATAATGTAATTAAAACACAATAGGT
1 AGTATAATGTAATTAAAACAAAATAGGT
599129 A
1 A
599130 ACCAAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (28 bp):
AGTATAATGTAATTAAAACAAAATAGGT
Found at i:600122 original size:10 final size:10
Alignment explanation
Indices: 600107--600142 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
600097 AAACGAGGAG
600107 AAAAAATAAT
1 AAAAAATAAT
600117 AAAAAATAA-
1 AAAAAATAAT
600126 ATAAAAATAAT
1 A-AAAAATAAT
600137 AAAAAA
1 AAAAAA
600143 CATTTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.04
10 22 0.92
11 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:600178 original size:36 final size:35
Alignment explanation
Indices: 600136--600494 Score: 237
Period size: 38 Copynumber: 9.9 Consensus size: 35
600126 ATAAAAATAA
*
600136 TAAAAAACATTTTTAAAACTACATAATATATATGTTT
1 TAAAAAA-ATTTTTAAAACTATATAATATATAT-TTT
*
600173 TAAAAAATAATTTTTAAAACTATATAATATATATGTTA
1 T-AAAAA-AATTTTTAAAACTATATAATATATAT-TTT
600211 TAAAAAAATAATTTTCAAAAGC-ATATAATATATATTTT
1 TAAAAAAAT--TTTT-AAAA-CTATATAATATATATTTT
*
600249 TAAAAATAATTTTCAAAACTATATAATATATATTTT
1 TAAAAA-AATTTTTAAAACTATATAATATATATTTT
*
600285 TAAAAACTAATTTTCAAAACTATATAATATATATATTT
1 TAAAAA--AATTTTTAAAACTATATAATATATAT-TTT
** * * * * *
600323 T-TCAACA-CTAT-ATATTATAT-ATATATA-TTT
1 TAAAAAAATTTTTAAAACTATATAATATATATTTT
* ** *
600353 TCAAAATGTTTTAAAAACTATATAATATATATATGTT
1 TAAAAAAATTTTTAAAACTATATAATATATAT-T-TT
*** *
600390 TTTTATAATATTTTAAAACTATATAATATATATATGTT
1 TAAAAAAAT-TTTTAAAACTATATAATATATAT-T-TT
** *
600428 T-TCAAAATGTTTTAAAAACTATATATTATATATATTT
1 TAAAAAAAT-TTTT-AAAACTATATAATATATAT-TTT
* ** * *
600465 TCAAAATGTTTTAAAAACTATATAACATAT
1 TAAAAAAATTTTTAAAACTATATAATATAT
600495 GTTTCCAAAA
Statistics
Matches: 263, Mismatches: 39, Indels: 41
0.77 0.11 0.12
Matches are distributed among these distances:
30 4 0.02
31 2 0.01
32 8 0.03
33 14 0.05
34 8 0.03
35 2 0.01
36 45 0.17
37 58 0.22
38 100 0.38
39 21 0.08
40 1 0.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (35 bp):
TAAAAAAATTTTTAAAACTATATAATATATATTTT
Found at i:600186 original size:38 final size:37
Alignment explanation
Indices: 600136--600323 Score: 256
Period size: 37 Copynumber: 5.0 Consensus size: 37
600126 ATAAAAATAA
* * *
600136 TAAAAAA-CATTTTTAAAACTACATAATATATATGTTT
1 TAAAAAATAATTTTCAAAACTATATAATATATAT-TTT
*
600173 TAAAAAATAATTTTTAAAACTATATAATATATATGTTAT
1 TAAAAAATAATTTTCAAAACTATATAATATATAT-TT-T
*
600212 AAAAAAATAATTTTCAAAAGC-ATATAATATATATTTT
1 TAAAAAATAATTTTCAAAA-CTATATAATATATATTTT
600249 T-AAAAATAATTTTCAAAACTATATAATATATATTTT
1 TAAAAAATAATTTTCAAAACTATATAATATATATTTT
*
600285 TAAAAACTAATTTTCAAAACTATATAATATATATATTT
1 TAAAAAATAATTTTCAAAACTATATAATATATAT-TTT
600323 T
1 T
600324 TCAACACTAT
Statistics
Matches: 139, Mismatches: 6, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
35 1 0.01
36 34 0.24
37 39 0.28
38 33 0.24
39 31 0.22
40 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (37 bp):
TAAAAAATAATTTTCAAAACTATATAATATATATTTT
Found at i:600258 original size:75 final size:75
Alignment explanation
Indices: 600144--600323 Score: 258
Period size: 73 Copynumber: 2.4 Consensus size: 75
600134 AATAAAAAAC
* * * *
600144 ATTTTTAAAACTACATAATATATATGTTTTAAAAAATAATTTTTAAAACTATATAATATATATGT
1 ATTTTCAAAACTATATAATATATATATTTTAAAAAATAATTTTCAAAACTATATAATATATAT-T
600209 TATAAAAAAATA
65 T-TAAAAAAATA
600221 ATTTTCAAAAGC-ATATAATATATAT-TTTT-AAAAATAATTTTCAAAACTATATAATATATATT
1 ATTTTCAAAA-CTATATAATATATATATTTTAAAAAATAATTTTCAAAACTATATAATATATATT
* *
600283 TTTAAAAACTA
65 TTAAAAAAATA
600294 ATTTTCAAAACTATATAATATATATATTTT
1 ATTTTCAAAACTATATAATATATATATTTT
600324 TCAACACTAT
Statistics
Matches: 95, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
72 1 0.01
73 31 0.33
74 6 0.06
75 31 0.33
76 4 0.04
77 21 0.22
78 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (75 bp):
ATTTTCAAAACTATATAATATATATATTTTAAAAAATAATTTTCAAAACTATATAATATATATTT
TAAAAAAATA
Found at i:600324 original size:75 final size:77
Alignment explanation
Indices: 600144--600324 Score: 255
Period size: 75 Copynumber: 2.4 Consensus size: 77
600134 AATAAAAAAC
* * * * *
600144 ATTTTTAAAACTACATAATATATATGTTTTAAAAAATAATTTTTAAAACTATATAATATATATGT
1 ATTTTCAAAACTATATAATATATATATTTTTAAAAATAATTTTCAAAACTATATAATATATATGT
600209 TATAAAAAAATA
66 TATAAAAAAATA
600221 ATTTTCAAAAGC-ATAT-A-ATATATATTTTTAAAAATAATTTTCAAAACTATATAATATATAT-
1 ATTTTCAAAA-CTATATAATATATATATTTTTAAAAATAATTTTCAAAACTATATAATATATATG
* *
600282 TT-TTAAAAACTA
65 TTATAAAAAAATA
600294 ATTTTCAAAACTATATAATATATATATTTTT
1 ATTTTCAAAACTATATAATATATATATTTTT
600325 CAACACTATA
Statistics
Matches: 93, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
72 1 0.01
73 22 0.24
74 3 0.03
75 53 0.57
76 1 0.01
77 12 0.13
78 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.44
Consensus pattern (77 bp):
ATTTTCAAAACTATATAATATATATATTTTTAAAAATAATTTTCAAAACTATATAATATATATGT
TATAAAAAAATA
Found at i:600325 original size:26 final size:28
Alignment explanation
Indices: 600294--600358 Score: 98
Period size: 26 Copynumber: 2.4 Consensus size: 28
600284 TTAAAAACTA
600294 ATTTTCAAAACTATATA-ATATATATAT
1 ATTTTCAAAACTATATATATATATATAT
*
600321 -TTTTCAACACTATATATTATATATATAT
1 ATTTTCAAAACTATATA-TATATATATAT
600349 ATTTTCAAAA
1 ATTTTCAAAA
600359 TGTTTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 15 0.45
28 10 0.30
29 8 0.24
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTTTCAAAACTATATATATATATATAT
Found at i:600384 original size:38 final size:38
Alignment explanation
Indices: 600333--600536 Score: 242
Period size: 38 Copynumber: 5.5 Consensus size: 38
600323 TTCAACACTA
*
600333 TATATTATATATATATATTTTCAAAATGTTTTAAAAAC
1 TATATAATATATATATATTTTCAAAATGTTTTAAAAAC
* * * *
600371 TATATAATATATATATGTTTTTTATAATATTTT-AAAAC
1 TATATAATATATATAT-ATTTTCAAAATGTTTTAAAAAC
*
600409 TATATAATATATATATGTTTTCAAAATGTTTTAAAAAC
1 TATATAATATATATATATTTTCAAAATGTTTTAAAAAC
600447 TATAT-AT-TATATATATTTTCAAAATGTTTTAAAAAC
1 TATATAATATATATATATTTTCAAAATGTTTTAAAAAC
* * * *
600483 --TAT-ATA-ACATATGTTTCCAAAATGTTTTAAAGAC
1 TATATAATATATATATATTTTCAAAATGTTTTAAAAAC
600517 TATAATATATATATATATAT
1 TAT-ATA-ATATATATATAT
600537 ATATATAATA
Statistics
Matches: 141, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
34 29 0.21
36 29 0.21
37 16 0.11
38 46 0.33
39 15 0.11
40 6 0.04
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (38 bp):
TATATAATATATATATATTTTCAAAATGTTTTAAAAAC
Found at i:602238 original size:19 final size:19
Alignment explanation
Indices: 602211--602280 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 19
602201 TTTATATCAT
*
602211 TAAAGTATAAAAATTATTA
1 TAAAATATAAAAATTATTA
* *
602230 TAAAATATATTAATTTAGTTA
1 TAAAATATA-AAAATTA-TTA
*
602251 TTTAAAATATAATAAATAATTA
1 --TAAAATATAA-AAATTATTA
602273 T-AAATATA
1 TAAAATATA
602281 TTATTATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 15 0.38
20 6 0.15
21 3 0.08
22 3 0.08
23 13 0.32
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TAAAATATAAAAATTATTA
Found at i:602294 original size:21 final size:21
Alignment explanation
Indices: 602227--602295 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 21
602217 ATAAAAATTA
*
602227 TTATAAAATATATTAATTTAGTTAT
1 TTAT-AAATATATT-A-TTA-TAAT
* *
602252 TTA-AAATATAATA-AATAA-
1 TTATAAATATATTATTATAAT
602270 TTATAAATATATTATTATAAT
1 TTATAAATATATTATTATAAT
602291 TTATA
1 TTATA
602296 TTATTTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
18 3 0.08
19 11 0.31
20 5 0.14
21 5 0.14
22 1 0.03
23 8 0.22
25 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (21 bp):
TTATAAATATATTATTATAAT
Found at i:611009 original size:2 final size:2
Alignment explanation
Indices: 610929--610994 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
610919 TTACAAAATA
610929 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
610971 AT AC AT TT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
610995 CAGCTCGAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:611774 original size:226 final size:228
Alignment explanation
Indices: 611364--611818 Score: 896
Period size: 226 Copynumber: 2.0 Consensus size: 228
611354 AATTGTCCAA
611364 AATCCTAACATAGTATTTTGCGCTAACTATCCTAGGAACAAACAGAGTATCAATCATGGTAAAAT
1 AATCCTAACATAGTATTTTGCGCTAACTATCCTAGGAACAAACAGAGTATCAATCATGGTAAAAT
611429 TACTATCTATGCTGATATGTAACAGATGATGTTCGGATTCTTCGATTCGATAACAAAATTTACAG
66 TACTATCTATGCTGATATGTAACAGATGATGTTCGGATTCTTCGATTCGATAACAAAATTTACAG
611494 CTCCTAGCCATGGTTTGCAGTTTGCTCTATCACACCAATTTCATCAGTAGGAACTGAACTCAATA
131 CTCCTAGCCATGGTTTGCAGTTTGCTCTATCACACCAATTTCATCAGTAGGAACTGAACTCAATA
611559 TCTCAGCATGAAAGA-TTTATGATCATCAGCTG
196 TCTCAGCATGAAAGATTTTATGATCATCAGCTG
611591 AATCCTAACATAGTA-TTTGCGCTAACTATCCTAGGAACAAACAGAGTATCAATCATGGTAAAAT
1 AATCCTAACATAGTATTTTGCGCTAACTATCCTAGGAACAAACAGAGTATCAATCATGGTAAAAT
611655 TACTATCTATGCTGATATGTAACAGATGATGTTCGGATTCTTCGATTCGATAACAAAATTTACAG
66 TACTATCTATGCTGATATGTAACAGATGATGTTCGGATTCTTCGATTCGATAACAAAATTTACAG
611720 CTCCTAGCCATGGTTTGCAGTTTGCTCTATCACACCAATTTCATCAGTAGGAACTGAACTCAATA
131 CTCCTAGCCATGGTTTGCAGTTTGCTCTATCACACCAATTTCATCAGTAGGAACTGAACTCAATA
611785 TCTCAGCATGAAAGATTTTATGATCATCAGCTG
196 TCTCAGCATGAAAGATTTTATGATCATCAGCTG
611818 A
1 A
611819 TCACAAAATA
Statistics
Matches: 227, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
226 194 0.85
227 33 0.15
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (228 bp):
AATCCTAACATAGTATTTTGCGCTAACTATCCTAGGAACAAACAGAGTATCAATCATGGTAAAAT
TACTATCTATGCTGATATGTAACAGATGATGTTCGGATTCTTCGATTCGATAACAAAATTTACAG
CTCCTAGCCATGGTTTGCAGTTTGCTCTATCACACCAATTTCATCAGTAGGAACTGAACTCAATA
TCTCAGCATGAAAGATTTTATGATCATCAGCTG
Found at i:622128 original size:12 final size:12
Alignment explanation
Indices: 622097--622122 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
622087 ACACAGCCGA
622097 AAACGCAAACAC
1 AAACGCAAACAC
622109 AAACGCAAACAC
1 AAACGCAAACAC
622121 AA
1 AA
622123 TGGCAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.31, G:0.08, T:0.00
Consensus pattern (12 bp):
AAACGCAAACAC
Found at i:623513 original size:27 final size:28
Alignment explanation
Indices: 623452--623555 Score: 165
Period size: 28 Copynumber: 3.8 Consensus size: 28
623442 TTGTTTACAT
*
623452 TATGTCGTCGAGCCAGTGTTTGAAACAC
1 TATGTCGTCGAGCCAGTGCTTGAAACAC
623480 TATGTCGTCGAGCCAGTGCTTG-AACAC
1 TATGTCGTCGAGCCAGTGCTTGAAACAC
*
623507 TATGTCGTCGAGCCAATGCTTGAAACAC
1 TATGTCGTCGAGCCAGTGCTTGAAACAC
* *
623535 TATGTTGTCGAACCAGTGCTT
1 TATGTCGTCGAGCCAGTGCTT
623556 AAAAGCAATT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
27 26 0.37
28 44 0.63
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (28 bp):
TATGTCGTCGAGCCAGTGCTTGAAACAC
Found at i:623536 original size:55 final size:55
Alignment explanation
Indices: 623452--623555 Score: 172
Period size: 55 Copynumber: 1.9 Consensus size: 55
623442 TTGTTTACAT
* * *
623452 TATGTCGTCGAGCCAGTGTTTGAAACACTATGTCGTCGAGCCAGTGCTTGAACAC
1 TATGTCGTCGAGCCAATGCTTGAAACACTATGTCGTCGAACCAGTGCTTGAACAC
*
623507 TATGTCGTCGAGCCAATGCTTGAAACACTATGTTGTCGAACCAGTGCTT
1 TATGTCGTCGAGCCAATGCTTGAAACACTATGTCGTCGAACCAGTGCTT
623556 AAAAGCAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (55 bp):
TATGTCGTCGAGCCAATGCTTGAAACACTATGTCGTCGAACCAGTGCTTGAACAC
Found at i:626565 original size:39 final size:38
Alignment explanation
Indices: 626492--626589 Score: 126
Period size: 39 Copynumber: 2.5 Consensus size: 38
626482 CATTTCCCAG
*
626492 AATCCCTAATTTCCCATTTTCATTTCCCTCTCGCACCTC
1 AATCCCTAA-TTCCCATTTTCAATTCCCTCTCGCACCTC
* *
626531 AATCCCTAATTCCCCTTTTACAATTCTCCT-TCGCATCTC
1 AATCCCTAATTCCCATTTT-CAATTC-CCTCTCGCACCTC
626570 AATCCCTAATTCACCATTTT
1 AATCCCTAATTC-CCATTTT
626590 TCTCTTCGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
38 9 0.17
39 34 0.65
40 9 0.17
ACGTcount: A:0.21, C:0.38, G:0.02, T:0.39
Consensus pattern (38 bp):
AATCCCTAATTCCCATTTTCAATTCCCTCTCGCACCTC
Found at i:631763 original size:39 final size:39
Alignment explanation
Indices: 631715--631812 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 39
631705 CAATTCCCAG
* *
631715 AATCTCTAATTTCCCATTTT-CATTTC-CCTCTCGCACCTC
1 AATCCCTAA-TTCCCATTTTACAATTCTCCT-TCGCACCTC
* *
631754 AATCCCTAATTCCCCTTTTACAATTCTCCTTCGCATCTC
1 AATCCCTAATTCCCATTTTACAATTCTCCTTCGCACCTC
631793 AATCCCTAATTCACCATTTT
1 AATCCCTAATTC-CCATTTT
631813 TCTCTTCGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
38 9 0.18
39 33 0.65
40 9 0.18
ACGTcount: A:0.21, C:0.37, G:0.02, T:0.40
Consensus pattern (39 bp):
AATCCCTAATTCCCATTTTACAATTCTCCTTCGCACCTC
Found at i:632042 original size:30 final size:30
Alignment explanation
Indices: 632008--632142 Score: 146
Period size: 30 Copynumber: 4.5 Consensus size: 30
631998 ATAATTTCTC
*
632008 CATCACTTTAGACACGTGATAACATCACAT
1 CATCACTTTAGACACGTGATAATATCACAT
* * *
632038 CATCACTTTAAACACGTGATAATATTACGT
1 CATCACTTTAGACACGTGATAATATCACAT
* * * *
632068 CATCACTTTGGACACATGACAATATCATAT
1 CATCACTTTAGACACGTGATAATATCACAT
* * *
632098 CATCACTTT-GAATATGTGATAAATGTCACAT
1 CATCACTTTAG-ACACGTGAT-AATATCACAT
632129 CATCACTTTAGACA
1 CATCACTTTAGACA
632143 TATGACACGT
Statistics
Matches: 84, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
29 1 0.01
30 63 0.75
31 19 0.23
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (30 bp):
CATCACTTTAGACACGTGATAATATCACAT
Found at i:632101 original size:60 final size:61
Alignment explanation
Indices: 632008--632149 Score: 171
Period size: 60 Copynumber: 2.3 Consensus size: 61
631998 ATAATTTCTC
* * *
632008 CATCACTTTAGACACGTGATAACATCACATCATCACTTTAAACACGTGATAATAT-T-ACGT
1 CATCACTTTAGACACATGACAACATCACATCATCACTTTAAACACGTGATAA-ATGTCACAT
* * * * * *
632068 CATCACTTTGGACACATGACAATATCATATCATCACTTTGAATATGTGATAAATGTCACAT
1 CATCACTTTAGACACATGACAACATCACATCATCACTTTAAACACGTGATAAATGTCACAT
*
632129 CATCACTTTAGACATATGACA
1 CATCACTTTAGACACATGACA
632150 CGTACCACAT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 2 0.03
60 45 0.65
61 22 0.32
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.31
Consensus pattern (61 bp):
CATCACTTTAGACACATGACAACATCACATCATCACTTTAAACACGTGATAAATGTCACAT
Found at i:635694 original size:20 final size:21
Alignment explanation
Indices: 635669--635720 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
635659 TTTTCCCGAT
*
635669 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
635689 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
635710 TCGCAATGCGA
1 TCGCAATGCGA
635721 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:635737 original size:20 final size:20
Alignment explanation
Indices: 635709--635844 Score: 107
Period size: 20 Copynumber: 6.7 Consensus size: 20
635699 AATTGGGAAA
635709 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
635729 ATTGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
635749 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
635770 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
635790 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
* *
635810 AATCGCAACGCGATAAT-ACAT
1 -ATCGCAATGCGATACTGAC-T
635831 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
635845 TTTCAAAGCG
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
19 4 0.04
20 47 0.48
21 45 0.46
22 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:635753 original size:61 final size:62
Alignment explanation
Indices: 635706--635838 Score: 173
Period size: 61 Copynumber: 2.2 Consensus size: 62
635696 GCGAATTGGG
* * * * *
635706 AAAATCGCAATGCGATACTGACTATT-GCAATGCGATACTGAC-T-ATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACT-TTCGCAACGCGATAAT-ACATAATCGCAACGCGATAATAC
635767 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATAATCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATAATCGCAACGCGATAATAC
*
635829 ATAATCGCAA
1 AAAATCGCAA
635839 TGCGATTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
60 4 0.06
61 33 0.52
62 26 0.41
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.22
Consensus pattern (62 bp):
AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATAATCGCAACGCGATAATAC
Found at i:635775 original size:21 final size:21
Alignment explanation
Indices: 635749--635844 Score: 115
Period size: 21 Copynumber: 4.6 Consensus size: 21
635739 GATACTGACT
* *
635749 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATAATACATA
* *
635770 ATCGCAACGAGATACTGAC-T-
1 ATCGCAACGCGATAAT-ACATA
*
635790 TTCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
635811 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
*
635832 ATCGCAATGCGAT
1 ATCGCAACGCGAT
635845 TTTCAAAGCG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 14 0.22
21 45 0.71
22 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGATAATACATA
Found at i:635795 original size:41 final size:41
Alignment explanation
Indices: 635739--635824 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
635729 ATTGCAATGC
*
635739 GATACTGACTATCGCAATGCGATAATACAAAATCGCAACGA
1 GATACTGACTATCGCAACGCGATAATACAAAATCGCAACGA
* * *
635780 GATACTGACTTTCGCAACGCGATAATACATAATCGCAACGC
1 GATACTGACTATCGCAACGCGATAATACAAAATCGCAACGA
635821 GATA
1 GATA
635825 ATACATAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (41 bp):
GATACTGACTATCGCAACGCGATAATACAAAATCGCAACGA
Found at i:636040 original size:22 final size:22
Alignment explanation
Indices: 636012--636055 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
636002 CACTCTCTCA
636012 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
636034 CCCATCTCTGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
636056 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:636344 original size:20 final size:20
Alignment explanation
Indices: 636319--636356 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
636309 CGATTCTCTC
636319 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
636339 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
636357 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:636547 original size:25 final size:24
Alignment explanation
Indices: 636493--636547 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
636483 TGTTTATTAT
* *
636493 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
636517 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
636543 TGTTT
1 TGTTT
636548 ATTGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:637698 original size:18 final size:18
Alignment explanation
Indices: 637677--637721 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
637667 TCCACTTCGG
*
637677 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
637695 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
637713 GAGCCATCA
1 GAGCCATCA
637722 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:638251 original size:19 final size:20
Alignment explanation
Indices: 638197--638263 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
638187 TAGTTTACTT
* *
638197 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
638217 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
638237 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
638256 TCGCAACG
1 TCGCAACG
638264 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:638271 original size:14 final size:14
Alignment explanation
Indices: 638252--638310 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
638242 ATGCGAAATG
638252 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
638266 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
638285 AAAATCGCAACGAC
1 AAAATCGCAACGAC
638299 AAAATCGCAACG
1 AAAATCGCAACG
638311 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:638278 original size:33 final size:33
Alignment explanation
Indices: 638236--638327 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
638226 GGAAATGGCT
638236 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
638269 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
638302 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
638328 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:638290 original size:19 final size:19
Alignment explanation
Indices: 638236--638332 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
638226 GGAAATGGCT
638236 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
638255 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
638269 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
638288 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
638302 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
638321 ATCGCAATGCGA
1 ATCGCAATGCGA
638333 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:638387 original size:14 final size:14
Alignment explanation
Indices: 638368--638420 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
638358 TTCGCATTGT
638368 GATTTTGTCGTTGC
1 GATTTTGTCGTTGC
*
638382 GATTTTCATTTCGCATTGC
1 GA-TTT--TGTCG--TTGC
638401 GATTTTGTCGTTGC
1 GATTTTGTCGTTGC
638415 GATTTT
1 GATTTT
638421 CATTTCGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 12 0.38
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 6 0.19
ACGTcount: A:0.11, C:0.15, G:0.23, T:0.51
Consensus pattern (14 bp):
GATTTTGTCGTTGC
Found at i:638394 original size:33 final size:33
Alignment explanation
Indices: 638344--638436 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
638334 TTGTGTTTCG
*
638344 CGTTGCGA-TTTCATTTCGCATTGTGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
638376 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
638409 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
638437 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 8 0.14
33 51 0.86
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:638402 original size:19 final size:18
Alignment explanation
Indices: 638339--638436 Score: 86
Period size: 18 Copynumber: 5.8 Consensus size: 18
638329 GCGATTTGTG
*
638339 TTTCGCGTTGCGATTTCA
1 TTTCGCATTGCGATTTCA
*
638357 TTTCGCATTGTGATTT--
1 TTTCGCATTGCGATTTCA
*
638373 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGA-TTTCA
638390 TTTCGCATTGCGATTT--
1 TTTCGCATTGCGATTTCA
*
638406 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGA-TTTCA
638423 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
638437 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 11 0.17
15 6 0.10
16 8 0.13
17 8 0.13
18 18 0.29
19 12 0.19
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.48
Consensus pattern (18 bp):
TTTCGCATTGCGATTTCA
Found at i:638455 original size:20 final size:20
Alignment explanation
Indices: 638430--638476 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
638420 TCATTTCGCA
638430 TTGCGATAGCCATTTCCACG
1 TTGCGATAGCCATTTCCACG
* * *
638450 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCACG
638470 TTGCGAT
1 TTGCGAT
638477 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:638938 original size:41 final size:42
Alignment explanation
Indices: 638842--638929 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
638832 GACTCACCTG
* *
638842 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* * *
638884 TCCTCCCTCAAGAGTCCCC-CCTACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
638925 TCATC
1 TCATC
638930 GTTGAAGAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.22
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:640364 original size:14 final size:14
Alignment explanation
Indices: 640345--640380 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
640335 ATTGTTTAAT
640345 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
640359 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
640373 TGATTTGT
1 TGATTTGT
640381 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:640544 original size:19 final size:19
Alignment explanation
Indices: 640520--640584 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
640510 GCAACGAGAG
640520 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
640539 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
640558 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
640572 AATCGCAATGCGA
1 AATCGCAATGCGA
640585 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:640628 original size:20 final size:20
Alignment explanation
Indices: 640603--640660 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
640593 TCGCATTGCG
*
640603 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
640623 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
640643 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
640661 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:642835 original size:12 final size:12
Alignment explanation
Indices: 642818--642842 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
642808 TCTTCGGGGA
642818 CTTTTTCTTCTT
1 CTTTTTCTTCTT
642830 CTTTTTCTTCTT
1 CTTTTTCTTCTT
642842 C
1 C
642843 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:643051 original size:24 final size:24
Alignment explanation
Indices: 643017--643070 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
643007 CTGAAACATC
*
643017 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
643041 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
643065 ATCAAA
1 ATCAAA
643071 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:643852 original size:20 final size:20
Alignment explanation
Indices: 643780--643851 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
643770 AACTTTGAAA
643780 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGAAAGTCAGT
643800 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGAAAGTCAGT
* *
643820 ATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGAAAGTCAGT
*
643840 ATTGCATTGCGA
1 ATCGCATTGCGA
643852 TTTTCCCAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
ATCGCATTGCGAAAGTCAGT
Found at i:645045 original size:2 final size:2
Alignment explanation
Indices: 645040--645084 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
645030 AAAATATTAA
645040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
645082 AT A
1 AT A
645085 AAATAATATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:645093 original size:10 final size:12
Alignment explanation
Indices: 645033--645093 Score: 74
Period size: 12 Copynumber: 5.3 Consensus size: 12
645023 TAGATAAAAA
645033 ATAT-TAAATAT
1 ATATATAAATAT
*
645044 ATATATATATAT
1 ATATATAAATAT
*
645056 ATATATATATAT
1 ATATATAAATAT
*
645068 ATATATATATAT
1 ATATATAAATAT
645080 ATATA-AAATA-
1 ATATATAAATAT
645090 ATAT
1 ATAT
645094 TTTTATTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
10 4 0.09
11 8 0.17
12 35 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATATATAAATAT
Found at i:647965 original size:20 final size:20
Alignment explanation
Indices: 647940--647980 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
647930 TCCGACATTC
647940 TCGAAAATAACCCTTTTGGT
1 TCGAAAATAACCCTTTTGGT
647960 TCGAAAATAACCCTTTTGGT
1 TCGAAAATAACCCTTTTGGT
647980 T
1 T
647981 AGCGTCATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (20 bp):
TCGAAAATAACCCTTTTGGT
Found at i:649065 original size:30 final size:26
Alignment explanation
Indices: 649004--649078 Score: 87
Period size: 26 Copynumber: 2.7 Consensus size: 26
648994 ATGTCGCCGC
*
649004 GTAGCCCCGGAGACTTCCAGAAGTCT
1 GTAGTCCCGGAGACTTCCAGAAGTCT
*
649030 GTAGTCCCGGCGACTTCCAGAAGTCGCAGT
1 GTAGTCCCGGAGACTTCCAGAAGT--C--T
*
649060 GTAGTCCTGGAGACTTCCA
1 GTAGTCCCGGAGACTTCCA
649079 CCGAGTAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 22 0.54
28 1 0.02
30 18 0.44
ACGTcount: A:0.21, C:0.29, G:0.28, T:0.21
Consensus pattern (26 bp):
GTAGTCCCGGAGACTTCCAGAAGTCT
Found at i:652546 original size:5 final size:5
Alignment explanation
Indices: 652536--652563 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
652526 ATTAGTTATT
652536 CGATC CGATC CGATC CGATC CGATC CGA
1 CGATC CGATC CGATC CGATC CGATC CGA
652564 ATAACACATA
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:0.21, C:0.39, G:0.21, T:0.18
Consensus pattern (5 bp):
CGATC
Found at i:654466 original size:426 final size:426
Alignment explanation
Indices: 653673--654530 Score: 1574
Period size: 426 Copynumber: 2.0 Consensus size: 426
653663 TTGAAATTGG
*
653673 AAATTTTAGTGACTAAATTGTAGCTTTTGAAAATTGCAAGGGCAAAGGTGAAAAATGGATTTTTA
1 AAATTTTAGTGACTAAATTGTAGCTTTTGAAAATTGCAAGGACAAAGGTGAAAAATGGATTTTTA
653738 TTTGTTCATCTTTGACCATGAAGATGATATAGATAATATGGTGTCATGGATGATGTTATAGCAAT
66 TTTGTTCATCTTTGACCATGAAGATGATATAGATAATATGGTGTCATGGATGATGTTATAGCAAT
*
653803 GTCAAAGTGGAAATTATCATATTTTGGTAAGGATAAAATTGTAATTTCTAATTAAATGAATTTTA
131 GTCAAAGTGGAAATTATCATATTTTGGTAAGGATAAAATGGTAATTTCTAATTAAATGAATTTTA
* *
653868 AATTTATTTTTAATACATTAAGACAAGTGTATATGTTAATTATGAAGAGAAAACAAGAACTTTCA
196 AATTCATTTATAATACATTAAGACAAGTGTATATGTTAATTATGAAGAGAAAACAAGAACTTTCA
* *
653933 GCCCCTATTCTTGCTCAAGTCGTGCACCATCGTAGCTACAAGGTAAGAATGACATTTTGGATTGT
261 GCCCCTATTCTTGCTCAAGTCGTGCACCACCGTAGCTACAAGGTAAGAATGACATTTTGAATTGT
* *
653998 AATACAACAAATTTTGGTTAGTGACCAAAATGTAAATTTTGAATGTTTAGTAGTTAAAGTATAAA
326 AATACAACAAATTTTAGTTAGTGACCAAAATGTAAATTTTGAATGTTTAGTAGTCAAAGTATAAA
*
654063 GTTTGGAAAAGTTTAGGGACCAAAGTGTAATTTTCA
391 GTTTGGAAAAGTTCAGGGACCAAAGTGTAATTTTCA
654099 AAATTTTAGTGACTAAATTGTAGCTTTTGAAAATTGCAAGGACAAAGGTGAAAAATGGATTTTTA
1 AAATTTTAGTGACTAAATTGTAGCTTTTGAAAATTGCAAGGACAAAGGTGAAAAATGGATTTTTA
*
654164 TTTGTTCATCTTTGACTATGAAGATGATATAGATAATATGGTGTCATGGATGATGTTATAGCAAT
66 TTTGTTCATCTTTGACCATGAAGATGATATAGATAATATGGTGTCATGGATGATGTTATAGCAAT
654229 GTCAAAGTGGAAATTATCATATTTTGGTAAGGATAAAATGGTAATTTCTAATTAAATGAATTTTA
131 GTCAAAGTGGAAATTATCATATTTTGGTAAGGATAAAATGGTAATTTCTAATTAAATGAATTTTA
654294 AATTCATTTATAATACATTAAGACAAGTGTATATGTTAATTATGAAGAGAAAACAAGAA-TTTCC
196 AATTCATTTATAATACATTAAGACAAGTGTATATGTTAATTATGAAGAGAAAACAAGAACTTT-C
* * *
654358 CGCCCCTATTCTTGCTCAAGTTGTGCACCACCTTAGCTACAAGGTAAGAATGACATTTTGAATTG
260 AGCCCCTATTCTTGCTCAAGTCGTGCACCACCGTAGCTACAAGGTAAGAATGACATTTTGAATTG
654423 TAATACAACAAATTTTAGTTAGTGACCAAAATGTAAATTTTGAATGTTTAGTAGTCAAAGTATAA
325 TAATACAACAAATTTTAGTTAGTGACCAAAATGTAAATTTTGAATGTTTAGTAGTCAAAGTATAA
*
654488 AGTTTGGAAAAGTTCAGGGACCGAAGTGTAATTTTCA
390 AGTTTGGAAAAGTTCAGGGACCAAAGTGTAATTTTCA
654525 AAATTT
1 AAATTT
654531 AGGTATTTTG
Statistics
Matches: 417, Mismatches: 14, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
425 3 0.01
426 414 0.99
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (426 bp):
AAATTTTAGTGACTAAATTGTAGCTTTTGAAAATTGCAAGGACAAAGGTGAAAAATGGATTTTTA
TTTGTTCATCTTTGACCATGAAGATGATATAGATAATATGGTGTCATGGATGATGTTATAGCAAT
GTCAAAGTGGAAATTATCATATTTTGGTAAGGATAAAATGGTAATTTCTAATTAAATGAATTTTA
AATTCATTTATAATACATTAAGACAAGTGTATATGTTAATTATGAAGAGAAAACAAGAACTTTCA
GCCCCTATTCTTGCTCAAGTCGTGCACCACCGTAGCTACAAGGTAAGAATGACATTTTGAATTGT
AATACAACAAATTTTAGTTAGTGACCAAAATGTAAATTTTGAATGTTTAGTAGTCAAAGTATAAA
GTTTGGAAAAGTTCAGGGACCAAAGTGTAATTTTCA
Found at i:654832 original size:16 final size:16
Alignment explanation
Indices: 654811--654841 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
654801 AGTGACTAAA
654811 TTGTAGCTTTTGAAAT
1 TTGTAGCTTTTGAAAT
654827 TTGTAGCTTTTGAAA
1 TTGTAGCTTTTGAAA
654842 ATTGCAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (16 bp):
TTGTAGCTTTTGAAAT
Found at i:656754 original size:21 final size:21
Alignment explanation
Indices: 656728--656768 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
656718 GTCGAGGGTT
656728 TCATAGGTCCTTCAGGACAAC
1 TCATAGGTCCTTCAGGACAAC
*
656749 TCATAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCAGGACAA
656769 AAATTTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCAGGACAAC
Found at i:657357 original size:21 final size:22
Alignment explanation
Indices: 657331--657377 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
657321 TACGGAAGTA
*
657331 CTGTAGCA-GGGTATCGGCTCC
1 CTGTAGCAGGGGAATCGGCTCC
*
657352 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGGCTCC
657374 CTGT
1 CTGT
657378 CAACAATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.15, C:0.26, G:0.34, T:0.26
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGGCTCC
Found at i:658775 original size:22 final size:21
Alignment explanation
Indices: 658730--658776 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
658720 TGTAGAAATA
* *
658730 CTGTAGCAGGGTATCGATTCC
1 CTGTAGCAGGGAATAGATTCC
*
658751 CTGTAGCAGGGGAATAGGTTCC
1 CTGTAGCA-GGGAATAGATTCC
658773 CTGT
1 CTGT
658777 CAACAATCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.28
Consensus pattern (21 bp):
CTGTAGCAGGGAATAGATTCC
Found at i:661530 original size:20 final size:20
Alignment explanation
Indices: 661500--661576 Score: 147
Period size: 20 Copynumber: 3.9 Consensus size: 20
661490 TTGAGCAATA
661500 CTAGT-AGTATCGATACTAC
1 CTAGTGAGTATCGATACTAC
661519 CTAGTGAGTATCGATACTAC
1 CTAGTGAGTATCGATACTAC
661539 CTAGTGAGTATCGATACTAC
1 CTAGTGAGTATCGATACTAC
661559 CTAGTGAGTATCGATACT
1 CTAGTGAGTATCGATACT
661577 TCCCTTACCT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 5 0.09
20 52 0.91
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (20 bp):
CTAGTGAGTATCGATACTAC
Found at i:663361 original size:23 final size:23
Alignment explanation
Indices: 663314--663361 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
663304 AATAACATAT
**
663314 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
*
663337 TAGGTAGCGCTTATGTAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
663360 TA
1 TA
663362 TGCATTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:663418 original size:23 final size:23
Alignment explanation
Indices: 663392--663439 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
663382 ATCAAGTACA
663392 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
663415 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
663438 AT
1 AT
663440 TGACCTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:663423 original size:87 final size:86
Alignment explanation
Indices: 663273--663437 Score: 294
Period size: 87 Copynumber: 1.9 Consensus size: 86
663263 CGGTTATGCT
*
663273 ATATCATTTAACCGAAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAAT
1 ATATCATTTAACCGAAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAAT
663338 AGGTAGCGCTTATGTAATAAA
66 AGGTAGCGCTTATGTAATAAA
* *
663359 ATATGCATTTAACCGGAAATATTATCAAGTACAATAACAAATTAGGTAGCGCTTATATAATGTAA
1 ATAT-CATTTAACCGAAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAA
663424 TAGGTAGCGCTTAT
65 TAGGTAGCGCTTAT
663438 ATTGACCTAT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 4 0.05
87 71 0.95
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (86 bp):
ATATCATTTAACCGAAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGTAAT
AGGTAGCGCTTATGTAATAAA
Found at i:663830 original size:198 final size:199
Alignment explanation
Indices: 663458--663942 Score: 549
Period size: 199 Copynumber: 2.4 Consensus size: 199
663448 TTTCTCATAA
* * * *
663458 AACCGGTTACATTATTAATTGACCTATTACATTATAAATATCGGTTTCGATGTTTTCGGGATCGA
1 AACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGATTTCGGGATCGA
* * * * *
663523 TACAATTTT-AAATGTATCGACACTTTATGCGTGCAATTCGTTTGTGCTTTATTTTGGAAAAAAA
66 TAC-TTTTTAAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCATTTTGGAAAAAAA
* * * * * *
663587 TATCGACACATATTTAAAGAGTGTCGATACATAATGTAGACCTATT-TGTTAATTAA-CCGGTAT
130 TATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCT-CTAATGAACCCGATAT
663650 ATTT-T
194 ATTTCT
* * *
663655 AACCGGTTACATTATAAATTTACCTGTTACATAATAATTATCGATTTCGATG-TTTCGAGGATCG
1 AACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGATTTCG-GGATCG
*
663719 ATACTTTTTACAAATGTATCGACACTTTATGCGTACACCTCGTTTG-CCATTCATTTTGGAAAAA
65 ATACTTTTTA-AAATGTATCGACACTTTATGCGTACAACTCGTTTGTCC-TTCATTTTGGAAAAA
** * * *
663783 TGTATCGACACAAATTAAAAAAGTGTTGATACTTTATAT-TA-ACCTATTCTCTCATGAACCCGA
128 AATATCGACACAAATTAAAAAAGTGTCGATAC-ATA-ATGTAGACCTATTCTCTAATGAACCCGA
663846 TATATTTCT
191 TATATTTCT
* * ** *
663855 -ACCGGTTATATTGA-AAATTTACCTATTACATTATAATTATCGGTCTCTTTGATTTTGGGATCG
1 AACCGGTTACATT-ATAAATTTACCTATTACATTATAATTATCGGTTTCGATGATTTCGGGATCG
*
663918 ATACTTGTTATAAATGTATCGACAC
65 ATACTTTTTA-AAATGTATCGACAC
663943 AAAATCTAAC
Statistics
Matches: 244, Mismatches: 33, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
196 9 0.04
197 57 0.23
198 84 0.34
199 86 0.35
200 8 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (199 bp):
AACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGATTTCGGGATCGA
TACTTTTTAAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCATTTTGGAAAAAAAT
ATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTAATGAACCCGATATAT
TTCT
Found at i:663940 original size:199 final size:196
Alignment explanation
Indices: 663458--663942 Score: 543
Period size: 198 Copynumber: 2.4 Consensus size: 196
663448 TTTCTCATAA
* * *
663458 AACCGGTTACATTATTAATTGACCTATTACATTATAAATATCGGTTTCGATGTTTTCGGGATCGA
1 AACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT-GGGATCGA
* * * * *
663523 TACAATTT-TAAATGTATCGACACTTTATGCGTGCAATTCGTTTGTGCTTTATTTTGGAAAAAAA
65 TAC-TTTTATAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCATTTTGGAAAAAAA
* * * * * *
663587 TATCGACACATATTTAAAGAGTGTCGATACATAATGTAGACCTATTTGTTAATTAACCGGTATAT
129 TATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTTGCTAATGAACCGATATAT
663652 TTT
194 TTT
* * * *
663655 AACCGGTTACATTATAAATTTACCTGTTACATAATAATTATCGATTTCGATGTTTCGAGGATCGA
1 AACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTG-GGATCGA
* * *
663720 TACTTTTTACAAATGTATCGACACTTTATGCGTACACCTCGTTTG-CCATTCATTTTGGAAAAAT
65 TAC-TTTTATAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCC-TTCATTTTGGAAAAAA
* * * *
663784 GTATCGACACAAATTAAAAAAGTGTTGATACTTTATAT-TA-ACCTATTCT-CTCATGAACCCGA
128 ATATCGACACAAATTAAAAAAGTGTCGATAC-ATA-ATGTAGACCTATT-TGCTAATGAA-CCGA
663846 TATATTTCT
189 TATATTT-T
* * **
663855 -ACCGGTTATATTGA-AAATTTACCTATTACATTATAATTATCGGTCTCTTTGATTTTGGGATCG
1 AACCGGTTACATT-ATAAATTTACCTATTACATTATAATTATCGGTTTCGATG-TTTTGGGATCG
663918 ATACTTGTTATAAATGTATCGACAC
64 ATACTT-TTATAAATGTATCGACAC
663943 AAAATCTAAC
Statistics
Matches: 242, Mismatches: 35, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
196 1 0.00
197 63 0.26
198 86 0.36
199 84 0.35
200 8 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (196 bp):
AACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTGGGATCGAT
ACTTTTATAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCATTTTGGAAAAAAATA
TCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTTGCTAATGAACCGATATATTT
T
Found at i:667451 original size:198 final size:198
Alignment explanation
Indices: 667100--668671 Score: 2152
Period size: 198 Copynumber: 7.9 Consensus size: 198
667090 GTAATTTTAA
* * * * * * *
667100 AAAGTATCGACACTAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAA-AACCG
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCT-TTTT-T-TTAATAACCG
* * * * * * * *
667164 ATAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATAGGTTTCGATGCTTT
63 GTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* ** * * *
667229 TAGGATAAACACTTTTTCTAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAAGTTATTAT
128 TGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTAT
667294 GGACAT
193 GGACAT
667300 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTA
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTA
* *
667365 TATTTAGACTGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGG
66 TATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
667430 GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
131 GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
667495 CAT
196 CAT
* *
667498 AAAGTGTCGACACAAATGTATAAAGTATAGATACATTATGTATACCTTTTTTTTAATAACTGGTA
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTA
*
667563 TATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGG
66 TATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
667628 GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
131 GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
667693 CAT
196 CAT
* * *
667696 AAAGTGTCGACACAAATATATAAAGTATCGATACATTATGTATACCTTTTCTTTAATAACTGGTA
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTA
667761 TATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGAT-TTTTTGG
66 TATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
667825 GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
131 GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
667890 CAT
196 CAT
* *
667893 AAAGTGTCGACACAAATGTATAAAGTATTGATACACTATGTATACC-TTTTTTTAATAACCGGTA
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTA
* *
667957 TATTTAGACCGGTTATATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGG
66 TATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
668022 GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
131 GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
668087 CAT
196 CAT
*
668090 AAAGTGTCGA-ACAAATGTATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAACAGG
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACC-TT-TTTTTTAATAACCGG
* * *
668154 TATATTTAGACTGGTTACATTGTTATTTTACCTATTACATTATAATTATGTGTTTCGATGTTTTT
64 TATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
* ** *
668219 GGGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGCAC----TT-----ATACATTCT
129 GGGATCGACACTTGTTATAAATGTATCGACAC-TTTTTCGTGAACTTGTTTGGAAAATTTATTAT
668275 GGACA-
193 GGACAT
* * * * * *
668280 ACATGTATCGACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCATAA-AAC
1 A-AAGTGTCGACACAAATGTATAAAGTATCGATACATTA-TGTATACCT-TTTT-T-TTAATAAC
* * * * * * * * *
668343 TGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTATATTATAGTTACGGGTTTCGATGTT
61 CGGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTT
* *
668408 TTTGGGATCGACACTTGATATAAATGTATCAACACTTATTT-GTGAACTTGTTTTGGTTGGAAAA
126 TTTGGGATCGACACTTGTTATAAATGTATCGACACTT-TTTCGTGAACTTG---T--TTGGAAAA
** *
668472 TACATTATGGACAC
185 TTTATTATGGACAT
* * * ** * * *
668486 AAAGTATCGACACAAATGTATAAAGTGTCGATACTTTATGTATATATCTTTTCTCATAATCCGGT
1 AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAA-CCGGT
* * * *
668551 ATATTTAGATCGGTTACATTGTTATTTTACCTATTACATTATAATTATGGGTCTCGATATTTTTG
65 ATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
* * * *
668616 GGATCGATACTTTTTATAAATGTATCGACACTTTGTTCATGCACTTGGTTTGGAAA
130 GGATCGACACTTGTTATAAATGTATCGACACTTT-TTCGTGAACTT-GTTTGGAAA
668672 TACATTCTGG
Statistics
Matches: 1241, Mismatches: 97, Indels: 67
0.88 0.07 0.05
Matches are distributed among these distances:
190 1 0.00
191 31 0.02
192 123 0.10
193 3 0.00
196 106 0.09
197 206 0.17
198 440 0.35
199 112 0.09
200 54 0.04
201 7 0.01
202 2 0.00
203 5 0.00
204 91 0.07
205 56 0.05
206 4 0.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (198 bp):
AAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTA
TATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
GATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGA
CAT
Found at i:668470 original size:593 final size:587
Alignment explanation
Indices: 667100--668671 Score: 2275
Period size: 593 Copynumber: 2.6 Consensus size: 587
667090 GTAATTTTAA
* *
667100 AAAGTATCGACACTAATTTAA-AAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCG
1 AAAGTATCGACAC-AA-ATAATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACTG
* * *
667164 ATAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATAGGTTTCGATGCTTT
64 GTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATGGGTTTCGATGTTTT
* ** * * *
667229 TAGGATAAACACTTTTTCTAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAAGTTATTAT
129 TGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTAT
667294 GGACATAAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAA
194 GGACATAAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACC-TTTTTTTAATAA
* *
667359 CCGGTATATTTAGACTGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGT
258 CCGGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGT
667424 TTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTAT
323 TTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTAT
667489 TATGGACATAAAGTGTCGACACAAATGTATAAAGTATAGATACATTATGTATACCTTTTTTTTAA
388 TATGGACATAAAGTGTCGACACAAATGTATAAAGTATAGATACATTATGTATACCTTTTTTTTAA
*
667554 TAACTGGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGA
453 TAACAGGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGA
*
667619 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATT
518 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAAC---TTT----AATA
*
667684 TATTATGGACAT
576 CATTATGGACAT
* * * *
667696 AAAGTGTCGACACAAATATATAAAGTATCGATACATTATGTATACC--TTTTCT-TTAATAACTG
1 AAAGTATCGACACAAATA-ATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAA-AACTG
* * * * *
667758 GTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGAT-TTTT
64 GTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATGGGTTTCGATGTTTT
667822 TGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTAT
129 TGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTAT
* *
667887 GGACATAAAGTGTCGACACAAATGTATAAAGTATTGATACACTATGTATACCTTTTTTTAATAAC
194 GGACATAAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTAATAAC
* *
667952 CGGTATATTTAGACCGGTTATATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTT
259 CGGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTT
668017 TTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATT
324 TTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATT
*
668082 ATGGACATAAAGTGTCGA-ACAAATGTATAAAGTATCGATACATTATGTATACCTTTCTTTTTTA
389 ATGGACATAAAGTGTCGACACAAATGTATAAAGTATAGATACATTATGTATACC-TT-TTTTTTA
* * * *
668146 ATAACAGGTATATTTAGACTGGTTACATTGTTATTTTACCTATTACATTATAATTATGTGTTTCG
452 ATAACAGGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCG
* *
668211 ATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGCAC-TT-ATACATTC
517 ATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC-TTTTTCGTGAACTTTAATACATTA
668274 TGGACA-
581 TGGACAT
*
668280 ACATGTATCGACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCATAAAACT
1 A-AAGTATCGACACAAAT-AATAAAGTGTCGATACATTA-TGTAGACCTATTTTCTCATAAAACT
* * *
668344 GGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTATATTATAGTTACGGGTTTCGATGTTT
63 GGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATGGGTTTCGATGTTT
* *
668409 TTGGGATCGACACTTGATATAAATGTATCAACACTTATTT-GTGAACTTGTTTTGGTTGGAAAAT
128 TTGGGATCGACACTTGTTATAAATGTATCGACACTT-TTTCGTGAACTTG---T--TTGGAAAAT
** * * * * **
668473 ACATTATGGACACAAAGTATCGACACAAATGTATAAAGTGTCGATACTTTATGTATATATCTTTT
187 TTATTATGGACATAAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCT-TTTT
* * * *
668538 CTCATAATCCGGTATATTTAGATCGGTTACATTGTTATTTTACCTATTACATTATAATTATGGGT
251 TTAATAA-CCGGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGT
* * * * * *
668603 CTCGATATTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTGTTCATGCACTTGGTTTG
315 TTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTT-TTCGTGAACTT-GTTTG
668668 GAAA
378 GAAA
668672 TACATTCTGG
Statistics
Matches: 880, Mismatches: 73, Indels: 45
0.88 0.07 0.05
Matches are distributed among these distances:
584 3 0.00
585 47 0.05
586 1 0.00
587 63 0.07
588 49 0.06
589 3 0.00
590 2 0.00
591 35 0.04
592 159 0.18
593 281 0.32
594 85 0.10
595 99 0.11
596 44 0.05
597 9 0.01
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (587 bp):
AAAGTATCGACACAAATAATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACTGGT
AAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
GGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGG
ACATAAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTAATAACCG
GTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGGGTTTCGATGTTTT
TGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTAT
GGACATAAAGTGTCGACACAAATGTATAAAGTATAGATACATTATGTATACCTTTTTTTTAATAA
CAGGTATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGT
TTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTTAATACATTATGGAC
AT
Found at i:669963 original size:6 final size:6
Alignment explanation
Indices: 669956--669989 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
669946 GTTTGGATCA
* *
669956 TCATCA TCATCT TCATCT TCATCG TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
669990 TGACCGCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.44
Consensus pattern (6 bp):
TCATCT
Found at i:670761 original size:2 final size:2
Alignment explanation
Indices: 670754--670789 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
670744 TAGTCTCCAG
670754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
670790 CATTCCCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:671120 original size:15 final size:15
Alignment explanation
Indices: 671096--671131 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
671086 ATTTCCTCAA
671096 AAGAGCTGGGTTGAG
1 AAGAGCTGGGTTGAG
*
671111 AAGAGGTGGGTTGAG
1 AAGAGCTGGGTTGAG
671126 AAGAGC
1 AAGAGC
671132 CCTGATTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.47, T:0.17
Consensus pattern (15 bp):
AAGAGCTGGGTTGAG
Found at i:671909 original size:198 final size:198
Alignment explanation
Indices: 671568--672532 Score: 1582
Period size: 198 Copynumber: 4.9 Consensus size: 198
671558 TGACCATTTA
*
671568 CATTCTGGATA-AAATGTATCGACACAAATTCAA-AGAGTGTCGATACTTTATGTACACATGTTT
1 CATTCTGGACACAAA-GTATCGACACAAATTCAACA-AGTGTCGATACTTTATGTACACATGTTT
* *
671631 TCTCATAAACCGATGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGAG
64 TCTCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGG
*
671696 TCTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTAT-GGTG-ACCTTGGTA
129 TCTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATT-TCGATGCA-CTTGGTA
*
671759 AGAAAAT
192 AGGAAAT
* * *
671766 CATTCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCAATACTTTATGTACACTTGTTTTC
1 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACATGTTTTC
* *
671831 TCATAAACCGGTATATTTAGACCGGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTC
66 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
* * * * *
671896 TCAATGATTTTGGGATCGATACTTTTTATAAATGTATCGACACATTAT-GGT-AACCTTAGTAAG
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATT-TCGATGCA-CTTGGTAAG
671959 GAAAT
194 GAAAT
*
671964 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTC
1 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACATGTTTTC
672029 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
66 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
* * *
672094 TCGATGTTTTTGGGATCGATACTTGTTATAAATGTATCGACATATTTCTATGCACTTGGTAAGGA
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCGATGCACTTGGTAAGGA
672159 AAT
196 AAT
672162 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACATGTTTTC
1 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACATGTTTTC
672227 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
66 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
* *
672292 TCGATGTTTTTGGGATTGATACTTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGA
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCGATGCACTTGGTAAGGA
*
672357 GAT
196 AAT
* * * *
672360 CATTCTGGATACAAAGTATGGACATAAATTCAACAAGTGTCGATACTTTATGTACACTTGTTTTC
1 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACATGTTTTC
*
672425 TCATAAACCGGTGTATTTACACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
66 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
*
672490 TCGATATTTTTGGGATCGATACTTTTTATAAATGTATCGACAC
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACAC
672533 GTATGTTTAC
Statistics
Matches: 724, Mismatches: 38, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
197 1 0.00
198 718 0.99
199 5 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (198 bp):
CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACATGTTTTC
TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCGATGCACTTGGTAAGGA
AAT
Found at i:674002 original size:17 final size:17
Alignment explanation
Indices: 673980--674015 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
673970 GAATCATTAG
673980 GATTAATATCTTTTCAT
1 GATTAATATCTTTTCAT
673997 GATTAATATCTTTTCAT
1 GATTAATATCTTTTCAT
674014 GA
1 GA
674016 AATATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (17 bp):
GATTAATATCTTTTCAT
Found at i:674340 original size:18 final size:18
Alignment explanation
Indices: 674317--674355 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
674307 TTCTCCTCAT
* *
674317 TTCCTCTATCTTTTCTTC
1 TTCCTCCATATTTTCTTC
674335 TTCCTCCATATTTTCTTC
1 TTCCTCCATATTTTCTTC
674353 TTC
1 TTC
674356 AAATTTTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.33, G:0.00, T:0.59
Consensus pattern (18 bp):
TTCCTCCATATTTTCTTC
Found at i:675056 original size:22 final size:23
Alignment explanation
Indices: 675028--675086 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 23
675018 AACCTGAATT
*
675028 TATAATAAAAT-TAATCATTTTA
1 TATAATAAAATACAATCATTTTA
*
675050 TATAATAACTATACAATCATTTTA
1 TATAATAA-AATACAATCATTTTA
675074 TATAA-AAAA-ACAA
1 TATAATAAAATACAA
675087 AAACATTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.12
22 9 0.28
23 4 0.12
24 15 0.47
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.37
Consensus pattern (23 bp):
TATAATAAAATACAATCATTTTA
Found at i:677254 original size:182 final size:179
Alignment explanation
Indices: 676934--677289 Score: 493
Period size: 182 Copynumber: 2.0 Consensus size: 179
676924 ATTAAAGTAC
* * *
676934 CGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTATCATTTTGATAACGGTTTTGTCATA
1 CGACACTTTCAACATAACCGATAGCGCTTTACCGGTTTTATCATTTCGAGAACGGTTTTGTCATA
* * *
676999 TTTTTACCTATTATATTATTATGGATCGATACATTTTCATAAAGTATCGACACTTTTTAGGTGCT
66 TTCTTACCTATTATATTACTATGGATCGATACATTTTCATAAAGTATCGACACTTTATAGGTGCT
*
677064 ACAACTTCTTCTCTTTTAAATT-ACGAAAGTGTCGATACTTATATTAATTTAT
131 ACAA---CTTCTCTTTTAAATTCA-AAAAGTGTCGATACTTATATTAATTTAT
* * ** * *
677116 CGACACTTTCAATATATCCGATAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAACATAACCGATAGCGCTTTACCGGTTTTATCATTTCGAGAACGGTTTTGTCATA
* *
677181 TTCTTACCTATTATATTGCTATGGATCGATATATTTGT-ATAAAGTATCGACACTTTATAGGCT-
66 TTCTTACCTATTATATTACTATGGATCGATACATTT-TCATAAAGTATCGACACTTTATAGG-TG
*
677244 CTATAACTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAA
129 CTACAACTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAA
677290 CGTATTGACA
Statistics
Matches: 155, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
179 37 0.24
180 1 0.01
182 115 0.74
183 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (179 bp):
CGACACTTTCAACATAACCGATAGCGCTTTACCGGTTTTATCATTTCGAGAACGGTTTTGTCATA
TTCTTACCTATTATATTACTATGGATCGATACATTTTCATAAAGTATCGACACTTTATAGGTGCT
ACAACTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAATTTAT
Found at i:677304 original size:20 final size:20
Alignment explanation
Indices: 677274--677322 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
677264 TCAAAAAGTG
*
677274 TCGATACTTATATTAACGTA
1 TCGACACTTATATTAACGTA
*
677294 TTGACACTTATATTAACGTA
1 TCGACACTTATATTAACGTA
677314 TCGACACTT
1 TCGACACTT
677323 TTAATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (20 bp):
TCGACACTTATATTAACGTA
Found at i:677440 original size:199 final size:200
Alignment explanation
Indices: 677100--677490 Score: 563
Period size: 199 Copynumber: 2.0 Consensus size: 200
677090 AAGTGTCGAT
** * *
677100 ACTTATATTAATTTATCGACACTTTCAATATATCCGATAGCTTTTTACCGGTTTTATCATTTCGA
1 ACTTATATTAACGTATCGACACTTTCAATATATACGATAGCTCTTTACCGGTTTTATCATTTCGA
* * * * *
677165 GACCTGTTTTGTCATATTCTTACCTATTATATTGCTATGGATCGATATATTTGTATAAAGTATCG
66 GACCGGTTTTGTCATATTCATACATATTATATTGCTATGGATCAATACATTTGTATAAAGTATCG
*
677230 ACACTTTATAGGCTCTA-TA-ACTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAACGT
131 ACACTTTATAGGCGCTATTACACTTCTCTTTTAAATTCAAAAAGTGTCGATACTTAT-TTAACGT
677293 ATTGAC
195 ATTGAC
* * * *
677299 ACTTATATTAACGTATCGACACTTTTAATATATATGGTAGCTCTTTACCGGTTTTATCATTTCGT
1 ACTTATATTAACGTATCGACACTTTCAATATATACGATAGCTCTTTACCGGTTTTATCATTTCGA
* * *
677364 GACCGGTTTTGTCATACTT-ATACATGTTATATTGTTATGGATCAATACATTTTTATAAAGTATC
66 GACCGGTTTTGTCATA-TTCATACATATTATATTGCTATGGATCAATACATTTGTATAAAGTATC
* *
677428 GACACTTTATAGGCGCTATTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAA
130 GACACTTTATAGGCGCTATTAC-ACTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATTTAA
677491 ATCTAATCGA
Statistics
Matches: 169, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
199 127 0.75
200 4 0.02
201 4 0.02
202 34 0.20
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (200 bp):
ACTTATATTAACGTATCGACACTTTCAATATATACGATAGCTCTTTACCGGTTTTATCATTTCGA
GACCGGTTTTGTCATATTCATACATATTATATTGCTATGGATCAATACATTTGTATAAAGTATCG
ACACTTTATAGGCGCTATTACACTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATTTAACGTA
TTGAC
Found at i:677891 original size:34 final size:34
Alignment explanation
Indices: 677848--677917 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
677838 AAAAATAGTA
*
677848 TAAAGGGTAAATTATAAGTTTACTCACTGAACTT
1 TAAAGGGTAAATTATAAGCTTACTCACTGAACTT
677882 TAAAGGGTAAATTATAAGCTTACTCACTGAACTT
1 TAAAGGGTAAATTATAAGCTTACTCACTGAACTT
677916 TA
1 TA
677918 CTCACTCTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (34 bp):
TAAAGGGTAAATTATAAGCTTACTCACTGAACTT
Found at i:678295 original size:26 final size:26
Alignment explanation
Indices: 678256--678307 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
678246 AAAATTCAAT
678256 GAGTAAGTGCGTAATTTACCCTAATA
1 GAGTAAGTGCGTAATTTACCCTAATA
*
678282 GAGTAAGTGTGTAATTTACCCTAATA
1 GAGTAAGTGCGTAATTTACCCTAATA
678308 TAAATAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (26 bp):
GAGTAAGTGCGTAATTTACCCTAATA
Found at i:683758 original size:21 final size:20
Alignment explanation
Indices: 683672--683829 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
683662 AAATGACCAA
**
683672 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
683691 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
683711 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
683731 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
683752 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
683773 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
683793 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
683814 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
683830 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:683820 original size:20 final size:20
Alignment explanation
Indices: 683796--684065 Score: 321
Period size: 20 Copynumber: 13.5 Consensus size: 20
683786 CGATTTTCCA
* ** *
683796 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
683816 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
683836 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
683856 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
683876 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
683896 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
683916 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
683936 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
683956 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
683976 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
683996 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
684016 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
684036 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
684056 AAATCACAAC
1 AAATCGCAAC
684066 ACTGAAATTT
Statistics
Matches: 219, Mismatches: 25, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
19 1 0.00
20 216 0.99
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:684787 original size:24 final size:24
Alignment explanation
Indices: 684748--684794 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
684738 AAATTTGGTC
684748 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
684772 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
684795 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:684986 original size:12 final size:12
Alignment explanation
Indices: 684969--684993 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
684959 ATATAATCCT
684969 GAAGAAGAAAAA
1 GAAGAAGAAAAA
684981 GAAGAAGAAAAA
1 GAAGAAGAAAAA
684993 G
1 G
684994 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:686315 original size:19 final size:20
Alignment explanation
Indices: 686252--686307 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
686242 GATTCTCTCG
686252 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCCGCA
686272 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCCGCA
686292 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
686308 GCAATGCGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.48
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCGCA
Found at i:686343 original size:14 final size:14
Alignment explanation
Indices: 686324--686378 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
686314 CGGAAATGAA
686324 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
686338 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
686357 AATCGCAACGAGAG
1 AATCGCAACGAGAG
686371 AATCGCAA
1 AATCGCAA
686379 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:686358 original size:33 final size:33
Alignment explanation
Indices: 686306--686397 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
686296 GATTTTCATT
686306 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
686340 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
686373 TCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
686398 TGCGAAATGA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 49 0.84
34 9 0.16
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:686400 original size:52 final size:52
Alignment explanation
Indices: 686338--686454 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
686328 GCAACGAGAG
686338 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
686390 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
686442 AATCGCATTGCGA
1 AATCGCAATGCGA
686455 TTCTCCCATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:686503 original size:19 final size:19
Alignment explanation
Indices: 686461--686560 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
686451 GCGATTCTCC
686461 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
686481 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
686500 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
686516 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
686533 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
686552 CATTGCGAT
1 CATTGCGAT
686561 AGTCAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:686557 original size:52 final size:53
Alignment explanation
Indices: 686444--686560 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
686434 GAAATTAAAA
686444 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
686497 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
686549 TCGCATTGCGAT
1 TCGCATTGCGAT
686561 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:686686 original size:14 final size:14
Alignment explanation
Indices: 686667--686703 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
686657 CATCAATTAC
686667 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
686681 ACAAATCATCTTTT
1 ACAAATCAACTTTT
686695 ACAAATCAA
1 ACAAATCAA
686704 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:688701 original size:14 final size:14
Alignment explanation
Indices: 688682--688738 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
688672 GCGAAATGAA
*
688682 AATCGCAACGACAG
1 AATCGCAACGAAAG
688696 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
688713 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
688729 AATCGCAACG
1 AATCGCAACG
688739 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:688709 original size:33 final size:33
Alignment explanation
Indices: 688663--688755 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
688653 GCGAAACCAA
*
688663 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
688696 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
688729 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
688756 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:688720 original size:19 final size:19
Alignment explanation
Indices: 688626--688760 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
688616 TAGTTTACTT
* *
688626 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
688646 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
688665 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
688684 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
688698 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
688717 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
688731 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
688750 TCGCAATGCGA
1 TCGCAACGCGA
688761 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:688778 original size:19 final size:19
Alignment explanation
Indices: 688756--688884 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
688746 AAAATCGCAA
688756 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
688775 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
688789 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
688808 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
688822 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
688841 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
688860 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
688880 TGCGA
1 TGCGA
688885 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:688798 original size:33 final size:33
Alignment explanation
Indices: 688756--688847 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
688746 AAAATCGCAA
688756 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
688789 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
688822 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
688848 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:689087 original size:93 final size:93
Alignment explanation
Indices: 688928--689401 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
688918 TTGAATGGAT
688928 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
688993 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
689021 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
689086 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
689114 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
689179 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
689207 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
689272 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
689300 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
689365 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
689393 AAATTTACT
1 AAATTTACT
689402 AAGCAATCTA
Statistics
Matches: 378, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 378 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:691126 original size:14 final size:14
Alignment explanation
Indices: 691107--691196 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
691097 TTGAAATGAA
691107 AATCGCAACGAGAG
1 AATCGCAACGAGAG
691121 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
691138 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
691154 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
691173 AATCGCAACGAGAG
1 AATCGCAACGAGAG
691187 AATCGCAACG
1 AATCGCAACG
691197 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:691144 original size:33 final size:33
Alignment explanation
Indices: 691099--691213 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
691089 TCTTTTGGTT
691099 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
691132 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
691165 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
691198 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
691214 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:691145 original size:19 final size:18
Alignment explanation
Indices: 691106--691218 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
691096 GTTGAAATGA
691106 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
691121 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
691138 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
691154 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
691171 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
691187 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
691204 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
691219 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:691249 original size:14 final size:14
Alignment explanation
Indices: 691230--691286 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
691220 TTTGGTTTCG
691230 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
691244 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
691263 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
691277 CGTTGCGATT
1 CGTTGCGATT
691287 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Done.