Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold50
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: 2541760
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Warning! 26494 characters in sequence are not A, C, G, or T
File 15 of 16
Found at i:2321375 original size:19 final size:19
Alignment explanation
Indices: 2321351--2321415 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
2321341 TTTCAACGAT
2321351 TTGTATCGATACAAAAATG
1 TTGTATCGATACAAAAATG
2321370 TTGTATCGAT---AAAA--
1 TTGTATCGATACAAAAATG
* *
2321384 -TGTATCGATACATAAGTG
1 TTGTATCGATACAAAAATG
*
2321402 TTGTATTGATACAA
1 TTGTATCGATACAA
2321416 TGTATCGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
13 9 0.25
16 6 0.17
19 21 0.58
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACAAAAATG
Found at i:2321425 original size:13 final size:13
Alignment explanation
Indices: 2321403--2321458 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 13
2321393 ACATAAGTGT
*
2321403 TGTATTGATACAA
1 TGTATCGATACAA
2321416 TGTATCGATACATAA
1 TGTATCGATAC--AA
2321431 GTTTGTATCGATACAA
1 ---TGTATCGATACAA
2321447 TGTATCGATACA
1 TGTATCGATACA
2321459 TAAGTTTGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
16 2 0.05
18 11 0.30
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2321444 original size:31 final size:32
Alignment explanation
Indices: 2321352--2321484 Score: 207
Period size: 31 Copynumber: 4.2 Consensus size: 32
2321342 TTCAACGATT
* * *
2321352 TGTATCGATACAAAAATGTTGTATCGATAAAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
2321384 TGTATCGATACATAAGTGTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2321416 TGTATCGATACATAAGT-TTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
2321447 TGTATCGATACATAAGT-TTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2321478 TGTATCG
1 TGTATCG
2321485 CTACGAAGCT
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
31 50 0.53
32 45 0.47
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:2321546 original size:13 final size:12
Alignment explanation
Indices: 2321506--2321584 Score: 62
Period size: 13 Copynumber: 6.9 Consensus size: 12
2321496 CTGCCAAGAA
2321506 ATGTATCGATAC
1 ATGTATCGATAC
* *
2321518 AT-TACCCA-A-
1 ATGTATCGATAC
2321527 ATGTATCGATAC
1 ATGTATCGATAC
2321539 ATTGTATCGATAC
1 A-TGTATCGATAC
* *
2321552 AT-TACCCA-A-
1 ATGTATCGATAC
2321561 ATGTATCGATAC
1 ATGTATCGATAC
2321573 ATTGTATCGATA
1 A-TGTATCGATA
2321585 TACTGATCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
9 4 0.08
10 10 0.20
11 10 0.20
12 5 0.10
13 22 0.43
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:2321550 original size:34 final size:34
Alignment explanation
Indices: 2321507--2321584 Score: 156
Period size: 34 Copynumber: 2.3 Consensus size: 34
2321497 TGCCAAGAAA
2321507 TGTATCGATACATTACCCAAATGTATCGATACAT
1 TGTATCGATACATTACCCAAATGTATCGATACAT
2321541 TGTATCGATACATTACCCAAATGTATCGATACAT
1 TGTATCGATACATTACCCAAATGTATCGATACAT
2321575 TGTATCGATA
1 TGTATCGATA
2321585 TACTGATCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (34 bp):
TGTATCGATACATTACCCAAATGTATCGATACAT
Found at i:2321651 original size:52 final size:52
Alignment explanation
Indices: 2321595--2321723 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
2321585 TACTGATCTT
*
2321595 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
2321647 TGTATCGATACATTCAGGCAACTTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2321699 TGTATCGATACATGCAGGGAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2321724 TCATATTTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2326493 original size:13 final size:13
Alignment explanation
Indices: 2326475--2326500 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2326465 CAATTTTTTA
2326475 TGTATCGATACAT
1 TGTATCGATACAT
2326488 TGTATCGATACAT
1 TGTATCGATACAT
2326501 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2328594 original size:21 final size:20
Alignment explanation
Indices: 2328565--2328607 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2328555 GGCTAGTGTG
* *
2328565 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
2328586 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
2328606 GG
1 GG
2328608 TGGTGCTGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:2331142 original size:15 final size:15
Alignment explanation
Indices: 2331122--2331152 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2331112 ATTACGTTTG
*
2331122 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2331137 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2331152 G
1 G
2331153 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2335230 original size:13 final size:13
Alignment explanation
Indices: 2335212--2335237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2335202 CAATTTTTTG
2335212 TGTATCGATACAT
1 TGTATCGATACAT
2335225 TGTATCGATACAT
1 TGTATCGATACAT
2335238 ACTTAGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2335252 original size:32 final size:33
Alignment explanation
Indices: 2335192--2335255 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2335182 TACAAGCCAA
** *
2335192 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTAGTGTATCGATACAT
2335225 TGTATCGATAC-ATACTTAGTGTATCGATACA
1 TGTATCGATACAATACTTAGTGTATCGATACA
2335256 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTAGTGTATCGATACAT
Found at i:2335404 original size:49 final size:49
Alignment explanation
Indices: 2335270--2335513 Score: 298
Period size: 49 Copynumber: 5.2 Consensus size: 49
2335260 TGGCTACTAC
*
2335270 ATTGGACTTAAAGATGATGGTGCCAATACGCTGATTCAAGG-CAGCGAT
1 ATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
* * * *
2335318 ATTGGACTT--A-A--A-GGTGCCAATGTGCTGATTCAGGGCCAGCTAC
1 ATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
2335361 ATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
1 ATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
* *
2335410 ATTGGACTTAAAG--G-T-GT--CAATGTGCTGATTCAAGGCCAGCTAT
1 ATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
* * *
2335453 ATTGGACTTAAAGATAAAGATGCCAATATGCTGATTCAAGGCCAGCGAT
1 ATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
*
2335502 ATTGGGCTTAAA
1 ATTGGACTTAAA
2335514 AGAAGATGCC
Statistics
Matches: 166, Mismatches: 17, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
42 20 0.12
43 52 0.31
45 4 0.02
46 3 0.02
47 2 0.01
48 10 0.06
49 75 0.45
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (49 bp):
ATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGAT
Found at i:2335449 original size:92 final size:92
Alignment explanation
Indices: 2335266--2335513 Score: 417
Period size: 92 Copynumber: 2.7 Consensus size: 92
2335256 AGTTTGGCTA
*
2335266 CTACATTGGACTTAAAGATGATGGTGCCAATACGCTGATTCAAGG-CAGCGATATTGGACTTAAA
1 CTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
*
2335330 GGTGCCAATGTGCTGATTCAGGGCCAG
66 GGTGCCAATGTGCTGATTCAAGGCCAG
2335357 CTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 CTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
*
2335422 GGTGTCAATGTGCTGATTCAAGGCCAG
66 GGTGCCAATGTGCTGATTCAAGGCCAG
* * * * *
2335449 CTATATTGGACTTAAAGATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
1 CTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
2335514 AGAAGATGCC
Statistics
Matches: 148, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
91 44 0.30
92 104 0.70
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (92 bp):
CTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
GGTGCCAATGTGCTGATTCAAGGCCAG
Found at i:2335597 original size:32 final size:33
Alignment explanation
Indices: 2335504--2335639 Score: 170
Period size: 33 Copynumber: 4.2 Consensus size: 33
2335494 CCAGCGATAT
* * *
2335504 TGGGC-TTAAAAGAA-GATGCCACCAACTTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
*
2335535 TGGGCTTTTGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
** * *
2335568 TGGGCTTTAG-AGGGGGTTGGCACCCACTTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
*
2335600 TGGGCTTTAGAAAAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
2335633 TGGGCTT
1 TGGGCTT
2335640 AAAAGGAAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
31 5 0.06
32 35 0.40
33 48 0.55
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (33 bp):
TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
Found at i:2335658 original size:36 final size:36
Alignment explanation
Indices: 2335588--2335704 Score: 102
Period size: 36 Copynumber: 3.3 Consensus size: 36
2335578 AGGGGGTTGG
* *
2335588 CACCCACTTGTGTGGGCTT--TA-GAAAAAG-GTTGC
1 CACCGACTTGTGTGGGCTTAAAAGGAAAAAGAG-TGC
2335621 CACCGACTTGTGTGGGCTTAAAAGGAAAAAGAGTGC
1 CACCGACTTGTGTGGGCTTAAAAGGAAAAAGAGTGC
* * *
2335657 CACGGA-GT-TGTGGGCTTTAAAAGGAAAAAAAGGTGC
1 CACCGACTTGTGTGGGC-TTAAAAGGAAAAAGA-GTGC
* *
2335693 CACGGAGTTGTG
1 CACCGACTTGTG
2335705 GGCTTTAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
33 18 0.26
34 7 0.10
35 16 0.23
36 25 0.36
37 2 0.03
38 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (36 bp):
CACCGACTTGTGTGGGCTTAAAAGGAAAAAGAGTGC
Found at i:2335721 original size:65 final size:62
Alignment explanation
Indices: 2335646--2335776 Score: 174
Period size: 65 Copynumber: 2.1 Consensus size: 62
2335636 GCTTAAAAGG
* * * * *
2335646 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGGAAAAAAAGGTGCCACGGAGTTGTGGGCTT
1 AAAAAGAGTGCCACGAAGTTGTGGACTTTGAAAA-G--AAAAAGGTGCCACAGAGTCGTGGAC-T
2335710 T
62 T
2335711 AAAAAGAGTGCCACGAAGTTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTCGTGGACTT
1 AAAAAGAGTGCCACGAAGTTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTCGTGGACTT
2335773 AAAA
1 AAAA
2335777 GGAACAAGGT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
62 6 0.10
63 22 0.37
65 28 0.47
66 4 0.07
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.20
Consensus pattern (62 bp):
AAAAAGAGTGCCACGAAGTTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTCGTGGACTT
Found at i:2335757 original size:34 final size:34
Alignment explanation
Indices: 2335640--2335938 Score: 279
Period size: 33 Copynumber: 9.0 Consensus size: 34
2335630 GTGTGGGCTT
* *
2335640 AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-
1 AAAA-GAAAAAG-GTGCCACGGAGTCGTGGACTTTG
* *
2335675 AAAAGGAAAAAAAGGTGCCACGGAGTTGTGGGCTTT-
1 AAAA-G--AAAAAGGTGCCACGGAGTCGTGGACTTTG
* * *
2335711 --AA-AAAGA-GTGCCACGAAGTTGTGGACTTTG
1 AAAAGAAAAAGGTGCCACGGAGTCGTGGACTTTG
*
2335741 AAAAGAAAAAGGTGCCACAGAGTCGTGGAC-TT-
1 AAAAGAAAAAGGTGCCACGGAGTCGTGGACTTTG
*
2335773 AAAAGGAACAAGGTGCCACGGAGTCGTGGAC-TT-
1 AAAA-GAAAAAGGTGCCACGGAGTCGTGGACTTTG
* *
2335806 --AA-AAAGA-GTGCCACGGAGTTGTGGACTTTG
1 AAAAGAAAAAGGTGCCACGGAGTCGTGGACTTTG
*
2335836 AAAAGAAAAAAGGTGCCACGAAGTCGTGGACTTTG
1 AAAAG-AAAAAGGTGCCACGGAGTCGTGGACTTTG
* *
2335871 AAGA-AAAAAGGTGCCACGAAGTCGTGGACTTTG
1 AAAAGAAAAAGGTGCCACGGAGTCGTGGACTTTG
*
2335904 AAGA-AAAAAGAGTGCCACGGAGTCGTGGACTTTG
1 AAAAGAAAAAG-GTGCCACGGAGTCGTGGACTTTG
2335938 A
1 A
2335939 GACAAAATGC
Statistics
Matches: 231, Mismatches: 17, Indels: 33
0.82 0.06 0.12
Matches are distributed among these distances:
28 18 0.08
29 25 0.11
30 4 0.02
31 2 0.01
32 8 0.03
33 71 0.31
34 45 0.19
35 30 0.13
36 22 0.10
37 6 0.03
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19
Consensus pattern (34 bp):
AAAAGAAAAAGGTGCCACGGAGTCGTGGACTTTG
Found at i:2335865 original size:96 final size:96
Alignment explanation
Indices: 2335640--2335938 Score: 368
Period size: 96 Copynumber: 3.0 Consensus size: 96
2335630 GTGTGGGCTT
* * * *
2335640 AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAAAGGTGCCACGGAGTTGTG
1 AAAA-GAAAAAG-GTGCCACGAAGTCGTGGAC-TTAAAAGG--AAAAAGGTGCCACGGAGTCGTG
* *
2335705 GGCTTTAAAAAGAGTGCCACGAAGTTGTGGACTTTG
61 GACTTTAAAAAGAGTGCCACGGAGTTGTGGACTTTG
*
2335741 AAAAGAAAAAGGTGCCAC-AGAGTCGTGGACTTAAAAGGAACAAGGTGCCACGGAGTCGTGGAC-
1 AAAAGAAAAAGGTGCCACGA-AGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTCGTGGACT
2335804 TTAAAAAGAGTGCCACGGAGTTGTGGACTTTG
65 TTAAAAAGAGTGCCACGGAGTTGTGGACTTTG
** * *
2335836 AAAAGAAAAAAGGTGCCACGAAGTCGTGGACTTTGAAGAAAAAAGGTGCCACGAAGTCGTGGACT
1 AAAAG-AAAAAGGTGCCACGAAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTCGTGGACT
*
2335901 TTGAAGAAAAAAGAGTGCCACGGAGTCGTGGACTTTG
65 TT-----AAAAAGAGTGCCACGGAGTTGTGGACTTTG
2335938 A
1 A
2335939 GACAAAATGC
Statistics
Matches: 176, Mismatches: 13, Indels: 17
0.85 0.06 0.08
Matches are distributed among these distances:
95 36 0.20
96 73 0.41
97 3 0.02
98 8 0.05
99 15 0.09
100 7 0.04
101 4 0.02
102 30 0.17
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19
Consensus pattern (96 bp):
AAAAGAAAAAGGTGCCACGAAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTCGTGGACTT
TAAAAAGAGTGCCACGGAGTTGTGGACTTTG
Found at i:2335959 original size:30 final size:31
Alignment explanation
Indices: 2335645--2335972 Score: 226
Period size: 33 Copynumber: 10.1 Consensus size: 31
2335635 GGCTTAAAAG
* * *
2335645 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
1 GAAAAA-AGTGCCAC-GAGTCGTGGACTTT-GAA
* *
2335679 GGAAAAAAAGGTGCCACGGAGTTGTGGGCTTT--A
1 -G-AAAAAA-GTGCCAC-GAGTCGTGGACTTTGAA
* *
2335712 -AAAAGAGTGCCACGAAGTTGTGGACTTTGAAAA
1 GAAAAAAGTGCCACG-AGTCGTGGACTTTG--AA
* **
2335745 GAAAAAGGTGCCACAGAGTCGTGGACTTAAAA
1 GAAAAAAGTGCCAC-GAGTCGTGGACTTTGAA
* *
2335777 GGAACAAGGTGCCACGGAGTCGTGGAC-TT--A
1 -GAAAAAAGTGCCAC-GAGTCGTGGACTTTGAA
* *
2335807 -AAAAGAGTGCCACGGAGTTGTGGACTTTGAAAA
1 GAAAAAAGTGCCAC-GAGTCGTGGACTTTG--AA
2335840 GAAAAAAGGTGCCACGAAGTCGTGGACTTTGAA
1 GAAAAAA-GTGCCACG-AGTCGTGGACTTTGAA
2335873 GAAAAAAGGTGCCACGAAGTCGTGGACTTTGAA
1 GAAAAAA-GTGCCACG-AGTCGTGGACTTTGAA
2335906 GAAAAAAGAGTGCCACGGAGTCGTGGACTTTG-A
1 G-AAAAA-AGTGCCAC-GAGTCGTGGACTTTGAA
* *
2335939 GACAAAA-TGCCTCTGAGTCGTGGACTTTG-A
1 GAAAAAAGTGCCAC-GAGTCGTGGACTTTGAA
2335969 GAAA
1 GAAA
2335973 GTATTTGAAG
Statistics
Matches: 252, Mismatches: 20, Indels: 47
0.79 0.06 0.15
Matches are distributed among these distances:
28 22 0.09
29 21 0.08
30 30 0.12
31 1 0.00
32 7 0.03
33 65 0.26
34 54 0.21
35 25 0.10
36 27 0.11
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.20
Consensus pattern (31 bp):
GAAAAAAGTGCCACGAGTCGTGGACTTTGAA
Found at i:2335964 original size:160 final size:160
Alignment explanation
Indices: 2335646--2335965 Score: 418
Period size: 160 Copynumber: 2.0 Consensus size: 160
2335636 GCTTAAAAGG
* * * *
2335646 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAAAGGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAAAGGTGCCACGAAGTCGTGGACTTT
* *
2335711 AAAAAGAGTGCCACGAAGTTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTCGTGGACTTAAA
66 AAAAAAAGTGCCACGAAGTCGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTCGTGGACTTAAA
**
2335776 AGGAACAAGGTGCCACGGAGTCGTGGACTT
131 AGGAACAAAATGCCACGGAGTCGTGGACTT
2335806 AAAAAGAGTGCCACGGAGTTGTGGACTTTGAAAA-G-AAAAAAGGTGCCACGAAGTCGTGGACTT
1 AAAAAGAGTGCCACGGAGTTGTGGACTTT-AAAAGGAAAAAAAGGTGCCACGAAGTCGTGGACTT
* *
2335869 TGAAGAAAAAAGGTGCCACGAAGTCGTGGACTTTGAAGA-AAAAAGAGTGCCACGGAGTCGTGGA
65 T--A-AAAAAA-GTGCCACGAAGTCGTGGACTTTGAAAAGAAAAAG-GTGCCACAGAGTCGTGGA
** * *
2335933 CTT-TGA-G-ACAAAATGCCTCTGAGTCGTGGACTT
125 CTTAAAAGGAACAAAATGCCACGGAGTCGTGGACTT
2335966 TGAGAAAGTA
Statistics
Matches: 140, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
159 26 0.19
160 51 0.36
161 6 0.04
162 12 0.09
163 45 0.32
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.20
Consensus pattern (160 bp):
AAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAAAGGTGCCACGAAGTCGTGGACTTT
AAAAAAAGTGCCACGAAGTCGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTCGTGGACTTAAA
AGGAACAAAATGCCACGGAGTCGTGGACTT
Found at i:2336102 original size:16 final size:17
Alignment explanation
Indices: 2336071--2336108 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2336061 GATGCAAATA
* *
2336071 ATGATGTTATTGATGTT
1 ATGATGTCATTGATGTC
2336088 ATGATGTCA-TGATGTC
1 ATGATGTCATTGATGTC
2336104 ATGAT
1 ATGAT
2336109 TACAGCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (17 bp):
ATGATGTCATTGATGTC
Found at i:2337277 original size:5 final size:5
Alignment explanation
Indices: 2337267--2337303 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
2337257 TGTGTGTGTT
2337267 TTTTG TTTTG -TTTG TTTT- TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
2337304 TTGTGTTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (5 bp):
TTTTG
Found at i:2337277 original size:18 final size:17
Alignment explanation
Indices: 2337254--2337307 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
2337244 TTTGCACTTT
2337254 TTTTGTGTGTGTTTTTTG
1 TTTTGT-TGTGTTTTTTG
*
2337272 TTTTGTTTGTTTTTTTTG
1 TTTTG-TTGTGTTTTTTG
*
2337290 TTTTGTTTTGTTTTTTG
1 TTTTGTTGTGTTTTTTG
2337307 T
1 T
2337308 GTTTACTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 11 0.34
18 20 0.62
19 1 0.03
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (17 bp):
TTTTGTTGTGTTTTTTG
Found at i:2337282 original size:9 final size:9
Alignment explanation
Indices: 2337254--2337303 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
2337244 TTTGCACTTT
*
2337254 TTTTGTGTG
1 TTTTGTTTG
2337263 TGTTT-TTTG
1 T-TTTGTTTG
2337272 TTTTGTTTG
1 TTTTGTTTG
*
2337281 TTTTTTTTG
1 TTTTGTTTG
2337290 TTTTGTTTTG
1 TTTTG-TTTG
2337300 TTTT
1 TTTT
2337304 TTGTGTTTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 3 0.09
9 21 0.60
10 11 0.31
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (9 bp):
TTTTGTTTG
Found at i:2337288 original size:13 final size:13
Alignment explanation
Indices: 2337251--2337302 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
2337241 GCCTTTGCAC
*
2337251 TTTTTTTGTGTGT
1 TTTTTTTGTTTGT
*
2337264 GTTTTTTGTTTTGT
1 TTTTTTTG-TTTGT
2337278 TTGTTTTT-TTTGT
1 TT-TTTTTGTTTGT
2337291 TTTGTTTTGTTT
1 TTT-TTTTGTTT
2337303 TTTGTGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 1 0.03
13 18 0.56
14 8 0.25
15 5 0.16
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (13 bp):
TTTTTTTGTTTGT
Found at i:2337310 original size:9 final size:9
Alignment explanation
Indices: 2337261--2337311 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
2337251 TTTTTTTGTG
2337261 TGTGTTTTT
1 TGTGTTTTT
2337270 TGT-TTTGTT
1 TGTGTTT-TT
2337279 TGT-TTTTT
1 TGTGTTTTT
2337287 T-TGTTTTGT
1 TGTGTTTT-T
*
2337296 TTTGTTTTT
1 TGTGTTTTT
2337305 TGTGTTT
1 TGTGTTT
2337312 ACTTTTGACT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
7 1 0.03
8 10 0.27
9 20 0.54
10 6 0.16
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (9 bp):
TGTGTTTTT
Found at i:2337317 original size:19 final size:19
Alignment explanation
Indices: 2337277--2337318 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2337267 TTTTGTTTTG
* **
2337277 TTTGTTTTTTTTGTTTTGT
1 TTTGTTTTTTGTGTTTACT
2337296 TTTGTTTTTTGTGTTTACT
1 TTTGTTTTTTGTGTTTACT
2337315 TTTG
1 TTTG
2337319 ACTTTTTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.02, C:0.02, G:0.17, T:0.79
Consensus pattern (19 bp):
TTTGTTTTTTGTGTTTACT
Found at i:2343207 original size:165 final size:164
Alignment explanation
Indices: 2343029--2343666 Score: 636
Period size: 165 Copynumber: 3.9 Consensus size: 164
2343019 GTTTACTAAC
* * * * * * * *
2343029 AATATTAGATGAATCTAAAAAATTTTAAATCAACAAAAGTACCC-CGAAAACATTTACGGAGTAG
1 AATATTTGATGAATTTTAAAAATTTTAAACCAAGAAAAATCCCCTCGAAAACATTTACGGAGAAG
* *
2343093 AAAACTCGGTTTTTTGAAAATAAAGAATTTTAAAGTAAAAAATGAAAAACTTATGAAAATAA-AA
66 AAAACTC-GTATTTTGAAAATAAAGAATTTTAAAG-AAAAAATGAAAAACTCATG-AAATAAGAA
* * *
2343157 AAATTTTTTAAAACTAATTTACTATAAATTAAATGAT
128 AAATTTTTTAAAACTGATTTAATATAAATTAAATAAT
* * *
2343194 GATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCCCCTTCGAAAATATTTACGGAGTA
1 AATATTTGATGAATTTTAAAAATTTTAAACCAAGAAAAATCCCC-TCGAAAACATTTACGGAG-A
*
2343259 A-AAAACTCTGTATTTT-AGAAATATAA-AA-TTT-AAGAAAAAAATGAAAAA-TCCTTGAAATA
64 AGAAAACTC-GTATTTTGA-AAATA-AAGAATTTTAAAG-AAAAAATGAAAAACT-CATGAAATA
* *
2343318 AGAAGAATTTTTTAAAACTGATTTAATGTAAATTAAATAAT
124 AGAAAAATTTTTTAAAACTGATTTAATATAAATTAAATAAT
** *
2343359 AATATTCAATGAATTTGAAAAATTTTAAACCAAGAAAAATCCCCTCGAAAACATTTACGGAGAAG
1 AATATTTGATGAATTTTAAAAATTTTAAACCAAGAAAAATCCCCTCGAAAACATTTACGGAGAAG
* * * * * * *
2343424 -AAACTCCATATTTCGAAAATAAGAAAATTTCAAGGAAAAAAT-AAAAAATCCATGAAATAAGAG
66 AAAACT-CGTATTTTGAAAATAA-AGAATTTTAAAGAAAAAATGAAAAACT-CATGAAATAAGAA
* * * *
2343487 GAATTTTTCAAAACTGATTTAATTTAAAGTAAATAAT
128 AAATTTTTTAAAACTGATTTAATATAAATTAAATAAT
* * * * *
2343524 AATATTTTATGAATTTTAAAAATTTTAAACTAAGAAAAATCCCC-CGAAAATATTTACTGAAAAG
1 AATATTTGATGAATTTTAAAAATTTTAAACCAAGAAAAATCCCCTCGAAAACATTTACGGAGAAG
* * * * * *
2343588 AAAACTTCGTATTTTAGAAACATAAGGGATTTCAAA-AGAAAATCAATAACTCATGAAATAA-AA
66 AAAAC-TCGTATTTT-GAAA-ATAAAGAATTTTAAAGAAAAAATGAAAAACTCATGAAATAAGAA
2343651 GAAATTTTTTAAAACT
128 -AAATTTTTTAAAACT
2343667 TTAAATGATA
Statistics
Matches: 397, Mismatches: 55, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
162 1 0.00
163 18 0.05
164 51 0.13
165 261 0.66
166 23 0.06
167 40 0.10
168 3 0.01
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (164 bp):
AATATTTGATGAATTTTAAAAATTTTAAACCAAGAAAAATCCCCTCGAAAACATTTACGGAGAAG
AAAACTCGTATTTTGAAAATAAAGAATTTTAAAGAAAAAATGAAAAACTCATGAAATAAGAAAAA
TTTTTTAAAACTGATTTAATATAAATTAAATAAT
Found at i:2343647 original size:330 final size:329
Alignment explanation
Indices: 2343029--2343666 Score: 758
Period size: 330 Copynumber: 1.9 Consensus size: 329
2343019 GTTTACTAAC
* * *
2343029 AATATTAGATGAATCTAAAAAATTTTAAATCAACAAAAGTACCCCGAAAACATTTACGGAGTAGA
1 AATATTAGATGAATCTAAAAAATTTTAAACCAACAAAAATACCCCGAAAACATTTACGGAGAAGA
** * * * * * *
2343094 AAACTCGGTTTTTTGAAAATAAAGAATTTTAAAGTAAAAAATGAAAAACTTATGAAAATAAAAAA
66 AAACTCCATATTTCGAAAATAAAGAAATTTAAAGGAAAAAATAAAAAACTCATGAAAATAAAAAA
* * * * *
2343159 ATTTTTTAAAACTAATTTACTATAAATTAAATGATGATATTTGATGAATTTTAAAAATTATAAAC
131 ATTTTTCAAAACTAATTTAATATAAAGTAAATAATAATATTTGATGAATTTTAAAAATTATAAAC
* *
2343224 CAAGAAAAATCCCCTTCGAAAATATTTACGGAGTAAAAAACTCTGTATTTTAGAAATATAAAATT
196 CAAGAAAAATCCCC-TCGAAAATATTTACGGAGAAAAAAACTCTGTATTTTAGAAACATAAAATT
* *
2343289 TAAGAAAAAAATGAAAAATCCTTGAAATAAGAAG-AATTTTTTAAAACTGATTTAATGTAAATTA
260 TAAGAAAAAAATCAAAAATCCATGAAATAA-AAGAAATTTTTTAAAACTGATTTAATGTAAATTA
2343353 AATAAT
324 AATAAT
* * * *
2343359 AATATTCA-ATGAATTTGAAAAATTTTAAACCAAGAAAAATCCCCTCGAAAACATTTACGGAGAA
1 AATATT-AGATGAATCTAAAAAATTTTAAACCAACAAAAATACCC-CGAAAACATTTACGGAGAA
*
2343423 G-AAACTCCATATTTCGAAAAT-AAGAAAATTTCAAGGAAAAAATAAAAAA-TCCATG-AAATAA
64 GAAAACTCCATATTTCGAAAATAAAG-AAATTTAAAGGAAAAAATAAAAAACT-CATGAAAATAA
** * * * *
2343484 GAGGAATTTTTCAAAACTGATTTAATTTAAAGTAAATAATAATATTTTATGAATTTTAAAAATTT
127 -AAAAATTTTTCAAAACTAATTTAATATAAAGTAAATAATAATATTTGATGAATTTTAAAAATTA
* *
2343549 TAAACTAAGAAAAATCCCC-CGAAAATATTTACTGA-AAAGAAAACT-TCGTATTTTAGAAACAT
191 TAAACCAAGAAAAATCCCCTCGAAAATATTTACGGAGAAA-AAAACTCT-GTATTTTAGAAACAT
* * *
2343611 AAGGGATTTCAA-AAGAAAATCAATAA-CTCATGAAATAAAAGAAATTTTTTAAAACT
254 AA--AATTT-AAGAAAAAAATCAAAAATC-CATGAAATAAAAGAAATTTTTTAAAACT
2343667 TTAAATGATA
Statistics
Matches: 260, Mismatches: 36, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
327 3 0.01
328 37 0.14
329 14 0.05
330 184 0.71
331 22 0.08
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (329 bp):
AATATTAGATGAATCTAAAAAATTTTAAACCAACAAAAATACCCCGAAAACATTTACGGAGAAGA
AAACTCCATATTTCGAAAATAAAGAAATTTAAAGGAAAAAATAAAAAACTCATGAAAATAAAAAA
ATTTTTCAAAACTAATTTAATATAAAGTAAATAATAATATTTGATGAATTTTAAAAATTATAAAC
CAAGAAAAATCCCCTCGAAAATATTTACGGAGAAAAAAACTCTGTATTTTAGAAACATAAAATTT
AAGAAAAAAATCAAAAATCCATGAAATAAAAGAAATTTTTTAAAACTGATTTAATGTAAATTAAA
TAAT
Found at i:2346606 original size:32 final size:32
Alignment explanation
Indices: 2346565--2346746 Score: 161
Period size: 32 Copynumber: 5.7 Consensus size: 32
2346555 GAGTAGGGAA
*
2346565 CTTATCAACCTCAATCCTCAAAGAGCAAGACG
1 CTTACCAACCTCAATCCTCAAAGAGCAAGACG
* * **
2346597 CCTACCAACCTCAATCCTCAAAGAGCCAGGTG
1 CTTACCAACCTCAATCCTCAAAGAGCAAGACG
* *
2346629 CTTACCAACCTCAATCCTCAAAGAGCAGGACA
1 CTTACCAACCTCAATCCTCAAAGAGCAAGACG
* * * * * * *
2346661 TTTACTAACCTTC-GTCCTCAAAGAGTAGGGCA
1 CTTACCAACC-TCAATCCTCAAAGAGCAAGACG
* * *
2346693 CTTACTAACCTCAATCCTGAAAAAGCAAGACG
1 CTTACCAACCTCAATCCTCAAAGAGCAAGACG
* *
2346725 -TCTACCTACCTTAATCCTCAAA
1 CT-TACCAACCTCAATCCTCAAA
2346747 AAGTAAAGTG
Statistics
Matches: 119, Mismatches: 28, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
31 3 0.03
32 114 0.96
33 2 0.02
ACGTcount: A:0.35, C:0.32, G:0.13, T:0.21
Consensus pattern (32 bp):
CTTACCAACCTCAATCCTCAAAGAGCAAGACG
Found at i:2346642 original size:64 final size:63
Alignment explanation
Indices: 2346551--2346746 Score: 207
Period size: 64 Copynumber: 3.1 Consensus size: 63
2346541 TTTTAGTCCA
* * *
2346551 CAAAGAGTAGGGAACTTATCAACCTCAATCCTCAAAGAGCAAGACGCCTACCAACCTCAATCCT
1 CAAAGAGCAGGG-ACTTACCAACCTCAATCCTCAAAGAGCAAGACGTCTACCAACCTCAATCCT
* * * * *
2346615 CAAAGAGCCAGGTG-CTTACCAACCTCAATCCTCAAAGAGCAGGACATTTACTAACCTTC-GTCC
1 CAAAGAG-CAGG-GACTTACCAACCTCAATCCTCAAAGAGCAAGACGTCTACCAACC-TCAATCC
2346678 T
63 T
* * * * * *
2346679 CAAAGAGTAGGGCACTTACTAACCTCAATCCTGAAAAAGCAAGACGTCTACCTACCTTAATCCT
1 CAAAGAGCAGGG-ACTTACCAACCTCAATCCTCAAAGAGCAAGACGTCTACCAACCTCAATCCT
2346743 CAAA
1 CAAA
2346747 AAGTAAAGTG
Statistics
Matches: 107, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 96 0.90
65 5 0.05
66 1 0.01
ACGTcount: A:0.36, C:0.30, G:0.14, T:0.20
Consensus pattern (63 bp):
CAAAGAGCAGGGACTTACCAACCTCAATCCTCAAAGAGCAAGACGTCTACCAACCTCAATCCT
Found at i:2347942 original size:166 final size:165
Alignment explanation
Indices: 2347625--2347945 Score: 353
Period size: 166 Copynumber: 1.9 Consensus size: 165
2347615 ATCAATTTTC
* * * * * *
2347625 AATTTTTAAAATTCATCAAATATTATTATTTGATTCATATCAAGTCCGTCTTGAAAAATTAATTC
1 AATTTTTAAAATTCATCAAAAATCATCATTTAATTCATATCAAATCAGTCTTGAAAAATTAATTC
* * * * * *
2347690 ATTTTCATGAGTTTTGAATTTTTTCTTTGAAATTCTCCTTTCCTCGAAAAACTGAGTTTCCTACT
66 ATTTTCATGAGTTTTCAATTTTTTCCTTGAAATCCTCATTT-CTCGAAAAACTAAATTTCCTACT
* ***
2347755 CCGTAAATATTTTTGGGGGGATTTTTCTAAGTTTAT
130 CCGTAAAAATTTCAAGGGGGATTTTTCTAAGTTTAT
* * * * *
2347791 AATTTTTAAAATTCATCAAAAATCATCATTTAATTTATATTAAATCAGTTTTGAAAAATTCATTT
1 AATTTTTAAAATTCATCAAAAATCATCATTTAATTCATATCAAATCAGTCTTGAAAAATTAATTC
* *
2347856 ATTTTCATGAGTTTTTCATTTTTTTCCTTGAAATGCCTCAATTT-TCGAAAAACTAAATTTTCTA
66 ATTTTCATGAG-TTTTCAATTTTTTCCTTGAAAT-CCTC-ATTTCTCGAAAAACTAAATTTCCTA
2347920 -T-C-TAATAAATGTTCAAGGGGGATTTT
128 CTCCGTAA-AAAT-TTCAAGGGGGATTTT
2347946 CTTCGATTTA
Statistics
Matches: 127, Mismatches: 23, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
164 3 0.02
165 4 0.03
166 78 0.61
167 36 0.28
168 3 0.02
169 3 0.02
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (165 bp):
AATTTTTAAAATTCATCAAAAATCATCATTTAATTCATATCAAATCAGTCTTGAAAAATTAATTC
ATTTTCATGAGTTTTCAATTTTTTCCTTGAAATCCTCATTTCTCGAAAAACTAAATTTCCTACTC
CGTAAAAATTTCAAGGGGGATTTTTCTAAGTTTAT
Found at i:2348562 original size:10 final size:10
Alignment explanation
Indices: 2348547--2348582 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 10
2348537 CTCAGCAAAG
2348547 AAAAGAGAAA
1 AAAAGAGAAA
2348557 AAAAGAAAGAAA
1 AAAAG--AGAAA
2348569 AAAAGAGAAA
1 AAAAGAGAAA
2348579 AAAA
1 AAAA
2348583 TAAGAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 14 0.58
12 10 0.42
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAGAGAAA
Found at i:2348569 original size:12 final size:12
Alignment explanation
Indices: 2348552--2348589 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
2348542 CAAAGAAAAG
2348552 AGAAAAAAAGAA
1 AGAAAAAAAGAA
2348564 AGAAAAAAAGAGA
1 AGAAAAAAAGA-A
2348577 A-AAAAATAAGAA
1 AGAAAAA-AAGAA
2348589 A
1 A
2348590 AATAGTGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 18 0.75
13 6 0.25
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (12 bp):
AGAAAAAAAGAA
Found at i:2348575 original size:22 final size:21
Alignment explanation
Indices: 2348547--2348591 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
2348537 CTCAGCAAAG
2348547 AAAAGAGAAAAAAAGAAAGAAA
1 AAAAGAGAAAAAAA-AAAGAAA
*
2348569 AAAAGAGAAAAAAATAAGAAA
1 AAAAGAGAAAAAAAAAAGAAA
2348590 AA
1 AA
2348592 TAGTGAGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (21 bp):
AAAAGAGAAAAAAAAAAGAAA
Found at i:2352217 original size:13 final size:13
Alignment explanation
Indices: 2352199--2352224 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2352189 CAATTTTTTG
2352199 TGTATCGATACAT
1 TGTATCGATACAT
2352212 TGTATCGATACAT
1 TGTATCGATACAT
2352225 ACTTACTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2352952 original size:21 final size:21
Alignment explanation
Indices: 2352911--2352954 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2352901 CTCCCCTTTA
* *
2352911 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
2352932 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
2352953 TC
1 TC
2352955 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:2356860 original size:15 final size:15
Alignment explanation
Indices: 2356840--2356870 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2356830 ATTTCGTTTG
*
2356840 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2356855 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2356870 G
1 G
2356871 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2358703 original size:21 final size:21
Alignment explanation
Indices: 2358674--2358718 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2358664 AAGTTTTCAT
*
2358674 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2358694 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2358716 TTT
1 TTT
2358719 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2360953 original size:13 final size:13
Alignment explanation
Indices: 2360935--2360960 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2360925 CAATTTTTTG
2360935 TGTATCGATACAT
1 TGTATCGATACAT
2360948 TGTATCGATACAT
1 TGTATCGATACAT
2360961 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2364456 original size:13 final size:13
Alignment explanation
Indices: 2364438--2364462 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2364428 TGCCAAAAAA
2364438 TGTATCGATACAT
1 TGTATCGATACAT
2364451 TGTATCGATACA
1 TGTATCGATACA
2364463 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2364529 original size:52 final size:52
Alignment explanation
Indices: 2364471--2364755 Score: 525
Period size: 52 Copynumber: 5.5 Consensus size: 52
2364461 CACTGATCTT
* *
2364471 TGTATCGATACATGCAGGCAAGTTTGCCCAGATGTATCAATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2364523 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2364575 TGTATCGATACATGCAGGCAAGTTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2364627 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2364679 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2364731 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2364756 TCATATTTCG
Statistics
Matches: 228, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 228 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2378581 original size:18 final size:15
Alignment explanation
Indices: 2378560--2378640 Score: 81
Period size: 16 Copynumber: 4.9 Consensus size: 15
2378550 TCCTCCACAA
2378560 AAAAAAAACCAAATAAAC
1 AAAAAAAA--AAA-AAAC
* *
2378578 AAAAAAAAAAAGAAG
1 AAAAAAAAAAAAAAC
2378593 AAAAAAAACAAAAAAC
1 AAAAAAAA-AAAAAAC
2378609 AAAAAAAAAACAAAAAC
1 -AAAAAAAAA-AAAAAC
2378626 AAAAAAAAAACAAAA
1 AAAAAAAAAA-AAAA
2378641 ACAACAACAA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
15 11 0.20
16 22 0.40
17 14 0.25
18 8 0.15
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.01
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:2378583 original size:16 final size:15
Alignment explanation
Indices: 2378561--2378656 Score: 76
Period size: 15 Copynumber: 6.3 Consensus size: 15
2378551 CCTCCACAAA
2378561 AAAAAAACCAAATAAAC
1 AAAAAAA-CAAA-AAAC
*
2378578 AAAAAAA-AAAAGAAGA
1 AAAAAAACAAAA-AA-C
2378594 AAAAAAACAAAAAAC
1 AAAAAAACAAAAAAC
2378609 AAAAAAA-AAACAAA-
1 AAAAAAACAAA-AAAC
*
2378623 AACAAAA-AAAAAAC
1 AAAAAAACAAAAAAC
*
2378637 AAAAACAAC-AACAAC
1 AAAAA-AACAAAAAAC
2378652 AAAAA
1 AAAAA
2378657 GGGTCCGGAT
Statistics
Matches: 67, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.04
14 17 0.25
15 27 0.40
16 9 0.13
17 11 0.16
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.01
Consensus pattern (15 bp):
AAAAAAACAAAAAAC
Found at i:2378601 original size:24 final size:23
Alignment explanation
Indices: 2378558--2378656 Score: 110
Period size: 23 Copynumber: 4.1 Consensus size: 23
2378548 CGTCCTCCAC
*
2378558 AAAAAAAAAACCAAATAAACAAAAA
1 AAAAAAAAAAAC-AA-AAACAAAAA
2378583 AAAAAAGAAGAAA-AAAAACAAAAA
1 AAAAAA-AA-AAACAAAAACAAAAA
2378607 ACAAAAAAAAAACAAAAACAAAAA
1 A-AAAAAAAAAACAAAAACAAAAA
* * *
2378631 AAAAACAAAAACAACAACAACAA
1 AAAAAAAAAAACAAAAACAAAAA
2378654 AAA
1 AAA
2378657 GGGTCCGGAT
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
23 25 0.38
24 24 0.36
25 13 0.20
26 2 0.03
27 2 0.03
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.01
Consensus pattern (23 bp):
AAAAAAAAAAACAAAAACAAAAA
Found at i:2378616 original size:17 final size:17
Alignment explanation
Indices: 2378559--2378641 Score: 84
Period size: 18 Copynumber: 4.9 Consensus size: 17
2378549 GTCCTCCACA
2378559 AAAAAAAAACCAAATAAAC
1 AAAAAAAAA-CAAA-AAAC
*
2378578 -AAAAAAAA-AAAGAA-
1 AAAAAAAAACAAAAAAC
*
2378592 GAAAAAAAACAAAAAAC
1 AAAAAAAAACAAAAAAC
2378609 AAAAAAAAA-ACAAAAAC
1 AAAAAAAAACA-AAAAAC
2378626 AAAAAAAAAACAAAAA
1 -AAAAAAAAACAAAAA
2378642 CAACAACAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
15 10 0.18
16 9 0.16
17 14 0.25
18 21 0.38
19 1 0.02
ACGTcount: A:0.87, C:0.10, G:0.02, T:0.01
Consensus pattern (17 bp):
AAAAAAAAACAAAAAAC
Found at i:2378642 original size:17 final size:17
Alignment explanation
Indices: 2378556--2378644 Score: 110
Period size: 17 Copynumber: 5.2 Consensus size: 17
2378546 GGCGTCCTCC
*
2378556 ACAAAAAAAAAAC-CAA
1 ACAAAAAAAAAACAAAA
* *
2378572 ATAAACAAAAAA-AAAA
1 ACAAAAAAAAAACAAAA
*
2378588 AGAAGAAAAAAAACAAAAA
1 ACAA-AAAAAAAAC-AAAA
2378607 ACAAAAAAAAAACAAAA
1 ACAAAAAAAAAACAAAA
2378624 ACAAAAAAAAAACAAAA
1 ACAAAAAAAAAACAAAA
2378641 ACAA
1 ACAA
2378645 CAACAACAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
16 15 0.24
17 32 0.51
18 9 0.14
19 7 0.11
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.01
Consensus pattern (17 bp):
ACAAAAAAAAAACAAAA
Found at i:2378652 original size:9 final size:9
Alignment explanation
Indices: 2378593--2378653 Score: 63
Period size: 9 Copynumber: 6.9 Consensus size: 9
2378583 AAAAAAGAAG
*
2378593 AAAAAAAAC
1 AAAAACAAC
2378602 AAAAAACAA-
1 -AAAAACAAC
*
2378611 AAAAAAAAC
1 AAAAACAAC
2378620 AAAAACAA-
1 AAAAACAAC
*
2378628 AAAAAAAAC
1 AAAAACAAC
2378637 AAAAACAAC
1 AAAAACAAC
*
2378646 AACAACAA
1 AAAAACAA
2378654 AAAGGGTCCG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
8 14 0.33
9 22 0.51
10 7 0.16
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAACAAC
Found at i:2378656 original size:1 final size:1
Alignment explanation
Indices: 2378558--2378641 Score: 69
Period size: 1 Copynumber: 84.0 Consensus size: 1
2378548 CGTCCTCCAC
** * * * * * * *
2378558 AAAAAAAAAACCAAATAAACAAAAAAAAAAAGAAGAAAAAAAACAAAAAACAAAAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2378623 AACAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAA
2378642 CAACAACAAC
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.87, C:0.10, G:0.02, T:0.01
Consensus pattern (1 bp):
A
Found at i:2380131 original size:29 final size:29
Alignment explanation
Indices: 2380090--2380402 Score: 421
Period size: 29 Copynumber: 10.7 Consensus size: 29
2380080 TCACCCTTCA
*
2380090 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
* * * *
2380119 AAAGCCCATAAGTCAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
*
2380147 AAAGCCCACAAGTCAGTGGCATATTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
* *
2380176 AAAGCCCACAAGTCAGTGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
* *
2380205 AAAGCCCACAAGTTAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
* * *
2380235 AAAGCCCACAAGTTAGTGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
*
2380264 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
2380294 AAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
*
2380323 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
* * * *
2380353 AAAGCCCACAAGTCAATGGTATCTCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCC
2380382 AAAGCCCACAAGTCAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
2380403 ACCTTCAAAA
Statistics
Matches: 247, Mismatches: 33, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
28 22 0.09
29 146 0.59
30 79 0.32
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTCC
Found at i:2380253 original size:59 final size:59
Alignment explanation
Indices: 2380086--2380407 Score: 488
Period size: 59 Copynumber: 5.5 Consensus size: 59
2380076 TTCCTCACCC
* * * * * *
2380086 TTCAAAAGCCCACAAGTCAGTGGCA-TCTTTTTCAAAGCCCATAAGTCAGTGGCAAC-C
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTT
**
2380143 TTCAAAAGCCCACAAGTCAGTGGCA-TATTTTCCAAAGCCCACAAGTCAGTGGTATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTT
* *
2380201 TTCAAAAGCCCACAAGTTAGTGGCACCCTTTTCCAAAGCCCACAAGTTAGTGGTATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTT
*
2380260 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTT
* * *
2380319 TTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAATGGTATCTC
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTT
*
2380378 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
2380408 CAAAAGCACA
Statistics
Matches: 244, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
57 51 0.21
58 24 0.10
59 169 0.69
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (59 bp):
TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTT
Found at i:2380448 original size:29 final size:29
Alignment explanation
Indices: 2380081--2380448 Score: 325
Period size: 29 Copynumber: 12.7 Consensus size: 29
2380071 AGATATTCCT
*
2380081 CACCC-TTCAAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAAGCCCACAAGTTAGTGG
** * *
2380109 CATCTTTTTC-AAAGCCCATAAGTCAGTGG
1 CA-CCCTTTCAAAAGCCCACAAGTTAGTGG
* *
2380138 CAACC-TTCAAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAAGCCCACAAGTTAGTGG
*** * *
2380166 CATATTTTCCAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAAGCCCACAAGTTAGTGG
* * *
2380195 TATCTTTTCAAAAGCCCACAAGTTAGTGG
1 CACCCTTTCAAAAGCCCACAAGTTAGTGG
*
2380224 CACCCTTTTCCAAAGCCCACAAGTTAGTGG
1 CACCC-TTTCAAAAGCCCACAAGTTAGTGG
* * * *
2380254 TATCTTTTCAAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAAGCCCACAAGTTAGTGG
* *
2380283 CACCCTTTTCCAAAGCCCACAAGTCAGTGG
1 CACCC-TTTCAAAAGCCCACAAGTTAGTGG
* * * *
2380313 CATCTTTTCCAAAGCCCACAAGTCAGTGG
1 CACCCTTTCAAAAGCCCACAAGTTAGTGG
* * *
2380342 CACCCTTTTCCAAAGCCCACAAGTCAATGG
1 CACCC-TTTCAAAAGCCCACAAGTTAGTGG
* * *
2380372 TA-TCTCTTCAAAAGCCCACAAGTCAGTGG
1 CACCCT-TTCAAAAGCCCACAAGTTAGTGG
* * *
2380401 CAACC-TTCAAAAGCACACAAGTTGGT-G
1 CACCCTTTCAAAAGCCCACAAGTTAGTGG
2380428 CAACCCTTTCAAAAGCCCACA
1 C-ACCCTTTCAAAAGCCCACA
2380449 CAAGTTGGTG
Statistics
Matches: 285, Mismatches: 44, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
27 5 0.02
28 44 0.15
29 157 0.55
30 79 0.28
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (29 bp):
CACCCTTTCAAAAGCCCACAAGTTAGTGG
Found at i:2380452 original size:31 final size:28
Alignment explanation
Indices: 2380377--2380458 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
2380367 AATGGTATCT
**
2380377 CTTCAAAAGCC-CACAAGTCAGTGGCAAC
1 CTTCAAAAGCCACACAAGTTGGT-GCAAC
2380405 CTTCAAAAG-CACACAAGTTGGTGCAACC
1 CTTCAAAAGCCACACAAGTTGGTGCAA-C
2380433 CTTTCAAAAGCCCACACAAGTTGGTG
1 C-TTCAAAAG-CCACACAAGTTGGTG
2380459 GCATCTTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.11
28 20 0.43
29 8 0.17
31 14 0.30
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.18
Consensus pattern (28 bp):
CTTCAAAAGCCACACAAGTTGGTGCAAC
Found at i:2380461 original size:118 final size:115
Alignment explanation
Indices: 2380081--2380448 Score: 463
Period size: 118 Copynumber: 3.2 Consensus size: 115
2380071 AGATATTCCT
* * * * *
2380081 CACCC-TTCAAAAGCCCACAAGTCAGTGGCA-TCTTTTTCAAAGCCCATAAGTCAGTGGCAAC-C
1 CACCCTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTC
**
2380143 TTCAAAAGCCCACAAGTCAGTGGCATATTTTCCAAAGCCCACAAGTCAGTGG
66 TTCAAAAGCCCACAAGTCAGTGGCA-ACCTTCCAAAGCCCACAAGTCAGT-G
* * * * * *
2380195 TATCTTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTTCCAAAGCCCACAAGTTAGTGGTATCTT
1 CACCCTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTC
*
2380260 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGG
66 TTCAAAAGCCCACAAGTCAGTGGCAACC--TTCCAAAGCCCACAAGTCAGT-G
* * * *
2380313 CATCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAATGGTATCTC
1 CACCCTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTC
* * **
2380378 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCACACAAGTTGGTG
66 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCCAAAGCCCACAAGTCAGTG
2380428 CAACCCTTTCAAAAGCCCACA
1 C-ACCCTTTCAAAAGCCCACA
2380449 CAAGTTGGTG
Statistics
Matches: 220, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
114 2 0.01
115 26 0.12
116 58 0.26
117 25 0.11
118 109 0.50
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (115 bp):
CACCCTTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGTATCTC
TTCAAAAGCCCACAAGTCAGTGGCAACCTTCCAAAGCCCACAAGTCAGTG
Found at i:2380522 original size:43 final size:43
Alignment explanation
Indices: 2380470--2380832 Score: 438
Period size: 43 Copynumber: 8.0 Consensus size: 43
2380460 CATCTTCTTC
*
2380470 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
2380513 TAAGTCCAATATAGCTGGCCTTGAGTCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
* *
2380562 TAAGTCCAATGTAGCTGGCCTTGAATCAGTACATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
2380605 TAAGTCCAATATAGCTAGCCTTGAGTCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
* *
2380654 TAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
2380697 CAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
*
2380746 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
*
2380789 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
2380832 T
1 T
2380833 TCCATCTTTA
Statistics
Matches: 278, Mismatches: 24, Indels: 36
0.82 0.07 0.11
Matches are distributed among these distances:
43 156 0.56
45 3 0.01
47 3 0.01
49 116 0.42
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (43 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT
Found at i:2380627 original size:92 final size:92
Alignment explanation
Indices: 2380465--2380885 Score: 698
Period size: 92 Copynumber: 4.5 Consensus size: 92
2380455 GGTGGCATCT
* *
2380465 TCTTCTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTG
1 TCTT-TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTG
*
2380530 GCCTTGAGTCAGCATATTGGCACCTTCA
65 GCCTTGAATCAGCATATTGGCACCTTCA
* *
2380558 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGTACATTGGCACCTTTAAGTCCAATATAGCTAG
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
*
2380623 CCTTGAGTCAGCATATTGGCACCTTCA
66 CCTTGAATCAGCATATTGGCACCTTCA
* *
2380650 TCTTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACCTTCAAGTCCAATATAGCTGG
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
*
2380715 CCTTGAATCAGCATATTGGCACCTTCT
66 CCTTGAATCAGCATATTGGCACCTTCA
2380742 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
2380807 CCTTGAATCAGCATATTGGCACCTTTTCCA
66 CCTTGAATCAGCATATTGGCACC--TT-CA
* *
2380837 TCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTT
2380886 TTCTCATCTT
Statistics
Matches: 309, Mismatches: 15, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
92 256 0.83
93 4 0.01
94 2 0.01
95 42 0.14
96 5 0.02
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGG
CCTTGAATCAGCATATTGGCACCTTCA
Found at i:2380864 original size:52 final size:55
Alignment explanation
Indices: 2380786--2380896 Score: 165
Period size: 52 Copynumber: 2.1 Consensus size: 55
2380776 ACATTGGCAC
* *
2380786 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* *
2380838 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
2380893 CTTT
1 CTTT
2380897 GAACCCAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
52 38 0.73
53 2 0.04
54 5 0.10
55 7 0.13
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:2384436 original size:52 final size:52
Alignment explanation
Indices: 2384358--2384487 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
2384348 CGAAATATGA
* *
2384358 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTAGGC
*
2384410 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTAGGC
*
2384462 AAACTTGCCTGCATGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACAT
2384488 CTGGGCAAAC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTAGGC
Found at i:2384483 original size:32 final size:32
Alignment explanation
Indices: 2384442--2384519 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
2384432 ACATTTTATA
2384442 ATGTATCGATACATCTAGGCAAACTTGCCTGC
1 ATGTATCGATACATCTAGGCAAACTTGCCTGC
*
2384474 ATGTATCGATACATCTGGGCAAACTTGCCTGC
1 ATGTATCGATACATCTAGGCAAACTTGCCTGC
2384506 ATGTATCGATACAT
1 ATGTATCGATACAT
2384520 TTTATAGTGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACATCTAGGCAAACTTGCCTGC
Found at i:2384532 original size:84 final size:84
Alignment explanation
Indices: 2384391--2384571 Score: 335
Period size: 84 Copynumber: 2.2 Consensus size: 84
2384381 CATTTCATAG
*
2384391 TGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACAT
1 TGTATCGATACATCTGGGCAAACTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACAT
2384456 CTAGGCAAACTTGCCTGCA
66 CTAGGCAAACTTGCCTGCA
*
2384475 TGTATCGATACATCTGGGCAAACTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACAT
1 TGTATCGATACATCTGGGCAAACTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACAT
*
2384540 CTGGGCAAACTTGCCTGCA
66 CTAGGCAAACTTGCCTGCA
2384559 TGTATCGATACAT
1 TGTATCGATACAT
2384572 TTTATAGTGT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 94 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (84 bp):
TGTATCGATACATCTGGGCAAACTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACAT
CTAGGCAAACTTGCCTGCA
Found at i:2384606 original size:136 final size:136
Alignment explanation
Indices: 2384362--2384622 Score: 477
Period size: 136 Copynumber: 1.9 Consensus size: 136
2384352 ATATGAAAAT
*
2384362 TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTA
1 TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAACTTGCCTGCATGTA
2384427 TCGATACATTTTATAATGTATCGATACATCTAGGCAAACTTGCCTGCATGTATCGATACATCTGG
66 TCGATACATTTTATAATGTATCGATACATCTAGGCAAACTTGCCTGCATGTATCGATACATCTGG
2384492 GCAAAC
131 GCAAAC
*
2384498 TTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAACTTGCCTGCATGTA
1 TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAACTTGCCTGCATGTA
* * *
2384563 TCGATACATTTTATAGTGTATCGATACATCTGGGCAAACTTGCCTGTATGTATCGATACA
66 TCGATACATTTTATAATGTATCGATACATCTAGGCAAACTTGCCTGCATGTATCGATACA
2384623 AAGATCAGTG
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
136 120 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (136 bp):
TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAACTTGCCTGCATGTA
TCGATACATTTTATAATGTATCGATACATCTAGGCAAACTTGCCTGCATGTATCGATACATCTGG
GCAAAC
Found at i:2384642 original size:52 final size:52
Alignment explanation
Indices: 2384475--2384622 Score: 287
Period size: 52 Copynumber: 2.8 Consensus size: 52
2384465 CTTGCCTGCA
2384475 TGTATCGATACATCTGGGCAAACTTGCCTGCATGTATCGATACATTTTATAG
1 TGTATCGATACATCTGGGCAAACTTGCCTGCATGTATCGATACATTTTATAG
2384527 TGTATCGATACATCTGGGCAAACTTGCCTGCATGTATCGATACATTTTATAG
1 TGTATCGATACATCTGGGCAAACTTGCCTGCATGTATCGATACATTTTATAG
*
2384579 TGTATCGATACATCTGGGCAAACTTGCCTGTATGTATCGATACA
1 TGTATCGATACATCTGGGCAAACTTGCCTGCATGTATCGATACA
2384623 AAGATCAGTG
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 95 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (52 bp):
TGTATCGATACATCTGGGCAAACTTGCCTGCATGTATCGATACATTTTATAG
Found at i:2384649 original size:13 final size:13
Alignment explanation
Indices: 2384631--2384655 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2384621 CAAAGATCAG
2384631 TGTATCGATACAA
1 TGTATCGATACAA
2384644 TGTATCGATACA
1 TGTATCGATACA
2384656 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2384730 original size:32 final size:32
Alignment explanation
Indices: 2384693--2384793 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
2384683 GGTAGTAGCT
* *
2384693 TACATTGTTTTGATACAAAACTTATGTATCGA
1 TACATTGTATTGATACAACACTTATGTATCGA
2384725 TACATTGTATTGATACAACACTTATGTATCGA
1 TACATTGTATTGATACAACACTTATGTATCGA
*
2384757 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATTGATACAACAC-TTATGTATCGA
2384790 TACA
1 TACA
2384794 AATCGTTGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 50 0.77
33 15 0.23
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (32 bp):
TACATTGTATTGATACAACACTTATGTATCGA
Found at i:2384739 original size:13 final size:13
Alignment explanation
Indices: 2384717--2384773 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
2384707 ACAAAACTTA
2384717 TGTATCGATACAT
1 TGTATCGATACAT
*
2384730 TGTATTGATACAACACTT
1 TGTATCGAT---ACA--T
2384748 ATGTATCGATACAT
1 -TGTATCGATACAT
2384762 TGTATCGATACA
1 TGTATCGATACA
2384774 ACACTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
14 1 0.03
16 6 0.17
18 1 0.03
19 8 0.22
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2387195 original size:21 final size:21
Alignment explanation
Indices: 2387171--2387222 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
2387161 TCACTTCATT
2387171 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
2387192 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
2387213 TCTTTTTGTC
1 TCTTTTTGTC
2387223 TAACTCACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.10, C:0.23, G:0.12, T:0.56
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:2389347 original size:27 final size:27
Alignment explanation
Indices: 2389281--2389350 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
2389271 TTTGGTTGAA
* * *
2389281 AATGGGGATGGAATGTCCTTTCGAAGG
1 AATGGGGTTGGAGTGTCCCTTCGAAGG
*
2389308 AATGGGGTTGGAGTGTCCCTTCGGAGG
1 AATGGGGTTGGAGTGTCCCTTCGAAGG
2389335 AATGGGGTTGGAGTGT
1 AATGGGGTTGGAGTGT
2389351 GCCCGATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.20, C:0.10, G:0.43, T:0.27
Consensus pattern (27 bp):
AATGGGGTTGGAGTGTCCCTTCGAAGG
Found at i:2391575 original size:13 final size:13
Alignment explanation
Indices: 2391557--2391617 Score: 62
Period size: 13 Copynumber: 5.2 Consensus size: 13
2391547 ATACAAAGAT
2391557 CAATGTATCGATA
1 CAATGTATCGATA
2391570 CAATGTATCGATA
1 CAATGTATCGATA
*
2391583 C-AT-T-TAG-T-
1 CAATGTATCGATA
*
2391591 -AATGTATCAATA
1 CAATGTATCGATA
2391603 CAATGTATCGATA
1 CAATGTATCGATA
2391616 CA
1 CA
2391618 TTTCCTTGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
8 2 0.05
9 2 0.05
10 3 0.08
11 2 0.05
12 2 0.05
13 27 0.71
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2391580 original size:33 final size:32
Alignment explanation
Indices: 2391538--2391618 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 32
2391528 AAAATTCCCA
*
2391538 AATGTATCGATACA-AAGATCAATGTATCGATAC
1 AATGTATCGATACATAAG-T-AATGTATCAATAC
*
2391571 AATGTATCGATACATTTAGTAATGTATCAATAC
1 AATGTATCGATACA-TAAGTAATGTATCAATAC
2391604 AATGTATCGATACAT
1 AATGTATCGATACAT
2391619 TTCCTTGCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
32 1 0.02
33 40 0.91
34 1 0.02
35 2 0.05
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (32 bp):
AATGTATCGATACATAAGTAATGTATCAATAC
Found at i:2391619 original size:33 final size:33
Alignment explanation
Indices: 2391558--2391620 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
2391548 TACAAAGATC
*
2391558 AATGTATCGATACAATGTATCGATACATTTAGT
1 AATGTATCAATACAATGTATCGATACATTTAGT
2391591 AATGTATCAATACAATGTATCGATACATTT
1 AATGTATCAATACAATGTATCGATACATTT
2391621 CCTTGCCAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (33 bp):
AATGTATCAATACAATGTATCGATACATTTAGT
Found at i:2391673 original size:19 final size:21
Alignment explanation
Indices: 2391649--2391701 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
2391639 AGCGATACAT
2391649 TGTATCGATACAA-CACT-TA
1 TGTATCGATACAATCACTCTA
* *
2391668 TGTATCGATACAATTACTCTT
1 TGTATCGATACAATCACTCTA
2391689 TGTATCGATACAA
1 TGTATCGATACAA
2391702 ATTGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (21 bp):
TGTATCGATACAATCACTCTA
Found at i:2393426 original size:49 final size:49
Alignment explanation
Indices: 2393232--2393713 Score: 437
Period size: 49 Copynumber: 10.0 Consensus size: 49
2393222 ATACGCGGCT
* ** * * *
2393232 AGCGATATTGGGCTCGAAGATGCAAAGAATGACAATGTGCTGATTCATGGCC
1 AGCGATATTGGACTTAAAGATG--AAG-ATGCCAATATGCTGATTCAAGGCC
* * * *
2393284 AGCGACATTAGACTT---GAGGAAGAATGCCAATGTGCTAAGA-T-AAGGCC
1 AGCGATATTGGACTTAAAGATGAAG-ATGCCAATATGCT--GATTCAAGGCC
2393331 AGCGATATTAGG-CTT-AAGAATGTTAAAGATGCCAATATGCTGATTCAAGGCCC
1 AGCGATATT-GGACTTAAAG-ATG---AAGATGCCAATATGCTGATTCAAGG-CC
* * * *
2393384 A-CGATATTGGACTTAAATATGAAGATACCAATGTACTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* *
2393432 GGCGACATTGGACTT-AA-A-G--G-TGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
*
2393475 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* *
2393524 AGCGACATTGGACTT-AA-A-G--G-TGCCAATATGCTGATTCAAAGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* * *
2393567 AGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGAC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* * * * * *
2393616 GGCGACATTGGTCTTAAAGATGAAGGTGTCAATATGGTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* * *
2393665 AGCAATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
2393714 GACGACATTA
Statistics
Matches: 359, Mismatches: 44, Indels: 57
0.78 0.10 0.12
Matches are distributed among these distances:
43 68 0.19
44 6 0.02
45 2 0.01
46 4 0.01
47 34 0.09
48 10 0.03
49 180 0.50
50 4 0.01
51 3 0.01
52 40 0.11
53 8 0.02
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (49 bp):
AGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
Found at i:2393515 original size:92 final size:92
Alignment explanation
Indices: 2393353--2393722 Score: 544
Period size: 92 Copynumber: 4.0 Consensus size: 92
2393343 CTTAAGAATG
* * *
2393353 TTAAAGATGCCAATATGCTGATTCAAGGCCCA-CGATATTGGACTTAAATATGAAGATACCAATG
1 TTAAAGGTGCCAATATGCTGATTCAAGG-CCAGCGATATTGGACTTAAAGATGAAGATGCCAATG
*
2393417 TACTGATTCAAGGCCGGCGACATTGGAC
65 TGCTGATTCAAGGCCGGCGACATTGGAC
2393445 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
*
2393510 GCTGATTCAAGGCCAGCGACATTGGAC
66 GCTGATTCAAGGCCGGCGACATTGGAC
* *
2393537 TTAAAGGTGCCAATATGCTGATTCAAAGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
* *
2393602 GCTGATTCAAGGACGGCGACATTGGTC
66 GCTGATTCAAGGCCGGCGACATTGGAC
* * * *
2393629 TTAAAGATGAAGGTGTCAATATGGTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGGTGC
1 TT----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGC
*
2393694 CAATGTGCTGATTCAAGGCCGACGACATT
60 CAATGTGCTGATTCAAGGCCGGCGACATT
2393723 AGGCTCGTGC
Statistics
Matches: 255, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
91 3 0.01
92 172 0.67
96 1 0.00
98 79 0.31
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
GCTGATTCAAGGCCGGCGACATTGGAC
Found at i:2393534 original size:141 final size:140
Alignment explanation
Indices: 2393264--2393722 Score: 472
Period size: 141 Copynumber: 3.2 Consensus size: 140
2393254 CAAAGAATGA
* * * *
2393264 CAATGTGCTGATTCATGGCCAGCGACATTAGACTTGAGGAAGAATGCCAATGTGCTAAGA-T-AA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTT-AAGAAG-GTGCCAATGTGCT--GATTCAA
2393327 GGCCAGCGATATTAGGCTT-AAGAATGTTAAAGATGCCAATATGCTGATTCAAGGCCCA-CGATA
62 GGCCAGCGATATT-GGCTTAAAG-ATG---AAGATGCCAATATGCTGATTCAAGG-CCAGCGATA
*
2393390 TTGGACTTAAATATGAAGATAC
121 TTGGACTTAAA-ATGAAG-TGC
* * *
2393412 CAATGTACTGATTCAAGGCCGGCGACATTGGACTT-A-AAGGTGCCAATATGCTGATTCAAGGCC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGAAGGTGCCAATGTGCTGATTCAAGGCC
* *
2393475 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT-
66 AGCGATATTGG-CTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
2393539 AAA-G--GTGC
130 AAATGAAGTGC
* * *
2393547 CAATATGCTGATTCAAAGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTT--A-A-GAAGGTGCCAATGTGCTGATTCAA
* * * * * * *
2393612 GGACGGCGACATTGGTCTTAAAGATGAAGGTGTCAATATGGTGATTCAAGGCCAGCAATATTGGA
62 GGCCAGCGATATTGG-CTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
2393677 CTTAAAGATGAAGGTGC
126 CTTAAA-ATGAA-GTGC
2393694 CAATGTGCTGATTCAAGGCC-GACGACATT
1 CAATGTGCTGATTCAAGGCCAG-CGACATT
2393723 AGGCTCGTGC
Statistics
Matches: 264, Mismatches: 29, Indels: 37
0.80 0.09 0.11
Matches are distributed among these distances:
135 32 0.12
136 1 0.00
138 1 0.00
139 2 0.01
140 5 0.02
141 116 0.44
142 4 0.02
143 4 0.02
144 33 0.12
145 6 0.02
146 1 0.00
147 28 0.11
148 31 0.12
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (140 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAGAAGGTGCCAATGTGCTGATTCAAGGCC
AGCGATATTGGCTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
AATGAAGTGC
Found at i:2393858 original size:34 final size:34
Alignment explanation
Indices: 2393818--2393925 Score: 114
Period size: 34 Copynumber: 3.2 Consensus size: 34
2393808 TAGGCTTAAA
* *
2393818 GGTGCCACAGAGTTGTGGACTT-ATAGAAAAAAG
1 GGTGCCACAGAGGTGTGGACTTAAAAGAAAAAAG
* **
2393851 GGATGCCACAGAGGTGTGGGCTTAAAAGGGAAAAG
1 GG-TGCCACAGAGGTGTGGACTTAAAAGAAAAAAG
** *
2393886 GGTGCCACAGAGGCATGGACTTAAAA-AGAAAA-
1 GGTGCCACAGAGGTGTGGACTTAAAAGAAAAAAG
2393918 GGTGCCAC
1 GGTGCCAC
2393926 GAAGTTGTAG
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
32 8 0.12
33 7 0.11
34 39 0.61
35 10 0.16
ACGTcount: A:0.36, C:0.15, G:0.33, T:0.16
Consensus pattern (34 bp):
GGTGCCACAGAGGTGTGGACTTAAAAGAAAAAAG
Found at i:2393959 original size:35 final size:33
Alignment explanation
Indices: 2393906--2393975 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 33
2393896 AGGCATGGAC
* *
2393906 TTAAAAAGAAAAGGTGCCACGAAGTTGTAGGCT
1 TTAAAAAGAAAAGATGCCACGAACTTGTAGGCT
* *
2393939 TTAAAAAGGAAAAAGATGCCACGGACTTGTGGGCT
1 TTAAAAA-G-AAAAGATGCCACGAACTTGTAGGCT
2393974 TT
1 TT
2393976 TGAAGGTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 7 0.23
34 1 0.03
35 23 0.74
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (33 bp):
TTAAAAAGAAAAGATGCCACGAACTTGTAGGCT
Found at i:2393995 original size:28 final size:28
Alignment explanation
Indices: 2393953--2394096 Score: 162
Period size: 28 Copynumber: 5.0 Consensus size: 28
2393943 AAAGGAAAAA
*
2393953 GATGCCACGGACTTGTGGGCTTTTGAAG
1 GATGCCACTGACTTGTGGGCTTTTGAAG
*
2393981 GTTGCCACTGACTTGTGGGCTTTTGAAG
1 GATGCCACTGACTTGTGGGCTTTTGAAG
* *
2394009 AAGATGCCACTGAATTATGGGCTTTTGAAG
1 --GATGCCACTGACTTGTGGGCTTTTGAAG
* * * * *
2394039 GTTGCGATTGACTTGTGGGCTTTGGAAAA
1 GATGCCACTGACTTGTGGGCTTTTG-AAG
* *
2394068 GATGCTACTAACTTGTGGGCTTTTGAAG
1 GATGCCACTGACTTGTGGGCTTTTGAAG
2394096 G
1 G
2394097 GTGAGGAATG
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
28 48 0.51
29 22 0.23
30 25 0.26
ACGTcount: A:0.21, C:0.15, G:0.32, T:0.33
Consensus pattern (28 bp):
GATGCCACTGACTTGTGGGCTTTTGAAG
Found at i:2394030 original size:58 final size:57
Alignment explanation
Indices: 2393949--2394096 Score: 208
Period size: 58 Copynumber: 2.6 Consensus size: 57
2393939 TTAAAAAGGA
* * *
2393949 AAAAGATGCCACGGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAAGATGCCACTGAATTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGG
* * *
2394006 AAGAAGATGCCACTGAATTATGGGCTTTTGAAGGTTGCGATTGACTTGTGGGCTTTGG
1 AA-AAGATGCCACTGAATTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGG
*
2394064 AAAAGATGCTACT-AACTTGTGGGCTTTTGAAGG
1 AAAAGATGCCACTGAA-TTGTGGGCTTTTGAAGG
2394097 GTGAGGAATG
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
56 2 0.02
57 28 0.35
58 51 0.63
ACGTcount: A:0.23, C:0.14, G:0.31, T:0.32
Consensus pattern (57 bp):
AAAAGATGCCACTGAATTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGG
Found at i:2395551 original size:8 final size:8
Alignment explanation
Indices: 2395527--2395558 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
2395517 TCCAGACCTT
2395527 TTTTTTTG
1 TTTTTTTG
2395535 TTTTGTTTG
1 TTTT-TTTG
2395544 TTTTTTTG
1 TTTTTTTG
2395552 TTTTTTT
1 TTTTTTT
2395559 TTGTGGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:2395559 original size:9 final size:9
Alignment explanation
Indices: 2395526--2395559 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2395516 ATCCAGACCT
2395526 TTTTTTTTG
1 TTTTTTTTG
*
2395535 TTTTGTTTG
1 TTTTTTTTG
2395544 -TTTTTTTG
1 TTTTTTTTG
2395552 TTTTTTTT
1 TTTTTTTT
2395560 TGTGGAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:2409478 original size:20 final size:20
Alignment explanation
Indices: 2409413--2409480 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 20
2409403 ATTTGCCTGC
*
2409413 ATGTATCGATGCATTGAATA
1 ATGTATCGATACATTGAATA
*
2409433 ATTTATCGATAC----AAT-
1 ATGTATCGATACATTGAATA
*
2409448 A--TATTGATACATTGAATA
1 ATGTATCGATACATTGAATA
2409466 ATGTATCGATACATT
1 ATGTATCGATACATT
2409481 TCCTTGGCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
13 8 0.22
15 1 0.03
16 3 0.08
17 3 0.08
18 1 0.03
20 21 0.57
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:2409651 original size:12 final size:12
Alignment explanation
Indices: 2409634--2409658 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2409624 TACATTCTAG
2409634 AAATGTATCGAT
1 AAATGTATCGAT
2409646 AAATGTATCGAT
1 AAATGTATCGAT
2409658 A
1 A
2409659 CATTTGGACA
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (12 bp):
AAATGTATCGAT
Found at i:2410166 original size:51 final size:51
Alignment explanation
Indices: 2410095--2410207 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 51
2410085 GAAATGATGG
* * * * *
2410095 GGTTAGAGTACCCCCAATGGTGAAAAATCGATATTTTGGAAATAAAAACAA
1 GGTTGGAGTATCCCCAATGGTGAAAAATCGATAATTTGAAAAAAAAAACAA
* *
2410146 GGTTGGAGTATCCCCGATGGTGAAAAATCGATAATTTGAAAAAAAAAACGA
1 GGTTGGAGTATCCCCAATGGTGAAAAATCGATAATTTGAAAAAAAAAACAA
*
2410197 GGTGGGAGTAT
1 GGTTGGAGTAT
2410208 TCCCTCAGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.23
Consensus pattern (51 bp):
GGTTGGAGTATCCCCAATGGTGAAAAATCGATAATTTGAAAAAAAAAACAA
Found at i:2416061 original size:40 final size:41
Alignment explanation
Indices: 2415995--2416117 Score: 148
Period size: 40 Copynumber: 3.1 Consensus size: 41
2415985 AGTCACATTT
* *
2415995 TTACCCAGATGTATCGATA-ATTTTTCAATGTATCGATATA
1 TTACCTAGATGTATCGATACATTTTTCAATGTATCGATACA
* *
2416035 TTACCTAGATG-ATCGATACATCTTTCAATGTATCAATACA
1 TTACCTAGATGTATCGATACATTTTTCAATGTATCGATACA
*
2416075 TGTA--T-GAATGTATTGATACATTTTTCAATGTATCGATACA
1 T-TACCTAG-ATGTATCGATACATTTTTCAATGTATCGATACA
2416115 TTA
1 TTA
2416118 TGTCCTTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
38 1 0.01
39 13 0.18
40 56 0.78
41 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (41 bp):
TTACCTAGATGTATCGATACATTTTTCAATGTATCGATACA
Found at i:2416116 original size:20 final size:20
Alignment explanation
Indices: 2416003--2416116 Score: 108
Period size: 20 Copynumber: 5.8 Consensus size: 20
2415993 TTTTACCCAG
2416003 ATGTATCGATA-ATTTTTCA
1 ATGTATCGATACATTTTTCA
* **
2416022 ATGTATCGATATA-TTACCTA
1 ATGTATCGATACATTTTTC-A
*
2416042 GATG-ATCGATACATCTTTCA
1 -ATGTATCGATACATTTTTCA
* * * *
2416062 ATGTATCAATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
2416082 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
2416102 ATGTATCGATACATT
1 ATGTATCGATACATT
2416117 ATGTCCTTTT
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
19 17 0.23
20 52 0.70
21 5 0.07
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2420441 original size:92 final size:92
Alignment explanation
Indices: 2420303--2420501 Score: 328
Period size: 92 Copynumber: 2.2 Consensus size: 92
2420293 ACAATGAAAA
*
2420303 ATGTATCGATACATTTTCTTTCCAGAATGCAAAACTTGCCTAGACATGGTCCTATATCGATACAT
1 ATGTATCGATACATTTTCTTTCCAGAATGCAAAACTTGCCTAGACATGGTCCCATATCGATACAT
*
2420368 TTCAGATATGTA-CTGATACATTTATTT
66 TTCAGATATGTATC-GATACATTCATTT
* * *
2420395 ATGTATCAATACATTTTCTTTCCAGAATGCAAAACTTGCTTGGACATGGTCCCATATCGATACAT
1 ATGTATCGATACATTTTCTTTCCAGAATGCAAAACTTGCCTAGACATGGTCCCATATCGATACAT
*
2420460 TTTAGATATGTATCGATACATTCATTT
66 TTCAGATATGTATCGATACATTCATTT
2420487 ATGTATCGATACATT
1 ATGTATCGATACATT
2420502 CACTATTTGT
Statistics
Matches: 99, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
92 98 0.99
93 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (92 bp):
ATGTATCGATACATTTTCTTTCCAGAATGCAAAACTTGCCTAGACATGGTCCCATATCGATACAT
TTCAGATATGTATCGATACATTCATTT
Found at i:2420491 original size:20 final size:20
Alignment explanation
Indices: 2420466--2420503 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2420456 ACATTTTAGA
2420466 TATGTATCGATACATTCATT
1 TATGTATCGATACATTCATT
2420486 TATGTATCGATACATTCA
1 TATGTATCGATACATTCA
2420504 CTATTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
TATGTATCGATACATTCATT
Found at i:2427364 original size:13 final size:13
Alignment explanation
Indices: 2427323--2427375 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
2427313 CCGTTAGAAG
2427323 CAATGTATCGATA
1 CAATGTATCGATA
2427336 CAA--T-TC-AT-
1 CAATGTATCGATA
2427344 C-ATGTATCGATA
1 CAATGTATCGATA
*
2427356 CATTGTATCGATA
1 CAATGTATCGATA
2427369 CAATGTA
1 CAATGTA
2427376 CCATGTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 19 0.59
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2427368 original size:33 final size:33
Alignment explanation
Indices: 2427326--2427388 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
2427316 TTAGAAGCAA
*
2427326 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATGT-ACCATGTATCGATACAT
2427359 TGTATCGATACAATGTACCATGTATCGATA
1 TGTATCGATACAATGTACCATGTATCGATA
2427389 GAAATAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:2427499 original size:81 final size:81
Alignment explanation
Indices: 2427359--2427555 Score: 259
Period size: 81 Copynumber: 2.4 Consensus size: 81
2427349 ATCGATACAT
* * * * * * *
2427359 TGTATCGATACAATGTACCATGTATCGATAGAAATAGTGATAGCGTAGCTACTGTCAGTTTTATA
1 TGTATCGATACAGTG-A-AATGTATCGATACAAATAATGATAGCGCAGCTACTGCCAGTTTCATA
2427424 TATCAATACAATCGTGCA
64 TATCAATACAATCGTGCA
* * *
2427442 TGTATCGATACAGTGAAATGTATCGATACAAATAATGGTAGGGCAGCTACTGCCAGTTTCATGTA
1 TGTATCGATACAGTGAAATGTATCGATACAAATAATGATAGCGCAGCTACTGCCAGTTTCATATA
* *
2427507 TCGATACAATTGTGCA
66 TCAATACAATCGTGCA
2427523 TGTATCGATACAGTGAACATGTATCGATACAAA
1 TGTATCGATACAGTGAA-ATGTATCGATACAAA
2427556 GCATAATGTA
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
81 71 0.70
82 16 0.16
83 14 0.14
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (81 bp):
TGTATCGATACAGTGAAATGTATCGATACAAATAATGATAGCGCAGCTACTGCCAGTTTCATATA
TCAATACAATCGTGCA
Found at i:2427526 original size:20 final size:20
Alignment explanation
Indices: 2427501--2427554 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
2427491 CTGCCAGTTT
* **
2427501 CATGTATCGATACAATTGTG
1 CATGTATCGATACAAGTGAA
2427521 CATGTATCGATAC-AGTGAA
1 CATGTATCGATACAAGTGAA
2427540 CATGTATCGATACAA
1 CATGTATCGATACAA
2427555 AGCATAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAAGTGAA
Found at i:2428151 original size:19 final size:21
Alignment explanation
Indices: 2428127--2428170 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2428117 AGGCTCTCGT
*
2428127 TAAAAAATTT-T-CCCTTTGA
1 TAAAAAATTTCTCCCCCTTGA
2428146 TAAAAAATTTCTCCCCCTTGA
1 TAAAAAATTTCTCCCCCTTGA
2428167 TAAA
1 TAAA
2428171 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 1 0.05
21 11 0.50
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (21 bp):
TAAAAAATTTCTCCCCCTTGA
Found at i:2429624 original size:20 final size:22
Alignment explanation
Indices: 2429585--2429629 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
2429575 GCAGTGGGTG
*
2429585 TGGGAGCTGCCCGATTGCGACC
1 TGGGAGCTGCCCGATCGCGACC
2429607 TGGGAG-TG-CCGATCGCGACC
1 TGGGAGCTGCCCGATCGCGACC
2429627 TGG
1 TGG
2429630 AGGTAGCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 2 0.09
22 6 0.27
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (22 bp):
TGGGAGCTGCCCGATCGCGACC
Found at i:2429992 original size:6 final size:6
Alignment explanation
Indices: 2429981--2430005 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2429971 GAAAGGATGT
2429981 TAGGAG TAGGAG TAGGAG TAGGAG T
1 TAGGAG TAGGAG TAGGAG TAGGAG T
2430006 TCGAACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.48, T:0.20
Consensus pattern (6 bp):
TAGGAG
Found at i:2430189 original size:18 final size:20
Alignment explanation
Indices: 2430148--2430190 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
2430138 CTATTGACCC
2430148 TAATTCACATCAAACAAGCA
1 TAATTCACATCAAACAAGCA
2430168 TAATTCA-AT-AACACAA-CA
1 TAATTCACATCAA-ACAAGCA
2430186 TAATT
1 TAATT
2430191 AAACACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.41
19 6 0.27
20 7 0.32
ACGTcount: A:0.51, C:0.21, G:0.02, T:0.26
Consensus pattern (20 bp):
TAATTCACATCAAACAAGCA
Found at i:2439297 original size:23 final size:23
Alignment explanation
Indices: 2439271--2439349 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 23
2439261 TTTTTTATCT
2439271 AGAGGGAGAAAATCTGATTATTA
1 AGAGGGAGAAAATCTGATTATTA
* **
2439294 AGAGGGAG-AAATTTTTTTATCT-
1 AGAGGGAGAAAATCTGATTAT-TA
* *
2439316 AGAGGGAGAAAATCCGATTATCA
1 AGAGGGAGAAAATCTGATTATTA
*
2439339 AGGGGGAGAAA
1 AGAGGGAGAAA
2439350 TTTTTATGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
22 17 0.39
23 27 0.61
ACGTcount: A:0.41, C:0.06, G:0.29, T:0.24
Consensus pattern (23 bp):
AGAGGGAGAAAATCTGATTATTA
Found at i:2439313 original size:22 final size:22
Alignment explanation
Indices: 2439261--2439326 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
2439251 TGAAAATAAA
2439261 TTTTTTATCTAGAGGGAGAAAAT
1 TTTTTTATCTAGAGGGAG-AAAT
* **
2439284 CTGATTAT-TAAGAGGGAGAAAT
1 TTTTTTATCT-AGAGGGAGAAAT
2439306 TTTTTTATCTAGAGGGAGAAA
1 TTTTTTATCTAGAGGGAGAAA
2439327 ATCCGATTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 21 0.60
23 14 0.40
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (22 bp):
TTTTTTATCTAGAGGGAGAAAT
Found at i:2439321 original size:45 final size:45
Alignment explanation
Indices: 2439261--2439354 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
2439251 TGAAAATAAA
* *
2439261 TTTTTTATCTAGAGGGAGAAAATCTGATTATTAAGAGGGAGAAAT
1 TTTTTTATCTAGAGGGAGAAAATCCGATTATCAAGAGGGAGAAAT
*
2439306 TTTTTTATCTAGAGGGAGAAAATCCGATTATCAAGGGGGAGAAAT
1 TTTTTTATCTAGAGGGAGAAAATCCGATTATCAAGAGGGAGAAAT
2439351 TTTT
1 TTTT
2439355 ATGAAATGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.34
Consensus pattern (45 bp):
TTTTTTATCTAGAGGGAGAAAATCCGATTATCAAGAGGGAGAAAT
Found at i:2439979 original size:19 final size:19
Alignment explanation
Indices: 2439955--2440011 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
2439945 TGTATCAATA
*
2439955 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGAT
2439974 CATTGTATCGATACATGGAT
1 CATTGTATCGATACAT-GAT
*
2439994 AATTGTATCGATACATGA
1 CATTGTATCGATACATGA
2440012 AACTGGCAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:2440000 original size:20 final size:20
Alignment explanation
Indices: 2439956--2440010 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2439946 GTATCAATAC
* *
2439956 ATTGTATCGATACAT-GTTC
1 ATTGTATCGATACATGGATA
2439975 ATTGTATCGATACATGGATA
1 ATTGTATCGATACATGGATA
2439995 ATTGTATCGATACATG
1 ATTGTATCGATACATG
2440011 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTGTATCGATACATGGATA
Found at i:2440067 original size:20 final size:20
Alignment explanation
Indices: 2440042--2440092 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2440032 CCATTGTTTC
* * *
2440042 TATCGATCCATGGTACATTG
1 TATCGATACATGATAAATTG
2440062 TATCGATACATGATAAATTG
1 TATCGATACATGATAAATTG
2440082 TATCGATACAT
1 TATCGATACAT
2440093 TGCTTCTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGATAAATTG
Found at i:2440843 original size:29 final size:29
Alignment explanation
Indices: 2440810--2440878 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
2440800 AACGTTTTTT
2440810 ATGCAAACATCAC-ATAAAACAACCATAAA
1 ATGCAAACATCACGATAAAACAACCAT-AA
* **
2440839 ATGCAAGCAAAACGGATAAAACAACCATAA
1 ATGCAAACATCAC-GATAAAACAACCATAA
2440869 A-GCAAACATC
1 ATGCAAACATC
2440879 GCATTTCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
29 16 0.50
30 3 0.09
31 13 0.41
ACGTcount: A:0.57, C:0.23, G:0.09, T:0.12
Consensus pattern (29 bp):
ATGCAAACATCACGATAAAACAACCATAA
Found at i:2442269 original size:20 final size:21
Alignment explanation
Indices: 2442244--2442283 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2442234 TTTGTTGGTG
*
2442244 ATTTTGATG-AAAAATGAAGT
1 ATTTTGAAGTAAAAATGAAGT
2442264 ATTTTGAAGTAAAAATGAAG
1 ATTTTGAAGTAAAAATGAAG
2442284 AAATTTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (21 bp):
ATTTTGAAGTAAAAATGAAGT
Found at i:2442488 original size:50 final size:50
Alignment explanation
Indices: 2442410--2442521 Score: 158
Period size: 50 Copynumber: 2.3 Consensus size: 50
2442400 ATAGTAACCC
* *
2442410 ATGTATCGATACA---AGGAATATTACATCGATACATCTGGGTTTTCTAG
1 ATGTATCGATACATTGAAGAATATTACATCGATACATCTGGGTTTTCCAG
* **
2442457 ATGTATTGATACATTGAAGAATATTGTATCGATACATCTGGGTTTTCCAG
1 ATGTATCGATACATTGAAGAATATTACATCGATACATCTGGGTTTTCCAG
2442507 ATGTATCGATACATT
1 ATGTATCGATACATT
2442522 CTTCAATGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
47 12 0.21
50 44 0.79
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (50 bp):
ATGTATCGATACATTGAAGAATATTACATCGATACATCTGGGTTTTCCAG
Found at i:2448644 original size:13 final size:13
Alignment explanation
Indices: 2448628--2448652 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2448618 AATTTATCAT
2448628 GTATCGATACAAA
1 GTATCGATACAAA
2448641 GTATCGATACAA
1 GTATCGATACAA
2448653 TGTACCATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACAAA
Found at i:2448645 original size:20 final size:20
Alignment explanation
Indices: 2448606--2448645 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2448596 GTTAGAAGTA
**
2448606 ATGTATCGATACAATTTATC
1 ATGTATCGATACAAAGTATC
2448626 ATGTATCGATACAAAGTATC
1 ATGTATCGATACAAAGTATC
2448646 GATACAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAAAGTATC
Found at i:2448664 original size:20 final size:18
Alignment explanation
Indices: 2448606--2448669 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 18
2448596 GTTAGAAGTA
2448606 ATGTATCGATACAATTTATC
1 ATGTATCGATACAA-TTA-C
2448626 ATGTATCGATAC-A--A-
1 ATGTATCGATACAATTAC
2448640 A-GTATCGATACAATGTACC
1 ATGTATCGATACAAT-TA-C
2448659 ATGTATCGATA
1 ATGTATCGATA
2448670 AAAATAGTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.27
14 2 0.05
16 1 0.03
17 1 0.03
19 2 0.05
20 21 0.57
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (18 bp):
ATGTATCGATACAATTAC
Found at i:2454595 original size:13 final size:13
Alignment explanation
Indices: 2454577--2454606 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2454567 ACAATTCATC
2454577 ATGTATCGATACA
1 ATGTATCGATACA
2454590 ATGTATCGATACA
1 ATGTATCGATACA
2454603 ATGT
1 ATGT
2454607 GCCATGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2454696 original size:19 final size:19
Alignment explanation
Indices: 2454652--2454723 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
2454642 CTGCCAGTTT
* **
2454652 CATGTATCGATACAATTGTG
1 CATGTATCGATAC-AGTGAA
2454672 CATGTATCGATACAGTGAA
1 CATGTATCGATACAGTGAA
2454691 CATGTATCGATACAGTGAA
1 CATGTATCGATACAGTGAA
*
2454710 CACGTATCGATACA
1 CATGTATCGATACA
2454724 ATATATTGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
19 35 0.73
20 13 0.27
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAGTGAA
Found at i:2455946 original size:28 final size:28
Alignment explanation
Indices: 2455906--2455977 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
2455896 GGAATAAAGC
** *
2455906 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2455934 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2455962 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2455978 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:2456035 original size:52 final size:52
Alignment explanation
Indices: 2455966--2456302 Score: 185
Period size: 52 Copynumber: 6.4 Consensus size: 52
2455956 AAATAACGAG
*
2455966 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
2456018 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * *
2456071 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
2456122 GTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
2456177 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * * *
2456231 GTTAGAGTATCCCCGACTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* *
2456282 GTTGGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
2456303 GAGAATTGAT
Statistics
Matches: 213, Mismatches: 45, Indels: 54
0.68 0.14 0.17
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 2 0.01
51 36 0.17
52 79 0.37
53 33 0.15
54 27 0.13
55 18 0.08
56 2 0.01
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:2456162 original size:28 final size:27
Alignment explanation
Indices: 2456122--2456192 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
2456112 TAAAACCGGA
**
2456122 GTTGGAGTATCCCCTCGGAAATAACGGG
1 GTTGGAGTATCCCCGAGG-AATAACGGG
* *
2456150 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCGAGGAATAACGGG
2456177 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
2456193 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 24 0.62
28 15 0.38
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACGGG
Found at i:2456205 original size:107 final size:106
Alignment explanation
Indices: 2455852--2456244 Score: 343
Period size: 107 Copynumber: 3.7 Consensus size: 106
2455842 CCTTCGAAAA
* * * * * * * *
2455852 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
* *
2455917 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
66 TATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-AT
* * * *
2455959 TAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGG-AATAAAACCGGAGTTGGA
* * ** * ** **
2456024 GTAT-CCC-C-G-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
65 GTATCCCCTCGGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * * * *
2456061 AAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGTT
1 -TAA-CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTAGTATTTTTG-GAATAAAACCGGAGTT
2456125 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
62 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
* * * *
2456170 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATTAGT-ATTTTTGG-AATAAAACCGGAGTTG
2456235 GAGTATCCCC
63 GAGTATCCCC
2456245 GACTATAGAA
Statistics
Matches: 220, Mismatches: 48, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 46 0.21
105 20 0.09
106 18 0.08
107 72 0.33
108 32 0.15
109 27 0.12
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (106 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
TATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:2456258 original size:212 final size:212
Alignment explanation
Indices: 2455899--2456304 Score: 629
Period size: 212 Copynumber: 1.9 Consensus size: 212
2455889 TATTTTGGGA
* * *
2455899 ATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
2455964 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
* * *
2456029 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGA
131 CCCGACTAAAGGAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTGGA
2456093 AAAATTAGTGTTTTAGCG
195 AAAATTAGTGTTTTAGCG
*
2456111 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
2456175 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
66 AGGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTA
* * * *
2456240 TCCCCGACTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTGTGG
129 TCCCCGACTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGG
2456304 A
194 A
2456305 GAATTGATAA
Statistics
Matches: 176, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 32 0.18
212 106 0.60
213 38 0.22
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
CCCGACTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:2458682 original size:13 final size:13
Alignment explanation
Indices: 2458664--2458689 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2458654 ACAAAGATCC
2458664 ATGTATCGATACA
1 ATGTATCGATACA
2458677 ATGTATCGATACA
1 ATGTATCGATACA
2458690 CAAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2458844 original size:21 final size:21
Alignment explanation
Indices: 2458820--2458876 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
2458810 CATTTGTAGG
2458820 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
2458841 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
2458862 ATGTATCGATACATT
1 ATGTATCGATACATT
2458877 TGGATAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:2458909 original size:16 final size:16
Alignment explanation
Indices: 2458888--2458919 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2458878 GGATAAATTT
2458888 TTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTCAA
2458904 TTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTCAA
2458920 ACACTTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTTTTTCAA
Found at i:2465239 original size:3 final size:3
Alignment explanation
Indices: 2465231--2465255 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2465221 TAACCTCTTG
2465231 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
2465256 CTTTAAGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:2468569 original size:21 final size:21
Alignment explanation
Indices: 2468543--2468587 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2468533 TCTTATATTG
* * *
2468543 ATACATTTATGAAATGTATCA
1 ATACATTGATAAAATGCATCA
2468564 ATACATTGATAAAATGCATCA
1 ATACATTGATAAAATGCATCA
2468585 ATA
1 ATA
2468588 TACATCTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (21 bp):
ATACATTGATAAAATGCATCA
Found at i:2470196 original size:10 final size:9
Alignment explanation
Indices: 2470172--2470197 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2470162 AATACTAGTG
2470172 CATTTTTTC
1 CATTTTTTC
2470181 CATTTTTTC
1 CATTTTTTC
2470190 CATTTTTT
1 CATTTTTT
2470198 GTTTCCCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (9 bp):
CATTTTTTC
Done.