Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 31 of 222
Found at i:9289504 original size:4 final size:4
Alignment explanation
Indices: 9289470--9289494 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9289460 GTGTACATGC
9289470 AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG A
9289495 CCAATGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:9291318 original size:35 final size:35
Alignment explanation
Indices: 9291272--9291675 Score: 223
Period size: 35 Copynumber: 11.3 Consensus size: 35
9291262 ACGAGATTTT
*
9291272 TTTTTGAAAACACGAAAATTTTCAAAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
** * *
9291307 TTTTTGAAAACACGAGGATTTTTGGAAATACGAAAA
1 TTTTTGAAAACACGAAAATTTTT-AAAACACGAAAA
* * *
9291343 TTTTAG-AAACATGAAAATTTTTAAAACACGACAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
* *
9291377 CTTTTG-AAGCACGAGAAATTTATTCAAAACAC-AAAA
1 TTTTTGAAAACACGA-AAATTT-TT-AAAACACGAAAA
** * * *****
9291413 AATTT-AAAACACGAACATTTTTTGAAACAATTTTTA
1 TTTTTGAAAACACGAA-AATTTTTAAAAC-ACGAAAA
* *
9291449 TTTTT-ATTTTTAAACAAGAAAAATTTTTAAAACACGAGAA
1 TTTTTGA-----AAACACG-AAAATTTTTAAAACACGAAAA
* * *
9291489 TTTTAG-AGACACGAAAATTCTTAAAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
* * * * **
9291523 TTTTTGAGAACACGACAATTTTGAAATACGCGAATT
1 TTTTTGAAAACACGAAAATTTTTAAA-ACACGAAAA
** * * *
9291559 TTTTTGAAAAC-CTG-ATTTTTTTGAAGCGCGAAAA
1 TTTTTGAAAACAC-GAAAATTTTTAAAACACGAAAA
** * * *
9291593 TTCGTG-AAACATGAGAATTGTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAATT-TTTAAAACACGAAAA
* *
9291628 TTTTTGAAAACACGAAAATTTTTGAAACATGAAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
9291663 TTTTTTGAAAACA
1 -TTTTTGAAAACA
9291676 AAAAAATATT
Statistics
Matches: 270, Mismatches: 76, Indels: 45
0.69 0.19 0.12
Matches are distributed among these distances:
33 5 0.02
34 59 0.22
35 96 0.36
36 79 0.29
37 7 0.03
40 6 0.02
41 16 0.06
42 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
Found at i:9291330 original size:53 final size:51
Alignment explanation
Indices: 9291272--9291666 Score: 208
Period size: 53 Copynumber: 7.4 Consensus size: 51
9291262 ACGAGATTTT
**
9291272 TTTTTGAAAACACGAAAATTTTCAAAACACGAAAATTTTTGAAAACACGAGGA
1 TTTTTG-AAACACGAAAATTTTCAAAACACGAAAATTTTT-AAAACACGACAA
* *
9291325 TTTTTGGAAATACGAAAATTTT-AGAAACATGAAAATTTTTAAAACACGACAA
1 TTTTT-GAAACACGAAAATTTTCA-AAACACGAAAATTTTTAAAACACGACAA
* * ** *
9291377 CTTTTGAAGCACGAGAAATTTATTCAAAACAC-AAAAAATTTAAAACACGAACAT
1 TTTTTGAAACACGA-AAA-TT-TTCAAAACACGAAAATTTTTAAAACACG-ACAA
***** * * *
9291431 TTTTTGAAACAATTTTTATTTTTATTTTTAAACAAGAAAAATTTTTAAAACACGAGAA
1 TTTTTGAAAC-ACGAAAATTTTCA-----AAACACG-AAAATTTTTAAAACACGACAA
* * *
9291489 TTTTAGAGACACGAAAATTCTT-AAAACACGAAAATTTTTGAGAACACGACAA
1 TTTTTGAAACACGAAAATT-TTCAAAACACGAAAATTTTT-AAAACACGACAA
* ** * ** * * * *
9291541 -TTTTGAAATACGCGAATTTTTTTGAAAAC-CTG-ATTTTTTTGAAGCGCGAAAA
1 TTTTTG-AA-ACACGAA-AATTTTCAAAACAC-GAAAATTTTTAAAACACGACAA
** * * * *
9291593 TTCGTGAAACATGAGAATTGTTGAAAACACGAAAATTTTTGAAAACACGAAAA
1 TTTTTGAAACACGAAAATT-TTCAAAACACGAAAATTTTT-AAAACACGACAA
*
9291646 TTTTTGAAACATGAAAATTTT
1 TTTTTGAAACACGAAAATTTT
9291667 TTGAAAACAA
Statistics
Matches: 254, Mismatches: 61, Indels: 55
0.69 0.16 0.15
Matches are distributed among these distances:
50 2 0.01
51 33 0.13
52 56 0.22
53 96 0.38
54 28 0.11
55 2 0.01
57 10 0.04
58 12 0.05
59 15 0.06
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (51 bp):
TTTTTGAAACACGAAAATTTTCAAAACACGAAAATTTTTAAAACACGACAA
Found at i:9291680 original size:18 final size:18
Alignment explanation
Indices: 9291272--9291675 Score: 221
Period size: 17 Copynumber: 22.7 Consensus size: 18
9291262 ACGAGATTTT
9291272 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
9291290 -TTTTCAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
**
9291307 TTTTTGAAAACACGAGGA
1 TTTTTGAAAACACGAAAA
* *
9291325 TTTTTGGAAATACGAAAA
1 TTTTTGAAAACACGAAAA
* *
9291343 TTTTAG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
*
9291360 TTTTT-AAAACACGACAA
1 TTTTTGAAAACACGAAAA
* *
9291377 CTTTTG-AAGCACGAGAAA
1 TTTTTGAAAACACGA-AAA
*
9291395 TTTATTCAAAACAC-AAAA
1 TTT-TTGAAAACACGAAAA
** *
9291413 AATTT-AAAACACGAACAT
1 TTTTTGAAAACACGAA-AA
*****
9291431 TTTTTG-AAACAATTTTTA
1 TTTTTGAAAAC-ACGAAAA
*
9291449 TTTTT-ATTTTTAAACAAGAAAAA
1 TTTTTGA-----AAACACG-AAAA
*
9291472 TTTTT-AAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* *
9291489 TTTTAG-AGACACGAAAA
1 TTTTTGAAAACACGAAAA
*
9291506 TTCTT-AAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
9291523 TTTTTGAGAACACGACAA
1 TTTTTGAAAACACGAAAA
* **
9291541 -TTTTGAAATACGCGAATT
1 TTTTTGAAA-ACACGAAAA
**
9291559 TTTTTGAAAAC-CTG-ATT
1 TTTTTGAAAACAC-GAAAA
* *
9291576 TTTTTG-AAGCGCGAAAA
1 TTTTTGAAAACACGAAAA
** * *
9291593 TTCGTG-AAACATGAGAA
1 TTTTTGAAAACACGAAAA
*
9291610 TTGTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
9291628 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
9291646 TTTTTG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
9291663 TTTTTTGAAAACA
1 -TTTTTGAAAACA
9291676 AAAAAATATT
Statistics
Matches: 291, Mismatches: 67, Indels: 55
0.70 0.16 0.13
Matches are distributed among these distances:
16 11 0.04
17 130 0.45
18 116 0.40
19 17 0.06
20 5 0.02
22 1 0.00
23 11 0.04
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:9291682 original size:36 final size:36
Alignment explanation
Indices: 9291460--9291687 Score: 103
Period size: 36 Copynumber: 6.4 Consensus size: 36
9291450 TTTTATTTTT
* *
9291460 AAACAAGAAAAATTTTT-AAAACACGAGAATTTTAG-
1 AAACAA-AAAAATTTTTGAAAACACGAAAATTTTTGA
* ** *
9291495 AGACACGAAAATTCTT-AAAACACGAAAATTTTTGA
1 AAACAAAAAAATTTTTGAAAACACGAAAATTTTTGA
* ** * * **
9291530 GAACACGACAA-TTTTGAAATACGCGAATTTTTTTGA
1 AAACAAAAAAATTTTTGAAA-ACACGAAAATTTTTGA
*** ** * * **
9291566 AAAC-CTGATTTTTTTG-AAGCGCGAAAATTCGTG-
1 AAACAAAAAAATTTTTGAAAACACGAAAATTTTTGA
** * *
9291599 AAACATGAGAATTGTTGAAAACACGAAAATTTTTGA
1 AAACAAAAAAATTTTTGAAAACACGAAAATTTTTGA
** *
9291635 AAACACGAAAATTTTTG-AAACATGAAAATTTTTTGA
1 AAACAAAAAAATTTTTGAAAACACGAAAA-TTTTTGA
9291671 AAACAAAAAAATATTTT
1 AAACAAAAAAAT-TTTT
9291688 TTTTTTGATC
Statistics
Matches: 143, Mismatches: 41, Indels: 16
0.71 0.20 0.08
Matches are distributed among these distances:
33 4 0.03
34 42 0.29
35 41 0.29
36 52 0.36
37 4 0.03
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30
Consensus pattern (36 bp):
AAACAAAAAAATTTTTGAAAACACGAAAATTTTTGA
Found at i:9291738 original size:17 final size:17
Alignment explanation
Indices: 9291703--9291744 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
9291693 TGATCATGGG
9291703 AATTTTTGAAAACGTGAA
1 AATTTTTGAAAACG-GAA
9291721 AATTTTTGAAACAC-GAA
1 AATTTTTGAAA-ACGGAA
*
9291738 AGTTTTT
1 AATTTTT
9291745 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 11 0.50
19 2 0.09
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (17 bp):
AATTTTTGAAAACGGAA
Found at i:9291811 original size:19 final size:19
Alignment explanation
Indices: 9291770--9291815 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
9291760 CGAAAATTTT
* *
9291770 TTTTTGAACACGAGAAAAT
1 TTTTTGAAAACGAGAAAAA
9291789 TTTTTGAAAAC-ATGAAAAA
1 TTTTTGAAAACGA-GAAAAA
9291808 -TTTTGAAA
1 TTTTTGAAA
9291816 CACCGAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.35
Consensus pattern (19 bp):
TTTTTGAAAACGAGAAAAA
Found at i:9291849 original size:18 final size:17
Alignment explanation
Indices: 9291789--9291852 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 17
9291779 ACGAGAAAAT
*
9291789 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACG-AAA
*
9291807 ATTTTG-AAACACCGAAA
1 TTTTTGAAAACA-CGAAA
*
9291824 -TCTTGAAAACACGAAGA
1 TTTTTGAAAACACGAA-A
9291841 TTTTTGAAAACA
1 TTTTTGAAAACA
9291853 ATTATTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 8 0.21
17 14 0.37
18 16 0.42
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
TTTTTGAAAACACGAAA
Found at i:9291918 original size:39 final size:40
Alignment explanation
Indices: 9291829--9291928 Score: 111
Period size: 38 Copynumber: 2.6 Consensus size: 40
9291819 CGAAATCTTG
* * *
9291829 AAAACACGAAGATTTTTGAAAACAATTATTATTTTAAAAA
1 AAAACACGAAAATTTATGAAAACAATGATTATTTTAAAAA
9291869 AAAA-A-GAAAATTTATGAAACACAA-GATT-TTTTAAAAA
1 AAAACACGAAAATTTATGAAA-ACAATGATTATTTTAAAAA
* *
9291906 AAAACACAAAAATTT-TCAAAACA
1 AAAACACGAAAATTTATGAAAACA
9291929 CTGAAATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
37 16 0.31
38 20 0.38
39 12 0.23
40 4 0.08
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.27
Consensus pattern (40 bp):
AAAACACGAAAATTTATGAAAACAATGATTATTTTAAAAA
Found at i:9291921 original size:22 final size:22
Alignment explanation
Indices: 9291885--9291926 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
9291875 AAAATTTATG
* * *
9291885 AAACACAAGATTTTTTAAAAAA
1 AAACACAAAAATTTTCAAAAAA
9291907 AAACACAAAAATTTTCAAAA
1 AAACACAAAAATTTTCAAAA
9291927 CACTGAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (22 bp):
AAACACAAAAATTTTCAAAAAA
Found at i:9291928 original size:17 final size:17
Alignment explanation
Indices: 9291906--9291996 Score: 92
Period size: 18 Copynumber: 5.2 Consensus size: 17
9291896 TTTTTAAAAA
* *
9291906 AAAACACAAAAATTTTC
1 AAAACACGAAAATTTTG
*
9291923 AAAACACTGAAATTTTTG
1 AAAACAC-GAAAATTTTG
** *
9291941 AAAACACGAGGATTTTT
1 AAAACACGAAAATTTTG
9291958 AAAACACGCAAAATTTTG
1 AAAACACG-AAAATTTTG
*
9291976 GAAACACGAAAATTTTTG
1 AAAACACGAAAA-TTTTG
9291994 AAA
1 AAA
9291997 TACGAAATTA
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
17 25 0.42
18 34 0.58
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.26
Consensus pattern (17 bp):
AAAACACGAAAATTTTG
Found at i:9291991 original size:35 final size:35
Alignment explanation
Indices: 9291906--9291992 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
9291896 TTTTTAAAAA
* * *
9291906 AAAACACAAAAATTTTCAAAACACTGAAATTTTTG
1 AAAACACGAAAATTTTTAAAACACTGAAAATTTTG
**
9291941 AAAACACGAGGATTTTTAAAACAC-GCAAAATTTTG
1 AAAACACGAAAATTTTTAAAACACTG-AAAATTTTG
*
9291976 GAAACACGAAAATTTTT
1 AAAACACGAAAATTTTT
9291993 GAAATACGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 1 0.02
35 42 0.98
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (35 bp):
AAAACACGAAAATTTTTAAAACACTGAAAATTTTG
Found at i:9292001 original size:17 final size:17
Alignment explanation
Indices: 9291907--9292003 Score: 88
Period size: 17 Copynumber: 5.6 Consensus size: 17
9291897 TTTTAAAAAA
* **
9291907 AAACACAAAAATTTTCA
1 AAACACGAAAATTTTTG
9291924 AAACACTG-AAATTTTTG
1 AAACAC-GAAAATTTTTG
** *
9291941 AAAACACGAGGATTTTTA
1 -AAACACGAAAATTTTTG
*
9291959 AAACACGCAAAATTTTGG
1 AAACACG-AAAATTTTTG
9291977 AAACACGAAAATTTTTG
1 AAACACGAAAATTTTTG
*
9291994 AAATACGAAA
1 AAACACGAAA
9292004 TTATTTTTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
17 39 0.61
18 25 0.39
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.26
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:9292010 original size:18 final size:19
Alignment explanation
Indices: 9291959--9292010 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 19
9291949 AGGATTTTTA
*
9291959 AAACACGCAAA-ATTTTGG
1 AAACACGAAAATATTTTGG
9291977 AAACACGAAAAT-TTTT-G
1 AAACACGAAAATATTTTGG
* *
9291994 AAATACGAAATTATTTT
1 AAACACGAAAATATTTT
9292011 TTTTAAAAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 11 0.38
18 18 0.62
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (19 bp):
AAACACGAAAATATTTTGG
Found at i:9292638 original size:7 final size:7
Alignment explanation
Indices: 9292626--9292676 Score: 59
Period size: 7 Copynumber: 7.3 Consensus size: 7
9292616 CTTTTTCTTC
9292626 CTTTTTT
1 CTTTTTT
9292633 CTTTTTT
1 CTTTTTT
9292640 CTTTTTTT
1 C-TTTTTT
9292648 CTTTTTT
1 CTTTTTT
*
9292655 CTTCTTT
1 CTTTTTT
* *
9292662 -TTCTTC
1 CTTTTTT
9292668 CTTTTTT
1 CTTTTTT
9292675 CT
1 CT
9292677 CTGCTGGGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
6 5 0.13
7 26 0.68
8 7 0.18
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
CTTTTTT
Found at i:9292647 original size:15 final size:15
Alignment explanation
Indices: 9292627--9292666 Score: 71
Period size: 15 Copynumber: 2.6 Consensus size: 15
9292617 TTTTTCTTCC
9292627 TTTTTTCTTTTTTCT
1 TTTTTTCTTTTTTCT
9292642 TTTTTTCTTTTTTCT
1 TTTTTTCTTTTTTCT
9292657 TCTTTTTCTT
1 T-TTTTTCTT
9292667 CCTTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTCTTTTTTCT
Found at i:9292953 original size:3 final size:3
Alignment explanation
Indices: 9292947--9292977 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
9292937 TTAAATTTTT
9292947 TTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC
9292978 AAAACCGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:9293473 original size:29 final size:29
Alignment explanation
Indices: 9293331--9293466 Score: 173
Period size: 29 Copynumber: 4.6 Consensus size: 29
9293321 AATTTATATG
* * *
9293331 AAGTTTAGGGGTAAAAATGTAAGTTTGATA
1 AAGTTTAGGGGTCAAAATGTAA-TTTCAAA
9293361 AAGTTTAGGGGTCAAAATGTAATTTCAAA
1 AAGTTTAGGGGTCAAAATGTAATTTCAAA
* * * *
9293390 AAGGTTAAGGGTAAAAATGTAATTTTGAAA
1 AAGTTTAGGGGTCAAAATGTAA-TTTCAAA
* *
9293420 AATTTTAGGGGTCAAAATATAATTTCAAA
1 AAGTTTAGGGGTCAAAATGTAATTTCAAA
9293449 AAGTTTAGGGGTCAAAAT
1 AAGTTTAGGGGTCAAAAT
9293467 ATGATTTTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
29 47 0.52
30 44 0.48
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.32
Consensus pattern (29 bp):
AAGTTTAGGGGTCAAAATGTAATTTCAAA
Found at i:9293474 original size:59 final size:59
Alignment explanation
Indices: 9293331--9293466 Score: 209
Period size: 59 Copynumber: 2.3 Consensus size: 59
9293321 AATTTATATG
* * *
9293331 AAGTTTAGGGGTAAAAATGTAAGTTTGATAAAGTTTAGGGGTCAAAATGTAATTTCAAA
1 AAGTTTAGGGGTAAAAATGTAATTTTGAAAAAGTTTAGGGGTCAAAATATAATTTCAAA
* * *
9293390 AAGGTTAAGGGTAAAAATGTAATTTTGAAAAATTTTAGGGGTCAAAATATAATTTCAAA
1 AAGTTTAGGGGTAAAAATGTAATTTTGAAAAAGTTTAGGGGTCAAAATATAATTTCAAA
*
9293449 AAGTTTAGGGGTCAAAAT
1 AAGTTTAGGGGTAAAAAT
9293467 ATGATTTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 68 1.00
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.32
Consensus pattern (59 bp):
AAGTTTAGGGGTAAAAATGTAATTTTGAAAAAGTTTAGGGGTCAAAATATAATTTCAAA
Found at i:9293491 original size:16 final size:16
Alignment explanation
Indices: 9293470--9293502 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9293460 TCAAAATATG
*
9293470 ATTTTTTTTATTTTTT
1 ATTTTTTTGATTTTTT
9293486 ATTTTTTTGATTTTTT
1 ATTTTTTTGATTTTTT
9293502 A
1 A
9293503 GAAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (16 bp):
ATTTTTTTGATTTTTT
Found at i:9297073 original size:18 final size:19
Alignment explanation
Indices: 9297033--9297074 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
9297023 TTTATGTTAT
* *
9297033 TTTTCTGTCTTTTTCATTC
1 TTTTCTGTCTTCTCCATTC
*
9297052 TTTTCTG-CTTCTCCATTG
1 TTTTCTGTCTTCTCCATTC
9297070 TTTTC
1 TTTTC
9297075 CTCCATTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.05, C:0.24, G:0.07, T:0.64
Consensus pattern (19 bp):
TTTTCTGTCTTCTCCATTC
Found at i:9297651 original size:11 final size:10
Alignment explanation
Indices: 9297623--9297670 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
9297613 AAAAAAGAAT
9297623 AGAAAAT-AA
1 AGAAAATAAA
9297632 AG-AAA-AAA
1 AGAAAATAAA
*
9297640 AGTAAATTAAA
1 AG-AAAATAAA
9297651 AGAAAATAAA
1 AGAAAATAAA
9297661 AGAAAA-AAA
1 AGAAAATAAA
9297670 A
1 A
9297671 TTAAATTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
8 7 0.21
9 6 0.18
10 15 0.45
11 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AGAAAATAAA
Found at i:9313869 original size:21 final size:21
Alignment explanation
Indices: 9313843--9313906 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
9313833 TTCGGGTGGA
*
9313843 TCAGCTCTTTTGAGCTTTTGT
1 TCAGCTCTTATGAGCTTTTGT
* *
9313864 TCAGCTCTTATGTGCTTCTGT
1 TCAGCTCTTATGAGCTTTTGT
9313885 TCAGCTCTTATGAGCTTTTGT
1 TCAGCTCTTATGAGCTTTTGT
9313906 T
1 T
9313907 GGCGTGTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.11, C:0.20, G:0.19, T:0.50
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTTTGT
Found at i:9314793 original size:30 final size:30
Alignment explanation
Indices: 9314757--9314925 Score: 248
Period size: 30 Copynumber: 5.6 Consensus size: 30
9314747 GTCTCATCCG
* *
9314757 TGTGTGACATACGGCCATGCGACACAGCCA
1 TGTGTGACACACGGCCATGCGACACGGCCA
9314787 TGTGTGACACACGGCCATGCGACACGGCCA
1 TGTGTGACACACGGCCATGCGACACGGCCA
*
9314817 TGTGTGACACACGGCCATGCGACACGGCTA
1 TGTGTGACACACGGCCATGCGACACGGCCA
* *
9314847 TGTGTGACACACGGCCATGCGACACGACCG
1 TGTGTGACACACGGCCATGCGACACGGCCA
* * * *
9314877 TGTATGACATACGACCATGCGACACGGCCG
1 TGTGTGACACACGGCCATGCGACACGGCCA
*
9314907 TGTGTGACACATGGCCATG
1 TGTGTGACACACGGCCATG
9314926 TAGGTTCAAA
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 125 1.00
ACGTcount: A:0.24, C:0.30, G:0.29, T:0.17
Consensus pattern (30 bp):
TGTGTGACACACGGCCATGCGACACGGCCA
Found at i:9314803 original size:17 final size:17
Alignment explanation
Indices: 9314757--9314865 Score: 89
Period size: 15 Copynumber: 7.1 Consensus size: 17
9314747 GTCTCATCCG
*
9314757 TGTGTGACATACGGCCA
1 TGTGTGACACACGGCCA
*
9314774 --TGCGACACA--GCCA
1 TGTGTGACACACGGCCA
9314787 TGTGTGACACACGGCCA
1 TGTGTGACACACGGCCA
*
9314804 --TGCG--ACACGGCCA
1 TGTGTGACACACGGCCA
9314817 TGTGTGACACACGGCCA
1 TGTGTGACACACGGCCA
* *
9314834 --TGCG--ACACGGCTA
1 TGTGTGACACACGGCCA
9314847 TGTGTGACACACGGCCA
1 TGTGTGACACACGGCCA
9314864 TG
1 TG
9314866 CGACACGACC
Statistics
Matches: 71, Mismatches: 9, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
13 21 0.30
15 27 0.38
17 23 0.32
ACGTcount: A:0.24, C:0.30, G:0.29, T:0.17
Consensus pattern (17 bp):
TGTGTGACACACGGCCA
Found at i:9314843 original size:13 final size:13
Alignment explanation
Indices: 9314767--9314872 Score: 59
Period size: 13 Copynumber: 7.2 Consensus size: 13
9314757 TGTGTGACAT
9314767 ACGGCCATGCGAC
1 ACGGCCATGCGAC
* *
9314780 ACAGCCATGTGTGACAC
1 ACGGCCA--TGCG--AC
9314797 ACGGCCATGCGAC
1 ACGGCCATGCGAC
*
9314810 ACGGCCATGTGTGACAC
1 ACGGCCA--TGCG--AC
9314827 ACGGCCATGCGAC
1 ACGGCCATGCGAC
* *
9314840 ACGGCTATGTGTGACAC
1 ACGGCCA--TGCG--AC
9314857 ACGGCCATGCGAC
1 ACGGCCATGCGAC
9314870 ACG
1 ACG
9314873 ACCGTGTATG
Statistics
Matches: 71, Mismatches: 10, Indels: 24
0.68 0.10 0.23
Matches are distributed among these distances:
13 28 0.39
15 18 0.25
17 25 0.35
ACGTcount: A:0.25, C:0.33, G:0.29, T:0.13
Consensus pattern (13 bp):
ACGGCCATGCGAC
Found at i:9315550 original size:21 final size:21
Alignment explanation
Indices: 9315524--9315565 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9315514 ATCCAATTGA
* *
9315524 ACGTAAGCTTGGGGCTATCGC
1 ACGTAAACTTGGGCCTATCGC
*
9315545 ACGTAAATTTGGGCCTATCGC
1 ACGTAAACTTGGGCCTATCGC
9315566 TTGTTAATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (21 bp):
ACGTAAACTTGGGCCTATCGC
Found at i:9315970 original size:15 final size:15
Alignment explanation
Indices: 9315950--9315980 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9315940 TCTTTAAATC
9315950 ATTCAAAAGAGTAAT
1 ATTCAAAAGAGTAAT
9315965 ATTCAAAAGAGTAAT
1 ATTCAAAAGAGTAAT
9315980 A
1 A
9315981 AATTGACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (15 bp):
ATTCAAAAGAGTAAT
Found at i:9317768 original size:31 final size:31
Alignment explanation
Indices: 9317733--9317801 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
9317723 AATATATCAG
9317733 GAAGTCGAATTGGCAATGAAAAAAGAAGCAT
1 GAAGTCGAATTGGCAATGAAAAAAGAAGCAT
9317764 GAAGTCGAATTGGCAATGAAAAAAGAAGCAT
1 GAAGTCGAATTGGCAATGAAAAAAGAAGCAT
9317795 GAAGTCG
1 GAAGTCG
9317802 GAAGTCATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.46, C:0.10, G:0.28, T:0.16
Consensus pattern (31 bp):
GAAGTCGAATTGGCAATGAAAAAAGAAGCAT
Found at i:9317955 original size:16 final size:17
Alignment explanation
Indices: 9317934--9317966 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9317924 TGAAAAATAA
9317934 TTAAAA-AAAAAGAAAG
1 TTAAAAGAAAAAGAAAG
*
9317950 TTAAAAGAACAAGAAAG
1 TTAAAAGAAAAAGAAAG
9317967 AAAAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.70, C:0.03, G:0.15, T:0.12
Consensus pattern (17 bp):
TTAAAAGAAAAAGAAAG
Found at i:9319053 original size:18 final size:20
Alignment explanation
Indices: 9319005--9319053 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 20
9318995 TCTTTAGTTC
*
9319005 TTTTA-TTATTTAGGTAACT
1 TTTTAGTTATTTAGGTAAAT
**
9319024 TTTTAGAAATTTA-G-AAAT
1 TTTTAGTTATTTAGGTAAAT
9319042 TTTTAGTTATTT
1 TTTTAGTTATTT
9319054 TATATATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 13 0.54
19 6 0.25
20 5 0.21
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (20 bp):
TTTTAGTTATTTAGGTAAAT
Found at i:9324266 original size:129 final size:129
Alignment explanation
Indices: 9324036--9324296 Score: 396
Period size: 129 Copynumber: 2.0 Consensus size: 129
9324026 TTCCAAGAAG
* * *
9324036 CTTTATGATGACAGTTTTGGAAAAGCGTATGAATTTTATCAGAAAATTTAATCGATGTGACTCTA
1 CTTTATGATGACAGTTTTAGAAAAGCGTATGAATTCTATCAGAAAATTTAATCGATGGGACTCTA
** * *
9324101 TTCATGAAGTGTATTGAAACTTCACCTAACAACAACTCAATATCCTCCTCATCCACAGCCTATC
66 TTCACAAAGTGTATTAAAACTTCACCTAACAACAACTCAATATCCTCCTCATCAACAGCCTATC
* * *
9324165 CTTTATGATGATAGTTTTAGACAAGTGTATGAATTCTATCAGAAAATTTAATCGATGGGACTCTA
1 CTTTATGATGACAGTTTTAGAAAAGCGTATGAATTCTATCAGAAAATTTAATCGATGGGACTCTA
* * * *
9324230 TTCACAAAGTGTATTAAAACTTCATCTACCAGCAACTCAATATCCTCCTCATCAATAGCCTATC
66 TTCACAAAGTGTATTAAAACTTCACCTAACAACAACTCAATATCCTCCTCATCAACAGCCTATC
9324294 CTT
1 CTT
9324297 CCTCCATCCT
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
129 118 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (129 bp):
CTTTATGATGACAGTTTTAGAAAAGCGTATGAATTCTATCAGAAAATTTAATCGATGGGACTCTA
TTCACAAAGTGTATTAAAACTTCACCTAACAACAACTCAATATCCTCCTCATCAACAGCCTATC
Found at i:9331671 original size:19 final size:19
Alignment explanation
Indices: 9331647--9331685 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
9331637 TCCGCAATCA
* *
9331647 TATTTCTAGATTTTCTTTT
1 TATTTCAAGATTTTATTTT
*
9331666 TATTTCAATATTTTATTTT
1 TATTTCAAGATTTTATTTT
9331685 T
1 T
9331686 CCCCGTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (19 bp):
TATTTCAAGATTTTATTTT
Found at i:9333942 original size:22 final size:23
Alignment explanation
Indices: 9333916--9333963 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
9333906 CAAAAAGACA
* *
9333916 ATTTTG-TGTGCGTGTAAAAACC
1 ATTTTGCTGTACGTGCAAAAACC
*
9333938 ATTTTGCTTTACGTGCAAAAACC
1 ATTTTGCTGTACGTGCAAAAACC
9333961 ATT
1 ATT
9333964 AAGGACAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (23 bp):
ATTTTGCTGTACGTGCAAAAACC
Found at i:9335404 original size:44 final size:44
Alignment explanation
Indices: 9335340--9335429 Score: 155
Period size: 44 Copynumber: 2.0 Consensus size: 44
9335330 TTGTTGTTGC
*
9335340 TATCATCTTCTAAAAGAACTCCATCAAGAGTCCCTGGACTTTCT
1 TATCATCTTCTAAAAGAACTCCATCAAGAGTCCCTAGACTTTCT
9335384 TATCATCTTCTACAAA-AACTCCATCAAGAGTCCCTAGACTTTCT
1 TATCATCTTCTA-AAAGAACTCCATCAAGAGTCCCTAGACTTTCT
9335428 TA
1 TA
9335430 ACCTTGCTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 41 0.93
45 3 0.07
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (44 bp):
TATCATCTTCTAAAAGAACTCCATCAAGAGTCCCTAGACTTTCT
Found at i:9336800 original size:48 final size:48
Alignment explanation
Indices: 9336729--9336823 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
9336719 TGTAAAAAGT
*
9336729 CTAGTTCTGAAACAACCTCCACTCACGATAGTCTCACTTTGGAATAGA
1 CTAGTTCTGAAACAACCTCCACTCACGATAGTCTCACTTCGGAATAGA
*
9336777 CTAGTTTTGAAACAACCTCCACTCACGATAGTCTCACTTCGGAATAG
1 CTAGTTCTGAAACAACCTCCACTCACGATAGTCTCACTTCGGAATAG
9336824 GATCTTTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (48 bp):
CTAGTTCTGAAACAACCTCCACTCACGATAGTCTCACTTCGGAATAGA
Found at i:9340680 original size:3 final size:3
Alignment explanation
Indices: 9340672--9340718 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
9340662 TTTTGTTTTC
9340672 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
9340719 AACATATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9354275 original size:13 final size:13
Alignment explanation
Indices: 9354257--9354287 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
9354247 CATAACATAC
9354257 GAGTTAGGTAAAT
1 GAGTTAGGTAAAT
9354270 GAGTTAGGTAAAT
1 GAGTTAGGTAAAT
*
9354283 CAGTT
1 GAGTT
9354288 TTGACTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.32
Consensus pattern (13 bp):
GAGTTAGGTAAAT
Found at i:9361979 original size:22 final size:22
Alignment explanation
Indices: 9361930--9361978 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
9361920 ATATAGTGGA
9361930 ATTTTTATTTTGAGTTTAATTT
1 ATTTTTATTTTGAGTTTAATTT
*
9361952 ATTTTTATTTT-A-TCTTATTTT
1 ATTTTTATTTTGAGT-TTAATTT
9361973 ATTTTT
1 ATTTTT
9361979 TTCCAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.52
22 11 0.44
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (22 bp):
ATTTTTATTTTGAGTTTAATTT
Found at i:9373800 original size:9 final size:9
Alignment explanation
Indices: 9373786--9373820 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
9373776 TATAGAGTGG
9373786 CATGCTTCA
1 CATGCTTCA
9373795 CATGCTTCA
1 CATGCTTCA
* *
9373804 TATGTTTCA
1 CATGCTTCA
9373813 CATGCTTC
1 CATGCTTC
9373821 CATTTCAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.20, C:0.29, G:0.11, T:0.40
Consensus pattern (9 bp):
CATGCTTCA
Found at i:9383330 original size:12 final size:13
Alignment explanation
Indices: 9383313--9383349 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
9383303 GAACAGGACA
9383313 CGAACCGAA-CTC
1 CGAACCGAAGCTC
9383325 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
9383337 CGAACCGTAGCTC
1 CGAACCGAAGCTC
9383350 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:9387999 original size:17 final size:17
Alignment explanation
Indices: 9387979--9388023 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
9387969 GCAGTCTCGG
*
9387979 TGAGCACATAGTGTTGA
1 TGAGCACACAGTGTTGA
* *
9387996 TGAGCTCACAGTGTTGG
1 TGAGCACACAGTGTTGA
*
9388013 TGAGCTCACAG
1 TGAGCACACAG
9388024 ATATGGTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (17 bp):
TGAGCACACAGTGTTGA
Found at i:9388015 original size:34 final size:34
Alignment explanation
Indices: 9387996--9388079 Score: 132
Period size: 34 Copynumber: 2.5 Consensus size: 34
9387986 ATAGTGTTGA
*
9387996 TGAGCTCACAGTGTTGGTGAGCTCACAGATATGG
1 TGAGCTCACAGTGTTGGTGAGCTCATAGATATGG
* * *
9388030 TGAGCTCATATTGTTGGTGAGCTTATAGATATGG
1 TGAGCTCACAGTGTTGGTGAGCTCATAGATATGG
9388064 TGAGCTCACAGTGTTG
1 TGAGCTCACAGTGTTG
9388080 AAGTCTGGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.23, C:0.14, G:0.31, T:0.32
Consensus pattern (34 bp):
TGAGCTCACAGTGTTGGTGAGCTCATAGATATGG
Found at i:9388030 original size:17 final size:16
Alignment explanation
Indices: 9387996--9388075 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 16
9387986 ATAGTGTTGA
*
9387996 TGAGCTCACAGTGTTGG
1 TGAGCTCACAGT-ATGG
9388013 TGAGCTCACAGATATGG
1 TGAGCTCACAG-TATGG
*
9388030 TGAGCTCATATTGT-TGG
1 TGAGCTCACA--GTATGG
* *
9388047 TGAGCTTATAGATATGG
1 TGAGCTCACAG-TATGG
9388064 TGAGCTCACAGT
1 TGAGCTCACAGT
9388076 GTTGAAGTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
15 1 0.02
16 2 0.04
17 47 0.89
18 2 0.04
19 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (16 bp):
TGAGCTCACAGTATGG
Found at i:9388032 original size:51 final size:51
Alignment explanation
Indices: 9387977--9388074 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
9387967 TCGCAGTCTC
*
9387977 GGTGAGCACATAGTGTTGATGAGCTCACAG-TGTTGGTGAGCTCACAGATAT
1 GGTGAGCACATAGTGTTGATGAGCTCACAGAT-ATGGTGAGCTCACAGATAT
* * * * *
9388028 GGTGAGCTCATATTGTTGGTGAGCTTATAGATATGGTGAGCTCACAG
1 GGTGAGCACATAGTGTTGATGAGCTCACAGATATGGTGAGCTCACAG
9388075 TGTTGAAGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
51 39 0.98
52 1 0.03
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.30
Consensus pattern (51 bp):
GGTGAGCACATAGTGTTGATGAGCTCACAGATATGGTGAGCTCACAGATAT
Found at i:9401864 original size:124 final size:124
Alignment explanation
Indices: 9401636--9401887 Score: 468
Period size: 124 Copynumber: 2.0 Consensus size: 124
9401626 ATGAAATATG
* *
9401636 AGCCCTCAAATAGAAATTCCAAATTACCATATTTTGTTACTCAAACTCAATGGTGAATGTTAAGT
1 AGCCCTCAAATAGAAATTCAAAATTACCATATTCTGTTACTCAAACTCAATGGTGAATGTTAAGT
*
9401701 ATGCATCAAACAAGGTATGCTCAATTTTCTACATATTTTTGATACATTTAGAGGATCAT
66 ATGCATCAAACAAGGTATGCTCAATTTTCAACATATTTTTGATACATTTAGAGGATCAT
9401760 AGCCCTCAAATAGAAATTCAAAATTACCATATTCTGTTACTCAAACTCAATGGTGAATGTTAAGT
1 AGCCCTCAAATAGAAATTCAAAATTACCATATTCTGTTACTCAAACTCAATGGTGAATGTTAAGT
*
9401825 ATGCATCAAACAAGGTATGCTCAATTTTCAACATTTTTTTGATACATTTAGAGGATCAT
66 ATGCATCAAACAAGGTATGCTCAATTTTCAACATATTTTTGATACATTTAGAGGATCAT
9401884 AGCC
1 AGCC
9401888 TCATAACCAA
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (124 bp):
AGCCCTCAAATAGAAATTCAAAATTACCATATTCTGTTACTCAAACTCAATGGTGAATGTTAAGT
ATGCATCAAACAAGGTATGCTCAATTTTCAACATATTTTTGATACATTTAGAGGATCAT
Found at i:9414815 original size:65 final size:65
Alignment explanation
Indices: 9414711--9414844 Score: 223
Period size: 65 Copynumber: 2.1 Consensus size: 65
9414701 AATTTGAATT
**
9414711 GCTTCTGTTAATGTGTTTTTTGTATGGCAGATTCGGACACTTGCAAAACCTTTGTCTTGGCTCCG
1 GCTTCTGTTAATGTGTTTTTTGTATGGCAGATTCGGACACTTGCAAAACCTTTACCTTGGCTCCG
** *
9414776 GCTTCTGTTTGTGTGTTTTTTGTGTGGCAGATTCGGACACTTGCAAAACCTTTACCTTGGCTCCG
1 GCTTCTGTTAATGTGTTTTTTGTATGGCAGATTCGGACACTTGCAAAACCTTTACCTTGGCTCCG
9414841 GCTT
1 GCTT
9414845 AGCGAACAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (65 bp):
GCTTCTGTTAATGTGTTTTTTGTATGGCAGATTCGGACACTTGCAAAACCTTTACCTTGGCTCCG
Found at i:9426264 original size:31 final size:31
Alignment explanation
Indices: 9426229--9426297 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
9426219 CTTAAAAGCC
* **
9426229 CAGTGACTTAAAT-AAAATTTTTTGAATGGTT
1 CAGTGACTTAAATGAAAA-CTTTTGAATAATT
9426260 CAGTGACTTAAATGAAAACTTTTGAATAATT
1 CAGTGACTTAAATGAAAACTTTTGAATAATT
9426291 CAGTGAC
1 CAGTGAC
9426298 CAAATTGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (31 bp):
CAGTGACTTAAATGAAAACTTTTGAATAATT
Found at i:9431104 original size:6 final size:6
Alignment explanation
Indices: 9431095--9431135 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
9431085 TCTCCTCTTC
*
9431095 CTCTAA CTCTAA CTCTTAA CTCTGA CTCTTAA CTCTAA CTC
1 CTCTAA CTCTAA CTC-TAA CTCTAA CTC-TAA CTCTAA CTC
9431136 CTGTCCTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.27, C:0.34, G:0.02, T:0.37
Consensus pattern (6 bp):
CTCTAA
Found at i:9431116 original size:13 final size:13
Alignment explanation
Indices: 9431098--9431135 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
9431088 CCTCTTCCTC
9431098 TAACTCTAACTCT
1 TAACTCTAACTCT
*
9431111 TAACTCTGACTCT
1 TAACTCTAACTCT
9431124 TAACTCTAACTC
1 TAACTCTAACTC
9431136 CTGTCCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.29, C:0.32, G:0.03, T:0.37
Consensus pattern (13 bp):
TAACTCTAACTCT
Found at i:9431122 original size:19 final size:19
Alignment explanation
Indices: 9431095--9431135 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
9431085 TCTCCTCTTC
9431095 CTCTAACTCTAACTCTTAA
1 CTCTAACTCTAACTCTTAA
*
9431114 CTCTGACTCTTAACTC-TAA
1 CTCTAACTC-TAACTCTTAA
9431133 CTC
1 CTC
9431136 CTGTCCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.27, C:0.34, G:0.02, T:0.37
Consensus pattern (19 bp):
CTCTAACTCTAACTCTTAA
Found at i:9435804 original size:21 final size:22
Alignment explanation
Indices: 9435757--9435823 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
9435747 TTGACACAGA
*
9435757 ATTAAATTATATATTTTATAAT
1 ATTAAAATATATATTTTATAAT
*
9435779 ATTAAAATATA-ATTTTATCAT
1 ATTAAAATATATATTTTATAAT
* * *
9435800 TTTAATATTTTATATATTTATAAT
1 ATTAA-AATATATAT-TTTATAAT
9435824 TTTTAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 13 0.36
22 14 0.39
23 2 0.06
24 7 0.19
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAAAATATATATTTTATAAT
Found at i:9435825 original size:16 final size:16
Alignment explanation
Indices: 9435786--9435826 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
9435776 AATATTAAAA
9435786 TATAATTTTATCATTT
1 TATAATTTTATCATTT
9435802 TA-ATATTTTAT-ATATT
1 TATA-ATTTTATCAT-TT
9435818 TATAATTTT
1 TATAATTTT
9435827 TAAAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.14
16 18 0.82
17 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TATAATTTTATCATTT
Found at i:9435839 original size:16 final size:16
Alignment explanation
Indices: 9435798--9435840 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
9435788 TAATTTTATC
* *
9435798 ATTTTAATATTTTATAT
1 ATTTTAAT-TTTTAAAA
9435815 ATTTATAATTTTTAAAA
1 ATTT-TAATTTTTAAAA
9435832 ATTTTAATT
1 ATTTTAATT
9435841 AAATTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 14 0.61
18 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTAATTTTTAAAA
Found at i:9435923 original size:30 final size:30
Alignment explanation
Indices: 9435889--9435983 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
9435879 ATCGTTAATT
9435889 TAAAATTTAATAAGTTATAAATAGCCTAAA
1 TAAAATTTAATAAGTTATAAATAGCCTAAA
* * * * *
9435919 TAAAA--AAATACAATTTTATCATAG-CTAATT
1 TAAAATTTAATA-AGTTATA-AATAGCCTAA-A
9435949 TAAAATTTAATAAGTTATAAATAGCCTAAA
1 TAAAATTTAATAAGTTATAAATAGCCTAAA
9435979 TAAAA
1 TAAAA
9435984 AAAAAATTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
28 4 0.08
29 9 0.18
30 23 0.47
31 9 0.18
32 4 0.08
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (30 bp):
TAAAATTTAATAAGTTATAAATAGCCTAAA
Found at i:9435931 original size:60 final size:60
Alignment explanation
Indices: 9435867--9435986 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
9435857 TAAGAGAAAG
* *
9435867 TACAATTTTATCATCGTTAATTTAAAATTTAATAAGTTATAAATAGCCTAAATAAAAAAA
1 TACAATTTTATCATAGCTAATTTAAAATTTAATAAGTTATAAATAGCCTAAATAAAAAAA
9435927 TACAATTTTATCATAGCTAATTTAAAATTTAATAAGTTATAAATAGCCTAAATAAAAAAA
1 TACAATTTTATCATAGCTAATTTAAAATTTAATAAGTTATAAATAGCCTAAATAAAAAAA
9435987 AAATTATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (60 bp):
TACAATTTTATCATAGCTAATTTAAAATTTAATAAGTTATAAATAGCCTAAATAAAAAAA
Found at i:9437116 original size:9 final size:9
Alignment explanation
Indices: 9437102--9437132 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
9437092 GTTAAACAAA
9437102 TCGAGTTAT
1 TCGAGTTAT
*
9437111 TCGAGTTAA
1 TCGAGTTAT
9437120 TCGAGTTAT
1 TCGAGTTAT
9437129 TCGA
1 TCGA
9437133 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:9437573 original size:30 final size:31
Alignment explanation
Indices: 9437521--9437579 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
9437511 CCAATTTTTT
*
9437521 TTTATTTTCCCTCTAAAATTTTACTCCCCTA
1 TTTACTTTCCCTCTAAAATTTTACTCCCCTA
* * *
9437552 TTTACTTTCCGTC-AAACTTTTATTCCCC
1 TTTACTTTCCCTCTAAAATTTTACTCCCC
9437580 AAAACTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.20, C:0.31, G:0.02, T:0.47
Consensus pattern (31 bp):
TTTACTTTCCCTCTAAAATTTTACTCCCCTA
Found at i:9438241 original size:5 final size:5
Alignment explanation
Indices: 9438231--9438272 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
9438221 AAAATTTTTT
9438231 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG AT
9438273 CGAATGCTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (5 bp):
ATTCG
Found at i:9445791 original size:3 final size:3
Alignment explanation
Indices: 9445783--9445828 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
9445773 TTCTATTCTG
9445783 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9445829 TTCTGTGCGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9447380 original size:26 final size:27
Alignment explanation
Indices: 9447329--9447390 Score: 108
Period size: 26 Copynumber: 2.3 Consensus size: 27
9447319 ATAAAAAAAC
9447329 CCAAAATATTATAACTTTTTTTATTTA
1 CCAAAATATTATAACTTTTTTTATTTA
*
9447356 TCAAAATATTATAA-TTTTTTTATTTA
1 CCAAAATATTATAACTTTTTTTATTTA
9447382 CCAAAATAT
1 CCAAAATAT
9447391 AAAAAAACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
26 20 0.61
27 13 0.39
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (27 bp):
CCAAAATATTATAACTTTTTTTATTTA
Found at i:9447468 original size:27 final size:27
Alignment explanation
Indices: 9447429--9447487 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
9447419 GCCTGATCAG
*
9447429 GCCAATCACATTGGAGGCACCAAAGGT
1 GCCAATCACATTGGAGGCACCAAAGGC
* * * *
9447456 GCCAATGAGATTGGCGGCACCAATGGC
1 GCCAATCACATTGGAGGCACCAAAGGC
9447483 GCCAA
1 GCCAA
9447488 AGGACTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.27, G:0.29, T:0.14
Consensus pattern (27 bp):
GCCAATCACATTGGAGGCACCAAAGGC
Found at i:9448054 original size:19 final size:19
Alignment explanation
Indices: 9447999--9448056 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
9447989 CTAATTAAGC
9447999 AATAACTCTATTTTAATTT
1 AATAACTCTATTTTAATTT
* * *
9448018 AATAA-ACTATTCTCATTT
1 AATAACTCTATTTTAATTT
9448036 AATAACTCTATTTTAATTT
1 AATAACTCTATTTTAATTT
9448055 AA
1 AA
9448057 AAAAATTAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAACTCTATTTTAATTT
Found at i:9448163 original size:18 final size:19
Alignment explanation
Indices: 9448134--9448224 Score: 114
Period size: 18 Copynumber: 4.9 Consensus size: 19
9448124 TCTAATTAAG
*
9448134 TAATAACTCTATTTTAATT
1 TAATAACACTATTTTAATT
* *
9448153 TAATAA-ACTATTCTCATT
1 TAATAACACTATTTTAATT
9448171 TAATAACACTATTTTAATT
1 TAATAACACTATTTTAATT
* *
9448190 TAATAA-ACTATTCTCATT
1 TAATAACACTATTTTAATT
*
9448208 TAATAACTCTATTTTAA
1 TAATAACACTATTTTAA
9448225 ATTTTAATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 31 0.52
19 29 0.48
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATAACACTATTTTAATT
Found at i:9448175 original size:37 final size:37
Alignment explanation
Indices: 9448134--9448224 Score: 173
Period size: 37 Copynumber: 2.5 Consensus size: 37
9448124 TCTAATTAAG
9448134 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
*
9448171 TAATAACACTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
9448208 TAATAACTCTATTTTAA
1 TAATAACTCTATTTTAA
9448225 ATTTTAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (37 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
Found at i:9448268 original size:136 final size:135
Alignment explanation
Indices: 9447983--9448256 Score: 381
Period size: 136 Copynumber: 2.0 Consensus size: 135
9447973 TAAGATATTT
*
9447983 AGAATTCTAATTAAGCAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATT
1 AGAATTCTAATTAAGCAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACACTATT
* * * *
9448048 TTAATTTAAAAAAATTAAGTAAATTATTTTAATTTAATTTTTTTAAAATTAAAATAGAGTTATTA
66 TTAATTTAAAAAAATTAAGTAAATAACTCTAATTTAA-TATTTTAAAATTAAAATAGAGTTATTA
9448113 AATGAG
130 AATGAG
*
9448119 AGAATTCTAATTAAGTAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACACTATT
1 AGAATTCTAATTAAGCAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACACTATT
* * * * * *
9448184 TTAATTTAATAAACTATTCTCATTTAATAACTCTATTTTAA-ATTTT-AATTTAAAATAGAGTTA
66 TTAATTTAA-AAA--AAT-TAAGTAAATAACTCTAATTTAATATTTTAAAATTAAAATAGAGTTA
9448247 TTAAATGAG
127 TTAAATGAG
9448256 A
1 A
9448257 ATAGTTTATT
Statistics
Matches: 122, Mismatches: 12, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
136 72 0.59
137 29 0.24
138 4 0.03
139 2 0.02
140 15 0.12
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (135 bp):
AGAATTCTAATTAAGCAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACACTATT
TTAATTTAAAAAAATTAAGTAAATAACTCTAATTTAATATTTTAAAATTAAAATAGAGTTATTAA
ATGAG
Found at i:9448284 original size:37 final size:37
Alignment explanation
Indices: 9448228--9448323 Score: 174
Period size: 37 Copynumber: 2.6 Consensus size: 37
9448218 ATTTTAAATT
*
9448228 TTAATTTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
*
9448265 TTAAATTAAAATAGTGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
9448302 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
9448324 CTTAATTAGA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:9448314 original size:18 final size:18
Alignment explanation
Indices: 9448228--9448315 Score: 104
Period size: 18 Copynumber: 4.8 Consensus size: 18
9448218 ATTTTAAATT
* *
9448228 TTAATTTAAAATAGAGTTA
1 TTAAATTAAAATAG-TTTA
* *
9448247 TTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGTTTA
9448265 TTAAATTAAAATAGTGTTA
1 TTAAATTAAAATAGT-TTA
* *
9448284 TTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGTTTA
9448302 TTAAATTAAAATAG
1 TTAAATTAAAATAG
9448316 AGTTATTACT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
18 31 0.53
19 27 0.47
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (18 bp):
TTAAATTAAAATAGTTTA
Found at i:9448604 original size:20 final size:20
Alignment explanation
Indices: 9448581--9448618 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9448571 TTATACTTTT
9448581 TAAAATAGT-TTTACTTTAGG
1 TAAAATA-TATTTACTTTAGG
9448601 TAAAATATATTTACTTTA
1 TAAAATATATTTACTTTA
9448619 ATAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (20 bp):
TAAAATATATTTACTTTAGG
Found at i:9448968 original size:26 final size:27
Alignment explanation
Indices: 9448938--9449000 Score: 119
Period size: 26 Copynumber: 2.4 Consensus size: 27
9448928 GTTTTTTTTT
9448938 ATATTTTGGTAAATAAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
9448964 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
9448991 ATATTTTGGT
1 ATATTTTGGT
9449001 TTTTTTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 21 0.58
27 15 0.42
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:9449459 original size:19 final size:20
Alignment explanation
Indices: 9449437--9449475 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9449427 CATTTTTTTT
*
9449437 ATTATA-AAAATTTTTAAAA
1 ATTATAGAAAACTTTTAAAA
9449456 ATTATAGAAAACTTTTAAAA
1 ATTATAGAAAACTTTTAAAA
9449476 TATATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
ATTATAGAAAACTTTTAAAA
Found at i:9449675 original size:20 final size:22
Alignment explanation
Indices: 9449652--9449698 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
9449642 ATTTTCATAT
9449652 TAAAATAAATT-AAATTTA-AA
1 TAAAATAAATTAAAATTTAGAA
**
9449672 TAAAA-ATTTTAAAATTTAGAA
1 TAAAATAAATTAAAATTTAGAA
9449693 TAAAAT
1 TAAAAT
9449699 TACTGATGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 12 0.55
21 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAAATAAATTAAAATTTAGAA
Found at i:9451501 original size:24 final size:24
Alignment explanation
Indices: 9451474--9451547 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 24
9451464 AGCACACCAA
9451474 AACTATAAGAAGCATAAGACCCTT
1 AACTATAAGAAGCATAAGACCCTT
* **
9451498 AACTAT---AAGC---ACA-CCAA
1 AACTATAAGAAGCATAAGACCCTT
9451515 AACTATAAGAAGCATAAGACCCTT
1 AACTATAAGAAGCATAAGACCCTT
9451539 AACTATAAG
1 AACTATAAG
9451548 GCAATATACA
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
17 8 0.22
18 2 0.05
20 4 0.11
21 4 0.11
23 2 0.05
24 17 0.46
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.19
Consensus pattern (24 bp):
AACTATAAGAAGCATAAGACCCTT
Found at i:9451520 original size:41 final size:41
Alignment explanation
Indices: 9451463--9451547 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
9451453 TCCTAAGCCA
9451463 AAGCACACCAAAACTATAAGAAGCATAAGACCCTTAACTAT
1 AAGCACACCAAAACTATAAGAAGCATAAGACCCTTAACTAT
9451504 AAGCACACCAAAACTATAAGAAGCATAAGACCCTTAACTAT
1 AAGCACACCAAAACTATAAGAAGCATAAGACCCTTAACTAT
9451545 AAG
1 AAG
9451548 GCAATATACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.49, C:0.24, G:0.11, T:0.16
Consensus pattern (41 bp):
AAGCACACCAAAACTATAAGAAGCATAAGACCCTTAACTAT
Found at i:9452972 original size:3 final size:3
Alignment explanation
Indices: 9452964--9452998 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
9452954 CTCAATAGAT
*
9452964 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9452999 TCTTCCTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:9464029 original size:20 final size:20
Alignment explanation
Indices: 9463976--9464043 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 20
9463966 TTAAAAAAAA
*
9463976 TAAAAA-TATTTTTATACCTTT
1 TAAAAATTATTTTTA-A-TTTT
* *
9463997 T-AAAATAAATTTTAATTTT
1 TAAAAATTATTTTTAATTTT
*
9464016 TAAAAATTATTTTTTGATTTT
1 TAAAAATTA-TTTTTAATTTT
9464037 TATAAAA
1 TA-AAAA
9464044 AAATAATAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 4 0.11
20 11 0.30
21 18 0.49
22 4 0.11
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (20 bp):
TAAAAATTATTTTTAATTTT
Found at i:9464703 original size:12 final size:12
Alignment explanation
Indices: 9464682--9464711 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
9464672 AAGATTCTTC
9464682 CTTTTCCTTTTT
1 CTTTTCCTTTTT
*
9464694 CTTTTTCTTTTT
1 CTTTTCCTTTTT
9464706 CTTTTC
1 CTTTTC
9464712 TTGTTGTACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
CTTTTCCTTTTT
Found at i:9464799 original size:5 final size:5
Alignment explanation
Indices: 9464785--9464817 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
9464775 TTATCATGTG
*
9464785 TATA- TATAT TATAT TATAT TAAAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
9464818 AGGTTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:9467976 original size:16 final size:16
Alignment explanation
Indices: 9467934--9467968 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
9467924 CAAAGTGATA
9467934 TATGTGATATGTCAAG
1 TATGTGATATGTCAAG
9467950 TATGTGATATGTCAAG
1 TATGTGATATGTCAAG
9467966 TAT
1 TAT
9467969 TTTATATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (16 bp):
TATGTGATATGTCAAG
Found at i:9468816 original size:14 final size:14
Alignment explanation
Indices: 9468766--9468817 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
9468756 AGCTTAAGGT
* *
9468766 TTTAATTAATTTAG
1 TTTAATTAATTAAA
9468780 TTTAATTAAATTAAA
1 TTTAATT-AATTAAA
* * *
9468795 TATGATTAGTTAAA
1 TTTAATTAATTAAA
9468809 TTTAATTAA
1 TTTAATTAA
9468818 AGTATAAAAG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:9469167 original size:13 final size:13
Alignment explanation
Indices: 9469149--9469173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9469139 GTGCATAAAT
9469149 TGAAAATTTTATG
1 TGAAAATTTTATG
9469162 TGAAAATTTTAT
1 TGAAAATTTTAT
9469174 AATTATAGAT
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:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TGAAAATTTTATG
Found at i:9472937 original size:26 final size:26
Alignment explanation
Indices: 9472908--9472967 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
9472898 ACATCATAGG
*
9472908 TTGTACATTTTCTCTTTTTGATGTTA
1 TTGTACATTTTCTCTTTTCGATGTTA
9472934 TTGTACATTTTCTCTTTTCGATGTTA
1 TTGTACATTTTCTCTTTTCGATGTTA
*
9472960 CTGTACAT
1 TTGTACAT
9472968 GCTTTGATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.57
Consensus pattern (26 bp):
TTGTACATTTTCTCTTTTCGATGTTA
Found at i:9476312 original size:31 final size:31
Alignment explanation
Indices: 9476213--9476317 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 31
9476203 TTTAATAAAT
* * * *
9476213 TTAAATTAATGTTTATCTAGTTAGAT-TTTTA
1 TTAATTTAATATTTATCTTGATA-ATATTTTA
* * * **
9476244 TTAATTTAATATTAAT-ATGA-GATATTAAA
1 TTAATTTAATATTTATCTTGATAATATTTTA
9476273 TTTAATTTAATATTTATCTTGATAATATTTTA
1 -TTAATTTAATATTTATCTTGATAATATTTTA
9476305 TTAATTTAATATT
1 TTAATTTAATATT
9476318 AATGTCATTA
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
28 2 0.04
29 3 0.05
30 16 0.29
31 29 0.52
32 6 0.11
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (31 bp):
TTAATTTAATATTTATCTTGATAATATTTTA
Found at i:9478602 original size:6 final size:6
Alignment explanation
Indices: 9478587--9478679 Score: 60
Period size: 6 Copynumber: 15.5 Consensus size: 6
9478577 ACGTACAACT
* * * * * * *
9478587 GTAATA GTAATG GTAAGA ATAATA ATAATA ATAATA ATAATA ATAATA
1 GTAATA GTAATA GTAATA GTAATA GTAATA GTAATA GTAATA GTAATA
* * * * * * *
9478635 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA GTA
1 GTAATA GTAATA GTAATA GTAATA GTAATA GTAATA GTAATA GTA
9478680 CGAAAACAAC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (6 bp):
GTAATA
Found at i:9478612 original size:3 final size:3
Alignment explanation
Indices: 9478604--9478676 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
9478594 TAATGGTAAG
9478604 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9478652 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
9478677 GTACGAAAAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9479455 original size:17 final size:18
Alignment explanation
Indices: 9479433--9479470 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9479423 AGAGAACATT
*
9479433 TTTTTG-TATTGATTTTC
1 TTTTTGATATAGATTTTC
*
9479450 TTTTTGATATAGTTTTTC
1 TTTTTGATATAGATTTTC
9479468 TTT
1 TTT
9479471 GAAAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.13, C:0.05, G:0.11, T:0.71
Consensus pattern (18 bp):
TTTTTGATATAGATTTTC
Found at i:9480687 original size:130 final size:129
Alignment explanation
Indices: 9480394--9480786 Score: 567
Period size: 130 Copynumber: 3.0 Consensus size: 129
9480384 CTACAACTTT
* * * * * * *
9480394 AGGGAGATAGGA-TTATCGGCTTCAATCTGATTCCTTACAGTTAAAGATAAGATTCGCCATTTTC
1 AGGGACATAGGACTTGT-GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCATCTTC
* * *
9480458 GATCTGCTCTGCTACTACTTAGGGAGACAAGATC-TGTAATTTCCAACATATTCCACTGCTAACC
65 GATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTTGTAATTTCCAACCTATTCCACTGCTAACC
* * *
9480522 AGGGACATAGGACTTGTGGCTTAAATCTACTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCG
1 AGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCATCTTCG
* *
9480587 ATCTGCTCCGCTCCTGCTTAGGGAGACAAGATCTTGTAATTTCCTAACCTATTCCACTGCTGACC
66 ATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTTGTAATTTCC-AACCTATTCCACTGCTAACC
* *
9480652 AGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCATCTTTG
1 AGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCATCTTCG
*
9480717 ATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTTGTAATTTCCCAACCTATTCCGCTGC-AACC
66 ATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTTGTAATTT-CCAACCTATTCCACTGCTAACC
9480781 GAGGGA
1 -AGGGA
9480787 GGCAAGGCTG
Statistics
Matches: 237, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
128 81 0.34
129 16 0.07
130 138 0.58
131 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (129 bp):
AGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCATCTTCG
ATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTTGTAATTTCCAACCTATTCCACTGCTAACC
Found at i:9480868 original size:88 final size:88
Alignment explanation
Indices: 9480773--9481249 Score: 731
Period size: 88 Copynumber: 5.4 Consensus size: 88
9480763 ACCTATTCCG
*
9480773 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTTGCTGTCAGCGCAGGAAGGCAAGA
1 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCAGCGCAGGAAGGCAAGA
*
9480838 TCTGCTATCTTTAACCTGCTCTA
66 TCTGCTATCTTTAACCTGCTCCA
* * * *
9480861 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGGTTCGTTGTCAGCGTAAGAAGGCAAGA
1 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCAGCGCAGGAAGGCAAGA
9480926 TCTGCTATCTTT-ACCTGCTCCA
66 TCTGCTATCTTTAACCTGCTCCA
* * * * * *
9480948 CTGCAATCGAGGGAGGCATGGCTTTGTTTCTTCGATCTGCTTCACTGTCAGCGGAGGAAGGCAAG
1 CTGCAACCGAGGGAGGCAAGGC-TGGTATCTTCGATCTGCTTCGCTGTCAGCGCAGGAAGGCAAG
*
9481013 ATTTGCTATCTTTAACCTGCTCCA
65 ATCTGCTATCTTTAACCTGCTCCA
* * * *
9481037 TTGCAACCGAGGGAGGGAAGGCTGGTATCTTCGATCTGCTTCGCTGTCATCGCAAGAAGGCAAGA
1 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCAGCGCAGGAAGGCAAGA
*
9481102 TCTGTTATCTTTAACCTGCTCCA
66 TCTGCTATCTTTAACCTGCTCCA
* **
9481125 CTGCAACCGAGGGAGCCAAGGCTGGTATCTTCGATCTGCTTCATTGTCAGCGCAGGAAGGCAAGA
1 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCAGCGCAGGAAGGCAAGA
*
9481190 TCTGCTATCTCTAACCTGCTCCA
66 TCTGCTATCTTTAACCTGCTCCA
*
9481213 CTGCAACCGAGGGAGGCAAGGCTGGTTTCTTCGATCT
1 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCT
9481250 TCACTAATCT
Statistics
Matches: 348, Mismatches: 39, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
87 29 0.08
88 291 0.84
89 28 0.08
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.27
Consensus pattern (88 bp):
CTGCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCAGCGCAGGAAGGCAAGA
TCTGCTATCTTTAACCTGCTCCA
Found at i:9481067 original size:43 final size:43
Alignment explanation
Indices: 9480773--9481243 Score: 223
Period size: 44 Copynumber: 10.7 Consensus size: 43
9480763 ACCTATTCCG
** * ***
9480773 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGCTTTG
1 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTTAACCTGCTCCA
* * * * *
9480816 CTGTC-AGCGCAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCTA
1 CTG-CAACCG-AGGGAGGCAAG-GCTGGTATCTTTAACCTGCTCCA
** * * * *
9480861 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTCGATCTGGTTCG
1 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTTAACCTGCTCCA
* * * * * *
9480904 TTGTC-AGCGTAAGAAGGCAAGATCTGCTATCTTT-ACCTGCTCCA
1 CTG-CAACCG-AGGGAGGCAAG-GCTGGTATCTTTAACCTGCTCCA
* * * * ** * *
9480948 CTGCAATCGAGGGAGGCATGGCTTTGTTTCTTCGATCTGCTTCA
1 CTGCAACCGAGGGAGGCAAGGC-TGGTATCTTTAACCTGCTCCA
* * * ** *
9480992 CTGTCAGCGGAGGAAGGCAAGATTTGCTATCTTTAACCTGCTCCA
1 CTG-CAACCGAGGGAGGCAAG-GCTGGTATCTTTAACCTGCTCCA
* * ** * * *
9481037 TTGCAACCGAGGGAGGGAAGGCTGGTATCTTCGATCTGCTTCG
1 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTTAACCTGCTCCA
* * * * *
9481080 CTGTC-ATCGCAAGAAGGCAAGATCTGTTATCTTTAACCTGCTCCA
1 CTG-CAACCG-AGGGAGGCAAG-GCTGGTATCTTTAACCTGCTCCA
* ** * *
9481125 CTGCAACCGAGGGAGCCAAGGCTGGTATCTTCGATCTGCTTCA
1 CTGCAACCGAGGGAGGCAAGGCTGGTATCTTTAACCTGCTCCA
* * * * * *
9481168 TTGTC-AGCGCAGGAAGGCAAGATCTGCTATCTCTAACCTGCTCCA
1 CTG-CAACCG-AGGGAGGCAAG-GCTGGTATCTTTAACCTGCTCCA
*
9481213 CTGCAACCGAGGGAGGCAAGGCTGGTTTCTT
1 CTGCAACCGAGGGAGGCAAGGCTGGTATCTT
9481244 CGATCTTCAC
Statistics
Matches: 298, Mismatches: 110, Indels: 40
0.67 0.25 0.09
Matches are distributed among these distances:
42 1 0.00
43 89 0.30
44 106 0.36
45 102 0.34
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.27
Consensus pattern (43 bp):
CTGCAACCGAGGGAGGCAAGGCTGGTATCTTTAACCTGCTCCA
Found at i:9487897 original size:3 final size:3
Alignment explanation
Indices: 9487875--9487953 Score: 131
Period size: 3 Copynumber: 26.3 Consensus size: 3
9487865 TAATGGTAAG
* *
9487875 AAT AAT AAC AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
9487923 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9487954 GTACGAAAAC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:9503445 original size:132 final size:132
Alignment explanation
Indices: 9503253--9503660 Score: 672
Period size: 132 Copynumber: 3.1 Consensus size: 132
9503243 TCAGTGAAAT
* *
9503253 CACAAGTCCTATATCCCTGACCAGCACTGGAATAGGTTTGGAAACTACAGATCTTATCTCCCTAA
1 CACAAGTCCTATATCCCTGGCCAGCAATGGAATAGGTTTGGAAACTACAGATCTTATCTCCCTAA
*** * *
9503318 GCAATAGTGGAGAAGATCGAAGATGAAAAATCTTATCTTCCCCAAAATTAAGGAAGCAGATTTAA
66 GCAATAGTGGAGAAGATCGAAGATGGCGAATCTTATCTTCCCCAGAAGTAAGGAAGCAGATTTAA
9503383 GC
131 GC
*
9503385 CACAAGTTCTATATCCCTGGCCAGCAATGGAATAGGTTTGGAAACTACAGATCTTATCTCCCTAA
1 CACAAGTCCTATATCCCTGGCCAGCAATGGAATAGGTTTGGAAACTACAGATCTTATCTCCCTAA
* * * * *
9503450 GCAATAGTGAAGTAGATCGAAGACGGCGAATCTTATCTTCCCTAGAAGTAAGGAAGCAAATTTAA
66 GCAATAGTGGAGAAGATCGAAGATGGCGAATCTTATCTTCCCCAGAAGTAAGGAAGCAGATTTAA
9503515 GC
131 GC
* * *
9503517 CACAAGTCCTATATCCCTGGCCAGTAGTGGAATAGGTTTGGAAATTACAGATCTTATCTCCCTAA
1 CACAAGTCCTATATCCCTGGCCAGCAATGGAATAGGTTTGGAAACTACAGATCTTATCTCCCTAA
9503582 GCAATAGTGGAGAAGATCGAAGATGGCGAATCTTATCTTCCCCAGAAGTAAGGAAGCAGATTTAA
66 GCAATAGTGGAGAAGATCGAAGATGGCGAATCTTATCTTCCCCAGAAGTAAGGAAGCAGATTTAA
9503647 GC
131 GC
9503649 CACAAGTCCTAT
1 CACAAGTCCTAT
9503661 GTCCTGGTCA
Statistics
Matches: 254, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 254 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (132 bp):
CACAAGTCCTATATCCCTGGCCAGCAATGGAATAGGTTTGGAAACTACAGATCTTATCTCCCTAA
GCAATAGTGGAGAAGATCGAAGATGGCGAATCTTATCTTCCCCAGAAGTAAGGAAGCAGATTTAA
GC
Found at i:9503963 original size:44 final size:40
Alignment explanation
Indices: 9503915--9504010 Score: 120
Period size: 40 Copynumber: 2.3 Consensus size: 40
9503905 TTGAAGTTGC
*
9503915 AGTGGGGCAGACCGAAAAACACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGACCG--AAACA-AG-TCTTATCTCCCTAAGCAGT
* * *
9503959 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGACCGAAACAAGTCTTATCTCCCTAAGCAGT
9503999 AGTGGAGCAGAC
1 AGTGGAGCAGAC
9504011 AGAAGAAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 30 0.64
41 2 0.04
42 3 0.06
44 12 0.26
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (40 bp):
AGTGGAGCAGACCGAAACAAGTCTTATCTCCCTAAGCAGT
Found at i:9504049 original size:44 final size:44
Alignment explanation
Indices: 9503851--9504225 Score: 180
Period size: 44 Copynumber: 8.7 Consensus size: 44
9503841 TCGTATCAGG
* * * * *
9503851 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTG-AGTAAGCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCA-A
* * *
9503895 TCTTATC-CCCTTGAAGTTGCAGTGGGGCAGACCGAA-AAACACAGA
1 TCTTATCTCCC-TGAAGTTGCAGTGGAGCAGACAGAAGAAA-TCA-A
** * *
9503940 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATC----G-CATCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAGAAGAAATCAA
** *
9503979 GTCTTATCTCCCT-AAGCAGTAGTGGAGCAGACAGAAGAAATCAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAA
* * *
9504023 TCCTATCTCCCTGAAGTTGCAGTGGAGC-GA-ATTAAAACAAT-AGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA-GAAGA-AATCA-A
* * * * **
9504067 TCTTATCTCCCT-AAGTAGTAGT--AG-AG-CAGATCG-CATCGGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAATC-AA
* *
9504107 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AGAAAACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAA
* ** * * *
9504150 GTCTTATCCCCCTGAAGTCACAGTGGGGCAGAC-TAAGAAAACAAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATC-AA
* *
9504195 TCTTATCCCCCTGAGGTTGCAGTGGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
9504226 TTGAAGTCGA
Statistics
Matches: 256, Mismatches: 45, Indels: 60
0.71 0.12 0.17
Matches are distributed among these distances:
39 4 0.02
40 45 0.18
41 13 0.05
42 1 0.00
43 32 0.12
44 141 0.55
45 17 0.07
46 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAA
Found at i:9504221 original size:256 final size:257
Alignment explanation
Indices: 9503764--9504226 Score: 630
Period size: 256 Copynumber: 1.8 Consensus size: 257
9503754 TGAAGTCGAT
* * ** * *
9503764 AATCCTATCTCCCTGAGGTTGTGTTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTGAAGTTGAGTTGGAGCAGATTAAAACAATAGATCTTATCTCCCTAAAGTAG
** * * * *
9503829 CAGTAGAGTGGATCGTATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGTAAGCAG
66 CAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGAAAACAA
* ** * * *
9503894 GTCTTATCCCCTTGAAGTTGCAGTGGGGCAGACCGAAAAACACAGATCTTATCTCCCTAAGCAGT
131 GTCTTATCCCCCTGAAGTCACAGTGGGGCAGACCGAAAAACACAAATCTTATCCCCCTAAGCAGC
9503959 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAATC
196 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAATC
9504021 AATCCTATCTCCCTGAAGTTGCAG-TGGAGC-GAATTAAAACAATAGATCTTATCTCCCT-AAGT
1 AATCCTATCTCCCTGAAGTTG-AGTTGGAGCAG-ATTAAAACAATAGATCTTATCTCCCTAAAGT
* * *
9504083 AGTAGTAGAGCAGATCGCATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGAAAAC
64 AGCAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGAAAAC
* *
9504148 AAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGA-CTAAGAAA-ACAAATCTTATCCCCCTGAGG
129 AAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGACCGAA-AAACACAAATCTTATCCCCCT-AAG
**
9504211 TTGCAGTGGAGCAGAT
192 CAGCAGTGGAGCAGAT
9504227 TGAAGTCGAT
Statistics
Matches: 177, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
255 18 0.10
256 109 0.62
257 49 0.28
258 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (257 bp):
AATCCTATCTCCCTGAAGTTGAGTTGGAGCAGATTAAAACAATAGATCTTATCTCCCTAAAGTAG
CAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGAAAACAA
GTCTTATCCCCCTGAAGTCACAGTGGGGCAGACCGAAAAACACAAATCTTATCCCCCTAAGCAGC
AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAATC
Found at i:9504256 original size:44 final size:43
Alignment explanation
Indices: 9504193--9504314 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 43
9504183 TAAGAAAACA
* * * *
9504193 AATCTTATCCCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGAT
1 AATCTTATCTCCCTAAGGTTGCAGTGGAGCAGATTAAAGT-AAT
* * *
9504237 AATCCTATCTCCCTAAGGTTG-TGTTGGAGCGGATTAAAGTAAT
1 AATCTTATCTCCCTAAGGTTGCAG-TGGAGCAGATTAAAGTAAT
* *
9504280 AGATCTTATCTCTCTGAA-GTTGCAGTAGAGCAGAT
1 A-ATCTTATCTCCCT-AAGGTTGCAGTGGAGCAGAT
9504315 CGCATCAAGT
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
43 4 0.06
44 55 0.89
45 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (43 bp):
AATCTTATCTCCCTAAGGTTGCAGTGGAGCAGATTAAAGTAAT
Found at i:9505006 original size:18 final size:18
Alignment explanation
Indices: 9504983--9505018 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
9504973 ATTACAGATC
9504983 ATTTTATTTATTTATTTT
1 ATTTTATTTATTTATTTT
9505001 ATTTTATTTATTTATTTT
1 ATTTTATTTATTTATTTT
9505019 GGCTATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
ATTTTATTTATTTATTTT
Found at i:9505018 original size:13 final size:13
Alignment explanation
Indices: 9504983--9505017 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
9504973 ATTACAGATC
9504983 ATTTTATTTATTT
1 ATTTTATTTATTT
9504996 ATTTTATTTTATTT
1 ATTTTA-TTTATTT
9505010 A-TTTATTT
1 ATTTTATTT
9505018 TGGCTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 10 0.48
14 8 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:9523663 original size:15 final size:15
Alignment explanation
Indices: 9523643--9523673 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9523633 GATGTCACAA
9523643 ACCTCAATCACAATG
1 ACCTCAATCACAATG
9523658 ACCTCAATCACAATG
1 ACCTCAATCACAATG
9523673 A
1 A
9523674 AAAAGTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.32, G:0.06, T:0.19
Consensus pattern (15 bp):
ACCTCAATCACAATG
Found at i:9525071 original size:19 final size:19
Alignment explanation
Indices: 9525049--9525105 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
9525039 CATAAAAATC
9525049 TTATAATTTTATAATTTTT
1 TTATAATTTTATAATTTTT
*
9525068 TTATAATATTTATGATTTTT
1 TTATAAT-TTTATAATTTTT
9525088 TTAGTAATTTT-TAATTTT
1 TTA-TAATTTTATAATTTT
9525106 AAAAGGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.38
20 17 0.50
21 4 0.12
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TTATAATTTTATAATTTTT
Found at i:9534184 original size:9 final size:9
Alignment explanation
Indices: 9534172--9534202 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
9534162 ATTAAACGAA
9534172 TCGAGTTAT
1 TCGAGTTAT
*
9534181 TCGAGTTAA
1 TCGAGTTAT
9534190 TCGAGTTAT
1 TCGAGTTAT
9534199 TCGA
1 TCGA
9534203 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:9534522 original size:30 final size:32
Alignment explanation
Indices: 9534471--9534531 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
9534461 AAACATTTTA
*
9534471 TTTTCCCCCAAAAATTTTTATTCCC-TCCCAC
1 TTTTCCCCCAAAAACTTTTATTCCCTTCCCAC
*
9534502 TTTT-CCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAAACTTTTATTCCCTTCCCA
9534532 TCCCACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (32 bp):
TTTTCCCCCAAAAACTTTTATTCCCTTCCCAC
Found at i:9535661 original size:146 final size:146
Alignment explanation
Indices: 9535396--9536560 Score: 1337
Period size: 146 Copynumber: 8.0 Consensus size: 146
9535386 TTTTAAGTAA
* ** * * * *
9535396 AGTTTCCTTTTATTTGGTAAAAAATTAATTTTGGAGAACTGACGGTTATAATGTCACTGATCACG
1 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGATATAGTGTCACTGATCACG
* * * * * * * * **
9535461 TAACAACTGAGAGAGAGACT-GGACCATAGATAGTTGAGAGTAAAAATACCATAATCACCCTAAT
66 TAACGACTGAGAGAGAGACTAGG-CGACAGAGAGTCGAGAGTAAAAAGATCATAATCGCCCTAGC
* *
9535525 AAAAAGGACCAAATTAG
130 AAAAAGGGCCACATTAG
*
9535542 TGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGATATAGTGTCACTGATCACG
1 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGATATAGTGTCACTGATCACG
* * * *
9535607 TAACGATTGAGAGAGAGACTAGGCGACAGATAGCCTAGAGTAAAAAGATCATAATCGCCCTAGCA
66 TAACGACTGAGAGAGAGACTAGGCGACAGAGAGTCGAGAGTAAAAAGATCATAATCGCCCTAGCA
9535672 AAAAGGGCCACATTAG
131 AAAAGGGCCACATTAG
* * * * *
9535688 ATTTTCTTTTTCTTTATTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCATTGATCACA
1 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGATATAGTGTCACTGATCACG
* * * * * * *
9535753 TAATGATTGAGAGAGACACTAGACCG-CAGATAGTCGAGAGTAAAAATATCATAATCGCCCTATC
66 TAACGACTGAGAGAGAGACTAG-GCGACAGAGAGTCGAGAGTAAAAAGATCATAATCGCCCTAGC
9535817 AAAAAGGGCCACATTAG
130 AAAAAGGGCCACATTAG
* * * * * *
9535834 AGTTACTTTTTATTTTTTAAAATATTAATTATGGAGAATTGACA-ATTATAATGTCACTTATCAC
1 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGA-TATAGTGTCACTGATCAC
* * * * * * * *
9535898 GCAACGATTGAGAGAGAGACTGGGCGGCGGACAGTCGAGAGT--AAAGACCATAATCGTCCTAGC
65 GTAACGACTGAGAGAGAGACTAGGCGACAGAGAGTCGAGAGTAAAAAGATCATAATCGCCCTAGC
9535961 AAAAAGGGCCACATTAG
130 AAAAAGGGCCACATTAG
** * * * *
9535978 AGTTTCTTTTTATTTGGTAAAAAATTAATTTTGGAGAACTGACGGTTATAGTGTCACTGATCATG
1 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGATATAGTGTCACTGATCACG
* *
9536043 TAACGACTGAGAGAGAGACTAGACGACAGAGAGTCGAGAGTAAAAAGATCATAATCGCCTTAGCA
66 TAACGACTGAGAGAGAGACTAGGCGACAGAGAGTCGAGAGTAAAAAGATCATAATCGCCCTAGCA
*
9536108 AAAAGGGCCACATTAA
131 AAAAGGGCCACATTAG
* * *
9536124 AATTTCTTTTTATTTATTAAAAAA--AA--TTAGAGAATCGACA-ATTATAGTGTCACTGATCAC
1 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGA-TATAGTGTCACTGATCAC
* * * * * * *
9536184 GTAACGACTGAGAAAGAGAGAGACTTGGCGATAGGGAGTCGGGAGTAGAAAGACCATAATCACCC
65 GTAACGACT--G--AGAGAGAGACTAGGCGACAGAGAGTCGAGAGTAAAAAGATCATAATCGCCC
*
9536249 TAGCAAAAAAGGCCACATTAG
126 TAGCAAAAAGGGCCACATTAG
* * * *
9536270 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACCGTTATAGTGTTACTGATCACT
1 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGATATAGTGTCACTGATCACG
* * *
9536335 TAACGACTGAGAGAGAGACTGGGCGACAGAGAGTTGAGAGTAAAAAGATCATAATCGCCTTAGCA
66 TAACGACTGAGAGAGAGACTAGGCGACAGAGAGTCGAGAGTAAAAAGATCATAATCGCCCTAGCA
*
9536400 AAAAGGGCCACATTAA
131 AAAAGGGCCACATTAG
* * * *
9536416 AGTTTCTTTTTATTTATTAAAAAAATAATTTTGAAGAATTGATA-ATTATAATGTCACTGATCAC
1 AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGA-TATAGTGTCACTGATCAC
* * * * * *
9536480 GTAATGACTGAGAGAGAGACTGGGTGACAGACG-GTCGAGGGTAAAAAGACCATATTCGCCCTAG
65 GTAACGACTGAGAGAGAGACTAGGCGACAGA-GAGTCGAGAGTAAAAAGATCATAATCGCCCTAG
* * *
9536544 CGAAAATGGCCATATTA
129 CAAAAAGGGCCACATTA
9536561 CATCCCTTTC
Statistics
Matches: 865, Mismatches: 135, Indels: 38
0.83 0.13 0.04
Matches are distributed among these distances:
142 36 0.04
144 124 0.14
145 2 0.00
146 659 0.76
147 5 0.01
148 3 0.00
150 36 0.04
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (146 bp):
AGTTTCTTTTTATTTATTAAAAAATTAATTTTGGAGAATTGACAGATATAGTGTCACTGATCACG
TAACGACTGAGAGAGAGACTAGGCGACAGAGAGTCGAGAGTAAAAAGATCATAATCGCCCTAGCA
AAAAGGGCCACATTAG
Found at i:9541954 original size:76 final size:75
Alignment explanation
Indices: 9541812--9541970 Score: 182
Period size: 76 Copynumber: 2.1 Consensus size: 75
9541802 TTTAAAAAAA
* * *
9541812 AAAC-TTAAGCCCCTACTTTTTTTTTTCACTCAGTTAGGTACTTAATCTTTTAAAATGTATAAAA
1 AAACTTTAAGCCCCTACTTTTTTTTTTCACTCAATTAGGTACTTAATCTTTCAAAATGCATAAAA
*
9541876 AAAGGCCCTT
66 AAAGGCCCTC
* *
9541886 AAACATTTAAGCCCCTACTTTTTTCTTTTGTACTCAATTGGGTACTTGAA-C-TTCAAAATGCAT
1 AAAC-TTTAAGCCCCTACTTTTTT-TTTT-CACTCAATTAGGTACTT-AATCTTTCAAAATGCAT
* *
9541949 -CAAAAAGGCTCTC
62 AAAAAAAGGCCCTC
9541962 AAACTTTAA
1 AAACTTTAA
9541971 AAAAAAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
74 4 0.06
75 5 0.07
76 32 0.44
77 14 0.19
78 15 0.21
79 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (75 bp):
AAACTTTAAGCCCCTACTTTTTTTTTTCACTCAATTAGGTACTTAATCTTTCAAAATGCATAAAA
AAAGGCCCTC
Found at i:9542130 original size:10 final size:10
Alignment explanation
Indices: 9542115--9542234 Score: 53
Period size: 10 Copynumber: 12.7 Consensus size: 10
9542105 ACACATGGTA
9542115 AAAAAATTAT
1 AAAAAATTAT
9542125 -AAAAA--AT
1 AAAAAATTAT
9542132 -AAAAATTAT
1 AAAAAATTAT
9542141 AAAAAAATT-T
1 -AAAAAATTAT
**
9542151 -AAATTTTAAT
1 AAAAAATT-AT
9542161 AAAAAA--AT
1 AAAAAATTAT
*
9542169 TAAAAA-TAT
1 AAAAAATTAT
**
9542178 CAAAATTTTAT
1 -AAAAAATTAT
* *
9542189 TAAAAATTAG
1 AAAAAATTAT
*
9542199 AAAAAATGAT
1 AAAAAATTAT
*
9542209 -AAAAATGAT
1 AAAAAATTAT
*
9542218 AAAAAATTGT
1 AAAAAATTAT
9542228 AAAAAAT
1 AAAAAAT
9542235 AATTTATCAA
Statistics
Matches: 82, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
7 7 0.09
8 12 0.15
9 18 0.22
10 32 0.39
11 13 0.16
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:9542137 original size:16 final size:16
Alignment explanation
Indices: 9542116--9542146 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9542106 CACATGGTAA
9542116 AAAAATTATAAAAAAT
1 AAAAATTATAAAAAAT
9542132 AAAAATTATAAAAAA
1 AAAAATTATAAAAAA
9542147 ATTTAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATTATAAAAAAT
Found at i:9542161 original size:29 final size:29
Alignment explanation
Indices: 9542129--9542204 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
9542119 AATTATAAAA
**
9542129 AATAAAAATTATAAAAAAATTTAAATTTT
1 AATAAAAATTATAAAAAAATCAAAATTTT
* *
9542158 AATAAAAA-AATTAAAAATATCAAAATTTT
1 AATAAAAATTA-TAAAAAAATCAAAATTTT
* *
9542187 ATTAAAAATTAGAAAAAA
1 AATAAAAATTATAAAAAA
9542205 TGATAAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
28 1 0.03
29 35 0.95
30 1 0.03
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (29 bp):
AATAAAAATTATAAAAAAATCAAAATTTT
Found at i:9542545 original size:19 final size:19
Alignment explanation
Indices: 9542523--9542631 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 19
9542513 ACTTTATAAA
*
9542523 ATTTTATAATTTTTTCTAT
1 ATTTTATAATTTTTTATAT
*
9542542 ATTTCTAT-ATATTTTATA-
1 ATTT-TATAATTTTTTATAT
*
9542560 ATTTT-TAATAATTTTTAAAT
1 ATTTTATAAT--TTTTTATAT
*
9542580 ATTTTA-AATTTTTTATTAAA
1 ATTTTATAATTTTTTA-T-AT
*
9542600 ATTTAATAA-TTTTTATA-
1 ATTTTATAATTTTTTATAT
9542617 ATTTTTATAATTTTT
1 A-TTTTATAATTTTT
9542632 ATTGATTTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
16 1 0.01
17 4 0.06
18 18 0.25
19 23 0.32
20 23 0.32
21 2 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTATAATTTTTTATAT
Found at i:9542634 original size:38 final size:37
Alignment explanation
Indices: 9542515--9542633 Score: 118
Period size: 38 Copynumber: 3.1 Consensus size: 37
9542505 TTTTTACGAC
* * *
9542515 TTTATAAAATTTTATAATTTTTTCTATATTTCTAT-ATAT
1 TTTATAAAATTTAATAA-TTTTTATA-ATTTTTATAAT-T
**
9542554 TTTATAATTTTTAATAATTTTTA-AATATTTTA-AATTT
1 TTTATAAAATTTAATAATTTTTATAAT-TTTTATAA-TT
9542591 TTTATTAAAATTTAATAATTTTTATAATTTTTATAATT
1 TTTA-TAAAATTTAATAATTTTTATAATTTTTATAATT
9542629 TTTAT
1 TTTAT
9542634 TGATTTTTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
36 2 0.03
37 12 0.18
38 34 0.51
39 19 0.28
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (37 bp):
TTTATAAAATTTAATAATTTTTATAATTTTTATAATT
Found at i:9542639 original size:28 final size:27
Alignment explanation
Indices: 9542454--9542643 Score: 95
Period size: 28 Copynumber: 6.7 Consensus size: 27
9542444 TTTTGGTACG
9542454 ATAA-TTTTATAATTCTTTTATGAA-TTTT
1 ATAATTTTTATAA-T-TTTTAT-AATTTTT
* * * *
9542482 ATATTTCTTTACATTTTTTATATTTTTT
1 ATAATT-TTTATAATTTTTATAATTTTT
** * *
9542510 ACGA-CTTTATAAAATTTTATAATTTTTT
1 ATAATTTTTAT-AATTTTTATAA-TTTTT
* *
9542538 CTATATTTCTAT-ATATTTTATAATTTTT
1 ATA-ATTTTTATAAT-TTTTATAATTTTT
9542566 AATAATTTTTA-AATATTTTA-AATTTTTT
1 -ATAATTTTTATAAT-TTTTATAA-TTTTT
* *
9542594 ATTAAAATTTAATAATTTTTATAATTTTT
1 A-T-AATTTTTATAATTTTTATAATTTTT
*
9542623 ATAATTTTTATTGATTTTTAT
1 ATAATTTTTA-TAATTTTTAT
9542644 TTTTTTTCAT
Statistics
Matches: 121, Mismatches: 25, Indels: 32
0.68 0.14 0.18
Matches are distributed among these distances:
26 4 0.03
27 18 0.15
28 55 0.45
29 30 0.25
30 14 0.12
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (27 bp):
ATAATTTTTATAATTTTTATAATTTTT
Found at i:9542644 original size:10 final size:9
Alignment explanation
Indices: 9542454--9542643 Score: 95
Period size: 9 Copynumber: 20.2 Consensus size: 9
9542444 TTTTGGTACG
9542454 ATAA-TTTT
1 ATAATTTTT
9542462 ATAATTCTTTT
1 ATAA-T-TTTT
9542473 ATGAA-TTTT
1 AT-AATTTTT
*
9542482 ATATTTCTTT
1 ATAATT-TTT
* *
9542492 ACATTTTTT
1 ATAATTTTT
*
9542501 ATATTTTTT
1 ATAATTTTT
** *
9542510 ACGA-CTTT
1 ATAATTTTT
*
9542518 ATAAAATTTT
1 AT-AATTTTT
9542528 ATAATTTTTT
1 ATAA-TTTTT
* *
9542538 CTATATTTCT
1 ATA-ATTTTT
9542548 AT-ATATTTT
1 ATAAT-TTTT
9542557 ATAATTTTT
1 ATAATTTTT
9542566 AATAATTTTT
1 -ATAATTTTT
9542576 A-AATATTTT
1 ATAAT-TTTT
9542585 A-AATTTTTT
1 ATAA-TTTTT
* *
9542594 ATTAAAATTTA
1 A-T-AATTTTT
9542605 ATAATTTTT
1 ATAATTTTT
9542614 ATAATTTTT
1 ATAATTTTT
9542623 ATAATTTTT
1 ATAATTTTT
*
9542632 ATTGATTTTT
1 A-TAATTTTT
9542642 AT
1 AT
9542644 TTTTTTTCAT
Statistics
Matches: 143, Mismatches: 20, Indels: 37
0.71 0.10 0.19
Matches are distributed among these distances:
8 14 0.10
9 69 0.48
10 45 0.31
11 11 0.08
12 4 0.03
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:9543053 original size:26 final size:24
Alignment explanation
Indices: 9543017--9543076 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
9543007 ATTAATAATA
*
9543017 TAATTTTTTATGTTAAAAAAATCTT
1 TAATTTATTATGTTAAAAAAAT-TT
*
9543042 TATATTTATTATGTTAACAAAATTT
1 TA-ATTTATTATGTTAAAAAAATTT
*
9543067 TAAATTATTA
1 TAATTTATTA
9543077 ATTTGAAGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.23
25 6 0.19
26 18 0.58
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (24 bp):
TAATTTATTATGTTAAAAAAATTT
Found at i:9544649 original size:19 final size:21
Alignment explanation
Indices: 9544627--9544667 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9544617 ATAATATATA
9544627 TTATA-TA-TAATATATTTTT
1 TTATATTAGTAATATATTTTT
9544646 TTATATTAGTAATATATTTTT
1 TTATATTAGTAATATATTTTT
9544667 T
1 T
9544668 CAACTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTATATTAGTAATATATTTTT
Found at i:9544675 original size:23 final size:21
Alignment explanation
Indices: 9544634--9544676 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9544624 ATATTATATA
*
9544634 TAATATATTTTTTTATATTAG
1 TAATATATTTTTTAATATTAG
9544655 TAATATATTTTTTCAACTATTA
1 TAATATATTTTTT-AA-TATTA
9544677 TTTTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 1 0.05
23 5 0.26
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (21 bp):
TAATATATTTTTTAATATTAG
Found at i:9556854 original size:22 final size:22
Alignment explanation
Indices: 9556790--9556857 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
9556780 TAGAAAGAGT
9556790 TGGTTTAAG-TTTGGT-CGAATA
1 TGGTTTAAGTTTTGGTACGAA-A
* * * *
9556811 TGGTTTAGGTTTAGTTATGAAA
1 TGGTTTAAGTTTTGGTACGAAA
*
9556833 TGGTATAAGTTTTGGTACGAAA
1 TGGTTTAAGTTTTGGTACGAAA
9556855 TGG
1 TGG
9556858 GTTTTTGATG
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
21 8 0.22
22 25 0.69
23 3 0.08
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.41
Consensus pattern (22 bp):
TGGTTTAAGTTTTGGTACGAAA
Found at i:9565989 original size:2 final size:2
Alignment explanation
Indices: 9565982--9566053 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
9565972 TTGGGTCATA
9565982 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
9566024 TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
9566054 ATGGGTTCGA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.01, C:0.00, G:0.49, T:0.50
Consensus pattern (2 bp):
TG
Found at i:9568992 original size:22 final size:22
Alignment explanation
Indices: 9568967--9569012 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
9568957 CACCTAACCA
9568967 AAACCTAATTAACTACACAACT
1 AAACCTAATTAACTACACAACT
9568989 AAACCTAATTAACTACACAACT
1 AAACCTAATTAACTACACAACT
9569011 AA
1 AA
9569013 CTTCGTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (22 bp):
AAACCTAATTAACTACACAACT
Found at i:9572375 original size:9 final size:9
Alignment explanation
Indices: 9572353--9572410 Score: 57
Period size: 9 Copynumber: 6.4 Consensus size: 9
9572343 TTTGGTTAAA
9572353 AATTAACCG
1 AATTAACCG
*
9572362 TATTAATCC-
1 AATTAA-CCG
9572371 AATTAACCG
1 AATTAACCG
*
9572380 AATTAACTG
1 AATTAACCG
9572389 AATT-ACTCG
1 AATTAAC-CG
*
9572398 AATTAACTG
1 AATTAACCG
9572407 AATT
1 AATT
9572411 GAATAATTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
8 4 0.10
9 32 0.80
10 4 0.10
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (9 bp):
AATTAACCG
Found at i:9572385 original size:27 final size:27
Alignment explanation
Indices: 9572353--9572410 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
9572343 TTTGGTTAAA
*
9572353 AATTAACCGTATTAATCCAATTAACCG
1 AATTAACCGAATTAATCCAATTAACCG
* * * *
9572380 AATTAACTGAATTACTCGAATTAACTG
1 AATTAACCGAATTAATCCAATTAACCG
9572407 AATT
1 AATT
9572411 GAATAATTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (27 bp):
AATTAACCGAATTAATCCAATTAACCG
Found at i:9572392 original size:18 final size:18
Alignment explanation
Indices: 9572353--9572410 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
9572343 TTTGGTTAAA
* *
9572353 AATTAACCGTATTAA-TCC
1 AATTAACCGAATTAACT-G
9572371 AATTAACCGAATTAACTG
1 AATTAACCGAATTAACTG
9572389 AATT-ACTCGAATTAACTG
1 AATTAAC-CGAATTAACTG
9572407 AATT
1 AATT
9572411 GAATAATTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.06
18 33 0.92
19 1 0.03
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (18 bp):
AATTAACCGAATTAACTG
Found at i:9572555 original size:18 final size:18
Alignment explanation
Indices: 9572532--9572575 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
9572522 AATTTTTATG
9572532 ATTGGGTTGGGTTAGG-TA
1 ATTGGGTTGGGTT-GGATA
9572550 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGATA
*
9572568 CTTGGGTT
1 ATTGGGTT
9572576 TGGATTGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Done.