Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 153 of 168
Found at i:45379604 original size:10 final size:10
Alignment explanation
Indices: 45379589--45379635 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
45379579 TTCTCTATAT
45379589 ATTTTTTAGA
1 ATTTTTTAGA
*
45379599 ATTTTTTGAAA
1 ATTTTTT-AGA
*
45379610 ATTTTATA-A
1 ATTTTTTAGA
45379619 ATTTTTT-GA
1 ATTTTTTAGA
45379628 ATTTTTTA
1 ATTTTTTA
45379636 AAATCAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 15 0.48
10 8 0.26
11 8 0.26
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (10 bp):
ATTTTTTAGA
Found at i:45379648 original size:29 final size:30
Alignment explanation
Indices: 45379584--45379654 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
45379574 TAACTTTCTC
* *
45379584 TATATATTTTTTAGAATTTTTTGAAAATTT
1 TATAAATTTTTTAGAATTTTTTGAAAATAT
45379614 TATAAATTTTTT-GAATTTTTT-AAAATCAAT
1 TATAAATTTTTTAGAATTTTTTGAAAAT--AT
45379644 T-TAAATTTTTT
1 TATAAATTTTTT
45379655 TTGTAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.14
29 19 0.51
30 13 0.35
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.59
Consensus pattern (30 bp):
TATAAATTTTTTAGAATTTTTTGAAAATAT
Found at i:45383712 original size:20 final size:20
Alignment explanation
Indices: 45383687--45383748 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
45383677 TTTTTGGTTA
*
45383687 AAAATTACCCCAATTACCCG
1 AAAATTACCCAAATTACCCG
*
45383707 AAAATTACCCGAATTACCCG
1 AAAATTACCCAAATTACCCG
45383727 AAAATTACCCAAATTACCCG
1 AAAATTACCCAAATTACCCG
45383747 AA
1 AA
45383749 TTACCTGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19
Consensus pattern (20 bp):
AAAATTACCCAAATTACCCG
Found at i:45383758 original size:9 final size:9
Alignment explanation
Indices: 45383689--45383760 Score: 81
Period size: 9 Copynumber: 7.6 Consensus size: 9
45383679 TTTGGTTAAA
*
45383689 AATTACCCC
1 AATTACCCG
45383698 AATTACCCG
1 AATTACCCG
45383707 AAAATTACCCG
1 --AATTACCCG
45383718 AATTACCCG
1 AATTACCCG
*
45383727 AAAATTACCCA
1 --AATTACCCG
45383738 AATTACCCG
1 AATTACCCG
*
45383747 AATTACCTG
1 AATTACCCG
45383756 AATTA
1 AATTA
45383761 AATCACTACA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
9 38 0.69
11 17 0.31
ACGTcount: A:0.40, C:0.29, G:0.07, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:45383802 original size:37 final size:37
Alignment explanation
Indices: 45383761--45383873 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
45383751 ACCTGAATTA
* *
45383761 AATCACTACATGATTAAAAACATTACATAAATCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
45383798 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
45383835 AATCACTACATAATTAAAAACATTACATAAGTC-TTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
45383871 AAT
1 AAT
45383874 TAACACATAA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 6 0.08
37 66 0.92
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (37 bp):
AATCACTACATAATTAAAAACATTACATAAGTCTTTG
Found at i:45383809 original size:20 final size:20
Alignment explanation
Indices: 45383784--45383847 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
45383774 TTAAAAACAT
45383784 TACATAAATCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
*** *
45383804 TACAT-AAT-TAAAAAT-AT
1 TACATAAATCTTTGAATCAC
*
45383821 TACATAAGTCTTTGAATCAC
1 TACATAAATCTTTGAATCAC
45383841 TACATAA
1 TACATAA
45383848 TTAAAAACAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 6 0.19
18 6 0.19
19 7 0.22
20 13 0.41
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (20 bp):
TACATAAATCTTTGAATCAC
Found at i:45383826 original size:17 final size:17
Alignment explanation
Indices: 45383804--45383864 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
45383794 TTTGAATCAC
45383804 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
45383821 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
45383841 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
45383858 TACATAA
1 TACATAA
45383865 GTCTTGAATT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 15 0.47
18 4 0.12
19 5 0.16
20 8 0.25
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:45385690 original size:12 final size:12
Alignment explanation
Indices: 45385673--45385698 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
45385663 TCAGTAGTTC
45385673 TGCTTTAAATTT
1 TGCTTTAAATTT
45385685 TGCTTTAAATTT
1 TGCTTTAAATTT
45385697 TG
1 TG
45385699 GTCTTTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.58
Consensus pattern (12 bp):
TGCTTTAAATTT
Found at i:45386567 original size:8 final size:8
Alignment explanation
Indices: 45386540--45386576 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
45386530 GGGTCTAGGT
45386540 ACTCGGCG
1 ACTCGGCG
*
45386548 ACTCCGGTG
1 ACT-CGGCG
45386557 ACTCGGCG
1 ACTCGGCG
45386565 ACTCGGCG
1 ACTCGGCG
45386573 ACTC
1 ACTC
45386577 CCGATTCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.14, C:0.38, G:0.32, T:0.16
Consensus pattern (8 bp):
ACTCGGCG
Found at i:45393677 original size:21 final size:21
Alignment explanation
Indices: 45393626--45393679 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
45393616 ATTTTTAGTA
*
45393626 AATA-TAATTTTTATATGTGT
1 AATATTAATTTTTATATGAGT
*
45393646 AATATTTATTTTTATATGAGT
1 AATATTAATTTTTATATGAGT
* *
45393667 -GTATTAAATTTTA
1 AATATTAATTTTTA
45393680 GTATTCTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
AATATTAATTTTTATATGAGT
Found at i:45398138 original size:17 final size:17
Alignment explanation
Indices: 45398100--45398150 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
45398090 GGACAAAGAA
*
45398100 AGAAAATTTTGGAACTT
1 AGAAAATTTTGAAACTT
*
45398117 AGAAAATTTTGAAATTT
1 AGAAAATTTTGAAACTT
* * *
45398134 GGAAAACTTGGAAACTT
1 AGAAAATTTTGAAACTT
45398151 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (17 bp):
AGAAAATTTTGAAACTT
Found at i:45398990 original size:27 final size:28
Alignment explanation
Indices: 45398960--45399016 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
45398950 TGAACTTGTC
45398960 AAATAGGGATTAAAT-TGAGAAA-TGTGA
1 AAATAGGGA-TAAATGTGAGAAATTGTGA
* * *
45398987 AAATTGTGATAAATGTGTGAAATTGTGA
1 AAATAGGGATAAATGTGAGAAATTGTGA
45399015 AA
1 AA
45399017 TTTTTGGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 5 0.20
27 13 0.52
28 7 0.28
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.30
Consensus pattern (28 bp):
AAATAGGGATAAATGTGAGAAATTGTGA
Found at i:45399002 original size:18 final size:19
Alignment explanation
Indices: 45398979--45399014 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
45398969 TTAAATTGAG
45398979 AAATGTG-AAAATTGTGAT
1 AAATGTGTAAAATTGTGAT
*
45398997 AAATGTGTGAAATTGTGA
1 AAATGTGTAAAATTGTGA
45399015 AATTTTTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (19 bp):
AAATGTGTAAAATTGTGAT
Found at i:45401014 original size:152 final size:152
Alignment explanation
Indices: 45400737--45401065 Score: 498
Period size: 152 Copynumber: 2.2 Consensus size: 152
45400727 CACGGCCTAG
* * *
45400737 CACACGGCTTG-GCACACGAGCGTGTAAGGCCATTTCGAAGGGAACACGGCTTGGCACACGAGCG
1 CACACGGCCTGAG-ACACGGGCGTGTAAGGCCATTTCGAAGGGAACACGGCTTAGCACACGAGCG
* *
45400801 TGTAGTCTGGCCGTGTGACCCAAGTCAGTGAGTTACACGGGGTAGGACACGGGCTGGGACACGAC
65 TGTAGTCTAGCCGTGTGACCCAAGTCAGTGAGTTACACGGGGTAGGACACGGGCTGAGACACGAC
**
45400866 CATGTGTCTTAAATTTGAATGCC
130 CATGTGTCCCAAATTTGAATGCC
* *
45400889 TACACGGCCTGAGACACGGGCGTGTAAGGCCATTTCGAAGGGAACACGGCTTAGCACACGGGCGT
1 CACACGGCCTGAGACACGGGCGTGTAAGGCCATTTCGAAGGGAACACGGCTTAGCACACGAGCGT
* * *
45400954 GTGGTCTAGTCGTGTGACCCAAGTCAGTGAGTTACACGGGGTAGGACACGGGCTGAGACACGATC
66 GTAGTCTAGCCGTGTGACCCAAGTCAGTGAGTTACACGGGGTAGGACACGGGCTGAGACACGACC
* * *
45401019 GTGTGTCCCCATTTTGAATGCC
131 ATGTGTCCCAAATTTGAATGCC
*
45401041 CACACGGCCTGAGACACAGGCGTGT
1 CACACGGCCTGAGACACGGGCGTGT
45401066 CACATGGCCG
Statistics
Matches: 159, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
152 158 0.99
153 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (152 bp):
CACACGGCCTGAGACACGGGCGTGTAAGGCCATTTCGAAGGGAACACGGCTTAGCACACGAGCGT
GTAGTCTAGCCGTGTGACCCAAGTCAGTGAGTTACACGGGGTAGGACACGGGCTGAGACACGACC
ATGTGTCCCAAATTTGAATGCC
Found at i:45406469 original size:61 final size:62
Alignment explanation
Indices: 45406389--45406519 Score: 210
Period size: 61 Copynumber: 2.1 Consensus size: 62
45406379 TTGTCCTACT
* * **
45406389 AATTGATTTTCTGTATTATTTCAACGGATTCTTCGCAAGTATTATATATTTATAA-TTTTTA
1 AATTTATTTTCTGTATTATTTCAACAGATTCTTCGCAAGTATTATATATACATAATTTTTTA
*
45406450 AATTTATTTTCTGTATTATTTCAACAGATTCTTCGTAAGTATTATATATACATAATTTTTTA
1 AATTTATTTTCTGTATTATTTCAACAGATTCTTCGCAAGTATTATATATACATAATTTTTTA
45406512 AATTTATT
1 AATTTATT
45406520 CAAAAACAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
61 50 0.78
62 14 0.22
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (62 bp):
AATTTATTTTCTGTATTATTTCAACAGATTCTTCGCAAGTATTATATATACATAATTTTTTA
Found at i:45412139 original size:6 final size:6
Alignment explanation
Indices: 45412128--45412153 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
45412118 TGAACAAATT
45412128 GGCCTA GGCCTA GGCCTA GGCCTA GG
1 GGCCTA GGCCTA GGCCTA GGCCTA GG
45412154 AGTTGTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (6 bp):
GGCCTA
Found at i:45419778 original size:27 final size:27
Alignment explanation
Indices: 45419725--45419779 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
45419715 TTCTTAATTT
*
45419725 AAAATTAAGTAAATTAATCCCTCTTTA
1 AAAATTAAGTAAATTAATCCATCTTTA
* *
45419752 AAAATTAGAGTAATTTAAT-CATTTTTA
1 AAAATTA-AGTAAATTAATCCATCTTTA
45419779 A
1 A
45419780 TTTTAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40
Consensus pattern (27 bp):
AAAATTAAGTAAATTAATCCATCTTTA
Found at i:45437984 original size:38 final size:39
Alignment explanation
Indices: 45437932--45438014 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
45437922 ATTTGCCGGC
45437932 TTACTGATTAGGCAC-TTATGTG-CCAACTACTGTTACTG
1 TTACTGATTAGGCACTTTATGTGTCCAA-TACTGTTACTG
* * *
45437970 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTAGGCACTTTATGTGTCCAATACTGTTACTG
45438009 TTACTG
1 TTACTG
45438015 TTACCGACTC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 14 0.35
39 23 0.57
40 3 0.08
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (39 bp):
TTACTGATTAGGCACTTTATGTGTCCAATACTGTTACTG
Found at i:45438013 original size:39 final size:39
Alignment explanation
Indices: 45437932--45438058 Score: 125
Period size: 45 Copynumber: 3.1 Consensus size: 39
45437922 ATTTGCCGGC
* * *
45437932 TTACTGATTAGGCAC-TTATGTG-CCAACTACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAA-TACTGTTACTG
45437970 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
*
45438009 TTACTG-TTACCGACTCTGTACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATT--CG-----GCACTTTGTGTGTCGAATACTGTTACTG
45438054 TTACT
1 TTACT
45438059 ATTACTATTA
Statistics
Matches: 76, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
38 16 0.21
39 23 0.30
40 5 0.07
45 32 0.42
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:45438032 original size:45 final size:45
Alignment explanation
Indices: 45437959--45438148 Score: 245
Period size: 45 Copynumber: 4.1 Consensus size: 45
45437949 ATGTGCCAAC
*
45437959 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
45438004 TACTGTTACTGTTACCGACTCTGTACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
*
45438049 TACTGTTACTATTACTATTATCGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTAC------CGATTCGGCACTTTGTGTGTCGAATACTGT
* * * *
45438100 TACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
45438145 TACT
1 TACT
45438149 ACTACCGTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
45 85 0.68
51 40 0.32
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:45438160 original size:96 final size:96
Alignment explanation
Indices: 45437957--45438168 Score: 300
Period size: 96 Copynumber: 2.2 Consensus size: 96
45437947 TTATGTGCCA
* * *
45437957 ACTACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGA
1 ACTACTGTTACTATTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAGA
* *
45438022 CTCTGTACTTTGTGTGTCGAATACTGTTACT
66 CTCAGCACTTTGTGTGTCGAATACTGTTACT
** *
45438053 GTTACTATTACTATTA-TCGATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAG
1 ACTACTGTTACTATTACT-GATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAG
* *
45438117 ATTCAGCACTTTGTGTGTTGAATACTGTTACT
65 ACTCAGCACTTTGTGTGTCGAATACTGTTACT
*
45438149 ACTACCGTTACTGATTACTG
1 ACTACTGTTACT-ATTACTG
45438169 TATACTGGTG
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
95 1 0.01
96 92 0.93
97 5 0.05
98 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (96 bp):
ACTACTGTTACTATTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAGA
CTCAGCACTTTGTGTGTCGAATACTGTTACT
Found at i:45441456 original size:24 final size:24
Alignment explanation
Indices: 45441428--45441479 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
45441418 TTAGTAAGTC
*
45441428 AAATAAACTATGCTAATAAATACT
1 AAATAAACTATACTAATAAATACT
* *
45441452 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
45441476 AAAT
1 AAAT
45441480 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:45448452 original size:8 final size:8
Alignment explanation
Indices: 45448439--45448469 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
45448429 GAAATGGACC
45448439 AATTATTT
1 AATTATTT
45448447 AATTATTT
1 AATTATTT
45448455 AATTATTT
1 AATTATTT
45448463 AATTATT
1 AATTATT
45448470 GAAATCGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
AATTATTT
Found at i:45449998 original size:16 final size:18
Alignment explanation
Indices: 45449944--45449998 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
45449934 TGCAATATTC
45449944 TTTTATTTTA--TAAATAA
1 TTTTATTTTATTTAAAT-A
45449961 CTTTCTATTTTATTTAAATA
1 -TTT-TATTTTATTTAAATA
45449981 TTTTATTTT-TTT-AATA
1 TTTTATTTTATTTAAATA
45449997 TT
1 TT
45449999 ATACTATACC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.18
17 3 0.09
18 9 0.26
19 10 0.29
20 1 0.03
21 5 0.15
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATTTTATTTAAATA
Found at i:45452875 original size:6 final size:6
Alignment explanation
Indices: 45452866--45452903 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
45452856 TTTCAATTTA
45452866 TAATCC TAATCC TAATCC TAATCC TAATCC TAATCC TA
1 TAATCC TAATCC TAATCC TAATCC TAATCC TAATCC TA
45452904 CTCATTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (6 bp):
TAATCC
Found at i:45454588 original size:51 final size:51
Alignment explanation
Indices: 45454512--45454610 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
45454502 AAAGTACAAC
45454512 CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAACTATTAGGGATGTA
1 CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAACTATTAGGGATGTA
*
45454563 CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAATTATTAGGGAT
1 CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAACTATTAGGGAT
45454611 TAGAAGTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (51 bp):
CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAACTATTAGGGATGTA
Found at i:45458581 original size:21 final size:21
Alignment explanation
Indices: 45458557--45458604 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
45458547 GCTTTTTAGG
* *
45458557 TTTTTAA-ATTTTTTTTCTTTA
1 TTTTTAATATTCTTTTT-TTGA
*
45458578 TTTTCAATATTCTTTTTTTGA
1 TTTTTAATATTCTTTTTTTGA
45458599 TTTTTA
1 TTTTTA
45458605 TTTTTTATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTTAATATTCTTTTTTTGA
Found at i:45459783 original size:13 final size:13
Alignment explanation
Indices: 45459761--45459790 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
45459751 CTAATTTATT
*
45459761 AAATTTTATATAA
1 AAATTATATATAA
45459774 AAATTATATATAA
1 AAATTATATATAA
45459787 AAAT
1 AAAT
45459791 GGTCAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTATATATAA
Found at i:45467226 original size:18 final size:19
Alignment explanation
Indices: 45467194--45467229 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
45467184 TAGCTAATAC
*
45467194 ATTAAAAAATTAATTAAAA
1 ATTAAAAAATAAATTAAAA
45467213 ATTAAAAAA-AAATTAAA
1 ATTAAAAAATAAATTAAA
45467230 TCAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
ATTAAAAAATAAATTAAAA
Found at i:45467235 original size:11 final size:11
Alignment explanation
Indices: 45467198--45467246 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
45467188 TAATACATTA
*
45467198 AAAAATTAATT
1 AAAAATTAAAT
*
45467209 AAAAATTAAAA
1 AAAAATTAAAT
45467220 AAAAATTAAAT
1 AAAAATTAAAT
*
45467231 CAAAA-TAAACT
1 AAAAATTAAA-T
45467242 AAAAA
1 AAAAA
45467247 ATACAAATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 4 0.12
11 28 0.88
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAAATTAAAT
Found at i:45467245 original size:23 final size:23
Alignment explanation
Indices: 45467196--45467248 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
45467186 GCTAATACAT
*
45467196 TAAAAAATTAATTAAAAATTAAA
1 TAAAAAATTAAATAAAAATTAAA
*
45467219 -AAAAAATTAAATCAAAA-TAAA
1 TAAAAAATTAAATAAAAATTAAA
45467240 CTAAAAAAT
1 -TAAAAAAT
45467249 ACAAATGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 15 0.58
23 7 0.27
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (23 bp):
TAAAAAATTAAATAAAAATTAAA
Found at i:45476537 original size:23 final size:22
Alignment explanation
Indices: 45476489--45476545 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
45476479 CCTCGGGTAA
*
45476489 ATTTTT-TTATTAAATATATAT
1 ATTTTTATTTTTAAATATATAT
45476510 ATTTTTATTTTTAAA-ATATACT
1 ATTTTTATTTTTAAATATATA-T
* *
45476532 ACTTTTAGTTTTAA
1 ATTTTTATTTTTAA
45476546 GTTTTATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTTTATTTTTAAATATATAT
Found at i:45477275 original size:23 final size:22
Alignment explanation
Indices: 45477218--45477275 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
45477208 TTTTAATTTA
*
45477218 CTTAATTTT-CGTTGTATTTTG
1 CTTAATTTTGCGTCGTATTTTG
*
45477239 CTTAATTGTAGCGTCGTATTTTG
1 CTTAATT-TTGCGTCGTATTTTG
45477262 CTTAATTTTCGCGT
1 CTTAATTTT-GCGT
45477276 TTGAATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 7 0.23
22 2 0.06
23 22 0.71
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.53
Consensus pattern (22 bp):
CTTAATTTTGCGTCGTATTTTG
Found at i:45487235 original size:21 final size:22
Alignment explanation
Indices: 45487211--45487263 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
45487201 TTTTAATTTA
45487211 CTTAATTTTCG-TTGTATTTTG
1 CTTAATTTTCGATTGTATTTTG
*
45487232 CTTAATTGTCGCATTGTATTTTG
1 CTTAATTTTCG-ATTGTATTTTG
*
45487255 ATTAATTTT
1 CTTAATTTT
45487264 TGCGTTTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
23 17 0.63
ACGTcount: A:0.19, C:0.09, G:0.13, T:0.58
Consensus pattern (22 bp):
CTTAATTTTCGATTGTATTTTG
Found at i:45487682 original size:5 final size:5
Alignment explanation
Indices: 45487674--45487708 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
45487664 TTCTTTTTAG
45487674 AATTT AATTT AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT
45487709 TACTTTGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:45503149 original size:14 final size:14
Alignment explanation
Indices: 45503126--45503165 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
45503116 ACAGAAAAGT
*
45503126 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
45503140 AAATCATTTTACGG
1 AAAACATTTTACAG
45503154 AAAACATTTTAC
1 AAAACATTTTAC
45503166 TGGTAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:45503150 original size:34 final size:35
Alignment explanation
Indices: 45503091--45503157 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
45503081 CAAACAGCAG
* * *
45503091 AAAATATTTTCTAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
45503126 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
45503158 CATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:45503663 original size:41 final size:40
Alignment explanation
Indices: 45503618--45503720 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 40
45503608 CAACTTCAAG
*
45503618 TCGATGAGGCACTGGGTGCCAATTTACTACTTCGGATTTAT
1 TCGATGAGGCACTGGGTGCCAATTTACTACTTC-GAATTAT
* **
45503659 TCGATGAGACACTGGGTGTTAATTTACTACTTCGAATTAT
1 TCGATGAGGCACTGGGTGCCAATTTACTACTTCGAATTAT
* *
45503699 CCAATGAGGCACTGGGTGCCAA
1 TCGATGAGGCACTGGGTGCCAA
45503721 ATTGGTGTGT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 23 0.43
41 30 0.57
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (40 bp):
TCGATGAGGCACTGGGTGCCAATTTACTACTTCGAATTAT
Found at i:45513337 original size:2 final size:2
Alignment explanation
Indices: 45513330--45513367 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
45513320 TGAATGATTG
45513330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45513368 TGTATGTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45517461 original size:15 final size:15
Alignment explanation
Indices: 45517441--45517471 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
45517431 AGGTTTTTGC
45517441 ATCTCAGAGGTCTAT
1 ATCTCAGAGGTCTAT
45517456 ATCTCAGAGGTCTAT
1 ATCTCAGAGGTCTAT
45517471 A
1 A
45517472 GCTTGTACAG
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:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (15 bp):
ATCTCAGAGGTCTAT
Found at i:45543065 original size:86 final size:87
Alignment explanation
Indices: 45542919--45543257 Score: 383
Period size: 86 Copynumber: 3.7 Consensus size: 87
45542909 TTAAAAAGAG
* * * * *
45542919 GTAAAGTAGTTTTATTTAATACCTAACAAGTTTTTTTTATGTTTGGAAACGTATTTTATTATTAA
1 GTAACGTAATTTTATTTAATACCTAAAAAGTTTTTTTTATGTTTGGAAATGTATTCTATTATTAA
45542984 TGACACTATTAAAAAAAGTGAA
66 TGACACTATTAAAAAAAGTGAA
* * *
45543006 GTAACGTAGTTTTATTTAATAACTAAAAAG-TTTTTGTATGTTTGGAAATGTATTCTATTATTAA
1 GTAACGTAATTTTATTTAATACCTAAAAAGTTTTTTTTATGTTTGGAAATGTATTCTATTATTAA
* *
45543070 TGACACTGTTAAGAAAAAAAAGGTAAA
66 TGACACTATT----AAAAAAA-GTGAA
45543097 GTAACGTAATTTTATTTAATACCTAAAAAGTTTTTTTTTTTTTTTTATGTTTGGAAATGTATTCT
1 GTAACGTAATTTTATTTAATACCTAAAAAG--------TTTTTTTTATGTTTGGAAATGTATTCT
* * * * *
45543162 ATTATTAATCACATTAATAAAAAATGGTGGA
58 ATTATTAATGACACTATTAAAAAA-AGTGAA
* * *
45543193 GTAACGTAATTTTATTTAATACCTACAATGTTTTTTTTATGTTTGGAAATGTATTTTATTATTAA
1 GTAACGTAATTTTATTTAATACCTAAAAAGTTTTTTTTATGTTTGGAAATGTATTCTATTATTAA
45543258 AAAAAGTGAA
Statistics
Matches: 216, Mismatches: 21, Indels: 29
0.81 0.08 0.11
Matches are distributed among these distances:
86 40 0.19
87 27 0.12
88 34 0.16
90 7 0.03
91 32 0.15
96 37 0.17
100 39 0.18
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (87 bp):
GTAACGTAATTTTATTTAATACCTAAAAAGTTTTTTTTATGTTTGGAAATGTATTCTATTATTAA
TGACACTATTAAAAAAAGTGAA
Found at i:45543214 original size:96 final size:99
Alignment explanation
Indices: 45543036--45543230 Score: 288
Period size: 96 Copynumber: 2.0 Consensus size: 99
45543026 AACTAAAAAG
*
45543036 TTTTTGTATGTTTGGAAATGTATTCTATTATTAATGACACTGTTAAGAAAAAAAAGGTAAAGTAA
1 TTTTTGTATGTTTGGAAATGTATTCTATTATTAAT-ACACTATTAAGAAAAAAAAGGTAAAGTAA
45543101 CGTAATTTTATTTAATACCTAAAAAGTTTTTTTTT
65 CGTAATTTTATTTAATACCTAAAAAGTTTTTTTTT
* * * **
45543136 TTTTTTTATGTTTGGAAATGTATTCTATTATTAAT-CAC-ATTAA-TAAAAAATGGTGGAGTAAC
1 TTTTTGTATGTTTGGAAATGTATTCTATTATTAATACACTATTAAGAAAAAAAAGGTAAAGTAAC
* *
45543198 GTAATTTTATTTAATACCTACAATGTTTTTTTT
66 GTAATTTTATTTAATACCTAAAAAGTTTTTTTT
45543231 ATGTTTGGAA
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
96 46 0.53
97 4 0.05
98 3 0.03
100 34 0.39
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (99 bp):
TTTTTGTATGTTTGGAAATGTATTCTATTATTAATACACTATTAAGAAAAAAAAGGTAAAGTAAC
GTAATTTTATTTAATACCTAAAAAGTTTTTTTTT
Found at i:45543273 original size:75 final size:75
Alignment explanation
Indices: 45543173--45543376 Score: 263
Period size: 71 Copynumber: 2.8 Consensus size: 75
45543163 TTATTAATCA
* * * * *
45543173 CATTAATAAAAAATGGTGGAGTAACGTAATTTTATTTAATACCTACAATGTTTTTTTTATGTTTG
1 CATTATTAAAAAA-AGTGAAGTAACGTAGTTTTATTTAATACCTACAATGTTTTTTTTATCTTTG
*
45543238 GAAATGTATTT
65 GAAATGTATTC
* * *
45543249 TATTATTAAAAAAAGTGAAGTAACGTAGTTTTATTTAATA-CT-C-TTTTTTTTTTTATCTTTGG
1 CATTATTAAAAAAAGTGAAGTAACGTAGTTTTATTTAATACCTACAATGTTTTTTTTATCTTTGG
45543311 AAATGTATTC
66 AAATGTATTC
* * *
45543321 CATTATT-AAAAAAGTGAAGTAACGTAGTTTTATTTAATACTTAAAAAGTTTTTTTT
1 CATTATTAAAAAAAGTGAAGTAACGTAGTTTTATTTAATACCTACAATGTTTTTTTT
45543377 TTAAATATAA
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
71 32 0.29
72 32 0.29
73 1 0.01
74 10 0.09
75 24 0.22
76 11 0.10
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (75 bp):
CATTATTAAAAAAAGTGAAGTAACGTAGTTTTATTTAATACCTACAATGTTTTTTTTATCTTTGG
AAATGTATTC
Found at i:45551073 original size:4 final size:4
Alignment explanation
Indices: 45551064--45551168 Score: 60
Period size: 4 Copynumber: 25.8 Consensus size: 4
45551054 GGGAAAGGAG
*
45551064 AAGA AAGA AAGA AAG- AA-A AAGA AAGAA AAGGA AAGGA AAGGA GAGGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAG-A AA-GA AA-GA AA-GA -AAGA
* *
45551111 AAGA AAG- AA-A AAGA AGGA AAGAA AAGGA AGGA GAAGA AA-A AA-A AAGA
1 AAGA AAGA AAGA AAGA AAGA AAG-A AA-GA AAGA -AAGA AAGA AAGA AAGA
*
45551158 AAGA AAAA AAG
1 AAGA AAGA AAG
45551169 GTGATCTTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
3 14 0.17
4 41 0.50
5 24 0.29
6 3 0.04
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:45551084 original size:10 final size:10
Alignment explanation
Indices: 45551071--45551165 Score: 68
Period size: 10 Copynumber: 9.3 Consensus size: 10
45551061 GAGAAGAAAG
45551071 AAAGAAAGAA
1 AAAGAAAGAA
45551081 AAAGAAAGAA
1 AAAGAAAGAA
* *
45551091 AAGGAAAGGA
1 AAAGAAAGAA
* * *
45551101 AAGGAGAG-G
1 AAAGAAAGAA
45551110 AAAGAAAGAA
1 AAAGAAAGAA
*
45551120 AAAGAAGGAA
1 AAAGAAAGAA
*
45551130 AGAA-AAGGAA
1 A-AAGAAAGAA
*
45551140 GGAGAAGAAAAAA
1 --A-AAGAAAGAA
45551153 AAAGAAAGAA
1 AAAGAAAGAA
45551163 AAA
1 AAA
45551166 AAGGTGATCT
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
9 6 0.09
10 52 0.75
11 3 0.04
12 4 0.06
13 4 0.06
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:45551103 original size:33 final size:33
Alignment explanation
Indices: 45551057--45551164 Score: 94
Period size: 33 Copynumber: 3.1 Consensus size: 33
45551047 AAGGAGAGGG
45551057 AAAGGAGAA-GAAAGAAAGAAAGAAAAAGAAAGA
1 AAAGGA-AAGGAAAGAAAGAAAGAAAAAGAAAGA
*
45551090 AAAGGAAAGGAAAGGAGAGGAAAGAAAGAAAAAG-AAGG
1 AAAGGAAAGG--A--A-A-GAAAGAAAGAAAAAGAAAGA
* * *
45551128 AAAGAAAAGGAAGGAGAAGAAAAAAAAAGAAAGA
1 AAAGGAAAGGAAAGA-AAGAAAGAAAAAGAAAGA
45551162 AAA
1 AAA
45551165 AAAGGTGATC
Statistics
Matches: 61, Mismatches: 5, Indels: 17
0.73 0.06 0.20
Matches are distributed among these distances:
32 4 0.07
33 19 0.31
34 7 0.11
35 1 0.02
36 1 0.02
37 1 0.02
38 13 0.21
39 15 0.25
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (33 bp):
AAAGGAAAGGAAAGAAAGAAAGAAAAAGAAAGA
Found at i:45551113 original size:43 final size:43
Alignment explanation
Indices: 45551055--45551165 Score: 145
Period size: 43 Copynumber: 2.6 Consensus size: 43
45551045 AGAAGGAGAG
45551055 GGAAAGGAGAAGAAAGAAAGAAAGAA-AAAGAAAGAAAAGGAAA
1 GGAAAGGAGAAGAAAGAAAGAAA-AAGAAAGAAAGAAAAGGAAA
* *
45551098 GGAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGG-AA
1 GGAAAGGAGAAGAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAA
* * *
45551140 GGAGAAGAAAAAAAAAGAAAGAAAAA
1 GGA-AAGGAGAAGAAAGAAAGAAAAA
45551166 AAGGTGATCT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
42 7 0.12
43 53 0.88
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (43 bp):
GGAAAGGAGAAGAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAA
Found at i:45551166 original size:14 final size:14
Alignment explanation
Indices: 45551067--45551167 Score: 76
Period size: 14 Copynumber: 7.1 Consensus size: 14
45551057 AAAGGAGAAG
*
45551067 AAAGAAAGAAAGAA
1 AAAGAAAGAAAAAA
*
45551081 AAAGAAAGAAAAGGA
1 AAAGAAAGAAAA-AA
* * * **
45551096 AAGGAAAGGAGAGG
1 AAAGAAAGAAAAAA
*
45551110 AAAGAAAGAAAAAG
1 AAAGAAAGAAAAAA
* **
45551124 AAGGAAAGAAAAGG
1 AAAGAAAGAAAAAA
*
45551138 AAGGAGAAGAAAAAA
1 AAAGA-AAGAAAAAA
45551153 AAAGAAAGAAAAAA
1 AAAGAAAGAAAAAA
45551167 A
1 A
45551168 GGTGATCTTT
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
14 49 0.70
15 21 0.30
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAAAA
Found at i:45551688 original size:158 final size:152
Alignment explanation
Indices: 45551496--45551969 Score: 526
Period size: 158 Copynumber: 3.0 Consensus size: 152
45551486 AAATGGTATA
* * * *
45551496 TTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTTCTAAAATAATATAAAATAATAAA
1 TTTAAAAAACAAAATAAATTAATAAATTTCAAACATAATGTACTGAAATAATATAAAATAATAAA
*
45551561 ATTAGAAAATATGATATTTTTT-AAAGTAATAAAATGCGGAGAAAAAAATACGAGCAAAGGGCCG
66 ATTAGAAAATAT-ATATTTTTTGAAAGTAATAAAATTCGGAGAAAAAAATACGAGCAAAGGGCCG
* *
45551625 AAGTAAGAGTTTTTTACTAAATTT
130 AAATAAG-GTTTTTTATTAAATTT
* *
45551649 TTTAAAAATTCAGAAAT-AATTAATACAAATATTTCAAACAAAATGTACTGAAATAATATAAAAT
1 TTTAAAAA-ACA-AAATAAATTAAT---AA-ATTTCAAACATAATGTACTGAAATAATATAAAAT
*
45551713 AATAAAA-TACGAAAATAATATATTTTTATCGAAAGTAATAAAATTC-GAAAAAAATAATACGAG
60 AATAAAATTA-GAAAAT-ATATATTTTT-T-GAAAGTAATAAAATTCGGAGAAAAA-AATACGAG
* *
45551776 CAAAGGGCAGAAATAAGGTTTTTTTTTTTAAATTT
120 CAAAGGGCCGAAATAAGG--TTTTTTATTAAATTT
* * * *
45551811 ATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTGAAATAATGTAAACTAATAA
1 -TTTAAAAAACAAAATAAATTAATAAATTTCAAACATAATGTACTGAAATAATATAAAATAATAA
* * ** *
45551876 AATTAGAAAATATAATATTTTTATTGAAAGTAATAAAATTCGG-GAAAATAGTACGAATAAATGG
65 AATTAGAAAATAT-ATA-TTTT-TTGAAAGTAATAAAATTCGGAGAAAAAAATACGAGCAAAGGG
* *
45551940 ACGAAATAAGGGTTTTTTATTAATTTT
127 CCGAAATAA-GGTTTTTTATTAAATTT
45551967 TTT
1 TTT
45551970 TGAACTTGCA
Statistics
Matches: 271, Mismatches: 28, Indels: 42
0.79 0.08 0.12
Matches are distributed among these distances:
153 8 0.03
154 9 0.03
155 5 0.02
156 13 0.05
157 24 0.09
158 121 0.45
159 13 0.05
160 9 0.03
161 39 0.14
162 22 0.08
163 8 0.03
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.32
Consensus pattern (152 bp):
TTTAAAAAACAAAATAAATTAATAAATTTCAAACATAATGTACTGAAATAATATAAAATAATAAA
ATTAGAAAATATATATTTTTTGAAAGTAATAAAATTCGGAGAAAAAAATACGAGCAAAGGGCCGA
AATAAGGTTTTTTATTAAATTT
Found at i:45554050 original size:11 final size:11
Alignment explanation
Indices: 45554031--45554100 Score: 65
Period size: 10 Copynumber: 6.5 Consensus size: 11
45554021 AAAAATTAAA
45554031 AAAAGTATTTTT
1 AAAA-TATTTTT
45554043 AAAATATTTTT
1 AAAATATTTTT
45554054 AAAATA-TTTT
1 AAAATATTTTT
***
45554064 AAAAT-TTAAA
1 AAAATATTTTT
*
45554074 AAAAGTATTTTA
1 AAAA-TATTTTT
45554086 AAAATA-TTTT
1 AAAATATTTTT
45554096 AAAAT
1 AAAAT
45554101 TAAAAAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
10 22 0.45
11 16 0.33
12 11 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:45554088 original size:31 final size:31
Alignment explanation
Indices: 45554043--45554108 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 31
45554033 AAGTATTTTT
*
45554043 AAAA-TATTTTTAAAATATTTTAAAATTTAAA
1 AAAAGTATTTTAAAAATATTTTAAAA-TTAAA
45554074 AAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAGTATTTTAAAAATATTTTAAAATTAAA
45554105 AAAA
1 AAAA
45554109 TTAAAAAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (31 bp):
AAAAGTATTTTAAAAATATTTTAAAATTAAA
Found at i:45554114 original size:8 final size:9
Alignment explanation
Indices: 45554096--45554151 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
45554086 AAAATATTTT
45554096 AAAATTAAA
1 AAAATTAAA
45554105 AAAATTAAA
1 AAAATTAAA
45554114 AAAGTATGTAAA
1 AAA--AT-TAAA
**
45554126 AAATATT-TT
1 AAA-ATTAAA
45554135 AAAATTAAA
1 AAAATTAAA
45554144 AAAATTAA
1 AAAATTAA
45554152 TATATTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 3 0.08
9 23 0.59
10 1 0.03
11 5 0.13
12 7 0.18
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (9 bp):
AAAATTAAA
Found at i:45554400 original size:59 final size:59
Alignment explanation
Indices: 45554303--45554425 Score: 237
Period size: 59 Copynumber: 2.1 Consensus size: 59
45554293 CCTCTAGTTG
*
45554303 CGAACATCTAGAACGTGACTGTCGACCTCCGAATAGGTATACCCCTATGACCACACCAT
1 CGAACATCTAGAACGTGACTGTCGACCTCCGAAAAGGTATACCCCTATGACCACACCAT
45554362 CGAACATCTAGAACGTGACTGTCGACCTCCGAAAAGGTATACCCCTATGACCACACCAT
1 CGAACATCTAGAACGTGACTGTCGACCTCCGAAAAGGTATACCCCTATGACCACACCAT
45554421 CGAAC
1 CGAAC
45554426 CATCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.32, C:0.33, G:0.17, T:0.19
Consensus pattern (59 bp):
CGAACATCTAGAACGTGACTGTCGACCTCCGAAAAGGTATACCCCTATGACCACACCAT
Found at i:45557687 original size:18 final size:17
Alignment explanation
Indices: 45557661--45557699 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
45557651 ATTTTCCTTC
45557661 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
45557678 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
45557696 CACA
1 CACA
45557700 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:45559887 original size:3 final size:3
Alignment explanation
Indices: 45559879--45559903 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
45559869 CTCCCCTTTC
45559879 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
45559904 ATTTTTATCC
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:45564801 original size:15 final size:15
Alignment explanation
Indices: 45564752--45564802 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
45564742 TTATTTCAAA
45564752 TTATATTTTAGTCAT
1 TTATATTTTAGTCAT
* **
45564767 TTAT-GTTT-GAAAT
1 TTATATTTTAGTCAT
45564780 GTTATATTTTAGTCAT
1 -TTATATTTTAGTCAT
45564796 TTATATT
1 TTATATT
45564803 ATCGTATTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 3 0.11
14 7 0.26
15 14 0.52
16 3 0.11
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.59
Consensus pattern (15 bp):
TTATATTTTAGTCAT
Found at i:45565757 original size:19 final size:19
Alignment explanation
Indices: 45565719--45565767 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
45565709 ACATTGGATG
**
45565719 AAATAAAAATTATTTGTAA
1 AAATAAAAATTATTAATAA
*
45565738 AAATAATAATTATTAATAA
1 AAATAAAAATTATTAATAA
*
45565757 AGAATTAAAAT
1 A-AATAAAAAT
45565768 ATAAACAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
AAATAAAAATTATTAATAA
Found at i:45568497 original size:21 final size:22
Alignment explanation
Indices: 45568451--45568508 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 22
45568441 GCTGTGCTTA
*
45568451 CTTA-ATTTTCTTTTTTTAAAT
1 CTTATATTCTCTTTTTTTAAAT
* *
45568472 ATTATATTCTCTTTTTTT-CAT
1 CTTATATTCTCTTTTTTTAAAT
*
45568493 CTTAT-TTCCCTTTTTT
1 CTTATATTCTCTTTTTT
45568509 AGCAAACTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 10 0.32
21 9 0.29
22 12 0.39
ACGTcount: A:0.17, C:0.16, G:0.00, T:0.67
Consensus pattern (22 bp):
CTTATATTCTCTTTTTTTAAAT
Found at i:45581728 original size:22 final size:20
Alignment explanation
Indices: 45581697--45581758 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
45581687 TCCAAAAAAC
*
45581697 AAAAATATTTTTATATTTTTT
1 AAAAATAATTTTATA-TTTTT
*
45581718 TAAAATAATTTTA-ATTTTT
1 AAAAATAATTTTATATTTTT
*
45581737 AAAAATAAATTTCATAATTTTT
1 AAAAAT-AATTTTAT-ATTTTT
45581759 GAGCATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.29
20 7 0.21
21 11 0.32
22 6 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
AAAAATAATTTTATATTTTT
Found at i:45582506 original size:2 final size:2
Alignment explanation
Indices: 45582501--45582525 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45582491 TTATTTAATA
45582501 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
45582526 GGTAAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45595969 original size:69 final size:69
Alignment explanation
Indices: 45595891--45596045 Score: 188
Period size: 69 Copynumber: 2.2 Consensus size: 69
45595881 GAAATTATAA
* * * *
45595891 ACGTAAGACCATAGTGAGACTATGGCCGTTGTTCGGATA-TAAGACCATGGTTGGACCATGGCAA
1 ACGTAAGACCATAGCGAGACTATGGCAGTTATT--GATACAAAGACCATGGTTGGACCATGGCAA
45595955 TG-TAT
64 TGATAT
* * *
45595960 ACGTAAGACCATAGCGAGGCTATGGTAGTTATTTATACGAAAGACCATGGTTGGACCATGGCAAT
1 ACGTAAGACCATAGCGAGACTATGGCAGTTATTGATAC-AAAGACCATGGTTGGACCATGGCAAT
45596025 GTATAT
65 G-ATAT
*
45596031 ATGTAAGACCATAGC
1 ACGTAAGACCATAGC
45596046 TGGGCTATGG
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
67 3 0.04
69 54 0.73
71 17 0.23
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (69 bp):
ACGTAAGACCATAGCGAGACTATGGCAGTTATTGATACAAAGACCATGGTTGGACCATGGCAATG
ATAT
Found at i:45606228 original size:50 final size:50
Alignment explanation
Indices: 45606108--45606351 Score: 312
Period size: 50 Copynumber: 4.9 Consensus size: 50
45606098 GATAATAACA
* * * ** * *
45606108 TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCT-CGG
* * *
45606157 TACCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
45606207 TGCCAACGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
45606257 TGCCAACGCCATGTCCCAGACATGGTATTACATGGGACCTCTCGTCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
45606307 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT
45606352 GATCTCAAGG
Statistics
Matches: 174, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
48 1 0.01
49 38 0.22
50 135 0.78
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:45606775 original size:30 final size:30
Alignment explanation
Indices: 45606741--45606798 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
45606731 CCTCGACTCT
45606741 AACTTTGGA-AAAATTACAATTTTTCCCCTA
1 AACTTT-GACAAAATTACAATTTTTCCCCTA
* * *
45606771 AACTTTTACATAATTACACTTTTTCCCC
1 AACTTTGACAAAATTACAATTTTTCCCC
45606799 AAAGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTTCCCCTA
Found at i:45618311 original size:15 final size:14
Alignment explanation
Indices: 45618293--45618339 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
45618283 ATAATAATTA
45618293 AAATAATAAGAAAAT
1 AAATAATAA-AAAAT
*
45618308 AAATAA-AAACAA-
1 AAATAATAAAAAAT
*
45618320 AAATAATAAAAATT
1 AAATAATAAAAAAT
45618334 AAATAA
1 AAATAA
45618340 AATGAAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
12 6 0.22
13 7 0.26
14 8 0.30
15 6 0.22
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (14 bp):
AAATAATAAAAAAT
Found at i:45619204 original size:22 final size:22
Alignment explanation
Indices: 45619179--45619256 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
45619169 GAAAATGAAA
45619179 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
45619201 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * * **
45619223 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAGC
45619245 CATGAGAGCTTA
1 CATGAGAGCTTA
45619257 CTTTTAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:45619990 original size:17 final size:17
Alignment explanation
Indices: 45619968--45620000 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
45619958 TTTGAATTAG
45619968 TGAATTTTGTGATTTAT
1 TGAATTTTGTGATTTAT
45619985 TGAATTTTGTGATTTA
1 TGAATTTTGTGATTTA
45620001 AAAAGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (17 bp):
TGAATTTTGTGATTTAT
Found at i:45621293 original size:46 final size:46
Alignment explanation
Indices: 45621223--45621361 Score: 242
Period size: 46 Copynumber: 3.0 Consensus size: 46
45621213 CATGGCAAAG
*
45621223 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
45621269 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
45621315 TGTGAAAAGTAGGTATGGTATTTCTGTGAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
45621361 T
1 T
45621362 ATAGCAATGT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 88 1.00
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:45626969 original size:13 final size:13
Alignment explanation
Indices: 45626946--45626979 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
45626936 AAAACCATAT
45626946 ATTTT-AATTTAA
1 ATTTTAAATTTAA
45626958 ATTTTAAATTTAA
1 ATTTTAAATTTAA
45626971 ATTGTTAAA
1 ATT-TTAAA
45626980 AGATTAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 10 0.50
14 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
ATTTTAAATTTAA
Found at i:45628999 original size:23 final size:23
Alignment explanation
Indices: 45628972--45629093 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
45628962 AGTGTTATTG
*
45628972 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
45628995 TTCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
45629018 AACAGTGGTAGTTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
45629041 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
45629064 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
45629087 ATCAGTG
1 ATCAGTG
45629094 TTGCACTTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 86 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:45629027 original size:46 final size:46
Alignment explanation
Indices: 45628974--45629093 Score: 204
Period size: 46 Copynumber: 2.6 Consensus size: 46
45628964 TGTTATTGAT
*
45628974 CAGTGGTAGCTTCGGCTACGTTTCAGTGGTAGCTTCAGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCAGCTACATAA
* *
45629020 CAGTGGTAGTTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCAGCTACATAA
*
45629066 CAGTGGTAGCTTCGGCTACATATCAGTG
1 CAGTGGTAGCTTCGGCTACATTTCAGTG
45629094 TTGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.31
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCAGCTACATAA
Found at i:45631134 original size:24 final size:24
Alignment explanation
Indices: 45631097--45631183 Score: 72
Period size: 24 Copynumber: 3.6 Consensus size: 24
45631087 GGACACACCA
*
45631097 CAACTCGTATGAGCTTATCGATTT
1 CAACTCGTATGAGCTTACCGATTT
45631121 CAACTCGTGA-GAGCTTACCGA-TT
1 CAACTCGT-ATGAGCTTACCGATTT
* * *
45631144 CATAGCTCGGAGGAGCTTACCGTTTAT
1 CA-A-CTCGTATGAGCTTACCGATT-T
*
45631171 C-ACTTGTATGAGC
1 CAACTCGTATGAGC
45631184 ATACATTTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
23 4 0.08
24 28 0.55
25 16 0.31
26 1 0.02
27 2 0.04
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (24 bp):
CAACTCGTATGAGCTTACCGATTT
Found at i:45633873 original size:26 final size:29
Alignment explanation
Indices: 45633851--45633905 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
45633841 ATATTATGTT
45633851 TTAAA-AATAATTATATTAATTATATATG
1 TTAAATAATAATTATATTAATTATATATG
*
45633879 TTAAATAATAATTATA-TATTTATATAT
1 TTAAATAATAATTATATTAATTATATAT
45633906 ATTGAATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TTAAATAATAATTATATTAATTATATATG
Found at i:45649174 original size:91 final size:86
Alignment explanation
Indices: 45649066--45649227 Score: 252
Period size: 91 Copynumber: 1.8 Consensus size: 86
45649056 GCAAAGACAG
*
45649066 AAATTTTCGTTTATTTTTTACACATGTTCTAGTATATAGGAAAATTTTTCATTTTAGTATATAGG
1 AAATTTTCATTTATTTTTTACACATGTTCTAGTATATAGGAAAA----T-ATTTTAGTATATAGG
45649131 TTAGCAATAAACTAATTCAATTGGTA
61 TTAGCAATAAACTAATTCAATTGGTA
* *
45649157 AAATTTTCATTTATTTTTTACGCATGTTTTAGTATATAGGAAAATATTTTAGTATATAGGTTAGC
1 AAATTTTCATTTATTTTTTACACATGTTCTAGTATATAGGAAAATATTTTAGTATATAGGTTAGC
45649222 AATAAA
66 AATAAA
45649228 TAGGCTTTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
86 26 0.38
87 1 0.01
91 41 0.60
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (86 bp):
AAATTTTCATTTATTTTTTACACATGTTCTAGTATATAGGAAAATATTTTAGTATATAGGTTAGC
AATAAACTAATTCAATTGGTA
Found at i:45656655 original size:25 final size:25
Alignment explanation
Indices: 45656614--45656792 Score: 75
Period size: 25 Copynumber: 7.2 Consensus size: 25
45656604 ACAAACCGCA
*
45656614 GCTCTTTTG-AGCGTCCCGATATATG
1 GCTC-TTTGAAGCTTCCCGATATATG
* * **
45656639 GCTCTTTGAAGCTTCCCAATAAAAA
1 GCTCTTTGAAGCTTCCCGATATATG
* * *
45656664 TCTCTTTCATGAGCTTCCCGAT-TAAAG
1 GCTCTTTGA--AGCTTCCCGATAT-ATG
* * *
45656691 ACTCTCTGGAGCTTCCCGATAT-TG
1 GCTCTTTGAAGCTTCCCGATATATG
* *
45656715 GCTCGCTTGAACCTTCCCG-TCAT-TG
1 GCTC-TTTGAAGCTTCCCGAT-ATATG
* *
45656740 GCTCGTATG-AGCTTCCCGTTA-ATG
1 GCTC-TTTGAAGCTTCCCGATATATG
* * * *
45656764 GCTCTTTGGAGCTTTCCGTTACATG
1 GCTCTTTGAAGCTTCCCGATATATG
45656789 GCTC
1 GCTC
45656793 ACATGGGCTT
Statistics
Matches: 118, Mismatches: 25, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
23 3 0.03
24 35 0.30
25 62 0.53
26 1 0.01
27 17 0.14
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.34
Consensus pattern (25 bp):
GCTCTTTGAAGCTTCCCGATATATG
Found at i:45656765 original size:24 final size:23
Alignment explanation
Indices: 45656672--45656792 Score: 73
Period size: 24 Copynumber: 5.0 Consensus size: 23
45656662 AATCTCTTTC
* *
45656672 ATGAGCTTCCCGATTAAAGACTCT
1 ATGAGCTTCCCG-TTAATGGCTCT
* * *
45656696 CTGGAGCTTCCCGATATTGGCTCGCT
1 AT-GAGCTTCCCGTTAATGGCT--CT
* * *
45656722 -TGAACCTTCCCGTCATTGGCTCGT
1 ATG-AGCTTCCCGTTAATGGCTC-T
45656746 ATGAGCTTCCCGTTAATGGCTCT
1 ATGAGCTTCCCGTTAATGGCTCT
* *
45656769 TTGGAGCTTTCCGTTACATGGCTC
1 AT-GAGCTTCCCGTTA-ATGGCTC
45656793 ACATGGGCTT
Statistics
Matches: 76, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
23 3 0.04
24 36 0.47
25 35 0.46
26 2 0.03
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (23 bp):
ATGAGCTTCCCGTTAATGGCTCT
Found at i:45659131 original size:28 final size:28
Alignment explanation
Indices: 45659066--45659137 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
45659056 GAGCCCTATA
*
45659066 CAATATCAGT-ACAATGTGGGCCTTAGCC
1 CAATA-CAGTAACAGTGTGGGCCTTAGCC
* * *
45659094 TATTATAGTAACAGTGTGGGCCTTAGCC
1 CAATACAGTAACAGTGTGGGCCTTAGCC
45659122 CAATACAGTAATCAGT
1 CAATACAGTAA-CAGT
45659138 ACAATGCAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
27 3 0.09
28 28 0.80
29 4 0.11
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (28 bp):
CAATACAGTAACAGTGTGGGCCTTAGCC
Found at i:45659308 original size:25 final size:25
Alignment explanation
Indices: 45659248--45659318 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
45659238 AATATCACAG
*
45659248 CAAAGCTGCCAGTAATAATAACGTA
1 CAAAGCTGCCAGTAATAGTAACGTA
* *
45659273 GCAAAGATGCCAGTAACAGTAACGCT-
1 -CAAAGCTGCCAGTAATAGTAACG-TA
45659299 CAAAGCTGCCAGTAATAGTA
1 CAAAGCTGCCAGTAATAGTA
45659319 TATGTGGCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 18 0.46
26 20 0.51
27 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (25 bp):
CAAAGCTGCCAGTAATAGTAACGTA
Found at i:45659526 original size:27 final size:27
Alignment explanation
Indices: 45659476--45659546 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
45659466 GCATAATACC
* * *
45659476 ATAACAGTCATTTCATCTCCTAGGGGT
1 ATAACAGTCATTTTACCTCATAGGGGT
*
45659503 ATAACAGTCATTTTACCTTATAGGGGT
1 ATAACAGTCATTTTACCTCATAGGGGT
***
45659530 ATTTTAGTCATTTTACC
1 ATAACAGTCATTTTACC
45659547 CTTCAAAGGT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (27 bp):
ATAACAGTCATTTTACCTCATAGGGGT
Found at i:45659557 original size:27 final size:27
Alignment explanation
Indices: 45659526--45659939 Score: 380
Period size: 27 Copynumber: 15.3 Consensus size: 27
45659516 TACCTTATAG
* * *
45659526 GGGTATTTTAGTCATTTTACCCTTCAA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* * * * * *
45659553 AGGTATTTCGATTATTTTACCTTTCAA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* *
45659580 GGGTATTTTGGTAATTTTACCTTTCAA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* * * *
45659607 TGGTATTTTGGTTATTTTACCATTCAGG
1 GGGTATTTTGGTAATTTTACCCTTC-GA
* * *
45659635 GGGAATTTCGGTAATTTTACCCTTTGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* * *
45659662 AGGTATTTCGATAATTTTACCCTTCGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* *
45659689 GGGTTTTTTGGTCATTTTACCCTTCGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
*** * *
45659716 GGGTATTTCAATCATTTTACCATTCGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* * *
45659743 GGGTATTTCGGTTATTTTACCCTT-TA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* *
45659769 GGGGTATTTTGGTTATTTTACCCTTTGA
1 -GGGTATTTTGGTAATTTTACCCTTCGA
* *
45659797 GGGTATTTCGGTTATTTTACCCTTCGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* * *
45659824 AGGTATTTTGATAATTTTAACCTTCGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* * * * **
45659851 GGGTATTTCGATAATTTTTCCTTTTAA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* *
45659878 GGGTATTTCGGTAATTTTACCCTTCAA
1 GGGTATTTTGGTAATTTTACCCTTCGA
*
45659905 GGGTATTTTGATAATTTTACCCTTCGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
45659932 GGGTATTT
1 GGGTATTT
45659940 CGGTCCCATT
Statistics
Matches: 320, Mismatches: 64, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
26 1 0.00
27 299 0.93
28 20 0.06
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.46
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACCCTTCGA
Found at i:45659760 original size:81 final size:81
Alignment explanation
Indices: 45659526--45659944 Score: 444
Period size: 81 Copynumber: 5.2 Consensus size: 81
45659516 TACCTTATAG
* * * * * * * *
45659526 GGGTATTTTAGTCATTTTACCCTTCAAAGGTATTTCGATTATTTTACCTTTCAAGGGTATTTTGG
1 GGGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTGA
* *
45659591 TAATTTTACCTTTCAA
66 TAATTTTACCCTTCGA
* * * * * * * *
45659607 TGGTATTTTGGTTATTTTACCATTCAGGGGGAATTTCGGTAATTTTACCCTTTGAAGGTATTTCG
1 GGGTATTTTGGTCATTTTACCCTTC-GAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTG
45659672 ATAATTTTACCCTTCGA
65 ATAATTTTACCCTTCGA
* ** * * * *
45659689 GGGTTTTTTGGTCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCATTCGAGGGTATTTCGG
1 GGGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTGA
* *
45659754 TTATTTTACCCTT-TA
66 TAATTTTACCCTTCGA
* * * *
45659769 GGGGTATTTTGGTTATTTTACCCTTTGAGGGTATTTCGGTTATTTTACCCTTCGAAGGTATTTTG
1 -GGGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTG
*
45659834 ATAATTTTAACCTTCGA
65 ATAATTTTACCCTTCGA
* * * * * ** *
45659851 GGGTATTTCGATAATTTTTCCTTTTAAGGGTATTTCGGTAATTTTACCCTTCAAGGGTATTTTGA
1 GGGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTGA
45659916 TAATTTTACCCTTCGA
66 TAATTTTACCCTTCGA
*
45659932 GGGTATTTCGGTC
1 GGGTATTTTGGTC
45659945 CCATTATGGC
Statistics
Matches: 277, Mismatches: 58, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
80 1 0.00
81 212 0.77
82 64 0.23
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.46
Consensus pattern (81 bp):
GGGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTGA
TAATTTTACCCTTCGA
Found at i:45663964 original size:79 final size:79
Alignment explanation
Indices: 45663874--45664031 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
45663864 TTGTGTGCGT
*
45663874 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCTGCTATACAAATTGGTGCCTT
1 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
45663939 GGAGGAGTTCTTTA
66 GGAGGAGTTCTTTA
45663953 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
1 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
45664018 GGAGGAGTTCTTTA
66 GGAGGAGTTCTTTA
45664032 AGAATCCTCA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.49
Consensus pattern (79 bp):
TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
GGAGGAGTTCTTTA
Found at i:45686629 original size:9 final size:9
Alignment explanation
Indices: 45686615--45686639 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
45686605 AAAATATTTA
45686615 TTTTAATAT
1 TTTTAATAT
45686624 TTTTAATAT
1 TTTTAATAT
45686633 TTTTAAT
1 TTTTAAT
45686640 GTATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTAATAT
Found at i:45687086 original size:21 final size:20
Alignment explanation
Indices: 45687039--45687087 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
45687029 GGATCCCCCG
45687039 CACCACCAACTCCCTCGCAA
1 CACCACCAACTCCCTCGCAA
** * *
45687059 CGTCACCAACTTCTTCCGCAA
1 CACCACCAACTCCCT-CGCAA
45687080 CACCACCA
1 CACCACCA
45687088 CGTCTGTCTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.29, C:0.51, G:0.06, T:0.14
Consensus pattern (20 bp):
CACCACCAACTCCCTCGCAA
Found at i:45689485 original size:16 final size:16
Alignment explanation
Indices: 45689461--45689493 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
45689451 TCTTGAAAAG
45689461 AAAAAAGAAT-TCTTT
1 AAAAAAGAATGTCTTT
45689476 AAAAATAGAATGTCTTT
1 AAAAA-AGAATGTCTTT
45689493 A
1 A
45689494 CAGTTTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (16 bp):
AAAAAAGAATGTCTTT
Found at i:45711984 original size:6 final size:6
Alignment explanation
Indices: 45711973--45712006 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
45711963 TATTCTGTTC
45711973 ATAAAT ATAAAT ATAAAT ATAAAT -TAAAT A-AAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
45712007 TATTTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 9 0.33
6 18 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAAAT
Found at i:45712015 original size:17 final size:18
Alignment explanation
Indices: 45711995--45712029 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
45711985 ATAAATATAA
45711995 ATTAAATAAA-ATTATTT
1 ATTAAATAAACATTATTT
*
45712012 ATTATATAAACATTATTT
1 ATTAAATAAACATTATTT
45712030 CGAATCAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAAATAAACATTATTT
Found at i:45713061 original size:15 final size:14
Alignment explanation
Indices: 45713037--45713067 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
45713027 AATTAGTACA
45713037 TTTTTTAAATTGAT
1 TTTTTTAAATTGAT
45713051 TTTTCTTAAATTGAT
1 TTTT-TTAAATTGAT
45713066 TT
1 TT
45713068 ACACAATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTTTTAAATTGAT
Found at i:45725089 original size:19 final size:20
Alignment explanation
Indices: 45725050--45725089 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
45725040 AAATATTAAA
* *
45725050 TATTAAAATTGATATAAACT
1 TATTAAAAGTGATAAAAACT
45725070 TATTAAAAGT-ATAAAAACT
1 TATTAAAAGTGATAAAAACT
45725089 T
1 T
45725090 GTCAATATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
TATTAAAAGTGATAAAAACT
Found at i:45725159 original size:10 final size:9
Alignment explanation
Indices: 45725108--45725159 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
45725098 TGTAAAAATA
*
45725108 TAAAAATTC
1 TAAAAATTT
45725117 TAATAAATTT
1 TAA-AAATTT
45725127 TAAAAATTT
1 TAAAAATTT
*
45725136 ATAAAACTTAT
1 -TAAAAATT-T
45725147 TAAAAATATT
1 TAAAAAT-TT
45725157 TAA
1 TAA
45725160 GATTAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
9 9 0.25
10 25 0.69
11 2 0.06
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (9 bp):
TAAAAATTT
Found at i:45725721 original size:9 final size:9
Alignment explanation
Indices: 45725680--45725881 Score: 56
Period size: 10 Copynumber: 21.2 Consensus size: 9
45725670 TTTTATTATT
45725680 TTTTTATAA
1 TTTTTATAA
*
45725689 GTTTATATCAA
1 -TTTTTAT-AA
*
45725700 TTTTGAT-A
1 TTTTTATAA
*
45725708 CTTTTATAA
1 TTTTTATAA
45725717 TTTTTATAGAA
1 TTTTTAT--AA
* *
45725728 TTTTAATACG
1 TTTTTATA-A
45725738 TTTTTATAAAA
1 TTTTTAT--AA
* *
45725749 TTTTAAATAT
1 TTTT-TATAA
45725759 TTTTTATTAA
1 TTTTTA-TAA
*
45725769 TTTATTAGAA
1 TTT-TTATAA
45725779 TTTATTAT--
1 TTT-TTATAA
* *
45725787 GTTTTATAT
1 TTTTTATAA
45725796 TTTTTATAA
1 TTTTTATAA
*
45725805 TATTTATAA
1 TTTTTATAA
*
45725814 GCTTTTTTTATAT
1 ----TTTTTATAA
*
45725827 TTTTTCTAA
1 TTTTTATAA
* *
45725836 GCTTATATCAA
1 -TTTTTAT-AA
*
45725847 TTTTCAT-A
1 TTTTTATAA
*
45725855 TTTTTTTAA
1 TTTTTATAA
45725864 TTTTTAT-A
1 TTTTTATAA
45725872 -TTTTATAA
1 TTTTTATAA
45725880 TT
1 TT
45725882 CCTTATGATT
Statistics
Matches: 138, Mismatches: 33, Indels: 43
0.64 0.15 0.20
Matches are distributed among these distances:
7 10 0.07
8 16 0.12
9 39 0.28
10 44 0.32
11 19 0.14
12 3 0.02
13 7 0.05
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:45725729 original size:28 final size:29
Alignment explanation
Indices: 45725681--45725746 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
45725671 TTTATTATTT
*
45725681 TTTTATAAGTTTATATCAATTTTGATAC-
1 TTTTATAAGTTTATATCAATTTTAATACG
* *
45725709 TTTTATAA-TTTTTATAGAATTTTAATACG
1 TTTTATAAGTTTATAT-CAATTTTAATACG
45725738 TTTTTATAA
1 -TTTTATAA
45725747 AATTTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 6 0.19
28 18 0.56
30 8 0.25
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.56
Consensus pattern (29 bp):
TTTTATAAGTTTATATCAATTTTAATACG
Found at i:45725822 original size:22 final size:22
Alignment explanation
Indices: 45725795--45725839 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
45725785 ATGTTTTATA
45725795 TTTTTTATAATATTTATAAGCT
1 TTTTTTATAATATTTATAAGCT
* * *
45725817 TTTTTTATATTTTTTCTAAGCT
1 TTTTTTATAATATTTATAAGCT
45725839 T
1 T
45725840 ATATCAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTTTTATAATATTTATAAGCT
Found at i:45726354 original size:19 final size:19
Alignment explanation
Indices: 45726330--45726384 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
45726320 TTAAATCATA
45726330 ATTAAATTAATTGTATAAT
1 ATTAAATTAATTGTATAAT
* * *
45726349 ATTAAAAAAATATTTATATAAT
1 ATT---AAATTAATTGTATAAT
45726371 ATTAAATTAATTGT
1 ATTAAATTAATTGT
45726385 GTTGGATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
19 11 0.41
22 16 0.59
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
ATTAAATTAATTGTATAAT
Found at i:45741264 original size:41 final size:40
Alignment explanation
Indices: 45741171--45741268 Score: 101
Period size: 43 Copynumber: 2.4 Consensus size: 40
45741161 AACTAAAGTT
*
45741171 ATATTTATAATTAAAATTTATTAAATTAAATTAAATTATTAA
1 ATATTTAT-ATTAAAATTTATTAAATTAAATAAAATTA-TAA
* *
45741213 ATCATATATATTAAAA-TTAGGTTATATTAAATAATAATTA-AA
1 AT-ATTTATATTAAAATTTA--TTAAATTAAATAA-AATTATAA
45741255 ATATTTATATTAAA
1 ATATTTATATTAAA
45741269 TAATTAAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
41 14 0.29
42 13 0.27
43 16 0.33
44 5 0.10
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (40 bp):
ATATTTATATTAAAATTTATTAAATTAAATAAAATTATAA
Found at i:45741266 original size:25 final size:28
Alignment explanation
Indices: 45741207--45741272 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 28
45741197 TAAATTAAAT
45741207 TATTAAATCATATATATTAAAATTAGGTTA
1 TATTAAAT-A-ATATATTAAAATTAGGTTA
*
45741237 TATTAAATAATA-ATTAAAA-TA-TTTA
1 TATTAAATAATATATTAAAATTAGGTTA
45741262 TATTAAATAAT
1 TATTAAATAAT
45741273 TAAAGAGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 14 0.40
26 2 0.06
27 7 0.20
28 3 0.09
29 1 0.03
30 8 0.23
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (28 bp):
TATTAAATAATATATTAAAATTAGGTTA
Found at i:45749546 original size:3 final size:3
Alignment explanation
Indices: 45749538--45749586 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
45749528 ATAAAGAATG
45749538 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
45749586 A
1 A
45749587 TGATTAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:45749629 original size:5 final size:6
Alignment explanation
Indices: 45749610--45749656 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
45749600 TTTGGAATTC
*
45749610 AAATAA AAATAA AAATAA AACATTAC AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AA-A-TAA AAATAA AAATAA AAATAA AAA
45749657 AATAAAGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 31 0.84
7 2 0.05
8 4 0.11
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:45749659 original size:20 final size:20
Alignment explanation
Indices: 45749614--45749668 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
45749604 GAATTCAAAT
*
45749614 AAAAATAAAAATAAAACATT
1 AAAAATAAAAATAAAACATA
*
45749634 ACAAATAAAAATAAAA-ATAA
1 AAAAATAAAAATAAAACAT-A
*
45749654 AAAAATAAAGATAAA
1 AAAAATAAAAATAAA
45749669 CTAAATTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAATAAAAATAAAACATA
Found at i:45749667 original size:26 final size:26
Alignment explanation
Indices: 45749609--45749668 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
45749599 ATTTGGAATT
* *
45749609 CAAATAAAAATAAAAATAAAACATTA
1 CAAATAAAAATAAAAATAAAAAAATA
45749635 CAAATAAAAATAAAAATAAAAAAATA
1 CAAATAAAAATAAAAATAAAAAAATA
45749661 -AAGATAAA
1 CAA-ATAAA
45749669 CTAAATTGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 2 0.06
26 29 0.94
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.17
Consensus pattern (26 bp):
CAAATAAAAATAAAAATAAAAAAATA
Found at i:45753174 original size:10 final size:10
Alignment explanation
Indices: 45753159--45753183 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
45753149 CCTGATATCA
45753159 CATACTTTCT
1 CATACTTTCT
45753169 CATACTTTCT
1 CATACTTTCT
45753179 CATAC
1 CATAC
45753184 AATATGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (10 bp):
CATACTTTCT
Found at i:45758155 original size:9 final size:9
Alignment explanation
Indices: 45758141--45758171 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
45758131 GTTAAACGAA
45758141 TCGAGTTAT
1 TCGAGTTAT
*
45758150 TCGAGTTAA
1 TCGAGTTAT
45758159 TCGAGTTAT
1 TCGAGTTAT
45758168 TCGA
1 TCGA
45758172 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:45758239 original size:9 final size:9
Alignment explanation
Indices: 45758225--45758252 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
45758215 TGAGTTTTCG
45758225 AATTCGAAT
1 AATTCGAAT
45758234 AATTCGAAT
1 AATTCGAAT
45758243 AATTCGAAT
1 AATTCGAAT
45758252 A
1 A
45758253 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:45759907 original size:40 final size:39
Alignment explanation
Indices: 45759852--45759983 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 39
45759842 ACTACTTTGG
*
45759852 CACCCAGTGCCTCATCAGATAATTTGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATC-GATAATCTGAAGTAGTAAATTGA
* * * * * *
45759892 CACCCAGTGTCTCATCGGTTAAACCG-A--AGTAAGTTGG
1 CACCCAGTGCCTCATC-GATAATCTGAAGTAGTAAATTGA
*
45759929 CACCCAGTGCCTCATCGAATAAATCTGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCG-AT-AATCTGAAGTAGTAAATTGA
*
45759970 CA-CCAGTGTCTCAT
1 CACCCAGTGCCTCAT
45759984 TGACTCGAAG
Statistics
Matches: 71, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
36 1 0.01
37 24 0.34
38 4 0.06
39 2 0.03
40 31 0.44
41 9 0.13
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGATAATCTGAAGTAGTAAATTGA
Found at i:45762823 original size:11 final size:11
Alignment explanation
Indices: 45762802--45762910 Score: 80
Period size: 11 Copynumber: 10.7 Consensus size: 11
45762792 AAATTTTTAT
45762802 TTTTAAAAAATA
1 TTTT-AAAAATA
45762814 TTTTAAAAATA
1 TTTTAAAAATA
45762825 --TT--AAATA
1 TTTTAAAAATA
45762832 -TTT-AAAATA
1 TTTTAAAAATA
45762841 -TTTAAAAAGTA
1 TTTTAAAAA-TA
45762852 TTTTAAAAATA
1 TTTTAAAAATA
45762863 TTTT--AAA-A
1 TTTTAAAAATA
*
45762871 -TTAAAAAATA
1 TTTTAAAAATA
* *
45762881 -ATAAAAAAGTA
1 TTTTAAAAA-TA
45762892 TTTTAAAAATA
1 TTTTAAAAATA
45762903 TTTTAAAA
1 TTTTAAAA
45762911 TAAAAAATAA
Statistics
Matches: 83, Mismatches: 4, Indels: 21
0.77 0.04 0.19
Matches are distributed among these distances:
7 7 0.08
8 3 0.04
9 16 0.19
10 12 0.14
11 27 0.33
12 18 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:45762845 original size:17 final size:18
Alignment explanation
Indices: 45762809--45762864 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 18
45762799 TATTTTTAAA
45762809 AAATATTTTAAAAATATT
1 AAATATTTTAAAAATATT
45762827 AAATA-TTT-AAAATATTT
1 AAATATTTTAAAAATA-TT
45762844 AAAAAGTATTTTAAAAATATT
1 --AAA-TATTTTAAAAATATT
45762865 TTAAAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
16 6 0.19
17 5 0.16
18 5 0.16
19 3 0.09
20 2 0.06
21 5 0.16
22 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATATTTTAAAAATATT
Found at i:45762869 original size:40 final size:40
Alignment explanation
Indices: 45762803--45762958 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
45762793 AATTTTTATT
* *
45762803 TTTAAAAAATATTTTAAAAATA--TTAAATATT-TAAAATA
1 TTTAAAAAGTATTTTAAAAATATTTTAAA-ATTAAAAAATA
45762841 TTTAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATA
1 TTTAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATA
* *
45762881 ATAAAAAAGTATTTTAAAAATATTTTAAAA-TAAAAAATA
1 TTTAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATA
45762920 ---AAAAA-TA-TTT-AAAATA-TTT-AAATTAAAAAAT-
1 TTTAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATA
*
45762951 TTAAAAAA
1 TTTAAAAA
45762959 TAAATATATT
Statistics
Matches: 107, Mismatches: 4, Indels: 18
0.83 0.03 0.14
Matches are distributed among these distances:
31 3 0.03
32 11 0.10
33 6 0.06
34 8 0.07
35 2 0.02
36 5 0.05
38 21 0.20
39 12 0.11
40 39 0.36
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (40 bp):
TTTAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATA
Found at i:45762942 original size:8 final size:9
Alignment explanation
Indices: 45762808--45762941 Score: 57
Period size: 9 Copynumber: 14.3 Consensus size: 9
45762798 TTATTTTTAA
45762808 AAAATATTTT
1 AAAATA-TTT
45762818 AAAA-ATATT
1 AAAATAT-TT
45762827 -AAATATTT
1 AAAATATTT
45762835 AAAATATTT
1 AAAATATTT
45762844 AAAAAGTATTTT
1 -AAAA-TA-TTT
45762856 AAAAATATTTT
1 -AAAATA-TTT
**
45762867 AAAAT-TAA
1 AAAATATTT
**
45762875 AAAATAATAA
1 AAAAT-ATTT
45762885 AAAAGTATTTT
1 AAAA-TA-TTT
45762896 AAAAATATTTT
1 -AAAATA-TTT
45762907 AAAATA---
1 AAAATATTT
**
45762913 AAAA-ATAA
1 AAAATATTT
45762921 AAAATATTT
1 AAAATATTT
45762930 AAAATATTT
1 AAAATATTT
45762939 AAA
1 AAA
45762942 TTAAAAAATT
Statistics
Matches: 103, Mismatches: 6, Indels: 31
0.74 0.04 0.22
Matches are distributed among these distances:
5 1 0.01
6 4 0.04
8 16 0.16
9 27 0.26
10 27 0.26
11 16 0.16
12 12 0.12
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (9 bp):
AAAATATTT
Found at i:45764873 original size:15 final size:16
Alignment explanation
Indices: 45764855--45764891 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
45764845 CTTATTATAA
*
45764855 AATAAATAA-ATAGAG
1 AATAAATAAGAAAGAG
45764870 AATAAATAAGAAAGAG
1 AATAAATAAGAAAGAG
45764886 AATAAA
1 AATAAA
45764892 GTTTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (16 bp):
AATAAATAAGAAAGAG
Found at i:45765353 original size:27 final size:27
Alignment explanation
Indices: 45765299--45765349 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
45765289 TGTCTTTCTT
*
45765299 CTCCTCTTCCTATCCCACGCTTTCACC
1 CTCCTCCTCCTATCCCACGCTTTCACC
* *
45765326 CTCCTCCTCCT-TCCCTCTCTTTCA
1 CTCCTCCTCCTATCCCACGCTTTCA
45765350 ACCCCACTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.08, C:0.53, G:0.02, T:0.37
Consensus pattern (27 bp):
CTCCTCCTCCTATCCCACGCTTTCACC
Found at i:45777312 original size:21 final size:21
Alignment explanation
Indices: 45777273--45777319 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
45777263 GTAATTTACT
*
45777273 CTTTTTTTTAAATCTTTGTTA
1 CTTTTTTTTAAATCATTGTTA
*
45777294 GTTTTTGTTTAAAT-ATTGTTA
1 CTTTTT-TTTAAATCATTGTTA
45777315 CTTTT
1 CTTTT
45777320 AATACAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.19, C:0.06, G:0.09, T:0.66
Consensus pattern (21 bp):
CTTTTTTTTAAATCATTGTTA
Found at i:45778819 original size:32 final size:32
Alignment explanation
Indices: 45778778--45778841 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
45778768 ATTCTCTGTC
45778778 CTATATCTAAGTTATGAATTTAGTCTTTGTAA
1 CTATATCTAAGTTATGAATTTAGTCTTTGTAA
45778810 CTATATCTAAGTTATGAATTTAGTCTTTGTAA
1 CTATATCTAAGTTATGAATTTAGTCTTTGTAA
45778842 TTTAATTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (32 bp):
CTATATCTAAGTTATGAATTTAGTCTTTGTAA
Found at i:45794867 original size:20 final size:20
Alignment explanation
Indices: 45794830--45794867 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
45794820 AAGTTAGAAT
*
45794830 TATGATATTTATTTTTATTA
1 TATGATATTTATTCTTATTA
45794850 TATGATTATTT-TTCTTAT
1 TATGA-TATTTATTCTTAT
45794868 ATTCCAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (20 bp):
TATGATATTTATTCTTATTA
Found at i:45795566 original size:163 final size:163
Alignment explanation
Indices: 45795318--45795808 Score: 973
Period size: 163 Copynumber: 3.0 Consensus size: 163
45795308 TAGTATTAAT
45795318 TTTGCTAATTGAGTTTTAGGTCAGATAAAATCGATATTGTTATTAATGTATGAAAATGTAAATTT
1 TTTGCTAATTGAGTTTTAGGTCAGATAAAATCGATATTGTTATTAATGTATGAAAATGTAAATTT
45795383 AAGTACGTTGAAGTGCATTATCTTATTATTTAAAGATTATAACTAATTTTAAGTATTATATAAAA
66 AAGTACGTTGAAGTGCATTATCTTATTATTTAAAGATTATAACTAATTTTAAGTATTATATAAAA
45795448 AAATAAATATGATTTTAAGTTATAAAATCAGAC
131 AAATAAATATGATTTTAAGTTATAAAATCAGAC
45795481 TTTGCTAATTGAGTTTTAGGTCAGATAAAATCGATATTGTTATTAATGTATGAAAATGTAAATTT
1 TTTGCTAATTGAGTTTTAGGTCAGATAAAATCGATATTGTTATTAATGTATGAAAATGTAAATTT
45795546 AAGTACGTTGAAGTGCATTATCTTATTATTTAAAGATTATAACTAATTTTAAGTATTATATAAAA
66 AAGTACGTTGAAGTGCATTATCTTATTATTTAAAGATTATAACTAATTTTAAGTATTATATAAAA
45795611 AAATAAATATGATTTTAAGTTATAAAATCAGAC
131 AAATAAATATGATTTTAAGTTATAAAATCAGAC
45795644 TTTGCTAATTGAGTTTTAGGTCAGATAAAATCGATATTGTTATTAATGTATGAAAATGTAAATTT
1 TTTGCTAATTGAGTTTTAGGTCAGATAAAATCGATATTGTTATTAATGTATGAAAATGTAAATTT
*
45795709 AAGTACGTTGAAGTGCATTATCTTATTATTTAAAGATTATAATTAATTTTAAGTATTATATAAAA
66 AAGTACGTTGAAGTGCATTATCTTATTATTTAAAGATTATAACTAATTTTAAGTATTATATAAAA
45795774 AAATAAATATGATTTTAAGTTATAAAATCAGAC
131 AAATAAATATGATTTTAAGTTATAAAATCAGAC
45795807 TT
1 TT
45795809 ATATAGAGCT
Statistics
Matches: 327, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 327 1.00
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (163 bp):
TTTGCTAATTGAGTTTTAGGTCAGATAAAATCGATATTGTTATTAATGTATGAAAATGTAAATTT
AAGTACGTTGAAGTGCATTATCTTATTATTTAAAGATTATAACTAATTTTAAGTATTATATAAAA
AAATAAATATGATTTTAAGTTATAAAATCAGAC
Found at i:45796975 original size:11 final size:11
Alignment explanation
Indices: 45796959--45796985 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
45796949 ATACACGGAT
45796959 AGATTTACTGG
1 AGATTTACTGG
45796970 AGATTTACTGG
1 AGATTTACTGG
45796981 AGATT
1 AGATT
45796986 AGTGATAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (11 bp):
AGATTTACTGG
Found at i:45819982 original size:2 final size:2
Alignment explanation
Indices: 45819977--45820012 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
45819967 CTCTCGCTCT
* *
45819977 CA CA CA CA CA CA CA CA CA CA CA CA AA CA CA AA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
45820013 AACATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:45820013 original size:6 final size:6
Alignment explanation
Indices: 45819978--45820016 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
45819968 TCTCGCTCTC
* * *
45819978 ACACAC ACACAC ACACAC ACACAA ACACAA ACACAA ACA
1 ACACAA ACACAA ACACAA ACACAA ACACAA ACACAA ACA
45820017 TATATAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (6 bp):
ACACAA
Found at i:45820013 original size:12 final size:12
Alignment explanation
Indices: 45819978--45820016 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
45819968 TCTCGCTCTC
*
45819978 ACACACACACAC
1 ACACACACACAA
45819990 ACACACACACAA
1 ACACACACACAA
*
45820002 ACACAAACACAA
1 ACACACACACAA
45820014 ACA
1 ACA
45820017 TATATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (12 bp):
ACACACACACAA
Found at i:45831734 original size:15 final size:17
Alignment explanation
Indices: 45831714--45831745 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
45831704 TTACAAACTA
45831714 TAAAAT-AT-AAATTAT
1 TAAAATAATAAAATTAT
45831729 TAAAATAATAAAATTAT
1 TAAAATAATAAAATTAT
45831746 ATTTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATAATAAAATTAT
Found at i:45844328 original size:14 final size:14
Alignment explanation
Indices: 45844311--45844338 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
45844301 TAATTATAAA
45844311 AATGTAAAAATATT
1 AATGTAAAAATATT
45844325 AATGTAAAAATATT
1 AATGTAAAAATATT
45844339 TATAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGTAAAAATATT
Found at i:45849830 original size:3 final size:3
Alignment explanation
Indices: 45849822--45849851 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
45849812 ATCTGACCCC
45849822 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
45849852 CAAGAGTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Done.