Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 187 of 208
Found at i:57124451 original size:25 final size:24
Alignment explanation
Indices: 57124350--57124475 Score: 127
Period size: 22 Copynumber: 5.3 Consensus size: 24
57124340 CACTAATGAA
* *
57124350 CAGAGAGCACTAAAGTGCTAT-A-
1 CAGAGAGCACCAACGTGCTATAAT
*
57124372 CAGAGAGCA-CAGATGTGCTA-AA-
1 CAGAGAGCACCA-ACGTGCTATAAT
** *
57124394 CAGAGAGCACTGACGTGCTAAAAT
1 CAGAGAGCACCAACGTGCTATAAT
*
57124418 CAGAGAGCACCAACGTGCTAGTAGT
1 CAGAGAGCACCAACGTGCTA-TAAT
57124443 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCT-ATAAT
57124468 CAGAGAGC
1 CAGAGAGC
57124476 GCGCTAAAGT
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
21 1 0.01
22 33 0.38
23 2 0.02
24 18 0.21
25 32 0.37
26 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.15
Consensus pattern (24 bp):
CAGAGAGCACCAACGTGCTATAAT
Found at i:57124773 original size:5 final size:5
Alignment explanation
Indices: 57124763--57124792 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
57124753 AGTTCCATAA
*
57124763 TATTT TATTT TACTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT
57124793 CTAAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:57126029 original size:21 final size:21
Alignment explanation
Indices: 57125976--57126030 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
57125966 TAAAGATTAT
57125976 TAATTTAAAA-TTGATATGCAA
1 TAATTTAAAATTTGATAT-CAA
*
57125997 T-ATATAATAATTTGAATAT-AA
1 TAATTTAA-AATTTG-ATATCAA
57126018 TAATTTAAAATTT
1 TAATTTAAAATTT
57126031 TAAAAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 5 0.18
21 11 0.39
22 8 0.29
23 4 0.14
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
TAATTTAAAATTTGATATCAA
Found at i:57126038 original size:9 final size:9
Alignment explanation
Indices: 57126024--57126066 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
57126014 ATAATAATTT
*
57126024 AAAATTTTA
1 AAAATTGTA
57126033 AAAATTGT-
1 AAAATTGTA
57126041 AAAATTGTAAA
1 AAAATTGT--A
57126052 AAAATTGTA
1 AAAATTGTA
57126061 AAAATT
1 AAAATT
57126067 ACAAAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
8 8 0.27
9 14 0.47
11 8 0.27
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (9 bp):
AAAATTGTA
Found at i:57126072 original size:19 final size:19
Alignment explanation
Indices: 57126032--57126075 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
57126022 TTAAAATTTT
*
57126032 AAAAATTGTAAAATTGTAA
1 AAAAATTGTAAAAATGTAA
57126051 AAAAATTGTAAAAAT-TACA
1 AAAAATTGTAAAAATGTA-A
57126070 AAAAAT
1 AAAAAT
57126076 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (19 bp):
AAAAATTGTAAAAATGTAA
Found at i:57126080 original size:16 final size:17
Alignment explanation
Indices: 57126059--57126098 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
57126049 AAAAAAATTG
57126059 TAAAAATT-ACAAAAAA
1 TAAAAATTAACAAAAAA
*
57126075 TAAAAATTAAATAAAAAA
1 TAAAAATT-AACAAAAAA
57126093 TAAAAA
1 TAAAAA
57126099 AGAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
18 13 0.62
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
TAAAAATTAACAAAAAA
Found at i:57126090 original size:18 final size:18
Alignment explanation
Indices: 57126069--57126120 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
57126059 TAAAAATTAC
57126069 AAAAAATAAAAATTAAAT
1 AAAAAATAAAAATTAAAT
**
57126087 AAAAAATAAAAAAGAAAT
1 AAAAAATAAAAATTAAAT
57126105 AAAAACACTAAAAATT
1 AAAAA-A-TAAAAATT
57126121 TTATTTTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 21 0.75
19 1 0.04
20 6 0.21
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (18 bp):
AAAAAATAAAAATTAAAT
Found at i:57127448 original size:28 final size:28
Alignment explanation
Indices: 57127408--57127464 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
57127398 TGCCGAATAA
57127408 AAATTGGATTTTTATGTCCGGGAAATGG
1 AAATTGGATTTTTATGTCCGGGAAATGG
57127436 AAATTGGATTTTTATGTCCGGGAAATGG
1 AAATTGGATTTTTATGTCCGGGAAATGG
57127464 A
1 A
57127465 TATCGACCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (28 bp):
AAATTGGATTTTTATGTCCGGGAAATGG
Found at i:57127658 original size:6 final size:6
Alignment explanation
Indices: 57127647--57127723 Score: 100
Period size: 6 Copynumber: 12.8 Consensus size: 6
57127637 AATTAGGTTT
* *
57127647 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG CGTGTG CGTGTG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * *
57127695 CGTGTG CGTGTG CGTGTG CGTGTG TGTGT
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGT
57127724 TTTTAAAATA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.00, C:0.08, G:0.49, T:0.43
Consensus pattern (6 bp):
TGTGTG
Found at i:57127668 original size:18 final size:18
Alignment explanation
Indices: 57127647--57127723 Score: 118
Period size: 18 Copynumber: 4.3 Consensus size: 18
57127637 AATTAGGTTT
*
57127647 TGTGTGTGTGTGTGTGTG
1 TGTGTGTGTGTGCGTGTG
57127665 TGTGTGTGTGTGCGTGTG
1 TGTGTGTGTGTGCGTGTG
*
57127683 CGTGTGTGTGTGCGTGTG
1 TGTGTGTGTGTGCGTGTG
* *
57127701 CGTGTGCGTGTGCGTGTG
1 TGTGTGTGTGTGCGTGTG
57127719 TGTGT
1 TGTGT
57127724 TTTTAAAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.00, C:0.08, G:0.49, T:0.43
Consensus pattern (18 bp):
TGTGTGTGTGTGCGTGTG
Found at i:57128012 original size:18 final size:19
Alignment explanation
Indices: 57127989--57128032 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
57127979 CAGAATTTTC
*
57127989 TGTTTCTCTAGCA-TGTTA
1 TGTTTCTCTACCATTGTTA
* *
57128007 TGTTTCTGTACCATTTTTA
1 TGTTTCTCTACCATTGTTA
57128026 TGTTTCT
1 TGTTTCT
57128033 TTATTTTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.57
Consensus pattern (19 bp):
TGTTTCTCTACCATTGTTA
Found at i:57128048 original size:7 final size:7
Alignment explanation
Indices: 57128036--57128080 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
57128026 TGTTTCTTTA
57128036 TTTTCTG
1 TTTTCTG
57128043 TTTTCTG
1 TTTTCTG
*
57128050 TTTTTTG
1 TTTTCTG
57128057 TTTTCTG
1 TTTTCTG
*
57128064 TTTTGCTA
1 TTTT-CTG
57128072 TTTTCTG
1 TTTTCTG
57128079 TT
1 TT
57128081 GAATGAAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.02, C:0.11, G:0.13, T:0.73
Consensus pattern (7 bp):
TTTTCTG
Found at i:57128062 original size:21 final size:22
Alignment explanation
Indices: 57128021--57128067 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
57128011 TCTGTACCAT
57128021 TTTTATGTTTCTTTATTTTCTG
1 TTTTATGTTTCTTTATTTTCTG
* *
57128043 TTTTCTGTTT-TTTGTTTTCTG
1 TTTTATGTTTCTTTATTTTCTG
57128064 TTTT
1 TTTT
57128068 GCTATTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.04, C:0.09, G:0.11, T:0.77
Consensus pattern (22 bp):
TTTTATGTTTCTTTATTTTCTG
Found at i:57128877 original size:25 final size:26
Alignment explanation
Indices: 57128847--57129124 Score: 130
Period size: 25 Copynumber: 10.7 Consensus size: 26
57128837 CTTAAATGTA
*
57128847 AACTTACATAA-TACATAATTTACAC
1 AACTTACATAACTACATAACTTACAC
*
57128872 AACTTACATAACCTACATAACTTACAT
1 AACTTACATAA-CTACATAACTTACAC
* * *
57128899 AA--TACA-AAGCTTACATAACTGAAAT
1 AACTTACATAA-C-TACATAACTTACAC
* * *
57128924 AGCTTACACAACTTACATAACTTACAT
1 AACTTACATAAC-TACATAACTTACAC
* *
57128951 AACTTACATAACTTACACAACTTACAT
1 AACTTACATAAC-TACATAACTTACAC
* *
57128978 AA--TACATAA-TAACTTACAACTTACAT
1 AACTTACATAACT-AC--ATAACTTACAC
* * ** *
57129004 AACATACATTACTTTGATAACTTACAT
1 AACTTACATAAC-TACATAACTTACAC
* * *
57129031 AAGTTACATAA-TACACAACTTACAT
1 AACTTACATAACTACATAACTTACAC
** * *
57129056 AGTTTACTTAA-TACATAACTTACAT
1 AACTTACATAACTACATAACTTACAC
*
57129081 AACTT--ATACACGTACATAACTTACAT
1 AACTTACATA-AC-TACATAACTTACAC
* *
57129107 AATTTACTTAA-TACATAA
1 AACTTACATAACTACATAA
57129125 ATATATATCA
Statistics
Matches: 205, Mismatches: 30, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
23 3 0.01
24 6 0.03
25 77 0.38
26 31 0.15
27 77 0.38
28 10 0.05
30 1 0.00
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (26 bp):
AACTTACATAACTACATAACTTACAC
Found at i:57128878 original size:9 final size:9
Alignment explanation
Indices: 57128807--57129113 Score: 228
Period size: 9 Copynumber: 34.4 Consensus size: 9
57128797 TTATTAATAT
57128807 TTACATAAAC
1 TTACAT-AAC
57128817 TTACATAAC
1 TTACATAAC
57128826 TATCACATAAAC
1 T-T-ACAT-AAC
*
57128838 TTAAATGTAAAC
1 TTACA--T-AAC
57128850 TTACATAA-
1 TTACATAAC
*
57128858 -TACATAAT
1 TTACATAAC
*
57128866 TTACACAAC
1 TTACATAAC
57128875 TTACATAAC
1 TTACATAAC
*
57128884 CTACATAAC
1 TTACATAAC
57128893 TTACATAA-
1 TTACATAAC
57128901 -TACA-AAGC
1 TTACATAA-C
57128909 TTACATAAC
1 TTACATAAC
* * *
57128918 TGAAATAGC
1 TTACATAAC
*
57128927 TTACACAAC
1 TTACATAAC
57128936 TTACATAAC
1 TTACATAAC
57128945 TTACATAAC
1 TTACATAAC
57128954 TTACATAAC
1 TTACATAAC
*
57128963 TTACACAAC
1 TTACATAAC
57128972 TTACATAATAC
1 TTACAT-A-AC
*
57128983 ATA-ATAAC
1 TTACATAAC
57128991 TTAC--AAC
1 TTACATAAC
57128998 TTACATAAC
1 TTACATAAC
* *
57129007 ATACATTAC
1 TTACATAAC
**
57129016 TTTGATAAC
1 TTACATAAC
*
57129025 TTACATAAG
1 TTACATAAC
57129034 TTACATAA-
1 TTACATAAC
*
57129042 -TACACAAC
1 TTACATAAC
**
57129050 TTACATAGT
1 TTACATAAC
*
57129059 TTACTTAA-
1 TTACATAAC
57129067 -TACATAAC
1 TTACATAAC
57129075 TTACATAAC
1 TTACATAAC
57129084 TT--ATACAC
1 TTACATA-AC
*
57129092 GTACATAAC
1 TTACATAAC
*
57129101 TTACATAAT
1 TTACATAAC
57129110 TTAC
1 TTAC
57129114 TTAATACATA
Statistics
Matches: 236, Mismatches: 38, Indels: 47
0.74 0.12 0.15
Matches are distributed among these distances:
6 2 0.01
7 33 0.14
8 7 0.03
9 154 0.65
10 18 0.08
11 9 0.04
12 13 0.06
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (9 bp):
TTACATAAC
Found at i:57128894 original size:43 final size:42
Alignment explanation
Indices: 57128847--57129109 Score: 197
Period size: 43 Copynumber: 6.3 Consensus size: 42
57128837 CTTAAATGTA
* *
57128847 AACTTACATAATACATAATTTACACAACTTACATAACCTACAT
1 AACTTACATAATACATAA-TTACATAACTTACATAACTTACAT
* * * *
57128890 AACTTACATAATACA-AAGCTTACATAACTGAAATAGCTTACAC
1 AACTTACATAATACATAA--TTACATAACTTACATAACTTACAT
*
57128933 AACTTACAT-A-AC----TTACATAACTTACATAACTTACAC
1 AACTTACATAATACATAATTACATAACTTACATAACTTACAT
* * *
57128969 AACTTACATAATACATAATAACTTACAACTTACATAACATACAT
1 AACTTACATAATACATAATTAC--ATAACTTACATAACTTACAT
* ** *
57129013 TACTTTGATAACTTACATAAGTTACATAA--TACACAACTTACAT
1 AACTTACATAA--TACATAA-TTACATAACTTACATAACTTACAT
** * *
57129056 AGTTTACTTAATACATAACTTACATAACTT--ATACACGTACAT
1 AACTTACATAATACATAA-TTACATAACTTACATA-ACTTACAT
57129098 AACTTACATAAT
1 AACTTACATAAT
57129110 TTACTTAATA
Statistics
Matches: 172, Mismatches: 33, Indels: 31
0.73 0.14 0.13
Matches are distributed among these distances:
36 30 0.17
37 1 0.01
38 2 0.01
41 19 0.11
42 22 0.13
43 60 0.35
44 25 0.15
45 3 0.02
46 7 0.04
47 3 0.02
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (42 bp):
AACTTACATAATACATAATTACATAACTTACATAACTTACAT
Found at i:57129113 original size:51 final size:50
Alignment explanation
Indices: 57128850--57129124 Score: 155
Period size: 52 Copynumber: 5.3 Consensus size: 50
57128840 AAATGTAAAC
* * * * *
57128850 TTACATAATACATAATTTACACAACTTACATAACCTACATAACTTACATAA-
1 TTACTTAATACATAACTTACATAACTTACACAA--TACACAACTTACATAAT
* * * * * *
57128901 -TAC-AAAGCTTACATAACTGAAATAGCTTACACAACTTACATAACTTACATAAC
1 TTACTTAA---TACATAACTTACATAACTTACACAA--TACACAACTTACATAAT
* * * *
57128954 TTACATAACTTACACAACTTACATAA--TACATAATAACTTACAACTTACATAAC
1 TTACTTAA--TACATAACTTACATAACTTACACAAT-AC--ACAACTTACATAAT
* * ** * * *
57129007 ATACATTACTTTGATAACTTACATAAGTTACATAATACACAACTTACATAGT
1 TTAC-TTA-ATACATAACTTACATAACTTACACAATACACAACTTACATAAT
* * *
57129059 TTACTTAATACATAACTTACATAACTTATACACGTACATAACTTACATAAT
1 TTACTTAATACATAACTTACATAACTTACACA-ATACACAACTTACATAAT
57129110 TTACTTAATACATAA
1 TTACTTAATACATAA
57129125 ATATATATCA
Statistics
Matches: 177, Mismatches: 33, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
49 2 0.01
50 23 0.13
51 35 0.20
52 57 0.32
53 29 0.16
54 21 0.12
55 10 0.06
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (50 bp):
TTACTTAATACATAACTTACATAACTTACACAATACACAACTTACATAAT
Found at i:57132758 original size:42 final size:41
Alignment explanation
Indices: 57132646--57132915 Score: 297
Period size: 42 Copynumber: 6.4 Consensus size: 41
57132636 AATCCCAAAA
* * *
57132646 TTAGTGGCGTTTTTTATAAAAGCGTCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTT-T-TAAGCGCCGCTAAAGAACATGATCT
* * * *
57132689 ATAGCGGCATTTTTTTACCAAGCGCCGCTAAAGAACATTATCT
1 TTAGCGGCGTTTTTTT--TAAGCGCCGCTAAAGAACATGATCT
* *
57132732 TTAGCGGCGTTTTTCTTTAAGCGCCGCTAAAGAATATTATCT
1 TTAGCGGCGTTTTT-TTTAAGCGCCGCTAAAGAACATGATCT
* * *
57132774 TTAGCGGCGATTTTTTGTAACCGCCACTAAAGAACATGATCT
1 TTAGCGGCG-TTTTTTTTAAGCGCCGCTAAAGAACATGATCT
** * * *
57132816 TTAGAAGCGTCTTTTATTAAGCGTCGCTAAAGAACATGATTT
1 TTAGCGGCGT-TTTTTTTAAGCGCCGCTAAAGAACATGATCT
*
57132858 TTAGCGGCGTCTTTTTTTAAACGCCGCTAAAGAACATGATCT
1 TTAGCGGCGT-TTTTTTTAAGCGCCGCTAAAGAACATGATCT
*
57132900 TTAGCGTCGTTTTTTT
1 TTAGCGGCGTTTTTTT
57132916 CTGTAAACGC
Statistics
Matches: 192, Mismatches: 31, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
41 7 0.04
42 132 0.69
43 51 0.27
44 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (41 bp):
TTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
Found at i:57136898 original size:2 final size:2
Alignment explanation
Indices: 57136891--57136916 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57136881 AGTAATTTAA
57136891 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
57136917 TCTTATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57137584 original size:17 final size:17
Alignment explanation
Indices: 57137562--57137600 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
57137552 AATATTTCTA
57137562 AAAATAAACATAATTTT
1 AAAATAAACATAATTTT
57137579 AAAATAAACATAATTTT
1 AAAATAAACATAATTTT
57137596 AAAAT
1 AAAAT
57137601 TTTAAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAAACATAATTTT
Found at i:57145644 original size:3 final size:3
Alignment explanation
Indices: 57145622--57145697 Score: 125
Period size: 3 Copynumber: 25.3 Consensus size: 3
57145612 AAGAAGGAAC
* * *
57145622 AAT AAC AAT AAT GAT 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
57145670 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
57145698 GGAATAAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:57147464 original size:44 final size:44
Alignment explanation
Indices: 57147416--57147906 Score: 130
Period size: 44 Copynumber: 11.2 Consensus size: 44
57147406 TATCTTGGAA
* * *
57147416 AGATAAGATTTGCCGTCTTCGATTTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
57147460 AGATAATATCTGTTATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * *
57147504 AGACAAGGCTCGGT-GGCTTAAATTTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
57147548 AGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
57147592 AGATAAGATCTG-CTATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGTC-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * *
57147636 AGACAAGGCTCGGT-GGCTTAAATCTACTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * * ** *
57147680 AGATGAGATTTGCCATCTTTGATCTGCTCCACTACTGGTTAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
57147724 AGATAAGATCT-ACAATCTTCAACCTGCTCCGCTACTACTCAGGG
1 AGATAAGATTTGTC-GTCTTCAATCTGCTCCACTACTGCTTAGGG
** * ** * * * *
57147768 AGGCAAGGCTCGGT-GGCTTAAATCTGCTTCCCATTA-T-CTT-GGAA
1 AGATAA-GATTTGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
** *
57147812 AGATAAGATTTACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
57147856 AGATAAGATCTG-CTATCTTCAACCTGCTCCGCTGCTGCTCAAGG
1 AGATAAGATTTGTC-GTCTTCAATCTGCTCCACTACTGCTTAGGG
57147900 AGATAAG
1 AGATAAG
57147907 GCTCGGGGGA
Statistics
Matches: 307, Mismatches: 111, Indels: 58
0.64 0.23 0.12
Matches are distributed among these distances:
42 17 0.06
43 24 0.08
44 231 0.75
45 23 0.07
46 12 0.04
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (44 bp):
AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:57147485 original size:132 final size:132
Alignment explanation
Indices: 57147327--57147912 Score: 904
Period size: 132 Copynumber: 4.4 Consensus size: 132
57147317 CAACTTCAGA
* * * * * *
57147327 GAGATAAGACCTG-TAATTTTCAACCTACTCCACTGCTGCTCAAGGAGATAAGGCTCGGTGGTTT
1 GAGATAAGATCTGCT-ATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTCGGTGGCTT
* *
57147391 AAATCTGCTTGCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATTTGCTCCACTACTGCTT
65 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTT
57147456 AGG
130 AGG
* *
57147459 GAGATAATATCTGTTATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTCGGTGGCTTA
1 GAGATAAGATCTGCTATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTCGGTGGCTTA
* *
57147524 AATTTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
66 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTA
57147589 GG
131 GG
57147591 GAGATAAGATCTGCTATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTCGGTGGCTTA
1 GAGATAAGATCTGCTATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTCGGTGGCTTA
* * * * *
57147656 AATCTACTTCCCACTATCTTGGAAAGATGAGATTTGCCATCTTTGATCTGCTCCACTACTGGTTA
66 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTA
57147721 GG
131 GG
* * * * * *
57147723 GAGATAAGATCTACAATCTTCAACCTGCTCCGCTACTACTCAGGGAGGCAAGGCTCGGTGGCTTA
1 GAGATAAGATCTGCTATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTCGGTGGCTTA
* *
57147788 AATCTGCTTCCCATTATCTTGGAAAGATAAGATTTACCGTCTTCGATCTGCTCCACTACTGCTTA
66 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTA
57147853 GG
131 GG
* * *
57147855 GAGATAAGATCTGCTATCTTCAACCTGCTCCGCTGCTGCTCAAGGAGATAAGGCTCGG
1 GAGATAAGATCTGCTATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTCGG
57147913 GGGATTTGAT
Statistics
Matches: 413, Mismatches: 40, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
132 412 1.00
133 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.30
Consensus pattern (132 bp):
GAGATAAGATCTGCTATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTCGGTGGCTTA
AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTA
GG
Found at i:57155325 original size:6 final size:6
Alignment explanation
Indices: 57155314--57155343 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
57155304 GAGATTGAAG
57155314 ATAAGC ATAAGC ATAAGC ATAAGC ATAAGC
1 ATAAGC ATAAGC ATAAGC ATAAGC ATAAGC
57155344 CGATGCCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
ATAAGC
Found at i:57155399 original size:3 final size:3
Alignment explanation
Indices: 57155393--57155429 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
57155383 AAGAAGACTT
57155393 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
57155430 ATAAAAGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:57161616 original size:37 final size:37
Alignment explanation
Indices: 57161569--57161639 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
57161559 AGTATTACTT
*
57161569 AATATTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
57161606 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
57161640 AAAAAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:57161644 original size:19 final size:19
Alignment explanation
Indices: 57161575--57161643 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
57161565 ACTTAATATT
57161575 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
57161594 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
57161612 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
57161631 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
57161644 AAATGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:57161795 original size:27 final size:27
Alignment explanation
Indices: 57161717--57161802 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 27
57161707 ACTTTTTTCC
* *
57161717 TTTGACACCA-TGGTGCCGCCAA-TGA
1 TTTGGCACCATTGGTGCCGCCAATTTA
* *
57161742 CTTTGGCACCATTGGTGACACCAATTTA
1 -TTTGGCACCATTGGTGCCGCCAATTTA
*
57161770 TTTGGCACCTTTGGTGCCGCCAATTTA
1 TTTGGCACCATTGGTGCCGCCAATTTA
*
57161797 ATTGGC
1 TTTGGC
57161803 CTGATCAGGC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
26 9 0.18
27 39 0.78
28 2 0.04
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (27 bp):
TTTGGCACCATTGGTGCCGCCAATTTA
Found at i:57162723 original size:22 final size:22
Alignment explanation
Indices: 57162676--57162723 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
57162666 AGGTACTTAA
*
57162676 TCTTCATTTTTTAGCTTTAGTC
1 TCTTCATTTTTTAGCTTTAATC
* * *
57162698 TCTTCGTTTTTTATCTTTAATT
1 TCTTCATTTTTTAGCTTTAATC
57162720 TCTT
1 TCTT
57162724 GGGTTCCTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.12, C:0.17, G:0.06, T:0.65
Consensus pattern (22 bp):
TCTTCATTTTTTAGCTTTAATC
Found at i:57166581 original size:7 final size:7
Alignment explanation
Indices: 57166565--57166606 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
57166555 AACTATCAAA
57166565 ACCC-TC
1 ACCCATC
57166571 ACCCATC
1 ACCCATC
57166578 ACCCATC
1 ACCCATC
57166585 ACCCATC
1 ACCCATC
57166592 ACCCATC
1 ACCCATC
57166599 ACCCATC
1 ACCCATC
57166606 A
1 A
57166607 TCTTCATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.11
7 31 0.89
ACGTcount: A:0.29, C:0.57, G:0.00, T:0.14
Consensus pattern (7 bp):
ACCCATC
Found at i:57172590 original size:42 final size:42
Alignment explanation
Indices: 57172527--57172637 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
57172517 ACAATGAGTT
* * * *
57172527 ACACGGCCTGGACACATGCCCATGTCCTTGCTCGTATGACTC
1 ACACGACCTGGGCACATGCCCATGTCCTTGCCCATATGACTC
* * *
57172569 ACACGACCTGGGCACACGCCCATGTCCTTGCCCATGTGGCTC
1 ACACGACCTGGGCACATGCCCATGTCCTTGCCCATATGACTC
* * *
57172611 ACATGACTTGAGCACATGCCCATGTCC
1 ACACGACCTGGGCACATGCCCATGTCC
57172638 CTGACTGTGT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.20, C:0.37, G:0.22, T:0.22
Consensus pattern (42 bp):
ACACGACCTGGGCACATGCCCATGTCCTTGCCCATATGACTC
Found at i:57172649 original size:42 final size:41
Alignment explanation
Indices: 57172539--57172649 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 41
57172529 ACGGCCTGGA
* * *
57172539 CACATGCCCATGTCCTTGCTCGTATGACTCACACGACCTGGG
1 CACATGCCCATGTCCTTGCT-GTGTGGCTCACACGACCTGAG
* ** * *
57172581 CACACGCCCATGTCCTTGCCCATGTGGCTCACATGACTTGAG
1 CACATGCCCATGTCCTTG-CTGTGTGGCTCACACGACCTGAG
*
57172623 CACATGCCCATGTCCCTGACTGTGTGG
1 CACATGCCCATGTCCTTG-CTGTGTGG
57172650 TTCTAAAGCA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
42 54 0.98
43 1 0.02
ACGTcount: A:0.18, C:0.35, G:0.23, T:0.24
Consensus pattern (41 bp):
CACATGCCCATGTCCTTGCTGTGTGGCTCACACGACCTGAG
Found at i:57178057 original size:21 final size:21
Alignment explanation
Indices: 57178031--57178073 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
57178021 TTGCATCTAG
*
57178031 ATATCAAA-CATGAGATCATTC
1 ATATCAAACCATAAG-TCATTC
57178052 ATATCAAACCATAAGTCATTC
1 ATATCAAACCATAAGTCATTC
57178073 A
1 A
57178074 ATTCGTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (21 bp):
ATATCAAACCATAAGTCATTC
Found at i:57178772 original size:9 final size:9
Alignment explanation
Indices: 57178752--57178793 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
57178742 ACCTAAAACA
57178752 TTATTT-AT
1 TTATTTAAT
57178760 TTATTTAAT
1 TTATTTAAT
57178769 TTATTTAATT
1 TTATTTAA-T
*
57178779 TTATTTAAA
1 TTATTTAAT
57178788 TTATTT
1 TTATTT
57178794 TCTCAACCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
8 6 0.19
9 16 0.52
10 9 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTATTTAAT
Found at i:57178941 original size:14 final size:13
Alignment explanation
Indices: 57178918--57178953 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
57178908 CTTATTTTAA
57178918 AATTTAATTAATT
1 AATTTAATTAATT
57178931 AATTATAATTAATT
1 AATT-TAATTAATT
*
57178945 AAATTAATT
1 AATTTAATT
57178954 CCTAAGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTTAATTAATT
Found at i:57182170 original size:21 final size:21
Alignment explanation
Indices: 57182144--57182192 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
57182134 TGAATACACC
57182144 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
*
57182165 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
57182186 AACAGAA
1 AACAGAA
57182193 AGCAAAACGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:57189760 original size:13 final size:13
Alignment explanation
Indices: 57189742--57189770 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
57189732 TTTTAGTTAT
57189742 TTAGGTTTAATAA
1 TTAGGTTTAATAA
57189755 TTAGGTTTAATAA
1 TTAGGTTTAATAA
57189768 TTA
1 TTA
57189771 ACTCTATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (13 bp):
TTAGGTTTAATAA
Found at i:57204042 original size:21 final size:21
Alignment explanation
Indices: 57203998--57204189 Score: 120
Period size: 21 Copynumber: 9.2 Consensus size: 21
57203988 TACATCGTTT
* *
57203998 CAGAAGCTC-GAA-AGCTGAA
1 CAGAAGCTCATAAGAGCTAAA
*
57204017 CAGAAGCTCATGAGAGCTAAA
1 CAGAAGCTCATAAGAGCTAAA
*
57204038 TAGAAGCTCATAAGAGCTAAA
1 CAGAAGCTCATAAGAGCTAAA
* * * *
57204059 CAGAAAC-CTATAAGGGTTGAA
1 CAGAAGCTC-ATAAGAGCTAAA
* *
57204080 CAGAAGCTCGTAAGAGCTTAA
1 CAGAAGCTCATAAGAGCTAAA
* * * *
57204101 CAGAAACTCACAAGAGTTGAA
1 CAGAAGCTCATAAGAGCTAAA
* * * *
57204122 TAGAAGCTCGTAAGGGCTGAA
1 CAGAAGCTCATAAGAGCTAAA
* * * * *
57204143 TAGAAACTCGTATGAGTTAAA
1 CAGAAGCTCATAAGAGCTAAA
* * *
57204164 CAGAAGCTCGTAAGAGATGAA
1 CAGAAGCTCATAAGAGCTAAA
57204185 CAGAA
1 CAGAA
57204190 AGTAAAACAC
Statistics
Matches: 133, Mismatches: 36, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
19 9 0.07
20 2 0.02
21 121 0.91
22 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.17
Consensus pattern (21 bp):
CAGAAGCTCATAAGAGCTAAA
Found at i:57204085 original size:42 final size:42
Alignment explanation
Indices: 57203998--57204190 Score: 173
Period size: 42 Copynumber: 4.6 Consensus size: 42
57203988 TACATCGTTT
* * * *
57203998 CAGAAGCTCG-AA-AGCTGAACAG-AAGCTCATGAGAGCTAAA
1 CAGAAGCTCGTAAGAGCTGAACAGAAACCT-ATAAGAGTTGAA
* * * *
57204038 TAGAAGCTCATAAGAGCTAAACAGAAACCTATAAGGGTTGAA
1 CAGAAGCTCGTAAGAGCTGAACAGAAACCTATAAGAGTTGAA
* *
57204080 CAGAAGCTCGTAAGAGCTTAACAGAAA-CTCACAAGAGTTGAA
1 CAGAAGCTCGTAAGAGCTGAACAGAAACCT-ATAAGAGTTGAA
* * * *
57204122 TAGAAGCTCGTAAGGGCTGAATAGAAACTCGTAT--GAGTTAAA
1 CAGAAGCTCGTAAGAGCTGAACAGAAAC-C-TATAAGAGTTGAA
*
57204164 CAGAAGCTCGTAAGAGATGAACAGAAA
1 CAGAAGCTCGTAAGAGCTGAACAGAAA
57204191 GTAAAACACG
Statistics
Matches: 123, Mismatches: 23, Indels: 12
0.78 0.15 0.08
Matches are distributed among these distances:
40 8 0.07
41 4 0.03
42 104 0.85
43 4 0.03
44 2 0.02
45 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.17
Consensus pattern (42 bp):
CAGAAGCTCGTAAGAGCTGAACAGAAACCTATAAGAGTTGAA
Found at i:57204179 original size:63 final size:63
Alignment explanation
Indices: 57203998--57204189 Score: 149
Period size: 63 Copynumber: 3.1 Consensus size: 63
57203988 TACATCGTTT
* * * * * * * * * *
57203998 CAGAAGCTCG-AA-AGCTGAACAGAAGCTCATGAGAGCTAAATAGAAGCTCATAAGAGCTAAA
1 CAGAAGCTCGTAAGGGCTGAACAGAAACTCGTAAGAGCTTAACAGAAACTCACAAGAGATGAA
* * * * *
57204059 CAGAAAC-CTATAAGGGTTGAACAGAAGCTCGTAAGAGCTTAACAGAAACTCACAAGAGTTGAA
1 CAGAAGCTC-GTAAGGGCTGAACAGAAACTCGTAAGAGCTTAACAGAAACTCACAAGAGATGAA
* * * * **
57204122 TAGAAGCTCGTAAGGGCTGAATAGAAACTCGTATGAG-TTAAACAGAAGCTCGTAAGAGATGAA
1 CAGAAGCTCGTAAGGGCTGAACAGAAACTCGTAAGAGCTT-AACAGAAACTCACAAGAGATGAA
57204185 CAGAA
1 CAGAA
57204190 AGTAAAACAC
Statistics
Matches: 102, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
60 1 0.01
61 6 0.06
62 4 0.04
63 90 0.88
64 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.17
Consensus pattern (63 bp):
CAGAAGCTCGTAAGGGCTGAACAGAAACTCGTAAGAGCTTAACAGAAACTCACAAGAGATGAA
Found at i:57206191 original size:15 final size:17
Alignment explanation
Indices: 57206149--57206193 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 17
57206139 GAAATAATAA
57206149 CTAATTAATTCAATTAACT
1 CTAA-TAATT-AATTAACT
57206168 CTAAT-ATTAATTAA-T
1 CTAATAATTAATTAACT
57206183 -TAATAATTAAT
1 CTAATAATTAAT
57206194 ATGCTTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.16
15 7 0.28
16 6 0.24
17 3 0.12
18 1 0.04
19 4 0.16
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (17 bp):
CTAATAATTAATTAACT
Found at i:57206446 original size:18 final size:17
Alignment explanation
Indices: 57206416--57206449 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
57206406 ATAACTATAG
57206416 TTTAAATTATAATTATT
1 TTTAAATTATAATTATT
57206433 TTTAAATGTATAATTAT
1 TTTAAAT-TATAATTAT
57206450 CACCACTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAATTATAATTATT
Found at i:57206850 original size:23 final size:23
Alignment explanation
Indices: 57206807--57206883 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
57206797 TATATTAAAT
*
57206807 ATATATATATTTATTTTTAATCAA
1 ATATATATA-TTATTTATAATCAA
57206831 ATATATATATTATTTATAATCAA
1 ATATATATATTATTTATAATCAA
* * *
57206854 ATATATATTTTATATAT-ATTAA
1 ATATATATATTATTTATAATCAA
57206876 ATATATAT
1 ATATATAT
57206884 TTAATATGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 12 0.24
23 28 0.57
24 9 0.18
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATATATTATTTATAATCAA
Found at i:57206870 original size:11 final size:11
Alignment explanation
Indices: 57206853--57206890 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
57206843 TTTATAATCA
57206853 AATATATATTT
1 AATATATATTT
* *
57206864 TATATATATTA
1 AATATATATTT
57206875 AATATATATTT
1 AATATATATTT
57206886 AATAT
1 AATAT
57206891 GGGTCGGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATATATATTT
Found at i:57210753 original size:76 final size:76
Alignment explanation
Indices: 57210627--57210782 Score: 276
Period size: 76 Copynumber: 2.1 Consensus size: 76
57210617 TTTACAATTT
* *
57210627 TTAATATTTATAACACCTTACACTCGACTCGAAAGATGACCGGATGCATGATGTTACATCGACTA
1 TTAATATTTATAACACCTTACACTCGACTCGAAAGATGACCAGATGCATGATGTCACATCGACTA
57210692 CCAAACTAACC
66 CCAAACTAACC
* *
57210703 TTAATATTTATAACACCTTACACTCGACTCGAAAGCTGACCAGATGCATGATGTCACATCGTCTA
1 TTAATATTTATAACACCTTACACTCGACTCGAAAGATGACCAGATGCATGATGTCACATCGACTA
57210768 CCAAACTAACC
66 CCAAACTAACC
57210779 TTAA
1 TTAA
57210783 GTAAGTTGAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (76 bp):
TTAATATTTATAACACCTTACACTCGACTCGAAAGATGACCAGATGCATGATGTCACATCGACTA
CCAAACTAACC
Found at i:57211043 original size:21 final size:21
Alignment explanation
Indices: 57211019--57211100 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
57211009 TGATATATAG
57211019 ACCTATGTTCT-AGTACCTTAT
1 ACCTATGTTCTGA-TACCTTAT
*
57211040 ACCTATATTCTGATACCTCT-T
1 ACCTATGTTCTGATACCT-TAT
** * *
57211061 GTCTATGTTCTGATACCTCAA
1 ACCTATGTTCTGATACCTTAT
57211082 ACCTATGTTCCT-ATACCTT
1 ACCTATGTT-CTGATACCTT
57211101 GGGTTTGAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
21 44 0.92
22 4 0.08
ACGTcount: A:0.23, C:0.27, G:0.09, T:0.41
Consensus pattern (21 bp):
ACCTATGTTCTGATACCTTAT
Found at i:57211727 original size:43 final size:43
Alignment explanation
Indices: 57211644--57211727 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
57211634 TTTCACATTA
*
57211644 ATAACATCTACATTAATAACAACATAAGATCATCAATTCATCT
1 ATAACATCTACATTAATAACAACATAAGATAATCAATTCATCT
* *
57211687 ATAACATCTAGATTACT-ACAACATCAAG-TAATCAACTTCAT
1 ATAACATCTACATTAATAACAACAT-AAGATAATCAA-TTCAT
57211728 GCATATTACC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 13 0.36
43 23 0.64
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (43 bp):
ATAACATCTACATTAATAACAACATAAGATAATCAATTCATCT
Found at i:57212859 original size:18 final size:19
Alignment explanation
Indices: 57212833--57212870 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
57212823 TATTTTGCCC
* *
57212833 AAACTAAAAA-CATTGTCA
1 AAACAAAAAATCAGTGTCA
57212851 AAACAAAAAATCAGTGTCA
1 AAACAAAAAATCAGTGTCA
57212870 A
1 A
57212871 TAACTACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.58, C:0.16, G:0.08, T:0.18
Consensus pattern (19 bp):
AAACAAAAAATCAGTGTCA
Found at i:57215180 original size:24 final size:25
Alignment explanation
Indices: 57215128--57215174 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
57215118 TGGCCCTCTA
*
57215128 GAGCTTCCCGTTATATAGTTCTTGC
1 GAGCTTCCCGTTATATAGCTCTTGC
*
57215153 GAGCTTCCCTTTA-ATAGCTCTT
1 GAGCTTCCCGTTATATAGCTCTT
57215175 CGGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTGC
Found at i:57215271 original size:25 final size:24
Alignment explanation
Indices: 57215243--57215290 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
57215233 GAGTGTCCTG
57215243 ATTAAAGGCTCTTTGCGAGCTTCCC
1 ATTAAAGGCTCTTTG-GAGCTTCCC
*
57215268 ATTAATGGCTCTTTGGAGCTTCC
1 ATTAAAGGCTCTTTGGAGCTTCC
57215291 TGATATTCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (24 bp):
ATTAAAGGCTCTTTGGAGCTTCCC
Found at i:57217416 original size:26 final size:26
Alignment explanation
Indices: 57217380--57217455 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
57217370 CCATGATTTA
* *
57217380 ATTATGATTAATTAATTATAATTAGT
1 ATTAAGATTAATTAATTATAATTAGC
*
57217406 ATTACGATTAATTAATTATAATTAGC
1 ATTAAGATTAATTAATTATAATTAGC
* *
57217432 ATTAAGATCAATTAATTATGATTA
1 ATTAAGATTAATTAATTATAATTA
57217456 AAGTAAGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (26 bp):
ATTAAGATTAATTAATTATAATTAGC
Found at i:57220177 original size:51 final size:50
Alignment explanation
Indices: 57220046--57220379 Score: 334
Period size: 51 Copynumber: 6.6 Consensus size: 50
57220036 GAAAGTGATG
*
57220046 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGATGG
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT-AT-C
* * * * *
57220096 GTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTTTC
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTATC
* ** * *
57220146 GATCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTGTCGGATGGTAATG
1 G-TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT-ATC
*
57220198 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGATGG
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT-AT-C
* * * * * * *
57220248 GTCGCATGTGTAGTACTATGTGCAGACTACTATGCGTGCCGGATAGTTTC
1 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTATC
* * * * *
57220298 GATCACGTGTGTAGTACTATATGCATGCTACTACGTGTATCGGATGGTAATG
1 G-TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT-ATC
* *
57220350 GTCACATGTGTAGTACTATGTGTAGGCTAC
1 GTCACGTGTGTAGTACTATGTGCAGGCTAC
57220380 AATGTGAACC
Statistics
Matches: 230, Mismatches: 45, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
49 3 0.01
50 79 0.34
51 142 0.62
52 6 0.03
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (50 bp):
GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTATC
Found at i:57220183 original size:28 final size:28
Alignment explanation
Indices: 57220152--57220234 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
57220142 TTTCGATCAT
57220152 GTGTGTAGTACTATGTGCAGGCTACTAC
1 GTGTGTAGTACTATGTGCAGGCTACTAC
* * * *
57220180 GTGTGTCGGA-T-GGT-AATGG-T-C-AC
1 GTGTGTAGTACTATGTGCA-GGCTACTAC
57220203 GTGTGTAGTACTATGTGCAGGCTACTAC
1 GTGTGTAGTACTATGTGCAGGCTACTAC
57220231 GTGT
1 GTGT
57220235 ACCGGAATGA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
23 10 0.25
24 2 0.05
25 6 0.15
26 6 0.15
27 2 0.05
28 14 0.35
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.33
Consensus pattern (28 bp):
GTGTGTAGTACTATGTGCAGGCTACTAC
Found at i:57220258 original size:101 final size:99
Alignment explanation
Indices: 57220052--57220379 Score: 342
Period size: 101 Copynumber: 3.2 Consensus size: 99
57220042 GATGGTCACG
* * * *
57220052 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG-ATGGGTCGCATGTGTAGTACTATG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTGCCGG-ATGTATCGGTCACGTGTGTAGTACTATG
* * **
57220116 TGCAGGCTACTATGCGTACCGGAT-A-GTTTCGATCA
65 TGCAGGCTACTACGTGTACCGGATGATGGGTCG--CA
*
57220151 TGTGTGTAGTACTATGTGCAGGCTACTACGTGTGTCGGATGGTAAT-GGTCACGTGTGTAGTACT
1 --TGTGTAGTACTATGTGCAGGCTACTACGTGTGCCGGAT-GT-ATCGGTCACGTGTGTAGTACT
57220215 ATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCA
62 ATGTGCAGGCTACTACGTGTACCGG-ATGATGGGTCGCA
* * * * * *
57220254 TGTGTAGTACTATGTGCAGACTACTATGCGTGCCGGATAGTTTCGATCACGTGTGTAGTACTATA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTGCCGGAT-GTATCGGTCACGTGTGTAGTACTATG
* * *
57220319 TGCATGCTACTACGTGTATCGGATGGTAAT-GGTCACA
65 TGCAGGCTACTACGTGTACCGGAT-G--ATGGGTCGCA
*
57220356 TGTGTAGTACTATGTGTAGGCTAC
1 TGTGTAGTACTATGTGCAGGCTAC
57220380 AATGTGAACC
Statistics
Matches: 196, Mismatches: 21, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
100 5 0.03
101 111 0.57
102 67 0.34
103 8 0.04
104 1 0.01
105 4 0.02
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (99 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTGCCGGATGTATCGGTCACGTGTGTAGTACTATGT
GCAGGCTACTACGTGTACCGGATGATGGGTCGCA
Found at i:57220328 original size:152 final size:152
Alignment explanation
Indices: 57220043--57220379 Score: 602
Period size: 152 Copynumber: 2.2 Consensus size: 152
57220033 AGTGAAAGTG
57220043 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCATGTGTA
1 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCATGTGTA
* * *
57220108 GTACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGATCATGTGTGTAGTACTATGTGCAGG
66 GTACTATGTGCAGACTACTATGCGTACCGGATAGTTTCGATCACGTGTGTAGTACTATATGCAGG
*
57220173 CTACTACGTGTGTCGGATGGTA
131 CTACTACGTGTATCGGATGGTA
57220195 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCATGTGTA
1 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCATGTGTA
* *
57220260 GTACTATGTGCAGACTACTATGCGTGCCGGATAGTTTCGATCACGTGTGTAGTACTATATGCATG
66 GTACTATGTGCAGACTACTATGCGTACCGGATAGTTTCGATCACGTGTGTAGTACTATATGCAGG
57220325 CTACTACGTGTATCGGATGGTA
131 CTACTACGTGTATCGGATGGTA
* *
57220347 ATGGTCACATGTGTAGTACTATGTGTAGGCTAC
1 ATGGTCACGTGTGTAGTACTATGTGCAGGCTAC
57220380 AATGTGAACC
Statistics
Matches: 177, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 177 1.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (152 bp):
ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCATGTGTA
GTACTATGTGCAGACTACTATGCGTACCGGATAGTTTCGATCACGTGTGTAGTACTATATGCAGG
CTACTACGTGTATCGGATGGTA
Found at i:57223713 original size:54 final size:54
Alignment explanation
Indices: 57223655--57223768 Score: 124
Period size: 54 Copynumber: 2.1 Consensus size: 54
57223645 GGACACACAG
* *
57223655 CCGTGTCTCATCCCGTGTCCTCGCCCGTGTAACTCAT-TGAGTTGCCCCACACT-C
1 CCGTGTCTCAGCCCGTGTCCTAGCCCGTGTAACTC-TCTGAGTTGCCCCACA-TGC
* * * * * *
57223709 CCGTGTGTCAGGCCGTGTGCTAGGCTGTGTAACTCTCTGAGTTTCCCCACATGC
1 CCGTGTCTCAGCCCGTGTCCTAGCCCGTGTAACTCTCTGAGTTGCCCCACATGC
57223763 CCGTGT
1 CCGTGT
57223769 GCCAGGCCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
53 2 0.04
54 48 0.96
ACGTcount: A:0.12, C:0.35, G:0.24, T:0.29
Consensus pattern (54 bp):
CCGTGTCTCAGCCCGTGTCCTAGCCCGTGTAACTCTCTGAGTTGCCCCACATGC
Found at i:57228582 original size:5 final size:5
Alignment explanation
Indices: 57228549--57228573 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
57228539 TTTTAATTCA
57228549 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
57228574 TTAATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:57235604 original size:34 final size:35
Alignment explanation
Indices: 57235560--57235626 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
57235550 CAGTAAAATA
* *
57235560 TTTTCCGTAAAATGATTT-TTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
57235594 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
57235627 CTGGTGTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:57235630 original size:14 final size:15
Alignment explanation
Indices: 57235554--57235630 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
57235544 GATTGTCAGT
* *
57235554 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
57235568 AAAATGATTTT-TGG
1 AAAATGATTTTCTGG
*
57235582 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
57235602 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
57235617 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
57235631 TGTTGATCCN
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.40
15 16 0.32
16 1 0.02
18 1 0.02
19 4 0.08
20 8 0.16
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:57257462 original size:13 final size:13
Alignment explanation
Indices: 57257444--57257470 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
57257434 TTTATTTTAG
57257444 TAATATTATATTT
1 TAATATTATATTT
57257457 TAATATTATATTT
1 TAATATTATATTT
57257470 T
1 T
57257471 TAAAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TAATATTATATTT
Found at i:57259217 original size:18 final size:19
Alignment explanation
Indices: 57259194--57259255 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
57259184 ATAATCAAAT
57259194 ATAATAAT-GTCAATAACA
1 ATAATAATAGTCAATAACA
*
57259212 ATAATAAATAGT-AATAAAA
1 ATAAT-AATAGTCAATAACA
*
57259231 ATAAAAATAGTCAATTAATCA
1 ATAATAATAGTCAA-TAA-CA
57259252 ATAA
1 ATAA
57259256 ATTAATGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 11 0.31
19 15 0.42
20 5 0.14
21 5 0.14
ACGTcount: A:0.61, C:0.06, G:0.05, T:0.27
Consensus pattern (19 bp):
ATAATAATAGTCAATAACA
Found at i:57268881 original size:113 final size:113
Alignment explanation
Indices: 57268683--57268909 Score: 454
Period size: 113 Copynumber: 2.0 Consensus size: 113
57268673 AATAAAGAGT
57268683 AAGTTTCTTCTCGTTTATTACTTCTAGCTCTGCGATATAGTTCCGGATTTTCCTTGCTATTTTAG
1 AAGTTTCTTCTCGTTTATTACTTCTAGCTCTGCGATATAGTTCCGGATTTTCCTTGCTATTTTAG
57268748 TTCCTGTCATGTATCTTCTTTCATATAAAAATTGGTTTCTGTTGAACC
66 TTCCTGTCATGTATCTTCTTTCATATAAAAATTGGTTTCTGTTGAACC
57268796 AAGTTTCTTCTCGTTTATTACTTCTAGCTCTGCGATATAGTTCCGGATTTTCCTTGCTATTTTAG
1 AAGTTTCTTCTCGTTTATTACTTCTAGCTCTGCGATATAGTTCCGGATTTTCCTTGCTATTTTAG
57268861 TTCCTGTCATGTATCTTCTTTCATATAAAAATTGGTTTCTGTTGAACC
66 TTCCTGTCATGTATCTTCTTTCATATAAAAATTGGTTTCTGTTGAACC
57268909 A
1 A
57268910 GATTAACCAA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (113 bp):
AAGTTTCTTCTCGTTTATTACTTCTAGCTCTGCGATATAGTTCCGGATTTTCCTTGCTATTTTAG
TTCCTGTCATGTATCTTCTTTCATATAAAAATTGGTTTCTGTTGAACC
Found at i:57275715 original size:9 final size:9
Alignment explanation
Indices: 57275698--57275734 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
57275688 TGAGTTTTCG
57275698 AATTCGAAT
1 AATTCGAAT
*
57275707 AACTCGAAT
1 AATTCGAAT
57275716 AATTCGAAT
1 AATTCGAAT
57275725 AATTCGAAT
1 AATTCGAAT
57275734 A
1 A
57275735 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:57276113 original size:17 final size:17
Alignment explanation
Indices: 57276086--57276147 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
57276076 ACTCCCCCTA
*
57276086 TTTACTTCCCCTCAAACT
1 TTTACTTCCCC-AAAACT
57276104 TTTA-TTCCCCAAAACTT
1 TTTACTTCCCCAAAAC-T
* *
57276121 TTTATTTTCCCCCTAAACT
1 TTTA-CTT-CCCCAAAACT
57276140 TTTACTTC
1 TTTACTTC
57276148 TCACCCTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 4 0.11
17 12 0.32
18 6 0.16
19 7 0.19
20 8 0.22
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTACTTCCCCAAAACT
Found at i:57276769 original size:5 final size:5
Alignment explanation
Indices: 57276759--57276784 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
57276749 CTCGAAAATT
57276759 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
57276785 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:57277526 original size:25 final size:25
Alignment explanation
Indices: 57277498--57277548 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
57277488 AAGTTCCTTT
57277498 TGTACAACGTAGTTTACCTCCTATA
1 TGTACAACGTAGTTTACCTCCTATA
57277523 TGTACAACGTAGTTTACCTCCTATA
1 TGTACAACGTAGTTTACCTCCTATA
57277548 T
1 T
57277549 ATACGGCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (25 bp):
TGTACAACGTAGTTTACCTCCTATA
Found at i:57283188 original size:13 final size:15
Alignment explanation
Indices: 57283157--57283187 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
57283147 AACAAGTAAA
57283157 TTTAAAATATTTATT
1 TTTAAAATATTTATT
57283172 TTTAAAAT-TTTATT
1 TTTAAAATATTTATT
57283186 TT
1 TT
57283188 ATTCAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTAAAATATTTATT
Found at i:57292102 original size:14 final size:15
Alignment explanation
Indices: 57292075--57292110 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
57292065 GACCAAGATA
57292075 ATAT-TTTATAATAT
1 ATATATTTATAATAT
57292089 ATATATTTATATATAT
1 ATATATTTATA-ATAT
57292105 ATATAT
1 ATATAT
57292111 ATGTGGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 6 0.30
16 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATATTTATAATAT
Found at i:57293560 original size:5 final size:5
Alignment explanation
Indices: 57293550--57293580 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
57293540 TGAGCATTCG
57293550 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
57293581 AATTTTCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:57299235 original size:29 final size:29
Alignment explanation
Indices: 57299193--57299273 Score: 153
Period size: 29 Copynumber: 2.8 Consensus size: 29
57299183 TTTGCCTTCG
*
57299193 GTTACATTTTAGTCACTTATGTTTGAAAT
1 GTTACGTTTTAGTCACTTATGTTTGAAAT
57299222 GTTACGTTTTAGTCACTTATGTTTGAAAT
1 GTTACGTTTTAGTCACTTATGTTTGAAAT
57299251 GTTACGTTTTAGTCACTTATGTT
1 GTTACGTTTTAGTCACTTATGTT
57299274 ATTATTTTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.23, C:0.11, G:0.16, T:0.49
Consensus pattern (29 bp):
GTTACGTTTTAGTCACTTATGTTTGAAAT
Found at i:57299424 original size:18 final size:16
Alignment explanation
Indices: 57299392--57299427 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
57299382 ATAGAATAAG
57299392 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
57299408 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATTA
57299426 AA
1 AA
57299428 AATTTTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:57300263 original size:18 final size:16
Alignment explanation
Indices: 57300240--57300275 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
57300230 GTTTAAAATT
57300240 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
57300258 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
57300274 TT
1 TT
57300276 CTCATCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:57304932 original size:23 final size:25
Alignment explanation
Indices: 57304894--57304940 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
57304884 TTCAATTGAA
*
57304894 AAATAATTGAAATATTATTTTAAAT
1 AAATAATTGAAATATTATTATAAAT
57304919 AAATAA-T-AAATATTATTATAAA
1 AAATAATTGAAATATTATTATAAA
57304941 AATATTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
24 1 0.05
25 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
AAATAATTGAAATATTATTATAAAT
Found at i:57305845 original size:29 final size:30
Alignment explanation
Indices: 57305785--57305848 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
57305775 TCAAAACTAC
57305785 ACATGAACTTTGATTTAATGTGCAATTGTAT
1 ACATGAACTTTGATTT-ATGTGCAATTGTAT
* *
57305816 ACATGAACTTTGATTT-TGTGTAATTTTAT
1 ACATGAACTTTGATTTATGTGCAATTGTAT
57305845 ACAT
1 ACAT
57305849 AAAATTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 15 0.48
31 16 0.52
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.45
Consensus pattern (30 bp):
ACATGAACTTTGATTTATGTGCAATTGTAT
Found at i:57305860 original size:30 final size:30
Alignment explanation
Indices: 57305785--57305861 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
57305775 TCAAAACTAC
*
57305785 ACATGAACTTTGATTTAATGTGCAATTGTAT
1 ACATAAACTTTGATTT-ATGTGCAATTGTAT
* * *
57305816 ACATGAACTTTGATTT-TGTGTAATTTTAT
1 ACATAAACTTTGATTTATGTGCAATTGTAT
*
57305845 ACATAAAATTTTGATTT
1 ACAT-AAACTTTGATTT
57305862 CATCCAATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 15 0.37
30 10 0.24
31 16 0.39
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (30 bp):
ACATAAACTTTGATTTATGTGCAATTGTAT
Found at i:57307383 original size:35 final size:34
Alignment explanation
Indices: 57307336--57307452 Score: 98
Period size: 35 Copynumber: 3.5 Consensus size: 34
57307326 AAACAGACTC
*
57307336 TAAA-TATTTTTATTATTTTTATTAATAAATCAA
1 TAAATTATTTTTATTAATTTTATTAATAAATCAA
* ** * * *
57307369 TAAATTATTATTTATTACTAGTATTTATATATTAA
1 TAAATTATT-TTTATTAATTTTATTAATAAATCAA
* *
57307404 TAAATTATGTTTTAGTAATTTTATT-ATTAAT-AA
1 TAAATTAT-TTTTATTAATTTTATTAATAAATCAA
*
57307437 T-AATTAATTTTATTAA
1 TAAATTATTTTTATTAA
57307453 CAATTTCCTA
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
31 8 0.12
32 5 0.07
33 7 0.10
34 8 0.12
35 38 0.57
36 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (34 bp):
TAAATTATTTTTATTAATTTTATTAATAAATCAA
Found at i:57312300 original size:27 final size:28
Alignment explanation
Indices: 57312236--57312306 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
57312226 AGTGGAGGGA
*
57312236 CTGCCACAGGCGGCACCAATGGTGCCAG
1 CTGCCACAGGCGGCACCAAAGGTGCCAG
* * *
57312264 -TGGCAGAGGCAGCACCAAAGGTG-CAG
1 CTGCCACAGGCGGCACCAAAGGTGCCAG
57312290 CTGCCACAGGCGGCACC
1 CTGCCACAGGCGGCACC
57312307 CCCCATTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
26 3 0.09
27 32 0.91
ACGTcount: A:0.24, C:0.34, G:0.34, T:0.08
Consensus pattern (28 bp):
CTGCCACAGGCGGCACCAAAGGTGCCAG
Found at i:57312823 original size:160 final size:160
Alignment explanation
Indices: 57312636--57313025 Score: 581
Period size: 160 Copynumber: 2.4 Consensus size: 160
57312626 GCGGCACCCC
* * *
57312636 CTTTGTTCGTATTTTTCTCTCTTTTTTCGGATTTTATTACTTTTAAAAAATATACTATTTTTGTA
1 CTTTGTTCGTATTTTTCT-TTTTTTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTA
57312701 TTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTATTGTT-GTGTG-TTTTTA
65 TTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTATT-TTAGTGTGCTTTTTA
*
57312764 TATAAATTTAGTAAAAAACCCTTATTTTGGCA
129 TAAAAATTTAGTAAAAAACCCTTATTTTGGCA
* * *
57312796 CTTTGTTCTTATTTTTCTTTTTTTTTTCAGATTTTATTACTTTCAAAAAATATATTATTTTCGTA
1 CTTTGTTCGTATTTTTC-TTTTTTTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTA
*
57312861 TTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGCTTTTTAT
65 TTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTATTTTAGTGTGCTTTTTAT
* *
57312926 AAAAATTTAGTGAAAAACCCTTATTTTGGCC
130 AAAAATTTAGTAAAAAACCCTTATTTTGGCA
* * * * * *
57312957 CTTTGTTCGTATTTTTC--TTTTTTTCGAATTTTATTACTTTCCATAAATATATTGTTTTCGTTT
1 CTTTGTTCGTATTTTTCTTTTTTTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
57313020 TTTATT
66 TTTATT
57313026 TCTTTTCATA
Statistics
Matches: 210, Mismatches: 17, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
158 46 0.22
159 2 0.01
160 110 0.52
161 52 0.25
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (160 bp):
CTTTGTTCGTATTTTTCTTTTTTTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
TTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTATTTTAGTGTGCTTTTTATA
AAAATTTAGTAAAAAACCCTTATTTTGGCA
Found at i:57313042 original size:51 final size:46
Alignment explanation
Indices: 57312962--57313076 Score: 106
Period size: 51 Copynumber: 2.3 Consensus size: 46
57312952 TGGCCCTTTG
* * *
57312962 TTCGTATTTTTCTTTTTTTCGAATTTTATTACTTTCCATAAATATATTGTT
1 TTCGT-TTTTTATTTTTTTCGAATCTTATT--TTTCCATAAACATA-T-TT
*
57313013 TTCGTTTTTTATTTCTTTTC-ATATCTTATTTTTTCATAAACATATTT
1 TTCGTTTTTTATTT-TTTTCGA-ATCTTATTTTTCCATAAACATATTT
*
57313060 TTCGGTATTTTATTTTT
1 TTC-GTTTTTTATTTTT
57313077 AATACTATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
47 7 0.12
48 11 0.20
49 12 0.21
50 9 0.16
51 17 0.30
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.63
Consensus pattern (46 bp):
TTCGTTTTTTATTTTTTTCGAATCTTATTTTTCCATAAACATATTT
Found at i:57313110 original size:16 final size:16
Alignment explanation
Indices: 57313089--57313119 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
57313079 TACTATTTTT
*
57313089 ATAAAAAAATCCGAAA
1 ATAAAAAAATACGAAA
57313105 ATAAAAAAATACGAA
1 ATAAAAAAATACGAA
57313120 TAAAGAGAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (16 bp):
ATAAAAAAATACGAAA
Found at i:57319123 original size:27 final size:27
Alignment explanation
Indices: 57319092--57319145 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
57319082 TTTATCGAGG
* *
57319092 TTATTAGTTTATTGATAAATGAATATT
1 TTATTAATTTATCGATAAATGAATATT
*
57319119 TTATTAATTTATCGATAAATTAATATT
1 TTATTAATTTATCGATAAATGAATATT
57319146 AATTCAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (27 bp):
TTATTAATTTATCGATAAATGAATATT
Found at i:57319272 original size:34 final size:37
Alignment explanation
Indices: 57319228--57319299 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 37
57319218 GAATCAAAGC
57319228 TAATTAGTTAATGTAA-C-AAA-AAAAAAGAGTTAAT
1 TAATTAGTTAATGTAACCAAAAGAAAAAAGAGTTAAT
*
57319262 TAATTGGTTAATGTAACCAAAAAGAAAAAAGAGTTAAT
1 TAATTAGTTAATGTAACC-AAAAGAAAAAAGAGTTAAT
57319300 GGTTTCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
34 15 0.45
35 1 0.03
37 3 0.09
38 14 0.42
ACGTcount: A:0.54, C:0.04, G:0.14, T:0.28
Consensus pattern (37 bp):
TAATTAGTTAATGTAACCAAAAGAAAAAAGAGTTAAT
Found at i:57326863 original size:51 final size:50
Alignment explanation
Indices: 57326681--57327232 Score: 470
Period size: 51 Copynumber: 10.9 Consensus size: 50
57326671 ACTATTATCA
* *
57326681 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AATTT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* * * * *
57326730 TTACGGTTCACGTAATAGCCTTCACATAGTACTATACACGTGATC-AAGTT
1 TT-CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* * *
57326780 TTACGATTCACGTAGTAGCCTTCACATAGTACTACATACGTGACTAAAGCTT
1 TT-CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TT
* * * * *
57326832 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCA-TT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTT
* * * *
57326882 TATCAATTCACGTAGTAACCTTCACACAGTACTACACACGTGACCAAAGTT
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* ** * * * * * *
57326933 TCTCGGTACATATTGTAGCCTTCACTTAGGACTGCACATGTGACCATTA-TT
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTT
* *
57326984 TATCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TT
* * * * * * * *
57327036 CTCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACTATTA-TT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTT
* *
57327086 TATCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TT
* * * * * *
57327138 CTC-AGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TGT
1 TTCGA-TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGT-T
* * * *
57327189 ATCGATTCAAGTAGTAGCCTTCACACAGTACTACACACGTGACC
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACC
57327233 GACACTTTCA
Statistics
Matches: 396, Mismatches: 90, Indels: 32
0.76 0.17 0.06
Matches are distributed among these distances:
49 2 0.01
50 91 0.23
51 290 0.73
52 13 0.03
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (50 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
Found at i:57326923 original size:102 final size:102
Alignment explanation
Indices: 57326682--57327232 Score: 779
Period size: 102 Copynumber: 5.4 Consensus size: 102
57326672 CTATTATCAT
* * * * * * **
57326682 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AA-TTTTTACGGTTCACGTAA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATTG
* * * * *
57326745 TAGCCTTCACATAGTACTATACACGTGATCAAGT-TTTA
65 TAGCCTTCACTTAGTACTACACATGTGA-CCATTATTTA
* * * *
57326783 -CGATTCACGTAGTAGCCTTCACATAGTACTACATACGTGACTAAAGCTTTTCGGTACACATAGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATTGT
*
57326847 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
* * *
57326884 TCAATTCACGTAGTAACCTTCACACAGTACTACACACGTGACCAAAG-TTTCTCGGTACATATTG
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTT-TCGGTACACATTG
* *
57326948 TAGCCTTCACTTAGGACTGCACATGTGACCATTATTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATTATTTA
*
57326986 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATTGT
*
57327051 AGCCTTCACTTAGTACTACACATGTGACTATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
* *
57327088 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCAGTACACATTGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATTGT
*
57327153 AGCCTTCACTTAGTACTACACATGTGACCATTATGTA
66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
*
57327190 TCGATTCAAGTAGTAGCCTTCACACAGTACTACACACGTGACC
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACC
57327233 GACACTTTCA
Statistics
Matches: 409, Mismatches: 35, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
100 40 0.10
101 43 0.11
102 324 0.79
103 2 0.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (102 bp):
TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATTGT
AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
Found at i:57336534 original size:20 final size:21
Alignment explanation
Indices: 57336496--57336535 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
57336486 GTTTTTATAT
57336496 TATTTTCATATATTATTATTA
1 TATTTTCATATATTATTATTA
57336517 TATTTT-ATA-ATGTATTATT
1 TATTTTCATATAT-TATTATT
57336536 CTTTAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 10 0.56
21 6 0.33
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
TATTTTCATATATTATTATTA
Found at i:57341414 original size:19 final size:19
Alignment explanation
Indices: 57341368--57341414 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
57341358 ACAAACTCTC
*
57341368 AAAAGCAAAGAAGCAACAA
1 AAAAGCAAAAAAGCAACAA
57341387 ACAAA-CAAAAAAGTC-ACAA
1 A-AAAGCAAAAAAG-CAACAA
57341406 AAAAGCAAA
1 AAAAGCAAA
57341415 TGCACTACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 3 0.12
19 17 0.71
20 4 0.17
ACGTcount: A:0.70, C:0.17, G:0.11, T:0.02
Consensus pattern (19 bp):
AAAAGCAAAAAAGCAACAA
Found at i:57342193 original size:26 final size:26
Alignment explanation
Indices: 57342143--57342193 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
57342133 AGCTGCGAGA
* *
57342143 AGAGAACAGAAAAAAAAAATTAGAAG
1 AGAGAAAAGAAAAAAAAAATGAGAAG
57342169 AGAGAAAAGAAAATAAAAAA-GAGAA
1 AGAGAAAAGAAAA-AAAAAATGAGAA
57342194 TACAATAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.06
Consensus pattern (26 bp):
AGAGAAAAGAAAAAAAAAATGAGAAG
Found at i:57349894 original size:18 final size:18
Alignment explanation
Indices: 57349871--57349905 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
57349861 TTTTAAATGT
57349871 TATTTTAATAAGTAATAA
1 TATTTTAATAAGTAATAA
* *
57349889 TATTTTATTAATTAATA
1 TATTTTAATAAGTAATA
57349906 TTATAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TATTTTAATAAGTAATAA
Found at i:57350079 original size:32 final size:32
Alignment explanation
Indices: 57350038--57350102 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
57350028 TTTTTCTTCA
*
57350038 ATTTTTTCATAGATTTTGAATCTTTGAAGCTT
1 ATTTTTTCATAGATTTTGAATCTATGAAGCTT
57350070 ATTTTTTCATAGATTTTGAATCTATGAAGCTT
1 ATTTTTTCATAGATTTTGAATCTATGAAGCTT
57350102 A
1 A
57350103 CTTTACATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (32 bp):
ATTTTTTCATAGATTTTGAATCTATGAAGCTT
Found at i:57366033 original size:36 final size:35
Alignment explanation
Indices: 57365991--57366077 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 35
57365981 TTCATCGAAT
*
57365991 GCATATATATATATTATTCAAATACATATGCCAAAA
1 GCATATATATATATTA-TCAAACACATATGCCAAAA
* * * *
57366027 GCATATACT-TATACTTATCAACCACATGTGCCGAAT
1 GCATATA-TATATA-TTATCAAACACATATGCCAAAA
*
57366063 GCACATATATATATT
1 GCATATATATATATT
57366078 TACTATAATC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
35 3 0.07
36 35 0.83
37 4 0.10
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (35 bp):
GCATATATATATATTATCAAACACATATGCCAAAA
Found at i:57366338 original size:41 final size:41
Alignment explanation
Indices: 57366283--57366474 Score: 294
Period size: 41 Copynumber: 4.7 Consensus size: 41
57366273 TTAATTTAAA
* * * * *
57366283 CAGATTCACTGGCACTTAGCTTGTTAGGCTTAAAGCTTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
57366325 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* * *
57366366 CAGATCACCAGCACTTAGCTTGCTAGGCTTATAGTCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
57366407 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
57366448 CAGTTCACCGGCACTTAGCCTGCTAGG
1 CAGATCACCGGCACTTAGCCTGCTAGG
57366475 TTTTAAAACC
Statistics
Matches: 138, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 134 0.97
42 4 0.03
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:57368716 original size:42 final size:42
Alignment explanation
Indices: 57368664--57368758 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 42
57368654 ACTCTCGGTA
*
57368664 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
* *
57368706 TCGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
57368748 TCGCACACTTA
1 TCGCACACTTA
57368759 TTGTCGTTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
Found at i:57370478 original size:17 final size:17
Alignment explanation
Indices: 57370456--57370488 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
57370446 TTTTAATTAG
57370456 TGAATTTTGTGATTTAT
1 TGAATTTTGTGATTTAT
57370473 TGAATTTTGTGATTTA
1 TGAATTTTGTGATTTA
57370489 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:57371726 original size:46 final size:46
Alignment explanation
Indices: 57371673--57371855 Score: 303
Period size: 46 Copynumber: 4.0 Consensus size: 46
57371663 TGGAAAATTT
* * *
57371673 TGAAAAGTAGGTCTGGTGTTTCAGTGAAGAAAGCTATACTGAGCTG
1 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGCTG
*
57371719 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTG
1 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGCTG
*
57371765 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTG
1 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGCTG
* *
57371811 TGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGCT
1 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGCT
57371856 ATAGCAATGT
Statistics
Matches: 130, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 130 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (46 bp):
TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGCTG
Found at i:57377217 original size:21 final size:21
Alignment explanation
Indices: 57377193--57377304 Score: 127
Period size: 21 Copynumber: 5.3 Consensus size: 21
57377183 GTGTTTTTCT
*
57377193 TTTTGTTTAGCTCTTTCGAGC
1 TTTTGTTTAGCTCTTACGAGC
57377214 TTTTGTTTAGCTCTTACGAGC
1 TTTTGTTTAGCTCTTACGAGC
* * * * *
57377235 TTCTGTTCAACTCTTATGA-A
1 TTTTGTTTAGCTCTTACGAGC
* *
57377255 TTTATGTTCAGCTCTTCCGAGC
1 TTT-TGTTTAGCTCTTACGAGC
57377277 TTTTGTTTAGCTCTTACGAGC
1 TTTTGTTTAGCTCTTACGAGC
*
57377298 TTCTGTT
1 TTTTGTT
57377305 GACGTATCTG
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
20 2 0.03
21 70 0.93
22 3 0.04
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (21 bp):
TTTTGTTTAGCTCTTACGAGC
Found at i:57377582 original size:17 final size:17
Alignment explanation
Indices: 57377533--57377583 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
57377523 ATAATGACGC
57377533 ATGATATATTAATAT-A
1 ATGATATATTAATATGA
*
57377549 TTGATATATTGAA-ATGA
1 ATGATATATT-AATATGA
57377566 ATGATATATGT-ATATGA
1 ATGATATAT-TAATATGA
57377583 A
1 A
57377584 GAAATGGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 12 0.41
17 16 0.55
18 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (17 bp):
ATGATATATTAATATGA
Found at i:57382441 original size:62 final size:62
Alignment explanation
Indices: 57382344--57382474 Score: 244
Period size: 62 Copynumber: 2.1 Consensus size: 62
57382334 CAAGTGTGAC
*
57382344 ATGTTGAGATAATAAGGTTATCGATGTTGAATTTATATGAAATATGTTCAAGTATGCTAACA
1 ATGTTGAGATAATAAGGTTATCAATGTTGAATTTATATGAAATATGTTCAAGTATGCTAACA
57382406 ATGTTGAGATAATAAGGTTATCAATGTTGAATTTATATGAAATATGTTCAAGTATGCTAACA
1 ATGTTGAGATAATAAGGTTATCAATGTTGAATTTATATGAAATATGTTCAAGTATGCTAACA
57382468 AGTGTTG
1 A-TGTTG
57382475 TTTTTTGATG
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 62 0.93
63 5 0.07
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (62 bp):
ATGTTGAGATAATAAGGTTATCAATGTTGAATTTATATGAAATATGTTCAAGTATGCTAACA
Found at i:57396578 original size:17 final size:16
Alignment explanation
Indices: 57396543--57396581 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
57396533 TAATATATAA
* *
57396543 ATAAATTTAAAATTTT
1 ATAAATTTAAAAATAT
57396559 ATAAATTTAAAAAATAT
1 ATAAATTT-AAAAATAT
57396576 ATAAAT
1 ATAAAT
57396582 ATATAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAAATTTAAAAATAT
Found at i:57396774 original size:18 final size:19
Alignment explanation
Indices: 57396739--57396777 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
57396729 AAGTACATAT
57396739 TTTTAAAAAAATTATAAAA
1 TTTTAAAAAAATTATAAAA
* *
57396758 TTTTGAAAATATT-TAAAA
1 TTTTAAAAAAATTATAAAA
57396776 TT
1 TT
57396778 CGAAGAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
TTTTAAAAAAATTATAAAA
Found at i:57398774 original size:65 final size:67
Alignment explanation
Indices: 57398659--57398790 Score: 164
Period size: 67 Copynumber: 2.0 Consensus size: 67
57398649 AGATGCACGA
57398659 GTCTGTAGGTGTTAAATATATATATGCGTGAGATTGGAGTCATAAATAT-A-ATATATATGAGTG
1 GTCTGTAGGTGTTAAATATATATATGCGTGAGATTGGAGTCATAAATATAATATATATATGAGTG
57398722 GG
66 GG
* * * ***
57398724 GTCTGTTGGTGTTAAACATATATATATGCGTGAGTTTGG-GT-TTTTTTATAATATATATATGAG
1 GTCTGTAGGTGTT-AA-ATATATATATGCGTGAGATTGGAGTCATAAATATAATATATATATGAG
57398787 TGGG
64 TGGG
57398791 TTTATATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
65 16 0.28
66 5 0.09
67 36 0.63
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.40
Consensus pattern (67 bp):
GTCTGTAGGTGTTAAATATATATATGCGTGAGATTGGAGTCATAAATATAATATATATATGAGTG
GG
Found at i:57412916 original size:21 final size:19
Alignment explanation
Indices: 57412881--57412925 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
57412871 CCATATTAGT
*
57412881 TTTTAATTTTTTTTAAAAA
1 TTTTAATTATTTTTAAAAA
*
57412900 TGTTTACATTATTTTTAATAA
1 T-TTTA-ATTATTTTTAAAAA
57412921 TTTTA
1 TTTTA
57412926 TATGTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 8 0.36
21 13 0.59
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTAATTATTTTTAAAAA
Found at i:57421703 original size:139 final size:139
Alignment explanation
Indices: 57421534--57421785 Score: 371
Period size: 139 Copynumber: 1.8 Consensus size: 139
57421524 TAGAAGAATT
* * * * * * *
57421534 GAACTCAAGACTCACTGATGTAATTACAACTATCTAACCATCTAACAAAAGGACTAATATGTTAA
1 GAACTCAAAACTCAATGATGTAAGTACAACTAACTAACCATCAAACAAAAGAACTAATATGCTAA
*
57421599 AAACATTAATTAAAA-TGTAAAAAGCTTCAAACAACATGAAATAAAAAAATATAAATACAAGTAG
66 AAA-AATAATTAAAATTGTAAAAAGCTTCAAACAACATGAAATAAAAAAATATAAATACAAGTAG
57421663 GAGATTAATC
130 GAGATTAATC
* *
57421673 GAACTCAAAACTCAATGATGTAAGTGCAACTAACTAACCATCAAACCAAAGAACTAATATGCTAA
1 GAACTCAAAACTCAATGATGTAAGTACAACTAACTAACCATCAAACAAAAGAACTAATATGCTAA
* * *
57421738 AAAAATAATTAAAATTTTAAAAAGCTTGAAGCAACATGAAATAAAAAA
66 AAAAATAATTAAAATTGTAAAAAGCTTCAAACAACATGAAATAAAAAA
57421786 TTACAAATGT
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
138 10 0.10
139 89 0.90
ACGTcount: A:0.52, C:0.15, G:0.10, T:0.23
Consensus pattern (139 bp):
GAACTCAAAACTCAATGATGTAAGTACAACTAACTAACCATCAAACAAAAGAACTAATATGCTAA
AAAAATAATTAAAATTGTAAAAAGCTTCAAACAACATGAAATAAAAAAATATAAATACAAGTAGG
AGATTAATC
Found at i:57421850 original size:139 final size:136
Alignment explanation
Indices: 57421484--57421853 Score: 324
Period size: 139 Copynumber: 2.7 Consensus size: 136
57421474 TGTTAAAGAA
*
57421484 AAAAAGCTTGAAGCAACATGAAGTAAAAAATACAAATGT-GT-AGA-AG-AATTGAACTCAAGAC
1 AAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATGTAGTAAGAGAGTAATTGAACTCAAGAC
** * ** ** * * * *
57421545 TCACTGATGTAATTAC-AACTATCTAACCATCTAACAAAAGGACTAATATGTTAAAAACATTAAT
66 TCAAGGTTAAAAGCACTAAC-AT-TAACCATCAAACAAAAGAACTAATATGCTAAAAACAATAAT
57421609 TAAAATGT
129 TAAAATGT
* * * ** * * * *
57421617 AAAAAGCTTCAAACAACATGAAATAAAAAAATATAAATACAAGTAGGAGATTAATCGAACTCAAA
1 AAAAAGCTTGAAGCAACATGAAAT-AAAAAATACAAAT-GTAGTAAGAGAGTAATTGAACTCAAG
* ** *
57421682 ACTCAATGATGTAAGTGCAACTAAC--TAACCATCAAACCAAAGAACTAATATGCTAAAAA-AAT
64 ACTCAA-GGT-TAAAAGC-ACTAACATTAACCATCAAACAAAAGAACTAATATGCTAAAAACAAT
*
57421744 AATTAAAATTTT
126 AATTAAAA-TGT
* *
57421756 AAAAAGCTTGAAGCAACATGAAATAAAAAATTACAAATGTGAGTAAGAGAGTAATTGAACCCGAG
1 AAAAAGCTTGAAGCAACATGAAATAAAAAA-TACAAATGT-AGTAAGAGAGTAATTGAACTCAAG
*
57421821 ACTTAAGGTTAAAAGCACTAACATTTAACCATC
64 ACTCAAGGTTAAAAGCACTAACA-TTAACCATC
57421854 TGGACAAAGC
Statistics
Matches: 180, Mismatches: 41, Indels: 26
0.73 0.17 0.11
Matches are distributed among these distances:
133 21 0.12
134 12 0.07
136 8 0.04
137 7 0.04
138 19 0.11
139 107 0.59
141 1 0.01
142 2 0.01
143 3 0.02
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (136 bp):
AAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATGTAGTAAGAGAGTAATTGAACTCAAGAC
TCAAGGTTAAAAGCACTAACATTAACCATCAAACAAAAGAACTAATATGCTAAAAACAATAATTA
AAATGT
Found at i:57429349 original size:25 final size:25
Alignment explanation
Indices: 57429313--57429379 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
57429303 TTACCAATAC
*
57429313 TCAGCTCACATGAGCTTCCCGTTAT
1 TCAGCTCGCATGAGCTTCCCGTTAT
57429338 TCAGCTCGCATGAGCTTCCCGTTAT
1 TCAGCTCGCATGAGCTTCCCGTTAT
* * *
57429363 TCTGCTCGGAAGAGCTT
1 TCAGCTCGCATGAGCTT
57429380 ACTGTTTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.18, C:0.30, G:0.21, T:0.31
Consensus pattern (25 bp):
TCAGCTCGCATGAGCTTCCCGTTAT
Found at i:57429400 original size:24 final size:24
Alignment explanation
Indices: 57429371--57429416 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
57429361 ATTCTGCTCG
*
57429371 GAAGAGCTTACTGTTTACAGCTTA
1 GAAGAGCTTACCGTTTACAGCTTA
57429395 GAAGAGCTTACCGTTTACAGCT
1 GAAGAGCTTACCGTTTACAGCT
57429417 CGTATGAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (24 bp):
GAAGAGCTTACCGTTTACAGCTTA
Found at i:57429425 original size:24 final size:24
Alignment explanation
Indices: 57429322--57429425 Score: 77
Period size: 25 Copynumber: 4.2 Consensus size: 24
57429312 CTCAGCTCAC
* *
57429322 ATGAGCTTCCCGTTATTCAGCTCG
1 ATGAGCTTACCGTTATACAGCTCG
* * *
57429346 CATGAGCTTCCCGTTATTCTGCTCGG
1 -ATGAGCTTACCGTTATACAGCTC-G
* * *
57429372 AAGAGCTTACTGTT-TACAGCTTAG
1 ATGAGCTTACCGTTATACAGC-TCG
*
57429396 AAGAGCTTACCGTT-TACAGCTCG
1 ATGAGCTTACCGTTATACAGCTCG
57429419 TATGAGC
1 -ATGAGC
57429426 ATACATGTAC
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
23 2 0.03
24 29 0.44
25 34 0.52
26 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (24 bp):
ATGAGCTTACCGTTATACAGCTCG
Found at i:57433016 original size:3 final size:3
Alignment explanation
Indices: 57433010--57433034 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
57433000 AACTACTATT
57433010 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
57433035 TGGCTACACT
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:57433083 original size:27 final size:27
Alignment explanation
Indices: 57433013--57433121 Score: 101
Period size: 27 Copynumber: 3.9 Consensus size: 27
57433003 TACTATTACA
* *
57433013 ACAACAACAACAACAACAACAATGGCT
1 ACAACGACAACTACAACAACAATGGCT
* * *
57433040 ACACTCTCAGCAGCTACAACAACAATGGCT
1 ACA-AC-GA-CAACTACAACAACAATGGCT
* ** *
57433070 ACAGCGGGAACTACAACACCAATGGCT
1 ACAACGACAACTACAACAACAATGGCT
*
57433097 ACAATGACAACTACAACAACAATGG
1 ACAACGACAACTACAACAACAATGG
57433122 GTATGAGACA
Statistics
Matches: 64, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
27 40 0.62
28 1 0.02
29 2 0.03
30 21 0.33
ACGTcount: A:0.45, C:0.29, G:0.14, T:0.12
Consensus pattern (27 bp):
ACAACGACAACTACAACAACAATGGCT
Found at i:57439719 original size:12 final size:12
Alignment explanation
Indices: 57439702--57439728 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
57439692 ACGTCATATT
57439702 CCAAAAAATTCC
1 CCAAAAAATTCC
57439714 CCAAAAAATTCC
1 CCAAAAAATTCC
57439726 CCA
1 CCA
57439729 TCTGCATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (12 bp):
CCAAAAAATTCC
Found at i:57441848 original size:17 final size:17
Alignment explanation
Indices: 57441813--57441845 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
57441803 TACGATTTGG
57441813 TTGAGAAACTTATTTAA
1 TTGAGAAACTTATTTAA
57441830 TTGAGAAA-TTATTTAA
1 TTGAGAAACTTATTTAA
57441846 ATTAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (17 bp):
TTGAGAAACTTATTTAA
Found at i:57442712 original size:92 final size:92
Alignment explanation
Indices: 57442603--57442820 Score: 332
Period size: 92 Copynumber: 2.4 Consensus size: 92
57442593 GTGATATCTA
*
57442603 AACTATCAAAATATGTTTTATTATGGTACCT-GTACTTTCATAAAATGTCAAATGT-GATACTTG
1 AACTATCAATATATGTTTTATTATGGTACCTGGT-CTTTCATAAAATGTCAAATGTAG-TACTTG
*
57442666 CACTTTGAAAATGTTCAATATGGTATTTG
64 CACTTTGAAAATGTCCAATATGGTATTTG
* * * *
57442695 AACTATCAATATGTGTTTTATTATGGTACTTGGTCTTTCATAAAATGTCAAATGTAGTATTTTCA
1 AACTATCAATATATGTTTTATTATGGTACCTGGTCTTTCATAAAATGTCAAATGTAGTACTTGCA
57442760 CTTTGAAAATGTCCAATATGGTATTTG
66 CTTTGAAAATGTCCAATATGGTATTTG
* *
57442787 AACTATCAATATATGCTTTATTATGGTACTTGGT
1 AACTATCAATATATGTTTTATTATGGTACCTGGT
57442821 GTTAACATCG
Statistics
Matches: 116, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
92 113 0.97
93 3 0.03
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (92 bp):
AACTATCAATATATGTTTTATTATGGTACCTGGTCTTTCATAAAATGTCAAATGTAGTACTTGCA
CTTTGAAAATGTCCAATATGGTATTTG
Found at i:57460834 original size:98 final size:98
Alignment explanation
Indices: 57460665--57460863 Score: 292
Period size: 98 Copynumber: 2.0 Consensus size: 98
57460655 GGTTACTTGC
* * *
57460665 ATTTCAATCAATTTTAGATTGGATTTTATTTAGAGGAGCTCGTGGGTCAGGTCAAATTTAGGGGC
1 ATTTCAATCAATTTTAGATTGGATTCTATCTAGAGGAGCTCGTGGGTCAGGTCAAATTCAGGGGC
*
57460730 GAAGTTAGAAAATTTTTTAGGGGCTAAAATTAA
66 GAAGTTAGAAAATTTTTTAGGGGCCAAAATTAA
* * * *
57460763 ATTTCAATCAATTTTAGATTGGATTCTATCTAGAAGTA-TTCGTGGGTCAGGTTAAATTCATGGG
1 ATTTCAATCAATTTTAGATTGGATTCTATCTAG-AGGAGCTCGTGGGTCAGGTCAAATTCAGGGG
* *
57460827 CGAAGTTATAAATTTTTTTAGGGGCCAAAATTAA
65 CGAAGTTAGAAAATTTTTTAGGGGCCAAAATTAA
57460861 ATT
1 ATT
57460864 ATAATTTTTA
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 87 0.97
99 3 0.03
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (98 bp):
ATTTCAATCAATTTTAGATTGGATTCTATCTAGAGGAGCTCGTGGGTCAGGTCAAATTCAGGGGC
GAAGTTAGAAAATTTTTTAGGGGCCAAAATTAA
Found at i:57467762 original size:20 final size:18
Alignment explanation
Indices: 57467712--57467763 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
57467702 CTACAAGATA
57467712 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
**
57467729 AATATTAAGGTAATCACTTT
1 AATATTAAATTAAT-A-TTT
57467749 AATATTAAATTAATA
1 AATATTAAATTAATA
57467764 AAATACTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 11 0.39
19 2 0.07
20 15 0.54
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:57469406 original size:15 final size:15
Alignment explanation
Indices: 57469382--57469413 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
57469372 TATGCAAGCA
*
57469382 AAATATAAAAGACAT
1 AAATACAAAAGACAT
57469397 AAATACAAAAGACAT
1 AAATACAAAAGACAT
57469412 AA
1 AA
57469414 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:57471291 original size:15 final size:16
Alignment explanation
Indices: 57471258--57471296 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
57471248 TTAATAATTT
*
57471258 TTTTGTTCAAAAACAA
1 TTTTATTCAAAAACAA
* *
57471274 TTTTATTCAAAAATAT
1 TTTTATTCAAAAACAA
57471290 TTTTATT
1 TTTTATT
57471297 TGTTATATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTTATTCAAAAACAA
Found at i:57476324 original size:31 final size:31
Alignment explanation
Indices: 57476276--57476334 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
57476266 CTAATCTTAG
*
57476276 TAATTATTCTCATATTAAAG-TCTAAATTTAA
1 TAATTATTCTCAAATTAAAGCTC-AAATTTAA
57476307 TAATTATT-TCTAAATTAAAGCTCAAATT
1 TAATTATTCTC-AAATTAAAGCTCAAATT
57476335 CTAAAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 2 0.08
31 21 0.84
32 2 0.08
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.44
Consensus pattern (31 bp):
TAATTATTCTCAAATTAAAGCTCAAATTTAA
Found at i:57482879 original size:9 final size:9
Alignment explanation
Indices: 57482865--57482922 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
57482855 GTAGTGATTC
*
57482865 AATTTGGTT
1 AATTCGGTT
*
57482874 AATTTGGTT
1 AATTCGGTT
*
57482883 AATTCGGGT
1 AATTCGGTT
57482892 AATTCGGTT
1 AATTCGGTT
*
57482901 AGTTCAGG-T
1 AATTC-GGTT
57482910 AATTCGGTT
1 AATTCGGTT
57482919 AATT
1 AATT
57482923 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
8 2 0.05
9 38 0.90
10 2 0.05
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:57482894 original size:18 final size:18
Alignment explanation
Indices: 57482873--57482922 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
57482863 TCAATTTGGT
* *
57482873 TAATTTGGTTAATTCGGG
1 TAATTCGGTTAATTCAGG
*
57482891 TAATTCGGTTAGTTCAGG
1 TAATTCGGTTAATTCAGG
57482909 TAATTCGGTTAATT
1 TAATTCGGTTAATT
57482923 TTTAACCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (18 bp):
TAATTCGGTTAATTCAGG
Found at i:57484589 original size:50 final size:50
Alignment explanation
Indices: 57484481--57484666 Score: 291
Period size: 50 Copynumber: 3.7 Consensus size: 50
57484471 ACATGTCAAA
** * * *
57484481 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAAC
**
57484532 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
*
57484582 GGCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
57484632 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
57484667 TTACCCAAAT
Statistics
Matches: 124, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 96 0.77
51 28 0.23
ACGTcount: A:0.19, C:0.31, G:0.24, T:0.25
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
Found at i:57494068 original size:44 final size:44
Alignment explanation
Indices: 57494003--57494389 Score: 364
Period size: 44 Copynumber: 8.6 Consensus size: 44
57493993 GAGTAACTGG
**
57494003 CAAGATCTATTTTCCTTCGATCTACTTCACGCCAGTACATGAAGA
1 CAAGATCTGCTTT-CTTCGATCTACTTCACGCCAGTACATGAAGA
* * ***
57494048 CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGA
1 CAAGATCTGCTTTCTTCGATCTACTTC-ACGCCAGTACATGAAGA
* * * *
57494093 CAAGATCTGCTCTCTTTGATCTACTTCATGCCAATACATGAAGA
1 CAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACATGAAGA
** *
57494137 CAAGATCTATTTTCTTCGATCTACTTCACGCCAATACATGAAGA
1 CAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACATGAAGA
* * * *** *
57494181 CAAGATCTGCTTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGG
1 CAAGATCTGC--TTT-CTTCGATCTACTTC-ACGCCAGTACATGAAGA
** *
57494229 CAAGATCTATTTTTCTTCAATCTACTTCACGCCAGTACATGAAGA
1 CAAGATCT-GCTTTCTTCGATCTACTTCACGCCAGTACATGAAGA
* * * * *** *
57494274 CAAGATCTGTTTTCTTTGATC-AGCTTCGCCACCAGTATGGGAAGG
1 CAAGATCTGCTTTCTTCGATCTA-CTTC-ACGCCAGTACATGAAGA
*
57494319 CAAGATCTG-TTATCTTTGATCTACTTCACGCCAGTACATGAAGA
1 CAAGATCTGCTT-TCTTCGATCTACTTCACGCCAGTACATGAAGA
*
57494363 CAAGATCTGCTTTCTTCGATCTGCTTC
1 CAAGATCTGCTTTCTTCGATCTACTTC
57494390 GCCACCAGTA
Statistics
Matches: 273, Mismatches: 58, Indels: 23
0.77 0.16 0.06
Matches are distributed among these distances:
43 1 0.00
44 120 0.44
45 102 0.37
46 16 0.06
47 16 0.06
48 18 0.07
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (44 bp):
CAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTACATGAAGA
Done.