Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 125 of 145
Found at i:41716119 original size:21 final size:21
Alignment explanation
Indices: 41716095--41716165 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
41716085 TTCTGCTCTG
* *
41716095 CTCTGCTTCCCTCACTGCAAC
1 CTCTGCTTCCCTCGCTGCAGC
41716116 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
41716137 CTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
41716158 CTCTGCTT
1 CTCTGCTT
41716166 TAAGTTGTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.06, C:0.48, G:0.15, T:0.31
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:41718142 original size:50 final size:49
Alignment explanation
Indices: 41718069--41718168 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 49
41718059 ATATTTTAAA
*
41718069 ATTATTAAGTTATGTAAATTATGTGAGTTGTTAAGTTATTAAGTTATGT
1 ATTATTAAATTATGTAAATTATGTGAGTTGTTAAGTTATTAAGTTATGT
*
41718118 ATTATGTAAATTATGTAAATTATGTGAGTTGTTAAGTTGTTAAGTTATGT
1 ATTAT-TAAATTATGTAAATTATGTGAGTTGTTAAGTTATTAAGTTATGT
41718168 A
1 A
41718169 AGTTATTATG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 5 0.10
50 43 0.90
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (49 bp):
ATTATTAAATTATGTAAATTATGTGAGTTGTTAAGTTATTAAGTTATGT
Found at i:41718195 original size:9 final size:8
Alignment explanation
Indices: 41718070--41718176 Score: 65
Period size: 9 Copynumber: 12.8 Consensus size: 8
41718060 TATTTTAAAA
41718070 TTATTAAG
1 TTATTAAG
*
41718078 TTATGTAAA
1 TTAT-TAAG
*
41718087 TTATGTGAG
1 TTAT-TAAG
*
41718096 TTGTTAAG
1 TTATTAAG
41718104 TTATTAAG
1 TTATTAAG
41718112 TTATGT-A-
1 TTAT-TAAG
*
41718119 TTATGTAAA
1 TTAT-TAAG
*
41718128 TTATGTAAA
1 TTAT-TAAG
*
41718137 TTATGTGAG
1 TTAT-TAAG
*
41718146 TTGTTAAG
1 TTATTAAG
*
41718154 TTGTTAAG
1 TTATTAAG
41718162 TTATGTAAG
1 TTAT-TAAG
41718171 TTATTA
1 TTATTA
41718177 TGTGAATTAT
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
7 6 0.07
8 36 0.43
9 41 0.49
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.49
Consensus pattern (8 bp):
TTATTAAG
Found at i:41720697 original size:9 final size:8
Alignment explanation
Indices: 41720652--41720723 Score: 62
Period size: 7 Copynumber: 9.2 Consensus size: 8
41720642 AAAAATTAAT
41720652 AACCCCTA
1 AACCCCTA
*
41720660 AATCCC-A
1 AACCCCTA
*
41720667 AATCCC-A
1 AACCCCTA
*
41720674 AACCCAT-
1 AACCCCTA
41720681 AACCCCTA
1 AACCCCTA
41720689 AATCCCCT-
1 AA-CCCCTA
41720697 AACCCCTA
1 AACCCCTA
*
41720705 AATCCCCTT
1 AA-CCCCTA
41720714 AACCCCTA
1 AACCCCTA
41720722 AA
1 AA
41720724 GCATAACCCC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
7 23 0.43
8 18 0.34
9 12 0.23
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.17
Consensus pattern (8 bp):
AACCCCTA
Found at i:41720702 original size:7 final size:7
Alignment explanation
Indices: 41720651--41720739 Score: 52
Period size: 7 Copynumber: 11.9 Consensus size: 7
41720641 TAAAAATTAA
41720651 TAACCCC
1 TAACCCC
*
41720658 TAAATCCC
1 T-AACCCC
* *
41720666 AAATCCC
1 TAACCCC
* *
41720673 AAACCCA
1 TAACCCC
41720680 TAACCCC
1 TAACCCC
41720687 TAAATCCCC
1 T-AA-CCCC
41720696 TAACCCC
1 TAACCCC
41720703 TAAATCCCC
1 T-AA-CCCC
41720712 TTAACCCC
1 -TAACCCC
** *
41720720 TAAAGCA
1 TAACCCC
41720727 TAACCCC
1 TAACCCC
41720734 TAACCC
1 TAACCC
41720740 TTGAACCACA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
7 37 0.58
8 15 0.23
9 11 0.17
10 1 0.02
ACGTcount: A:0.36, C:0.46, G:0.01, T:0.17
Consensus pattern (7 bp):
TAACCCC
Found at i:41720718 original size:17 final size:16
Alignment explanation
Indices: 41720651--41720723 Score: 89
Period size: 16 Copynumber: 4.7 Consensus size: 16
41720641 TAAAAATTAA
41720651 TAACCCCTAAAT-CCC
1 TAACCCCTAAATCCCC
* * *
41720666 AAATCCC-AAA-CCCA
1 TAACCCCTAAATCCCC
41720680 TAACCCCTAAATCCCC
1 TAACCCCTAAATCCCC
41720696 TAACCCCTAAATCCCC
1 TAACCCCTAAATCCCC
41720712 TTAACCCCTAAA
1 -TAACCCCTAAA
41720724 GCATAACCCC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
14 10 0.21
15 8 0.17
16 19 0.40
17 11 0.23
ACGTcount: A:0.37, C:0.45, G:0.00, T:0.18
Consensus pattern (16 bp):
TAACCCCTAAATCCCC
Found at i:41721012 original size:31 final size:32
Alignment explanation
Indices: 41720954--41721015 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
41720944 GAAACGGATG
* *
41720954 AAATTTGGTATAAAAATTTTTATTTTTTTATA
1 AAATTTGGTATAAAAATATGTATTTTTTTATA
41720986 AAATTTGGTATAAAAA-ATGTATTTTTTTAT
1 AAATTTGGTATAAAAATATGTATTTTTTTAT
41721016 CCAATAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (32 bp):
AAATTTGGTATAAAAATATGTATTTTTTTATA
Found at i:41721784 original size:8 final size:7
Alignment explanation
Indices: 41721761--41721872 Score: 52
Period size: 7 Copynumber: 15.4 Consensus size: 7
41721751 CTAACCATTG
41721761 AAACCCT
1 AAACCCT
41721768 AAACCCT
1 AAACCCT
41721775 AAATCCCT
1 AAA-CCCT
*
41721783 AACCCCT
1 AAACCCT
* *
41721790 AAAGCAT
1 AAACCCT
41721797 -AACCC-
1 AAACCCT
41721802 ATAACCCTT
1 A-AACCC-T
41721811 AAATCCCCT
1 AAA--CCCT
*
41721820 TAACCCTT
1 AAACCC-T
* *
41721828 AAAGCAT
1 AAACCCT
41721835 -AACACCT
1 AAAC-CCT
*
41721842 AACCCCT
1 AAACCCT
*
41721849 AAACCTT
1 AAACCCT
41721856 AAATCCC-
1 AAA-CCCT
41721863 AAACCCT
1 AAACCCT
41721870 AAA
1 AAA
41721873 TCCATACCCC
Statistics
Matches: 77, Mismatches: 16, Indels: 24
0.66 0.14 0.21
Matches are distributed among these distances:
6 8 0.10
7 46 0.60
8 16 0.21
9 4 0.05
10 3 0.04
ACGTcount: A:0.41, C:0.38, G:0.02, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:41721806 original size:21 final size:20
Alignment explanation
Indices: 41721779--41721851 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 20
41721769 AACCCTAAAT
41721779 CCCTAACCCCTAAAGCATAA
1 CCCTAACCCCTAAAGCATAA
* *
41721799 CCCATAA-CCCTTAA--AT-C
1 CCC-TAACCCCTAAAGCATAA
*
41721816 CCCTTAACCCTTAAAGCATAA
1 CCC-TAACCCCTAAAGCATAA
41721837 CACCTAACCCCTAAA
1 C-CCTAACCCCTAAA
41721852 CCTTAAATCC
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
17 6 0.15
18 7 0.17
20 11 0.28
21 14 0.35
22 2 0.05
ACGTcount: A:0.38, C:0.40, G:0.03, T:0.19
Consensus pattern (20 bp):
CCCTAACCCCTAAAGCATAA
Found at i:41721831 original size:38 final size:35
Alignment explanation
Indices: 41721769--41721851 Score: 105
Period size: 38 Copynumber: 2.3 Consensus size: 35
41721759 TGAAACCCTA
41721769 AACCCTAAATCCCTAACCCCTAAAGCATAAC-CCAT
1 AACCCTAAATCCCTAACCCCTAAAGCATAACACC-T
*
41721804 AACCCTTAAATCCCCTTAACCCTTAAAGCATAACACCT
1 AACCC-TAAAT-CCC-TAACCCCTAAAGCATAACACCT
41721842 AACCCCTAAA
1 AA-CCCTAAA
41721852 CCTTAAATCC
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
35 5 0.12
36 5 0.12
37 3 0.07
38 24 0.57
39 5 0.12
ACGTcount: A:0.40, C:0.39, G:0.02, T:0.19
Consensus pattern (35 bp):
AACCCTAAATCCCTAACCCCTAAAGCATAACACCT
Found at i:41722486 original size:115 final size:114
Alignment explanation
Indices: 41722087--41722757 Score: 835
Period size: 114 Copynumber: 5.9 Consensus size: 114
41722077 TAAATTATTT
* ** *
41722087 TAAATCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCTACTAAATCCCCGAAAGCACAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* * * * * *
41722152 GGTGTTGTTGGGCTTA-GTTTTTCTTCCGGGGCTTTCCCAAAAATGCCGC
66 GGCGTCGTTGGGCTTAGGTTTTT-TTGCGGCGCTTTCTCAAAAACGCCGC
* * *
41722201 TAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAAACAG-CGCTAAATCCCCGAAAACTCAGGAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC-GCCGCTAAATCCCCGAAAGCTCAGAAAA
* * * *
41722265 CGACATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACACCGC
65 CGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
* *
41722315 TAAAGCCATGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCTCGAAAAGCTCAGAAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCG-AAAGCTCAGAAAA
* * *
41722380 TGGCATCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTCTCAAAAACGCCGC
65 CGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
* * * * * *
41722430 TAAAAGCCCTGAGCATTAGCTGCGCTTTATTAAAAACGTCACTAAATCCCGGAAAGCTCAGCAAA
1 T-AAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA
** * *
41722495 CGGCGTCGTTGGGCTTAGGTTTTTTTGCGATGCTTTTTCAAAAACGCCGT
65 CGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
** * * * * * *
41722545 TTTATCCCTCAGCATTAGCGGCGCTTTATTAAAAATGCCGCTAAATCCCAGAAAGCTCAGAAAAT
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* *
41722610 GGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTCTCAAAAACGTCGC
66 GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
* * * * *
41722659 TAAAGCCCTGAGCATTAGCGACGCTTTCTTGAAAATGCCGCTAAATCCCCGAAAGCTCGGTAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
** *
41722724 GATGTCGTTGGGCTTAGG-TTTTTTACGGCGCTTT
66 GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTT
41722758 TTGGAAATCA
Statistics
Matches: 480, Mismatches: 72, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
113 15 0.03
114 302 0.63
115 120 0.25
116 43 0.09
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (114 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
Found at i:41730938 original size:41 final size:43
Alignment explanation
Indices: 41730888--41730996 Score: 141
Period size: 41 Copynumber: 2.6 Consensus size: 43
41730878 CAATTTTTGT
* * *
41730888 TTACGTGTAAGACCATGTCTGGGACATTGGCATCG-TATTTAA
1 TTACATGTAAGACCATGTCTGGGACAGTGGCATCGATATGTAA
* *
41730930 TT-CATGTAAGACCCTGTCTGGGACAGTGGCATCGATATGTGA
1 TTACATGTAAGACCATGTCTGGGACAGTGGCATCGATATGTAA
* *
41730972 TTACATGTAAGACCACGTTTGGGAC
1 TTACATGTAAGACCATGTCTGGGAC
41730997 GACGGCATTG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 29 0.51
42 9 0.16
43 19 0.33
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
TTACATGTAAGACCATGTCTGGGACAGTGGCATCGATATGTAA
Found at i:41738315 original size:27 final size:27
Alignment explanation
Indices: 41738247--41738387 Score: 180
Period size: 27 Copynumber: 5.2 Consensus size: 27
41738237 TTGATGTCAA
41738247 AAAATTATCGAAATACCC-CTGAAGGGT
1 AAAATTATCGAAATACCCTC-GAAGGGT
*
41738274 AAAAGTTATCGAAATACCC-CTGAAGGGA
1 AAAA-TTATCGAAATACCCTC-GAAGGGT
*
41738302 AAAATTA-CTAAAATACCCTCGAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
*
41738329 AAAATTATCGAAATGCCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
41738356 AAAATTACCGAAATACCCTGGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
41738383 AAAAT
1 AAAAT
41738388 AACCATTATA
Statistics
Matches: 102, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.01
27 73 0.72
28 28 0.27
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.21
Consensus pattern (27 bp):
AAAATTATCGAAATACCCTCGAAGGGT
Found at i:41738657 original size:26 final size:26
Alignment explanation
Indices: 41738589--41738685 Score: 124
Period size: 26 Copynumber: 3.8 Consensus size: 26
41738579 CAAATAATGT
41738589 TACTGGCAGCTTTGCTGCG-AACTGA
1 TACTGGCAGCTTTGCTGCGAAACTGA
* * * *
41738614 TACTGGCAGCTCTACTGCGAAATTGT
1 TACTGGCAGCTTTGCTGCGAAACTGA
* **
41738640 TACTGGCAACTTTGCTGCGTTACTGA
1 TACTGGCAGCTTTGCTGCGAAACTGA
41738666 TACTGGCAGCTTTGCTGCGA
1 TACTGGCAGCTTTGCTGCGA
41738686 TATTAGCGTG
Statistics
Matches: 58, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
25 17 0.29
26 41 0.71
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.31
Consensus pattern (26 bp):
TACTGGCAGCTTTGCTGCGAAACTGA
Found at i:41738684 original size:52 final size:51
Alignment explanation
Indices: 41738586--41738685 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 51
41738576 CCACAAATAA
*
41738586 TGTTACTGGCAGCTTTGCTGCGAACTGATACTGGCAGCTCTACTGCGAAAT
1 TGTTACTGGCAACTTTGCTGCGAACTGATACTGGCAGCTCTACTGCGAAAT
* * *
41738637 TGTTACTGGCAACTTTGCTGCGTTACTGATACTGGCAGCTTTGCTGCGA
1 TGTTACTGGCAACTTTGCTGCG-AACTGATACTGGCAGCTCTACTGCGA
41738686 TATTAGCGTG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 21 0.48
52 23 0.52
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (51 bp):
TGTTACTGGCAACTTTGCTGCGAACTGATACTGGCAGCTCTACTGCGAAAT
Found at i:41738835 original size:28 final size:29
Alignment explanation
Indices: 41738791--41738914 Score: 96
Period size: 30 Copynumber: 4.2 Consensus size: 29
41738781 CTGCATTTGT
*
41738791 ACTGATTACTGTTTTGGGCTAAGGCCCAC
1 ACTGATTACTGTATTGGGCTAAGGCCCAC
41738820 ACTG-TTACTGTATTGGGCTAAGGCCTACAC
1 ACTGATTACTGTATTGGGCTAAGGCC--CAC
* **
41738850 TCTGA-TACTACATTGGGCTATA-GCTCACAC
1 ACTGATTACTGTATTGGGCTA-AGGC-C-CAC
* * *
41738880 ACT-ACTACTGTATAGGGCTCAA-GCCCAG
1 ACTGATTACTGTATTGGGCT-AAGGCCCAC
41738908 ACTGATT
1 ACTGATT
41738915 CTGCATGTTG
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
28 25 0.32
29 8 0.10
30 41 0.53
31 3 0.04
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (29 bp):
ACTGATTACTGTATTGGGCTAAGGCCCAC
Found at i:41741063 original size:12 final size:12
Alignment explanation
Indices: 41741046--41741079 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41741036 ACTATATGAT
41741046 TTTATTTTGGAC
1 TTTATTTTGGAC
*
41741058 TTTATTATGGAC
1 TTTATTTTGGAC
*
41741070 TTTAATTTGG
1 TTTATTTTGG
41741080 GTTTGTCTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.56
Consensus pattern (12 bp):
TTTATTTTGGAC
Found at i:41742395 original size:43 final size:42
Alignment explanation
Indices: 41742317--41742402 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 42
41742307 AAGGCACCAA
*
41742317 GAAAAGAGAAATCAGCAGCTCCTTGAATACCGTCCCTTGCAT
1 GAAAAGAGAAATCAGCAGCTCCTTGAATACCGTCCCATGCAT
* ***
41742359 GAAAATGAGAAATCAGCAGCTCCTTTAATGTTGTCCCATGCAT
1 GAAAA-GAGAAATCAGCAGCTCCTTGAATACCGTCCCATGCAT
41742402 G
1 G
41742403 CTTGCTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 5 0.13
43 33 0.87
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (42 bp):
GAAAAGAGAAATCAGCAGCTCCTTGAATACCGTCCCATGCAT
Found at i:41747361 original size:18 final size:18
Alignment explanation
Indices: 41747340--41747399 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
41747330 GATTGAGAGC
41747340 GAAAAAGAATTTGAGAAA
1 GAAAAAGAATTTGAGAAA
* *
41747358 G-AAAAGAAAATTGAAAAA
1 GAAAAAG-AATTTGAGAAA
** *
41747376 GAAAGTGAGTTTGGAGAAA
1 GAAAAAGAATTT-GAGAAA
41747395 GAAAA
1 GAAAA
41747400 GAAAATGAGC
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
17 5 0.16
18 14 0.45
19 12 0.39
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (18 bp):
GAAAAAGAATTTGAGAAA
Found at i:41753315 original size:39 final size:39
Alignment explanation
Indices: 41753261--41753358 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 39
41753251 TAATTTAGTT
* * * *
41753261 TGAGTCTTTAATTATGTCATAATTTGAACATCATTAATA
1 TGAGTTTTTAATTATGTCATAATCTAAACAACATTAATA
41753300 TGAGTTTTTAATTATGTCATAATCTAAACAACATTAATA
1 TGAGTTTTTAATTATGTCATAATCTAAACAACATTAATA
* *
41753339 AG-GGTTTTAATTATGTCATA
1 TGAGTTTTTAATTATGTCATA
41753359 GTTTAGGACA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 17 0.32
39 36 0.68
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (39 bp):
TGAGTTTTTAATTATGTCATAATCTAAACAACATTAATA
Found at i:41755912 original size:18 final size:18
Alignment explanation
Indices: 41755891--41755942 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 18
41755881 CTCGCAATCT
41755891 TTTTCTTTTTCAATCTCG
1 TTTTCTTTTTCAATCTCG
* *
41755909 TTTTGCTTTCTTCACTCTCT
1 TTTT-CTTT-TTCAATCTCG
41755929 TTTTCTTTTTCAAT
1 TTTTCTTTTTCAAT
41755943 TTCTTTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 9 0.31
19 8 0.28
20 12 0.41
ACGTcount: A:0.10, C:0.23, G:0.04, T:0.63
Consensus pattern (18 bp):
TTTTCTTTTTCAATCTCG
Found at i:41755947 original size:18 final size:18
Alignment explanation
Indices: 41755888--41755949 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 18
41755878 CTGCTCGCAA
41755888 TCTTTTTCTTTTTCAATC
1 TCTTTTTCTTTTTCAATC
* *
41755906 TCGTTTTGCTTTCTTCACTC
1 TC-TTTTTCTTT-TTCAATC
*
41755926 TCTTTTTCTTTTTCAATT
1 TCTTTTTCTTTTTCAATC
41755944 TCTTTT
1 TCTTTT
41755950 ATGCTTATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 13 0.35
19 16 0.43
20 8 0.22
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.66
Consensus pattern (18 bp):
TCTTTTTCTTTTTCAATC
Found at i:41763688 original size:33 final size:34
Alignment explanation
Indices: 41763625--41763691 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
41763615 TTCTGGATTG
*
41763625 CTTTCTTCACTCATTTCTTTTGTAAACTTTCTTT
1 CTTTCTTCACTCATTTCTTTTGCAAACTTTCTTT
*
41763659 CTTT-TTCACTCGATTTCTTTT-CAAGCTTTCTTT
1 CTTTCTTCACTC-ATTTCTTTTGCAAACTTTCTTT
41763692 TAATTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 17 0.57
34 13 0.43
ACGTcount: A:0.13, C:0.24, G:0.04, T:0.58
Consensus pattern (34 bp):
CTTTCTTCACTCATTTCTTTTGCAAACTTTCTTT
Found at i:41773356 original size:24 final size:24
Alignment explanation
Indices: 41773324--41773372 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
41773314 TGGTCCCACA
41773324 TTCATGCTGTCCATTGCATGTACC
1 TTCATGCTGTCCATTGCATGTACC
41773348 TTCATGCTGTCCATTGCATGTACC
1 TTCATGCTGTCCATTGCATGTACC
41773372 T
1 T
41773373 GGCACCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.29, G:0.16, T:0.39
Consensus pattern (24 bp):
TTCATGCTGTCCATTGCATGTACC
Found at i:41780610 original size:33 final size:32
Alignment explanation
Indices: 41780545--41780610 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 32
41780535 TTTTTCTTGA
*
41780545 TTTCTTTCTTCACTCGTTTCTTATGCAGACTC
1 TTTCTTTCTTCACTCGTTTCTTATGCAAACTC
* *
41780577 TTTCTTTTTCTCACTCGATTTCTT-TTCAAACTC
1 TTTCTTTCT-TCACTCG-TTTCTTATGCAAACTC
41780610 T
1 T
41780611 CTTTCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 8 0.28
33 15 0.52
34 6 0.21
ACGTcount: A:0.14, C:0.27, G:0.06, T:0.53
Consensus pattern (32 bp):
TTTCTTTCTTCACTCGTTTCTTATGCAAACTC
Found at i:41780623 original size:6 final size:6
Alignment explanation
Indices: 41780612--41780678 Score: 95
Period size: 6 Copynumber: 11.7 Consensus size: 6
41780602 TCAAACTCTC
*
41780612 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTT-AT TTTC-- TTTCAA
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
*
41780657 TTTCTT TTTCAT TTTCAT TTTC
1 TTTCAT TTTCAT TTTCAT TTTC
41780679 TCGCTCGCAC
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
4 4 0.07
5 5 0.09
6 46 0.84
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCAT
Found at i:41791039 original size:39 final size:38
Alignment explanation
Indices: 41790976--41791067 Score: 139
Period size: 39 Copynumber: 2.4 Consensus size: 38
41790966 TGTCCTAAAC
*
41790976 TATGACATAATTAAAACCCTTATTAATGTTGTTCAAAT
1 TATGACATAATTAAAACCCATATTAATGTTGTTCAAAT
* * *
41791014 TATGACACAATTAAAAGCTCATATTAATGTTGTTCGAAT
1 TATGACATAATTAAAA-CCCATATTAATGTTGTTCAAAT
41791053 TATGACATAATTAAA
1 TATGACATAATTAAA
41791068 GACTCAAACT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 15 0.31
39 33 0.69
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (38 bp):
TATGACATAATTAAAACCCATATTAATGTTGTTCAAAT
Found at i:41793946 original size:15 final size:15
Alignment explanation
Indices: 41793910--41793939 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41793900 ATATGCTGAT
41793910 TTCTTTTTTTCACAA
1 TTCTTTTTTTCACAA
41793925 TTCTTTTTTTCACAA
1 TTCTTTTTTTCACAA
41793940 GTTTTTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTCTTTTTTTCACAA
Found at i:41795310 original size:92 final size:92
Alignment explanation
Indices: 41795180--41795383 Score: 243
Period size: 92 Copynumber: 2.2 Consensus size: 92
41795170 TAATATGGAG
* * * * *
41795180 CATGCACCCGATTATGCATG-AA-TATCGAGAGTTGTTTTTTAGCTGGACATTCATGTATCTT-T
1 CATGCACCCGATTGTGCATGAAAGT-TCGA-AGCTATTTTTTAGCTGAACATACATGTATCTTCT
* **
41795242 CAGATTCAATAAAGCTACTTTATTGAAGAA
64 -AGATTCAACAAAGCTACTTTAAAGAAGAA
** *
41795272 CATGCACCTTATTGTGCATGAAAGTTCGAAGCTATTTTTTAGCTGAATATACATGTATCTTCTAG
1 CATGCACCCGATTGTGCATGAAAGTTCGAAGCTATTTTTTAGCTGAACATACATGTATCTTCTAG
* *
41795337 ATTCAACGAAGCTGCTTTAAAGAAGAA
66 ATTCAACAAAGCTACTTTAAAGAAGAA
41795364 CATGCACCCGATTGTGCATG
1 CATGCACCCGATTGTGCATG
41795384 TATTTTGAGA
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
92 86 0.91
93 7 0.07
94 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (92 bp):
CATGCACCCGATTGTGCATGAAAGTTCGAAGCTATTTTTTAGCTGAACATACATGTATCTTCTAG
ATTCAACAAAGCTACTTTAAAGAAGAA
Found at i:41796908 original size:16 final size:16
Alignment explanation
Indices: 41796869--41796910 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
41796859 AATGAGCCAT
*
41796869 ATCCATGAATCCAGCC
1 ATCCATGTATCCAGCC
41796885 ATCCATGTATCCAGCC
1 ATCCATGTATCCAGCC
*
41796901 ATTCATGTAT
1 ATCCATGTAT
41796911 GCTCCCATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.29
Consensus pattern (16 bp):
ATCCATGTATCCAGCC
Found at i:41798492 original size:20 final size:20
Alignment explanation
Indices: 41798469--41798538 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 20
41798459 GTCTTTGCTG
41798469 AATTAAATATGTCCTGATTT
1 AATTAAATATGTCCTGATTT
* *
41798489 AATT-AATATG-CTTTGTTTTTGTT
1 AATTAAATATGTC-CTG---AT-TT
41798512 GAATTAAATATGTCCTGATTT
1 -AATTAAATATGTCCTGATTT
41798533 AATTAA
1 AATTAA
41798539 GTTTGTCTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
18 1 0.03
19 8 0.21
20 10 0.26
21 2 0.05
22 2 0.05
23 2 0.05
24 4 0.11
25 8 0.21
26 1 0.03
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (20 bp):
AATTAAATATGTCCTGATTT
Found at i:41798496 original size:44 final size:44
Alignment explanation
Indices: 41798447--41798538 Score: 166
Period size: 44 Copynumber: 2.1 Consensus size: 44
41798437 ATATAAGTCT
41798447 TTAATATGCTTTGTCTTTGCTGAATTAAATATGTCCTGATTTAA
1 TTAATATGCTTTGTCTTTGCTGAATTAAATATGTCCTGATTTAA
* *
41798491 TTAATATGCTTTGTTTTTGTTGAATTAAATATGTCCTGATTTAA
1 TTAATATGCTTTGTCTTTGCTGAATTAAATATGTCCTGATTTAA
41798535 TTAA
1 TTAA
41798539 GTTTGTCTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.50
Consensus pattern (44 bp):
TTAATATGCTTTGTCTTTGCTGAATTAAATATGTCCTGATTTAA
Found at i:41799795 original size:12 final size:13
Alignment explanation
Indices: 41799773--41799799 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41799763 GTAATCGTAG
41799773 TTTCAAAAAAAAT
1 TTTCAAAAAAAAT
41799786 TTTCAAAAAAAAT
1 TTTCAAAAAAAAT
41799799 T
1 T
41799800 CAAATCTAAA
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:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (13 bp):
TTTCAAAAAAAAT
Found at i:41807703 original size:12 final size:12
Alignment explanation
Indices: 41807682--41807759 Score: 51
Period size: 12 Copynumber: 6.9 Consensus size: 12
41807672 GTGCGAGCGA
*
41807682 GAAAATGAAAAT
1 GAAAAAGAAAAT
*
41807694 GAAAAAGAAATT
1 GAAAAAGAAAAT
41807706 G--AAAGAAAA-
1 GAAAAAGAAAAT
* *
41807715 GAAAAAGAGATT
1 GAAAAAGAAAAT
* *
41807727 GAAAAATAAATT
1 GAAAAAGAAAAT
41807739 G--AAAGAAAA-
1 GAAAAAGAAAAT
41807748 GAAAAAGGAAAA
1 GAAAAA-GAAAA
41807760 GACATTGTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
9 2 0.04
10 13 0.25
11 9 0.18
12 27 0.53
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (12 bp):
GAAAAAGAAAAT
Found at i:41807720 original size:21 final size:22
Alignment explanation
Indices: 41807688--41807730 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
41807678 GCGAGAAAAT
41807688 GAAAATGAAAAAGAAATTGAAA
1 GAAAATGAAAAAGAAATTGAAA
*
41807710 GAAAA-GAAAAAGAGATTGAAA
1 GAAAATGAAAAAGAAATTGAAA
41807731 AATAAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (22 bp):
GAAAATGAAAAAGAAATTGAAA
Found at i:41807785 original size:33 final size:33
Alignment explanation
Indices: 41807748--41807849 Score: 90
Period size: 33 Copynumber: 3.1 Consensus size: 33
41807738 TGAAAGAAAA
41807748 GAAAAAGGAAAAGACATTGTAAAGAAAACGAGT
1 GAAAAAGGAAAAGACATTGTAAAGAAAACGAGT
*
41807781 G-AAAAGGAAAAAGAGC-TTG-AACAGAAATCGAGT
1 GAAAAAGG-AAAAGA-CATTGTAA-AGAAAACGAGT
*
41807814 GAAAAA-G-AAAGAAAGTTTGTAAA-AGAAACGAGT
1 GAAAAAGGAAAAGACA--TTGTAAAGA-AAACGAGT
41807847 GAA
1 GAA
41807850 GAGAGTAATC
Statistics
Matches: 57, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
31 5 0.09
32 9 0.16
33 36 0.63
34 7 0.12
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAAAGGAAAAGACATTGTAAAGAAAACGAGT
Found at i:41816035 original size:13 final size:13
Alignment explanation
Indices: 41816019--41816064 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
41816009 TTTATATTCT
41816019 TTTTTTTCAC-AAA
1 TTTTTTT-ACGAAA
41816032 TTTTTTTACGAAA
1 TTTTTTTACGAAA
* *
41816045 TTTTTTTATGAAG
1 TTTTTTTACGAAA
41816058 TTTTTTT
1 TTTTTTT
41816065 CAGCTAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 2 0.07
13 28 0.93
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTTTTTACGAAA
Found at i:41817127 original size:16 final size:16
Alignment explanation
Indices: 41817106--41817147 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
41817096 AATGAGCCAT
41817106 ATCCATG-ATTCCAGCC
1 ATCCATGTA-TCCAGCC
41817122 ATCCATGTATCCAGCC
1 ATCCATGTATCCAGCC
*
41817138 ATTCATGTAT
1 ATCCATGTAT
41817148 GCTCCCATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (16 bp):
ATCCATGTATCCAGCC
Found at i:41822138 original size:21 final size:21
Alignment explanation
Indices: 41822087--41822142 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
41822077 TCACTCTCTT
**
41822087 TTTCAATTTCTTTCTCTTTTTC
1 TTTCAATTTCTTT-TCCATTTC
**
41822109 -TTCTTTTTCTTTTCCATTTC
1 TTTCAATTTCTTTTCCATTTC
41822129 TTTCAATTTCTTTT
1 TTTCAATTTCTTTT
41822143 TCAATGTTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCAATTTCTTTTCCATTTC
Found at i:41822154 original size:13 final size:12
Alignment explanation
Indices: 41822083--41822155 Score: 50
Period size: 12 Copynumber: 6.5 Consensus size: 12
41822073 AGTCTCACTC
41822083 TCTTTTTCAATT
1 TCTTTTTCAATT
*
41822095 TCTTTCTC--TT
1 TCTTTTTCAATT
* **
41822105 T-TTCTTCTTTT
1 TCTTTTTCAATT
*
41822116 TC-TTTTCCATT
1 TCTTTTTCAATT
41822127 TC--TTTCAATT
1 TCTTTTTCAATT
41822137 TCTTTTTCAATGT
1 TCTTTTTCAAT-T
41822150 TCTTTT
1 TCTTTT
41822156 CTCGCTCACA
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
9 4 0.08
10 12 0.25
11 11 0.23
12 14 0.29
13 7 0.15
ACGTcount: A:0.10, C:0.21, G:0.01, T:0.68
Consensus pattern (12 bp):
TCTTTTTCAATT
Found at i:41822156 original size:12 final size:11
Alignment explanation
Indices: 41822114--41822156 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
41822104 TTTTCTTCTT
*
41822114 TTTCTTTTCCA
1 TTTCTTTTCAA
41822125 TTTC-TTTCAA
1 TTTCTTTTCAA
41822135 TTTCTTTTTCAA
1 TTTC-TTTTCAA
41822147 TGTTCTTTTC
1 T-TTCTTTTC
41822157 TCGCTCACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 9 0.32
11 4 0.14
12 12 0.43
13 3 0.11
ACGTcount: A:0.12, C:0.21, G:0.02, T:0.65
Consensus pattern (11 bp):
TTTCTTTTCAA
Found at i:41824576 original size:22 final size:21
Alignment explanation
Indices: 41824551--41824593 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
41824541 TTTAACACTT
* *
41824551 AACTAAATTAATTAAATATTTA
1 AACTAAACTAACTAAA-ATTTA
41824573 AACTAAACTAACTAAAATTTA
1 AACTAAACTAACTAAAATTTA
41824594 TTTAAGCAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (21 bp):
AACTAAACTAACTAAAATTTA
Found at i:41825354 original size:91 final size:92
Alignment explanation
Indices: 41825190--41825359 Score: 200
Period size: 91 Copynumber: 1.9 Consensus size: 92
41825180 GCATGAATCT
** * * **
41825190 TTCATTAACTAGCTTCAATATATCAGCAAGATACATGAACATTCAGCTGAATAATAGCTCCCTTC
1 TTCATTAACTAGCTTCAATATATCAGCAAGATACATGAACATTCAAATGAAAAACAGCTCCCAAC
* *
41825255 ATTCATGCATAATTAGGTACGTTACTC
66 ATTAATGCACAATTAGGTACGTTACTC
* * * **
41825282 TTCATT-ACATAGCTT-AATGTATCAGCTAGGTACATGAATGTTCAAATGAAAAACAGCTCCCAA
1 TTCATTAAC-TAGCTTCAATATATCAGCAAGATACATGAACATTCAAATGAAAAACAGCTCCCAA
41825345 CATTAATGCACAATT
65 CATTAATGCACAATT
41825360 CGGGTGCACG
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
91 52 0.81
92 12 0.19
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (92 bp):
TTCATTAACTAGCTTCAATATATCAGCAAGATACATGAACATTCAAATGAAAAACAGCTCCCAAC
ATTAATGCACAATTAGGTACGTTACTC
Found at i:41829220 original size:47 final size:49
Alignment explanation
Indices: 41829168--41829268 Score: 161
Period size: 50 Copynumber: 2.1 Consensus size: 49
41829158 TAAATGTCGA
* *
41829168 AATTATTTAAGCAACTAAA-ATAA-AAAAACAACTTAATTCATTAAACT
1 AATTATTTAAGCAACTAAAGAAAATAAAAACAACTTAATTAATTAAACT
41829215 AATTATTTAAGCAACTAAAGAAAATTAAAAACAACTTAATTAATTAAACT
1 AATTATTTAAGCAACTAAAGAAAA-TAAAAACAACTTAATTAATTAAACT
41829265 AATT
1 AATT
41829269 TAACTAAACA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
47 19 0.39
48 3 0.06
50 27 0.55
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (49 bp):
AATTATTTAAGCAACTAAAGAAAATAAAAACAACTTAATTAATTAAACT
Found at i:41837327 original size:43 final size:43
Alignment explanation
Indices: 41837280--41837452 Score: 346
Period size: 43 Copynumber: 4.0 Consensus size: 43
41837270 AACATGCCAC
41837280 CCTCAAACGGATGGCCAAACCGAGGTAGTAAATCGTGTACTAT
1 CCTCAAACGGATGGCCAAACCGAGGTAGTAAATCGTGTACTAT
41837323 CCTCAAACGGATGGCCAAACCGAGGTAGTAAATCGTGTACTAT
1 CCTCAAACGGATGGCCAAACCGAGGTAGTAAATCGTGTACTAT
41837366 CCTCAAACGGATGGCCAAACCGAGGTAGTAAATCGTGTACTAT
1 CCTCAAACGGATGGCCAAACCGAGGTAGTAAATCGTGTACTAT
41837409 CCTCAAACGGATGGCCAAACCGAGGTAGTAAATCGTGTACTAT
1 CCTCAAACGGATGGCCAAACCGAGGTAGTAAATCGTGTACTAT
41837452 C
1 C
41837453 AACTTTGCTT
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 130 1.00
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (43 bp):
CCTCAAACGGATGGCCAAACCGAGGTAGTAAATCGTGTACTAT
Found at i:41839756 original size:20 final size:21
Alignment explanation
Indices: 41839719--41839758 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
41839709 AGATTGTTTG
41839719 AGCTCATTTCAATTTATTTCC
1 AGCTCATTTCAATTTATTTCC
*
41839740 AGCTCATTT-ACTTTATTTC
1 AGCTCATTTCAATTTATTTC
41839759 TAGAATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.50
Consensus pattern (21 bp):
AGCTCATTTCAATTTATTTCC
Found at i:41841131 original size:14 final size:14
Alignment explanation
Indices: 41841107--41841149 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
41841097 TCCAAAGTAG
41841107 GTTCGTGAAAAAAAA
1 GTTC-TGAAAAAAAA
*
41841122 GTTTTGAAAAAAAA
1 GTTCTGAAAAAAAA
*
41841136 GTTCCGAAAAAAAA
1 GTTCTGAAAAAAAA
41841150 TTTGTGCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 22 0.88
15 3 0.12
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.21
Consensus pattern (14 bp):
GTTCTGAAAAAAAA
Found at i:41841625 original size:33 final size:33
Alignment explanation
Indices: 41841583--41841651 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
41841573 TCTGTGTGTA
41841583 TAAATAAACTGTTTTATAATAATGTCCTGAGAG
1 TAAATAAACTGTTTTATAATAATGTCCTGAGAG
41841616 TAAATAAACTGTTTTATAATAATGTCCTGAGAG
1 TAAATAAACTGTTTTATAATAATGTCCTGAGAG
41841649 TAA
1 TAA
41841652 TATGATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (33 bp):
TAAATAAACTGTTTTATAATAATGTCCTGAGAG
Found at i:41852710 original size:38 final size:39
Alignment explanation
Indices: 41852659--41852735 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
41852649 CTTATCACAT
*
41852659 ATTAAAGATGTTCAAATTATGACATAGTTAAA-ACTCAA
1 ATTAAAGATGTTCAAATTATGACATAATTAAAGACTCAA
* *
41852697 ATTAATGATGTTCAAATTATGGCATAATTAAAGACTCAA
1 ATTAAAGATGTTCAAATTATGACATAATTAAAGACTCAA
41852736 CTTTAATAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 29 0.83
39 6 0.17
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.32
Consensus pattern (39 bp):
ATTAAAGATGTTCAAATTATGACATAATTAAAGACTCAA
Found at i:41853205 original size:11 final size:11
Alignment explanation
Indices: 41853187--41853216 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
41853177 AGTAAAACCC
41853187 AAATATAAAAT
1 AAATATAAAAT
*
41853198 ATATATAAAAT
1 AAATATAAAAT
41853209 AAATATAA
1 AAATATAA
41853217 TAAAAGTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:41866220 original size:9 final size:9
Alignment explanation
Indices: 41866196--41866232 Score: 56
Period size: 10 Copynumber: 3.9 Consensus size: 9
41866186 ATTTATTAAC
41866196 AAACACATT
1 AAACACATT
41866205 AAAACACATT
1 -AAACACATT
41866215 AAACACATTT
1 AAACACA-TT
41866225 AAACACAT
1 AAACACAT
41866233 ATTAGACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.57, C:0.22, G:0.00, T:0.22
Consensus pattern (9 bp):
AAACACATT
Found at i:41866220 original size:19 final size:19
Alignment explanation
Indices: 41866196--41866232 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41866186 ATTTATTAAC
41866196 AAACACATTAAAACACATT
1 AAACACATTAAAACACATT
*
41866215 AAACACATTTAAACACAT
1 AAACACATTAAAACACAT
41866233 ATTAGACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.22, G:0.00, T:0.22
Consensus pattern (19 bp):
AAACACATTAAAACACATT
Found at i:41866386 original size:54 final size:53
Alignment explanation
Indices: 41866323--41866450 Score: 161
Period size: 54 Copynumber: 2.4 Consensus size: 53
41866313 TGCAACAATA
* *
41866323 AATTATTCCAGAAACTAAATTAACTAAGATGAGCTTAATTATA-TAAGATGAGT
1 AATTATTCCAGAAACTAAATTAACTAAGATGAACTCAATTA-ACTAAGATGAGT
*
41866376 AATTAATTCCAGCAAC-ATAATTAACTAAGATGAACTCAATTAACTAAGATGAGT
1 AATT-ATTCCAGAAACTA-AATTAACTAAGATGAACTCAATTAACTAAGATGAGT
**
41866430 AATTCATTCCAGTGACTAAAT
1 AATT-ATTCCAGAAACTAAAT
41866451 ACTTATTTCA
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
53 6 0.09
54 58 0.89
55 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (53 bp):
AATTATTCCAGAAACTAAATTAACTAAGATGAACTCAATTAACTAAGATGAGT
Found at i:41868168 original size:18 final size:18
Alignment explanation
Indices: 41868142--41868184 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
41868132 TTACTTTTTA
*
41868142 TTTCATTTTCAATAT-CTT
1 TTTCTTTTTCAAT-TGCTT
41868160 TTTCTTTTTCAATTGCTT
1 TTTCTTTTTCAATTGCTT
41868178 TTTCTTT
1 TTTCTTT
41868185 CTTTTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.14, C:0.16, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTCTTTTTCAATTGCTT
Found at i:41868564 original size:17 final size:17
Alignment explanation
Indices: 41868542--41868580 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
41868532 TTCTTGAATA
41868542 TTCATG-GGATGCTTGTC
1 TTCATGAGGAT-CTTGTC
41868559 TTCATGAGGATCTTGTC
1 TTCATGAGGATCTTGTC
41868576 TTCAT
1 TTCAT
41868581 TCCTCAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.44
Consensus pattern (17 bp):
TTCATGAGGATCTTGTC
Found at i:41870368 original size:19 final size:19
Alignment explanation
Indices: 41870341--41870378 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
41870331 TTATTCCAGC
41870341 AACTAAATTAACTAAGATG
1 AACTAAATTAACTAAGATG
*
41870360 AACTTAATTAACTAAGATG
1 AACTAAATTAACTAAGATG
41870379 CGTAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (19 bp):
AACTAAATTAACTAAGATG
Found at i:41870394 original size:54 final size:54
Alignment explanation
Indices: 41870331--41870456 Score: 198
Period size: 54 Copynumber: 2.3 Consensus size: 54
41870321 CAACAATAAA
* **
41870331 TTATTCCAGCAACTAAATTAACTAAGATGAACTTAATTAACTAAGATGCGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATAAGTAAT
* * *
41870385 TTATTCCAGCAACTTAATTAATTAAGATGAACTCAATTAACTAGGATAAGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATAAGTAAT
41870439 TTATTCCAGCAACTAAAT
1 TTATTCCAGCAACTAAAT
41870457 ACTTACTCCA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (54 bp):
TTATTCCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAGATAAGTAAT
Found at i:41876812 original size:21 final size:22
Alignment explanation
Indices: 41876788--41876834 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
41876778 AATTCTCACC
* *
41876788 AAATGAACAGAATTTCATT-CA
1 AAATGAACAAAAGTTCATTACA
*
41876809 AAATGATCAAAAGTTCATTACA
1 AAATGAACAAAAGTTCATTACA
41876831 AAAT
1 AAAT
41876835 CTGATTTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.28
Consensus pattern (22 bp):
AAATGAACAAAAGTTCATTACA
Found at i:41881771 original size:20 final size:21
Alignment explanation
Indices: 41881738--41881777 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
41881728 AAGTTTTTTG
41881738 AGCTCAATTGAGCTCATTTCC
1 AGCTCAATTGAGCTCATTTCC
*
41881759 AGCTCAA-TGAGCTCGTTTC
1 AGCTCAATTGAGCTCATTTC
41881778 AATCTTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.33
Consensus pattern (21 bp):
AGCTCAATTGAGCTCATTTCC
Found at i:41883301 original size:21 final size:19
Alignment explanation
Indices: 41883257--41883314 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
41883247 AAAATTTGAA
41883257 AAAATTCAAAAAAAAA-TC
1 AAAATTCAAAAAAAAAGTC
41883275 AGAAATTCGAAAAAAAAAGTTC
1 A-AAATTC-AAAAAAAAAG-TC
*
41883297 AAAATTATAAAAAAAAAG
1 AAAATT-CAAAAAAAAAG
41883315 GAAATTTGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 1 0.03
19 6 0.18
20 9 0.26
21 15 0.44
22 3 0.09
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (19 bp):
AAAATTCAAAAAAAAAGTC
Found at i:41886699 original size:20 final size:21
Alignment explanation
Indices: 41886669--41886707 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41886659 CTTGTTGAGA
41886669 TCAATTGAGCTCATTTCCAGC
1 TCAATTGAGCTCATTTCCAGC
*
41886690 TCAA-TGAGCTCGTTTCCA
1 TCAATTGAGCTCATTTCCA
41886708 TCTTTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.33
Consensus pattern (21 bp):
TCAATTGAGCTCATTTCCAGC
Found at i:41890160 original size:15 final size:15
Alignment explanation
Indices: 41890140--41890175 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
41890130 TAACTGATAA
*
41890140 GGAGTCATTCCTAAT
1 GGAGTCATTCCTAAC
41890155 GGAGTCATTCCTAAC
1 GGAGTCATTCCTAAC
41890170 GGAGTC
1 GGAGTC
41890176 TTAAATGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (15 bp):
GGAGTCATTCCTAAC
Found at i:41890977 original size:8 final size:8
Alignment explanation
Indices: 41890964--41890992 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
41890954 TTTTAATTGA
41890964 TATTTTAT
1 TATTTTAT
41890972 TATTTTAT
1 TATTTTAT
41890980 TATTTTAT
1 TATTTTAT
41890988 TATTT
1 TATTT
41890993 AAGTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:41894950 original size:50 final size:50
Alignment explanation
Indices: 41894840--41895291 Score: 327
Period size: 50 Copynumber: 8.8 Consensus size: 50
41894830 ATTTGGGTAA
* * * *
41894840 AGAGATCCCATGTAAGACCATGTATGGGACATGGAATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
**
41894896 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
41894946 AGAGGTCCCCCGTAAGACCATGCCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * * *
41894996 AGAACTCCCATGTAAGACCATATCTGGGATATGGAATTGG-A-AGTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** *
41895045 AAACATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCATCGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
* * * * * * *
41895101 AGAAGTCTCACGTAAGACCATGTCAGGGACATGCCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
41895151 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
41895201 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * * *
41895250 AAACATCTCATGTAAGACCATGCCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41895292 TGTTATTATC
Statistics
Matches: 314, Mismatches: 72, Indels: 27
0.76 0.17 0.07
Matches are distributed among these distances:
48 2 0.01
49 73 0.23
50 156 0.50
52 2 0.01
53 5 0.02
54 1 0.00
55 2 0.01
56 73 0.23
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:41895143 original size:155 final size:149
Alignment explanation
Indices: 41894901--41895184 Score: 343
Period size: 155 Copynumber: 1.9 Consensus size: 149
41894891 TTATGAGAGG
** * * *
41894901 TCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTAGCACCGAGATGAGAAGTCCCACGTAAGACCA
* * * * *
41894966 TGCCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGGGATATGGA
66 TGCCAGGGACATGCCATGGGCACCGAGATGAGAACTCCCACGTAAGACCATATCTGGGACATGGA
41895031 ATTGGAAGTACAAGAAACA
131 ATTGGAAGTACAAGAAACA
*
41895050 TCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCATCGAGGTTATGAGAAGTCTCACGTA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTAGCA-C--CGA-G--ATGAGAAGTCCCACGTA
* * * * ** * *
41895115 AGACCATGTCAGGGACATGCCGTTGGCACTGAGATGAGAGGTCCCCCGTAAGACCATGTCTGGGA
60 AGACCATGCCAGGGACATGCCATGGGCACCGAGATGAGAACTCCCACGTAAGACCATATCTGGGA
41895180 CATGG
125 CATGG
41895185 CATGGGCACC
Statistics
Matches: 110, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
149 34 0.31
150 1 0.01
152 3 0.03
153 1 0.01
155 71 0.65
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.21
Consensus pattern (149 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTAGCACCGAGATGAGAAGTCCCACGTAAGACCA
TGCCAGGGACATGCCATGGGCACCGAGATGAGAACTCCCACGTAAGACCATATCTGGGACATGGA
ATTGGAAGTACAAGAAACA
Found at i:41895196 original size:205 final size:205
Alignment explanation
Indices: 41894844--41895284 Score: 731
Period size: 205 Copynumber: 2.2 Consensus size: 205
41894834 GGGTAAAGAG
* * * * * *
41894844 ATCCCATGTAAGACCATGTATGGGACATGGAATTGGCATCATTGAGGTTATGAGAGGTCCCATGT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCATCGAGGTTATGAGAAGTCCCACGT
* **
41894909 AAGACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGCCTGGG
66 AAGACCATGTCAGGGACATGCCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGCCTGGG
41894974 ACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGGGATATGGA-ATTGGAA
131 ACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGGGATAT-GACATTGGAA
41895038 GTACAAGAAAC
195 GTACAAGAAAC
*
41895049 ATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCATCGAGGTTATGAGAAGTCTCACGT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCATCGAGGTTATGAGAAGTCCCACGT
* *
41895114 AAGACCATGTCAGGGACATGCCGTTGGCACTGAGATGAGAGGTCCCCCGTAAGACCATGTCTGGG
66 AAGACCATGTCAGGGACATGCCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGCCTGGG
*
41895179 ACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGCAG
131 ACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGAAG
41895244 TACAAGAAAC
196 TACAAGAAAC
* *
41895254 ATCTCATGTAAGACCATGCCTGGGACATGGC
1 ATCCCATGTAAGACCATGTCTGGGACATGGC
41895285 TTTGGCATGT
Statistics
Matches: 220, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
204 2 0.01
205 218 0.99
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.22
Consensus pattern (205 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCATCGAGGTTATGAGAAGTCCCACGT
AAGACCATGTCAGGGACATGCCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGCCTGGG
ACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGAAG
TACAAGAAAC
Found at i:41899078 original size:81 final size:82
Alignment explanation
Indices: 41898975--41899138 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 82
41898965 GTTCGGTCTA
41898975 TTTCATTGGTTACTCCAAGAAAAGTTAGGATGATTACGCCATGAAGAATTGTTGAAGTTGGACTG
1 TTTCATTGGTTACTCCAAGAAAAGTTAGGATGATTACGCCATGAAGAATTGTTGAAGTTGGACTG
41899040 GGGTCCTTGTCCACTCC
66 GGGTCCTTGTCCACTCC
41899057 TTTCATTGG-TACTCCAAGAAAAGTTAGGATGATTACGCCATGAAGAATTGTTGAAGTTGGACTG
1 TTTCATTGGTTACTCCAAGAAAAGTTAGGATGATTACGCCATGAAGAATTGTTGAAGTTGGACTG
41899121 GGGTCCTTGTCCACTCC
66 GGGTCCTTGTCCACTCC
41899138 T
1 T
41899139 ATTTTGATAT
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 73 0.89
82 9 0.11
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (82 bp):
TTTCATTGGTTACTCCAAGAAAAGTTAGGATGATTACGCCATGAAGAATTGTTGAAGTTGGACTG
GGGTCCTTGTCCACTCC
Found at i:41918957 original size:18 final size:18
Alignment explanation
Indices: 41918930--41918971 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
41918920 TGCTGGAATA
*
41918930 AATTAATTAAGTT-AGTTT
1 AATTAATTAA-TTAAGCTT
*
41918948 AATTAGTTAATTAAGCTT
1 AATTAATTAATTAAGCTT
41918966 AATTAA
1 AATTAA
41918972 ATGTTGAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (18 bp):
AATTAATTAATTAAGCTT
Found at i:41923747 original size:18 final size:18
Alignment explanation
Indices: 41923720--41923761 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
41923710 AGCTGGAATA
*
41923720 AATTAATTAAGTT-AGTTT
1 AATTAATTAA-TTCAGCTT
*
41923738 AATTAGTTAATTCAGCTT
1 AATTAATTAATTCAGCTT
41923756 AATTAA
1 AATTAA
41923762 ATGTTGAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (18 bp):
AATTAATTAATTCAGCTT
Found at i:41932457 original size:18 final size:17
Alignment explanation
Indices: 41932434--41932472 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
41932424 CTCTATTTGC
41932434 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
41932452 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
41932470 TCT
1 TCT
41932473 GTCTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:41936062 original size:22 final size:21
Alignment explanation
Indices: 41936033--41936074 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
41936023 TAAAAACCAA
41936033 ATGGCCAAAAAATGTGAAAGG
1 ATGGCCAAAAAATGTGAAAGG
* *
41936054 ATGGTCCAATAAGTGTGAAAG
1 ATGG-CCAAAAAATGTGAAAG
41936075 CTTTGATAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.43, C:0.10, G:0.29, T:0.19
Consensus pattern (21 bp):
ATGGCCAAAAAATGTGAAAGG
Found at i:41945818 original size:24 final size:25
Alignment explanation
Indices: 41945772--41945818 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
41945762 AGGAATTTGG
*
41945772 CTAAATGAATTGATGATGGAAATGA
1 CTAAATGAATTGATGATGAAAATGA
* *
41945797 CTAAGTGAA-TGATGGTGAAAAT
1 CTAAATGAATTGATGATGAAAAT
41945819 TCGGCTAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.28
Consensus pattern (25 bp):
CTAAATGAATTGATGATGAAAATGA
Found at i:41950525 original size:70 final size:70
Alignment explanation
Indices: 41950411--41950551 Score: 219
Period size: 70 Copynumber: 2.0 Consensus size: 70
41950401 GTCATTTGCA
* * *
41950411 ATCTTTTGCAAGTTTAACATTAATTTGATTAAACTCATCATAGTTAATGATTGAGTTGCTAGACT
1 ATCTTTTGCAAGCTGAACATTAATTTGATTAAACTCATCATAGTTAATAATTGAGTTGCTAGACT
41950476 TTATT
66 TTATT
* * * *
41950481 ATCTTTTGCAAGCTGAACTTTAATTTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGACT
1 ATCTTTTGCAAGCTGAACATTAATTTGATTAAACTCATCATAGTTAATAATTGAGTTGCTAGACT
41950546 TTATT
66 TTATT
41950551 A
1 A
41950552 AACTCATCTT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (70 bp):
ATCTTTTGCAAGCTGAACATTAATTTGATTAAACTCATCATAGTTAATAATTGAGTTGCTAGACT
TTATT
Found at i:41950549 original size:40 final size:40
Alignment explanation
Indices: 41950505--41950590 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
41950495 GAACTTTAAT
41950505 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGAC
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGAC
* *
41950545 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGTTGGAT
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGAC
41950585 TTTATT
1 TTTATT
41950591 TTTGTTAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (40 bp):
TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGAC
Found at i:41950688 original size:10 final size:10
Alignment explanation
Indices: 41950673--41950708 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
41950663 AACTTAATAA
41950673 GTGTTTAAAT
1 GTGTTTAAAT
41950683 GTGTTT-AAT
1 GTGTTTAAAT
41950692 GTGTTTTAAAT
1 GTG-TTTAAAT
41950703 GTGTTT
1 GTGTTT
41950709 GATTGTAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 6 0.25
10 12 0.50
11 6 0.25
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (10 bp):
GTGTTTAAAT
Found at i:41950705 original size:11 final size:11
Alignment explanation
Indices: 41950676--41950708 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
41950666 TTAATAAGTG
41950676 TTTAAATGTG-
1 TTTAAATGTGT
41950686 TTT-AATGTGT
1 TTTAAATGTGT
41950696 TTTAAATGTGT
1 TTTAAATGTGT
41950707 TT
1 TT
41950709 GATTGTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.29
10 6 0.29
11 9 0.43
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (11 bp):
TTTAAATGTGT
Found at i:41950861 original size:21 final size:23
Alignment explanation
Indices: 41950807--41950871 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 23
41950797 ATACAAGGGG
*
41950807 CTGTTACATCAATTAAAGGAGAT
1 CTGTTACATCATTTAAAGGAGAT
**
41950830 CACTATACATCATTTAAAGGAG-T
1 CTGT-TACATCATTTAAAGGAGAT
41950853 -TGTTACATCATTTAAAGGA
1 CTGTTACATCATTTAAAGGA
41950872 AAACATTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 16 0.44
22 1 0.03
23 3 0.08
24 16 0.44
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (23 bp):
CTGTTACATCATTTAAAGGAGAT
Found at i:41955129 original size:70 final size:70
Alignment explanation
Indices: 41955016--41955156 Score: 228
Period size: 70 Copynumber: 2.0 Consensus size: 70
41955006 GTCATTTGCA
41955016 ATCTTTTACAAGATAAACTTTAATTTTATTAAACTCATCTTAGTTAATAATTCAGTTGCTGGACT
1 ATCTTTTACAAGATAAACTTTAATTTTATTAAACTCATCTTAGTTAATAATTCAGTTGCTGGACT
41955081 TTATT
66 TTATT
* * * * * *
41955086 ATCTTTTGCAAGCTGAACTTTAATTTTATTAAATTCATCTTAGTTAATAATTGAGTTGTTGGACT
1 ATCTTTTACAAGATAAACTTTAATTTTATTAAACTCATCTTAGTTAATAATTCAGTTGCTGGACT
41955151 TTATT
66 TTATT
41955156 A
1 A
41955157 AACTCATCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (70 bp):
ATCTTTTACAAGATAAACTTTAATTTTATTAAACTCATCTTAGTTAATAATTCAGTTGCTGGACT
TTATT
Found at i:41955154 original size:40 final size:40
Alignment explanation
Indices: 41955110--41955195 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
41955100 GAACTTTAAT
*
41955110 TTTATTAAATTCATCTTAGTTAATAATTGAGTTGTTGGAC
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGTTGGAC
41955150 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGTTGGAC
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGTTGGAC
41955190 TTTATT
1 TTTATT
41955196 TCTATTAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (40 bp):
TTTATTAAACTCATCTTAGTTAATAATTGAGTTGTTGGAC
Found at i:41955299 original size:9 final size:9
Alignment explanation
Indices: 41955278--41955322 Score: 63
Period size: 9 Copynumber: 4.7 Consensus size: 9
41955268 AACTTAATAA
41955278 GTGTTTAAAT
1 GTGTTT-AAT
41955288 GTGTTTAAT
1 GTGTTTAAT
41955297 GTGTTTAAT
1 GTGTTTAAT
41955306 GTGTTTTTAAT
1 GTG--TTTAAT
41955317 GTGTTT
1 GTGTTT
41955323 GATTGTAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 18 0.55
10 6 0.18
11 9 0.27
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.58
Consensus pattern (9 bp):
GTGTTTAAT
Found at i:41955316 original size:11 final size:11
Alignment explanation
Indices: 41955291--41955322 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
41955281 TTTAAATGTG
41955291 TTTAATGTG--
1 TTTAATGTGTT
41955300 TTTAATGTGTT
1 TTTAATGTGTT
41955311 TTTAATGTGTT
1 TTTAATGTGTT
41955322 T
1 T
41955323 GATTGTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
11 12 0.57
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (11 bp):
TTTAATGTGTT
Found at i:41955316 original size:20 final size:19
Alignment explanation
Indices: 41955278--41955322 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
41955268 AACTTAATAA
41955278 GTGTTTAAATGTGTTTAAT
1 GTGTTTAAATGTGTTTAAT
41955297 GTGTTT-AATGTGTTTTTAAT
1 GTGTTTAAATGTG--TTTAAT
41955317 GTGTTT
1 GTGTTT
41955323 GATTGTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.25
19 6 0.25
20 12 0.50
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.58
Consensus pattern (19 bp):
GTGTTTAAATGTGTTTAAT
Found at i:41962540 original size:25 final size:25
Alignment explanation
Indices: 41962512--41962564 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
41962502 AACTGACGAG
* *
41962512 ATTGGTCCAGAAGACTGGATGATGC
1 ATTGGTCCAAAAGACTGGACGATGC
41962537 ATTGGTCCAAAAGACTGGACGATGC
1 ATTGGTCCAAAAGACTGGACGATGC
41962562 ATT
1 ATT
41962565 ATGGGCCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (25 bp):
ATTGGTCCAAAAGACTGGACGATGC
Found at i:41978218 original size:17 final size:18
Alignment explanation
Indices: 41978183--41978220 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
41978173 ATCGTTTCTA
*
41978183 TTTACAAAAACCTTAGTT
1 TTTACAAAAACCATAGTT
*
41978201 TTTAGAAAAACCAT-GTT
1 TTTACAAAAACCATAGTT
41978218 TTT
1 TTT
41978221 GTTGAGTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (18 bp):
TTTACAAAAACCATAGTT
Found at i:41990271 original size:17 final size:17
Alignment explanation
Indices: 41990249--41990305 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
41990239 ACCACAGGGG
41990249 ACACATGGCTGTGTGTC
1 ACACATGGCTGTGTGTC
* *
41990266 ACACATGAC--TGAG--
1 ACACATGGCTGTGTGTC
* *
41990279 ACACATGCCCGTGTGTC
1 ACACATGGCTGTGTGTC
41990296 ACACATGGCT
1 ACACATGGCT
41990306 AAGACACACG
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
13 8 0.27
15 6 0.20
17 16 0.53
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.23
Consensus pattern (17 bp):
ACACATGGCTGTGTGTC
Found at i:41990284 original size:30 final size:30
Alignment explanation
Indices: 41990248--41990322 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
41990238 AACCACAGGG
* *
41990248 GACACATGGCTGTGTGTCACACATGACTGA
1 GACACATGCCTGTGTGTCACACATGACTAA
* *
41990278 GACACATGCCCGTGTGTCACACATGGCTAA
1 GACACATGCCTGTGTGTCACACATGACTAA
*
41990308 GACACACGCCTGTGT
1 GACACATGCCTGTGT
41990323 CTCTGCCCGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.21
Consensus pattern (30 bp):
GACACATGCCTGTGTGTCACACATGACTAA
Found at i:42004344 original size:130 final size:130
Alignment explanation
Indices: 42004110--42004369 Score: 495
Period size: 130 Copynumber: 2.0 Consensus size: 130
42004100 TAGGTTCATT
*
42004110 ACACATGTCATGTTCCCTAGAGAGCAGATCAGTGAAGATAGCAGATCTTATCTCCCTAAGCAGTA
1 ACACATGTCATGTTCCCTAGAGAGCAGATCAGTGAAGATAGAAGATCTTATCTCCCTAAGCAGTA
42004175 GTGGAGCATATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
66 GTGGAGCATATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
42004240 ACACATGTCATGTTCCCTAGAGAGCAGATCAGTGAAGATAGAAGATCTTATCTCCCTAAGCAGTA
1 ACACATGTCATGTTCCCTAGAGAGCAGATCAGTGAAGATAGAAGATCTTATCTCCCTAAGCAGTA
42004305 GTGGAGCATATCGAAGACGGCAAATTCTTATCTTT-CAAGATAGTGGGAAGCAGATTTAAGCCAC
66 GTGGAGCATATCGAAGACGGCAAA-TCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
42004369 C
130 C
42004370 GAACCTTGTT
Statistics
Matches: 128, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
130 118 0.92
131 10 0.08
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (130 bp):
ACACATGTCATGTTCCCTAGAGAGCAGATCAGTGAAGATAGAAGATCTTATCTCCCTAAGCAGTA
GTGGAGCATATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC
Found at i:42004441 original size:88 final size:88
Alignment explanation
Indices: 42004290--42004486 Score: 308
Period size: 88 Copynumber: 2.2 Consensus size: 88
42004280 GAAGATCTTA
* *
42004290 TCTCCCTAAGCAGTAGTGGAGCATATCGAAGACGGCAAATTCTTATCTTTCAAGATAGTGGGAAG
1 TCTCCCTAAGCAGTAGTGGAGCATATCAAAGACGACAAATTCTTATCTTTCAAGATAGTGGGAAG
42004355 CAGATTTAAGCCACCGAA-CCTTG
66 CAGATTTAAGCCACC-AAGCCTTG
*
42004378 TTTCCCTAAGCAGTAGTGGAGCATATCAAAGACGACAAA-TCTTATCTTTCCAAGATAGTGGGAA
1 TCTCCCTAAGCAGTAGTGGAGCATATCAAAGACGACAAATTCTTATCTTT-CAAGATAGTGGGAA
42004442 GCAGATTTAAGCCACCAAGCCTTG
65 GCAGATTTAAGCCACCAAGCCTTG
* * *
42004466 TCTCCTTGAGCAGCAGTGGAG
1 TCTCCCTAAGCAGTAGTGGAG
42004487 TAGGTTGAAA
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
87 12 0.12
88 88 0.88
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (88 bp):
TCTCCCTAAGCAGTAGTGGAGCATATCAAAGACGACAAATTCTTATCTTTCAAGATAGTGGGAAG
CAGATTTAAGCCACCAAGCCTTG
Found at i:42004529 original size:45 final size:45
Alignment explanation
Indices: 42004478--42004618 Score: 126
Period size: 45 Copynumber: 3.2 Consensus size: 45
42004468 TCCTTGAGCA
* * **
42004478 GCAGTGGAGTAGGTTGAAAAT-AGCAGGTCTTATCCCCCTGAGGTT
1 GCAGTGGAGTAGATCGAAAATGA-CAAATCTTATCCCCCTGAGGTT
* * * *
42004523 GCAGTGGGGTAGATCGAAGATGATAAATCTTATCTCCCTGAGGTT
1 GCAGTGGAGTAGATCGAAAATGACAAATCTTATCCCCCTGAGGTT
* * * *
42004568 GCAGTGGAGCAGA-CAGAGAA-GACAAGTCTTATCCCCCTGAAGTT
1 GCAGTGGAGTAGATC-GAAAATGACAAATCTTATCCCCCTGAGGTT
*
42004612 CCAGTGG
1 GCAGTGG
42004619 GCCAGACTGA
Statistics
Matches: 77, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
44 27 0.35
45 49 0.64
46 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (45 bp):
GCAGTGGAGTAGATCGAAAATGACAAATCTTATCCCCCTGAGGTT
Found at i:42004617 original size:44 final size:42
Alignment explanation
Indices: 42004504--42004649 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 42
42004494 AAAATAGCAG
* * *
42004504 GTCTTATCCCCCTGAGGTTGCAGTGGGGTAGATCGAAGATGATAA
1 GTCTTATCCCCCTGAGGTTGCAGT-GGGCAGA-CG-AGAAGACAA
* *
42004549 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAGACAGAGAAGACAA
1 GTCTTATCCCCCTGAGGTTGCAGTGG-GCAGAC-GAGAAGACAA
* * *
42004593 GTCTTATCCCCCTGAAGTTCCAGTGGGCCAGACTGAGAATAGCAA
1 GTCTTATCCCCCTGAGGTTGCAGTGGG-CAGAC-GAGAAGA-CAA
*
42004638 TTCTTACTCCCC
1 GTCTTA-TCCCC
42004650 AGGCGATGCA
Statistics
Matches: 84, Mismatches: 12, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
43 1 0.01
44 43 0.51
45 35 0.42
46 5 0.06
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (42 bp):
GTCTTATCCCCCTGAGGTTGCAGTGGGCAGACGAGAAGACAA
Found at i:42004721 original size:50 final size:50
Alignment explanation
Indices: 42004664--42004825 Score: 164
Period size: 50 Copynumber: 3.2 Consensus size: 50
42004654 GATGCAGTGG
*
42004664 AACAGATTAAAGCCACAA-AGGTGAATCTTGCTTCCCCGACATTGCAGTTA
1 AACAGATTAAAGCTACAACA-GTGAATCTTGCTTCCCCGACATTGCAGTTA
* ** * * * ** * **
42004714 AAAAGATTAAAGCTACAACAGCCAATCTTACTTCCCGGGCGGTGTAGTGG
1 AACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTA
* * **
42004764 AACAGATTGAAGCTACAACAGTGAATCTTGCTTCCTCGACATCACAGTTA
1 AACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTA
42004814 AACAGATTAAAG
1 AACAGATTAAAG
42004826 TTACGAGTTA
Statistics
Matches: 83, Mismatches: 28, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
50 82 0.99
51 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (50 bp):
AACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTA
Found at i:42004812 original size:100 final size:100
Alignment explanation
Indices: 42004639--42004825 Score: 268
Period size: 100 Copynumber: 1.9 Consensus size: 100
42004629 GAATAGCAAT
42004639 TCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAAAGGTGAATCTTGCTTCCCCGAC
1 TCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAAAGGTGAATCTTGCTTCCCCGAC
**
42004704 ATTGCAGTTAAAAAGATTAAAGCTACAACAGCCAA
66 ATCACAGTTAAAAAGATTAAAGCTACAACAGCCAA
* * * * * * *
42004739 TCTTACTTCCCGGGCGGTGTAGTGGAACAGATTGAAGCTACAACA-GTGAATCTTGCTTCCTCGA
1 TCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAA-AGGTGAATCTTGCTTCCCCGA
*
42004803 CATCACAGTTAAACAGATTAAAG
65 CATCACAGTTAAAAAGATTAAAG
42004826 TTACGAGTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
100 75 0.99
101 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (100 bp):
TCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAAAGGTGAATCTTGCTTCCCCGAC
ATCACAGTTAAAAAGATTAAAGCTACAACAGCCAA
Found at i:42005566 original size:26 final size:23
Alignment explanation
Indices: 42005529--42005578 Score: 57
Period size: 23 Copynumber: 2.0 Consensus size: 23
42005519 ACTTTTACAG
42005529 ACAGACAGAGAAAATTACAAAAAAAT
1 ACAGACAGAG-AAA-T-CAAAAAAAT
42005555 ACAG-CAGAAGAAATCAAAAAAAT
1 ACAGACAG-AGAAATCAAAAAAAT
42005578 A
1 A
42005579 AAAAAAGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 10 0.43
24 1 0.04
25 6 0.26
26 6 0.26
ACGTcount: A:0.66, C:0.12, G:0.12, T:0.10
Consensus pattern (23 bp):
ACAGACAGAGAAATCAAAAAAAT
Found at i:42007738 original size:25 final size:25
Alignment explanation
Indices: 42007709--42007827 Score: 111
Period size: 25 Copynumber: 4.8 Consensus size: 25
42007699 TCCTGTACAT
42007709 GTATGCTCATACGAGCTGT-GAATCA
1 GTATGCTCATACGAGCTGTAG-ATCA
* *
42007734 ATATGCCCACT-CGAGCTGTAGAT-A
1 GTATGCTCA-TACGAGCTGTAGATCA
* **
42007758 GGTATGCTC-TCACGAGCTGTAAATTG
1 -GTATGCTCAT-ACGAGCTGTAGATCA
*
42007784 GTATGCTCACACGAGCTGTAGATCA
1 GTATGCTCATACGAGCTGTAGATCA
*
42007809 GTATGCTCACACGAGCTGT
1 GTATGCTCATACGAGCTGT
42007828 GAGTCGGAAC
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
23 1 0.01
24 1 0.01
25 73 0.95
26 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (25 bp):
GTATGCTCATACGAGCTGTAGATCA
Found at i:42007774 original size:50 final size:50
Alignment explanation
Indices: 42007709--42007829 Score: 147
Period size: 50 Copynumber: 2.4 Consensus size: 50
42007699 TCCTGTACAT
*
42007709 GTATGCTCAT-ACGAGCTGTGAATCAATATGCCCACTCGAGCTGTAGAT-A
1 GTATGCTC-TCACGAGCTGTGAATCAATATGCCCACACGAGCTGTAGATCA
* *** *
42007758 GGTATGCTCTCACGAGCTGTAAATTGGTATGCTCACACGAGCTGTAGATCA
1 -GTATGCTCTCACGAGCTGTGAATCAATATGCCCACACGAGCTGTAGATCA
*
42007809 GTATGCTCACACGAGCTGTGA
1 GTATGCTCTCACGAGCTGTGA
42007830 GTCGGAACGT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
49 1 0.02
50 59 0.97
51 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (50 bp):
GTATGCTCTCACGAGCTGTGAATCAATATGCCCACACGAGCTGTAGATCA
Found at i:42009016 original size:17 final size:17
Alignment explanation
Indices: 42008996--42009028 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42008986 TTAATAACCC
42008996 AATTAAATTAATTCTAT
1 AATTAAATTAATTCTAT
*
42009013 AATTAATTTAATTCTA
1 AATTAAATTAATTCTA
42009029 GCGACAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTAAATTAATTCTAT
Found at i:42019918 original size:16 final size:16
Alignment explanation
Indices: 42019897--42019928 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42019887 GTTTTGTTGC
*
42019897 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
42019913 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
42019929 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:42020214 original size:51 final size:50
Alignment explanation
Indices: 42020156--42020447 Score: 208
Period size: 51 Copynumber: 5.8 Consensus size: 50
42020146 CCGGTTCACA
* *
42020156 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGGTACA-G
* * * * *
42020207 TAGTAGCCTACACATAGTACTACACACGTGA--TTGAAGTTATCCGGGTTGCA-
1 TAGTAGCCTACACATAGTACTACACATGTGACCAT-CA-CTATCC-GG-TACAG
* * * * *
42020258 TAGTAGCTTGCACATAGTACTACAGATGCGACCTATCA-T-TCTGGTACATG
1 TAGTAGCCTACACATAGTACTACACATGTGACC-ATCACTATCCGGTACA-G
* * * * *
42020308 TAATAGCCTACACATAGTACTACACACGTGA--TTGAAGCTATCCGGGTTGCA-
1 TAGTAGCCTACACATAGTACTACACATGTGACCAT-CA-CTATCC-GG-TACAG
* * * *
42020359 TAGTAGCCTGCACATAGTACTACAGATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTACACATAGTACTACACATGTGACC-ATCACTATCCGGTACA-G
42020409 TAGTAGCCTACACATAGTACTACACATGTGACCATCACT
1 TAGTAGCCTACACATAGTACTACACATGTGACCATCACT
42020448 TTCACTTTCA
Statistics
Matches: 182, Mismatches: 38, Indels: 43
0.69 0.14 0.16
Matches are distributed among these distances:
47 1 0.01
48 7 0.04
49 9 0.05
50 62 0.34
51 90 0.49
52 3 0.02
53 8 0.04
54 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGGTACAG
Found at i:42020335 original size:101 final size:101
Alignment explanation
Indices: 42020154--42020439 Score: 466
Period size: 101 Copynumber: 2.8 Consensus size: 101
42020144 TACCGGTTCA
* * * *
42020154 CATAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTATCCGATACACGTAGTAGCCTAC
1 CATAGTAGCCTGCACATAGTACTACAGATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTAC
*
42020218 ACATAGTACTACACACGTGATTGAAGTTATCCGGGTTG
64 ACATAGTACTACACACGTGATTGAAGCTATCCGGGTTG
* * *
42020256 CATAGTAGCTTGCACATAGTACTACAGATGCGACCTATCATTCTGGTACATGTAATAGCCTACAC
1 CATAGTAGCCTGCACATAGTACTACAGATGCGACCTATCATTCTGGTACACGTAGTAGCCTACAC
42020321 ATAGTACTACACACGTGATTGAAGCTATCCGGGTTG
66 ATAGTACTACACACGTGATTGAAGCTATCCGGGTTG
42020357 CATAGTAGCCTGCACATAGTACTACAGATGCGACCTATCATTCTGGTACACGTAGTAGCCTACAC
1 CATAGTAGCCTGCACATAGTACTACAGATGCGACCTATCATTCTGGTACACGTAGTAGCCTACAC
*
42020422 ATAGTACTACACATGTGA
66 ATAGTACTACACACGTGA
42020440 CCATCACTTT
Statistics
Matches: 171, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
101 134 0.78
102 33 0.19
103 4 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACAGATGCGACCTATCATTCTGGTACACGTAGTAGCCTACAC
ATAGTACTACACACGTGATTGAAGCTATCCGGGTTG
Found at i:42023575 original size:25 final size:25
Alignment explanation
Indices: 42023547--42023623 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
42023537 TTTTCTCACT
*
42023547 CGAGCTATAGATCGATATGCTCTCA
1 CGAGCTGTAGATCGATATGCTCTCA
* * * *
42023572 CGAGCTGTAAATTGGTATGCTCACA
1 CGAGCTGTAGATCGATATGCTCTCA
42023597 CGAGCTGTAGATC-AGTATGCTCTCA
1 CGAGCTGTAGATCGA-TATGCTCTCA
42023622 CG
1 CG
42023624 CACTCTAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (25 bp):
CGAGCTGTAGATCGATATGCTCTCA
Found at i:42023595 original size:50 final size:50
Alignment explanation
Indices: 42023512--42023774 Score: 148
Period size: 50 Copynumber: 5.2 Consensus size: 50
42023502 CCTGTACATG
* * * * *
42023512 TATGCTCAT-ACGAGCTGTGAATCGGTTTTCTCACTCGAGCTATAGATCGA
1 TATGCTC-TCACGAGCTGTAAATTGGTATGCTCACTCGAGCTGTAGATCGA
*
42023562 TATGCTCTCACGAGCTGTAAATTGGTATGCTCACACGAGCTGTAGATC-A
1 TATGCTCTCACGAGCTGTAAATTGGTATGCTCACTCGAGCTGTAGATCGA
* * * * *
42023611 GTATGCTCTCACGCA-CTCTAACTCATATAACTGTAAT-CT-A-TCAAATCCTGTACAT-G-
1 -TATGCTCTCACG-AGCTGTAA---AT-T---GGT-ATGCTCACTC-GA-GCTGTAGATCGA
* * * * * *
42023667 TATGCTCAT-ACGAGCTGTGAATCGGTTTTCTCACTCGAGCTATAGATCGG
1 TATGCTC-TCACGAGCTGTAAATTGGTATGCTCACTCGAGCTGTAGATCGA
* * * *
42023717 TATGCTCTCACGAGCTATAAATTGGTATGCTCACACGAACTGTAGATCGG
1 TATGCTCTCACGAGCTGTAAATTGGTATGCTCACTCGAGCTGTAGATCGA
42023767 TATGCTCT
1 TATGCTCT
42023775 AACGCACTGT
Statistics
Matches: 162, Mismatches: 29, Indels: 44
0.69 0.12 0.19
Matches are distributed among these distances:
47 1 0.01
48 10 0.06
49 6 0.04
50 107 0.66
51 1 0.01
52 2 0.01
53 2 0.01
54 2 0.01
55 15 0.09
56 3 0.02
57 11 0.07
58 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (50 bp):
TATGCTCTCACGAGCTGTAAATTGGTATGCTCACTCGAGCTGTAGATCGA
Found at i:42023715 original size:25 final size:25
Alignment explanation
Indices: 42023666--42023773 Score: 110
Period size: 25 Copynumber: 4.3 Consensus size: 25
42023656 TCCTGTACAT
* *
42023666 GTATGCTCATACGAGCTGT-GAATCG
1 GTATGCTCACACGAGCTATAG-ATCG
* * *
42023691 GTTTTCTCACTCGAGCTATAGATCG
1 GTATGCTCACACGAGCTATAGATCG
* * *
42023716 GTATGCTCTCACGAGCTATAAATTG
1 GTATGCTCACACGAGCTATAGATCG
* *
42023741 GTATGCTCACACGAACTGTAGATCG
1 GTATGCTCACACGAGCTATAGATCG
42023766 GTATGCTC
1 GTATGCTC
42023774 TAACGCACTG
Statistics
Matches: 66, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
25 65 0.98
26 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (25 bp):
GTATGCTCACACGAGCTATAGATCG
Found at i:42023760 original size:155 final size:155
Alignment explanation
Indices: 42023473--42023782 Score: 575
Period size: 155 Copynumber: 2.0 Consensus size: 155
42023463 ACATTGTGTG
42023473 CTAACTCATATAACTGTAATCTATCAAATCCTGTACATGTATGCTCATACGAGCTGTGAATCGGT
1 CTAACTCATATAACTGTAATCTATCAAATCCTGTACATGTATGCTCATACGAGCTGTGAATCGGT
* *
42023538 TTTCTCACTCGAGCTATAGATCGATATGCTCTCACGAGCTGTAAATTGGTATGCTCACACGAGCT
66 TTTCTCACTCGAGCTATAGATCGATATGCTCTCACGAGCTATAAATTGGTATGCTCACACGAACT
*
42023603 GTAGATCAGTATGCTCTCACGCACT
131 GTAGATCAGTATGCTCTAACGCACT
42023628 CTAACTCATATAACTGTAATCTATCAAATCCTGTACATGTATGCTCATACGAGCTGTGAATCGGT
1 CTAACTCATATAACTGTAATCTATCAAATCCTGTACATGTATGCTCATACGAGCTGTGAATCGGT
*
42023693 TTTCTCACTCGAGCTATAGATCGGTATGCTCTCACGAGCTATAAATTGGTATGCTCACACGAACT
66 TTTCTCACTCGAGCTATAGATCGATATGCTCTCACGAGCTATAAATTGGTATGCTCACACGAACT
*
42023758 GTAGATCGGTATGCTCTAACGCACT
131 GTAGATCAGTATGCTCTAACGCACT
42023783 GTAGGTCGGA
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 150 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (155 bp):
CTAACTCATATAACTGTAATCTATCAAATCCTGTACATGTATGCTCATACGAGCTGTGAATCGGT
TTTCTCACTCGAGCTATAGATCGATATGCTCTCACGAGCTATAAATTGGTATGCTCACACGAACT
GTAGATCAGTATGCTCTAACGCACT
Found at i:42023783 original size:25 final size:24
Alignment explanation
Indices: 42023709--42023791 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 24
42023699 ACTCGAGCTA
* *
42023709 TAGATCGGTATGCTCTCACGAGCTA
1 TAGATCGGTATGCTCTAACGA-CTG
* *
42023734 TAAATTGGTATGCTC-ACACGAACTG
1 TAGATCGGTATGCTCTA-ACG-ACTG
42023759 TAGATCGGTATGCTCTAACGCACTG
1 TAGATCGGTATGCTCTAACG-ACTG
*
42023784 TAGGTCGG
1 TAGATCGG
42023792 AACGTAGCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 45 0.96
26 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (24 bp):
TAGATCGGTATGCTCTAACGACTG
Found at i:42024192 original size:16 final size:17
Alignment explanation
Indices: 42024171--42024205 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42024161 TCAATTTAAC
42024171 CCAAAATCA-TATTTTG
1 CCAAAATCATTATTTTG
*
42024187 CCAAAATTATTATTTTG
1 CCAAAATCATTATTTTG
42024204 CC
1 CC
42024206 CCTATACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (17 bp):
CCAAAATCATTATTTTG
Found at i:42025183 original size:6 final size:6
Alignment explanation
Indices: 42025172--42025215 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
42025162 GGTCGAACCC
42025172 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TT
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TT
42025216 ACATCGATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCCT
Found at i:42025520 original size:35 final size:35
Alignment explanation
Indices: 42025481--42025557 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
42025471 TATCTACTAT
* **
42025481 TCCTTCAAGGTGACATCATGTGGATGATATACAGG
1 TCCTTCAAGGTGACACCATGTAAATGATATACAGG
** * *
42025516 TCCTTCGGGGTGACACCGTGTAAATGATATATAGG
1 TCCTTCAAGGTGACACCATGTAAATGATATACAGG
*
42025551 TTCTTCA
1 TCCTTCA
42025558 GGGCAACTAT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (35 bp):
TCCTTCAAGGTGACACCATGTAAATGATATACAGG
Found at i:42041593 original size:9 final size:9
Alignment explanation
Indices: 42041576--42041621 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
42041566 TGAGTTTTAG
42041576 AATTCGAAT
1 AATTCGAAT
*
42041585 AACTCGAAT
1 AATTCGAAT
42041594 AATTCGAAT
1 AATTCGAAT
42041603 AATTCGAAT
1 AATTCGAAT
42041612 AATTCGAAT
1 AATTCGAAT
42041621 A
1 A
42041622 TCAAACTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42050091 original size:19 final size:19
Alignment explanation
Indices: 42050067--42050137 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
42050057 TATTCATAAA
*
42050067 AAAGGGAGGAAATCAGTGT
1 AAAGGGAGAAAATCAGTGT
*
42050086 AAAGGG-GAAAAGTTAGTGT
1 AAAGGGAGAAAA-TCAGTGT
* * *
42050105 AAAAAGAAAAAAATCAGTGT
1 -AAAGGGAGAAAATCAGTGT
42050125 AAAGGGAGGAAAA
1 AAAGGGA-GAAAA
42050138 AAAATCAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
18 4 0.10
19 17 0.44
20 14 0.36
21 4 0.10
ACGTcount: A:0.52, C:0.03, G:0.31, T:0.14
Consensus pattern (19 bp):
AAAGGGAGAAAATCAGTGT
Found at i:42050137 original size:20 final size:20
Alignment explanation
Indices: 42050067--42050137 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
42050057 TATTCATAAA
42050067 AAAGGGAGG-AAATCAGTGT
1 AAAGGGAGGAAAATCAGTGT
*
42050086 AAA-GG-GGAAAAGTTAGTGT
1 AAAGGGAGGAAAA-TCAGTGT
** **
42050105 AAAAAGAAAAAAATCAGTGT
1 AAAGGGAGGAAAATCAGTGT
42050125 AAAGGGAGGAAAA
1 AAAGGGAGGAAAA
42050138 AAAATCAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
17 2 0.05
18 5 0.13
19 12 0.31
20 16 0.41
21 4 0.10
ACGTcount: A:0.52, C:0.03, G:0.31, T:0.14
Consensus pattern (20 bp):
AAAGGGAGGAAAATCAGTGT
Found at i:42050969 original size:24 final size:24
Alignment explanation
Indices: 42050942--42051056 Score: 96
Period size: 23 Copynumber: 4.9 Consensus size: 24
42050932 TTATTGTATA
*
42050942 TTATTATTTTAGATTTATCATGTT
1 TTATTATTTTAAATTTATCATGTT
* *
42050966 TTATTATTTGT-AATTTATCA-ATA
1 TTATTATTT-TAAATTTATCATGTT
*
42050989 TTATTATTTTAAATTCATC--GTT
1 TTATTATTTTAAATTTATCATGTT
**
42051011 AACATTATTTTAAATTTATCATG-T
1 -TTATTATTTTAAATTTATCATGTT
* *
42051035 ATATTTATTTCAAATTTATCAT
1 TTA-TTATTTTAAATTTATCAT
42051057 TAATATTTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
22 2 0.03
23 35 0.47
24 35 0.47
25 2 0.03
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (24 bp):
TTATTATTTTAAATTTATCATGTT
Found at i:42051062 original size:24 final size:23
Alignment explanation
Indices: 42050904--42051179 Score: 135
Period size: 24 Copynumber: 12.0 Consensus size: 23
42050894 CTTATTATCA
*
42050904 TTAAATTAATCATTAATATTA-T
1 TTAAATTTATCATTAATATTATT
* * ** *
42050926 CTAAGTTTATTGTATATTATTATT
1 TTAAATTTATCAT-TAATATTATT
* **
42050950 TTAGATTTATCATGTTTTATTATT
1 TTAAATTTATCAT-TAATATTATT
* *
42050974 TGT-AATTTATCAATATTATTATT
1 T-TAAATTTATCATTAATATTATT
* * *
42050997 TTAAATTCATCGTTAACATTATT
1 TTAAATTTATCATTAATATTATT
42051020 TTAAATTTATCATGT-ATATTTATT
1 TTAAATTTATCAT-TAATA-TTATT
*
42051044 TCAAATTTATCATTAATA-T-TT
1 TTAAATTTATCATTAATATTATT
* *
42051065 TTAAATTTATTATATACTATTATT
1 TTAAATTTATCAT-TAATATTATT
** *
42051089 TTGGATTTATCA-CATATGATTATT
1 TTAAATTTATCATTA-AT-ATTATT
* * *
42051113 CTAGAA-TTATCATCAA-A-AATT
1 TTA-AATTTATCATTAATATTATT
*
42051134 TTAAATTTTAT-ATGTATTATTATT
1 TTAAA-TTTATCAT-TAATATTATT
* *
42051158 TCAAATTTATTA-T-ATATTATT
1 TTAAATTTATCATTAATATTATT
42051179 T
1 T
42051180 ATTGTAAATT
Statistics
Matches: 191, Mismatches: 43, Indels: 41
0.69 0.16 0.15
Matches are distributed among these distances:
20 2 0.01
21 28 0.15
22 22 0.12
23 54 0.28
24 81 0.42
25 4 0.02
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (23 bp):
TTAAATTTATCATTAATATTATT
Found at i:42051190 original size:69 final size:68
Alignment explanation
Indices: 42051014--42051192 Score: 175
Period size: 69 Copynumber: 2.6 Consensus size: 68
42051004 CATCGTTAAC
* * * *
42051014 ATTATTTTAAATTTATCATGTA-TATTTATTTCAAATTTATCATTAATATTTTTAAATTTATTAT
1 ATTATTTTAAATTTATCATATATTATTTATTT-AAA-TTATCATCAAAAATTTTAAATTTATTAT
42051078 ATACT
64 ATACT
** * *
42051083 ATTATTTTGGATTTATCACATATGA-TTATTCTAGAATTATCATCAAAAATTTTAAATTT-TATA
1 ATTATTTTAAATTTATCATATATTATTTATT-TA-AATTATCATCAAAAATTTTAAATTTAT-TA
* *
42051146 TGTATT
63 TATACT
* *
42051152 ATTATTTCAAATTTATTATATATTATTTATTGTAAATTATC
1 ATTATTTTAAATTTATCATATATTATTTATT-TAAATTATC
42051193 CAATTCATTT
Statistics
Matches: 88, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
68 1 0.01
69 76 0.86
70 11 0.12
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (68 bp):
ATTATTTTAAATTTATCATATATTATTTATTTAAATTATCATCAAAAATTTTAAATTTATTATAT
ACT
Found at i:42051191 original size:24 final size:23
Alignment explanation
Indices: 42051133--42051191 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 23
42051123 CATCAAAAAT
42051133 TTTAAATT-TTATATGTATTATTA
1 TTTAAATTATTATA-GTATTATTA
42051156 TTTCAAATTTATTATA-TATTATTTA
1 TTT-AAA-TTATTATAGTATTA-TTA
42051181 TTGTAAATTAT
1 TT-TAAATTAT
42051192 CCAATTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
23 3 0.10
24 12 0.39
25 10 0.32
26 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (23 bp):
TTTAAATTATTATAGTATTATTA
Found at i:42051280 original size:23 final size:23
Alignment explanation
Indices: 42051238--42051282 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42051228 AATTGTACAT
*
42051238 TCATATATATTATTTGTTTTAAC
1 TCATATATATTATTTATTTTAAC
42051261 TCATATATA-TAGTTTATTTTAA
1 TCATATATATTA-TTTATTTTAA
42051283 AATTTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (23 bp):
TCATATATATTATTTATTTTAAC
Found at i:42054692 original size:22 final size:22
Alignment explanation
Indices: 42054667--42054709 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42054657 AAAAAAAGAG
42054667 AAAAAAACATCAAAATCAAAAT
1 AAAAAAACATCAAAATCAAAAT
**
42054689 AAAAAGTCATCAAAATCAAAA
1 AAAAAAACATCAAAATCAAAA
42054710 ATGAAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.70, C:0.14, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAAAAACATCAAAATCAAAAT
Found at i:42057056 original size:44 final size:44
Alignment explanation
Indices: 42057001--42057759 Score: 439
Period size: 44 Copynumber: 17.6 Consensus size: 44
42056991 AAACCAATCC
* * *
42057001 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
* * * * *
42057045 TATCTATCTGAAGTTGCAGTAGAGCAGA-TCACATC-TAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
* * * *
42057086 CATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAC-CA-ATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATT-AA-AATCACAGATCT
* *
42057130 TATCTC-CTTGAAGTTGCAGTGGAGCGGATTAAAA-CATAGATCT
1 TATCTCTC-TGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
* * ***
42057173 TATCTCTCTGAAGTTGTAG-AGAGCAGA-TCGCATC-CAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
* * * ***
42057213 TATCTCTTTGAAGTTGCAGTGGGGCAGACTAAAGAT-GGTGAATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAA-ATCACAG-ATCT
* * * * * ** * *
42057258 TATATCCCTAAAGTTGCAGCGGAGCAGATTGAAGCCA-ATAATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACA-GATCT
* *
42057302 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGC-TAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAAT-CACAGATCT
* * *
42057346 TATCTCTCTGAAGTTGCAGTAGAGCAGA-TCACATC-CAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
* * * *
42057387 TATCTCCCTGAAGTTGCAGTAGAGCAGACTGAATAAAC-CA-ATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA-TTAA-AATCACAGATCT
* * *
42057431 TATCTC-CTTGAAGTTGCAGTGGAGCAGATTGAATAA-AATA-ATCC
1 TATCTCTC-TGAAGTTGCAGTGGAGCAGATT-AA-AATCACAGATCT
* * * **
42057475 TATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAGTGATGGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
* * * *** *
42057519 TATCTCTCCGAAGTTGTAGTAGAGCAGA-TCGCAT--CAGGTCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
* ** *
42057560 TATCT-TCCTAAAGTTGCAGTGGAGCAGA-CGAAATAAACCA-ATCT
1 TATCTCT-CTGAAGTTGCAGTGGAGCAGATTAAAAT-CA-CAGATCT
* * * *
42057604 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAAAAATC-
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
* * * * **
42057647 TATCTCTCTGAAGTTGCAGTGAATCAGATCAAAATGATGGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
* * ****
42057691 TATCTCTCTGAAGTTGCAGTAGAGAAGATCGCTA-CA-AG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
* *
42057732 TATCTCGCTGAAGTTGTAGTGGAGCAGA
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA
42057760 CTGAAGATAG
Statistics
Matches: 549, Mismatches: 128, Indels: 79
0.73 0.17 0.10
Matches are distributed among these distances:
40 21 0.04
41 123 0.22
42 19 0.03
43 79 0.14
44 271 0.49
45 36 0.07
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCT
Found at i:42057457 original size:173 final size:173
Alignment explanation
Indices: 42057087--42057764 Score: 859
Period size: 173 Copynumber: 3.9 Consensus size: 173
42057077 ATCTAGTCTC
* *
42057087 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-AAACCAATCCTATCTCCTTGAAGTTGCAGTG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAAA-TAATCCTATCTCCCTGAAGTTGCAGTG
* * *
42057151 GAGCGGATTAAAA-CATAGATCTTATCTCTCTGAAGTTGTAG-AGAGCAGATCGCATCCAGTCTT
65 GAGCAGATTAAAATGATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTT
** * * * ****
42057214 ATCTCTTTGAAGTTGCAGTGGGGCAGACTAAAGATGGTGAATCTT
130 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATA-AACCAATCTT
* * * *
42057259 ATATCCCTAAAGTTGCAGCGGAGCAGATTGAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAAATAATCCTATCTCCCTGAAGTTGCAGTGG
* *
42057324 AGCAGATTAAAATGCTAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAGTCTTA
66 AGCAGATTAAAATGATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTA
*
42057389 TCTCCCTGAAGTTGCAGTAGAGCAGACTGAATAAACCAATCTT
131 TCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAAACCAATCTT
* ** *
42057432 ATCTCCTTGAAGTTGCAGTGGAGCAGATTGAATAAAATAATCCTATCTCTCTGAAGTTGCAGTGG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAAATAATCCTATCTCCCTGAAGTTGCAGTGG
* * * * *
42057497 AGCGGATTAAAGTGATGGATCTTATCTCTCCGAAGTTGTAGTAGAGCAGATCGCAT-CAGGTCTT
66 AGCAGATTAAAATGATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCA-GTCTT
* *
42057561 ATCTTCCTAAAGTTGCAGTGGAGCAGAC-GAAATAAACCAATCTT
130 ATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AATAAACCAATCTT
* * *
42057605 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAAA-AAT-CTATCTCTCTGAAGTTGCAGTG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATT-GAAGCAAATAATCCTATCTCCCTGAAGTTGCAGTG
* * * * * *
42057668 AATCAGATCAAAATGATGGATCTTATCTCTCTGAAGTTGCAGTAGAGAAGATCGC-TACAAGTCT
65 GAGCAGATTAAAATGATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCAT-CCAGTCT
* *
42057732 TATCTCGCTGAAGTTGTAGTGGAGCAGACTGAA
129 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA
42057765 GATAGCAAAT
Statistics
Matches: 441, Mismatches: 56, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
171 1 0.00
172 170 0.39
173 216 0.49
174 54 0.12
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (173 bp):
ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAAATAATCCTATCTCCCTGAAGTTGCAGTGG
AGCAGATTAAAATGATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTA
TCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAAACCAATCTT
Found at i:42057561 original size:129 final size:125
Alignment explanation
Indices: 42057001--42057636 Score: 359
Period size: 129 Copynumber: 4.9 Consensus size: 125
42056991 AAACCAATCC
* * * * * * *
42057001 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTATCTGAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTAGAGCAGACT-GAA-TACA-ATCTTATCT-CCTGAAGTTGCAGTG
* * * * * *
42057066 GAGCAGA-TCACAT---CTAGTCTCATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAA
62 GAGCAGATTGA-ATAAACTAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATT--A-AATCCAG
*
42057127 TCC
123 TCT
* * * * * * *
42057130 TATCTCCTTGAAGTTGCAGTGGAGCGGA-TTAAAACATAGATCTTATCTCTCTGAAGTTGTAG-A
1 TATCTCCCTGAAGTTGCAGTAGAGCAGACTGAATAC--A-ATCTTATCTC-CTGAAGTTGCAGTG
* * * * * * * ** *
42057193 GAGCAGATCGCAT---CCAGTCTTATCTCTTTGAAGTTGCAGTGGGGCAGACTAAAGATGGTGAA
62 GAGCAGATTGAATAAACTAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGA-TTAA-AT--CCAG
42057255 TCT
123 TCT
* * ** * * * *
42057258 TATATCCCTAAAGTTGCAGCGGAGCAGATTGAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTAGAGCAGACTGAA---TACAATCTTATCT-CCTGAAGTTGCAGTG
* * * *
42057323 GAGCAGATT-AA-AATGCTAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAGTC
62 GAGCAGATTGAATAA-ACTA-ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAATCCAGTC
42057386 T
125 T
42057387 TATCTCCCTGAAGTTGCAGTAGAGCAGACTGAATAAACCAATCTTATCTCCTTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAT--A-CAATCTTATCTCC-TGAAGTTGCAGTG
* * * *
42057452 GAGCAGATTGAATAAAATAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAGT-GATGGA
62 GAGCAGATTGAATAAACTAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAA-TCCA--G-
42057516 TCT
123 TCT
* * * *
42057519 TATCTCTCC-GAAGTTGTAGTAGAGCAGA-TCGCAT-CAGGTCTTATCTTCCTAAAGTTGCAGTG
1 TATCTC-CCTGAAGTTGCAGTAGAGCAGACT-GAATACA-ATCTTATC-TCCTGAAGTTGCAGTG
* * *
42057581 GAGCAGA-CGAAATAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
62 GAGCAGATTG-AATAAACTAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAA
42057637 ACCAAAAATC
Statistics
Matches: 407, Mismatches: 66, Indels: 68
0.75 0.12 0.13
Matches are distributed among these distances:
125 1 0.00
126 4 0.01
127 42 0.10
128 57 0.14
129 213 0.52
130 18 0.04
131 6 0.01
132 36 0.09
133 30 0.07
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (125 bp):
TATCTCCCTGAAGTTGCAGTAGAGCAGACTGAATACAATCTTATCTCCTGAAGTTGCAGTGGAGC
AGATTGAATAAACTAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAATCCAGTCT
Found at i:42058196 original size:19 final size:19
Alignment explanation
Indices: 42058172--42058237 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 19
42058162 TATTCATAAA
*
42058172 AAAGGGAGGAAATCAGTGT
1 AAAGGGAGAAAATCAGTGT
42058191 AAAGGG-GAAAAGTCAGTGT
1 AAAGGGAGAAAA-TCAGTGT
* *
42058210 AAAGAGAAAAAAATCAGTGT
1 AAAG-GGAGAAAATCAGTGT
42058230 AAAGGGAG
1 AAAGGGAG
42058238 GGAAAAAGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 4 0.10
19 19 0.49
20 12 0.31
21 4 0.10
ACGTcount: A:0.48, C:0.05, G:0.33, T:0.14
Consensus pattern (19 bp):
AAAGGGAGAAAATCAGTGT
Done.