Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 104 of 109
Found at i:33229854 original size:45 final size:45
Alignment explanation
Indices: 33229777--33229876 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 45
33229767 GTTTAACTAA
* *
33229777 AAAAATATAAAGTTTAGAAATTGAGAAATTGAAAAG-TAAAATTTG
1 AAAAATATGAAGTCTAGAAATTGAGAAATTGAAAAGTTAAAA-TTG
* * * *
33229822 AAAAATATGAAGTCTAGATATTGA-AATTTTGAAATGTTCAAATTG
1 AAAAATATGAAGTCTAGAAATTGAGAA-ATTGAAAAGTTAAAATTG
33229867 AAAAAT-TGAA
1 AAAAATATGAA
33229877 AATAAAAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
44 6 0.13
45 37 0.79
46 4 0.09
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (45 bp):
AAAAATATGAAGTCTAGAAATTGAGAAATTGAAAAGTTAAAATTG
Found at i:33229923 original size:10 final size:10
Alignment explanation
Indices: 33229894--33229932 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
33229884 AACAAAGTAT
33229894 ATAAATTTTA
1 ATAAATTTTA
33229904 GATAAATTTTA
1 -ATAAATTTTA
*
33229915 ATAATTTTTA
1 ATAAATTTTA
*
33229925 AAAAATTT
1 ATAAATTT
33229933 CAAATAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (10 bp):
ATAAATTTTA
Found at i:33236812 original size:21 final size:22
Alignment explanation
Indices: 33236713--33236851 Score: 87
Period size: 21 Copynumber: 6.6 Consensus size: 22
33236703 TTCCGTGTTT
*
33236713 GCTTTCAGTTTAGCTCTTATGA
1 GCTTTCAGTTTAACTCTTATGA
**
33236735 GC-TT-AAATTAACT-TATATGA
1 GCTTTCAGTTTAACTCT-TATGA
* *
33236755 G-TTTCAGTTTAACCCTTTTGA
1 GCTTTCAGTTTAACTCTTATGA
* * *
33236776 G-TTTCAATTTAGCTCTTTTGA
1 GCTTTCAGTTTAACTCTTATGA
33236797 GCTTT-AGTTTAACTCTTAT-A
1 GCTTTCAGTTTAACTCTTATGA
* * * * *
33236817 GGTTTCCGTTCAGCTTTTATGA
1 GCTTTCAGTTTAACTCTTATGA
*
33236839 GC-TTCCGTTTAAC
1 GCTTTCAGTTTAAC
33236852 CTTTATGGGT
Statistics
Matches: 89, Mismatches: 21, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
19 1 0.01
20 19 0.21
21 61 0.69
22 8 0.09
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (22 bp):
GCTTTCAGTTTAACTCTTATGA
Found at i:33236879 original size:42 final size:42
Alignment explanation
Indices: 33236750--33236879 Score: 111
Period size: 42 Copynumber: 3.1 Consensus size: 42
33236740 AATTAACTTA
* * * **
33236750 TATGAGTTTCAGTTTAACCCTT-TTGAGTTTCAATTTAGCTCT
1 TATGAGCTTCAGTTTAACTCTTATAG-GTTTCCGTTTAGCTCT
* * * *
33236792 TTTGAGCTTTAGTTTAACTCTTATAGGTTTCCGTTCAGCTTT
1 TATGAGCTTCAGTTTAACTCTTATAGGTTTCCGTTTAGCTCT
* * * *
33236834 TATGAGCTTCCGTTTAAC-CTTTATGGGTTTTCGTTTAGCACT
1 TATGAGCTTCAGTTTAACTC-TTATAGGTTTCCGTTTAGCTCT
33236876 TATG
1 TATG
33236880 TGGAACCTTT
Statistics
Matches: 69, Mismatches: 17, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
41 1 0.01
42 66 0.96
43 2 0.03
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACTCTTATAGGTTTCCGTTTAGCTCT
Found at i:33238088 original size:22 final size:24
Alignment explanation
Indices: 33238058--33238102 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
33238048 CTATCAAAAT
33238058 ATCAAATC-TCT-AAGATTACATA
1 ATCAAATCTTCTAAAGATTACATA
*
33238080 ATCATATCTTCTAAAGATTACAT
1 ATCAAATCTTCTAAAGATTACAT
33238103 TTAATATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 10 0.50
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (24 bp):
ATCAAATCTTCTAAAGATTACATA
Found at i:33245860 original size:83 final size:85
Alignment explanation
Indices: 33245706--33245875 Score: 247
Period size: 83 Copynumber: 2.0 Consensus size: 85
33245696 CAACCAGTGA
* *
33245706 TGAATTGACGGATAAGTCCATGGTGGATCCATGGCAAAATGTGAAAATTAGGTATGGTGTTTCAA
1 TGAATTGACGGATAAGTCCATGGTGGATCCATGACAAAATGTGAAAAGTAGGTATGGTGTTTCAA
*
33245771 TTAAGAAAACCAT-CTGAGT
66 TGAAGAAAACCATACTGAGT
* **
33245790 TGAATTGACGGATAAGTCCATGGTGGAT-CAT-ACTGAGTTGTGAAAAGTAGGTATGGTGTTTCA
1 TGAATTGACGGATAAGTCCATGGTGGATCCATGAC-AAAATGTGAAAAGTAGGTATGGTGTTTCA
*
33245853 GTGAAGAAAACCATACTGAGT
65 ATGAAGAAAACCATACTGAGT
33245874 TG
1 TG
33245876 TGAAAAGTAG
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
82 1 0.01
83 40 0.52
84 36 0.47
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (85 bp):
TGAATTGACGGATAAGTCCATGGTGGATCCATGACAAAATGTGAAAAGTAGGTATGGTGTTTCAA
TGAAGAAAACCATACTGAGT
Found at i:33245885 original size:46 final size:46
Alignment explanation
Indices: 33245818--33246012 Score: 345
Period size: 46 Copynumber: 4.2 Consensus size: 46
33245808 CATGGTGGAT
33245818 CATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAAC
1 CATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAAC
33245864 CATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAAC
1 CATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAAC
*
33245910 CATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAAC
1 CATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAAC
* * * *
33245956 CATACTGAGTTGTAAAAAGTAGGTATGGTATTTCCGTGAATAAAAC
1 CATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAAC
33246002 CATACTGAGTT
1 CATACTGAGTT
33246013 ATAGCATTGT
Statistics
Matches: 143, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 143 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (46 bp):
CATACTGAGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAAC
Found at i:33249820 original size:175 final size:175
Alignment explanation
Indices: 33249524--33249874 Score: 641
Period size: 175 Copynumber: 2.0 Consensus size: 175
33249514 ACTTGAAATA
33249524 TTTTGGTATATATATGAAATGAATTAATGAAACTATACGTATGTTTGCAAATATGGTTGGTAAGT
1 TTTTGGTATATATATGAAATGAATTAATGAAACTATACGTATGTTTGCAAATATGGTTGGTAAGT
33249589 TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCATTTTGACACCAAATG
66 TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCATTTTGACACCAAATG
*
33249654 TAATAG-TCTTATACCGGGTCTGTACGATTAGACCAGGTATAGGGT
131 TAATAGCT-TTATACCGGGTCTGTACAATTAGACCAGGTATAGGGT
*
33249699 TTTTGGTATATATATTAAATGAATTAATGAAACTATACGTATGTTTGCAAATATGGTTGGTAAGT
1 TTTTGGTATATATATGAAATGAATTAATGAAACTATACGTATGTTTGCAAATATGGTTGGTAAGT
* *
33249764 TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGTTATAACCGTTTTGACACCAAATG
66 TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCATTTTGACACCAAATG
*
33249829 TAATAGCTTTATACTGGGTCTGTACAATTAGACCAGGTATAGGGT
131 TAATAGCTTTATACCGGGTCTGTACAATTAGACCAGGTATAGGGT
33249874 T
1 T
33249875 GTTACAGGTC
Statistics
Matches: 170, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
175 169 0.99
176 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (175 bp):
TTTTGGTATATATATGAAATGAATTAATGAAACTATACGTATGTTTGCAAATATGGTTGGTAAGT
TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCATTTTGACACCAAATG
TAATAGCTTTATACCGGGTCTGTACAATTAGACCAGGTATAGGGT
Found at i:33252131 original size:7 final size:7
Alignment explanation
Indices: 33252119--33252148 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
33252109 TTGCTAAAAA
33252119 GTTTAGG
1 GTTTAGG
33252126 GTTTAGG
1 GTTTAGG
33252133 GTTTAGG
1 GTTTAGG
33252140 GTTTAGG
1 GTTTAGG
33252147 GT
1 GT
33252149 AAGAATTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:33256234 original size:2 final size:2
Alignment explanation
Indices: 33256227--33256256 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33256217 GTTTGATAAG
33256227 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33256257 GTATTTATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33256467 original size:2 final size:2
Alignment explanation
Indices: 33256462--33256497 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
33256452 ACACACAGAG
33256462 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33256498 TTGTATGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33257904 original size:24 final size:26
Alignment explanation
Indices: 33257868--33257919 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
33257858 TTTCTTACTT
* *
33257868 AAACATAATAAATATTAT-TATATTA
1 AAACATAAAAAATATTATAAATATTA
*
33257893 AAAC-TAAAAAATTTTATAAATATTA
1 AAACATAAAAAATATTATAAATATTA
33257918 AA
1 AA
33257920 TCACACTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (26 bp):
AAACATAAAAAATATTATAAATATTA
Found at i:33259223 original size:24 final size:26
Alignment explanation
Indices: 33259187--33259238 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
33259177 TTTCTTACTT
* *
33259187 AAACATAATAAATATTAT-TATATTA
1 AAACATAAAAAATATTATAAATATTA
*
33259212 AAAC-TAAAAAATTTTATAAATATTA
1 AAACATAAAAAATATTATAAATATTA
33259237 AA
1 AA
33259239 TCACACTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (26 bp):
AAACATAAAAAATATTATAAATATTA
Found at i:33260542 original size:24 final size:26
Alignment explanation
Indices: 33260506--33260557 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
33260496 TTTCTTACTT
* *
33260506 AAACATAATAAATATTAT-TATATTA
1 AAACATAAAAAATATTATAAATATTA
*
33260531 AAAC-TAAAAAATTTTATAAATATTA
1 AAACATAAAAAATATTATAAATATTA
33260556 AA
1 AA
33260558 TCACACTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (26 bp):
AAACATAAAAAATATTATAAATATTA
Found at i:33261861 original size:24 final size:26
Alignment explanation
Indices: 33261825--33261876 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
33261815 TTTCTTACTT
* *
33261825 AAACATAATAAATATTAT-TATATTA
1 AAACATAAAAAATATTATAAATATTA
*
33261850 AAAC-TAAAAAATTTTATAAATATTA
1 AAACATAAAAAATATTATAAATATTA
33261875 AA
1 AA
33261877 TCACACTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (26 bp):
AAACATAAAAAATATTATAAATATTA
Found at i:33262677 original size:12 final size:13
Alignment explanation
Indices: 33262655--33262685 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
33262645 TCACAAGAAA
33262655 GAATATTGAATTT
1 GAATATTGAATTT
33262668 GAAT-TTGAATTT
1 GAATATTGAATTT
33262680 GAATAT
1 GAATAT
33262686 GTTCTTACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (13 bp):
GAATATTGAATTT
Found at i:33264634 original size:24 final size:21
Alignment explanation
Indices: 33264601--33264643 Score: 59
Period size: 24 Copynumber: 1.9 Consensus size: 21
33264591 TGTCATGTCA
33264601 TTTTTAATTAATATCTTAAATGT
1 TTTTTAATTAA-AT-TTAAATGT
33264624 TTTTATAATTAAATTTAAAT
1 TTTT-TAATTAAATTTAAAT
33264644 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 6 0.32
24 7 0.37
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTTAATTAAATTTAAATGT
Found at i:33265914 original size:21 final size:21
Alignment explanation
Indices: 33265880--33265920 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
33265870 CGCCAACTAA
**
33265880 TTATTAAATCAATTAATTATT
1 TTATTAAAAAAATTAATTATT
*
33265901 TTATTAAAAAAATTATTTAT
1 TTATTAAAAAAATTAATTAT
33265921 GAATATTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATTAAAAAAATTAATTATT
Found at i:33300349 original size:20 final size:20
Alignment explanation
Indices: 33300326--33300365 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
33300316 GATAAATAAT
33300326 AAATAT-AAGAGAAGCTTTTG
1 AAATATGAAGAGAAG-TTTTG
33300346 AAATATGAAGAGAAGTTTTG
1 AAATATGAAGAGAAGTTTTG
33300366 GTACGTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.30
Consensus pattern (20 bp):
AAATATGAAGAGAAGTTTTG
Found at i:33305128 original size:14 final size:15
Alignment explanation
Indices: 33305089--33305128 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
33305079 ATCAATAAAT
*
33305089 AATTTAAAAATTATA
1 AATTCAAAAATTATA
33305104 AATTCAAAAAATTA-A
1 AATTC-AAAAATTATA
33305119 AATTCAAAAA
1 AATTCAAAAA
33305129 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 10 0.43
16 8 0.35
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTCAAAAATTATA
Found at i:33305129 original size:15 final size:16
Alignment explanation
Indices: 33305094--33305130 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
33305084 TAAATAATTT
33305094 AAAAATTATAAATTCA
1 AAAAATTATAAATTCA
33305110 AAAAATTA-AAATTCA
1 AAAAATTATAAATTCA
33305125 AAAAAT
1 AAAAAT
33305131 ATTAAAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAATTATAAATTCA
Found at i:33307050 original size:3 final size:3
Alignment explanation
Indices: 33307042--33307075 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
33307032 TTCCTGTTAC
33307042 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
33307076 GATATCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:33309136 original size:17 final size:17
Alignment explanation
Indices: 33309103--33309137 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
33309093 TAACCGGTTC
* *
33309103 AATTAAAAATTATTAAA
1 AATTAAAAATAAATAAA
33309120 AATTAAAAATAAATAAA
1 AATTAAAAATAAATAAA
33309137 A
1 A
33309138 TAAATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATTAAAAATAAATAAA
Found at i:33316087 original size:42 final size:42
Alignment explanation
Indices: 33316034--33316117 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 42
33316024 ACCAAAAATT
33316034 TATTTTAAAAATTAAAACAAAATT-AAAAGTATTTTAATAAAAA
1 TATTTTAAAAATTAAAA-AAAATTAAAAAGTATTTTAA-AAAAA
33316077 TATTTT-AAAATTAAAAAAAATTAAAAAAGTATTTTAAAAAA
1 TATTTTAAAAATTAAAAAAAATT-AAAAAGTATTTTAAAAAA
33316118 TTTAAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
41 6 0.15
42 14 0.36
43 19 0.49
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (42 bp):
TATTTTAAAAATTAAAAAAAATTAAAAAGTATTTTAAAAAAA
Found at i:33323831 original size:134 final size:136
Alignment explanation
Indices: 33323681--33323952 Score: 530
Period size: 134 Copynumber: 2.0 Consensus size: 136
33323671 ACTCACTTAC
33323681 TTTCCCTCTAATAAAAAAATTATTTGACCATTTAATTTTTAAGCAAATTTTAATTTAATGTAAAT
1 TTTCCCTCTAATAAAAAAATTATTTGACCATTTAATTTTTAAGCAAATTTTAATTTAATGTAAAT
33323746 GTATGTCACATTAATAATTAATTATTTTTTAAAATTAAAAAATATATTTTTATATTTTTT-A-AA
66 GTATGTCACATTAATAATTAATTATTTTTTAAAATTAAAAAATATATTTTTATATTTTTTAATAA
33323809 TATTAA
131 TATTAA
33323815 TTTCCCTCTAATAAAAAAATTATTTGACCATTTAATTTTTAAGCAAATTTTAATTTAATGTAAAT
1 TTTCCCTCTAATAAAAAAATTATTTGACCATTTAATTTTTAAGCAAATTTTAATTTAATGTAAAT
33323880 GTATGTCACATTAATAATTAATTATTTTTTAAAATTAAAAAATATATTTTTATATTTTTTAATAA
66 GTATGTCACATTAATAATTAATTATTTTTTAAAATTAAAAAATATATTTTTATATTTTTTAATAA
33323945 TATTAA
131 TATTAA
33323951 TT
1 TT
33323953 AATGTGATTT
Statistics
Matches: 136, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
134 125 0.92
135 1 0.01
136 10 0.07
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.48
Consensus pattern (136 bp):
TTTCCCTCTAATAAAAAAATTATTTGACCATTTAATTTTTAAGCAAATTTTAATTTAATGTAAAT
GTATGTCACATTAATAATTAATTATTTTTTAAAATTAAAAAATATATTTTTATATTTTTTAATAA
TATTAA
Found at i:33325385 original size:26 final size:25
Alignment explanation
Indices: 33325309--33325388 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
33325299 ATTATTATTG
*
33325309 TTAAATTATATTTAATAATAATTTTA
1 TTAAATTATATTT-ATAATAATCTTA
* *
33325335 TTAAAATATGA-TTA-AAT-TTCTTA
1 TTAAATTAT-ATTTATAATAATCTTA
*
33325358 TTAAATTATATTTAGTAATAATCCTA
1 TTAAATTATATTTA-TAATAATCTTA
33325384 TTAAA
1 TTAAA
33325389 ATTTAATAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
22 1 0.02
23 15 0.35
24 3 0.07
25 4 0.09
26 19 0.44
27 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (25 bp):
TTAAATTATATTTATAATAATCTTA
Found at i:33332635 original size:94 final size:94
Alignment explanation
Indices: 33332531--33332714 Score: 305
Period size: 94 Copynumber: 2.0 Consensus size: 94
33332521 TAATTGAGAA
*
33332531 AAAAAAGTACCTGCTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGGAAGCG
1 AAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGGAAGCG
33332596 CACAGAGGCAATGAAAGAGGAAGCATGAG
66 CACAGAGGCAATGAAAGAGGAAGCATGAG
* ** *
33332625 AAAAAGGTACCTACTGCAAGAATGGTATTGCCAGCTCTAGAACTTCAAAAACAAAAAGGGAAGCG
1 AAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGGAAGCG
**
33332690 CGTAGAGGCAATGAAAGAGGAAGCA
66 CACAGAGGCAATGAAAGAGGAAGCA
33332715 CTCAGGCTAA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 83 1.00
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (94 bp):
AAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGGAAGCG
CACAGAGGCAATGAAAGAGGAAGCATGAG
Found at i:33337377 original size:24 final size:24
Alignment explanation
Indices: 33337350--33337444 Score: 68
Period size: 24 Copynumber: 3.9 Consensus size: 24
33337340 GAGTTATCCG
33337350 TTAAGCTTGCATGAGCTTTCTGAT
1 TTAAGCTTGCATGAGCTTTCTGAT
*
33337374 TTAAGATCTT--ATGAGCTTTCTGTT
1 TTAAG--CTTGCATGAGCTTTCTGAT
* * * *
33337398 ATTAAGCCTGGATAAGCTTTCCGAT
1 -TTAAGCTTGCATGAGCTTTCTGAT
** **
33337423 ACAAGCTCACATGAGCTTTCTG
1 TTAAGCTTGCATGAGCTTTCTG
33337445 TTATTTGGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
23 2 0.04
24 32 0.60
25 16 0.30
26 3 0.06
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (24 bp):
TTAAGCTTGCATGAGCTTTCTGAT
Found at i:33338778 original size:199 final size:199
Alignment explanation
Indices: 33338428--33338864 Score: 653
Period size: 199 Copynumber: 2.2 Consensus size: 199
33338418 TCGTGTGTGA
* *
33338428 CACACAGCCTAGCACATGGG-AGTGTGATTTGGTCGTGTGTCCCCTGTATCTTTAAAATTGCAAA
1 CACACAGCTTAGCACATGGGCA-TGTGGTTTGGTCGTGTGTCCCCTGTATCTTTAAAATTGCAAA
33338492 ACAAAATGCTCAAGTATTTTCACACGAGCAGGCACACGGACGTCTGTCTCAGTCGTATATGGCAC
65 ACAAAATGCTCAAGTATTTTCACACGAGCAGGCACACGGACGTCTGTCTCAGTCGTATATGGCAC
* * * * *
33338557 ACGACCTGGTACACGGGCGTGTGACTTGACCGTGTGGCTCCTGCACCTAATTAATGTAAATTAAA
130 ACGACCTGGCACACGAGCGTGTGACTTGACCATGTGGCTCCTACACCTAATTAAAGTAAATTAAA
*
33338622 TTATT
195 ATATT
* * *
33338627 CACACAACTTAGCACATGGGCATGTGGTTTGGTCGTGTGTCTCTTGTATCTTTAAAATTGCAAAA
1 CACACAGCTTAGCACATGGGCATGTGGTTTGGTCGTGTGTCCCCTGTATCTTTAAAATTGCAAAA
* * * * * *
33338692 CATAATGTTCAGGTATTTTCACATGGGCAGGCACACGGACGTCTGTCTCAGTCGTATGTGGCACA
66 CAAAATGCTCAAGTATTTTCACACGAGCAGGCACACGGACGTCTGTCTCAGTCGTATATGGCACA
*
33338757 CGGCCTGGCACACGAGCGTGTGACTTGACCATGTGGCTCCTACACCTAATTAAAGTAAATTAAAA
131 CGACCTGGCACACGAGCGTGTGACTTGACCATGTGGCTCCTACACCTAATTAAAGTAAATTAAAA
*
33338822 TGTT
196 TATT
* *
33338826 CACACAGCTTAGCACACT-AGCATGTGGTTTGGCCGTGTG
1 CACACAGCTTAGCACA-TGGGCATGTGGTTTGGTCGTGTG
33338865 ACCCAAGTCT
Statistics
Matches: 214, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
199 212 0.99
200 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (199 bp):
CACACAGCTTAGCACATGGGCATGTGGTTTGGTCGTGTGTCCCCTGTATCTTTAAAATTGCAAAA
CAAAATGCTCAAGTATTTTCACACGAGCAGGCACACGGACGTCTGTCTCAGTCGTATATGGCACA
CGACCTGGCACACGAGCGTGTGACTTGACCATGTGGCTCCTACACCTAATTAAAGTAAATTAAAA
TATT
Found at i:33344244 original size:25 final size:25
Alignment explanation
Indices: 33344213--33344270 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
33344203 GGAGAGCTAT
**
33344213 TAACGGGAAGCTCGCAAGAACCATA
1 TAACGGGAAGCTCAAAAGAACCATA
*
33344238 TAACGGGAAGCTCAAAAGAGCCATA
1 TAACGGGAAGCTCAAAAGAACCATA
*
33344263 TATCGGGA
1 TAACGGGA
33344271 TGTTTATGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.14
Consensus pattern (25 bp):
TAACGGGAAGCTCAAAAGAACCATA
Found at i:33344627 original size:11 final size:10
Alignment explanation
Indices: 33344611--33344667 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
33344601 TATACAAATG
33344611 AATTTAACATC
1 AATTT-ACATC
33344622 AATTTA-ATAC
1 AATTTACAT-C
33344632 AATTTACATTC
1 AATTTACA-TC
33344643 AATTT-CATAC
1 AATTTACAT-C
33344653 AATTTACATTC
1 AATTTACA-TC
33344664 AATT
1 AATT
33344668 CAATCCAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
9 3 0.08
10 16 0.40
11 19 0.47
12 2 0.05
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (10 bp):
AATTTACATC
Found at i:33344636 original size:10 final size:10
Alignment explanation
Indices: 33344611--33344677 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 10
33344601 TATACAAATG
*
33344611 AATTTAACATC
1 AATTTAATA-C
33344622 AATTTAATAC
1 AATTTAATAC
*
33344632 AATTTACATTC
1 AATTTA-ATAC
*
33344643 AATTTCATAC
1 AATTTAATAC
*
33344653 AATTTACATTC
1 AATTTA-ATAC
* *
33344664 AATTCAATCC
1 AATTTAATAC
33344674 AATT
1 AATT
33344678 CACATCTTAG
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
10 22 0.48
11 24 0.52
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTTAATAC
Found at i:33344637 original size:21 final size:21
Alignment explanation
Indices: 33344611--33344682 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
33344601 TATACAAATG
33344611 AATTTAACA-TCAATTTAATAC
1 AATTT-ACATTCAATTTAATAC
*
33344632 AATTTACATTCAATTTCATAC
1 AATTTACATTCAATTTAATAC
* *
33344653 AATTTACATTCAATTCAATCC
1 AATTTACATTCAATTTAATAC
*
33344674 AATTCACAT
1 AATTTACAT
33344683 CTTAGGCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
20 3 0.07
21 42 0.93
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (21 bp):
AATTTACATTCAATTTAATAC
Found at i:33345183 original size:11 final size:11
Alignment explanation
Indices: 33345167--33345195 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
33345157 TTTTAGGAAA
33345167 GATGATAAAAT
1 GATGATAAAAT
33345178 GATGATAAAAT
1 GATGATAAAAT
33345189 GATGATA
1 GATGATA
33345196 TTTTATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.28
Consensus pattern (11 bp):
GATGATAAAAT
Found at i:33346240 original size:32 final size:32
Alignment explanation
Indices: 33346199--33346263 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
33346189 GCTTGGTGAG
33346199 AAAAAAAGAAAAAATTGAATAGTTAGGTAATC
1 AAAAAAAGAAAAAATTGAATAGTTAGGTAATC
* *
33346231 AAAAAAAGAAAAATTTGAATAGTTATGTAATC
1 AAAAAAAGAAAAAATTGAATAGTTAGGTAATC
33346263 A
1 A
33346264 TTTTGTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.25
Consensus pattern (32 bp):
AAAAAAAGAAAAAATTGAATAGTTAGGTAATC
Found at i:33348873 original size:199 final size:201
Alignment explanation
Indices: 33348533--33348933 Score: 788
Period size: 199 Copynumber: 2.0 Consensus size: 201
33348523 CCATTTAAGC
33348533 TTGAAGGTTCATTCGAAATTTAAAAAGATTTGGATAAAAATATTAAGCTTAAAAAATAAATTTTG
1 TTGAAGGTTCATTCGAAATTTAAAAAGATTTGGATAAAAATATTAAGCTTAAAAAATAAATTTTG
33348598 ACAAAAATTTGGACCCATTTAACTTATGAATTGAGCTTGGACTCGAGCTTGAATATTCAAGACCC
66 ACAAAAATTTGGACCCATTTAACTTATGAATTGAGCTTGGACTCGAGCTTGAATATTCAAGACCC
33348663 GAATCAACCCGACCTGACTCACTTTTAAATTTATAATGTTTTATATTATCTTATTC-TTTT-CAT
131 GAATCAACCCGACCTGACTCACTTTTAAATTTATAATGTTTTATATTATCTTATTCTTTTTACAT
33348726 ATTATA
196 ATTATA
33348732 TTGAAGGTTCATTCGAAATTTAAAAAGATTTGGATAAAAATATTAAGCTTAAAAAATAAATTTTG
1 TTGAAGGTTCATTCGAAATTTAAAAAGATTTGGATAAAAATATTAAGCTTAAAAAATAAATTTTG
33348797 ACAAAAATTTGGACCCATTTAACTTATGAATTGAGCTTGGACTCGAGCTTGAATATTCAAGACCC
66 ACAAAAATTTGGACCCATTTAACTTATGAATTGAGCTTGGACTCGAGCTTGAATATTCAAGACCC
33348862 GAATCAACCCGACCTGACTCACTTTTAAATTTATAATGTTTTATATTATCTTATTCTTTTTACAT
131 GAATCAACCCGACCTGACTCACTTTTAAATTTATAATGTTTTATATTATCTTATTCTTTTTACAT
33348927 ATTATA
196 ATTATA
33348933 T
1 T
33348934 AATTTATAAC
Statistics
Matches: 200, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
199 186 0.93
200 4 0.02
201 10 0.05
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (201 bp):
TTGAAGGTTCATTCGAAATTTAAAAAGATTTGGATAAAAATATTAAGCTTAAAAAATAAATTTTG
ACAAAAATTTGGACCCATTTAACTTATGAATTGAGCTTGGACTCGAGCTTGAATATTCAAGACCC
GAATCAACCCGACCTGACTCACTTTTAAATTTATAATGTTTTATATTATCTTATTCTTTTTACAT
ATTATA
Found at i:33349658 original size:107 final size:107
Alignment explanation
Indices: 33349522--33349791 Score: 436
Period size: 109 Copynumber: 2.5 Consensus size: 107
33349512 GAAAAACGAA
* *
33349522 AAAAAAAATTTTGGGTGCTGGCCTATCAATGGCCGGCACCCAGTACAAATTAAAAAAAATA-TAT
1 AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAAAATTAT
*
33349586 TTTTTTTCGTGTCAGAATGAGATATAAATATACG-AAAAAAT
66 TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT
*
33349627 AAAAAAAATTTCTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAAAAT
1 AAAAAAAA-TT-TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAA-TTAAAAAAAAAAT
33349692 TATTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT
63 TATTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT
* *
33349737 AAAAAGAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGTATAAATTAAA
1 AAAAA-AAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTAAA
33349792 TTTTTTTTCG
Statistics
Matches: 152, Mismatches: 7, Indels: 9
0.90 0.04 0.05
Matches are distributed among these distances:
105 8 0.05
106 2 0.01
107 37 0.24
108 16 0.11
109 72 0.47
110 14 0.09
111 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (107 bp):
AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAAAATTAT
TTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT
Found at i:33350012 original size:105 final size:104
Alignment explanation
Indices: 33349794--33350230 Score: 574
Period size: 106 Copynumber: 4.1 Consensus size: 104
33349784 AAATTAAATT
* *
33349794 TTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTAAAAAAATTTGTA
1 TTTTTTCGTATATTTATATCTGATTCTAACAC-AAAAAAAA-AAATTTTTTT---TAAATTTGTA
* * ** * * *
33349859 CTAGGTGTCAACCATTAACAGGCAAACACCCAAA-TTTTTTTTA
61 CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTA
*
33349902 TTTTTTTCGTATATTTATAT-TAGATTCTAACACAAAAAAAAAAGATTTTTTTTAAATTTGTATT
1 -TTTTTTCGTATATTTATATCT-GATTCTAACACAAAAAAAAAA-ATTTTTTTTAAATTTGTACT
*
33349966 GGGTGCCGGCCATTGACAGGCCAGTACCCAAATTTTTTTTTA
63 GGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTA
* * * *
33350008 TTTTTTTGTATATTTATATCTGATTCTGACACGAAAAAAAAGAATTTTTTTTAAAAATTGTACTG
1 TTTTTTCGTATATTTATATCTGATTCTAACAC-AAAAAAAAAAATTTTTTTT-AAATTTGTACTG
* *
33350073 GTTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTAA
64 GGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTA
* *
33350114 TTTTTTCGTATATTTATATCTGATTCTAACACGAAAAAAAGAATTTTTTTT-AATTTGTACTGGG
1 TTTTTTCGTATATTTATATCTGATTCTAACACAAAAAAAAAAATTTTTTTTAAATTTGTACTGGG
*
33350178 TGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTCG
66 TGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTT-A
33350218 TTTTTTCGTATAT
1 TTTTTTCGTATAT
33350231 CAGTATTATA
Statistics
Matches: 295, Mismatches: 26, Indels: 19
0.87 0.08 0.06
Matches are distributed among these distances:
103 48 0.16
104 13 0.04
105 89 0.30
106 97 0.33
107 2 0.01
108 17 0.06
109 29 0.10
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (104 bp):
TTTTTTCGTATATTTATATCTGATTCTAACACAAAAAAAAAAATTTTTTTTAAATTTGTACTGGG
TGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTA
Found at i:33373371 original size:24 final size:24
Alignment explanation
Indices: 33373343--33373395 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
33373333 TTAGTAAGTC
* *
33373343 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
33373367 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
33373391 AAATA
1 AAATA
33373396 TTCTAGAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:33375199 original size:8 final size:8
Alignment explanation
Indices: 33375188--33375228 Score: 82
Period size: 8 Copynumber: 5.1 Consensus size: 8
33375178 AAAACTAAAC
33375188 CCCGAAAA
1 CCCGAAAA
33375196 CCCGAAAA
1 CCCGAAAA
33375204 CCCGAAAA
1 CCCGAAAA
33375212 CCCGAAAA
1 CCCGAAAA
33375220 CCCGAAAA
1 CCCGAAAA
33375228 C
1 C
33375229 AAGAATCCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.49, C:0.39, G:0.12, T:0.00
Consensus pattern (8 bp):
CCCGAAAA
Found at i:33381191 original size:16 final size:17
Alignment explanation
Indices: 33381151--33381194 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
33381141 TCTCAAATTT
33381151 ACGAATGAGAAAAACAAC
1 ACGAAT-AGAAAAACAAC
* *
33381169 TCGAATAGAAAAACAAG
1 ACGAATAGAAAAACAAC
33381186 AC-AATAGAA
1 ACGAATAGAA
33381195 CAATGTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.61, C:0.14, G:0.16, T:0.09
Consensus pattern (17 bp):
ACGAATAGAAAAACAAC
Found at i:33385347 original size:16 final size:17
Alignment explanation
Indices: 33385323--33385355 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
33385313 TTTCTTTTAT
33385323 CAATATAA-TATAAAAA
1 CAATATAATTATAAAAA
*
33385339 CAATTTAATTATAAAAA
1 CAATATAATTATAAAAA
33385356 TTTACGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
CAATATAATTATAAAAA
Found at i:33389568 original size:50 final size:51
Alignment explanation
Indices: 33389473--33389591 Score: 177
Period size: 50 Copynumber: 2.4 Consensus size: 51
33389463 ACTTCTGATC
* *
33389473 AGTGATAAGTGATAAGTGGTGGCTTTAGCTACACTTATCTAATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGAGACA
* *
33389524 AGTGATAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGAGATA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGAGACA
* *
33389574 AGAGATAAATGATAAGTG
1 AGTGATAAGTGATAAGTG
33389592 ATTCCGTGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 40 0.65
51 22 0.35
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.29
Consensus pattern (51 bp):
AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGAGACA
Found at i:33391082 original size:12 final size:12
Alignment explanation
Indices: 33391065--33391089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33391055 CATGCCATAT
33391065 AAATCATATGTA
1 AAATCATATGTA
33391077 AAATCATATGTA
1 AAATCATATGTA
33391089 A
1 A
33391090 CACATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
AAATCATATGTA
Found at i:33398346 original size:18 final size:20
Alignment explanation
Indices: 33398308--33398358 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
33398298 CCCCAAATTA
*
33398308 TATATTTTTTTATTTTGATT
1 TATATTTTTTTATATTGATT
33398328 T-TGATTTTTTT-TATT-ATT
1 TAT-ATTTTTTTATATTGATT
33398346 TATATTTTTTTAT
1 TATATTTTTTTAT
33398359 GCTTTAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 12 0.44
19 6 0.22
20 9 0.33
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (20 bp):
TATATTTTTTTATATTGATT
Found at i:33399372 original size:25 final size:25
Alignment explanation
Indices: 33399338--33399410 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 25
33399328 ATTAATATCC
*
33399338 AAAT-AAGTAATAAATAATAAAATA
1 AAATAAAGTAATAAATAATAAAAGA
33399362 AAATAAAGTAATAAATAA-AGTAAAGA
1 AAATAAAGTAATAAATAATA--AAAGA
33399388 AAATAAA-TAAATAAATAATAAAA
1 AAATAAAGT-AATAAATAATAAAA
33399411 ATTGGGTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
24 5 0.12
25 17 0.40
26 20 0.47
27 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (25 bp):
AAATAAAGTAATAAATAATAAAAGA
Found at i:33399380 original size:4 final size:4
Alignment explanation
Indices: 33399346--33399409 Score: 53
Period size: 4 Copynumber: 15.5 Consensus size: 4
33399336 CCAAATAAGT
*
33399346 AATA AAT- AATAA AATAA AATA AAGT- AATA AATA AAGTA AAGAA AATA
1 AATA AATA AAT-A AAT-A AATA AA-TA AATA AATA AA-TA AA-TA AATA
33399393 AATA AATA AAT- AATA AA
1 AATA AATA AATA AATA AA
33399410 AATTGGGTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
3 7 0.13
4 28 0.54
5 17 0.33
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:33399385 original size:22 final size:22
Alignment explanation
Indices: 33399346--33399402 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
33399336 CCAAATAAGT
33399346 AATAAAT-AATAAAATAAA-ATA
1 AATAAATAAATAAAATAAAGA-A
*
33399367 AAGT-AATAAATAAAGTAAAGAA
1 AA-TAAATAAATAAAATAAAGAA
33399389 AATAAATAAATAAA
1 AATAAATAAATAAA
33399403 TAATAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 6 0.19
22 24 0.77
23 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (22 bp):
AATAAATAAATAAAATAAAGAA
Found at i:33399412 original size:17 final size:16
Alignment explanation
Indices: 33399346--33399410 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 16
33399336 CCAAATAAGT
33399346 AATAAATAATAAAATAA
1 AATAAATAATAAAAT-A
33399363 AATAAAGTAAT-AAATA
1 AATAAA-TAATAAAATA
* *
33399379 AAGTAAAGAAAATAAATA
1 AA-TAAATAATA-AAATA
33399397 AATAAATAATAAAA
1 AATAAATAATAAAA
33399411 ATTGGGTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 8 0.20
17 21 0.52
18 11 0.28
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.22
Consensus pattern (16 bp):
AATAAATAATAAAATA
Found at i:33406547 original size:18 final size:18
Alignment explanation
Indices: 33406511--33406545 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
33406501 AAAATTTTAA
33406511 AATTTTATTTATATTTTT
1 AATTTTATTTATATTTTT
*
33406529 AATTTT-TTTGTATTTTT
1 AATTTTATTTATATTTTT
33406546 TAGATTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
AATTTTATTTATATTTTT
Found at i:33416347 original size:50 final size:54
Alignment explanation
Indices: 33416242--33416347 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
33416232 TTCCGAAAGG
* *
33416242 TTCTCGTCCATTTGTCCTTCACGACATTCACCCTTCTGTTGAGAATGTGATTCT
1 TTCTCATCCACTTGTCCTTCACGACATTCACCCTTCTGTTGAGAATGTGATTCT
33416296 TTCTCATCCACTTGTCCTTCACGA-ATTCACCC-T-T-TTGAGAATGTGATTCT
1 TTCTCATCCACTTGTCCTTCACGACATTCACCCTTCTGTTGAGAATGTGATTCT
33416346 TT
1 TT
33416348 AAGCTATCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
50 18 0.36
51 1 0.02
52 1 0.02
53 8 0.16
54 22 0.44
ACGTcount: A:0.18, C:0.27, G:0.13, T:0.42
Consensus pattern (54 bp):
TTCTCATCCACTTGTCCTTCACGACATTCACCCTTCTGTTGAGAATGTGATTCT
Found at i:33418659 original size:10 final size:10
Alignment explanation
Indices: 33418635--33418681 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
33418625 GAGTCATAAC
33418635 TTTTTAATAAT
1 TTTTTAAT-AT
33418646 TTTTTAATA-
1 TTTTTAATAT
*
33418655 CTTTT-ATAT
1 TTTTTAATAT
*
33418664 TTTTTACTAT
1 TTTTTAATAT
33418674 TTTTTAAT
1 TTTTTAAT
33418682 TTATATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
8 3 0.10
9 8 0.27
10 11 0.37
11 8 0.27
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:33418704 original size:25 final size:24
Alignment explanation
Indices: 33418657--33418706 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
33418647 TTTTAATACT
* *
33418657 TTTATATTTTTTACTATTTTTTAA
1 TTTATATTTTTTACAATTATTTAA
33418681 TTTATATTTTTTACAATTAATTTAA
1 TTTATATTTTTTACAATT-ATTTAA
33418706 T
1 T
33418707 AATCTTGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTATATTTTTTACAATTATTTAA
Found at i:33418928 original size:117 final size:118
Alignment explanation
Indices: 33418711--33418945 Score: 463
Period size: 117 Copynumber: 2.0 Consensus size: 118
33418701 TTTAATAATC
33418711 TTGTAAAATTAGGGAAAAGACCGAAAGTATTAAATTTTTAAGTATAACCTCTGGTGTAGCAAATT
1 TTGTAAAATTAGGGAAAAGACCGAAAGTATTAAATTTTTAAGTATAACCTCTGGTGTAGCAAATT
33418776 TAAACCTAAAAAACTTAGGACAAATTACTAAAATAGTTACTTTTGTTTGTCTT
66 TAAACCTAAAAAACTTAGGACAAATTACTAAAATAGTTACTTTTGTTTGTCTT
33418829 TTGTAAAATT-GGGAAAAGACCGAAAGTATTAAATTTTTAAGTATAACCTCTGGTGTAGCAAATT
1 TTGTAAAATTAGGGAAAAGACCGAAAGTATTAAATTTTTAAGTATAACCTCTGGTGTAGCAAATT
33418893 TAAACCTAAAAAACTTAGGACAAATTACTAAAATAGTTACTTTTGTTTGTCTT
66 TAAACCTAAAAAACTTAGGACAAATTACTAAAATAGTTACTTTTGTTTGTCTT
33418946 AGATTACATT
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
117 107 0.91
118 10 0.09
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (118 bp):
TTGTAAAATTAGGGAAAAGACCGAAAGTATTAAATTTTTAAGTATAACCTCTGGTGTAGCAAATT
TAAACCTAAAAAACTTAGGACAAATTACTAAAATAGTTACTTTTGTTTGTCTT
Found at i:33421271 original size:41 final size:42
Alignment explanation
Indices: 33421233--33421316 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
33421223 TTCAATTTTT
*
33421233 TTACTATTATAATC-AATATCTGTTTTTATAACAAAATTTAA
1 TTACTATTATAATCAAATATCTATTTTTATAACAAAATTTAA
33421274 TTACTATTATAATCAAATATCTATTTTTATAACAAAATTTAA
1 TTACTATTATAATCAAATATCTATTTTTATAACAAAATTTAA
33421316 T
1 T
33421317 ACCCAGAACT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 14 0.34
42 27 0.66
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.46
Consensus pattern (42 bp):
TTACTATTATAATCAAATATCTATTTTTATAACAAAATTTAA
Found at i:33421311 original size:20 final size:20
Alignment explanation
Indices: 33421247--33421311 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 20
33421237 TATTATAATC
*
33421247 AATATCTGTTTTTATAACAA
1 AATATCTATTTTTATAACAA
33421267 AAT-T-TAATTACTATTATAATC-A
1 AATATCT-ATT--T-TTATAA-CAA
33421289 AATATCTATTTTTATAACAA
1 AATATCTATTTTTATAACAA
33421309 AAT
1 AAT
33421312 TTAATACCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 16
0.68 0.02 0.30
Matches are distributed among these distances:
18 1 0.03
19 4 0.11
20 13 0.36
21 2 0.06
22 10 0.28
23 5 0.14
24 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (20 bp):
AATATCTATTTTTATAACAA
Found at i:33430148 original size:9 final size:8
Alignment explanation
Indices: 33430119--33430146 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
33430109 TTATTTTTAA
33430119 TTTTGATT
1 TTTTGATT
33430127 TTTTGATT
1 TTTTGATT
33430135 TTTTGATT
1 TTTTGATT
33430143 TTTT
1 TTTT
33430147 TGTAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (8 bp):
TTTTGATT
Found at i:33431831 original size:36 final size:35
Alignment explanation
Indices: 33431754--33431832 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 35
33431744 GTCCCTACCC
** *
33431754 TTTAAAATTACATAAATTTTAAAAAATATTTTTTG
1 TTTAAAAAAACATAAATTTTAAAAAATATTATTTG
*
33431789 TATTAAAAAAACATAAAATTTTAAAATATATGTATTT-
1 T-TTAAAAAAACAT-AAATTTTAAAAAATAT-TATTTG
33431826 TTTAAAA
1 TTTAAAA
33431833 TATTAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 1 0.03
36 16 0.43
37 16 0.43
38 4 0.11
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (35 bp):
TTTAAAAAAACATAAATTTTAAAAAATATTATTTG
Found at i:33432152 original size:10 final size:10
Alignment explanation
Indices: 33432137--33432168 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
33432127 TAGCATTGAA
33432137 TTTTAGATTT
1 TTTTAGATTT
33432147 TTTTAGATTT
1 TTTTAGATTT
*
33432157 TTTTATATTT
1 TTTTAGATTT
33432167 TT
1 TT
33432169 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (10 bp):
TTTTAGATTT
Found at i:33432167 original size:17 final size:17
Alignment explanation
Indices: 33432146--33432179 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
33432136 ATTTTAGATT
33432146 TTTTTAGATTTTTTTATA
1 TTTTTA-ATTTTTTTATA
33432164 TTTTTAATTTTTTTAT
1 TTTTTAATTTTTTTAT
33432180 TTTATGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTAATTTTTTTATA
Found at i:33432177 original size:10 final size:9
Alignment explanation
Indices: 33432137--33432182 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 9
33432127 TAGCATTGAA
33432137 TTTTAGATTT
1 TTTTA-ATTT
33432147 TTTTAGATTT
1 TTTTA-ATTT
*
33432157 TTTT-ATAT
1 TTTTAATTT
33432165 TTTTAATTT
1 TTTTAATTT
33432174 TTTT-ATTT
1 TTTTAATTT
33432182 T
1 T
33432183 ATGAGTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 12 0.36
9 7 0.21
10 14 0.42
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (9 bp):
TTTTAATTT
Found at i:33432216 original size:24 final size:24
Alignment explanation
Indices: 33432189--33432239 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
33432179 TTTTATGAGT
* * *
33432189 TATTATTATTTTTCATTTTTTAAA
1 TATTATTATTTTTAATATTTAAAA
* *
33432213 TATTTTTGTTTTTAATATTTAAAA
1 TATTATTATTTTTAATATTTAAAA
33432237 TAT
1 TAT
33432240 GAAAAAATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
TATTATTATTTTTAATATTTAAAA
Found at i:33433436 original size:40 final size:41
Alignment explanation
Indices: 33433392--33433470 Score: 99
Period size: 40 Copynumber: 1.9 Consensus size: 41
33433382 AAATACAATG
* *
33433392 CAAAATC-TCAAAAACTTTTGATTTTG-TTTTTATTTGACTT
1 CAAAATCTTCAAAAA-ATTTGAATTTGATTTTTATTTGACTT
*
33433432 CAAAATCTTTAAAAAATTTGAATTTGACTTTTTATTTGA
1 CAAAATCTTCAAAAAATTTGAATTTGA-TTTTTATTTGA
33433471 TTTATTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 16 0.48
41 6 0.18
42 11 0.33
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (41 bp):
CAAAATCTTCAAAAAATTTGAATTTGATTTTTATTTGACTT
Found at i:33435502 original size:31 final size:31
Alignment explanation
Indices: 33435453--33435527 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
33435443 TGATTTGGTG
* * *
33435453 TAATTATACACATAAAACTTGAATTTTGGTT
1 TAATTGTATACATAAAACTTGAATTTTGATT
* *
33435484 T-ATATGTATACATGAAACTTTAATTTTGATT
1 TAAT-TGTATACATAAAACTTGAATTTTGATT
33435515 TAATTGTATACAT
1 TAATTGTATACAT
33435528 TTAAAAAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 2 0.05
31 33 0.89
32 2 0.05
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.45
Consensus pattern (31 bp):
TAATTGTATACATAAAACTTGAATTTTGATT
Found at i:33444270 original size:16 final size:17
Alignment explanation
Indices: 33444237--33444277 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
33444227 AATAAAAAAA
*
33444237 ATAAAAAA-TTGAAGGG
1 ATAAAAAACTAGAAGGG
33444253 ATAAAAAACTAGAA-GG
1 ATAAAAAACTAGAAGGG
*
33444269 ATGAAAAAC
1 ATAAAAAAC
33444278 ATAATTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.61, C:0.05, G:0.20, T:0.15
Consensus pattern (17 bp):
ATAAAAAACTAGAAGGG
Found at i:33447397 original size:5 final size:5
Alignment explanation
Indices: 33447389--33447414 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
33447379 AAACAGATAA
33447389 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
33447415 GATATTATAG
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:33450580 original size:14 final size:14
Alignment explanation
Indices: 33450542--33450580 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
33450532 TGTTTTTGAG
33450542 TTTATGATATTTTAT
1 TTTAT-ATATTTTAT
* *
33450557 TCTATTTATTTTAT
1 TTTATATATTTTAT
33450571 TTTATATATT
1 TTTATATATT
33450581 ATGTTATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTATATATTTTAT
Found at i:33450920 original size:12 final size:12
Alignment explanation
Indices: 33450903--33450930 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
33450893 AAACGTACAT
33450903 AATGGCCAACCA
1 AATGGCCAACCA
33450915 AATGGCCAACCA
1 AATGGCCAACCA
33450927 AATG
1 AATG
33450931 AGGAAACACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.29, G:0.18, T:0.11
Consensus pattern (12 bp):
AATGGCCAACCA
Found at i:33458760 original size:46 final size:46
Alignment explanation
Indices: 33458693--33458869 Score: 300
Period size: 46 Copynumber: 3.8 Consensus size: 46
33458683 AGTGTGGAAT
33458693 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
33458739 GTAGGTATGGTATTTCAGTAAAGAAAACTATACTGAGTTGTGAGAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* * *
33458785 GTATGTATGGTATTTCAGTAACGAAAACCATACTAAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
*
33458831 GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTT
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
33458870 ATAGCATTGT
Statistics
Matches: 120, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 120 1.00
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
Found at i:33461509 original size:23 final size:23
Alignment explanation
Indices: 33461476--33461523 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
33461466 TCAAAAATGA
33461476 TTTTTGAAAAA-TTGATTAATTTT
1 TTTTTGAAAAAGTTGA-TAATTTT
*
33461499 TTTTTGGAAAAGTTGATAATTTT
1 TTTTTGAAAAAGTTGATAATTTT
33461522 TT
1 TT
33461524 ATGTTTGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (23 bp):
TTTTTGAAAAAGTTGATAATTTT
Found at i:33461850 original size:19 final size:19
Alignment explanation
Indices: 33461826--33461865 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
33461816 GGTCCAACTA
*
33461826 TCATAAAATATTATTT-TTT
1 TCATAAAA-ATAATTTATTT
33461845 TCATAAAAATAATTTATTT
1 TCATAAAAATAATTTATTT
33461864 TC
1 TC
33461866 CAAAAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (19 bp):
TCATAAAAATAATTTATTT
Found at i:33464264 original size:27 final size:25
Alignment explanation
Indices: 33464205--33464271 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 25
33464195 ACAATTCCAA
* *
33464205 CCTAACATTTGAAACATTATTTAAG
1 CCTAACATTTAAAACATTAGTTAAG
*
33464230 AC-AACATTTAAAACATATAGTTATAG
1 CCTAACATTTAAAACAT-TAGTTA-AG
33464256 CCTAACATTTAAAACA
1 CCTAACATTTAAAACA
33464272 ACATTAAGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 13 0.37
25 6 0.17
26 3 0.09
27 13 0.37
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.31
Consensus pattern (25 bp):
CCTAACATTTAAAACATTAGTTAAG
Found at i:33473609 original size:14 final size:16
Alignment explanation
Indices: 33473592--33473623 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
33473582 ATATTTAAAA
33473592 TTTAATTT-ATAT-AT
1 TTTAATTTGATATGAT
33473606 TTTAATTTGATATGAT
1 TTTAATTTGATATGAT
33473622 TT
1 TT
33473624 GATCCTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTAATTTGATATGAT
Found at i:33474821 original size:272 final size:272
Alignment explanation
Indices: 33474335--33474879 Score: 1081
Period size: 272 Copynumber: 2.0 Consensus size: 272
33474325 ATTGGGTTGA
33474335 TTGAGATGATCGGACTACCTAACCCATGAATACCTTCATTTACCATCAAAGAGCAACTAACATAT
1 TTGAGATGATCGGACTACCTAACCCATGAATACCTTCATTTACCATCAAAGAGCAACTAACATAT
33474400 TTCTTTTAAAAAAAAATTCATTTTTTTATATTTTTCATAAATTTAGAAATTTTAAAATGATGTTT
66 TTCTTTTAAAAAAAAATTCATTTTTTTATATTTTTCATAAATTTAGAAATTTTAAAATGATGTTT
33474465 TAAATTTTTTTCATAATTTTTTTATATTTTTAGAAAAGAAAATGTTTTTTTTATAATTTTTATTT
131 TAAATTTTTTTCATAATTTTTTTATATTTTTAGAAAAGAAAATGTTTTTTTTATAATTTTTATTT
33474530 AAAAATTATTTTTTATACTTTTAAAGTAAACCAAAATTAAAAAATAATAAACGTTGATGGTTTAA
196 AAAAATTATTTTTTATACTTTTAAAGTAAACCAAAATTAAAAAATAATAAACGTTGATGGTTTAA
*
33474595 ACCTCAACGATT
261 ACATCAACGATT
33474607 TTGAGATGATCGGACTACCTAACCCATGAATACCTTCATTTACCATCAAAGAGCAACTAACATAT
1 TTGAGATGATCGGACTACCTAACCCATGAATACCTTCATTTACCATCAAAGAGCAACTAACATAT
33474672 TTCTTTTAAAAAAAAATTCATTTTTTTATATTTTTCATAAATTTAGAAATTTTAAAATGATGTTT
66 TTCTTTTAAAAAAAAATTCATTTTTTTATATTTTTCATAAATTTAGAAATTTTAAAATGATGTTT
33474737 TAAATTTTTTTCATAATTTTTTTATATTTTTAGAAAAGAAAATGTTTTTTTTATAATTTTTATTT
131 TAAATTTTTTTCATAATTTTTTTATATTTTTAGAAAAGAAAATGTTTTTTTTATAATTTTTATTT
33474802 AAAAATTATTTTTTATACTTTTAAAGTAAACCAAAATTAAAAAATAATAAACGTTGATGGTTTAA
196 AAAAATTATTTTTTATACTTTTAAAGTAAACCAAAATTAAAAAATAATAAACGTTGATGGTTTAA
33474867 ACATCAACGATT
261 ACATCAACGATT
33474879 T
1 T
33474880 AACAACAATA
Statistics
Matches: 272, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
272 272 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.43
Consensus pattern (272 bp):
TTGAGATGATCGGACTACCTAACCCATGAATACCTTCATTTACCATCAAAGAGCAACTAACATAT
TTCTTTTAAAAAAAAATTCATTTTTTTATATTTTTCATAAATTTAGAAATTTTAAAATGATGTTT
TAAATTTTTTTCATAATTTTTTTATATTTTTAGAAAAGAAAATGTTTTTTTTATAATTTTTATTT
AAAAATTATTTTTTATACTTTTAAAGTAAACCAAAATTAAAAAATAATAAACGTTGATGGTTTAA
ACATCAACGATT
Found at i:33492980 original size:93 final size:93
Alignment explanation
Indices: 33492821--33493012 Score: 273
Period size: 93 Copynumber: 2.1 Consensus size: 93
33492811 TATTTCATAA
*
33492821 TTCTTTGATATTTAAGAAGTATTCTGTCAATTCTGAACAACCAAGACCATATAACAAACCAGCAT
1 TTCTTTGATATTTAAGAAGTATTCTGTCAATTCTCAACAACCAAGACCATATAACAAACCAGCAT
* *
33492886 ATTTCTCAGTCG-ACCAACTAAAGAAGTT
66 ATTTCTCAGCCGAACC-ACTAAAGAAATT
* * *
33492914 TTCTTTGAT-TTATTAGAGAGTATTCTGTCCATTCTCAAC-ACCAAGACCATATAACACACCAGC
1 TTCTTTGATATT-TAAGA-AGTATTCTGTCAATTCTCAACAACCAAGACCATATAACAAACCAGC
*
33492977 ATATTTCTCGGCCGAACCACTAAAGAAATT
64 ATATTTCTCAGCCGAACCACTAAAGAAATT
33493007 TTCTTT
1 TTCTTT
33493013 CAGTTTCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
92 2 0.02
93 65 0.73
94 22 0.25
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.32
Consensus pattern (93 bp):
TTCTTTGATATTTAAGAAGTATTCTGTCAATTCTCAACAACCAAGACCATATAACAAACCAGCAT
ATTTCTCAGCCGAACCACTAAAGAAATT
Found at i:33494497 original size:17 final size:17
Alignment explanation
Indices: 33494475--33494509 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
33494465 TGTTTATGGA
33494475 TATTA-TTTATTATTTAT
1 TATTATTTTA-TATTTAT
33494492 TATTATTTTATATTTAT
1 TATTATTTTATATTTAT
33494509 T
1 T
33494510 TTTGTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTATTTTATATTTAT
Found at i:33496246 original size:17 final size:17
Alignment explanation
Indices: 33496224--33496258 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
33496214 TGTTTATGGA
33496224 TATTA-TTTATTATTTAT
1 TATTATTTTA-TATTTAT
33496241 TATTATTTTATATTTAT
1 TATTATTTTATATTTAT
33496258 T
1 T
33496259 TTTGTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTATTTTATATTTAT
Found at i:33507336 original size:17 final size:17
Alignment explanation
Indices: 33507304--33507382 Score: 67
Period size: 17 Copynumber: 4.7 Consensus size: 17
33507294 AGAAATTGTG
33507304 ATAATTATACATTTATAA
1 ATAATTATA-ATTTATAA
33507322 ATAATTATAATTTATTAA
1 ATAATTATAATTTA-TAA
* * *
33507340 A-AATTA-AACTTGTTA
1 ATAATTATAATTTATAA
*
33507355 A-AATTACACATTTA-AA
1 ATAATTATA-ATTTATAA
33507371 ATAATTATAATT
1 ATAATTATAATT
33507383 ATTAATTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
15 8 0.16
16 10 0.20
17 19 0.38
18 13 0.26
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (17 bp):
ATAATTATAATTTATAA
Found at i:33507341 original size:49 final size:47
Alignment explanation
Indices: 33507288--33507387 Score: 121
Period size: 50 Copynumber: 2.1 Consensus size: 47
33507278 ATAATTGAAA
* *
33507288 TAAAA-TAGAAATTGTGATAATTATACATTTATAAATAATTATAATTTAT
1 TAAAATTA-AAATTGTGAAAATTACACATTTA-AAATAATTATAA-TTAT
* *
33507337 TAAAAATTAAACTTGTTAAAATTACACATTTAAAATAATTATAATTAT
1 T-AAAATTAAAATTGTGAAAATTACACATTTAAAATAATTATAATTAT
33507385 TAA
1 TAA
33507388 TTAAAAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
47 2 0.04
48 5 0.11
49 13 0.29
50 23 0.51
51 2 0.04
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (47 bp):
TAAAATTAAAATTGTGAAAATTACACATTTAAAATAATTATAATTAT
Found at i:33509814 original size:5 final size:5
Alignment explanation
Indices: 33509804--33509829 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
33509794 TGAGCATTCG
33509804 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
33509830 AATTTTCGAG
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:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:33510591 original size:9 final size:9
Alignment explanation
Indices: 33510573--33510607 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
33510563 TATAGTTTGA
*
33510573 TATTCAAAT
1 TATTCGAAT
33510582 TATTCGAAT
1 TATTCGAAT
*
33510591 TATTCGAGT
1 TATTCGAAT
33510600 TATTCGAA
1 TATTCGAA
33510608 ATCGAAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (9 bp):
TATTCGAAT
Found at i:33510680 original size:9 final size:9
Alignment explanation
Indices: 33510663--33510693 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
33510653 TCGAGTTGAT
33510663 TCGAATAAC
1 TCGAATAAC
*
33510672 TCGATTAAC
1 TCGAATAAC
33510681 TCGAATAAC
1 TCGAATAAC
33510690 TCGA
1 TCGA
33510694 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:33513989 original size:11 final size:11
Alignment explanation
Indices: 33513973--33514020 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
33513963 CTTAATCACT
33513973 TTAATATTAAA
1 TTAATATTAAA
33513984 TTAATATTAAGA
1 TTAATATTAA-A
33513996 -TAATTATT---
1 TTAA-TATTAAA
33514004 TTAATATTAAA
1 TTAATATTAAA
33514015 TTAATA
1 TTAATA
33514021 AAATCCTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
8 4 0.13
9 3 0.10
11 19 0.61
12 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:33515753 original size:27 final size:27
Alignment explanation
Indices: 33515721--33515787 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
33515711 ATAAAAAATA
*
33515721 ACCAAAATGT-TATAACTTTTTTTATTT
1 ACCAAAATATATATAA-TTTTTTTATTT
* *
33515748 ACCAAAAAATATATAATTTTTTTGTTT
1 ACCAAAATATATATAATTTTTTTATTT
*
33515775 ACGAAAATATATA
1 ACCAAAATATATA
33515788 AAAAAACCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (27 bp):
ACCAAAATATATATAATTTTTTTATTT
Found at i:33525765 original size:27 final size:27
Alignment explanation
Indices: 33525733--33525799 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
33525723 ATAAAAAATA
*
33525733 ACCAAAATGT-TATAACTTTTTTTATTT
1 ACCAAAATATATATAA-TTTTTTTATTT
* *
33525760 ACCAAAAAATATATAATTTTTTTGTTT
1 ACCAAAATATATATAATTTTTTTATTT
*
33525787 ACGAAAATATATA
1 ACCAAAATATATA
33525800 AAAAAACCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (27 bp):
ACCAAAATATATATAATTTTTTTATTT
Found at i:33525887 original size:27 final size:27
Alignment explanation
Indices: 33525857--33525923 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
33525847 CGCCAATGGG
33525857 ATTGGCGGCACCAAAGGTGCCAA-AGCC
1 ATTGGCGGCACCAAAGGTGCCAATA-CC
*
33525884 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAAAGGTGCCAATACC
33525911 ATTGGCGGCACCA
1 ATTGGCGGCACCA
33525924 CTATATATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAATACC
Found at i:33525982 original size:4 final size:4
Alignment explanation
Indices: 33525968--33526101 Score: 86
Period size: 4 Copynumber: 34.0 Consensus size: 4
33525958 GAAGGAGAGG
* *
33525968 GAAA TAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AA -AAA GAAT
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
* ** *
33526014 GGAA GAAA -AGG GAAG GAGAA GAGAA -AAA -AAA GAAA GAAA G-AA G-AA
1 GAAA GAAA GAAA GAAA GA-AA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
* *
33526059 GAAAA TGAAA GGAGAA GAAA -AAA GAAA GAAG GAAG GAAA GAAA
1 G-AAA -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
33526102 AGGAAAGGAG
Statistics
Matches: 107, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
3 19 0.18
4 70 0.65
5 15 0.14
6 3 0.03
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:33526047 original size:41 final size:40
Alignment explanation
Indices: 33526001--33526146 Score: 158
Period size: 41 Copynumber: 3.6 Consensus size: 40
33525991 AGAAAGAAAG
*
33526001 AAAGAAAAAGAATGGAAGAAAAGGGAAGGAGAAGAGAAAAA
1 AAAGAAAAAGAA-GGAAGAAAAGGAAAGGAGAAGAGAAAAA
*
33526042 AAAGAAAGAAAGAA-GAAGAAAATGAAAGGAGAAGA-AAAAA
1 AAAG-AA-AAAGAAGGAAGAAAAGGAAAGGAGAAGAGAAAAA
*
33526082 GAAAG--AAGGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAA
1 -AAAGAAAAAGAAGG-AAGAAAAGGAAAGGAGAAGAGAAAAA
* * *
33526122 AAAGAAGAAGAGGGAAG-GAAGGAAA
1 AAAGAAAAAGAAGGAAGAAAAGGAAA
33526147 AAAAAGAAAA
Statistics
Matches: 89, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
37 5 0.06
38 1 0.01
39 30 0.34
40 13 0.15
41 32 0.36
42 2 0.02
43 6 0.07
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.01
Consensus pattern (40 bp):
AAAGAAAAAGAAGGAAGAAAAGGAAAGGAGAAGAGAAAAA
Found at i:33526085 original size:17 final size:17
Alignment explanation
Indices: 33525968--33526132 Score: 90
Period size: 19 Copynumber: 9.1 Consensus size: 17
33525958 GAAGGAGAGG
33525968 GAAATAAAGAAAG-A-AA
1 GAAA-AAAGAAAGAAGAA
33525984 GAAAGAAAGAAAG-A-AA
1 GAAA-AAAGAAAGAAGAA
*
33526000 GAAAGAA-AAAGAATGGAA
1 GAAAAAAGAAAGAA--GAA
**
33526018 GAAAAGGGAAGGAGAAGAGA
1 GAAAAAAGAA--AGAAGA-A
*
33526038 AAAAAAAGAAAGAAAGAA
1 GAAAAAAGAAAG-AAGAA
*
33526056 GAAGAAAATGAAAGGAGAA
1 GAA-AAAA-GAAAGAAGAA
33526075 GAAAAAAGAAAGAAGGAA
1 GAAAAAAGAAAGAA-GAA
*
33526093 GGAAAGAAAAGGAAAGGAGAA
1 -G-AA-AAAA-GAAAGAAGAA
33526114 GAGAAAAA-AAAGAAGAA
1 GA-AAAAAGAAAGAAGAA
33526131 GA
1 GA
33526133 GGGAAGGAAG
Statistics
Matches: 119, Mismatches: 13, Indels: 33
0.72 0.08 0.20
Matches are distributed among these distances:
14 4 0.03
15 3 0.03
16 19 0.16
17 16 0.13
18 18 0.15
19 25 0.21
20 17 0.14
21 11 0.09
22 6 0.05
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (17 bp):
GAAAAAAGAAAGAAGAA
Found at i:33526093 original size:65 final size:64
Alignment explanation
Indices: 33525977--33526099 Score: 144
Period size: 65 Copynumber: 1.9 Consensus size: 64
33525967 GGAAATAAAG
** *
33525977 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAATGGAAGAAAAGGGAAGGAGAAGAGAAAAA
1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAATAAAAGAAAAAGGAAGGA-AAGAGAAAAA
* *
33526042 AAAGAAAGAAAG-AAG-AAGAAAATGAAAGGAGAAGAA-AAAAGAAAGAAGGAAGGAAAGA
1 AAAGAAAGAAAGAAAGAAAG-AAA-GAAAGAAAAAGAATAAAAGAAA-AAGGAAGGAAAGA
33526100 AAAGGAAAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
63 3 0.06
64 16 0.32
65 31 0.62
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (64 bp):
AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAATAAAAGAAAAAGGAAGGAAAGAGAAAAA
Found at i:33526115 original size:16 final size:15
Alignment explanation
Indices: 33525981--33526115 Score: 56
Period size: 12 Copynumber: 10.0 Consensus size: 15
33525971 ATAAAGAAAG
33525981 AAAGAAA-GA-AAG-
1 AAAGAAAGGAGAAGA
33525993 AAAGAAA-GA-AAGA
1 AAAGAAAGGAGAAGA
*
33526006 AAA-AGAATG-GAAGA
1 AAAGA-AAGGAGAAGA
*
33526020 AAAGGGAAGGAGAAGA
1 AAA-GAAAGGAGAAGA
*
33526036 GAA-AAA--A-AAG-
1 AAAGAAAGGAGAAGA
*
33526046 AAAGAAAGAAGAAGA
1 AAAGAAAGGAGAAGA
33526061 AAATGAAAGGAGAAG-
1 AAA-GAAAGGAGAAGA
33526076 AAA-AAA-GA-AAG-
1 AAAGAAAGGAGAAGA
*
33526087 -AAGGAAGGA-AAGA
1 AAAGAAAGGAGAAGA
33526100 AAAGGAAAGGAGAAGA
1 AAA-GAAAGGAGAAGA
33526116 GAAAAAAAAG
Statistics
Matches: 96, Mismatches: 8, Indels: 34
0.70 0.06 0.25
Matches are distributed among these distances:
10 4 0.04
11 11 0.11
12 21 0.22
13 9 0.09
14 15 0.16
15 15 0.16
16 21 0.22
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.01
Consensus pattern (15 bp):
AAAGAAAGGAGAAGA
Found at i:33526126 original size:39 final size:40
Alignment explanation
Indices: 33526001--33526130 Score: 167
Period size: 39 Copynumber: 3.2 Consensus size: 40
33525991 AGAAAGAAAG
*
33526001 AAAGAA-AAAGAATGGAAGAAAAGGGAAGGAGAAGAGAAAAA
1 AAAGAAGAAAGAA--GAAGAAAAGGAAAGGAGAAGAGAAAAA
*
33526042 AAAGAAAGAAAGAAGAAGAAAATGAAAGGAGAAGA-AAAAA
1 AAAG-AAGAAAGAAGAAGAAAAGGAAAGGAGAAGAGAAAAA
* *
33526082 GAAAGAAGGAAGGA-AAGAAAAGGAAAGGAGAAGAGAAAAA
1 -AAAGAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAGAAAAA
33526122 AAAGAAGAA
1 AAAGAAGAA
33526131 GAGGGAAGGA
Statistics
Matches: 79, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
39 27 0.34
40 17 0.22
41 27 0.34
42 2 0.03
43 6 0.08
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (40 bp):
AAAGAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAGAAAAA
Found at i:33526140 original size:30 final size:27
Alignment explanation
Indices: 33526096--33526158 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
33526086 GAAGGAAGGA
*
33526096 AAGAAAAGGAAAGGAGAAGAGAAAAAAAAG
1 AAGAAGAGGAAA-G-GAAG-GAAAAAAAAG
*
33526126 AAGAAGAGGGAAGGAAGGAAAAAAAAG
1 AAGAAGAGGAAAGGAAGGAAAAAAAAG
33526153 AA-AAGA
1 AAGAAGA
33526159 AAAGATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 4 0.13
27 12 0.39
28 4 0.13
29 1 0.03
30 10 0.32
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (27 bp):
AAGAAGAGGAAAGGAAGGAAAAAAAAG
Found at i:33526144 original size:39 final size:39
Alignment explanation
Indices: 33526014--33526146 Score: 162
Period size: 39 Copynumber: 3.4 Consensus size: 39
33526004 GAAAAAGAAT
*
33526014 GGAAGAAAAGGGAAGGAGAAGAGAAAAAAAAGAAAGAAAG
1 GGAAGAAAAGGAAAGGAGAAGAGAAAAAAAAG-AAGAAAG
* * *
33526054 AAGAAGAAAATGAAAGGAGAAGA-AAAAAGAAAGAAGGAAG
1 -GGAAGAAAAGGAAAGGAGAAGAGAAAAA-AAAGAAGAAAG
*
33526094 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAGAAGAAGAG
1 GGAAGAAAAGGAAAGGAGAAGAGAAAAAAAAGAAGAA-AG
*
33526134 GGAAG-GAAGGAAA
1 GGAAGAAAAGGAAA
33526147 AAAAAGAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
39 34 0.43
40 22 0.28
41 23 0.29
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (39 bp):
GGAAGAAAAGGAAAGGAGAAGAGAAAAAAAAGAAGAAAG
Found at i:33526162 original size:80 final size:75
Alignment explanation
Indices: 33525973--33526163 Score: 195
Period size: 80 Copynumber: 2.5 Consensus size: 75
33525963 AGAGGGAAAT
*
33525973 AAAGAAAGAAAG-A-AAG-AAAG-AAAG-AAAG-AAAGAAAAAGAATGGAAGAAAAGGGAAGGAG
1 AAAGAAAGAAAGAAGAAGAAAAGAAAAGAAAAGAAAAGAAAAAGAATGGAAGAAAAGGAAAGGAG
33526032 AAGAGAAAAA
66 AAGAGAAAAA
33526042 AAAGAAAGAAAGAAGAAGAAAATGAAAGGAGAAGAA-AAAAGAAAGAAGGAA-GGAAAGAAAAGG
1 AAAGAAAGAAAGAAGAAGAAAA-GAAA--AGAA-AAGAAAAGAAA-AA-GAATGG-AAGAAAAGG
33526105 AAAGGAGAAGAGAAAAA
59 AAAGGAGAAGAGAAAAA
33526122 AAAG-AAGAAGAGGGAAGGAAGGAAAA-AAAAGAAAAGAAAAGA
1 AAAGAAAGAA-A--GAA-GAA-GAAAAGAAAAGAAAAGAAAAGA
33526164 TAATTTTTTT
Statistics
Matches: 102, Mismatches: 1, Indels: 27
0.78 0.01 0.21
Matches are distributed among these distances:
69 12 0.12
70 1 0.01
71 3 0.03
72 3 0.03
73 1 0.01
74 2 0.02
76 2 0.02
77 1 0.01
78 9 0.09
79 11 0.11
80 43 0.42
82 6 0.06
83 3 0.03
84 5 0.05
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (75 bp):
AAAGAAAGAAAGAAGAAGAAAAGAAAAGAAAAGAAAAGAAAAAGAATGGAAGAAAAGGAAAGGAG
AAGAGAAAAA
Found at i:33526875 original size:74 final size:77
Alignment explanation
Indices: 33526791--33526936 Score: 192
Period size: 75 Copynumber: 1.9 Consensus size: 77
33526781 ATTTCGGGTT
*
33526791 TTTTACC-AAAATATTACAAAAAAATAAAAAAAT-ACGAAAATATTATAA-ACTTT-TTTATTTA
1 TTTTACCAAAAATATT--AAAAAAATAAAAAAATAACCAAAATATTATAAGACTTTATTTATTTA
*
33526852 CCAGAATAATGAGA
64 CCAAAATAATGAGA
* * **
33526866 TTTTACAAAAAATATTAAAAAAATAAAAAAATAACCAAAATGTTATAAGTTTTTATTTATTTACC
1 TTTTACCAAAAATATTAAAAAAATAAAAAAATAACCAAAATATTATAAGACTTTATTTATTTACC
33526931 AAAATA
66 AAAATA
33526937 TATATTTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
74 16 0.26
75 19 0.31
76 11 0.18
77 15 0.25
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (77 bp):
TTTTACCAAAAATATTAAAAAAATAAAAAAATAACCAAAATATTATAAGACTTTATTTATTTACC
AAAATAATGAGA
Found at i:33530013 original size:3 final size:3
Alignment explanation
Indices: 33530005--33530103 Score: 198
Period size: 3 Copynumber: 33.0 Consensus size: 3
33529995 TTTTGCTAAC
33530005 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
33530053 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
33530101 CAA
1 CAA
33530104 TAATAATAAT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:33530108 original size:3 final size:3
Alignment explanation
Indices: 33530102--33530129 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
33530092 CAACAACAAC
33530102 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
33530130 CTAACTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:33530270 original size:10 final size:11
Alignment explanation
Indices: 33530253--33530281 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
33530243 AAAAAAATAC
33530253 CTTCTTTTTCT
1 CTTCTTTTTCT
33530264 C-TCTTTTTCT
1 CTTCTTTTTCT
33530274 CTTCTTTT
1 CTTCTTTT
33530282 CCGCAGCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:33530412 original size:27 final size:27
Alignment explanation
Indices: 33530366--33530466 Score: 134
Period size: 27 Copynumber: 3.7 Consensus size: 27
33530356 AATACGAGTA
33530366 GTGCCGCCAAT--CAGTATGGCACCATTG
1 GTGCCGCCAATGGCA-T-TGGCACCATTG
33530393 GTGCCGCCAATGGCATTGGCACCATTG
1 GTGCCGCCAATGGCATTGGCACCATTG
** *
33530420 GTGCCGCCAATGGTTTTGGCACCTTTG
1 GTGCCGCCAATGGCATTGGCACCATTG
*
33530447 GTGCCGCCAATGGCTTTGGC
1 GTGCCGCCAATGGCATTGGC
33530467 GTGACCAAGG
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
27 65 0.96
28 1 0.01
29 2 0.03
ACGTcount: A:0.16, C:0.29, G:0.30, T:0.26
Consensus pattern (27 bp):
GTGCCGCCAATGGCATTGGCACCATTG
Found at i:33530553 original size:27 final size:27
Alignment explanation
Indices: 33530523--33530574 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
33530513 TTTTGTTTTT
33530523 TATATATTTTGGTAAATAAAAAAAATA
1 TATATATTTTGGTAAATAAAAAAAATA
*
33530550 TATATTTTTTGGTAAATAAAAAAAA
1 TATATATTTTGGTAAATAAAAAAAA
33530575 GTTATAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (27 bp):
TATATATTTTGGTAAATAAAAAAAATA
Found at i:33530580 original size:27 final size:26
Alignment explanation
Indices: 33530522--33530580 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 26
33530512 TTTTTGTTTT
33530522 TTATATATTTTGGTAAATAAAAAAAA
1 TTATATATTTTGGTAAATAAAAAAAA
*
33530548 TATATATTTTTTGGTAAATAAAAAAAA
1 T-TATATATTTTGGTAAATAAAAAAAA
33530575 GTTATA
1 -TTATA
33530581 ACATTTTAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 1 0.03
27 28 0.93
28 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (26 bp):
TTATATATTTTGGTAAATAAAAAAAA
Found at i:33536509 original size:15 final size:15
Alignment explanation
Indices: 33536475--33536526 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
33536465 AGAGTAAAAT
*
33536475 GAAAATTGGGAAGATG
1 GAAAATT-GAAAGATG
* *
33536491 GAAAATTGAAGGGTG
1 GAAAATTGAAAGATG
33536506 GAAAAATTGAAAGATG
1 G-AAAATTGAAAGATG
33536522 GAAAA
1 GAAAA
33536527 ATGGAAAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 10 0.33
16 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (15 bp):
GAAAATTGAAAGATG
Found at i:33536511 original size:16 final size:16
Alignment explanation
Indices: 33536485--33536534 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
33536475 GAAAATTGGG
33536485 AAGATGG-AAAATTGA
1 AAGATGGAAAAATTGA
* *
33536500 AGGGTGGAAAAATTGA
1 AAGATGGAAAAATTGA
*
33536516 AAGATGGAAAAATGGA
1 AAGATGGAAAAATTGA
33536532 AAG
1 AAG
33536535 TAATTTTCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 5 0.17
16 24 0.83
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (16 bp):
AAGATGGAAAAATTGA
Found at i:33536993 original size:35 final size:35
Alignment explanation
Indices: 33536947--33537022 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
33536937 TTCTTGCAAA
* *
33536947 GCTTTTTGAACTTTTTGTGTGAATATACTTTTGTT
1 GCTTTTTGAACTATTTGAGTGAATATACTTTTGTT
*
33536982 GCTTTTTGAACTATTTGAGTGAATATATTTTTGTT
1 GCTTTTTGAACTATTTGAGTGAATATACTTTTGTT
33537017 G-TTTTT
1 GCTTTTT
33537023 ACTAGAAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 5 0.13
35 33 0.87
ACGTcount: A:0.18, C:0.07, G:0.17, T:0.58
Consensus pattern (35 bp):
GCTTTTTGAACTATTTGAGTGAATATACTTTTGTT
Found at i:33542264 original size:15 final size:16
Alignment explanation
Indices: 33542238--33542267 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33542228 CGAATCTCAG
33542238 CTCTTGTTTCTCTTCT
1 CTCTTGTTTCTCTTCT
33542254 CTCTT-TTTCTCTTC
1 CTCTTGTTTCTCTTC
33542268 GAACAACGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.63
Consensus pattern (16 bp):
CTCTTGTTTCTCTTCT
Found at i:33544758 original size:18 final size:18
Alignment explanation
Indices: 33544720--33544755 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33544710 TTATTATTTT
*
33544720 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
33544738 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
33544756 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:33545445 original size:14 final size:14
Alignment explanation
Indices: 33545426--33545453 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33545416 TGTAGAACTT
33545426 TTTTAGAATTTTTA
1 TTTTAGAATTTTTA
33545440 TTTTAGAATTTTTA
1 TTTTAGAATTTTTA
33545454 ATATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTTAGAATTTTTA
Found at i:33545469 original size:18 final size:17
Alignment explanation
Indices: 33545446--33545508 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 17
33545436 TTTATTTTAG
*
33545446 AATTTTTAATATATATTT
1 AATTTTTAAAATAT-TTT
33545464 AATTTTTTAAAATATTTT
1 AA-TTTTTAAAATATTTT
*
33545482 GATTTTTTAAAATTATTTT
1 -AATTTTTAAAA-TATTTT
33545501 GAATTTTT
1 -AATTTTT
33545509 TCTGAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
18 14 0.36
19 25 0.64
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
AATTTTTAAAATATTTT
Found at i:33545472 original size:19 final size:19
Alignment explanation
Indices: 33545448--33545509 Score: 74
Period size: 18 Copynumber: 3.3 Consensus size: 19
33545438 TATTTTAGAA
*
33545448 TTTTTAATATATATTTAAT
1 TTTTTAAAATATATTTAAT
*
33545467 TTTTTAAAATAT-TTTGAT
1 TTTTTAAAATATATTTAAT
33545485 TTTTTAAAAT-TATTTTGAAT
1 TTTTTAAAATATA-TTT-AAT
33545505 TTTTT
1 TTTTT
33545510 CTGAAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.03
18 15 0.41
19 14 0.38
20 7 0.19
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTTAAAATATATTTAAT
Found at i:33549465 original size:25 final size:25
Alignment explanation
Indices: 33549415--33549463 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
33549405 AGTTTTCATC
* *
33549415 AAATATATTTATTTATTTTTTAAAT
1 AAATATAATTATTTATTTTGTAAAT
*
33549440 AAATATAATTATTTGTATTTGTAA
1 AAATATAATTATTTAT-TTTGTAA
33549464 TATGTAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
AAATATAATTATTTATTTTGTAAAT
Found at i:33549471 original size:7 final size:7
Alignment explanation
Indices: 33549459--33549533 Score: 68
Period size: 7 Copynumber: 11.0 Consensus size: 7
33549449 TATTTGTATT
33549459 TGTAATA
1 TGTAATA
33549466 TGTAATA
1 TGTAATA
33549473 TGTAATA
1 TGTAATA
33549480 TGTAATA
1 TGTAATA
33549487 TGTAA-A
1 TGTAATA
* *
33549493 TATAAAA
1 TGTAATA
* *
33549500 TGGCATTA
1 T-GTAATA
33549508 TGTTAATA
1 TG-TAATA
33549516 -GTAATA
1 TGTAATA
33549522 T-TAATA
1 TGTAATA
33549528 T-TAATA
1 TGTAATA
33549534 ATTTATGAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
6 21 0.37
7 30 0.53
8 6 0.11
ACGTcount: A:0.45, C:0.01, G:0.12, T:0.41
Consensus pattern (7 bp):
TGTAATA
Found at i:33553102 original size:19 final size:19
Alignment explanation
Indices: 33553066--33553105 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33553056 TTTATATTTT
*
33553066 TTTAAAAAATTTGTAAAAA
1 TTTAAAAAATTTGAAAAAA
*
33553085 TTTAAAAAATTCTAAAAAAA
1 TTTAAAAAATT-TGAAAAAA
33553105 T
1 T
33553106 ATGTGAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
TTTAAAAAATTTGAAAAAA
Found at i:33556372 original size:100 final size:100
Alignment explanation
Indices: 33556199--33556400 Score: 395
Period size: 100 Copynumber: 2.0 Consensus size: 100
33556189 CTCCATTTGG
33556199 ATTTACAACTACCATCAGTGAGATAGAATCTTAAAGCATATGCCTTTTCACTGTACCCTTTTTGT
1 ATTTACAACTACCATCAGTGAGATAGAATCTTAAAGCATATGCCTTTTCACTGTACCCTTTTTGT
*
33556264 TGTTTGGATTATTAATGGTGAATTGCATCTCCACC
66 TGTTTGGATTATTAATGGTGAACTGCATCTCCACC
33556299 ATTTACAACTACCATCAGTGAGATAGAATCTTAAAGCATATGCCTTTTCACTGTACCCTTTTTGT
1 ATTTACAACTACCATCAGTGAGATAGAATCTTAAAGCATATGCCTTTTCACTGTACCCTTTTTGT
33556364 TGTTTGGATTATTAATGGTGAACTGCATCTCCACC
66 TGTTTGGATTATTAATGGTGAACTGCATCTCCACC
33556399 AT
1 AT
33556401 CTCACCACAC
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (100 bp):
ATTTACAACTACCATCAGTGAGATAGAATCTTAAAGCATATGCCTTTTCACTGTACCCTTTTTGT
TGTTTGGATTATTAATGGTGAACTGCATCTCCACC
Found at i:33556793 original size:21 final size:21
Alignment explanation
Indices: 33556743--33556794 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
33556733 ACCATTGTTT
* *
33556743 CTAATCTCACTGCTACAATAT
1 CTAATCTCACCGCTACAATAA
* * *
33556764 CCAAACTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAATAA
33556785 CTAATCTCAC
1 CTAATCTCAC
33556795 TGCCACCGCT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.35, G:0.06, T:0.25
Consensus pattern (21 bp):
CTAATCTCACCGCTACAATAA
Found at i:33564090 original size:15 final size:15
Alignment explanation
Indices: 33564072--33564102 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33564062 ATTAAAATGA
33564072 TAAAATTATAATATT
1 TAAAATTATAATATT
33564087 TAAAATTATAATATT
1 TAAAATTATAATATT
33564102 T
1 T
33564103 TGTGTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATTATAATATT
Found at i:33574971 original size:2 final size:2
Alignment explanation
Indices: 33574964--33575042 Score: 126
Period size: 2 Copynumber: 40.5 Consensus size: 2
33574954 CTGACTCCCT
33574964 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
33575006 TC TC TC TC T- TT TC TG T- TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
33575043 TTTCTGTGTT
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 71 0.97
ACGTcount: A:0.00, C:0.46, G:0.01, T:0.53
Consensus pattern (2 bp):
TC
Found at i:33577593 original size:3 final size:3
Alignment explanation
Indices: 33577580--33577610 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
33577570 CTTTGTTTCT
33577580 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
33577611 TTAATTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:33580288 original size:21 final size:22
Alignment explanation
Indices: 33580257--33580312 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
33580247 ATAGTAATAA
*
33580257 TTAAAAT-TAAATTTTAAAA-T
1 TTAAAATATAAATTTAAAAATT
* *
33580277 TTGAAATATAAAAATTAAAAATT
1 TTAAAATAT-AAATTTAAAAATT
33580300 TTAAAATATAAAT
1 TTAAAATATAAAT
33580313 AAAAAAAGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 6 0.21
21 1 0.04
22 12 0.43
23 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TTAAAATATAAATTTAAAAATT
Found at i:33580305 original size:15 final size:15
Alignment explanation
Indices: 33580257--33580311 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
33580247 ATAGTAATAA
33580257 TTAAAATT--AAATT
1 TTAAAATTAAAAATT
** *
33580270 TTAAAATTTGAAATA
1 TTAAAATTAAAAATT
*
33580285 TAAAAATTAAAAATT
1 TTAAAATTAAAAATT
33580300 TTAAAATATAAA
1 TTAAAAT-TAAA
33580312 TAAAAAAAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
13 8 0.24
15 21 0.64
16 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
TTAAAATTAAAAATT
Done.