Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 76 of 128
Found at i:24895497 original size:126 final size:125
Alignment explanation
Indices: 24895250--24895563 Score: 430
Period size: 126 Copynumber: 2.4 Consensus size: 125
24895240 GCTGCTCAGA
* * * * *
24895250 GAGATAGGGTTCACGATCTTCAACCTATTCTATTGCTGACCAGGGAGATAGGACCTACAATCTTC
1 GAGATAGGATTCACAATCTTTAACCTATTC-ACTGCTGTCCAGGGAGATAGGA--T----TCTTC
* * *
24895315 AATCTATTCCAATGCTGCCCAGGGAGATAGAATTCTCAATTTTCAACCTATTCCACTGCAGACCA
59 AATCTATTCCAATGCTGCCCAAGGAGATAGAATTCTCAATCTTCAACATATTCCACTGCAGACCA
24895380 GG
124 GG
*
24895382 GAGATAGGATTCACAATCTTTAACCTATTACACTGCTGTCCAGGGAGATAGGATTCTTTAATCTA
1 GAGATAGGATTCACAATCTTTAACCTATT-CACTGCTGTCCAGGGAGATAGGATTCTTCAATCTA
* * *
24895447 TTCCACTGCTGCCTAAGGAGATAGAATTCTCAATCTTCAACATATTCCACTGCTGACCAGG
65 TTCCAATGCTGCCCAAGGAGATAGAATTCTCAATCTTCAACATATTCCACTGCAGACCAGG
*
24895508 GAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGAGAGATAGGATTC
1 GAGATAGGATTCACAATCTTTAACCTATT-CACTGCTGTCCAGGGAGATAGGATTC
24895564 ACAATCTTTA
Statistics
Matches: 167, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
126 119 0.71
130 1 0.01
132 46 0.28
133 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (125 bp):
GAGATAGGATTCACAATCTTTAACCTATTCACTGCTGTCCAGGGAGATAGGATTCTTCAATCTAT
TCCAATGCTGCCCAAGGAGATAGAATTCTCAATCTTCAACATATTCCACTGCAGACCAGG
Found at i:24895662 original size:88 final size:88
Alignment explanation
Indices: 24895603--24895925 Score: 547
Period size: 88 Copynumber: 3.7 Consensus size: 88
24895593 GGGGAGATAG
* * * * *
24895603 GGCTGGGGTCATCAATCTGCTTCGCTGTCGGTGTAAGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
24895668 TCCGCTGCAACCTAGGGAGGCAA
66 TCCGCTGCAACCTAGGGAGGCAA
*
24895691 GGCTGGTGTCTTCGATCTGCTTCGCTGTCTGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
24895756 TCCGCTGCAACCTAGGGAGGCAA
66 TCCGCTGCAACCTAGGGAGGCAA
* * *
24895779 GGCTGGTATCTTCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGT
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
24895844 TCCGCTGCAACCCAAGGAGGCAA
66 TCCGCTGCAACCTAGGGAGGCAA
24895867 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
24895926 CTGATCTGCT
Statistics
Matches: 221, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 221 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCTAGGGAGGCAA
Found at i:24895733 original size:44 final size:44
Alignment explanation
Indices: 24895685--24895911 Score: 149
Period size: 44 Copynumber: 5.2 Consensus size: 44
24895675 CAACCTAGGG
* *
24895685 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCTGTGCAGGA
1 AGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGGTGCAGGA
* * * ** * * *** *
24895729 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-C-AACCTAGGG
1 AGGCAAG-GCTGGTATCTTCGATCTGCTTCGCTGTCGGTGC-AGGA
*
24895773 AGGCAAGGCTGGTATCTTCGATCTGCTTTGCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGGTGCAGGA
* * * ** * ****
24895817 AGGCAAGATCTGCTATTTTTAACCTG-TTCCGCTG-CAACCCAAGG-
1 AGGCAAG-GCTGGTATCTTCGATCTGCTT-CGCTGTCGGTGC-AGGA
*
24895861 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGGTGCAGGA
24895905 AGGCAAG
1 AGGCAAG
24895912 ATCTGCTATT
Statistics
Matches: 127, Mismatches: 46, Indels: 20
0.66 0.24 0.10
Matches are distributed among these distances:
43 38 0.30
44 51 0.40
45 38 0.30
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (44 bp):
AGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGTCGGTGCAGGA
Found at i:24902094 original size:23 final size:23
Alignment explanation
Indices: 24902036--24902094 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
24902026 ATATCGTGAT
*
24902036 AACAAATACAATAGTAATAAATAC
1 AACAAATA-AATAGAAATAAATAC
*
24902060 AAC-AATGGAATAGAAATAATATA-
1 AACAAAT-AAATAGAAATAA-ATAC
24902083 AACAAATAAATA
1 AACAAATAAATA
24902095 AATAAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.64, C:0.08, G:0.07, T:0.20
Consensus pattern (23 bp):
AACAAATAAATAGAAATAAATAC
Found at i:24902103 original size:18 final size:18
Alignment explanation
Indices: 24902073--24902113 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
24902063 AATGGAATAG
*
24902073 AAAT-AATATAAACAAAT
1 AAATAAATAAAAACAAAT
24902090 AAATAAATAAAAACAAAT
1 AAATAAATAAAAACAAAT
*
24902108 CAATAA
1 AAATAA
24902114 CATGTAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (18 bp):
AAATAAATAAAAACAAAT
Found at i:24902503 original size:17 final size:17
Alignment explanation
Indices: 24902481--24902524 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
24902471 TAGGAAATAA
*
24902481 AAAATGTATATGTCTAT
1 AAAATGTATATGTATAT
*
24902498 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
24902515 -ATATGTATAT
1 AAAATGTATAT
24902525 AAAAGTTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:24902652 original size:3 final size:3
Alignment explanation
Indices: 24902644--24902682 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
24902634 GTATATATAG
* *
24902644 TAA TAA TAA TAA TAA TGA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
24902683 CTTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:24903078 original size:21 final size:21
Alignment explanation
Indices: 24902999--24903077 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
24902989 AAATTAAATC
24902999 TCTAAGATTACA-AAATCATA
1 TCTAAGATTACATAAATCATA
*
24903019 TCTTCTAAGATTGCATAAATCATA
1 ---TCTAAGATTACATAAATCATA
* *
24903043 TCTAAGATTGCATATATCATA
1 TCTAAGATTACATAAATCATA
24903064 TCTAAGATTACATA
1 TCTAAGATTACATA
24903078 TCCTTGAAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
21 33 0.63
23 11 0.21
24 8 0.15
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (21 bp):
TCTAAGATTACATAAATCATA
Found at i:24914462 original size:18 final size:18
Alignment explanation
Indices: 24914439--24914474 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24914429 ATTTATTTAC
24914439 TATTAACATAAATATTAA
1 TATTAACATAAATATTAA
* *
24914457 TATTAATATAAATTTTAA
1 TATTAACATAAATATTAA
24914475 ATTTATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTAACATAAATATTAA
Found at i:24914487 original size:21 final size:20
Alignment explanation
Indices: 24914457--24914495 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
24914447 TAAATATTAA
24914457 TATTAATATAAATTTTAAATT
1 TATTAATAT-AATTTTAAATT
* *
24914478 TATTATTATATTTTTAAA
1 TATTAATATAATTTTAAA
24914496 ATATTTATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTAATATAATTTTAAATT
Found at i:24918897 original size:3 final size:3
Alignment explanation
Indices: 24918889--24918921 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
24918879 TGATCTATAC
24918889 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
24918922 ATCAAATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:24921699 original size:63 final size:63
Alignment explanation
Indices: 24921632--24921767 Score: 272
Period size: 63 Copynumber: 2.2 Consensus size: 63
24921622 CAAAACTGTT
24921632 TTGAATAATAACAGTTGGGAAACTTTGAAAAATCACCATAAATGGAGGAAAATGAATTAGAGG
1 TTGAATAATAACAGTTGGGAAACTTTGAAAAATCACCATAAATGGAGGAAAATGAATTAGAGG
24921695 TTGAATAATAACAGTTGGGAAACTTTGAAAAATCACCATAAATGGAGGAAAATGAATTAGAGG
1 TTGAATAATAACAGTTGGGAAACTTTGAAAAATCACCATAAATGGAGGAAAATGAATTAGAGG
24921758 TTGAATAATA
1 TTGAATAATA
24921768 TATGAAATTG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 73 1.00
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.25
Consensus pattern (63 bp):
TTGAATAATAACAGTTGGGAAACTTTGAAAAATCACCATAAATGGAGGAAAATGAATTAGAGG
Found at i:24921852 original size:45 final size:45
Alignment explanation
Indices: 24921788--24921877 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
24921778 AATCTGGATG
24921788 GGTTTATTTTCAAATGAAAGAAATAGAGCAAGCAAAAGAGTTGTA
1 GGTTTATTTTCAAATGAAAGAAATAGAGCAAGCAAAAGAGTTGTA
24921833 GGTTTATTTTCAAATGAAAGAAATAGAGCAAGCAAAAGAGTTGTA
1 GGTTTATTTTCAAATGAAAGAAATAGAGCAAGCAAAAGAGTTGTA
24921878 TATTTGGGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (45 bp):
GGTTTATTTTCAAATGAAAGAAATAGAGCAAGCAAAAGAGTTGTA
Found at i:24928877 original size:33 final size:33
Alignment explanation
Indices: 24928813--24929038 Score: 167
Period size: 33 Copynumber: 6.5 Consensus size: 33
24928803 ATATAAAGGG
*
24928813 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
24928840 GGTTGCTAAGTGCTGATTCCTCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
24928873 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
24928915 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
24928948 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
24928990 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
24929023 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
24929039 ATCCACCGGT
Statistics
Matches: 159, Mismatches: 16, Indels: 42
0.73 0.07 0.19
Matches are distributed among these distances:
27 21 0.13
31 2 0.01
32 2 0.01
33 57 0.36
34 5 0.03
35 2 0.01
36 4 0.03
37 7 0.04
38 6 0.04
39 4 0.03
40 2 0.01
41 6 0.04
42 41 0.26
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:24928932 original size:42 final size:42
Alignment explanation
Indices: 24928873--24929009 Score: 184
Period size: 42 Copynumber: 3.5 Consensus size: 42
24928863 ATTCATTGGT
24928873 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
* *
24928915 GGTTGCTAAGTGCTGATTCC-CCG-A-C-T-CAT-TG---GT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
*
24928948 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
24928990 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
24929010 CCGACTCATT
Statistics
Matches: 80, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
33 20 0.25
34 3 0.04
35 1 0.01
36 3 0.04
37 3 0.04
38 3 0.04
39 3 0.04
40 1 0.01
41 3 0.04
42 40 0.50
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
Found at i:24928959 original size:75 final size:75
Alignment explanation
Indices: 24928836--24929046 Score: 386
Period size: 75 Copynumber: 2.8 Consensus size: 75
24928826 TGATTCCCCC
* *
24928836 AAGGGGTTGCTAAGTGCTGATTCCTCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
24928901 TTAAATGTGA
66 TTAAATGTGA
*
24928911 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
24928976 TTAAATGTGA
66 TTAAATGTGA
*
24928986 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
24929047 GTAATGGATA
Statistics
Matches: 131, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 131 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.31
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:24943743 original size:22 final size:25
Alignment explanation
Indices: 24943718--24943765 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 25
24943708 ATGTACATTG
24943718 TTTATTTCAAAT-CT-ATT-TCCAA
1 TTTATTTCAAATACTAATTATCCAA
24943740 TTTATTTCAAATACTAATTATCCAA
1 TTTATTTCAAATACTAATTATCCAA
24943765 T
1 T
24943766 GTTCTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.52
23 2 0.09
24 3 0.13
25 6 0.26
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTATTTCAAATACTAATTATCCAA
Found at i:24944050 original size:73 final size:72
Alignment explanation
Indices: 24943955--24944100 Score: 258
Period size: 73 Copynumber: 2.0 Consensus size: 72
24943945 GATTAAAATT
*
24943955 ATTATTGCTATTTGCATTTACCTATTATTTACTTGTTATTTTTTAGTGTGTTTGTGGATTACCAT
1 ATTATTGCTATTTGCATTTACCTATTATTTACTTGTTATTTTTTAGTGTG-TT-TGGAGTACCAT
24944020 TTATCTTGA
64 TTATCTTGA
24944029 ATTATTGCTA-TTGCATTTACCTATTATTTACTTGTTATTTTTTAGTGTGTTTGGAGTACCATTT
1 ATTATTGCTATTTGCATTTACCTATTATTTACTTGTTATTTTTTAGTGTGTTTGGAGTACCATTT
24944093 ATCTTGA
66 ATCTTGA
24944100 A
1 A
24944101 CATTGTATAT
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
71 20 0.28
72 2 0.03
73 39 0.55
74 10 0.14
ACGTcount: A:0.21, C:0.11, G:0.14, T:0.54
Consensus pattern (72 bp):
ATTATTGCTATTTGCATTTACCTATTATTTACTTGTTATTTTTTAGTGTGTTTGGAGTACCATTT
ATCTTGA
Found at i:24945245 original size:17 final size:17
Alignment explanation
Indices: 24945223--24945255 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
24945213 TAGAATTGGG
24945223 TTGAGAAAATTATTTAA
1 TTGAGAAAATTATTTAA
*
24945240 TTGAGAAATTTATTTA
1 TTGAGAAAATTATTTA
24945256 TTTATTTATT
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:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (17 bp):
TTGAGAAAATTATTTAA
Found at i:24945256 original size:4 final size:4
Alignment explanation
Indices: 24945247--24945271 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
24945237 TAATTGAGAA
24945247 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
24945272 AATTAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:24945649 original size:19 final size:22
Alignment explanation
Indices: 24945611--24945659 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
24945601 AAATAGTGAG
*
24945611 AATT-TATTTTCTAAGTAT-A-
1 AATTCTATTTTCTAAGAATAAC
24945630 AATTCTATTTTCTAA-AATAAC
1 AATTCTATTTTCTAAGAATAAC
24945651 AATTCTATT
1 AATTCTATT
24945660 GGTTTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 6 0.23
20 11 0.42
21 9 0.35
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (22 bp):
AATTCTATTTTCTAAGAATAAC
Found at i:24954095 original size:25 final size:26
Alignment explanation
Indices: 24954062--24954115 Score: 101
Period size: 25 Copynumber: 2.1 Consensus size: 26
24954052 GGATGTAAGC
24954062 AAATCTTTGCTTAGTAAGTTCGTAAT
1 AAATCTTTGCTTAGTAAGTTCGTAAT
24954088 AAAT-TTTGCTTAGTAAGTTCGTAAT
1 AAATCTTTGCTTAGTAAGTTCGTAAT
24954113 AAA
1 AAA
24954116 CTTAAACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (26 bp):
AAATCTTTGCTTAGTAAGTTCGTAAT
Found at i:24955805 original size:10 final size:11
Alignment explanation
Indices: 24955782--24955806 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24955772 ACAACAATTC
24955782 AAAAACATTAA
1 AAAAACATTAA
24955793 AAAAACATTAA
1 AAAAACATTAA
24955804 AAA
1 AAA
24955807 CGGAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAACATTAA
Found at i:24955997 original size:12 final size:12
Alignment explanation
Indices: 24955971--24956003 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
24955961 CATTATTAAC
24955971 TTATA-ATAATA
1 TTATATATAATA
*
24955982 TTATATATAATT
1 TTATATATAATA
24955994 TTATATATAA
1 TTATATATAA
24956004 ACCATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATATATAATA
Found at i:24961790 original size:20 final size:20
Alignment explanation
Indices: 24961765--24961802 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
24961755 ATTTTAGGTG
24961765 AAAACGAGTAAATTGACAAA
1 AAAACGAGTAAATTGACAAA
24961785 AAAACGAGTAAATTGACA
1 AAAACGAGTAAATTGACA
24961803 TAATCGGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.58, C:0.11, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAACGAGTAAATTGACAAA
Found at i:24962342 original size:101 final size:102
Alignment explanation
Indices: 24962226--24962408 Score: 271
Period size: 101 Copynumber: 1.8 Consensus size: 102
24962216 AGTGATGGTA
* *
24962226 ACGTGTGTAGTACTATTTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGTAC
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGTAC
24962289 TATGTGCAGGCTACTATGCATACCGGATAGCTTCGATC
65 TATGTGCAGGCTACTATGCATACCGGATAGCTTCGATC
* * * * *
24962327 ACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGATAGTGATGTTCACATGTGTTGTGCT
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTACT
*
24962392 ATGTGCATGCTACTATG
66 ATGTGCAGGCTACTATG
24962409 TGAACTGGTA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
101 37 0.51
102 31 0.43
103 4 0.06
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (102 bp):
ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTACT
ATGTGCAGGCTACTATGCATACCGGATAGCTTCGATC
Found at i:24962369 original size:51 final size:50
Alignment explanation
Indices: 24962226--24962406 Score: 159
Period size: 51 Copynumber: 3.6 Consensus size: 50
24962216 AGTGATGGTA
* *
24962226 ACGTGTGTAGTACTATTTGCAGGCTACTACGTGTACCAGA-ATGATAGGTC
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA-GATAGATC
* * * ** * * *
24962276 GCATGTGTAGTACTATGTGCAGGCTACTATGCATACCGGATAGCTTCGATC
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAG-ATAGATC
* * *
24962327 ACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGATAG-TGATGTTC
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGAT-A-GATC
* * * *
24962378 ACATGTGTTGTGCTATGTGCATGCTACTA
1 ACGTGTGTAGTACTATGTGCAGGCTACTA
24962407 TGTGAACTGG
Statistics
Matches: 102, Mismatches: 25, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
49 1 0.01
50 34 0.33
51 67 0.66
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (50 bp):
ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGATAGATC
Found at i:24962655 original size:16 final size:16
Alignment explanation
Indices: 24962634--24962665 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24962624 TGATTGAAAG
*
24962634 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
24962650 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
24962666 GCAACAAAAC
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:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:24974991 original size:99 final size:99
Alignment explanation
Indices: 24974820--24975197 Score: 595
Period size: 99 Copynumber: 3.9 Consensus size: 99
24974810 AAAACATGTG
* * * * * *
24974820 AGGTATGAAAGTGTTAACATATCATGTTGCGTATTTGATATTCTGTATGATTAATAAAGTG-ACT
1 AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTC-
24974884 GCACTTATTATGTTGAAAATGAATGGGAATGAATC
65 GCACTTATTATGTTGAAAATGAATGGGAATGAATC
24974919 AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
1 AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
* *
24974984 CACTTATTATGTTGAAAATGAATGGAAATTAATC
66 CACTTATTATGTTGAAAATGAATGGGAATGAATC
*
24975018 AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTTG
1 AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
24975083 CACTTATTATGTTGAAAATGAATGGGAATGAATC
66 CACTTATTATGTTGAAAATGAATGGGAATGAATC
* * *
24975117 AAGTATGAAAGTGTTAATATATCATGTTGCATACTTGATATACTGTATG-TTGATAAAGTGTTCG
1 AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
*
24975181 --CTCATTATG-TGAAAATG
66 CACTTATTATGTTGAAAATG
24975198 CTTTTGGTTT
Statistics
Matches: 262, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
95 8 0.03
96 8 0.03
98 14 0.05
99 231 0.88
100 1 0.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (99 bp):
AGGTATGAAAATGTTAATATATCATGTTGCATACTTGATATTCTGTATGATTGATAAAGTGTTCG
CACTTATTATGTTGAAAATGAATGGGAATGAATC
Found at i:24986335 original size:42 final size:43
Alignment explanation
Indices: 24986278--24986382 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 43
24986268 AGAAACCGTG
* *
24986278 AGGGTTGAATAGAAGCTCATA-AGAGCTGAATGGAAACCCATA
1 AGGGTTGAACAGAAGCTCATACAGAGCTAAATGGAAACCCATA
* *
24986320 AGGGTTAAACAGAAGCTCA-ACAGAGCTAAATGGAAACCCATT
1 AGGGTTGAACAGAAGCTCATACAGAGCTAAATGGAAACCCATA
* *
24986362 AGGGTTGAACGGAAACTCATA
1 AGGGTTGAACAGAAGCTCATA
24986383 TGAGTTAAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.02
42 52 0.96
43 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (43 bp):
AGGGTTGAACAGAAGCTCATACAGAGCTAAATGGAAACCCATA
Found at i:24998558 original size:19 final size:19
Alignment explanation
Indices: 24998536--24998572 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24998526 AAATGATATT
24998536 ATATAAAAAAAATAAAAAC
1 ATATAAAAAAAATAAAAAC
**
24998555 ATATAAAATTAATAAAAA
1 ATATAAAAAAAATAAAAA
24998573 TGCGTTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (19 bp):
ATATAAAAAAAATAAAAAC
Found at i:25003532 original size:17 final size:17
Alignment explanation
Indices: 25003512--25003544 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25003502 GTATGTATAA
25003512 TTGAAT-TGTAAATTGAT
1 TTGAATGTG-AAATTGAT
25003529 TTGAATGTGAAATTGA
1 TTGAATGTGAAATTGA
25003545 ATATTGACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (17 bp):
TTGAATGTGAAATTGAT
Found at i:25009583 original size:2 final size:2
Alignment explanation
Indices: 25009576--25009602 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25009566 CTAACATTCT
25009576 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
25009603 TCAAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25011269 original size:21 final size:21
Alignment explanation
Indices: 25011229--25011269 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25011219 AATTTTAAAA
* *
25011229 TATTTTTAAAATATATTTTTT
1 TATTTTTAAAATAAAATTTTT
25011250 TATTTTTAAAATAAAATTTT
1 TATTTTTAAAATAAAATTTT
25011270 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTTAAAATAAAATTTTT
Found at i:25029131 original size:16 final size:17
Alignment explanation
Indices: 25029110--25029145 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
25029100 TCCTTCTTTC
25029110 TCTTTTTC-TTTTTCTT
1 TCTTTTTCGTTTTTCTT
*
25029126 TCTTTTTCGTTTTTGTT
1 TCTTTTTCGTTTTTCTT
25029143 TCT
1 TCT
25029146 CTGTTTTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.78
Consensus pattern (17 bp):
TCTTTTTCGTTTTTCTT
Found at i:25029202 original size:5 final size:5
Alignment explanation
Indices: 25029192--25029220 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
25029182 TTTATTTGTT
25029192 TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATA
25029221 TATTTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:25040424 original size:43 final size:43
Alignment explanation
Indices: 25040357--25040479 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
25040347 TTTTCGAAAA
25040357 GTGTTTTCGTGTAAGACCACGTCTAGGAC-GTTGGCATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTAGGACAG-TGGCATCGACTT
* *
25040400 GTGTTTTCGTGTAAGGCTC-TGTCTAGGACAGTGGCATCGA-TCT
1 GTGTTTTCGTGTAAGAC-CACGTCTAGGACAGTGGCATCGACT-T
* * * *
25040443 GTGGTTACATGTAAGACCACGTCTGGGAC-GTTGGCAT
1 GTGTTTTCGTGTAAGACCACGTCTAGGACAG-TGGCAT
25040480 TGTACGAGCC
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
42 3 0.04
43 62 0.93
44 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.32
Consensus pattern (43 bp):
GTGTTTTCGTGTAAGACCACGTCTAGGACAGTGGCATCGACTT
Found at i:25042918 original size:15 final size:15
Alignment explanation
Indices: 25042898--25042926 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25042888 TCTTCTTACT
25042898 GATTTATTAATTATC
1 GATTTATTAATTATC
25042913 GATTTATTAATTAT
1 GATTTATTAATTAT
25042927 TGTCATTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (15 bp):
GATTTATTAATTATC
Found at i:25045125 original size:35 final size:35
Alignment explanation
Indices: 25045086--25045206 Score: 161
Period size: 35 Copynumber: 3.5 Consensus size: 35
25045076 TACACAGTTA
* *
25045086 ACCATCCAACACACTAGATGCTCATAAGAGCCAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCTAGT
* **
25045121 ACCATCCAACATACCAGATGCTCATAAGAAATAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCTAGT
* *
25045156 ACCATCCAACACACCAGATGCTTAGAAGAGCTAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCTAGT
* *
25045191 ACCATCTAGCACACCA
1 ACCATCCAACACACCA
25045207 AATAACATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 74 1.00
ACGTcount: A:0.39, C:0.31, G:0.13, T:0.17
Consensus pattern (35 bp):
ACCATCCAACACACCAGATGCTCATAAGAGCTAGT
Found at i:25057991 original size:68 final size:69
Alignment explanation
Indices: 25057892--25058019 Score: 213
Period size: 68 Copynumber: 1.9 Consensus size: 69
25057882 TCTAAATTTA
25057892 AAAAAAAGCCTAAAAGCCCAAATAAAAAAATCGACATATATAGTTAATTTAGCCCAACTTTCTCT
1 AAAAAAAGCCTAAAAGCCCAAATAAAAAAATCGACATATATAGTTAATTTAGCCCAACTTTCTCT
25057957 CTCC
66 CTCC
* * * *
25057961 AAAAATAGCCT-AAATCTCAAATAAAAAAATCGACATATATAGTTAATTTAGCCTAACTT
1 AAAAAAAGCCTAAAAGCCCAAATAAAAAAATCGACATATATAGTTAATTTAGCCCAACTT
25058020 ATCATTTAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
68 45 0.82
69 10 0.18
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (69 bp):
AAAAAAAGCCTAAAAGCCCAAATAAAAAAATCGACATATATAGTTAATTTAGCCCAACTTTCTCT
CTCC
Found at i:25068467 original size:16 final size:16
Alignment explanation
Indices: 25068435--25068476 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
25068425 GGTTGGAGTG
*
25068435 AATGGAATAAGACTGT
1 AATGGAATAAGAATGT
25068451 AATGGAAT-AGAAATGT
1 AATGGAATAAG-AATGT
*
25068467 ACTGGAATAA
1 AATGGAATAA
25068477 AGTTGTAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 19 0.86
17 1 0.05
ACGTcount: A:0.48, C:0.05, G:0.24, T:0.24
Consensus pattern (16 bp):
AATGGAATAAGAATGT
Found at i:25068748 original size:62 final size:58
Alignment explanation
Indices: 25068680--25068827 Score: 174
Period size: 62 Copynumber: 2.5 Consensus size: 58
25068670 TTTTAATAAG
* *
25068680 ATTATTAGTAAATATAATTTAATAAATATAGAAAGTAAATAATTAAATCATATT-TCAATATA
1 ATTATTATTAAATATAATTTAATAAA-AT---AA-TAAATAATTAAATAATATTCTCAATATA
* * *
25068742 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAATATTCTTAATATA
1 ATTATTATTAAATATAATTTAATAAAATAATAAATAATTAAATAATATTCTCAATATA
25068800 ATTATTATTAAAATATGAA-TTAATAAAA
1 ATTATTATT-AAATAT-AATTTAATAAAA
25068828 ATCATAACAT
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
57 16 0.21
58 18 0.23
59 15 0.19
60 2 0.03
61 2 0.03
62 25 0.32
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAATAATAAATAATTAAATAATATTCTCAATATA
Found at i:25069695 original size:14 final size:14
Alignment explanation
Indices: 25069671--25069704 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
25069661 CATTGTACAA
25069671 TATAT-ATAAGAAT
1 TATATGATAAGAAT
25069684 TATATGATAAGAAT
1 TATATGATAAGAAT
25069698 TATATGA
1 TATATGA
25069705 ATCCATCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (14 bp):
TATATGATAAGAAT
Found at i:25070871 original size:157 final size:158
Alignment explanation
Indices: 25070571--25070889 Score: 595
Period size: 157 Copynumber: 2.0 Consensus size: 158
25070561 GCAAAAAATG
25070571 ATAATAAATCTCATCATTAATATTATTATAATAAATTATAATAAAAAATAGAGATTAATTAATGA
1 ATAATAAATCTCA-CATTAATATTATTATAATAAATTATAATAAAAAATAGAGATTAATTAATGA
25070636 ATTCATTAGTGAGAGCTAAACTTTATGATAAAGATAAAGAAACACAGGAGGAACCCATATACAAC
65 ATTCATTAGTGAGAGCTAAACTTTATGATAAAGATAAAGAAACACAGGAGGAACCCATATACAAC
* *
25070701 TTCAGACGAAGTATACGCTTTAGGTCAAC
130 TTCAGACAAAGTATACACTTTAGGTCAAC
25070730 ATAATAAATCTC-CATTAATATTATTATAATAAATTATAATAAAAAATAGAGATTAATTAATGAA
1 ATAATAAATCTCACATTAATATTATTATAATAAATTATAATAAAAAATAGAGATTAATTAATGAA
*
25070794 TTCATTAGTGAGAGCTAAACTTTATGATATAGATAAAGAAACACAGGAGGAACCCATATACAACT
66 TTCATTAGTGAGAGCTAAACTTTATGATAAAGATAAAGAAACACAGGAGGAACCCATATACAACT
25070859 TCAGACAAAGTATACACTTTAGGTCAAC
131 TCAGACAAAGTATACACTTTAGGTCAAC
25070887 ATA
1 ATA
25070890 TATGTCTGTC
Statistics
Matches: 157, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
157 145 0.92
159 12 0.08
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (158 bp):
ATAATAAATCTCACATTAATATTATTATAATAAATTATAATAAAAAATAGAGATTAATTAATGAA
TTCATTAGTGAGAGCTAAACTTTATGATAAAGATAAAGAAACACAGGAGGAACCCATATACAACT
TCAGACAAAGTATACACTTTAGGTCAAC
Found at i:25072666 original size:9 final size:9
Alignment explanation
Indices: 25072652--25072688 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
25072642 TATAGTTTAA
25072652 TATTCGAAT
1 TATTCGAAT
25072661 TATTCGAAT
1 TATTCGAAT
*
25072670 TATTCGAGT
1 TATTCGAAT
25072679 TATTCGAAT
1 TATTCGAAT
25072688 T
1 T
25072689 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:25072735 original size:58 final size:59
Alignment explanation
Indices: 25072671--25072785 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 59
25072661 TATTCGAATT
25072671 ATTCGAGTT-ATTCGAAT-TCGAA-AACTCAACTCGATTCGAACTCGAAATTCGAAAAAAA
1 ATTCGAGTTGATTCGAATATCGAATAACTCAACTCG-TT-GAACTCGAAATTCGAAAAAAA
* * *
25072729 ATTCGAGTTGATTCGAATAACTCGAATAACTCGATTCGTTTAACTCGAAATTCGAAA
1 ATTCGAGTTGATTCGAAT-A-TCGAATAACTCAACTCGTTGAACTCGAAATTCGAAA
25072786 TTTTTTTCGA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
58 9 0.18
59 8 0.16
61 16 0.33
62 7 0.14
63 9 0.18
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (59 bp):
ATTCGAGTTGATTCGAATATCGAATAACTCAACTCGTTGAACTCGAAATTCGAAAAAAA
Found at i:25076322 original size:18 final size:18
Alignment explanation
Indices: 25076289--25076346 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
25076279 AAGGTTTTCT
25076289 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
*
25076304 TATTGTTGATAGTGACGA
1 TATTGATGATAGTGACGA
* *
25076322 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
25076340 TATTGAT
1 TATTGAT
25076347 CATGACCTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 10 0.28
16 1 0.03
18 25 0.69
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.40
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:25087087 original size:31 final size:31
Alignment explanation
Indices: 25087049--25087110 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
25087039 GGCTCGTGTA
25087049 AGTAGGAAATAGAAAATATCTATTCTAGTTC
1 AGTAGGAAATAGAAAATATCTATTCTAGTTC
25087080 AGTAGGAAATAGAAAATATCTATTCTAGTTC
1 AGTAGGAAATAGAAAATATCTATTCTAGTTC
25087111 TATCATCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (31 bp):
AGTAGGAAATAGAAAATATCTATTCTAGTTC
Found at i:25093986 original size:26 final size:25
Alignment explanation
Indices: 25093955--25094010 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
25093945 GAAGCTCTGG
*
25093955 AGAGCCATTAATCAAAAAGCTCATAA
1 AGAGCCATTAATCAAAAAGCTC-CAA
* * *
25093981 AGAGCCTTTAATCGAGAAGCTCCAA
1 AGAGCCATTAATCAAAAAGCTCCAA
25094006 AGAGC
1 AGAGC
25094011 TATATATCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (25 bp):
AGAGCCATTAATCAAAAAGCTCCAA
Found at i:25100794 original size:25 final size:25
Alignment explanation
Indices: 25100763--25100866 Score: 111
Period size: 25 Copynumber: 4.2 Consensus size: 25
25100753 AGCCCTCTCT
*
25100763 TGAGCCATATAACAGGAAGCTCGTG
1 TGAGCCATATAACAGGAAGCTCATG
* * * *
25100788 TGAGCCATGTAACGGGAAGCTTATT
1 TGAGCCATATAACAGGAAGCTCATG
* * *
25100813 TGGGCTATATAACAGGAAGCTCATA
1 TGAGCCATATAACAGGAAGCTCATG
* *
25100838 AGAGCCATAT-TCAGGAAGCTCATG
1 TGAGCCATATAACAGGAAGCTCATG
25100862 TGAGC
1 TGAGC
25100867 TAATAACGGG
Statistics
Matches: 62, Mismatches: 17, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
24 16 0.26
25 46 0.74
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (25 bp):
TGAGCCATATAACAGGAAGCTCATG
Found at i:25100889 original size:48 final size:50
Alignment explanation
Indices: 25100763--25100906 Score: 127
Period size: 50 Copynumber: 2.9 Consensus size: 50
25100753 AGCCCTCTCT
* * ** ** * *
25100763 TGAGCCATATAACAGGAAGCTCGTGTGAGCCATGTAA-CGGGAAGCTTATT
1 TGAGCTATATAACAGGAAGCTCATAAGAGCCAT-TAATTAGGAAGCTCATG
*
25100813 TGGGCTATATAACAGGAAGCTCATAAGAGCCA-T-ATTCAGGAAGCTCATG
1 TGAGCTATATAACAGGAAGCTCATAAGAGCCATTAATT-AGGAAGCTCATG
* *
25100862 TGAGCTA-ATAACGGGTAGCTC-TGAAGAGCCATTAATTAGGAAGCT
1 TGAGCTATATAACAGGAAGCTCAT-AAGAGCCATTAATTAGGAAGCT
25100907 TCGGATAGCC
Statistics
Matches: 77, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
47 2 0.03
48 21 0.27
49 24 0.31
50 30 0.39
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (50 bp):
TGAGCTATATAACAGGAAGCTCATAAGAGCCATTAATTAGGAAGCTCATG
Found at i:25107169 original size:18 final size:18
Alignment explanation
Indices: 25107130--25107169 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25107120 CGCATAAAAA
* *
25107130 GAAAGTAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
*
25107148 GAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
25107166 GAAA
1 GAAA
25107170 AAAGGGGGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.12
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:25113283 original size:23 final size:23
Alignment explanation
Indices: 25113255--25113311 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
25113245 AGTCTAAGAA
*
25113255 ATAAAATTAAAAA-AACAAAAAAC
1 ATAAAAATAAAAATAA-AAAAAAC
*
25113278 A-AAAAATAAAAATAAAAAAAAG
1 ATAAAAATAAAAATAAAAAAAAC
25113300 ATAAAAATAAAA
1 ATAAAAATAAAA
25113312 GTGAAGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (23 bp):
ATAAAAATAAAAATAAAAAAAAC
Found at i:25113290 original size:6 final size:6
Alignment explanation
Indices: 25113253--25113311 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
25113243 GAAGTCTAAG
* *
25113253 AAATAA AATTAA AAA-AA CAAA-AA ACA-AA AAATAA AAATAA AAA-AA
1 AAATAA AAATAA AAATAA -AAATAA AAATAA AAATAA AAATAA AAATAA
*
25113298 AGATAA AAATAA AA
1 AAATAA AAATAA AA
25113312 GTGAAGAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
5 12 0.27
6 32 0.73
ACGTcount: A:0.83, C:0.03, G:0.02, T:0.12
Consensus pattern (6 bp):
AAATAA
Found at i:25113298 original size:17 final size:18
Alignment explanation
Indices: 25113273--25113311 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
25113263 AAAAAAACAA
25113273 AAAACAAAAAATAAAAAT
1 AAAACAAAAAATAAAAAT
*
25113291 AAAA-AAAAGATAAAAAT
1 AAAACAAAAAATAAAAAT
25113308 AAAA
1 AAAA
25113312 GTGAAGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.10
Consensus pattern (18 bp):
AAAACAAAAAATAAAAAT
Found at i:25113303 original size:11 final size:12
Alignment explanation
Indices: 25113253--25113311 Score: 54
Period size: 11 Copynumber: 5.2 Consensus size: 12
25113243 GAAGTCTAAG
*
25113253 AAATAAAATTAA
1 AAATAAAAATAA
25113265 AAA-AACAAA-AA
1 AAATAA-AAATAA
*
25113276 ACA-AAAAATAA
1 AAATAAAAATAA
25113287 AAATAAAAA-AA
1 AAATAAAAATAA
*
25113298 AGATAAAAATAA
1 AAATAAAAATAA
25113310 AA
1 AA
25113312 GTGAAGAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
10 3 0.08
11 22 0.58
12 13 0.34
ACGTcount: A:0.83, C:0.03, G:0.02, T:0.12
Consensus pattern (12 bp):
AAATAAAAATAA
Found at i:25114857 original size:12 final size:12
Alignment explanation
Indices: 25114829--25114906 Score: 63
Period size: 12 Copynumber: 6.4 Consensus size: 12
25114819 AGGTAGCAAG
25114829 AATAATAATATAA
1 AATAATAATA-AA
*
25114842 AATAATACTAAA
1 AATAATAATAAA
25114854 AATAATAATAAA
1 AATAATAATAAA
*
25114866 AGCT-A-AATAGCAA
1 A-ATAATAATA--AA
25114879 AATAA-AATAAA
1 AATAATAATAAA
**
25114890 AATAAGCATAAA
1 AATAATAATAAA
25114902 AATAA
1 AATAA
25114907 AATTAATTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
11 11 0.20
12 26 0.47
13 18 0.33
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.22
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:25115871 original size:109 final size:109
Alignment explanation
Indices: 25115699--25115914 Score: 290
Period size: 109 Copynumber: 2.0 Consensus size: 109
25115689 ACTACAGTAT
*
25115699 TCACACGACCTAGGACACGCCCGTATGTCCAGGCCGTGTGTGCCAAGCCATATGGACCACCTCAA
1 TCACACGACCTAGGACACACCCGTATGTCCAGGCCGTGTGTGCCAAGCCATATGGACCACCTCAA
25115764 GCAGTGTAATGATCGAAATATGGAAAAAAAATAAGTCCCAGGAC
66 GCAGTGTAATGATCGAAATATGGAAAAAAAATAAGTCCCAGGAC
* * ** * * * *
25115808 TCACACGGCCTAGGACACACCCGTGTGTCGTGGCC-TGTGTCGTCAAGTCGTGTGGACCACCTCA
1 TCACACGACCTAGGACACACCCGTATGTCCAGGCCGTGTGT-GCCAAGCCATATGGACCACCTCA
* * * * *
25115872 GGCTGTGTAATGATTGAAATTTGGAAAAAAAATAAGTCTCAGG
65 AGCAGTGTAATGATCGAAATATGGAAAAAAAATAAGTCCCAGG
25115915 CCGTGTTACC
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
108 5 0.05
109 87 0.95
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (109 bp):
TCACACGACCTAGGACACACCCGTATGTCCAGGCCGTGTGTGCCAAGCCATATGGACCACCTCAA
GCAGTGTAATGATCGAAATATGGAAAAAAAATAAGTCCCAGGAC
Found at i:25118750 original size:42 final size:42
Alignment explanation
Indices: 25118648--25118743 Score: 156
Period size: 42 Copynumber: 2.3 Consensus size: 42
25118638 GATTTATTCA
* * *
25118648 AGGCTCCCGCTCATCCATGCACCAAGGTGCCGATGGTGCTCG
1 AGGCTCCCGCACATCCAAGCAACAAGGTGCCGATGGTGCTCG
*
25118690 AGGCTCCCGCACATCCAAGCAACAAGGTGTCGATGGTGCTCG
1 AGGCTCCCGCACATCCAAGCAACAAGGTGCCGATGGTGCTCG
25118732 AGGCTCCCGCAC
1 AGGCTCCCGCAC
25118744 GACCAAGGGC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (42 bp):
AGGCTCCCGCACATCCAAGCAACAAGGTGCCGATGGTGCTCG
Found at i:25120411 original size:20 final size:20
Alignment explanation
Indices: 25120371--25120422 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
25120361 TTGGAGCCAG
*
25120371 AGATATCGATACCAAAGAAA
1 AGATATTGATACCAAAGAAA
* **
25120391 ATATATTGATACCAATTAAA
1 AGATATTGATACCAAAGAAA
*
25120411 AGGTATTGATAC
1 AGATATTGATAC
25120423 TGGATCGATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (20 bp):
AGATATTGATACCAAAGAAA
Found at i:25120581 original size:21 final size:20
Alignment explanation
Indices: 25120557--25120607 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
25120547 GGAGCAATAC
* *
25120557 TAACTTGTTTTAAAGCAATTT
1 TAACTTGATTGAAA-CAATTT
* *
25120578 TAACTCGATTGAAACCATTT
1 TAACTTGATTGAAACAATTT
25120598 TAACTTGATT
1 TAACTTGATT
25120608 AAAAGTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (20 bp):
TAACTTGATTGAAACAATTT
Found at i:25125931 original size:3 final size:3
Alignment explanation
Indices: 25125923--25125947 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25125913 TAAATAAACT
25125923 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
25125948 CCAACACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:25126469 original size:23 final size:23
Alignment explanation
Indices: 25126437--25126485 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
25126427 TTTTTTTAAA
* *
25126437 AAATTGCAAATGAAATTATATAT
1 AAATTACAAATGAAATTATACAT
*
25126460 AAATTACAAATGCAATTATACAT
1 AAATTACAAATGAAATTATACAT
25126483 AAA
1 AAA
25126486 AAACATATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (23 bp):
AAATTACAAATGAAATTATACAT
Found at i:25126588 original size:24 final size:25
Alignment explanation
Indices: 25126561--25126624 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
25126551 ACAAAATAAA
25126561 TTATACATAAAAATATATAC-CAAT
1 TTATACATAAAAATATATACTCAAT
*
25126585 TTATA-AGTGAAAAA-ATATACTTAAT
1 TTATACA-T-AAAAATATATACTCAAT
*
25126610 TATATCCATAAAAAT
1 T-TATACATAAAAAT
25126625 GTACTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
23 1 0.03
24 12 0.38
25 14 0.44
26 4 0.12
27 1 0.03
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.34
Consensus pattern (25 bp):
TTATACATAAAAATATATACTCAAT
Found at i:25127426 original size:25 final size:25
Alignment explanation
Indices: 25127376--25127428 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
25127366 TAAAGGAAGA
*
25127376 AAATAATGTCAATAATAGAATTAAT
1 AAATAATGTCAATAATAGAATAAAT
*
25127401 AAATAATGTTATATAATA-AATAAAT
1 AAATAATGTCA-ATAATAGAATAAAT
25127426 AAA
1 AAA
25127429 AAGAAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (25 bp):
AAATAATGTCAATAATAGAATAAAT
Found at i:25129881 original size:27 final size:28
Alignment explanation
Indices: 25129831--25129893 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 28
25129821 TACATAGTAC
* *
25129831 ATATATATGTGTGGTTTTGCTATATATA
1 ATATATATGTGAGGTTTTACTATATATA
*
25129859 ATATATATGT-AGGTTTTATTATATATA
1 ATATATATGTGAGGTTTTACTATATATA
25129886 ATATATAT
1 ATATATAT
25129894 ATGCATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 22 0.69
28 10 0.31
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.51
Consensus pattern (28 bp):
ATATATATGTGAGGTTTTACTATATATA
Found at i:25130259 original size:17 final size:18
Alignment explanation
Indices: 25130224--25130261 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
25130214 TGTGAGCCAA
**
25130224 TTATATTTGTAAATTATG
1 TTATATTTGTAAACCATG
25130242 TTATATTT-TAAACCATG
1 TTATATTTGTAAACCATG
25130259 TTA
1 TTA
25130262 ACTTGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (18 bp):
TTATATTTGTAAACCATG
Found at i:25130297 original size:36 final size:36
Alignment explanation
Indices: 25130256--25130327 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
25130246 ATTTTAAACC
*
25130256 ATGTTAACTTGGTGAATTATATTATTATGGGGAACT
1 ATGTTAACTTGGTGAATTATATTAATATGGGGAACT
* * * *
25130292 ATGTTAATTTGGTGATTTGTATTAATATGGTGAACT
1 ATGTTAACTTGGTGAATTATATTAATATGGGGAACT
25130328 GTATTAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.44
Consensus pattern (36 bp):
ATGTTAACTTGGTGAATTATATTAATATGGGGAACT
Found at i:25130322 original size:18 final size:18
Alignment explanation
Indices: 25130265--25130335 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
25130255 CATGTTAACT
* * *
25130265 TGGTGAATTATATTATTA
1 TGGTGAACTGTATTAATA
* * * *
25130283 TGGGGAACTATGTTAATT
1 TGGTGAACTGTATTAATA
**
25130301 TGGTGATTTGTATTAATA
1 TGGTGAACTGTATTAATA
25130319 TGGTGAACTGTATTAAT
1 TGGTGAACTGTATTAAT
25130336 TTGCCAGACT
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.45
Consensus pattern (18 bp):
TGGTGAACTGTATTAATA
Found at i:25130335 original size:36 final size:36
Alignment explanation
Indices: 25130259--25130338 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
25130249 TTAAACCATG
* * *
25130259 TTAACTTGGTGAATTATATTATTATGGGGAACTATG
1 TTAATTTGGTGAATTATATTAATATGGGGAACTATA
* * * *
25130295 TTAATTTGGTGATTTGTATTAATATGGTGAACTGTA
1 TTAATTTGGTGAATTATATTAATATGGGGAACTATA
25130331 TTAATTTG
1 TTAATTTG
25130339 CCAGACTATG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (36 bp):
TTAATTTGGTGAATTATATTAATATGGGGAACTATA
Found at i:25131021 original size:51 final size:51
Alignment explanation
Indices: 25130916--25131024 Score: 143
Period size: 51 Copynumber: 2.1 Consensus size: 51
25130906 TATAATGGAG
* *
25130916 TATGAACTATTATTTTGCATGGATTGTTATTCGGTATGAATTGATATTTCA
1 TATGAACTATTATTTTGCATGGATTGTCATTCGGTATGAACTGATATTTCA
*
25130967 TATGAACTATTATTTTGCAT-GAGTTGTCATTTGGTATGAACT-ATTACTTT-A
1 TATGAACTATTATTTTGCATGGA-TTGTCATTCGGTATGAACTGA-TA-TTTCA
25131018 TATGAAC
1 TATGAAC
25131025 AGATGTTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
50 3 0.06
51 46 0.88
52 3 0.06
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (51 bp):
TATGAACTATTATTTTGCATGGATTGTCATTCGGTATGAACTGATATTTCA
Found at i:25135311 original size:29 final size:31
Alignment explanation
Indices: 25135261--25135321 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 31
25135251 TTCGGTATTT
**
25135261 AGAATTTAGTTTTTCTATTTTT-AT-TTTTA
1 AGAATTTAACTTTTCTATTTTTCATATTTTA
25135290 AGAATTTAACTTTTCT-TCTTTTCATATTTTA
1 AGAATTTAACTTTTCTAT-TTTTCATATTTTA
25135321 A
1 A
25135322 CACAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 1 0.04
29 18 0.67
30 2 0.07
31 6 0.22
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (31 bp):
AGAATTTAACTTTTCTATTTTTCATATTTTA
Found at i:25137277 original size:11 final size:11
Alignment explanation
Indices: 25137257--25137286 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
25137247 TAATAAAAAA
25137257 TAAAAATATTT
1 TAAAAATATTT
*
25137268 TAAAAGTATTT
1 TAAAAATATTT
25137279 TAAAAATA
1 TAAAAATA
25137287 AAAAATAAAA
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:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:25137297 original size:13 final size:13
Alignment explanation
Indices: 25137279--25137306 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
25137269 AAAAGTATTT
25137279 TAAAAATAAAAAA
1 TAAAAATAAAAAA
25137292 TAAAAATAAAAAA
1 TAAAAATAAAAAA
25137305 TA
1 TA
25137307 TATATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:25137394 original size:13 final size:13
Alignment explanation
Indices: 25137376--25137401 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25137366 NNNNNNNNNN
25137376 AAAATAAAAAATA
1 AAAATAAAAAATA
25137389 AAAATAAAAAATA
1 AAAATAAAAAATA
25137402 TATATTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:25138277 original size:18 final size:19
Alignment explanation
Indices: 25138239--25138277 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
25138229 TCCTTCATAT
25138239 GCACCACCTTTTCTAGGTG
1 GCACCACCTTTTCTAGGTG
25138258 GCACCA-CTTATTCT-GGTG
1 GCACCACCTT-TTCTAGGTG
25138276 GC
1 GC
25138278 TATAGTCGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (19 bp):
GCACCACCTTTTCTAGGTG
Found at i:25140045 original size:13 final size:13
Alignment explanation
Indices: 25140027--25140087 Score: 104
Period size: 13 Copynumber: 4.7 Consensus size: 13
25140017 CTCAAATTTT
25140027 TCAAAAGCACTTC
1 TCAAAAGCACTTC
25140040 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
25140053 TGAAAAGTACTTC
1 TCAAAAGCACTTC
25140066 TCAAAAGCACTTC
1 TCAAAAGCACTTC
25140079 TCAAAAGCA
1 TCAAAAGCA
25140088 ATGAAGAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:25140314 original size:13 final size:13
Alignment explanation
Indices: 25140290--25140324 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
25140280 CTCAAATTTT
25140290 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
25140303 TTAAAAGTACTTC
1 TCAAAAGCACTTC
25140316 TCAAAAGCA
1 TCAAAAGCA
25140325 ATGAAGAACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:25142084 original size:207 final size:207
Alignment explanation
Indices: 25141843--25142261 Score: 829
Period size: 207 Copynumber: 2.0 Consensus size: 207
25141833 TGCTCACCCT
*
25141843 TATTTATAGATTAATTTAGATATATATATATATATATTGGTACACGGACAAAAGGAATTTAAGGA
1 TATTTATAGATTAATGTAGATATATATATATATATATTGGTACACGGACAAAAGGAATTTAAGGA
25141908 AAAATAATAATAAATGATTTTTTTTTTAGAAACCATTTAAAACTCGTGATTTAATGTATTAGACA
66 AAAATAATAATAAATGATTTTTTTTTTAGAAACCATTTAAAACTCGTGATTTAATGTATTAGACA
25141973 AAAACATGGAATTTTGAGTGCTATCATAATTTGTTGGTTAAGGTAAAGTAGTTTCAAGATATACA
131 AAAACATGGAATTTTGAGTGCTATCATAATTTGTTGGTTAAGGTAAAGTAGTTTCAAGATATACA
25142038 AATATAATTCCG
196 AATATAATTCCG
25142050 TATTTATAGATTAATGTAGATATATATATATATATATTGGTACACGGACAAAAGGAATTTAAGGA
1 TATTTATAGATTAATGTAGATATATATATATATATATTGGTACACGGACAAAAGGAATTTAAGGA
25142115 AAAATAATAATAAATGATTTTTTTTTTAGAAACCATTTAAAACTCGTGATTTAATGTATTAGACA
66 AAAATAATAATAAATGATTTTTTTTTTAGAAACCATTTAAAACTCGTGATTTAATGTATTAGACA
25142180 AAAACATGGAATTTTGAGTGCTATCATAATTTGTTGGTTAAGGTAAAGTAGTTTCAAGATATACA
131 AAAACATGGAATTTTGAGTGCTATCATAATTTGTTGGTTAAGGTAAAGTAGTTTCAAGATATACA
25142245 AATATAATTCCG
196 AATATAATTCCG
25142257 TATTT
1 TATTT
25142262 GATTCTCTCT
Statistics
Matches: 211, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 211 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (207 bp):
TATTTATAGATTAATGTAGATATATATATATATATATTGGTACACGGACAAAAGGAATTTAAGGA
AAAATAATAATAAATGATTTTTTTTTTAGAAACCATTTAAAACTCGTGATTTAATGTATTAGACA
AAAACATGGAATTTTGAGTGCTATCATAATTTGTTGGTTAAGGTAAAGTAGTTTCAAGATATACA
AATATAATTCCG
Found at i:25147409 original size:29 final size:29
Alignment explanation
Indices: 25147367--25147425 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
25147357 TAATAATGTT
25147367 AATGATTATTAAGAATTAAATCAAATCAA
1 AATGATTATTAAGAATTAAATCAAATCAA
25147396 AATGATTATTAAGAATTAAATCAAATCAA
1 AATGATTATTAAGAATTAAATCAAATCAA
25147425 A
1 A
25147426 TTTTCATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (29 bp):
AATGATTATTAAGAATTAAATCAAATCAA
Found at i:25148933 original size:15 final size:14
Alignment explanation
Indices: 25148904--25148958 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 14
25148894 TAAGTAAAAA
25148904 AATATAAAATTTAT
1 AATATAAAATTTAT
*
25148918 AATATATAACTTTAT
1 AATATA-AAATTTAT
25148933 AA-A-AAAATTTAT
1 AATATAAAATTTAT
*
25148945 AA-ATAAAACTTAT
1 AATATAAAATTTAT
25148958 A
1 A
25148959 TAACTTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
12 10 0.28
13 10 0.28
14 7 0.19
15 9 0.25
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATAAAATTTAT
Found at i:25148969 original size:27 final size:27
Alignment explanation
Indices: 25148909--25148961 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
25148899 AAAAAAATAT
*
25148909 AAAATTTATAATATATAACTTTATAAA
1 AAAATTTATAATATAAAACTTTATAAA
25148936 AAAATTTATAA-ATAAAACTTATATAA
1 AAAATTTATAATATAAAACTT-TATAA
25148962 CTTAATTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAATTTATAATATAAAACTTTATAAA
Found at i:25148987 original size:123 final size:127
Alignment explanation
Indices: 25148825--25149062 Score: 439
Period size: 123 Copynumber: 1.9 Consensus size: 127
25148815 TTTAATTATA
25148825 AAAACTTATATAAACTTAATTTGAAGAAAGACTTATGCTAAATTATATCACTTTGTATAATACAT
1 AAAACTTATATAAACTTAATTTGAAGAAAGACTTATGCTAAATTATATCACTTTGTATAATACAT
25148890 AAATTAAGTAAAAAAATATAAAA-TT-TATAATATATAA-CTTTATAAAAAAATTTATAAAT
66 AAATTAAGTAAAAAAATATAAAATTTATATAATATATAACCTTTATAAAAAAATTTATAAAT
25148949 AAAACTTATAT-AACTTAATTTGAAGAAAGACTTATGCTAAATTATATCACTTTGTATAATACAT
1 AAAACTTATATAAACTTAATTTGAAGAAAGACTTATGCTAAATTATATCACTTTGTATAATACAT
25149013 AAATTAAGTAAAAAAATATAAAATTTAATATAATATATAACCTTTATAAA
66 AAATTAAGTAAAAAAATATAAAATTT-ATATAATATATAACCTTTATAAA
25149063 TAATGCTTTA
Statistics
Matches: 110, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
123 76 0.69
124 13 0.12
126 12 0.11
127 9 0.08
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (127 bp):
AAAACTTATATAAACTTAATTTGAAGAAAGACTTATGCTAAATTATATCACTTTGTATAATACAT
AAATTAAGTAAAAAAATATAAAATTTATATAATATATAACCTTTATAAAAAAATTTATAAAT
Found at i:25154716 original size:3 final size:3
Alignment explanation
Indices: 25154702--25154738 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
25154692 GATAGAAATG
*
25154702 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
25154739 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25157094 original size:106 final size:106
Alignment explanation
Indices: 25156909--25157595 Score: 1329
Period size: 106 Copynumber: 6.5 Consensus size: 106
25156899 TTAAAATTAA
* * *
25156909 AAAGGATATTTGGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
1 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
*
25156974 AATTTCCAAACGCAAAACATTGCGTTATTTTGTAATTTTTG
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTG
25157015 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
1 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
*
25157080 AATTTCCAAACGCAAAACATTGCGTTATTTTGTAATTTTTG
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTG
25157121 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
1 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
25157186 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTG
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTG
25157227 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
1 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
25157292 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTG
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTG
25157333 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
1 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
25157398 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTG
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTG
25157439 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
1 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
25157504 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTG
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTG
25157545 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTA
1 AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTA
25157596 CGGCCATCGA
Statistics
Matches: 577, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 577 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (106 bp):
AAAGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCG
AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTG
Found at i:25161443 original size:178 final size:178
Alignment explanation
Indices: 25161144--25161472 Score: 595
Period size: 178 Copynumber: 1.8 Consensus size: 178
25161134 AACGAGTGTA
*
25161144 GAAAGGTAATGAAATAGTAAGTTCATACTTGAAGTGTAAAATGACGAAAAAGGGGATAATGAGTT
1 GAAAGGTAATGAAATAGTAAGTTCATACTTAAAGTGTAAAATGACGAAAAAGGGGATAATGAGTT
25161209 GAATTGATGTTGTTATTTAAGCTAAAGTGATATTTTCATTGCAAAATTGAGAATTTCATAAATGC
66 GAATTGATGTTGTTATTTAAGCTAAAGTGATATTTTCATTGCAAAATTGAGAATTTCATAAATGC
*
25161274 GTTAATGAATGGTATAATCGAGGTCATTTTACCAAAATAGTCCAAATG
131 GTCAATGAATGGTATAATCGAGGTCATTTTACCAAAATAGTCCAAATG
* * *
25161322 GAAAGGTAATGAAATAGTAAGTTCATACTTAAAGTGTACAATGACTAAAAAGGGGATGATGAGTT
1 GAAAGGTAATGAAATAGTAAGTTCATACTTAAAGTGTAAAATGACGAAAAAGGGGATAATGAGTT
* *
25161387 GAATTGATGTTGTTATTTAAGCTAAAGTGATATTTTCATTGCAAAGTTGAGAATTTCATAAATGT
66 GAATTGATGTTGTTATTTAAGCTAAAGTGATATTTTCATTGCAAAATTGAGAATTTCATAAATGC
25161452 GTCAATGAATGGTATAATCGA
131 GTCAATGAATGGTATAATCGA
25161473 TAAACGTTGA
Statistics
Matches: 144, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
178 144 1.00
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (178 bp):
GAAAGGTAATGAAATAGTAAGTTCATACTTAAAGTGTAAAATGACGAAAAAGGGGATAATGAGTT
GAATTGATGTTGTTATTTAAGCTAAAGTGATATTTTCATTGCAAAATTGAGAATTTCATAAATGC
GTCAATGAATGGTATAATCGAGGTCATTTTACCAAAATAGTCCAAATG
Found at i:25163915 original size:30 final size:31
Alignment explanation
Indices: 25163871--25163929 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
25163861 ATTCATATAT
* *
25163871 ATATCTCATGTCACATAGCATGTTTCATTCC
1 ATATCTCATATCACATAGCATGTATCATTCC
*
25163902 ATAT-TCATATCACATATCATGTATCATT
1 ATATCTCATATCACATAGCATGTATCATT
25163930 TATATCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.41
Consensus pattern (31 bp):
ATATCTCATATCACATAGCATGTATCATTCC
Found at i:25172964 original size:16 final size:17
Alignment explanation
Indices: 25172943--25172976 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
25172933 TCAGTGTTGT
25172943 AAAATAAA-CAAGAAAA
1 AAAATAAAGCAAGAAAA
*
25172959 AAAATAAAGGAAGAAAA
1 AAAATAAAGCAAGAAAA
25172976 A
1 A
25172977 GAAGAGGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAATAAAGCAAGAAAA
Found at i:25174186 original size:22 final size:22
Alignment explanation
Indices: 25174141--25174188 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
25174131 AGTGATTTGA
* * *
25174141 TAAATATCACAAATTCAAATAT
1 TAAATATCACAAAATAAAAGAT
25174163 TAAATATCACAAAATAAAAGAT
1 TAAATATCACAAAATAAAAGAT
25174185 TAAA
1 TAAA
25174189 AGAGATGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATATCACAAAATAAAAGAT
Found at i:25175359 original size:62 final size:59
Alignment explanation
Indices: 25175247--25175384 Score: 168
Period size: 62 Copynumber: 2.3 Consensus size: 59
25175237 TTAATATAAC
* * ** * * *
25175247 ATTTGGTATTTGAATTTAACACTTTTTCCTAATTTGGTACTTAAACTTTTTTTGGCTCA
1 ATTTGGTACTTGAACTTAACACTTTTTCCTAATTTAATACCTAAACTTTTTTGGGCCCA
*
25175306 ATTTGGTACTTGAACTTAGACATTTTTTTCCCTAATTTAATACCTAAACTTTTTTGGGCCCA
1 ATTTGGTACTTGAACTTA-ACA-CTTTTT-CCTAATTTAATACCTAAACTTTTTTGGGCCCA
*
25175368 ATTTGGTACCTGAACTT
1 ATTTGGTACTTGAACTT
25175385 GGCACCTAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 16 0.24
60 3 0.04
61 5 0.07
62 43 0.64
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (59 bp):
ATTTGGTACTTGAACTTAACACTTTTTCCTAATTTAATACCTAAACTTTTTTGGGCCCA
Found at i:25176489 original size:62 final size:59
Alignment explanation
Indices: 25176377--25176514 Score: 168
Period size: 62 Copynumber: 2.3 Consensus size: 59
25176367 TTAATATAAC
* * ** * * *
25176377 ATTTGGTATTTGAATTTAACACTTTTTCCTAATTTGGTACTTAAACTTTTTTTGGCTCA
1 ATTTGGTACTTGAACTTAACACTTTTTCCTAATTTAATACCTAAACTTTTTTGGGCCCA
*
25176436 ATTTGGTACTTGAACTTAGACATTTTTTTCCCTAATTTAATACCTAAACTTTTTTGGGCCCA
1 ATTTGGTACTTGAACTTA-ACA-CTTTTT-CCTAATTTAATACCTAAACTTTTTTGGGCCCA
*
25176498 ATTTGGTACCTGAACTT
1 ATTTGGTACTTGAACTT
25176515 GGCACCTAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 16 0.24
60 3 0.04
61 5 0.07
62 43 0.64
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (59 bp):
ATTTGGTACTTGAACTTAACACTTTTTCCTAATTTAATACCTAAACTTTTTTGGGCCCA
Found at i:25181974 original size:105 final size:105
Alignment explanation
Indices: 25181784--25181995 Score: 347
Period size: 105 Copynumber: 2.0 Consensus size: 105
25181774 GTTTTTTTAT
* * *
25181784 TCTATTTTCTTTATTTTTTCATTTTTTATTAATTAATAATGTAATTATTATTATTAATATTATTA
1 TCTATTTTCTTCATTTTTTCATTATTAATTAATTAATAATGTAA-TATTATTATTAATATTATTA
*
25181849 TCCCTTTTTAATTCTTGTATGTAATTTTTTTTAATGTATATA
65 TCCCTTTTTAATTCTCGTATGTAA-TTTTTTTAATGTATATA
25181891 TCTATTTTCTTCATTTTTTCATTAATTAATTAATTAATAATGT-A-ATTATTATTAATATTATTA
1 TCTATTTTCTTCATTTTTTCATT-ATTAATTAATTAATAATGTAATATTATTATTAATATTATTA
25181954 TCCCTTTTTAATTCTCGTATGTAATTTTTTTAATGTATATA
65 TCCCTTTTTAATTCTCGTATGTAATTTTTTTAATGTATATA
25181995 T
1 T
25181996 ATGTATTTTT
Statistics
Matches: 100, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
104 18 0.18
105 42 0.42
107 23 0.23
108 17 0.17
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.59
Consensus pattern (105 bp):
TCTATTTTCTTCATTTTTTCATTATTAATTAATTAATAATGTAATATTATTATTAATATTATTAT
CCCTTTTTAATTCTCGTATGTAATTTTTTTAATGTATATA
Found at i:25182048 original size:105 final size:105
Alignment explanation
Indices: 25181830--25182017 Score: 276
Period size: 105 Copynumber: 1.8 Consensus size: 105
25181820 TAATGTAATT
* *
25181830 ATTATTATTAATATTATTATCCCTTTTTAATTCTTGTATGTAATTTTTTTTAATGTATATATCTA
1 ATTATTATTAATATTATTATCCCTTTTTAATTCTCGTATGTAATTTTTTTTAATGTATATATATA
* * **
25181895 TTTTCTTCATTTTTTCATTAATTAATTAATTAATAATGTA
66 TTTTCTTCATTTTTTCATGAAATAATTAATTAATAACATA
*
25181935 ATTATTATTAATATTATTATCCCTTTTTAATTCTCGTATGTAA-TTTTTTTAATGTATATATATG
1 ATTATTATTAATATTATTATCCCTTTTTAATTCTCGTATGTAATTTTTTTTAATGTATATATATA
25181999 TATTT-TT-ATTTTTT-ATGAA
66 T-TTTCTTCATTTTTTCATGAA
25182018 CATATTTTTC
Statistics
Matches: 78, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
102 4 0.05
103 7 0.09
104 22 0.28
105 45 0.58
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.59
Consensus pattern (105 bp):
ATTATTATTAATATTATTATCCCTTTTTAATTCTCGTATGTAATTTTTTTTAATGTATATATATA
TTTTCTTCATTTTTTCATGAAATAATTAATTAATAACATA
Found at i:25186494 original size:24 final size:24
Alignment explanation
Indices: 25186467--25186512 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25186457 AGAACAGTCC
* *
25186467 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
25186491 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
25186513 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Found at i:25194626 original size:44 final size:43
Alignment explanation
Indices: 25194571--25195334 Score: 277
Period size: 44 Copynumber: 17.7 Consensus size: 43
25194561 CCAGTAATCC
* *
25194571 TATCTCCCTGAAGTTGCAGTGGATCAGATTAAAACCTTGGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACC-TGGATCT
* *** * *
25194615 TATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATCTAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTGGATCT
* * **
25194655 TATCTC-CTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAG-TCT
1 TATCTCTC-TGAAGTTGCAGTGGAGCAGATTAA--AACCTGGATCT
* *
25194699 TATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGA--TGGCAAATCT
1 TATCTCT-CTGAAGTTGCAGTGGA-GCAGA-TTAAAACCTGG---ATCT
* *
25194744 TATCTCCCTGAAGTTGCAGTGGATCAGATTAAAACCTTGGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACC-TGGATCT
* *** * *
25194788 TATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATCTAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTGGATCT
* * * * **
25194828 TATCTC-CTTGAAGTTGCAGTGGGGTAGACTAAATAAGCAAG-TCT
1 TATCTCTC-TGAAGTTGCAGTGGAGCAGA-TTAA-AACCTGGATCT
* * * *
25194872 TATCT-TCCTGAAGATGCAGT-GAGGCAGACT--GACGATGGCAAATCT
1 TATCTCT-CTGAAGTTGCAGTGGA-GCAGATTAAAAC-CTGG---ATCT
* * * * *
25194917 TATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCC-GATAATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTG--GATCT
* * *
25194961 TATCTC-CTTGAAGTTGTAGTGGAGCGGGTTAAAACCTTGGATCT
1 TATCTCTC-TGAAGTTGCAGTGGAGCAGATTAAAACC-TGGATCT
* * ** * *
25195005 TATCTATCTGAAGTTGCAG-AGAGCAGA-T--CGCATGTAGTCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTGGA-TCT
* * * ** *
25195045 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAG-CCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAA--AACCTGGATCT
* *
25195089 TATC-CTCCTGAAGTTGCAGT-GAGGCAGACTAAAGA--TGGCAAATCG
1 TATCTCT-CTGAAGTTGCAGTGGA-GCAGATTAAA-ACCTGG---ATCT
* * * *
25195134 TATCTCCCTGATGTTGCAGTGGAGCAGGTTAAAGCCGATGG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACC--TGGATCT
* **
25195178 TATCTCTCTGAAGTTACAGTGGAGTGGATTAAAACCTTGGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACC-TGGATCT
* *** * *
25195222 TATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATCTAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTGGATCT
* *
25195262 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA---GGAAGTCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAA--AACCTGG-A-TCT
**
25195306 TATCTCTCTGAAGTTGCAGCAGAGCAGAT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGAT
25195335 CACATCAAAT
Statistics
Matches: 527, Mismatches: 124, Indels: 138
0.67 0.16 0.17
Matches are distributed among these distances:
39 5 0.01
40 83 0.16
41 36 0.07
42 14 0.03
43 35 0.07
44 258 0.49
45 80 0.15
46 9 0.02
47 4 0.01
48 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (43 bp):
TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTGGATCT
Found at i:25194944 original size:89 final size:88
Alignment explanation
Indices: 25194652--25194949 Score: 335
Period size: 89 Copynumber: 3.4 Consensus size: 88
25194642 TCGCATCTAG
* * *
25194652 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAATAAGCAAGTCTTAT-CTCCTGAAGTTGCA
*
25194717 GTGAGGCAGACTGAAGATGGCAAA
65 GTGAGGCAGACTGACGATGGCAAA
* * **
25194741 TCTTATCTCCCTGAAGTTGCAGTGGA-TCAGA-TTAA-AACCTTGGATCTTATCTCTCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGT-AGACTAAATAAGC-AAG-TCTTATCTC-CTGAAGTT
* * *
25194803 GCAGAGA-GCAGA-T--CGCAT--CTAG
62 GCAGTGAGGCAGACTGACG-ATGGCAAA
* * *
25194825 TCTTATCTCCTTGAAGTTGCAGTGGGGTAGACTAAATAAGCAAGTCTTATCTTCCTGAAGATGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAATAAGCAAGTCTTATC-TCCTGAAGTTGCA
25194890 GTGAGGCAGACTGACGATGGCAAA
65 GTGAGGCAGACTGACGATGGCAAA
*
25194914 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAA
25194950 GCCGATAATC
Statistics
Matches: 170, Mismatches: 24, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
84 49 0.29
85 13 0.08
86 6 0.04
87 6 0.04
88 13 0.08
89 83 0.49
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAATAAGCAAGTCTTATCTCCTGAAGTTGCAG
TGAGGCAGACTGACGATGGCAAA
Found at i:25194965 original size:89 final size:86
Alignment explanation
Indices: 25194566--25194981 Score: 306
Period size: 89 Copynumber: 4.8 Consensus size: 86
25194556 GGTAGCCAGT
* * **
25194566 AATCCTATCTCCCTGAAGTTGCAGTGGA-TCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGT-AGATTAAAGCC--AAATCTTATCTC-CTGAAGTT
* *
25194630 GCAGAGA-GCAGA-T--CGCAT--CT
62 GCAGTGAGGCAGACTGACG-ATGGCA
* * * * *
25194650 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAG-CAAGTCTTATCCTCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-TTA--AAGCCAAATCTTAT-CTCCTGAAGTT
*
25194714 GCAGTGAGGCAGACTGAAGATGGCA
62 GCAGTGAGGCAGACTGACGATGGCA
* **
25194739 AATCTTATCTCCCTGAAGTTGCAGTGGA-TCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGT-AGATTAAAGCC--AAATCTTATCTC-CTGAAGTT
* *
25194803 GCAGAGA-GCAGA-T--CGCAT--CT
62 GCAGTGAGGCAGACTGACG-ATGGCA
* * * * * *
25194823 AGTCTTATCTCCTTGAAGTTGCAGTGGGGTAGACTAAATAAG-CAAGTCTTATCTTCCTGAAGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-T-TA-AAGCCAAATCTTATC-TCCTGAAGTT
25194887 GCAGTGAGGCAGACTGACGATGGCA
62 GCAGTGAGGCAGACTGACGATGGCA
*
25194912 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCGATAATCCTATCTCCTTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCC-A-AATCTTATCTCC-TGAAGTTG
*
25194977 TAGTG
63 CAGTG
25194982 GAGCGGGTTA
Statistics
Matches: 258, Mismatches: 42, Indels: 59
0.72 0.12 0.16
Matches are distributed among these distances:
84 97 0.38
85 20 0.08
86 12 0.05
87 12 0.05
88 18 0.07
89 99 0.38
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (86 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAAATCTTATCTCCTGAAGTTGCAG
TGAGGCAGACTGACGATGGCA
Found at i:25194967 original size:217 final size:216
Alignment explanation
Indices: 25194650--25195324 Score: 916
Period size: 217 Copynumber: 3.1 Consensus size: 216
25194640 GATCGCATCT
* * *
25194650 AGTCTTATCTCCTTGAAGTTGCAGTG-GAGCAGACT-AAG-TAAGCAAGTCTTATC-CTCCTGAA
1 AGTCTTATCTCC-TGAAGTTGCAGTGAG-GCAGACTAAAGAT-GGCAAATCGTATCTC-CCTGAA
* * *
25194711 GTTGCAGT-GAGGCAGACTGAAGATGGC-A-AATCTTATCTCCCTGAAGTTGCAGTGGATCAGAT
62 GTTGCAGTGGA-GCAGA-TTAA-A-GCCGATAATCTTATCTCCCTGAAGTTGCAGTGGATCGGAT
*
25194773 TAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTG
123 TAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTG
* * *
25194838 AAGTTGCAGTGGGGTAGACTAAATAAGCA
188 AAGTTGCAGTGGAGCAGACTAAGTAAGCA
* * * *
25194867 AGTCTTATCTTCCTGAAGATGCAGTGAGGCAGACTGACGATGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATC-TCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCGTATCTCCCTGAAGTT
* * * * * *
25194932 GCAGTGGAGTAGATTAAAGCCGATAATCCTATCTCCTTGAAGTTGTAGTGGAGCGGGTTAAAACC
65 GCAGTGGAGCAGATTAAAGCCGATAATCTTATCTCCCTGAAGTTGCAGTGGATCGGATTAAAACC
* *
25194997 TTGGATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATGTAGTCTTATCTCCCTGAAGTTGC
130 TTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGC
25195062 AGTGGAGCAGACTAAGTAAGCA
195 AGTGGAGCAGACTAAGTAAGCA
* *
25195084 AGCCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCGTATCTCCCTGATGTT
1 AGTCTTAT-CTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCGTATCTCCCTGAAGTT
* ** * *
25195149 GCAGTGGAGCAGGTTAAAGCCGATGGTCTTATCTCTCTGAAGTTACAGTGGAGT-GGATTAAAAC
65 GCAGTGGAGCAGATTAAAGCCGATAATCTTATCTCCCTGAAGTTGCAGTGGA-TCGGATTAAAAC
25195213 CTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTG
129 CTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTG
*
25195278 CAGTGGAGCAGACTAAGTAAGGA
194 CAGTGGAGCAGACTAAGTAAGCA
25195301 AGTCTTATCTCTCTGAAGTTGCAG
1 AGTCTTATCTC-CTGAAGTTGCAG
25195325 CAGAGCAGAT
Statistics
Matches: 407, Mismatches: 40, Indels: 22
0.87 0.09 0.05
Matches are distributed among these distances:
215 2 0.00
216 5 0.01
217 360 0.88
218 36 0.09
219 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (216 bp):
AGTCTTATCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCGTATCTCCCTGAAGTTG
CAGTGGAGCAGATTAAAGCCGATAATCTTATCTCCCTGAAGTTGCAGTGGATCGGATTAAAACCT
TGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCA
GTGGAGCAGACTAAGTAAGCA
Found at i:25194976 original size:173 final size:173
Alignment explanation
Indices: 25194566--25194949 Score: 689
Period size: 173 Copynumber: 2.2 Consensus size: 173
25194556 GGTAGCCAGT
*
25194566 AATCCTATCTCCCTGAAGTTGCAGTGGATCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGATCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
*
25194631 CAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAG
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAG
*
25194696 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
131 TCTTATCCTCCTGAAGATGCAGTGAGGCAGACTGAAGATGGCA
25194739 AATCTTATCTCCCTGAAGTTGCAGTGGATCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGATCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
* *
25194804 CAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGGGTAGACTAAATAAGCAAG
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAG
* *
25194869 TCTTATCTTCCTGAAGATGCAGTGAGGCAGACTGACGATGGCA
131 TCTTATCCTCCTGAAGATGCAGTGAGGCAGACTGAAGATGGCA
25194912 AATCTTATCTCCCTGAAGTTGCAGTGGAGT-AGATTAAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGA-TCAGATTAAA
25194950 GCCGATAATC
Statistics
Matches: 203, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
173 202 1.00
174 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (173 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGATCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTTG
CAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAG
TCTTATCCTCCTGAAGATGCAGTGAGGCAGACTGAAGATGGCA
Found at i:25195291 original size:390 final size:387
Alignment explanation
Indices: 25194565--25195324 Score: 1030
Period size: 390 Copynumber: 2.0 Consensus size: 387
25194555 CGGTAGCCAG
* *
25194565 TAATCCTATCTCCCTGAAGTTGCAGTGGATCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
1 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTTGGATCTTATCTATCTGAAGTT
*
25194630 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAA
66 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAA
* * *
25194695 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTG
131 GCCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCGTATCTCCCTGAAGTTG
* * * *** *
25194760 CAGTGGATCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
196 CAGTGGAGCAGATTAAAACCATGGATCTTATCTCTCTGAAGTTACAGAGAGCAGATAAAACCTAG
* * * *
25194825 TCTTATCTCCTTGAAGTTGCAGTGGGGTAGACTAAATAAGCAAGTCTTATCTTCCTGAAGATGCA
261 TCTTATCTCCTTGAAGTTGCAGTAGAGCAGACTAAAT-A-CAAGTCTTATCTCCCTGAAGATGCA
* *
25194890 GTGAGGCAGACTGACG-ATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCG
324 GTGAGGCAGACT-AAGTAAGG-AAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCG
25194954 A
387 A
* * * *
25194955 TAATCCTATCTCCTTGAAGTTGTAGTGGAGCGGGTTAAAACCTTGGATCTTATCTATCTGAAGTT
1 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTTGGATCTTATCTATCTGAAGTT
*
25195020 GCAGAGAGCAGATCGCATGTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAA
66 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAA
*
25195085 GCCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCGTATCTCCCTGATGTTG
131 GCCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCGTATCTCCCTGAAGTTG
* * * **
25195150 CAGTGGAGCAGGTTAAAGCCGATGG-TCTTATCTCTCTGAAGTTACAGTGGAGTGGATTAAAACC
196 CAGTGGAGCAGATTAAAACC-ATGGATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-TAAAACC
* ** *
25195214 TTGGATCTTATCT-CTCTGAAGTTGCAG-AGAGCAGA-TCGCAT-CTAGTCTTATCTCCCTGAAG
258 -TAG-TCTTATCTCCT-TGAAGTTGCAGTAGAGCAGACT-AAATACAAGTCTTATCTCCCTGAAG
* * *
25195275 TTGCAGTG-GAGCAGACTAAGTAAGGAAGTCTTATCTCTCTGAAGTTGCAG
319 ATGCAGTGAG-GCAGACTAAGTAAGGAAATCTTATCTCCCTGAAGTTGCAG
25195325 CAGAGCAGAT
Statistics
Matches: 324, Mismatches: 37, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
389 26 0.08
390 256 0.79
391 8 0.02
392 4 0.01
393 11 0.03
394 19 0.06
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (387 bp):
TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTTGGATCTTATCTATCTGAAGTT
GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAA
GCCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCGTATCTCCCTGAAGTTG
CAGTGGAGCAGATTAAAACCATGGATCTTATCTCTCTGAAGTTACAGAGAGCAGATAAAACCTAG
TCTTATCTCCTTGAAGTTGCAGTAGAGCAGACTAAATACAAGTCTTATCTCCCTGAAGATGCAGT
GAGGCAGACTAAGTAAGGAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCGA
Found at i:25196904 original size:135 final size:136
Alignment explanation
Indices: 25196660--25196932 Score: 512
Period size: 135 Copynumber: 2.0 Consensus size: 136
25196650 CTCTAAATTA
25196660 TTAGCGTGTTCAATAGGGTCCTCCAATCTTCAATTATTCACGAATTTGCCCCAGTTTTTTTTGTT
1 TTAGCGTGTTC-ATAGGGTCCTCCAATCTTCAATTATTCACGAATTTGCCCCAGTTTTTTTTGTT
*
25196725 TTTACAATTCAATCTAGGTTTTTTATTCTATTTTCTTCATTTTTTCATTAATTAATTAATTAATA
65 TTTACAATTCAATCTAGGTTTTTTATTCTATATTCTTCATTTTTTCATTAATTAATTAATTAATA
25196790 ATGTAAT
130 ATGTAAT
25196797 TTAGCGTGTTC-TAGGGTCCTCCAATCTTCAATTATTCACGAATTTGCCCCAGTTTTTTTTGTTT
1 TTAGCGTGTTCATAGGGTCCTCCAATCTTCAATTATTCACGAATTTGCCCCAGTTTTTTTTGTTT
*
25196861 TTACAATTCAATCTAGGTTTTTTATTCTCTATTCTTCATTTTTTCATTAATTAATTAATTAATAA
66 TTACAATTCAATCTAGGTTTTTTATTCTATATTCTTCATTTTTTCATTAATTAATTAATTAATAA
25196926 TGTAAT
131 TGTAAT
25196932 T
1 T
25196933 ATTATTAATA
Statistics
Matches: 134, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
135 123 0.92
137 11 0.08
ACGTcount: A:0.25, C:0.16, G:0.10, T:0.50
Consensus pattern (136 bp):
TTAGCGTGTTCATAGGGTCCTCCAATCTTCAATTATTCACGAATTTGCCCCAGTTTTTTTTGTTT
TTACAATTCAATCTAGGTTTTTTATTCTATATTCTTCATTTTTTCATTAATTAATTAATTAATAA
TGTAAT
Found at i:25198701 original size:12 final size:12
Alignment explanation
Indices: 25198679--25198722 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
25198669 TTTTTAAAAA
*
25198679 ATATCTTTATAT
1 ATATATTTATAT
*
25198691 TTATATTTATAT
1 ATATATTTATAT
* *
25198703 ATACATGTATAT
1 ATATATTTATAT
25198715 ATATATTT
1 ATATATTT
25198723 TTCTTATACT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (12 bp):
ATATATTTATAT
Found at i:25207011 original size:23 final size:24
Alignment explanation
Indices: 25206979--25207023 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
25206969 TGCATGTTTA
25206979 TTTCTTATTTTCAATTTGTTTTGT
1 TTTCTTATTTTCAATTTGTTTTGT
* *
25207003 TTTC-TATTTTTATTTTGTTTT
1 TTTCTTATTTTCAATTTGTTTT
25207024 TAGTTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.11, C:0.07, G:0.07, T:0.76
Consensus pattern (24 bp):
TTTCTTATTTTCAATTTGTTTTGT
Found at i:25207024 original size:24 final size:25
Alignment explanation
Indices: 25206979--25207029 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
25206969 TGCATGTTTA
25206979 TTTCTTATTTTCAATTTGTTTT-GT
1 TTTCTTATTTTCAATTTGTTTTAGT
* *
25207003 TTTC-TATTTTTATTTTGTTTTTAGT
1 TTTCTTATTTTCAATTTG-TTTTAGT
25207028 TT
1 TT
25207030 GTTTAGTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.48
24 8 0.35
25 4 0.17
ACGTcount: A:0.12, C:0.06, G:0.08, T:0.75
Consensus pattern (25 bp):
TTTCTTATTTTCAATTTGTTTTAGT
Found at i:25208721 original size:17 final size:17
Alignment explanation
Indices: 25208681--25208718 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
25208671 TACTATTAAG
*
25208681 TTAAACATTAAATTTAC
1 TTAAATATTAAATTTAC
*
25208698 TTTAATATTAAATTTA-
1 TTAAATATTAAATTTAC
25208714 TTAAA
1 TTAAA
25208719 ATAATATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATATTAAATTTAC
Found at i:25213253 original size:43 final size:43
Alignment explanation
Indices: 25213135--25213275 Score: 117
Period size: 43 Copynumber: 3.3 Consensus size: 43
25213125 CGGGTAAGTC
* * * * *
25213135 GAAGCAATTATACTGACATACGAGGTGCATTATCGAACGAACT
1 GAAGCAATTATACTGACACACGAGATGCATCATAGAACAAACT
* * * * * *
25213178 GAAGCAATTATACTGGCACGC-ATAGTGTATCATAGAATAAATT
1 GAAGCAATTATACTGACACACGAGA-TGCATCATAGAACAAACT
* *
25213221 GAAGCAATTATACTAACACACGAGATGCATCATCAG-ACGAACT
1 GAAGCAATTATACTGACACACGAGATGCATCAT-AGAACAAACT
25213264 GCAA-CAATTATA
1 G-AAGCAATTATA
25213276 TTGGCACGCT
Statistics
Matches: 75, Mismatches: 19, Indels: 8
0.74 0.19 0.08
Matches are distributed among these distances:
42 1 0.01
43 68 0.91
44 6 0.08
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (43 bp):
GAAGCAATTATACTGACACACGAGATGCATCATAGAACAAACT
Found at i:25221320 original size:41 final size:43
Alignment explanation
Indices: 25221254--25221368 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
25221244 TAACGCATAT
* ** * *
25221254 CGATGCCACTGTCCTTGACAGGGTCTTATACG-ATTCAT-AC-A
1 CGATGCCAATGTCCCAGACATGGTCTTACACGTATTC-TCACTA
* * *
25221295 CGATGCCAATGTCCCAGACTTGGTCTTACACGTTTTCTCACTT
1 CGATGCCAATGTCCCAGACATGGTCTTACACGTATTCTCACTA
25221338 CGATGCCAATGTCCCAGACATGGTCTTACAC
1 CGATGCCAATGTCCCAGACATGGTCTTACAC
25221369 AAAATCACAC
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 27 0.44
42 5 0.08
43 30 0.48
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.30
Consensus pattern (43 bp):
CGATGCCAATGTCCCAGACATGGTCTTACACGTATTCTCACTA
Found at i:25221546 original size:31 final size:30
Alignment explanation
Indices: 25221511--25221575 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
25221501 TTCGATAATA
*
25221511 TATATCCATATACGAATCAAATTCGGCAATG
1 TATATCCATATA-AAATCAAATTCGGCAATG
* *
25221542 TATATCTATTTAAAATCAAATTCGGCAATG
1 TATATCCATATAAAATCAAATTCGGCAATG
25221572 TATA
1 TATA
25221576 AAACTTATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 21 0.68
31 10 0.32
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (30 bp):
TATATCCATATAAAATCAAATTCGGCAATG
Found at i:25228788 original size:31 final size:31
Alignment explanation
Indices: 25228747--25228830 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
25228737 ATCTAATGCT
*
25228747 CAAATC-AATTCAGTAATATATATCTATATA
1 CAAATCAAATTCAGCAATATATATCTATATA
* * * *
25228777 CAAATCAAATTCGGCAGTGTATATTTATATA
1 CAAATCAAATTCAGCAATATATATCTATATA
* *
25228808 CAAATCAAATTCGGCAATGTATA
1 CAAATCAAATTCAGCAATATATA
25228831 AAACATATAC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 6 0.13
31 41 0.87
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (31 bp):
CAAATCAAATTCAGCAATATATATCTATATA
Found at i:25232372 original size:57 final size:57
Alignment explanation
Indices: 25232304--25232439 Score: 150
Period size: 57 Copynumber: 2.4 Consensus size: 57
25232294 TAATGAAAAA
* *
25232304 TTTCAGCTTAACGAGCTTTTTTACCCTAACTTTTGCTTATGTCAT-CTAAGTAAAGAT
1 TTTCAGCTTAACGAGCTTTTTTACCCTAACTTTTGCTTAAGTCATCCAAAG-AAAGAT
* * * * ** *
25232361 TTTCAACTTAAC-ATGGTTTTTTTCTCTAACTTTTGCTTAAGTTTTCCAAAGAAGGAT
1 TTTCAGCTTAACGA-GCTTTTTTACCCTAACTTTTGCTTAAGTCATCCAAAGAAAGAT
*
25232418 TTTTAGCTTAACGAGCTTTTTT
1 TTTCAGCTTAACGAGCTTTTTT
25232440 GTGCACTTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
56 1 0.02
57 58 0.91
58 5 0.08
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (57 bp):
TTTCAGCTTAACGAGCTTTTTTACCCTAACTTTTGCTTAAGTCATCCAAAGAAAGAT
Found at i:25235916 original size:25 final size:25
Alignment explanation
Indices: 25235896--25236011 Score: 108
Period size: 25 Copynumber: 4.6 Consensus size: 25
25235886 GTATATTGGA
* *
25235896 AAGCTCTTGCGAGCCAAATATCGGG
1 AAGCTCATGAGAGCCAAATATCGGG
* *
25235921 ACGCTCATGAGAGCC-ATTAATCGGG
1 AAGCTCATGAGAGCCAAAT-ATCGGG
*
25235946 AAGCTCATGAGAGCCAAATATTGGG
1 AAGCTCATGAGAGCCAAATATCGGG
* * * * *
25235971 ATGCTCATAATAGCTAAATAACGGG
1 AAGCTCATGAGAGCCAAATATCGGG
* *
25235996 AAGCTCGTGCGAGCCA
1 AAGCTCATGAGAGCCA
25236012 TGGTGTGTCT
Statistics
Matches: 70, Mismatches: 19, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
24 2 0.03
25 66 0.94
26 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (25 bp):
AAGCTCATGAGAGCCAAATATCGGG
Found at i:25235950 original size:50 final size:50
Alignment explanation
Indices: 25235896--25236011 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
25235886 GTATATTGGA
* * * *
25235896 AAGCTCTTGCGAGCCAAATATCGGGACGCTCATGAGAGC-CATTAATCGGG
1 AAGCTCATGCGAGCCAAATATCGGGACGCTCATAAGAGCTAAATAA-CGGG
* * * *
25235946 AAGCTCATGAGAGCCAAATATTGGGATGCTCATAATAGCTAAATAACGGG
1 AAGCTCATGCGAGCCAAATATCGGGACGCTCATAAGAGCTAAATAACGGG
*
25235996 AAGCTCGTGCGAGCCA
1 AAGCTCATGCGAGCCA
25236012 TGGTGTGTCT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 51 0.93
51 4 0.07
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (50 bp):
AAGCTCATGCGAGCCAAATATCGGGACGCTCATAAGAGCTAAATAACGGG
Found at i:25237973 original size:40 final size:38
Alignment explanation
Indices: 25237894--25238020 Score: 92
Period size: 40 Copynumber: 3.1 Consensus size: 38
25237884 TGTTAAATTG
* * * * *
25237894 TAATTAAAATATATTTATATTAAAAAATAAATTTATAAAA
1 TAATTATATTATATTTAT-TTAAATAATATATAT-TAAAA
25237934 TAATTATATTATATTTATGTTAAATAATAGTATATTAAAA
1 TAATTATATTATATTTAT-TTAAATAATA-TATATTAAAA
* * * *
25237974 TTATGTCATATTAAATCTTAATTAAAATAGTATTATATTAAAA
1 TAAT-T-ATATTATAT-TT-ATTTAAATAATA-TATATTAAAA
25238017 TAAT
1 TAAT
25238021 AAAATTGAGG
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
40 33 0.47
41 4 0.06
42 8 0.11
43 23 0.33
44 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (38 bp):
TAATTATATTATATTTATTTAAATAATATATATTAAAA
Found at i:25237977 original size:26 final size:24
Alignment explanation
Indices: 25237931--25237979 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
25237921 TAAATTTATA
* *
25237931 AAATAATTATATTATATTTATGTT
1 AAATAATTATATTAAAATTATGTT
25237955 AAATAATAGTATATTAAAATTATGT
1 AAATAAT--TATATTAAAATTATGT
25237980 CATATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
26 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (24 bp):
AAATAATTATATTAAAATTATGTT
Found at i:25240568 original size:18 final size:20
Alignment explanation
Indices: 25240515--25240582 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
25240505 CGAGATGCTA
*
25240515 AACAAGGCA-CAAATGTGCAT
1 AACAGGGCACCAAA-GTGCAT
*
25240535 -ACAGGAGCACCGAAGTGCA-
1 AACAGG-GCACCAAAGTGCAT
25240554 AA-AGGGCACCAAAGTGCAT
1 AACAGGGCACCAAAGTGCAT
25240573 AACAGGGCAC
1 AACAGGGCAC
25240583 AGATGTGCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 12 0.30
19 9 0.22
20 16 0.40
21 3 0.08
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (20 bp):
AACAGGGCACCAAAGTGCAT
Found at i:25240571 original size:38 final size:40
Alignment explanation
Indices: 25240498--25240592 Score: 101
Period size: 38 Copynumber: 2.4 Consensus size: 40
25240488 ACAATATCAT
25240498 GGAGCACCG-AGATGCTAAACAAGGCACAAATGTGCAT-ACA
1 GGAGCACCGAAG-TGC-AAACAAGGCACAAATGTGCATAACA
*
25240538 GGAGCACCGAAGTGCAAA-AGGGCACCAAA-GTGCATAACA
1 GGAGCACCGAAGTGCAAACAAGGCA-CAAATGTGCATAACA
* *
25240577 GG-GCACAGATGTGCAA
1 GGAGCACCGAAGTGCAA
25240593 TTAGGGATAC
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
38 23 0.47
39 12 0.24
40 12 0.24
41 2 0.04
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.11
Consensus pattern (40 bp):
GGAGCACCGAAGTGCAAACAAGGCACAAATGTGCATAACA
Found at i:25240590 original size:20 final size:20
Alignment explanation
Indices: 25240515--25240591 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
25240505 CGAGATGCTA
*
25240515 AACAAGGCACA-AATGTGCAT
1 AACAGGGCACAGAA-GTGCAT
*
25240535 -ACAGGAGCACCGAAGTGCA-
1 AACAGG-GCACAGAAGTGCAT
25240554 AA-AGGGCACCA-AAGTGCAT
1 AACAGGGCA-CAGAAGTGCAT
*
25240573 AACAGGGCACAGATGTGCA
1 AACAGGGCACAGAAGTGCA
25240592 ATTAGGGATA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
18 10 0.22
19 12 0.26
20 22 0.48
21 2 0.04
ACGTcount: A:0.40, C:0.22, G:0.27, T:0.10
Consensus pattern (20 bp):
AACAGGGCACAGAAGTGCAT
Found at i:25243310 original size:13 final size:14
Alignment explanation
Indices: 25243287--25243316 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
25243277 GTTGTAAAGT
25243287 TTTATTTTTATTTA
1 TTTATTTTTATTTA
25243301 TTTA-TTTTATTTA
1 TTTATTTTTATTTA
25243314 TTT
1 TTT
25243317 TTACTTAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:25243310 original size:19 final size:20
Alignment explanation
Indices: 25243284--25243336 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
25243274 CAAGTTGTAA
*
25243284 AGTTTTATTTTTATTTATTT
1 AGTTTTATTTTTATTTACTT
25243304 A-TTTTATTTATT-TTTACTT
1 AGTTTTATTT-TTATTTACTT
*
25243323 AGTTTAATTTTTAT
1 AGTTTTATTTTTAT
25243337 GTAAATATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.72
Consensus pattern (20 bp):
AGTTTTATTTTTATTTACTT
Found at i:25249844 original size:15 final size:15
Alignment explanation
Indices: 25249824--25249854 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25249814 TATTTATATT
*
25249824 AAATAAATATACTAC
1 AAATAAATATAATAC
25249839 AAATAAATATAATAC
1 AAATAAATATAATAC
25249854 A
1 A
25249855 TTAATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAAATATAATAC
Done.