Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 20 of 163
Found at i:5643650 original size:29 final size:29
Alignment explanation
Indices: 5643618--5644012 Score: 248
Period size: 30 Copynumber: 13.4 Consensus size: 29
5643608 GGGAAAACTC
*
5643618 GAGGTCAAAATGTGATTTTGGAGAAGTTT
1 GAGGTCAAAATGTAATTTTGGAGAAGTTT
* ** * *
5643647 GAGGTTAAAACATGATTTTGG-GAAG-GT
1 GAGGTCAAAATGTAATTTTGGAGAAGTTT
*
5643674 GTAGGGATCAAAATGCAATTTTGGAGAAGTTT
1 G-A-GG-TCAAAATGTAATTTTGGAGAAGTTT
*
5643706 G-GAGTCAAAATATAATTTTGGAGAAGTTT
1 GAG-GTCAAAATGTAATTTTGGAGAAGTTT
*
5643735 G-GGTTCAAAATGTATTTTTGGAGAAGTTT
1 GAGG-TCAAAATGTAATTTTGGAGAAGTTT
* *
5643764 AAGGGTCAAAATATAATTTTGGA-AAGGTTT
1 GA-GGTCAAAATGTAATTTTGGAGAA-GTTT
* *
5643794 AGGGGTCAAAATGTAATTTTGGAAAAGTTT
1 -GAGGTCAAAATGTAATTTTGGAGAAGTTT
* * * *
5643824 AATGGTTAAAATGTAATTTTGGAAAAATTT
1 GA-GGTCAAAATGTAATTTTGGAGAAGTTT
* * *
5643854 AAGGGTAAAAATGTAATTTTGGAAAAGTTT
1 GA-GGTCAAAATGTAATTTTGGAGAAGTTT
* * * * **
5643884 AGGGGTCAAAATATAATTTTGAAAAAAGTAA
1 -GAGGTCAAAATGTAATTTTG-GAGAAGTTT
* * * * *
5643915 G-GGTTAAAATGTATTTTTGGAAAAAATTA
1 GAGGTCAAAATGTAATTTTGG-AGAAGTTT
* * * * *
5643944 GGGGTTAAAATGTAATTTTGGAAAAATTA
1 GAGGTCAAAATGTAATTTTGGAGAAGTTT
* * *
5643973 GGGGTGAAAATGTAATTTTAGA-AAG-TT
1 GAGGTCAAAATGTAATTTTGGAGAAGTTT
5644000 GAGGGGTCAAAAT
1 GA--GGTCAAAAT
5644013 ATAGTTTTAG
Statistics
Matches: 300, Mismatches: 47, Indels: 38
0.78 0.12 0.10
Matches are distributed among these distances:
27 4 0.01
28 8 0.03
29 129 0.43
30 143 0.48
31 14 0.05
32 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (29 bp):
GAGGTCAAAATGTAATTTTGGAGAAGTTT
Found at i:5643695 original size:59 final size:59
Alignment explanation
Indices: 5643558--5644020 Score: 312
Period size: 60 Copynumber: 7.8 Consensus size: 59
5643548 CGGGGAATAC
* * * * *** *** *
5643558 GGGATCAAAATGTAAATTTGGAAAAGTTTAGGGGGTGAAAATGCGATTTTGGGAAAACTC
1 GGGATCAAAATGTAATTTTGGAGAAGTTTA-AGGGTCAAAATATAATTTTGGGAAGGTTA
* * * * *
5643618 GAGG-TCAAAATGTGATTTTGGAGAAGTTTGA-GGTTAAAACATGATTTTGGGAAGGTGTA
1 G-GGATCAAAATGTAATTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTGGGAAGGT-TA
* *
5643677 GGGATCAAAATGCAATTTTGGAGAAGTTT--GGAGTCAAAATATAATTTTGGAGAA-GTTT
1 GGGATCAAAATGTAATTTTGGAGAAGTTTAAGG-GTCAAAATATAATTTTGG-GAAGGTTA
* * *
5643735 GGGTTCAAAATGTATTTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTGGAAAGGTTTA
1 GGGATCAAAATGTAATTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTGGGAAGG-TTA
* * * * * * **
5643795 GGGGTCAAAATGTAATTTTGGAAAAGTTTAATGGTTAAAATGTAATTTTGGAAAAATTTAA
1 GGGATCAAAATGTAATTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTGG-GAAGGTT-A
* * * ** * *
5643856 GGG-TAAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATATAATTTTGAAAAAAGTAA
1 GGGATCAAAATGTAATTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTG-GGAAGGTTA
* * * ** * * * * **
5643915 GGG-TTAAAATGTATTTTTGGAAAAAATTAGGGGTTAAAATGTAATTTTGGAAAAATTA
1 GGGATCAAAATGTAATTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTGGGAAGGTTA
* * * * * *
5643973 GGGGTGAAAATGTAATTTTAGA-AAGTTGAGGGGTCAAAATATAGTTTT
1 GGGATCAAAATGTAATTTTGGAGAAGTTTAAGGGTCAAAATATAATTTT
5644021 AGAAAAATTA
Statistics
Matches: 331, Mismatches: 58, Indels: 30
0.79 0.14 0.07
Matches are distributed among these distances:
58 79 0.24
59 120 0.36
60 123 0.37
61 9 0.03
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (59 bp):
GGGATCAAAATGTAATTTTGGAGAAGTTTAAGGGTCAAAATATAATTTTGGGAAGGTTA
Found at i:5644025 original size:29 final size:28
Alignment explanation
Indices: 5643562--5644012 Score: 292
Period size: 29 Copynumber: 15.2 Consensus size: 28
5643552 GAATACGGGA
*
5643562 TCAAAATGTAAATTTGGAAAAGTTTAGGGGG
1 TCAAAATGTAATTTTGG-AAAG-TTA-GGGG
* ** ** * *
5643593 TGAAAATGCGATTTTGGGAAAACTCGAGG
1 TCAAAATGTAATTTT-GGAAAGTTAGGGG
* * *
5643622 TCAAAATGTGATTTTGGAGAAGTTTGAGG
1 TCAAAATGTAATTTTGGA-AAGTTAGGGG
* ** * * *
5643651 TTAAAACATGATTTTGGGAAGGTGTAGGGA
1 TCAAAATGTAATTTT-GGAAAGT-TAGGGG
* * *
5643681 TCAAAATGCAATTTTGGAGAAGTTTGGAG
1 TCAAAATGTAATTTTGGA-AAGTTAGGGG
* * *
5643710 TCAAAATATAATTTTGGAGAAGTTTGGGT
1 TCAAAATGTAATTTTGGA-AAGTTAGGGG
* *
5643739 TCAAAATGTATTTTTGGAGAAGTTTAAGGG
1 TCAAAATGTAATTTTGGA-AAG-TTAGGGG
*
5643769 TCAAAATATAATTTTGGAAAGGTTTAGGGG
1 TCAAAATGTAATTTTGGAAA-G-TTAGGGG
**
5643799 TCAAAATGTAATTTTGGAAAAGTTTAATGG
1 TCAAAATGTAATTTTGG-AAAG-TTAGGGG
* * *
5643829 TTAAAATGTAATTTTGGAAAAATTTAAGGG
1 TCAAAATGTAATTTTGG--AAAGTTAGGGG
*
5643859 TAAAAATGTAATTTTGGAAAAGTTTAGGGG
1 TCAAAATGTAATTTTGG-AAAG-TTAGGGG
* * *
5643889 TCAAAATATAATTTTGAAAAAAG-TAAGGG
1 TCAAAATGTAATTTTG--GAAAGTTAGGGG
* * *
5643918 TTAAAATGTATTTTTGGAAAAAATTAGGGG
1 TCAAAATGTAATTTTGG--AAAGTTAGGGG
* *
5643948 TTAAAATGTAATTTTGGAAAAATTAGGGG
1 TCAAAATGTAATTTTGG-AAAGTTAGGGG
* *
5643977 TGAAAATGTAATTTTAGAAAGTTGAGGGG
1 TCAAAATGTAATTTTGGAAAGTT-AGGGG
5644006 TCAAAAT
1 TCAAAAT
5644013 ATAGTTTTAG
Statistics
Matches: 339, Mismatches: 65, Indels: 34
0.77 0.15 0.08
Matches are distributed among these distances:
28 8 0.02
29 154 0.45
30 150 0.44
31 25 0.07
32 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (28 bp):
TCAAAATGTAATTTTGGAAAGTTAGGGG
Found at i:5644044 original size:30 final size:30
Alignment explanation
Indices: 5643735--5644042 Score: 258
Period size: 30 Copynumber: 10.3 Consensus size: 30
5643725 GGAGAAGTTT
* **
5643735 GGGTTCAAAATGTATTTTTGGAGAAGTTTA-A
1 GGGTT-AAAATGTAATTTTGGA-AAAATTAGA
* * **
5643766 GGGTCAAAATATAATTTTGGAAAGGTTTAG-
1 GGGTTAAAATGTAATTTTGGAAA-AATTAGA
* *
5643796 GGGTCAAAATGTAATTTTGGAAAAGTTTA-A
1 GGGTTAAAATGTAATTTTGGAAAA-ATTAGA
*
5643826 TGGTTAAAATGTAATTTTGGAAAAATTTA-A
1 GGGTTAAAATGTAATTTTGGAAAAA-TTAGA
* *
5643856 GGGTAAAAATGTAATTTTGGAAAAGTTTAG-
1 GGGTTAAAATGTAATTTTGGAAAA-ATTAGA
* * * *
5643886 GGGTCAAAATATAATTTTGAAAAAAGTA-A
1 GGGTTAAAATGTAATTTTGGAAAAATTAGA
*
5643915 GGGTTAAAATGTATTTTTGGAAAAAATTAG-
1 GGGTTAAAATGTAATTTTGG-AAAAATTAGA
5643945 GGGTTAAAATGTAATTTTGGAAAAATTAG-
1 GGGTTAAAATGTAATTTTGGAAAAATTAGA
* * *
5643974 GGGTGAAAATGTAATTTTAG-AAAGTT-GA
1 GGGTTAAAATGTAATTTTGGAAAAATTAGA
* * * *
5644002 GGGGTCAAAATATAGTTTTAGAAAAATTAGA
1 -GGGTTAAAATGTAATTTTGGAAAAATTAGA
5644033 GGGTTAAAAT
1 GGGTTAAAAT
5644043 ATGATTTTTA
Statistics
Matches: 233, Mismatches: 30, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.00
28 5 0.02
29 64 0.27
30 157 0.67
31 6 0.03
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.34
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTTGGAAAAATTAGA
Found at i:5644903 original size:6 final size:6
Alignment explanation
Indices: 5644892--5644996 Score: 78
Period size: 6 Copynumber: 18.0 Consensus size: 6
5644882 TAAATGGACT
* * *
5644892 TTTAAA TTTAAA --TAAA TTTAAA TTTAAAA TGT--A TTGGACA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TT-TAAA T-TTAAA
* * * *
5644939 TTTAAA TTAAAA TTTAAA -GTAAA TTTAAA TTAAAA TTTAAA -GTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
5644985 TTTAAA TTTAAA
1 TTTAAA TTTAAA
5644997 ATTTGTCTTA
Statistics
Matches: 77, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
4 6 0.08
5 8 0.10
6 52 0.68
7 10 0.13
8 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:5644953 original size:12 final size:12
Alignment explanation
Indices: 5644936--5645000 Score: 89
Period size: 12 Copynumber: 5.5 Consensus size: 12
5644926 TGGACATTTT
5644936 AAATTTAAATTA
1 AAATTTAAATTA
*
5644948 AAATTTAAAGT-
1 AAATTTAAATTA
5644959 AAATTTAAATTA
1 AAATTTAAATTA
*
5644971 AAATTTAAAGT-
1 AAATTTAAATTA
5644982 AAATTTAAATTTA
1 AAATTTAAA-TTA
5644995 AAATTT
1 AAATTT
5645001 GTCTTATTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
11 19 0.41
12 21 0.46
13 6 0.13
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
AAATTTAAATTA
Found at i:5644962 original size:11 final size:11
Alignment explanation
Indices: 5644935--5644990 Score: 76
Period size: 11 Copynumber: 4.9 Consensus size: 11
5644925 TTGGACATTT
*
5644935 TAAATTTAAAT
1 TAAATTTAAAG
5644946 TAAAATTTAAAG
1 T-AAATTTAAAG
*
5644958 TAAATTTAAAT
1 TAAATTTAAAG
5644969 TAAAATTTAAAG
1 T-AAATTTAAAG
5644981 TAAATTTAAA
1 TAAATTTAAA
5644991 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
11 20 0.50
12 20 0.50
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAG
Found at i:5644963 original size:17 final size:17
Alignment explanation
Indices: 5644964--5644996 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5644954 AAAGTAAATT
5644964 TAAATTAAAATTTAAAG
1 TAAATTAAAATTTAAAG
*
5644981 TAAATTTAAATTTAAA
1 TAAATTAAAATTTAAA
5644997 ATTTGTCTTA
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:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAATTAAAATTTAAAG
Found at i:5644965 original size:23 final size:23
Alignment explanation
Indices: 5644935--5645000 Score: 123
Period size: 23 Copynumber: 2.8 Consensus size: 23
5644925 TTGGACATTT
5644935 TAAATTTAAATTAAAATTTAAAG
1 TAAATTTAAATTAAAATTTAAAG
5644958 TAAATTTAAATTAAAATTTAAAG
1 TAAATTTAAATTAAAATTTAAAG
5644981 TAAATTTAAATTTAAAATTT
1 TAAATTTAAA-TTAAAATTT
5645001 GTCTTATTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 33 0.79
24 9 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
TAAATTTAAATTAAAATTTAAAG
Found at i:5645539 original size:39 final size:39
Alignment explanation
Indices: 5645503--5645652 Score: 156
Period size: 39 Copynumber: 3.8 Consensus size: 39
5645493 ATTGGATGGT
* *
5645503 TGCAATCTGCCCCAGACTTGGGGTAAAAGATCGGATGAC
1 TGCAATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGAC
* * * * *
5645542 TGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGGTTGAA
1 TGCAATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGAC
** * * * *
5645581 TGTGATTTGCCCCAGGCTTGGGGTAAAAGATCGAATGGC
1 TGCAATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGAC
* * *
5645620 TGCAATTTGCCCCAGGCTCAGGGTAAGAGATCG
1 TGCAATCTGCCCCAGGCTCGGGGTAAAAGATCG
5645653 AAATTTTCAA
Statistics
Matches: 88, Mismatches: 23, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (39 bp):
TGCAATCTGCCCCAGGCTCGGGGTAAAAGATCGGATGAC
Found at i:5645575 original size:78 final size:78
Alignment explanation
Indices: 5645485--5645650 Score: 217
Period size: 78 Copynumber: 2.1 Consensus size: 78
5645475 TTATTTTTTT
* ** *
5645485 GGTAAGATATTGGATGGTTGCAATCTGCCCCAGACTTGGGGTAAAAGATCGGATGACTGCAATCT
1 GGTAAGAGATTGGATGAATGCAATCTGCCCCAGACTTGGGGTAAAAGATCGAATGACTGCAATCT
5645550 GCCCCAGGCTC-G
66 GCCCCAGGCTCAG
* ** * * * *
5645562 AGGTAAGAGATTGGTTGAATGTGATTTGCCCCAGGCTTGGGGTAAAAGATCGAATGGCTGCAATT
1 -GGTAAGAGATTGGATGAATGCAATCTGCCCCAGACTTGGGGTAAAAGATCGAATGACTGCAATC
5645627 TGCCCCAGGCTCAG
65 TGCCCCAGGCTCAG
5645641 GGTAAGAGAT
1 GGTAAGAGAT
5645651 CGAAATTTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
78 75 0.99
79 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (78 bp):
GGTAAGAGATTGGATGAATGCAATCTGCCCCAGACTTGGGGTAAAAGATCGAATGACTGCAATCT
GCCCCAGGCTCAG
Found at i:5647952 original size:3 final size:3
Alignment explanation
Indices: 5647944--5647970 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5647934 GGTCATCCCT
5647944 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
5647971 AATATCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:5652075 original size:17 final size:17
Alignment explanation
Indices: 5652052--5652176 Score: 153
Period size: 17 Copynumber: 7.3 Consensus size: 17
5652042 CCAAACCCAT
5652052 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
5652070 -TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
5652086 TTTAAGTTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
5652103 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
* * *
5652120 TTTAAATTTAATTTGAG
1 TTTAAATTTATTTTAAA
5652137 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
5652155 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
5652172 TTTAA
1 TTTAA
5652177 TTAAAATGTC
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
16 1 0.01
17 77 0.85
18 13 0.14
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:5652089 original size:6 final size:6
Alignment explanation
Indices: 5652080--5652160 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
5652070 TTAAATTTGT
* * **
5652080 TTTAAA TTTAAG TTT-AT TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
5652126 TTT-AA TTTGAG TTTAAA TTT-AT TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
5652161 ATTATTATAA
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
5 16 0.28
6 38 0.66
7 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:5652199 original size:14 final size:15
Alignment explanation
Indices: 5652175--5652211 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5652165 TTATAAATTT
*
5652175 AATTA-AAATGTC-C
1 AATTACAAATGTCTA
5652188 AATTACAAATGTCTA
1 AATTACAAATGTCTA
5652203 AATTACAAA
1 AATTACAAA
5652212 GGCCAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.24
14 7 0.33
15 9 0.43
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (15 bp):
AATTACAAATGTCTA
Found at i:5654072 original size:32 final size:32
Alignment explanation
Indices: 5654031--5654132 Score: 138
Period size: 32 Copynumber: 3.2 Consensus size: 32
5654021 CCTGAACATG
*
5654031 TTTTGACCCCAAAACTTTTTTAAAAAATTATA
1 TTTTGACCCCAAAACTTTTTTAAAAAATTACA
5654063 TTTTGACCCCAAAA-TTTTTCT--AAAATTACA
1 TTTTGACCCCAAAACTTTTT-TAAAAAATTACA
* * *
5654093 CTTTGACCCCAAAACTTTCTAAAAAAATTACA
1 TTTTGACCCCAAAACTTTTTTAAAAAATTACA
5654125 TTTTGACC
1 TTTTGACC
5654133 TTAAACTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
30 21 0.34
31 9 0.15
32 31 0.51
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (32 bp):
TTTTGACCCCAAAACTTTTTTAAAAAATTACA
Found at i:5654142 original size:31 final size:32
Alignment explanation
Indices: 5654032--5654147 Score: 103
Period size: 32 Copynumber: 3.7 Consensus size: 32
5654022 CTGAACATGT
*** * *
5654032 TTTGACCCCAAAACTTTTTTAAAAAATTATAT
1 TTTGACCCCAAAACTTTCCAAAAAAATTACAC
* * *
5654064 TTTGACCCCAAAATTTTTC--TAAAATTACAC
1 TTTGACCCCAAAACTTTCCAAAAAAATTACAC
* *
5654094 TTTGACCCCAAAACTTTCTAAAAAAATTACAT
1 TTTGACCCCAAAACTTTCCAAAAAAATTACAC
**
5654126 TTTGA-CCTTAAACTTTCCAAAA
1 TTTGACCCCAAAACTTTCCAAAA
5654148 TTCCATTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
30 24 0.35
31 14 0.20
32 31 0.45
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.36
Consensus pattern (32 bp):
TTTGACCCCAAAACTTTCCAAAAAAATTACAC
Found at i:5654162 original size:29 final size:27
Alignment explanation
Indices: 5654116--5654219 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 27
5654106 ACTTTCTAAA
* *
5654116 AAAATTACATTTTGACCTTAAACTTTCC
1 AAAATTCCATTTTAACC-TAAACTTTCC
5654144 AAAATTCCATTTTTAACCT-AA-TTTCACCC
1 AAAATTCCA-TTTTAACCTAAACTTT---CC
* *
5654173 AAAATTACCATTTTACCCCTAAACTTTCT
1 AAAATT-CCATTTTA-ACCTAAACTTTCC
5654202 AAAATTCCATTTTTAACC
1 AAAATTCCA-TTTTAACC
5654220 CCGATTTCAC
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
26 3 0.05
27 2 0.03
28 14 0.23
29 32 0.52
30 6 0.10
31 2 0.03
32 3 0.05
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.38
Consensus pattern (27 bp):
AAAATTCCATTTTAACCTAAACTTTCC
Found at i:5654186 original size:30 final size:30
Alignment explanation
Indices: 5654142--5654362 Score: 105
Period size: 29 Copynumber: 7.5 Consensus size: 30
5654132 CTTAAACTTT
5654142 CCAAAATT-CCATTTTTAACCTAATTTCAC
1 CCAAAATTACCATTTTTAACCTAATTTCAC
*
5654171 CCAAAATTACCA-TTTTACCCCTAAACTTT---
1 CCAAAATTACCATTTTTA-ACCT-AA-TTTCAC
* **
5654200 CTAAAATT-CCATTTTTAACCCCGATTTCAC
1 CCAAAATTACCATTTTTAA-CCTAATTTCAC
* * * *
5654230 CTAAAATTACCA-TTTTACCCCCAAACTT--C
1 CCAAAATTACCATTTTTA--ACCTAATTTCAC
* *
5654259 CCTAAA-TCCCATTTTTAACCTCAATTTCAC
1 CCAAAATTACCATTTTTAACCT-AATTTCAC
* *
5654289 CTAAAATTACCA-TTTTACCCTCGAATCTT---
1 CCAAAATTACCATTTTTAACCT--AAT-TTCAC
*
5654318 CCAAAATT-CCATTTTTAACCCCAATTTCA-
1 CCAAAATTACCATTTTTAA-CCTAATTTCAC
*
5654347 TCAAAATTACCATTTT
1 CCAAAATTACCATTTT
5654363 GTCCCCCCGA
Statistics
Matches: 144, Mismatches: 24, Indels: 47
0.67 0.11 0.22
Matches are distributed among these distances:
27 7 0.05
28 18 0.12
29 56 0.39
30 41 0.28
31 17 0.12
32 5 0.03
ACGTcount: A:0.33, C:0.30, G:0.01, T:0.36
Consensus pattern (30 bp):
CCAAAATTACCATTTTTAACCTAATTTCAC
Found at i:5654250 original size:59 final size:59
Alignment explanation
Indices: 5654116--5654362 Score: 324
Period size: 59 Copynumber: 4.2 Consensus size: 59
5654106 ACTTTCTAAA
* * *
5654116 AAAATTA-CATTTTGA-CCTTAAACTTTCCAAAATTCCATTTTTAA-CCTAATTTCACCC
1 AAAATTACCATTTT-ACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCT
* *
5654173 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCT
* * * * *
5654232 AAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTTTAACCTCAATTTCACCT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCT
* * *
5654291 AAAATTACCATTTTACCCTCGAATC-TTCCAAAATTCCATTTTTAACCCCAATTTCATC-
1 AAAATTACCATTTTACCC-CTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCT
5654349 AAAATTACCATTTT
1 AAAATTACCATTTT
5654363 GTCCCCCCGA
Statistics
Matches: 167, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
57 8 0.05
58 47 0.28
59 108 0.65
60 4 0.02
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.37
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCT
Found at i:5654265 original size:29 final size:30
Alignment explanation
Indices: 5654166--5654362 Score: 128
Period size: 29 Copynumber: 6.7 Consensus size: 30
5654156 TTAACCTAAT
* *
5654166 TTCACCCAAAATTACCATTTTACCCCTAAAC
1 TTCACCTAAAATTACCATTTTACCCC-CAAC
* * * *
5654197 TT--TCTAAAATT-CCATTTTTAACCCCGAT
1 TTCACCTAAAATTACCA-TTTTACCCCCAAC
5654225 TTCACCTAAAATTACCATTTTACCCCCAAAC
1 TTCACCTAAAATTACCATTTTACCCCC-AAC
* * * *
5654256 TTC-CCT-AAA-TCCCATTTTTAACCTCAAT
1 TTCACCTAAAATTACCA-TTTTACCCCCAAC
*
5654284 TTCACCTAAAATTACCATTTTACCCTCGAATC
1 TTCACCTAAAATTACCATTTTACCC-CCAA-C
* *
5654316 TT--CC-AAAATT-CCATTTTTAACCCCAAT
1 TTCACCTAAAATTACCA-TTTTACCCCCAAC
*
5654343 TTCATC-AAAATTACCATTTT
1 TTCACCTAAAATTACCATTTT
5654363 GTCCCCCCGA
Statistics
Matches: 128, Mismatches: 23, Indels: 32
0.70 0.13 0.17
Matches are distributed among these distances:
27 2 0.02
28 21 0.16
29 53 0.41
30 35 0.27
31 15 0.12
32 2 0.02
ACGTcount: A:0.32, C:0.30, G:0.01, T:0.36
Consensus pattern (30 bp):
TTCACCTAAAATTACCATTTTACCCCCAAC
Found at i:5654383 original size:59 final size:57
Alignment explanation
Indices: 5654144--5654392 Score: 261
Period size: 59 Copynumber: 4.2 Consensus size: 57
5654134 TAAACTTTCC
* * **
5654144 AAAATTCCATTTTTAA-CCTAATTTCACCCAAAATTACCATTTTACCCCTAAACTTTCT
1 AAAATTCCATTTTTAACCCCAATTTCACCTAAAATTACCATTTTACCCCCGAA--TTCT
* *
5654202 AAAATTCCATTTTTAACCCCGATTTCACCTAAAATTACCATTTTACCCCCAAACTTCCCT
1 AAAATTCCATTTTTAACCCCAATTTCACCTAAAATTACCATTTTACCCCCGAA-TT--CT
* * * *
5654262 -AAATCCCATTTTTAACCTCAATTTCACCTAAAATTACCATTTTACCCTCGAATCTTCC
1 AAAATTCCATTTTTAACCCCAATTTCACCTAAAATTACCATTTTACCCCCGAA--TTCT
* * *
5654320 AAAATTCCATTTTTAACCCCAATTTCATC-AAAATTACCATTTTGTCCCCCCGAGAGTCT
1 AAAATTCCATTTTTAACCCCAATTTCACCTAAAATTACCA-TTT-TACCCCCGA-ATTCT
5654379 AAAATTACCATTTT
1 AAAATT-CCATTTT
5654393 GCCCCTGGGT
Statistics
Matches: 164, Mismatches: 18, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
58 29 0.18
59 115 0.70
60 19 0.12
61 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36
Consensus pattern (57 bp):
AAAATTCCATTTTTAACCCCAATTTCACCTAAAATTACCATTTTACCCCCGAATTCT
Found at i:5658828 original size:19 final size:19
Alignment explanation
Indices: 5658801--5658847 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
5658791 AAACCCAAAT
*
5658801 AAAAA-AAAAGAAGAAGAA
1 AAAAACAAAAAAAGAAGAA
*
5658819 CAAAACAAAAAAAGAAGAA
1 AAAAACAAAAAAAGAAGAA
5658838 AAAAACAAAA
1 AAAAACAAAA
5658848 CAAAAAAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAAAAGAAGAA
Found at i:5658828 original size:24 final size:24
Alignment explanation
Indices: 5658801--5658854 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
5658791 AAACCCAAAT
*
5658801 AAAAAAA-AAGAAGAAGAACAAAAC
1 AAAAAAAGAAGAA-AAAAACAAAAC
5658825 AAAAAAAGAAGAAAAAAACAAAAC
1 AAAAAAAGAAGAAAAAAACAAAAC
5658849 AAAAAA
1 AAAAAA
5658855 GGGTCAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.83, C:0.07, G:0.09, T:0.00
Consensus pattern (24 bp):
AAAAAAAGAAGAAAAAAACAAAAC
Found at i:5659695 original size:12 final size:12
Alignment explanation
Indices: 5659671--5659713 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
5659661 AAATATAATA
5659671 AAAAAAGAGAAAG
1 AAAAAAGA-AAAG
5659684 AAAAAAGAAAAG
1 AAAAAAGAAAAG
* *
5659696 CAAAAACAAGAAG
1 AAAAAAGAA-AAG
5659709 AAAAA
1 AAAAA
5659714 CAAAATAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:5661055 original size:50 final size:50
Alignment explanation
Indices: 5661001--5661143 Score: 132
Period size: 51 Copynumber: 2.8 Consensus size: 50
5660991 AACACAACAA
* *
5661001 GGAAAGGTCTAAGTTACAATGGCAGACCATATACCTCAAAAGCATG-GAAG
1 GGAAAGGTCTAAGTCACAATGGCAGACCATATACCTCAAAAGCA-GAAAAG
* * *
5661051 GGAAAGATCTAAGATCGCAATGGCAGATCCAGTAT---TGCAAAAACAGAAAAG
1 GGAAAGGTCTAAG-TCACAATGGCAGA-CCA-TATACCT-CAAAAGCAGAAAAG
* * * *
5661102 GGAAAGGTCTAAGTCACAACGGCGGACCGTGTACCTCAAAAG
1 GGAAAGGTCTAAGTCACAATGGCAGACCATATACCTCAAAAG
5661144 ACACGACGAG
Statistics
Matches: 73, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
48 2 0.03
49 2 0.03
50 29 0.40
51 34 0.47
52 3 0.04
53 3 0.04
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (50 bp):
GGAAAGGTCTAAGTCACAATGGCAGACCATATACCTCAAAAGCAGAAAAG
Found at i:5661164 original size:101 final size:101
Alignment explanation
Indices: 5660989--5661212 Score: 272
Period size: 101 Copynumber: 2.2 Consensus size: 101
5660979 TCAGCACCAC
* * * *
5660989 AAAACACAACAA-GGAAAGGTCTAAGTTACAATGGCAGACCATATACCTCAAAAGCATGGAAGGG
1 AAAACACAA-AAGGGAAAGGTCTAAGTCACAACGGCAGACCATATACCTCAAAAGCATCGAAGAG
* * * **
5661053 AAAGATCTAAGATCGCAATGGCAGATCCAGTATTGCA
65 AAAGATCTAAGACCACAACGGCAGATCCAGTACCGCA
* * * * *
5661090 AAAACAGAAAAGGGAAAGGTCTAAGTCACAACGGCGGACCGTGTACCTCAAAAGACA-CGACGAG
1 AAAACACAAAAGGGAAAGGTCTAAGTCACAACGGCAGACCATATACCTCAAAAG-CATCGAAGAG
5661154 AAAGATCTAAGACCACAACGGCAGATCCAGTACCGCA
65 AAAGATCTAAGACCACAACGGCAGATCCAGTACCGCA
* *
5661191 AAAAGACAAAAGGGAAAAGTCT
1 AAAACACAAAAGGGAAAGGTCT
5661213 TTATCTCTCT
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
100 2 0.02
101 100 0.96
102 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (101 bp):
AAAACACAAAAGGGAAAGGTCTAAGTCACAACGGCAGACCATATACCTCAAAAGCATCGAAGAGA
AAGATCTAAGACCACAACGGCAGATCCAGTACCGCA
Found at i:5661193 original size:51 final size:51
Alignment explanation
Indices: 5661052--5661207 Score: 133
Period size: 51 Copynumber: 3.1 Consensus size: 51
5661042 GCATGGAAGG
* * ** *
5661052 GAAAGATCTAAGATCGCAATGGCAGATCCAGTATTGCAAAA-ACAGAAAAGG
1 GAAAGATCTAAGATCACAACGGCAGATCCAGTACCGCAAAAGACAG-AAAGA
* * * * *
5661103 GAAAGGTCTAAG-TCACAACGGCGGA-CCGTGTACCTCAAAAGACACG-ACGA
1 GAAAGATCTAAGATCACAACGGCAGATCC-AGTACCGCAAAAGACA-GAAAGA
* *
5661153 GAAAGATCTAAGACCACAACGGCAGATCCAGTACCGCAAAAAGACA-AAAGG
1 GAAAGATCTAAGATCACAACGGCAGATCCAGTACCGC-AAAAGACAGAAAGA
5661204 GAAA
1 GAAA
5661208 AGTCTTTATC
Statistics
Matches: 81, Mismatches: 17, Indels: 14
0.72 0.15 0.12
Matches are distributed among these distances:
49 2 0.02
50 31 0.38
51 37 0.46
52 11 0.14
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (51 bp):
GAAAGATCTAAGATCACAACGGCAGATCCAGTACCGCAAAAGACAGAAAGA
Found at i:5661393 original size:94 final size:94
Alignment explanation
Indices: 5661210--5661529 Score: 488
Period size: 94 Copynumber: 3.4 Consensus size: 94
5661200 AAGGGAAAAG
* * *
5661210 TCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATAAAGCTTT-AAATGTCAATTTTTTTTTATC
1 TCTTCATCTCTCTGAAGTTATAGTAAGAGCAAGATGAA-TTTTCAAATGTC-A-TTTTTTTTATC
5661274 CTCTTGAAGTTATAGTAAA-ATTGGATAATGAA
63 CTCTTGAAGTTATAGTAAAGA-TGGATAATGAA
5661306 TCTTCATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCATTTTTTTTATCCTC
1 TCTTCATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCATTTTTTTTATCCTC
5661371 TTGAAGTTATAGTAAAGATGGATAATGAA
66 TTGAAGTTATAGTAAAGATGGATAATGAA
*
5661400 TCTTCATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCA--ATTTTTATCCTC
1 TCTTCATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCATTTTTTTTATCCTC
*
5661463 TTGAAGTTATAGTAAAGATGGATAATGAG
66 TTGAAGTTATAGTAAAGATGGATAATGAA
* * *
5661492 TCTTTATCTCTCTGAAATTGA-AGTAAGAGTAAGATGAA
1 TCTTCATCTCTCTGAAGTT-ATAGTAAGAGCAAGATGAA
5661530 GCACCAACAT
Statistics
Matches: 213, Mismatches: 8, Indels: 10
0.92 0.03 0.04
Matches are distributed among these distances:
92 72 0.34
93 1 0.00
94 92 0.43
95 5 0.02
96 43 0.20
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (94 bp):
TCTTCATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCATTTTTTTTATCCTC
TTGAAGTTATAGTAAAGATGGATAATGAA
Found at i:5661552 original size:92 final size:92
Alignment explanation
Indices: 5661493--5662579 Score: 1817
Period size: 92 Copynumber: 11.8 Consensus size: 92
5661483 GATAATGAGT
*
5661493 CTTTATCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
1 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
*
5661558 AAATTGAAGTAGAGCTGGATATCAAGA
66 AAATTGAAGTAGAGCTGGATATCAAGC
*
5661585 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCTTATCCTCTTG
1 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
5661650 AAATTGAAGTAGAGCTGGATATCAAGC
66 AAATTGAAGTAGAGCTGGATATCAAGC
* * *
5661677 CTTTGTCCCTCTGAAATTGAAGTAAGAGCT-AGATAAAGCATCAAACATCATTTTCCTATCCTCT
1 CTTTGTCTCTCTGAAATTGAAGTAAGAG-TAAGATGAAGCA-CCAACATCATTTTCCTATCCTCT
5661741 TGAAATTGAAGTAGAGCTGGATATCAAGC
64 TGAAATTGAAGTAGAGCTGGATATCAAGC
* * * *
5661770 CTTTGTCCCTCTAAAATTGAAGTAAGAGCT-AGATAAAGCATCAAACATCATTTTCCTATCCTCT
1 CTTTGTCTCTCTGAAATTGAAGTAAGAG-TAAGATGAAGCA-CCAACATCATTTTCCTATCCTCT
*
5661834 TGAAATTGAAGTAGAGCTGGATAACAAGC
64 TGAAATTGAAGTAGAGCTGGATATCAAGC
5661863 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
1 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
*
5661928 AAATTGAAGTAGAGATGGATATCAAGC
66 AAATTGAAGTAGAGCTGGATATCAAGC
*
5661955 CTTTGTCTCTGTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
1 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
5662020 AAATTGAAGTAGAGCTGGATATCAAGC
66 AAATTGAAGTAGAGCTGGATATCAAGC
*
5662047 CTTTGTCTCTGTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
1 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
5662112 AAATTGAAGTAGAGCTGGATATCAAGC
66 AAATTGAAGTAGAGCTGGATATCAAGC
* * *
5662139 CTTTGTCCCTCTGAAATTGAAGTAAGAGCT-AGATAAAGCATCAAACATCATTTTCCTATCCTCT
1 CTTTGTCTCTCTGAAATTGAAGTAAGAG-TAAGATGAAGCA-CCAACATCATTTTCCTATCCTCT
5662203 TGAAATTGAAGTAGAGCTGGATATCAAGC
64 TGAAATTGAAGTAGAGCTGGATATCAAGC
* * *
5662232 CTTTGTCCCTCTGAAATTGAAGTAAGAG-ATAGATAAAGCATCAAACATCATTTTCCTATCCTCT
1 CTTTGTCTCTCTGAAATTGAAGTAAGAGTA-AGATGAAGCA-CCAACATCATTTTCCTATCCTCT
* *
5662296 TGAAATTGAAGTAAAGCTGGATAACAAGC
64 TGAAATTGAAGTAGAGCTGGATATCAAGC
5662325 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
1 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
5662390 AAATTGAAGTAGAGCTGGATATCAAGC
66 AAATTGAAGTAGAGCTGGATATCAAGC
5662417 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
1 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
* *
5662482 AAATTGAGGTAGAGCTGGATATCAAGT
66 AAATTGAAGTAGAGCTGGATATCAAGC
* * *
5662509 CTTTGTCCCTCTGAAATTGAAGTAAGAGCAAGATGAAGCACCGACATC-TTTTCCTATCCTC-TG
1 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
5662572 AAATTGAA
66 AAATTGAA
5662580 TAAGAGCAAG
Statistics
Matches: 953, Mismatches: 34, Indels: 18
0.95 0.03 0.02
Matches are distributed among these distances:
90 9 0.01
91 13 0.01
92 576 0.60
93 354 0.37
94 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (92 bp):
CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
AAATTGAAGTAGAGCTGGATATCAAGC
Found at i:5661559 original size:46 final size:46
Alignment explanation
Indices: 5661509--5661651 Score: 105
Period size: 46 Copynumber: 3.1 Consensus size: 46
5661499 CTCTCTGAAA
5661509 TTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTC
1 TTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTC
* * * * * * * * ****
5661555 TTGAAAT-TGAAGTAGAGCTGGA-TATCAAGA-C-TTTGTCTCTCTGAAA
1 TTGAAGTAAG-AGTA-AGATGAAGCACCAACATCATTT-TC-CTATCCTC
*
5661601 TTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCTTATCCTC
1 TTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTC
5661647 TTGAA
1 TTGAA
5661652 ATTGAAGTAG
Statistics
Matches: 64, Mismatches: 25, Indels: 16
0.61 0.24 0.15
Matches are distributed among these distances:
44 3 0.05
45 9 0.14
46 40 0.62
47 9 0.14
48 3 0.05
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (46 bp):
TTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTC
Found at i:5661950 original size:370 final size:369
Alignment explanation
Indices: 5661456--5662579 Score: 1909
Period size: 370 Copynumber: 3.0 Consensus size: 369
5661446 TGTCAATTTT
* * * ** * *
5661456 TATCCTCTTGAAGTT-ATAGTAAAGATGGATAATGAGTCTTTATCTCTCTGAAATTGAAGTAAGA
1 TATCCTCTTGAAATTGA-AGTAGAGCTGGATAACAAGCCTTTGTCTCTCTGAAATTGAAGTAAGA
*
5661520 GTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGA
65 GTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGC
*
5661585 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCTTATCCTCTTG
130 CTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTG
* *
5661650 AAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAGCT-AGATAAA
195 AAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAG-TAAGATGAA
*
5661714 GCATCAAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCC
259 GCA-CCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCC
*
5661779 TCTAAAATTGAAGTAAGAGCTAGATAAAGCATCAAACATCATTTTCC
323 TCTGAAATTGAAGTAAGAGCTAGATAAAGCATCAAACATCATTTTCC
5661826 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAG
*
5661891 TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGATGGATATCAAGCC
66 TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCC
*
5661956 TTTGTCTCTGTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGA
131 TTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGA
*
5662021 AATTGAAGTAGAGCTGGATATCAAGCCTTTGTCTCTGTGAAATTGAAGTAAGAGTAAGATGAAGC
196 AATTGAAGTAGAGCTGGATATCAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGC
5662086 ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCT
261 ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCT
5662151 GAAATTGAAGTAAGAGCTAGATAAAGCATCAAACATCATTTTCC
326 GAAATTGAAGTAAGAGCTAGATAAAGCATCAAACATCATTTTCC
* *
5662195 TATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAG
* * * *
5662260 -ATAGATAAAGCATCAAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAG
66 TA-AGATGAAGCA-CCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAG
5662324 CCTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTT
129 CCTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTT
5662389 GAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAA
194 GAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAA
* *
5662454 GCACCAACATCATTTTCCTATCCTCTTGAAATTGAGGTAGAGCTGGATATCAAGTCTTTGTCCCT
259 GCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCT
* * **
5662519 CTGAAATTGAAGTAAGAGCAAGATGAAGCA-CCGACATC-TTTTCC
324 CTGAAATTGAAGTAAGAGCTAGATAAAGCATCAAACATCATTTTCC
5662563 TATCCTC-TGAAATTGAA
1 TATCCTCTTGAAATTGAA
5662580 TAAGAGCAAG
Statistics
Matches: 719, Mismatches: 31, Indels: 11
0.94 0.04 0.01
Matches are distributed among these distances:
367 10 0.01
368 14 0.02
369 185 0.26
370 509 0.71
371 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (369 bp):
TATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAG
TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCC
TTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGA
AATTGAAGTAGAGCTGGATATCAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGC
ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCT
GAAATTGAAGTAAGAGCTAGATAAAGCATCAAACATCATTTTCC
Found at i:5662228 original size:462 final size:462
Alignment explanation
Indices: 5661456--5662579 Score: 2040
Period size: 462 Copynumber: 2.4 Consensus size: 462
5661446 TGTCAATTTT
* * * * *
5661456 TATCCTCTTGAAGTT-ATAGTAAAGATGGATAAT-GAGTCTTTATCTCTCTGAAATTGAAGTAAG
1 TATCCTCTTGAAATTGA-AGTAGAGATGGAT-ATCAAGCCTTTGTCTCTCTGAAATTGAAGTAAG
5661519 AGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAG
64 AGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAG
*
5661584 ACTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCTTATCCTCTT
129 ACTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTT
5661649 GAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAA
194 GAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAA
5661714 GCATCAAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCC
259 GCATCAAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCC
*
5661779 TCTAAAATTGAAGTAAGAGCTAGATAAAGCATCAAACATCATTTTCCTATCCTCTTGAAATTGAA
324 TCTAAAATTGAAGTAAGAGATAGATAAAGCATCAAACATCATTTTCCTATCCTCTTGAAATTGAA
*
5661844 GTAGAGCTGGATAACAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACA
389 GTAAAGCTGGATAACAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACA
5661909 TCATTTTCC
454 TCATTTTCC
*
5661918 TATCCTCTTGAAATTGAAGTAGAGATGGATATCAAGCCTTTGTCTCTGTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGATGGATATCAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAG
*
5661983 TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCC
66 TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGAC
*
5662048 TTTGTCTCTGTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGA
131 TTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGA
5662113 AATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAAGC
196 AATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAAGC
5662178 ATCAAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTC
261 ATCAAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTC
*
5662243 TGAAATTGAAGTAAGAGATAGATAAAGCATCAAACATCATTTTCCTATCCTCTTGAAATTGAAGT
326 TAAAATTGAAGTAAGAGATAGATAAAGCATCAAACATCATTTTCCTATCCTCTTGAAATTGAAGT
5662308 AAAGCTGGATAACAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATC
391 AAAGCTGGATAACAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATC
5662373 ATTTTCC
456 ATTTTCC
*
5662380 TATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGATGGATATCAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAG
* *
5662445 TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAGGTAGAGCTGGATATCAAGTC
66 TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGAC
* * *
5662510 TTTGTCCCTCTGAAATTGAAGTAAGAGCAAGATGAAGCACCGACATC-TTTTCCTATCCTC-TGA
131 TTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGA
5662573 AATTGAA
196 AATTGAA
5662580 TAAGAGCAAG
Statistics
Matches: 640, Mismatches: 20, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
460 10 0.02
461 15 0.02
462 614 0.96
463 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (462 bp):
TATCCTCTTGAAATTGAAGTAGAGATGGATATCAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAG
TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGAC
TTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGA
AATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAGTAAGAGCTAGATAAAGC
ATCAAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTC
TAAAATTGAAGTAAGAGATAGATAAAGCATCAAACATCATTTTCCTATCCTCTTGAAATTGAAGT
AAAGCTGGATAACAAGCCTTTGTCTCTCTGAAATTGAAGTAAGAGTAAGATGAAGCACCAACATC
ATTTTCC
Found at i:5662341 original size:40 final size:40
Alignment explanation
Indices: 5662292--5662441 Score: 117
Period size: 40 Copynumber: 3.5 Consensus size: 40
5662282 TTTTCCTATC
5662292 CTCT-TGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGT
1 CTCTCTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGT
* *
5662331 CTCTCTGAAATTGAAGTAAGAG-TAAGATGAAGCACCAACATCATTT-T
1 CTCTCTGAAATTGAAGTAA-AGCT-GGAT-AA-CA--AGC--C-TTTGT
* *
5662378 CCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGT
1 -C--T-CTC-TGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGT
5662423 CTCTCTGAAATTGAAGTAA
1 CTCTCTGAAATTGAAGTAA
5662442 GAGTAAGATG
Statistics
Matches: 87, Mismatches: 7, Indels: 33
0.69 0.06 0.26
Matches are distributed among these distances:
39 4 0.05
40 28 0.32
41 8 0.09
42 3 0.03
43 2 0.02
44 4 0.05
45 4 0.05
47 4 0.05
48 4 0.05
49 2 0.02
50 2 0.02
51 8 0.09
52 14 0.16
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (40 bp):
CTCTCTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGT
Found at i:5663206 original size:17 final size:17
Alignment explanation
Indices: 5663183--5663307 Score: 153
Period size: 17 Copynumber: 7.3 Consensus size: 17
5663173 CCAAACCCAT
5663183 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
5663201 -TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
5663217 TTTAAGTTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
5663234 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
* * *
5663251 TTTAAATTTAATTTGAG
1 TTTAAATTTATTTTAAA
5663268 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
5663286 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
5663303 TTTAA
1 TTTAA
5663308 TTAAAATGTC
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
16 1 0.01
17 77 0.85
18 13 0.14
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:5663220 original size:6 final size:6
Alignment explanation
Indices: 5663211--5663291 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
5663201 TTAAATTTGT
* * **
5663211 TTTAAA TTTAAG TTT-AT TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
5663257 TTT-AA TTTGAG TTTAAA TTT-AT TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
5663292 ATTATTATAA
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
5 16 0.28
6 38 0.66
7 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:5663330 original size:14 final size:15
Alignment explanation
Indices: 5663306--5663342 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5663296 TTATAAATTT
*
5663306 AATTA-AAATGTC-C
1 AATTACAAATGTCTA
5663319 AATTACAAATGTCTA
1 AATTACAAATGTCTA
5663334 AATTACAAA
1 AATTACAAA
5663343 GGCCAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.24
14 7 0.33
15 9 0.43
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (15 bp):
AATTACAAATGTCTA
Found at i:5665188 original size:32 final size:31
Alignment explanation
Indices: 5665147--5665257 Score: 120
Period size: 30 Copynumber: 3.6 Consensus size: 31
5665137 CCTGAACATG
*
5665147 TTTTGACCCCAAAACTTTTTTAAAAAAATATA
1 TTTTGACCCCAAAAC-TTTTTAAAAAAATACA
* *
5665179 TTTTGACCCCAAAACTTTTT-CAAAATTACA
1 TTTTGACCCCAAAACTTTTTAAAAAAATACA
* *
5665209 CTTT-ATCCCCAAAACTTTCTAAAAAAATTACA
1 TTTTGA-CCCCAAAACTTTTTAAAAAAA-TACA
*
5665241 TTTTGA-CCCTAAACTTT
1 TTTTGACCCCAAAACTTT
5665258 CCAAAATTCC
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
29 1 0.02
30 23 0.35
31 19 0.29
32 22 0.33
33 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.37
Consensus pattern (31 bp):
TTTTGACCCCAAAACTTTTTAAAAAAATACA
Found at i:5665258 original size:31 final size:32
Alignment explanation
Indices: 5665147--5665263 Score: 118
Period size: 32 Copynumber: 3.8 Consensus size: 32
5665137 CCTGAACATG
* *
5665147 TTTTGACCCCAAAACTTTTTTAAAAAAA-TATA
1 TTTTGACCCCAAAAC-TTTCTAAAAAAATTACA
**
5665179 TTTTGACCCCAAAACTTT-T-TCAAAATTACA
1 TTTTGACCCCAAAACTTTCTAAAAAAATTACA
*
5665209 CTTT-ATCCCCAAAACTTTCTAAAAAAATTACA
1 TTTTGA-CCCCAAAACTTTCTAAAAAAATTACA
* *
5665241 TTTTGA-CCCTAAACTTTCCAAAA
1 TTTTGACCCCAAAACTTTCTAAAA
5665264 TTCCATTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.07
30 19 0.27
31 19 0.27
32 27 0.38
33 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (32 bp):
TTTTGACCCCAAAACTTTCTAAAAAAATTACA
Found at i:5665270 original size:28 final size:27
Alignment explanation
Indices: 5665232--5665330 Score: 94
Period size: 29 Copynumber: 3.5 Consensus size: 27
5665222 ACTTTCTAAA
*
5665232 AAAATTACATTTTGACCCTAAACTTTCC
1 AAAATTCCATTTT-ACCCTAAACTTTCC
*
5665260 AAAATTCCATTTTTAACCT-AA-TTTCACCC
1 AAAATTCCA-TTTTACCCTAAACTTT---CC
*
5665289 AAAATTACCATTTTACCCCTAAACTTTCT
1 AAAATT-CCATTTTA-CCCTAAACTTTCC
5665318 AAAATTCCATTTT
1 AAAATTCCATTTT
5665331 TAACCCCGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
26 3 0.05
27 2 0.03
28 19 0.32
29 24 0.41
30 6 0.10
31 2 0.03
32 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.38
Consensus pattern (27 bp):
AAAATTCCATTTTACCCTAAACTTTCC
Found at i:5665290 original size:29 final size:30
Alignment explanation
Indices: 5665258--5665361 Score: 94
Period size: 29 Copynumber: 3.5 Consensus size: 30
5665248 CCTAAACTTT
5665258 CCAAAATT-CCATTTTTAACCTAATTTCAC
1 CCAAAATTACCATTTTTAACCTAATTTCAC
*
5665287 CCAAAATTACCA-TTTTACCCCTAAACTTT---
1 CCAAAATTACCATTTTTA-ACCT-AA-TTTCAC
* **
5665316 CTAAAATT-CCATTTTTAACCCCGATTTCAC
1 CCAAAATTACCATTTTTAA-CCTAATTTCAC
5665346 CCAAAATTACCATTTT
1 CCAAAATTACCATTTT
5665362 ACCCCCAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
27 3 0.05
28 4 0.07
29 27 0.46
30 13 0.22
31 9 0.15
32 3 0.05
ACGTcount: A:0.34, C:0.29, G:0.01, T:0.37
Consensus pattern (30 bp):
CCAAAATTACCATTTTTAACCTAATTTCAC
Found at i:5665309 original size:58 final size:59
Alignment explanation
Indices: 5665232--5665478 Score: 306
Period size: 59 Copynumber: 4.2 Consensus size: 59
5665222 ACTTTCTAAA
*
5665232 AAAATTA-CATTTTGA-CCCTAAACTTTCCAAAATTCCATTTTTAA-CCTAATTTCACCC
1 AAAATTACCATTTT-ACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCC
* *
5665289 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCC
* * * * * * * *
5665348 AAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTTTAAACTCGATTTCACCT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCC
* * **
5665407 AAAATTACCATTTTACCCTCGAATC-TTCCAAAATTCCATTTTTAACCCCAATTT-AATC
1 AAAATTACCATTTTACCC-CTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCC
5665465 AAAATTACCATTTT
1 AAAATTACCATTTT
5665479 GTCCCCCTCG
Statistics
Matches: 164, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
57 8 0.05
58 49 0.30
59 103 0.63
60 4 0.02
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCC
Found at i:5665414 original size:118 final size:116
Alignment explanation
Indices: 5665232--5665484 Score: 323
Period size: 117 Copynumber: 2.2 Consensus size: 116
5665222 ACTTTCTAAA
* * * *
5665232 AAAATTA-CATTTTGACCCTAAACTTTCCAAAATTCCATTTTTAACCTAATTTCACCCAAAATTA
1 AAAATTACCATTTTGACCCCAAACTTCCCAAAATCCCATTTTTAAACTAATTTCACCCAAAATTA
* * * *
5665296 CCATTTTACCC-CTAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCC
66 CCATTTTACCCTCGAAAC-TTCCAAAATTCCATTTTTAACCCCAATTT-AACC
* * *
5665348 AAAATTACCATTTT-ACCCCCAAACTTCCCTAAATCCCATTTTTAAACTCGATTTCACCTAAAAT
1 AAAATTACCATTTTGA-CCCCAAACTTCCCAAAATCCCATTTTTAAACT-AATTTCACCCAAAAT
* *
5665412 TACCATTTTACCCTCGAATCTTCCAAAATTCCATTTTTAACCCCAATTTAATC
64 TACCATTTTACCCTCGAAACTTCCAAAATTCCATTTTTAACCCCAATTTAACC
*
5665465 AAAATTACCATTTTGTCCCC
1 AAAATTACCATTTTGACCCC
5665485 CTCGAGAGTC
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
116 8 0.07
117 53 0.45
118 53 0.45
119 4 0.03
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36
Consensus pattern (116 bp):
AAAATTACCATTTTGACCCCAAACTTCCCAAAATCCCATTTTTAAACTAATTTCACCCAAAATTA
CCATTTTACCCTCGAAACTTCCAAAATTCCATTTTTAACCCCAATTTAACC
Found at i:5665449 original size:29 final size:28
Alignment explanation
Indices: 5665256--5665455 Score: 81
Period size: 29 Copynumber: 6.8 Consensus size: 28
5665246 ACCCTAAACT
* *
5665256 TTCCAAAATTCCATTTTTA-ACCTAAT-
1 TTCCAAAATTCCATTTTTACCCCGAATC
* *
5665282 TTCACCCAAAATTACCA-TTTTACCCCTAAAC
1 TT---CCAAAATT-CCATTTTTACCCCGAATC
* *
5665313 TTTCTAAAATTCCATTTTTAACCCCGATTTC
1 -TTCCAAAATTCCATTTTT-ACCCCGA-ATC
** * *
5665344 ACCCAAAATTACCA-TTTTACCCCCAAAC
1 TTCCAAAATT-CCATTTTTACCCCGAATC
* * * *
5665372 TTCCCTAAATCCCATTTTTAAACTCG-AT-
1 TT-CCAAAATTCCATTTTT-ACCCCGAATC
5665400 TTCACCTAAAATTACCA-TTTTACCCTCGAATC
1 TT--CC-AAAATT-CCATTTTTACCC-CGAATC
5665432 TTCCAAAATTCCATTTTTAACCCC
1 TTCCAAAATTCCATTTTT-ACCCC
5665456 AATTTAATCA
Statistics
Matches: 127, Mismatches: 25, Indels: 41
0.66 0.13 0.21
Matches are distributed among these distances:
26 2 0.02
28 12 0.09
29 56 0.44
30 44 0.35
31 9 0.07
32 4 0.03
ACGTcount: A:0.32, C:0.31, G:0.01, T:0.35
Consensus pattern (28 bp):
TTCCAAAATTCCATTTTTACCCCGAATC
Found at i:5668137 original size:39 final size:40
Alignment explanation
Indices: 5668065--5668163 Score: 146
Period size: 39 Copynumber: 2.5 Consensus size: 40
5668055 TGGGACAAGT
* *
5668065 CTCTTCCAAAAAGTGTCCATCCAATATGAAAAGGGTTGTGA
1 CTCTT-CAAAAGGTGTCCATCCAATATGAAAAGGGTTGTAA
* *
5668106 CTTTTCAAAAGGTGTCTATCCAATATG-AAAGGGTTGTAA
1 CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGGTTGTAA
5668145 CTCTTCAAAAGGTGTCCAT
1 CTCTTCAAAAGGTGTCCAT
5668164 TAAGTGCATA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 28 0.54
40 20 0.38
41 4 0.08
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (40 bp):
CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGGTTGTAA
Found at i:5673105 original size:39 final size:40
Alignment explanation
Indices: 5673034--5673111 Score: 122
Period size: 39 Copynumber: 1.9 Consensus size: 40
5673024 AAAAGTGTCC
*
5673034 ATCTAATATGAAAAAGAGTTGTGACTTTTCAAAAGGTGTGT
1 ATCTAATATG-AAAAGAGTTGTGACTCTTCAAAAGGTGTGT
*
5673075 ATCTAATATG-AAAGGGTTGTGACTCTTCAAAAGGTGT
1 ATCTAATATGAAAAGAGTTGTGACTCTTCAAAAGGTGT
5673112 TTATTGAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 25 0.71
41 10 0.29
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (40 bp):
ATCTAATATGAAAAGAGTTGTGACTCTTCAAAAGGTGTGT
Found at i:5678206 original size:18 final size:18
Alignment explanation
Indices: 5678185--5678219 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5678175 TTGAAAATTT
*
5678185 TCATATTTAATAAATAGA
1 TCATATTTAAAAAATAGA
*
5678203 TCATCTTTAAAAAATAG
1 TCATATTTAAAAAATAG
5678220 GGATTATCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (18 bp):
TCATATTTAAAAAATAGA
Found at i:5679517 original size:25 final size:24
Alignment explanation
Indices: 5679489--5679536 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
5679479 TCAGAAATTA
*
5679489 AATTCAATTTTAGATTTTAAATTTT
1 AATTCAATCTTA-ATTTTAAATTTT
5679514 AATTCAATCTTAATTTTAAATTT
1 AATTCAATCTTAATTTTAAATTT
5679537 ATTGTAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (24 bp):
AATTCAATCTTAATTTTAAATTTT
Found at i:5679548 original size:17 final size:17
Alignment explanation
Indices: 5679528--5679590 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
5679518 CAATCTTAAT
5679528 TTTAAATTTATTGTAAG
1 TTTAAATTTATTGTAAG
** *
5679545 TTTAAGCTTATTCG-GAG
1 TTTAAATTTATT-GTAAG
* *
5679562 TTTAAATTTATTTTAAA
1 TTTAAATTTATTGTAAG
*
5679579 TTTAAAATTATT
1 TTTAAATTTATT
5679591 TTCGAATTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
17 34 0.97
18 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTGTAAG
Found at i:5679598 original size:18 final size:17
Alignment explanation
Indices: 5679562--5679616 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
5679552 TTATTCGGAG
*
5679562 TTTAAATTTATTTTAAA
1 TTTAAAATTATTTTAAA
*
5679579 TTTAAAATTATTTTCGAA
1 TTTAAAATTATTTT-AAA
5679597 -TTAAAA--A-TTTAAA
1 TTTAAAATTATTTTAAA
5679610 TTTAAAA
1 TTTAAAA
5679617 AGTTTAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 2 0.06
14 9 0.27
15 1 0.03
17 19 0.58
18 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TTTAAAATTATTTTAAA
Found at i:5680361 original size:3 final size:3
Alignment explanation
Indices: 5680346--5680394 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
5680336 TTCTTTATAT
* * *
5680346 TAA TAA TAT TAA TAA TAA TAA TAG TAA TAAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
5680392 TAA
1 TAA
5680395 AAAAGAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:5680380 original size:19 final size:19
Alignment explanation
Indices: 5680346--5680395 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
5680336 TTCTTTATAT
*
5680346 TAATAAT-ATTAATAATAA
1 TAATAATAATAAATAATAA
* *
5680364 TAATAGTAATAAATAATAT
1 TAATAATAATAAATAATAA
5680383 TAATAATAATAAA
1 TAATAATAATAAA
5680396 AAAGAAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
TAATAATAATAAATAATAA
Found at i:5681558 original size:30 final size:29
Alignment explanation
Indices: 5681513--5681822 Score: 276
Period size: 29 Copynumber: 10.7 Consensus size: 29
5681503 CTAAACTGTT
* * *
5681513 CAAAAATTATATTTTGACCCCCAAACTTC
1 CAAAAATTACATTTTTACCCCAAAACTTC
* *** *
5681542 TC-CAAATTACATTTTTGACCTTGAAACTTT
1 -CAAAAATTACATTTTT-ACCCCAAAACTTC
* *
5681572 AAAAAATTACATTTTTATCCCTAAAA-TTC
1 CAAAAATTACATTTTTA-CCCCAAAACTTC
* *
5681601 CAAAAATTACATTTTTACCCTAAAACTTT
1 CAAAAATTACATTTTTACCCCAAAACTTC
**
5681630 CAAAAATTACATTTTTACCCTTAAACTTC
1 CAAAAATTACATTTTTACCCCAAAACTTC
**
5681659 CAAAAATGCCATTTTTAACCCCAAAACTTC
1 CAAAAATTACATTTTT-ACCCCAAAACTTC
** *
5681689 CAAAAATTACCA--TTT-CCCCCGAACTTT
1 CAAAAATTA-CATTTTTACCCCAAAACTTC
**
5681716 C-AAAATTACATTTTTAACATCAAAACTTC
1 CAAAAATTACATTTTT-ACCCCAAAACTTC
*
5681745 CAAAAATTACATTTTTACCCCTAAACTTC
1 CAAAAATTACATTTTTACCCCAAAACTTC
* *
5681774 CAAAAATTCCATTTTTGGCCCCAAAACTTC
1 CAAAAATTACATTTTT-ACCCCAAAACTTC
5681804 C-AAAATTACCA-TTTTACCC
1 CAAAAATTA-CATTTTTACCC
5681823 TTGGACATCC
Statistics
Matches: 229, Mismatches: 38, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
25 2 0.01
26 7 0.03
27 13 0.06
28 11 0.05
29 119 0.52
30 75 0.33
31 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.34
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCCAAAACTTC
Found at i:5681760 original size:115 final size:113
Alignment explanation
Indices: 5681603--5681817 Score: 349
Period size: 115 Copynumber: 1.9 Consensus size: 113
5681593 TAAAATTCCA
* * * *
5681603 AAAATTACATTTTTACCCTAAAACTTTCAAAAATTACATTTTTACCCTTAAACTTCCAAAAATGC
1 AAAATTACATTTTTAACATAAAACTTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATGC
5681668 CATTTTTAACCCCAAAACTTCCAAAAATTACCATTTCCCCCGAACTTTC
66 CATTTTTAACCCCAAAACTTCC-AAAATTACCATTTCCCCCGAACTTTC
*
5681717 AAAATTACATTTTTAACATCAAAACTTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATT
1 AAAATTACATTTTTAACAT-AAAACTTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATG
**
5681782 CCATTTTTGGCCCCAAAACTTCCAAAATTACCATTT
65 CCATTTTTAACCCCAAAACTTCCAAAATTACCATTT
5681818 TACCCTTGGA
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
114 30 0.32
115 63 0.68
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.33
Consensus pattern (113 bp):
AAAATTACATTTTTAACATAAAACTTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATGC
CATTTTTAACCCCAAAACTTCCAAAATTACCATTTCCCCCGAACTTTC
Found at i:5681872 original size:173 final size:174
Alignment explanation
Indices: 5681530--5681846 Score: 417
Period size: 173 Copynumber: 1.8 Consensus size: 174
5681520 TATATTTTGA
* * * ** * *
5681530 CCCCCAAACTTCTCCAAATTACATTTTTGACCTTGAAACTTTAAAAAATTACATTTTTATCCCTA
1 CCCCCAAACTTCTCAAAATTACATTTTTAACATCAAAACTTCAAAAAATTACATTTTTACCCCTA
* *
5681595 AAATTCCAAAAATTACATTTTTACCCTAAAACTTTCAAAAATTACATTTTTACCCTTAAACTTCC
66 AAATTCCAAAAATTACATTTTTACCCCAAAACTTTCAAAAATTACATTTTTACCCTTAAACATCC
5681660 AAAAATGCCATTTTTAACCCCAAAACTTCCAAAAATTACCATTT
131 AAAAATGCCATTTTTAACCCCAAAACTTCCAAAAATTACCATTT
* *
5681704 CCCCCGAACTT-TCAAAATTACATTTTTAACATCAAAACTTCCAAAAATTACATTTTTACCCCTA
1 CCCCCAAACTTCTCAAAATTACATTTTTAACATCAAAACTTCAAAAAATTACATTTTTACCCCTA
* * * * **
5681768 AACTTCCAAAAATTCCATTTTTGGCCCCAAAAC-TTCCAAAATTACCA-TTTTACCCTTGGACAT
66 AAATTCCAAAAATTACATTTTT-ACCCCAAAACTTTCAAAAATTA-CATTTTTACCCTTAAACAT
* *
5681831 CCACAACT-CCATTTTT
129 CCAAAAATGCCATTTTT
5681847 TGATCCTAAT
Statistics
Matches: 122, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
172 8 0.07
173 94 0.77
174 20 0.16
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.34
Consensus pattern (174 bp):
CCCCCAAACTTCTCAAAATTACATTTTTAACATCAAAACTTCAAAAAATTACATTTTTACCCCTA
AAATTCCAAAAATTACATTTTTACCCCAAAACTTTCAAAAATTACATTTTTACCCTTAAACATCC
AAAAATGCCATTTTTAACCCCAAAACTTCCAAAAATTACCATTT
Found at i:5686097 original size:4 final size:4
Alignment explanation
Indices: 5686090--5686148 Score: 61
Period size: 4 Copynumber: 15.2 Consensus size: 4
5686080 AAAAAGAGAG
* * *
5686090 AGAA AGAA AGAAA AAAA AGAG AGAA AGAA A-AA AGAA A-AA A-AG AGAA
1 AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
5686136 AGAA AGAA AGAA A
1 AGAA AGAA AGAA A
5686149 AACAAGGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
3 8 0.17
4 35 0.76
5 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:5686103 original size:21 final size:21
Alignment explanation
Indices: 5686079--5686150 Score: 90
Period size: 21 Copynumber: 3.2 Consensus size: 21
5686069 GTGTTATCAA
5686079 AAAAAAGAGAGAGAAAGAAAG
1 AAAAAAGAGAGAGAAAGAAAG
*
5686100 AAAAAAAAGAGAGAAAGAAAAAAG
1 AAAAAAGAGAGAGAAAG---AAAG
*
5686124 AAAAAAAGAGAAAGAAAGAAAG
1 -AAAAAAGAGAGAGAAAGAAAG
5686146 AAAAA
1 AAAAA
5686151 CAAGGAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
21 21 0.48
22 4 0.09
24 4 0.09
25 15 0.34
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AAAAAAGAGAGAGAAAGAAAG
Found at i:5686129 original size:46 final size:43
Alignment explanation
Indices: 5686078--5686171 Score: 134
Period size: 46 Copynumber: 2.1 Consensus size: 43
5686068 CGTGTTATCA
*
5686078 AAAAAAAGAGAGAGAAAGAAAGAAAAAAAAGAGAGAAAGAAAAAAG
1 AAAAAAAGAGAAAGAAAGAAAGAAAAAAAAG-GA-AAA-AAAAAAG
* *
5686124 AAAAAAAGAGAAAGAAAGAAAGAAAAACAAGGAAAAAAAGAAG
1 AAAAAAAGAGAAAGAAAGAAAGAAAAAAAAGGAAAAAAAAAAG
5686167 AAAAA
1 AAAAA
5686172 TGGGTCGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 11 0.24
44 3 0.07
45 2 0.04
46 29 0.64
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (43 bp):
AAAAAAAGAGAAAGAAAGAAAGAAAAAAAAGGAAAAAAAAAAG
Found at i:5686167 original size:25 final size:23
Alignment explanation
Indices: 5686078--5686171 Score: 90
Period size: 23 Copynumber: 4.2 Consensus size: 23
5686068 CGTGTTATCA
* *
5686078 AAAAAAAGAGAGAGA-AAGAAAG
1 AAAAAAAGAGAAAAAGAAGAAAG
* *
5686100 AAAAAAAAGAGAGAAAGAAAAAAG
1 -AAAAAAAGAGAAAAAGAAGAAAG
*
5686124 AAAAAAAGAGAAAGA-AAGAAAG
1 AAAAAAAGAGAAAAAGAAGAAAG
5686146 AAAAACAAG-GAAAAA-AAG-AAG
1 AAAAA-AAGAGAAAAAGAAGAAAG
5686167 AAAAA
1 AAAAA
5686172 TGGGTCGAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.13
22 19 0.30
23 30 0.48
24 6 0.10
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (23 bp):
AAAAAAAGAGAAAAAGAAGAAAG
Found at i:5687011 original size:13 final size:12
Alignment explanation
Indices: 5686986--5687075 Score: 56
Period size: 13 Copynumber: 7.0 Consensus size: 12
5686976 TTCAATGAAT
5686986 AAAAGAAAAGAA
1 AAAAGAAAAGAA
5686998 AAAAGAAGAAGAAA
1 AAAAGAA-AAG-AA
* *
5687012 AACAAAAACAAAAA
1 AA-AAGAA-AAGAA
*
5687026 CAAAATAAAAGAAA
1 -AAAAGAAAAG-AA
* *
5687040 AAAACAAAATAA
1 AAAAGAAAAGAA
*
5687052 AATAAAAAAAG-A
1 AA-AAGAAAAGAA
5687064 AAAAGAAAAGAA
1 AAAAGAAAAGAA
5687076 GAGATCGAGG
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
11 7 0.11
12 15 0.25
13 19 0.31
14 12 0.20
15 8 0.13
ACGTcount: A:0.82, C:0.04, G:0.10, T:0.03
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:5687030 original size:18 final size:18
Alignment explanation
Indices: 5687021--5687066 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
5687011 AAACAAAAAC
5687021 AAAAACAAAATAAAAGAA
1 AAAAACAAAATAAAAGAA
*
5687039 AAAAACAAAATAAAATAA
1 AAAAACAAAATAAAAGAA
*
5687057 AAAAAGAAAA
1 AAAAACAAAA
5687067 AGAAAAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.85, C:0.04, G:0.04, T:0.07
Consensus pattern (18 bp):
AAAAACAAAATAAAAGAA
Found at i:5687520 original size:106 final size:107
Alignment explanation
Indices: 5687332--5687536 Score: 349
Period size: 106 Copynumber: 1.9 Consensus size: 107
5687322 TTGGGGCACC
* * *
5687332 TAACCCTATTCTTTGCTCACTTTGTGTTTGGCAATTCTTTGACCAATATGAGTCATTTTTAATCT
1 TAACCCTATTCTTTGCTCACTTTATATTTGGCAATCCTTTGACCAATATGAGTCATTTTTAATCT
5687397 TTTCATTCATGTAAGCTTTGCCTCCAATAAAATTCATCCACT
66 TTTCATTCATGTAAGCTTTGCCTCCAATAAAATTCATCCACT
* *
5687439 TAACCCTATTCTTTGCTCACTTTATATTTGGC-ATCCTTTGACTAATATGAGTCATTTTTTATCT
1 TAACCCTATTCTTTGCTCACTTTATATTTGGCAATCCTTTGACCAATATGAGTCATTTTTAATCT
*
5687503 TTTCATTCATGTGAGCTTTGCCTCCAATAAAATT
66 TTTCATTCATGTAAGCTTTGCCTCCAATAAAATT
5687537 TCATTCGCCT
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
106 62 0.67
107 30 0.33
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.44
Consensus pattern (107 bp):
TAACCCTATTCTTTGCTCACTTTATATTTGGCAATCCTTTGACCAATATGAGTCATTTTTAATCT
TTTCATTCATGTAAGCTTTGCCTCCAATAAAATTCATCCACT
Found at i:5688185 original size:51 final size:50
Alignment explanation
Indices: 5688064--5688418 Score: 248
Period size: 51 Copynumber: 7.1 Consensus size: 50
5688054 CAGGTTTAAC
* * * ***
5688064 AGGGAAAGATCTAAGCCGCGATGGTGGATCCAGTA-C-CGTGAAGAC-AA
1 AGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAAAGACAAA
*
5688111 AGGGAAAGATCTAAGACCGCAACGACGGATCCAGTACCACAAAAAGACAAA
1 AGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACAAAAAGACAAA
* * * *
5688162 AGGGGAAAGGTCTAAGTCGCAACGGCGGA-CC-GTGCACCTCAAAAA-ACACGA
1 A-GGGAAAGATCTAAGCCGCAACGGCGGATCCAGT--ACCACAAAAAGACA-AA
* * * * *** *
5688213 CGGGAAAGATCTAAGATCGTAACGGCGGATCTAGTA-C-CGTGAAGACATA
1 AGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACAAAAAGACAAA
* * * * * *
5688262 AGGGAAAGATCTAAGCCACAACAGTGGATCCAGTACCACGAAGATATC-AA
1 AGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAAAGA-CAAA
* * ** *
5688312 A-GGAAAGATCTAAGCCGTAATGGCGGA-CCATGTACC-TTAGAAGACAATA
1 AGGGAAAGATCTAAGCCGCAACGGCGGATCCA-GTACCACAAAAAGACAA-A
* *
5688361 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATACAAA
1 AGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACAAAAAGACAAA
5688412 AGGGAAA
1 AGGGAAA
5688419 AGTTTAAGTC
Statistics
Matches: 237, Mismatches: 49, Indels: 40
0.73 0.15 0.12
Matches are distributed among these distances:
47 16 0.07
48 37 0.16
49 50 0.21
50 47 0.20
51 62 0.26
52 23 0.10
53 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.13
Consensus pattern (50 bp):
AGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACAAAAAGACAAA
Found at i:5688385 original size:148 final size:149
Alignment explanation
Indices: 5688064--5688398 Score: 392
Period size: 148 Copynumber: 2.3 Consensus size: 149
5688054 CAGGTTTAAC
* * *
5688064 AGGGAAAGATCTAAG-CCGCGATGGTGGATCCAGTACCGTGAAGACAAAGGGAAAGATCTAAGAC
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTGAAGACAAAGGGAAAGATCTAAGAC
* * *
5688128 CGCAACGACGGATCCAGTACCACAAAAAGACAAAAGGGGAAAGGTCTAAGTCGCAACGGCGGACC
66 CACAACGACGGATCCAGTACCACAAAAAGACAAAA-GGGAAAGATCTAAGCCGCAACGGCGGACC
* *
5688193 GTGCACCTCAAAAAACACGA
130 ATGCACCTCAAAAAACAAGA
* * * *
5688213 CGGGAAAGATCTAAGATCGTAACGGCGGATCTAGTACCGTGAAGACATAAGGGAAAGATCTAAG-
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTGAAGACA-AAGGGAAAGATCTAAGA
* * * * * *
5688277 CCACAAC-AGTGGATCCAGTACCACGAAGATATC-AAA-GGAAAGATCTAAGCCGTAATGGCGGA
65 CCACAACGA-CGGATCCAGTACCACAAAAAGA-CAAAAGGGAAAGATCTAAGCCGCAACGGCGGA
* * * * *
5688339 CCATGTACCTTAGAAGACAATA
128 CCATGCACCTCAAAAAACAAGA
5688361 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACC
1 AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACC
5688399 ACAAAGATAC
Statistics
Matches: 155, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
148 71 0.46
149 15 0.10
150 52 0.34
151 17 0.11
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13
Consensus pattern (149 bp):
AGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTGAAGACAAAGGGAAAGATCTAAGAC
CACAACGACGGATCCAGTACCACAAAAAGACAAAAGGGAAAGATCTAAGCCGCAACGGCGGACCA
TGCACCTCAAAAAACAAGA
Found at i:5688468 original size:100 final size:99
Alignment explanation
Indices: 5688253--5688454 Score: 241
Period size: 100 Copynumber: 2.0 Consensus size: 99
5688243 CTAGTACCGT
* * *
5688253 GAAGAC-ATAAGGGAAAGATCTAAGCCACAACAGTGGATCCAGTACCACGAAGATATCAAAGGAA
1 GAAGACAATAAGAGAAAGATCTAAGCCACAACAGCGGATCCAGTACCACAAAGATATCAAAGGAA
* *
5688317 AGATCTAAGCCGTAATGGCGGACCATGTACCTTA
66 AGATCTAAGCCGCAATGGCGAACCATGTACCTTA
* * *
5688351 GAAGACAATAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATA-CAAAAGG
1 GAAGACAATAAGAGAAAGATCTAAG-CCACAACAGCGGATCCAGTACCACAAAGATATC-AAA-G
* *
5688415 GAAA-AGTTTAAGTCGCAATGGCGAACCCA-GTACCTTA
63 GAAAGA-TCTAAGCCGCAATGGCGAA-CCATGTACCTTA
5688452 GAA
1 GAA
5688455 ACATGACGAG
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
98 6 0.07
99 19 0.21
100 31 0.34
101 31 0.34
102 3 0.03
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (99 bp):
GAAGACAATAAGAGAAAGATCTAAGCCACAACAGCGGATCCAGTACCACAAAGATATCAAAGGAA
AGATCTAAGCCGCAATGGCGAACCATGTACCTTA
Found at i:5689562 original size:205 final size:206
Alignment explanation
Indices: 5688865--5690083 Score: 1609
Period size: 205 Copynumber: 6.0 Consensus size: 206
5688855 TACCAACTCG
* * * * *
5688865 AGGCTCAATGCAAGTAAATCTTCGAACCCCAACTTTCTGATGAGACACAGAG-AGACAGGTCGAA
1 AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAG-CAGGTCGAA
* * * *
5688929 GTAATAAAATGGTTAACTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAG
65 GCAATAAAATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAG
* * *
5688994 ACACAGTGAAGCGAATTGAAACAAGTGATGCGATCATCTTCCTGATGAGACACTGAGAAGAAGAC
130 ACACAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGAC
*
5689059 CAAATCAAACCT
195 CAAATCAAACCC
* * ** *
5689071 AGACTCGATATGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAG
1 AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAG
* *
5689136 CAATAAAATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTTGTCTTCCTGATAAGA
66 CAATAAAATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
* * * * * *
5689201 CACAGAGAAACGAATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAG-TGTAC
131 CACAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAG-AC
*
5689265 CAACTC-AA--C
195 CAAATCAAACCC
* * * *
5689274 --GCTCAATGCGAGGAAATCTTCGAACCCCAACTTCTTGATGAGACACTAAGAAGCAGGTCGAAG
1 AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAG
* * * *
5689337 CAAT-AAATGGTTAGCTTCCTGATAAGACACTTAGAAGTGGACCAAATTCGTCTTCCTGAGGATA
66 CAATAAAATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
5689401 TC-CAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGAC
131 -CACAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGAC
5689465 CAAATCAAACCC
195 CAAATCAAACCC
*
5689477 AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
1 AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAG
* * *
5689542 TAAT-AAATGGTTAGCTTCCTGATGAGGCACTGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGA
66 CAATAAAATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
* * * *
5689606 TC-CAGAGAAGCGAATTAAAACAAGTGATGTGGTCATCTTCCTTATGAGACACGGAGAAGTAGAC
131 -CACAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGAC
*
5689670 CAAATCAAACCT
195 CAAATCAAACCC
* *
5689682 AGGCTCAATGCGAGCAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAG
1 AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAG
* * * *
5689746 CAATAAAATGGTTAGCTTCCTAATGAGATACAGAGAAGTGGACCAAATTCATCTTCCTGATGAGA
66 CAATAAAATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
* *
5689811 CACAGAGAAGCGAATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTAAGAAGAAGACC
131 CACAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACC
5689876 AAATCAAACCC
196 AAATCAAACCC
* * * * * * **
5689887 AAGCTTAATGCGAACAAATCTTCGAACCCTAGCTTTCTGATGAGATACTGAGAAGCAGGTTAAAG
1 AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAG
* * * ** ** *
5689952 CAATAAAGTGGTCAGCTTCCTGATGAGACACAGAGAAGTAAACCAAACCCGTCTTCCTGATGAAA
66 CAATAAAATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
* * * * * * * * *
5690017 CACAGAGAAGTGGATCAAAACAAATGACGCGGTCATCCTCCT-ATTGAAATACTGAGAAGAAGGC
131 CACAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGA-TGAGACACTGAGAAGAAGAC
5690081 CAA
195 CAA
5690084 GTTAATGAAA
Statistics
Matches: 894, Mismatches: 106, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
200 113 0.13
201 62 0.07
203 1 0.00
204 41 0.05
205 362 0.40
206 313 0.35
207 2 0.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (206 bp):
AGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAG
CAATAAAATGGTTAGCTTCCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA
CACAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACC
AAATCAAACCC
Found at i:5690485 original size:17 final size:17
Alignment explanation
Indices: 5690465--5690527 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
5690455 CAATCTTAAT
5690465 TTTAAATTTATTGTAAG
1 TTTAAATTTATTGTAAG
** *
5690482 TTTAAGCTTATTCG-GAG
1 TTTAAATTTATT-GTAAG
* *
5690499 TTTAAATTTATTTTAAA
1 TTTAAATTTATTGTAAG
*
5690516 TTTAAAATTATT
1 TTTAAATTTATT
5690528 TTTGAATTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
17 34 0.97
18 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTGTAAG
Found at i:5690530 original size:18 final size:17
Alignment explanation
Indices: 5690499--5690553 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
5690489 TTATTCGGAG
*
5690499 TTTAAATTTATTTTAAA
1 TTTAAAATTATTTTAAA
*
5690516 TTTAAAATTATTTTTGAA
1 TTTAAAATTA-TTTTAAA
5690534 -TTAAAA--A-TTTAAA
1 TTTAAAATTATTTTAAA
5690547 TTTAAAA
1 TTTAAAA
5690554 AGTTTAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 5 0.15
14 6 0.18
15 1 0.03
17 15 0.45
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAAAATTATTTTAAA
Found at i:5691257 original size:3 final size:3
Alignment explanation
Indices: 5691249--5691297 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
5691239 TTCTTTATAT
* *
5691249 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
5691295 TAA
1 TAA
5691298 AAAAGAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5692501 original size:29 final size:29
Alignment explanation
Indices: 5692432--5692648 Score: 185
Period size: 29 Copynumber: 7.4 Consensus size: 29
5692422 AACTGTTGAG
* * *
5692432 AAATTATATTTTGACCC-CAAACTTCTC-C
1 AAATTACATTTTGACCCTGAAACTTC-CAA
* * *
5692460 AAATTATACTTTTGACCTTGAAACTTCTAA
1 AAATTACA-TTTTGACCCTGAAACTTCCAA
* *
5692490 AAATTACATTTTTATCCTTG-AACTTCCAA
1 AAATTACATTTTGA-CCCTGAAACTTCCAA
**
5692519 AAATTACATTTTTGACCCCAAAACTTCCAA
1 AAATTACA-TTTTGACCCTGAAACTTCCAA
*
5692549 AAATTACATTTTTACCCCT-AAACTTCCAA
1 AAATTACATTTTGA-CCCTGAAACTTCCAA
** *
5692578 AAATGCCATTTTTGACCCTAAAACTTCCAA
1 AAATTACA-TTTTGACCCTGAAACTTCCAA
5692608 AAATTACCATTTT-ACCCCTG-AACTTCCAA
1 AAATTA-CATTTTGA-CCCTGAAACTTCCAA
*
5692637 AAATTCCATTTT
1 AAATTACATTTT
5692649 TTGATCTCTA
Statistics
Matches: 158, Mismatches: 20, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
28 14 0.09
29 71 0.45
30 71 0.45
31 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
AAATTACATTTTGACCCTGAAACTTCCAA
Found at i:5692646 original size:59 final size:59
Alignment explanation
Indices: 5692469--5692649 Score: 265
Period size: 59 Copynumber: 3.1 Consensus size: 59
5692459 CAAATTATAC
* * * * * *
5692469 TTTTGACCTTGAAACTTCTAAAAATTACATTTTTATCCTTGAACTTCCAAAAATTACAT
1 TTTTGACCCTAAAACTTCCAAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCAT
* * *
5692528 TTTTGACCCCAAAACTTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATGCCAT
1 TTTTGACCCTAAAACTTCCAAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCAT
5692587 TTTTGACCCTAAAACTTCCAAAAATTACCA-TTTTACCCCTGAACTTCCAAAAATTCCAT
1 TTTTGACCCTAAAACTTCCAAAAATTA-CATTTTTACCCCTGAACTTCCAAAAATTCCAT
5692646 TTTT
1 TTTT
5692650 TGATCTCTAT
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
59 107 0.98
60 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (59 bp):
TTTTGACCCTAAAACTTCCAAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCAT
Found at i:5692649 original size:29 final size:29
Alignment explanation
Indices: 5692480--5692649 Score: 209
Period size: 29 Copynumber: 5.8 Consensus size: 29
5692470 TTTGACCTTG
* * *
5692480 AAACTTCTAAAAATTACATTTTTATCCTT
1 AAACTTCCAAAAATTACATTTTTACCCCT
* *
5692509 GAACTTCCAAAAATTACATTTTTGACCCCA
1 AAACTTCCAAAAATTACATTTTT-ACCCCT
5692539 AAACTTCCAAAAATTACATTTTTACCCCT
1 AAACTTCCAAAAATTACATTTTTACCCCT
**
5692568 AAACTTCCAAAAATGCCATTTTTGA-CCCT
1 AAACTTCCAAAAATTACATTTTT-ACCCCT
5692597 AAAACTTCCAAAAATTACCA-TTTTACCCCT
1 -AAACTTCCAAAAATTA-CATTTTTACCCCT
* *
5692627 GAACTTCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATTACATTTTT
5692650 TGATCTCTAT
Statistics
Matches: 122, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
28 2 0.02
29 70 0.57
30 48 0.39
31 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCCT
Found at i:5694571 original size:13 final size:14
Alignment explanation
Indices: 5694523--5694582 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
5694513 TAGATCAATT
* *
5694523 TAAAATTTCATATA
1 TAAAATTACACATA
* *
5694537 TAAAATTATACAAAA
1 TAAAATTACAC-ATA
5694552 TTAAAATTA-ACATA
1 -TAAAATTACACATA
5694566 TAAAATTACACAT-
1 TAAAATTACACATA
5694579 TAAA
1 TAAA
5694583 CTAAAATTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 12 0.32
14 14 0.37
15 4 0.11
16 8 0.21
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAATTACACATA
Found at i:5697049 original size:3 final size:3
Alignment explanation
Indices: 5697041--5697068 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5697031 AAATATTCAC
5697041 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5697069 ATATTATTAT
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):
ATA
Found at i:5709961 original size:39 final size:40
Alignment explanation
Indices: 5709904--5709983 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
5709894 AAGAGGTATG
*
5709904 TCCAATATGAAAATGGTTGTGACTCTTC-AAAAGATGTCCA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAAG-TGTCCA
*
5709944 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAAGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAAGTGTCCA
5709983 T
1 T
5709984 TGAGTGCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 24 0.65
40 13 0.35
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGGTTGTGACTCTTCAAAAAGTGTCCA
Found at i:5724019 original size:49 final size:49
Alignment explanation
Indices: 5723922--5724019 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
5723912 CTATAATTTC
* * *
5723922 ACTAAATTCCATTATTATTTATTCTCTTTTCAAATATGGACAAGGTAAT
1 ACTAAATTCCATTATTACTTATTCTCTTTTCAAATATCGACAAAGTAAT
* * *
5723971 ACTACATTCTATTATTACTTATTCTCTTTTCAAATATCGAGAAAGTAAT
1 ACTAAATTCCATTATTACTTATTCTCTTTTCAAATATCGACAAAGTAAT
5724020 GCAACTTATC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (49 bp):
ACTAAATTCCATTATTACTTATTCTCTTTTCAAATATCGACAAAGTAAT
Found at i:5727178 original size:52 final size:52
Alignment explanation
Indices: 5727104--5727290 Score: 243
Period size: 52 Copynumber: 3.6 Consensus size: 52
5727094 GTATATGAAA
* *
5727104 AGGTTCGATGACTATGTGTCATCATGAGTATATGAATCCCTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATG
*
5727156 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAC-AGATTATG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGA-ATTATG
* * * * * *
5727208 AGGTCCGATGATTATGTGTCATCGTGAGTGTATGATTCCTTTACGGAA-CAAG
1 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTAC-GAATTATG
**
5727260 AGGTCTAATGACTATGTGTCATCATGAGTAT
1 AGGTCCGATGACTATGTGTCATCATGAGTAT
5727291 TAAATGGAAT
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
51 1 0.01
52 116 0.97
53 1 0.01
54 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATG
Found at i:5732886 original size:29 final size:28
Alignment explanation
Indices: 5732843--5733063 Score: 162
Period size: 29 Copynumber: 7.7 Consensus size: 28
5732833 AAATTGTTCA
* *
5732843 AAAATTATATTTTGACCCCCAAACTTCTC
1 AAAATTACATTTTGACCCCTAAACTTC-C
* * * *
5732872 CAAATTATATTTTGACCTCGAAACTTCC
1 AAAATTACATTTTGACCCCTAAACTTCC
* *
5732900 AAAAATTACATTTTTATCCCTAAACTTCC
1 -AAAATTACATTTTGACCCCTAAACTTCC
* * *
5732929 AAAATTACATTTTTACCTCTAAACTTCTA
1 AAAATTACATTTTGACCCCTAAACTTC-C
** *
5732958 AAAATGCCATTTTTGA-CCTTAAAACTTCC
1 AAAATTACA-TTTTGACCCCT-AAACTTCC
* *
5732987 AAAAATTACCATTTT-A-CCCTCGAACTTCA
1 -AAAATTA-CATTTTGACCCCT-AAACTTCC
* *
5733016 AAAATTCCACTTTTGACCCCAAAACTTCC
1 AAAATTACA-TTTTGACCCCTAAACTTCC
5733045 AAAATTACCATTTT-ACCCC
1 AAAATTA-CATTTTGACCCC
5733064 CGAACATCCA
Statistics
Matches: 153, Mismatches: 29, Indels: 21
0.75 0.14 0.10
Matches are distributed among these distances:
27 2 0.01
28 41 0.27
29 82 0.54
30 26 0.17
31 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATTACATTTTGACCCCTAAACTTCC
Found at i:5732953 original size:57 final size:58
Alignment explanation
Indices: 5732841--5733058 Score: 205
Period size: 58 Copynumber: 3.8 Consensus size: 58
5732831 CTAAATTGTT
* * * * * *
5732841 CAAAAATTATATTTTGACCCCCAAACTTCTCCAAATTA-TATTTTGACCTCGAAACTTC
1 CAAAAATTACATTTTGACCCCTAAACTTC-CAAAATTACCATTTTTACCTCTAAACTTC
* *
5732899 CAAAAATTACATTTTTATCCCTAAACTTCCAAAATTA-CATTTTTACCTCTAAACTTC
1 CAAAAATTACATTTTGACCCCTAAACTTCCAAAATTACCATTTTTACCTCTAAACTTC
* ** * *
5732956 TAAAAATGCCATTTTTGA-CCTTAAAACTTCCAAAAATTACCA-TTTTACC-CTCGAACTT-
1 CAAAAATTACA-TTTTGACCCCT-AAACTTCC-AAAATTACCATTTTTACCTCT-AAACTTC
* *
5733014 CAAAAATTCCACTTTTGACCCCAAAACTTCCAAAATTACCATTTT
1 CAAAAATTACA-TTTTGACCCCTAAACTTCCAAAATTACCATTTT
5733059 ACCCCCGAAC
Statistics
Matches: 134, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
57 45 0.34
58 66 0.49
59 21 0.16
60 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (58 bp):
CAAAAATTACATTTTGACCCCTAAACTTCCAAAATTACCATTTTTACCTCTAAACTTC
Found at i:5732989 original size:87 final size:88
Alignment explanation
Indices: 5732839--5733058 Score: 227
Period size: 87 Copynumber: 2.5 Consensus size: 88
5732829 CCCTAAATTG
* * * * * *
5732839 TTCAAAAATTATA-TTTTGACCCCCAAACTTCTCCAAATTA-TA-TTTTGACCTCGAAACTTCCA
1 TTCAAAAATTACACTTTTGACCCCAAAACTTC-CAAAAATACCATTTTTGACCTCAAAACTTCCA
5732901 AAAATTA-CATTTTTATCCCT-AAAC
65 AAAATTACCA-TTTTA-CCCTCAAAC
* * * * * * *
5732925 TTCCAAAATTACA-TTTTTACCTCTAAACTTCTAAAAATGCCATTTTTGACCTTAAAACTTCCAA
1 TTCAAAAATTACACTTTTGACCCCAAAACTTCCAAAAATACCATTTTTGACCTCAAAACTTCCAA
*
5732989 AAATTACCATTTTACCCTCGAAC
66 AAATTACCATTTTACCCTCAAAC
* *
5733012 TTCAAAAATTCCACTTTTGACCCCAAAACTTCCAAAATTACCATTTT
1 TTCAAAAATTACACTTTTGACCCCAAAACTTCCAAAAATACCATTTT
5733059 ACCCCCGAAC
Statistics
Matches: 108, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
85 4 0.04
86 31 0.29
87 44 0.41
88 29 0.27
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (88 bp):
TTCAAAAATTACACTTTTGACCCCAAAACTTCCAAAAATACCATTTTTGACCTCAAAACTTCCAA
AAATTACCATTTTACCCTCAAAC
Found at i:5733073 original size:28 final size:28
Alignment explanation
Indices: 5732980--5733076 Score: 115
Period size: 29 Copynumber: 3.4 Consensus size: 28
5732970 TTGACCTTAA
*
5732980 AACTTCCAAAAATTACCATTTTACCCTCG
1 AACTTCC-AAAATTACCATTTTACCCCCG
* **
5733009 AACTTCAAAAATT-CCACTTTTGACCCCAA
1 AACTTCCAAAATTACCA-TTTT-ACCCCCG
5733038 AACTTCCAAAATTACCATTTTACCCCCG
1 AACTTCCAAAATTACCATTTTACCCCCG
*
5733066 AACATCCAAAA
1 AACTTCCAAAA
5733077 ACTCTATTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
27 3 0.05
28 25 0.44
29 26 0.46
30 3 0.05
ACGTcount: A:0.38, C:0.32, G:0.03, T:0.27
Consensus pattern (28 bp):
AACTTCCAAAATTACCATTTTACCCCCG
Found at i:5733077 original size:29 final size:28
Alignment explanation
Indices: 5732984--5733077 Score: 102
Period size: 28 Copynumber: 3.3 Consensus size: 28
5732974 CCTTAAAACT
*
5732984 TCCAAAAATTACCATTTTACCCTCGAAC
1 TCCAAAAATTACCATTTTACCCCCGAAC
* **
5733012 TTCAAAAATT-CCACTTTTGACCCCAAAAC
1 TCCAAAAATTACCA-TTTT-ACCCCCGAAC
5733041 TTCC-AAAATTACCATTTTACCCCCGAAC
1 -TCCAAAAATTACCATTTTACCCCCGAAC
5733069 ATCCAAAAA
1 -TCCAAAAA
5733078 CTCTATTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
27 3 0.06
28 24 0.45
29 21 0.40
30 5 0.09
ACGTcount: A:0.38, C:0.32, G:0.03, T:0.27
Consensus pattern (28 bp):
TCCAAAAATTACCATTTTACCCCCGAAC
Found at i:5734102 original size:26 final size:28
Alignment explanation
Indices: 5734073--5734125 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
5734063 ACATATTCTT
*
5734073 TTTGAAATTTT-AGTAA-TTTATATAAA
1 TTTGAAATTTTAAATAATTTTATATAAA
*
5734099 TTTGAATTTTTAAATAATTTTATATAA
1 TTTGAAATTTTAAATAATTTTATATAA
5734126 GTTTCTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 10 0.43
27 4 0.17
28 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (28 bp):
TTTGAAATTTTAAATAATTTTATATAAA
Found at i:5736421 original size:3 final size:3
Alignment explanation
Indices: 5736415--5736450 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
5736405 ATAATAATAA
5736415 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CTAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
5736451 GACATTCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5744678 original size:49 final size:49
Alignment explanation
Indices: 5744607--5744799 Score: 260
Period size: 49 Copynumber: 3.8 Consensus size: 49
5744597 TTATAATTTC
* * *
5744607 ACTAAATTCCATTATTATTTATTCTCTTTTCAAATATGGACAAGGTAAT
1 ACTACATTCTATTATTACTTATTCTCTTTTCAAATATGGACAAGGTAAT
5744656 ACTACATTCTATTATTACTTATTCTCTTTTCAAATATGGACAAGGTAAT
1 ACTACATTCTATTATTACTTATTCTCTTTTCAAATATGGACAAGGTAAT
*
5744705 ACTACATTTTCAAATATGGACAATTACTTATTCTCTTTTCAAATATGGACAAGGTAAT
1 ACTACA--TTC---TAT----TATTACTTATTCTCTTTTCAAATATGGACAAGGTAAT
*
5744763 ACTACATTCTATTATTACTTATTCTCTGTTCAAATAT
1 ACTACATTCTATTATTACTTATTCTCTTTTCAAATAT
5744800 CGAGAAAGTA
Statistics
Matches: 129, Mismatches: 6, Indels: 18
0.84 0.04 0.12
Matches are distributed among these distances:
49 75 0.58
51 3 0.02
53 3 0.02
54 3 0.02
56 3 0.02
58 42 0.33
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (49 bp):
ACTACATTCTATTATTACTTATTCTCTTTTCAAATATGGACAAGGTAAT
Found at i:5744724 original size:29 final size:29
Alignment explanation
Indices: 5744682--5744770 Score: 112
Period size: 29 Copynumber: 3.1 Consensus size: 29
5744672 ACTTATTCTC
5744682 TTTTCAAATATGGACAAGGTAATACTACA
1 TTTTCAAATATGGACAAGGTAATACTACA
* *
5744711 TTTTCAAATATGGACAA-TTACTTATTCT-C-
1 TTTTCAAATATGGACAAGGTA---ATACTACA
5744740 TTTTCAAATATGGACAAGGTAATACTACA
1 TTTTCAAATATGGACAAGGTAATACTACA
5744769 TT
1 TT
5744771 CTATTATTAC
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
27 4 0.08
28 3 0.06
29 36 0.72
30 3 0.06
31 4 0.08
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (29 bp):
TTTTCAAATATGGACAAGGTAATACTACA
Found at i:5747970 original size:52 final size:52
Alignment explanation
Indices: 5747896--5748082 Score: 243
Period size: 52 Copynumber: 3.6 Consensus size: 52
5747886 GTATATGAAA
* * *
5747896 AGGTTCGATGACTATGTGTCATCATGAGTATATGAATCCCTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
5747948 AGGTCCGGTGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGG-TTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAC-GGATTATG
* * * ** *
5748000 AGGTCCGATGATTATGTGTCAACGTGAGTGTAT-AATTCCTTTACGGAACAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAA-TCCTTTACGGATTATG
*
5748052 AGGTCCAATGACTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
5748083 TAAATGGAAT
Statistics
Matches: 117, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
51 4 0.03
52 111 0.95
53 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:5754554 original size:52 final size:52
Alignment explanation
Indices: 5754475--5754623 Score: 199
Period size: 52 Copynumber: 2.9 Consensus size: 52
5754465 CGTTAATGAA
* *
5754475 AAGGTCCGATGACTATGTGCCATCGTGAGTATCTGAATCCCTTACAAATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCCTTACAAATTAT
* * * *
5754527 GAGGTCCGGTGACTATGTGTCATCGTGAGTATATGAATCCTTTACAAATTTT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCCTTACAAATTAT
* * * * *
5754579 AAGGTCCAATGACTATGTGTCATCATGAGTGTATGATTCCTTTAC
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCCTTAC
5754624 GGAACAAGAG
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 85 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCCTTACAAATTAT
Found at i:5761104 original size:24 final size:24
Alignment explanation
Indices: 5761043--5761105 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
5761033 TAGACTAATA
* *
5761043 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
5761067 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
5761091 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
5761106 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:5762747 original size:24 final size:24
Alignment explanation
Indices: 5762685--5762748 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
5762675 CTAGACTAAT
*
5762685 AAGAGTTTAACTCAAACAAATAAA
1 AAGAGTTTAACTGAAACAAATAAA
* * *
5762709 CAGAGTTTAATTGAAACAATTAAA
1 AAGAGTTTAACTGAAACAAATAAA
5762733 AAGAGTTTAACTGAAA
1 AAGAGTTTAACTGAAA
5762749 GATTATTTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (24 bp):
AAGAGTTTAACTGAAACAAATAAA
Found at i:5767712 original size:250 final size:250
Alignment explanation
Indices: 5767018--5767880 Score: 1076
Period size: 250 Copynumber: 3.4 Consensus size: 250
5767008 ATATATATAG
* * *
5767018 ACAAGGAAATGCTACCTACCAATAAATCTAATTCATCACAAGAAAAAAATATAAAAT-ATTTTAA
1 ACAAAGAAATGCAACCAACCAATAAATCTAATTCATCACAAGAAAAAAATATAAAATGATTTT-A
* *
5767082 ATAGA-AAAAATGA-TTTTATTCATTCAGTCATTATTTTTGGACGCTCGTTGAAGATTTTTTCGT
65 A-AGACAAAAATGATTTTTATTCATTCAATCATTATTTTTGGACGCTCGTTGAAAATTTTTT-GT
*
5767145 ACGATAAATATTAGAAGAATTTCAAAAGAAAAAAATCACCCACACACAATTTATCTTATAAAAAT
128 ACGATGAATATTAGAAGAATTTCAAAAGAAAAAAATCACCCACACACAATTTATCTTATAAAAAT
* *
5767210 TTTGACCCACTATAATTTCACTAAACTCTATTATTAATTACTCTGTTTGCAAATATGA
193 TTTGACCCACTATAATTCCACTAAACTCCATTATTAATTACTCTGTTTGCAAATATGA
* ** * * * *
5767268 ACAAAGTAATGCAACCAATTAATAAATCTGATTCAT-ATCAATAAAAAAATAGAAAATGTTTTTG
1 ACAAAGAAATGCAACCAACCAATAAATCTAATTCATCA-CAAGAAAAAAATATAAAATGATTTT-
* * * * * *
5767332 ACAGACAAAAATGATTTTTATTCATTCAATCGTTATTTTTGGGCCCGCTTGTTCAAGATTTTTTT
64 AAAGACAAAAATGATTTTTATTCATTCAATCATTATTTTT-GG-ACGCTCGTTGAA-AATTTTTT
* ** **** * *
5767397 GTATGATGAATGGTAGAAGAATTTTGGGAGAAGAAACATCACCCACACACACTTTATCTTATAAA
126 GTACGATGAATATTAGAAGAATTTCAAAAGAA-AAAAATCACCCACACACAATTTATCTTATAAA
* * * *
5767462 AATTTTGACCCCACTATAATTCCATTAAACTCCATTATTAATTATTCTCTTTTCAAATAT-A
190 AATTTTGA-CCCACTATAATTCCACTAAACTCCATTATTAATTACTCTGTTTGCAAATATGA
* * * *
5767523 GACAAGGAAATGCTACCTACCAATAAATCTAATTCATCACAAGAAAAAAATATACAAT-ATTTTA
1 -ACAAAGAAATGCAACCAACCAATAAATCTAATTCATCACAAGAAAAAAATATAAAATGATTTTA
* *
5767587 AATAGAAAAATGA-TTTTATTCATTCAATCATTATTTTTGGACGCTCGTTGAAAATTTTTTGTAC
65 AAGACAAAAATGATTTTTATTCATTCAATCATTATTTTTGGACGCTCGTTGAAAATTTTTTGTAC
*
5767651 GATGAATATTAGAAGAATTTCAAAAGAAAACAAATCACCCACACACAGTTTATCTTATAAAAATT
130 GATGAATATTAGAAGAATTTCAAAAGAAAA-AAATCACCCACACACAATTTATCTTATAAAAATT
* *
5767716 TTGACCCACTATAAATCCACTAAACTCCATTACTAATTACTCTGTTTGCAAATATGA
194 TTGACCCACTATAATTCCACTAAACTCCATTATTAATTACTCTGTTTGCAAATATGA
* * * * *
5767773 ACAAAGTAATGCAACCAATCAATAAATCTAATTCATAACAA-ATAAAAAATAAAAAAAATGTTTT
1 ACAAAGAAATGCAACCAACCAATAAATCTAATTCATCACAAGA-AAAAAAT--ATAAAATGATTT
**
5767837 TAACAGACAAAAATGATTTTTATTCATTCAATTGTTATTTTTGG
63 TAA-AGACAAAAATGATTTTTATTCATTCAATCATTATTTTTGG
5767881 GCCCGCTCGT
Statistics
Matches: 512, Mismatches: 82, Indels: 34
0.82 0.13 0.05
Matches are distributed among these distances:
248 1 0.00
249 90 0.18
250 118 0.23
251 27 0.05
252 31 0.06
253 36 0.07
254 69 0.13
255 49 0.10
256 90 0.18
257 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (250 bp):
ACAAAGAAATGCAACCAACCAATAAATCTAATTCATCACAAGAAAAAAATATAAAATGATTTTAA
AGACAAAAATGATTTTTATTCATTCAATCATTATTTTTGGACGCTCGTTGAAAATTTTTTGTACG
ATGAATATTAGAAGAATTTCAAAAGAAAAAAATCACCCACACACAATTTATCTTATAAAAATTTT
GACCCACTATAATTCCACTAAACTCCATTATTAATTACTCTGTTTGCAAATATGA
Found at i:5771996 original size:40 final size:40
Alignment explanation
Indices: 5771952--5772102 Score: 187
Period size: 40 Copynumber: 3.8 Consensus size: 40
5771942 CAATGCTATC
* *
5771952 ACTGAACTAGCAGTGACACTGTAAACACTGTGACATTACT
1 ACTGAACTAGCAGTGACACTGTAAACACTGCGATATTACT
* *
5771992 ACTGAATTGGCAGTGACACTGTAAACACTGCGATATTACT
1 ACTGAACTAGCAGTGACACTGTAAACACTGCGATATTACT
* * * * * *
5772032 ATTAAACTGGTAGTGAAACTGTAAACACTGCAATATTA-T
1 ACTGAACTAGCAGTGACACTGTAAACACTGCGATATTACT
*
5772071 CACTGAACTAGCTGTGACACTGTAAACACTGC
1 -ACTGAACTAGCAGTGACACTGTAAACACTGC
5772103 TAGACTGTCA
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 1 0.01
40 93 0.99
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (40 bp):
ACTGAACTAGCAGTGACACTGTAAACACTGCGATATTACT
Found at i:5772118 original size:40 final size:40
Alignment explanation
Indices: 5772044--5772119 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
5772034 TAAACTGGTA
* * *
5772044 GTGAAACTGTAAACACTGCAATATTATCACTGAACTAGCT
1 GTGAAACTGTAAACACTGCAAGACTATCAATGAACTAGCT
* * *
5772084 GTGACACTGTAAACACTGCTAGACTGTCAATGAACT
1 GTGAAACTGTAAACACTGCAAGACTATCAATGAACT
5772120 GTAATACCAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (40 bp):
GTGAAACTGTAAACACTGCAAGACTATCAATGAACTAGCT
Found at i:5772247 original size:51 final size:51
Alignment explanation
Indices: 5772192--5772293 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
5772182 CTACGAATTA
* *
5772192 AGTTGATGAGATTTACAAAGTATTGTTGTGTTTCACACTAACTCATTTAAT
1 AGTTGATGAGATTTACAAAGTATCGTTATGTTTCACACTAACTCATTTAAT
*
5772243 AGTTGATGAGATTTACAAAGTATCGTTATGTTTCACACTAACTCGTTTAAT
1 AGTTGATGAGATTTACAAAGTATCGTTATGTTTCACACTAACTCATTTAAT
5772294 GCTATTTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (51 bp):
AGTTGATGAGATTTACAAAGTATCGTTATGTTTCACACTAACTCATTTAAT
Found at i:5775436 original size:16 final size:16
Alignment explanation
Indices: 5775415--5775453 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
5775405 GTTTGGTTCG
5775415 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAA
*
5775431 CTGTAATGGAATAGGA
1 CTGTAATGGAATAGAA
5775447 CTGTAAT
1 CTGTAAT
5775454 CAGTAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAGAA
Found at i:5775692 original size:58 final size:58
Alignment explanation
Indices: 5775623--5775734 Score: 165
Period size: 58 Copynumber: 1.9 Consensus size: 58
5775613 AATTTTAATG
* * *
5775623 ATTATTATTAAATATAATTTAATAAAAATATTA-ATTAATTTAATTATATT-TTAACATA
1 ATTATTATTAAATACAATTTAAT-AAAATAATATA-TAATTTAATAATATTATTAACATA
5775681 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAATATTATTAA
1 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAATATTATTAA
5775735 AATATGAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
57 22 0.45
58 27 0.55
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (58 bp):
ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAATATTATTAACATA
Found at i:5775755 original size:25 final size:24
Alignment explanation
Indices: 5775727--5775777 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5775717 ATTTAATAAT
*
5775727 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
5775752 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
5775776 AT
1 AT
5775778 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:5784135 original size:16 final size:18
Alignment explanation
Indices: 5784110--5784151 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5784100 ATATGGGACA
*
5784110 AAAATGAGAA-TGATGTG
1 AAAATGAGAATTGAAGTG
5784127 AAAAT-AGAATTGAAGTG
1 AAAATGAGAATTGAAGTG
5784144 AAATATGA
1 AAA-ATGA
5784152 TTTTTACCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 14 0.67
18 2 0.10
19 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
AAAATGAGAATTGAAGTG
Found at i:5786354 original size:18 final size:18
Alignment explanation
Indices: 5786331--5786365 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5786321 CTTCTGCAGT
*
5786331 TCGAGGTCGTGGTAGTAC
1 TCGAGGTCGTGCTAGTAC
*
5786349 TCGAGGTGGTGCTAGTA
1 TCGAGGTCGTGCTAGTA
5786366 GCAGAGGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.14, G:0.40, T:0.29
Consensus pattern (18 bp):
TCGAGGTCGTGCTAGTAC
Found at i:5797597 original size:7 final size:6
Alignment explanation
Indices: 5797574--5797607 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
5797564 TTGTTAAATT
*
5797574 ATTTTA ATTTTA ATTTTAA ATTTTA CTTTTA ATT
1 ATTTTA ATTTTA ATTTT-A ATTTTA ATTTTA ATT
5797608 CACTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:5803355 original size:20 final size:20
Alignment explanation
Indices: 5803330--5803370 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5803320 ATACATAGAA
5803330 CGAAATTTTTTATTCCAGCC
1 CGAAATTTTTTATTCCAGCC
5803350 CGAAATTTTTTATTCCAGCC
1 CGAAATTTTTTATTCCAGCC
5803370 C
1 C
5803371 TTCTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (20 bp):
CGAAATTTTTTATTCCAGCC
Found at i:5806092 original size:23 final size:23
Alignment explanation
Indices: 5806060--5806126 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
5806050 GACGTGGCAT
* *
5806060 CCAGTCAGCAGCTTCTAGAAGAC
1 CCAGTTAGCAGCTTCCAGAAGAC
5806083 CCAGTTAGCAGCTTCCAGAAGAC
1 CCAGTTAGCAGCTTCCAGAAGAC
5806106 CCAGTTAGCAGCTTCCAGAAG
1 CCAGTTAGCAGCTTCCAGAAG
5806127 GTCTAGTCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (23 bp):
CCAGTTAGCAGCTTCCAGAAGAC
Found at i:5812573 original size:5 final size:5
Alignment explanation
Indices: 5812556--5812588 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
5812546 AACCCATTGT
5812556 TTTTA TTTT- TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5812589 TCGTTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTA
Found at i:5812588 original size:24 final size:24
Alignment explanation
Indices: 5812556--5812646 Score: 69
Period size: 24 Copynumber: 3.8 Consensus size: 24
5812546 AACCCATTGT
5812556 TTTTATTTTTTTTATTTTATTTTA
1 TTTTATTTTTTTTATTTTATTTTA
* *
5812580 TTTTATTTTTCGTTA-TTTAATTTA
1 TTTTATTTTT-TTTATTTTATTTTA
** * * *
5812604 -TTTCGTTTATTTATATTATTATA
1 TTTTATTTTTTTTATTTTATTTTA
*
5812627 TTTTTACTTATTTTTATTTT
1 -TTTTA-TTTTTTTTATTTT
5812647 TGGTATTTTA
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
22 3 0.06
23 12 0.25
24 18 0.38
25 6 0.12
26 9 0.19
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTATTTTTTTTATTTTATTTTA
Found at i:5812622 original size:18 final size:18
Alignment explanation
Indices: 5812576--5812623 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
5812566 TTTATTTTAT
5812576 TTTATTT-TATT-TTTCG
1 TTTATTTATATTATTTCG
5812592 -TTATTTA-ATTTATTTCG
1 TTTATTTATA-TTATTTCG
5812609 TTTATTTATATTATT
1 TTTATTTATATTATT
5812624 ATATTTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
15 7 0.26
16 2 0.07
17 5 0.19
18 12 0.44
19 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (18 bp):
TTTATTTATATTATTTCG
Found at i:5813604 original size:12 final size:13
Alignment explanation
Indices: 5813589--5813617 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5813579 CAAAAGGTTC
5813589 AAAAAAAA-GAGA
1 AAAAAAAAGGAGA
5813601 AAAAAAAAGGAGA
1 AAAAAAAAGGAGA
5813614 AAAA
1 AAAA
5813618 GAAGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGGAGA
Found at i:5813813 original size:105 final size:105
Alignment explanation
Indices: 5813631--5813842 Score: 388
Period size: 105 Copynumber: 2.0 Consensus size: 105
5813621 GAAAAAATGG
*
5813631 TTGCTTAAACTTCTTTGCTTGTCTCATTATATTGGTTCGATTCGTGGCTTGAACTTCAATATTTT
1 TTGCTTAAACTTCTTTGCTTGTCTCATTATATTGGTTCGATTCGTGGCTTGAACTTCAACATTTT
*
5813696 GCATCTTTTGTCTTGGCATTTTACCATACATTTTTTGCCT
66 GCATCTTTTGTCTTGGCATTTTACCACACATTTTTTGCCT
* *
5813736 TTGCTTAAACTTTTTTGCTTGTCTCATTATATTGGTTCGATTCGTGGTTTGAACTTCAACATTTT
1 TTGCTTAAACTTCTTTGCTTGTCTCATTATATTGGTTCGATTCGTGGCTTGAACTTCAACATTTT
5813801 GCATCTTTTGTCTTGGCATTTTACCACACATTTTTTGCCT
66 GCATCTTTTGTCTTGGCATTTTACCACACATTTTTTGCCT
5813841 TT
1 TT
5813843 TTCCTACCTT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.50
Consensus pattern (105 bp):
TTGCTTAAACTTCTTTGCTTGTCTCATTATATTGGTTCGATTCGTGGCTTGAACTTCAACATTTT
GCATCTTTTGTCTTGGCATTTTACCACACATTTTTTGCCT
Found at i:5816140 original size:26 final size:26
Alignment explanation
Indices: 5816104--5816155 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
5816094 TTGAAATATG
5816104 TCGCAGGTGACATGTTTAAGGAAGTT
1 TCGCAGGTGACATGTTTAAGGAAGTT
5816130 TCGCAGGTGACATGTTTAAGGAAGTT
1 TCGCAGGTGACATGTTTAAGGAAGTT
5816156 CCAGCTTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.31
Consensus pattern (26 bp):
TCGCAGGTGACATGTTTAAGGAAGTT
Found at i:5820788 original size:33 final size:34
Alignment explanation
Indices: 5820741--5820820 Score: 103
Period size: 33 Copynumber: 2.4 Consensus size: 34
5820731 ACTTATATTT
* *
5820741 AATGAATGTA-TTAGAATAGATGTATTTAGT-TC
1 AATGAATGTATTTAGAAAAGATGTATCTAGTATC
5820773 AATGAATGTATTTAGAAAAGATGTATCTAGTAGTC
1 AATGAATGTATTTAGAAAAGATGTATCTAGTA-TC
*
5820808 -ATGCATGTATTTA
1 AATGAATGTATTTA
5820821 ACTAGGATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 10 0.24
33 18 0.43
34 12 0.29
35 2 0.05
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.39
Consensus pattern (34 bp):
AATGAATGTATTTAGAAAAGATGTATCTAGTATC
Found at i:5826508 original size:41 final size:41
Alignment explanation
Indices: 5826447--5826679 Score: 281
Period size: 41 Copynumber: 5.7 Consensus size: 41
5826437 TACATAAATA
* * *
5826447 CCGCAAAAGGT-AGAGCAATAGTGGTGCTTATGGGAAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
*
5826487 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
* * *
5826528 CCG-TAAAGATCAGAGCAATAGCGGCGCTTATGAGAAAACG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
* * ** *
5826568 CTGATAAAGGTCAGAGCAATAGCAACGCTTATGGGCAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
* * *
5826609 CCGCTAAAGGTCAGAGCAATAGCCGCGCTTATGAGAAAGCC
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
* ** *
5826650 CCACTAAAAATCAAAGCAATAGCGGCGCTT
1 CCGCTAAAGGTCAGAGCAATAGCGGCGCTT
5826680 TCTAAAGGTC
Statistics
Matches: 164, Mismatches: 27, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
40 45 0.27
41 119 0.73
ACGTcount: A:0.33, C:0.22, G:0.29, T:0.16
Consensus pattern (41 bp):
CCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCG
Found at i:5826543 original size:81 final size:82
Alignment explanation
Indices: 5826458--5826679 Score: 302
Period size: 81 Copynumber: 2.7 Consensus size: 82
5826448 CGCAAAAGGT
* * *
5826458 AGAGCAATAGTGGTGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGC
1 AGAGCAATAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGC
5826523 AAGCGCCG-TAAAGATC
66 AAGCGCCGCTAAAGATC
* * * **
5826539 AGAGCAATAGCGGCGCTTATGAGAAAACGCTGATAAAGGTCAGAGCAATAGCAACGCTTATGGGC
1 AGAGCAATAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGC
*
5826604 AAGCGCCGCTAAAGGTC
66 AAGCGCCGCTAAAGATC
* * * ** *
5826621 AGAGCAATAGCCGCGCTTATGAGAAAGCCCCACTAAAAATCAAAGCAATAGCGGCGCTT
1 AGAGCAATAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
5826680 TCTAAAGGTC
Statistics
Matches: 120, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
81 65 0.54
82 55 0.46
ACGTcount: A:0.33, C:0.22, G:0.29, T:0.16
Consensus pattern (82 bp):
AGAGCAATAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGC
AAGCGCCGCTAAAGATC
Found at i:5829053 original size:12 final size:12
Alignment explanation
Indices: 5829036--5829060 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5829026 CATTAGATGG
5829036 TTTTCTTAATCT
1 TTTTCTTAATCT
5829048 TTTTCTTAATCT
1 TTTTCTTAATCT
5829060 T
1 T
5829061 CTTTTATAGA
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:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTCTTAATCT
Found at i:5834352 original size:25 final size:26
Alignment explanation
Indices: 5834324--5834447 Score: 74
Period size: 25 Copynumber: 4.7 Consensus size: 26
5834314 ATCAGGATTT
5834324 TTATCAAAATAATATAA-AAAATTAA
1 TTATCAAAATAATATAACAAAATTAA
* * *
5834349 TTATGAAAATAATATAAGATTTAAATTAT
1 TTATCAAAATAATATAACA---AAATTAA
* * ** *
5834378 TTATAAAAATAGAAAATAATCAGGATT-T
1 TTATCAAAAT--AATATAA-CAAAATTAA
*
5834406 TTTTCAAAATAATATAA-AAAATTAA
1 TTATCAAAATAATATAACAAAATTAA
* *
5834431 TTATGAAAATAACATAA
1 TTATCAAAATAATATAA
5834448 GATTTAAATT
Statistics
Matches: 75, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
24 4 0.05
25 30 0.40
26 7 0.09
28 9 0.12
29 18 0.24
31 6 0.08
32 1 0.01
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCAAAATAATATAACAAAATTAA
Found at i:5834375 original size:29 final size:29
Alignment explanation
Indices: 5834342--5834458 Score: 77
Period size: 29 Copynumber: 4.2 Consensus size: 29
5834332 ATAATATAAA
5834342 AAATTAATTATGAAAATAATATAAGATTT
1 AAATTAATTATGAAAATAATATAAGATTT
* * * * *
5834371 AAATTATTTATAAAAATAGA-A-AATAATC
1 AAATTAATTATGAAAATA-ATATAAGATTT
* * * *
5834399 AGGATT-TTTTTCAAAATAATATAA-A---
1 A-AATTAATTATGAAAATAATATAAGATTT
*
5834424 AAATTAATTATGAAAATAACATAAGATTT
1 AAATTAATTATGAAAATAATATAAGATTT
5834453 AAATTA
1 AAATTA
5834459 TTTTTAAAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
24 3 0.05
25 15 0.23
26 1 0.02
27 1 0.02
28 17 0.26
29 28 0.42
30 1 0.02
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.36
Consensus pattern (29 bp):
AAATTAATTATGAAAATAATATAAGATTT
Found at i:5834402 original size:82 final size:82
Alignment explanation
Indices: 5834306--5834472 Score: 307
Period size: 82 Copynumber: 2.0 Consensus size: 82
5834296 AGAATGAGAA
*
5834306 AGAAAATAATCAGGATTTTTATCAAAATAATATAAAAAATTAATTATGAAAATAATATAAGATTT
1 AGAAAATAATCAGGATTTTTATCAAAATAATATAAAAAATTAATTATGAAAATAACATAAGATTT
5834371 AAATTATTTATAAAAAT
66 AAATTATTTATAAAAAT
*
5834388 AGAAAATAATCAGGATTTTTTTCAAAATAATATAAAAAATTAATTATGAAAATAACATAAGATTT
1 AGAAAATAATCAGGATTTTTATCAAAATAATATAAAAAATTAATTATGAAAATAACATAAGATTT
*
5834453 AAATTATTTTTAAAAAT
66 AAATTATTTATAAAAAT
5834470 AGA
1 AGA
5834473 GTATTTTTTA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (82 bp):
AGAAAATAATCAGGATTTTTATCAAAATAATATAAAAAATTAATTATGAAAATAACATAAGATTT
AAATTATTTATAAAAAT
Found at i:5839603 original size:5 final size:5
Alignment explanation
Indices: 5839595--5839631 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
5839585 TAATTAAATT
5839595 ATTTA ATTTA ATTTA ATTTA ATTT- ATATT- ATTTA ATT
1 ATTTA ATTTA ATTTA ATTTA ATTTA AT-TTA ATTTA ATT
5839632 ATATTGTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTA
Found at i:5839615 original size:15 final size:14
Alignment explanation
Indices: 5839592--5839636 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
5839582 AGTTAATTAA
5839592 ATTATTTAATTTA-
1 ATTATTTAATTTAT
5839605 ATTTAATTTAATTTAT
1 A-TT-ATTTAATTTAT
5839621 ATTATTTAA-TTAT
1 ATTATTTAATTTAT
5839634 ATT
1 ATT
5839637 GTACATTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.28
14 8 0.28
15 12 0.41
16 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTTAATTTAT
Found at i:5841842 original size:16 final size:15
Alignment explanation
Indices: 5841803--5841846 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
5841793 GTATCTACTG
*
5841803 CTTCTTTGTTATGCT
1 CTTCTTTGTTCTGCT
*
5841818 GTT-TTTGTTCTGCT
1 CTTCTTTGTTCTGCT
5841832 ACTTCTTTGTTCTGC
1 -CTTCTTTGTTCTGC
5841847 AGGTTACTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 10 0.42
15 4 0.17
16 10 0.42
ACGTcount: A:0.05, C:0.20, G:0.16, T:0.59
Consensus pattern (15 bp):
CTTCTTTGTTCTGCT
Found at i:5842047 original size:15 final size:16
Alignment explanation
Indices: 5842027--5842056 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5842017 AAAATTCAAT
5842027 TAATTCGA-TTAATTG
1 TAATTCGATTTAATTG
5842042 TAATTCGATTTAATT
1 TAATTCGATTTAATT
5842057 AACCGATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (16 bp):
TAATTCGATTTAATTG
Found at i:5842683 original size:3 final size:3
Alignment explanation
Indices: 5842677--5842703 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5842667 GCCAACAACA
5842677 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
5842704 GAAGATGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.