Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 51 of 66
Found at i:18422283 original size:79 final size:79
Alignment explanation
Indices: 18422174--18422331 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
18422164 TACTTTTATG
18422174 TCTGCTGCTCAAAAGCTGAAGACAGAATTAAGACTCAAAGCTAATGAAACAGTAGGTGTGTTTTC
1 TCTGCTGCTCAAAAGCTGAAGACAGAATTAAGACTCAAAGCTAATGAAACAGTAGGTGTGTTTTC
18422239 TTTGCTCAATGTAA
66 TTTGCTCAATGTAA
*
18422253 TCTGCTGCTCAAAAGCTGAAGACAGTATTAAGACTCAAAGCTAATGAAACAGTAGGTGTGTTTTC
1 TCTGCTGCTCAAAAGCTGAAGACAGAATTAAGACTCAAAGCTAATGAAACAGTAGGTGTGTTTTC
18422318 TTTGCTCAATGTAA
66 TTTGCTCAATGTAA
18422332 CGGTACTTGT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (79 bp):
TCTGCTGCTCAAAAGCTGAAGACAGAATTAAGACTCAAAGCTAATGAAACAGTAGGTGTGTTTTC
TTTGCTCAATGTAA
Found at i:18427516 original size:2 final size:2
Alignment explanation
Indices: 18427509--18427536 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18427499 CCATTACATC
18427509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18427537 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18427571 original size:2 final size:2
Alignment explanation
Indices: 18427566--18427593 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18427556 AGAGAAGAAN
18427566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18427594 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18430179 original size:147 final size:146
Alignment explanation
Indices: 18429889--18430172 Score: 324
Period size: 147 Copynumber: 2.0 Consensus size: 146
18429879 AGGACAAATT
** *
18429889 GATTAAAGATGTAGAGAAGGTTGAATATTTGAAGAAAAATGGAGAAAGTGAAAATAAAATTGAAG
1 GATTAAAGATGTAGAGAAGGTTGAATATTAAAAGAAAAATGGAGAAAGTGAAAACAAAATTGAAG
* * * * * **
18429954 ATGAATTGGCGGAAACAAAAGAAGTTTCTGACCAGGTTGTTGAGAATATTGAGTTGCAGGAGACA
66 AGGAATTGGCGGAAACAAAAGAAGTTTCTGACAAGATGGTTGAGAATATTAAACTGCAGGAGACA
18430019 GAAGAAACTGGGGAACA
131 -AAGAAACTGGGGAACA
* * **
18430036 GATTGAAGATGTAGAGAAGGTTGAA-AGTGTAAAAG-AAAATGGAGAAAGTGAAGACGTAATTGA
1 GATTAAAGATGTAGAGAAGGTTGAATA-T-TAAAAGAAAAATGGAGAAAGTGAAAACAAAATTGA
* ** * * * *
18430099 AGAGGAATTGGTGGAAACAGGAGAAGTTTCTGATAAGATGGTTGGGGATATTAAACTGCTGG-GA
64 AGAGGAATTGGCGGAAACAAAAGAAGTTTCTGACAAGATGGTTGAGAATATTAAACTGCAGGAGA
18430163 C-AAGAAACTG
129 CAAAGAAACTG
18430173 CTGGGGAGAT
Statistics
Matches: 114, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
144 9 0.08
146 4 0.04
147 97 0.85
148 4 0.04
ACGTcount: A:0.42, C:0.06, G:0.31, T:0.22
Consensus pattern (146 bp):
GATTAAAGATGTAGAGAAGGTTGAATATTAAAAGAAAAATGGAGAAAGTGAAAACAAAATTGAAG
AGGAATTGGCGGAAACAAAAGAAGTTTCTGACAAGATGGTTGAGAATATTAAACTGCAGGAGACA
AAGAAACTGGGGAACA
Found at i:18431476 original size:145 final size:146
Alignment explanation
Indices: 18431203--18431495 Score: 561
Period size: 145 Copynumber: 2.0 Consensus size: 146
18431193 CTCATTTAGC
18431203 CATTTAGGACCGCAGTTGCTGATTGCTTATACTATCTTGTATTGTCCTTTAGAAGCAATTATATG
1 CATTTAGGACCGCAGTTGCTGATTGCTTATACTATCTTGTATTGTCCTTTAGAAGCAATTATATG
* *
18431268 TGCTTAACATGCATTTAGGGACTATTTTATGAAAACACCTTCGTTTAAGCTTTTTGGAACTTTGT
66 TGCATAACATGCATTGAGGGACTATTTTATGAAAACACCTTCGTTTAAGCTTTTTGGAACTTTGT
18431333 TATGTTTGTGTTGCAG
131 TATGTTTGTGTTGCAG
18431349 CATTTAGGA-CGCAGTTGCTGATTGCTTATACTATCTTGTATTGTCCTTTAGAAGCAATTATATG
1 CATTTAGGACCGCAGTTGCTGATTGCTTATACTATCTTGTATTGTCCTTTAGAAGCAATTATATG
18431413 TGCATAACATGCATTGAGGGACTATTTTATGAAAACACCTTCGTTTAAGCTTTTTGGAACTTTGT
66 TGCATAACATGCATTGAGGGACTATTTTATGAAAACACCTTCGTTTAAGCTTTTTGGAACTTTGT
18431478 TATGTTTGTGTTGCAG
131 TATGTTTGTGTTGCAG
18431494 CA
1 CA
18431496 GGCAGGACCG
Statistics
Matches: 145, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
145 136 0.94
146 9 0.06
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (146 bp):
CATTTAGGACCGCAGTTGCTGATTGCTTATACTATCTTGTATTGTCCTTTAGAAGCAATTATATG
TGCATAACATGCATTGAGGGACTATTTTATGAAAACACCTTCGTTTAAGCTTTTTGGAACTTTGT
TATGTTTGTGTTGCAG
Found at i:18434301 original size:3 final size:3
Alignment explanation
Indices: 18434293--18434320 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
18434283 GTAGTAATAA
18434293 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
18434321 TTCCACGTTC
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:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:18435808 original size:22 final size:23
Alignment explanation
Indices: 18435780--18435836 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
18435770 GAATGAAATT
*
18435780 ATAAAATTTTTAAA-AAATAAAA
1 ATAAAATTTTTAAATAAAAAAAA
*
18435802 ATAAAATTTTAAAATAAAAAAAA
1 ATAAAATTTTTAAATAAAAAAAA
18435825 ATATAAATTTTT
1 ATA-AAATTTTT
18435837 GTAATTTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 13 0.43
23 10 0.33
24 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
ATAAAATTTTTAAATAAAAAAAA
Found at i:18437173 original size:21 final size:21
Alignment explanation
Indices: 18437149--18437200 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
18437139 ATATGACACG
18437149 ACACGATTAATAACACATTTA
1 ACACGATTAATAACACATTTA
18437170 ACACGATTAATAACACATTTA
1 ACACGATTAATAACACATTTA
*
18437191 ACAAGATTAA
1 ACACGATTAA
18437201 ATAAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.27
Consensus pattern (21 bp):
ACACGATTAATAACACATTTA
Found at i:18449641 original size:2 final size:2
Alignment explanation
Indices: 18449634--18449673 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
18449624 TCACTATGAC
18449634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18449674 GTTTGTTCGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18450089 original size:2 final size:2
Alignment explanation
Indices: 18450082--18450107 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18450072 ATCGAAAGAG
18450082 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
18450108 TTTTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18459354 original size:27 final size:29
Alignment explanation
Indices: 18459298--18459358 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
18459288 TAAAAATCAA
**
18459298 GTTACATGTTTTATTTAAAAAATATTATT
1 GTTACATGTCATATTTAAAAAATATTATT
18459327 GTTACATGTCATATTT-AAAAATA-TATT
1 GTTACATGTCATATTTAAAAAATATTATT
18459354 GTTAC
1 GTTAC
18459359 GCACTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 9 0.30
28 7 0.23
29 14 0.47
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.48
Consensus pattern (29 bp):
GTTACATGTCATATTTAAAAAATATTATT
Found at i:18459651 original size:27 final size:28
Alignment explanation
Indices: 18459606--18459675 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
18459596 TTACCCGTTA
* ** *
18459606 TATTTAAAAAATATTGTTATGACATGCC
1 TATTTAAAAAAAAAAGTTATGACACGCC
* *
18459634 -ATTTAAAAAAAAAAGTTATTATACGCC
1 TATTTAAAAAAAAAAGTTATGACACGCC
*
18459661 TTTTTAAAAAAAAAA
1 TATTTAAAAAAAAAA
18459676 ATTGTTATAC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 21 0.62
28 13 0.38
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (28 bp):
TATTTAAAAAAAAAAGTTATGACACGCC
Found at i:18460834 original size:38 final size:37
Alignment explanation
Indices: 18460791--18460871 Score: 99
Period size: 38 Copynumber: 2.2 Consensus size: 37
18460781 TATGAAATCT
* * *
18460791 TGAAATAGTATAGTTGAATGTAAGTTTTGCTTATAATA
1 TGAAATAGTATAGTTAAATGCAA-TTTTACTTATAATA
* * *
18460829 TGAAATATTGTAGTTAAATGCAATTTTACTTGTAATA
1 TGAAATAGTATAGTTAAATGCAATTTTACTTATAATA
18460866 TGAAAT
1 TGAAAT
18460872 CCTGTTATCT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 18 0.49
38 19 0.51
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (37 bp):
TGAAATAGTATAGTTAAATGCAATTTTACTTATAATA
Found at i:18461049 original size:22 final size:22
Alignment explanation
Indices: 18461008--18461059 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
18460998 TACAAACCAA
* *
18461008 TTAC-AAAAATATCCACTTTAG
1 TTACAAAAAAGATCCACTTTAC
18461029 TTACAAAAAAGAT-CACGTTTAC
1 TTACAAAAAAGATCCAC-TTTAC
18461051 TTACAAAAA
1 TTACAAAAA
18461060 TATAAACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.29
Consensus pattern (22 bp):
TTACAAAAAAGATCCACTTTAC
Found at i:18461080 original size:22 final size:20
Alignment explanation
Indices: 18461008--18461080 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
18460998 TACAAACCAA
18461008 TTACAAAAATATCCACTTTAG
1 TTACAAAAATAT-CACTTTAG
* *
18461029 TTACAAAAAAGATCACGTTTAC
1 TTAC-AAAAATATCAC-TTTAG
* *
18461051 TTACAAAAATATAAACTTTGG
1 TTACAAAAATAT-CACTTTAG
18461072 TTACAAAAA
1 TTACAAAAA
18461081 GAATTATAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 26 0.60
22 17 0.40
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (20 bp):
TTACAAAAATATCACTTTAG
Found at i:18465708 original size:20 final size:21
Alignment explanation
Indices: 18465669--18465708 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
18465659 TTAGAAACAT
* *
18465669 TTATTTATTAAATTTTCTTTC
1 TTATTTATTAAAATTCCTTTC
18465690 TTATTT-TTAAAATTCCTTT
1 TTATTTATTAAAATTCCTTT
18465709 TTTCTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTTATTAAAATTCCTTTC
Found at i:18465906 original size:6 final size:6
Alignment explanation
Indices: 18465895--18465924 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
18465885 GTCGACTGAG
18465895 TGAGCT TGAGCT TGAGCT TGAGCT TGAGCT
1 TGAGCT TGAGCT TGAGCT TGAGCT TGAGCT
18465925 GCACTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
TGAGCT
Found at i:18479738 original size:26 final size:26
Alignment explanation
Indices: 18479707--18479795 Score: 83
Period size: 26 Copynumber: 3.4 Consensus size: 26
18479697 TGTGATTAAT
*
18479707 ATTAATTGATTAATTATTTTAAATTA
1 ATTAATTAATTAATTATTTTAAATTA
* * *
18479733 ATTAATTAACTAATTA-CTT-AGTTA
1 ATTAATTAATTAATTATTTTAAATTA
* * *
18479757 ATTTAATTTATAAAATATTTTAAATTA
1 A-TTAATTAATTAATTATTTTAAATTA
18479784 ATTAATTTAATT
1 ATTAA-TTAATT
18479796 CTTTAAAACT
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
24 5 0.11
25 13 0.28
26 20 0.43
27 9 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
ATTAATTAATTAATTATTTTAAATTA
Found at i:18481942 original size:32 final size:33
Alignment explanation
Indices: 18481894--18481963 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 33
18481884 TAAATTTATC
* *
18481894 TTTTATTAGTTTAAAAATTACTATTA-CATATA
1 TTTTATTAATTAAAAAATTACTATTATCATATA
*
18481926 TTTTATTAATTAAAAAATTACTATTATTATATA
1 TTTTATTAATTAAAAAATTACTATTATCATATA
18481959 TTTTA
1 TTTTA
18481964 AAAAAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 24 0.71
33 10 0.29
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (33 bp):
TTTTATTAATTAAAAAATTACTATTATCATATA
Found at i:18481976 original size:35 final size:32
Alignment explanation
Indices: 18481906--18481977 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
18481896 TTATTAGTTT
** *
18481906 AAAAATTACTATTACATATATTTTATTAATTA
1 AAAAATTACTATTACATATATTTTAAAAATAA
*
18481938 AAAAATTACTATTATTATATATTTTAAAAAAATAA
1 AAAAATTACTATTA-CATATATTTT--AAAAATAA
18481973 AAAAA
1 AAAAA
18481978 ATATTGAGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 14 0.42
33 9 0.27
35 10 0.30
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (32 bp):
AAAAATTACTATTACATATATTTTAAAAATAA
Found at i:18497000 original size:33 final size:33
Alignment explanation
Indices: 18496920--18496983 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
18496910 TTAAAATATT
** *
18496920 AAAATAATAAAAAATATTAATATTTAACTTTAA
1 AAAATAATTTAAAATATTAATATTTAACATTAA
*
18496953 AAAATAATTTAAAATATTAATGTTTAA-ATTA
1 AAAATAATTTAAAATATTAATATTTAACATTA
18496984 TACAATACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (33 bp):
AAAATAATTTAAAATATTAATATTTAACATTAA
Found at i:18498885 original size:39 final size:36
Alignment explanation
Indices: 18498840--18498935 Score: 95
Period size: 39 Copynumber: 2.5 Consensus size: 36
18498830 ATTGAATAAT
*
18498840 TTATAAATTAATATTATAAAATTAATTA-AACTATTTA
1 TTATAAATTAATATTATAAAA-TAATTATAAATA-TTA
* *
18498877 TACTATAAATTTTATATTTTAAAATAATTATAAATATTA
1 T--TATAAA-TTAATATTATAAAATAATTATAAATATTA
*
18498916 TTATATAATTATTATTATAA
1 TTATA-AATTAATATTATAA
18498936 TAATCTATCT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
37 14 0.29
38 2 0.04
39 16 0.33
40 16 0.33
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (36 bp):
TTATAAATTAATATTATAAAATAATTATAAATATTA
Found at i:18498928 original size:14 final size:14
Alignment explanation
Indices: 18498905--18498939 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
18498895 TTAAAATAAT
*
18498905 TATAAATATTATTA
1 TATAATTATTATTA
18498919 TATAATTATTATTA
1 TATAATTATTATTA
18498933 TAATAAT
1 T-ATAAT
18498940 CTATCTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATAATTATTATTA
Found at i:18499434 original size:23 final size:23
Alignment explanation
Indices: 18499408--18499461 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 23
18499398 GTTGTATGTA
18499408 ATTGATTTTGGCT-TTTGTTCCTC
1 ATTGATTTT-GCTATTTGTTCCTC
**
18499431 ATTGTGATTTTTTTATTTGTTCCTC
1 A-T-TGATTTTGCTATTTGTTCCTC
18499456 ATTGAT
1 ATTGAT
18499462 GATTGTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 5 0.19
24 3 0.12
25 18 0.69
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.59
Consensus pattern (23 bp):
ATTGATTTTGCTATTTGTTCCTC
Found at i:18499449 original size:25 final size:28
Alignment explanation
Indices: 18499421--18499479 Score: 88
Period size: 25 Copynumber: 2.2 Consensus size: 28
18499411 GATTTTGGCT
*
18499421 TTTGTTCCTCATTG-TGATT-T-TTTTA
1 TTTGTTCCTCATTGATGATTGTATGTTA
18499446 TTTGTTCCTCATTGATGATTGTATGTTA
1 TTTGTTCCTCATTGATGATTGTATGTTA
18499474 TTTGTT
1 TTTGTT
18499480 TTATTTTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 14 0.47
26 5 0.17
27 1 0.03
28 10 0.33
ACGTcount: A:0.14, C:0.10, G:0.15, T:0.61
Consensus pattern (28 bp):
TTTGTTCCTCATTGATGATTGTATGTTA
Found at i:18507784 original size:29 final size:30
Alignment explanation
Indices: 18507729--18507785 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
18507719 ATATTTAATC
* *
18507729 AAGTTTTTATATATTTATTTTGAATTAAAT
1 AAGTTTTTATATATTAATATTGAATTAAAT
18507759 AAGTTTTTATA-ATTAATAATT-AATTAA
1 AAGTTTTTATATATTAAT-ATTGAATTAA
18507786 TTACTATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (30 bp):
AAGTTTTTATATATTAATATTGAATTAAAT
Found at i:18508669 original size:2 final size:2
Alignment explanation
Indices: 18508662--18508689 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18508652 ATGAATAATC
18508662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18508690 TTTTGTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18519847 original size:25 final size:25
Alignment explanation
Indices: 18519813--18519865 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
18519803 CCAAAGCAGT
18519813 TGTTAACTTGTAACCTCAGGCTGTC
1 TGTTAACTTGTAACCTCAGGCTGTC
18519838 TGTTAACTTGTAACCTCAGGCTGTC
1 TGTTAACTTGTAACCTCAGGCTGTC
18519863 TGT
1 TGT
18519866 GCCATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (25 bp):
TGTTAACTTGTAACCTCAGGCTGTC
Found at i:18528197 original size:39 final size:39
Alignment explanation
Indices: 18528144--18528223 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
18528134 TTAAAAGGTA
* *
18528144 AACAATGTAAATAATTTCTAAACTTATCAATTTTATATT
1 AACAATATAAATAATTTCTAAACTAATCAATTTTATATT
* * * *
18528183 AACAATATAGATAATTTTTAAACTAATCTATTTTATTTT
1 AACAATATAAATAATTTCTAAACTAATCAATTTTATATT
18528222 AA
1 AA
18528224 AAATTATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.45
Consensus pattern (39 bp):
AACAATATAAATAATTTCTAAACTAATCAATTTTATATT
Found at i:18531670 original size:15 final size:15
Alignment explanation
Indices: 18531650--18531719 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
18531640 TAATCCATTA
18531650 TATTTAAATTTAATT
1 TATTTAAATTTAATT
18531665 TATTTAAATTTAA--
1 TATTTAAATTTAATT
*
18531678 -A--TAAAGATTAATT
1 TATTTAAA-TTTAATT
* *
18531691 ACATTTAAATTTAATC
1 -TATTTAAATTTAATT
18531707 TATTTAAATTTAA
1 TATTTAAATTTAA
18531720 AAGAAATATC
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
10 4 0.09
11 4 0.09
12 1 0.02
15 26 0.59
16 5 0.11
17 4 0.09
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (15 bp):
TATTTAAATTTAATT
Found at i:18531675 original size:21 final size:21
Alignment explanation
Indices: 18531651--18531720 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
18531641 AATCCATTAT
18531651 ATTTAAATTTAATTTATTTAA
1 ATTTAAATTTAATTTATTTAA
* * * *
18531672 ATTTAAA-TAAAGATTAATTAC
1 ATTTAAATTTAA-TTTATTTAA
*
18531693 ATTTAAATTTAATCTATTTAA
1 ATTTAAATTTAATTTATTTAA
18531714 ATTTAAA
1 ATTTAAA
18531721 AGAAATATCC
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
20 3 0.08
21 32 0.84
22 3 0.08
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (21 bp):
ATTTAAATTTAATTTATTTAA
Found at i:18547081 original size:2 final size:2
Alignment explanation
Indices: 18547069--18547102 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
18547059 GCATATAATT
*
18547069 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18547103 CAAAATGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:18547525 original size:11 final size:11
Alignment explanation
Indices: 18547502--18547543 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 11
18547492 CCAGCAGCAC
18547502 CTTTTATTT-TT
1 CTTTT-TTTCTT
18547513 CTTTTTTTCTT
1 CTTTTTTTCTT
18547524 C-TTTTTTCTT
1 CTTTTTTTCTT
18547534 CTTTCTTTTC
1 CTTT-TTTTC
18547544 CCTGTCGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.46
11 10 0.36
12 5 0.18
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (11 bp):
CTTTTTTTCTT
Found at i:18549353 original size:28 final size:28
Alignment explanation
Indices: 18549321--18549410 Score: 117
Period size: 28 Copynumber: 3.2 Consensus size: 28
18549311 CTAAAGTGGC
*
18549321 TGAATACTTTTAACTCACCAGAAATGGA
1 TGAATACTTTTAACTCACTAGAAATGGA
* *
18549349 TGAATATTTTTAACCCACTAGAAATGGA
1 TGAATACTTTTAACTCACTAGAAATGGA
* * * *
18549377 TGGATACTTTTAACTAATTAGAAGTGGA
1 TGAATACTTTTAACTCACTAGAAATGGA
18549405 TGAATA
1 TGAATA
18549411 GTGATGAGAT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (28 bp):
TGAATACTTTTAACTCACTAGAAATGGA
Found at i:18570675 original size:20 final size:21
Alignment explanation
Indices: 18570638--18570681 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
18570628 TCCGAATGTT
18570638 AGAAATATTTGAAAAGAAAGA
1 AGAAATATTTGAAAAGAAAGA
**
18570659 AGAAAT-TTTGAGTAGAAAGA
1 AGAAATATTTGAAAAGAAAGA
18570679 AGA
1 AGA
18570682 GGATGAGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (21 bp):
AGAAATATTTGAAAAGAAAGA
Found at i:18580238 original size:20 final size:20
Alignment explanation
Indices: 18580173--18580230 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
18580163 ACATATATGG
*
18580173 ATAGATAACCAGATCTATCC
1 ATAGATAGCCAGATCTATCC
18580193 ATAGATAGCCAGATCTATCC
1 ATAGATAGCCAGATCTATCC
18580213 ATAGATAGCCAGATCTAT
1 ATAGATAGCCAGATCTAT
18580231 TGATAGATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (20 bp):
ATAGATAGCCAGATCTATCC
Found at i:18587950 original size:23 final size:23
Alignment explanation
Indices: 18587924--18587977 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
18587914 CTGTGTGAGG
* *
18587924 ATGTGACACACCGTGGTGTGAAT
1 ATGTGACACACCATGGTGAGAAT
** *
18587947 ATGTGACATGCCATGGTGAGCAT
1 ATGTGACACACCATGGTGAGAAT
18587970 ATGTGACA
1 ATGTGACA
18587978 TGGTAGGGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (23 bp):
ATGTGACACACCATGGTGAGAAT
Found at i:18588054 original size:23 final size:23
Alignment explanation
Indices: 18588028--18588093 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
18588018 TGTGACATAG
18588028 CATGATGAGAATCTGTGACACGA
1 CATGATGAGAATCTGTGACACGA
* * *
18588051 CATGTTGA-AATCGTGTAAGACGA
1 CATGATGAGAATC-TGTGACACGA
* **
18588074 CAAGGCGAGAATCTGTGACA
1 CATGATGAGAATCTGTGACA
18588094 TGATAGGGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 4 0.12
23 25 0.76
24 4 0.12
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (23 bp):
CATGATGAGAATCTGTGACACGA
Found at i:18593092 original size:31 final size:31
Alignment explanation
Indices: 18593043--18593153 Score: 134
Period size: 31 Copynumber: 3.6 Consensus size: 31
18593033 TCATGACACT
* *
18593043 TAGCGTGTAACAACATTTTACTTGGTATGCA
1 TAGCATGTAACAAGATTTTACTTGGTATGCA
*
18593074 TAGCATGTAATAAGATTTTACTTGGTATGCA
1 TAGCATGTAACAAGATTTTACTTGGTATGCA
* * *
18593105 TAACATGTAACAACG-TTTAACTTGGTATACA
1 TAGCATGTAACAA-GATTTTACTTGGTATGCA
* *
18593136 TAGCTTGTAACAACATTT
1 TAGCATGTAACAAGATTT
18593154 ATTTCTTTCT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
31 67 0.99
32 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (31 bp):
TAGCATGTAACAAGATTTTACTTGGTATGCA
Found at i:18595550 original size:81 final size:81
Alignment explanation
Indices: 18595465--18595654 Score: 204
Period size: 81 Copynumber: 2.3 Consensus size: 81
18595455 CCTTTCAATT
* ** * * *
18595465 AGTTGATGCTGAAGGAGACCATGTTCCTCAAGCTGATGTGATTGTCGATGCA-TCTGCGGGAGAG
1 AGTTGAAGCTGAAGGAGACCATGTTCCTCAAGCCAATGTGATAGTCGAGGCAGT-TGCGGCAGAG
* *
18595529 GAGGGGGACCTT-CACTC
65 GAGGAGAACCTTGCA-TC
* * * * *
18595546 AGTTGAGGCTGAAGGAAACCATGTTCCTCAGGCCAATGTGGTAGTCGAGGCAGTTGCGGCAGGGG
1 AGTTGAAGCTGAAGGAGACCATGTTCCTCAAGCCAATGTGATAGTCGAGGCAGTTGCGGCAGAGG
*
18595611 ATGAGAACCTTGCATC
66 AGGAGAACCTTGCATC
* *
18595627 AGCTCAAGCTGAAGGAGACCATGTTCCT
1 AGTTGAAGCTGAAGGAGACCATGTTCCT
18595655 TAGGCAGATG
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
81 87 0.97
82 3 0.03
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.23
Consensus pattern (81 bp):
AGTTGAAGCTGAAGGAGACCATGTTCCTCAAGCCAATGTGATAGTCGAGGCAGTTGCGGCAGAGG
AGGAGAACCTTGCATC
Found at i:18595678 original size:81 final size:81
Alignment explanation
Indices: 18595553--18595738 Score: 196
Period size: 81 Copynumber: 2.3 Consensus size: 81
18595543 CTCAGTTGAG
* * * * * *
18595553 GCTGAAGGAAACCATGTTCCTCAGGCCAATGTGGTAGTCGAGGCAGTTG-CGGCAGGGGATGAGA
1 GCTGAAGGAGACCATGTTCCTTAGGCCAATGCGGTAGTCAAGGCAGCTGTAGG-AGGGGATGAGA
18595617 ACCTTGCATCAGCTCAA
65 ACCTTGCATCAGCTCAA
* * * *
18595634 GCTGAAGGAGACCATGTTCCTTAGG-CAGATGCGTTAGTTAAGGCAGCTGTAGGAGGGGATGGGC
1 GCTGAAGGAGACCATGTTCCTTAGGCCA-ATGCGGTAGTCAAGGCAGCTGTAGGAGGGGATGAGA
* * * *
18595698 ACTTTGCATCAGTTTAG
65 ACCTTGCATCAGCTCAA
* *
18595715 GCTAAAGGGGACCATGTTCCTTAG
1 GCTGAAGGAGACCATGTTCCTTAG
18595739 AGCACTCTTG
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
80 2 0.02
81 83 0.95
82 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (81 bp):
GCTGAAGGAGACCATGTTCCTTAGGCCAATGCGGTAGTCAAGGCAGCTGTAGGAGGGGATGAGAA
CCTTGCATCAGCTCAA
Found at i:18597160 original size:76 final size:76
Alignment explanation
Indices: 18597057--18597347 Score: 256
Period size: 76 Copynumber: 3.9 Consensus size: 76
18597047 ACAAGCGTGT
* * *
18597057 CGTGTCA--CCATAATACTGCAACGACTCAGCTTGCCACCACAAGATGTCAACAACATCTAACAA
1 CGTGTCACCCCATAATACTGCAACGACTCAGCGTGTCACCACAAGATGTCAACGACATCTAACAA
* **
18597120 TTGGAGCATGG
66 TTGGAACATAA
* * * * * * * *
18597131 CTTGTCATCCCATAATACTACAATGACTCAACGTGTCATCACAAGATGTTAATGACATCTAACAA
1 CGTGTCACCCCATAATACTGCAACGACTCAGCGTGTCACCACAAGATGTCAACGACATCTAACAA
*
18597196 TTGGAACGTAA
66 TTGGAACATAA
* * *
18597207 CGTGTCACCCCATAATATTGCAACCATTCAGCGTGTCACCACAAGATGTCAACGACATCTAACAA
1 CGTGTCACCCCATAATACTGCAACGACTCAGCGTGTCACCACAAGATGTCAACGACATCTAACAA
* **
18597272 ---G--CGTGG
66 TTGGAACATAA
* * * * * * * *
18597278 CATGTCACCCTAAAATACTGCAACGACAT-GGTGTGTCACCATAAGATGTAAACAACATCTAACA
1 CGTGTCACCCCATAATACTGCAACGAC-TCAGCGTGTCACCACAAGATGTCAACGACATCTAACA
18597342 ATTGGA
65 ATTGGA
18597348 GCGTGTAACA
Statistics
Matches: 172, Mismatches: 38, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
71 55 0.32
72 1 0.01
73 1 0.01
74 7 0.04
76 108 0.63
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (76 bp):
CGTGTCACCCCATAATACTGCAACGACTCAGCGTGTCACCACAAGATGTCAACGACATCTAACAA
TTGGAACATAA
Found at i:18600916 original size:24 final size:24
Alignment explanation
Indices: 18600889--18600969 Score: 110
Period size: 23 Copynumber: 3.4 Consensus size: 24
18600879 TCAATCATGT
* *
18600889 TGTTACACGTCATGCTCAAAAAAA
1 TGTTACATGTCATGTTCAAAAAAA
18600913 TGTTACATGTCATGTTC-AAAAAA
1 TGTTACATGTCATGTTCAAAAAAA
* *
18600936 TGTTACATGCCATGTTCAATAAAAG
1 TGTTACATGTCATGTTCAA-AAAAA
18600961 TGTTACATG
1 TGTTACATG
18600970 CCATTTGCTA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
23 22 0.43
24 16 0.31
25 13 0.25
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (24 bp):
TGTTACATGTCATGTTCAAAAAAA
Found at i:18616695 original size:35 final size:34
Alignment explanation
Indices: 18616624--18616702 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 34
18616614 AAAATAAAAT
*
18616624 AAATAAATAATAATCAATTAATCTTATCAAGTTTTA
1 AAATAAA-AATAATCAATTAATCTTAACAAG-TTTA
*
18616660 AAATAAAAATAATCAATTCTATCTTAACACA-TTTA
1 AAATAAAAATAATCAATT-AATCTTAACA-AGTTTA
*
18616695 AAAGAAAA
1 AAATAAAA
18616703 GGTAAAAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
35 22 0.58
36 15 0.39
37 1 0.03
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (34 bp):
AAATAAAAATAATCAATTAATCTTAACAAGTTTA
Found at i:18617766 original size:3 final size:3
Alignment explanation
Indices: 18617758--18617797 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
18617748 TAACTCACAA
18617758 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
18617798 TTGCCTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:18618638 original size:37 final size:37
Alignment explanation
Indices: 18618557--18618638 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
18618547 CCATGCCATT
* * * *
18618557 GGAGTTAATTGTGGATTTATTTCTTATCTATGCCAAT
1 GGAGTTAATTATGGATTTATTTCTTACCTATACCAAA
18618594 GGAGTTAATTATGGATTTATTT-TTGACCTATACCAAA
1 GGAGTTAATTATGGATTTATTTCTT-ACCTATACCAAA
*
18618631 GGGGTTAA
1 GGAGTTAA
18618639 GTGTGATCGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 2 0.05
37 37 0.95
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (37 bp):
GGAGTTAATTATGGATTTATTTCTTACCTATACCAAA
Found at i:18634094 original size:36 final size:36
Alignment explanation
Indices: 18634046--18634123 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
18634036 GTGATAGAGG
* *
18634046 GAGTTGGTCACAAATCGTTTTTAAAGGAAAAAATCT
1 GAGTTGGCCACAAATCGTTTTTAAAAGAAAAAATCT
* *
18634082 GAGTTGGCCACAAATCGTTTTTAAAAGAGATAATCT
1 GAGTTGGCCACAAATCGTTTTTAAAAGAAAAAATCT
18634118 GA-TTGG
1 GAGTTGG
18634124 TTCATCAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
35 4 0.11
36 34 0.89
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (36 bp):
GAGTTGGCCACAAATCGTTTTTAAAAGAAAAAATCT
Found at i:18641322 original size:30 final size:30
Alignment explanation
Indices: 18641277--18641341 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
18641267 CTTTTATACC
* *
18641277 CAGAAGAAAGAGGGCAAAACGGTGTCGTTT
1 CAGAGGAAAGAGGGCAAAACGGCGTCGTTT
*
18641307 CAGAGGAAGGAGGGCAAAACGGCGTCGTTT
1 CAGAGGAAAGAGGGCAAAACGGCGTCGTTT
18641337 CAGAG
1 CAGAG
18641342 AGGCAAGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.15, G:0.37, T:0.14
Consensus pattern (30 bp):
CAGAGGAAAGAGGGCAAAACGGCGTCGTTT
Found at i:18652131 original size:22 final size:21
Alignment explanation
Indices: 18652079--18652134 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
18652069 TCCCACAGAT
* *
18652079 CAACAACGAATCTCTCACAAA
1 CAACAACAAATCACTCACAAA
18652100 CAACAACAAATCACTCACAAA
1 CAACAACAAATCACTCACAAA
*
18652121 CTAGCAACAAATCA
1 C-AACAACAAATCA
18652135 GCAGTAGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.52, C:0.32, G:0.04, T:0.12
Consensus pattern (21 bp):
CAACAACAAATCACTCACAAA
Found at i:18652501 original size:29 final size:31
Alignment explanation
Indices: 18652454--18652512 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
18652444 GAATTCTGAT
*
18652454 TTTTTTTTCTTCTGCCTTGTTCACT-TCTAA
1 TTTTTTTTCTTCTACCTTGTTCACTCTCTAA
*
18652484 TTTTTTTT-TTCTATCTTGTTCACTCTCTA
1 TTTTTTTTCTTCTACCTTGTTCACTCTCTA
18652513 CTGTACATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.10, C:0.22, G:0.05, T:0.63
Consensus pattern (31 bp):
TTTTTTTTCTTCTACCTTGTTCACTCTCTAA
Found at i:18667879 original size:13 final size:13
Alignment explanation
Indices: 18667861--18667886 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18667851 TTTGACTTCT
18667861 TTCAACCAGTTTC
1 TTCAACCAGTTTC
18667874 TTCAACCAGTTTC
1 TTCAACCAGTTTC
18667887 AGATCACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (13 bp):
TTCAACCAGTTTC
Found at i:18677610 original size:20 final size:20
Alignment explanation
Indices: 18677593--18677630 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
18677583 TCTCAAATCT
18677593 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
18677613 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
18677631 GGGGTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:18687289 original size:13 final size:15
Alignment explanation
Indices: 18687271--18687302 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
18687261 ACAAACTTTG
18687271 TAATA-TAT-ACATA
1 TAATATTATAACATA
18687284 TAATATTATAACATA
1 TAATATTATAACATA
18687299 TAAT
1 TAAT
18687303 TTGTGTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 3 0.18
15 9 0.53
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATATTATAACATA
Found at i:18704328 original size:43 final size:43
Alignment explanation
Indices: 18704279--18704485 Score: 132
Period size: 43 Copynumber: 4.8 Consensus size: 43
18704269 CTTTATACTC
* *
18704279 AAGGTAAGATTGCCATAATTAAT-TGCCACACATATTATCACAA
1 AAGGTAAGATTTCCATAATTAATAT-CCACACACATTATCACAA
* * **
18704322 AAGGTAAGATTTCTATAATTAATATCCATACACATTATCATTA
1 AAGGTAAGATTTCCATAATTAATATCCACACACATTATCACAA
* * * * ***
18704365 AGGGTAAGATTTCCATAATCAATACCCATATGTATTATCATC-A
1 AAGGTAAGATTTCCATAATTAATATCCACACACATTATCA-CAA
* * * * ** * *
18704408 ATGATAAGATTTCCATAATCAATACCCATGCATACTATCATC-A
1 AAGGTAAGATTTCCATAATTAATATCCACACACATTATCA-CAA
* * * * *
18704451 AGGGTAAGATTTTCATAATCAATACCCATACACAT
1 AAGGTAAGATTTCCATAATTAATATCCACACACAT
18704486 ATATTAAGAT
Statistics
Matches: 136, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
43 135 0.99
44 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (43 bp):
AAGGTAAGATTTCCATAATTAATATCCACACACATTATCACAA
Found at i:18704381 original size:86 final size:86
Alignment explanation
Indices: 18704247--18704487 Score: 236
Period size: 86 Copynumber: 2.8 Consensus size: 86
18704237 TATGGTTAGA
* * ** * * **
18704247 TTCCATAATCAATACCTATTCACTTTAT-ACTCAA-GGTAAGATTGCCATAATTAATTGCCACAC
1 TTCCATAATCAATACCCATACACACTATCA-TCAAGGGTAAGATTTCCATAATCAATACCCACAC
*
18704310 ATATTATCA-CAAAAGGTAAGAT
65 ATATTATCATC-AAAGATAAGAT
* * * * * * **
18704332 TTCTATAATTAATATCCATACACATTATCATTAAGGGTAAGATTTCCATAATCAATACCCATATG
1 TTCCATAATCAATACCCATACACACTATCATCAAGGGTAAGATTTCCATAATCAATACCCACACA
*
18704397 TATTATCATCAATGATAAGAT
66 TATTATCATCAAAGATAAGAT
* * *
18704418 TTCCATAATCAATACCCATGCATACTATCATCAAGGGTAAGATTTTCATAATCAATACCCATACA
1 TTCCATAATCAATACCCATACACACTATCATCAAGGGTAAGATTTCCATAATCAATACCC--ACA
18704483 CATAT
64 CATAT
18704488 ATTAAGATTT
Statistics
Matches: 124, Mismatches: 27, Indels: 7
0.78 0.17 0.04
Matches are distributed among these distances:
85 25 0.20
86 93 0.75
87 1 0.01
88 5 0.04
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (86 bp):
TTCCATAATCAATACCCATACACACTATCATCAAGGGTAAGATTTCCATAATCAATACCCACACA
TATTATCATCAAAGATAAGAT
Found at i:18708037 original size:34 final size:34
Alignment explanation
Indices: 18708014--18708128 Score: 142
Period size: 34 Copynumber: 3.3 Consensus size: 34
18708004 GTGTAATACA
18708014 TGGTGCTGAAACTTTGACCTTGGCATGTAACATC
1 TGGTGCTGAAACTTTGACCTTGGCATGTAACATC
* *
18708048 TAGTG-TTAAAGCTTTGACCTTGGCAACATGTAACATC
1 TGGTGCTGAAA-CTTTGACCTTGG---CATGTAACATC
* * *
18708085 TGATACTGAAACTTTGACCTTGGCATGTAATATC
1 TGGTGCTGAAACTTTGACCTTGGCATGTAACATC
18708119 TGGTGCTGAA
1 TGGTGCTGAA
18708129 GTCTTGGCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
33 4 0.06
34 34 0.51
37 25 0.37
38 4 0.06
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (34 bp):
TGGTGCTGAAACTTTGACCTTGGCATGTAACATC
Found at i:18708100 original size:37 final size:35
Alignment explanation
Indices: 18708019--18708109 Score: 107
Period size: 37 Copynumber: 2.6 Consensus size: 35
18708009 ATACATGGTG
18708019 CTGAAACTTTGACCTTGG--CATGTAACATCTAGT
1 CTGAAACTTTGACCTTGGCACATGTAACATCTAGT
* *
18708052 GTTAAAGCTTTGACCTTGGCAACATGTAACATCT-GAT
1 CTGAAA-CTTTGACCTTGGC-ACATGTAACATCTAG-T
18708089 ACTGAAACTTTGACCTTGGCA
1 -CTGAAACTTTGACCTTGGCA
18708110 TGTAATATCT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
33 4 0.08
34 12 0.25
36 2 0.04
37 26 0.54
38 4 0.08
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (35 bp):
CTGAAACTTTGACCTTGGCACATGTAACATCTAGT
Found at i:18708147 original size:28 final size:28
Alignment explanation
Indices: 18708103--18708158 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
18708093 AAACTTTGAC
* * *
18708103 CTTGGCATGTAATATCTGGTGCTGAAGT
1 CTTGGCATGTAACATCTAGTGCTAAAGT
18708131 CTTGGCATGTAACATCTAGTGCTAAAGT
1 CTTGGCATGTAACATCTAGTGCTAAAGT
18708159 TTTGATGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (28 bp):
CTTGGCATGTAACATCTAGTGCTAAAGT
Found at i:18708647 original size:34 final size:34
Alignment explanation
Indices: 18708599--18708690 Score: 103
Period size: 34 Copynumber: 2.7 Consensus size: 34
18708589 TAACCATAAA
*
18708599 AAAGATTCAGCACCAGATATTACATGTCAAGATC
1 AAAGATTCAGCACCAGATATTACATGCCAAGATC
* * * * *
18708633 AAAGTTTCAGCACCAGATGTTGCATGCCAAGGTT
1 AAAGATTCAGCACCAGATATTACATGCCAAGATC
* * *
18708667 AAAGCTTCAACACCATATATTACA
1 AAAGATTCAGCACCAGATATTACA
18708691 CATCAAAGCT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (34 bp):
AAAGATTCAGCACCAGATATTACATGCCAAGATC
Found at i:18711135 original size:30 final size:30
Alignment explanation
Indices: 18711095--18711157 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
18711085 CGAAAACAGA
* *
18711095 AATATTTATATGCA-ATGATATGCATAATGC
1 AATATATATATACATATGATATGC-TAATGC
* *
18711125 AATATATATATATATATGTTATGCTAATGC
1 AATATATATATACATATGATATGCTAATGC
18711155 AAT
1 AAT
18711158 TGTCTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (30 bp):
AATATATATATACATATGATATGCTAATGC
Found at i:18711235 original size:20 final size:21
Alignment explanation
Indices: 18711166--18711238 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
18711156 ATTGTCTATT
18711166 TTTTATTTATCATTTTTTATTA
1 TTTTATTTATCATTTTTT-TTA
*
18711188 -TTTATTTATTATTTTATTTTA
1 TTTTATTTATCATTTT-TTTTA
*
18711209 TTCTT-TATTATCATATTTTTTA
1 TT-TTAT-TTATCATTTTTTTTA
18711231 TTTTATTT
1 TTTTATTT
18711239 CTAATTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
21 21 0.49
22 12 0.28
23 10 0.23
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTATTTATCATTTTTTTTA
Found at i:18711245 original size:27 final size:27
Alignment explanation
Indices: 18711194--18711257 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
18711184 ATTATTTATT
*
18711194 TATTATTTTATTTTATTCTTTATTATCA
1 TATT-TTTTATTTTATTCTTAATTATCA
*
18711222 TATTTTTTATTTTATT-TCTAATTATTA
1 TATTTTTTATTTTATTCT-TAATTATCA
18711249 T-TTTTTTAT
1 TATTTTTTAT
18711258 ACCTTACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 9 0.27
27 20 0.61
28 4 0.12
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (27 bp):
TATTTTTTATTTTATTCTTAATTATCA
Found at i:18711399 original size:31 final size:32
Alignment explanation
Indices: 18711351--18711412 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
18711341 TGAACAAAAA
*
18711351 TTTTATTTTTTTTATTATACTAT-TTTTTTATT
1 TTTTATTTTTTTCATTATA-TATATTTTTTATT
18711383 TTTTA-TTTTTTCATTATATATATTTTTTAT
1 TTTTATTTTTTTCATTATATATATTTTTTAT
18711413 ATATTTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 3 0.11
31 20 0.71
32 5 0.18
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTTATTTTTTTCATTATATATATTTTTTATT
Found at i:18711415 original size:15 final size:15
Alignment explanation
Indices: 18711358--18711416 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
18711348 AAATTTTATT
18711358 TTTTTTAT-TATACTA
1 TTTTTTATATATA-TA
* *
18711373 TTTTTT-TATTTTTTA
1 TTTTTTATA-TATATA
18711388 TTTTTTCATTATATATA
1 TTTTTT-A-TATATATA
18711405 TTTTTTATATAT
1 TTTTTTATATAT
18711417 TTGAAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 1 0.03
15 19 0.54
16 3 0.09
17 10 0.29
18 2 0.06
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTATATATATA
Found at i:18711605 original size:10 final size:10
Alignment explanation
Indices: 18711592--18711628 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
18711582 GTATTTTGTA
18711592 TTTTTTTATT
1 TTTTTTTATT
18711602 TTTTTTTATT
1 TTTTTTTATT
*
18711612 TTTTATTATT
1 TTTTTTTATT
18711622 ATTTTTT
1 -TTTTTT
18711629 GTAAGAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 19 0.79
11 5 0.21
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:18711964 original size:14 final size:14
Alignment explanation
Indices: 18711945--18711975 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
18711935 ATTTTTATAT
18711945 TATATATATATTTA
1 TATATATATATTTA
18711959 TATATATATATTTA
1 TATATATATATTTA
18711973 TAT
1 TAT
18711976 TCCCCTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATATATATTTA
Found at i:18717100 original size:56 final size:54
Alignment explanation
Indices: 18717031--18717179 Score: 165
Period size: 54 Copynumber: 2.7 Consensus size: 54
18717021 TAAAAAAGGT
* * *
18717031 TATTACACGCCATGTTGAAAAAAATATATTGTTATTACACACCATATTCAAATACA
1 TATTACAC-CCATGTTGAAAAAAATATATT-TTGTTACACACCATATACAAAAACA
* * * * *
18717087 TTTTACACACCATGTTG-TAAAAATAAATTTTGTTATACACCATGTACAAAAACA
1 TATTACAC-CCATGTTGAAAAAAATATATTTTGTTACACACCATATACAAAAACA
*
18717141 TATTACACCTCATGTTGAAAAAAAAATATTATTGTTACA
1 TATTACACC-CATGTTGAAAAAAATATATT-TTGTTACA
18717180 TGCTATGTTG
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
53 1 0.01
54 34 0.45
55 19 0.25
56 22 0.29
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (54 bp):
TATTACACCCATGTTGAAAAAAATATATTTTGTTACACACCATATACAAAAACA
Found at i:18717188 original size:32 final size:32
Alignment explanation
Indices: 18717151--18717223 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 32
18717141 TATTACACCT
18717151 CATGTTGAAAAAAAAATATTATTGTTACATGC
1 CATGTTGAAAAAAAAATATTATTGTTACATGC
* * *
18717183 TATGTTG---AAAAACTATTGTTGTTACATGC
1 CATGTTGAAAAAAAAATATTATTGTTACATGC
*
18717212 CATGTTCAAAAA
1 CATGTTGAAAAA
18717224 TTTTTTATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
29 25 0.76
32 8 0.24
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (32 bp):
CATGTTGAAAAAAAAATATTATTGTTACATGC
Found at i:18717193 original size:29 final size:29
Alignment explanation
Indices: 18717161--18717223 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
18717151 CATGTTGAAA
* *
18717161 AAAAAATATTATTGTTACATGCTATGTTG
1 AAAAAATATTATTGTTACATGCCATGTTC
* *
18717190 AAAAACTATTGTTGTTACATGCCATGTTC
1 AAAAAATATTATTGTTACATGCCATGTTC
18717219 AAAAA
1 AAAAA
18717224 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (29 bp):
AAAAAATATTATTGTTACATGCCATGTTC
Found at i:18719149 original size:14 final size:15
Alignment explanation
Indices: 18719127--18719177 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
18719117 ATTAATCATT
18719127 TTTTATTATTTTTTA
1 TTTTATTATTTTTTA
18719142 TTTT-TTATTTTTTCA
1 TTTTATTATTTTTT-A
* * *
18719157 ATTTACTTAATGTTTA
1 TTTTA-TTATTTTTTA
18719173 TTTTA
1 TTTTA
18719178 AAATAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 9 0.31
15 8 0.28
16 5 0.17
17 7 0.24
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTATTATTTTTTA
Found at i:18723100 original size:35 final size:35
Alignment explanation
Indices: 18723056--18723248 Score: 233
Period size: 35 Copynumber: 5.5 Consensus size: 35
18723046 TATTATACAG
* * * *
18723056 AGAACAACTAGAACAAGTGAAGTGTTACTTCTCAC
1 AGAACAACTAGAACAAGTGAAGCGCTACTTCACAT
* *
18723091 AGAACAACTAGAACAAGTGAAGCGTTACTTCACGT
1 AGAACAACTAGAACAAGTGAAGCGCTACTTCACAT
* * * *
18723126 AGAACAACTAGACCAAGTAAAGTGCTACTTCACGT
1 AGAACAACTAGAACAAGTGAAGCGCTACTTCACAT
* *
18723161 AGAATAACTAGAACAAGTGAAGCGCTACTTCATAT
1 AGAACAACTAGAACAAGTGAAGCGCTACTTCACAT
* * * *
18723196 AGAACAACTAGAATAAGTGAAACACTACTTAACAT
1 AGAACAACTAGAACAAGTGAAGCGCTACTTCACAT
*
18723231 AGAACAACTAGAATAAGT
1 AGAACAACTAGAACAAGT
18723249 AGAGTACTAC
Statistics
Matches: 138, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 138 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.21
Consensus pattern (35 bp):
AGAACAACTAGAACAAGTGAAGCGCTACTTCACAT
Found at i:18723249 original size:105 final size:105
Alignment explanation
Indices: 18723056--18723259 Score: 266
Period size: 105 Copynumber: 1.9 Consensus size: 105
18723046 TATTATACAG
* * * **
18723056 AGAACAACTAGAACAAGTGAAGTGTTACTTCTCACAGAACAACTAGAACAAGTGAAGCGTTACTT
1 AGAACAACTAGAACAAGTGAAGCGCTACTTCTCACAGAACAACTAGAACAAGTGAAACACTACTT
* * * *
18723121 CACGTAGAACAACTAGACCAAGTAAAGTGCTACTTCACGT
66 AACATAGAACAACTAGAACAAGTAAAGTACTACTTCACGT
* * *
18723161 AGAATAACTAGAACAAGTGAAGCGCTACTTCAT-ATAGAACAACTAGAATAAGTGAAACACTACT
1 AGAACAACTAGAACAAGTGAAGCGCTACTTC-TCACAGAACAACTAGAACAAGTGAAACACTACT
* *
18723225 TAACATAGAACAACTAGAATAAGTAGAGTACTACT
65 TAACATAGAACAACTAGAACAAGTAAAGTACTACT
18723260 CCATATGGAA
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
105 83 0.99
106 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.21
Consensus pattern (105 bp):
AGAACAACTAGAACAAGTGAAGCGCTACTTCTCACAGAACAACTAGAACAAGTGAAACACTACTT
AACATAGAACAACTAGAACAAGTAAAGTACTACTTCACGT
Found at i:18723258 original size:35 final size:35
Alignment explanation
Indices: 18723056--18723283 Score: 226
Period size: 35 Copynumber: 6.5 Consensus size: 35
18723046 TATTATACAG
* * *
18723056 AGAACAACTAGAACAAGTGAAGTGTTACTTCTCAC
1 AGAACAACTAGAACAAGTGAAGTGCTACTTCACAT
* * *
18723091 AGAACAACTAGAACAAGTGAAGCGTTACTTCACGT
1 AGAACAACTAGAACAAGTGAAGTGCTACTTCACAT
* * *
18723126 AGAACAACTAGACCAAGTAAAGTGCTACTTCACGT
1 AGAACAACTAGAACAAGTGAAGTGCTACTTCACAT
* * *
18723161 AGAATAACTAGAACAAGTGAAGCGCTACTTCATAT
1 AGAACAACTAGAACAAGTGAAGTGCTACTTCACAT
* *** *
18723196 AGAACAACTAGAATAAGTGAAACACTACTTAACAT
1 AGAACAACTAGAACAAGTGAAGTGCTACTTCACAT
* * * *
18723231 AGAACAACTAGAATAAGT-AGAGTACTACTCCATAT
1 AGAACAACTAGAACAAGTGA-AGTGCTACTTCACAT
*
18723266 GGAACAACTA-ATACAAGT
1 AGAACAACTAGA-ACAAGT
18723284 AAAACAGCTG
Statistics
Matches: 164, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
34 2 0.01
35 162 0.99
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (35 bp):
AGAACAACTAGAACAAGTGAAGTGCTACTTCACAT
Found at i:18723275 original size:105 final size:105
Alignment explanation
Indices: 18723056--18723283 Score: 262
Period size: 105 Copynumber: 2.2 Consensus size: 105
18723046 TATTATACAG
* * * **
18723056 AGAACAACTAGAACAAGTGAAGTGTTACTTCTCACAGAACAACTAGAACAAGTGAAGCGTTACTT
1 AGAACAACTAGAACAAGTGAAGCGCTACTTCTCACAGAACAACTAGAACAAGTGAAACACTACTT
* * * * * *
18723121 CACGTAGAACAACTAGACCAAGTAAAGTGCTACTTCACGT
66 AACATAGAACAACTAGAACAAGTAAAGTACTACTCCACAT
* * *
18723161 AGAATAACTAGAACAAGTGAAGCGCTACTTCAT-ATAGAACAACTAGAATAAGTGAAACACTACT
1 AGAACAACTAGAACAAGTGAAGCGCTACTTC-TCACAGAACAACTAGAACAAGTGAAACACTACT
* * *
18723225 TAACATAGAACAACTAGAATAAGTAGAGTACTACTCCATAT
65 TAACATAGAACAACTAGAACAAGTAAAGTACTACTCCACAT
*
18723266 GGAACAACTA-ATACAAGT
1 AGAACAACTAGA-ACAAGT
18723284 AAAACAGCTG
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
104 1 0.01
105 100 0.98
106 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (105 bp):
AGAACAACTAGAACAAGTGAAGCGCTACTTCTCACAGAACAACTAGAACAAGTGAAACACTACTT
AACATAGAACAACTAGAACAAGTAAAGTACTACTCCACAT
Found at i:18724063 original size:13 final size:13
Alignment explanation
Indices: 18724032--18724077 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
18724022 AGGTTAAGAC
18724032 ATTCTC-CTCTAA
1 ATTCTCTCTCTAA
18724044 AGCTTCTCTCTCTAA
1 A--TTCTCTCTCTAA
18724059 ATTCTCTCTCT-A
1 ATTCTCTCTCTAA
18724071 ATTCTCT
1 ATTCTCT
18724078 TCTTATTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.29
13 10 0.32
14 5 0.16
15 7 0.23
ACGTcount: A:0.20, C:0.33, G:0.02, T:0.46
Consensus pattern (13 bp):
ATTCTCTCTCTAA
Found at i:18726440 original size:33 final size:33
Alignment explanation
Indices: 18726398--18726472 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
18726388 CAACACAAGG
18726398 TTAGCATGCATTAGCTTAATTTATTTTTCCATT
1 TTAGCATGCATTAGCTTAATTTATTTTTCCATT
18726431 TTAGCATGCATTAGCTTAATTTATTTTTCCATT
1 TTAGCATGCATTAGCTTAATTTATTTTTCCATT
18726464 TTAGCATGC
1 TTAGCATGC
18726473 TTTTATAAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (33 bp):
TTAGCATGCATTAGCTTAATTTATTTTTCCATT
Found at i:18730924 original size:37 final size:38
Alignment explanation
Indices: 18730876--18730953 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
18730866 ATAAACTACC
18730876 TAACCCCACTAACTTAAACGTAATAA-TAAACTGACTT
1 TAACCCCACTAACTTAAACGTAATAAGTAAACTGACTT
* * * *
18730913 TAACTCCACTAACTTAAACTTGATAAGTAAATTGACTT
1 TAACCCCACTAACTTAAACGTAATAAGTAAACTGACTT
18730951 TAA
1 TAA
18730954 TAAAACTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 23 0.64
38 13 0.36
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (38 bp):
TAACCCCACTAACTTAAACGTAATAAGTAAACTGACTT
Found at i:18735491 original size:2 final size:2
Alignment explanation
Indices: 18735486--18735515 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18735476 ATATATATAT
*
18735486 AC AC AC AC AC AC AC AC AC AC AT AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
18735516 TCATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:18735520 original size:12 final size:12
Alignment explanation
Indices: 18735486--18735520 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
18735476 ATATATATAT
*
18735486 ACACACACACAC
1 ACACACACATAC
18735498 ACACACACATAC
1 ACACACACATAC
*
18735510 ACACACTCATA
1 ACACACACATA
18735521 TATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.43, G:0.00, T:0.09
Consensus pattern (12 bp):
ACACACACATAC
Found at i:18735523 original size:2 final size:2
Alignment explanation
Indices: 18735518--18735547 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18735508 ACACACACTC
18735518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18735548 NAAGTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18735823 original size:2 final size:2
Alignment explanation
Indices: 18735818--18735844 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18735808 ACACATGCTC
18735818 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
18735845 ATTGTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18735844 original size:320 final size:318
Alignment explanation
Indices: 18735230--18735812 Score: 968
Period size: 320 Copynumber: 1.8 Consensus size: 318
18735220 AAGACATTAC
*
18735230 AAGTTAATTAAAAATCATAGTTTCATTAATTAATTTAATTAACTATATAGGTTTATCCTTAATTA
1 AAGTCAATTAAAAATCATAGTTTCATTAATTAATTTAATTAACTATATAGGTTTATCCTTAATTA
*
18735295 CAAGAAATTAAAAAAATAACTAAGTTTCCAAACTATTCTAATTTCACAACTTCCCTTTACATTTA
66 CAAGAAATTAAAAAAATAACTAAGTTTCCAAACTATTCTAATCTCACAACTTCCCTTTACATTTA
* * * * *
18735360 TATATTATAAATTTATATAAATAAAGGTATATATATTGTAGTTAATAATTTTATGAGTTATAATT
131 TATATTATAAATTTATATAAACAAAAGTATATATATTATAATTAATAATTTTATAAGTTATAATT
* * * *
18735425 TTTATAATGTTAATACAAAATAGAAAGTAAATATGTTTACATTTAAAGTACATATATATATACAC
196 TTTATAATATTAATACAAAATAAAAAATAAATATATTTACATTTAAAGTACATATATATATACAC
18735490 ACACACACACACACACATACACACACTCATATATATATATATATATATATATATATAT
261 ACACACACACACACACATACACACACTCATATATATATATATATATATATATATATAT
* *
18735548 NAAGTCAATTAATAATCATAGTTTCATTAATTAATTTAATTAACTATATAGGTTTGTCCTTAATT
1 -AAGTCAATTAAAAATCATAGTTTCATTAATTAATTTAATTAACTATATAGGTTTATCCTTAATT
* *
18735613 ACAATAAATTAAAAAAAATAACTAAGTTTCCAAACTATTCTAATCTCACAACTTCCCTTTAGATT
65 ACAAGAAATT-AAAAAAATAACTAAGTTTCCAAACTATTCTAATCTCACAACTTCCCTTTACATT
* *
18735678 TATATATTATAAGTTTATATAAACAAAAGTATATATATTATAATTAATACTTTTATAAGTTATAA
129 TATATATTATAAATTTATATAAACAAAAGTATATATATTATAATTAATAATTTTATAAGTTATAA
* * *
18735743 TTTTTGTAATATTAATACAAAATAAAAAATAAATATATTTATATTTAAAGTACATATATATTTAC
194 TTTTTATAATATTAATACAAAATAAAAAATAAATATATTTACATTTAAAGTACATATATATATAC
18735808 ACACA
259 ACACA
18735813 TGCTCATATA
Statistics
Matches: 243, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
319 70 0.29
320 173 0.71
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (318 bp):
AAGTCAATTAAAAATCATAGTTTCATTAATTAATTTAATTAACTATATAGGTTTATCCTTAATTA
CAAGAAATTAAAAAAATAACTAAGTTTCCAAACTATTCTAATCTCACAACTTCCCTTTACATTTA
TATATTATAAATTTATATAAACAAAAGTATATATATTATAATTAATAATTTTATAAGTTATAATT
TTTATAATATTAATACAAAATAAAAAATAAATATATTTACATTTAAAGTACATATATATATACAC
ACACACACACACACACATACACACACTCATATATATATATATATATATATATATATAT
Found at i:18736971 original size:7 final size:7
Alignment explanation
Indices: 18736959--18736984 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18736949 TAGAAATCTT
18736959 TTCTCCC
1 TTCTCCC
18736966 TTCTCCC
1 TTCTCCC
18736973 TTCTCCC
1 TTCTCCC
18736980 TTCTC
1 TTCTC
18736985 TTGACCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (7 bp):
TTCTCCC
Found at i:18737279 original size:440 final size:441
Alignment explanation
Indices: 18736193--18737410 Score: 2076
Period size: 440 Copynumber: 2.8 Consensus size: 441
18736183 TAAAATACCT
* * * *
18736193 TAACTTTATATAACCGGGTCGAGTATCTACAGATACCTTATAATAAGACACCCATTACTATCCCT
1 TAACTTTATATAACCGGGTCGAGTATCTGCAGATGCCTTATAATAAGACACCTATTACCATCCCT
18736258 AAATTTCACTTGTTTTTGTTGATTATCTTATGTTGGTTAAAAGTCAAAATTTAGTTACTTCACTT
66 AAATTTCACTTGTTTTTGTTGATTATCTTATGTTGGTTAAAAGTCAAAATTTAGTTACTTCACTT
*
18736323 AATGAAACTGTGTCGTATAGGTAGTTGTATGAGTCATTGTGCCAGGGAATTTTTCATTGATCCCA
131 AGTGAAACTGTGTCGTATAGGTAGTTGTATGAGTCATTGTGCCAGGGAATTTTTCATTGATCCCA
* *
18736388 GCACCCTCGGTCTTTGTAATGTCAGATGGCCTCATTTGGTTTGTTATTTCTTTTACATTTTCTCT
196 GCACCCTCGGTCTTTGTAATGTTAGATGGCCTCATCTGGTTTGTTATTTCTTTTACATTTTCTCT
*
18736453 CTCTTTGAACAACATATATATTGGTTGTTGAATGAAATGTGGTGAAGCCATTTTGGTGAATTAGA
261 CTCTTTGAACAACATATATATTGGTTGTTGAATGAAACGTGGTGAAGCCATTTTGGTGAATTAGA
18736518 AATC-TTT-T--C-T-T-CCTTCTCCCTTCTCTTGACCATTTTGGTGAATTAGAACTCGATTTAG
326 AATCTTTTCTCCCTTCTCCCTTCTCCCTTCTCTTGACCATTTTGGTGAATTAGAACTCGATTTAG
*
18736576 GTAGTGAAATCACTACCCAAACCCATCCCAAACCTAGTTATAGGATACCTTC
391 GTAGTGAAATCACTACCCAAACCCATCCCAAACCTAGTTATAGGATA-CTCC
*
18736628 TAACTTTATATAACCGGATCGAGTATCTGCAGATGCCTTATAATAAGACACCTATTACCATCCCT
1 TAACTTTATATAACCGGGTCGAGTATCTGCAGATGCCTTATAATAAGACACCTATTACCATCCCT
18736693 AAATTTCACTTGTTTTTGTTGATTATCTTATGTTGGTTAAAAGTCAAAATTTAGTTACTTCACTT
66 AAATTTCACTTGTTTTTGTTGATTATCTTATGTTGGTTAAAAGTCAAAATTTAGTTACTTCACTT
*
18736758 AGTGAAACTGTGTCGTTTAGGTAGTTGTATGAGTCATTGTGCCAGGGAATTTTTCATTGATCCCA
131 AGTGAAACTGTGTCGTATAGGTAGTTGTATGAGTCATTGTGCCAGGGAATTTTTCATTGATCCCA
18736823 GCACCCTCGGTCTTTGTAATGTTAGATGGCCTCATCTGGTTTGTTATTTCTTTTACATTTTCTCT
196 GCACCCTCGGTCTTTGTAATGTTAGATGGCCTCATCTGGTTTGTTATTTCTTTTACATTTTCTCT
18736888 CTCTTTGAACAACATATATATTGGTTGTTGAATGAAACGTGGTGAAGCCATTTTGGTGAATTAGA
261 CTCTTTGAACAACATATATATTGGTTGTTGAATGAAACGTGGTGAAGCCATTTTGGTGAATTAGA
18736953 AATCTTTTCTCCCTTCTCCCTTCTCCCTTCTCTTGACCATTTTGGTGAATTAGAACTCGATTTAG
326 AATCTTTTCTCCCTTCTCCCTTCTCCCTTCTCTTGACCATTTTGGTGAATTAGAACTCGATTTAG
* * ** * *
18737018 GTAGTGAAATCATTACCCGAACCTGTCCCAAA-CTTGATTATAGGGTA-TCC
391 GTAGTGAAATCACTACCCAAACCCATCCCAAACCTAG-TTATAGGATACTCC
* **
18737068 TAACTTTATATAATCGGGTCGAGTATCTGCAGATGCCTTATAATAAGATGCCTATTACCATCCCT
1 TAACTTTATATAACCGGGTCGAGTATCTGCAGATGCCTTATAATAAGACACCTATTACCATCCCT
*
18737133 AAATTTCACTTGTTTTTATTGATTATCTTATGTTGGTTAAAAGTCAAAATTTAGTTACTTCACTT
66 AAATTTCACTTGTTTTTGTTGATTATCTTATGTTGGTTAAAAGTCAAAATTTAGTTACTTCACTT
* * * * *
18737198 AGTGAATCTGTGTTGTATAGGTAGTTGAATTAGTCATTGTGCTAGGGAATTTTTCATTGATCCCA
131 AGTGAAACTGTGTCGTATAGGTAGTTGTATGAGTCATTGTGCCAGGGAATTTTTCATTGATCCCA
* * * * *
18737263 TCACCCTTGATCTTTGTAATGCTAGATGGCCTCATCTGGTTTGCTATTTCTTTTACATTTTCTCT
196 GCACCCTCGGTCTTTGTAATGTTAGATGGCCTCATCTGGTTTGTTATTTCTTTTACATTTTCTCT
18737328 CTCTTTGAACAACATATATATTGGTTGTTGAATGAAACGTGGTGAAGCCATTTTGGTGAATTAGA
261 CTCTTTGAACAACATATATATTGGTTGTTGAATGAAACGTGGTGAAGCCATTTTGGTGAATTAGA
18737393 AATCTTTTCTCCCTTCTC
326 AATCTTTTCTCCCTTCTC
18737411 TCTTGACTAT
Statistics
Matches: 742, Mismatches: 33, Indels: 11
0.94 0.04 0.01
Matches are distributed among these distances:
435 319 0.43
436 3 0.00
437 1 0.00
439 1 0.00
440 330 0.44
441 4 0.01
442 84 0.11
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (441 bp):
TAACTTTATATAACCGGGTCGAGTATCTGCAGATGCCTTATAATAAGACACCTATTACCATCCCT
AAATTTCACTTGTTTTTGTTGATTATCTTATGTTGGTTAAAAGTCAAAATTTAGTTACTTCACTT
AGTGAAACTGTGTCGTATAGGTAGTTGTATGAGTCATTGTGCCAGGGAATTTTTCATTGATCCCA
GCACCCTCGGTCTTTGTAATGTTAGATGGCCTCATCTGGTTTGTTATTTCTTTTACATTTTCTCT
CTCTTTGAACAACATATATATTGGTTGTTGAATGAAACGTGGTGAAGCCATTTTGGTGAATTAGA
AATCTTTTCTCCCTTCTCCCTTCTCCCTTCTCTTGACCATTTTGGTGAATTAGAACTCGATTTAG
GTAGTGAAATCACTACCCAAACCCATCCCAAACCTAGTTATAGGATACTCC
Found at i:18760051 original size:9 final size:9
Alignment explanation
Indices: 18760020--18760091 Score: 56
Period size: 9 Copynumber: 7.4 Consensus size: 9
18760010 GTAGACACCT
*
18760020 AAATAAACA
1 AAATAAATA
18760029 AAATTAAAATTA
1 AAA-T-AAA-TA
*
18760041 AATTAAATA
1 AAATAAATA
18760050 AAATAAA-A
1 AAATAAATA
18760058 TAAATAAATA
1 -AAATAAATA
18760068 AAATAAATA
1 AAATAAATA
*
18760077 ATAATTAAAAA
1 A-AA-TAAATA
18760088 AAAT
1 AAAT
18760092 GAGATGGCTG
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
8 1 0.02
9 29 0.56
10 9 0.17
11 10 0.19
12 3 0.06
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.25
Consensus pattern (9 bp):
AAATAAATA
Found at i:18761016 original size:9 final size:9
Alignment explanation
Indices: 18760984--18761008 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
18760974 CCACAAAAAG
18760984 AAAAAAATC
1 AAAAAAATC
18760993 AAAAAAATC
1 AAAAAAATC
18761002 AAAAAAA
1 AAAAAAA
18761009 GGAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATC
Found at i:18761794 original size:12 final size:11
Alignment explanation
Indices: 18761771--18761859 Score: 60
Period size: 12 Copynumber: 7.9 Consensus size: 11
18761761 ATTTTTAGAT
18761771 AAAAA-AATAA
1 AAAAATAATAA
18761781 AAAAATATATAA
1 AAAAATA-ATAA
*
18761793 AATAATAAT-A
1 AAAAATAATAA
18761803 AAAAA-AATAA
1 AAAAATAATAA
* *
18761813 TGATAATAATAA
1 -AAAAATAATAA
18761825 AATGAAA-AATAA
1 AA--AAATAATAA
*
18761837 ATAAATAATAA
1 AAAAATAATAA
18761848 TAATAAATAATA
1 -AA-AAATAATA
18761860 TAATTGGAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
9 3 0.05
10 14 0.23
11 12 0.20
12 22 0.36
13 10 0.16
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:18761799 original size:3 final size:3
Alignment explanation
Indices: 18761784--18761863 Score: 58
Period size: 3 Copynumber: 26.0 Consensus size: 3
18761774 AAAATAAAAA
* * *
18761784 AAT ATAT AA- AAT AAT AAT AAA AAA AAT AAT GAT AAT AAT AA- AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
18761828 GAAA AAT AAAT AAAT AAT AAT AAT AAAT AAT -AT AAT
1 -AAT AAT -AAT -AAT AAT AAT AAT -AAT AAT AAT AAT
18761864 TGGAAGAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
2 6 0.09
3 43 0.67
4 15 0.23
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:18761811 original size:24 final size:25
Alignment explanation
Indices: 18761780--18761861 Score: 91
Period size: 24 Copynumber: 3.4 Consensus size: 25
18761770 TAAAAAAATA
18761780 AAAAAATATATAAAATAATAATAA-
1 AAAAAATATATAAAATAATAATAAT
*
18761804 AAAAAATA-ATGATAATAATAA-AAT
1 AAAAAATATAT-AAAATAATAATAAT
* *
18761828 GAAAAATAAAT-AAATAATAATAAT
1 AAAAAATATATAAAATAATAATAAT
*
18761852 AAATAATATA
1 AAAAAATATA
18761862 ATTGGAAGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 12 0.25
24 34 0.71
25 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (25 bp):
AAAAAATATATAAAATAATAATAAT
Found at i:18761812 original size:32 final size:34
Alignment explanation
Indices: 18761771--18761862 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 34
18761761 ATTTTTAGAT
*
18761771 AAAAAAATAA-AAAAATATATAAAAT-AATAATA
1 AAAAAAATAATAAAAATATATAAAATGAAAAATA
* *
18761803 AAAAAAATAATGATAATA-ATAAAATGAAAAATA
1 AAAAAAATAATAAAAATATATAAAATGAAAAATA
18761836 AATAAATAATAATAATAAATAATATAA
1 AA-AAA-AATAATAA-AAAT-ATATAA
18761863 TTGGAAGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
32 17 0.35
33 13 0.27
34 3 0.06
35 7 0.15
36 3 0.06
37 1 0.02
38 4 0.08
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (34 bp):
AAAAAAATAATAAAAATATATAAAATGAAAAATA
Found at i:18761821 original size:29 final size:31
Alignment explanation
Indices: 18761771--18761859 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 31
18761761 ATTTTTAGAT
18761771 AAAA-AAATAAA-AA-AATATATAAAATAATA
1 AAAATAAATAAATAATAATA-ATAAAATAATA
* *
18761800 ATAA-AAA-AAATAATGATAATAATAA-AATGA
1 AAAATAAATAAATAATAATAATAA-AATAAT-A
18761830 AAAATAAATAAATAATAATAAT-AAATAATA
1 AAAATAAATAAATAATAATAATAAAATAATA
18761860 TAATTGGAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
28 3 0.06
29 15 0.31
30 12 0.24
31 7 0.14
32 12 0.24
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (31 bp):
AAAATAAATAAATAATAATAATAAAATAATA
Found at i:18778644 original size:2 final size:2
Alignment explanation
Indices: 18778637--18778671 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
18778627 CAGCCATGCA
18778637 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
18778672 ATTACTTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18779947 original size:18 final size:18
Alignment explanation
Indices: 18779924--18779994 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
18779914 AATTAATAAT
*
18779924 ACGTTTAACGCGATTAAC
1 ACGTTTAACACGATTAAC
* *
18779942 ACGTTTAATACTATTAAC
1 ACGTTTAACACGATTAAC
18779960 ACGTTTAACACGATTAAC
1 ACGTTTAACACGATTAAC
*
18779978 ACGTTTAACATGATTAA
1 ACGTTTAACACGATTAA
18779995 ATAAAAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (18 bp):
ACGTTTAACACGATTAAC
Found at i:18779949 original size:9 final size:9
Alignment explanation
Indices: 18779924--18779987 Score: 76
Period size: 9 Copynumber: 7.1 Consensus size: 9
18779914 AATTAATAAT
18779924 ACGTTTAAC
1 ACGTTTAAC
* *
18779933 GCGATTAAC
1 ACGTTTAAC
*
18779942 ACGTTTAAT
1 ACGTTTAAC
18779951 AC-TATTAAC
1 ACGT-TTAAC
18779960 ACGTTTAAC
1 ACGTTTAAC
*
18779969 ACGATTAAC
1 ACGTTTAAC
18779978 ACGTTTAAC
1 ACGTTTAAC
18779987 A
1 A
18779988 TGATTAAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
8 1 0.02
9 43 0.96
10 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (9 bp):
ACGTTTAAC
Found at i:18779958 original size:27 final size:27
Alignment explanation
Indices: 18779920--18779994 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
18779910 ACACAATTAA
* *
18779920 TAATACGTTTAACGCGATTAACACGTT
1 TAATACGTTTAACACGATTAACACGAT
*
18779947 TAATAC-TATTAACACGTTTAACACGAT
1 TAATACGT-TTAACACGATTAACACGAT
* *
18779974 TAACACGTTTAACATGATTAA
1 TAATACGTTTAACACGATTAA
18779995 ATAAAAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 1 0.03
27 38 0.95
28 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (27 bp):
TAATACGTTTAACACGATTAACACGAT
Found at i:18779994 original size:9 final size:9
Alignment explanation
Indices: 18779928--18779994 Score: 71
Period size: 9 Copynumber: 7.4 Consensus size: 9
18779918 AATAATACGT
*
18779928 TTAACGCGA
1 TTAACACGA
*
18779937 TTAACACGT
1 TTAACACGA
* *
18779946 TTAATACTA
1 TTAACACGA
*
18779955 TTAACACGT
1 TTAACACGA
18779964 TTAACACGA
1 TTAACACGA
*
18779973 TTAACACGT
1 TTAACACGA
*
18779982 TTAACATGA
1 TTAACACGA
18779991 TTAA
1 TTAA
18779995 ATAAAAATAT
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (9 bp):
TTAACACGA
Found at i:18780278 original size:18 final size:18
Alignment explanation
Indices: 18780257--18780302 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
18780247 TGTCACGTAT
*
18780257 ACACGTTTAAACACGATA
1 ACACGATTAAACACGATA
18780275 ACACGATTAAACACGATA
1 ACACGATTAAACACGATA
18780293 ACACGATTAA
1 ACACGATTAA
18780303 GTAAACGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.48, C:0.22, G:0.11, T:0.20
Consensus pattern (18 bp):
ACACGATTAAACACGATA
Found at i:18780287 original size:10 final size:10
Alignment explanation
Indices: 18780257--18780302 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 10
18780247 TGTCACGTAT
*
18780257 ACACGTTTAA
1 ACACGATTAA
18780267 ACACGA-T-A
1 ACACGATTAA
18780275 ACACGATTAA
1 ACACGATTAA
18780285 ACACGA-T-A
1 ACACGATTAA
18780293 ACACGATTAA
1 ACACGATTAA
18780303 GTAAACGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
8 14 0.45
9 4 0.13
10 13 0.42
ACGTcount: A:0.48, C:0.22, G:0.11, T:0.20
Consensus pattern (10 bp):
ACACGATTAA
Found at i:18783971 original size:14 final size:14
Alignment explanation
Indices: 18783952--18783984 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
18783942 GAAAGTTCAC
18783952 TTCTTCAAGGAAAA
1 TTCTTCAAGGAAAA
18783966 TTCTTCAAGGAAAA
1 TTCTTCAAGGAAAA
18783980 TTCTT
1 TTCTT
18783985 GGATATGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (14 bp):
TTCTTCAAGGAAAA
Found at i:18787380 original size:2 final size:2
Alignment explanation
Indices: 18787373--18787418 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
18787363 TACTTTGGTT
18787373 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18787415 TA TA
1 TA TA
18787419 NATTATGGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18792064 original size:86 final size:86
Alignment explanation
Indices: 18791956--18792131 Score: 327
Period size: 86 Copynumber: 2.0 Consensus size: 86
18791946 ATTTATTATT
*
18791956 AATTATAAATTTTATATTATATAAAAATACTTTTTATACTTTTATAAATAAAAAATAAAATTAAC
1 AATTATAAAATTTATATTATATAAAAATACTTTTTATACTTTTATAAATAAAAAATAAAATTAAC
18792021 TTTTTTCATTATGAACAAAAG
66 TTTTTTCATTATGAACAAAAG
18792042 NAATTATAAAATTTATA-TATATAAAAATACTTTTTATACTTTTATAAATAAAAAATAAAATTAA
1 -AATTATAAAATTTATATTATATAAAAATACTTTTTATACTTTTATAAATAAAAAATAAAATTAA
18792106 CTTTTTTCATTATGAACAAAAG
65 CTTTTTTCATTATGAACAAAAG
18792128 AATT
1 AATT
18792132 TATGATTAAT
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
85 4 0.05
86 69 0.78
87 15 0.17
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (86 bp):
AATTATAAAATTTATATTATATAAAAATACTTTTTATACTTTTATAAATAAAAAATAAAATTAAC
TTTTTTCATTATGAACAAAAG
Found at i:18800520 original size:3 final size:3
Alignment explanation
Indices: 18800512--18800541 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
18800502 TTTACTCCTT
18800512 TTA TTA TTA TTA TTA TTA TTA TTA GTTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT
18800542 TTTTAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18801734 original size:3 final size:3
Alignment explanation
Indices: 18801726--18801818 Score: 54
Period size: 3 Copynumber: 31.3 Consensus size: 3
18801716 ACACCTAAAA
** *
18801726 AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAAT AAT TTT AAAT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT -AAT AAT AAT
* *
18801774 AA- AAT AA- ACT AA- AAT -AT AA- AAT AAT -AT AAA AAT AAAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT
18801815 AAT A
1 AAT A
18801819 TATATAAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
2 11 0.15
3 45 0.63
4 15 0.21
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:18801794 original size:17 final size:16
Alignment explanation
Indices: 18801772--18801827 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
18801762 TTAAATTATA
18801772 ATAAAATAAACTAAAAT
1 ATAAAATAAA-TAAAAT
18801789 ATAAAATAATATAAAA-
1 ATAAAATAA-ATAAAAT
18801805 AT-AAATAAATAATATAT
1 ATAAAATAAATAA-A-AT
18801822 ATAAAA
1 ATAAAA
18801828 AAAAGGGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.12
15 7 0.21
16 3 0.09
17 16 0.47
18 4 0.12
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATAAATAAAAT
Found at i:18815179 original size:62 final size:62
Alignment explanation
Indices: 18815024--18815326 Score: 470
Period size: 62 Copynumber: 5.0 Consensus size: 62
18815014 CATTAAAGAA
* * *
18815024 TTTAAATCGAACCTATTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAA---T-
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTG
* * *
18815082 TTTAAATCAAACCTGTTGTAAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTCAATTTTG
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTG
*
18815144 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTG
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTG
*
18815206 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAAGAATTTTAATTTTG
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTG
* * * *
18815268 TTCAAATTGAATCTGTTGTGAGATAGGTCGAGCCAAGATTAAGTCTAAGAATTTTAATT
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATT
18815327 GAATTTGTTC
Statistics
Matches: 226, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
58 53 0.23
61 1 0.00
62 172 0.76
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (62 bp):
TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTG
Found at i:18815650 original size:11 final size:11
Alignment explanation
Indices: 18815634--18815658 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18815624 GTACGCCCAG
18815634 CCATCCCTTCC
1 CCATCCCTTCC
18815645 CCATCCCTTCC
1 CCATCCCTTCC
18815656 CCA
1 CCA
18815659 ACCACCCCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.64, G:0.00, T:0.24
Consensus pattern (11 bp):
CCATCCCTTCC
Found at i:18815862 original size:17 final size:17
Alignment explanation
Indices: 18815836--18815868 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18815826 CCAGCCACAG
18815836 AAACAAAAAGCAAAAAC
1 AAACAAAAAGCAAAAAC
*
18815853 AAACACAAAGCAAAAA
1 AAACAAAAAGCAAAAA
18815869 AGAAAAAGGA
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:0.76, C:0.18, G:0.06, T:0.00
Consensus pattern (17 bp):
AAACAAAAAGCAAAAAC
Found at i:18816907 original size:13 final size:13
Alignment explanation
Indices: 18816889--18816924 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
18816879 TAAAAAAAAT
18816889 ATGATAAATAATA
1 ATGATAAATAATA
18816902 ATGATAAATAATA
1 ATGATAAATAATA
*
18816915 ACGATAAATA
1 ATGATAAATA
18816925 TATGAAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (13 bp):
ATGATAAATAATA
Found at i:18844285 original size:13 final size:12
Alignment explanation
Indices: 18844261--18844291 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
18844251 GACAATAAAA
18844261 AGAGAATTAGAG
1 AGAGAATTAGAG
18844273 AGAGAATTTAGAG
1 AGAGAA-TTAGAG
18844286 AGAGAA
1 AGAGAA
18844292 GCTTTCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (12 bp):
AGAGAATTAGAG
Found at i:18844581 original size:29 final size:29
Alignment explanation
Indices: 18844515--18844586 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
18844505 AAAAGAGGTA
* * *
18844515 TACATGAAAAGGTACAAAAGCAGAAGCTG
1 TACATGAATAGGTACAAAAGAAAAAGCTG
*
18844544 -A-ATGAGAATAGGTACAAGAGAAAAAGCTG
1 TACAT--GAATAGGTACAAAAGAAAAAGCTG
18844573 TACATGAATAGGTA
1 TACATGAATAGGTA
18844587 TACGAGAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.06
28 1 0.03
29 29 0.83
30 1 0.03
31 2 0.06
ACGTcount: A:0.49, C:0.10, G:0.25, T:0.17
Consensus pattern (29 bp):
TACATGAATAGGTACAAAAGAAAAAGCTG
Found at i:18844900 original size:35 final size:35
Alignment explanation
Indices: 18844829--18844951 Score: 147
Period size: 35 Copynumber: 3.5 Consensus size: 35
18844819 GTAGTGCTCT
* * * * *
18844829 ACTTATTCTAGTTGTTCTATGTTAAGTAGTGTTTC
1 ACTTGTTCTAGTTGTTCTACGTGAAGTAGCGCTTC
* *
18844864 ACTTGTTCTAATTGTTCTACGTGAAGGAGCGCTTC
1 ACTTGTTCTAGTTGTTCTACGTGAAGTAGCGCTTC
* * *
18844899 ACTTGTTCTAGTCGTTTTACGTGAAGTAGCACTTC
1 ACTTGTTCTAGTTGTTCTACGTGAAGTAGCGCTTC
*
18844934 ACTTGTTCTAGTTATTCT
1 ACTTGTTCTAGTTGTTCT
18844952 CTGTATAATA
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 73 1.00
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.45
Consensus pattern (35 bp):
ACTTGTTCTAGTTGTTCTACGTGAAGTAGCGCTTC
Found at i:18845254 original size:21 final size:21
Alignment explanation
Indices: 18845215--18845254 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18845205 TTGTGTAAGG
* *
18845215 TGTAATGCCAATTTTTTTTTT
1 TGTAATGCCAATATCTTTTTT
*
18845236 TGTAATGTCAATATCTTTT
1 TGTAATGCCAATATCTTTT
18845255 GTAATATTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (21 bp):
TGTAATGCCAATATCTTTTTT
Found at i:18846419 original size:17 final size:20
Alignment explanation
Indices: 18846399--18846446 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
18846389 TTGACTTTTT
18846399 TTTTATTATTT-TT-TTA-A
1 TTTTATTATTTGTTATTATA
18846416 TTTTATTCATTTGTTATTATTA
1 TTTTATT-ATTTGTTATTA-TA
18846438 TTTTATTAT
1 TTTTATTAT
18846447 ATATATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.27
18 4 0.15
19 2 0.08
20 3 0.12
21 2 0.08
22 8 0.31
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTATTATTTGTTATTATA
Found at i:18846586 original size:14 final size:15
Alignment explanation
Indices: 18846567--18846611 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
18846557 NNNNNNNNTT
*
18846567 TTTATATTTTAT-TA
1 TTTATATTATATATA
18846581 TTTATA-TATATATA
1 TTTATATTATATATA
18846595 TTTATA-TATATATA
1 TTTATATTATATATA
18846609 TTT
1 TTT
18846612 GACAAATACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 4 0.14
14 25 0.86
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTATATTATATATA
Found at i:18850025 original size:102 final size:102
Alignment explanation
Indices: 18849868--18850143 Score: 290
Period size: 102 Copynumber: 2.7 Consensus size: 102
18849858 AGAAATGAGC
* * * * * *
18849868 GATAAAGCTAGCGGCTAATAGCATAACATCATTACAGCCAAATTATGAGCGATAAAGCTAGCGAC
1 GATAAAGCTAGCGACCAATAGAATAATATCATTACAGCCAAAATAAGAGCGATAAAGCTAGCGAC
*
18849933 TGGAATATGAGTAATAAATTATGATCAAAGAATAAG-A
66 T-GAATATGAGTAATAAACTATGATCAAAGAATAAGCA
* * * * *
18849970 GATAAAGCTCGCGACCAATAGAAAAATATCATTGCAGCCAAAATAAGAGCAATAAAGCTTGCGAC
1 GATAAAGCTAGCGACCAATAGAATAATATCATTACAGCCAAAATAAGAGCGATAAAGCTAGCGAC
* * * * * * *
18850035 CGAAGTAAGAGTGATGAACTATGGTTAAAGAATGAGCA
66 TGAA-TATGAGTAATAAACTATGATCAAAGAATAAGCA
* *
18850073 -ATAAAG-TTGACGACCAATAGAATAATATAATTACAGCCAAAATATA-AGCGATAAAGCTAGCG
1 GATAAAGCTAG-CGACCAATAGAATAATATCATTACAGCCAAAATA-AGAGCGATAAAGCTAGCG
*
18850135 GCTGAATAT
64 ACTGAATAT
18850144 AATTTTTTTT
Statistics
Matches: 142, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
101 7 0.05
102 133 0.94
103 2 0.01
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (102 bp):
GATAAAGCTAGCGACCAATAGAATAATATCATTACAGCCAAAATAAGAGCGATAAAGCTAGCGAC
TGAATATGAGTAATAAACTATGATCAAAGAATAAGCA
Found at i:18851729 original size:35 final size:35
Alignment explanation
Indices: 18851614--18851834 Score: 178
Period size: 35 Copynumber: 6.3 Consensus size: 35
18851604 CCAAGTGAAG
* **
18851614 TAGTTATTCTAT-TCGAAGTAGCTATTCTACTTGTAT-
1 TAGTTGTTCTATGT-GAAGTAGCGCTT-TACTTGT-TC
* * ** * *
18851650 TAGTTGTTCCATATGAAGTAATGCTTTATTTATTC
1 TAGTTGTTCTATGTGAAGTAGCGCTTTACTTGTTC
* * *
18851685 TAGTTGTTCTATGTTAAGTAGTGTTTTACTTGTTC
1 TAGTTGTTCTATGTGAAGTAGCGCTTTACTTGTTC
* * *
18851720 TAGTTGTTCTACGTGAAGTAGCGCTTCACTTGTTT
1 TAGTTGTTCTATGTGAAGTAGCGCTTTACTTGTTC
* * * *
18851755 TAGTTATTCTACGTGAAGTAGCACTTCACTTGTTC
1 TAGTTGTTCTATGTGAAGTAGCGCTTTACTTGTTC
* * *
18851790 TAGTTATTCTGTGTGAAGTAGCACTTCT-CTTGTTC
1 TAGTTGTTCTATGTGAAGTAGCGCTT-TACTTGTTC
*
18851825 TACTTGTTCT
1 TAGTTGTTCT
18851835 CTGTATAATA
Statistics
Matches: 153, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
34 1 0.01
35 133 0.87
36 18 0.12
37 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (35 bp):
TAGTTGTTCTATGTGAAGTAGCGCTTTACTTGTTC
Found at i:18858147 original size:29 final size:29
Alignment explanation
Indices: 18858112--18858167 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
18858102 TCATCTCTAC
*
18858112 GTTTTATCCTTATTATTTGTCCCTCTTAT
1 GTTTTATCCTTATCATTTGTCCCTCTTAT
18858141 GTTTTATCCTTATCATTTGTCCCTCTT
1 GTTTTATCCTTATCATTTGTCCCTCTT
18858168 GATATATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.23, G:0.07, T:0.57
Consensus pattern (29 bp):
GTTTTATCCTTATCATTTGTCCCTCTTAT
Found at i:18859265 original size:13 final size:13
Alignment explanation
Indices: 18859242--18859267 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18859232 TTTCATTTAC
18859242 TCTACACATTATT
1 TCTACACATTATT
18859255 TCTACACATTATT
1 TCTACACATTATT
18859268 GAAACACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
TCTACACATTATT
Found at i:18862868 original size:18 final size:18
Alignment explanation
Indices: 18862845--18862880 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
18862835 TTCAAGAACA
18862845 GATGCTTCATCCGTTATT
1 GATGCTTCATCCGTTATT
18862863 GATGCTTCATCCGTTATT
1 GATGCTTCATCCGTTATT
18862881 CTCGTAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (18 bp):
GATGCTTCATCCGTTATT
Found at i:18871430 original size:131 final size:131
Alignment explanation
Indices: 18871217--18871460 Score: 314
Period size: 131 Copynumber: 1.9 Consensus size: 131
18871207 GAATAGCTAC
* * * * *
18871217 AAAATTAAAGGAAAAAGTGTTGCTGAAAATTGAAGCTGATAAACTATTCAAACAAGTATGAGGTA
1 AAAATTAAAGGAAAAAGTGTTGCTGAAAATTGAAGCTAATAAACTATGCAAACAAATATGAAGCA
*
18871282 TGATACATTATTCTTAAGGATA-ATTTC-CGTCAAAAAATTAAGAGAAAACTCTTTTTGAATAAT
66 TGATACACTATTCTTAAGGATACATTTCAC-T-AAAAAATTAAGAGAAAACTCTTTTTGAATAAT
18871345 TAG
129 TAG
* * *
18871348 AAAATTAAAGGAAAAAGTGCTT-TTGAAAATTGAAGCTAATAACCTATGCAAACAAATTTGAAGC
1 AAAATTAAAGGAAAAAGTG-TTGCTGAAAATTGAAGCTAATAAACTATGCAAACAAATATGAAGC
* * * * *
18871412 GTGATACACTGTTTTTAAGGATACTTTTCACTAGAAAATTAAGAGAAAA
65 ATGATACACTATTCTTAAGGATACATTTCACTAAAAAATTAAGAGAAAA
18871461 AGTACTATAA
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
131 88 0.92
132 7 0.07
133 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.30
Consensus pattern (131 bp):
AAAATTAAAGGAAAAAGTGTTGCTGAAAATTGAAGCTAATAAACTATGCAAACAAATATGAAGCA
TGATACACTATTCTTAAGGATACATTTCACTAAAAAATTAAGAGAAAACTCTTTTTGAATAATTA
G
Done.