Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 62 of 79
Found at i:20293936 original size:53 final size:53
Alignment explanation
Indices: 20293856--20293962 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
20293846 AAACACGAAA
*
20293856 TTCAGACCGGACAAAATTTAGTGATTACAATATTAATATAATTTTTGTATGTC
1 TTCAGACCGGACAAAATTCAGTGATTACAATATTAATATAATTTTTGTATGTC
*
20293909 TTCAGACCGGACAAAATTCAGTGATTACAATATTAATGTAATTTTTGTATGTC
1 TTCAGACCGGACAAAATTCAGTGATTACAATATTAATATAATTTTTGTATGTC
20293962 T
1 T
20293963 ATGAGATATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (53 bp):
TTCAGACCGGACAAAATTCAGTGATTACAATATTAATATAATTTTTGTATGTC
Found at i:20296603 original size:21 final size:21
Alignment explanation
Indices: 20296579--20296619 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20296569 TTATTTTTAG
*
20296579 TTTAATATATATTTTTTATTT
1 TTTAATAAATATTTTTTATTT
* *
20296600 TTTAGTAAATCTTTTTTATT
1 TTTAATAAATATTTTTTATT
20296620 AAATTTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTAATAAATATTTTTTATTT
Found at i:20297040 original size:32 final size:33
Alignment explanation
Indices: 20296981--20297042 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
20296971 ACTAATATAT
**
20296981 TATATATAATTTTACATTTTAAAAAATAATTCA
1 TATATATAATTTTACATGCTAAAAAATAATTCA
*
20297014 TATATA-AATTTTACATGCTAAGAAATAAT
1 TATATATAATTTTACATGCTAAAAAATAAT
20297043 AATATTTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (33 bp):
TATATATAATTTTACATGCTAAAAAATAATTCA
Found at i:20305323 original size:19 final size:19
Alignment explanation
Indices: 20305299--20305411 Score: 172
Period size: 19 Copynumber: 5.8 Consensus size: 19
20305289 AATTTTTGAG
20305299 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
20305318 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
20305337 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
20305358 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
20305377 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
20305396 GATATGCAATATTAGA
1 GATATGCAATCTTAGA
20305412 ATATATGATT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 67 0.79
21 18 0.21
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:20305344 original size:40 final size:40
Alignment explanation
Indices: 20305300--20305405 Score: 189
Period size: 40 Copynumber: 2.7 Consensus size: 40
20305290 ATTTTTGAGG
20305300 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGAT
*
20305340 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGAT
20305380 ATAT--AATCTTAGATATGATATGCAAT
1 ATATGCAATCTTAGATATGATATGCAAT
20305406 ATTAGAATAT
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
38 22 0.34
40 43 0.66
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCTAGATATGAT
Found at i:20305575 original size:24 final size:22
Alignment explanation
Indices: 20305543--20305597 Score: 83
Period size: 24 Copynumber: 2.4 Consensus size: 22
20305533 TCATTGTAAA
20305543 GAAGAAAAAAAGAAAAAAGAGGAG
1 GAAGAAAAAAAGAAAAAAG-GG-G
20305567 GAAGAAAAAAAGAAAAAAGGGG
1 GAAGAAAAAAAGAAAAAAGGGG
*
20305589 GGAGAAAAA
1 GAAGAAAAA
20305598 GAGGAGGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 9 0.30
23 2 0.07
24 19 0.63
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (22 bp):
GAAGAAAAAAAGAAAAAAGGGG
Found at i:20306601 original size:98 final size:98
Alignment explanation
Indices: 20306432--20306686 Score: 510
Period size: 98 Copynumber: 2.6 Consensus size: 98
20306422 NNNNNNNNNN
20306432 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAAAG
1 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAAAG
20306497 GAAATATTCCGAGTTTGGGATTCTAGAGGAATC
66 GAAATATTCCGAGTTTGGGATTCTAGAGGAATC
20306530 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAAAG
1 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAAAG
20306595 GAAATATTCCGAGTTTGGGATTCTAGAGGAATC
66 GAAATATTCCGAGTTTGGGATTCTAGAGGAATC
20306628 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAA
1 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAA
20306687 ATTTTATTGT
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 157 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.37
Consensus pattern (98 bp):
GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAAAG
GAAATATTCCGAGTTTGGGATTCTAGAGGAATC
Found at i:20312431 original size:29 final size:29
Alignment explanation
Indices: 20312386--20312451 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
20312376 ATGGGTTTAA
20312386 ATTAATTATTATTTAAGTAAATAGATATTT
1 ATTAATTATTATTTAAGTAAA-AGATATTT
* *
20312416 ATTATTTATT-TTTAAGTAAAATATATTT
1 ATTAATTATTATTTAAGTAAAAGATATTT
*
20312444 CTTAATTA
1 ATTAATTA
20312452 AATAATTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 13 0.41
29 10 0.31
30 9 0.28
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (29 bp):
ATTAATTATTATTTAAGTAAAAGATATTT
Found at i:20312899 original size:41 final size:36
Alignment explanation
Indices: 20312848--20312940 Score: 107
Period size: 37 Copynumber: 2.4 Consensus size: 36
20312838 GAATATATGT
*
20312848 GTGGAATTGAATTGAATATATTGACTTGAAAAATGGAAAA
1 GTGGAATTGAATTGAAT-TA-TGA-TTG-AAAATGAAAAA
*
20312888 GT-GAATTTTGAATTGAATTATGATTGAAAGTGAAAAA
1 GTGGAA--TTGAATTGAATTATGATTGAAAATGAAAAA
20312925 GTGGAATTGAATTGAA
1 GTGGAATTGAATTGAA
20312941 ATGTGAATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
36 10 0.21
37 11 0.23
38 6 0.12
39 6 0.12
40 4 0.08
41 11 0.23
ACGTcount: A:0.43, C:0.01, G:0.24, T:0.32
Consensus pattern (36 bp):
GTGGAATTGAATTGAATTATGATTGAAAATGAAAAA
Found at i:20312923 original size:36 final size:41
Alignment explanation
Indices: 20312848--20312940 Score: 110
Period size: 36 Copynumber: 2.4 Consensus size: 41
20312838 GAATATATGT
20312848 GTGGAATTGAATTGAATATATTGACTTGAAAAATGG-AAAA
1 GTGGAATTGAATTGAATATATTGACTTGAAAAATGGAAAAA
*
20312888 GT-GAATTTTGAATTGAAT-TA-TGA-TTG-AAAGT-GAAAAA
1 GTGGAA--TTGAATTGAATATATTGACTTGAAAAATGGAAAAA
20312925 GTGGAATTGAATTGAA
1 GTGGAATTGAATTGAA
20312941 ATGTGAATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
36 11 0.23
37 10 0.21
38 6 0.12
39 6 0.12
40 4 0.08
41 11 0.23
ACGTcount: A:0.43, C:0.01, G:0.24, T:0.32
Consensus pattern (41 bp):
GTGGAATTGAATTGAATATATTGACTTGAAAAATGGAAAAA
Found at i:20317939 original size:20 final size:20
Alignment explanation
Indices: 20317914--20317953 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20317904 CAGAAAATGA
*
20317914 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
20317934 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
20317954 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:20317969 original size:14 final size:15
Alignment explanation
Indices: 20317893--20317969 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
20317883 GATTGGCAGT
* *
20317893 AAAATGTTTTTC-AG
1 AAAATGATTTTCTGG
20317907 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
20317921 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
20317941 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
20317956 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
20317970 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
13 4 0.08
14 21 0.42
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:20318031 original size:32 final size:32
Alignment explanation
Indices: 20317946--20318031 Score: 84
Period size: 33 Copynumber: 2.6 Consensus size: 32
20317936 TCTGTAAAAT
* * **
20317946 GATTTACTGGAAAATATTTTCTGGTGTTTGATT
1 GATTT-CTTGAAAATATTTTCTGCTGTTTGACA
* *
20317979 GA-ATCTGTGTAAAATGTTTTCTGCTGTTTGACA
1 GATTTCT-TG-AAAATATTTTCTGCTGTTTGACA
20318012 GATTTCTTGAAAATATTTTC
1 GATTTCTTGAAAATATTTTC
20318032 CGGAAAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
31 2 0.05
32 12 0.29
33 25 0.60
34 3 0.07
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.47
Consensus pattern (32 bp):
GATTTCTTGAAAATATTTTCTGCTGTTTGACA
Found at i:20318062 original size:20 final size:20
Alignment explanation
Indices: 20318037--20318116 Score: 92
Period size: 20 Copynumber: 4.0 Consensus size: 20
20318027 TTTTCCGGAA
20318037 AAATTGTTTTTACATATATT
1 AAATTGTTTTTACATATATT
20318057 AAATTGTTTTTACATATATAT
1 AAATTGTTTTTACATATAT-T
* ** *
20318078 TAATAAATTTTT--ATATTTT
1 AAAT-TGTTTTTACATATATT
20318097 AAATTGTTTTTACATATATT
1 AAATTGTTTTTACATATATT
20318117 GCAATGATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
18 5 0.10
19 4 0.08
20 30 0.62
21 4 0.08
22 5 0.10
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (20 bp):
AAATTGTTTTTACATATATT
Found at i:20319190 original size:17 final size:15
Alignment explanation
Indices: 20319166--20319208 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
20319156 GTGTATATAT
*
20319166 AAAAACAAATGTTTG
1 AAAAACAAATGTTTC
20319181 AATGAAACAAATGTTTC
1 AA--AAACAAATGTTTC
20319198 AAAAACAAATG
1 AAAAACAAATG
20319209 CCATGCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 11 0.44
17 14 0.56
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (15 bp):
AAAAACAAATGTTTC
Found at i:20320852 original size:13 final size:13
Alignment explanation
Indices: 20320834--20320859 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20320824 CCAGAAACTG
20320834 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
20320847 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
20320860 TACCCATTTG
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:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ATTTGCAGAAAAC
Found at i:20321036 original size:14 final size:14
Alignment explanation
Indices: 20321017--20321046 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20321007 AACAAAACTA
20321017 GCAGAGAAGATGAG
1 GCAGAGAAGATGAG
*
20321031 GCAGAGATGATGAG
1 GCAGAGAAGATGAG
20321045 GC
1 GC
20321047 TGCAATCGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.10, G:0.43, T:0.10
Consensus pattern (14 bp):
GCAGAGAAGATGAG
Found at i:20321106 original size:24 final size:24
Alignment explanation
Indices: 20321069--20321114 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
20321059 GGTGAAGAGA
*
20321069 GTGAAGAGAGGAGCTATGGAAAGG
1 GTGAAGAAAGGAGCTATGGAAAGG
* *
20321093 GTGAAGAAATGAGCTGTGGAAA
1 GTGAAGAAAGGAGCTATGGAAA
20321115 TGGTTTCAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.04, G:0.41, T:0.15
Consensus pattern (24 bp):
GTGAAGAAAGGAGCTATGGAAAGG
Found at i:20326057 original size:13 final size:13
Alignment explanation
Indices: 20326039--20326064 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20326029 ATATAACACT
20326039 ATCAAACTCATAA
1 ATCAAACTCATAA
20326052 ATCAAACTCATAA
1 ATCAAACTCATAA
20326065 GTTAGTATAC
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:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
ATCAAACTCATAA
Found at i:20326664 original size:9 final size:9
Alignment explanation
Indices: 20326650--20326680 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20326640 GTTAAACGAA
20326650 TCGAGTTAT
1 TCGAGTTAT
*
20326659 TCGAGTTAA
1 TCGAGTTAT
20326668 TCGAGTTAT
1 TCGAGTTAT
20326677 TCGA
1 TCGA
20326681 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:20326751 original size:9 final size:9
Alignment explanation
Indices: 20326734--20326770 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20326724 TGAGTTTTCG
20326734 AATTCGAAT
1 AATTCGAAT
*
20326743 AACTCGAAT
1 AATTCGAAT
20326752 AATTCGAAT
1 AATTCGAAT
20326761 AATTCGAAT
1 AATTCGAAT
20326770 A
1 A
20326771 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:20327587 original size:5 final size:5
Alignment explanation
Indices: 20327577--20327612 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
20327567 CTCGAAAATT
20327577 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
20327613 CGAATGCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:20333188 original size:21 final size:21
Alignment explanation
Indices: 20333162--20333214 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
20333152 TCAAATATTA
* *
20333162 AATAATCCACAAACATTAGTT
1 AATAATCCACAAACATCAATT
* *
20333183 AATAAT--GCAACCATCAATT
1 AATAATCCACAAACATCAATT
20333202 AATAATCCACAAA
1 AATAATCCACAAA
20333215 TCAAATATCA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
19 15 0.62
21 9 0.38
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.25
Consensus pattern (21 bp):
AATAATCCACAAACATCAATT
Found at i:20333229 original size:23 final size:26
Alignment explanation
Indices: 20333201--20333265 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 26
20333191 AACCATCAAT
*
20333201 TAATAATCCACAAAT-CAAATATC-A
1 TAATAATCCACAAATACAAATACCAA
*
20333225 -AATAATCCATAAATACCAAATACCAA
1 TAATAATCCACAAATA-CAAATACCAA
20333251 TTAATAATCCACAAA
1 -TAATAATCCACAAA
20333266 CTCATTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 13 0.39
25 7 0.21
26 1 0.03
28 12 0.36
ACGTcount: A:0.55, C:0.22, G:0.00, T:0.23
Consensus pattern (26 bp):
TAATAATCCACAAATACAAATACCAA
Found at i:20337698 original size:99 final size:98
Alignment explanation
Indices: 20337537--20337753 Score: 301
Period size: 99 Copynumber: 2.2 Consensus size: 98
20337527 TTTAAAGCTT
* * * * *
20337537 GCTGATTTACGATCACAGCTTTAGTTCATTGATTTATGATCATGAACAATTCATTAAGAGTTCGC
1 GCTGATTTATGATCACAACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTCCC
* *
20337602 CGATTTACGATCGCAACTATCATTTTTAAC-TCTC
66 CAATTTACGATCGCAACT-TCA-TTTAAACATCTC
*
20337636 GCTGATTTATGATCACAACTTCAGTTTATTGATTTACGATCATGAACAATTCATTAAGAGTTCCC
1 GCTGATTTATGATCACAACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTCCC
* * *
20337701 CAATTTATGATCGCAACTTCATTTAAACATTTT
66 CAATTTACGATCGCAACTTCATTTAAACATCTC
*
20337734 GCTAATTTATGATCACAACT
1 GCTGATTTATGATCACAACT
20337754 GCCATTTTTA
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
97 6 0.06
98 24 0.23
99 75 0.71
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (98 bp):
GCTGATTTATGATCACAACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTCCC
CAATTTACGATCGCAACTTCATTTAAACATCTC
Found at i:20337801 original size:134 final size:134
Alignment explanation
Indices: 20337604--20338307 Score: 736
Period size: 134 Copynumber: 5.4 Consensus size: 134
20337594 GAGTTCGCCG
* ** *
20337604 ATTTACGATCGCAACTATCATTTTTAACTCTCGCTGATTTATGATCACAACTTCAGTTTATTGAT
1 ATTTACGATCACAACTATCATTTTTAAAGCTCGCTGATTTATGATCACAACTTCAGTTCATTGAT
* * * * *
20337669 TTACGATCATGAACAATTCATTAAGAGTTCCCCAATTTATGATCGCAACTTCATTTAAACATTTT
66 TTACGATCATGAACAATTCATTAAGAGTTCGCCAATTTACGATCGCAACTCCATTTAAATAGTTT
20337734 GCTA
131 GCTA
* ** * * * *
20337738 ATTTATGATCACAACTGCCATTTTTAAAGCTCGTTGATTTACGACCACAACTTTAGTTCATTGAT
1 ATTTACGATCACAACTATCATTTTTAAAGCTCGCTGATTTATGATCACAACTTCAGTTCATTGAT
* * * *
20337803 TTACGATCATGAATAATTCATTAAGAGCTCGCCGATTTACGATCGCAACTCTATTTAAATAGTTT
66 TTACGATCATGAACAATTCATTAAGAGTTCGCCAATTTACGATCGCAACTCCATTTAAATAGTTT
20337868 GCTA
131 GCTA
* * * * *
20337872 ATTTTACGATCATAACTGTCATTTTTAAAGCTCACTGATTTATAATCACAACTTCAATTCATTGA
1 A-TTTACGATCACAACTATCATTTTTAAAGCTCGCTGATTTATGATCACAACTTCAGTTCATTGA
* * * * * * *
20337937 TTTATGATTATGAACAATTCATTAAGAGTTCGTCGATTTACGATTGCAACTCCTTTTAAATAATT
65 TTTACGATCATGAACAATTCATTAAGAGTTCGCCAATTTACGATCGCAACTCCATTTAAATAGTT
20338002 TGCTA
130 TGCTA
* * * *
20338007 ATTTACGATTACAACTATCATTTTTAAAGCTTGTTGATTTATG------A-TT-AG-----TG-C
1 ATTTACGATCACAACTATCATTTTTAAAGCTCGCTGATTTATGATCACAACTTCAGTTCATTGAT
* ** * *
20338058 TTACGATCATGAATAATTCATTAAGAGTTC-ATAGATTTATGATCGCAACTCCATTTAAACAGTT
66 TTACGATCATGAACAATTCATTAAGAGTTCGCCA-ATTTACGATCGCAACTCCATTTAAATAGTT
*
20338122 TGCTG
130 TGCTA
** * * *
20338127 ATTTACGATCACATTTATCATTTTTAAAGCTCGCTGATTTACGATCACAGCTTCAGTTCATTTAT
1 ATTTACGATCACAACTATCATTTTTAAAGCTCGCTGATTTATGATCACAACTTCAGTTCATTGAT
* * * *
20338192 TTATGATCATGAACAATTCATTAAGAGTTTGTCAATTTACGATCGCAACTCCATTTAAATAGTTC
66 TTACGATCATGAACAATTCATTAAGAGTTCGCCAATTTACGATCGCAACTCCATTTAAATAGTTT
** *
20338257 ATTG
131 GCTA
* * * ** * *
20338261 ATTTATGATCACAATTGTCATTTTTAAAATTGGCTGGTTTATGATCA
1 ATTTACGATCACAACTATCATTTTTAAAGCTCGCTGATTTATGATCA
20338308 TGAACAATTC
Statistics
Matches: 466, Mismatches: 87, Indels: 34
0.79 0.15 0.06
Matches are distributed among these distances:
120 93 0.20
121 2 0.00
126 1 0.00
127 4 0.01
128 3 0.01
133 1 0.00
134 246 0.53
135 116 0.25
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.39
Consensus pattern (134 bp):
ATTTACGATCACAACTATCATTTTTAAAGCTCGCTGATTTATGATCACAACTTCAGTTCATTGAT
TTACGATCATGAACAATTCATTAAGAGTTCGCCAATTTACGATCGCAACTCCATTTAAATAGTTT
GCTA
Found at i:20338165 original size:120 final size:120
Alignment explanation
Indices: 20337946--20338167 Score: 318
Period size: 120 Copynumber: 1.9 Consensus size: 120
20337936 ATTTATGATT
* * * * *
20337946 ATGAACAATTCATTAAGAGTTCGTCGATTTACGATTGCAACTCCTTTTAAATAATTTGCTAATTT
1 ATGAACAATTCATTAAGAGTTCATAGATTTACGATCGCAACTCCATTTAAACAATTTGCTAATTT
* * *
20338011 ACGATTACAACTATCATTTTTAAAGCTTGTTGATTTATGATTAGTGCTTACGATC
66 ACGATCACAACTATCATTTTTAAAGCTCGCTGATTTATGATTAGTGCTTACGATC
* * * *
20338066 ATGAATAATTCATTAAGAGTTCATAGATTTATGATCGCAACTCCATTTAAACAGTTTGCTGATTT
1 ATGAACAATTCATTAAGAGTTCATAGATTTACGATCGCAACTCCATTTAAACAATTTGCTAATTT
**
20338131 ACGATCACATTTATCATTTTTAAAGCTCGCTGATTTA
66 ACGATCACAACTATCATTTTTAAAGCTCGCTGATTTA
20338168 CGATCACAGC
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
120 88 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (120 bp):
ATGAACAATTCATTAAGAGTTCATAGATTTACGATCGCAACTCCATTTAAACAATTTGCTAATTT
ACGATCACAACTATCATTTTTAAAGCTCGCTGATTTATGATTAGTGCTTACGATC
Found at i:20338283 original size:36 final size:35
Alignment explanation
Indices: 20338226--20338383 Score: 92
Period size: 35 Copynumber: 4.5 Consensus size: 35
20338216 GAGTTTGTCA
* * *
20338226 ATTTACGATCGCAACTCCATTTAAATAGTTCATTG
1 ATTTACGATCACAATTTCATTTAAATAGTTCATTG
* ***
20338261 ATTTATGATCACAATTGTCATTTTTAAA-A-TTGGCTG
1 ATTTACGATCACAATT-TCA--TTTAAATAGTTCATTG
* * * * *
20338297 GTTTATGATCATGAACAA-TTCA-TT-AAGAGTTCGTCG
1 ATTTACGATC----ACAATTTCATTTAAATAGTTCATTG
* *
20338333 ATTTACGACCACAATTCCATTTAAATAGTTCATTG
1 ATTTACGATCACAATTTCATTTAAATAGTTCATTG
20338368 ATTTACGATCACAATT
1 ATTTACGATCACAATT
20338384 GACATTTTTA
Statistics
Matches: 92, Mismatches: 19, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
32 4 0.04
33 3 0.03
34 4 0.04
35 40 0.43
36 26 0.28
37 1 0.01
38 9 0.10
39 1 0.01
40 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (35 bp):
ATTTACGATCACAATTTCATTTAAATAGTTCATTG
Found at i:20338378 original size:107 final size:107
Alignment explanation
Indices: 20338190--20338415 Score: 355
Period size: 107 Copynumber: 2.1 Consensus size: 107
20338180 CAGTTCATTT
* * *
20338190 ATTTATGATCATGAACAATTCATTAAGAGTTTGTCAATTTACGATCGCAACTCCATTTAAATAGT
1 ATTTATGATCATGAACAATTCATTAAGAGTTCGTCAATTTACGACCACAACTCCATTTAAATAGT
* *
20338255 TCATTGATTTATGATCACAATTGTCATTTTTAAA-ATTGGCTG
66 TCATTGATTTACGATCACAATTGACATTTTTAAAGATT-GCTG
* * *
20338297 GTTTATGATCATGAACAATTCATTAAGAGTTCGTCGATTTACGACCACAATTCCATTTAAATAGT
1 ATTTATGATCATGAACAATTCATTAAGAGTTCGTCAATTTACGACCACAACTCCATTTAAATAGT
*
20338362 TCATTGATTTACGATCACAATTGACATTTTTAAAGCTTGCTG
66 TCATTGATTTACGATCACAATTGACATTTTTAAAGATTGCTG
20338404 ATTTATGATCAT
1 ATTTATGATCAT
20338416 AGTTTCAGTT
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
107 106 0.98
108 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (107 bp):
ATTTATGATCATGAACAATTCATTAAGAGTTCGTCAATTTACGACCACAACTCCATTTAAATAGT
TCATTGATTTACGATCACAATTGACATTTTTAAAGATTGCTG
Found at i:20338743 original size:11 final size:11
Alignment explanation
Indices: 20338729--20338753 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20338719 GATGGGGATA
20338729 AATTATTATAG
1 AATTATTATAG
20338740 AATTATTATAG
1 AATTATTATAG
20338751 AAT
1 AAT
20338754 ATATCATAAC
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
AATTATTATAG
Found at i:20341111 original size:2 final size:2
Alignment explanation
Indices: 20341104--20341128 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20341094 TTAAATTATG
20341104 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20341129 GGCAATCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20358641 original size:54 final size:54
Alignment explanation
Indices: 20358544--20358646 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
20358534 CTTGTTGAGC
* * * * *
20358544 AAGAGTGATCTTGTTTAGAGGGGGGTTGAACTATAATGGATTAACTTTTTGGAA
1 AAGAGTGATCATGTTTAGAGGGAGGTGGAACTACAATGAATTAACTTTTTGGAA
*
20358598 AAGAGTGATCATGTTTAGAGTGAGGTGGAAGC-ACAATGAATTAACTTTT
1 AAGAGTGATCATGTTTAGAGGGAGGTGGAA-CTACAATGAATTAACTTTT
20358647 GGGCAATAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 41 0.98
55 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.28, T:0.33
Consensus pattern (54 bp):
AAGAGTGATCATGTTTAGAGGGAGGTGGAACTACAATGAATTAACTTTTTGGAA
Found at i:20366625 original size:18 final size:18
Alignment explanation
Indices: 20366592--20366626 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20366582 TCCAGCAGAT
* *
20366592 GGCATACTGACTTGTTGA
1 GGCATACTAACCTGTTGA
20366610 GGCATACTAACCTGTTG
1 GGCATACTAACCTGTTG
20366627 TGGAGAGCTG
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:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (18 bp):
GGCATACTAACCTGTTGA
Found at i:20370142 original size:56 final size:57
Alignment explanation
Indices: 20370040--20370150 Score: 134
Period size: 56 Copynumber: 2.0 Consensus size: 57
20370030 AATTAAACTT
** * * * *
20370040 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGCCAAGTTCAAGTACTAAATTGAG
1 AAAAAAAGTTTAAATACCAAATTAAGAAAAAATACAAAATTCAAGTACTAAATTGAG
* * *
20370097 AAAAAAA-TTTAAATACCAAATTAAGAAAAAATATAAAATTTAAGTATTAAATTG
1 AAAAAAAGTTTAAATACCAAATTAAGAAAAAATACAAAATTCAAGTACTAAATTG
20370151 GATCAAATCA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
56 38 0.84
57 7 0.16
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.26
Consensus pattern (57 bp):
AAAAAAAGTTTAAATACCAAATTAAGAAAAAATACAAAATTCAAGTACTAAATTGAG
Found at i:20386043 original size:21 final size:20
Alignment explanation
Indices: 20386009--20386068 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
20385999 CTTGAACTTT
*
20386009 AAACTCAAACCCTTGAACCCC
1 AAACCCAAA-CCTTGAACCCC
* * *
20386030 GAACCCTAAACCTTAAATCCC
1 AAACCC-AAACCTTGAACCCC
*
20386051 AAACCCAAACCCTGAACC
1 AAACCCAAACCTTGAACC
20386069 TTGAGGTTCG
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
20 9 0.30
21 18 0.60
22 3 0.10
ACGTcount: A:0.40, C:0.42, G:0.05, T:0.13
Consensus pattern (20 bp):
AAACCCAAACCTTGAACCCC
Found at i:20388363 original size:63 final size:64
Alignment explanation
Indices: 20388291--20388421 Score: 237
Period size: 64 Copynumber: 2.1 Consensus size: 64
20388281 ACACTTTAAT
*
20388291 TTTATTTAGTTATGTTTTAAAA-TTTATATTTTTCCATTCTTTGATTGGTTGAGCATATAAATA
1 TTTATTTAGTTATGTTTTAAAATTTTATATTTTTCCATTCTTTAATTGGTTGAGCATATAAATA
*
20388354 TTTATTTAGTTATGTTTTAAAATTTTATATTTTTCCATTCTTTAATTGGTTGAGCATATAAATC
1 TTTATTTAGTTATGTTTTAAAATTTTATATTTTTCCATTCTTTAATTGGTTGAGCATATAAATA
20388418 TTTA
1 TTTA
20388422 CGAGGACACG
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
63 22 0.34
64 43 0.66
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (64 bp):
TTTATTTAGTTATGTTTTAAAATTTTATATTTTTCCATTCTTTAATTGGTTGAGCATATAAATA
Found at i:20393846 original size:4 final size:4
Alignment explanation
Indices: 20393839--20393865 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20393829 AATAGTTTTT
20393839 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
20393866 TATCAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:20394241 original size:55 final size:55
Alignment explanation
Indices: 20394180--20394283 Score: 145
Period size: 55 Copynumber: 1.9 Consensus size: 55
20394170 TCGTCTTAAT
* * * * *
20394180 TGTTGGAATACTGCTTCTTTTGAATATATTTTTTATATGTTTAAATTGATTGTCA
1 TGTTGGAATACTACTTCTTTTGAACAGATTGTTTATATGCTTAAATTGATTGTCA
* *
20394235 TGTTGGAATACTATTTCTTTTGAACCGATTGTTTATATGCTTAAATTGA
1 TGTTGGAATACTACTTCTTTTGAACAGATTGTTTATATGCTTAAATTGA
20394284 CTGTTACATA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 42 1.00
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (55 bp):
TGTTGGAATACTACTTCTTTTGAACAGATTGTTTATATGCTTAAATTGATTGTCA
Found at i:20397204 original size:21 final size:21
Alignment explanation
Indices: 20397178--20397219 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20397168 CTAAATCGAA
20397178 GGGGCTTAAAGGCAACCCACT
1 GGGGCTTAAAGGCAACCCACT
20397199 GGGGCTTAAAGGCAACCCACT
1 GGGGCTTAAAGGCAACCCACT
20397220 AACAAAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (21 bp):
GGGGCTTAAAGGCAACCCACT
Found at i:20405433 original size:21 final size:21
Alignment explanation
Indices: 20405409--20405458 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
20405399 TAAATTCGAG
20405409 ACCTTAAACT-TTAAATCTAAA
1 ACCTTAAACTCTTAAA-CTAAA
*
20405430 ACCTTAAA-TCTTAAACTCAA
1 ACCTTAAACTCTTAAACTAAA
*
20405450 ACTTTAAAC
1 ACCTTAAAC
20405459 ATGCGGATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (21 bp):
ACCTTAAACTCTTAAACTAAA
Found at i:20405732 original size:32 final size:32
Alignment explanation
Indices: 20405696--20405759 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
20405686 CGAAAAAAGT
* *
20405696 AAGTGCATCTATAGATAAATAGTATATCTACG
1 AAGTGCACCTATACATAAATAGTATATCTACG
20405728 AAGTGCACCTATACATAAATAGTATATCTACG
1 AAGTGCACCTATACATAAATAGTATATCTACG
20405760 GTAAGTAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (32 bp):
AAGTGCACCTATACATAAATAGTATATCTACG
Found at i:20415964 original size:80 final size:81
Alignment explanation
Indices: 20415837--20415998 Score: 317
Period size: 80 Copynumber: 2.0 Consensus size: 81
20415827 AGTTCGACTT
20415837 TGTTGCTTGTATGAGTGCCTTCTTTGGTGTCGTTTTCTTTTCCATCGAGATCGACCTTCTAATAG
1 TGTTGCTTGTATGAGTGCCTTCTTTGGTGTCGTTTTCTTTTCCATCGAGATCGACCTTCTAATAG
20415902 CTATG-GGAACATAAG
66 CTATGAGGAACATAAG
20415917 TGTTGCTTGTATGAGTGCCTTCTTTGGTGTCGTTTTCTTTTCCATCGAGATCGACCTTCTAATAG
1 TGTTGCTTGTATGAGTGCCTTCTTTGGTGTCGTTTTCTTTTCCATCGAGATCGACCTTCTAATAG
20415982 CTATGAGGAACATAAG
66 CTATGAGGAACATAAG
20415998 T
1 T
20415999 AGATTATTGA
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 70 0.86
81 11 0.14
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (81 bp):
TGTTGCTTGTATGAGTGCCTTCTTTGGTGTCGTTTTCTTTTCCATCGAGATCGACCTTCTAATAG
CTATGAGGAACATAAG
Found at i:20421480 original size:22 final size:23
Alignment explanation
Indices: 20421455--20421509 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
20421445 ATTTATTATT
*
20421455 TTAATATTATTTCTTT-TCCATA
1 TTAATATTATTTCTTTATCAATA
* *
20421477 TTAAT-TTATTTTTTTATTAATA
1 TTAATATTATTTCTTTATCAATA
20421499 TTAATATTATT
1 TTAATATTATT
20421510 ATTATTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.32
22 14 0.50
23 5 0.18
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (23 bp):
TTAATATTATTTCTTTATCAATA
Found at i:20421509 original size:3 final size:3
Alignment explanation
Indices: 20421490--20421523 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
20421480 ATTTATTTTT
* *
20421490 TTA TTA ATA TTA ATA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20421524 CGTTCGTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:20425716 original size:64 final size:64
Alignment explanation
Indices: 20425595--20425717 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
20425585 TCCCGATCGG
* * * * ***
20425595 TATTAATCCTGCATGTGTTGTAGATATACCACAGCTCTTTGTGAGCGTCCTTTTATATGATCAA
1 TATTAATCCTGCATGTATTGCAGACATACCACAGCTCTTTATGAGCGTCCCGATATATGATCAA
* *
20425659 TATTGATCCTGTATGTATTGCAGACATACCACAGCTCTTTATGAGCGTCCCGATATATG
1 TATTAATCCTGCATGTATTGCAGACATACCACAGCTCTTTATGAGCGTCCCGATATATG
20425718 GCACTTCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (64 bp):
TATTAATCCTGCATGTATTGCAGACATACCACAGCTCTTTATGAGCGTCCCGATATATGATCAA
Found at i:20425801 original size:24 final size:25
Alignment explanation
Indices: 20425753--20425801 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
20425743 CTCGCTTGAA
* *
20425753 CTTCCTGATATATGGTTATTCGGAG
1 CTTCCTGATATATAGCTATTCGGAG
20425778 CTTCCTGATA-ATAGCTATTCGGAG
1 CTTCCTGATATATAGCTATTCGGAG
20425802 TTACCCGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (25 bp):
CTTCCTGATATATAGCTATTCGGAG
Found at i:20429951 original size:33 final size:33
Alignment explanation
Indices: 20429906--20429969 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
20429896 AAAAATTATA
* *
20429906 TTTAATACAATAAAATATTTATTATATTTATTT
1 TTTAATACAATAAAACATTTACTATATTTATTT
*
20429939 TTTAATATAATAAAACATTTACTATATTTAT
1 TTTAATACAATAAAACATTTACTATATTTAT
20429970 AGTAGTGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (33 bp):
TTTAATACAATAAAACATTTACTATATTTATTT
Found at i:20430969 original size:2 final size:2
Alignment explanation
Indices: 20430962--20430992 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20430952 TTTGTAAGAT
20430962 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 A
20430993 TAACCAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20446723 original size:41 final size:41
Alignment explanation
Indices: 20446678--20446757 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
20446668 CCTAATTGGA
* * *
20446678 AAAATAATTTCCTTATTTTAATAAACTACTAAAAGATAAGG
1 AAAATAATTACATTATTCTAATAAACTACTAAAAGATAAGG
* * *
20446719 AAAATAATTAGATTATTCTGATAGACTACTAAAAGATAA
1 AAAATAATTACATTATTCTAATAAACTACTAAAAGATAA
20446758 AATAAAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.33
Consensus pattern (41 bp):
AAAATAATTACATTATTCTAATAAACTACTAAAAGATAAGG
Found at i:20454772 original size:15 final size:15
Alignment explanation
Indices: 20454750--20454788 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
20454740 CACGACAAAT
20454750 TCCCTCTCCTTATCC
1 TCCCTCTCCTTATCC
* * *
20454765 TTCCTCTCTTTCTCC
1 TCCCTCTCCTTATCC
20454780 TCCCTCTCC
1 TCCCTCTCC
20454789 CTCCTCTCCT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.54, G:0.00, T:0.44
Consensus pattern (15 bp):
TCCCTCTCCTTATCC
Found at i:20459507 original size:17 final size:16
Alignment explanation
Indices: 20459484--20459549 Score: 73
Period size: 17 Copynumber: 4.1 Consensus size: 16
20459474 TTTAGGCAGC
20459484 AAAAGAAGAAAAAGAG
1 AAAAGAAGAAAAAGAG
20459500 ACAAAGAAG-AAAAGA-
1 A-AAAGAAGAAAAAGAG
*
20459515 AGAAGAAGAAAAAGGAG
1 AAAAGAAGAAAAA-GAG
*
20459532 AAAAGAAAAAAATAGAG
1 AAAAGAAGAAAA-AGAG
20459549 A
1 A
20459550 TGCCAACTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
14 6 0.14
15 5 0.12
16 9 0.21
17 21 0.50
18 1 0.02
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAAAAGAG
Found at i:20459541 original size:14 final size:14
Alignment explanation
Indices: 20459489--20459541 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
20459479 GCAGCAAAAG
20459489 AAGAAAAA-GAGACA
1 AAGAAAAAGGAGA-A
*
20459503 AAGAAGAAAAGAAGAA
1 AAG-A-AAAAGGAGAA
20459519 GAAGAAAAAGGAGAA
1 -AAGAAAAAGGAGAA
20459534 AAGAAAAA
1 AAGAAAAA
20459542 AATAGAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 11 0.33
15 10 0.30
16 6 0.18
17 6 0.18
ACGTcount: A:0.74, C:0.02, G:0.25, T:0.00
Consensus pattern (14 bp):
AAGAAAAAGGAGAA
Found at i:20460081 original size:5 final size:5
Alignment explanation
Indices: 20460071--20460109 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
20460061 ACACATTTGT
20460071 ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTT
1 ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTT
20460110 TCTAAATGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTC
Found at i:20460683 original size:21 final size:21
Alignment explanation
Indices: 20460659--20460713 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
20460649 GGCAACCTCC
* *
20460659 TGCTGAGTTAGGGTAGTCTCT
1 TGCTGAGTTAGGGTAGCCTAT
* *
20460680 TGCTGATTTGGGGTAGCCTAT
1 TGCTGAGTTAGGGTAGCCTAT
* *
20460701 TACTAAGTTAGGG
1 TGCTGAGTTAGGG
20460714 CAACCACTTG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.13, G:0.33, T:0.36
Consensus pattern (21 bp):
TGCTGAGTTAGGGTAGCCTAT
Found at i:20463199 original size:5 final size:5
Alignment explanation
Indices: 20463189--20463227 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
20463179 GTTGATAGAG
*
20463189 AAAAT AAAAT AAACA- AAAAT ATAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAA
20463228 AACATTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.03
5 28 0.93
6 1 0.03
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:20468127 original size:45 final size:45
Alignment explanation
Indices: 20468062--20468217 Score: 201
Period size: 45 Copynumber: 3.5 Consensus size: 45
20468052 AGTCAGATAA
* *
20468062 GTTGCTATGTGCTGATTCCACCGGGTACCATTGATTATAAAGGTG
1 GTTGCTATGTGCTGATTCCACCGGATATCATTGATTATAAAGGTG
* * * **
20468107 GTTGCTATGTGCTGACTCCACCAGAAATCATTGAAAATAAAGGTG
1 GTTGCTATGTGCTGATTCCACCGGATATCATTGATTATAAAGGTG
* *
20468152 GTTGCTATGTGCTGATTCCACCGAATATAATTGATTAT-AAGAGTG
1 GTTGCTATGTGCTGATTCCACCGGATATCATTGATTATAAAG-GTG
20468197 GTT-CTATGTGCTGA-TCCACCG
1 GTTGCTATGTGCTGATTCCACCG
20468218 TGTAACGGTT
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
43 7 0.07
44 14 0.15
45 75 0.78
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (45 bp):
GTTGCTATGTGCTGATTCCACCGGATATCATTGATTATAAAGGTG
Found at i:20481465 original size:85 final size:87
Alignment explanation
Indices: 20481345--20481517 Score: 323
Period size: 85 Copynumber: 2.0 Consensus size: 87
20481335 TAAAGCGGTT
*
20481345 TCAAAAACAAGGTATCGAGACCTCGATTTTATAAACTAAACTATAAATTTTTTTATAAATATTTA
1 TCAAAAACAAGGTATCGAGACCTCGATTTTATAAACTAAACTATAAATATTTTTATAAATATTTA
20481410 CGGAGTGTCA-T-AGTTAGTAG
66 CGGAGTGTCATTGAGTTAGTAG
20481430 TCAAAAACAAGGTATCGAGACCTCGATTTTATAAACTAAACTATAAATATTTTTATAAATATTTA
1 TCAAAAACAAGGTATCGAGACCTCGATTTTATAAACTAAACTATAAATATTTTTATAAATATTTA
20481495 CGGAGTGTCATTGAGTTAGTAG
66 CGGAGTGTCATTGAGTTAGTAG
20481517 T
1 T
20481518 AAAGTTTCAT
Statistics
Matches: 85, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
85 74 0.87
86 1 0.01
87 10 0.12
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (87 bp):
TCAAAAACAAGGTATCGAGACCTCGATTTTATAAACTAAACTATAAATATTTTTATAAATATTTA
CGGAGTGTCATTGAGTTAGTAG
Found at i:20482780 original size:105 final size:101
Alignment explanation
Indices: 20482599--20482792 Score: 237
Period size: 105 Copynumber: 1.9 Consensus size: 101
20482589 GACGGATAAG
* * * *
20482599 ACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTTAGCTATGGCATTTTAATGAA
1 ACCATGGTTGAACCATGGCAATATTTAAATGTAAGACCATAGCTGAGCTATGACATTATAATGAA
* *
20482664 AAGATCATAATTGGGTTATGGCACCTTGAATGTAAA
66 AAGACCATAATTGGCTTATGGCACCTTGAATGTAAA
* *
20482700 ACCATGGTTGAACCATGGCAATATATATACATGTGTAAGACCATAGCTGGGCTATGACATTCAT-
1 ACCATGGTTGAACCATGGCAATAT-T-TA-A-ATGTAAGACCATAGCTGAGCTATGACATT-ATA
* * *
20482764 ATGATAATACCGTAATTGGCTTATGGCAC
61 ATGAAAAGACCATAATTGGCTTATGGCAC
20482793 TACAAATGTA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
101 23 0.30
102 1 0.01
103 2 0.03
104 1 0.01
105 49 0.64
106 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (101 bp):
ACCATGGTTGAACCATGGCAATATTTAAATGTAAGACCATAGCTGAGCTATGACATTATAATGAA
AAGACCATAATTGGCTTATGGCACCTTGAATGTAAA
Found at i:20483220 original size:19 final size:20
Alignment explanation
Indices: 20483196--20483247 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
20483186 TCCGGTAGTT
*
20483196 TTTGCAATGTAAAT-TTTGG
1 TTTGCAATGTAAATGGTTGG
*
20483215 TTTGC-ATGTACATGGTTGG
1 TTTGCAATGTAAATGGTTGG
20483234 TTTGGCAATG-AAAT
1 TTT-GCAATGTAAAT
20483248 AGTTTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 7 0.26
19 12 0.44
20 5 0.19
21 3 0.11
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (20 bp):
TTTGCAATGTAAATGGTTGG
Found at i:20494281 original size:37 final size:37
Alignment explanation
Indices: 20494240--20494396 Score: 224
Period size: 37 Copynumber: 4.2 Consensus size: 37
20494230 CAATCACTCG
* * *
20494240 TAAGAGCTAATCCACCCGATAACACGCCAGACGCTCA
1 TAAGAGCTAGTCCACCCGATAACACGCTAGATGCTCA
* *
20494277 TAAGATCTAGTCCACCCGATAACAAGCTAGATGCTCA
1 TAAGAGCTAGTCCACCCGATAACACGCTAGATGCTCA
*
20494314 TAAGAGCTAGTCCACCCGATAACAAGCTAGATGCTCA
1 TAAGAGCTAGTCCACCCGATAACACGCTAGATGCTCA
* * * *
20494351 TAAGAGCTAGTCCACCCAATAGCACGTTAGATGCTTA
1 TAAGAGCTAGTCCACCCGATAACACGCTAGATGCTCA
20494388 TAAGAGCTA
1 TAAGAGCTA
20494397 ATCAAACCGA
Statistics
Matches: 109, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 109 1.00
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (37 bp):
TAAGAGCTAGTCCACCCGATAACACGCTAGATGCTCA
Found at i:20494323 original size:17 final size:17
Alignment explanation
Indices: 20494301--20494360 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
20494291 CCCGATAACA
20494301 AGCTAGATGCTCATAAG
1 AGCTAGATGCTCATAAG
* * *
20494318 AGCTAG-TCCACCCGATAACA
1 AGCTAGAT--GCTC-ATAA-G
20494338 AGCTAGATGCTCATAAG
1 AGCTAGATGCTCATAAG
20494355 AGCTAG
1 AGCTAG
20494361 TCCACCCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 1 0.03
17 12 0.38
18 6 0.19
19 6 0.19
20 6 0.19
21 1 0.03
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (17 bp):
AGCTAGATGCTCATAAG
Found at i:20494343 original size:20 final size:20
Alignment explanation
Indices: 20494283--20494343 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
20494273 CTCATAAGAT
20494283 CTAGTCCACCCGATAACAAG
1 CTAGTCCACCCGATAACAAG
* * *
20494303 CTAGAT--GCTC-ATAA-GAG
1 CTAG-TCCACCCGATAACAAG
20494320 CTAGTCCACCCGATAACAAG
1 CTAGTCCACCCGATAACAAG
20494340 CTAG
1 CTAG
20494344 ATGCTCATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
16 1 0.03
17 6 0.20
18 6 0.20
19 6 0.20
20 10 0.33
21 1 0.03
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.18
Consensus pattern (20 bp):
CTAGTCCACCCGATAACAAG
Found at i:20495166 original size:19 final size:19
Alignment explanation
Indices: 20495139--20495197 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 19
20495129 TCAATGAAAA
*
20495139 CTTCTAGAATTTTTAACAG
1 CTTCAAGAATTTTTAACAG
20495158 CTTCAAGAA-----AA-A-
1 CTTCAAGAATTTTTAACAG
*
20495170 CTTCTAGAATTTTTAACAG
1 CTTCAAGAATTTTTAACAG
20495189 CTTCAAGAA
1 CTTCAAGAA
20495198 CGAAGGTACG
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 2 0.07
17 2 0.07
18 1 0.03
19 16 0.53
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (19 bp):
CTTCAAGAATTTTTAACAG
Found at i:20495171 original size:31 final size:31
Alignment explanation
Indices: 20495135--20495197 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
20495125 TTAATCAATG
20495135 AAAACTTCTAGAATTTTTAACAGCTTCAAGA
1 AAAACTTCTAGAATTTTTAACAGCTTCAAGA
20495166 AAAACTTCTAGAATTTTTAACAGCTTCAAGA
1 AAAACTTCTAGAATTTTTAACAGCTTCAAGA
20495197 A
1 A
20495198 CGAAGGTACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
AAAACTTCTAGAATTTTTAACAGCTTCAAGA
Found at i:20496092 original size:13 final size:13
Alignment explanation
Indices: 20496076--20496100 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20496066 AATCAGACTC
20496076 ATAAATATTTATA
1 ATAAATATTTATA
20496089 ATAAATATTTAT
1 ATAAATATTTAT
20496101 GAAGCTAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAAATATTTATA
Found at i:20498764 original size:15 final size:14
Alignment explanation
Indices: 20498741--20498777 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
20498731 CAAATGGCAG
*
20498741 ACATATTTGAATAC
1 ACATATTTGAATAA
20498755 ACAGTATTTGAATAA
1 ACA-TATTTGAATAA
20498770 ACATATTT
1 ACATATTT
20498778 AAAGTACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (14 bp):
ACATATTTGAATAA
Found at i:20506102 original size:27 final size:28
Alignment explanation
Indices: 20506050--20506113 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
20506040 GTTATATTTG
* *
20506050 TAAAATTTTATAAATAGTTTTAATAAAA
1 TAAAATTTAAGAAATAGTTTTAATAAAA
* *
20506078 TAAAATTTAAGAATATATTTTATAATTAAA
1 TAAAATTTAAGAA-ATAGTTT-TAATAAAA
20506108 TAAAAT
1 TAAAAT
20506114 AAATTTTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 11 0.37
29 6 0.20
30 13 0.43
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (28 bp):
TAAAATTTAAGAAATAGTTTTAATAAAA
Found at i:20508476 original size:18 final size:18
Alignment explanation
Indices: 20508432--20508479 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
20508422 CTTTATATCA
20508432 TTCAGGGATTTTAAATTC
1 TTCAGGGATTTTAAATTC
*
20508450 TTCTGGGATTTTAAA-TC
1 TTCAGGGATTTTAAATTC
*
20508467 TTTCAAGGATTTT
1 -TTCAGGGATTTT
20508480 CATATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (18 bp):
TTCAGGGATTTTAAATTC
Found at i:20512779 original size:104 final size:104
Alignment explanation
Indices: 20512605--20512801 Score: 304
Period size: 104 Copynumber: 1.9 Consensus size: 104
20512595 TTCACACGGG
* *
20512605 CAAGGACATGGGCATGAGTCCAGGTCGTGTAACTCACTGTTTATGATTTAGAATCACACGGCCAG
1 CAAGGACATGGGCATGAGTCCAGGCCGTGTAACTCACTGTTTATGATTTAGAATCACACGGCCAA
* * *
20512670 GGACATAGGCGTGTGCCCAGGCCGTGTGACCCACACAGA
66 CGACATAGGCGTATGCCCAAGCCGTGTGACCCACACAGA
* * *
20512709 CAAGGACATGGGCGTGTGTCCAGGCCGTGTAACTCACTGTTTATGATTTAGAATCACACGGGCAA
1 CAAGGACATGGGCATGAGTCCAGGCCGTGTAACTCACTGTTTATGATTTAGAATCACACGGCCAA
* *
20512774 CGACATGGGCGTATGTCCAAGCCGTGTG
66 CGACATAGGCGTATGCCCAAGCCGTGTG
20512802 GCATTTAAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
104 83 1.00
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (104 bp):
CAAGGACATGGGCATGAGTCCAGGCCGTGTAACTCACTGTTTATGATTTAGAATCACACGGCCAA
CGACATAGGCGTATGCCCAAGCCGTGTGACCCACACAGA
Found at i:20518305 original size:6 final size:6
Alignment explanation
Indices: 20518289--20518368 Score: 51
Period size: 6 Copynumber: 13.8 Consensus size: 6
20518279 TTCTATCGTC
* * *
20518289 CTTTTT C-TTTT CTTTTT C-CTTT CTTATT C-TCTT -TTTTT CTTTCTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT-TT
* * * * *
20518334 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
20518369 ATATTTTTGT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
5 15 0.24
6 42 0.68
7 5 0.08
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:20518330 original size:20 final size:20
Alignment explanation
Indices: 20518301--20518338 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20518291 TTTTCTTTTC
20518301 TTTTTCCTTTCTTATTCTCT
1 TTTTTCCTTTCTTATTCTCT
* *
20518321 TTTTTTCTTTCTTCTTCT
1 TTTTTCCTTTCTTATTCT
20518339 TCTTCTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTCCTTTCTTATTCTCT
Found at i:20518335 original size:3 final size:3
Alignment explanation
Indices: 20518329--20518366 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
20518319 CTTTTTTTCT
20518329 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
20518367 TTATATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:20519228 original size:104 final size:102
Alignment explanation
Indices: 20519075--20519375 Score: 320
Period size: 92 Copynumber: 3.0 Consensus size: 102
20519065 TCCAGGCCTT
* * * * **
20519075 TAACTCACTATTTATGATTTGGAATCACACGGTCAGGGATATGAACGTGTGCCCAGTTCGTGT-A
1 TAACTCACTGTTTATGATTTAGAATCACACGGCCAGGGACATGGGCGTGTGCCCAGTTCGTGTGA
20519139 AGCCAAACGAGAAAGGATATGGGCGTGTGTCCAAGCCGTG
66 A-CCAAACGAG-AAGGA-ATGGGCGTGTGTCCAAGCCGTG
*
20519179 TAACTCACTGTTTATGATTTAGAATAACACGGCCAGGGACATGGGCGTGTGCCCAGGTT-GTGTG
1 TAACTCACTGTTTATGATTTAGAATCACACGGCCAGGGACATGGGCGTGTGCCCA-GTTCGTGTG
*
20519243 AACCACAC--G--GG--T----GTGTGTCCAAGCCGTG
65 AACCAAACGAGAAGGAATGGGCGTGTGTCCAAGCCGTG
* * * ** *
20519271 TAACTCACTGTTTATGATTTAGAATCACACGGGCAAGGACATAGGCGTGTGCCCAGGCCATGTGA
1 TAACTCACTGTTTATGATTTAGAATCACACGGCCAGGGACATGGGCGTGTGCCCAGTTCGTGTGA
* *
20519336 ACCATACGAGCAAGGACATGGGCGTGTGTCCAGGCCGTG
66 ACCAAACGAG-AAGGA-ATGGGCGTGTGTCCAAGCCGTG
20519375 T
1 T
20519376 GGCATCTGAA
Statistics
Matches: 165, Mismatches: 17, Indels: 30
0.78 0.08 0.14
Matches are distributed among these distances:
91 1 0.01
92 78 0.47
94 1 0.01
96 1 0.01
97 2 0.01
99 2 0.01
100 1 0.01
102 1 0.01
104 73 0.44
105 5 0.03
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (102 bp):
TAACTCACTGTTTATGATTTAGAATCACACGGCCAGGGACATGGGCGTGTGCCCAGTTCGTGTGA
ACCAAACGAGAAGGAATGGGCGTGTGTCCAAGCCGTG
Found at i:20519957 original size:23 final size:22
Alignment explanation
Indices: 20519931--20519973 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
20519921 AACTGATATG
20519931 TTCTGT-ATCTGAACTAGAATCGC
1 TTCTGTCATCT-AACT-GAATCGC
20519954 TTCTGTCATCTAACTGAATC
1 TTCTGTCATCTAACTGAATC
20519974 TTGGAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (22 bp):
TTCTGTCATCTAACTGAATCGC
Found at i:20528335 original size:19 final size:21
Alignment explanation
Indices: 20528291--20528340 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
20528281 TCTCTCTCAA
20528291 CAAAAATTACAAAATAATTTT
1 CAAAAATTACAAAATAATTTT
20528312 CAAAAATT-CAAAAT-ATTTAT
1 CAAAAATTACAAAATAATTT-T
*
20528332 AAAAAATTA
1 CAAAAATTA
20528341 AAATTTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.15
20 14 0.54
21 8 0.31
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (21 bp):
CAAAAATTACAAAATAATTTT
Found at i:20528361 original size:65 final size:65
Alignment explanation
Indices: 20528292--20528419 Score: 152
Period size: 65 Copynumber: 2.0 Consensus size: 65
20528282 CTCTCTCAAC
* * * * *
20528292 AAAAATTACAAAATAATTTTCAAAAATTC-AAAATATTTATAAAAAA-TTAAAATTTATATTTTT
1 AAAAATTACAAAAT--TTTTAAAAAAATCTAAAAAATGTATAAAAAAGTTAAAATTTAAATTTTT
20528355 AA
64 AA
* * *
20528357 AAAAATTATAAGATTTTTAAAAAAATCTAAAAAATGTATAAAAAAGTTAAGATTTAAATTTTT
1 AAAAATTACAAAATTTTTAAAAAAATCTAAAAAATGTATAAAAAAGTTAAAATTTAAATTTTT
20528420 TTTCTAAAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
63 11 0.21
64 15 0.28
65 27 0.51
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (65 bp):
AAAAATTACAAAATTTTTAAAAAAATCTAAAAAATGTATAAAAAAGTTAAAATTTAAATTTTTAA
Found at i:20530065 original size:18 final size:19
Alignment explanation
Indices: 20530044--20530087 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
20530034 AAAATTTTGA
*
20530044 GAATTTTTATAA-TATTTT
1 GAATTTTTAAAATTATTTT
*
20530062 GAATTTTAAAAATTATTTT
1 GAATTTTTAAAATTATTTT
20530081 -AATTTTT
1 GAATTTTT
20530088 TTTGTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
GAATTTTTAAAATTATTTT
Found at i:20534167 original size:41 final size:42
Alignment explanation
Indices: 20534081--20534184 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 42
20534071 GGCTTAGCGC
* * * *
20534081 CTAGCAGGCTTATTACCAGTGAAACAATATCAGATTTTACGT
1 CTAGCAGGCTTATTGCCGGTGAAACAATATCAGACTATACGT
* *
20534123 CTAGCAGGCTTATTGCCGGTGAAAC-ATTTCAGACTATATGT
1 CTAGCAGGCTTATTGCCGGTGAAACAATATCAGACTATACGT
* * *
20534164 CTAGAAGGCTAAGTGCCGGTG
1 CTAGCAGGCTTATTGCCGGTG
20534185 TACTGAATCT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 30 0.57
42 23 0.43
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (42 bp):
CTAGCAGGCTTATTGCCGGTGAAACAATATCAGACTATACGT
Found at i:20542528 original size:2 final size:2
Alignment explanation
Indices: 20542523--20542560 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
20542513 ATAAAAAAGT
*
20542523 TA TA TA T- TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20542561 TTAGGTATGC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:20550235 original size:15 final size:15
Alignment explanation
Indices: 20550215--20550244 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20550205 TAAAAAATAC
20550215 TCATTTGGTAACAAT
1 TCATTTGGTAACAAT
20550230 TCATTTGGTAACAAT
1 TCATTTGGTAACAAT
20550245 GTAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
TCATTTGGTAACAAT
Found at i:20557987 original size:17 final size:17
Alignment explanation
Indices: 20557952--20558004 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
20557942 AGCTCACATT
* * *
20557952 TTTTGGTGAGTTTGCAG
1 TTTTGGTGAGCTCGTAG
20557969 TTTTGGTGAGCTCGTAG
1 TTTTGGTGAGCTCGTAG
*
20557986 TTCTGGTGAGCTCGTAG
1 TTTTGGTGAGCTCGTAG
20558003 TT
1 TT
20558005 CACAGTTCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.11, C:0.11, G:0.34, T:0.43
Consensus pattern (17 bp):
TTTTGGTGAGCTCGTAG
Found at i:20560009 original size:16 final size:17
Alignment explanation
Indices: 20559983--20560014 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20559973 CTTCCCTTCA
20559983 ACTGCTTTAGTAGGTAG
1 ACTGCTTTAGTAGGTAG
20560000 ACTG-TTTAGTAGGTA
1 ACTGCTTTAGTAGGTA
20560015 AACAACAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.09, G:0.28, T:0.38
Consensus pattern (17 bp):
ACTGCTTTAGTAGGTAG
Found at i:20565184 original size:43 final size:43
Alignment explanation
Indices: 20565086--20565484 Score: 518
Period size: 43 Copynumber: 9.3 Consensus size: 43
20565076 AGGTTACGTT
* * *
20565086 TTTAGCGGCGTTTCTG-CAAGAAGCGCCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGACAA-AAGCGCCGCTAAAGGTCATGATC
* * *
20565128 TTTCGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATC
* * *
20565171 TTTAGCGCCGTTTGTGACAAAAGCCCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATC
* * *
20565214 TTTAGCGGCATTTGTGACAAAAGCGCCGCTACAGGTCAAGATC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATC
* *
20565257 TTTAGCGGCGTTTGTGACTAAAGCGCC-CTAAAGGTCAAGATC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATC
* * *
20565299 TTTAGCGGTGTTTGTGACAAAAGTGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATC
*
20565342 TTTAGCAGC-TTTGTGACAAAAGCGCCGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATC
*** * * *
20565384 TTTAGCAATGTTTGTGACAAAAGTGCCACTAAAGGTCAAGATC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATC
* *
20565427 TTTAACGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATC
*
20565470 TTTAGCGACGTTTGT
1 TTTAGCGGCGTTTGT
20565485 TCACATTAGC
Statistics
Matches: 312, Mismatches: 41, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
42 106 0.34
43 206 0.66
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATC
Found at i:20565314 original size:128 final size:128
Alignment explanation
Indices: 20565073--20565476 Score: 521
Period size: 128 Copynumber: 3.2 Consensus size: 128
20565063 ATATATTTTT
* * * * * *
20565073 TAAAGGTTACGTT-TTTAGCGGCGTTTCTG-CAAGAAGCGCCGCTAAAGGT-TTGTTCTTTCGCG
1 TAAAGGTCATGTTCTTTAGCGGC-TTTGTGACAA-AAGCGCCGCTAAAGGTCATGATCTTTAGCG
* * * * *
20565135 GCGTTTGTGA-TAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGCCGTTTGTGACAAAAGCCCCG
64 GCGTTTGTGACT-AAAGCGCCACTAAAGGTCAAGATCTTTAGCGGCGTTTGTGACAAAAGCGCCG
20565199 C
128 C
* *
20565200 TAAAGGTCATGTTCTTTAGCGGCATTTGTGACAAAAGCGCCGCTACAGGTCAAGATCTTTAGCGG
1 TAAAGGTCATGTTCTTTAGCGGC-TTTGTGACAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGG
* *
20565265 CGTTTGTGACTAAAGCGCC-CTAAAGGTCAAGATCTTTAGCGGTGTTTGTGACAAAAGTGCCGC
65 CGTTTGTGACTAAAGCGCCACTAAAGGTCAAGATCTTTAGCGGCGTTTGTGACAAAAGCGCCGC
* ***
20565328 TAAAGGTCATGTTCTTTAGCAGCTTTGTGACAAAAGCGCCGCTAAAGGTCATGATCTTTAGCAAT
1 TAAAGGTCATGTTCTTTAGCGGCTTTGTGACAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGC
* * * *
20565393 GTTTGTGACAAAAGTGCCACTAAAGGTCAAGATCTTTAACGGCGTTTGTGATAAAAGCGCCGC
66 GTTTGTGACTAAAGCGCCACTAAAGGTCAAGATCTTTAGCGGCGTTTGTGACAAAAGCGCCGC
*
20565456 TAAAGGTCATGATCTTTAGCG
1 TAAAGGTCATGTTCTTTAGCG
20565477 ACGTTTGTTC
Statistics
Matches: 243, Mismatches: 29, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
127 64 0.26
128 148 0.61
129 30 0.12
130 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (128 bp):
TAAAGGTCATGTTCTTTAGCGGCTTTGTGACAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGC
GTTTGTGACTAAAGCGCCACTAAAGGTCAAGATCTTTAGCGGCGTTTGTGACAAAAGCGCCGC
Found at i:20565335 original size:85 final size:86
Alignment explanation
Indices: 20565086--20565484 Score: 518
Period size: 85 Copynumber: 4.7 Consensus size: 86
20565076 AGGTTACGTT
* * * * *
20565086 TTTAGCGGCGTTTCTG-CAAGAAGCGCCGCTAAAGGT-TTGTTCTTTCGCGGCGTTTGTGATAAA
1 TTTAGCGGCGTTTGTGACAA-AAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGACAAA
* *
20565149 AGCGCCGCTAAAGGTCATGTTC
65 AGCGCCGCTAAAGGTCAAGATC
* * * *
20565171 TTTAGCGCCGTTTGTGACAAAAGCCCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGACAAAA
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGACAAAA
*
20565236 GCGCCGCTACAGGTCAAGATC
66 GCGCCGCTAAAGGTCAAGATC
* * *
20565257 TTTAGCGGCGTTTGTGACTAAAGCGCC-CTAAAGGTCAAGATCTTTAGCGGTGTTTGTGACAAAA
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGACAAAA
* * *
20565321 GTGCCGCTAAAGGTCATGTTC
66 GCGCCGCTAAAGGTCAAGATC
* ***
20565342 TTTAGCAGC-TTTGTGACAAAAGCGCCGCTAAAGGTCATGATCTTTAGCAATGTTTGTGACAAAA
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGACAAAA
* *
20565406 GTGCCACTAAAGGTCAAGATC
66 GCGCCGCTAAAGGTCAAGATC
* * *
20565427 TTTAACGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGACGTTTGT
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGT
20565485 TCACATTAGC
Statistics
Matches: 276, Mismatches: 34, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
84 16 0.06
85 146 0.53
86 114 0.41
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGACAAAA
GCGCCGCTAAAGGTCAAGATC
Found at i:20566940 original size:17 final size:17
Alignment explanation
Indices: 20566914--20566959 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
20566904 AGCTCACATT
20566914 TTTTGGTGAGCTCGTAG
1 TTTTGGTGAGCTCGTAG
*
20566931 TTTTGATGAGCTCGTAG
1 TTTTGGTGAGCTCGTAG
*
20566948 TTCTGGTGAGCT
1 TTTTGGTGAGCT
20566960 TGCAATTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.13, C:0.13, G:0.33, T:0.41
Consensus pattern (17 bp):
TTTTGGTGAGCTCGTAG
Found at i:20583792 original size:22 final size:22
Alignment explanation
Indices: 20583764--20583815 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
20583754 GTTAATCTAC
*
20583764 CTCGAGACATTGG-AAATTGTGT
1 CTCGAGAC-TTGGTAAATTATGT
**
20583786 CTCGAGACTTGGTCCATTATGT
1 CTCGAGACTTGGTAAATTATGT
20583808 CTCGAGAC
1 CTCGAGAC
20583816 CAACCTCCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (22 bp):
CTCGAGACTTGGTAAATTATGT
Found at i:20584570 original size:19 final size:19
Alignment explanation
Indices: 20584548--20584585 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20584538 TGCATTAAGA
20584548 ATAAAAAAAACAATTATAT
1 ATAAAAAAAACAATTATAT
* *
20584567 ATAAAAATATCAATTATAT
1 ATAAAAAAAACAATTATAT
20584586 TAATGTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAAAAAAAACAATTATAT
Found at i:20593063 original size:16 final size:16
Alignment explanation
Indices: 20593042--20593074 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20593032 TTAATTGTTT
20593042 TAATCTAGTTAATTTA
1 TAATCTAGTTAATTTA
20593058 TAATCTAGTTAATTTA
1 TAATCTAGTTAATTTA
20593074 T
1 T
20593075 TGACAAGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (16 bp):
TAATCTAGTTAATTTA
Found at i:20596525 original size:22 final size:22
Alignment explanation
Indices: 20596463--20596544 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
20596453 TCATCCTATA
*
20596463 AAAGGGCTCTCATACGTCCCCT
1 AAAGGGCTCTCATACGTCCCAT
* * * * *
20596485 GAGGGGTTCTCAAATGTCCCAT
1 AAAGGGCTCTCATACGTCCCAT
* *
20596507 AAAGGGCTCTTATACGTCCCGCAG
1 AAAGGGCTCTCATACGT-CC-CAT
*
20596531 AAGGGGCTCTCATA
1 AAAGGGCTCTCATA
20596545 TACAGGTGTG
Statistics
Matches: 43, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
22 27 0.63
23 2 0.05
24 14 0.33
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.23
Consensus pattern (22 bp):
AAAGGGCTCTCATACGTCCCAT
Found at i:20597830 original size:100 final size:99
Alignment explanation
Indices: 20597657--20597857 Score: 375
Period size: 100 Copynumber: 2.0 Consensus size: 99
20597647 CCAACCTGCC
*
20597657 ACTTATCTTTAATTACAAAAAGAACTTACCAGAATAGAAAACTTTTCAATTTAATCCGCAATTCT
1 ACTTATCTTTAATTACAAAAAGAACTTACCAGAATAGAAAAATTTTCAATTTAATCCGCAATTCT
20597722 CCTTTGCAACATACGACTTAACAAATATGGGTGCA
66 CCTTTGCAA-ATACGACTTAACAAATATGGGTGCA
*
20597757 ACTTATCTTTAATTACAAAAAGAACTTACCAGAATAGAAAAATTTTCAATTTAATCTGCAATTCT
1 ACTTATCTTTAATTACAAAAAGAACTTACCAGAATAGAAAAATTTTCAATTTAATCCGCAATTCT
20597822 CCTTTGCAAATACGACTTAACAAATATGGGTGCA
66 CCTTTGCAAATACGACTTAACAAATATGGGTGCA
20597856 AC
1 AC
20597858 AATATCTACA
Statistics
Matches: 99, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
99 27 0.27
100 72 0.73
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (99 bp):
ACTTATCTTTAATTACAAAAAGAACTTACCAGAATAGAAAAATTTTCAATTTAATCCGCAATTCT
CCTTTGCAAATACGACTTAACAAATATGGGTGCA
Found at i:20617110 original size:22 final size:22
Alignment explanation
Indices: 20617062--20617111 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
20617052 CAATAACAAT
* *
20617062 AAAATAGTAGCAATATAATAGC
1 AAAATAGTAGCAATACAACAGC
*
20617084 GAAATAGTAGCAA-AGCAACAGC
1 AAAATAGTAGCAATA-CAACAGC
20617106 AAAATA
1 AAAATA
20617112 ACTTATTTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (22 bp):
AAAATAGTAGCAATACAACAGC
Found at i:20620472 original size:22 final size:21
Alignment explanation
Indices: 20620442--20620482 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
20620432 GATATGATAA
*
20620442 TTTTATTTATGTTATTTTTAAT
1 TTTTATTTAT-TCATTTTTAAT
*
20620464 TTTTGTTTATTCATTTTTA
1 TTTTATTTATTCATTTTTA
20620483 TTGGTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTTATTTATTCATTTTTAAT
Found at i:20628409 original size:54 final size:54
Alignment explanation
Indices: 20628307--20628476 Score: 196
Period size: 54 Copynumber: 3.1 Consensus size: 54
20628297 CAAGTCAGTC
* * * * * *
20628307 AGTTACATGGCCTAACACACGGCTTGATACATGGGCGTGTGTGACAACTTAGTG
1 AGTTACACGACCTAGCACACGGCTTGACACACGGGCGTGTGTGGCAACTTAGTG
* * *
20628361 AGGTACACGACCTAGCACACGGTTTGACACACAGGCGTGTGTGGCAACTTAGTG
1 AGTTACACGACCTAGCACACGGCTTGACACACGGGCGTGTGTGGCAACTTAGTG
* * *** * *
20628415 AGTTAGACGACCTAGCACATGGCCCAACACACGGGCATGAGTGGCAACTTAGTG
1 AGTTACACGACCTAGCACACGGCTTGACACACGGGCGTGTGTGGCAACTTAGTG
20628469 AGTTACAC
1 AGTTACAC
20628477 AGGTGAGGAC
Statistics
Matches: 96, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (54 bp):
AGTTACACGACCTAGCACACGGCTTGACACACGGGCGTGTGTGGCAACTTAGTG
Found at i:20630201 original size:72 final size:73
Alignment explanation
Indices: 20630113--20630249 Score: 195
Period size: 74 Copynumber: 1.9 Consensus size: 73
20630103 AATTAGTTAT
* * *
20630113 ATATCACAATTTCCATTTCATAAACTCAATG-ATAAGTCATTTCATATACATGCCTTTTCAATCC
1 ATATCACAATTCCCATTTCATAAACTCAATGAATAACTCATTTCATATACATACCTTTTCAATCC
20630177 CTTTACAC
66 CTTTACAC
* * * *
20630185 ATATTACAATTCCCATTTCGTAAGCTCAATGACATAACTCATTTCATATACATACTTTTTCAATC
1 ATATCACAATTCCCATTTCATAAACTCAATGA-ATAACTCATTTCATATACATACCTTTTCAATC
20630250 AAGCTCATTA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 27 0.48
74 29 0.52
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (73 bp):
ATATCACAATTCCCATTTCATAAACTCAATGAATAACTCATTTCATATACATACCTTTTCAATCC
CTTTACAC
Found at i:20644348 original size:31 final size:31
Alignment explanation
Indices: 20644281--20644350 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
20644271 TATATGAAGA
*
20644281 ATGATAGATCATGGAAAATAAAAAATTGTTC
1 ATGATCGATCATGGAAAATAAAAAATTGTTC
20644312 ATGATCGATCATGGAAAATAAAAAATTGTTC
1 ATGATCGATCATGGAAAATAAAAAATTGTTC
20644343 ATGATCGA
1 ATGATCGA
20644351 GATGAGTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.29
Consensus pattern (31 bp):
ATGATCGATCATGGAAAATAAAAAATTGTTC
Found at i:20645298 original size:18 final size:18
Alignment explanation
Indices: 20645275--20645309 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20645265 TTTGTTATAT
*
20645275 TTTTTTATTATTCATTTA
1 TTTTTTATTATTAATTTA
20645293 TTTTTTATTATTAATTT
1 TTTTTTATTATTAATTT
20645310 TAGCTGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTATTATTAATTTA
Found at i:20645300 original size:15 final size:15
Alignment explanation
Indices: 20645263--20645311 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
20645253 CTTGCTTTAA
*
20645263 ATTTTGTTA-TATTT
1 ATTTTATTATTATTT
20645277 -TTTTATTATTCATTT
1 ATTTTATTATT-ATTT
*
20645292 ATTTT-TTATTATTA
1 ATTTTATTATTATTT
20645306 ATTTTA
1 ATTTTA
20645312 GCTGTGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 7 0.24
14 9 0.31
15 9 0.31
16 4 0.14
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
ATTTTATTATTATTT
Found at i:20649080 original size:43 final size:43
Alignment explanation
Indices: 20648915--20649146 Score: 168
Period size: 42 Copynumber: 5.5 Consensus size: 43
20648905 ATTGATTCAA
* * *
20648915 TTTATCCGATGATGCACT-TATGTGTCAGTATAATTTCTTTGG
1 TTTATCCGATGATGCACTATATGTGCCAATATAATTGCTTTGG
* * * * * *
20648957 TATATCTGATGATGCA-TTTACGTGCCAATATATTTGCTTTAG
1 TTTATCCGATGATGCACTATATGTGCCAATATAATTGCTTTGG
** ** * * *
20648999 TACATCTAATGATGCA-TTTATGTGCCAACATGATTGCTTTGG
1 TTTATCCGATGATGCACTATATGTGCCAATATAATTGCTTTGG
* * * *
20649041 TTTATCCGATGATGCACTATGTGTGCTAGTATAATTGCTTCGG
1 TTTATCCGATGATGCACTATATGTGCCAATATAATTGCTTTGG
** * *
20649084 TTCGTCCGATGATACAACTTATATGT--TAATATAATTGCTTTGG
1 TTTATCCGATGATGC-AC-TATATGTGCCAATATAATTGCTTTGG
* **
20649127 CTTGCCCGATGATGCACTAT
1 TTTATCCGATGATGCACTAT
20649147 GGGTGCCAGT
Statistics
Matches: 150, Mismatches: 36, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
41 4 0.03
42 81 0.54
43 57 0.38
44 2 0.01
45 6 0.04
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (43 bp):
TTTATCCGATGATGCACTATATGTGCCAATATAATTGCTTTGG
Found at i:20658704 original size:7 final size:7
Alignment explanation
Indices: 20658692--20658736 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
20658682 TTTAAAAATA
20658692 AATTTAT
1 AATTTAT
20658699 AATTTAT
1 AATTTAT
20658706 AATTTAT
1 AATTTAT
20658713 AATTTAT
1 AATTTAT
20658720 AATTTAT
1 AATTTAT
20658727 AATTT-T
1 AATTTAT
20658733 AATT
1 AATT
20658737 GAAAGTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.13
7 33 0.87
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTAT
Found at i:20658773 original size:17 final size:17
Alignment explanation
Indices: 20658751--20658785 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20658741 GTAAAATTAT
*
20658751 TTTAAATTTGTCTTGCA
1 TTTAAATTTGACTTGCA
20658768 TTTAAATTTGACTTGCA
1 TTTAAATTTGACTTGCA
20658785 T
1 T
20658786 GTATTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.51
Consensus pattern (17 bp):
TTTAAATTTGACTTGCA
Found at i:20660097 original size:47 final size:47
Alignment explanation
Indices: 20659963--20660100 Score: 170
Period size: 47 Copynumber: 2.9 Consensus size: 47
20659953 AAAAAAAAAA
* * * *
20659963 TTGACTGGTTATAGTTTTAAATAAAGAAAAT-GAGAGAGGAAAAACTT
1 TTGACTGGTTATAGTTTCAAACAGAGAAAATGGA-AGAAGAAAAACTT
* * * *
20660010 TTGACTGGTTATAGTTTCAAACAGAGGAAACGGGACAAGAAAAACTT
1 TTGACTGGTTATAGTTTCAAACAGAGAAAATGGAAGAAGAAAAACTT
* *
20660057 TTGACTAGTTATAGTTTGAAACAGAGAAAATGGAAGAAGAAAAA
1 TTGACTGGTTATAGTTTCAAACAGAGAAAATGGAAGAAGAAAAA
20660101 AGGGTGTTAG
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
47 75 0.99
48 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.22, T:0.25
Consensus pattern (47 bp):
TTGACTGGTTATAGTTTCAAACAGAGAAAATGGAAGAAGAAAAACTT
Found at i:20663004 original size:14 final size:14
Alignment explanation
Indices: 20662985--20663011 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20662975 AACTACCATC
20662985 CTAGACAATCTTCT
1 CTAGACAATCTTCT
20662999 CTAGACAATCTTC
1 CTAGACAATCTTC
20663012 ATAGTCAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (14 bp):
CTAGACAATCTTCT
Found at i:20669801 original size:18 final size:18
Alignment explanation
Indices: 20669780--20669818 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
20669770 CTTACCCATA
20669780 AATGTCCACTAACCCTTT
1 AATGTCCACTAACCCTTT
*
20669798 AATGTCCAGTAACCCTTT
1 AATGTCCACTAACCCTTT
20669816 AAT
1 AAT
20669819 TGGTCTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (18 bp):
AATGTCCACTAACCCTTT
Found at i:20677927 original size:28 final size:28
Alignment explanation
Indices: 20677885--20677945 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
20677875 ATACAGATAC
20677885 CATAACCTAAAGCTTGTGTGAA-CCATTT
1 CATAACCTAAAGCTTGTGT-AAGCCATTT
*
20677913 CATAACCTAAGGCTTGTGTAAGCCATTT
1 CATAACCTAAAGCTTGTGTAAGCCATTT
20677941 CATAA
1 CATAA
20677946 ATAAAAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (28 bp):
CATAACCTAAAGCTTGTGTAAGCCATTT
Found at i:20683056 original size:25 final size:26
Alignment explanation
Indices: 20683014--20683066 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
20683004 ACTCATTTCC
20683014 TCTCATCATTCACTAACCTCTTATTT
1 TCTCATCATTCACTAACCTCTTATTT
*
20683040 TCTC-TCATTCA-TAAACCTTTTATTT
1 TCTCATCATTCACT-AACCTCTTATTT
20683065 TC
1 TC
20683067 CCCTTCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 1 0.04
25 20 0.80
26 4 0.16
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (26 bp):
TCTCATCATTCACTAACCTCTTATTT
Found at i:20684202 original size:15 final size:16
Alignment explanation
Indices: 20684182--20684218 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
20684172 TCTTATTTAA
20684182 TTATTTTTTTAT-TCT
1 TTATTTTTTTATGTCT
20684197 TTA-TTTTTTATGTCT
1 TTATTTTTTTATGTCT
*
20684212 TTCTTTT
1 TTATTTT
20684219 CAGGTCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 8 0.42
15 8 0.42
16 3 0.16
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (16 bp):
TTATTTTTTTATGTCT
Found at i:20684205 original size:14 final size:15
Alignment explanation
Indices: 20684186--20684218 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20684176 ATTTAATTAT
20684186 TTTTTTAT-TCTTTA
1 TTTTTTATGTCTTTA
*
20684200 TTTTTTATGTCTTTC
1 TTTTTTATGTCTTTA
20684215 TTTT
1 TTTT
20684219 CAGGTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTTTATGTCTTTA
Found at i:20686584 original size:12 final size:12
Alignment explanation
Indices: 20686567--20686617 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
20686557 ACTTAATCAC
20686567 TTTAATATTAAA
1 TTTAATATTAAA
*
20686579 TTTAAT-CTAATA
1 TTTAATATTAA-A
*
20686591 TTTATTAGATTAAA
1 TTTA--ATATTAAA
20686605 TTTAATATTAAA
1 TTTAATATTAAA
20686617 T
1 T
20686618 CTTATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
11 3 0.10
12 19 0.61
14 6 0.19
15 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:20686596 original size:21 final size:21
Alignment explanation
Indices: 20686572--20686613 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20686562 ATCACTTTAA
*
20686572 TATTAAATTTAATCTAATATT
1 TATTAAATTAAATCTAATATT
* *
20686593 TATTAGATTAAATTTAATATT
1 TATTAAATTAAATCTAATATT
20686614 AAATCTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTAAATTAAATCTAATATT
Found at i:20693510 original size:12 final size:12
Alignment explanation
Indices: 20693493--20693522 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20693483 TTAGGCTGTT
*
20693493 ACACGGCTTAGC
1 ACACGGCCTAGC
20693505 ACACGGCCTAGC
1 ACACGGCCTAGC
20693517 ACACGG
1 ACACGG
20693523 GCGTGTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.37, G:0.27, T:0.10
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:20705568 original size:28 final size:28
Alignment explanation
Indices: 20705528--20705587 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
20705518 TTGTTTGATT
* *
20705528 GAAAATGGTTTCCAAAAAATGATTTCTA
1 GAAAATAGTTTCCAAAAAATAATTTCTA
* *
20705556 GAAAATAGTTTCCGAAAAATAATTTCTG
1 GAAAATAGTTTCCAAAAAATAATTTCTA
20705584 GAAA
1 GAAA
20705588 GTGGCTTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (28 bp):
GAAAATAGTTTCCAAAAAATAATTTCTA
Found at i:20715084 original size:16 final size:16
Alignment explanation
Indices: 20715063--20715112 Score: 100
Period size: 16 Copynumber: 3.1 Consensus size: 16
20715053 TGGTTCGCTA
20715063 TATTGGATTAGAGGTG
1 TATTGGATTAGAGGTG
20715079 TATTGGATTAGAGGTG
1 TATTGGATTAGAGGTG
20715095 TATTGGATTAGAGGTG
1 TATTGGATTAGAGGTG
20715111 TA
1 TA
20715113 ATAGCTAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (16 bp):
TATTGGATTAGAGGTG
Found at i:20715177 original size:44 final size:45
Alignment explanation
Indices: 20715093--20715183 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
20715083 GGATTAGAGG
* * *
20715093 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
20715138 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
20715182 TG
1 TG
20715184 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:20718702 original size:76 final size:76
Alignment explanation
Indices: 20718576--20719446 Score: 1733
Period size: 76 Copynumber: 11.5 Consensus size: 76
20718566 TAACATTTTC
20718576 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
20718641 GAACTGCAGAA
66 GAACTGCAGAA
20718652 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
20718717 GAACTGCAGAA
66 GAACTGCAGAA
20718728 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
20718793 GAACTGCAGAA
66 GAACTGCAGAA
20718804 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
20718869 GAACTGCAGAA
66 GAACTGCAGAA
20718880 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
20718945 GAACTGCAGAA
66 GAACTGCAGAA
20718956 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
20719021 GAACTGCAGAA
66 GAACTGCAGAA
20719032 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
20719097 GAACTGCAGAA
66 GAACTGCAGAA
20719108 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
20719173 GAACTGCAGAA
66 GAACTGCAGAA
20719184 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
20719249 GAACTGCAGAA
66 GAACTGCAGAA
20719260 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
20719325 GAACTGCAGAA
66 GAACTGCAGAA
20719336 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
20719401 GAACTGCAGAA
66 GAACTGCAGAA
*
20719412 ATCTTACCTATTTTTGCTACTTTCAGATGACCAAA
1 ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAA
20719447 AGAACTCAAT
Statistics
Matches: 794, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 794 1.00
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (76 bp):
ATCTTACCTATTTTTGCTACTTTCAGAGGACCAAATTACAACAGAACAAACAAACAAAAGAACTC
GAACTGCAGAA
Found at i:20727380 original size:13 final size:13
Alignment explanation
Indices: 20727364--20727392 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
20727354 TATGAGCTTA
20727364 AATCATGATCAAT
1 AATCATGATCAAT
20727377 AATCATGATCAAT
1 AATCATGATCAAT
20727390 AAT
1 AAT
20727393 ACGCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (13 bp):
AATCATGATCAAT
Found at i:20728456 original size:84 final size:84
Alignment explanation
Indices: 20728345--20728897 Score: 910
Period size: 84 Copynumber: 6.6 Consensus size: 84
20728335 CAAAGGACCC
*
20728345 CGGTGGAATCAGCACTTTA-CAACCACCTTATAATCAATGATACGGGGAATCAGTACATAGCAAC
1 CGGTGGAATCAGCAC-TTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAAC
20728409 CCCTTTCACAATCAAGGATA
65 CCCTTTCACAATCAAGGATA
* * *
20728429 CAGTGGAATCAGCACTTAGCAAGCACCTTATAATCAATGATACGTGGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
* *
20728494 CCTTTTACAGTCAAGGATA
66 CCTTTCACAATCAAGGATA
* *
20728513 CGGTGGAATCAACACTTAGCAACCACCTTATAATCAATGATACGGGGAATTAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
*
20728578 CCTTTCACAGTCAAGGATA
66 CCTTTCACAATCAAGGATA
* * * *
20728597 CGGTGGAATCAGCACTTAGTAACCACCTTAAAATCAATGATACAGGGAATCAGCACATAACAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
20728662 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* *
20728681 CAGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAACCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
*
20728746 CATTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* *
20728765 CGGTGGAATCAGCCCTTAGCAACCACCTTATAATCAATGATACAGGGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
20728830 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* *
20728849 CGGTGGAATCAACACTTAGAAACCACCTTATAATCAATGATACGGGGAA
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAA
20728898 NNNNNNNNNN
Statistics
Matches: 433, Mismatches: 35, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
83 3 0.01
84 430 0.99
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
CCTTTCACAATCAAGGATA
Found at i:20731683 original size:30 final size:30
Alignment explanation
Indices: 20731649--20731711 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
20731639 TCTTAGCAAT
*
20731649 AAATTTTG-GAGGTATCTAATTAAAATTTCA
1 AAATTTTGAG-GGTATCTAATGAAAATTTCA
* * *
20731679 AAATTTTTAGGGTGTTTAATGAAAATTTCA
1 AAATTTTGAGGGTATCTAATGAAAATTTCA
20731709 AAA
1 AAA
20731712 AATATTGGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (30 bp):
AAATTTTGAGGGTATCTAATGAAAATTTCA
Found at i:20732046 original size:31 final size:31
Alignment explanation
Indices: 20732000--20732071 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
20731990 AATTTGATGC
* * *
20732000 AATTATACACGTGAAACTCTAATTGTTGTTT
1 AATTATATACTTGAAACTCTAATTGTTATTT
* * *
20732031 AATTGTATACTTGAAACTTTAATTTTTATTT
1 AATTATATACTTGAAACTCTAATTGTTATTT
20732062 AATTATATAC
1 AATTATATAC
20732072 AATTAGAGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (31 bp):
AATTATATACTTGAAACTCTAATTGTTATTT
Found at i:20732241 original size:29 final size:30
Alignment explanation
Indices: 20732198--20732254 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
20732188 GAATTTGATC
20732198 AAATCAAAATCTCATGTATAAAATTGCACA
1 AAATCAAAATCTCATGTATAAAATTGCACA
* *
20732228 AAATCAAAGT-TCATGTATACAATTGCA
1 AAATCAAAATCTCATGTATAAAATTGCA
20732255 TATTAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (30 bp):
AAATCAAAATCTCATGTATAAAATTGCACA
Done.