Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397269.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.1, whole genome shotgun sequence
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: 5666189
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 144833 characters in sequence are not A, C, G, or T
File 10 of 14
Found at i:3824838 original size:7 final size:7
Alignment explanation
Indices: 3824826--3824854 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3824816 ATTGGTACAA
3824826 GCAGCAG
1 GCAGCAG
3824833 GCAGCAG
1 GCAGCAG
3824840 GCAGCAG
1 GCAGCAG
3824847 GCAGCAG
1 GCAGCAG
3824854 G
1 G
3824855 GTAAATGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.45, T:0.00
Consensus pattern (7 bp):
GCAGCAG
Found at i:3839409 original size:33 final size:32
Alignment explanation
Indices: 3839372--3839469 Score: 133
Period size: 33 Copynumber: 3.0 Consensus size: 32
3839362 AGATAGTTGT
*
3839372 ATAGGTTCTGCTTGATCCTTTAAAAGGCAAGTG
1 ATAGGTTCTGCTTGATCC-TTAAAAAGCAAGTG
*
3839405 ATAGGTTCTGCTTGATCCTTAAAAAAACAAGTG
1 ATAGGTTCTGCTTGATCCTT-AAAAAGCAAGTG
* * *
3839438 ATAGATTCTGTTTGATCCTTGAAAAGCAAGTG
1 ATAGGTTCTGCTTGATCCTTAAAAAGCAAGTG
3839470 TAACGATTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
32 12 0.21
33 46 0.79
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (32 bp):
ATAGGTTCTGCTTGATCCTTAAAAAGCAAGTG
Found at i:3842994 original size:35 final size:34
Alignment explanation
Indices: 3842915--3843004 Score: 108
Period size: 35 Copynumber: 2.6 Consensus size: 34
3842905 TCTACTGGTT
* *
3842915 ATATAATTAATCATCCTACATAAACTTACTAGCA
1 ATATAATTAATCATCTTACATAAACCTACTAGCA
* * *
3842949 ATAAAATTAATCATCTTTCATAAAACCTACTAGGA
1 ATATAATTAATCATCTTACAT-AAACCTACTAGCA
* *
3842984 ATATAGTTAATTATCTTACAT
1 ATATAATTAATCATCTTACAT
3843005 TATGGTTCCT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
34 18 0.39
35 28 0.61
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (34 bp):
ATATAATTAATCATCTTACATAAACCTACTAGCA
Found at i:3848601 original size:17 final size:17
Alignment explanation
Indices: 3848579--3848615 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3848569 ATTTAAGGAT
3848579 TGCTCCCCGTAAATATA
1 TGCTCCCCGTAAATATA
* *
3848596 TGCTCCCCTTTAATATA
1 TGCTCCCCGTAAATATA
3848613 TGC
1 TGC
3848616 ATTGAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.30, G:0.11, T:0.35
Consensus pattern (17 bp):
TGCTCCCCGTAAATATA
Found at i:3853472 original size:21 final size:22
Alignment explanation
Indices: 3853446--3853491 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3853436 TTGAGTAGTT
*
3853446 AATTTAAT-TTATTTTA-ATTA
1 AATTTTATGTTATTTTATATTA
*
3853466 AATTTTATGTTATTTTATTTTA
1 AATTTTATGTTATTTTATATTA
3853488 AATT
1 AATT
3853492 ACTTTAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 8 0.36
22 7 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
AATTTTATGTTATTTTATATTA
Found at i:3865833 original size:13 final size:13
Alignment explanation
Indices: 3865815--3865842 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3865805 TAAATGAGTG
3865815 ATTAATTTATTGA
1 ATTAATTTATTGA
3865828 ATTAATTTATTGA
1 ATTAATTTATTGA
3865841 AT
1 AT
3865843 AACTTAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (13 bp):
ATTAATTTATTGA
Found at i:3872498 original size:32 final size:32
Alignment explanation
Indices: 3872457--3872518 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
3872447 AACATTTGTG
3872457 TTTTTATTTTAAGTCAAATAAATTCTTATATT
1 TTTTTATTTTAAGTCAAATAAATTCTTATATT
* *
3872489 TTTTTATTTTGAGTCAAATAAATTTTTATA
1 TTTTTATTTTAAGTCAAATAAATTCTTATA
3872519 ATTAAAACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (32 bp):
TTTTTATTTTAAGTCAAATAAATTCTTATATT
Found at i:3872602 original size:21 final size:21
Alignment explanation
Indices: 3872576--3872618 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3872566 ATATGTATGA
*
3872576 TATAATAT-ATTAATTTGATAT
1 TATAATATGATT-ATATGATAT
3872597 TATAATATGATTATATGATAT
1 TATAATATGATTATATGATAT
3872618 T
1 T
3872619 TTTTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
TATAATATGATTATATGATAT
Found at i:3874634 original size:2 final size:2
Alignment explanation
Indices: 3874629--3874654 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3874619 CAAAGTGTTC
3874629 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
3874655 TACAATTAAT
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:3877394 original size:22 final size:22
Alignment explanation
Indices: 3877369--3877420 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
3877359 TGATCCAATT
*
3877369 TTAGGCACTACGTGACCCCTTA
1 TTAGGCACTACGTGACCCCATA
* *
3877391 TTAGGCATTGCGTGACCCCATA
1 TTAGGCACTACGTGACCCCATA
3877413 TTAGGCAC
1 TTAGGCAC
3877421 GTTACTTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (22 bp):
TTAGGCACTACGTGACCCCATA
Found at i:3882587 original size:22 final size:23
Alignment explanation
Indices: 3882561--3882612 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
3882551 GGTTACGATT
3882561 CTTAATAAT-CAGTCATGCAATG
1 CTTAATAATCCAGTCATGCAATG
*
3882583 CTTAAT-ATCCAGTGATGCAATG
1 CTTAATAATCCAGTCATGCAATG
3882605 CTTAATAA
1 CTTAATAA
3882613 ATATTCACGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 2 0.07
22 24 0.89
23 1 0.04
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (23 bp):
CTTAATAATCCAGTCATGCAATG
Found at i:3882832 original size:36 final size:37
Alignment explanation
Indices: 3882785--3882865 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
3882775 ATGGTGAGAA
* **
3882785 AGTTATATGGT-GATATAGA-CTTCGATGTTGTTGGAG
1 AGTTAGATGGTAGATATAGACCTT-GATGGCGTTGGAG
3882821 AGTTAGATGGTGAGATATAGACCTTGATGGCGTTGGAG
1 AGTTAGATGGT-AGATATAGACCTTGATGGCGTTGGAG
*
3882859 AGCTAGA
1 AGTTAGA
3882866 CTGGATGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 10 0.26
38 25 0.66
39 3 0.08
ACGTcount: A:0.27, C:0.07, G:0.33, T:0.32
Consensus pattern (37 bp):
AGTTAGATGGTAGATATAGACCTTGATGGCGTTGGAG
Found at i:3884929 original size:4 final size:4
Alignment explanation
Indices: 3884920--3884957 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
3884910 AATTTACCCT
* *
3884920 TACA TACA TACA TGCA TACA TGCA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
3884958 TATATGTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:3890577 original size:22 final size:22
Alignment explanation
Indices: 3890552--3890594 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3890542 CATGAGTTGT
3890552 GCATTGCGTGACTTGTTTGTAA
1 GCATTGCGTGACTTGTTTGTAA
*
3890574 GCATTGTGTGACTTGTTTGTA
1 GCATTGCGTGACTTGTTTGTA
3890595 GTAATTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.44
Consensus pattern (22 bp):
GCATTGCGTGACTTGTTTGTAA
Found at i:3890601 original size:22 final size:22
Alignment explanation
Indices: 3890554--3890609 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
3890544 TGAGTTGTGC
* *
3890554 ATTGCGTGACTTGTTTGTAAGC
1 ATTGTGTGACTTGTTTGTAAGA
3890576 ATTGTGTGACTTGTTTGT-AGTA
1 ATTGTGTGACTTGTTTGTAAG-A
*
3890598 ATTGTGTTACTT
1 ATTGTGTGACTT
3890610 TATCTACTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.18, C:0.09, G:0.25, T:0.48
Consensus pattern (22 bp):
ATTGTGTGACTTGTTTGTAAGA
Found at i:3893954 original size:35 final size:35
Alignment explanation
Indices: 3893909--3894051 Score: 142
Period size: 35 Copynumber: 4.0 Consensus size: 35
3893899 CCTTAAAAAA
*
3893909 CCCAATTAACTTAATTATTTAATTTAATCAATTAGG
1 CCCAA-TAACTTAATTAATTAATTTAATCAATTAGG
* ** *
3893945 CCCAATAACTTGATTAAACAAATTTAATCGATTAGG
1 CCCAATAACTTAATT-AATTAATTTAATCAATTAGG
* ** * *
3893981 CTCAATAACTTAATTGTTTAATTTAATTAATTAGC
1 CCCAATAACTTAATTAATTAATTTAATCAATTAGG
* ** *
3894016 CCCAATGACTTAATTAAACAATTTAATGAATTAGG
1 CCCAATAACTTAATTAATTAATTTAATCAATTAGG
3894051 C
1 C
3894052 ACAACTTAAT
Statistics
Matches: 84, Mismatches: 22, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
35 50 0.60
36 34 0.40
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (35 bp):
CCCAATAACTTAATTAATTAATTTAATCAATTAGG
Found at i:3893969 original size:36 final size:36
Alignment explanation
Indices: 3893929--3894078 Score: 148
Period size: 35 Copynumber: 4.3 Consensus size: 36
3893919 TTAATTATTT
*
3893929 AATTTAATCAATTAGGCCCAATAACTTGATTAAACA
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACA
* * ****
3893965 AATTTAATCGATTAGGCTCAATAACTTAATT-GTTT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACA
* * *
3894000 AATTTAATTAATTAGCCCCAATGACTTAATTAAAC-
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACA
* *
3894035 AATTTAATGAATTAGG--C-ACAACTTAATTAAACA
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACA
*
3894068 ATTTTAATCAA
1 AATTTAATCAA
3894079 GTGCTTGAGA
Statistics
Matches: 91, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
32 13 0.14
33 10 0.11
35 40 0.44
36 28 0.31
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (36 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAACA
Found at i:3894001 original size:71 final size:70
Alignment explanation
Indices: 3893915--3894051 Score: 204
Period size: 71 Copynumber: 1.9 Consensus size: 70
3893905 AAAACCCAAT
* *
3893915 TAACTTAATTATTTAATTTAATCAATTAGGCCCAATAACTTGATTAAACAAATTTAATCG-ATTA
1 TAACTTAATTATTTAATTTAATCAATTAGCCCCAATAACTTAATTAAAC-AATTTAAT-GAATTA
3893979 GGCTCAA
64 GGCTCAA
* * *
3893986 TAACTTAATTGTTTAATTTAATTAATTAGCCCCAATGACTTAATTAAACAATTTAATGAATTAGG
1 TAACTTAATTATTTAATTTAATCAATTAGCCCCAATAACTTAATTAAACAATTTAATGAATTAGG
3894051 C
66 C
3894052 ACAACTTAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
69 1 0.02
70 15 0.25
71 44 0.73
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (70 bp):
TAACTTAATTATTTAATTTAATCAATTAGCCCCAATAACTTAATTAAACAATTTAATGAATTAGG
CTCAA
Found at i:3897712 original size:16 final size:17
Alignment explanation
Indices: 3897691--3897724 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3897681 GCTCCCTGTA
*
3897691 TCTCTCCTGC-CTTTCT
1 TCTCTCCGGCGCTTTCT
3897707 TCTCTCCGGCGCTTTCT
1 TCTCTCCGGCGCTTTCT
3897724 T
1 T
3897725 AACAACTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.00, C:0.41, G:0.12, T:0.47
Consensus pattern (17 bp):
TCTCTCCGGCGCTTTCT
Found at i:3897968 original size:30 final size:30
Alignment explanation
Indices: 3897932--3897993 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
3897922 GCTGATGCAC
**
3897932 ACCTAGCTCTATGTTTACTCTAAGCAAATG
1 ACCTAGCTCTACATTTACTCTAAGCAAATG
*
3897962 ACCTAGCTCTACATTTACTTTAAGCAAATG
1 ACCTAGCTCTACATTTACTCTAAGCAAATG
3897992 AC
1 AC
3897994 TTATTTGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.32
Consensus pattern (30 bp):
ACCTAGCTCTACATTTACTCTAAGCAAATG
Found at i:3904476 original size:9 final size:9
Alignment explanation
Indices: 3904464--3904510 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
3904454 TCCATCGTCT
3904464 TCATCTTCA
1 TCATCTTCA
*
3904473 TCATCATCA
1 TCATCTTCA
*
3904482 TCATATTCA
1 TCATCTTCA
*
3904491 TCATCTGCA
1 TCATCTTCA
3904500 TTC-TCTTCA
1 -TCATCTTCA
3904509 TC
1 TC
3904511 TACAACCTGC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
8 2 0.06
9 27 0.87
10 2 0.06
ACGTcount: A:0.23, C:0.32, G:0.02, T:0.43
Consensus pattern (9 bp):
TCATCTTCA
Found at i:3909923 original size:33 final size:33
Alignment explanation
Indices: 3909886--3909950 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
3909876 GCATACTATG
* *
3909886 TCATCATCCATAATGACATGTTAACATACCACA
1 TCATCATCCATAATAACATATTAACATACCACA
* **
3909919 TCATCATCTATTGTAACATATTAACATACCAC
1 TCATCATCCATAATAACATATTAACATACCAC
3909951 GTCAGCTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (33 bp):
TCATCATCCATAATAACATATTAACATACCACA
Found at i:3910424 original size:22 final size:23
Alignment explanation
Indices: 3910377--3910440 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
3910367 ATTATCTAAT
**
3910377 TATTCATAACTTAATATTAATTA
1 TATTCATTTCTTAATATTAATTA
*
3910400 TATT-ATTTCTTAATGTT-ATTGA
1 TATTCATTTCTTAATATTAATT-A
**
3910422 TATTCATTTAATAATATTA
1 TATTCATTTCTTAATATTA
3910441 TCTAACTAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 3 0.09
22 15 0.47
23 14 0.44
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (23 bp):
TATTCATTTCTTAATATTAATTA
Found at i:3910608 original size:16 final size:15
Alignment explanation
Indices: 3910583--3910621 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 15
3910573 TATTGAATAT
3910583 TTTAATTATTTAATAAA
1 TTTAA-TATTTAA-AAA
3910600 TTTAATATTTAAAAA
1 TTTAATATTTAAAAA
3910615 TATTAAT
1 T-TTAAT
3910622 TATGATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTAATATTTAAAAA
Found at i:3911556 original size:10 final size:10
Alignment explanation
Indices: 3911541--3911573 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3911531 ATGTCACATC
3911541 AACATAGCAA
1 AACATAGCAA
3911551 AACATAGCAA
1 AACATAGCAA
3911561 AACAT--CAA
1 AACATAGCAA
3911569 AACAT
1 AACAT
3911574 CATATCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
10 15 0.65
ACGTcount: A:0.61, C:0.21, G:0.06, T:0.12
Consensus pattern (10 bp):
AACATAGCAA
Found at i:3921759 original size:35 final size:35
Alignment explanation
Indices: 3921720--3921940 Score: 214
Period size: 35 Copynumber: 6.3 Consensus size: 35
3921710 TTAATCATTT
*
3921720 AATTTAACCAATTAAGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAAGCCCAATAACTTAATTAAAC
* * * *
3921755 AATTTAATTATTTAAGCCCAACAATTTAATTAAAC
1 AATTTAATCAATTAAGCCCAATAACTTAATTAAAC
* * *
3921790 AATTTTAATCAATTAGGCCCAATGACTTAATGAAAC
1 AA-TTTAATCAATTAAGCCCAATAACTTAATTAAAC
* * *
3921826 AAATTTAATCAATTAAGCCTAATGACTTAATTAAAT
1 -AATTTAATCAATTAAGCCCAATAACTTAATTAAAC
* ** * * *
3921862 AATTTAATTAATTGGGCTCAATGACTTAATTAAAT
1 AATTTAATCAATTAAGCCCAATAACTTAATTAAAC
* * *
3921897 AATTTAATTAATT-AG-GC-ACAACTTAATTAAAC
1 AATTTAATCAATTAAGCCCAATAACTTAATTAAAC
3921929 AATTTTAATCAA
1 AA-TTTAATCAA
3921941 GTGCTTAAGA
Statistics
Matches: 156, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
32 14 0.09
33 9 0.06
34 1 0.01
35 75 0.48
36 55 0.35
37 2 0.01
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (35 bp):
AATTTAATCAATTAAGCCCAATAACTTAATTAAAC
Found at i:3921803 original size:71 final size:71
Alignment explanation
Indices: 3921722--3921940 Score: 257
Period size: 71 Copynumber: 3.1 Consensus size: 71
3921712 AATCATTTAA
* * * * *
3921722 TTTAACCAATTAAGCCCAATAACTTAATTAAACAATTTAATTATTTAAGCCCAACAATTTAATTA
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAATTA
3921787 AACAAT
66 AACAAT
* * * **
3921793 TTTAATCAATTAGGCCCAATGACTTAATGAAACAAATTTAATCAATTAAGCCTAATGACTTAATT
1 TTTAATCAATTAGGCCCAATGACTTAATTAAAC-AATTTAATTAATTAAGCCCAACAACTTAATT
*
3921858 AAATAA-
65 AAACAAT
* * * * *
3921864 TTTAATTAATTGGGCTCAATGACTTAATTAAATAATTTAATTAATT-AG-GC-ACAACTTAATTA
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAATTA
3921926 AACAAT
66 AACAAT
3921932 TTTAATCAA
1 TTTAATCAA
3921941 GTGCTTAAGA
Statistics
Matches: 123, Mismatches: 23, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
67 14 0.11
68 8 0.07
69 2 0.02
70 12 0.10
71 57 0.46
72 30 0.24
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (71 bp):
TTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAATTA
AACAAT
Found at i:3921949 original size:107 final size:106
Alignment explanation
Indices: 3921720--3921940 Score: 268
Period size: 107 Copynumber: 2.1 Consensus size: 106
3921710 TTAATCATTT
* * *
3921720 AATTTAACCAATTAAGCCCAATAACTTAATTAAACAATTTAATTATTTAAGCCCAACAATTTAAT
1 AATTTAATCAATTAAGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAAT
*
3921785 TAAACAATTTTAATCAATTAGGCCCAATGACTTAATGAAACA
66 TAAACAATTTTAATCAATTAGGCACAA-GACTTAATGAAACA
* * * ** * **
3921827 AATTTAATCAATTAAGCCTAATGACTTAATTAAATAATTTAATTAATTGGGCTCAATGACTTAAT
1 AATTTAATCAATTAAGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAAT
* * *
3921892 TAAATAA-TTTAATTAATTAGGCAC-A-ACTTAATTAAACA
66 TAAACAATTTTAATCAATTAGGCACAAGACTTAATGAAACA
*
3921930 ATTTTAATCAA
1 AATTTAATCAA
3921941 GTGCTTAAGA
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
103 22 0.22
105 1 0.01
106 15 0.15
107 60 0.61
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (106 bp):
AATTTAATCAATTAAGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAAT
TAAACAATTTTAATCAATTAGGCACAAGACTTAATGAAACA
Found at i:3930589 original size:46 final size:46
Alignment explanation
Indices: 3930522--3930614 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
3930512 TAAGCACCGT
*
3930522 CTAAACTGAATAGGGAGCAAAAAAAAAGTGTTAAGAATCAAGTCAG
1 CTAAACTCAATAGGGAGCAAAAAAAAAGTGTTAAGAATCAAGTCAG
*
3930568 CTAAACTCAATAGGGAGCAAAAAAAAGGTGTTAAGAATCAAGTCAG
1 CTAAACTCAATAGGGAGCAAAAAAAAAGTGTTAAGAATCAAGTCAG
3930614 C
1 C
3930615 ATCTCAGTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.48, C:0.13, G:0.22, T:0.17
Consensus pattern (46 bp):
CTAAACTCAATAGGGAGCAAAAAAAAAGTGTTAAGAATCAAGTCAG
Found at i:3945217 original size:21 final size:21
Alignment explanation
Indices: 3945169--3945236 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
3945159 GGATATGTTC
3945169 ATGCAGTTCATGACAAAGACTA
1 ATGCA-TTCATGACAAAGACTA
** *
3945191 GCGCATTCATAACAAAGACTA
1 ATGCATTCATGACAAAGACTA
* * *
3945212 ATGCATTTATGATAAGGACTA
1 ATGCATTCATGACAAAGACTA
3945233 ATGC
1 ATGC
3945237 CTCCATTCAA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 34 0.92
22 3 0.08
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (21 bp):
ATGCATTCATGACAAAGACTA
Found at i:3947185 original size:45 final size:45
Alignment explanation
Indices: 3947076--3947185 Score: 121
Period size: 45 Copynumber: 2.4 Consensus size: 45
3947066 AAAACCTTTT
3947076 TCTTTATTTATTTTATTTTTAGTTATTTATTTATTTCTACATTAA
1 TCTTTATTTATTTTATTTTTAGTTATTTATTTATTTCTACATTAA
**********
3947121 TCNNNNNNNNNNTTATTTTTAGTTATTTATTTATTTCTACATTAA
1 TCTTTATTTATTTTATTTTTAGTTATTTATTTATTTCTACATTAA
*
3947166 TCTTTATTTATTTTCTTTTT
1 TCTTTATTTATTTTATTTTT
3947186 GTAGTAAAAA
Statistics
Matches: 44, Mismatches: 21, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.62
Consensus pattern (45 bp):
TCTTTATTTATTTTATTTTTAGTTATTTATTTATTTCTACATTAA
Found at i:3954937 original size:48 final size:47
Alignment explanation
Indices: 3954784--3954968 Score: 208
Period size: 49 Copynumber: 3.8 Consensus size: 47
3954774 ACGTGGGTTG
* **
3954784 ACAAATTACATAAATTTAAAAGCCCAATATCTGTTTATTCTAGCTTAA
1 ACAAATCACATAAATAGAAAAGCCCAATATCTGTTTATTCTA-CTTAA
* * * * * **
3954832 ATAAATCATATAAATAGAATAAAACCCAACATCTGTTTATTTTACCCAA
1 ACAAATCACATAAATAG-A-AAAGCCCAATATCTGTTTATTCTACTTAA
* *
3954881 ACAAATCACATAAATAGAAAAGCACAATATTTGTTTATTCTGACTTAA
1 ACAAATCACATAAATAGAAAAGCCCAATATCTGTTTATTCT-ACTTAA
*
3954929 ACAAATCACATAAATAGAATAAGCCCAATATTTGTTTATT
1 ACAAATCACATAAATAGAA-AAGCCCAATATCTGTTTATT
3954969 TTTATATCAA
Statistics
Matches: 113, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
47 18 0.16
48 36 0.32
49 38 0.34
50 21 0.19
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (47 bp):
ACAAATCACATAAATAGAAAAGCCCAATATCTGTTTATTCTACTTAA
Found at i:3954972 original size:97 final size:97
Alignment explanation
Indices: 3954784--3954970 Score: 261
Period size: 97 Copynumber: 1.9 Consensus size: 97
3954774 ACGTGGGTTG
* ** * * *
3954784 ACAAATTACATAAATTTAAAAGCCCAATATCTGTTTATTCTAGCTTAAATAAATCATATAAATAG
1 ACAAATCACATAAATAGAAAAGCACAATATCTGTTTATTCTAGCTTAAACAAATCACATAAATAG
3954849 AATAAAACCCAACATCTGTTTATTTTACCCAA
66 AATAAAACCCAACATCTGTTTATTTTACCCAA
*
3954881 ACAAATCACATAAATAGAAAAGCACAATATTTGTTTATTCT-GACTTAAACAAATCACATAAATA
1 ACAAATCACATAAATAGAAAAGCACAATATCTGTTTATTCTAG-CTTAAACAAATCACATAAATA
* * *
3954945 GAAT-AAGCCCAATATTTGTTTATTTT
65 GAATAAAACCCAACATCTGTTTATTTT
3954971 TATATCAAGA
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
96 20 0.25
97 59 0.75
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.33
Consensus pattern (97 bp):
ACAAATCACATAAATAGAAAAGCACAATATCTGTTTATTCTAGCTTAAACAAATCACATAAATAG
AATAAAACCCAACATCTGTTTATTTTACCCAA
Found at i:3955959 original size:41 final size:41
Alignment explanation
Indices: 3955902--3955981 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
3955892 TGGATTTTTA
3955902 AAAAAAGATTCTTATTATCTTTTTACAAAAACTAAAATATC
1 AAAAAAGATTCTTATTATCTTTTTACAAAAACTAAAATATC
3955943 AAAAAAGATTCTTATTATCTTTTTACAAAAACTAAAATA
1 AAAAAAGATTCTTATTATCTTTTTACAAAAACTAAAATA
3955982 AAATTTTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.36
Consensus pattern (41 bp):
AAAAAAGATTCTTATTATCTTTTTACAAAAACTAAAATATC
Found at i:3959689 original size:17 final size:17
Alignment explanation
Indices: 3959667--3959699 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3959657 TACTACTAGC
3959667 AATAATA-TACACAAAGG
1 AATAATACTACA-AAAGG
3959684 AATAATACTACAAAAG
1 AATAATACTACAAAAG
3959700 AAAGGCTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.61, C:0.12, G:0.09, T:0.18
Consensus pattern (17 bp):
AATAATACTACAAAAGG
Found at i:3963845 original size:16 final size:16
Alignment explanation
Indices: 3963824--3963854 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3963814 CCAACAAATG
*
3963824 CAAATGTAATTCAAAA
1 CAAATGAAATTCAAAA
3963840 CAAATGAAATTCAAA
1 CAAATGAAATTCAAA
3963855 TTCATACCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (16 bp):
CAAATGAAATTCAAAA
Found at i:3965026 original size:17 final size:18
Alignment explanation
Indices: 3965001--3965034 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3964991 GATTATTTCA
3965001 TTCCATCC-TATTCTTTG
1 TTCCATCCTTATTCTTTG
*
3965018 TTCCTTCCTTATTCTTT
1 TTCCATCCTTATTCTTT
3965035 TGTTTAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.09, C:0.29, G:0.03, T:0.59
Consensus pattern (18 bp):
TTCCATCCTTATTCTTTG
Found at i:3967469 original size:16 final size:16
Alignment explanation
Indices: 3967448--3967479 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3967438 CTCAAGATAA
3967448 TGTTAAAAGGAAAACT
1 TGTTAAAAGGAAAACT
3967464 TGTTAAAAGGAAAACT
1 TGTTAAAAGGAAAACT
3967480 CCTTAACGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (16 bp):
TGTTAAAAGGAAAACT
Found at i:3967485 original size:16 final size:16
Alignment explanation
Indices: 3967450--3967485 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3967440 CAAGATAATG
**
3967450 TTAAAAGGAAAACTTG
1 TTAAAAGGAAAACTCC
3967466 TTAAAAGGAAAACTCC
1 TTAAAAGGAAAACTCC
3967482 TTAA
1 TTAA
3967486 CGTAGTAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (16 bp):
TTAAAAGGAAAACTCC
Found at i:3980461 original size:50 final size:50
Alignment explanation
Indices: 3980399--3980498 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
3980389 TTTATAAAGC
* * * *
3980399 ATCTTTAAAAGATAAAAGGGAAAAATATTGAAACAAATTTTGTTCAAGAT
1 ATCTCTAAAAGATAAAAAGAAAAAATATCGAAACAAATTTTGTTCAAGAT
3980449 ATCTCTAAAAGATAAAAAGAAAAAATATCGAAACAAATTTTGTTCAAGAT
1 ATCTCTAAAAGATAAAAAGAAAAAATATCGAAACAAATTTTGTTCAAGAT
3980499 GATAGCCAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (50 bp):
ATCTCTAAAAGATAAAAAGAAAAAATATCGAAACAAATTTTGTTCAAGAT
Found at i:3980661 original size:32 final size:32
Alignment explanation
Indices: 3980623--3980712 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
3980613 TTGGTTGATG
*
3980623 TGTTTTGATATAACTCTATTAGGAAGTTGGTA
1 TGTTTTGATATAACTCTATTAAGAAGTTGGTA
* *
3980655 TGTTTTGCTATAACTCTATTAAGAAGTTGGTG
1 TGTTTTGATATAACTCTATTAAGAAGTTGGTA
* * *
3980687 TGTGTT-AGTATAAGTTTATTAAGAAG
1 TGTTTTGA-TATAACTCTATTAAGAAG
3980713 ATTTTTTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (32 bp):
TGTTTTGATATAACTCTATTAAGAAGTTGGTA
Found at i:3983675 original size:28 final size:28
Alignment explanation
Indices: 3983643--3983786 Score: 96
Period size: 29 Copynumber: 4.9 Consensus size: 28
3983633 TTGCAACTTT
3983643 AACATGTTTGTCTTAATTTAAACAAAAA
1 AACATGTTTGTCTTAATTTAAACAAAAA
*
3983671 AACATGTTTGGTTTTAATTTAGATA-AGAAAA
1 AACATGTTT-GTCTTAATTTA-A-ACA-AAAA
* * * * * *
3983702 AATATTTTTTGTCTTAATCTAGATAAGAA
1 AACA-TGTTTGTCTTAATTTAAACAAAAA
*
3983731 AACATATTTGTCTCT-ATTTAAACAAGATAA
1 AACATGTTTGTCT-TAATTTAAACAA-A-AA
* *
3983761 AATAT-TTTGTCTTAATTAAAGACAAA
1 AACATGTTTGTCTTAATTTAA-ACAAA
3983787 TGTTGTCTTA
Statistics
Matches: 90, Mismatches: 15, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
28 25 0.28
29 31 0.34
30 13 0.14
31 17 0.19
32 4 0.04
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAAACAAAAA
Found at i:3983719 original size:31 final size:31
Alignment explanation
Indices: 3983649--3983739 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
3983639 CTTTAACATG
* *
3983649 TTTGTCTTAATTTA-A-ACA-AAAAAACATGT
1 TTTGTCTTAATTTAGATA-AGAAAAAATATTT
* *
3983678 TTGGTTTTAATTTAGATAAGAAAAAATATTT
1 TTTGTCTTAATTTAGATAAGAAAAAATATTT
* *
3983709 TTTGTCTTAATCTAGATAAGAAAACATATTT
1 TTTGTCTTAATTTAGATAAGAAAAAATATTT
3983740 GTCTCTATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 12 0.24
30 2 0.04
31 37 0.73
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
TTTGTCTTAATTTAGATAAGAAAAAATATTT
Found at i:3986860 original size:84 final size:84
Alignment explanation
Indices: 3986757--3986918 Score: 254
Period size: 84 Copynumber: 1.9 Consensus size: 84
3986747 GCAAATTGGA
*
3986757 AAAAAGATTAAAAAAATATTGCACAATTCAATGAACAACAAAAC-ATAAAAAAGAAAATATTGCC
1 AAAAAGATTAAAAAAATATTGCACAATCCAATGAACAAC-AAACTATAAAAAAGAAAATATTGCC
3986821 TAAAATTCGAAGCAGAGGGT
65 TAAAATTCGAAGCAGAGGGT
** * * *
3986841 AAAAAGATTAAAATCATATTGTACAATCCAATGAACAACAAACTATAAAAAAGAAGATATTGTCT
1 AAAAAGATTAAAAAAATATTGCACAATCCAATGAACAACAAACTATAAAAAAGAAAATATTGCCT
3986906 AAAATTCGAAGCA
66 AAAATTCGAAGCA
3986919 TATTGTTAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
83 4 0.06
84 67 0.94
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (84 bp):
AAAAAGATTAAAAAAATATTGCACAATCCAATGAACAACAAACTATAAAAAAGAAAATATTGCCT
AAAATTCGAAGCAGAGGGT
Found at i:3990419 original size:29 final size:29
Alignment explanation
Indices: 3990375--3990466 Score: 130
Period size: 29 Copynumber: 3.2 Consensus size: 29
3990365 TTGTTTTTTC
*
3990375 CTTTTTCTCTTATACCTGTTCACGTATAG
1 CTTTTTCTCTTGTACCTGTTCACGTATAG
* * *
3990404 CTTTTTCTCTTGTACCTATTCATGTACAG
1 CTTTTTCTCTTGTACCTGTTCACGTATAG
**
3990433 CTTCCTCTCTTGTACCTGTTCACGTATAG
1 CTTTTTCTCTTGTACCTGTTCACGTATAG
3990462 CTTTT
1 CTTTT
3990467 CTTTATTAGC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.15, C:0.26, G:0.11, T:0.48
Consensus pattern (29 bp):
CTTTTTCTCTTGTACCTGTTCACGTATAG
Found at i:3996684 original size:58 final size:58
Alignment explanation
Indices: 3996609--3996722 Score: 201
Period size: 58 Copynumber: 2.0 Consensus size: 58
3996599 GTGATTGCAA
3996609 GCAGCATGATGAATGTGGTAACTAAATACTTTCTAGTAATGTTTTCAAGGGCTCAGAG
1 GCAGCATGATGAATGTGGTAACTAAATACTTTCTAGTAATGTTTTCAAGGGCTCAGAG
* * *
3996667 GCAGTATGATGAATGTGGTAACTAGATGCTTTCTAGTAATGTTTTCAAGGGCTCAG
1 GCAGCATGATGAATGTGGTAACTAAATACTTTCTAGTAATGTTTTCAAGGGCTCAG
3996723 GGAGAAGGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (58 bp):
GCAGCATGATGAATGTGGTAACTAAATACTTTCTAGTAATGTTTTCAAGGGCTCAGAG
Found at i:3997205 original size:22 final size:22
Alignment explanation
Indices: 3997143--3997216 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
3997133 ACTGCATGAC
* *
3997143 TGGTTTTTAGGTATTATGTGAT
1 TGGTTTTTAGGCATTACGTGAT
* * *
3997165 T-GATTCTAAGCATTACGTGAT
1 TGGTTTTTAGGCATTACGTGAT
*
3997186 TGGTTTTTAGGCATTGCGTGAT
1 TGGTTTTTAGGCATTACGTGAT
*
3997208 TGATTTTTA
1 TGGTTTTTA
3997217 AGTAATGCCT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 16 0.39
22 25 0.61
ACGTcount: A:0.20, C:0.07, G:0.24, T:0.49
Consensus pattern (22 bp):
TGGTTTTTAGGCATTACGTGAT
Found at i:3997299 original size:22 final size:23
Alignment explanation
Indices: 3997228--3997307 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
3997218 GTAATGCCTA
* *
3997228 AGTCACACAATGGCTTACTAACT
1 AGTCACGCAATAGCTTACTAACT
* * *
3997251 AGTTACGCAATAGCTTATTAACA
1 AGTCACGCAATAGCTTACTAACT
*
3997274 AGTCACGCAAT-GCTTACCAACT
1 AGTCACGCAATAGCTTACTAACT
*
3997296 AGTCACGTAATA
1 AGTCACGCAATA
3997308 CCTAATAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
22 18 0.39
23 28 0.61
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (23 bp):
AGTCACGCAATAGCTTACTAACT
Found at i:3997349 original size:21 final size:22
Alignment explanation
Indices: 3997316--3997373 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
3997306 TACCTAATAA
**
3997316 TAAGTCATGTAATGCT-CAAAG
1 TAAGTCACATAATGCTACAAAG
*
3997337 TCAGTCACATAATG-TACAAAG
1 TAAGTCACATAATGCTACAAAG
*
3997358 TAAGTCACGTAATGCT
1 TAAGTCACATAATGCT
3997374 TAAAAATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (22 bp):
TAAGTCACATAATGCTACAAAG
Found at i:3997622 original size:60 final size:60
Alignment explanation
Indices: 3997504--3997624 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
3997494 CTTAACAAAG
* * *
3997504 AATACTCAAAATGTTCAAAAGTTTTTCTTCATATATCAAAAATCATTCCAAATACTTAAA
1 AATACTCAAAACGTTCAAAAGTTTTTCTTCATATATCAAAAATCACTCAAAATACTTAAA
* * *
3997564 AATACTCAAAACGCTT-AAAAG-TTTTCTTCGTATATCAAAAATTACTCTAAAATGCTTAAA
1 AATACTCAAAACG-TTCAAAAGTTTTTCTTCATATATCAAAAATCACTC-AAAATACTTAAA
3997624 A
1 A
3997625 CGCTTTAACG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 23 0.43
60 28 0.53
61 2 0.04
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.34
Consensus pattern (60 bp):
AATACTCAAAACGTTCAAAAGTTTTTCTTCATATATCAAAAATCACTCAAAATACTTAAA
Found at i:4006202 original size:34 final size:34
Alignment explanation
Indices: 4006159--4006227 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
4006149 AATACATATA
4006159 TAAATAATGATAAACTTGTCAGTTGTGATTTTAT
1 TAAATAATGATAAACTTGTCAGTTGTGATTTTAT
4006193 TAAATAATGATAAACTTGTCAGTTGTGATTTTAT
1 TAAATAATGATAAACTTGTCAGTTGTGATTTTAT
4006227 T
1 T
4006228 GAAGTAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (34 bp):
TAAATAATGATAAACTTGTCAGTTGTGATTTTAT
Found at i:4006527 original size:103 final size:103
Alignment explanation
Indices: 4006408--4006616 Score: 337
Period size: 103 Copynumber: 2.0 Consensus size: 103
4006398 TATTATTTGA
* * **
4006408 GCAAGTGACCTGTATAAATGTTGCATAAGGATTTGAAGAATTTTTACACCTAATTCCATTGATGG
1 GCAAGTGACCTATATAAATGTTGCAGAAGGATTTGAAGAACGTTTACACCTAATTCCATTGATGG
* *
4006473 CTGAGGTTATCAAGTAAAGAAAACAATAAAAATTCTCT
66 CTCAGGTTATCAAGCAAAGAAAACAATAAAAATTCTCT
* **
4006511 GCAAGTGACCTATATAAATGTTGCAGAAGGTTTTGAAGAACGTTTATGCCTAATTCCATTGATGG
1 GCAAGTGACCTATATAAATGTTGCAGAAGGATTTGAAGAACGTTTACACCTAATTCCATTGATGG
4006576 CTCAGGTTATCAAGCAAAGAAAACAATAAAAATTCTCT
66 CTCAGGTTATCAAGCAAAGAAAACAATAAAAATTCTCT
4006614 GCA
1 GCA
4006617 TCATTTTTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (103 bp):
GCAAGTGACCTATATAAATGTTGCAGAAGGATTTGAAGAACGTTTACACCTAATTCCATTGATGG
CTCAGGTTATCAAGCAAAGAAAACAATAAAAATTCTCT
Found at i:4026522 original size:35 final size:35
Alignment explanation
Indices: 4026457--4026533 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
4026447 AGACGTTGCA
**
4026457 CCTGATCCTACAAAAGGCTAGTTGTGAAGGTTACG
1 CCTGATCCTACAAAAGGCTAGTTGCAAAGGTTACG
* * *
4026492 CTTGATCCTGCAAAAGGC-ATGTTGCAAAGGTTATG
1 CCTGATCCTACAAAAGGCTA-GTTGCAAAGGTTACG
4026527 CCTGATC
1 CCTGATC
4026534 ATATTGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (35 bp):
CCTGATCCTACAAAAGGCTAGTTGCAAAGGTTACG
Found at i:4034991 original size:30 final size:31
Alignment explanation
Indices: 4034907--4034982 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
4034897 ATTTATAATG
* * *
4034907 TCCACAATAGCTAAACAAGATATA--CAATA
1 TCCACAATAACTAAGCAAGATATATTGAATA
4034936 TCCACAATAACTAAGCAAGATATATTGAATA
1 TCCACAATAACTAAGCAAGATATATTGAATA
*
4034967 TCCATAATAAC-AAGCA
1 TCCACAATAACTAAGCA
4034983 CATAATATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 22 0.54
30 5 0.12
31 14 0.34
ACGTcount: A:0.50, C:0.20, G:0.08, T:0.22
Consensus pattern (31 bp):
TCCACAATAACTAAGCAAGATATATTGAATA
Found at i:4035996 original size:19 final size:19
Alignment explanation
Indices: 4035972--4036013 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4035962 GAGAGGAGAC
* * *
4035972 AATTTTAAAGCTTGATTCT
1 AATTTTAAACCTAGATACT
4035991 AATTTTAAACCTAGATACT
1 AATTTTAAACCTAGATACT
4036010 AATT
1 AATT
4036014 GTGAGAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (19 bp):
AATTTTAAACCTAGATACT
Found at i:4039080 original size:68 final size:67
Alignment explanation
Indices: 4038986--4039279 Score: 270
Period size: 68 Copynumber: 4.3 Consensus size: 67
4038976 GATGAATGCC
* * * * *
4038986 ATAAGATTATGTATATGATGTAAATTCCATATACTATATGAGATGATCAAGTATGCACGGTGTAT
1 ATAAGATTATGTATATGATGTATATTCCATATACTACATGAGATGATTAAGTATGCATGAT-TAT
4039051 ACT
65 ACT
* * * **
4039054 ATAAAATTGTGTATATGATGTGA-ATTCCATATACCATTTGAGGA-GATTAAGTATGCATGATTA
1 ATAAGATTATGTATATGATGT-ATATTCCATATACTACATGA-GATGATTAAGTATGCATGATTA
*
4039117 -ATGT
64 TA-CT
* * * *
4039121 CATGAGATTATGTATATGATTTATATTCCATATACTACGTGAGATGATTAAGTATGCATGCTTAA
1 -ATAAGATTATGTATATGATGTATATTCCATATACTACATGAGATGATTAAGTATGCATGATT-A
* *
4039186 TGCC
64 TACT
* * * * * *
4039190 ATGAGATTATGTGTATGATGTATATTCCATATACTACATGAGATGATTGAGCAAGCATGATAAAT
1 ATAAGATTATGTATATGATGTATATTCCATATACTACATGAGATGATTAAGTATGCATGAT-TAT
* *
4039255 GCC
65 ACT
*
4039258 ATGAGATTATGTATATGATGTA
1 ATAAGATTATGTATATGATGTA
4039280 AAGTCTATAT
Statistics
Matches: 189, Mismatches: 28, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
66 1 0.01
67 6 0.03
68 178 0.94
69 4 0.02
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (67 bp):
ATAAGATTATGTATATGATGTATATTCCATATACTACATGAGATGATTAAGTATGCATGATTATA
CT
Found at i:4039218 original size:136 final size:136
Alignment explanation
Indices: 4038974--4039281 Score: 361
Period size: 136 Copynumber: 2.3 Consensus size: 136
4038964 CATGTTTGGT
* * *
4038974 ATGATGAATGCCATAAGATTATGTATATGATGTAAATTCCATATACTATATGAGATGATCAAGTA
1 ATGATAAATGCCATGAGATTATGTATATGATGTAAATTCCATATACTACATGAGATGATCAAGTA
* * * **
4039039 TGCACGGTGTATACTATAAAATTGTGTATATGATGTGAATTCCATATACCATTTGAGGA-GATTA
66 TGCACGCTGTATACCATAAAATTATGTATATGATGTGAATTCCATATACCACATGA-GATGATTA
* *
4039103 AGTATGC
130 AGCAAGC
* * * * * *
4039110 ATGATTAATGTCATGAGATTATGTATATGATTTATATTCCATATACTACGTGAGATGATTAAGTA
1 ATGATAAATGCCATGAGATTATGTATATGATGTAAATTCCATATACTACATGAGATGATCAAGTA
* * * * * *
4039175 TGCATGCT-TAATGCCATGAGATTATGTGTATGATGT-ATATTCCATATACTACATGAGATGATT
66 TGCACGCTGT-ATACCATAAAATTATGTATATGATGTGA-ATTCCATATACCACATGAGATGATT
*
4039238 GAGCAAGC
129 AAGCAAGC
4039246 ATGATAAATGCCATGAGATTATGTATATGATGTAAA
1 ATGATAAATGCCATGAGATTATGTATATGATGTAAA
4039282 GTCTATATGT
Statistics
Matches: 143, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
135 4 0.03
136 139 0.97
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (136 bp):
ATGATAAATGCCATGAGATTATGTATATGATGTAAATTCCATATACTACATGAGATGATCAAGTA
TGCACGCTGTATACCATAAAATTATGTATATGATGTGAATTCCATATACCACATGAGATGATTAA
GCAAGC
Found at i:4039415 original size:18 final size:19
Alignment explanation
Indices: 4039389--4039436 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
4039379 GTGATAAGTA
* *
4039389 AAAAAAATATTTTA-AACT
1 AAAATAATATTTTATAAAT
4039407 AAAATAATATTTTATAAAT
1 AAAATAATATTTTATAAAT
*
4039426 AAAATATTATT
1 AAAATAATATT
4039437 AAAATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:4039433 original size:16 final size:17
Alignment explanation
Indices: 4039412--4039454 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
4039402 AAACTAAAAT
4039412 AATATTTTATAAATA-A
1 AATATTTTATAAATATA
*
4039428 AATATTATTA-AAATATT
1 AATATT-TTATAAATATA
4039445 AATATTTTAT
1 AATATTTTAT
4039455 TTATTAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTTTATAAATATA
Found at i:4044854 original size:23 final size:23
Alignment explanation
Indices: 4044828--4044874 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
4044818 CTGAGAACAA
**
4044828 TTTAGAATTTCATTTT-AACTATG
1 TTTAGAAGATCATTTTCAAC-ATG
4044851 TTTAGAAGATCATTTTCAACATG
1 TTTAGAAGATCATTTTCAACATG
4044874 T
1 T
4044875 ATGATAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (23 bp):
TTTAGAAGATCATTTTCAACATG
Found at i:4045162 original size:20 final size:20
Alignment explanation
Indices: 4045137--4045176 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4045127 ATTCAAGTAG
4045137 TTATTTGCAACAAGGACAAC
1 TTATTTGCAACAAGGACAAC
4045157 TTATTTGCAACAAGGACAAC
1 TTATTTGCAACAAGGACAAC
4045177 ATATAGACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (20 bp):
TTATTTGCAACAAGGACAAC
Found at i:4045582 original size:21 final size:21
Alignment explanation
Indices: 4045556--4045595 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4045546 AAACCCCATG
*
4045556 TTGGCGTTATGGCACCAAATT
1 TTGGCGTTATGACACCAAATT
*
4045577 TTGGCGTTGTGACACCAAA
1 TTGGCGTTATGACACCAAA
4045596 CTTACTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (21 bp):
TTGGCGTTATGACACCAAATT
Found at i:4048283 original size:36 final size:36
Alignment explanation
Indices: 4048233--4048318 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
4048223 ATCTAACAAT
**
4048233 TTAATTAAA-AATTTTAATCAAGGAGGCCTAATGAC
1 TTAATTAAACAATTTTAATCAACAAGGCCTAATGAC
*
4048268 TT-ATCTAAACAATTTTAATCAACAAGGCCTAATGAG
1 TTAAT-TAAACAATTTTAATCAACAAGGCCTAATGAC
4048304 TTAATTAAACAATTT
1 TTAATTAAACAATTT
4048319 AATTAATTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
34 2 0.04
35 6 0.13
36 35 0.78
37 2 0.04
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (36 bp):
TTAATTAAACAATTTTAATCAACAAGGCCTAATGAC
Found at i:4051294 original size:31 final size:30
Alignment explanation
Indices: 4051237--4051294 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
4051227 TGCCTTTTCT
* *
4051237 ATGGAGTATAACCTTTCTCTACCTTTTAAA
1 ATGGAGTATAACCTTACACTACCTTTTAAA
*
4051267 ATGGAGGTATAACCTTACACTATCTTTT
1 ATGGA-GTATAACCTTACACTACCTTTT
4051295 CCAATAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (30 bp):
ATGGAGTATAACCTTACACTACCTTTTAAA
Found at i:4056738 original size:58 final size:58
Alignment explanation
Indices: 4056648--4056763 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
4056638 ACCCCTCATC
4056648 TCAAACTCTTCAAACCCTAAGTCAAAAACTACCAAAAACAATGGTTAAATCTTCACTA
1 TCAAACTCTTCAAACCCTAAGTCAAAAACTACCAAAAACAATGGTTAAATCTTCACTA
4056706 TCAAACTCTTCAAACCCTAAGTCAAAAACTACCAAAAACAATGGTTAAATCTTCACTA
1 TCAAACTCTTCAAACCCTAAGTCAAAAACTACCAAAAACAATGGTTAAATCTTCACTA
4056764 CCAAGTGATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (58 bp):
TCAAACTCTTCAAACCCTAAGTCAAAAACTACCAAAAACAATGGTTAAATCTTCACTA
Found at i:4059673 original size:74 final size:72
Alignment explanation
Indices: 4059510--4059693 Score: 201
Period size: 74 Copynumber: 2.5 Consensus size: 72
4059500 GACAAATAAA
* ** *
4059510 ACTTAATCAACTAAGAAGTATGGTTAGCCAGCTAAAAGCTTACGGTCCAAAATTTGATTGCTAGA
1 ACTTAATCAACTAAGAAGTATGGTTAGCCAGCTAAGAGC-TACACTCCAAAATTTGATTGATAGA
4059575 CAGAGAAG
65 CAGAGAAG
* * * *
4059583 GCTTAGTCGACTAAGAAGTATTGTTAGCCAGCTAAGAG-TACACTACCAGAGAATTTGATT-ATA
1 ACTTAATCAACTAAGAAGTATGGTTAGCCAGCTAAGAGCTACACT-CCA-A-AATTTGATTGAT-
4059646 AGACAGAGAAG
62 AGACAGAGAAG
* * * *
4059657 ACTTAATCAACCAAGAAGCATGGTTAGTCAACTAAGA
1 ACTTAATCAACTAAGAAGTATGGTTAGCCAGCTAAGA
4059694 TCACACTGTT
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
71 4 0.04
72 3 0.03
73 35 0.38
74 49 0.54
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (72 bp):
ACTTAATCAACTAAGAAGTATGGTTAGCCAGCTAAGAGCTACACTCCAAAATTTGATTGATAGAC
AGAGAAG
Found at i:4060966 original size:72 final size:72
Alignment explanation
Indices: 4060848--4061083 Score: 192
Period size: 73 Copynumber: 3.2 Consensus size: 72
4060838 ACCCAAAACT
* * * * * * *
4060848 TTTCTGTTATCTAAGAATCGATCTTTGCATTCTTGAG-ATATCGATTCTTCTTGTCACATTTAAA
1 TTTCTATTTTCTAAGAATCAATCATTCCATTCTTGAGCA-GT-GATTCTTCTTGTCTCATTTAAA
4060912 GTCTAAAGC
64 GTCTAAAGC
* *
4060921 TTTCTATTTTCTAAGAATCAAT-ATTCCATTCTTGAGCAGTTGATTCTTCTT-ACTTCATTTAGA
1 TTTCTATTTTCTAAGAATCAATCATTCCATTCTTGAGCAG-TGATTCTTCTTGTC-TCATTTAAA
* *
4060984 GTTTGAAGC
64 GTCTAAAGC
* * * * * * * *
4060993 TTTCTATTTTTTGAGAATCATTCTTTCCATTCTTGAGTAGTCAGTTCTTCTTGTCTCACTTCAAG
1 TTTCTATTTTCTAAGAATCAATCATTCCATTCTTGAGCAGTGA-TTCTTCTTGTCTCATTTAAAG
* *
4061058 TCCAAATC
65 TCTAAAGC
*
4061066 TTT-TGGTTTTCTAAGAAT
1 TTTCT-ATTTTCTAAGAAT
4061084 TGATCTTTGC
Statistics
Matches: 128, Mismatches: 28, Indels: 14
0.75 0.16 0.08
Matches are distributed among these distances:
71 1 0.01
72 58 0.45
73 68 0.53
74 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.46
Consensus pattern (72 bp):
TTTCTATTTTCTAAGAATCAATCATTCCATTCTTGAGCAGTGATTCTTCTTGTCTCATTTAAAGT
CTAAAGC
Found at i:4062922 original size:35 final size:35
Alignment explanation
Indices: 4062868--4062939 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
4062858 ATCGAGCAAT
* * ** *
4062868 AACCTTCACAATGATTTTTAATGAGCTCAACTACA
1 AACCATCACAATGAGTTTTAACAAGCTCAACCACA
*
4062903 AACCATCACAATGGGTTTTAACAAGCTCAACCACA
1 AACCATCACAATGAGTTTTAACAAGCTCAACCACA
4062938 AA
1 AA
4062940 TCGTTCCTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (35 bp):
AACCATCACAATGAGTTTTAACAAGCTCAACCACA
Found at i:4065046 original size:81 final size:81
Alignment explanation
Indices: 4064943--4065104 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
4064933 TTAAACCATG
4064943 CTTAGCTTTGCCATATTAAAGTATTTTAAAGAGGTGTATTTACTCACCTGTTTGAAACGTATCCA
1 CTTAGCTTTGCCATATTAAAGTATTTTAAAGAGGTGTATTTACTCACCTGTTTGAAACGTATCCA
4065008 ACCTTTTGTTGACTTT
66 ACCTTTTGTTGACTTT
4065024 CTTAGCTTTGCCATATTAAAGTATTTTAAAGAGGTGTATTTACTCACCTGTTTGAAACGTATCCA
1 CTTAGCTTTGCCATATTAAAGTATTTTAAAGAGGTGTATTTACTCACCTGTTTGAAACGTATCCA
4065089 ACCTTTTGTTGACTTT
66 ACCTTTTGTTGACTTT
4065105 TGACGAGTAC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (81 bp):
CTTAGCTTTGCCATATTAAAGTATTTTAAAGAGGTGTATTTACTCACCTGTTTGAAACGTATCCA
ACCTTTTGTTGACTTT
Found at i:4071489 original size:2 final size:2
Alignment explanation
Indices: 4071476--4071506 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4071466 AACTTCAACA
*
4071476 AT AT AC 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 AT AT A
4071507 ATAAGGGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4073493 original size:16 final size:16
Alignment explanation
Indices: 4073474--4073504 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4073464 ATAAAAATAA
4073474 AAAAAAATCAAAATCC
1 AAAAAAATCAAAATCC
*
4073490 AAAACAATCAAAATC
1 AAAAAAATCAAAATC
4073505 TAAATTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.19, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAAATCAAAATCC
Found at i:4083986 original size:13 final size:14
Alignment explanation
Indices: 4083963--4083996 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
4083953 TTTAGAATAG
4083963 TTTTAGTTTTAAAA
1 TTTTAGTTTTAAAA
4083977 TTTT-GTTTTAAAA
1 TTTTAGTTTTAAAA
4083990 TTTTAGT
1 TTTTAGT
4083997 GTTTGGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (14 bp):
TTTTAGTTTTAAAA
Found at i:4091427 original size:72 final size:73
Alignment explanation
Indices: 4091343--4091485 Score: 189
Period size: 72 Copynumber: 2.0 Consensus size: 73
4091333 TTGAGACATT
* ** * ** * *
4091343 CCTTAGAAGTATCGAGACATCATCTCTGAAGCCCCAAATTCTAGAATTCGAGTGTTAATGTATCA
1 CCTTAGAAGTATCGAAACATCATCTCAAAAGCCCAAAATTCTAGAAAACAAGTGTCAATGTATCA
4091408 AGACTTAA
66 AGACTTAA
* *
4091416 CCTT-GAAGTATCGAAACATCATCTCAAAAGTCCAAAATTCTAGAAAACAAGTGTCAATGTATCG
1 CCTTAGAAGTATCGAAACATCATCTCAAAAGCCCAAAATTCTAGAAAACAAGTGTCAATGTATCA
4091480 AGACTT
66 AGACTT
4091486 GTCCTCAAGG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
72 56 0.93
73 4 0.07
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (73 bp):
CCTTAGAAGTATCGAAACATCATCTCAAAAGCCCAAAATTCTAGAAAACAAGTGTCAATGTATCA
AGACTTAA
Found at i:4091512 original size:21 final size:21
Alignment explanation
Indices: 4091469--4091512 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
4091459 AAAACAAGTG
* **
4091469 TCAATGTATCGAGACTTGTCC
1 TCAAGGTATCGAGACTTCACC
*
4091490 TCAAGGTATTGAGACTTCACC
1 TCAAGGTATCGAGACTTCACC
4091511 TC
1 TC
4091513 TAGGCTTCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (21 bp):
TCAAGGTATCGAGACTTCACC
Found at i:4091625 original size:71 final size:72
Alignment explanation
Indices: 4091471--4091626 Score: 181
Period size: 72 Copynumber: 2.2 Consensus size: 72
4091461 AACAAGTGTC
* * * * * * *
4091471 AATGTATCGAGACTTGTCCTCAAGGTATTGAGACTTCACCTCTAGGCTTCAAATTTCCATAAGGC
1 AATGTATCAAGACATGGCCTCAAGGTATCGAGACATCACCACTAGACTTCAAATTTCCATAAGGC
*
4091536 AAGTGCA
66 AAGCGCA
* *
4091543 AATGTATCAAGACATGGCTTCAAGGTATCGAGACATCATCACTAGACTTC-AATTTCCA-AAGAG
1 AATGTATCAAGACATGGCCTCAAGGTATCGAGACATCACCACTAGACTTCAAATTTCCATAAG-G
* *
4091606 CATGCGCT
65 CAAGCGCA
4091614 AATGTATCAAGAC
1 AATGTATCAAGAC
4091627 CCACATTTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
70 3 0.04
71 27 0.38
72 41 0.58
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (72 bp):
AATGTATCAAGACATGGCCTCAAGGTATCGAGACATCACCACTAGACTTCAAATTTCCATAAGGC
AAGCGCA
Found at i:4103032 original size:5 final size:5
Alignment explanation
Indices: 4103022--4103050 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
4103012 AAGATAGATG
4103022 CCCTC CCCT- CCCTC CCCTC CCCTC CCCTC
1 CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC
4103051 ATTAGTAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.79, G:0.00, T:0.21
Consensus pattern (5 bp):
CCCTC
Found at i:4104876 original size:16 final size:16
Alignment explanation
Indices: 4104855--4104894 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
4104845 ATAATGTAAG
*
4104855 ATTACAATGCAATCAT
1 ATTACAACGCAATCAT
4104871 ATTACAACGCAATCAT
1 ATTACAACGCAATCAT
4104887 ATTACAAC
1 ATTACAAC
4104895 CAAGGGATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.28
Consensus pattern (16 bp):
ATTACAACGCAATCAT
Found at i:4105048 original size:26 final size:26
Alignment explanation
Indices: 4105017--4105119 Score: 84
Period size: 26 Copynumber: 3.8 Consensus size: 26
4105007 TTTGTAATGT
*
4105017 TATAATTAAAATAAAAAATATTAAAA
1 TATAATAAAAATAAAAAATATTAAAA
*
4105043 TATAATATATAATATAAAAAATTATATTAAA
1 TATAATA-A-AA-ATAAAAAA-TAT-TAAAA
* *
4105074 GA-AATAAAAATAAAAAATA-TAATAT
1 TATAATAAAAATAAAAAATATTAA-AA
* *
4105099 TCTAATAAAAATAAAATATAT
1 TATAATAAAAATAAAAAATAT
4105120 GACATTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
24 2 0.03
25 1 0.02
26 24 0.39
27 9 0.15
28 4 0.07
29 9 0.15
30 7 0.11
31 5 0.08
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (26 bp):
TATAATAAAAATAAAAAATATTAAAA
Found at i:4119314 original size:2 final size:2
Alignment explanation
Indices: 4119307--4119334 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4119297 GGCATGCACA
4119307 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
4119335 TTCTTATAAA
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:4122792 original size:2 final size:2
Alignment explanation
Indices: 4122785--4122812 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4122775 TTGATCCACT
4122785 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
4122813 AATTATTTGG
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):
TA
Found at i:4123245 original size:21 final size:19
Alignment explanation
Indices: 4123207--4123245 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
4123197 TTAGCAACAT
*
4123207 ATTTTAAATGTCGTCATAA
1 ATTTTAAATGTAGTCATAA
4123226 ATTTTAATATTGTAGTCATA
1 ATTTTAA-A-TGTAGTCATA
4123246 TCATATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 1 0.06
21 9 0.53
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (19 bp):
ATTTTAAATGTAGTCATAA
Found at i:4140610 original size:28 final size:28
Alignment explanation
Indices: 4140578--4140738 Score: 162
Period size: 29 Copynumber: 5.5 Consensus size: 28
4140568 CAACTTTAAC
* *
4140578 ATGTTTGCCTTAATTTAAACAAGAAAAT
1 ATGTTTGTCTTAATTTAGACAAGAAAAT
* *
4140606 ATGTTTAGTCTTAATTTAGAGAAAAAAAT
1 ATGTTT-GTCTTAATTTAGACAAGAAAAT
4140635 ATGTTTGTCTTAATTTAAGACAAGAAAAAT
1 ATGTTTGTCTTAATTT-AGACAAG-AAAAT
* * *
4140665 ATATTTTGTCTTAATCTAGACAAGAAAAC
1 AT-GTTTGTCTTAATTTAGACAAGAAAAT
* *
4140694 ATATTTGCCTCT-ATTTAGACAAGATAAAAT
1 ATGTTTGTCT-TAATTTAGACAAG--AAAAT
*
4140724 ATTTTTGTCTTAATT
1 ATGTTTGTCTTAATT
4140739 AAAGATAAGA
Statistics
Matches: 110, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
28 32 0.29
29 37 0.34
30 29 0.26
31 12 0.11
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.39
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAT
Found at i:4140710 original size:59 final size:58
Alignment explanation
Indices: 4140575--4140737 Score: 199
Period size: 59 Copynumber: 2.8 Consensus size: 58
4140565 AGACAACTTT
* * *
4140575 AACATGTTTGCCTTAATTTAA-ACAAG-AAAATATGTTTAGTCTTAATTTAGAGAAAAA
1 AACATGTTTGCCTTAATTTAAGACAAGAAAAATAT-TTTTGTCTTAATCTAGACAAAAA
* * *
4140632 AATATGTTTGTCTTAATTTAAGACAAGAAAAATATATTTTGTCTTAATCTAGACAAGAA
1 AACATGTTTGCCTTAATTTAAGACAAGAAAAATAT-TTTTGTCTTAATCTAGACAAAAA
*
4140691 AACATATTTGCCTCT-ATTT-AGACAAGATAAAATATTTTTGTCTTAAT
1 AACATGTTTGCCT-TAATTTAAGACAAGA-AAAATATTTTTGTCTTAAT
4140738 TAAAGATAAG
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
57 19 0.21
58 25 0.27
59 47 0.51
60 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (58 bp):
AACATGTTTGCCTTAATTTAAGACAAGAAAAATATTTTTGTCTTAATCTAGACAAAAA
Found at i:4143041 original size:15 final size:15
Alignment explanation
Indices: 4143021--4143050 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4143011 AGAGCAGGGT
4143021 TCGAATCCTTTCTCC
1 TCGAATCCTTTCTCC
4143036 TCGAATCCTTTCTCC
1 TCGAATCCTTTCTCC
4143051 CTCAATTATA
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:0.13, C:0.40, G:0.07, T:0.40
Consensus pattern (15 bp):
TCGAATCCTTTCTCC
Found at i:4143082 original size:28 final size:28
Alignment explanation
Indices: 4143042--4143097 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
4143032 CTCCTCGAAT
4143042 CCTTTCTCCCTCAATTATAAAAATAAAA
1 CCTTTCTCCCTCAATTATAAAAATAAAA
4143070 CCTTTCTCCCTCAATTATAAAAATAAAA
1 CCTTTCTCCCTCAATTATAAAAATAAAA
4143098 AAATAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (28 bp):
CCTTTCTCCCTCAATTATAAAAATAAAA
Found at i:4143834 original size:7 final size:7
Alignment explanation
Indices: 4143822--4143856 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
4143812 AGGATAAGGT
4143822 TGAGCAC
1 TGAGCAC
4143829 TGAGCAC
1 TGAGCAC
4143836 TGAGCAC
1 TGAGCAC
4143843 TGAGCAC
1 TGAGCAC
4143850 TTGAGCA
1 -TGAGCA
4143857 GCGAGTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.17
Consensus pattern (7 bp):
TGAGCAC
Found at i:4145981 original size:72 final size:72
Alignment explanation
Indices: 4145905--4146060 Score: 183
Period size: 72 Copynumber: 2.2 Consensus size: 72
4145895 CTGACAATAA
* * * *
4145905 GTCTCGATACTTTGGCA-CTTGCTCTCTAAAAATGGA-AGTTTGGAAGTGAAGTCTCGAA-ACTT
1 GTCTCAATACTTTGG-AGCTTGCTCTCTAAAAAT-CACAATTTGGAAGTGAAGTCTC-AATACCT
*
4145967 TGAAGCTTGG
63 TCAAGCTTGG
* * * *
4145977 GTCTCAATACTTTTGAGCTTGCTCTCTAAAACTCACAATTTGGAGGTGAAGTCTCAATTCCTTCA
1 GTCTCAATACTTTGGAGCTTGCTCTCTAAAAATCACAATTTGGAAGTGAAGTCTCAATACCTTCA
4146042 AGCTTGG
66 AGCTTGG
4146049 GTCTCAATACTT
1 GTCTCAATACTT
4146061 CATCACTTGT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
71 4 0.06
72 68 0.94
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (72 bp):
GTCTCAATACTTTGGAGCTTGCTCTCTAAAAATCACAATTTGGAAGTGAAGTCTCAATACCTTCA
AGCTTGG
Found at i:4146416 original size:2 final size:2
Alignment explanation
Indices: 4146411--4146440 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4146401 CTCTCTTTAG
4146411 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4146441 GGTTTACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4147180 original size:7 final size:7
Alignment explanation
Indices: 4147168--4147196 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
4147158 ATTTAATTTA
4147168 ATTATAT
1 ATTATAT
4147175 ATTATAT
1 ATTATAT
4147182 ATTATAT
1 ATTATAT
4147189 ATTATAT
1 ATTATAT
4147196 A
1 A
4147197 AATAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATTATAT
Found at i:4150794 original size:15 final size:14
Alignment explanation
Indices: 4150770--4150799 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4150760 TCAACAAGAG
4150770 AAACTGGATTCATC
1 AAACTGGATTCATC
4150784 AAACTTGGATTCATC
1 AAAC-TGGATTCATC
4150799 A
1 A
4150800 GGCGCAGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (14 bp):
AAACTGGATTCATC
Found at i:4156020 original size:62 final size:62
Alignment explanation
Indices: 4155923--4156047 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
4155913 ACCTAGAAGC
4155923 AATTTTGAGAAGAGGAAAAGTAAAGGTGGGACAAACAACGTTTATAATACTGAAACTAGTAA
1 AATTTTGAGAAGAGGAAAAGTAAAGGTGGGACAAACAACGTTTATAATACTGAAACTAGTAA
4155985 AATTTTGAGAAGAGGAAAAGTAAAGGTGGGACAAACAACGTTTATAATACTGAAACTAGTAA
1 AATTTTGAGAAGAGGAAAAGTAAAGGTGGGACAAACAACGTTTATAATACTGAAACTAGTAA
4156047 A
1 A
4156048 GACACACAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.22
Consensus pattern (62 bp):
AATTTTGAGAAGAGGAAAAGTAAAGGTGGGACAAACAACGTTTATAATACTGAAACTAGTAA
Found at i:4157437 original size:56 final size:56
Alignment explanation
Indices: 4157351--4157466 Score: 205
Period size: 56 Copynumber: 2.1 Consensus size: 56
4157341 ACTAATAATA
* *
4157351 TCAATGCAAGTTTTACCAGCAAATAAACTAAAGGATACACATTGTTTCTATTTATC
1 TCAATACAAGTTTTACCAGCAAATAAACTAAAGGATACACAGTGTTTCTATTTATC
*
4157407 TCAATACAAGTTTTACTAGCAAATAAACTAAAGGATACACAGTGTTTCTATTTATC
1 TCAATACAAGTTTTACCAGCAAATAAACTAAAGGATACACAGTGTTTCTATTTATC
4157463 TCAA
1 TCAA
4157467 CCATTTTCCT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (56 bp):
TCAATACAAGTTTTACCAGCAAATAAACTAAAGGATACACAGTGTTTCTATTTATC
Found at i:4160200 original size:16 final size:17
Alignment explanation
Indices: 4160164--4160200 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4160154 TTTTAAAAAG
*
4160164 AATATTTAAATTTTATT
1 AATATATAAATTTTATT
4160181 AATATATAAATTTT-TT
1 AATATATAAATTTTATT
4160197 AATA
1 AATA
4160201 AAATATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATATATAAATTTTATT
Found at i:4162362 original size:30 final size:30
Alignment explanation
Indices: 4162318--4162380 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
4162308 ACTATTAATC
*
4162318 ATAAAGGTTAATTTGGCTCAAAATAAAAAT
1 ATAAAGGTTAATTTGGCTCAAAACAAAAAT
* *
4162348 ATAAAGAGTT-ATTTGGTTCAAAACAAAAGT
1 ATAAAG-GTTAATTTGGCTCAAAACAAAAAT
4162378 ATA
1 ATA
4162381 GGGACTTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.30
Consensus pattern (30 bp):
ATAAAGGTTAATTTGGCTCAAAACAAAAAT
Found at i:4167752 original size:16 final size:17
Alignment explanation
Indices: 4167721--4167753 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4167711 CACTTCAGTC
4167721 TTTAAAGGCATCTTTGA
1 TTTAAAGGCATCTTTGA
*
4167738 TTTAAA-GCCTCTTTGA
1 TTTAAAGGCATCTTTGA
4167754 CCTGGCTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (17 bp):
TTTAAAGGCATCTTTGA
Found at i:4174249 original size:12 final size:12
Alignment explanation
Indices: 4174232--4174256 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4174222 TCCTCCTTAG
4174232 AGTTTTTTTTTA
1 AGTTTTTTTTTA
4174244 AGTTTTTTTTTA
1 AGTTTTTTTTTA
4174256 A
1 A
4174257 AATTTTGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (12 bp):
AGTTTTTTTTTA
Found at i:4174462 original size:20 final size:19
Alignment explanation
Indices: 4174426--4174467 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
4174416 ATAATATATT
4174426 TATATTTCAAAAAATAATAA
1 TATATTTCAAAAAATAA-AA
*
4174446 TATATTT-AAATATATAAAA
1 TATATTTCAAA-AAATAAAA
4174465 TAT
1 TAT
4174468 TCAAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATTTCAAAAAATAAAA
Found at i:4174464 original size:26 final size:26
Alignment explanation
Indices: 4174410--4174466 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
4174400 TTATATTAAT
* *
4174410 AAAATAATAATATATTTATATTTCAA
1 AAAATAATAATATATTTAAATATCAA
*
4174436 AAAATAATAATATATTTAAATAT-AT
1 AAAATAATAATATATTTAAATATCAA
4174461 AAAATA
1 AAAATA
4174467 TTCAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
AAAATAATAATATATTTAAATATCAA
Found at i:4174467 original size:17 final size:16
Alignment explanation
Indices: 4174437--4174475 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
4174427 ATATTTCAAA
* *
4174437 AAATAATAATATATTT
1 AAATAATAAAATATTC
4174453 AAATATATAAAATATTC
1 AAATA-ATAAAATATTC
4174470 AAATAA
1 AAATAA
4174476 ATCTTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAATAAAATATTC
Found at i:4174604 original size:33 final size:33
Alignment explanation
Indices: 4174562--4174639 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
4174552 AATATATTAC
*
4174562 AATTGATGATAATACGATATACTAGCATATCAT
1 AATTGATGATAATACGATATACTAACATATCAT
**
4174595 AATTGATGATAATGTGATATACTAACATATCAT
1 AATTGATGATAATACGATATACTAACATATCAT
4174628 AATTGATGATAA
1 AATTGATGATAA
4174640 CGTGACATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.35
Consensus pattern (33 bp):
AATTGATGATAATACGATATACTAACATATCAT
Found at i:4176558 original size:2 final size:2
Alignment explanation
Indices: 4176551--4176597 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4176541 GAAAGTTATG
4176551 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
4176593 TA TA T
1 TA TA T
4176598 CCATAAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4177069 original size:178 final size:173
Alignment explanation
Indices: 4176770--4177126 Score: 518
Period size: 178 Copynumber: 2.0 Consensus size: 173
4176760 AACTGACATG
* * * * * *
4176770 AGCATACCACATGTTGTTTTAATATGGAAAATCATTAAATAGTTTCGTATGTATGTAACCACATA
1 AGCATACCACATATTGTTCTAATATGGAAAATCATTAAACAGTTTCATATGCACGTAACCACATA
**
4176835 TATAAACATATAAGTCATACCATAGGTAAATAATCTCATAATATTCCAACTATCAAATAAACATG
66 TATAAACATATAAGTCATACCATAGGTAAATAATCTCATAATATTCCAACTATCAAATAAACAAA
*
4176900 CCTAACCTTGATGTATCAATGCACATCTCGTGTGCTCAATATATATAT
131 CCTAACCTTGATATATCAATG--CA--T-GTGTGCTCAATATATATAT
* * *
4176948 AGCATACCACATATTGTTCTAATATGGAAAATCATTCAACATTTTCATATGCACGTAACCACCTA
1 AGCATACCACATATTGTTCTAATATGGAAAATCATTAAACAGTTTCATATGCACGTAACCACATA
* * *
4177013 TATGAACATATAAGTCATACCATAGGTAAATATTCTCATAATATTCCAATTATCAAATAAACAAA
66 TATAAACATATAAGTCATACCATAGGTAAATAATCTCATAATATTCCAACTATCAAATAAACAAA
*
4177078 CCTAACCTTGATATTTCAATGCATGTGTGCTCAATATATATAT
131 CCTAACCTTGATATATCAATGCATGTGTGCTCAATATATATAT
4177121 A-CATAC
1 AGCATAC
4177127 ATACATACAT
Statistics
Matches: 163, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
172 5 0.03
173 20 0.12
174 1 0.01
176 2 0.01
178 135 0.83
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (173 bp):
AGCATACCACATATTGTTCTAATATGGAAAATCATTAAACAGTTTCATATGCACGTAACCACATA
TATAAACATATAAGTCATACCATAGGTAAATAATCTCATAATATTCCAACTATCAAATAAACAAA
CCTAACCTTGATATATCAATGCATGTGTGCTCAATATATATAT
Found at i:4180598 original size:21 final size:21
Alignment explanation
Indices: 4180545--4180600 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
4180535 GCCTTCTAGG
**
4180545 TATCAATACCTAAGGGAAGGT
1 TATCAATACCTTTGGGAAGGT
*
4180566 T-TCCAATTCCTTTGGGAAGGT
1 TAT-CAATACCTTTGGGAAGGT
4180587 TATCAATACCTTTG
1 TATCAATACCTTTG
4180601 TGGCAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (21 bp):
TATCAATACCTTTGGGAAGGT
Found at i:4183782 original size:22 final size:22
Alignment explanation
Indices: 4183756--4183832 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
4183746 GAACATGTAG
4183756 ATAATGTAAAACTGACTCCATA
1 ATAATGTAAAACTGACTCCATA
* * *
4183778 ATAAT-TAAAAAATAGAAT-GATA
1 ATAATGT-AAAACT-GACTCCATA
* *
4183800 GATAATGAAAAACTGACTCCACA
1 -ATAATGTAAAACTGACTCCATA
*
4183823 ATAATTTAAA
1 ATAATGTAAA
4183833 TTAGAATGAT
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
21 1 0.03
22 24 0.60
23 15 0.38
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (22 bp):
ATAATGTAAAACTGACTCCATA
Found at i:4183804 original size:45 final size:44
Alignment explanation
Indices: 4183753--4183844 Score: 139
Period size: 45 Copynumber: 2.1 Consensus size: 44
4183743 TAGGAACATG
* *
4183753 TAGATAATGTAAAACTGACTCCATAATAATTAAAAAATAGAATGA
1 TAGATAATGAAAAACTGACTCCACAATAATT-AAAAATAGAATGA
* *
4183798 TAGATAATGAAAAACTGACTCCACAATAATTTAAATTAGAATGA
1 TAGATAATGAAAAACTGACTCCACAATAATTAAAAATAGAATGA
4183842 TAG
1 TAG
4183845 TTAACACATT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 14 0.33
45 29 0.67
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (44 bp):
TAGATAATGAAAAACTGACTCCACAATAATTAAAAATAGAATGA
Found at i:4185759 original size:5 final size:5
Alignment explanation
Indices: 4185751--4185784 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
4185741 AAATACAAAT
4185751 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
4185785 TGTGCGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:4187046 original size:36 final size:36
Alignment explanation
Indices: 4186991--4187080 Score: 135
Period size: 36 Copynumber: 2.5 Consensus size: 36
4186981 TGCGATATGA
* *
4186991 GAGTGCACACGACGATAATGGTGGTGTGCGGTGTGG
1 GAGTGCACATGACGATAATGGTGGTGTACGGTGTGG
* *
4187027 GAGTGCACATGACGGTAATGGTGTTGTACGGTGTGG
1 GAGTGCACATGACGATAATGGTGGTGTACGGTGTGG
*
4187063 GAGTGCACATGAAGATAA
1 GAGTGCACATGACGATAA
4187081 CAGCTATGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.24, C:0.12, G:0.40, T:0.23
Consensus pattern (36 bp):
GAGTGCACATGACGATAATGGTGGTGTACGGTGTGG
Found at i:4188365 original size:16 final size:16
Alignment explanation
Indices: 4188339--4188424 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 16
4188329 ATTTTCAATC
4188339 ATAATTTAGTTATTTTT
1 ATAA-TTAGTTATTTTT
4188356 ATAATTAGTTTATTTTT
1 ATAATTAG-TTATTTTT
* * *
4188373 A-AGTGAGTTATTTTA
1 ATAATTAGTTATTTTT
*
4188388 AT-TTTATGTTATTTCTT
1 ATAATTA-GTTATTT-TT
*
4188405 TTAATTTAGTTATTATTT
1 ATAA-TTAGTTATT-TTT
4188423 AT
1 AT
4188425 TAGTTTTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
15 10 0.19
16 15 0.28
17 15 0.28
18 9 0.17
19 4 0.08
ACGTcount: A:0.28, C:0.01, G:0.08, T:0.63
Consensus pattern (16 bp):
ATAATTAGTTATTTTT
Found at i:4199491 original size:26 final size:26
Alignment explanation
Indices: 4199462--4199513 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
4199452 ATAAACACAA
*
4199462 GTCCATTATCCATAAAGATTTTGATT
1 GTCCACTATCCATAAAGATTTTGATT
*
4199488 GTCCACTATCCATCAAGATTTTGATT
1 GTCCACTATCCATAAAGATTTTGATT
4199514 CTACCATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (26 bp):
GTCCACTATCCATAAAGATTTTGATT
Found at i:4203496 original size:23 final size:24
Alignment explanation
Indices: 4203466--4203513 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
4203456 ATGTCACAAG
4203466 GCATGCCAGAA-GAAAGTAA-AGAA
1 GCATGCCA-AATGAAAGTAACAGAA
4203489 GCATGCCAAATTGAAAGTAACAGAA
1 GCATGCCAAA-TGAAAGTAACAGAA
4203514 TGAATTAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 2 0.09
23 8 0.36
24 8 0.36
25 4 0.18
ACGTcount: A:0.50, C:0.15, G:0.23, T:0.12
Consensus pattern (24 bp):
GCATGCCAAATGAAAGTAACAGAA
Found at i:4209547 original size:22 final size:22
Alignment explanation
Indices: 4209512--4209662 Score: 119
Period size: 23 Copynumber: 6.8 Consensus size: 22
4209502 ATGTTGTGAA
* *
4209512 CGTGTGACACTTTTTGAAC-TTG
1 CGTGTAACA-TTTTTGAACATGG
* *
4209534 CGTGTAACCA-TTTTAAACAAGG
1 CGTGTAA-CATTTTTGAACATGG
*
4209556 CGTGTAACACTTTTTGAAC-TTG
1 CGTGTAACA-TTTTTGAACATGG
* *
4209578 CATGTAACATTTTTGAACATAG
1 CGTGTAACATTTTTGAACATGG
* *
4209600 CGTGTATCATATTTTAAACATGG
1 CGTGTAACAT-TTTTGAACATGG
* *
4209623 CGTGTAACATTTTTTAAAAATGG
1 CGTGTAACA-TTTTTGAACATGG
* *
4209646 CCTGTAACATATTTGAA
1 CGTGTAACATTTTTGAA
4209663 AAATAACGTG
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
21 18 0.17
22 39 0.38
23 46 0.44
24 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (22 bp):
CGTGTAACATTTTTGAACATGG
Found at i:4209603 original size:44 final size:44
Alignment explanation
Indices: 4209512--4209662 Score: 141
Period size: 44 Copynumber: 3.4 Consensus size: 44
4209502 ATGTTGTGAA
*
4209512 CGTGTGACACTTTTTGAACTTGCGTGTAACCA-TTTTAAACAAGG
1 CGTGTAACACTTTTTGAACTTGCGTGTAA-CATTTTTAAACAAGG
* *
4209556 CGTGTAACACTTTTTGAACTTGCATGTAACATTTTTGAACATA-G
1 CGTGTAACACTTTTTGAACTTGCGTGTAACATTTTTAAACA-AGG
* * *
4209600 CGTGTATCA-TATTTTAAACATGGCGTGTAACATTTTTTAAA-AATGG
1 CGTGTAACACT-TTTTGAAC-TTGCGTGTAACA-TTTTTAAACAA-GG
* *
4209646 CCTGTAACA-TATTTGAA
1 CGTGTAACACTTTTTGAA
4209663 AAATAACGTG
Statistics
Matches: 88, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
43 3 0.03
44 52 0.59
45 17 0.19
46 16 0.18
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (44 bp):
CGTGTAACACTTTTTGAACTTGCGTGTAACATTTTTAAACAAGG
Found at i:4209619 original size:23 final size:23
Alignment explanation
Indices: 4209580--4209677 Score: 99
Period size: 23 Copynumber: 4.3 Consensus size: 23
4209570 TGAACTTGCA
* *
4209580 TGTAACAT-TTTTGAACATAGCG
1 TGTAACATATTTTAAAAATAGCG
* * *
4209602 TGTATCATATTTTAAACATGGCG
1 TGTAACATATTTTAAAAATAGCG
* * *
4209625 TGTAACATTTTTTAAAAATGGCC
1 TGTAACATATTTTAAAAATAGCG
* *
4209648 TGTAACATATTTGAAAAATAACG
1 TGTAACATATTTTAAAAATAGCG
4209671 TGTAACA
1 TGTAACA
4209678 ACATGATAGA
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
22 7 0.11
23 56 0.89
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (23 bp):
TGTAACATATTTTAAAAATAGCG
Found at i:4211038 original size:31 final size:31
Alignment explanation
Indices: 4211003--4211267 Score: 361
Period size: 31 Copynumber: 8.6 Consensus size: 31
4210993 AGAAAGAAAT
* * *
4211003 AAATGTTGTTACATGCCATGCATATCAAGTA
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* * * *
4211034 AAATGTTGTTACATGCAATGCATATCAAGTA
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* ** *
4211065 AAATGTTATTACACGCCATGCATATTAAGTA
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* *
4211096 AAATGTTGTTACACACAATGCATAACAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
*
4211127 AAATGTTGTTACACGCCATACATAACAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
* * *
4211158 AAATGTTGTTACATGCCATGTATATCAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
*
4211189 AAATGTTGTTACACGCAATGCATAACAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
4211220 -AATGTTGTTACACGCCATGCATAACAAGTC
1 AAATGTTGTTACACGCCATGCATAACAAGTC
4211250 AAATGTTGTTACACGCCA
1 AAATGTTGTTACACGCCA
4211268 ACTCTAACAC
Statistics
Matches: 210, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
30 29 0.14
31 181 0.86
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (31 bp):
AAATGTTGTTACACGCCATGCATAACAAGTC
Found at i:4211302 original size:123 final size:124
Alignment explanation
Indices: 4211055--4211294 Score: 299
Period size: 123 Copynumber: 2.0 Consensus size: 124
4211045 CATGCAATGC
* **
4211055 ATATCAAGTAAAATGTTATTACACGCCATGCATATTAAGTAAAATGTTGTTACACACAATGCATA
1 ATATCAAGTAAAATGTTATTACACGCAATGCATAACAAGTAAAATGTTGTTACACACAATGCATA
*** * * *
4211120 ACAAGTCAAATGTTGTTACACGCCATACATAACAAGTCAAATGTTGTTACATGCCATGT
66 ACAAGTCAAATGTTGTTACACGCCATACATAACAAGTCAAATGCAATAAAATACCATGT
* * * * *
4211179 ATATCAAGTCAAATGTTGTTACACGCAATGCATAACAAGT-CAATGTTGTTACACGCCATGCATA
1 ATATCAAGTAAAATGTTATTACACGCAATGCATAACAAGTAAAATGTTGTTACACACAATGCATA
* *
4211243 ACAAGTCAAATGTTGTTACACGCCA-ACTCTAACACGTC-AAT-CAATAAAATAC
66 ACAAGTCAAATGTTGTTACACGCCATAC-ATAACAAGTCAAATGCAATAAAATAC
4211295 AATATGTAGT
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
121 5 0.05
122 5 0.05
123 54 0.55
124 35 0.35
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (124 bp):
ATATCAAGTAAAATGTTATTACACGCAATGCATAACAAGTAAAATGTTGTTACACACAATGCATA
ACAAGTCAAATGTTGTTACACGCCATACATAACAAGTCAAATGCAATAAAATACCATGT
Found at i:4212009 original size:47 final size:46
Alignment explanation
Indices: 4211919--4212078 Score: 169
Period size: 47 Copynumber: 3.5 Consensus size: 46
4211909 CATCTGACAC
* * * * *
4211919 ACTCTAAACCCTAGCATGTCATAGATTCCCTCCATGGTATGTCACCA
1 ACTCTGAACCCTGGCGTGTCACAGATTCCCTCCATGGTGTGTCA-CA
* * * * *
4211966 ACCCTGAACGCTGGCGTGTCACAGATTTCTTCCATGGCGTGTCA-A
1 ACTCTGAACCCTGGCGTGTCACAGATTCCCTCCATGGTGTGTCACA
* * *
4212011 ACTTTGAACCCTGGTGTGTCACAGATTCCCTCCGTGGTGTGTCACAA
1 ACTCTGAACCCTGGCGTGTCACAGATTCCCTCCATGGTGTGTCAC-A
*
4212058 ACTCTGAACCCTAGCGTGTCA
1 ACTCTGAACCCTGGCGTGTCA
4212079 TAAACCCTGA
Statistics
Matches: 90, Mismatches: 21, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
45 37 0.41
47 53 0.59
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (46 bp):
ACTCTGAACCCTGGCGTGTCACAGATTCCCTCCATGGTGTGTCACA
Found at i:4212083 original size:24 final size:24
Alignment explanation
Indices: 4212049--4212104 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
4212039 CCTCCGTGGT
*
4212049 GTGTCACAAACTCTGAACCCTAGC
1 GTGTCACAAACCCTGAACCCTAGC
* *
4212073 GTGTCATAAACCCTGAACCCTAGT
1 GTGTCACAAACCCTGAACCCTAGC
4212097 GTGTCACA
1 GTGTCACA
4212105 GAGTCCCTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (24 bp):
GTGTCACAAACCCTGAACCCTAGC
Found at i:4212123 original size:23 final size:23
Alignment explanation
Indices: 4212095--4212141 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4212085 CTGAACCCTA
*
4212095 GTGTGTCACAGAGTCCCTCAATG
1 GTGTGTCACAAAGTCCCTCAATG
* *
4212118 GTGTGTCACAAATTCCCTCCATG
1 GTGTGTCACAAAGTCCCTCAATG
4212141 G
1 G
4212142 CATGTCAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (23 bp):
GTGTGTCACAAAGTCCCTCAATG
Found at i:4212147 original size:23 final size:23
Alignment explanation
Indices: 4212098--4212148 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
4212088 AACCCTAGTG
* **
4212098 TGTCACAGAGTCCCTCAATGGTG
1 TGTCACAAAGTCCCTCAATGGCA
* *
4212121 TGTCACAAATTCCCTCCATGGCA
1 TGTCACAAAGTCCCTCAATGGCA
4212144 TGTCA
1 TGTCA
4212149 AACTCTGAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (23 bp):
TGTCACAAAGTCCCTCAATGGCA
Found at i:4212170 original size:22 final size:22
Alignment explanation
Indices: 4212144--4212205 Score: 124
Period size: 22 Copynumber: 2.8 Consensus size: 22
4212134 CTCCATGGCA
4212144 TGTCAAACTCTGAACTATATCG
1 TGTCAAACTCTGAACTATATCG
4212166 TGTCAAACTCTGAACTATATCG
1 TGTCAAACTCTGAACTATATCG
4212188 TGTCAAACTCTGAACTAT
1 TGTCAAACTCTGAACTAT
4212206 GACATGTCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (22 bp):
TGTCAAACTCTGAACTATATCG
Done.