Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 11 of 161
Found at i:3615911 original size:55 final size:54
Alignment explanation
Indices: 3615819--3615969 Score: 169
Period size: 55 Copynumber: 2.8 Consensus size: 54
3615809 ATATTGAGTC
* * *
3615819 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAAT
* ** ** *
3615873 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCAAAT
* **
3615928 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCT
3615970 GTACAATTCA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 37 0.45
55 45 0.55
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAAT
Found at i:3615981 original size:55 final size:54
Alignment explanation
Indices: 3615819--3615997 Score: 147
Period size: 55 Copynumber: 3.3 Consensus size: 54
3615809 ATATTGAGTC
* *
3615819 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGC-TACGTAA-TCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCGTAC--AATTCAATT
*
3615873 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCG--C-ATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTG-CGTACAAT--TCAATT
* ** *
3615928 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCTGTACAATTCAATCC
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGC-GTACAATTCAAT-T
*
3615984 CGCGCACTTAGTGC
1 CGCACACTTAGTGC
3615998 CAATATCATG
Statistics
Matches: 103, Mismatches: 8, Indels: 26
0.75 0.06 0.19
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 34 0.33
55 48 0.47
56 16 0.16
57 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCGTACAATTCAATT
Found at i:3622838 original size:40 final size:38
Alignment explanation
Indices: 3622794--3623076 Score: 147
Period size: 38 Copynumber: 7.4 Consensus size: 38
3622784 GAATCCAGTC
*
3622794 ACCAGCACAAAACCTACAGGACTTTAAGCTCGAATATAAT
1 ACCAGCACAAAACCTACAGGA-TTTAA-CCCGAATATAAT
* * * * *
3622834 ACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAAT
1 ACCAGCACAAAACCTACAGGATTTAACCCGAATATAAT
* * * * ** *
3622872 ACCAGCACGAAGCCTGCGGGATAAAACCC-AGATATAGT
1 ACCAGCACAAAACCTACAGGATTTAACCCGA-ATATAAT
* * * * ** *
3622910 ACCAGCACTAAGCCTGCGGGATAAAACCCGGATATAAT
1 ACCAGCACAAAACCTACAGGATTTAACCCGAATATAAT
** * * * ** * *
3622948 ACCAGCATGAAGCCTGCGGGATAAAACACGGATATAAT
1 ACCAGCACAAAACCTACAGGATTTAACCCGAATATAAT
* * * ** *
3622986 ACCAGCACTAAGCCTGC-GGTATAAAACCCGGATATAAT
1 ACCAGCACAAAACCTACAGG-ATTTAACCCGAATATAAT
* * * * *
3623024 ACCAGCACTAAGCCAACGGGATTTAACCCGGATATAAT
1 ACCAGCACAAAACCTACAGGATTTAACCCGAATATAAT
*
3623062 ACCAGCACTAAACCT
1 ACCAGCACAAAACCT
3623077 GCGGGATAAA
Statistics
Matches: 213, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
37 2 0.01
38 187 0.88
39 7 0.03
40 17 0.08
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.17
Consensus pattern (38 bp):
ACCAGCACAAAACCTACAGGATTTAACCCGAATATAAT
Found at i:3622872 original size:38 final size:38
Alignment explanation
Indices: 3622827--3623097 Score: 418
Period size: 38 Copynumber: 7.1 Consensus size: 38
3622817 TTAAGCTCGA
**
3622827 ATATAATACCAGCACTAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACTAAGCCTGCGGGATAAAACCCGG
* *
3622865 ATATAATACCAGCACGAAGCCTGCGGGATAAAACCCAG
1 ATATAATACCAGCACTAAGCCTGCGGGATAAAACCCGG
*
3622903 ATATAGTACCAGCACTAAGCCTGCGGGATAAAACCCGG
1 ATATAATACCAGCACTAAGCCTGCGGGATAAAACCCGG
*
3622941 ATATAATACCAGCA-TGAAGCCTGCGGGATAAAACACGG
1 ATATAATACCAGCACT-AAGCCTGCGGGATAAAACCCGG
*
3622979 ATATAATACCAGCACTAAGCCTGCGGTATAAAACCCGG
1 ATATAATACCAGCACTAAGCCTGCGGGATAAAACCCGG
** **
3623017 ATATAATACCAGCACTAAGCCAACGGGATTTAACCCGG
1 ATATAATACCAGCACTAAGCCTGCGGGATAAAACCCGG
*
3623055 ATATAATACCAGCACTAAACCTGCGGGATAAAACCCGG
1 ATATAATACCAGCACTAAGCCTGCGGGATAAAACCCGG
3623093 ATATA
1 ATATA
3623098 CATCAAATAC
Statistics
Matches: 210, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
37 1 0.00
38 208 0.99
39 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.17
Consensus pattern (38 bp):
ATATAATACCAGCACTAAGCCTGCGGGATAAAACCCGG
Found at i:3626714 original size:40 final size:40
Alignment explanation
Indices: 3626512--3626714 Score: 193
Period size: 40 Copynumber: 5.1 Consensus size: 40
3626502 CGAAATTTAA
** *
3626512 CCGGATATAGCT-ACTCGTTCAAAT-CCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
3626551 CCGGTTATAGTAACTCGCATAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
3626591 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTATC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
3626630 CCGGA-ATTAGTATCTTGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * * *
3626670 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACCTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
3626710 CCGGA
1 CCGGA
3626715 CATCATTCAA
Statistics
Matches: 135, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
38 3 0.02
39 49 0.36
40 71 0.53
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:3632251 original size:117 final size:117
Alignment explanation
Indices: 3632045--3632371 Score: 514
Period size: 117 Copynumber: 2.8 Consensus size: 117
3632035 TTTGGTTTGT
*
3632045 TGGTTATTTGTGATTTATTATTGCAATTTTAGTGTCGCAATGTAGGGTTTGTTTTGTCGATTTGT
1 TGGTTATTTGTGATTTATTATTGCAATTTTAGTGCCGCAATGTAGGGTTTGTTTTGTCGATTTGT
* *
3632110 GATGCGACAGTGGTCTCGATGTTGTTGATAAAGCTATTGTTAAAATTGTAGA
66 GATGCGACAGTGGTCCCGATGTTGTTGATAAAGATATTGTTAAAATTGTAGA
* *
3632162 TGGTTATTTGTGATTTATTATTGCAATTTCAATG-CGACAATGTAGGGTTTGTTTTGTCGATTTG
1 TGGTTATTTGTGATTTATTATTGCAATTTTAGTGCCG-CAATGTAGGGTTTGTTTTGTCGATTTG
* *
3632226 TGATGCGACAGTGGTCCCAATGTTGTTGATAAAGATATTGTTAAAATTGTATA
65 TGATGCGACAGTGGTCCCGATGTTGTTGATAAAGATATTGTTAAAATTGTAGA
* **
3632279 TGGTTATTTTTGATTTATTATTGCTGTTTTAGTGCCGCAATGTA-GGTTTGTTTTGTCGATTTGT
1 TGGTTATTTGTGATTTATTATTGCAATTTTAGTGCCGCAATGTAGGGTTTGTTTTGTCGATTTGT
* * *
3632343 GATACGATAGTGGTCCTGATGTTGTTGAT
66 GATGCGACAGTGGTCCCGATGTTGTTGAT
3632372 TATTGTTACC
Statistics
Matches: 193, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
116 47 0.24
117 144 0.75
118 2 0.01
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.45
Consensus pattern (117 bp):
TGGTTATTTGTGATTTATTATTGCAATTTTAGTGCCGCAATGTAGGGTTTGTTTTGTCGATTTGT
GATGCGACAGTGGTCCCGATGTTGTTGATAAAGATATTGTTAAAATTGTAGA
Found at i:3632920 original size:33 final size:32
Alignment explanation
Indices: 3632879--3632955 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
3632869 GTTGACTGCT
*
3632879 TGGG-AGGGTGATGTTAAATAGGTAGAAGTTGA
1 TGGGAAGGGTGATGATAAA-AGGTAGAAGTTGA
* * *
3632911 TGGGAAGGGTGATGATGAAGGGTAGAATTTGA
1 TGGGAAGGGTGATGATAAAAGGTAGAAGTTGA
3632943 TGGTGAA-GGTGAT
1 TGG-GAAGGGTGAT
3632956 CTGGAAAGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 24 0.62
33 15 0.38
ACGTcount: A:0.30, C:0.00, G:0.43, T:0.27
Consensus pattern (32 bp):
TGGGAAGGGTGATGATAAAAGGTAGAAGTTGA
Found at i:3632935 original size:32 final size:32
Alignment explanation
Indices: 3632899--3633018 Score: 95
Period size: 32 Copynumber: 3.7 Consensus size: 32
3632889 ATGTTAAATA
3632899 GGTAGAAGTTGATGGGAAGGGTGATGATGAAG
1 GGTAGAAGTTGATGGGAAGGGTGATGATGAAG
* *
3632931 GGTAGAATTTGATGGTGAA-GGTGAT-CTGGAAAG
1 GGTAGAAGTTGATGG-GAAGGGTGATGAT-G-AAG
* * *
3632964 GGTA-AAATTG-TAGGGGAGGGTGATGTAAGAAG
1 GGTAGAAGTTGAT-GGGAAGGGTGATG-ATGAAG
* * *
3632996 GGTACAAGCTGATGGGGAGGGTG
1 GGTAGAAGTTGATGGGAAGGGTG
3633019 TGTCTGCTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
31 4 0.06
32 41 0.58
33 25 0.35
34 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.45, T:0.23
Consensus pattern (32 bp):
GGTAGAAGTTGATGGGAAGGGTGATGATGAAG
Found at i:3639839 original size:18 final size:18
Alignment explanation
Indices: 3639816--3639860 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3639806 GTTGAAAAAT
3639816 ATGTTGACAAAGACATTA
1 ATGTTGACAAAGACATTA
*
3639834 ATGTTGACAAAGGCATTA
1 ATGTTGACAAAGACATTA
*
3639852 GTGTTGACA
1 ATGTTGACA
3639861 CAGCCTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (18 bp):
ATGTTGACAAAGACATTA
Found at i:3642901 original size:24 final size:24
Alignment explanation
Indices: 3642874--3642934 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
3642864 TTCGAGTCTC
* *
3642874 TGTATTTAGTAGGATTTGA-GCCGG
1 TGTATTTAGTAGG-CTTCATGCCGG
*
3642898 TGTATTTAGCAGGCTTCATGCCGG
1 TGTATTTAGTAGGCTTCATGCCGG
*
3642922 TGTGTTTAGTAGG
1 TGTATTTAGTAGG
3642935 TACTGTGTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.18, C:0.11, G:0.33, T:0.38
Consensus pattern (24 bp):
TGTATTTAGTAGGCTTCATGCCGG
Found at i:3650113 original size:69 final size:69
Alignment explanation
Indices: 3650002--3650143 Score: 248
Period size: 69 Copynumber: 2.1 Consensus size: 69
3649992 TACCTTCATA
* *
3650002 AAGTGCCATTCAAAAATCTTTGAATCGTATTCCATTTGTAGAAGTATGCAATTTGACGATCAATT
1 AAGTGCCATTCAAAAATCCTGGAATCGTATTCCATTTGTAGAAGTATGCAATTTGACGATCAATT
3650067 GCAT
66 GCAT
*
3650071 AAGTGCCATTCAAAAATCCTGGAATCGTATTCCATTTGTAGAAGTGTGCAATTTGACGATCAATT
1 AAGTGCCATTCAAAAATCCTGGAATCGTATTCCATTTGTAGAAGTATGCAATTTGACGATCAATT
*
3650136 GCGT
66 GCAT
3650140 AAGT
1 AAGT
3650144 CTCATCGAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (69 bp):
AAGTGCCATTCAAAAATCCTGGAATCGTATTCCATTTGTAGAAGTATGCAATTTGACGATCAATT
GCAT
Found at i:3654683 original size:32 final size:34
Alignment explanation
Indices: 3654615--3654692 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 34
3654605 GTTAGGTTAC
*
3654615 TTTTAAATTTCAGTTTTTAAATTAAATCTTTGAT
1 TTTTAAATTTAAGTTTTTAAATTAAATCTTTGAT
* * *
3654649 TTTTAAATTTAAG-TTTT-AATTAGATTTTTTAT
1 TTTTAAATTTAAGTTTTTAAATTAAATCTTTGAT
*
3654681 TTTAAAATTTAA
1 TTTTAAATTTAA
3654693 TTCTTATGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 23 0.59
33 4 0.10
34 12 0.31
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58
Consensus pattern (34 bp):
TTTTAAATTTAAGTTTTTAAATTAAATCTTTGAT
Found at i:3654684 original size:25 final size:25
Alignment explanation
Indices: 3654646--3654694 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3654636 TTAAATCTTT
**
3654646 GATTTTTAAATTTAAGTTTTAATTA
1 GATTTTTAAATTTAAAATTTAATTA
* *
3654671 GATTTTTTATTTTAAAATTTAATT
1 GATTTTTAAATTTAAAATTTAATT
3654695 CTTATGTTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (25 bp):
GATTTTTAAATTTAAAATTTAATTA
Found at i:3656817 original size:8 final size:8
Alignment explanation
Indices: 3656793--3656830 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
3656783 GAGGAGACGA
3656793 TGGTGATGG
1 TGGTGA-GG
*
3656802 TAGTGAGG
1 TGGTGAGG
3656810 TGGTGAGG
1 TGGTGAGG
3656818 TGGTGAGG
1 TGGTGAGG
3656826 TGGTG
1 TGGTG
3656831 GTTTGGTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 22 0.81
9 5 0.19
ACGTcount: A:0.13, C:0.00, G:0.58, T:0.29
Consensus pattern (8 bp):
TGGTGAGG
Found at i:3662086 original size:20 final size:19
Alignment explanation
Indices: 3662040--3662089 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
3662030 GTGCAAGCAG
*
3662040 GGGCACCGTAGTGTGAACA
1 GGGCACCGAAGTGTGAACA
3662059 GGGACACCGAAGTGT-ATACAA
1 GGG-CACCGAAGTGTGA-AC-A
3662080 GGGCACCGAA
1 GGGCACCGAA
3662090 ATGCAAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.15
20 19 0.70
21 4 0.15
ACGTcount: A:0.32, C:0.22, G:0.34, T:0.12
Consensus pattern (19 bp):
GGGCACCGAAGTGTGAACA
Found at i:3662330 original size:21 final size:21
Alignment explanation
Indices: 3662305--3662345 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3662295 TATGTATTTA
3662305 TACAATTTACCAGCAACAATT
1 TACAATTTACCAGCAACAATT
3662326 TACAATTTACCAGCAACAAT
1 TACAATTTACCAGCAACAAT
3662346 AACTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (21 bp):
TACAATTTACCAGCAACAATT
Found at i:3664739 original size:18 final size:18
Alignment explanation
Indices: 3664712--3664746 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3664702 TGCCAATTTA
*
3664712 TGAAACTGTGATGTTGTG
1 TGAAACTGTGATATTGTG
*
3664730 TGAAATTGTGATATTGT
1 TGAAACTGTGATATTGT
3664747 TTCTGTGATG
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:0.26, C:0.03, G:0.29, T:0.43
Consensus pattern (18 bp):
TGAAACTGTGATATTGTG
Found at i:3666911 original size:9 final size:9
Alignment explanation
Indices: 3666893--3666940 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
3666883 GTCAACAAAT
3666893 AATT-TAAA
1 AATTATAAA
*
3666901 AATCATAAA
1 AATTATAAA
3666910 AATTA-AAA
1 AATTATAAA
*
3666918 AATTAAAACA
1 AATTATAA-A
3666928 AATTATAAA
1 AATTATAAA
3666937 AATT
1 AATT
3666941 TCATAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 11 0.32
9 15 0.44
10 8 0.24
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (9 bp):
AATTATAAA
Found at i:3666935 original size:27 final size:29
Alignment explanation
Indices: 3666900--3666954 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
3666890 AATAATTTAA
3666900 AAATCATAAAAA-TT-AAAAAATTAAAAC
1 AAATCATAAAAATTTCAAAAAATTAAAAC
* *
3666927 AAATTATAAAAATTTCATAAAATTAAAA
1 AAATCATAAAAATTTCAAAAAATTAAAA
3666955 TAATTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.46
28 2 0.08
29 11 0.46
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.27
Consensus pattern (29 bp):
AAATCATAAAAATTTCAAAAAATTAAAAC
Found at i:3667131 original size:17 final size:16
Alignment explanation
Indices: 3667109--3667149 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
3667099 GGCCAAATTT
3667109 AATTAAAAAAAGAAAAA
1 AATTAAAAAAA-AAAAA
*
3667126 AATTAACAAAAAAATAA
1 AATTAA-AAAAAAAAAA
3667143 AATTAAA
1 AATTAAA
3667150 GGCTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.73
18 5 0.23
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (16 bp):
AATTAAAAAAAAAAAA
Found at i:3667640 original size:17 final size:17
Alignment explanation
Indices: 3667620--3667668 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 17
3667610 TTTCAGTGAA
3667620 AATTATTTTTGAAAAAT
1 AATTATTTTTGAAAAAT
*
3667637 AA-T-TTTTAG-AAAAT
1 AATTATTTTTGAAAAAT
3667651 AATTTATTTTATGAAAAA
1 AA-TTATTTT-TGAAAAA
3667669 ATTAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 7 0.28
15 5 0.20
16 2 0.08
17 6 0.24
18 1 0.04
19 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
AATTATTTTTGAAAAAT
Found at i:3667641 original size:14 final size:14
Alignment explanation
Indices: 3667617--3667655 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3667607 TTTTTTCAGT
*
3667617 GAAAATTATTTTT-
1 GAAAATAATTTTTA
3667630 GAAAAATAATTTTTA
1 G-AAAATAATTTTTA
3667645 GAAAATAATTT
1 GAAAATAATTT
3667656 ATTTTATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (14 bp):
GAAAATAATTTTTA
Found at i:3668128 original size:23 final size:26
Alignment explanation
Indices: 3668095--3668157 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 26
3668085 TATTTTAAAA
*
3668095 AAAATACTCATA-TTTATA-TA-ATT
1 AAAATATTCATATTTTATACTAGATT
3668118 AAAATATTCATATTTTTATACTAGATT
1 AAAATATTCATA-TTTTATACTAGATT
3668145 AAAATATGTCATA
1 AAAATAT-TCATA
3668158 AGTCCTTGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
23 11 0.32
25 6 0.18
26 2 0.06
27 10 0.29
28 5 0.15
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (26 bp):
AAAATATTCATATTTTATACTAGATT
Found at i:3672012 original size:25 final size:25
Alignment explanation
Indices: 3671978--3672028 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3671968 TAATTGCAGA
3671978 AAAAAAATTAATTACAATAAAAAAT
1 AAAAAAATTAATTACAATAAAAAAT
3672003 AAAAAAATTAATTACAATAAAAAAT
1 AAAAAAATTAATTACAATAAAAAAT
3672028 A
1 A
3672029 TCTATAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAAAATTAATTACAATAAAAAAT
Found at i:3672461 original size:18 final size:18
Alignment explanation
Indices: 3672438--3672473 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3672428 TGATTTTTTT
*
3672438 TTTTACTTTTCATATTTG
1 TTTTACTGTTCATATTTG
*
3672456 TTTTACTGTTCATGTTTG
1 TTTTACTGTTCATATTTG
3672474 GGACCTATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.11, G:0.11, T:0.64
Consensus pattern (18 bp):
TTTTACTGTTCATATTTG
Found at i:3675121 original size:11 final size:11
Alignment explanation
Indices: 3675105--3675129 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3675095 ATGGTCGCCA
3675105 CCGTGGAACCG
1 CCGTGGAACCG
3675116 CCGTGGAACCG
1 CCGTGGAACCG
3675127 CCG
1 CCG
3675130 CGTCTAGCGG
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:0.16, C:0.40, G:0.36, T:0.08
Consensus pattern (11 bp):
CCGTGGAACCG
Found at i:3676189 original size:50 final size:50
Alignment explanation
Indices: 3676135--3676283 Score: 172
Period size: 50 Copynumber: 3.0 Consensus size: 50
3676125 TATGATGTCG
* *
3676135 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTATTCCACTGCACCGCCA
1 GGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTATTCCACTGCAACGCCA
* * * ** * * *
3676185 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCAATGTCG
1 GGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTATTCCACTGCAACGCCA
* * * *
3676235 GGGAAGCAAGATTCACCGATGTAGCTTTAATCTGTTCCACTGCATCGCC
1 GGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTATTCCACTGCAACGCC
3676284 TGGGGGATAA
Statistics
Matches: 79, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 79 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (50 bp):
GGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTATTCCACTGCAACGCCA
Found at i:3676485 original size:44 final size:44
Alignment explanation
Indices: 3676309--3677089 Score: 171
Period size: 44 Copynumber: 16.7 Consensus size: 44
3676299 GCTTCTTCGG
* * * * *
3676309 TCTGTTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATGCGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAA
* * * * *
3676350 TCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTT-TA-TTTTAA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TTCTAGCTTCAA
* * * * *
3676394 TCTACTCCACTATAATCTCAAGGAGATAGGATTACTAGCTTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAA
* *
3676438 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAA
* ** * *
3676482 TCTGATGCGATCTACTCTACTGTAACCTCAGAAAGATAAGATCCTT-TA-TTTTAA
1 TC---T--G--CT-C-C-ACTGTAATCTCAGGGAGATAAGAT--TTCTAGCTTCAA
* * * * *
3676536 TCCGCTCCACTGTAATCTCATGGAGAT-AGGTTACTAGCTTCTA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAA
* *
3676579 TCTGCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGT-AA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCT-TCAA
* * * *
3676623 TCTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTT-TA-TTTTAA
1 TC---T--G--CT-C-C-ACTGTAATCTCAGGGAGATAAGAT--TTCTAGCTTCAA
* * *
3676677 TCCGCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGT-AA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCT-TCAA
* * ** * *
3676721 TCTGATGCGATCTACTCTATTGTAACCTCAGAAAGATAAGATCCTT-TA-TTTTAA
1 TC---T--G--CT-C-C-ACTGTAATCTCAGGGAGATAAGAT--TTCTAGCTTCAA
* * *
3676775 TCCGCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGT-AA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCT-TCAA
* * * *
3676819 TCTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTT-TA-TTTTAA
1 TC---T--G--CT-C-C-ACTGTAATCTCAGGGAGATAAGAT--TTCTAGCTTCAA
* * * * *
3676873 TCCGCTCCACTGTAATTTCAGGGAGATAGGATTACTAGCTTCCA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAA
* ** * *
3676917 CCTGCTCTGCTGTAATATCAGGGAGATAAGATTTCTGGCTTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAA
* * * *
3676961 TCTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTT-TA-TTTTAA
1 TC---T--G--CT-C-C-ACTGTAATCTCAGGGAGATAAGAT--TTCTAGCTTCAA
* * * * ** *
3677015 TCCGGTCCACTGTAATTTCAGGGAGATAGGATTAGTAGCTTCCA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAA
** *
3677059 TCTGCTCTGCTGTAATCTTAGGGAGATAAGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGA
3677090 CTTGTTTTCT
Statistics
Matches: 529, Mismatches: 125, Indels: 169
0.64 0.15 0.21
Matches are distributed among these distances:
40 1 0.00
41 26 0.05
42 9 0.02
43 38 0.07
44 254 0.48
45 9 0.02
46 5 0.01
47 12 0.02
49 10 0.02
51 10 0.02
52 5 0.01
53 7 0.01
54 128 0.24
55 5 0.01
56 10 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (44 bp):
TCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAA
Found at i:3676646 original size:141 final size:142
Alignment explanation
Indices: 3676341--3676709 Score: 616
Period size: 141 Copynumber: 2.6 Consensus size: 142
3676331 GAGATAAGAC
* ** *
3676341 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTACTCCACTA
1 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
3676406 TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
3676471 TCTGGCTTCAAT
131 TCTGGCTTCAAT
*
3676483 CTGATGCGATCTACTCTACTGTAACCTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * *
3676548 TAATCTCATGGAGATAGG-TTACTAGCTTCTATCTGCTCCTCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
3676612 TCTGGCTGT-AAT
131 TCTGGCT-TCAAT
*
3676624 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCTCTG
1 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
3676689 TAATCTCAGGGAGATAAGATT
66 TAATCTCAAGGAGATAGGATT
3676710 TCTGGCTGTA
Statistics
Matches: 213, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
141 133 0.62
142 80 0.38
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:3676712 original size:98 final size:98
Alignment explanation
Indices: 3676582--3676905 Score: 603
Period size: 98 Copynumber: 3.3 Consensus size: 98
3676572 GCTTCTATCT
3676582 GCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTA
1 GCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTA
3676647 ACCTCAGAGAGATAAGATCCTTTATTTTAATCC
66 ACCTCAGAGAGATAAGATCCTTTATTTTAATCC
*
3676680 GCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTATTGTA
1 GCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTA
*
3676745 ACCTCAGAAAGATAAGATCCTTTATTTTAATCC
66 ACCTCAGAGAGATAAGATCCTTTATTTTAATCC
3676778 GCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTA
1 GCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTA
3676843 ACCTCAGAGAGATAAGATCCTTTATTTTAATCC
66 ACCTCAGAGAGATAAGATCCTTTATTTTAATCC
* * *
3676876 GCTCCACTGTAATTTCAGGGAGATAGGATT
1 GCTCCTCTGTAATCTCAGGGAGATAAGATT
3676906 ACTAGCTTCC
Statistics
Matches: 219, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 219 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (98 bp):
GCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTA
ACCTCAGAGAGATAAGATCCTTTATTTTAATCC
Found at i:3676997 original size:142 final size:142
Alignment explanation
Indices: 3676784--3677089 Score: 551
Period size: 142 Copynumber: 2.2 Consensus size: 142
3676774 ATCCGCTCCT
3676784 CTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTAACCTCA
1 CTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTAACCTCA
3676849 GAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATTTCAGGGAGATAGGATTACTAGCTT
66 GAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATTTCAGGGAGATAGGATTACTAGCTT
3676914 CCACCTGCTCTG
131 CCACCTGCTCTG
*
3676926 CTGTAATATCAGGGAGATAAGATTTCTGGCT-TCAATCTGATGCGATCTACTCTACTGTAACCTC
1 CTGTAATCTCAGGGAGATAAGATTTCTGGCTGT-AATCTGATGCGATCTACTCTACTGTAACCTC
* *
3676990 AGAGAGATAAGATCCTTTATTTTAATCCGGTCCACTGTAATTTCAGGGAGATAGGATTAGTAGCT
65 AGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATTTCAGGGAGATAGGATTACTAGCT
*
3677055 TCCATCTGCTCTG
130 TCCACCTGCTCTG
*
3677068 CTGTAATCTTAGGGAGATAAGA
1 CTGTAATCTCAGGGAGATAAGA
3677090 CTTGTTTTCT
Statistics
Matches: 157, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
141 1 0.01
142 156 0.99
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (142 bp):
CTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTAACCTCA
GAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATTTCAGGGAGATAGGATTACTAGCTT
CCACCTGCTCTG
Found at i:3677002 original size:196 final size:190
Alignment explanation
Indices: 3676582--3676948 Score: 508
Period size: 196 Copynumber: 1.9 Consensus size: 190
3676572 GCTTCTATCT
3676582 GCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTA
1 GCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTA
* *
3676647 ACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCTCTGTAATCTCAGGGAGATAAGATTTC
66 ACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTAC
* * * * * * *
3676712 TGGCTGTAATCTGATGCGATCTACTCTATTGTAACCTCAGAAAGATAAGATCCTTTATTTTAATC
131 TAGC-GT-ATC----GCGACCTACTCTACTGTAACATCAGAAAGATAAGATCCTTCAATCTAATC
3676777 C
190 C
3676778 GCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTA
1 GCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTA
* *
3676843 ACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATTTCAGGGAGATAGGATTAC
66 ACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTAC
* * * **
3676908 TAGC-T-TC-C-ACCTGCTCTGCTGTAATATCAGGGAGATAAGAT
131 TAGCGTATCGCGACCTACTCTACTGTAACATCAGAAAGATAAGAT
3676949 TTCTGGCTTC
Statistics
Matches: 158, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
186 25 0.16
187 1 0.01
192 2 0.01
194 1 0.01
196 129 0.82
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (190 bp):
GCTCCTCTGTAATCTCAGGGAGATAAGATTTCTGGCTGTAATCTGATGCGATCTACTCTACTGTA
ACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTAC
TAGCGTATCGCGACCTACTCTACTGTAACATCAGAAAGATAAGATCCTTCAATCTAATCC
Found at i:3678575 original size:15 final size:15
Alignment explanation
Indices: 3678541--3678574 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3678531 TTATTTTTAC
*
3678541 TTTTTCATTTTTCCA
1 TTTTTCATTTTCCCA
3678556 TTTTTCATTTTCCC-
1 TTTTTCATTTTCCCA
3678570 TTTTT
1 TTTTT
3678575 TTGACTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTCATTTTCCCA
Found at i:3679415 original size:8 final size:8
Alignment explanation
Indices: 3679402--3679441 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
3679392 CCTTGGCTTC
3679402 TCCTTTTT
1 TCCTTTTT
3679410 TCCTTTTT
1 TCCTTTTT
3679418 T-CTTTTT
1 TCCTTTTT
* *
3679425 TCCTTCTC
1 TCCTTTTT
3679433 TCCTTTTT
1 TCCTTTTT
3679441 T
1 T
3679442 ATTTTCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (8 bp):
TCCTTTTT
Found at i:3679451 original size:6 final size:6
Alignment explanation
Indices: 3679437--3679476 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
3679427 CTTCTCTCCT
* * *
3679437 TTTTTA TTTTCA TTTTGA CTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
3679477 TCTTCTCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.15, C:0.05, G:0.10, T:0.70
Consensus pattern (6 bp):
TTTTGA
Found at i:3685389 original size:19 final size:21
Alignment explanation
Indices: 3685354--3685394 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
3685344 AATTTTTTTG
3685354 AAAAGTCACAATATTTTAAAT
1 AAAAGTCACAATATTTTAAAT
3685375 AAAA-TCACAAT-TTTTAAAT
1 AAAAGTCACAATATTTTAAAT
3685394 A
1 A
3685395 TAAGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
20 7 0.35
21 4 0.20
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAAGTCACAATATTTTAAAT
Found at i:3685408 original size:17 final size:17
Alignment explanation
Indices: 3685383--3685420 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3685373 ATAAAATCAC
*
3685383 AATTTTTAAATATAAGAA
1 AATTTTAAAATATAA-AA
3685401 AATTTTAAAATATAAAA
1 AATTTTAAAATATAAAA
3685418 AAT
1 AAT
3685421 CCATATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTTTAAAATATAAAA
Found at i:3686522 original size:26 final size:26
Alignment explanation
Indices: 3686493--3686549 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
3686483 TATGAGCCTA
*
3686493 CCTTGCAAG-TTGGGTCTGCAAACTCC
1 CCTTGC-AGTTTGGGTCTACAAACTCC
* * *
3686519 CCTTACTGTTTGGGTCTACGAACTCC
1 CCTTGCAGTTTGGGTCTACAAACTCC
3686545 CCTTG
1 CCTTG
3686550 TTGTCCTCTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.16, C:0.32, G:0.21, T:0.32
Consensus pattern (26 bp):
CCTTGCAGTTTGGGTCTACAAACTCC
Found at i:3688130 original size:211 final size:211
Alignment explanation
Indices: 3687764--3688187 Score: 769
Period size: 211 Copynumber: 2.0 Consensus size: 211
3687754 AAGGTCGCTA
*
3687764 AAGCCTTAGGGGCAGTTGTTGAGAGTCAGTCATGGCCACATGGAATTTATGGCAATTTTGAAAAC
1 AAGCCTTAGGGGCAGTTGTTGAGAGTCAGTCATGGCCACATGGAATTTATGGCAATTTTAAAAAC
* *
3687829 AACGAATTGGTCTAAATTCTGATCGGTCTTCGAAAGGAGCCTATGAACTATTTCTATAATTATTG
66 AACGAATTGGTCCAAATTCTGATCGGTCTTCGAAAGAAGCCTATGAACTATTTCTATAATTATTG
* *
3687894 TGGGATAAAGTCTCGTCCGTTGATGGTGGCCTCCTTGTGGGTAGAAAGGTTGTTCCAATTAATCT
131 TGGGATAAAGCCTCGTCCATTGATGGTGGCCTCCTTGTGGGTAGAAAGGTTGTTCCAATTAATCT
*
3687959 GTTAATTACTCCCATT
196 GTTAAGTACTCCCATT
*
3687975 AAGCCTTAGGGGCAGTTGTTGAGAGTCGGTCATGGCCACATGGAATTTATGGCAATTTTAAAAAC
1 AAGCCTTAGGGGCAGTTGTTGAGAGTCAGTCATGGCCACATGGAATTTATGGCAATTTTAAAAAC
3688040 AACGAATTGGTCCAAATTCTGATCGGTCTTCGAAAGAAGCC-AGTGAACTATTTCTATAATTATT
66 AACGAATTGGTCCAAATTCTGATCGGTCTTCGAAAGAAGCCTA-TGAACTATTTCTATAATTATT
3688104 GTGGGATAAAGCCTCGTCCATTGATGGTGGCCTCCTTGTGGGTAGAAAGGTTGTTCCAATTAATC
130 GTGGGATAAAGCCTCGTCCATTGATGGTGGCCTCCTTGTGGGTAGAAAGGTTGTTCCAATTAATC
3688169 TGTTAAGTACTCCCATT
195 TGTTAAGTACTCCCATT
3688186 AA
1 AA
3688188 TGTTAGGATT
Statistics
Matches: 205, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
210 1 0.00
211 204 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (211 bp):
AAGCCTTAGGGGCAGTTGTTGAGAGTCAGTCATGGCCACATGGAATTTATGGCAATTTTAAAAAC
AACGAATTGGTCCAAATTCTGATCGGTCTTCGAAAGAAGCCTATGAACTATTTCTATAATTATTG
TGGGATAAAGCCTCGTCCATTGATGGTGGCCTCCTTGTGGGTAGAAAGGTTGTTCCAATTAATCT
GTTAAGTACTCCCATT
Found at i:3689915 original size:71 final size:71
Alignment explanation
Indices: 3689746--3689917 Score: 177
Period size: 71 Copynumber: 2.4 Consensus size: 71
3689736 GGATAGTTGG
* *
3689746 GAGTTTTTAACTCTCATTAAATGTTTGGAGGGCTGCAGTCTTAAACCTGTGAGCCATAAAATGGC
1 GAGTTTTTAACTCTCATTAAATGTTTGGAGGGCTGCAGTATTAAACCTGTGAGCCATAAAATGAC
3689811 AGCTAA
66 AGCTAA
* * * * * * * *
3689817 GAGTTTTTAACTGTCCTTAACTATTTGG-GGGACTG-AGATATTGAACTTGTGAGCCTTAATATG
1 GAGTTTTTAACTCTCATTAAATGTTTGGAGGG-CTGCAG-TATTAAACCTGTGAGCCATAAAATG
* *
3689880 ACCGCTAG
64 ACAGCTAA
* * *
3689888 GATTTTTTAACTCTCGTTAATTGTTTGGAG
1 GAGTTTTTAACTCTCATTAAATGTTTGGAG
3689918 AACAACTGAA
Statistics
Matches: 81, Mismatches: 17, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
70 5 0.06
71 75 0.93
72 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (71 bp):
GAGTTTTTAACTCTCATTAAATGTTTGGAGGGCTGCAGTATTAAACCTGTGAGCCATAAAATGAC
AGCTAA
Found at i:3690057 original size:71 final size:70
Alignment explanation
Indices: 3689931--3690551 Score: 441
Period size: 71 Copynumber: 8.8 Consensus size: 70
3689921 AACTGAAAGC
* * * * * * * * *
3689931 TTTTAACTCTCGCTAATTGTTTGGGGAGCTACAGCCTTAAACCTAT-AAGCTTTAAAGCGAAAAT
1 TTTTAACTCTTGCTAACTATTTGGGG-GCTGCAGTCTTAAACCT-TCGAGCCTTAAAGTGATAAT
3689995 TGAGAGT
64 TGAGAGT
* * * * *
3690002 TTTTAACTGTTGCTAACTGTCTGGAGGGCTGCAGTCTTAAACTTTCGAGCCTTAAAGTGATAGTT
1 TTTTAACTCTTGCTAACTATTTGG-GGGCTGCAGTCTTAAACCTTCGAGCCTTAAAGTGATAATT
* *
3690067 GGGAGC
65 GAGAGT
* * ** * * * *
3690073 TTTTAACTCTCT-TTAACTATTTGGGGGGTGTGGTTTTAAACCTGCAAGCCTTAAAGTGATAGTT
1 TTTTAACTCT-TGCTAACTATTTGGGGGCTGCAGTCTTAAACCTTCGAGCCTTAAAGTGATAATT
3690137 -AGGAGT
65 GA-GAGT
* * * *
3690143 TTTTAACTCTTACTAATTATTTGGGGGGCTGCAGTCTTAAACTTTTGAGCCTTAAAGTGATAATT
1 TTTTAACTCTTGCTAACTATTT-GGGGGCTGCAGTCTTAAACCTTCGAGCCTTAAAGTGATAATT
*
3690208 GAGAGC
65 GAGAGT
* * * * * *
3690214 TTTTAACTCTGGCTAACTATTTGGGGGGCTGCAGTCTTAGACCTACGAGCATTAAAGTGACAGTT
1 TTTTAACTCTTGCTAACTATTT-GGGGGCTGCAGTCTTAAACCTTCGAGCCTTAAAGTGATA-AT
3690279 TG-GAGT
64 TGAGAGT
* * * * *
3690285 TTTTAACTCTTGCTAATTGTTTGGGCGGTTGCGGTCTTAAACCTTCGAGCCTTAAAGTGATAGTT
1 TTTTAACTCTTGCTAACTATTTGGG-GGCTGCAGTCTTAAACCTTCGAGCCTTAAAGTGATAATT
* *
3690350 GGGAGC
65 GAGAGT
** * * * * * *
3690356 TTTTAACTCTCACTTACTATTTGGGGGGCTACGGTCTTAAACCTAT-GAGTCTTAAAGTGACATT
1 TTTTAACTCTTGCTAACTATTT-GGGGGCTGCAGTCTTAAACCT-TCGAGCCTTAAAGTGATAAT
* *
3690420 TGGGAGC
64 TGAGAGT
* * * * * * * **
3690427 TTTTAACTCATGCTAACTATTTGGGGGGCTACGGTATTGAACCTACGAGCCTTAATA-TG-CACC
1 TTTTAACTCTTGCTAACTATTT-GGGGGCTGCAGTCTTAAACCTTCGAGCCTTAA-AGTGATAAT
*
3690490 TGGGAGT
64 TGAGAGT
* * * *
3690497 TTTTAACT-TTCGCTAACTATTTGAGGAGTTGTAGTCTTAAA-CTTGTGAGCCTTAA
1 TTTTAACTCTT-GCTAACTATTTG-GGGGCTGCAGTCTTAAACCTT-CGAGCCTTAA
3690552 TTTTGATAAA
Statistics
Matches: 441, Mismatches: 92, Indels: 35
0.78 0.16 0.06
Matches are distributed among these distances:
69 5 0.01
70 107 0.24
71 317 0.72
72 12 0.03
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (70 bp):
TTTTAACTCTTGCTAACTATTTGGGGGCTGCAGTCTTAAACCTTCGAGCCTTAAAGTGATAATTG
AGAGT
Found at i:3690335 original size:142 final size:141
Alignment explanation
Indices: 3689928--3690519 Score: 600
Period size: 142 Copynumber: 4.2 Consensus size: 141
3689918 AACAACTGAA
* * * * * *
3689928 AGCTTTTAACTCTCGCTAATTGTTTGGGGAGCTACAGCCTTAAACCTATAAGCTTTAAAGCGA-A
1 AGCTTTTAACTCTCGCTAACTATTTGGGGGGCTACAGTCTTAAACCTACAAGC-TTAAAGTGACA
** * * * * *
3689992 AATTGAGAGTTTTTAACTGTTGCTAACTGTCTGGAGGGCTGCAGTCTTAAACTTTCGAGCCTTAA
65 GTTTG-GAGTTTTTAACTCTTGCTAACTATTTGGGGGGCTGCAGTCTTAAACCTTCGAGCCTTAA
3690057 AGTGATAGTTGGG
129 AGTGATAGTTGGG
** *** * * *
3690070 AGCTTTTAACTCTCTTTAACTATTTGGGGGG-TGTGGTTTTAAACCTGCAAGCCTTAAAGTGATA
1 AGCTTTTAACTCTCGCTAACTATTTGGGGGGCTACAGTCTTAAACCTACAAG-CTTAAAGTGACA
* * * * *
3690134 GTTAGGAGTTTTTAACTCTTACTAATTATTTGGGGGGCTGCAGTCTTAAACTTTTGAGCCTTAAA
65 GTTTGGAGTTTTTAACTCTTGCTAACTATTTGGGGGGCTGCAGTCTTAAACCTTCGAGCCTTAAA
* *
3690199 GTGATAATTGAG
130 GTGATAGTTGGG
* * * *
3690211 AGCTTTTAACTCTGGCTAACTATTTGGGGGGCTGCAGTCTTAGACCTACGAGCATTAAAGTGACA
1 AGCTTTTAACTCTCGCTAACTATTTGGGGGGCTACAGTCTTAAACCTACAAGC-TTAAAGTGACA
* * * * *
3690276 GTTTGGAGTTTTTAACTCTTGCTAATTGTTTGGGCGGTTGCGGTCTTAAACCTTCGAGCCTTAAA
65 GTTTGGAGTTTTTAACTCTTGCTAACTATTTGGGGGGCTGCAGTCTTAAACCTTCGAGCCTTAAA
3690341 GTGATAGTTGGG
130 GTGATAGTTGGG
* * * **
3690353 AGCTTTTAACTCTCACTTACTATTTGGGGGGCTACGGTCTTAAACCTATGAGTCTTAAAGTGACA
1 AGCTTTTAACTCTCGCTAACTATTTGGGGGGCTACAGTCTTAAACCTACAAG-CTTAAAGTGACA
* * * * * * *
3690418 -TTTGGGAGCTTTTAACTCATGCTAACTATTTGGGGGGCTACGGTATTGAACCTACGAGCCTTAA
65 GTTT-GGAGTTTTTAACTCTTGCTAACTATTTGGGGGGCTGCAGTCTTAAACCTTCGAGCCTTAA
* **
3690482 TA-TG-CACCTGGG
129 -AGTGATAGTTGGG
* *
3690494 AGTTTTTAACTTTCGCTAACTATTTG
1 AGCTTTTAACTCTCGCTAACTATTTG
3690520 AGGAGTTGTA
Statistics
Matches: 374, Mismatches: 69, Indels: 15
0.82 0.15 0.03
Matches are distributed among these distances:
141 143 0.38
142 229 0.61
143 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (141 bp):
AGCTTTTAACTCTCGCTAACTATTTGGGGGGCTACAGTCTTAAACCTACAAGCTTAAAGTGACAG
TTTGGAGTTTTTAACTCTTGCTAACTATTTGGGGGGCTGCAGTCTTAAACCTTCGAGCCTTAAAG
TGATAGTTGGG
Found at i:3690475 original size:213 final size:209
Alignment explanation
Indices: 3689928--3690519 Score: 641
Period size: 212 Copynumber: 2.8 Consensus size: 209
3689918 AACAACTGAA
* * * * * *
3689928 AGCTTTTAACTCTCGCTAATTGTTTGGGGAGCTACAGCCTTAAACCTATAAGCTTTAAAGCGAAA
1 AGCTTTTAACTCTCACTAATTATTTGGGGGGCTACAGTCTTAAACCTATGAGC-TTAAAGTGAAA
* * * * * * *
3689993 ATTGAGAGTTTTTAACTGTTGCTAACTGTCTGGAGGGCTGCAGTCTTAAACTTTCGAGCCTTAAA
65 ATTGAGAGCTTTTAACT-CTGCTAACTATTTGGGGGGCTGCAGTCTT-AACCTACGAGCCTTAAA
* * * *
3690058 GTGATAGTTGGGAGCTTTTAACTCTCTTTAACTATTTGGGGGGTGTGGTTTTAAACCTGCAAGCC
128 GTGACAGTTGGGAGCTTTTAACTCTCTCTAACTATTTGGGGGGTGCGGTCTTAAACCTGCAAGCC
3690123 TTAAAGTGATAGTTAGG
193 TTAAAGTGATAGTTAGG
* * * * * *
3690140 AGTTTTTAACTCTTACTAATTATTTGGGGGGCTGCAGTCTTAAACTTTTGAGCCTTAAAGTGATA
1 AGCTTTTAACTCTCACTAATTATTTGGGGGGCTACAGTCTTAAACCTATGAG-CTTAAAGTGAAA
*
3690205 ATTGAGAGCTTTTAACTCTGGCTAACTATTTGGGGGGCTGCAGTCTTAGACCTACGAGCATTAAA
65 ATTGAGAGCTTTTAACTCT-GCTAACTATTTGGGGGGCTGCAGTCTTA-ACCTACGAGCCTTAAA
* * * * * * *
3690270 GTGACAGTTTGGAGTTTTTAACTCT-TGCTAATTGTTTGGGCGGTTGCGGTCTTAAACCTTCGAG
128 GTGACAGTTGGGAGCTTTTAACTCTCT-CTAACTATTTGGG-GGGTGCGGTCTTAAACCTGCAAG
*
3690334 CCTTAAAGTGATAGTTGGG
191 CCTTAAAGTGATAGTTAGG
* * * *
3690353 AGCTTTTAACTCTCACTTACTATTTGGGGGGCTACGGTCTTAAACCTATGAGTCTTAAAGTGACA
1 AGCTTTTAACTCTCACTAATTATTTGGGGGGCTACAGTCTTAAACCTATGAG-CTTAAAGTGAAA
* * * * *
3690418 TTTGGGAGCTTTTAACTCATGCTAACTATTTGGGGGGCTACGGTATTGAACCTACGAGCCTTAAT
65 ATTGAGAGCTTTTAACTC-TGCTAACTATTTGGGGGGCTGCAGTCTT-AACCTACGAGCCTTAA-
** * * *
3690483 A-TG-CACCTGGGAGTTTTTAACTTTCGCTAACTATTTG
127 AGTGACAGTTGGGAGCTTTTAACTCTCTCTAACTATTTG
3690520 AGGAGTTGTA
Statistics
Matches: 316, Mismatches: 55, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
211 3 0.01
212 162 0.51
213 148 0.47
214 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (209 bp):
AGCTTTTAACTCTCACTAATTATTTGGGGGGCTACAGTCTTAAACCTATGAGCTTAAAGTGAAAA
TTGAGAGCTTTTAACTCTGCTAACTATTTGGGGGGCTGCAGTCTTAACCTACGAGCCTTAAAGTG
ACAGTTGGGAGCTTTTAACTCTCTCTAACTATTTGGGGGGTGCGGTCTTAAACCTGCAAGCCTTA
AAGTGATAGTTAGG
Found at i:3690503 original size:283 final size:283
Alignment explanation
Indices: 3689919--3690524 Score: 691
Period size: 283 Copynumber: 2.1 Consensus size: 283
3689909 TGTTTGGAGA
* * * * *
3689919 ACAACTGAAAGCTTTTAACTCTCGCTAATTGTTTGGGGAGCTACAGCCTTAAACCTATAAGCTTT
1 ACAACTGAGAGCTTTTAACTCTCGCTAACTATTTGGGGAGCTACAGCCTTAAACCTACAAGCATT
* *
3689984 AAAGCGAAAATTGAGAGTTTTTAACTGTTGCTAACTGTCTGGAGGGCTGCAGTCTTAAACTTTCG
66 AAAGCGAAAATTGAGAGTTTTTAACTCTTGCTAACTGTCTGGAGGGCTGCAGTCTTAAACCTTCG
* ** *
3690049 AGCCTTAAAGTGATAGTTGGGAGCTTTTAACTCTCTTTAACTATTTGGGGGGTGTGGTTTTAAAC
131 AGCCTTAAAGTGATAGTTGGGAGCTTTTAACTCTCCTTAACTATTTGGGGGGTACGGTCTTAAAC
* * * * * * *
3690114 CTGCAAGCCTTAAAGTGATAGTTAGGAGTTTTTAACTCTTACTAATTATTTGGGGGGCTGCAGTC
196 CTACAAGCCTTAAAGTGACAGTTAGGAGCTTTTAACTCATACTAACTATTTGGGGGGCTACAGTA
* **
3690179 TTAAACTTTTGAGCCTTAAAGTG
261 TTAAACCTACGAGCCTTAAAGTG
* * * * * * * *
3690202 ATAATTGAGAGCTTTTAACTCTGGCTAACTATTTGGGGGGCTGCAGTCTTAGACCTACGAGCATT
1 ACAACTGAGAGCTTTTAACTCTCGCTAACTATTTGGGGAGCTACAGCCTTAAACCTACAAGCATT
* ** * * * *
3690267 AAAGTGACAGTTTG-GAGTTTTTAACTCTTGCTAATTGTTTGG-GCGGTTGCGGTCTTAAACCTT
66 AAAGCGA-AAATTGAGAGTTTTTAACTCTTGCTAACTGTCTGGAG-GGCTGCAGTCTTAAACCTT
3690330 CGAGCCTTAAAGTGATAGTTGGGAGCTTTTAACTCTCACTT-ACTATTTGGGGGGCTACGGTCTT
129 CGAGCCTTAAAGTGATAGTTGGGAGCTTTTAACTCTC-CTTAACTATTTGGGGGG-TACGGTCTT
** * * * *
3690394 AAACCTATGAGTCTTAAAGTGACATTTGGGAGCTTTTAACTCATGCTAACTATTTGGGGGGCTAC
192 AAACCTACAAGCCTTAAAGTGACAGTTAGGAGCTTTTAACTCATACTAACTATTTGGGGGGCTAC
* *
3690459 GGTATTGAACCTACGAGCCTTAATA-TG
257 AGTATTAAACCTACGAGCCTTAA-AGTG
* * * * *
3690486 -CACCTGGGAGTTTTTAACTTTCGCTAACTATTTGAGGAG
1 ACAACTGAGAGCTTTTAACTCTCGCTAACTATTTGGGGAG
3690525 TTGTAGTCTT
Statistics
Matches: 265, Mismatches: 53, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
282 1 0.00
283 179 0.68
284 84 0.32
285 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (283 bp):
ACAACTGAGAGCTTTTAACTCTCGCTAACTATTTGGGGAGCTACAGCCTTAAACCTACAAGCATT
AAAGCGAAAATTGAGAGTTTTTAACTCTTGCTAACTGTCTGGAGGGCTGCAGTCTTAAACCTTCG
AGCCTTAAAGTGATAGTTGGGAGCTTTTAACTCTCCTTAACTATTTGGGGGGTACGGTCTTAAAC
CTACAAGCCTTAAAGTGACAGTTAGGAGCTTTTAACTCATACTAACTATTTGGGGGGCTACAGTA
TTAAACCTACGAGCCTTAAAGTG
Found at i:3702556 original size:50 final size:50
Alignment explanation
Indices: 3702499--3702598 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
3702489 ATGTTAGTTA
3702499 AATTAAATGTTTATTATGTTGTTTTTAATGTAAATGAATTAATATATATG
1 AATTAAATGTTTATTATGTTGTTTTTAATGTAAATGAATTAATATATATG
3702549 AATTAAATGTTTATTATGTTGTTTTTAATGTAAATGAATTAATATATATG
1 AATTAAATGTTTATTATGTTGTTTTTAATGTAAATGAATTAATATATATG
3702599 TAAATGTATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (50 bp):
AATTAAATGTTTATTATGTTGTTTTTAATGTAAATGAATTAATATATATG
Found at i:3702613 original size:20 final size:19
Alignment explanation
Indices: 3702576--3702617 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
3702566 GTTGTTTTTA
3702576 ATGTAAATGAATTAATATAT
1 ATGTAAATGAATTAATAT-T
*
3702596 ATGTAAATGTATCT-ATATT
1 ATGTAAATGAAT-TAATATT
3702615 ATG
1 ATG
3702618 ACGAATTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 15 0.75
21 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (19 bp):
ATGTAAATGAATTAATATT
Found at i:3706298 original size:26 final size:26
Alignment explanation
Indices: 3706269--3706321 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
3706259 CTAATCAAAA
* *
3706269 AGGGGTTGCTGAGTGCAGATTCCCCG
1 AGGGGTTGCTAAGTGCAGATTCACCG
*
3706295 AGGGGTTGCTAAGTGCTGATTCACCG
1 AGGGGTTGCTAAGTGCAGATTCACCG
3706321 A
1 A
3706322 ATTATTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.25
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCAGATTCACCG
Found at i:3706387 original size:43 final size:41
Alignment explanation
Indices: 3706295--3706390 Score: 104
Period size: 43 Copynumber: 2.3 Consensus size: 41
3706285 AGATTCCCCG
* *
3706295 AGGGGTTGCTAAGTGCTGATTCACCGAATTATTGATTCTAA
1 AGGGGTTGCTAAGTGCTAATTCACCGAATCATTGATTCTAA
* * *
3706336 AGGTGGTTGCTAAGTGCTAATTCCATC-ATATCCTTGATTGTTAA
1 AGG-GGTTGCTAAGTGCTAATT-CACCGA-ATCATTGATT-CTAA
3706380 AGGGGTTGCTA
1 AGGGGTTGCTA
3706391 TGTACTGATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
41 3 0.07
42 18 0.39
43 19 0.41
44 6 0.13
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGCTAATTCACCGAATCATTGATTCTAA
Found at i:3708470 original size:3 final size:3
Alignment explanation
Indices: 3708462--3708486 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3708452 TTTTTATGTC
3708462 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3708487 TTCTTGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3710156 original size:65 final size:65
Alignment explanation
Indices: 3710080--3710203 Score: 223
Period size: 65 Copynumber: 1.9 Consensus size: 65
3710070 AAGCAATAAT
*
3710080 TAATTTAGCCACAACTCTCCATA-AAAAGTTATCGAATCTCAATGAAATAAGAAATAGAATAAAG
1 TAATTTAGCCACAACCCTCCATACAAAA-TTATCGAATCTCAATGAAATAAGAAATAGAATAAAG
3710144 C
65 C
3710145 TAATTTAGCCACAACCCTCCATACAAAATTATCGAATCTCAATGAAATAAGAAATAGAA
1 TAATTTAGCCACAACCCTCCATACAAAATTATCGAATCTCAATGAAATAAGAAATAGAA
3710204 GCCAATCAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 53 0.93
66 4 0.07
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.24
Consensus pattern (65 bp):
TAATTTAGCCACAACCCTCCATACAAAATTATCGAATCTCAATGAAATAAGAAATAGAATAAAGC
Found at i:3718786 original size:50 final size:50
Alignment explanation
Indices: 3718728--3718851 Score: 167
Period size: 50 Copynumber: 2.5 Consensus size: 50
3718718 TATTGAGGTT
* * * *
3718728 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
** *
3718778 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
**
3718828 ATGAGAACTCCCATGTAAGACCAT
1 ATGAGAGGTCCCATGTAAGACCAT
3718852 ATATGGGATA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
Found at i:3719148 original size:20 final size:20
Alignment explanation
Indices: 3719123--3719171 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3719113 TGAGTTATTT
3719123 AAGTAAGCAAGTAAGCAAAC
1 AAGTAAGCAAGTAAGCAAAC
* *
3719143 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGCAAAC
3719163 AAG-AAGCAA
1 AAGTAAGCAA
3719172 AGACCATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.57, C:0.08, G:0.24, T:0.10
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGCAAAC
Found at i:3722288 original size:49 final size:49
Alignment explanation
Indices: 3722235--3722339 Score: 174
Period size: 49 Copynumber: 2.1 Consensus size: 49
3722225 AACGAGAAGA
*
3722235 AAAAGAAAAAAAGATAATGAATCCGGAAAGTGGAATTTCTAAGCGAGAG
1 AAAAGAAAAAAAGATAATGAATCCAGAAAGTGGAATTTCTAAGCGAGAG
* * *
3722284 AAAAGAAAAAAGGATAGTGAATCCAGAAAGTGGAATTTCTATGCGAGAG
1 AAAAGAAAAAAAGATAATGAATCCAGAAAGTGGAATTTCTAAGCGAGAG
3722333 AAAAGAA
1 AAAAGAA
3722340 GATTCAGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.51, C:0.08, G:0.25, T:0.16
Consensus pattern (49 bp):
AAAAGAAAAAAAGATAATGAATCCAGAAAGTGGAATTTCTAAGCGAGAG
Found at i:3740733 original size:42 final size:42
Alignment explanation
Indices: 3740686--3740920 Score: 310
Period size: 42 Copynumber: 5.6 Consensus size: 42
3740676 TTGAGATTTC
* * * *
3740686 AGACTTTACGCCTAGCAGGCTTATTGCTAGTGAAACAATATT
1 AGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAATAATATT
*
3740728 AGACTTTACGTCTAGCAGGCTTAAAGCCAGTGAAATAAT-TT
1 AGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAATAATATT
* * * * *
3740769 CAAACTTTACGTCTAGCAGGCTTATTGCTAGTGAAACAATATC
1 -AGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAATAATATT
* *
3740812 AGATTTTACGTCTAGCAGGCTTAATGCCAGTGAAATAATTTT
1 AGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAATAATATT
* *
3740854 AGACTTTACGTCTAGCAGGCTTAATACCAGTGAAATAATATC
1 AGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAATAATATT
* *
3740896 AGACTTTACATCTAGCAGACTTAAT
1 AGACTTTACGTCTAGCAGGCTTAAT
3740921 TCAGGTGAAA
Statistics
Matches: 167, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
41 2 0.01
42 164 0.98
43 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (42 bp):
AGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAATAATATT
Found at i:3740920 original size:84 final size:84
Alignment explanation
Indices: 3740681--3740957 Score: 378
Period size: 84 Copynumber: 3.3 Consensus size: 84
3740671 TGAAATTGAG
* *
3740681 ATTTCAGACTTTACGCCTAGCAGGCTTATTGCTAGTGAAACAATATTAGACTTTACGTCTAGCAG
1 ATTTCAGACTTTACGTCTAGCAGGCTTATTGCTAGTGAAACAATATCAGACTTTACGTCTAGCAG
*
3740746 GCTTAAAGCCAGTGAAATA
66 GCTTAATGCCAGTGAAATA
* *
3740765 ATTTCAAACTTTACGTCTAGCAGGCTTATTGCTAGTGAAACAATATCAGATTTTACGTCTAGCAG
1 ATTTCAGACTTTACGTCTAGCAGGCTTATTGCTAGTGAAACAATATCAGACTTTACGTCTAGCAG
3740830 GCTTAATGCCAGTGAAATA
66 GCTTAATGCCAGTGAAATA
* * * * * *
3740849 ATTTTAGACTTTACGTCTAGCAGGCTTAATACCAGTGAAATAATATCAGACTTTACATCTAGCAG
1 ATTTCAGACTTTACGTCTAGCAGGCTTATTGCTAGTGAAACAATATCAGACTTTACGTCTAGCAG
* * *
3740914 ACTTAAT-TCAGGTGAAA-C
66 GCTTAATGCCA-GTGAAATA
* * *
3740932 ATTTCAGACTATATGTCTAGTAGGCT
1 ATTTCAGACTTTACGTCTAGCAGGCT
3740958 AAGTGCCGGT
Statistics
Matches: 172, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
83 24 0.14
84 148 0.86
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (84 bp):
ATTTCAGACTTTACGTCTAGCAGGCTTATTGCTAGTGAAACAATATCAGACTTTACGTCTAGCAG
GCTTAATGCCAGTGAAATA
Found at i:3740929 original size:42 final size:41
Alignment explanation
Indices: 3740684--3740957 Score: 289
Period size: 42 Copynumber: 6.6 Consensus size: 41
3740674 AATTGAGATT
* * * *
3740684 TCAGACTTTACGCCTAGCAGGCTTATTGCTAGTGAAACAATA
1 TCAGACTTTACGTCTAGCAGGCTTAAT-CCAGTGAAATAATA
* * *
3740726 TTAGACTTTACGTCTAGCAGGCTTAAAGCCAGTGAAATAATT
1 TCAGACTTTACGTCTAGCAGGCTT-AATCCAGTGAAATAATA
* * * *
3740768 TCAAACTTTACGTCTAGCAGGCTTATTGCTAGTGAAACAATA
1 TCAGACTTTACGTCTAGCAGGCTTAAT-CCAGTGAAATAATA
* *
3740810 TCAGATTTTACGTCTAGCAGGCTTAATGCCAGTGAAATAATT
1 TCAGACTTTACGTCTAGCAGGCTTAAT-CCAGTGAAATAATA
*
3740852 TTAGACTTTACGTCTAGCAGGCTTAATACCAGTGAAATAATA
1 TCAGACTTTACGTCTAGCAGGCTTAAT-CCAGTGAAATAATA
* * * * *
3740894 TCAGACTTTACATCTAGCAGACTTAATTCAGGTGAAA-CATT
1 TCAGACTTTACGTCTAGCAGGCTTAATCCA-GTGAAATAATA
* * *
3740935 TCAGACTATATGTCTAGTAGGCT
1 TCAGACTTTACGTCTAGCAGGCT
3740958 AAGTGCCGGT
Statistics
Matches: 194, Mismatches: 35, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
41 23 0.12
42 170 0.88
43 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (41 bp):
TCAGACTTTACGTCTAGCAGGCTTAATCCAGTGAAATAATA
Found at i:3740932 original size:126 final size:126
Alignment explanation
Indices: 3740684--3740918 Score: 364
Period size: 126 Copynumber: 1.9 Consensus size: 126
3740674 AATTGAGATT
* *
3740684 TCAGACTTTACGCCTAGCAGGCTTATTGCTAGTGAAACAATATTAGACTTTACGTCTAGCAGGCT
1 TCAGACTTTACGCCTAGCAGGCTTAATGCCAGTGAAACAATATTAGACTTTACGTCTAGCAGGCT
* * *
3740749 TAAAGCCAGTGAAATAATTTCAAACTTTACGTCTAGCAGGCTTATTGCTAGTGAAACAATA
66 TAAAGCCAGTGAAATAATATCAAACTTTACATCTAGCAGACTTATTGCTAGTGAAACAATA
* * * *
3740810 TCAGATTTTACGTCTAGCAGGCTTAATGCCAGTGAAATAATTTTAGACTTTACGTCTAGCAGGCT
1 TCAGACTTTACGCCTAGCAGGCTTAATGCCAGTGAAACAATATTAGACTTTACGTCTAGCAGGCT
*
3740875 TAATA-CCAGTGAAATAATATCAGACTTTACATCTAGCAGACTTA
66 TAA-AGCCAGTGAAATAATATCAAACTTTACATCTAGCAGACTTA
3740919 ATTCAGGTGA
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
126 97 0.99
127 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (126 bp):
TCAGACTTTACGCCTAGCAGGCTTAATGCCAGTGAAACAATATTAGACTTTACGTCTAGCAGGCT
TAAAGCCAGTGAAATAATATCAAACTTTACATCTAGCAGACTTATTGCTAGTGAAACAATA
Found at i:3748960 original size:117 final size:117
Alignment explanation
Indices: 3748749--3748978 Score: 406
Period size: 117 Copynumber: 2.0 Consensus size: 117
3748739 AAGTATGATT
*
3748749 TGTAAACTCTTTTATGATTAAACATGGACTACAATGAACATGTGTTTGCTATTAAGAATTTTTCG
1 TGTAAACTCTTTTATGATTAAACATGGACTACAACGAACATGTGTTTGCTATTAAGAATTTTTCG
3748814 AGGAATTATTTTGTGTATGTGAAACTGAGATTTCAGACTTTACACCTAACAA
66 AGGAATTATTTTGTGTATGTGAAACTGAGATTTCAGACTTTACACCTAACAA
* * *
3748866 TGTAAACTCTTTTATGATTGAACATGGACTACAACGAACATGTGTTTTCTATTAAGAATTTTTCT
1 TGTAAACTCTTTTATGATTAAACATGGACTACAACGAACATGTGTTTGCTATTAAGAATTTTTCG
* *
3748931 AGGAATTATTTTGTGTATGTGAAATTGAGATTTCAGACTTTACGCCTA
66 AGGAATTATTTTGTGTATGTGAAACTGAGATTTCAGACTTTACACCTA
3748979 GCAGGCTTAT
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
117 107 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.39
Consensus pattern (117 bp):
TGTAAACTCTTTTATGATTAAACATGGACTACAACGAACATGTGTTTGCTATTAAGAATTTTTCG
AGGAATTATTTTGTGTATGTGAAACTGAGATTTCAGACTTTACACCTAACAA
Found at i:3749012 original size:42 final size:42
Alignment explanation
Indices: 3748960--3749104 Score: 186
Period size: 42 Copynumber: 3.5 Consensus size: 42
3748950 TGAAATTGAG
* * *
3748960 ATTTCAGACTTTACGCCTAGCAGGCTTATTGCTAGTGAAACA
1 ATTTCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACA
* *
3749002 ATATT-AGACTTTACGTCTAGCAGGCTTAAAGCCAGTGAAATA
1 AT-TTCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACA
* *
3749044 ATTTCAAACTTTACGTCTAGCAGGCTTAATGCCGGTGAAAC-
1 ATTTCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACA
* *
3749085 ATTTCAGACTATATGTCTAG
1 ATTTCAGACTTTACGTCTAG
3749105 TAGGTTAGGT
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
41 19 0.21
42 68 0.76
43 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (42 bp):
ATTTCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACA
Found at i:3759604 original size:41 final size:41
Alignment explanation
Indices: 3759553--3759709 Score: 192
Period size: 41 Copynumber: 3.9 Consensus size: 41
3759543 TGTCAATCAT
* *
3759553 ATAGCCGAAGCTATTATAATTCCGCACACTAAGTGTCATAC
1 ATAGCCAAAGCTATTATAATTCTGCACACTAAGTGTCATAC
* * *
3759594 ATAGCCGAAGCTATTATAATTATGCACATTAAGTGTC-TAAC
1 ATAGCCAAAGCTATTATAATTCTGCACACTAAGTGTCAT-AC
* * *
3759635 ATAGCCAAAACTATTATAATTCTGCACACTAAGTGCCATAT
1 ATAGCCAAAGCTATTATAATTCTGCACACTAAGTGTCATAC
** *
3759676 ATAGCCAAAGCTATTCCAAAT-TGCACACTAAGTG
1 ATAGCCAAAGCTATTATAATTCTGCACACTAAGTG
3759710 CCATTAATAA
Statistics
Matches: 101, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
40 14 0.14
41 86 0.85
42 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (41 bp):
ATAGCCAAAGCTATTATAATTCTGCACACTAAGTGTCATAC
Found at i:3759727 original size:40 final size:40
Alignment explanation
Indices: 3759657--3759737 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
3759647 ATTATAATTC
*
3759657 TGCACACTAAGTGCCATATATAGCCAAAGCTAT-TCCAAAT
1 TGCACACTAAGTGCCATATATAACCAAAGCTATCT-CAAAT
**
3759697 TGCACACTAAGTGCCAT-TAATAACTGAAGCTATCTCAAAT
1 TGCACACTAAGTGCCATAT-ATAACCAAAGCTATCTCAAAT
3759737 T
1 T
3759738 TCATATTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 1 0.03
40 34 0.94
41 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.27
Consensus pattern (40 bp):
TGCACACTAAGTGCCATATATAACCAAAGCTATCTCAAAT
Found at i:3761839 original size:15 final size:15
Alignment explanation
Indices: 3761819--3761850 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3761809 CATTTCACTA
*
3761819 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
3761834 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
3761849 TT
1 TT
3761851 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:3768617 original size:18 final size:19
Alignment explanation
Indices: 3768586--3768629 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
3768576 TCTTAGAAAT
3768586 CTTAGGATACCCTACTTGA
1 CTTAGGATACCCTACTTGA
*
3768605 CTTAGGA-ACCCTATTTGA
1 CTTAGGATACCCTACTTGA
*
3768623 TTTAGGA
1 CTTAGGA
3768630 GAAGGTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (19 bp):
CTTAGGATACCCTACTTGA
Found at i:3780150 original size:17 final size:16
Alignment explanation
Indices: 3780107--3780153 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
3780097 AATTTAGAAT
*
3780107 AATTTTTGAATTAGTG
1 AATTTTTGATTTAGTG
*
3780123 AATTTTTTGATTTATTG
1 AA-TTTTTGATTTAGTG
3780140 AATTTTGTGATTTA
1 AATTTT-TGATTTA
3780154 AAAAGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (16 bp):
AATTTTTGATTTAGTG
Found at i:3780959 original size:46 final size:46
Alignment explanation
Indices: 3780892--3780984 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
3780882 CATGGCAAAG
*
3780892 TGTGAAACGTAGGTATGGTA-TTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTTC-GTGAAGAAAACCATACTGAGT
3780938 TGTGAAAAGTAGGTATGGTATTTTCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTTCGTGAAGAAAACCATACTGAGT
3780984 T
1 T
3780985 ATAGCAATGT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 41 0.91
47 4 0.09
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTTCGTGAAGAAAACCATACTGAGT
Found at i:3796717 original size:68 final size:67
Alignment explanation
Indices: 3796608--3796777 Score: 173
Period size: 68 Copynumber: 2.5 Consensus size: 67
3796598 TTCTCTAGTT
* * *** * *
3796608 AATATGAGATTAAAATTAACTTTTTAATTAAAATGGTGAAGAAGTAAGTTATGTGAGTATTC-TT
1 AATATG-GATTAAAATTAACTTTTTAATGAAAGTAACGAAGAAGTAAGCTATG-AAGTATTCTTT
*
3796672 AGCC
64 AACC
* * *
3796676 AATGTGGAATTGAAATTAACTTTTTAATGAAAGTAACGAAGAAGTGAGCTATGAAGTATTCTTTA
1 AATATGG-ATTAAAATTAACTTTTTAATGAAAGTAACGAAGAAGTAAGCTATGAAGTATTCTTTA
*
3796741 ATC
65 ACC
*
3796744 AATATGGATTAAAACTAA-TCTTTTAATGAAAGTA
1 AATATGGATTAAAATTAACT-TTTTAATGAAAGTA
3796778 GTGAAAAAAT
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
66 1 0.01
67 31 0.37
68 52 0.62
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.35
Consensus pattern (67 bp):
AATATGGATTAAAATTAACTTTTTAATGAAAGTAACGAAGAAGTAAGCTATGAAGTATTCTTTAA
CC
Found at i:3802557 original size:27 final size:27
Alignment explanation
Indices: 3802519--3802573 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3802509 ATAGGGGGAA
*
3802519 TTCAAGGGCAGGCAGGGGGCTTGTTCT
1 TTCAAGGGCAGGCAGGAGGCTTGTTCT
* *
3802546 TTCAAGTGCAGGCAGGAGTCTTGTTCT
1 TTCAAGGGCAGGCAGGAGGCTTGTTCT
3802573 T
1 T
3802574 AAAAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.35, T:0.31
Consensus pattern (27 bp):
TTCAAGGGCAGGCAGGAGGCTTGTTCT
Found at i:3811651 original size:49 final size:49
Alignment explanation
Indices: 3811490--3812520 Score: 1880
Period size: 49 Copynumber: 21.2 Consensus size: 49
3811480 AATTCTAAAT
*
3811490 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
* * *
3811537 TGTGAATAGGGCCTAATGGCTGATGTGATGAATGTGAAAGTG--TATATA
1 TGTG-ATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
*
3811585 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3811634 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3811683 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3811732 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3811781 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3811830 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3811879 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3811928 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3811977 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3812026 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3812075 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3812124 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3812173 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3812222 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3812271 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3812320 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3812369 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3812418 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
* * ** * * * *
3812465 TGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATA-A-A
1 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
3812512 TGTGATAAG
1 TGTGATAAG
3812521 TCCCGAAGGG
Statistics
Matches: 965, Mismatches: 14, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
47 87 0.09
48 46 0.05
49 832 0.86
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (49 bp):
TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
Found at i:3812694 original size:37 final size:37
Alignment explanation
Indices: 3812638--3812716 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
3812628 TCGAGCTCTA
* * *
3812638 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
* *
3812675 AAGACCCTATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
3812712 AAGAC
1 AAGAC
3812717 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:3822416 original size:24 final size:24
Alignment explanation
Indices: 3822384--3822430 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3822374 TTTATTGCAA
* *
3822384 TATTGAGTGGCTTGTCCACAACGC
1 TATTAAGTGGCTTGACCACAACGC
*
3822408 TATTAAGTGGTTTGACCACAACG
1 TATTAAGTGGCTTGACCACAACG
3822431 ATACAAGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (24 bp):
TATTAAGTGGCTTGACCACAACGC
Found at i:3833453 original size:2 final size:2
Alignment explanation
Indices: 3833446--3833491 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
3833436 GTCTCCTTCC
* * *
3833446 CT CT CT CT CT CT CT CT CT CC CT CC CT CC CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3833488 CT CT
1 CT CT
3833492 TCGTTCAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (2 bp):
CT
Found at i:3833470 original size:24 final size:24
Alignment explanation
Indices: 3833437--3833488 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
3833427 CCCTTTCATG
* *
3833437 TCTCCTTCCCTCTCTCTCTCTCTC
1 TCTCCCTCCCTCCCTCTCTCTCTC
3833461 TCTCCCTCCCTCCCTCTCTCTCTC
1 TCTCCCTCCCTCCCTCTCTCTCTC
3833485 TCTC
1 TCTC
3833489 TCTTCGTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (24 bp):
TCTCCCTCCCTCCCTCTCTCTCTC
Found at i:3833478 original size:28 final size:28
Alignment explanation
Indices: 3833438--3833491 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
3833428 CCTTTCATGT
*
3833438 CTCCTTCCCTCTCTCTCTCTCTCTCTCC
1 CTCCCTCCCTCTCTCTCTCTCTCTCTCC
3833466 CTCCCTCCCTCTCTCTCTCTCTCTCT
1 CTCCCTCCCTCTCTCTCTCTCTCTCT
3833492 TCGTTCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (28 bp):
CTCCCTCCCTCTCTCTCTCTCTCTCTCC
Found at i:3836741 original size:9 final size:9
Alignment explanation
Indices: 3836727--3836752 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3836717 TAAATAGTTC
3836727 GAGTTATTT
1 GAGTTATTT
3836736 GAGTTATTT
1 GAGTTATTT
3836745 GAGTTATT
1 GAGTTATT
3836753 CGGATCAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (9 bp):
GAGTTATTT
Found at i:3842462 original size:27 final size:26
Alignment explanation
Indices: 3842432--3842547 Score: 169
Period size: 27 Copynumber: 4.3 Consensus size: 26
3842422 CCAAAATAGA
*
3842432 TAAAATGACCAAAATACCCTCATAGGG
1 TAAAATGACCGAAATACCC-CATAGGG
3842459 TAAAATGACCGAAATACCCCAATAGGG
1 TAAAATGACCGAAATACCCC-ATAGGG
* *
3842486 TAAAATGATCGAAATACCCTATAGGG
1 TAAAATGACCGAAATACCCCATAGGG
*
3842512 TAGAATGACCGAAATAACCCCATAGGG
1 TAAAATGACCGAAAT-ACCCCATAGGG
3842539 TAAAATGAC
1 TAAAATGAC
3842548 TGTTATACCC
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
26 20 0.25
27 60 0.75
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (26 bp):
TAAAATGACCGAAATACCCCATAGGG
Found at i:3842511 original size:53 final size:54
Alignment explanation
Indices: 3842432--3842547 Score: 182
Period size: 53 Copynumber: 2.2 Consensus size: 54
3842422 CCAAAATAGA
3842432 TAAAATGACCAAAATACCCTCATAGGGTAAAATGACCGAAAT-ACCCCAATAGGG
1 TAAAATGACCAAAATACCCTCATAGGGTAAAATGACCGAAATAACCCC-ATAGGG
* * *
3842486 TAAAATGATCGAAATACCCT-ATAGGGTAGAATGACCGAAATAACCCCATAGGG
1 TAAAATGACCAAAATACCCTCATAGGGTAAAATGACCGAAATAACCCCATAGGG
3842539 TAAAATGAC
1 TAAAATGAC
3842548 TGTTATACCC
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
53 34 0.60
54 23 0.40
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (54 bp):
TAAAATGACCAAAATACCCTCATAGGGTAAAATGACCGAAATAACCCCATAGGG
Found at i:3844895 original size:21 final size:21
Alignment explanation
Indices: 3844871--3844914 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3844861 GAAGTTCGAG
*
3844871 TTGTATCTGTAGAAC-CCATAA
1 TTGTATCGGTAGAACTCC-TAA
3844892 TTGTATCGGTAGAACTCCTAA
1 TTGTATCGGTAGAACTCCTAA
3844913 TT
1 TT
3844915 CTACTAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (21 bp):
TTGTATCGGTAGAACTCCTAA
Found at i:3848212 original size:40 final size:40
Alignment explanation
Indices: 3848129--3848220 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
3848119 CATTTGAATG
*
3848129 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGAT
* ** *
3848169 ATATCCGGGCTAAGACCCGAGGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGAT
3848209 ATATCC-GGCTAA
1 ATATCCGGGCTAA
3848221 ATTCCGAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 6 0.13
40 41 0.87
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGAT
Found at i:3851442 original size:21 final size:20
Alignment explanation
Indices: 3851390--3851439 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3851380 GAATTTTCTT
*
3851390 GAAAAATTAATTTTGATCAG
1 GAAAAATTAATTTTGATCAA
*
3851410 GAAAAATTAATTTTGATTAA
1 GAAAAATTAATTTTGATCAA
*
3851430 GTAAAATTAA
1 GAAAAATTAA
3851440 ATTCATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (20 bp):
GAAAAATTAATTTTGATCAA
Found at i:3855465 original size:12 final size:12
Alignment explanation
Indices: 3855448--3855474 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3855438 GTAAAATAAG
3855448 TAAGAGGCCTTT
1 TAAGAGGCCTTT
3855460 TAAGAGGCCTTT
1 TAAGAGGCCTTT
3855472 TAA
1 TAA
3855475 TGCGAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (12 bp):
TAAGAGGCCTTT
Found at i:3857197 original size:40 final size:41
Alignment explanation
Indices: 3857135--3857399 Score: 428
Period size: 40 Copynumber: 6.5 Consensus size: 41
3857125 TTTAACATAT
*
3857135 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCCGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* *
3857176 TCACCGGCAC-TAGCCTACTAGGTTTATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
3857216 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTAATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* * *
3857257 TCACCGACAC-TAGGCTGCTAGGTTTATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
3857297 TCACCGGCACTTAGCTTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
3857338 TCACCGGCAC-TAGCCTGCTAGGTTTATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
3857378 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
3857400 ACATAAAGTC
Statistics
Matches: 205, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
40 111 0.54
41 94 0.46
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:3857278 original size:81 final size:81
Alignment explanation
Indices: 3857135--3857399 Score: 476
Period size: 81 Copynumber: 3.3 Consensus size: 81
3857125 TTTAACATAT
* *
3857135 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCCGATCACCGGCACTAGCCTACTAGGTT
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTAGCCTGCTAGGTT
3857200 TATAACCTGGTTCAGA
66 TATAACCTGGTTCAGA
* * *
3857216 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTAATTCAGATCACCGACACTAGGCTGCTAGGTT
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTAGCCTGCTAGGTT
3857281 TATAACCTGGTTCAGA
66 TATAACCTGGTTCAGA
*
3857297 TCACCGGCACTTAGCTTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTAGCCTGCTAGGTT
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTAGCCTGCTAGGTT
3857362 TATAACCTGGTTCAGA
66 TATAACCTGGTTCAGA
3857378 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
3857400 ACATAAAGTC
Statistics
Matches: 174, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 174 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (81 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTAGCCTGCTAGGTT
TATAACCTGGTTCAGA
Found at i:3865199 original size:40 final size:41
Alignment explanation
Indices: 3865138--3865402 Score: 464
Period size: 40 Copynumber: 6.5 Consensus size: 41
3865128 TTTAACATAT
*
3865138 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTCATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
3865179 TCACCGGCAC-TAGCCTGCTAGGTTTATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
3865219 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
3865260 TCACCGGCAC-TAGCCTGCTAGGTTTATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
3865300 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
3865341 TCACCGGCAC-TAGCCTGCTAGGTTTATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
3865381 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
3865403 ACATAAAGTC
Statistics
Matches: 213, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
40 115 0.54
41 98 0.46
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:3865273 original size:81 final size:81
Alignment explanation
Indices: 3865138--3865402 Score: 512
Period size: 81 Copynumber: 3.3 Consensus size: 81
3865128 TTTAACATAT
*
3865138 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTCATTCAGATCACCGGCACTAGCCTGCTAGGTT
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTAGCCTGCTAGGTT
3865203 TATAACCTGGTTCAGA
66 TATAACCTGGTTCAGA
3865219 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTAGCCTGCTAGGTT
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTAGCCTGCTAGGTT
3865284 TATAACCTGGTTCAGA
66 TATAACCTGGTTCAGA
*
3865300 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAATCACCGGCACTAGCCTGCTAGGTT
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTAGCCTGCTAGGTT
3865365 TATAACCTGGTTCAGA
66 TATAACCTGGTTCAGA
3865381 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
3865403 ACATAAAGTC
Statistics
Matches: 182, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 182 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (81 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTAGCCTGCTAGGTT
TATAACCTGGTTCAGA
Found at i:3872747 original size:58 final size:58
Alignment explanation
Indices: 3872685--3872801 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
3872675 TCAATGATAT
3872685 AATCATCCATATATCATTATTTTCACACATATAAATATCAAGACTAAATTTTTTAAAC
1 AATCATCCATATATCATTATTTTCACACATATAAATATCAAGACTAAATTTTTTAAAC
*
3872743 AATCATCCATATATCATTATTTTCACACATATAAATATCATGACTAAATTTTTTAAAC
1 AATCATCCATATATCATTATTTTCACACATATAAATATCAAGACTAAATTTTTTAAAC
3872801 A
1 A
3872802 TTTGATCAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (58 bp):
AATCATCCATATATCATTATTTTCACACATATAAATATCAAGACTAAATTTTTTAAAC
Found at i:3872793 original size:29 final size:29
Alignment explanation
Indices: 3872703--3872794 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 29
3872693 ATATATCATT
*
3872703 ATTTTCACACATATAAATATCAAGACTAA
1 ATTTTCACACATATAAATATCATGACTAA
* * ** * *
3872732 ATTTTTTAAACAATCATCCATAT-ATCA-T-T
1 A-TTTTCACAC-AT-ATAAATATCATGACTAA
3872761 ATTTTCACACATATAAATATCATGACTAA
1 ATTTTCACACATATAAATATCATGACTAA
3872790 ATTTT
1 ATTTT
3872795 TTAAACATTT
Statistics
Matches: 44, Mismatches: 13, Indels: 12
0.64 0.19 0.17
Matches are distributed among these distances:
26 6 0.14
27 5 0.11
28 8 0.18
29 7 0.16
30 8 0.18
31 4 0.09
32 6 0.14
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.39
Consensus pattern (29 bp):
ATTTTCACACATATAAATATCATGACTAA
Found at i:3873569 original size:50 final size:50
Alignment explanation
Indices: 3873506--3873693 Score: 205
Period size: 50 Copynumber: 3.7 Consensus size: 50
3873496 TATCATTCGA
* *
3873506 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTCCGG
1 TACATGTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTTTCCGG
* * * * *
3873556 TTCATGTAGTAGCCTGCACATAGTACTACAAACGTGATCGAAGTTATCTGG
1 TACATGTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTT-TCCGG
* * * * * *** *
3873607 TACGTATAGTAGCCTGCACATAGTACTATACATGCGATCTTTCATTCCGG
1 TACATGTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTTTCCGG
* *
3873657 TACACGTAGTAGCCTACACATAGTACTACACACGTGA
1 TACATGTAGTAGCCTGCACATAGTACTACACACGTGA
3873694 CCATCACTTT
Statistics
Matches: 110, Mismatches: 27, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
50 73 0.66
51 37 0.34
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (50 bp):
TACATGTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTTTCCGG
Found at i:3873655 original size:101 final size:101
Alignment explanation
Indices: 3873512--3873693 Score: 256
Period size: 101 Copynumber: 1.8 Consensus size: 101
3873502 TCGATACACG
* * * * * *
3873512 TAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTCCGGTTCATGTAGTAGCCTGCACAT
1 TAGTAGCCTGCACATAGTACTACACACGCGATCAAACATTCCGGTACACGTAGTAGCCTACACAT
3873577 AGTACTACAAACGTGATCGAAGTTATCTGGTACGTA
66 AGTACTACAAACGTGATCGAAGTTATCTGGTACGTA
* * ***
3873613 TAGTAGCCTGCACATAGTACTATACATGCGATCTTTCATTCCGGTACACGTAGTAGCCTACACAT
1 TAGTAGCCTGCACATAGTACTACACACGCGATCAAACATTCCGGTACACGTAGTAGCCTACACAT
*
3873678 AGTACTACACACGTGA
66 AGTACTACAAACGTGA
3873694 CCATCACTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 69 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (101 bp):
TAGTAGCCTGCACATAGTACTACACACGCGATCAAACATTCCGGTACACGTAGTAGCCTACACAT
AGTACTACAAACGTGATCGAAGTTATCTGGTACGTA
Found at i:3876966 original size:73 final size:73
Alignment explanation
Indices: 3876879--3877031 Score: 306
Period size: 73 Copynumber: 2.1 Consensus size: 73
3876869 TCTCTAAACT
3876879 TTCTCTATATAAAGAGAGCATTGAGTCGTTATTTACACACACTTGAATTTAAGAGAAACTTGTAG
1 TTCTCTATATAAAGAGAGCATTGAGTCGTTATTTACACACACTTGAATTTAAGAGAAACTTGTAG
3876944 AGAGCAAA
66 AGAGCAAA
3876952 TTCTCTATATAAAGAGAGCATTGAGTCGTTATTTACACACACTTGAATTTAAGAGAAACTTGTAG
1 TTCTCTATATAAAGAGAGCATTGAGTCGTTATTTACACACACTTGAATTTAAGAGAAACTTGTAG
3877017 AGAGCAAA
66 AGAGCAAA
3877025 TTCTCTA
1 TTCTCTA
3877032 AAGAGATTAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 80 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (73 bp):
TTCTCTATATAAAGAGAGCATTGAGTCGTTATTTACACACACTTGAATTTAAGAGAAACTTGTAG
AGAGCAAA
Found at i:3904201 original size:21 final size:21
Alignment explanation
Indices: 3904176--3904215 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3904166 TTTAATATAA
3904176 TAATACCTT-ATTATATTATTT
1 TAATACCTTAATTA-ATTATTT
*
3904197 TAATACTTTAATTAATTAT
1 TAATACCTTAATTAATTAT
3904216 GACCCTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATACCTTAATTAATTATTT
Found at i:3912467 original size:16 final size:16
Alignment explanation
Indices: 3912446--3912476 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3912436 TCTTCAAACA
*
3912446 AAGAAAGATTACGCCC
1 AAGAAAGAGTACGCCC
3912462 AAGAAAGAGTACGCC
1 AAGAAAGAGTACGCC
3912477 TTAGAGTATT
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:0.45, C:0.23, G:0.23, T:0.10
Consensus pattern (16 bp):
AAGAAAGAGTACGCCC
Found at i:3915406 original size:21 final size:21
Alignment explanation
Indices: 3915349--3915409 Score: 86
Period size: 22 Copynumber: 2.9 Consensus size: 21
3915339 TGATCAAGTG
* *
3915349 TTGAACGACGTTGACTGATCG
1 TTGAACGACGTTGATTGATCA
*
3915370 TTGACCCGACGTTGATTGATCA
1 TTGA-ACGACGTTGATTGATCA
3915392 TTGAACGACGTTGATTGA
1 TTGAACGACGTTGATTGA
3915410 CTACGTGGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (21 bp):
TTGAACGACGTTGATTGATCA
Found at i:3915788 original size:13 final size:14
Alignment explanation
Indices: 3915765--3915796 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3915755 TACAAAAAAA
3915765 TATTATAAATTTTT
1 TATTATAAATTTTT
3915779 TATT-TAAATTTTT
1 TATTATAAATTTTT
3915792 T-TTAT
1 TATTAT
3915797 TTTAAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.12
13 11 0.65
14 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTATAAATTTTT
Found at i:3924807 original size:11 final size:11
Alignment explanation
Indices: 3924791--3924816 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3924781 TTTTTTTTAA
3924791 TTTTAAAATAC
1 TTTTAAAATAC
3924802 TTTTAAAATAC
1 TTTTAAAATAC
3924813 TTTT
1 TTTT
3924817 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:3924827 original size:40 final size:40
Alignment explanation
Indices: 3924783--3924905 Score: 187
Period size: 40 Copynumber: 3.1 Consensus size: 40
3924773 TATTTTTATT
*
3924783 TTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAAA
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAA
**
3924823 TTTTTTAATTTTAAAATATTTTTAAAATA-TATTTTTTATT
1 TTTTTTAATTTTAAAATATTTTTAAAATACT-TTTTTTAAA
*
3924863 TTTTTTAATTTTAAAATATTTTTAAAGTACTTTTTTT-AA
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAA
3924902 TTTT
1 TTTT
3924906 CAAAATAAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
39 5 0.07
40 69 0.92
41 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (40 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAA
Found at i:3931343 original size:55 final size:54
Alignment explanation
Indices: 3931248--3931397 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
3931238 CTACTTTGTT
* ** * *
3931248 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
3931302 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
3931357 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
3931398 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:3931360 original size:27 final size:27
Alignment explanation
Indices: 3931220--3931397 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
3931210 TAAATTGTAC
3931220 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
3931247 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
3931273 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
3931301 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
3931329 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
3931356 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
3931383 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
3931398 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:3931361 original size:82 final size:81
Alignment explanation
Indices: 3931221--3931376 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
3931211 AAATTGTACA
* * * *
3931221 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
3931286 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
3931302 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
3931365 TGTGCGAGTTGA
63 TGTGCGAATTGA
3931377 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:3939313 original size:27 final size:27
Alignment explanation
Indices: 3939282--3939459 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3939272 TAAATTGTAC
3939282 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
3939309 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3939335 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
3939363 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
3939391 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3939418 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
3939445 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
3939460 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:3939396 original size:82 final size:81
Alignment explanation
Indices: 3939283--3939438 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3939273 AAATTGTACA
* *
3939283 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
3939347 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
3939364 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
3939429 TGCGAGTTGA
65 TGCGAATTGA
3939439 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:3939450 original size:82 final size:81
Alignment explanation
Indices: 3939279--3939459 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
3939269 GATTAAATTG
* *
3939279 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
3939344 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
3939360 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
3939424 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
3939442 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
3939460 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:3941532 original size:37 final size:37
Alignment explanation
Indices: 3941482--3941556 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3941472 ATGGAAAGAC
3941482 ACAATTCAAGAAGAATTAAATTCACTTTCTAAACGTA
1 ACAATTCAAGAAGAATTAAATTCACTTTCTAAACGTA
3941519 ACAATTCAAGAAGAATTAAATTCACTTTCTAAACGTA
1 ACAATTCAAGAAGAATTAAATTCACTTTCTAAACGTA
3941556 A
1 A
3941557 TGTTTTTGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (37 bp):
ACAATTCAAGAAGAATTAAATTCACTTTCTAAACGTA
Found at i:3941872 original size:18 final size:19
Alignment explanation
Indices: 3941844--3941879 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3941834 AGTGAAATTT
3941844 ATTTAAAAATCCCAGAAGA
1 ATTTAAAAATCCCAGAAGA
*
3941863 ATTT-AAAATCCCTGAAG
1 ATTTAAAAATCCCAGAAG
3941880 GATATAGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.25
Consensus pattern (19 bp):
ATTTAAAAATCCCAGAAGA
Found at i:3944711 original size:136 final size:136
Alignment explanation
Indices: 3944467--3944739 Score: 397
Period size: 136 Copynumber: 2.0 Consensus size: 136
3944457 GCCCATACAT
*** *
3944467 TCATGCAGACAACCTTCTTTGTGTTAGCCAAACATGGGTCCGTGTTCAAAGATCAATCATTCCTT
1 TCATGCAGACAACCTTCTTTGTGTTAGCCAAACACAAGTCCGTATTCAAAGATCAATCATTCCTT
* *
3944532 TCATTTCCTTTGTCATGCTAGCTAGTCTGGTTTGTAATGTACCTACCTTACCT-GAGGCCACATA
66 TCATTTCCTTTGCCATGCTAGCTAGTCTGGTTTGCAATGTACCTACCTTA-CTAGAGGCCACATA
3944596 ACCATTG
130 ACCATTG
* * * ** *
3944603 TCATGCAGACAACCTTCTTTGTGTTGGCCAAACCCAATTTTGTATTCAGAGATCAA-CAATTCCT
1 TCATGCAGACAACCTTCTTTGTGTTAGCCAAACACAAGTCCGTATTCAAAGATCAATC-ATTCCT
*
3944667 TTCATTTCCTTTGCCATGCTAGCTAGTCTGGTTTGCAATGTACCTGCCTTACTAGAGGCCACATA
65 TTCATTTCCTTTGCCATGCTAGCTAGTCTGGTTTGCAATGTACCTACCTTACTAGAGGCCACATA
3944732 ACCATTG
130 ACCATTG
3944739 T
1 T
3944740 TCATATACTA
Statistics
Matches: 122, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
135 3 0.02
136 119 0.98
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.34
Consensus pattern (136 bp):
TCATGCAGACAACCTTCTTTGTGTTAGCCAAACACAAGTCCGTATTCAAAGATCAATCATTCCTT
TCATTTCCTTTGCCATGCTAGCTAGTCTGGTTTGCAATGTACCTACCTTACTAGAGGCCACATAA
CCATTG
Found at i:3955428 original size:29 final size:30
Alignment explanation
Indices: 3955395--3955453 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 30
3955385 AAATTATTAT
*
3955395 TTTTTTGTGATTTTTG-TTGAAAAAGACTA
1 TTTTTTGTCATTTTTGATTGAAAAAGACTA
*
3955424 TTTTTTTTCATTTTTGAAATTGAAAAAGAC
1 TTTTTTGTCATTTTTG--ATTGAAAAAGAC
3955454 CAAAGGAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.56
32 11 0.44
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.51
Consensus pattern (30 bp):
TTTTTTGTCATTTTTGATTGAAAAAGACTA
Found at i:3955428 original size:30 final size:30
Alignment explanation
Indices: 3955392--3955453 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 30
3955382 TTTAAATTAT
*
3955392 TATTTTTTTGTGATTTTTG-TTGAAAAAGAC
1 TATTTTTTT-TCATTTTTGATTGAAAAAGAC
3955422 TATTTTTTTTCATTTTTGAAATTGAAAAAGAC
1 TATTTTTTTTCATTTTTG--ATTGAAAAAGAC
3955454 CAAAGGAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 8 0.29
30 9 0.32
32 11 0.39
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.52
Consensus pattern (30 bp):
TATTTTTTTTCATTTTTGATTGAAAAAGAC
Found at i:3957498 original size:79 final size:81
Alignment explanation
Indices: 3957396--3957579 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
3957386 GCTCCTCGTT
* *
3957396 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACC
*
3957458 CGGAT-TTAGTAAC-TCGCA
63 CGGATATT-GTAACTTAGCA
**
3957476 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
*
3957540 ATATTGTCACTTAGCA
66 ATATTGTAACTTAGCA
3957556 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
3957580 CATCATTCAA
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 14 0.15
79 56 0.61
80 22 0.24
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATTGTAACTTAGCA
Found at i:3957513 original size:39 final size:41
Alignment explanation
Indices: 3957396--3957579 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 41
3957386 GCTCCTCGTT
* *
3957396 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATCTCGCA
* *
3957436 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAA-CTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
3957476 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
* * *
3957515 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCA
3957556 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
3957580 CATCATTCAA
Statistics
Matches: 128, Mismatches: 7, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
38 3 0.02
39 48 0.38
40 66 0.52
41 11 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
Found at i:3959885 original size:20 final size:20
Alignment explanation
Indices: 3959860--3959904 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3959850 TAAATACACA
3959860 TAATTAAAACT-AGACACAAT
1 TAATT-AAACTAAGACACAAT
**
3959880 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
3959900 TAATT
1 TAATT
3959905 CGGTTGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:3963119 original size:26 final size:26
Alignment explanation
Indices: 3963062--3963130 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
3963052 TTTACATGAA
* *
3963062 TGCTCACCCGAGTTGTGAAATGGGTC
1 TGCTCACACGAGCTGTGAAATGGGTC
*
3963088 TACTCACACGAGCTGTGAAATGGG-C
1 TGCTCACACGAGCTGTGAAATGGGTC
* *
3963113 TTGCTCACATGGGCTGTG
1 -TGCTCACACGAGCTGTG
3963131 GGTCGAAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 1 0.03
26 35 0.97
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.26
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATGGGTC
Found at i:3965918 original size:53 final size:54
Alignment explanation
Indices: 3965836--3965941 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 54
3965826 AGTCCATGGC
* * * *
3965836 ACCATATCGTGTAATACCATAACTAGTGGGTTATGGTATCATA-TGGAAAGAAT
1 ACCATATCATGTAAGACCATAACTAGTGGGTTAGGGCATCATATTGGAAAGAAT
* *
3965889 ACCATATCATGTAAGACCATAATTTGTGGGTTAGGGCATCATATTGGAAAGAA
1 ACCATATCATGTAAGACCATAACTAGTGGGTTAGGGCATCATATTGGAAAGAA
3965942 CTAAGGGGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 37 0.80
54 9 0.20
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (54 bp):
ACCATATCATGTAAGACCATAACTAGTGGGTTAGGGCATCATATTGGAAAGAAT
Found at i:3967213 original size:30 final size:30
Alignment explanation
Indices: 3967179--3967394 Score: 151
Period size: 30 Copynumber: 7.2 Consensus size: 30
3967169 TGACCAATGG
3967179 AAAGGGATAGCTTCGACTATCAAATTATGA
1 AAAGGGATAGCTTCGACTATCAAATTATGA
* *
3967209 AAAGGGATGGCTTC-AGCTATCGAATTATGA
1 AAAGGGATAGCTTCGA-CTATCAAATTATGA
*
3967239 AAAGGGATAGGGCTTC-AGCTATCGAATTATGA
1 AAAGGGATA--GCTTCGA-CTATCAAATTATGA
* * *
3967271 AAAGGGATA-ATGACGACCATCAACA--ATGA
1 AAAGGGATAGCT-TCGACTATCAA-ATTATGA
* * *
3967300 AAAGGGAT-GGTGACGACCATCAACA--ATGA
1 AAAGGGATAGCT-TCGACTATCAA-ATTATGA
* * * * *
3967329 GAAGGGATGGCTTCGGCGATCAAAATATGA
1 AAAGGGATAGCTTCGACTATCAAATTATGA
* * *
3967359 AAAGGGACAGCTTCGACTATCGAACTATGA
1 AAAGGGATAGCTTCGACTATCAAATTATGA
3967389 AAAGGG
1 AAAGGG
3967395 GTGGTAATAG
Statistics
Matches: 156, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.01
29 48 0.31
30 75 0.48
31 2 0.01
32 30 0.19
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.20
Consensus pattern (30 bp):
AAAGGGATAGCTTCGACTATCAAATTATGA
Found at i:3967258 original size:32 final size:31
Alignment explanation
Indices: 3967179--3967279 Score: 154
Period size: 30 Copynumber: 3.3 Consensus size: 31
3967169 TGACCAATGG
*
3967179 AAAGGGATA-GCTTC-GACTATCAAATTATGA
1 AAAGGGATAGGCTTCAG-CTATCGAATTATGA
3967209 AAAGGGAT-GGCTTCAGCTATCGAATTATGA
1 AAAGGGATAGGCTTCAGCTATCGAATTATGA
3967239 AAAGGGATAGGGCTTCAGCTATCGAATTATGA
1 AAAGGGATA-GGCTTCAGCTATCGAATTATGA
3967271 AAAGGGATA
1 AAAGGGATA
3967280 ATGACGACCA
Statistics
Matches: 66, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
30 34 0.52
31 1 0.02
32 31 0.47
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.25
Consensus pattern (31 bp):
AAAGGGATAGGCTTCAGCTATCGAATTATGA
Found at i:3967351 original size:29 final size:29
Alignment explanation
Indices: 3967267--3967338 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
3967257 CTATCGAATT
**
3967267 ATGAAAAGGGATAATGACGACCATCAACA
1 ATGAAAAGGGATGGTGACGACCATCAACA
3967296 ATGAAAAGGGATGGTGACGACCATCAACA
1 ATGAAAAGGGATGGTGACGACCATCAACA
*
3967325 ATGAGAAGGGATGG
1 ATGAAAAGGGATGG
3967339 CTTCGGCGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (29 bp):
ATGAAAAGGGATGGTGACGACCATCAACA
Found at i:3968848 original size:27 final size:27
Alignment explanation
Indices: 3968810--3968872 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
3968800 GGTGTTACAA
* * *
3968810 GAAGTCTTTGTGGCAATCTATGAAAAT
1 GAAGCCTTTGTGGCAATCTATAAAAAC
3968837 GAAGCCTTTGTGGCAATCTATAAAAAC
1 GAAGCCTTTGTGGCAATCTATAAAAAC
3968864 GAATGCCTT
1 GAA-GCCTT
3968873 CTTGGTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (27 bp):
GAAGCCTTTGTGGCAATCTATAAAAAC
Found at i:3969037 original size:27 final size:27
Alignment explanation
Indices: 3969007--3969058 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3968997 TGGAAGAATA
*
3969007 ATATGTATGGCGAACTCTAAAGGAAAG
1 ATATGTATGGCAAACTCTAAAGGAAAG
* *
3969034 ATATGTATGGTAAACTGTAAAGGAA
1 ATATGTATGGCAAACTCTAAAGGAA
3969059 TGGCTCCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (27 bp):
ATATGTATGGCAAACTCTAAAGGAAAG
Found at i:3974073 original size:57 final size:58
Alignment explanation
Indices: 3973978--3974092 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 58
3973968 ATATAAATAG
* * * * *
3973978 AAATGGAGAAATGAGAAACATTTGGAAATTATTATGGTTTTCTCCTAAATGAAAATGA
1 AAATAGAGAAATGAGAAACATTTGAAAATGAATATGGTTTTCTCCAAAATGAAAATGA
* *
3974036 AAATAGAGAAATGA-AATCATTTGAAAATGAATGTGGTTTTCTCCAAAATGAAAATGA
1 AAATAGAGAAATGAGAAACATTTGAAAATGAATATGGTTTTCTCCAAAATGAAAATGA
3974093 CTTGGAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 37 0.74
58 13 0.26
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (58 bp):
AAATAGAGAAATGAGAAACATTTGAAAATGAATATGGTTTTCTCCAAAATGAAAATGA
Found at i:3976775 original size:13 final size:13
Alignment explanation
Indices: 3976749--3976792 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
3976739 ATTATGAGTT
3976749 AAATGTGTAA-ATG
1 AAATG-GTAAGATG
3976762 AAATGGTAAGATG
1 AAATGGTAAGATG
* *
3976775 AAATGTTTAGATG
1 AAATGGTAAGATG
3976788 AAATG
1 AAATG
3976793 CTTATATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 4 0.14
13 24 0.86
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (13 bp):
AAATGGTAAGATG
Found at i:3976801 original size:13 final size:13
Alignment explanation
Indices: 3976759--3976803 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
3976749 AAATGTGTAA
* *
3976759 ATGAAATGGTAAG
1 ATGAAATGCTTAG
*
3976772 ATGAAATGTTTAG
1 ATGAAATGCTTAG
*
3976785 ATGAAATGCTTAT
1 ATGAAATGCTTAG
3976798 ATGAAA
1 ATGAAA
3976804 AAAAAAGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.31
Consensus pattern (13 bp):
ATGAAATGCTTAG
Found at i:3976801 original size:26 final size:26
Alignment explanation
Indices: 3976749--3976803 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
3976739 ATTATGAGTT
*
3976749 AAATGTGTAAATGAAATGGTAAGATG
1 AAATGTGTAAATGAAATGCTAAGATG
* * * *
3976775 AAATGTTTAGATGAAATGCTTATATG
1 AAATGTGTAAATGAAATGCTAAGATG
3976801 AAA
1 AAA
3976804 AAAAAAGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.22, T:0.31
Consensus pattern (26 bp):
AAATGTGTAAATGAAATGCTAAGATG
Done.