Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 43
Found at i:3768672 original size:14 final size:14
Alignment explanation
Indices: 3768641--3768698 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
3768631 CTCATTCATC
3768641 AGAA-AAGAAAAA-
1 AGAAGAAGAAAAAG
3768653 AG-AGAAGAAAAAG
1 AGAAGAAGAAAAAG
*
3768666 AGAAGAAAGAAAAAT
1 AGAAG-AAGAAAAAG
* *
3768681 AGAAAAAAAAAAAG
1 AGAAGAAGAAAAAG
3768695 AGAA
1 AGAA
3768699 AATAAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
11 1 0.03
12 10 0.26
13 2 0.05
14 13 0.34
15 12 0.32
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.02
Consensus pattern (14 bp):
AGAAGAAGAAAAAG
Found at i:3768677 original size:27 final size:29
Alignment explanation
Indices: 3768644--3768698 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
3768634 ATTCATCAGA
* *
3768644 AAAGAAAAA-AG-AGAAGAAAAAGAGAAG
1 AAAGAAAAATAGAAAAAAAAAAAGAGAAG
3768671 AAAGAAAAATAGAAAAAAAAAAAGAGAA
1 AAAGAAAAATAGAAAAAAAAAAAGAGAA
3768699 AATAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.38
28 2 0.08
29 13 0.54
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (29 bp):
AAAGAAAAATAGAAAAAAAAAAAGAGAAG
Found at i:3768687 original size:9 final size:8
Alignment explanation
Indices: 3768643--3768693 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
3768633 CATTCATCAG
3768643 AAAAGAAA
1 AAAAGAAA
3768651 AAAGAGAAGA
1 AAA-AGAA-A
3768661 AAAAGAGAA
1 AAAAGA-AA
*
3768670 GAAAGAAA
1 AAAAGAAA
*
3768678 AATAGAAA
1 AAAAGAAA
3768686 AAAA-AAA
1 AAAAGAAA
3768693 A
1 A
3768694 GAGAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
7 4 0.11
8 14 0.39
9 13 0.36
10 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (8 bp):
AAAAGAAA
Found at i:3768698 original size:26 final size:28
Alignment explanation
Indices: 3768644--3768707 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
3768634 ATTCATCAGA
* *
3768644 AAAGAAAAA-AGAGAAGAAAAAGAGAAG
1 AAAGAAAAATAGAGAAAAAAAAAAGAAG
3768671 AAAGAAAAATAGA-AAAAAAAAAAG-AG
1 AAAGAAAAATAGAGAAAAAAAAAAGAAG
3768697 AAA-ATAAAATA
1 AAAGA-AAAATA
3768708 ATAAGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 1 0.03
26 11 0.33
27 18 0.55
28 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (28 bp):
AAAGAAAAATAGAGAAAAAAAAAAGAAG
Found at i:3768705 original size:15 final size:14
Alignment explanation
Indices: 3768660--3768705 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
3768650 AAAAGAGAAG
*
3768660 AAAAAGAGAAGAAAG
1 AAAAAGAGAA-AAAA
*
3768675 AAAAATAGAAAAAA
1 AAAAAGAGAAAAAA
*
3768689 AAAAAGAGAAAATA
1 AAAAAGAGAAAAAA
3768703 AAA
1 AAA
3768706 TAATAAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 18 0.67
15 9 0.33
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (14 bp):
AAAAAGAGAAAAAA
Found at i:3768710 original size:29 final size:30
Alignment explanation
Indices: 3768660--3768717 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
3768650 AAAAGAGAAG
3768660 AAAAAGAGAAGAAAGAAAAAT-AGAAAAAA
1 AAAAAGAGAAGAAAGAAAAATAAGAAAAAA
3768689 AAAAAGAGAA-AATA-AAATAATAAGAAAAA
1 AAAAAGAGAAGAA-AGAAA-AATAAGAAAAA
3768718 TTGAATCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 5 0.19
29 14 0.54
30 7 0.27
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (30 bp):
AAAAAGAGAAGAAAGAAAAATAAGAAAAAA
Found at i:3770588 original size:54 final size:54
Alignment explanation
Indices: 3770505--3770713 Score: 233
Period size: 54 Copynumber: 3.9 Consensus size: 54
3770495 GAAATCTGGG
* * * * *
3770505 CAGAAGTCACAAGAAAGAATGAATATATTGTCAAATGTTTTACAAACATCTGTA
1 CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGTA
* * * * *
3770559 CAGAAGCCACAGGAAAGGACGAATGTATTGTCAAATATATTACGAACATCTATG
1 CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGTA
* * * *
3770613 CAGAAGACACAGGAAATGATGAATGTGTTGTCAAATGTTTCACGAACATCTG-A
1 CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGTA
* * *
3770666 GCAGAAGCCACATGG-AATGATGAATGTGTTGTCAAATGTTTTATGAAC
1 -CAGAAGCCACA-GGAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
3770714 TAATGATTAT
Statistics
Matches: 131, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
54 129 0.98
55 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (54 bp):
CAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGTA
Found at i:3770698 original size:108 final size:108
Alignment explanation
Indices: 3770504--3770702 Score: 269
Period size: 108 Copynumber: 1.8 Consensus size: 108
3770494 AGAAATCTGG
* *
3770504 GCAGAAGTCACAAGAAAGAATGAATATATTGTCAAATGTTTTACAAACATCTGTACAGAAGCCAC
1 GCAGAAGACACAAGAAAGAATGAATATATTGTCAAATGTTTCACAAACATCTGTACAGAAGCCAC
3770569 AGGAAAGGACGAATGTATTGTCAAATATATTACGAACATCTAT
66 AGGAAAGGACGAATGTATTGTCAAATATATTACGAACATCTAT
* * * *
3770612 GCAGAAGACACAGGAAATG-ATGAATGTGTTGTCAAATGTTTCACGAACATCTG-AGCAGAAGCC
1 GCAGAAGACACAAGAAA-GAATGAATATATTGTCAAATGTTTCACAAACATCTGTA-CAGAAGCC
* * *
3770675 ACATGG-AATGATGAATGTGTTGTCAAAT
64 ACA-GGAAAGGACGAATGTATTGTCAAAT
3770703 GTTTTATGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
107 1 0.01
108 75 0.95
109 3 0.04
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (108 bp):
GCAGAAGACACAAGAAAGAATGAATATATTGTCAAATGTTTCACAAACATCTGTACAGAAGCCAC
AGGAAAGGACGAATGTATTGTCAAATATATTACGAACATCTAT
Found at i:3771856 original size:36 final size:34
Alignment explanation
Indices: 3771803--3771921 Score: 98
Period size: 36 Copynumber: 3.3 Consensus size: 34
3771793 TTCAAATAGC
3771803 AATTTATCTCACTTGAGATTGTTTTTATTAAAACA
1 AATTT-TCTCACTTGAGATTGTTTTTATTAAAACA
** *
3771838 AACTATTTCTCACTTGAGAAAG-TTTCACTTGAAATAGC-
1 AA-T-TTTCTCACTTGAGATTGTTTTTA-TT-AAA-A-CA
*
3771876 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTT-TCTCACTTGAGATTGTTTTTATTAAAAC-A
3771912 AATGTTTCTC
1 AAT-TTTCTC
3771922 GATAGAGAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 21
0.70 0.07 0.22
Matches are distributed among these distances:
34 1 0.02
35 7 0.11
36 28 0.42
37 23 0.35
38 6 0.09
39 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (34 bp):
AATTTTCTCACTTGAGATTGTTTTTATTAAAACA
Found at i:3771920 original size:73 final size:73
Alignment explanation
Indices: 3771796--3771980 Score: 282
Period size: 73 Copynumber: 2.5 Consensus size: 73
3771786 GGATATTTTC
* * *
3771796 AAATAGCAATTTATCTCACTTGAGATTGTTTTTATTAAAACAAACTATTTCTC-ACTTGAGAAAG
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATATTTCTCGA-TAGAGAAAG
* *
3771860 TTTCACTTG
65 TTTAACTCG
*
3771869 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATGTTTCTCGATAGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATATTTCTCGATAGAGAAAGT
3771934 TTAACTCG
66 TTAACTCG
* *
3771942 AAATAACAATTTATCTTACTTGAGATTGTTTTTCTTAAA
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAA
3771981 TCATTTCAAG
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
73 102 0.99
74 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (73 bp):
AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATATTTCTCGATAGAGAAAGT
TTAACTCG
Found at i:3772031 original size:19 final size:19
Alignment explanation
Indices: 3772007--3772070 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
3771997 TTCATAATCT
3772007 GAAGAACTCGTCTGAAGAG
1 GAAGAACTCGTCTGAAGAG
* ***
3772026 GAAGAA-TGAGTTCAT-AATTT
1 GAAGAACT-CG-TC-TGAAGAG
3772046 GAAGAACTCGTCTGAAGAG
1 GAAGAACTCGTCTGAAGAG
3772065 GAAGAA
1 GAAGAA
3772071 GAAGTTCATA
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 2 0.06
19 17 0.53
20 11 0.34
21 2 0.06
ACGTcount: A:0.41, C:0.11, G:0.28, T:0.20
Consensus pattern (19 bp):
GAAGAACTCGTCTGAAGAG
Found at i:3772041 original size:39 final size:39
Alignment explanation
Indices: 3771988--3772248 Score: 380
Period size: 39 Copynumber: 6.7 Consensus size: 39
3771978 AAATCATTTC
*
3771988 AAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAGG
1 AAGAAGAAGTTCATAATCTGAAGAACTCATCTGAAGAGG
* *
3772027 AAGAATG-AGTTCATAATTTGAAGAACTCGTCTGAAGAGG
1 AAGAA-GAAGTTCATAATCTGAAGAACTCATCTGAAGAGG
* *
3772066 AAGAAGAAGTTCATAGTCTGAAGAACTCGTCTGAAGAGG
1 AAGAAGAAGTTCATAATCTGAAGAACTCATCTGAAGAGG
* * *
3772105 AAAAAGGAGTTCATAATCTGAAGAACTCATTTGAAGAGG
1 AAGAAGAAGTTCATAATCTGAAGAACTCATCTGAAGAGG
* *
3772144 AAGAAGAAGTTCATAGTCTGAAGAACTCATATGAAGAGG
1 AAGAAGAAGTTCATAATCTGAAGAACTCATCTGAAGAGG
* *
3772183 AAGAAGGAGTTTATAATCTGAAGAACTCATCTGAAGAGG
1 AAGAAGAAGTTCATAATCTGAAGAACTCATCTGAAGAGG
* *
3772222 AAGAAGAAATTCATAGTCTGAAGAACT
1 AAGAAGAAGTTCATAATCTGAAGAACT
3772249 TATTCAACTT
Statistics
Matches: 200, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
38 1 0.00
39 198 0.99
40 1 0.00
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (39 bp):
AAGAAGAAGTTCATAATCTGAAGAACTCATCTGAAGAGG
Found at i:3772078 original size:78 final size:78
Alignment explanation
Indices: 3771988--3772248 Score: 432
Period size: 78 Copynumber: 3.3 Consensus size: 78
3771978 AAATCATTTC
* * *
3771988 AAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAATGAGTTCATAATTTGAAGAAC
1 AAGAAGAAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAAC
*
3772053 TCGTCTGAAGAGG
66 TCATCTGAAGAGG
*
3772066 AAGAAGAAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAAAAGGAGTTCATAATCTGAAGAAC
1 AAGAAGAAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAAC
*
3772131 TCATTTGAAGAGG
66 TCATCTGAAGAGG
* * *
3772144 AAGAAGAAGTTCATAGTCTGAAGAACTCATATGAAGAGGAAGAAGGAGTTTATAATCTGAAGAAC
1 AAGAAGAAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAAC
3772209 TCATCTGAAGAGG
66 TCATCTGAAGAGG
*
3772222 AAGAAGAAATTCATAGTCTGAAGAACT
1 AAGAAGAAGTTCATAGTCTGAAGAACT
3772249 TATTCAACTT
Statistics
Matches: 171, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 171 1.00
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (78 bp):
AAGAAGAAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAAC
TCATCTGAAGAGG
Found at i:3773693 original size:28 final size:27
Alignment explanation
Indices: 3773662--3773724 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 27
3773652 AATTTAATCA
3773662 CTTATTTTAATTTTTTACCATAAGTTTT
1 CTTATTTT-ATTTTTTACCATAAGTTTT
3773690 C-----TTATTTTTTACCATAAGTTTT
1 CTTATTTTATTTTTTACCATAAGTTTT
3773712 CTTATTTTTATTT
1 CTTA-TTTTATTT
3773725 ACTCCTATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
22 20 0.69
23 2 0.07
28 7 0.24
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.63
Consensus pattern (27 bp):
CTTATTTTATTTTTTACCATAAGTTTT
Found at i:3773738 original size:27 final size:22
Alignment explanation
Indices: 3773671--3773720 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
3773661 ACTTATTTTA
3773671 ATTTTTTACCATAAGTTTTCTT
1 ATTTTTTACCATAAGTTTTCTT
3773693 ATTTTTTACCATAAGTTTTCTT
1 ATTTTTTACCATAAGTTTTCTT
3773715 ATTTTT
1 ATTTTT
3773721 ATTTACTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTTTTACCATAAGTTTTCTT
Found at i:3773843 original size:11 final size:12
Alignment explanation
Indices: 3773810--3773848 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
3773800 TTTCAATATG
*
3773810 TTTAAGTTATTGT
1 TTTAA-TTATTAT
3773823 TTTAATTATTAT
1 TTTAATTATTAT
3773835 TTT-ATTATTAT
1 TTTAATTATTAT
3773846 TTT
1 TTT
3773849 CATTTTAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 11 0.44
12 9 0.36
13 5 0.20
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (12 bp):
TTTAATTATTAT
Found at i:3774156 original size:141 final size:139
Alignment explanation
Indices: 3773891--3774145 Score: 329
Period size: 141 Copynumber: 1.8 Consensus size: 139
3773881 TTAAATAATA
** *
3773891 ATATTTATTTATTTTTAATATTAAGAAAGGGGATGTCTTAAAGTAACTAGATGTCATTTTCTGGT
1 ATATTTATTTATTTTTAATATTAAGAAAGGGGATGTCTTAAAACAACTAGATGTCATTTTCTGAT
** * **
3773956 ATTTTTAAATAAATAAAATATTATATTTAATTTAGTTTAGTTTTATTTAAATTATTTTTTAGGAA
66 ATTTTTAAATAAATAAAATATTATATTTAATTTAGTAAAATCATATTTAAATTATTTTTTAGGAA
3774021 AAAAATATC
131 AAAAATATC
*
3774030 ATATTTATTTATTTGTTAATGTTAAAGAAA-GGGACTGTCTTAAAACAACTAGATGTCATTTTCT
1 ATATTTATTTATTT-TTAATATT-AAGAAAGGGGA-TGTCTTAAAACAACTAGATGTCATTTTCT
* *
3774094 GATATTTTTAAATGAAT-AAATATTTTATTTATAATTTA-TAAAAATCAT-TTTA
63 GATATTTTTAAATAAATAAAATATTATA-TT-TAATTTAGT-AAAATCATATTTA
3774146 TATATGTTTT
Statistics
Matches: 99, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
139 14 0.14
140 20 0.20
141 55 0.56
142 10 0.10
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (139 bp):
ATATTTATTTATTTTTAATATTAAGAAAGGGGATGTCTTAAAACAACTAGATGTCATTTTCTGAT
ATTTTTAAATAAATAAAATATTATATTTAATTTAGTAAAATCATATTTAAATTATTTTTTAGGAA
AAAAATATC
Found at i:3777736 original size:19 final size:20
Alignment explanation
Indices: 3777712--3777783 Score: 92
Period size: 19 Copynumber: 3.5 Consensus size: 20
3777702 ATGCAAAAAT
3777712 GGTATCGATACCATAAT-TG
1 GGTATCGATACCATAATATG
3777731 GGTATCGATACCATAATATG
1 GGTATCGATACCATAATATG
** *
3777751 GTAGTATCGATACCATGGTAGG
1 G--GTATCGATACCATAATATG
3777773 GGTATCGATAC
1 GGTATCGATAC
3777784 TGAGGAGCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
19 17 0.36
20 13 0.28
22 17 0.36
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (20 bp):
GGTATCGATACCATAATATG
Found at i:3778199 original size:56 final size:56
Alignment explanation
Indices: 3778118--3778430 Score: 443
Period size: 55 Copynumber: 5.6 Consensus size: 56
3778108 TAAGTGTGCA
* * * **
3778118 AAAACTTAAAAAATTCATACAAAGTGAATGAATTTGTGTATGGGCACTATATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * *
3778174 AAAACTTAATAAATTAATACTAAGTGGATGAATTTACGTATGGGCACTATATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * **
3778230 AAAACTTAAGAAATTCATTCTAAGTGGATGAATTTCCATATATGCACTATATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
*
3778286 AAAA-TTAAGAAATTTATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
3778341 AAAA-TTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTATATGTGC
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * *
3778396 AAAAC-TAGGAAATTCATACTAAGTGTATAAATTTC
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTC
3778431 TTAGTGGGTG
Statistics
Matches: 232, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
55 129 0.56
56 103 0.44
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (56 bp):
AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
Found at i:3782082 original size:20 final size:21
Alignment explanation
Indices: 3782057--3782108 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3782047 TTTTCCCAAT
*
3782057 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3782077 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3782098 TCGCAATGCGA
1 TCGCAATGCGA
3782109 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3782122 original size:20 final size:20
Alignment explanation
Indices: 3782097--3782150 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
3782087 AATTGGGAAA
3782097 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTTACT
*
3782117 ATCGCAATTCGATACTTACT
1 ATCGCAATGCGATACTTACT
3782137 ATCGCAATGCGATA
1 ATCGCAATGCGATA
3782151 ATACAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (20 bp):
ATCGCAATGCGATACTTACT
Found at i:3782203 original size:61 final size:61
Alignment explanation
Indices: 3782094--3782210 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
3782084 GCGAATTGGG
* * * ** * *
3782094 AAAATCGCAATGCGATACTTACTATCGCAATTCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
3782155 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
3782211 TTACATAGCG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:3782207 original size:20 final size:20
Alignment explanation
Indices: 3782159--3782211 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3782149 TAATACAAAA
* *
3782159 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
3782179 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
3782199 TCGCAACGCGATT
1 TCGCAACGCGATT
3782212 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:3782814 original size:19 final size:19
Alignment explanation
Indices: 3782767--3782808 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3782757 ACGAGAGAAT
*
3782767 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
3782786 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
3782805 CGCA
1 CGCA
3782809 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:3782826 original size:19 final size:19
Alignment explanation
Indices: 3782804--3782893 Score: 144
Period size: 19 Copynumber: 4.7 Consensus size: 19
3782794 GAAACAAAAA
* *
3782804 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
3782823 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3782842 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
3782861 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
3782881 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3782894 GTCTGGTCGC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
19 48 0.73
20 18 0.27
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3782881 original size:39 final size:38
Alignment explanation
Indices: 3782804--3782893 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 38
3782794 GAAACAAAAA
*
3782804 TCGCATTGCGATTTTTATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
3782842 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
3782881 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3782894 GTCTGGTCGC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 22 0.44
39 28 0.56
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (38 bp):
TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
Found at i:3782904 original size:39 final size:39
Alignment explanation
Indices: 3782804--3782904 Score: 116
Period size: 39 Copynumber: 2.6 Consensus size: 39
3782794 GAAACAAAAA
* * **
3782804 TCGCATTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
1 TCGCGTTGCGATTTCTAGGTCGCGGTTGCGATTTTCATT
* **
3782842 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTCTAGGTCGCGGTTGCGATTTTCATT
3782881 TCGCGTTGCGATTGTCT-GGTCGCG
1 TCGCGTTGCGATT-TCTAGGTCGCG
3782905 ATAGTCATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
38 22 0.39
39 33 0.58
40 2 0.04
ACGTcount: A:0.10, C:0.20, G:0.25, T:0.46
Consensus pattern (39 bp):
TCGCGTTGCGATTTCTAGGTCGCGGTTGCGATTTTCATT
Found at i:3782935 original size:14 final size:14
Alignment explanation
Indices: 3782918--3782953 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3782908 GTCATTTCGC
*
3782918 GTTGCGATTCTCTA
1 GTTGCGATTCTATA
*
3782932 GTTGCGATTCTATC
1 GTTGCGATTCTATA
3782946 GTTGCGAT
1 GTTGCGAT
3782954 AGTCATTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (14 bp):
GTTGCGATTCTATA
Found at i:3782939 original size:33 final size:33
Alignment explanation
Indices: 3782866--3782939 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
3782856 TTATTTCGCG
** * *
3782866 GTTGCGATTTTCATTTCGCGTTGCGATTGTCTG
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTA
*
3782899 GTCGCGATAGTCATTTCGCGTTGCGATTCTCTA
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTA
3782932 GTTGCGAT
1 GTTGCGAT
3782940 TCTATCGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.12, C:0.20, G:0.27, T:0.41
Consensus pattern (33 bp):
GTTGCGATAGTCATTTCGCGTTGCGATTCTCTA
Found at i:3782979 original size:20 final size:20
Alignment explanation
Indices: 3782945--3782994 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3782935 GCGATTCTAT
**
3782945 CGTTGCGATAGTCATT-TCCG
1 CGTTGCGATTCTCATTAT-CG
*
3782965 CGTTGCGATTCTCATTATCT
1 CGTTGCGATTCTCATTATCG
3782985 CGTTGCGATT
1 CGTTGCGATT
3782995 TTTATTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTCTCATTATCG
Found at i:3785085 original size:21 final size:21
Alignment explanation
Indices: 3785061--3785127 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3785051 TCATTCCTCG
3785061 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
3785082 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3785103 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3785124 AGAG
1 AGAG
3785128 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3785085 original size:42 final size:42
Alignment explanation
Indices: 3785009--3785127 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
3784999 GACTCACCTG
* * * * * * *
3785009 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
3785051 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
3785093 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
3785128 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:3786498 original size:14 final size:14
Alignment explanation
Indices: 3786479--3786514 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3786469 ATTGTTTAAT
3786479 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3786493 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3786507 TGATTTGT
1 TGATTTGT
3786515 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3786715 original size:19 final size:19
Alignment explanation
Indices: 3786693--3786810 Score: 58
Period size: 19 Copynumber: 6.7 Consensus size: 19
3786683 CGAAATTAAA
3786693 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3786712 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * *
3786727 -CCTCGTTTCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
3786745 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
3786759 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
3786778 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
3786797 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
3786811 AGACATTAAG
Statistics
Matches: 69, Mismatches: 19, Indels: 21
0.63 0.17 0.19
Matches are distributed among these distances:
14 18 0.26
16 3 0.04
17 3 0.04
19 35 0.51
20 10 0.14
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:3786744 original size:33 final size:31
Alignment explanation
Indices: 3786696--3786790 Score: 127
Period size: 33 Copynumber: 2.9 Consensus size: 31
3786686 AATTAAATTC
*
3786696 GCGTTGCGATTTTCATTTCGCATTGCGATTCCC
1 GCGTTGCGATTTTCATTTCGCATTGCGATT--A
* *
3786729 TCGTTTCGATTTTCATTTCGCATTGCGAAATTA
1 GCGTTGCGATTTTCATTTCGCATTGCG--ATTA
3786762 GCGTTGCGATTTTCATTTCGCATTGCGAT
1 GCGTTGCGATTTTCATTTCGCATTGCGAT
3786791 AGTAATTTCC
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
31 2 0.04
33 50 0.91
35 3 0.05
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (31 bp):
GCGTTGCGATTTTCATTTCGCATTGCGATTA
Found at i:3789101 original size:12 final size:12
Alignment explanation
Indices: 3789084--3789108 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3789074 TCTTCAGGGA
3789084 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3789096 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3789108 C
1 C
3789109 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3789317 original size:24 final size:24
Alignment explanation
Indices: 3789283--3789336 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3789273 CTGAAACATC
* *
3789283 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
3789307 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
3789331 ATCAAA
1 ATCAAA
3789337 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:3790416 original size:20 final size:20
Alignment explanation
Indices: 3790391--3790448 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
3790381 ATTCATTTGA
3790391 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
3790411 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
3790431 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
3790449 CGCAATGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:3790491 original size:14 final size:14
Alignment explanation
Indices: 3790472--3790525 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
3790462 GAAAATCGCA
3790472 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
3790486 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
3790503 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
3790519 TTGCGAT
1 TTGCGAT
3790526 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:3790491 original size:33 final size:33
Alignment explanation
Indices: 3790454--3790524 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
3790444 AAAATCGCAA
3790454 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
3790487 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
3790520 TGCGA
1 TGCGA
3790525 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:3790525 original size:33 final size:33
Alignment explanation
Indices: 3790467--3790544 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
3790457 GAAATGAAAA
***
3790467 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
3790500 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
3790533 TCGCGTTGCGAT
1 TCGCATTGCGAT
3790545 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:3790651 original size:14 final size:14
Alignment explanation
Indices: 3790632--3790668 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3790622 CATCAATTAA
3790632 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3790646 ACAAATCATCTTTT
1 ACAAATCAACATTT
3790660 ACAAATCAA
1 ACAAATCAA
3790669 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3792589 original size:19 final size:19
Alignment explanation
Indices: 3792535--3792601 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
3792525 GAAACTTAAA
3792535 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* * *
3792554 ATCACAACACAGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
3792574 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
3792593 ATCGCAACG
1 ATCGCAACG
3792602 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 22 0.59
20 15 0.41
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3792609 original size:14 final size:14
Alignment explanation
Indices: 3792590--3792647 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3792580 ATGCGAAATG
3792590 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3792604 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
3792620 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3792636 AAAATCGCAACG
1 AAAATCGCAACG
3792648 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3792632 original size:32 final size:33
Alignment explanation
Indices: 3792574--3792652 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
3792564 AGAAATGGCT
*
3792574 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
3792607 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
3792639 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
3792653 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:3793107 original size:20 final size:20
Alignment explanation
Indices: 3793082--3793124 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3793072 AATAGTTTCT
3793082 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
3793102 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
3793122 GAA
1 GAA
3793125 TTCGACTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:3793430 original size:22 final size:22
Alignment explanation
Indices: 3793403--3793446 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3793393 GATGGAGATA
3793403 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
3793425 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
3793447 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:3793695 original size:20 final size:20
Alignment explanation
Indices: 3793634--3793747 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
3793624 GATTATGTAT
3793634 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
3793654 AACCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3793674 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
3793694 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
3793715 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3793735 TATCGCATTGCGA
1 TATCGCGTTGCGA
3793748 TTTTCCCAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.78
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:3793751 original size:41 final size:41
Alignment explanation
Indices: 3793614--3793749 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 41
3793604 CGCTTTGAAA
*
3793614 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * * *
3793655 ACCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
3793695 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
3793736 ATCGCATTGCGATT
1 ATCGCATTGCGATT
3793750 TTCCCAATTC
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.39
41 41 0.54
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:3793766 original size:21 final size:21
Alignment explanation
Indices: 3793737--3793829 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
3793727 ATAGTCAGTA
3793737 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
3793758 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
3793778 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
3793799 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
3793819 TCGCATTGCGA
1 TCGCATTGCGA
3793830 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:3793767 original size:41 final size:41
Alignment explanation
Indices: 3793676--3793810 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
3793666 AAAGTCAGTA
* * * ** *
3793676 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
3793716 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
3793758 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
3793799 TCGCGTTGCGAT
1 TCGCGTTGCGAT
3793811 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:3793811 original size:41 final size:41
Alignment explanation
Indices: 3793737--3793829 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
3793727 ATAGTCAGTA
3793737 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
3793778 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
3793819 TCGCATTGCGA
1 TCGCATTGCGA
3793830 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:3794281 original size:15 final size:15
Alignment explanation
Indices: 3794261--3794297 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3794251 TGAGACATTA
*
3794261 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
3794276 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
3794291 CCCGCCC
1 CCCGCCC
3794298 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:3801570 original size:6 final size:6
Alignment explanation
Indices: 3801559--3801589 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3801549 GGATTACTAC
*
3801559 GGTGGA GGTGGA GGTGGA GGTGGA TGTGGA G
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA G
3801590 AGAATAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.65, T:0.19
Consensus pattern (6 bp):
GGTGGA
Found at i:3809551 original size:20 final size:20
Alignment explanation
Indices: 3809513--3809551 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3809503 TCTGTTAGTT
* *
3809513 ATTAGATAGGATCAATTTTA
1 ATTAGATAGAACCAATTTTA
*
3809533 ATTAGATAGAACCAGTTTT
1 ATTAGATAGAACCAATTTT
3809552 TATTCTGTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (20 bp):
ATTAGATAGAACCAATTTTA
Found at i:3809559 original size:52 final size:51
Alignment explanation
Indices: 3809496--3809611 Score: 189
Period size: 52 Copynumber: 2.3 Consensus size: 51
3809486 TTAACTAGAT
*
3809496 ATTTTATTCTGTTAGTTATTAGATAGGATCAATTTTAATTAGATAGAA-CC
1 ATTTTATTCTGTTAGTTATTAGACAGGATCAATTTTAATTAGATAGAATCC
*
3809546 AGTTTTTATTCTGTTAGTTATTAGACAGGATCAGTTTTAATTAGATAGAATCC
1 A--TTTTATTCTGTTAGTTATTAGACAGGATCAATTTTAATTAGATAGAATCC
3809599 ATTTTATTCTGTT
1 ATTTTATTCTGTT
3809612 GCTAATTTTA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
50 1 0.02
51 12 0.20
52 45 0.74
53 3 0.05
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (51 bp):
ATTTTATTCTGTTAGTTATTAGACAGGATCAATTTTAATTAGATAGAATCC
Found at i:3812229 original size:27 final size:27
Alignment explanation
Indices: 3812199--3812254 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3812189 ATTCATATTT
3812199 CTGTAACTAATCCTAGGATTTCACAAC
1 CTGTAACTAATCCTAGGATTTCACAAC
3812226 CTGTAACTAATCCTAGGATTTCACAAC
1 CTGTAACTAATCCTAGGATTTCACAAC
3812253 CT
1 CT
3812255 ATAAATTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (27 bp):
CTGTAACTAATCCTAGGATTTCACAAC
Found at i:3814723 original size:20 final size:20
Alignment explanation
Indices: 3814698--3814789 Score: 67
Period size: 20 Copynumber: 5.0 Consensus size: 20
3814688 TCTGCTAGTT
3814698 ATTAGATATG-ATCAGTTTTA
1 ATTAGATA-GAATCAGTTTTA
*
3814718 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
3814738 ATT--CT-G--TTAG--TT-
1 ATTAGATAGAATCAGTTTTA
*
3814750 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
3814770 ATTAGATAGAATCAATTTTA
1 ATTAGATAGAATCAGTTTTA
3814790 TTCTGTTGCT
Statistics
Matches: 56, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
12 3 0.05
13 2 0.04
14 1 0.02
15 4 0.07
17 4 0.07
18 1 0.02
19 3 0.05
20 38 0.68
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:3814749 original size:52 final size:51
Alignment explanation
Indices: 3814681--3814796 Score: 196
Period size: 52 Copynumber: 2.3 Consensus size: 51
3814671 TTAACTACAT
* *
3814681 ATTTTATTCTGCTAGTTATTAGATATGATCAGTTTTAATTAGATAGAATCA
1 ATTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCA
*
3814732 GTTTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCA
1 -ATTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCA
3814784 ATTTTATTCTGTT
1 ATTTTATTCTGTT
3814797 GCTAATTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 12 0.20
52 48 0.80
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (51 bp):
ATTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCA
Found at i:3825568 original size:63 final size:59
Alignment explanation
Indices: 3825428--3825576 Score: 178
Period size: 63 Copynumber: 2.5 Consensus size: 59
3825418 AAATGACACC
* *
3825428 ATAAATCTAGCACATAGAGT-AACAAAAGGCAGAGTGCTACAGATCAAAAGATAACATG
1 ATAAATCTAGCACATAGAGTAAACAAAAGGCAGAGTGCAACAGATCAAAAAATAACATG
* * *
3825486 ATAAATCTAGCACATAGAGTAGCAACAAAAGGCAGATTGCAACA-ATTCAAAAACAATTATATG
1 ATAAATCTAGCACATAGAGTA--AACAAAAGGCAGAGTGCAACAGA-TC-AAAA-AATAACATG
*
3825549 GTAAATCTAGCACATAGAGT-AACAAAAG
1 ATAAATCTAGCACATAGAGTAAACAAAAG
3825577 AGTGCAACAA
Statistics
Matches: 79, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
58 20 0.25
60 9 0.11
61 21 0.27
62 4 0.05
63 25 0.32
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (59 bp):
ATAAATCTAGCACATAGAGTAAACAAAAGGCAGAGTGCAACAGATCAAAAAATAACATG
Found at i:3826880 original size:50 final size:49
Alignment explanation
Indices: 3826756--3826880 Score: 146
Period size: 50 Copynumber: 2.5 Consensus size: 49
3826746 GTAGTAGTAA
* *
3826756 AGCGCG-CCCCTGAATCGCGCTATACACTGATTTGGCGTCACGTGGGTAT
1 AGCGCGCCCCCTG-ATCGCGCTATACACTGATCTGGCGCCACGTGGGTAT
* **
3826805 AGCGCGCCCCCT-ATCCCGCGATATACGGTGATCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGAT--CGCGCTATACACTGATCTGGCGCCACGTGGGTAT
*
3826855 AGCTCGCCCCCTGATCTGCGCTATAC
1 AGCGCGCCCCCTGATC-GCGCTATAC
3826881 CTGGGTATCT
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
48 2 0.03
49 7 0.11
50 53 0.83
51 2 0.03
ACGTcount: A:0.17, C:0.34, G:0.27, T:0.22
Consensus pattern (49 bp):
AGCGCGCCCCCTGATCGCGCTATACACTGATCTGGCGCCACGTGGGTAT
Found at i:3826997 original size:10 final size:10
Alignment explanation
Indices: 3826982--3827021 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
3826972 TTTATCACAC
3826982 CAAATTCTCT
1 CAAATTCTCT
3826992 CAAATTCTCT
1 CAAATTCTCT
3827002 -AAATTTCTCT
1 CAAA-TTCTCT
*
3827012 CAAATACTCT
1 CAAATTCTCT
3827022 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:3827334 original size:111 final size:111
Alignment explanation
Indices: 3827149--3827480 Score: 547
Period size: 111 Copynumber: 3.0 Consensus size: 111
3827139 GAAAATCATT
* * * * *
3827149 TATCTCTACACTTTGCTGATACAGTAATGTTTAAACGTTTTAATTTAATTTAAATTATTTGTAAT
1 TATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAAT
* * *
3827214 ATTTAGTTGATTTATTTAATGCATGGTTATTAGATTAAAAATTAAA
66 AATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAA
3827260 TATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAAT
1 TATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAAT
3827325 AATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAA
66 AATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAA
* * *
3827371 TATCTCGACACTTTGTTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAAT
1 TATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAAT
* *
3827436 AATTAATTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 AATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
3827481 TTTTTGTAAT
Statistics
Matches: 208, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 208 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (111 bp):
TATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAAT
AATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAA
Found at i:3828608 original size:23 final size:23
Alignment explanation
Indices: 3828582--3828696 Score: 149
Period size: 23 Copynumber: 5.0 Consensus size: 23
3828572 CACCACAGCT
*
3828582 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
3828605 CGTAGAATTGCACCGTAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
3828628 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
3828651 CGTAGAATTGCACCGTAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
3828674 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
3828697 TATAAGATTT
Statistics
Matches: 75, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:3828654 original size:46 final size:46
Alignment explanation
Indices: 3828582--3828696 Score: 221
Period size: 46 Copynumber: 2.5 Consensus size: 46
3828572 CACCACAGCT
*
3828582 CGTATAAATGCACCGAAGTGCCACGTAGAATTGCACCGTAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCACGTAGAATTGCACCGTAGTGTCG
3828628 CGTAGAAATGCACCGAAGTGCCACGTAGAATTGCACCGTAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCACGTAGAATTGCACCGTAGTGTCG
3828674 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
3828697 TATAAGATTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (46 bp):
CGTAGAAATGCACCGAAGTGCCACGTAGAATTGCACCGTAGTGTCG
Found at i:3829105 original size:2 final size:2
Alignment explanation
Indices: 3829098--3829161 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
3829088 ATTCATCTTC
3829098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3829140 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
3829162 CATTTTTCCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3831639 original size:16 final size:16
Alignment explanation
Indices: 3831618--3831651 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3831608 CATTAAAATC
3831618 AACCTATATGTGACGA
1 AACCTATATGTGACGA
3831634 AACCTATATGTGACGA
1 AACCTATATGTGACGA
3831650 AA
1 AA
3831652 GAGATATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (16 bp):
AACCTATATGTGACGA
Found at i:3841311 original size:12 final size:12
Alignment explanation
Indices: 3841294--3841330 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3841284 ATTTATAAGA
3841294 GAGGAGAGATGC
1 GAGGAGAGATGC
*
3841306 GA-G-GAGATGT
1 GAGGAGAGATGC
3841316 GAGGAGAGATGC
1 GAGGAGAGATGC
3841328 GAG
1 GAG
3841331 AACCGGAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.32, C:0.05, G:0.51, T:0.11
Consensus pattern (12 bp):
GAGGAGAGATGC
Found at i:3841574 original size:51 final size:51
Alignment explanation
Indices: 3841471--3841593 Score: 122
Period size: 51 Copynumber: 2.4 Consensus size: 51
3841461 CCCCTACGTG
* * * * *
3841471 GCGTATAGCGCAG-AGCAGGGGGCGCGCTATACCCCACGTGTAACCCAGTCA
1 GCGTATAGCGCGGTA-CAGGGGGCGCACTATACCCCACGTGGAACCAAATCA
* **
3841522 GCGTATAGCGCGGTACAGGGGGCGCACTATACTCCACGTGGCGCCAAATCA
1 GCGTATAGCGCGGTACAGGGGGCGCACTATACCCCACGTGGAACCAAATCA
* * * *
3841573 GCATATAACGTGGTTCAGGGG
1 GCGTATAGCGCGGTACAGGGG
3841594 ACGCGCTTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
51 58 0.98
52 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.33, T:0.16
Consensus pattern (51 bp):
GCGTATAGCGCGGTACAGGGGGCGCACTATACCCCACGTGGAACCAAATCA
Found at i:3842732 original size:33 final size:33
Alignment explanation
Indices: 3842652--3842732 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
3842642 TTATAAATTA
*
3842652 TATATAAAAATATAATATAAATTAATATTATTTAT
1 TATAT-AAAATATAATAT-AATTAATATTATTGAT
* * *
3842687 AATATTATAATATAATAT-ATTTATATTATTGAT
1 TATA-TAAAATATAATATAATTAATATTATTGAT
3842720 TATATAGAAATAT
1 TATATA-AAATAT
3842733 TTTATATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
32 2 0.05
33 21 0.55
35 14 0.37
36 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (33 bp):
TATATAAAATATAATATAATTAATATTATTGAT
Found at i:3842740 original size:70 final size:66
Alignment explanation
Indices: 3842635--3842774 Score: 147
Period size: 70 Copynumber: 2.1 Consensus size: 66
3842625 TAAAAAGTAT
* *
3842635 TATTTTATTATAAATTATATATAAAAATATAATATAAATTAATATTATTTATAATA-TTATAATA
1 TATTTTATTATAAATTATATAGAAAAATATAATATAAACTAATA-TA--TATAATATTTATAATA
3842699 TAATA
63 TAA-A
** * * * * *
3842704 TATTTATATTATTGATTATATAGAAATATTTTATATATACTAATATATATAATATTTATATTATA
1 TATTT-TATTATAAATTATATAGAAAAATATAATATAAACTAATATATATAATATTTATAATATA
3842769 AA
65 AA
3842771 TATT
1 TATT
3842775 ATTCTAATGT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
67 12 0.20
68 10 0.17
69 7 0.12
70 31 0.52
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (66 bp):
TATTTTATTATAAATTATATAGAAAAATATAATATAAACTAATATATATAATATTTATAATATAA
A
Found at i:3843377 original size:17 final size:18
Alignment explanation
Indices: 3843340--3843385 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
3843330 ATTATAATAA
3843340 AATTAAAATCTGTGAAAG
1 AATTAAAATCTGTGAAAG
*
3843358 AATTAAAATCTGT-CAAG
1 AATTAAAATCTGTGAAAG
3843375 AATTAAAATCT
1 AATTAAAATCT
3843386 AATTCGATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (18 bp):
AATTAAAATCTGTGAAAG
Found at i:3849607 original size:37 final size:37
Alignment explanation
Indices: 3849557--3849630 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
3849547 TTTTGTATGG
3849557 GTTGTAAGGCCTCTGAGGAGGTCCCGAAAAGTTACCA
1 GTTGTAAGGCCTCTGAGGAGGTCCCGAAAAGTTACCA
3849594 GTTGTAAGGCCTCTGAGGAGGTCCCGAAAAGTTACCA
1 GTTGTAAGGCCTCTGAGGAGGTCCCGAAAAGTTACCA
3849631 ATGTCATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (37 bp):
GTTGTAAGGCCTCTGAGGAGGTCCCGAAAAGTTACCA
Found at i:3852013 original size:23 final size:23
Alignment explanation
Indices: 3851983--3852026 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3851973 TAAGGTATGT
3851983 GTAGAATTGCACCGGAGTGCCGC
1 GTAGAATTGCACCGGAGTGCCGC
*
3852006 GTAGAATTGCACCGTAGTGCC
1 GTAGAATTGCACCGGAGTGCC
3852027 ATATAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.25, G:0.32, T:0.20
Consensus pattern (23 bp):
GTAGAATTGCACCGGAGTGCCGC
Found at i:3852214 original size:103 final size:103
Alignment explanation
Indices: 3852035--3852260 Score: 400
Period size: 103 Copynumber: 2.2 Consensus size: 103
3852025 CCATATAATA
*
3852035 ATGT-CCATAAGGACCACATATCATTCCTTAATAATCATATACACATGCCAAGGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACACATGCCAAGGATCAAGTATGT
3852099 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
65 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
3852138 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACACATGCCAAGGATCAAGTATGTG
*
3852203 TCTCACCAGACTTCACACATGTTCCAAAGAATATATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
3852241 ATGTCCCGAAGGACCACATA
1 ATGTCCCAAAGGACCACATA
3852261 GACCCTCTAC
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 115 0.97
104 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACACATGCCAAGGATCAAGTATGTG
TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:3852751 original size:20 final size:20
Alignment explanation
Indices: 3852726--3852763 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3852716 CTTTTTTTTA
*
3852726 TGGGGGAATCGGTTCCTCCC
1 TGGGGGAATCGATTCCTCCC
*
3852746 TGGGGGTATCGATTCCTC
1 TGGGGGAATCGATTCCTC
3852764 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.34, T:0.29
Consensus pattern (20 bp):
TGGGGGAATCGATTCCTCCC
Found at i:3852815 original size:21 final size:21
Alignment explanation
Indices: 3852791--3852833 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3852781 TCATATTCGT
* *
3852791 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
3852812 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
3852833 T
1 T
3852834 AGCTCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:3856133 original size:36 final size:38
Alignment explanation
Indices: 3856092--3856191 Score: 89
Period size: 38 Copynumber: 2.7 Consensus size: 38
3856082 GAAATCTTAC
*
3856092 CTCACTTGAGATAGTTTTCCTTAAAAC-AAAA-TTCGT
1 CTCACTTGAGATAGTTTTCCTTAAAACAAAAATTTCAT
* * * * * * *
3856128 GTCACTAGGGAGAG-TTTCTATTGAAACAAAAATTTTAT
1 CTCACTTGAGATAGTTTTC-CTTAAAACAAAAATTTCAT
*
3856166 CTCACTTGAGATAGTTTTCCTCAAAA
1 CTCACTTGAGATAGTTTTCCTTAAAA
3856192 ATGAATTTAG
Statistics
Matches: 45, Mismatches: 15, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
35 4 0.09
36 16 0.36
37 4 0.09
38 17 0.38
39 4 0.09
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (38 bp):
CTCACTTGAGATAGTTTTCCTTAAAACAAAAATTTCAT
Found at i:3856319 original size:71 final size:70
Alignment explanation
Indices: 3856155--3856711 Score: 574
Period size: 71 Copynumber: 7.9 Consensus size: 70
3856145 CTATTGAAAC
* ** * * * * *
3856155 AAAAATTTTATCTCACTTGAGATAGTTTT-CCTCAAAAATGAATTTAGTATCACTTGAGACAATC
1 AAAAATTTCATCTCACTTGAGATA-TTTTCCCTTGAAAAT---TTTCGTCTCACTCGAGACAGTT
*
3856219 TC-CTTGAA
62 TCTCTCGAA
*
3856227 AAAAATTGT-ATCTCACATGAGATATTTTCCCTTGAAAATTTTCGT-TGCACTCGAGAC-GATTT
1 AAAAATT-TCATCTCACTTGAGATATTTTCCCTTGAAAATTTTCGTCT-CACTCGAGACAG-TTT
*
3856289 CTCTCAAA
63 CTCTCGAA
* *
3856297 ACAAAATTTCATCTCACTTGAGATATTTTCTCTTGAAAATTTTCGTCTCACTCGAGACAATTTCT
1 A-AAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTCGAGACAGTTTCT
3856362 CTC---
65 CTCGAA
* * * * * * *
3856365 AAAAATTGCATCTCACTTAAGATATTTCCCCTTGAATATTTTCGTCTCACTTGATACAGTTCCTC
1 AAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTCGAGACAGTTTCTC
3856430 TCGGAA
66 TC-GAA
* * * * *
3856436 AAAAATTTTATCTCACTCGAGATATTTTCCCTTGAAAAATTTTCGTCTTACTCGAGACAGTTCCA
1 AAAAATTTCATCTCACTTGAGATATTTTCCCTTG-AAAATTTTCGTCTCACTCGAGACAGTTTCT
3856501 CTCGATA
65 CTCGA-A
* * *
3856508 TAAAATTTCATCTCACTCGAGATATTTTCCCTTGAAAATTTTTCGTCTCACTCGAGATAGTTTCT
1 AAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAA-TTTTCGTCTCACTCGAGACAGTTTCT
3856573 CTCGAA
65 CTCGAA
* *
3856579 ACAAAATTTCATCTCAC-TGAGATATTTTCCCTTGAAAATTTTCGTCTCACTTGAGACTGTTTCT
1 A-AAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTCGAGACAGTTTCT
*
3856643 CTCCAA
65 CTCGAA
* * * * * * * *
3856649 ATAAAATTTCATCACACTTGATATTTTTTCTCTTAAAAATTTTCTTCTCACTAGAGATAGTTT
1 A-AAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTCGAGACAGTTT
3856712 TCTATCAAGA
Statistics
Matches: 414, Mismatches: 53, Indels: 37
0.82 0.11 0.07
Matches are distributed among these distances:
67 57 0.14
68 2 0.00
69 17 0.04
70 49 0.12
71 155 0.37
72 133 0.32
73 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.38
Consensus pattern (70 bp):
AAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTCGAGACAGTTTCTC
TCGAA
Found at i:3858298 original size:22 final size:20
Alignment explanation
Indices: 3858240--3858298 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
3858230 TTTTGTTTTG
* *
3858240 ATTTTGTTTTAATTTTATTT
1 ATTTTTTTTTCATTTTATTT
*
3858260 CTTTTTTTCTTCTATTTTATTT
1 ATTTTTTT-TTC-ATTTTATTT
3858282 ATTTATTATTTTCATTT
1 ATTT-TT-TTTTCATTT
3858299 CTTTGGTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 6 0.19
21 2 0.06
22 16 0.52
23 5 0.16
24 2 0.06
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.75
Consensus pattern (20 bp):
ATTTTTTTTTCATTTTATTT
Found at i:3858403 original size:20 final size:21
Alignment explanation
Indices: 3858378--3858416 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3858368 ATCCTTTATA
3858378 TTTTAAT-GTTTTCTTTTTCT
1 TTTTAATCGTTTTCTTTTTCT
*
3858398 TTTTAATCTTTTTCTTTTT
1 TTTTAATCGTTTTCTTTTT
3858417 AATTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTTAATCGTTTTCTTTTTCT
Found at i:3858425 original size:15 final size:15
Alignment explanation
Indices: 3858389--3858419 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3858379 TTTAATGTTT
3858389 TCTTTTTCTTTTTAA
1 TCTTTTTCTTTTTAA
3858404 TCTTTTTCTTTTTAA
1 TCTTTTTCTTTTTAA
3858419 T
1 T
3858420 TATTTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTTTTCTTTTTAA
Found at i:3858525 original size:15 final size:18
Alignment explanation
Indices: 3858486--3858525 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3858476 ATGCACTTGT
3858486 TTATTTGTTTATCTTTAC
1 TTATTTGTTTATCTTTAC
3858504 TTTATTTG-TTA-CTTTA-
1 -TTATTTGTTTATCTTTAC
3858520 TTATTT
1 TTATTT
3858526 TTATCTGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.29
17 5 0.24
18 3 0.14
19 7 0.33
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.70
Consensus pattern (18 bp):
TTATTTGTTTATCTTTAC
Found at i:3861550 original size:23 final size:23
Alignment explanation
Indices: 3861517--3861579 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
3861507 ATTATTATAT
3861517 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
3861540 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
3861563 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
3861580 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 33 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:3875477 original size:22 final size:22
Alignment explanation
Indices: 3875452--3875502 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3875442 AACAGATTTA
3875452 TCTTTTTAGAAAAGAGATCGAT
1 TCTTTTTAGAAAAGAGATCGAT
* * *
3875474 TCTTTTTTGTAAAGGGATCGAT
1 TCTTTTTAGAAAAGAGATCGAT
*
3875496 CCTTTTT
1 TCTTTTT
3875503 CTGGAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (22 bp):
TCTTTTTAGAAAAGAGATCGAT
Found at i:3875549 original size:50 final size:51
Alignment explanation
Indices: 3875463--3875559 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 51
3875453 CTTTTTAGAA
* * * *
3875463 AAGAGATCGATTCTTTTTTGTAAAGGGATCGATCCTTTTTCTGGAAAATGC
1 AAGAGATCGATTCTTTATTGTAAAGCGATCAATCCTTTTTCTAGAAAATGC
3875514 AAGAGATCGA-TCATTTATT-TAAAGCGATCAATCCTTTTTCTAGAAA
1 AAGAGATCGATTC-TTTATTGTAAAGCGATCAATCCTTTTTCTAGAAA
3875560 TTTTCATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
50 26 0.63
51 15 0.37
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (51 bp):
AAGAGATCGATTCTTTATTGTAAAGCGATCAATCCTTTTTCTAGAAAATGC
Found at i:3888931 original size:20 final size:19
Alignment explanation
Indices: 3888880--3888935 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 19
3888870 ATAAATGAAT
*
3888880 AAAATAAATAAATATTGA-
1 AAAATAAATAAATAATGAG
*
3888898 ATAA-AAAT-AATAATGAG
1 AAAATAAATAAATAATGAG
3888915 AAAATAAATAAAGTAAT-AG
1 AAAATAAATAAA-TAATGAG
3888934 AA
1 AA
3888936 GAATTCAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 7 0.23
17 7 0.23
18 7 0.23
19 6 0.19
20 4 0.13
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (19 bp):
AAAATAAATAAATAATGAG
Found at i:3891280 original size:21 final size:21
Alignment explanation
Indices: 3891212--3891282 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
3891202 TGTTGCAAGA
* *
3891212 AAGGGATCGATCCTTTAAGGG
1 AAGGGATCGATCCTTTTAGTG
*
3891233 AAAGAGATCGATCCTTTTCA-TCG
1 -AAGGGATCGATCCTTTT-AGT-G
*
3891256 -AGGGATCGATCCTTTTTGTG
1 AAGGGATCGATCCTTTTAGTG
3891276 AAGGGAT
1 AAGGGAT
3891283 ATATTCTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.03
21 22 0.55
22 15 0.38
23 2 0.05
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTAGTG
Found at i:3896724 original size:18 final size:18
Alignment explanation
Indices: 3896688--3896725 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3896678 TTTAAGAAAA
*
3896688 TAAATTTTAAATCGCTTT
1 TAAATTTTAAATAGCTTT
3896706 TAAATTTTGAAATAG-TTT
1 TAAATTTT-AAATAGCTTT
3896724 TA
1 TA
3896726 GAAAATACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (18 bp):
TAAATTTTAAATAGCTTT
Found at i:3903656 original size:18 final size:18
Alignment explanation
Indices: 3903620--3903657 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3903610 TTTAAGAAAA
*
3903620 TAAATTTTAAATCGCTTT
1 TAAATTTTAAATAGCTTT
3903638 TAAATTTTGAAATAG-TTT
1 TAAATTTT-AAATAGCTTT
3903656 TA
1 TA
3903658 GAAAATACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (18 bp):
TAAATTTTAAATAGCTTT
Found at i:3905269 original size:11 final size:10
Alignment explanation
Indices: 3905251--3905304 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
3905241 TCTATTTATG
*
3905251 TTTATTTTAT
1 TTTATTTTTT
3905261 TTTATTTTTT
1 TTTATTTTTT
*
3905271 TACTATTTTTT
1 T-TTATTTTTT
*
3905282 ATTATTTGTTT
1 TTTATTT-TTT
3905293 TTTATTTATTT
1 TTTATTT-TTT
3905304 T
1 T
3905305 AATTAAGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
10 15 0.42
11 21 0.58
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:3905278 original size:21 final size:21
Alignment explanation
Indices: 3905253--3905305 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3905243 TATTTATGTT
3905253 TATTTTATTTTATTT-TTTTAC
1 TATTTTATTTTATTTGTTTT-C
*
3905274 TATTTT-TTATTATTTGTTTTT
1 TATTTTATT-TTATTTGTTTTC
3905295 TA-TTTATTTTA
1 TATTTTATTTTA
3905306 ATTAAGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 8 0.29
21 16 0.57
22 4 0.14
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (21 bp):
TATTTTATTTTATTTGTTTTC
Found at i:3908435 original size:15 final size:15
Alignment explanation
Indices: 3908423--3908457 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3908413 GTTCTCATGG
*
3908423 ACATTATCATCATCA
1 ACATCATCATCATCA
3908438 ACATCATCATCATCA
1 ACATCATCATCATCA
*
3908453 TCATC
1 ACATC
3908458 CACATGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.31, G:0.00, T:0.31
Consensus pattern (15 bp):
ACATCATCATCATCA
Found at i:3908436 original size:3 final size:3
Alignment explanation
Indices: 3908428--3908457 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3908418 CATGGACATT
*
3908428 ATC ATC ATC AAC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
3908458 CACATGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:3912045 original size:11 final size:11
Alignment explanation
Indices: 3912029--3912057 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3912019 ATGTCCTAAA
3912029 TTGATACTTGT
1 TTGATACTTGT
3912040 TTGATACTTGT
1 TTGATACTTGT
3912051 TTGATAC
1 TTGATAC
3912058 AATCTGTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (11 bp):
TTGATACTTGT
Found at i:3913470 original size:35 final size:35
Alignment explanation
Indices: 3913419--3913489 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
3913409 ATATAATGAA
* *
3913419 TGTTTGGTATGTTATGGTTGCAAGCATGATCAATT
1 TGTTTGGTATGCTATGGTTGCAAGCATAATCAATT
*
3913454 TGTTTGGTATGCTATGGTTGCATGCATAATCAATT
1 TGTTTGGTATGCTATGGTTGCAAGCATAATCAATT
3913489 T
1 T
3913490 TGTGATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.23, C:0.10, G:0.24, T:0.44
Consensus pattern (35 bp):
TGTTTGGTATGCTATGGTTGCAAGCATAATCAATT
Found at i:3914399 original size:19 final size:19
Alignment explanation
Indices: 3914375--3914413 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3914365 TCGAATGCAT
3914375 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
3914394 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
3914413 T
1 T
3914414 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:3914430 original size:65 final size:63
Alignment explanation
Indices: 3914312--3914520 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 63
3914302 TATTCAAAGG
* *
3914312 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGGTGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATAT-TTTCAAACATCGAATGCA
*
3914374 TTC
61 TTT
3914377 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
3914442 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATA-TTTTCAAACATCGAATGCATTT
*
3914506 CATGCATCGATGCAC
1 CATGCACCGATGCAC
3914521 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.06
64 53 0.42
65 64 0.51
66 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTTTCAAACATCGAATGCATTT
Found at i:3914514 original size:64 final size:65
Alignment explanation
Indices: 3914361--3914521 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
3914351 GAATTAATTG
* * *** *
3914361 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
3914426 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
3914489 A
65 A
3914490 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
3914522 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:3914536 original size:64 final size:64
Alignment explanation
Indices: 3914361--3914541 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
3914351 GAATTAATTG
* * * *
3914361 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
3914426 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
3914490 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
3914542 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
64 51 0.52
65 48 0.48
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:3920347 original size:20 final size:21
Alignment explanation
Indices: 3920318--3920373 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
3920308 TTTGCGCTTC
*
3920318 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
3920338 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
3920360 ATGCATCGATGCAT
1 ATGCATCGATGCAT
3920374 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:3921956 original size:21 final size:21
Alignment explanation
Indices: 3921914--3921957 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3921904 ACCCCGGGAG
*
3921914 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
3921935 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
3921956 CT
1 CT
3921958 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:3923018 original size:19 final size:19
Alignment explanation
Indices: 3922994--3923032 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3922984 TCGAATGCAT
3922994 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
3923013 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
3923032 T
1 T
3923033 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:3923049 original size:65 final size:63
Alignment explanation
Indices: 3922931--3923139 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 63
3922921 TATTCAAAGG
* *
3922931 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATAT-TTTCAAACATCGAATGCA
*
3922993 TTC
61 TTT
*
3922996 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGTATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
3923061 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATA-TTTTCAAACATCGAATGCATTT
*
3923125 CATGCATCGATGCAC
1 CATGCACCGATGCAC
3923140 ACTTGGTGCA
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.42
65 63 0.51
66 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTTTCAAACATCGAATGCATTT
Found at i:3923137 original size:64 final size:65
Alignment explanation
Indices: 3922980--3923140 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
3922970 GAATTAATTG
* * *** *
3922980 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* * **
3923045 AACATCGAATGTATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
3923108 A
65 A
3923109 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
3923141 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.43
65 47 0.57
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:3923155 original size:64 final size:64
Alignment explanation
Indices: 3922931--3923160 Score: 216
Period size: 64 Copynumber: 3.6 Consensus size: 64
3922921 TATTCAAAGG
* * * *
3922931 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
3922993 TTC
62 TTT
* * * *
3922996 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGTATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** **
3923061 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
3923125 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
3923161 AGTGTTCCAA
Statistics
Matches: 137, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
63 6 0.04
64 68 0.50
65 63 0.46
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:3926668 original size:16 final size:16
Alignment explanation
Indices: 3926642--3926675 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3926632 ACTCATTAAT
3926642 AATATTTTTATAAATGA
1 AATATTTTTATAAA-GA
3926659 AATA-TTTTATAAAGA
1 AATATTTTTATAAAGA
3926674 AA
1 AA
3926676 AATATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 9 0.53
17 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
AATATTTTTATAAAGA
Found at i:3928328 original size:2 final size:2
Alignment explanation
Indices: 3928323--3928357 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3928313 ATAGAGAGTA
3928323 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3928358 GGGTTAGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3929547 original size:15 final size:15
Alignment explanation
Indices: 3929509--3929551 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 15
3929499 ATTATACTAT
*
3929509 TTTTTATTATTATTT
1 TTTTTATTATTATTA
3929524 TTGCCTTTATTATTATTA
1 TT---TTTATTATTATTA
3929542 TTTTTATTAT
1 TTTTTATTAT
3929552 ATATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 10 0.42
18 14 0.58
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (15 bp):
TTTTTATTATTATTA
Found at i:3929556 original size:2 final size:2
Alignment explanation
Indices: 3929549--3929593 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
3929539 TTATTTTTAT
*
3929549 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3929589 TA TA T
1 TA TA T
3929594 TTTATTATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:3929594 original size:12 final size:12
Alignment explanation
Indices: 3929533--3929601 Score: 70
Period size: 12 Copynumber: 5.6 Consensus size: 12
3929523 TTTGCCTTTA
3929533 TTATTAT-TATTT
1 TTATTATATA-TT
3929545 TTATTATATA-T
1 TTATTATATATT
*
3929556 ATATATATATATAT
1 TTAT-TATATAT-T
*
3929570 ATATATATATATT
1 TTAT-TATATATT
3929583 TTATTATATATT
1 TTATTATATATT
3929595 TTATTAT
1 TTATTAT
3929602 GTTTTTCATT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
11 4 0.08
12 28 0.55
13 6 0.12
14 13 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTATATATT
Found at i:3929618 original size:11 final size:11
Alignment explanation
Indices: 3929581--3929619 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
3929571 TATATATATA
*
3929581 TTTTATTATAT
1 TTTTATTATGT
3929592 ATTTTATTATGT
1 -TTTTATTATGT
3929604 TTTTCATTATGT
1 TTTT-ATTATGT
3929616 TTTT
1 TTTT
3929620 TTGCCTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.72
Consensus pattern (11 bp):
TTTTATTATGT
Found at i:3929883 original size:15 final size:16
Alignment explanation
Indices: 3929863--3929892 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3929853 TTGTTACCTT
3929863 TTTATTT-ATTTTTTC
1 TTTATTTCATTTTTTC
3929878 TTTATTTCATTTTTT
1 TTTATTTCATTTTTT
3929893 TACTTTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTATTTCATTTTTTC
Found at i:3934564 original size:84 final size:83
Alignment explanation
Indices: 3934387--3935170 Score: 813
Period size: 84 Copynumber: 9.4 Consensus size: 83
3934377 ATCATAACTC
* * * * * *
3934387 AAGGGTTGTCTGTCAGCC-AAGACCTTCGAGTTCAACTATGCTCAGCTCCAAGGCATATCATTTA
1 AAGGGTTATCTGCCA-CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
* * *
3934451 CAGCATAGCTCAAGGCTAG
65 CAGCATAACTCAAGTCGAG
* * * * * *
3934470 AGGGGCTATCTGCCACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCGAGGCATATCGTTTG
1 AAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
* * *
3934535 CAACATAACTTACGTCGAG
65 CAGCATAACTCAAGTCGAG
* *
3934554 AAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTACGCTCAGATCCAAGGCACATCATTTG
1 AAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
* *
3934619 CAGCATAGCTTAAGTCGAG
65 CAGCATAACTCAAGTCGAG
* * * * * * * * *
3934638 AAGGGTTGTCTG---CCAAAGACCCTCGAGTTAGATTACACTCAACTTCGAGGGCACATCATTTA
1 AAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTG
* * **
3934700 CAACATAACTCAAGGCTCG
65 CAGCATAACTCAAGTCGAG
** * * * * *
3934719 AAGGGTTATCTATCACCAAAAGACCATCGAGTTTGACTACGCTCATCTCTAAGGCATATCATTTG
1 AAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
*
3934784 CAGCATAACTTAAGTCGAG
65 CAGCATAACTCAAGTCGAG
* *
3934803 AAGGGTTATCTACCAACGAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
1 AAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
* *
3934868 CAGCATAACTCAAGGCTAG
65 CAGCATAACTCAAGTCGAG
* * * *
3934887 AAGGGTTATATGCCAACCAAAGACCTTCTAGTTTGACTACACTCAGCTCCAAGGCACATCATTTG
1 AAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
* * *
3934952 CAGCATAGCTCAAGGCTAG
65 CAGCATAACTCAAGTCGAG
* *
3934971 AAGGGCTATCTGCCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTG
1 AAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
* * *
3935036 CAGCATAGCTTAAGTCGAT
65 CAGCATAACTCAAGTCGAG
* * * * * * *
3935055 AAGGGCTATCTGCTAATCGAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTA
1 AAGGGTTATCTGC-CACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
**
3935120 CAATATAACTCAAGGT-GAG
65 CAGCATAACTCAA-GTCGAG
* *
3935139 AAGGGTTATCTGTCATCAAAGACCTTCGAGTT
1 AAGGGTTATCTGCCACCAAAGACCTTCGAGTT
3935171 TGATTACATT
Statistics
Matches: 586, Mismatches: 103, Indels: 24
0.82 0.14 0.03
Matches are distributed among these distances:
80 24 0.04
81 38 0.06
82 2 0.00
83 31 0.05
84 458 0.78
85 33 0.06
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (83 bp):
AAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGC
AGCATAACTCAAGTCGAG
Found at i:3936411 original size:18 final size:18
Alignment explanation
Indices: 3936390--3936465 Score: 55
Period size: 21 Copynumber: 3.9 Consensus size: 18
3936380 CATTTTAGTC
*
3936390 ATTTTCTTATTTTTATTT
1 ATTTTTTTATTTTTATTT
*
3936408 ATTTATTTTTTATTTGTTGTTT
1 A--T-TTTTTTATTT-TTATTT
*
3936430 A-TTTTTTACTTTTACTTTT
1 ATTTTTTTATTTTTA--TTT
3936449 ATTTTTATTATTTTTAT
1 ATTTTT-TTATTTTTAT
3936466 CTAATATCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
17 2 0.04
18 10 0.22
19 5 0.11
20 5 0.11
21 17 0.38
22 6 0.13
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.76
Consensus pattern (18 bp):
ATTTTTTTATTTTTATTT
Found at i:3936494 original size:2 final size:2
Alignment explanation
Indices: 3936487--3936522 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3936477 TTTATATGTT
3936487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3936523 ATTATATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3936623 original size:3 final size:3
Alignment explanation
Indices: 3936615--3936724 Score: 75
Period size: 3 Copynumber: 35.7 Consensus size: 3
3936605 GTTTTTGTCT
*
3936615 TTA TTA TTA TTA TTG TTA TTA TATA TTA TTA TTA TTA TTA TATA TT-
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA
* * * * *
3936661 TTA TTT TTT TTCA TTA TGT- TTT TTG TCT- TTA TTA TTA TTA TTG TATA
1 TTA TTA TTA TT-A TTA T-TA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA
3936708 TT- TTA TTA TTA TATA TT
1 TTA TTA TTA TTA T-TA TT
3936725 CTATTTTTTC
Statistics
Matches: 89, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
2 6 0.07
3 68 0.76
4 15 0.17
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3936664 original size:28 final size:25
Alignment explanation
Indices: 3936614--3936724 Score: 86
Period size: 25 Copynumber: 4.4 Consensus size: 25
3936604 AGTTTTTGTC
* *
3936614 TTTATTATTATTATTGTTATTATAT
1 TTTATTATTATTATTATTATTTTAT
*
3936639 ATTATTATTATTATTATATATTTTAT
1 TTTATTATTATTATTAT-TATTTTAT
* *
3936665 TTT-TT-TTCATTA-TGTT-TTTTGT
1 TTTATTATT-ATTATTATTATTTTAT
*
3936687 CTTTATTATTATTATTGTATATTTTAT
1 -TTTATTATTATTATTAT-TATTTTAT
3936714 TATTATATATT
1 T-TTAT-TATT
3936725 CTATTTTTTC
Statistics
Matches: 69, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
22 5 0.07
23 4 0.06
24 10 0.14
25 26 0.38
26 11 0.16
27 9 0.13
28 4 0.06
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTATTATTATTATTATTATTTTAT
Found at i:3936715 original size:15 final size:15
Alignment explanation
Indices: 3936690--3936729 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3936680 TTTTTGTCTT
*
3936690 TATTATTATTATTGTA
1 TATT-TTATTATTATA
3936706 TATTTTATTATTATA
1 TATTTTATTATTATA
*
3936721 TATTCTATT
1 TATTTTATT
3936730 TTTTCTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (15 bp):
TATTTTATTATTATA
Found at i:3936732 original size:49 final size:49
Alignment explanation
Indices: 3936640--3936733 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
3936630 TTATTATATA
* * *
3936640 TTATTATTATTATTATATATTTTATTTTTTTTCATTATGTTTTTTGTCT
1 TTATTATTATTATTATATATTTTATTTTATATCATTATATTTTTTGTCT
* *
3936689 TTATTATTATTATTGTATATTTTATTATTATAT-ATTCTATTTTTT
1 TTATTATTATTATTATATATTTTATT-TTATATCATTATATTTTTT
3936734 CTTAACATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 35 0.90
50 4 0.10
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (49 bp):
TTATTATTATTATTATATATTTTATTTTATATCATTATATTTTTTGTCT
Done.