Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold678
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1173314
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 74412 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:3087 original size:2 final size:2
Alignment explanation
Indices: 3080--3108 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3070 CTTTGCTTTG
3080 CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3109 TTCTTTACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:11095 original size:11 final size:11
Alignment explanation
Indices: 11067--11112 Score: 58
Period size: 11 Copynumber: 4.0 Consensus size: 11
11057 AAGTAAAACC
11067 CTGGGTTTACTTT
1 CTGGGTTTAC--T
11080 CTGGGTTTACT
1 CTGGGTTTACT
11091 CTGGGTTTACT
1 CTGGGTTTACT
11102 -TCGGGTTTACT
1 CT-GGGTTTACT
11113 AGAGTGGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 1 0.03
11 21 0.66
13 10 0.31
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (11 bp):
CTGGGTTTACT
Found at i:11099 original size:24 final size:22
Alignment explanation
Indices: 11067--11112 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 22
11057 AAGTAAAACC
11067 CTGGGTTTACTTTCTGGGTTTACT
1 CTGGGTTTAC-TTC-GGGTTTACT
11091 CTGGGTTTACTTCGGGTTTACT
1 CTGGGTTTACTTCGGGTTTACT
11113 AGAGTGGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 9 0.41
23 3 0.14
24 10 0.45
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (22 bp):
CTGGGTTTACTTCGGGTTTACT
Found at i:11127 original size:11 final size:11
Alignment explanation
Indices: 11120--11150 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
11110 ACTAGAGTGG
11120 ACCCAGAGTAA
1 ACCCAGAGTAA
*
11131 ACCCAAAGTAA
1 ACCCAGAGTAA
11142 ACCCAGAGT
1 ACCCAGAGT
11151 GGACACAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.29, G:0.16, T:0.10
Consensus pattern (11 bp):
ACCCAGAGTAA
Found at i:11375 original size:11 final size:10
Alignment explanation
Indices: 11358--11391 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
11348 AATTTTTAAA
11358 AAGTAAACCC
1 AAGTAAACCC
11368 AGAGTAAACCCC
1 A-AGTAAA-CCC
11380 AAGTAAACCC
1 AAGTAAACCC
11390 AA
1 AA
11392 AAAGTAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 6 0.27
11 12 0.55
12 4 0.18
ACGTcount: A:0.50, C:0.29, G:0.12, T:0.09
Consensus pattern (10 bp):
AAGTAAACCC
Found at i:17334 original size:18 final size:18
Alignment explanation
Indices: 17311--17352 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
17301 CCAACTGATG
*
17311 TATTATTACTATCACTAT
1 TATTATTAATATCACTAT
*
17329 TATTATTAATATTACTAT
1 TATTATTAATATCACTAT
17347 TATTAT
1 TATTAT
17353 CATTATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATTAATATCACTAT
Found at i:17335 original size:6 final size:6
Alignment explanation
Indices: 17311--17370 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
17301 CCAACTGATG
* * * * * *
17311 TATTAT TACTAT CACTAT TATTAT TAATAT TACTAT TATTAT CATTAT
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
*
17359 TATCAT TATTAT
1 TATTAT TATTAT
17371 AATCATTTGA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (6 bp):
TATTAT
Found at i:23359 original size:2 final size:2
Alignment explanation
Indices: 23352--23389 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
23342 CATGTATATC
23352 AG AG AG AG AG AG AG AG AG -G AG AG -G AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
23390 GGGGATCGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27938 original size:2 final size:2
Alignment explanation
Indices: 27931--27993 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
27921 CTTATATGGA
27931 CT CT CT CT CT CT CT CT CT CT CT CT CT CT 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
27973 CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT C
27994 AACTAACACA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:34661 original size:2 final size:2
Alignment explanation
Indices: 34654--34686 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34644 AACTGCTTTT
34654 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
34687 AGCTACTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39004 original size:12 final size:12
Alignment explanation
Indices: 38987--39012 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38977 AACATGTAGA
38987 ATATTCTATTCT
1 ATATTCTATTCT
38999 ATATTCTATTCT
1 ATATTCTATTCT
39011 AT
1 AT
39013 TCTTTTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATTCTATTCT
Found at i:41331 original size:11 final size:11
Alignment explanation
Indices: 41315--41345 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
41305 ATTTATTTGC
41315 CATCTTCAAGT
1 CATCTTCAAGT
41326 CATCTTCAAGT
1 CATCTTCAAGT
*
41337 CATATTCAA
1 CATCTTCAA
41346 AGAGAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.35
Consensus pattern (11 bp):
CATCTTCAAGT
Found at i:43567 original size:2 final size:2
Alignment explanation
Indices: 43560--43595 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
43550 NNNNNNNNNN
43560 AT AT AT AT AT AT AT GAT 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
43596 CACATTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:45391 original size:21 final size:21
Alignment explanation
Indices: 45365--45420 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
45355 AGAAAGTTCC
45365 TAAAGGGGTCAAATTGGTAAG
1 TAAAGGGGTCAAATTGGTAAG
45386 TAAAGGGGTCAAATTGGTAAG
1 TAAAGGGGTCAAATTGGTAAG
*
45407 TAAAAGGGTCAAAT
1 TAAAGGGGTCAAAT
45421 ATCTGCAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.41, C:0.05, G:0.30, T:0.23
Consensus pattern (21 bp):
TAAAGGGGTCAAATTGGTAAG
Found at i:50150 original size:21 final size:21
Alignment explanation
Indices: 50124--50177 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
50114 AAAGTTCCTC
50124 AAGGGGTCAAATTGGTAAGTA
1 AAGGGGTCAAATTGGTAAGTA
*
50145 AAGGGGTCAAACTGGTAAGTA
1 AAGGGGTCAAATTGGTAAGTA
* *
50166 AAAGGTTCAAAT
1 AAGGGGTCAAAT
50178 ATCTGCAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.30, T:0.22
Consensus pattern (21 bp):
AAGGGGTCAAATTGGTAAGTA
Found at i:53512 original size:2 final size:2
Alignment explanation
Indices: 53505--53539 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53495 NNNNNNNNNN
53505 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
53540 CACACACTCT
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:57120 original size:11 final size:11
Alignment explanation
Indices: 57099--57170 Score: 58
Period size: 11 Copynumber: 6.7 Consensus size: 11
57089 TTTAAGCTGC
57099 CTTTAAG-CAT
1 CTTTAAGCCAT
57109 CTTTAAGCCAT
1 CTTTAAGCCAT
* **
57120 CTTTACGCTTT
1 CTTTAAGCCAT
* *
57131 CTTAAAACCAT
1 CTTTAAGCCAT
**
57142 CTTTCTG-CAT
1 CTTTAAGCCAT
*
57152 CTTTAAGCCAG
1 CTTTAAGCCAT
57163 CTTTAAGC
1 CTTTAAGC
57171 GGCATATTTC
Statistics
Matches: 45, Mismatches: 15, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
10 15 0.33
11 30 0.67
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39
Consensus pattern (11 bp):
CTTTAAGCCAT
Found at i:57123 original size:21 final size:21
Alignment explanation
Indices: 57099--57170 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
57089 TTTAAGCTGC
57099 CTTTAAGCATCTTTAAGCCAT
1 CTTTAAGCATCTTTAAGCCAT
* * * *
57120 CTTTACGCTTTCTTAAAACCAT
1 CTTTAAGC-ATCTTTAAGCCAT
** *
57142 CTTTCTGCATCTTTAAGCCAG
1 CTTTAAGCATCTTTAAGCCAT
57163 CTTTAAGC
1 CTTTAAGC
57171 GGCATATTTC
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
21 22 0.58
22 16 0.42
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39
Consensus pattern (21 bp):
CTTTAAGCATCTTTAAGCCAT
Found at i:59085 original size:15 final size:15
Alignment explanation
Indices: 59065--59093 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59055 AGTGGAGCCT
59065 CAGATATCCGGACGC
1 CAGATATCCGGACGC
59080 CAGATATCCGGACG
1 CAGATATCCGGACG
59094 AGTCACTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.14
Consensus pattern (15 bp):
CAGATATCCGGACGC
Found at i:61380 original size:12 final size:11
Alignment explanation
Indices: 61339--61390 Score: 68
Period size: 12 Copynumber: 4.5 Consensus size: 11
61329 CCATATTAAC
61339 AAAAAAACAAA
1 AAAAAAACAAA
61350 AACAAAAACAAA
1 AA-AAAAACAAA
*
61362 AACAAAACAAA
1 AAAAAAACAAA
*
61373 ACAAAAAAGAAA
1 A-AAAAAACAAA
61385 AAAAAA
1 AAAAAA
61391 TCAGGAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
11 16 0.44
12 20 0.56
ACGTcount: A:0.87, C:0.12, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:61386 original size:6 final size:6
Alignment explanation
Indices: 61341--61379 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
61331 ATATTAACAA
61341 AAAAAC AAAAAC AAAAAC AAAAAC -AAAAC -AAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
61380 AGAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:61390 original size:17 final size:16
Alignment explanation
Indices: 61342--61389 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
61332 TATTAACAAA
61342 AAAACAAAAACAAAAAC
1 AAAA-AAAAACAAAAAC
61359 AAAAACAAAAC-AAAAC
1 AAAAA-AAAACAAAAAC
61375 AAAAAAGAAA-AAAAA
1 AAAAAA-AAACAAAAA
61390 ATCAGGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 18 0.64
17 9 0.32
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAAAAC
Found at i:65330 original size:13 final size:13
Alignment explanation
Indices: 65312--65338 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
65302 CCTATCAGCG
65312 CAGTGGTTAACTA
1 CAGTGGTTAACTA
65325 CAGTGGTTAACTA
1 CAGTGGTTAACTA
65338 C
1 C
65339 GAATCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (13 bp):
CAGTGGTTAACTA
Found at i:67569 original size:156 final size:157
Alignment explanation
Indices: 67262--67577 Score: 607
Period size: 156 Copynumber: 2.0 Consensus size: 157
67252 GTCGCTCTAT
*
67262 ATTTCCCATTCGAAAAAGGGTAGGAAAAGTGTCAAATTTTGATTGATTTTGATTGAATTATTAAA
1 ATTTCCCATTCGAAAAAGGGTAAGAAAAGTGTCAAATTTTGATTGATTTTGATTGAATTATTAAA
67327 ATAGCGTCACTACTGCCAGTGAATGCAAATAATTCAAATTAATAGGTGAAAAACATATTTCATGT
66 ATAGCGTCACTACTGCCAGTGAATGCAAATAATTCAAATTAATAGGTGAAAAACATATTTCATGT
67392 CAACTCTTTTATAAGATAACACAACAA
131 CAACTCTTTTATAAGATAACACAACAA
67419 ATTTCCCATTCGAAAAA-GGTAAGAAAAGTGTCAAATTTTGATTGATTTTGATTGAATTATTAAA
1 ATTTCCCATTCGAAAAAGGGTAAGAAAAGTGTCAAATTTTGATTGATTTTGATTGAATTATTAAA
67483 ATAGCGTCACTACTGCCAGTGAATGCAAATAATTCAAATTAATAGGTGAAAAACATATTTCATGT
66 ATAGCGTCACTACTGCCAGTGAATGCAAATAATTCAAATTAATAGGTGAAAAACATATTTCATGT
*
67548 CAGCTCTTTTATAAGATAACACAACAA
131 CAACTCTTTTATAAGATAACACAACAA
67575 ATT
1 ATT
67578 AATGTACCTG
Statistics
Matches: 157, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
156 140 0.89
157 17 0.11
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (157 bp):
ATTTCCCATTCGAAAAAGGGTAAGAAAAGTGTCAAATTTTGATTGATTTTGATTGAATTATTAAA
ATAGCGTCACTACTGCCAGTGAATGCAAATAATTCAAATTAATAGGTGAAAAACATATTTCATGT
CAACTCTTTTATAAGATAACACAACAA
Found at i:72366 original size:2 final size:2
Alignment explanation
Indices: 72359--72419 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
72349 ATCTTTAATC
72359 CT CT CT CT CT CT CT CT CT CT CT CT CT CT 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
72401 CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
72420 ACGCATGTGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:88885 original size:60 final size:59
Alignment explanation
Indices: 88817--88935 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 59
88807 TTCTGAAAAA
*
88817 CCAAAAGAATG-CTGACACAAATAAAATTGTAAACCGTGTAGATTCATAATATGAATGGC
1 CCAAAAGAATGCCT-ACACAAATAAAATTGTAAAACGTGTAGATTCATAATATGAATGGC
*
88876 NCCAAAAGAATGCCTACACAAATAAAATTGTAAAATGTGTAGATTCATAATATGAATGGC
1 -CCAAAAGAATGCCTACACAAATAAAATTGTAAAACGTGTAGATTCATAATATGAATGGC
88936 AGATGCTAGG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
60 54 0.96
61 2 0.04
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.24
Consensus pattern (59 bp):
CCAAAAGAATGCCTACACAAATAAAATTGTAAAACGTGTAGATTCATAATATGAATGGC
Found at i:97711 original size:28 final size:28
Alignment explanation
Indices: 97648--97936 Score: 273
Period size: 28 Copynumber: 10.4 Consensus size: 28
97638 CTCTGTTTTT
* * *
97648 GACTCTGTTTCTCTAC-ACTCTGTTATA
1 GACTCTGCTTCTCTACAACCCTGTTGTA
*
97675 GACTCTGCTTCTCTACAATCCTGTTGTA
1 GACTCTGCTTCTCTACAACCCTGTTGTA
* * * * *
97703 GCCTATGCTTCTCAACAACACTGTTGCA
1 GACTCTGCTTCTCTACAACCCTGTTGTA
* *
97731 GACTCTGATTCTCTACAACCCTGTTATA
1 GACTCTGCTTCTCTACAACCCTGTTGTA
* * * *
97759 GGCTCTGATT-TCTTATAACCCTGATGTA
1 GACTCTGCTTCTC-TACAACCCTGTTGTA
*
97787 GACTCTGCTTCTTTACAACCCTGTTGTA
1 GACTCTGCTTCTCTACAACCCTGTTGTA
* ** *
97815 GATTCTGCTTCAATACACACTCTG--GTA
1 GACTCTGCTTCTCTACA-ACCCTGTTGTA
* * *
97842 GAATCTGCTTCTCTACAACTCTGCTGTA
1 GACTCTGCTTCTCTACAACCCTGTTGTA
** * *
97870 GGTTCTGTTTCTCTAC-ACTCTGTTGTA
1 GACTCTGCTTCTCTACAACCCTGTTGTA
97897 GACTCTGCTTCTCTACAACCCTGTTGTA
1 GACTCTGCTTCTCTACAACCCTGTTGTA
*
97925 AACTCTGCTTCT
1 GACTCTGCTTCT
97937 ATACGCTCTG
Statistics
Matches: 213, Mismatches: 42, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
26 6 0.03
27 57 0.27
28 144 0.68
29 6 0.03
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (28 bp):
GACTCTGCTTCTCTACAACCCTGTTGTA
Found at i:97796 original size:84 final size:83
Alignment explanation
Indices: 97648--97936 Score: 231
Period size: 83 Copynumber: 3.5 Consensus size: 83
97638 CTCTGTTTTT
* * * * *
97648 GACTCTGTTTCTCTACACTCTGTTATAGACTCTGCTTCTCTACAATCCTGTTGTAGCCTATGCTT
1 GACTCTGATTCTCTACACCCTGTTATAGACTCTGCTTCTCTACAACCCTGATGTAGACTATGCTT
97713 CTCAACAACACTGTTGCA
66 CTCAACAACACTGTTGCA
* * * *
97731 GACTCTGATTCTCTACAACCCTGTTATAGGCTCTGATT-TCTTATAACCCTGATGTAGACTCTGC
1 GACTCTGATTCTCTAC-ACCCTGTTATAGACTCTGCTTCTC-TACAACCCTGATGTAGACTATGC
** * *
97795 TTCTTTACAACCCTGTTGTA
64 TTCTCAACAACACTGTTGCA
* * ** * * ** * * * ** * *
97815 GATTCTGCTTCAATACACACTCTGGTAGAATCTGCTTCTCTACAACTCTGCTGTAGGTTCTGTTT
1 GACTCTGATTCTCTACACCCTGTTATAGACTCTGCTTCTCTACAACCCTGATGTAGACTATGCTT
* * *
97880 CTCTAC-ACTCTGTTGTA
66 CTCAACAACACTGTTGCA
* * *
97897 GACTCTGCTTCTCTACAACCCTGTTGTAAACTCTGCTTCT
1 GACTCTGATTCTCTAC-ACCCTGTTATAGACTCTGCTTCT
97937 ATACGCTCTG
Statistics
Matches: 162, Mismatches: 40, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
82 23 0.14
83 73 0.45
84 66 0.41
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (83 bp):
GACTCTGATTCTCTACACCCTGTTATAGACTCTGCTTCTCTACAACCCTGATGTAGACTATGCTT
CTCAACAACACTGTTGCA
Found at i:97946 original size:55 final size:55
Alignment explanation
Indices: 97648--97957 Score: 300
Period size: 55 Copynumber: 5.6 Consensus size: 55
97638 CTCTGTTTTT
* * * *
97648 GACTCTGTTTCTCTACACTCTGTTATAGACTCTGCTTCTCTACAATCCTGTTGTA
1 GACTCTGCTTCTATACACTCTGTTGTAGACTCTGCTTCTCTACAACCCTGTTGTA
* * * * * *
97703 GCCTATGCTTCTCA-ACAACACTGTTGCAGACTCTGATTCTCTACAACCCTGTTATA
1 GACTCTGCTTCT-ATAC-ACTCTGTTGTAGACTCTGCTTCTCTACAACCCTGTTGTA
* * * * *
97759 GGCTCTGATTTCTTATA-ACCCTGATGTAGACTCTGCTTCTTTACAACCCTGTTGTA
1 GACTCTG-CTTC-TATACACTCTGTTGTAGACTCTGCTTCTCTACAACCCTGTTGTA
* * * * * * * *
97815 GATTCTGCTTCAATACACACTCTGGTAGAATCTGCTTCTCTACAACTCTGCTGTA
1 GACTCTGCTTCTATACACTCTGTTGTAGACTCTGCTTCTCTACAACCCTGTTGTA
** * *
97870 GGTTCTGTTTCTCTACACTCTGTTGTAGACTCTGCTTCTCTACAACCCTGTTGTA
1 GACTCTGCTTCTATACACTCTGTTGTAGACTCTGCTTCTCTACAACCCTGTTGTA
* * *
97925 AACTCTGCTTCTATACGCTCTGTTGTAAACTCT
1 GACTCTGCTTCTATACACTCTGTTGTAGACTCT
97958 ATAAACATAT
Statistics
Matches: 201, Mismatches: 48, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
54 3 0.01
55 116 0.58
56 76 0.38
57 4 0.02
58 2 0.01
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.38
Consensus pattern (55 bp):
GACTCTGCTTCTATACACTCTGTTGTAGACTCTGCTTCTCTACAACCCTGTTGTA
Found at i:98199 original size:2 final size:2
Alignment explanation
Indices: 98192--98236 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
98182 TGCTCATATT
98192 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
98234 TC T
1 TC T
98237 GAGAACTGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:99187 original size:17 final size:17
Alignment explanation
Indices: 99160--99192 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
99150 TTCATTAGAT
99160 TTTTCATCATTTATTTCA
1 TTTTCATCATTT-TTTCA
99178 TTTT-ATCATTTTTTC
1 TTTTCATCATTTTTTC
99193 TCAAAAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTCATCATTTTTTCA
Found at i:104366 original size:21 final size:21
Alignment explanation
Indices: 104329--104368 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
104319 AAAATCGGTA
*
104329 AGAAAAAAAAGGAGAAGAATG
1 AGAAAAAAAAGAAGAAGAATG
104350 AGAAAAAAAA-AACGAAGAA
1 AGAAAAAAAAGAA-GAAGAA
104369 AAACAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.03
Consensus pattern (21 bp):
AGAAAAAAAAGAAGAAGAATG
Found at i:105550 original size:438 final size:437
Alignment explanation
Indices: 104735--105731 Score: 1516
Period size: 438 Copynumber: 2.3 Consensus size: 437
104725 ATGGTTGTAC
* * * *
104735 ATTG-TAAAGCTCAATATTTTGAGCATCTTTTGTTTAATACTGCTT-TCCAGAATTTTCCTCTAT
1 ATTGTTAAA-CTCAATATTTTGAGCATCTTTTGTTCAATATTGCTTAT-CAAAATTTTCCTCCAT
* * * * * *
104798 TTTGAGATATTGAGGATCAAAATTTTGGACTTCTGGTCCCTTAAAATCCTTAACTACATAACATA
64 TTTGAGATATTGAGGATCAAAGTTTTAGACTTCTGGCCCCTTAAAATCCCTAATTACGTAACATA
* * *
104863 GGAGTAAATGTTTGCCATATATAGGTGAATACCGTTAGAATGAACATAATTGCTTCTATAACGTA
129 GGAGTAAATGATTGCCATATATAGGTGAATACCGTTAGAATAAACATAATTGCATCTATAACGTA
104928 TCACAAAACATTTCACAGTAAAAAGTTATCATTAAAAGACTTTAGAGCCCCCTCAGCCCCTTATT
194 TCACAAAACATTTCACAGTAAAAAGTTATCATTAAAAGACTTTAGAGCCCCCTCAGCCCCTTATT
** * * * * *
104993 TGAAGGGTCAGCCCCTTTTTCTTGATGTCATAAGAATGTTCTTGTCAATTCAAACACATTTTGTT
259 TGAAGGACCAGCCCCTCTTTCATGATGTCATAAGAAAGCTCTTGTCAAATCAAACACATTTTGTT
* *** *
105058 CAAGAAGTGTTTAGAAATTCTGTACCGTTCTCGAGATATCTTGAGAGGGTCGTTTTAGGGGCCGA
324 CAACAAGAAATTACAAATTCTGTACCGTTCTCGAGATATCTTGAGAGGGTCGTTTTAGGGGCCGA
*
105123 CCTTGTAACTCCCTTTAAGGACCGCATAACAAAGAAAGTATGGTTGATT
389 CCCTGTAACTCCCTTTAAGGACCGCATAACAAAGAAAGTATGGTTGATT
* *
105172 ATTGTTAAACTCAATATTTTGAGCATCTTTTATTCAATATTGCTTATCAAAATGTTCCTCCATTT
1 ATTGTTAAACTCAATATTTTGAGCATCTTTTGTTCAATATTGCTTATCAAAATTTTCCTCCATTT
*
105237 TGAGATATTGAGGATCAAAGTTTTAGACTTCTGGCCCCTTAAAATCCCTAATTACGTAATATAGG
66 TGAGATATTGAGGATCAAAGTTTTAGACTTCTGGCCCCTTAAAATCCCTAATTACGTAACATAGG
105302 AGTAAATGATTGCCATATATAGGTGAATACCGTTAGAATAAACATAATTGCATCTATAAACGTAT
131 AGTAAATGATTGCCATATATAGGTGAATACCGTTAGAATAAACATAATTGCATCTAT-AACGTAT
* * *
105367 CACAAAATATTTCACAGTAAAAAGTTATCATTAAAATACTTTAGAGTCCCCTCAGCCCCTTATTT
195 CACAAAACATTTCACAGTAAAAAGTTATCATTAAAAGACTTTAGAGCCCCCTCAGCCCCTTATTT
* * *
105432 GAAGGACCAGCCCCTCTTTCATGATTTCA-AATGAAAGCTCTTGTCAAATCTAACACTTTTTGTT
260 GAAGGACCAGCCCCTCTTTCATGATGTCATAA-GAAAGCTCTTGTCAAATCAAACACATTTTGTT
* *
105496 CAACAAGAAATTACAAATTTTGTACCGTTCTCGAGATATTTTGAGAGGGTCGTTTTAGGGGCCGA
324 CAACAAGAAATTACAAATTCTGTACCGTTCTCGAGATATCTTGAGAGGGTCGTTTTAGGGGCCGA
*
105561 CCCTGTAACTCCCTTTAAGGACCGCATAACAAAGAAATTATGGTTGATT
389 CCCTGTAACTCCCTTTAAGGACCGCATAACAAAGAAAGTATGGTTGATT
* * *
105610 ATTGTTAAGCTCAATATTTTGAGCATCGTTTGTTCAATATTGCTTATCAATATTTTCCTCCATTT
1 ATTGTTAAACTCAATATTTTGAGCATCTTTTGTTCAATATTGCTTATCAAAATTTTCCTCCATTT
* * * *
105675 TGAAATATTGAGCATCAAAGTTTTAGACTTCTGGCCCC-TAGAAACCCCTCATTACGT
66 TGAGATATTGAGGATCAAAGTTTTAGACTTCTGGCCCCTTA-AAATCCCTAATTACGT
105732 TACACATGAT
Statistics
Matches: 508, Mismatches: 47, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
437 168 0.33
438 340 0.67
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.35
Consensus pattern (437 bp):
ATTGTTAAACTCAATATTTTGAGCATCTTTTGTTCAATATTGCTTATCAAAATTTTCCTCCATTT
TGAGATATTGAGGATCAAAGTTTTAGACTTCTGGCCCCTTAAAATCCCTAATTACGTAACATAGG
AGTAAATGATTGCCATATATAGGTGAATACCGTTAGAATAAACATAATTGCATCTATAACGTATC
ACAAAACATTTCACAGTAAAAAGTTATCATTAAAAGACTTTAGAGCCCCCTCAGCCCCTTATTTG
AAGGACCAGCCCCTCTTTCATGATGTCATAAGAAAGCTCTTGTCAAATCAAACACATTTTGTTCA
ACAAGAAATTACAAATTCTGTACCGTTCTCGAGATATCTTGAGAGGGTCGTTTTAGGGGCCGACC
CTGTAACTCCCTTTAAGGACCGCATAACAAAGAAAGTATGGTTGATT
Found at i:106437 original size:58 final size:62
Alignment explanation
Indices: 106344--106579 Score: 208
Period size: 58 Copynumber: 4.0 Consensus size: 62
106334 AGAAGCAGAA
* * * *
106344 GAAAAAGAATCCGAAGAATAACAATAAGGTATTCCGTTGGAAACGTAAGA-CCT-T-ATAAT
1 GAAAAAGAAACCGAAGAATAACAAGAGGGTATTCCGTTGGAAACGGAAGACCCTATAATAAT
* * *
106403 -AAAAAGAAACTGAACAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAATAAT
1 GAAAAAGAAACCGAAGAATAACAAGAGGGTATTCCGTTGGAAACGGAAGACCCT-ATAATAAT
** ** *
106465 GAAAAAGAAACCGAAGAATAACAAGA--G-AAACCGAAGAAAACGGAAGACCC--TAATAA-
1 GAAAAAGAAACCGAAGAATAACAAGAGGGTATTCCGTTGGAAACGGAAGACCCTATAATAAT
* * * * * *
106521 GGAAAAGAAA-CAATAGAATAATAAGCGGGTCTTCCGTCGGAAACGGAAGACCCTA-AATA
1 GAAAAAGAAACCGA-AGAATAACAAGAGGGTATTCCGTTGGAAACGGAAGACCCTATAATA
106580 TACAGTTTTA
Statistics
Matches: 141, Mismatches: 25, Indels: 21
0.75 0.13 0.11
Matches are distributed among these distances:
55 2 0.01
56 19 0.13
57 6 0.04
58 43 0.30
59 20 0.14
60 21 0.15
61 2 0.01
62 5 0.04
63 23 0.16
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.15
Consensus pattern (62 bp):
GAAAAAGAAACCGAAGAATAACAAGAGGGTATTCCGTTGGAAACGGAAGACCCTATAATAAT
Found at i:114026 original size:1 final size:1
Alignment explanation
Indices: 114020--114044 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
114010 CTATTCAATA
114020 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
114045 AAAAAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:116678 original size:2 final size:2
Alignment explanation
Indices: 116673--116739 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
116663 TGTGTGTGAG
116673 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
116715 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
116740 TAGTTCATCC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:117153 original size:110 final size:110
Alignment explanation
Indices: 116960--117161 Score: 350
Period size: 110 Copynumber: 1.8 Consensus size: 110
116950 GTTTTGTTTT
* * *
116960 TTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGAAACTAACACAG
1 TTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACATAAAAAAAACCCTGAAACTAACACAG
*
117025 AATATACAAGATGTACACAACAGGTGTTATGTGCATAGGTGCATG
66 AATATACAAGATATACACAACAGGTGTTATGTGCATAGGTGCATG
* *
117070 TTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACATAAAAAAAACCCTGGAATTAACACAG
1 TTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACATAAAAAAAACCCTGAAACTAACACAG
117135 AATATACAAGATATACACAACAGGTGT
66 AATATACAAGATATACACAACAGGTGT
117162 GGCGTGTGCC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 86 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (110 bp):
TTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACATAAAAAAAACCCTGAAACTAACACAG
AATATACAAGATATACACAACAGGTGTTATGTGCATAGGTGCATG
Found at i:117194 original size:110 final size:110
Alignment explanation
Indices: 116965--117188 Score: 295
Period size: 110 Copynumber: 2.0 Consensus size: 110
116955 GTTTTTTTGT
* * *
116965 GTATATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGAAACTAACACAGAATAT
1 GTATATCTAATTAGAGTCTATTGTTTGTCCAACATAAAAAAAACCCTGAAACTAACACAGAATAT
* * * ** ** *
117030 ACAAGATGTACACAACAGGTGTTATGTGCATAGGTGCATGTTTGT
66 ACAAGATATACACAACAGGTGTCATGTGCACAGGTGCACATCAGG
* *
117075 GTATATCTAATTAGAGTCTATTGTTTGTCCAACATAAAAAAAACCCTGGAATTAACACAGAATAT
1 GTATATCTAATTAGAGTCTATTGTTTGTCCAACATAAAAAAAACCCTGAAACTAACACAGAATAT
* *
117140 ACAAGATATACACAACAGGTGTGGCGTGTGCCCAGGTGCACATCAGG
66 ACAAGATATACACAACAGGTGT--CATGTGCACAGGTGCACATCAGG
117187 GT
1 GT
117189 TTCTAAAGGC
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
110 81 0.84
112 16 0.16
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (110 bp):
GTATATCTAATTAGAGTCTATTGTTTGTCCAACATAAAAAAAACCCTGAAACTAACACAGAATAT
ACAAGATATACACAACAGGTGTCATGTGCACAGGTGCACATCAGG
Found at i:121404 original size:12 final size:12
Alignment explanation
Indices: 121380--121436 Score: 89
Period size: 12 Copynumber: 4.8 Consensus size: 12
121370 ATCACATTTT
121380 GTCTGTC-GTCC
1 GTCTGTCTGTCC
121391 GTCTGTCTGTCC
1 GTCTGTCTGTCC
*
121403 GTCCGTCTGTCC
1 GTCTGTCTGTCC
*
121415 GTCCGTCTGTCC
1 GTCTGTCTGTCC
121427 GTCTGTCTGT
1 GTCTGTCTGT
121437 AAACTTTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
11 7 0.16
12 36 0.84
ACGTcount: A:0.00, C:0.35, G:0.26, T:0.39
Consensus pattern (12 bp):
GTCTGTCTGTCC
Found at i:121434 original size:4 final size:4
Alignment explanation
Indices: 121379--121436 Score: 55
Period size: 4 Copynumber: 14.8 Consensus size: 4
121369 GATCACATTT
* * * * *
121379 TGTC TGTC -GTC CGTC TGTC TGTC CGTC CGTC TGTC CGTC CGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
*
121426 CGTC TGTC TGT
1 TGTC TGTC TGT
121437 AAACTTTTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
3 3 0.07
4 43 0.93
ACGTcount: A:0.00, C:0.34, G:0.26, T:0.40
Consensus pattern (4 bp):
TGTC
Found at i:121888 original size:170 final size:166
Alignment explanation
Indices: 121606--121957 Score: 598
Period size: 170 Copynumber: 2.1 Consensus size: 166
121596 AGAAATTTTC
*
121606 AAAAATCTTCTTCTCATGAACCATAAGACCAGCAAAGCTGAAACTTGTGTGGAAGCATCTTCAGG
1 AAAAATCTTCTTCTCATGAACCATAAGACCAGCAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* *
121671 TAGTGTAGATTCTAATTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACACTGGGGGGG
66 TAGTGTAGATTCTAATTTGTGAAATTCACGACCCCCGGGGGTAGGGTGGGGCCACAAT----GGG
* *
121736 GGGTCAAAGTTTTACATAGGAATATACA-GAGTAAATCTTT
127 GGGTCAAAGTTTAACAAAGGAATATACATG-GTAAATCTTT
121776 AAAAATCTTCTTCTCATGAACCATAAGACCAGCAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCATGAACCATAAGACCAGCAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
121841 TAGTGTAGATTCTAATTTGTGAAATTCACGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
66 TAGTGTAGATTCTAATTTGTGAAATTCACGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
*
121906 CAAAGTTTAACAAAGGAATATATATGGTAAATCTTT
131 CAAAGTTTAACAAAGGAATATACATGGTAAATCTTT
121942 AAAAATCTTCTTCTCA
1 AAAAATCTTCTTCTCA
121958 GAAACTAATC
Statistics
Matches: 175, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
166 54 0.31
167 1 0.01
170 120 0.69
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (166 bp):
AAAAATCTTCTTCTCATGAACCATAAGACCAGCAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCTAATTTGTGAAATTCACGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT
CAAAGTTTAACAAAGGAATATACATGGTAAATCTTT
Found at i:123542 original size:15 final size:15
Alignment explanation
Indices: 123522--123559 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
123512 AATGCACCCC
**
123522 CTTTTTTTTTTCTTT
1 CTTTTTTTTTAATTT
123537 CTTTTTTTTTAATTT
1 CTTTTTTTTTAATTT
123552 -TTTTTTTT
1 CTTTTTTTT
123560 ACAGTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.87
Consensus pattern (15 bp):
CTTTTTTTTTAATTT
Found at i:123746 original size:4 final size:4
Alignment explanation
Indices: 123708--123741 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
123698 TGAAAAGTTT
*
123708 ACAG ACGG ACAG ACAG ACAG ACAG ACAG ACAG AC
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG AC
123742 GGACGACGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.47, C:0.26, G:0.26, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:134951 original size:206 final size:205
Alignment explanation
Indices: 134597--135008 Score: 815
Period size: 206 Copynumber: 2.0 Consensus size: 205
134587 CAAACCTTAT
134597 ACTTATGACAAAGTTTGTATCTAGCATTTATGATAATAAAACTAATTCAAGTATAGCTGTTTCAT
1 ACTTATGACAAAGTTTGTATCTAGCATTTATGATAATAAAACTAATTCAAGTATAGCTGTTTCAT
134662 TGAAAAGATTAACATAAAGATATGCAGTTTATGTATCAGTTTTTATATGAAGCAGTTCTTGCTTC
66 TGAAAAGATTAACATAAAGATATGCAGTTTATGTATCAGTTTTTATATGAAGCAGTTCTTGCTTC
134727 CATGTTATGATATTTATTGTTGTCTACAGCAGGGTTGTTATTTCTTTGGCAGAGCTGTGATATGT
131 CATGTTATGATATTTATTGTTGTCTACAGCAGGGTTGTTATTTCTTTGGCAGAGCTGTGATATGT
134792 GGAGTGTAGG
196 GGAGTGTAGG
134802 NACTTATGACAAAGTTTGTATCTAGCATTTATGATAATAAAACTAATTCAAGTATAGCTGTTTCA
1 -ACTTATGACAAAGTTTGTATCTAGCATTTATGATAATAAAACTAATTCAAGTATAGCTGTTTCA
134867 TTGAAAAGATTAACATAAAGATATGCAGTTTATGTATCAGTTTTTATATGAAGCAGTTCTTGCTT
65 TTGAAAAGATTAACATAAAGATATGCAGTTTATGTATCAGTTTTTATATGAAGCAGTTCTTGCTT
134932 CCATGTTATGATATTTATTGTTGTCTACAGCAGGGTTGTTATTTCTTTGGCAGAGCTGTGATATG
130 CCATGTTATGATATTTATTGTTGTCTACAGCAGGGTTGTTATTTCTTTGGCAGAGCTGTGATATG
134997 TGGAGTGTAGG
195 TGGAGTGTAGG
135008 A
1 A
135009 GTCATTCTGT
Statistics
Matches: 206, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
205 1 0.00
206 205 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (205 bp):
ACTTATGACAAAGTTTGTATCTAGCATTTATGATAATAAAACTAATTCAAGTATAGCTGTTTCAT
TGAAAAGATTAACATAAAGATATGCAGTTTATGTATCAGTTTTTATATGAAGCAGTTCTTGCTTC
CATGTTATGATATTTATTGTTGTCTACAGCAGGGTTGTTATTTCTTTGGCAGAGCTGTGATATGT
GGAGTGTAGG
Found at i:148413 original size:12 final size:12
Alignment explanation
Indices: 148396--148423 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
148386 CAGTAGACTG
148396 ACATTGACACAT
1 ACATTGACACAT
148408 ACATTGACACAT
1 ACATTGACACAT
148420 ACAT
1 ACAT
148424 GTACTGTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (12 bp):
ACATTGACACAT
Found at i:160139 original size:2 final size:2
Alignment explanation
Indices: 160134--160175 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
160124 TGTATATATA
*
160134 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
160176 GTTCTGCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.02, G:0.50, T:0.48
Consensus pattern (2 bp):
TG
Found at i:177709 original size:42 final size:42
Alignment explanation
Indices: 177647--177982 Score: 378
Period size: 42 Copynumber: 8.0 Consensus size: 42
177637 GGACTATGTC
* *
177647 GTCCACAGGTACATATACCCCACACAACCCATACTCATATCA
1 GTCCACAGGTACATATACCCCACACAACCCATACTCACATTA
* * * *
177689 CTGCACAGGTACATATACCCCACACAACCCATACTCATATCA
1 GTCCACAGGTACATATACCCCACACAACCCATACTCACATTA
* *
177731 CTGCACAGGTACATATACCCCACA-ATA-CCACTACTCACATTA
1 GTCCACAGGTACATATACCCCACACA-ACCCA-TACTCACATTA
* *
177773 GTCCACAGGTACATATACCCAACACTA-CCACTACTCACATTA
1 GTCCACAGGTACATATACCCCACACAACCCA-TACTCACATTA
* *
177815 GTCCACAGGTACATATACCCCACACTTACAC-TACTCACATTA
1 GTCCACAGGTACATATACCCCACAC-AACCCATACTCACATTA
* * *
177857 GTCCATAGGTACATATACCCCACACTTACAC-TACTCACATTA
1 GTCCACAGGTACATATACCCCACAC-AACCCATACTCACATTA
* * * *
177899 GTCCATAGGTACATATACCCCACACAACCCATACTTATATCA
1 GTCCACAGGTACATATACCCCACACAACCCATACTCACATTA
* * *
177941 CTGCACAGGTACATATACCCCACACTA-CCACTACTCACATTA
1 GTCCACAGGTACATATACCCCACACAACCCA-TACTCACATTA
177983 TTACTTGTTA
Statistics
Matches: 264, Mismatches: 23, Indels: 14
0.88 0.08 0.05
Matches are distributed among these distances:
41 10 0.04
42 251 0.95
43 2 0.01
44 1 0.00
ACGTcount: A:0.35, C:0.36, G:0.07, T:0.22
Consensus pattern (42 bp):
GTCCACAGGTACATATACCCCACACAACCCATACTCACATTA
Found at i:177872 original size:126 final size:125
Alignment explanation
Indices: 177647--177982 Score: 469
Period size: 126 Copynumber: 2.7 Consensus size: 125
177637 GGACTATGTC
177647 GTCCACAGGTACATATACCCCACACAACCCATACTCATATCACTGCACAGGTACATATACCCCAC
1 GTCCACAGGTACATATACCCCACACAACCCATACTCATATCACTGCACAGGTACATATACCCCAC
* * * * *
177712 ACAACCCATACTCATATCACTGCACAGGTACATATACCCCACA-ATACCACTACTCACATTA
66 ACTACAC-TACTCACATTACTCCACAGGTACATATACCCCACACATA-CACTACTCACATTA
* * * * * *
177773 GTCCACAGGTACATATACCCAACACTA-CCACTACTCACATTAGTCCACAGGTACATATACCCCA
1 GTCCACAGGTACATATACCCCACACAACCCA-TACTCATATCACTGCACAGGTACATATACCCCA
* * *
177837 CACTTACACTACTCACATTAGTCCATAGGTACATATACCCCACACTTACACTACTCACATTA
65 CAC-TACACTACTCACATTACTCCACAGGTACATATACCCCACACATACACTACTCACATTA
* *
177899 GTCCATAGGTACATATACCCCACACAACCCATACTTATATCACTGCACAGGTACATATACCCCAC
1 GTCCACAGGTACATATACCCCACACAACCCATACTCATATCACTGCACAGGTACATATACCCCAC
177964 ACTACCACTACTCACATTA
66 ACTA-CACTACTCACATTA
177983 TTACTTGTTA
Statistics
Matches: 183, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
125 5 0.03
126 170 0.93
127 8 0.04
ACGTcount: A:0.35, C:0.36, G:0.07, T:0.22
Consensus pattern (125 bp):
GTCCACAGGTACATATACCCCACACAACCCATACTCATATCACTGCACAGGTACATATACCCCAC
ACTACACTACTCACATTACTCCACAGGTACATATACCCCACACATACACTACTCACATTA
Found at i:179883 original size:24 final size:24
Alignment explanation
Indices: 179856--179905 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
179846 GGGATCCAGG
*
179856 AAGAAGGAAGAGTTAAAAAAAAAA
1 AAGAAAGAAGAGTTAAAAAAAAAA
* * *
179880 AAGAAATAGGATTTAAAAAAAAAA
1 AAGAAAGAAGAGTTAAAAAAAAAA
179904 AA
1 AA
179906 TTATACACCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (24 bp):
AAGAAAGAAGAGTTAAAAAAAAAA
Found at i:181413 original size:15 final size:15
Alignment explanation
Indices: 181389--181418 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
181379 GAAATATCAG
*
181389 CCCCGGGGGTGATAC
1 CCCCGAGGGTGATAC
181404 CCCCGAGGGTGATAC
1 CCCCGAGGGTGATAC
181419 AGCACTAGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.33, G:0.37, T:0.13
Consensus pattern (15 bp):
CCCCGAGGGTGATAC
Found at i:193997 original size:2 final size:2
Alignment explanation
Indices: 193990--194048 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
193980 GGAGGGATTA
193990 CT CT CT CT CT CT -T CT CT CT CT CT CT CT 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
194031 CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
194049 GAGCAATCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:194366 original size:13 final size:15
Alignment explanation
Indices: 194348--194384 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
194338 TTGCAAAAAA
194348 AAAAAAC-AAC-AAC
1 AAAAAACAAACAAAC
194361 AAAAAACAAACAAAC
1 AAAAAACAAACAAAC
194376 -AAAAACAAA
1 AAAAAACAAA
194385 AGGCGGTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 12 0.55
15 3 0.14
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAACAAACAAAC
Found at i:194384 original size:21 final size:20
Alignment explanation
Indices: 194342--194385 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
194332 TACATCTTGC
194342 AAAAAAAAA-AAACAACAACA
1 AAAAAAAAACAAACAA-AACA
*
194362 AAAAACAAACAAACAAAAACA
1 AAAAAAAAACAAAC-AAAACA
194383 AAA
1 AAA
194386 GGCGGTAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 11 0.52
22 2 0.10
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAAAAAACAAACAAAACA
Found at i:197626 original size:11 final size:11
Alignment explanation
Indices: 197598--197627 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
197588 TAAGCTGTAT
197598 AAAAAAA-AAA
1 AAAAAAAGAAA
197608 AAAAAAAGAAA
1 AAAAAAAGAAA
197619 AAAAAAAGA
1 AAAAAAAGA
197628 TCACTGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:201166 original size:15 final size:15
Alignment explanation
Indices: 201146--201174 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
201136 TATGGGGGAG
201146 CTCCAATGCCTGGCC
1 CTCCAATGCCTGGCC
201161 CTCCAATGCCTGGC
1 CTCCAATGCCTGGC
201175 TATTACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.45, G:0.21, T:0.21
Consensus pattern (15 bp):
CTCCAATGCCTGGCC
Found at i:205869 original size:4 final size:4
Alignment explanation
Indices: 205860--205903 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
205850 TACCCTTGTG
* *
205860 TGTC TGTC TGTC TGTC TGTC CGTC CGTC TGTC TGTC TGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
205904 CGTCCGTAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.00, C:0.30, G:0.25, T:0.45
Consensus pattern (4 bp):
TGTC
Found at i:205888 original size:24 final size:24
Alignment explanation
Indices: 205861--205910 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
205851 ACCCTTGTGT
205861 GTCTGTCTGTCTGTCTGTCCGTCC
1 GTCTGTCTGTCTGTCTGTCCGTCC
205885 GTCTGTCTGTCTGTCTGTCCGTCC
1 GTCTGTCTGTCTGTCTGTCCGTCC
205909 GT
1 GT
205911 AACAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.00, C:0.32, G:0.26, T:0.42
Consensus pattern (24 bp):
GTCTGTCTGTCTGTCTGTCCGTCC
Found at i:206212 original size:167 final size:166
Alignment explanation
Indices: 205934--207060 Score: 1602
Period size: 166 Copynumber: 6.8 Consensus size: 166
205924 GTCGCATTTA
*
205934 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTT-AGGCATGCCATAT
* ** * *
205999 CGTGGGATATATTTTTGTACCAATCAGACGTCAACCACCAGTTAAATGATGACTTTGATTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATTTT
*
206064 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
206101 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGT-TAGGCATGCCATAT
* *
206166 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGAAGACTTTGTTTA-TTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATTTT
*
206230 TTAGCCAAAATTTTCAAACAAATTGTCGTCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
206267 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTG-TTAGGCATGCCATAT
* * * * * *
206332 GGTGGGATGTATTTTTGTACCAATCAGACATCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATTTT
*
206397 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * * *
206434 TCTCAGCATCTATATATCGGAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTT-AGGCATGCCATAT
* * * * * *
206499 CATGGAATATATTTTTGTACCATTTGGACGTCATCTTCCTGTTAAATGACGACTTTGTTTA-TTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATTTT
* *
206563 TTAGCCAAAATTTTCAAACAAATTGTCGTCAAAAATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * *
206600 TCTCAGCAGCTATTTATCACAGATGCTTGAAATTTTAACACACTATTTGTTTTGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTG-TTAGGCATGCCATAT
* * * *
206665 TGTGGGATATATTTTTGTATCAATCGGACATCAACTTCCTGTTAAATAATGACTTTGTTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATTTT
*
206730 TT-GCCAAAATTTTCAAACAAATTTTCGTCAAATATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * *
206766 TCTCAGCAGCTATTTATTGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTT-AGGCATGCCATAT
*
206831 CGTGGGATATATTTTTGTACCAATCGGACGTCATCTTCCTGTTAAATGA-GTACTTTGTTTA--T
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGATG-ACTTTGTTTATTT
*
206893 TTTAGCCAAAATTTTCAAACAAATTTTCCTCAAAGATT
129 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
206931 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTG-TTAGGCATGCCATAT
* * * * * * *
206996 TGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATG-TCGACTTTGCTTATTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAT-GACTTTGTTTATTT
207060 T
129 T
207061 GCATATTCAC
Statistics
Matches: 863, Mismatches: 83, Indels: 28
0.89 0.09 0.03
Matches are distributed among these distances:
164 4 0.00
165 144 0.17
166 444 0.51
167 270 0.31
168 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (166 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAGGCATGCCATATC
GTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGATGACTTTGTTTATTTTT
TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:206540 original size:333 final size:333
Alignment explanation
Indices: 205934--207060 Score: 1767
Period size: 333 Copynumber: 3.4 Consensus size: 333
205924 GTCGCATTTA
* * *
205934 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* * ** * * *
205999 CGTGGGATATATTTTTGTACCAATCAGACGTCAACCACCAGTTAAATGATGACTTTGATTATTTT
66 TGTGGGATATATTTTTGTACCAATCAGACATCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
*
206064 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTGTTTATCGCAGATGCTT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTT
* *
206129 GAAATTTTTACACAGTATTTG-TATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAG
196 GAAATTTTTACACAGTGTTTGTTA-AGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGG
*
206193 ACGTCAACTTCCTGTTAAATGAAGACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTGTCG
260 ACGTCATCTTCCTGTTAAATGAAGACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTGTCG
206258 TCAAAGATT
325 TCAAAGATT
*
206267 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* *
206332 GGTGGGATGTATTTTTGTACCAATCAGACATCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
66 TGTGGGATATATTTTTGTACCAATCAGACATCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* * *
206397 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCATCTATATATCGGAGATGCTT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTT
* * * *
206462 GAAATTTTTACACAGTGTTTGTTAAGGCATGCCATATCATGGAATATATTTTTGTACCATTTGGA
196 GAAATTTTTACACAGTGTTTGTTAAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGGA
*
206527 CGTCATCTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTGTCGT
261 CGTCATCTTCCTGTTAAATGAAGACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTGTCGT
*
206592 CAAAAATT
326 CAAAGATT
* * *
206600 TCTCAGCAGCTATTTATCACAGATGCTTGAAATTTTAACACACTATTTGTTTTGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* * * * *
206665 TGTGGGATATATTTTTGTATCAATCGGACATCAACTTCCTGTTAAATAATGACTTTGTTTATTTT
66 TGTGGGATATATTTTTGTACCAATCAGACATCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* * * *
206730 TT-GCCAAAATTTTCAAACAAATTTTCGTCAAATATTTCTCAGCAGCTATTTATTGCAGATGCTT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTT
206794 GAAATTTTTACACAGTGTTTGTTAAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGGA
196 GAAATTTTTACACAGTGTTTGTTAAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGGA
* *
206859 CGTCATCTTCCTGTTAAATG-AGTACTTTGTTTA-TTTTAGCCAAAATTTTCAAACAAATTTTCC
261 CGTCATCTTCCTGTTAAATGAAG-ACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTGTCG
206922 TCAAAGATT
325 TCAAAGATT
*
206931 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* * *** * * *
206996 TGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
66 TGTGGGATATATTTTTGTACCAATCAGACATCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
207061 GCATATTCAC
Statistics
Matches: 729, Mismatches: 63, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
331 154 0.21
332 147 0.20
333 426 0.58
334 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (333 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
TGTGGGATATATTTTTGTACCAATCAGACATCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTT
GAAATTTTTACACAGTGTTTGTTAAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGGA
CGTCATCTTCCTGTTAAATGAAGACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTGTCGT
CAAAGATT
Found at i:218082 original size:2 final size:2
Alignment explanation
Indices: 218075--218106 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
218065 AAACTGAAAT
218075 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
218107 TATTTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:219697 original size:2 final size:2
Alignment explanation
Indices: 219690--219743 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
219680 CTAGACAAAC
219690 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
219732 GA GA GA GA GA GA
1 GA GA GA GA GA GA
219744 TTACAAGATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:220935 original size:32 final size:32
Alignment explanation
Indices: 220893--220957 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
220883 ATATATAAAG
** *
220893 CCCTTATGTTAAATTCATGTACATCCTCAATT
1 CCCTTATGTTAAATTCATACACATCCGCAATT
*
220925 CCCTTTTGTTAAATTCATACACATCCGCAATT
1 CCCTTATGTTAAATTCATACACATCCGCAATT
220957 C
1 C
220958 TTGAATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.38
Consensus pattern (32 bp):
CCCTTATGTTAAATTCATACACATCCGCAATT
Found at i:221080 original size:2 final size:2
Alignment explanation
Indices: 221073--221125 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
221063 TTCGTTATAT
221073 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
221115 GA GA GA GA GA G
1 GA GA GA GA GA G
221126 TACTTACACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:229768 original size:2 final size:2
Alignment explanation
Indices: 229761--229806 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
229751 NNNNGCACCC
229761 CT CT CT CT CT CT CT CT CT CT CT CT CT CT 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
229803 CT CT
1 CT CT
229807 ATATATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:229811 original size:2 final size:2
Alignment explanation
Indices: 229806--229832 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
229796 TCTCTCTCTC
229806 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
229833 CATAATTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:242708 original size:438 final size:438
Alignment explanation
Indices: 241854--242800 Score: 1592
Period size: 438 Copynumber: 2.2 Consensus size: 438
241844 ATTACACAAT
* *
241854 AAAGTGGTATTGAAGAAAGACTTTAGAGCCCTTTTGGCCCCTAAATTGAAGGGCCAGCCCCTTTT
1 AAAGTGCTATAGAAGAAAGACTTTAGAGCCCTTTTGGCCCCTAAATTGAAGGGCCAGCCCCTTTT
*
241919 TCTTGGCATTATATGAAAGGTCTTCTGATATCAAACATATTTTGTCCAACAAGTGTTTAGAAATT
66 TCTTGGCATTATATGAAAGGACTTCTGATATCAAACATATTTTGTCCAACAAGTGTTTAGAAATT
* *
241984 CTTTGCCGTTTTTGAGATATCTGGGATAGGACGTTTTAGGGGTCGACCCCTTATCTCCATATTGG
131 CTTTGCCGTTTTTGAGATATCTGGGATAGGACATTTTAGGGGCCGACCCCTTATCTCCATATTGG
*
242049 GGCCAGATATCGAAATTTTTATGATTTATATATTGTTTAAAACATCATTCTAAGCATCTTTTATT
196 GGCCAGATAACGAAATTTTTATGATTTATATATTGTTTAAAACATCATTCTAAGCATCTTTTATT
* *
242114 CTATATTGCTTTTCAAAATATTTGTCCTTTTTGATATATAATTGATCGAAGTTGTGGACTTCTGG
261 CTATATTACTTCTCAAAATATTTGTCCTTTTTGATATATAATTGATCGAAGTTGTGGACTTCTGG
* *
242179 CCCCTGAAAACCCCTAATTACGTAACGCATGATAAATTTTTTTATAATGTATAGTTTTATAAGTG
326 CCCCTGAAAACCCCTAATTACGTAACGCATGATAAATATTTTTATAATGTATAGTTTTATAAGAG
*
242244 AAAGATAAACAATTTGCTTTTTAAACATATTACAAAATATTTCTCAGA
391 AAAGATAAACAATTTGCTTCTTAAACATATTACAAAATATTTCTCAGA
* *
242292 AAAGTGCTATAGAAGAAAGACTTTAGAGCCCTTTTGGTCCCTAAATTGAAGGGTCAGCCCCTTTT
1 AAAGTGCTATAGAAGAAAGACTTTAGAGCCCTTTTGGCCCCTAAATTGAAGGGCCAGCCCCTTTT
* *
242357 TCTTGGCATTATGTGAAAGGACTTCTGATATCAAACATATTTTGTTCAACAAGTGTTTAGAAATT
66 TCTTGGCATTATATGAAAGGACTTCTGATATCAAACATATTTTGTCCAACAAGTGTTTAGAAATT
* * *
242422 CTTTGTCGTTTTTGAGCTATCTGGGATAGGACATTTTAGGGGCCGACCCCTTATCTCCTTATTGG
131 CTTTGCCGTTTTTGAGATATCTGGGATAGGACATTTTAGGGGCCGACCCCTTATCTCCATATTGG
*
242487 GGCCAGATAACG-AATCTTTTATGATTTATATATTGTTTAAATCATCATTCTAAGCATCTTTTAT
196 GGCCAGATAACGAAAT-TTTTATGATTTATATATTGTTTAAAACATCATTCTAAGCATCTTTTAT
*
242551 TCTATATTACTTCTCAAAATATTTGTCCTTTTTGATATATAATTGATCGAAGTTTTGGACTTCTG
260 TCTATATTACTTCTCAAAATATTTGTCCTTTTTGATATATAATTGATCGAAGTTGTGGACTTCTG
*
242616 GCCCCTTAAAACCCCTAATTACGTAACGCATGATAAA-ATTTTTATAATGTATAGTTTTATAAGA
325 GCCCCTGAAAACCCCTAATTACGTAACGCATGATAAATATTTTTATAATGTATAGTTTTATAAGA
* *
242680 GAAAGATAAACATTTTCGCTTCTTAAACATATTACAAAATATTTCTCAGT
390 GAAAGATAAACAATTT-GCTTCTTAAACATATTACAAAATATTTCTCAGA
* * * ***
242730 AAAGTGCTATAGAAGAAAGACTTTTGAGCCCTTTTGACCCCTAATTTGAAAAAACCAGCCCCTTT
1 AAAGTGCTATAGAAGAAAGACTTTAGAGCCCTTTTGGCCCCTAAATTG-AAGGGCCAGCCCCTTT
242795 TTCTTG
65 TTCTTG
242801 ATATAAAACG
Statistics
Matches: 475, Mismatches: 31, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
437 43 0.09
438 414 0.87
439 18 0.04
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.38
Consensus pattern (438 bp):
AAAGTGCTATAGAAGAAAGACTTTAGAGCCCTTTTGGCCCCTAAATTGAAGGGCCAGCCCCTTTT
TCTTGGCATTATATGAAAGGACTTCTGATATCAAACATATTTTGTCCAACAAGTGTTTAGAAATT
CTTTGCCGTTTTTGAGATATCTGGGATAGGACATTTTAGGGGCCGACCCCTTATCTCCATATTGG
GGCCAGATAACGAAATTTTTATGATTTATATATTGTTTAAAACATCATTCTAAGCATCTTTTATT
CTATATTACTTCTCAAAATATTTGTCCTTTTTGATATATAATTGATCGAAGTTGTGGACTTCTGG
CCCCTGAAAACCCCTAATTACGTAACGCATGATAAATATTTTTATAATGTATAGTTTTATAAGAG
AAAGATAAACAATTTGCTTCTTAAACATATTACAAAATATTTCTCAGA
Found at i:255061 original size:12 final size:13
Alignment explanation
Indices: 255036--255062 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
255026 ACACAATTTT
255036 AATCATTAAAAAA
1 AATCATTAAAAAA
255049 AATCATTAAAAAA
1 AATCATTAAAAAA
255062 A
1 A
255063 CAAGTTTACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (13 bp):
AATCATTAAAAAA
Found at i:256807 original size:24 final size:24
Alignment explanation
Indices: 256761--256809 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
256751 ATATATATAT
* *
256761 ATATAAAACACAAATTAACAACCA
1 ATATAAAACAAAAATTAAAAACCA
256785 ATATAAAA-AAAAATTAAAAAACCA
1 ATATAAAACAAAAATT-AAAAACCA
256809 A
1 A
256810 AAACAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.16
Consensus pattern (24 bp):
ATATAAAACAAAAATTAAAAACCA
Found at i:260623 original size:68 final size:68
Alignment explanation
Indices: 260539--260816 Score: 466
Period size: 68 Copynumber: 4.1 Consensus size: 68
260529 ATGGACAGAT
** * *
260539 TATGAGTGTTACGGTTCTGTTAACTGACAGTGTTCGGACCTGACTGTTCCGGACTCCCTGACGGA
1 TATGAGTGTTACGGTTCTGTTATTTTACAGTGTTCGGACTTGACTGTTCCGGACTCCCTGACGGA
260604 AAC
66 AAC
*
260607 TATGAGTGTTACGGTTCTGTTATTTTACAGTGTTCGGACTTGACTGTACCGGACTCCCTGACGGA
1 TATGAGTGTTACGGTTCTGTTATTTTACAGTGTTCGGACTTGACTGTTCCGGACTCCCTGACGGA
260672 AAC
66 AAC
* *
260675 TATGAGTGTTATGGTTCTGTTATTTTACAGTGTTCGGACTTGACTGTTCCAGACTCCCTGACGGA
1 TATGAGTGTTACGGTTCTGTTATTTTACAGTGTTCGGACTTGACTGTTCCGGACTCCCTGACGGA
260740 AAC
66 AAC
* * *
260743 TATGAGTGTTATGATTCTGTTATTTTACAGTGTTCGGACTTGACTGTTCTGGACTCCCTGACGGA
1 TATGAGTGTTACGGTTCTGTTATTTTACAGTGTTCGGACTTGACTGTTCCGGACTCCCTGACGGA
260808 AAC
66 AAC
260811 TATGAG
1 TATGAG
260817 CTGGGATGTA
Statistics
Matches: 199, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 199 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (68 bp):
TATGAGTGTTACGGTTCTGTTATTTTACAGTGTTCGGACTTGACTGTTCCGGACTCCCTGACGGA
AAC
Found at i:261900 original size:17 final size:17
Alignment explanation
Indices: 261878--261912 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
261868 ATCTCTATTA
*
261878 AATTTTCAGTAATTCCT
1 AATTTTCAATAATTCCT
261895 AATTTTCAATAATTCCT
1 AATTTTCAATAATTCCT
261912 A
1 A
261913 CTTATCCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (17 bp):
AATTTTCAATAATTCCT
Found at i:272917 original size:21 final size:22
Alignment explanation
Indices: 272854--272934 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 22
272844 TCCCGAAAAA
* *
272854 AAACGCGAAAGTTTCGCGAG--
1 AAACGCGTAACTTTCGCGAGAT
* **
272874 GAACGCGTAACTTTTTC-AGAT
1 AAACGCGTAACTTTCGCGAGAT
272895 AAACGCGTAACTTTCGCGA-AT
1 AAACGCGTAACTTTCGCGAGAT
**
272916 AAACGCAAAACTTTCGCGA
1 AAACGCGTAACTTTCGCGA
272935 TATTTATAAC
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.04
20 12 0.25
21 33 0.69
22 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (22 bp):
AAACGCGTAACTTTCGCGAGAT
Found at i:273059 original size:7 final size:6
Alignment explanation
Indices: 273042--273112 Score: 58
Period size: 6 Copynumber: 12.0 Consensus size: 6
273032 ATTGCATGTT
* * * *
273042 TTTTTG TTTTTG TATTT- TTGTTG TTTTTTG TTGTTG TTGTTG TTGTTT-
1 TTTTTG TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG TT-TTTG
*
273090 TTTTTG -TTTTG TTTTTT TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG
273113 GGGGGGGGGG
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
5 11 0.21
6 34 0.65
7 7 0.13
ACGTcount: A:0.01, C:0.00, G:0.18, T:0.80
Consensus pattern (6 bp):
TTTTTG
Found at i:273068 original size:9 final size:9
Alignment explanation
Indices: 273038--273107 Score: 58
Period size: 8 Copynumber: 7.8 Consensus size: 9
273028 CAGTATTGCA
273038 TGTTTTT-T
1 TGTTTTTGT
273046 TGTTTTTG-
1 TGTTTTTGT
*
273054 TATTTTTGT
1 TGTTTTTGT
273063 TGTTTTTTGT
1 TG-TTTTTGT
273073 TGTTGTTGTTGT
1 TG-T-TT-TTGT
*
273085 TGTTTTTTT
1 TGTTTTTGT
273094 TG-TTTTGT
1 TGTTTTTGT
273102 T-TTTTT
1 TGTTTTT
273108 TTTTGGGGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
8 24 0.46
9 6 0.12
10 13 0.25
11 3 0.06
12 6 0.12
ACGTcount: A:0.01, C:0.00, G:0.19, T:0.80
Consensus pattern (9 bp):
TGTTTTTGT
Found at i:273068 original size:22 final size:22
Alignment explanation
Indices: 273040--273112 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
273030 GTATTGCATG
* *
273040 TTTTTTTGTTTTTGTATTTTTGTT
1 TTTTTTTGTTGTTG--TTGTTGTT
*
273064 GTTTTTTGTTGTTGTTGTTGTT
1 TTTTTTTGTTGTTGTTGTTGTT
*
273086 GTTTTTT-TTGTT-TTGTT-TT
1 TTTTTTTGTTGTTGTTGTTGTT
273105 TTTTTTTG
1 TTTTTTTG
273113 GGGGGGGGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
19 8 0.18
20 5 0.11
21 5 0.11
22 14 0.32
24 12 0.27
ACGTcount: A:0.01, C:0.00, G:0.18, T:0.81
Consensus pattern (22 bp):
TTTTTTTGTTGTTGTTGTTGTT
Found at i:273108 original size:9 final size:9
Alignment explanation
Indices: 273040--273112 Score: 60
Period size: 9 Copynumber: 7.9 Consensus size: 9
273030 GTATTGCATG
273040 TTTTTTTG-
1 TTTTTTTGT
* *
273048 TTTTTGTAT
1 TTTTTTTGT
*
273057 TTTTGTTGT
1 TTTTTTTGT
273066 TTTTTGTTGT
1 TTTTT-TTGT
273076 TGTTGTTGTTGT
1 T-TT-TT-TTGT
273088 TTTTTTTGT
1 TTTTTTTGT
*
273097 TTTGTTT-T
1 TTTTTTTGT
273105 TTTTTTTG
1 TTTTTTTG
273113 GGGGGGGGGG
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
8 13 0.25
9 20 0.38
10 7 0.13
11 4 0.08
12 8 0.15
ACGTcount: A:0.01, C:0.00, G:0.18, T:0.81
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:283838 original size:8 final size:8
Alignment explanation
Indices: 283827--283864 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
283817 TGAAAAGTTT
283827 ACGGACAG
1 ACGGACAG
283835 ACGGACAG
1 ACGGACAG
283843 ACGGACAG
1 ACGGACAG
*
283851 ACAGACAG
1 ACGGACAG
283859 ACGGAC
1 ACGGAC
283865 GACAGACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.39, C:0.26, G:0.34, T:0.00
Consensus pattern (8 bp):
ACGGACAG
Found at i:283848 original size:16 final size:16
Alignment explanation
Indices: 283827--283872 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
283817 TGAAAAGTTT
*
283827 ACGGACAGACGGACAG
1 ACGGACAGACAGACAG
283843 ACGGACAGACAGACAG
1 ACGGACAGACAGACAG
283859 ACGGAC-GACAGACA
1 ACGGACAGACAGACA
283873 AAATGTGATC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.41, C:0.26, G:0.33, T:0.00
Consensus pattern (16 bp):
ACGGACAGACAGACAG
Found at i:283855 original size:4 final size:4
Alignment explanation
Indices: 283830--283872 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
283820 AAAGTTTACG
* * *
283830 GACA GACG GACA GACG GACA GACA GACA GACG GAC- GACA GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
283873 AAATGTGATC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.42, C:0.26, G:0.33, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:286673 original size:22 final size:22
Alignment explanation
Indices: 286645--286688 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
286635 GCAAAAGAGC
286645 AGTACTGCAGTTATTGTGAATG
1 AGTACTGCAGTTATTGTGAATG
286667 AGTACTGCAGTTATTGTGAATG
1 AGTACTGCAGTTATTGTGAATG
286689 GGTCTCTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.36
Consensus pattern (22 bp):
AGTACTGCAGTTATTGTGAATG
Found at i:287249 original size:18 final size:18
Alignment explanation
Indices: 287226--287272 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
287216 ACAATCACTA
* *
287226 GATTTAGCTACGTAGCTT
1 GATTTACCTACATAGCTT
287244 GATTTACCTACATAGCTT
1 GATTTACCTACATAGCTT
*
287262 TATTTACCTAC
1 GATTTACCTAC
287273 CTGAAGTAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (18 bp):
GATTTACCTACATAGCTT
Found at i:287834 original size:18 final size:18
Alignment explanation
Indices: 287811--287857 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
287801 CCTACTTCAG
*
287811 GTAGGTAAAT-AAAGCTAT
1 GTAGGTAAATCAAA-CTAC
287829 GTAGGTAAATCAAACTAC
1 GTAGGTAAATCAAACTAC
*
287847 GTAGCTAAATC
1 GTAGGTAAATC
287858 TAGTGATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 23 0.88
19 3 0.12
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (18 bp):
GTAGGTAAATCAAACTAC
Found at i:290546 original size:2 final size:2
Alignment explanation
Indices: 290539--290586 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
290529 GTCTAGCAAA
*
290539 CT CT CT CT CT CT CT CA CT CT CT CT CT CT 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
290581 CT CT CT
1 CT CT CT
290587 TTGATATTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:300032 original size:182 final size:181
Alignment explanation
Indices: 299725--300087 Score: 717
Period size: 182 Copynumber: 2.0 Consensus size: 181
299715 TAAAGTAATG
299725 CATTTATAATAAATATACATAAAAATTTATATTTATAGACACATGAAGACATACATTTGTAGCCA
1 CATTTATAATAAATATACATAAAAATTTATATTTATAGACACATGAAGACATACATTTGTAGCCA
299790 TTGTCTGCTAGGCTGGTGGACATAACAGCTTGTGTGAGGACAGGATGGATTGAGAGTTCATTTGG
66 TTGTCTGCTAGGCTGGTGGACATAACAGCTTGTGTGAGGACAGGATGGATTGAGAGTTCATTTGG
299855 CTCCATAGAGTCATCTGGGTAAGAACATGGATTGTTGATTTCCTGTCAGAC
131 CTCCATAGAGTCATCTGGGTAAGAACATGGATTGTTGATTTCCTGTCAGAC
299906 NCATTTATAATAAATATACATAAAAATTTATATTTATAGACACATGAAGACATACATTTGTAGCC
1 -CATTTATAATAAATATACATAAAAATTTATATTTATAGACACATGAAGACATACATTTGTAGCC
299971 ATTGTCTGCTAGGCTGGTGGACATAACAGCTTGTGTGAGGACAGGATGGATTGAGAGTTCATTTG
65 ATTGTCTGCTAGGCTGGTGGACATAACAGCTTGTGTGAGGACAGGATGGATTGAGAGTTCATTTG
300036 GCTCCATAGAGTCATCTGGGTAAGAACATGGATTGTTGATTTCCTGTCAGAC
130 GCTCCATAGAGTCATCTGGGTAAGAACATGGATTGTTGATTTCCTGTCAGAC
300088 GAAAATAAAT
Statistics
Matches: 181, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
182 181 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (181 bp):
CATTTATAATAAATATACATAAAAATTTATATTTATAGACACATGAAGACATACATTTGTAGCCA
TTGTCTGCTAGGCTGGTGGACATAACAGCTTGTGTGAGGACAGGATGGATTGAGAGTTCATTTGG
CTCCATAGAGTCATCTGGGTAAGAACATGGATTGTTGATTTCCTGTCAGAC
Found at i:311725 original size:14 final size:14
Alignment explanation
Indices: 311706--311733 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
311696 GACGTTATGC
311706 ATGTTAACAAAGCT
1 ATGTTAACAAAGCT
311720 ATGTTAACAAAGCT
1 ATGTTAACAAAGCT
311734 CGAGTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
ATGTTAACAAAGCT
Found at i:325394 original size:180 final size:180
Alignment explanation
Indices: 325092--325628 Score: 1011
Period size: 180 Copynumber: 3.0 Consensus size: 180
325082 ACCCTACATG
* *
325092 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATTG
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
325157 GAAATCAAAATCCTAGCAATATGCACACCTGTGATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTGTGATATATGTACAATTGATCTGCAAAAGAACAAC
*
325222 TTCATATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTATCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTATCC
*
325272 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
325337 GAAATCAAAATCCTAGCAATATGCACACCTGTGATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTGTGATATATGTACAATTGATCTGCAAAAGAACAAC
325402 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTATCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTATCC
*
325452 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTAGATAAATTATCG
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
*
325517 GAAATCAAAATCCTAGCAATATGCATACCTGTGATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTGTGATATATGTACAATTGATCTGCAAAAGAACAAC
*
325582 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATAAGGGTA
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTA
325629 CCTTTTTGGC
Statistics
Matches: 349, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
180 349 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (180 bp):
TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
GAAATCAAAATCCTAGCAATATGCACACCTGTGATATATGTACAATTGATCTGCAAAAGAACAAC
TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTATCC
Found at i:338575 original size:15 final size:14
Alignment explanation
Indices: 338555--338584 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
338545 TTTTGGGTTG
338555 TTTTTTTGTTTGTTT
1 TTTTTTTGTTT-TTT
338570 TTTTTTTGTTTTTT
1 TTTTTTTGTTTTTT
338584 T
1 T
338585 AGATGTGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (14 bp):
TTTTTTTGTTTTTT
Found at i:338584 original size:11 final size:12
Alignment explanation
Indices: 338552--338584 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
338542 TGTTTTTGGG
338552 TTGTTTTTTTGT
1 TTGTTTTTTTGT
338564 TTGTTTTTTT-T
1 TTGTTTTTTTGT
338575 TTGTTTTTTT
1 TTGTTTTTTT
338585 AGATGTGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (12 bp):
TTGTTTTTTTGT
Found at i:346005 original size:21 final size:21
Alignment explanation
Indices: 345958--346033 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
345948 TTACGGATCC
* *
345958 TAAACTATAGTTAACGATTTG
1 TAAACTATAGTTTACGATATG
* *
345979 TTAACTATAGTTTAC-ATCTG
1 TAAACTATAGTTTACGATATG
345999 TGAAACTATA-TTTCACGA-ATG
1 T-AAACTATAGTTT-ACGATATG
346020 TAAACTATAGTTTA
1 TAAACTATAGTTTA
346034 AGAATGATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 17 0.37
21 28 0.61
22 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (21 bp):
TAAACTATAGTTTACGATATG
Found at i:346038 original size:20 final size:21
Alignment explanation
Indices: 346001--346053 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
345991 TACATCTGTG
*
346001 AAACTATA-TTTCACGAATG-T
1 AAACTATAGTTT-AAGAATGAT
346021 AAACTATAGTTTAAGAATGAT
1 AAACTATAGTTTAAGAATGAT
*
346042 AATC-ATAGTTTA
1 AAACTATAGTTTA
346054 TCTATCTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (21 bp):
AAACTATAGTTTAAGAATGAT
Found at i:346139 original size:20 final size:20
Alignment explanation
Indices: 346091--346140 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
346081 ATTTTGCGGA
*
346091 TAAATATAGATTCACATTTG
1 TAAATATAGATTCACATTCG
*
346111 TTAATTATA-ATTCACATTCG
1 -TAAATATAGATTCACATTCG
346131 TAAACTATAG
1 TAAA-TATAG
346141 TTAAGAGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.12
20 14 0.58
21 7 0.29
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (20 bp):
TAAATATAGATTCACATTCG
Found at i:346917 original size:20 final size:21
Alignment explanation
Indices: 346892--346985 Score: 74
Period size: 20 Copynumber: 4.7 Consensus size: 21
346882 TTTATACTCA
346892 TAAACTAT-GTTTAACAGACG
1 TAAACTATAGTTTAACAGACG
346912 TAAACTATAGTTT-AC-GAACG
1 TAAACTATAGTTTAACAG-ACG
* * *
346932 TGAATTATAG-TTAA-GGACG
1 TAAACTATAGTTTAACAGACG
* *
346951 ATAAACTAT-GATTAACAAACG
1 -TAAACTATAGTTTAACAGACG
*
346972 TAAATTATAGTTTA
1 TAAACTATAGTTTA
346986 TCTCTCAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
19 7 0.12
20 40 0.69
21 11 0.19
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (21 bp):
TAAACTATAGTTTAACAGACG
Found at i:347202 original size:20 final size:21
Alignment explanation
Indices: 347125--347215 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 21
347115 ATCTGATAGA
347125 TATAGTTTCACA-ATCGTGAAAC
1 TATAGTTT-ACAGAT-GTGAAAC
* *
347147 TATA-TTTACCATATCT-AAAC
1 TATAGTTTA-CAGATGTGAAAC
347167 TATAGTTTAC-GAATGT-AAAC
1 TATAGTTTACAG-ATGTGAAAC
*
347187 TATAGTTTACAGATGTGAATC
1 TATAGTTTACAGATGTGAAAC
347208 TATA-TTTA
1 TATAGTTTA
347216 TCAGCAAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
20 35 0.59
21 18 0.31
22 6 0.10
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (21 bp):
TATAGTTTACAGATGTGAAAC
Found at i:347549 original size:39 final size:40
Alignment explanation
Indices: 347506--347600 Score: 156
Period size: 39 Copynumber: 2.4 Consensus size: 40
347496 TGTTTTCAGT
*
347506 GTTAACTATAGTTTACAGATGTGAAACATAGACTATCG-C
1 GTTAACTATAGTTTACAGATGTGAAACATAGACTAACGTC
*
347545 GTTAACTATAGTTTACAGATGTGAAACATAGATTAACGTC
1 GTTAACTATAGTTTACAGATGTGAAACATAGACTAACGTC
*
347585 GGTAACTATAGTTTAC
1 GTTAACTATAGTTTAC
347601 GATCCGTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 36 0.69
40 16 0.31
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (40 bp):
GTTAACTATAGTTTACAGATGTGAAACATAGACTAACGTC
Found at i:347609 original size:20 final size:20
Alignment explanation
Indices: 347547--347618 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
347537 ACTATCGCGT
**
347547 TAACTATAGTTTACAGATGTG
1 TAACTATAGTTTAC-GATCCG
* * *
347568 AAAC-ATAGATTAACG-TCGG
1 TAACTATAG-TTTACGATCCG
347587 TAACTATAGTTTACGATCCG
1 TAACTATAGTTTACGATCCG
347607 TAAACTATAGTT
1 T-AACTATAGTT
347619 AACAGTCGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
19 10 0.25
20 13 0.32
21 17 0.43
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (20 bp):
TAACTATAGTTTACGATCCG
Found at i:347621 original size:40 final size:41
Alignment explanation
Indices: 347508--347626 Score: 142
Period size: 39 Copynumber: 3.0 Consensus size: 41
347498 TTTTCAGTGT
* * *
347508 TAACTATAGTTTACAGATGTGAAACATAGACTATC-G-CGT
1 TAACTATAGTTTACAGATGTGAAACATAGATTAACAGTCGG
347547 TAACTATAGTTTACAGATGTGAAACATAGATTAAC-GTCGG
1 TAACTATAGTTTACAGATGTGAAACATAGATTAACAGTCGG
347587 TAACTATAGTTTAC-GATCCGT-AAACTATAG-TTAACAGTCG
1 TAACTATAGTTTACAGAT--GTGAAAC-ATAGATTAACAGTCG
347627 ATAAACCTAG
Statistics
Matches: 72, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
39 37 0.51
40 25 0.35
41 10 0.14
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (41 bp):
TAACTATAGTTTACAGATGTGAAACATAGATTAACAGTCGG
Found at i:355290 original size:24 final size:24
Alignment explanation
Indices: 355263--355310 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
355253 CAGAATGACT
355263 TATGTTTATTCTTACT-AAGAAAAA
1 TATGTTTATTCTTA-TAAAGAAAAA
355287 TATGTTTATTCTTATAAAGAAAAA
1 TATGTTTATTCTTATAAAGAAAAA
355311 GAAAAGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (24 bp):
TATGTTTATTCTTATAAAGAAAAA
Found at i:364481 original size:22 final size:22
Alignment explanation
Indices: 364451--364492 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
364441 ATGCGAAGAA
364451 TTCACATGA-ACTTCATGCGAAT
1 TTCACATGAGA-TTCATGCGAAT
*
364473 TTCATATGAGATTCATGCGA
1 TTCACATGAGATTCATGCGA
364493 GCCACTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (22 bp):
TTCACATGAGATTCATGCGAAT
Found at i:369173 original size:12 final size:12
Alignment explanation
Indices: 369153--369186 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
369143 ATGCAACATA
369153 TTTAACTTTATG
1 TTTAACTTTATG
* *
369165 TTTACCTTTATT
1 TTTAACTTTATG
369177 TTTAACTTTA
1 TTTAACTTTA
369187 CCTTTTTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.62
Consensus pattern (12 bp):
TTTAACTTTATG
Found at i:369203 original size:12 final size:12
Alignment explanation
Indices: 369188--369217 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
369178 TTAACTTTAC
369188 CTTTTTCTTCTT
1 CTTTTTCTTCTT
369200 CTTTTTCTTCTT
1 CTTTTTCTTCTT
369212 CTTTTT
1 CTTTTT
369218 TGATTCCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:372325 original size:15 final size:15
Alignment explanation
Indices: 372307--372337 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
372297 CCATTCGAAT
*
372307 TCTTTCTTTTCTTTC
1 TCTTTCTATTCTTTC
372322 TCTTTCTATTCTTTC
1 TCTTTCTATTCTTTC
372337 T
1 T
372338 AGTCGATCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTTTCTATTCTTTC
Found at i:373214 original size:49 final size:47
Alignment explanation
Indices: 373145--373276 Score: 147
Period size: 47 Copynumber: 2.8 Consensus size: 47
373135 ACAAAATCGA
*** * *
373145 CACTAACGTGCGGAAATCCAGCACAGATAGCCCGATATCACACACACTC
1 CACTAACGTGCGGGGTTCCAGCACAGATAGCCCAACAT-A-ACACACTC
* * *
373194 CACTAACGTGCGGGGTTCCAGCACAGTTAGCCCAACATAACACTCTG
1 CACTAACGTGCGGGGTTCCAGCACAGATAGCCCAACATAACACACTC
** *
373241 TGCTAACGTGCGGGGTTCCAGCACAGCTAGCCCAAC
1 CACTAACGTGCGGGGTTCCAGCACAGATAGCCCAAC
373277 CGTTCTCTTC
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
47 39 0.54
48 1 0.01
49 32 0.44
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (47 bp):
CACTAACGTGCGGGGTTCCAGCACAGATAGCCCAACATAACACACTC
Found at i:376128 original size:90 final size:85
Alignment explanation
Indices: 375975--376161 Score: 311
Period size: 90 Copynumber: 2.1 Consensus size: 85
375965 GTGGTTTGGT
* *
375975 ATGACACAATATTGTAAAATATAATACGACATTGTATCAAATCATGTTATACAAGATCATATGGT
1 ATGACACAATATTGTAAAATATAATAAGACATTGTATCAAATCATGCTATACAAGATCATATGGT
376040 GCAATATCATACGATACAAGATCAA
66 GC-A-AT-ATA--ATACAAGATCAA
376065 ATGACACAATATTGTAAAATATAATAAGACATTGTATCAAATCATGCTATACAAGATCATATGGT
1 ATGACACAATATTGTAAAATATAATAAGACATTGTATCAAATCATGCTATACAAGATCATATGGT
376130 GCAATATAATACAAGATCAA
66 GCAATATAATACAAGATCAA
376150 ATGACACAATAT
1 ATGACACAATAT
376162 CGTATCACAT
Statistics
Matches: 95, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
85 24 0.25
87 3 0.03
88 2 0.02
89 1 0.01
90 65 0.68
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (85 bp):
ATGACACAATATTGTAAAATATAATAAGACATTGTATCAAATCATGCTATACAAGATCATATGGT
GCAATATAATACAAGATCAA
Found at i:376168 original size:20 final size:20
Alignment explanation
Indices: 376145--376202 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
376135 ATAATACAAG
*
376145 ATCAAATGACACAATATCGT
1 ATCAAATGACACAATATCGC
* * *
376165 ATCACATGATACAATATTGC
1 ATCAAATGACACAATATCGC
*
376185 ATCATATGACACAATATC
1 ATCAAATGACACAATATC
376203 ATGTAATATG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (20 bp):
ATCAAATGACACAATATCGC
Found at i:386726 original size:3 final size:3
Alignment explanation
Indices: 386718--386747 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
386708 GGCAGGCAAA
386718 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
386748 CTATAATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:389212 original size:174 final size:174
Alignment explanation
Indices: 388908--389223 Score: 390
Period size: 174 Copynumber: 1.8 Consensus size: 174
388898 ATGTATTCTG
** * *
388908 AGGATGCTTCCACACAAGTTTCAGCTTTCCTGACTGACTGGTTTCTGAGAAGAAATTTTTTAAAA
1 AGGATGCTTCCACACAAGTTTCAGCTTTCCTGACCAACTAGTTTCTGAAAAGAAATTTTTTAAAA
* * * * ** *
388973 TATTTACTCTTTATATTCCTATATAAAAATTCGACCCCCCATCTCCTTATTGTCGCACAACCCTA
66 TATTAACTCTTTATATTCATATATAAAAAATCGACCCCCCA-CCCCCCATGGTCGCACAACCCTA
389038 CCCCTGGGGGTCATGATTTTCACAACTTTGAATTTAAACTAACTA
130 CCCCTGGGGGTCATGATTTTCACAACTTTGAATTTAAACTAACTA
*
389083 AGGATGCTTCCACA-AAGTTTCAGCTTTCCTTG-CCAATTAGTTTCTGAAAAGAAGA-TTTTT-A
1 AGGATGCTTCCACACAAGTTTCAGCTTTCC-TGACCAACTAGTTTCTGAAAAGAA-ATTTTTTAA
* * * * *
389144 AATATTAACTCTTTATATTCATTTGTAAAAAATCGAACAACCCCC-CCCCCCATGGTTGCCCCAC
64 AATATTAACTCTTTATATTCATATATAAAAAATCG-AC--CCCCCACCCCCCATGGTCGCACAAC
389208 CCTACCCCTGGGGGTC
126 CCTACCCCTGGGGGTC
389224 TTTGAAACTA
Statistics
Matches: 119, Mismatches: 17, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
173 31 0.26
174 66 0.55
175 17 0.14
176 5 0.04
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (174 bp):
AGGATGCTTCCACACAAGTTTCAGCTTTCCTGACCAACTAGTTTCTGAAAAGAAATTTTTTAAAA
TATTAACTCTTTATATTCATATATAAAAAATCGACCCCCCACCCCCCATGGTCGCACAACCCTAC
CCCTGGGGGTCATGATTTTCACAACTTTGAATTTAAACTAACTA
Found at i:397487 original size:27 final size:27
Alignment explanation
Indices: 397456--397922 Score: 702
Period size: 27 Copynumber: 17.3 Consensus size: 27
397446 TCCATTTTGA
*
397456 GTATGCCATGGGCAATAAGACAGGTGT
1 GTATGCCATGGGCAATTAGACAGGTGT
*
397483 GTATGCCATGGGCAATAAGACAGGTGT
1 GTATGCCATGGGCAATTAGACAGGTGT
*
397510 GTATGCCAAGGGCAATTAGACAGGTGT
1 GTATGCCATGGGCAATTAGACAGGTGT
* * *
397537 GTATGCCATGAGCTATTAGACAGATGT
1 GTATGCCATGGGCAATTAGACAGGTGT
*
397564 GTATGCCATGGGCAATTAGACAGGTGA
1 GTATGCCATGGGCAATTAGACAGGTGT
*
397591 GTATGCCATGGGCAATTAGACAGGTGA
1 GTATGCCATGGGCAATTAGACAGGTGT
* *
397618 GTATGCCATGGGCAATTACACAGGTGA
1 GTATGCCATGGGCAATTAGACAGGTGT
397645 GTATGCCATGGGCAATTAGACAGGTGT
1 GTATGCCATGGGCAATTAGACAGGTGT
* * *
397672 GTATGCCATGAGCTATTAAACAGGTGT
1 GTATGCCATGGGCAATTAGACAGGTGT
* *
397699 GTATGCCATTGGCAATTAGACAGGTGA
1 GTATGCCATGGGCAATTAGACAGGTGT
*
397726 GTATGCCATGGGCAATTAGACAGGTGA
1 GTATGCCATGGGCAATTAGACAGGTGT
*
397753 GTATGCCATGGGCAATTAGACAGGTGA
1 GTATGCCATGGGCAATTAGACAGGTGT
* *
397780 GTATGCCATGGGCAATAAGACAGGTGA
1 GTATGCCATGGGCAATTAGACAGGTGT
* *
397807 ATATGCCATGGGCAATTAGAAAGGTGT
1 GTATGCCATGGGCAATTAGACAGGTGT
397834 GTATGCCACT-GGCAATTAGACAGGTGT
1 GTATGCCA-TGGGCAATTAGACAGGTGT
* * *
397861 GTATGCCATTGGCAATTACACAGGTCT
1 GTATGCCATGGGCAATTAGACAGGTGT
397888 GTATGCCATGGGCAATTAGACAGGTGT
1 GTATGCCATGGGCAATTAGACAGGTGT
397915 GTATGCCA
1 GTATGCCA
397923 GGTGCGTATG
Statistics
Matches: 404, Mismatches: 34, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
26 1 0.00
27 402 1.00
28 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (27 bp):
GTATGCCATGGGCAATTAGACAGGTGT
Found at i:397959 original size:27 final size:27
Alignment explanation
Indices: 397921--398929 Score: 1462
Period size: 27 Copynumber: 37.4 Consensus size: 27
397911 GTGTGTATGC
*
397921 CAGGTGCGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
*
397948 CAGGTGAGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
** *
397975 CAGGTGAATATGCCATGGGCAATAAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
**
398002 CAGGTGAATATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
*
398029 AAGGTGTGTATGCCACT-GGCAATTAGA
1 CAGGTGTGTATGCCA-TGGGCAATTAGA
* *
398056 CAGGTGTGTATGCCATTGGCAATTACA
1 CAGGTGTGTATGCCATGGGCAATTAGA
*
398083 CAGGTCTGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
398110 CAGGTGTGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
*
398137 CAGGTGTGTATGCCATGGGCAATTACA
1 CAGGTGTGTATGCCATGGGCAATTAGA
*
398164 CAGATGTGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
398191 CAGGTGTGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
398218 CAGGTGTGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* *
398245 CAAGTGTGTATGCCATGGGCAGTTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* * *
398272 CAGGTGAGTATACCATTGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* *
398299 CAGGTGTGTATGGCATTGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
*
398326 CAGGTGTGTATGGCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
*
398353 CAGGTGAGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
** *
398380 CAGGTGAATATGCCATGGGCAATAAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
398407 CAGGTGTGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* ** *
398434 CAGGTGAGTATGCCATGGTTAATAAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* * *
398461 CAGGTGAGTATGCCATTGGCAATTACA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* *
398488 CAGGTCTGTATGCCATGGGCAATTACA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* *
398515 CAGGTGTGTATTCCATGGGCAATTACA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* * *
398542 CAGGTCTGTATGGCATGGACAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
398569 CAGGTGTGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* *
398596 CAGGTGAGTTTGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
*
398623 CAGGTGTGTATGCCAAGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
*
398650 CAGGTGTTTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* *
398677 CAGGTGAGTATGCCATGGGCAATAAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* * *
398704 CAGGTGAGTATGCCATGAGCTATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* *
398731 CAGATGAGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
*
398758 CAGGTGTGTATGCCAAGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* *
398785 CAGGTGAGTATGCCATAGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
398812 CAGGTGTGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
398839 CAGGTGTGTATGCCATGGGCAATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* *
398866 CAGGTGAGTATGCCATGGGCAATAAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
* * * *
398893 CAGGTGAGTATGCCATAGCCTATTAGA
1 CAGGTGTGTATGCCATGGGCAATTAGA
*
398920 CCGGTGTGTA
1 CAGGTGTGTA
398930 ACTAAAAAAA
Statistics
Matches: 891, Mismatches: 89, Indels: 4
0.91 0.09 0.00
Matches are distributed among these distances:
26 1 0.00
27 889 1.00
28 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (27 bp):
CAGGTGTGTATGCCATGGGCAATTAGA
Found at i:397962 original size:67 final size:67
Alignment explanation
Indices: 397854--397989 Score: 209
Period size: 67 Copynumber: 2.0 Consensus size: 67
397844 GGCAATTAGA
* * * **
397854 CAGGTGTGTATGCCATTGGCAATTACACAGGTCTGTATGCCATGGGCAATTAGACAGGTGTGTAT
1 CAGGTGCGTATGCCATGGGCAATTACACAGGTCAGTATGCCATGGGCAATTAGACAGGTGAATAT
397919 GC
66 GC
* *
397921 CAGGTGCGTATGCCATGGGCAATTAGACAGGTGAGTATGCCATGGGCAATTAGACAGGTGAATAT
1 CAGGTGCGTATGCCATGGGCAATTACACAGGTCAGTATGCCATGGGCAATTAGACAGGTGAATAT
397986 GC
66 GC
397988 CA
1 CA
397990 TGGGCAATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (67 bp):
CAGGTGCGTATGCCATGGGCAATTACACAGGTCAGTATGCCATGGGCAATTAGACAGGTGAATAT
GC
Found at i:402486 original size:33 final size:33
Alignment explanation
Indices: 402404--403307 Score: 962
Period size: 33 Copynumber: 25.8 Consensus size: 33
402394 CACATAGGAA
* *
402404 GTATAATAGGGTAAGATATGGCTAACAGATAAAAA
1 GTATAATAGGGTAAGATATGGCTAACACAT--AAG
*
402439 GTATTATAGGGTAAGATATGGCTAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
402472 GTATAATAGGGTAAGATATGGCTAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
* * *
402505 ATAAAATAGGGTAAGATATGTCCAAGATATGTCCAACACATAAG
1 GTATAATAGGGTAAGATA--T----G----G-CTAACACATAAG
*
402549 GTATAATAGGGTAAGATGTGGCTAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
402582 GTATAATAGGGTAAGATATGGCTAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
* * *
402615 ATAAAATAGGGTAAGATATGTCCAAGATATGTCCAACACATAAG
1 GTATAATAGGGTAAGATA--T----G----G-CTAACACATAAG
*
402659 GTATAATAGGGTAAGATGTGGCTAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
*
402692 GTATAATAGGGTAAGATATGTCCAAGATATGTCCAACACATAAG
1 GTATAATAGGGTAAGATA--T----G----G-CTAACACATAAG
*
402736 GTATAATAGGGTAAGATGTGGCTAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
* *
402769 GTATAATAGGGTAAGATATGTCCAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
* *
402802 GTATAATAGGGTAAGATATGTCCAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
*
402835 GTATAATAGGGTAAGATGTGGCTAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
402868 GTATAATAGGGTAAGATATGGCTAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
* * *
402901 ATAAAATAGGGTAAGATATGTCCAAGATATGTCCAACACATAAG
1 GTATAATAGGGTAAGATA--T----G----G-CTAACACATAAG
* *
402945 GTATAATAGGGTAAGATGTGGCTAACACATAAT
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
* *
402978 GTATAATAGGGTAAGATATGTCCAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
*
403011 GTATAATAGGGTAAGATGTGGCTAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
* *
403044 GTATAATAGGGTAAGATATGTCCAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
* * *
403077 GTATAATAGGGTAAGATGTGGCTAACAGATAAAAA
1 GTATAATAGGGTAAGATATGGCTAACACAT--AAG
*
403112 GTATTATAGGGTAAGATATGGCTAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
* *
403145 GTATAATAGGGTAAGATATGTCCAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
* * *
403178 GTATAATAGGGTAAGATGTGGCTAACAGATAAAAA
1 GTATAATAGGGTAAGATATGGCTAACACAT--AAG
*
403213 GTATTATAGGGTAAGATATGGCTAACACATAAG
1 GTATAATAGGGTAAGATATGGCTAACACATAAG
403246 GTATAATAGGGTAAGATATGGCTAACACATAAGAG
1 GTATAATAGGGTAAGATATGGCTAACACAT-A-AG
* * * *
403281 GTATTATAGGATAAGATTTAGCTAACA
1 GTATAATAGGGTAAGATATGGCTAACA
403308 GATACCAGTA
Statistics
Matches: 745, Mismatches: 74, Indels: 100
0.81 0.08 0.11
Matches are distributed among these distances:
33 503 0.68
34 5 0.01
35 115 0.15
38 4 0.01
39 4 0.01
42 4 0.01
43 4 0.01
44 106 0.14
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (33 bp):
GTATAATAGGGTAAGATATGGCTAACACATAAG
Found at i:402637 original size:110 final size:108
Alignment explanation
Indices: 402439--403265 Score: 815
Period size: 110 Copynumber: 7.8 Consensus size: 108
402429 CAGATAAAAA
*
402439 GTATTATAGGGTAAGATATGGCTAACACATAAGGTATAATAGGGTAAGATATGGCTAACACATAA
1 GTATAATAGGGTAAGATATGGCTAACACATAAGGTATAATAGGGTAAGATATGGCTAACACATAA
*
402504 GATAAAATAGGGTAAGATATGTCCAAGATATGTCCAACACATAAG
66 GGTAAAATAGGGTAAGATATGT--AAGATATGTCCAACACATAAG
*
402549 GTATAATAGGGTAAGATGTGGCTAACACATAAGGTATAATAGGGTAAGATATGGCTAACACATAA
1 GTATAATAGGGTAAGATATGGCTAACACATAAGGTATAATAGGGTAAGATATGGCTAACACATAA
*
402614 GATAAAATAGGGTAAGATATGTCCAAGATATGTCCAACACATAAG
66 GGTAAAATAGGGTAAGATATGT--AAGATATGTCCAACACATAAG
* * * *
402659 GTATAATAGGGTAAGATGTGGCTAACACATAAGGTATAATAGGGTAAGATATGTC-CA-AGAT-A
1 GTATAATAGGGTAAGATATGGCTAACACATAAGGTATAATAGGGTAAGATATGGCTAACACATAA
* * * * * *
402721 TGTCCAACACATAAGGTATA-ATAGGGTAAGATGTGGCTAACACATAAG
66 GGT--AA-A-ATAGGGTA-AGATA-TGTAAGATATGTCCAACACATAAG
* * * *
402769 GTATAATAGGGTAAGATATGTCCAACACATAAGGTATAATAGGGTAAGATATGTCCAACACATAA
1 GTATAATAGGGTAAGATATGGCTAACACATAAGGTATAATAGGGTAAGATATGGCTAACACATAA
* *
402834 GGTATAATAGGGTAAG--ATGT--G----G-CTAACACATAAG
66 GGTAAAATAGGGTAAGATATGTAAGATATGTCCAACACATAAG
* * * * *
402868 GTATAATAGGGTAAGATATGGCTAACACATAAGATAAAATAGGGTAAGATATGTC-CA-AGAT-A
1 GTATAATAGGGTAAGATATGGCTAACACATAAGGTATAATAGGGTAAGATATGGCTAACACATAA
* * * * * * *
402930 TGTCCAACACATAAGGTATA-ATAGGGTAAGATGTGGCTAACACATAAT
66 GGT--AA-A-ATAGGGTA-AGATA-TGTAAGATATGTCCAACACATAAG
* * *
402978 GTATAATAGGGTAAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAA
1 GTATAATAGGGTAAGATATGGCTAACACATAAGGTATAATAGGGTAAGATATGGCTAACACATAA
*
403043 GGTATAATA--G---G----GTAAGATATGTCCAACACATAAG
66 GGTAAAATAGGGTAAGATATGTAAGATATGTCCAACACATAAG
* * * *
403077 GTATAATAGGGTAAGATGTGGCTAACAGATAAAAAGTATTATAGGGTAAGATATGGCTAACACAT
1 GTATAATAGGGTAAGATATGGCTAACACAT--AAGGTATAATAGGGTAAGATATGGCTAACACAT
*
403142 AAGGTATAATA--G---G----GTAAGATATGTCCAACACATAAG
64 AAGGTAAAATAGGGTAAGATATGTAAGATATGTCCAACACATAAG
* * * *
403178 GTATAATAGGGTAAGATGTGGCTAACAGATAAAAAGTATTATAGGGTAAGATATGGCTAACACAT
1 GTATAATAGGGTAAGATATGGCTAACACAT--AAGGTATAATAGGGTAAGATATGGCTAACACAT
*
403243 AAGGTATAATAGGGTAAGATATG
64 AAGGTAAAATAGGGTAAGATATG
403266 GCTAACACAT
Statistics
Matches: 624, Mismatches: 53, Indels: 80
0.82 0.07 0.11
Matches are distributed among these distances:
96 3 0.00
97 3 0.00
98 2 0.00
99 109 0.17
100 8 0.01
101 143 0.23
102 1 0.00
103 3 0.00
104 1 0.00
105 1 0.00
106 3 0.00
107 4 0.01
108 4 0.01
109 14 0.02
110 296 0.47
111 14 0.02
112 9 0.01
113 6 0.01
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (108 bp):
GTATAATAGGGTAAGATATGGCTAACACATAAGGTATAATAGGGTAAGATATGGCTAACACATAA
GGTAAAATAGGGTAAGATATGTAAGATATGTCCAACACATAAG
Found at i:402715 original size:176 final size:165
Alignment explanation
Indices: 402638--403307 Score: 890
Period size: 176 Copynumber: 3.9 Consensus size: 165
402628 AGATATGTCC
402638 AAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAAGGTATAATAGGG
1 AAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAAGGTATAATA--G
402703 TAAGATATGTCCAAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAA
64 ---G----GT--AAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAA
* *
402768 GGTATAATAGGGTAAGATATGTCCAACACATAAGGTATAATAGGGT
120 GGTATAATAGGGTAAGATATGGCTAACACATAAGGTATAATAGGGT
402814 AAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAAGGTATAATAGGG
1 AAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAAGGTATAATAGGG
* * * * *
402879 TAAGATATGGCTAACACATAAGATAAAATAGGGTAAGATATGTCCAAGATATGTCCAACACATAA
66 TAAGATATGTCCAACACATAAGGTATAATAGGGTAAG--ATGT----G----G-CTAACACATAA
* *
402944 GGTATAATAGGGTAAGATGTGGCTAACACATAATGTATAATAGGGT
120 GGTATAATAGGGTAAGATATGGCTAACACATAAGGTATAATAGGGT
402990 AAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAAGGTATAATAGGG
1 AAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAAGGTATAATAGGG
* * *
403055 TAAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACAGATAAAAAGTATTATA
66 TAAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACAT--AAGGTATAATA
403120 GGGTAAGATATGGCTAACACATAAGGTATAATAGGGT
129 GGGTAAGATATGGCTAACACATAAGGTATAATAGGGT
* * *
403157 AAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACAGATAAAAAGTATTATAG
1 AAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACAT--AAGGTATAATAG
* * * *
403222 GGTAAGATATGGCTAACACATAAGGTATAATAGGGTAAGATATGGCTAACACATAAGAGGTATTA
64 GGTAAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACAT-A-AGGTATAA
* * *
403287 TAGGATAAGATTTAGCTAACA
127 TAGGGTAAGATATGGCTAACA
403308 GATACCAGTA
Statistics
Matches: 448, Mismatches: 30, Indels: 39
0.87 0.06 0.08
Matches are distributed among these distances:
165 39 0.09
166 1 0.00
167 100 0.22
168 2 0.00
169 85 0.19
170 1 0.00
171 2 0.00
174 5 0.01
175 1 0.00
176 212 0.47
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (165 bp):
AAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAAGGTATAATAGGG
TAAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAAGGTATAATAGG
GTAAGATATGGCTAACACATAAGGTATAATAGGGT
Found at i:403009 original size:209 final size:209
Alignment explanation
Indices: 402539--403307 Score: 1018
Period size: 209 Copynumber: 3.7 Consensus size: 209
402529 AGATATGTCC
* *
402539 AACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAAGGTATAATAGGGTAAGATATGGC
1 AACACATAAGGTATAATAGGGTAAGATATGGCCAACACATAAGGTATAATAGGGTAAGATATGGC
* *
402604 TAACACATAAGATAAAATAGGGTAAGATATGTCCAAGATATGTCCAACACATAAGGTATAATAGG
66 TAACACATAAGGTATAATAGGGTAAGATA--T----G----G-CCAACACATAAGGTATAATAGG
* *
402669 GTAAGATGTGGCTAACACATAAGGTATAATAGGGTAAGATATGTCCAAGATATGTCCAACACATA
120 GTAAGATGTGGCTAACACATAAGATAAAATAGGGTAAGATATGTCCAAGATATGTCCAACACATA
402734 AGGTATAATAGGGTAAGATGTGGCT
185 AGGTATAATAGGGTAAGATGTGGCT
* *
402759 AACACATAAGGTATAATAGGGTAAGATATGTCCAACACATAAGGTATAATAGGGTAAGATATGTC
1 AACACATAAGGTATAATAGGGTAAGATATGGCCAACACATAAGGTATAATAGGGTAAGATATGGC
* * * *
402824 CAACACATAAGGTATAATAGGGTAAGATGTGGCTAACACATAAGGTATAATAGGGTAAGATATGG
66 TAACACATAAGGTATAATAGGGTAAGATATGGCCAACACATAAGGTATAATAGGGTAAGATGTGG
402889 CTAACACATAAGATAAAATAGGGTAAGATATGTCCAAGATATGTCCAACACATAAGGTATAATAG
131 CTAACACATAAGATAAAATAGGGTAAGATATGTCCAAGATATGTCCAACACATAAGGTATAATAG
402954 GGTAAGATGTGGCT
196 GGTAAGATGTGGCT
* * *
402968 AACACATAATGTATAATAGGGTAAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGGC
1 AACACATAAGGTATAATAGGGTAAGATATGGCCAACACATAAGGTATAATAGGGTAAGATATGGC
*
403033 TAACACATAAGGTATAATAGGGTAAGATATGTCCAACACATAAGGTATAATAGGGTAAGATGTGG
66 TAACACATAAGGTATAATAGGGTAAGATATGGCCAACACATAAGGTATAATAGGGTAAGATGTGG
** * * *
403098 CT-A-AC---AGATAAAA-A--GTATTATAGGGT--AAGATATGGCTAACACATAAGGTATAATA
131 CTAACACATAAGATAAAATAGGGTAAGATA-TGTCCAAGATATGTCCAACACATAAGGTATAATA
* * *
403153 GGGTAAGATATGTCC
195 GGGTAAGATGTGGCT
* * * * *
403168 AACACATAAGGTATAATAGGGTAAGATGTGGCTAACAGATAAAAAGTATTATAGGGTAAGATATG
1 AACACATAAGGTATAATAGGGTAAGATATGGCCAACACAT--AAGGTATAATAGGGTAAGATATG
* * *
403233 GCTAACACATAAGGTATAATAGGGTAAGATATGGCTAACACATAAGAGGTATTATAGGATAAGAT
64 GCTAACACATAAGGTATAATAGGGTAAGATATGGCCAACACAT-A-AGGTATAATAGGGTAAGAT
* *
403298 TTAGCTAACA
127 GTGGCTAACA
403308 GATACCAGTA
Statistics
Matches: 500, Mismatches: 42, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
200 74 0.15
201 6 0.01
202 63 0.13
203 2 0.00
204 29 0.06
205 1 0.00
206 1 0.00
207 2 0.00
208 1 0.00
209 232 0.46
210 1 0.00
214 1 0.00
218 1 0.00
220 86 0.17
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.24
Consensus pattern (209 bp):
AACACATAAGGTATAATAGGGTAAGATATGGCCAACACATAAGGTATAATAGGGTAAGATATGGC
TAACACATAAGGTATAATAGGGTAAGATATGGCCAACACATAAGGTATAATAGGGTAAGATGTGG
CTAACACATAAGATAAAATAGGGTAAGATATGTCCAAGATATGTCCAACACATAAGGTATAATAG
GGTAAGATGTGGCT
Found at i:403364 original size:35 final size:35
Alignment explanation
Indices: 403213--403476 Score: 271
Period size: 35 Copynumber: 7.3 Consensus size: 35
403203 CAGATAAAAA
** * *
403213 GTATTATAGGGTAAGATATGGCTAACACA-TA-AG
1 GTATTATAGAATAAGATATAGCTAACACAGAAGAG
* ** * *
403246 GTATAATAGGGTAAGATATGGCTAACACATAAGAG
1 GTATTATAGAATAAGATATAGCTAACACAGAAGAG
* *
403281 GTATTATAGGATAAGATTTAGCTAACAGATACCAGTAAGAG
1 GTATTATAGAATAAGATATAGCTAAC----A-CAG-AAGAG
*
403322 GTTTTATAGAATAAGATATAGCTAACACAGAAGAG
1 GTATTATAGAATAAGATATAGCTAACACAGAAGAG
* *
403357 GTATTATAGAATAAGATAAAGCTAACACAAAAGAG
1 GTATTATAGAATAAGATATAGCTAACACAGAAGAG
403392 GTATTATTATAATAGAATAAGATATAGCTAACACAGAAGAG
1 G---TA-T-T-ATAGAATAAGATATAGCTAACACAGAAGAG
403433 GTATTATAGAATAAGATATAGCTAACACAGAAGAG
1 GTATTATAGAATAAGATATAGCTAACACAGAAGAG
*
403468 GTATCATAG
1 GTATTATAG
403477 GGTTATATGT
Statistics
Matches: 201, Mismatches: 16, Indels: 26
0.83 0.07 0.11
Matches are distributed among these distances:
33 28 0.14
34 1 0.00
35 100 0.50
36 4 0.02
37 2 0.01
38 4 0.02
39 2 0.01
40 3 0.01
41 57 0.28
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (35 bp):
GTATTATAGAATAAGATATAGCTAACACAGAAGAG
Found at i:403471 original size:76 final size:77
Alignment explanation
Indices: 403247--403471 Score: 285
Period size: 76 Copynumber: 2.9 Consensus size: 77
403237 ACACATAAGG
** * * * * * *
403247 TATAATAGGGTAAGATATGGCTAACACATAAGAGGTATTATAGGATAAGATTTAGCTAACAGATA
1 TATAATAGAATAAGATATAGCTAACACAGAAGAGGTATTATAGAATAAGATATAGCTAACACAAA
** *
403312 CCA-GTAAGAGGT
66 AGAGGTATGA-GT
* *
403324 T-TTATAGAATAAGATATAGCTAACACAGAAGAGGTATTATAGAATAAGATAAAGCTAACACAAA
1 TATAATAGAATAAGATATAGCTAACACAGAAGAGGTATTATAGAATAAGATATAGCTAACACAAA
*
403388 AGAGGTATTA-T
66 AGAGGTATGAGT
*
403399 TATAATAGAATAAGATATAGCTAACACAGAAGAGGTATTATAGAATAAGATATAGCTAACACAGA
1 TATAATAGAATAAGATATAGCTAACACAGAAGAGGTATTATAGAATAAGATATAGCTAACACAAA
403464 AGAGGTAT
66 AGAGGTAT
403472 CATAGGGTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
75 2 0.02
76 122 0.95
77 5 0.04
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.25
Consensus pattern (77 bp):
TATAATAGAATAAGATATAGCTAACACAGAAGAGGTATTATAGAATAAGATATAGCTAACACAAA
AGAGGTATGAGT
Found at i:403753 original size:24 final size:25
Alignment explanation
Indices: 403700--403753 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
403690 TTCTTATACA
***
403700 AGGAGCATTTCATACACCTTTTCCT
1 AGGAGCATTTCATACACCACATCCT
403725 AGGAGCATTTCATAC-CCACATCCT
1 AGGAGCATTTCATACACCACATCCT
403749 AGGAG
1 AGGAG
403754 TAGCTCACAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (25 bp):
AGGAGCATTTCATACACCACATCCT
Found at i:408829 original size:18 final size:18
Alignment explanation
Indices: 408808--408852 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
408798 GGACTGTAGG
408808 ATAGGTC-CAGTCTGTAAA
1 ATAGGTCACAGT-TGTAAA
408826 ATAGGTCAACAGTTGTAAA
1 ATAGGTC-ACAGTTGTAAA
408845 ATAGGTCA
1 ATAGGTCA
408853 ACAACTGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 13 0.52
20 4 0.16
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (18 bp):
ATAGGTCACAGTTGTAAA
Found at i:408844 original size:19 final size:20
Alignment explanation
Indices: 408815--408855 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
408805 AGGATAGGTC
408815 CAGTCTGTAAAATAGGTCAA
1 CAGTCTGTAAAATAGGTCAA
408835 CAGT-TGTAAAATAGGTCAA
1 CAGTCTGTAAAATAGGTCAA
408854 CA
1 CA
408856 ACTGTCACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (20 bp):
CAGTCTGTAAAATAGGTCAA
Found at i:411123 original size:30 final size:30
Alignment explanation
Indices: 411084--411215 Score: 221
Period size: 30 Copynumber: 4.4 Consensus size: 30
411074 TCAATTTTTT
* * *
411084 CTGATAATTTTTAAAGA-TATTAATCACTTA
1 CTGACAATTTTTTAAGACT-TTCATCACTTA
411114 CTGACAATTTTTTAAGACTTTCATCACTTA
1 CTGACAATTTTTTAAGACTTTCATCACTTA
411144 CTGACAATTTTTTAAGACTTTCATCACTTA
1 CTGACAATTTTTTAAGACTTTCATCACTTA
411174 CTGACAATTTTTTAAGACTTTCATCACTTA
1 CTGACAATTTTTTAAGACTTTCATCACTTA
411204 CTGACAATTTTT
1 CTGACAATTTTT
411216 CCAGTGTCCT
Statistics
Matches: 98, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
30 97 0.99
31 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (30 bp):
CTGACAATTTTTTAAGACTTTCATCACTTA
Found at i:411757 original size:39 final size:39
Alignment explanation
Indices: 411712--412136 Score: 338
Period size: 39 Copynumber: 11.4 Consensus size: 39
411702 ATGCATGTAA
411712 TGACAAGTATTGAGTCTACTGACTTTGTGTGACATTAGC
1 TGACAAGTATTGAGTCTACTGACTTTGTGTGACATTAGC
* * ** * *
411751 TGACAAGTATTGAGTCTTCTGTCTTAATGTGTCATTTGC
1 TGACAAGTATTGAGTCTACTGACTTTGTGTGACATTAGC
* * * *
411790 TGCCAAGTATTGAG---ACT-ACTGTGTAATGACTTTA--
1 TGACAAGTATTGAGTCTACTGACTTTGT-GTGACATTAGC
*
411824 TG---AGTATTGAGTCTATTGAC--TGTGTGACATTAGC
1 TGACAAGTATTGAGTCTACTGACTTTGTGTGACATTAGC
411858 TGACAAGTATTGAGTCTACTGACTTTGTGTGACATTAGC
1 TGACAAGTATTGAGTCTACTGACTTTGTGTGACATTAGC
**
411897 TGACAAGTATTGAGTCTACTGACTTTGTGCAACATTAGC
1 TGACAAGTATTGAGTCTACTGACTTTGTGTGACATTAGC
*
411936 TGACAAGTATTGAGTCTACTGACTTT-TGTGTCATT-GC
1 TGACAAGTATTGAGTCTACTGACTTTGTGTGACATTAGC
* * * * *
411973 TGACAAGTATTAACT-TA-AGACTACTGTGTG--A-TAAC
1 TGACAAGTATTGAGTCTACTGACT-TTGTGTGACATTAGC
* ** *
412008 TTTATGAGTATTGAGTCTATTGAC--TGTGTGACATTAG-
1 -TGACAAGTATTGAGTCTACTGACTTTGTGTGACATTAGC
* ** * * * *
412045 TTATTAGTTATTGAGACTGCTGTCTTTATGTGACATTAGC
1 TGACAAG-TATTGAGTCTACTGACTTTGTGTGACATTAGC
* * * *
412085 TGATAAAGTAGTGAGTCTACTGAC-ATGTGTGTCATTAGC
1 TGA-CAAGTATTGAGTCTACTGACTTTGTGTGACATTAGC
412124 TGAC-AGTATTGAG
1 TGACAAGTATTGAG
412137 ACTCCTGTGT
Statistics
Matches: 305, Mismatches: 55, Indels: 54
0.74 0.13 0.13
Matches are distributed among these distances:
31 9 0.03
32 7 0.02
33 3 0.01
34 7 0.02
35 17 0.06
36 26 0.09
37 59 0.19
38 11 0.04
39 150 0.49
40 14 0.05
41 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (39 bp):
TGACAAGTATTGAGTCTACTGACTTTGTGTGACATTAGC
Found at i:411855 original size:107 final size:108
Alignment explanation
Indices: 411717--411917 Score: 305
Period size: 107 Copynumber: 1.9 Consensus size: 108
411707 TGTAATGACA
* *
411717 AGTATTGAGTCTACTGACTTTGTGTGACATTAGCTGACAAGTATTGAGTCTTCTGTCTTAATGTG
1 AGTATTGAGTCTACTGAC-TTGTGTGACATTAGCTGACAAGTATTGAGTCTACTGACTTAATGTG
* * *
411782 TCATTTGCTGCCAAGTATTGAGACTACTGTGTAATGACTTTATG
65 ACATTAGCTGACAAGTATTGAGACTACTGTGTAATGACTTTATG
* **
411826 AGTATTGAGTCTATTGAC-TGTGTGACATTAGCTGACAAGTATTGAGTCTACTGACTTTGTGTGA
1 AGTATTGAGTCTACTGACTTGTGTGACATTAGCTGACAAGTATTGAGTCTACTGACTTAATGTGA
*
411890 CATTAGCTGACAAGTATTGAGTCTACTG
66 CATTAGCTGACAAGTATTGAGACTACTG
411918 ACTTTGTGCA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
107 66 0.80
109 17 0.20
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (108 bp):
AGTATTGAGTCTACTGACTTGTGTGACATTAGCTGACAAGTATTGAGTCTACTGACTTAATGTGA
CATTAGCTGACAAGTATTGAGACTACTGTGTAATGACTTTATG
Done.