Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007849.1 Hibiscus syriacus cultivar Beakdansim tig00110206_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3141433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 12
Found at i:6516 original size:21 final size:19
Alignment explanation
Indices: 6479--6519 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
6469 TAATATAATA
*
6479 TTTTTATATTTTTTCTTAT
1 TTTTTATATTTTGTCTTAT
6498 TTTTTAATAATTTTGTCTTAT
1 TTTTT-AT-ATTTTGTCTTAT
6519 T
1 T
6520 ACACGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTATATTTTGTCTTAT
Found at i:14328 original size:32 final size:33
Alignment explanation
Indices: 14281--14348 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 33
14271 AAAAACAAAC
*
14281 GAAAGAAAGACGACACCAGCGTTTCACTGGAGG
1 GAAAGAAAGACGACACCAACGTTTCACTGGAGG
*
14314 GAAAGACA-ACGACACCAACGTTTCACTGGAGG
1 GAAAGAAAGACGACACCAACGTTTCACTGGAGG
14346 GAA
1 GAA
14349 TTGGTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 26 0.79
33 7 0.21
ACGTcount: A:0.38, C:0.22, G:0.28, T:0.12
Consensus pattern (33 bp):
GAAAGAAAGACGACACCAACGTTTCACTGGAGG
Found at i:23445 original size:2 final size:2
Alignment explanation
Indices: 23440--23464 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23430 TATATTTTTG
23440 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
23465 ACTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27185 original size:73 final size:73
Alignment explanation
Indices: 27066--27215 Score: 264
Period size: 73 Copynumber: 2.1 Consensus size: 73
27056 TGGGCATCAC
* * *
27066 CAAAATATTGTTTTGGTATACAATATCATGTATCTATTTCGGTTGCTCATAGAATCTAAGATTTG
1 CAAAATATTGTTTTGGTATACAATATCATGTAGCTATTTAGGTTGCTCATAGAATCTAAGATATG
27131 TTCAGTTG
66 TTCAGTTG
*
27139 CAAAATATTGTTTTGGTATACAATATCATGTAGCTATTTATGTTGCTCATAGAATCTAAGATATG
1 CAAAATATTGTTTTGGTATACAATATCATGTAGCTATTTAGGTTGCTCATAGAATCTAAGATATG
27204 TTCAGTTG
66 TTCAGTTG
27212 CAAA
1 CAAA
27216 GTTCTAATTC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (73 bp):
CAAAATATTGTTTTGGTATACAATATCATGTAGCTATTTAGGTTGCTCATAGAATCTAAGATATG
TTCAGTTG
Found at i:31027 original size:2 final size:2
Alignment explanation
Indices: 31022--31081 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
31012 TAAAAAAAAC
31022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31064 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
31082 TAAATTGAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40484 original size:20 final size:20
Alignment explanation
Indices: 40436--40497 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
40426 AACTTAAATC
*
40436 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
40456 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
40474 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
40493 AAAAT
1 AAAAT
40498 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:40565 original size:52 final size:53
Alignment explanation
Indices: 40493--40602 Score: 204
Period size: 52 Copynumber: 2.1 Consensus size: 53
40483 TATATGATAT
*
40493 AAAATTAAATATCTATAATATAATATTAAAAATTTAATATTTAATTTATTTAA
1 AAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
40546 AAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
1 AAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
40598 AAAAT
1 AAAAT
40603 ATTAAAATTA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 50 0.89
53 6 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (53 bp):
AAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAA
Found at i:40582 original size:28 final size:28
Alignment explanation
Indices: 40493--40584 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 28
40483 TATATGATAT
40493 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATATCTATAATATAATATTAA
* *
40522 AAATTTAATAT-T-TAAT-TTAT-TTAA
1 AAAATTAATATCTATAATATAATATTAA
40546 AAAATTAATATCTATAATATAATATTAA
1 AAAATTAATATCTATAATATAATATTAA
40574 AAAATTAATAT
1 AAAATTAATAT
40585 TTAATTTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
24 14 0.25
25 4 0.07
26 8 0.15
27 4 0.07
28 20 0.36
29 5 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAATTAATATCTATAATATAATATTAA
Found at i:40607 original size:26 final size:24
Alignment explanation
Indices: 40518--40602 Score: 116
Period size: 24 Copynumber: 3.4 Consensus size: 24
40508 TAATATAATA
*
40518 TTAAAAATTTAATATTTAATTTAT
1 TTAAAAAATTAATATTTAATTTAT
*
40542 TTAAAAAATTAATATCTATAATATAAT
1 TTAAAAAATTAATAT-T-TAAT-TTAT
40569 ATTAAAAAATTAATATTTAATTTAT
1 -TTAAAAAATTAATATTTAATTTAT
40594 TTAAAAAAT
1 TTAAAAAAT
40603 ATTAAAATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
24 23 0.43
25 4 0.07
26 8 0.15
27 4 0.07
28 15 0.28
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAAAAAATTAATATTTAATTTAT
Found at i:40639 original size:12 final size:12
Alignment explanation
Indices: 40599--40644 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
40589 TTTATTTAAA
40599 AAATATTAAAATT
1 AAATA-TAAAATT
*
40612 AAA-ATCAAA-T
1 AAATATAAAATT
40622 ATAATATAAAATT
1 A-AATATAAAATT
40635 AAATATAAAA
1 AAATATAAAA
40645 CCTCTTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
10 2 0.07
11 6 0.21
12 15 0.54
13 5 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATATAAAATT
Found at i:44643 original size:11 final size:11
Alignment explanation
Indices: 44627--44652 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44617 TTATTTTATT
44627 AATTTGTTAAA
1 AATTTGTTAAA
44638 AATTTGTTAAA
1 AATTTGTTAAA
44649 AATT
1 AATT
44653 CTTTTTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
AATTTGTTAAA
Found at i:47895 original size:4 final size:4
Alignment explanation
Indices: 47886--47926 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
47876 AGCAGATATA
47886 ATAC ATAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
47927 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
4 33 0.94
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:49108 original size:23 final size:23
Alignment explanation
Indices: 49046--49096 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
49036 CAGCTCATAT
* *
49046 AATTGCAACGAAGTGCCACGTAG
1 AATTGCACCGGAGTGCCACGTAG
*
49069 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCACGTAG
49092 AATTG
1 AATTG
49097 TACTGTAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCACGTAG
Found at i:53815 original size:23 final size:23
Alignment explanation
Indices: 53789--53852 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
53779 CAACTCATAT
53789 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
53812 AATTGCATCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
53835 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
53853 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:57944 original size:2 final size:2
Alignment explanation
Indices: 57937--58030 Score: 188
Period size: 2 Copynumber: 47.0 Consensus size: 2
57927 ACATACATAC
57937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57979 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58021 AT AT AT AT AT
1 AT AT AT AT AT
58031 CCATCTAAAA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59603 original size:21 final size:21
Alignment explanation
Indices: 59579--59618 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
59569 AAACCTGCTG
59579 AAGTAATTATGAATTAAAAAT
1 AAGTAATTATGAATTAAAAAT
*
59600 AAGTAATTGTGAATTAAAA
1 AAGTAATTATGAATTAAAA
59619 GTCCATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (21 bp):
AAGTAATTATGAATTAAAAAT
Found at i:61547 original size:2 final size:2
Alignment explanation
Indices: 61536--61568 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
61526 AAATAATAAA
61536 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61569 CGGGTCGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:62019 original size:2 final size:2
Alignment explanation
Indices: 62012--62038 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
62002 ATCACTTTGC
62012 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
62039 ATCTTGAATC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71916 original size:101 final size:101
Alignment explanation
Indices: 71742--71936 Score: 356
Period size: 101 Copynumber: 1.9 Consensus size: 101
71732 CCGCACAGGC
*
71742 TGCATCCAACACATATTTGGCATGGATATGAGAGAATGATACTCTGAAATATATGGGAAAACTTT
1 TGCATCCAACACATATTTGGCATGGATATGAGAGAATGATACTCGGAAATATATGGGAAAACTTT
71807 GAGCAATTTTAAAAGGCGTTCA-TTCATTCGTTTTG
66 GAGCAATTTTAAAAGGCGTTCATTTCATTCGTTTTG
*
71842 TGCATCCAACACATATTTTGGCATGGATATGAGAGAATGATACTCGGAAATATATGGGAGAACTT
1 TGCATCCAACACATA-TTTGGCATGGATATGAGAGAATGATACTCGGAAATATATGGGAAAACTT
71907 TGAGCAATTTTAAAAGGCGTTCATTTCATT
65 TGAGCAATTTTAAAAGGCGTTCATTTCATT
71937 TTGTGTAATT
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
100 15 0.16
101 70 0.77
102 6 0.07
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (101 bp):
TGCATCCAACACATATTTGGCATGGATATGAGAGAATGATACTCGGAAATATATGGGAAAACTTT
GAGCAATTTTAAAAGGCGTTCATTTCATTCGTTTTG
Found at i:73092 original size:16 final size:16
Alignment explanation
Indices: 73071--73104 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
73061 GATTCTAGCT
73071 GCATCGTGGATGCTGC
1 GCATCGTGGATGCTGC
73087 GCATCGTGGATGCTGC
1 GCATCGTGGATGCTGC
73103 GC
1 GC
73105 TTTGTCTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.26, G:0.38, T:0.24
Consensus pattern (16 bp):
GCATCGTGGATGCTGC
Found at i:76954 original size:33 final size:33
Alignment explanation
Indices: 76836--77095 Score: 115
Period size: 32 Copynumber: 7.5 Consensus size: 33
76826 TTAATCATAA
*
76836 TATATAATTTTAAAAATGATTTGTGAAA-ATATAT
1 TATAT-ATTTTAAAAAT-ATTTTTGAAACATATAT
** * *
76870 TAT-GGTTTTGAAAATATGTTTTAAAAACATATA-
1 TATATATTTTAAAAATAT-TTTT-GAAACATATAT
*
76903 T-T-TAGTTT-AAAATAATTTTTGAAACATATAT
1 TATATATTTTAAAAAT-ATTTTTGAAACATATAT
76934 TATATATTTTAAAAATATTTTTGAAAACTTGTATATAT
1 TATATATTTTAAAAATATTTTTG-AAAC----ATATAT
* ** * *
76972 TATATAGTTTTGAAAAAAAAATTTGAAAACGTATAA
1 TATATA-TTTT-AAAAATATTTTTG-AAACATATAT
*
77008 TATAGTTTTTTAAAAA-A-TTTTGAAAACGTATAATATATAT
1 TATA-TATTTTAAAAATATTTTTG-AAAC-------ATATAT
* *
77048 ATATATATTTTAAAAATACTTTTGAAA-ATGTAT
1 -TATATATTTTAAAAATATTTTTGAAACATATAT
*
77081 AATATATTTTAAAAA
1 TATATATTTTAAAAA
77096 AAAATTTTTT
Statistics
Matches: 178, Mismatches: 22, Indels: 54
0.70 0.09 0.21
Matches are distributed among these distances:
30 9 0.05
31 12 0.07
32 33 0.19
33 30 0.17
34 18 0.10
35 5 0.03
36 12 0.07
37 1 0.01
38 12 0.07
39 4 0.02
40 29 0.16
41 8 0.04
42 5 0.03
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (33 bp):
TATATATTTTAAAAATATTTTTGAAACATATAT
Found at i:76977 original size:75 final size:71
Alignment explanation
Indices: 76898--77096 Score: 172
Period size: 73 Copynumber: 2.7 Consensus size: 71
76888 TTTTAAAAAC
*
76898 ATATATTTAGTTTAAAATAATTTTTGAAACATATATTATATATTTTAAAAATATTTTTGAAAACT
1 ATATATTTA-TTTAAAA-AAATTTTGAAACATATATTATATATTTTAAAAA-A-TTTTGAAAAC-
76963 TGTAT-ATAT-T
61 -GTATAATATAT
** * * * *
76973 ATATAGTTT-TGAAAAAAAAATTTGAAAACGTATAATATAGTTTTTTAAAAAATTTTGAAAACGT
1 ATATA-TTTATTTAAAAAAATTTTG-AAACATATATTATA-TATTTTAAAAAATTTTGAAAACGT
77037 ATAATATAT
63 ATAATATAT
* * * *
77046 ATATATATATTTTAAAAATACTTTTGAAA-ATGTATAATATATTTTAAAAAA
1 ATATATTTA-TTTAAAAA-AATTTTGAAACATATATTATATATTTTAAAAAA
77097 AAATTTTTTG
Statistics
Matches: 99, Mismatches: 17, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
71 4 0.04
72 17 0.17
73 28 0.28
74 27 0.27
75 20 0.20
76 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.44
Consensus pattern (71 bp):
ATATATTTATTTAAAAAAATTTTGAAACATATATTATATATTTTAAAAAATTTTGAAAACGTATA
ATATAT
Found at i:76999 original size:40 final size:38
Alignment explanation
Indices: 76928--77102 Score: 122
Period size: 38 Copynumber: 4.7 Consensus size: 38
76918 TTTTTGAAAC
* **
76928 ATATATTATATATTTTAAAAATATTTTTGAAAACTTGT
1 ATATATTATATATTTTAAAAAAAAATTTGAAAACTTGT
76966 ATATATTATATAGTTTTGAAAAAAAAATTTGAAAAC--GT
1 ATATATTATATA-TTTT-AAAAAAAAATTTGAAAACTTGT
* * *
77004 ATA-A-TATAGT-TTTT-TAAAAAATTTTGAAAACGTATAAT
1 ATATATTATA-TATTTTAAAAAAAAATTTGAAAAC-T-T-GT
* **
77042 ATATATATATATATTTTAAAAATACTTTTGAAAA--TG-
1 ATATAT-TATATATTTTAAAAAAAAATTTGAAAACTTGT
77078 -TATA--ATATATTTTAAAAAAAAATTT
1 ATATATTATATATTTTAAAAAAAAATTT
77103 TTTGAAAACA
Statistics
Matches: 111, Mismatches: 13, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
32 18 0.16
33 15 0.14
35 8 0.07
36 4 0.04
37 2 0.02
38 22 0.20
39 5 0.05
40 16 0.14
41 8 0.07
42 13 0.12
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.43
Consensus pattern (38 bp):
ATATATTATATATTTTAAAAAAAAATTTGAAAACTTGT
Found at i:77098 original size:75 final size:74
Alignment explanation
Indices: 76919--77131 Score: 220
Period size: 75 Copynumber: 2.9 Consensus size: 74
76909 TTAAAATAAT
* * * * *
76919 TTTTGAAACATATATTATATATTTTAAAAATATTTTTGAAAACT-T-GTATATAT-TATATAGTT
1 TTTTGAAA-ATGTATAATATATTTTAAAAAAAATTTTGAAAACTATAATATATATATATATA-TT
76981 TTGAAAAAAAA
64 TTGAAAAAAAA
* * **
76992 ATTTGAAAACGTATAATATAGTTTTTTAAAAAATTTTGAAAACGTATAATATATATATATATATT
1 TTTTGAAAATGTATAATATA-TTTTAAAAAAAATTTTGAAAAC-TATAATATATATATATATATT
* *
77057 TT-AAAAATAC
64 TTGAAAAAAAA
*
77067 TTTTGAAAATGTATAATATATTTTAAAAAAAAATTTTTTGAAAAC-ATAATATATAGATATATAT
1 TTTTGAAAATGTATAATATATTTT-AAAAAAAA--TTTTGAAAACTATAATATATATATATATAT
77131 T
63 T
77132 AGAAAAATGA
Statistics
Matches: 116, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
72 9 0.08
73 25 0.22
74 5 0.04
75 50 0.43
76 11 0.09
77 16 0.14
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (74 bp):
TTTTGAAAATGTATAATATATTTTAAAAAAAATTTTGAAAACTATAATATATATATATATATTTT
GAAAAAAAA
Found at i:82586 original size:39 final size:40
Alignment explanation
Indices: 82487--82588 Score: 102
Period size: 39 Copynumber: 2.6 Consensus size: 40
82477 GTATGTTTTT
* * *
82487 CTGAAAACTGTTTGA-GCGAGAATACGGAAATGCATTCTG
1 CTGAAAACTGCTCGATGCGAGAATACGGAAATGCATCCTG
* * * * *
82526 CTTAAAACTGCTGGAT-TGAGAATATGGAGATGCATCCTG
1 CTGAAAACTGCTCGATGCGAGAATACGGAAATGCATCCTG
*
82565 CTGGAAACTGCTCG-TGCGAGAATA
1 CTGAAAACTGCTCGATGCGAGAATA
82589 AGACTTCTGG
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
38 1 0.02
39 49 0.98
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (40 bp):
CTGAAAACTGCTCGATGCGAGAATACGGAAATGCATCCTG
Found at i:85169 original size:194 final size:195
Alignment explanation
Indices: 84806--85200 Score: 701
Period size: 195 Copynumber: 2.0 Consensus size: 195
84796 CACCCCAATT
84806 AAATTTTGGCAGCTTCATTCTTTAAGTACCAGTTGTCAAACATCCATGTTCAACACATATATGGA
1 AAATTTTGGCAGCTTCATTCTTTAAGTACCAGTTGTCAAACATCCATGTTCAACACA-ATATGGA
84871 CACAATATGTCAATATGACCCTCCAAAACCCTCCAAATGCCGAAAAAATTTAGAAAATTTTGAGC
65 CACAATATGTCAATATGACCCTCCAAAACCCTCCAAATGCCGAAAAAATTTAGAAAATTTTGAGC
84936 ATATCGTTCAAATTACATAGCATCCGGATGCAGTTTTCCA-TTATACGTATTCCATCTAGACGCT
130 A-ATCGTTCAAATTACATAGCATCCGGATGCAGTTTTCCATTTATACGTATTCCATCTAGACGCT
85000 CA
194 CA
85002 AAATTTTGGCAGCTTCATTCTTTAAGTACCAG-TGTCAAACATCCATGTTCAACAC-ATATGGAC
1 AAATTTTGGCAGCTTCATTCTTTAAGTACCAGTTGTCAAACATCCATGTTCAACACAATATGGAC
85065 ACAAGTATGTCAATATGACCCTCCAAAAACCCTCCAAATGCACGAAAAAATTTAG-AAATTTTGA
66 ACAA-TATGTCAATATGACCCTCC-AAAACCCTCCAAATGC-CGAAAAAATTTAGAAAATTTTGA
85129 GC-ATCGTATCAAATTACATAGCATCCGGATGCAGTTTTCCATTTATACGTATTCCATCTAGACG
128 GCAATCGT-TCAAATTACATAGCATCCGGATGCAGTTTTCCATTTATACGTATTCCATCTAGACG
85193 CTCA
192 CTCA
85197 AAAT
1 AAAT
85201 ATTTTCAACT
Statistics
Matches: 194, Mismatches: 0, Indels: 11
0.95 0.00 0.05
Matches are distributed among these distances:
193 17 0.09
194 52 0.27
195 80 0.41
196 45 0.23
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.30
Consensus pattern (195 bp):
AAATTTTGGCAGCTTCATTCTTTAAGTACCAGTTGTCAAACATCCATGTTCAACACAATATGGAC
ACAATATGTCAATATGACCCTCCAAAACCCTCCAAATGCCGAAAAAATTTAGAAAATTTTGAGCA
ATCGTTCAAATTACATAGCATCCGGATGCAGTTTTCCATTTATACGTATTCCATCTAGACGCTCA
Found at i:90784 original size:2 final size:2
Alignment explanation
Indices: 90777--90810 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
90767 TGATGTGGAA
90777 AT AT AT AT AT AT AT AT A- 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
90811 AGGTGATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:90796 original size:17 final size:17
Alignment explanation
Indices: 90776--90811 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
90766 ATGATGTGGA
90776 AATATATATATATATAT
1 AATATATATATATATAT
90793 AATATATATATATATAT
1 AATATATATATATATAT
90810 AA
1 AA
90812 GGTGATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATATATATATATAT
Found at i:90797 original size:15 final size:15
Alignment explanation
Indices: 90779--90808 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
90769 ATGTGGAAAT
90779 ATATATATATATATA
1 ATATATATATATATA
90794 ATATATATATATATA
1 ATATATATATATATA
90809 TAAGGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:104890 original size:21 final size:21
Alignment explanation
Indices: 104864--104903 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
104854 ATAATTATTT
104864 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
104885 AAAAAATTTAATAAAAATA
1 AAAAAATTAAATAAAAATA
104904 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:105189 original size:29 final size:29
Alignment explanation
Indices: 105157--105248 Score: 68
Period size: 29 Copynumber: 3.2 Consensus size: 29
105147 TTAGCTTGTG
105157 AGTTTGAGTTGACTTGAACTTACTTTTAA
1 AGTTTGAGTTGACTTGAACTTACTTTTAA
* * * *
105186 AGTTTTCAAGTT--C--GAGTCTTTAGCTTGTGA
1 AG-TTT-GAGTTGACTTGA-AC-TTA-CTTTTAA
105216 -GTTTGAGTTGACTTGAACTTACTTTTAA
1 AGTTTGAGTTGACTTGAACTTACTTTTAA
105244 AGTTT
1 AGTTT
105249 TCAAGTTCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 20
0.62 0.11 0.27
Matches are distributed among these distances:
27 6 0.13
28 9 0.20
29 15 0.33
30 9 0.20
31 6 0.13
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.46
Consensus pattern (29 bp):
AGTTTGAGTTGACTTGAACTTACTTTTAA
Found at i:105210 original size:58 final size:58
Alignment explanation
Indices: 105146--105261 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
105136 CTTGATAATT
105146 TTTAGCTTGTGAGTTTGAGTTGACTTGAACTTACTTTTAAAGTTTTCAAGTTCGAGTC
1 TTTAGCTTGTGAGTTTGAGTTGACTTGAACTTACTTTTAAAGTTTTCAAGTTCGAGTC
105204 TTTAGCTTGTGAGTTTGAGTTGACTTGAACTTACTTTTAAAGTTTTCAAGTTCGAGTC
1 TTTAGCTTGTGAGTTTGAGTTGACTTGAACTTACTTTTAAAGTTTTCAAGTTCGAGTC
105262 GAGCTCAGCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.45
Consensus pattern (58 bp):
TTTAGCTTGTGAGTTTGAGTTGACTTGAACTTACTTTTAAAGTTTTCAAGTTCGAGTC
Found at i:105282 original size:58 final size:57
Alignment explanation
Indices: 105162--105289 Score: 152
Period size: 58 Copynumber: 2.2 Consensus size: 57
105152 TTGTGAGTTT
* * * * *
105162 GAGTTGACTTGAACTTACTTTTAAAGTTTTCAAGTTCGAGTCTTTAGCTTGTGAGTTT
1 GAGTTGACTTGAACTTACTTTTAAAGTTTTCAAGTTCGAGTC-TGAGCTAGTCAATTC
105220 GAGTTGACTTGAACTTACTTTTAAAGTTTTCAAGTTCGAGTC-GAGCTCAG-CAATACTC
1 GAGTTGACTTGAACTTACTTTTAAAGTTTTCAAGTTCGAGTCTGAGCT-AGTCAAT--TC
105278 GAGTTCGACTTG
1 GAGTT-GACTTG
105290 GCTCGTTTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
56 6 0.10
57 1 0.02
58 48 0.79
59 6 0.10
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (57 bp):
GAGTTGACTTGAACTTACTTTTAAAGTTTTCAAGTTCGAGTCTGAGCTAGTCAATTC
Found at i:108931 original size:21 final size:21
Alignment explanation
Indices: 108907--108953 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
108897 TACTTACTTG
*
108907 TTTATGTTTAATATT-TTATAT
1 TTTATG-TTAAAATTATTATAT
* *
108928 TTTAAGTTAAAATTATTTTAT
1 TTTATGTTAAAATTATTATAT
108949 TTTAT
1 TTTAT
108954 TTTTTAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTATGTTAAAATTATTATAT
Found at i:115155 original size:18 final size:18
Alignment explanation
Indices: 115132--115210 Score: 121
Period size: 18 Copynumber: 4.6 Consensus size: 18
115122 TGTTTATGAG
115132 GGAATTGGAATATGTGAA
1 GGAATTGGAATATGTGAA
115150 GGAATTGGAATATGTGAA
1 GGAATTGGAATATGTGAA
115168 GGAATTGGAATA--TGAA
1 GGAATTGGAATATGTGAA
*
115184 GGAATTGGATTATGT--A
1 GGAATTGGAATATGTGAA
115200 GGAATTGGAAT
1 GGAATTGGAAT
115211 CCAATTCCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
16 26 0.46
18 31 0.54
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATATGTGAA
Found at i:116026 original size:259 final size:255
Alignment explanation
Indices: 115734--116273 Score: 743
Period size: 264 Copynumber: 2.1 Consensus size: 255
115724 TTTTCACCCT
115734 AAACCCGACCCGACTCGACCCGAATACCACACTTTAAAAACCCGACCCGACCCGAACAAAATAAA
1 AAACCCGACCCGACTCGACCCGAATACCACAC-TTAAAAA----ACCCGACCCGAACAAAATAAA
*
115799 GTTTCATCCGAACCGACCCGAATATATGAATT-A-T-AA-ATCCGACCCGACCCGAAATAATAAA
61 GTTTCATCCGAACCGACCCGAATATATGAATTAATTCAACACCCGACCCGACCCGAAATAATAAA
*
115860 AAATTATTTTTATTTAATAAAAACAGTGAATTAATCCGACCCAACCCGAA-T-TATATATATTTT
126 AAATTATTTTTATTTAATAAAAACAGTGAATTAATCCGACCCAACACGAATTATATATATATTTT
*
115923 CGGGTCGGTCC-GATTTTTTTCACCCTAAACCCGAACCCGATCCGACCCGACCCGAATATCACAC
191 CGGGTCGGTCCAG-TTTTTTTCACCCCAAACCCGAA-CC--T--GACCCGACCCGAATATCACAC
115987 TTAAAA
250 TTAAAA
*
115993 AAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCGAACAAAATAAAGTTTC
1 AAACCCGACCCGACTCGACCCGAATACCACACTTAAAAAACCCGACCCGAACAAAATAAAGTTTC
* *
116058 ATCCGACCCGACCCGAATATATGAATTAGAAATTCAACCCGACCCGACCCGACCCGAAATATTAA
66 ATCCGAACCGACCCGAATATATGAATT---AATTCAA--C-ACCCGACCCGACCCGAAATAATAA
* * *
116123 AAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACATGAATTATATATATATTT
125 AAAATTATTTTTATTTAATAAAAACAGTGAATTAATCCGACCCAACACGAATTATATATATATTT
* **
116188 TCGGGTCGGTCCAGTTTTTTTCACCCCAAACCCGAACCTGACCCTACTTGAATATCACACTTAAA
190 TCGGGTCGGTCCAGTTTTTTTCACCCCAAACCCGAACCTGACCCGACCCGAATATCACACTTAAA
116253 A
255 A
* * *
116254 AAACCAGATCCGACCCGACC
1 AAACCCGACCCGACTCGACC
116274 AAAATAAAAT
Statistics
Matches: 253, Mismatches: 15, Indels: 24
0.87 0.05 0.08
Matches are distributed among these distances:
254 52 0.21
258 8 0.03
259 32 0.13
260 2 0.01
261 41 0.16
263 1 0.00
264 69 0.27
265 3 0.01
266 44 0.17
267 1 0.00
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.23
Consensus pattern (255 bp):
AAACCCGACCCGACTCGACCCGAATACCACACTTAAAAAACCCGACCCGAACAAAATAAAGTTTC
ATCCGAACCGACCCGAATATATGAATTAATTCAACACCCGACCCGACCCGAAATAATAAAAAATT
ATTTTTATTTAATAAAAACAGTGAATTAATCCGACCCAACACGAATTATATATATATTTTCGGGT
CGGTCCAGTTTTTTTCACCCCAAACCCGAACCTGACCCGACCCGAATATCACACTTAAAA
Found at i:116040 original size:37 final size:38
Alignment explanation
Indices: 115956--116042 Score: 149
Period size: 38 Copynumber: 2.3 Consensus size: 38
115946 CCTAAACCCG
*
115956 AACCCGATCCGACCCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGACCCGACCCGAATATCACACTTAAAAA
*
115994 AACCCGACCCGACTCGACCCGAATATCACACTT-AAAA
1 AACCCGACCCGACCCGACCCGAATATCACACTTAAAAA
116031 AACCCGACCCGA
1 AACCCGACCCGA
116043 ACAAAATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 16 0.34
38 31 0.66
ACGTcount: A:0.38, C:0.39, G:0.11, T:0.11
Consensus pattern (38 bp):
AACCCGACCCGACCCGACCCGAATATCACACTTAAAAA
Found at i:118127 original size:19 final size:20
Alignment explanation
Indices: 118103--118141 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
118093 AGTTTATGCA
118103 TTTTAAAAATTT-ATTATTT
1 TTTTAAAAATTTCATTATTT
*
118122 TTTTAAAATTTTCATTATTT
1 TTTTAAAAATTTCATTATTT
118142 CCCTTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAAAATTTCATTATTT
Found at i:121272 original size:20 final size:19
Alignment explanation
Indices: 121249--121294 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
121239 CGATATACCA
121249 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
121269 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
121289 GGTAAA
1 GGTAAA
121295 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:121438 original size:20 final size:19
Alignment explanation
Indices: 121415--121461 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
121405 CGATATAACA
*
121415 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
121435 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
121455 GGTAAAA
1 GGTAAAA
121462 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:121633 original size:24 final size:24
Alignment explanation
Indices: 121606--121658 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
121596 TGTATCGATT
121606 AAATATAA-ATAACATATCCGATGA
1 AAATATAAGATAA-ATATCCGATGA
* *
121630 AAATATAAGCTAAATATCCTATGA
1 AAATATAAGATAAATATCCGATGA
121654 AAATA
1 AAATA
121659 GATAGAACGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (24 bp):
AAATATAAGATAAATATCCGATGA
Found at i:123157 original size:23 final size:23
Alignment explanation
Indices: 123126--123189 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
123116 ATAGGTAAAC
*
123126 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
123149 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
123172 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
123190 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:123196 original size:23 final size:23
Alignment explanation
Indices: 123126--123198 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
123116 ATAGGTAAAC
* **
123126 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
123149 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
123172 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
123195 ATAT
1 ATAT
123199 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:135314 original size:2 final size:2
Alignment explanation
Indices: 135307--135341 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
135297 AAACTTTAAA
135307 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
135342 AGTATAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:135480 original size:21 final size:20
Alignment explanation
Indices: 135456--135503 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
135446 AAACACATGT
*
135456 TTAATAGAATTTATATATTTA
1 TTAATAGAATTTA-ATAATTA
**
135477 TTAATTATTATTTAATAATTA
1 TTAA-TAGAATTTAATAATTA
135498 TTAATA
1 TTAATA
135504 CTAAAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 14 0.61
22 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTAATAGAATTTAATAATTA
Found at i:135490 original size:14 final size:14
Alignment explanation
Indices: 135466--135500 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
135456 TTAATAGAAT
*
135466 TTATATATTTATTAA
1 TTAT-TATTTAATAA
135481 TTATTATTTAATAA
1 TTATTATTTAATAA
135495 TTATTA
1 TTATTA
135501 ATACTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTATTTAATAA
Found at i:137449 original size:29 final size:29
Alignment explanation
Indices: 137409--137480 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
137399 AAAAATCGAA
*
137409 TTAAAAGGGGACGGGGAAAACCGTTTATG
1 TTAAACGGGGACGGGGAAAACCGTTTATG
*
137438 TTAAACGGGGACGGGGAAAACTGTTTATG
1 TTAAACGGGGACGGGGAAAACCGTTTATG
137467 TTAAACGGGGACGG
1 TTAAACGGGGACGG
137481 AGACGGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.32, C:0.11, G:0.36, T:0.21
Consensus pattern (29 bp):
TTAAACGGGGACGGGGAAAACCGTTTATG
Found at i:137600 original size:2 final size:2
Alignment explanation
Indices: 137593--137651 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
137583 TAAATTAAAA
*
137593 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
137634 TT A- AT TT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
137652 CCCGGCCCGA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:160977 original size:21 final size:21
Alignment explanation
Indices: 160944--160983 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
160934 CTTCCTATCC
*
160944 TCCTTTTTATTCTCCTTCTTT
1 TCCTTTTCATTCTCCTTCTTT
* *
160965 TCCTTTTCCTTCTCTTTCT
1 TCCTTTTCATTCTCCTTCT
160984 ATTCTTTGTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.65
Consensus pattern (21 bp):
TCCTTTTCATTCTCCTTCTTT
Found at i:162754 original size:16 final size:14
Alignment explanation
Indices: 162724--162750 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
162714 TTTTGTTTAA
162724 TAACATGATTTTTG
1 TAACATGATTTTTG
162738 TAACATGATTTTT
1 TAACATGATTTTT
162751 TTGTCTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (14 bp):
TAACATGATTTTTG
Found at i:171898 original size:46 final size:46
Alignment explanation
Indices: 171841--171928 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
171831 CGGTAGAGCA
* *
171841 CTACTTAAAATGTTATTTTTTTTACAGAAAATATTAATATCAAATG
1 CTACCTAAAATGTTATTTTTTCTACAGAAAATATTAATATCAAATG
* * *
171887 CTACCTAAAATGTTATTTTTTCTACTGGAAATGTTAATATCA
1 CTACCTAAAATGTTATTTTTTCTACAGAAAATATTAATATCA
171929 CAAATATTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (46 bp):
CTACCTAAAATGTTATTTTTTCTACAGAAAATATTAATATCAAATG
Found at i:174702 original size:20 final size:20
Alignment explanation
Indices: 174648--174703 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
174638 ATTAAAATGG
174648 TTAACTATTGAATTAATTTAAT
1 TTAA-TATTGAATTAATTT-AT
* *
174670 TGAATAATG-ATTAATATT-T
1 TTAATATTGAATTAAT-TTAT
174689 TTAATATTGAATTAA
1 TTAATATTGAATTAA
174704 CAATTAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 8 0.29
20 11 0.39
21 6 0.21
22 3 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (20 bp):
TTAATATTGAATTAATTTAT
Found at i:176288 original size:2 final size:2
Alignment explanation
Indices: 176281--176312 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
176271 AATCGCATCT
*
176281 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
176313 ATTACTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:177923 original size:21 final size:21
Alignment explanation
Indices: 177897--178020 Score: 72
Period size: 21 Copynumber: 5.6 Consensus size: 21
177887 GTTATGTATT
* *
177897 GCAGCAACATCAATTCGAGCA
1 GCAGCAACAGCAATTCGAACA
*
177918 GCAGCAACAGCAATTTGAACA
1 GCAGCAACAGCAATTCGAACA
* * *
177939 GCATCAACAGGAACAGCA-TC-AGCT
1 GCAGCAACA-G--CA--ATTCGAACA
* * *
177963 GCAGCAGCAACATCAATTCGAGCA
1 GCAGCAACAGC---AATTCGAACA
177987 GCAGCAACAGCAATTCGAACA
1 GCAGCAACAGCAATTCGAACA
*
178008 GCATCAACAGCAA
1 GCAGCAACAGCAA
178021 CAGCATCAAC
Statistics
Matches: 78, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
21 48 0.62
22 2 0.03
23 2 0.03
24 24 0.31
25 1 0.01
26 1 0.01
ACGTcount: A:0.40, C:0.28, G:0.19, T:0.12
Consensus pattern (21 bp):
GCAGCAACAGCAATTCGAACA
Found at i:177988 original size:69 final size:69
Alignment explanation
Indices: 177897--178106 Score: 288
Period size: 69 Copynumber: 3.1 Consensus size: 69
177887 GTTATGTATT
* *
177897 GCAGCAACATCAATTCGAGCAGCAGCAACAGCAATTTGAACAGCATCAACAGGAACAGCATCAGC
1 GCAGCAACATCAATTCGAGCAGCAGCAACAGCAATTCGAACAGCATCAACAGCAACAGCATCAGC
177962 TGCA
66 TGCA
177966 GCAGCAACATCAATTCGAGCAGCAGCAACAGCAATTCGAACAGCATCAACAGCAACAGCATCA--
1 GCAGCAACATCAATTCGAGCAGCAGCAACAGCAATTCGAACAGCATCAACAGCAACAGCATCAGC
*
178029 -ACA
66 TGCA
* * * * * * *
178032 GCAACAGCATC-A-GC-TGCAGCAGCAACATCAATTCGAACACCATCAACAGCAACAGCATCCGC
1 GCAGCAACATCAATTCGAGCAGCAGCAACAGCAATTCGAACAGCATCAACAGCAACAGCATCAGC
178094 TGCA
66 TGCA
178098 GCAGCAACA
1 GCAGCAACA
178107 ATTCTTACAG
Statistics
Matches: 125, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
63 42 0.34
64 1 0.01
65 1 0.01
66 20 0.16
69 61 0.49
ACGTcount: A:0.40, C:0.31, G:0.18, T:0.11
Consensus pattern (69 bp):
GCAGCAACATCAATTCGAGCAGCAGCAACAGCAATTCGAACAGCATCAACAGCAACAGCATCAGC
TGCA
Found at i:178024 original size:15 final size:15
Alignment explanation
Indices: 178004--178090 Score: 84
Period size: 15 Copynumber: 5.6 Consensus size: 15
177994 CAGCAATTCG
178004 AACAGCATCAACAGC
1 AACAGCATCAACAGC
178019 AACAGCATCAACAGC
1 AACAGCATCAACAGC
* *
178034 AACAGCATCAGCTGC
1 AACAGCATCAACAGC
* * * *
178049 AGCAGCAACATCAATTC
1 AACAGCATCAAC-A-GC
*
178066 GAACACCATCAACAGC
1 -AACAGCATCAACAGC
178082 AACAGCATC
1 AACAGCATC
178091 CGCTGCAGCA
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
15 45 0.80
16 1 0.02
17 2 0.04
18 8 0.14
ACGTcount: A:0.43, C:0.33, G:0.14, T:0.10
Consensus pattern (15 bp):
AACAGCATCAACAGC
Found at i:178036 original size:21 final size:21
Alignment explanation
Indices: 178012--178058 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
178002 CGAACAGCAT
178012 CAACAGCAACAGCAT-CAACAG
1 CAACAGCAACAGC-TGCAACAG
* *
178033 CAACAGCATCAGCTGCAGCAG
1 CAACAGCAACAGCTGCAACAG
178054 CAACA
1 CAACA
178059 TCAATTCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.43, C:0.34, G:0.17, T:0.06
Consensus pattern (21 bp):
CAACAGCAACAGCTGCAACAG
Found at i:186552 original size:2 final size:2
Alignment explanation
Indices: 186541--186573 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
186531 ACTATAAACA
186541 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
186574 GCATATACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:186986 original size:66 final size:66
Alignment explanation
Indices: 186868--187034 Score: 167
Period size: 66 Copynumber: 2.5 Consensus size: 66
186858 ATTTATAATA
* * *
186868 GGTATCGATACCCCCCATAGGGTATCGGTACCCCTACAGCAATATGGAATTTTCATC-TT-AAGG
1 GGTATCGATACCCCCTATAGGGTATCGATACCCTTACAGCAATATGGAATTTT--TCGTTCAAGG
186931 TGG
64 TGG
** * * **
186934 GGTATCGATACCCCCTATAGGGTATCGATACCCTTATTGCATTCTGTTATTTTTCGTTCAAGGTG
1 GGTATCGATACCCCCTATAGGGTATCGATACCCTTACAGCAATATGGAATTTTTCGTTCAAGGTG
186999 G
66 G
* * * * *
187000 GGTATAGATACACCTTCATAGGGTACCAATACCCT
1 GGTATCGATACCCCCT-ATAGGGTATCGATACCCT
187035 CTGCCCAGAA
Statistics
Matches: 84, Mismatches: 14, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
64 2 0.02
65 2 0.02
66 64 0.76
67 16 0.19
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (66 bp):
GGTATCGATACCCCCTATAGGGTATCGATACCCTTACAGCAATATGGAATTTTTCGTTCAAGGTG
G
Found at i:196334 original size:2 final size:2
Alignment explanation
Indices: 196327--196357 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
196317 ACATACATAC
196327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
196358 AAAAGAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:198746 original size:13 final size:14
Alignment explanation
Indices: 198728--198762 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
198718 TGTGTGTTTA
198728 TGTTCGTTTAT-TG
1 TGTTCGTTTATGTG
*
198741 TGTTCGTTTATGTT
1 TGTTCGTTTATGTG
198755 TGTTCGTT
1 TGTTCGTT
198763 CGTGTTCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.06, C:0.09, G:0.23, T:0.63
Consensus pattern (14 bp):
TGTTCGTTTATGTG
Found at i:198751 original size:23 final size:23
Alignment explanation
Indices: 198683--198775 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 23
198673 TTACTTTTTT
*
198683 TTTATATTCGTTTGTTGTGTTCG
1 TTTATGTTCGTTTGTTGTGTTCG
** *
198706 AATAAGTT--TTT-TTGTG-T-G
1 TTTATGTTCGTTTGTTGTGTTCG
*
198724 TTTATGTTCGTTTATTGTGTTCG
1 TTTATGTTCGTTTGTTGTGTTCG
* *
198747 TTTATGTTTGTTCGTTCGTGTTCG
1 TTTATGTTCGTTTGTT-GTGTTCG
198771 TTTAT
1 TTTAT
198776 TTATTTAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
18 6 0.11
19 1 0.02
20 8 0.15
21 8 0.15
22 1 0.02
23 18 0.33
24 12 0.22
ACGTcount: A:0.11, C:0.08, G:0.22, T:0.60
Consensus pattern (23 bp):
TTTATGTTCGTTTGTTGTGTTCG
Found at i:199350 original size:21 final size:21
Alignment explanation
Indices: 199302--199342 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
199292 CCAGATTCGC
*
199302 AACGTGAACTTCGACTATCGT
1 AACGCGAACTTCGACTATCGT
199323 AACGCGAACTTCGACTATCG
1 AACGCGAACTTCGACTATCG
199343 CTTTGCGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
AACGCGAACTTCGACTATCGT
Found at i:199457 original size:76 final size:76
Alignment explanation
Indices: 199329--199472 Score: 252
Period size: 76 Copynumber: 1.9 Consensus size: 76
199319 TCGTAACGCG
*
199329 AACTTCGACTATCGCTTTGCGATTTACATATTCGCATTACGATAGTCCAAGTTCGCATTGCGATA
1 AACTTCGACTATCGCATTGCGATTTACATATTCGCATTACGATAGTCCAAGTTCGCATTGCGATA
199394 GTCGAATCGCA
66 GTCGAATCGCA
* * *
199405 AACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCTAAGTTCGCGTTGCGATA
1 AACTTCGACTATCGCATTGCGATTTACATATTCGCATTACGATAGTCCAAGTTCGCATTGCGATA
199470 GTC
66 GTC
199473 CAAGTTCGCG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (76 bp):
AACTTCGACTATCGCATTGCGATTTACATATTCGCATTACGATAGTCCAAGTTCGCATTGCGATA
GTCGAATCGCA
Found at i:199488 original size:23 final size:21
Alignment explanation
Indices: 199435--199532 Score: 92
Period size: 21 Copynumber: 4.6 Consensus size: 21
199425 GATTTACATA
* *
199435 TTCGCATTGCGATAGTCTAAG
1 TTCGCGTTGCGATAGTCCAAG
199456 TTCGCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
199477 TTCGCGCGTTGCGATTTATTCCAAA
1 TT--CGCGTTGCGA--TAGTCCAAG
*
199502 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
199521 TTCACGTTGCGA
1 TTCGCGTTGCGA
199533 ATCTGGAAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
19 8 0.12
21 37 0.58
23 10 0.16
25 9 0.14
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:208273 original size:17 final size:17
Alignment explanation
Indices: 208253--208291 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
208243 AATATATATT
208253 TAAT-TTATAATAATAAA
1 TAATATTATAA-AATAAA
*
208270 TAATATTATAACATAAA
1 TAATATTATAAAATAAA
208287 TAATA
1 TAATA
208292 AATAACATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATATTATAAAATAAA
Found at i:214409 original size:202 final size:202
Alignment explanation
Indices: 214020--214432 Score: 654
Period size: 202 Copynumber: 2.0 Consensus size: 202
214010 TTCACCCGAT
* * * *
214020 CCGACCCAACCCGAATATATGACTTAGAAACCCGACCCGACCCGAAATAATAATAAAAAATATTT
1 CCGACCCGACCCGAATATATGACTTAGAAACCCGACCAGACCCGAAACAATAAAAAAAAATATTT
*
214085 TTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATTATATATAGAGGGGTATTATTGTAATTA
66 TTATTCAATAAAAACAATGACTTAATTGAAAAAAAATTATATATAGAGGGGTATTATTGTAATTA
214150 TCCCTAAATATATAGGGAAAGATTATATATATTTTTCGAGTCGGGTCGGACCGGATTTTTTCCAC
131 TCCCTAAATATATAGGGAAAGATTATATATATTTTTCGAGTCGGGTCGGACCGGATTTTTTCCAC
214215 CCTAAAC
196 CCTAAAC
* *
214222 CCGACCCGACCCGAATATATGTCTTAGAAACCCGACTAGACCCGAAACAATAAAAAAATATATAT
1 CCGACCCGACCCGAATATATGACTTAGAAACCCGACCAGACCCGAAACAATAAAAAAA-A-ATAT
214287 TTTTATTCAATAAAAACAATGACTTAATTG-AAAAAAATTATATATAGAGGGGTATTATTGTAAT
64 TTTTATTCAATAAAAACAATGACTTAATTGAAAAAAAATTATATATAGAGGGGTATTATTGTAAT
* * * *
214351 TATCCCTAAATATATACGGTAAA-ATTATAT-TTTTTTTTGAGTCGGGTCAGG-TCGGATTTTTT
129 TATCCCTAAATATATA-GGGAAAGATTATATATATTTTTCGAGTCGGGTC-GGACCGGATTTTTT
214413 CCACCCTAAAC
192 CCACCCTAAAC
*
214424 CCAACCCGA
1 CCGACCCGA
214433 ATAGTGAATT
Statistics
Matches: 195, Mismatches: 12, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
202 97 0.50
203 60 0.31
204 38 0.19
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (202 bp):
CCGACCCGACCCGAATATATGACTTAGAAACCCGACCAGACCCGAAACAATAAAAAAAAATATTT
TTATTCAATAAAAACAATGACTTAATTGAAAAAAAATTATATATAGAGGGGTATTATTGTAATTA
TCCCTAAATATATAGGGAAAGATTATATATATTTTTCGAGTCGGGTCGGACCGGATTTTTTCCAC
CCTAAAC
Found at i:221799 original size:13 final size:13
Alignment explanation
Indices: 221781--221810 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
221771 TATTTAGGTC
*
221781 AGTTTTATGTGTT
1 AGTTTTATGTGTG
221794 AGTTTTATGTGTG
1 AGTTTTATGTGTG
221807 AGTT
1 AGTT
221811 GTTTTGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.57
Consensus pattern (13 bp):
AGTTTTATGTGTG
Found at i:235364 original size:14 final size:15
Alignment explanation
Indices: 235333--235370 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
235323 ATATACATAT
*
235333 AATAATAATAACATG
1 AATAATAATAAAATG
235348 AATAATAA-AAAATG
1 AATAATAATAAAATG
235362 AATAA-AATA
1 AATAATAATA
235371 TCCATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (15 bp):
AATAATAATAAAATG
Found at i:235804 original size:37 final size:36
Alignment explanation
Indices: 235761--235862 Score: 165
Period size: 34 Copynumber: 2.9 Consensus size: 36
235751 ATAGTAGAAC
235761 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
235798 GT-TATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 -TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
235832 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
235863 TAGAACGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
33 1 0.02
34 32 0.52
37 27 0.44
38 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:236709 original size:105 final size:104
Alignment explanation
Indices: 236410--237430 Score: 1479
Period size: 105 Copynumber: 9.9 Consensus size: 104
236400 CATTGTTCCA
* * * ** *
236410 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTTTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG-ATTGGGAAATTG-TTGTTGACAAG
* * * *
236475 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
236516 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGAATCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
*
236577 GCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
236616 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GGATTGGGAAATTGTTGTTGACAAGC
*
236681 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
236721 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
236782 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
236821 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
236882 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
236921 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAA-TTGTTGTTGACAAG
*
236985 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
237026 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
*
237087 GCGGTCCCGT--TCGTGAAGTTGAACTTGCGTTGTCTGG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
237124 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAA-TTGTTGTTGACAAG
*
237188 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
237229 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAATTGTTGTTGACAAGC
237294 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
237334 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GGATTGGG-AAATTG-TTGTTGACAA
* *
237399 CCAGCGGTCCCTTCGTCGTGAAGTTAAACTTG
63 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
237431 ACTCTAAAGC
Statistics
Matches: 843, Mismatches: 51, Indels: 41
0.90 0.05 0.04
Matches are distributed among these distances:
98 63 0.07
100 292 0.35
101 11 0.01
102 18 0.02
103 32 0.04
104 8 0.01
105 339 0.40
106 40 0.05
107 40 0.05
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (104 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:236763 original size:205 final size:206
Alignment explanation
Indices: 236410--237430 Score: 1521
Period size: 205 Copynumber: 5.0 Consensus size: 206
236400 CATTGTTCCA
* * * *
236410 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTTTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAA-TGGGAAA-T-TTTGTTGACAAC
* * * * *
236475 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGTTGTGAAG
63 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
**
236540 TTGAAATTGAATCTGAA-T-GAAA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
128 TTGAAATTGGCTCTGAATTGGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
* *
236602 CTTACGTTGTCTGG
193 CTTGCATTGTCTGG
* * *
236616 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GGAATGGGAAATT-TTGTTGACAACC
* *
236681 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
236746 TGAAATTGGCTCTGAA-T-GAAA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
129 TGAAATTGGCTCTGAATTGGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
236808 TTGCGTTGTCTGG
194 TTGCATTGTCTGG
*
236821 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATTTTGTTGACAAGCAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATGGGAAATTTTGTTGACAACCAG
*
236883 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTA
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
236948 AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGA-ATTGGAAAGTT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
237013 TTGCATTGTCTGG
194 TTGCATTGTCTGG
* *
237026 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATTTTGTTGACAAGCAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATGGGAAATTTTGTTGACAACCAG
*
237088 CGGTCCCGT--TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
237151 AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGA-ATTGGAAAGTT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
237216 TTGCATTGTCTGG
194 TTGCATTGTCTGG
* *
237229 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GAATGGGAAATT-TTGTTGACAACC
*
237294 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * * *
237359 TGAAATTGGCTCTAAAATTGGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
129 TGAAATTGGCTCT-GAATT-GG-AAAGT-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
*
237424 AAACTTG
190 GAACTTG
237431 ACTCTAAAGC
Statistics
Matches: 759, Mismatches: 38, Indels: 30
0.92 0.05 0.04
Matches are distributed among these distances:
200 88 0.12
201 6 0.01
202 1 0.00
203 175 0.23
204 3 0.00
205 303 0.40
206 40 0.05
207 8 0.01
208 21 0.03
210 67 0.09
211 3 0.00
212 43 0.06
213 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (206 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATGGGAAATTTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAATTGGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCATTGTCTGG
Found at i:236956 original size:305 final size:309
Alignment explanation
Indices: 236410--237430 Score: 1623
Period size: 305 Copynumber: 3.3 Consensus size: 309
236400 CATTGTTCCA
* * * *
236410 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTTTGGAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTAGAA-C-TGAAATTGTTTGTTGACAA
* * * * *
236474 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGTTGTGAA
63 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
**
236539 GTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
128 GTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* *
236604 TACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTG
193 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG
236669 TTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
258 TTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
*
236721 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAA-TGAAA-T-TTTGTTGACAAGCA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAGAACTGAAATTGTTTGTTGACAACCA
236782 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
236847 GAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
131 GAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
236912 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAGATTGGAAAGTTGTTG
196 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTG
*
236977 TTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
261 TTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
*
237026 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAA-TGAAA-T-TTTGTTGACAAGCA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAGAACTGAAATTGTTTGTTGACAACCA
*
237087 GCGGTCCCGT--TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
237150 GAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGA-A-T-GAAA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
237215 CTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGT
191 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGT
* * *
237280 TATTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
256 TGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* * *
237334 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAGAACT--G-AAATTGTTTGTTGACAA
*
237399 CCAGCGGTCCCTTCGTCGTGAAGTTAAACTTG
63 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
237431 ACTCTAAAGC
Statistics
Matches: 667, Mismatches: 28, Indels: 24
0.93 0.04 0.03
Matches are distributed among these distances:
303 67 0.10
304 1 0.00
305 316 0.47
306 5 0.01
307 6 0.01
308 189 0.28
309 2 0.00
310 4 0.01
311 34 0.05
312 2 0.00
313 3 0.00
314 1 0.00
315 21 0.03
317 16 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (309 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAGAACTGAAATTGTTTGTTGACAACCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTG
TTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
Found at i:238101 original size:22 final size:22
Alignment explanation
Indices: 238024--238094 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
238014 TTGTGTTTGG
*
238024 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
238046 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
238068 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
238090 TCAAA
1 TCAAA
238095 AGATTGATGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:238810 original size:8 final size:7
Alignment explanation
Indices: 238720--238807 Score: 50
Period size: 8 Copynumber: 11.1 Consensus size: 7
238710 TTTTTGTCCC
238720 TTTTTCT
1 TTTTTCT
*
238727 TTTTGCTT
1 TTTTTC-T
*
238735 TTTGCTTTT
1 TTT--TTCT
238744 TTTTTCT
1 TTTTTCT
238751 TTTGTTCT
1 TTT-TTCT
*
238759 TGTTTCT
1 TTTTTCT
238766 CTTTTTCTT
1 -TTTTTC-T
*
238775 TGTTTTTT
1 T-TTTTCT
238783 TTTTTGCT
1 TTTTT-CT
238791 TTTTTGCT
1 TTTTT-CT
238799 TCTTTTCT
1 T-TTTTCT
238807 T
1 T
238808 CTTGATTGGA
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
7 19 0.30
8 31 0.48
9 13 0.20
10 1 0.02
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (7 bp):
TTTTTCT
Found at i:241935 original size:2 final size:2
Alignment explanation
Indices: 241930--241959 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
241920 GGAAAAAGAA
241930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
241960 CAAAGTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:242489 original size:14 final size:15
Alignment explanation
Indices: 242459--242495 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
242449 ATATACATAT
*
242459 ATAATAATAACATGA
1 ATAATAATAAAATGA
242474 ATAATAA-AAAATGA
1 ATAATAATAAAATGA
242488 ATAA-AATA
1 ATAATAATA
242496 TCCATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.55
15 7 0.35
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (15 bp):
ATAATAATAAAATGA
Found at i:242929 original size:37 final size:36
Alignment explanation
Indices: 242886--242987 Score: 165
Period size: 34 Copynumber: 2.9 Consensus size: 36
242876 ATAGTAGAAC
242886 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
242923 GT-TATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 -TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
242957 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
242988 TAGAACGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
33 1 0.02
34 32 0.52
37 27 0.44
38 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:243818 original size:2 final size:2
Alignment explanation
Indices: 243813--243891 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
243803 AGAATTGTAA
243813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
243855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
243892 AACTTATATT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:244334 original size:9 final size:9
Alignment explanation
Indices: 244322--244371 Score: 55
Period size: 9 Copynumber: 5.0 Consensus size: 9
244312 ATATATAATA
244322 TTTTATATT
1 TTTTATATT
244331 TTTTATATT
1 TTTTATATT
244340 AATTATATATAATT
1 --TT-T-TAT-ATT
244354 TTTTATATT
1 TTTTATATT
244363 TTTTATATT
1 TTTTATATT
244372 AATTATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 21 0.58
10 3 0.08
11 3 0.08
12 3 0.08
13 3 0.08
14 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTATATT
Found at i:244352 original size:32 final size:32
Alignment explanation
Indices: 244311--244435 Score: 189
Period size: 32 Copynumber: 3.9 Consensus size: 32
244301 TATATATATA
244311 TATATATAATATTTTATATTTTTTATATTAAT
1 TATATATAATATTTTATATTTTTTATATTAAT
*
244343 TATATATAATTTTTTATATTTTTTATATTAATT
1 TATATATAATATTTTATATTTTTTATATTAA-T
244376 ATATATATAATATTTTATA-TTTTTATATTAAT
1 -TATATATAATATTTTATATTTTTTATATTAAT
** *
244408 TATATATAATAAATAATATTTTTTATAT
1 TATATATAATATTTTATATTTTTTATAT
244436 ATATTTTTAT
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
31 15 0.18
32 40 0.47
33 13 0.15
34 17 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (32 bp):
TATATATAATATTTTATATTTTTTATATTAAT
Found at i:244441 original size:13 final size:12
Alignment explanation
Indices: 244299--244447 Score: 72
Period size: 11 Copynumber: 13.4 Consensus size: 12
244289 GTCCCGATTA
* *
244299 TATATATATATA
1 TATATATATTTT
*
244311 TATATATAATATT
1 TATATAT-ATTTT
244324 T-TATAT-TTTT
1 TATATATATTTT
* *
244334 TATAT-TAATTA
1 TATATATATTTT
244345 TATATA-ATTTT
1 TATATATATTTT
244356 T-TATAT-TTTT
1 TATATATATTTT
* *
244366 TATAT-TAATTA
1 TATATATATTTT
* *
244377 TATATATAATAT
1 TATATATATTTT
244389 T-T-TATATTTT
1 TATATATATTTT
* *
244399 TATAT-TAATTA
1 TATATATATTTT
***
244410 TATATA-ATAAA
1 TATATATATTTT
244421 TA-ATAT-TTTT
1 TATATATATTTT
244431 TATATATATTTT
1 TATATATATTTT
244443 TATAT
1 TATAT
244448 TTTTAATGAA
Statistics
Matches: 103, Mismatches: 20, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
10 28 0.27
11 43 0.42
12 27 0.26
13 5 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATATTTT
Found at i:253609 original size:17 final size:17
Alignment explanation
Indices: 253582--253620 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
253572 AATTTACAAT
253582 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
253598 TAATTATAAATAATATC
1 TAATTATAAATAATATC
253615 TAATTA
1 TAATTA
253621 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:253749 original size:9 final size:9
Alignment explanation
Indices: 253735--253760 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
253725 TATATTTAAA
253735 GGTTAATTC
1 GGTTAATTC
253744 GGTTAATTC
1 GGTTAATTC
253753 GGTTAATT
1 GGTTAATT
253761 AACCGATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (9 bp):
GGTTAATTC
Found at i:255162 original size:21 final size:21
Alignment explanation
Indices: 255137--255184 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
255127 TAAGTGAAAG
*
255137 ATTGTTAGATTAAAATTTATA
1 ATTGTCAGATTAAAATTTATA
*
255158 ATTGTCGGATTAAAATTTATA
1 ATTGTCAGATTAAAATTTATA
255179 ATTGTC
1 ATTGTC
255185 GAGACCTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (21 bp):
ATTGTCAGATTAAAATTTATA
Found at i:255185 original size:21 final size:21
Alignment explanation
Indices: 255144--255185 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
255134 AAGATTGTTA
255144 GATTAAAATTTATAATTGTCG
1 GATTAAAATTTATAATTGTCG
255165 GATTAAAATTTATAATTGTCG
1 GATTAAAATTTATAATTGTCG
255186 AGACCTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (21 bp):
GATTAAAATTTATAATTGTCG
Found at i:261802 original size:33 final size:31
Alignment explanation
Indices: 261745--261845 Score: 136
Period size: 33 Copynumber: 3.3 Consensus size: 31
261735 CTTTATTTTG
*
261745 TTCGGGTCGGGTCAGGTTTTTTAAGTGTGATA
1 TTCGGGTC-GGTCGGGTTTTTTAAGTGTGATA
261777 TTCGGGTCGAGTCGGAGTTTTTTAAGTGTGATA
1 TTCGGGTCG-GTCGG-GTTTTTTAAGTGTGATA
*
261810 TTCGGGTC-G--GGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGTCGGGTTTTTTAAGTGTGATA
261838 TTCGGGTC
1 TTCGGGTC
261846 ATGTCGAGTT
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
28 24 0.37
29 2 0.03
31 2 0.03
32 12 0.18
33 25 0.38
ACGTcount: A:0.15, C:0.10, G:0.34, T:0.42
Consensus pattern (31 bp):
TTCGGGTCGGTCGGGTTTTTTAAGTGTGATA
Found at i:261827 original size:28 final size:27
Alignment explanation
Indices: 261751--261845 Score: 118
Period size: 28 Copynumber: 3.3 Consensus size: 27
261741 TTTGTTCGGG
*
261751 TCGGGTCAGGTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
261778 TCGGGTCGAGTCGGAGTTTTTTAAGTGTGATAT
1 TC--G--G-GTCGG-GTTTTTTAAGTGTGATAT
261811 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGG-TTTTTTAAGTGTGATAT
261839 TCGGGTC
1 TCGGGTC
261846 ATGTCGAGTT
Statistics
Matches: 60, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
27 3 0.05
28 29 0.48
29 2 0.03
31 2 0.03
32 4 0.07
33 20 0.33
ACGTcount: A:0.16, C:0.09, G:0.33, T:0.42
Consensus pattern (27 bp):
TCGGGTCGGGTTTTTTAAGTGTGATAT
Found at i:262426 original size:18 final size:18
Alignment explanation
Indices: 262403--262445 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
262393 CGACAAATTT
262403 CAATTCCTTCACAGATTC
1 CAATTCCTTCACAGATTC
*
262421 CAATTCCTTCACAGATTT
1 CAATTCCTTCACAGATTC
262439 CAATTCC
1 CAATTCC
262446 CTCATGAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.33, G:0.05, T:0.35
Consensus pattern (18 bp):
CAATTCCTTCACAGATTC
Found at i:265515 original size:24 final size:24
Alignment explanation
Indices: 265471--265517 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
265461 ATAAAGAACC
*
265471 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
265495 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
265518 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:266964 original size:28 final size:26
Alignment explanation
Indices: 266913--266981 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 26
266903 TCATAATCAG
* *
266913 AAATCATATACAAAATTGCAGTAACTAT
1 AAATCATATA-AAAATTACAGTAAAT-T
*
266941 AAATCATATAAAAATATACGGTAAATT
1 AAATCATATAAAAAT-TACAGTAAATT
266968 AGATATCATATAAA
1 A-A-ATCATATAAA
266982 TAGTATTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 7 0.20
28 18 0.51
29 10 0.29
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (26 bp):
AAATCATATAAAAATTACAGTAAATT
Found at i:269988 original size:82 final size:83
Alignment explanation
Indices: 269827--270028 Score: 212
Period size: 82 Copynumber: 2.4 Consensus size: 83
269817 AGTCGATTAT
* * * *
269827 ATTGAAAGTTTTGCCCTTTAATGAGGAAAC-GATGTTAGAATTTACACCTTTAAGGTTGAAGTTC
1 ATTGAAAATTTTACCCTTTAATGAGG-AACTGATGTTAGAATTTACACATTTAAGGTTGAAGTTA
* *
269891 AACTAAAAGAGTTAATTAA
65 AACTAAAAGAATTAATCAA
* * * * * *
269910 ATTG-GAATTTTACCTTTTAATGAGGAACTGGTGTTAGAATTTATATATTTAAGGTTTAA-TTGA
1 ATTGAAAATTTTACCCTTTAATGAGGAACTGATGTTAGAATTTACACATTTAAGGTTGAAGTT-A
* * *
269973 AACTGAAATAATTAATCAT
65 AACTAAAAGAATTAATCAA
* *
269992 ATTGAAAATTTTACCCTTTACTGAGGAACTGAAGTTA
1 ATTGAAAATTTTACCCTTTAATGAGGAACTGATGTTA
270029 CAGTTTGGAG
Statistics
Matches: 96, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
81 5 0.05
82 60 0.62
83 31 0.32
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (83 bp):
ATTGAAAATTTTACCCTTTAATGAGGAACTGATGTTAGAATTTACACATTTAAGGTTGAAGTTAA
ACTAAAAGAATTAATCAA
Found at i:270319 original size:83 final size:82
Alignment explanation
Indices: 270236--270388 Score: 184
Period size: 82 Copynumber: 1.9 Consensus size: 82
270226 ATAATTTTAC
* * *
270236 CCCTT-AATCAGTAACTGAAGTTAGAATTTAGAGCTAGT-AGGTTGAAGTGAAACTTAAAGAATC
1 CCCTTCAATCAGTAACTGAAGTCACAATTTAGAG-T-GTAAGGTTGAAGTGAAACATAAAGAATC
270299 AATTAAATCGGAAATGTTA
64 AATTAAATCGGAAATGTTA
* * * * * * *
270318 CCTTTCAATGAGTAACTGAAGTCACAATTTGGAGTTTAAGGTTGAATTGAAACATCAAGATTCAA
1 CCCTTCAATCAGTAACTGAAGTCACAATTTAGAGTGTAAGGTTGAAGTGAAACATAAAGAATCAA
270383 TTAAAT
66 TTAAAT
270389 TGAATAATTT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
81 1 0.02
82 34 0.58
83 24 0.41
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (82 bp):
CCCTTCAATCAGTAACTGAAGTCACAATTTAGAGTGTAAGGTTGAAGTGAAACATAAAGAATCAA
TTAAATCGGAAATGTTA
Found at i:295437 original size:108 final size:108
Alignment explanation
Indices: 295224--295439 Score: 416
Period size: 108 Copynumber: 2.0 Consensus size: 108
295214 CCTTTTACCC
295224 TTTTAGTTCTCATTCACTTAATTATTCATCCTACCCAACATTTTAATTAATTCCTTCACTTTTCG
1 TTTTAGTTCTCATTCACTTAATTATTCATCCTACCCAACATTTTAATTAATTCCTTCACTTTTCG
295289 ATTAATTTAATTGATCACTGACATATTAAAATCTTAACACTTT
66 ATTAATTTAATTGATCACTGACATATTAAAATCTTAACACTTT
295332 TTTTAGTTCTCATTCACTTAATTATTCATCCTACCCAACATTTTAATTAATTCCTTCACTTTTCG
1 TTTTAGTTCTCATTCACTTAATTATTCATCCTACCCAACATTTTAATTAATTCCTTCACTTTTCG
295397 ATTAATTTAATTTGATCACTGACATATTAAAATCTT-ACACTTT
66 ATTAATTTAA-TTGATCACTGACATATTAAAATCTTAACACTTT
295440 AATCACTAAC
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
108 82 0.77
109 25 0.23
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (108 bp):
TTTTAGTTCTCATTCACTTAATTATTCATCCTACCCAACATTTTAATTAATTCCTTCACTTTTCG
ATTAATTTAATTGATCACTGACATATTAAAATCTTAACACTTT
Found at i:297460 original size:31 final size:31
Alignment explanation
Indices: 297423--297567 Score: 236
Period size: 31 Copynumber: 4.7 Consensus size: 31
297413 AGTCCATAGA
* * * *
297423 TTCCGAAGAACCTAGGTAATCATTCCATATG
1 TTCCGAAGAACATAGGTAAACAGTCCGTATG
* *
297454 TCCCGAAGGACATAGGTAAACAGTCCGTATG
1 TTCCGAAGAACATAGGTAAACAGTCCGTATG
297485 TTCCGAAGAACATAGGTAAACAGTCCGTATG
1 TTCCGAAGAACATAGGTAAACAGTCCGTATG
297516 TTCCGAAGAACATAGGTAAACAGTCCGTATG
1 TTCCGAAGAACATAGGTAAACAGTCCGTATG
297547 TTCCGAAGAACATAGGTAAAC
1 TTCCGAAGAACATAGGTAAAC
297568 CCTCGACCCT
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 106 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (31 bp):
TTCCGAAGAACATAGGTAAACAGTCCGTATG
Found at i:298447 original size:21 final size:21
Alignment explanation
Indices: 298417--298461 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
298407 ATTCTGTCGT
* *
298417 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
298438 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
298459 TTG
1 TTG
298462 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:308605 original size:23 final size:23
Alignment explanation
Indices: 308571--308618 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
308561 GTAGGCTCTG
*
308571 AGGCCCCGAGAACCTTCTTGGGT
1 AGGCCCCAAGAACCTTCTTGGGT
*
308594 AGGCCCCAAGAACTTTCTTGGGT
1 AGGCCCCAAGAACCTTCTTGGGT
308617 AG
1 AG
308619 ACTCTCAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.27, G:0.29, T:0.23
Consensus pattern (23 bp):
AGGCCCCAAGAACCTTCTTGGGT
Found at i:317454 original size:24 final size:24
Alignment explanation
Indices: 317427--317476 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
317417 TATTATTTTT
317427 AAAAAA-TATTTTTAAAAGTAAAAA
1 AAAAAATTA-TTTTAAAAGTAAAAA
* *
317451 AAAAAATTATTTTAAAATTATAAA
1 AAAAAATTATTTTAAAAGTAAAAA
317475 AA
1 AA
317477 TATAGTTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (24 bp):
AAAAAATTATTTTAAAAGTAAAAA
Found at i:325944 original size:23 final size:23
Alignment explanation
Indices: 325918--325968 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
325908 GCCATCCGAC
*
325918 CGAGGCCACCCGAACGAGCTATG
1 CGAGGCCACCCGAACAAGCTATG
* * * *
325941 CGAGGGCATCTGAGCAAGCTATG
1 CGAGGCCACCCGAACAAGCTATG
325964 CGAGG
1 CGAGG
325969 GAATCCGAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.35, T:0.12
Consensus pattern (23 bp):
CGAGGCCACCCGAACAAGCTATG
Found at i:326071 original size:23 final size:23
Alignment explanation
Indices: 326045--326119 Score: 84
Period size: 23 Copynumber: 3.4 Consensus size: 23
326035 TTGCCCTCGA
326045 ATGCCATCGCATAGCTCGTTCGG
1 ATGCCATCGCATAGCTCGTTCGG
* *
326068 ATGCCCTCACATAGCTCGTTCGG
1 ATGCCATCGCATAGCTCGTTCGG
* *
326091 ATGGCATCGGAT-GCTC--TCGG
1 ATGCCATCGCATAGCTCGTTCGG
*
326111 ATGGCATCG
1 ATGCCATCG
326120 GATGCTTTCG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 13 0.28
22 4 0.09
23 29 0.63
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.25
Consensus pattern (23 bp):
ATGCCATCGCATAGCTCGTTCGG
Found at i:326112 original size:20 final size:20
Alignment explanation
Indices: 326087--326140 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
326077 CATAGCTCGT
326087 TCGGATGGCATCGGATGCTC
1 TCGGATGGCATCGGATGCTC
*
326107 TCGGATGGCATCGGATGCTT
1 TCGGATGGCATCGGATGCTC
*
326127 TCGGATGGCCTCGG
1 TCGGATGGCATCGG
326141 TCGGATGGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.13, C:0.24, G:0.37, T:0.26
Consensus pattern (20 bp):
TCGGATGGCATCGGATGCTC
Found at i:326146 original size:14 final size:14
Alignment explanation
Indices: 326127--326168 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
326117 TCGGATGCTT
326127 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
326141 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
326155 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
326169 ATGCCCAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:326508 original size:29 final size:29
Alignment explanation
Indices: 326466--326554 Score: 160
Period size: 29 Copynumber: 3.1 Consensus size: 29
326456 AACACCCCAC
326466 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
*
326495 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
*
326524 AGGTCGCTCGGATGCCATGACGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
326553 AG
1 AG
326555 CTCACTGTAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.19, C:0.35, G:0.30, T:0.16
Consensus pattern (29 bp):
AGGTCGCTCGGATGCCATGGCGACCTCCA
Found at i:330767 original size:26 final size:26
Alignment explanation
Indices: 330708--330768 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
330698 TTATAGTTTT
330708 ATAAAAA-TTTAAGGGTTTTTTTTAA
1 ATAAAAATTTTAAGGGTTTTTTTTAA
* *
330733 A-ATATAATTTTAA-GTTTTTATTTTAA
1 ATA-AAAATTTTAAGGGTTTT-TTTTAA
330759 ATAAAAATTT
1 ATAAAAATTT
330769 CAAAATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
24 1 0.03
25 9 0.31
26 18 0.62
27 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.51
Consensus pattern (26 bp):
ATAAAAATTTTAAGGGTTTTTTTTAA
Found at i:331506 original size:22 final size:21
Alignment explanation
Indices: 331469--331520 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
331459 TTCAGAATAT
*
331469 AAAAAATTTCTCAAAAACAAC
1 AAAAAATGTCTCAAAAACAAC
* *
331490 AAATAAATGTCTTAAAAAGAAC
1 AAA-AAATGTCTCAAAAACAAC
331512 AAAAAATGT
1 AAAAAATGT
331521 ACTGAACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.21
Consensus pattern (21 bp):
AAAAAATGTCTCAAAAACAAC
Found at i:334385 original size:117 final size:119
Alignment explanation
Indices: 334218--334431 Score: 326
Period size: 117 Copynumber: 1.8 Consensus size: 119
334208 TAATTAATTT
* *
334218 TTTAACTGTTAATCGAACTGATTTTTTATAAAAAAAATATCAATCGAATTGAACAAAGTTT-GAT
1 TTTAACTGTTAACCGAACTGA-TTTTTATAAAAAAAATATCAATCAAATTGAACAAA-TTTCGAT
* * *
334282 TAATTCAACAGGTAAAATTAAATTTTTATATATTTTTTGAATTAATTAAATTTTTC
64 TAATTCAACAGGTAAAACTAAATATATATATATTTTTTGAATTAATTAAATTTTTC
*
334338 TTTAACTGTTAACCGAATTGA-TTTT-TAAAAAAAATATCAATCAAATTGAACAAATTTCGATTA
1 TTTAACTGTTAACCGAACTGATTTTTATAAAAAAAATATCAATCAAATTGAACAAATTTCGATTA
*
334401 ATTCAACCGGTAAAACTAAATATATATATAT
66 ATTCAACAGGTAAAACTAAATATATATATAT
334432 ATATATATAT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
116 3 0.03
117 60 0.70
118 4 0.05
120 19 0.22
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (119 bp):
TTTAACTGTTAACCGAACTGATTTTTATAAAAAAAATATCAATCAAATTGAACAAATTTCGATTA
ATTCAACAGGTAAAACTAAATATATATATATTTTTTGAATTAATTAAATTTTTC
Found at i:334427 original size:2 final size:2
Alignment explanation
Indices: 334420--334451 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
334410 GTAAAACTAA
334420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
334452 TATTTTTAGA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:334589 original size:2 final size:2
Alignment explanation
Indices: 334582--334616 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
334572 TATGTATTTA
334582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
334617 TTAATATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:334623 original size:14 final size:15
Alignment explanation
Indices: 334580--334630 Score: 68
Period size: 16 Copynumber: 3.4 Consensus size: 15
334570 AATATGTATT
334580 TAATATATATATATA
1 TAATATATATATATA
334595 TATATATATATATATA
1 TA-ATATATATATATA
* *
334611 TAATATTTA-ATATT
1 TAATATATATATATA
334625 TAATAT
1 TAATAT
334631 CTTCAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 10 0.30
15 8 0.24
16 15 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TAATATATATATATA
Found at i:335960 original size:20 final size:20
Alignment explanation
Indices: 335924--335961 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
335914 ATCTTATTCC
**
335924 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
335944 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
335962 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:352248 original size:21 final size:21
Alignment explanation
Indices: 352224--352264 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
352214 GGTAAAAAAT
*
352224 TACCTAAAACATTATTATTTC
1 TACCTAAAACATTAATATTTC
352245 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
352265 TTTAACAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:354626 original size:6 final size:6
Alignment explanation
Indices: 354615--354640 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
354605 AGAATAAAAT
354615 ATATGC ATATGC ATATGC ATATGC AT
1 ATATGC ATATGC ATATGC ATATGC AT
354641 TGTGTAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (6 bp):
ATATGC
Found at i:355822 original size:33 final size:33
Alignment explanation
Indices: 355774--355862 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
355764 AGTTGAAAGG
* * * *
355774 GAGGAAGGCGAGTTCTTCCCAGATGGGGACGTC
1 GAGGAAGGTGAGTTCTTACCAAATGGGAACGTC
*
355807 GAGGAAGGTGGGTTCTTACCAAATGGGAACGTC
1 GAGGAAGGTGAGTTCTTACCAAATGGGAACGTC
*
355840 GAGGAAGGTGAGTTCTTTCCAAA
1 GAGGAAGGTGAGTTCTTACCAAA
355863 GGGGGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (33 bp):
GAGGAAGGTGAGTTCTTACCAAATGGGAACGTC
Found at i:357761 original size:3 final size:3
Alignment explanation
Indices: 357742--357776 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
357732 ATATTATAAA
357742 TAT TAAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
357777 CTTTAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 24 0.80
4 6 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:361050 original size:21 final size:21
Alignment explanation
Indices: 361028--361121 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
361018 CCAAGGATGA
*
361028 GAAGACCATTCATAAAGGCGA-
1 GAAGACCATTCATAAAGAC-AT
361049 GAAGACCATTCATAAAGACAT
1 GAAGACCATTCATAAAGACAT
361070 GAAGACTC-TTCATAAAGACAT
1 GAAGAC-CATTCATAAAGACAT
*
361091 GAAGACCCTTCATAAAGACAT
1 GAAGACCATTCATAAAGACAT
* *
361112 GGAGATCATT
1 GAAGACCATT
361122 TCGCATTGGA
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
20 2 0.03
21 63 0.95
22 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (21 bp):
GAAGACCATTCATAAAGACAT
Found at i:362971 original size:20 final size:21
Alignment explanation
Indices: 362938--362984 Score: 87
Period size: 20 Copynumber: 2.3 Consensus size: 21
362928 TTTGAAAATG
362938 TTTTTGTTGTTTTTTCTCAAC
1 TTTTTGTTGTTTTTTCTCAAC
362959 TTTTTGTTG-TTTTTCTCAAC
1 TTTTTGTTGTTTTTTCTCAAC
362979 TTTTTG
1 TTTTTG
362985 AAAGGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.09, C:0.13, G:0.11, T:0.68
Consensus pattern (21 bp):
TTTTTGTTGTTTTTTCTCAAC
Found at i:363712 original size:18 final size:19
Alignment explanation
Indices: 363681--363739 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 19
363671 TGTAGAAAGA
363681 GAAAAAGAAAAGAAAAAAT
1 GAAAAAGAAAAGAAAAAAT
*
363700 GAAAAA-AAGAGAAAAAAAT
1 GAAAAAGAAAAG-AAAAAAT
*
363719 GGAAATAAAAAAATGAAAAAA
1 -GAAA-AAGAAAA-GAAAAAA
363740 AAAAAAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 4 0.12
19 13 0.39
20 4 0.12
21 2 0.06
22 9 0.27
23 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (19 bp):
GAAAAAGAAAAGAAAAAAT
Found at i:363717 original size:13 final size:13
Alignment explanation
Indices: 363676--363750 Score: 55
Period size: 13 Copynumber: 5.6 Consensus size: 13
363666 AGAAATGTAG
*
363676 AAAGAGAAAAAGA
1 AAAGAGAAAAAAA
363689 AAAGA-AAAAATGAA
1 AAAGAGAAAAA--AA
* *
363703 AAAAAGAGAAAAA
1 AAAGAGAAAAAAA
*
363716 AATG-GAAATAAAA
1 AAAGAGAAA-AAAA
*
363729 AAATGAAAAAAAAA
1 AAA-GAGAAAAAAA
363743 AAAGAGAA
1 AAAGAGAA
363751 GGAAAGAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
12 8 0.17
13 19 0.40
14 13 0.28
15 7 0.15
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (13 bp):
AAAGAGAAAAAAA
Found at i:363744 original size:14 final size:14
Alignment explanation
Indices: 363711--363745 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
363701 AAAAAAAGAG
* *
363711 AAAAAAATGGAAAT
1 AAAAAAATGAAAAA
363725 AAAAAAATGAAAAA
1 AAAAAAATGAAAAA
363739 AAAAAAA
1 AAAAAAA
363746 GAGAAGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (14 bp):
AAAAAAATGAAAAA
Found at i:365223 original size:124 final size:125
Alignment explanation
Indices: 365003--365245 Score: 355
Period size: 124 Copynumber: 2.0 Consensus size: 125
364993 TGTGATATGT
* * *
365003 TGGGGCATGACTGAACCCACATCATGTTGAGATGGCAAGATTCAAACCAAGGAGGCATGAAGAAT
1 TGGGGAATGACTGAACCCACATCATATTGAGATGGCAAGATTCAAACCAAGAAGGCATGAAGAAT
* * *
365068 GAGCCTTACAATTTGAGGTGATGAGGCATTTTGAAGGCCCGTACCAGT-TAAGACACTGA
66 AAGCCTTACAATCTGAGATGATGAGGCATTTTGAAGGCCCGTACCAGTATAAGACACTGA
* * * *
365127 TGGGGAATGACTGAACCCACATCATATTGAGA-GGACAAGATTTAGACCAAGAAGGCATTAAGAG
1 TGGGGAATGACTGAACCCACATCATATTGAGATGG-CAAGATTCAAACCAAGAAGGCATGAAGAA
* *
365191 TAAGCCTTACAATCTGAGATGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGA
65 TAAGCCTTACAATCTGAGATGATGAGGCATTTTGAAGGCCCGTACCAGTATAAGA
365246 TGATGTTGCG
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
123 2 0.02
124 98 0.93
125 5 0.05
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (125 bp):
TGGGGAATGACTGAACCCACATCATATTGAGATGGCAAGATTCAAACCAAGAAGGCATGAAGAAT
AAGCCTTACAATCTGAGATGATGAGGCATTTTGAAGGCCCGTACCAGTATAAGACACTGA
Done.