Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 16 of 26
Found at i:6252861 original size:24 final size:24
Alignment explanation
Indices: 6252774--6252861 Score: 90
Period size: 24 Copynumber: 3.6 Consensus size: 24
6252764 TTGTATATTA
*
6252774 TATATTTTATTTTAGTTT-ATTTTACT
1 TATATTTTA-TTTATTTTAATTTT--T
* **
6252800 TATATTATATAAATTTTAATTTTT
1 TATATTTTATTTATTTTAATTTTT
6252824 TATATTTTATTTATTTTAATTTTT
1 TATATTTTATTTATTTTAATTTTT
6252848 TAT-TTTTATATTAT
1 TATATTTTAT-TTAT
6252862 ATATTTTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
23 6 0.11
24 29 0.55
25 5 0.09
26 13 0.25
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (24 bp):
TATATTTTATTTATTTTAATTTTT
Found at i:6252880 original size:13 final size:14
Alignment explanation
Indices: 6252553--6252881 Score: 59
Period size: 15 Copynumber: 22.8 Consensus size: 14
6252543 TTTAATACAT
*
6252553 TTATATTTTTTATTA
1 TTATATATTTTA-TA
6252568 TTA-AT-TTTTATA
1 TTATATATTTTATA
*
6252580 TAATATCATCTCTTA-A
1 TTATAT-AT-T-TTATA
*
6252596 ATATAT-TTTTA-A
1 TTATATATTTTATA
6252608 TGTCATATATTTTAT-
1 T-T-ATATATTTTATA
6252623 TT-T-TA-TTTATTA
1 TTATATATTTTA-TA
6252635 TTATA-ATCTTATATA
1 TTATATAT-TT-TATA
*
6252650 TTTTAT-TTTTA-A
1 TTATATATTTTATA
* *
6252662 TATATTTATTTTTTA
1 T-TATATATTTTATA
6252677 TTAT-TAATTTTTATA
1 TTATAT-A-TTTTATA
6252692 TTATATCATCTCTTA-A
1 TTATAT-AT-T-TTATA
*
6252708 ATATAT-TTTTA-A
1 TTATATATTTTATA
*
6252720 TGTCATATATTTTATTT
1 T-T-ATATATTTTA-TA
* *
6252737 TTAATATATTTATTTT
1 TT-ATATATTT-TATA
6252753 TTATTATTAATTTGTATA
1 TTA-TA-T-ATTT-TATA
*
6252771 TTATATATTTTATT
1 TTATATATTTTATA
* *
6252785 TTAGTTTATTTTA-C
1 TTA-TATATTTTATA
* *
6252799 TTATAT-TATATAAA
1 TTATATAT-TTTATA
* *
6252813 TTTTAATTTTTTATA
1 TTAT-ATATTTTATA
*
6252828 TTTTATTTATTTTA-A
1 --TTATATATTTTATA
* *
6252843 TTTTTTATTTTTATA
1 TTATATA-TTTTATA
*
6252858 TTATATATTTTATT
1 TTATATATTTTATA
6252872 TTA-ATATTTT
1 TTATATATTTT
6252882 TATAATAATA
Statistics
Matches: 237, Mismatches: 34, Indels: 88
0.66 0.09 0.25
Matches are distributed among these distances:
10 4 0.02
11 3 0.01
12 18 0.08
13 37 0.16
14 49 0.21
15 63 0.27
16 40 0.17
17 14 0.06
18 9 0.04
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (14 bp):
TTATATATTTTATA
Found at i:6252882 original size:14 final size:14
Alignment explanation
Indices: 6252812--6252884 Score: 60
Period size: 15 Copynumber: 5.1 Consensus size: 14
6252802 TATTATATAA
*
6252812 ATTTTAATTTTTTAT
1 ATTTTAATATTTT-T
* *
6252827 ATTTTATTTATTTTA
1 ATTTTA-ATATTTTT
*
6252842 ATTTT-TTATTTTT
1 ATTTTAATATTTTT
*
6252855 ATATT-ATATATTTT
1 ATTTTAATAT-TTTT
6252869 ATTTTAATATTTTT
1 ATTTTAATATTTTT
6252883 AT
1 AT
6252885 AATAATATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
13 14 0.29
14 14 0.29
15 15 0.31
16 5 0.10
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTAATATTTTT
Found at i:6252897 original size:19 final size:19
Alignment explanation
Indices: 6252873--6252915 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6252863 TATTTTATTT
*
6252873 TAATAT-TTTTATAATAATA
1 TAATATATTTT-TAATAAAA
6252892 TAATATATTTTTAATAAAA
1 TAATATATTTTTAATAAAA
6252911 TAATA
1 TAATA
6252916 AAGTTAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATATATTTTTAATAAAA
Found at i:6252898 original size:34 final size:33
Alignment explanation
Indices: 6252833--6252902 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
6252823 TTATATTTTA
** * *
6252833 TTTATTTTAATTTTTTATTTTTATATTATATAT
1 TTTATTTTAATTTTTTATAATAATATAATATAT
6252866 TTTATTTTAATATTTTTATAATAATATAATATAT
1 TTTATTTTAAT-TTTTTATAATAATATAATATAT
6252900 TTT
1 TTT
6252903 TAATAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 11 0.34
34 21 0.66
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (33 bp):
TTTATTTTAATTTTTTATAATAATATAATATAT
Found at i:6253352 original size:2 final size:2
Alignment explanation
Indices: 6253345--6253378 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6253335 TCTTGCCCAA
6253345 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
6253379 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6259826 original size:98 final size:98
Alignment explanation
Indices: 6259692--6259889 Score: 342
Period size: 98 Copynumber: 2.0 Consensus size: 98
6259682 ATTTTCAATA
* *
6259692 TCATAAATTAACATGCTATCCCATTTAATAATATTTGCATTTCAGACCACTTAATGGGATACTTG
1 TCATAAATTAACATGCTATCCCATTTAATAACATTTGCATTTCAGACAACTTAATGGGATACTTG
* *
6259757 AACATGGGTAATACACATTTTGCATGCTTAACC
66 AACATGGGTAATAAACATTTTGCATACTTAACC
* *
6259790 TCATAAATTAACATGCTATTCCATTTGATAACATTTGCATTTCAGACAACTTAATGGGATACTTG
1 TCATAAATTAACATGCTATCCCATTTAATAACATTTGCATTTCAGACAACTTAATGGGATACTTG
6259855 AACATGGGTAATAAACATTTTGCATACTTAACC
66 AACATGGGTAATAAACATTTTGCATACTTAACC
6259888 TC
1 TC
6259890 CAACCTTAAT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (98 bp):
TCATAAATTAACATGCTATCCCATTTAATAACATTTGCATTTCAGACAACTTAATGGGATACTTG
AACATGGGTAATAAACATTTTGCATACTTAACC
Found at i:6261151 original size:54 final size:54
Alignment explanation
Indices: 6261069--6261177 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
6261059 CAACAAAAGG
6261069 TTCAAGCTCGATCTCTATTAAATTTTAATCAATTTGTCCATTTTCTCATATTCC
1 TTCAAGCTCGATCTCTATTAAATTTTAATCAATTTGTCCATTTTCTCATATTCC
* *
6261123 TTCAAGCTCGATCTCTATTAAATTTTAATCAATTTGTCTATTTTCTTATATTCC
1 TTCAAGCTCGATCTCTATTAAATTTTAATCAATTTGTCCATTTTCTCATATTCC
6261177 T
1 T
6261178 ATAGGAATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.49
Consensus pattern (54 bp):
TTCAAGCTCGATCTCTATTAAATTTTAATCAATTTGTCCATTTTCTCATATTCC
Found at i:6262343 original size:15 final size:15
Alignment explanation
Indices: 6262313--6262364 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
6262303 CGTTTGGTAC
6262313 ATTACAATGCAATGTG
1 ATTACAA-GCAATGTG
*
6262329 ATTACAAGTAATGTG
1 ATTACAAGCAATGTG
*
6262344 ATTGCAAGCAATGTG
1 ATTACAAGCAATGTG
6262359 ATTACA
1 ATTACA
6262365 GGAAAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 25 0.78
16 7 0.22
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (15 bp):
ATTACAAGCAATGTG
Found at i:6262610 original size:21 final size:21
Alignment explanation
Indices: 6262584--6262651 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
6262574 CATATATTTT
6262584 TTTTATTTTATTATTATAATA
1 TTTTATTTTATTATTATAATA
*
6262605 TTTTATATTATT-TT-TAATA
1 TTTTATTTTATTATTATAATA
6262624 TATTTATATTT-TTATTATTAAT-
1 T-TTTAT-TTTATTATTA-TAATA
6262646 TTTTAT
1 TTTTAT
6262652 ATAATATCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 6 0.15
20 9 0.22
21 20 0.50
22 1 0.03
23 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTATTTTATTATTATAATA
Found at i:6262627 original size:14 final size:14
Alignment explanation
Indices: 6262608--6262717 Score: 63
Period size: 14 Copynumber: 7.8 Consensus size: 14
6262598 TATAATATTT
6262608 TATATTATTTTTAA
1 TATATTATTTTTAA
*
6262622 TATATTTATATTTTTA
1 TATA-TTAT-TTTTAA
6262638 T-TATTAATTTTTATA
1 TATATT-ATTTTTA-A
*
6262653 TAATATCATATTTTAA
1 T-ATATTAT-TTTTAA
6262669 -ATA-TATTTTTAA
1 TATATTATTTTTAA
*
6262681 TGTCA-T-TTTTTAA
1 TAT-ATTATTTTTAA
*
6262694 TATATT-TTTTATAT
1 TATATTATTTT-TAA
6262708 TATA-TATTTT
1 TATATTATTTT
6262718 ATTTTATTGT
Statistics
Matches: 77, Mismatches: 7, Indels: 24
0.71 0.06 0.22
Matches are distributed among these distances:
12 7 0.09
13 18 0.23
14 25 0.32
15 10 0.13
16 9 0.12
17 8 0.10
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (14 bp):
TATATTATTTTTAA
Found at i:6262635 original size:17 final size:16
Alignment explanation
Indices: 6262613--6262654 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 16
6262603 TATTTTATAT
6262613 TATTTTTAATATATTTA
1 TATTTTT-ATATATTTA
6262630 TATTTTTAT-TA-TTA
1 TATTTTTATATATTTA
6262644 -ATTTTTATATA
1 TATTTTTATATA
6262655 ATATCATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 2 0.08
16 2 0.08
17 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTTATATATTTA
Found at i:6262643 original size:29 final size:30
Alignment explanation
Indices: 6262605--6262681 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
6262595 TATTATAATA
*
6262605 TTTTATATTATTTTTAATAT-AT-TTATAT
1 TTTTATATTATTTTTAATATAATATCATAT
6262633 TTTTATTATTAATTTTT-ATATAATATCATA-
1 TTTTA-TATT-ATTTTTAATATAATATCATAT
*
6262663 TTTTAAATATATTTTTAAT
1 TTTTATAT-TATTTTTAAT
6262682 GTCATTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
28 5 0.12
29 16 0.39
30 16 0.39
31 4 0.10
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (30 bp):
TTTTATATTATTTTTAATATAATATCATAT
Found at i:6262680 original size:12 final size:11
Alignment explanation
Indices: 6262660--6262707 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
6262650 ATATAATATC
*
6262660 ATATTTTAAAT
1 ATATTTTTAAT
6262671 ATATTTTTAAT
1 ATATTTTTAAT
*
6262682 GTCATTTTTTAAT
1 AT-A-TTTTTAAT
*
6262695 ATATTTTTTAT
1 ATATTTTTAAT
6262706 AT
1 AT
6262708 TATATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 20 0.65
12 2 0.06
13 9 0.29
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (11 bp):
ATATTTTTAAT
Found at i:6262681 original size:25 final size:25
Alignment explanation
Indices: 6262653--6262712 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
6262643 AATTTTTATA
6262653 TAATATCATATTTTAAATATATTTT
1 TAATATCATATTTTAAATATATTTT
* *
6262678 TAATGTCAT-TTTTTAATATATTTT
1 TAATATCATATTTTAAATATATTTT
* *
6262702 TTATATTATAT
1 TAATATCATAT
6262713 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (25 bp):
TAATATCATATTTTAAATATATTTT
Found at i:6262725 original size:109 final size:107
Alignment explanation
Indices: 6262514--6262725 Score: 297
Period size: 109 Copynumber: 2.0 Consensus size: 107
6262504 ATATAAGTTT
6262514 ATATATTTATATTTTTTATATAATTTTTATATATATCATTCTTAAATATATTTTTAATGTCATAT
1 ATATATTTATATTTTTTATATAATTTTTATATATATCATTCTTAAATATATTTTTAATGTCATAT
* *
6262579 ATTTTTTTTATTTTATTATTATAATATTTTATATTATTTTTA
66 ATTTTATATATTTTATTATTATAATATTTTATATTATTTTTA
*
6262621 ATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATGTC
1 ATATATTTATATTTTTTA-TA-TAATTTTTATAT-ATATCAT-TCTTAAATATATTTTTAATGTC
* *
6262685 AT-T-TTTTAATATATTTTTTATATTAT-ATATTTTATTTTATT
62 ATATATTTT-ATATATTTTAT-TATTATAATATTTTATATTATT
6262726 GTTTTACCTA
Statistics
Matches: 94, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
106 6 0.06
107 13 0.14
108 16 0.17
109 30 0.32
110 29 0.31
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (107 bp):
ATATATTTATATTTTTTATATAATTTTTATATATATCATTCTTAAATATATTTTTAATGTCATAT
ATTTTATATATTTTATTATTATAATATTTTATATTATTTTTA
Found at i:6262742 original size:110 final size:106
Alignment explanation
Indices: 6262521--6262760 Score: 274
Period size: 110 Copynumber: 2.2 Consensus size: 106
6262511 TTTATATATT
*
6262521 TATAT-TTTTTATATAATTTTTATATATATCATTCTTAAATATATTTTTAATGTCATATATTTTT
1 TATATATTTTTATATAATTTTTATATATATCATTCTTAAATATATTTTTAATGTCATATATTTTA
* *
6262585 TTTATTTTATTATTATAATATTTTATATTATTTTTAATATA
66 TATATTTTATTATTATAATATTTTATATTATTTTTAACATA
* *
6262626 TTTATATTTTTATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATGTCAT-T-T
1 TATATATTTTTA-TA-TAATTTTTATAT-ATATCAT-TCTTAAATATATTTTTAATGTCATATAT
* * * *
6262689 TTTAATATATTTTTTATATTAT-ATATTTTATTTTATTGTTTTACCTA
62 TTT-ATATATTTTAT-TATTATAATATTTTATATTATT-TTTAACATA
***
6262736 TATATATAAATAT-TAATTTTTATAT
1 TATATATTTTTATATAATTTTTATAT
6262761 TTTATTTTTT
Statistics
Matches: 114, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
105 4 0.04
106 6 0.05
107 14 0.12
108 16 0.14
109 31 0.27
110 43 0.38
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (106 bp):
TATATATTTTTATATAATTTTTATATATATCATTCTTAAATATATTTTTAATGTCATATATTTTA
TATATTTTATTATTATAATATTTTATATTATTTTTAACATA
Found at i:6270713 original size:3 final size:3
Alignment explanation
Indices: 6270705--6270736 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6270695 TCCATAATGC
6270705 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6270737 ATTTATCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:6285560 original size:2 final size:2
Alignment explanation
Indices: 6285553--6285583 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6285543 ACTCGTGTAT
*
6285553 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6285584 TAAATTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6285926 original size:11 final size:11
Alignment explanation
Indices: 6285910--6285934 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6285900 TATAACATGA
6285910 TTTTTTCTTTT
1 TTTTTTCTTTT
6285921 TTTTTTCTTTT
1 TTTTTTCTTTT
6285932 TTT
1 TTT
6285935 CCACATACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:6289995 original size:24 final size:24
Alignment explanation
Indices: 6289950--6289995 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
6289940 GGGAGCAAAG
*
6289950 GAGGAGGAGGAGGATGCAGAGGGA
1 GAGGAGGAGGAGGAGGCAGAGGGA
6289974 GAGGAGGAGGAGGAAGGC-GAGG
1 GAGGAGGAGGAGG-AGGCAGAGG
6289996 AAGTGTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.33, C:0.04, G:0.61, T:0.02
Consensus pattern (24 bp):
GAGGAGGAGGAGGAGGCAGAGGGA
Found at i:6294067 original size:17 final size:17
Alignment explanation
Indices: 6294045--6294077 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6294035 CCACAGGCCA
6294045 TACCCATAGAGGCAAAG
1 TACCCATAGAGGCAAAG
6294062 TACCCATAGAGGCAAA
1 TACCCATAGAGGCAAA
6294078 AAAAAGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.24, G:0.21, T:0.12
Consensus pattern (17 bp):
TACCCATAGAGGCAAAG
Found at i:6303645 original size:21 final size:20
Alignment explanation
Indices: 6303612--6303654 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
6303602 AAAATATTAA
*
6303612 AAATAATTTTTTA-TATATTT
1 AAATAATTATTTAGTA-ATTT
6303632 AAATATATTATTTAGTAATTT
1 AAATA-ATTATTTAGTAATTT
6303653 AA
1 AA
6303655 TCATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 13 0.65
22 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
AAATAATTATTTAGTAATTT
Found at i:6315490 original size:31 final size:31
Alignment explanation
Indices: 6315455--6315516 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
6315445 TGCAAGCATC
6315455 AATTTAGCCAATGATAATATGTTATGAATTA
1 AATTTAGCCAATGATAATATGTTATGAATTA
* * *
6315486 AATTTGGTCAATGATAGTATGTTATGAATTA
1 AATTTAGCCAATGATAATATGTTATGAATTA
6315517 TATAGAGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.40
Consensus pattern (31 bp):
AATTTAGCCAATGATAATATGTTATGAATTA
Found at i:6316224 original size:17 final size:19
Alignment explanation
Indices: 6316202--6316245 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
6316192 TTAAATTATT
6316202 AATTTAGATATA-AAAA-A
1 AATTTAGATATACAAAATA
*
6316219 AATTTATATATACAAAATA
1 AATTTAGATATACAAAATA
*
6316238 AAATTAGA
1 AATTTAGA
6316246 CAAATATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 11 0.50
18 4 0.18
19 7 0.32
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (19 bp):
AATTTAGATATACAAAATA
Found at i:6316313 original size:15 final size:15
Alignment explanation
Indices: 6316289--6316318 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6316279 AAATGCGATC
*
6316289 TTTAATCTAAAAAAT
1 TTTAACCTAAAAAAT
6316304 TTTAACCTAAAAAAT
1 TTTAACCTAAAAAAT
6316319 ATAACTTAAA
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:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTAACCTAAAAAAT
Found at i:6316331 original size:12 final size:12
Alignment explanation
Indices: 6316314--6316365 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
6316304 TTTAACCTAA
*
6316314 AAAATATAACTT
1 AAAATATAACAT
6316326 AAAATATTAA-AT
1 AAAATA-TAACAT
*
6316338 AAAATAAAAACAT
1 AAAAT-ATAACAT
6316351 AAAATATAA-AT
1 AAAATATAACAT
6316362 AAAA
1 AAAA
6316366 AATTATAGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 6 0.18
12 17 0.50
13 11 0.32
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAATATAACAT
Found at i:6317448 original size:19 final size:19
Alignment explanation
Indices: 6317394--6317453 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
6317384 TCAAATTAAA
6317394 AAATAAATTA-AA-ATTTT
1 AAATAAATTATAATATTTT
*
6317411 AATTATAAATTGTTAATATTTT
1 AA--ATAAATT-ATAATATTTT
6317433 AAATAAATTATAATATTTT
1 AAATAAATTATAATATTTT
6317452 AA
1 AA
6317454 TAGTTTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
17 2 0.06
19 18 0.50
20 7 0.19
21 2 0.06
22 7 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
AAATAAATTATAATATTTT
Found at i:6317666 original size:28 final size:26
Alignment explanation
Indices: 6317623--6317675 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
6317613 TTTTTATCAC
**
6317623 TTAATATTTTGTTATTTTAAATAAATTA
1 TTAATATTTTAATA-TTTAAA-AAATTA
6317651 TTAATATTTTAATATTTAAAAAATT
1 TTAATATTTTAATATTTAAAAAATT
6317676 TAAAAATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 6 0.26
28 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
TTAATATTTTAATATTTAAAAAATTA
Found at i:6317717 original size:190 final size:189
Alignment explanation
Indices: 6317458--6317905 Score: 582
Period size: 190 Copynumber: 2.4 Consensus size: 189
6317448 TTTTAATAGT
* *
6317458 TTAATATTTAAAAATTTAAAAAATTGAGAAAAATTAAATAAAAAATAAATGCTCATATTAAAATT
1 TTAATATTTAAAAATTTAAAAAATT-AGAAAAATTAAAGAAAAAATAAATGATCATATTAAAATT
*
6317523 TTAATTAAAAATTATTAATACTTTAATAAATTACAAAAATAATATTGCAAATTAAAAAACATAAA
65 TTAATTAAAAATTAGTAATACTTTAATAAATTACAAAAATAATATTGC--A--AAAAAACATAAA
* *
6317588 TTATAATAAAAATATATTTTTATC-TTTTTTATCACTTAATATTTTGTTATTTTAAATAAATTA
126 TTATAATAAAAATATATTTATATCTTTTTTTATCACTTAATATTTTGTTATTTCAAATAAATTA
* * * * * *
6317651 TTAATATTTTAATATTTAAAAAATT-TAAAAA-TAGAGAAAAAATAAGTGATCATATTAAACTTT
1 TTAATATTTAAAAATTTAAAAAATTAGAAAAATTAAAGAAAAAATAAATGATCATATTAAAATTT
* * * * *
6317714 TAATTAAAAATTAGTAGTACTTTAATAAATTATAAAAATGATGTTTCAAAAAAACATAAATTATA
66 TAATTAAAAATTAGTAATACTTTAATAAATTACAAAAATAATATTGCAAAAAAACATAAATTATA
6317779 ATAAAAATATATTTATATCTTTTTTTATCACTTAATATTTTGTTATTTCAAATAAATTA
131 ATAAAAATATATTTATATCTTTTTTTATCACTTAATATTTTGTTATTTCAAATAAATTA
* * * * * * * * *
6317838 -TATTTTATTAATATTTTAATATA-GAGAAAAATTAAATAAAAAATAAATGATCATATTAATATT
1 TTAATAT-TTAAAAATTTAAAAAATTAGAAAAATTAAAGAAAAAATAAATGATCATATTAAAATT
6317901 TTAAT
65 TTAAT
6317906 ATATTGTAAA
Statistics
Matches: 220, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
186 39 0.18
187 53 0.24
188 32 0.15
190 68 0.31
191 5 0.02
193 23 0.10
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (189 bp):
TTAATATTTAAAAATTTAAAAAATTAGAAAAATTAAAGAAAAAATAAATGATCATATTAAAATTT
TAATTAAAAATTAGTAATACTTTAATAAATTACAAAAATAATATTGCAAAAAAACATAAATTATA
ATAAAAATATATTTATATCTTTTTTTATCACTTAATATTTTGTTATTTCAAATAAATTA
Found at i:6320930 original size:17 final size:18
Alignment explanation
Indices: 6320892--6320928 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
6320882 TGAAGACTTA
6320892 TTCTGTTTTCCTCAATTT
1 TTCTGTTTTCCTCAATTT
6320910 TTCTGTTTTCCTCAATTT
1 TTCTGTTTTCCTCAATTT
6320928 T
1 T
6320929 CTTGTAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.22, G:0.05, T:0.62
Consensus pattern (18 bp):
TTCTGTTTTCCTCAATTT
Found at i:6332470 original size:36 final size:36
Alignment explanation
Indices: 6332405--6332473 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
6332395 TCTTCCAGAG
* *
6332405 GTTAGTGCTGCATGTTTTCTAAACTTGGTTGCTCCT
1 GTTAGTGCTGCATGTTTCCTAAACCTGGTTGCTCCT
*
6332441 GTTAGTGCTGCA-GCTTTCCTACACCTGGTTGCT
1 GTTAGTGCTGCATG-TTTCCTAAACCTGGTTGCT
6332474 GGTCTTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 1 0.03
36 28 0.97
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.41
Consensus pattern (36 bp):
GTTAGTGCTGCATGTTTCCTAAACCTGGTTGCTCCT
Found at i:6338932 original size:77 final size:76
Alignment explanation
Indices: 6338803--6338954 Score: 286
Period size: 77 Copynumber: 2.0 Consensus size: 76
6338793 AGGACTTAAC
*
6338803 TGAGAGATTATTTGTCTAAATGAATCTAAGTTAACAAATGGCATGTCTTAATCATGGACTTAGTA
1 TGAGAGATTATTTGTCTAAATGAATCTAAGTTAACAAATGGCATGTCTTAATCATGGACATAGTA
6338868 ACCTAGAATTT
66 ACCTAGAATTT
6338879 TGAGAGATTATTTGTCTAAATGAATCTTAAGTTAACAAATGGCATGTCTTAATCATGGACATAGT
1 TGAGAGATTATTTGTCTAAATGAATC-TAAGTTAACAAATGGCATGTCTTAATCATGGACATAGT
6338944 AACCTAGAATT
65 AACCTAGAATT
6338955 ATCCATACTT
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
76 26 0.35
77 48 0.65
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (76 bp):
TGAGAGATTATTTGTCTAAATGAATCTAAGTTAACAAATGGCATGTCTTAATCATGGACATAGTA
ACCTAGAATTT
Found at i:6359833 original size:22 final size:22
Alignment explanation
Indices: 6359793--6359834 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6359783 TGTTGTATAC
* *
6359793 TTTATTTTTAGGTTTTTCATTT
1 TTTATTTTTAGCTTGTTCATTT
*
6359815 TTTATTTTTATCTTGTTCAT
1 TTTATTTTTAGCTTGTTCAT
6359835 GGAGTCGTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.71
Consensus pattern (22 bp):
TTTATTTTTAGCTTGTTCATTT
Found at i:6362197 original size:13 final size:14
Alignment explanation
Indices: 6362160--6362197 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
6362150 AAAGAAAAAT
6362160 AAAAACAAAATCACA
1 AAAAACAAAA-CACA
*
6362175 AAAAA-AAAAAACA
1 AAAAACAAAACACA
6362188 AAAAACAAAA
1 AAAAACAAAA
6362198 TCCAAGCTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 8 0.38
14 8 0.38
15 5 0.24
ACGTcount: A:0.84, C:0.13, G:0.00, T:0.03
Consensus pattern (14 bp):
AAAAACAAAACACA
Found at i:6370185 original size:19 final size:19
Alignment explanation
Indices: 6370163--6370199 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6370153 AGTATTTGAA
*
6370163 AAAGAAAAGAGTAACAGAG
1 AAAGAAAAGAGAAACAGAG
6370182 AAAGAAAAGAGAAACAGA
1 AAAGAAAAGAGAAACAGA
6370200 AATTAGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.24, T:0.03
Consensus pattern (19 bp):
AAAGAAAAGAGAAACAGAG
Found at i:6374344 original size:28 final size:28
Alignment explanation
Indices: 6374241--6374482 Score: 117
Period size: 28 Copynumber: 8.8 Consensus size: 28
6374231 CTTTTTTATC
* * * *
6374241 ATGACGTGTAATAATTACATTTTTCAAT
1 ATGACGTGTAACAACTAAATTTTTAAAT
* * *
6374269 ATAACGTGTAACAATTAAA-TTTCAACAT
1 ATGACGTGTAACAACTAAATTTTTAA-AT
* *
6374297 -TG-TGTGTAAC-ACTTATATTTTTAAAT
1 ATGACGTGTAACAAC-TAAATTTTTAAAT
* *
6374323 ATGACGTGTAATAACTAAATTTTCAACAT
1 ATGACGTGTAACAACTAAATTTTTAA-AT
* * * * *
6374352 A-G-TGTATAACAACTATATTTTTCAAC
1 ATGACGTGTAACAACTAAATTTTTAAAT
* * * * *
6374378 ATGGCATATAACAACTAGATTTTCAACAT
1 ATGACGTGTAACAACTAAATTTTTAA-AT
* * **
6374407 A--ACATGTAACAACTACATTTTTTGAT
1 ATGACGTGTAACAACTAAATTTTTAAAT
*
6374433 ATGATGTGTAACAACTAAATTTTTAACAT
1 ATGACGTGTAACAACTAAATTTTTAA-AT
* *
6374462 A--ACATGTAACAACTATATTTT
1 ATGACGTGTAACAACTAAATTTT
6374483 GAAAAAGAAT
Statistics
Matches: 160, Mismatches: 41, Indels: 27
0.70 0.18 0.12
Matches are distributed among these distances:
25 1 0.01
26 17 0.11
27 63 0.39
28 69 0.43
29 10 0.06
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (28 bp):
ATGACGTGTAACAACTAAATTTTTAAAT
Found at i:6374372 original size:55 final size:55
Alignment explanation
Indices: 6374259--6374482 Score: 227
Period size: 55 Copynumber: 4.1 Consensus size: 55
6374249 TAATAATTAC
* * ****
6374259 ATTTTTCAATATAACGTGTAACAATTAAA-TTTCAACATTGTGTGTAAC-ACTTAT
1 ATTTTTCAATATGACGTGTAACAACTAAATTTTCAACATAACATGTAACAAC-TAT
* * *** *
6374313 ATTTTTAAATATGACGTGTAATAACTAAATTTTCAACATAGTGTATAACAACTAT
1 ATTTTTCAATATGACGTGTAACAACTAAATTTTCAACATAACATGTAACAACTAT
* * * * * *
6374368 ATTTTTCAACATGGCATATAACAACTAGATTTTCAACATAACATGTAACAACTAC
1 ATTTTTCAATATGACGTGTAACAACTAAATTTTCAACATAACATGTAACAACTAT
** * *
6374423 ATTTTTTGATATGATGTGTAACAACTAAATTTTTAACATAACATGTAACAACTAT
1 ATTTTTCAATATGACGTGTAACAACTAAATTTTCAACATAACATGTAACAACTAT
6374478 ATTTT
1 ATTTT
6374483 GAAAAAGAAT
Statistics
Matches: 140, Mismatches: 28, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
54 25 0.18
55 113 0.81
56 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (55 bp):
ATTTTTCAATATGACGTGTAACAACTAAATTTTCAACATAACATGTAACAACTAT
Found at i:6374469 original size:27 final size:27
Alignment explanation
Indices: 6374329--6374482 Score: 119
Period size: 27 Copynumber: 5.6 Consensus size: 27
6374319 AAATATGACG
* * ***
6374329 TGTAATAACTAAATTTTCAACATAGTG
1 TGTAACAACTAAATTTTTAACATAACA
* * **
6374356 TATAACAACTATATTTTTCAACATGGCA
1 TGTAACAACTAAATTTTT-AACATAACA
* * *
6374384 TATAACAACTAGATTTTCAACATAACA
1 TGTAACAACTAAATTTTTAACATAACA
* * * * **
6374411 TGTAACAACTACATTTTTTGATATGATG
1 TGTAACAACTA-AATTTTTAACATAACA
6374439 TGTAACAACTAAATTTTTAACATAACA
1 TGTAACAACTAAATTTTTAACATAACA
*
6374466 TGTAACAACTATATTTT
1 TGTAACAACTAAATTTT
6374483 GAAAAAGAAT
Statistics
Matches: 98, Mismatches: 27, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
27 57 0.58
28 41 0.42
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (27 bp):
TGTAACAACTAAATTTTTAACATAACA
Found at i:6377011 original size:15 final size:15
Alignment explanation
Indices: 6376993--6377058 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
6376983 TTAGAATTGT
6376993 ATTTTATTTAATTTA
1 ATTTTATTTAATTTA
*
6377008 ATTTTAGTTAATTTA
1 ATTTTATTTAATTTA
*
6377023 AGATTTATTT--TTTA
1 A-TTTTATTTAATTTA
*
6377037 TATTTTATTTAGATTGA
1 -ATTTTATTTA-ATTTA
6377054 ATTTT
1 ATTTT
6377059 TTTTCTTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 11 0.27
15 16 0.39
16 11 0.27
17 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (15 bp):
ATTTTATTTAATTTA
Found at i:6378038 original size:24 final size:24
Alignment explanation
Indices: 6377993--6378038 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
6377983 CCATAACAAA
* *
6377993 CCAAGAAAAGCCCAATCTTCTAAG
1 CCAAGAAAAGCCCAACCCTCTAAG
* *
6378017 CCAAGAGACGCCCAACCCTCTA
1 CCAAGAAAAGCCCAACCCTCTA
6378039 GAAGACCGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.37, G:0.13, T:0.13
Consensus pattern (24 bp):
CCAAGAAAAGCCCAACCCTCTAAG
Found at i:6388216 original size:18 final size:18
Alignment explanation
Indices: 6388178--6388216 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6388168 AGAAAAATTA
* *
6388178 CAATTAGAATCATCAAAT
1 CAATTAGAATAACCAAAT
*
6388196 CAATTAGAATAACCAAGT
1 CAATTAGAATAACCAAAT
6388214 CAA
1 CAA
6388217 CCAAATCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.08, T:0.23
Consensus pattern (18 bp):
CAATTAGAATAACCAAAT
Found at i:6419231 original size:16 final size:15
Alignment explanation
Indices: 6419198--6419238 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
6419188 CATATGAATC
6419198 AATTTTATTAAAGAT
1 AATTTTATTAAAGAT
6419213 AATTTTATTTAAA-ATT
1 AATTTTA-TTAAAGA-T
6419229 AATTTT-TTAA
1 AATTTTATTAA
6419239 CTAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.17
15 8 0.33
16 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
AATTTTATTAAAGAT
Found at i:6441169 original size:27 final size:27
Alignment explanation
Indices: 6441106--6441266 Score: 130
Period size: 27 Copynumber: 6.0 Consensus size: 27
6441096 TTGGAACTAT
*
6441106 CTTAGGCGTTTCTGTGCTTGGAAC-GC
1 CTTAGGCGTTTCTGTGCTTGGAACACC
* *
6441132 CTTGGGTGTTTCTGTGCTTGGAACACC
1 CTTAGGCGTTTCTGTGCTTGGAACACC
* * * * *
6441159 CTTAGGTGTTTTTATACTTGGAACGCC
1 CTTAGGCGTTTCTGTGCTTGGAACACC
* * * * *
6441186 TTTGGGAGTTTCTGCGCTTGGAACGTCC
1 CTTAGGCGTTTCTGTGCTTGGAAC-ACC
* * * *
6441214 C-TGGGCGTTTCTATACTTGAAACACC
1 CTTAGGCGTTTCTGTGCTTGGAACACC
*
6441240 C-TAGACGTTTCTGTGCTTGGAACACC
1 CTTAGGCGTTTCTGTGCTTGGAACACC
6441266 C
1 C
6441267 CTAAGTGCTT
Statistics
Matches: 105, Mismatches: 28, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
26 46 0.44
27 57 0.54
28 2 0.02
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.35
Consensus pattern (27 bp):
CTTAGGCGTTTCTGTGCTTGGAACACC
Found at i:6441229 original size:54 final size:53
Alignment explanation
Indices: 6441106--6441266 Score: 164
Period size: 54 Copynumber: 3.0 Consensus size: 53
6441096 TTGGAACTAT
* * * *
6441106 CTTAGGCGTTTCTGTGCTTGGAACGCCTTGGGTGTTTCTGTGCTTGGAACACC
1 CTTAGGCGTTTCTATACTTGGAACGCCTTGGGAGTTTCTGCGCTTGGAACACC
* * *
6441159 CTTAGGTGTTTTTATACTTGGAACGCCTTTGGGAGTTTCTGCGCTTGGAACGTCC
1 CTTAGGCGTTTCTATACTTGGAACGCC-TTGGGAGTTTCTGCGCTTGGAAC-ACC
* * * * * *
6441214 C-TGGGCGTTTCTATACTTGAAACACCCT-AGACGTTTCTGTGCTTGGAACACC
1 CTTAGGCGTTTCTATACTTGGAACGCCTTGGGA-GTTTCTGCGCTTGGAACACC
6441266 C
1 C
6441267 CTAAGTGCTT
Statistics
Matches: 89, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
52 5 0.06
53 40 0.45
54 41 0.46
55 3 0.03
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.35
Consensus pattern (53 bp):
CTTAGGCGTTTCTATACTTGGAACGCCTTGGGAGTTTCTGCGCTTGGAACACC
Found at i:6441404 original size:53 final size:53
Alignment explanation
Indices: 6441285--6441572 Score: 233
Period size: 53 Copynumber: 5.4 Consensus size: 53
6441275 TTCTGTAGGT
* ** * * * * *
6441285 GCTTCTGCGCTTGGAACTCTTTTAGGCGCTTCTATACTTGGAATGCCCCTGGAC
1 GCTTCTGCGCTTGGAACAC-CCTAAGCGCTTTTGTACTTGGAACGCCCCTGGGC
** * * * ** *
6441339 GCTTCTATGCTTGGAACACCCTGAGCGTTTTTGTATTTGGAACGCCTTTGGGT
1 GCTTCTGCGCTTGGAACACCCTAAGCGCTTTTGTACTTGGAACGCCCCTGGGC
* *
6441392 GCTTCTGCGCTTGGAACTCCCTTAAGCGCTTTTGTACTTGAAACGCCCCTGGGC
1 GCTTCTGCGCTTGGAACACCC-TAAGCGCTTTTGTACTTGGAACGCCCCTGGGC
* * ** * *
6441446 GCTTCTGCGTTTGGAACGCCCTAAGCGCTTTTGCGCTTGGGACG-CCCTGGGT
1 GCTTCTGCGCTTGGAACACCCTAAGCGCTTTTGTACTTGGAACGCCCCTGGGC
** * *
6441498 GCTTCTGTACTTGGAACA-CCT-TG-GACATTTATGTACTTGGAATGCCCCTGGGC
1 GCTTCTGCGCTTGGAACACCCTAAGCG-C-TTT-TGTACTTGGAACGCCCCTGGGC
* *
6441551 GTTTCTGCACTTGGAACACCCT
1 GCTTCTGCGCTTGGAACACCCT
6441573 TGGGCGCTTC
Statistics
Matches: 183, Mismatches: 45, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
49 1 0.01
50 2 0.01
51 6 0.03
52 30 0.16
53 81 0.44
54 63 0.34
ACGTcount: A:0.15, C:0.27, G:0.26, T:0.32
Consensus pattern (53 bp):
GCTTCTGCGCTTGGAACACCCTAAGCGCTTTTGTACTTGGAACGCCCCTGGGC
Found at i:6441478 original size:107 final size:106
Alignment explanation
Indices: 6441282--6441514 Score: 268
Period size: 107 Copynumber: 2.2 Consensus size: 106
6441272 TGCTTCTGTA
** * * * *
6441282 GGTGCTTCTGCGCTTGGAACTCTTTTAGGCGCTTCTATACTTGGAATGCCCCTGGACGCTTCTAT
1 GGTGCTTCTGCGCTTGGAACTCCCTTAAGCGCTTCTATACTTGAAACGCCCCTGGACGCTTCTAC
* * * * *
6441347 GCTTGGAACACCCTGAGCGTTTTTGTATTTGGAACGCCTTTG
66 GCTTGGAACACCCTAAGCGCTTTTGCACTTGGAACGCC-CTG
* * * *
6441389 GGTGCTTCTGCGCTTGGAACTCCCTTAAGCGCTTTTGTACTTGAAACGCCCCTGGGCGCTTCTGC
1 GGTGCTTCTGCGCTTGGAACTCCCTTAAGCGCTTCTATACTTGAAACGCCCCTGGACGCTTCTAC
* * * *
6441454 GTTTGGAACGCCCTAAGCGCTTTTGCGCTTGGGACGCCCTG
66 GCTTGGAACACCCTAAGCGCTTTTGCACTTGGAACGCCCTG
**
6441495 GGTGCTTCTGTACTTGGAAC
1 GGTGCTTCTGCGCTTGGAAC
6441515 ACCTTGGACA
Statistics
Matches: 105, Mismatches: 21, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
106 20 0.19
107 85 0.81
ACGTcount: A:0.14, C:0.27, G:0.27, T:0.33
Consensus pattern (106 bp):
GGTGCTTCTGCGCTTGGAACTCCCTTAAGCGCTTCTATACTTGAAACGCCCCTGGACGCTTCTAC
GCTTGGAACACCCTAAGCGCTTTTGCACTTGGAACGCCCTG
Found at i:6441576 original size:27 final size:27
Alignment explanation
Indices: 6441309--6441594 Score: 116
Period size: 27 Copynumber: 10.7 Consensus size: 27
6441299 AACTCTTTTA
* * * *
6441309 GGCGCTTCTATACTTGGAATGCCCCTG
1 GGCGTTTCTGTACTTGGAACGCCCTTG
* * * * *
6441336 GACGCTTCTATGCTTGGAACACCC-TG
1 GGCGTTTCTGTACTTGGAACGCCCTTG
* * * *
6441362 AGCGTTTTTGTATTTGGAACGCCTTTG
1 GGCGTTTCTGTACTTGGAACGCCCTTG
* * ** * *
6441389 GGTGCTTCTGCGCTTGGAACTCCCTTA
1 GGCGTTTCTGTACTTGGAACGCCCTTG
* * *
6441416 AGCGCTTT-TGTACTTGAAACGCCCCTG
1 GGCG-TTTCTGTACTTGGAACGCCCTTG
* *** *
6441443 GGCGCTTCTGCGTTTGGAACGCCC-TA
1 GGCGTTTCTGTACTTGGAACGCCCTTG
* ** *
6441469 AGCGCTTT-TGCGCTTGGGACGCCC-TG
1 GGCG-TTTCTGTACTTGGAACGCCCTTG
* * *
6441495 GGTGCTTCTGTACTTGGAAC-ACCTTG
1 GGCGTTTCTGTACTTGGAACGCCCTTG
* * * * *
6441521 GACATTTATGTACTTGGAATGCCCCTG
1 GGCGTTTCTGTACTTGGAACGCCCTTG
* *
6441548 GGCGTTTCTGCACTTGGAACACCCTTG
1 GGCGTTTCTGTACTTGGAACGCCCTTG
* * *
6441575 GGCGCTTCTATACTTAGAAC
1 GGCGTTTCTGTACTTGGAAC
6441595 ACCTTAGACA
Statistics
Matches: 182, Mismatches: 70, Indels: 14
0.68 0.26 0.05
Matches are distributed among these distances:
25 4 0.02
26 65 0.36
27 111 0.61
28 2 0.01
ACGTcount: A:0.16, C:0.27, G:0.26, T:0.31
Consensus pattern (27 bp):
GGCGTTTCTGTACTTGGAACGCCCTTG
Found at i:6463506 original size:6 final size:6
Alignment explanation
Indices: 6463495--6463537 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
6463485 GGAATGGAAA
* * *
6463495 CAATGG CAATGG CAATGG CAAAGG CAAAGG CAAAGG CAATGG C
1 CAATGG CAATGG CAATGG CAATGG CAATGG CAATGG CAATGG C
6463538 CACGATGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.40, C:0.19, G:0.33, T:0.09
Consensus pattern (6 bp):
CAATGG
Found at i:6463512 original size:12 final size:12
Alignment explanation
Indices: 6463495--6463537 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
6463485 GGAATGGAAA
*
6463495 CAATGGCAATGG
1 CAATGGCAAAGG
6463507 CAATGGCAAAGG
1 CAATGGCAAAGG
*
6463519 CAAAGGCAAAGG
1 CAATGGCAAAGG
6463531 CAATGGC
1 CAATGGC
6463538 CACGATGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.33, T:0.09
Consensus pattern (12 bp):
CAATGGCAAAGG
Found at i:6466404 original size:2 final size:2
Alignment explanation
Indices: 6466369--6466394 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6466359 TTGATGGATT
6466369 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
6466395 CCCATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6481024 original size:12 final size:12
Alignment explanation
Indices: 6481007--6481043 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
6480997 AATAAAATAA
6481007 ATAAATATTCAT
1 ATAAATATTCAT
*
6481019 ATAAATATTTAT
1 ATAAATATTCAT
*
6481031 AAAAATATTCAT
1 ATAAATATTCAT
6481043 A
1 A
6481044 ACACTCTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAAATATTCAT
Found at i:6496759 original size:29 final size:28
Alignment explanation
Indices: 6496700--6496759 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
6496690 GAGTGTTGGA
*
6496700 AGTTTATTTACATTTATTTCTTTAAGTT
1 AGTTTATTTACATTTATTTCTTTAAGAT
* *
6496728 AGTTTATATTATATGTT-TTTCTTTCAGAT
1 AGTTTAT-TTACAT-TTATTTCTTTAAGAT
6496757 AGT
1 AGT
6496760 AGACGTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.26
29 18 0.67
30 2 0.07
ACGTcount: A:0.25, C:0.07, G:0.10, T:0.58
Consensus pattern (28 bp):
AGTTTATTTACATTTATTTCTTTAAGAT
Found at i:6496920 original size:21 final size:22
Alignment explanation
Indices: 6496894--6496934 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
6496884 TTACTCAATA
6496894 TAAATAATT-TAATAG-TAATTT
1 TAAAT-ATTATAATAGATAATTT
6496915 TAAATATTATAATAGATAAT
1 TAAATATTATAATAGATAAT
6496935 AATATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 11 0.61
22 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
TAAATATTATAATAGATAATTT
Found at i:6497060 original size:35 final size:35
Alignment explanation
Indices: 6496890--6497060 Score: 109
Period size: 36 Copynumber: 4.8 Consensus size: 35
6496880 TATATTACTC
* *
6496890 AATATAAATAAT-TTAATAGTAATTTTAAA-TATTAT
1 AATATAAATAATATTAATA-AAATATTAAATTA-TAT
* * * * *
6496925 AATAGATAATAATATTAATAATATAATGAATTATTT
1 AATATA-AATAATATTAATAAAATATTAAATTATAT
*
6496961 AATATTAAAT-TTAATTAATTAAAATATTAAATTATAT
1 AATA-TAAATAAT-ATTAA-TAAAATATTAAATTATAT
** * * * *
6496998 AATATTGATTATTTTTATCAAAA-ATTAAATTACAT
1 AATATAAATAATATTAAT-AAAATATTAAATTATAT
6497033 AATATCAAATAATATTAAT-AAATATTAA
1 AATAT-AAATAATATTAATAAAATATTAA
6497061 TAAACTGTAT
Statistics
Matches: 102, Mismatches: 24, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
34 3 0.03
35 28 0.27
36 43 0.42
37 28 0.27
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (35 bp):
AATATAAATAATATTAATAAAATATTAAATTATAT
Found at i:6497162 original size:19 final size:19
Alignment explanation
Indices: 6497134--6497185 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
6497124 GTACATTATT
*
6497134 AATAAATATTAAATTATGA
1 AATAATTATTAAATTATGA
*
6497153 AATAATTATTAAACTATGA
1 AATAATTATTAAATTATGA
* *
6497172 TA-AATTATTGAATT
1 AATAATTATTAAATT
6497186 TAATTAATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (19 bp):
AATAATTATTAAATTATGA
Found at i:6498610 original size:22 final size:23
Alignment explanation
Indices: 6498570--6498613 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
6498560 GCATTGCGTG
6498570 ACTTGTTTTGTAAGTATTGTGTA
1 ACTTGTTTTGTAAGTATTGTGTA
6498593 ACTTG-TTTGT-AGTAATTGTGT
1 ACTTGTTTTGTAAGT-ATTGTGT
6498614 TGCTTTATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.15
22 12 0.60
23 5 0.25
ACGTcount: A:0.20, C:0.05, G:0.23, T:0.52
Consensus pattern (23 bp):
ACTTGTTTTGTAAGTATTGTGTA
Found at i:6499685 original size:186 final size:188
Alignment explanation
Indices: 6499369--6499835 Score: 618
Period size: 186 Copynumber: 2.5 Consensus size: 188
6499359 AAGAGAAGCA
* *
6499369 AACGTGAATGGATGTTAGGCATTGTGTGACCTATTATTAGGTATTGCGAGACT-GAGTTATAGGC
1 AACGTGAATGGATATTAGGCATTGAGTGACCTATTATTAGGTATTGCGAGACTAG-GTTATAGGC
* * ** * * *
6499433 ACTACATGAATTGTGCAATGCATATATTCTATTCAGACATTGTGTGATTGGTTTGTATGTATATC
65 ACTACGTGAATTGTGCAATGCATATCTTCTATTCAGACATTGCATGACTGGTTTGAATGGATATC
* * *
6499498 GTGACTTGTTGTTATGTATTGCATGACGTTGGGCTAGTATGTGA-T-TTATGTTGGCAT
130 GTGACTTGTTGTTATGTATTGCATGACATTGGGCCAGTATGTGACTGTTATATTGGCAT
*
6499555 AACGTGAATGGATATTAGGCATTGAGTGACCTATTATTAGGTATTGTGAGACTAGGTTATAGGCA
1 AACGTGAATGGATATTAGGCATTGAGTGACCTATTATTAGGTATTGCGAGACTAGGTTATAGGCA
* * *
6499620 CTATGTGAATTGTGCAATGCATATCTTCTATTGAGATATTGCATGACTGGTTTGAATGGATATCG
66 CTACGTGAATTGTGCAATGCATATCTTCTATTCAGACATTGCATGACTGGTTTGAATGGATATCG
* *
6499685 TGACTTGTTGTTATGTATTGCGTGATATTGGGCCAGTATGTGACTGGTTATATTGGCAT
131 TGACTTGTTGTTATGTATTGCATGACATTGGGCCAGTATGTGACT-GTTATATTGGCAT
* * * * * * * * *
6499744 AATGTGAGTAGATATTAGGCATCGAGTGACTTATTGTTA-GTCATTACAAGACTAGGTTATAGGT
1 AACGTGAATGGATATTAGGCATTGAGTGACCTATTATTAGGT-ATTGCGAGACTAGGTTATAGGC
* *
6499808 GCTGCGTGAATTGTGCAATGCATATCTT
65 ACTACGTGAATTGTGCAATGCATATCTT
6499836 GTGTCAAGAT
Statistics
Matches: 245, Mismatches: 31, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
186 154 0.63
187 2 0.01
188 2 0.01
189 87 0.36
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.38
Consensus pattern (188 bp):
AACGTGAATGGATATTAGGCATTGAGTGACCTATTATTAGGTATTGCGAGACTAGGTTATAGGCA
CTACGTGAATTGTGCAATGCATATCTTCTATTCAGACATTGCATGACTGGTTTGAATGGATATCG
TGACTTGTTGTTATGTATTGCATGACATTGGGCCAGTATGTGACTGTTATATTGGCAT
Found at i:6499890 original size:189 final size:186
Alignment explanation
Indices: 6499369--6499893 Score: 495
Period size: 186 Copynumber: 2.8 Consensus size: 186
6499359 AAGAGAAGCA
* * * * * *
6499369 AACGTGAATGGATGTTAGGCATTGTGTGACCTATTATTAGGTATTGCGAGACT-GAGTTATAGGC
1 AACGTGAATAGATATTAGGCATCGAGTGACCTATTATTAGGTATTACAAGACTAG-GTTATAGGC
* * * ** * * * *
6499433 ACTACATGAATTGTGCAATGCATATATTCTATTC-AGACATTGTGTGATTGGTTTGTATGTATAT
65 ACTACGTGAATTGTGCAATGCATATCTTCTA-TCAAGATATTGCATGACTCGTTTGAATGCATAT
* ** * * *
6499497 CGTGACTTGTTGTTATGTATTGCATGACGTTGGGCTAGTATGTGATTTATGTTGGCAT
129 CATGACTAATTGTTATGTATTGCATGACATTGGGCCAGTATGTGATTTATATTGGCAT
* * ***
6499555 AACGTGAATGGATATTAGGCATTGAGTGACCTATTATTAGGTATTGTGAGACTAGGTTATAGGCA
1 AACGTGAATAGATATTAGGCATCGAGTGACCTATTATTAGGTATTACAAGACTAGGTTATAGGCA
* ** * * *
6499620 CTATGTGAATTGTGCAATGCATATCTTCTATTGAGATATTGCATGACTGGTTTGAATGGATATCG
66 CTACGTGAATTGTGCAATGCATATCTTCTATCAAGATATTGCATGACTCGTTTGAATGCATATCA
** * *
6499685 TGACTTGTTGTTATGTATTGCGTGATATTGGGCCAGTATGTGACTGGTTATATTGGCAT
131 TGACTAATTGTTATGTATTGCATGACATTGGGCCAGTATGTGA-T--TTATATTGGCAT
* * * * *
6499744 AATGTGAGTAGATATTAGGCATCGAGTGACTTATTGTTA-GTCATTACAAGACTAGGTTATAGGT
1 AACGTGAATAGATATTAGGCATCGAGTGACCTATTATTAGGT-ATTACAAGACTAGGTTATAGGC
* * * * * * *
6499808 GCTGCGTGAATTGTGCAATGCATATCTTGTGTCAAGATATTTCTTGACTACTTTTG-ATGCAT-T
65 ACTACGTGAATTGTGCAATGCATATCTTCTATCAAGATATTGCATGACT-CGTTTGAATGCATAT
6499871 GCATGACTAATAT-TTATGTATTG
129 -CATGACTAAT-TGTTATGTATTG
6499894 TGAGACTTGT
Statistics
Matches: 287, Mismatches: 43, Indels: 15
0.83 0.12 0.04
Matches are distributed among these distances:
185 1 0.00
186 152 0.53
187 2 0.01
188 3 0.01
189 124 0.43
190 5 0.02
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (186 bp):
AACGTGAATAGATATTAGGCATCGAGTGACCTATTATTAGGTATTACAAGACTAGGTTATAGGCA
CTACGTGAATTGTGCAATGCATATCTTCTATCAAGATATTGCATGACTCGTTTGAATGCATATCA
TGACTAATTGTTATGTATTGCATGACATTGGGCCAGTATGTGATTTATATTGGCAT
Found at i:6503965 original size:46 final size:46
Alignment explanation
Indices: 6503847--6503966 Score: 150
Period size: 46 Copynumber: 2.6 Consensus size: 46
6503837 TATAAAAAAG
* * * *
6503847 TCACACGATTTCATATCAACTAGTAAAGCAATTCCATAATAATTAC
1 TCACACGATTTCATATTAACTAGTAATGCAACTCCATAATAACTAC
* * * * *
6503893 TCACACGATTTTATAATAACTAGTAATGCGACTCCATATTTACTAC
1 TCACACGATTTCATATTAACTAGTAATGCAACTCCATAATAACTAC
*
6503939 TCACGCGATTTCATATTAACTAGTAATG
1 TCACACGATTTCATATTAACTAGTAATG
6503967 TGATTTTATA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (46 bp):
TCACACGATTTCATATTAACTAGTAATGCAACTCCATAATAACTAC
Found at i:6503971 original size:23 final size:23
Alignment explanation
Indices: 6503899--6504091 Score: 91
Period size: 23 Copynumber: 8.4 Consensus size: 23
6503889 TTACTCACAC
* * * *
6503899 GATTTTATAATAACTAGTAATGC
1 GATTTCATATTAACTAGTAACGT
* * * * * *
6503922 GACTCCATATTTACTACTCACGC
1 GATTTCATATTAACTAGTAACGT
*
6503945 GATTTCATATTAACTAGTAATGT
1 GATTTCATATTAACTAGTAACGT
* * *
6503968 GATTTTATAATAACTAGTAACAT
1 GATTTCATATTAACTAGTAACGT
* * * * * *
6503991 GACTCCATATTTACTACTCATGT
1 GATTTCATATTAACTAGTAACGT
* * **
6504014 GATTTCATATCAA-TCAGTCATAT
1 GATTTCATATTAACT-AGTAACGT
* *
6504037 GATTCCATAATAACTAGTAACGT
1 GATTTCATATTAACTAGTAACGT
* * * * *
6504060 GACTCCATATTTACCACTAACGT
1 GATTTCATATTAACTAGTAACGT
6504083 GATTTCATA
1 GATTTCATA
6504092 ATAATTAATA
Statistics
Matches: 121, Mismatches: 47, Indels: 4
0.70 0.27 0.02
Matches are distributed among these distances:
22 1 0.01
23 119 0.98
24 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (23 bp):
GATTTCATATTAACTAGTAACGT
Found at i:6503986 original size:69 final size:69
Alignment explanation
Indices: 6503899--6504091 Score: 262
Period size: 69 Copynumber: 2.8 Consensus size: 69
6503889 TTACTCACAC
* * * *
6503899 GATTTTATAATAACTAGTAATGCGACTCCATATTTACTACTCACGCGATTTCATATTAA-CTAGT
1 GATTTTATAATAACTAGTAACGTGACTCCATATTTACTACTCACGTGATTTCATATCAATC-AGT
*
6503963 AATGT
65 AATAT
* * *
6503968 GATTTTATAATAACTAGTAACATGACTCCATATTTACTACTCATGTGATTTCATATCAATCAGTC
1 GATTTTATAATAACTAGTAACGTGACTCCATATTTACTACTCACGTGATTTCATATCAATCAGTA
6504033 ATAT
66 ATAT
** * *
6504037 GATTCCATAATAACTAGTAACGTGACTCCATATTTACCACTAACGTGATTTCATA
1 GATTTTATAATAACTAGTAACGTGACTCCATATTTACTACTCACGTGATTTCATA
6504092 ATAATTAATA
Statistics
Matches: 109, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
69 108 0.99
70 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (69 bp):
GATTTTATAATAACTAGTAACGTGACTCCATATTTACTACTCACGTGATTTCATATCAATCAGTA
ATAT
Found at i:6504000 original size:46 final size:46
Alignment explanation
Indices: 6503950--6504061 Score: 111
Period size: 46 Copynumber: 2.4 Consensus size: 46
6503940 CACGCGATTT
*
6503950 CATATTAACTAGTAATGTGATTTTATAAT-AA-CTAGTAACATGACTC
1 CATATTAACTAGTAATGTGATTTCAT-ATCAATC-AGTAACATGACTC
* * * * * *
6503996 CATATTTACTACTCATGTGATTTCATATCAATCAGTCATATGATTC
1 CATATTAACTAGTAATGTGATTTCATATCAATCAGTAACATGACTC
* *
6504042 CATAATAACTAGTAACGTGA
1 CATATTAACTAGTAATGTGA
6504062 CTCCATATTT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
45 2 0.04
46 49 0.94
47 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (46 bp):
CATATTAACTAGTAATGTGATTTCATATCAATCAGTAACATGACTC
Found at i:6504284 original size:24 final size:26
Alignment explanation
Indices: 6504228--6504287 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
6504218 TGAACAAATT
*
6504228 TTGTTACACGCCATATTCAAAAAAAA
1 TTGTTACACACCATATTCAAAAAAAA
* * *
6504254 TTATTACACACCATGTT-TAAAAAAA
1 TTGTTACACACCATATTCAAAAAAAA
6504279 -TGTTACACA
1 TTGTTACACA
6504288 TCGTTTTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 8 0.28
25 7 0.24
26 14 0.48
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (26 bp):
TTGTTACACACCATATTCAAAAAAAA
Found at i:6504519 original size:27 final size:27
Alignment explanation
Indices: 6504486--6504557 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
6504476 ATATGCAATG
6504486 ATTTTGCTACAAGCCATGTGAATAACA
1 ATTTTGCTACAAGCCATGTGAATAACA
* *
6504513 ATTTTGCTACCCA-CCATGTGCATAACA
1 ATTTTGCTA-CAAGCCATGTGAATAACA
* **
6504540 CTTTT-CTACTTGCCATGT
1 ATTTTGCTACAAGCCATGT
6504558 TCAAAAACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 9 0.24
27 26 0.68
28 2 0.05
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (27 bp):
ATTTTGCTACAAGCCATGTGAATAACA
Found at i:6505061 original size:18 final size:18
Alignment explanation
Indices: 6505040--6505074 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6505030 AAAGCTTAGA
6505040 GAGTTGACAGAGTTGAGG
1 GAGTTGACAGAGTTGAGG
* *
6505058 GAGTTGAGATAGTTGAG
1 GAGTTGACAGAGTTGAG
6505075 CATTAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.43, T:0.26
Consensus pattern (18 bp):
GAGTTGACAGAGTTGAGG
Found at i:6505909 original size:2 final size:2
Alignment explanation
Indices: 6505902--6505938 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6505892 ACATGTATAA
6505902 AG AG 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 AG AG A
6505939 TATCACTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6520985 original size:26 final size:27
Alignment explanation
Indices: 6520931--6521009 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 27
6520921 GGGCTACAGC
* *
6520931 CCAGCCCGCCAAGAGGCCCAAG-AGGGTG
1 CCAGCCCACCAAGA--CCCATGTAGGGTG
*
6520959 CCAGCCC-TCAAGACCCATGTAGGGTG
1 CCAGCCCACCAAGACCCATGTAGGGTG
6520985 CCAGCCCACCAAGACCCATGTAGGG
1 CCAGCCCACCAAGACCCATGTAGGG
6521010 ATTTCCCTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
25 5 0.11
26 13 0.28
27 21 0.46
28 7 0.15
ACGTcount: A:0.25, C:0.37, G:0.29, T:0.09
Consensus pattern (27 bp):
CCAGCCCACCAAGACCCATGTAGGGTG
Found at i:6521080 original size:15 final size:15
Alignment explanation
Indices: 6521060--6521116 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
6521050 TCCCAAATGG
6521060 TTTTGGAGGGAAATC
1 TTTTGGAGGGAAATC
*
6521075 TTTTGGAAGGAAATC
1 TTTTGGAGGGAAATC
*
6521090 CTTTGGAGGGAAA--
1 TTTTGGAGGGAAATC
*
6521103 ATTTGGAGGGAAAT
1 TTTTGGAGGGAAAT
6521117 GGGTGGGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
13 12 0.32
15 25 0.68
ACGTcount: A:0.32, C:0.05, G:0.33, T:0.30
Consensus pattern (15 bp):
TTTTGGAGGGAAATC
Found at i:6521109 original size:13 final size:13
Alignment explanation
Indices: 6521091--6521115 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6521081 AAGGAAATCC
6521091 TTTGGAGGGAAAA
1 TTTGGAGGGAAAA
6521104 TTTGGAGGGAAA
1 TTTGGAGGGAAA
6521116 TGGGTGGGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (13 bp):
TTTGGAGGGAAAA
Found at i:6526159 original size:14 final size:14
Alignment explanation
Indices: 6526140--6526167 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6526130 TGGGGGAGGG
6526140 TGTCACGGGCCACA
1 TGTCACGGGCCACA
6526154 TGTCACGGGCCACA
1 TGTCACGGGCCACA
6526168 GCCCAGACCC
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:0.21, C:0.36, G:0.29, T:0.14
Consensus pattern (14 bp):
TGTCACGGGCCACA
Found at i:6526225 original size:27 final size:27
Alignment explanation
Indices: 6526193--6526250 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
6526183 GAGGCCCAAG
*
6526193 AGGGTGCCAGCCCTCCAAGACCCATGT
1 AGGGTGCCAGCCCACCAAGACCCATGT
6526220 AGGGTGCCAGCCCACCAAGACCCATGT
1 AGGGTGCCAGCCCACCAAGACCCATGT
6526247 AGGG
1 AGGG
6526251 ATTTCCCTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.24, C:0.34, G:0.29, T:0.12
Consensus pattern (27 bp):
AGGGTGCCAGCCCACCAAGACCCATGT
Found at i:6526313 original size:15 final size:15
Alignment explanation
Indices: 6526295--6526343 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
6526285 TTTCCCTCCC
6526295 AAATGTTTTGGAGGG
1 AAATGTTTTGGAGGG
**
6526310 AAATCCTTTGGAGGG
1 AAATGTTTTGGAGGG
6526325 AAAT-TTTTGGAGGG
1 AAATGTTTTGGAGGG
6526339 AAATG
1 AAATG
6526344 GGTGGGGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 13 0.43
15 17 0.57
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.31
Consensus pattern (15 bp):
AAATGTTTTGGAGGG
Found at i:6530998 original size:23 final size:23
Alignment explanation
Indices: 6530972--6531022 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
6530962 AATATATGGA
*
6530972 TTAAAAATTTCAT-TCATTATTTT
1 TTAAAAATTTCATGGCA-TATTTT
* *
6530995 TTAAAATTTTGATGGCATATTTT
1 TTAAAAATTTCATGGCATATTTT
6531018 TTAAA
1 TTAAA
6531023 CCAAAAAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (23 bp):
TTAAAAATTTCATGGCATATTTT
Found at i:6539842 original size:2 final size:2
Alignment explanation
Indices: 6539835--6539873 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6539825 GATGTTCGAA
6539835 AT 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 AT A
6539874 ACTTGGAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6542121 original size:15 final size:16
Alignment explanation
Indices: 6542095--6542124 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6542085 TTTTTAATTT
6542095 TTAAAAATTAAAATCA
1 TTAAAAATTAAAATCA
6542111 TTAAAAA-TAAAATC
1 TTAAAAATTAAAATC
6542125 CACATAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAAATTAAAATCA
Found at i:6542289 original size:15 final size:14
Alignment explanation
Indices: 6542248--6542305 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 14
6542238 TATATGAGCA
*
6542248 AATAAAATATAATT
1 AATAAAATATAAAT
*
6542262 AA-AAAACATAAAT
1 AATAAAATATAAAT
6542275 AATAATAATATAAAT
1 AATAA-AATATAAAT
*
6542290 AGAAAAAAT-TAAAT
1 A-ATAAAATATAAAT
6542304 AA
1 AA
6542306 AAACTTTACC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
13 12 0.32
14 10 0.27
15 12 0.32
16 3 0.08
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (14 bp):
AATAAAATATAAAT
Found at i:6542304 original size:29 final size:27
Alignment explanation
Indices: 6542248--6542305 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
6542238 TATATGAGCA
*
6542248 AATAAAATATAATTAAAAAACATAAAT
1 AATAAAATATAAATAAAAAACATAAAT
6542275 AATAATAATATAAATAGAAAAA-ATTAAAT
1 AATAA-AATATAAATA-AAAAACA-TAAAT
6542304 AA
1 AA
6542306 AAACTTTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 5 0.19
28 10 0.37
29 12 0.44
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (27 bp):
AATAAAATATAAATAAAAAACATAAAT
Found at i:6555243 original size:37 final size:38
Alignment explanation
Indices: 6555202--6555276 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 38
6555192 TGTTTAAAGG
* * *
6555202 GAAGAGTTTTATCTTGCAGA-GAATCTTAGTTTGATTA
1 GAAGAGTTTTATCTTGCAAAGGAATCCTAGTTTAATTA
6555239 GAAGAGTTTTATCTTGCAAAGGAATCCTAGTTTAATTA
1 GAAGAGTTTTATCTTGCAAAGGAATCCTAGTTTAATTA
6555277 TATCAAGAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 19 0.56
38 15 0.44
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (38 bp):
GAAGAGTTTTATCTTGCAAAGGAATCCTAGTTTAATTA
Found at i:6556437 original size:23 final size:24
Alignment explanation
Indices: 6556411--6556455 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
6556401 TTTTTTATTA
6556411 ATTAATATATAAATT-AATAATTT
1 ATTAATATATAAATTAAATAATTT
* *
6556434 ATTAATTTATTAATTAAATAAT
1 ATTAATATATAAATTAAATAAT
6556456 ATCTTGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTAATATATAAATTAAATAATTT
Found at i:6556467 original size:20 final size:19
Alignment explanation
Indices: 6556438--6556496 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
6556428 TAATTTATTA
6556438 ATTT-ATTAATTAAATAAT
1 ATTTGATTAATTAAATAAT
*
6556456 ATCTTGATTAATTAATTAAT
1 AT-TTGATTAATTAAATAAT
*
6556476 -TTTTA-TAATCTAAATAAT
1 ATTTGATTAAT-TAAATAAT
6556494 ATT
1 ATT
6556497 AATTTATAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 4 0.12
18 12 0.35
19 5 0.15
20 13 0.38
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTGATTAATTAAATAAT
Found at i:6561747 original size:29 final size:30
Alignment explanation
Indices: 6561714--6561770 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
6561704 GTTCCCCACA
*
6561714 CATTTCCCTCCAAAA-TTTTCCCTCCAAGG
1 CATTTCCCTCCAAAAGATTTCCCTCCAAGG
6561743 CATTTCCCTCCAAAAGATTTCCCTCCAA
1 CATTTCCCTCCAAAAGATTTCCCTCCAA
6561771 AACATTTGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.26, C:0.39, G:0.05, T:0.30
Consensus pattern (30 bp):
CATTTCCCTCCAAAAGATTTCCCTCCAAGG
Found at i:6561772 original size:15 final size:15
Alignment explanation
Indices: 6561715--6561777 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
6561705 TTCCCCACAC
6561715 ATTTCCCTCCAAAA-
1 ATTTCCCTCCAAAAG
* *
6561729 TTTTCCCTCC-AAGG
1 ATTTCCCTCCAAAAG
6561743 CATTTCCCTCCAAAAG
1 -ATTTCCCTCCAAAAG
*
6561759 ATTTCCCTCCAAAAC
1 ATTTCCCTCCAAAAG
6561774 ATTT
1 ATTT
6561778 GGGAGGGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
13 2 0.05
14 9 0.22
15 27 0.66
16 3 0.07
ACGTcount: A:0.29, C:0.35, G:0.05, T:0.32
Consensus pattern (15 bp):
ATTTCCCTCCAAAAG
Found at i:6561777 original size:30 final size:29
Alignment explanation
Indices: 6561713--6561777 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
6561703 GGTTCCCCAC
* *
6561713 ACATTTCCCTCCAAAATTTTCCCTCCAAG
1 ACATTTCCCTCCAAAAATTTCCCTCCAAA
*
6561742 GCATTTCCCTCCAAAAGATTTCCCTCCAAA
1 ACATTTCCCTCCAAAA-ATTTCCCTCCAAA
6561772 ACATTT
1 ACATTT
6561778 GGGAGGGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.29, C:0.35, G:0.05, T:0.31
Consensus pattern (29 bp):
ACATTTCCCTCCAAAAATTTCCCTCCAAA
Found at i:6562343 original size:51 final size:51
Alignment explanation
Indices: 6562283--6562638 Score: 312
Period size: 51 Copynumber: 7.0 Consensus size: 51
6562273 TTGCCTGACT
* * * *
6562283 CTGTCGGGCTGTCTCGCCCAAGGTCCTGTTCTGTGCGCCCCGGCTGGCACC
1 CTGTCGGGCTGGCTCGCCCAAGGGCCTGTGCTGTGCGCCCCTGCTGGCACC
* * * *
6562334 CTGTCGGGCTGGCTCGCCCAAGGGCCTGTGCCGTGCGCCCCTCCTAGCATC
1 CTGTCGGGCTGGCTCGCCCAAGGGCCTGTGCTGTGCGCCCCTGCTGGCACC
* * * * * * *
6562385 CTGTCGGGCTAGCTCGCTC-AGGAGCCGGTGCTGTGCACCCTTGCTAGCATC
1 CTGTCGGGCTGGCTCGCCCAAGG-GCCTGTGCTGTGCGCCCCTGCTGGCACC
* **
6562436 CTGTCGGGCTGGCTCGCCCATGGGCCTGTGAC-GTGCGCCCCTAATGGCATCC
1 CTGTCGGGCTGGCTCGCCCAAGGGCCTGTG-CTGTGCGCCCCTGCTGGCA-CC
* * * * *
6562488 C-ATCGGGAC-GGCTCGCCCAAGGGCCTATGATGTGCGCCCTTGTTGGCACC
1 CTGTCGGG-CTGGCTCGCCCAAGGGCCTGTGCTGTGCGCCCCTGCTGGCACC
* * * * * *
6562538 CTGCCGGGCTGGCTCGCCTAGGGGCCTATGCGGTGCACCCCTGCTGGCACC
1 CTGTCGGGCTGGCTCGCCCAAGGGCCTGTGCTGTGCGCCCCTGCTGGCACC
* * *
6562589 TTGTCGGGC-GAGCTCGCCC-AGGGTCCTGTGTTGTGC-ACCCTAGCTGGCAC
1 CTGTCGGGCTG-GCTCGCCCAAGGG-CCTGTGCTGTGCGCCCCT-GCTGGCAC
6562639 GTTGCACTTG
Statistics
Matches: 245, Mismatches: 49, Indels: 22
0.78 0.16 0.07
Matches are distributed among these distances:
50 15 0.06
51 224 0.91
52 6 0.02
ACGTcount: A:0.10, C:0.37, G:0.33, T:0.21
Consensus pattern (51 bp):
CTGTCGGGCTGGCTCGCCCAAGGGCCTGTGCTGTGCGCCCCTGCTGGCACC
Found at i:6562637 original size:153 final size:153
Alignment explanation
Indices: 6562283--6562638 Score: 350
Period size: 153 Copynumber: 2.3 Consensus size: 153
6562273 TTGCCTGACT
* * * ** *
6562283 CTGTCGGGCTGTCTCGCCCAAGGTCCTGT-TCTGTGCGCCCCGGCTGGCACCCTGTCGGGCTGGC
1 CTGTCGGGCTGGCTCGCCCAGGGTCCTGTGT-TGTGCACCCTAGCTGGCACCCTATCGGGCTGGC
* * * *
6562347 TCGCCCAAGGGCCTGTGCCGTGCGCCCCTCCTAGCATCCTGTCGGGCTAGCTCGCTCAGGAGCCG
65 TCGCCCAAGGGCCTATGACGTGCGCCCCTCCTAGCACCCTGCCGGGCTAGCTCGCTCAGGAGCCG
* * *
6562412 GTGCTGTGCACCCTTGCTAGCATC
130 ATGCGGTGCACCCCTGCTAGCATC
** * *
6562436 CTGTCGGGCTGGCTCGCCCATGGG-CCTGTGACGTGCGCCCCTA-ATGGCATCCC-ATCGGGAC-
1 CTGTCGGGCTGGCTCGCCCA-GGGTCCTGTGTTGTGC-ACCCTAGCTGGCA-CCCTATCGGG-CT
* * ** * * *
6562497 GGCTCGCCCAAGGGCCTATGATGTGCGCCCTTGTTGGCACCCTGCCGGGCTGGCTCGC-CTAGGG
62 GGCTCGCCCAAGGGCCTATGACGTGCGCCCCTCCTAGCACCCTGCCGGGCTAGCTCGCTC-AGGA
* *
6562561 GCCTATGCGGTGCACCCCTGCTGGCA-C
126 GCCGATGCGGTGCACCCCTGCTAGCATC
6562588 CTTGTCGGGC-GAGCTCGCCCAGGGTCCTGTGTTGTGCACCCTAGCTGGCAC
1 C-TGTCGGGCTG-GCTCGCCCAGGGTCCTGTGTTGTGCACCCTAGCTGGCAC
6562639 GTTGCACTTG
Statistics
Matches: 164, Mismatches: 29, Indels: 21
0.77 0.14 0.10
Matches are distributed among these distances:
152 13 0.08
153 142 0.87
154 9 0.05
ACGTcount: A:0.10, C:0.37, G:0.33, T:0.21
Consensus pattern (153 bp):
CTGTCGGGCTGGCTCGCCCAGGGTCCTGTGTTGTGCACCCTAGCTGGCACCCTATCGGGCTGGCT
CGCCCAAGGGCCTATGACGTGCGCCCCTCCTAGCACCCTGCCGGGCTAGCTCGCTCAGGAGCCGA
TGCGGTGCACCCCTGCTAGCATC
Found at i:6564855 original size:20 final size:20
Alignment explanation
Indices: 6564830--6564894 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
6564820 TTATTTTGAA
6564830 TAATTTAAATATTAATATTT
1 TAATTTAAATATTAATATTT
6564850 TAATTTAAAAATATTTCTTAATATTT
1 TAATTT--AAATA----TTAATATTT
*
6564876 TAAATTAAATATTAATATT
1 TAATTTAAATATTAATATT
6564895 AATCAAACCT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
20 14 0.37
22 5 0.13
24 5 0.13
26 14 0.37
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTTAAATATTAATATTT
Found at i:6564896 original size:26 final size:27
Alignment explanation
Indices: 6564837--6564897 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
6564827 GAATAATTTA
*
6564837 AATATTAATATTTTAATTTAAAAATATT
1 AATATTAATATTTTAAATT-AAAATATT
*
6564865 --TCTTAATATTTTAAATT-AAATATT
1 AATATTAATATTTTAAATTAAAATATT
6564889 AATATTAAT
1 AATATTAAT
6564898 CAAACCTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 7 0.25
26 21 0.75
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
AATATTAATATTTTAAATTAAAATATT
Found at i:6582684 original size:3 final size:3
Alignment explanation
Indices: 6582678--6582704 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6582668 AAAAAGATCG
6582678 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
6582705 TTGGTTGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6591918 original size:16 final size:18
Alignment explanation
Indices: 6591887--6591931 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 18
6591877 GATTGCTTTT
6591887 ATTATAATTATTTCCTTA
1 ATTATAATTATTTCCTTA
*
6591905 ATTAT-ATT-TTTCCTTT
1 ATTATAATTATTTCCTTA
6591921 ATTA-AATTATT
1 ATTATAATTATT
6591932 CAAAACTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 14 0.58
17 5 0.21
18 5 0.21
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTATAATTATTTCCTTA
Found at i:6602923 original size:6 final size:6
Alignment explanation
Indices: 6602912--6602936 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6602902 AAAAGATTTG
6602912 CTGCCC CTGCCC CTGCCC CTGCCC C
1 CTGCCC CTGCCC CTGCCC CTGCCC C
6602937 ATCCCACCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.16, T:0.16
Consensus pattern (6 bp):
CTGCCC
Found at i:6604823 original size:15 final size:17
Alignment explanation
Indices: 6604792--6604823 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
6604782 AAAAATGTAG
6604792 GCAATCACCCACCACCA
1 GCAATCACCCACCACCA
6604809 GCAA-CACCC-CCACCA
1 GCAATCACCCACCACCA
6604824 CACCCCACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.34, C:0.56, G:0.06, T:0.03
Consensus pattern (17 bp):
GCAATCACCCACCACCA
Found at i:6604834 original size:21 final size:22
Alignment explanation
Indices: 6604797--6604840 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
6604787 TGTAGGCAAT
6604797 CACCCACCACCAGCAACACCCC
1 CACCCACCACCAGCAACACCCC
*
6604819 CACCACACC-CCA-CAACCCCCC
1 CACC-CACCACCAGCAACACCCC
6604840 C
1 C
6604841 CCTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.30, C:0.68, G:0.02, T:0.00
Consensus pattern (22 bp):
CACCCACCACCAGCAACACCCC
Found at i:6609400 original size:41 final size:40
Alignment explanation
Indices: 6609309--6609405 Score: 106
Period size: 41 Copynumber: 2.4 Consensus size: 40
6609299 ATTTGATTTT
** * *
6609309 AAATAAAAATATTA-AAATTTTATTTTTTTTGTAAATTATA
1 AAATAAAAAT-TTATAAATTTTATTTTAATTATAAAATATA
* *
6609349 ATATCAAAATTTATAAATTTTATTTATAATTATAAAATATA
1 AAATAAAAATTTATAAATTTTATTT-TAATTATAAAATATA
*
6609390 AAATAAAAATTAATAA
1 AAATAAAAATTTATAA
6609406 TGAAAATATA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
39 3 0.07
40 19 0.41
41 24 0.52
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (40 bp):
AAATAAAAATTTATAAATTTTATTTTAATTATAAAATATA
Found at i:6621453 original size:48 final size:50
Alignment explanation
Indices: 6621401--6621494 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
6621391 TTATTGCTCT
* * *
6621401 TTATCTATGTTT-TTGTGTG-TTTTGGACATTGCAACCTGATTATTATTG
1 TTATCTACGTTTCTTCTGTGTTTTTAGACATTGCAACCTGATTATTATTG
6621449 TTATCTACGTTTCTTCTGTGTTTTTAGACATTGCAACCTGATTATT
1 TTATCTACGTTTCTTCTGTGTTTTTAGACATTGCAACCTGATTATT
6621495 CTCAACTGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 11 0.27
49 6 0.15
50 24 0.59
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (50 bp):
TTATCTACGTTTCTTCTGTGTTTTTAGACATTGCAACCTGATTATTATTG
Found at i:6633818 original size:57 final size:57
Alignment explanation
Indices: 6633739--6633903 Score: 280
Period size: 57 Copynumber: 2.9 Consensus size: 57
6633729 GACACGCATA
*
6633739 ACAGCAG-TAA-ATATTTGCATTCTATTCTGCTTTATTGTTACACTGATCAATGCTG
1 ACAGCAGTTAATATATTTGCATTCTATTCTGCTTTATTGTTAAACTGATCAATGCTG
* *
6633794 ACAGCAGTTAATATATTTGCATTCTATTCTGCTTTTTTGTTAAACTGATCAGTGCTG
1 ACAGCAGTTAATATATTTGCATTCTATTCTGCTTTATTGTTAAACTGATCAATGCTG
*
6633851 ACAGCAGTAAATATATTTGCATTCTATTCTGCTTTATTGTTAAACTGATCAAT
1 ACAGCAGTTAATATATTTGCATTCTATTCTGCTTTATTGTTAAACTGATCAAT
6633904 ACTGCCAAAA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
55 7 0.07
56 3 0.03
57 92 0.90
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (57 bp):
ACAGCAGTTAATATATTTGCATTCTATTCTGCTTTATTGTTAAACTGATCAATGCTG
Found at i:6641321 original size:32 final size:30
Alignment explanation
Indices: 6641237--6641337 Score: 91
Period size: 32 Copynumber: 3.4 Consensus size: 30
6641227 ATAAAAATTT
* * * *
6641237 AAATAAATTTTAAAATTTTTATTAT-ATTC
1 AAATAAATTTTTATATTTTTATTTTAAATC
*
6641266 -AATCAAA-TTTTATATTTTTATTTTGAATC
1 AAAT-AAATTTTTATATTTTTATTTTAAATC
* *
6641295 AAATAATTTTTTATATTTTTTTATTTTAAATT
1 AAATAAATTTTTATA--TTTTTATTTTAAATC
6641327 AAATAAATTTT
1 AAATAAATTTT
6641338 ATGATTAATC
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
28 17 0.29
29 8 0.14
30 10 0.17
32 23 0.40
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (30 bp):
AAATAAATTTTTATATTTTTATTTTAAATC
Found at i:6662747 original size:9 final size:10
Alignment explanation
Indices: 6662721--6662746 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6662711 CTTTGAATGC
6662721 AAAAAAATAA
1 AAAAAAATAA
6662731 AAAAAAATAA
1 AAAAAAATAA
6662741 AAAAAA
1 AAAAAA
6662747 TGAAGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:6678587 original size:14 final size:14
Alignment explanation
Indices: 6678565--6678608 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
6678555 CATTATTCTA
6678565 TTTATTTTTATTTAT
1 TTTA-TTTTATTTAT
6678580 TTTATTTTATTTAT
1 TTTATTTTATTTAT
6678594 TTTATATTT-TTTAT
1 TTTAT-TTTATTTAT
6678608 T
1 T
6678609 AAAATGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 21 0.75
15 7 0.25
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:6679195 original size:26 final size:26
Alignment explanation
Indices: 6679160--6679227 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 26
6679150 GTTATGTTAA
*
6679160 AAAAATAATATTATTATAAA-TCATGATT
1 AAAAA-AATATTATTACAAACT-AT-ATT
6679188 -AAAAAATATTATTACAAACTATATT
1 AAAAAAATATTATTACAAACTATATT
6679213 GAAAAAAATATTATT
1 -AAAAAAATATTATT
6679228 GTTATACGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 3 0.08
26 15 0.42
27 18 0.50
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (26 bp):
AAAAAAATATTATTACAAACTATATT
Found at i:6679451 original size:30 final size:29
Alignment explanation
Indices: 6679387--6679461 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
6679377 CGTTATGTTA
*
6679387 AAAAAAATATTATTCTTACACCTCATATT
1 AAAAAAATATTATTATTACACCTCATATT
* * *
6679416 GAAAAAATATTATTATTGCACTTTACAT-TT
1 AAAAAAATATTATTATTACAC-CT-CATATT
*
6679446 AAAAAAATTTTATTAT
1 AAAAAAATATTATTAT
6679462 ATGTCTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 18 0.47
30 17 0.45
31 3 0.08
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.41
Consensus pattern (29 bp):
AAAAAAATATTATTATTACACCTCATATT
Found at i:6699641 original size:39 final size:39
Alignment explanation
Indices: 6699587--6699667 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
6699577 TCGGGTTCCA
6699587 TTGAGAATAGTAAACCTTTTTAGTTGAATATGAGGTTGG
1 TTGAGAATAGTAAACCTTTTTAGTTGAATATGAGGTTGG
6699626 TTGAGAATAGTAAACCTTTTTAGTTGAATATGAGGTTGG
1 TTGAGAATAGTAAACCTTTTTAGTTGAATATGAGGTTGG
6699665 TTG
1 TTG
6699668 GTTTTGATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.40
Consensus pattern (39 bp):
TTGAGAATAGTAAACCTTTTTAGTTGAATATGAGGTTGG
Found at i:6702359 original size:14 final size:14
Alignment explanation
Indices: 6702340--6702368 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6702330 ATGCACTGCA
6702340 TAATATTATTTTGC
1 TAATATTATTTTGC
6702354 TAATATTATTTTGC
1 TAATATTATTTTGC
6702368 T
1 T
6702369 TTCTCAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
TAATATTATTTTGC
Found at i:6711889 original size:21 final size:21
Alignment explanation
Indices: 6711863--6711906 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
6711853 TAAGTCAAGT
6711863 TTAATTTTATTCAAGAGATTG
1 TTAATTTTATTCAAGAGATTG
*
6711884 TTAATTTTATTCAAGGGATTG
1 TTAATTTTATTCAAGAGATTG
6711905 TT
1 TT
6711907 TGCAGAGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.50
Consensus pattern (21 bp):
TTAATTTTATTCAAGAGATTG
Found at i:6712318 original size:17 final size:17
Alignment explanation
Indices: 6712296--6712329 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6712286 AGTGAGTTTA
6712296 AGATTGATCTTATAATC
1 AGATTGATCTTATAATC
6712313 AGATTGATCTTATAATC
1 AGATTGATCTTATAATC
6712330 TCTATTGCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
AGATTGATCTTATAATC
Found at i:6718541 original size:3 final size:3
Alignment explanation
Indices: 6718535--6718560 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6718525 ACCACCAAAA
6718535 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
6718561 AATTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6719703 original size:17 final size:17
Alignment explanation
Indices: 6719681--6719859 Score: 66
Period size: 16 Copynumber: 10.9 Consensus size: 17
6719671 AAAATATTTT
6719681 ATAATATTATAAT-TAAA
1 ATAATA-TATAATATAAA
6719698 ATAATATATAATAT-AA
1 ATAATATATAATATAAA
* *
6719714 AGAATA-AAAAT-TAAAA
1 ATAATATATAATAT-AAA
* *
6719730 ATAA-ATAAAATAAAAAA
1 ATAATATATAAT-ATAAA
* *
6719747 ATTAATAT-TTATATAAT
1 A-TAATATATAATATAAA
* *
6719764 ATAGATAAACAA-ATTAAA
1 ATA-ATATATAATA-TAAA
6719782 ATAAAATATATAATATAAA
1 AT--AATATATAATATAAA
6719801 A-AATAT-T--TA-AGAA
1 ATAATATATAATATA-AA
*
6719814 ATAATATATAATATATA
1 ATAATATATAATATAAA
6719831 A-AAT-TATAATA-ATAA
1 ATAATATATAATATA-AA
*
6719846 ATAAAATA-AATATA
1 ATAATATATAATATA
6719860 TGACATTAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 48
0.65 0.09 0.26
Matches are distributed among these distances:
12 1 0.01
13 5 0.04
14 7 0.06
15 16 0.13
16 39 0.32
17 26 0.21
18 12 0.10
19 13 0.11
20 2 0.02
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (17 bp):
ATAATATATAATATAAA
Found at i:6719737 original size:24 final size:25
Alignment explanation
Indices: 6719705--6719855 Score: 85
Period size: 29 Copynumber: 5.6 Consensus size: 25
6719695 AAAATAATAT
*
6719705 ATAATATAAAGA-ATAAAAATTAAAA
1 ATAATATAAA-ATAAAAAAATTAAAA
6719730 ATAA-ATAAAATAAAAAAATTAATATTTA
1 ATAATATAAAATAAAAAAATTAA-A---A
* *
6719758 TATAATAT-AGATAAACAAATTAAAA
1 -ATAATATAAAATAAAAAAATTAAAA
*
6719783 TAAAATATATAATATAAAAAATATTTAAGAA
1 -ATAATATA-AA-ATAAAAAA-A-TTAA-AA
* *
6719814 ATAATATATAATATATAAAATTATAATA
1 ATAATATAAAATA-AAAAAATTA-AA-A
6719842 ATAA-ATAAAATAAA
1 ATAATATAAAATAAA
6719856 TATATGACAT
Statistics
Matches: 99, Mismatches: 11, Indels: 31
0.70 0.08 0.22
Matches are distributed among these distances:
23 1 0.01
24 15 0.15
25 13 0.13
26 1 0.01
27 12 0.12
28 19 0.19
29 23 0.23
30 13 0.13
31 2 0.02
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (25 bp):
ATAATATAAAATAAAAAAATTAAAA
Found at i:6719816 original size:32 final size:34
Alignment explanation
Indices: 6719780--6720076 Score: 109
Period size: 34 Copynumber: 8.6 Consensus size: 34
6719770 AAACAAATTA
*
6719780 AAATAAAATATATAATATA-AAAAATAT-TTAAG
1 AAATAAAATATATAATATATAAAAATATAATAAG
* *
6719812 AAAT--AATATATAATATATAAAATTATAATAAT
1 AAATAAAATATATAATATATAAAAATATAATAAG
* * * *
6719844 AAATAAAATAAATATATGACATTAAATATATTTAAATATG
1 AAATAAAATATATA-AT-ATA-TAAA-A-ATAT-AATAAG
* * * * * *
6719884 ATATTATATAAATTAATA-ATATAAATATAATATATT
1 AAATAAAATATA-TAATATATAAAAATATAATA-A-G
* *
6719920 AAATATAAATATA-AAAATTATAATAATA-AATAA-
1 AAATA-AAATATATAATA-TATAAAAATATAATAAG
* *
6719953 AAATAAAATATATGATAT-TAAAAATATATTTAAG
1 AAATAAAATATATAATATATAAAAATATA-ATAAG
* * * *
6719987 AAATGAATTATATAA-AAATTAATAATATAAATATA-
1 AAATAAAATATATAATATA-TAAAAATAT-AATA-AG
* *
6720022 AATTATTAAATATA-AA-ATATAAAATATTATAATAAT
1 AA--ATAAAATATATAATATATAAAA-A-TATAATAAG
*
6720058 AAATAAAA-ATAAAATATAT
1 AAATAAAATATATAATATAT
6720077 GATATTAAAA
Statistics
Matches: 196, Mismatches: 38, Indels: 59
0.67 0.13 0.20
Matches are distributed among these distances:
30 13 0.07
31 14 0.07
32 20 0.10
33 14 0.07
34 30 0.15
35 30 0.15
36 23 0.12
37 30 0.15
38 2 0.01
39 3 0.02
40 15 0.08
41 2 0.01
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (34 bp):
AAATAAAATATATAATATATAAAAATATAATAAG
Found at i:6719905 original size:13 final size:14
Alignment explanation
Indices: 6719889--6720075 Score: 98
Period size: 14 Copynumber: 13.8 Consensus size: 14
6719879 ATATGATATT
6719889 ATATAAAT-TAATA
1 ATATAAATATAATA
6719902 ATATAAATATAAT-
1 ATATAAATATAATA
6719915 ATATTAAATAT-A-A
1 ATA-TAAATATAATA
* *
6719928 ATATAAAAATTATA
1 ATATAAATATAATA
6719942 ATAATAAATA-AA-A
1 AT-ATAAATATAATA
*
6719955 ATA-AAATAT-ATG
1 ATATAAATATAATA
*
6719967 ATATTAA-A-AATA
1 ATATAAATATAATA
* * *
6719979 TATTTAAGAAATGAATT
1 -ATATAA-ATAT-AATA
*
6719996 ATATAAAAATTAATA
1 ATATAAATA-TAATA
6720011 ATATAAATATAA-A
1 ATATAAATATAATA
*
6720024 TTATTAAATATAA-A
1 ATA-TAAATATAATA
*
6720038 ATATAAAATATTATA
1 ATAT-AAATATAATA
6720053 ATAATAAATA-AA-A
1 AT-ATAAATATAATA
6720066 ATA-AAATATA
1 ATATAAATATA
6720076 TGATATTAAA
Statistics
Matches: 137, Mismatches: 16, Indels: 43
0.70 0.08 0.22
Matches are distributed among these distances:
11 11 0.08
12 15 0.11
13 32 0.23
14 39 0.28
15 29 0.21
16 8 0.06
17 3 0.02
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
ATATAAATATAATA
Found at i:6720014 original size:15 final size:14
Alignment explanation
Indices: 6719700--6720131 Score: 93
Period size: 14 Copynumber: 30.3 Consensus size: 14
6719690 TAATTAAAAT
6719700 AATATATAATATAAA
1 AATA-ATAATATAAA
*
6719715 GAATAAAAAT-TAAA
1 -AATAATAATATAAA
*
6719729 AATAAATAAAATAAA
1 AAT-AATAATATAAA
**
6719744 AA-AATTAATATTTA
1 AATAA-TAATATAAA
* *
6719758 TATAATATAGATAAA
1 AATAATA-ATATAAA
* *
6719773 CAA-ATTAAAAT-AA
1 -AATAATAATATAAA
6719786 AATATATAATATAAAA
1 AATA-ATAATAT-AAA
* * *
6719802 AATATTTAAGA-AAT
1 AATA-ATAATATAAA
6719816 AATATATAATATATAA
1 AATA-ATAATATA-AA
*
6719832 AATTATAATAATAAA
1 AATAATAAT-ATAAA
*
6719847 TAA-AATAAATATATGAC
1 -AATAAT-AATATA--AA
* *
6719864 ATTAAATATATTTAAA
1 AAT-AATA-ATATAAA
* * *
6719880 TATGATATTATATAA
1 AATAATAATATA-AA
*
6719895 ATTAATAATATAAA
1 AATAATAATATAAA
* *
6719909 TATAAT-ATAT-TA
1 AATAATAATATAAA
6719921 AAT-ATAAATATAAA
1 AATAAT-AATATAAA
* *
6719935 AATTATAATA-ATA
1 AATAATAATATAAA
6719948 AATAA-AA-AT-AA
1 AATAATAATATAAA
*
6719959 AATATATGATATTAAA
1 AATA-ATAATA-TAAA
*
6719975 AAT-AT-ATTTAAGA
1 AATAATAATATAA-A
*
6719988 AATGAATTATATAAA
1 AAT-AATAATATAAA
6720003 AATTAATAATATAAA
1 AA-TAATAATATAAA
* *
6720018 TATAA-ATTATTAAA
1 AATAATAATA-TAAA
*
6720032 TATAA-AATATAAA
1 AATAATAATATAAA
* *
6720045 ATATTATAATA-ATA
1 A-ATAATAATATAAA
6720059 AATAA-AA-AT-AA
1 AATAATAATATAAA
* *
6720070 AATATATGATATTAA
1 AATA-ATAATATAAA
*
6720085 AAT-AT-ATTTAAGA
1 AATAATAATATAA-A
*
6720098 AATGATATTATATAAA
1 AAT-A-ATAATATAAA
6720114 AATTAATAATA-AAA
1 AA-TAATAATATAAA
6720128 AATA
1 AATA
6720132 TAAATATATT
Statistics
Matches: 305, Mismatches: 61, Indels: 103
0.65 0.13 0.22
Matches are distributed among these distances:
11 14 0.05
12 18 0.06
13 48 0.16
14 84 0.28
15 78 0.26
16 48 0.16
17 8 0.03
18 7 0.02
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
AATAATAATATAAA
Found at i:6720085 original size:111 final size:111
Alignment explanation
Indices: 6719816--6720144 Score: 516
Period size: 111 Copynumber: 3.0 Consensus size: 111
6719806 TTTAAGAAAT
* *
6719816 AATATATAATATATAAAATTATAATAATAAAT-AAAAT-AAATATATGACATT-AAATATATTTA
1 AATATAAAATATA-AAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAATATATTTA
*
6719878 A-ATATGATATTATAT--AAATTAATAATATAAATAT-AATATATTA
65 AGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
6719921 AATAT-AAATATAAAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTA
1 AATATAAAATATAAAAATTATAATAATAAATAAAAATAAAATATATGATATT-AAAATATATTTA
6719985 AGAAATGA-ATTATATAAAAATTAATAATATAAATATAAAT-TATTA
65 AGAAATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
6720030 AATATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAATATATTTA
1 AATATAAAATATAAAA-ATTATAATAATAAATAAAAATAAAATATATGATATTAAAATATATTTA
*
6720095 AGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
65 AGAAATGATATTATATAAAAATTAATAAT-ATAAATATAAATATATTA
6720143 AA
1 AA
6720145 CTTATATTTT
Statistics
Matches: 207, Mismatches: 4, Indels: 18
0.90 0.02 0.08
Matches are distributed among these distances:
103 18 0.09
104 11 0.05
105 18 0.09
107 19 0.09
108 5 0.02
109 29 0.14
110 33 0.16
111 56 0.27
112 11 0.05
113 7 0.03
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (111 bp):
AATATAAAATATAAAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAATATATTTAA
GAAATGATATTATATAAAAATTAATAATATAAATATAAATATATTA
Found at i:6720343 original size:15 final size:15
Alignment explanation
Indices: 6720289--6720334 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
6720279 TGTTATTTTC
* *
6720289 CTTGTAATCACATTG
1 CTTGCAATCACATTA
6720304 CTTGCAATCACATTA
1 CTTGCAATCACATTA
6720319 CTTGCAATCACATTA
1 CTTGCAATCACATTA
6720334 C
1 C
6720335 CTGTAATCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (15 bp):
CTTGCAATCACATTA
Found at i:6727460 original size:2 final size:2
Alignment explanation
Indices: 6727453--6727488 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6727443 TTGGTGAAGT
6727453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6727489 AATAGTTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6743109 original size:13 final size:13
Alignment explanation
Indices: 6743091--6743117 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6743081 TGATCAAGTG
6743091 CATTACCAGAGCT
1 CATTACCAGAGCT
6743104 CATTACCAGAGCT
1 CATTACCAGAGCT
6743117 C
1 C
6743118 GCTGTTATCA
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:0.33, G:0.15, T:0.22
Consensus pattern (13 bp):
CATTACCAGAGCT
Found at i:6747100 original size:22 final size:22
Alignment explanation
Indices: 6747061--6747103 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6747051 ATTGAAGCAA
*
6747061 CCAAATTCAATTGGCAACTATT
1 CCAAATTCAATTCGCAACTATT
* *
6747083 CCAAATTCACTTCTCAACTAT
1 CCAAATTCAATTCGCAACTAT
6747104 AAACTTCCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (22 bp):
CCAAATTCAATTCGCAACTATT
Found at i:6752563 original size:4 final size:4
Alignment explanation
Indices: 6752554--6752606 Score: 70
Period size: 4 Copynumber: 13.2 Consensus size: 4
6752544 CATATACATA
* * *
6752554 TATG TATG TATG TATG TATG TATG TATG TATG TGTG TGTG TGTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
6752602 AATG T
1 TATG T
6752607 TATCATTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:6759769 original size:23 final size:23
Alignment explanation
Indices: 6759739--6759785 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
6759729 AACACCCTCA
6759739 AATTGCATTATTGCATTTTCTTT
1 AATTGCATTATTGCATTTTCTTT
6759762 AATTGCATTATTGCATTTTCTTT
1 AATTGCATTATTGCATTTTCTTT
6759785 A
1 A
6759786 GTTTCAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (23 bp):
AATTGCATTATTGCATTTTCTTT
Found at i:6761983 original size:19 final size:20
Alignment explanation
Indices: 6761927--6761983 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
6761917 TTGGAAGAAG
*
6761927 AAAAATAATATAAT-ATTTAA
1 AAAAATTATA-AATAATTTAA
*
6761947 AAAAATTATAAATTATTTAA
1 AAAAATTATAAATAATTTAA
*
6761967 TAAAATT-TAAATAATTT
1 AAAAATTATAAATAATTT
6761984 TTTATTATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.36
20 21 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATTATAAATAATTTAA
Found at i:6762315 original size:22 final size:22
Alignment explanation
Indices: 6762282--6762323 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
6762272 TTAACTAAAA
6762282 AATATAAAAATTTAATTAAATGT
1 AATATAAAAA-TTAATTAAATGT
*
6762305 AATA-AAAAATTATTTAAAT
1 AATATAAAAATTAATTAAAT
6762324 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AATATAAAAATTAATTAAATGT
Done.