Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 116 of 129
Found at i:20825710 original size:30 final size:30
Alignment explanation
Indices: 20825674--20825746 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
20825664 TTTATTTAGA
*
20825674 TAAAAATTAAAAAATTATTTGGA-TCCAAAT
1 TAAAAATTAAAAAATTA-TGGGAGTCCAAAT
*** *
20825704 TAAAAATTAAATGCTTATGGGAGTGCAAAT
1 TAAAAATTAAAAAATTATGGGAGTCCAAAT
20825734 TAAAAATTAAAAA
1 TAAAAATTAAAAA
20825747 TTAAAAATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 4 0.11
30 31 0.89
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.30
Consensus pattern (30 bp):
TAAAAATTAAAAAATTATGGGAGTCCAAAT
Found at i:20825752 original size:6 final size:7
Alignment explanation
Indices: 20825730--20825755 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20825720 ATGGGAGTGC
20825730 AAATTAA
1 AAATTAA
20825737 AAATTAA
1 AAATTAA
20825744 AAATTAA
1 AAATTAA
20825751 AAATT
1 AAATT
20825756 TATTTGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AAATTAA
Found at i:20830868 original size:30 final size:30
Alignment explanation
Indices: 20830834--20830898 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
20830824 TCATAAATTT
* *
20830834 TTTATTTCGAATTAGTTGAATTATTAAATA
1 TTTATTTCGAATTAATTGAACTATTAAATA
** * *
20830864 TTTATTTTTATTTAATTGAACTCTTAAATA
1 TTTATTTCGAATTAATTGAACTATTAAATA
20830894 TTTAT
1 TTTAT
20830899 CTTAATCCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (30 bp):
TTTATTTCGAATTAATTGAACTATTAAATA
Found at i:20830916 original size:30 final size:30
Alignment explanation
Indices: 20830857--20830920 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
20830847 AGTTGAATTA
* * ** *
20830857 TTAAATATTTATTTTTATTTAATTGAACTC
1 TTAAATATTTATCTTAATCCAATTAAACTC
20830887 TTAAATATTTATCTTAATCCAATTAAACTC
1 TTAAATATTTATCTTAATCCAATTAAACTC
20830917 TTAA
1 TTAA
20830921 TTCGTTGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (30 bp):
TTAAATATTTATCTTAATCCAATTAAACTC
Found at i:20835044 original size:8 final size:8
Alignment explanation
Indices: 20835024--20835064 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
20835014 ATATTATTTT
20835024 TAAA-ATA
1 TAAATATA
*
20835031 TAAATATT
1 TAAATATA
20835039 TAAATATA
1 TAAATATA
*
20835047 TAATTATA
1 TAAATATA
20835055 TAAATATA
1 TAAATATA
20835063 TA
1 TA
20835065 TTAAAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAATATA
Found at i:20840532 original size:31 final size:31
Alignment explanation
Indices: 20840494--20840560 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
20840484 CATAAGCCTA
* *
20840494 ATAATATAGGTTCTGTCCTTGGTGCTCAATT
1 ATAATATAGGTTCTGTACTTAGTGCTCAATT
20840525 ATAATATAGGTTCTGTACTTAGTGCTCAATT
1 ATAATATAGGTTCTGTACTTAGTGCTCAATT
20840556 ATAAT
1 ATAAT
20840561 GATATGTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.42
Consensus pattern (31 bp):
ATAATATAGGTTCTGTACTTAGTGCTCAATT
Found at i:20840949 original size:12 final size:10
Alignment explanation
Indices: 20840921--20840945 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20840911 ATGTGAAAAA
20840921 ATTTTAATAT
1 ATTTTAATAT
20840931 ATTTTAATAT
1 ATTTTAATAT
20840941 ATTTT
1 ATTTT
20840946 TTAAATGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:20841096 original size:17 final size:16
Alignment explanation
Indices: 20841076--20841110 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
20841066 ATTTTATCTA
*
20841076 TTTATTAATTTATATTT
1 TTTATTAAATTAT-TTT
20841093 TTTATTAAATTATTTT
1 TTTATTAAATTATTTT
20841109 TT
1 TT
20841111 AAAAAGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATTAAATTATTTT
Found at i:20841936 original size:3 final size:3
Alignment explanation
Indices: 20841928--20841954 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20841918 GGCATGAATC
20841928 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
20841955 AGAATTGATA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20842937 original size:25 final size:25
Alignment explanation
Indices: 20842903--20842957 Score: 89
Period size: 22 Copynumber: 2.3 Consensus size: 25
20842893 TCCAAAATTA
20842903 ATAAAATATTATTTTT--TA-AAAT
1 ATAAAATATTATTTTTAATATAAAT
20842925 ATAAAATATTATTTTTAATATAAAT
1 ATAAAATATTATTTTTAATATAAAT
20842950 ATAAAATA
1 ATAAAATA
20842958 AATAAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.53
24 2 0.07
25 12 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAAAATATTATTTTTAATATAAAT
Found at i:20842952 original size:6 final size:6
Alignment explanation
Indices: 20842941--20842985 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
20842931 TATTATTTTT
20842941 AATATA AATATA AA-AT- AA-ATA AATATA AA-A-A AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
20842984 AA
1 AA
20842986 ATTAAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 7 0.20
5 6 0.17
6 22 0.63
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (6 bp):
AATATA
Found at i:20842978 original size:16 final size:16
Alignment explanation
Indices: 20842941--20842986 Score: 76
Period size: 15 Copynumber: 2.9 Consensus size: 16
20842931 TATTATTTTT
*
20842941 AATATAAATATAAAAT
1 AATATAAATATAAAAA
20842957 AA-ATAAATATAAAAA
1 AATATAAATATAAAAA
20842972 AATATAAATATAAAA
1 AATATAAATATAAAA
20842987 TTAAATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATATAAATATAAAAA
Found at i:20842979 original size:31 final size:33
Alignment explanation
Indices: 20842941--20843008 Score: 104
Period size: 31 Copynumber: 2.1 Consensus size: 33
20842931 TATTATTTTT
20842941 AATATAAATATAAAA-TAAATAAAT-ATAAAAA
1 AATATAAATATAAAATTAAATAAATAATAAAAA
* *
20842972 AATATAAATATAAAATTAAATAATTAATTAAAA
1 AATATAAATATAAAATTAAATAAATAATAAAAA
20843005 AATA
1 AATA
20843009 ATTTTTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 15 0.45
32 8 0.24
33 10 0.30
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (33 bp):
AATATAAATATAAAATTAAATAAATAATAAAAA
Found at i:20842993 original size:12 final size:13
Alignment explanation
Indices: 20842941--20842993 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
20842931 TATTATTTTT
20842941 AATATAAATATAA
1 AATATAAATATAA
20842954 AATAAATAAATATAAAAA
1 AAT--ATAAATAT---AA
20842972 AATATAAATATAA
1 AATATAAATATAA
20842985 AAT-TAAATA
1 AATATAAATA
20842994 ATTAATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
12 6 0.17
13 8 0.23
15 8 0.23
16 8 0.23
18 5 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATATAAATATAA
Found at i:20842994 original size:10 final size:11
Alignment explanation
Indices: 20842941--20842994 Score: 53
Period size: 10 Copynumber: 5.0 Consensus size: 11
20842931 TATTATTTTT
20842941 AATATAAATATA
1 AATATAAATA-A
20842953 AA-ATAAAT-A
1 AATATAAATAA
20842962 AATATAAA-AA
1 AATATAAATAA
20842972 AATATAAATATA
1 AATATAAATA-A
20842984 AA-ATTAAATAA
1 AATA-TAAATAA
20842995 TTAATTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
9 3 0.08
10 14 0.38
11 9 0.24
12 11 0.30
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATATAAATAA
Found at i:20842994 original size:16 final size:16
Alignment explanation
Indices: 20842940--20842987 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
20842930 ATATTATTTT
20842940 TAATATAAATATAAAA
1 TAATATAAATATAAAA
20842956 TAA-ATAAATATAAAA
1 TAATATAAATATAAAA
*
20842971 AAATATAAATATAAAA
1 TAATATAAATATAAAA
20842987 T
1 T
20842988 TAAATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 14 0.48
16 15 0.52
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAATATAAATATAAAA
Found at i:20845750 original size:20 final size:21
Alignment explanation
Indices: 20845725--20845765 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
20845715 TTTAAAATTC
*
20845725 ATTTATATTTATTT-GGGTTT
1 ATTTATATTCATTTAGGGTTT
*
20845745 ATTTATGTTCATTTAGGGTTT
1 ATTTATATTCATTTAGGGTTT
20845766 GCTTGTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.20, C:0.02, G:0.17, T:0.61
Consensus pattern (21 bp):
ATTTATATTCATTTAGGGTTT
Found at i:20846403 original size:19 final size:20
Alignment explanation
Indices: 20846360--20846403 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
20846350 AAAAGTAGAA
*
20846360 AAATTTTTGCAATAATCTTG
1 AAATTTTTGCAAAAATCTTG
* *
20846380 TAATTTTTG-AAAAATTTTG
1 AAATTTTTGCAAAAATCTTG
20846399 AAATT
1 AAATT
20846404 GAGTTCTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (20 bp):
AAATTTTTGCAAAAATCTTG
Found at i:20846693 original size:13 final size:13
Alignment explanation
Indices: 20846656--20846697 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
20846646 ATTTTACATA
* *
20846656 TTATTTTCATTGT
1 TTATTTTGATTAT
*
20846669 TT-TTTGGATTAT
1 TTATTTTGATTAT
20846681 TTATTTTGATTAT
1 TTATTTTGATTAT
20846694 TTAT
1 TTAT
20846698 GTCATTTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.19, C:0.02, G:0.10, T:0.69
Consensus pattern (13 bp):
TTATTTTGATTAT
Found at i:20847328 original size:25 final size:25
Alignment explanation
Indices: 20847300--20847350 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
20847290 GCTAAAAAGA
*
20847300 TAATTTAAAATAATTACTATCAATT
1 TAATTTAAAATAATTACGATCAATT
*
20847325 TAATTTAAAATAATTACGATTAATT
1 TAATTTAAAATAATTACGATCAATT
20847350 T
1 T
20847351 GTGGACATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (25 bp):
TAATTTAAAATAATTACGATCAATT
Found at i:20847964 original size:17 final size:19
Alignment explanation
Indices: 20847938--20847980 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
20847928 AATTTATTCA
20847938 TTTTTAA-T-TAATGTAAT
1 TTTTTAATTATAATGTAAT
* *
20847955 TTTTTTATTATAATTTAAT
1 TTTTTAATTATAATGTAAT
20847974 TTTTTAA
1 TTTTTAA
20847981 AAGTAACCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 6 0.29
18 1 0.05
19 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTTAATTATAATGTAAT
Found at i:20848420 original size:25 final size:27
Alignment explanation
Indices: 20848374--20848423 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
20848364 GTGTGGGTCA
*
20848374 ATATTATATATACAAACCAAAAAATAT
1 ATATTATATATACAAACAAAAAAATAT
*
20848401 ATATTATA-ATA-GAACAAAAAAAT
1 ATATTATATATACAAACAAAAAAAT
20848424 TAAGAGGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 3 0.14
27 8 0.38
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (27 bp):
ATATTATATATACAAACAAAAAAATAT
Found at i:20851843 original size:15 final size:15
Alignment explanation
Indices: 20851820--20851851 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20851810 AGACAATAGC
20851820 AAATAAACTATTATT
1 AAATAAACTATTATT
*
20851835 AAATCAACTATTATT
1 AAATAAACTATTATT
20851850 AA
1 AA
20851852 TACCTTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATAAACTATTATT
Found at i:20860922 original size:52 final size:52
Alignment explanation
Indices: 20860849--20860993 Score: 186
Period size: 52 Copynumber: 2.8 Consensus size: 52
20860839 TATAACCATA
* * *
20860849 CAAACTTACCCATTAAAAATCTCTTTTCTCTTAGAATTCTTCTCTTATAAGT
1 CAAACTTACCTATTAAGAATCTCTTTTCTCTTATAATTCTTCTCTTATAAGT
* * * *
20860901 CAAACTTGCCTATTAAGAATCTCTTTCCT-TTGATAATTCTTCTTTTGTAAGT
1 CAAACTTACCTATTAAGAATCTCTTTTCTCTT-ATAATTCTTCTCTTATAAGT
*
20860953 CAAACTTATCTATTAAGAATCATC-TTTCTCTTATAATTCTT
1 CAAACTTACCTATTAAGAATC-TCTTTTCTCTTATAATTCTT
20860994 TTTTTACAAG
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
51 2 0.03
52 74 0.93
53 4 0.05
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.45
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCTCTTTTCTCTTATAATTCTTCTCTTATAAGT
Found at i:20863760 original size:3 final size:3
Alignment explanation
Indices: 20863747--20863786 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
20863737 TGTTAATGAT
20863747 TAA TGAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20863787 ATTTATAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20868868 original size:29 final size:29
Alignment explanation
Indices: 20868831--20868886 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
20868821 TTTTAAAAAA
* *
20868831 ATTTCAATCACTT-TATTTTTAAAATTTTT
1 ATTTCAATCA-TTCAATTTTGAAAATTTTT
*
20868860 ATTTTAATCATTCAATTTTGAAAATTT
1 ATTTCAATCATTCAATTTTGAAAATTT
20868887 AAAATTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (29 bp):
ATTTCAATCATTCAATTTTGAAAATTTTT
Found at i:20874992 original size:13 final size:13
Alignment explanation
Indices: 20874968--20875001 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
20874958 GTATTATGCA
*
20874968 AAAAAATGCCTTG
1 AAAAAATTCCTTG
*
20874981 AATAAATTCCTTG
1 AAAAAATTCCTTG
20874994 AAAAAATT
1 AAAAAATT
20875002 ATAACAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (13 bp):
AAAAAATTCCTTG
Found at i:20875572 original size:187 final size:185
Alignment explanation
Indices: 20875072--20875970 Score: 933
Period size: 187 Copynumber: 4.9 Consensus size: 185
20875062 TTTATATTAA
* * * * *
20875072 AAGACGCATTTTATAATCTCAATAATTTTGAAAAGAAAATTATTGAAGGCGTTTGTTCTCAAAAA
1 AAGACGCCTTTAATAATCTCAAAAATTTTTAAAATAAAATTATTGAAGGCGTTTGTTCT-AAAAA
* *
20875137 AATACCTTCAATAATTATGTACATAAATTAAAAGAAATCAGTGAAGG-TGTTTTTCTAG-ATAAA
65 AATACCTTTAATAATTATGTACATAAATT-AAA-AAATTAGTGAAGGCT-TTTTTCTAGAATAAA
* * * * *
20875200 CGCCTTCATTAACCATCTTAAAATTTGTGTAGTAAAATAGT-AA-AGGTGTTTTTCACT-G
127 CGCCTTCACTAACCATCTTAAAATTTGAGTAGTGAAATATTGAATACGT-TTTTT-ACTAG
* ** * *
20875258 AAAAATACCTTTAATAATCTCAAAAA-TTTTAAAAAAAAATTATTGAATGCG-TTGTTCTAAAAA
1 -AAGACGCCTTTAATAATCTCAAAAATTTTTAAAATAAAATTATTGAAGGCGTTTGTTCTAAAAA
*
20875321 AAT-GCTTTAATAATTATGTACATAAATTAAAAGGAATTAGTGAAGGCATTTTTT-TAGAATAAA
65 AATACCTTTAATAATTATGTACATAAATTAAAA--AATTAGTGAAGGC-TTTTTTCTAGAATAAA
* *
20875384 CGCCGTCACTAACAATCTTAAAATTTGAGTAGTGAAATATTGAATACGTTTTTTACTAG
127 CGCCTTCACTAACCATCTTAAAATTTGAGTAGTGAAATATTGAATACGTTTTTTACTAG
*
20875443 AAGACGCCTTTAATAATC-CTAAAAATTTTTAAAATAAAATTATTAAAGGCGTTTGTTCTAAAAA
1 AAGACGCCTTTAATAATCTC-AAAAATTTTTAAAATAAAATTATTGAAGGCGTTTGTTCTAAAAA
* * *
20875507 AATGCCTTTAATAATTATGTACA-AAATTTTAAAAAATTTATTGAAGGCTTTTTTCTGGAATAAA
65 AATACCTTTAATAATTATGTACATAAA--TTAAAAAA-TTAGTGAAGGCTTTTTTCTAGAATAAA
* * ** ** ** *
20875571 CGTCTTCACTAACCGTCTTAAAATTTGAGTTTTGGTATATTGAAGGCGTTTTTCACTAG
127 CGCCTTCACTAACCATCTTAAAATTTGAGTAGTGAAATATTGAATACGTTTTTTACTAG
* * *
20875630 AAGACACCTTTAATAATCTTAAAAATTTTTAAAATGAAATTATTGAAGGCGTTTGTTCT-AAAAA
1 AAGACGCCTTTAATAATCTCAAAAATTTTTAAAATAAAATTATTGAAGGCGTTTGTTCTAAAAAA
* * * * *
20875694 ATACCTTCAATAATTATGTACATAAATGAAATGAAATTAGTGAATGCGTTTTTCTAGAATAAACA
66 ATACCTTTAATAATTATGTACATAAATTAAA--AAATTAGTGAAGGCTTTTTTCTAGAATAAACG
* * *
20875759 CTTTCACTAACCATATTAAAATTTGAATAGTGAAATA-T---T--G---------A-
129 CCTTCACTAACCATCTTAAAATTTGAGTAGTGAAATATTGAATACGTTTTTTACTAG
* *
20875800 AAGACGCCTTTAATAATCTCAATAATTGTTT-TAA-AAAATTATTGAAGGCGTTTGTTCTAAAAA
1 AAGACGCCTTTAATAATCTCAAAAATT-TTTAAAATAAAATTATTGAAGGCGTTTGTTCTAAAAA
* * * *
20875863 AAAACCTTTAATAATTATGTACATAAATTAAAAAGAATTAGTAAATG-TAGTTTTCTAGAATAAA
65 AATACCTTTAATAATTATGTACATAAATT-AAAA-AATTAGTGAAGGCT-TTTTTCTAGAATAAA
* *
20875927 CGCCTTCACTAATCGTCTTAAAATTTGAGTAGTGAAATATTGAA
127 CGCCTTCACTAACCATCTTAAAATTTGAGTAGTGAAATATTGAA
20875971 GGTATTTTAC
Statistics
Matches: 605, Mismatches: 78, Indels: 71
0.80 0.10 0.09
Matches are distributed among these distances:
169 24 0.04
170 114 0.19
171 8 0.01
180 1 0.00
181 1 0.00
182 3 0.00
183 38 0.06
184 76 0.13
185 43 0.07
186 128 0.21
187 163 0.27
188 6 0.01
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (185 bp):
AAGACGCCTTTAATAATCTCAAAAATTTTTAAAATAAAATTATTGAAGGCGTTTGTTCTAAAAAA
ATACCTTTAATAATTATGTACATAAATTAAAAAATTAGTGAAGGCTTTTTTCTAGAATAAACGCC
TTCACTAACCATCTTAAAATTTGAGTAGTGAAATATTGAATACGTTTTTTACTAG
Found at i:20875919 original size:170 final size:169
Alignment explanation
Indices: 20875630--20875970 Score: 472
Period size: 170 Copynumber: 2.0 Consensus size: 169
20875620 TTTTCACTAG
*
20875630 AAGACACCTTTAATAATCTTAAAAATTTTTAAAATGAAATTATTGAAGGCGTTTGTTCTAAAAAA
1 AAGACACCTTTAATAATCTCAAAAATTTTTAAAA-GAAATTATTGAAGGCGTTTGTTCTAAAAAA
* * * * *
20875695 TACCTTCAATAATTATGTACATAAATGAAATGAAATTAGTGAATGCGTTTTTCTAGAATAAACAC
65 AACCTTCAATAATTATGTACATAAATAAAAAGAAATTAGTAAATGAGTTTTTCTAGAATAAACAC
*
20875760 TTTCACTAACCATATTAAAATTTGAATAGTGAAATATTGA
130 CTTCACTAACCATATTAAAATTTGAATAGTGAAATATTGA
* * *
20875800 AAGACGCCTTTAATAATCTCAATAATTGTTTTAAA-AAATTATTGAAGGCGTTTGTTCTAAAAAA
1 AAGACACCTTTAATAATCTCAAAAATT-TTTAAAAGAAATTATTGAAGGCGTTTGTTCT-AAAAA
*
20875864 AAACCTTTAATAATTATGTACATAAATTAAAAAG-AATTAGTAAATGTAG-TTTTCTAGAATAAA
64 AAACCTTCAATAATTATGTACATAAA-TAAAAAGAAATTAGTAAATG-AGTTTTTCTAGAATAAA
* * * * *
20875927 CGCCTTCACTAATCGTCTTAAAATTTGAGTAGTGAAATATTGA
127 CACCTTCACTAACCATATTAAAATTTGAATAGTGAAATATTGA
20875970 A
1 A
20875971 GGTATTTTAC
Statistics
Matches: 151, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
169 23 0.15
170 116 0.77
171 12 0.08
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (169 bp):
AAGACACCTTTAATAATCTCAAAAATTTTTAAAAGAAATTATTGAAGGCGTTTGTTCTAAAAAAA
ACCTTCAATAATTATGTACATAAATAAAAAGAAATTAGTAAATGAGTTTTTCTAGAATAAACACC
TTCACTAACCATATTAAAATTTGAATAGTGAAATATTGA
Found at i:20876029 original size:125 final size:123
Alignment explanation
Indices: 20875891--20876124 Score: 297
Period size: 125 Copynumber: 1.9 Consensus size: 123
20875881 GTACATAAAT
* * * **
20875891 TAAAAAGAATTAGTAAATGTAGTTTTCTAGAATAAACGCCTTCACTAATCGTCTTAAAATTTGAG
1 TAAAAAGAATTAGTAAAGGCAGTTTTCTAGAATAAACGCCTTCAATAA-CCCCTTAAAATTTGAG
* *
20875956 TAGTGAAATATTGAAGGTATTTTACACTAGAAGATGCCTTCAATAAATTTTTTTAAAAAA
65 TAGTGAAATATTAAAGGCATTTTACA-TAGAAGATGCCTTCAATAAATTTTTTTAAAAAA
* * * * * *
20876016 TAAAACGAATTAGTCAAGGCATTTTTTTAGAATAAATGCCTTCAATAACCCCTTAAAATTTTAGT
1 TAAAAAGAATTAGTAAAGGCAGTTTTCTAGAATAAACGCCTTCAATAACCCCTTAAAATTTGAGT
* ** *
20876081 AGTGTAATATTAAAGGCATTTTGTATAGAAGATGCCTTTAATAA
66 AGTGAAATATTAAAGGCATTTTACATAGAAGATGCCTTCAATAA
20876125 TCCTAAACAA
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
123 18 0.20
124 34 0.37
125 40 0.43
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (123 bp):
TAAAAAGAATTAGTAAAGGCAGTTTTCTAGAATAAACGCCTTCAATAACCCCTTAAAATTTGAGT
AGTGAAATATTAAAGGCATTTTACATAGAAGATGCCTTCAATAAATTTTTTTAAAAAA
Found at i:20885977 original size:21 final size:21
Alignment explanation
Indices: 20885928--20885974 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 21
20885918 TCGTCATTAT
20885928 AATTATGTTCTTATGATAATAA
1 AATTAT-TTCTTATGATAATAA
20885950 AATTATTTCTTAT--T-ATAA
1 AATTATTTCTTATGATAATAA
20885968 AATTATT
1 AATTATT
20885975 ATTGATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
21 7 0.28
22 6 0.24
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (21 bp):
AATTATTTCTTATGATAATAA
Found at i:20889526 original size:11 final size:11
Alignment explanation
Indices: 20889510--20889534 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20889500 GGGGCAAACA
20889510 TTTTATTTTAT
1 TTTTATTTTAT
20889521 TTTTATTTTAT
1 TTTTATTTTAT
20889532 TTT
1 TTT
20889535 CATGCATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:20897669 original size:89 final size:89
Alignment explanation
Indices: 20897515--20897683 Score: 230
Period size: 89 Copynumber: 1.9 Consensus size: 89
20897505 ATCATTTCTT
* ** * * * *
20897515 ATGATTCATGGTTTCATCTTGTTCATTTATTTTTAACCTCAACTCGATCCTGATCACTTTGTTTT
1 ATGATTCATGGTTTCATCATAATAATTTATTTTTAACATCAACTCAATCCTGATCACTTTATTTT
**
20897580 GACTTGTGGTTTCATCCCGATTAC
66 GACTCATGGTTTCATCCCGATTAC
* * *
20897604 ATGATTCGTGGTTTCATCATAATAATTTATTTTTGACATCGACTCAATCCTGATCACTTTATTTT
1 ATGATTCATGGTTTCATCATAATAATTTATTTTTAACATCAACTCAATCCTGATCACTTTATTTT
20897669 GACTCATGGTTTCAT
66 GACTCATGGTTTCAT
20897684 TCCACTTATT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 68 1.00
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.46
Consensus pattern (89 bp):
ATGATTCATGGTTTCATCATAATAATTTATTTTTAACATCAACTCAATCCTGATCACTTTATTTT
GACTCATGGTTTCATCCCGATTAC
Found at i:20897695 original size:63 final size:63
Alignment explanation
Indices: 20897628--20897746 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
20897618 CATCATAATA
*
20897628 ATTTATTTTTGACATCGACTCA-ATCCTGATCACTTTATTTTGACTCATGGTTTCATTCCACTT
1 ATTTATTTTTGACATCAACT-AGATCCTGATCACTTTATTTTGACTCATGGTTTCATTCCACTT
* * * * **
20897691 ATTTATTTTTGACCTCAACTAGGTCTTGGTCACTTTATTTTGACTTGTGGTTTCAT
1 ATTTATTTTTGACATCAACTAGATCCTGATCACTTTATTTTGACTCATGGTTTCAT
20897747 CCCGATCACA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 1 0.02
63 47 0.98
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.48
Consensus pattern (63 bp):
ATTTATTTTTGACATCAACTAGATCCTGATCACTTTATTTTGACTCATGGTTTCATTCCACTT
Found at i:20897765 original size:89 final size:89
Alignment explanation
Indices: 20897672--20897978 Score: 350
Period size: 89 Copynumber: 3.4 Consensus size: 89
20897662 TTATTTTGAC
* *
20897672 TCATGGTTTCAT-TCCACTTATTTATTTTTGACCTCAACT-AGGTCTTGGTCACTTTATTTTGAC
1 TCATGGTTTCATCTCGA-TCATTTATTTTTGACCTCAACTCA-GTCTTGGTCACTTTATTTTGAC
*
20897735 TTGTGGTTTCATCCCGATCACATGAT
64 TCGTGGTTTCATCCCGATCACATGAT
* *
20897761 TCATGGTTTCATCT-GATCATTTATTTTTTTACCTCAACTCAATCTTGGTCACTTTATTTTGACT
1 TCATGGTTTCATCTCGATCATTTA-TTTTTGACCTCAACTCAGTCTTGGTCACTTTATTTTGACT
* * * *
20897825 CATGATTTCATCTCGATCACATGGT
65 CGTGGTTTCATCCCGATCACATGAT
** ** * * * * * *
20897850 TTGTGGTTTTGTCTTGATTATTTATTTTTAACTTCGACTCAGTCCTGGTCACTTTATTTTGACTC
1 TCATGGTTTCATCTCGATCATTTATTTTTGACCTCAACTCAGTCTTGGTCACTTTATTTTGACTC
* *
20897915 GTGGTTTCATCCCAATCATATGAT
66 GTGGTTTCATCCCGATCACATGAT
* * *
20897939 TTATGGTTTCATCTTGATCATTTATTTTTGACCTCGACTC
1 TCATGGTTTCATCTCGATCATTTATTTTTGACCTCAACTC
20897979 GTGGTTTCAT
Statistics
Matches: 183, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
88 6 0.03
89 167 0.91
90 10 0.05
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.47
Consensus pattern (89 bp):
TCATGGTTTCATCTCGATCATTTATTTTTGACCTCAACTCAGTCTTGGTCACTTTATTTTGACTC
GTGGTTTCATCCCGATCACATGAT
Found at i:20897801 original size:152 final size:152
Alignment explanation
Indices: 20897539--20897835 Score: 434
Period size: 152 Copynumber: 2.0 Consensus size: 152
20897529 CATCTTGTTC
* * *
20897539 ATTTATTTTTAACCTCAACTCGATCCTGATCACTTTGTTTTGACTTGTGGTTTCATCCCGATTAC
1 ATTTATTTTTAACCTCAACTAGATCCTGATCACTTTATTTTGACTTGTGGTTTCATCCCGATCAC
* *
20897604 ATGATTCGTGGTTTCATCATAATAATTTATTTTTGACATCGACTCAATCCTGATCACTTTATTTT
66 ATGATTCATGGTTTCATCATAATAATTTATTTTTGACATCAACTCAATCCTGATCACTTTATTTT
*
20897669 GACTCATGGTTTCATTCCACTT
131 GACTCATGATTTCATTCCACTT
* * * *
20897691 ATTTATTTTTGACCTCAACTAGGTCTTGGTCACTTTATTTTGACTTGTGGTTTCATCCCGATCAC
1 ATTTATTTTTAACCTCAACTAGATCCTGATCACTTTATTTTGACTTGTGGTTTCATCCCGATCAC
* * * * * *
20897756 ATGATTCATGGTTTCATC-TGATCATTTATTTTTTTACCTCAACTCAATCTTGGTCACTTTATTT
66 ATGATTCATGGTTTCATCATAATAATTTA-TTTTTGACATCAACTCAATCCTGATCACTTTATTT
20897820 TGACTCATGATTTCAT
130 TGACTCATGATTTCAT
20897836 CTCGATCACA
Statistics
Matches: 128, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
151 8 0.06
152 120 0.94
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.46
Consensus pattern (152 bp):
ATTTATTTTTAACCTCAACTAGATCCTGATCACTTTATTTTGACTTGTGGTTTCATCCCGATCAC
ATGATTCATGGTTTCATCATAATAATTTATTTTTGACATCAACTCAATCCTGATCACTTTATTTT
GACTCATGATTTCATTCCACTT
Found at i:20897981 original size:64 final size:64
Alignment explanation
Indices: 20897910--20898042 Score: 185
Period size: 64 Copynumber: 2.1 Consensus size: 64
20897900 ACTTTATTTT
* * * * *
20897910 GACTCGTGGTTTCATCCCAATCATATGATTTATGGTTTCATCTTGATCATTTATTTTTGACCTC
1 GACTCGTGGTTTCATCCCAATCACATGATTCATGGTTTCATCCTAATCATTTATTTTAGACCTC
** * *
20897974 GACTCGTGGTTTCATCCTGATCACATGATTCATGGTTTTATCCTAATGATTTATTTTAGACCTC
1 GACTCGTGGTTTCATCCCAATCACATGATTCATGGTTTCATCCTAATCATTTATTTTAGACCTC
20898038 GACTC
1 GACTC
20898043 AGTCCTAGTC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (64 bp):
GACTCGTGGTTTCATCCCAATCACATGATTCATGGTTTCATCCTAATCATTTATTTTAGACCTC
Found at i:20897996 original size:153 final size:153
Alignment explanation
Indices: 20897821--20898132 Score: 358
Period size: 153 Copynumber: 2.0 Consensus size: 153
20897811 ACTTTATTTT
* * ** * * * * *
20897821 GACTCATGATTTCATCTCGATCACATGGTTTGTGGTTTTGTCTTGATTATTTATTTTTA-ACTTC
1 GACTCGTGATTTCATCTCGATCACATGATTCATGGTTTTATCCTAATGATTTA-TTTTAGACCTC
* * * *
20897885 GACTCAGTCCTGGTCACTTTATTTTGACTCGTGGTTTCATCCCAATCATATGATTTATGGTTTCA
65 GACTCAGTCCTAGTCACTTTATTTTGACTCGTAGTTTCATCCCAATCACATGATTCATGGTTTCA
** * *
20897950 TCTTGATCATTTATTTTTGACCTC
130 TCCCGAACATTTATTTTGGACCTC
*
20897974 GACTCGTGGTTTCATC-CTGATCACATGATTCATGGTTTTATCCTAATGATTTATTTTAGACCTC
1 GACTCGTGATTTCATCTC-GATCACATGATTCATGGTTTTATCCTAATGATTTATTTTAGACCTC
* * ** ** * *
20898038 GACTCAGTCCTAGTCACTTTATTTTGATTTGTAGTTTTGTTTCGATCACATGATTCATGGTTTTA
65 GACTCAGTCCTAGTCACTTTATTTTGACTCGTAGTTTCATCCCAATCACATGATTCATGGTTTCA
20898103 TCCCGAACATTTATTTTGGACCTC
130 TCCCGAACATTTATTTTGGACCTC
20898127 GACTCG
1 GACTCG
20898133 ATCCTGGTCA
Statistics
Matches: 131, Mismatches: 26, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
152 6 0.05
153 125 0.95
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.45
Consensus pattern (153 bp):
GACTCGTGATTTCATCTCGATCACATGATTCATGGTTTTATCCTAATGATTTATTTTAGACCTCG
ACTCAGTCCTAGTCACTTTATTTTGACTCGTAGTTTCATCCCAATCACATGATTCATGGTTTCAT
CCCGAACATTTATTTTGGACCTC
Found at i:20898172 original size:89 final size:89
Alignment explanation
Indices: 20897974--20898172 Score: 242
Period size: 89 Copynumber: 2.2 Consensus size: 89
20897964 TTTTGACCTC
* * *
20897974 GACTCGTGGTTTCATC-CTGATCACATGATTCATGGTTTTATCCTAATGATTTATTTTAGACCTC
1 GACTCGTGGTTTCGTCTC-GATCACATGATTCATGGTTTTATCCGAATCATTTATTTTAGACCTC
*
20898038 GACTCAGTCCTAGTCACTTTATTTT
65 GACTCAGTCCTAGTCACCTTATTTT
* * * * * *
20898063 GATTTGTAGTTTTGTTTCGATCACATGATTCATGGTTTTATCCCGAA-CATTTATTTTGGACCTC
1 GACTCGTGGTTTCGTCTCGATCACATGATTCATGGTTTTAT-CCGAATCATTTATTTTAGACCTC
*
20898127 GACTC-GATCCTGGTCACCTTATTTT
65 GACTCAG-TCCTAGTCACCTTATTTT
*
20898152 GACTCATGGTTTCGTCTCGAT
1 GACTCGTGGTTTCGTCTCGAT
20898173 TACTTGATCT
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
88 1 0.01
89 84 0.93
90 5 0.06
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.43
Consensus pattern (89 bp):
GACTCGTGGTTTCGTCTCGATCACATGATTCATGGTTTTATCCGAATCATTTATTTTAGACCTCG
ACTCAGTCCTAGTCACCTTATTTT
Found at i:20898536 original size:52 final size:52
Alignment explanation
Indices: 20898433--20898543 Score: 134
Period size: 52 Copynumber: 2.1 Consensus size: 52
20898423 AGACACCTAC
* * * *
20898433 TTGTGTCCAGTCCCAAGTAGGCCCATTAACATCTAGGCCTAATTGGACCCAT
1 TTGTGTCCAGGCCCAAATAGGCCCATTAACATCTAAGCCTAATAGGACCCAT
* * *
20898485 TTGTGTTCAGGCCCAAATAGGCCCATTGACGTCTAAGCCTAACTAGG-CCCAT
1 TTGTGTCCAGGCCCAAATAGGCCCATTAACATCTAAGCCTAA-TAGGACCCAT
*
20898537 TTATGTC
1 TTGTGTC
20898544 TAAGCTCGGT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
52 46 0.94
53 3 0.06
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (52 bp):
TTGTGTCCAGGCCCAAATAGGCCCATTAACATCTAAGCCTAATAGGACCCAT
Found at i:20899591 original size:15 final size:14
Alignment explanation
Indices: 20899554--20899599 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
20899544 CGATCATAGA
20899554 TTTTTT-TTTTTAT
1 TTTTTTATTTTTAT
*
20899567 ATTTTATATTTTTAT
1 -TTTTTTATTTTTAT
20899582 TTATTTTA-TTTTAT
1 TT-TTTTATTTTTAT
20899596 TTTT
1 TTTT
20899600 AACCTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 15 0.54
15 11 0.39
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTATTTTTAT
Found at i:20899591 original size:22 final size:21
Alignment explanation
Indices: 20899553--20899599 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
20899543 CCGATCATAG
20899553 ATTTTTTTTTTTATATTTTAT
1 ATTTTTTTTTTTATATTTTAT
20899574 ATTTTTATTTATTT-TATTTTAT
1 ATTTTT-TTT-TTTATATTTTAT
20899596 -TTTT
1 ATTTT
20899600 AACCTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.42
22 11 0.46
23 3 0.12
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (21 bp):
ATTTTTTTTTTTATATTTTAT
Found at i:20899626 original size:30 final size:31
Alignment explanation
Indices: 20899573--20899631 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
20899563 TTATATTTTA
*
20899573 TATTTTTATTTATTTTATTTTATTTTTAACC
1 TATTTTTATTTATTTGATTTTATTTTTAACC
*
20899604 TATTTTTATTT-TTTGGTTTTATTTTTAA
1 TATTTTTATTTATTTGATTTTATTTTTAA
20899632 ACGAGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (31 bp):
TATTTTTATTTATTTGATTTTATTTTTAACC
Found at i:20899718 original size:24 final size:26
Alignment explanation
Indices: 20899679--20899726 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
20899669 AAAAAGTAAA
20899679 AAAAAAATGAAGTTCTAAAAAAAAAG
1 AAAAAAATGAAGTTCTAAAAAAAAAG
*
20899705 AAAAAAAT-AA-TTCTACAAAAAA
1 AAAAAAATGAAGTTCTAAAAAAAA
20899727 TCCCTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 2 0.10
26 8 0.38
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (26 bp):
AAAAAAATGAAGTTCTAAAAAAAAAG
Found at i:20899772 original size:19 final size:19
Alignment explanation
Indices: 20899748--20899784 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20899738 AAAAATGATA
*
20899748 AAATAAAAAAATAGTTTTC
1 AAATAAAAAAATAATTTTC
*
20899767 AAATAAATAAATAATTTT
1 AAATAAAAAAATAATTTT
20899785 TGTCCTCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
AAATAAAAAAATAATTTTC
Found at i:20900761 original size:61 final size:61
Alignment explanation
Indices: 20900645--20900761 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 61
20900635 GATATTCAAG
* **
20900645 TTATGATTTTTATGGTTTTAAAGTATGAGTTGTAATTTATAATTTTTTAAATAATTATAAT
1 TTATGATTTTTATGGTTTTAAACTATGAGTTGTAATTTATAATTCATTAAATAATTATAAT
* *
20900706 TTATGATTTTTATGGTTTTAAACTATGAGTTGTAATTTTTTAA-TCATTAACTAATT
1 TTATGATTTTTATGGTTTTAAACTATGAGTTGTAA-TTTATAATTCATTAAATAATT
20900762 GAAATAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
61 44 0.88
62 6 0.12
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.54
Consensus pattern (61 bp):
TTATGATTTTTATGGTTTTAAACTATGAGTTGTAATTTATAATTCATTAAATAATTATAAT
Found at i:20902332 original size:46 final size:45
Alignment explanation
Indices: 20902265--20902351 Score: 102
Period size: 46 Copynumber: 1.9 Consensus size: 45
20902255 GAATCGATTG
* * ** *
20902265 TTTTTTATAAGAGAAGACATAACTTAGGGATAAAAGAAAGGTCGT
1 TTTTTTATAAAAAAAGACATAACTTACAGATAAAAAAAAGGTCGT
* *
20902310 TTTTTTATAAAAAAAGGTCATAATTTACAGATAAAAAAAAGG
1 TTTTTTATAAAAAAA-GACATAACTTACAGATAAAAAAAAGG
20902352 ATTTTAGATG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
45 13 0.38
46 21 0.62
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (45 bp):
TTTTTTATAAAAAAAGACATAACTTACAGATAAAAAAAAGGTCGT
Found at i:20904644 original size:17 final size:17
Alignment explanation
Indices: 20904622--20904654 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20904612 TTTTTGTTAA
*
20904622 TAAAAAATTAAAAAAAT
1 TAAAAAATGAAAAAAAT
20904639 TAAAAAATGAAAAAAA
1 TAAAAAATGAAAAAAA
20904655 GCTGAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAAAAATGAAAAAAAT
Found at i:20905184 original size:16 final size:17
Alignment explanation
Indices: 20905163--20905201 Score: 64
Period size: 15 Copynumber: 2.4 Consensus size: 17
20905153 AAAAAGAGAT
20905163 AGAGAAAAGAAGGGG-A
1 AGAGAAAAGAAGGGGAA
20905179 AGAG-AAAGAAGGGGAA
1 AGAGAAAAGAAGGGGAA
20905195 AGAGAAA
1 AGAGAAA
20905202 TCTGGTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 9 0.43
17 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (17 bp):
AGAGAAAAGAAGGGGAA
Found at i:20905188 original size:15 final size:16
Alignment explanation
Indices: 20905163--20905201 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
20905153 AAAAAGAGAT
20905163 AGAGAAAAGAAGGGG-A
1 AGAG-AAAGAAGGGGAA
20905179 AGAGAAAGAAGGGGAA
1 AGAGAAAGAAGGGGAA
20905195 AGAGAAA
1 AGAGAAA
20905202 TCTGGTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAAGGGGAA
Found at i:20905669 original size:62 final size:60
Alignment explanation
Indices: 20905561--20905743 Score: 227
Period size: 62 Copynumber: 3.1 Consensus size: 60
20905551 TTTTCAATGA
* *
20905561 TTTTCTT-AAAATAAAATTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAATAAAATTTTCAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAAT
20905620 TTTTCTTGAAAATAAAATTTTCAAAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAATAAAATTTTC--AAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAAT
* * * * *
20905682 TTTTCTTG-----AAAATTATC-AAAAAAACATTTCTAAGGAAAAGTTGAAAGTACCAAT
1 TTTTCTTGAAAATAAAATTTTCAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAAT
*
20905736 TTTGCTTG
1 TTTTCTTG
20905744 TATAAAAGCA
Statistics
Matches: 113, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
54 40 0.35
57 8 0.07
59 7 0.06
60 14 0.12
62 44 0.39
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.36
Consensus pattern (60 bp):
TTTTCTTGAAAATAAAATTTTCAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAAT
Found at i:20908973 original size:15 final size:15
Alignment explanation
Indices: 20908950--20908981 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20908940 TGCATGTATG
*
20908950 CATTTTCATTCATTA
1 CATTCTCATTCATTA
20908965 CATTCTCATTCATTA
1 CATTCTCATTCATTA
20908980 CA
1 CA
20908982 ATTAACAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (15 bp):
CATTCTCATTCATTA
Found at i:20916210 original size:14 final size:15
Alignment explanation
Indices: 20916193--20916226 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
20916183 AAAAAAAAAG
*
20916193 AAAATTGAAAGA-AA
1 AAAATTGAAAAATAA
20916207 AAAATTGAAAAATAA
1 AAAATTGAAAAATAA
20916222 AAAAT
1 AAAAT
20916227 AAAAAGACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (15 bp):
AAAATTGAAAAATAA
Found at i:20916225 original size:15 final size:14
Alignment explanation
Indices: 20916185--20916226 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
20916175 AAAAAAGAAA
20916185 AAAAAAAGAAAATTG
1 AAAAAAA-AAAATTG
*
20916200 AAAGAAAAAAATTG
1 AAAAAAAAAAATTG
20916214 AAAAATAAAAAAT
1 AAAAA-AAAAAAT
20916227 AAAAAGACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAAATTG
Found at i:20917307 original size:46 final size:46
Alignment explanation
Indices: 20917234--20917325 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
20917224 TCTTTTATTT
*
20917234 TTCAAAGTTGTGGTGCTTCTATTTAGAGGAGCAATTTATTTTTCAA
1 TTCAAAGTTGTGGTGCTTCTATATAGAGGAGCAATTTATTTTTCAA
*
20917280 TTCAAAGTTGTGGTGGC-TCTGTATAGAGGAGCAATTTATTTTTCAA
1 TTCAAAGTTGTGGT-GCTTCTATATAGAGGAGCAATTTATTTTTCAA
20917326 AGTTGTGGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 41 0.95
47 2 0.05
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (46 bp):
TTCAAAGTTGTGGTGCTTCTATATAGAGGAGCAATTTATTTTTCAA
Found at i:20917341 original size:41 final size:41
Alignment explanation
Indices: 20917227--20917482 Score: 230
Period size: 41 Copynumber: 6.1 Consensus size: 41
20917217 CAAAAAGTCT
* *
20917227 TTTATTTTTCAAAGTTGTGGTGCTTCTATTTAGAGGAGCAA
1 TTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAAGAGCAA
* * * *
20917268 TTTATTTTTCAATTCAAAGTTGTGGTGGCTCTGTATAGAGGAGCAA
1 TTTA--TTT---TTCAAAGTTGTGGTGCCTCTATTTAGAAGAGCAA
* **
20917314 TTTATTTTTCAAAGTTGTGGTGCCTCTGTTTA-AAGAAAACA
1 TTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAAGAGCA-A
* * * *
20917355 TTTATTTTTCAAAGTAGTAGTGCCTTTTTTTAGAAGAGCAA
1 TTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAAGAGCAA
* ** * * *
20917396 TTTTTTTTTTTAAGTTATGATGTCTCTATTTAGAAGAGCAA
1 TTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAAGAGCAA
* * *
20917437 TTAATTTTTCAAAGTTTTGGTGCCTCTATTCAG-AGAAGC-A
1 TTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAAG-AGCAA
20917477 TTTATT
1 TTTATT
20917483 ATCAATTGAG
Statistics
Matches: 173, Mismatches: 34, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
40 12 0.07
41 116 0.67
42 5 0.03
43 3 0.02
44 3 0.02
46 34 0.20
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (41 bp):
TTTATTTTTCAAAGTTGTGGTGCCTCTATTTAGAAGAGCAA
Found at i:20917462 original size:123 final size:126
Alignment explanation
Indices: 20917227--20917463 Score: 302
Period size: 123 Copynumber: 1.9 Consensus size: 126
20917217 CAAAAAGTCT
* * * *
20917227 TTTATTTTTCAAAGTTGTGGTGCTTCTATTTAGAGGAGCAATTTATTTTTCAATTCAAAGTTGTG
1 TTTATTTTTCAAAGTAGTAGTGCTTCTATTTAGAAGAGCAATTTATTTTT--ATTCAAAGTTATG
* * * *
20917292 GTGGCTCTGTATAGAGGAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAAAGAAAACA
64 ATGGCTCTATATAGAAGAGCAATTAATTTTTCAAAGTTGTGGTGCCTCTGTTTAAAGAAAACA
* *
20917355 TTTATTTTTCAAAGTAGTAGTGCCTT-TTTTTAGAAGAGCAATTT-TTTTT-TT-TAAGTTATGA
1 TTTATTTTTCAAAGTAGTAGTG-CTTCTATTTAGAAGAGCAATTTATTTTTATTCAAAGTTATGA
* * *
20917416 TGTCTCTATTTAGAAGAGCAATTAATTTTTCAAAGTTTTGGTGCCTCT
65 TGGCTCTATATAGAAGAGCAATTAATTTTTCAAAGTTGTGGTGCCTCT
20917464 ATTCAGAGAA
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
123 49 0.52
124 2 0.02
127 5 0.05
128 36 0.38
129 3 0.03
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (126 bp):
TTTATTTTTCAAAGTAGTAGTGCTTCTATTTAGAAGAGCAATTTATTTTTATTCAAAGTTATGAT
GGCTCTATATAGAAGAGCAATTAATTTTTCAAAGTTGTGGTGCCTCTGTTTAAAGAAAACA
Found at i:20918680 original size:61 final size:58
Alignment explanation
Indices: 20918574--20918924 Score: 304
Period size: 61 Copynumber: 6.0 Consensus size: 58
20918564 TGATTTTTTC
* * * * * *
20918574 AAAATAAAATTTTCAAAAAAAATATTTTTGAGGAAAAATTAAAAGTATCAATTTTTCTTG
1 AAAATAAAA--TTAAAAAAAAACATTTCTAAGGAAAAGTTAAAAGTATCAATTTTTCTTA
* ** *
20918634 AAAATAAAATTTAAAAAAAAAAACATTTTTAAAAAAAAGTTGAAAGTATCAA-TTTTCTTTA
1 AAAATAAAA-TT--AAAAAAAAACATTTCTAAGGAAAAGTTAAAAGTATCAATTTTTC-TTA
* *
20918695 AAAATAAAATTTTTAAAAGAAAACATTT-TCAAGGAAAAGTTAAAAGTATCAATTTTCCTTA
1 AAAATAAAA---TTAAAAAAAAACATTTCT-AAGGAAAAGTTAAAAGTATCAATTTTTCTTA
* * * * *
20918756 AAAAT--TA-T-AAAAAAAATATTTCTAAGGAAAAGTTGGAAA-TACCAATTTTTCTAA
1 AAAATAAAATTAAAAAAAAACATTTCTAAGGAAAAGTT-AAAAGTATCAATTTTTCTTA
** ** *
20918810 AAAATAAAATTATCAAAAAACATTTCTAAGGAAAAGTTGGAATTATCAATTTTT-TTA
1 AAAATAAAATTAAAAAAAAACATTTCTAAGGAAAAGTTAAAAGTATCAATTTTTCTTA
** * *
20918867 AAAAGTAAAATTACCAAAAAACATTTCTGAGGAAGAGTTAAAAGTATCAATTTTTCTT
1 AAAA-TAAAATTAAAAAAAAACATTTCTAAGGAAAAGTTAAAAGTATCAATTTTTCTT
20918925 GTATAAAAGT
Statistics
Matches: 242, Mismatches: 33, Indels: 33
0.79 0.11 0.11
Matches are distributed among these distances:
54 39 0.16
55 5 0.02
56 1 0.00
57 10 0.04
58 77 0.32
59 6 0.02
60 15 0.06
61 82 0.34
62 4 0.02
63 3 0.01
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (58 bp):
AAAATAAAATTAAAAAAAAACATTTCTAAGGAAAAGTTAAAAGTATCAATTTTTCTTA
Found at i:20921219 original size:230 final size:233
Alignment explanation
Indices: 20920812--20921276 Score: 553
Period size: 230 Copynumber: 2.0 Consensus size: 233
20920802 AAATTTTAAC
** * *
20920812 AAATATCATATATGAGTTTAGTAAAATCAAAATTGTATTTTTTATCTTTCATATTAATGCAAATA
1 AAATATCATATACCAGTTTAGAAAAATCAAAATTGTATTTTTTATCTTTCATATTAATACAAATA
* * * *
20920877 ATGACATATAATTTTTATATAAAATATAATATATATATGAATACACAAATTATTAATATTTTACA
66 ATGACATATAATTTTTATATAAAATATAATATATACATAAATACACAAATTATTAATATGTTAAA
* * ** * ** *
20920942 TAATATTAATACATGAATTGTCTGCTTTATATATACATGATTTCATCTAACTTTGCATTTCTTTC
131 GAATACTAATACACAAATTATCTAATTTATATATACATGAATTCATCTAACTTTGCATTTCTTTC
* *
20921007 ATATTTTTTAAAAATA-TTATAATTTATTCCTTTTTCA
196 ACATTTTTCAAAAATATTTATAATTTATTCCTTTTTCA
* * * ** *
20921044 AAATATCATATACCAGTTT-GAAAAAATTAAAATTTTATTTTTTATTTTTTGTATTGATACAAAT
1 AAATATCATATACCAGTTTAG-AAAAATCAAAATTGTATTTTTTATCTTTCATATTAATACAAAT
* * * * * *
20921108 TATTATATATGATTTTTATAT-AAA-ATAATATATACATAAATATATAAATTATTAATATGTTAA
65 AATGACATATAATTTTTATATAAAATATAATATATACATAAATACACAAATTATTAATATGTTAA
**
20921171 AGGTTACTAATACACAAATTATC-AATTCTATATATACATGAATTCATCTAACTTTGCATTTCTT
130 AGAATACTAATACACAAATTATCTAATT-TATATATACATGAATTCATCTAACTTTGCATTTCTT
* * * *
20921235 TCGCATTTTTCACAAATATTTGTAATTTCTTCCTTTTTCA
194 TCACATTTTTCAAAAATATTTATAATTTATTCCTTTTTCA
20921275 AA
1 AA
20921277 GTACCCTAGG
Statistics
Matches: 194, Mismatches: 36, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
229 2 0.01
230 98 0.51
231 25 0.13
232 69 0.36
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (233 bp):
AAATATCATATACCAGTTTAGAAAAATCAAAATTGTATTTTTTATCTTTCATATTAATACAAATA
ATGACATATAATTTTTATATAAAATATAATATATACATAAATACACAAATTATTAATATGTTAAA
GAATACTAATACACAAATTATCTAATTTATATATACATGAATTCATCTAACTTTGCATTTCTTTC
ACATTTTTCAAAAATATTTATAATTTATTCCTTTTTCA
Found at i:20923706 original size:37 final size:35
Alignment explanation
Indices: 20923655--20923743 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 35
20923645 TATATTGCAA
* *
20923655 TTATTATTTTTTATTT-TTTCATGTTATGTTATGATTT
1 TTATT-TTTTTTATTTATTTCATCTAATG-TAT-ATTT
*
20923692 TTATTTTTTATTATTTATTTGATCTAATGTATATTT
1 TTATTTTTT-TTATTTATTTCATCTAATGTATATTT
*
20923728 TTATTTTTATT-TTTAT
1 TTATTTTTTTTATTTAT
20923744 AAATTACAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 2 0.04
36 16 0.35
37 14 0.30
38 9 0.20
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.71
Consensus pattern (35 bp):
TTATTTTTTTTATTTATTTCATCTAATGTATATTT
Found at i:20923886 original size:15 final size:14
Alignment explanation
Indices: 20923849--20923890 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
20923839 AAATTTAACA
*
20923849 TTATTATTGTATTT
1 TTATTATTTTATTT
20923863 TTATTATTTTATTT
1 TTATTATTTTATTT
*
20923877 TATGTTATTTTATT
1 T-TATTATTTTATT
20923891 GTAAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (14 bp):
TTATTATTTTATTT
Found at i:20928391 original size:26 final size:27
Alignment explanation
Indices: 20928353--20928413 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
20928343 AAGTAGTAAT
20928353 AAAAA-TTACTGTAACTGCAATT-AAA
1 AAAAATTTACTGTAACTGCAATTGAAA
* * **
20928378 AAAAATTTATTGTAATTGTGATTGAAA
1 AAAAATTTACTGTAACTGCAATTGAAA
20928405 AAAAATTTA
1 AAAAATTTA
20928414 ATAAGAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 5 0.17
26 13 0.43
27 12 0.40
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (27 bp):
AAAAATTTACTGTAACTGCAATTGAAA
Found at i:20932006 original size:23 final size:24
Alignment explanation
Indices: 20931980--20932039 Score: 59
Period size: 27 Copynumber: 2.4 Consensus size: 24
20931970 AAATTAACCT
20931980 AATAGTTT-ATTAATTTATTTATC
1 AATAGTTTAATTAATTTATTTATC
*
20932003 AATATTTTAACCATTAATTTATTTATC
1 AATAGTTT-A--ATTAATTTATTTATC
* *
20932030 ACTATTTTAA
1 AATAGTTTAA
20932040 CCTTACTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 7 0.23
24 1 0.03
26 1 0.03
27 22 0.71
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (24 bp):
AATAGTTTAATTAATTTATTTATC
Found at i:20932019 original size:27 final size:27
Alignment explanation
Indices: 20931988--20932041 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
20931978 CTAATAGTTT
20931988 ATTAATTTATTTATCAATATTTTAACC
1 ATTAATTTATTTATCAATATTTTAACC
*
20932015 ATTAATTTATTTATCACTATTTTAACC
1 ATTAATTTATTTATCAATATTTTAACC
20932042 TTACTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTAATTTATTTATCAATATTTTAACC
Found at i:20936139 original size:20 final size:20
Alignment explanation
Indices: 20936114--20936153 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
20936104 GCTGCTGCTA
20936114 ATGAATAAATTATGTAATTT
1 ATGAATAAATTATGTAATTT
*
20936134 ATGAATAAATTTTGTAATTT
1 ATGAATAAATTATGTAATTT
20936154 TTTATTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (20 bp):
ATGAATAAATTATGTAATTT
Found at i:20939814 original size:18 final size:18
Alignment explanation
Indices: 20939791--20939829 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
20939781 TTTGTTCTAA
* *
20939791 ATTTTTACTTTAATTATT
1 ATTTTTAATATAATTATT
*
20939809 ATTTTTAATATAATTTTT
1 ATTTTTAATATAATTATT
20939827 ATT
1 ATT
20939830 CTAAAAAAAT
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:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTAATATAATTATT
Found at i:20941060 original size:194 final size:193
Alignment explanation
Indices: 20940734--20941089 Score: 458
Period size: 194 Copynumber: 1.8 Consensus size: 193
20940724 AAAAAATAAA
* ** *
20940734 ATAAAAAATAAAAAAATTTTGAGAATAAATATTAATTATCCAATGATGGAATTTATAAAAATTTC
1 ATAAAAAAAAAAAAAATTTTGAGAATAAATACAAATTATCCAAGGATGGAATTTATAAAAATTTC
* * *
20940799 AAATGATAAATTTTTATAAAATTTCTAGGTGATAAGTTTTATCTAAATTTGTCCCAAATTATGGA
66 AAATGATAAATTTCTATAAAATTTCTAGGTGAGAAATTTTATCTAAATTTGTCCCAAATTATGGA
20940864 ATAATTTAGAT-AGAATTTCAATAACAA-TAATTAATATTTATTTTCAAAACAAAAACATAAAAC
131 ATAATTTAGATGA-AATTTCAATAA-AAGTAATTAATATTTATTTTCAAAACAAAAACATAAAAC
*
20940927 ATAAAAAAAAAATAAAGATTTTG-GAA-AAATACAAATTA-CCTAAGGAT-GAGATTTTTAAAAA
1 ATAAAAAAAAAA-AAA-ATTTTGAGAATAAATACAAATTATCC-AAGGATGGA-ATTTATAAAAA
* * * *
20940988 TTTCAAATGGTAAAGTTTCTA-AGAAATCTT-TAGGTGAGAAATTTTTTCTAAATTTGTTCTAAA
62 TTTCAAATGATAAA-TTTCTATA-AAAT-TTCTAGGTGAGAAATTTTATCTAAATTTGTCCCAAA
*
20941051 TTGTGGAATAATTTAGATGAAATTTCAATAAAAGTAATT
124 TTATGGAATAATTTAGATGAAATTTCAATAAAAGTAATT
20941090 GTATTCTTTT
Statistics
Matches: 141, Mismatches: 13, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
192 4 0.03
193 52 0.37
194 76 0.54
195 9 0.06
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.36
Consensus pattern (193 bp):
ATAAAAAAAAAAAAAATTTTGAGAATAAATACAAATTATCCAAGGATGGAATTTATAAAAATTTC
AAATGATAAATTTCTATAAAATTTCTAGGTGAGAAATTTTATCTAAATTTGTCCCAAATTATGGA
ATAATTTAGATGAAATTTCAATAAAAGTAATTAATATTTATTTTCAAAACAAAAACATAAAAC
Found at i:20945422 original size:16 final size:16
Alignment explanation
Indices: 20945403--20945436 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20945393 AGAAAGGGAA
20945403 AAAATGAAAAAAAATG
1 AAAATGAAAAAAAATG
* *
20945419 AAAATGAGAGAAAATG
1 AAAATGAAAAAAAATG
20945435 AA
1 AA
20945437 TACTCAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (16 bp):
AAAATGAAAAAAAATG
Found at i:20946059 original size:22 final size:21
Alignment explanation
Indices: 20946017--20946063 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
20946007 AGCCTGTGAG
20946017 TTATGATCGAATGATAAAAAT
1 TTATGATCGAATGATAAAAAT
20946038 ATTATGGATC-AATGGAT-AAAAT
1 -TTAT-GATCGAAT-GATAAAAAT
20946060 TTAT
1 TTAT
20946064 TCTGAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.17
22 12 0.52
23 7 0.30
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36
Consensus pattern (21 bp):
TTATGATCGAATGATAAAAAT
Found at i:20946168 original size:63 final size:63
Alignment explanation
Indices: 20946069--20946197 Score: 179
Period size: 63 Copynumber: 2.0 Consensus size: 63
20946059 TTTATTCTGA
* *
20946069 AATGGCTAGTACTAAGAAACTTATAAGTGGTGACCCAGTGATGG-GTGACAAAAATTGTTTTGG
1 AATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATGGAG-GACAAAAATTGTTTTGG
* * ** *
20946132 AATGGCTAGTACTGAGAAACCTATGAGTAGTGACCCAGTGATGGAGGATGAAACTTGTTTTGG
1 AATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATGGAGGACAAAAATTGTTTTGG
20946195 AAT
1 AAT
20946198 TGTTAATGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 57 0.98
64 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (63 bp):
AATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATGGAGGACAAAAATTGTTTTGG
Found at i:20946220 original size:63 final size:63
Alignment explanation
Indices: 20946069--20946220 Score: 171
Period size: 63 Copynumber: 2.4 Consensus size: 63
20946059 TTTATTCTGA
* * * *
20946069 AATGGCTAGTACTAAGAAACTTATAAGTGGTGACCCAGTGATGGGTGACAAAAATTGTTTTGG
1 AATGGCTAATACTGAGAAACTTATGAGTAGTGACCCAGTGATGGGTGACAAAAATTGTTTTGG
* * ** *
20946132 AATGGCTAGTACTGAGAAACCTATGAGTAGTGACCCAGTGATGGAG-GATGAAACTTGTTTTGG
1 AATGGCTAATACTGAGAAACTTATGAGTAGTGACCCAGTGATGG-GTGACAAAAATTGTTTTGG
* * * *
20946195 AATTGTTAATGCTGAGAAGCTTATGA
1 AATGGCTAATACTGAGAAACTTATGA
20946221 ATGGTGATCA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
63 74 0.99
64 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (63 bp):
AATGGCTAATACTGAGAAACTTATGAGTAGTGACCCAGTGATGGGTGACAAAAATTGTTTTGG
Found at i:20947150 original size:42 final size:42
Alignment explanation
Indices: 20947065--20947155 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
20947055 CATGATTGTC
* * **
20947065 GAAGAGCATTTTATTTTTCTAAAGTTGTGGTGCCTCTGTTTA
1 GAAGAGCATTTTATTTTTCTAAAGTCGTGGAGCCTCTAATTA
* *
20947107 GAGGAGCA-TTTATTTTTCTTAAAGTCGTTGAGCCTCTAATTA
1 GAAGAGCATTTTATTTTTC-TAAAGTCGTGGAGCCTCTAATTA
20947149 GAAGAGC
1 GAAGAGC
20947156 TTTGTTTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 10 0.24
42 31 0.76
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (42 bp):
GAAGAGCATTTTATTTTTCTAAAGTCGTGGAGCCTCTAATTA
Found at i:20947764 original size:14 final size:14
Alignment explanation
Indices: 20947747--20947781 Score: 56
Period size: 12 Copynumber: 2.6 Consensus size: 14
20947737 GTGAAAAAAT
20947747 AAAATTTTTTTTTG
1 AAAATTTTTTTTTG
20947761 AAAA--TTTTTTTG
1 AAAATTTTTTTTTG
20947773 AAAATTTTT
1 AAAATTTTT
20947782 AGATTTTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 12 0.63
14 7 0.37
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (14 bp):
AAAATTTTTTTTTG
Found at i:20947770 original size:12 final size:12
Alignment explanation
Indices: 20947753--20947781 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
20947743 AAATAAAATT
20947753 TTTTTTTGAAAA
1 TTTTTTTGAAAA
20947765 TTTTTTTGAAAA
1 TTTTTTTGAAAA
20947777 TTTTT
1 TTTTT
20947782 AGATTTTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (12 bp):
TTTTTTTGAAAA
Found at i:20948336 original size:12 final size:12
Alignment explanation
Indices: 20948321--20948361 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
20948311 GTATTTTTTT
20948321 TATTTTATTTAG
1 TATTTTATTTAG
20948333 TATTTTATTTATG
1 TATTTTATTTA-G
*
20948346 TA-ATT-TTTAG
1 TATTTTATTTAG
20948356 TATTTT
1 TATTTT
20948362 TGCATAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 3 0.12
11 6 0.24
12 13 0.52
13 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (12 bp):
TATTTTATTTAG
Found at i:20948337 original size:21 final size:20
Alignment explanation
Indices: 20948299--20948362 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
20948289 GCCAAGCTGC
*
20948299 TTTTA-TTTTTTGGTATTTT
1 TTTTATTTTTTTAGTATTTT
20948318 TTTTATTTTATTTAGTATTTT
1 TTTTATTTT-TTTAGTATTTT
*
20948339 ATTTATGTAATTTTTAGTATTTT
1 TTTTAT-T--TTTTTAGTATTTT
20948362 T
1 T
20948363 GCATAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.14
20 3 0.08
21 15 0.41
22 1 0.03
23 11 0.30
24 2 0.05
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (20 bp):
TTTTATTTTTTTAGTATTTT
Found at i:20948853 original size:26 final size:25
Alignment explanation
Indices: 20948799--20948851 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
20948789 AATGATGAGA
*
20948799 TTCTAAAAATTTTAAATGATAAATT
1 TTCTAAAAATTTTAAATGAGAAATT
*
20948824 TTCTAAGAAATCTTTAAGTGAGAAATT
1 TTCTAA-AAAT-TTTAAATGAGAAATT
20948851 T
1 T
20948852 CTTTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.25
26 4 0.17
27 14 0.58
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (25 bp):
TTCTAAAAATTTTAAATGAGAAATT
Found at i:20949098 original size:65 final size:59
Alignment explanation
Indices: 20948927--20949113 Score: 196
Period size: 59 Copynumber: 3.0 Consensus size: 59
20948917 TTATTTTTTT
* * *
20948927 TTAAAACAAAAAAAAAGGAAAAAAATTTCTAAATAAGCCCAAATGGTGAAAATTTTAGAAA
1 TTAAAA-AAAAAAAAAAG-AAAAAATTTCTGAATAAGCCCAAATGGTGAAAAATTTAGAAA
* * * * *
20948988 TTAAAAAAAAAAAAAAGAAAATATTTTTAGATTGA-CCTAAATGGTGAAAAATTTAGAAA
1 TTAAAAAAAAAAAAAAGAAAAAATTTCT-GAATAAGCCCAAATGGTGAAAAATTTAGAAA
* *
20949047 TAATAATAAAAAAAAAGAAATAAGAAGAATTTCTGAATAAGCCCAAATGGTGAAAAATTTAAAAA
1 T--TAA-AAAAAAAAA-AAAGAA-AA-AATTTCTGAATAAGCCCAAATGGTGAAAAATTTAGAAA
20949112 TT
1 TT
20949114 CTGAAAAGAG
Statistics
Matches: 103, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
59 32 0.31
60 13 0.13
61 9 0.09
62 9 0.09
63 6 0.06
64 6 0.06
65 28 0.27
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (59 bp):
TTAAAAAAAAAAAAAAGAAAAAATTTCTGAATAAGCCCAAATGGTGAAAAATTTAGAAA
Found at i:20952102 original size:18 final size:18
Alignment explanation
Indices: 20952038--20952105 Score: 72
Period size: 18 Copynumber: 3.8 Consensus size: 18
20952028 TGATGTGGCA
*
20952038 CTAACATGTC-GGTCGAC
1 CTAACATGTCAAGTCGAC
20952055 CTAACATGTCAAGTCAGTA-
1 CTAACATGTCAAGTC-G-AC
20952074 C-AA-ATGATCAAGTCGAC
1 CTAACATG-TCAAGTCGAC
20952091 CTAACATGTCAAGTC
1 CTAACATGTCAAGTC
20952106 AGTATAAAGG
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
16 1 0.02
17 15 0.35
18 21 0.49
19 5 0.12
20 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (18 bp):
CTAACATGTCAAGTCGAC
Found at i:20952295 original size:233 final size:233
Alignment explanation
Indices: 20951888--20952318 Score: 808
Period size: 233 Copynumber: 1.8 Consensus size: 233
20951878 GATGGGCAAG
* *
20951888 TCAGTAAAGATCAGGTCGGCAAAAAAGTAGGAAAAAAATAGAGAAGTGAATGGGATGAACTTGCC
1 TCAGTAAAGATCAGGTCGGCAAAAAAATAGGAAAAAAAGAGAGAAGTGAATGGGATGAACTTGCC
20951953 TTCATGGTGCTTTAGTCTTTATATTTATAGATAAGTTGAGGGGGATTATAAAAGGATAATTAGGA
66 TTCATGGTGCTTTAGTCTTTATATTTATAGATAAGTTGAGGGGGATTATAAAAGGATAATTAGGA
*
20952018 AAGGTCGAGCTGATGTGGCACTAACATGTCGGTCGACCTAACATGTCAAGTCAGTACAAATGATC
131 AAGGTCGAGCTGAGGTGGCACTAACATGTCGGTCGACCTAACATGTCAAGTCAGTACAAATGATC
20952083 AAGTCGACCTAACATGTCAAGTCAGTATAAAGGGATAA
196 AAGTCGACCTAACATGTCAAGTCAGTATAAAGGGATAA
20952121 TCAGTAAAGATCAGGTCGGCAAAAAAATAGGAAAAAAAGAGAGAAGTGAATGGGATGAACTTGCC
1 TCAGTAAAGATCAGGTCGGCAAAAAAATAGGAAAAAAAGAGAGAAGTGAATGGGATGAACTTGCC
*
20952186 TTCATGGTGCTTTAGTCTTTATATTTATAGATAAGTTGAGGGGGATTATAAAGGGATAATTAGGA
66 TTCATGGTGCTTTAGTCTTTATATTTATAGATAAGTTGAGGGGGATTATAAAAGGATAATTAGGA
* *
20952251 AAGGTTGAGTTGAGGTGGCACTAACATGTCGGTCGACCTAACATGTCAAGTCAGTACAAATGATC
131 AAGGTCGAGCTGAGGTGGCACTAACATGTCGGTCGACCTAACATGTCAAGTCAGTACAAATGATC
20952316 AAG
196 AAG
20952319 ATATCCCTAA
Statistics
Matches: 192, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
233 192 1.00
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.26
Consensus pattern (233 bp):
TCAGTAAAGATCAGGTCGGCAAAAAAATAGGAAAAAAAGAGAGAAGTGAATGGGATGAACTTGCC
TTCATGGTGCTTTAGTCTTTATATTTATAGATAAGTTGAGGGGGATTATAAAAGGATAATTAGGA
AAGGTCGAGCTGAGGTGGCACTAACATGTCGGTCGACCTAACATGTCAAGTCAGTACAAATGATC
AAGTCGACCTAACATGTCAAGTCAGTATAAAGGGATAA
Found at i:20955673 original size:34 final size:34
Alignment explanation
Indices: 20955634--20955732 Score: 161
Period size: 34 Copynumber: 3.0 Consensus size: 34
20955624 TTATAATTTA
20955634 TGAATAATTAGATTGAAGGCCTTCAATAATTGCT
1 TGAATAATTAGATTGAAGGCCTTCAATAATTGCT
*
20955668 TGAATAATTAGATTGAAGGCCTTTAATAA----T
1 TGAATAATTAGATTGAAGGCCTTCAATAATTGCT
20955698 TGAATAATTAGATTGAAGGCCTTCAATAATTGCT
1 TGAATAATTAGATTGAAGGCCTTCAATAATTGCT
20955732 T
1 T
20955733 AGATTATATT
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
30 29 0.49
34 30 0.51
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (34 bp):
TGAATAATTAGATTGAAGGCCTTCAATAATTGCT
Found at i:20955703 original size:30 final size:30
Alignment explanation
Indices: 20955634--20955729 Score: 147
Period size: 30 Copynumber: 3.1 Consensus size: 30
20955624 TTATAATTTA
20955634 TGAATAATTAGATTGAAGGCCTTCAATAATTGCT
1 TGAATAATTAGATTGAAGGCCTTCAATAA----T
*
20955668 TGAATAATTAGATTGAAGGCCTTTAATAAT
1 TGAATAATTAGATTGAAGGCCTTCAATAAT
20955698 TGAATAATTAGATTGAAGGCCTTCAATAAT
1 TGAATAATTAGATTGAAGGCCTTCAATAAT
20955728 TG
1 TG
20955730 CTTAGATTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
30 32 0.53
34 28 0.47
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (30 bp):
TGAATAATTAGATTGAAGGCCTTCAATAAT
Found at i:20959675 original size:11 final size:11
Alignment explanation
Indices: 20959659--20959706 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
20959649 ATAAATTTTT
20959659 TTTTTTGGAAA
1 TTTTTTGGAAA
20959670 TTTTTTGGAAA
1 TTTTTTGGAAA
* *
20959681 -ATTTT-CAAA
1 TTTTTTGGAAA
*
20959690 TTTTTGGGAAA
1 TTTTTTGGAAA
20959701 TTTTTT
1 TTTTTT
20959707 TGCATCGGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
9 3 0.10
10 7 0.24
11 19 0.66
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (11 bp):
TTTTTTGGAAA
Found at i:20959705 original size:20 final size:20
Alignment explanation
Indices: 20959667--20959704 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20959657 TTTTTTTTGG
*
20959667 AAATTTTTTGGAAAATTTTC
1 AAATTTTTGGGAAAATTTTC
20959687 AAATTTTTGGG-AAATTTT
1 AAATTTTTGGGAAAATTTT
20959705 TTTGCATCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (20 bp):
AAATTTTTGGGAAAATTTTC
Found at i:20960251 original size:23 final size:22
Alignment explanation
Indices: 20960221--20960283 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
20960211 GCCAAGCCAC
20960221 TTTTATTTTTTGGTATTTTTTTA
1 TTTTATTTTTT-GTATTTTTTTA
20960244 TTTTA-TTTTT-TATTTTATTTA
1 TTTTATTTTTTGTATTTT-TTTA
*
20960265 -TGTATTTTTTAGTATTTTT
1 TTTTATTTTTT-GTATTTTT
20960284 GATGATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 6 0.17
23 11 0.31
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (22 bp):
TTTTATTTTTTGTATTTTTTTA
Found at i:20960252 original size:12 final size:12
Alignment explanation
Indices: 20960237--20960263 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20960227 TTTTTGGTAT
20960237 TTTTTTATTTTA
1 TTTTTTATTTTA
20960249 TTTTTTATTTTA
1 TTTTTTATTTTA
20960261 TTT
1 TTT
20960264 ATGTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:20960259 original size:20 final size:20
Alignment explanation
Indices: 20960234--20960275 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
20960224 TATTTTTTGG
*
20960234 TATTTT-TTTATTTTATTTTT
1 TATTTTATTTA-TGTATTTTT
20960254 TATTTTATTTATGTATTTTT
1 TATTTTATTTATGTATTTTT
20960274 TA
1 TA
20960276 GTATTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (20 bp):
TATTTTATTTATGTATTTTT
Found at i:20960317 original size:13 final size:13
Alignment explanation
Indices: 20960299--20960323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20960289 TTAAATTCAA
20960299 AAAAAATAAAAAT
1 AAAAAATAAAAAT
20960312 AAAAAATAAAAA
1 AAAAAATAAAAA
20960324 AATTTTGAGA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:20960624 original size:195 final size:191
Alignment explanation
Indices: 20960298--20960665 Score: 471
Period size: 195 Copynumber: 1.9 Consensus size: 191
20960288 ATTAAATTCA
** *
20960298 AAAAAAATAAAAATAAAAAATAAAAAAATTTTGAGAATAAATATTAATTATCCAATGATGGAATT
1 AAAAAAATAAAAATAAAAAATAAAAAAATTTTGAGAATAAATACAAATTATCCAAGGATGGAATT
* * *
20960363 TATAAAAATTTCAAATGATAAATTTTTATAAAATTCTAGGTGATAAGTTTTATCTAAATTTGTCC
66 TATAAAAATTTCAAATGATAAATTTCTATAAAATTCTAGGTGAGAAATTTTATCTAAATTTGTCC
20960428 CAAATTATGGAATAATTTAGAT-AGAATTTCAATAACAA-TAATTAATATTTATTTTCAAAAC
131 CAAATTATGGAATAATTTAGATGA-AATTTCAATAA-AAGTAATTAATATTTATTTTCAAAAC
*
20960489 AAAAACATAAAACATAAAAAAATAAATAAAGATTTTG-GAA-AAATACAAATTA-CCTAAGGAT-
1 AAAAAAATAAAA-AT-AAAAAATAAA-AAA-ATTTTGAGAATAAATACAAATTATCC-AAGGATG
* * * * *
20960550 GAGATTTTTAGAAATTTCAAATGGTAAAGTTTCTA-AGAAATCTTTAGGTGAGAAATTTTTTCTA
61 GA-ATTTATAAAAATTTCAAATGATAAA-TTTCTATA-AAAT-TCTAGGTGAGAAATTTTATCTA
*
20960614 AATTTGTCCCAAATTGTGGAATAATTTAGATGAAATTTCAATAAAAGTAATT
122 AATTTGTCCCAAATTATGGAATAATTTAGATGAAATTTCAATAAAAGTAATT
20960666 GTATTCTTTT
Statistics
Matches: 153, Mismatches: 13, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
191 11 0.07
192 6 0.04
193 48 0.31
194 17 0.11
195 70 0.46
196 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (191 bp):
AAAAAAATAAAAATAAAAAATAAAAAAATTTTGAGAATAAATACAAATTATCCAAGGATGGAATT
TATAAAAATTTCAAATGATAAATTTCTATAAAATTCTAGGTGAGAAATTTTATCTAAATTTGTCC
CAAATTATGGAATAATTTAGATGAAATTTCAATAAAAGTAATTAATATTTATTTTCAAAAC
Found at i:20965624 original size:22 final size:21
Alignment explanation
Indices: 20965583--20965629 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
20965573 AGCCTGTGAG
20965583 TTATGATCGAATGATAAAAAT
1 TTATGATCGAATGATAAAAAT
20965604 ATTATGGATC-AATAGAT-AAAAT
1 -TTAT-GATCGAAT-GATAAAAAT
20965626 TTAT
1 TTAT
20965630 TCTGAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.17
22 12 0.52
23 7 0.30
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (21 bp):
TTATGATCGAATGATAAAAAT
Found at i:20965731 original size:63 final size:63
Alignment explanation
Indices: 20965621--20965741 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 63
20965611 ATCAATAGAT
* *
20965621 AAAATTTATTCTGAAATGGCTAGTACTAAGAAACCTATAAGTGGTGACCCAGTGATGGGTGAC
1 AAAAATTATTCTGAAATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATGGGTGAC
* * * *
20965684 AAAAATTATTTTGGAATGGCTAGTACTGAGAAACCTATGAGTAGTGACCCAGTGATGG
1 AAAAATTATTCTGAAATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATGG
20965742 AAGATGAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (63 bp):
AAAAATTATTCTGAAATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATGGGTGAC
Found at i:20965759 original size:63 final size:63
Alignment explanation
Indices: 20965621--20965763 Score: 178
Period size: 63 Copynumber: 2.3 Consensus size: 63
20965611 ATCAATAGAT
* * * * **
20965621 AAAATTTATTCTGAAATGGCTAGTACTAAGAAACCTATAAGTGGTGACCCAGTGATGGGTGAC
1 AAAAATTATTTTGGAATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATGGAAGAC
* * *
20965684 AAAAATTATTTTGGAATGGCTAGTACTGAGAAACCTATGAGTAGTGACCCAGTGATGGAAGAT
1 AAAAATTATTTTGGAATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATGGAAGAC
* * *
20965747 GAAACTTGTTTTGGAAT
1 AAAAATTATTTTGGAAT
20965764 TGTTAATGCT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (63 bp):
AAAAATTATTTTGGAATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATGGAAGAC
Found at i:20966707 original size:42 final size:42
Alignment explanation
Indices: 20966633--20966720 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
20966623 GATTGTCGAA
** * **
20966633 GAGCATTTTATTTTTCTAAAGTTGTGGTGCCTCTGTTTAGAG
1 GAGCATTTTATTTTTCTAAAGTCCTGGAGCCTCTAATTAGAG
*
20966675 GAGCA-TTTATTTTTCTTAAAGTCCTTGAGCCTCTAATTAGAG
1 GAGCATTTTATTTTTC-TAAAGTCCTGGAGCCTCTAATTAGAG
20966717 GAGC
1 GAGC
20966721 TTTGTTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 10 0.26
42 29 0.74
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.41
Consensus pattern (42 bp):
GAGCATTTTATTTTTCTAAAGTCCTGGAGCCTCTAATTAGAG
Found at i:20967658 original size:12 final size:12
Alignment explanation
Indices: 20967643--20967683 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
20967633 GGTATTTTTT
20967643 TATTTTATTTAG
1 TATTTTATTTAG
20967655 TATTTTATTTATG
1 TATTTTATTTA-G
*
20967668 TA-ATT-TTTAG
1 TATTTTATTTAG
20967678 TATTTT
1 TATTTT
20967684 TGCATAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 3 0.12
11 6 0.24
12 13 0.52
13 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (12 bp):
TATTTTATTTAG
Found at i:20968322 original size:60 final size:59
Alignment explanation
Indices: 20968258--20968435 Score: 164
Period size: 60 Copynumber: 2.9 Consensus size: 59
20968248 TTTTAAAACA
**
20968258 AAAAAAAAGGAAAAAAATTTCTAAATAAGCCCAAATGGTGAAAATTTTAG-AATTTTCAAG
1 AAAAAAAA-GAAAAAAATTTCTAAATAAGCCCAAATGGTGAAAATTTTAGAAATAAT-AAG
* * * * *
20968318 AAAAAAAA-AAGAAAATATTTTTAGAT-TGACCCAAATGGTGAAAAATTTAGAAATAATAAT
1 AAAAAAAAGAA-AAAA-ATTTCTAAATAAG-CCCAAATGGTGAAAATTTTAGAAATAATAAG
* *
20968378 AAAAAAAAGAAATAAGAAGAATTTCTGAATAAGCCCAAATGGTGAAAATTTTAAAAAT
1 AAAAAAAAG--A-AA-AA-AATTTCTAAATAAGCCCAAATGGTGAAAATTTTAGAAAT
20968436 TCTGAAAAAG
Statistics
Matches: 94, Mismatches: 13, Indels: 18
0.75 0.10 0.14
Matches are distributed among these distances:
58 2 0.02
59 5 0.05
60 46 0.49
61 4 0.04
63 2 0.02
64 33 0.35
65 2 0.02
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.25
Consensus pattern (59 bp):
AAAAAAAAGAAAAAAATTTCTAAATAAGCCCAAATGGTGAAAATTTTAGAAATAATAAG
Found at i:20970910 original size:18 final size:18
Alignment explanation
Indices: 20970889--20970936 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
20970879 TAATATGAAT
* *
20970889 TATAATATATAATTTTTA
1 TATAATATATAATATATA
*
20970907 TATAAAATATAATATATA
1 TATAATATATAATATATA
*
20970925 TAAAATATATAA
1 TATAATATATAA
20970937 ATTATCAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAATATATAATATATA
Found at i:20972547 original size:41 final size:42
Alignment explanation
Indices: 20972450--20972547 Score: 101
Period size: 41 Copynumber: 2.3 Consensus size: 42
20972440 TTCAAAATTA
* * * *
20972450 TAAAAAATTATAAGACTTTTCAATATATTGGTAAAACCTTTTTT
1 TAAAAAATTAT-TGACCTTCCAATATATTGGT-AAACCTTTTCT
* *
20972494 TAATAAAA-TATTGACCTTCCAATATGTTGGT-AAGCTTTTCT
1 TAA-AAAATTATTGACCTTCCAATATATTGGTAAACCTTTTCT
20972535 TAAAAAATTATTG
1 TAAAAAATTATTG
20972548 CTTTTTTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
40 4 0.09
41 16 0.35
43 16 0.35
44 6 0.13
45 4 0.09
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (42 bp):
TAAAAAATTATTGACCTTCCAATATATTGGTAAACCTTTTCT
Found at i:20972705 original size:4 final size:4
Alignment explanation
Indices: 20972696--20972749 Score: 63
Period size: 4 Copynumber: 13.0 Consensus size: 4
20972686 AAACAAGTAG
* * *
20972696 ATAA ATAA ATGA ATAA ATAA ATAA ATAA GTAA ATAAA ACAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA
20972745 GATAA
1 -ATAA
20972750 GCATATAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
4 35 0.83
5 7 0.17
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:20973718 original size:18 final size:18
Alignment explanation
Indices: 20973692--20973732 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20973682 CTTACTGGGC
20973692 TTAAAG-CCCATAATCAAT
1 TTAAAGCCCCAT-ATCAAT
*
20973710 TTAAGGCCCCATATCAAT
1 TTAAAGCCCCATATCAAT
20973728 TTAAA
1 TTAAA
20973733 TGCTTGATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (18 bp):
TTAAAGCCCCATATCAAT
Found at i:20975875 original size:27 final size:28
Alignment explanation
Indices: 20975826--20975879 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
20975816 TGGATGGGTG
*
20975826 AAAAAATGAAGAAAGGGAAAAAATGAAA
1 AAAAAATGAAGAAAGAGAAAAAATGAAA
* *
20975854 AAAAAATGAA-ATAGAGAGAAAATGAA
1 AAAAAATGAAGAAAGAGAAAAAATGAA
20975880 TACTCAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.09
Consensus pattern (28 bp):
AAAAAATGAAGAAAGAGAAAAAATGAAA
Found at i:20976503 original size:22 final size:21
Alignment explanation
Indices: 20976461--20976507 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
20976451 AGCCTGTGAG
20976461 TTATGATCGAATGATAAAAAT
1 TTATGATCGAATGATAAAAAT
20976482 ATTATGGATC-AATGGAT-AAAAT
1 -TTAT-GATCGAAT-GATAAAAAT
20976504 TTAT
1 TTAT
20976508 TCTGAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.17
22 12 0.52
23 7 0.30
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36
Consensus pattern (21 bp):
TTATGATCGAATGATAAAAAT
Found at i:20976612 original size:63 final size:63
Alignment explanation
Indices: 20976513--20976641 Score: 179
Period size: 63 Copynumber: 2.0 Consensus size: 63
20976503 TTTATTCTGA
* *
20976513 AATGGCTAGTACTAAGAAACTTATAAGTGGTGACCCAGTGATGG-GTGACAAAAATTGTTTTGG
1 AATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATGGAG-GACAAAAATTGTTTTGG
* * ** *
20976576 AATGGCTAGTACTGAGAAACCTATGAGTAGTGACCCAGTGATGGAGGATGAAACTTGTTTTGG
1 AATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATGGAGGACAAAAATTGTTTTGG
20976639 AAT
1 AAT
20976642 TGTTAATGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 57 0.98
64 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (63 bp):
AATGGCTAGTACTAAGAAACCTATAAGTAGTGACCCAGTGATGGAGGACAAAAATTGTTTTGG
Found at i:20976664 original size:63 final size:63
Alignment explanation
Indices: 20976513--20976664 Score: 171
Period size: 63 Copynumber: 2.4 Consensus size: 63
20976503 TTTATTCTGA
* * * *
20976513 AATGGCTAGTACTAAGAAACTTATAAGTGGTGACCCAGTGATGGGTGACAAAAATTGTTTTGG
1 AATGGCTAATACTGAGAAACTTATGAGTAGTGACCCAGTGATGGGTGACAAAAATTGTTTTGG
* * ** *
20976576 AATGGCTAGTACTGAGAAACCTATGAGTAGTGACCCAGTGATGGAG-GATGAAACTTGTTTTGG
1 AATGGCTAATACTGAGAAACTTATGAGTAGTGACCCAGTGATGG-GTGACAAAAATTGTTTTGG
* * * *
20976639 AATTGTTAATGCTGAGAAGCTTATGA
1 AATGGCTAATACTGAGAAACTTATGA
20976665 ATGGTGATCA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
63 74 0.99
64 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (63 bp):
AATGGCTAATACTGAGAAACTTATGAGTAGTGACCCAGTGATGGGTGACAAAAATTGTTTTGG
Found at i:20977590 original size:41 final size:41
Alignment explanation
Indices: 20977507--20977595 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
20977497 CATGATTGTC
* * **
20977507 GAAGAGCATTTTATTTTCTAAAGTTGTGGTGCCTCTGTTTA
1 GAAGAGCATTTTATTTTCTAAAGTCGTGGAGCCTCTAATTA
* *
20977548 GAGGAGCA-TTTATTTTCTTAAAGTCGTTGAGCCTCTAATTA
1 GAAGAGCATTTTATTTTC-TAAAGTCGTGGAGCCTCTAATTA
20977589 GAAGAGC
1 GAAGAGC
20977596 TTTGTTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 9 0.22
41 31 0.77
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.38
Consensus pattern (41 bp):
GAAGAGCATTTTATTTTCTAAAGTCGTGGAGCCTCTAATTA
Found at i:20978766 original size:12 final size:12
Alignment explanation
Indices: 20978751--20978791 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
20978741 GGTATTTTTT
20978751 TATTTTATTTAG
1 TATTTTATTTAG
20978763 TATTTTATTTATG
1 TATTTTATTTA-G
*
20978776 TA-ATT-TTTAG
1 TATTTTATTTAG
20978786 TATTTT
1 TATTTT
20978792 TACATAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 3 0.12
11 6 0.24
12 13 0.52
13 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (12 bp):
TATTTTATTTAG
Found at i:20979000 original size:12 final size:13
Alignment explanation
Indices: 20978983--20979011 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
20978973 ATTTATTTTC
20978983 AAAACAAAAAA-A
1 AAAACAAAAAACA
20978995 AAAACAAAAAACA
1 AAAACAAAAAACA
20979008 AAAA
1 AAAA
20979012 ATAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAACA
Found at i:20979263 original size:26 final size:27
Alignment explanation
Indices: 20979232--20979285 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
20979222 AATGATGAGA
*
20979232 TTCTAAAAAAT-TTTAAATGATAAATT
1 TTCTAAAAAATCTTTAAATGAGAAATT
* *
20979258 TTCTAAGAAATCTTTAAGTGAGAAATT
1 TTCTAAAAAATCTTTAAATGAGAAATT
20979285 T
1 T
20979286 CTTTAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (27 bp):
TTCTAAAAAATCTTTAAATGAGAAATT
Found at i:20980591 original size:30 final size:31
Alignment explanation
Indices: 20980530--20980605 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
20980520 AATTAAAAAA
* *
20980530 AAAAGTTTGATCACTTAATTTTTTAAAAATTT
1 AAAA-TTTGATCACTTAAGTTTTGAAAAATTT
** * *
20980562 TTATTTTGATCACTT-AGTTTTGGAAAATTT
1 AAAATTTGATCACTTAAGTTTTGAAAAATTT
20980592 AAAATTTGATCACT
1 AAAATTTGATCACT
20980606 CAAAAATAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
30 23 0.66
31 11 0.31
32 1 0.03
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (31 bp):
AAAATTTGATCACTTAAGTTTTGAAAAATTT
Found at i:20982023 original size:18 final size:18
Alignment explanation
Indices: 20982002--20982048 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
20981992 TAATATGAAT
* *
20982002 TATAATATATAATTTTTA
1 TATAATATATAATATATA
*
20982020 TATAAAATATAATATATA
1 TATAATATATAATATATA
20982038 TA-AATATATAA
1 TATAATATATAA
20982049 ATTATCAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATAATATATAATATATA
Found at i:20982058 original size:15 final size:17
Alignment explanation
Indices: 20982018--20982061 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
20982008 ATATAATTTT
20982018 TATATAAA-ATATAATA
1 TATATAAATATATAATA
20982034 TATATAAATATATAA-A
1 TATATAAATATATAATA
*
20982050 T-TATCAATATAT
1 TATATAAATATAT
20982062 TACATAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 10 0.38
16 10 0.38
17 6 0.23
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TATATAAATATATAATA
Found at i:20983655 original size:41 final size:42
Alignment explanation
Indices: 20983558--20983655 Score: 101
Period size: 41 Copynumber: 2.3 Consensus size: 42
20983548 TTCAAAATTA
* * * *
20983558 TAAAAAATTATAAGACTTTTCAATATATTGGTAAAACCTTTTTT
1 TAAAAAATTAT-TGACCTTCCAATATATTGGT-AAACCTTTTCT
* *
20983602 TAATAAAA-TATTGACCTTCCAATATGTTGGT-AAGCTTTTCT
1 TAA-AAAATTATTGACCTTCCAATATATTGGTAAACCTTTTCT
20983643 TAAAAAATTATTG
1 TAAAAAATTATTG
20983656 CTTTTTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
40 4 0.09
41 16 0.35
43 16 0.35
44 6 0.13
45 4 0.09
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (42 bp):
TAAAAAATTATTGACCTTCCAATATATTGGTAAACCTTTTCT
Found at i:20983812 original size:4 final size:4
Alignment explanation
Indices: 20983803--20983856 Score: 63
Period size: 4 Copynumber: 13.0 Consensus size: 4
20983793 AAACAAGTAG
* * *
20983803 ATAA ATAA ATGA ATAA ATAA ATAA ATAA GTAA ATAAA ACAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA
20983852 GATAA
1 -ATAA
20983857 GCATATAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
4 35 0.83
5 7 0.17
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:20984373 original size:35 final size:36
Alignment explanation
Indices: 20984334--20984419 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 36
20984324 ACAATAGACT
*
20984334 AAATCCCAATTAAAAAAAAAAAAAACC-AAGTTCAA
1 AAATCCCAATTAAAAAAAAAAAAAACCAAAATTCAA
* * *
20984369 AAATCCCAA--AAAAGAAAATAAAGCCAAAAATTCAA
1 AAATCCCAATTAAAAAAAAAAAAAACC-AAAATTCAA
20984404 AAA-CCCAATTAAAAAA
1 AAATCCCAATTAAAAAA
20984420 TTTCCTTAGC
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
33 13 0.31
34 5 0.12
35 19 0.45
36 5 0.12
ACGTcount: A:0.66, C:0.17, G:0.03, T:0.13
Consensus pattern (36 bp):
AAATCCCAATTAAAAAAAAAAAAAACCAAAATTCAA
Found at i:20996221 original size:59 final size:59
Alignment explanation
Indices: 20996149--20996348 Score: 282
Period size: 60 Copynumber: 3.4 Consensus size: 59
20996139 TATTTTTGGA
20996149 GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAGGTTTTGAG
1 GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAGGTTTTGAG
* * * * *
20996208 GAAAAGTTAAAAGTATCAATTTTTCTTAGAAATCAAAGTTTCAAAAAAAAGGGTTTTGAG
1 GAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTTCAAAAAAAAAGGTTTTGAG
*
20996268 GAAAAGTTGAAAGTATCAATTTTCCTT-AAAAT-AAATTTCCAAAAAAAATA-TTTTTG-G
1 GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTT-CAAAAAAAA-AGGTTTTGAG
20996325 AGAAAAGTTGAAAGTATCAATTTT
1 -GAAAAGTTGAAAGTATCAATTTT
20996349 TCCTACACAA
Statistics
Matches: 126, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
57 6 0.05
58 37 0.29
59 34 0.27
60 49 0.39
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.33
Consensus pattern (59 bp):
GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAGGTTTTGAG
Found at i:21000227 original size:8 final size:8
Alignment explanation
Indices: 21000183--21000244 Score: 58
Period size: 8 Copynumber: 7.8 Consensus size: 8
21000173 ACAATGGATG
21000183 AAAAATGA
1 AAAAATGA
21000191 GAAAAGA-GA
1 -AAAA-ATGA
21000200 AAAAA--A
1 AAAAATGA
*
21000206 AAAAAGGGA
1 AAAAA-TGA
21000215 AAAAATGA
1 AAAAATGA
*
21000223 GAAAATGA
1 AAAAATGA
21000231 AAAAATGA
1 AAAAATGA
21000239 AAAAAT
1 AAAAAT
21000245 CCAAATTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
6 6 0.13
7 1 0.02
8 26 0.57
9 12 0.26
10 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (8 bp):
AAAAATGA
Found at i:21001516 original size:41 final size:40
Alignment explanation
Indices: 21001466--21002039 Score: 697
Period size: 41 Copynumber: 14.1 Consensus size: 40
21001456 ATGATTGTCT
21001466 AGGAG-AATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAG
1 AGGAGCAATTTAC-TTTTCAAAGTTCGTTGCCTCTGTTTAG
* *
21001506 AGGAGCAATTTACTTTTTCAAAGTT-GTGGTACCTCTATTTAG
1 AGGAGCAATTTAC-TTTTCAAAGTTCGT--TGCCTCTGTTTAG
*
21001548 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAG
*
21001588 AGGAGCAATTTACTTTTCCAAAG-TCGTGGTCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTTCGTTG-CCTCTGTTTAG
21001629 AGGAGCAATTTACTTTTCCAAAGTTCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTTCGTTGCCTCTGTTTAG
* *
21001670 AGGAGCAATTTACTTTTCCAAG-TCGTGGTACCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTCGT--T-GCCTCTGTTTAG
*
21001712 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAA
1 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAG
* * *
21001752 AGGAGC-ATATACTTTTCAAAGTGT-GGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGT-TCGTTGCCTCTGTTTAG
21001791 AGGAGCAATTTACTTTTC-AAGTTCGTTG-CTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAG
21001829 AGGAGCAATTTAC-TTTCAAAGTTCCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTT-CGTTGCCTCTGTTTAG
*
21001869 ATGGAGCAATTTTACTTTTCCAAAGTT-GTGGTACCTCTGTTTAG
1 A-GGAGCAA-TTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAG
* *
21001913 AGGAGCAATTTACTTTCCAAAG-TCGTGGTGCCTCTGCTTAG
1 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
*
21001954 AGGAGCAATTTACTTTTCAAAG-TCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
*
21001995 AGGAGCAATTTATGTTTCTCAAAG-TCGTTGAGCCTCTGTTTAG
1 AGGAGCAATTTA-CTTT-TCAAAGTTCGTT--GCCTCTGTTTAG
21002038 AG
1 AG
21002040 AAGCTTTGGT
Statistics
Matches: 479, Mismatches: 27, Indels: 53
0.86 0.05 0.09
Matches are distributed among these distances:
37 4 0.01
38 29 0.06
39 48 0.10
40 84 0.18
41 176 0.37
42 81 0.17
43 37 0.08
44 20 0.04
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (40 bp):
AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAG
Found at i:21001576 original size:82 final size:81
Alignment explanation
Indices: 21001466--21002039 Score: 785
Period size: 82 Copynumber: 7.0 Consensus size: 81
21001456 ATGATTGTCT
21001466 AGGAG-AATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGT
1 AGGAGCAATTTAC-TTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTAC-TTTTCAAAGT
* *
21001530 TGTGGTACCTCTATTTAG
64 CGTGGTACCTCTGTTTAG
*
21001548 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTATTTAGAGGAGCAATTTACTTTTCCAAAGTC
1 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTC
21001613 GTGGT-CCTCTGTTTAG
65 GTGGTACCTCTGTTTAG
*
21001629 AGGAGCAATTTACTTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAGTC
1 AGGAGCAATTTACTTTT-CAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
21001694 GTGGTACCCTCTGTTTAG
65 GTGGTA-CCTCTGTTTAG
* *
21001712 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAAAGGAGC-ATATACTTTTCAAAGT-G
1 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCG
21001775 TGGTACCTCTGTTTAG
66 TGGTACCTCTGTTTAG
21001791 AGGAGCAATTTACTTTTC-AAGTTCGTTG-CTCTGTTTAGAGGAGCAATTTAC-TTTCAAAGTTC
1 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-T-
*
21001853 CGT--TGCCTCTGTTTAG
64 CGTGGTACCTCTGTTTAG
* *
21001869 ATGGAGCAATTTTACTTTTCCAAAGTT-GTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAA
1 A-GGAGCAA-TTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAA
* *
21001933 AGTCGTGGTGCCTCTGCTTAG
61 AGTCGTGGTACCTCTGTTTAG
* *
21001954 AGGAGCAATTTACTTTTCAAAG-TCGTGGTACCTCTGTTTAGAGGAGCAATTTATGTTTCTCAAA
1 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTA-CTTT-TCAAA
*
21002018 GTCGTTG-AGCCTCTGTTTAG
62 GTCGTGGTA-CCTCTGTTTAG
21002038 AG
1 AG
21002040 AAGCTTTGGT
Statistics
Matches: 450, Mismatches: 19, Indels: 44
0.88 0.04 0.09
Matches are distributed among these distances:
77 23 0.05
78 29 0.06
79 36 0.08
80 17 0.04
81 60 0.13
82 161 0.36
83 51 0.11
84 53 0.12
85 20 0.04
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (81 bp):
AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCG
TGGTACCTCTGTTTAG
Found at i:21002084 original size:25 final size:25
Alignment explanation
Indices: 21002050--21002138 Score: 99
Period size: 25 Copynumber: 3.5 Consensus size: 25
21002040 AAGCTTTGGT
*
21002050 AAAAA-AAAAAAACAACGCAAGAAA
1 AAAAACAAAAAAACAACACAAGAAA
21002074 AAAAACAAAAAAACAACACAAGAAA
1 AAAAACAAAAAAACAACACAAGAAA
* * * *
21002099 AAAACCAAAAAAAACAAAAAAACACAA
1 AAAAAC-AAAAAAACAACACAAGA-AA
*
21002126 AAAAATAAAAAAA
1 AAAAACAAAAAAA
21002139 GAAAGACAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
24 5 0.09
25 23 0.42
26 21 0.38
27 6 0.11
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.01
Consensus pattern (25 bp):
AAAAACAAAAAAACAACACAAGAAA
Found at i:21002085 original size:8 final size:8
Alignment explanation
Indices: 21002072--21002129 Score: 62
Period size: 8 Copynumber: 6.9 Consensus size: 8
21002062 CAACGCAAGA
21002072 AAAAAAAC
1 AAAAAAAC
21002080 AAAAAAAC
1 AAAAAAAC
* * *
21002088 AACACAAG
1 AAAAAAAC
21002096 AAAAAAACC
1 AAAAAAA-C
21002105 AAAAAAAAC
1 -AAAAAAAC
21002114 AAAAAAAC
1 AAAAAAAC
21002122 ACAAAAAA
1 A-AAAAAA
21002130 ATAAAAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
8 27 0.66
9 7 0.17
10 7 0.17
ACGTcount: A:0.83, C:0.16, G:0.02, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:21002136 original size:34 final size:34
Alignment explanation
Indices: 21002071--21002136 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
21002061 ACAACGCAAG
* *
21002071 AAAAAAAACAAAAAAACAACACAAGAAAAAAACC
1 AAAAAAAACAAAAAAACAACAAAAAAAAAAAACC
21002105 AAAAAAAACAAAAAAAC-ACAAAAAAATAAAAA
1 AAAAAAAACAAAAAAACAACAAAAAAA-AAAAA
21002137 AAGAAAGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.02
Consensus pattern (34 bp):
AAAAAAAACAAAAAAACAACAAAAAAAAAAAACC
Done.