Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 176 of 187
Found at i:52733298 original size:15 final size:15
Alignment explanation
Indices: 52733278--52733306 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52733268 GGTTCCCAGG
52733278 ATTGAAAATTTGAAA
1 ATTGAAAATTTGAAA
52733293 ATTGAAAATTTGAA
1 ATTGAAAATTTGAA
52733307 TAGGATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (15 bp):
ATTGAAAATTTGAAA
Found at i:52733438 original size:12 final size:13
Alignment explanation
Indices: 52733407--52733439 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
52733397 TTTTAGGTAT
52733407 TAATAAAATAATA
1 TAATAAAATAATA
52733420 TAA-AAAATAATA
1 TAATAAAATAATA
52733432 -AATAAAAT
1 TAATAAAAT
52733440 TTGCAAATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 14 0.74
13 3 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
TAATAAAATAATA
Found at i:52734171 original size:17 final size:17
Alignment explanation
Indices: 52734133--52734165 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
52734123 GTACATGGTT
*
52734133 GTGTGGTCAACATGCCA
1 GTGTGGTCAACACGCCA
52734150 GTGTGGTCAACACGCC
1 GTGTGGTCAACACGCC
52734166 CATGTGAAAA
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:0.21, C:0.27, G:0.30, T:0.21
Consensus pattern (17 bp):
GTGTGGTCAACACGCCA
Found at i:52734386 original size:20 final size:20
Alignment explanation
Indices: 52734341--52734386 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
52734331 ATTTCCAATA
*
52734341 TTTATCAAGATTATCGAAAGG
1 TTTATCAAGA-TATCGAAAAG
52734362 TTTATCAAGA-ATCGAAAAAG
1 TTTATCAAGATATCG-AAAAG
52734382 TTTAT
1 TTTAT
52734387 TTAATCGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 9 0.39
21 10 0.43
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (20 bp):
TTTATCAAGATATCGAAAAG
Found at i:52734622 original size:17 final size:16
Alignment explanation
Indices: 52734608--52734640 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
52734598 AAAGAAAAAT
52734608 GAAAGAAAATAAAAAGA
1 GAAA-AAAATAAAAAGA
52734625 GAAAAAAATAAAAAGA
1 GAAAAAAATAAAAAGA
52734641 TGGAGAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (16 bp):
GAAAAAAATAAAAAGA
Found at i:52735878 original size:19 final size:19
Alignment explanation
Indices: 52735856--52735893 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
52735846 AAAAAAACTT
*
52735856 ATTTTACTAAATAACCCAA
1 ATTTAACTAAATAACCCAA
52735875 ATTTAACTAAATAACCCAA
1 ATTTAACTAAATAACCCAA
52735894 CCTAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (19 bp):
ATTTAACTAAATAACCCAA
Found at i:52735972 original size:38 final size:41
Alignment explanation
Indices: 52735920--52736010 Score: 143
Period size: 38 Copynumber: 2.3 Consensus size: 41
52735910 TTAAAAATGA
*
52735920 TATTTAATACAATAAAATATTTATTATATTTATT-T-GTGT
1 TATTTAATATAATAAAATATTTATTATATTTATTGTAGTGT
52735959 T-TTTAATATAATAAAATATTTATTATATTTATTGTAGTGT
1 TATTTAATATAATAAAATATTTATTATATTTATTGTAGTGT
*
52735999 TATTTAAAATAA
1 TATTTAATATAA
52736011 ACAGATTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
38 31 0.66
39 2 0.04
40 5 0.11
41 9 0.19
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (41 bp):
TATTTAATATAATAAAATATTTATTATATTTATTGTAGTGT
Found at i:52742766 original size:15 final size:15
Alignment explanation
Indices: 52742746--52742774 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52742736 GGTTCCCGGG
52742746 ATTGAAAATTTGAAA
1 ATTGAAAATTTGAAA
52742761 ATTGAAAATTTGAA
1 ATTGAAAATTTGAA
52742775 TAGGATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (15 bp):
ATTGAAAATTTGAAA
Found at i:52742950 original size:28 final size:27
Alignment explanation
Indices: 52742884--52742950 Score: 62
Period size: 29 Copynumber: 2.4 Consensus size: 27
52742874 TTAATAAAAT
* **
52742884 AAAATAATAAATAATAAATAAAATTTG
1 AAAATGATAAATAATAAATAAAATTAA
* * *
52742911 CAAATGCTTAAATCAATAATTAAAATTAA
1 AAAATG-ATAAAT-AATAAATAAAATTAA
52742940 AAAATGATAAA
1 AAAATGATAAA
52742951 ATTTCTATTT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
27 4 0.13
28 9 0.30
29 17 0.57
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAATGATAAATAATAAATAAAATTAA
Found at i:52746803 original size:11 final size:11
Alignment explanation
Indices: 52746787--52746813 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
52746777 CTTAACCATT
52746787 ATATTATTTTA
1 ATATTATTTTA
52746798 ATATTATTTTA
1 ATATTATTTTA
52746809 ATATT
1 ATATT
52746814 TTAATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTATTTTA
Found at i:52748334 original size:18 final size:17
Alignment explanation
Indices: 52748301--52748339 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
52748291 TTTTATAAAT
52748301 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
52748319 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
52748336 TGTG
1 TGTG
52748340 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:52760488 original size:129 final size:130
Alignment explanation
Indices: 52760339--52760592 Score: 456
Period size: 129 Copynumber: 2.0 Consensus size: 130
52760329 TCGAGTCTTG
52760339 CCTAAATCAGGTTTAATTGACCTCTTTATAGACTTTATTGATAGGCCACTCAAATCTCTTAAG-A
1 CCTAAATCAGGTTTAATTGACCTCTTTATAGACTTTATTGATAGGCCACTCAAATCTCTTAAGAA
* *
52760403 AATATCTCTCTTTGTGGTGGTTGATTGTTTTTTTCTAGTATGCTCATTTTATTACCCTCTCCCAT
66 AATATCTCTCTTTGTCGTGGTTGATTGTTTTTTTCTACTATGCTCATTTTATTACCCTCTCCCAT
* *
52760468 CCTAAATCAGGTTTAATTGACCTCTTTATAGACTTTATTGATAGGCTACTCAAATCTCTTGAGAA
1 CCTAAATCAGGTTTAATTGACCTCTTTATAGACTTTATTGATAGGCCACTCAAATCTCTTAAGAA
*
52760533 AATATCTCTTTTTGTCGTGGTTGATTGTTTTTTTCTACTATGCTCATTTTATTACCCTCT
66 AATATCTCTCTTTGTCGTGGTTGATTGTTTTTTTCTACTATGCTCATTTTATTACCCTCT
52760593 TTCATCCTTA
Statistics
Matches: 119, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
129 61 0.51
130 58 0.49
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.44
Consensus pattern (130 bp):
CCTAAATCAGGTTTAATTGACCTCTTTATAGACTTTATTGATAGGCCACTCAAATCTCTTAAGAA
AATATCTCTCTTTGTCGTGGTTGATTGTTTTTTTCTACTATGCTCATTTTATTACCCTCTCCCAT
Found at i:52765052 original size:12 final size:12
Alignment explanation
Indices: 52765020--52765054 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
52765010 GCACATTTTG
52765020 TTCTTATTATTA
1 TTCTTATTATTA
*
52765032 TTCTCATTATTA
1 TTCTTATTATTA
*
52765044 TTGTTATTATT
1 TTCTTATTATT
52765055 TATTTTTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.66
Consensus pattern (12 bp):
TTCTTATTATTA
Found at i:52765066 original size:7 final size:7
Alignment explanation
Indices: 52765047--52765095 Score: 53
Period size: 7 Copynumber: 6.6 Consensus size: 7
52765037 ATTATTATTG
*
52765047 TTATTAT
1 TTATTTT
52765054 TTATTTT
1 TTATTTT
*
52765061 TCATTTTT
1 TTA-TTTT
52765069 TTATTTT
1 TTATTTT
52765076 TTATTTT
1 TTATTTT
52765083 TTAGATTTT
1 TT--ATTTT
52765092 TTAT
1 TTAT
52765096 ATTAATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
7 23 0.64
8 6 0.17
9 7 0.19
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (7 bp):
TTATTTT
Found at i:52765090 original size:16 final size:15
Alignment explanation
Indices: 52765047--52765095 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
52765037 ATTATTATTG
*
52765047 TTATTATTT-ATTTT
1 TTATTTTTTGATTTT
* *
52765061 TCATTTTTTTATTTT
1 TTATTTTTTGATTTT
52765076 TTATTTTTTAGATTTT
1 TTATTTTTT-GATTTT
52765092 TTAT
1 TTAT
52765096 ATTAATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 7 0.24
15 13 0.45
16 9 0.31
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (15 bp):
TTATTTTTTGATTTT
Found at i:52765091 original size:22 final size:22
Alignment explanation
Indices: 52765047--52765092 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
52765037 ATTATTATTG
**
52765047 TTATTATTTATTTTTCATTTTT
1 TTATTATTTATTTTTCAGATTT
* *
52765069 TTATTTTTTATTTTTTAGATTT
1 TTATTATTTATTTTTCAGATTT
52765091 TT
1 TT
52765093 TATATTAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (22 bp):
TTATTATTTATTTTTCAGATTT
Found at i:52771829 original size:26 final size:26
Alignment explanation
Indices: 52771799--52771853 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
52771789 TTTGGTGAGC
*
52771799 TCATAGTTCGCAGGTGAACTTGCAGT
1 TCATAGTTCGCAGGTGAACTCGCAGT
* *
52771825 TCATAGTTCGTAGGTGAGCTCGCAGT
1 TCATAGTTCGCAGGTGAACTCGCAGT
52771851 TCA
1 TCA
52771854 CAATTAGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (26 bp):
TCATAGTTCGCAGGTGAACTCGCAGT
Found at i:52775031 original size:13 final size:13
Alignment explanation
Indices: 52775013--52775177 Score: 118
Period size: 13 Copynumber: 12.5 Consensus size: 13
52775003 TAAATTTTAG
*
52775013 TAAGTAATGTATT
1 TAAGTAATATATT
*
52775026 TAAGTAACATATT
1 TAAGTAATATATT
* *
52775039 AAAGTAATAAATT
1 TAAGTAATATATT
** *
52775052 TAAACAA-ATTTT
1 TAAGTAATATATT
*
52775064 AGTAAGTAATGTATT
1 --TAAGTAATATATT
*
52775079 TAAGTAACATATT
1 TAAGTAATATATT
*
52775092 TAAGTAATAAATT
1 TAAGTAATATATT
** *
52775105 TAACCAA-ATTTT
1 TAAGTAATATATT
* *
52775117 AGTAAGTAGTGTATT
1 --TAAGTAATATATT
*
52775132 TAAGTAATTTATT
1 TAAGTAATATATT
52775145 TAAGTAATATATT
1 TAAGTAATATATT
*
52775158 CAAGTAATATATT
1 TAAGTAATATATT
*
52775171 AAAGTAA
1 TAAGTAA
52775178 ATTTTAGTAA
Statistics
Matches: 114, Mismatches: 32, Indels: 12
0.72 0.20 0.08
Matches are distributed among these distances:
12 6 0.05
13 93 0.82
14 9 0.08
15 6 0.05
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:52775068 original size:53 final size:53
Alignment explanation
Indices: 52775004--52775153 Score: 255
Period size: 53 Copynumber: 2.8 Consensus size: 53
52774994 ATATATACTT
*
52775004 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTAAAGTAATAAATTTAAAC
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAAAC
*
52775057 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAACC
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAAAC
* **
52775110 AAATTTTAGTAAGTAGTGTATTTAAGTAATTTATTTAAGTAATA
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATA
52775154 TATTCAAGTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 92 1.00
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (53 bp):
AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAAAC
Found at i:52775204 original size:66 final size:66
Alignment explanation
Indices: 52775066--52775204 Score: 161
Period size: 66 Copynumber: 2.1 Consensus size: 66
52775056 CAAATTTTAG
* * ** * *
52775066 TAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAACCAAATTTTAGTAAGTAGTGTAT
1 TAAGTAATGTATTTAAGTAACATATTCAAGTAATAAATTAAACCAAATTTTAGTAAAAAATATAT
52775131 T
66 T
* * * ** *
52775132 TAAGTAATTTATTTAAGTAATATATTCAAGTAATATATTAAAGTAAATTTTAGTAAAAAATATGT
1 TAAGTAATGTATTTAAGTAACATATTCAAGTAATAAATTAAACCAAATTTTAGTAAAAAATATAT
52775197 T
66 T
*
52775198 TTAGTAA
1 TAAGTAA
52775205 GTAATGTAAG
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (66 bp):
TAAGTAATGTATTTAAGTAACATATTCAAGTAATAAATTAAACCAAATTTTAGTAAAAAATATAT
T
Found at i:52776906 original size:40 final size:40
Alignment explanation
Indices: 52776851--52776948 Score: 169
Period size: 40 Copynumber: 2.5 Consensus size: 40
52776841 TCCACGTCAG
*
52776851 CGCGATTTGCTGACGTGGACACAAATAGCGCCCTCTAGGA
1 CGCGATTTGCTGACGTGGACACAAATAACGCCCTCTAGGA
*
52776891 CGCGATTTGCTGACGTGGACACAAATAACTCCCTCTAGGA
1 CGCGATTTGCTGACGTGGACACAAATAACGCCCTCTAGGA
*
52776931 CGCGATTTACTGACGTGG
1 CGCGATTTGCTGACGTGG
52776949 CATGAACAGT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (40 bp):
CGCGATTTGCTGACGTGGACACAAATAACGCCCTCTAGGA
Found at i:52784042 original size:13 final size:15
Alignment explanation
Indices: 52784011--52784065 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
52784001 AAAATTTGAA
*
52784011 TTGAAGATTTGAAACT
1 TTGAATATTTG-AACT
52784027 TTGAATATTTG-A-T
1 TTGAATATTTGAACT
* *
52784040 TTGTAGATTTGTAACT
1 TTGAATATTTG-AACT
52784056 TTGAATATTT
1 TTGAATATTT
52784066 TGGTATGCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 10 0.32
14 1 0.03
15 1 0.03
16 19 0.61
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (15 bp):
TTGAATATTTGAACT
Found at i:52784047 original size:29 final size:29
Alignment explanation
Indices: 52784004--52784065 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
52783994 CGAATATAAA
52784004 ATTTGAATTGAAGATTTGAAACTTTGAAT
1 ATTTGAATTGAAGATTTGAAACTTTGAAT
* * *
52784033 ATTTGATTTGTAGATTTGTAACTTTGAAT
1 ATTTGAATTGAAGATTTGAAACTTTGAAT
52784062 ATTT
1 ATTT
52784066 TGGTATGCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.48
Consensus pattern (29 bp):
ATTTGAATTGAAGATTTGAAACTTTGAAT
Found at i:52785642 original size:31 final size:29
Alignment explanation
Indices: 52785592--52785675 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 29
52785582 TCTCTTGAAT
* *
52785592 AAAATA-TTTTTATTTAAATAATA-ATGAA
1 AAAATATTTTTTACTAAAATAATATAT-AA
52785620 AATTAATATTTTTTACTAAAATAATATATAA
1 AA--AATATTTTTTACTAAAATAATATATAA
* *
52785651 AAAAGAATTATTTACTAAAATAATA
1 AAAA-TATTTTTTACTAAAATAATA
52785676 CACAAACTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
28 2 0.04
29 2 0.04
30 22 0.47
31 19 0.40
32 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAATATTTTTTACTAAAATAATATATAA
Found at i:52785901 original size:66 final size:66
Alignment explanation
Indices: 52785832--52786112 Score: 388
Period size: 66 Copynumber: 4.3 Consensus size: 66
52785822 ATTTTGAATT
* * *
52785832 TTTGAATAGGAAAGGTAAGATAGGTGGAAAACGATTATAAAATTTGAAGATAGGCGGGTTTGAAA
1 TTTGAATAGGAATGGTAAGATAGGTGGAAAACGACTATAAAATTTGAAGATAGGCGGATTTGAAA
*
52785897 T
66 A
* * *
52785898 TTTGAATAGGAATGGTAAGATAAGTGGAAAACGACTATAAAATCTGAAGATAGGTGGATTTGAAA
1 TTTGAATAGGAATGGTAAGATAGGTGGAAAACGACTATAAAATTTGAAGATAGGCGGATTTGAAA
52785963 A
66 A
* * * * * *
52785964 TTTGATTAAGG-ATGGTAAGATAGATGGAAAAAGACTGTAAAATTTAAAGATA-GCGGGTTTGAA
1 TTTGAAT-AGGAATGGTAAGATAGGTGGAAAACGACTATAAAATTTGAAGATAGGCGGATTTGAA
52786027 AA
65 AA
* *
52786029 TTTAAATAGGAATGGTAAGATAGGTGGAAAACGACTATAAAATTTGAAGATAGGCAGATTTGAAA
1 TTTGAATAGGAATGGTAAGATAGGTGGAAAACGACTATAAAATTTGAAGATAGGCGGATTTGAAA
52786094 A
66 A
52786095 TTTGAATTA-GAATGGTAA
1 TTTGAA-TAGGAATGGTAA
52786113 AATGACTAAG
Statistics
Matches: 186, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
64 3 0.02
65 53 0.28
66 125 0.67
67 5 0.03
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.27
Consensus pattern (66 bp):
TTTGAATAGGAATGGTAAGATAGGTGGAAAACGACTATAAAATTTGAAGATAGGCGGATTTGAAA
A
Found at i:52786070 original size:131 final size:132
Alignment explanation
Indices: 52785832--52786112 Score: 406
Period size: 131 Copynumber: 2.1 Consensus size: 132
52785822 ATTTTGAATT
* * * * *
52785832 TTTGAA-TAGGAAAGGTAAGATAGGTGGAAAACGATTATAAAATTTGAAGATAGGCGGGTTTGAA
1 TTTGAATTA-GAATGGTAAGATAGATGGAAAAAGACTATAAAATTTAAAGATAGGCGGGTTTGAA
* * **
52785896 ATTTTGAATAGGAATGGTAAGATAAGTGGAAAACGACTATAAAATCTGAAGATAGGTGGATTTGA
65 AATTTAAATAGGAATGGTAAGATAAGTGGAAAACGACTATAAAATCTGAAGATAGGCAGATTTGA
52785961 AAA
130 AAA
* *
52785964 TTTG-ATTAAGGATGGTAAGATAGATGGAAAAAGACTGTAAAATTTAAAGATA-GCGGGTTTGAA
1 TTTGAATT-AGAATGGTAAGATAGATGGAAAAAGACTATAAAATTTAAAGATAGGCGGGTTTGAA
* *
52786027 AATTTAAATAGGAATGGTAAGATAGGTGGAAAACGACTATAAAATTTGAAGATAGGCAGATTTGA
65 AATTTAAATAGGAATGGTAAGATAAGTGGAAAACGACTATAAAATCTGAAGATAGGCAGATTTGA
52786092 AAA
130 AAA
52786095 TTTGAATTAGAATGGTAA
1 TTTGAATTAGAATGGTAA
52786113 AATGACTAAG
Statistics
Matches: 132, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
131 87 0.66
132 44 0.33
133 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.26, T:0.27
Consensus pattern (132 bp):
TTTGAATTAGAATGGTAAGATAGATGGAAAAAGACTATAAAATTTAAAGATAGGCGGGTTTGAAA
ATTTAAATAGGAATGGTAAGATAAGTGGAAAACGACTATAAAATCTGAAGATAGGCAGATTTGAA
AA
Found at i:52797526 original size:5 final size:5
Alignment explanation
Indices: 52797518--52797553 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
52797508 GAGATGAAAT
52797518 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
52797554 ATATTTATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (5 bp):
TCGAA
Found at i:52800860 original size:31 final size:30
Alignment explanation
Indices: 52800799--52800861 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
52800789 TAGTAAATAA
* * **
52800799 TTTTTATATTATTTTAATCAAAAAGTTTAT
1 TTTTTATATTATTTAAATAAAAAAAATTAT
52800829 TTTTTATTATTATTTAAATAAAAAAAATTAT
1 TTTTTA-TATTATTTAAATAAAAAAAATTAT
52800860 TT
1 TT
52800862 AAGAGAATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 6 0.21
31 22 0.79
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTTTATATTATTTAAATAAAAAAAATTAT
Found at i:52801153 original size:25 final size:24
Alignment explanation
Indices: 52801125--52801172 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
52801115 TAAAAGTATT
52801125 TATA-TTATATTATATTAATATTTTA
1 TATATTTATATT-TATTAA-ATTTTA
*
52801150 TATATTTTTATTTATTAAATTTT
1 TATATTTATATTTATTAAATTTT
52801173 TTTATATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 10 0.48
26 6 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TATATTTATATTTATTAAATTTTA
Found at i:52807306 original size:13 final size:13
Alignment explanation
Indices: 52807288--52807335 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
52807278 AGTTCTTCAT
52807288 TGCTTTTGA-AGAG
1 TGCTTTTGAGA-AG
52807301 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
52807314 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
52807327 TACTTTTGA
1 TGCTTTTGA
52807336 AAATTTTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
13 32 0.97
14 1 0.03
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:52812944 original size:15 final size:15
Alignment explanation
Indices: 52812924--52812952 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52812914 CTTGCTTCGT
52812924 TGTTTAATAGGTGCG
1 TGTTTAATAGGTGCG
52812939 TGTTTAATAGGTGC
1 TGTTTAATAGGTGC
52812953 TCTGTAAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.31, T:0.41
Consensus pattern (15 bp):
TGTTTAATAGGTGCG
Found at i:52813625 original size:19 final size:18
Alignment explanation
Indices: 52813586--52813654 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
52813576 TATGTTACCC
* *
52813586 TAAACCCTAAACTAAATCA
1 TAAACCATAAACTTAA-CA
*
52813605 TAAGCCATAAACCTTAACA
1 TAAACCATAAA-CTTAACA
* *
52813624 TAAATCATAAACTTAAACC
1 TAAACCATAAACTT-AACA
*
52813643 TAAACCCTAAAC
1 TAAACCATAAAC
52813655 ACTGAATCTT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 3 0.08
19 33 0.82
20 4 0.10
ACGTcount: A:0.51, C:0.26, G:0.01, T:0.22
Consensus pattern (18 bp):
TAAACCATAAACTTAACA
Found at i:52813653 original size:26 final size:26
Alignment explanation
Indices: 52813586--52813653 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
52813576 TATGTTACCC
*
52813586 TAAACCCTAAA-CTAAATCATAAGCCA
1 TAAA-CCTAAACCTAAATCATAAGACA
* * *
52813612 TAAACCTTAACATAAATCATAA-ACT
1 TAAACCTAAACCTAAATCATAAGACA
52813637 TAAACCTAAACCCTAAA
1 TAAACCTAAA-CCTAAA
52813654 CACTGAATCT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 15 0.44
26 19 0.56
ACGTcount: A:0.51, C:0.25, G:0.01, T:0.22
Consensus pattern (26 bp):
TAAACCTAAACCTAAATCATAAGACA
Found at i:52813803 original size:22 final size:21
Alignment explanation
Indices: 52813769--52814602 Score: 206
Period size: 22 Copynumber: 39.5 Consensus size: 21
52813759 TACTAAATCG
*
52813769 TAAATATTAAAACCCTAAACCT
1 TAAATCTT-AAACCCTAAACCT
**
52813791 TAAATGCTTAAACCCTACCCCT
1 TAAAT-CTTAAACCCTAAACCT
* * *
52813813 AAAATC-TAAATCTTAAACCT
1 TAAATCTTAAACCCTAAACCT
*
52813833 T--A----AAACCTTAAACCT
1 TAAATCTTAAACCCTAAACCT
* * *
52813848 CAAATGTATAAACCATAAACCT
1 TAAATCT-TAAACCCTAAACCT
* *
52813870 TAAACAC-TAAACTCTTAAACCT
1 TAAA-TCTTAAAC-CCTAAACCT
* * * * *
52813892 AAAACCTAAAAACCTAAAACT
1 TAAATCTTAAACCCTAAACCT
* *
52813913 TAAATCCTAAACCTTAAA-CT
1 TAAATCTTAAACCCTAAACCT
***
52813933 TCAAACTCTTAAATATTAAATCC-
1 T-AAA-TCTTAAACCCTAAA-CCT
* * *
52813956 TAAACCTTAAATCCTAAACTT
1 TAAATCTTAAACCCTAAACCT
* *
52813977 TAAATGCATAAACCCTAAAACTT
1 TAAAT-CTTAAACCCT-AAACCT
* * *
52814000 TAAACCTTAAA-ACTCAA---
1 TAAATCTTAAACCCTAAACCT
* * *
52814017 -AAA-CATAAACCCTAATCCC
1 TAAATCTTAAACCCTAAACCT
* *
52814036 TAAATGTTTAAACACTAAACCT
1 TAAAT-CTTAAACCCTAAACCT
* * *** *
52814058 TAAACCTCAAATATATAAACCC
1 TAAATCTTAAA-CCCTAAACCT
** *
52814080 TAAA-CATTAAATTCTAAATCT
1 TAAATC-TTAAACCCTAAACCT
* **
52814101 TAAACCTTAAACTTTAAACCT
1 TAAATCTTAAACCCTAAACCT
* * *
52814122 CAAATATATAAACCCTAAACAT
1 TAAATCT-TAAACCCTAAACCT
*
52814144 TAAAT-TCTAAACCTTAAACCT
1 TAAATCT-TAAACCCTAAACCT
* *
52814165 TAAAATCTTAAA-TCTCAAACCC
1 T-AAATCTTAAACCCT-AAACCT
*
52814187 TAAACCTTAAACGCCTAAACAC-
1 TAAATCTTAAAC-CCTAAAC-CT
*
52814209 TAAAACTTTAAACCCTAAACCT
1 TAAATC-TTAAACCCTAAACCT
* *
52814231 TAAAACTTTAAAACCTAAAACC-
1 TAAATC-TTAAACCCT-AAACCT
* *
52814253 TAAA-CTCTAAACCTTAAACTT
1 TAAATCT-TAAACCCTAAACCT
* * ** * *
52814274 TAAAGCCCTAAATACTAAATCA
1 TAAA-TCTTAAACCCTAAACCT
52814296 TAAA-CTTTAAACCCTAAACCT
1 TAAATC-TTAAACCCTAAACCT
* * * * *
52814317 CAAATACATAAATCTTAAAACCC
1 TAAAT-CTTAAACCCT-AAACCT
*
52814340 TAAA-CTTTAAACCTTAAACCT
1 TAAATC-TTAAACCCTAAACCT
**
52814361 TAAA-CTT-----C-AAATGT
1 TAAATCTTAAACCCTAAACCT
* * **
52814375 ATAAACCCTAAACCCTAAACTA
1 -TAAATCTTAAACCCTAAACCT
*
52814397 TAAACT-TTAAAACCCTAAACCC
1 TAAA-TCTT-AAACCCTAAACCT
* * *
52814419 TAAATCTTAAATGCATAAACCA
1 TAAATCTTAAA-CCCTAAACCT
* * *
52814441 TAAACCATAAACCCTAATCCT
1 TAAATCTTAAACCCTAAACCT
* *
52814462 TAAATCATAAACCCTAAACTT
1 TAAATCTTAAACCCTAAACCT
* * * *
52814483 TAAACCCTAAACCTTAAATACT
1 TAAATCTTAAACCCTAAA-CCT
* *
52814505 TAAAACCCTAAACCCTAAA-CT
1 T-AAATCTTAAACCCTAAACCT
* * *
52814526 CTAAACCTTAAATCATAAACCT
1 -TAAATCTTAAACCCTAAACCT
52814548 TAAA-CTTTAAACCCTAAACCT
1 TAAATC-TTAAACCCTAAACCT
** *
52814569 TAAATACTTAAATACTAAAATCT
1 TAAAT-CTTAAACCCT-AAACCT
52814592 TAAATCTTAAA
1 TAAATCTTAAA
52814603 TTATAAACCC
Statistics
Matches: 601, Mismatches: 144, Indels: 134
0.68 0.16 0.15
Matches are distributed among these distances:
14 4 0.01
15 21 0.03
16 8 0.01
17 1 0.00
18 1 0.00
20 28 0.05
21 223 0.37
22 249 0.41
23 65 0.11
24 1 0.00
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.27
Consensus pattern (21 bp):
TAAATCTTAAACCCTAAACCT
Found at i:52813845 original size:7 final size:7
Alignment explanation
Indices: 52813778--52814714 Score: 310
Period size: 7 Copynumber: 129.6 Consensus size: 7
52813768 GTAAATATTA
*
52813778 AAACCCT
1 AAACCTT
52813785 AAACCTT
1 AAACCTT
*
52813792 AAATGCTT
1 AAA-CCTT
*
52813800 AAACCCT
1 AAACCTT
** *
52813807 ACCCCTA
1 AAACCTT
*
52813814 AAATC-T
1 AAACCTT
*
52813820 AAATCTT
1 AAACCTT
52813827 AAACCTT
1 AAACCTT
52813834 AAAACCTT
1 -AAACCTT
*
52813842 AAACCTC
1 AAACCTT
**
52813849 AAATGTAT
1 AAACCT-T
*
52813857 AAACCAT
1 AAACCTT
52813864 AAACCTT
1 AAACCTT
52813871 AAACAC-T
1 AAAC-CTT
52813878 AAACTCTT
1 AAAC-CTT
*
52813886 AAACCTA
1 AAACCTT
*
52813893 AAACCTAA
1 AAACCT-T
52813901 AAACC-T
1 AAACCTT
*
52813907 AAAACTT
1 AAACCTT
52813914 AAATCC-T
1 AAA-CCTT
52813921 AAACCTT
1 AAACCTT
52813928 AAA-CTT
1 AAACCTT
52813934 CAAACTCTT
1 -AAAC-CTT
**
52813943 AAATATT
1 AAACCTT
52813950 AAATCC-T
1 AAA-CCTT
52813957 AAACCTT
1 AAACCTT
52813964 AAATCC-T
1 AAA-CCTT
*
52813971 AAACTTT
1 AAACCTT
* *
52813978 AAATGCAT
1 AAA-CCTT
*
52813986 AAACCCTA
1 AAA-CCTT
*
52813994 AAACTTT
1 AAACCTT
52814001 AAACCTT
1 AAACCTT
* *
52814008 AAAACTCA
1 AAACCT-T
* *
52814016 AAAACAT
1 AAACCTT
*
52814023 AAACCCT
1 AAACCTT
* *
52814030 AATCCCT
1 AAACCTT
**
52814037 AAATGTTT
1 AAA-CCTT
52814045 AAACAC-T
1 AAAC-CTT
52814052 AAACCTT
1 AAACCTT
*
52814059 AAACCTC
1 AAACCTT
**
52814066 AAATATAT
1 AAACCT-T
*
52814074 AAACCCT
1 AAACCTT
*
52814081 AAACATT
1 AAACCTT
*
52814088 AAA-TTCT
1 AAACCT-T
*
52814095 AAATCTT
1 AAACCTT
52814102 AAACCTT
1 AAACCTT
*
52814109 AAACTTT
1 AAACCTT
*
52814116 AAACCTC
1 AAACCTT
**
52814123 AAATATAT
1 AAACCT-T
*
52814131 AAACCCT
1 AAACCTT
*
52814138 AAACATT
1 AAACCTT
*
52814145 AAA-TTCT
1 AAACCT-T
52814152 AAACCTT
1 AAACCTT
52814159 AAACCTT
1 AAACCTT
*
52814166 AAAATCTT
1 -AAACCTT
* *
52814174 AAATCTC
1 AAACCTT
*
52814181 AAACCCT
1 AAACCTT
52814188 AAACCTT
1 AAACCTT
*
52814195 AAACGCCT
1 AAAC-CTT
*
52814203 AAACACTA
1 AAAC-CTT
*
52814211 AAACTTT
1 AAACCTT
*
52814218 AAACCCT
1 AAACCTT
52814225 AAACCTT
1 AAACCTT
*
52814232 AAAACTTT
1 -AAACCTT
*
52814240 AAAACCTA
1 -AAACCTT
52814248 AAACC-T
1 AAACCTT
52814254 AAA-CTCT
1 AAACCT-T
52814261 AAACCTT
1 AAACCTT
*
52814268 AAACTTT
1 AAACCTT
*
52814275 AAAGCCCT
1 AAA-CCTT
*
52814283 AAATAC-T
1 AAA-CCTT
* *
52814290 AAATCAT
1 AAACCTT
*
52814297 AAACTTT
1 AAACCTT
*
52814304 AAACCCT
1 AAACCTT
*
52814311 AAACCTC
1 AAACCTT
* *
52814318 AAATACAT
1 AAA-CCTT
*
52814326 AAATCTT
1 AAACCTT
*
52814333 AAAACCCT
1 -AAACCTT
*
52814341 AAACTTT
1 AAACCTT
52814348 AAACCTT
1 AAACCTT
52814355 AAACCTT
1 AAACCTT
52814362 AAA-CTT
1 AAACCTT
**
52814368 CAAATGTAT
1 -AAACCT-T
*
52814377 AAACCCT
1 AAACCTT
*
52814384 AAACCCT
1 AAACCTT
52814391 AAA-CTAT
1 AAACCT-T
*
52814398 AAACTTT
1 AAACCTT
*
52814405 AAAACCCT
1 -AAACCTT
*
52814413 AAACCCT
1 AAACCTT
*
52814420 AAATCTT
1 AAACCTT
* *
52814427 AAATGCAT
1 AAA-CCTT
*
52814435 AAACCAT
1 AAACCTT
*
52814442 AAACCAT
1 AAACCTT
*
52814449 AAACCCT
1 AAACCTT
*
52814456 AATCCTT
1 AAACCTT
* *
52814463 AAATCAT
1 AAACCTT
*
52814470 AAACCCT
1 AAACCTT
*
52814477 AAACTTT
1 AAACCTT
*
52814484 AAACCCT
1 AAACCTT
52814491 AAACCTT
1 AAACCTT
*
52814498 AAATACTT
1 AAA-CCTT
*
52814506 AAAACCCT
1 -AAACCTT
*
52814514 AAACCCT
1 AAACCTT
52814521 AAA-CTCT
1 AAACCT-T
52814528 AAACCTT
1 AAACCTT
* *
52814535 AAATCAT
1 AAACCTT
52814542 AAACCTT
1 AAACCTT
*
52814549 AAACTTT
1 AAACCTT
*
52814556 AAACCCT
1 AAACCTT
52814563 AAACCTT
1 AAACCTT
*
52814570 AAATACTT
1 AAA-CCTT
* *
52814578 AAATACTA
1 AAA-CCTT
*
52814586 AAATCTT
1 AAACCTT
*
52814593 AAATCTT
1 AAACCTT
*
52814600 AAA-TTAT
1 AAACCT-T
*
52814607 AAACCCT
1 AAACCTT
*
52814614 AAACCCT
1 AAACCTT
*
52814621 AAA-TTT
1 AAACCTT
*
52814627 CAAATACTT
1 -AAA-CCTT
*
52814636 AAACCCTA
1 AAA-CCTT
*
52814644 AAATCTT
1 AAACCTT
52814651 AAAACCTT
1 -AAACCTT
52814659 AAA-CTAT
1 AAACCT-T
*
52814666 AAATCTT
1 AAACCTT
52814673 AAAACCTT
1 -AAACCTT
*
52814681 AAACTTT
1 AAACCTT
*
52814688 AAATCCTAA
1 AAA-CCT-T
52814697 AAACCTT
1 AAACCTT
*
52814704 AAACTTT
1 AAACCTT
52814711 AAAC
1 AAAC
52814715 TATAAATTCT
Statistics
Matches: 688, Mismatches: 181, Indels: 122
0.69 0.18 0.12
Matches are distributed among these distances:
5 1 0.00
6 33 0.05
7 475 0.69
8 167 0.24
9 12 0.02
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.27
Consensus pattern (7 bp):
AAACCTT
Found at i:52814011 original size:15 final size:15
Alignment explanation
Indices: 52813825--52814013 Score: 51
Period size: 15 Copynumber: 13.0 Consensus size: 15
52813815 AATCTAAATC
*
52813825 TTAAACCTTAAAACC
1 TTAAACCTTAAAACT
* **
52813840 TTAAACCTCAAATGT
1 TTAAACCTTAAAACT
* * *
52813855 ATAAACCAT-AAACC
1 TTAAACCTTAAAACT
52813869 TTAAACAC-T-AAACT
1 TTAAAC-CTTAAAACT
52813883 CTTAAACC-TAAAACCT
1 -TTAAACCTTAAAA-CT
**
52813899 AAAAACC-TAAAAC-
1 TTAAACCTTAAAACT
*
52813912 TTAAATCC-T-AAACC
1 TTAAA-CCTTAAAACT
*
52813926 TTAAA-CTTCAAACT
1 TTAAACCTTAAAACT
** *
52813940 CTTAAATATTAAATC-
1 -TTAAACCTTAAAACT
* *
52813955 CTAAACCTTAAATC-
1 TTAAACCTTAAAACT
* * *
52813969 CTAAACTTTAAATGC-
1 TTAAACCTTAAA-ACT
* *
52813984 ATAAACCCTAAAACT
1 TTAAACCTTAAAACT
52813999 TTAAACCTTAAAACT
1 TTAAACCTTAAAACT
52814014 CAAAAACATA
Statistics
Matches: 131, Mismatches: 31, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
12 1 0.01
13 8 0.06
14 50 0.38
15 65 0.50
16 7 0.05
ACGTcount: A:0.48, C:0.24, G:0.01, T:0.28
Consensus pattern (15 bp):
TTAAACCTTAAAACT
Found at i:52814121 original size:57 final size:57
Alignment explanation
Indices: 52814043--52814183 Score: 221
Period size: 57 Copynumber: 2.5 Consensus size: 57
52814033 CCCTAAATGT
* *
52814043 TTAAACAC-TAAACCTTAAACCTCAAATATATAAACCCTAAACATTAAATTCTAAATC
1 TTAAAC-CTTAAACTTTAAACCTCAAATATATAAACCCTAAACATTAAATTCTAAACC
52814100 TTAAACCTTAAACTTTAAACCTCAAATATATAAACCCTAAACATTAAATTCTAAACC
1 TTAAACCTTAAACTTTAAACCTCAAATATATAAACCCTAAACATTAAATTCTAAACC
* *
52814157 TTAAACCTTAAAATCTTAAATCTCAAA
1 TTAAACCTTAAACT-TTAAACCTCAAA
52814184 CCCTAAACCT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
56 1 0.01
57 66 0.85
58 11 0.14
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (57 bp):
TTAAACCTTAAACTTTAAACCTCAAATATATAAACCCTAAACATTAAATTCTAAACC
Found at i:52814147 original size:36 final size:36
Alignment explanation
Indices: 52813913--52814572 Score: 130
Period size: 36 Copynumber: 18.5 Consensus size: 36
52813903 ACCTAAAACT
* *
52813913 TAAATCCTAAACCTTAAACTTCAAACTCTTAAATAT-
1 TAAACCCTAAACCTTAAACTTTAAAC-CTTAAATATA
* * * **
52813949 TAAATCCTAAACCTTAAA-TCCTAAACTTTAAATGCA
1 TAAACCCTAAACCTTAAACT-TTAAACCTTAAATATA
* * * * * *
52813985 TAAACCCTAAAACTTTAAACCTTAAAACTCAAAAACA
1 TAAACCCT-AAACCTTAAACTTTAAACCTTAAATATA
* * * **
52814022 TAAACCCTAATCCCTAAATGTTTAAACAC-TAAACCT-
1 TAAACCCTAAACCTTAAA-CTTTAAAC-CTTAAATATA
** ** * *
52814058 TAAA-CCTCAAATATATAAACCCTAAACATTAAAT-TC
1 TAAACCCT-AAACCT-TAAACTTTAAACCTTAAATATA
* * *
52814094 TAAATCTTAAACCTTAAACTTTAAACCTCAAATATA
1 TAAACCCTAAACCTTAAACTTTAAACCTTAAATATA
*
52814130 TAAACCCTAAACATTAAA-TTCTAAACCTTAAACCT-TA
1 TAAACCCTAAACCTTAAACTT-TAAACCTTAAA--TATA
* * * * ** ****
52814167 -AAATCTTAAATCTCAAACCCTAAACCTTAAACGCC
1 TAAACCCTAAACCTTAAACTTTAAACCTTAAATATA
* * ** *
52814202 TAAACACTAAAACTTTAAACCCTAAACCTTAAA-ACTT
1 TAAACCCT-AAACCTTAAACTTTAAACCTTAAATA-TA
* *
52814239 TAAAACCTAAAACC-TAAACTCTAAACCTTAAACT-T-
1 TAAACCCT-AAACCTTAAACTTTAAACCTTAAA-TATA
* *
52814274 TAAAGCCCTAAA---T--AC--TAAATCATAAACT-T-
1 TAAA-CCCTAAACCTTAAACTTTAAACCTTAAA-TATA
* * * **
52814303 TAAACCCTAAACCTCAAA-TACATAAATCTTAAA-ACCC
1 TAAACCCTAAACCTTAAACT--TTAAACCTTAAATA-TA
** * *
52814340 TAAACTTTAAACCTTAAACCTTAAA-CTTCAAATGTA
1 TAAACCCTAAACCTTAAACTTTAAACCTT-AAATATA
* * * **
52814376 TAAACCCTAAACCCTAAACTATAAACTTTAAA-ACCC
1 TAAACCCTAAACCTTAAACTTTAAACCTTAAATA-TA
* * * **
52814412 TAAACCCTAAATCTTAAA-TGCATAAACCATAAA-CCA
1 TAAACCCTAAACCTTAAACT--TTAAACCTTAAATATA
* * *
52814448 TAAACCCTAATCCTTAAA-TCATAAACCCTAAACT-T-
1 TAAACCCTAAACCTTAAACT-TTAAACCTTAAA-TATA
* * ***
52814483 TAAACCCTAAACCTTAAATACTTAAAACCCTAAA-CCC
1 TAAACCCTAAACCTT-AA-ACTTTAAACCTTAAATATA
* *
52814520 TAAACTCTAAACCTTAAA-TCATAAACCTTAAACT-T-
1 TAAACCCTAAACCTTAAACT-TTAAACCTTAAA-TATA
52814555 TAAACCCTAAACCTTAAA
1 TAAACCCTAAACCTTAAA
52814573 TACTTAAATA
Statistics
Matches: 461, Mismatches: 111, Indels: 105
0.68 0.16 0.16
Matches are distributed among these distances:
28 7 0.02
29 16 0.03
31 2 0.00
33 2 0.00
34 1 0.00
35 92 0.20
36 211 0.46
37 127 0.28
38 3 0.01
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.27
Consensus pattern (36 bp):
TAAACCCTAAACCTTAAACTTTAAACCTTAAATATA
Found at i:52814191 original size:57 final size:57
Alignment explanation
Indices: 52814057--52814270 Score: 200
Period size: 57 Copynumber: 3.6 Consensus size: 57
52814047 ACACTAAACC
* * *
52814057 TTAAACCTCAAATATATAAACCCTAAACATTAAATTCTAAATCTTAAACCTTAAACT
1 TTAAACCTCAAATACATAAACCCTAAACATTAAATTCTAAACCTTAAACCTTAAAAT
*
52814114 TTAAACCTCAAATATATAAACCCTAAACATTAAATTCTAAACCTTAAACCTTAAAAT
1 TTAAACCTCAAATACATAAACCCTAAACATTAAATTCTAAACCTTAAACCTTAAAAT
* * * *
52814171 CTTAAATCTCAAACCCTAAACCTTAAACGCCTAAACACTAAAACTT-TAAACCCTAAACCTTAAA
1 -TTAAACCTCAAA---T--A-CATAAAC-CCTAAACA-TTAAA-TTCTAAACCTTAAACCTTAAA
52814235 ACT
56 A-T
* * *
52814238 TTAAAACCT-AAA-ACCTAAACTCTAAACCTTAAA
1 TT-AAACCTCAAATACATAAACCCTAAACATTAAA
52814271 CTTTAAAGCC
Statistics
Matches: 133, Mismatches: 12, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
57 59 0.44
58 17 0.13
59 6 0.05
60 1 0.01
61 1 0.01
63 1 0.01
64 5 0.04
65 8 0.06
66 27 0.20
67 8 0.06
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (57 bp):
TTAAACCTCAAATACATAAACCCTAAACATTAAATTCTAAACCTTAAACCTTAAAAT
Found at i:52814283 original size:29 final size:28
Alignment explanation
Indices: 52813856--52814566 Score: 173
Period size: 29 Copynumber: 24.9 Consensus size: 28
52813846 CTCAAATGTA
* * *
52813856 TAAACCATAAACCTTAAACACTAAACTC
1 TAAACCTTAAACTTTAAACCCTAAACTC
* * * *
52813884 TTAAACCTAAAACCTAAAAACCTAAAACT-
1 -TAAACCTTAAACTTTAAACCCT-AAACTC
* *
52813913 TAAATCC-TAAACCTTAAA-CTTCAAACTC
1 TAAA-CCTTAAACTTTAAACCCT-AAACTC
** * *
52813941 TTAAATATTAAA-TCCTAAACCTTAAA-TCC
1 -TAAACCTTAAACT-TTAAACCCTAAACT-C
* * *
52813970 TAAACTTTAAA-TGCATAAACCCTAAAACTT
1 TAAACCTTAAACT--TTAAACCCT-AAACTC
** * * *
52814000 TAAACCTTAAAACTCAAAAACATAAACCC
1 TAAACCTT-AAACTTTAAACCCTAAACTC
* * * *
52814029 TAATCCCTAAATGTTTAAACACTAAAC-C
1 TAAACCTTAAA-CTTTAAACCCTAAACTC
*
52814057 TTAAACCTCAAA-TATATAAACCCTAAACAT-
1 -TAAACCTTAAACT-T-TAAACCCTAAAC-TC
* * *
52814087 TAAA-TTCTAAA-TCTTAAACCTTAAACTT
1 TAAACCT-TAAACT-TTAAACCCTAAACTC
*
52814115 TAAACCTCAAA-TATATAAACCCTAAACAT-
1 TAAACCTTAAACT-T-TAAACCCTAAAC-TC
* * * *
52814144 TAAA-TTCTAAACCTTAAACCTTAAAATC
1 TAAACCT-TAAACTTTAAACCCTAAACTC
* * ** * *
52814172 TTAAATCTCAAACCCTAAACCTTAAACGCC
1 -TAAACCTTAAACTTTAAACCCTAAAC-TC
*
52814202 TAAACACTAAAACTTTAAACCCTAAAC-C
1 TAAAC-CTTAAACTTTAAACCCTAAACTC
* * *
52814230 TTAAAACTTTAAAAC-CTAAAACCTAAACTC
1 -T-AAACCTT-AAACTTTAAACCCTAAACTC
52814260 TAAACCTTAAACTTTAAAGCCCTAAA-TAC
1 TAAACCTTAAACTTTAAA-CCCTAAACT-C
* *
52814289 TAAATCATAAACTTTAAACCCTAAAC-C
1 TAAACCTTAAACTTTAAACCCTAAACTC
* * * *
52814316 TCAAATACATAAATCTTAAAACCCTAAACTT
1 T-AAA-CCTTAAA-CTTTAAACCCTAAACTC
*
52814347 TAAACCTTAAACCTTAAA--CT----TC
1 TAAACCTTAAACTTTAAACCCTAAACTC
** ** *
52814369 -AAATGTATAAACCCTAAACCCTAAACTA
1 TAAACCT-TAAACTTTAAACCCTAAACTC
* **
52814397 TAAACTTTAAAACCCTAAACCCTAAA-TC
1 TAAACCTT-AAACTTTAAACCCTAAACTC
* * ** * *
52814425 TTAAATGCATAAACCATAAACCATAAACCC
1 -TAAA-CCTTAAACTTTAAACCCTAAACTC
* * *
52814455 TAATCCTTAAA-TCATAAACCCTAAACTT
1 TAAACCTTAAACT-TTAAACCCTAAACTC
* * * * *
52814483 TAAACCCTAAACCTTAAATACTTAAAACCC
1 TAAACCTTAAACTTTAAA-CCCT-AAACTC
* * *
52814513 TAAACCCTAAACTCTAAACCTTAAA-TC
1 TAAACCTTAAACTTTAAACCCTAAACTC
52814540 ATAAACCTTAAACTTTAAACCCTAAAC
1 -TAAACCTTAAACTTTAAACCCTAAAC
52814567 CTTAAATACT
Statistics
Matches: 509, Mismatches: 112, Indels: 122
0.69 0.15 0.16
Matches are distributed among these distances:
21 4 0.01
22 11 0.02
24 2 0.00
26 2 0.00
27 17 0.03
28 146 0.29
29 230 0.45
30 91 0.18
31 5 0.01
32 1 0.00
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.26
Consensus pattern (28 bp):
TAAACCTTAAACTTTAAACCCTAAACTC
Found at i:52814451 original size:72 final size:72
Alignment explanation
Indices: 52814375--52814580 Score: 263
Period size: 72 Copynumber: 2.9 Consensus size: 72
52814365 CTTCAAATGT
* * ** * *
52814375 ATAAACCCTAAACCCTAAA-CTATAAACTTTAAAACCCTAAACCCTAAATCTTAAATGCAT-AAA
1 ATAAACCCTAAACCTTAAATC-ATAAACCTT-AAACTTTAAACCCTAAACCTTAAATACATAAAA
52814438 CCATAAACC
64 CCATAAACC
* * *
52814447 ATAAACCCTAATCCTTAAATCATAAACCCTAAACTTTAAACCCTAAACCTTAAATACTTAAAACC
1 ATAAACCCTAAACCTTAAATCATAAACCTTAAACTTTAAACCCTAAACCTTAAATACATAAAACC
*
52814512 CTAAACC
66 ATAAACC
* * *
52814519 CTAAACTCTAAACCTTAAATCATAAACCTTAAACTTTAAACCCTAAACCTTAAATACTTAAA
1 ATAAACCCTAAACCTTAAATCATAAACCTTAAACTTTAAACCCTAAACCTTAAATACATAAA
52814581 TACTAAAATC
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
71 24 0.20
72 93 0.79
73 1 0.01
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.25
Consensus pattern (72 bp):
ATAAACCCTAAACCTTAAATCATAAACCTTAAACTTTAAACCCTAAACCTTAAATACATAAAACC
ATAAACC
Found at i:52814594 original size:58 final size:58
Alignment explanation
Indices: 52814532--52814691 Score: 153
Period size: 58 Copynumber: 2.7 Consensus size: 58
52814522 AACTCTAAAC
** *
52814532 CTTAAATCATAAACCT-TAAACTTTAAACCCTAAACCTT-AAATACTTAAATACTAAAAT
1 CTTAAATCATAAA-CTATAAACCCTAAACCCTAAA-CTTCAAATACTTAAACACTAAAAT
* * * *
52814590 CTTAAATCTTAAATTATAAACCCTAAACCCTAAATTTCAAATACTTAAACCCTAAAAT
1 CTTAAATCATAAACTATAAACCCTAAACCCTAAACTTCAAATACTTAAACACTAAAAT
* * * * * *
52814648 CTTAAAACCTTAAACTATAAATCTTAAAACCTTAAACTTTAAAT
1 CTT-AAATCATAAACTATAAACCCT-AAACCCTAAACTTCAAAT
52814692 CCTAAAAACC
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
57 3 0.04
58 49 0.58
59 17 0.20
60 15 0.18
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (58 bp):
CTTAAATCATAAACTATAAACCCTAAACCCTAAACTTCAAATACTTAAACACTAAAAT
Found at i:52814653 original size:51 final size:50
Alignment explanation
Indices: 52814482--52814645 Score: 149
Period size: 51 Copynumber: 3.2 Consensus size: 50
52814472 ACCCTAAACT
* *
52814482 TTAAACCCTAAACCTTAAA-TACTTAAAACCCTAAACCCTAAA-CTCTAAA-CC
1 TTAAACCCTAAACCTTAAATTA--T-AAACCCTAAACCCTAAATTTC-AAATAC
* * *
52814533 TTAAATCATAAACCTTAAACTT-TAAACCCTAAACCTTAAATACTT-AAATAC
1 TTAAACCCTAAACCTTAAA-TTATAAACCCTAAACCCTAAAT--TTCAAATAC
* * * *
52814584 TAAAATCTTAAATCTTAAATTATAAACCCTAAACCCTAAATTTCAAATAC
1 TTAAACCCTAAACCTTAAATTATAAACCCTAAACCCTAAATTTCAAATAC
52814634 TTAAACCCTAAA
1 TTAAACCCTAAA
52814646 ATCTTAAAAC
Statistics
Matches: 93, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
49 18 0.19
50 21 0.23
51 52 0.56
52 1 0.01
53 1 0.01
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (50 bp):
TTAAACCCTAAACCTTAAATTATAAACCCTAAACCCTAAATTTCAAATAC
Found at i:52814672 original size:22 final size:22
Alignment explanation
Indices: 52814644--52814713 Score: 113
Period size: 22 Copynumber: 3.1 Consensus size: 22
52814634 TTAAACCCTA
*
52814644 AAATCTTAAAACCTTAAACTAT
1 AAATCTTAAAACCTTAAACTTT
52814666 AAATCTTAAAACCTTAAACTTT
1 AAATCTTAAAACCTTAAACTTT
*
52814688 AAATCCTAAAAACCTTAAACTTT
1 AAAT-CTTAAAACCTTAAACTTT
52814711 AAA
1 AAA
52814714 CTATAAATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
22 25 0.56
23 20 0.44
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATCTTAAAACCTTAAACTTT
Found at i:52814720 original size:23 final size:22
Alignment explanation
Indices: 52814651--52814720 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 22
52814641 CTAAAATCTT
*
52814651 AAAACCTTAAACTATAAATCTT-
1 AAAACCTTAAACTTTAAA-CTTA
*
52814673 AAAACCTTAAACTTTAAATCCTA
1 AAAACCTTAAACTTTAAA-CTTA
52814696 AAAACCTTAAACTTTAAACTATA
1 AAAACCTTAAACTTTAAACT-TA
52814719 AA
1 AA
52814721 TTCTAAACCC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 21 0.49
23 22 0.51
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAACCTTAAACTTTAAACTTA
Found at i:52814804 original size:45 final size:45
Alignment explanation
Indices: 52814751--52814860 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 45
52814741 TTTGGTTTGC
52814751 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
* * ***
52814796 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
52814840 TG--A---AATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
52814861 TAAAGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 15 0.26
42 1 0.02
44 18 0.32
45 23 0.40
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (45 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
Found at i:52815026 original size:18 final size:17
Alignment explanation
Indices: 52815005--52815039 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52814995 TTATTATTAA
*
52815005 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
52815023 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
52815040 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:52815146 original size:18 final size:17
Alignment explanation
Indices: 52815123--52815159 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
52815113 AATTATTATT
52815123 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
52815139 AAATATATGATTTAATA
1 AAATATATGATTTAATA
52815156 AAAT
1 AAAT
52815160 TCTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:52815148 original size:59 final size:58
Alignment explanation
Indices: 52815081--52815266 Score: 175
Period size: 59 Copynumber: 3.1 Consensus size: 58
52815071 CTCAAATCAT
*
52815081 AATATATGATACTATAAAATATAATTTGAAATAATTATTATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTT-AAATAATTATTATTAAATATATTTTAATAAA
* * * * *
52815140 AATATATGAT-TTAATAAAATTCTTAATATTAAAT-ATTCTTATATGAAT-T-TTCTAA-AATCA
1 AATATATGATACT-ATAAAA-T-ATAAT-TTAAATAATTATTAT-TAAATATATTTTAATAA--A
* *
52815200 TAATATATAATACTATAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAA
1 -AATATATGATACTATAAAATATAATTTAA-ATAATTATTATTAAATATATTTTAATAAA
52815260 AATATAT
1 AATATAT
52815267 AATTTATCAT
Statistics
Matches: 100, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
58 6 0.06
59 38 0.38
60 20 0.20
61 31 0.31
62 5 0.05
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (58 bp):
AATATATGATACTATAAAATATAATTTAAATAATTATTATTAAATATATTTTAATAAA
Found at i:52815204 original size:120 final size:120
Alignment explanation
Indices: 52814985--52815272 Score: 479
Period size: 120 Copynumber: 2.4 Consensus size: 120
52814975 TTAATCATAT
52814985 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * * *
52815050 CAATATTCTTCTATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
52815105 TTTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
52815169 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
65 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
52815225 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTA
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTA
52815273 TCATCATACT
Statistics
Matches: 156, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
119 2 0.01
120 152 0.97
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:52815218 original size:61 final size:60
Alignment explanation
Indices: 52815020--52815220 Score: 155
Period size: 61 Copynumber: 3.3 Consensus size: 60
52815010 TTTTAATTAA
* * * * *
52815020 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTCTATGAATTTACTCAAATCAT
1 AATATATAATCTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCT-AAATCAT
* * * * * * *
52815081 AATATATGATACT-ATAAAA-T-ATAAT-TTGAAATAATTATTAT-TAAATATATT-TTAATTAA
1 AATATATAAT-CTAATAAAATTCTTAATATT-AAAT-ATTCTTATATGAAT-T-TTCTAAATCAT
* *
52815140 AATATATGATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
1 AATATATAATCTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCT-AAATCAT
52815201 AATATATAATACT-ATAAAAT
1 AATATATAAT-CTAATAAAAT
52815221 ATAATTTAAC
Statistics
Matches: 106, Mismatches: 21, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
58 2 0.02
59 33 0.31
60 19 0.18
61 48 0.45
62 4 0.04
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.43
Consensus pattern (60 bp):
AATATATAATCTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAATCAT
Found at i:52818221 original size:7 final size:7
Alignment explanation
Indices: 52818195--52818273 Score: 61
Period size: 7 Copynumber: 11.0 Consensus size: 7
52818185 TTATAAATAC
52818195 TAAACCT
1 TAAACCT
* *
52818202 TAACCCC
1 TAAACCT
52818209 TAAACCT
1 TAAACCT
52818216 TAAACCT
1 TAAACCT
***
52818223 TAAATAA
1 TAAACCT
52818230 TAAACCT
1 TAAACCT
**
52818237 TAAAATAT
1 T-AAACCT
52818245 TAAACCT
1 TAAACCT
52818252 TAAAACAC-
1 T-AAAC-CT
52818260 TAAACCT
1 TAAACCT
52818267 TAAACCT
1 TAAACCT
52818274 CAAAACATGA
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
6 1 0.02
7 42 0.78
8 10 0.19
9 1 0.02
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAACCT
Found at i:52818248 original size:15 final size:15
Alignment explanation
Indices: 52818215--52818270 Score: 78
Period size: 15 Copynumber: 3.8 Consensus size: 15
52818205 CCCCTAAACC
52818215 TTAAACCTT-AAATA
1 TTAAACCTTAAAATA
*
52818229 ATAAACCTTAAAATA
1 TTAAACCTTAAAATA
*
52818244 TTAAACCTTAAAACA
1 TTAAACCTTAAAATA
*
52818259 CTAAACCTTAAA
1 TTAAACCTTAAA
52818271 CCTCAAAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
14 8 0.22
15 29 0.78
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.29
Consensus pattern (15 bp):
TTAAACCTTAAAATA
Found at i:52818400 original size:14 final size:14
Alignment explanation
Indices: 52818368--52818419 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
52818358 ACACAATCCT
52818368 TAAACCTTAAA-TA
1 TAAACCTTAAACTA
* *
52818381 TAAACCATAAACTC
1 TAAACCTTAAACTA
52818395 TAAACCTTAAACTA
1 TAAACCTTAAACTA
*
52818409 TAAACTTTAAA
1 TAAACCTTAAA
52818420 ATCATAAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
13 10 0.30
14 23 0.70
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAACCTTAAACTA
Found at i:52818428 original size:15 final size:14
Alignment explanation
Indices: 52818368--52818428 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
52818358 ACACAATCCT
52818368 TAAACCTT-AAATA
1 TAAACCTTAAAATA
* * *
52818381 TAAACCATAAACTC
1 TAAACCTTAAAATA
*
52818395 TAAACCTTAAACTA
1 TAAACCTTAAAATA
*
52818409 TAAACTTTAAAATCA
1 TAAACCTTAAAAT-A
52818424 TAAAC
1 TAAAC
52818429 AATAAAACCC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
13 7 0.18
14 26 0.67
15 6 0.15
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAACCTTAAAATA
Found at i:52818434 original size:15 final size:14
Alignment explanation
Indices: 52818416--52818492 Score: 57
Period size: 15 Copynumber: 5.3 Consensus size: 14
52818406 CTATAAACTT
*
52818416 TAAAATCATAAACAA
1 TAAAACCATAAAC-A
*
52818431 TAAAACCCTAAACA
1 TAAAACCATAAACA
* *
52818445 TAAATCC-TAAAACCT
1 TAAAACCAT-AAA-CA
*
52818460 TAAAACCATAAGCCA
1 TAAAACCATAA-ACA
*
52818475 TAAAACCCTAAACA
1 TAAAACCATAAACA
52818489 TAAA
1 TAAA
52818493 CCTTAAAACT
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
13 1 0.02
14 16 0.33
15 31 0.63
16 1 0.02
ACGTcount: A:0.57, C:0.23, G:0.01, T:0.18
Consensus pattern (14 bp):
TAAAACCATAAACA
Found at i:52818463 original size:44 final size:43
Alignment explanation
Indices: 52818349--52818576 Score: 168
Period size: 44 Copynumber: 5.4 Consensus size: 43
52818339 ACCCTAATTT
* * *
52818349 AAACCCTAAACACAATCCTTAAACCTT-AAAT-ATAAACCAT-
1 AAACCCTAAACATAAACCTAAAACCTTAAAATCATAAACCATA
* * * *
52818389 AAACTCTAAACCTTAAA-CTATAAACTTTAAAATCATAAACAATA
1 AAACCCTAAA-CATAAACCTA-AAACCTTAAAATCATAAACCATA
* *
52818433 AAACCCTAAACATAAATCCTAAAACCTTAAAACCATAAGCCATA
1 AAACCCTAAACATAAA-CCTAAAACCTTAAAATCATAAACCATA
* ** *
52818477 AAACCCTAAACATAAACCTTAAAA-CTTTAACCCAT-AATC-T-
1 AAACCCTAAACATAAACC-TAAAACCTTAAAATCATAAACCATA
* * * * *
52818517 AAACCCTAAACACAAACTTTAAA-CTCTAAAATTATAAACCTTA
1 AAACCCTAAACATAAACCTAAAACCT-TAAAATCATAAACCATA
* *
52818560 AAACACAAAACATAAAC
1 AAACCCTAAACATAAAC
52818577 TTTAAAATCC
Statistics
Matches: 148, Mismatches: 28, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
39 6 0.04
40 32 0.22
41 13 0.09
42 7 0.05
43 38 0.26
44 49 0.33
45 3 0.02
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (43 bp):
AAACCCTAAACATAAACCTAAAACCTTAAAATCATAAACCATA
Found at i:52818499 original size:21 final size:21
Alignment explanation
Indices: 52818349--52818591 Score: 99
Period size: 21 Copynumber: 11.5 Consensus size: 21
52818339 ACCCTAATTT
* *
52818349 AAACCCTAAACACAATCCTT-
1 AAACCCTAAACATAAACCTTA
* * *
52818369 AAACCTTAAATATAAACCAT-
1 AAACCCTAAACATAAACCTTA
* *
52818389 AAACTCTAAACCTTAAA-C-TA
1 AAACCCTAAA-CATAAACCTTA
** **
52818409 TAAACTTTAAAATCATAAACAATA
1 -AAACCCT-AAA-CATAAACCTTA
52818433 AAACCCTAAACATAAATCC-TA
1 AAACCCTAAACATAAA-CCTTA
* * *
52818454 AAACCTTAAAACCATAAGCCATA
1 AAACCCT-AAA-CATAAACCTTA
52818477 AAACCCTAAACATAAACCTTA
1 AAACCCTAAACATAAACCTTA
** * *
52818498 AAACTTTAACCCAT-AATC-T-
1 AAACCCTAA-ACATAAACCTTA
* *
52818517 AAACCCTAAACACAAA-CTTT
1 AAACCCTAAACATAAACCTTA
* *
52818537 AAACTCTAAAATTATAAACCTTA
1 AAACCCT-AAA-CATAAACCTTA
* * *
52818560 AAACACAAAACATAAACTTTA
1 AAACCCTAAACATAAACCTTA
*
52818581 AAATCCTAAAC
1 AAACCCTAAAC
52818592 CTTAAAACCA
Statistics
Matches: 166, Mismatches: 40, Indels: 33
0.69 0.17 0.14
Matches are distributed among these distances:
18 3 0.02
19 11 0.07
20 31 0.19
21 63 0.38
22 30 0.18
23 26 0.16
24 2 0.01
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.23
Consensus pattern (21 bp):
AAACCCTAAACATAAACCTTA
Found at i:52818568 original size:36 final size:36
Alignment explanation
Indices: 52818512--52818621 Score: 109
Period size: 36 Copynumber: 3.1 Consensus size: 36
52818502 TTTAACCCAT
*
52818512 AATC-TAAACCCT-AAACACAAACTTTAAACTCTAA
1 AATCATAAACCTTAAAACACAAACTTTAAACTCTAA
* * *
52818546 AATTATAAACCTTAAAACACAAAAC-ATAAACTTTAA
1 AATCATAAACCTTAAAACAC-AAACTTTAAACTCTAA
* * *
52818582 AATCCTAAACCTTAAAACCATAAACTTTAAAATCCTAA
1 AATCATAAACCTTAAAA-CACAAACTTTAAACT-CTAA
52818620 AA
1 AA
52818622 CACTAAATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
34 3 0.05
35 7 0.12
36 34 0.57
37 11 0.18
38 5 0.08
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.25
Consensus pattern (36 bp):
AATCATAAACCTTAAAACACAAACTTTAAACTCTAA
Found at i:52818596 original size:15 final size:15
Alignment explanation
Indices: 52818572--52818620 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
52818562 ACACAAAACA
52818572 TAAACTTTAAAATCC
1 TAAACTTTAAAATCC
*
52818587 TAAACCTTAAAA-CC
1 TAAACTTTAAAATCC
52818601 ATAAACTTTAAAATCC
1 -TAAACTTTAAAATCC
52818617 TAAA
1 TAAA
52818621 ACACTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 2 0.07
15 26 0.87
16 2 0.07
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAACTTTAAAATCC
Found at i:52818679 original size:27 final size:27
Alignment explanation
Indices: 52818640--52818705 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
52818630 TTTAAACCCT
*
52818640 AAATCTTAGACCTTAAACCATAAACAC
1 AAATCTTAAACCTTAAACCATAAACAC
* * *
52818667 AAATTTTAAACCTTAAACCCTAAATAC
1 AAATCTTAAACCTTAAACCATAAACAC
*
52818694 AAACCTTAAACC
1 AAATCTTAAACC
52818706 CTAACATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (27 bp):
AAATCTTAAACCTTAAACCATAAACAC
Found at i:52822258 original size:8 final size:8
Alignment explanation
Indices: 52822245--52822269 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
52822235 TGTTTTTTTG
52822245 ATTGATGA
1 ATTGATGA
52822253 ATTGATGA
1 ATTGATGA
52822261 ATTGATGA
1 ATTGATGA
52822269 A
1 A
52822270 CAATACAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (8 bp):
ATTGATGA
Found at i:52827984 original size:103 final size:103
Alignment explanation
Indices: 52827864--52828057 Score: 300
Period size: 103 Copynumber: 1.9 Consensus size: 103
52827854 AAGCAGCAAC
* * * *
52827864 AATACAAGCTAAGCAGCAG-TAAAAGCAAGTTTCCTTTAAGGTCCAAAAACCAATGCCTACCTAT
1 AATACAAGCTAAACAGCAGAT-AAAGCAAGTTTCCTTTAAAGTCCAAAAAACAATGCCTACCGAT
52827928 GTATGCTTTCAAAAGCAAGCAGGAGCAACAATTGTAACT
65 GTATGCTTTCAAAAGCAAGCAGGAGCAACAATTGTAACT
* *
52827967 AATACAAGCTAAACAGCAGATAAAGCAAGTTTCCTTTAAAGTTCAAAAAACAATGCCTGCCGATG
1 AATACAAGCTAAACAGCAGATAAAGCAAGTTTCCTTTAAAGTCCAAAAAACAATGCCTACCGATG
* *
52828032 TATGCTTTCAGAAGCAAGCAGTAGCA
66 TATGCTTTCAAAAGCAAGCAGGAGCA
52828058 GAAAGAACAA
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
103 81 0.99
104 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (103 bp):
AATACAAGCTAAACAGCAGATAAAGCAAGTTTCCTTTAAAGTCCAAAAAACAATGCCTACCGATG
TATGCTTTCAAAAGCAAGCAGGAGCAACAATTGTAACT
Found at i:52834190 original size:18 final size:17
Alignment explanation
Indices: 52834163--52834209 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
52834153 AATAAAAAAT
* *
52834163 AAATTTTAAAAAATTATA
1 AAATTATAAAAAATGA-A
52834181 AAATTAT-AAAAATGAA
1 AAATTATAAAAAATGAA
52834197 AAATTATATAAAA
1 AAATTATA-AAAA
52834210 GTTAGAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 8 0.32
17 7 0.28
18 10 0.40
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AAATTATAAAAAATGAA
Found at i:52836157 original size:22 final size:21
Alignment explanation
Indices: 52836128--52836168 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
52836118 AAAAACTAAT
*
52836128 TTTAGATTAATATTATAAAAA
1 TTTAGATTAAAATTATAAAAA
*
52836149 TTTATGATTAAAATTTTAAA
1 TTTA-GATTAAAATTATAAA
52836169 TGATTTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTAGATTAAAATTATAAAAA
Found at i:52838536 original size:39 final size:39
Alignment explanation
Indices: 52838464--52838538 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
52838454 AATTGGTTAA
* *
52838464 TAAATCATATTTTATAAATAATGGATAGGATTTTTTTAT
1 TAAAACATATTTTATAAATAATGGATAGCATTTTTTTAT
*
52838503 TAAAACATATTTTATAATTAATGGAT-GCCATTTTTT
1 TAAAACATATTTTATAAATAATGGATAG-CATTTTTT
52838539 AGCTTTACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.48
Consensus pattern (39 bp):
TAAAACATATTTTATAAATAATGGATAGCATTTTTTTAT
Found at i:52839716 original size:48 final size:49
Alignment explanation
Indices: 52839624--52839720 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 49
52839614 TGAGGGAATT
* * * *
52839624 CTGTTGAATCCTTTATCGTTGCGAGATTAGGCTGACTTCGGTGTTTTTA
1 CTGTTGAATCCATCATCATTGCGAGATTAGGCTGACTTAGGTGTTTTTA
52839673 CTGTTGAATCCATCATCATTGCGAG-TTAGGCTGACTTAGGTGTTTTTA
1 CTGTTGAATCCATCATCATTGCGAGATTAGGCTGACTTAGGTGTTTTTA
52839721 AGCAAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 22 0.50
49 22 0.50
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (49 bp):
CTGTTGAATCCATCATCATTGCGAGATTAGGCTGACTTAGGTGTTTTTA
Found at i:52844808 original size:49 final size:48
Alignment explanation
Indices: 52844736--52844832 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 48
52844726 TGAGGGAATT
* * * *
52844736 CTGTTGAATCCTTTATCGTTGCGAGATTAGGCTAACTTCGGTGTTTTTA
1 CTGTTGAATCCATTATCATTGCGAG-TTAGGCTAACTTAGGCGTTTTTA
*
52844785 CTGTTGAATCCATTATCATTGCGAGTTAGGCTGACTTAGGCGTTTTTA
1 CTGTTGAATCCATTATCATTGCGAGTTAGGCTAACTTAGGCGTTTTTA
52844833 AGCAAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 20 0.47
49 23 0.53
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (48 bp):
CTGTTGAATCCATTATCATTGCGAGTTAGGCTAACTTAGGCGTTTTTA
Found at i:52845466 original size:12 final size:11
Alignment explanation
Indices: 52845438--52845471 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
52845428 TTATTTTTTT
52845438 TATTTTTAAAA
1 TATTTTTAAAA
52845449 TATTTTTAAAA
1 TATTTTTAAAA
52845460 TACTTTTTAAAA
1 TA-TTTTTAAAA
52845472 AAAATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:52848500 original size:27 final size:27
Alignment explanation
Indices: 52848468--52848535 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
52848458 ATGCACTTCG
52848468 GTGCTTACTGCTACGTGATTAAACTAT
1 GTGCTTACTGCTACGTGATTAAACTAT
* * * ** *
52848495 GTGCTTACCGTTATGTGATTGCACTTT
1 GTGCTTACTGCTACGTGATTAAACTAT
*
52848522 GTTCTTACTGCTAC
1 GTGCTTACTGCTAC
52848536 ATGAAATGCA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (27 bp):
GTGCTTACTGCTACGTGATTAAACTAT
Found at i:52849374 original size:20 final size:20
Alignment explanation
Indices: 52849270--52849366 Score: 169
Period size: 20 Copynumber: 4.8 Consensus size: 20
52849260 AAAATATTGA
*
52849270 TACTTTGAAG-AAAGTAGAGG
1 TACTTTG-AGCAAAGTATAGG
52849290 TACTTTGAGCAAAGTATAGG
1 TACTTTGAGCAAAGTATAGG
52849310 TACTTTGAGCAAAGTATAGG
1 TACTTTGAGCAAAGTATAGG
52849330 TACTTTGAGCAAAGTATAGG
1 TACTTTGAGCAAAGTATAGG
52849350 TACTTTGAGCAAAGTAT
1 TACTTTGAGCAAAGTAT
52849367 CGATACTTAC
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
19 2 0.03
20 73 0.97
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (20 bp):
TACTTTGAGCAAAGTATAGG
Found at i:52857613 original size:2 final size:2
Alignment explanation
Indices: 52857608--52857634 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52857598 TTTTTTTCAT
52857608 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
52857635 TAAAAACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52866519 original size:12 final size:13
Alignment explanation
Indices: 52866491--52866528 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
52866481 AATGGCATAG
52866491 AAATAATATAAAC
1 AAATAATATAAAC
*
52866504 AAATAA-ATAAAT
1 AAATAATATAAAC
52866516 AAATAATAATAAA
1 AAATAAT-ATAAA
52866529 ATTCATAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 6 0.27
14 5 0.23
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAATATAAAC
Found at i:52867610 original size:4 final size:4
Alignment explanation
Indices: 52867601--52867649 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
52867591 NNNNNNNTAA
*
52867601 AAAT AAAT -AAT AAAT -AAT AAAT -AAT AAAT -AAT AAAT AAAA AAACT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T
52867646 AAAT
1 AAAT
52867650 CGAGCTTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 12 0.32
4 23 0.61
5 3 0.08
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:52867614 original size:7 final size:7
Alignment explanation
Indices: 52867598--52867638 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
52867588 NNNNNNNNNN
52867598 TAAA-AA
1 TAAATAA
52867604 TAAATAA
1 TAAATAA
52867611 TAAATAA
1 TAAATAA
52867618 TAAATAA
1 TAAATAA
52867625 TAAATAA
1 TAAATAA
52867632 TAAATAA
1 TAAATAA
52867639 AAAAACTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.12
7 30 0.88
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAATAA
Found at i:52867628 original size:21 final size:20
Alignment explanation
Indices: 52867598--52867649 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
52867588 NNNNNNNNNN
52867598 TAAAAATAAATAATAAATAA
1 TAAAAATAAATAATAAATAA
52867618 TAAATAATAAATAATAAATAA
1 TAAA-AATAAATAATAAATAA
52867639 -AAAAACTAAAT
1 TAAAAA-TAAAT
52867650 CGAGCTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.07
20 12 0.40
21 16 0.53
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
TAAAAATAAATAATAAATAA
Found at i:52867933 original size:23 final size:22
Alignment explanation
Indices: 52867907--52867951 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
52867897 AAATTAAATC
52867907 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
52867930 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACAAATCATATCT
52867952 AAGATTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:52867954 original size:19 final size:20
Alignment explanation
Indices: 52867907--52867977 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 20
52867897 AAATTAAATC
* *
52867907 TCTAAGATTACAAAATCATA
1 TCTAAGATTGCAATATCATA
52867927 TCTTCTAAGATTGC-ATATCATA
1 ---TCTAAGATTGCAATATCATA
*
52867949 TCTAAGATTTCATATATCATA
1 TCTAAGATTGCA-ATATCATA
52867970 TCTAAGAT
1 TCTAAGAT
52867978 AATATCTAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
19 10 0.23
21 16 0.37
22 7 0.16
23 10 0.23
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.38
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Found at i:52871513 original size:26 final size:26
Alignment explanation
Indices: 52871473--52871531 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
52871463 ACATATTTTC
* * **
52871473 TCAAAATTTTTCCTAGGGCAAAATTG
1 TCAAAATATTACCTAGGGCAAAATCA
*
52871499 TCAAAATATTACCTAGGGTAAAATCA
1 TCAAAATATTACCTAGGGCAAAATCA
52871525 TCAAAAT
1 TCAAAAT
52871532 TTTGCTGAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (26 bp):
TCAAAATATTACCTAGGGCAAAATCA
Found at i:52874459 original size:23 final size:23
Alignment explanation
Indices: 52874416--52874459 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
52874406 TTCTTATCCT
* *
52874416 TACATTTAAATTCTTGGCCCATC
1 TACATTTAAATTCCTGACCCATC
52874439 TACATTTAAATTCCTGACCCA
1 TACATTTAAATTCCTGACCCA
52874460 AGCAGCTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (23 bp):
TACATTTAAATTCCTGACCCATC
Found at i:52877302 original size:23 final size:24
Alignment explanation
Indices: 52877265--52877313 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
52877255 TTAAGCTTTT
* *
52877265 AATAGGATTTATTTAGGTAAAAAG
1 AATAGGATCTATTTAAGTAAAAAG
52877289 AATAGG-TCTATTTAAGTAAAAAG
1 AATAGGATCTATTTAAGTAAAAAG
52877312 AA
1 AA
52877314 ATGAAATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (24 bp):
AATAGGATCTATTTAAGTAAAAAG
Found at i:52877542 original size:21 final size:21
Alignment explanation
Indices: 52877503--52877542 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52877493 GTATTAAAAA
* *
52877503 CAAATTTAAAAATACAAAGTT
1 CAAATTAAAAAAAACAAAGTT
*
52877524 CAAATTAAAAAAAATAAAG
1 CAAATTAAAAAAAACAAAG
52877543 GAAAACAAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (21 bp):
CAAATTAAAAAAAACAAAGTT
Found at i:52882151 original size:57 final size:59
Alignment explanation
Indices: 52882038--52882185 Score: 194
Period size: 57 Copynumber: 2.5 Consensus size: 59
52882028 AATTGACGGT
52882038 AAAAATGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCAGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC-AT-CTGATATAGCCCTCCAGAAGAATATGTG-G
*
52882101 AAAAAGATCTAGCCCGGACGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCAGAAGAATATGTGG
* * *
52882157 AAAATAGATTTAGCCCGGATGGGTAATCC
1 AAAA-AGATCTAGCCCGGACGGGTGATCC
52882186 GAATTAGGGT
Statistics
Matches: 79, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
56 5 0.06
57 45 0.57
58 1 0.01
59 1 0.01
61 1 0.01
62 21 0.27
63 5 0.06
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (59 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCAGAAGAATATGTGG
Found at i:52882416 original size:67 final size:67
Alignment explanation
Indices: 52882308--52882438 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 67
52882298 TTTATATTAT
** *
52882308 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAAGTTTGCGGGAGTGTGTTCTCTT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAAGTTCACGGGAGTGTGGTCTCTT
52882373 GC
66 GC
*
52882375 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCACGGGAGTGTGGTCTCT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAAGTTCACGGGAGTGTGGTCTCT
52882439 GAATTGAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.28
Consensus pattern (67 bp):
AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAAGTTCACGGGAGTGTGGTCTCTT
GC
Found at i:52884198 original size:49 final size:49
Alignment explanation
Indices: 52884051--52884198 Score: 215
Period size: 49 Copynumber: 3.0 Consensus size: 49
52884041 AACATGTGAA
* *
52884051 TATGTGATTATGTGATTTCCGTGTAAGGCCATAGTTGGGCTATGGCATCAG
1 TATGTGA-TATGTGA-TTCCGTGTAAGACCATAGTTGGGCTATGGCATCGG
* *
52884102 TAAGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGG
1 TATGTGATATGTGATTCCGTGTAAGACCATAGTTGGGCTATGGCATCGG
* * *
52884151 TATGTGATATGTGATTACGTGTAAGACCATAGTTGGACTAAGGCATCG
1 TATGTGATATGTGATTCCGTGTAAGACCATAGTTGGGCTATGGCATCG
52884199 AGAAAATAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
49 75 0.85
50 7 0.08
51 6 0.07
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (49 bp):
TATGTGATATGTGATTCCGTGTAAGACCATAGTTGGGCTATGGCATCGG
Found at i:52885546 original size:15 final size:15
Alignment explanation
Indices: 52885526--52885555 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52885516 TATATACACT
*
52885526 TATATCAAATATATA
1 TATATCAAAAATATA
52885541 TATATCAAAAATATA
1 TATATCAAAAATATA
52885556 AAGAATAAAA
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:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
TATATCAAAAATATA
Found at i:52885618 original size:2 final size:2
Alignment explanation
Indices: 52885611--52885637 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52885601 GACATAAGAG
52885611 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
52885638 CACTCACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52885946 original size:41 final size:41
Alignment explanation
Indices: 52885771--52885939 Score: 275
Period size: 41 Copynumber: 4.1 Consensus size: 41
52885761 AATTCATCAT
* *
52885771 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
52885812 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* * *
52885853 ATTCATATCACCGGCACTTAGCCTGCGAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
52885894 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
52885935 ATTCA
1 ATTCA
52885940 ATTCACCAAT
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 117 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
Found at i:52885946 original size:82 final size:82
Alignment explanation
Indices: 52885777--52885939 Score: 317
Period size: 82 Copynumber: 2.0 Consensus size: 82
52885767 TCATATTCGG
*
52885777 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCGAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
52885842 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
52885859 ATCACCGGCACTTAGCCTGCGAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCGAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
52885924 TTTATAACCTGATTCA
66 TTTATAACCTGATTCA
52885940 ATTCACCAAT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (82 bp):
ATCACCGGCACTTAGCCTGCGAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
TTTATAACCTGATTCAT
Found at i:52886189 original size:15 final size:16
Alignment explanation
Indices: 52886167--52886213 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
52886157 ATCCACATAT
52886167 ATATATATATTACACAC
1 ATATATATA-TACACAC
*
52886184 ATATATATATTCACAC
1 ATATATATATACACAC
*
52886200 AT-TATATAAACACA
1 ATATATATATACACA
52886214 ATCATAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 10 0.37
16 8 0.30
17 9 0.33
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATATATATACACAC
Found at i:52886189 original size:17 final size:16
Alignment explanation
Indices: 52886167--52886207 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
52886157 ATCCACATAT
52886167 ATATATATATTACACAC
1 ATATATATATT-CACAC
52886184 ATATATATATTCACAC
1 ATATATATATTCACAC
52886200 AT-TATATA
1 ATATATATA
52886208 AACACAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
17 11 0.46
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATATATATTCACAC
Found at i:52886206 original size:19 final size:18
Alignment explanation
Indices: 52886160--52886207 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
52886150 TTGTTCGATC
52886160 CACATATATATATATATTA
1 CACAT-TATATATATATTA
*
52886179 CACA-CATATATATATTCA
1 CACATTATATATATATT-A
52886197 CACATTATATA
1 CACATTATATA
52886208 AACACAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 11 0.44
18 5 0.20
19 9 0.36
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.38
Consensus pattern (18 bp):
CACATTATATATATATTA
Found at i:52889995 original size:16 final size:17
Alignment explanation
Indices: 52889973--52890014 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
52889963 TCAAATCAAT
*
52889973 GAAAAATAAAAAATAAA
1 GAAAAATAAAAAAAAAA
52889990 -AAAAATAAAAAAAAAA
1 GAAAAATAAAAAAAAAA
52890006 GAAAAATAA
1 GAAAAATAA
52890015 GAGGACCAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.10
Consensus pattern (17 bp):
GAAAAATAAAAAAAAAA
Found at i:52890000 original size:10 final size:9
Alignment explanation
Indices: 52889980--52890014 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
52889970 AATGAAAAAT
52889980 AAAAAATAA
1 AAAAAATAA
52889989 AAAAAATAA
1 AAAAAATAA
52889998 AAAAAA-AA
1 AAAAAATAA
*
52890006 GAAAAATAA
1 AAAAAATAA
52890015 GAGGACCAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.09
Consensus pattern (9 bp):
AAAAAATAA
Found at i:52893336 original size:22 final size:22
Alignment explanation
Indices: 52893306--52893398 Score: 116
Period size: 22 Copynumber: 4.3 Consensus size: 22
52893296 GTTGAAATTG
**
52893306 GAGC-TAGTACGTTAGCCATGA
1 GAGCTTAGTACGTTAAACATGA
**
52893327 GAGCTTAGTACGTTAGCCATGA
1 GAGCTTAGTACGTTAAACATGA
* * *
52893349 GGGTTTAGTTCGTTAAACATGA
1 GAGCTTAGTACGTTAAACATGA
52893371 GAGCTTAGTACGTTAAACATGA
1 GAGCTTAGTACGTTAAACATGA
52893393 GAGCTT
1 GAGCTT
52893399 TTGGTAGATG
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
21 4 0.06
22 59 0.94
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (22 bp):
GAGCTTAGTACGTTAAACATGA
Found at i:52894416 original size:19 final size:20
Alignment explanation
Indices: 52894380--52894434 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
52894370 ATGATCATTT
52894380 TTATTTTTAATATTAATA-TAA
1 TTATTTTT-AT-TTAATATTAA
52894401 TTATTTTTATTTAATATTAA
1 TTATTTTTATTTAATATTAA
52894421 -TATTTTTATTTAAT
1 TTATTTTTATTTAAT
52894435 TAGATTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 20 0.61
20 5 0.15
21 8 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTTTTATTTAATATTAA
Found at i:52895818 original size:28 final size:30
Alignment explanation
Indices: 52895770--52895825 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
52895760 TTAAATAAAA
52895770 AATTTATAAATAAAACAAATAACATAATTT
1 AATTTATAAATAAAACAAATAACATAATTT
* *
52895800 AATTTA-AACTAAAA-AAATATCATAAT
1 AATTTATAAATAAAACAAATAACATAAT
52895826 AAAACTTGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.46
29 7 0.29
30 6 0.25
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (30 bp):
AATTTATAAATAAAACAAATAACATAATTT
Found at i:52898697 original size:14 final size:14
Alignment explanation
Indices: 52898592--52898706 Score: 54
Period size: 14 Copynumber: 8.2 Consensus size: 14
52898582 AGACTCTCAC
*
52898592 ATGTGGATTCATAA
1 ATGTGGATTCATAG
* *
52898606 ATGTGGATTTATAC
1 ATGTGGATTCATAG
** *
52898620 ATGCAGATCCATAG
1 ATGTGGATTCATAG
* *
52898634 ATGCGGATCCATACG
1 ATGTGGATTCATA-G
* *
52898649 -TGTTGATTTATAG
1 ATGTGGATTCATAG
* ** *
52898662 AT-TCAGATTTGTAC
1 ATGT-GGATTCATAG
*
52898676 ATGCGGATTCATAG
1 ATGTGGATTCATAG
*
52898690 ATGTGGATCCATAG
1 ATGTGGATTCATAG
52898704 ATG
1 ATG
52898707 CGAATTAATA
Statistics
Matches: 75, Mismatches: 22, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
13 2 0.03
14 72 0.96
15 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (14 bp):
ATGTGGATTCATAG
Found at i:52898707 original size:28 final size:28
Alignment explanation
Indices: 52898676--52898768 Score: 69
Period size: 28 Copynumber: 3.3 Consensus size: 28
52898666 AGATTTGTAC
* *
52898676 ATGCGGATTCATAGATGTGGATCCATAG
1 ATGCGGATTCATACATGTAGATCCATAG
* * **
52898704 ATGCGAATTAATACATGTAGATTTATAG
1 ATGCGGATTCATACATGTAGATCCATAG
* * * ** *
52898732 ACGCAGATTCATAAATACAGATTCATAG
1 ATGCGGATTCATACATGTAGATCCATAG
*
52898760 ATGCAGATT
1 ATGCGGATT
52898769 GTCCTGCAGA
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (28 bp):
ATGCGGATTCATACATGTAGATCCATAG
Found at i:52898752 original size:14 final size:14
Alignment explanation
Indices: 52898735--52898768 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
52898725 TTTATAGACG
52898735 CAGATTCATAAATA
1 CAGATTCATAAATA
* *
52898749 CAGATTCATAGATG
1 CAGATTCATAAATA
52898763 CAGATT
1 CAGATT
52898769 GTCCTGCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (14 bp):
CAGATTCATAAATA
Found at i:52898755 original size:70 final size:70
Alignment explanation
Indices: 52898625--52898762 Score: 168
Period size: 70 Copynumber: 2.0 Consensus size: 70
52898615 TATACATGCA
* * * * ** ** * * *
52898625 GATCCATAGATGCGGATCCATACGTGTTGATTTATAGATTCAGATTTGTACATGCGGATTCATAG
1 GATCCATAGATGCGAATCAATACATGTAGATTTATAGACGCAGATTCATAAATACAGATTCATAG
52898690 ATGTG
66 ATGTG
*
52898695 GATCCATAGATGCGAATTAATACATGTAGATTTATAGACGCAGATTCATAAATACAGATTCATAG
1 GATCCATAGATGCGAATCAATACATGTAGATTTATAGACGCAGATTCATAAATACAGATTCATAG
52898760 ATG
66 ATG
52898763 CAGATTGTCC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
70 56 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (70 bp):
GATCCATAGATGCGAATCAATACATGTAGATTTATAGACGCAGATTCATAAATACAGATTCATAG
ATGTG
Found at i:52901072 original size:20 final size:19
Alignment explanation
Indices: 52901048--52901098 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
52901038 AGGTTAATTA
52901048 ACTTAATTAAT-TATATTTT
1 ACTTAATTAATCT-TATTTT
52901067 ATCTTAATTAATCTTATTTT
1 A-CTTAATTAATCTTATTTT
52901087 ACTTAATTAATC
1 ACTTAATTAATC
52901099 AACATATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 12 0.40
20 17 0.57
21 1 0.03
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (19 bp):
ACTTAATTAATCTTATTTT
Found at i:52904809 original size:2 final size:2
Alignment explanation
Indices: 52904802--52904846 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
52904792 ATGGGAGATA
52904802 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52904844 AT A
1 AT A
52904847 AGCATGATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52906468 original size:25 final size:25
Alignment explanation
Indices: 52906440--52906511 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
52906430 TTTCATTCTT
*
52906440 ATTTTACCCTAGTAAAATTTTGACA
1 ATTTTACCCTAGTAAAATTTTAACA
* * *
52906465 ATTTTAGCCTTAGTAAAAATTTAACG
1 ATTTTA-CCCTAGTAAAATTTTAACA
* *
52906491 ATTTTGCCCGTGGTAAAATTT
1 ATTTTACCC-TAGTAAAATTT
52906512 CGAGAAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
25 8 0.22
26 29 0.78
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (25 bp):
ATTTTACCCTAGTAAAATTTTAACA
Found at i:52906682 original size:17 final size:18
Alignment explanation
Indices: 52906660--52906693 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52906650 CAAATGGATT
*
52906660 ATTTCCTTTTCC-TTTTC
1 ATTTCCATTTCCATTTTC
52906677 ATTTCCATTTCCATTTT
1 ATTTCCATTTCCATTTT
52906694 TGGAAACTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTCCATTTCCATTTTC
Found at i:52909247 original size:64 final size:64
Alignment explanation
Indices: 52909144--52909270 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 64
52909134 GTAATTGTTC
52909144 AAAAACATTGTCTTGACATCTATTTTCCAGATCTCGTAATCAAGAGTCGCCATAATAGATAGTT
1 AAAAACATTGTCTTGACATCTATTTTCCAGATCTCGTAATCAAGAGTCGCCATAATAGATAGTT
* * * *
52909208 AAAAACATTGTCTTGACATCTATTTTCTAGATCTTGTAATCGAGAGTCGCCATAATGGATAGT
1 AAAAACATTGTCTTGACATCTATTTTCCAGATCTCGTAATCAAGAGTCGCCATAATAGATAGT
52909271 AATTTATGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (64 bp):
AAAAACATTGTCTTGACATCTATTTTCCAGATCTCGTAATCAAGAGTCGCCATAATAGATAGTT
Found at i:52911746 original size:49 final size:49
Alignment explanation
Indices: 52911690--52911823 Score: 144
Period size: 49 Copynumber: 2.7 Consensus size: 49
52911680 TAACCACATT
* * *
52911690 TATCTGGCAGTTTATTTGGAATTTCTAGTGGCTT-TTCCACATATATCTG
1 TATCTGGCAGCTTATCTGCAATTTCTAGTGGCTTGTT-CACATATATCTG
* * *
52911739 TATCTGGCAGCTTGTCTGCAATTTTTAGTGGCTTGTTCATATATATCTG
1 TATCTGGCAGCTTATCTGCAATTTCTAGTGGCTTGTTCACATATATCTG
* * * * * *
52911788 TATTTGGTAGCTTGTCTGCAATATCTGGTGGGTTGT
1 TATCTGGCAGCTTATCTGCAATTTCTAGTGGCTTGT
52911824 CTACATTGTG
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 70 0.97
50 2 0.03
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (49 bp):
TATCTGGCAGCTTATCTGCAATTTCTAGTGGCTTGTTCACATATATCTG
Found at i:52918144 original size:26 final size:25
Alignment explanation
Indices: 52918070--52918145 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 25
52918060 TCTCATCCCT
* *
52918070 ATTTTTCCACCAGTAAAATTTTAACA
1 ATTTTTCC-CTAGTAAAATTTTGACA
* * *
52918096 ATTTTACCCTTGGTAAAATTTTGACG
1 ATTTTTCCC-TAGTAAAATTTTGACA
52918122 ATTTTTCCTCTAGTAAAATTTTGA
1 ATTTTTCC-CTAGTAAAATTTTGA
52918146 GAAAATATGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 1 0.02
26 39 0.95
27 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (25 bp):
ATTTTTCCCTAGTAAAATTTTGACA
Found at i:52922513 original size:17 final size:17
Alignment explanation
Indices: 52922493--52922530 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
52922483 TTCAATTAAT
52922493 TTAAATAAATAAATTTC
1 TTAAATAAATAAATTTC
* *
52922510 TTAATTAAATAATTTTC
1 TTAAATAAATAAATTTC
52922527 TTAA
1 TTAA
52922531 CTCAATTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATAAATAAATTTC
Found at i:52938554 original size:27 final size:27
Alignment explanation
Indices: 52938524--52938630 Score: 110
Period size: 27 Copynumber: 4.0 Consensus size: 27
52938514 AAATATCCCC
* *
52938524 GATGGGTAAAATAACCGAAATGCCGTT
1 GATGGGTAAAATGACCGAAATGCCCTT
*
52938551 GATGGGTAAAATGACCGTAATGCCCTT
1 GATGGGTAAAATGACCGAAATGCCCTT
* * *
52938578 G-TAGGGTAAAATGACCGTAATACCCCT
1 GAT-GGGTAAAATGACCGAAATGCCCTT
* *
52938605 -ATAGGGTAAAATGTCCGTAATGCCCT
1 GAT-GGGTAAAATGACCGAAATGCCCT
52938631 GGTGGGAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
26 1 0.01
27 69 0.99
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (27 bp):
GATGGGTAAAATGACCGAAATGCCCTT
Found at i:52938721 original size:24 final size:24
Alignment explanation
Indices: 52938688--52938746 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
52938678 TATGTGGTTA
52938688 AATGACTGATTTGTCTGTG-TTTGG
1 AATGACTGATTTGTCTGTGATTT-G
* *
52938712 TATGACTGATTTGTTTGTGATTTG
1 AATGACTGATTTGTCTGTGATTTG
52938736 AATGACTGATT
1 AATGACTGATT
52938747 CTGAGCATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.20, C:0.07, G:0.25, T:0.47
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTG
Found at i:52938848 original size:27 final size:27
Alignment explanation
Indices: 52938810--52938874 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
52938800 ATAGAGGAAG
52938810 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTGGCT-TGGCCACATA
52938835 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
*
52938863 TACTATTACTGG
1 TACTGTTACTGG
52938875 CAGCTTTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
27 27 0.77
28 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:52938880 original size:27 final size:27
Alignment explanation
Indices: 52938828--52938880 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
52938818 TGGTGGCTCT
* **
52938828 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAATCACTATTACTGGCAGCTTG
52938855 GCCACATAT-ACTATTACTGGCAGCTT
1 GCCACA-ATCACTATTACTGGCAGCTT
52938881 TGCTGCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTATTACTGGCAGCTTG
Found at i:52938990 original size:32 final size:32
Alignment explanation
Indices: 52938949--52939081 Score: 108
Period size: 32 Copynumber: 4.2 Consensus size: 32
52938939 CATATTACCA
* *
52938949 TTACCGATGGCTGTGTGACGGTCATTTCACTG
1 TTACTGATGGCTGTGTGACGATCATTTCACTG
* * *
52938981 TTACTGATGGCTGTGTGCCTATCATATCACTG
1 TTACTGATGGCTGTGTGACGATCATTTCACTG
* * *
52939013 CTACTGATGGCTTTGT-ACCGATCATGTT-ACCG
1 TTACTGATGGCTGTGTGA-CGATCAT-TTCACTG
* ** * *
52939045 TTACTGATGGTTGTCCGTCGATCATATCACTG
1 TTACTGATGGCTGTGTGACGATCATTTCACTG
*
52939077 CTACT
1 TTACT
52939082 AATGACTTTG
Statistics
Matches: 77, Mismatches: 20, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
31 1 0.01
32 75 0.97
33 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (32 bp):
TTACTGATGGCTGTGTGACGATCATTTCACTG
Found at i:52939022 original size:64 final size:64
Alignment explanation
Indices: 52938918--52939081 Score: 152
Period size: 64 Copynumber: 2.6 Consensus size: 64
52938908 GCTGCGATGC
* * *** * * *
52938918 TACTGATGGCTTTATGCCAATCATATTACCATTACCGATGGCTGTGTGA-CGGTCAT-TTCACTG
1 TACTGATGGCTGTATGCCAATCATATCACTGCTACTGATGGCTGTGT-ACCGATCATGTT-ACCG
52938981 T
64 T
* * *
52938982 TACTGATGGCTGTGTGCCTATCATATCACTGCTACTGATGGCTTTGTACCGATCATGTTACCGT
1 TACTGATGGCTGTATGCCAATCATATCACTGCTACTGATGGCTGTGTACCGATCATGTTACCGT
* ** * *
52939046 TACTGATGGTTGTCCGTCGATCATATCACTGCTACT
1 TACTGATGGCTGTATGCCAATCATATCACTGCTACT
52939082 AATGACTTTG
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
63 1 0.01
64 79 0.96
65 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (64 bp):
TACTGATGGCTGTATGCCAATCATATCACTGCTACTGATGGCTGTGTACCGATCATGTTACCGT
Found at i:52939094 original size:96 final size:96
Alignment explanation
Indices: 52938915--52939103 Score: 225
Period size: 96 Copynumber: 2.0 Consensus size: 96
52938905 TTTGCTGCGA
* ** * *
52938915 TGCTACTGATGGCTTTATGCCAATCATATTACCATTACCGATGGCTGTGTGACGGTCATTTCACT
1 TGCTACTGATGGCTTTATACCAATCATATTACCATTACCGATGGCTGTCCGACGATCATATCACT
* * * *
52938980 GTTACTGATGGCTGTGTGCCTATCATATCAC
66 GCTACTAATGACTGTGTGCCAATCATATCAC
* * * * * * *
52939011 TGCTACTGATGGCTTTGTACCGATCATGTTACCGTTACTGATGGTTGTCCGTCGATCATATCACT
1 TGCTACTGATGGCTTTATACCAATCATATTACCATTACCGATGGCTGTCCGACGATCATATCACT
*
52939076 GCTACTAATGACTTTGTGCCAATCATAT
66 GCTACTAATGACTGTGTGCCAATCATAT
52939104 TATTGTACTT
Statistics
Matches: 76, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
96 76 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (96 bp):
TGCTACTGATGGCTTTATACCAATCATATTACCATTACCGATGGCTGTCCGACGATCATATCACT
GCTACTAATGACTGTGTGCCAATCATATCAC
Found at i:52939371 original size:28 final size:28
Alignment explanation
Indices: 52939338--52939391 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
52939328 CATACTGATA
*
52939338 CTGTATCGGGCTTAGGCCCACACTGTTT
1 CTGTATCGGGCTAAGGCCCACACTGTTT
*
52939366 CTGTATTGGGCTAAGGCCCACACTGT
1 CTGTATCGGGCTAAGGCCCACACTGT
52939392 ACTGTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.30
Consensus pattern (28 bp):
CTGTATCGGGCTAAGGCCCACACTGTTT
Found at i:52947031 original size:55 final size:56
Alignment explanation
Indices: 52946890--52947036 Score: 161
Period size: 55 Copynumber: 2.6 Consensus size: 56
52946880 TAATACTGAG
* * * *
52946890 TCTGGTGCCAGCCATTGACAGGCCAGTACCAAATTTTTTTTTTTAAAAAAAACACGTAC
1 TCTGGTGCCGGCCATTGACAGGCCAGCACCAAATTCTTTTTTCT---AAAAACACGTAC
* * * *
52946949 TCTAGTGCTGGCCATTGACATGCCAGCACCAAATTCTTTTTTCT-AAAACTCGTAC
1 TCTGGTGCCGGCCATTGACAGGCCAGCACCAAATTCTTTTTTCTAAAAACACGTAC
* * *
52947004 TTTGGTGCCGGCCATTAACAGGTCAGCACCAAA
1 TCTGGTGCCGGCCATTGACAGGCCAGCACCAAA
52947037 AAAATTTATT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
55 37 0.50
59 37 0.50
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (56 bp):
TCTGGTGCCGGCCATTGACAGGCCAGCACCAAATTCTTTTTTCTAAAAACACGTAC
Found at i:52947088 original size:54 final size:53
Alignment explanation
Indices: 52947013--52947304 Score: 374
Period size: 54 Copynumber: 5.4 Consensus size: 53
52947003 CTTTGGTGCC
* * *
52947013 GGCCATTAACAGGTCAGCACCAAAAAAATTTATTTTTTTTTGGTACTTGGTGGT
1 GGCCATTGACAGGCCAACACCAAAAAAATTTATTTTTTTTT-GTACTTGGTGGT
*
52947067 GGCCATTGATAGGCCAACACCAAAAAAATTTGATTTTTTTTTTGTACTTGGTGGT
1 GGCCATTGACAGGCCAACACCAAAAAAATTT-A-TTTTTTTTTGTACTTGGTGGT
* *
52947122 GGTCATTGACAGGCCAACA-CAAAAAAA-TTAATTTTTTTTGTACTTGGTGGT
1 GGCCATTGACAGGCCAACACCAAAAAAATTTATTTTTTTTTGTACTTGGTGGT
* * * * * *
52947173 GGCCATTGACAGGTCAGCACAAAAAAAAATTGATTTATTTCTGTACTTGGTGGT
1 GGCCATTGACAGGCCAACAC-CAAAAAAATTTATTTTTTTTTGTACTTGGTGGT
* *
52947227 GGCCATTGACAGGCCAGCA-TAAAAAAATTTTGATTTTTTTTTTGTACTTGGTGGT
1 GGCCATTGACAGGCCAACACCAAAAAAA-TTT-A-TTTTTTTTTGTACTTGGTGGT
52947282 GGCCATTGACAGGCCAACACCAA
1 GGCCATTGACAGGCCAACACCAA
52947305 TTTTTTTTTA
Statistics
Matches: 207, Mismatches: 22, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
51 36 0.17
52 8 0.04
53 11 0.05
54 74 0.36
55 67 0.32
56 11 0.05
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (53 bp):
GGCCATTGACAGGCCAACACCAAAAAAATTTATTTTTTTTTGTACTTGGTGGT
Found at i:52947187 original size:160 final size:160
Alignment explanation
Indices: 52947013--52947301 Score: 465
Period size: 160 Copynumber: 1.8 Consensus size: 160
52947003 CTTTGGTGCC
* * * * *
52947013 GGCCATTAACAGGTCAGCAC-CAAAAAAATTTATTTTTTTTTGGTACTTGGTGGTGGCCATTGAT
1 GGCCATTAACAGGTCAGCACAAAAAAAAATTGATTTATTTCT-GTACTTGGTGGTGGCCATTGAC
*
52947077 AGGCCAACACCAAAAAAA-TTTGATTTTTTTTTTGTACTTGGTGGTGGTCATTGACAGGCCAACA
65 AGGCCAACA-CAAAAAAATTTTGATTTTTTTTTTGTACTTGGTGGTGGCCATTGACAGGCCAACA
52947141 CAAAAAAATTAATTTTTTTTGTACTTGGTGGT
129 CAAAAAAATTAATTTTTTTTGTACTTGGTGGT
*
52947173 GGCCATTGACAGGTCAGCACAAAAAAAAATTGATTTATTTCTGTACTTGGTGGTGGCCATTGACA
1 GGCCATTAACAGGTCAGCACAAAAAAAAATTGATTTATTTCTGTACTTGGTGGTGGCCATTGACA
* *
52947238 GGCCAGCATAAAAAAATTTTGATTTTTTTTTTGTACTTGGTGGTGGCCATTGACAGGCCAACAC
66 GGCCAACACAAAAAAATTTTGATTTTTTTTTTGTACTTGGTGGTGGCCATTGACAGGCCAACAC
52947302 CAATTTTTTT
Statistics
Matches: 118, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
159 7 0.06
160 94 0.80
161 17 0.14
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (160 bp):
GGCCATTAACAGGTCAGCACAAAAAAAAATTGATTTATTTCTGTACTTGGTGGTGGCCATTGACA
GGCCAACACAAAAAAATTTTGATTTTTTTTTTGTACTTGGTGGTGGCCATTGACAGGCCAACACA
AAAAAATTAATTTTTTTTGTACTTGGTGGT
Done.