Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 81 of 210
Found at i:28275745 original size:17 final size:17
Alignment explanation
Indices: 28275723--28275820 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
28275713 AATTCAAGAC
28275723 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
28275740 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
28275759 CTTATGTAATATTTTTAA
1 -TTATGTAATGTTTTTAA
* **
28275777 TTATGTAGTGATTTAAAGA
1 TTATGTAATG-TTTTTA-A
*
28275796 TTTATGTAATGCTTTTAA
1 -TTATGTAATGTTTTTAA
28275814 TTATGTA
1 TTATGTA
28275821 GTGATTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 24 0.41
18 9 0.16
19 8 0.14
20 17 0.29
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:28275802 original size:20 final size:18
Alignment explanation
Indices: 28275738--28275829 Score: 71
Period size: 17 Copynumber: 5.0 Consensus size: 18
28275728 TAATGTTTTT
*
28275738 AATTATGTAGTGATTCAA
1 AATTATGTAGTGATTTAA
* **
28275756 AGACTTATGTAAT-ATTTTT
1 A-A-TTATGTAGTGATTTAA
28275775 AATTATGTAGTGATTTAA
1 AATTATGTAGTGATTTAA
* * *
28275793 AGATTTATGTAATGCTTT-T
1 A-A-TTATGTAGTGATTTAA
28275812 AATTATGTAGTGATTTAA
1 AATTATGTAGTGATTTAA
28275830 TTCGGGTAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
17 20 0.36
18 8 0.15
19 7 0.13
20 20 0.36
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (18 bp):
AATTATGTAGTGATTTAA
Found at i:28275827 original size:37 final size:37
Alignment explanation
Indices: 28275718--28275829 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
28275708 GTGTTAATTC
*
28275718 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
*
28275755 AAGACTTATGTAATATTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
* *
28275792 AAGATTTATGTAATGCTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
28275829 A
1 A
28275830 TTCGGGTAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
Found at i:28275845 original size:9 final size:10
Alignment explanation
Indices: 28275830--28275908 Score: 96
Period size: 9 Copynumber: 8.2 Consensus size: 10
28275820 AGTGATTTAA
28275830 TTCGGGTAAT
1 TTCGGGTAAT
28275840 TT-GGGTAATT
1 TTCGGGTAA-T
28275850 TTCGGGTAA-
1 TTCGGGTAAT
28275859 TTCGGGTAATT
1 TTCGGGTAA-T
28275870 TTCGGGTAA-
1 TTCGGGTAAT
28275879 TTCGGGT-AT
1 TTCGGGTAAT
*
28275888 TTCGGGT-TT
1 TTCGGGTAAT
28275897 TTCGGGTAAT
1 TTCGGGTAAT
28275907 TT
1 TT
28275909 TTAACCAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
8 1 0.02
9 37 0.61
10 8 0.13
11 15 0.25
ACGTcount: A:0.16, C:0.09, G:0.30, T:0.44
Consensus pattern (10 bp):
TTCGGGTAAT
Found at i:28275855 original size:20 final size:20
Alignment explanation
Indices: 28275830--28275909 Score: 119
Period size: 20 Copynumber: 4.1 Consensus size: 20
28275820 AGTGATTTAA
*
28275830 TTCGGGTAATTTGGGTAATT
1 TTCGGGTAATTCGGGTAATT
28275850 TTCGGGTAATTCGGGTAATT
1 TTCGGGTAATTCGGGTAATT
28275870 TTCGGGTAATTCGGGT-A-T
1 TTCGGGTAATTCGGGTAATT
**
28275888 TTCGGGTTTTTCGGGTAATT
1 TTCGGGTAATTCGGGTAATT
28275908 TT
1 TT
28275910 TAACCAAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
18 15 0.27
19 2 0.04
20 38 0.69
ACGTcount: A:0.16, C:0.09, G:0.30, T:0.45
Consensus pattern (20 bp):
TTCGGGTAATTCGGGTAATT
Found at i:28275869 original size:29 final size:30
Alignment explanation
Indices: 28275827--28275909 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 30
28275817 TGTAGTGATT
28275827 TAATTCGGGTAATTT-GGGTAATTTTCGGG
1 TAATTCGGGTAATTTCGGGTAATTTTCGGG
28275856 TAATTCGGGTAATTTTCGGGTAA--TTCGGG
1 TAATTCGGGTAA-TTTCGGGTAATTTTCGGG
* *
28275885 TATTTCGGGT-TTTTCGGGTAATTTT
1 TAATTCGGGTAATTTCGGGTAATTTT
28275910 TAACCAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
27 10 0.21
29 29 0.60
30 3 0.06
31 6 0.12
ACGTcount: A:0.18, C:0.08, G:0.29, T:0.45
Consensus pattern (30 bp):
TAATTCGGGTAATTTCGGGTAATTTTCGGG
Found at i:28276031 original size:29 final size:29
Alignment explanation
Indices: 28275970--28276031 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
28275960 TTATTAACCG
* * **
28275970 AAAAAAATTTCGGTTCGGTTAATTATTTT
1 AAAAAAAATTCGGTTCGGTTAATCATTAA
28275999 AAAAAAAATTCGGTTCGGTTAA-CAGTTAA
1 AAAAAAAATTCGGTTCGGTTAATCA-TTAA
28276028 AAAA
1 AAAA
28276032 TTTGGGAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.34
Consensus pattern (29 bp):
AAAAAAAATTCGGTTCGGTTAATCATTAA
Found at i:28276227 original size:39 final size:39
Alignment explanation
Indices: 28276148--28276237 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
28276138 TAAAAAATAT
* *
28276148 TTATATTAAAAAACATTACCAAAAATATAATAAATGTTTTA
1 TTATATTAAAAAAC--TACAAAAAATATAATAAATATTTTA
28276189 TTATATTAAAAAAC-ACAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAACTACAAA-AAATATAATAAATATTTTA
*
28276228 TTGTATTAAA
1 TTATATTAAA
28276238 TATAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
38 4 0.09
39 27 0.60
41 14 0.31
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (39 bp):
TTATATTAAAAAACTACAAAAAATATAATAAATATTTTA
Found at i:28285421 original size:16 final size:16
Alignment explanation
Indices: 28285399--28285435 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
28285389 NNNNNNAATT
28285399 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
28285416 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
28285431 TAATA
1 TAATA
28285436 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:28285486 original size:15 final size:15
Alignment explanation
Indices: 28285468--28285524 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
28285458 ATTCAATATT
28285468 AATATTTTAACAATA
1 AATATTTTAACAATA
*
28285483 AATATTTATTACAATTATA
1 AATATTT-TAAC-A--ATA
* *
28285502 AATATATTAATAATA
1 AATATTTTAACAATA
28285517 AATATTTT
1 AATATTTT
28285525 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 3 0.09
17 2 0.06
18 2 0.06
19 9 0.27
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAACAATA
Found at i:28286958 original size:6 final size:6
Alignment explanation
Indices: 28286947--28286971 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28286937 TGGCGACCCC
28286947 CGTTTT CGTTTT CGTTTT CGTTTT C
1 CGTTTT CGTTTT CGTTTT CGTTTT C
28286972 AAAATCCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.16, T:0.64
Consensus pattern (6 bp):
CGTTTT
Found at i:28289373 original size:33 final size:33
Alignment explanation
Indices: 28289291--28289373 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 33
28289281 CATTCAAACC
* * ** *
28289291 ATGGTCTTACGTTCAAGGTGCCATAACCCAATT
1 ATGGTCTTACATTTAAAATGCCATAACCCAACT
* * *
28289324 ATGGTCTTTTCA-TTAAAATGCCATAGCCCAGCT
1 ATGGTC-TTACATTTAAAATGCCATAACCCAACT
28289357 ATGGTCTTACATTTAAA
1 ATGGTCTTACATTTAAA
28289374 CATTGTCATG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
32 4 0.10
33 32 0.82
34 3 0.08
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (33 bp):
ATGGTCTTACATTTAAAATGCCATAACCCAACT
Found at i:28294585 original size:20 final size:21
Alignment explanation
Indices: 28294550--28294593 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
28294540 TTTTTTCTTT
*
28294550 CTAGTTGTACTTTTATTTTTTG
1 CTAGTTGTA-TTTTATTTTATG
28294572 CTAGTTGT-TTTTATTTTATG
1 CTAGTTGTATTTTATTTTATG
28294592 CT
1 CT
28294594 GAGACTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
22 8 0.38
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.64
Consensus pattern (21 bp):
CTAGTTGTATTTTATTTTATG
Found at i:28307807 original size:5 final size:5
Alignment explanation
Indices: 28307788--28307820 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
28307778 CCAAATCGAC
28307788 AACAA AACTAA AACAA AACAA AACAA AACAA AA
1 AACAA AAC-AA AACAA AACAA AACAA AACAA AA
28307821 TTCAGTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.18, G:0.00, T:0.03
Consensus pattern (5 bp):
AACAA
Found at i:28308920 original size:12 final size:12
Alignment explanation
Indices: 28308903--28308955 Score: 58
Period size: 11 Copynumber: 4.6 Consensus size: 12
28308893 TTTTCACAAA
28308903 CAAATTCTCTCT
1 CAAATTCTCTCT
28308915 CAAATT-TCCTCT
1 CAAATTCT-CTCT
* *
28308927 CAATTTC-CTTT
1 CAAATTCTCTCT
28308938 CAAATT-TCTCT
1 CAAATTCTCTCT
28308949 CAAATTC
1 CAAATTC
28308956 ATATTTAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 18 0.55
12 15 0.45
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.43
Consensus pattern (12 bp):
CAAATTCTCTCT
Found at i:28308933 original size:11 final size:12
Alignment explanation
Indices: 28308911--28308954 Score: 65
Period size: 11 Copynumber: 3.8 Consensus size: 12
28308901 AACAAATTCT
28308911 CTCTCAAATTTC
1 CTCTCAAATTTC
28308923 CTCTC-AATTTC
1 CTCTCAAATTTC
*
28308934 CTTTCAAATTT-
1 CTCTCAAATTTC
28308945 CTCTCAAATT
1 CTCTCAAATT
28308955 CATATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:28311438 original size:15 final size:15
Alignment explanation
Indices: 28311414--28311489 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
28311404 TAAAAATTCC
*
28311414 AAACCCTAAACCTAA
1 AAACCATAAACCTAA
*
28311429 AAACCATAAACC-AT
1 AAACCATAAACCTAA
* *
28311443 AAACCTAAAAACC-AT
1 AAACC-ATAAACCTAA
* *
28311458 AAACCCTAAACATAA
1 AAACCATAAACCTAA
28311473 AAACCATAAACCCTAA
1 AAACCATAAA-CCTAA
28311489 A
1 A
28311490 CATAAAACTT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
14 10 0.20
15 34 0.69
16 5 0.10
ACGTcount: A:0.58, C:0.29, G:0.00, T:0.13
Consensus pattern (15 bp):
AAACCATAAACCTAA
Found at i:28311439 original size:7 final size:7
Alignment explanation
Indices: 28311414--28311495 Score: 69
Period size: 7 Copynumber: 11.4 Consensus size: 7
28311404 TAAAAATTCC
*
28311414 AAACCCT
1 AAACCAT
*
28311421 AAACCTAA
1 AAACC-AT
28311429 AAACCAT
1 AAACCAT
28311436 AAACCAT
1 AAACCAT
*
28311443 AAACCTAA
1 AAACC-AT
28311451 AAACCAT
1 AAACCAT
*
28311458 AAACCCT
1 AAACCAT
28311465 AAA-CAT
1 AAACCAT
28311471 AAAAACCAT
1 --AAACCAT
*
28311480 AAACCCT
1 AAACCAT
28311487 AAA-CAT
1 AAACCAT
28311493 AAA
1 AAA
28311496 ACTTCAGACC
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
6 7 0.11
7 37 0.61
8 14 0.23
9 3 0.05
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.13
Consensus pattern (7 bp):
AAACCAT
Found at i:28311463 original size:44 final size:44
Alignment explanation
Indices: 28311351--28311876 Score: 410
Period size: 44 Copynumber: 12.2 Consensus size: 44
28311341 CCCTAATCCT
* * * * *
28311351 AACCCTTAACTTAAAAACCCT-AACCCTTCAA-TTAAAAACGCT-
1 AACCCTAAACCTAAAAACCATAAACCC-TAAACTTAAAAACCCTA
* * * *
28311393 AACCCTTAACTTAAAAATTCC--AAACCCTAAACCTAAAAACCATA
1 AACCCTAAACCTAAAAA--CCATAAACCCTAAACTTAAAAACCCTA
* * *
28311437 AACCATAAACCTAAAAACCATAAACCCTAAACATAAAAACCATA
1 AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCTA
* * *
28311481 AACCCTAAACAT-AAAA-CTTCAGACCCTAAACTTAAAAA-CCTCA
1 AACCCTAAACCTAAAAACCAT-AAACCCTAAACTTAAAAACCCT-A
*
28311524 AACCCTAAACCTAAAAA-CAT-AACCCTTAACTT-AAAACCCTA
1 AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCTA
* ** * * ** **
28311565 AACCCTAAACTTAAAAACTTTAAACACTAAAATT-TTAACTTTAA
1 AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCT-A
* *
28311609 AACCCT-AACTCT--AATCC-T-AACCCTTAACTTAAAAA-CCTCA
1 AACCCTAAAC-CTAAAAACCATAAACCCTAAACTTAAAAACCCT-A
* * * * *
28311649 AACCCTTAATCTAAAAACCATAGACCTTAAACTTAAAAATCCTA
1 AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCTA
* * *
28311693 AACTCTAAACCAAAAAACCATAAACCCTAAACTTAAAAACCCCA
1 AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCTA
* *
28311737 AACACTAAACCTAAAAA-CACT-AACCCTTAACTTAAAAACCCTA
1 AACCCTAAACCTAAAAACCA-TAAACCCTAAACTTAAAAACCCTA
* * * * *
28311780 AACCATAAACC-ATAAAACCTTAAACCTTAAACTTAAAAACCATG
1 AACCCTAAACCTA-AAAACCATAAACCCTAAACTTAAAAACCCTA
* *
28311824 AACCTTAAACCTAAAAACCCTAAACCCTAAACTTAAAAACCCTA
1 AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCTA
*
28311868 AACCTTAAA
1 AACCCTAAA
28311877 ACCTTAACTT
Statistics
Matches: 389, Mismatches: 68, Indels: 52
0.76 0.13 0.10
Matches are distributed among these distances:
40 19 0.05
41 26 0.07
42 48 0.12
43 98 0.25
44 194 0.50
45 4 0.01
ACGTcount: A:0.50, C:0.29, G:0.01, T:0.21
Consensus pattern (44 bp):
AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCTA
Found at i:28311790 original size:29 final size:29
Alignment explanation
Indices: 28311758--28311897 Score: 92
Period size: 29 Copynumber: 4.8 Consensus size: 29
28311748 TAAAAACACT
*
28311758 AACCCTTAACTTAAAAACCCTAAACCATA
1 AACCCTAAACTTAAAAACCCTAAACCATA
* * * *
28311787 AACCATAAAACCTT--AAACCTTAAACTTAAA
1 AACCCT-AAA-CTTAAAAACCCTAAAC-CATA
* * *
28311817 AACCATGAACCTT--AAA-CCTAAAAACCCTA
1 AACCCT-AAACTTAAAAACCCT--AAACCATA
*
28311846 AACCCTAAACTTAAAAACCCTAAACCTTA
1 AACCCTAAACTTAAAAACCCTAAACCATA
* *
28311875 AAACCTTAACTTAAAAACCCTAA
1 AACCCTAAACTTAAAAACCCTAA
28311898 CCCTTAAGTT
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
28 7 0.08
29 55 0.63
30 19 0.22
31 6 0.07
ACGTcount: A:0.50, C:0.29, G:0.01, T:0.21
Consensus pattern (29 bp):
AACCCTAAACTTAAAAACCCTAAACCATA
Found at i:28311819 original size:15 final size:14
Alignment explanation
Indices: 28311801--28311890 Score: 51
Period size: 15 Copynumber: 6.2 Consensus size: 14
28311791 ATAAAACCTT
28311801 AAACCTTAAACTTAA
1 AAACCTTAAACTT-A
* *
28311816 AAACCATGAACCTT-
1 AAACC-TTAAACTTA
* *
28311830 AAACCTAAAAACCCT-
1 AAACCT-TAAA-CTTA
*
28311845 AAACCCTAAACTTAA
1 AAACCTTAAACTT-A
*
28311860 AAACCCTAAACCTTA
1 AAACCTTAAA-CTTA
28311875 AAACCTT-AACTTA
1 AAACCTTAAACTTA
28311888 AAA
1 AAA
28311891 ACCCTAACCC
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
13 10 0.17
14 12 0.20
15 29 0.48
16 9 0.15
ACGTcount: A:0.51, C:0.27, G:0.01, T:0.21
Consensus pattern (14 bp):
AAACCTTAAACTTA
Found at i:28311854 original size:16 final size:15
Alignment explanation
Indices: 28311845--28311897 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
28311835 TAAAAACCCT
*
28311845 AAACCCTAAACTTAA
1 AAACCCTAAACCTAA
*
28311860 AAACCCTAAACCTTA
1 AAACCCTAAACCTAA
* *
28311875 AAA-CCTTAACTTAA
1 AAACCCTAAACCTAA
28311889 AAACCCTAA
1 AAACCCTAA
28311898 CCCTTAAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (15 bp):
AAACCCTAAACCTAA
Found at i:28311876 original size:7 final size:7
Alignment explanation
Indices: 28311772--28311883 Score: 66
Period size: 7 Copynumber: 15.3 Consensus size: 7
28311762 CTTAACTTAA
*
28311772 AAACCCT
1 AAACCTT
*
28311779 AAACCAT
1 AAACCTT
*
28311786 AAACCATA
1 AAACC-TT
28311794 AAACCTT
1 AAACCTT
28311801 AAACCTT
1 AAACCTT
28311808 AAA-CTT
1 AAACCTT
*
28311814 AAAAACCAT
1 --AAACCTT
*
28311823 GAACCTT
1 AAACCTT
*
28311830 AAACCTAA
1 AAACCT-T
*
28311838 AAACCCT
1 AAACCTT
*
28311845 AAACCCT
1 AAACCTT
28311852 AAA-CTT
1 AAACCTT
*
28311858 AAAAACCCT
1 --AAACCTT
28311867 AAACCTT
1 AAACCTT
28311874 AAAACCTT
1 -AAACCTT
28311882 AA
1 AA
28311884 CTTAAAAACC
Statistics
Matches: 82, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
6 5 0.06
7 50 0.61
8 23 0.28
9 4 0.05
ACGTcount: A:0.51, C:0.29, G:0.01, T:0.20
Consensus pattern (7 bp):
AAACCTT
Found at i:28311876 original size:22 final size:22
Alignment explanation
Indices: 28311348--28311876 Score: 312
Period size: 22 Copynumber: 24.6 Consensus size: 22
28311338 TAACCCTAAT
*
28311348 CCTAACCCTT-AACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* *
28311369 CCTAACCCTTCAA-TTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* * *
28311390 GCTAACCCTT-AACTTAAAAATT
1 CCTAAACCTTAAACTTAAAAA-C
* *
28311412 CC-AAACCCTAAACCTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* * *
28311433 CATAAACCATAAACCTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* * *
28311455 CATAAACCCTAAACATAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* * *
28311477 CATAAACCCTAAACAT-AAAA-
1 CCTAAACCTTAAACTTAAAAAC
* * *
28311497 CTTCAGACCCTAAACTTAAAAA-
1 CCT-AAACCTTAAACTTAAAAAC
* *
28311519 CCTCAAACCCTAAACCTAAAAA-
1 CCT-AAACCTTAAACTTAAAAAC
* *
28311541 CATAACCCTT-AACTT-AAAAC
1 CCTAAACCTTAAACTTAAAAAC
*
28311561 CCTAAACCCTAAACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
** * **
28311583 TTTAAACAC-TAAAATT-TTAAC
1 CCTAAAC-CTTAAACTTAAAAAC
** * *
28311604 TTTAAAACCCT-AACTCT---AAT
1 CCT-AAACCTTAAACT-TAAAAAC
*
28311624 CCTAACCCTT-AACTTAAAAA-
1 CCTAAACCTTAAACTTAAAAAC
*
28311644 CCTCAAACCCTTAATC-TAAAAAC
1 CCT-AAA-CCTTAAACTTAAAAAC
* * *
28311667 CATAGACCTTAAACTTAAAAAT
1 CCTAAACCTTAAACTTAAAAAC
**
28311689 CCTAAA-CTCTAAACCAAAAAAC
1 CCTAAACCT-TAAACTTAAAAAC
* *
28311711 CATAAACCCTAAACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* *
28311733 CCCAAACAC-TAAACCTAAAAAC
1 CCTAAAC-CTTAAACTTAAAAAC
* *
28311755 ACTAACCCTT-AACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* *
28311776 CCTAAACCATAAAC-CATAAAAC
1 CCTAAACCTTAAACTTA-AAAAC
*
28311798 CTTAAACCTTAAACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* * *
28311820 CATGAACCTTAAACCTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
*
28311842 CCTAAACCCTAAACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
28311864 CCTAAACCTTAAA
1 CCTAAACCTTAAA
28311877 ACCTTAACTT
Statistics
Matches: 407, Mismatches: 72, Indels: 57
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.00
19 13 0.03
20 21 0.05
21 107 0.26
22 257 0.63
23 8 0.02
ACGTcount: A:0.50, C:0.29, G:0.01, T:0.21
Consensus pattern (22 bp):
CCTAAACCTTAAACTTAAAAAC
Found at i:28311902 original size:29 final size:29
Alignment explanation
Indices: 28311839--28311904 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
28311829 TAAACCTAAA
*
28311839 AACCC-TAAACCCTAAACTTAAAAACCCT
1 AACCCTTAAAACCTAAACTTAAAAACCCT
* *
28311867 AAACCTTAAAACCTTAACTTAAAAACCCT
1 AACCCTTAAAACCTAAACTTAAAAACCCT
28311896 AACCCTTAA
1 AACCCTTAA
28311905 GTTAAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (29 bp):
AACCCTTAAAACCTAAACTTAAAAACCCT
Found at i:28315071 original size:125 final size:125
Alignment explanation
Indices: 28314828--28315391 Score: 722
Period size: 125 Copynumber: 4.5 Consensus size: 125
28314818 CAAACATGCT
* * *
28314828 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTATTCTCATAAAGCATCCTGGTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTA
* * *
28314893 GAAGCGA-TTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTTCAGGATCA
66 GAAGC-ATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
* * * *
28314953 ACTATATCAAAAGCGCGTCCACGAGGGTGCGATTTCAGAAATTCTTCTCA-AATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCT
* * * * *
28315017 TGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTT-TTTCAGAACCT
65 AGAAGCA-TTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
* * *
28315078 ACTGTAGCAAAAGCGCGTCTACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTA
* *
28315143 GAAGCAATTTTATACTATTTTCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
66 GAAGCATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
* * * * * * *
28315203 ATTGTAGCAAAAGCGCGTCCAGGAGAGCTCGATTTCACAAATTCTTCGCATATAGCATCCTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTA
*
28315268 GAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCT
66 GAAGCA-TTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
* * * * * * * * * *
28315328 ACTGTAGCAAAAGCGAGTACACGTGGGCGCGACTGCAAAAATCCTTCTAATAAATCATTCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
28315392 TTGATTTTAT
Statistics
Matches: 377, Mismatches: 56, Indels: 12
0.85 0.13 0.03
Matches are distributed among these distances:
124 42 0.11
125 254 0.67
126 81 0.21
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (125 bp):
ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTA
GAAGCATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
Found at i:28315267 original size:250 final size:249
Alignment explanation
Indices: 28314826--28315359 Score: 863
Period size: 250 Copynumber: 2.1 Consensus size: 249
28314816 CCCAAACATG
28314826 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTATTCTCATAAAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGT-CACGTGGGCGCGATTTCACAAATTATTCTCATAAAGCATCCTGG
* * *
28314891 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTTCAGGATCAACT
65 TAGAAGCAATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCAGGACCAACT
* * * *
28314956 ATATCAAAAGCGCGTCCACGAGGGTGCGATTTCAGAAATTCTTCTCAAATAGCATCCTGCTTGAA
130 ATAGCAAAAGCGCGTCCACGAGGCTGCGATTTCACAAATTCTTCGCAAATAGCATCCTGCTTGAA
*
28315021 GCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTTCAGAAC
195 GCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTCCAGAAC
*
28315076 CTACTGTAGCAAAAGCGCGTCTACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTC-ACGTGGGCGCGATTTCACAAATTATTCTCATAAAGCATCCTGG
* * *
28315141 TAGAAGCAATTTTATACTATTTTCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAATT
65 TAGAAGCAATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCAGGACCAACT
* * *
28315206 GTAGCAAAAGCGCGTCCAGGAGAGCT-CGATTTCACAAATTCTTCGCATATAGCATCCTGCTTGA
130 ATAGCAAAAGCGCGTCCACGAG-GCTGCGATTTCACAAATTCTTCGCAAATAGCATCCTGCTTGA
* *
28315270 AGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
194 AGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTCCAGAAC
*
28315326 CTACTGTAGCAAAAGCGAGTACACGTGGGCGCGA
1 CTACTGTAGCAAAAGCGCGT-CACGTGGGCGCGA
28315360 CTGCAAAAAT
Statistics
Matches: 263, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
249 1 0.00
250 259 0.98
251 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (249 bp):
CTACTGTAGCAAAAGCGCGTCACGTGGGCGCGATTTCACAAATTATTCTCATAAAGCATCCTGGT
AGAAGCAATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCAGGACCAACTA
TAGCAAAAGCGCGTCCACGAGGCTGCGATTTCACAAATTCTTCGCAAATAGCATCCTGCTTGAAG
CATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTCCAGAAC
Found at i:28320297 original size:12 final size:11
Alignment explanation
Indices: 28320282--28320324 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 11
28320272 TAAAAAATAT
28320282 AAATATATAAA
1 AAATATATAAA
28320293 TAAATATATAAA
1 -AAATATATAAA
28320305 AAA-AT-T-AA
1 AAATATATAAA
28320313 AAATATATAAA
1 AAATATATAAA
28320324 A
1 A
28320325 TCTAGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
8 5 0.18
9 3 0.11
10 3 0.11
11 6 0.21
12 11 0.39
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATATATAAA
Found at i:28321669 original size:79 final size:79
Alignment explanation
Indices: 28321535--28321682 Score: 217
Period size: 79 Copynumber: 1.9 Consensus size: 79
28321525 ACTTACCTTT
* * *
28321535 TATATTGACATATGCAATCATGAAGATATAAGTTGACTTTTATGATCTTTTGTATCTTTATATTA
1 TATATTAACATATGCAATCATGAAGATATAAGCTGACTTTTATGATCTTTGGTATCTTTATATTA
28321600 AGGATAATTGATGA
66 AGGATAATTGATGA
* * * *
28321614 TATATTAAGATATGCAATCCATGAATATATGAGCTGA-TTTTATTATCTTTGGTATCTTTATATT
1 TATATTAACATATGCAAT-CATGAAGATATAAGCTGACTTTTATGATCTTTGGTATCTTTATATT
28321678 AAGGA
65 AAGGA
28321683 CAATGAATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
79 46 0.75
80 15 0.25
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (79 bp):
TATATTAACATATGCAATCATGAAGATATAAGCTGACTTTTATGATCTTTGGTATCTTTATATTA
AGGATAATTGATGA
Found at i:28330972 original size:18 final size:16
Alignment explanation
Indices: 28330941--28330982 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
28330931 TTGAGTAAAT
28330941 AAATATAT-TTTATACTA
1 AAATATATATTTATA--A
28330958 AAATATATATTTATAA
1 AAATATATATTTATAA
28330974 AAATATATA
1 AAATATATA
28330983 AAAAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.42
17 8 0.33
18 6 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATATATATTTATAA
Found at i:28331360 original size:214 final size:213
Alignment explanation
Indices: 28330967--28331409 Score: 671
Period size: 214 Copynumber: 2.1 Consensus size: 213
28330957 AAAATATATA
* * * *
28330967 TTTATAAAAATATATAAAAAATTTATTATTAGTGGAATTAAGGGTAAAGCCAAAAAAATTTTTTG
1 TTTAT-AAATTATATAAAAAATTTATTATTAGTGAAATCAAGGGTAAAGCAAAAAAAATTTTTTG
* *
28331032 GGTAAAATTAATTTATGTATTTTTTACTATGTTAAAAATACAATTTCACCATTTTAATAGCCTAA
65 GGTAAAATTAATTTATGTATTTTTTACGATATTAAAAATACAATTTCACCATTTTAATAGCCTAA
** * *
28331097 ATTTTTATAATTTTTAAATAATTAAATTAAAATTTTATCATTCTTAAGGGTTAAAGTGTAATTTT
130 ATTTTTATAATTTAAAAAAAATTAAATTAAAATTTTATCATTCTTAAGGGTTAAAGTATAATTTT
28331162 ACCAATACAAATTTAAAAT
195 ACCAATACAAATTTAAAAT
* *
28331181 TTTATAAATTATATCAACAAA-TTATTCTTAGTGAAATCAAGGGTAAAGACAAAAAAATTATTTT
1 TTTATAAATTATAT-AAAAAATTTATTATTAGTGAAATCAAGGGTAAAG-CAAAAAAA--A-TTT
*
28331245 TTTGGGTAAAATTAATTTATGTA-TTTTTACGATATTAAAAATACAATTT-ATCATTTTAATAGC
61 TTTGGGTAAAATTAATTTATGTATTTTTTACGATATTAAAAATACAATTTCACCATTTTAATAGC
28331308 CTAAATTTTTATAA-TTAAAAAAAATTAAATTAAAATTTTATCA-TCTTTAAGGGTTAAAGTATA
126 CTAAATTTTTATAATTTAAAAAAAATTAAATTAAAATTTTATCATTC-TTAAGGGTTAAAGTATA
28331371 ATTTTACCAATACAAATTTAAAAT
190 ATTTTACCAATACAAATTTAAAAT
28331395 TTTATAAATTATATA
1 TTTATAAATTATATA
28331410 GGGACTTAAA
Statistics
Matches: 210, Mismatches: 13, Indels: 13
0.89 0.06 0.06
Matches are distributed among these distances:
213 35 0.17
214 97 0.46
215 27 0.13
216 25 0.12
217 26 0.12
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.42
Consensus pattern (213 bp):
TTTATAAATTATATAAAAAATTTATTATTAGTGAAATCAAGGGTAAAGCAAAAAAAATTTTTTGG
GTAAAATTAATTTATGTATTTTTTACGATATTAAAAATACAATTTCACCATTTTAATAGCCTAAA
TTTTTATAATTTAAAAAAAATTAAATTAAAATTTTATCATTCTTAAGGGTTAAAGTATAATTTTA
CCAATACAAATTTAAAAT
Found at i:28338884 original size:17 final size:17
Alignment explanation
Indices: 28338862--28338897 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28338852 CTAAACCATG
28338862 CTTCAAAGTTGACTCTT
1 CTTCAAAGTTGACTCTT
28338879 CTTCAAAGTTGACTCTT
1 CTTCAAAGTTGACTCTT
28338896 CT
1 CT
28338898 AAACCCATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.25, G:0.11, T:0.42
Consensus pattern (17 bp):
CTTCAAAGTTGACTCTT
Found at i:28342251 original size:17 final size:17
Alignment explanation
Indices: 28342229--28342262 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28342219 AAATAATAGT
28342229 AAAATAAAATTTTCAAC
1 AAAATAAAATTTTCAAC
28342246 AAAATAAAATTTTCAAC
1 AAAATAAAATTTTCAAC
28342263 CTCGAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAAAATTTTCAAC
Found at i:28345268 original size:13 final size:14
Alignment explanation
Indices: 28345234--28345270 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
28345224 TATTTATAAA
*
28345234 AAATATATTATTTT
1 AAATATATTATATT
28345248 AAAT-TATT-TATT
1 AAATATATTATATT
28345260 AAATATATTAT
1 AAATATATTAT
28345271 TTTCTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 7 0.35
13 8 0.40
14 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AAATATATTATATT
Found at i:28345423 original size:31 final size:30
Alignment explanation
Indices: 28345388--28345472 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
28345378 TGATGCGCAA
*
28345388 ATCAACTACCTTTTTTAGCTGAAATAATTTT
1 ATCAACTA-CTTTTTTAGCTTAAATAATTTT
28345419 ATCAAACTA-TCTTTTTAGCTTAAATAATTTT
1 ATC-AACTACT-TTTTTAGCTTAAATAATTTT
*
28345450 -T-ATCTACTTTTTTAGCTTAAATA
1 ATCAACTACTTTTTTAGCTTAAATA
28345473 CCAATTTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
28 19 0.39
29 1 0.02
30 2 0.04
31 22 0.45
32 5 0.10
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (30 bp):
ATCAACTACTTTTTTAGCTTAAATAATTTT
Found at i:28345977 original size:31 final size:30
Alignment explanation
Indices: 28345942--28346026 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
28345932 TGATGCGCAA
*
28345942 ATCAACTACCTTTTTTAGCTGAAATAATTTT
1 ATCAACTA-CTTTTTTAGCTTAAATAATTTT
28345973 ATCAAACTA-TCTTTTTAGCTTAAATAATTTT
1 ATC-AACTACT-TTTTTAGCTTAAATAATTTT
*
28346004 -T-ATCTACTTTTTTAGCTTAAATA
1 ATCAACTACTTTTTTAGCTTAAATA
28346027 CCAATTTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
28 19 0.39
29 1 0.02
30 2 0.04
31 22 0.45
32 5 0.10
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (30 bp):
ATCAACTACTTTTTTAGCTTAAATAATTTT
Found at i:28346310 original size:554 final size:556
Alignment explanation
Indices: 28345249--28346359 Score: 2208
Period size: 554 Copynumber: 2.0 Consensus size: 556
28345239 TATTATTTTA
28345249 AATTATTTATTAAATATATTATTTTCTATAAAATTTGAAACTCTTCACCCAAAATTGAGGAGTTG
1 AATTATTTATTAAATATATTATTTTCTATAAAATTTGAAACTCTTCACCCAAAATTGAGGAGTTG
28345314 GGATTAAAAAAGTAATGAGTTTTTAATTTTGAACCTGGAATAAGCTGATTCGAAAAGTGAAGGCT
66 GGATTAAAAAAGTAATGAGTTTTTAATTTTGAACCTGGAATAAGCTGATTCGAAAAGTGAAGGCT
28345379 GATGCGCAAATCAACTACCTTTTTTAGCTGAAATAATTTTATCAAACTATCTTTTTAGCTTAAAT
131 GATGCGCAAATCAACTACCTTTTTTAGCTGAAATAATTTTATCAAACTATCTTTTTAGCTTAAAT
28345444 AATTTTTATCTACTTTTTTAGCTTAAATACCAATTTAAAAACAACAACAACAAAAATCTATTGAA
196 AATTTTTATCTACTTTTTTAGCTTAAATACCAATTTAAAAACAACAACAACAAAAATCTATTGAA
28345509 CGTTATAAAGAAATTAATTACATTTTATTTTTTTACCCTAAACTTGGTAATCAAGTCTAACTTGA
261 CGTTATAAAGAAATTAATTACATTTTATTTTTTTACCCTAAACTTGGTAATCAAGTCTAACTTGA
28345574 TACTTAATATTGTTTTTAGTTTACTTCGATACCTAAATTAATAATTTGATTTATTTTGATTTTTA
326 TACTTAATATTGTTTTTAGTTTACTTCGATACCTAAATTAATAATTTGATTTATTTTGATTTTTA
28345639 AACTTAGAAAATTTAAAAGTTTAACAACGTAATACTCTAAAAATGTGTCATGTCATCAAATTTTG
391 AACTTAGAAAATTTAAAAGTTTAACAACGTAATACTCTAAAAATGTGTCATGTCATCAAATTTTG
28345704 ATAAAATCTAAATTCAAATATTTTTTTTAAATAAATTGAGTTGCCACAATTAAAAAAATAGACCT
456 ATAAAATCTAAATTCAAATATTTTTTTTAAATAAATTGAGTTGCCACAATTAAAAAAATAGACCT
28345769 ACATTAAATTATTGACCAATTGACCAAAAATTGCCC
521 ACATTAAATTATTGACCAATTGACCAAAAATTGCCC
28345805 AATTATTTA-T-AATATATTATTTTCTATAAAATTTGAAACTCTTCACCCAAAATTGAGGAGTTG
1 AATTATTTATTAAATATATTATTTTCTATAAAATTTGAAACTCTTCACCCAAAATTGAGGAGTTG
28345868 GGATTAAAAAAGTAATGAGTTTTTAATTTTGAACCTGGAATAAGCTGATTCGAAAAGTGAAGGCT
66 GGATTAAAAAAGTAATGAGTTTTTAATTTTGAACCTGGAATAAGCTGATTCGAAAAGTGAAGGCT
28345933 GATGCGCAAATCAACTACCTTTTTTAGCTGAAATAATTTTATCAAACTATCTTTTTAGCTTAAAT
131 GATGCGCAAATCAACTACCTTTTTTAGCTGAAATAATTTTATCAAACTATCTTTTTAGCTTAAAT
28345998 AATTTTTATCTACTTTTTTAGCTTAAATACCAATTTAAAAACAACAACAACAAAAATCTATTGAA
196 AATTTTTATCTACTTTTTTAGCTTAAATACCAATTTAAAAACAACAACAACAAAAATCTATTGAA
28346063 CGTTATAAAGAAATTAATTACATTTTATTTTTTTACCCTAAACTTGGTAATCAAGTCTAACTTGA
261 CGTTATAAAGAAATTAATTACATTTTATTTTTTTACCCTAAACTTGGTAATCAAGTCTAACTTGA
28346128 TACTTAATATTGTTTTTAGTTTACTTCGATACCTAAATTAATAATTTGATTTATTTTGATTTTTA
326 TACTTAATATTGTTTTTAGTTTACTTCGATACCTAAATTAATAATTTGATTTATTTTGATTTTTA
28346193 AACTTAGAAAATTTAAAAGTTTAACAACGTAATACTCTAAAAATGTGTCATGTCATCAAATTTTG
391 AACTTAGAAAATTTAAAAGTTTAACAACGTAATACTCTAAAAATGTGTCATGTCATCAAATTTTG
28346258 ATAAAATCTAAATTCAAATATTTTTTTTAAATAAATTGAGTTGCCACAATTAAAAAAATAGACCT
456 ATAAAATCTAAATTCAAATATTTTTTTTAAATAAATTGAGTTGCCACAATTAAAAAAATAGACCT
28346323 ACATTAAATTATTGACCAATTGACCAAAAATTGCCC
521 ACATTAAATTATTGACCAATTGACCAAAAATTGCCC
28346359 A
1 A
28346360 TTTCCAAAAA
Statistics
Matches: 555, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
554 545 0.98
555 1 0.00
556 9 0.02
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (556 bp):
AATTATTTATTAAATATATTATTTTCTATAAAATTTGAAACTCTTCACCCAAAATTGAGGAGTTG
GGATTAAAAAAGTAATGAGTTTTTAATTTTGAACCTGGAATAAGCTGATTCGAAAAGTGAAGGCT
GATGCGCAAATCAACTACCTTTTTTAGCTGAAATAATTTTATCAAACTATCTTTTTAGCTTAAAT
AATTTTTATCTACTTTTTTAGCTTAAATACCAATTTAAAAACAACAACAACAAAAATCTATTGAA
CGTTATAAAGAAATTAATTACATTTTATTTTTTTACCCTAAACTTGGTAATCAAGTCTAACTTGA
TACTTAATATTGTTTTTAGTTTACTTCGATACCTAAATTAATAATTTGATTTATTTTGATTTTTA
AACTTAGAAAATTTAAAAGTTTAACAACGTAATACTCTAAAAATGTGTCATGTCATCAAATTTTG
ATAAAATCTAAATTCAAATATTTTTTTTAAATAAATTGAGTTGCCACAATTAAAAAAATAGACCT
ACATTAAATTATTGACCAATTGACCAAAAATTGCCC
Found at i:28347861 original size:26 final size:26
Alignment explanation
Indices: 28347830--28347889 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
28347820 GTCTCGATAT
*
28347830 AAGGCTCTTTGTAAGCTTCCCGCTTA
1 AAGGCTCTTTGTAAGCTTCCCGATTA
*
28347856 AAGGCTCTTTGTAAGCTTCCTGATTA
1 AAGGCTCTTTGTAAGCTTCCCGATTA
*
28347882 ATGGCTCT
1 AAGGCTCT
28347890 CCTGAGCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (26 bp):
AAGGCTCTTTGTAAGCTTCCCGATTA
Found at i:28351298 original size:25 final size:24
Alignment explanation
Indices: 28351270--28351323 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
28351260 TATATTATGT
28351270 TTTTATT-TTATAAATTATTTTTGAA
1 TTTTATTATTAT-AATTATTTTT-AA
* *
28351295 TTTTTTTATTATTATTATTTTTAA
1 TTTTATTATTATAATTATTTTTAA
28351319 TTTTA
1 TTTTA
28351324 GAATTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 6 0.24
25 15 0.60
26 4 0.16
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTATTATTATAATTATTTTTAA
Found at i:28368713 original size:23 final size:21
Alignment explanation
Indices: 28368687--28368732 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
28368677 CATACTTTGT
*
28368687 TTATAGCATTTTATTATATATTA
1 TTATA-CATATTATT-TATATTA
28368710 TTATACATATTATTTATATTA
1 TTATACATATTATTTATATTA
28368731 TT
1 TT
28368733 GTTAGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 8 0.36
23 5 0.23
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATACATATTATTTATATTA
Found at i:28375719 original size:72 final size:71
Alignment explanation
Indices: 28375602--28375772 Score: 216
Period size: 72 Copynumber: 2.4 Consensus size: 71
28375592 AGATCGAGCA
* * * *
28375602 TTAGCGGCATTTTCTAAAAAGCGCTGCAATAAACATAAGCCCAACGATGCCGTTTTCTGAGCTTT
1 TTAGCGGCATTTT-TAGAAAGCGCCGCAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCTTT
28375667 CGAGGAT
65 CGAGGAT
* * * *
28375674 TTAGCGGCATTTTTGTGAAAGCGCCGCAAAAAACCTAAGCTCAACGACGCCGTTTTGTGAGCTTT
1 TTAGCGGCATTTTT-AGAAAGCGCCGCAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCTTT
* *
28375739 TGGGGAT
65 CGAGGAT
*
28375746 TTAGCGGCGTTTTTAAGAAAGCGCCGC
1 TTAGCGGCATTTTT-AGAAAGCGCCGC
28375773 TAATGCTCAG
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
71 1 0.01
72 84 0.99
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (71 bp):
TTAGCGGCATTTTTAGAAAGCGCCGCAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCTTTC
GAGGAT
Found at i:28375905 original size:73 final size:72
Alignment explanation
Indices: 28375786--28375961 Score: 253
Period size: 73 Copynumber: 2.4 Consensus size: 72
28375776 TGCTCAGGGC
* * *** *
28375786 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACGTGGTTTTGTGAGCT
1 TTTAGCGGCGTTTTT-AGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
28375851 TTGGGGGA
65 TTGGGGGA
* *
28375859 TTTAGCGGCGTTTTTCAGGATGCGCCGCAAAAAACGTAAGCCAAAACGACACCGTTTTATGAGCT
1 TTTAGCGGCGTTTTT-AGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
28375924 TTGGGGGA
65 TTGGGGGA
28375932 TTTAGCGGCGTTTTTAGGAAAGCGCCGCAA
1 TTTAGCGGCGTTTTTAGG-AAGCGCCGCAA
28375962 TGCTCAGGGC
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 3 0.03
73 89 0.97
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (72 bp):
TTTAGCGGCGTTTTTAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCTT
TGGGGGA
Found at i:28375929 original size:186 final size:185
Alignment explanation
Indices: 28375602--28376072 Score: 594
Period size: 186 Copynumber: 2.5 Consensus size: 185
28375592 AGATCGAGCA
* * * * *
28375602 TTAGCGGCATTTTCTAA-AAAGCGCTGCAATAAACATAAGCC-CAACGATGCCGTTTTCTGAGCT
1 TTAGCGGCGTTTT-TAAGAAAGCGCCGCAA-AAACCTAAGCCAAAACGATGCCGTTTTGTGAGCT
* * ** *
28375665 TTCGAGGATTTAGCGGCATTTTTGTGAAAGCGCCGCAAAAAACCTAAGCTCAACGACGCCGTTTT
64 TTCGGGGATTTAGCGGCGTTTTTCAGAAAGCGCCGCAAAAAACCTAAGCTCAACGACACCGTTTT
*
28375730 GTGAGCTTTT-GGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
129 ATGAGCTTTTGGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC-AATGCTCAGGGCT
* **
28375787 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACGTGGTTTTGTGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAA-AACCTAAGCCAAAACGATGCCGTTTTGTGAGCTT
* * * *
28375852 TGGGGGATTTAGCGGCGTTTTTCAGGATGCGCCGCAAAAAACGTAAGC-CAAAACGACACCGTTT
65 TCGGGGATTTAGCGGCGTTTTTCAGAAAGCGCCGCAAAAAACCTAAGCTC--AACGACACCGTTT
*
28375916 TATGAGC-TTTGGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCAATGCTCAGGGCT
128 TATGAGCTTTTGGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCAATGCTCAGGGCT
* ** * * *
28375973 TTAGCAGCGTTTTCGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCATTTTGTGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGC-AAAAACCTAAGCCAAAACGATGCCGTTTTGTGAGCTT
*
28376038 TCGGGGATTTAGCGGCGTTTTT-ATGTAAGCGCCGC
65 TCGGGGATTTAGCGGCGTTTTTCA-GAAAGCGCCGC
28376073 TAATGCTCAG
Statistics
Matches: 247, Mismatches: 31, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
184 4 0.02
185 34 0.14
186 156 0.63
187 53 0.21
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (185 bp):
TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAACCTAAGCCAAAACGATGCCGTTTTGTGAGCTTT
CGGGGATTTAGCGGCGTTTTTCAGAAAGCGCCGCAAAAAACCTAAGCTCAACGACACCGTTTTAT
GAGCTTTTGGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCAATGCTCAGGGCT
Found at i:28376131 original size:114 final size:111
Alignment explanation
Indices: 28375859--28376186 Score: 442
Period size: 113 Copynumber: 2.9 Consensus size: 111
28375849 CTTTGGGGGA
* * * * *
28375859 TTTAGCGGCGTTTTTCAGGATGCGCCGCAAAAAACGTAAGCCAAAACGACACCGTTTTATGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCT
28375924 TTGGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCAATGCTCAGGGC
66 TT-GGGGATTTAGCGGCGTTTTTA-GAAAGCGCCGCAATGCTCAGGGC
* ** * * * * *
28375972 TTTAGCAGCGTTTTCGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCATTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCT
*
28376037 TTCGGGGATTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGCTCAGGGC
66 TT-GGGGATTTAGCGGCGTTTTTA-GAAAGCGCCGC-AATGCTCAGGGC
* *
28376086 TTTAGCGGCGTTTTTAATAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCT
*
28376151 TT-GGGATTTAGCGGCGTTTTTGAGGAAGCGCCGCAA
66 TTGGGGATTTAGCGGCGTTTTT-AGAAAGCGCCGCAA
28376187 AAAACCTAAG
Statistics
Matches: 187, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
111 2 0.01
112 29 0.16
113 87 0.47
114 69 0.37
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (111 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCT
TTGGGGATTTAGCGGCGTTTTTAGAAAGCGCCGCAATGCTCAGGGC
Found at i:28376202 original size:71 final size:71
Alignment explanation
Indices: 28376086--28376257 Score: 256
Period size: 71 Copynumber: 2.4 Consensus size: 71
28376076 TGCTCAGGGC
** **
28376086 TTTAGCGGCGTTTTTAATAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCT
1 TTTAGCGGCGTTTTT-AGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
28376151 TT-GGGA
65 TTCGGGA
28376157 TTTAGCGGCGTTTTTGAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
1 TTTAGCGGCGTTTTT-AGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
28376222 TTCGGGGA
65 TTC-GGGA
*
28376230 TTTAGCGACGTTTTTAGGAAAGCGCCGC
1 TTTAGCGGCGTTTTTAGG-AAGCGCCGC
28376258 TAATGCTCAG
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
71 62 0.67
72 3 0.03
73 27 0.29
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (71 bp):
TTTAGCGGCGTTTTTAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCTT
TCGGGA
Found at i:28376222 original size:185 final size:186
Alignment explanation
Indices: 28375972--28376444 Score: 680
Period size: 185 Copynumber: 2.5 Consensus size: 186
28375962 TGCTCAGGGC
* * * * ** *
28375972 TTTAGCAGCGTTTTCGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCATTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTGTGAGCT
* *
28376037 TTCGGGGATTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
66 TTCGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
* * * *
28376102 ATAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCTTT-GGGA
131 AGAAAGCGCCACAAAAAACCTAAGCCAAAACAACGCCGTTTTATGAGCTTTCGGGA
* *
28376157 TTTAGCGGCGTTTTTGAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTGTGAGCT
* *
28376222 TTCGGGGATTTAGCGACGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
66 TTCGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
* * *
28376287 AGAAAGCGCCACAGAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCTTTCGGGGA
131 AGAAAGCGCCACAAAAAACCTAAGCCAAAACAACGCCGTTTTATGAGCTTTC-GGGA
* * * *
28376344 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACATCGCTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTGTGAGCT
* *
28376409 TTGGGGGATTTAGCGGCGTTTATGAGG-AAGCGCCGC
66 TTCGGGGATTTAGCGGCGTTT-TTAGGAAAGCGCCGC
28376445 AAAAAACCTA
Statistics
Matches: 256, Mismatches: 29, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
185 161 0.63
187 91 0.36
188 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (186 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTGTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
AGAAAGCGCCACAAAAAACCTAAGCCAAAACAACGCCGTTTTATGAGCTTTCGGGA
Found at i:28376305 original size:114 final size:114
Alignment explanation
Indices: 28376157--28376371 Score: 349
Period size: 114 Copynumber: 1.9 Consensus size: 114
28376147 AGCTTTGGGA
* * *
28376157 TTTAGCGGCGTTTTTGAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAACACCGTTTTATGAGCT
*
28376222 TTCGGGGATTTAGCGACGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* ** *
28376271 TTTAGCGGCGTTTTTGAGAAAGCGCCACAGAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAACACCGTTTTATGAGCT
*
28376336 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
66 TTCGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGC
28376372 AAAGAACCTA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 92 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAACACCGTTTTATGAGCT
TTCGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:28376369 original size:299 final size:299
Alignment explanation
Indices: 28375673--28376371 Score: 1161
Period size: 299 Copynumber: 2.3 Consensus size: 299
28375663 CTTTCGAGGA
* * * * *
28375673 TTTAGCGGCATTTTTGTGAAAGCGCCGCAAAAAACCTAAGCTC--AACGACGCCGTTTTGTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGC-CAAAACAATGCCGTTTTGTGAGC
*
28375736 TTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTT
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTT
* * *
28375801 AAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACGTGGTTTTGTGAGCTTTGGGGGATTTAGCG
130 AAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCTTT-GGGGATTTAGCG
* * *
28375866 GCGTTTTTCAGGATGCGCCGCAAAAAACGTAAGCCAAAACGACACCGTTTTATGAGCTTTGGGGG
194 GCGTTTTTCAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCTTTCGGGG
*
28375931 ATTTAGCGGCGTTTTTAGGAAAGCGCCGCAATGCTCAGGGC
259 ATTTAGCGACGTTTTTAGGAAAGCGCCGCAATGCTCAGGGC
* * *
28375972 TTTAGCAGCGTTTTCGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCATTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCT
* *
28376037 TTCGGGGATTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
*
28376102 ATAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCTTT-GGGATTTAGCGGC
131 AGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCTTTGGGGATTTAGCGGC
*
28376166 GTTTTTGAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCTTTCGGGGAT
196 GTTTTTCAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCTTTCGGGGAT
28376231 TTAGCGACGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
261 TTAGCGACGTTTTTAGGAAAGCGCCGC-AATGCTCAGGGC
*
28376271 TTTAGCGGCGTTTTTGAGAAAGCGCCACAGAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCT
28376336 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
28376372 AAAGAACCTA
Statistics
Matches: 371, Mismatches: 26, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
298 101 0.27
299 143 0.39
300 127 0.34
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (299 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
AGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCTTTGGGGATTTAGCGGC
GTTTTTCAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCTTTCGGGGAT
TTAGCGACGTTTTTAGGAAAGCGCCGCAATGCTCAGGGC
Found at i:28376390 original size:73 final size:69
Alignment explanation
Indices: 28376271--28376510 Score: 290
Period size: 73 Copynumber: 3.4 Consensus size: 69
28376261 TGCTCAGGGC
* *
28376271 TTTAGCGGCGTTTTTGAGAAAGCGCCACAGAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCA-AAAACCTAAGCCAAAACAAT--CG-TTTGTGAGCT
28376336 TTCGGGGA
62 TTCGGGGA
28376344 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACATCGCTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAA-AACCTAAGCCAAAAC-A-ATCG-TTTGTGAGCT
*
28376409 TTGGGGGA
62 TTCGGGGA
* * * * *
28376417 TTTAGCGGCGTTTATGAGGAAGCGCCGCAAAAAACCTAAGCC--AA-AA-CGATTATGAGCTTTC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGC-AAAAACCTAAGCCAAAACAATCGTTTGTGAGCTTTC
28376478 GGGGA
65 GGGGA
*
28376483 TTTAGCGGCGTTTTTAGGAAAGCGCCGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGC
28376511 TAATGCTTAG
Statistics
Matches: 149, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
66 39 0.26
67 2 0.01
68 1 0.01
69 1 0.01
71 2 0.01
72 2 0.01
73 96 0.64
74 4 0.03
75 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (69 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAACCTAAGCCAAAACAATCGTTTGTGAGCTTTCG
GGGA
Found at i:28376713 original size:14 final size:14
Alignment explanation
Indices: 28376694--28376798 Score: 61
Period size: 14 Copynumber: 7.4 Consensus size: 14
28376684 TATCACTATA
*
28376694 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
28376708 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* **
28376722 GTTTAGAGTTTAAA
1 GTTTAGGGTTTATG
*
28376736 GTTTAGGTGTTACCAT-
1 GTTTAGG-GTT--TATG
*
28376752 -TTTAAGGTTTATG
1 GTTTAGGGTTTATG
* *
28376765 GATTATGGGTTTAGG
1 GTTTA-GGGTTTATG
* *
28376780 GGTTATGGTTTATG
1 GTTTAGGGTTTATG
28376794 GTTTA
1 GTTTA
28376799 AAGGCTGGGG
Statistics
Matches: 67, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
12 2 0.03
14 45 0.67
15 19 0.28
17 1 0.01
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.48
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:28376777 original size:22 final size:21
Alignment explanation
Indices: 28376752--28376799 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
28376742 GTGTTACCAT
*
28376752 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGGTTATGGATTAT-GG
* *
28376774 TTTAGGGGTTATGGTTTATGG
1 TTTAAGGGTTATGGATTATGG
28376795 TTTAA
1 TTTAA
28376800 AGGCTGGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (21 bp):
TTTAAGGGTTATGGATTATGG
Found at i:28376993 original size:26 final size:26
Alignment explanation
Indices: 28376942--28376993 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
28376932 GATAATATTA
*
28376942 ATTTGGTTCTTCAAAATCATGTGAAG
1 ATTTGGTTCTTCAAAATCATGAGAAG
28376968 ATTTGGTTCTTCAAAATCGAT-AGAAG
1 ATTTGGTTCTTCAAAATC-ATGAGAAG
28376994 CTATATCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (26 bp):
ATTTGGTTCTTCAAAATCATGAGAAG
Found at i:28377188 original size:21 final size:21
Alignment explanation
Indices: 28377164--28377217 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
28377154 ATTTAAAGGT
28377164 TTAGGGGTTAGTAGTTAGGG-G
1 TTAGGGGTTAG-AGTTAGGGAG
* *
28377185 TTAGAGGTTAAGAGTTAGGGAT
1 TTAGGGGTT-AGAGTTAGGGAG
28377207 TTAGGGGTTAG
1 TTAGGGGTTAG
28377218 GATTTAGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (21 bp):
TTAGGGGTTAGAGTTAGGGAG
Found at i:28377220 original size:14 final size:14
Alignment explanation
Indices: 28377163--28377225 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
28377153 GATTTAAAGG
*
28377163 TTTAGGGGTTAGTA
1 TTTAGGGGTTAGGA
*
28377177 GTTAGGGGTTA-GA
1 TTTAGGGGTTAGGA
* * *
28377190 GGTTAAGAGTTAGGGA
1 -TTTAGGGGTTA-GGA
28377206 TTTAGGGGTTAGGA
1 TTTAGGGGTTAGGA
28377220 TTTAGG
1 TTTAGG
28377226 AATTTAAGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
13 1 0.03
14 28 0.72
15 8 0.21
16 2 0.05
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (14 bp):
TTTAGGGGTTAGGA
Found at i:28377224 original size:22 final size:21
Alignment explanation
Indices: 28377161--28377251 Score: 87
Period size: 22 Copynumber: 4.3 Consensus size: 21
28377151 GGGATTTAAA
*
28377161 GGTTTAGGGGTTAGTAGTTAG
1 GGTTTAGGGGTTAGGAGTTAG
* * *
28377182 GGGTTAGAGGTTAAGAGTTAG
1 GGTTTAGGGGTTAGGAGTTAG
*
28377203 GGATTTAGGGGTTAGGATTTAG
1 GG-TTTAGGGGTTAGGAGTTAG
* *
28377225 GAATTTAAGGGTT-GG-GTTAG
1 G-GTTTAGGGGTTAGGAGTTAG
28377245 GGTTTAG
1 GGTTTAG
28377252 ATTAATTACT
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
19 4 0.07
20 5 0.09
21 21 0.38
22 25 0.45
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (21 bp):
GGTTTAGGGGTTAGGAGTTAG
Found at i:28377514 original size:29 final size:29
Alignment explanation
Indices: 28377481--28377554 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
28377471 TATTTTTCGT
28377481 GATTTAAAATTTTAAAATAAATTTT-AAAA
1 GATTTAAAATTTTAAAA-AAATTTTAAAAA
*
28377510 GATTTCAAAATTTTTAAAAAATTTTAAAAA
1 GATTT-AAAATTTTAAAAAAATTTTAAAAA
*
28377540 GAATTTAAACTTTTA
1 G-ATTTAAAATTTTA
28377555 TTTTTATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 12 0.31
30 23 0.59
31 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (29 bp):
GATTTAAAATTTTAAAAAAATTTTAAAAA
Found at i:28377526 original size:19 final size:19
Alignment explanation
Indices: 28377502--28377538 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28377492 TTAAAATAAA
*
28377502 TTTTAAAAGATTTCAAAAT
1 TTTTAAAAAATTTCAAAAT
*
28377521 TTTTAAAAAATTTTAAAA
1 TTTTAAAAAATTTCAAAA
28377539 AGAATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (19 bp):
TTTTAAAAAATTTCAAAAT
Found at i:28377529 original size:10 final size:10
Alignment explanation
Indices: 28377486--28377539 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
28377476 TTCGTGATTT
28377486 AAAATTTTAAA
1 AAAATTTT-AA
28377497 ATAAATTTTAA
1 A-AAATTTTAA
* *
28377508 AAGA-TTTCA
1 AAAATTTTAA
*
28377517 AAATTTTTAA
1 AAAATTTTAA
28377527 AAAATTTTAA
1 AAAATTTTAA
28377537 AAA
1 AAA
28377540 GAATTTAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
9 6 0.17
10 18 0.51
11 4 0.11
12 7 0.20
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:28379021 original size:20 final size:20
Alignment explanation
Indices: 28378982--28379023 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
28378972 TTGTTAGAGT
*
28378982 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
28379002 TAATATAGTCAAAACCGTTG
1 TAATATAGTCAAAACAGTTG
28379022 TA
1 TA
28379024 CCGTTGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:28379052 original size:15 final size:15
Alignment explanation
Indices: 28379032--28379062 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28379022 TACCGTTGTA
28379032 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
28379047 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
28379062 A
1 A
28379063 AAGATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:28383732 original size:20 final size:20
Alignment explanation
Indices: 28383707--28383749 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
28383697 ATGTTAGAGT
*
28383707 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
28383727 TAATATAGTCAAAACCGTTG
1 TAATATAGTCAAAACAGTTG
28383747 TAA
1 TAA
28383750 GTCTGTTAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:28383769 original size:15 final size:15
Alignment explanation
Indices: 28383749--28383779 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28383739 AACCGTTGTA
28383749 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
28383764 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
28383779 A
1 A
28383780 AAGATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:28385909 original size:23 final size:23
Alignment explanation
Indices: 28385883--28385948 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
28385873 ATATGTTGTT
28385883 AATTGATA-TGTTAAAGTGCTGCA
1 AATTGA-AGTGTTAAAGTGCTGCA
*
28385906 AATTGAAGTGTTTAAA-TGCTGTA
1 AATTGAAGTG-TTAAAGTGCTGCA
*
28385929 ACTTGAAGTGTTAAAGTGCT
1 AATTGAAGTGTTAAAGTGCT
28385949 ACTTTCCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.16
23 27 0.71
24 5 0.13
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (23 bp):
AATTGAAGTGTTAAAGTGCTGCA
Found at i:28388062 original size:23 final size:23
Alignment explanation
Indices: 28388028--28388106 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 23
28388018 TTTGGTTTAA
28388028 TTTA-TTTTTATATTATATCTAT
1 TTTATTTTTTATATTATATCTAT
28388050 TTTATTTTTTATA-TATATTCTAAT
1 TTTATTTTTTATATTATA-TCT-AT
*
28388074 TTTATTTATT-TATT-T-T-TAT
1 TTTATTTTTTATATTATATCTAT
28388093 TTCTATTTTTTATA
1 TT-TATTTTTTATA
28388107 CATTATATAC
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
19 4 0.08
20 8 0.16
21 3 0.06
22 8 0.16
23 14 0.29
24 12 0.24
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTATTTTTTATATTATATCTAT
Found at i:28388093 original size:25 final size:25
Alignment explanation
Indices: 28388027--28388102 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
28388017 TTTTGGTTTA
28388027 ATTTATTT-TTATATTATATCT-ATTTT
1 ATTTATTTATT-T-TTAT-TCTAATTTT
* *
28388053 ATTT-TTTATATATATTCTAATTTT
1 ATTTATTTATTTTTATTCTAATTTT
*
28388077 ATTTATTTATTTTTATTTCTATTTTT
1 ATTTATTTATTTTTA-TTCTAATTTT
28388103 TATACATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
23 3 0.07
24 12 0.29
25 12 0.29
26 14 0.34
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (25 bp):
ATTTATTTATTTTTATTCTAATTTT
Found at i:28388993 original size:23 final size:24
Alignment explanation
Indices: 28388959--28389011 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
28388949 TTTGGTTTAA
28388959 TTTA-TTTTTATAT-TATATCT-AT
1 TTTATTTTTTATATATAT-TCTAAT
28388981 TTTATTTTTTATATATATTCTAAT
1 TTTATTTTTTATATATATTCTAAT
28389005 TTTATTT
1 TTTATTT
28389012 ACTCTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.14
23 12 0.43
24 12 0.43
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTATTTTTTATATATATTCTAAT
Found at i:28390865 original size:23 final size:23
Alignment explanation
Indices: 28390834--28390886 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
28390824 TTTTGTTATG
* *
28390834 TATATATATGCATGCATATATTTT
1 TATA-ATATACATACATATATTTT
* *
28390858 TATAATATACGTACATATTTTTT
1 TATAATATACATACATATATTTT
28390881 TATAAT
1 TATAAT
28390887 TTATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.51
Consensus pattern (23 bp):
TATAATATACATACATATATTTT
Found at i:28390893 original size:2 final size:2
Alignment explanation
Indices: 28390888--28390963 Score: 52
Period size: 2 Copynumber: 39.5 Consensus size: 2
28390878 TTTTATAATT
* * *
28390888 TA TA TA TA TA CA TA CT- TA TA TA TA TA TT TA T- TA TA TC T- TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
28390928 TA -A TT TA TA TA TA TA TA TA TA TG TA CA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28390964 CTTTTTGCAT
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
1 4 0.07
2 51 0.91
3 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28390899 original size:27 final size:27
Alignment explanation
Indices: 28390881--28390963 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 27
28390871 CATATTTTTT
28390881 TATA-ATTTATATATATACATACTTATA
1 TATATATTTAT-TATATACATACTTATA
*
28390908 TATATATTTATTATAT-CTTATAATT-TA
1 TATATATTTATTATATAC--ATACTTATA
* * *
28390935 TATATATATATATATGTACATACATATA
1 TATATATTTAT-TATATACATACTTATA
28390963 T
1 T
28390964 CTTTTTGCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
26 1 0.02
27 25 0.56
28 18 0.40
29 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (27 bp):
TATATATTTATTATATACATACTTATA
Found at i:28395591 original size:42 final size:41
Alignment explanation
Indices: 28395483--28395602 Score: 116
Period size: 41 Copynumber: 2.9 Consensus size: 41
28395473 GCACTTTAAC
* ** * *
28395483 AAAACGCCACTAAAACCCTTAGAATTAGCGGCAG-TTACTAA
1 AAAACGCCGCTAAAACCCCAAGCATTAGCGGC-GCTTAATAA
** * * *
28395524 AAAACGCCGCTAAAAGTCTAAGCATTAGTGGTGCTTAATAA
1 AAAACGCCGCTAAAACCCCAAGCATTAGCGGCGCTTAATAA
*
28395565 AAAACGCCGCTAAAAACCCCGAGCATTAGCGGCGCTTA
1 AAAACGCCGCT-AAAACCCCAAGCATTAGCGGCGCTTA
28395603 CCTAAAACCG
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
40 1 0.02
41 42 0.67
42 20 0.32
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
AAAACGCCGCTAAAACCCCAAGCATTAGCGGCGCTTAATAA
Found at i:28395619 original size:83 final size:82
Alignment explanation
Indices: 28395483--28395634 Score: 184
Period size: 83 Copynumber: 1.8 Consensus size: 82
28395473 GCACTTTAAC
** *
28395483 AAAACGCCACTAAAACCCTTAGAATTAGCGGCAGTTACTAAAAAACGCCGCTAAAAGTCTA-AGC
1 AAAACGCCACTAAAACCCCGAGAATTAGCGGCAGTTACTAAAAAACGCAGCTAAAAG-CTAGAGC
28395547 ATTAGTGGTGCTTAATAA
65 ATTAGTGGTGCTTAATAA
* * * *
28395565 AAAACGCCGCTAAAAACCCCGAGCATTAGCGGC-GCTTACCT-AAAACCGCAGCTAATAGCTAGA
1 AAAACGCCACT-AAAACCCCGAGAATTAGCGGCAG-TTA-CTAAAAAACGCAGCTAAAAGCTAGA
28395628 GCATTAG
63 GCATTAG
28395635 CAGCGCTACG
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
82 14 0.24
83 43 0.73
84 2 0.03
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (82 bp):
AAAACGCCACTAAAACCCCGAGAATTAGCGGCAGTTACTAAAAAACGCAGCTAAAAGCTAGAGCA
TTAGTGGTGCTTAATAA
Found at i:28396061 original size:15 final size:17
Alignment explanation
Indices: 28396041--28396073 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
28396031 TTGGTAGAGA
28396041 ATTGATTT-AT-TCGAG
1 ATTGATTTGATATCGAG
28396056 ATTGATTTGATATCGAG
1 ATTGATTTGATATCGAG
28396073 A
1 A
28396074 GAAAAAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.42
Consensus pattern (17 bp):
ATTGATTTGATATCGAG
Found at i:28401550 original size:73 final size:72
Alignment explanation
Indices: 28401436--28401578 Score: 241
Period size: 73 Copynumber: 2.0 Consensus size: 72
28401426 TCTTTTCAAA
* * * *
28401436 CTCAAGTTTTAAACGATCTCAGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACAATCTCAAGAATTAAGAAAAGACCGTGTCCTAACTTACT-GGCATGATCCC
28401501 TTTTTTTT
65 TTTTTTTT
28401509 CTCAAGTTTTAAACAATCTCAAGAATTAAGAAAAGACCGTGTCCTAACTTACTGGCATGATCCCT
1 CTCAAGTTTTAAACAATCTCAAGAATTAAGAAAAGACCGTGTCCTAACTTACTGGCATGATCCCT
28401574 TTTTT
66 TTTTT
28401579 AAATCTGAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
72 17 0.26
73 49 0.74
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (72 bp):
CTCAAGTTTTAAACAATCTCAAGAATTAAGAAAAGACCGTGTCCTAACTTACTGGCATGATCCCT
TTTTTTT
Found at i:28408307 original size:40 final size:40
Alignment explanation
Indices: 28408249--28408325 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
28408239 TCGAGTGGAT
*
28408249 TATGTTAGATATTTGTCCCTATGAACCTGGAAGTGTTAGA
1 TATGTTAGATATTCGTCCCTATGAACCTGGAAGTGTTAGA
28408289 TATGTTAGATATTCGTCCCTATGAACCTGGAAGTGTT
1 TATGTTAGATATTCGTCCCTATGAACCTGGAAGTGTT
28408326 CTAAATAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (40 bp):
TATGTTAGATATTCGTCCCTATGAACCTGGAAGTGTTAGA
Found at i:28413804 original size:44 final size:44
Alignment explanation
Indices: 28413421--28413985 Score: 263
Period size: 44 Copynumber: 12.6 Consensus size: 44
28413411 AAGATAATAG
* * *
28413421 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCGA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CCA
* * * *
28413466 ATCTTATTTTCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAGATTACA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT--A--CCA
* * * * * *
28413516 GATTTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T-CATAT-CAA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* * * * * * *
28413558 ACCTTATCTCCCTAAAGTTGCAATGGAGCAGGTTAAAAATAAATCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT--ACCA
* * * *
28413604 ATTTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAAACGGGTTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG--AA---GATACCA
* * * *
28413653 ATCTTATCTCCCTAAAGTTGCAGCGGAGAAGATGGAAGCCATA--A
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--ATACCA
* * * * *
28413697 ACCTTATCCCCCTGAAGTTACAGTGGGGCAGGTTGAA-ATTA-CA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TACCA
* * *
28413740 AGTCTTATCCCCCTGAAGTTGCAATGGAGCAGGTTGAAGATACCA
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* * * * *
28413785 ATCTTATCTCTCTGAAGTTGCGGTGGAGCAAATTGAAGTTACTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* * * * ** * ***
28413829 GTCCTATCTCTCTGAAGTTGCAGAGGAGTGGATT-AAAATGATGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ACCA
* * * * * *
28413873 ATCTTATTTCTCTAAAGTTGCAGTAGAGCAGA-T---CATATCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* * * * * *
28413913 AACATTATCTTCTTGAAGTTGCGGTGGAGCAGATTGAAGTTACTA
1 ATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* * *
28413958 GTCCTATCTCCCTGAAGTTGCAGAGGAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAG
28413986 TGGATCAAAA
Statistics
Matches: 381, Mismatches: 110, Indels: 59
0.69 0.20 0.11
Matches are distributed among these distances:
40 4 0.01
41 50 0.13
42 5 0.01
43 9 0.02
44 171 0.45
45 41 0.11
46 31 0.08
47 6 0.02
48 2 0.01
49 33 0.09
50 2 0.01
51 27 0.07
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
Found at i:28413949 original size:129 final size:129
Alignment explanation
Indices: 28413788--28414050 Score: 431
Period size: 129 Copynumber: 2.0 Consensus size: 129
28413778 GATACCAATC
*
28413788 TTATCTCTCTGAAGTTGCGGTGGAGCAAATTGAAGTTACTAGTCCTATCTCTCTGAAGTTGCAGA
1 TTATCTCTCTGAAGTTGCGGTGGAGCAAATTGAAGTTACTAGTCCTATCTCCCTGAAGTTGCAGA
* *
28413853 GGAGTGGATTAAAATGATGGATCTTATTTCTCTAAAGTTGCA-GTAGAGCAGATCATATCAAACA
66 GGAGTGGATCAAAATGATGGATCTTATCTCTCTAAAGTTG-AGGTAGAGCAGATCATATCAAACA
*
28413917 TTATCT-TCTTGAAGTTGCGGTGGAGCAGATTGAAGTTACTAGTCCTATCTCCCTGAAGTTGCAG
1 TTATCTCTC-TGAAGTTGCGGTGGAGCAAATTGAAGTTACTAGTCCTATCTCCCTGAAGTTGCAG
* * *
28413981 AGGAGTGGATCAAAATTATGGATCTTATCTCTCTGAAGTTGAGGTAGAGCAGATCATATCAAACC
65 AGGAGTGGATCAAAATGATGGATCTTATCTCTCTAAAGTTGAGGTAGAGCAGATCATATCAAACA
28414046 TTATC
1 TTATC
28414051 CCCCAGAAGT
Statistics
Matches: 125, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
128 3 0.02
129 122 0.98
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (129 bp):
TTATCTCTCTGAAGTTGCGGTGGAGCAAATTGAAGTTACTAGTCCTATCTCCCTGAAGTTGCAGA
GGAGTGGATCAAAATGATGGATCTTATCTCTCTAAAGTTGAGGTAGAGCAGATCATATCAAACA
Found at i:28414102 original size:129 final size:129
Alignment explanation
Indices: 28413832--28414105 Score: 311
Period size: 129 Copynumber: 2.1 Consensus size: 129
28413822 GTTACTAGTC
* *
28413832 CTATCTCTCTGAAGTTGCAGAGGAGTGGATTAAAATGATGGATCTTATTTCTCTAAAGTTGCAGT
1 CTATCTCTCTGAAGTTGCAGAGGAGTGGATCAAAATGATGGATCTTATCTCTCTAAAGTTGCAGT
** ** * * * *** * * *
28413897 AGAGCAGATCATATCAAACATTATCTTCTTGAAGTTGCGGTGGAGCAGATTGAAGTTACTAGTC
66 AGAGCAGATCATATCAAACATTATCCCCCAGAAGTTGCAGCGGAGCAGATTAAAAACAATAATA
* * *
28413961 CTATCTCCCTGAAGTTGCAGAGGAGTGGATCAAAATTATGGATCTTATCTCTCTGAAGTTG-AGG
1 CTATCTCTCTGAAGTTGCAGAGGAGTGGATCAAAATGATGGATCTTATCTCTCTAAAGTTGCA-G
* * *
28414025 TAGAGCAGATCATATCAAACCTTATCCCCCAGAAGTTGTAGCGGAGCGGA-TAAAAACAATGAAT
65 TAGAGCAGATCATATCAAACATTATCCCCCAGAAGTTGCAGCGGAGCAGATTAAAAACAAT-AAT
28414089 A
129 A
28414090 CTATAC-CTCTGAAGTT
1 CTAT-CTCTCTGAAGTT
28414106 ACAGTAGGTT
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
128 6 0.05
129 113 0.94
130 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (129 bp):
CTATCTCTCTGAAGTTGCAGAGGAGTGGATCAAAATGATGGATCTTATCTCTCTAAAGTTGCAGT
AGAGCAGATCATATCAAACATTATCCCCCAGAAGTTGCAGCGGAGCAGATTAAAAACAATAATA
Found at i:28416033 original size:73 final size:73
Alignment explanation
Indices: 28415952--28416095 Score: 270
Period size: 73 Copynumber: 2.0 Consensus size: 73
28415942 TCTTTTCAAA
*
28415952 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAGAGATCGTATCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTATCCTAACTTACTGGGCATGATCCC
28416017 TTTTTTTT
66 TTTTTTTT
*
28416025 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTATCCTAACTTACTGGGCATGATCCC
28416090 TTTTTT
66 TTTTTT
28416096 AAATCTGAGA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (73 bp):
CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTATCCTAACTTACTGGGCATGATCCC
TTTTTTTT
Found at i:28417160 original size:22 final size:19
Alignment explanation
Indices: 28417120--28417163 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
28417110 TGTTGTTTTA
*
28417120 TTGCTATTTTTCCATTGTT
1 TTGCTATTTTTCCACTGTT
28417139 TTGCTATTGCTTTCCCACTGTT
1 TTGCTATT--TTT-CCACTGTT
28417161 TTG
1 TTG
28417164 ATACCATTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.09, C:0.20, G:0.14, T:0.57
Consensus pattern (19 bp):
TTGCTATTTTTCCACTGTT
Found at i:28418921 original size:41 final size:40
Alignment explanation
Indices: 28418876--28419043 Score: 161
Period size: 40 Copynumber: 4.2 Consensus size: 40
28418866 AAATAGGGTT
* * *
28418876 TTAGCGGCG-TTTGGACAAAAAACGCCACTAAAAATCGAGCA
1 TTAGCGGCGCTTT-GAC-AAAAACGCCGCTAAAGATCGAGTA
*
28418917 TTAGCGGCGCTTT-ACGTAAAACGCCGCTAAAGATCGAGTA
1 TTAGCGGCGCTTTGAC-AAAAACGCCGCTAAAGATCGAGTA
28418957 TTAGCGGCGCATTTTG--AAAAACGCCGCTAAAGATCGAGTA
1 TTAGCGGCGC--TTTGACAAAAACGCCGCTAAAGATCGAGTA
* * *
28418997 TTAGCGGTGCATTTTG--AAAAACGCCGCTAAAAAT-AAGTA
1 TTAGCGGCGC--TTTGACAAAAACGCCGCTAAAGATCGAGTA
28419036 TTAGCGGC
1 TTAGCGGC
28419044 ATTTTCCAAG
Statistics
Matches: 113, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
39 11 0.10
40 87 0.77
41 9 0.08
42 6 0.05
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGCTTTGACAAAAACGCCGCTAAAGATCGAGTA
Found at i:28419062 original size:39 final size:40
Alignment explanation
Indices: 28418893--28419043 Score: 207
Period size: 40 Copynumber: 3.8 Consensus size: 40
28418883 CGTTTGGACA
* * *
28418893 AAAAACGCCACTAAAAATCGAGCATTAGCGGCGC-TTTACG
1 AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCATTT-TG
* *
28418933 TAAAACGCCGCTAAAGATCGAGTATTAGCGGCGCATTTTG
1 AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCATTTTG
* *
28418973 AAAAACGCCGCTAAAGATCGAGTATTAGCGGTGCATTTTG
1 AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCATTTTG
*
28419013 AAAAACGCCGCTAAAAAT-AAGTATTAGCGGC
1 AAAAACGCCGCTAAAAATCGAGTATTAGCGGC
28419044 ATTTTCCAAG
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 11 0.11
40 86 0.86
41 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCATTTTG
Found at i:28419068 original size:39 final size:39
Alignment explanation
Indices: 28418934--28419068 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 39
28418924 CGCTTTACGT
* * * * *
28418934 AAAACGCCGCTAAAGATCGAGTATTAGCGGCGCATTTTGA
1 AAAACGCCGCAAAAAAT-AAGTATTAGCGGTGCATTTTCA
* * * *
28418974 AAAACGCCGCTAAAGATCGAGTATTAGCGGTGCATTTTGA
1 AAAACGCCGCAAAAAAT-AAGTATTAGCGGTGCATTTTCA
*
28419014 AAAACGCCGCTAAAAATAAGTATTAGC-G-GCATTTTCCA
1 AAAACGCCGCAAAAAATAAGTATTAGCGGTGCATTTT-CA
*
28419052 AGAAGCGCCGCAAAAAA
1 A-AAACGCCGCAAAAAA
28419069 AGGAAAGCGG
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
37 7 0.08
38 3 0.03
39 22 0.25
40 55 0.63
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (39 bp):
AAAACGCCGCAAAAAATAAGTATTAGCGGTGCATTTTCA
Found at i:28419166 original size:41 final size:41
Alignment explanation
Indices: 28419109--28419277 Score: 239
Period size: 41 Copynumber: 4.1 Consensus size: 41
28419099 TTTTGAGGCA
*
28419109 TTTAGCGGCGTTTTTGGGAAAGTGCCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
28419150 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
* ** *
28419191 TTTAGCTGCGTTTTTGGGAAAGCGCCGCTAATGCTCAAGGA
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
** * * * *
28419232 TTTAGCGGCGTTTTTTAGAATGTGCCGCTAATGCTCGTGCC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
28419273 TTTAG
1 TTTAG
28419278 TTCAAAAACG
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 114 1.00
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
Found at i:28420772 original size:109 final size:109
Alignment explanation
Indices: 28420604--28420891 Score: 472
Period size: 109 Copynumber: 2.7 Consensus size: 109
28420594 GTCAATCGAG
* * * *
28420604 AAATCGAAACCCAGCACATTAGGGCACG-TTCCTCGAATTTCCAAACGCTAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* * * *
28420668 TTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAATGAGAA
66 TTGAAAATTTTAAAAGGACATTTAACCATTTGGTTGAACGAGAA
28420712 AAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
*
28420777 TTAAAAATTTTAAAAGGACATTTAACCATTTGGTTGAACGAGAA
66 TTGAAAATTTTAAAAGGACATTTAACCATTTGGTTGAACGAGAA
*
28420821 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTA-T
1 AAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
28420885 TTGAAAA
66 TTGAAAA
28420892 AATTTCCTTT
Statistics
Matches: 168, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
108 33 0.20
109 135 0.80
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (109 bp):
AAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TTGAAAATTTTAAAAGGACATTTAACCATTTGGTTGAACGAGAA
Found at i:28421896 original size:12 final size:12
Alignment explanation
Indices: 28421866--28421901 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
28421856 ACTGCTTTTA
* *
28421866 ATATATATATAT
1 ATATATGTATGT
28421878 ATATATGTATGT
1 ATATATGTATGT
28421890 ATATATGTATGT
1 ATATATGTATGT
28421902 GAAAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (12 bp):
ATATATGTATGT
Found at i:28422895 original size:20 final size:20
Alignment explanation
Indices: 28422873--28422935 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
28422863 TTCGTGATTT
28422873 AAAATTTTAAAATGAATTTTA
1 AAAATTTTAAAATG-ATTTTA
**
28422894 AAAGATTTT-AAATCTTTTTA
1 AAA-ATTTTAAAATGATTTTA
*
28422914 AAAATTTTAAAAAGATTTTA
1 AAAATTTTAAAATGATTTTA
28422934 AA
1 AA
28422936 CTTTTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.14
20 18 0.51
21 7 0.20
22 5 0.14
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.43
Consensus pattern (20 bp):
AAAATTTTAAAATGATTTTA
Found at i:28422903 original size:10 final size:10
Alignment explanation
Indices: 28422876--28422935 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
28422866 GTGATTTAAA
28422876 ATTTTAAAATG
1 ATTTTAAAA-G
28422887 AATTTTAAAAG
1 -ATTTTAAAAG
**
28422898 ATTTTAAATC
1 ATTTTAAAAG
*
28422908 TTTTTAAAA-
1 ATTTTAAAAG
28422917 ATTTTAAAAAG
1 ATTTT-AAAAG
28422928 ATTTTAAA
1 ATTTTAAA
28422936 CTTTTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
9 4 0.10
10 22 0.54
11 6 0.15
12 9 0.22
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (10 bp):
ATTTTAAAAG
Found at i:28427190 original size:16 final size:16
Alignment explanation
Indices: 28427169--28427202 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28427159 ATAAAAATAA
*
28427169 TTTTAATTAATTAATT
1 TTTTAATTAAATAATT
28427185 TTTTAATTAAATAATT
1 TTTTAATTAAATAATT
28427201 TT
1 TT
28427203 CTCAACCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAATTAAATAATT
Found at i:28427781 original size:17 final size:16
Alignment explanation
Indices: 28427759--28427809 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
28427749 TTTAAAAAGT
28427759 AAATAAAAATGAAATCA
1 AAATAAAAATGAAA-CA
*
28427776 AAATAAACATGAAA-A
1 AAATAAAAATGAAACA
*
28427791 CTAATAAAAAT-AAACA
1 -AAATAAAAATGAAACA
28427807 AAA
1 AAA
28427810 GCAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.16
Consensus pattern (16 bp):
AAATAAAAATGAAACA
Found at i:28428540 original size:26 final size:26
Alignment explanation
Indices: 28428511--28428563 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
28428501 ATAGCCATAT
*
28428511 TACAACCATTTATTTTCTATTCTTTG
1 TACAACCATTGATTTTCTATTCTTTG
28428537 TACAACCATTGATTTTCTATTCTTTG
1 TACAACCATTGATTTTCTATTCTTTG
28428563 T
1 T
28428564 CTTTTGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.53
Consensus pattern (26 bp):
TACAACCATTGATTTTCTATTCTTTG
Found at i:28429129 original size:44 final size:44
Alignment explanation
Indices: 28429031--28429129 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 44
28429021 TACATTGCGT
* * * *
28429031 CTTGTTGTTTCGATCCACTCTACTACAACTTCAGAGAGATACAA
1 CTTGTAGTTTCAATCCACTCTACTACAACTTCAGAGAGACAAAA
* * *
28429075 CTCGTAGTTTCAATCCACTCTGCTGCAACTTCAG-GAGGACAAAA
1 CTTGTAGTTTCAATCCACTCTACTACAACTTCAGAGA-GACAAAA
* *
28429119 TTTGTGGTTTC
1 CTTGTAGTTTC
28429130 TTTTGTCTAC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
43 2 0.05
44 42 0.95
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32
Consensus pattern (44 bp):
CTTGTAGTTTCAATCCACTCTACTACAACTTCAGAGAGACAAAA
Found at i:28429237 original size:44 final size:43
Alignment explanation
Indices: 28429139--28429368 Score: 157
Period size: 44 Copynumber: 5.4 Consensus size: 43
28429129 CTTTTGTCTA
* * * ***
28429139 CTCCACTGCAACTTCAGGGCGATAAGA-CTG-GATGCGATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCTGTGTTTTAATCTG
* *
28429180 CTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCG
1 CTCCACTGCAACTTCAGAGAGATAAGATCTGT-GTTTTAATCTG
* * * * * **
28429224 CTCCATTGCAACTTCAGGGAGATAGGAT-TAATTTCTTTTGTCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCT-GTGT-TTTAATCTG
* ** * * * **
28429268 CTCCACTACTGCTT-AGGGAGATCAGA-CT-TGATGGAATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCTGTGTTTTAATCTG
* *
28429308 CTCTAGTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCTGT-GTTTTAATCTG
28429352 CTCCACTGCAACTTCAG
1 CTCCACTGCAACTTCAG
28429369 GAAGATAGGA
Statistics
Matches: 138, Mismatches: 41, Indels: 17
0.70 0.21 0.09
Matches are distributed among these distances:
40 14 0.10
41 35 0.25
42 5 0.04
43 14 0.10
44 70 0.51
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGAGAGATAAGATCTGTGTTTTAATCTG
Found at i:28429335 original size:128 final size:129
Alignment explanation
Indices: 28429126--28429380 Score: 388
Period size: 128 Copynumber: 2.0 Consensus size: 129
28429116 AAATTTGTGG
* *
28429126 TTTCTTTTGTCTACTCCACTGCAACTTCAGGGCGATAAGACTGGATGCGATCTGCTCTACTGCAA
1 TTTCTTTTGTCTACTCCACTACAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAA
* *
28429191 CTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCATTGCAACTTCAGGGAGATAGGATTAA
66 CTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTAA
* ** * * *
28429255 TTTCTTTTGTCTGCTCCACTACTGCTT-AGGGAGATCAGACTTGATG-GAATCTGCTCTAGTGCA
1 TTTCTTTTGTCTACTCCACTACAACTTCAGGGAGATAAGACTGGATGCG-ATCTGCTCTACTGCA
*
28429318 ACTTCAGAGAGATAAGATCTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGAAGATAGGATT
65 ACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATT
28429381 CGTCGTCTTC
Statistics
Matches: 114, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
127 1 0.01
128 90 0.79
129 23 0.20
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (129 bp):
TTTCTTTTGTCTACTCCACTACAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAA
CTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTAA
Found at i:28429441 original size:50 final size:50
Alignment explanation
Indices: 28429398--28429893 Score: 172
Period size: 50 Copynumber: 10.0 Consensus size: 50
28429388 TTCATTTTAA
* *
28429398 TTAACTACAATGTCGGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
* * * ** **
28429448 TTAATTGCAATATCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGC
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
** * **** * * * *
28429498 TCCACTGCACCGCCAGGGAAGTAAGATTCA-CTTTCGTGGCTTCAATCTTT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTT-GCGGCTTCAATCTTT
* * * * * ** **
28429548 TAAATTACAATGTCGAGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
** * **** ** * *** *
28429598 TCCACTGCACCGCCAAGGAAGTAAGATTCGTAGTTGTGGCTTCAATCTTT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
* * * * * ** *
28429648 TTAATTGCAATGTCGGGGAA-CAAGATTCGCCATTGTAGCTTCAATCTGT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
** * ** * * *
28429697 TCCACTGC-ATCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
1 TTAACTACAAT-ATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
* * * * * * ** *
28429747 TCAATTGCAATGTCGGGGAA-CAAGATTCGCCATTGTAGCTTCAATCTGT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
** * ** * * * *
28429796 TCCACTGCACCACCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
* * * * * * * **
28429846 TAAATTACAATGTCCGTGAAGTAAGATTCACCGTCGTAGCTTCAATCT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCT
28429894 GCTCCACTGT
Statistics
Matches: 329, Mismatches: 111, Indels: 12
0.73 0.25 0.03
Matches are distributed among these distances:
48 2 0.01
49 74 0.22
50 249 0.76
51 4 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (50 bp):
TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
Found at i:28429717 original size:99 final size:100
Alignment explanation
Indices: 28429413--28429902 Score: 689
Period size: 99 Copynumber: 4.9 Consensus size: 100
28429403 TACAATGTCG
* * *
28429413 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGCAAGATTCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCA
*
28429478 CTGTTGTAGCTTCAATCTGCTCCACTGCACCGCCA
66 CCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCA
* * *
28429513 GGGAAGTAAGATTCA-CTTTCGTGGCTTCAATCTTTTAAATTACAATGTCGAGGAAGCAAGATTC
1 GGGAAGTAAGATTCACCGTT-GTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTC
*
28429577 ACCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCA
65 ACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCA
* *** * *
28429613 AGGAAGTAAGATTCGTAGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAA-CAAGATTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCA
* * *
28429677 CCATTGTAGCTTCAATCTGTTCCACTGCATCGCCA
66 CCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCA
* * * *
28429712 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTCAATTGCAATGTCGGGGAA-CAAGATTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCA
* * *
28429776 CCATTGTAGCTTCAATCTGTTCCACTGCACCACCA
66 CCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCA
* * * *
28429811 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTACAATGTCCGTGAAGTAAGATTCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCA
*
28429876 CCGTCGTAGCTTCAATCTGCTCCACTG
66 CCGTTGTAGCTTCAATCTGCTCCACTG
28429903 TAATGCCAAA
Statistics
Matches: 349, Mismatches: 38, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
99 183 0.52
100 164 0.47
101 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (100 bp):
GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCA
CCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCA
Found at i:28436700 original size:4 final size:4
Alignment explanation
Indices: 28436691--28436715 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28436681 TCTTATCATG
28436691 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
28436716 TTTATAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:28436826 original size:26 final size:25
Alignment explanation
Indices: 28436781--28436871 Score: 103
Period size: 26 Copynumber: 3.4 Consensus size: 25
28436771 GGAAACTTAG
28436781 AATAATATATATACACTAAAACTGTTTA
1 AATAA-ATA-ATACA-TAAAACTGTTTA
* *
28436809 ATATAAATAATACATAAAAATCTTTAA
1 A-ATAAATAATACATAAAACTGTTT-A
28436836 AATAAATAATA-ATAAAACTGTTTA
1 AATAAATAATACATAAAACTGTTTA
28436860 AATGAAATAATA
1 AAT-AAATAATA
28436872 TAAAAAAATC
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
24 4 0.07
25 18 0.32
26 19 0.34
27 7 0.12
28 4 0.07
29 4 0.07
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (25 bp):
AATAAATAATACATAAAACTGTTTA
Found at i:28436877 original size:25 final size:24
Alignment explanation
Indices: 28436798--28436877 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 24
28436788 TATATACACT
28436798 AAAACTGTTTAATATAAATAATACATA
1 AAAACTGTTTAA-ATAAATAAT--ATA
*
28436825 AAAATCT-TTAAAATAAATAATA-A
1 AAAA-CTGTTTAAATAAATAATATA
28436848 TAAAACTGTTTAAATGAAATAATATA
1 -AAAACTGTTTAAAT-AAATAATATA
28436874 AAAA
1 AAAA
28436878 AATCTAAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
23 3 0.07
24 11 0.24
25 12 0.26
26 10 0.22
27 8 0.17
28 2 0.04
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAACTGTTTAAATAAATAATATA
Found at i:28440982 original size:21 final size:21
Alignment explanation
Indices: 28440956--28440998 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28440946 CTGAATGTCA
28440956 AGATCATTGTAGTCGAACTTT
1 AGATCATTGTAGTCGAACTTT
28440977 AGATCATTGTAGTCGAACTTT
1 AGATCATTGTAGTCGAACTTT
28440998 A
1 A
28440999 ATTAAAGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (21 bp):
AGATCATTGTAGTCGAACTTT
Found at i:28441558 original size:30 final size:30
Alignment explanation
Indices: 28441522--28441581 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
28441512 TTGCATAAAT
28441522 GACCCAATATGTTTATACTTCTTCTCCATC
1 GACCCAATATGTTTATACTTCTTCTCCATC
28441552 GACCCAATATGTTTATACTTCTTCTCCATC
1 GACCCAATATGTTTATACTTCTTCTCCATC
28441582 CCAACAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (30 bp):
GACCCAATATGTTTATACTTCTTCTCCATC
Found at i:28442364 original size:3 final size:3
Alignment explanation
Indices: 28442358--28442442 Score: 152
Period size: 3 Copynumber: 28.3 Consensus size: 3
28442348 CTCCTCCTCC
28442358 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
28442406 TCT TCT TCT TCT TCT ACT TCT TCT TCT TCT TTT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
28442443 TTATTGCCCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:28443588 original size:20 final size:20
Alignment explanation
Indices: 28443563--28443603 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28443553 CTTCAAAACC
* *
28443563 ACACCTGAATTAAATTTAAT
1 ACACCTGAACTAAATTCAAT
28443583 ACACCTGAACTAAATTCAAT
1 ACACCTGAACTAAATTCAAT
28443603 A
1 A
28443604 ATATGAGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.29
Consensus pattern (20 bp):
ACACCTGAACTAAATTCAAT
Found at i:28444919 original size:25 final size:26
Alignment explanation
Indices: 28444877--28444931 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
28444867 TGCATCACAA
*
28444877 TATTTTTATAAAGATTTT-AATTAAT
1 TATTTTTATAAACATTTTAAATTAAT
* * *
28444902 TATTTTTATAATCCTTTTAAATTATT
1 TATTTTTATAAACATTTTAAATTAAT
28444928 TATT
1 TATT
28444932 ATATCAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTTTTATAAACATTTTAAATTAAT
Found at i:28455401 original size:5 final size:5
Alignment explanation
Indices: 28455391--28455416 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28455381 AATTAAAAAA
28455391 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
28455417 TAATCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:28456042 original size:70 final size:71
Alignment explanation
Indices: 28455962--28456119 Score: 166
Period size: 69 Copynumber: 2.3 Consensus size: 71
28455952 AATTGTAAAA
* *
28455962 ATTTCATTTAAGATTTTAATTA-GA-GTTTTAAAATAGAATATTAGAATTTTTACA-TTAGTTAA
1 ATTTTATTTAAGATTTTAATTACCAGGTTTTAAAATAG-AT-TTAGAATTTTTACATTTAG-TAA
*
28456024 -AGTTTAGG
63 GAGTTTAAG
* * * * *
28456032 ATTTTATTTAA-ATTTT-TTTACCAGGTTTTAAATTAGATTTAGGATTTTTATATTTAGTAAGAT
1 ATTTTATTTAAGATTTTAATTACCAGGTTTTAAAATAGATTTAGAATTTTTACATTTAGTAAGAG
28456095 TTTAAG
66 TTTAAG
*
28456101 ATTTTATTTGAGATTTTAA
1 ATTTTATTTAAGATTTTAA
28456120 ACTTCGCCTT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
68 18 0.25
69 28 0.39
70 26 0.36
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.51
Consensus pattern (71 bp):
ATTTTATTTAAGATTTTAATTACCAGGTTTTAAAATAGATTTAGAATTTTTACATTTAGTAAGAG
TTTAAG
Found at i:28457438 original size:15 final size:15
Alignment explanation
Indices: 28457415--28457444 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28457405 TCACAATAAA
*
28457415 TAAATAAATAAATAC
1 TAAACAAATAAATAC
28457430 TAAACAAATAAATAC
1 TAAACAAATAAATAC
28457445 ATACTAATGA
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:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAACAAATAAATAC
Found at i:28457457 original size:19 final size:19
Alignment explanation
Indices: 28457411--28457451 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
28457401 AACATCACAA
*
28457411 TAAATAAATAAATAAATAC
1 TAAACAAATAAATAAATAC
*
28457430 TAAACAAATAAATACATAC
1 TAAACAAATAAATAAATAC
28457449 TAA
1 TAA
28457452 TGAAATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAACAAATAAATAAATAC
Found at i:28459882 original size:15 final size:15
Alignment explanation
Indices: 28459859--28459888 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28459849 AGCCAATAAA
*
28459859 TAAATAAATAAATAC
1 TAAACAAATAAATAC
28459874 TAAACAAATAAATAC
1 TAAACAAATAAATAC
28459889 ATACTAATGA
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:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAACAAATAAATAC
Found at i:28459901 original size:19 final size:19
Alignment explanation
Indices: 28459855--28459895 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
28459845 AACAAGCCAA
*
28459855 TAAATAAATAAATAAATAC
1 TAAACAAATAAATAAATAC
*
28459874 TAAACAAATAAATACATAC
1 TAAACAAATAAATAAATAC
28459893 TAA
1 TAA
28459896 TGAAATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAACAAATAAATAAATAC
Found at i:28460219 original size:388 final size:388
Alignment explanation
Indices: 28459503--28460284 Score: 1564
Period size: 388 Copynumber: 2.0 Consensus size: 388
28459493 CCGAGTAAGA
28459503 ACTAATGAAATGTTTAAAAATCATATGTGCAATTTCGATTGTATTTGAAAATACAACATTTAAAA
1 ACTAATGAAATGTTTAAAAATCATATGTGCAATTTCGATTGTATTTGAAAATACAACATTTAAAA
28459568 CAAAAAGATGTCATACACGATTAACAATAATAACACTATCTACATTGAGCATGATCATGGTGTAC
66 CAAAAAGATGTCATACACGATTAACAATAATAACACTATCTACATTGAGCATGATCATGGTGTAC
28459633 TATATATAAATAAACAATTATATGGCATCGATGCTAACGAATCCTAATGCTAACAAGCATGAGAT
131 TATATATAAATAAACAATTATATGGCATCGATGCTAACGAATCCTAATGCTAACAAGCATGAGAT
28459698 ATAATGATAATGTAAATGGCAATATAACAATAACATTCATAACAACAACAATAACATAATTATAA
196 ATAATGATAATGTAAATGGCAATATAACAATAACATTCATAACAACAACAATAACATAATTATAA
28459763 TACCAAAACTTGAAAGTGTTTAAAGAATAGCAAATAAATAAACAATGAAATAAATAACAAGAAGG
261 TACCAAAACTTGAAAGTGTTTAAAGAATAGCAAATAAATAAACAATGAAATAAATAACAAGAAGG
28459828 ATGGCCAAAACAAAATGAACAAGCCAATAAATAAATAAATAAATACTAAACAAATAAATACAT
326 ATGGCCAAAACAAAATGAACAAGCCAATAAATAAATAAATAAATACTAAACAAATAAATACAT
28459891 ACTAATGAAATGTTTAAAAATCATATGTGCAATTTCGATTGTATTTGAAAATACAACATTTAAAA
1 ACTAATGAAATGTTTAAAAATCATATGTGCAATTTCGATTGTATTTGAAAATACAACATTTAAAA
28459956 CAAAAAGATGTCATACACGATTAACAATAATAACACTATCTACATTGAGCATGATCATGGTGTAC
66 CAAAAAGATGTCATACACGATTAACAATAATAACACTATCTACATTGAGCATGATCATGGTGTAC
28460021 TATATATAAATAAACAATTATATGGCATCGATGCTAACGAATCCTAATGCTAACAAGCATGAGAT
131 TATATATAAATAAACAATTATATGGCATCGATGCTAACGAATCCTAATGCTAACAAGCATGAGAT
28460086 ATAATGATAATGTAAATGGCAATATAACAATAACATTCATAACAACAACAATAACATAATTATAA
196 ATAATGATAATGTAAATGGCAATATAACAATAACATTCATAACAACAACAATAACATAATTATAA
28460151 TACCAAAACTTGAAAGTGTTTAAAGAATAGCAAATAAATAAACAATGAAATAAATAACAAGAAGG
261 TACCAAAACTTGAAAGTGTTTAAAGAATAGCAAATAAATAAACAATGAAATAAATAACAAGAAGG
28460216 ATGGCCAAAACAAAATGAACAAGCCAATAAATAAATAAATAAATACTAAACAAATAAATACAT
326 ATGGCCAAAACAAAATGAACAAGCCAATAAATAAATAAATAAATACTAAACAAATAAATACAT
28460279 ACTAAT
1 ACTAAT
28460285 ATAAGTTTGA
Statistics
Matches: 394, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
388 394 1.00
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.26
Consensus pattern (388 bp):
ACTAATGAAATGTTTAAAAATCATATGTGCAATTTCGATTGTATTTGAAAATACAACATTTAAAA
CAAAAAGATGTCATACACGATTAACAATAATAACACTATCTACATTGAGCATGATCATGGTGTAC
TATATATAAATAAACAATTATATGGCATCGATGCTAACGAATCCTAATGCTAACAAGCATGAGAT
ATAATGATAATGTAAATGGCAATATAACAATAACATTCATAACAACAACAATAACATAATTATAA
TACCAAAACTTGAAAGTGTTTAAAGAATAGCAAATAAATAAACAATGAAATAAATAACAAGAAGG
ATGGCCAAAACAAAATGAACAAGCCAATAAATAAATAAATAAATACTAAACAAATAAATACAT
Found at i:28460270 original size:15 final size:15
Alignment explanation
Indices: 28460247--28460276 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28460237 AGCCAATAAA
*
28460247 TAAATAAATAAATAC
1 TAAACAAATAAATAC
28460262 TAAACAAATAAATAC
1 TAAACAAATAAATAC
28460277 ATACTAATAT
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:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAACAAATAAATAC
Found at i:28460270 original size:19 final size:19
Alignment explanation
Indices: 28460243--28460283 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
28460233 AACAAGCCAA
*
28460243 TAAATAAATAAATAAATAC
1 TAAACAAATAAATAAATAC
*
28460262 TAAACAAATAAATACATAC
1 TAAACAAATAAATAAATAC
28460281 TAA
1 TAA
28460284 TATAAGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAACAAATAAATAAATAC
Found at i:28462740 original size:15 final size:15
Alignment explanation
Indices: 28462717--28462746 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28462707 AGCCAATAAA
*
28462717 TAAATAAATAAATAC
1 TAAACAAATAAATAC
28462732 TAAACAAATAAATAC
1 TAAACAAATAAATAC
28462747 ATACTAATAT
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:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAACAAATAAATAC
Found at i:28462740 original size:19 final size:19
Alignment explanation
Indices: 28462713--28462753 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
28462703 AACAAGCCAA
*
28462713 TAAATAAATAAATAAATAC
1 TAAACAAATAAATAAATAC
*
28462732 TAAACAAATAAATACATAC
1 TAAACAAATAAATAAATAC
28462751 TAA
1 TAA
28462754 TATAAGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAACAAATAAATAAATAC
Found at i:28463626 original size:20 final size:19
Alignment explanation
Indices: 28463576--28463628 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
28463566 TTGTATATAT
* *
28463576 AAAAAGATAAAAAGAATGA
1 AAAAAGAAAAAAAGAATCA
28463595 AAAAA-ATCAAAAAATGAATCA
1 AAAAAGA--AAAAAA-GAATCA
28463616 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
28463629 ATCACCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 1 0.04
19 5 0.18
20 11 0.39
21 10 0.36
22 1 0.04
ACGTcount: A:0.77, C:0.04, G:0.09, T:0.09
Consensus pattern (19 bp):
AAAAAGAAAAAAAGAATCA
Found at i:28467027 original size:17 final size:17
Alignment explanation
Indices: 28466976--28467027 Score: 86
Period size: 17 Copynumber: 3.0 Consensus size: 17
28466966 GGATCCAATG
*
28466976 GAAACACGAGAATTTTT
1 GAAACACGAAAATTTTT
28466993 GAAAACACGAAAATTTTT
1 G-AAACACGAAAATTTTT
28467011 GAAACACGAAAATTTTT
1 GAAACACGAAAATTTTT
28467028 ATAAATTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 17 0.52
18 16 0.48
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (17 bp):
GAAACACGAAAATTTTT
Found at i:28467437 original size:9 final size:8
Alignment explanation
Indices: 28467423--28467469 Score: 51
Period size: 8 Copynumber: 5.5 Consensus size: 8
28467413 AGAATGGGTC
28467423 TTTTTCTCT
1 TTTTTCT-T
28467432 TTTTTCTT
1 TTTTTCTT
28467440 TTTTTCTT
1 TTTTTCTT
28467448 CCTTTCTTCTT
1 --TTT-TTCTT
28467459 TTTTT-TT
1 TTTTTCTT
28467466 TTTT
1 TTTT
28467470 GCCTGGGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 6 0.17
8 11 0.31
9 10 0.29
10 3 0.09
11 5 0.14
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:28467785 original size:7 final size:7
Alignment explanation
Indices: 28467775--28467853 Score: 90
Period size: 7 Copynumber: 11.0 Consensus size: 7
28467765 ATTTTTTTCC
28467775 TTTCTTT
1 TTTCTTT
28467782 TTTCTTT
1 TTTCTTT
28467789 TTTCTTT
1 TTTCTTT
28467796 TTTCTTT
1 TTTCTTT
28467803 TTTCTTT
1 TTTCTTT
28467810 CCTTT-TTT
1 --TTTCTTT
28467818 TCTTCTTT
1 T-TTCTTT
*
28467826 TTT-TTCC
1 TTTCTT-T
*
28467833 TTTCTTC
1 TTTCTTT
28467840 TTTCTTT
1 TTTCTTT
28467847 TTTCTTT
1 TTTCTTT
28467854 CCTTTTCCTT
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
6 3 0.05
7 49 0.77
8 9 0.14
9 3 0.05
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTCTTT
Found at i:28467824 original size:37 final size:37
Alignment explanation
Indices: 28467757--28467878 Score: 112
Period size: 37 Copynumber: 3.3 Consensus size: 37
28467747 ACCCGATTTC
28467757 TCCTTT-TTATTTT-TTTCCTTTCTTTTTTCTTTTTTCT
1 TCCTTTCTT-TTTTCTTTCCTTTCTTTTTTCTTTTTT-T
*
28467794 T-TTTTCTTTTTTCTTTCCTTT-TTTTCTTCTTTTTTT
1 TCCTTTCTTTTTTCTTTCCTTTCTTTT-TTCTTTTTTT
* * *
28467830 TCCTTTCTTCTTTCTTT--TTTCTTTCCTTTTCCTTTTTC
1 TCCTTTCTTTTTTCTTTCCTTTC-TT--TTTTCTTTTTTT
28467868 TCCTTTCTTTT
1 TCCTTTCTTTT
28467879 CCGTTCAGCC
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
35 3 0.04
36 13 0.18
37 35 0.49
38 18 0.25
39 2 0.03
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (37 bp):
TCCTTTCTTTTTTCTTTCCTTTCTTTTTTCTTTTTTT
Found at i:28467825 original size:44 final size:46
Alignment explanation
Indices: 28467766--28467859 Score: 140
Period size: 44 Copynumber: 2.1 Consensus size: 46
28467756 CTCCTTTTTA
* *
28467766 TTTTTTTCCTTTCTTTTTTCTT-TTTTCTTTTTTCTTTTTTCTTTCC
1 TTTTTTTCCTTTCTTTTTT-TTCCTTTCTTCTTTCTTTTTTCTTTCC
28467812 TTTTTTT-C-TTCTTTTTTTTCCTTTCTTCTTTCTTTTTTCTTTCC
1 TTTTTTTCCTTTCTTTTTTTTCCTTTCTTCTTTCTTTTTTCTTTCC
28467856 TTTT
1 TTTT
28467860 CCTTTTTCTC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 2 0.04
44 35 0.78
45 1 0.02
46 7 0.16
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (46 bp):
TTTTTTTCCTTTCTTTTTTTTCCTTTCTTCTTTCTTTTTTCTTTCC
Done.