Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 273 of 356
Found at i:89474706 original size:27 final size:27
Alignment explanation
Indices: 89474663--89474728 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
89474653 CCACCAAGAC
89474663 AGTAAACACGGGATAGTCTATTGG-AAT
1 AGTAAACACGGGATAGT-TATTGGAAAT
* *
89474690 AGTAAACACATGG-TAGTTCTTGGAAAT
1 AGTAAACAC-GGGATAGTTATTGGAAAT
*
89474717 AATAAACACGGG
1 AGTAAACACGGG
89474729 GATTACGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 7 0.21
27 24 0.73
28 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (27 bp):
AGTAAACACGGGATAGTTATTGGAAAT
Found at i:89476385 original size:18 final size:18
Alignment explanation
Indices: 89476359--89476411 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
89476349 GCTTAATTCT
*
89476359 AAATTAATAAAAAAATAA
1 AAATAAATAAAAAAATAA
*
89476377 AAATAAATAATAAAACTAA
1 AAATAAATAA-AAAAATAA
* *
89476396 ATA-AAATAAAATAATA
1 AAATAAATAAAAAAATA
89476412 TCTTCTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 5 0.17
18 15 0.52
19 9 0.31
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAATAAAAAAATAA
Found at i:89477396 original size:305 final size:305
Alignment explanation
Indices: 89476845--89477460 Score: 1207
Period size: 305 Copynumber: 2.0 Consensus size: 305
89476835 AACTAAATAA
89476845 TTTCATTAAATTGAGTTTGAATCAATAATTTGCAAGGCATTTATTAATGAACTACTCATTAGAAA
1 TTTCATTAAATTGAGTTTGAATCAATAATTTGCAAGGCATTTATTAATGAACTACTCATTAGAAA
*
89476910 AATTAAATTATTGACATGGTCAAACCTTTTTACGCGAACTAGGATGACAACCCAAGCACCTTAGC
66 AATTAAATTATTGACATGGTCAAACCTTTTTACGCGAACTAGGATGACAACCCAAGCACCCTAGC
89476975 CCGGTTACTCAGTTCAAACAGTCTTAAAATTTTATTTATTTATTTTTTTGTGTGAGTGAAGGCTA
131 CCGGTTACTCAGTTCAAACAGTCTTAAAATTTTATTTATTTATTTTTTTGTGTGAGTGAAGGCTA
89477040 AGTTAGCGGAATGTTTATAAGCTACCGACTTGTCACTCGGACTTTTTTACGTGAGATAAGATGAC
196 AGTTAGCGGAATGTTTATAAGCTACCGACTTGTCACTCGGACTTTTTTACGTGAGATAAGATGAC
*
89477105 AACCCAATCACCTTACCCCATTTACTCAATCCGGTCTTTCGAAAC
261 AACCCAAGCACCTTACCCCATTTACTCAATCCGGTCTTTCGAAAC
89477150 TTTCATTAAATTGAGTTTGAATCAATAATTTGCAAGGCATTTATTAATGAACTACTCATTAGAAA
1 TTTCATTAAATTGAGTTTGAATCAATAATTTGCAAGGCATTTATTAATGAACTACTCATTAGAAA
89477215 AATTAAATTATTGACATGGTCAAACCTTTTTACGCGAACTAGGATGACAACCCAAGCACCCTAGC
66 AATTAAATTATTGACATGGTCAAACCTTTTTACGCGAACTAGGATGACAACCCAAGCACCCTAGC
89477280 CCGGTTACTCAGTTCAAACAGTCTTAAAATTTTATTTATTTATTTTTTTGTGTGAGTGAAGGCTA
131 CCGGTTACTCAGTTCAAACAGTCTTAAAATTTTATTTATTTATTTTTTTGTGTGAGTGAAGGCTA
89477345 AGTTAGCGGAATGTTTATAAGCTACCGACTTGTCACTCGGACTTTTTTACGTGAGATAAGATGAC
196 AGTTAGCGGAATGTTTATAAGCTACCGACTTGTCACTCGGACTTTTTTACGTGAGATAAGATGAC
89477410 AACCCAAGCACCTTACCCCATTTACTCAATCCGGTCTTTCGAAAC
261 AACCCAAGCACCTTACCCCATTTACTCAATCCGGTCTTTCGAAAC
89477455 -TTCATT
1 TTTCATT
89477461 CATAACTTGA
Statistics
Matches: 309, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
304 6 0.02
305 303 0.98
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (305 bp):
TTTCATTAAATTGAGTTTGAATCAATAATTTGCAAGGCATTTATTAATGAACTACTCATTAGAAA
AATTAAATTATTGACATGGTCAAACCTTTTTACGCGAACTAGGATGACAACCCAAGCACCCTAGC
CCGGTTACTCAGTTCAAACAGTCTTAAAATTTTATTTATTTATTTTTTTGTGTGAGTGAAGGCTA
AGTTAGCGGAATGTTTATAAGCTACCGACTTGTCACTCGGACTTTTTTACGTGAGATAAGATGAC
AACCCAAGCACCTTACCCCATTTACTCAATCCGGTCTTTCGAAAC
Found at i:89487086 original size:23 final size:24
Alignment explanation
Indices: 89487051--89487104 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
89487041 AGCCTAATCG
89487051 TAAATTAATAAAA-TAAAATAAAAA
1 TAAATTAATAAAACT-AAATAAAAA
89487075 TAAA-TAATAAAACTAAATAAAACA
1 TAAATTAATAAAACTAAATAAAA-A
89487099 -AAATTA
1 TAAATTA
89487105 TATCTTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (24 bp):
TAAATTAATAAAACTAAATAAAAA
Found at i:89491279 original size:2 final size:2
Alignment explanation
Indices: 89491272--89491304 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
89491262 TTAGTTGAAA
89491272 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
89491305 AGCCCATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:89497770 original size:15 final size:16
Alignment explanation
Indices: 89497750--89497784 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
89497740 GAAAGTAGAT
*
89497750 TAAAAAATT-TAAAAA
1 TAAAAAATTGAAAAAA
89497765 TAAAAAATTGAAAAAA
1 TAAAAAATTGAAAAAA
89497781 TAAA
1 TAAA
89497785 CTCTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
TAAAAAATTGAAAAAA
Found at i:89502106 original size:24 final size:24
Alignment explanation
Indices: 89502053--89502101 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
89502043 ATTTGTTTTA
*
89502053 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
89502077 ATATTTGATTTATTATATTTTTAAA
1 ATATTTG-TTT-TTATATTTTTAAA
89502102 AATTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:89504880 original size:5 final size:5
Alignment explanation
Indices: 89504856--89504932 Score: 58
Period size: 5 Copynumber: 15.8 Consensus size: 5
89504846 TTTATATAAA
* *
89504856 TATAT TAT-T TA-AT T-TGAT TATAT TATTAT TTTAT TATAT TGTAATT
1 TATAT TATAT TATAT TAT-AT TATAT TA-TAT TATAT TATAT TAT-A-T
89504902 TATAT TA-AT TATAT TATA- -ATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
89504933 AAATAAATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
3 3 0.05
4 9 0.16
5 36 0.62
6 7 0.12
7 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:89504912 original size:21 final size:22
Alignment explanation
Indices: 89504857--89504930 Score: 84
Period size: 21 Copynumber: 3.5 Consensus size: 22
89504847 TTATATAAAT
89504857 ATATTAT-TTAATT-TGATTATA
1 ATATTATATTAATTAT-ATTATA
* * *
89504878 TTATTAT-TTTATTATATTGTA
1 ATATTATATTAATTATATTATA
89504899 AT-TTATATTAATTATATTATA
1 ATATTATATTAATTATATTATA
89504920 ATATTATATTA
1 ATATTATATTA
89504931 TAAAATAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 4 0.09
21 31 0.70
22 9 0.20
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (22 bp):
ATATTATATTAATTATATTATA
Found at i:89505490 original size:8 final size:8
Alignment explanation
Indices: 89505479--89505510 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
89505469 TGTGAAAATG
89505479 TGTGAATT
1 TGTGAATT
89505487 TGTGAATT
1 TGTGAATT
89505495 TGTGAATT
1 TGTGAATT
89505503 TGTGAATT
1 TGTGAATT
89505511 GAATATTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (8 bp):
TGTGAATT
Found at i:89511437 original size:23 final size:23
Alignment explanation
Indices: 89511384--89511445 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
89511374 ATTATAGCAA
*
89511384 TGGAAAAATAAATTAAATTTTTC
1 TGGAAATATAAATTAAATTTTTC
** * *
89511407 TAAAAAATATAATTTAAATTTTTG
1 T-GGAAATATAAATTAAATTTTTC
89511431 TGGAAATATTAAATT
1 TGGAAATA-TAAATT
89511446 TTACTTATTC
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (23 bp):
TGGAAATATAAATTAAATTTTTC
Found at i:89515760 original size:35 final size:35
Alignment explanation
Indices: 89515721--89515886 Score: 199
Period size: 35 Copynumber: 4.6 Consensus size: 35
89515711 CATGGCAAAG
89515721 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
* *
89515756 TGTGAAAAGTAGGTATGGTATCATCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
*
89515791 TGTCAAATGTAGGTATGGAATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGT
** * *
89515831 TAAGAAATGTAGGTATGGCAT-TTCCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGT
*
89515866 TGTAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
89515887 TTCAATGAGG
Statistics
Matches: 111, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
34 1 0.01
35 77 0.69
37 2 0.02
38 4 0.04
40 27 0.24
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
Found at i:89515831 original size:75 final size:74
Alignment explanation
Indices: 89515725--89515891 Score: 202
Period size: 75 Copynumber: 2.3 Consensus size: 74
89515715 GCAAAGTGTG
** *
89515725 AAATGTAGGTATGG--TATC--ATCCATACTGAGTTGTGAAAAGTAGGTATGGTATCAT-CCATA
1 AAATGTAGGTATGGATTATCAAATCCATACTGAGTTAAGAAAAGTAGGTATGGCAT-ATCCCATA
*
89515785 CCGAGTTGTC
65 CCGAGTTGTA
* *
89515795 AAATGTAGGTATGGAATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCCCATA
1 AAATGTAGGTATGG-ATTATCAAATCCATACTGAGTTAAGAAAAGTAGGTATGGCATATCCCATA
*
89515860 CTGAGTTGTA
65 CCGAGTTGTA
89515870 AAATGTAGGTATGGTATT-TCAA
1 AAATGTAGGTATGG-ATTATCAA
89515892 TGAGGAAAAC
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 14 0.17
73 4 0.05
74 5 0.06
75 60 0.72
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (74 bp):
AAATGTAGGTATGGATTATCAAATCCATACTGAGTTAAGAAAAGTAGGTATGGCATATCCCATAC
CGAGTTGTA
Found at i:89518997 original size:42 final size:43
Alignment explanation
Indices: 89518884--89519012 Score: 120
Period size: 43 Copynumber: 3.0 Consensus size: 43
89518874 GGATATATAT
* * * * *
89518884 ATACAATGCCAATGTTCCAGAC-GTGGTCTTACATGTAATAAAAC
1 ATACGATGCCAATGTCCCAGACAG-GGTCTTACACGTAA-AACAG
* * *
89518928 AT-TGATGCCACTGTCCCAGACAGGGTCTTACACG-AAATCAG
1 ATACGATGCCAATGTCCCAGACAGGGTCTTACACGTAAAACAG
* * *
89518969 ATACGATGCCAATGTCCTAGGCATGGTCTTACACGTAAAACAG
1 ATACGATGCCAATGTCCCAGACAGGGTCTTACACGTAAAACAG
89519012 A
1 A
89519013 AGTCGATGTC
Statistics
Matches: 68, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
41 4 0.06
42 29 0.43
43 32 0.47
44 3 0.04
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (43 bp):
ATACGATGCCAATGTCCCAGACAGGGTCTTACACGTAAAACAG
Found at i:89520574 original size:15 final size:15
Alignment explanation
Indices: 89520539--89520568 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
89520529 TTTAATCCTT
*
89520539 TATAAATTATAAAGA
1 TATAAATTATAAAAA
89520554 TATAAATTATAAAAA
1 TATAAATTATAAAAA
89520569 ATTAAAATTT
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:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
TATAAATTATAAAAA
Found at i:89521106 original size:16 final size:15
Alignment explanation
Indices: 89521087--89521139 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 15
89521077 TGTCTTTAGG
*
89521087 TTTTGTTTTGATTGTT
1 TTTTATTTTG-TTGTT
89521103 TTTTATTTTGTTG-T
1 TTTTATTTTGTTGTT
*
89521117 TTTTATTTT-TTATT
1 TTTTATTTTGTTGTT
89521131 TTTTATTTT
1 TTTTATTTT
89521140 TTATGGGTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 2 0.06
14 20 0.59
15 3 0.09
16 9 0.26
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.81
Consensus pattern (15 bp):
TTTTATTTTGTTGTT
Found at i:89521111 original size:21 final size:21
Alignment explanation
Indices: 89521087--89521132 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
89521077 TGTCTTTAGG
*
89521087 TTTTGTT-TTGATTGTTTTTTA
1 TTTTGTTGTT-ATTATTTTTTA
*
89521108 TTTTGTTGTTTTTATTTTTTA
1 TTTTGTTGTTATTATTTTTTA
89521129 TTTT
1 TTTT
89521133 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.09, C:0.00, G:0.11, T:0.80
Consensus pattern (21 bp):
TTTTGTTGTTATTATTTTTTA
Found at i:89521126 original size:7 final size:7
Alignment explanation
Indices: 89521101--89521143 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
89521091 GTTTTGATTG
89521101 TTTTTTA
1 TTTTTTA
89521108 TTTTGTT-
1 TTTT-TTA
*
89521115 GTTTTTA
1 TTTTTTA
89521122 TTTTTTA
1 TTTTTTA
89521129 TTTTTTA
1 TTTTTTA
89521136 TTTTTTA
1 TTTTTTA
89521143 T
1 T
89521144 GGGTACACCG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 2 0.06
7 28 0.88
8 2 0.06
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.84
Consensus pattern (7 bp):
TTTTTTA
Found at i:89521944 original size:2 final size:2
Alignment explanation
Indices: 89521937--89521971 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
89521927 CCCCAAACAA
89521937 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
89521972 AGGCAATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:89524922 original size:81 final size:81
Alignment explanation
Indices: 89524819--89524988 Score: 313
Period size: 81 Copynumber: 2.1 Consensus size: 81
89524809 GAAATTAAAA
*
89524819 CCAAAGAAGGATGCAGAGCTGAAGCCCATGAATGATATATTTGGTGACAATTTAAATATAATAAA
1 CCAAAGAAGGATGCAGAGCTGAAGCCAATGAATGATATATTTGGTGACAATTTAAATATAATAAA
89524884 AGACACTGAACTGAAG
66 AGACACTGAACTGAAG
* *
89524900 CCAAAGACGGATGCAGAGCTGAAGCCAATGAATGATATTTTTGGTGACAATTTAAATATAATAAA
1 CCAAAGAAGGATGCAGAGCTGAAGCCAATGAATGATATATTTGGTGACAATTTAAATATAATAAA
89524965 AGACACTGAACTGAAG
66 AGACACTGAACTGAAG
89524981 CCAAAGAA
1 CCAAAGAA
89524989 TAATTCTTTC
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.22
Consensus pattern (81 bp):
CCAAAGAAGGATGCAGAGCTGAAGCCAATGAATGATATATTTGGTGACAATTTAAATATAATAAA
AGACACTGAACTGAAG
Found at i:89532569 original size:21 final size:22
Alignment explanation
Indices: 89532537--89532586 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
89532527 ACTAACCTAC
*
89532537 TAATTGATATTATTGTG-ATTA
1 TAATTGATATTATTATGAATTA
89532558 TAATT-ATAATTATTATGAATTA
1 TAATTGAT-ATTATTATGAATTA
*
89532580 TGATTGA
1 TAATTGA
89532587 ACTTTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 13 0.54
22 8 0.33
23 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (22 bp):
TAATTGATATTATTATGAATTA
Found at i:89534888 original size:16 final size:15
Alignment explanation
Indices: 89534858--89534892 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
89534848 TGCAAGCAAG
*
89534858 GGCTTTAGTTGAAAA
1 GGCTTCAGTTGAAAA
89534873 GGCTTCAGTTGAAAA
1 GGCTTCAGTTGAAAA
*
89534888 AGCTT
1 GGCTT
89534893 TAGGTATGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (15 bp):
GGCTTCAGTTGAAAA
Found at i:89542099 original size:19 final size:21
Alignment explanation
Indices: 89542057--89542099 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
89542047 ACTGTAATAA
* *
89542057 TTGTGAATTGATCTTTTGGGT
1 TTGTAAATTGATCTTTTGGAT
89542078 TTGTAAATTG-TC-TTTGGAT
1 TTGTAAATTGATCTTTTGGAT
89542097 TTG
1 TTG
89542100 CCTTGCATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.16, C:0.05, G:0.26, T:0.53
Consensus pattern (21 bp):
TTGTAAATTGATCTTTTGGAT
Found at i:89549104 original size:20 final size:20
Alignment explanation
Indices: 89549079--89549119 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
89549069 CAACTATGTC
*
89549079 TCTTCCATTATTAGCAAAGT
1 TCTTCCATCATTAGCAAAGT
*
89549099 TCTTCCATCATTAGTAAAGT
1 TCTTCCATCATTAGCAAAGT
89549119 T
1 T
89549120 ATGCCAAGAC
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:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (20 bp):
TCTTCCATCATTAGCAAAGT
Found at i:89554116 original size:4 final size:4
Alignment explanation
Indices: 89554107--89554137 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
89554097 AATGATATAT
89554107 AATA AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AAT
89554138 GTTAAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:89554270 original size:3 final size:3
Alignment explanation
Indices: 89554262--89554289 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
89554252 TATATATATG
89554262 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
89554290 ATGAACAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:89556004 original size:27 final size:27
Alignment explanation
Indices: 89555957--89556114 Score: 191
Period size: 27 Copynumber: 5.9 Consensus size: 27
89555947 CGAGGCTGCT
* *
89555957 AGATATTGTGAC-GAAGTCACCAGATAC
1 AGATATTGTGGCAG-AGCCACCAGATAC
89555984 AGATATTGTGGCAGAGCCACCAGA-AC
1 AGATATTGTGGCAGAGCCACCAGATAC
89556010 AGATATATGTGGCAGAGCCACCAGAT-C
1 AGATAT-TGTGGCAGAGCCACCAGATAC
* *
89556037 AGATAATCGTGGCATAGCCACCAGA-AC
1 AGAT-ATTGTGGCAGAGCCACCAGATAC
89556064 AGATATATGTGGCAGAGCCACCAGAT-C
1 AGATAT-TGTGGCAGAGCCACCAGATAC
*
89556091 AGATAATTGTGGCATAGCCACCAG
1 AGAT-ATTGTGGCAGAGCCACCAG
89556115 GACGCTTCCT
Statistics
Matches: 116, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
26 10 0.09
27 101 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (27 bp):
AGATATTGTGGCAGAGCCACCAGATAC
Found at i:89556049 original size:54 final size:54
Alignment explanation
Indices: 89555974--89556114 Score: 248
Period size: 54 Copynumber: 2.6 Consensus size: 54
89555964 GTGACGAAGT
*
89555974 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
89556028 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
89556082 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
89556115 GACGCTTCCT
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
53 5 0.06
54 78 0.94
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:89557763 original size:26 final size:26
Alignment explanation
Indices: 89557733--89557840 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
89557723 TGAAATTCCC
89557733 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
89557759 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
89557785 ATCATGAAATATTTAACTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
89557811 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
89557837 ATCA
1 ATCA
89557841 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:89562801 original size:27 final size:27
Alignment explanation
Indices: 89562754--89562910 Score: 153
Period size: 27 Copynumber: 5.8 Consensus size: 27
89562744 CGAGGCTGCT
* *
89562754 AGATATTGTGAC-GAAGTCACCAGATAC
1 AGATATTGTGGCAG-AGCCACCAGATAC
89562781 AGATATTGTGGCAGAGCCACCAGA-AC
1 AGATATTGTGGCAGAGCCACCAGATAC
*
89562807 AGATATATGTGGCAGAGCCACCAGAT-G
1 AGATAT-TGTGGCAGAGCCACCAGATAC
* *
89562834 AGATAATCGTGGCATAGCCACCAGA-AC
1 AGAT-ATTGTGGCAGAGCCACCAGATAC
* *
89562861 AGATATATGTGGCAAAGCCACTAGAT-C
1 AGATAT-TGTGGCAGAGCCACCAGATAC
* *
89562888 AGATAATTGTGGCATAGACACCA
1 AGAT-ATTGTGGCAGAGCCACCA
89562911 AGACGCTTCC
Statistics
Matches: 110, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
26 10 0.09
27 95 0.86
28 5 0.05
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.19
Consensus pattern (27 bp):
AGATATTGTGGCAGAGCCACCAGATAC
Found at i:89562846 original size:54 final size:54
Alignment explanation
Indices: 89562754--89562910 Score: 210
Period size: 54 Copynumber: 2.9 Consensus size: 54
89562744 CGAGGCTGCT
* * * *
89562754 AGATAT-TGTGACGAAGTCACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAAC
1 AGATATATGTGGCAAAGCCACCAGAT-CAGATAATTGTGGCATAGCCACCAGAAC
* * *
89562807 AGATATATGTGGCAGAGCCACCAGATGAGATAATCGTGGCATAGCCACCAGAAC
1 AGATATATGTGGCAAAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGAAC
* *
89562861 AGATATATGTGGCAAAGCCACTAGATCAGATAATTGTGGCATAGACACCA
1 AGATATATGTGGCAAAGCCACCAGATCAGATAATTGTGGCATAGCCACCA
89562911 AGACGCTTCC
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 10 0.11
54 80 0.89
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.19
Consensus pattern (54 bp):
AGATATATGTGGCAAAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGAAC
Found at i:89564564 original size:26 final size:26
Alignment explanation
Indices: 89564534--89564586 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
89564524 AATTACCATT
*
89564534 ATGGAACATTTACCTAACCTATTATC
1 ATGGAACATTTACCTAACCCATTATC
89564560 ATGGAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
89564586 A
1 A
89564587 ATTTGTATCA
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:0.36, C:0.25, G:0.08, T:0.32
Consensus pattern (26 bp):
ATGGAACATTTACCTAACCCATTATC
Found at i:89569313 original size:40 final size:40
Alignment explanation
Indices: 89569264--89569401 Score: 138
Period size: 40 Copynumber: 3.5 Consensus size: 40
89569254 AATATACAAG
* *
89569264 TTTGGCACCCAGTGTCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGTCTCATCGGATAATCCGAAGTAATAA
* * *
89569304 TTTGACACCCAGTGTCTCATCAGCTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGTCTCATCGGATAATCCGAAGTAATAA
* * * * *
89569342 -TTGACACTCAATGCCTCATCGAATATATCCGAAATAATAA
1 TTTGACACCCAGTGTCTCATCGGATA-ATCCGAAGTAATAA
**
89569382 TTTGACACTTAGTGTCTCAT
1 TTTGACACCCAGTGTCTCAT
89569402 TGACTCGAAG
Statistics
Matches: 78, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 19 0.24
38 9 0.12
39 2 0.03
40 32 0.41
41 16 0.21
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (40 bp):
TTTGACACCCAGTGTCTCATCGGATAATCCGAAGTAATAA
Found at i:89570310 original size:17 final size:17
Alignment explanation
Indices: 89570288--89570336 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
89570278 TCCTTCTTTC
*
89570288 TTTCCTTTTTCTTTCTT
1 TTTCCTTTTTCTTTCAT
*
89570305 TTTCCTTTTTGTTTCAT
1 TTTCCTTTTTCTTTCAT
*
89570322 TTTCTTTCTTTCTTT
1 TTTCCTT-TTTCTTT
89570337 TCTATTCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 21 0.78
18 6 0.22
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTCCTTTTTCTTTCAT
Found at i:89570312 original size:11 final size:10
Alignment explanation
Indices: 89570284--89570332 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
89570274 TTTCTCCTTC
89570284 TTTCTTTCCTT
1 TTTCTTT-CTT
89570295 TTTCTTTCTT
1 TTTCTTTCTT
89570305 TTTC---CTT
1 TTTCTTTCTT
* *
89570312 TTTGTTTCAT
1 TTTCTTTCTT
89570322 TTTCTTTCTT
1 TTTCTTTCTT
89570332 T
1 T
89570333 CTTTTCTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
7 6 0.19
10 18 0.58
11 7 0.23
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:89570919 original size:23 final size:20
Alignment explanation
Indices: 89570863--89570908 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
89570853 TGTAAGTTGA
89570863 TTATATAAACATAATATTAT
1 TTATATAAACATAATATTAT
89570883 TTATATAAACATAATATTAT
1 TTATATAAACATAATATTAT
*
89570903 TCATAT
1 TTATAT
89570909 TATTTACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATATAAACATAATATTAT
Found at i:89572395 original size:13 final size:13
Alignment explanation
Indices: 89572377--89572402 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89572367 ATTCTATGGC
89572377 TTTATTTTATTAT
1 TTTATTTTATTAT
89572390 TTTATTTTATTAT
1 TTTATTTTATTAT
89572403 GCCGCCTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTTATTAT
Found at i:89572597 original size:21 final size:21
Alignment explanation
Indices: 89572545--89572590 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
89572535 AATTATCTAT
89572545 TGAAACGTTAAAATTTTTCAA
1 TGAAACGTTAAAATTTTTCAA
89572566 TGAAACGTTAAAATTTTTCAA
1 TGAAACGTTAAAATTTTTCAA
89572587 TGAA
1 TGAA
89572591 GCTTTAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (21 bp):
TGAAACGTTAAAATTTTTCAA
Found at i:89575631 original size:40 final size:39
Alignment explanation
Indices: 89575533--89575755 Score: 241
Period size: 40 Copynumber: 5.6 Consensus size: 39
89575523 TCCTCGTTCA
* * * * *
89575533 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
89575572 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
89575611 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
89575651 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* * * * * *
89575691 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
* *
89575732 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
89575756 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
Found at i:89575755 original size:120 final size:119
Alignment explanation
Indices: 89575533--89575755 Score: 272
Period size: 120 Copynumber: 1.9 Consensus size: 119
89575523 TCCTCGTTCA
* * * *
89575533 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
* *
89575598 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
66 TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
89575652 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA
* *
89575716 TATATTC-ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
64 TATA-ACAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA
89575756 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
119 37 0.43
120 44 0.51
121 6 0.07
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:89583496 original size:38 final size:39
Alignment explanation
Indices: 89583415--89583497 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 39
89583405 TCCTCGTTCA
* * **
89583415 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACATAACCCGGTATTAACAACTCACAC
*
89583454 AATGCCTTCGGGAC-TAACCCGG-ATTAACAACTCGCAC
1 AATGCCTTCGGGACATAACCCGGTATTAACAACTCACAC
89583491 GAATGCC
1 -AATGCC
89583498 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
37 11 0.29
38 13 0.34
39 14 0.37
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (39 bp):
AATGCCTTCGGGACATAACCCGGTATTAACAACTCACAC
Found at i:89600482 original size:40 final size:40
Alignment explanation
Indices: 89600370--89600534 Score: 228
Period size: 40 Copynumber: 4.2 Consensus size: 40
89600360 TCCTCGTTCA
* * * ** *
89600370 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
89600409 AATGCCTTCGGGAC-TAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* *
89600448 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
89600488 AATGCCTTCGGGACTTAACCTGGATTT-ACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
89600527 AATGCCTT
1 AATGCCTT
89600535 TGGATCTTAG
Statistics
Matches: 114, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
38 19 0.17
39 47 0.41
40 48 0.42
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:89600524 original size:79 final size:78
Alignment explanation
Indices: 89600370--89600534 Score: 251
Period size: 78 Copynumber: 2.1 Consensus size: 78
89600360 TCCTCGTTCA
* * *
89600370 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTAACCCGGATTT
1 AATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACAATGCCTTCGGGACTAACCCGGATTT
89600435 AACAACTCGCACG
66 AACAACTCGCACG
* * *
89600448 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCTTCGGGACTTAACCTGGAT
1 AATGCCTTCGGGACATAACCCGGCTTTAATAACTCACAC-AATGCCTTCGGGAC-TAACCCGGAT
89600513 TT-ACAACTCGCACG
64 TTAACAACTCGCACG
89600527 AATGCCTT
1 AATGCCTT
89600535 TGGATCTTAG
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
78 34 0.43
79 34 0.43
80 11 0.14
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (78 bp):
AATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACAATGCCTTCGGGACTAACCCGGATTT
AACAACTCGCACG
Found at i:89600574 original size:79 final size:79
Alignment explanation
Indices: 89600370--89600590 Score: 216
Period size: 79 Copynumber: 2.8 Consensus size: 79
89600360 TCCTCGTTCA
* * * * *
89600370 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCA-CACAATGCCTTCGGGAC-TAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATATAATAACT-AGCACAATGCCTTCGGGACTTAACCCGGAT
89600433 TTAACAACTCGCACG
65 TTAACAACTCGCACG
* * * *
89600448 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCTTCGGGACTTAACCTGGAT
1 AATGCCTTCGGGACTTAACCCGGATATAATAACTAGCAC-AATGCCTTCGGGACTTAACCCGGAT
89600513 TT-ACAACTCGCACG
65 TTAACAACTCGCACG
* ** * *** * *
89600527 AATGCCTT-TGGATCTTAGTCCGGATATATTCGGTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGA-CTTAACCCGGATATAAT-AACTAGCACAATGCCTTCGGGACTTAACCCGGA
89600591 CAGCATTCAA
Statistics
Matches: 119, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
78 36 0.30
79 67 0.56
80 16 0.13
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAACCCGGATATAATAACTAGCACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACG
Found at i:89609814 original size:27 final size:27
Alignment explanation
Indices: 89609784--89609961 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
89609774 ATATCGAGTC
* * * *
89609784 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
89609811 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
89609838 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
89609866 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
89609893 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
89609920 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
89609947 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
89609962 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:89609923 original size:82 final size:81
Alignment explanation
Indices: 89609805--89609960 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
89609795 TGCTATATAA
*
89609805 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
89609870 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
89609887 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
89609951 CACTTAGTGC
65 CACTTAGTGC
89609961 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:89617986 original size:27 final size:27
Alignment explanation
Indices: 89617956--89618133 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
89617946 ATATCGAGTC
* * * *
89617956 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
89617983 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
89618010 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
89618038 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
89618065 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
89618092 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
89618119 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
89618134 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:89618095 original size:82 final size:81
Alignment explanation
Indices: 89617977--89618132 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
89617967 TGCTATATAA
*
89617977 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
89618042 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
89618059 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
89618123 CACTTAGTGC
65 CACTTAGTGC
89618133 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:89623938 original size:40 final size:40
Alignment explanation
Indices: 89623893--89623982 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 40
89623883 TATTATTTCA
*
89623893 ATTTTAATTTTCAGAATTT-CA-ATCAAAACTTTTAATTCT
1 ATTTTTATTTT-AGAATTTCCAGATCAAAACTTTTAATTCT
* *** *
89623932 GTTTTTATTTTATTTTTTCCAGATCAAATCTTTTAATTCT
1 ATTTTTATTTTAGAATTTCCAGATCAAAACTTTTAATTCT
89623972 ATTTTT-TTTTA
1 ATTTTTATTTTA
89623983 TTTTTTTCAG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
38 4 0.10
39 16 0.38
40 22 0.52
ACGTcount: A:0.28, C:0.11, G:0.03, T:0.58
Consensus pattern (40 bp):
ATTTTTATTTTAGAATTTCCAGATCAAAACTTTTAATTCT
Found at i:89623990 original size:40 final size:40
Alignment explanation
Indices: 89623914--89623988 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
89623904 CAGAATTTCA
*
89623914 ATCAAAACTTTTAATTCTGTTTTTATTTTATTTTTTCCAG
1 ATCAAAACTTTTAATTCTATTTTTATTTTATTTTTTCCAG
*
89623954 ATCAAATCTTTTAATTCTATTTTT-TTTTATTTTTT
1 ATCAAAACTTTTAATTCTATTTTTATTTTATTTTTT
89623989 TCAGGTACGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
39 11 0.33
40 22 0.67
ACGTcount: A:0.24, C:0.11, G:0.03, T:0.63
Consensus pattern (40 bp):
ATCAAAACTTTTAATTCTATTTTTATTTTATTTTTTCCAG
Found at i:89638091 original size:19 final size:20
Alignment explanation
Indices: 89638047--89638092 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
89638037 ATGAGATTAT
89638047 TAAAA-ATATATATGAAAAA
1 TAAAACATATATATGAAAAA
* **
89638066 TATAACATATA-ATGAAATG
1 TAAAACATATATATGAAAAA
89638085 TAAAACAT
1 TAAAACAT
89638093 CAAGGGTCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (20 bp):
TAAAACATATATATGAAAAA
Found at i:89638660 original size:62 final size:61
Alignment explanation
Indices: 89638562--89638741 Score: 266
Period size: 55 Copynumber: 3.0 Consensus size: 61
89638552 TACAAGTGTG
89638562 ATTTAAGTTTAACTCACTTATACAA-CTGCAACCTCTCTCATATACTTCGAACTAAATTACTTT
1 ATTTAAG-TTAACTCACTTAT-CAAGCTGCAACCTCTCTCATATA-TTCGAACTAAATTACTTT
*
89638625 ATTTAAGTTAACTCACTTATCAAGCTGCAACCTCTCTC----A--CGAACTAAATTAATTT
1 ATTTAAGTTAACTCACTTATCAAGCTGCAACCTCTCTCATATATTCGAACTAAATTACTTT
89638680 ATTTAAGTTAACTCACTTATCAAGCTGCAACCTCTCTCATATAATTCGAACTAAATTACTTT
1 ATTTAAGTTAACTCACTTATCAAGCTGCAACCTCTCTCATAT-ATTCGAACTAAATTACTTT
89638742 CCCTATAAGT
Statistics
Matches: 107, Mismatches: 2, Indels: 17
0.85 0.02 0.13
Matches are distributed among these distances:
55 53 0.50
58 1 0.01
60 1 0.01
61 3 0.03
62 42 0.39
63 7 0.07
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (61 bp):
ATTTAAGTTAACTCACTTATCAAGCTGCAACCTCTCTCATATATTCGAACTAAATTACTTT
Found at i:89640362 original size:26 final size:26
Alignment explanation
Indices: 89640333--89640414 Score: 164
Period size: 26 Copynumber: 3.2 Consensus size: 26
89640323 TGATACAAAT
89640333 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89640359 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89640385 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89640411 TGAT
1 TGAT
89640415 GGGAATTTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:89648388 original size:26 final size:26
Alignment explanation
Indices: 89648359--89648466 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
89648349 TGATACAAAT
89648359 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
89648385 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
89648411 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89648437 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89648463 TGAT
1 TGAT
89648467 GGGAATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:89657777 original size:351 final size:351
Alignment explanation
Indices: 89657134--89657836 Score: 1397
Period size: 351 Copynumber: 2.0 Consensus size: 351
89657124 TGGCCAACCA
89657134 TGCTGCTGTTATGTTTTTGTTGAATGCATACAGCTTGTATGCATGCTGCAGCAAGTGTGCATGTT
1 TGCTGCTGTTATGTTTTTGTTGAATGCATACAGCTTGTATGCATGCTGCAGCAAGTGTGCATGTT
89657199 GTAGCAACATATTTTCTATTTTAGTTGAAATGTAGTTTAGTTTCATTGAAAATGAACTTAGTTGT
66 GTAGCAACATATTTTCTATTTTAGTTGAAATGTAGTTTAGTTTCATTGAAAATGAACTTAGTTGT
89657264 TGATGTTTTGATAGGTTTAGGTGATGACTGAGCTGATAATTCAGCTTATTCATGTGTACAAGCAA
131 TGATGTTTTGATAGGTTTAGGTGATGACTGAGCTGATAATTCAGCTTATTCATGTGTACAAGCAA
89657329 TGTTTATCAAGTTACTAGGCTACTTAGTAGTAGTAGGTAGTATTTGGTGATGTATTTGGCTATAA
196 TGTTTATCAAGTTACTAGGCTACTTAGTAGTAGTAGGTAGTATTTGGTGATGTATTTGGCTATAA
89657394 ATGTATTGTTTTCATACTAAATGAGTAAGCAGATCAGTTATAAAAAAATCAGATTGCTTCCTTGC
261 ATGTATTGTTTTCATACTAAATGAGTAAGCAGATCAGTTATAAAAAAATCAGATTGCTTCCTTGC
89657459 TACACGTTTGTGAGCAAGTAAAACTT
326 TACACGTTTGTGAGCAAGTAAAACTT
*
89657485 TGCTGCTGTTATGTTTTTGTTGAGTGCATACAGCTTGTATGCATGCTGCAGCAAGTGTGCATGTT
1 TGCTGCTGTTATGTTTTTGTTGAATGCATACAGCTTGTATGCATGCTGCAGCAAGTGTGCATGTT
89657550 GTAGCAACATATTTTCTATTTTAGTTGAAATGTAGTTTAGTTTCATTGAAAATGAACTTAGTTGT
66 GTAGCAACATATTTTCTATTTTAGTTGAAATGTAGTTTAGTTTCATTGAAAATGAACTTAGTTGT
89657615 TGATGTTTTGATAGGTTTAGGTGATGACTGAGCTGATAATTCAGCTTATTCATGTGTACAAGCAA
131 TGATGTTTTGATAGGTTTAGGTGATGACTGAGCTGATAATTCAGCTTATTCATGTGTACAAGCAA
89657680 TGTTTATCAAGTTACTAGGCTACTTAGTAGTAGTAGGTAGTATTTGGTGATGTATTTGGCTATAA
196 TGTTTATCAAGTTACTAGGCTACTTAGTAGTAGTAGGTAGTATTTGGTGATGTATTTGGCTATAA
89657745 ATGTATTGTTTTCATACTAAATGAGTAAGCAGATCAGTTATAAAAAAATCAGATTGCTTCCTTGC
261 ATGTATTGTTTTCATACTAAATGAGTAAGCAGATCAGTTATAAAAAAATCAGATTGCTTCCTTGC
89657810 TACACGTTTGTGAGCAAGTAAAACTT
326 TACACGTTTGTGAGCAAGTAAAACTT
89657836 T
1 T
89657837 TCTTGCATTT
Statistics
Matches: 351, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
351 351 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.39
Consensus pattern (351 bp):
TGCTGCTGTTATGTTTTTGTTGAATGCATACAGCTTGTATGCATGCTGCAGCAAGTGTGCATGTT
GTAGCAACATATTTTCTATTTTAGTTGAAATGTAGTTTAGTTTCATTGAAAATGAACTTAGTTGT
TGATGTTTTGATAGGTTTAGGTGATGACTGAGCTGATAATTCAGCTTATTCATGTGTACAAGCAA
TGTTTATCAAGTTACTAGGCTACTTAGTAGTAGTAGGTAGTATTTGGTGATGTATTTGGCTATAA
ATGTATTGTTTTCATACTAAATGAGTAAGCAGATCAGTTATAAAAAAATCAGATTGCTTCCTTGC
TACACGTTTGTGAGCAAGTAAAACTT
Found at i:89661510 original size:5 final size:5
Alignment explanation
Indices: 89661500--89661524 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
89661490 TTTAAAAATC
89661500 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
89661525 GAAGAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:89661802 original size:40 final size:41
Alignment explanation
Indices: 89661747--89661829 Score: 159
Period size: 40 Copynumber: 2.0 Consensus size: 41
89661737 AAGATACTTG
89661747 TCATATGAACAATCTCCTTTTAAGT-CTCATGAAAGTTAAC
1 TCATATGAACAATCTCCTTTTAAGTCCTCATGAAAGTTAAC
89661787 TCATATGAACAATCTCCTTTTAAGTCCTCATGAAAGTTAAC
1 TCATATGAACAATCTCCTTTTAAGTCCTCATGAAAGTTAAC
89661828 TC
1 TC
89661830 TATAACGTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 25 0.60
41 17 0.40
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.35
Consensus pattern (41 bp):
TCATATGAACAATCTCCTTTTAAGTCCTCATGAAAGTTAAC
Found at i:89663217 original size:22 final size:21
Alignment explanation
Indices: 89663170--89663217 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
89663160 TTTTATTTGG
* *
89663170 AATTTAATTTTAGGATTTTAG
1 AATTTAAGTTTAGGATTTTAA
* *
89663191 TATTTAAGGTTTAGGGTTTTAA
1 AATTTAA-GTTTAGGATTTTAA
89663213 AATTT
1 AATTT
89663218 TATAAGAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (21 bp):
AATTTAAGTTTAGGATTTTAA
Found at i:89666373 original size:26 final size:26
Alignment explanation
Indices: 89666315--89666399 Score: 113
Period size: 26 Copynumber: 3.3 Consensus size: 26
89666305 CTGGAGGCCT
89666315 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
89666339 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
89666365 AGCCCTTTTCAATAAACTGAGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
89666391 AGCCCTTTT
1 AGCCCTTTT
89666400 GCACTTCCTC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
23 5 0.09
24 5 0.09
25 10 0.19
26 33 0.62
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:89666474 original size:20 final size:20
Alignment explanation
Indices: 89666449--89666523 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
89666439 TTATGAATAC
89666449 ATCATGTGCACT-TCATACAT
1 ATCATGTGCA-TATCATACAT
89666469 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
89666489 GTCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
89666509 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
89666524 TCCCACGTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.16
19 1 0.02
20 40 0.78
21 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:89669232 original size:18 final size:18
Alignment explanation
Indices: 89669193--89669232 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
89669183 TGAATTGCCA
*
89669193 GTGTAATCGCACACGTCC
1 GTGTAATCGCACACATCC
*
89669211 GTGTAATCGCACACATCT
1 GTGTAATCGCACACATCC
89669229 GTGT
1 GTGT
89669233 GGTACACACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.28
Consensus pattern (18 bp):
GTGTAATCGCACACATCC
Found at i:89672385 original size:19 final size:19
Alignment explanation
Indices: 89672361--89672441 Score: 108
Period size: 19 Copynumber: 4.1 Consensus size: 19
89672351 ATGCACTAAA
*
89672361 AATTAATTAAATATTAATT
1 AATTAATTAAAAATTAATT
89672380 AATTAATTAAAAATTAATT
1 AATTAATTAAAAATTAATT
89672399 AATTAATTAAACAATTAATT
1 AATTAATTAAA-AATTAATT
**
89672419 AAACAATGTAAACAATTAATT
1 AATTAAT-TAAA-AATTAATT
89672440 AA
1 AA
89672442 AAATTTTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 29 0.51
20 13 0.23
21 15 0.26
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (19 bp):
AATTAATTAAAAATTAATT
Found at i:89672401 original size:15 final size:15
Alignment explanation
Indices: 89672357--89672404 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
89672347 AAATATGCAC
*
89672357 TAAAAATTAATTAAA
1 TAAAAATTAATTAAT
**
89672372 TATTAATTAATTAAT
1 TAAAAATTAATTAAT
89672387 TAAAAATTAATTAAT
1 TAAAAATTAATTAAT
89672402 TAA
1 TAA
89672405 TTAAACAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAAATTAATTAAT
Found at i:89672421 original size:12 final size:11
Alignment explanation
Indices: 89672357--89672446 Score: 72
Period size: 11 Copynumber: 8.7 Consensus size: 11
89672347 AAATATGCAC
89672357 TAAAAATTAAT
1 TAAAAATTAAT
*
89672368 TAAATATTAAT
1 TAAAAATTAAT
89672379 T---AATTAAT
1 TAAAAATTAAT
89672387 TAAAAATTAAT
1 TAAAAATTAAT
89672398 T---AATTAAT
1 TAAAAATTAAT
89672406 TAAACAATTAAT
1 TAAA-AATTAAT
89672418 TAAACAATGT-A-
1 TAAA-AAT-TAAT
*
89672429 -AACAATTAAT
1 TAAAAATTAAT
89672439 TAAAAATT
1 TAAAAATT
89672447 TTAAAGAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
8 16 0.25
9 4 0.06
10 2 0.03
11 25 0.39
12 16 0.25
13 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (11 bp):
TAAAAATTAAT
Found at i:89672439 original size:4 final size:4
Alignment explanation
Indices: 89672361--89672420 Score: 70
Period size: 4 Copynumber: 15.5 Consensus size: 4
89672351 ATGCACTAAA
* *
89672361 AATT AATT AAAT -ATT AATT AATT AATT AA-A AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT
**
89672407 AAAC AATT AATT AA
1 AATT AATT AATT AA
89672421 ACAATGTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 4 0.09
4 42 0.91
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (4 bp):
AATT
Found at i:89672451 original size:21 final size:21
Alignment explanation
Indices: 89672373--89672456 Score: 77
Period size: 21 Copynumber: 4.1 Consensus size: 21
89672363 TTAATTAAAT
**
89672373 ATTAATTAATTAA-TTAAA-A
1 ATTAATTAAACAATTTAAACA
**
89672392 ATTAATTAATTAA-TTAAACA
1 ATTAATTAAACAATTTAAACA
*
89672412 ATTAATTAAACAATGTAAACA
1 ATTAATTAAACAATTTAAACA
*
89672433 ATTAATTAAA-AATTTTAAAGA
1 ATTAATTAAACAA-TTTAAACA
89672454 ATT
1 ATT
89672457 CTAAACGTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 18 0.32
20 14 0.25
21 25 0.44
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
ATTAATTAAACAATTTAAACA
Found at i:89672919 original size:41 final size:42
Alignment explanation
Indices: 89672841--89672945 Score: 151
Period size: 41 Copynumber: 2.5 Consensus size: 42
89672831 TGGTCCCAGC
*
89672841 TTGGACTTTTC-CAAGGGCTAGAGCGTCACTCACTCGATTTTG
1 TTGGAC-TTTCGCAAGGGCTCGAGCGTCACTCACTCGATTTTG
* *
89672883 TTGGAGTTTCGCAAGGGCTCGA-CGTCACTCAGTCGATTTTG
1 TTGGACTTTCGCAAGGGCTCGAGCGTCACTCACTCGATTTTG
*
89672924 TTGGACTTTTGCAAGGGCTCGA
1 TTGGACTTTCGCAAGGGCTCGA
89672946 ATGTCGAGCG
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
41 42 0.74
42 15 0.26
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (42 bp):
TTGGACTTTCGCAAGGGCTCGAGCGTCACTCACTCGATTTTG
Found at i:89677741 original size:26 final size:26
Alignment explanation
Indices: 89677712--89677819 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
89677702 TGGTACAAAT
89677712 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
89677738 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89677764 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
89677790 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89677816 TGAT
1 TGAT
89677820 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:89695350 original size:42 final size:41
Alignment explanation
Indices: 89695246--89695350 Score: 149
Period size: 41 Copynumber: 2.5 Consensus size: 41
89695236 CGCTCGACAT
*
89695246 TCGAGCCCTTGCAAAAGTCCAACAAAATCGACTGAGTGACG
1 TCGAGCCCTTGGAAAAGTCCAACAAAATCGACTGAGTGACG
* *
89695287 TCGAGCCCTTGCG-AAACTCCAACAAAATCGAGTGAGTGACG
1 TCGAGCCCTTG-GAAAAGTCCAACAAAATCGACTGAGTGACG
*
89695328 CTCTAGCCCTTGGAAAAGTCCAA
1 -TCGAGCCCTTGGAAAAGTCCAA
89695351 GCTGGGACCA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
41 38 0.68
42 18 0.32
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (41 bp):
TCGAGCCCTTGGAAAAGTCCAACAAAATCGACTGAGTGACG
Found at i:89695760 original size:21 final size:22
Alignment explanation
Indices: 89695736--89695787 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
89695726 TAACGTTTAG
*
89695736 AATTCTTTAAAATT-TTTAATT
1 AATTGTTTAAAATTGTTTAATT
*
89695757 AATTGTTT-ACATTGTTTAATT
1 AATTGTTTAAAATTGTTTAATT
89695778 AATTGTTTAA
1 AATTGTTTAA
89695788 TTAATTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 4 0.15
21 22 0.81
22 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (22 bp):
AATTGTTTAAAATTGTTTAATT
Found at i:89695779 original size:4 final size:4
Alignment explanation
Indices: 89695772--89695831 Score: 70
Period size: 4 Copynumber: 15.5 Consensus size: 4
89695762 TTTACATTGT
** *
89695772 TTAA TTAA TTGT TTAA TTAA TTAA TTAA TT-T TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA
*
89695819 -TAT TTAA TTAA TT
1 TTAA TTAA TTAA TT
89695832 TTTAGTGCAT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 4 0.09
4 42 0.91
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (4 bp):
TTAA
Found at i:89695782 original size:12 final size:11
Alignment explanation
Indices: 89695746--89695835 Score: 72
Period size: 11 Copynumber: 8.7 Consensus size: 11
89695736 AATTCTTTAA
89695746 AATTTTTAATT
1 AATTTTTAATT
89695757 AATTGTTTACA-T
1 AATT-TTTA-ATT
*
89695769 --TGTTTAATT
1 AATTTTTAATT
89695778 AATTGTTTAATT
1 AATT-TTTAATT
89695790 AA---TTAATT
1 AATTTTTAATT
89695798 AATTTTTAATT
1 AATTTTTAATT
89695809 AA---TTAATT
1 AATTTTTAATT
*
89695817 AATATTTAATT
1 AATTTTTAATT
89695828 AATTTTTA
1 AATTTTTA
89695836 GTGCATATTT
Statistics
Matches: 64, Mismatches: 3, Indels: 24
0.70 0.03 0.26
Matches are distributed among these distances:
8 17 0.27
9 5 0.08
10 1 0.02
11 26 0.41
12 14 0.22
13 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTTTAATT
Found at i:89695807 original size:19 final size:20
Alignment explanation
Indices: 89695751--89695831 Score: 112
Period size: 19 Copynumber: 4.1 Consensus size: 20
89695741 TTTAAAATTT
**
89695751 TTAATTAATTGTTTACATTGT
1 TTAATTAATTGTTTA-ATTAA
89695772 TTAATTAATTGTTTAATTAA
1 TTAATTAATTGTTTAATTAA
89695792 TTAATTAATT-TTTAATTAA
1 TTAATTAATTGTTTAATTAA
*
89695811 TTAATTAA-TATTTAATTAA
1 TTAATTAATTGTTTAATTAA
89695830 TT
1 TT
89695832 TTTAGTGCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
18 1 0.02
19 28 0.49
20 13 0.23
21 15 0.26
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (20 bp):
TTAATTAATTGTTTAATTAA
Found at i:89695808 original size:15 final size:15
Alignment explanation
Indices: 89695788--89695835 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
89695778 AATTGTTTAA
89695788 TTAATTAATTAATTT
1 TTAATTAATTAATTT
*
89695803 TTAATTAATTAATTA
1 TTAATTAATTAATTT
* *
89695818 ATATTTAATTAATTT
1 TTAATTAATTAATTT
89695833 TTA
1 TTA
89695836 GTGCATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTAATTAATTT
Found at i:89701690 original size:20 final size:19
Alignment explanation
Indices: 89701657--89701735 Score: 85
Period size: 20 Copynumber: 4.2 Consensus size: 19
89701647 GATACGTGGA
89701657 TATGATAT--ACATGATTG
1 TATGATATGCACATGATTG
*
89701674 ATATGATATGCACATGACATG
1 -TATGATATGCACATGA-TTG
89701695 TATGATATGCACATGATATG
1 TATGATATGCACATGAT-TG
89701715 TATGA-AGTGCACATGA-TG
1 TATGATA-TGCACATGATTG
89701733 TAT
1 TAT
89701736 TCATAAATGC
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
18 13 0.24
19 1 0.02
20 38 0.70
21 2 0.04
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.34
Consensus pattern (19 bp):
TATGATATGCACATGATTG
Found at i:89701810 original size:26 final size:25
Alignment explanation
Indices: 89701781--89701863 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 25
89701771 GAGGAAGTGC
89701781 AAAAGGGCTTATGCCTCAGTTTATTG
1 AAAAGGGCTTATGCC-CAGTTTATTG
**
89701807 AAAAGGGCTTATGCCCAGTTTACCG
1 AAAAGGGCTTATGCCCAGTTTATTG
89701832 AAAA-GGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATG-CCCAGTTTATTG
89701854 AAAAGAGGCT
1 AAAAG-GGCT
89701864 AGGCCTCCAG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
22 4 0.08
23 5 0.10
24 14 0.28
25 12 0.24
26 15 0.30
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTATGCCCAGTTTATTG
Found at i:89701847 original size:24 final size:26
Alignment explanation
Indices: 89701781--89701850 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
89701771 GAGGAAGTGC
* **
89701781 AAAAGGGCTTATGCCTCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
89701807 AAAAGGGCTTATG-CCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
89701832 AAAA-GGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
89701851 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.05
24 12 0.30
25 13 0.32
26 13 0.32
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:89704927 original size:22 final size:21
Alignment explanation
Indices: 89704902--89704950 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
89704892 TATTCTTATA
* *
89704902 AAATTTTAAAACCCTAAACCTT
1 AAATTCTAAAACCCTAAA-ATT
* *
89704924 AAATACTAAAATCCTAAAATT
1 AAATTCTAAAACCCTAAAATT
89704945 AAATTC
1 AAATTC
89704951 CAAATAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATTCTAAAACCCTAAAATT
Found at i:89717047 original size:41 final size:42
Alignment explanation
Indices: 89716969--89717073 Score: 142
Period size: 41 Copynumber: 2.5 Consensus size: 42
89716959 TGGTCCCAGC
*
89716969 TTGGACTTTTC-CAAGGGCTGGAGCGTCACTCACTCGATTTTG
1 TTGGAC-TTTCGCAAGGGCTCGAGCGTCACTCACTCGATTTTG
* **
89717011 TTGGAGTTTCGCAAGGGCTCGA-CGTCACTCGGTCGATTTTG
1 TTGGACTTTCGCAAGGGCTCGAGCGTCACTCACTCGATTTTG
*
89717052 TTGGACTTTTGCAAGGGCTCGA
1 TTGGACTTTCGCAAGGGCTCGA
89717074 ATGTCGAGCG
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 41 0.73
42 15 0.27
ACGTcount: A:0.16, C:0.22, G:0.30, T:0.32
Consensus pattern (42 bp):
TTGGACTTTCGCAAGGGCTCGAGCGTCACTCACTCGATTTTG
Found at i:89723455 original size:41 final size:40
Alignment explanation
Indices: 89723387--89723500 Score: 115
Period size: 40 Copynumber: 2.8 Consensus size: 40
89723377 TATAATCTCG
* *
89723387 CACACTAAGTGCCTTTCATAGTTGAAGCTATCT-CAACCTCA
1 CACACTAAGTGCCTAT-ATAGTCGAAGCTATCTCCAA-CTCA
* * * *
89723428 CACACTAAGTGCCATATATAGCCGAAGCTAT-TCCGATTCC
1 CACACTAAGTGCC-TATATAGTCGAAGCTATCTCCAACTCA
*
89723468 CACACTAAGTGCTTTATATAGTCGAAGCTATCT
1 CACACTAAGTGC-CTATATAGTCGAAGCTATCT
89723501 AGAAATGCAC
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
40 31 0.51
41 28 0.46
42 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (40 bp):
CACACTAAGTGCCTATATAGTCGAAGCTATCTCCAACTCA
Found at i:89725302 original size:16 final size:16
Alignment explanation
Indices: 89725271--89725313 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
89725261 CGTAAATTAG
*
89725271 ATTTAAAATAATATAAA
1 ATTTATAAT-ATATAAA
*
89725288 ATTTATAATATATAAC
1 ATTTATAATATATAAA
*
89725304 TTTTATAATA
1 ATTTATAATA
89725314 AAAAAACTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTATAATATATAAA
Found at i:89727578 original size:2 final size:2
Alignment explanation
Indices: 89727571--89727631 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
89727561 CACCTTTTTC
89727571 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
89727613 CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
89727632 ACTTCTGTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:89728718 original size:41 final size:41
Alignment explanation
Indices: 89728647--89728783 Score: 195
Period size: 41 Copynumber: 3.3 Consensus size: 41
89728637 AGCTTGGACT
* *
89728647 TTTC-CAAGGGCTGAAGCGTCACTCGCTCGATTTTGTTGGAG
1 TTTCGCAAGGGCT-CAGCGTCACTCGGTCGATTTTGTTGGAG
*
89728688 ATTCGCAAGGGCTCAGCGTCACTCGGTCGATTTTGTTGGAG
1 TTTCGCAAGGGCTCAGCGTCACTCGGTCGATTTTGTTGGAG
* * *
89728729 TTTCGCAAGGGCTCAGCGACACTCGGTCGATTTTGTTAGAC
1 TTTCGCAAGGGCTCAGCGTCACTCGGTCGATTTTGTTGGAG
*
89728770 TTTTGCAAGGGCTC
1 TTTCGCAAGGGCTC
89728784 TAATGTCGAG
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 79 0.91
42 8 0.09
ACGTcount: A:0.18, C:0.23, G:0.29, T:0.31
Consensus pattern (41 bp):
TTTCGCAAGGGCTCAGCGTCACTCGGTCGATTTTGTTGGAG
Found at i:89741195 original size:32 final size:32
Alignment explanation
Indices: 89741159--89741230 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
89741149 TAATATTGGA
89741159 TAATTATTTGATACACATGAAGCACATATTTT
1 TAATTATTTGATACACATGAAGCACATATTTT
89741191 TAATTATTTGATACACATGAAGCACATATTTT
1 TAATTATTTGATACACATGAAGCACATATTTT
89741223 TAACTTAT
1 TAA-TTAT
89741231 AACATCCCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
32 35 0.90
33 4 0.10
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (32 bp):
TAATTATTTGATACACATGAAGCACATATTTT
Found at i:89742292 original size:23 final size:22
Alignment explanation
Indices: 89742256--89742298 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
89742246 CAGAAAATTT
*
89742256 TGCCAATAATAATGCAGATAAGC
1 TGCCAATAAAAATGC-GATAAGC
*
89742279 TGCCAGTAAAAATGCGATAA
1 TGCCAATAAAAATGCGATAA
89742299 ATCACCGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (22 bp):
TGCCAATAAAAATGCGATAAGC
Found at i:89746517 original size:93 final size:93
Alignment explanation
Indices: 89746358--89746529 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
89746348 CGCCCATAAG
* * * *
89746358 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAGGTGAACTTGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
89746423 ACAAGTTCGGATGCCTAGTTACATTTCA
66 ACAAGTTCGGATGCCTAGTTACATTTCA
* *
89746451 CGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
89746516 ACAAGTTCGGATGC
66 ACAAGTTCGGATGC
89746530 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACAAGTTCGGATGCCTAGTTACATTTCA
Found at i:89746523 original size:46 final size:46
Alignment explanation
Indices: 89746351--89746526 Score: 162
Period size: 46 Copynumber: 3.8 Consensus size: 46
89746341 TGTAACCCGC
* * * *
89746351 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCAT
* * * *
89746397 CCATAGGTGAACTTGGACTCAACTCAACAAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACAAGTTCGGA---C-A-TTCGCAT
* * **
89746447 --TTCA-CGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCAT
*
89746490 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACAAGTTCGGA
89746527 TGCTCAACCA
Statistics
Matches: 100, Mismatches: 21, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 58 0.58
47 26 0.26
48 1 0.01
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCAT
Found at i:89746545 original size:46 final size:45
Alignment explanation
Indices: 89746403--89746545 Score: 105
Period size: 46 Copynumber: 3.1 Consensus size: 45
89746393 GCATCCATAG
* *
89746403 GTGAACTTGGACTCAACTCAACAAGTTCGGATGC-CTAGTTA-CATTTCA
1 GTGAACTCGGACTCAACTCAACAAGTTCGGATGCTC-A---ACCATCT-A
* ** * * * *
89746451 -CGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCAT-AA
1 GTGAACTCGGACTCAACTCAACAAGTTCGG--ATGCTCAACCATCTA
89746496 GTGAACTCGGACTCAACTCAACAAGTTCGGATGCTCAACCATCCTA
1 GTGAACTCGGACTCAACTCAACAAGTTCGGATGCTCAACCAT-CTA
89746542 GTGA
1 GTGA
89746546 CATGTCACTT
Statistics
Matches: 74, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 31 0.42
47 28 0.38
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (45 bp):
GTGAACTCGGACTCAACTCAACAAGTTCGGATGCTCAACCATCTA
Found at i:89750375 original size:15 final size:15
Alignment explanation
Indices: 89750355--89750415 Score: 97
Period size: 15 Copynumber: 4.1 Consensus size: 15
89750345 TATGCGATGA
89750355 ATTGATTGAATTTAT
1 ATTGATTGAATTTAT
*
89750370 ATTGATTGAAATTAT
1 ATTGATTGAATTTAT
*
89750385 TTTGATTGAATTTAT
1 ATTGATTGAATTTAT
89750400 ATTGATTGAA-TTAT
1 ATTGATTGAATTTAT
89750414 AT
1 AT
89750416 AATATATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
14 6 0.14
15 36 0.86
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (15 bp):
ATTGATTGAATTTAT
Found at i:89750392 original size:30 final size:29
Alignment explanation
Indices: 89750356--89750413 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
89750346 ATGCGATGAA
89750356 TTGATTGAATTTATATTGATTGAAATTATT
1 TTGATTGAATTTATATTGATTG-AATTATT
89750386 TTGATTGAATTTATATTGATTGAATTAT
1 TTGATTGAATTTATATTGATTGAATTAT
89750414 ATAATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (29 bp):
TTGATTGAATTTATATTGATTGAATTATT
Found at i:89750846 original size:21 final size:23
Alignment explanation
Indices: 89750787--89750852 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
89750777 GCTTTATCAA
89750787 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* ** *
89750810 TCAGGCACCTCGTGTGTTGT-TT
1 TCAGGCACTTTATGTGTCGTATT
89750832 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
89750853 ACTGATCAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
21 14 0.41
22 4 0.12
23 16 0.47
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.42
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:89760637 original size:119 final size:118
Alignment explanation
Indices: 89760494--89760720 Score: 341
Period size: 119 Copynumber: 1.9 Consensus size: 118
89760484 AGAGGACTTT
* * *
89760494 GATTTTTGGGGGTAAATAGGGAGAAATAAAATATTTTTG-GGGATTTTGATTTTTGGGAGTAAAA
1 GATTTTTGGGGGTAAAGAGGGAGAAATAAAATATTTTTGAGGGATTTGGATTTTGGGGAGTAAAA
89760558 -GGGGGAGAGAAAGTAAAAAATTTTGAAGGTAAGGGGGATAAAAATTCGTGGGGG
66 TGGGGGAGAGAAA-T-AAAAATTTTGAAGGTAAGGGGGATAAAAATTCGTGGGGG
89760612 GATTTTTGGGGGGTAAAGAGGGAGAAATAAAATATTTTTGAGGGATTTGGATTTTGGGGAGTAAA
1 GATTTTT-GGGGGTAAAGAGGGAGAAATAAAATATTTTTGAGGGATTTGGATTTTGGGGAGTAAA
* * * * *
89760677 ATGGGGGGGGGGAATAAAATTTTTGGAGGTAAGGGGGATAAAAA
65 ATGGGGGAGAGAAATAAAAATTTTGAAGGTAAGGGGGATAAAAA
89760721 GTTTGCGAGG
Statistics
Matches: 98, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
118 7 0.07
119 58 0.59
120 24 0.24
121 9 0.09
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (118 bp):
GATTTTTGGGGGTAAAGAGGGAGAAATAAAATATTTTTGAGGGATTTGGATTTTGGGGAGTAAAA
TGGGGGAGAGAAATAAAAATTTTGAAGGTAAGGGGGATAAAAATTCGTGGGGG
Found at i:89762782 original size:57 final size:59
Alignment explanation
Indices: 89762682--89762819 Score: 153
Period size: 57 Copynumber: 2.4 Consensus size: 59
89762672 CATTACAGAA
*
89762682 AGGATTTAG-CTCGGATGAGTAATCCTAATATAAGCCCTCTTGAGCATATGTT-TCA-ATT
1 AGGATTTAGCCT-GGATGAGTAATCCTAATATAAGCCCTCTTGAGCATATGTTAT-AGACT
* * * * *
89762740 AGGATTTAGCCTGGATTAGTTATCTTAAT-TAAGCTCTTTTGAGCATATGTTATAGACT
1 AGGATTTAGCCTGGATGAGTAATCCTAATATAAGCCCTCTTGAGCATATGTTATAGACT
89762798 -GGATTTAGCCTGGACTG-GTAAT
1 AGGATTTAGCCTGGA-TGAGTAAT
89762820 TCAGATTAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
57 39 0.57
58 27 0.40
59 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (59 bp):
AGGATTTAGCCTGGATGAGTAATCCTAATATAAGCCCTCTTGAGCATATGTTATAGACT
Found at i:89762828 original size:57 final size:57
Alignment explanation
Indices: 89762740--89762934 Score: 148
Period size: 57 Copynumber: 3.4 Consensus size: 57
89762730 TGTTTCAATT
* * * * * ** * * *
89762740 AGGATTTAGCCTGGATTAGTTATCTTAATTAAGCTCTTTTGAGCATATGTTATAGAC
1 AGGATTTAGCCTGGACTGGTAATCTCAATTAAACTCTTAAGAGCATATGTCACAGAA
*
89762797 TGGATTTAGCCTGGACTGGTAAT-TCAGATTAAACTCTTAAGAGCATATGTCACAGAA
1 AGGATTTAGCCTGGACTGGTAATCTCA-ATTAAACTCTTAAGAGCATATGTCACAGAA
* * * * * * * *
89762854 AGAATTTAGTCTGGACTGGTAATCCTGACA--AAGCTCTT-AGAGAACACGTTACAGATA
1 AGGATTTAGCCTGGACTGGTAAT-CTCA-ATTAAACTCTTAAGAGCATATGTCACAGA-A
89762911 A-GATTTAGCCTGGACTGGTAATCT
1 AGGATTTAGCCTGGACTGGTAATCT
89762935 TGTTGTATGA
Statistics
Matches: 111, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
55 2 0.02
56 34 0.31
57 72 0.65
59 3 0.03
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.32
Consensus pattern (57 bp):
AGGATTTAGCCTGGACTGGTAATCTCAATTAAACTCTTAAGAGCATATGTCACAGAA
Found at i:89762927 original size:56 final size:56
Alignment explanation
Indices: 89762799--89762933 Score: 157
Period size: 56 Copynumber: 2.4 Consensus size: 56
89762789 TTATAGACTG
* * * * *
89762799 GATTTAGCCTGGACTGGTAATTCAGATTAAACTCTTAAGAGCATATGTCACAGAAA
1 GATTTAGCCTGGACTGGTAATCCAGATCAAACTCTTAAGAGAACACGTCACAGAAA
* * *
89762855 GAATTTAGTCTGGACTGGTAATCCTGA-CAAAGCTCTT-AGAGAACACGTTACAGATAA
1 G-ATTTAGCCTGGACTGGTAATCCAGATCAAA-CTCTTAAGAGAACACGTCACAGA-AA
89762912 GATTTAGCCTGGACTGGTAATC
1 GATTTAGCCTGGACTGGTAATC
89762934 TTGTTGTATG
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
56 37 0.55
57 30 0.45
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (56 bp):
GATTTAGCCTGGACTGGTAATCCAGATCAAACTCTTAAGAGAACACGTCACAGAAA
Found at i:89765637 original size:55 final size:53
Alignment explanation
Indices: 89765549--89765803 Score: 227
Period size: 55 Copynumber: 4.8 Consensus size: 53
89765539 ATTAGGGTTG
* **
89765549 AAGGATACCGTGTAAGACCATG-CTAAGGTATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGTC-AAGACATGGC-ATTGGTAA-GTTTCTAAGGC
* * * *
89765604 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTT--TCTAAGGC
* * * *
89765659 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTC-TAAGGC
* *
89765712 AAGGATACCATGTAAGACCATGTCAAGACATGGAAATGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCTAAGGC
* * * ** *
89765761 AAGGATACCACGTTAGACCATGACAATTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAG
89765804 GTACCCGTGT
Statistics
Matches: 166, Mismatches: 27, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
49 37 0.22
52 7 0.04
53 41 0.25
54 11 0.07
55 65 0.39
56 5 0.03
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCTAAGGC
Found at i:89765755 original size:108 final size:110
Alignment explanation
Indices: 89765559--89765756 Score: 294
Period size: 108 Copynumber: 1.8 Consensus size: 110
89765549 AAGGATACCG
* * *
89765559 TGTAAGACCATGCTAAGGTATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGACCA
1 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
* *
89765624 TGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCA
66 TGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTCCCA
* *
89765669 TGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAGACC
1 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGACC
*
89765731 ATGTCAAGACATGGAAATGGTAAGTT
65 ATGTCAAGACATGGAAATGATAAGTT
89765757 TCAAAAGGAT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.59
109 7 0.09
110 22 0.28
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.24
Consensus pattern (110 bp):
TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
TGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTCCCA
Found at i:89766016 original size:16 final size:16
Alignment explanation
Indices: 89765995--89766025 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89765985 ATAAATTTGA
89765995 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
89766011 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
89766026 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:89773218 original size:55 final size:53
Alignment explanation
Indices: 89773130--89773384 Score: 227
Period size: 55 Copynumber: 4.8 Consensus size: 53
89773120 ATTAGGGTTT
* **
89773130 AAGGATACCGTGTAAGACCATG-CTAAGGTATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGTC-AAGACATGGC-ATTGGTAA-GTTTCTAAGGC
* * * *
89773185 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTT--TCTAAGGC
* * * *
89773240 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTC-TAAGGC
* *
89773293 AAGGATACCATGTAAGACCATGTCAAGACATGGAAATGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCTAAGGC
* * * ** *
89773342 AAGGATACCACGTTAGACCATGACAATTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAG
89773385 GTACCCGTGT
Statistics
Matches: 166, Mismatches: 27, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
49 37 0.22
52 7 0.04
53 41 0.25
54 11 0.07
55 65 0.39
56 5 0.03
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCTAAGGC
Found at i:89773336 original size:108 final size:110
Alignment explanation
Indices: 89773140--89773337 Score: 294
Period size: 108 Copynumber: 1.8 Consensus size: 110
89773130 AAGGATACCG
* * *
89773140 TGTAAGACCATGCTAAGGTATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGACCA
1 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
* *
89773205 TGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCA
66 TGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTCCCA
* *
89773250 TGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAGACC
1 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGACC
*
89773312 ATGTCAAGACATGGAAATGGTAAGTT
65 ATGTCAAGACATGGAAATGATAAGTT
89773338 TCAAAAGGAT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.59
109 7 0.09
110 22 0.28
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.24
Consensus pattern (110 bp):
TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
TGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTCCCA
Found at i:89773602 original size:16 final size:16
Alignment explanation
Indices: 89773581--89773611 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89773571 ATAAATTTGA
89773581 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
89773597 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
89773612 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:89776694 original size:48 final size:48
Alignment explanation
Indices: 89776623--89776903 Score: 287
Period size: 48 Copynumber: 5.9 Consensus size: 48
89776613 AGGGAAACTT
* * * * *
89776623 GCCGATGCCTTGTCCCAAACATGGTCTTACATTGGCTCACATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAG
* * *
89776671 GCCGATGCCATGTCCCAGGCATGGTCTTACACTAGCTCTCATGTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAG
* * * *
89776719 ACCGATGCCATATCCCAGACATGGTCTTACACTGGCTCACACGTCAAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAG
* * * * * *
89776767 GCCGATGCCATGTCCCAGACATGGTCATACACTAGCTCTCGTCTAAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAG
** * * * * **
89776815 GATGATGCCATGTCCCAAACATGATCTTACACTGGCTCTCATGAT-GTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATG-TCAAG
* *
89776863 GCCGATGCCATGTCCC-GACATGGTCTTACATTAGCACACAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT
89776904 ATGACCCAAA
Statistics
Matches: 188, Mismatches: 44, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
47 19 0.10
48 168 0.89
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCAAG
Found at i:89776790 original size:96 final size:97
Alignment explanation
Indices: 89776624--89776897 Score: 367
Period size: 96 Copynumber: 2.9 Consensus size: 97
89776614 GGGAAACTTG
* *
89776624 CCGATGCCTTGTCCCAAACATGGTCTTACATTGGCTCACATGTCGAGGCCGATGCCATGTCCCAG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCCAG
* * *
89776689 GCATGGTCTTACACTAGCTCTCATGTCAAT-A
66 ACATGGTCTTACACTAGCTCTCATCTAAATGA
* * * *
89776720 CCGATGCCATATCCCAGACATGGTCTTACACTGGCTCACACGTCAAGGCCGATGCCATGTCCCAG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCCAG
* *
89776785 ACATGGTCATACACTAGCTCTCGTCTAAATGA
66 ACATGGTCTTACACTAGCTCTCATCTAAATGA
* * * *
89776817 -TGATGCCATGTCCCAAACATGATCTTACACTGGCTCTCATGAT-GTGGCCGATGCCATGTCCC-
1 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATG-TCGAGGCCGATGCCATGTCCCA
*
89776879 GACATGGTCTTACATTAGC
65 GACATGGTCTTACACTAGC
89776898 ACACATATGA
Statistics
Matches: 155, Mismatches: 21, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
95 17 0.11
96 136 0.88
97 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.26
Consensus pattern (97 bp):
CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCCAG
ACATGGTCTTACACTAGCTCTCATCTAAATGA
Found at i:89780738 original size:40 final size:40
Alignment explanation
Indices: 89780694--89780771 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
89780684 ATTTTTAAAA
*
89780694 AAAAAACGCCGCAAT-AGATCGAGCTTTAGCGGCGTTTTTG
1 AAAAAACGCCGCAATAAG-TCGACCTTTAGCGGCGTTTTTG
* * *
89780734 AAAAAGCGCCGCTATAAGTCGACCTTTAGTGGCGTTTT
1 AAAAAACGCCGCAATAAGTCGACCTTTAGCGGCGTTTT
89780772 ACCAAAACGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (40 bp):
AAAAAACGCCGCAATAAGTCGACCTTTAGCGGCGTTTTTG
Found at i:89780911 original size:74 final size:74
Alignment explanation
Indices: 89780759--89780929 Score: 191
Period size: 74 Copynumber: 2.3 Consensus size: 74
89780749 AAGTCGACCT
* * ***
89780759 TTAGTGGCGTTTTACC-AAAACGCCGCTAAAAGGTTAAGAAAAATGGCGTCGTTTTACATGAGCT
1 TTAGCGGCGTTTTCCCAAAAACGCCGCTAAAAGGTTAAGAAAAACAACGTCGTTTTACATGAGCT
* *
89780823 TCATTGGCA
66 TCAGTGACA
* * * * *
89780832 GTAGCGGCGTTTTCCCAAAAACGTCGCTAAAATGTTAAGCAAAACAACGTCGTTTTATATGAGCT
1 TTAGCGGCGTTTTCCCAAAAACGCCGCTAAAAGGTTAAGAAAAACAACGTCGTTTTACATGAGCT
*
89780897 TCAGTGATA
66 TCAGTGACA
* * *
89780906 TTAGCGGTGCTTTCCTAAAAACGC
1 TTAGCGGCGTTTTCCCAAAAACGC
89780930 TGTAATAGCT
Statistics
Matches: 79, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
73 13 0.16
74 66 0.84
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (74 bp):
TTAGCGGCGTTTTCCCAAAAACGCCGCTAAAAGGTTAAGAAAAACAACGTCGTTTTACATGAGCT
TCAGTGACA
Found at i:89781767 original size:15 final size:14
Alignment explanation
Indices: 89781749--89781791 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
89781739 ATTTAATATT
89781749 TTATAGGTTTAGGGG
1 TTAT-GGTTTAGGGG
*
89781764 TTATGGGTTTAAGGG
1 TTAT-GGTTTAGGGG
*
89781779 TTATGATTTAGGG
1 TTATGGTTTAGGG
89781792 TTGATGATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (14 bp):
TTATGGTTTAGGGG
Found at i:89781798 original size:14 final size:13
Alignment explanation
Indices: 89781756--89781821 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 13
89781746 ATTTTATAGG
*
89781756 TTTAGGGGTTATGGG
1 TTTA-GGGTTAT-GA
89781771 TTTAAGGGTTATGA
1 TTT-AGGGTTATGA
89781785 TTTAGGGTTGATGA
1 TTTAGGGTT-ATGA
**
89781799 TTTATGTTTTATGA
1 TTTA-GGGTTATGA
89781813 TTTAGGGTT
1 TTTAGGGTT
89781822 TGAGGTTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
13 9 0.21
14 20 0.47
15 13 0.30
16 1 0.02
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (13 bp):
TTTAGGGTTATGA
Found at i:89781837 original size:28 final size:28
Alignment explanation
Indices: 89781779--89781837 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
89781769 GGTTTAAGGG
**
89781779 TTATGATTTAGGGTTGATGATTTATGTT
1 TTATGATTTAGGGTTGATGATTTATAAT
*
89781807 TTATGATTTAGGGTTTGA-GGTTTATAAT
1 TTATGATTTAGGG-TTGATGATTTATAAT
89781835 TTA
1 TTA
89781838 GAATGTTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (28 bp):
TTATGATTTAGGGTTGATGATTTATAAT
Found at i:89782214 original size:14 final size:14
Alignment explanation
Indices: 89782197--89782236 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
89782187 AAGGTCTAGT
89782197 GTTTGGGGTTTAAG
1 GTTTGGGGTTTAAG
* *
89782211 GTTTGGAGTTTATG
1 GTTTGGGGTTTAAG
*
89782225 GTTTAGGGTTTA
1 GTTTGGGGTTTA
89782237 TGGAATAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.47
Consensus pattern (14 bp):
GTTTGGGGTTTAAG
Found at i:89782221 original size:21 final size:21
Alignment explanation
Indices: 89782178--89782236 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
89782168 TAGGGGTTAA
* *
89782178 TTAGGGTTTAAGGTCTAGTGT
1 TTAGGGTTTAAGGTTTAGAGT
* *
89782199 TTGGGGTTTAAGGTTTGGAGT
1 TTAGGGTTTAAGGTTTAGAGT
* *
89782220 TTATGGTTTAGGGTTTA
1 TTAGGGTTTAAGGTTTA
89782237 TGGAATAGGG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.02, G:0.36, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTAAGGTTTAGAGT
Found at i:89782383 original size:14 final size:14
Alignment explanation
Indices: 89782349--89782383 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
89782339 TTTTAGGGTG
*
89782349 TTAGGGTTTAATGT
1 TTAGGGTTTAAAGT
89782363 TTA-GGTTTAAAGT
1 TTAGGGTTTAAAGT
89782376 TTAGGGTT
1 TTAGGGTT
89782384 ATATTTAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.49
Consensus pattern (14 bp):
TTAGGGTTTAAAGT
Found at i:89782478 original size:7 final size:7
Alignment explanation
Indices: 89782468--89782569 Score: 50
Period size: 7 Copynumber: 14.6 Consensus size: 7
89782458 GATTTAGGAT
89782468 TTTAGGG
1 TTTAGGG
*
89782475 TTTAGAG
1 TTTAGGG
89782482 TTT-GTGG
1 TTTAG-GG
*
89782489 ATT-GGG
1 TTTAGGG
*
89782495 TTTTGTGG
1 TTTAG-GG
**
89782503 TTTATAG
1 TTTAGGG
*
89782510 TTTGGGG
1 TTTAGGG
89782517 TTTAGGG
1 TTTAGGG
89782524 TTT-GGTG
1 TTTAGG-G
*
89782531 TTTGGGG
1 TTTAGGG
*
89782538 TTTAGAG
1 TTTAGGG
89782545 TTT-GGAG
1 TTTAGG-G
*
89782552 TTTAGAG
1 TTTAGGG
*
89782559 TTTGGGG
1 TTTAGGG
89782566 TTTA
1 TTTA
89782570 ATTTTGGAAT
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
6 8 0.11
7 54 0.77
8 8 0.11
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:89782525 original size:21 final size:21
Alignment explanation
Indices: 89782492--89782548 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
89782482 TTTGTGGATT
*
89782492 GGGTTTTGTGGTTT-ATAGTTTG
1 GGGTTTAG-GGTTTGAT-GTTTG
*
89782514 GGGTTTAGGGTTTGGTGTTTG
1 GGGTTTAGGGTTTGATGTTTG
*
89782535 GGGTTTAGAGTTTG
1 GGGTTTAGGGTTTG
89782549 GAGTTTAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.09, C:0.00, G:0.42, T:0.49
Consensus pattern (21 bp):
GGGTTTAGGGTTTGATGTTTG
Found at i:89782526 original size:14 final size:14
Alignment explanation
Indices: 89782516--89782569 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
89782506 ATAGTTTGGG
* * *
89782516 GTTTAGGGTTTGGT
1 GTTTGGGGTTTAGA
89782530 GTTTGGGGTTTAGA
1 GTTTGGGGTTTAGA
*
89782544 GTTTGGAGTTTAGA
1 GTTTGGGGTTTAGA
89782558 GTTTGGGGTTTA
1 GTTTGGGGTTTA
89782570 ATTTTGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.13, C:0.00, G:0.41, T:0.46
Consensus pattern (14 bp):
GTTTGGGGTTTAGA
Found at i:89782549 original size:21 final size:21
Alignment explanation
Indices: 89782508--89782554 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
89782498 TGTGGTTTAT
*
89782508 AGTTTGGGGTTTAGGGTTTGG
1 AGTTTGGGGTTTAGAGTTTGG
*
89782529 TGTTTGGGGTTTAGAGTTTGG
1 AGTTTGGGGTTTAGAGTTTGG
89782550 AGTTT
1 AGTTT
89782555 AGAGTTTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.11, C:0.00, G:0.43, T:0.47
Consensus pattern (21 bp):
AGTTTGGGGTTTAGAGTTTGG
Found at i:89782568 original size:21 final size:21
Alignment explanation
Indices: 89782516--89782568 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
89782506 ATAGTTTGGG
* * *
89782516 GTTTAGGGTTTGGTGTTTGGG
1 GTTTAGGGTTTGGAGTTTAGA
*
89782537 GTTTAGAGTTTGGAGTTTAGA
1 GTTTAGGGTTTGGAGTTTAGA
*
89782558 GTTTGGGGTTT
1 GTTTAGGGTTT
89782569 AATTTTGGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.11, C:0.00, G:0.42, T:0.47
Consensus pattern (21 bp):
GTTTAGGGTTTGGAGTTTAGA
Found at i:89783504 original size:24 final size:24
Alignment explanation
Indices: 89783474--89783519 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
89783464 GTCAGGTAAC
89783474 TTTAATTTCTAAGTCTCTGTTTCT
1 TTTAATTTCTAAGTCTCTGTTTCT
89783498 TTTAATTTCTAAGTCTCTGTTT
1 TTTAATTTCTAAGTCTCTGTTT
89783520 ACAAATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (24 bp):
TTTAATTTCTAAGTCTCTGTTTCT
Found at i:89783647 original size:11 final size:11
Alignment explanation
Indices: 89783631--89783655 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
89783621 ACAACTTACT
89783631 TTTTACTGATG
1 TTTTACTGATG
89783642 TTTTACTGATG
1 TTTTACTGATG
89783653 TTT
1 TTT
89783656 CATGGCCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTTACTGATG
Found at i:89784620 original size:25 final size:25
Alignment explanation
Indices: 89784592--89784658 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
89784582 CTAATTCAAA
89784592 ACTCACCATTTCAATTGTTCCCACC
1 ACTCACCATTTCAATTGTTCCCACC
*
89784617 ACTCACCATTTCAATTGTTTCCACC
1 ACTCACCATTTCAATTGTTCCCACC
* * *
89784642 ACGCATCGTTTCAATTG
1 ACTCACCATTTCAATTG
89784659 ATTTCACAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.24, C:0.34, G:0.07, T:0.34
Consensus pattern (25 bp):
ACTCACCATTTCAATTGTTCCCACC
Found at i:89786341 original size:39 final size:39
Alignment explanation
Indices: 89786298--89786467 Score: 223
Period size: 39 Copynumber: 4.3 Consensus size: 39
89786288 GGTCTTTAAC
** * *
89786298 CCGGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCAGACCTCATGT
* * * *
89786337 CCGGATATATTTCTAGCATATAGCTTGCAGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCAGACCTCATGT
* *
89786376 CCGGAAATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCAGACCTCATGT
* *
89786415 CCGGATATATTTCTAGCATATAGCCTGCAGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCAGACCTCATGT
89786454 CCGGATATATTTTC
1 CCGGATAT-TTTTC
89786468 AATCTCATAC
Statistics
Matches: 111, Mismatches: 19, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
39 107 0.96
40 4 0.04
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCAGACCTCATGT
Done.