Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 187 of 190
Found at i:55803967 original size:41 final size:41
Alignment explanation
Indices: 55803897--55804047 Score: 182
Period size: 40 Copynumber: 3.7 Consensus size: 41
55803887 ACCAAAAATT
55803897 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAAATTAAAAAAAGTATTTTAAAAA
* *
55803941 TATTTTAAAATTAAAAAAAATTAAAAAAA-TTTTTTAAAAT
1 TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAA
* * * * *
55803981 TTTTTTAAAATTTAACAAAATTTAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAA
*
55804022 TATTTTAAAA-TAAAGAAAA-TAAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAA
55804048 TAATAAAAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
39 6 0.06
40 41 0.44
41 32 0.34
42 3 0.03
43 6 0.06
44 6 0.06
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (41 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:55804022 original size:11 final size:11
Alignment explanation
Indices: 55804006--55804031 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55803996 CAAAATTTAA
55804006 AAAAGTATTTT
1 AAAAGTATTTT
55804017 AAAAGTATTTT
1 AAAAGTATTTT
55804028 AAAA
1 AAAA
55804032 TAAAGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:55806124 original size:11 final size:12
Alignment explanation
Indices: 55806108--55806144 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
55806098 AAAAATAGGG
55806108 ATTTAAGAG-AA
1 ATTTAAGAGCAA
55806119 ATTTAAGAGCAA
1 ATTTAAGAGCAA
*
55806131 A-TTGAGAGCAA
1 ATTTAAGAGCAA
55806142 ATT
1 ATT
55806145 GAGATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (12 bp):
ATTTAAGAGCAA
Found at i:55806154 original size:11 final size:11
Alignment explanation
Indices: 55806124--55806148 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55806114 GAGAAATTTA
55806124 AGAGCAAATTG
1 AGAGCAAATTG
55806135 AGAGCAAATTG
1 AGAGCAAATTG
55806146 AGA
1 AGA
55806149 TTAAATATGG
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:0.48, C:0.08, G:0.28, T:0.16
Consensus pattern (11 bp):
AGAGCAAATTG
Found at i:55806161 original size:51 final size:51
Alignment explanation
Indices: 55806100--55806248 Score: 141
Period size: 51 Copynumber: 3.0 Consensus size: 51
55806090 AAATAATTAA
* * **
55806100 AAATAGGGATTTAAGAGAAATTTAAGAGCAAATTGAGAGCAAATTGAGATT
1 AAATATGGATTTAAGAGAAATTTAAGAGCAAATTGAGAGAAAATTGAGAGG
* *
55806151 AAATATGGATTTGAGAGAAATTTGGAAG-G-AAATTGAGAGGAAATTGAGAGG
1 AAATATGGATTTAAGAGAAATTT--AAGAGCAAATTGAGAGAAAATTGAGAGG
*
55806202 AAAT-TGAGA---AAG-GATTAATTTGAGAGCAAATTGAGAGAAAATTGAGA
1 AAATATG-GATTTAAGAGA--AATTTAAGAGCAAATTGAGAGAAAATTGAGA
55806249 AAGGATTAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
47 4 0.05
48 3 0.04
49 24 0.29
50 2 0.02
51 46 0.55
52 1 0.01
53 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.24
Consensus pattern (51 bp):
AAATATGGATTTAAGAGAAATTTAAGAGCAAATTGAGAGAAAATTGAGAGG
Found at i:55806173 original size:11 final size:11
Alignment explanation
Indices: 55806161--55806248 Score: 81
Period size: 11 Copynumber: 7.5 Consensus size: 11
55806151 AAATATGGAT
55806161 TTGAGA-GAAA
1 TTGAGAGGAAA
55806171 TTTG-GAAGGAAA
1 -TTGAGA-GGAAA
55806183 TTGAGAGGAAA
1 TTGAGAGGAAA
55806194 TTGAGAGGAAA
1 TTGAGAGGAAA
55806205 TTGAGAAAGGATTAA
1 TTGAG--AGGA--AA
*
55806220 TTTGAGAGCAAA
1 -TTGAGAGGAAA
*
55806232 TTGAGAGAAAA
1 TTGAGAGGAAA
55806243 TTGAGA
1 TTGAGA
55806249 AAGGATTAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
10 2 0.03
11 43 0.64
12 8 0.12
13 4 0.06
14 3 0.04
15 2 0.03
16 5 0.07
ACGTcount: A:0.45, C:0.01, G:0.31, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:55808660 original size:15 final size:15
Alignment explanation
Indices: 55808640--55808668 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55808630 TTTTAATCAC
55808640 TTGTAGACTCATTTA
1 TTGTAGACTCATTTA
55808655 TTGTAGACTCATTT
1 TTGTAGACTCATTT
55808669 TTGCCAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (15 bp):
TTGTAGACTCATTTA
Found at i:55815730 original size:25 final size:24
Alignment explanation
Indices: 55815702--55815756 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
55815692 GAGTCGAACT
*
55815702 CGAATTT-AATATTTTTTATTTAGGC
1 CGAATTTAAATA-TATTT-TTTAGGC
55815727 CGAACTTTAAATATATTTTTTAGGC
1 CGAA-TTTAAATATATTTTTTAGGC
55815752 CGAAT
1 CGAAT
55815757 AAACCCGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 1 0.04
25 15 0.56
26 7 0.26
27 4 0.15
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (24 bp):
CGAATTTAAATATATTTTTTAGGC
Found at i:55821866 original size:22 final size:24
Alignment explanation
Indices: 55821841--55821889 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
55821831 GGTGAATTTT
* *
55821841 TTTTCGAGAA-TTAAATTATAA-A
1 TTTTCAAGAAGTTAAAATATAATA
*
55821863 TTTTTAAGAAGTTAAAATATAATA
1 TTTTCAAGAAGTTAAAATATAATA
55821887 TTT
1 TTT
55821890 GATTTCATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 8 0.36
23 10 0.45
24 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (24 bp):
TTTTCAAGAAGTTAAAATATAATA
Found at i:55822180 original size:19 final size:19
Alignment explanation
Indices: 55822156--55822268 Score: 145
Period size: 19 Copynumber: 5.8 Consensus size: 19
55822146 AATTTTTGAG
55822156 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
** *
55822175 GATATGCAATCCAATATAT
1 GATATGCAATCTTAGATAT
55822194 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
55822215 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
55822234 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
55822253 GACATGCAATCTTAGA
1 GATATGCAATCTTAGA
55822269 ATATATGATT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 63 0.80
21 16 0.20
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:55822201 original size:40 final size:40
Alignment explanation
Indices: 55822157--55822263 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 40
55822147 ATTTTTGAGG
* *
55822157 ATATGCAATCTTAGATATGATATGCAATCCAATATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
**
55822197 ATATGCAATCTTAGATATGATATGCAATCTTAGAGATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
*
55822237 ATAT--AATCTTAGATATGACATGCAATC
1 ATATGCAATCTTAGATATGATATGCAATC
55822264 TTAGAATATA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 22 0.35
40 40 0.65
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
Found at i:55822888 original size:21 final size:21
Alignment explanation
Indices: 55822864--55822903 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
55822854 TTATTCTAAT
* *
55822864 TTTTTTTATCTATATATATTC
1 TTTTTATATCTACATATATTC
*
55822885 TTTTTATATGTACATATAT
1 TTTTTATATCTACATATAT
55822904 ATATATTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTTTATATCTACATATATTC
Found at i:55823323 original size:9 final size:9
Alignment explanation
Indices: 55823311--55823335 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55823301 GATGATGTAT
55823311 TTATTATTG
1 TTATTATTG
55823320 TTATTATTG
1 TTATTATTG
55823329 TTATTAT
1 TTATTAT
55823336 AGCATTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTATTG
Found at i:55823445 original size:36 final size:36
Alignment explanation
Indices: 55823398--55823473 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
55823388 AGATAGATTT
55823398 TTTTTTTTTAAATTGAGATCATGTTCGTATTTAAGA
1 TTTTTTTTTAAATTGAGATCATGTTCGTATTTAAGA
55823434 TTTTTTTTTAAATTGAGATCATGTTCGTATTTAAGA
1 TTTTTTTTTAAATTGAGATCATGTTCGTATTTAAGA
55823470 TTTT
1 TTTT
55823474 CAAGGGAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.55
Consensus pattern (36 bp):
TTTTTTTTTAAATTGAGATCATGTTCGTATTTAAGA
Found at i:55823484 original size:36 final size:36
Alignment explanation
Indices: 55823407--55823486 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
55823397 TTTTTTTTTT
*****
55823407 AAATTGAGATCATGTTCGTATTTAAGATTTTTTTTT
1 AAATTGAGATCATGTTCGTATTTAAGATTTTCAAGG
55823443 AAATTGAGATCATGTTCGTATTTAAGATTTTCAAGG
1 AAATTGAGATCATGTTCGTATTTAAGATTTTCAAGG
*
55823479 GAATTGAG
1 AAATTGAG
55823487 CCCTAACGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (36 bp):
AAATTGAGATCATGTTCGTATTTAAGATTTTCAAGG
Found at i:55823696 original size:99 final size:97
Alignment explanation
Indices: 55823587--55823844 Score: 252
Period size: 98 Copynumber: 2.6 Consensus size: 97
55823577 ATTCAACACG
* * ** *
55823587 TTGTGTCCTAACGTATTGGATGTGA-CGCATTGATTTCTCGAAATAA-AGAT-TTTTTTTAAATA
1 TTGTGCCCTAACGTATTGGGTGTGATCGC-TT-AAATCTCG-AATAAGAGATGTTCTTTTAAA-A
*
55823649 ATAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAA
62 A-AAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAA
** * * * *
55823686 TTGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGAAA
1 TTGTGCCCTAACGTATTGGGTGTGATCGCTTAAATCTCGAATAAG-AGATGTTCTTTTAAAAAAA
*
55823751 AGGAAATATTCCGAGTTTGGGATTCTAGAGGAA
65 AGGAAATATTCCGAGTTTGGGATTCTAAAGGAA
* ** * * * *
55823784 TCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATGAGTGGATGTTCTTTTAAA
1 TTGTGCCCTAACGTATTGGGTGTGATCGCTTAAATCTCGAATAAG-AGATGTTCTTTTAAA
55823845 GTTTTATTGT
Statistics
Matches: 140, Mismatches: 15, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
97 4 0.03
98 97 0.69
99 29 0.21
100 10 0.07
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (97 bp):
TTGTGCCCTAACGTATTGGGTGTGATCGCTTAAATCTCGAATAAGAGATGTTCTTTTAAAAAAAA
GGAAATATTCCGAGTTTGGGATTCTAAAGGAA
Found at i:55823765 original size:98 final size:98
Alignment explanation
Indices: 55823651--55823845 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
55823641 TTTAAATAAT
* *
55823651 AAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCT
1 AAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCT
55823716 TAAATCTTGGATAAGTGGATGTTCTTTTAAAGA
66 TAAATCTTGGATAAGTGGATGTTCTTTTAAAGA
*
55823749 AAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCT
1 AAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCT
*
55823814 TAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TAAATCTTGGATAAGTGGATGTTCTTTTAAAG
55823846 TTTTATTGTA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (98 bp):
AAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCT
TAAATCTTGGATAAGTGGATGTTCTTTTAAAGA
Found at i:55829073 original size:12 final size:12
Alignment explanation
Indices: 55829056--55829085 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
55829046 TGTTAAAGAG
55829056 GCTGAAACTGAA
1 GCTGAAACTGAA
55829068 GCTGAAACTGAA
1 GCTGAAACTGAA
*
55829080 GTTGAA
1 GCTGAA
55829086 CTTTCATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (12 bp):
GCTGAAACTGAA
Found at i:55830124 original size:21 final size:23
Alignment explanation
Indices: 55830092--55830135 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
55830082 TAATATTCTA
*
55830092 ATTTTAAAAATTC-AATTAAAAT
1 ATTTTAAAAATTCGAAATAAAAT
55830114 ATTTT-AAAATTCGAAATAAAAT
1 ATTTTAAAAATTCGAAATAAAAT
55830136 TTAAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (23 bp):
ATTTTAAAAATTCGAAATAAAAT
Found at i:55837981 original size:19 final size:21
Alignment explanation
Indices: 55837957--55838000 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
55837947 AAAAATTGAC
55837957 ATATATTTTT-AT-TTTTATT
1 ATATATTTTTAATATTTTATT
55837976 ATATATTTTTAATATTTTATT
1 ATATATTTTTAATATTTTATT
55837997 ATAT
1 ATAT
55838001 CTTTCACCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 10 0.43
20 2 0.09
21 11 0.48
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
ATATATTTTTAATATTTTATT
Found at i:55838124 original size:21 final size:21
Alignment explanation
Indices: 55838065--55838126 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
55838055 TTCTTTTATT
* * *
55838065 AATATAAGTATATATTAAATA
1 AATATAATTTTATATTTAATA
* *
55838086 TA-ATAATTTTCA-AGTTAATA
1 AATATAATTTT-ATATTTAATA
55838106 AATATAATTTTATATTTAATA
1 AATATAATTTTATATTTAATA
55838127 GAATTCTATG
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (21 bp):
AATATAATTTTATATTTAATA
Found at i:55845669 original size:21 final size:21
Alignment explanation
Indices: 55845598--55845670 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
55845588 GGCTGCACAA
* * * *
55845598 AAACACATAAGTGCTAAACGA
1 AAACCCATAAGAGCTGAACGG
* *
55845619 AAACCCGTAAGAGTTGAACGG
1 AAACCCATAAGAGCTGAACGG
* * *
55845640 AAGCTCATAGGAGCTGAACGG
1 AAACCCATAAGAGCTGAACGG
55845661 AAACCCATAA
1 AAACCCATAA
55845671 AGGTTAATCT
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.14
Consensus pattern (21 bp):
AAACCCATAAGAGCTGAACGG
Found at i:55845686 original size:42 final size:42
Alignment explanation
Indices: 55845640--55845772 Score: 160
Period size: 42 Copynumber: 3.2 Consensus size: 42
55845630 AGTTGAACGG
* * * *
55845640 AAGCTCATAGGAGCTGAACGGAAACCCATAAAGGTTAATCTA
1 AAGCTCAAAAGAGCTGAACTGAAACCCATAAGGGTTAATCTA
* * * *
55845682 AAGCTCAAAAGAGCTAAACTGAAACCCATTAGGGTTAAACTG
1 AAGCTCAAAAGAGCTGAACTGAAACCCATAAGGGTTAATCTA
* *
55845724 AAGCTCAAAAGAGCTGAACTGAAACCTAGAAGGGTTAATCTGA
1 AAGCTCAAAAGAGCTGAACTGAAACCCATAAGGGTTAATCT-A
55845767 AA-CTCA
1 AAGCTCA
55845773 TATGAGTTAA
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 74 0.97
43 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (42 bp):
AAGCTCAAAAGAGCTGAACTGAAACCCATAAGGGTTAATCTA
Found at i:55845743 original size:21 final size:21
Alignment explanation
Indices: 55845682--55845746 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
55845672 GGTTAATCTA
55845682 AAGCTCAAAAGAGCTAAACTG
1 AAGCTCAAAAGAGCTAAACTG
* * ** * *
55845703 AAACCCATTAGGGTTAAACTG
1 AAGCTCAAAAGAGCTAAACTG
*
55845724 AAGCTCAAAAGAGCTGAACTG
1 AAGCTCAAAAGAGCTAAACTG
55845745 AA
1 AA
55845747 ACCTAGAAGG
Statistics
Matches: 31, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (21 bp):
AAGCTCAAAAGAGCTAAACTG
Found at i:55847807 original size:13 final size:13
Alignment explanation
Indices: 55847791--55847815 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55847781 AACTATTTAT
55847791 AAATATAGTTAAC
1 AAATATAGTTAAC
55847804 AAATATAGTTAA
1 AAATATAGTTAA
55847816 GTTTAGACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
AAATATAGTTAAC
Found at i:55848264 original size:9 final size:9
Alignment explanation
Indices: 55848242--55848279 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
55848232 AGTGTAAATT
*
55848242 AATTTTTAT
1 AATTTTTAA
*
55848251 CATTTTTAA
1 AATTTTTAA
55848260 AATTTTTAA
1 AATTTTTAA
55848269 AA-TTTTAA
1 AATTTTTAA
55848277 AAT
1 AAT
55848280 GACTAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (9 bp):
AATTTTTAA
Found at i:55864033 original size:89 final size:89
Alignment explanation
Indices: 55863879--55864056 Score: 275
Period size: 89 Copynumber: 2.0 Consensus size: 89
55863869 TCTCAAATCA
* *
55863879 GATTAGCCACCCAAAGTAGCCATATTTTATAAAACTAAAAAATTATGAATATGATGGTTGTGTAT
1 GATTAGCCACCCAAAGTAGCCATATTTTATAAAACTAAAAAATTATGAATATGATGATTGAGTAT
55863944 TAGTTCAATTCATATTATTATTGT
66 TAGTTCAATTCATATTATTATTGT
* * * *
55863968 GATTAGTCACTCAAAGTAGTCATATTTTATAAAATTAAAAAATTATGAATATGATGATTGAGTAT
1 GATTAGCCACCCAAAGTAGCCATATTTTATAAAACTAAAAAATTATGAATATGATGATTGAGTAT
** *
55864033 TAGTTCGGTTTATATTATTATTGT
66 TAGTTCAATTCATATTATTATTGT
55864057 TGTTACAGTT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.40
Consensus pattern (89 bp):
GATTAGCCACCCAAAGTAGCCATATTTTATAAAACTAAAAAATTATGAATATGATGATTGAGTAT
TAGTTCAATTCATATTATTATTGT
Found at i:55864140 original size:17 final size:19
Alignment explanation
Indices: 55864118--55864157 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
55864108 CTATTTGTCA
55864118 AATTGGT-A-ATCATTGAG
1 AATTGGTGATATCATTGAG
55864135 AATTGGTGGATATCATTGAG
1 AATTGGT-GATATCATTGAG
55864155 AAT
1 AAT
55864158 GTGTACCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
19 1 0.05
20 12 0.60
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (19 bp):
AATTGGTGATATCATTGAG
Found at i:55865800 original size:3 final size:3
Alignment explanation
Indices: 55865792--55865836 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
55865782 AGATTCACAT
55865792 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55865837 TACTATATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55868744 original size:19 final size:18
Alignment explanation
Indices: 55868720--55868770 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
55868710 ATAAATTTAA
*
55868720 AAAATTATACAATAGTAAC
1 AAAATTATACAATA-AAAC
*
55868739 AAAATTA-GCAATAAAAC
1 AAAATTATACAATAAAAC
55868756 AATAATTATACAATA
1 AA-AATTATACAATA
55868771 TCCAAACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 5 0.19
18 10 0.37
19 12 0.44
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.25
Consensus pattern (18 bp):
AAAATTATACAATAAAAC
Found at i:55869278 original size:20 final size:20
Alignment explanation
Indices: 55869241--55869281 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
55869231 ATATATTTTG
*
55869241 ATTTTATATTTTTAAAATTT
1 ATTTTATATCTTTAAAATTT
* *
55869261 ATTTTTTATCTTTGAAATTT
1 ATTTTATATCTTTAAAATTT
55869281 A
1 A
55869282 AAATTTTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTTATATCTTTAAAATTT
Found at i:55871092 original size:4 final size:4
Alignment explanation
Indices: 55871085--55871109 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55871075 GCATGCATGA
55871085 ATCC ATCC ATCC ATCC ATCC ATCC A
1 ATCC ATCC ATCC ATCC ATCC ATCC A
55871110 AGTGCTGTAT
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:0.28, C:0.48, G:0.00, T:0.24
Consensus pattern (4 bp):
ATCC
Found at i:55880505 original size:3 final size:3
Alignment explanation
Indices: 55880497--55880524 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
55880487 GTCCCTTGTC
55880497 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
55880525 TTTCGCAAGT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:55884956 original size:60 final size:60
Alignment explanation
Indices: 55884863--55884979 Score: 225
Period size: 60 Copynumber: 1.9 Consensus size: 60
55884853 CAATAATACT
55884863 AAAGTACCATTGACATAACTTGTCTTAAACCTGCAGCTATCGAACCCCAACATTTGAACC
1 AAAGTACCATTGACATAACTTGTCTTAAACCTGCAGCTATCGAACCCCAACATTTGAACC
*
55884923 AAAGTACCATTGACATAACTTGTCTTAACCCTGCAGCTATCGAACCCCAACATTTGA
1 AAAGTACCATTGACATAACTTGTCTTAAACCTGCAGCTATCGAACCCCAACATTTGA
55884980 CCTATTGATC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (60 bp):
AAAGTACCATTGACATAACTTGTCTTAAACCTGCAGCTATCGAACCCCAACATTTGAACC
Found at i:55886897 original size:22 final size:22
Alignment explanation
Indices: 55886869--55886914 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
55886859 CGATTATTGT
55886869 AGGATTGTTTTATAATAAGAAA
1 AGGATTGTTTTATAATAAGAAA
55886891 AGGATTGTTTTATAATAAGAAA
1 AGGATTGTTTTATAATAAGAAA
55886913 AG
1 AG
55886915 CAATTAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.35
Consensus pattern (22 bp):
AGGATTGTTTTATAATAAGAAA
Found at i:55896457 original size:27 final size:27
Alignment explanation
Indices: 55896413--55896467 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
55896403 ATACGTGTTT
*** *
55896413 ATGTTCATTTACTTAATGCTCATGAAC
1 ATGTTCATTTAAACAATGCTCAAGAAC
*
55896440 ATGTTCATTTAAACAATGTTCAAGAAC
1 ATGTTCATTTAAACAATGCTCAAGAAC
55896467 A
1 A
55896468 ATATTCATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (27 bp):
ATGTTCATTTAAACAATGCTCAAGAAC
Found at i:55901707 original size:2 final size:2
Alignment explanation
Indices: 55901700--55901729 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55901690 NNNNNNNNAT
55901700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55901730 CAATGTCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55923591 original size:31 final size:29
Alignment explanation
Indices: 55923553--55923633 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 29
55923543 AATCTCAAAA
55923553 TTATATATAAATTTTAATTTAACGTGTA-ATT
1 TTATATATAAATTTTAATTT--CGTGTAGA-T
* *
55923584 TTATATATAAATCTTAATTTTGTGTAGAT
1 TTATATATAAATTTTAATTTCGTGTAGAT
*
55923613 TTATACATAAAATTTTAATTT
1 TTATATAT-AAATTTTAATTT
55923634 GATCAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 13 0.30
30 12 0.27
31 19 0.43
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (29 bp):
TTATATATAAATTTTAATTTCGTGTAGAT
Found at i:55923634 original size:29 final size:28
Alignment explanation
Indices: 55923553--55923634 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
55923543 AATCTCAAAA
55923553 TTATATAT-AAATTTTAATTTAACGTGTAAT
1 TTATATATAAAATTTTAATTT---GTGTAAT
*
55923583 TT-TATATATAAATCTTAATTTTGTGTAGAT
1 TTATATATA-AAATTTTAA-TTTGTGTA-AT
*
55923613 TTATACATAAAATTTTAATTTG
1 TTATATATAAAATTTTAATTTG
55923635 ATCAATTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
29 14 0.32
30 14 0.32
31 13 0.30
32 3 0.07
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (28 bp):
TTATATATAAAATTTTAATTTGTGTAAT
Found at i:55926070 original size:8 final size:8
Alignment explanation
Indices: 55926057--55926081 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
55926047 CTAACTAGCT
55926057 TCGCTTTA
1 TCGCTTTA
55926065 TCGCTTTA
1 TCGCTTTA
55926073 TCGCTTTA
1 TCGCTTTA
55926081 T
1 T
55926082 TATTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.12, T:0.52
Consensus pattern (8 bp):
TCGCTTTA
Found at i:55932105 original size:25 final size:26
Alignment explanation
Indices: 55932073--55932127 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
55932063 AATTTTAAAA
* * *
55932073 TATTTTTAAAATAATTTTTTG-TTTT
1 TATTTTTAAAACAAATTTTTGATGTT
55932098 TATTTTTAAAACAAATTTTTGATGTT
1 TATTTTTAAAACAAATTTTTGATGTT
55932124 TATT
1 TATT
55932128 AAAAAAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (26 bp):
TATTTTTAAAACAAATTTTTGATGTT
Found at i:55935018 original size:15 final size:15
Alignment explanation
Indices: 55934998--55935051 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
55934988 TACTTAATTT
*
55934998 AAAATTTAATTAATC
1 AAAACTTAATTAATC
* *
55935013 AAAA-TTAAGTAATT
1 AAAACTTAATTAATC
*
55935027 AAACCTTAATTAATC
1 AAAACTTAATTAATC
55935042 AAAACTTAAT
1 AAAACTTAAT
55935052 CATACTCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 11 0.34
15 21 0.66
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (15 bp):
AAAACTTAATTAATC
Found at i:55941473 original size:25 final size:25
Alignment explanation
Indices: 55941425--55941473 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
55941415 TATTAGTATT
* *
55941425 TTAAAAACTCAATTAAATTTTGAAA
1 TTAAAAACTCAATTAAAATCTGAAA
55941450 TTAAAAA-TCGAATTAAAATCTGAA
1 TTAAAAACTC-AATTAAAATCTGAA
55941474 TAAAAGTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (25 bp):
TTAAAAACTCAATTAAAATCTGAAA
Found at i:55946265 original size:31 final size:30
Alignment explanation
Indices: 55946229--55946328 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 30
55946219 ATTTTTGGGT
55946229 CTAATTTAGTACTCGAATTTGACAATTTTTC
1 CTAATTTAGTACTCGAATTTGAC-ATTTTTC
*
55946260 CTAATTTAGTA-TCTAAGTTT----TTTTGTC
1 CTAATTTAGTACTCGAA-TTTGACATTTT-TC
*
55946287 C-AATTTAGTACTTGAATTTGACACTTTTTC
1 CTAATTTAGTACTCGAATTTGACA-TTTTTC
*
55946317 CTAATTTGGTAC
1 CTAATTTAGTAC
55946329 CCAAACTTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
26 16 0.29
27 6 0.11
30 7 0.12
31 27 0.48
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (30 bp):
CTAATTTAGTACTCGAATTTGACATTTTTC
Found at i:55958646 original size:37 final size:37
Alignment explanation
Indices: 55958596--55958670 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
55958586 TATCGATGAG
55958596 GCTTTCCCTATTGTATACAGCATTCTTTGACTACTCC
1 GCTTTCCCTATTGTATACAGCATTCTTTGACTACTCC
*
55958633 GCTTTCCCTATTGTATACAGCGTTCTTTGACTACTCC
1 GCTTTCCCTATTGTATACAGCATTCTTTGACTACTCC
55958670 G
1 G
55958671 TTAACTTCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.17, C:0.29, G:0.13, T:0.40
Consensus pattern (37 bp):
GCTTTCCCTATTGTATACAGCATTCTTTGACTACTCC
Found at i:55959304 original size:14 final size:15
Alignment explanation
Indices: 55959279--55959317 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
55959269 TTAGATATAA
*
55959279 TTATTATTTAAATAT
1 TTATTATATAAATAT
55959294 TT-TTATATAAATAT
1 TTATTATATAAATAT
55959308 TTATTATATA
1 TTATTATATA
55959318 CTGATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATATAAATAT
Found at i:55960504 original size:3 final size:3
Alignment explanation
Indices: 55960496--55960542 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
55960486 CATATTCCCC
55960496 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
55960543 TGTGTAGGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55961305 original size:24 final size:25
Alignment explanation
Indices: 55961278--55961326 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
55961268 TAAAATTGAT
* *
55961278 ATAAAATTTTTAAA-ATTATAAAAA
1 ATAAAACTTATAAATATTATAAAAA
55961302 ATAAAACTTATAAATATTATAAAAA
1 ATAAAACTTATAAATATTATAAAAA
55961327 TATATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAAAACTTATAAATATTATAAAAA
Found at i:55961325 original size:18 final size:20
Alignment explanation
Indices: 55961301--55961344 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
55961291 AATTATAAAA
*
55961301 AATAAAACT-TATAA-ATAT
1 AATAAAAATATATAATATAT
*
55961319 TATAAAAATATATAATATAT
1 AATAAAAATATATAATATAT
55961339 AATAAA
1 AATAAA
55961345 TTCTAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 7 0.33
19 5 0.24
20 9 0.43
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AATAAAAATATATAATATAT
Found at i:55961329 original size:11 final size:10
Alignment explanation
Indices: 55961192--55961456 Score: 51
Period size: 9 Copynumber: 27.7 Consensus size: 10
55961182 ATATTTTTTC
55961192 TATAAAAAT-
1 TATAAAAATA
55961201 TATTAAAAAT-
1 TA-TAAAAATA
*
55961211 CATAAAAATA
1 TATAAAAATA
*
55961221 TATCAAAGAAAA
1 TAT-AAA-AATA
55961233 TTATAAAACATAGA
1 -TATAAAA-AT--A
*
55961247 TATATTAAATA
1 TATA-AAAATA
55961258 T-TAAAAATA
1 TATAAAAATA
*
55961267 T-TAAAATTGA
1 TATAAAAAT-A
55961277 TAT-AAAAT-
1 TATAAAAATA
* *
55961285 TTTTAAAAT-
1 TATAAAAATA
55961294 TAT-AAAA-A
1 TATAAAAATA
*
55961302 -ATAAAACT-
1 TATAAAAATA
*
55961310 TATAAATAT-
1 TATAAAAATA
55961319 TATAAAAATA
1 TATAAAAATA
55961329 TAT---AATA
1 TATAAAAATA
55961336 TATAATAAAT-
1 TATAA-AAATA
*
55961346 TCTAATAAAT-
1 TATAA-AAATA
*
55961356 TACAAAAA-A
1 TATAAAAATA
*
55961365 TATAAAATTA
1 TATAAAAATA
55961375 -ATAAAAACT-
1 TATAAAAA-TA
*
55961384 TATTTAAAATA
1 TA-TAAAAATA
*
55961395 T-TTAAAAT-
1 TATAAAAATA
*
55961403 T-TAAAAACA
1 TATAAAAATA
* *
55961412 TATTAGAAT-
1 TATAAAAATA
*
55961421 TCTTAAAAAT-
1 T-ATAAAAATA
* *
55961431 TATAAATATT
1 TATAAAAATA
55961441 TATAAAAATA
1 TATAAAAATA
55961451 T-TAAAA
1 TATAAAA
55961457 TTGATATTAA
Statistics
Matches: 192, Mismatches: 33, Indels: 62
0.67 0.11 0.22
Matches are distributed among these distances:
7 9 0.05
8 15 0.08
9 77 0.40
10 56 0.29
11 16 0.08
12 7 0.04
13 9 0.05
14 3 0.02
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (10 bp):
TATAAAAATA
Found at i:55961380 original size:17 final size:17
Alignment explanation
Indices: 55961276--55961381 Score: 51
Period size: 17 Copynumber: 6.1 Consensus size: 17
55961266 ATTAAAATTG
**
55961276 ATATAAAATTTTTAAAA
1 ATATAAAATTAATAAAA
*
55961293 TTATAAAA--AATAAAA
1 ATATAAAATTAATAAAA
*
55961308 CTTATAAATATT-ATAAAA
1 -ATATAAA-ATTAATAAAA
55961326 ATATATAATATATAAT-AAA
1 ATATA-AA-AT-TAATAAAA
* *
55961345 TTCTAATAAATTACA-AAAA
1 ATAT-A-AAATTA-ATAAAA
55961364 ATATAAAATTAATAAAA
1 ATATAAAATTAATAAAA
55961381 A
1 A
55961382 CTTATTTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
15 5 0.07
16 8 0.11
17 23 0.33
18 14 0.20
19 14 0.20
20 6 0.09
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAAATTAATAAAA
Found at i:55961455 original size:19 final size:19
Alignment explanation
Indices: 55961389--55961455 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
55961379 AAACTTATTT
55961389 AAAATATTTAAA-ATTTA-A
1 AAAATA-TTAAATATTTATA
*
55961407 AAACATATTAGAAT-TCT-TA
1 AAA-ATATTA-AATATTTATA
55961426 AAAAT-TATAAATATTTATA
1 AAAATAT-TAAATATTTATA
55961445 AAAATATTAAA
1 AAAATATTAAA
55961456 ATTGATATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 15
0.70 0.04 0.27
Matches are distributed among these distances:
17 4 0.10
18 12 0.31
19 22 0.56
20 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (19 bp):
AAAATATTAAATATTTATA
Found at i:55961773 original size:24 final size:26
Alignment explanation
Indices: 55961737--55961785 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
55961727 CCAAATCAAT
55961737 TAAATAAAATATTAA-AAATAAAAAA
1 TAAATAAAATATTAAGAAATAAAAAA
55961762 TAAA-AAAATATTAAGAAATAAAAA
1 TAAATAAAATATTAAGAAATAAAAA
55961786 TGGATTCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (26 bp):
TAAATAAAATATTAAGAAATAAAAAA
Found at i:55962790 original size:135 final size:134
Alignment explanation
Indices: 55962547--55962815 Score: 439
Period size: 135 Copynumber: 2.0 Consensus size: 134
55962537 AAAATAAAAG
* * * *
55962547 CATCCAATATACAGTATAACTACAAGAAATAAAGAAATTCATGATAATTTCCTAAGAAATCAACT
1 CATCCAAGATACAGTATAACCACAAGAAATAAAGAAACTCATGATAAATTCCTAAGAAATCAACT
* * *
55962612 AGGAATCTTCAATCTTGACAACAATTTGCTTCATAATCTGCTTCAATGGTGTTTTTTTTAGTTGT
66 AGGAATCTTCAATCTTGACAACAATTTGCTTCACAATCGGCTTCAATGGTG-TTTTTTGAGTTGT
55962677 TTTCT
130 TTTCT
* *
55962682 CATCCAAGATACAGTATAACCACAATAAATAAAGGAACTCATGATAAATTCCTAAGAAATCAACT
1 CATCCAAGATACAGTATAACCACAAGAAATAAAGAAACTCATGATAAATTCCTAAGAAATCAACT
*
55962747 AGGAATCTTCAATCTTGACAATAATTTGCTTCACAATCGGCTTCAATGGTGTTTTTTGAGTTGTT
66 AGGAATCTTCAATCTTGACAACAATTTGCTTCACAATCGGCTTCAATGGTGTTTTTTGAGTTGTT
55962812 TTCT
131 TTCT
55962816 TGAATATTAT
Statistics
Matches: 124, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
134 17 0.14
135 107 0.86
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (134 bp):
CATCCAAGATACAGTATAACCACAAGAAATAAAGAAACTCATGATAAATTCCTAAGAAATCAACT
AGGAATCTTCAATCTTGACAACAATTTGCTTCACAATCGGCTTCAATGGTGTTTTTTGAGTTGTT
TTCT
Found at i:55963301 original size:21 final size:22
Alignment explanation
Indices: 55963277--55963321 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
55963267 TTATATAATT
*
55963277 TTTATAGAACTTT-AACATGTA
1 TTTATAAAACTTTAAACATGTA
* *
55963298 TTTATAAAATTTTAAATATGTA
1 TTTATAAAACTTTAAACATGTA
55963320 TT
1 TT
55963322 ATTAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (22 bp):
TTTATAAAACTTTAAACATGTA
Found at i:55963339 original size:9 final size:9
Alignment explanation
Indices: 55963327--55963399 Score: 58
Period size: 9 Copynumber: 7.9 Consensus size: 9
55963317 GTATTATTAA
55963327 TTTTATAAT
1 TTTTATAAT
*
55963336 TTTTATAAAA
1 TTTTAT-AAT
* *
55963346 TATTAGAAT
1 TTTTATAAT
* *
55963355 TTATTAGAAA
1 TT-TTATAAT
55963365 TTTTAT-AT
1 TTTTATAAT
55963373 TTTTGATAAT
1 TTTT-ATAAT
*
55963383 GTTTATAAT
1 TTTTATAAT
55963392 TTTTATAA
1 TTTTATAA
55963400 GTTCACATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
8 5 0.10
9 26 0.52
10 19 0.38
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (9 bp):
TTTTATAAT
Found at i:55963367 original size:38 final size:38
Alignment explanation
Indices: 55963298--55963381 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
55963288 TTAACATGTA
* **
55963298 TTTATAAAATTTTAAATATGTATTATTAATTTTATAATT
1 TTTATAAAATATTAAATATGTATTAGAAATTTTAT-ATT
55963337 TTTATAAAATATTAGAAT-T-TATTAGAAATTTTATATT
1 TTTATAAAATATTA-AATATGTATTAGAAATTTTATATT
55963374 TTTGATAA
1 TTT-ATAA
55963382 TGTTTATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
37 6 0.15
38 17 0.43
39 14 0.35
40 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (38 bp):
TTTATAAAATATTAAATATGTATTAGAAATTTTATATT
Found at i:55963387 original size:18 final size:17
Alignment explanation
Indices: 55963366--55963412 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
55963356 TATTAGAAAT
55963366 TTTATATTTTTGATAATG
1 TTTATATTTTTGATAA-G
55963384 TTTATAATTTTT-ATAAG
1 TTTAT-ATTTTTGATAAG
* *
55963401 TTCACATTTTTG
1 TTTATATTTTTG
55963413 TGTTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 6 0.24
17 4 0.16
18 9 0.36
19 6 0.24
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.60
Consensus pattern (17 bp):
TTTATATTTTTGATAAG
Found at i:55963395 original size:19 final size:17
Alignment explanation
Indices: 55963324--55963399 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 17
55963314 TATGTATTAT
55963324 TAATTTTATAATTTTTA
1 TAATTTTATAATTTTTA
* *
55963341 TAAAATATTAGAATTTATTA
1 T--AATTTTATAATTT-TTA
*
55963361 GAAATTTTAT-ATTTTTGA
1 -TAATTTTATAATTTTT-A
55963379 TAATGTTTATAATTTTTA
1 TAAT-TTTATAATTTTTA
55963397 TAA
1 TAA
55963400 GTTCACATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
17 6 0.13
18 14 0.30
19 23 0.50
20 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TAATTTTATAATTTTTA
Found at i:55967507 original size:37 final size:37
Alignment explanation
Indices: 55967416--55967546 Score: 181
Period size: 37 Copynumber: 3.5 Consensus size: 37
55967406 ACCAGTTTGA
* * * *
55967416 CACCCAGTGCCTCATCGGATAATTCGAAATGATAATTTGA
1 CACCCAGTGCCTCATCGGCTAAATCG-AA-G-TAAATTGG
* *
55967456 CACCCAGTGTCTCATCGGCTAAACCGAAGTAAATTGG
1 CACCCAGTGCCTCATCGGCTAAATCGAAGTAAATTGG
55967493 CACCCAGTGCCTCATCGGCTAAATCGAAGTAAATTGG
1 CACCCAGTGCCTCATCGGCTAAATCGAAGTAAATTGG
55967530 CACCCAGTGCCTCATCG
1 CACCCAGTGCCTCATCG
55967547 AATATATCTA
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
37 58 0.70
38 1 0.01
39 2 0.02
40 22 0.27
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGCTAAATCGAAGTAAATTGG
Found at i:55968559 original size:22 final size:22
Alignment explanation
Indices: 55968512--55968569 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
55968502 GATTCTTTTC
*
55968512 TTTA-TTTATTACATTTACTAA
1 TTTATTTTATTATATTTACTAA
*
55968533 TTTATTTTATTATATTTACT-T
1 TTTATTTTATTATATTTACTAA
*
55968554 TATTATTATATTATAT
1 T-TTATTTTATTATAT
55968570 ATATTTACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.16
22 27 0.84
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATTTTATTATATTTACTAA
Found at i:55968586 original size:26 final size:25
Alignment explanation
Indices: 55968513--55968587 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 25
55968503 ATTCTTTTCT
*
55968513 TTAT-TTATTACATTTAC-T-AAT-
1 TTATATTATTATATTTACTTAAATA
* * *
55968534 TTATTTTATTATATTTACTTTATTA
1 TTATATTATTATATTTACTTAAATA
55968559 TTATATTATATATATTTACTTAAATA
1 TTATATTAT-TATATTTACTTAAATA
55968585 TTA
1 TTA
55968588 AGTAATACAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.09
22 12 0.27
23 1 0.02
24 2 0.05
25 8 0.18
26 17 0.39
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (25 bp):
TTATATTATTATATTTACTTAAATA
Found at i:55968599 original size:26 final size:26
Alignment explanation
Indices: 55968544--55968601 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
55968534 TTATTTTATT
* * * *
55968544 ATATTTACTTTATTATTATATTATAT
1 ATATTTACTTAAATATTATATAATAC
55968570 ATATTTACTTAAATATTA-AGTAATAC
1 ATATTTACTTAAATATTATA-TAATAC
55968596 ATATTT
1 ATATTT
55968602 TATTAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATTTACTTAAATATTATATAATAC
Found at i:55968653 original size:15 final size:15
Alignment explanation
Indices: 55968635--55968664 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55968625 TATTTTTACA
55968635 CATGTAATAACTGTT
1 CATGTAATAACTGTT
55968650 CATGTAATAACTGTT
1 CATGTAATAACTGTT
55968665 ACCGTCCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
CATGTAATAACTGTT
Found at i:55969591 original size:32 final size:33
Alignment explanation
Indices: 55969548--55969610 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
55969538 TAATCAAAAA
* **
55969548 ATTTAGTTTTTTTTTTTTTGGCTTCAATCAAGT
1 ATTTAGTTTTTTTATTTACGGCTTCAATCAAGT
*
55969581 ATTTA-TTTTTTTATTTACGGCTTTAATCAA
1 ATTTAGTTTTTTTATTTACGGCTTCAATCAA
55969611 TCATGTGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (33 bp):
ATTTAGTTTTTTTATTTACGGCTTCAATCAAGT
Found at i:55970155 original size:23 final size:22
Alignment explanation
Indices: 55970125--55970169 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
55970115 TTGACAATAA
55970125 TTAGAACAAAAATATAAACAATT
1 TTAGAACAAAAATA-AAACAATT
* *
55970148 TTAGAACAATAATAAAATAATT
1 TTAGAACAAAAATAAAACAATT
55970170 AAAAACAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (22 bp):
TTAGAACAAAAATAAAACAATT
Found at i:55979391 original size:22 final size:21
Alignment explanation
Indices: 55979351--55979392 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
55979341 CAAAATGGAA
55979351 TATTATTATTGTAGAGCTTAT
1 TATTATTATTGTAGAGCTTAT
* *
55979372 TATTATTTATTTTAGGGCTTA
1 TATTA-TTATTGTAGAGCTTA
55979393 ACCACCTCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.55
Consensus pattern (21 bp):
TATTATTATTGTAGAGCTTAT
Found at i:55988415 original size:3 final size:3
Alignment explanation
Indices: 55988399--55988436 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
55988389 ATTGGATTGT
55988399 GAA G-A GAA GAAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GA
55988437 GAGGATATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:55989097 original size:21 final size:23
Alignment explanation
Indices: 55989057--55989098 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
55989047 ATACTTAAAA
55989057 TTTCTTTCTATGTTCAAATTAAT
1 TTTCTTTCTATGTTCAAATTAAT
*
55989080 TTTCTTT-T-TGTTCTAATTA
1 TTTCTTTCTATGTTCAAATTA
55989099 GTATCCGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.62
Consensus pattern (23 bp):
TTTCTTTCTATGTTCAAATTAAT
Found at i:55993072 original size:21 final size:21
Alignment explanation
Indices: 55993048--55993097 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
55993038 TTTTGCTTCT
55993048 AAATAACACAAA-TAAAATATA
1 AAATAACACAAACTAAAAT-TA
* *
55993069 AAATAAAAGAAACTAAAATTA
1 AAATAACACAAACTAAAATTA
*
55993090 AACTAACA
1 AAATAACA
55993098 GATTATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.70, C:0.10, G:0.02, T:0.18
Consensus pattern (21 bp):
AAATAACACAAACTAAAATTA
Found at i:55998851 original size:2 final size:2
Alignment explanation
Indices: 55998844--55998876 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55998834 CAGCCGCGGG
55998844 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
55998877 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:55998881 original size:2 final size:2
Alignment explanation
Indices: 55998876--55998904 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55998866 TCTCTCTCTC
55998876 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55998905 GTGTGTACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56005467 original size:45 final size:46
Alignment explanation
Indices: 56005394--56005500 Score: 148
Period size: 46 Copynumber: 2.4 Consensus size: 46
56005384 ACGTATGATT
* *
56005394 ACTTATCAC-TTGTC-CCTAATCAGATAAGTATAGCT-AGGCTATC
1 ACTTATCACTTTGTCACCTAATCAGATAAGTATAGCTAAAGCTACC
* * *
56005437 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
1 ACTTATCACTTTGTCACCTAATCAGATAAGTATAGCTAAAGCTACC
56005483 ACTTATCACTTTGTCACC
1 ACTTATCACTTTGTCACC
56005501 ACTTATCATT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 9 0.16
44 5 0.09
45 18 0.33
46 23 0.42
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (46 bp):
ACTTATCACTTTGTCACCTAATCAGATAAGTATAGCTAAAGCTACC
Found at i:56005503 original size:18 final size:17
Alignment explanation
Indices: 56005480--56005513 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
56005470 AGCTAAAGCT
56005480 ACCACTTATCACTTTGTC
1 ACCACTTATCA-TTTGTC
56005498 ACCACTTATCATTTGT
1 ACCACTTATCATTTGT
56005514 TCCTGATCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.24, C:0.29, G:0.06, T:0.41
Consensus pattern (17 bp):
ACCACTTATCATTTGTC
Found at i:56005535 original size:62 final size:64
Alignment explanation
Indices: 56005436--56005561 Score: 222
Period size: 62 Copynumber: 2.0 Consensus size: 64
56005426 GCTAGGCTAT
56005436 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC
56005500 CACTTATCA-TTTGTTC-C-TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC
1 CACTTATCACTTTG-TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC
56005562 TTGATCAGAT
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
62 45 0.74
63 5 0.08
64 11 0.18
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.35
Consensus pattern (64 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC
Found at i:56005573 original size:46 final size:46
Alignment explanation
Indices: 56005498--56005616 Score: 199
Period size: 46 Copynumber: 2.6 Consensus size: 46
56005488 TCACTTTGTC
56005498 ACCACTTATCA-TTTGTTC-C-TGATCAGATAAGTGTAGCTAAAGCT
1 ACCACTTATCACTTTG-TCACTTGATCAGATAAGTGTAGCTAAAGCT
56005542 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
*
56005588 ACCACTTATCACTTTGTTACTTGATCAGA
1 ACCACTTATCACTTTGTCACTTGATCAGA
56005617 AGTACTCAAA
Statistics
Matches: 71, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
44 13 0.18
45 5 0.07
46 53 0.75
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (46 bp):
ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
Found at i:56005582 original size:108 final size:107
Alignment explanation
Indices: 56005394--56005604 Score: 359
Period size: 108 Copynumber: 2.0 Consensus size: 107
56005384 ACGTATGATT
* *
56005394 ACTTATCACTTGTCCCTAATCAGATAAGTATAGCTAGGCTATCACTTATCACTTTGTCACTTGAT
1 ACTTATCACTTGTCCCTAATCAGATAAGTATAGCTAAGCTACCACTTATCACTTTGTCACTTGAT
56005459 CAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACC
66 CAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACC
* * * *
56005501 ACTTATCATTTGTTCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGA
1 ACTTATCACTTGTCCCTAATCAGATAAGTATAGCT-AAGCTACCACTTATCACTTTGTCACTTGA
56005566 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGT
65 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGT
56005605 TACTTGATCA
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
107 31 0.32
108 66 0.68
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (107 bp):
ACTTATCACTTGTCCCTAATCAGATAAGTATAGCTAAGCTACCACTTATCACTTTGTCACTTGAT
CAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACC
Found at i:56007320 original size:3 final size:3
Alignment explanation
Indices: 56007301--56007342 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
56007291 AATTTATTTC
* * *
56007301 ATA AT- ATA ATA ACA ATA ATA TTA ATA ATA ACA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
56007343 AAAAATAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:56014461 original size:39 final size:40
Alignment explanation
Indices: 56014418--56014500 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
56014408 GGCCTAGCCG
56014418 AATA-TAAT-AAATATATTTTTTTTTATTTTTTAATTTTAA
1 AATATTAATAAAAT-TATTTTTTTTTATTTTTTAATTTTAA
** * *
56014457 AATATTTTTAAAATTCTTTTTTTTTATTTTTTATTTTTAA
1 AATATTAATAAAATTATTTTTTTTTATTTTTTAATTTTAA
56014497 AATA
1 AATA
56014501 AATTTTAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 4 0.11
40 30 0.79
41 4 0.11
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (40 bp):
AATATTAATAAAATTATTTTTTTTTATTTTTTAATTTTAA
Found at i:56014919 original size:5 final size:6
Alignment explanation
Indices: 56014909--56014934 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
56014899 TTTAAATCAA
56014909 ATTTTT ATTTTT ATTTTT ATTTTT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT AT
56014935 CTAAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:56019453 original size:21 final size:20
Alignment explanation
Indices: 56019429--56019469 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
56019419 TTTTTGGTAC
56019429 TCTTTAATATTTTTTGATATT
1 TCTTT-ATATTTTTTGATATT
* *
56019450 TCTTTGTATTTTTTTATATT
1 TCTTTATATTTTTTGATATT
56019470 CTCTCCTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.71
Consensus pattern (20 bp):
TCTTTATATTTTTTGATATT
Found at i:56022071 original size:29 final size:29
Alignment explanation
Indices: 56022039--56022097 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
56022029 ATTAACAATC
56022039 AAGGAAAGCGAACCAAAATAATATATGAA
1 AAGGAAAGCGAACCAAAATAATATATGAA
56022068 AAGGAAAGCGAACCAAAATAATATATGAA
1 AAGGAAAGCGAACCAAAATAATATATGAA
56022097 A
1 A
56022098 CAATTTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.14
Consensus pattern (29 bp):
AAGGAAAGCGAACCAAAATAATATATGAA
Found at i:56022199 original size:26 final size:26
Alignment explanation
Indices: 56022170--56022238 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
56022160 AAAAGGTTTC
*
56022170 AAATAAACAATATAAAAAAAACTTAA
1 AAATAAATAATATAAAAAAAACTTAA
* * * * *
56022196 AAATGAATAATA-ACAAAACAGTTTA
1 AAATAAATAATATAAAAAAAACTTAA
56022221 AAATAAATAATATAAAAA
1 AAATAAATAATATAAAAA
56022239 TAACATATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
25 20 0.59
26 14 0.41
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.22
Consensus pattern (26 bp):
AAATAAATAATATAAAAAAAACTTAA
Found at i:56022238 original size:25 final size:25
Alignment explanation
Indices: 56022160--56022238 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
56022150 AGTAAATGAT
* * *
56022160 AAAAGGTTTCAAATAAACAATATAAA
1 AAAAAGTTTAAAATAAATAATAT-AA
* * *
56022186 AAAAACTTAAAAATGAATAATA-ACA
1 AAAAAGTTTAAAATAAATAATATA-A
*
56022211 AAACAGTTTAAAATAAATAATATAA
1 AAAAAGTTTAAAATAAATAATATAA
56022236 AAA
1 AAA
56022239 TAACATATAA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
24 1 0.02
25 23 0.56
26 17 0.41
ACGTcount: A:0.66, C:0.06, G:0.05, T:0.23
Consensus pattern (25 bp):
AAAAAGTTTAAAATAAATAATATAA
Found at i:56022369 original size:27 final size:27
Alignment explanation
Indices: 56022260--56022397 Score: 114
Period size: 27 Copynumber: 5.3 Consensus size: 27
56022250 ACAATTTTTT
56022260 TAAATAATAT-ATAAAAAT--TTTAAA
1 TAAATAATATAATAAAAATAGTTTAAA
* *
56022284 T-GATAATAT-AT-ATAATAGTTTAAAA
1 TAAATAATATAATAAAAATAGTTT-AAA
* *
56022309 TAAGTAATATAATAAAAA-AATTTAAA
1 TAAATAATATAATAAAAATAGTTTAAA
**
56022335 TAAATAATA-GGTAAAAATAGTTTAGAA
1 TAAATAATATAATAAAAATAGTTTA-AA
* *
56022362 TAAATAATATATATAAAAA-ACTTAAAA
1 TAAATAATATA-ATAAAAATAGTTTAAA
56022389 TAAATAATA
1 TAAATAATA
56022398 ACAAAAGAGC
Statistics
Matches: 90, Mismatches: 14, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
22 4 0.04
23 9 0.10
24 4 0.04
25 10 0.11
26 22 0.24
27 28 0.31
28 7 0.08
29 6 0.07
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (27 bp):
TAAATAATATAATAAAAATAGTTTAAA
Found at i:56025653 original size:20 final size:19
Alignment explanation
Indices: 56025629--56025740 Score: 84
Period size: 20 Copynumber: 5.7 Consensus size: 19
56025619 AATATTTAGC
56025629 ATAATTTTTGGTATTTCTT
1 ATAATTTTTGGTATTTCTT
** * *
56025648 CATAATAATTGATATACTCTT
1 -ATAATTTTTGGTAT-TTCTT
* *
56025669 ATAATGTTTGATATTTCTT
1 ATAATTTTTGGTATTTCTT
* *
56025688 CATAATTTTCGGTACACTT-TT
1 -ATAATTTTTGGT--ATTTCTT
56025709 ATAATTTTTGGTATTCTCTT
1 ATAATTTTTGGTATT-TCTT
56025729 ATAA-TTTTGGTA
1 ATAATTTTTGGTA
56025741 CAGTTTCGAA
Statistics
Matches: 73, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.03
19 13 0.18
20 49 0.67
21 6 0.08
22 3 0.04
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (19 bp):
ATAATTTTTGGTATTTCTT
Found at i:56025711 original size:40 final size:39
Alignment explanation
Indices: 56025629--56025742 Score: 140
Period size: 40 Copynumber: 2.9 Consensus size: 39
56025619 AATATTTAGC
* * *
56025629 ATAATTTTTGGTATTTCTTCATAATAATTGATATACTCTT
1 ATAATTTTTGGTATTTCTTCATAAT-TTTGGTACACTCTT
* * *
56025669 ATAATGTTTGATATTTCTTCATAATTTTCGGTACACTTTT
1 ATAATTTTTGGTATTTCTTCATAATTTT-GGTACACTCTT
56025709 ATAATTTTTGGTATTCTCTT-ATAATTTTGGTACA
1 ATAATTTTTGGTATT-TCTTCATAATTTTGGTACA
56025743 GTTTCGAACT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
39 8 0.12
40 52 0.81
41 4 0.06
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.53
Consensus pattern (39 bp):
ATAATTTTTGGTATTTCTTCATAATTTTGGTACACTCTT
Found at i:56026938 original size:11 final size:11
Alignment explanation
Indices: 56026908--56026955 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
56026898 AAATATAGAA
56026908 ATTTAG-TTTT
1 ATTTAGATTTT
** *
56026918 ATAAAGATTTC
1 ATTTAGATTTT
56026929 ATTTAGATTTT
1 ATTTAGATTTT
*
56026940 ATTCAGATTTT
1 ATTTAGATTTT
56026951 ATTTA
1 ATTTA
56026956 CTAAAGAATA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
10 4 0.14
11 25 0.86
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.56
Consensus pattern (11 bp):
ATTTAGATTTT
Found at i:56026947 original size:22 final size:21
Alignment explanation
Indices: 56026908--56026955 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
56026898 AAATATAGAA
56026908 ATTTAGTTTTATAAAGATTTC
1 ATTTAGTTTTATAAAGATTTC
** *
56026929 ATTTAGATTTTATTCAGATTTT
1 ATTTAG-TTTTATAAAGATTTC
56026951 ATTTA
1 ATTTA
56026956 CTAAAGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.56
Consensus pattern (21 bp):
ATTTAGTTTTATAAAGATTTC
Found at i:56030231 original size:29 final size:29
Alignment explanation
Indices: 56030185--56030240 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
56030175 CATAAATTTT
*
56030185 AAATTTAATCCTTGTACTT-TTATTTATAG
1 AAATTTAATCCTTCTACTTATT-TTTATAG
56030214 AAATTTAAT-CTATCTACTTATTTTTAT
1 AAATTTAATCCT-TCTACTTATTTTTAT
56030241 TAGTATTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 2 0.08
29 20 0.83
30 2 0.08
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.54
Consensus pattern (29 bp):
AAATTTAATCCTTCTACTTATTTTTATAG
Found at i:56033768 original size:2 final size:2
Alignment explanation
Indices: 56033755--56033789 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
56033745 TACGGTTATT
*
56033755 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56033790 CTTGAAACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:56038176 original size:30 final size:29
Alignment explanation
Indices: 56038105--56038179 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
56038095 TTCTAAATTG
* * *
56038105 AAAAGTGAAATAATTTAATTTTAAAATTTT
1 AAAAGT-AAATAATTAAATCTCAAAATTTT
*
56038135 AAAA-TATAATAATTAAATCTCAAATTTTAT
1 AAAAGTA-AATAATTAAATCTCAAAATTT-T
56038165 AAAAGTAAATAATTA
1 AAAAGTAAATAATTA
56038180 GCAACATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 1 0.03
29 18 0.47
30 17 0.45
31 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.39
Consensus pattern (29 bp):
AAAAGTAAATAATTAAATCTCAAAATTTT
Found at i:56041406 original size:23 final size:23
Alignment explanation
Indices: 56041366--56041423 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
56041356 CCGACCCATT
**
56041366 TTTTAATAAATACC-AAAAATTTA
1 TTTTAA-AAATACCAAAAAAAGTA
*
56041389 TTTTAAAAATACATAAAAAAAGTA
1 TTTTAAAAATAC-CAAAAAAAGTA
56041413 TTTTAAAAATA
1 TTTTAAAAATA
56041424 TTTTAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.20
23 6 0.20
24 18 0.60
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (23 bp):
TTTTAAAAATACCAAAAAAAGTA
Found at i:56041437 original size:40 final size:38
Alignment explanation
Indices: 56041392--56041478 Score: 95
Period size: 41 Copynumber: 2.2 Consensus size: 38
56041382 AAATTTATTT
56041392 TAAAAATACATAAAA-AAAGTATTTTAAAAATATTTTAAAA
1 TAAAAATACATAAAATAAAGTA-TTT-AAAATA-TTTAAAA
** *
56041432 TAAAAAAGTATTTAAAATAAAGTATTTAAAATATTTAAAT
1 T-AAAAA-TACATAAAATAAAGTATTTAAAATATTTAAAA
56041472 TAAAAAT
1 TAAAAAT
56041479 TAAAAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
38 1 0.02
39 5 0.12
40 8 0.20
41 11 0.27
42 10 0.24
43 6 0.15
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (38 bp):
TAAAAATACATAAAATAAAGTATTTAAAATATTTAAAA
Found at i:56041443 original size:18 final size:16
Alignment explanation
Indices: 56041417--56041464 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
56041407 AAAGTATTTT
56041417 AAAAATATTTTAAAATA
1 AAAAATA-TTTAAAATA
56041434 AAAAAGTATTTAAAAT-
1 AAAAA-TATTTAAAATA
*
56041450 -AAAGTATTTAAAATA
1 AAAAATATTTAAAATA
56041465 TTTAAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.36
15 3 0.11
17 13 0.46
18 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (16 bp):
AAAAATATTTAAAATA
Found at i:56041463 original size:14 final size:14
Alignment explanation
Indices: 56041436--56041464 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56041426 TTAAAATAAA
56041436 AAAGTATTTAAAAT
1 AAAGTATTTAAAAT
56041450 AAAGTATTTAAAAT
1 AAAGTATTTAAAAT
56041464 A
1 A
56041465 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (14 bp):
AAAGTATTTAAAAT
Found at i:56041485 original size:23 final size:23
Alignment explanation
Indices: 56041428--56041487 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
56041418 AAAATATTTT
56041428 AAAA-TAAAAAAGTATTTAAAATA
1 AAAATTAAAAAA-TATTTAAAATA
* * *
56041451 AAGTATT-TAAAATATTTAAATTA
1 AA-AATTAAAAAATATTTAAAATA
56041474 AAAATTAAAAAATA
1 AAAATTAAAAAATA
56041488 AATATATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
22 3 0.10
23 20 0.69
24 5 0.17
25 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (23 bp):
AAAATTAAAAAATATTTAAAATA
Found at i:56056860 original size:22 final size:22
Alignment explanation
Indices: 56056817--56056860 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
56056807 TATAAAATAA
*
56056817 TTATTAAACGATTCAATAATTT
1 TTATTAAACGATTAAATAATTT
** *
56056839 TTATTAAATTATTAAATTATTT
1 TTATTAAACGATTAAATAATTT
56056861 AAAATTTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (22 bp):
TTATTAAACGATTAAATAATTT
Found at i:56063542 original size:22 final size:22
Alignment explanation
Indices: 56063516--56063578 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
56063506 CATGGCTCTC
56063516 CTCTCTTTCTCTCGCTCTTTCA
1 CTCTCTTTCTCTCGCTCTTTCA
56063538 CTCTCCTTTC-CTCGC-CATTTCA
1 CTCT-CTTTCTCTCGCTC-TTTCA
*
56063560 CT-TCTTT-TCTC-CTCGTTCA
1 CTCTCTTTCTCTCGCTCTTTCA
56063579 ATCCGCCGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
19 5 0.14
20 8 0.22
21 2 0.06
22 16 0.44
23 5 0.14
ACGTcount: A:0.06, C:0.41, G:0.05, T:0.48
Consensus pattern (22 bp):
CTCTCTTTCTCTCGCTCTTTCA
Found at i:56064068 original size:2 final size:2
Alignment explanation
Indices: 56064061--56064094 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56064051 AACTTTCGGA
56064061 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
56064095 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:56074594 original size:25 final size:25
Alignment explanation
Indices: 56074543--56074594 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
56074533 TTTTTACAAA
*
56074543 TTTAGAATTTAGTTCTATTTTTATT
1 TTTAGAATTTAGTTCTACTTTTATT
56074568 TTTAGAAATTTAGTCTCT-CTTTT-TT
1 TTTAG-AATTTAGT-TCTACTTTTATT
56074593 TT
1 TT
56074595 ATATTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 9 0.38
26 12 0.50
27 3 0.12
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.63
Consensus pattern (25 bp):
TTTAGAATTTAGTTCTACTTTTATT
Found at i:56076142 original size:22 final size:23
Alignment explanation
Indices: 56076117--56076161 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
56076107 TTAATTTAAA
*
56076117 ATTTAATACT-TTTATATATATT
1 ATTTAATAATATTTATATATATT
56076139 ATTTAATAATAATTTATATATAT
1 ATTTAATAAT-ATTTATATATAT
56076162 AGTACTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
24 11 0.55
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTAATAATATTTATATATATT
Found at i:56087530 original size:24 final size:25
Alignment explanation
Indices: 56087503--56087550 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
56087493 AGATGAAAGT
56087503 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
56087527 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
56087551 TATGGGAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:56095507 original size:18 final size:19
Alignment explanation
Indices: 56095479--56095514 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
56095469 TTTGTTTTGA
56095479 GATGTTTAATTATATGATC
1 GATGTTTAATTATATGATC
56095498 GATG-TTAATTATATGAT
1 GATGTTTAATTATATGAT
56095515 TGGGATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (19 bp):
GATGTTTAATTATATGATC
Found at i:56099890 original size:32 final size:36
Alignment explanation
Indices: 56099845--56099921 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 36
56099835 GTTCATTTTA
56099845 ATTCATATACAATTC-ATT-CAA-TTTA-TCACTAT
1 ATTCATATACAATTCTATTGCAATTTTACTCACTAT
56099877 ATTCA-ATATCAATTCTATTGCAATTTTACTCACTA-
1 ATTCATATA-CAATTCTATTGCAATTTTACTCACTAT
56099912 ATATCATATA
1 AT-TCATATA
56099922 ACAAAAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
31 3 0.08
32 11 0.29
33 3 0.08
34 3 0.08
35 6 0.16
36 9 0.24
37 3 0.08
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.43
Consensus pattern (36 bp):
ATTCATATACAATTCTATTGCAATTTTACTCACTAT
Found at i:56101266 original size:35 final size:34
Alignment explanation
Indices: 56101218--56101284 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
56101208 GCGTGTTCTC
* *
56101218 TTTCTTTTTCTTCTTTCTCTT-TTTCTTTCTCAAT
1 TTTCTTTTGCTTCTCTCT-TTCTTTCTTTCTCAAT
*
56101252 TTTCGTTTTGCTTCTCTGTTTCTTTCTTTCTCA
1 TTTC-TTTTGCTTCTCTCTTTCTTTCTTTCTCA
56101285 TTTCTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 6 0.21
35 22 0.79
ACGTcount: A:0.04, C:0.24, G:0.04, T:0.67
Consensus pattern (34 bp):
TTTCTTTTGCTTCTCTCTTTCTTTCTTTCTCAAT
Found at i:56101892 original size:7 final size:7
Alignment explanation
Indices: 56101880--56101906 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
56101870 CGCTTAACTT
56101880 ATAATTA
1 ATAATTA
56101887 ATAATTA
1 ATAATTA
56101894 ATAATTA
1 ATAATTA
56101901 ATAATT
1 ATAATT
56101907 TTTCTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATAATTA
Found at i:56102141 original size:31 final size:29
Alignment explanation
Indices: 56102103--56102163 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 29
56102093 AGCCTCAAAA
56102103 TTATATATGAATTTTGATTTAATGTGTAATT
1 TTATATATGAATTTTGATTT--TGTGTAATT
56102134 TTATATATGAATTTTGATTTTGTGTAATT
1 TTATATATGAATTTTGATTTTGTGTAATT
56102163 T
1 T
56102164 CATACACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.33
31 20 0.67
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (29 bp):
TTATATATGAATTTTGATTTTGTGTAATT
Found at i:56102332 original size:31 final size:32
Alignment explanation
Indices: 56102291--56102378 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 32
56102281 AATAAATGTA
*
56102291 TATAA-TTGAACCAAAATTAAAGTTTCAT-T-
1 TATAATTTGAACCAAAATTAAAGTTCCATATG
* * *
56102320 TATACATTTGAACCACAATAAAAATTCCATATG
1 TATA-ATTTGAACCAAAATTAAAGTTCCATATG
56102353 TATAATTT-AACC-AAATTAAAG-TCCAT
1 TATAATTTGAACCAAAATTAAAGTTCCAT
56102379 GTATCAAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
29 9 0.19
30 7 0.15
31 23 0.48
32 5 0.10
33 4 0.08
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (32 bp):
TATAATTTGAACCAAAATTAAAGTTCCATATG
Found at i:56102823 original size:23 final size:22
Alignment explanation
Indices: 56102778--56102830 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
56102768 ATAAAAGTAA
* *
56102778 TAAATTTTAATTAAGATATTATT
1 TAAATTTTAATAAAAATATTA-T
56102801 TAAATTTTATATAAAAATA-TAT
1 TAAATTTTA-ATAAAAATATTAT
56102823 T-AATTTTA
1 TAAATTTTA
56102831 CTTTATTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 7 0.26
22 2 0.07
23 11 0.41
24 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TAAATTTTAATAAAAATATTAT
Found at i:56107141 original size:2 final size:2
Alignment explanation
Indices: 56107134--56107160 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56107124 GAAACTAGAA
56107134 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 A
56107161 ATATGAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56114189 original size:13 final size:11
Alignment explanation
Indices: 56114157--56114199 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
56114147 CATTTTTTTA
*
56114157 AATAAAATAAT
1 AATAAAATATT
56114168 AAT-AAATATCT
1 AATAAAATAT-T
56114179 AAGTAAAATATT
1 AA-TAAAATATT
56114191 AATAAAATA
1 AATAAAATA
56114200 ATATTGAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:56114578 original size:3 final size:3
Alignment explanation
Indices: 56114570--56114634 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
56114560 CTACTTCTTA
56114570 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56114618 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
56114635 ACCCCTCAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:56115268 original size:20 final size:20
Alignment explanation
Indices: 56115240--56115300 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
56115230 TTATTCTACA
56115240 TCTTAAATTTTTTATTGATT
1 TCTTAAATTTTTTATTGATT
* * * *
56115260 TCTTTAATTCTTTAATAATAT
1 TCTTAAATTTTTTATTGAT-T
56115281 T-TTAAATTTTTTATTGATT
1 TCTTAAATTTTTTATTGATT
56115300 T
1 T
56115301 AAAATATGCC
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TCTTAAATTTTTTATTGATT
Found at i:56124474 original size:17 final size:16
Alignment explanation
Indices: 56124452--56124487 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
56124442 AATTTGATCA
56124452 TTTTTAGTTCCTGTAAT
1 TTTTTAGTT-CTGTAAT
*
56124469 TTTTTAGTTTTGTAAT
1 TTTTTAGTTCTGTAAT
56124485 TTT
1 TTT
56124488 AGTCTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.67
Consensus pattern (16 bp):
TTTTTAGTTCTGTAAT
Found at i:56125545 original size:41 final size:41
Alignment explanation
Indices: 56125469--56125695 Score: 161
Period size: 41 Copynumber: 5.5 Consensus size: 41
56125459 CTTTCGAGCT
* * * * * * *
56125469 TTTTTAAAAAAGCACCGCTAATGCTCAGAGC-TTTAGCTGTG
1 TTTTTGAAAAAGCGCCGCTAAAGATC-GGGCTTTTAGCGGCG
* * *
56125510 TTTTTGATAAAGCGCGGCTAAAGATCTGGCTTTTAGCGGCG
1 TTTTTGAAAAAGCGCCGCTAAAGATCGGGCTTTTAGCGGCG
* * * **
56125551 GTTCTAAAAAAGTACCGCTAAAGATCGGGCTTTTAGCGGCG
1 TTTTTGAAAAAGCGCCGCTAAAGATCGGGCTTTTAGCGGCG
* * * * * ** *
56125592 TTTTTGAAAAAGCGTCGCTAATGCTAAGAGC-TGCAGCGGCA
1 TTTTTGAAAAAGCGCCGCTAAAGAT-CGGGCTTTTAGCGGCG
* * * * *
56125633 TTTTTGAAAATGCGCCGCCAATGCTCTGGCTTTTAGCGGCG
1 TTTTTGAAAAAGCGCCGCTAAAGATCGGGCTTTTAGCGGCG
*
56125674 TTTTTAAAAAAGCGCCGCTAAA
1 TTTTTGAAAAAGCGCCGCTAAA
56125696 ACATTTTATC
Statistics
Matches: 139, Mismatches: 44, Indels: 6
0.74 0.23 0.03
Matches are distributed among these distances:
40 4 0.03
41 132 0.95
42 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (41 bp):
TTTTTGAAAAAGCGCCGCTAAAGATCGGGCTTTTAGCGGCG
Found at i:56125622 original size:123 final size:123
Alignment explanation
Indices: 56125469--56125695 Score: 285
Period size: 123 Copynumber: 1.8 Consensus size: 123
56125459 CTTTCGAGCT
* ** * ** * *
56125469 TTTTTAAAAAAGCACCGCTAATGCTCAGAGCTTTAGCTGTGTTTTTGATAAA-GCGCGGCTAAAG
1 TTTTTAAAAAAGCACCGCTAATGCTAAGAGCTGCAGCGGCATTTTTGA-AAATGCGCCGCCAAAG
*
56125533 ATCTGGCTTTTAGCGGCGGTTCTAAAAAAGTACCGCTAAAGATCGGGCTTTTAGCGGCG
65 ATCTGGCTTTTAGCGGCGGTTCTAAAAAAGCACCGCTAAAGATCGGGCTTTTAGCGGCG
* ** * *
56125592 TTTTTGAAAAAGCGTCGCTAATGCTAAGAGCTGCAGCGGCATTTTTGAAAATGCGCCGCCAATGC
1 TTTTTAAAAAAGCACCGCTAATGCTAAGAGCTGCAGCGGCATTTTTGAAAATGCGCCGCCAAAGA
* * *
56125657 TCTGGCTTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAAA
66 TCTGGCTTTTAGCGGCGGTTCTAAAAAAGCACCGCTAAA
56125696 ACATTTTATC
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
122 3 0.03
123 83 0.97
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (123 bp):
TTTTTAAAAAAGCACCGCTAATGCTAAGAGCTGCAGCGGCATTTTTGAAAATGCGCCGCCAAAGA
TCTGGCTTTTAGCGGCGGTTCTAAAAAAGCACCGCTAAAGATCGGGCTTTTAGCGGCG
Found at i:56125630 original size:82 final size:82
Alignment explanation
Indices: 56125544--56125694 Score: 185
Period size: 82 Copynumber: 1.8 Consensus size: 82
56125534 TCTGGCTTTT
* * * * *
56125544 AGCGGCGGTTCTAAAAAAGTACCGCTAAAGATCGGGCTTTTAGCGGCGTTTTTGAAAAAGCGTCG
1 AGCGGCAGTTCTAAAAAAGCACCGCCAAAGATCGGGCTTTTAGCGGCGTTTTTAAAAAAGCGCCG
56125609 CTAATGCTAAGAGCTGC
66 CTAATGCTAAGAGCTGC
* * * * * * * *
56125626 AGCGGCATTTTTGAAAATGCGCCGCCAATGCTCTGGCTTTTAGCGGCGTTTTTAAAAAAGCGCCG
1 AGCGGCAGTTCTAAAAAAGCACCGCCAAAGATCGGGCTTTTAGCGGCGTTTTTAAAAAAGCGCCG
56125691 CTAA
66 CTAA
56125695 AACATTTTAT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
82 56 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (82 bp):
AGCGGCAGTTCTAAAAAAGCACCGCCAAAGATCGGGCTTTTAGCGGCGTTTTTAAAAAAGCGCCG
CTAATGCTAAGAGCTGC
Found at i:56125731 original size:20 final size:18
Alignment explanation
Indices: 56125706--56125743 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
56125696 ACATTTTATC
56125706 TGTTTATTTACTATTCAATT
1 TGTTTATTTA-TATT-AATT
56125726 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
56125744 AAAATTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.63
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:56126128 original size:14 final size:15
Alignment explanation
Indices: 56126102--56126134 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
56126092 AACATTTATA
56126102 GATTATGGAATTAGG
1 GATTATGGAATTAGG
56126117 GATTAT-GAATTAGG
1 GATTATGGAATTAGG
56126131 GATT
1 GATT
56126135 TCGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Done.