Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 46 of 206
Found at i:13075043 original size:26 final size:25
Alignment explanation
Indices: 13074868--13075081 Score: 134
Period size: 26 Copynumber: 8.6 Consensus size: 25
13074858 TATATATATA
*
13074868 TATATTATTTATTTTAGATTTTTTT
1 TATATTATTTATTTTAAATTTTTTT
* * * *
13074893 ACATATTATTTCTTTTAAACTATTTTA
1 -TATATTATTTATTTTAAA-TTTTTTT
* * * **
13074920 TGTAATGTTTATTTTAAA-TTGCTT
1 TATATTATTTATTTTAAATTTTTTT
* * * *
13074944 TAAATTATTTATTTCAAACTATTTTA
1 TATATTATTTATTTTAAA-TTTTTTT
* *
13074970 TATTTTATTTATGTT-AATTTTTTT
1 TATATTATTTATTTTAAATTTTTTT
* * **
13074994 TACATTGTTTATTTTGAACCTTTTTT
1 TATATTATTTATTTT-AAATTTTTTT
*
13075020 TGTATTATTTATTTTAAA---TTTT
1 TATATTATTTATTTTAAATTTTTTT
*
13075042 T-TATTATTTACTTTAAATTTTTTT
1 TATATTATTTATTTTAAATTTTTTT
13075066 GTATATTATTTTATTT
1 -TATATTA-TTTATTT
13075082 CATTTGTCTT
Statistics
Matches: 136, Mismatches: 41, Indels: 21
0.69 0.21 0.11
Matches are distributed among these distances:
21 15 0.11
22 5 0.04
24 35 0.26
25 5 0.04
26 65 0.48
27 11 0.08
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (25 bp):
TATATTATTTATTTTAAATTTTTTT
Found at i:13075078 original size:22 final size:22
Alignment explanation
Indices: 13075014--13075078 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 22
13075004 ATTTTGAACC
13075014 TTTTTTTGTATTATTTATTTTAAA
1 TTTTTTTGTA-TA-TTATTTTAAA
*
13075038 TTTTTTAT-TAT-TTACTTTAAA
1 TTTTTT-TGTATATTATTTTAAA
13075059 TTTTTTTGTATATTATTTTA
1 TTTTTTTGTATATTATTTTA
13075079 TTTCATTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
20 1 0.03
21 18 0.50
22 7 0.19
23 1 0.03
24 8 0.22
25 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.71
Consensus pattern (22 bp):
TTTTTTTGTATATTATTTTAAA
Found at i:13075394 original size:18 final size:17
Alignment explanation
Indices: 13075364--13075397 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13075354 GCTATTATTC
13075364 AAAAAAGGAAATATTTT
1 AAAAAAGGAAATATTTT
*
13075381 AAAATAAGGCAATATTT
1 AAAA-AAGGAAATATTT
13075398 CGCGTTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (17 bp):
AAAAAAGGAAATATTTT
Found at i:13078912 original size:113 final size:110
Alignment explanation
Indices: 13078640--13078970 Score: 396
Period size: 113 Copynumber: 3.0 Consensus size: 110
13078630 AAAATAAGAA
* * * ** *
13078640 TTAGCGGCGCTTTTGCT-AAAGCGCCGC-AAAAAACTAAGCCCAACGATGCCGTTTTCTAAGCTT
1 TTAGCGGCGCTTTT-ATGAAAGCGCCGCAAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTT
* * *
13078703 CTGGGGGGGTTTAGCGGCGTTTTTAATAATGCGCAGCTAATGCAGGGCT
65 -T-CGGGGGTTTAGCGGCGTTTTTAATAAAGCGC-GCTAATGCTGGGCT
* * * * *
13078752 TTAGCGGCGTTTTTATGGAAGCGACGCAAAAAAATTAAACCTAACGACACCGTTTTCTTTGCTTT
1 TTAGCGGCGCTTTTATGAAAGCGCCGCAAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTTT
* * *
13078817 CGGGGGTTTAGCGGTGTTTTTAGTAAAGCGTCGCTAATGCTGGGTTT
66 CGGGGGTTTAGCGGCGTTTTTAATAAAGCG-CGCTAATGCTGGG-CT
*
13078864 TTAGTGGCGCTTTTATGAAAGCGCCGCAAAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTT
1 TTAGCGGCGCTTTTATGAAAGCGCCGC-AAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTT
* *
13078929 TCAGGGTTTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCT
65 TCGGGGGTTTAGCGGCGTTTTTAATAAAGCG-CGCTAATGCT
13078971 CAGGGATTTA
Statistics
Matches: 186, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
111 38 0.20
112 47 0.25
113 101 0.54
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (110 bp):
TTAGCGGCGCTTTTATGAAAGCGCCGCAAAAAAATTAAACCCAACGACACCGTTTTCTTAGCTTT
CGGGGGTTTAGCGGCGTTTTTAATAAAGCGCGCTAATGCTGGGCT
Found at i:13079236 original size:31 final size:32
Alignment explanation
Indices: 13079201--13079263 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
13079191 GGTTTAAGGG
*
13079201 TTAGGTGTTATGATTT-AGGGGTTAGGGGGAT
1 TTAGGGGTTATGATTTAAGGGGTTAGGGGGAT
* *
13079232 TTAGGGGTTATGCTTTAAGGGGTTATGGGGAT
1 TTAGGGGTTATGATTTAAGGGGTTAGGGGGAT
13079264 ATATTTAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.19, C:0.02, G:0.41, T:0.38
Consensus pattern (32 bp):
TTAGGGGTTATGATTTAAGGGGTTAGGGGGAT
Found at i:13081296 original size:52 final size:52
Alignment explanation
Indices: 13081230--13081328 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
13081220 TGAAATAAGA
*
13081230 AAATTCAAACTAGGGTTAAGAAAGTAAGAACATTTTTAGGTATTAATACGGT
1 AAATTCAAACTAGGGTTAAGAAAGTAAGAACATTTTTAGGTAATAATACGGT
*
13081282 AAATTCAAATTAGGGTTAAGAAAGTAAGAACATTTTTAGGTAATAAT
1 AAATTCAAACTAGGGTTAAGAAAGTAAGAACATTTTTAGGTAATAAT
13081329 TTACATAACC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.31
Consensus pattern (52 bp):
AAATTCAAACTAGGGTTAAGAAAGTAAGAACATTTTTAGGTAATAATACGGT
Found at i:13082603 original size:52 final size:52
Alignment explanation
Indices: 13082531--13082735 Score: 177
Period size: 52 Copynumber: 4.1 Consensus size: 52
13082521 GTATATAACT
* *
13082531 TAATACATAATAACACAATACATAA-TTGGTCTATAAGCTTGCATAACTTACA
1 TAATACATAATAACACAATACATAACTT-ATATATAAGCTTGCATAACTTACA
* *
13082583 TAATACATAATAACATAATACATAACTTATATATAAGCTTGTATAACTTACA
1 TAATACATAATAACACAATACATAACTTATATATAAGCTTGCATAACTTACA
* * *
13082635 TAATA-ACT--T----C----CGTAACTTATATATAATCTGAT-AAT-ACATTACA
1 TAATACA-TAATAACACAATACATAACTTATATATAAGCT--TGCATAAC-TTACA
* *
13082678 TAATACATAATAACATAATACATAACTTATATTATAATCTTGCATAACTTACA
1 TAATACATAATAACACAATACATAACTTATA-TATAAGCTTGCATAACTTACA
13082731 TAATA
1 TAATA
13082736 ACTTACATAA
Statistics
Matches: 123, Mismatches: 11, Indels: 37
0.72 0.06 0.22
Matches are distributed among these distances:
42 19 0.15
43 13 0.11
44 2 0.02
45 1 0.01
50 1 0.01
51 1 0.01
52 52 0.42
53 24 0.20
54 10 0.08
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (52 bp):
TAATACATAATAACACAATACATAACTTATATATAAGCTTGCATAACTTACA
Found at i:13082629 original size:21 final size:20
Alignment explanation
Indices: 13082603--13082660 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
13082593 TAACATAATA
*
13082603 CATAACTTATATATAAGCTTG
1 CATAACTTATATATAA-CTTC
* *
13082624 TATAACTTACATAATAACTTC
1 CATAACTTATAT-ATAACTTC
*
13082645 CGTAACTTATATATAA
1 CATAACTTATATATAA
13082661 TCTGATAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 4 0.13
21 22 0.73
22 4 0.13
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (20 bp):
CATAACTTATATATAACTTC
Found at i:13082682 original size:12 final size:14
Alignment explanation
Indices: 13082665--13082701 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
13082655 ATATAATCTG
13082665 ATAATACAT-T-AC
1 ATAATACATATAAC
13082677 ATAATACATAATAAC
1 ATAATACAT-ATAAC
13082692 ATAATACATA
1 ATAATACATA
13082702 ACTTATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
14 2 0.09
15 11 0.50
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAATACATATAAC
Found at i:13082695 original size:8 final size:7
Alignment explanation
Indices: 13082665--13082702 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
13082655 ATATAATCTG
13082665 ATAATAC
1 ATAATAC
13082672 AT--TAC
1 ATAATAC
13082677 ATAATAC
1 ATAATAC
13082684 ATAATAAC
1 ATAAT-AC
13082692 ATAATAC
1 ATAATAC
13082699 ATAA
1 ATAA
13082703 CTTATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (7 bp):
ATAATAC
Found at i:13082723 original size:22 final size:21
Alignment explanation
Indices: 13082665--13082751 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 21
13082655 ATATAATCTG
13082665 ATAAT-ACATTACATAA--TAC
1 ATAATAAC-TTACATAACTTAC
*
13082684 ATAATAACATAATACATAACTTAT
1 ATAATAAC-T--TACATAACTTAC
* *
13082708 ATTATAATCTTGCATAACTTAC
1 ATAATAA-CTTACATAACTTAC
13082730 ATAATAACTTACATAACTTAC
1 ATAATAACTTACATAACTTAC
13082751 A
1 A
13082752 CATATTCATT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
19 5 0.09
20 4 0.07
21 14 0.25
22 23 0.41
24 9 0.16
25 1 0.02
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.34
Consensus pattern (21 bp):
ATAATAACTTACATAACTTAC
Found at i:13082738 original size:12 final size:12
Alignment explanation
Indices: 13082721--13082745 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13082711 ATAATCTTGC
13082721 ATAACTTACATA
1 ATAACTTACATA
13082733 ATAACTTACATA
1 ATAACTTACATA
13082745 A
1 A
13082746 CTTACACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:13083117 original size:191 final size:187
Alignment explanation
Indices: 13082748--13083178 Score: 665
Period size: 191 Copynumber: 2.3 Consensus size: 187
13082738 TTACATAACT
* * *
13082748 TACACATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAAT-AATAAATTTATAACTTA
1 TACATATATTCATTTATGTATGTGAGCTATATTTAAATTTTATTAATAAATAAATTTATAACTTA
13082812 AATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTAAA
66 AATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTAAA
* ** *
13082877 TTTTATTAATAATCATTTTTATAACTTAAATAAGTATTACTATTTTTTTTTAATATTTA
131 TTTTATTAATAATAAAATTTATAACTTAAATAAATATTACTATTTTTTTTT-ATA-TTA
* *
13082936 TACATATATTCATTTTATGTATGTGAGCTATATTTTAAATTTTATTAATAAATCATTTTATAACT
1 TACATATATTCA-TTTATGTATGTGAGCTATA-TTTAAATTTTATTAATAAATAAATTTATAACT
13083001 TAAATAAGTATTACTATTTTTTTTAATATTATACATATATTCATTTACG-ATGTAAGCTATATTT
64 TAAATAAGTATTACTA-TTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTATATTT
13083065 AAATTTTATTAATAATAAAATTTATAACTTTAAATAAATATTACTA-TTTTTTTTATATTA
128 AAATTTTATTAATAATAAAATTTATAAC-TTAAATAAATATTACTATTTTTTTTTATATTA
*
13083125 TACATATATTCCA-TTATGCATGTGAAGCTATATTTAAATTTTATTAAT-AATAAA
1 TACATATATT-CATTTATGTATGTG-AGCTATATTTAAATTTTATTAATAAATAAA
13083179 ATTANNNNNN
Statistics
Matches: 224, Mismatches: 12, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
187 4 0.02
188 37 0.17
189 37 0.17
190 21 0.09
191 77 0.34
192 48 0.21
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (187 bp):
TACATATATTCATTTATGTATGTGAGCTATATTTAAATTTTATTAATAAATAAATTTATAACTTA
AATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTAAA
TTTTATTAATAATAAAATTTATAACTTAAATAAATATTACTATTTTTTTTTATATTA
Found at i:13083123 original size:93 final size:94
Alignment explanation
Indices: 13082748--13083181 Score: 655
Period size: 93 Copynumber: 4.6 Consensus size: 94
13082738 TTACATAACT
*
13082748 TACACATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAAT-AAATTTATAACTTA
1 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAAATTTATAACTTA
13082812 AATAAGTATTACTA-TTTTTTTAATATTA
66 AATAAGTATTACTATTTTTTTTAATATTA
* **
13082840 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATCATTTTTATAACTTA
1 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAAATTTATAACTTA
13082905 AATAAGTATTACTATTTTTTTTTAATATTTA
66 AATAAGTATTACTA-TTTTTTTTAATA-TTA
* * * *
13082936 TACATATATTCATTTTATGTATGTGAGCTATATTTTAAATTTTATTAATAA-ATCATTTTATAAC
1 TACATATATTCA-TTTACGTATGTAAGCTATA-TTTAAATTTTATTAATAATA-AAATTTATAAC
13083000 TTAAATAAGTATTACTATTTTTTTTAATATTA
63 TTAAATAAGTATTACTATTTTTTTTAATATTA
13083032 TACATATATTCATTTACG-ATGTAAGCTATATTTAAATTTTATTAATAATAAAATTTATAACTTT
1 TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAAATTTATAAC-TT
*
13083096 AAATAAATATTACTATTTTTTTT-ATATTA
65 AAATAAGTATTACTATTTTTTTTAATATTA
* *
13083125 TACATATATTCCA-TTATGCATGTGAAGCTATATTTAAATTTTATTAATAATAAAATT
1 TACATATATT-CATTTACGTATGT-AAGCTATATTTAAATTTTATTAATAATAAAATT
13083182 ANNNNNNNNN
Statistics
Matches: 316, Mismatches: 14, Indels: 21
0.90 0.04 0.06
Matches are distributed among these distances:
92 49 0.16
93 73 0.23
94 42 0.13
95 49 0.16
96 30 0.09
97 29 0.09
98 44 0.14
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (94 bp):
TACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAAATTTATAACTTA
AATAAGTATTACTATTTTTTTTAATATTA
Found at i:13086184 original size:21 final size:21
Alignment explanation
Indices: 13086158--13086250 Score: 114
Period size: 21 Copynumber: 4.3 Consensus size: 21
13086148 CAACAACTTA
**
13086158 AAGCAGAGGCAGCAATGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
13086179 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
13086200 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
13086221 AAGCAGCGAGAGAAGCAGCGAGAG
1 AAGCA--GAG-GCAGCAGCGAGAG
13086245 AAGCAG
1 AAGCAG
13086251 CGATAGAAGC
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
21 43 0.68
22 1 0.02
23 3 0.05
24 16 0.25
ACGTcount: A:0.39, C:0.18, G:0.41, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:13086228 original size:12 final size:12
Alignment explanation
Indices: 13086190--13086262 Score: 98
Period size: 12 Copynumber: 6.3 Consensus size: 12
13086180 AGCAGAGGCC
13086190 GCAGCGAGAGAA
1 GCAGCGAGAGAA
**
13086202 GCA--GAG-GCT
1 GCAGCGAGAGAA
13086211 GCAGCGAGAGAA
1 GCAGCGAGAGAA
13086223 GCAGCGAGAGAA
1 GCAGCGAGAGAA
13086235 GCAGCGAGAGAA
1 GCAGCGAGAGAA
*
13086247 GCAGCGATAGAA
1 GCAGCGAGAGAA
13086259 GCAG
1 GCAG
13086263 AGGTTCCAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
9 4 0.08
10 3 0.06
11 3 0.06
12 43 0.81
ACGTcount: A:0.38, C:0.18, G:0.41, T:0.03
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:13086866 original size:42 final size:42
Alignment explanation
Indices: 13086729--13087076 Score: 457
Period size: 42 Copynumber: 8.2 Consensus size: 42
13086719 TTTAAACAAG
* * * * * *
13086729 CGCTATAGAACATTA-CTTTTAGAGGCGTTTTCTTTCAAAGTGC
1 CGCTAAAGAACATGATC-TTTAGTGGCG-TTTATTTCTAAGCGC
*
13086772 CGCTAAAGAACATGATCTTTAGCGGCGTTT-TTGTCCTAAGCGC
1 CGCTAAAGAACATGATCTTTAGTGGCGTTTATT-T-CTAAGCGC
13086815 CGCTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGC
1 CGCTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGC
*
13086857 CGCTAAAGAACATGCTCTTTAGTGGCGTTTATTTCTAAGCGC
1 CGCTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGC
* * *
13086899 CGCTAAAGAACATGGTCTTTAGTGGCGTTTATTTTTTAGCGC
1 CGCTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGC
* *
13086941 CGCTAAAGAACATGATCTTTAGTGGCGTTTATTTTTTAGCGC
1 CGCTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGC
* * * *
13086983 CGTTAAAGAACATGATCTTTAGCGGCGATTCTTTCTAAGCGC
1 CGCTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGC
*
13087025 CGCTAAAGAACATGATCTTTAGTGGCGTTTTTTTCTGTAAGCGC
1 CGCTAAAGAACATGATCTTTAGTGGCGTTTATTTC--TAAGCGC
*
13087069 CGCAAAAG
1 CGCTAAAG
13087077 TTTACGACGG
Statistics
Matches: 277, Mismatches: 22, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
41 2 0.01
42 200 0.72
43 58 0.21
44 17 0.06
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (42 bp):
CGCTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGC
Found at i:13087107 original size:84 final size:80
Alignment explanation
Indices: 13086770--13087116 Score: 358
Period size: 84 Copynumber: 4.1 Consensus size: 80
13086760 CTTTCAAAGT
* * *
13086770 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTGTCCTAAGCGCCGCTAAAGAACATGATCTTT
1 GCCGCTAAAGAACATGATCTTTAGTGGCGTTTTT-TTCTAAGCGCCGCTAAAGAACAGGA-CTTT
13086835 AGTGGCGTTTATTTCTAAGC
64 AGTGGCGTTTA--T-TAAGC
* * *
13086855 GCCGCTAAAGAACATGCTCTTTAGTGGCGTTTATTTCTAAGCGCCGCTAAAGAACATGGTCTTTA
1 GCCGCTAAAGAACATGATCTTTAGTGGCGTTTTTTTCTAAGCGCCGCTAAAGAACA-GGACTTTA
*
13086920 GTGGCGTTTATTTTTTAGC
65 GTGGCGTTTA---TTAAGC
* * *
13086939 GCCGCTAAAGAACATGATCTTTAGTGGCGTTTATTTT-TTAGCGCCGTTAAAGAACATGATCTTT
1 GCCGCTAAAGAACATGATCTTTAGTGGCGTTT-TTTTCTAAGCGCCGCTAAAGAACAGGA-CTTT
* *
13087003 AGCGGCGATTCTTTCTAAGC
64 AGTGGCG-TT-TAT-TAAGC
* *
13087023 GCCGCTAAAGAACATGATCTTTAGTGGCGTTTTTTTCTGTAAGCGCCGCAAAAGTTTACGACGGA
1 GCCGCTAAAGAACATGATCTTTAGTGGCGTTTTTTTC--TAAGCGCCGCTAAAG--AAC-A-GGA
*
13087088 -TTTAGTGGCGTTTA-AAAGC
60 CTTTAGTGGCGTTTATTAAGC
13087107 GCCGCTAAAG
1 GCCGCTAAAG
13087117 GCAAAAAAAA
Statistics
Matches: 224, Mismatches: 24, Indels: 29
0.81 0.09 0.10
Matches are distributed among these distances:
83 6 0.03
84 148 0.66
85 40 0.18
86 14 0.06
87 2 0.01
88 11 0.05
89 1 0.00
90 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (80 bp):
GCCGCTAAAGAACATGATCTTTAGTGGCGTTTTTTTCTAAGCGCCGCTAAAGAACAGGACTTTAG
TGGCGTTTATTAAGC
Found at i:13087108 original size:126 final size:123
Alignment explanation
Indices: 13086758--13087116 Score: 420
Period size: 126 Copynumber: 2.8 Consensus size: 123
13086748 TAGAGGCGTT
* * * * *
13086758 TTCTTTCAAAGTGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTGTCCTAAGCGCCGCTAAAG
1 TTCTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTTTTTTCTTAAGCGCCGCTAAAG
* * *
13086823 AACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCGCTAAAGAACATGCTCTTTAGTGGCGT
66 AACATGA-CTTTAGTGGCGTTTA--T-TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGA
* *
13086885 TTATTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCGTTTATTTT-TT-AGCGCCGCTAAA
1 TTCTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTT-TTTTCTTAAGCGCCGCTAAA
* *
13086948 GAACATGATCTTTAGTGGCGTTTATTTTTTAGCGCCGTTAAAGAACATGATCTTTAGCGGCGA
65 GAACATGA-CTTTAGTGGCGTTTA---TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGA
*
13087011 TTCTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTTTTTTCTGTAAGCGCCGCAAAA
1 TTCTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTTTTTTCT-TAAGCGCCGCTAAA
* * *
13087076 GTTTACGACGGA-TTTAGTGGCGTTTA-AAAGCGCCGCTAAAG
65 G--AAC-A-TGACTTTAGTGGCGTTTATTAAGCGCCGCTAAAG
13087117 GCAAAAAAAA
Statistics
Matches: 203, Mismatches: 20, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
125 4 0.02
126 121 0.60
127 44 0.22
128 15 0.07
130 16 0.08
131 1 0.00
132 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (123 bp):
TTCTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTTTTTTCTTAAGCGCCGCTAAAG
AACATGACTTTAGTGGCGTTTATTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGA
Found at i:13090643 original size:2 final size:2
Alignment explanation
Indices: 13090636--13090661 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13090626 CCTTCATTGG
13090636 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
13090662 ATTTATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:13093075 original size:44 final size:45
Alignment explanation
Indices: 13093013--13093108 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 45
13093003 TCGTATATTC
* * *
13093013 TTTGA-TTCAGTATTTAAACATGTAATAACTGGTG-AAGCCAATG
1 TTTGAGTTCAGTATTTAAACAAGTAAGAACTGGTGAAAGCCAATA
* *
13093056 TTTGAGTTCTGTATTTAAACAAGTAAGAACTGGTGAAAGGCAATA
1 TTTGAGTTCAGTATTTAAACAAGTAAGAACTGGTGAAAGCCAATA
13093101 TTTGAGTT
1 TTTGAGTT
13093109 GAGAGAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 5 0.11
44 26 0.57
45 15 0.33
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.35
Consensus pattern (45 bp):
TTTGAGTTCAGTATTTAAACAAGTAAGAACTGGTGAAAGCCAATA
Found at i:13096277 original size:15 final size:15
Alignment explanation
Indices: 13096257--13096286 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13096247 ATAGCTTATA
13096257 GTACAAGTTAAATTT
1 GTACAAGTTAAATTT
*
13096272 GTACAATTTAAATTT
1 GTACAAGTTAAATTT
13096287 ATTTAATACT
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:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (15 bp):
GTACAAGTTAAATTT
Found at i:13096478 original size:31 final size:30
Alignment explanation
Indices: 13096419--13096484 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
13096409 TTTTTAATCA
* * *
13096419 CAAATGGTACTTAAATTATATTATGTTACT
1 CAAATGGTACCTAAATCATATTATGTTACC
13096449 CAAAGTGGTACCTAAATCATATT-TCGTTACC
1 CAAA-TGGTACCTAAATCATATTAT-GTTACC
13096480 CAAAT
1 CAAAT
13096485 TACCTCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (30 bp):
CAAATGGTACCTAAATCATATTATGTTACC
Found at i:13113251 original size:45 final size:45
Alignment explanation
Indices: 13113187--13113278 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
13113177 AAAGAAAAGA
13113187 ATGTGCATGAGATGCATTGTTGTTAATTCATTGACATGTATGTAT
1 ATGTGCATGAGATGCATTGTTGTTAATTCATTGACATGTATGTAT
13113232 ATGTGCATGAGATGCATTGTTGTTAATTCATTGACATGTATGTAT
1 ATGTGCATGAGATGCATTGTTGTTAATTCATTGACATGTATGTAT
13113277 AT
1 AT
13113279 ATGTATTTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (45 bp):
ATGTGCATGAGATGCATTGTTGTTAATTCATTGACATGTATGTAT
Found at i:13122888 original size:17 final size:18
Alignment explanation
Indices: 13122863--13122897 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
13122853 TTTAGTTTTC
*
13122863 AAATTAAAT-AAAGTAGA
1 AAATAAAATAAAAGTAGA
13122880 AAATAAAATAAAAGTAGA
1 AAATAAAATAAAAGTAGA
13122898 GGAAGTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (18 bp):
AAATAAAATAAAAGTAGA
Found at i:13133223 original size:35 final size:35
Alignment explanation
Indices: 13133177--13133243 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
13133167 TAATTGACAG
13133177 ATTAACATAAAGACTGAAAGAAAGAAATAAAATCA
1 ATTAACATAAAGACTGAAAGAAAGAAATAAAATCA
13133212 ATTAACATAAAGACTGAAAGAAAGAAATAAAA
1 ATTAACATAAAGACTGAAAGAAAGAAATAAAA
13133244 GAATAAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.64, C:0.07, G:0.12, T:0.16
Consensus pattern (35 bp):
ATTAACATAAAGACTGAAAGAAAGAAATAAAATCA
Found at i:13139156 original size:25 final size:26
Alignment explanation
Indices: 13139123--13139171 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
13139113 AAAAACTGCT
*
13139123 TTTTTACTATTTTGTTGCT-CTTTTC
1 TTTTAACTATTTTGTTGCTACTTTTC
13139148 TTTTAACTATTTTGTTGCTACTTT
1 TTTTAACTATTTTGTTGCTACTTT
13139172 CTTATTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.12, C:0.14, G:0.08, T:0.65
Consensus pattern (26 bp):
TTTTAACTATTTTGTTGCTACTTTTC
Found at i:13149876 original size:22 final size:22
Alignment explanation
Indices: 13149841--13149882 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13149831 TCCTTTTCAT
*
13149841 AATTTAAGCTTAATT-TTTATC
1 AATTTAAGCCTAATTCTTTATC
13149862 AATTTCAAGCCTAATTCTTTA
1 AATTT-AAGCCTAATTCTTTA
13149883 ATTTCTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (22 bp):
AATTTAAGCCTAATTCTTTATC
Found at i:13156777 original size:5 final size:5
Alignment explanation
Indices: 13156767--13156791 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
13156757 AGAATGAGAT
13156767 GGATA GGATA GGATA GGATA GGATA
1 GGATA GGATA GGATA GGATA GGATA
13156792 CAGAGAGATT
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:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (5 bp):
GGATA
Found at i:13164157 original size:13 final size:13
Alignment explanation
Indices: 13164128--13164166 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
13164118 TTACATTTTA
13164128 TTTATTAAA-AAT
1 TTTATTAAATAAT
*
13164140 ATTATTAAATAAT
1 TTTATTAAATAAT
13164153 TTTATTAAAATAAT
1 TTTATT-AAATAAT
13164167 AAATTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 8 0.35
13 8 0.35
14 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTATTAAATAAT
Found at i:13166259 original size:17 final size:18
Alignment explanation
Indices: 13166225--13166281 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
13166215 TTAACTATTA
13166225 ATTATTATATTTAATTTT
1 ATTATTATATTTAATTTT
*
13166243 ATTATTA-ATTTATTTTT
1 ATTATTATATTTAATTTT
* *
13166260 ATAAATTATTTTTTAATTTT
1 AT-TATTA-TATTTAATTTT
13166280 AT
1 AT
13166282 AAATTATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 11 0.34
18 11 0.34
20 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTATTATATTTAATTTT
Found at i:13166279 original size:20 final size:20
Alignment explanation
Indices: 13166251--13166288 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13166241 TTATTATTAA
*
13166251 TTTATTTTTATAAATTATTT
1 TTTAATTTTATAAATTATTT
13166271 TTTAATTTTATAAATTAT
1 TTTAATTTTATAAATTAT
13166289 AATTACGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTAATTTTATAAATTATTT
Found at i:13174419 original size:11 final size:11
Alignment explanation
Indices: 13174399--13174506 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
13174389 TAAAAATTAA
13174399 AAAAAGTATTTT
1 AAAAA-TATTTT
13174411 AAAAATATTTT
1 AAAAATATTTT
13174422 --AAA-A--TT
1 AAAAATATTTT
* * *
13174428 AAAAAAAATTA
1 AAAAATATTTT
13174439 AAAAAGTATTTT
1 AAAAA-TATTTT
*
13174451 AAAAAAATTTT
1 AAAAATATTTT
13174462 --AAA-A-TTT
1 AAAAATATTTT
13174469 AAAAA-ATTTAAT
1 AAAAATATTT--T
*
13174481 AAAAGTATTTT
1 AAAAATATTTT
*
13174492 AAAAGTATTTT
1 AAAAATATTTT
13174503 AAAA
1 AAAA
13174507 TTAAAAAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 25
0.72 0.06 0.23
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 5 0.06
9 11 0.14
10 2 0.03
11 33 0.42
12 18 0.23
13 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:13174442 original size:41 final size:41
Alignment explanation
Indices: 13174366--13174522 Score: 212
Period size: 40 Copynumber: 3.8 Consensus size: 41
13174356 ATAAATACCA
13174366 AAAAATTATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTT
1 AAAAA-TATTTT-AAAATT-AAA-AAAAATTAAAAAAAGTATTTT
13174411 AAAAATATTTTAAAATTAAAAAAAATT-AAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
* * * *
13174451 AAAAAAATTTTAAAATTTAAAAAATTTAATAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
*
13174492 AAAAGTATTTTAAAATT-AAAAAAA-TAAAAAA
1 AAAAATATTTTAAAATTAAAAAAAATTAAAAAA
13174523 TAATAAAAAT
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
39 6 0.06
40 43 0.42
41 34 0.33
42 3 0.03
43 6 0.06
44 6 0.06
45 5 0.05
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (41 bp):
AAAAATATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
Found at i:13175296 original size:22 final size:20
Alignment explanation
Indices: 13175259--13175304 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
13175249 CTCTTTCAAC
*
13175259 AAAAAAATTAAAAATTTCTA
1 AAAAAAATAAAAAATTTCTA
*
13175279 AAAAAAATCAAAATAATTTTTA
1 AAAAAAAT-AAAA-AATTTCTA
13175301 AAAA
1 AAAA
13175305 TCCAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 3 0.14
22 11 0.50
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAAATAAAAAATTTCTA
Found at i:13175315 original size:18 final size:19
Alignment explanation
Indices: 13175281--13175321 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13175271 AATTTCTAAA
*
13175281 AAAAATCAAAATAATTTTT
1 AAAAATCAAAATAATTTAT
*
13175300 AAAAATCCAAAT-ATTTAT
1 AAAAATCAAAATAATTTAT
13175318 AAAA
1 AAAA
13175322 TTTCCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATCAAAATAATTTAT
Found at i:13180401 original size:2 final size:2
Alignment explanation
Indices: 13180389--13180469 Score: 51
Period size: 2 Copynumber: 41.0 Consensus size: 2
13180379 ATAAGATAAA
* * * *
13180389 AT AT AT GT AT AT AT AT AT AT GT GT AT AT AT AT AT AG AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
13180430 AA AG AA ACT AT AT TT CA- AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
13180470 GAATACGTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
1 3 0.05
2 59 0.94
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:13180408 original size:14 final size:14
Alignment explanation
Indices: 13180389--13180422 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
13180379 ATAAGATAAA
13180389 ATATATGTATATAT
1 ATATATGTATATAT
*
13180403 ATATATGTGTATAT
1 ATATATGTATATAT
13180417 ATATAT
1 ATATAT
13180423 AGATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (14 bp):
ATATATGTATATAT
Found at i:13180408 original size:16 final size:16
Alignment explanation
Indices: 13180389--13180423 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
13180379 ATAAGATAAA
13180389 ATATATGTATATATAT
1 ATATATGTATATATAT
*
13180405 ATATGTGTATATATAT
1 ATATATGTATATATAT
13180421 ATA
1 ATA
13180424 GATATAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (16 bp):
ATATATGTATATATAT
Found at i:13180610 original size:3 final size:3
Alignment explanation
Indices: 13180602--13180696 Score: 70
Period size: 3 Copynumber: 30.7 Consensus size: 3
13180592 AAGCTATTAT
*
13180602 ATA ATA ATA ATA ATA ATA CGATA AGTA ACA ATA AT- ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA --ATA A-TA ATA ATA ATA AT-A ATA ATA ATA
* * * *
13180650 TTA ATA ATA ATA ACA ATA ATGA A-A GATA ATA AT- ATA TTA AAA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA -ATA ATA ATA ATA ATA ATA ATA
13180695 AT
1 AT
13180697 GAGGAAAATA
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
2 5 0.07
3 57 0.78
4 8 0.11
5 3 0.04
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:13181386 original size:18 final size:18
Alignment explanation
Indices: 13181355--13181401 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
13181345 AACAGTTTCG
13181355 AAAGAAAGAA-AAAAATAA
1 AAAGAAA-AATAAAAATAA
*
13181373 AGAGAAAAATAAAAATAA
1 AAAGAAAAATAAAAATAA
*
13181391 AAAGGAAAATA
1 AAAGAAAAATA
13181402 GAACTTGTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.09
Consensus pattern (18 bp):
AAAGAAAAATAAAAATAA
Found at i:13181783 original size:27 final size:28
Alignment explanation
Indices: 13181735--13181789 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
13181725 GTTTTGGGCC
*
13181735 TGTTGGGTATTTGGGCTTGGTT-TAATT
1 TGTTGGGTACTTGGGCTTGGTTGTAATT
*
13181762 TGTTGGGT-CTTGGGTTTGGGTTGTAATT
1 TGTTGGGTACTTGGGCTT-GGTTGTAATT
13181790 GGGTTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 12 0.50
28 5 0.21
ACGTcount: A:0.09, C:0.04, G:0.36, T:0.51
Consensus pattern (28 bp):
TGTTGGGTACTTGGGCTTGGTTGTAATT
Found at i:13182329 original size:132 final size:132
Alignment explanation
Indices: 13182105--13182373 Score: 432
Period size: 132 Copynumber: 2.0 Consensus size: 132
13182095 CATCATTGTT
13182105 GATCTGCTCCACTACTGCCTAGGGGGACAGAATCTACAATCTTCGACCTATTCCACTACTGCTTA
1 GATCTGCTCCACTACTGCCTAGGGGGACAGAATCTACAATCTTCGACCTATTCCACTACTGCTTA
* *
13182170 GGGTGATAGGGCTAACGGTTTAAATCTGCTTCTCCACTGTCTTGAGAAGATAAAATTCACCATCT
66 GGGTGATAGGACTAACGGATTAAATCTGCTTCTCCACTGTCTTGAGAAGATAAAATTCACCATCT
13182235 TC
131 TC
* * * *
13182237 GATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCGACCTATTCCACTATTGCTTA
1 GATCTGCTCCACTACTGCCTAGGGGGACAGAATCTACAATCTTCGACCTATTCCACTACTGCTTA
* * * *
13182302 GGAG-GATAGGACTAATGGATTAAATCTGCTTCTCCACTGTCTTGGGAAGGTAAGATTCACCATC
66 GG-GTGATAGGACTAACGGATTAAATCTGCTTCTCCACTGTCTTGAGAAGATAAAATTCACCATC
13182366 TTC
130 TTC
13182369 GATCT
1 GATCT
13182374 TCAATTTATT
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
132 125 0.99
133 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
GATCTGCTCCACTACTGCCTAGGGGGACAGAATCTACAATCTTCGACCTATTCCACTACTGCTTA
GGGTGATAGGACTAACGGATTAAATCTGCTTCTCCACTGTCTTGAGAAGATAAAATTCACCATCT
TC
Found at i:13182448 original size:95 final size:95
Alignment explanation
Indices: 13182360--13182660 Score: 469
Period size: 95 Copynumber: 3.2 Consensus size: 95
13182350 GGTAAGATTC
* * *
13182360 ACCATCTTCGATCTTCAATTTATTCCACTGCCAACCAGAGAGATAGAATTATCGACTTCAATGTA
1 ACCATCTTTGATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATCGGCTTCAATGTA
13182425 CTCCACTGTAGTCACAGAGAGGTAAAATCT
66 CTCCACTGTAGTCACAGAGAGGTAAAATCT
*
13182455 ACCATCTTTGATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTA
1 ACCATCTTTGATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATCGGCTTCAATGTA
*
13182520 CTCCACTGTAATCACA-AGGAGGTAAAATCT
66 CTCCACTGTAGTCACAGA-GAGGTAAAATCT
* * * * *
13182550 GCCATCTTTGATCTTCAATCTATTCCACTGCTAACCAGAGAGATAGAATTATAGGTTTCAATATA
1 ACCATCTTTGATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATCGGCTTCAATGTA
* *
13182615 CTCCACTGTAGTCACAGGGAGGTAGAATCT
66 CTCCACTGTAGTCACAGAGAGGTAAAATCT
*
13182645 GCCATCTTTGATCTTC
1 ACCATCTTTGATCTTC
13182661 TCCTTTTTGG
Statistics
Matches: 190, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
94 1 0.01
95 189 0.99
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (95 bp):
ACCATCTTTGATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTATCGGCTTCAATGTA
CTCCACTGTAGTCACAGAGAGGTAAAATCT
Found at i:13182782 original size:62 final size:62
Alignment explanation
Indices: 13182713--13182837 Score: 178
Period size: 62 Copynumber: 2.0 Consensus size: 62
13182703 TTGCAAACTA
*
13182713 TGGTGTCTTCGATCTACTTCACTGTCAGTACAAGAAGGCAAGATCTGCTACCTTCAGTCTGC
1 TGGTGTCTTCGATCTACTTCACCGTCAGTACAAGAAGGCAAGATCTGCTACCTTCAGTCTGC
* * ** * * *
13182775 TGGTGTCTTTGATCTGCTTTGCCGTCAGTACAGGAAGGCAAGATCTGCTATCTTTAGTCTGC
1 TGGTGTCTTCGATCTACTTCACCGTCAGTACAAGAAGGCAAGATCTGCTACCTTCAGTCTGC
13182837 T
1 T
13182838 CCACTGTTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (62 bp):
TGGTGTCTTCGATCTACTTCACCGTCAGTACAAGAAGGCAAGATCTGCTACCTTCAGTCTGC
Found at i:13182974 original size:45 final size:45
Alignment explanation
Indices: 13182846--13183234 Score: 200
Period size: 44 Copynumber: 8.8 Consensus size: 45
13182836 CTCCACTGTT
*
13182846 AATGCAGGAAGACAAGATCTGTTGTCTTCAACCAGC-TCTGCTA-C
1 AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTC-GCTATC
* * * * * *
13182890 AACTG-A-GAGAGGCAAGGTTTG-TGTCTTCGACCTGATTCGCTATT
1 AA-TGCAGGA-AGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
*
13182934 AATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTTCGCTA-C
1 AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
* * * * * * *
13182978 AA--CCGAGAGAGGCAAGGTTTG-TGTCTTCGATCTGCTTCGCTGTC
1 AATGCAG-GA-AGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
* *
13183022 AAGGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGC-TCTACTA-C
1 AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTC-GCTATC
* * * * * * * * * *
13183066 AA-CCGAGAAAGGTAAGGTTTG-CGTCTTCGATCTGCTTCGCTGTC
1 AATGC-AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
* * * *
13183110 AAGGCAGGAAGGCAGGATCTGTTGTCTTCAACCAGCTCCACTA-C
1 AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
* * * * * * *
13183154 AA--CCGAGAGAGGCAAGGTTTG-TGTCTTCGATCTGCTTCGCTGTC
1 AATGCAG-GA-AGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
* * * *
13183198 AAGGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCT
1 AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCT
13183235 CCACTGCAAC
Statistics
Matches: 248, Mismatches: 72, Indels: 49
0.67 0.20 0.13
Matches are distributed among these distances:
42 4 0.02
43 67 0.27
44 110 0.44
45 63 0.25
46 4 0.02
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (45 bp):
AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTTCGCTATC
Found at i:13183311 original size:87 final size:88
Alignment explanation
Indices: 13182832--13183575 Score: 837
Period size: 88 Copynumber: 8.5 Consensus size: 88
13182822 CTATCTTTAG
* * * * ** *
13182832 TCTGCTCCACTGTTAATGCAGGAAGACAAGATCTGTTGTCTTCAACCAGCTCTGCTACAACTGAG
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTCCACTACAACCGAG
13182897 AGAGGCAAGGTTTGTGTCTTCGA
66 AGAGGCAAGGTTTGTGTCTTCGA
* * * * *
13182920 CCTGATTCGCTATTAATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTTCGCTACAACCGAG
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTCCACTACAACCGAG
13182985 AGAGGCAAGGTTTGTGTCTTCGA
66 AGAGGCAAGGTTTGTGTCTTCGA
* * * *
13183008 TCTGCTTCGCTGTCAAGGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCTACTACAACCGAG
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTCCACTACAACCGAG
* * *
13183073 AAAGGTAAGGTTTGCGTCTTCGA
66 AGAGGCAAGGTTTGTGTCTTCGA
* * * *
13183096 TCTGCTTCGCTGTCAAGGCAGGAAGGCAGGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAG
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTCCACTACAACCGAG
13183161 AGAGGCAAGGTTTGTGTCTTCGA
66 AGAGGCAAGGTTTGTGTCTTCGA
* * * * *
13183184 TCTGCTTCGCTGTCAAGGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTCCACTACAACCGA-
*
13183249 G-GAGGCAAGGTTTTGTGT-TT-TA
65 GAGAGGCAAGG-TTTGTGTCTTCGA
* * * * *
13183271 TCTGCTTCGCTGTTAATGTAGGAAGGTAAAATCTGCTATCTTCAACCAGCTCCACTATAACCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTCCACTACAACCGA-
* *
13183336 G-GAGGCAGGGCTTTAT-T-TTCGA
65 GAGAGGCAAGG-TTTGTGTCTTCGA
* * * *
13183358 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTACACTGCAACCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTCCACTACAACCGA-
**
13183423 G-GAGGCAAGGCTTCAT-T-TTCGA
65 GAGAGGCAAGG-TTTGTGTCTTCGA
* * * * * ** *
13183445 TCTACTTCGCTGTCAATGCAGGAAAGCAAGATCTGTTGTCTTCAACCAGCTCCATTGTAATCGAT
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTCCACTACAACCGA-
*
13183510 G-GAGGCAAGGCTT-TG-CTTTCGA
65 GAGAGGCAAGGTTTGTGTC-TTCGA
* * * *
13183532 TCTGCTTCACTGTTAACGCAGGAAAGCAAGATCTGCTATCTTCA
1 TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTATCTTCA
13183576 CTAATATGTT
Statistics
Matches: 578, Mismatches: 72, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
85 1 0.00
86 4 0.01
87 258 0.45
88 307 0.53
89 8 0.01
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (88 bp):
TCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGTTATCTTCAACCAGCTCCACTACAACCGAG
AGAGGCAAGGTTTGTGTCTTCGA
Found at i:13185275 original size:41 final size:41
Alignment explanation
Indices: 13185220--13185315 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
13185210 TCATTTCATA
* *
13185220 TTTTATTTTGACTTTGATTTTGATTTTAATTGATTTTCT-T-
1 TTTTCTTTTCACTTTGATTTTGATTTTAATT-ATTTTCTCTC
*
13185260 TTTTGCTTTTCACTTTGATTTTGATTTTAATTTTTTTCTCTC
1 TTTT-CTTTTCACTTTGATTTTGATTTTAATTATTTTCTCTC
13185302 TTTTCTTTTC-CTTT
1 TTTTCTTTTCACTTT
13185316 TTTTTTGAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 14 0.28
41 32 0.64
42 4 0.08
ACGTcount: A:0.12, C:0.11, G:0.07, T:0.69
Consensus pattern (41 bp):
TTTTCTTTTCACTTTGATTTTGATTTTAATTATTTTCTCTC
Found at i:13189896 original size:2 final size:2
Alignment explanation
Indices: 13189884--13189976 Score: 66
Period size: 2 Copynumber: 47.0 Consensus size: 2
13189874 TATAGATAAA
* * * * *
13189884 AT AT AT GT AT AT AT AT AT GT GT AT AT AT AT AG AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
13189926 A- AA AG AA ACT AT AT TT CA- AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
13189967 AT AT AT AT AT
1 AT AT AT AT AT
13189977 GAATACGTAT
Statistics
Matches: 73, Mismatches: 13, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
1 3 0.04
2 69 0.95
3 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:13190119 original size:3 final size:3
Alignment explanation
Indices: 13190111--13190199 Score: 56
Period size: 3 Copynumber: 28.7 Consensus size: 3
13190101 AAGCTATTAT
* * *
13190111 ATA ATA ATA ATA CGATA AGAA ACA ATA AT- ATAA ATA ATA ATA TTA ATA
1 ATA ATA ATA ATA --ATA A-TA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
* * * *
13190159 ATA ATA ACA ATA ATGA AAA ATA ATA AT- ATA TTA AAA ATA AT
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA AT
13190200 GAGGAAAATA
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
2 4 0.06
3 53 0.80
4 6 0.09
5 3 0.05
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:13190151 original size:12 final size:12
Alignment explanation
Indices: 13190134--13190188 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
13190124 GATAAGAAAC
13190134 AATAATATAAAT
1 AATAATATAAAT
*
13190146 AATAATATTAAT
1 AATAATATAAAT
13190158 AATAATA-ACAAT
1 AATAATATA-AAT
*
13190170 AATGA-A-AAAT
1 AATAATATAAAT
13190180 AATAATATA
1 AATAATATA
13190189 TTAAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 7 0.19
11 3 0.08
12 26 0.72
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (12 bp):
AATAATATAAAT
Found at i:13190896 original size:18 final size:18
Alignment explanation
Indices: 13190815--13190909 Score: 66
Period size: 18 Copynumber: 4.9 Consensus size: 18
13190805 TATAGTTTTT
13190815 AAATATAAAAGAAAAATAA
1 AAATA-AAAAGAAAAATAA
*
13190834 AAATAAAAATAAAGAATACA
1 AAATAAAAAGAAA-AATA-A
** *
13190854 AACAGTTTCGAAAGAAAGA-AA
1 AA-A---TAAAAAGAAAAATAA
*
13190875 AAATAAAGAGAAAAATAA
1 AAATAAAAAGAAAAATAA
*
13190893 AAATAAAAAGGAAAATA
1 AAATAAAAAGAAAAATA
13190910 GAACTTGTAC
Statistics
Matches: 58, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
17 8 0.14
18 24 0.41
19 9 0.16
20 4 0.07
21 4 0.07
22 1 0.02
23 1 0.02
24 7 0.12
ACGTcount: A:0.73, C:0.03, G:0.11, T:0.14
Consensus pattern (18 bp):
AAATAAAAAGAAAAATAA
Found at i:13191291 original size:27 final size:28
Alignment explanation
Indices: 13191243--13191297 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
13191233 GTTTTGGGCC
*
13191243 TGTTGGGTATTTGGGCTTGGTT-TAATT
1 TGTTGGGTACTTGGGCTTGGTTGTAATT
*
13191270 TGTTGGGT-CTTGGGTTTGGGTTGTAATT
1 TGTTGGGTACTTGGGCTT-GGTTGTAATT
13191298 GGGTTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 12 0.50
28 5 0.21
ACGTcount: A:0.09, C:0.04, G:0.36, T:0.51
Consensus pattern (28 bp):
TGTTGGGTACTTGGGCTTGGTTGTAATT
Found at i:13192762 original size:10 final size:10
Alignment explanation
Indices: 13192747--13192910 Score: 89
Period size: 10 Copynumber: 16.2 Consensus size: 10
13192737 GAAGGAGAGG
13192747 GAAAGAAGAA
1 GAAAGAAGAA
13192757 GAAAGAAAGAAA
1 GAAAG-AAG-AA
13192769 GAAAGAA-AA
1 GAAAGAAGAA
13192778 GGAAAGAA-AA
1 -GAAAGAAGAA
* *
13192788 GGAAAGGAGAG
1 -GAAAGAAGAA
13192799 GAAAG-A-AA
1 GAAAGAAGAA
13192807 GAAA-AAGAA
1 GAAAGAAGAA
13192816 GGAAAGAA-AA
1 -GAAAGAAGAA
13192826 GGAAAGGAGAAGAA
1 -G-AA--AGAAGAA
*
13192840 GAAAAAAGAAA
1 GAAAGAAG-AA
13192851 GAAA-AAGAA
1 GAAAGAAGAA
13192860 GGAAAGAA-AA
1 -GAAAGAAGAA
*
13192870 GGAAAGGAGAA
1 -GAAAGAAGAA
13192881 GAGAAG-AGAA
1 GA-AAGAAGAA
*
13192891 -AAAAAAGAA
1 GAAAGAAGAA
13192900 G-AAGAAGAA
1 GAAAGAAGAA
13192909 GA
1 GA
13192911 GGGAAGGAAA
Statistics
Matches: 127, Mismatches: 7, Indels: 40
0.73 0.04 0.23
Matches are distributed among these distances:
8 8 0.06
9 20 0.16
10 60 0.47
11 23 0.18
12 9 0.07
13 5 0.04
14 2 0.02
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
GAAAGAAGAA
Found at i:13192803 original size:38 final size:39
Alignment explanation
Indices: 13192756--13192932 Score: 167
Period size: 38 Copynumber: 4.5 Consensus size: 39
13192746 GGAAAGAAGA
*
13192756 AGAAAGAAAGAAAGAAAGAAAAGGAAAGAAAAGGAAAGG
1 AGAAGGAAAGAAAGAAAGAAAAGGAAAGAAAAGGAAAGG
13192795 AG-AGGAAAGAAAGAAA-AAGAAGGAAAGAAAAGGAAAGG
1 AGAAGGAAAGAAAGAAAGAA-AAGGAAAGAAAAGGAAAGG
13192833 AGAAGAAGAAA-AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
1 AGAAG--GAAAGAAAGAAAG---AA-AAGGAAAGAAAAGGAAAGG
*
13192877 AGAA-G--AGAAGAGAAA-AAAAAG-AAGAAGAA-GAAGAGG
1 AGAAGGAAAGAA-AGAAAGAAAAGGAAAGAA-AAGGAA-AGG
*
13192913 -GAAGGAAAGAAAAAAAGAAA
1 AGAAGGAAAGAAAGAAAGAAA
13192933 TAAAAGGTAA
Statistics
Matches: 119, Mismatches: 3, Indels: 33
0.77 0.02 0.21
Matches are distributed among these distances:
35 11 0.09
36 9 0.08
37 8 0.07
38 41 0.34
39 5 0.04
40 9 0.08
41 10 0.08
44 26 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (39 bp):
AGAAGGAAAGAAAGAAAGAAAAGGAAAGAAAAGGAAAGG
Found at i:13192870 original size:82 final size:84
Alignment explanation
Indices: 13192750--13192937 Score: 255
Period size: 82 Copynumber: 2.3 Consensus size: 84
13192740 GGAGAGGGAA
13192750 AGAAGAAGAAAGAAAGAAAGAAAGAAAAGGAAAGAAAAGGAAAGGAG-AG-GAA-AGAAAGAAAA
1 AGAAGAAGAAA-AAAGAAAGAAA-AAAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAA-AAAA
*
13192812 AGAAGGA-AAGAAAAGGAAAGG
63 AGAAGAAGAAGAAAAGGAAAGG
13192833 AGAAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAAAAAAAG
1 AGAAGAAGAAAAAAGAAAGAAAAA-AAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAAAAAAAG
* *
13192898 AAGAAGAAGAAGAGGGAAGG
65 AAGAAGAAGAAAAGGAAAGG
*
13192918 A-AAG-A-AAAAAAGAAATAAAA
1 AGAAGAAGAAAAAAGAAAGAAAA
13192938 GGTAATTTTT
Statistics
Matches: 96, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
81 2 0.02
82 46 0.48
83 14 0.15
84 16 0.17
85 18 0.19
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (84 bp):
AGAAGAAGAAAAAAGAAAGAAAAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAAAAAAAGA
AGAAGAAGAAAAGGAAAGG
Found at i:13192918 original size:46 final size:44
Alignment explanation
Indices: 13192750--13192937 Score: 206
Period size: 44 Copynumber: 4.5 Consensus size: 44
13192740 GGAGAGGGAA
13192750 AGAAGAAGAAAGAAAGAAAGAAAGAA-AAGGAAAGAAAAGGAAAGG
1 AGAAGAAGAAA-AAAGAAAGAAA-AAGAAGGAAAGAAAAGGAAAGG
13192795 AG-AG--G---AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
1 AGAAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
13192833 AGAAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
1 AGAAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
* * * *
13192877 AGAAG-AG--AAGAGAAA-AAAAAGAAGAAGAAGAAGAGGGAAGG
1 AGAAGAAGAAAAAAGAAAGAAAAAGAAGGA-AAGAAAAGGAAAGG
*
13192918 A-AAG-A-AAAAAAGAAATAAAA
1 AGAAGAAGAAAAAAGAAAGAAAA
13192938 GGTAATTTTT
Statistics
Matches: 127, Mismatches: 5, Indels: 25
0.81 0.03 0.16
Matches are distributed among these distances:
37 2 0.02
38 32 0.25
39 2 0.02
40 14 0.11
41 28 0.22
42 5 0.04
43 2 0.02
44 40 0.31
45 2 0.02
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (44 bp):
AGAAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
Found at i:13193952 original size:162 final size:159
Alignment explanation
Indices: 13193551--13194024 Score: 508
Period size: 160 Copynumber: 3.0 Consensus size: 159
13193541 NNNNNNNNNN
13193551 TCTTACACCAAATTAATTTAAAAAACACACTAAATTAATAAATTTCAAACATTATGCACTGAAAT
1 TCTTACACCAAATTAATTT-AAAAACACACTAAATTAATAAATTTCAAACATTATGCACTGAAAT
* *
13193616 AATGTAAAAGTATAAAATTAGAAATTAAGATATTTTTTAAAGTAAT-GAAATGCGGAGAAAAAAT
65 AATGTAAAATTATAAAATTAGAAATTAAGATATTTTTTAAAGTAATAAAAATGCGGAGAAAAAAT
*
13193680 ACGAACAAATGGCCGAAGTAAGAGTGTATT
130 ACGAACAAAGGGCCGAAGTAAGAGTGTATT
* * * * **
13193710 AC-TA-A-C---TT-TTTTAAAAATTCAGA-AATAATTAATACAAATATTTCAAACAAAATGCAC
1 TCTTACACCAAATTAATTTAAAAA--CACACTA-AATTAAT---AA-ATTTCAAACATTATGCAC
* * * *
13193767 TGAAATAATATAAAATAATAAAA-TACGAAAATAATATATTTTTATTGAAAGTAATAAAAAT-CG
59 TGAAATAATGTAAAATTATAAAATTA-GAAATTAAGATA-TTTT-TT-AAAGTAATAAAAATGCG
* * * * * *
13193830 G-GAAAATAATACGAGCAAAGGGCAG-GGATAAGGGTTTTTT
120 GAGAAAA-AATACGAACAAAGGGCCGAAG-TAAGAGTGTATT
13193870 TCTTACACCAAATTAATTTAAAACACACACTAAATTAATAAATTTCAAACATTATGCACTGAAAT
1 TCTTACACCAAATTAATTTAAAA-ACACACTAAATTAATAAATTTCAAACATTATGCACTGAAAT
*
13193935 AATGTAAAATTATAAAATTAGAAATTAAGATATTTTTTAAAGTAAT-AAAATACGGAGAAAAAAA
65 AATGTAAAATTATAAAATTAGAAATTAAGATATTTTTTAAAGTAATAAAAATGCGGAG-AAAAAA
* *
13193999 TAAGAACAAATGGCCGAAGTAAGAGT
129 TACGAACAAAGGGCCGAAGTAAGAGT
13194025 TTTTTACTAA
Statistics
Matches: 252, Mismatches: 35, Indels: 55
0.74 0.10 0.16
Matches are distributed among these distances:
151 5 0.02
152 4 0.02
153 12 0.05
156 5 0.02
157 47 0.19
158 11 0.04
159 20 0.08
160 59 0.23
161 15 0.06
162 48 0.19
163 5 0.02
166 12 0.05
167 8 0.03
168 1 0.00
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.28
Consensus pattern (159 bp):
TCTTACACCAAATTAATTTAAAAACACACTAAATTAATAAATTTCAAACATTATGCACTGAAATA
ATGTAAAATTATAAAATTAGAAATTAAGATATTTTTTAAAGTAATAAAAATGCGGAGAAAAAATA
CGAACAAAGGGCCGAAGTAAGAGTGTATT
Found at i:13195841 original size:18 final size:18
Alignment explanation
Indices: 13195818--13195854 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
13195808 ATCCCAATGA
13195818 TTGCCACCACCTTCTTCT
1 TTGCCACCACCTTCTTCT
*
13195836 TTGCCACCAGCTTCTTCT
1 TTGCCACCACCTTCTTCT
13195854 T
1 T
13195855 CACCACCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.41, G:0.08, T:0.41
Consensus pattern (18 bp):
TTGCCACCACCTTCTTCT
Found at i:13195860 original size:18 final size:18
Alignment explanation
Indices: 13195821--13195862 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
13195811 CCAATGATTG
**
13195821 CCACCACCTTCTTCTTTG
1 CCACCACCTTCTTCTTCA
*
13195839 CCACCAGCTTCTTCTTCA
1 CCACCACCTTCTTCTTCA
13195857 CCACCA
1 CCACCA
13195863 ATCATATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.48, G:0.05, T:0.31
Consensus pattern (18 bp):
CCACCACCTTCTTCTTCA
Found at i:13196594 original size:43 final size:42
Alignment explanation
Indices: 13196476--13196599 Score: 114
Period size: 43 Copynumber: 2.9 Consensus size: 42
13196466 CCACTAATCC
* *
13196476 TAATAACTAAC--ACAATAATAATATTAATAATTTTATACTCAAAA
1 TAATAACTAACTAACAATAATAATA-TAGT--TTTT-TACTAAAAA
* *
13196520 TAAT-ACTAACTAA-AATTATTAAT-TAGGTTTTTACTAAAAA
1 TAATAACTAACTAACAA-TAATAATATAGTTTTTTACTAAAAA
*
13196560 TAATAACTAACTAACTATAATAATACTAGTTTTTTACTAA
1 TAATAACTAACTAACAATAATAATA-TAGTTTTTTACTAA
13196600 CTAGTTTATT
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
40 12 0.18
41 19 0.29
42 1 0.02
43 21 0.32
44 6 0.09
45 7 0.11
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.38
Consensus pattern (42 bp):
TAATAACTAACTAACAATAATAATATAGTTTTTTACTAAAAA
Found at i:13196656 original size:63 final size:63
Alignment explanation
Indices: 13196554--13196726 Score: 303
Period size: 63 Copynumber: 2.7 Consensus size: 63
13196544 AGGTTTTTAC
*
13196554 TAAAAATAATAACTAACTA-ACTATAATAATACTAGTTTTTTACTAACTAGTTTATTTTGGTAAA
1 TAAAAATAATAACTAACCATA--ATAATAATACTAGTTTTTTACTAACTAGTTTATTTTGGTAAA
*
13196618 TAAAAATAATAACTAACCATAATAATAAAACTAGTTTTTTACTAACTAGTTTATTTTGGTAAA
1 TAAAAATAATAACTAACCATAATAATAATACTAGTTTTTTACTAACTAGTTTATTTTGGTAAA
13196681 TAAAAATAATAACTAACCATAATAATAATACTAGTTTTTTACTAAC
1 TAAAAATAATAACTAACCATAATAATAATACTAGTTTTTTACTAAC
13196727 AATAATACTA
Statistics
Matches: 105, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
63 86 0.82
64 18 0.17
65 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (63 bp):
TAAAAATAATAACTAACCATAATAATAATACTAGTTTTTTACTAACTAGTTTATTTTGGTAAA
Found at i:13196752 original size:63 final size:63
Alignment explanation
Indices: 13196554--13196772 Score: 221
Period size: 63 Copynumber: 3.5 Consensus size: 63
13196544 AGGTTTTTAC
* * * * **
13196554 TAAAAATAATAACTAACTA-ACTATAATAATACTAGTTTTTTACTAACTAGTTTATTTTGGTAAA
1 TAAAAATAATAACTAACCATA--ATAATAATACTAGTTTTTTACTAACTAATATATCTAAGTAAA
* * * * **
13196618 TAAAAATAATAACTAACCATAATAATAAAACTAGTTTTTTACTAACTAGTTTATTTTGGTAAA
1 TAAAAATAATAACTAACCATAATAATAATACTAGTTTTTTACTAACTAATATATCTAAGTAAA
13196681 TAAAAATAATAACTAACCATAATAATAATACTAGTTTTTTACTAAC-AATA-ATACTAAGTAACA
1 TAAAAATAATAACTAACCATAATAATAATACTAGTTTTTTACTAACTAATATAT-CTAAGTAA-A
*** **
13196744 TCTTAATAATAA-TAATAATAATAATAATA
1 TAAAAATAATAACTAACCATAATAATAATA
13196773 ATAATAATAA
Statistics
Matches: 139, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
61 2 0.01
62 22 0.16
63 96 0.69
64 18 0.13
65 1 0.01
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (63 bp):
TAAAAATAATAACTAACCATAATAATAATACTAGTTTTTTACTAACTAATATATCTAAGTAAA
Found at i:13196755 original size:3 final size:3
Alignment explanation
Indices: 13196747--13196817 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
13196737 AGTAACATCT
13196747 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13196795 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
13196818 CGAACTAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:13197098 original size:27 final size:27
Alignment explanation
Indices: 13197060--13197150 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
13197050 ACGAGTAGTC
13197060 CCGCCAATCAGTATGGCACCATTGGTG
1 CCGCCAATCAGTATGGCACCATTGGTG
* *
13197087 CCGCCAACCAGTATGGCACCATCGGTG
1 CCGCCAATCAGTATGGCACCATTGGTG
*
13197114 CCGCCAATCAGT-TAGGCACCTTTGGTG
1 CCGCCAATCAGTAT-GGCACCATTGGTG
13197141 CCGCCAATCA
1 CCGCCAATCA
13197151 AAAACCCTCC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
26 1 0.02
27 57 0.98
ACGTcount: A:0.22, C:0.34, G:0.24, T:0.20
Consensus pattern (27 bp):
CCGCCAATCAGTATGGCACCATTGGTG
Found at i:13197422 original size:16 final size:17
Alignment explanation
Indices: 13197401--13197438 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 17
13197391 TTAAAAAATA
13197401 TTTTTTTCTT-TC-AAC
1 TTTTTTTCTTGTCAAAC
13197416 TTTTTTTCTTGTCAAAC
1 TTTTTTTCTTGTCAAAC
13197433 TTTTTT
1 TTTTTT
13197439 CTAAAGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.48
16 2 0.10
17 9 0.43
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTTTTCTTGTCAAAC
Found at i:13207571 original size:25 final size:28
Alignment explanation
Indices: 13207543--13207609 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 28
13207533 AAAAAAAAAA
13207543 CAAAATATTATAA-T-TTT-TTATTTAC
1 CAAAATATTATAATTATTTCTTATTTAC
13207568 CAAAATATTATAATTATTTCCATTATTTAC
1 CAAAATATTATAATTATTT-C-TTATTTAC
13207598 CAAAATA-TATAA
1 CAAAATATTATAA
13207610 AAAAAACCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
25 13 0.35
26 1 0.03
27 3 0.08
29 5 0.14
30 15 0.41
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (28 bp):
CAAAATATTATAATTATTTCTTATTTAC
Found at i:13207736 original size:27 final size:27
Alignment explanation
Indices: 13207667--13207737 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
13207657 AGGCCAATGG
* *
13207667 CATTGGCGGCACCAAAGGTGCCAAAGC
1 CATTGGCGGCACCAATGGTGCCAAAAC
13207694 CATTGGCGGCACCAATGGTGCCAAAAC
1 CATTGGCGGCACCAATGGTGCCAAAAC
13207721 CATTGGCGGCACCAATG
1 CATTGGCGGCACCAATG
13207738 CCATAATAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (27 bp):
CATTGGCGGCACCAATGGTGCCAAAAC
Found at i:13207786 original size:4 final size:4
Alignment explanation
Indices: 13207779--13207904 Score: 61
Period size: 4 Copynumber: 31.0 Consensus size: 4
13207769 GGAGGAGAGG
* * *
13207779 GAAA GAAA GAAA GAAA GAAA GGAAG GAAG GAGAG GAAA GAAA G-AA -AAA
1 GAAA GAAA GAAA GAAA GAAA -GAAA GAAA GA-AA GAAA GAAA GAAA GAAA
* *
13207827 GAAG GAAA GAAAA GGAAA G-GA GAAGA GAAA -AAA -AAA GGAAA G-AA
1 GAAA GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA -GAAA GAAA
13207871 GAAA -AAGA GGAAA GGAGAA GAAA -AAA GAAA GAAA
1 GAAA GAA-A -GAAA -GA-AA GAAA GAAA GAAA GAAA
13207905 AGGAAAGGAG
Statistics
Matches: 100, Mismatches: 6, Indels: 32
0.72 0.04 0.23
Matches are distributed among these distances:
3 20 0.20
4 49 0.49
5 26 0.26
6 5 0.05
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:13207832 original size:18 final size:17
Alignment explanation
Indices: 13207778--13207904 Score: 79
Period size: 17 Copynumber: 7.5 Consensus size: 17
13207768 GGGAGGAGAG
*
13207778 GGAAAGAAAGAAAGAAA
1 GGAAAGAAAGAAAAAAA
* ** *
13207795 -GAAAGGAAGGAAGGAGA
1 GGAAA-GAAAGAAAAAAA
13207812 GGAAAGAAAGAAAAAGAA
1 GGAAAGAAAGAAAAA-AA
**
13207830 GGAAAG-AA-AAGGAAA
1 GGAAAGAAAGAAAAAAA
13207845 GGAGAAGAGAA-AAAAAAA
1 GGA-AAGA-AAGAAAAAAA
*
13207863 GGAAAG-AAGAAAAAGA
1 GGAAAGAAAGAAAAAAA
13207879 GGAAAGGAGAAG-AAAAAA
1 GGAAA-GA-AAGAAAAAAA
13207897 -GAAAGAAA
1 GGAAAGAAA
13207905 AGGAAAGGAG
Statistics
Matches: 87, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
15 9 0.10
16 23 0.26
17 26 0.30
18 26 0.30
19 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
GGAAAGAAAGAAAAAAA
Found at i:13207873 original size:44 final size:42
Alignment explanation
Indices: 13207778--13207906 Score: 121
Period size: 42 Copynumber: 3.1 Consensus size: 42
13207768 GGGAGGAGAG
* *
13207778 GGAAAGAAAGAAAGAAAGAAAGG-AAGGA-AGGAGAGGAAAGAAA
1 GGAAAG-AAG-AAGAAAGAAAGGAAAGGAGAAGAGA-AAAAGAAA
*
13207821 -GAAA-AAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAA
1 GGAAAGAAGAA-GAAAG-AAAGGAAAGGAGAAGAGAAAAAGAAA
13207863 GGAAAGAAGAA-AAAG--AGGAAAGGAGAAGA-AAAAAGAAA
1 GGAAAGAAGAAGAAAGAAAGGAAAGGAGAAGAGAAAAAGAAA
*
13207901 GAAAAG
1 GGAAAG
13207907 GAAAGGAGAA
Statistics
Matches: 75, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
38 13 0.17
39 16 0.21
40 8 0.11
41 5 0.07
42 19 0.25
43 9 0.12
44 5 0.07
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (42 bp):
GGAAAGAAGAAGAAAGAAAGGAAAGGAGAAGAGAAAAAGAAA
Found at i:13207925 original size:29 final size:27
Alignment explanation
Indices: 13207781--13207924 Score: 93
Period size: 27 Copynumber: 5.3 Consensus size: 27
13207771 AGGAGAGGGA
13207781 AAGAAAGAAAGAAAG-AAAGG-AAGGAAG
1 AAGAAA-AAAGAAAGAAAAGGAAAGG-AG
* ** *
13207808 GAGAGGAAAGAAAGAAAAAG-AAGGA-
1 AAGAAAAAAGAAAGAAAAGGAAAGGAG
* * ** *
13207833 AAG-AAAAGGAAAGGAGAAGAGAAAAAAA
1 AAGAAAAAAGAAA-GAAAAG-GAAAGGAG
* *
13207861 AAGGAAAGAAGAAA-AAGAGGAAAGGAG
1 AA-GAAAAAAGAAAGAAAAGGAAAGGAG
13207888 AAGAAAAAAGAAAGAAAAGGAAAGGAG
1 AAGAAAAAAGAAAGAAAAGGAAAGGAG
13207915 AAGAGAAAAA
1 AAGA-AAAAA
13207925 AAAAAGATGA
Statistics
Matches: 87, Mismatches: 21, Indels: 17
0.70 0.17 0.14
Matches are distributed among these distances:
24 6 0.07
25 6 0.07
26 20 0.23
27 37 0.43
28 10 0.11
29 1 0.01
30 7 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (27 bp):
AAGAAAAAAGAAAGAAAAGGAAAGGAG
Found at i:13207928 original size:33 final size:35
Alignment explanation
Indices: 13207778--13207963 Score: 113
Period size: 34 Copynumber: 5.3 Consensus size: 35
13207768 GGGAGGAGAG
*
13207778 GGAAAGAAAGAAAGA-AAG-AAAGG-AAGGAAGGAGA
1 GGAAA-AAAAAAAGAGAAGAAAAGGAAAGGAAGGA-A
* *
13207812 GGAAAGAAAGAAAA-AGAAGGAAAGAAAAGGAAAGGAGA
1 GGAAA-AAA-AAAAGAGAAGAAAAGGAAAGG-AAGGA-A
* * * *
13207850 AGAGAAAAAAAAAG-GAA-AGAAGAAAAAG-AGGAAA
1 GGA-AAAAAAAAAGAGAAGAAAAGGAAAGGAAGG-AA
*
13207884 GGAGAAGAAAAAAGA-AAGAAAAGGAAAGG-A-GAA
1 GGA-AAAAAAAAAGAGAAGAAAAGGAAAGGAAGGAA
* *
13207917 GAGAAAAAAAAAAGATGAAGAAGAGGGAAGGAAGGAA
1 G-GAAAAAAAAAAGA-GAAGAAAAGGAAAGGAAGGAA
13207954 GGAAAAAAAA
1 GGAAAAAAAA
13207964 GAAAAAAAAG
Statistics
Matches: 123, Mismatches: 14, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
33 13 0.11
34 31 0.25
35 28 0.23
36 22 0.18
37 15 0.12
38 12 0.10
39 2 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.01
Consensus pattern (35 bp):
GGAAAAAAAAAAGAGAAGAAAAGGAAAGGAAGGAA
Found at i:13207946 original size:29 final size:29
Alignment explanation
Indices: 13207878--13207931 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
13207868 GAAGAAAAAG
*
13207878 AGGAAAGGAG-A-AGAAAAAAGAAAGAAA
1 AGGAAAGGAGAAGAGAAAAAAAAAAGAAA
13207905 AGGAAAGGAGAAGAGAAAAAAAAAAGA
1 AGGAAAGGAGAAGAGAAAAAAAAAAGA
13207932 TGAAGAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.42
28 1 0.04
29 13 0.54
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (29 bp):
AGGAAAGGAGAAGAGAAAAAAAAAAGAAA
Found at i:13207974 original size:62 final size:64
Alignment explanation
Indices: 13207809--13207968 Score: 186
Period size: 66 Copynumber: 2.5 Consensus size: 64
13207799 GGAAGGAAGG
13207809 AGAGGAAA-GA-AAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAGGAAAGAAG
1 AGAGGAAAGGAGAAG-AAAA-AA-GAAAGAAAAGGAAAGGAGAAGAG-AAAAAAAA-GAAAGAAG
13207872 AAAA
61 AAAA
* *
13207876 AGAGGAAAGGAGAAGAAAAAAGAAAGAAAAGGAAAGGAGAAGAG-AAAAAAA-AAAGATGAAGA
1 AGAGGAAAGGAGAAGAAAAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAGAAAGAAGAAAA
* *
13207938 AGAGGGAAGGAAGGAAGGAAAAA-AAAGAAAA
1 AGAGGAAAGG-A-GAAGAAAAAAGAAAGAAAA
13207969 AAAAGGTAAT
Statistics
Matches: 85, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
62 18 0.21
63 9 0.11
64 16 0.19
66 23 0.27
67 10 0.12
68 6 0.07
69 3 0.04
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (64 bp):
AGAGGAAAGGAGAAGAAAAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAGAAAGAAGAAAA
Found at i:13207998 original size:18 final size:18
Alignment explanation
Indices: 13207975--13208011 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13207965 AAAAAAAAGG
13207975 TAATTTTTTT-TATAAATT
1 TAATTTTTTTGTA-AAATT
13207993 TAATTTTTTTGTAAAATT
1 TAATTTTTTTGTAAAATT
13208011 T
1 T
13208012 GGGTGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TAATTTTTTTGTAAAATT
Found at i:13213726 original size:18 final size:18
Alignment explanation
Indices: 13213700--13213734 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13213690 CCCAATGATC
13213700 GCCACCACCTGCTTCTTG
1 GCCACCACCTGCTTCTTG
* *
13213718 GCCAGCACCTTCTTCTT
1 GCCACCACCTGCTTCTT
13213735 CACCACCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.43, G:0.14, T:0.31
Consensus pattern (18 bp):
GCCACCACCTGCTTCTTG
Found at i:13214566 original size:24 final size:24
Alignment explanation
Indices: 13214539--13214586 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
13214529 CTTAATCCCC
* *
13214539 CACCACCACAGTAGTAATAATAAT
1 CACCACCACAATAATAATAATAAT
* *
13214563 CACCCCCATAATAATAATAATAAT
1 CACCACCACAATAATAATAATAAT
13214587 AATAATAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.25, G:0.04, T:0.23
Consensus pattern (24 bp):
CACCACCACAATAATAATAATAAT
Found at i:13214576 original size:3 final size:3
Alignment explanation
Indices: 13214570--13214623 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
13214560 AATCACCCCC
13214570 ATA 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 ATA
13214618 ATA ATA
1 ATA ATA
13214624 CTATCAATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13214751 original size:11 final size:11
Alignment explanation
Indices: 13214731--13214770 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
13214721 TAAAAAATAC
13214731 CTTCTTTTTCT
1 CTTCTTTTTCT
*
13214742 CTTCTCTTTCT
1 CTTCTTTTTCT
13214753 C-TCTTTTTCT
1 CTTCTTTTTCT
13214763 CTTCTTTT
1 CTTCTTTT
13214771 CCATAGCACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:13214758 original size:21 final size:20
Alignment explanation
Indices: 13214733--13214771 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
13214723 AAAAATACCT
13214733 TCTTTTTCTCTTCTCTTTCTC
1 TCTTTTTCTCTTCT-TTTCTC
13214754 TCTTTTTCTCTTCTTTTC
1 TCTTTTTCTCTTCTTTTC
13214772 CATAGCACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TCTTTTTCTCTTCTTTTCTC
Found at i:13214899 original size:27 final size:27
Alignment explanation
Indices: 13214855--13214928 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
13214845 AATACGAGTA
*
13214855 GTGCCGCCAGTGCCTTTGGCACCATTG
1 GTGCCGCCAATGCCTTTGGCACCATTG
** *
13214882 GTGCCGCCAATGGTTTTGGCACCTTTG
1 GTGCCGCCAATGCCTTTGGCACCATTG
* *
13214909 GTGCTGCCAATGCCATTGGC
1 GTGCCGCCAATGCCTTTGGC
13214929 CTGATTAGGC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.12, C:0.30, G:0.30, T:0.28
Consensus pattern (27 bp):
GTGCCGCCAATGCCTTTGGCACCATTG
Found at i:13215004 original size:27 final size:29
Alignment explanation
Indices: 13214973--13215041 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 29
13214963 TTATTTTTTG
*
13214973 ATATATTTTGGTAAATAATAAAAATAATT
1 ATATATTTTGGTAAATAAAAAAAATAATT
*
13215002 ATAATATTTTGGTAAATAAAAAAAATTA-T
1 AT-ATATTTTGGTAAATAAAAAAAATAATT
13215031 A-ATATTTTGGT
1 ATATATTTTGGT
13215042 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 10 0.27
29 4 0.11
30 23 0.62
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAATAATT
Found at i:13215009 original size:30 final size:27
Alignment explanation
Indices: 13214975--13215041 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
13214965 ATTTTTTGAT
13214975 ATATTTTGGTAAATAATAAAAATAATTATA
1 ATATTTTGGTAAAT-A-AAAAA-AATTATA
13215005 ATATTTTGGTAAATAAAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAAATTATA
13215032 ATATTTTGGT
1 ATATTTTGGT
13215042 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
27 17 0.46
28 5 0.14
29 1 0.03
30 14 0.38
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAATTATA
Found at i:13215726 original size:17 final size:18
Alignment explanation
Indices: 13215694--13215729 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
13215684 ATATTATTTT
13215694 TTAATTATTTAAAATATA
1 TTAATTATTTAAAATATA
*
13215712 TTAATT-TTTATAATATA
1 TTAATTATTTAAAATATA
13215729 T
1 T
13215730 GACAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATTTAAAATATA
Found at i:13232416 original size:19 final size:20
Alignment explanation
Indices: 13232371--13232422 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
13232361 TATCTAATTA
13232371 TAAATATTTAATATTATATT
1 TAAATATTTAATATTATATT
13232391 TAAATATTTAA-A-TATAGTT
1 TAAATATTTAATATTATA-TT
*
13232410 TATATATTCTAAT
1 TAAATATT-TAAT
13232423 TAAATTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 4 0.14
19 10 0.36
20 14 0.50
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TAAATATTTAATATTATATT
Found at i:13232680 original size:13 final size:13
Alignment explanation
Indices: 13232657--13232708 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
13232647 AGCACTCAAA
13232657 TTTTACAAAAGCAC
1 TTTT-CAAAAGCAC
* *
13232671 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
**
13232684 TTTTCAAAAATAC
1 TTTTCAAAAGCAC
13232697 TTTTCAAAAGCA
1 TTTTCAAAAGCA
13232709 ATAAAGAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 29 0.91
14 3 0.09
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:13234507 original size:2 final size:2
Alignment explanation
Indices: 13234500--13234525 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13234490 TCTTCCCTTC
13234500 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
13234526 GCTCAACACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:13242801 original size:18 final size:18
Alignment explanation
Indices: 13242778--13242820 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
13242768 GTTCAATGTG
13242778 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
13242796 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
13242814 TAATTAA
1 TAATTAA
13242821 AAACCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:13244855 original size:8 final size:8
Alignment explanation
Indices: 13244842--13244906 Score: 76
Period size: 8 Copynumber: 7.9 Consensus size: 8
13244832 ATCACAATTT
13244842 AATAAACA
1 AATAAACA
13244850 AATAAACGA
1 AATAAAC-A
*
13244859 AATGAAATA
1 AAT-AAACA
* *
13244868 ATTGAACA
1 AATAAACA
13244876 AATAAACA
1 AATAAACA
*
13244884 AACAAACA
1 AATAAACA
13244892 AATAAACA
1 AATAAACA
13244900 AATAAAC
1 AATAAAC
13244907 CAACAACACC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
8 37 0.79
9 7 0.15
10 3 0.06
ACGTcount: A:0.69, C:0.12, G:0.05, T:0.14
Consensus pattern (8 bp):
AATAAACA
Found at i:13244887 original size:12 final size:12
Alignment explanation
Indices: 13244872--13244912 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
13244862 GAAATAATTG
13244872 AACAAATAAACA
1 AACAAATAAACA
* *
13244884 AACAAACAAATA
1 AACAAATAAACA
*
13244896 AACAAATAAACC
1 AACAAATAAACA
13244908 AACAA
1 AACAA
13244913 CACCACATGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.73, C:0.20, G:0.00, T:0.07
Consensus pattern (12 bp):
AACAAATAAACA
Found at i:13245116 original size:13 final size:13
Alignment explanation
Indices: 13245098--13245127 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13245088 TGACATAGTT
13245098 TAAAATAAATAAA
1 TAAAATAAATAAA
13245111 TAAAATAAATAAA
1 TAAAATAAATAAA
13245124 -AAAA
1 TAAAA
13245128 CACAGAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:13248100 original size:104 final size:104
Alignment explanation
Indices: 13247966--13248335 Score: 490
Period size: 104 Copynumber: 3.6 Consensus size: 104
13247956 AAAGAACTTA
* * *
13247966 GTTGCGAGCTTAACTCAGCTAACTTTTAATCATCAGCTGGGAATGTAGGTCCGCGAGCTGTTTCG
1 GTTGCGAGCTTAACTCAGCTAACATTTAATCATCAGTTGGGAACGTAGGTCCGCGAGCTGTTTCG
* *
13248031 GAGTTGCGAGCTTAACTCGACTAACCCAAATAACTGGAG
66 GAGTTGCGAGCTTAACTCGGCTAACTCAAATAACTGGAG
* * * * *
13248070 GTTGCGAGCTTAACTCAGCTAACCTTTAATCATTAGTTGGGAACGTAGGTCAGCAAGTTGTTTCG
1 GTTGCGAGCTTAACTCAGCTAACATTTAATCATCAGTTGGGAACGTAGGTCCGCGAGCTGTTTCG
* *
13248135 GAGTTACGAGCTTAACTCGGCTAACTCAAATAATTGGA-
66 GAGTTGCGAGCTTAACTCGGCTAACTCAAATAACTGGAG
* * * * * ** * **
13248173 GTTGTGAGCTTAACTCATCCAACATTTAATCATCAATTGGGAACATAGGTCCATGAGCTATTTTA
1 GTTGCGAGCTTAACTCAGCTAACATTTAATCATCAGTTGGGAACGTAGGTCCGCGAGCTGTTTCG
*
13248238 GAGTTGTGAGCTTAACTCGGCTAACTCAAATAACTGGAG
66 GAGTTGCGAGCTTAACTCGGCTAACTCAAATAACTGGAG
* * * *
13248277 GTTTCGAGCTTAACTCAGCTAACATTTAATCATTAGTTGGGAATGTAAGTCCGCGAGCT
1 GTTGCGAGCTTAACTCAGCTAACATTTAATCATCAGTTGGGAACGTAGGTCCGCGAGCT
13248336 ATTTTAAAGG
Statistics
Matches: 225, Mismatches: 40, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
103 85 0.38
104 140 0.62
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (104 bp):
GTTGCGAGCTTAACTCAGCTAACATTTAATCATCAGTTGGGAACGTAGGTCCGCGAGCTGTTTCG
GAGTTGCGAGCTTAACTCGGCTAACTCAAATAACTGGAG
Found at i:13248427 original size:69 final size:69
Alignment explanation
Indices: 13248314--13248512 Score: 204
Period size: 69 Copynumber: 2.9 Consensus size: 69
13248304 AATCATTAGT
* * **
13248314 TGGGAATGTAAGTCCGCGAGCTATTTTAAAGGCTACGATATTAAATCAGCGAGCCTTTATAATAT
1 TGGGAATGTAGGTCCGCGAGCTATTTGAAAGGCTACGATATTAAATCAAAGAGCCTTTATAATAT
*
13248379 CAGC
66 CAAC
* * ** * *
13248383 TGGGAATGTAGGTCCGTGAGCTGTTTGAGGGGCTGCGATCTTAAATCAAAGAGCCTTTATAATAT
1 TGGGAATGTAGGTCCGCGAGCTATTTGAAAGGCTACGATATTAAATCAAAGAGCCTTTATAATAT
13248448 CAAC
66 CAAC
* * * * * * *
13248452 TAGGAACGTAGGTCCGCAAGCTGCTTTTG--AGGTTACGATTTTAAATCAATGAGCCTTTATA
1 TGGGAATGTAGGTCCGCGAGCT--ATTTGAAAGGCTACGATATTAAATCAAAGAGCCTTTATA
13248513 TAGAAGGTCG
Statistics
Matches: 107, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
69 103 0.96
71 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (69 bp):
TGGGAATGTAGGTCCGCGAGCTATTTGAAAGGCTACGATATTAAATCAAAGAGCCTTTATAATAT
CAAC
Found at i:13248527 original size:16 final size:16
Alignment explanation
Indices: 13248508--13248539 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
13248498 CAATGAGCCT
13248508 TTATATAGAAGGTCGC
1 TTATATAGAAGGTCGC
13248524 TTATATAGAAGGTCGC
1 TTATATAGAAGGTCGC
13248540 GGTATGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (16 bp):
TTATATAGAAGGTCGC
Found at i:13249397 original size:15 final size:15
Alignment explanation
Indices: 13249377--13249406 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13249367 CAAAATTTTG
13249377 ACAAGAACATAACAA
1 ACAAGAACATAACAA
13249392 ACAAGAACATAACAA
1 ACAAGAACATAACAA
13249407 TGTGATAACA
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:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (15 bp):
ACAAGAACATAACAA
Found at i:13254219 original size:34 final size:35
Alignment explanation
Indices: 13254163--13254229 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
13254153 CAAACACCAA
* *
13254163 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
*
13254198 AAAACATTTTCCA-AAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAA
13254230 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
Found at i:13269111 original size:58 final size:57
Alignment explanation
Indices: 13268979--13269113 Score: 182
Period size: 58 Copynumber: 2.3 Consensus size: 57
13268969 TTTAATTCAT
* **
13268979 ATAATAATTATATTAAGAATTTTATTAAATTATATATTATTTTATTAAATTATATTTA
1 ATAATAATTATATTAA-AATATGGTTAAATTATATATTATTTTATTAAATTATATTTA
* * *
13269037 ATAATAATTATGTTAAAATATGGTTAAATTATTTATTATTTTTATTAAATTATTTTTA
1 ATAATAATTATATTAAAATATGGTTAAATTATATATTA-TTTTATTAAATTATATTTA
13269095 ATAATAATCT-TATTAAAAT
1 ATAATAAT-TATATTAAAAT
13269114 TTAATAACAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
57 18 0.26
58 49 0.72
59 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (57 bp):
ATAATAATTATATTAAAATATGGTTAAATTATATATTATTTTATTAAATTATATTTA
Found at i:13269314 original size:16 final size:16
Alignment explanation
Indices: 13269289--13269331 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
13269279 GATTGTAGCT
13269289 CTATTCAATTACAGCC
1 CTATTCAATTACAGCC
*
13269305 CTATTTAATTACAGCC
1 CTATTCAATTACAGCC
* *
13269321 TTATTCCATTA
1 CTATTCAATTA
13269332 GAGTGAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.40
Consensus pattern (16 bp):
CTATTCAATTACAGCC
Found at i:13270812 original size:21 final size:19
Alignment explanation
Indices: 13270786--13270825 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
13270776 TGCAATTTAA
13270786 TAATTTTCTTTTATGTTCTTT
1 TAATTTTCTTTT-T-TTCTTT
13270807 TAATTTTCTTTTTTTCTTT
1 TAATTTTCTTTTTTTCTTT
13270826 ATTTTCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (19 bp):
TAATTTTCTTTTTTTCTTT
Found at i:13270817 original size:11 final size:11
Alignment explanation
Indices: 13270786--13270818 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
13270776 TGCAATTTAA
13270786 TAATTTTCTTT
1 TAATTTTCTTT
*
13270797 T-ATGTTCTTT
1 TAATTTTCTTT
13270807 TAATTTTCTTT
1 TAATTTTCTTT
13270818 T
1 T
13270819 TTTCTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.73
Consensus pattern (11 bp):
TAATTTTCTTT
Found at i:13270930 original size:32 final size:32
Alignment explanation
Indices: 13270869--13270933 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
13270859 TCCTCCCTTC
***
13270869 TCCATTTCTTTTAGTGTAATTTTTCTATGTTT
1 TCCATTTCTTTTAACATAATTTTTCTATGTTT
13270901 TCCATTTCTTTTAACATAACTTTTT-TATGTTT
1 TCCATTTCTTTTAACATAA-TTTTTCTATGTTT
13270933 T
1 T
13270934 TGAAACAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 24 0.83
33 5 0.17
ACGTcount: A:0.18, C:0.14, G:0.06, T:0.62
Consensus pattern (32 bp):
TCCATTTCTTTTAACATAATTTTTCTATGTTT
Found at i:13275508 original size:16 final size:17
Alignment explanation
Indices: 13275477--13275510 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
13275467 AATTTAACTT
13275477 TAATTAAATATTTAAAA
1 TAATTAAATATTTAAAA
*
13275494 TAATT-AATTTTTAAAA
1 TAATTAAATATTTAAAA
13275510 T
1 T
13275511 TATAAACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTAAATATTTAAAA
Found at i:13277187 original size:14 final size:14
Alignment explanation
Indices: 13277168--13277195 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13277158 TCACGATGTG
13277168 TATGTATGTATATA
1 TATGTATGTATATA
13277182 TATGTATGTATATA
1 TATGTATGTATATA
13277196 GATACACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (14 bp):
TATGTATGTATATA
Found at i:13280631 original size:17 final size:17
Alignment explanation
Indices: 13280605--13280648 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
13280595 CATCCACTAC
* *
13280605 ATATAAATACACTTACT
1 ATATATATACACATACT
*
13280622 ATATATATACACATATT
1 ATATATATACACATACT
13280639 ATATATATAC
1 ATATATATAC
13280649 GGACACAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATATATACACATACT
Found at i:13286739 original size:16 final size:18
Alignment explanation
Indices: 13286717--13286761 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
13286707 TTATTATTTG
*
13286717 TTTTATAATATTTTAA-A
1 TTTTATAATATTTAAACA
13286734 -TTTAT-AT-TTTAAACA
1 TTTTATAATATTTAAACA
13286749 TTTTATAATATTT
1 TTTTATAATATTT
13286762 GTTTATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 5 0.22
15 3 0.13
16 10 0.43
17 2 0.09
18 3 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATAATATTTAAACA
Found at i:13291509 original size:23 final size:23
Alignment explanation
Indices: 13291483--13291539 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
13291473 TATATTTACT
*
13291483 TTATAGAATATTTAG-TTTTATTA
1 TTATA-AATATTTAGCATTTATTA
13291506 TTATAATATATTTAGCATTTATTA
1 TTATAA-ATATTTAGCATTTATTA
*
13291530 GTATAAATAT
1 TTATAAATAT
13291540 CTTTGTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 1 0.03
23 17 0.57
24 12 0.40
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.53
Consensus pattern (23 bp):
TTATAAATATTTAGCATTTATTA
Found at i:13300509 original size:18 final size:17
Alignment explanation
Indices: 13300482--13300539 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
13300472 CAGCTCACAT
*
13300482 CTTTGGTGAGCTCGCAA
1 CTTTGGTGAGCTCGCAC
*
13300499 CTTTGGGTGAGCTTGCAC
1 CTTT-GGTGAGCTCGCAC
**
13300517 CTTTCATGAGCTCGCAC
1 CTTTGGTGAGCTCGCAC
13300534 CTTTGG
1 CTTTGG
13300540 GAAGTTTGCA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
17 18 0.55
18 15 0.45
ACGTcount: A:0.14, C:0.26, G:0.28, T:0.33
Consensus pattern (17 bp):
CTTTGGTGAGCTCGCAC
Found at i:13308919 original size:23 final size:22
Alignment explanation
Indices: 13308874--13308919 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
13308864 GAGAAATACA
* *
13308874 TATTTTAATTTTAATTTTTATT
1 TATTTTAATTTTAACTTTAATT
*
13308896 TATTTGTATTTTTAACTTTAATT
1 TATTT-TAATTTTAACTTTAATT
13308919 T
1 T
13308920 TTATATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TATTTTAATTTTAACTTTAATT
Found at i:13308934 original size:29 final size:29
Alignment explanation
Indices: 13308876--13308935 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
13308866 GAAATACATA
* *
13308876 TTTTAATTTTAATTTTTATTTATTTGTAT
1 TTTTAACTTTAATTTTTATATATTTGTAT
13308905 TTTTAACTTTAATTTTTATATATATT-TAT
1 TTTTAACTTTAATTTTTATATAT-TTGTAT
13308934 TT
1 TT
13308936 ATTTATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (29 bp):
TTTTAACTTTAATTTTTATATATTTGTAT
Found at i:13308959 original size:14 final size:14
Alignment explanation
Indices: 13308890--13308947 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
13308880 AATTTTAATT
*
13308890 TTTATTTATTTGTA
1 TTTATTTATTTATA
*
13308904 TTT-TTAACTTTA-A
1 TTTATTTA-TTTATA
*
13308917 -TT-TTTATATATA
1 TTTATTTATTTATA
13308929 TTTATTTATTTATA
1 TTTATTTATTTATA
13308943 TTTAT
1 TTTAT
13308948 ATTTTTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
11 3 0.09
12 6 0.17
13 6 0.17
14 20 0.57
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (14 bp):
TTTATTTATTTATA
Found at i:13315178 original size:36 final size:36
Alignment explanation
Indices: 13315126--13315204 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
13315116 ATCTTTGCTG
* * * *
13315126 GAGGATTCACATGGTGCAACAAATTGGGCTTTACAA
1 GAGGGTTCACATGGTGCAACAAACTAGGCTTCACAA
* *
13315162 GAGGGTTCACATGGTGCAGCGAACTAGGCTTCACAA
1 GAGGGTTCACATGGTGCAACAAACTAGGCTTCACAA
13315198 GAGGGTT
1 GAGGGTT
13315205 TGCATAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (36 bp):
GAGGGTTCACATGGTGCAACAAACTAGGCTTCACAA
Found at i:13316579 original size:17 final size:16
Alignment explanation
Indices: 13316555--13316650 Score: 77
Period size: 17 Copynumber: 5.6 Consensus size: 16
13316545 GCTTGCAGCC
13316555 TTGGTGAGCTCACAAT
1 TTGGTGAGCTCACAAT
* * * *
13316571 ATTGATGAGATCGCAGT
1 -TTGGTGAGCTCACAAT
13316588 CTTGGTGAGCTCGTAC-AT
1 -TTGGTGAGCTC--ACAAT
13316606 TTGGTGAGCTCACAATT
1 TTGGTGAGCTCACAA-T
*
13316623 TTGGTGAGCTCTCAACT
1 TTGGTGAGCTCACAA-T
13316640 TTGGGTGAGCT
1 TT-GGTGAGCT
13316651 TACATCTTTG
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
15 2 0.03
16 1 0.02
17 50 0.79
18 9 0.14
19 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (16 bp):
TTGGTGAGCTCACAAT
Found at i:13316659 original size:18 final size:18
Alignment explanation
Indices: 13316608--13316661 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
13316598 TCGTACATTT
*
13316608 GGTGAGCTCACAAT-TTT-
1 GGTGAGCTTAC-ATCTTTG
*
13316625 GGTGAGCTCT-CAACTTTG
1 GGTGAGCT-TACATCTTTG
13316643 GGTGAGCTTACATCTTTG
1 GGTGAGCTTACATCTTTG
13316661 G
1 G
13316662 TAAGCTCGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.43
18 16 0.53
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (18 bp):
GGTGAGCTTACATCTTTG
Found at i:13316661 original size:35 final size:35
Alignment explanation
Indices: 13316589--13316693 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 35
13316579 GATCGCAGTC
* *
13316589 TTGGTGAGCTCGT-ACATTT-GGTGAGCTCACAAT-T
1 TTGGTAAGCTCGTAAC-TTTGGGTGAGCTTAC-ATCT
*
13316623 TTGGTGAGCTC-TCAACTTTGGGTGAGCTTACATCT
1 TTGGTAAGCTCGT-AACTTTGGGTGAGCTTACATCT
* * *
13316658 TTGGTAAGCTCGTACCTTTGGG-GAGTTTGCATCT
1 TTGGTAAGCTCGTAACTTTGGGTGAGCTTACATCT
13316692 TT
1 TT
13316694 ACGACCTATG
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
33 1 0.02
34 28 0.46
35 31 0.51
36 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.38
Consensus pattern (35 bp):
TTGGTAAGCTCGTAACTTTGGGTGAGCTTACATCT
Found at i:13320167 original size:26 final size:26
Alignment explanation
Indices: 13320138--13320219 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
13320128 TGATGAGGCT
*
13320138 TAAAATAAGTTACTTGTGTAGTGGAA
1 TAAAATAAGTTACTTGTATAGTGGAA
* * * **
13320164 TAAAA-ATGTTAACCATG-ATA-AGGCT
1 TAAAATAAGTT-A-CTTGTATAGTGGAA
13320189 TAAAATAAGTTACTTGTATAGTGGAA
1 TAAAATAAGTTACTTGTATAGTGGAA
13320215 TAAAA
1 TAAAA
13320220 ATGTTAACCA
Statistics
Matches: 40, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
24 3 0.08
25 15 0.38
26 19 0.47
27 3 0.08
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (26 bp):
TAAAATAAGTTACTTGTATAGTGGAA
Found at i:13320191 original size:51 final size:51
Alignment explanation
Indices: 13320128--13320232 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
13320118 TAAAGTCAGT
* *
13320128 TGATGAGGCTTAAAATAAGTTACTTGTGTAGTGGAATAAAAATGTTAACCA
1 TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
13320179 TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
1 TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
13320230 TGA
1 TGA
13320233 ATTTGAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (51 bp):
TGATAAGGCTTAAAATAAGTTACTTGTATAGTGGAATAAAAATGTTAACCA
Found at i:13328001 original size:14 final size:14
Alignment explanation
Indices: 13327982--13328012 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
13327972 TGGAATGAAA
13327982 TTATTTTTTTCTCT
1 TTATTTTTTTCTCT
13327996 TTA-TTTTTTCTCT
1 TTATTTTTTTCTCT
13328009 TTAT
1 TTAT
13328013 ACAGGCTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.81
14 3 0.19
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATTTTTTTCTCT
Found at i:13328675 original size:16 final size:15
Alignment explanation
Indices: 13328656--13328685 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
13328646 TCATATATAT
13328656 ATATATATATATTTAG
1 ATATATAT-TATTTAG
13328672 ATATATATTATTTA
1 ATATATATTATTTA
13328686 TACTTTAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATATATTATTTAG
Found at i:13335047 original size:17 final size:19
Alignment explanation
Indices: 13335012--13335049 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
13335002 TTAACTTTTC
13335012 TTATTTTTATCAGATTATT
1 TTATTTTTATCAGATTATT
13335031 TTATTTTT-TCA-ATTATT
1 TTATTTTTATCAGATTATT
13335048 TT
1 TT
13335050 TTTCAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 8 0.42
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATTTTTATCAGATTATT
Done.