Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold254
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: 856998
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 28123 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:2736 original size:8 final size:7
Alignment explanation
Indices: 2718--2837 Score: 50
Period size: 7 Copynumber: 17.0 Consensus size: 7
2708 ATCAATTAAT
2718 CTAAACC
1 CTAAACC
2725 CTAAACCC
1 CTAAA-CC
2733 CT-AACC
1 CTAAACC
* *
2739 CTTATCTC
1 CTAAAC-C
*
2747 TTAAACC
1 CTAAACC
*
2754 CTAAATC
1 CTAAACC
* *
2761 ATAAAAC
1 CTAAACC
*
2768 ATAAACC
1 CTAAACC
*
2775 CTAACCC
1 CTAAACC
*
2782 CT-AACTT
1 CTAAAC-C
*
2789 CTAACCC
1 CTAAACC
*
2796 CTAACCC
1 CTAAACC
2803 CT-AACC
1 CTAAACC
2809 CTTAAACC
1 C-TAAACC
*
2817 C-CAACC
1 CTAAACC
2823 CTTAAACC
1 C-TAAACC
*
2831 ATAAACC
1 CTAAACC
2838 ATAATCTATA
Statistics
Matches: 85, Mismatches: 19, Indels: 18
0.70 0.16 0.15
Matches are distributed among these distances:
6 15 0.18
7 51 0.60
8 19 0.22
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:2806 original size:14 final size:14
Alignment explanation
Indices: 2773--2823 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
2763 AAAACATAAA
2773 CCCTAACCCCTAAC
1 CCCTAACCCCTAAC
**
2787 TTCTAACCCCTAAC
1 CCCTAACCCCTAAC
*
2801 CCCTAACCCTTAAAC
1 CCCTAACCCCT-AAC
2816 CCC-AACCC
1 CCCTAACCC
2824 TTAAACCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 25 0.81
15 6 0.19
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (14 bp):
CCCTAACCCCTAAC
Found at i:2822 original size:21 final size:20
Alignment explanation
Indices: 2769--2837 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
2759 TCATAAAACA
*
2769 TAAACCCTAACCCCTAA-CT
1 TAAACCCCAACCCCTAACCT
*
2788 TCTAACCCCTAACCCCTAACCCT
1 T-AAACCCC-AACCCCTAA-CCT
* *
2811 TAAACCCCAACCCTTAAACCA
1 TAAACCCCAACCCCT-AACCT
2832 TAAACC
1 TAAACC
2838 ATAATCTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
19 1 0.03
20 5 0.12
21 23 0.57
22 8 0.20
23 3 0.08
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.19
Consensus pattern (20 bp):
TAAACCCCAACCCCTAACCT
Found at i:2824 original size:14 final size:15
Alignment explanation
Indices: 2789--2830 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
2779 CCCCTAACTT
*
2789 CTAACCCCT-AACCC
1 CTAACCCTTAAACCC
2803 CTAACCCTTAAACCC
1 CTAACCCTTAAACCC
2818 C-AACCCTTAAACC
1 CTAACCCTTAAACC
2831 ATAAACCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 20 0.77
15 6 0.23
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (15 bp):
CTAACCCTTAAACCC
Found at i:3863 original size:40 final size:40
Alignment explanation
Indices: 3804--3922 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 40
3794 TTAAATCCCT
3804 GAGCATTAGCGGCGCTTTTTAGAAAAACGCCGCTAAAAACA
1 GAGCATTAGCGGCGCTTTTT-GAAAAACGCCGCTAAAAACA
* * * ** *
3845 GAGCATTTGCGGCG-TTTTTGTGAAAGCGCCGCTAAAGCCCC
1 GAGCATTAGCGGCGCTTTTTG-AAAAACGCCGCTAAA-AACA
*
3886 GACCATTAGCGGCGCTTTTTGAAAAACGCCGCTAAAA
1 GAGCATTAGCGGCGCTTTTTGAAAAACGCCGCTAAAA
3923 CCCTGAAAGC
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
39 1 0.02
40 18 0.28
41 39 0.61
42 6 0.09
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (40 bp):
GAGCATTAGCGGCGCTTTTTGAAAAACGCCGCTAAAAACA
Found at i:4046 original size:40 final size:40
Alignment explanation
Indices: 4002--4095 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 40
3992 AGTGCTTATT
* * * * *
4002 TTTAGCGGCCTTTTCCATAAGGCGTAGCTAATGTTCGATC
1 TTTAGCGGCGTTTTCCAAAAAGCGCAGCTAATGCTCGATC
*
4042 TTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGATC
1 TTTAGCGGCGTTTTCCAAAAAGCGCAGCTAATGCTCGATC
4082 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
4096 TTATCCAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (40 bp):
TTTAGCGGCGTTTTCCAAAAAGCGCAGCTAATGCTCGATC
Found at i:4518 original size:18 final size:18
Alignment explanation
Indices: 4487--4525 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4477 GATTTTGAAA
*
4487 AAATATATAAAAATTTAT
1 AAATATATAAAAATATAT
**
4505 AAATATATTTAAATATAT
1 AAATATATAAAAATATAT
4523 AAA
1 AAA
4526 GGGAATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATATAAAAATATAT
Found at i:5462 original size:16 final size:18
Alignment explanation
Indices: 5427--5464 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
5417 ATTTCTTTTT
5427 ATATTCTATTATTGTTAA
1 ATATTCTATTATTGTTAA
*
5445 ATATT-TATTCTT-TTAA
1 ATATTCTATTATTGTTAA
5461 ATAT
1 ATAT
5465 GCAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (18 bp):
ATATTCTATTATTGTTAA
Found at i:5822 original size:201 final size:197
Alignment explanation
Indices: 5505--5904 Score: 516
Period size: 201 Copynumber: 2.0 Consensus size: 197
5495 ATAAATTAAT
* ** * *
5505 GAACTATATTTTAATTAAATTGATTTATTTTATTTTTAATATACTTAAATTGAGAAAAAATTCAA
1 GAACTATATTTTAATTAAATTAAACTAATTTATTTTTAATATACTTAAATAGAGAAAAAATTCAA
** * ** *
5570 TTTTTAATTTTAAAAAATTGATTAAATTTTTTTATTTAAATTTATTAATTTTGAAGTAGATTAAT
66 TTTGAAATTTTAAAAAATTAATTAAATTTTTAGATTTAAATTTATTAATTTTGAAGTAAATTAAT
* * *
5635 ATAATGTGAATTCTAATTTTAAATATTAATTAATTTTAGTTTAAATAAAATAATAAAATTACTTA
131 ATAATGTAAATTCTAATTTTAAATATGAATTAATTTAAGTTTAAAT-AAATAAT-AAATTACTTA
5700 TTTA
194 TTTA
* * **
5704 GAACTATATTTTAATTAAATTAAACTAATTTATTTTT-TTATACTTAAATAGATAAACTTTATT-
1 GAACTATATTTTAATTAAATTAAACTAATTTATTTTTAATATACTTAAATAGAGAAA--AAATTC
*
5767 AAGTTTGAAATTTTGAAAAATCTAATTAAATTTTTAGATTTAAATTTATTAATTTTGAAGTAAAT
64 AA-TTTGAAATTTTAAAAAAT-TAATTAAATTTTTAGATTTAAATTTATTAATTTTGAAGTAAAT
* * * * *
5832 TATTATATTGTAAATTCTATTTTTAAATATGAATTCATTTAAGTTTAAATTAATAATAAATTACT
127 TAATATAATGTAAATTCTAATTTTAAATATGAATTAATTTAAGTTTAAATAAATAATAAATTACT
5897 TATTTA
192 TATTTA
5903 GA
1 GA
5905 TAGCATATTT
Statistics
Matches: 173, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
198 16 0.09
199 51 0.29
200 24 0.14
201 82 0.47
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (197 bp):
GAACTATATTTTAATTAAATTAAACTAATTTATTTTTAATATACTTAAATAGAGAAAAAATTCAA
TTTGAAATTTTAAAAAATTAATTAAATTTTTAGATTTAAATTTATTAATTTTGAAGTAAATTAAT
ATAATGTAAATTCTAATTTTAAATATGAATTAATTTAAGTTTAAATAAATAATAAATTACTTATT
TA
Found at i:6118 original size:19 final size:21
Alignment explanation
Indices: 6091--6132 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
6081 CTTATAATAC
*
6091 ATATTATGTA-GATATA-GAT
1 ATATAATGTATGATATATGAT
6110 ATATAATGTATGATATATGAT
1 ATATAATGTATGATATATGAT
6131 AT
1 AT
6133 TTTTATGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 6 0.30
21 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (21 bp):
ATATAATGTATGATATATGAT
Found at i:9680 original size:43 final size:43
Alignment explanation
Indices: 9632--9788 Score: 244
Period size: 43 Copynumber: 3.7 Consensus size: 43
9622 TTATCTTTAA
*
9632 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTATACAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTATACAC
* * * *
9675 AAACGCCACTAAAAATCATGTTCTTTAGCGGCGCTACT-TCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCT-TTATACAC
*
9718 AAACGTCGCTAAAGATCATGTTCTTTAGCGGCGCTTTATACAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTATACAC
9761 AAACGCCGCTAAAGATCATGTTCTTTAG
1 AAACGCCGCTAAAGATCATGTTCTTTAG
9789 TGGCAATTTT
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 99 0.98
44 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTATACAC
Found at i:10277 original size:67 final size:66
Alignment explanation
Indices: 10154--10290 Score: 211
Period size: 67 Copynumber: 2.1 Consensus size: 66
10144 CTCGCTGCAG
* *
10154 CCTCTGCTTCTCTGGATGCCGCATCAGCTTTAAGTTGTCGCTGGAGTTCTTCATATTTCTTTTGA
1 CCTCTGCTTCTCTCGATGCCGCATCAGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
10219 A
66 A
* * * *
10220 CCTCTGCTTCTCTCGCTGTCGCATCTGCTTTTGAGTTGTAGCTGGAGTTCTTCATATTTCTTTTG
1 CCTCTGCTTCTCTCGATGCCGCATCAGC-TTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTG
10285 AA
65 AA
10287 CCTC
1 CCTC
10291 AACTGTGGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
66 24 0.38
67 40 0.62
ACGTcount: A:0.13, C:0.26, G:0.19, T:0.42
Consensus pattern (66 bp):
CCTCTGCTTCTCTCGATGCCGCATCAGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
A
Found at i:10776 original size:11 final size:11
Alignment explanation
Indices: 10760--10786 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
10750 CGGCAGCAGC
10760 CCATAATACCA
1 CCATAATACCA
10771 CCATAATACCA
1 CCATAATACCA
10782 CCATA
1 CCATA
10787 TCAATTAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (11 bp):
CCATAATACCA
Found at i:11316 original size:6 final size:6
Alignment explanation
Indices: 11305--11357 Score: 63
Period size: 6 Copynumber: 8.3 Consensus size: 6
11295 ACACATGTTA
11305 AATAAC AATAAC AAATAAC AAATAAC AATAAC AATGAGA- AATAAC AATAAC
1 AATAAC AATAAC -AATAAC -AATAAC AATAAC AAT-A-AC AATAAC AATAAC
11356 AA
1 AA
11358 ATAAACAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 1 0.02
6 24 0.56
7 17 0.40
8 1 0.02
ACGTcount: A:0.68, C:0.13, G:0.04, T:0.15
Consensus pattern (6 bp):
AATAAC
Found at i:11322 original size:13 final size:13
Alignment explanation
Indices: 11304--11361 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
11294 TACACATGTT
11304 AAATAACAATAAC
1 AAATAACAATAAC
11317 AAATAACAAATAAC
1 AAATAAC-AATAAC
* *
11331 -AATAACAATGAG
1 AAATAACAATAAC
11343 AAATAACAATAAC
1 AAATAACAATAAC
11356 AAATAA
1 AAATAA
11362 ACAGTTCTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
12 4 0.10
13 29 0.74
14 6 0.15
ACGTcount: A:0.69, C:0.12, G:0.03, T:0.16
Consensus pattern (13 bp):
AAATAACAATAAC
Found at i:14667 original size:82 final size:81
Alignment explanation
Indices: 14571--14835 Score: 302
Period size: 82 Copynumber: 3.2 Consensus size: 81
14561 GGTGTTTTTA
* * * * * *
14571 AAAAAGCGCCGCTAAAGGCCTGAGA-ATTAGCGCCACATCCATAAAAACGCCACTAAATCCCAGA
1 AAAAA-CGCCGCTAAA-GCCT-AGACATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGA
*
14635 ATATTAGCGGCGCATAAAT
63 ACATTAGCGGCGCATAAAT
* *
14654 AAAAACGCCGCTAAAG-CTCAGAACATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCACATAA
1 AAAAACGCCGCTAAAGCCT-AG-ACATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGAA
* *
14718 CATTAGCGGCGCTTACAT
64 CATTAGCGGCGCATAAAT
14736 AAAAACGCCGCTAAAGCACATA-ACATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGAA
1 AAAAACGCCGCTAAAGC-C-TAGACATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGAA
* **
14800 CATTAGCGGCGCTTCCAT
64 CATTAGCGGCGCATAAAT
* *
14818 AAAATCACCGCTAAAGCC
1 AAAAACGCCGCTAAAGCC
14836 CCCGAAAAGT
Statistics
Matches: 160, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
80 4 0.03
81 3 0.02
82 145 0.91
83 5 0.03
84 2 0.01
85 1 0.01
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16
Consensus pattern (81 bp):
AAAAACGCCGCTAAAGCCTAGACATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGAACA
TTAGCGGCGCATAAAT
Found at i:14704 original size:123 final size:124
Alignment explanation
Indices: 14571--14833 Score: 336
Period size: 123 Copynumber: 2.1 Consensus size: 124
14561 GGTGTTTTTA
* * *
14571 AAAAAGCGCCGCTAAAGGC-C-TGAGA-ATTAGCGCCACATCCATAAAAACGCCACTAAATCCCA
1 AAAAA-CGCCGCTAAAGGCACAT-A-ACATTAGCGCCACATACATAAAAACGCCACTAAAGCACA
* *
14633 GAATATTAGCGGCGCATAAATAAAAACGCCGCTAAAGCTCAGAACATTAGCGGCGCTTACAT
63 GAACATTAGCGGCGCATAAATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
* * * * *
14695 AAAAACGCCGCTAAA-GCACATAACATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCACATAA
1 AAAAACGCCGCTAAAGGCACATAACATTAGCGCCACATACATAAAAACGCCACTAAAGCACAGAA
* * *
14759 CATTAGCGGCGCTTACATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTCCAT
66 CATTAGCGGCGCATAAATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
* *
14818 AAAATCACCGCTAAAG
1 AAAAACGCCGCTAAAG
14834 CCCCCGAAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
122 3 0.03
123 111 0.93
124 6 0.05
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (124 bp):
AAAAACGCCGCTAAAGGCACATAACATTAGCGCCACATACATAAAAACGCCACTAAAGCACAGAA
CATTAGCGGCGCATAAATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
Found at i:14717 original size:21 final size:21
Alignment explanation
Indices: 14691--14758 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
14681 AGCGGCGCTT
14691 ACATAAAAACGCCGCTAAAGC
1 ACATAAAAACGCCGCTAAAGC
* * *
14712 ACATAACATTAGCGGCGCT-TA--
1 ACATAA-A--AACGCCGCTAAAGC
14733 -CATAAAAACGCCGCTAAAGC
1 ACATAAAAACGCCGCTAAAGC
14753 ACATAA
1 ACATAA
14759 CATTAGCGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
17 7 0.21
18 1 0.03
19 1 0.03
20 5 0.15
21 11 0.32
22 1 0.03
23 1 0.03
24 7 0.21
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (21 bp):
ACATAAAAACGCCGCTAAAGC
Found at i:14835 original size:41 final size:41
Alignment explanation
Indices: 14610--14836 Score: 337
Period size: 41 Copynumber: 5.5 Consensus size: 41
14600 GCGCCACATC
* * * *
14610 CATAAAAACGCCACTAAATCCCAGAATATTAGCGGCGCATA
1 CATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTA
* *
14651 AATAAAAACGCCGCTAAAGCTCAGAACATTAGCGGCGCTTA
1 CATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTA
* *
14692 CATAAAAACGCCGCTAAAGCACATAACATTAGCGGCGCTTA
1 CATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTA
* *
14733 CATAAAAACGCCGCTAAAGCACATAACATTAGCGGCGCTTA
1 CATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTA
*
14774 CATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTC
1 CATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTA
* *
14815 CATAAAATCACCGCTAAAGCCC
1 CATAAAAACGCCGCTAAAGCCC
14837 CCGAAAAGTC
Statistics
Matches: 172, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 172 1.00
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.16
Consensus pattern (41 bp):
CATAAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTA
Found at i:17560 original size:27 final size:27
Alignment explanation
Indices: 17509--17561 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
17499 AAAGAAATGG
*
17509 AGAAGGAAGGAAAACAGAGAGAGAAGC
1 AGAAGGAAGGAAAACAAAGAGAGAAGC
17536 AGAAGAGAATGGAAAA-AAAGA-AGAAG
1 AGAAG-GAA-GGAAAACAAAGAGAGAAG
17562 AAAGTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 10 0.43
28 7 0.30
29 6 0.26
ACGTcount: A:0.60, C:0.04, G:0.34, T:0.02
Consensus pattern (27 bp):
AGAAGGAAGGAAAACAAAGAGAGAAGC
Found at i:22043 original size:22 final size:23
Alignment explanation
Indices: 22004--22058 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
21994 AAAAGTGGAA
22004 TTAA-TTTTATTCTAGTTTTGGT
1 TTAAGTTTTATTCTAGTTTTGGT
* *
22026 TTAAGTTTTATT-TTGTTTTGTT
1 TTAAGTTTTATTCTAGTTTTGGT
22048 TTAAAGTTTTA
1 TT-AAGTTTTA
22059 ATTATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.20, C:0.02, G:0.13, T:0.65
Consensus pattern (23 bp):
TTAAGTTTTATTCTAGTTTTGGT
Found at i:22866 original size:21 final size:21
Alignment explanation
Indices: 22806--22883 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
22796 CATGAGCTGG
* *
22806 CCACACGG-CTATGTAACTCTA
1 CCACACGGTC-ATGTACCTCCA
22827 CCACACGAG-CATGTACCT-CA
1 CCACACG-GTCATGTACCTCCA
*
22847 GCCACACGGTCATGTGCCTCCA
1 -CCACACGGTCATGTACCTCCA
*
22869 TCACACGGTCATGTA
1 CCACACGGTCATGTA
22884 GACTCCTCAC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.04
21 42 0.88
22 4 0.08
ACGTcount: A:0.26, C:0.36, G:0.18, T:0.21
Consensus pattern (21 bp):
CCACACGGTCATGTACCTCCA
Found at i:22893 original size:21 final size:21
Alignment explanation
Indices: 22849--22899 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
22839 GTACCTCAGC
*
22849 CACACGGTCATGTGCCTCCAT
1 CACACGGTCATGTGACTCCAT
22870 CACACGGTCATGTAGACTCC-T
1 CACACGGTCATGT-GACTCCAT
*
22891 CACATGGTC
1 CACACGGTC
22900 TGGTTCCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.24
Consensus pattern (21 bp):
CACACGGTCATGTGACTCCAT
Found at i:22909 original size:17 final size:18
Alignment explanation
Indices: 22887--22920 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22877 TCATGTAGAC
*
22887 TCCTC-ACATGGTCTGGT
1 TCCTCAACATGGCCTGGT
22904 TCCTCAACATGGCCTGG
1 TCCTCAACATGGCCTGG
22921 GCACACGGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.32, G:0.24, T:0.29
Consensus pattern (18 bp):
TCCTCAACATGGCCTGGT
Found at i:25892 original size:15 final size:14
Alignment explanation
Indices: 25869--25902 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
25859 CACATCCCAA
25869 AAATCGAGTTAGTAG
1 AAATCGAGTTAGT-G
*
25884 AAATTGAGTTAGTG
1 AAATCGAGTTAGTG
25898 AAATC
1 AAATC
25903 AAGAGTGGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (14 bp):
AAATCGAGTTAGTG
Found at i:36700 original size:22 final size:21
Alignment explanation
Indices: 36652--36700 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
36642 AAAACAGAAA
*
36652 AATATTTTTATATTAATATTT
1 AATAATTTTATATTAATATTT
36673 ATATAATTTTATAATTAA-ATTT
1 A-ATAATTTTAT-ATTAATATTT
36695 GAATAA
1 -AATAA
36701 AAACTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 17 0.71
23 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
AATAATTTTATATTAATATTT
Found at i:37693 original size:30 final size:30
Alignment explanation
Indices: 37655--37718 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
37645 AAAAAAAGTG
* *
37655 TTGCT-TTTCCTTGCT-TTTTTT-ACTTTTT
1 TTGCTATTTTCTTGCTATTTTTTCAC-TATT
*
37683 TTGCTATTTTCTTGTTATTTTTTCACTATT
1 TTGCTATTTTCTTGCTATTTTTTCACTATT
37713 TTGCTA
1 TTGCTA
37719 CCATTTCACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 5 0.17
29 8 0.27
30 15 0.50
31 2 0.07
ACGTcount: A:0.09, C:0.16, G:0.08, T:0.67
Consensus pattern (30 bp):
TTGCTATTTTCTTGCTATTTTTTCACTATT
Found at i:42089 original size:6 final size:6
Alignment explanation
Indices: 42062--42090 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
42052 AATTTAATTA
42062 TAATAT T-ATAT TAATAT TAATAT TAATAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT
42091 ACAATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATAT
Found at i:49294 original size:2 final size:2
Alignment explanation
Indices: 49181--49279 Score: 198
Period size: 2 Copynumber: 49.5 Consensus size: 2
49171 CATATATATA
49181 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
49223 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
49265 TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
49280 TGCTTTTAAG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:57377 original size:21 final size:22
Alignment explanation
Indices: 57353--57393 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
57343 TCAAGGTTTC
57353 AAATTA-ATATACTCTAACATG
1 AAATTAGATATACTCTAACATG
* *
57374 AAATTAGTTATACTGTAACA
1 AAATTAGATATACTCTAACA
57394 AGATTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (22 bp):
AAATTAGATATACTCTAACATG
Found at i:65328 original size:22 final size:22
Alignment explanation
Indices: 65300--65341 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
65290 GATGATGACC
65300 ACTTTTTTT-TTAATTTTAATTT
1 ACTTTTTTTATT-ATTTTAATTT
65322 ACTTTTTTTATTATTTTAAT
1 ACTTTTTTTATTATTTTAAT
65342 ATTTTAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
ACTTTTTTTATTATTTTAATTT
Found at i:69381 original size:17 final size:18
Alignment explanation
Indices: 69345--69382 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
69335 AGTTTGAAAC
*
69345 AAAACAAAAAGTTTTAGA
1 AAAACAAAAAATTTTAGA
*
69363 AAAATAAAAAATTTT-GA
1 AAAACAAAAAATTTTAGA
69380 AAA
1 AAA
69383 TAGGGGTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (18 bp):
AAAACAAAAAATTTTAGA
Found at i:73595 original size:29 final size:28
Alignment explanation
Indices: 73563--73618 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
73553 AGTGTTTTGC
* * *
73563 CATTAATGTATTACTTTTAAGTATTTTTT
1 CATTAATATAATAATTTT-AGTATTTTTT
73592 CATTAATATAATAATTTTAGTATTTTT
1 CATTAATATAATAATTTTAGTATTTTT
73619 ATTTTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (28 bp):
CATTAATATAATAATTTTAGTATTTTTT
Found at i:73634 original size:28 final size:28
Alignment explanation
Indices: 73603--73658 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
73593 ATTAATATAA
*
73603 TAATTTT-AGTATTTTTATTTTTTAGTTT
1 TAATTTTGAGTA-TTTTAATTTTTAGTTT
73631 TAATTTTGAGTATTTTAATTTTTAGTTT
1 TAATTTTGAGTATTTTAATTTTTAGTTT
73659 ATTTATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (28 bp):
TAATTTTGAGTATTTTAATTTTTAGTTT
Found at i:73648 original size:15 final size:14
Alignment explanation
Indices: 73603--73652 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
73593 ATTAATATAA
73603 TAATTTTAGTATTT
1 TAATTTTAGTATTT
* *
73617 TTATTTT-TTAGTTT
1 TAATTTTAGTA-TTT
73631 TAATTTTGAGTATTT
1 TAATTTT-AGTATTT
73646 TAATTTT
1 TAATTTT
73653 TAGTTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 2 0.07
14 15 0.52
15 10 0.34
16 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (14 bp):
TAATTTTAGTATTT
Found at i:80251 original size:19 final size:20
Alignment explanation
Indices: 80211--80253 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
80201 TATAAGAGAA
*
80211 TTAATTTTTTATATTTTATT
1 TTAATTTTTTATATATTATT
*
80231 TTAA-TTTTTATAATATTTTT
1 TTAATTTTTTAT-ATATTATT
80251 TTA
1 TTA
80254 TTTATAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTAATTTTTTATATATTATT
Found at i:80630 original size:32 final size:32
Alignment explanation
Indices: 80594--80656 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
80584 TTATAAACTT
* *
80594 ATAAATTAATTACTTAAATTTAATAACTCATG
1 ATAAATTAATAAATTAAATTTAATAACTCATG
* *
80626 ATAAATTAATAAATTTAATTTGATAACTCAT
1 ATAAATTAATAAATTAAATTTAATAACTCAT
80657 TGATTAACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (32 bp):
ATAAATTAATAAATTAAATTTAATAACTCATG
Found at i:85233 original size:20 final size:20
Alignment explanation
Indices: 85197--85234 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
85187 AAAATATCTT
**
85197 TTGACCATTAACTTTAATAG
1 TTGACCATTAAAGTTAATAG
85217 TTGACCATTAAAGTTAAT
1 TTGACCATTAAAGTTAAT
85235 TGCCCCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (20 bp):
TTGACCATTAAAGTTAATAG
Found at i:85351 original size:37 final size:37
Alignment explanation
Indices: 85307--85388 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 37
85297 GCAGGAAAAA
* *
85307 TTATAAAAAATA-AAA-ATCAATAAAATTTATTAAATT
1 TTATAAAAAATATAAATATCAATAAAA-ATATAAAATT
*
85343 TTAATAAAAAATATAAATATCATTAAAAATATAAAATT
1 TT-ATAAAAAATATAAATATCAATAAAAATATAAAATT
85381 TTATAAAA
1 TTATAAAA
85389 TTTTATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
36 2 0.05
37 16 0.40
38 13 0.32
39 9 0.22
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (37 bp):
TTATAAAAAATATAAATATCAATAAAAATATAAAATT
Found at i:85385 original size:10 final size:10
Alignment explanation
Indices: 85372--85398 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
85362 TCATTAAAAA
85372 TATAAAATTT
1 TATAAAATTT
85382 TATAAAATTT
1 TATAAAATTT
85392 TATAAAA
1 TATAAAA
85399 ATCATAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TATAAAATTT
Found at i:85416 original size:48 final size:48
Alignment explanation
Indices: 85317--85417 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 48
85307 TTATAAAAAA
* *
85317 TAAAAATCAATAAAATTTATTAAATTTTAATAAAAAATATAAATATCAT
1 TAAAAAT-AATAAAATTTATAAAATTTTAATAAAAAATATAAAGATCAT
*
85366 TAAAAAT-ATAAAATTTTATAAAATTTT-AT-AAAAATCATAAAAGATTAT
1 TAAAAATAATAAAA-TTTATAAAATTTTAATAAAAAAT-AT-AAAGATCAT
85414 TAAA
1 TAAA
85418 TGTATATAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
46 6 0.13
47 10 0.22
48 23 0.50
49 7 0.15
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (48 bp):
TAAAAATAATAAAATTTATAAAATTTTAATAAAAAATATAAAGATCAT
Found at i:85655 original size:10 final size:10
Alignment explanation
Indices: 85631--85682 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
85621 CTTTTACAAA
85631 TTTTATATTT
1 TTTTATATTT
* *
85641 CTTTATTTTT
1 TTTTATATTT
85651 TTTTATAATTT
1 TTTTAT-ATTT
*
85662 TTCTATATTT
1 TTTTATATTT
* *
85672 CTATATATTT
1 TTTTATATTT
85682 T
1 T
85683 ATAATTTTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
10 25 0.76
11 8 0.24
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTATATTT
Found at i:85707 original size:28 final size:28
Alignment explanation
Indices: 85651--85710 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
85641 CTTTATTTTT
* *
85651 TTTTATAATTTTTCTATATTTCTATATA
1 TTTTATAATTTTTATAAATTTCTATATA
*
85679 TTTTATAATTTTTAATAAATTTTTA-ATA
1 TTTTATAATTTTT-ATAAATTTCTATATA
85707 TTTT
1 TTTT
85711 TTTACTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTATAATTTTTATAAATTTCTATATA
Found at i:85976 original size:88 final size:84
Alignment explanation
Indices: 85839--85997 Score: 205
Period size: 88 Copynumber: 1.8 Consensus size: 84
85829 ATTTTGGCAG
* *
85839 TTCAAATACCCAATTGAGCAAAAAAAAAAAGGGCTTAATGTTTTCTTTTTTTGAAAAATTTTGAG
1 TTCAAATACCCAATTGAGC-AAAAAAAAAAGGGCTTAATG--CTCTTTTTTTGAAAAAGTTTGAG
85904 GGCCTTTTTGTGTATTTTAAAAT
63 GG-CTTTTTGTGTATTTTAAAAT
* *
85927 TTCAAGTACCCAATTGAATGC-AAAAAAAAATGGCTTAATTGCT-TTTTTTTGAAAAAGTTTGAG
1 TTCAAATACCCAATTG-A-GCAAAAAAAAAAGGGCTTAA-TGCTCTTTTTTTGAAAAAGTTTGAG
85990 GGCTTTTT
63 GGCTTTTT
85998 ATACCCTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
85 6 0.09
86 21 0.33
87 1 0.02
88 31 0.48
89 3 0.05
90 2 0.03
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (84 bp):
TTCAAATACCCAATTGAGCAAAAAAAAAAGGGCTTAATGCTCTTTTTTTGAAAAAGTTTGAGGGC
TTTTTGTGTATTTTAAAAT
Found at i:87936 original size:28 final size:27
Alignment explanation
Indices: 87884--87937 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
87874 AAAGAATATT
*
87884 TTTAAAAAATAAATTTTGCTTAAAATTC
1 TTTAAAAAATAAATTTT-CTAAAAATTC
87912 TTTAAAAAATCATAATTTT-TAAAAAT
1 TTTAAAAAAT-A-AATTTTCTAAAAAT
87938 ACAAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 16 0.70
29 1 0.04
30 6 0.26
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (27 bp):
TTTAAAAAATAAATTTTCTAAAAATTC
Found at i:88262 original size:308 final size:309
Alignment explanation
Indices: 87925--88542 Score: 1229
Period size: 308 Copynumber: 2.0 Consensus size: 309
87915 AAAAAATCAT
87925 AATTTTTAAAAATACAAATTAATATAAAAAGTTTTAAAATAAATTCAAAAAAATTATTATATATT
1 AATTTTTAAAAATACAAATTAATATAAAAAGTTTTAAAATAAATTCAAAAAAATTATTATATATT
87990 ACAAAAAATAAAAATAAATTGTAGGTTATATTTTTAAAAAAATTATTAAATTATAAAAAATTCAA
66 ACAAAAAATAAAAATAAATTGTAGGTTATATTTTTAAAAAAATTATTAAATTATAAAAAATTCAA
88055 TAAACTTTTAAAAGATCCAAAATTTTGAAAAAAAATGTATGAAAATTTTTGAAAAAGAAAAAATG
131 TAAACTTTTAAAAGATCCAAAATTTTGAAAAAAAATGTATGAAAATTTTTGAAAAAGAAAAAATG
88120 ACGATTTTTTTTGTAAGTAGCACGGTATCACTTTTAAATTTTGATTTTTTTTTCAAAAAATAGTA
196 ACGATTTTTTTTGTAAGTAGCACGGTATCACTTTTAAATTTTGATTTTTTTTTCAAAAAATAGTA
88185 TAAAATTAAATAGCCATAATTGAAATTAATTTTGATATTTTCATAATTG
261 TAAAATTAAATAGCCATAATTGAAATTAATTTTGATATTTTCATAATTG
88234 AATTTTT-AAAATACAAATTAATATAAAAAGTTTTAAAATAAATTCAAAAAAATTATTATATATT
1 AATTTTTAAAAATACAAATTAATATAAAAAGTTTTAAAATAAATTCAAAAAAATTATTATATATT
88298 ACAAAAAATAAAAATAAATTGTAGGTTATATTTTTAAAAAAATTATTAAATTATAAAAAATTCAA
66 ACAAAAAATAAAAATAAATTGTAGGTTATATTTTTAAAAAAATTATTAAATTATAAAAAATTCAA
88363 TAAACTTTTAAAAGATCCAAAATTTTGAAAAAAAATGTATGAAAATTTTTGAAAAAGAAAAAATG
131 TAAACTTTTAAAAGATCCAAAATTTTGAAAAAAAATGTATGAAAATTTTTGAAAAAGAAAAAATG
88428 ACGATTTTTTTTGTAAGTAGCACGGTATCACTTTTAAATTTTGATTTTTTTTTCAAAAAATAGTA
196 ACGATTTTTTTTGTAAGTAGCACGGTATCACTTTTAAATTTTGATTTTTTTTTCAAAAAATAGTA
88493 TAAAATTAAATAGCCATAATTGAAATTAATTTTGATATTTTCATAATTG
261 TAAAATTAAATAGCCATAATTGAAATTAATTTTGATATTTTCATAATTG
88542 A
1 A
88543 CTGGAGTCCG
Statistics
Matches: 309, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
308 302 0.98
309 7 0.02
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.38
Consensus pattern (309 bp):
AATTTTTAAAAATACAAATTAATATAAAAAGTTTTAAAATAAATTCAAAAAAATTATTATATATT
ACAAAAAATAAAAATAAATTGTAGGTTATATTTTTAAAAAAATTATTAAATTATAAAAAATTCAA
TAAACTTTTAAAAGATCCAAAATTTTGAAAAAAAATGTATGAAAATTTTTGAAAAAGAAAAAATG
ACGATTTTTTTTGTAAGTAGCACGGTATCACTTTTAAATTTTGATTTTTTTTTCAAAAAATAGTA
TAAAATTAAATAGCCATAATTGAAATTAATTTTGATATTTTCATAATTG
Found at i:89361 original size:126 final size:125
Alignment explanation
Indices: 89136--89424 Score: 461
Period size: 126 Copynumber: 2.3 Consensus size: 125
89126 TAATTTAAAA
* * **
89136 AAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGCTCGTGAAAAAATAATTTCGAGAAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCAGAAAAAATAATTTCGAGAAGACGTTT
*
89201 CTAACCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
66 CTAACCAAATAGTGTCAAAAACACTTTAAGCAGGATGCATTGTCAGC-AAAGTACTGAAAG
*
89262 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCAGAAAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCAGAAAAAATAATTTCGAGAAGACGTTT
* * *
89327 CTGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAAAGTACTGAAAG
66 CTAACCAAATAGTGTCAAAAACACTTTAAGCAGGATGCATTGTCAGCAAAGTACTGAAAG
** *
89387 AAGCTCTTACGTGGACGTGCTTTTGCTACAGTAGCTCC
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCC
89425 TGTTTGGCTT
Statistics
Matches: 151, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
125 48 0.32
126 103 0.68
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (125 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCAGAAAAAATAATTTCGAGAAGACGTTT
CTAACCAAATAGTGTCAAAAACACTTTAAGCAGGATGCATTGTCAGCAAAGTACTGAAAG
Found at i:91580 original size:7 final size:7
Alignment explanation
Indices: 91570--91602 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
91560 CATAATACAT
91570 AATACTA
1 AATACTA
91577 AATACTA
1 AATACTA
91584 AATACTA
1 AATACTA
91591 AATACTA
1 AATACTA
91598 AATAC
1 AATAC
91603 CAATCGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:92825 original size:11 final size:11
Alignment explanation
Indices: 92811--92869 Score: 77
Period size: 11 Copynumber: 5.4 Consensus size: 11
92801 AGCATTTTTA
92811 AGAGGAATTTG
1 AGAGGAATTTG
92822 AGAGGAATTTG
1 AGAGGAATTTG
92833 AGAGGAATTTG
1 AGAGGAATTTG
92844 AGA-GAATATTG
1 AGAGGAAT-TTG
*
92855 -GAGAGAAATTG
1 AGAG-GAATTTG
92866 AGAG
1 AGAG
92870 AAAGGATTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
10 6 0.14
11 31 0.72
12 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.36, T:0.24
Consensus pattern (11 bp):
AGAGGAATTTG
Found at i:93928 original size:6 final size:6
Alignment explanation
Indices: 93917--93947 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
93907 TGGCATAAAC
93917 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
93948 ATATTGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:95273 original size:9 final size:9
Alignment explanation
Indices: 95229--95295 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
95219 TTGCGATCTG
95229 ATTATTAAT-
1 ATTATT-ATC
*
95238 ATTGTTATC
1 ATTATTATC
*
95247 ATTATTATA
1 ATTATTATC
*
95256 ATTA-CATC
1 ATTATTATC
95264 ATTATTATC
1 ATTATTATC
95273 ATAGTATTAT-
1 AT--TATTATC
95283 ATTATTTATC
1 ATTA-TTATC
95293 ATT
1 ATT
95296 TATCATTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
8 10 0.22
9 25 0.54
10 5 0.11
11 6 0.13
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (9 bp):
ATTATTATC
Found at i:102369 original size:65 final size:65
Alignment explanation
Indices: 102265--102395 Score: 226
Period size: 65 Copynumber: 2.0 Consensus size: 65
102255 ACATGTCAAC
* * *
102265 ATCCTTACCATTAATTTCAAAAATATCTAATAACTAGAATGTTCATATATAATATCTAGTCTTCT
1 ATCCTTACCATTAATTTAAAAAAAATCTAATAACTAGAATGTTCATATATAATATCTAGCCTTCT
*
102330 ATCCTTACCATTAATTTAAAAAAAATCTAATAACTAGAATGTTCATGTATAATATCTAGCCTTCT
1 ATCCTTACCATTAATTTAAAAAAAATCTAATAACTAGAATGTTCATATATAATATCTAGCCTTCT
102395 A
1 A
102396 GAGAATATCC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (65 bp):
ATCCTTACCATTAATTTAAAAAAAATCTAATAACTAGAATGTTCATATATAATATCTAGCCTTCT
Found at i:109936 original size:29 final size:29
Alignment explanation
Indices: 109894--109959 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
109884 CACGAGTGTG
109894 TGGGCCCACTTAGGTCGAGTAATGGGCCT
1 TGGGCCCACTTAGGTCGAGTAATGGGCCT
*
109923 TGGGCCCACTTAGGTCGAGTAATTGGCCT
1 TGGGCCCACTTAGGTCGAGTAATGGGCCT
109952 TGGGCCCA
1 TGGGCCCA
109960 TTTACACTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (29 bp):
TGGGCCCACTTAGGTCGAGTAATGGGCCT
Found at i:110047 original size:27 final size:27
Alignment explanation
Indices: 109982--110211 Score: 297
Period size: 27 Copynumber: 8.7 Consensus size: 27
109972 TGATCGAAAG
* * * * *
109982 ACCCTCATATGGTAGAATAACCGAAAT
1 ACCCCCATAGGGTAAAATGACCAAAAT
110009 A-CCCCATAGGGTAAAATGACCAAAAT
1 ACCCCCATAGGGTAAAATGACCAAAAT
110035 ACCCCCATAGGGTAAAATGACCAAAAT
1 ACCCCCATAGGGTAAAATGACCAAAAT
* ***
110062 A-CCCCATAGGATAAAATGATTGAAAT
1 ACCCCCATAGGGTAAAATGACCAAAAT
110088 ACCCCCATA-GG-AAAATGACCAAAAT
1 ACCCCCATAGGGTAAAATGACCAAAAT
* * *
110113 ACCCCTATACGGTAAAATGAACAAAAT
1 ACCCCCATAGGGTAAAATGACCAAAAT
*
110140 ACCCCCATAGGGTAAAACGACCAAAAT
1 ACCCCCATAGGGTAAAATGACCAAAAT
110167 ACCCCCATAGGGTAAAATGACCAAAAT
1 ACCCCCATAGGGTAAAATGACCAAAAT
**
110194 ACCATCATAGGGTAAAAT
1 ACCCCCATAGGGTAAAAT
110212 TACTATGATA
Statistics
Matches: 177, Mismatches: 22, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
25 19 0.11
26 46 0.26
27 112 0.63
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.17
Consensus pattern (27 bp):
ACCCCCATAGGGTAAAATGACCAAAAT
Found at i:110068 original size:53 final size:53
Alignment explanation
Indices: 109982--110211 Score: 302
Period size: 53 Copynumber: 4.3 Consensus size: 53
109972 TGATCGAAAG
* * * * *
109982 ACCCTCATATGGTAGAATAACCGAAATACCCCATAGGGTAAAATGACCAAAAT
1 ACCCCCATAGGGTAAAATGACCAAAATACCCCATAGGGTAAAATGACCAAAAT
* ***
110035 ACCCCCATAGGGTAAAATGACCAAAATACCCCATAGGATAAAATGATTGAAAT
1 ACCCCCATAGGGTAAAATGACCAAAATACCCCATAGGGTAAAATGACCAAAAT
* *
110088 ACCCCCATA-GG-AAAATGACCAAAATACCCCTATACGGTAAAATGAACAAAAT
1 ACCCCCATAGGGTAAAATGACCAAAATACCCC-ATAGGGTAAAATGACCAAAAT
*
110140 ACCCCCATAGGGTAAAACGACCAAAATACCCCCATAGGGTAAAATGACCAAAAT
1 ACCCCCATAGGGTAAAATGACCAAAATA-CCCCATAGGGTAAAATGACCAAAAT
**
110194 ACCATCATAGGGTAAAAT
1 ACCCCCATAGGGTAAAAT
110212 TACTATGATA
Statistics
Matches: 153, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
51 19 0.12
52 27 0.18
53 55 0.36
54 48 0.31
55 4 0.03
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.17
Consensus pattern (53 bp):
ACCCCCATAGGGTAAAATGACCAAAATACCCCATAGGGTAAAATGACCAAAAT
Found at i:117251 original size:41 final size:41
Alignment explanation
Indices: 117206--117288 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
117196 GGAATCTACA
117206 CTCACGAG-AAAACTAGCCCTTCTTGCCACAATTGAAACATT
1 CTCACGAGCAAAA-TAGCCCTTCTTGCCACAATTGAAACATT
*
117247 CTCACGAGCAAAATGGCCCTTCTTGCCACAATTGAAACATT
1 CTCACGAGCAAAATAGCCCTTCTTGCCACAATTGAAACATT
117288 C
1 C
117289 ACCATCCCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 36 0.90
42 4 0.10
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (41 bp):
CTCACGAGCAAAATAGCCCTTCTTGCCACAATTGAAACATT
Found at i:118415 original size:19 final size:19
Alignment explanation
Indices: 118378--118415 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
118368 CATTATAAGC
*
118378 AATAAATAACTTAATAACT
1 AATAAATAACTTAAAAACT
118397 AATAAATTAAC-TAAAAACT
1 AATAAA-TAACTTAAAAACT
118416 TACACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAAATAACTTAAAAACT
Found at i:121966 original size:33 final size:32
Alignment explanation
Indices: 121923--122033 Score: 85
Period size: 33 Copynumber: 3.6 Consensus size: 32
121913 AATCAGTCTA
*
121923 GGCCTGAGCCCTATACAATATCAGTACAGTGTG
1 GGCCTTAGCCCT-TACAATATCAGTACAGTGTG
* *
121956 GGCCTTAGCCCGTTACAATAACA--A-TGTGTG
1 GGCCTTAGCCC-TTACAATATCAGTACAGTGTG
*
121986 GGCCTTA-ACC---CAATAT-AGTAACAGTGTG
1 GGCCTTAGCCCTTACAATATCAGT-ACAGTGTG
*
122014 GGCCTTAGCCCAATACAATA
1 GGCCTTAGCCC-TTACAATA
122034 ATTAGTAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
24 1 0.02
25 5 0.08
27 1 0.02
28 12 0.20
29 4 0.07
30 12 0.20
31 1 0.02
33 24 0.39
34 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (32 bp):
GGCCTTAGCCCTTACAATATCAGTACAGTGTG
Found at i:121987 original size:30 final size:28
Alignment explanation
Indices: 121948--122034 Score: 111
Period size: 28 Copynumber: 3.0 Consensus size: 28
121938 CAATATCAGT
**
121948 ACAGTGTGGGCCTTAGCCCGTTACAATA
1 ACAGTGTGGGCCTTAGCCCAATACAATA
* * *
121976 ACAATGTGTGGGCCTTAACCCAATATAGTA
1 AC-A-GTGTGGGCCTTAGCCCAATACAATA
122006 ACAGTGTGGGCCTTAGCCCAATACAATA
1 ACAGTGTGGGCCTTAGCCCAATACAATA
122034 A
1 A
122035 TTAGTAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 25 0.51
29 2 0.04
30 22 0.45
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCCAATACAATA
Found at i:122025 original size:28 final size:28
Alignment explanation
Indices: 121938--122028 Score: 103
Period size: 28 Copynumber: 3.2 Consensus size: 28
121928 GAGCCCTATA
121938 CAATATCAGT-ACAGTGTGGGCCTTAGCC
1 CAATAT-AGTAACAGTGTGGGCCTTAGCC
** * * *
121966 CGTTACAATAACAATGTGTGGGCCTTAACC
1 CAATATAGTAAC-A-GTGTGGGCCTTAGCC
121996 CAATATAGTAACAGTGTGGGCCTTAGCC
1 CAATATAGTAACAGTGTGGGCCTTAGCC
122024 CAATA
1 CAATA
122029 CAATAATTAG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
27 2 0.04
28 24 0.48
29 2 0.04
30 22 0.44
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (28 bp):
CAATATAGTAACAGTGTGGGCCTTAGCC
Found at i:122174 original size:26 final size:26
Alignment explanation
Indices: 122145--122221 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 26
122135 GCACCAATAT
*
122145 CGCAGCAAAGCTGCCAGTAATAGTGA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
* *
122171 CGCAGCAAAACTGCCAGAAATAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
** *
122197 CGCATTAAAGCTGCCAGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAATAGTA
122222 TACGTGGCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAATAGTAA
Found at i:122429 original size:27 final size:27
Alignment explanation
Indices: 122399--122615 Score: 199
Period size: 27 Copynumber: 8.0 Consensus size: 27
122389 TAAAACAGTT
* * *
122399 ATTTTAACCTATGGGGGTATTTTGATC
1 ATTTTACCCTTTGAGGGTATTTTGATC
* *
122426 ATTTTACCCTTTAAGGGTA-TTTCAGTC
1 ATTTTACCCTTTGAGGGTATTTTGA-TC
* *
122453 ATTTTACCCTTCG-GAGGTATTTTGGTC
1 ATTTTACCCTTTGAG-GGTATTTTGATC
* *
122480 ATCTTACCCTTTGAGGGTA-TTTCAGTC
1 ATTTTACCCTTTGAGGGTATTTTGA-TC
* * *
122507 ATTTTACCCTTCGGGGGTATTTTGGTC
1 ATTTTACCCTTTGAGGGTATTTTGATC
* *
122534 ATTTTACTCTTTGAGGGTA-TTTCAGTC
1 ATTTTACCCTTTGAGGGTATTTTGA-TC
* * *
122561 ATTTTATCCTTTAAGGGTATTTCGATC
1 ATTTTACCCTTTGAGGGTATTTTGATC
* *
122588 ATTTTCCCCTTCGAGGGTATTTTGATC
1 ATTTTACCCTTTGAGGGTATTTTGATC
122615 A
1 A
122616 GGAGGGGTGA
Statistics
Matches: 149, Mismatches: 33, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
26 11 0.07
27 128 0.86
28 10 0.07
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.45
Consensus pattern (27 bp):
ATTTTACCCTTTGAGGGTATTTTGATC
Found at i:122472 original size:54 final size:54
Alignment explanation
Indices: 122414--122609 Score: 268
Period size: 54 Copynumber: 3.6 Consensus size: 54
122404 AACCTATGGG
*
122414 GGTATTTTGATCATTTTACCCTTTAAGGGTATTTCAGTCATTTTACCCTTCGGA
1 GGTATTTTGATCATTTTACCCTTTGAGGGTATTTCAGTCATTTTACCCTTCGGA
* * *
122468 GGTATTTTGGTCATCTTACCCTTTGAGGGTATTTCAGTCATTTTACCCTTCGGG
1 GGTATTTTGATCATTTTACCCTTTGAGGGTATTTCAGTCATTTTACCCTTCGGA
* * * **
122522 GGTATTTTGGTCATTTTACTCTTTGAGGGTATTTCAGTCATTTTATCCTT-TAA
1 GGTATTTTGATCATTTTACCCTTTGAGGGTATTTCAGTCATTTTACCCTTCGGA
* * *
122575 GGGTATTTCGATCATTTTCCCCTTCGAGGGTATTT
1 -GGTATTTTGATCATTTTACCCTTTGAGGGTATTT
122610 TGATCAGGAG
Statistics
Matches: 126, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
54 126 1.00
ACGTcount: A:0.17, C:0.18, G:0.19, T:0.45
Consensus pattern (54 bp):
GGTATTTTGATCATTTTACCCTTTGAGGGTATTTCAGTCATTTTACCCTTCGGA
Found at i:122553 original size:81 final size:81
Alignment explanation
Indices: 122413--122611 Score: 240
Period size: 81 Copynumber: 2.5 Consensus size: 81
122403 TAACCTATGG
* ** ** **
122413 GGGTATTTTGATCATTTTACCCTTTAAGGGTATTTCAGTCATTTTACCCTTCGGAGGTATTTTGG
1 GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCGGAGGTATTTCAG
*
122478 TCATCTTACCCTTTGA
66 TCATCTTACCCTTTAA
* * *
122494 GGGTATTTC-AGTCATTTTACCCTTCGGGGGTATTTTGGTCATTTTACTCTT-TGAGGGTATTTC
1 GGGTATTTCGA-TCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCGGA-GGTATTTC
* *
122557 AGTCATTTTATCCTTTAA
64 AGTCATCTTACCCTTTAA
*
122575 GGGTATTTCGATCATTTTCCCCTTCGAGGGTATTTTG
1 GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTTG
122612 ATCAGGAGGG
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
80 3 0.03
81 96 0.96
82 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.45
Consensus pattern (81 bp):
GGGTATTTCGATCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCGGAGGTATTTCAG
TCATCTTACCCTTTAA
Found at i:124947 original size:27 final size:27
Alignment explanation
Indices: 124878--124950 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
124868 AAAATGATTG
*
124878 AAATACCCTCATAGGATAAAATGACCA
1 AAATACCCTCATAGGGTAAAATGACCA
*
124905 AAATACCC-CTGTAGGGTAAAATGACCA
1 AAATACCCTC-ATAGGGTAAAATGACCA
124932 AAATACCCTCATAGGGTAA
1 AAATACCCTCATAGGGTAA
124951 TGTTGGAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
26 1 0.02
27 39 0.95
28 1 0.02
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (27 bp):
AAATACCCTCATAGGGTAAAATGACCA
Found at i:126586 original size:81 final size:81
Alignment explanation
Indices: 126449--126703 Score: 411
Period size: 81 Copynumber: 3.1 Consensus size: 81
126439 ATACTCTAAC
* *
126449 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTATAATGA
1 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCGTAGGGTAAAATGA
* *
126514 CCGAAATACCCTCGTA
66 CCAAAATACCCCCGTA
* * * * *
126530 GGGTAAAATGATCGAAATACCCCTATAGGGTAAAATGATCGAAATACCCCTGTAGGGTAAAATGA
1 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCGTAGGGTAAAATGA
126595 CCAAAATACCCCCGTA
66 CCAAAATACCCCCGTA
*
126611 AGGTAAAATGACCCAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCGTAGGGTAAAATGA
1 AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCGTAGGGTAAAATGA
*
126676 CCAAAATACCCCCATA
66 CCAAAATACCCCCGTA
126692 AGGTAAAATGAC
1 AGGTAAAATGAC
126704 TGTTATACTC
Statistics
Matches: 158, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 158 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.17
Consensus pattern (81 bp):
AGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCGTAGGGTAAAATGA
CCAAAATACCCCCGTA
Found at i:126711 original size:27 final size:27
Alignment explanation
Indices: 126450--126703 Score: 373
Period size: 27 Copynumber: 9.4 Consensus size: 27
126440 TACTCTAACA
126450 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
126477 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
126504 GGTATAATGACCGAAATACCCTCGTAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
126531 GGTAAAATGATCGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* **
126558 GGTAAAATGATCGAAATACCCCTGTAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
126585 GGTAAAATGACCAAAATACCCCCGTAA
1 GGTAAAATGACCGAAATACCCCCATAG
*
126612 GGTAAAATGACCCAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
126639 GGTAAAATGACCGAAATACCCCCGTAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
126666 GGTAAAATGACCAAAATACCCCCATAA
1 GGTAAAATGACCGAAATACCCCCATAG
126693 GGTAAAATGAC
1 GGTAAAATGAC
126704 TGTTATACTC
Statistics
Matches: 206, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 206 1.00
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.17
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCCCATAG
Found at i:126881 original size:26 final size:26
Alignment explanation
Indices: 126850--126904 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
126840 TGGAGGAAGT
*
126850 ATACTGTTACTGGCAGCTTTGCTACG
1 ATACTGTTACTAGCAGCTTTGCTACG
* *
126876 ATACTGTTACTAGTAGCTTTGCTGCG
1 ATACTGTTACTAGCAGCTTTGCTACG
126902 ATA
1 ATA
126905 TTGGTGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (26 bp):
ATACTGTTACTAGCAGCTTTGCTACG
Found at i:129961 original size:16 final size:18
Alignment explanation
Indices: 129932--129965 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
129922 TTATTTTAAA
129932 AAAATACAACAGTAAAAT
1 AAAATACAACAGTAAAAT
129950 AAAATA-AA-AGTAAAAT
1 AAAATACAACAGTAAAAT
129966 CCCTATAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (18 bp):
AAAATACAACAGTAAAAT
Found at i:133036 original size:14 final size:15
Alignment explanation
Indices: 133009--133053 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
132999 TATCATCAGG
*
133009 TATATTTTACTATAAT
1 TATA-TTTATTATAAT
133025 T-TATTTATTAT-AT
1 TATATTTATTATAAT
133038 TATATTTATTATAAT
1 TATATTTATTATAAT
133053 T
1 T
133054 GAAGATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 3 0.12
14 17 0.65
15 5 0.19
16 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTTATTATAAT
Found at i:137608 original size:107 final size:107
Alignment explanation
Indices: 137449--137702 Score: 348
Period size: 107 Copynumber: 2.4 Consensus size: 107
137439 GCGATGTCTG
* * * * *
137449 AGATTCTACATATGTTGCGGAATCTCGACAGCTTGTATGAGCAGCATCGTGAATTGGTGAATTGA
1 AGATCCTACATATGTTGCGGATTCTCGACAGCTTGTGTGAGCAGCATCGTGAACTGGTGAATAGA
* ** *
137514 ATGGCTACTCTATTATGATGACATAGACCGTTCCGATGGTTA
66 ATGGCTACTCTATTATGATGACATAGACCATTCAAATGGCTA
*
137556 AGATCCTACATATGTTGCGGATTCTCGACAGCTTGTGTGAGTAGCATCGTGAACTGGTGAATAGA
1 AGATCCTACATATGTTGCGGATTCTCGACAGCTTGTGTGAGCAGCATCGTGAACTGGTGAATAGA
** * *
137621 ATGGCTACTCTATTATGATGTTATAGTCCATTCAAATGGCTG
66 ATGGCTACTCTATTATGATGACATAGACCATTCAAATGGCTA
* *
137663 AGATCTTGCATATGTTGCGGATTCTC-ATCAGCTTGTGTGA
1 AGATCCTACATATGTTGCGGATTCTCGA-CAGCTTGTGTGA
137703 ACAATCTCGT
Statistics
Matches: 130, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
106 1 0.01
107 129 0.99
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (107 bp):
AGATCCTACATATGTTGCGGATTCTCGACAGCTTGTGTGAGCAGCATCGTGAACTGGTGAATAGA
ATGGCTACTCTATTATGATGACATAGACCATTCAAATGGCTA
Found at i:139939 original size:25 final size:26
Alignment explanation
Indices: 139911--139968 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
139901 ACAGATCTTA
139911 TGAGCTTCCCGATT-A-TGGCTCTTTG
1 TGAGCTTCCCG-TTAATTGGCTCTTTG
139936 TGAGCTTCCCGTTAATTGGCTCTTTG
1 TGAGCTTCCCGTTAATTGGCTCTTTG
139962 TGAGCTT
1 TGAGCTT
139969 TCTGATAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 2 0.06
25 12 0.39
26 17 0.55
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.41
Consensus pattern (26 bp):
TGAGCTTCCCGTTAATTGGCTCTTTG
Found at i:140086 original size:25 final size:25
Alignment explanation
Indices: 140057--140105 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
140047 TATTGGATCG
*
140057 CATGAGCTTCCCGTTACATGGCTCA
1 CATGAGCTTCCCATTACATGGCTCA
*
140082 CATGAGCTTCCCATTATATGGCTC
1 CATGAGCTTCCCATTACATGGCTC
140106 GAGAAAGTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.20, C:0.31, G:0.18, T:0.31
Consensus pattern (25 bp):
CATGAGCTTCCCATTACATGGCTCA
Found at i:142089 original size:26 final size:26
Alignment explanation
Indices: 142027--142089 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
142017 GAAAGGTACG
* *
142027 TATATGAAATAAGCTATAATGTTGAG
1 TATATGAAATGAGCTATAATGTTGAA
*
142053 TATATGAAATGAGCTATGATGTTGAA
1 TATATGAAATGAGCTATAATGTTGAA
*
142079 TATATAAAATG
1 TATATGAAATG
142090 GATAGTATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (26 bp):
TATATGAAATGAGCTATAATGTTGAA
Found at i:146610 original size:15 final size:15
Alignment explanation
Indices: 146592--146625 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
146582 CAAAACTAAG
146592 ATTTTTAAAATATTT
1 ATTTTTAAAATATTT
*
146607 ATTTTTACAATATTT
1 ATTTTTAAAATATTT
146622 ATTT
1 ATTT
146626 AAAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTTAAAATATTT
Found at i:150780 original size:16 final size:14
Alignment explanation
Indices: 150745--150808 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 14
150735 GCAATTTATT
150745 TTTTCTCTTTTATGTTC
1 TTTTCT-TTTT-T-TTC
150762 TTTTAACTTTTTTTTC
1 TTTT--CTTTTTTTTC
150778 TTTTCTTTTTTTTCC
1 TTTTCTTTTTTTT-C
*
150793 TTTCTCTTTTGTTTC
1 TTT-TCTTTTTTTTC
150808 T
1 T
150809 CCCTTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
14 9 0.21
15 6 0.14
16 16 0.38
17 5 0.12
18 4 0.10
19 2 0.05
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:150789 original size:15 final size:16
Alignment explanation
Indices: 150768--150807 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
150758 GTTCTTTTAA
150768 CTTTTTTTT-CTTT-T
1 CTTTTTTTTCCTTTCT
150782 CTTTTTTTTCCTTTCT
1 CTTTTTTTTCCTTTCT
*
150798 CTTTTGTTTC
1 CTTTTTTTTC
150808 TCCCTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.39
15 4 0.17
16 10 0.43
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (16 bp):
CTTTTTTTTCCTTTCT
Found at i:155353 original size:107 final size:107
Alignment explanation
Indices: 155202--155399 Score: 256
Period size: 107 Copynumber: 1.9 Consensus size: 107
155192 CGATGCTGCT
* ** * * **
155202 CACACAAGCTACAGAGAATCCGCAATGATGTAGGATCTCAAGCCATTG-TAACGGTTTGTATCAC
1 CACACAAGCTACAGAGAATCCGAAAAAATGCAGGATCTCAAGCCATCGCT-ACAATTTGTATCAC
* *
155266 CGGTACATATTACCTGTTAAATAATCATCGACTCACAATGTTG
65 CGGTACATAATACCTGCTAAATAATCATCGACTCACAATGTTG
* *
155309 CACACAAGCTATAGAGAATCTGAAACAAATGCAGGATCTC-AGCCATCGCTACAATTTGTATCAC
1 CACACAAGCTACAGAGAATCCGAAA-AAATGCAGGATCTCAAGCCATCGCTACAATTTGTATCAC
*
155373 CGGTACATAATACCTGCTAAATGATCA
65 CGGTACATAATACCTGCTAAATAATCA
155400 CCCAGCTCAA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
107 65 0.84
108 12 0.16
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (107 bp):
CACACAAGCTACAGAGAATCCGAAAAAATGCAGGATCTCAAGCCATCGCTACAATTTGTATCACC
GGTACATAATACCTGCTAAATAATCATCGACTCACAATGTTG
Found at i:164816 original size:3 final size:3
Alignment explanation
Indices: 164808--164856 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
164798 AACCTTTTTG
*
164808 TAT TAT TAT TAT GTAT ATAT TAT CAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
164855 TA
1 TA
164857 AGCTCTTCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:169959 original size:46 final size:45
Alignment explanation
Indices: 169892--169979 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 45
169882 AGGAGAAGCG
* *
169892 ACCAAGGTGAAAACCCACAAAGGGCGCCTTGATTCCTAAAAAAAAC
1 ACCAAAGTGAAAACCCACAAAGGGCGCCTTGAGTCC-AAAAAAAAC
* *
169938 ACCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGTCCAAAAAA
1 ACCAAAGTGAAAACCCACAAAGGGCGCCTTGAGTCCAAAAAA
169980 TAAAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 6 0.16
46 32 0.84
ACGTcount: A:0.43, C:0.25, G:0.19, T:0.12
Consensus pattern (45 bp):
ACCAAAGTGAAAACCCACAAAGGGCGCCTTGAGTCCAAAAAAAAC
Found at i:171422 original size:88 final size:87
Alignment explanation
Indices: 171246--171424 Score: 189
Period size: 88 Copynumber: 2.0 Consensus size: 87
171236 AATAGATCAG
* * ** *
171246 TGAAGAGAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAAAGAACAGATCTTGCCTTCCCACACTAACAGCGAAGCAGATCGAAGACACCAGCCTT-CCT
*** *
171311 CCCTGGGTTGCAGCGGAGCAGGT
65 CCCTGGAAAGCAGCGGAACAGGT
* * * *
171334 TGAAAAGAACAGATCTTGCCTTCCCATACTAACGGCGAAGCAGATCGAAGATACTAGTCCTAT-C
1 TGAAAAGAACAGATCTTGCCTTCCCACACTAACAGCGAAGCAGATCGAAGACACCAG-CCT-TCC
* *
171398 TCCCTGGAAAGCAGTGGAATAGGT
64 TCCCTGGAAAGCAGCGGAACAGGT
171422 TGA
1 TGA
171425 GGATTGTAAG
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
88 70 0.95
89 3 0.04
90 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.20
Consensus pattern (87 bp):
TGAAAAGAACAGATCTTGCCTTCCCACACTAACAGCGAAGCAGATCGAAGACACCAGCCTTCCTC
CCTGGAAAGCAGCGGAACAGGT
Found at i:171455 original size:44 final size:44
Alignment explanation
Indices: 171389--171601 Score: 279
Period size: 44 Copynumber: 4.8 Consensus size: 44
171379 CGAAGATACT
** *
171389 AGTCCTATCTCCCTGGAAAGCAGTGGAATAGGTTGAGGATTGTA
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTA
171433 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTG-A
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTA
* * ** *
171476 GAATTCTATCTCCCTGGGT-AATAGTGGAATAGATTGAAGATTGTA
1 -AGTCCTATCTCCCT-GGTCAGCAGTGGAATAGGTTGAAGATTGTA
*
171521 GGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGA
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-A
* *
171566 A-TTCTATCTCCCTGGTCAGCAGTGGAATAGATTGAA
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAA
171602 AAATTACAAA
Statistics
Matches: 147, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
43 4 0.03
44 138 0.94
45 5 0.03
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (44 bp):
AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTA
Found at i:171505 original size:88 final size:89
Alignment explanation
Indices: 171393--171601 Score: 325
Period size: 88 Copynumber: 2.4 Consensus size: 89
171383 GATACTAGTC
* *
171393 CTATCTCCCT-GGAAAGCAGTGGAATAGGTTGAGGATTGTAAGTCCTATCTCCCTGGTCAGCAGT
1 CTATCTCCCTGGGAAAGCAGTGGAATAGATTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGT
171457 GGAATAGGTTGAAGATTGAGAATT
66 GGAATAGGTTGAAGATTGAGAATT
* * *
171481 CTATCTCCCTGGGTAA-TAGTGGAATAGATTGAAGATTGTAGGTCCTATCTCCCTGGTCAGCAGT
1 CTATCTCCCTGGGAAAGCAGTGGAATAGATTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGT
*
171545 GGAATAGGTTGAAGATTGTGAATT
66 GGAATAGGTTGAAGATTGAGAATT
**
171569 CTATCTCCCT-GGTCAGCAGTGGAATAGATTGAA
1 CTATCTCCCTGGGAAAGCAGTGGAATAGATTGAA
171602 AAATTACAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
87 4 0.04
88 103 0.93
89 4 0.04
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (89 bp):
CTATCTCCCTGGGAAAGCAGTGGAATAGATTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGT
GGAATAGGTTGAAGATTGAGAATT
Found at i:171664 original size:132 final size:131
Alignment explanation
Indices: 171390--171689 Score: 338
Period size: 132 Copynumber: 2.3 Consensus size: 131
171380 GAAGATACTA
* *
171390 GTCCTATCTCCCTGGAAAGCAGTGGAATAGGTTGAGGATTGTAAGTCCTATCTCCCTGGTCAGCA
1 GTCCTATCTCCCTGG-CAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCA
* * * * ** * * ****
171455 GTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGTAATAGTGGAATAGATTGAAGATTGT
65 GTGGAATAGATTGAAAATTGACAAATCTATCTCCCTAAGTAATAGTGGAACAGATCGAAGACCCC
171520 AG
130 AG
*
171522 GTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAA-TTCTATCTCCCTGGTCAGC
1 GTCCTATCTCCCTGG-CAGCAGTGGAATAGGTTGAAGATTGT-AAGTCCTATCTCCCTGGTCAGC
* *
171586 AGTGGAATAGATTGAAAAATT-ACAAATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGAC
64 AGTGGAATAGATTG-AAAATTGACAAATC-TATCTCCCTAAGTAATAGTGGAACAGATCGAAGAC
171650 CCCA-
127 CCCAG
* *
171654 G-CCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAA
1 GTCC-TATCTCCCTG-GCAGCAGTGGAATAGGTTGAA
171690 AAAAAATTAC
Statistics
Matches: 143, Mismatches: 20, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
131 2 0.01
132 104 0.73
133 37 0.26
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (131 bp):
GTCCTATCTCCCTGGCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAG
TGGAATAGATTGAAAATTGACAAATCTATCTCCCTAAGTAATAGTGGAACAGATCGAAGACCCCA
G
Found at i:171949 original size:217 final size:215
Alignment explanation
Indices: 171692--172131 Score: 623
Period size: 217 Copynumber: 2.0 Consensus size: 215
171682 AGGTTGAAAA
* *
171692 AAAATTACAGATCTTATATCTCTAAAGTTGAAGTAGAGTAGATCGCATCAGGTCTTATCTCCTTG
1 AAAATAACAGATCTTATATCTCTAAAGTTGAAGTAGAGTAGATCGCATCAGGTCTTATCTCCGTG
* * *
171757 AGGTTACAACGGAGCAGACCGAAGAAACGGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGA
66 AGGTTACAACGGAGCAGAACGAAGAAACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGA
** * * * *
171822 AGATGGTGGATTTTATCTCCCTTAG-GTTACAGTAGAGTAGATTGAAGCCACTAATCCTATCT-C
131 AGATGGCAGATCTTATCTCCCTAAGAG-T--AGTAGAGCAGATTGAAGACACTAATCCTATCTCC
* *
171885 TCTGAGGTTGCAGTGGAGTGGATT
193 T-TAAAGTTGCAGTGGAGTGGATT
* * *
171909 AAAATAACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCGTG
1 AAAATAACAGATCTTATATCTCTAAAGTTGAAGTAGAGTAGATCGCATCAGGTCTTATCTCCGTG
* *
171974 AGGTTGCAGCGGAGCAGAACGAAGAAACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGA
66 AGGTTACAACGGAGCAGAACGAAGAAACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGA
* * * *
172039 AGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATAGTAGTCCTATCTCCTT
131 AGATGGCAGATCTTATCTCCCTAAG-AGTAGTAGAGCAGATTGAAGACACTAATCCTATCTCCTT
172104 AAAGTTGCAGTGGAGTGGATT
195 AAAGTTGCAGTGGAGTGGATT
172125 AAAATAA
1 AAAATAA
172132 ATCTTATCTC
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
216 53 0.27
217 143 0.72
218 1 0.01
219 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (215 bp):
AAAATAACAGATCTTATATCTCTAAAGTTGAAGTAGAGTAGATCGCATCAGGTCTTATCTCCGTG
AGGTTACAACGGAGCAGAACGAAGAAACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGA
AGATGGCAGATCTTATCTCCCTAAGAGTAGTAGAGCAGATTGAAGACACTAATCCTATCTCCTTA
AAGTTGCAGTGGAGTGGATT
Found at i:172049 original size:44 final size:44
Alignment explanation
Indices: 171984--172087 Score: 156
Period size: 44 Copynumber: 2.4 Consensus size: 44
171974 AGGTTGCAGC
*
171984 GGAGCAGAACGAAGA-AACAGATCTTATCTCCCTAAGCAATAGT
1 GGAGCAGATCGAAGATAACAGATCTTATCTCCCTAAGCAATAGT
** *
172027 GGAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGT
1 GGAGCAGATCGAAGATAACAGATCTTATCTCCCTAAGCAATAGT
*
172071 GGAGCAGATTGAAGATA
1 GGAGCAGATCGAAGATA
172088 GTAGTCCTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
43 14 0.26
44 40 0.74
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (44 bp):
GGAGCAGATCGAAGATAACAGATCTTATCTCCCTAAGCAATAGT
Found at i:172118 original size:44 final size:44
Alignment explanation
Indices: 171979--172101 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 44
171969 CCGTGAGGTT
* * * *
171979 GCAGCGGAGCAGAACGAAGA-AACAGATCTTATCTCCCTAAGCA
1 GCAGTGGAGCAGATCGAAGATAGCAGATCCTATCTCCCTAAGCA
** * *
172022 ATAGTGGAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCA
1 GCAGTGGAGCAGATCGAAGATAGCAGATCCTATCTCCCTAAGCA
* * *
172066 GTAGTGGAGCAGATTGAAGATAGTAG-TCCTATCTCC
1 GCAGTGGAGCAGATCGAAGATAGCAGATCCTATCTCC
172102 TTAAAGTTGC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 25 0.37
44 43 0.63
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (44 bp):
GCAGTGGAGCAGATCGAAGATAGCAGATCCTATCTCCCTAAGCA
Found at i:176507 original size:257 final size:258
Alignment explanation
Indices: 176040--176555 Score: 1025
Period size: 257 Copynumber: 2.0 Consensus size: 258
176030 CATCTTATCA
176040 TTCAATTTAGTTTATTCAAATTTTAACTTCGAAGGATCGTATTTTAGAATCTTTTCAGAATTTCA
1 TTCAATTTAGTTTATTCAAATTTTAACTTCGAAGGATCGTATTTTAGAATCTTTTCAGAATTTCA
176105 ATACTAAGACATTAAGCAATCAATTCGGTACCAATTTTTGGGCATCACGAGGGTGCTAACCCTTT
66 ATACTAAGACATTAAGCAATCAATTCGGTACCAATTTTTGGGCATCACGAGGGTGCTAACCCTTT
176170 CTCGTGCTTAACCGACTCCCGAACCTATTTTCTCAAAATCTGTAGACCTAAAATCGTTTTCAAGG
131 CTCGTGCTTAACCGACTCCCGAACCTATTTTCTCAAAATCTGTAGACCTAAAATCGTTTTCAAGG
176235 TGATCCGATCACACCTTCAATAAAGTTCGGTGGCGACTCCATTTCCATTTTCAAAATCGATTC
196 TGATCCGATCACACCTTCAATAAAGTTCGGTGGCGACTCCATTTCCATTTTCAAAATCGATTC
176298 TTCAATTTAG-TTATTCAAATTTTAACTTCGAAGGATCGTATTTTAGAATCTTTTCAGAATTTCA
1 TTCAATTTAGTTTATTCAAATTTTAACTTCGAAGGATCGTATTTTAGAATCTTTTCAGAATTTCA
176362 ATACTAAGACATTAAGCAATCAATTCGGTACCAATTTTTGGGCATCACGAGGGTGCTAACCCTTT
66 ATACTAAGACATTAAGCAATCAATTCGGTACCAATTTTTGGGCATCACGAGGGTGCTAACCCTTT
176427 CTCGTGCTTAACCGACTCCCGAACCTATTTTCTCAAAATCTGTAGACCTAAAATCGTTTTCAAGG
131 CTCGTGCTTAACCGACTCCCGAACCTATTTTCTCAAAATCTGTAGACCTAAAATCGTTTTCAAGG
176492 TGATCCGATCACACCTTCAATAAAGTTCGGTGGCGACTCCATTTCCATTTTCAAAATCGATTC
196 TGATCCGATCACACCTTCAATAAAGTTCGGTGGCGACTCCATTTCCATTTTCAAAATCGATTC
176555 T
1 T
176556 CATTTTAAAA
Statistics
Matches: 258, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
257 248 0.96
258 10 0.04
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (258 bp):
TTCAATTTAGTTTATTCAAATTTTAACTTCGAAGGATCGTATTTTAGAATCTTTTCAGAATTTCA
ATACTAAGACATTAAGCAATCAATTCGGTACCAATTTTTGGGCATCACGAGGGTGCTAACCCTTT
CTCGTGCTTAACCGACTCCCGAACCTATTTTCTCAAAATCTGTAGACCTAAAATCGTTTTCAAGG
TGATCCGATCACACCTTCAATAAAGTTCGGTGGCGACTCCATTTCCATTTTCAAAATCGATTC
Found at i:179562 original size:26 final size:25
Alignment explanation
Indices: 179526--179591 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
179516 ATAAAATACA
*
179526 TCTTTGCATTCATTTTTGAGCCAA-TAT
1 TCTTT-CATTC-TTTTTGA-ACAATTAT
*
179553 TCTTTCATTCTTTTTGAATAATTAT
1 TCTTTCATTCTTTTTGAACAATTAT
179578 TCTTTCATTCTTTT
1 TCTTTCATTCTTTT
179592 GGATTTTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 2 0.06
25 24 0.67
26 5 0.14
27 5 0.14
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.58
Consensus pattern (25 bp):
TCTTTCATTCTTTTTGAACAATTAT
Found at i:180670 original size:18 final size:18
Alignment explanation
Indices: 180647--180718 Score: 76
Period size: 18 Copynumber: 4.0 Consensus size: 18
180637 AAAAAATCAG
180647 AATCAAAAATAA-AAAAA
1 AATCAAAAATAACAAAAA
* *
180664 AAGTCAAAATTAAAAAAAA
1 AA-TCAAAAATAACAAAAA
**
180683 AATCAATCATAATCAAAAA
1 AATCAAAAATAA-CAAAAA
180702 AAT-AAAAATAACAAAAA
1 AATCAAAAATAACAAAAA
180719 GAAAAGGAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
17 8 0.18
18 22 0.49
19 15 0.33
ACGTcount: A:0.75, C:0.08, G:0.01, T:0.15
Consensus pattern (18 bp):
AATCAAAAATAACAAAAA
Found at i:183108 original size:44 final size:44
Alignment explanation
Indices: 183056--183179 Score: 203
Period size: 44 Copynumber: 2.8 Consensus size: 44
183046 GAAGATACTA
*
183056 GTCCTATCTCCCTGGTCAGCAGTGGAATAGATTGAAGATTGTAG
1 GTCCTATCTCCCTGGTCAGTAGTGGAATAGATTGAAGATTGTAG
* *
183100 GTCCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTTG
1 GTCCTATCTCCCTGGTCAGTAGTGGAATAGATTGAAGATTGTAG
* *
183144 ATTCTATCTCCCTGGTCAGTAGTGGAATAGATTGAA
1 GTCCTATCTCCCTGGTCAGTAGTGGAATAGATTGAA
183180 AAATTACAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 74 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (44 bp):
GTCCTATCTCCCTGGTCAGTAGTGGAATAGATTGAAGATTGTAG
Found at i:183500 original size:44 final size:43
Alignment explanation
Indices: 183452--183593 Score: 128
Period size: 44 Copynumber: 3.3 Consensus size: 43
183442 GAAGCCACTA
* *
183452 ATCTTATCTCCCTGAGGTTACAGTGGAGCGGATTAAAATAACAG
1 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAGA-TAAAATAACAG
* * * * ***
183496 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCAT--CAG
1 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATAAAATAACAG
* * *
183537 GTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACATAAGA-AACAG
1 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAG--ATAAAATAACAG
183581 ATCTTATCTCCCT
1 ATCTTATCTCCCT
183594 AAGCAATAGT
Statistics
Matches: 75, Mismatches: 19, Indels: 8
0.74 0.19 0.08
Matches are distributed among these distances:
41 28 0.37
43 6 0.08
44 41 0.55
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (43 bp):
ATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATAAAATAACAG
Found at i:183522 original size:216 final size:216
Alignment explanation
Indices: 183270--183708 Score: 639
Period size: 216 Copynumber: 2.0 Consensus size: 216
183260 AGGTTGAAAA
* *
183270 AAAATTACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCTTG
1 AAAATAACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTG
* * * *
183335 AGGTTGCAGCAGAGCAGACCGAAGAAA-GGGTCTTATCTCCCTAAGCAGTAGTCGAGCAGATCGA
66 AGGTTGCAGCAGAGCAGACAGAAGAAACAGATCTTATCTCCCTAAGCAATAGTCGAGCAGATCGA
** * * * *
183399 AGATGGTGGATTTTACCTCCCTGAGTTTA-CAGTGGAGTAGATTGAAGCCACTAATCTTATCTCC
131 AGATGGAAGATCTTACCTCCCTAAG--TAGCAGTGGAGCAGATTGAAGCCACTAATCCTATCTCC
*
183463 CTGAGGTTACAGTGGAGCGGATT
194 CTGAAGTTACAGTGGAGCGGATT
*
183486 AAAATAACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTG
1 AAAATAACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTG
* * *
183551 AGGTTGCAGCGGAGCAGACATAAGAAACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGA
66 AGGTTGCAGCAGAGCAGACAGAAGAAACAGATCTTATCTCCCTAAGCAATAGTCGAGCAGATCGA
* * * *
183616 AGATGGAAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATTGAAGCCAGTAGTCCTATCTCCCT
131 AGATGGAAGATCTTACCTCCCTAAGTAGCAGTGGAGCAGATTGAAGCCACTAATCCTATCTCCCT
* *
183681 GAAGTTGCAGTGGAGTGGATT
196 GAAGTTACAGTGGAGCGGATT
183702 AAAATAA
1 AAAATAA
183709 ATCTTATCTG
Statistics
Matches: 198, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
215 2 0.01
216 143 0.72
217 53 0.27
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (216 bp):
AAAATAACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTG
AGGTTGCAGCAGAGCAGACAGAAGAAACAGATCTTATCTCCCTAAGCAATAGTCGAGCAGATCGA
AGATGGAAGATCTTACCTCCCTAAGTAGCAGTGGAGCAGATTGAAGCCACTAATCCTATCTCCCT
GAAGTTACAGTGGAGCGGATT
Found at i:183760 original size:216 final size:215
Alignment explanation
Indices: 183270--183760 Score: 526
Period size: 216 Copynumber: 2.3 Consensus size: 215
183260 AGGTTGAAAA
* * * * * * * * * *
183270 AAAATTACAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCTTG
1 AAAATAACAGATCTTATCTCTCCGAAGTTGCAGGAGAGCAGATAGAAGCAGATCTTATCTCCCTG
* * * *
183335 AGGTTGCAGCAGAGCAGACCGAAGAAAGGGTCTTATCTCCCTAAGCAGTAGTCGAGCAGATCGAA
66 AGGTTGCAGCAGAGCAGACAGAAGAAAAGATCTTATCTCCCTAAGCAATAGTCGAGCAGATCGAA
** * * * *
183400 GATGGTGGATTTTACCTCCCTGAGTTTACAGTGGAGTAGATTGAAGCCACTAATCTTATCTCCCT
131 GATGGAAGATCTTACCTCCCTAAG-TTACAGTGGAGCAGATTGAAGCCACTAATCCTATCTCCCT
*
183465 GAGGTTACAGTGGAGCGGATT
195 GAAGTTACAGTGGAGCGGATT
* * * * * * *
183486 AAAATAACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTG
1 AAAATAACAGATCTTATCTCTCCGAAGTTGCAGGAGAGCAGATAGAAGCAGATCTTATCTCCCTG
* * *
183551 AGGTTGCAGCGGAGCAGACATAAGAAACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGA
66 AGGTTGCAGCAGAGCAGACAGAAGAAA-AGATCTTATCTCCCTAAGCAATAGTCGAGCAGATCGA
* * * *
183616 AGATGGAAGATCTTATCTCCCTAAG-TAGTAGTGGAGCAGATTGAAGCCAGTAGTCCTATCTCCC
130 AGATGGAAGATCTTACCTCCCTAAGTTA-CAGTGGAGCAGATTGAAGCCACTAATCCTATCTCCC
* *
183680 TGAAGTTGCAGTGGAGTGGATT
194 TGAAGTTACAGTGGAGCGGATT
*
183702 AAAAT-A-A-ATCTTATCTGC-CCGAGGTTGCAGCGA-AGCAGACTGAGTAAGCAGATCTTATC
1 AAAATAACAGATCTTATCT-CTCCGAAGTTGCAG-GAGAGCAGA-T-AG-AAGCAGATCTTATC
183761 CTCCTAAAGA
Statistics
Matches: 237, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
213 24 0.10
214 4 0.02
215 4 0.02
216 152 0.64
217 53 0.22
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (215 bp):
AAAATAACAGATCTTATCTCTCCGAAGTTGCAGGAGAGCAGATAGAAGCAGATCTTATCTCCCTG
AGGTTGCAGCAGAGCAGACAGAAGAAAAGATCTTATCTCCCTAAGCAATAGTCGAGCAGATCGAA
GATGGAAGATCTTACCTCCCTAAGTTACAGTGGAGCAGATTGAAGCCACTAATCCTATCTCCCTG
AAGTTACAGTGGAGCGGATT
Found at i:189727 original size:15 final size:16
Alignment explanation
Indices: 189707--189741 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
189697 ATCCTTATTT
*
189707 AAATAAAAT-ACAGTA
1 AAATAAAATAAAAGTA
189722 AAATAAAATAAAAGTA
1 AAATAAAATAAAAGTA
189738 AAAT
1 AAAT
189742 CCCTATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (16 bp):
AAATAAAATAAAAGTA
Found at i:191950 original size:13 final size:13
Alignment explanation
Indices: 191934--191963 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
191924 TCCATAAAAA
191934 AATTAAATAATAT
1 AATTAAATAATAT
*
191947 AATTAAATAGTAT
1 AATTAAATAATAT
191960 AATT
1 AATT
191964 CTAGTGGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
AATTAAATAATAT
Found at i:196948 original size:18 final size:19
Alignment explanation
Indices: 196909--196949 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
196899 CAACAAAAAA
*
196909 AAAATTCAAAACAATTTTT
1 AAAATTCAAAACAATTTAT
*
196928 AAAATTCAAAA-TATTTAT
1 AAAATTCAAAACAATTTAT
196946 AAAA
1 AAAA
196950 ATTATAAAAT
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:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTCAAAACAATTTAT
Found at i:205014 original size:16 final size:16
Alignment explanation
Indices: 204993--205047 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
204983 TCTAGGTATG
204993 TGAAGAGACTTGAAAA
1 TGAAGAGACTTGAAAA
*
205009 TGAAGAG--TTAGAAATG
1 TGAAGAGACTT-GAAA-A
*
205025 TGAAGAGACTTGAAGA
1 TGAAGAGACTTGAAAA
205041 TGAAGAG
1 TGAAGAG
205048 TTACACACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 21 0.66
17 3 0.09
18 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.31, T:0.20
Consensus pattern (16 bp):
TGAAGAGACTTGAAAA
Found at i:205027 original size:32 final size:32
Alignment explanation
Indices: 204990--205050 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
204980 GTTTCTAGGT
204990 ATGTGAAGAGACTTGAAAATGAAGAGTTAGAA
1 ATGTGAAGAGACTTGAAAATGAAGAGTTAGAA
*
205022 ATGTGAAGAGACTTGAAGATGAAGAGTTA
1 ATGTGAAGAGACTTGAAAATGAAGAGTTA
205051 CACACATGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.30, T:0.23
Consensus pattern (32 bp):
ATGTGAAGAGACTTGAAAATGAAGAGTTAGAA
Found at i:206213 original size:61 final size:61
Alignment explanation
Indices: 206118--206301 Score: 368
Period size: 61 Copynumber: 3.0 Consensus size: 61
206108 TGCAGCCAGA
206118 TTAAAACTGGCTCAAAGTATTATTATACTATCCCTTAGATACCATTAATAGAGGCTATGGG
1 TTAAAACTGGCTCAAAGTATTATTATACTATCCCTTAGATACCATTAATAGAGGCTATGGG
206179 TTAAAACTGGCTCAAAGTATTATTATACTATCCCTTAGATACCATTAATAGAGGCTATGGG
1 TTAAAACTGGCTCAAAGTATTATTATACTATCCCTTAGATACCATTAATAGAGGCTATGGG
206240 TTAAAACTGGCTCAAAGTATTATTATACTATCCCTTAGATACCATTAATAGAGGCTATGGG
1 TTAAAACTGGCTCAAAGTATTATTATACTATCCCTTAGATACCATTAATAGAGGCTATGGG
206301 T
1 T
206302 CATGGTTAGA
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 123 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (61 bp):
TTAAAACTGGCTCAAAGTATTATTATACTATCCCTTAGATACCATTAATAGAGGCTATGGG
Found at i:216853 original size:19 final size:19
Alignment explanation
Indices: 216831--216876 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
216821 ATCCAAACAA
*
216831 TAAAATCTATCAATTTTTT
1 TAAAATCAATCAATTTTTT
**
216850 TAAAATCAATTTATTTTTT
1 TAAAATCAATCAATTTTTT
*
216869 AAAAATCA
1 TAAAATCA
216877 TTTTCGGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (19 bp):
TAAAATCAATCAATTTTTT
Found at i:224090 original size:9 final size:9
Alignment explanation
Indices: 224081--224122 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
224071 CAAATTTAAA
224081 AAATAAAA-
1 AAATAAAAT
224089 AAGAT-AAAT
1 AA-ATAAAAT
*
224098 AAATTAAAT
1 AAATAAAAT
224107 AAATAAAAT
1 AAATAAAAT
224116 AAATAAA
1 AAATAAA
224123 TTTTTTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:224099 original size:13 final size:12
Alignment explanation
Indices: 224081--224123 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
224071 CAAATTTAAA
224081 AAATAAAAAAGAT
1 AAATAAAAAA-AT
*
224094 AAATAAATTAAAT
1 AAATAAA-AAAAT
224107 AAATAAAATAAAT
1 AAATAAAA-AAAT
224120 AAAT
1 AAAT
224124 TTTTTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 24 0.92
14 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:224101 original size:4 final size:4
Alignment explanation
Indices: 224077--224123 Score: 51
Period size: 4 Copynumber: 11.2 Consensus size: 4
224067 AATACAAATT
*
224077 TAAA -AAA TAAA AAAGA TAAA TAAA TTAAA TAAA TAAAA TAAA TAAA T
1 TAAA TAAA TAAA TAA-A TAAA TAAA -TAAA TAAA T-AAA TAAA TAAA T
224124 TTTTTTATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 3 0.08
4 23 0.62
5 11 0.30
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:225438 original size:81 final size:81
Alignment explanation
Indices: 225340--225598 Score: 509
Period size: 81 Copynumber: 3.2 Consensus size: 81
225330 TTTGTTCCAG
*
225340 TTTTTTTTTTTTTTTGGTTTTAGTCTTCTTTGTTATTGTTCTAGGCCTATCTTTTAGTTTCTTGA
1 TTTTTTTTTTTTTTTGGTTTTAGTCGTCTTTGTTATTGTTCTAGGCCTATCTTTTAGTTTCTTGA
225405 AAAATTTCTGGATTCT
66 AAAATTTCTGGATTCT
225421 TTTTTTTTTTTTTTTGGTTTTAGTCGTCTTTGTTATTGTTCTAGGCCTATCTTTTAGTTTCTTGA
1 TTTTTTTTTTTTTTTGGTTTTAGTCGTCTTTGTTATTGTTCTAGGCCTATCTTTTAGTTTCTTGA
225486 AAAATTTCTGGATTCT
66 AAAATTTCTGGATTCT
225502 TTTTTTTTTTTTTTTGGTTTTAGTCGTCTTTGTTATTGTTCTAGGCCTATCTTTTAGTTTCTTGA
1 TTTTTTTTTTTTTTTGGTTTTAGTCGTCTTTGTTATTGTTCTAGGCCTATCTTTTAGTTTCTTGA
225567 AAAATTTCTGGATTCT
66 AAAATTTCTGGATTCT
225583 TTTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTTG
225599 CAATGATAGT
Statistics
Matches: 177, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 177 1.00
ACGTcount: A:0.13, C:0.10, G:0.14, T:0.63
Consensus pattern (81 bp):
TTTTTTTTTTTTTTTGGTTTTAGTCGTCTTTGTTATTGTTCTAGGCCTATCTTTTAGTTTCTTGA
AAAATTTCTGGATTCT
Found at i:246197 original size:3 final size:3
Alignment explanation
Indices: 246189--246262 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
246179 AATCATTAAA
246189 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
246237 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
246263 ACCAATCCAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:246461 original size:108 final size:109
Alignment explanation
Indices: 246263--246480 Score: 429
Period size: 108 Copynumber: 2.0 Consensus size: 109
246253 ATAATAATAA
246263 ACCAATCCAAATGATTATTTTAACTTGGTTCAACCGGTTTGTATTAGTTTGTGGGTCAATTGGTC
1 ACCAATCCAAATGATTATTTTAACTTGGTTCAACCGGTTTGTATTAGTTTGTGGGTCAATTGGTC
246328 TGATATCTCTCTCGAAATCGATATCCCAATTGCTTCAAACAACC
66 TGATATCTCTCTCGAAATCGATATCCCAATTGCTTCAAACAACC
246372 ACCAATCC-AATGATTATTTTAACTTGGTTCAACCGGTTTGTATTAGTTTGTGGGTCAATTGGTC
1 ACCAATCCAAATGATTATTTTAACTTGGTTCAACCGGTTTGTATTAGTTTGTGGGTCAATTGGTC
246436 TGATATCTCTCTCGAAATCGATATCCCAATTGCTTCAAACAACC
66 TGATATCTCTCTCGAAATCGATATCCCAATTGCTTCAAACAACC
246480 A
1 A
246481 TGGTTGTAAG
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 101 0.93
109 8 0.07
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (109 bp):
ACCAATCCAAATGATTATTTTAACTTGGTTCAACCGGTTTGTATTAGTTTGTGGGTCAATTGGTC
TGATATCTCTCTCGAAATCGATATCCCAATTGCTTCAAACAACC
Found at i:255544 original size:14 final size:14
Alignment explanation
Indices: 255521--255551 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
255511 CTGACAATTC
*
255521 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
255535 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
255549 TTA
1 TTA
255552 AAATAATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:262661 original size:31 final size:30
Alignment explanation
Indices: 262616--262711 Score: 156
Period size: 30 Copynumber: 3.2 Consensus size: 30
262606 AGTCGATAGG
*
262616 TATATTCTTTTTGTTTACTAATGTAGTGCA
1 TATATTCTTTTTGTTTACTAATGTAATGCA
*
262646 TATATTCTTTTTTGTTTACTAATGTATTGCA
1 TATATTC-TTTTTGTTTACTAATGTAATGCA
*
262677 TATATTATTTTTGTTTACTAATGTAATGCA
1 TATATTCTTTTTGTTTACTAATGTAATGCA
262707 TATAT
1 TATAT
262712 AATAATGTGT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
30 34 0.55
31 28 0.45
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.55
Consensus pattern (30 bp):
TATATTCTTTTTGTTTACTAATGTAATGCA
Found at i:270527 original size:162 final size:161
Alignment explanation
Indices: 270145--270537 Score: 547
Period size: 161 Copynumber: 2.4 Consensus size: 161
270135 GCTCCCAATT
* * *
270145 GGAAGTGTCAGACATAAACCTCCAAAGTTTAAGGGAAGTAGAAGTTAGAAACTACAATAATTTGA
1 GGAAGTGTCAAACATAAGCCTCCAAAGTTTAAGGGAAGTAGAAGTTAGAAACTGCAATAATTTGA
* * * * *
270210 GGTATCCCTTCCCAATGGCTATTTCTAATAGCCTTGGGAGATTGCAAGCTTTGAAGATATGAGAC
66 GGTATCCCTTCCCAATGGCTATTGCTAATAGCCTTAGGAGATTGCAAACTCTGAAGATAAGAGAC
270275 TGCTCCCAATTGAAAGAACAATCCAAGGCTC
131 TGCTCCCAATTGAAAGAACAATCCAAGGCTC
** * *
270306 AAAAGTGTCAAACATAAGCCTCCAAAGTTTAAGGGAAGTAGAAGTCAGAAACGGCAATAATTTGA
1 GGAAGTGTCAAACATAAGCCTCCAAAGTTTAAGGGAAGTAGAAGTTAGAAACTGCAATAATTTGA
* * * * * * *
270371 TGTATCTCTTCCCAATGTCTATTGCTAATAGCCTTAGGAGGTTGCAAACTCTGCAGATAAGTGAT
66 GGTATCCCTTCCCAATGGCTATTGCTAATAGCCTTAGGAGATTGCAAACTCTGAAGATAAGAGAC
* *
270436 TGCTCCCAATT-AGAAGAAATAATCCAAGGTTC
131 TGCTCCCAATTGA-AAG-AACAATCCAAGGCTC
*
270468 GGAAGTGTCAAACATAAGCCTCCAAAGTTTAAGGGAAGTAAAAGTT-GAAAACTGCAATAATTTG
1 GGAAGTGTCAAACATAAGCCTCCAAAGTTTAAGGGAAGTAGAAGTTAG-AAACTGCAATAATTTG
270532 AGGTAT
65 AGGTAT
270538 TGGGGGATTG
Statistics
Matches: 202, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
160 1 0.00
161 126 0.62
162 75 0.37
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (161 bp):
GGAAGTGTCAAACATAAGCCTCCAAAGTTTAAGGGAAGTAGAAGTTAGAAACTGCAATAATTTGA
GGTATCCCTTCCCAATGGCTATTGCTAATAGCCTTAGGAGATTGCAAACTCTGAAGATAAGAGAC
TGCTCCCAATTGAAAGAACAATCCAAGGCTC
Found at i:272403 original size:14 final size:14
Alignment explanation
Indices: 272384--272422 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
272374 TTGTTTCACT
* *
272384 GAAAATGGCTTCTG
1 GAAAATGACTTCTA
*
272398 GAAAATGATTTCTA
1 GAAAATGACTTCTA
272412 GAAAATGACTT
1 GAAAATGACTT
272423 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (14 bp):
GAAAATGACTTCTA
Found at i:272751 original size:13 final size:13
Alignment explanation
Indices: 272735--272764 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
272725 AACAAAATTG
272735 ACAAAAAAAATCA
1 ACAAAAAAAATCA
*
272748 ACAAAAAAAATGA
1 ACAAAAAAAATCA
272761 ACAA
1 ACAA
272765 TATCAGCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.13, G:0.03, T:0.07
Consensus pattern (13 bp):
ACAAAAAAAATCA
Found at i:273538 original size:43 final size:43
Alignment explanation
Indices: 273477--273698 Score: 225
Period size: 43 Copynumber: 5.1 Consensus size: 43
273467 AAAAAACATA
*
273477 GCTAAAGACCATGACATTTAGCGGCGCCTTTATCACAAACGCC
1 GCTAAAGACCATGACATTTAGCGGCGCTTTTATCACAAACGCC
* *
273520 GCTAAAGACCATGACATTTAGCAGCGCTTTTATCATAATCATAAACACC
1 GCTAAAGACCATGACATTTAGCGGCGCTTTTATC---A-C--AAACGCC
* * *
273569 GTTAAAGACCATGACCTTT--CGACGCTTTTATCACAAACGCC
1 GCTAAAGACCATGACATTTAGCGGCGCTTTTATCACAAACGCC
* * * ** *
273610 ACTAAAAACCATGACATTTAGCGACGCTTTGGTCACAAAC-AC
1 GCTAAAGACCATGACATTTAGCGGCGCTTTTATCACAAACGCC
* * * *
273652 ACTAAAGAACATGACTTTTAGCGGCGCTTTTGTCACAAACGCC
1 GCTAAAGACCATGACATTTAGCGGCGCTTTTATCACAAACGCC
273695 GCTA
1 GCTA
273699 TATAACAAGC
Statistics
Matches: 148, Mismatches: 22, Indels: 18
0.79 0.12 0.10
Matches are distributed among these distances:
41 21 0.14
42 36 0.24
43 54 0.36
44 1 0.01
46 1 0.01
47 12 0.08
49 23 0.16
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (43 bp):
GCTAAAGACCATGACATTTAGCGGCGCTTTTATCACAAACGCC
Found at i:274156 original size:43 final size:43
Alignment explanation
Indices: 274109--274306 Score: 242
Period size: 43 Copynumber: 4.7 Consensus size: 43
274099 AAAAAAAGGT
*
274109 CGCTAAAGACCATGACCTTTAGTGGCGCTTTTATCACAAACGC
1 CGCTAAAGACCATGACCTTTAGCGGCGCTTTTATCACAAACGC
* * * *
274152 CGCTAAAGACAATGACTTTTAGCGGTGCTTTTATCATAAACGC
1 CGCTAAAGACCATGACCTTTAGCGGCGCTTTTATCACAAACGC
* *
274195 CGC-AAA-A-GATGACCTTTAGCGACGCTTTTATCACAAACGC
1 CGCTAAAGACCATGACCTTTAGCGGCGCTTTTATCACAAACGC
* * *
274235 CGCTAAAGACCATGACTTTTAGCGGCGCTTTTGTCACAAACGT
1 CGCTAAAGACCATGACCTTTAGCGGCGCTTTTATCACAAACGC
* * * *
274278 CGCTATAGAACA-AACCTTTAGTGGCGCTT
1 CGCTAAAGACCATGACCTTTAGCGGCGCTT
274307 CTCACAAAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
40 31 0.23
41 4 0.03
42 18 0.14
43 79 0.60
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (43 bp):
CGCTAAAGACCATGACCTTTAGCGGCGCTTTTATCACAAACGC
Found at i:274223 original size:83 final size:83
Alignment explanation
Indices: 274120--274276 Score: 260
Period size: 83 Copynumber: 1.9 Consensus size: 83
274110 GCTAAAGACC
* * *
274120 ATGACCTTTAGTGGCGCTTTTATCACAAACGCCGCTAAAGACAATGACTTTTAGCGGTGCTTTTA
1 ATGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAAAGACAATGACTTTTAGCGGCGCTTTTA
*
274185 TCATAAACGCCGCAAAAG
66 TCACAAACGCCGCAAAAG
* *
274203 ATGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAAAGACCATGACTTTTAGCGGCGCTTTTG
1 ATGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAAAGACAATGACTTTTAGCGGCGCTTTTA
274268 TCACAAACG
66 TCACAAACG
274277 TCGCTATAGA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 68 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (83 bp):
ATGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAAAGACAATGACTTTTAGCGGCGCTTTTA
TCACAAACGCCGCAAAAG
Found at i:274324 original size:83 final size:82
Alignment explanation
Indices: 274123--274314 Score: 235
Period size: 83 Copynumber: 2.3 Consensus size: 82
274113 AAAGACCATG
*
274123 ACCTTTAGTGGCGCTTTTATCACAAACGCCGCTAAAGACAATGACTTTTAGCGGTGCTTTTATCA
1 ACCTTTAGTGGCGC-TTTATCACAAACGCCGCTAAAGACAATGACTTTTAGCGGCGCTTTTATCA
* * *
274188 TAAACGCCGCAAAAGATG
65 CAAACGCCGCAAAACATA
* * * *
274206 ACCTTTAGCGACGCTTTTATCACAAACGCCGCTAAAGACCATGACTTTTAGCGGCGCTTTTGTCA
1 ACCTTTAGTGGCGC-TTTATCACAAACGCCGCTAAAGACAATGACTTTTAGCGGCGCTTTTATCA
*
274271 CAAACGTCGCTATAGAACA-A
65 CAAACGCCGC-A-A-AACATA
*
274291 ACCTTTAGTGGCGC-TTCTCACAAA
1 ACCTTTAGTGGCGCTTTATCACAAA
274315 AACTGCTAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
83 77 0.82
84 1 0.01
85 13 0.14
86 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (82 bp):
ACCTTTAGTGGCGCTTTATCACAAACGCCGCTAAAGACAATGACTTTTAGCGGCGCTTTTATCAC
AAACGCCGCAAAACATA
Found at i:274915 original size:18 final size:18
Alignment explanation
Indices: 274877--274912 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
274867 TTATTATTTT
*
274877 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
274895 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
274913 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:275910 original size:43 final size:43
Alignment explanation
Indices: 275844--275934 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
275834 CACATTGCAA
* * *
275844 GGTAATAAATAATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAATAATACAATACATTTACTTAATCAAGAAAATCTT
*
275887 GGTAATAAA-AGATATAATACATTTACTTAATCAAGAAAATCTT
1 GGTAATAAATA-ATACAATACATTTACTTAATCAAGAAAATCTT
275930 -GTAAT
1 GGTAAT
275935 GAACTCATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 6 0.14
43 37 0.86
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (43 bp):
GGTAATAAATAATACAATACATTTACTTAATCAAGAAAATCTT
Found at i:275947 original size:14 final size:14
Alignment explanation
Indices: 275928--275955 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
275918 CAAGAAAATC
275928 TTGTAATGAACTCA
1 TTGTAATGAACTCA
275942 TTGTAATGAACTCA
1 TTGTAATGAACTCA
275956 AAGCAATGAG
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:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
TTGTAATGAACTCA
Found at i:279693 original size:19 final size:19
Alignment explanation
Indices: 279669--279729 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 19
279659 ACTAATGAAT
279669 AATTTAAAAATTATAAAAA
1 AATTTAAAAATTATAAAAA
*
279688 AATTTAAAAA-TAAAAATAA
1 AATTTAAAAATTATAAA-AA
279707 AAGTTTATAAGTAATTATAAAAA
1 AA-TTTA-AA--AATTATAAAAA
279730 TTAGCATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 5 0.15
19 14 0.41
20 4 0.12
21 2 0.06
23 4 0.12
24 5 0.15
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
AATTTAAAAATTATAAAAA
Done.