Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015326.1 Kokia drynarioides strain JFW-HI SEQ_130372, whole genome shotgun sequence
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: 219308
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 129 characters in sequence are not A, C, G, or T
Found at i:54 original size:10 final size:11
Alignment explanation
Indices: 24--64 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
14 TTATATTTAA
24 AAAATAATTTT
1 AAAATAATTTT
*
35 AAATTAATTTT
1 AAAATAATTTT
46 AAAAT-ATTTT
1 AAAATAATTTT
*
56 AAAAAAATT
1 AAAATAATT
65 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:64 original size:21 final size:22
Alignment explanation
Indices: 24--64 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
14 TTATATTTAA
**
24 AAAATAATTTTAAATTAATTTT
1 AAAATAATTTTAAAAAAATTTT
46 AAAAT-ATTTTAAAAAAATT
1 AAAATAATTTTAAAAAAATT
65 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATAATTTTAAAAAAATTTT
Found at i:88 original size:18 final size:16
Alignment explanation
Indices: 51--89 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
41 ATTTTAAAAT
*
51 ATTTTAAAAAAATTAT
1 ATTTTAAAAAAATTAA
67 ATTTTAAAAAATAATTAA
1 ATTTT-AAAAA-AATTAA
85 ATTTT
1 ATTTT
90 GTTGACGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 5 0.25
18 10 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTTAAAAAAATTAA
Found at i:2412 original size:32 final size:32
Alignment explanation
Indices: 2376--2439 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2366 ATTGTCGAGT
2376 TTGTCTTTGCTCAACAAATGACCCTTCACATC
1 TTGTCTTTGCTCAACAAATGACCCTTCACATC
2408 TTGTCTTTGCTCAACAAATGACCCTTCACATC
1 TTGTCTTTGCTCAACAAATGACCCTTCACATC
2440 CTCGAACGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.31, G:0.09, T:0.34
Consensus pattern (32 bp):
TTGTCTTTGCTCAACAAATGACCCTTCACATC
Found at i:3089 original size:15 final size:13
Alignment explanation
Indices: 3057--3083 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3047 ATAAATTGAG
3057 AAATTGAACACAC
1 AAATTGAACACAC
3070 AAATTGAACACAC
1 AAATTGAACACAC
3083 A
1 A
3084 TCAATTTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (13 bp):
AAATTGAACACAC
Found at i:5790 original size:26 final size:26
Alignment explanation
Indices: 5761--5812 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
5751 ATATAGGAAT
5761 CAAACAAGGTTAATGATAACTGCAAA
1 CAAACAAGGTTAATGATAACTGCAAA
*
5787 CAAACAAGGTTAATGATAAGTGCAAA
1 CAAACAAGGTTAATGATAACTGCAAA
5813 AGTAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.19
Consensus pattern (26 bp):
CAAACAAGGTTAATGATAACTGCAAA
Found at i:6607 original size:35 final size:34
Alignment explanation
Indices: 6563--6671 Score: 90
Period size: 33 Copynumber: 3.4 Consensus size: 34
6553 TAAATACTTA
6563 GATTT-TATTCTCAATTATGAGTGCTTAATTCTT
1 GATTTATATTCTCAATTATGAGTGCTTAATTCTT
*** * *
6596 GATTTA-ATAT-TC--TTA--AGCAATAAATACTT
1 GATTTATAT-TCTCAATTATGAGTGCTTAATTCTT
6625 AGATTT-TATTCTCAATTATGAGTGCTTAATTCTT
1 -GATTTATATTCTCAATTATGAGTGCTTAATTCTT
6659 GATTTAGTATTCT
1 GATTTA-TATTCT
6672 TAAGATATTA
Statistics
Matches: 55, Mismatches: 10, Indels: 20
0.65 0.12 0.24
Matches are distributed among these distances:
29 10 0.18
30 9 0.16
31 3 0.05
32 3 0.05
33 14 0.25
34 10 0.18
35 6 0.11
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (34 bp):
GATTTATATTCTCAATTATGAGTGCTTAATTCTT
Found at i:6618 original size:63 final size:63
Alignment explanation
Indices: 6532--6675 Score: 245
Period size: 63 Copynumber: 2.3 Consensus size: 63
6522 ATTCTGTCAT
** *
6532 TTGATTTTTTATT-TTACGCAATAAATACTTAGATTTTATTCTCAATTATGAGTGCTTAATTC
1 TTGATTTAATATTCTTAAGCAATAAATACTTAGATTTTATTCTCAATTATGAGTGCTTAATTC
6594 TTGATTTAATATTCTTAAGCAATAAATACTTAGATTTTATTCTCAATTATGAGTGCTTAATTC
1 TTGATTTAATATTCTTAAGCAATAAATACTTAGATTTTATTCTCAATTATGAGTGCTTAATTC
*
6657 TTGATTTAGTATTCTTAAG
1 TTGATTTAATATTCTTAAG
6676 ATATTAATTC
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
62 11 0.14
63 66 0.86
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (63 bp):
TTGATTTAATATTCTTAAGCAATAAATACTTAGATTTTATTCTCAATTATGAGTGCTTAATTC
Found at i:13026 original size:27 final size:28
Alignment explanation
Indices: 12996--13057 Score: 92
Period size: 27 Copynumber: 2.2 Consensus size: 28
12986 AGAAAAGTGT
*
12996 AAAAAAAT-TAAAAATTATTATAAA-TG
1 AAAAAAATATAAAAATTATTAAAAATTG
13022 AAAAAAATATAAAAATTATTAAAAATTG
1 AAAAAAATATAAAAATTATTAAAAATTG
13050 CAAAAAAA
1 -AAAAAAA
13058 GCAGTTTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 8 0.25
27 15 0.47
28 2 0.06
29 7 0.22
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (28 bp):
AAAAAAATATAAAAATTATTAAAAATTG
Found at i:13102 original size:28 final size:29
Alignment explanation
Indices: 13062--13126 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
13052 AAAAAAGCAG
**
13062 TTTCTATAATTTTTGTAA-TTTTAATGAT
1 TTTCTATAATTTTTAAAATTTTTAATGAT
*
13090 TTTCTATAATTTTTAAAATTTTTAATGCT
1 TTTCTATAATTTTTAAAATTTTTAATGAT
*
13119 TTTATATA
1 TTTCTATA
13127 TAAAACTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.50
29 16 0.50
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (29 bp):
TTTCTATAATTTTTAAAATTTTTAATGAT
Found at i:13178 original size:3 final size:3
Alignment explanation
Indices: 13170--13198 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
13160 TCACATGCAA
13170 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
13199 AAGACAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16307 original size:21 final size:21
Alignment explanation
Indices: 16283--16323 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16273 TTGTTATCCT
16283 TGCTGTCA-ATGGCAATGGCAA
1 TGCTG-CACATGGCAATGGCAA
*
16304 TGCTGCACATGGCATTGGCA
1 TGCTGCACATGGCAATGGCA
16324 CTGGCACTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (21 bp):
TGCTGCACATGGCAATGGCAA
Found at i:35070 original size:31 final size:31
Alignment explanation
Indices: 35033--35093 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
35023 ATGATTATTG
*
35033 AATTATTTAAAAGTTTTCATTTAAGTCATTA
1 AATTATTTAAAAGTTTTCATTCAAGTCATTA
* *
35064 AATTATTTGAAAGTTTTTATTCAAGTCATT
1 AATTATTTAAAAGTTTTCATTCAAGTCATT
35094 GGAAGATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (31 bp):
AATTATTTAAAAGTTTTCATTCAAGTCATTA
Found at i:36779 original size:24 final size:25
Alignment explanation
Indices: 36739--36796 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
36729 TAAAGACAAT
*
36739 ATATACATAACATATAATA-AAATA
1 ATATACATAACATATAAAATAAATA
*
36763 ATATACAT-ATATGATAAAATAAATA
1 ATATACATAACAT-ATAAAATAAATA
*
36788 A-ATAAATAA
1 ATATACATAA
36797 AATCAGGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 3 0.11
24 18 0.64
25 7 0.25
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (25 bp):
ATATACATAACATATAAAATAAATA
Found at i:36887 original size:30 final size:30
Alignment explanation
Indices: 36846--37009 Score: 161
Period size: 30 Copynumber: 5.5 Consensus size: 30
36836 AAATCAAAAG
* *
36846 TTTTGGAAAATTTGGGGGTCAAATTGGAAT
1 TTTTTGAAAATTTAGGGGTCAAATTGGAAT
* *** *
36876 TTTTTGGAAATTTAGTACT-AAATTCGAAT
1 TTTTTGAAAATTTAGGGGTCAAATTGGAAT
* *
36905 TTTTTGGAAAATTTAGGAGTCAAATTTGAAT
1 TTTTT-GAAAATTTAGGGGTCAAATTGGAAT
*
36936 TTTTAT-AAAATTTACGGGTCAAATTGGAAT
1 TTTT-TGAAAATTTAGGGGTCAAATTGGAAT
** * *
36966 TTTTAAAAAATTTAGGGCTCAAATTAGAAT
1 TTTTTGAAAATTTAGGGGTCAAATTGGAAT
*
36996 TTTTAGAAAATTTA
1 TTTTTGAAAATTTA
37010 AGGTTAAAAC
Statistics
Matches: 111, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
29 14 0.13
30 83 0.75
31 13 0.12
32 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.41
Consensus pattern (30 bp):
TTTTTGAAAATTTAGGGGTCAAATTGGAAT
Found at i:37956 original size:16 final size:16
Alignment explanation
Indices: 37928--37969 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
37918 GGTTTGTATA
37928 TATTT-TTTAATTTTAT
1 TATTTATTT-ATTTTAT
*
37944 TATTTATTTATTTTTT
1 TATTTATTTATTTTAT
37960 TATTTATTTA
1 TATTTATTTA
37970 ATTAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTTATTTATTTTAT
Found at i:37994 original size:14 final size:14
Alignment explanation
Indices: 37977--38003 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
37967 TTAATTAATA
37977 AATAATAATAAAAT
1 AATAATAATAAAAT
37991 AATAATAATAAAA
1 AATAATAATAAAA
38004 ATTTTGGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:38470 original size:45 final size:45
Alignment explanation
Indices: 38406--38507 Score: 168
Period size: 45 Copynumber: 2.3 Consensus size: 45
38396 TTCTTGTAGC
38406 TTCAATTTGCCCCTCTATAGCTTTAGGGGTAAAAGATTGAATTGT
1 TTCAATTTGCCCCTCTATAGCTTTAGGGGTAAAAGATTGAATTGT
* * * *
38451 TTCAATTTGTCCTTCTATAGCTTTAGGGGTAAAAGGTTGGATTGT
1 TTCAATTTGCCCCTCTATAGCTTTAGGGGTAAAAGATTGAATTGT
38496 TTCAATTTGCCC
1 TTCAATTTGCCC
38508 TAAGGTCGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (45 bp):
TTCAATTTGCCCCTCTATAGCTTTAGGGGTAAAAGATTGAATTGT
Found at i:38638 original size:50 final size:50
Alignment explanation
Indices: 38584--38691 Score: 112
Period size: 50 Copynumber: 2.2 Consensus size: 50
38574 GTCCTTATGA
* * *
38584 CTTCAATCTGATCCTCTATAGCTTTAGGTGA-ATGAGATTCT-CCATTGCGG
1 CTTCAATCTGACCCTCTACAGCTTTACGT-ATATGAGATT-TGCCATTGCGG
* ** *
38634 CTTCATTCTTCCCCTTTACAGCTTTACGTATATGAGATTTGCCATTGCGG
1 CTTCAATCTGACCCTCTACAGCTTTACGTATATGAGATTTGCCATTGCGG
*
38684 CATCAATC
1 CTTCAATC
38692 CATTCTTCTA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
49 2 0.04
50 45 0.96
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (50 bp):
CTTCAATCTGACCCTCTACAGCTTTACGTATATGAGATTTGCCATTGCGG
Found at i:38822 original size:40 final size:40
Alignment explanation
Indices: 38759--38888 Score: 165
Period size: 39 Copynumber: 3.3 Consensus size: 40
38749 TATAACTTTA
38759 GGGGTAAAAGAT-TAGATTGCTTCAATCTGCCCCATGGTC
1 GGGGTAAAAGATCTAGATTGCTTCAATCTGCCCCATGGTC
* * * * *
38798 GGGGTAAGAGATCTAGATTACTTCAATCTACCCTATGGTT
1 GGGGTAAAAGATCTAGATTGCTTCAATCTGCCCCATGGTC
* * *
38838 AGGGTAAAAGATCT-GATGGCTTTAATCTGCCCCATGGTC
1 GGGGTAAAAGATCTAGATTGCTTCAATCTGCCCCATGGTC
*
38877 GAGGTAAAAGAT
1 GGGGTAAAAGAT
38889 TCGAAGTTGT
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 40 0.53
40 35 0.47
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (40 bp):
GGGGTAAAAGATCTAGATTGCTTCAATCTGCCCCATGGTC
Found at i:45239 original size:17 final size:17
Alignment explanation
Indices: 45219--45304 Score: 111
Period size: 17 Copynumber: 5.1 Consensus size: 17
45209 CCAATTTTAA
45219 ATTTTAAAATTTAAA-TT
1 ATTTT-AAATTTAAATTT
*
45236 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
* *
45253 ATTTTAAATTAAAACTT
1 ATTTTAAATTTAAATTT
* *
45270 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
45287 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
45304 A
1 A
45305 ATTAAAAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
16 8 0.14
17 50 0.86
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:45272 original size:34 final size:33
Alignment explanation
Indices: 45219--45302 Score: 123
Period size: 34 Copynumber: 2.5 Consensus size: 33
45209 CCAATTTTAA
*
45219 ATTTTAAAATTTAAATTATTTTAAGTTTAAATTT
1 ATTTT-AAATTAAAATTATTTTAAGTTTAAATTT
*
45253 ATTTTAAATTAAAACTTATTTTGAGTTTAAATTT
1 ATTTTAAATTAAAA-TTATTTTAAGTTTAAATTT
*
45287 ATTTTAAATTTAAATT
1 ATTTTAAATTAAAATT
45303 TAATTAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 10 0.22
34 36 0.78
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (33 bp):
ATTTTAAATTAAAATTATTTTAAGTTTAAATTT
Found at i:45307 original size:5 final size:6
Alignment explanation
Indices: 45214--45305 Score: 50
Period size: 6 Copynumber: 15.8 Consensus size: 6
45204 TGAACCCAAT
* * *
45214 TTTAAA TTTTAAAA TTTAAA -TT-AT TTTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA -TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * *
45261 TTAAAA CTT-AT TTTGAG TTTAAA TTT-AT TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
45306 TTAAAAAAAA
Statistics
Matches: 64, Mismatches: 15, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
4 1 0.02
5 15 0.23
6 39 0.61
7 6 0.09
8 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:49107 original size:124 final size:125
Alignment explanation
Indices: 48886--49130 Score: 422
Period size: 124 Copynumber: 2.0 Consensus size: 125
48876 TCATATCTTG
*
48886 TTGCACCTTCGTTAATTTTTCATGCAGCTGATCCTGCATTTCCTTTTGCATTTGCTCCAACCTTT
1 TTGCACCTTCGTTAATTGTTCATGCAGCTGATCCTGCATTTCCTTTTGCATTTGCTCCAACCTTT
*
48951 CCAATTGCTGATTCATCGCTCTTGTCTTGGCACGAGTGTAATAACGAAGTGGTTTTGCAT
66 CCAATCGCTGATTCATCGCTCTTGTCTTGGCACGAGTGTAATAACGAAGTGGTTTTGCAT
*
49011 TTGCACCTTCGTTAATTGTTCATGCAGCTGAT-CTGCATTTCCTTTTGCATTTGCTCTAACCTTT
1 TTGCACCTTCGTTAATTGTTCATGCAGCTGATCCTGCATTTCCTTTTGCATTTGCTCCAACCTTT
* *
49075 CCAATCGCTGA-TCTATCGCTCTTGTCTTGGCACGAGTGTAGTAACGGAGTGGTTTT
66 CCAATCGCTGATTC-ATCGCTCTTGTCTTGGCACGAGTGTAATAACGAAGTGGTTTT
49131 TCCAGAGTAA
Statistics
Matches: 114, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
123 2 0.02
124 81 0.71
125 31 0.27
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.40
Consensus pattern (125 bp):
TTGCACCTTCGTTAATTGTTCATGCAGCTGATCCTGCATTTCCTTTTGCATTTGCTCCAACCTTT
CCAATCGCTGATTCATCGCTCTTGTCTTGGCACGAGTGTAATAACGAAGTGGTTTTGCAT
Found at i:52810 original size:30 final size:30
Alignment explanation
Indices: 52745--52988 Score: 203
Period size: 29 Copynumber: 8.3 Consensus size: 30
52735 AAATAAAATC
* * ** *
52745 GGGTCAAACTTGAATTTTTAGAAGCTCTA-
1 GGGTCAAATTTGAATTTTTTGAAAATTTAG
* * *
52774 GGGTCAAATTAGAAGTTTTGGAAAATTTAG
1 GGGTCAAATTTGAATTTTTTGAAAATTTAG
* *
52804 GGGTCAAATTAGAATTTTTTGAAAATTTAA
1 GGGTCAAATTTGAATTTTTTGAAAATTTAG
* **
52834 GGCT-AAATTTGAATTTTTAAAAAATTTAG
1 GGGTCAAATTTGAATTTTTTGAAAATTTAG
* * *
52863 GGGTTAATTTTGAA-TTTTTGGAAATTT-G
1 GGGTCAAATTTGAATTTTTTGAAAATTTAG
* * *
52891 GGGTTCAAAATTAAAATTTTTGAGAAATTTAG
1 GGG-TCAAATTTGAATTTTTTGA-AAATTTAG
* * *
52923 GGGTTAAATTTGAATTTTTAGAAAAATT-G
1 GGGTCAAATTTGAATTTTTTGAAAATTTAG
* *
52952 GAGTCAAATTTGAA-TTTTTAAAAATTTAG
1 GGGTCAAATTTGAATTTTTTGAAAATTTAG
*
52981 AGGTCAAA
1 GGGTCAAA
52989 ACATGATTTT
Statistics
Matches: 170, Mismatches: 38, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
28 14 0.08
29 83 0.49
30 49 0.29
31 20 0.12
32 4 0.02
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTTGAAAATTTAG
Found at i:52988 original size:89 final size:89
Alignment explanation
Indices: 52754--52989 Score: 250
Period size: 89 Copynumber: 2.7 Consensus size: 89
52744 CGGGTCAAAC
* ** * * *
52754 TTGAATTTTTAGAAGCTCTAGG-GTCAAATTAGAAGTTTTGGAAAATTTAGGGGTC-AAATTAGA
1 TTGAATTTTTAAAAAATTTAGGAGTCAAATTTGAA-TTTTTGAAAATTTAGGGGTCAAAATTAGA
*
52817 ATTTTTTGAAAATTTAAGGCTAAAT
65 AATTTTTGAAAATTTAAGGCTAAAT
* * * *
52842 TTGAATTTTTAAAAAATTTAGGGGTTAATTTTGAATTTTTGGAAATTT-GGGGTTCAAAATTA-A
1 TTGAATTTTTAAAAAATTTAGGAGTCAAATTTGAATTTTTGAAAATTTAGGGG-TCAAAATTAGA
* *
52905 AATTTTTGAGAAATTTAGGGGTTAAAT
65 AATTTTTGA-AAATTTA-AGGCTAAAT
* *
52932 TTGAATTTTTAGAAAAA-TT-GGAGTCAAATTTGAATTTTTAAAAATTTAGAGGTCAAAA
1 TTGAATTTTTA-AAAAATTTAGGAGTCAAATTTGAATTTTTGAAAATTTAGGGGTCAAAA
52990 CATGATTTTA
Statistics
Matches: 123, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
87 4 0.03
88 40 0.33
89 51 0.41
90 23 0.19
91 5 0.04
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40
Consensus pattern (89 bp):
TTGAATTTTTAAAAAATTTAGGAGTCAAATTTGAATTTTTGAAAATTTAGGGGTCAAAATTAGAA
ATTTTTGAAAATTTAAGGCTAAAT
Found at i:59825 original size:30 final size:29
Alignment explanation
Indices: 59791--59853 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
59781 ATATTAAAAC
*
59791 TATACATAAAGTTCGATTTAATGTGCATGT
1 TATACATAAACTTCGATTTAATGTG-ATGT
* * * *
59821 TATACATGAACTTTGATTTTATGTGATTT
1 TATACATAAACTTCGATTTAATGTGATGT
59850 TATA
1 TATA
59854 TATGAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (29 bp):
TATACATAAACTTCGATTTAATGTGATGT
Found at i:64449 original size:15 final size:17
Alignment explanation
Indices: 64428--64469 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
64418 TAAACTTTTA
64428 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
64444 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
64460 AAAATTATAA
1 AAAATTATAA
64470 TTTTATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 2 0.09
17 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:64461 original size:24 final size:23
Alignment explanation
Indices: 64418--64490 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 23
64408 AAATATAATT
*
64418 TAAACTTTTAAAAATTATAAAAATA
1 TAAA-TTTT-AAAATCATAAAAATA
* *
64443 TAAATTATTAAAATGATAAAATTA
1 TAAATT-TTAAAATCATAAAAATA
**
64467 T-AATTTTATTATCATAAAAATA
1 TAAATTTTAAAATCATAAAAATA
64489 TA
1 TA
64491 CGATTAATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
22 14 0.35
23 4 0.10
24 16 0.40
25 6 0.15
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (23 bp):
TAAATTTTAAAATCATAAAAATA
Found at i:64490 original size:22 final size:23
Alignment explanation
Indices: 64428--64490 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
64418 TAAACTTTTA
*
64428 AAAATTATAAAAATATAAATTATT
1 AAAATCATAAAAATAT-AATTATT
* *
64452 AAAATGATAAAATTATAATT-TT
1 AAAATCATAAAAATATAATTATT
**
64474 ATTATCATAAAAATATA
1 AAAATCATAAAAATATA
64491 CGATTAATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 15 0.45
23 4 0.12
24 14 0.42
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAATCATAAAAATATAATTATT
Found at i:68385 original size:15 final size:16
Alignment explanation
Indices: 68345--68377 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
68335 CTAATTTAAA
*
68345 TAAAATAAATGTAATT
1 TAAAAAAAATGTAATT
68361 TAAAAAAAAT-TAATT
1 TAAAAAAAATGTAATT
68376 TA
1 TA
68378 GTAAAAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TAAAAAAAATGTAATT
Found at i:69811 original size:110 final size:111
Alignment explanation
Indices: 69639--69861 Score: 412
Period size: 110 Copynumber: 2.0 Consensus size: 111
69629 TGGAAATTAA
*
69639 AAAAATATAACCACTAAGAATGATCAAATTAATGAACGTAGATTAAATTTATAACTTTACACATA
1 AAAAATATAACCACTAAGAATGATCAAATTAATGAACGTAGATTAAATCTATAACTTTACACATA
69704 ATACAATAATAATAACATAATTTAATCAAATATATTTAACTGTTAT
66 ATACAATAATAATAACATAATTTAATCAAATATATTTAACTGTTAT
* *
69750 AAAAATATAACCACTAAGAATGATC-TATTAGTGAACGTAGATTAAATCTATAACTTTACACATA
1 AAAAATATAACCACTAAGAATGATCAAATTAATGAACGTAGATTAAATCTATAACTTTACACATA
69814 ATACAATAATAATAACATAATTTAATCAAATATATTTAACTGTTAT
66 ATACAATAATAATAACATAATTTAATCAAATATATTTAACTGTTAT
69860 AA
1 AA
69862 TTGAGTCTGA
Statistics
Matches: 109, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
110 84 0.77
111 25 0.23
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (111 bp):
AAAAATATAACCACTAAGAATGATCAAATTAATGAACGTAGATTAAATCTATAACTTTACACATA
ATACAATAATAATAACATAATTTAATCAAATATATTTAACTGTTAT
Found at i:70203 original size:17 final size:15
Alignment explanation
Indices: 70181--70214 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
70171 TTCATACTAT
70181 TTCATTTTCATTATAAA
1 TTCATTTTC-TTA-AAA
70198 TTCATTTTCTTAAAA
1 TTCATTTTCTTAAAA
70213 TT
1 TT
70215 AAATAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 3 0.18
17 9 0.53
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (15 bp):
TTCATTTTCTTAAAA
Found at i:75766 original size:6 final size:6
Alignment explanation
Indices: 75752--75832 Score: 64
Period size: 6 Copynumber: 14.0 Consensus size: 6
75742 TTTAATTTAT
* * *
75752 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
75798 TTT-AA TGTAAA TTTAAA TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
75833 AGTCCAAAAC
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
4 2 0.03
5 14 0.24
6 37 0.63
7 6 0.10
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:75768 original size:17 final size:17
Alignment explanation
Indices: 75745--75832 Score: 95
Period size: 17 Copynumber: 5.1 Consensus size: 17
75735 ATTGTTTTTT
75745 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
75762 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* * *
75779 AATTAATCTTAAAATTA
1 AATTTATTTTAAATTTA
* *
75796 AATTTAATGTAAATTTA
1 AATTTATTTTAAATTTA
* *
75813 AATTTAATTTCAAAATTA
1 AATTT-ATTTTAAATTTA
75831 AA
1 AA
75833 AGTCCAAAAC
Statistics
Matches: 56, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
17 46 0.82
18 10 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:75819 original size:23 final size:23
Alignment explanation
Indices: 75769--75819 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
75759 TTAGATTTAT
75769 TTTAAATTTAAATTAATCTTAAA
1 TTTAAATTTAAATTAATCTTAAA
*
75792 ATTAAATTT-AATGTAAAT-TTAAA
1 TTTAAATTTAAAT-T-AATCTTAAA
75815 TTTAA
1 TTTAA
75820 TTTCAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 3 0.12
23 18 0.75
24 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTAAATTTAAATTAATCTTAAA
Found at i:76657 original size:13 final size:13
Alignment explanation
Indices: 76639--76694 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
76629 TGATTTAAGT
76639 TATTATTAATTAA
1 TATTATTAATTAA
76652 TATTA-TAATATAA
1 TATTATTAAT-TAA
* * *
76665 TAGTATAAATTAT
1 TATTATTAATTAA
76678 TA-T-TTAATTAA
1 TATTATTAATTAA
76689 TATTAT
1 TATTAT
76695 CTTATTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
11 8 0.24
12 6 0.18
13 17 0.50
14 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
TATTATTAATTAA
Found at i:76941 original size:14 final size:14
Alignment explanation
Indices: 76922--76948 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
76912 GCTTAAACGA
76922 AAAAGGGAAGGAAG
1 AAAAGGGAAGGAAG
76936 AAAAGGGAAGGAA
1 AAAAGGGAAGGAA
76949 AAAGAAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AAAAGGGAAGGAAG
Found at i:77356 original size:17 final size:18
Alignment explanation
Indices: 77334--77367 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
77324 TAAATGAGTT
77334 AATTAGGAT-TAAATTGA
1 AATTAGGATATAAATTGA
*
77351 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
77368 GATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGA
Found at i:89953 original size:48 final size:48
Alignment explanation
Indices: 89898--89999 Score: 136
Period size: 48 Copynumber: 2.1 Consensus size: 48
89888 TCTTATTTTA
*
89898 TATTGAAACAAACCAATATTATTGCAATATTTA-GCAGTAAAAAATTGG
1 TATTGAAACAAACCAATATTATTGCAATA-TTAGGCAGTAAAAAATTAG
* * * *
89946 TATTGAAAGAAACCCATATTATTGTAATATTAGGTAGTAAAAAATTAG
1 TATTGAAACAAACCAATATTATTGCAATATTAGGCAGTAAAAAATTAG
89994 T-TTGAA
1 TATTGAA
90000 GCTCTAGAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
47 8 0.17
48 40 0.83
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (48 bp):
TATTGAAACAAACCAATATTATTGCAATATTAGGCAGTAAAAAATTAG
Found at i:91995 original size:162 final size:162
Alignment explanation
Indices: 91818--92142 Score: 596
Period size: 162 Copynumber: 2.0 Consensus size: 162
91808 CGATATATTA
91818 ATTATGAAGGGAATTAATTAAGGTTAATTAAATGGTTTATTAATTTAATCATAAAAGTCTTAAAA
1 ATTATGAAGGGAATTAATTAAGGTTAATTAAATGGTTTATTAATTTAATCATAAAAGTCTTAAAA
* * *
91883 TTTACAAGTTTGTCAGTGGGTATATATATGAATTAAAAGAAAGGAAAATGAATAGAATTCCTCTA
66 TTTACAAGTTTGCCAGTGGGTATATATATGAATTAAAAGAAAGAAAAATGAAAAGAATTCCTCTA
*
91948 ATTTTTCATCATCTTCTTCTTCATTCGGCTAG
131 ATTTTTCATCATCATCTTCTTCATTCGGCTAG
91980 ATTATGAAGGGAATTAATTAAGGTTAATTAAATGGTTTATTAATTTAATCATAAAAGTCTTAAAA
1 ATTATGAAGGGAATTAATTAAGGTTAATTAAATGGTTTATTAATTTAATCATAAAAGTCTTAAAA
*
92045 TTTACAAGTTTGCCATTGGGTATATATATGAATTAAAAGAAAGAAAAATGAAAAGAATTCCTCTA
66 TTTACAAGTTTGCCAGTGGGTATATATATGAATTAAAAGAAAGAAAAATGAAAAGAATTCCTCTA
*
92110 ATTTTTCATCATCATCTTCTTCATTCGGTTAG
131 ATTTTTCATCATCATCTTCTTCATTCGGCTAG
92142 A
1 A
92143 GGAAGAATAT
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
162 157 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (162 bp):
ATTATGAAGGGAATTAATTAAGGTTAATTAAATGGTTTATTAATTTAATCATAAAAGTCTTAAAA
TTTACAAGTTTGCCAGTGGGTATATATATGAATTAAAAGAAAGAAAAATGAAAAGAATTCCTCTA
ATTTTTCATCATCATCTTCTTCATTCGGCTAG
Found at i:92871 original size:17 final size:18
Alignment explanation
Indices: 92845--92925 Score: 83
Period size: 18 Copynumber: 4.5 Consensus size: 18
92835 AAGGAATAGA
92845 ATACTGGCTC-TTTGAGC
1 ATACTGGCTCATTTGAGC
*
92862 ATATTGGCTCATTTGAGC
1 ATACTGGCTCATTTGAGC
* **
92880 ATACTGGCTCGTAAGAGC
1 ATACTGGCTCATTTGAGC
* * *
92898 AATACTGGCTTATTAGAGT
1 -ATACTGGCTCATTTGAGC
92917 ATACTGGCT
1 ATACTGGCT
92926 TGTAAGAGCA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
17 9 0.17
18 30 0.57
19 14 0.26
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (18 bp):
ATACTGGCTCATTTGAGC
Found at i:92904 original size:19 final size:19
Alignment explanation
Indices: 92876--92968 Score: 84
Period size: 19 Copynumber: 5.0 Consensus size: 19
92866 TGGCTCATTT
92876 GAGC-ATACTGGCTCGTAA
1 GAGCAATACTGGCTCGTAA
** *
92894 GAGCAATACTGGCTTATTA
1 GAGCAATACTGGCTCGTAA
* *
92913 GAG-TATACTGGCTTGTAA
1 GAGCAATACTGGCTCGTAA
* *
92931 GAGCAATACTAGCTCGTTTA
1 GAGCAATACTGGCTCG-TAA
*
92951 -AGCACTACTGGCTCGTAA
1 GAGCAATACTGGCTCGTAA
92969 AAGATTTCTA
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
18 21 0.36
19 36 0.61
20 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (19 bp):
GAGCAATACTGGCTCGTAA
Found at i:92921 original size:37 final size:37
Alignment explanation
Indices: 92845--92968 Score: 128
Period size: 37 Copynumber: 3.4 Consensus size: 37
92835 AAGGAATAGA
** * *
92845 ATACTGGCTC-TTTGAGC-ATATTGGCTCATTTGAGC
1 ATACTGGCTCGTAAGAGCAATACTGGCTCATTAGAGC
* *
92880 ATACTGGCTCGTAAGAGCAATACTGGCTTATTAGAGT
1 ATACTGGCTCGTAAGAGCAATACTGGCTCATTAGAGC
* * *
92917 ATACTGGCTTGTAAGAGCAATACTAGCTCGTTTA-AGC
1 ATACTGGCTCGTAAGAGCAATACTGGCTC-ATTAGAGC
92954 ACTACTGGCTCGTAA
1 A-TACTGGCTCGTAA
92969 AAGATTTCTA
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
35 10 0.14
36 5 0.07
37 43 0.59
38 15 0.21
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (37 bp):
ATACTGGCTCGTAAGAGCAATACTGGCTCATTAGAGC
Found at i:92933 original size:18 final size:19
Alignment explanation
Indices: 92876--92940 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 19
92866 TGGCTCATTT
*
92876 GAGC-ATACTGGCTCGTAA
1 GAGCAATACTGGCTTGTAA
* *
92894 GAGCAATACTGGCTTATTA
1 GAGCAATACTGGCTTGTAA
*
92913 GAG-TATACTGGCTTGTAA
1 GAGCAATACTGGCTTGTAA
92931 GAGCAATACT
1 GAGCAATACT
92941 AGCTCGTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 19 0.50
19 19 0.50
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (19 bp):
GAGCAATACTGGCTTGTAA
Found at i:94936 original size:37 final size:38
Alignment explanation
Indices: 94908--94986 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
94898 ATTTTTGGAA
* *
94908 TGCATCCAAGACTATCGTTGCATAAATATTCTTCAAAT
1 TGCATCCAAAACTATCGCTGCATAAATATTCTTCAAAT
* *
94946 TGCATCCAAAACTTTCGCTGCATAAGTATTCTTC-AAT
1 TGCATCCAAAACTATCGCTGCATAAATATTCTTCAAAT
94983 TGCA
1 TGCA
94987 CCCAGGAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 7 0.19
38 30 0.81
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (38 bp):
TGCATCCAAAACTATCGCTGCATAAATATTCTTCAAAT
Found at i:95004 original size:37 final size:38
Alignment explanation
Indices: 94926--95005 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 38
94916 AGACTATCGT
* * *
94926 TGCATAAATATTCTTCAAATTGCATCCAAAACTTTCGC
1 TGCATAAATATTCTTCAAATTGCACCCAAAACTGTCAC
* *
94964 TGCATAAGTATTCTTC-AATTGCACCCAGGAA-TGTCAC
1 TGCATAAATATTCTTCAAATTGCACCCA-AAACTGTCAC
95001 TGCAT
1 TGCAT
95006 GAACATGTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 19 0.53
38 17 0.47
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (38 bp):
TGCATAAATATTCTTCAAATTGCACCCAAAACTGTCAC
Found at i:95869 original size:16 final size:16
Alignment explanation
Indices: 95848--95878 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
95838 TTGTGAATCC
95848 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
95864 CATTTTATCTTTATT
1 CATTTTACCTTTATT
95879 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:99410 original size:37 final size:37
Alignment explanation
Indices: 99315--99410 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 37
99305 TTCCGGAATG
*
99315 CACCCAACACTATCGCTGCATAAATATTCTTCAAATTA
1 CACCCAA-AATATCGCTGCATAAATATTCTTCAAATTA
* * * *
99353 CATCCAAAACTTTCGTTGCATAAGTATTCTTC-AATTA
1 CACCCAAAA-TATCGCTGCATAAATATTCTTCAAATTA
*
99390 CACCCAAGAATATCACTGCAT
1 CACCCAA-AATATCGCTGCAT
99411 GAACTTGTCT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 20 0.43
38 27 0.57
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.30
Consensus pattern (37 bp):
CACCCAAAATATCGCTGCATAAATATTCTTCAAATTA
Found at i:108168 original size:35 final size:36
Alignment explanation
Indices: 108116--108215 Score: 141
Period size: 35 Copynumber: 2.8 Consensus size: 36
108106 AAGGAATAGA
* *
108116 ATACTGACTCGTTTGAGCTTACTGGCTCGTTTAAGC
1 ATACTGGCTCGTTTGAGCATACTGGCTCGTTTAAGC
* *
108152 ATACTGGCTTG-TTGAGCATACTGGCTCG-TTGAGC
1 ATACTGGCTCGTTTGAGCATACTGGCTCGTTTAAGC
*
108186 ATACTGGCTCGTTTGAGCATATTGGCTCGT
1 ATACTGGCTCGTTTGAGCATACTGGCTCGT
108216 AAGAGCAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
34 15 0.27
35 32 0.57
36 9 0.16
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (36 bp):
ATACTGGCTCGTTTGAGCATACTGGCTCGTTTAAGC
Found at i:108171 original size:17 final size:18
Alignment explanation
Indices: 108116--108215 Score: 141
Period size: 18 Copynumber: 5.7 Consensus size: 18
108106 AAGGAATAGA
*
108116 ATACTGACTCGTTTGAGC
1 ATACTGGCTCGTTTGAGC
* *
108134 TTACTGGCTCGTTTAAGC
1 ATACTGGCTCGTTTGAGC
*
108152 ATACTGGCTTG-TTGAGC
1 ATACTGGCTCGTTTGAGC
108169 ATACTGGCTCG-TTGAGC
1 ATACTGGCTCGTTTGAGC
108186 ATACTGGCTCGTTTGAGC
1 ATACTGGCTCGTTTGAGC
*
108204 ATATTGGCTCGT
1 ATACTGGCTCGT
108216 AAGAGCAATA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
17 32 0.44
18 41 0.56
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
ATACTGGCTCGTTTGAGC
Found at i:108221 original size:18 final size:18
Alignment explanation
Indices: 108116--108242 Score: 98
Period size: 18 Copynumber: 7.1 Consensus size: 18
108106 AAGGAATAGA
* **
108116 ATACTGACTCGTTTGAGC
1 ATACTGGCTCGTAAGAGC
* *
108134 TTACTGGCTCGTTTA-AGC
1 ATACTGGCTCG-TAAGAGC
* *
108152 ATACTGGCTTGT-TGAGC
1 ATACTGGCTCGTAAGAGC
*
108169 ATACTGGCTCGT-TGAGC
1 ATACTGGCTCGTAAGAGC
**
108186 ATACTGGCTCGTTTGAGC
1 ATACTGGCTCGTAAGAGC
*
108204 ATATTGGCTCGTAAGAGC
1 ATACTGGCTCGTAAGAGC
* *
108222 AATACTGACTTGTAAGAGC
1 -ATACTGGCTCGTAAGAGC
108241 AT
1 AT
108243 TTTTGGATCA
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
17 32 0.35
18 43 0.47
19 17 0.18
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (18 bp):
ATACTGGCTCGTAAGAGC
Found at i:113159 original size:32 final size:34
Alignment explanation
Indices: 113120--113182 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
113110 TTTTTTTTAC
113120 TGTTTTGGTG-T-TCTTTTTACTGTTTTGATTGT
1 TGTTTTGGTGCTATCTTTTTACTGTTTTGATTGT
*
113152 TGTTTTGGTGCTATTTTTTTACTGTTTTGAT
1 TGTTTTGGTGCTATCTTTTTACTGTTTTGAT
113183 GATGTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 10 0.36
33 1 0.04
34 17 0.61
ACGTcount: A:0.08, C:0.06, G:0.21, T:0.65
Consensus pattern (34 bp):
TGTTTTGGTGCTATCTTTTTACTGTTTTGATTGT
Found at i:113204 original size:37 final size:34
Alignment explanation
Indices: 113133--113206 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
113123 TTTGGTGTTC
*
113133 TTTTTACTGTTTTGATTGTTGTTTTGGTGCTATT
1 TTTTTACTGTTTTGATTGTTGTTTTGGTACTATT
* *
113167 TTTTTACTGTTTTGATGATGTTATTTTTGTTACTATT
1 TTTTTACTGTTTTGAT--TGTT-GTTTTGGTACTATT
113204 TTT
1 TTT
113207 GTTGTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 16 0.47
36 4 0.12
37 14 0.41
ACGTcount: A:0.12, C:0.05, G:0.16, T:0.66
Consensus pattern (34 bp):
TTTTTACTGTTTTGATTGTTGTTTTGGTACTATT
Found at i:113212 original size:24 final size:24
Alignment explanation
Indices: 113154--113286 Score: 116
Period size: 24 Copynumber: 5.7 Consensus size: 24
113144 TTGATTGTTG
* * *
113154 TTTTGGTGCTATTTTT-TTACTGT
1 TTTTGTTGTTATTTTTGTTACTAT
*
113177 TTTGATGATGTTATTTTTGTTACTAT
1 TTT--TGTTGTTATTTTTGTTACTAT
*
113203 TTTTGTTGTTATTTTTGTTACTGT
1 TTTTGTTGTTATTTTTGTTACTAT
* *
113227 TTCTGTTGCTATTTTTG-T--TAT
1 TTTTGTTGTTATTTTTGTTACTAT
* **
113248 TTTTGTTGTT-GTTTTGTTGTTA-
1 TTTTGTTGTTATTTTTGTTACTAT
113270 TTTTGTTGTTATTTTTG
1 TTTTGTTGTTATTTTTG
113287 CTGTTGTTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
20 5 0.05
21 11 0.12
22 10 0.11
23 11 0.12
24 34 0.37
25 11 0.12
26 9 0.10
ACGTcount: A:0.10, C:0.05, G:0.17, T:0.68
Consensus pattern (24 bp):
TTTTGTTGTTATTTTTGTTACTAT
Found at i:113245 original size:33 final size:34
Alignment explanation
Indices: 113191--113286 Score: 124
Period size: 33 Copynumber: 2.8 Consensus size: 34
113181 ATGATGTTAT
*
113191 TTTTGTTACTATTTTTGTTGTTATTTTTGTTACTG
1 TTTTGTTGCTA-TTTTGTTGTTATTTTTGTTACTG
**
113226 TTTCTGTTGCTA-TTT-TTGTTATTTTTGTTGTTG
1 TTT-TGTTGCTATTTTGTTGTTATTTTTGTTACTG
*
113259 TTTTGTTGTTATTTTGTTGTTATTTTTG
1 TTTTGTTGCTATTTTGTTGTTATTTTTG
113287 CTGTTGTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.13
33 22 0.41
34 15 0.28
35 3 0.06
36 7 0.13
ACGTcount: A:0.08, C:0.04, G:0.17, T:0.71
Consensus pattern (34 bp):
TTTTGTTGCTATTTTGTTGTTATTTTTGTTACTG
Found at i:113256 original size:12 final size:12
Alignment explanation
Indices: 113185--113303 Score: 104
Period size: 12 Copynumber: 10.3 Consensus size: 12
113175 GTTTTGATGA
113185 TGTTATTTTTGT
1 TGTTATTTTTGT
**
113197 TACTATTTTTGT
1 TGTTATTTTTGT
113209 TGTTATTTTTGT
1 TGTTATTTTTGT
** * *
113221 TACTGTTTCTGT
1 TGTTATTTTTGT
*
113233 TGCTA--TTT-T
1 TGTTATTTTTGT
113242 TGTTATTTTTGT
1 TGTTATTTTTGT
*
113254 TGTT-GTTTTGT
1 TGTTATTTTTGT
113265 TGTTA-TTTTGT
1 TGTTATTTTTGT
*
113276 TGTTATTTTTGC
1 TGTTATTTTTGT
* *
113288 TGTTGTTTTGGT
1 TGTTATTTTTGT
113300 TGTT
1 TGTT
113304 TGGATGTTAT
Statistics
Matches: 85, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
9 5 0.06
10 2 0.02
11 24 0.28
12 54 0.64
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:113264 original size:11 final size:11
Alignment explanation
Indices: 113248--113303 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
113238 TTTTTGTTAT
113248 TTTTGTTGTTG
1 TTTTGTTGTTG
*
113259 TTTTGTTGTTA
1 TTTTGTTGTTG
*
113270 TTTTGTTGTTAT
1 TTTTGTTGTT-G
*
113282 TTTTGCTGTTG
1 TTTTGTTGTTG
113293 TTTTGGTTGTT
1 TTTT-GTTGTT
113304 TGGATGTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
11 24 0.63
12 14 0.37
ACGTcount: A:0.04, C:0.02, G:0.23, T:0.71
Consensus pattern (11 bp):
TTTTGTTGTTG
Found at i:113492 original size:19 final size:19
Alignment explanation
Indices: 113431--113494 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
113421 TATAAAGAAT
*
113431 TTTAATGTATTTTACA-TTTG
1 TTTAATGT-TTTTA-AGTTTA
*
113451 TTT-AT-TTTTTAATGTTTGT
1 TTTAATGTTTTTAA-GTTT-A
113470 TTTAATGTTTTTAAGTTTA
1 TTTAATGTTTTTAAGTTTA
113489 TTTAAT
1 TTTAAT
113495 ATATTATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
16 1 0.03
17 5 0.14
18 4 0.11
19 11 0.30
20 9 0.24
21 7 0.19
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (19 bp):
TTTAATGTTTTTAAGTTTA
Found at i:126308 original size:3 final size:3
Alignment explanation
Indices: 126300--126338 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
126290 ATTTGCTTGA
*
126300 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
126339 GTTCTTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:127800 original size:337 final size:337
Alignment explanation
Indices: 127185--127859 Score: 1269
Period size: 337 Copynumber: 2.0 Consensus size: 337
127175 TTCTCCAATT
127185 ATCTGTTCTCATTGTTTGATTCAGCTAATCATTGGAACATTGTTTTCTCTGATACAACACTGAAA
1 ATCTGTTCTCATTGTTTGATTCAGCTAATCATTGGAACATTGTTTTCTCTGATACAACACTGAAA
127250 CATTGTTGGTAAGTTAATTAACAATTTAAAATAAGTGCGAGGTGGAGAAAAAAATGTTCTTATTT
66 CATTGTTGGTAAGTTAATTAACAATTTAAAATAAGTGCGAGGTGGAGAAAAAAATGTTCTTATTT
* *
127315 GAAGCCATTAATTGCATGCATCTGTCCATATTCAAAAGGACTATGATTTGATAGACCAAGCAATG
131 GAAGCCATTAATTGCATGCATCTATCCATATTCAAAAGGACTATGATTTGATAGACCAAACAATG
127380 TTAAGATGTTTGATTTAACATTAATTGATTAAATTGTAAGAATCATTACAAATTTACAATGATAA
196 TTAAGATGTTTGATTTAACATTAATTGATTAAATTGTAAGAATCATTACAAATTTACAATGATAA
127445 GTTTGATGCTTGTTTTTCTTTTAACATTTCATATTTAAATAAAATATTGATTGAATTAAATTATT
261 GTTTGATGCTTGTTTTTCTTTTAACATTTCATATTTAAATAAAATATTGATTGAATTAAATTATT
*
127510 GGTATAAGTGTG
326 GGTATAAATGTG
127522 ATCTGTTCTCATTGTTTGATTCAGCTAATCATTGGAACATTGTTTTCTCTGATACAACACTGAAA
1 ATCTGTTCTCATTGTTTGATTCAGCTAATCATTGGAACATTGTTTTCTCTGATACAACACTGAAA
*
127587 CATTGTTGGTAAGTTAATTAACAATTTAAAATAATTGCGAGGTGGAGAAAAAAATGTTCTTATTT
66 CATTGTTGGTAAGTTAATTAACAATTTAAAATAAGTGCGAGGTGGAGAAAAAAATGTTCTTATTT
*
127652 GAAGTCATTAATTGCATGCATCTATCCATATTCAAAAGGACTATGATTTGATAGACCAAACAATG
131 GAAGCCATTAATTGCATGCATCTATCCATATTCAAAAGGACTATGATTTGATAGACCAAACAATG
* * *
127717 TTAAGATGTTTGATTTAATATTAATTGATTAAATTGTAAGAATCATTACAAATTTATAATGTTAA
196 TTAAGATGTTTGATTTAACATTAATTGATTAAATTGTAAGAATCATTACAAATTTACAATGATAA
*
127782 GTTTGATGTTTGTTTTTCTTTTAACATTTCATATTTAAATAAAATATTGATTGAATTAAATTATT
261 GTTTGATGCTTGTTTTTCTTTTAACATTTCATATTTAAATAAAATATTGATTGAATTAAATTATT
127847 GGTATAAATGTG
326 GGTATAAATGTG
127859 A
1 A
127860 GTTTGGTTCA
Statistics
Matches: 329, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
337 329 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (337 bp):
ATCTGTTCTCATTGTTTGATTCAGCTAATCATTGGAACATTGTTTTCTCTGATACAACACTGAAA
CATTGTTGGTAAGTTAATTAACAATTTAAAATAAGTGCGAGGTGGAGAAAAAAATGTTCTTATTT
GAAGCCATTAATTGCATGCATCTATCCATATTCAAAAGGACTATGATTTGATAGACCAAACAATG
TTAAGATGTTTGATTTAACATTAATTGATTAAATTGTAAGAATCATTACAAATTTACAATGATAA
GTTTGATGCTTGTTTTTCTTTTAACATTTCATATTTAAATAAAATATTGATTGAATTAAATTATT
GGTATAAATGTG
Found at i:132005 original size:14 final size:15
Alignment explanation
Indices: 131971--132004 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
131961 ATCAATCATT
131971 AAAAAA-AAAAAGAA
1 AAAAAAGAAAAAGAA
131985 AAAAAAGAAAAAGAA
1 AAAAAAGAAAAAGAA
132000 AAAAA
1 AAAAA
132005 GGGGGTGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAGAA
Found at i:132775 original size:19 final size:19
Alignment explanation
Indices: 132751--132791 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
132741 CCGCACAAGT
132751 TTTTTACCATTTATTTTTG
1 TTTTTACCATTTATTTTTG
***
132770 TTTTTATTTTTTATTTTTG
1 TTTTTACCATTTATTTTTG
132789 TTT
1 TTT
132792 ATTTTGTAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTTACCATTTATTTTTG
Found at i:141025 original size:14 final size:15
Alignment explanation
Indices: 140991--141024 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
140981 ATCAATCATT
140991 AAAAAA-AAAAAGAA
1 AAAAAAGAAAAAGAA
141005 AAAAAAGAAAAAGAA
1 AAAAAAGAAAAAGAA
141020 AAAAA
1 AAAAA
141025 GGGGGTGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAGAA
Found at i:141795 original size:19 final size:19
Alignment explanation
Indices: 141771--141811 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
141761 CCGCACAAGT
141771 TTTTTACCATTTATTTTTG
1 TTTTTACCATTTATTTTTG
***
141790 TTTTTATTTTTTATTTTTG
1 TTTTTACCATTTATTTTTG
141809 TTT
1 TTT
141812 ATTTTGTAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTTACCATTTATTTTTG
Found at i:148977 original size:79 final size:79
Alignment explanation
Indices: 148881--149118 Score: 449
Period size: 79 Copynumber: 3.0 Consensus size: 79
148871 TTAGAGAGAG
148881 AAATCAGTTCAATGAAATCGATTTTTGCATTTTTAACCATGAATACCAATTCCCTAAGTCCCTGT
1 AAATCAGTTCAATGAAATCGATTTTTGCATTTTTAACCATGAATACCAATTCCCTAAGTCCCTGT
148946 CAAATAGTTGGAAA
66 CAAATAGTTGGAAA
*
148960 AAATCAGTTCAATGAAATCGATTTTTGCATTTTTAACCACGAATACCAATTCCCTAAGTCCCTGT
1 AAATCAGTTCAATGAAATCGATTTTTGCATTTTTAACCATGAATACCAATTCCCTAAGTCCCTGT
149025 CAAATAGTTGGAAAA
66 CAAATAGTTGG-AAA
*
149040 AAATCAGTTCCATGAAATCGATTTTTGCATTTTTAACCATGAATACCAATTCCCTAAGTCCCTGT
1 AAATCAGTTCAATGAAATCGATTTTTGCATTTTTAACCATGAATACCAATTCCCTAAGTCCCTGT
149105 CAAATAGTTGGAAA
66 CAAATAGTTGGAAA
149119 GTAGTAAAAA
Statistics
Matches: 155, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
79 78 0.50
80 77 0.50
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (79 bp):
AAATCAGTTCAATGAAATCGATTTTTGCATTTTTAACCATGAATACCAATTCCCTAAGTCCCTGT
CAAATAGTTGGAAA
Found at i:149084 original size:80 final size:80
Alignment explanation
Indices: 148881--149118 Score: 451
Period size: 80 Copynumber: 3.0 Consensus size: 80
148871 TTAGAGAGAG
148881 AAATCAGTTCAATGAAATCGATTTTTGCATTTTTAACCATGAATACCAATTCCCTAAGTCCCTGT
1 AAATCAGTTCAATGAAATCGATTTTTGCATTTTTAACCATGAATACCAATTCCCTAAGTCCCTGT
148946 CAAATAGTTGG-AAA
66 CAAATAGTTGGAAAA
*
148960 AAATCAGTTCAATGAAATCGATTTTTGCATTTTTAACCACGAATACCAATTCCCTAAGTCCCTGT
1 AAATCAGTTCAATGAAATCGATTTTTGCATTTTTAACCATGAATACCAATTCCCTAAGTCCCTGT
149025 CAAATAGTTGGAAAA
66 CAAATAGTTGGAAAA
*
149040 AAATCAGTTCCATGAAATCGATTTTTGCATTTTTAACCATGAATACCAATTCCCTAAGTCCCTGT
1 AAATCAGTTCAATGAAATCGATTTTTGCATTTTTAACCATGAATACCAATTCCCTAAGTCCCTGT
149105 CAAATAGTTGGAAA
66 CAAATAGTTGGAAA
149119 GTAGTAAAAA
Statistics
Matches: 155, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
79 75 0.48
80 80 0.52
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (80 bp):
AAATCAGTTCAATGAAATCGATTTTTGCATTTTTAACCATGAATACCAATTCCCTAAGTCCCTGT
CAAATAGTTGGAAAA
Found at i:155428 original size:41 final size:41
Alignment explanation
Indices: 155362--155511 Score: 201
Period size: 41 Copynumber: 3.6 Consensus size: 41
155352 TACGCTCTAT
* *
155362 CGAGTCAGAAGTGTTCCTTTAAATATAATCTCATGCTCATCC
1 CGAGTCATAAGTCTTCCTTT-AATATAATCTCATGCTCATCC
* *
155404 TGAGTCATAAGTCTTCCTTTAATATAATTTCATGCTCATCC
1 CGAGTCATAAGTCTTCCTTTAATATAATCTCATGCTCATCC
** *
155445 CGAGTCACGAGTCTTCCTTTACTATAATCTCATGCTCATCC
1 CGAGTCATAAGTCTTCCTTTAATATAATCTCATGCTCATCC
* * *
155486 CCAATCATGAGTCTTCCTTTAATATA
1 CGAGTCATAAGTCTTCCTTTAATATA
155512 TCAAGTGATT
Statistics
Matches: 95, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 78 0.82
42 17 0.18
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (41 bp):
CGAGTCATAAGTCTTCCTTTAATATAATCTCATGCTCATCC
Found at i:156043 original size:85 final size:85
Alignment explanation
Indices: 155900--156069 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
155890 TAACACAACA
*
155900 CATAATCCGTTAAACGTTTCATTGTCACCTGAATTCAACTATATCATTTCTTCACTTACAACCAT
1 CATAATCCGTTAAACGTTTCATTGTCACCTGAATTCAACTATATCATTTATTCACTTACAACCAT
155965 GCCCCTCAATACAATTTCAT
66 GCCCCTCAATACAATTTCAT
155985 CATAATCCGTTAAACGTTTCATTGTCACCTGAATTCAACTATATCATTTATTCACTTACAACCAT
1 CATAATCCGTTAAACGTTTCATTGTCACCTGAATTCAACTATATCATTTATTCACTTACAACCAT
156050 GCCCCTCAATACAATTTCAT
66 GCCCCTCAATACAATTTCAT
156070 TTCAATTTGA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (85 bp):
CATAATCCGTTAAACGTTTCATTGTCACCTGAATTCAACTATATCATTTATTCACTTACAACCAT
GCCCCTCAATACAATTTCAT
Found at i:157608 original size:21 final size:21
Alignment explanation
Indices: 157584--157627 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
157574 AATTCACATA
* *
157584 TAATAAGACTATGTAAATATT
1 TAATAAAAATATGTAAATATT
*
157605 TAATAAAAATATTTAAATATT
1 TAATAAAAATATGTAAATATT
157626 TA
1 TA
157628 CAGCCTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (21 bp):
TAATAAAAATATGTAAATATT
Found at i:174520 original size:25 final size:25
Alignment explanation
Indices: 174472--174521 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
174462 TTTAGTGATT
*
174472 TATTTTTTAAAATTCAAGTATATATA
1 TATTTTTCAAAATTCAAG-ATATATA
174498 TATTTTTCAATAATTCAAG-TATAT
1 TATTTTTCAA-AATTCAAGATATAT
174522 TAATATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 9 0.41
27 8 0.36
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (25 bp):
TATTTTTCAAAATTCAAGATATATA
Found at i:177057 original size:9 final size:9
Alignment explanation
Indices: 177043--177115 Score: 65
Period size: 9 Copynumber: 7.4 Consensus size: 9
177033 TCAAACTCAT
177043 CCATGCCGC
1 CCATGCCGC
177052 CCATGCCGCC
1 CCATGCCG-C
*
177062 CATCATGTCGC
1 C--CATGCCGC
177073 CCATGCCGC
1 CCATGCCGC
*
177082 CCATGCCACC
1 CCATGCC-GC
*
177092 CATCATGTCGC
1 C--CATGCCGC
177103 CCATGCCGC
1 CCATGCCGC
177112 CCAT
1 CCAT
177116 TCCCCCGAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
9 33 0.63
10 4 0.08
11 4 0.08
12 11 0.21
ACGTcount: A:0.15, C:0.51, G:0.18, T:0.16
Consensus pattern (9 bp):
CCATGCCGC
Found at i:177068 original size:21 final size:21
Alignment explanation
Indices: 177044--177085 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
177034 CAAACTCATC
177044 CATGCCGCCCATGCCGCCCAT
1 CATGCCGCCCATGCCGCCCAT
*
177065 CATGTCGCCCATGCCGCCCAT
1 CATGCCGCCCATGCCGCCCAT
177086 GCCACCCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.50, G:0.19, T:0.17
Consensus pattern (21 bp):
CATGCCGCCCATGCCGCCCAT
Found at i:177079 original size:30 final size:30
Alignment explanation
Indices: 177043--177115 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
177033 TCAAACTCAT
*
177043 CCATGCCGCCCATGCCGCCCATCATGTCGC
1 CCATGCCGCCCATGCCACCCATCATGTCGC
177073 CCATGCCGCCCATGCCACCCATCATGTCGC
1 CCATGCCGCCCATGCCACCCATCATGTCGC
177103 CCATGCCGCCCAT
1 CCATGCCGCCCAT
177116 TCCCCCGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.15, C:0.51, G:0.18, T:0.16
Consensus pattern (30 bp):
CCATGCCGCCCATGCCACCCATCATGTCGC
Found at i:177098 original size:21 final size:21
Alignment explanation
Indices: 177074--177115 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
177064 TCATGTCGCC
177074 CATGCCGCCCATGCCACCCAT
1 CATGCCGCCCATGCCACCCAT
* *
177095 CATGTCGCCCATGCCGCCCAT
1 CATGCCGCCCATGCCACCCAT
177116 TCCCCCGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17
Consensus pattern (21 bp):
CATGCCGCCCATGCCACCCAT
Found at i:177957 original size:27 final size:27
Alignment explanation
Indices: 177916--177971 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
177906 TGTTGAAACA
*
177916 TATAGCATGATCTAATAGAAATTATGC
1 TATAGCATGACCTAATAGAAATTATGC
177943 TATAGCATGACCTAATAGAAATTATGC
1 TATAGCATGACCTAATAGAAATTATGC
177970 TA
1 TA
177972 ATGCAATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (27 bp):
TATAGCATGACCTAATAGAAATTATGC
Found at i:179611 original size:13 final size:15
Alignment explanation
Indices: 179593--179633 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
179583 AACGATAACG
179593 TAAATAATTAAAAC-
1 TAAATAATTAAAACA
* *
179607 T-AATATTTCAAACA
1 TAAATAATTAAAACA
179621 TAAATAATTAAAA
1 TAAATAATTAAAA
179634 TGTAATAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
13 10 0.48
14 2 0.10
15 9 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAATAATTAAAACA
Found at i:179646 original size:28 final size:28
Alignment explanation
Indices: 179593--179646 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
179583 AACGATAACG
**
179593 TAAATAATTAAAACTAATATTTCAAACA
1 TAAATAATTAAAACTAATATAACAAACA
*
179621 TAAATAATTAAAATGTAATA-AACAAA
1 TAAATAATTAAAA-CTAATATAACAAA
179647 TGTGAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 17 0.77
29 5 0.23
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (28 bp):
TAAATAATTAAAACTAATATAACAAACA
Found at i:183389 original size:27 final size:25
Alignment explanation
Indices: 183358--183414 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
183348 TAAAGTTAGA
* *
183358 TAAAATTTGAAATTTAATTTTTATATT
1 TAAAAATT-AAATTAAATTTTT-TATT
*
183385 TAAAAAATTAAATTAAATTTTTTTTT
1 T-AAAAATTAAATTAAATTTTTTATT
183411 TAAA
1 TAAA
183415 GTTTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 3 0.12
26 4 0.15
27 13 0.50
28 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TAAAAATTAAATTAAATTTTTTATT
Found at i:183696 original size:7 final size:7
Alignment explanation
Indices: 183684--183708 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
183674 AAATTTTAGA
183684 TAAATTT
1 TAAATTT
183691 TAAATTT
1 TAAATTT
183698 TAAATTT
1 TAAATTT
183705 TAAA
1 TAAA
183709 ACGTAGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:185113 original size:54 final size:54
Alignment explanation
Indices: 185050--185152 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
185040 GGTTCGCTAG
*
185050 TTAGACTGACAAGCTAGGGTTCACT-AGTTGAGTTGTGAACTAAGGGTTCGTCAA
1 TTAGACTGACAAGCTAGGGTTC-CTCAGTTGAGTTGCGAACTAAGGGTTCGTCAA
* * * * * *
185104 TTAGTCTGACGAGCTGGGGTTCGTCATTTGAGTTGCGAACTAGGGGTTC
1 TTAGACTGACAAGCTAGGGTTCCTCAGTTGAGTTGCGAACTAAGGGTTC
185153 ACTATACAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 1 0.02
54 40 0.98
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (54 bp):
TTAGACTGACAAGCTAGGGTTCCTCAGTTGAGTTGCGAACTAAGGGTTCGTCAA
Found at i:185149 original size:27 final size:27
Alignment explanation
Indices: 185077--185152 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
185067 GGTTCACTAG
* *
185077 TTGAGTTGTGAACTAAGGGTTCGTCAA
1 TTGAGTTGCGAACTAGGGGTTCGTCAA
* *
185104 TT-AGTCTGACGAGCT-GGGGTTCGTCAT
1 TTGAGT-TG-CGAACTAGGGGTTCGTCAA
185131 TTGAGTTGCGAACTAGGGGTTC
1 TTGAGTTGCGAACTAGGGGTTC
185153 ACTATACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
26 8 0.20
27 25 0.62
28 7 0.17
ACGTcount: A:0.20, C:0.14, G:0.33, T:0.33
Consensus pattern (27 bp):
TTGAGTTGCGAACTAGGGGTTCGTCAA
Found at i:187208 original size:24 final size:24
Alignment explanation
Indices: 187179--187227 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
187169 GATAGTATAT
*
187179 ACCGGCACGAAGCCTACTTGGCAC
1 ACCGGCACGAAGCCTACTAGGCAC
*
187203 ACCGGCACGAAGCCTGCTAGGCAC
1 ACCGGCACGAAGCCTACTAGGCAC
187227 A
1 A
187228 AAGCCCGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.37, G:0.27, T:0.10
Consensus pattern (24 bp):
ACCGGCACGAAGCCTACTAGGCAC
Found at i:187247 original size:37 final size:37
Alignment explanation
Indices: 187201--187275 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
187191 CCTACTTGGC
* *
187201 ACACCGGCACGAAGCCTGCTAGGCACAAAGCCCGAAT
1 ACACCGGCACGAAGCCTACTAGGCACAAAGCCCAAAT
187238 ACACCGGCACGAAGCCTACTAGGCACAAAGCCCAAAT
1 ACACCGGCACGAAGCCTACTAGGCACAAAGCCCAAAT
187275 A
1 A
187276 TTTAGATGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.35, G:0.21, T:0.08
Consensus pattern (37 bp):
ACACCGGCACGAAGCCTACTAGGCACAAAGCCCAAAT
Found at i:187976 original size:43 final size:43
Alignment explanation
Indices: 187858--187976 Score: 193
Period size: 43 Copynumber: 2.8 Consensus size: 43
187848 GAGGAAAAAT
* * * *
187858 GCCGCTATAGAACATGGTCTTTAGCGGCGCTTATCTCACAAAC
1 GCCGCTAAAGACCATGGTCTTTAGCGGCGCTTTTCCCACAAAC
187901 GCCGCTAAAGACCATGGTCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGACCATGGTCTTTAGCGGCGCTTTTCCCACAAAC
*
187944 GCCGCTAAAGACCATGGTCTTTAGCGGTGCTTT
1 GCCGCTAAAGACCATGGTCTTTAGCGGCGCTTT
187977 GTCTTTATTG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (43 bp):
GCCGCTAAAGACCATGGTCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:195628 original size:41 final size:41
Alignment explanation
Indices: 195581--195737 Score: 162
Period size: 41 Copynumber: 3.9 Consensus size: 41
195571 CGGTGTTTTT
* *
195581 CCCATAAGCGCCGTTATTGCTCTGACTTTTAGCGGCGCTTG
1 CCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTG
* * *
195622 CCCATAAGCGCCGCTATTGCTTTGACCTTTACTCTGAC-CTTG
1 CCCATAAGCGCCGCTATTGCTCTGACCTTTA-GC-GGCGCTTG
* * *
195664 --GA-AAGCGCCGCTATTGCTCTGACCTTTAGCGTCGCTTT
1 CCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTG
* * *
195702 CCCATAAGCACCGCTATTGCTCTAACTTTTA-CGGCG
1 CCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
195738 TTTATATAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 25 0.26
40 6 0.06
41 51 0.54
42 5 0.05
43 2 0.02
ACGTcount: A:0.17, C:0.31, G:0.20, T:0.31
Consensus pattern (41 bp):
CCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTG
Found at i:195733 original size:80 final size:80
Alignment explanation
Indices: 195586--195733 Score: 224
Period size: 80 Copynumber: 1.9 Consensus size: 80
195576 TTTTTCCCAT
* * * * *
195586 AAGCGCCGTTATTGCTCTGACTTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTTTGACCTT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCACCGCTATTGCTCTAACCTT
195651 TACTCTGACCTTGGA
66 TACTCTGACCTTGGA
* * *
195666 AAGCGCCGCTATTGCTCTGACCTTTAGCGTCGCTTTCCCATAAGCACCGCTATTGCTCTAACTTT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCACCGCTATTGCTCTAACCTT
195731 TAC
66 TAC
195734 GGCGTTTATA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 60 1.00
ACGTcount: A:0.18, C:0.30, G:0.20, T:0.32
Consensus pattern (80 bp):
AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCACCGCTATTGCTCTAACCTT
TACTCTGACCTTGGA
Found at i:198712 original size:27 final size:27
Alignment explanation
Indices: 198689--198752 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
198679 AGAAATTCGC
198689 TTCAGAATACGCCATGAAGGAATTTCA
1 TTCAGAATACGCCATGAAGGAATTTCA
* *
198716 TTCAGAATATGTCATGAA-GACATTTCA
1 TTCAGAATACGCCATGAAGGA-ATTTCA
*
198743 TTCAAAATAC
1 TTCAGAATAC
198753 ACCACACAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (27 bp):
TTCAGAATACGCCATGAAGGAATTTCA
Found at i:199710 original size:21 final size:21
Alignment explanation
Indices: 199685--199756 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
199675 TAGTGCAGTT
* *
199685 TTCTACCGATACAAGTGTCAG
1 TTCTACCGATACAAGTCTCAC
* *
199706 TTCTATCGAAACAAGTCTCAC
1 TTCTACCGATACAAGTCTCAC
* * *
199727 TTTTACTGATACAAGTCTTAC
1 TTCTACCGATACAAGTCTCAC
199748 TTCTACCGA
1 TTCTACCGA
199757 CACCAAAAAC
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (21 bp):
TTCTACCGATACAAGTCTCAC
Found at i:202186 original size:41 final size:42
Alignment explanation
Indices: 202112--202210 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 42
202102 ATAACAGCAC
202112 CATAAGTTGGTTTTCCATTTCAACAACCCCAATACCAGC-AGTCA
1 CATAAGTTGGTTTTCCATTTCAACAA--CCAATACCAGCTA-TCA
*
202156 CATAAGTTGGTTTTCCATTTCAACAA-CAATACTAGCTATCA
1 CATAAGTTGGTTTTCCATTTCAACAACCAATACCAGCTATCA
*
202197 TATAAGTTGGTTTT
1 CATAAGTTGGTTTT
202211 TCACAACAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
41 25 0.48
42 1 0.02
44 26 0.50
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (42 bp):
CATAAGTTGGTTTTCCATTTCAACAACCAATACCAGCTATCA
Found at i:202221 original size:3 final size:3
Alignment explanation
Indices: 202213--202237 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
202203 TTGGTTTTTC
202213 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
202238 TAATCTTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:202221 original size:41 final size:41
Alignment explanation
Indices: 202112--202225 Score: 113
Period size: 41 Copynumber: 2.7 Consensus size: 41
202102 ATAACAGCAC
**
202112 CATAAGTTGGTTTTCCATTTCAACAACCCCAATACCAGCAGTCA
1 CATAAGTTGGTTTTCCA---CAACAACAACAATACCAGCAGTCA
*** *
202156 CATAAGTTGGTTTTCCATTTCAACAACAATACTAGCTA-TCA
1 CATAAGTTGGTTTTCCACAACAACAACAATACCAGC-AGTCA
* *
202197 TATAAGTTGGTTTTTCACAACAACAACAA
1 CATAAGTTGGTTTTCCACAACAACAACAA
202226 CAACAACAAC
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
41 40 0.69
42 1 0.02
44 17 0.29
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.31
Consensus pattern (41 bp):
CATAAGTTGGTTTTCCACAACAACAACAATACCAGCAGTCA
Found at i:202522 original size:3 final size:3
Alignment explanation
Indices: 202509--202569 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
202499 TCTCCATTTC
* * * *
202509 TCT TAT TCT TCT TCT TC- TCC TCC TCC TCT TCT TCT TCT TCCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT
202553 TC- TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT
202570 ACTATCCAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
2 6 0.12
3 42 0.82
4 3 0.06
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:202567 original size:20 final size:21
Alignment explanation
Indices: 202515--202568 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
202505 TTTCTCTTAT
202515 TCTTCTTCTTC-TCCTCCTCC
1 TCTTCTTCTTCTTCCTCCTCC
* *
202535 TCTTCTTCTTCTTCCT-TTTC
1 TCTTCTTCTTCTTCCTCCTCC
202555 TCTTCTTCTTCTTC
1 TCTTCTTCTTCTTC
202569 TACTATCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (21 bp):
TCTTCTTCTTCTTCCTCCTCC
Found at i:204291 original size:31 final size:29
Alignment explanation
Indices: 204241--204305 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 29
204231 TAGTTTATTT
*
204241 TTTTATAATTTTAAAAGATTAAATTAAAA
1 TTTTATAATTTTAAAAGATTAAAATAAAA
* *
204270 TTTTATCATTTTTAAAAAGATTAAAATACAA
1 TTTTAT-AATTTT-AAAAGATTAAAATAAAA
204301 TTTTA
1 TTTTA
204306 CTTTTACTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 6 0.19
30 5 0.16
31 20 0.65
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (29 bp):
TTTTATAATTTTAAAAGATTAAAATAAAA
Found at i:213609 original size:2 final size:2
Alignment explanation
Indices: 213602--213633 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
213592 TAATCAAATT
213602 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
213634 CCTGGACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:213829 original size:3 final size:3
Alignment explanation
Indices: 213823--213859 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
213813 TTAACAATAA
213823 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
213860 AAAAATCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:215937 original size:7 final size:8
Alignment explanation
Indices: 215917--215941 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
215907 TAGTTGTTAT
215917 ATTTTTAA
1 ATTTTTAA
215925 ATTTTTAA
1 ATTTTTAA
215933 ATTTTTAA
1 ATTTTTAA
215941 A
1 A
215942 ATTTCAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTTTAA
Found at i:216160 original size:29 final size:29
Alignment explanation
Indices: 216098--216160 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
216088 AATAATCTAT
216098 ATTTTTATAATTTTTAAAGGATTAAATTA
1 ATTTTTATAATTTTTAAAGGATTAAATTA
* * *
216127 TTTTTTTTCATTTTT-AAGG-TTAAAATGTA
1 ATTTTTATAATTTTTAAAGGATT-AAAT-TA
216156 ATTTT
1 ATTTT
216161 ATCATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.07
28 8 0.29
29 18 0.64
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (29 bp):
ATTTTTATAATTTTTAAAGGATTAAATTA
Found at i:218347 original size:58 final size:60
Alignment explanation
Indices: 218255--218571 Score: 199
Period size: 59 Copynumber: 5.4 Consensus size: 60
218245 CTTGGGGGGT
* ** * * *
218255 AAAATGGTAAATTTTGGAAGTTTCGGGGGCAAAATGGTAATCTTGGGAA-ATTCGGGGTTA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTAAAAATGGAAATCTTGGGAAGATTCGGCGTCA
* * * *
218315 AAAATGGAATTTTTGGATGTTT-GGGGTAAAAAT-GAAATTTTTGGAAGTTTCGGCGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGAAATCTTGGGAAGATTCGGCGTCA
* * * *
218373 AAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAAT-GAGATTTTCGGG-AG-TTCTAGG-GT-A
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-AAAAATGGAAATCTT-GGGAAGATTC--GGCGTCA
* ** * * * *
218432 AAAATGGAATTTTTAGAAGTTTCAAGGTAAAAAATAGG--ATTTTGGGAAGTTTGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-AAAAAT-GGAAATCTTGGGAAGATTCGGCGTCA
* * * * ** * * * *
218491 AAAATGAAATTTTTGAAAGTTTCGGGGTTAAAATGG-AATTTTTAGAAGTTTTGGGGACA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGAAATCTTGGGAAGATTCGGCGTCA
*
218550 AAAATGGGATTTTTGGAAGTTT
1 AAAATGGAATTTTTGGAAGTTT
218572 TAGAGTAAAA
Statistics
Matches: 211, Mismatches: 33, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
57 12 0.06
58 63 0.30
59 105 0.50
60 26 0.12
61 5 0.02
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (60 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGAAATCTTGGGAAGATTCGGCGTCA
Found at i:218444 original size:59 final size:57
Alignment explanation
Indices: 218313--218630 Score: 243
Period size: 59 Copynumber: 5.4 Consensus size: 57
218303 AATTCGGGGT
* * * * *
218313 TAAAAATGGAATTTTTGGATGTTT-GGGGTAAAAATGAAATTTTTGGAAGTTTCGGCG
1 TAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGAGATTTTTGGGAGTTTAGG-G
* *
218370 TCAAAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTCGGGAGTTCTAGGG
1 T-AAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAAATGAGATTTTTGGGAGTT-TAGGG
* * *
218430 TAAAAATGGAATTTTTAGAAGTTTCAAGGTAAAAAAT-AGGA-TTTTGGGAAGTTTGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAAATGA-GATTTTTGGG-AGTTT-AGGG
* * * * * * *
218489 TAAAAATGAAATTTTTGAAAGTTTCGGGGTTAAAATG-GAATTTTTAGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGAG-ATTTTTGGGAG-TTTAGGG
* * * * *
218547 ACAAAAATGGGATTTTTGGAAGTTT-TAGAGTAAAAAATG-GTATTTTTAGGAGTTCGAGGG
1 -TAAAAATGGAATTTTTGGAAGTTTCGAG-GT-AAAAATGAG-ATTTTTGGGAGTT-TAGGG
**
218607 TAAAAACAGAATTTTTGGAAGTTT
1 TAAAAATGGAATTTTTGGAAGTTT
218631 AGGGACCTTT
Statistics
Matches: 210, Mismatches: 36, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
57 2 0.01
58 42 0.20
59 122 0.58
60 41 0.20
61 3 0.01
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (57 bp):
TAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGAGATTTTTGGGAGTTTAGGG
Found at i:218572 original size:30 final size:29
Alignment explanation
Indices: 218250--218630 Score: 263
Period size: 30 Copynumber: 13.0 Consensus size: 29
218240 GGATACTTGG
* *
218250 GGGGT-AAAATGGTAAATTTTGGAAGTTTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTT
** * * * *
218279 GGGGGCAAAATGGTAATCTTGGGAA-ATTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTT
*
218308 GGGGTTAAAAATGGAATTTTTGGATG-TTT
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTT
* *
218337 GGGGTAAAAATGAAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* * *
218366 GGCGTCAAAAATGGGATTTTTGGAAGTTTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
* * * *
218396 GAGGTCAAAAAT-GAGATTTTCGGGAGTTCT
1 GGGGT-AAAAATGGA-ATTTTTGGAAGTTTT
* * *
218426 AGGGTAAAAATGGAATTTTTAGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
** * *
218455 AAGGTAAAAAATAGG-ATTTTGGGAAGTTTG
1 GGGGT-AAAAAT-GGAATTTTTGGAAGTTTT
* * *
218485 GGGGTAAAAATGAAATTTTTGAAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* *
218514 GGGGTTAAAATGGAATTTTTAGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* *
218543 GGGGACAAAAATGGGATTTTTGGAAGTTTT
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTT
* * * *
218573 AGAGTAAAAAATGGTATTTTTAGG-AG-TTC
1 GGGGT-AAAAATGGAATTTTT-GGAAGTTTT
**
218602 GAGGGTAAAAACAGAATTTTTGGAAGTTT
1 G-GGGTAAAAATGGAATTTTTGGAAGTTT
218631 AGGGACCTTT
Statistics
Matches: 276, Mismatches: 60, Indels: 31
0.75 0.16 0.08
Matches are distributed among these distances:
28 22 0.08
29 114 0.41
30 136 0.49
31 4 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTT
Found at i:218580 original size:88 final size:88
Alignment explanation
Indices: 218313--218634 Score: 296
Period size: 89 Copynumber: 3.6 Consensus size: 88
218303 AATTCGGGGT
* * * * * * *
218313 TAAAAATGGAATTTTTGGATGTTT-GGGGTAAAAATGAAATTTTTGGAAGTTTCGGCGTCAAAAA
1 TAAAAATGAAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTTAGAAGTTTAGGGGACAAAAA
*
218377 TGGGATTTTTGGAAG-TTTCGAGG
66 TGGGATTTTTGGAAGTTTTAGA-G
* * * * * *
218400 TCAAAAATGAGATTTTCGGGAG-TTCTAGGGTAAAAATGGAATTTTTAGAAGTTTCAAGGTA-AA
1 T-AAAAATGAAATTTTTGGAAGTTTC-GGGGTAAAAATGGAATTTTTAGAAGTTT-AGGGGACAA
* * ** *
218463 AAATAGGATTTTGGGAAGTTTGGGGG
63 AAATGGGATTTTTGGAAGTTTTAGAG
* * *
218489 TAAAAATGAAATTTTTGAAAGTTTCGGGGTTAAAATGGAATTTTTAGAAGTTTTGGGGACAAAAA
1 TAAAAATGAAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTTAGAAGTTTAGGGGACAAAAA
218554 TGGGATTTTTGGAAGTTTTAGAG
66 TGGGATTTTTGGAAGTTTTAGAG
** ** *
218577 TAAAAAATGGTATTTTTAGG-AG-TTCGAGGGTAAAAACAGAATTTTTGGAAGTTTAGGG
1 T-AAAAATGAAATTTTT-GGAAGTTTCG-GGGTAAAAATGGAATTTTTAGAAGTTTAGGG
218635 ACCTTTAGGG
Statistics
Matches: 185, Mismatches: 40, Indels: 18
0.76 0.16 0.07
Matches are distributed among these distances:
87 6 0.03
88 85 0.46
89 89 0.48
90 5 0.03
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (88 bp):
TAAAAATGAAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTTAGAAGTTTAGGGGACAAAAA
TGGGATTTTTGGAAGTTTTAGAG
Done.