Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 51 of 203
Found at i:16593659 original size:61 final size:60
Alignment explanation
Indices: 16593593--16593783 Score: 174
Period size: 61 Copynumber: 3.2 Consensus size: 60
16593583 TTTTAATTAA
* *
16593593 AATATATAATTTAATAAAATTCTTAATAATCAATATTTTTATCTGAATTTACTAAAATAAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTATTAT-TGAATTTAATAAAATAAT
* * * * * * ** *
16593654 AATATATGATACT-ATAAAATATATT-TTAA-C-ATAATTATTATTAAATATAATTTAATAAA
1 AATATATAAT-TTAATAAAAT-TCTTAATAATCAAT-ATTATTATTGAATTTAATAAAATAAT
* * * *
16593713 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTATTAT-TGAATTTAATAAAATAAT
16593774 AATATATAAT
1 AATATATAAT
16593784 ACTATATAAT
Statistics
Matches: 98, Mismatches: 24, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
58 4 0.04
59 32 0.33
60 15 0.15
61 43 0.44
62 4 0.04
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTATTATTGAATTTAATAAAATAAT
Found at i:16593696 original size:120 final size:120
Alignment explanation
Indices: 16593554--16593796 Score: 387
Period size: 120 Copynumber: 2.0 Consensus size: 120
16593544 TAATTTAATC
* *
16593554 ATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAA
1 ATATTTAAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAA
* * * * *
16593619 TAATCAATATTTTTATCTGAATTTACTAAAATAATAATATATGATACTATAAAAT
66 TAATAAATATTCTTATATGAATTTAATAAAATAATAATATATAATACTATAAAAT
*
16593674 ATATTTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAA
1 ATATTTAAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAA
* * *
16593739 TATTAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAAT
66 TAATAAATATTCTTATATGAATTTAATAAAATAATAATATATAATACTATAAAAT
16593794 ATA
1 ATA
16593797 GATTAATAAT
Statistics
Matches: 112, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
120 112 1.00
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (120 bp):
ATATTTAAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAA
TAATAAATATTCTTATATGAATTTAATAAAATAATAATATATAATACTATAAAAT
Found at i:16593779 original size:59 final size:57
Alignment explanation
Indices: 16593584--16593779 Score: 154
Period size: 56 Copynumber: 3.3 Consensus size: 57
16593574 TTAAATATAT
* * * *
16593584 TTTAATTAAA-AT-ATATAATTTAATAAAATTCTTAATAATCAATATTTTTATCTGAA
1 TTTAATAAAATATAATATAATTTAATAAAATTCTTAAT-ATAAATATTATTATATGAA
* * *
16593640 TTTACTAAAATAATAATATATGATACTATAA-AATATATT-TTAACATAATTATTATTAAATAT-
1 TTTAATAAAAT-ATAATATA--AT--T-TAATAA-A-ATTCTTAATATAAATATTATT--ATATG
16593702 AA
56 AA
*
16593704 TTTAATAAAA-AT-ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
1 TTTAATAAAATATAATATAATTTAATAAAATTCTTAATA-TAAATATTATTATATGAA
16593760 TTTAATAAAATCATAATATA
1 TTTAATAAAAT-ATAATATA
16593780 TAATACTATA
Statistics
Matches: 110, Mismatches: 11, Indels: 35
0.71 0.07 0.22
Matches are distributed among these distances:
55 7 0.06
56 29 0.26
57 12 0.11
58 4 0.04
59 12 0.11
61 7 0.06
62 2 0.02
63 12 0.11
64 19 0.17
65 6 0.05
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (57 bp):
TTTAATAAAATATAATATAATTTAATAAAATTCTTAATATAAATATTATTATATGAA
Found at i:16598766 original size:18 final size:20
Alignment explanation
Indices: 16598743--16598786 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
16598733 AAATCAATAA
*
16598743 ATGATAAT-TATTTA-AATT
1 ATGATAATGTATTTATAAAT
16598761 ATGATAATGTATTTATAAAT
1 ATGATAATGTATTTATAAAT
16598781 ATGATA
1 ATGATA
16598787 TGATTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 6 0.26
20 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (20 bp):
ATGATAATGTATTTATAAAT
Found at i:16602089 original size:218 final size:219
Alignment explanation
Indices: 16601699--16602094 Score: 659
Period size: 219 Copynumber: 1.8 Consensus size: 219
16601689 TCAAGTTTTT
* * * * *
16601699 TTTTTTTAAATAATTCACGCTAGACCGTGATGAATGCAAAGTGCCACTTGATCTGTAGAGGTGTG
1 TTTTTTTAAATAATCCACACTAGACCATGATGAATGCAAAGTGCCACTTGATCTGTAGAGATGGG
* *
16601764 TGAAATCAGTTCTGTCAAAGCTGTAGTTAAATCTTTTTCCGGGATTTTTCCCCTCTAGAGTTTGA
66 TGAAATCAGTTCTGTCAAAGCTGTAGTTAAATCTTTTTCCAGGATTTTTCCCCTCTAGAATTTGA
16601829 AGCTCCAATTAAGTGACATTTGCCAAGGTGTTGCAATTAGGTTGGAATACTTATTTTGCAAAATT
131 AGCTCCAATTAAGTGACATTTGCCAAGGTGTTGCAATTAGGTTGGAATACTTATTTTGCAAAATT
16601894 TTGGATGGGGGTGAATCTGTAAGG
196 TTGGATGGGGGTGAATCTGTAAGG
** * *
16601918 TTTTTTTCTATAATCCACACTAGACCATGATGAATGCAAAGTGCCTCTTGGTCTGTAGAGATGGG
1 TTTTTTTAAATAATCCACACTAGACCATGATGAATGCAAAGTGCCACTTGATCTGTAGAGATGGG
* *
16601983 TGAAATCAGTTCTGTCAAAGCTGTAGTT-AATCTTTTTCTAGGCTTTTTCCCCTCTAGAATTTGA
66 TGAAATCAGTTCTGTCAAAGCTGTAGTTAAATCTTTTTCCAGGATTTTTCCCCTCTAGAATTTGA
*
16602047 AGCTCCAATTAAGTGACATTTGCCAGGGTGTTGCAATTAGGTTGGAAT
131 AGCTCCAATTAAGTGACATTTGCCAAGGTGTTGCAATTAGGTTGGAAT
16602095 GTTCATTTCA
Statistics
Matches: 163, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
218 79 0.48
219 84 0.52
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (219 bp):
TTTTTTTAAATAATCCACACTAGACCATGATGAATGCAAAGTGCCACTTGATCTGTAGAGATGGG
TGAAATCAGTTCTGTCAAAGCTGTAGTTAAATCTTTTTCCAGGATTTTTCCCCTCTAGAATTTGA
AGCTCCAATTAAGTGACATTTGCCAAGGTGTTGCAATTAGGTTGGAATACTTATTTTGCAAAATT
TTGGATGGGGGTGAATCTGTAAGG
Found at i:16602111 original size:218 final size:219
Alignment explanation
Indices: 16601699--16602138 Score: 652
Period size: 218 Copynumber: 2.0 Consensus size: 219
16601689 TCAAGTTTTT
* * * * *
16601699 TTTTTTTAAATAATTCACGCTAGACCGTGATGAATGCAAAGTGCCACTTGATCTGTAGAGGTGTG
1 TTTTTTTAAATAATCCACACTAGACCATGATGAATGCAAAGTGCCACTTGATCTGTAGAGATGGG
* *
16601764 TGAAATCAGTTCTGTCAAAGCTGTAGTTAAATCTTTTTCCGGGATTTTTCCCCTCTAGAGTTTGA
66 TGAAATCAGTTCTGTCAAAGCTGTAGTTAAATCTTTTTCCAGGATTTTTCCCCTCTAGAATTTGA
**
16601829 AGCTCCAATTAAGTGACATTTGCCAAGGTGTTGCAATTAGGTTGGAATACTTATTTTGCAAAATT
131 AGCTCCAATTAAGTGACATTTGCCAAGGTGTTGCAATTAGGTTGGAATACTTATTTCACAAAATT
* * *
16601894 TTGG-ATGGGGGTGAATCTGTAAGG
196 CTGGTA-GGAGGTGAAGCTGTAAGG
** * *
16601918 TTTTTTTCTATAATCCACACTAGACCATGATGAATGCAAAGTGCCTCTTGGTCTGTAGAGATGGG
1 TTTTTTTAAATAATCCACACTAGACCATGATGAATGCAAAGTGCCACTTGATCTGTAGAGATGGG
* *
16601983 TGAAATCAGTTCTGTCAAAGCTGTAGTT-AATCTTTTTCTAGGCTTTTTCCCCTCTAGAATTTGA
66 TGAAATCAGTTCTGTCAAAGCTGTAGTTAAATCTTTTTCCAGGATTTTTCCCCTCTAGAATTTGA
* *
16602047 AGCTCCAATTAAGTGACATTTGCCAGGGTGTTGCAATTAGGTTGGAAT-GTTCATTTCACAAAAT
131 AGCTCCAATTAAGTGACATTTGCCAAGGTGTTGCAATTAGGTTGGAATACTT-ATTTCACAAAAT
*
16602111 TCTGGTAGGAGGTGAAGGTGTAAGG
195 TCTGGTAGGAGGTGAAGCTGTAAGG
16602136 TTT
1 TTT
16602139 GGTGATTCAT
Statistics
Matches: 198, Mismatches: 21, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
217 2 0.01
218 111 0.56
219 85 0.43
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (219 bp):
TTTTTTTAAATAATCCACACTAGACCATGATGAATGCAAAGTGCCACTTGATCTGTAGAGATGGG
TGAAATCAGTTCTGTCAAAGCTGTAGTTAAATCTTTTTCCAGGATTTTTCCCCTCTAGAATTTGA
AGCTCCAATTAAGTGACATTTGCCAAGGTGTTGCAATTAGGTTGGAATACTTATTTCACAAAATT
CTGGTAGGAGGTGAAGCTGTAAGG
Found at i:16605100 original size:26 final size:27
Alignment explanation
Indices: 16605049--16605110 Score: 108
Period size: 26 Copynumber: 2.3 Consensus size: 27
16605039 AAAAAATAAT
16605049 CAAAATATTATAACTTTTTTTTATTTAC
1 CAAAATATTATAAC-TTTTTTTATTTAC
16605077 CAAAATATTATAA-TTTTTTTATTTAC
1 CAAAATATTATAACTTTTTTTATTTAC
16605103 CAAAATAT
1 CAAAATAT
16605111 ACAAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 21 0.62
28 13 0.38
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (27 bp):
CAAAATATTATAACTTTTTTTATTTAC
Found at i:16605279 original size:27 final size:27
Alignment explanation
Indices: 16605226--16605282 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
16605216 TTTGGGGGGA
* *
16605226 GAAGGAGAGGGAAAGAAAGGAAGGAAG
1 GAAGGAGAGGGAAAGAAAGAAAAGAAG
16605253 GAAGGAGA-GGAAAGAAAGAAAAAGAAG
1 GAAGGAGAGGGAAAGAAAG-AAAAGAAG
16605280 GAA
1 GAA
16605283 AGAAAAAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (27 bp):
GAAGGAGAGGGAAAGAAAGAAAAGAAG
Found at i:16605298 original size:39 final size:41
Alignment explanation
Indices: 16605250--16605400 Score: 165
Period size: 39 Copynumber: 3.8 Consensus size: 41
16605240 GAAAGGAAGG
16605250 AAGG-AAGGAG-AG-GAAAGAAAGAAAAAGAAGGAAAGAAA
1 AAGGAAAGGAGAAGAGAAAGAAAGAAAAAGAAGGAAAGAAA
*
16605288 AAGGAAAGGAGAAGAGAAA-AAA-AAAACGAA-G-AAGAAGA
1 AAGGAAAGGAGAAGAGAAAGAAAGAAAAAGAAGGAAAGAA-A
*
16605326 AGAGGAAAGGAGAAGAAAAAAGAAAGAAAAAGAAGGAAAG-AA
1 A-AGGAAAGGAGAAG-AGAAAGAAAGAAAAAGAAGGAAAGAAA
* * * *
16605368 AAGGAAATGAGAAAAGAAAAAAAGAAGAAGAAG
1 AAGGAAAGGAGAAGAGAAAGAAAGAAAAAGAAG
16605401 AGGGAAGTAA
Statistics
Matches: 95, Mismatches: 8, Indels: 18
0.79 0.07 0.15
Matches are distributed among these distances:
37 5 0.05
38 7 0.07
39 26 0.27
40 25 0.26
41 18 0.19
42 9 0.09
43 2 0.02
44 3 0.03
ACGTcount: A:0.68, C:0.01, G:0.30, T:0.01
Consensus pattern (41 bp):
AAGGAAAGGAGAAGAGAAAGAAAGAAAAAGAAGGAAAGAAA
Found at i:16605309 original size:34 final size:34
Alignment explanation
Indices: 16605254--16605365 Score: 88
Period size: 35 Copynumber: 3.2 Consensus size: 34
16605244 GGAAGGAAGG
* *
16605254 AAGGAGAGGA-AAGAAAGAAAAAGAAGGAAAGAAA
1 AAGGAAAGGAGAAGAGA-AAAAAGAAGGAAAGAAA
* *
16605288 AAGGAAAGGAGAAGAGAAAAAAAAAACGAAGAAGAAGA
1 AAGGAAAGGAGAAGAG-AAAAAAGAA-GGA-AAGAA-A
* *
16605326 AGAGGAAAGGAG-A-AGAAAAAAGAAAGAAA-AAG
1 A-AGGAAAGGAGAAGAGAAAAAAGAAGGAAAGAAA
16605358 AAGGAAAG
1 AAGGAAAG
16605366 AAAAGGAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
31 7 0.11
32 1 0.02
33 2 0.03
34 11 0.17
35 12 0.19
36 11 0.17
37 7 0.11
38 3 0.05
39 10 0.16
ACGTcount: A:0.68, C:0.01, G:0.31, T:0.00
Consensus pattern (34 bp):
AAGGAAAGGAGAAGAGAAAAAAGAAGGAAAGAAA
Found at i:16605419 original size:73 final size:72
Alignment explanation
Indices: 16605287--16605432 Score: 163
Period size: 75 Copynumber: 2.0 Consensus size: 72
16605277 AAGGAAAGAA
* *
16605287 AAAGGAAAGGAGAAGAGAAAAAAAAAACGAAGAAGAAGAAGAGGAAAGGAGAAGAAAAAAGAAAG
1 AAAGAAAAGGAGAAGAGAAAAAAAAAAC-AAGAAGAAGAAGAGGAAAGAAGAAG-AAAAA-AAAG
*
16605352 AAAAAGAAGG
63 AAAAAAAAGG
* * * *
16605362 AAAGAAAAGGA-AATGAGAAAAGAAAAA-AAGAAGAAGAAGAGGGAAGTAAG-GGGAAAAAAAGA
1 AAAGAAAAGGAGAA-GAGAAAAAAAAAACAAGAAGAAGAAGAGGAAAG-AAGAAGAAAAAAAAGA
16605424 AAAAAAAGG
64 AAAAAAAGG
16605433 TAATTTTATT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
71 13 0.21
72 4 0.06
73 19 0.31
74 4 0.06
75 22 0.35
ACGTcount: A:0.68, C:0.01, G:0.30, T:0.01
Consensus pattern (72 bp):
AAAGAAAAGGAGAAGAGAAAAAAAAAACAAGAAGAAGAAGAGGAAAGAAGAAGAAAAAAAAGAAA
AAAAAGG
Found at i:16605427 original size:81 final size:80
Alignment explanation
Indices: 16605263--16605428 Score: 219
Period size: 81 Copynumber: 2.0 Consensus size: 80
16605253 GAAGGAGAGG
* *
16605263 AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAGAGAAAAAAAAAACGAAGAAGAAGAAG
1 AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAAAGAAAAAAAAAAAGAAGAAGAAGAAG
*
16605328 AGGAAAGGAGAAGAAA
66 AGGAAA-GAAAAGAAA
* *
16605344 AAAGAAAGAAAAAGAAGGAAAG-AAAAGGAAATGAGAAAAGAAAAAAAGAAGAAGAAGAGGGAAG
1 AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAAAGAAAAAAA-AA-AAGAAGA-AGAAG
*
16605408 TAAGGGGAAA-AAAAGAAA
63 -AAGAGGAAAGAAAAGAAA
16605426 AAA
1 AAA
16605429 AAGGTAATTT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
80 23 0.31
81 24 0.32
82 16 0.21
83 4 0.05
84 8 0.11
ACGTcount: A:0.69, C:0.01, G:0.29, T:0.01
Consensus pattern (80 bp):
AAAGAAAGAAAAAGAAGGAAAGAAAAAGGAAAGGAGAAAAGAAAAAAAAAAAGAAGAAGAAGAAG
AGGAAAGAAAAGAAA
Found at i:16606114 original size:64 final size:64
Alignment explanation
Indices: 16606038--16606169 Score: 187
Period size: 64 Copynumber: 2.1 Consensus size: 64
16606028 AAGGAAAGGG
16606038 TTTTTTCGGGTTTTTTACCAAAATATTACAAA-AAATAAAAAAAAT-ACCAAAATATTATAAACT
1 TTTTTTCGGGTTTTTTACCAAAATATTACAAATAAA-AAAAAAAATAACCAAAATATTAT-AACT
16606101 T
64 T
* * * * *
16606102 TTTTTTCGGGTTTTTTACTAAATTATTATAAATAAAAATAAAAATAACTAAAATATTATAACTT
1 TTTTTTCGGGTTTTTTACCAAAATATTACAAATAAAAAAAAAAATAACCAAAATATTATAACTT
16606166 TTTT
1 TTTT
16606170 ATTTACCAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
64 46 0.75
65 15 0.25
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (64 bp):
TTTTTTCGGGTTTTTTACCAAAATATTACAAATAAAAAAAAAAATAACCAAAATATTATAACTT
Found at i:16606638 original size:15 final size:16
Alignment explanation
Indices: 16606618--16606647 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16606608 GTACTGAAAT
16606618 AATAT-AAAATAATAA
1 AATATAAAAATAATAA
16606633 AATATAAAAATAATA
1 AATATAAAAATAATA
16606648 TATTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATATAAAAATAATAA
Found at i:16609477 original size:16 final size:15
Alignment explanation
Indices: 16609456--16609485 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16609446 AATAAAAATA
16609456 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
16609472 TATTATTTTATATT
1 TATTATTTTATATT
16609486 ATTTCAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:16609947 original size:26 final size:26
Alignment explanation
Indices: 16609912--16609965 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
16609902 TATTTTTATT
*
16609912 TTTTGGTAAATAAAAAAATTATAATA
1 TTTTGATAAATAAAAAAATTATAATA
16609938 TTTTGATAAATAAAAAAATTATAATA
1 TTTTGATAAATAAAAAAATTATAATA
16609964 TT
1 TT
16609966 GTGGTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (26 bp):
TTTTGATAAATAAAAAAATTATAATA
Found at i:16610016 original size:63 final size:65
Alignment explanation
Indices: 16609949--16610080 Score: 169
Period size: 66 Copynumber: 2.0 Consensus size: 65
16609939 TTTGATAAAT
16609949 AAAAAAATTATAATATTGTGG-TTATTTTTA-TTTTTTTATAATAATTTAGTAAAAAACCCGAAA
1 AAAAAAATTATAATATTGTGGATTATTTTTATTTTTTTTATAATAATTTAGTAAAAAACCCGAAA
** * * * * * *
16610012 AAAAAGTTTATAATATTTTGGTATTTTTTTTATTTTTTTTGTAATATTTTGGTAAAAAACCCTAA
1 AAAAAAATTATAATATTGTGG-ATTATTTTTATTTTTTTTATAATAATTTAGTAAAAAACCCGAA
16610077 A
65 A
16610078 AAA
1 AAA
16610081 CTCTTTTCCT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
63 18 0.31
65 8 0.14
66 32 0.55
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (65 bp):
AAAAAAATTATAATATTGTGGATTATTTTTATTTTTTTTATAATAATTTAGTAAAAAACCCGAAA
Found at i:16610750 original size:24 final size:24
Alignment explanation
Indices: 16610718--16610767 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
16610708 CTCTTCTCTT
16610718 CTTCGTTTTTTCTCTTCTCCTTTC
1 CTTCGTTTTTTCTCTTCTCCTTTC
* *
16610742 CTTCTTTTTTTTTCTTCTCCTTTC
1 CTTCGTTTTTTCTCTTCTCCTTTC
16610766 CT
1 CT
16610768 CTTCTTCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (24 bp):
CTTCGTTTTTTCTCTTCTCCTTTC
Found at i:16610775 original size:19 final size:19
Alignment explanation
Indices: 16610753--16610822 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
16610743 TTCTTTTTTT
16610753 TTCTTCTCCTTTCCTCTTC
1 TTCTTCTCCTTTCCTCTTC
*
16610772 TTCTTCTTCTTTCTCTCTT-
1 TTCTTCTCCTTTC-CTCTTC
* *
16610791 TTTTTCTCTCTTTCCTCTCC
1 TTCTTCTC-CTTTCCTCTTC
*
16610811 TTCCT-TCCTTTC
1 TTCTTCTCCTTTC
16610823 TTTCTTTCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
18 5 0.12
19 24 0.57
20 13 0.31
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (19 bp):
TTCTTCTCCTTTCCTCTTC
Found at i:16612364 original size:15 final size:15
Alignment explanation
Indices: 16612353--16612388 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
16612343 GCCGGAGTCT
16612353 GATGAAGAGGAGGAA
1 GATGAAGAGGAGGAA
* *
16612368 GATGAAGAGGATGAT
1 GATGAAGAGGAGGAA
16612383 GATGAA
1 GATGAA
16612389 TATGATCCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.42, T:0.14
Consensus pattern (15 bp):
GATGAAGAGGAGGAA
Found at i:16618227 original size:27 final size:27
Alignment explanation
Indices: 16618197--16618287 Score: 119
Period size: 27 Copynumber: 3.4 Consensus size: 27
16618187 CCTATGGAAG
* * *
16618197 AGGCGGCACCAGTCACGCCTTTCCCAT
1 AGGCGGCATCGGTCACGCCTTCCCCAT
*
16618224 AGGCGGTATCGGTCACGCCTTCCCCAT
1 AGGCGGCATCGGTCACGCCTTCCCCAT
* * *
16618251 AGGCGGCATCGGTGATGCCATCCCCAT
1 AGGCGGCATCGGTCACGCCTTCCCCAT
16618278 AGGCGGCATC
1 AGGCGGCATC
16618288 CACTCCCCCC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.18, C:0.36, G:0.27, T:0.19
Consensus pattern (27 bp):
AGGCGGCATCGGTCACGCCTTCCCCAT
Found at i:16621825 original size:37 final size:37
Alignment explanation
Indices: 16621760--16621868 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
16621750 TACGTATGAT
* *
16621760 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
16621795 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
16621832 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
16621869 TAAAGCTATC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 10 0.14
36 3 0.04
37 56 0.81
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:16621911 original size:52 final size:52
Alignment explanation
Indices: 16621832--16622146 Score: 379
Period size: 52 Copynumber: 6.2 Consensus size: 52
16621822 TAAGTGTAGC
* * *
16621832 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
16621885 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAA-CTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCC-AAAGCTATCACTTAT
* * *
16621937 CAC---T---TTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
*
16621983 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAA-CTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCC-AAAGCTATCACTTAT
* * *
16622035 CAC---T---TTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
* * *
16622081 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACCTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
16622133 CACTTTGTCACTTG
1 CACTTT-TCACTTG
16622147 ATCAGAAGTA
Statistics
Matches: 226, Mismatches: 19, Indels: 34
0.81 0.07 0.12
Matches are distributed among these distances:
45 4 0.02
46 78 0.35
49 1 0.00
52 123 0.54
53 20 0.09
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
Found at i:16621942 original size:98 final size:98
Alignment explanation
Indices: 16621832--16622152 Score: 579
Period size: 98 Copynumber: 3.3 Consensus size: 98
16621822 TAAGTGTAGC
* ** *
16621832 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
16621897 GTCACTTGATCAGATAAGTGTAGCCGAAACTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAACTAT
16621930 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
16621995 GTCACTTGATCAGATAAGTGTAGCCGAAACTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAACTAT
16622028 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
*
16622093 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAACTAT
* *
16622126 CACCTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCTCTTGATCAGA
16622153 AGTACTCAAA
Statistics
Matches: 216, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 216 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (98 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAACTAT
Found at i:16627298 original size:24 final size:24
Alignment explanation
Indices: 16627268--16627314 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
16627258 ATATATGAAA
* *
16627268 AATAAATTTTAAATATTTTTAAAC
1 AATAAATATTAAATATTTATAAAC
*
16627292 AATAAATATTAATTATTTATAAA
1 AATAAATATTAAATATTTATAAA
16627315 ATTTAATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AATAAATATTAAATATTTATAAAC
Found at i:16627905 original size:24 final size:24
Alignment explanation
Indices: 16627873--16627918 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16627863 CTAATTAAAT
* *
16627873 TTTATAAATAATTAATATTTATTG
1 TTTAAAAATAATTAAAATTTATTG
*
16627897 TTTAAAAATATTTAAAATTTAT
1 TTTAAAAATAATTAAAATTTAT
16627919 ATTTCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAAATAATTAAAATTTATTG
Found at i:16628155 original size:13 final size:13
Alignment explanation
Indices: 16628137--16628161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16628127 CTTCTCCACG
16628137 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
16628150 TTTTCAAAAGCA
1 TTTTCAAAAGCA
16628162 TTGCCAAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:16628607 original size:27 final size:27
Alignment explanation
Indices: 16628566--16628626 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
16628556 AGCAACAGGA
* *
16628566 GCCGCCTTTGGGGAAGGCATGACCGAT
1 GCCGCCTCTGAGGAAGGCATGACCGAT
* *
16628593 GCCGCCTCTGAGGAAGGCGTGACCGGT
1 GCCGCCTCTGAGGAAGGCATGACCGAT
16628620 GCCGCCT
1 GCCGCCT
16628627 TTTCCCCAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.15, C:0.31, G:0.38, T:0.16
Consensus pattern (27 bp):
GCCGCCTCTGAGGAAGGCATGACCGAT
Found at i:16628686 original size:27 final size:27
Alignment explanation
Indices: 16628607--16628675 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
16628597 CCTCTGAGGA
*
16628607 AGGCGTGACCGGTGCCGCCTTTTCCCC
1 AGGCGTGACCGGTGCCGCCTCTTCCCC
16628634 AGGCGTGACCGGTGCCGCCTCTTCCCC
1 AGGCGTGACCGGTGCCGCCTCTTCCCC
16628661 AGGCGTGACCGGTGC
1 AGGCGTGACCGGTGC
16628676 TGTCCCGTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.09, C:0.39, G:0.33, T:0.19
Consensus pattern (27 bp):
AGGCGTGACCGGTGCCGCCTCTTCCCC
Found at i:16628765 original size:27 final size:26
Alignment explanation
Indices: 16628699--16628756 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
16628689 CATCACTTTT
16628699 TTTTGTCAGTTTATTTTTTTAAACAG
1 TTTTGTCAGTTTATTTTTTTAAACAG
16628725 TTTTGTCAGTTTATTTTTTTAAACAG
1 TTTTGTCAGTTTATTTTTTTAAACAG
16628751 TTTTGT
1 TTTTGT
16628757 TTTTTTTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (26 bp):
TTTTGTCAGTTTATTTTTTTAAACAG
Found at i:16629219 original size:20 final size:21
Alignment explanation
Indices: 16629179--16629229 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
16629169 CGATTTCTGC
*
16629179 TTCTTCTTCTCTACGTTTCTT
1 TTCTTCTTCTCTACATTTCTT
*
16629200 TTCTTC-TCTTTACATTTCTT
1 TTCTTCTTCTCTACATTTCTT
16629220 TTCTT-TTCTC
1 TTCTTCTTCTC
16629230 CATTTTATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.06, C:0.27, G:0.02, T:0.65
Consensus pattern (21 bp):
TTCTTCTTCTCTACATTTCTT
Found at i:16630932 original size:21 final size:21
Alignment explanation
Indices: 16630891--16630933 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
16630881 AATAAAGTAG
* *
16630891 ATTATATATTATTTTTATAGT
1 ATTACATATTATATTTATAGT
16630912 ATTACATATTATGATTT-TAGT
1 ATTACATATTAT-ATTTATAGT
16630933 A
1 A
16630934 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTACATATTATATTTATAGT
Found at i:16630987 original size:57 final size:56
Alignment explanation
Indices: 16630925--16631042 Score: 139
Period size: 57 Copynumber: 2.1 Consensus size: 56
16630915 ACATATTATG
* *
16630925 ATTTTAGTAAATTCATA-TAAGAATAATTATATTAAGAATTTTATTAAATTATATATT
1 ATTTTAGTAAATT-ATATTAAGAATAATTATATTAA-AATATGATTAAATTATATATT
* * * * *
16630982 ATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAGATTATTTATT
1 ATTTTAGTAAATTATA-TTAAGAATAATTATATTAAAATATGATTAAATTATATATT
16631039 ATTT
1 ATTT
16631043 ATATTAACAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
56 3 0.06
57 33 0.63
58 16 0.31
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (56 bp):
ATTTTAGTAAATTATATTAAGAATAATTATATTAAAATATGATTAAATTATATATT
Found at i:16631181 original size:23 final size:23
Alignment explanation
Indices: 16631155--16631201 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
16631145 CTATTACAAC
*
16631155 ATCATTCCATTCTACCAAACACA
1 ATCATTCCATTCAACCAAACACA
16631178 ATCATTCCATTCAACCAAACACA
1 ATCATTCCATTCAACCAAACACA
16631201 A
1 A
16631202 GAATACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (23 bp):
ATCATTCCATTCAACCAAACACA
Found at i:16631269 original size:45 final size:44
Alignment explanation
Indices: 16631180--16631272 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
16631170 CAAACACAAT
16631180 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
* *
16631224 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGTTTTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGTTCTATTC
16631269 CATT
1 CATT
16631273 ACACCTCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.49
45 22 0.49
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:16631292 original size:24 final size:24
Alignment explanation
Indices: 16631275--16631325 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
16631265 ATTCCATTAC
16631275 ACCTCTATACCTCTATTCCAGCGA
1 ACCTCTATACCTCTATTCCAGCGA
16631299 ACCTCTATACCTCTATTCCAGCGA
1 ACCTCTATACCTCTATTCCAGCGA
16631323 ACC
1 ACC
16631326 AAATGTGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.39, G:0.08, T:0.27
Consensus pattern (24 bp):
ACCTCTATACCTCTATTCCAGCGA
Found at i:16633567 original size:31 final size:31
Alignment explanation
Indices: 16633523--16633592 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
16633513 TAAATTTAGT
* * *
16633523 CCTCAAAGTTTACATATTATGTTAATCTAGC
1 CCTCAATGATTACATATTATGTCAATCTAGC
*
16633554 TCTCAATGATTACATATTATGTCAATCTAGC
1 CCTCAATGATTACATATTATGTCAATCTAGC
16633585 CCTCAATG
1 CCTCAATG
16633593 TTGCTTGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.37
Consensus pattern (31 bp):
CCTCAATGATTACATATTATGTCAATCTAGC
Found at i:16634169 original size:45 final size:45
Alignment explanation
Indices: 16634104--16634234 Score: 253
Period size: 45 Copynumber: 2.9 Consensus size: 45
16634094 AATGGCTATG
*
16634104 GTGGCGGCAATGGATGGAGTTCATCATCCCCAATGCCACCACCAA
1 GTGGTGGCAATGGATGGAGTTCATCATCCCCAATGCCACCACCAA
16634149 GTGGTGGCAATGGATGGAGTTCATCATCCCCAATGCCACCACCAA
1 GTGGTGGCAATGGATGGAGTTCATCATCCCCAATGCCACCACCAA
16634194 GTGGTGGCAATGGATGGAGTTCATCATCCCCAATGCCACCA
1 GTGGTGGCAATGGATGGAGTTCATCATCCCCAATGCCACCA
16634235 GGACCAATTT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 85 1.00
ACGTcount: A:0.26, C:0.29, G:0.25, T:0.20
Consensus pattern (45 bp):
GTGGTGGCAATGGATGGAGTTCATCATCCCCAATGCCACCACCAA
Found at i:16634292 original size:21 final size:21
Alignment explanation
Indices: 16634233--16634297 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 21
16634223 CCAATGCCAC
16634233 CAGGACCAATTTATAGTGGTT
1 CAGGACCAATTTATAGTGGTT
*
16634254 CAGGAAGACAATTTTATAGTGGTT
1 CAGG-A-CCAA-TTTATAGTGGTT
16634278 CAGGACCAATTTATAGTGGT
1 CAGGACCAATTTATAGTGGT
16634298 GAAGCAACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 15 0.38
22 4 0.10
23 4 0.10
24 16 0.41
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (21 bp):
CAGGACCAATTTATAGTGGTT
Found at i:16635752 original size:13 final size:13
Alignment explanation
Indices: 16635734--16635758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16635724 TATTAATCCC
16635734 GTTAAAATTTTTA
1 GTTAAAATTTTTA
16635747 GTTAAAATTTTT
1 GTTAAAATTTTT
16635759 GGTGACATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
GTTAAAATTTTTA
Found at i:16639248 original size:59 final size:59
Alignment explanation
Indices: 16639145--16639256 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 59
16639135 ACTAACTACT
** *** *
16639145 TGGAAAAAAAAAAGTTTAGGTGCCAATTTAAACATTGTTGCCAAGTTTAGGTACCTAAC
1 TGGAAAAAAAAAACCTTAGGTGCCAATTTAAACATTGCAACCAAGTTCAGGTACCTAAC
* * *
16639204 TGGATAAAAAAAACCTTAGGTGCCAATTTGAACCTTGCAACCAAGTTCAGGTA
1 TGGAAAAAAAAAACCTTAGGTGCCAATTTAAACATTGCAACCAAGTTCAGGTA
16639257 ACAAAATGTA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 44 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (59 bp):
TGGAAAAAAAAAACCTTAGGTGCCAATTTAAACATTGCAACCAAGTTCAGGTACCTAAC
Found at i:16643489 original size:31 final size:30
Alignment explanation
Indices: 16643445--16643503 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
16643435 TAGCGCAAAA
*
16643445 TCAAAATTCATGTATGATATTGTATATTTGG
1 TCAAAATTCATGTATAATATTG-ATATTTGG
* * *
16643476 TCAAAGTTTATGTATAATTTTGATATTT
1 TCAAAATTCATGTATAATATTGATATTT
16643504 ACCACCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (30 bp):
TCAAAATTCATGTATAATATTGATATTTGG
Found at i:16644336 original size:15 final size:17
Alignment explanation
Indices: 16644293--16644339 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
16644283 AAAAATAGAA
16644293 ATAAATATATAAAATTTTC
1 ATAAAT-TATAAAA-TTTC
*
16644312 ATAAAATATAAAA-TT-
1 ATAAATTATAAAATTTC
16644327 ATAAATTATAAAA
1 ATAAATTATAAAA
16644340 AATATTAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 12 0.46
16 2 0.08
18 7 0.27
19 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAATTATAAAATTTC
Found at i:16652848 original size:17 final size:18
Alignment explanation
Indices: 16652822--16652856 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
16652812 TACACTCTAG
16652822 AAATAAAAATA-TAAATA
1 AAATAAAAATATTAAATA
*
16652839 AAATATAAATATTAAATA
1 AAATAAAAATATTAAATA
16652857 TGAAGATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAAAATATTAAATA
Found at i:16652854 original size:7 final size:6
Alignment explanation
Indices: 16652822--16652884 Score: 56
Period size: 6 Copynumber: 10.0 Consensus size: 6
16652812 TACACTCTAG
* *
16652822 AAATAA AAATAT AAATA- AAATAT AAATATT AAATAT GAAGATTT GAAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATA-T AAATAT -AA-ATAT -AAATAT
*
16652873 ATATAT AAATAT
1 AAATAT AAATAT
16652885 TTAAGTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
5 5 0.10
6 26 0.54
7 11 0.23
8 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (6 bp):
AAATAT
Found at i:16655888 original size:3 final size:3
Alignment explanation
Indices: 16655880--16655921 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
16655870 CGTAGAACAA
16655880 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
16655922 CATTGTAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16656586 original size:7 final size:7
Alignment explanation
Indices: 16656566--16656598 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
16656556 TTTTAAATCT
16656566 AGATTCG
1 AGATTCG
16656573 -GAGTTCG
1 AGA-TTCG
16656580 AGATTCG
1 AGATTCG
16656587 AGATTCG
1 AGATTCG
16656594 AGATT
1 AGATT
16656599 TGATGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 2 0.08
7 20 0.83
8 2 0.08
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (7 bp):
AGATTCG
Found at i:16664535 original size:15 final size:15
Alignment explanation
Indices: 16664515--16664559 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
16664505 CAAGAACAAG
*
16664515 AGCAACAACAGCAGC
1 AGCAACAACAACAGC
16664530 AGCAACAACAACAGC
1 AGCAACAACAACAGC
*
16664545 AGCAGCAACAACAGC
1 AGCAACAACAACAGC
16664560 TTCTTGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.49, C:0.33, G:0.18, T:0.00
Consensus pattern (15 bp):
AGCAACAACAACAGC
Found at i:16664538 original size:18 final size:18
Alignment explanation
Indices: 16664517--16664557 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
16664507 AGAACAAGAG
16664517 CAACAACAGCAGCAGCAA
1 CAACAACAGCAGCAGCAA
16664535 CAACAACAGCAGCAGCAA
1 CAACAACAGCAGCAGCAA
16664553 CAACA
1 CAACA
16664558 GCTTCTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.34, G:0.15, T:0.00
Consensus pattern (18 bp):
CAACAACAGCAGCAGCAA
Found at i:16669953 original size:29 final size:29
Alignment explanation
Indices: 16669920--16669980 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
16669910 GAGAAATTGA
* * *
16669920 ATAGTTGGGTGACAATTTTGTAACTTTTC
1 ATAGTTGGATGACAATTTTATAAATTTTC
**
16669949 ATAGTTGGATGATTATTTTATAAATTTTC
1 ATAGTTGGATGACAATTTTATAAATTTTC
16669978 ATA
1 ATA
16669981 ATTGAGTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.48
Consensus pattern (29 bp):
ATAGTTGGATGACAATTTTATAAATTTTC
Found at i:16673584 original size:31 final size:31
Alignment explanation
Indices: 16673546--16673605 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
16673536 CATGTTCTTC
16673546 GAACTATTCAAAAGCTTTTATTTAAGTCACT
1 GAACTATTCAAAAGCTTTTATTTAAGTCACT
** *
16673577 GAACTATTTGAAAGTTTTTATTTAAGTCA
1 GAACTATTCAAAAGCTTTTATTTAAGTCA
16673606 TTGAGTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (31 bp):
GAACTATTCAAAAGCTTTTATTTAAGTCACT
Found at i:16685281 original size:19 final size:19
Alignment explanation
Indices: 16685239--16685283 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
16685229 TTTAAAATCC
*
16685239 GAATTTGTGTATTTATATT
1 GAATTTGGGTATTTATATT
*
16685258 AAATTTGGGTATTT-TATTT
1 GAATTTGGGTATTTATA-TT
16685277 GAATTTG
1 GAATTTG
16685284 AATTAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.56
Consensus pattern (19 bp):
GAATTTGGGTATTTATATT
Found at i:16686183 original size:24 final size:25
Alignment explanation
Indices: 16686156--16686212 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
16686146 AATTAAATTA
*
16686156 TAATAAAATATAATTTTATCA-TTT
1 TAATAAAATATAATTTTATAATTTT
* *
16686180 TAATAATATATATTTTTATAATTTT
1 TAATAAAATATAATTTTATAATTTT
16686205 TAA-AAAAT
1 TAATAAAAT
16686213 TAAATTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 22 0.79
25 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TAATAAAATATAATTTTATAATTTT
Found at i:16687588 original size:26 final size:28
Alignment explanation
Indices: 16687559--16687638 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 28
16687549 TATTAAAGCC
16687559 AAACTCAAGTACCAAATTAGAAA-AA-A
1 AAACTCAAGTACCAAATTAGAAATAAGA
* *
16687585 AAACTCAGGTACCAAATT-GAACATTGAAGTC
1 AAACTCAAGTACCAAATTAGAA-A-T-AAG-A
16687616 AAACTCAAGTACCAAATTAGAAA
1 AAACTCAAGTACCAAATTAGAAA
16687639 GGAAAACTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 3 0.07
26 18 0.41
29 2 0.05
31 18 0.41
32 3 0.07
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.19
Consensus pattern (28 bp):
AAACTCAAGTACCAAATTAGAAATAAGA
Found at i:16687621 original size:57 final size:57
Alignment explanation
Indices: 16687558--16687671 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
16687548 ATATTAAAGC
* *
16687558 CAAACTCAAGTACCAAATTAGAAAAAAAAACTCAGGTACCAAATTGAACATTGAAGT
1 CAAACTCAAGTACCAAATTAGAAAAAAAAACTCAGGTACCAAATTAAACATGGAAGT
** **
16687615 CAAACTCAAGTACCAAATTAGAAAGGAAAACTTGGGTACCAAATTAAACATGGAAGT
1 CAAACTCAAGTACCAAATTAGAAAAAAAAACTCAGGTACCAAATTAAACATGGAAGT
16687672 AAAATTCACC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (57 bp):
CAAACTCAAGTACCAAATTAGAAAAAAAAACTCAGGTACCAAATTAAACATGGAAGT
Found at i:16693521 original size:17 final size:17
Alignment explanation
Indices: 16693499--16693532 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16693489 AATTAAAATT
16693499 CCTATTTTCATATTAAC
1 CCTATTTTCATATTAAC
16693516 CCTATTTTCATATTAAC
1 CCTATTTTCATATTAAC
16693533 TCATTCTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (17 bp):
CCTATTTTCATATTAAC
Found at i:16694572 original size:28 final size:28
Alignment explanation
Indices: 16694531--16694589 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
16694521 GTTCAACTGA
*
16694531 AAAAATTGATTTATTTCATTAAATAAAT
1 AAAAATTGACTTATTTCATTAAATAAAT
*
16694559 AAAAATTGACTTATTTCTTTAAATAAAT
1 AAAAATTGACTTATTTCATTAAATAAAT
16694587 AAA
1 AAA
16694590 TAAAACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (28 bp):
AAAAATTGACTTATTTCATTAAATAAAT
Found at i:16698988 original size:21 final size:22
Alignment explanation
Indices: 16698962--16699008 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
16698952 CTCTGCTCAA
*
16698962 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
16698983 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
16699005 ACTC
1 ACTC
16699009 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:16725267 original size:19 final size:19
Alignment explanation
Indices: 16725245--16725301 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
16725235 ACATTATATT
16725245 TTATTTTAATTATTATTTG
1 TTATTTTAATTATTATTTG
* *
16725264 TTATTTTCATTGAAT-TTTG
1 TTATTTTAATT-ATTATTTG
*
16725283 TTACTTTTACTT-TTATTTG
1 TTA-TTTTAATTATTATTTG
16725302 GTTGAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 1 0.03
19 21 0.70
20 8 0.27
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (19 bp):
TTATTTTAATTATTATTTG
Found at i:16727492 original size:123 final size:124
Alignment explanation
Indices: 16727275--16727571 Score: 353
Period size: 123 Copynumber: 2.4 Consensus size: 124
16727265 TTATCAAATT
* ** * *
16727275 AATTAATTAATTAAGTGTTTTGATAAATTTAAGTTTCTTGTTTATTAATTTTTTTTAAGATTAAT
1 AATTAATTAATTAAGTGTTTTGATAAATTTAAATTTCTTACTTATTAA-TATTGTTAAGATTAAT
** * * * *
16727340 GAAAATTTTAAAACTTTAAGATACAAAATTTCATAAAATTTTGATTGTCATCTATTATCA
65 GAAAAAATAAAAACTTTAAGATAAAAAATTTCATAAAACTTTAATTGTCATCTATTATCA
* * *
16727400 AATTAATTAATTAGGTTTTTTTATAAATTTAAATTTCTTACTTATTAA-ATTGTTAAGATTAATG
1 AATTAATTAATTAAGTGTTTTGATAAATTTAAATTTCTTACTTATTAATATTGTTAAGATTAATG
* * *
16727464 AAAAAATAAAAACTTTAGGATAAAAAATTTCATAAAACTTTAATTTTTATCTATTATCA
66 AAAAAATAAAAACTTTAAGATAAAAAATTTCATAAAACTTTAATTGTCATCTATTATCA
* * * *
16727523 AATTAATTCATTAACAAAGTGTTTTGATAAAATTAATTTTCTTAATTAT
1 AATTAATTAATT----AAGTGTTTTGATAAATTTAAATTTCTTACTTAT
16727572 AAATCAATAA
Statistics
Matches: 144, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
123 75 0.52
125 42 0.29
127 27 0.19
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (124 bp):
AATTAATTAATTAAGTGTTTTGATAAATTTAAATTTCTTACTTATTAATATTGTTAAGATTAATG
AAAAAATAAAAACTTTAAGATAAAAAATTTCATAAAACTTTAATTGTCATCTATTATCA
Found at i:16735405 original size:41 final size:41
Alignment explanation
Indices: 16735360--16735443 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
16735350 CGGATCATTA
16735360 TGGGTTTATGTCATTTTAAATTTCGAGATATTTTAAGTTCG
1 TGGGTTTATGTCATTTTAAATTTCGAGATATTTTAAGTTCG
16735401 TGGGTTTATGTCATTTTAAATTTCGAGATATTTTAAGTTCG
1 TGGGTTTATGTCATTTTAAATTTCGAGATATTTTAAGTTCG
16735442 TG
1 TG
16735444 TGCAAGGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (41 bp):
TGGGTTTATGTCATTTTAAATTTCGAGATATTTTAAGTTCG
Found at i:16755523 original size:23 final size:22
Alignment explanation
Indices: 16755483--16755526 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
16755473 TATTTTTTTC
*
16755483 AAATAAAATTTAATTCTAATTG
1 AAATAAAATATAATTCTAATTG
16755505 AAATAAAATAATAATTCTAATT
1 AAATAAAAT-ATAATTCTAATT
16755527 CCAACATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATAAAATATAATTCTAATTG
Found at i:16762912 original size:34 final size:35
Alignment explanation
Indices: 16762854--16762920 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
16762844 CAAACACTAG
* *
16762854 AAAATATTTTTCAGTGAATCATTTTACAGAAAAGT
1 AAAACATTTTTCAGTAAATCATTTTACAGAAAAGT
*
16762889 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTTCAGTAAATCATTTTACAGAAAA
16762921 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.34
Consensus pattern (35 bp):
AAAACATTTTTCAGTAAATCATTTTACAGAAAAGT
Found at i:16765767 original size:30 final size:28
Alignment explanation
Indices: 16765718--16765786 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
16765708 GCATATTTGG
*
16765718 AATTTAGTTTTGTTATTTT-ATTTTTAAA
1 AATTTAGTTTTGTTATTTTAAATTTT-AA
*
16765746 AATTTAGTCTTTTTATATTTTAAATTTTAA
1 AATTTAGT-TTTGT-TATTTTAAATTTTAA
16765776 AATTTAAGTTT
1 AATTT-AGTTT
16765787 ACTTAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.23
29 4 0.11
30 15 0.43
31 8 0.23
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (28 bp):
AATTTAGTTTTGTTATTTTAAATTTTAA
Found at i:16767481 original size:26 final size:27
Alignment explanation
Indices: 16767428--16767490 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 27
16767418 AAAAAAAATA
16767428 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTT
*
16767455 ACCAAAATATTATAA-TTTTTTTGTTT
1 ACCAAAATATTATAACTTTTTTTATTT
16767481 ACCAAAATAT
1 ACCAAAATAT
16767491 ACAAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 20 0.57
27 15 0.43
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.48
Consensus pattern (27 bp):
ACCAAAATATTATAACTTTTTTTATTT
Found at i:16767588 original size:27 final size:27
Alignment explanation
Indices: 16767550--16767601 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
16767540 GGCCAATTAC
*
16767550 ATTGGCGGCACCAAAGGTGTCAAAGAG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
*
16767577 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAAAGGTGCCAAAG
16767602 GACTAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGAG
Found at i:16768144 original size:19 final size:19
Alignment explanation
Indices: 16768120--16768178 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
16768110 TCTAATTAAG
16768120 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
16768139 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
16768157 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
16768176 TAA
1 TAA
16768179 AAAATTTAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:16768262 original size:98 final size:94
Alignment explanation
Indices: 16768150--16768328 Score: 263
Period size: 98 Copynumber: 1.9 Consensus size: 94
16768140 AATAAACTAT
*
16768150 TCTCATTTAATAACTCTATTTTAA-TTTAAAAAATTTAAGTAAACTATTTTAATTTAAATTTTTT
1 TCTCATTTAATAACTCTATTTTAATTTTAAAAAAATT---T-AA-T-TTTTAATTTAAATTTTTT
16768214 -AAATTAAAATAGAGTTATTACTTAATTAGAATTC
60 AAAATTAAAATAGAGTTATTACTTAATTAGAATTC
*
16768248 TCTCATTTAATAACTCTATTTTAATTTTTAAAAAAATTTAATTTTTAATTTAATTTTTTTAAAAT
1 TCTCATTTAATAACTCTATTTTAA-TTTTAAAAAAATTTAATTTTTAATTTAAATTTTTTAAAAT
16768313 TAAAATAGAGTTATTA
65 TAAAATAGAGTTATTA
16768329 AATGAGAATA
Statistics
Matches: 76, Mismatches: 2, Indels: 9
0.87 0.02 0.10
Matches are distributed among these distances:
94 17 0.22
95 21 0.28
96 2 0.03
97 1 0.01
98 24 0.32
100 11 0.14
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.49
Consensus pattern (94 bp):
TCTCATTTAATAACTCTATTTTAATTTTAAAAAAATTTAATTTTTAATTTAAATTTTTTAAAATT
AAAATAGAGTTATTACTTAATTAGAATTC
Found at i:16768356 original size:18 final size:19
Alignment explanation
Indices: 16768309--16768365 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
16768299 AATTTTTTTA
16768309 AAATTAAAATAGAGTTATT
1 AAATTAAAATAGAGTTATT
* * *
16768328 AAATGAGAATAG-TTTATT
1 AAATTAAAATAGAGTTATT
*
16768346 AAATTAAAATAGAATTATT
1 AAATTAAAATAGAGTTATT
16768365 A
1 A
16768366 CTTAATTAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (19 bp):
AAATTAAAATAGAGTTATT
Found at i:16776232 original size:13 final size:13
Alignment explanation
Indices: 16776209--16776249 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
16776199 AATTCAACTA
16776209 AATATTTAAACAT
1 AATATTTAAACAT
16776222 AAT-TCTTAAACGA-
1 AATAT-TTAAAC-AT
16776235 AATATTTAAACAT
1 AATATTTAAACAT
16776248 AA
1 AA
16776250 AATATATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (13 bp):
AATATTTAAACAT
Found at i:16780140 original size:16 final size:18
Alignment explanation
Indices: 16780119--16780155 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
16780109 TAATTTTTAT
*
16780119 AAAAATA-TAATACA-TA
1 AAAAATACTAAAACATTA
16780135 AAAAATACTAAAACATTA
1 AAAAATACTAAAACATTA
16780153 AAA
1 AAA
16780156 TAAATGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAAATACTAAAACATTA
Found at i:16781440 original size:24 final size:24
Alignment explanation
Indices: 16781413--16781464 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16781403 TTAGTAAGTC
*
16781413 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
16781437 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
16781461 AAAT
1 AAAT
16781465 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:16783777 original size:13 final size:12
Alignment explanation
Indices: 16783744--16783777 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16783734 TTAATTTAAA
16783744 TAATTAAAATAT
1 TAATTAAAATAT
*
16783756 TAATAAAAATATT
1 TAATTAAAATA-T
16783769 TAATTAAAA
1 TAATTAAAA
16783778 CATGAATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATTAAAATAT
Found at i:16786387 original size:29 final size:29
Alignment explanation
Indices: 16786355--16786419 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
16786345 GTTTTTACTT
16786355 TTTTTTAATTT-TGAATTTAGT-CTTTATA
1 TTTTTTAATTTATGAATTTAGTCCTTT-TA
16786383 CTTTTATT--TTTATGAATTTAGTCCTTTTA
1 -TTTT-TTAATTTATGAATTTAGTCCTTTTA
16786412 TTTTTTAA
1 TTTTTTAA
16786420 AATATAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
27 2 0.06
28 7 0.23
29 16 0.52
30 6 0.19
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (29 bp):
TTTTTTAATTTATGAATTTAGTCCTTTTA
Found at i:16796227 original size:26 final size:26
Alignment explanation
Indices: 16796198--16796252 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
16796188 CTTTCTGAAA
* *
16796198 CTTTTGGTTTAATTCTGGTTTTAGTC
1 CTTTTGGTTTAATTCAGGCTTTAGTC
16796224 CTTTTGGTTTAATTCAGGCTTTAGTC
1 CTTTTGGTTTAATTCAGGCTTTAGTC
16796250 CTT
1 CTT
16796253 CTAAAATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.13, C:0.15, G:0.18, T:0.55
Consensus pattern (26 bp):
CTTTTGGTTTAATTCAGGCTTTAGTC
Found at i:16819118 original size:394 final size:393
Alignment explanation
Indices: 16818200--16819232 Score: 1439
Period size: 394 Copynumber: 2.6 Consensus size: 393
16818190 TATGATTAAA
* **
16818200 GGTATGTTCATTTAACATAAGCTATAATTCACTACATGTTGGATGATGTTTGCTTTTATGGCAAA
1 GGTATGTTCATTTAACATAAGCTATAATTCACTACATGTTGGATCATG-TTGCTTTTATGATAAA
* *
16818265 TAAAAATATGAATCTCATAGGTTAGTAATTATCTAGCTCTTGAAGTAATACGAGACTTCAGAAAT
65 TAAAAATATGAATCTCATAGGTTAGTAATTATCTAGCTCTCGAAGTAATACAAGACTTCAGAAAT
* * **
16818330 TCATGACCGAATGAACCTTGATCCATCCATTTTTGTTGTTCCTACTGAAAATGAGATCAATGTAA
130 TCATGACCGAACGAACCTTGATCCATCCATTTTTGTTGTTCCTATTGAAAATGAGATTGATGTAA
* * *
16818395 AAGCTT-CCAGTTTTGTATCTTGTTGAACTTTCTGAATAATTGCTTTGTCTCTTCCCTTTGTTCT
195 AAACTTCCCAGTTTTGTATCTTGTTGAACTTTCTGATTAATTGCTTCGTCTCTTCCCTTTGTTCT
* * *
16818459 CTCATATATGTGTGTTAGCAAGTTAAATTGGAGTTTCTGTGTAAGTTCAGAATTAAGAATTTTTG
260 CTCATATATGTGTGTTAGCAAGTTAAATTGGAATTTCTGTGCAACTTCAGAATTAAGAATTTTTG
** * * * *
16818524 AGCGATGGGGCTGGAGTTCGCTAGAAACTTATGATGAAACTATCTTGTGTATAATCAATGACCAA
325 AGCGACAGGGCTGGAATTCGCTAGAAACTTATAATGAAAATATATTGTGTATAATCAATGACCAA
16818589 AAGC
390 AAGC
* * * *
16818593 GGTATGTTCATTTAACATAAGCTATAATTCACTACGTGTTGGATCATGTTGCTCTCATGATGAAT
1 GGTATGTTCATTTAACATAAGCTATAATTCACTACATGTTGGATCATGTTGCTTTTATGATAAAT
*
16818658 AAAAATATGCATCTCATA--TCTAGTAATTATCTAGCTCTCGAAGTAATA-AGAGACTTCAGAAA
66 AAAAATATGAATCTCATAGGT-TAGTAATTATCTAGCTCTCGAAGTAATACA-AGACTTCAGAAA
*
16818720 TTCATGACCGAACGAACCTTGATCCATTCATTTTTGTTGTTCCTATTGAAAATGAGATTGATGTA
129 TTCATGACCGAACGAACCTTGATCCATCCATTTTTGTTGTTCCTATTGAAAATGAGATTGATGT-
* * * * *
16818785 AAAAATTTCCCA-TTTCTGTATCGTGTTAAACTTTCTGATTAGTTGCTTCGACTCTTCCCTTTGT
193 AAAAACTTCCCAGTTT-TGTATCTTGTTGAACTTTCTGATTAATTGCTTCGTCTCTTCCCTTTGT
* * *
16818849 TC-CGTCATATGTGTGTGTTAGGAGGTTAAATT-GAATTCTCTGTGCAACTTCAGAATTAAGAAT
257 TCTC-TCATATATGTGTGTTAGCAAGTTAAATTGGAATT-TCTGTGCAACTTCAGAATTAAGAA-
* * * * *
16818912 TTTTTGTGTGACAGTGCTGGAATTCGCTAGAAACTTATAATGAAAATATATTTTGTATAATTAAT
319 TTTTTGAGCGACAGGGCTGGAATTCGCTAGAAACTTATAATGAAAATATATTGTGTATAATCAAT
16818977 GACCAAAA-C
384 GACCAAAAGC
* * *
16818986 TGGTATGTTCATTTAATACAAGCTATAATTCACTACATTTTGGATCATGTTGCTTTTATGATAAA
1 -GGTATGTTCATTTAACATAAGCTATAATTCACTACATGTTGGATCATGTTGCTTTTATGATAAA
* * *
16819051 TGAAAATATGAATCTCATAGGTTAGTAACTT-TCTAGCTCTCAAAGTGATACAAGACTTCAG-AA
65 TAAAAATATGAATCTCATAGGTTAGTAA-TTATCTAGCTCTCGAAGTAATACAAGACTTCAGAAA
*
16819114 TTCATGA-C---CGAACCTTGATCCATCCATTTTTGTTGTTCCTATTGAAAATGATATTGATGT-
129 TTCATGACCGAACGAACCTTGATCCATCCATTTTTGTTGTTCCTATTGAAAATGAGATTGATGTA
*
16819174 AAAAGTTCCCAGTTTTGTATCTTGTTGAACTTTCTGATTAATTGCTTCGTCTCTTCCCT
194 AAAACTTCCCAGTTTTGTATCTTGTTGAACTTTCTGATTAATTGCTTCGTCTCTTCCCT
16819233 CCATTCTCTA
Statistics
Matches: 568, Mismatches: 58, Indels: 33
0.86 0.09 0.05
Matches are distributed among these distances:
388 50 0.09
389 3 0.01
390 51 0.09
391 98 0.17
392 43 0.08
393 142 0.25
394 145 0.26
395 32 0.06
396 4 0.01
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (393 bp):
GGTATGTTCATTTAACATAAGCTATAATTCACTACATGTTGGATCATGTTGCTTTTATGATAAAT
AAAAATATGAATCTCATAGGTTAGTAATTATCTAGCTCTCGAAGTAATACAAGACTTCAGAAATT
CATGACCGAACGAACCTTGATCCATCCATTTTTGTTGTTCCTATTGAAAATGAGATTGATGTAAA
AACTTCCCAGTTTTGTATCTTGTTGAACTTTCTGATTAATTGCTTCGTCTCTTCCCTTTGTTCTC
TCATATATGTGTGTTAGCAAGTTAAATTGGAATTTCTGTGCAACTTCAGAATTAAGAATTTTTGA
GCGACAGGGCTGGAATTCGCTAGAAACTTATAATGAAAATATATTGTGTATAATCAATGACCAAA
AGC
Found at i:16822129 original size:32 final size:32
Alignment explanation
Indices: 16822059--16822133 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 32
16822049 TATGTCGAAT
16822059 TTTAAATATAAAAATAATTCAAACTCGAAATAA
1 TTTAAATATAAAAATAA-TCAAACTCGAAATAA
* *
16822092 ATTAAATCTAAAAATACA-CAAA-TCTGAAATAA
1 TTTAAATATAAAAATA-ATCAAACTC-GAAATAA
16822124 TTTAAA-ATAA
1 TTTAAATATAA
16822134 TTTGAATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
31 5 0.14
32 16 0.44
33 14 0.39
34 1 0.03
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (32 bp):
TTTAAATATAAAAATAATCAAACTCGAAATAA
Found at i:16825939 original size:27 final size:27
Alignment explanation
Indices: 16825901--16825956 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
16825891 CATCACTATC
16825901 AGAAACCTTACCAAAGAAAGGCAGGTG
1 AGAAACCTTACCAAAGAAAGGCAGGTG
16825928 AGAAACCTTACCAAAGAAAGGCAGGTG
1 AGAAACCTTACCAAAGAAAGGCAGGTG
16825955 AG
1 AG
16825957 TTTGCATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.45, C:0.18, G:0.27, T:0.11
Consensus pattern (27 bp):
AGAAACCTTACCAAAGAAAGGCAGGTG
Found at i:16826908 original size:17 final size:17
Alignment explanation
Indices: 16826863--16826916 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
16826853 TTTAAAAAAA
*
16826863 TATTTATATTATATTATTT
1 TATTTAT-TAATATT-TTT
16826882 TAATTT-TTAATATTTTT
1 T-ATTTATTAATATTTTT
16826899 TATTTATTAATGATTTTT
1 TATTTATTAAT-ATTTTT
16826917 ATATAGCCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.13
17 9 0.29
18 12 0.39
19 2 0.06
20 4 0.13
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TATTTATTAATATTTTT
Found at i:16830122 original size:25 final size:26
Alignment explanation
Indices: 16830072--16830123 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
16830062 ATACATGGAC
**
16830072 AAAATTTTAACAGTAGAAATGGATAA
1 AAAATTTTAACAGTAGAAATCAATAA
16830098 AAAATTTTAACAG-A-ATAATCAATAA
1 AAAATTTTAACAGTAGA-AATCAATAA
16830123 A
1 A
16830124 TACTATTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 1 0.04
25 9 0.39
26 13 0.57
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.27
Consensus pattern (26 bp):
AAAATTTTAACAGTAGAAATCAATAA
Found at i:16833904 original size:39 final size:39
Alignment explanation
Indices: 16833840--16834419 Score: 736
Period size: 39 Copynumber: 14.9 Consensus size: 39
16833830 GCTGTTCAGN
*
16833840 GAAGAAATTGAAGGAAGCTCATGAACGAGAAGAGAGAAG-
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGA-AAGA
** * * * *
16833879 GAAGAAAGAGAAGGAGGCACGTGAACTAGAAGAGAAGGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
* * *
16833918 GAAAAAATTGAAGGAAGCTCATGAACGAGAAGAGAATGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
* * * * *
16833957 GAGGAGATTGAGGGAGGCTCGTGAACGAGAAGAGATAGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
*
16833996 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAATGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
* * * *
16834035 GAAGAGATTGAGGGAGGCTCGTGAGCGAGAAGAGAAAGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
* * *
16834074 GAAGAAA--G-AGGAGGCACATGAACGAGAAGAGAAAGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
*
16834110 GAAGAAATTGAAGGAAGCTCGTGAACTAGAAGAGAAAGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
*
16834149 GAAGAAATTGAAGGAAGCTCGTGAACTAGAAGAGAAAGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
* *
16834188 GAAGAAATTGAAGGAAGCTTGTGAACGAGAAGAGAATGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
* * ** **
16834227 GAGGAGATTGAAGGAAATTCGTGAACGAGAAGAGATTGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
*
16834266 GAAGAGATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
* * * *
16834305 GAAGAAGTTGAAAGAAGCTCGTGAACAAGAAGAGAATGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
* *
16834344 GAAGAGATTGAAGGAAGCTCGTGAACGAGAAGAGAATGA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
* * *
16834383 CAAGAGATTGAAGGAAGCTCGTGAGCGAGAAGAGAAA
1 GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAA
16834420 TTGAAGGAAG
Statistics
Matches: 468, Mismatches: 69, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
36 31 0.07
37 1 0.00
38 3 0.01
39 433 0.93
ACGTcount: A:0.46, C:0.08, G:0.35, T:0.12
Consensus pattern (39 bp):
GAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGA
Found at i:16834480 original size:30 final size:30
Alignment explanation
Indices: 16834392--16834485 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
16834382 ACAAGAGATT
* **
16834392 GAAGGAAGCTCGTGAGCGAGAAGAGAAATT
1 GAAGGAAGCTCGTGAACGAGAAGAGAAAGA
16834422 GAAGGAAGCTCGTGAACGAGAAGAGAAAGA
1 GAAGGAAGCTCGTGAACGAGAAGAGAAAGA
* *
16834452 GAAGGAGGCACGTGAACGAGAAGAGAAAGA
1 GAAGGAAGCTCGTGAACGAGAAGAGAAAGA
16834482 GAAG
1 GAAG
16834486 AAAGAGAAGG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.45, C:0.10, G:0.38, T:0.07
Consensus pattern (30 bp):
GAAGGAAGCTCGTGAACGAGAAGAGAAAGA
Found at i:16834488 original size:69 final size:70
Alignment explanation
Indices: 16834324--16834514 Score: 169
Period size: 69 Copynumber: 2.8 Consensus size: 70
16834314 GAAAGAAGCT
* * * *
16834324 CGTGAACAAGAAGAGAATGAGAAGAGATTGAAGGAAGCTCGTGAACGAGAAGAGAATGACAAGAG
1 CGTGAACGAGAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGACAAGAG
*
16834389 ATTGA
66 ATGGA
* * * * *
16834394 AG-GAAGCTCGTG-AGCGAGA-AG-AGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGAGAA
1 CGTGAA---CGAGAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGACAA
16834455 G-GA-GGCA
63 GAGATGG-A
** * * *
16834462 CGTGAACGAGAAGAGAAAGAGAAGAAAGAGAAGGAGGCACGTGAACTAGAAGA
1 CGTGAACGAGAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGA
16834515 AAGTGAGAAG
Statistics
Matches: 94, Mismatches: 19, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
66 3 0.03
67 6 0.06
68 6 0.06
69 70 0.74
70 3 0.03
71 4 0.04
72 2 0.02
ACGTcount: A:0.46, C:0.09, G:0.36, T:0.09
Consensus pattern (70 bp):
CGTGAACGAGAAGAGAAAGAGAAGAAATTGAAGGAAGCTCGTGAACGAGAAGAGAAAGACAAGAG
ATGGA
Found at i:16837243 original size:29 final size:29
Alignment explanation
Indices: 16837179--16837243 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
16837169 TTTAATATGG
* *
16837179 TATTTGTGTTAGTTTTTGGTCTAATCTGC
1 TATTTGTGTTAGTTTTTGGTCCAATCTGA
* * *
16837208 TACTTGTGTTA-TGTTTTGGTCCAGTTTGA
1 TATTTGTGTTAGT-TTTTGGTCCAATCTGA
16837237 TATTTGT
1 TATTTGT
16837244 ATTTGATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.14, C:0.09, G:0.22, T:0.55
Consensus pattern (29 bp):
TATTTGTGTTAGTTTTTGGTCCAATCTGA
Found at i:16838964 original size:24 final size:24
Alignment explanation
Indices: 16838932--16838981 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
16838922 ATGACTCCGT
*
16838932 TGCTTTATGTATTTCTTTCGTCTA
1 TGCTTTATGTATTTATTTCGTCTA
16838956 TGCTTTATGTATTTATTTCGTCTA
1 TGCTTTATGTATTTATTTCGTCTA
16838980 TG
1 TG
16838982 GTTCACTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.58
Consensus pattern (24 bp):
TGCTTTATGTATTTATTTCGTCTA
Found at i:16839082 original size:12 final size:12
Alignment explanation
Indices: 16839065--16839089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16839055 ATTTTATAAC
16839065 ATAAATTTTGTT
1 ATAAATTTTGTT
16839077 ATAAATTTTGTT
1 ATAAATTTTGTT
16839089 A
1 A
16839090 ATAGCTTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (12 bp):
ATAAATTTTGTT
Found at i:16843786 original size:53 final size:53
Alignment explanation
Indices: 16843705--16843867 Score: 227
Period size: 53 Copynumber: 3.1 Consensus size: 53
16843695 TTTTTAACCG
**
16843705 ATTGGCTTGACGCTCACATTCGAGACACGAAATTCGTCCTCCAAAAGCCGGTC
1 ATTGGCTCAACGCTCACATTCGAGACACGAAATTCGTCCTCCAAAAGCCGGTC
* * *
16843758 GTTGGCTCAACGCTCACATTCGAGACACGAAATTCATCCTCCAAAAGTCGGTC
1 ATTGGCTCAACGCTCACATTCGAGACACGAAATTCGTCCTCCAAAAGCCGGTC
* * * * * *
16843811 ATTGGCTCGACGCTCACATTCGAGACGCGGAATACGTCCTCCAAAATCCGATC
1 ATTGGCTCAACGCTCACATTCGAGACACGAAATTCGTCCTCCAAAAGCCGGTC
16843864 ATTG
1 ATTG
16843868 TCGCCAATTT
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 96 1.00
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (53 bp):
ATTGGCTCAACGCTCACATTCGAGACACGAAATTCGTCCTCCAAAAGCCGGTC
Found at i:16848152 original size:72 final size:75
Alignment explanation
Indices: 16848056--16848226 Score: 258
Period size: 76 Copynumber: 2.3 Consensus size: 75
16848046 GACAAACTCG
* * *
16848056 AGAAGGACGAGGCCTTGAAGAAAGCCGAGGTTAAAGAATCTC-G-A-GAACTGAAAATCGAACAC
1 AGAAGGACGAAGCCTCGAAGAAAGCCGAGGTTAAAGAATCCCAGAATGAACTGAAAATCGAACAC
*
16848118 AAGTATCTCA
66 AAATATCTCA
*
16848128 AGAAGGACGAAGCCTCGAAGAAAGCCGAGGTTAAAGAATCCCAAGAATGAATTGAAAATCGAACA
1 AGAAGGACGAAGCCTCGAAGAAAGCCGAGGTTAAAGAATCCC-AGAATGAACTGAAAATCGAACA
16848193 CAAATATCTCA
65 CAAATATCTCA
*
16848204 AGAAAGACGAAGCCTCGAAGAAA
1 AGAAGGACGAAGCCTCGAAGAAA
16848227 TCCAAAATTT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
72 39 0.44
74 1 0.01
75 1 0.01
76 48 0.54
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (75 bp):
AGAAGGACGAAGCCTCGAAGAAAGCCGAGGTTAAAGAATCCCAGAATGAACTGAAAATCGAACAC
AAATATCTCA
Found at i:16853031 original size:20 final size:19
Alignment explanation
Indices: 16852986--16853034 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
16852976 GTACATTCAC
**
16852986 GATTTAAATAAAAAAACGA
1 GATTTAAATAAAAAAAAAA
*
16853005 GACTTTAATTAGAAAAAAAAA
1 GA-TTTAAATA-AAAAAAAAA
16853026 GATTTAAAT
1 GATTTAAAT
16853035 GCCCTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.08
20 13 0.54
21 9 0.38
ACGTcount: A:0.59, C:0.04, G:0.10, T:0.27
Consensus pattern (19 bp):
GATTTAAATAAAAAAAAAA
Found at i:16867317 original size:24 final size:24
Alignment explanation
Indices: 16867257--16867324 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
16867247 AATATTGGCA
* * *
16867257 ATATATATATGTATTAAGTATATGT
1 ATATATATATGTA-CATGTATATGC
* * *
16867282 TTACATACATGTACATGTATATGC
1 ATATATATATGTACATGTATATGC
*
16867306 ATATATATATGTACTTGTA
1 ATATATATATGTACATGTA
16867325 CTTAGGGGGG
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
24 23 0.70
25 10 0.30
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (24 bp):
ATATATATATGTACATGTATATGC
Found at i:16870899 original size:128 final size:129
Alignment explanation
Indices: 16870646--16870880 Score: 316
Period size: 128 Copynumber: 1.8 Consensus size: 129
16870636 TAGGCATTAG
* * *
16870646 GGTCTAAGTTCTAAGTCTTACTATGTGTAAATGTGTGTTCAGTATAATTTTACTATTGTCCTTGT
1 GGTCTAAGTTCTAAGTCTTACAATGCGTAAATATGTGTTCAGTATAATTTTACTATTGTCCTTGT
* * * **
16870711 TTAGAATCGTACAATTTCTAAAGGGACTAATAAGGAAATTTTCCATTTTGAGGGGCTGGTTTAC
66 TTAAAATCGTACAATTTCTAAAGGGACTAACAAGGAAATTTACCATTTAAAGGGGCTGGTTTAC
* *
16870775 GGTCTAAGTTCTAAGTCTTACAATGCGTAAATATG-GCTT-GGTGTAATTTTACTATTGTCCTTG
1 GGTCTAAGTTCTAAGTCTTACAATGCGTAAATATGTG-TTCAGTATAATTTTACTATTGTCCTTG
* *
16870838 TTTAAAATCTTACCATTT-TAAAGGGACT-ACAAGGAAATCTTAC
65 TTTAAAATCGTACAATTTCTAAAGGGACTAACAAGGAAAT-TTAC
16870881 TATGTGTAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
126 9 0.10
127 13 0.14
128 38 0.40
129 34 0.36
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.39
Consensus pattern (129 bp):
GGTCTAAGTTCTAAGTCTTACAATGCGTAAATATGTGTTCAGTATAATTTTACTATTGTCCTTGT
TTAAAATCGTACAATTTCTAAAGGGACTAACAAGGAAATTTACCATTTAAAGGGGCTGGTTTAC
Found at i:16900656 original size:21 final size:21
Alignment explanation
Indices: 16900632--16900674 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
16900622 CCATTTCAGG
16900632 TTTGAGTTATTTTGGATTTGA
1 TTTGAGTTATTTTGGATTTGA
*
16900653 TTTGGGTTATTTTGGATTTGA
1 TTTGAGTTATTTTGGATTTGA
16900674 T
1 T
16900675 GATTCGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (21 bp):
TTTGAGTTATTTTGGATTTGA
Found at i:16901128 original size:14 final size:14
Alignment explanation
Indices: 16901106--16901135 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16901096 TTTATTATTA
16901106 TTTAAGATTTAGGG
1 TTTAAGATTTAGGG
*
16901120 TTTAGGATTTAGGG
1 TTTAAGATTTAGGG
16901134 TT
1 TT
16901136 GCTAGAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (14 bp):
TTTAAGATTTAGGG
Found at i:16905234 original size:83 final size:82
Alignment explanation
Indices: 16905077--16905239 Score: 222
Period size: 83 Copynumber: 2.0 Consensus size: 82
16905067 ATGAAGAATC
* *
16905077 TTCAATTCAGTCATCTTATAAATAAAGAAATTATAAATTAATATGTAGTGAAATTGCACTTTAAC
1 TTCAATTCAGTCATCTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTGCACTTTAAC
* *
16905142 TCTCTAAAATATAAAAAA
66 CCCCTAAAATA-AAAAAA
* * *
16905160 TTCAATTCAGTCCTCTTATGAATAAAGAAATTATAAATTAATA-ATAGTAAAATTGCA-TTTAGC
1 TTCAATTCAGTCATCTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTGCACTTTA-A
16905223 CCCCCTAAAAATAAAAA
65 CCCCCT-AAAATAAAAA
16905240 TAAAAATTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 4 0.06
82 20 0.28
83 47 0.66
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (82 bp):
TTCAATTCAGTCATCTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTGCACTTTAAC
CCCCTAAAATAAAAAAA
Found at i:16905296 original size:23 final size:23
Alignment explanation
Indices: 16905270--16905330 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
16905260 TTCAAGAAAG
16905270 ATAAAATTATATATTAATACATA
1 ATAAAATTATATATTAATACATA
* * * *
16905293 ATAAACTTACATTTTAATTCATA
1 ATAAAATTATATATTAATACATA
*
16905316 A-AAAAATATA-ATTAA
1 ATAAAATTATATATTAA
16905331 ATTCCATCTT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 4 0.13
22 6 0.20
23 20 0.67
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (23 bp):
ATAAAATTATATATTAATACATA
Found at i:16905505 original size:10 final size:10
Alignment explanation
Indices: 16905490--16905520 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
16905480 AGTTGCAACC
16905490 CCCCTCCCCA
1 CCCCTCCCCA
16905500 CCCCTCCCCA
1 CCCCTCCCCA
*
16905510 CCCATCCCCA
1 CCCCTCCCCA
16905520 C
1 C
16905521 ATGGTTCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.13, C:0.77, G:0.00, T:0.10
Consensus pattern (10 bp):
CCCCTCCCCA
Found at i:16908380 original size:133 final size:133
Alignment explanation
Indices: 16908140--16908382 Score: 296
Period size: 133 Copynumber: 1.8 Consensus size: 133
16908130 TCGTGGTCCA
* * * * *
16908140 TTAATGATTTTTCTCTAATCATGGGAGTTAGGTGAGATGGCAAGGATTATTCCTACCTTAACCAA
1 TTAATGATTTTTCTCTAATCACGGAAGTTAAGTGAGATAGCAAGGATTATCCCTACCTTAACCAA
* * * ** * *
16908205 TGTTTGAGGGTTTAATTTTCACTCTGGGTATGGAGCAGCTTTAAAGCTCATGGTCAGCATTTACT
66 TGGTCGAGAGTTTAATTTTCACTCTAAGTATGGAACAACTTTAAAGCTCATGGTCAGCATTTACT
16908270 GCC
131 GCC
*
16908273 TTAATGATTTTTCTTTAATCACGGAAGTTAAGTGAGATAGCACA-GATT-TCCCCTACCTTAACC
1 TTAATGATTTTTCTCTAATCACGGAAGTTAAGTGAGATAGCA-AGGATTAT-CCCTACCTTAACC
*
16908336 AGTGGTCGAGAGTTTAATTCTT-AC-CTTAAGTATGGAACAACTTTAAA
64 AATGGTCGAGAGTTTAATT-TTCACTC-TAAGTATGGAACAACTTTAAA
16908383 TCTCGTGACC
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
132 2 0.02
133 87 0.95
134 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (133 bp):
TTAATGATTTTTCTCTAATCACGGAAGTTAAGTGAGATAGCAAGGATTATCCCTACCTTAACCAA
TGGTCGAGAGTTTAATTTTCACTCTAAGTATGGAACAACTTTAAAGCTCATGGTCAGCATTTACT
GCC
Found at i:16908399 original size:133 final size:133
Alignment explanation
Indices: 16908140--16908412 Score: 295
Period size: 133 Copynumber: 2.1 Consensus size: 133
16908130 TCGTGGTCCA
* * * * *
16908140 TTAATGATTTTTCTCTAATCATGGGAGTTAGGTGAGATGGCAAGGATTATTCCTACCTTAACCAA
1 TTAATGATTTTTCTCTAATCACGGAAGTTAAGTGAGATAGCAAGGATTATCCCTACCTTAACCAA
* * * ** * * **
16908205 TGTTTGAGGGTTTAATTTTCACTCTGGGTATGGAGCAGCTTTAAAGCTCATGGTCAGCATTTACT
66 TGGTCGAGAGTTTAATTTTCACTCTAAGTATGGAACAACTTTAAAGCTCATGACCAGCATTTACT
16908270 GC-C
131 -CAC
*
16908273 TTAATGATTTTTCTTTAATCACGGAAGTTAAGTGAGATAGCACA-GATT-TCCCCTACCTTAACC
1 TTAATGATTTTTCTCTAATCACGGAAGTTAAGTGAGATAGCA-AGGATTAT-CCCTACCTTAACC
* * * *
16908336 AGTGGTCGAGAGTTTAATTCTT-AC-CTTAAGTATGGAACAACTTTAAATCTCGTGACCATCATT
64 AATGGTCGAGAGTTTAATT-TTCACTC-TAAGTATGGAACAACTTTAAAGCTCATGACCAGCATT
16908399 TACTCAC
127 TACTCAC
16908406 TTAATGA
1 TTAATGA
16908413 ACCTATAAAA
Statistics
Matches: 116, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
132 3 0.03
133 110 0.95
134 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (133 bp):
TTAATGATTTTTCTCTAATCACGGAAGTTAAGTGAGATAGCAAGGATTATCCCTACCTTAACCAA
TGGTCGAGAGTTTAATTTTCACTCTAAGTATGGAACAACTTTAAAGCTCATGACCAGCATTTACT
CAC
Found at i:16926153 original size:107 final size:107
Alignment explanation
Indices: 16926026--16926297 Score: 378
Period size: 101 Copynumber: 2.6 Consensus size: 107
16926016 AAAACGAATT
16926026 TTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAATTTTTTTTCTTTTTTT
1 TTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAATTTTTTTTCTTTTTTT
* *
16926091 GTATCAGAGTCAGATATCAGTATACAAAAAAAATAAAAAAAA
66 GCATCAGAATCAGATATCAGTATACAAAAAAAATAAAAAAAA
* * * *
16926133 TTTTTTGGGTGTTGGCCTGTCAATGGCCAGCACCCAGTACAATTTT-AA---TTTTTC--TTCTC
1 TTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAATTTTTTTTCTTTTTTT
* *
16926192 GCGTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAAA
66 GCATCAGAATCAGATATCAGTATACAAAAAAAATAAAAAAAA
** * * *
16926234 AATTTTGGGTGCTGGCCTATCAATGGCCGGCACCCAGTACAA-TTAAAATTTTTTTCCTTTTTTT
1 TTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAATTTTTTTTCTTTTTTT
16926298 TTTAAATTGT
Statistics
Matches: 142, Mismatches: 17, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
100 2 0.01
101 80 0.56
103 6 0.04
104 5 0.04
106 5 0.04
107 44 0.31
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (107 bp):
TTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAATTTTTTTTCTTTTTTT
GCATCAGAATCAGATATCAGTATACAAAAAAAATAAAAAAAA
Found at i:16928445 original size:4 final size:4
Alignment explanation
Indices: 16928438--16928467 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
16928428 TTTTTTTATC
16928438 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
16928468 CCTAAAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:16931608 original size:2 final size:2
Alignment explanation
Indices: 16931603--16931628 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16931593 TATGTATATA
16931603 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
16931629 CATGTGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:16933589 original size:23 final size:22
Alignment explanation
Indices: 16933539--16933595 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
16933529 TAATATTTTA
*
16933539 ATAAATAAAAAATAAAAAAATT
1 ATAAATATAAAATAAAAAAATT
16933561 ATTAAATATAAAATAATAAATAA-T
1 A-TAAATATAAAATAA-AAA-AATT
16933585 ATAAATATAAA
1 ATAAATATAAA
16933596 CCTACCAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 1 0.03
23 23 0.74
24 5 0.16
25 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
ATAAATATAAAATAAAAAAATT
Found at i:16935907 original size:16 final size:16
Alignment explanation
Indices: 16935886--16935919 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16935876 TATAGATCGA
* *
16935886 ATTAATTTGGGTTTAG
1 ATTAATTCGGGTTCAG
16935902 ATTAATTCGGGTTCAG
1 ATTAATTCGGGTTCAG
16935918 AT
1 AT
16935920 CATTTTTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.44
Consensus pattern (16 bp):
ATTAATTCGGGTTCAG
Found at i:16946292 original size:101 final size:104
Alignment explanation
Indices: 16946070--16946293 Score: 310
Period size: 101 Copynumber: 2.2 Consensus size: 104
16946060 AACGAATTTT
* * * *
16946070 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAATTTTTTTTCTTTTTTTGT
1 TTTTGGGTGCTGGCCTGTCAATGGCCAGCACCCAGTACAATTTTAAA--TTTTTTC-TTTCTCGC
* **
16946135 ATCAGAGTCAGATATCAGTATACAAAAAAAATAAAAAAAATT
63 ATCAGAATCAGATATCAGTATACAAAAAAAATAAAAAAAAAA
* *
16946177 TTTTGGGTGTTGGCCTGTCAATGGCCAGCACCCAGTACAATTTT-AA-TTTTTC-TTCTCGCGTC
1 TTTTGGGTGCTGGCCTGTCAATGGCCAGCACCCAGTACAATTTTAAATTTTTTCTTTCTCGCATC
*
16946239 AGAATCAGATATCAGTATACGAAAAAAATAAAAAAAAAA
66 AGAATCAGATATCAGTATACAAAAAAAATAAAAAAAAAA
16946278 TTTTGGGTGCTGGCCT
1 TTTTGGGTGCTGGCCT
16946294 TTTTTTTTCG
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
101 56 0.53
103 6 0.06
106 2 0.02
107 42 0.40
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (104 bp):
TTTTGGGTGCTGGCCTGTCAATGGCCAGCACCCAGTACAATTTTAAATTTTTTCTTTCTCGCATC
AGAATCAGATATCAGTATACAAAAAAAATAAAAAAAAAA
Found at i:16948299 original size:4 final size:4
Alignment explanation
Indices: 16948292--16948321 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
16948282 TTTTTTTATC
16948292 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
16948322 CCTAAAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:16951462 original size:2 final size:2
Alignment explanation
Indices: 16951457--16951482 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16951447 TATGTATATA
16951457 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
16951483 CATGTGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:16953447 original size:23 final size:22
Alignment explanation
Indices: 16953397--16953453 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
16953387 TAATATTTTA
*
16953397 ATAAATAAAAAATAAAAAAATT
1 ATAAATATAAAATAAAAAAATT
16953419 ATTAAATATAAAATAATAAATAA-T
1 A-TAAATATAAAATAA-AAA-AATT
16953443 ATAAATATAAA
1 ATAAATATAAA
16953454 CCTACCAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 1 0.03
23 23 0.74
24 5 0.16
25 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
ATAAATATAAAATAAAAAAATT
Found at i:16955765 original size:16 final size:16
Alignment explanation
Indices: 16955744--16955777 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16955734 TATAGATCGA
* *
16955744 ATTAATTTGGGTTTAG
1 ATTAATTCGGGTTCAG
16955760 ATTAATTCGGGTTCAG
1 ATTAATTCGGGTTCAG
16955776 AT
1 AT
16955778 CATTTTTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.44
Consensus pattern (16 bp):
ATTAATTCGGGTTCAG
Found at i:16975757 original size:14 final size:14
Alignment explanation
Indices: 16975740--16975780 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
16975730 TTTTAAAATA
16975740 ATATATTTATATTT
1 ATATATTTATATTT
*
16975754 ATATTTTTA-ATTT
1 ATATATTTATATTT
16975767 A-ATATTTAATATTT
1 ATATATTT-ATATTT
16975781 TTATGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 5 0.22
13 6 0.26
14 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATATTTATATTT
Found at i:16981682 original size:4 final size:4
Alignment explanation
Indices: 16981673--16981706 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
16981663 TTCCGGCTTT
*
16981673 TGTA TGTA TGTA TGTA TGTA TGTA TGTA GGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
16981707 AAAGTTACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (4 bp):
TGTA
Found at i:16985468 original size:86 final size:87
Alignment explanation
Indices: 16985362--16985695 Score: 225
Period size: 88 Copynumber: 3.9 Consensus size: 87
16985352 GATCTGCAAT
* *
16985362 TCTTCAACCAGCTCCACTACAAC-CGAGAGAGGTAAGG-TTTGTCTTCGACCTGCTTCACTGTCA
1 TCTTCAACCAACTCCACTAC-ACTCGAGAGAGGCAAGGCTTTGTCTTCGACCTGCTTCACTGTCA
16985425 ACGCAGGAAGATAAAATCAGTTG
65 ACGCAGGAAGATAAAATCAGTTG
** * * * *
16985448 TCTTCAACCAACTCTTCTACACTCGAGAGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAA
1 TCTTCAACCAACTCCACTACACTCGAGAGAGGCAAGGCTTTGTCTTCGACCTGCTTCACTGTCAA
* ** * * * *
16985513 CGTAGGAAGGCAAGATCTGCTA
66 CGCAGGAAGATAAAATCAGTTG
* * * * * *
16985535 TCTTCAACCAGCTCCACTGCAAC-CGATG-GAGGCAAGGCTTTGTTTTTCGATCTACTTCGCTGT
1 TCTTCAACCAACTCCACTAC-ACTCGA-GAGAGGCAAGGCTTTG-TCTTCGACCTGCTTCACTGT
* * ** * * * *
16985598 TAATGCAGGAAGGCAAGATCTGCTA
63 CAACGCAGGAAGATAAAATCAGTTG
* * * * * *
16985623 TCTTCAACCAGCTCCACTGTA-AC-CAATGA-AGGCAAAGC-TTGTTTTCGATCTGCTTCGCTGT
1 TCTTCAACCAACTCCAC--TACACTCGA-GAGAGGCAAGGCTTTGTCTTCGACCTGCTTCACTGT
*
16985684 TAACGCAGGAAG
63 CAACGCAGGAAG
16985696 GCAAGATCTG
Statistics
Matches: 213, Mismatches: 27, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
85 2 0.01
86 60 0.28
87 74 0.35
88 76 0.36
90 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.28
Consensus pattern (87 bp):
TCTTCAACCAACTCCACTACACTCGAGAGAGGCAAGGCTTTGTCTTCGACCTGCTTCACTGTCAA
CGCAGGAAGATAAAATCAGTTG
Found at i:16985539 original size:87 final size:88
Alignment explanation
Indices: 16985351--16985725 Score: 451
Period size: 87 Copynumber: 4.3 Consensus size: 88
16985341 CAGGGAGATC
* * * *
16985351 AGATCTGCAATTCTTCAACCAGCTCCACTACAACCGA-GAGAGGTAAGG-TTTGTCTTCGACCTG
1 AGATCTGCTA-TCTTCAACCAGCTCCACTACAACCGATGAGAGGCAAGGCTTTGTTTTCGATCTG
* * **
16985414 CTTCACTGTCAACGCAGGAAGATA
65 CTTCGCTGTTAACGCAGGAAGGCA
* * * * * **
16985438 AAATCAGTTGTCTTCAACCAACTCTTCTAC-ACTCGA-GAGAGGCAAGGCTTTGTTTTCGATCTG
1 AGATCTGCTATCTTCAACCAGCTCCACTACAAC-CGATGAGAGGCAAGGCTTTGTTTTCGATCTG
*
16985501 CTTCGCTGTTAACGTAGGAAGGCA
65 CTTCGCTGTTAACGCAGGAAGGCA
* *
16985525 AGATCTGCTATCTTCAACCAGCTCCACTGCAACCGATG-GAGGCAAGGCTTTGTTTTTCGATCTA
1 AGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGAGAGGCAAGGCTTTG-TTTTCGATCTG
*
16985589 CTTCGCTGTTAATGCAGGAAGGCA
65 CTTCGCTGTTAACGCAGGAAGGCA
** * *
16985613 AGATCTGCTATCTTCAACCAGCTCCACTGTAACCAATGA-AGGCAAAGC-TTGTTTTCGATCTGC
1 AGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGAGAGGCAAGGCTTTGTTTTCGATCTGC
16985676 TTCGCTGTTAACGCAGGAAGGCA
66 TTCGCTGTTAACGCAGGAAGGCA
*
16985699 AGATCTGCT-TCTTTAACCAGCTCCACT
1 AGATCTGCTATCTTCAACCAGCTCCACT
16985726 GNNNNNNNNN
Statistics
Matches: 249, Mismatches: 33, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
85 19 0.08
86 72 0.29
87 79 0.32
88 79 0.32
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (88 bp):
AGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGAGAGGCAAGGCTTTGTTTTCGATCTGC
TTCGCTGTTAACGCAGGAAGGCA
Found at i:16985654 original size:44 final size:43
Alignment explanation
Indices: 16985518--16985726 Score: 110
Period size: 44 Copynumber: 4.8 Consensus size: 43
16985508 GTTAACGTAG
*
16985518 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGAT
1 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGTAACC-AT
* * * * * * * * * *
16985562 GGAGGCAAGGCTTTG-T-TTTTCGATCTA-CTTCGCTGTTAATGCAG
1 GAAGGCAA-GATCTGCTATCTTC-AACCAGCTCCACTG-TAA-CCAT
16985606 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGTAACCAAT
1 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGTAACC-AT
* * * * * * *
16985650 GAAGGCAA-AGCTTG-T-T-TTCGATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAGATC-TGCTATCTTCAACCAGCTCCACTG-TAAC-CAT
*
16985692 GAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTG
1 GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTG
16985727 NNNNNNNNNN
Statistics
Matches: 116, Mismatches: 35, Indels: 28
0.65 0.20 0.16
Matches are distributed among these distances:
41 12 0.10
42 16 0.14
43 23 0.20
44 50 0.43
45 15 0.13
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (43 bp):
GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTGTAACCAT
Found at i:17003289 original size:27 final size:27
Alignment explanation
Indices: 17003259--17003369 Score: 132
Period size: 27 Copynumber: 4.1 Consensus size: 27
17003249 TGAAAATCAC
* * *
17003259 GGTCCCTTGTATCAACATACCTTTGTT
1 GGTCCCTTGGATCGACATACCTCTGTT
* *
17003286 GGTCCCTCGGATCGACGTACCTCTGTT
1 GGTCCCTTGGATCGACATACCTCTGTT
* *
17003313 GGTCTCTTGGATCGACATACCTTTGTT
1 GGTCCCTTGGATCGACATACCTCTGTT
* * *
17003340 GATCCCTTGTATCGACGTACCTCTGTT
1 GGTCCCTTGGATCGACATACCTCTGTT
17003367 GGT
1 GGT
17003370 TTCCGAAATA
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.37
Consensus pattern (27 bp):
GGTCCCTTGGATCGACATACCTCTGTT
Found at i:17003355 original size:54 final size:54
Alignment explanation
Indices: 17003259--17003369 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 54
17003249 TGAAAATCAC
* *
17003259 GGTCCCTTGTATCAACATACCTTTGTTGGTCCCTCGGATCGACGTACCTCTGTT
1 GGTCCCTTGGATCAACATACCTTTGTTGATCCCTCGGATCGACGTACCTCTGTT
* * * *
17003313 GGTCTCTTGGATCGACATACCTTTGTTGATCCCTTGTATCGACGTACCTCTGTT
1 GGTCCCTTGGATCAACATACCTTTGTTGATCCCTCGGATCGACGTACCTCTGTT
17003367 GGT
1 GGT
17003370 TTCCGAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.37
Consensus pattern (54 bp):
GGTCCCTTGGATCAACATACCTTTGTTGATCCCTCGGATCGACGTACCTCTGTT
Found at i:17010139 original size:12 final size:13
Alignment explanation
Indices: 17010122--17010151 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
17010112 TTTTTCTCTG
17010122 AAAATTAAAA-AA
1 AAAATTAAAACAA
17010134 AAAATTAAAACAA
1 AAAATTAAAACAA
17010147 AAAAT
1 AAAAT
17010152 GAGAAAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAATTAAAACAA
Found at i:17011254 original size:40 final size:41
Alignment explanation
Indices: 17011192--17011300 Score: 109
Period size: 40 Copynumber: 2.7 Consensus size: 41
17011182 CTCTCTCAAC
* *
17011192 AAAAATTACAAAAAAAA-T-TAAAATAATTTTCGAAAATTCT
1 AAAAATTATAAAAAAAACTCTAAAATAATTTT-GAAAATTAT
* * * *
17011232 AAATATT-T-ATAAAAACTCTAAAATTTATTTTTAAAATTAT
1 AAAAATTATAAAAAAAACTCTAAAA-TAATTTTGAAAATTAT
*
17011272 AAAAATTATAAAAAAAATTCTAAAATAAT
1 AAAAATTATAAAAAAAACTCTAAAATAAT
17011301 AACATTGGGA
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
38 6 0.11
39 1 0.02
40 24 0.44
41 10 0.19
42 13 0.24
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.35
Consensus pattern (41 bp):
AAAAATTATAAAAAAAACTCTAAAATAATTTTGAAAATTAT
Found at i:17011257 original size:18 final size:19
Alignment explanation
Indices: 17011224--17011259 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17011214 ATAATTTTCG
*
17011224 AAAATTCTAAATATTTATA
1 AAAACTCTAAATATTTATA
17011243 AAAACTCTAAA-ATTTAT
1 AAAACTCTAAATATTTAT
17011260 TTTTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAACTCTAAATATTTATA
Found at i:17016317 original size:18 final size:17
Alignment explanation
Indices: 17016281--17016319 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
17016271 AAAATAATTT
*
17016281 AATTAAAACTTAAAAAA
1 AATTAAAACATAAAAAA
*
17016298 AATTAAAACCATAAACAA
1 AATTAAAA-CATAAAAAA
17016316 AATT
1 AATT
17016320 TCAAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (17 bp):
AATTAAAACATAAAAAA
Found at i:17021610 original size:16 final size:17
Alignment explanation
Indices: 17021583--17021616 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17021573 ATAGCAAAAC
17021583 AATTATATTATTATTTA
1 AATTATATTATTATTTA
*
17021600 AATTA-ATTATTTTTTA
1 AATTATATTATTATTTA
17021616 A
1 A
17021617 GAGCTTCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTATATTATTATTTA
Done.