Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 40 of 221
Found at i:11093300 original size:79 final size:82
Alignment explanation
Indices: 11093183--11093367 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
11093173 GCTACTCGTT
* * *
11093183 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
11093246 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* * **
11093263 CAAATGCCTTCAGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
11093326 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
11093343 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
11093368 CATCATTCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.60
80 33 0.37
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:11093367 original size:40 final size:40
Alignment explanation
Indices: 11093165--11093367 Score: 218
Period size: 40 Copynumber: 5.1 Consensus size: 40
11093155 GGAATTTAAT
** *
11093165 CGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGCC
1 CGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCC
* * *
11093205 CGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
* *
11093245 CGGATTTAGTAACTCGCACAAATGCCTTCAGG-CTTAGCC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
* *
11093284 CGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCC
* * *
11093324 CGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCC
1 CGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCC
11093364 CGGA
1 CGGA
11093368 CATCATTCAA
Statistics
Matches: 137, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 90 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
Found at i:11097326 original size:24 final size:24
Alignment explanation
Indices: 11097284--11097333 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
11097274 AATCAAAGTC
* * *
11097284 AAATATATTATGTTAATAAATGCT
1 AAATATATTATATGAATAAATACT
*
11097308 AAATATATTATATGCATAAATACT
1 AAATATATTATATGAATAAATACT
11097332 AA
1 AA
11097334 TTCTTCTAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
AAATATATTATATGAATAAATACT
Found at i:11098558 original size:37 final size:37
Alignment explanation
Indices: 11098508--11098585 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
11098498 CCATTATTTC
11098508 TTGATTGCTCTTTATAAATTGATTTGTTAAAATGATG
1 TTGATTGCTCTTTATAAATTGATTTGTTAAAATGATG
11098545 TTGATTGCTCTTTATAAATTGATTTGTTAAAATGATG
1 TTGATTGCTCTTTATAAATTGATTTGTTAAAATGATG
11098582 TTGA
1 TTGA
11098586 ATGATACTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.49
Consensus pattern (37 bp):
TTGATTGCTCTTTATAAATTGATTTGTTAAAATGATG
Found at i:11110702 original size:16 final size:17
Alignment explanation
Indices: 11110681--11110712 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11110671 CCCAATGAAA
11110681 GAAAGAGA-GAGAAGAC
1 GAAAGAGAGGAGAAGAC
11110697 GAAAGAGAGGAGAAGA
1 GAAAGAGAGGAGAAGA
11110713 ACTTGTGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.56, C:0.03, G:0.41, T:0.00
Consensus pattern (17 bp):
GAAAGAGAGGAGAAGAC
Found at i:11122664 original size:5 final size:6
Alignment explanation
Indices: 11122629--11122663 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
11122619 ATTGCATATA
**
11122629 ATTTTT ATTTTT CCTTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
11122664 AATCGTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:11126052 original size:16 final size:17
Alignment explanation
Indices: 11126026--11126064 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
11126016 CTGAATATGA
* *
11126026 TGAGTATTGGAAGGCAC
1 TGAGAATTGGAAGCCAC
11126043 -GAGAATTGGAAGCCAC
1 TGAGAATTGGAAGCCAC
11126059 TGAGAA
1 TGAGAA
11126065 CCTGAACAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.18
Consensus pattern (17 bp):
TGAGAATTGGAAGCCAC
Found at i:11133976 original size:18 final size:19
Alignment explanation
Indices: 11133943--11133980 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
11133933 CAGGAAAAAC
11133943 GTCTTGAAACTCCTTAACT
1 GTCTTGAAACTCCTTAACT
*
11133962 GTCTTGATA-TCCTTAACT
1 GTCTTGAAACTCCTTAACT
11133980 G
1 G
11133981 AAGTGTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (19 bp):
GTCTTGAAACTCCTTAACT
Found at i:11137239 original size:17 final size:18
Alignment explanation
Indices: 11137205--11137239 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11137195 CCATGATGTT
*
11137205 CGCCCGTGTGGGCCCACA
1 CGCCCGTGTGGACCCACA
11137223 CGCCCGTGT-GACCCACA
1 CGCCCGTGTGGACCCACA
11137240 TGACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.14, C:0.46, G:0.29, T:0.11
Consensus pattern (18 bp):
CGCCCGTGTGGACCCACA
Found at i:11139198 original size:23 final size:24
Alignment explanation
Indices: 11139157--11139204 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
11139147 TGCCAATACT
11139157 TGGAACCAAAGTTTATTCGGTAAA
1 TGGAACCAAAGTTTATTCGGTAAA
*
11139181 TGGAATCAAA-TTTATTCGGTAAA
1 TGGAACCAAAGTTTATTCGGTAAA
11139204 T
1 T
11139205 AATAGTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (24 bp):
TGGAACCAAAGTTTATTCGGTAAA
Found at i:11140255 original size:39 final size:39
Alignment explanation
Indices: 11140154--11140415 Score: 368
Period size: 39 Copynumber: 6.6 Consensus size: 39
11140144 TTGAATGTTG
* *
11140154 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
11140193 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
11140234 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
11140273 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
11140312 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* * * *
11140351 TCCGAGCTAAGCCCGAAGGCATTTGTGCAAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
*
11140390 TCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
11140416 AACGAGGAGC
Statistics
Matches: 205, Mismatches: 13, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
39 149 0.73
40 44 0.21
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:11147570 original size:39 final size:40
Alignment explanation
Indices: 11147469--11147691 Score: 298
Period size: 39 Copynumber: 5.7 Consensus size: 40
11147459 TTGAATGTTG
* *
11147469 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
11147508 ATCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
11147549 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
11147588 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
11147627 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
11147666 TCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
11147692 AACGAGGAGC
Statistics
Matches: 168, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
39 112 0.67
40 44 0.26
41 11 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:11149092 original size:9 final size:9
Alignment explanation
Indices: 11149078--11149103 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
11149068 TAATTAAATG
11149078 ATTAGTAAA
1 ATTAGTAAA
11149087 ATTAGTAAA
1 ATTAGTAAA
11149096 ATTAGTAA
1 ATTAGTAA
11149104 TATGAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.35
Consensus pattern (9 bp):
ATTAGTAAA
Found at i:11149860 original size:23 final size:22
Alignment explanation
Indices: 11149826--11149868 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
11149816 AAACTATATT
11149826 TCATGTTTAATT-AGTTAAAAA
1 TCATGTTTAATTAAGTTAAAAA
11149847 TCATGTCTTAAATTAAGTTAAA
1 TCATGT-TT-AATTAAGTTAAA
11149869 TGTAATGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 4 0.21
24 7 0.37
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (22 bp):
TCATGTTTAATTAAGTTAAAAA
Found at i:11150348 original size:85 final size:84
Alignment explanation
Indices: 11150205--11150438 Score: 328
Period size: 85 Copynumber: 2.8 Consensus size: 84
11150195 ACCACCGCTG
* * * *
11150205 ATTTGTAGTTACTGCCACTTATTGTGGGTGCACAATATATTTGAAGATTAAACAAACTGTCACTT
1 ATTTGCAGTTACTGCCACTT-TTGTAGGTGCACAACATATTTGTAGATTAAACAAACTGTCACTT
11150270 GGCTCATGATCGAACCACAT
65 GGCTCATGATCGAACCACAT
*
11150290 ATTTGCAGTTATTGCCACTTGTTGTAGGTGCACAACATATTTGTAGATTAAACAAACTGTCACTT
1 ATTTGCAGTTACTGCCACTT-TTGTAGGTGCACAACATATTTGTAGATTAAACAAACTGTCACTT
*
11150355 GGTTCATGATCGAACCACAT
65 GGCTCATGATCGAACCACAT
* * * * **
11150375 ATTTGCAGTTACTGCTACTTATG-A-GTGCACATCATATTTGTAGATTAAATAAACTACCACTTG
1 ATTTGCAGTTACTGCCACTTTTGTAGGTGCACAACATATTTGTAGATTAAACAAACTGTCACTTG
11150438 G
66 G
11150439 TTCGTAATTG
Statistics
Matches: 135, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
82 36 0.27
83 1 0.01
84 2 0.01
85 96 0.71
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (84 bp):
ATTTGCAGTTACTGCCACTTTTGTAGGTGCACAACATATTTGTAGATTAAACAAACTGTCACTTG
GCTCATGATCGAACCACAT
Found at i:11150482 original size:48 final size:48
Alignment explanation
Indices: 11150411--11150519 Score: 218
Period size: 48 Copynumber: 2.3 Consensus size: 48
11150401 GCACATCATA
11150411 TTTGTAGATTAAATAAACTACCACTTGGTTCGTAATTGAACCACACTG
1 TTTGTAGATTAAATAAACTACCACTTGGTTCGTAATTGAACCACACTG
11150459 TTTGTAGATTAAATAAACTACCACTTGGTTCGTAATTGAACCACACTG
1 TTTGTAGATTAAATAAACTACCACTTGGTTCGTAATTGAACCACACTG
11150507 TTTGTAGATTAAA
1 TTTGTAGATTAAA
11150520 CTGACACTCT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 61 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (48 bp):
TTTGTAGATTAAATAAACTACCACTTGGTTCGTAATTGAACCACACTG
Found at i:11151100 original size:28 final size:28
Alignment explanation
Indices: 11151069--11151177 Score: 119
Period size: 28 Copynumber: 3.9 Consensus size: 28
11151059 GTAATATTTG
* *
11151069 AAAAATAGGGGTAACATTGTGAAATCTA
1 AAAAATAGGGGTAAAATTGTAAAATCTA
* *
11151097 AAAAACTTGGGGTAAAATTGTAAAATCTT
1 AAAAA-TAGGGGTAAAATTGTAAAATCTA
* * * * *
11151126 GAAAATAAGGGAAAAAATATAAAATCTA
1 AAAAATAGGGGTAAAATTGTAAAATCTA
*
11151154 AAAAGTAGGGGTAAAATTGTAAAA
1 AAAAATAGGGGTAAAATTGTAAAA
11151178 CTTGAAAAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
28 40 0.63
29 23 0.37
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (28 bp):
AAAAATAGGGGTAAAATTGTAAAATCTA
Found at i:11151119 original size:57 final size:56
Alignment explanation
Indices: 11151058--11151190 Score: 151
Period size: 56 Copynumber: 2.4 Consensus size: 56
11151048 AAGGGAAAGC
* * * * * * * *
11151058 TGTAATATTTGAAAAATAGGGGTAACATTGTGAAATCTAAAAAACTTGGGGTAAAAT
1 TGTAAAATTTGAAAAATAAGGGAAAAAATATAAAATCT-AAAAACTAGGGGTAAAAT
*
11151115 TGTAAAATCTTG-AAAATAAGGGAAAAAATATAAAATCTAAAAAGTAGGGGTAAAAT
1 TGTAAAAT-TTGAAAAATAAGGGAAAAAATATAAAATCTAAAAACTAGGGGTAAAAT
*
11151171 TGTAAAACTTGAAAAATAAG
1 TGTAAAATTTGAAAAATAAG
11151191 AGACACACAG
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
55 3 0.05
56 31 0.48
57 27 0.42
58 3 0.05
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (56 bp):
TGTAAAATTTGAAAAATAAGGGAAAAAATATAAAATCTAAAAACTAGGGGTAAAAT
Found at i:11151186 original size:29 final size:27
Alignment explanation
Indices: 11151066--11151188 Score: 97
Period size: 28 Copynumber: 4.4 Consensus size: 27
11151056 GCTGTAATAT
* *
11151066 TTGAAAAATAGGGGTAACATTGTGAAA
1 TTGAAAAATAGGGGTAAAATTGTAAAA
* *
11151093 TCTAAAAAACTTGGGGTAAAATTGTAAAA
1 T-TGAAAAA-TAGGGGTAAAATTGTAAAA
* * * *
11151122 TCTTG-AAAATAAGGGAAAAAATATAAAA
1 --TTGAAAAATAGGGGTAAAATTGTAAAA
11151150 TCT-AAAAAGTAGGGGTAAAATTGTAAAA
1 T-TGAAAAA-TAGGGGTAAAATTGTAAAA
11151178 CTTGAAAAATA
1 -TTGAAAAATA
11151189 AGAGACACAC
Statistics
Matches: 73, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
26 1 0.01
27 6 0.08
28 38 0.52
29 26 0.36
30 1 0.01
31 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.25
Consensus pattern (27 bp):
TTGAAAAATAGGGGTAAAATTGTAAAA
Found at i:11155510 original size:38 final size:38
Alignment explanation
Indices: 11155466--11155539 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
11155456 TGCCTACTAT
11155466 TACTGTTAAACCAAACACATGTTAAGCATGTCTACTGC
1 TACTGTTAAACCAAACACATGTTAAGCATGTCTACTGC
* ** *
11155504 TACTGTTGAACTGAATACATGTTAAGCATGTCTACT
1 TACTGTTAAACCAAACACATGTTAAGCATGTCTACT
11155540 ATTTTACATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (38 bp):
TACTGTTAAACCAAACACATGTTAAGCATGTCTACTGC
Found at i:11159763 original size:59 final size:59
Alignment explanation
Indices: 11159695--11159809 Score: 185
Period size: 59 Copynumber: 1.9 Consensus size: 59
11159685 GGTTGAATGC
* *
11159695 ATACCTTCTGAAGCTAAAGAATGGCAAATAACGTTGTTGGTTGGATTCCTTTGGACGAT
1 ATACCTTCTGAAACTAAAGAATGGCAAATAACGTTGTTGGTTAGATTCCTTTGGACGAT
* * *
11159754 ATACCTTCTGAAATTGAAGAATGGCAAATAATGTTGTTGGTTAGATTCCTTTGGAC
1 ATACCTTCTGAAACTAAAGAATGGCAAATAACGTTGTTGGTTAGATTCCTTTGGAC
11159810 AATGTTAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (59 bp):
ATACCTTCTGAAACTAAAGAATGGCAAATAACGTTGTTGGTTAGATTCCTTTGGACGAT
Found at i:11160153 original size:17 final size:17
Alignment explanation
Indices: 11160131--11160170 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
11160121 TCCACCAAGA
* *
11160131 AATACTATTCGCCGGGC
1 AATACTATTAGCCAGGC
11160148 AATACTATTAGCCAGGC
1 AATACTATTAGCCAGGC
*
11160165 TATACT
1 AATACT
11160171 TATACGCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (17 bp):
AATACTATTAGCCAGGC
Found at i:11162522 original size:14 final size:14
Alignment explanation
Indices: 11162503--11162530 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11162493 GTTTAAAGAT
11162503 GATTAAAAACTAAG
1 GATTAAAAACTAAG
11162517 GATTAAAAACTAAG
1 GATTAAAAACTAAG
11162531 TAAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
GATTAAAAACTAAG
Found at i:11172164 original size:50 final size:50
Alignment explanation
Indices: 11172075--11172250 Score: 190
Period size: 50 Copynumber: 3.4 Consensus size: 50
11172065 CTGTACTACT
* * * **
11172075 AATGCCATATCCCAAATATGGTCTTATATGGGAGTTCTCATATCGGTGCC
1 AATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCC
* * * *
11172125 CATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCC
1 AATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCC
* *
11172175 AACGCCATGTCCCAAACATGGTCTTACATGGGACCTCCCATAGTCTTAGTGATGCC
1 AATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATA-TC---G-G-TGCC
*
11172231 AATGCCATGTCCCAGACATG
1 AATGCCATGTCCCAAACATG
11172251 CTATTACTGG
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
50 77 0.75
51 2 0.02
54 1 0.01
55 1 0.01
56 22 0.21
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
AATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCC
Found at i:11172600 original size:30 final size:30
Alignment explanation
Indices: 11172564--11172622 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
11172554 TCCTTGACTC
11172564 AAACTTTAGAAAAATTACAATTTTTCCCCT
1 AAACTTTAGAAAAATTACAATTTTTCCCCT
* * * *
11172594 AAACTTTTGCATAATTACACTTTTTCCCC
1 AAACTTTAGAAAAATTACAATTTTTCCCC
11172623 AAAGCTCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
AAACTTTAGAAAAATTACAATTTTTCCCCT
Found at i:11177987 original size:21 final size:22
Alignment explanation
Indices: 11177943--11177987 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
11177933 GAACAAATTG
*
11177943 TTGATCCTATTTCTTTTTTGAT
1 TTGATCCTATTTCTTTTCTGAT
11177965 TTGAT-CTA-TTCTTTTCTGTAT
1 TTGATCCTATTTCTTTTCTG-AT
11177986 TT
1 TT
11177988 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 7 0.33
22 5 0.24
ACGTcount: A:0.13, C:0.13, G:0.09, T:0.64
Consensus pattern (22 bp):
TTGATCCTATTTCTTTTCTGAT
Found at i:11178043 original size:21 final size:23
Alignment explanation
Indices: 11178019--11178061 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
11178009 TTAATTTTTT
*
11178019 AAAACATATTT-CTTCT-TTTAG
1 AAAACAGATTTGCTTCTCTTTAG
*
11178040 AAAAGAGATTTGCTTCTCTTTA
1 AAAACAGATTTGCTTCTCTTTA
11178062 TAATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (23 bp):
AAAACAGATTTGCTTCTCTTTAG
Found at i:11180074 original size:21 final size:22
Alignment explanation
Indices: 11180030--11180074 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
11180020 GAACAAATTG
*
11180030 TTGATCCTATTTCTTTTTTGAT
1 TTGATCCTATTTCTTTTCTGAT
11180052 TTGAT-CTA-TTCTTTTCTGTAT
1 TTGATCCTATTTCTTTTCTG-AT
11180073 TT
1 TT
11180075 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 7 0.33
22 5 0.24
ACGTcount: A:0.13, C:0.13, G:0.09, T:0.64
Consensus pattern (22 bp):
TTGATCCTATTTCTTTTCTGAT
Found at i:11180130 original size:21 final size:23
Alignment explanation
Indices: 11180106--11180148 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
11180096 TTAATTTTTT
*
11180106 AAAACATATTT-CTTCT-TTTAG
1 AAAACAGATTTGCTTCTCTTTAG
*
11180127 AAAAGAGATTTGCTTCTCTTTA
1 AAAACAGATTTGCTTCTCTTTA
11180149 TAATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (23 bp):
AAAACAGATTTGCTTCTCTTTAG
Found at i:11182614 original size:21 final size:23
Alignment explanation
Indices: 11182572--11182614 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
11182562 TAATTAATTA
*
11182572 TAAAGAGAAGCAAATCTCTTTTC
1 TAAAGAGAAGCAAATATCTTTTC
*
11182595 TAAA-AGAAG-AAATATGTTTT
1 TAAAGAGAAGCAAATATCTTTT
11182615 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (23 bp):
TAAAGAGAAGCAAATATCTTTTC
Found at i:11188838 original size:27 final size:27
Alignment explanation
Indices: 11188800--11188854 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
11188790 TGTTTTTCTA
11188800 CTATTGAAGATACAGATTCGTCGTATC
1 CTATTGAAGATACAGATTCGTCGTATC
*
11188827 CTATTGAAGATACAGATTCTTCGTATC
1 CTATTGAAGATACAGATTCGTCGTATC
11188854 C
1 C
11188855 CATGTATGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (27 bp):
CTATTGAAGATACAGATTCGTCGTATC
Found at i:11204766 original size:17 final size:17
Alignment explanation
Indices: 11204744--11204778 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
11204734 TTGGCATCCA
11204744 TATGTTAATGAAAACCC
1 TATGTTAATGAAAACCC
*
11204761 TATGTTAATGACAACCC
1 TATGTTAATGAAAACCC
11204778 T
1 T
11204779 TTGTCATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (17 bp):
TATGTTAATGAAAACCC
Found at i:11207766 original size:49 final size:49
Alignment explanation
Indices: 11207543--11207825 Score: 271
Period size: 49 Copynumber: 5.7 Consensus size: 49
11207533 AATAATGGTT
* * * * ** *
11207543 ACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATGAAAGGTC
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGAATCGGAAAG-TTGATC
* * * * * * * *
11207593 GCATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGATAGTTTCGATC
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGAATCGGAAAG-TT-GATC
* * * ** *
11207644 ACGTGTGTAGTACTATGTGCAAGATACTACGTGTAAT-GCATATTTATGGTC
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTG-AATCGGA-AAGT-TGATC
**
11207695 ACGTAAGTAGTACTATGTGCAGGCTACTACGTGAATCGGAAAGTTGATC
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGAATCGGAAAGTTGATC
* *
11207744 ATGTGTGTAGTACTATGTGCAGGCTACTACGTGAATCGAAAAGTTGATC
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGAATCGGAAAGTTGATC
*
11207793 ACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTG
11207826 TATTGAATGA
Statistics
Matches: 190, Mismatches: 38, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
49 80 0.42
50 42 0.22
51 66 0.35
52 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (49 bp):
ACGTGTGTAGTACTATGTGCAGGCTACTACGTGAATCGGAAAGTTGATC
Found at i:11214790 original size:15 final size:16
Alignment explanation
Indices: 11214770--11214799 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11214760 TGGTGACTTA
11214770 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
11214785 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
11214800 AGCATGTTTG
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:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:11216725 original size:86 final size:86
Alignment explanation
Indices: 11216579--11216742 Score: 222
Period size: 86 Copynumber: 1.9 Consensus size: 86
11216569 TCTAGAACAT
* * **
11216579 TGGTGGTTCATCCACAAATTACTGAAAAATTTTATCAACAAATGAGTTTTGCATTTACAACAAGT
1 TGGTGGTTCATCCACAAATTACTGAAAAATTTTACCAACAAATGAGTTGTGCATCCACAACAAGT
*
11216644 GGCAATTTATTTGCATATTAC
66 AGCAATTTATTTGCATATTAC
* * * *
11216665 TGGTGGTTCATCCACAAATTACTGACAACTTTTACCTACAGAT-ATGTTGTGCATCCACAACAAG
1 TGGTGGTTCATCCACAAATTACTGAAAAATTTTACCAACAAATGA-GTTGTGCATCCACAACAAG
*
11216729 TAGCATTTTATTTG
65 TAGCAATTTATTTG
11216743 TCAATGTTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
85 1 0.01
86 66 0.99
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (86 bp):
TGGTGGTTCATCCACAAATTACTGAAAAATTTTACCAACAAATGAGTTGTGCATCCACAACAAGT
AGCAATTTATTTGCATATTAC
Found at i:11217334 original size:20 final size:21
Alignment explanation
Indices: 11217311--11217351 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
11217301 TAGCATGCAT
*
11217311 GGTATTTAAAT-TGAATTTAG
1 GGTATTGAAATATGAATTTAG
*
11217331 GGTATTGAAATATGGATTTAG
1 GGTATTGAAATATGAATTTAG
11217352 AATTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (21 bp):
GGTATTGAAATATGAATTTAG
Found at i:11227314 original size:139 final size:137
Alignment explanation
Indices: 11227014--11227518 Score: 663
Period size: 139 Copynumber: 3.6 Consensus size: 137
11227004 ATGTAGTATT
* * * *
11227014 AATTAATTAATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGATACGAAAATTAA
1 AATTTATTAATATAAACAGTTATATTAATTAATTTTGATCAAAATATAAAAGACATGAAAATTAA
* * * *
11227079 TATTCTTTTGGAAATAATATAATTAATATATGAATTTTATTCATACAAAATGTTAATTTTATATG
66 TATTCTTTTGAAAAGAATATAATT-ATATATGAATTTTATTCATACAAAATATTAATTTTATATA
*
11227144 TTTTACCG
130 TTTTATCG
* *
11227152 AATTTATTAATATAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAA
1 AATTTATTAATATAAACAGTTATATTAATTAATTTTGATCAAAATATAAAAGACATGAAAATTAA
* *
11227217 TATTCTTTTGAAAAAAGAATATAATTATATATAAATTTGATTCATACAAAATATTAATTTTATAT
66 TATTCTTTTG--AAAAGAATATAATTATATATGAATTTTATTCATACAAAATATTAATTTTATAT
11227282 ATTTTATCG
129 ATTTTATCG
* * * **
11227291 AATTTATTAATATAAATAGTTATATTAATTAATTTCTG-TCAAATTATAAAAAAACATGAATGTT
1 AATTTATTAATATAAACAGTTATATTAATTAATTT-TGATCAAAATAT-AAAAGACATGAAAATT
* * * * *
11227355 AATATTCTTTTGGAAAGAATATAATAAATATATGAATTTTATTCATGCAAAATAGTAATTGTATA
64 AATATTCTTTTGAAAAGAATATAAT-TATATATGAATTTTATTCATACAAAATATTAATTTTATA
*
11227420 TATTTTATTG
128 TATTTTATCG
* * * * *
11227430 AATTTATTAATATAAACAGTTATATTAATTTA-TTTCAGTCAAAGTATAAAATATATGAAAATTA
1 AATTTATTAATATAAACAGTTATATTAATTAATTTTGA-TCAAAATATAAAAGACATGAAAATTA
*
11227494 ATATACTTTTGAAAAGAATATAATT
65 ATATTCTTTTGAAAAGAATATAATT
11227519 TTTTTTCTAA
Statistics
Matches: 321, Mismatches: 39, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
137 1 0.00
138 118 0.37
139 164 0.51
140 38 0.12
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (137 bp):
AATTTATTAATATAAACAGTTATATTAATTAATTTTGATCAAAATATAAAAGACATGAAAATTAA
TATTCTTTTGAAAAGAATATAATTATATATGAATTTTATTCATACAAAATATTAATTTTATATAT
TTTATCG
Found at i:11227586 original size:74 final size:75
Alignment explanation
Indices: 11227499--11227644 Score: 258
Period size: 76 Copynumber: 1.9 Consensus size: 75
11227489 AATTAATATA
*
11227499 CTTTTGAAAAGAATATAA-TTTTTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAATA
1 CTTTTGAAAAGAATATAACTTTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGGGAATA
11227563 ATCCTATACT
66 ATCCTATACT
*
11227573 CTTTTGGAAAGAATATAACTTTTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGGGAAT
1 CTTTTGAAAAGAATATAAC-TTTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGGGAAT
11227638 AATCCTA
65 AATCCTA
11227645 GTTTTCCTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
74 17 0.25
76 51 0.75
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (75 bp):
CTTTTGAAAAGAATATAACTTTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGGGAATA
ATCCTATACT
Found at i:11228904 original size:17 final size:15
Alignment explanation
Indices: 11228882--11228916 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
11228872 ATAAAAAACT
11228882 AAAAATTAACTAAGTAA
1 AAAAATTAA--AAGTAA
11228899 AAAAATTAAAAGTAA
1 AAAAATTAAAAGTAA
11228914 AAA
1 AAA
11228917 TTCCAATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
17 9 0.50
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (15 bp):
AAAAATTAAAAGTAA
Found at i:11229216 original size:104 final size:105
Alignment explanation
Indices: 11229097--11229305 Score: 402
Period size: 104 Copynumber: 2.0 Consensus size: 105
11229087 ATTTACTACG
11229097 AAACTGCATGAATTAGAGCTCAAAAGGTACTAAAAAGCCAATATATTTTTGTG-TTCCAATAACT
1 AAACTGCATGAATTAGAGCTCAAAAGGTACTAAAAAGCCAATATATTTTTGTGTTTCCAATAACT
11229161 TAACTAGGTTACTCTAATAATATTAGATACCTAGAGGCAA
66 TAACTAGGTTACTCTAATAATATTAGATACCTAGAGGCAA
*
11229201 AAACTGCATGAATTAGAGCTCAAAATGTACTAAAAAGCCAATATATTTTTGTGTTTCCAATAACT
1 AAACTGCATGAATTAGAGCTCAAAAGGTACTAAAAAGCCAATATATTTTTGTGTTTCCAATAACT
11229266 TAACTAGGTTACTCTAATAATATTAGATACCTAGAGGCAA
66 TAACTAGGTTACTCTAATAATATTAGATACCTAGAGGCAA
11229306 GTGATCTGTC
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 52 0.50
105 51 0.50
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (105 bp):
AAACTGCATGAATTAGAGCTCAAAAGGTACTAAAAAGCCAATATATTTTTGTGTTTCCAATAACT
TAACTAGGTTACTCTAATAATATTAGATACCTAGAGGCAA
Found at i:11242335 original size:50 final size:50
Alignment explanation
Indices: 11242232--11242411 Score: 189
Period size: 50 Copynumber: 3.5 Consensus size: 50
11242222 GGGAATGAGA
** *
11242232 TCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-C--CGAG---ATGAGAGG
* ** *
11242288 TCCCATGTAAAACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGG
** * **
11242338 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGG
*
11242388 TCCCATGTAAGACCATATCTGGGA
1 TCCCATGTAAGACCATGTCTGGGA
11242412 TATGACATTG
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
50 70 0.65
53 3 0.03
55 1 0.01
56 33 0.31
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGG
Found at i:11242423 original size:100 final size:103
Alignment explanation
Indices: 11242238--11242424 Score: 227
Period size: 100 Copynumber: 1.8 Consensus size: 103
11242228 GAGATCCCAT
* **
11242238 GTAAGACCATGTCTGGGACATGGCATTAGCATCATTGAGATTATGAGAGGTCCCATGTAAAACCA
1 GTAAGACCATGTCTGGGACATGGCATGAGCATC--T-AGATTATGAGAACTCCCATGTAAAACCA
* ***
11242303 TGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCCC
63 TATCTGGGACATGACATTGGCACCGAGATGAGAGGTCCCCC
* * *
11242344 GTAAGACCATGTCTGGGACATGGCATGGGCA-C-CGA-TATGAGAACTCCCATGTAAGACCATAT
1 GTAAGACCATGTCTGGGACATGGCATGAGCATCTAGATTATGAGAACTCCCATGTAAAACCATAT
*
11242406 CTGGGATATGACATTGGCA
66 CTGGGACATGACATTGGCA
11242425 GTACAGAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
100 38 0.54
101 2 0.03
105 1 0.01
106 29 0.41
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (103 bp):
GTAAGACCATGTCTGGGACATGGCATGAGCATCTAGATTATGAGAACTCCCATGTAAAACCATAT
CTGGGACATGACATTGGCACCGAGATGAGAGGTCCCCC
Found at i:11242682 original size:4 final size:4
Alignment explanation
Indices: 11242673--11242711 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
11242663 AAGAGTAATT
* * *
11242673 TAAG TAAG TAAG TAAG TAAA CAAG TAAG TGAG TAAG TAA
1 TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAA
11242712 AAAAGCGAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.23, T:0.23
Consensus pattern (4 bp):
TAAG
Found at i:11242699 original size:20 final size:20
Alignment explanation
Indices: 11242674--11242712 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11242664 AGAGTAATTT
11242674 AAGTAAGTAAGTAAGTAAAC
1 AAGTAAGTAAGTAAGTAAAC
*
11242694 AAGTAAGTGAGTAAGTAAA
1 AAGTAAGTAAGTAAGTAAA
11242713 AAAGCGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.21
Consensus pattern (20 bp):
AAGTAAGTAAGTAAGTAAAC
Found at i:11244398 original size:50 final size:50
Alignment explanation
Indices: 11244270--11244461 Score: 163
Period size: 50 Copynumber: 3.7 Consensus size: 50
11244260 GGGAATGATA
**
11244270 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C---GA-A-TATGAGAAC
*** * * *
11244326 TCCCCCATAAGACCATGCCTGGGACATGGCTTTGGCACCAATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAATATGAGAAC
* * * * *
11244376 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA-GTACA-GAAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAATATGAGAAC
* * *
11244424 ATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
11244462 TGTATTATCA
Statistics
Matches: 111, Mismatches: 24, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
48 5 0.05
49 34 0.31
50 37 0.33
51 1 0.01
52 1 0.01
55 1 0.01
56 32 0.29
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAATATGAGAAC
Found at i:11244670 original size:4 final size:4
Alignment explanation
Indices: 11244661--11244699 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
11244651 AAGAGTTATT
* * *
11244661 TAAG TAAG TAAG TAAG TAAA CAAG TAAG TGAG TAAG TAA
1 TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAA
11244700 AGAAGCGAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.23, T:0.23
Consensus pattern (4 bp):
TAAG
Found at i:11244687 original size:20 final size:20
Alignment explanation
Indices: 11244662--11244700 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11244652 AGAGTTATTT
11244662 AAGTAAGTAAGTAAGTAAAC
1 AAGTAAGTAAGTAAGTAAAC
*
11244682 AAGTAAGTGAGTAAGTAAA
1 AAGTAAGTAAGTAAGTAAA
11244701 GAAGCGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.21
Consensus pattern (20 bp):
AAGTAAGTAAGTAAGTAAAC
Found at i:11245946 original size:12 final size:12
Alignment explanation
Indices: 11245929--11245967 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11245919 ATAAGTTATT
11245929 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
11245941 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
11245953 TAAGTGAGTAAG
1 TAAGTAAGCAAG
11245965 TAA
1 TAA
11245968 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:11247216 original size:12 final size:12
Alignment explanation
Indices: 11247199--11247237 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11247189 ATAAGTTATT
11247199 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
11247211 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
11247223 TAAGTGAGTAAG
1 TAAGTAAGCAAG
11247235 TAA
1 TAA
11247238 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:11247812 original size:12 final size:12
Alignment explanation
Indices: 11247795--11247833 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11247785 ATGAGTTATT
11247795 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
11247807 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
11247819 TAAGTGAGTAAG
1 TAAGTAAGCAAG
11247831 TAA
1 TAA
11247834 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:11248250 original size:596 final size:596
Alignment explanation
Indices: 11247118--11248871 Score: 3238
Period size: 596 Copynumber: 2.9 Consensus size: 596
11247108 CCAAGGATAG
*
11247118 TATAAGGATTGAGAATATCTCAGTTATCAGTTCAGAAAGAAATTTCAGCAAGGGAGGAGTAAGTT
1 TATAAGGATTGAGAATATCTCAGTTATCAGTTGAGAAAGAAATTTCAGCAAGGGAGGAGTAAGTT
*
11247183 ATAATCATAAGTTATTTAAGTAAGCAAGTAAGTAAACAAGTAAGTGAGTAAGTAAAGAAGCGAGT
66 ATAATCATGAGTTATTTAAGTAAGCAAGTAAGTAAACAAGTAAGTGAGTAAGTAAAGAAGCGAGT
11247248 AAAGATTCTAATGTTTGATGAAATTTATGAGTGTGATTATTTATGATAAATGTTGTTATTTATTT
131 AAAGATTCTAATGTTTGATGAAATTTATGAGTGTGATTATTTATGATAAATGTTGTTATTTATTT
*
11247313 ACTTGTAAACTTACTAAGCTTTATGCTTACTTTCTTTATTTTCCTTATTTTTATAGTATCGTCAA
196 ACTTGTAAACTTACTAAGCTTTATGCTTACTTTCTTTATTTTCCTTATTTTTATAGTATCGCCAA
11247378 GTCAGTTCGAGGATCACAAAGACGTCGGAGTTCTTCTCACACTATATACAGACATCTCGGTATTA
261 GTCAGTTCGAGGATCACAAAGACGTCGGAGTTCTTCTCACACTATATACAGACATCTCGGTATTA
*
11247443 TGTGATTTCAAAATGTGTAAAGCTATGGCATGTATCGAGACTTAGTCATTTTGAGCGTGTTTATA
326 TGTGATTTCAAAATGTGTAAAGCTATGGCATGTATAGAGACTTAGTCATTTTGAGCGTGTTTATA
** *
11247508 TGATATGGCCAATGGTTAGCTATTGTAATGGCTAATTAAGAACATGTGTGGTGTTATGAATGCCT
391 TGATATGGTGAATGGTTAGCTATTGCAATGGCTAATTAAGAACATGTGTGGTGTTATGAATGCCT
* *
11247573 AGGTGATAGTTTATGCCTAGAAAATATGAAAGAGTAAAAATTTGCAATGAAACAGTTTTGGGGCA
456 AGGTGATAGTTTATACCTAGAAAATATGAAAGAGTAAAAATTTGCAATGAAACAGTTTTGGGACA
** * *
11247638 ACAATAGTGACATGACTTTGAAAAATCACCAGGGATAATATACTTTCAATAAGCATTATAATAAA
521 ACAGCAGTGACATGACTTTGAAAAATCACCAGGGATAGTATACTTTCAATAAGCATAATAATAAA
11247703 TTCAGGTGAGT
586 TTCAGGTGAGT
11247714 TATAAGGATTGAGAATATCTCAGTTATCAGTTGAGAAAGAAATTTCAGCAAGGGAGGAGTAAGTT
1 TATAAGGATTGAGAATATCTCAGTTATCAGTTGAGAAAGAAATTTCAGCAAGGGAGGAGTAAGTT
11247779 ATAATCATGAGTTATTTAAGTAAGCAAGTAAGTAAACAAGTAAGTGAGTAAGTAAAGAAGCGAGT
66 ATAATCATGAGTTATTTAAGTAAGCAAGTAAGTAAACAAGTAAGTGAGTAAGTAAAGAAGCGAGT
11247844 AAAGATTCTAATGTTTGATGAAATTTATGAGTGTGATTATTTATGATAAATGTTGTTATTTATTT
131 AAAGATTCTAATGTTTGATGAAATTTATGAGTGTGATTATTTATGATAAATGTTGTTATTTATTT
*
11247909 ACTTGTAAACTTACTAAGCTTTATGCTTACTTTCTTTATTTTCCTTATTTTTATAGTATTGCCAA
196 ACTTGTAAACTTACTAAGCTTTATGCTTACTTTCTTTATTTTCCTTATTTTTATAGTATCGCCAA
* * *
11247974 GTCAGTTCGAGGGTCACACAGACGCCGGAGTTCTTCTCACACTATATACAGACATCTCGGTATTA
261 GTCAGTTCGAGGATCACAAAGACGTCGGAGTTCTTCTCACACTATATACAGACATCTCGGTATTA
* * * * * *
11248039 TGTGATTTCGAAATGCGGAAAGCTATGGCATGTATAGAGACTTAGTCATTTTAAGTGTGTTTTTA
326 TGTGATTTCAAAATGTGTAAAGCTATGGCATGTATAGAGACTTAGTCATTTTGAGCGTGTTTATA
*
11248104 TAATATGGTGAATGGTTAGCTATTGCAATGGCTAATTAAGAACATGTGTGGTGTTATGAATGCCT
391 TGATATGGTGAATGGTTAGCTATTGCAATGGCTAATTAAGAACATGTGTGGTGTTATGAATGCCT
*
11248169 AGGTGATAGTTTATACCTAGAAAATATGAAAGAGTCAAAATTTGCAATGAAACAGTTTTGGGACA
456 AGGTGATAGTTTATACCTAGAAAATATGAAAGAGTAAAAATTTGCAATGAAACAGTTTTGGGACA
*
11248234 ACAGCAGTGACATGACTTTGAAAAATCACAAGGGATAGTATACTTTCAATAAGCATAATAATAAA
521 ACAGCAGTGACATGACTTTGAAAAATCACCAGGGATAGTATACTTTCAATAAGCATAATAATAAA
*
11248299 TTTAGGTGAGT
586 TTCAGGTGAGT
11248310 TATAAGGATTGAGAATATCTCAGTTATCAGTTGAGAAAGAAATTTCAGCAAGGGAGGAGTAAGTT
1 TATAAGGATTGAGAATATCTCAGTTATCAGTTGAGAAAGAAATTTCAGCAAGGGAGGAGTAAGTT
*
11248375 ATAATCATGAGTTATTTAAGTAAGAAAGTAAGTAAACAAGTAAGTGAGTAAGTAAAGAAGCGAGT
66 ATAATCATGAGTTATTTAAGTAAGCAAGTAAGTAAACAAGTAAGTGAGTAAGTAAAGAAGCGAGT
11248440 AAAGATTCTAATGTTTGATGAAATTTATGAGTGTGATTATTTATGATAAATGTTGTTATTTATTT
131 AAAGATTCTAATGTTTGATGAAATTTATGAGTGTGATTATTTATGATAAATGTTGTTATTTATTT
11248505 ACTTGTAAACTTACTAAGCTTTATGCTTACTTTCTTTATTTTCCTTATTTTTATAGTATCGCCAA
196 ACTTGTAAACTTACTAAGCTTTATGCTTACTTTCTTTATTTTCCTTATTTTTATAGTATCGCCAA
11248570 GTCAGTTCGAGGATCACAAAGACGTCGGAGTTCTTCTCACACTATATACAGACATCTCGGTATTA
261 GTCAGTTCGAGGATCACAAAGACGTCGGAGTTCTTCTCACACTATATACAGACATCTCGGTATTA
* *
11248635 TGTGATTTCAAAATTTGTAAAGCTATGGCATGTATAGAGACTTAGTCATTTTGAGCGTGTTTGTA
326 TGTGATTTCAAAATGTGTAAAGCTATGGCATGTATAGAGACTTAGTCATTTTGAGCGTGTTTATA
11248700 TGATATGGTGAATGGTTAGCTATTGCAATGGCTAATTAAGAACATGTGTGGTGTTATGAATGCCT
391 TGATATGGTGAATGGTTAGCTATTGCAATGGCTAATTAAGAACATGTGTGGTGTTATGAATGCCT
11248765 AGGTGATAGTTTATACCTAGAAAATATGAAAGAGTAAAAATTTGCAATGAAACAGTTTTGGGACA
456 AGGTGATAGTTTATACCTAGAAAATATGAAAGAGTAAAAATTTGCAATGAAACAGTTTTGGGACA
11248830 ACAGCAGTGACATGACTTTGAAAAATCACCAGGGATAGTATA
521 ACAGCAGTGACATGACTTTGAAAAATCACCAGGGATAGTATA
11248872 AATGAATTAG
Statistics
Matches: 1116, Mismatches: 42, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
596 1116 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (596 bp):
TATAAGGATTGAGAATATCTCAGTTATCAGTTGAGAAAGAAATTTCAGCAAGGGAGGAGTAAGTT
ATAATCATGAGTTATTTAAGTAAGCAAGTAAGTAAACAAGTAAGTGAGTAAGTAAAGAAGCGAGT
AAAGATTCTAATGTTTGATGAAATTTATGAGTGTGATTATTTATGATAAATGTTGTTATTTATTT
ACTTGTAAACTTACTAAGCTTTATGCTTACTTTCTTTATTTTCCTTATTTTTATAGTATCGCCAA
GTCAGTTCGAGGATCACAAAGACGTCGGAGTTCTTCTCACACTATATACAGACATCTCGGTATTA
TGTGATTTCAAAATGTGTAAAGCTATGGCATGTATAGAGACTTAGTCATTTTGAGCGTGTTTATA
TGATATGGTGAATGGTTAGCTATTGCAATGGCTAATTAAGAACATGTGTGGTGTTATGAATGCCT
AGGTGATAGTTTATACCTAGAAAATATGAAAGAGTAAAAATTTGCAATGAAACAGTTTTGGGACA
ACAGCAGTGACATGACTTTGAAAAATCACCAGGGATAGTATACTTTCAATAAGCATAATAATAAA
TTCAGGTGAGT
Found at i:11252166 original size:51 final size:51
Alignment explanation
Indices: 11252090--11252192 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 51
11252080 AGTGAACTTG
*
11252090 TACCAAATATAATTACCTGAAAAAGAGAAAAGAAAATCATGGACAGTTGGA
1 TACCAAATATAACTACCTGAAAAAGAGAAAAGAAAATCATGGACAGTTGGA
* ** **
11252141 TACCAGATATAACTACCTGAAAAAGAGGGAAGAAAATCATGGATTGTTGGA
1 TACCAAATATAACTACCTGAAAAAGAGAAAAGAAAATCATGGACAGTTGGA
11252192 T
1 T
11252193 TTACTCTAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.21
Consensus pattern (51 bp):
TACCAAATATAACTACCTGAAAAAGAGAAAAGAAAATCATGGACAGTTGGA
Found at i:11254293 original size:40 final size:40
Alignment explanation
Indices: 11254210--11254472 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
11254200 TTGAATGTTG
* * * * * *
11254210 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
11254250 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
11254290 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
11254330 TCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
11254370 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
11254410 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
11254449 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
11254473 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:11254492 original size:79 final size:80
Alignment explanation
Indices: 11254249--11254507 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
11254239 AAGTGAATAT
* * * * * * *
11254249 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
11254313 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
11254329 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
11254394 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* ** *
11254409 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
11254473 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
11254488 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
11254508 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:11274677 original size:40 final size:40
Alignment explanation
Indices: 11274594--11274856 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
11274584 TTGAATGCTG
* * * * * *
11274594 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
11274634 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
11274674 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
11274714 TCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
11274754 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
11274794 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
11274833 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
11274857 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:11274876 original size:79 final size:80
Alignment explanation
Indices: 11274633--11274891 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
11274623 AAGTGAATAT
* * * * * * *
11274633 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
11274697 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
11274713 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
11274778 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* ** *
11274793 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
11274857 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
11274872 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
11274892 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:11293899 original size:21 final size:21
Alignment explanation
Indices: 11293856--11293902 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
11293846 GCGGCGGTTA
* *
11293856 TGGTTCCTCCGACGGGGATTT
1 TGGTTCCTCCGAAGGGCATTT
11293877 TGGTTCCTCCGATAGGGCA-TT
1 TGGTTCCTCCGA-AGGGCATTT
11293898 TGGTT
1 TGGTT
11293903 TTCGAAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.11, C:0.21, G:0.32, T:0.36
Consensus pattern (21 bp):
TGGTTCCTCCGAAGGGCATTT
Found at i:11294843 original size:7 final size:7
Alignment explanation
Indices: 11294833--11294858 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
11294823 TTATATACAT
11294833 AATACTA
1 AATACTA
11294840 AATACTA
1 AATACTA
11294847 AATACTA
1 AATACTA
11294854 AATAC
1 AATAC
11294859 CAATAGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:11295064 original size:20 final size:20
Alignment explanation
Indices: 11295027--11295064 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11295017 ATTATTTTTA
*
11295027 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
11295047 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
11295065 TACCTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:11295998 original size:17 final size:16
Alignment explanation
Indices: 11295968--11296001 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
11295958 ACGATTTAAA
11295968 AAAAATTTTAAAAAAT
1 AAAAATTTTAAAAAAT
*
11295984 AAAAATTATTTAAAAAT
1 AAAAATT-TTAAAAAAT
11296001 A
1 A
11296002 GGGATTTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATTTTAAAAAAT
Found at i:11296052 original size:51 final size:52
Alignment explanation
Indices: 11295997--11296097 Score: 134
Period size: 51 Copynumber: 2.0 Consensus size: 52
11295987 AATTATTTAA
*
11295997 AAATAGGGATTTAAGAGAAATTTAAGAGGAAA-TTGAGAGCAAA-TTGAGATT
1 AAATAGGGATTTAAGAGAAATTT-AGAAGAAATTTGAGAGCAAATTTGAGATT
* * * *
11296048 AAATATGGATTTGAGAGAAATTTGGAAGAAATTTGAGAGGAAATTTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGAAATTTGAGAGCAAATTTGAGA
11296098 GAGGATTAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 6 0.14
51 31 0.72
52 6 0.14
ACGTcount: A:0.46, C:0.01, G:0.27, T:0.27
Consensus pattern (52 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGAAATTTGAGAGCAAATTTGAGATT
Found at i:11296070 original size:11 final size:11
Alignment explanation
Indices: 11296056--11296099 Score: 63
Period size: 11 Copynumber: 3.9 Consensus size: 11
11296046 TTAAATATGG
11296056 ATTTGAGAGAA
1 ATTTGAGAGAA
11296067 ATTTG-GAAGAA
1 ATTTGAG-AGAA
11296078 ATTTGAGAGGAA
1 ATTTGAGA-GAA
11296090 ATTTGAGAGA
1 ATTTGAGAGA
11296100 GGATTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.03
11 17 0.57
12 12 0.40
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:11296092 original size:12 final size:12
Alignment explanation
Indices: 11296056--11296098 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
11296046 TTAAATATGG
11296056 ATTTGAGA-GAA
1 ATTTGAGAGGAA
*
11296067 ATTTG-GAAGAA
1 ATTTGAGAGGAA
11296078 ATTTGAGAGGAA
1 ATTTGAGAGGAA
11296090 ATTTGAGAG
1 ATTTGAGAG
11296099 AGGATTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 2 0.07
11 13 0.45
12 14 0.48
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:11297404 original size:9 final size:9
Alignment explanation
Indices: 11297344--11297499 Score: 68
Period size: 9 Copynumber: 16.4 Consensus size: 9
11297334 GACATGTGCC
*
11297344 AAAAATGAT
1 AAAAATTAT
11297353 AAAAA--AT
1 AAAAATTAT
*
11297360 AAAAATAAT
1 AAAAATTAT
11297369 AAAAATTATT
1 AAAAATTA-T
**
11297379 AAATTTTAAT
1 AAAAATT-AT
11297389 AAAAAATTAT
1 -AAAAATTAT
*
11297399 AAAAATTGTAA
1 AAAAA-T-TAT
11297410 AAAATATATAT
1 AAAA-AT-TAT
*
11297421 AAAAAATTGT
1 -AAAAATTAT
**
11297431 AAAGTTTTAT
1 AAA-AATTAT
*
11297441 AAAAATCAT
1 AAAAATTAT
11297450 AAAAATTAT
1 AAAAATTAT
11297459 -AAAATATAT
1 AAAAAT-TAT
*
11297468 AGAAA-TAT
1 AAAAATTAT
* *
11297476 AGAAATATAGA
1 AAAAAT-TA-T
11297487 AAAAATTAT
1 AAAAATTAT
11297496 AAAA
1 AAAA
11297500 CTTTATAAAT
Statistics
Matches: 112, Mismatches: 20, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
7 7 0.06
8 13 0.12
9 40 0.36
10 25 0.22
11 22 0.20
12 5 0.04
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:11297404 original size:22 final size:22
Alignment explanation
Indices: 11297365--11297432 Score: 70
Period size: 21 Copynumber: 3.1 Consensus size: 22
11297355 AAAATAAAAA
* *
11297365 TAAT-AAAAATTAT-TAAATTT
1 TAATAAAAAATTATAAAAATTG
11297385 TAATAAAAAATTATAAAAATTG
1 TAATAAAAAATTATAAAAATTG
*
11297407 TAA-AAAATATATATAAAAAATTG
1 TAATAAAAAAT-TAT-AAAAATTG
11297430 TAA
1 TAA
11297433 AGTTTTATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.10
21 15 0.37
22 11 0.27
23 11 0.27
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (22 bp):
TAATAAAAAATTATAAAAATTG
Found at i:11297475 original size:8 final size:8
Alignment explanation
Indices: 11297464--11297488 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11297454 ATTATAAAAT
11297464 ATATAGAA
1 ATATAGAA
11297472 ATATAGAA
1 ATATAGAA
11297480 ATATAGAA
1 ATATAGAA
11297488 A
1 A
11297489 AAATTATAAA
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:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
ATATAGAA
Found at i:11297796 original size:9 final size:9
Alignment explanation
Indices: 11297772--11297893 Score: 52
Period size: 9 Copynumber: 12.8 Consensus size: 9
11297762 AAATTTTACC
11297772 ATTTTTATA
1 ATTTTTATA
* *
11297781 TTATTTTATG
1 AT-TTTTATA
11297791 ATTTTTATA
1 ATTTTTATA
*
11297800 ATTTTTTTTCTA
1 A---TTTTTATA
11297812 ATTTTTAATA
1 ATTTTT-ATA
*
11297822 TGTTTTTAT-
1 -ATTTTTATA
11297831 ATTTTTATTAA
1 ATTTTTA-T-A
* *
11297842 AATTTAATA
1 ATTTTTATA
11297851 ATTTTTATA
1 ATTTTTATA
** *
11297860 ACCTTTATTG
1 ATTTTTA-TA
11297870 ATTTTTAT-
1 ATTTTTATA
11297878 -TTTTTATAA
1 ATTTTTAT-A
11297887 ATTTTTA
1 ATTTTTA
11297894 CTACATGTCA
Statistics
Matches: 83, Mismatches: 17, Indels: 25
0.66 0.14 0.20
Matches are distributed among these distances:
7 7 0.08
8 6 0.07
9 28 0.34
10 24 0.29
11 10 0.12
12 8 0.10
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
ATTTTTATA
Found at i:11297806 original size:19 final size:19
Alignment explanation
Indices: 11297726--11297806 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
11297716 TTAAAGGGCA
*
11297726 TTTTTATGCA-TTTTATACT
1 TTTTTATG-ATTTTTATAAT
* *
11297745 TTTTTATGACTTTTATAAA
1 TTTTTATGATTTTTATAAT
* **
11297764 ATTTTACCATTTTTAT-AT
1 TTTTTATGATTTTTATAAT
11297782 TATTTTATGATTTTTATAAT
1 T-TTTTATGATTTTTATAAT
11297802 TTTTT
1 TTTTT
11297807 TTCTAATTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
18 2 0.04
19 44 0.90
20 3 0.06
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTTATGATTTTTATAAT
Found at i:11301533 original size:21 final size:20
Alignment explanation
Indices: 11301507--11301574 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
11301497 TTGTTTTGAG
11301507 TACTGAATTGAATTGTGAAGT
1 TACTGAATTGAATTGTGAA-T
*
11301528 TACTGAA-T--ATTGTTATAT
1 TACTGAATTGAATTGTGA-AT
*
11301546 GTACTGCATTGAATTGTGAAAT
1 -TACTGAATTGAATTGTG-AAT
11301568 TACTGAA
1 TACTGAA
11301575 GTAATGAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
18 7 0.19
19 7 0.19
20 2 0.05
21 13 0.35
22 7 0.19
23 1 0.03
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (20 bp):
TACTGAATTGAATTGTGAAT
Found at i:11301538 original size:40 final size:40
Alignment explanation
Indices: 11301471--11301574 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 40
11301461 AGACTGACAT
* * * *
11301471 TGAACTGAATTATGGAA-TACTGAATATTGTTTTGA-GTAC
1 TGAATTGAATTGTGAAATTACTGAATATTGTTAT-ATGTAC
*
11301510 TGAATTGAATTGTGAAGTTACTGAATATTGTTATATGTAC
1 TGAATTGAATTGTGAAATTACTGAATATTGTTATATGTAC
*
11301550 TGCATTGAATTGTGAAATTACTGAA
1 TGAATTGAATTGTGAAATTACTGAA
11301575 GTAATGAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
39 14 0.25
40 42 0.75
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (40 bp):
TGAATTGAATTGTGAAATTACTGAATATTGTTATATGTAC
Found at i:11301821 original size:38 final size:39
Alignment explanation
Indices: 11301774--11301859 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 39
11301764 ATATGCCGAC
* ** * *
11301774 TACTTTTACTATTACTGATTTGACAC-TTGTGTGTCGAA
1 TACTATTACTATTACCAATTCGACACTTTGTGTGTCAAA
* *
11301812 TACTATTACTCTTACCAATTCGGCACTTTGTGTGTCAAA
1 TACTATTACTATTACCAATTCGACACTTTGTGTGTCAAA
*
11301851 TACTGTTAC
1 TACTATTAC
11301860 CGTTATTGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
38 20 0.51
39 19 0.49
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (39 bp):
TACTATTACTATTACCAATTCGACACTTTGTGTGTCAAA
Found at i:11301883 original size:45 final size:44
Alignment explanation
Indices: 11301818--11302031 Score: 215
Period size: 45 Copynumber: 4.9 Consensus size: 44
11301808 CGAATACTAT
* *
11301818 TACTCTTACCAATTCGGCACTTTGTGTGTCAAATACTGTTACCG
1 TACTGTTACCGATTCGGCACTTTGTGTGTCAAATACTGTTACCG
* * * * *
11301862 TTATTGTTACCGATTCAGCACTTTGTGTGTCGAATATTGTTACCAT
1 -TACTGTTACCGATTCGGCACTTTGTGTGTCAAATACTGTTACC-G
* *
11301908 TACTGTTGCCGATTCGGCACTTTGTGTGTCGAATACTG-T----
1 TACTGTTACCGATTCGGCACTTTGTGTGTCAAATACTGTTACCG
* * * *
11301947 TACTGTTACTGATTTGTCACTTTTTGTGT-AGAATACTGTTACCG
1 TACTGTTACCGATTCGGCACTTTGTGTGTCA-AATACTGTTACCG
* * *
11301991 TACTGTTACAGATTTGGCACTTTGTGTGTTAAATACTGTTA
1 TACTGTTACCGATTCGGCACTTTGTGTGTCAAATACTGTTA
11302032 TTGTTACTGT
Statistics
Matches: 141, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
39 31 0.22
40 1 0.01
44 37 0.26
45 72 0.51
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (44 bp):
TACTGTTACCGATTCGGCACTTTGTGTGTCAAATACTGTTACCG
Found at i:11301950 original size:39 final size:39
Alignment explanation
Indices: 11301774--11302038 Score: 172
Period size: 45 Copynumber: 6.4 Consensus size: 39
11301764 ATATGCCGAC
* * * * *
11301774 TACTTTTACTATTACTGATTTGACAC-TTGTGTGTCGAA
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
* * * *
11301812 TACTATTACTCTTACCAATTCGGCACTTTGTGTGTCAAA
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
*
11301851 TACTGTTACCGTTATTGTTACCGATTCAGCACTTTGTGTGTCGAA
1 TACTGTTA-C-----TGTTACCGATTCGGCACTTTGTGTGTCGAA
* *
11301896 TATTGTTACCATTACTGTTGCCGATTCGGCACTTTGTGTGTCGAA
1 TACTG------TTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
* * * * *
11301941 TACTGTTACTGTTACTGATTTGTCACTTTTTGTGTAGAA
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
* * **
11301980 TACTGTTACCGTACTGTTACAGATTTGGCACTTTGTGTGTTAAA
1 TACTG-T----TACTGTTACCGATTCGGCACTTTGTGTGTCGAA
*
11302024 TACTGTTATTGTTAC
1 TACTGTTACTGTTAC
11302039 TGTTACTGCT
Statistics
Matches: 181, Mismatches: 28, Indels: 35
0.74 0.11 0.14
Matches are distributed among these distances:
38 20 0.11
39 59 0.33
40 2 0.01
43 1 0.01
44 33 0.18
45 62 0.34
50 1 0.01
51 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.43
Consensus pattern (39 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
Found at i:11302029 original size:83 final size:84
Alignment explanation
Indices: 11301774--11302040 Score: 239
Period size: 83 Copynumber: 3.2 Consensus size: 84
11301764 ATATGCCGAC
* * * * *
11301774 TACTTTTACTATTACTGATTTGACAC-TTGTGTGTCGAATACTATTA-C--T-C--TTACCA-AT
1 TACTGTTACTGTTACTGATTTGTCACTTTGTGTGTAGAATACTGTTACCAGTACTGTTA-CAGAT
11301831 TCGGCACTTTGTGTGTCAAA
65 TCGGCACTTTGTGTGTCAAA
* * * * *
11301851 TACTGTTACCGTTATTGTTACCGATTCAG-CACTTTGTGTGTCGAATATTGTTACCATTACTGTT
1 TACTGTTA-C-----TGTTACTGATT-TGTCACTTTGTGTGTAGAATACTGTTACCAGTACTGTT
* * *
11301915 GCCGATTCGGCACTTTGTGTGTCGAA
59 ACAGATTCGGCACTTTGTGTGTCAAA
*
11301941 TACTGTTACTGTTACTGATTTGTCACTTTTTGTGTAGAATACTGTTACC-GTACTGTTACAGATT
1 TACTGTTACTGTTACTGATTTGTCACTTTGTGTGTAGAATACTGTTACCAGTACTGTTACAGATT
* *
11302005 TGGCACTTTGTGTGTTAAA
66 CGGCACTTTGTGTGTCAAA
*
11302024 TACTGTTATTGTTACTG
1 TACTGTTACTGTTACTG
11302041 TTACTGCTAC
Statistics
Matches: 153, Mismatches: 21, Indels: 26
0.76 0.10 0.13
Matches are distributed among these distances:
77 7 0.05
78 1 0.01
83 57 0.37
84 52 0.34
85 1 0.01
87 1 0.01
88 1 0.01
89 2 0.01
90 31 0.20
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (84 bp):
TACTGTTACTGTTACTGATTTGTCACTTTGTGTGTAGAATACTGTTACCAGTACTGTTACAGATT
CGGCACTTTGTGTGTCAAA
Found at i:11304416 original size:19 final size:18
Alignment explanation
Indices: 11304394--11304438 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
11304384 ATTAACCATA
*
11304394 TATTTAGTTATTTATTTTT
1 TATTTAGTTAATT-TTTTT
*
11304413 TATTTAATTTAATTTTTTT
1 TATTT-AGTTAATTTTTTT
11304432 TATTTAG
1 TATTTAG
11304439 CTTTTCATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 6 0.27
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (18 bp):
TATTTAGTTAATTTTTTT
Found at i:11306688 original size:13 final size:13
Alignment explanation
Indices: 11306672--11306701 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11306662 TCCATAAATC
11306672 CACAACATATTTT
1 CACAACATATTTT
*
11306685 CACAATATATTTT
1 CACAACATATTTT
11306698 CACA
1 CACA
11306702 TATAAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (13 bp):
CACAACATATTTT
Found at i:11313703 original size:35 final size:36
Alignment explanation
Indices: 11313655--11313723 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
11313645 ATTTGTTAGA
11313655 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
11313691 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAA
11313724 ATGATTGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (36 bp):
TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
Found at i:11315022 original size:32 final size:33
Alignment explanation
Indices: 11314986--11315071 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
11314976 ACTTTTCCGA
* *
11314986 AAAATATTTT-CAGGAAATCAATCAAACAGCAG
1 AAAATATTTTACAGCAAATCAATCAAACACCAG
*
11315018 AAAATATTTTACA-CAGATTCAATCAAACACCAG
1 AAAATATTTTACAGCA-AATCAATCAAACACCAG
* *
11315051 AAAATATTTTCCAGTAAATCA
1 AAAATATTTTACAGCAAATCA
11315072 TTTTACAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
32 11 0.24
33 33 0.73
34 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.08, T:0.26
Consensus pattern (33 bp):
AAAATATTTTACAGCAAATCAATCAAACACCAG
Found at i:11315069 original size:14 final size:15
Alignment explanation
Indices: 11315047--11315123 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
11315037 CAATCAAACA
11315047 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
11315061 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
11315076 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
11315096 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
11315110 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
11315124 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:11315088 original size:20 final size:20
Alignment explanation
Indices: 11315063--11315102 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11315053 AATATTTTCC
*
11315063 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
11315083 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
11315103 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:11315108 original size:34 final size:35
Alignment explanation
Indices: 11315051--11315117 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
11315041 CAAACACCAG
*
11315051 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
11315086 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
11315118 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:11315124 original size:14 final size:14
Alignment explanation
Indices: 11315086--11315125 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
11315076 ACAGAAAAGT
*
11315086 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
11315100 AAATCATTTTACGG
1 AAAACATTTTACAG
11315114 AAAACATTTTAC
1 AAAACATTTTAC
11315126 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:11315480 original size:17 final size:17
Alignment explanation
Indices: 11315450--11315483 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11315440 TTTTATATTT
*
11315450 TATAAATATTATAATAA
1 TATAAATATAATAATAA
*
11315467 TATAATTATAATAATAA
1 TATAAATATAATAATAA
11315484 CATTATTTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAAATATAATAATAA
Found at i:11316658 original size:11 final size:11
Alignment explanation
Indices: 11316641--11316680 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
11316631 TAATAACTAT
11316641 AAAATAATAGC
1 AAAATAATAGC
*
11316652 AATATAATAGC
1 AAAATAATAGC
* *
11316663 AAAATAACAAC
1 AAAATAATAGC
11316674 AAAATAA
1 AAAATAA
11316681 CATCAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.68, C:0.10, G:0.05, T:0.17
Consensus pattern (11 bp):
AAAATAATAGC
Found at i:11316680 original size:22 final size:22
Alignment explanation
Indices: 11316641--11316698 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 22
11316631 TAATAACTAT
* * * *
11316641 AAAATAATAGCAATATAATAGC
1 AAAATAACAACAAAATAACAGC
*
11316663 AAAATAACAACAAAATAACATC
1 AAAATAACAACAAAATAACAGC
*
11316685 -AAATAACAATAAAA
1 AAAATAACAACAAAA
11316699 AAAAGAGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.67, C:0.12, G:0.03, T:0.17
Consensus pattern (22 bp):
AAAATAACAACAAAATAACAGC
Found at i:11318124 original size:15 final size:17
Alignment explanation
Indices: 11318094--11318126 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11318084 TGTTAGCACT
11318094 TAAAATATATTATATAG
1 TAAAATATATTATATAG
11318111 TAAAATA-ATATATATA
1 TAAAATATAT-TATATA
11318127 CAAAAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAAATATATTATATAG
Found at i:11318620 original size:9 final size:9
Alignment explanation
Indices: 11318606--11318633 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
11318596 TGAGTTTTCG
11318606 AATTCGAAT
1 AATTCGAAT
11318615 AATTCGAAT
1 AATTCGAAT
11318624 AATTCGAAT
1 AATTCGAAT
11318633 A
1 A
11318634 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:11322469 original size:29 final size:28
Alignment explanation
Indices: 11322433--11322510 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
11322423 TCATGAGATT
11322433 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
11322463 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
11322490 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
11322511 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:11322728 original size:174 final size:174
Alignment explanation
Indices: 11322463--11322964 Score: 950
Period size: 174 Copynumber: 2.9 Consensus size: 174
11322453 AAATTGTACA
* * *
11322463 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* * *
11322528 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
11322593 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
11322637 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
11322702 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
11322767 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
11322811 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
11322876 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
11322941 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
11322965 ACCTTGAGTT
Statistics
Matches: 322, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 322 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:11324941 original size:23 final size:24
Alignment explanation
Indices: 11324880--11324930 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
11324870 TTTATTTAAT
*
11324880 TTTAAA-TCTAATATTATTTTGGTG
1 TTTAAACT-TAATATTATTTTAGTG
11324904 TTTAAACTTAATATTATTTTAGT-
1 TTTAAACTTAATATTATTTTAGTG
11324927 TTTA
1 TTTA
11324931 TTATTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 4 0.16
24 20 0.80
25 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTAAACTTAATATTATTTTAGTG
Found at i:11325044 original size:69 final size:67
Alignment explanation
Indices: 11324961--11325129 Score: 171
Period size: 69 Copynumber: 2.4 Consensus size: 67
11324951 ATTGTACATT
* * * *
11324961 ATTATCTTAGATTTATCATGCATTATTATTTGTAATTTATCAATATTATTATTTTAAATTCATCA
1 ATTAT-TTAAATTTATCATGTATTATTATTT-AAATTTATCAATAATA-T-TTTTAAATTCATCA
11325026 T-TAAC
62 TATAAC
* *
11325031 ATTATTTAAATTTATCATGTA-TATTTATCTTAAATTTATCATTAATATTTTTAAATTTATCATA
1 ATTATTTAAATTTATCATGTATTA-TTAT-TTAAATTTATCAATAATATTTTTAAATTCATCATA
**
11325095 TATT
64 TAAC
* *
11325099 ATTATTTTGAATTTATCACGTATTATTATTT
1 ATTA-TTTAAATTTATCATGTATTATTATTT
11325130 TTAGAATTAT
Statistics
Matches: 84, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
67 14 0.17
68 11 0.13
69 50 0.60
70 9 0.11
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (67 bp):
ATTATTTAAATTTATCATGTATTATTATTTAAATTTATCAATAATATTTTTAAATTCATCATATA
AC
Found at i:11325058 original size:13 final size:12
Alignment explanation
Indices: 11325014--11325080 Score: 61
Period size: 13 Copynumber: 5.7 Consensus size: 12
11325004 TATTATTATT
*
11325014 TTAAATTCATCA
1 TTAAATTTATCA
11325026 TTAACA-TTAT--
1 TTAA-ATTTATCA
11325036 TTAAATTTATCA
1 TTAAATTTATCA
*
11325048 TGTATATTTATC-
1 T-TAAATTTATCA
11325060 TTAAATTTATCA
1 TTAAATTTATCA
11325072 TTAATATTT
1 TTAA-ATTT
11325081 TTAAATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
9 1 0.02
10 8 0.18
11 9 0.20
12 13 0.29
13 14 0.31
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.52
Consensus pattern (12 bp):
TTAAATTTATCA
Found at i:11325084 original size:45 final size:46
Alignment explanation
Indices: 11324958--11325116 Score: 171
Period size: 45 Copynumber: 3.5 Consensus size: 46
11324948 TTTATTGTAC
* * * ** *
11324958 ATTATTATCTTAGATTTATCATGCATTATTATTTGTAATTTATCA-AT
1 ATTATTATTTTAAATTTATCAT-TAACATTATTT-AAATTTATCATAT
* *
11325005 ATTATTATTTTAAATTCATCATTAACATTATTTAAATTTATCATGT
1 ATTATTATTTTAAATTTATCATTAACATTATTTAAATTTATCATAT
* *
11325051 A-TATTTATCTTAAATTTATCATTAATATT-TTTAAATTTATCATAT
1 ATTA-TTATTTTAAATTTATCATTAACATTATTTAAATTTATCATAT
*
11325096 ATTATTATTTTGAATTTATCA
1 ATTATTATTTTAAATTTATCA
11325117 CGTATTATTA
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
45 42 0.44
46 34 0.36
47 19 0.20
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (46 bp):
ATTATTATTTTAAATTTATCATTAACATTATTTAAATTTATCATAT
Found at i:11325154 original size:70 final size:68
Alignment explanation
Indices: 11325011--11325184 Score: 183
Period size: 70 Copynumber: 2.5 Consensus size: 68
11325001 CAATATTATT
* ** * *
11325011 ATTTTAAATTCATCATTAACATTA-TTTAAATTTATCATGTATATTTATCTTAAATTTATCATTA
1 ATTTTAAATTTATCATTATTATTATTTTAAATTTATCACGTATATTTATCTTAAATTTATCATCA
*
11325075 ATA
66 AAA
* * *
11325078 TTTTTAAATTTATCATATATTATTATTTTGAATTTATCACGTAT-TATTATTTTTAGAA-TTATC
1 ATTTTAAATTTATCAT-TATTATTATTTTAAATTTATCACGTATAT-TTA-TCTTA-AATTTATC
11325141 ATCAAAA
62 ATCAAAA
* *
11325148 ATTTTAAATTTATTATGTATTATTATTTCAAATTTAT
1 ATTTTAAATTTATCAT-TATTATTATTTTAAATTTAT
11325185 TATATATTGT
Statistics
Matches: 88, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
67 14 0.16
68 7 0.08
69 19 0.22
70 46 0.52
71 2 0.02
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (68 bp):
ATTTTAAATTTATCATTATTATTATTTTAAATTTATCACGTATATTTATCTTAAATTTATCATCA
AAA
Found at i:11325187 original size:24 final size:23
Alignment explanation
Indices: 11324958--11325184 Score: 164
Period size: 24 Copynumber: 9.8 Consensus size: 23
11324948 TTTATTGTAC
* *
11324958 ATTATTATCTTAGATTTATCATGC
1 ATTATTAT-TTAAATTTATCATGT
* *
11324982 ATTATTATTTGTAATTTATCA-AT
1 ATTATTATTT-AAATTTATCATGT
*
11325005 ATTATTATTTTAAATTCATCAT-T
1 ATTATTA-TTTAAATTTATCATGT
**
11325028 AACATTATTTAAATTTATCATGT
1 ATTATTATTTAAATTTATCATGT
11325051 A-TATTTATCTTAAATTTATCAT-T
1 ATTA-TTAT-TTAAATTTATCATGT
* *
11325074 AATATT-TTTAAATTTATCATAT
1 ATTATTATTTAAATTTATCATGT
* *
11325096 ATTATTATTTTGAATTTATCACGT
1 ATTATTA-TTTAAATTTATCATGT
*
11325120 ATTATTATTTTTAGAA-TTATCAT-C
1 ATTATTA--TTTA-AATTTATCATGT
** * *
11325144 AAAAAT-TTTAAATTTATTATGT
1 ATTATTATTTAAATTTATCATGT
11325166 ATTATTATTTCAAATTTAT
1 ATTATTATTT-AAATTTAT
11325185 TATATATTGT
Statistics
Matches: 162, Mismatches: 25, Indels: 32
0.74 0.11 0.15
Matches are distributed among these distances:
20 2 0.01
21 23 0.14
22 24 0.15
23 36 0.22
24 65 0.40
25 10 0.06
26 2 0.01
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.54
Consensus pattern (23 bp):
ATTATTATTTAAATTTATCATGT
Found at i:11325481 original size:12 final size:12
Alignment explanation
Indices: 11325453--11325484 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
11325443 TTACATGTAA
*
11325453 TTTTAAATGATT
1 TTTTTAATGATT
11325465 TTTTTAATGATT
1 TTTTTAATGATT
11325477 TTTTTAAT
1 TTTTTAAT
11325485 TTGTTTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (12 bp):
TTTTTAATGATT
Found at i:11326061 original size:13 final size:13
Alignment explanation
Indices: 11326043--11326068 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11326033 AAATCATTTA
11326043 GGTACCAATTTTG
1 GGTACCAATTTTG
11326056 GGTACCAATTTTG
1 GGTACCAATTTTG
11326069 TCATTCGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
GGTACCAATTTTG
Found at i:11328428 original size:16 final size:16
Alignment explanation
Indices: 11328407--11328450 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
11328397 ATGTGCAGAC
11328407 CCATGTTATATGCGAA
1 CCATGTTATATGCGAA
**
11328423 CCATGTCGTATGCGAA
1 CCATGTTATATGCGAA
*
11328439 CCTGTGTTATAT
1 CC-ATGTTATAT
11328451 ACTAACCCTG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (16 bp):
CCATGTTATATGCGAA
Found at i:11328516 original size:17 final size:17
Alignment explanation
Indices: 11328490--11328567 Score: 57
Period size: 17 Copynumber: 4.6 Consensus size: 17
11328480 TGTTATAACC
*
11328490 ATGTGTGAACCCATAAT
1 ATGTGCGAACCCATAAT
**
11328507 ATGTGCGAACCCATACC
1 ATGTGCGAACCCATAAT
* * **
11328524 ATGTGAGAACTCATGTT
1 ATGTGCGAACCCATAAT
* * *
11328541 GTATGCGAACCCATGAT
1 ATGTGCGAACCCATAAT
*
11328558 ATATGCGAAC
1 ATGTGCGAAC
11328568 TTATGTTATA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (17 bp):
ATGTGCGAACCCATAAT
Found at i:11328577 original size:17 final size:17
Alignment explanation
Indices: 11328530--11328579 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
11328520 TACCATGTGA
*
11328530 GAACTCATGTTGTATGC
1 GAACTCATGTTATATGC
* *
11328547 GAACCCATGATATATGC
1 GAACTCATGTTATATGC
*
11328564 GAACTTATGTTATATG
1 GAACTCATGTTATATG
11328580 TGAGCTACAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (17 bp):
GAACTCATGTTATATGC
Found at i:11328721 original size:17 final size:18
Alignment explanation
Indices: 11328681--11328723 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
11328671 GTGAACTGTG
*
11328681 TTATATTATGCGAGCTCTA
1 TTATATTA-GCGAGCCCTA
*
11328700 CTATATTA-CGAGCCCTA
1 TTATATTAGCGAGCCCTA
11328717 TTATATT
1 TTATATT
11328724 GTGTACTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
19 7 0.33
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (18 bp):
TTATATTAGCGAGCCCTA
Found at i:11329953 original size:18 final size:18
Alignment explanation
Indices: 11329930--11329966 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
11329920 GTCCAATTGA
11329930 GTAGATGCTTTGTCTTGG
1 GTAGATGCTTTGTCTTGG
11329948 GTAGATGCTTTGTCTTGG
1 GTAGATGCTTTGTCTTGG
11329966 G
1 G
11329967 CATCGAAGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.35, T:0.43
Consensus pattern (18 bp):
GTAGATGCTTTGTCTTGG
Found at i:11340168 original size:23 final size:23
Alignment explanation
Indices: 11340117--11340161 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
11340107 GTGTTATTGA
11340117 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
11340140 TCAGTGGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
11340162 ATTAGTGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:11341893 original size:41 final size:39
Alignment explanation
Indices: 11341773--11341908 Score: 150
Period size: 40 Copynumber: 3.5 Consensus size: 39
11341763 ACTAGTTTGG
*
11341773 CACCCAGTGCCTCATCGAATAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAATAATCCGAAGTAAT-AATTGA
* * ** * *
11341813 CACCTAGTGTCTCATCGGCTAAACTGAAGT-A-AATTGA
1 CACCCAGTGCCTCATCGAATAATCCGAAGTAATAATTGA
11341850 CACCCAGTGCCTCATCGAATTAATCCGAAGTAAATAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCCGAAGT-AATAATTGA
* *
11341891 CACACAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
11341909 CTCGAAGTCG
Statistics
Matches: 77, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
37 21 0.27
38 9 0.12
39 1 0.01
40 24 0.31
41 22 0.29
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGAATAATCCGAAGTAATAATTGA
Found at i:11342717 original size:10 final size:10
Alignment explanation
Indices: 11342694--11342759 Score: 53
Period size: 10 Copynumber: 6.2 Consensus size: 10
11342684 TAGTTTTTCC
11342694 TTTCTTTC-T
1 TTTCTTTCTT
11342703 TTTCTTTCTT
1 TTTCTTTCTT
*
11342713 TTTCTTTCTA
1 TTTCTTTCTT
11342723 TTTCGTTTAACCTT
1 TTTC-TTT---CTT
*
11342737 CTATCTTTCTT
1 -TTTCTTTCTT
*
11342748 TTTGTTTCTT
1 TTTCTTTCTT
11342758 TT
1 TT
11342760 ATTTATTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
9 8 0.17
10 24 0.52
11 6 0.13
14 5 0.11
15 3 0.07
ACGTcount: A:0.06, C:0.20, G:0.03, T:0.71
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:11342809 original size:26 final size:26
Alignment explanation
Indices: 11342758--11342823 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
11342748 TTTGTTTCTT
* *
11342758 TTAT-TTAT-TATATTTACTTTATTA
1 TTATATTATATATATTTACTTAAATA
11342782 TTATATTATATATATTTACTTAAATA
1 TTATATTATATATATTTACTTAAATA
*
11342808 TTA-AGTAATATATATT
1 TTATA-TTATATATATT
11342824 ATAATAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 4 0.11
25 5 0.14
26 27 0.75
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (26 bp):
TTATATTATATATATTTACTTAAATA
Found at i:11344646 original size:53 final size:52
Alignment explanation
Indices: 11344563--11344687 Score: 151
Period size: 53 Copynumber: 2.4 Consensus size: 52
11344553 GGCGCTGAAG
* * * * * *
11344563 GACCATATCATGTATGACCATAATTGGTGGGCTATAACTTCATTTGGAAAGAA
1 GACCATATCGTGTAAGA-CATAACTGGTGGGCTATAACATCATATAGAAAGAA
* *
11344616 GACCATATCGTGTAAGACAGTAACTGGTGGGTTATGACATCATATAGAAAGAA
1 GACCATATCGTGTAAGACA-TAACTGGTGGGCTATAACATCATATAGAAAGAA
*
11344669 GAACATATCGTGTAAGACA
1 GACCATATCGTGTAAGACA
11344688 CATTTATGGC
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 2 0.03
53 60 0.97
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.26
Consensus pattern (52 bp):
GACCATATCGTGTAAGACATAACTGGTGGGCTATAACATCATATAGAAAGAA
Found at i:11348693 original size:30 final size:30
Alignment explanation
Indices: 11348657--11348720 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
11348647 AATTTAAGGG
11348657 ACATAATTTCCTAACTGGGGGAGAGTTGTA
1 ACATAATTTCCTAACTGGGGGAGAGTTGTA
*
11348687 ACATAATTTCCTAAGTGGGGGAGAGTTGTA
1 ACATAATTTCCTAACTGGGGGAGAGTTGTA
11348717 ACAT
1 ACAT
11348721 CTCGTCCGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (30 bp):
ACATAATTTCCTAACTGGGGGAGAGTTGTA
Found at i:11350233 original size:27 final size:29
Alignment explanation
Indices: 11350195--11350272 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 29
11350185 CTGGAAGGGT
*
11350195 AAGCCTTCGTGGTGAAG-CTCTT-AAAGG-
1 AAGCCTTTGTGGTGAAGACT-TTAAAAGGA
* *
11350222 ATGCCTTTGTGGCG-AGACTTTAAAAGGA
1 AAGCCTTTGTGGTGAAGACTTTAAAAGGA
11350250 AAGCCTTTGTGGTG-AGTACTTTA
1 AAGCCTTTGTGGTGAAG-ACTTTA
11350273 TGAAAAGGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
26 4 0.10
27 18 0.43
28 14 0.33
29 6 0.14
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (29 bp):
AAGCCTTTGTGGTGAAGACTTTAAAAGGA
Found at i:11352212 original size:18 final size:19
Alignment explanation
Indices: 11352189--11352227 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
11352179 CTAAATCATG
11352189 AATTAA-AATAAAAAATAA
1 AATTAATAATAAAAAATAA
**
11352207 AATTAATTTTAAAAAATAA
1 AATTAATAATAAAAAATAA
11352226 AA
1 AA
11352228 CAATAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AATTAATAATAAAAAATAA
Found at i:11368289 original size:18 final size:18
Alignment explanation
Indices: 11368266--11368307 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
11368256 CACCACCACT
*
11368266 CCACCTTCAACTT-CGCCA
1 CCACCTACAACTTCCG-CA
11368284 CCACCTACAACTTCCGCA
1 CCACCTACAACTTCCGCA
11368302 CCACCT
1 CCACCT
11368308 CCTTCAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.24, C:0.52, G:0.05, T:0.19
Consensus pattern (18 bp):
CCACCTACAACTTCCGCA
Found at i:11372867 original size:18 final size:18
Alignment explanation
Indices: 11372838--11372888 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
11372828 TTTAAGTTTA
11372838 TAATTTTT-TATATTATG
1 TAATTTTTATATATTATG
*
11372855 TTATTTTTATATATTATG
1 TAATTTTTATATATTATG
*
11372873 TAATTTATAATATATT
1 TAATTT-TTATATATT
11372889 TAAAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 7 0.24
18 14 0.48
19 8 0.28
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (18 bp):
TAATTTTTATATATTATG
Found at i:11380294 original size:3 final size:3
Alignment explanation
Indices: 11380277--11380341 Score: 60
Period size: 3 Copynumber: 22.0 Consensus size: 3
11380267 AGGTTAGATC
* * * * * *
11380277 AAT AAA AAT -AT AAT AAT AGT AGT AGT AAT AAT AAT AAT AAT ATT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
11380324 AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT
11380342 GAAGCTCAAG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11382377 original size:132 final size:131
Alignment explanation
Indices: 11382126--11382910 Score: 1097
Period size: 132 Copynumber: 5.9 Consensus size: 131
11382116 TAAATCTGCT
* * * * **
11382126 TTAAATCTGCTTCCCTACTACTTTGGGAAGATAAGATTCGCCATTTTTTTATCTACTCCACTACT
1 TTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACC-GTCTTCGATCTACTCCACTACT
* * *
11382191 GCTTAGGGAGACAAGATCTATATTCTTCAACCTACTCCACTGCTACTCAAGGAGAT-GAGATTAG
65 GCTTAGGGAGAC-AGATCTACATTCTTCAACCTACTCCACTGCTGCTCAGGGAGATAG-GATTAG
*
11382255 TAGC
128 TGGC
* * * *
11382259 CTAAATATGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTG
1 TTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTACTCCACTACTG
* *
11382324 CTTAGAGAGAGCAGATCTACATTCTTCAACCTACTCCATTGCTGCTCAGGGAGAT-GAGATTAGT
66 CTTAGGGAGA-CAGATCTACATTCTTCAACCTACTCCACTGCTGCTCAGGGAGATAG-GATTAGT
*
11382388 AGC
129 GGC
* * * * *
11382391 CTAAATCTGCTTCCCTACTATCTTGGGAAGATAAGATTCACCGTTTTCGATCTGCTCCGCTACTG
1 TTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTACTCCACTACTG
11382456 CTTAGGGAGACCAGATCTACATTCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTG
66 CTTAGGGAGA-CAGATCTACATTCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTG
11382521 GC
130 GC
*
11382523 TTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCAATCTACTCCACTACTG
1 TTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTACTCCACTACTG
* *
11382588 CTCAGGGAGACCAGATCTACATTCTTCAACCTACTCCACTGTTGCTCAGGGAGATAGGATTAGTG
66 CTTAGGGAGA-CAGATCTACATTCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTG
11382653 GC
130 GC
* * * * *
11382655 TTAAATCTGCTTCTCTACTACCTTGGGAATATAAGATTCACCGTCTTTGATCTGCTCTACTACTG
1 TTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTACTCCACTACTG
* *
11382720 CTTAGGGAAACAAGATCTACATTCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTGGTG
66 CTTAGGGAGAC-AGATCTACATTCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTG
11382785 GC
130 GC
* * * * * *
11382787 TTAAATCTGCTTCTCTACTACTTTGGGAAGATAAGACTCAACGTCTTCGATCTACTCCGCTATTG
1 TTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTACTCCACTACTG
* * * *
11382852 CTTAGAGAGACATGATCTACAATATTCAACCTACTCCACTGCTGCTCAAGGAGATAGGA
66 CTTAGGGAGACA-GATCTACATTCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGA
11382911 CTTGTTTTCT
Statistics
Matches: 594, Mismatches: 54, Indels: 9
0.90 0.08 0.01
Matches are distributed among these distances:
131 2 0.00
132 552 0.93
133 40 0.07
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (131 bp):
TTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTACTCCACTACTG
CTTAGGGAGACAGATCTACATTCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGG
C
Found at i:11382622 original size:44 final size:43
Alignment explanation
Indices: 11382445--11382641 Score: 132
Period size: 44 Copynumber: 4.5 Consensus size: 43
11382435 TTTCGATCTG
* *
11382445 CTCCGCTACTGCTTAGGGAGACCAGATCTACATTCTTCAACCTA
1 CTCCACTACTGCTCAGGGAGACCAGAT-TACATTCTTCAACCTA
* * * * * * *
11382489 CTCCACTGCTGCTCAGGGAGA-TAGGATTA-GTGGCTTAAATCTG
1 CTCCACTACTGCTCAGGGAGACCA-GATTACAT-TCTTCAACCTA
* * ** ** *
11382532 CTTCC-CTACTAC-CTTGGGAAGATAAGATTCACCGTCTTCAATCTA
1 C-TCCACTACTGCTC-AGGG-AGACCAGATT-ACATTCTTCAACCTA
11382577 CTCCACTACTGCTCAGGGAGACCAGATCTACATTCTTCAACCTA
1 CTCCACTACTGCTCAGGGAGACCAGAT-TACATTCTTCAACCTA
**
11382621 CTCCACTGTTGCTCAGGGAGA
1 CTCCACTACTGCTCAGGGAGA
11382642 TAGGATTAGT
Statistics
Matches: 115, Mismatches: 27, Indels: 22
0.70 0.16 0.13
Matches are distributed among these distances:
42 2 0.02
43 19 0.17
44 72 0.63
45 21 0.18
46 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (43 bp):
CTCCACTACTGCTCAGGGAGACCAGATTACATTCTTCAACCTA
Found at i:11393066 original size:16 final size:16
Alignment explanation
Indices: 11393045--11393078 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
11393035 TTTTATGATG
*
11393045 AAATGCTATGCAATCA
1 AAATGCCATGCAATCA
11393061 AAATGCCATGCAATCA
1 AAATGCCATGCAATCA
11393077 AA
1 AA
11393079 GCAAAACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (16 bp):
AAATGCCATGCAATCA
Found at i:11394271 original size:13 final size:13
Alignment explanation
Indices: 11394253--11394277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11394243 GAATATTTTG
11394253 AAAATTTACAGAT
1 AAAATTTACAGAT
11394266 AAAATTTACAGA
1 AAAATTTACAGA
11394278 ATTGAAGCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (13 bp):
AAAATTTACAGAT
Found at i:11394543 original size:4 final size:4
Alignment explanation
Indices: 11394534--11394571 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
11394524 TTTTCCTTCG
11394534 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA- AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
11394572 CCGAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:11403156 original size:12 final size:12
Alignment explanation
Indices: 11403134--11403166 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11403124 CCATAGAAAC
11403134 ATGCA-TTGCAT
1 ATGCATTTGCAT
11403145 ATGCATTTGCAT
1 ATGCATTTGCAT
*
11403157 TTGCATTTGC
1 ATGCATTTGC
11403167 GTACCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (12 bp):
ATGCATTTGCAT
Found at i:11403687 original size:31 final size:29
Alignment explanation
Indices: 11403644--11403711 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
11403634 TTTTATAAAT
* *
11403644 AATTAATATTTAT-TAATTAAAAATATTTAC
1 AATTTATATTTATAT-ATT-AAAATATTAAC
11403674 AATTTATATTTTATATATTAAAATATTAAC
1 AATTTATA-TTTATATATTAAAATATTAAC
*
11403704 AAGTTATA
1 AATTTATA
11403712 ATAATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 24 0.73
31 8 0.24
32 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (29 bp):
AATTTATATTTATATATTAAAATATTAAC
Done.