Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 175 of 210
Found at i:52280438 original size:18 final size:20
Alignment explanation
Indices: 52280402--52280453 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
52280392 CTCAAAAAAG
52280402 TATTTAATATTTTTAATAAT
1 TATTTAATATTTTTAATAAT
52280422 TATTTAA-ATTTTT-ATAAT
1 TATTTAATATTTTTAATAAT
**
52280440 TATAAAATATTTTT
1 TATTTAATATTTTT
52280454 TTCATATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 10 0.34
19 12 0.41
20 7 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTAATATTTTTAATAAT
Found at i:52280711 original size:19 final size:19
Alignment explanation
Indices: 52280687--52280728 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
52280677 TATACATTTG
52280687 ATTTTATCTATA-TTTATAA
1 ATTTTAT-TATATTTTATAA
*
52280706 ATTTTATTTTATTTTATAA
1 ATTTTATTATATTTTATAA
52280725 ATTT
1 ATTT
52280729 AAAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTATTATATTTTATAA
Found at i:52284255 original size:18 final size:18
Alignment explanation
Indices: 52284203--52284258 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
52284193 AATAAAATTT
* *
52284203 ATTTTTAAAAA-ATTATAG
1 ATTTATAAAAATATTA-AA
*
52284221 ATTTGTAAAACATTATTAAA
1 ATTTATAAAA-A-TATTAAA
52284241 ATTTATAAAAATATTAAA
1 ATTTATAAAAATATTAAA
52284259 TAAAAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 16 0.50
19 2 0.06
20 10 0.31
21 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (18 bp):
ATTTATAAAAATATTAAA
Found at i:52284567 original size:14 final size:16
Alignment explanation
Indices: 52284543--52284580 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
52284533 TAAAATTAAA
52284543 ATTTATTTAAAAT-TT
1 ATTTATTTAAAATATT
52284558 ATTT-TTTAAAATATT
1 ATTTATTTAAAATATT
52284573 ATTTATTT
1 ATTTATTT
52284581 TTATATATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 10 0.48
16 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTATTTAAAATATT
Found at i:52284825 original size:23 final size:23
Alignment explanation
Indices: 52284782--52284830 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
52284772 TAATTTTTAA
*
52284782 TTTTTTTAAACTTTATTTAATAT
1 TTTTTTTAAACTTTATCTAATAT
* *
52284805 TTTTTTATAAATTTTA-CTAATGT
1 TTTTTT-TAAACTTTATCTAATAT
52284828 TTT
1 TTT
52284831 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTTTAAACTTTATCTAATAT
Found at i:52287489 original size:26 final size:26
Alignment explanation
Indices: 52287460--52287611 Score: 162
Period size: 26 Copynumber: 5.8 Consensus size: 26
52287450 GGAAAAACAA
* * *
52287460 GCCTTGAGCTGGTGGTTATGTAGTAG
1 GCCTTGAGCCGGTGGTTATTTAGCAG
52287486 GCCTTGAGCCGGTGGTTATTTAGCAG
1 GCCTTGAGCCGGTGGTTATTTAGCAG
* * * *
52287512 GCCTCGAGCCAGTGTTTATTTAGCAA
1 GCCTTGAGCCGGTGGTTATTTAGCAG
* * *
52287538 GCATTGAGCCGGTGTTTATTTAGCAA
1 GCCTTGAGCCGGTGGTTATTTAGCAG
**
52287564 GCCTTGAGTTGGTGGTTATTTAGCAG
1 GCCTTGAGCCGGTGGTTATTTAGCAG
* *
52287590 GCTTTGAGCTGGT-GTATATTTA
1 GCCTTGAGCCGGTGGT-TATTTA
52287612 TCAAGTATTA
Statistics
Matches: 108, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
25 2 0.02
26 106 0.98
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (26 bp):
GCCTTGAGCCGGTGGTTATTTAGCAG
Found at i:52287583 original size:52 final size:52
Alignment explanation
Indices: 52287457--52287616 Score: 185
Period size: 52 Copynumber: 3.1 Consensus size: 52
52287447 ATTGGAAAAA
* * * *
52287457 CAAGCCTTGAGCTGGTGGTTATGTAGTAGGCCTTGAGCCGGTGGTTATTTAG
1 CAAGCCTTGAGCTGGTGGTTATTTAGCAGGCATTGAGCCGGTGTTTATTTAG
* * ** * *
52287509 CAGGCCTCGAGCCAGTGTTTATTTAGCAAGCATTGAGCCGGTGTTTATTTAG
1 CAAGCCTTGAGCTGGTGGTTATTTAGCAGGCATTGAGCCGGTGTTTATTTAG
* * * * *
52287561 CAAGCCTTGAGTTGGTGGTTATTTAGCAGGCTTTGAGCTGGTGTATATTTAT
1 CAAGCCTTGAGCTGGTGGTTATTTAGCAGGCATTGAGCCGGTGTTTATTTAG
52287613 CAAG
1 CAAG
52287617 TATTATGTAT
Statistics
Matches: 87, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 87 1.00
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (52 bp):
CAAGCCTTGAGCTGGTGGTTATTTAGCAGGCATTGAGCCGGTGTTTATTTAG
Found at i:52287610 original size:78 final size:78
Alignment explanation
Indices: 52287457--52287616 Score: 194
Period size: 78 Copynumber: 2.1 Consensus size: 78
52287447 ATTGGAAAAA
* * * *
52287457 CAAGCCTTGAGCTGGTGGTTATGTAGTAGGCCTTGAGCCGGTGGTTATTTAGCAGGCCTCGAGCC
1 CAAGCATTGAGCCGGTGGTTATGTAGCAAGCCTTGAGCCGGTGGTTATTTAGCAGGCCTCGAGCC
*
52287522 AGTGTTTATTTAG
66 AGTGTATATTTAG
* * ** * * *
52287535 CAAGCATTGAGCCGGTGTTTATTTAGCAAGCCTTGAGTTGGTGGTTATTTAGCAGGCTTTGAGCT
1 CAAGCATTGAGCCGGTGGTTATGTAGCAAGCCTTGAGCCGGTGGTTATTTAGCAGGCCTCGAGCC
* *
52287600 GGTGTATATTTAT
66 AGTGTATATTTAG
52287613 CAAG
1 CAAG
52287617 TATTATGTAT
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (78 bp):
CAAGCATTGAGCCGGTGGTTATGTAGCAAGCCTTGAGCCGGTGGTTATTTAGCAGGCCTCGAGCC
AGTGTATATTTAG
Found at i:52288771 original size:29 final size:29
Alignment explanation
Indices: 52288739--52288816 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
52288729 GTCACACAGT
*
52288739 CGTGTACCACACACGGTCTCCCACATGAC
1 CGTGTGCCACACACGGTCTCCCACATGAC
* * * * *
52288768 CGTGTGCCACATATGGTTTCCTACATGGC
1 CGTGTGCCACACACGGTCTCCCACATGAC
*
52288797 CGTGTGCAACACACGGTCTC
1 CGTGTGCCACACACGGTCTC
52288817 TCATACGGCC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.21, C:0.35, G:0.22, T:0.23
Consensus pattern (29 bp):
CGTGTGCCACACACGGTCTCCCACATGAC
Found at i:52295733 original size:21 final size:21
Alignment explanation
Indices: 52295709--52295751 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
52295699 CATGAGATTA
*
52295709 TAGGATTTCAACAATTCATTG
1 TAGGATTTCAAAAATTCATTG
52295730 TAGGATTTCAAAAATTCATTG
1 TAGGATTTCAAAAATTCATTG
52295751 T
1 T
52295752 GTTTCTCTTC
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:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (21 bp):
TAGGATTTCAAAAATTCATTG
Found at i:52298495 original size:23 final size:23
Alignment explanation
Indices: 52298462--52298505 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
52298452 CACAATATGT
*
52298462 TTATCCACTTCGGCGGTGTTCAA
1 TTATCCACTTCGGCGATGTTCAA
*
52298485 TTATCCGCTTCGGCGATGTTC
1 TTATCCACTTCGGCGATGTTC
52298506 CATTTTGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.27, G:0.23, T:0.36
Consensus pattern (23 bp):
TTATCCACTTCGGCGATGTTCAA
Found at i:52318271 original size:3 final size:3
Alignment explanation
Indices: 52318265--52318330 Score: 56
Period size: 3 Copynumber: 24.0 Consensus size: 3
52318255 TTTTGAAGTA
* *
52318265 TAT TAT TAT T-T TAT TA- TAT TGT AAAT TA- TAT TA- TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
52318306 TAT TAT TA- TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
52318331 ATTTTAAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
2 14 0.27
3 36 0.71
4 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:52318280 original size:8 final size:8
Alignment explanation
Indices: 52318263--52318333 Score: 90
Period size: 8 Copynumber: 8.8 Consensus size: 8
52318253 TTTTTTGAAG
52318263 TATATTAT
1 TATATTAT
*
52318271 TATTTTAT
1 TATATTAT
*
52318279 TATATT-G
1 TATATTAT
*
52318286 TAAATTATAT
1 TATA-T-TAT
52318296 TATATTAT
1 TATATTAT
52318304 TATATTAT
1 TATATTAT
52318312 TATATTAT
1 TATATTAT
52318320 TATATTAT
1 TATATTAT
52318328 TATATT
1 TATATT
52318334 TTAAATAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
7 3 0.06
8 46 0.85
9 2 0.04
10 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:52318563 original size:13 final size:13
Alignment explanation
Indices: 52318532--52318572 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
52318522 GACGAAACAG
*
52318532 AGAAGGAAAG-AA
1 AGAAAGAAAGAAA
*
52318544 GGAAAGAAAGAAA
1 AGAAAGAAAGAAA
52318557 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
52318570 AGA
1 AGA
52318573 GAAAATTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGAAA
Found at i:52319357 original size:27 final size:30
Alignment explanation
Indices: 52319318--52319374 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
52319308 AAATAAGGTG
*
52319318 AATATCGATATTGAATTAAA-TGAATTAAA
1 AATATCGATATTGAATAAAAGTGAATTAAA
52319347 AATAT-GA-ATTGAATAAAAGTGAATTAAA
1 AATATCGATATTGAATAAAAGTGAATTAAA
52319375 TTATGATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 10 0.38
28 11 0.42
29 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.32
Consensus pattern (30 bp):
AATATCGATATTGAATAAAAGTGAATTAAA
Found at i:52330496 original size:26 final size:27
Alignment explanation
Indices: 52330447--52330501 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
52330437 TTTAATTTAA
**
52330447 AAAATAAAAAAATATTTTTTGAAAATG
1 AAAATAAAAAAATATTTTCAGAAAATG
* *
52330474 AAAAT-AAAAAATGTTTTCAGAAATTG
1 AAAATAAAAAAATATTTTCAGAAAATG
52330500 AA
1 AA
52330502 CAAAGCATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (27 bp):
AAAATAAAAAAATATTTTCAGAAAATG
Found at i:52339864 original size:19 final size:20
Alignment explanation
Indices: 52339840--52339877 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
52339830 TGACACTTAC
52339840 ATGTGTAGTT-AATCAATAG
1 ATGTGTAGTTAAATCAATAG
52339859 ATGTGTAGTTAAATCAATA
1 ATGTGTAGTTAAATCAATA
52339878 CCCAAGTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (20 bp):
ATGTGTAGTTAAATCAATAG
Found at i:52341930 original size:18 final size:16
Alignment explanation
Indices: 52341887--52341930 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 16
52341877 TAGAATCAAT
*
52341887 AAAATGAAAAATAATA
1 AAAATTAAAAATAATA
52341903 AAAATATAAAAATTAAATA
1 AAAAT-TAAAAA-T-AATA
52341922 AAAATTAAA
1 AAAATTAAA
52341931 GGGTTAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 5 0.21
17 5 0.21
18 5 0.21
19 9 0.38
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAATTAAAAATAATA
Found at i:52344467 original size:22 final size:22
Alignment explanation
Indices: 52344434--52344494 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
52344424 GCCCGGCTCG
* *
52344434 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
52344457 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
52344479 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
52344495 TTATTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:52344507 original size:16 final size:16
Alignment explanation
Indices: 52344470--52344509 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
52344460 TTAATAAAAT
* * *
52344470 TAAAACTAATTGTTAT
1 TAAAATTAATTATTAG
52344486 TAAAATTAATTATTAG
1 TAAAATTAATTATTAG
52344502 TAAAATTA
1 TAAAATTA
52344510 TCAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTATTAG
Found at i:52344588 original size:59 final size:59
Alignment explanation
Indices: 52344520--52344659 Score: 262
Period size: 59 Copynumber: 2.4 Consensus size: 59
52344510 TCAAATTATT
*
52344520 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
52344579 AATTATTAATTGTATTAGTTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
52344638 AATTATTAATTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
52344660 ATTAATTGTT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 78 1.00
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:52344653 original size:9 final size:9
Alignment explanation
Indices: 52344641--52344668 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
52344631 TTTATCAAAT
52344641 TATTAATTG
1 TATTAATTG
52344650 TATTAATTG
1 TATTAATTG
52344659 TATTAATTG
1 TATTAATTG
52344668 T
1 T
52344669 TGTAACAAAA
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:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:52354174 original size:22 final size:24
Alignment explanation
Indices: 52354136--52354180 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
52354126 TACAATAATA
52354136 AATTTAGTCTTTAATTT-TTTTTC
1 AATTTAGTCTTTAATTTCTTTTTC
*
52354159 AATTTA-TCTTTTATTTCTTTTT
1 AATTTAGTCTTTAATTTCTTTTT
52354181 TGGTTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.69
Consensus pattern (24 bp):
AATTTAGTCTTTAATTTCTTTTTC
Found at i:52354384 original size:17 final size:17
Alignment explanation
Indices: 52354364--52354470 Score: 55
Period size: 16 Copynumber: 6.4 Consensus size: 17
52354354 ATTTAAATAT
52354364 TATAAAATATTAAAAAA
1 TATAAAATATTAAAAAA
* *
52354381 TAT-ACATAATAAAATAA
1 TATAAAATATTAAAA-AA
* *
52354398 -CTCAAA-ATTAAAAAA
1 TATAAAATATTAAAAAA
* *
52354413 TAT-ACATAATAAAATAA
1 TATAAAATATTAAAA-AA
* *
52354430 -CTCAAA-ATTAAAAAA
1 TATAAAATATTAAAAAA
*
52354445 TATAAAAAATTCATAAAAA
1 TATAAAATATT-A-AAAAA
52354464 TATAAAA
1 TATAAAA
52354471 AAATTACATG
Statistics
Matches: 67, Mismatches: 13, Indels: 18
0.68 0.13 0.18
Matches are distributed among these distances:
15 6 0.09
16 34 0.51
17 14 0.21
18 1 0.01
19 12 0.18
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (17 bp):
TATAAAATATTAAAAAA
Found at i:52354409 original size:16 final size:16
Alignment explanation
Indices: 52354390--52354442 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
52354380 ATATACATAA
52354390 TAAAATAACTCAAAAT
1 TAAAATAACTCAAAAT
* *
52354406 TAAAA-AATATACATAA-
1 TAAAATAA-CT-CAAAAT
52354422 TAAAATAACTCAAAAT
1 TAAAATAACTCAAAAT
52354438 TAAAA
1 TAAAA
52354443 AATATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
15 6 0.21
16 17 0.59
17 6 0.21
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAAATAACTCAAAAT
Found at i:52354413 original size:32 final size:32
Alignment explanation
Indices: 52354372--52354448 Score: 154
Period size: 32 Copynumber: 2.4 Consensus size: 32
52354362 ATTATAAAAT
52354372 ATTAAAAAATATACATAATAAAATAACTCAAA
1 ATTAAAAAATATACATAATAAAATAACTCAAA
52354404 ATTAAAAAATATACATAATAAAATAACTCAAA
1 ATTAAAAAATATACATAATAAAATAACTCAAA
52354436 ATTAAAAAATATA
1 ATTAAAAAATATA
52354449 AAAAATTCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (32 bp):
ATTAAAAAATATACATAATAAAATAACTCAAA
Found at i:52354414 original size:18 final size:18
Alignment explanation
Indices: 52354391--52354446 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
52354381 TATACATAAT
52354391 AAAATAACTCAAAATTAA
1 AAAATAACTCAAAATTAA
*
52354409 AAAAT-A-T--ACA-TAA
1 AAAATAACTCAAAATTAA
52354422 TAAAATAACTCAAAATTAA
1 -AAAATAACTCAAAATTAA
52354441 AAAATA
1 AAAATA
52354447 TAAAAAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 1 0.03
16 2 0.07
17 1 0.03
18 13 0.43
19 3 0.10
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATAACTCAAAATTAA
Found at i:52364871 original size:44 final size:44
Alignment explanation
Indices: 52364801--52364908 Score: 148
Period size: 44 Copynumber: 2.5 Consensus size: 44
52364791 CTAAAGTTCC
* * * *
52364801 TTTCCCAC-AAATGCCGCTAAAGAACATGACATTTAGTGGCGCT
1 TTTCCCACAAAACGCCGCTAAACAACATGACATTTAGCGGCACT
*
52364844 TTTCCCACAAAACGCCGCTAAACAACATGACCTTTAGCGGCACT
1 TTTCCCACAAAACGCCGCTAAACAACATGACATTTAGCGGCACT
*
52364888 TTTACCA-AAAACGCCGCTAAA
1 TTTCCCACAAAACGCCGCTAAA
52364909 GGTCATATTC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 22 0.38
44 36 0.62
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (44 bp):
TTTCCCACAAAACGCCGCTAAACAACATGACATTTAGCGGCACT
Found at i:52368937 original size:18 final size:20
Alignment explanation
Indices: 52368906--52368943 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
52368896 CAAATTAGAA
52368906 ATAAATAAATAAACAAAAAT
1 ATAAATAAATAAACAAAAAT
52368926 ATAAAT-AA-AAACAAAAAT
1 ATAAATAAATAAACAAAAAT
52368944 TATTAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
ATAAATAAATAAACAAAAAT
Found at i:52374049 original size:22 final size:23
Alignment explanation
Indices: 52374015--52374059 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
52374005 TTAAGGTTTT
**
52374015 AAAATTAATTAAATCAATTATTA
1 AAAATTAATTAAAAAAATTATTA
*
52374038 AAAATTTA-TAAAAAAATTATTA
1 AAAATTAATTAAAAAAATTATTA
52374060 TTAAAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATTAATTAAAAAAATTATTA
Found at i:52377847 original size:20 final size:20
Alignment explanation
Indices: 52377822--52377863 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
52377812 AAGTTTAGTA
52377822 TTTACT-TTTTTATTAAAATG
1 TTTACTATTTTT-TTAAAATG
52377842 TTTACTCATTTTTTTAAAATG
1 TTTACT-ATTTTTTTAAAATG
52377863 T
1 T
52377864 AATTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 9 0.45
22 5 0.25
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTACTATTTTTTTAAAATG
Found at i:52378189 original size:63 final size:63
Alignment explanation
Indices: 52378008--52378192 Score: 217
Period size: 63 Copynumber: 2.9 Consensus size: 63
52377998 TGGTACTGTT
* * * ** * * *
52378008 AATATAAAGTACCTTAATAAAACACATATTGATAGTTTAAGTACGACATTGGATAATTTGTGAA
1 AATATAAA-TACCATAATAAAACACATATTGATAGTTCAAGTACCACATTAAACATTTTATGAA
* * ** * * *
52378072 CATACAAATACCATAATAAAATGCATATTAATAGTTCAGGTACCAAATTAAACATTTTATGAA
1 AATATAAATACCATAATAAAACACATATTGATAGTTCAAGTACCACATTAAACATTTTATGAA
*
52378135 AATATAAATACCATAATAAAACACATATTGATAGTTCAAATACCACATTAAACATTTT
1 AATATAAATACCATAATAAAACACATATTGATAGTTCAAGTACCACATTAAACATTTT
52378193 CAATACTACA
Statistics
Matches: 98, Mismatches: 23, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
63 92 0.94
64 6 0.06
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (63 bp):
AATATAAATACCATAATAAAACACATATTGATAGTTCAAGTACCACATTAAACATTTTATGAA
Found at i:52384777 original size:15 final size:15
Alignment explanation
Indices: 52384753--52384794 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
52384743 ACTTTGTTAA
* *
52384753 AATTTTTTTTATCTG
1 AATTTATTTTATATG
52384768 AATTTATTTT-TATG
1 AATTTATTTTATATG
*
52384782 GATTTATTTTATA
1 AATTTATTTTATA
52384795 ATTATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (15 bp):
AATTTATTTTATATG
Found at i:52385197 original size:23 final size:21
Alignment explanation
Indices: 52385164--52385206 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
52385154 TTGAAGTATG
52385164 GAAAAAAATAAAAATTAAAAT
1 GAAAAAAATAAAAATTAAAAT
*
52385185 GAAAAAATGATAAAAGTTAAAA
1 GAAAAAA--ATAAAAATTAAAA
52385207 CAATACATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (21 bp):
GAAAAAAATAAAAATTAAAAT
Found at i:52393735 original size:17 final size:17
Alignment explanation
Indices: 52393684--52393724 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
52393674 AATTTATATA
52393684 TTATATATTAA-ATTAT
1 TTATATATTAATATTAT
**
52393700 CAATATATTAATATTAT
1 TTATATATTAATATTAT
52393717 TTATATAT
1 TTATATAT
52393725 AATGTTAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATATATTAATATTAT
Found at i:52404213 original size:18 final size:19
Alignment explanation
Indices: 52404176--52404213 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
52404166 GGGTTTTTTT
52404176 TGTTTTTTTTAGTTATAAA
1 TGTTTTTTTTAGTTATAAA
*
52404195 TGTTTTTTTTTGTTA-AAA
1 TGTTTTTTTTAGTTATAAA
52404213 T
1 T
52404214 TTAGTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.66
Consensus pattern (19 bp):
TGTTTTTTTTAGTTATAAA
Found at i:52404605 original size:3 final size:3
Alignment explanation
Indices: 52404597--52404643 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
52404587 CACGATTTTC
*
52404597 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TATT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
52404642 TA
1 TA
52404644 CTATATTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:52404619 original size:14 final size:14
Alignment explanation
Indices: 52404600--52404637 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
52404590 GATTTTCTAT
52404600 TATTATTATTATTA
1 TATTATTATTATTA
52404614 TATTATTATTATTA
1 TATTATTATTATTA
52404628 T-TTATTATTA
1 TATTATTATTA
52404638 CTATTACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:52404650 original size:21 final size:21
Alignment explanation
Indices: 52404596--52404651 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
52404586 CCACGATTTT
*
52404596 CTATTATTATTA-TTATTATA
1 CTATTACTATTATTTATTATA
* *
52404616 TTATTATTATTATTTATTATTA
1 CTATTACTATTATTTATTA-TA
52404638 CTATTACTA-TATTT
1 CTATTACTATTATTT
52404652 TCTATATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.35
21 11 0.35
22 9 0.29
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
CTATTACTATTATTTATTATA
Found at i:52406632 original size:18 final size:17
Alignment explanation
Indices: 52406611--52406644 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52406601 TTTTTATAGT
52406611 TTTTTAATTTTCACATAC
1 TTTTTAA-TTTCACATAC
*
52406629 TTTTTTATTTCACATA
1 TTTTTAATTTCACATA
52406645 TATACCTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTAATTTCACATAC
Found at i:52412112 original size:144 final size:144
Alignment explanation
Indices: 52411850--52412151 Score: 471
Period size: 144 Copynumber: 2.1 Consensus size: 144
52411840 CATGGAAGTT
* *
52411850 GGGATTGAACCAGAAAGCCCATTAAAATGAAGCACAAGATTGCCCAAGTTAGTCAAGTTTCCTAT
1 GGGATAGAACCAGAAAGCCCATTAAAATGAAGCACAAGATTACCCAAGTTAGTCAAGTTTCCTAT
* * *
52411915 GGAATCAGGGATGAGACCAGTGAGATTATTGTCCGATAACTGCAAGTCGAAAAGAGATTTGAGCA
66 GGAATCAGGGATGACACCAGTGAGATTATTGTACGATAACTGAAAGTCGAAAAGAGATTTGAGCA
52411980 TCCCTATCTCACTG
131 TCCCTATCTCACTG
* *
52411994 GGGATAGAACCAGAAAGCCCATTAAAATTAAGCACAAGATTATCCAAGTTAGTCAAGTTTCCTAT
1 GGGATAGAACCAGAAAGCCCATTAAAATGAAGCACAAGATTACCCAAGTTAGTCAAGTTTCCTAT
* * * *
52412059 GGAATGAGGGATGACACCAGTGAGATTATTGTACGCTAACTGAAACG-CTAAAAGCGATTTGAGC
66 GGAATCAGGGATGACACCAGTGAGATTATTGTACGATAACTGAAA-GTCGAAAAGAGATTTGAGC
* *
52412123 ATTCCTATCTCATTG
130 ATCCCTATCTCACTG
52412138 GGGATAGAACCAGA
1 GGGATAGAACCAGA
52412152 GAGATTATTA
Statistics
Matches: 144, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
144 143 0.99
145 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (144 bp):
GGGATAGAACCAGAAAGCCCATTAAAATGAAGCACAAGATTACCCAAGTTAGTCAAGTTTCCTAT
GGAATCAGGGATGACACCAGTGAGATTATTGTACGATAACTGAAAGTCGAAAAGAGATTTGAGCA
TCCCTATCTCACTG
Found at i:52415341 original size:24 final size:23
Alignment explanation
Indices: 52415314--52415362 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
52415304 TAGTATTTTG
* *
52415314 ATATCTAATATTTTTAAACAATTA
1 ATATATAATATTTGTAAA-AATTA
*
52415338 ATATATATTATTTGTAAAAATTA
1 ATATATAATATTTGTAAAAATTA
52415361 AT
1 AT
52415363 TTGAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATATAATATTTGTAAAAATTA
Found at i:52417771 original size:21 final size:21
Alignment explanation
Indices: 52417699--52417771 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
52417689 TGACAGGAGT
* *
52417699 ACACGCCCGTGT-GTCTGGGGG
1 ACACGCCCGTGTGGT-TGAGAG
* * * *
52417720 ACACACCCATGTGATTGAGAT
1 ACACGCCCGTGTGGTTGAGAG
* *
52417741 ACATGGCCGTGTGGTTGAGAG
1 ACACGCCCGTGTGGTTGAGAG
52417762 ACACGCCCGT
1 ACACGCCCGT
52417772 ATGACTGAGG
Statistics
Matches: 37, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 36 0.97
22 1 0.03
ACGTcount: A:0.21, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
ACACGCCCGTGTGGTTGAGAG
Found at i:52427839 original size:158 final size:159
Alignment explanation
Indices: 52427549--52427864 Score: 476
Period size: 158 Copynumber: 2.0 Consensus size: 159
52427539 ATATACCATC
* *
52427549 CTTTTTTGGCTTCTAGTTCTTGTACTCGTACTAGACTGAGACAAAAAAAATCACAACCCCAAATT
1 CTTTTTTAGCTTCTAGTTCTTGTACTCATACTAGACTGAGACAAAAAAAATCACAACCCCAAATT
* * * * * * *
52427614 AGATTTAAATATTTTGAAATTTGATAGTAAAAAAGTGTTTACGATATAACTGTGATCTAGTTGTG
66 AGACTTAAACATTTCGAAACTTGATAATAAAAAAGTGTTTACGATATAACCGTGATCCAGTTGTG
* *
52427679 TTAGGTTGAATGCATTG-TCTTCTGTTGTT
131 TTAGGTTGAAGGCA-TGATCTTATGTTGTT
*
52427708 CTTTTTATAGCTTCTAGTTCTTGTACTCATACTAGACT-A-AGAAAAAAAATCACAACCCCAAAT
1 CTTTTT-TAGCTTCTAGTTCTTGTACTCATACTAGACTGAGACAAAAAAAATCACAACCCCAAAT
*
52427771 TAGACTTAAACATTTCGAAACTTGATAATAAAAAAGTGTTTACGATATACCCGTGATCCAGTTGT
65 TAGACTTAAACATTTCGAAACTTGATAATAAAAAAGTGTTTACGATATAACCGTGATCCAGTTGT
52427836 GTTAGGTTGAAGGCATGATCTTATGTTGT
130 GTTAGGTTGAAGGCATGATCTTATGTTGT
52427865 AACCCTCACC
Statistics
Matches: 142, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
157 2 0.01
158 104 0.73
159 7 0.05
160 29 0.20
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (159 bp):
CTTTTTTAGCTTCTAGTTCTTGTACTCATACTAGACTGAGACAAAAAAAATCACAACCCCAAATT
AGACTTAAACATTTCGAAACTTGATAATAAAAAAGTGTTTACGATATAACCGTGATCCAGTTGTG
TTAGGTTGAAGGCATGATCTTATGTTGTT
Found at i:52428385 original size:15 final size:15
Alignment explanation
Indices: 52428365--52428395 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
52428355 CTACATTACT
52428365 TCCTCTTATCCACTA
1 TCCTCTTATCCACTA
52428380 TCCTCTTATCCACTA
1 TCCTCTTATCCACTA
52428395 T
1 T
52428396 TCTGGTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.39, G:0.00, T:0.42
Consensus pattern (15 bp):
TCCTCTTATCCACTA
Found at i:52429401 original size:18 final size:18
Alignment explanation
Indices: 52429378--52429416 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
52429368 CAATTGTACT
52429378 CATCATGAAAACTTTTCA
1 CATCATGAAAACTTTTCA
*
52429396 CATCATGGAAACTTTTCA
1 CATCATGAAAACTTTTCA
52429414 CAT
1 CAT
52429417 GAATGCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (18 bp):
CATCATGAAAACTTTTCA
Found at i:52429680 original size:3 final size:3
Alignment explanation
Indices: 52429672--52429701 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
52429662 CTTTTACAAG
52429672 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52429702 CATCATCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:52429955 original size:3 final size:3
Alignment explanation
Indices: 52429947--52429972 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52429937 TTCTTGAAGC
52429947 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
52429973 TAAAAAGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:52431216 original size:29 final size:29
Alignment explanation
Indices: 52431184--52431274 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
52431174 TCAAAAATAA
*
52431184 AAAAAATATAAACAAAAA-CCTCCAAAATC
1 AAAAAACATAAACAAAAATCC-CCAAAATC
* * *
52431213 AAAAACCCTAAGCAAAAATCCCCAAAATC
1 AAAAAACATAAACAAAAATCCCCAAAATC
** * * * *
52431242 AAAACCCCTAACCCAAAATCCCCAAACTC
1 AAAAAACATAAACAAAAATCCCCAAAATC
52431271 AAAA
1 AAAA
52431275 TCCCTAAACA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 51 0.96
30 2 0.04
ACGTcount: A:0.57, C:0.31, G:0.01, T:0.11
Consensus pattern (29 bp):
AAAAAACATAAACAAAAATCCCCAAAATC
Found at i:52431264 original size:15 final size:15
Alignment explanation
Indices: 52431227--52431283 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
52431217 ACCCTAAGCA
*
52431227 AAAATCCCCAAAATC
1 AAAATCCCCAAACTC
* *
52431242 AAAA-CCCCTAACCC
1 AAAATCCCCAAACTC
52431256 AAAATCCCCAAACTC
1 AAAATCCCCAAACTC
*
52431271 AAAATCCCTAAAC
1 AAAATCCCCAAAC
52431284 ATAAACCGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 11 0.31
15 24 0.69
ACGTcount: A:0.49, C:0.39, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAATCCCCAAACTC
Found at i:52431279 original size:29 final size:29
Alignment explanation
Indices: 52431196--52431281 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
52431186 AAAATATAAA
* *
52431196 CAAAAACCTCCAAAATCAAAAACCCTAAGC
1 CAAAATCC-CCAAAATCAAAAACCCTAACC
* *
52431226 AAAAATCCCCAAAATCAAAACCCCTAACC
1 CAAAATCCCCAAAATCAAAAACCCTAACC
* *
52431255 CAAAATCCCCAAACTCAAAATCCCTAA
1 CAAAATCCCCAAAATCAAAAACCCTAA
52431282 ACATAAACCG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 43 0.88
30 6 0.12
ACGTcount: A:0.51, C:0.36, G:0.01, T:0.12
Consensus pattern (29 bp):
CAAAATCCCCAAAATCAAAAACCCTAACC
Found at i:52437359 original size:143 final size:143
Alignment explanation
Indices: 52437101--52437389 Score: 515
Period size: 143 Copynumber: 2.0 Consensus size: 143
52437091 ACTTGGAACT
* *
52437101 AAGGAAATGTGCAAGTGTACAAAATCGTATCAAGTAATAAAGTGACAACTAATGTCGAGCTATCG
1 AAGGAAATGTGCAAGTGTACAAAATCATACCAAGTAATAAAGTGACAACTAATGTCGAGCTATCG
* *
52437166 TATCCATAGGAACTGTGAAAGAGAATATTTATGAAATGCAAATTTAAACAATTTGGTGATGGAAA
66 TATCCATAGGAACTATGAAAGAGAATATTTATGAAATGCAAATTTAAACAATTTGGTGATGAAAA
52437231 ATATGTTGATTTG
131 ATATGTTGATTTG
* *
52437244 AAGGAAATGTGCAAGTGTACAAAATCATACCAAGTAATAAAGTGACAAGTAATGTCGAGTTATCG
1 AAGGAAATGTGCAAGTGTACAAAATCATACCAAGTAATAAAGTGACAACTAATGTCGAGCTATCG
*
52437309 TATCCATAGGTACTATGAAAGAGAATATTTATGAAATGCAAATTTAAACAATTTGGTGATGAAAA
66 TATCCATAGGAACTATGAAAGAGAATATTTATGAAATGCAAATTTAAACAATTTGGTGATGAAAA
52437374 ATATGTTGATTTG
131 ATATGTTGATTTG
52437387 AAG
1 AAG
52437390 TGGTGATATA
Statistics
Matches: 139, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
143 139 1.00
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (143 bp):
AAGGAAATGTGCAAGTGTACAAAATCATACCAAGTAATAAAGTGACAACTAATGTCGAGCTATCG
TATCCATAGGAACTATGAAAGAGAATATTTATGAAATGCAAATTTAAACAATTTGGTGATGAAAA
ATATGTTGATTTG
Found at i:52441751 original size:37 final size:37
Alignment explanation
Indices: 52441701--52441774 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
52441691 TAGACTCATG
52441701 AAGTCAAACATGTCCCAAAAGTGTAGCATAAAGCTAA
1 AAGTCAAACATGTCCCAAAAGTGTAGCATAAAGCTAA
52441738 AAGTCAAACATGTCCCAAAAGTGTAGCATAAAGCTAA
1 AAGTCAAACATGTCCCAAAAGTGTAGCATAAAGCTAA
52441775 CACTCTCCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.19
Consensus pattern (37 bp):
AAGTCAAACATGTCCCAAAAGTGTAGCATAAAGCTAA
Found at i:52442105 original size:82 final size:82
Alignment explanation
Indices: 52441968--52442126 Score: 318
Period size: 82 Copynumber: 1.9 Consensus size: 82
52441958 ATCAAACACT
52441968 TAACACTTACTGATTATCCGTACACTATCTCATGTTAGCATCTTTTGAAAAACACTACCACTATC
1 TAACACTTACTGATTATCCGTACACTATCTCATGTTAGCATCTTTTGAAAAACACTACCACTATC
52442033 ATATAACATATAACATA
66 ATATAACATATAACATA
52442050 TAACACTTACTGATTATCCGTACACTATCTCATGTTAGCATCTTTTGAAAAACACTACCACTATC
1 TAACACTTACTGATTATCCGTACACTATCTCATGTTAGCATCTTTTGAAAAACACTACCACTATC
52442115 ATATAACATATA
66 ATATAACATATA
52442127 TTTCATGTAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.33
Consensus pattern (82 bp):
TAACACTTACTGATTATCCGTACACTATCTCATGTTAGCATCTTTTGAAAAACACTACCACTATC
ATATAACATATAACATA
Found at i:52453560 original size:20 final size:20
Alignment explanation
Indices: 52453525--52453612 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
52453515 TTTTGAAACA
52453525 ATTTTAAAATCAAGTTAAAATG
1 ATTTT-AAA-CAAGTTAAAATG
*
52453547 ATTTTAACCAAGTTAAAATG
1 ATTTTAAACAAGTTAAAATG
*
52453567 ATTTTAAACAAGTCAAAATTG
1 ATTTTAAACAAGTTAAAA-TG
* * *
52453588 -TTTCAATCAAGTTAAAATC
1 ATTTTAAACAAGTTAAAATG
52453607 ATTTTA
1 ATTTTA
52453613 GCACATCAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.02
20 46 0.82
21 4 0.07
22 5 0.09
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (20 bp):
ATTTTAAACAAGTTAAAATG
Found at i:52453579 original size:40 final size:41
Alignment explanation
Indices: 52453525--52453612 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 41
52453515 TTTTGAAACA
* * *
52453525 ATTTTAAAATCAAGTTAAAA-TGATTTTAACCAAGTTAAAATG
1 ATTTT-AAATCAAGTCAAAATTG-TTTCAACCAAGTTAAAATC
*
52453567 ATTTTAAA-CAAGTCAAAATTGTTTCAATCAAGTTAAAATC
1 ATTTTAAATCAAGTCAAAATTGTTTCAACCAAGTTAAAATC
52453607 ATTTTA
1 ATTTTA
52453613 GCACATCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 31 0.76
41 5 0.12
42 5 0.12
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (41 bp):
ATTTTAAATCAAGTCAAAATTGTTTCAACCAAGTTAAAATC
Found at i:52453599 original size:60 final size:60
Alignment explanation
Indices: 52453532--52453649 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
52453522 ACAATTTTAA
* * *
52453532 AATCAAGTTAAAATGATTTTAACCA-AGTTAAAATGATTTT-AAACAAGTCAAAATTGTTTC
1 AATCAAGTTAAAATCATTTT-ACCACA-TCAAAATCATTTTCAAACAAGTCAAAATTGTTTC
* *
52453592 AATCAAGTTAAAATCATTTTAGCACATCAAAATCATTTTCAAACAAGTCAGAATTGTT
1 AATCAAGTTAAAATCATTTTACCACATCAAAATCATTTTCAAACAAGTCAAAATTGTT
52453650 CCATGCTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 14 0.27
60 37 0.73
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (60 bp):
AATCAAGTTAAAATCATTTTACCACATCAAAATCATTTTCAAACAAGTCAAAATTGTTTC
Found at i:52454028 original size:42 final size:42
Alignment explanation
Indices: 52453969--52454053 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
52453959 TTGGGAATCA
52453969 ATTAGAGGGTATAAATACCATCTTCCAAAGACCTACAACAAT
1 ATTAGAGGGTATAAATACCATCTTCCAAAGACCTACAACAAT
*
52454011 ATTAGGGGGTATAAATACCATCTTCCAAAGACCTACAACAAT
1 ATTAGAGGGTATAAATACCATCTTCCAAAGACCTACAACAAT
52454053 A
1 A
52454054 AGAAAGCACT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (42 bp):
ATTAGAGGGTATAAATACCATCTTCCAAAGACCTACAACAAT
Found at i:52460991 original size:6 final size:6
Alignment explanation
Indices: 52460980--52461009 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
52460970 TGGAAGACCA
52460980 TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT
1 TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT
52461010 GTAGATGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
TCTGAT
Found at i:52466079 original size:21 final size:22
Alignment explanation
Indices: 52466036--52466079 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
52466026 TTATTTGATT
* *
52466036 TTAAAAATACAAGAGTTATTAA
1 TTAAAAATACAAAAGTTAATAA
*
52466058 TTAAAAATA-AAAATTTAATAA
1 TTAAAAATACAAAAGTTAATAA
52466079 T
1 T
52466080 ATGTTTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (22 bp):
TTAAAAATACAAAAGTTAATAA
Found at i:52466101 original size:12 final size:12
Alignment explanation
Indices: 52466086--52466110 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52466076 TAATATGTTT
52466086 ATTAATTAAAAA
1 ATTAATTAAAAA
52466098 ATTAATTAAAAA
1 ATTAATTAAAAA
52466110 A
1 A
52466111 AATTTGAAAC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAATTAAAAA
Found at i:52466249 original size:3 final size:3
Alignment explanation
Indices: 52466241--52466269 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
52466231 ATATTAATTA
52466241 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
52466270 AACTTGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52466724 original size:18 final size:19
Alignment explanation
Indices: 52466701--52466736 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52466691 TAAAAGATTA
*
52466701 TTTATATA-ATTTTTAGAG
1 TTTATATATATATTTAGAG
52466719 TTTATATATATATTTAGA
1 TTTATATATATATTTAGA
52466737 TTATTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (19 bp):
TTTATATATATATTTAGAG
Found at i:52470482 original size:18 final size:18
Alignment explanation
Indices: 52470459--52470497 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
52470449 TGGATGAACA
*
52470459 TCTAATTCTGATTCTGAT
1 TCTAATGCTGATTCTGAT
*
52470477 TCTAATGCTGATTCTGGT
1 TCTAATGCTGATTCTGAT
52470495 TCT
1 TCT
52470498 GATGTAGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (18 bp):
TCTAATGCTGATTCTGAT
Found at i:52472712 original size:29 final size:29
Alignment explanation
Indices: 52472679--52472736 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
52472669 TCAATTTATT
*
52472679 TTTGTTAATTTAGTAATCCAAAATAGAAA
1 TTTGTTAATTTAATAATCCAAAATAGAAA
52472708 TTTGTTAATTTAATAATCCAAAATAGAAA
1 TTTGTTAATTTAATAATCCAAAATAGAAA
52472737 CTGATCAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.38
Consensus pattern (29 bp):
TTTGTTAATTTAATAATCCAAAATAGAAA
Found at i:52473364 original size:16 final size:15
Alignment explanation
Indices: 52473322--52473365 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
52473312 AAAAATTATA
52473322 TAAAAATAATTTTTT
1 TAAAAATAATTTTTT
*
52473337 TAAATCATAATTATTTT
1 TAAA-AATAATT-TTTT
*
52473354 TAAAAAAAATTT
1 TAAAAATAATTT
52473366 ACGTTAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAAATAATTTTTT
Found at i:52476798 original size:24 final size:24
Alignment explanation
Indices: 52476771--52476834 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 24
52476761 AATAAAACTT
52476771 ATTAAAAATAT-AAGAA-ATATATAA
1 ATTAAAAAT-TCAA-AATATATATAA
52476795 ATTATAAAACTTCAAAATATATATAA
1 ATTA-AAAA-TTCAAAATATATATAA
* *
52476821 ATTGAAAATGCAAA
1 ATTAAAAATTCAAA
52476835 TAAAAAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
24 9 0.26
25 11 0.32
26 14 0.41
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (24 bp):
ATTAAAAATTCAAAATATATATAA
Found at i:52477979 original size:25 final size:25
Alignment explanation
Indices: 52477950--52478000 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
52477940 GTCAACAAGA
52477950 GAGTTTAGTTCCACTAGAACTACTT
1 GAGTTTAGTTCCACTAGAACTACTT
52477975 GAGTTTAGTTCCACTAGAACTACTT
1 GAGTTTAGTTCCACTAGAACTACTT
52478000 G
1 G
52478001 TTTAGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (25 bp):
GAGTTTAGTTCCACTAGAACTACTT
Found at i:52480231 original size:19 final size:19
Alignment explanation
Indices: 52480203--52480256 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
52480193 AAAATTCAAT
52480203 AAAATATAAAAATTATTTTA
1 AAAAT-TAAAAATTATTTTA
*
52480223 AAAATT-AAAATTAATTTA
1 AAAATTAAAAATTATTTTA
*
52480241 AAAAGTATAAAATTAT
1 AAAATTA-AAAATTAT
52480257 AAAAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 16 0.55
19 1 0.03
20 12 0.41
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATTAAAAATTATTTTA
Found at i:52480232 original size:18 final size:20
Alignment explanation
Indices: 52480211--52480256 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 20
52480201 ATAAAATATA
52480211 AAAATTATTTTAAAAA-T-T
1 AAAATTATTTTAAAAAGTAT
*
52480229 AAAATTAATTTAAAAAGTAT
1 AAAATTATTTTAAAAAGTAT
52480249 AAAATTAT
1 AAAATTAT
52480257 AAAAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.62
19 1 0.04
20 8 0.33
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAATTATTTTAAAAAGTAT
Found at i:52482175 original size:91 final size:91
Alignment explanation
Indices: 52481996--52482187 Score: 273
Period size: 91 Copynumber: 2.1 Consensus size: 91
52481986 GGCAATTTAT
*
52481996 CTACAAACACTGGTGGTTTATCCACAAACATACTGCCAACTTTTATTTGCAAACTCATTATGCAT
1 CTACAAACACTAGTGGTTTATCCACAAACATACTGCCAACTTTTATTTGCAAACTCATTATGCAT
*
52482061 TCACAACCTACTGGTAGCATATTAAC
66 TCACAACCTACTAGTAGCATATTAAC
* * * * * *
52482087 CTTCAAACACTAGTGGTTTATCCAC-AACTTTTACTGGCAACTTTTATTTGCAAACTCGTTGTGT
1 CTACAAACACTAGTGGTTTATCCACAAAC--ATACTGCCAACTTTTATTTGCAAACTCATTATGC
52482151 ATTCACAACC-ACTAGTAGCATATTAAC
64 ATTCACAACCTACTAGTAGCATATTAAC
52482178 CTAC-AACACT
1 CTACAAACACT
52482188 TGTAATTCAT
Statistics
Matches: 90, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
90 9 0.10
91 42 0.47
92 39 0.43
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (91 bp):
CTACAAACACTAGTGGTTTATCCACAAACATACTGCCAACTTTTATTTGCAAACTCATTATGCAT
TCACAACCTACTAGTAGCATATTAAC
Found at i:52482892 original size:50 final size:50
Alignment explanation
Indices: 52482817--52483001 Score: 235
Period size: 50 Copynumber: 3.7 Consensus size: 50
52482807 TTTTTTGTAC
* * * * ** *
52482817 TGCCAATGCCATATCCCAGATATGGTTTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * ** *
52482867 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
52482917 TGCCAACGCCATGTCCCAGACATGGTCTTACATTGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
52482967 TGCCAACGCCATGTCCCAGACATGGTCTTATATGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGG
52483002 AAATCACATA
Statistics
Matches: 115, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 115 1.00
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:52482948 original size:100 final size:100
Alignment explanation
Indices: 52482817--52482996 Score: 261
Period size: 100 Copynumber: 1.8 Consensus size: 100
52482807 TTTTTTGTAC
* * * ** * *
52482817 TGCCAATGCCATATCCCAGATATGGTTTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTC
*
52482882 CTAGACATGGTCTTACGGGGGACCTCTCATCTTGG
66 CCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
* * *
52482917 TGCCAACGCCATGTCCCAGACATGGTCTTACATTGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTC
52482982 CCAGACATGGTCTTA
66 CCAGACATGGTCTTA
52482997 TATGGAAATC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 69 1.00
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (100 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTC
CCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
Found at i:52486634 original size:229 final size:228
Alignment explanation
Indices: 52486213--52486666 Score: 517
Period size: 229 Copynumber: 2.0 Consensus size: 228
52486203 GACATCTTTT
* *
52486213 TCTGAAACAATAGTCCACCATTTCTTTCAAAAAGTTTTTGTTTAAGTTTTATGTACTTTCTTTTC
1 TCTGAAACAATAATCCACCATTTCTTTCAAAAAGTTTTTGTTTAAGTTTAATGTACTTTC--TTC
*
52486278 TGCAGTATCTTACAAAACCACCAAACCCCAGCAATTAGAAACAAGAGCCCTATACTTAAACCTGC
64 TGCAGTATCTTACAAAACCACCAAACCCCAGCAATTAGAAACAAGAGCCCTAAACTTAAACCTGC
** * * *
52486343 ATGAGATCAAAATAAATATGTCGATACCACTTATTTGATTAACTCCTAACATAGTCAATGTTACC
129 ATGAGATCAAAATAAATATGT--AT--CACTTAAATCATCAACTCCTAAAATAGTCAATGTTACC
* *
52486408 ATTTATGCTACCG-TTTG-AATAAAATTTAGATGGCCATA
190 ATTTAAGCTA-CGATTTGAAATAAAAATTAGATGGCCATA
* * * *
52486446 TCTGAACCAATAATCCACCATTTCTTTCGAAGAGTTTTTGTTTGAGTTTAATGTAC-TTC-TCTG
1 TCTGAAACAATAATCCACCATTTCTTTCAAAAAGTTTTTGTTTAAGTTTAATGTACTTTCTTCTG
* * * * * *
52486509 CAGTATTTTATAAAGCCACCATACCCC-GACAATTAGAAATAAGATCCCTAAACTTAACCCAACA
66 CAGTATCTTACAAAACCACCAAACCCCAG-CAATTAGAAACAAGAGCCCTAAACTT-A---AAC-
* * * *
52486573 TCTGCATGAGATCCAAATAAATATGT-T-ACTTAAATCATCAGCTCCTAAAATCGTTAATGTTAC
125 -CTGCATGAGATCAAAATAAATATGTATCACTTAAATCATCAACTCCTAAAATAGTCAATGTTAC
52486636 CATTTAAGCTACGATTTGAAATAAAAATTAG
189 CATTTAAGCTACGATTTGAAATAAAAATTAG
52486667 TTGGACATGT
Statistics
Matches: 188, Mismatches: 24, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
228 3 0.02
229 92 0.49
230 12 0.06
232 4 0.02
233 53 0.28
235 24 0.13
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.33
Consensus pattern (228 bp):
TCTGAAACAATAATCCACCATTTCTTTCAAAAAGTTTTTGTTTAAGTTTAATGTACTTTCTTCTG
CAGTATCTTACAAAACCACCAAACCCCAGCAATTAGAAACAAGAGCCCTAAACTTAAACCTGCAT
GAGATCAAAATAAATATGTATCACTTAAATCATCAACTCCTAAAATAGTCAATGTTACCATTTAA
GCTACGATTTGAAATAAAAATTAGATGGCCATA
Found at i:52490499 original size:42 final size:42
Alignment explanation
Indices: 52490257--52490496 Score: 383
Period size: 42 Copynumber: 5.7 Consensus size: 42
52490247 GGCGGCGCTT
*
52490257 CGCCTCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAA
1 CGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAA
*
52490299 GGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAA
1 CGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAA
52490341 CGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAA
1 CGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAA
52490383 CGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAA
1 CGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAA
** *
52490425 CGCAGCTAAAGACCATGTTCTTTAGCGGCGTTTAGAAAAAAAA
1 CGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAG-AAAAAAA
* * * *
52490468 CGCCGC-AAATATCATGTTTTTTAGCGGCG
1 CGCCTCTAAAGACCATGTTCTTTAGCGGCG
52490497 TTTTTGTTTG
Statistics
Matches: 187, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
42 175 0.94
43 12 0.06
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (42 bp):
CGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAA
Found at i:52490847 original size:21 final size:21
Alignment explanation
Indices: 52490798--52490847 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
52490788 TTTTGGACTG
*
52490798 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
52490819 TTCCGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
52490840 CTCTGCTT
1 CTCTGCTT
52490848 TAAGTTGTAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.46, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:52494641 original size:9 final size:9
Alignment explanation
Indices: 52494623--52494856 Score: 213
Period size: 9 Copynumber: 25.8 Consensus size: 9
52494613 TGATATATTT
52494623 TTATGTAAG
1 TTATGTAAG
*
52494632 TTATGCAAG
1 TTATGTAAG
52494641 TTTATGTAAG
1 -TTATGTAAG
52494651 TTATGTAAG
1 TTATGTAAG
*
52494660 TTACT-TAAT
1 TTA-TGTAAG
52494669 TTATGTAAG
1 TTATGTAAG
*
52494678 TTATGGAAG
1 TTATGTAAG
* *
52494687 TTATTTAAT
1 TTATGTAAG
*
52494696 TTATGTAGG
1 TTATGTAAG
52494705 TTATGTAAG
1 TTATGTAAG
* *
52494714 TTATTTAAT
1 TTATGTAAG
*
52494723 TTATGCAAG
1 TTATGTAAG
*
52494732 TTTATGTATG
1 -TTATGTAAG
*
52494742 TTATGTAGG
1 TTATGTAAG
*
52494751 TTACT-TAAT
1 TTA-TGTAAG
52494760 TTATGTAAG
1 TTATGTAAG
52494769 TTATGTAAG
1 TTATGTAAG
* *
52494778 TTATTTAAT
1 TTATGTAAG
*
52494787 TTATGTAGG
1 TTATGTAAG
52494796 TTATGTAAG
1 TTATGTAAG
*
52494805 TTATGTAAC
1 TTATGTAAG
* *
52494814 TTATTTAAT
1 TTATGTAAG
52494823 TTAT-TCAAG
1 TTATGT-AAG
52494832 TTATGTAAG
1 TTATGTAAG
* * *
52494841 TAATTTAAT
1 TTATGTAAG
52494850 TTATGTA
1 TTATGTA
52494857 TAAGCTTGTA
Statistics
Matches: 179, Mismatches: 38, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
8 3 0.02
9 158 0.88
10 18 0.10
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:52497634 original size:43 final size:42
Alignment explanation
Indices: 52497575--52497659 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
52497565 TAATTAATCG
* * *
52497575 TAAATCCTAAACCCCAA-ACTATATAACCTTTAACCTTAAACCC
1 TAAATCCTAAACCCCAACAC-ATA-AAACTTAAACCCTAAACCC
52497618 TAAATCCT-AACACCCAACACATAAAACTTAAACCCTAAACCC
1 TAAATCCTAAAC-CCCAACACATAAAACTTAAACCCTAAACCC
52497660 GTCAATTAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 19 0.51
43 16 0.43
44 2 0.05
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (42 bp):
TAAATCCTAAACCCCAACACATAAAACTTAAACCCTAAACCC
Found at i:52497747 original size:25 final size:26
Alignment explanation
Indices: 52497716--52497767 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
52497706 TATCGTAAAC
* * *
52497716 ATTAACCGTAGATCTTAAACCC-TAA
1 ATTAACCATAAATATTAAACCCGTAA
52497741 ATTAACCATAAATATTAAACCCGTAA
1 ATTAACCATAAATATTAAACCCGTAA
52497767 A
1 A
52497768 CCACAAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.27
Consensus pattern (26 bp):
ATTAACCATAAATATTAAACCCGTAA
Found at i:52498629 original size:113 final size:114
Alignment explanation
Indices: 52498512--52498739 Score: 377
Period size: 113 Copynumber: 2.0 Consensus size: 114
52498502 TTTTCCCTAG
*** *
52498512 CGCCGCTAATAATGTGCTTCAGCGGCGATTTTATAGAAACGCCACCAATTCTACTATACCTCAAT
1 CGCCGCTAATAATCCACTTCAGCGGCGATTTTACAGAAACGCCACCAATTCTACTATACCTCAAT
*
52498577 CTTGTACGCTGCGTTTTGTTTAACA-TTTTTGCGGCGCTTACAAACAAA
66 CCTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCGCTTACAAACAAA
* *
52498625 CGCCGCTAATGATCCACTTCAGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAAT
1 CGCCGCTAATAATCCACTTCAGCGGCGATTTTACAGAAACGCCACCAATTCTACTATACCTCAAT
*
52498690 CCTGTATGCTGCGTTTTGTTTAACATTTTTTGCGGCGCTTACAAACAAA
66 CCTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCGCTTACAAACAAA
52498739 C
1 C
52498740 NNNNNNNNNN
Statistics
Matches: 106, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
113 82 0.77
114 24 0.23
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (114 bp):
CGCCGCTAATAATCCACTTCAGCGGCGATTTTACAGAAACGCCACCAATTCTACTATACCTCAAT
CCTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCGCTTACAAACAAA
Found at i:52499040 original size:114 final size:114
Alignment explanation
Indices: 52498840--52499130 Score: 521
Period size: 114 Copynumber: 2.6 Consensus size: 114
52498830 NNNNNNNNNN
*
52498840 CCTCAAACTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAA
1 CCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAA
*
52498905 TGATACACTTCAGTAGCGTTTTTACAGAAACGCCACCAATTCTACTATA
66 TGATACACTTCAGCAGCGTTTTTACAGAAACGCCACCAATTCTACTATA
52498954 CCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAA
1 CCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAA
* *
52499019 TGATCCACTTCAGCGGCGTTTTTACAGAAACGCCACCAATTCTACTATA
66 TGATACACTTCAGCAGCGTTTTTACAGAAACGCCACCAATTCTACTATA
* *
52499068 CCTCAATCTTGTACGCTGTGTTTTGTTTAACA-TTGTTGCGGCGCTTACAAACAAACGCCGCTA
1 CCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTA
52499131 CTGCTATATT
Statistics
Matches: 171, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
113 30 0.18
114 141 0.82
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (114 bp):
CCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAA
TGATACACTTCAGCAGCGTTTTTACAGAAACGCCACCAATTCTACTATA
Found at i:52500004 original size:23 final size:23
Alignment explanation
Indices: 52499961--52500004 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
52499951 TTTATAGAAT
*
52499961 TAAAATTAAATTGATATAATTTA
1 TAAAATTAAATTGATAAAATTTA
*
52499984 TAAATATTAAA-TGTTAAAATT
1 TAAA-ATTAAATTGATAAAATT
52500005 ACTATTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
TAAAATTAAATTGATAAAATTTA
Found at i:52504057 original size:19 final size:19
Alignment explanation
Indices: 52504033--52504069 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52504023 TAAATTTGCT
*
52504033 ATTATTATCATTATTATTA
1 ATTATTATCATTACTATTA
*
52504052 ATTATTATTATTACTATT
1 ATTATTATCATTACTATT
52504070 TACTCATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTATTATCATTACTATTA
Found at i:52504176 original size:37 final size:37
Alignment explanation
Indices: 52504122--52504192 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
52504112 ATATATATAC
*
52504122 ATACTTATATATATTTTT-TATATTTTATAATTTTTAT
1 ATACATATATATATTTTTATAT-TTTTATAATTTTTAT
*
52504159 ATACATATATATCTTTTTATATTTTTATAATTTT
1 ATACATATATATATTTTTATATTTTTATAATTTT
52504193 ATTCATTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.63
Consensus pattern (37 bp):
ATACATATATATATTTTTATATTTTTATAATTTTTAT
Found at i:52507486 original size:15 final size:15
Alignment explanation
Indices: 52507474--52507505 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
52507464 AAATAAAAAG
*
52507474 AAAAATAAAAAAATA
1 AAAAACAAAAAAATA
52507489 AAAAACAAAAAAATA
1 AAAAACAAAAAAATA
52507504 AA
1 AA
52507506 CTCTACCGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAAACAAAAAAATA
Found at i:52508999 original size:45 final size:45
Alignment explanation
Indices: 52508890--52509148 Score: 263
Period size: 45 Copynumber: 5.8 Consensus size: 45
52508880 CTAAATATAA
* * * * * * * *
52508890 CAGATCTTGCCTTCTTATACTGATAGCGCAGAAGATCGAAGACAT
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGATTGAAGATAG
* *
52508935 CA-ACCTTGCCTTCTTGTACTGACAGCGGAGCAGATTGAAGATAG
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGATTGAAGATAG
* * * * *
52508979 CAGATCTTACCTTCCTGTACTGACAGCGAAGAAGATCGAAGA-CG
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGATTGAAGATAG
* * *
52509023 CCAG-TCTTGCCTTCCTGTACTGACAGTGGAGTAGACTGAAGATAG
1 -CAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGATTGAAGATAG
* * *
52509068 CAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGAAAA
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGATTGAAGATAG
* * * *
52509113 CAGATCTCGCCTTCCCGTACTGACAGTGAAGCAGAT
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGAT
52509149 CAAAAGCACC
Statistics
Matches: 179, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
44 72 0.40
45 107 0.60
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (45 bp):
CAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGATTGAAGATAG
Found at i:52509109 original size:89 final size:89
Alignment explanation
Indices: 52508872--52509140 Score: 315
Period size: 89 Copynumber: 3.0 Consensus size: 89
52508862 AAATTGCAGC
* * * * * * * *
52508872 GGAGTAGACTAAATATAACAGATCTTGCCTTCTTATACTGATAGCGCAGAAGATCGAAGACATCA
1 GGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGAAGATCGAAGACAACA
** * *
52508937 ACCTTGCCTTCTTGTACTGACAGC
66 GTCTTGCCTTCCTGTACTGACAGT
* * * **
52508961 GGAGCAGATTGAAGATAGCAGATCTTACCTTCCTGTACTGACAGCGAAGAAGATCGAAGACGCCA
1 GGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGAAGATCGAAGACAACA
52509026 GTCTTGCCTTCCTGTACTGACAGT
66 GTCTTGCCTTCCTGTACTGACAGT
* * *
52509050 GGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGA-CTGAAGAAAAC
1 GGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGAAGATC-GAAGACAAC
* *
52509114 AGATCTCGCCTTCCCGTACTGACAGT
65 AG-TCTTGCCTTCCTGTACTGACAGT
52509140 G
1 G
52509141 AAGCAGATCA
Statistics
Matches: 152, Mismatches: 26, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
88 1 0.01
89 129 0.85
90 22 0.14
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (89 bp):
GGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGAAGATCGAAGACAACA
GTCTTGCCTTCCTGTACTGACAGT
Found at i:52509297 original size:131 final size:131
Alignment explanation
Indices: 52509155--52509983 Score: 1255
Period size: 131 Copynumber: 6.3 Consensus size: 131
52509145 AGATCAAAAG
* * * *
52509155 CACCAGTCCTATCTCCTTGAGCAGTAGTCGAGTAGGTTAAAGATTGTAGATCTTATCTCCCTAAG
1 CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
* *
52509220 CAGTAGTGGAGCAGATTGAAGACGGCAAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAG
52509285 C
131 C
* * * *
52509286 CACCAGTCCTATTTCCCTGAGTAGTAGTAGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
1 CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
** * *
52509351 CAGTAGTGGAGCAGATCGAAGACGATGAATCTTATCTTCCCGAGATAGTAAGAAGTAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAG
52509416 C
131 C
* * * * * *
52509417 CACCAGTCCTATCTCTCTAAACAACAATGGAGTAGGTTGAAGATTGTAAATCTTATCTCCCTAAG
1 CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
* *** * *
52509482 CAGTAGTGGAGCATATCGAAGATAACAAACCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAG
52509547 C
131 C
* *
52509548 CACCAGTCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCTTAAG
1 CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
* * * *
52509613 TAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTCCCG-GAATAGTAGGAAGTAGATTTAA
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAG-ATAGTAGGAAGCAGATTTAA
52509677 GC
130 GC
52509679 CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
1 CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
* * *
52509744 CAGTAGTGGAGCAGATCGAAGACGGCGAATATTATCTTCTCAAGATAGTAGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAG
52509809 C
131 C
* * *
52509810 CACCACTCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAAATCTTATCTCCCTAAG
1 CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
*
52509875 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCTGAGATAGTAGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAG
52509940 C
131 C
* * * *
52509941 CACCAATCCTATCTCCCTGAGCAGTAGTGGAGCAGATTGAAGA
1 CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGA
52509984 CAGGCTACAA
Statistics
Matches: 628, Mismatches: 68, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
130 1 0.00
131 626 1.00
132 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (131 bp):
CACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAG
CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAG
C
Found at i:52510067 original size:44 final size:44
Alignment explanation
Indices: 52510019--52510163 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 44
52510009 AATTATAGAG
* * * *
52510019 GAGCAGATTAAAACCACAAACCTTATCTCTCTGAAGTTGTAGTA
1 GAGCAGATTAAAACAACAAACCTTATCCCCCTGAAGTTGCAGTA
* * * *
52510063 GAGCAGGTTGAAATAACAAACCTTATCCCCCTGAAGTTGCAGTG
1 GAGCAGATTAAAACAACAAACCTTATCCCCCTGAAGTTGCAGTA
* * * * * * * *
52510107 GAGCAGACTGAAGCTACTAATCC-TATCTCCCTGAAGTTACAGTG
1 GAGCAGATTAAAACAAC-AAACCTTATCCCCCTGAAGTTGCAGTA
*
52510151 GAGCGGATTAAAA
1 GAGCAGATTAAAA
52510164 ACGATGAATC
Statistics
Matches: 80, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
44 76 0.95
45 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (44 bp):
GAGCAGATTAAAACAACAAACCTTATCCCCCTGAAGTTGCAGTA
Found at i:52512025 original size:45 final size:43
Alignment explanation
Indices: 52511982--52512065 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
52511972 TTCAAATTTC
*
52511982 TTTATATATATACATA-CTTATATATTTTTTATATTTTATAATT
1 TTTATATAAATACATATCTT-TATATTTTTTATATTTTATAATT
* *
52512025 TTTATATAAATATATATCTTTTTATCTTTTTATAATTTTAT
1 TTTATATAAATACATATCTTTATAT-TTTTTAT-ATTTTAT
52512066 TCATTTTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
43 18 0.51
44 10 0.29
45 7 0.20
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (43 bp):
TTTATATAAATACATATCTTTATATTTTTTATATTTTATAATT
Found at i:52519022 original size:20 final size:22
Alignment explanation
Indices: 52518994--52519037 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
52518984 AGCATCATGT
*
52518994 ATAACCAAA-CTCAT-ATATAA
1 ATAAACAAATCTCATAATATAA
*
52519014 ATAAACAAATCTTATAATATAA
1 ATAAACAAATCTCATAATATAA
52519036 AT
1 AT
52519038 CAAAGTAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 4 0.20
22 8 0.40
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAACAAATCTCATAATATAA
Found at i:52526839 original size:24 final size:24
Alignment explanation
Indices: 52526783--52526828 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
52526773 AAGCCTAATT
*
52526783 CTAATTAATGTAAAATATATTATG
1 CTAATAAATGTAAAATATATTATG
*
52526807 CTAATAAATGTTAAATATATTA
1 CTAATAAATGTAAAATATATTA
52526829 GACTACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (24 bp):
CTAATAAATGTAAAATATATTATG
Found at i:52528859 original size:24 final size:24
Alignment explanation
Indices: 52528803--52528848 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
52528793 AAGCCTAATT
*
52528803 CTAATTAATGTAAAATATATTATG
1 CTAATAAATGTAAAATATATTATG
*
52528827 CTAATAAATGTTAAATATATTA
1 CTAATAAATGTAAAATATATTA
52528849 GACTACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (24 bp):
CTAATAAATGTAAAATATATTATG
Found at i:52529078 original size:24 final size:24
Alignment explanation
Indices: 52529051--52529097 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
52529041 ATAATAAATA
*
52529051 TTTTACATATTTTTAAAAAGTTTG
1 TTTTAAATATTTTTAAAAAGTTTG
52529075 TTTTAAATATTTTTAAAAAGTTT
1 TTTTAAATATTTTTAAAAAGTTT
52529098 ATTTATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (24 bp):
TTTTAAATATTTTTAAAAAGTTTG
Found at i:52530973 original size:16 final size:16
Alignment explanation
Indices: 52530938--52530976 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
52530928 AATTATGGAA
*
52530938 ATATATAAAAACATGT
1 ATATATAAAAACATGC
**
52530954 ATATATAAAAGTATGC
1 ATATATAAAAACATGC
52530970 ATATATA
1 ATATATA
52530977 TGTACACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (16 bp):
ATATATAAAAACATGC
Found at i:52530974 original size:18 final size:17
Alignment explanation
Indices: 52530918--52530977 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 17
52530908 ATATATGTGT
* *
52530918 ATATACATAAAATTATGG
1 ATATATATAAAAATAT-G
* *
52530936 AAATATATAAAAACATG
1 ATATATATAAAAATATG
*
52530953 -TATATATAAAAGTATG
1 ATATATATAAAAATATG
52530969 CATATATAT
1 -ATATATAT
52530978 GTACACTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
16 13 0.39
17 1 0.03
18 19 0.58
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.33
Consensus pattern (17 bp):
ATATATATAAAAATATG
Found at i:52531258 original size:10 final size:10
Alignment explanation
Indices: 52531233--52531276 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
52531223 AAAATAGTAG
*
52531233 TAAAAAAATC
1 TAAAAAAATA
52531243 TCAAAAAAATA
1 T-AAAAAAATA
52531254 TAAAAAAATA
1 TAAAAAAATA
*
52531264 -CAAAAAATA
1 TAAAAAAATA
52531273 TAAA
1 TAAA
52531277 TTACATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 8 0.28
10 12 0.41
11 9 0.31
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:52531341 original size:30 final size:29
Alignment explanation
Indices: 52531307--52531372 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
52531297 TTTTTAAAAT
*
52531307 TTACATTTTGACCCCAAA-ATTTTCTTTAAA
1 TTACATTTTGACCCCAAATA-TTTC-GTAAA
* *
52531337 TTACATATTGACCCCTAATATTTCGTAAA
1 TTACATTTTGACCCCAAATATTTCGTAAA
52531366 TTACATT
1 TTACATT
52531373 CGGGCCCCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 10 0.32
30 20 0.65
31 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (29 bp):
TTACATTTTGACCCCAAATATTTCGTAAA
Found at i:52531705 original size:21 final size:21
Alignment explanation
Indices: 52531656--52531696 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
52531646 CGGCAACCAA
*
52531656 AGAAACAA-AAAAAATAGCAG
1 AGAAAAAAGAAAAAATAGCAG
52531676 AGAAAAAAGAAAAAATAGCAG
1 AGAAAAAAGAAAAAATAGCAG
52531697 CAAGCAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.71, C:0.07, G:0.17, T:0.05
Consensus pattern (21 bp):
AGAAAAAAGAAAAAATAGCAG
Found at i:52531998 original size:15 final size:16
Alignment explanation
Indices: 52531975--52532004 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52531965 AAGAGAAGAA
52531975 GAAGAAAGAAAGGAGG
1 GAAGAAAGAAAGGAGG
52531991 GAAG-AAGAAAGGAG
1 GAAGAAAGAAAGGAG
52532005 AGAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (16 bp):
GAAGAAAGAAAGGAGG
Found at i:52532058 original size:22 final size:21
Alignment explanation
Indices: 52532005--52532064 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
52531995 AAGAAAGGAG
52532005 AGAAAA-AAAATAGAAAAAGAA
1 AGAAAACAAAATA-AAAAAGAA
*
52532026 AGAAAATAAAATAAAATAA-AA
1 AGAAAACAAAATAAAA-AAGAA
52532047 AGATAAACAAAA-AAAAAA
1 AGA-AAACAAAATAAAAAA
52532065 TCAGTCGGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 2 0.06
21 18 0.51
22 15 0.43
ACGTcount: A:0.82, C:0.02, G:0.08, T:0.08
Consensus pattern (21 bp):
AGAAAACAAAATAAAAAAGAA
Found at i:52532058 original size:27 final size:26
Alignment explanation
Indices: 52532007--52532064 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
52531997 GAAAGGAGAG
*
52532007 AAAAAAAATAGAAAAAGAAAGAAAATA
1 AAAAAAAATAGAAAAAGAAACAAAA-A
* *
52532034 AAATAAAATA-AAAAGATAAACAAAAA
1 AAAAAAAATAGAAAA-AGAAACAAAAA
52532060 AAAAA
1 AAAAA
52532065 TCAGTCGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.83, C:0.02, G:0.07, T:0.09
Consensus pattern (26 bp):
AAAAAAAATAGAAAAAGAAACAAAAA
Found at i:52532216 original size:17 final size:18
Alignment explanation
Indices: 52532183--52532218 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
52532173 AGCCCAAGAG
52532183 AAAAAAAACAAGCAGCAAA
1 AAAAAAAACAA-CAGCAAA
52532202 AAAAAAAACAA-AGCAAA
1 AAAAAAAACAACAGCAAA
52532219 GCAGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.78, C:0.14, G:0.08, T:0.00
Consensus pattern (18 bp):
AAAAAAAACAACAGCAAA
Found at i:52532687 original size:20 final size:20
Alignment explanation
Indices: 52532662--52532699 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52532652 AAAAATATTC
52532662 AAAAATCCTCGTATTTTAAT
1 AAAAATCCTCGTATTTTAAT
* *
52532682 AAAAATTCTCGTGTTTTA
1 AAAAATCCTCGTATTTTA
52532700 GGATCCCGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAAATCCTCGTATTTTAAT
Found at i:52532843 original size:17 final size:17
Alignment explanation
Indices: 52532816--52532861 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
52532806 AAAAAAATCG
52532816 TGTTTCAAAAATTT-TCA
1 TGTTTC-AAAATTTCTCA
*
52532833 TGTCTTCAAAATTTCTCG
1 TGT-TTCAAAATTTCTCA
52532851 TGTTTCAAAAT
1 TGTTTCAAAAT
52532862 AATAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (17 bp):
TGTTTCAAAATTTCTCA
Found at i:52532974 original size:18 final size:18
Alignment explanation
Indices: 52532951--52532985 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52532941 TTTTTCAAAA
*
52532951 AAAAAATTCTCGTGTTTC
1 AAAAAATTATCGTGTTTC
52532969 AAAAAATTATCGTGTTT
1 AAAAAATTATCGTGTTT
52532986 TTTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (18 bp):
AAAAAATTATCGTGTTTC
Found at i:52533044 original size:18 final size:18
Alignment explanation
Indices: 52532952--52533373 Score: 110
Period size: 17 Copynumber: 22.8 Consensus size: 18
52532942 TTTTCAAAAA
*
52532952 AAAAATTCTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
52532969 AAAAAATTATCGTGTTTTTTT
1 -AAAAATTTTCGTG--TTTTC
** *
52532990 AAAAA-ACTCGTG-TTTA
1 AAAAATTTTCGTGTTTTC
*
52533006 AAAAATTTT-ATGTTTTC
1 AAAAATTTTCGTGTTTTC
*
52533023 -AAAACTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
** *
52533040 AAAAATTTTTATGTTTTTAA
1 AAAAATTTTCGTG-TTTT-C
*
52533060 AAAAATTTTCGCGTTTTC
1 AAAAATTTTCGTGTTTTC
* * *
52533078 AAAAAAAAATATCCTG-TTTC
1 ---AAAAATTTTCGTGTTTTC
52533098 --AAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
52533114 AAAAATTTCTCGT-ATTTC
1 AAAAATTT-TCGTGTTTTC
*
52533132 AAAAAAATTTTCACTTTTTGTGTTTGTAA
1 --AAAAATTTT--C-----GTGTTT-T-C
52533161 AAAAATTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
**
52533178 AAAAATATTCTCG-CATTTC
1 AAAAAT-TT-TCGTGTTTTC
*
52533197 AAAATTTTTTTAAATCGTG-TTTC
1 AAAA---ATTT---TCGTGTTTTC
* *
52533220 AAAAAAATGTCGTGTTTT-
1 -AAAAATTTTCGTGTTTTC
52533238 AAAAATTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* * *
52533255 TAAAATTTCCCTGTTTT-
1 AAAAATTTTCGTGTTTTC
** *
52533272 AAAAATTCCCGTGTTTTTAA
1 AAAAATTTTCGTG-TTTT-C
*
52533292 AAAAATGTT-GTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
52533308 AAAAATTTTTGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
52533325 TAAAATCTTCGTG-TTT-
1 AAAAATTTTCGTGTTTTC
* *
52533341 ACAAATTCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
52533359 AAAAATTCTCGTGTT
1 AAAAATTTTCGTGTT
52533374 AAAAAAAAAC
Statistics
Matches: 299, Mismatches: 58, Indels: 94
0.66 0.13 0.21
Matches are distributed among these distances:
15 8 0.03
16 41 0.14
17 74 0.25
18 60 0.20
19 37 0.12
20 36 0.12
21 16 0.05
22 1 0.00
23 7 0.02
24 4 0.01
25 1 0.00
26 2 0.01
27 11 0.04
28 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:52533044 original size:35 final size:33
Alignment explanation
Indices: 52532997--52533061 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 33
52532987 TTTAAAAAAC
52532997 TCGTGTTTAAAAAATTTTATGTTTTCAAAACTT
1 TCGTGTTTAAAAAATTTTATGTTTTCAAAACTT
* *
52533030 TCGTGTTTTCAAAAATTTTTATGTTTTTAAAA
1 TCGTG-TTT-AAAAAATTTTATGTTTTCAAAA
52533062 AAATTTTCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.18
34 3 0.11
35 20 0.71
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (33 bp):
TCGTGTTTAAAAAATTTTATGTTTTCAAAACTT
Found at i:52533183 original size:17 final size:17
Alignment explanation
Indices: 52533161--52533448 Score: 116
Period size: 17 Copynumber: 16.1 Consensus size: 17
52533151 GTGTTTGTAA
52533161 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
**
52533178 AAAAATATTCTCGCATTTC
1 AAAAAT-TT-TCGTGTTTC
*
52533197 AAAATTTTTTTAAATCGTGTTTC
1 AAAA---ATTT---TCGTGTTTC
* * *
52533220 AAAAAAATGTCGTGTTTT
1 -AAAAATTTTCGTGTTTC
52533238 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* * * *
52533255 TAAAATTTCCCTGTTTT
1 AAAAATTTTCGTGTTTC
** *
52533272 AAAAATTCCCGTGTTTTTAA
1 AAAAATTTTCGTG--TTT-C
*
52533292 AAAAATGTT-GTGTTTC
1 AAAAATTTTCGTGTTTC
*
52533308 AAAAATTTTTGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
52533325 TAAAATCTTCGTGTTT-
1 AAAAATTTTCGTGTTTC
* *
52533341 ACAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* **
52533359 AAAAATTCTCGTGTTAAAA
1 AAAAATTTTCGTGTT--TC
* * *
52533378 AAAAACTTTCGTTCTTTTA
1 AAAAATTTTCG-T-GTTTC
* *
52533397 AAAAAATTTC-TGCTTC
1 AAAAATTTTCGTGTTTC
* *
52533413 AAAAATCTTCGTG-TTA
1 AAAAATTTTCGTGTTTC
*
52533429 AAAAATTTCTCATGTTTC
1 AAAAATTT-TCGTGTTTC
52533447 AA
1 AA
52533449 TCGGATCACG
Statistics
Matches: 200, Mismatches: 50, Indels: 41
0.69 0.17 0.14
Matches are distributed among these distances:
16 36 0.18
17 78 0.39
18 26 0.13
19 36 0.18
20 7 0.04
21 5 0.03
22 1 0.00
23 7 0.04
24 4 0.02
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:52533305 original size:70 final size:69
Alignment explanation
Indices: 52533212--52533363 Score: 209
Period size: 70 Copynumber: 2.2 Consensus size: 69
52533202 TTTTTTAAAT
*
52533212 CGTG-TTTCAAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAAT-TTCCCTGTTTTAAA
1 CGTGTTTTCAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTTCTAAAATCTT-CCTG-TTTAAA
52533275 AATTCC
64 AATTCC
* * * * *
52533281 CGTGTTTTTAAAAAAATGTTGTGTTTCAAAAATTTTTGTGTTTCTAAAATCTTCGTGTTTACAAA
1 CGTGTTTTCAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTTCTAAAATCTTCCTGTTTAAAAA
*
52533346 TTCT
66 TTCC
52533350 CGTGTTTTCAAAAA
1 CGTGTTTTCAAAAA
52533364 TTCTCGTGTT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
69 27 0.37
70 44 0.60
71 2 0.03
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (69 bp):
CGTGTTTTCAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTTCTAAAATCTTCCTGTTTAAAAA
TTCC
Found at i:52533380 original size:18 final size:18
Alignment explanation
Indices: 52533343--52533381 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
52533333 TCGTGTTTAC
***
52533343 AAATTCTCGTGTTTTCAA
1 AAATTCTCGTGTTAAAAA
52533361 AAATTCTCGTGTTAAAAA
1 AAATTCTCGTGTTAAAAA
52533379 AAA
1 AAA
52533382 ACTTTCGTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (18 bp):
AAATTCTCGTGTTAAAAA
Found at i:52537175 original size:8 final size:9
Alignment explanation
Indices: 52537155--52537204 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
52537145 ATAATCCCAT
*
52537155 AAAAATTAT
1 AAAAATTAG
52537164 AAAAA-TAG
1 AAAAATTAG
52537172 AAAAATTAG
1 AAAAATTAG
* *
52537181 AAAGATTTAA
1 AAA-AATTAG
52537191 AAAAATTA-
1 AAAAATTAG
52537199 AAAAAT
1 AAAAAT
52537205 ATTTTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 13 0.37
9 15 0.43
10 7 0.20
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (9 bp):
AAAAATTAG
Found at i:52537232 original size:21 final size:19
Alignment explanation
Indices: 52537172--52537235 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 19
52537162 ATAAAAATAG
* *
52537172 AAAAATTAGAAAGATTTAA
1 AAAAATTAAAAAGATTTTA
*
52537191 AAAAATTAAAAAATATTTTTA
1 AAAAATT-AAAAAGA-TTTTA
*
52537212 AAAAATTATATAAGATATTTA
1 AAAAATTA-AAAAGAT-TTTA
52537233 AAA
1 AAA
52537236 GACGACAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 7 0.19
20 7 0.19
21 22 0.61
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
AAAAATTAAAAAGATTTTA
Found at i:52542649 original size:144 final size:143
Alignment explanation
Indices: 52542204--52542638 Score: 470
Period size: 144 Copynumber: 3.0 Consensus size: 143
52542194 GATAAGCTGC
* * *
52542204 TCAAGTTTCCTATGGAAGTAGGGATTTGTCCAGAGAATGTGTTATTAGACAGA-CACAACTGACT
1 TCAAGTTTCCTATCGAAGTAGGGATTTGTCCAGAGAATGTGTTATTAGACAGATC-CAATTCACT
* * * * * *
52542268 CAGAGATTTAAGCATCCCTACCTCTTCAGGTATCAATCCAAAAAACATATTGTCAAAAAGGCTAA
65 GAGAGATTTAAGCATCCCTACCTCTTTAGGTATCAATCCAGAAAACATATTTTGAAAAAGGATAA
52542333 GAGTAGTTAAGTCGG
130 GAGTAGTTAAGT-GG
* * * * *
52542348 TCAAGTTTCCTTTGGAAGTAGGGATTTGTCCAAAGAATGTGTTACTAGACAGATCCAATTTACTG
1 TCAAGTTTCCTATCGAAGTAGGGATTTGTCCAGAGAATGTGTTATTAGACAGATCCAATTCACTG
* * ** * * *
52542413 AGAGATTTAAGCATCCCTACCTCTTTAGGGATGACGCCACTG-AGA-TTATTATCGTACAAAA--
66 AGAGATTTAAGCATCCCTACCTCTTTAGGTATCAATCCA--GAAAACATATT-TTG-A-AAAAGG
*** *
52542474 A-AAGA-TGAACCAAGTTGC
126 ATAAGAGT-AGTTAAG-TGG
* *
52542492 TTAAGTTTCCTATCGAAGTAGGGATTTGTCCAGAGAATGTGTTATTGGACAGATCCAATTCACTG
1 TCAAGTTTCCTATCGAAGTAGGGATTTGTCCAGAGAATGTGTTATTAGACAGATCCAATTCACTG
* *
52542557 AGAGATTTAAGCATCCCTACCTCTTTAGGTATCAATCCAGAAAACATATTTTGAGAAAGGGTAAG
66 AGAGATTTAAGCATCCCTACCTCTTTAGGTATCAATCCAGAAAACATATTTTGAAAAAGGATAAG
52542622 AGTAGTTAAGCTGG
131 AGTAGTTAAG-TGG
52542636 TCA
1 TCA
52542639 TGCTCCCTAT
Statistics
Matches: 233, Mismatches: 44, Indels: 28
0.76 0.14 0.09
Matches are distributed among these distances:
141 3 0.01
142 2 0.01
143 5 0.02
144 213 0.91
145 5 0.02
146 1 0.00
147 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (143 bp):
TCAAGTTTCCTATCGAAGTAGGGATTTGTCCAGAGAATGTGTTATTAGACAGATCCAATTCACTG
AGAGATTTAAGCATCCCTACCTCTTTAGGTATCAATCCAGAAAACATATTTTGAAAAAGGATAAG
AGTAGTTAAGTGG
Found at i:52547476 original size:21 final size:21
Alignment explanation
Indices: 52547452--52547492 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52547442 AATATTTAAA
52547452 TTCAAAAAACTATTAAAAAAG
1 TTCAAAAAACTATTAAAAAAG
* * *
52547473 TTCATAAAAGTCTTAAAAAA
1 TTCAAAAAACTATTAAAAAA
52547493 TTAGCATGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.27
Consensus pattern (21 bp):
TTCAAAAAACTATTAAAAAAG
Found at i:52548315 original size:10 final size:9
Alignment explanation
Indices: 52548302--52548405 Score: 58
Period size: 10 Copynumber: 11.3 Consensus size: 9
52548292 GAAAGAGAGG
52548302 GAAAGAAGAA
1 GAAAGAA-AA
52548312 GAAAG-AAA
1 GAAAGAAAA
52548320 GAAAGAAAA
1 GAAAGAAAA
* *
52548329 GGAAAGGAGAG
1 -GAAA-GAAAA
52548340 GAAAG-AAA
1 GAAAGAAAA
52548348 GAAA-AAGAA
1 GAAAGAA-AA
52548357 GGAAAGAAAA
1 -GAAAGAAAA
*
52548367 GGAAAG--GA
1 -GAAAGAAAA
52548375 GAAGAGAAAA
1 GAA-AGAAAA
*
52548385 -AAAAAAAA
1 GAAAGAAAA
52548393 GAAAGAAGAA
1 GAAAGAA-AA
52548403 GAA
1 GAA
52548406 GAGGGGAGGA
Statistics
Matches: 74, Mismatches: 8, Indels: 24
0.70 0.08 0.23
Matches are distributed among these distances:
7 3 0.04
8 21 0.28
9 14 0.19
10 31 0.42
11 5 0.07
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (9 bp):
GAAAGAAAA
Found at i:52548319 original size:4 final size:4
Alignment explanation
Indices: 52548302--52548399 Score: 50
Period size: 4 Copynumber: 24.8 Consensus size: 4
52548292 GAAAGAGAGG
*
52548302 GAAA G-AA G-AA GAAA GAAA GAAA GAAAA GGAAA GGAGAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA -GA-AA GAAA GAAA
* *
52548348 G-AA -AAA GAAG GAAA GAAAA GGAAA G-GA GAAGA GAAA -AAA -AAA -AAA
1 GAAA GAAA GAAA GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA
52548393 GAAA GAA
1 GAAA GAA
52548400 GAAGAAGAGG
Statistics
Matches: 77, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
3 21 0.27
4 32 0.42
5 21 0.27
6 3 0.04
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:52548332 original size:28 final size:28
Alignment explanation
Indices: 52548291--52548436 Score: 96
Period size: 28 Copynumber: 5.4 Consensus size: 28
52548281 TGGGGGGAAG
* *
52548291 AGAAAGAGAGGGAAAGAAGAAGAAAGAA
1 AGAAAGAAAAGGAAAGAAGAAGAAAGAA
* *
52548319 AGAAAGAAAAGGAAAGGAGAGGAAAGAA
1 AGAAAGAAAAGGAAAGAAGAAGAAAGAA
*
52548347 AGAAA-AAGAAGGAAAGAA-AAGGAAAG-G
1 AGAAAGAA-AAGGAAAGAAGAA-GAAAGAA
*
52548374 AGAAGAGAAAA--AAA-AAAAAGAAAG-A
1 AGAA-AGAAAAGGAAAGAAGAAGAAAGAA
* * *
52548399 AG-AAGAAGAGGGGAGGAAGGAA-AAAGAA
1 AGAAAGAA-AAGGAAAGAA-GAAGAAAGAA
52548427 AGAAA-AAAAG
1 AGAAAGAAAAG
52548437 TAATTTTTTA
Statistics
Matches: 93, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
23 4 0.04
24 2 0.02
25 9 0.10
26 6 0.06
27 15 0.16
28 53 0.57
29 4 0.04
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (28 bp):
AGAAAGAAAAGGAAAGAAGAAGAAAGAA
Found at i:52548334 original size:5 final size:5
Alignment explanation
Indices: 52548312--52548374 Score: 53
Period size: 5 Copynumber: 13.4 Consensus size: 5
52548302 GAAAGAAGAA
* * * *
52548312 GAAA- GAAA- GAAAG AAAAG GAAAG GAGAG GAAA- GAAAG AAAAA G-AAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
*
52548358 GAAAG AAAAG GAAAG GA
1 GAAAG GAAAG GAAAG GA
52548375 GAAGAGAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
4 15 0.33
5 31 0.67
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:52548343 original size:38 final size:37
Alignment explanation
Indices: 52548292--52548436 Score: 146
Period size: 38 Copynumber: 4.0 Consensus size: 37
52548282 GGGGGGAAGA
52548292 GAAA-GAGAGGGAAAGAAGAAGAAAGAAAGAAAGAAAAG
1 GAAAGGAGA-GGAAAGAAGAA-AAAGAAAGAAAGAAAAG
*
52548330 GAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAG
1 GAAAGGAGAGGAAAG-AAGAAAAAGAAAGAAAGAAAAG
*
52548368 GAAAGGAGAAGAGAA-AA-AAAAA-AAAGAAAGAAGAA-
1 GAAAGGAGAGGA-AAGAAGAAAAAGAAAGAAAGAA-AAG
*
52548403 GAAGAGGGGAGG-AAG--GAAAAAGAAAGAAA-AAAAG
1 GAA-AGGAGAGGAAAGAAGAAAAAGAAAGAAAGAAAAG
52548437 TAATTTTTTA
Statistics
Matches: 93, Mismatches: 5, Indels: 22
0.77 0.04 0.18
Matches are distributed among these distances:
33 2 0.02
34 9 0.10
35 19 0.20
36 13 0.14
37 2 0.02
38 37 0.40
39 11 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (37 bp):
GAAAGGAGAGGAAAGAAGAAAAAGAAAGAAAGAAAAG
Done.