Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 200 of 204
Found at i:59218561 original size:11 final size:10
Alignment explanation
Indices: 59218547--59218663 Score: 64
Period size: 11 Copynumber: 11.5 Consensus size: 10
59218537 AAAAATTAAA
59218547 AAAAGTATTTT
1 AAAA-TATTTT
59218558 AAAATATTTTT
1 AAAATA-TTTT
59218569 AAAATATTTT
1 AAAATATTTT
*
59218579 -AAA-A-TTA
1 AAAATATTTT
* **
59218586 AAAAAATTAA
1 AAAATATTTT
59218596 AAAATTATTTT
1 AAAA-TATTTT
59218607 AAAATTATTTT
1 AAAA-TATTTT
**
59218618 AAAAT-TAGT
1 AAAATATTTT
**
59218627 AAAA-ATTAAA
1 AAAATATT-TT
59218637 AAAAGTATTTT
1 AAAA-TATTTT
59218648 AAAAATATTTT
1 -AAAATATTTT
59218659 AAAAT
1 AAAAT
59218664 TTAAAAAAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
7 2 0.02
8 4 0.05
9 11 0.13
10 22 0.26
11 38 0.45
12 7 0.08
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (10 bp):
AAAATATTTT
Found at i:59218703 original size:11 final size:11
Alignment explanation
Indices: 59218521--59218662 Score: 69
Period size: 10 Copynumber: 13.9 Consensus size: 11
59218511 GGCCCATTTT
59218521 TATTTT-AAAA
1 TATTTTAAAAA
59218531 -ATTTTAAAAA
1 TATTTTAAAAA
**
59218541 -ATTAAAAAAA
1 TATTTTAAAAA
59218551 GTATTTT-AAAA
1 -TATTTTAAAAA
*
59218562 TATTTTTAAAA
1 TATTTTAAAAA
59218573 TATTTT--AAA
1 TATTTTAAAAA
59218582 -A--TTAAAAA
1 TATTTTAAAAA
* *
59218590 -AATTAAAAAA
1 TATTTTAAAAA
*
59218600 TTATTTTAAAAT
1 -TATTTTAAAAA
59218612 TATTTT-AAAA
1 TATTTTAAAAA
**
59218622 T-TAGT-AAAA
1 TATTTTAAAAA
**
59218631 -ATTAAAAAAA
1 TATTTTAAAAA
59218641 GTATTTTAAAAA
1 -TATTTTAAAAA
59218653 TATTTTAAAA
1 TATTTTAAAA
59218663 TTTAAAAAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
6 2 0.02
8 5 0.05
9 15 0.15
10 32 0.31
11 30 0.29
12 18 0.18
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:59218704 original size:41 final size:40
Alignment explanation
Indices: 59218521--59218712 Score: 228
Period size: 41 Copynumber: 4.8 Consensus size: 40
59218511 GGCCCATTTT
* **
59218521 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAGTATTTTAAAA-
1 TATTTTAAAAATATTT-TAAAATTAAAAAAA--ATTAAAAAAG
* *
59218562 TATTTTTAAAATATTTTAAAATT-AAAAAAATTAAAAAAT
1 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAG
* **
59218601 TATTTTAAAATTATTTTAAAATTAGTAAAAATTAAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAAATT-AAAAAAG
59218642 TATTTTAAAAATATTTTAAAATTTAAAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTTAAAA-TTAAAAAAAATTAAAAAAG
* *
59218683 TATGTAAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAA
59218713 TAAATATATT
Statistics
Matches: 132, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
38 7 0.05
39 21 0.16
40 22 0.17
41 69 0.52
42 13 0.10
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (40 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAG
Found at i:59218973 original size:4 final size:4
Alignment explanation
Indices: 59218964--59219022 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
59218954 TAATTTTCAT
59218964 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
59219012 ATAC ATAC ATA
1 ATAC ATAC ATA
59219023 TCTTTTAGCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:59224665 original size:32 final size:32
Alignment explanation
Indices: 59224605--59224665 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
59224595 GGCTGTAATA
* *
59224605 TTTGATGCTTTGTTTTCTTTTGAGTATTTTGG
1 TTTGATGCTTTGATTTCTGTTGAGTATTTTGG
*
59224637 TTTGATGCTTTTGATTTGTGTTGA-TATTT
1 TTTGATGC-TTTGATTTCTGTTGAGTATTT
59224666 GAGTGTAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 13 0.52
33 12 0.48
ACGTcount: A:0.11, C:0.05, G:0.21, T:0.62
Consensus pattern (32 bp):
TTTGATGCTTTGATTTCTGTTGAGTATTTTGG
Found at i:59231007 original size:16 final size:16
Alignment explanation
Indices: 59230982--59231020 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
59230972 TTGGTTCGCT
*
59230982 GTAATAGAATAGAGGC
1 GTAATAGAATAGAGAC
*
59230998 GTAATGGAATAGAGAC
1 GTAATAGAATAGAGAC
59231014 GTAATAG
1 GTAATAG
59231021 GTAATTCTTT
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:0.44, C:0.05, G:0.31, T:0.21
Consensus pattern (16 bp):
GTAATAGAATAGAGAC
Found at i:59231080 original size:44 final size:46
Alignment explanation
Indices: 59231000--59231092 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 46
59230990 ATAGAGGCGT
* * *
59231000 AATGGAATAGAGACGTAATAGGTAATTCTTTTGTTTGGTTGAGTGG
1 AATGGAATAGAGACATAATAGGTAATTCTTGTGTTTGGTTGAATGG
*
59231046 AATGGAATAGAGGCATAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGACATAATAGGTAATTCTTGTGTTTGGTTGAATGG
59231090 AAT
1 AAT
59231093 AGAGGTGTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 23 0.53
45 3 0.07
46 17 0.40
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGACATAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:59231089 original size:39 final size:44
Alignment explanation
Indices: 59231000--59231097 Score: 116
Period size: 46 Copynumber: 2.3 Consensus size: 44
59230990 ATAGAGGCGT
* * *
59231000 AATGGAATAGAGACGTAATAGGTAATTCTTTTGTTTGGTTGAGTGG
1 AATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTT--GTGG
59231046 AATGGAATAGAGGCATAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTGTGG
59231085 AATGGAATAGAGG
1 AATGGAATAGAGG
59231098 TGTAATAGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
39 14 0.29
40 1 0.02
43 1 0.02
44 13 0.27
45 3 0.06
46 17 0.35
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTGTGG
Found at i:59231391 original size:59 final size:57
Alignment explanation
Indices: 59231248--59231600 Score: 206
Period size: 59 Copynumber: 6.3 Consensus size: 57
59231238 TGGTTGTTAT
* * *
59231248 TAAATATAATTTAATAAAAATATATAAT-TTAATAAAAT-T-GTTAATAAAT-ATTCTTA
1 TAAATATAATTTAATAATAATATATAATATT-ATAAAATATAATT--TAAATAATTATTA
* * ** *
59231304 TATGAATTTACTAAAATCATAATATATAATATTATAAAATATAATTTAAAATAATTATTA
1 TA--AATATAATTTAATAATAATATATAATATTATAAAATATAATTT-AAATAATTATTA
* * **
59231364 GTAAATATCATTTAATAATAATATATAAT-TTAATAAAAT-T--CTT--ATTTTTA-TA
1 -TAAATATAATTTAATAATAATATATAATATT-ATAAAATATAATTTAAATAATTATTA
* * * ** * *
59231416 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTA
1 TAAATATAATTTAATAATAATATATAATATTATAAAATATAATTT-AAATAATTATTA
* **
59231474 GTAAATATAATTTAATAATAATATATAAT-TTAATAAAAT-T--CTT--ATTCTTA-TA
1 -TAAATATAATTTAATAATAATATATAATATT-ATAAAATATAATTTAAATAATTATTA
* * * * *
59231526 TGAAT-TTATTAAAATCATAATATATAATACTATAAAATATAATTTAAATAATTATTA
1 TAAATATAATT-TAATAATAATATATAATATTATAAAATATAATTTAAATAATTATTA
59231583 TTAAATATAATTT-ATAAT
1 -TAAATATAATTTAATAAT
59231601 CTACTTTATT
Statistics
Matches: 218, Mismatches: 50, Indels: 57
0.67 0.15 0.18
Matches are distributed among these distances:
50 4 0.02
51 54 0.25
52 8 0.04
53 10 0.05
54 4 0.02
56 11 0.05
57 11 0.05
58 39 0.18
59 67 0.31
60 8 0.04
61 2 0.01
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (57 bp):
TAAATATAATTTAATAATAATATATAATATTATAAAATATAATTTAAATAATTATTA
Found at i:59231437 original size:51 final size:51
Alignment explanation
Indices: 59231381--59231553 Score: 150
Period size: 51 Copynumber: 3.2 Consensus size: 51
59231371 TCATTTAATA
* *
59231381 ATAATATATAATTTAATAAAATTCTTATTTTTATATGAATTTACTAAAATC
1 ATAATATATAATTTAATAAAATTCTTATTATTATATGAATTTAATAAAATC
* * * * * ** *
59231432 ATAATATATAATACTATAAAATATAATT-TAAAATAATTATTAGTAAATATAATTTAATA
1 ATAATATATAAT--T-T--AATAAAATTCT--TATTATTA-TA-TGAATTTAATAAAATC
* *
59231491 ATAATATATAATTTAATAAAATTCTTATTCTTATATGAATTTATTAAAATC
1 ATAATATATAATTTAATAAAATTCTTATTATTATATGAATTTAATAAAATC
59231542 ATAATATATAAT
1 ATAATATATAAT
59231554 ACTATAAAAT
Statistics
Matches: 92, Mismatches: 20, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
51 34 0.37
52 2 0.02
53 6 0.07
54 9 0.10
55 2 0.02
56 9 0.10
57 6 0.07
58 2 0.02
59 22 0.24
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (51 bp):
ATAATATATAATTTAATAAAATTCTTATTATTATATGAATTTAATAAAATC
Found at i:59231454 original size:110 final size:110
Alignment explanation
Indices: 59231248--59231600 Score: 566
Period size: 110 Copynumber: 3.2 Consensus size: 110
59231238 TGGTTGTTAT
* *
59231248 TAAATATAATTTAATAAAAATATATAATTTAATAAAATTGTTAATAAATATTCTTATATGAATTT
1 TAAATATAATTTAATAATAATATATAATTTAATAAAATT-CT--T--AT-TT-TTATATGAATTT
*
59231313 ACTAAAATCATAATATATAATATTATAAAATATAATTTAAAATAATTATTAG
59 ACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTAG
*
59231365 TAAATATCATTTAATAATAATATATAATTTAATAAAATTCTTATTTTTATATGAATTTACTAAAA
1 TAAATATAATTTAATAATAATATATAATTTAATAAAATTCTTATTTTTATATGAATTTACTAAAA
59231430 TCATAATATATAATACTATAAAATATAATTTAAAATAATTATTAG
66 TCATAATATATAATACTATAAAATATAATTTAAAATAATTATTAG
* *
59231475 TAAATATAATTTAATAATAATATATAATTTAATAAAATTCTTATTCTTATATGAATTTATTAAAA
1 TAAATATAATTTAATAATAATATATAATTTAATAAAATTCTTATTTTTATATGAATTTACTAAAA
*
59231540 TCATAATATATAATACTATAAAATATAATTT-AAATAATTATTAT
66 TCATAATATATAATACTATAAAATATAATTTAAAATAATTATTAG
59231584 TAAATATAATTT-ATAAT
1 TAAATATAATTTAATAAT
59231601 CTACTTTATT
Statistics
Matches: 228, Mismatches: 8, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
108 5 0.02
109 24 0.11
110 156 0.68
111 2 0.01
112 2 0.01
114 1 0.00
116 1 0.00
117 37 0.16
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (110 bp):
TAAATATAATTTAATAATAATATATAATTTAATAAAATTCTTATTTTTATATGAATTTACTAAAA
TCATAATATATAATACTATAAAATATAATTTAAAATAATTATTAG
Found at i:59233053 original size:49 final size:49
Alignment explanation
Indices: 59232981--59233085 Score: 156
Period size: 49 Copynumber: 2.1 Consensus size: 49
59232971 CTTAAGAAAA
* ** * *
59232981 AAAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTAT
1 AAAATTAAAATTAAGTTCAATATCATGAATCAAAAACTCAACACTGTAT
*
59233030 AAAATTAAAATTGAGTTCAATATCATGAATCAAAAACTCAACACTGTAT
1 AAAATTAAAATTAAGTTCAATATCATGAATCAAAAACTCAACACTGTAT
59233079 AAAATTA
1 AAAATTA
59233086 TAACACATGA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.30
Consensus pattern (49 bp):
AAAATTAAAATTAAGTTCAATATCATGAATCAAAAACTCAACACTGTAT
Found at i:59235000 original size:55 final size:55
Alignment explanation
Indices: 59234870--59234983 Score: 201
Period size: 55 Copynumber: 2.1 Consensus size: 55
59234860 CAAACCACAT
* *
59234870 TTTTCTTTAAAGAATTTTTAGAAGCACTTTCAATCATAATAACAATGAATACTTG
1 TTTTCTTTAAACAATTTTTACAAGCACTTTCAATCATAATAACAATGAATACTTG
*
59234925 TTTTCTTTAAACAATTTTTACAAGCACTTTCAATCATAATAACAATGAATATTTG
1 TTTTCTTTAAACAATTTTTACAAGCACTTTCAATCATAATAACAATGAATACTTG
59234980 TTTT
1 TTTT
59234984 TTAATCAAGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (55 bp):
TTTTCTTTAAACAATTTTTACAAGCACTTTCAATCATAATAACAATGAATACTTG
Found at i:59235147 original size:66 final size:64
Alignment explanation
Indices: 59234972--59235156 Score: 309
Period size: 64 Copynumber: 2.9 Consensus size: 64
59234962 AATAACAATG
* *
59234972 AATATTTGTTTTTTAATCAAGTTGTTTACTTGATTATATCTAATGATCAAATTTTAATATATCC
1 AATATTTGTTTTTTAATCAAGTTGTTTACTTGATTATATCTAATGATCCAATTTTAATATATCA
*
59235036 AATAATTGTTTTTTAATCAAGTTGTTTACTTGATTATATCTAATGATCCAATTTTAATATGTTAT
1 AATATTTGTTTTTTAATCAAGTTGTTTACTTGATTATATCTAATGATCCAATTTTAATA---TAT
59235101 -A
63 CA
59235102 AATATTTGTTTTTTAATCAAGTTGTTTACTTGATTATATCTAATGATCCAATTTT
1 AATATTTGTTTTTTAATCAAGTTGTTTACTTGATTATATCTAATGATCCAATTTT
59235157 TATTTTATTT
Statistics
Matches: 114, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
64 57 0.50
66 54 0.47
67 3 0.03
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.51
Consensus pattern (64 bp):
AATATTTGTTTTTTAATCAAGTTGTTTACTTGATTATATCTAATGATCCAATTTTAATATATCA
Found at i:59235314 original size:32 final size:32
Alignment explanation
Indices: 59235273--59235334 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
59235263 TAAAAATATT
59235273 TTTAATTAATGCGTTGTATATGAATATACACA
1 TTTAATTAATGCGTTGTATATGAATATACACA
*
59235305 TTTAATTAATGTGTTGTATATGAATATACA
1 TTTAATTAATGCGTTGTATATGAATATACA
59235335 TTAGTGCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (32 bp):
TTTAATTAATGCGTTGTATATGAATATACACA
Found at i:59235574 original size:25 final size:25
Alignment explanation
Indices: 59235540--59235601 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
59235530 CAATTTACTG
59235540 GAATTGCAACTATAAAAAACCTCTT
1 GAATTGCAACTATAAAAAACCTCTT
*
59235565 GAATTGCAACTATAAAATACCTCTT
1 GAATTGCAACTATAAAAAACCTCTT
59235590 GAATTGCAACTA
1 GAATTGCAACTA
59235602 GAGCTTCAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (25 bp):
GAATTGCAACTATAAAAAACCTCTT
Found at i:59250666 original size:23 final size:22
Alignment explanation
Indices: 59250619--59250662 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
59250609 ATAAAATTAT
* *
59250619 TAAATATTAAAATAATATAATA
1 TAAATATTAAAAAAATATAAAA
59250641 TAAATATTTAAAAAAAT-TAAAA
1 TAAATA-TTAAAAAAATATAAAA
59250663 ATAATATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATATTAAAAAAATATAAAA
Found at i:59263514 original size:19 final size:20
Alignment explanation
Indices: 59263492--59263532 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
59263482 AATTGATAAA
* *
59263492 TATTTTTATATTTAA-ATTT
1 TATTTATATATTAAATATTT
59263511 TATTTATATATTAAATATTT
1 TATTTATATATTAAATATTT
59263531 TA
1 TA
59263533 AAAATATCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTATATATTAAATATTT
Found at i:59266896 original size:38 final size:33
Alignment explanation
Indices: 59266866--59266930 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
59266856 ATTGTCACAC
59266866 ATGTAAAAATATAATATATTATATATAAATTTAA
1 ATGTAAAAA-ATAATATATTATATATAAATTTAA
* * *
59266900 ATTTTAAAAATAATATTTTATATATAAATTT
1 ATGTAAAAAATAATATATTATATATAAATTT
59266931 TATATTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (33 bp):
ATGTAAAAAATAATATATTATATATAAATTTAA
Found at i:59266932 original size:13 final size:13
Alignment explanation
Indices: 59266897--59266935 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
59266887 TATATAAATT
* *
59266897 TAAATTTTAAAAA
1 TAAATTTTATATA
59266910 TAATATTTTATATA
1 TAA-ATTTTATATA
59266924 TAAATTTTATAT
1 TAAATTTTATAT
59266936 TTTTGAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAAATTTTATATA
Found at i:59272865 original size:53 final size:53
Alignment explanation
Indices: 59272785--59272889 Score: 210
Period size: 53 Copynumber: 2.0 Consensus size: 53
59272775 TCCTGTAAGG
59272785 ATCAATACCATGTTCATAGTGGTTATGAAATCTGTTGACACTGATATCCTTAT
1 ATCAATACCATGTTCATAGTGGTTATGAAATCTGTTGACACTGATATCCTTAT
59272838 ATCAATACCATGTTCATAGTGGTTATGAAATCTGTTGACACTGATATCCTTA
1 ATCAATACCATGTTCATAGTGGTTATGAAATCTGTTGACACTGATATCCTTA
59272890 CTCAATAACC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (53 bp):
ATCAATACCATGTTCATAGTGGTTATGAAATCTGTTGACACTGATATCCTTAT
Found at i:59275837 original size:6 final size:6
Alignment explanation
Indices: 59275826--59275852 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
59275816 TTGTTTTCTT
59275826 AAATGG AAATGG AAATGG AAATGG AAA
1 AAATGG AAATGG AAATGG AAATGG AAA
59275853 ATGATATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.15
Consensus pattern (6 bp):
AAATGG
Found at i:59278391 original size:33 final size:33
Alignment explanation
Indices: 59278349--59278414 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
59278339 CATGCATTAC
*
59278349 GAATCGGGACTTATCTTTACTGGATGTTTGAAA
1 GAATCGGGACTTATCTTTACTGGATGTCTGAAA
59278382 GAATCGGGACTTATCTTTACTGGATGTCTGAAA
1 GAATCGGGACTTATCTTTACTGGATGTCTGAAA
59278415 AAATGACCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (33 bp):
GAATCGGGACTTATCTTTACTGGATGTCTGAAA
Found at i:59281655 original size:27 final size:29
Alignment explanation
Indices: 59281622--59281680 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
59281612 CGTTAAATTT
59281622 AAAATAGCTTTTA-A-ATTTTAATTTTTA
1 AAAATAGCTTTTATAGATTTTAATTTTTA
* * *
59281649 AAAATAGTTTTTATAGTTTTTTATTTTTA
1 AAAATAGCTTTTATAGATTTTAATTTTTA
59281678 AAA
1 AAA
59281681 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 12 0.44
28 1 0.04
29 14 0.52
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (29 bp):
AAAATAGCTTTTATAGATTTTAATTTTTA
Found at i:59290556 original size:13 final size:13
Alignment explanation
Indices: 59290538--59290563 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59290528 TATTATTTTG
59290538 TATACATGCTATA
1 TATACATGCTATA
59290551 TATACATGCTATA
1 TATACATGCTATA
59290564 ATCTTTTTAT
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:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
TATACATGCTATA
Found at i:59290621 original size:67 final size:67
Alignment explanation
Indices: 59290547--59290686 Score: 246
Period size: 67 Copynumber: 2.1 Consensus size: 67
59290537 GTATACATGC
*
59290547 TATATATACATGC-TATAATCTTTTTATGTATTTCTAATATACATGCTATATATATAGTAAAATG
1 TATATATACATCCAT-TAATCTTTTTATGTATTTCTAATATACATGCTATATATATAGTAAAATG
59290611 ATA
65 ATA
*
59290614 TATATATATATCCATTAATCTTTTTATGTATTTCTAATATACATGCTATATATATAGTAAAATGA
1 TATATATACATCCATTAATCTTTTTATGTATTTCTAATATACATGCTATATATATAGTAAAATGA
59290679 TA
66 TA
59290681 TATATA
1 TATATA
59290687 ATCTACACTA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
67 69 0.99
68 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (67 bp):
TATATATACATCCATTAATCTTTTTATGTATTTCTAATATACATGCTATATATATAGTAAAATGA
TA
Found at i:59290718 original size:65 final size:67
Alignment explanation
Indices: 59290574--59290719 Score: 156
Period size: 67 Copynumber: 2.2 Consensus size: 67
59290564 ATCTTTTTAT
* * * * ***
59290574 GTATTTCTAATATACATGCTATATATATAGTAAAATGATATATATATATATCCATTAATCTTTTT
1 GTATTTCAAATATACATGCTATATATATAGTAAAATGATATATATATATATACATAAATCATGAG
*
59290639 AT
66 AA
* *
59290641 GTATTTCTAATATACATGCTATATATATAGTAAAATGATATATATA-ATCTACACTAAAT-ATGA
1 GTATTTCAAATATACATGCTATATATATAGTAAAATGATATATATATATATACA-TAAATCATGA
59290704 GAA
65 GAA
59290707 G-ATTAT-AAATATA
1 GTATT-TCAAATATA
59290720 ATAATCTATA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
65 9 0.13
66 9 0.13
67 50 0.74
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (67 bp):
GTATTTCAAATATACATGCTATATATATAGTAAAATGATATATATATATATACATAAATCATGAG
AA
Found at i:59317696 original size:21 final size:21
Alignment explanation
Indices: 59317667--59317709 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
59317657 CTGAATATAA
*
59317667 TAAATATATATTTTTT-ATTTT
1 TAAAAATAT-TTTTTTAATTTT
59317688 TAAAAATATTTTTTTAATTTT
1 TAAAAATATTTTTTTAATTTT
59317709 T
1 T
59317710 TTAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TAAAAATATTTTTTTAATTTT
Found at i:59318867 original size:31 final size:31
Alignment explanation
Indices: 59318809--59318871 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
59318799 AAAAAATTAT
* * *
59318809 TGAATTATTCAAAATTTTTTATTTAAGTCAC
1 TGAACTATTCAAAAGTTTTTATCTAAGTCAC
*
59318840 TGAACTATTTAAAAGTTTTTATCTAAGTCAC
1 TGAACTATTCAAAAGTTTTTATCTAAGTCAC
59318871 T
1 T
59318872 ACTTTGTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTTTTATCTAAGTCAC
Found at i:59325696 original size:22 final size:24
Alignment explanation
Indices: 59325684--59325738 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 24
59325674 AAATTTATAT
59325684 TAAATATATAATAATACTTTAATA
1 TAAATATATAATAATACTTTAATA
* *
59325708 TAAATAT-TAA-AATAATGTAATA
1 TAAATATATAATAATACTTTAATA
59325730 TAAATATAT
1 TAAATATAT
59325739 TTTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 17 0.61
23 4 0.14
24 7 0.25
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAATATATAATAATACTTTAATA
Found at i:59333988 original size:20 final size:20
Alignment explanation
Indices: 59333954--59333995 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
59333944 AACTATTTAA
** *
59333954 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
59333974 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
59333994 AT
1 AT
59333996 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:59334714 original size:26 final size:26
Alignment explanation
Indices: 59334675--59334733 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
59334665 AATGAAAGTG
59334675 GAAATTA--AAGAGGTCCCACTCCAT
1 GAAATTATTAAGAGGTCCCACTCCAT
*
59334699 GAAATTATTAAGAGGTCCCAGTCCAT
1 GAAATTATTAAGAGGTCCCACTCCAT
59334725 GAAATTATT
1 GAAATTATT
59334734 GCACCCTCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 7 0.22
26 25 0.78
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (26 bp):
GAAATTATTAAGAGGTCCCACTCCAT
Found at i:59334939 original size:45 final size:45
Alignment explanation
Indices: 59334888--59334973 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
59334878 ATTTGCATAA
59334888 AAAATAATTTTAACTATTAAATTTATTTTTTTATCAAATCATTTC
1 AAAATAATTTTAACTATTAAATTTATTTTTTTATCAAATCATTTC
59334933 AAAATAATTTTAACTATTAAATTTATTTTTTTATCAAATCA
1 AAAATAATTTTAACTATTAAATTTATTTTTTTATCAAATCA
59334974 ATACAGGGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (45 bp):
AAAATAATTTTAACTATTAAATTTATTTTTTTATCAAATCATTTC
Found at i:59338479 original size:300 final size:302
Alignment explanation
Indices: 59337848--59338485 Score: 956
Period size: 302 Copynumber: 2.1 Consensus size: 302
59337838 TAAGCATATC
* ** * * *
59337848 AATAAACCCAATTTATTCCCAAATTCTTCTGAACATCCATTGAAACTCAATAAGTAAATATTAGA
1 AATAAACCCAACTTATTTTCAAATTCTTCTGAACATCAATCGAAACTCAATAAGTAAATATCAGA
* * *
59337913 TTATGCATAAAAACAAGCTAATGACTTCATCATAGTCATCGAAAGCATAAATCAAATTAAAAAAC
66 TTATGAACAAAAACAAGCTAATGAATTCATCATAGTCATCGAAAGCATAAATCAAATTAAAAAAC
* *
59337978 CCATAATATTTCAACAACTACAAACCCTTTGAACAACACATTTATCAACAGAAAATACAACCTAC
131 ACATAAAATTTCAACAACTACAAACCCTTTGAACAACACATTTATCAACAGAAAATACAACCTAC
*
59338043 CAAAAGGACCAGCAAGTTAAGCACAAAACTAACTACAACACAATTCTTCTAAGATATTCCATATT
196 CAAAAGGACCAGCAAGTTAAACACAAAACTAACTACAACACAATTCTTCTAAGATATTCCATATT
* * * **
59338108 TATAGGGATAGCTTTAGGGCACTAGCATATCAACGTATTGCA
261 TATAAGGATAGCATTAAGGCACTAGCATATCAACACATTGCA
**
59338150 AATAAACCCAACTTATTTTCAAATTCTTCTGAACATCAATCGAAACTTGATAAGTAAATATCAGA
1 AATAAACCCAACTTATTTTCAAATTCTTCTGAACATCAATCGAAACTCAATAAGTAAATATCAGA
* * * * *
59338215 TTATGAACAGAAACAAGCTAATGAATTCATTATCGTCATTGAAAGCATAAATCCAATT-AAAAAC
66 TTATGAACAAAAACAAGCTAATGAATTCATCATAGTCATCGAAAGCATAAATCAAATTAAAAAAC
* * *
59338279 ACATAAAATTTCAACAACTACAAGCCCTTTGAACAATACATTTATCAACAGAAAATAGAACCTAC
131 ACATAAAATTTCAACAACTACAAACCCTTTGAACAACACATTTATCAACAGAAAATACAACCTAC
* * * * *
59338344 CGAAAGGACCAGCAAGTTAAACACTAAATTAACTAC-AGACAATTCTTCTAAGATATTCCATTTT
196 CAAAAGGACCAGCAAGTTAAACACAAAACTAACTACAACACAATTCTTCTAAGATATTCCATATT
* *
59338408 TGTAAGGATAGCATTAAGGCACTAGCATATCAATACATTGCA
261 TATAAGGATAGCATTAAGGCACTAGCATATCAACACATTGCA
59338450 AATAAACCCAACTTATTTTCAAATTCTTCTGAACAT
1 AATAAACCCAACTTATTTTCAAATTCTTCTGAACAT
59338486 TAGATTATGA
Statistics
Matches: 302, Mismatches: 34, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
300 97 0.32
301 98 0.32
302 107 0.35
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.27
Consensus pattern (302 bp):
AATAAACCCAACTTATTTTCAAATTCTTCTGAACATCAATCGAAACTCAATAAGTAAATATCAGA
TTATGAACAAAAACAAGCTAATGAATTCATCATAGTCATCGAAAGCATAAATCAAATTAAAAAAC
ACATAAAATTTCAACAACTACAAACCCTTTGAACAACACATTTATCAACAGAAAATACAACCTAC
CAAAAGGACCAGCAAGTTAAACACAAAACTAACTACAACACAATTCTTCTAAGATATTCCATATT
TATAAGGATAGCATTAAGGCACTAGCATATCAACACATTGCA
Found at i:59340172 original size:2 final size:2
Alignment explanation
Indices: 59340165--59340220 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
59340155 TATAATACTC
59340165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59340207 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
59340221 TTCTTAACAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59347126 original size:33 final size:32
Alignment explanation
Indices: 59347089--59347150 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
59347079 TTTATTGGGT
*
59347089 ACGGTTCGATTTAATTTTATGATAACATAAGGA
1 ACGGTTCGACTTAATTTTATGATAA-ATAAGGA
59347122 ACGGTTCGACTTAATTTTATGATAAATAA
1 ACGGTTCGACTTAATTTTATGATAAATAA
59347151 TTATGGTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (32 bp):
ACGGTTCGACTTAATTTTATGATAAATAAGGA
Found at i:59347340 original size:18 final size:16
Alignment explanation
Indices: 59347309--59347343 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
59347299 CGTACTATTC
59347309 AAATAATAACATACTA
1 AAATAATAACATACTA
59347325 AAATATATATACATACTA
1 AAATA-ATA-ACATACTA
59347343 A
1 A
59347344 TCATATGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 3 0.18
18 9 0.53
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAACATACTA
Found at i:59348626 original size:18 final size:19
Alignment explanation
Indices: 59348587--59348627 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
59348577 ATGCATGGCA
*
59348587 ATGTTTATATATAGTATTT
1 ATGTTTATATACAGTATTT
59348606 ATGTTT-TATACA-TATTAT
1 ATGTTTATATACAGTATT-T
59348624 ATGT
1 ATGT
59348628 ATATCAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 4 0.20
18 10 0.50
19 6 0.30
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
ATGTTTATATACAGTATTT
Found at i:59351427 original size:15 final size:14
Alignment explanation
Indices: 59351402--59351435 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
59351392 ATTATATTTA
*
59351402 AAATGTTTTTATAT
1 AAATTTTTTTATAT
59351416 ATAATTTTTTTATAT
1 A-AATTTTTTTATAT
59351431 AAATT
1 AAATT
59351436 AACAATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
AAATTTTTTTATAT
Found at i:59355132 original size:32 final size:32
Alignment explanation
Indices: 59355083--59355145 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
59355073 ATTAGCTCTC
59355083 TTAAATTTTTGAAAATTT-TGTATTAGGCCCCT
1 TTAAATTTTTGAAAATTTAT-TATTAGGCCCCT
* *
59355115 TTAAAGTTTTT-AGAATTTATTATTATGCCCC
1 TTAAA-TTTTTGAAAATTTATTATTAGGCCCC
59355146 AAAATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.48
Consensus pattern (32 bp):
TTAAATTTTTGAAAATTTATTATTAGGCCCCT
Found at i:59363334 original size:24 final size:24
Alignment explanation
Indices: 59363307--59363361 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
59363297 GACTTAATAT
59363307 TTTTGTTGTTTAACGGTTTAATCC
1 TTTTGTTGTTTAACGGTTTAATCC
* *
59363331 TTTTGTTGTTTATCGGTTTAGTCC
1 TTTTGTTGTTTAACGGTTTAATCC
59363355 TTTTGTT
1 TTTTGTT
59363362 TGAAGTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.60
Consensus pattern (24 bp):
TTTTGTTGTTTAACGGTTTAATCC
Found at i:59371089 original size:17 final size:18
Alignment explanation
Indices: 59371051--59371091 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
59371041 GAGTTTTGAC
* *
59371051 TTTACATTATATTTGTGA
1 TTTATATTATATTTATGA
59371069 -TTATATTATATTTAT-A
1 TTTATATTATATTTATGA
59371085 TTTATAT
1 TTTATAT
59371092 ATTTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (18 bp):
TTTATATTATATTTATGA
Found at i:59371692 original size:14 final size:14
Alignment explanation
Indices: 59371675--59371739 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
59371665 TACAATATCT
*
59371675 AAATAATAATAATA
1 AAATAATAACAATA
59371689 AAATAATAACAATA
1 AAATAATAACAATA
* * *
59371703 TAATAGTGA-AATA
1 AAATAATAACAATA
*
59371716 ACAGTAA-AACAATGA
1 A-AATAATAACAAT-A
59371731 AAATAATAA
1 AAATAATAA
59371740 AAACAATAAC
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
13 5 0.13
14 29 0.76
15 4 0.11
ACGTcount: A:0.66, C:0.05, G:0.06, T:0.23
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:59376032 original size:2 final size:2
Alignment explanation
Indices: 59376025--59376056 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
59376015 ATTGGACTGA
59376025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59376057 CTTTTAGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59377236 original size:16 final size:17
Alignment explanation
Indices: 59377211--59377248 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
59377201 TTAGTAAAAA
59377211 TTAA-AATTTAT-CATT
1 TTAATAATTTATACATT
59377226 TTAATAATTTATACATT
1 TTAATAATTTATACATT
59377243 TATAAT
1 T-TAAT
59377249 TTTTAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 5 0.25
18 4 0.20
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATAATTTATACATT
Found at i:59377551 original size:9 final size:9
Alignment explanation
Indices: 59377537--59377614 Score: 56
Period size: 9 Copynumber: 9.0 Consensus size: 9
59377527 TTTTATTTTT
59377537 TATTTTTAA
1 TATTTTTAA
*
59377546 TATTTTAAA
1 TATTTTTAA
59377555 TATTTTTTAA
1 TA-TTTTTAA
*
59377565 -AATTTT--
1 TATTTTTAA
**
59377571 TATTTAAAA
1 TATTTTTAA
59377580 TATTTTTAA
1 TATTTTTAA
*
59377589 AATTTTTAA
1 TATTTTTAA
**
59377598 T-TTTAAAA
1 TATTTTTAA
59377606 TATTTTTAA
1 TATTTTTAA
59377615 AATACTTTTT
Statistics
Matches: 50, Mismatches: 14, Indels: 10
0.68 0.19 0.14
Matches are distributed among these distances:
7 3 0.06
8 10 0.20
9 31 0.62
10 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TATTTTTAA
Found at i:59377574 original size:25 final size:24
Alignment explanation
Indices: 59377546--59377640 Score: 115
Period size: 24 Copynumber: 3.9 Consensus size: 24
59377536 TTATTTTTAA
59377546 TATTTTAAATATTTTTTAAAATTTT
1 TATTTTAAA-ATTTTTTAAAATTTT
59377571 TA-TTTAAAATATTTTTAAAATTTT
1 TATTTTAAAAT-TTTTTAAAATTTT
*
59377595 TAATTTTAAAATATTTTTAAAATACTT
1 T-ATTTTAAAAT-TTTTTAAAAT-TTT
59377622 T-TTTT-AAATTTTTTAAAAT
1 TATTTTAAAATTTTTTAAAAT
59377641 AAATTTTTGG
Statistics
Matches: 65, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
23 12 0.18
24 24 0.37
25 7 0.11
26 19 0.29
27 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTTAAAATTTTTTAAAATTTT
Found at i:59377576 original size:24 final size:24
Alignment explanation
Indices: 59377546--59377640 Score: 115
Period size: 26 Copynumber: 3.9 Consensus size: 24
59377536 TTATTTTTAA
*
59377546 TATTTTAAATATTTTTTAAAATTTT
1 TATTTAAAATA-TTTTTAAAATTTT
59377571 TATTTAAAATATTTTTAAAATTTT
1 TATTTAAAATATTTTTAAAATTTT
59377595 TAATTTTAAAATATTTTTAAAATACTTT
1 T-A-TTTAAAATATTTTTAAAAT--TTT
59377623 T-TTT-AAAT-TTTTTAAAAT
1 TATTTAAAATATTTTTAAAAT
59377641 AAATTTTTGG
Statistics
Matches: 65, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
23 10 0.15
24 18 0.28
25 14 0.22
26 19 0.29
28 4 0.06
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTAAAATATTTTTAAAATTTT
Found at i:59377612 original size:17 final size:16
Alignment explanation
Indices: 59377581--59377614 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59377571 TATTTAAAAT
*
59377581 ATTTTTAAAATTTTTA
1 ATTTTAAAAATTTTTA
59377597 ATTTTAAAATATTTTTA
1 ATTTTAAAA-ATTTTTA
59377614 A
1 A
59377615 AATACTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTAAAAATTTTTA
Found at i:59378318 original size:3 final size:3
Alignment explanation
Indices: 59378312--59378342 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
59378302 AATTTTTTTG
59378312 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
59378343 TACTTGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:59379208 original size:93 final size:93
Alignment explanation
Indices: 59379031--59379243 Score: 234
Period size: 93 Copynumber: 2.3 Consensus size: 93
59379021 TTTATTAGAA
* * *
59379031 AAAAAATCTAAAATTTATTCTAAAAAAGAAAAAAATAAAGGAATTTAAAAATTAAAATGATTTTC
1 AAAAAAT-TAAAATTAATTCTAAAAAAGAAAAAAATAAAGGAAATTAAAAAATAAAATGATTTTC
** *
59379096 CTCTAAAAATTAGTTTTTCCCATTTTACT
65 CTCTAAAAACAAGTGTTTCCCATTTTACT
* * *
59379125 -GAAAATTAAAATTAATTTTAAAAAGGAAAAAAAGTAAAGGAAATTAAAAACATAAAATG-TTTT
1 AAAAAATTAAAATTAATTCTAAAAAAGAAAAAAA-TAAAGGAAATTAAAAA-ATAAAATGATTTT
* * ** *
59379188 -TTTTAAATCCCAAGTGTTTCCCATTTTATT
64 CCTCTAAA-AACAAGTGTTTCCCATTTTACT
*
59379218 AAAAAAATAAAATTAATTCTAAAAAA
1 AAAAAATTAAAATTAATTCTAAAAAA
59379244 ATAAGTAACT
Statistics
Matches: 97, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
92 29 0.30
93 40 0.41
94 28 0.29
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.33
Consensus pattern (93 bp):
AAAAAATTAAAATTAATTCTAAAAAAGAAAAAAATAAAGGAAATTAAAAAATAAAATGATTTTCC
TCTAAAAACAAGTGTTTCCCATTTTACT
Found at i:59383743 original size:14 final size:16
Alignment explanation
Indices: 59383724--59383757 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
59383714 TGGGTGACTT
59383724 AAATAATC-AATT-TC
1 AAATAATCGAATTATC
59383738 AAATAATCGAATTATC
1 AAATAATCGAATTATC
59383754 AAAT
1 AAAT
59383758 CGTAACTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 4 0.22
16 6 0.33
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATAATCGAATTATC
Found at i:59383838 original size:11 final size:11
Alignment explanation
Indices: 59383822--59383852 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
59383812 CTATATATAT
*
59383822 AATTTATCCAA
1 AATTTACCCAA
59383833 AATTTACCCAA
1 AATTTACCCAA
59383844 AATTTACCC
1 AATTTACCC
59383853 TTTGTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (11 bp):
AATTTACCCAA
Found at i:59384113 original size:12 final size:13
Alignment explanation
Indices: 59384098--59384126 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
59384088 TTGTTAAAAA
59384098 TTAATA-TTTTTG
1 TTAATATTTTTTG
59384110 TTAATATTTTTTG
1 TTAATATTTTTTG
59384123 TTAA
1 TTAA
59384127 AAAATGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (13 bp):
TTAATATTTTTTG
Found at i:59388347 original size:18 final size:20
Alignment explanation
Indices: 59388318--59388356 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
59388308 ATTGCACTAA
59388318 ACATTCTTAAATT-ATCTCT
1 ACATTCTTAAATTGATCTCT
59388337 ACATT-TTAAATTGATCTCT
1 ACATTCTTAAATTGATCTCT
59388356 A
1 A
59388357 AACTTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.46
Consensus pattern (20 bp):
ACATTCTTAAATTGATCTCT
Found at i:59391215 original size:2 final size:2
Alignment explanation
Indices: 59391208--59391242 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
59391198 TACGTATTAT
59391208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59391243 TAGATTGTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59391619 original size:18 final size:18
Alignment explanation
Indices: 59391593--59391627 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59391583 CTCTTTATAT
*
59391593 TATACAGAAATATAAAAA
1 TATAAAGAAATATAAAAA
*
59391611 TATAAAGAAGTATAAAA
1 TATAAAGAAATATAAAA
59391628 TACTCTTCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.03, G:0.09, T:0.23
Consensus pattern (18 bp):
TATAAAGAAATATAAAAA
Found at i:59402689 original size:2 final size:2
Alignment explanation
Indices: 59402682--59402718 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
59402672 AAAGACACTA
* *
59402682 AT AT AT AT AT AT AT AT AT AG AT AT AT AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59402719 ATTACCTGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (2 bp):
AT
Found at i:59402697 original size:10 final size:10
Alignment explanation
Indices: 59402682--59402718 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
59402672 AAAGACACTA
*
59402682 ATATATATAT
1 ATATATATAG
59402692 ATATATATAG
1 ATATATATAG
59402702 ATATATATAG
1 ATATATATAG
59402712 ATATATA
1 ATATATA
59402719 ATTACCTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (10 bp):
ATATATATAG
Found at i:59407864 original size:2 final size:2
Alignment explanation
Indices: 59407857--59407884 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59407847 AATAATTGAA
59407857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59407885 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59407999 original size:2 final size:2
Alignment explanation
Indices: 59407992--59408022 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
59407982 NNNAATTAGA
59407992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59408023 AAATAATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59410442 original size:29 final size:29
Alignment explanation
Indices: 59410400--59410458 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
59410390 TCCAAAAAAG
59410400 AAAAGCTATCATCCAAAAGTGATATTATT
1 AAAAGCTATCATCCAAAAGTGATATTATT
59410429 AAAAGCTATCATCCAAAAGTGATATTATT
1 AAAAGCTATCATCCAAAAGTGATATTATT
59410458 A
1 A
59410459 TATTTTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.31
Consensus pattern (29 bp):
AAAAGCTATCATCCAAAAGTGATATTATT
Found at i:59423227 original size:7 final size:7
Alignment explanation
Indices: 59423217--59423241 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
59423207 AAGTCAAAGG
59423217 AAAATTA
1 AAAATTA
59423224 AAAATTA
1 AAAATTA
59423231 AAAATTA
1 AAAATTA
59423238 AAAA
1 AAAA
59423242 ACTTCAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:59432249 original size:232 final size:231
Alignment explanation
Indices: 59431837--59432256 Score: 644
Period size: 232 Copynumber: 1.8 Consensus size: 231
59431827 GAGGAGACCA
* * * *
59431837 CAACAAGCCGAAAGTCACCAGAGATATAACAAAAATCCCATTAAAACATAAGTTAAGAAGGCCGA
1 CAACAAGCCAAAAGTCACCAGAGATATAAAAAAAATCCCATTAAAACAAAAGTTAAGAAGACCGA
* * *
59431902 GAACACGACTAGATATAAGACATAAATCAAGTTTCCTTTGTGTAAGACCTATGTTACTCTGGCTC
66 GAACACGACTACATATAAGACATAAATCAAGTTTCCTTCGTGTAAGACCTATGTTACACTGGCTC
**
59431967 TTCATTTTTCTTTTAAGCACCCAATTCCAACACTTGTGTCCAACGTATATTTGGACATTGGCATG
131 TTCATTTTTCTTTTAAGCACCCAATTCCAACACTCATGTCCAACGTATATTTGGACATTGGCATG
59432032 TACAGCGTATATCTAGACATTGGTTTGCAAGGGGAC
196 TACAGCGTATATCTAGACATTGGTTTGCAAGGGGAC
* *
59432068 CAACAAGGCAAAAGTCACC-GAAGATATAAAAAAAATCCCATTAAAACAAAAAGTTAAGAATACC
1 CAACAAGCCAAAAGTCACCAG-AGATATAAAAAAAATCCCATTAAAAC-AAAAGTTAAGAAGACC
** *
59432132 GAGAACGTGACTACATATAAGACATAAATCAAGTTTCCTTCGTGTAAGACCTATGTTGCACTGGC
64 GAGAACACGACTACATATAAGACATAAATCAAGTTTCCTTCGTGTAAGACCTATGTTACACTGGC
* * ** *
59432197 TCTTCATTTTTCTTTTAAGTACTCAATTCCAACACTCATGTCTGATGTATATTTGGACAT
129 TCTTCATTTTTCTTTTAAGCACCCAATTCCAACACTCATGTCCAACGTATATTTGGACAT
59432257 AAGTTGTCCA
Statistics
Matches: 168, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
230 1 0.01
231 42 0.25
232 125 0.74
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (231 bp):
CAACAAGCCAAAAGTCACCAGAGATATAAAAAAAATCCCATTAAAACAAAAGTTAAGAAGACCGA
GAACACGACTACATATAAGACATAAATCAAGTTTCCTTCGTGTAAGACCTATGTTACACTGGCTC
TTCATTTTTCTTTTAAGCACCCAATTCCAACACTCATGTCCAACGTATATTTGGACATTGGCATG
TACAGCGTATATCTAGACATTGGTTTGCAAGGGGAC
Found at i:59432706 original size:187 final size:187
Alignment explanation
Indices: 59432391--59432768 Score: 686
Period size: 187 Copynumber: 2.0 Consensus size: 187
59432381 CAATTCAATG
*
59432391 AATCACATCCTCAGAGGAGAACATATTGTAAAACAATTCCATTACCATGATAAATGCCAGATATA
1 AATCACATCCTCAGAGGAGAACATATTGTAAAACAATTCCATTACCATGATAAATGCCAAATATA
*
59432456 ACGGATCAAATTCATAGTACAAATAGATATAACAAAGAAAAATGTATCGGTTTAGCATGAGACAT
66 ACGGATCAAATTCATAGTACAAATAGATATAACAAAGAAAAATGGATCGGTTTAGCATGAGACAT
* * *
59432521 GGTTAATAGAACTACATGCATCACGTAATATAGATTAAGAAGGATTTGCAAAACTTA
131 GGTTAATAGAACTAAATGCATCACATAATATAGAGTAAGAAGGATTTGCAAAACTTA
*
59432578 AATCACATCCTCCA-AGGAGAATATATTGTAAAACAATTCCATTACCATGATAAATGCCAAATAT
1 AATCACATCCT-CAGAGGAGAACATATTGTAAAACAATTCCATTACCATGATAAATGCCAAATAT
59432642 AACGGATCAAATTCATAGTACAAATAGATATAACAAAGAAAAATGGATCGGTTTAGCATGAGACA
65 AACGGATCAAATTCATAGTACAAATAGATATAACAAAGAAAAATGGATCGGTTTAGCATGAGACA
59432707 TGGTTAATAGAACTAAATGCATCACATAATATAGAGTAAGAAGGATTTGCAAAACTTA
130 TGGTTAATAGAACTAAATGCATCACATAATATAGAGTAAGAAGGATTTGCAAAACTTA
59432765 AATC
1 AATC
59432769 GATGTAATAA
Statistics
Matches: 184, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
187 182 0.99
188 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (187 bp):
AATCACATCCTCAGAGGAGAACATATTGTAAAACAATTCCATTACCATGATAAATGCCAAATATA
ACGGATCAAATTCATAGTACAAATAGATATAACAAAGAAAAATGGATCGGTTTAGCATGAGACAT
GGTTAATAGAACTAAATGCATCACATAATATAGAGTAAGAAGGATTTGCAAAACTTA
Found at i:59435379 original size:68 final size:68
Alignment explanation
Indices: 59435270--59435405 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
59435260 AATTTTACCT
59435270 GTAATAATTCTATATGTTAATCAATATGATCATAATTTAAATTCTTAAAAAGAACATAAGGGACT
1 GTAATAATTCTATATGTTAATCAATATGATCATAATTTAAATTCTTAAAAAGAACATAAGGGACT
59435335 AAA
66 AAA
59435338 GTAATAATTCTATATGTTAATCAATATGATCATAATTTAAATTCTTAAAAAGAACATAAGGGACT
1 GTAATAATTCTATATGTTAATCAATATGATCATAATTTAAATTCTTAAAAAGAACATAAGGGACT
59435403 AAA
66 AAA
59435406 ATTAGAATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (68 bp):
GTAATAATTCTATATGTTAATCAATATGATCATAATTTAAATTCTTAAAAAGAACATAAGGGACT
AAA
Found at i:59441374 original size:18 final size:18
Alignment explanation
Indices: 59441351--59441407 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
59441341 ATTTAAGTCC
59441351 AATTATTAACACTGTTAA
1 AATTATTAACACTGTTAA
* **
59441369 AATTATTTA-A--G-TCC
1 AATTATTAACACTGTTAA
59441383 AATTATTAACACTGTTAA
1 AATTATTAACACTGTTAA
59441401 AATTATT
1 AATTATT
59441408 TTTTAAATTC
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 9 0.31
15 2 0.07
17 2 0.07
18 16 0.55
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (18 bp):
AATTATTAACACTGTTAA
Found at i:59441380 original size:32 final size:32
Alignment explanation
Indices: 59441341--59441408 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
59441331 AGATTTTAAA
59441341 ATTTAAGTCCAATTATTAACACTGTTAAAATT
1 ATTTAAGTCCAATTATTAACACTGTTAAAATT
59441373 ATTTAAGTCCAATTATTAACACTGTTAAAATT
1 ATTTAAGTCCAATTATTAACACTGTTAAAATT
59441405 ATTT
1 ATTT
59441409 TTTAAATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.43
Consensus pattern (32 bp):
ATTTAAGTCCAATTATTAACACTGTTAAAATT
Found at i:59446722 original size:15 final size:15
Alignment explanation
Indices: 59446702--59446736 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
59446692 AAATTCTCTT
59446702 ATAAATAAATAAATA
1 ATAAATAAATAAATA
* *
59446717 ATAAATTAATATATA
1 ATAAATAAATAAATA
59446732 ATAAA
1 ATAAA
59446737 ATTATACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAATAAATAAATA
Found at i:59447842 original size:37 final size:36
Alignment explanation
Indices: 59447799--59447927 Score: 109
Period size: 37 Copynumber: 3.5 Consensus size: 36
59447789 CCACCTTCAT
* *
59447799 CCGATTTGCTTCCTTGTTTCATTGCTTTTCTTTTCTG
1 CCGATTTGCTTCC-AGTTTCATTTCTTTTCTTTTCTG
* **
59447836 CCGATTTGGTTCCAGTTT-ATTTTCTTACCTTTTCTG
1 CCGATTTGCTTCCAGTTTCA-TTTCTTTTCTTTTCTG
* * * * *
59447872 CCGATTTGCTCCCCCGATTCTTTTCTTTTCTATTTCGG
1 CCGATTTGCT-TCCAGTTTCATTTCTTTTCT-TTTCTG
59447910 CCGATTTGC-TCACAGTTT
1 CCGATTTGCTTC-CAGTTT
59447928 ATGCTGATTT
Statistics
Matches: 71, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
35 1 0.01
36 27 0.38
37 29 0.41
38 14 0.20
ACGTcount: A:0.09, C:0.26, G:0.14, T:0.50
Consensus pattern (36 bp):
CCGATTTGCTTCCAGTTTCATTTCTTTTCTTTTCTG
Found at i:59449080 original size:69 final size:71
Alignment explanation
Indices: 59448954--59449084 Score: 185
Period size: 69 Copynumber: 1.9 Consensus size: 71
59448944 GTTCTGGACA
* * *
59448954 TTGTTTTGATAGTCTGCTGGAAAATGTTATTTTAGTTTGTTAGTGAGTAGAAGATGAAACTGTTG
1 TTGTTTTGATAGTCTGCTGGAAAATGTTACTTGAGTTTGTTAGTCAGTAGAAGATGAAACTGTTG
59449019 TGGCAG
66 TGGCAG
* ** *
59449025 TTGTTTTGATTGTCTGCTGGAACTTGTT-CTTGA-TTTGTTAGTCAGTAGAATATGAAACTG
1 TTGTTTTGATAGTCTGCTGGAAAATGTTACTTGAGTTTGTTAGTCAGTAGAAGATGAAACTG
59449085 GAACTTTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
69 25 0.47
70 3 0.06
71 25 0.47
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.43
Consensus pattern (71 bp):
TTGTTTTGATAGTCTGCTGGAAAATGTTACTTGAGTTTGTTAGTCAGTAGAAGATGAAACTGTTG
TGGCAG
Found at i:59450297 original size:37 final size:37
Alignment explanation
Indices: 59450245--59450333 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 37
59450235 ATCATAAATA
59450245 AATAAACTAATCAATGTTCA-AACTTTGAACATGCTTT
1 AATAAACTAATCAATG-TCAGAACTTTGAACATGCTTT
* * *
59450282 ATTAAACTAATCAATGTGAGGACTTTGAACATGCTTT
1 AATAAACTAATCAATGTCAGAACTTTGAACATGCTTT
*
59450319 AATGAACTAATCAAT
1 AATAAACTAATCAAT
59450334 ATATTTATAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 2 0.04
37 44 0.96
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (37 bp):
AATAAACTAATCAATGTCAGAACTTTGAACATGCTTT
Found at i:59450499 original size:33 final size:33
Alignment explanation
Indices: 59450391--59450506 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
59450381 CAATGTATAC
*
59450391 TTAGATCAATTATACATACACCAACAATTAATT
1 TTAGGTCAATTATACATACACCAACAATTAATT
* * * *
59450424 TTAGGGT-AAATAAAAATAAACCAACAATTAATT
1 TTA-GGTCAATTATACATACACCAACAATTAATT
*
59450457 TGAGGTCAATTATACATACACCAACAATTAATT
1 TTAGGTCAATTATACATACACCAACAATTAATT
59450490 TTAGGTCAATTATACAT
1 TTAGGTCAATTATACAT
59450507 GCTTTATAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 3 0.04
33 65 0.93
34 2 0.03
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.32
Consensus pattern (33 bp):
TTAGGTCAATTATACATACACCAACAATTAATT
Found at i:59454029 original size:18 final size:17
Alignment explanation
Indices: 59454001--59454035 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
59453991 ATTATTAAGA
*
59454001 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
59454018 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
59454036 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:59454412 original size:16 final size:16
Alignment explanation
Indices: 59454391--59454426 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
59454381 AATTTGCTAT
59454391 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
59454407 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
59454423 TACA
1 TACA
59454427 GTGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:59463839 original size:21 final size:21
Alignment explanation
Indices: 59463813--59463855 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
59463803 ATCAGTCTCA
59463813 ACTCCACTCATCCCACAAGTT
1 ACTCCACTCATCCCACAAGTT
59463834 ACTCCACTCATCCCACAAGTT
1 ACTCCACTCATCCCACAAGTT
59463855 A
1 A
59463856 GTCTTGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.42, G:0.05, T:0.23
Consensus pattern (21 bp):
ACTCCACTCATCCCACAAGTT
Found at i:59468751 original size:16 final size:16
Alignment explanation
Indices: 59468730--59468761 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
59468720 TGTTGTACTA
59468730 CGTGTATCTCATGCTG
1 CGTGTATCTCATGCTG
59468746 CGTGTATCTCATGCTG
1 CGTGTATCTCATGCTG
59468762 ATGTATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.25, G:0.25, T:0.38
Consensus pattern (16 bp):
CGTGTATCTCATGCTG
Found at i:59472006 original size:24 final size:24
Alignment explanation
Indices: 59471957--59472006 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
59471947 TCTCAACTAA
* *
59471957 TAATATATTTATTTAGATAATTTT
1 TAATAAATTTATTTAGATAATATT
*
59471981 TAATAAATTTA-TTGGATAATAATT
1 TAATAAATTTATTTAGATAAT-ATT
59472005 TA
1 TA
59472007 TTGATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (24 bp):
TAATAAATTTATTTAGATAATATT
Found at i:59474575 original size:13 final size:13
Alignment explanation
Indices: 59474557--59474582 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59474547 GTAACTTTTT
59474557 AAAATTGAGTGAC
1 AAAATTGAGTGAC
59474570 AAAATTGAGTGAC
1 AAAATTGAGTGAC
59474583 CAAACGTAAA
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:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (13 bp):
AAAATTGAGTGAC
Found at i:59474908 original size:18 final size:19
Alignment explanation
Indices: 59474874--59474909 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
59474864 CATTACATCG
*
59474874 ATATCATTTTTATGATTAC
1 ATATCATTTTTACGATTAC
59474893 ATATCA-TTTTACGATTA
1 ATATCATTTTTACGATTA
59474910 AACTCGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (19 bp):
ATATCATTTTTACGATTAC
Found at i:59487605 original size:130 final size:131
Alignment explanation
Indices: 59487362--59487609 Score: 408
Period size: 130 Copynumber: 1.9 Consensus size: 131
59487352 GTGCTGAAAT
* * * *
59487362 GAAGAGAATTCAGGCCAACTACAATGATATGGGGATACCTAGTAATGGTTATCGTGATGCCGACT
1 GAAGAGAATTCAGGCCAACTACAATGATATGGGGATACCTAGTAATGGTTATCATGATACCAACA
*
59487427 CCCCAAGATCCCCAATCTTAAGAATTTTATGGGTATCGTGAAACCCAAGCCTGGGTAATGGTTAT
66 CCCCAAGATCCCCAATCTCAAGAATTTTATGGGTATCGTGAAACCCAAGCCTGGGTAATGGTTAT
59487492 A
131 A
59487493 GAAGAGAATTCAGGCCAACTACAATGATATGGGGATACCTAGTAAT-GTTATCATGATACCAACA
1 GAAGAGAATTCAGGCCAACTACAATGATATGGGGATACCTAGTAATGGTTATCATGATACCAACA
* * * *
59487557 CCCTAAGATTCCCAATCTCAAGAATTTTGTGGGTATCGTGACACCCAAGCCTG
66 CCCCAAGATCCCCAATCTCAAGAATTTTATGGGTATCGTGAAACCCAAGCCTG
59487610 AGTATCGCGA
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
130 62 0.57
131 46 0.43
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (131 bp):
GAAGAGAATTCAGGCCAACTACAATGATATGGGGATACCTAGTAATGGTTATCATGATACCAACA
CCCCAAGATCCCCAATCTCAAGAATTTTATGGGTATCGTGAAACCCAAGCCTGGGTAATGGTTAT
A
Found at i:59491550 original size:23 final size:23
Alignment explanation
Indices: 59491523--59491598 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
59491513 AGTGTTATTG
*
59491523 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
59491546 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
59491569 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
59491592 ATCAGTG
1 ATCAGTG
59491599 TGGCACTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:59492705 original size:2 final size:2
Alignment explanation
Indices: 59492698--59492730 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59492688 NNNNNNNNNN
59492698 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
59492731 ATAATAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:59494605 original size:31 final size:31
Alignment explanation
Indices: 59494565--59494624 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
59494555 TAAAATTACA
*
59494565 CTCATAAATTTTCT-TAAAATTCTAATTAGATG
1 CTCATAAATTTT-TGAAAAATT-TAATTAGATG
59494597 CTCA-AAATTTTTGAAAAATTTAATTAGA
1 CTCATAAATTTTTGAAAAATTTAATTAGA
59494625 CCCCTTAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 9 0.35
31 13 0.50
32 4 0.15
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.42
Consensus pattern (31 bp):
CTCATAAATTTTTGAAAAATTTAATTAGATG
Found at i:59496782 original size:12 final size:12
Alignment explanation
Indices: 59496765--59496790 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
59496755 TAGGAATCCC
59496765 AAAACTTTTGCA
1 AAAACTTTTGCA
59496777 AAAACTTTTGCA
1 AAAACTTTTGCA
59496789 AA
1 AA
59496791 TTCTAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (12 bp):
AAAACTTTTGCA
Found at i:59496873 original size:30 final size:29
Alignment explanation
Indices: 59496839--59496903 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
59496829 AACCCTCTAA
* *
59496839 AATTACA-CTCATAAATTTTCTTAAAATTTT
1 AATTACAGCTCA-AAATTTT-TGAAAAATTT
*
59496869 AATTAGATGCTCAAAATTTTTGAAAAATTT
1 AATTACA-GCTCAAAATTTTTGAAAAATTT
59496899 AATTA
1 AATTA
59496904 GACCCCTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 19 0.63
31 7 0.23
32 4 0.13
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (29 bp):
AATTACAGCTCAAAATTTTTGAAAAATTT
Found at i:59496904 original size:30 final size:32
Alignment explanation
Indices: 59496846--59496905 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
59496836 TAAAATTACA
* *
59496846 CTCATAAATTTTCTTAAAATTTTAATTAGATG
1 CTCATAAATTTTCTGAAAAATTTAATTAGATG
59496878 CTCA-AAATTTT-TGAAAAATTTAATTAGA
1 CTCATAAATTTTCTGAAAAATTTAATTAGA
59496906 CCCCTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 15 0.58
31 7 0.27
32 4 0.15
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (32 bp):
CTCATAAATTTTCTGAAAAATTTAATTAGATG
Found at i:59498788 original size:100 final size:99
Alignment explanation
Indices: 59498615--59498798 Score: 235
Period size: 100 Copynumber: 1.8 Consensus size: 99
59498605 GTGTGTGTGT
* * * * * *
59498615 ATATATATATTATTTAAGCCCTTAATTGAGCTTGTGTCACCAGTCAAATGGGCACTAACTTGGTT
1 ATATATATATTATTTAAGCCCCTAATTGAGCTTGCGTCACCAGTCAAATGGACACCAACTCGATT
59498680 AGGAAAATTACAAAAATATTATTTTGTATTTAAA
66 AGGAAAATTACAAAAATATTATTTTGTATTTAAA
* * * * * *
59498714 ATATATACTATTATTTAAGCCCCTGATTGAGTTTGCGTCACGAGTCAACTGGACCCCAGCTCGAT
1 ATATATA-TATTATTTAAGCCCCTAATTGAGCTTGCGTCACCAGTCAAATGGACACCAACTCGAT
59498779 TA-GAGAAATTACAAAAATAT
65 TAGGA-AAATTACAAAAATAT
59498799 CCGTTCATAT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
99 9 0.13
100 62 0.87
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (99 bp):
ATATATATATTATTTAAGCCCCTAATTGAGCTTGCGTCACCAGTCAAATGGACACCAACTCGATT
AGGAAAATTACAAAAATATTATTTTGTATTTAAA
Found at i:59498810 original size:100 final size:99
Alignment explanation
Indices: 59498615--59498826 Score: 219
Period size: 100 Copynumber: 2.1 Consensus size: 99
59498605 GTGTGTGTGT
* * * * * *
59498615 ATATATATATTATTTAAGCCCTTAATTGAGCTTGTGTCACCAGTCAAATGGGCACTAACTTGGTT
1 ATATATATATTATTTAAGCCCCTAATTGAGCTTGCGTCACCAGTCAAATGGACACCAACTCGATT
* * **
59498680 AGGAAAATTACAAAAATATTATTTTGTATTTAAA
66 AGGAAAATTACAAAAATATCAGTTCATATTTAAA
* * * * * *
59498714 ATATATACTATTATTTAAGCCCCTGATTGAGTTTGCGTCACGAGTCAACTGGACCCCAGCTCGAT
1 ATATATA-TATTATTTAAGCCCCTAATTGAGCTTGCGTCACCAGTCAAATGGACACCAACTCGAT
* *
59498779 TA-GAGAAATTACAAAAATATCCGTTCATATTTGAA
65 TAGGA-AAATTACAAAAATATCAGTTCATATTTAAA
*
59498814 ATAAATTATATTA
1 ATATA-TATATTA
59498827 CTCGGGAGTA
Statistics
Matches: 91, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
99 9 0.10
100 80 0.88
101 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (99 bp):
ATATATATATTATTTAAGCCCCTAATTGAGCTTGCGTCACCAGTCAAATGGACACCAACTCGATT
AGGAAAATTACAAAAATATCAGTTCATATTTAAA
Found at i:59499808 original size:16 final size:16
Alignment explanation
Indices: 59499764--59499810 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
59499754 GTCACATTCC
59499764 AAGTTTGAATCATTTTA
1 AAGTTTG-ATCATTTTA
*
59499781 AATTTTGATCATTTT-
1 AAGTTTGATCATTTTA
*
59499796 GAGTTTGAGTCATTT
1 AAGTTTGA-TCATTT
59499811 ATAATTTCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 6 0.23
16 14 0.54
17 6 0.23
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (16 bp):
AAGTTTGATCATTTTA
Found at i:59505480 original size:2 final size:2
Alignment explanation
Indices: 59505473--59505520 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
59505463 TACCCAAATC
*
59505473 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59505515 AT AT AT
1 AT AT AT
59505521 TAGGTACACT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59506387 original size:15 final size:17
Alignment explanation
Indices: 59506355--59506395 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
59506345 ACCCTTATTA
*
59506355 TATATATACTAGAGAAT
1 TATATTTACTAGAGAAT
59506372 TATATTTACTA-A-AAT
1 TATATTTACTAGAGAAT
59506387 TATATTTAC
1 TATATTTAC
59506396 AAATAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.52
16 1 0.04
17 10 0.43
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (17 bp):
TATATTTACTAGAGAAT
Found at i:59508585 original size:2 final size:2
Alignment explanation
Indices: 59508578--59508618 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
59508568 TATATGTTTG
59508578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59508619 ACTTTTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59515024 original size:46 final size:45
Alignment explanation
Indices: 59514957--59515219 Score: 301
Period size: 46 Copynumber: 6.2 Consensus size: 45
59514947 TTTGAGTACT
* *
59514957 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
59515003 TCTGATCAAATGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
59515039 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
59515075 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
59515121 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
59515167 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
59515212 TCTGATCA
1 TCTGATCA
59515220 GGGGCAAGTG
Statistics
Matches: 197, Mismatches: 10, Indels: 21
0.86 0.04 0.09
Matches are distributed among these distances:
36 63 0.32
38 1 0.01
39 1 0.01
40 3 0.02
41 1 0.01
42 4 0.02
43 2 0.01
44 1 0.01
45 21 0.11
46 100 0.51
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.30
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:59515038 original size:36 final size:36
Alignment explanation
Indices: 59514993--59515101 Score: 191
Period size: 36 Copynumber: 3.0 Consensus size: 36
59514983 GGTAGCTTTA
* *
59514993 GCTACACTTATCTGATCAAATGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
59515029 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
59515065 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
59515101 G
1 G
59515102 TTAGCCTTAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:59515049 original size:21 final size:20
Alignment explanation
Indices: 59515021--59515086 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
59515011 AATGAAAAAG
59515021 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
* **
59515041 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGCTATACTTATC
59515057 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
59515077 TGATCAAGTG
1 TGAT-AAGTG
59515087 ACAAAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:59518296 original size:28 final size:26
Alignment explanation
Indices: 59518259--59518317 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 26
59518249 TTTTCCATAG
59518259 TTTTAGGGTTAGATTTCTTTTCTTTTCAT
1 TTTTAGGGTTAGA-TT-TTTTCTTTT-AT
59518288 TTTTA-GGTTAGATTTTTTCTTTTAT
1 TTTTAGGGTTAGATTTTTTCTTTTAT
59518313 TTTTA
1 TTTTA
59518318 TATTATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.23
26 9 0.30
27 2 0.07
28 7 0.23
29 5 0.17
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.66
Consensus pattern (26 bp):
TTTTAGGGTTAGATTTTTTCTTTTAT
Found at i:59518315 original size:5 final size:5
Alignment explanation
Indices: 59518315--59518356 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
59518305 TCTTTTATTT
*
59518315 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TCATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT
59518357 TTGTTTTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:59522276 original size:586 final size:587
Alignment explanation
Indices: 59521160--59522338 Score: 2227
Period size: 586 Copynumber: 2.0 Consensus size: 587
59521150 TAAATGTTAG
59521160 TAGGCTATAAATACAAATTTATAAGCCTTTCATTTTAGATTTTGTTGGCTGGTAGTTTCTTTTAG
1 TAGGCTATAAATACAAATTTATAAGCCTTTCATTTTAGATTTTGTTGGCTGGTAGTTTCTTTTAG
59521225 TTTTCCATAGTTTTAGGATTAGATGTCCTTTCTTTTCATTTTTAGATTAGATTTTCTCTTTTCTT
66 TTTTCCATAGTTTTAGGATTAGATGTCCTTTCTTTTCATTTTTAGATTAGATTTTCTCTTTTCTT
59521290 ATTAGACTACTTTTTTTTTCTTTTTTTTTTGTTAAAGAATCTTGTAAATGAAGATGGATTAAACC
131 ATTAGACTACTTTTTTTTTC---TTTTTTTGTTAAAGAATCTTGTAAATGAAGATGGATTAAACC
59521355 TTTGGGTGTCATTGGTTCCACATCTAAATGAGCATTTCATACCCTTCTCTTTATATTGTGCATAT
193 TTTGGGTGTCATTGGTTCCACATCTAAATGAGCATTTCATACCCTTCTCTTTATATTGTGCATAT
59521420 CAATTGTTCGATGAAATGCCTATTTGGGTGCTAAGTTTTATCAATGCAAAATTCTTTGATGGTTG
258 CAATTGTTCGATGAAATGCCTATTTGGGTGCTAAGTTTTATCAATGCAAAATTCTTTGATGGTTG
* *
59521485 GTTGATTTATTATTTGTTATTTTAAGTTAATGTTTATGCTTGATTAATTGGTTGTTTGATTATAT
323 GTTGATTTATTATTTATTATTTTAAGTTAATGTTTATGCTTGATTAATTGGTTGTTTGATTACAT
*
59521550 TGAAATGCTTAATAAACTAGATTTGACGCCTTTAGTGAAAAATCTAGATAAATGAGACCGAGAGG
388 TGAAATGCTTAATAAACTAGAATTGACGCCTTTAGTGAAAAATCTAGATAAATGAGACCGAGAGG
59521615 AGAGTTTATCATTAGATAGTTCGATAAAATTATGCCAAATAGTGAAACCGAAAGGAGATCTATAT
453 AGAGTTTATCATTAGATAGTTCGATAAAATTATGCCAAATAGTGAAACCGAAAGGAGATCTATAT
*
59521680 GCCTACGTGATACCGAGAGGAGAGCTTAGGAGGTCTCTTTTAGTTTAAGATGAGACCAATAGGAG
518 GCCTACGTGATACCGAGAGGAGAGCTTAGGAGGTATCTTTTAGTTTAAGATGAGACCAATAGGAG
59521745 ATTTC
583 ATTTC
59521750 TAGGCTATAAATACAAATTTATAAGCCTTTCATTTTAGATTTTGTTGGCTGGTAGTTTCTTTTAG
1 TAGGCTATAAATACAAATTTATAAGCCTTTCATTTTAGATTTTGTTGGCTGGTAGTTTCTTTTAG
59521815 TTTTCCATAGTTTTAGGATTAGATGTCCTTTCTTTTCATTTTTAGATTAGATTTTCTCTTTTCTT
66 TTTTCCATAGTTTTAGGATTAGATGTCCTTTCTTTTCATTTTTAGATTAGATTTTCTCTTTTCTT
59521880 ATTAGACTACTTTTTTTTTC-TTTTTTGTTAAAGAATCTTGTAAATGAAGATGGATTAAACCTTT
131 ATTAGACTACTTTTTTTTTCTTTTTTTGTTAAAGAATCTTGTAAATGAAGATGGATTAAACCTTT
59521944 GGGTGTCATTGGTTCCACATCTAAATGAGCATTTCATACCCTTCTCTTTATATTGTGCATATCAA
196 GGGTGTCATTGGTTCCACATCTAAATGAGCATTTCATACCCTTCTCTTTATATTGTGCATATCAA
* * *
59522009 TTGTTCGATGAAATGCCTATTTTGGTGCTAAGTTTTATCAATGCTAAATTGTTTGATGGTTGGTT
261 TTGTTCGATGAAATGCCTATTTGGGTGCTAAGTTTTATCAATGCAAAATTCTTTGATGGTTGGTT
*
59522074 GATTTATTATTTATTATTTTAAGTTAATGTTTGTGCTTGATTAATTGGTTGTTTGATTACATTGA
326 GATTTATTATTTATTATTTTAAGTTAATGTTTATGCTTGATTAATTGGTTGTTTGATTACATTGA
59522139 AATGCTTAATAAACTAGAATTGACGCCTTTAGTGAAAAATCTAGATAAATGAGACCGAGAGGAGA
391 AATGCTTAATAAACTAGAATTGACGCCTTTAGTGAAAAATCTAGATAAATGAGACCGAGAGGAGA
*
59522204 GTTTATCATTAGATAGTTCGATAAAATTGTGCCAAATAGT-AAGACCGAAAGGAGATCTATATGC
456 GTTTATCATTAGATAGTTCGATAAAATTATGCCAAATAGTGAA-ACCGAAAGGAGATCTATATGC
59522268 CTACGTGATACCGAGAGGAGAGCTTAGGAGGTATCTTTTAGTTTAAGATGAGACCAATAGGAGAT
520 CTACGTGATACCGAGAGGAGAGCTTAGGAGGTATCTTTTAGTTTAAGATGAGACCAATAGGAGAT
59522333 TTC
585 TTC
59522336 TAG
1 TAG
59522339 CTAAAAGTGG
Statistics
Matches: 579, Mismatches: 9, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
585 2 0.00
586 427 0.74
590 150 0.26
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (587 bp):
TAGGCTATAAATACAAATTTATAAGCCTTTCATTTTAGATTTTGTTGGCTGGTAGTTTCTTTTAG
TTTTCCATAGTTTTAGGATTAGATGTCCTTTCTTTTCATTTTTAGATTAGATTTTCTCTTTTCTT
ATTAGACTACTTTTTTTTTCTTTTTTTGTTAAAGAATCTTGTAAATGAAGATGGATTAAACCTTT
GGGTGTCATTGGTTCCACATCTAAATGAGCATTTCATACCCTTCTCTTTATATTGTGCATATCAA
TTGTTCGATGAAATGCCTATTTGGGTGCTAAGTTTTATCAATGCAAAATTCTTTGATGGTTGGTT
GATTTATTATTTATTATTTTAAGTTAATGTTTATGCTTGATTAATTGGTTGTTTGATTACATTGA
AATGCTTAATAAACTAGAATTGACGCCTTTAGTGAAAAATCTAGATAAATGAGACCGAGAGGAGA
GTTTATCATTAGATAGTTCGATAAAATTATGCCAAATAGTGAAACCGAAAGGAGATCTATATGCC
TACGTGATACCGAGAGGAGAGCTTAGGAGGTATCTTTTAGTTTAAGATGAGACCAATAGGAGATT
TC
Found at i:59530432 original size:90 final size:90
Alignment explanation
Indices: 59530228--59530435 Score: 215
Period size: 90 Copynumber: 2.3 Consensus size: 90
59530218 GATAGTTTAT
* * * *
59530228 CTACAAACACTAGTGGTAT-ATCCACAAAATTTATTGGCAGCCTTGATCTACAAACCCATTGCGT
1 CTAC-AACACTTGTGGT-TCATCCACAAAATTTATTGACAGCCTTCATCTACAAACCCATTGCGA
*
59530292 ATTCACAAACACTGGCAGCGTATTAAC
64 ATTCACAAACACTGGCAGCCTATTAAC
* * * * * * * * ** *
59530319 TTGCAACA-TTGGTAGCTCGTCCACAATATTTATTGACAGCTTTCATCTGCAAACCTGTTGTGAA
1 CTACAACACTT-GTGGTTCATCCACAAAATTTATTGACAGCCTTCATCTACAAACCCATTGCGAA
59530383 TTCAC-AACTACTGGCAGCCTATTAAC
65 TTCACAAAC-ACTGGCAGCCTATTAAC
59530409 CTACAACACTTGTGGTTCATCCACAAA
1 CTACAACACTTGTGGTTCATCCACAAA
59530436 CTCGAGTGTC
Statistics
Matches: 91, Mismatches: 22, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
89 5 0.05
90 82 0.90
91 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (90 bp):
CTACAACACTTGTGGTTCATCCACAAAATTTATTGACAGCCTTCATCTACAAACCCATTGCGAAT
TCACAAACACTGGCAGCCTATTAAC
Found at i:59532953 original size:28 final size:28
Alignment explanation
Indices: 59532913--59532973 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
59532903 TATAGTAATT
*
59532913 AAAAACATGTTATTTAAAAAATAATTAA
1 AAAAACATATTATTTAAAAAATAATTAA
*
59532941 AAAAACATATTATTTAAAAACTAATTAA
1 AAAAACATATTATTTAAAAAATAATTAA
59532969 AAAAA
1 AAAAA
59532974 TTAAACGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAAACATATTATTTAAAAAATAATTAA
Found at i:59535100 original size:21 final size:21
Alignment explanation
Indices: 59535076--59535115 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
59535066 TGATGAAATA
*
59535076 TATTTAAA-ATTTAAATATTTT
1 TATTCAAATATTT-AATATTTT
59535097 TATTCAAATATTTAATATT
1 TATTCAAATATTTAATATT
59535116 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTCAAATATTTAATATTTT
Found at i:59535541 original size:22 final size:25
Alignment explanation
Indices: 59535516--59535568 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
59535506 ATATTACTTA
*
59535516 AAATTAATT-AT-AATATATA-ATT
1 AAATTAATTGATAAATATAAATATT
*
59535538 AAATTATTTGATAAATATAAATATT
1 AAATTAATTGATAAATATAAATATT
59535563 AAATTA
1 AAATTA
59535569 TAGAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.31
23 2 0.08
24 7 0.27
25 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
AAATTAATTGATAAATATAAATATT
Found at i:59539237 original size:2 final size:2
Alignment explanation
Indices: 59539230--59539261 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
59539220 TTAAGCACTA
59539230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59539262 CAAATTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59539713 original size:20 final size:21
Alignment explanation
Indices: 59539679--59539733 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
59539669 ACAAATAATT
59539679 TAAAAATTATAAAATA-TTCAA
1 TAAAAATTATAAAATAGTTC-A
59539700 TAAAAATTAT-AAATAGTTCA
1 TAAAAATTATAAAATAGTTCA
* *
59539720 TAAAATTTCTAAAA
1 TAAAAATTATAAAA
59539734 AATTAGCACG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (21 bp):
TAAAAATTATAAAATAGTTCA
Found at i:59545187 original size:18 final size:19
Alignment explanation
Indices: 59545152--59545197 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
59545142 AATTAAATTC
*
59545152 TAGATTTGTTTTTAC-TT-T
1 TAGATTT-TATTTACTTTGT
59545170 TAGATTTTATTTATCTTTGT
1 TAGATTTTATTTA-CTTTGT
59545190 TAGATTTT
1 TAGATTTT
59545198 GCCTTTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.21
18 8 0.33
19 2 0.08
20 9 0.38
ACGTcount: A:0.20, C:0.04, G:0.11, T:0.65
Consensus pattern (19 bp):
TAGATTTTATTTACTTTGT
Found at i:59548688 original size:2 final size:2
Alignment explanation
Indices: 59548683--59548709 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59548673 TATGATTTTA
59548683 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
59548710 CAAGAACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59571485 original size:17 final size:17
Alignment explanation
Indices: 59571465--59571510 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
59571455 CTAAATATAT
*
59571465 AATATTACTCTAATGTA
1 AATATTACTATAATGTA
** *
59571482 AATATTAAAATAATGTT
1 AATATTACTATAATGTA
59571499 AATATTACTATA
1 AATATTACTATA
59571511 TAAAATAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (17 bp):
AATATTACTATAATGTA
Found at i:59581230 original size:9 final size:9
Alignment explanation
Indices: 59581216--59581467 Score: 224
Period size: 9 Copynumber: 30.3 Consensus size: 9
59581206 AATTTATGTA
59581216 TTATGTAAG
1 TTATGTAAG
59581225 TTATGTAAG
1 TTATGTAAG
*
59581234 TTGTGT-A-
1 TTATGTAAG
59581241 TTATGTAAG
1 TTATGTAAG
59581250 TTATGT-A-
1 TTATGTAAG
59581257 TTATGTAAG
1 TTATGTAAG
59581266 TTATGTAAG
1 TTATGTAAG
*
59581275 TTGTGT-A-
1 TTATGTAAG
*
59581282 TTACGTAAG
1 TTATGTAAG
59581291 TTATGT-A-
1 TTATGTAAG
*
59581298 TTACGTAAG
1 TTATGTAAG
* *
59581307 TTGTG-CA-
1 TTATGTAAG
*
59581314 TTATGAAAG
1 TTATGTAAG
59581323 TTATGTAAG
1 TTATGTAAG
*
59581332 TTGTGT-A-
1 TTATGTAAG
59581339 TTATGTAAG
1 TTATGTAAG
59581348 TTATGTAAG
1 TTATGTAAG
59581357 TTATGT-A-
1 TTATGTAAG
59581364 TTATGTAAG
1 TTATGTAAG
59581373 TTATGTAAG
1 TTATGTAAG
*
59581382 TTGTGT-A-
1 TTATGTAAG
*
59581389 TTACGTAAG
1 TTATGTAAG
59581398 TTATGT-A-
1 TTATGTAAG
59581405 TTATGTAAG
1 TTATGTAAG
*
59581414 TTGTGT-A-
1 TTATGTAAG
*
59581421 TTA--TAGGG
1 TTATGTA-AG
59581429 TTATGTAAG
1 TTATGTAAG
59581438 TTATGTAAG
1 TTATGTAAG
59581447 TTATGTAAG
1 TTATGTAAG
*
59581456 TTGTGTAAG
1 TTATGTAAG
59581465 TTA
1 TTA
59581468 AGCATTATGT
Statistics
Matches: 195, Mismatches: 25, Indels: 46
0.73 0.09 0.17
Matches are distributed among these distances:
5 1 0.01
7 47 0.24
8 22 0.11
9 123 0.63
10 2 0.01
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:59581230 original size:16 final size:16
Alignment explanation
Indices: 59581225--59581495 Score: 191
Period size: 16 Copynumber: 17.5 Consensus size: 16
59581215 ATTATGTAAG
*
59581225 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
59581241 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
59581257 TTATGT-A---A-G--
1 TTATGTAAGTTATGTA
*
59581266 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
*
59581282 TTACGTAAGTTATGTA
1 TTATGTAAGTTATGTA
* * *
59581298 TTACGTAAGTTGTGCA
1 TTATGTAAGTTATGTA
59581314 TTATG-AA---A-G--
1 TTATGTAAGTTATGTA
*
59581323 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
59581339 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
59581356 GTTATGT-A-TTATGTAA
1 -TTATGTAAGTTATGT-A
*
59581372 GTTATGTAAGTTGTGTA
1 -TTATGTAAGTTATGTA
*
59581389 TTACGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
59581405 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
*
59581421 TTA--TAGGGTTATGTAA
1 TTATGTA-AGTTATGT-A
59581437 GTTATGTAAGTTATGTAA
1 -TTATGTAAGTTATGT-A
* * *
59581455 GTTGTGTAAGTTAAGCA
1 -TTATGTAAGTTATGTA
*
59581472 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
*
59581488 TAATGTAA
1 TTATGTAA
59581496 TTAAGTTATG
Statistics
Matches: 206, Mismatches: 26, Indels: 46
0.74 0.09 0.17
Matches are distributed among these distances:
9 11 0.05
10 3 0.01
11 2 0.01
12 1 0.00
14 4 0.02
15 9 0.04
16 133 0.65
17 8 0.04
18 33 0.16
19 2 0.01
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:59581246 original size:25 final size:24
Alignment explanation
Indices: 59581209--59581411 Score: 200
Period size: 25 Copynumber: 8.3 Consensus size: 24
59581199 TGATATAAAT
59581209 TTATGTATTATGTAAGTTATGTAA
1 TTATGTATTATGTAAGTTATGTAA
*
59581233 GTTGTGTATTATGTAAGTTATGT-A
1 -TTATGTATTATGTAAGTTATGTAA
*
59581257 TTATGTAAGTTATGTAAGTTGTGT-A
1 TTATGT-A-TTATGTAAGTTATGTAA
* *
59581282 TTACGTAAGTTATGT-A-TTACGTAA
1 TTATGT-A-TTATGTAAGTTATGTAA
* * *
59581306 GTTGTGCATTATGAAAGTTATGTAA
1 -TTATGTATTATGTAAGTTATGTAA
*
59581331 GTTGTGTATTATGTAAGTTATGTAA
1 -TTATGTATTATGTAAGTTATGTAA
59581356 GTTATGTATTATGTAAGTTATGTAA
1 -TTATGTATTATGTAAGTTATGTAA
* *
59581381 GTTGTGTATTACGTAAGTTATGT-A
1 -TTATGTATTATGTAAGTTATGTAA
59581405 TTATGTA
1 TTATGTA
59581412 AGTTGTGTAT
Statistics
Matches: 155, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
23 20 0.13
24 7 0.05
25 128 0.83
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.47
Consensus pattern (24 bp):
TTATGTATTATGTAAGTTATGTAA
Found at i:59581257 original size:41 final size:41
Alignment explanation
Indices: 59581209--59581495 Score: 286
Period size: 41 Copynumber: 7.0 Consensus size: 41
59581199 TGATATAAAT
*
59581209 TTATGTATTATGTAAGTTATGTAAGTTGTGTATTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAGTTATGTATTATGTAAG
* *
59581250 TTATGTATTATGTAAGTTATGTAAGTTGTGTATTACGTAAG
1 TTATGTATTATGTAAGTTATGTAAGTTATGTATTATGTAAG
* * * *
59581291 TTATGTATTACGTAAGTTGTG-CA-TTATGAAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAGTTATG-TA-TTATGTAAG
*
59581332 TTGTGTATTATGTAAGTTATGTAAGTTATGTATTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAGTTATGTATTATGTAAG
* *
59581373 TTATGTAAGTTGTGT-A-TTACGTAAGTTATGTATTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAGTTATGTATTATGTAAG
* *
59581414 TTGTGTATTA--TAGGGTTATGTAAGTTATGTAAGTTATGTAAG
1 TTATGTATTATGTA-AGTTATGTAAGTTATGT-A-TTATGTAAG
* * *
59581456 TTGTGTA--A-GTTAAGCATTATGTAAGTTGTGTATAATGTAA
1 TTATGTATTATG-TAAG--TTATGTAAGTTATGTATTATGTAA
59581496 TTAAGTTATG
Statistics
Matches: 209, Mismatches: 22, Indels: 30
0.80 0.08 0.11
Matches are distributed among these distances:
37 1 0.00
39 6 0.03
40 18 0.09
41 137 0.66
42 23 0.11
43 24 0.11
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.46
Consensus pattern (41 bp):
TTATGTATTATGTAAGTTATGTAAGTTATGTATTATGTAAG
Found at i:59581668 original size:29 final size:28
Alignment explanation
Indices: 59581622--59581676 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
59581612 GTGTCAAAAA
* * * *
59581622 TTAACTTTAGTTTTTATCCAAATAAATAT
1 TTAACTTGAATTTGTAT-CAAAGAAATAT
59581651 TTAACTTGAATTTGTATCAAAGAAAT
1 TTAACTTGAATTTGTATCAAAGAAAT
59581677 TTGTTTATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 8 0.36
29 14 0.64
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (28 bp):
TTAACTTGAATTTGTATCAAAGAAATAT
Found at i:59584905 original size:2 final size:2
Alignment explanation
Indices: 59584898--59584922 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59584888 GTTACCATAC
59584898 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
59584923 ATGATGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59593179 original size:216 final size:216
Alignment explanation
Indices: 59592837--59593273 Score: 750
Period size: 216 Copynumber: 2.0 Consensus size: 216
59592827 AATAAGAGAT
* *
59592837 TGCAAGGAGGTTGATTTAGAGGGCATGCAATTGGAACCCCATAAGAATCTCTCTCATTTGAAGAT
1 TGCAAAGAGGTTGATTTAGAGGGCATGCAATGGGAACCCCATAAGAATCTCTCTCATTTGAAGAT
59592902 TGATAATATTCCAAAGCTGGTGTCTCTCCCCATTTGGCTTCAACATCTTGTTCAATTGAAAACAT
66 TGATAATATTCCAAAGCTGGTGTCTCTCCCCATTTGGCTTCAACATCTTGTTCAATTGAAAACAT
* * *
59592967 TAAAAATTCATAACTGCATTGGATTGAGGTCACT-CTTTCCTGTGATCCAACATCTCACTTTCGT
131 TAAAAATTCATAACTGCAATGGATTGAGGTCACTGC-TTCCTGTGATCAAACATCTCACTTTCCT
* *
59593031 TGAAGATTTTGAAGTAAAGGAC
195 TGAAAAGTTTGAAGTAAAGGAC
*
59593053 TGCAAAGAGGTTGATTTAGAGGGCATGCAATGGGAACCCCTTAAGAATCTCTCTCATTTGAAGAT
1 TGCAAAGAGGTTGATTTAGAGGGCATGCAATGGGAACCCCATAAGAATCTCTCTCATTTGAAGAT
*
59593118 TGATAATATTCCAAAGCTGGTGTCTCTCCCCATTTGGCTTCAACATCTTGTTCAGTTGAAAACAT
66 TGATAATATTCCAAAGCTGGTGTCTCTCCCCATTTGGCTTCAACATCTTGTTCAATTGAAAACAT
* *
59593183 TAATAATTCATAACTGCAATGGATTGAGGTCACTGCTTCCTGTGTTCAAACATCTCACTTTCCTT
131 TAAAAATTCATAACTGCAATGGATTGAGGTCACTGCTTCCTGTGATCAAACATCTCACTTTCCTT
*
59593248 GAAAAGTTTGCAGTAAAGGAC
196 GAAAAGTTTGAAGTAAAGGAC
59593269 TGCAA
1 TGCAA
59593274 GGAGCTGGAG
Statistics
Matches: 208, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
216 207 1.00
217 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (216 bp):
TGCAAAGAGGTTGATTTAGAGGGCATGCAATGGGAACCCCATAAGAATCTCTCTCATTTGAAGAT
TGATAATATTCCAAAGCTGGTGTCTCTCCCCATTTGGCTTCAACATCTTGTTCAATTGAAAACAT
TAAAAATTCATAACTGCAATGGATTGAGGTCACTGCTTCCTGTGATCAAACATCTCACTTTCCTT
GAAAAGTTTGAAGTAAAGGAC
Found at i:59596773 original size:9 final size:9
Alignment explanation
Indices: 59596759--59597027 Score: 258
Period size: 9 Copynumber: 32.2 Consensus size: 9
59596749 ATGTATTGTA
59596759 TAAGTTATG
1 TAAGTTATG
*
59596768 TAAGTTGTG
1 TAAGTTATG
*
59596777 T-A-TTATA
1 TAAGTTATG
59596784 TAAGTTATG
1 TAAGTTATG
59596793 TAAGTTATG
1 TAAGTTATG
59596802 T-A-TTATG
1 TAAGTTATG
59596809 TAAGTTATG
1 TAAGTTATG
*
59596818 TAAGTTGTG
1 TAAGTTATG
*
59596827 T-A-TTACG
1 TAAGTTATG
59596834 TAAGTTATG
1 TAAGTTATG
59596843 T-A-TTATG
1 TAAGTTATG
*
59596850 TAAGTTGTG
1 TAAGTTATG
59596859 T-A-TTATG
1 TAAGTTATG
*
59596866 AAAGTTATG
1 TAAGTTATG
*
59596875 TAAGTTGTG
1 TAAGTTATG
59596884 T-A-TTATG
1 TAAGTTATG
59596891 TAAGTTATG
1 TAAGTTATG
59596900 TAAGTTATG
1 TAAGTTATG
59596909 T-A-TTATG
1 TAAGTTATG
*
59596916 AAAGTTATG
1 TAAGTTATG
*
59596925 TAAGTTGTG
1 TAAGTTATG
59596934 T-A-TTATG
1 TAAGTTATG
59596941 TAAGTTATG
1 TAAGTTATG
*
59596950 TAAGTTGTG
1 TAAGTTATG
59596959 T-A-TTA--
1 TAAGTTATG
*
59596964 TAGGGTTATG
1 TA-AGTTATG
59596974 TAAGTTATG
1 TAAGTTATG
59596983 TAAGTTATG
1 TAAGTTATG
*
59596992 TAAGTTGTG
1 TAAGTTATG
59597001 T-A-TTATG
1 TAAGTTATG
59597008 TAAGTTATG
1 TAAGTTATG
*
59597017 TAAGTTGTG
1 TAAGTTATG
59597026 TA
1 TA
59597028 TAATGTAATT
Statistics
Matches: 212, Mismatches: 25, Indels: 46
0.75 0.09 0.16
Matches are distributed among these distances:
5 1 0.00
7 46 0.22
8 22 0.10
9 141 0.67
10 2 0.01
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:59596782 original size:16 final size:16
Alignment explanation
Indices: 59596763--59597018 Score: 196
Period size: 16 Copynumber: 16.0 Consensus size: 16
59596753 ATTGTATAAG
*
59596763 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
*
59596779 TTATATAAGTTATGTAA
1 TTATGTAAGTTATGT-A
59596796 GTTATGT-A-TTATGTAA
1 -TTATGTAAGTTATGT-A
*
59596812 GTTATGTAAGTTGTGTA
1 -TTATGTAAGTTATGTA
*
59596829 TTACGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
59596845 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
59596861 TTATG-AA---A-G--
1 TTATGTAAGTTATGTA
*
59596870 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
59596886 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
*
59596903 GTTATGT-A-TTATGAAA
1 -TTATGTAAGTTATG-TA
*
59596919 GTTATGTAAGTTGTGTA
1 -TTATGTAAGTTATGTA
59596936 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
* **
59596953 GTTGTGT-A-TTATAGGG
1 -TTATGTAAGTTAT-GTA
59596969 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
*
59596986 GTTATGTAAGTTGTGTA
1 -TTATGTAAGTTATGTA
59597003 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
59597019 AGTTGTGTAT
Statistics
Matches: 194, Mismatches: 23, Indels: 46
0.74 0.09 0.17
Matches are distributed among these distances:
9 5 0.03
10 2 0.01
11 1 0.01
14 1 0.01
15 7 0.04
16 123 0.63
17 16 0.08
18 39 0.20
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:59596785 original size:25 final size:25
Alignment explanation
Indices: 59596750--59596844 Score: 145
Period size: 25 Copynumber: 3.8 Consensus size: 25
59596740 TATAAATTTA
*
59596750 TGTATTGTATAAGTTATGTAAGTTG
1 TGTATTATATAAGTTATGTAAGTTG
*
59596775 TGTATTATATAAGTTATGTAAGTTA
1 TGTATTATATAAGTTATGTAAGTTG
*
59596800 TGTATTATGTAAGTTATGTAAGTTG
1 TGTATTATATAAGTTATGTAAGTTG
**
59596825 TGTATTACGTAAGTTATGTA
1 TGTATTATATAAGTTATGTA
59596845 TTATGTAAGT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (25 bp):
TGTATTATATAAGTTATGTAAGTTG
Found at i:59596874 original size:25 final size:25
Alignment explanation
Indices: 59596845--59597002 Score: 219
Period size: 25 Copynumber: 6.3 Consensus size: 25
59596835 AAGTTATGTA
59596845 TTATGTAAGTTGTGTATTATGAAAG
1 TTATGTAAGTTGTGTATTATGAAAG
*
59596870 TTATGTAAGTTGTGTATTATGTAAG
1 TTATGTAAGTTGTGTATTATGAAAG
*
59596895 TTATGTAAGTTATGTATTATGAAAG
1 TTATGTAAGTTGTGTATTATGAAAG
*
59596920 TTATGTAAGTTGTGTATTATGTAAG
1 TTATGTAAGTTGTGTATTATGAAAG
**
59596945 TTATGTAAGTTGTGTATTAT-AGGG
1 TTATGTAAGTTGTGTATTATGAAAG
* *
59596969 TTATGTAAGTTATGTAAGTTATGTAAG
1 TTATGTAAGTTGTGT-A-TTATGAAAG
*
59596996 TTGTGTA
1 TTATGTA
59597003 TTATGTAAGT
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.13
25 91 0.78
26 4 0.03
27 7 0.06
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (25 bp):
TTATGTAAGTTGTGTATTATGAAAG
Found at i:59596989 original size:67 final size:65
Alignment explanation
Indices: 59596903--59597028 Score: 225
Period size: 67 Copynumber: 1.9 Consensus size: 65
59596893 AGTTATGTAA
59596903 GTTATGTATTATGAAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTATTATAGG
1 GTTATGTATTATGAAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTATTATAGG
*
59596968 GTTATGTAAGTTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTAT
1 GTTATGT-A-TTATGAAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTAT
59597029 AATGTAATTA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 7 0.12
66 1 0.02
67 50 0.86
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.47
Consensus pattern (65 bp):
GTTATGTATTATGAAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTATTATAGG
Done.