Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 83 of 128
Found at i:27319635 original size:23 final size:24
Alignment explanation
Indices: 27319596--27319649 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
27319586 TTATGGACTG
27319596 TTTTTA-TTGGACCTTTAATATTAT
1 TTTTTATTTGGA-CTTTAATATTAT
* *
27319620 TTTTTATTTGGA-TTTATTTTTAT
1 TTTTTATTTGGACTTTAATATTAT
*
27319643 TTATTAT
1 TTTTTAT
27319650 ATTTTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 15 0.58
24 6 0.23
25 5 0.19
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (24 bp):
TTTTTATTTGGACTTTAATATTAT
Found at i:27319636 original size:17 final size:16
Alignment explanation
Indices: 27319616--27319671 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
27319606 ACCTTTAATA
27319616 TTATTTTTTATTTGGAT
1 TTATTTTTTATTT-GAT
27319633 TTA-TTTTTATTT-AT
1 TTATTTTTTATTTGAT
27319647 TATATTTTTTATTTG-T
1 T-TATTTTTTATTTGAT
*
27319663 TTGTTTTTT
1 TTATTTTTT
27319672 TGAAATGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 3 0.09
15 9 0.26
16 20 0.57
17 3 0.09
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (16 bp):
TTATTTTTTATTTGAT
Found at i:27320111 original size:43 final size:44
Alignment explanation
Indices: 27320057--27320598 Score: 321
Period size: 43 Copynumber: 12.3 Consensus size: 44
27320047 TCGTCTACTG
* * *
27320057 CTGCTCAGGGAGGCAAGGCTGGTGTCTTT-GATCTGCTCTACTA
1 CTGCTTAGGGAGACAAGGCTGGTGTCTTTCGATCTGCTCCACTA
* * * * * * * * * *
27320100 CTGCTTAGGGAGATAA-GATATGTAATTTTTCAACCTACTCCATTG
1 CTGCTTAGGGAGACAAGGCT-GGT-GTCTTTCGATCTGCTCCACTA
* * * *
27320145 TTGCTGAGGGAGAGAAGGCTGGGGTCTTT-GATCTGCTCCACTA
1 CTGCTTAGGGAGACAAGGCTGGTGTCTTTCGATCTGCTCCACTA
* ** * * * * * * *
27320188 CTGCTTAGGGAGATAATATCTGTATTTTTTTTCAACCTACTCCACTG
1 CTGCTTAGGGAGACAA-GGCTG--GTGTCTTTCGATCTGCTCCACTA
* * *
27320235 CTGCTCAGGGAGACAAGGCTGGGGT-TTTCTATCTGCTCCACTA
1 CTGCTTAGGGAGACAAGGCTGGTGTCTTTCGATCTGCTCCACTA
* * * * * * * *
27320278 CTGCTTAGGGAGATAAGATCTGTATTTATTTCAACCTACTCCACTA
1 CTGCTTAGGGAGACAAG-GCTG-GTGTCTTTCGATCTGCTCCACTA
* *
27320324 CTGCTCAGGAAGACAAGGCTGG-GTC-TTCGATCTGCTCCACTA
1 CTGCTTAGGGAGACAAGGCTGGTGTCTTTCGATCTGCTCCACTA
*
27320366 CTGCTTAGGGAGACAAGGCTGGGGTC-TTCGATCTGCTCCACTA
1 CTGCTTAGGGAGACAAGGCTGGTGTCTTTCGATCTGCTCCACTA
* * * * * * * * *
27320409 CTGCCTAGGGAGATAAGATCTGTATTTATTTCAACCTACTCCACTA
1 CTGCTTAGGGAGACAAG-GCTG-GTGTCTTTCGATCTGCTCCACTA
* *
27320455 CTGCTCAGGAAGACAAGGCTGG-GTC-TTCGATCTGCTCCACTA
1 CTGCTTAGGGAGACAAGGCTGGTGTCTTTCGATCTGCTCCACTA
* * * * * * * * *
27320497 CTGCTTAGGGAGATAAGATCTGTATTTATTTCAACCTACTCCACTG
1 CTGCTTAGGGAGACAAG-GCTG-GTGTCTTTCGATCTGCTCCACTA
* * * * *
27320543 CTACTTAGGGAGACAAGGATGGGGTC-TTCAATTTGCTCCACTA
1 CTGCTTAGGGAGACAAGGCTGGTGTCTTTCGATCTGCTCCACTA
27320586 CTGCTTAGGGAGA
1 CTGCTTAGGGAGA
27320599 TAAGATCTGT
Statistics
Matches: 364, Mismatches: 116, Indels: 38
0.70 0.22 0.07
Matches are distributed among these distances:
42 64 0.18
43 131 0.36
44 19 0.05
45 33 0.09
46 93 0.26
47 24 0.07
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (44 bp):
CTGCTTAGGGAGACAAGGCTGGTGTCTTTCGATCTGCTCCACTA
Found at i:27320172 original size:88 final size:88
Alignment explanation
Indices: 27320053--27320378 Score: 476
Period size: 88 Copynumber: 3.7 Consensus size: 88
27320043 CGCTTCGTCT
* * *
27320053 ACTGCTGCTCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTCTACTACTGCTTAGGGAGATAAGA
1 ACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGA
* *
27320118 TATGTAATTTTTCAACCTACTCC
66 TCTGTATTTTTTCAACCTACTCC
* * * * *
27320141 ATTGTTGCTGAGGGAGAGAAGGCTGGGGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAATA
1 ACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGA
27320206 TCTGTATTTTTTTTCAACCTACTCC
66 TCTGTA--TTTTTTCAACCTACTCC
*
27320231 ACTGCTGCTCAGGGAGACAAGGCTGGGGT-TTTCTATCTGCTCCACTACTGCTTAGGGAGATAAG
1 ACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTT-GATCTGCTCCACTACTGCTTAGGGAGATAAG
27320295 ATCTGTATTTATTTCAACCTACTCC
65 ATCTGTATTT-TTTCAACCTACTCC
* * *
27320320 ACTACTGCTCAGGAAGACAAGGCT-GGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 ACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTTGATCTGCTCCACTACTGCTTAGGGAGA
27320379 CAAGGCTGGG
Statistics
Matches: 213, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
88 95 0.45
89 41 0.19
90 77 0.36
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (88 bp):
ACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGA
TCTGTATTTTTTCAACCTACTCC
Found at i:27320350 original size:178 final size:178
Alignment explanation
Indices: 27320053--27320378 Score: 503
Period size: 178 Copynumber: 1.8 Consensus size: 178
27320043 CGCTTCGTCT
* * *
27320053 ACTGCTGCTCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTCTACTACTGCTTAGGGAGATAAGA
1 ACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGA
* ** * * * *
27320118 TATGTAATTTTTCAACCTACTCCATTGTTGCTGAGGGAGAGAAGGCTGGGGTCTTTGATCTGCTC
66 TATGTAATTTTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGGTCTTCGATCTGCTC
27320183 CACTACTGCTTAGGGAGATAATATCTGTATTTTTTTTCAACCTACTCC
131 CACTACTGCTTAGGGAGATAATATCTGTATTTTTTTTCAACCTACTCC
*
27320231 ACTGCTGCTCAGGGAGACAAGGCTGGGGT-TTTCTATCTGCTCCACTACTGCTTAGGGAGATAAG
1 ACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTT-GATCTGCTCCACTACTGCTTAGGGAGATAAG
* *
27320295 ATCTGTATTTATTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCT-GGGTCTTCGATCTGC
65 ATATGTAATT-TTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGGTCTTCGATCTGC
27320359 TCCACTACTGCTTAGGGAGA
129 TCCACTACTGCTTAGGGAGA
27320379 CAAGGCTGGG
Statistics
Matches: 133, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
177 3 0.02
178 98 0.74
179 32 0.24
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (178 bp):
ACTGCTGCTCAGGGAGACAAGGCTGGGGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGA
TATGTAATTTTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGGTCTTCGATCTGCTC
CACTACTGCTTAGGGAGATAATATCTGTATTTTTTTTCAACCTACTCC
Found at i:27320376 original size:131 final size:131
Alignment explanation
Indices: 27320227--27320509 Score: 521
Period size: 131 Copynumber: 2.2 Consensus size: 131
27320217 TTTCAACCTA
* * * * *
27320227 CTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTTTTCTATCTGCTCCACTACTGCTTAGGGAGAT
1 CTCCACTACTGCTTAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTACTGCCTAGGGAGAT
27320292 AAGATCTGTATTTATTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGTCTTCGATCT
66 AAGATCTGTATTTATTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGTCTTCGATCT
27320357 G
131 G
27320358 CTCCACTACTGCTTAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTACTGCCTAGGGAGAT
1 CTCCACTACTGCTTAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTACTGCCTAGGGAGAT
27320423 AAGATCTGTATTTATTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGTCTTCGATCT
66 AAGATCTGTATTTATTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGTCTTCGATCT
27320488 G
131 G
27320489 CTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGA
27320510 TAAGATCTGT
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 147 1.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (131 bp):
CTCCACTACTGCTTAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTACTGCCTAGGGAGAT
AAGATCTGTATTTATTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGTCTTCGATCT
G
Found at i:27320508 original size:88 final size:89
Alignment explanation
Indices: 27320358--27320651 Score: 482
Period size: 89 Copynumber: 3.3 Consensus size: 89
27320348 CTTCGATCTG
* * *
27320358 CTCCACTACTGCTTAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTACTGCCTAGGGAGAT
1 CTCCACTACTACTCAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGAT
27320423 AAGATCTGTATTTATTTCAACCTA
66 AAGATCTGTATTTATTTCAACCTA
* *
27320447 CTCCACTACTGCTCAGGAAGACAAGGCT-GGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGAT
1 CTCCACTACTACTCAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGAT
27320511 AAGATCTGTATTTATTTCAACCTA
66 AAGATCTGTATTTATTTCAACCTA
* * * * *
27320535 CTCCACTGCTACTTAGGGAGACAAGGATGGGGTCTTCAATTTGCTCCACTACTGCTTAGGGAGAT
1 CTCCACTACTACTCAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGAT
27320600 AAGATCTGTATTTATTTCAACCTA
66 AAGATCTGTATTTATTTCAACCTA
*
27320624 CTCCACTGCTACTCAGGGAGACAAGGCT
1 CTCCACTACTACTCAGGGAGACAAGGCT
27320652 TTGTGGTTTC
Statistics
Matches: 192, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
88 82 0.43
89 110 0.57
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (89 bp):
CTCCACTACTACTCAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGAT
AAGATCTGTATTTATTTCAACCTA
Found at i:27320590 original size:131 final size:130
Alignment explanation
Indices: 27320227--27320559 Score: 360
Period size: 131 Copynumber: 2.5 Consensus size: 130
27320217 TTTCAACCTA
* * * * * * * * * *
27320227 CTCCACTGCTGCTCAGGGAGACAAGGCTGGGGTTTTCTATCTGCTCCACTACTGCTTAGGGAGAT
1 CTCCACTACTGCTTAGGGAGACAAGGCTGAGGTCTTCAACCTACTCCACTACTACCTAGGGAGAC
** *
27320292 AAGATCTGTATTTATTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGTCTTCGATCT
66 AAGA-CTGTAGGTACTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGTCTTCGATCT
27320357 G
130 G
* * * * * *
27320358 CTCCACTACTGCTTAGGGAGACAAGGCTGGGGTCTTCGATCTGCTCCACTACTGCCTAGGGAGAT
1 CTCCACTACTGCTTAGGGAGACAAGGCTGAGGTCTTCAACCTACTCCACTACTACCTAGGGAGAC
** *
27320423 AAGATCTGTATTTATTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGTCTTCGATCT
66 AAGA-CTGTAGGTACTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGTCTTCGATCT
27320488 G
130 G
* * ** * * *
27320489 CTCCACTACTGCTTAGGGAGATAAGATCTGTATTTATTTCAACCTACTCCACTGCTACTTAGGGA
1 CTCCACTACTGCTTAGGGAGACAAG-GCTG-AGGT-CTTCAACCTACTCCACTACTACCTAGGGA
27320554 GACAAG
63 GACAAG
27320560 GATGGGGTCT
Statistics
Matches: 181, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
131 150 0.83
132 3 0.02
133 1 0.01
134 27 0.15
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.29
Consensus pattern (130 bp):
CTCCACTACTGCTTAGGGAGACAAGGCTGAGGTCTTCAACCTACTCCACTACTACCTAGGGAGAC
AAGACTGTAGGTACTTCAACCTACTCCACTACTGCTCAGGAAGACAAGGCTGGGTCTTCGATCTG
Found at i:27320632 original size:43 final size:43
Alignment explanation
Indices: 27320496--27320633 Score: 131
Period size: 43 Copynumber: 3.1 Consensus size: 43
27320486 CTGCTCCACT
27320496 ACTGCTTAGGGAGATAAGATCTGTATTTATTTCAACCTACTCC
1 ACTGCTTAGGGAGATAAGATCTGTATTTATTTCAACCTACTCC
* ** * * *
27320539 ACTGCTACTTAGGGAGACAAGGATGGGGTCTTCAATTTGC-TCC-ACT--
1 ACTG---CTTAGGGAGATAA-GAT-CTGTATT-TATTT-CAACCTACTCC
27320585 ACTGCTTAGGGAGATAAGATCTGTATTTATTTCAACCTACTCC
1 ACTGCTTAGGGAGATAAGATCTGTATTTATTTCAACCTACTCC
27320628 ACTGCT
1 ACTGCT
27320634 ACTCAGGGAG
Statistics
Matches: 72, Mismatches: 12, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
39 1 0.01
40 6 0.08
41 7 0.10
42 3 0.04
43 22 0.31
46 16 0.22
47 3 0.04
48 7 0.10
49 6 0.08
50 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (43 bp):
ACTGCTTAGGGAGATAAGATCTGTATTTATTTCAACCTACTCC
Found at i:27321786 original size:42 final size:42
Alignment explanation
Indices: 27321737--27321850 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
27321727 AGATCGTCAT
* * *
27321737 ATGCCCCAATCTAATCAAAATTTGAACTGCTCAGATCACCTC
1 ATGCCCCATTCTAATCAATATTTGAACCGCTCAGATCACCTC
** * * *
27321779 ATGCCCCATTCTGGTTAATATTTGAGCCGCTCAGATTACCTC
1 ATGCCCCATTCTAATCAATATTTGAACCGCTCAGATCACCTC
* * *
27321821 ATGCCCTATTCCAATCAATATTTGAGCCGC
1 ATGCCCCATTCTAATCAATATTTGAACCGC
27321851 CTTTTTGAGT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (42 bp):
ATGCCCCATTCTAATCAATATTTGAACCGCTCAGATCACCTC
Found at i:27323417 original size:42 final size:42
Alignment explanation
Indices: 27323368--27323481 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
27323358 AGATCGTCAT
* * *
27323368 ATGCCCCAATCTAATCAAAATTTGAACTGCTCAGATCACCTC
1 ATGCCCCATTCTAATCAATATTTGAACCGCTCAGATCACCTC
** * * *
27323410 ATGCCCCATTCTGGTTAATATTTGAGCCGCTCAGATTACCTC
1 ATGCCCCATTCTAATCAATATTTGAACCGCTCAGATCACCTC
* * *
27323452 ATGCCCTATTCCAATCAATATTTGAGCCGC
1 ATGCCCCATTCTAATCAATATTTGAACCGC
27323482 CTTTTTGAGT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (42 bp):
ATGCCCCATTCTAATCAATATTTGAACCGCTCAGATCACCTC
Found at i:27330318 original size:21 final size:21
Alignment explanation
Indices: 27330279--27330318 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27330269 ATTGCTCTAA
* *
27330279 ATTTCTCTTCAATCCATTTCT
1 ATTTCTCCTCAAACCATTTCT
*
27330300 ATTTCTCCTCAAACTATTT
1 ATTTCTCCTCAAACCATTT
27330319 TGACAATTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTCTCCTCAAACCATTTCT
Found at i:27334723 original size:18 final size:19
Alignment explanation
Indices: 27334697--27334745 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
27334687 TTATTAACCG
*
27334697 ATTTGTTTAT-TACTCAAA
1 ATTTATTTATATACTCAAA
*
27334715 ATTTATTTATAATTCTCAAA
1 ATTTATTTAT-ATACTCAAA
27334735 ATTTATTTATA
1 ATTTATTTATA
27334746 ATTTGGCAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 9 0.33
19 1 0.04
20 17 0.63
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTTATTTATATACTCAAA
Found at i:27334734 original size:20 final size:20
Alignment explanation
Indices: 27334709--27334748 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
27334699 TTGTTTATTA
27334709 CTCAAAATTTATTTATAATT
1 CTCAAAATTTATTTATAATT
27334729 CTCAAAATTTATTTATAATT
1 CTCAAAATTTATTTATAATT
27334749 TGGCAGTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
CTCAAAATTTATTTATAATT
Found at i:27341103 original size:11 final size:11
Alignment explanation
Indices: 27341089--27341118 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
27341079 AAAATAAAAA
27341089 TAAAATTATTT
1 TAAAATTATTT
*
27341100 TAAAAGTATTT
1 TAAAATTATTT
27341111 TAAAATTA
1 TAAAATTA
27341119 AAAAATAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:27341132 original size:41 final size:43
Alignment explanation
Indices: 27341059--27341143 Score: 120
Period size: 41 Copynumber: 2.0 Consensus size: 43
27341049 TAAACATTAA
* *
27341059 AAAATTATTTTAAAAATAAAAAAATAAAAATAAAATTAT-TTT
1 AAAAGTATTTTAAAAATAAAAAAATAAAAATAAAAATATATTT
* *
27341101 AAAAGTATTTT-AAAATTAAAAAATAAGAATAAAAATATATTT
1 AAAAGTATTTTAAAAATAAAAAAATAAAAATAAAAATATATTT
27341143 A
1 A
27341144 TTATATTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 24 0.63
42 14 0.37
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (43 bp):
AAAAGTATTTTAAAAATAAAAAAATAAAAATAAAAATATATTT
Found at i:27341665 original size:9 final size:9
Alignment explanation
Indices: 27341653--27341709 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
27341643 AATTTTTAAA
27341653 AATAATTTT
1 AATAATTTT
27341662 AATAATTTT
1 AATAATTTT
* *
27341671 TATACTTTT
1 AATAATTTT
27341680 CAAATAATTTT
1 --AATAATTTT
*
27341691 AATGATTTT
1 AATAATTTT
*
27341700 TA-AATTTT
1 AATAATTTT
27341708 AA
1 AA
27341710 AAAATTAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
8 6 0.16
9 25 0.66
11 7 0.18
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (9 bp):
AATAATTTT
Found at i:27341704 original size:20 final size:20
Alignment explanation
Indices: 27341658--27341704 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
27341648 TTAAAAATAA
*
27341658 TTTT-AATAATTTTTATACT
1 TTTTAAATAATTTTAATACT
*
27341677 TTTCAAATAATTTTAATGA-T
1 TTTTAAATAATTTTAAT-ACT
27341697 TTTTAAAT
1 TTTTAAAT
27341705 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 3 0.13
20 19 0.83
21 1 0.04
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTAAATAATTTTAATACT
Found at i:27342051 original size:19 final size:20
Alignment explanation
Indices: 27342029--27342066 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27342019 AAATATTTTT
27342029 AATATT-ATTAAAAATTTAA
1 AATATTAATTAAAAATTTAA
*
27342048 AATATTAATTAAATATTTA
1 AATATTAATTAAAAATTTA
27342067 TATGTCATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATATTAATTAAAAATTTAA
Found at i:27349143 original size:103 final size:102
Alignment explanation
Indices: 27348902--27349142 Score: 273
Period size: 103 Copynumber: 2.4 Consensus size: 102
27348892 TTTAAAAGTG
* *
27348902 TTTTTTAATTTAAA-ATTTTTTAAAAAATAATATTTTATTTGGTGGAGCCATATAGAATGGCGCC
1 TTTTTTAATCTAAATA-ATTTT-AAAAATAATATTTTATTTGGTGGAGCCATATAGAATGGCGCC
*
27348966 ACCAGTGTATTATGTATATATATATTTTAAAATGTATTA
64 ACCAGTGTATTACGTATATATATATTTTAAAATGTATTA
* ** * *
27349005 TTTTTTAATTTAAATTTTTTTTAAAAATAATATTTTATTTGGTGGAGCCATATAGAATGGTGCCT
1 TTTTTTAATCTAAA-TAATTTTAAAAATAATATTTTATTTGGTGGAGCCATATAGAATGGCGCCA
* *
27349070 CCAGTGTACTGTACG-GT-T-T-T-TTTT-AAATGTGTTA
65 CCAGTGTA-T-TACGTATATATATATTTTAAAATGTATTA
*
27349104 GTTTTTTAATCTAAA-AATTTTAAAAATGATATTTTATTT
1 -TTTTTTAATCTAAATAATTTTAAAAATAATATTTTATTT
27349143 TGGTATGGCT
Statistics
Matches: 123, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
98 21 0.17
99 9 0.07
100 17 0.14
101 1 0.01
102 1 0.01
103 64 0.52
104 7 0.06
105 3 0.02
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (102 bp):
TTTTTTAATCTAAATAATTTTAAAAATAATATTTTATTTGGTGGAGCCATATAGAATGGCGCCAC
CAGTGTATTACGTATATATATATTTTAAAATGTATTA
Found at i:27353659 original size:46 final size:46
Alignment explanation
Indices: 27353592--27353841 Score: 410
Period size: 46 Copynumber: 5.4 Consensus size: 46
27353582 NNNNNNNNNN
* *
27353592 AAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGATGTTTCGGTA
1 AAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTCGGTA
*
27353638 AAGAAAACCACACTGAGTTGTGAAAAGTAGGTATGGTATTTCGGTA
1 AAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTCGGTA
27353684 AAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTCGGTA
1 AAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTCGGTA
* * *
27353730 AAGAAAACCATACTGAGTTATGAAAAGTAGGTGTGGTATTTCAGTA
1 AAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTCGGTA
* *
27353776 AAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTCCGTG
1 AAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTCGGTA
*
27353822 AAGAAAAATCATACTGAGTT
1 AAG-AAAACCATACTGAGTT
27353842 ATAGCAATGT
Statistics
Matches: 191, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
46 176 0.92
47 15 0.08
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (46 bp):
AAGAAAACCATACTGAGTTGTGAAAAGTAGGTATGGTATTTCGGTA
Found at i:27357883 original size:6 final size:6
Alignment explanation
Indices: 27357874--27357907 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
27357864 GAGAAAAAGA
27357874 ATGGTT ATGGTT ATGGTT ATGGTT ATGGTT ATGG
1 ATGGTT ATGGTT ATGGTT ATGGTT ATGGTT ATGG
27357908 GTTGGGTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (6 bp):
ATGGTT
Found at i:27358566 original size:20 final size:20
Alignment explanation
Indices: 27358512--27358569 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
27358502 AAATTATAAA
*
27358512 AATTTTAAGTAAT-TAAAAT
1 AATTTTAACTAATATAAAAT
* **
27358531 AATTTTTACTATATATAATTT
1 AATTTTAACTA-ATATAAAAT
*
27358552 AATTTTAATTAATATAAA
1 AATTTTAACTAATATAAA
27358570 TAAGGAGAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 9 0.30
20 8 0.27
21 13 0.43
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
AATTTTAACTAATATAAAAT
Found at i:27361129 original size:114 final size:114
Alignment explanation
Indices: 27360929--27361264 Score: 507
Period size: 114 Copynumber: 3.0 Consensus size: 114
27360919 CTGGTGTGCT
* *
27360929 CATATT-TCAACTATGAACCAAATGTTTCTTTTATATGTAAAAATATTGCTGCTTTGCTGCTCTA
1 CATATTCT-AACTATGAACCAAATATTTCTTTTACATGTAAAAATATTGCTGCTTTGCTGCTCTA
* * * * **
27360993 ATTTGTTTCTATTAACACGTAAAATGTGGAATCATCATTCAACTTTCTTG
65 ACTTGTTTTTATTAACATGTAAAATGTGGAATCATCATTCAACTTGCCCG
*
27361043 CATATTCTAATTATGAACCAAATATTTCTTTTACATGTAAAAATATTGCTGCTTTGCTGCTCTAA
1 CATATTCTAACTATGAACCAAATATTTCTTTTACATGTAAAAATATTGCTGCTTTGCTGCTCTAA
*
27361108 CTTGTTTTTAGTAACATGTAAAATGTGGAATCATCATTCAACTTGCCCG
66 CTTGTTTTTATTAACATGTAAAATGTGGAATCATCATTCAACTTGCCCG
* *
27361157 CATATTCTAACTATGAACCAAATATTTC--TTACATGTAAAATTATTGCTGCTTTGCTGGTCTAA
1 CATATTCTAACTATGAACCAAATATTTCTTTTACATGTAAAAATATTGCTGCTTTGCTGCTCTAA
* * *
27361220 CTTGTTTTTATTAACATGTAAAATGTGGGATTATCATTGAACTTG
66 CTTGTTTTTATTAACATGTAAAATGTGGAATCATCATTCAACTTG
27361265 GTTCCCCTGT
Statistics
Matches: 204, Mismatches: 17, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
112 74 0.36
114 129 0.63
115 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (114 bp):
CATATTCTAACTATGAACCAAATATTTCTTTTACATGTAAAAATATTGCTGCTTTGCTGCTCTAA
CTTGTTTTTATTAACATGTAAAATGTGGAATCATCATTCAACTTGCCCG
Found at i:27363296 original size:187 final size:187
Alignment explanation
Indices: 27362981--27363354 Score: 748
Period size: 187 Copynumber: 2.0 Consensus size: 187
27362971 TATTTGTTTC
27362981 AATAAACTCTGATTAGTCTAGATTATTTTATTATTATTTGACCTACGAATTTAGCCTATAAATAG
1 AATAAACTCTGATTAGTCTAGATTATTTTATTATTATTTGACCTACGAATTTAGCCTATAAATAG
27363046 GCTCTTTTACAACTTTAGAAAATACACCCATTAGATATTAGAACTCATAACACATTTAGAAAATT
66 GCTCTTTTACAACTTTAGAAAATACACCCATTAGATATTAGAACTCATAACACATTTAGAAAATT
27363111 TTGTGTTTACATTTTGAGGGTTCTTTGTTTTTGGATTTTCAGGTTTTCGAGGTTTAG
131 TTGTGTTTACATTTTGAGGGTTCTTTGTTTTTGGATTTTCAGGTTTTCGAGGTTTAG
27363168 AATAAACTCTGATTAGTCTAGATTATTTTATTATTATTTGACCTACGAATTTAGCCTATAAATAG
1 AATAAACTCTGATTAGTCTAGATTATTTTATTATTATTTGACCTACGAATTTAGCCTATAAATAG
27363233 GCTCTTTTACAACTTTAGAAAATACACCCATTAGATATTAGAACTCATAACACATTTAGAAAATT
66 GCTCTTTTACAACTTTAGAAAATACACCCATTAGATATTAGAACTCATAACACATTTAGAAAATT
27363298 TTGTGTTTACATTTTGAGGGTTCTTTGTTTTTGGATTTTCAGGTTTTCGAGGTTTAG
131 TTGTGTTTACATTTTGAGGGTTCTTTGTTTTTGGATTTTCAGGTTTTCGAGGTTTAG
27363355 TTTTTAACTC
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 187 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (187 bp):
AATAAACTCTGATTAGTCTAGATTATTTTATTATTATTTGACCTACGAATTTAGCCTATAAATAG
GCTCTTTTACAACTTTAGAAAATACACCCATTAGATATTAGAACTCATAACACATTTAGAAAATT
TTGTGTTTACATTTTGAGGGTTCTTTGTTTTTGGATTTTCAGGTTTTCGAGGTTTAG
Found at i:27364218 original size:6 final size:6
Alignment explanation
Indices: 27364209--27364248 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
27364199 GAGAAAGAGA
27364209 ATGGTT ATGGTT ATGGTT ATGGTT ATGGTT ATGGTT ATGG
1 ATGGTT ATGGTT ATGGTT ATGGTT ATGGTT ATGGTT ATGG
27364249 GTTGGGTCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.47
Consensus pattern (6 bp):
ATGGTT
Found at i:27365745 original size:23 final size:22
Alignment explanation
Indices: 27365706--27365749 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
27365696 TAATAAAAAA
27365706 TTAATTTTCAATATTATTTTAT
1 TTAATTTTCAATATTATTTTAT
*
27365728 TTAATATTTCAATTTTATTTTA
1 TTAAT-TTTCAATATTATTTTA
27365750 ATAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (22 bp):
TTAATTTTCAATATTATTTTAT
Found at i:27365760 original size:13 final size:14
Alignment explanation
Indices: 27365744--27365785 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
27365734 TTTCAATTTT
27365744 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
27365757 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
27365772 ATTTTAAATAATAT
1 ATTTT-AATAATAT
27365786 TCTTCATATC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:27365770 original size:16 final size:16
Alignment explanation
Indices: 27365748--27365784 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
27365738 AATTTTATTT
27365748 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
27365765 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
27365780 TAATA
1 TAATA
27365785 TTCTTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:27367599 original size:2 final size:2
Alignment explanation
Indices: 27367586--27367615 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
27367576 TTTATAGGTG
27367586 AT AT AGT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A
27367616 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27367668 original size:2 final size:2
Alignment explanation
Indices: 27367615--27367650 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
27367605 ATATATATAT
27367615 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
27367651 TACGGATTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27376726 original size:12 final size:12
Alignment explanation
Indices: 27376704--27376736 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
27376694 AAAAAACAAT
27376704 TATAT-TATTTA
1 TATATATATTTA
27376715 TATATATATTTA
1 TATATATATTTA
*
27376727 TATTTATATT
1 TATATATATT
27376737 AAATCACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TATATATATTTA
Found at i:27387927 original size:24 final size:24
Alignment explanation
Indices: 27387895--27387942 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
27387885 TCGTATCAGG
27387895 TAATGAAGTTAATCACCTATGCAC
1 TAATGAAGTTAATCACCTATGCAC
27387919 TAATGAAGTTAATCACCTATGCAC
1 TAATGAAGTTAATCACCTATGCAC
27387943 CCAATATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (24 bp):
TAATGAAGTTAATCACCTATGCAC
Found at i:27394959 original size:29 final size:29
Alignment explanation
Indices: 27394916--27394984 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
27394906 TGAAAAAAAT
27394916 CAATTGAGCCACTACACCAAATCTGCACC
1 CAATTGAGCCACTACACCAAATCTGCACC
* *
27394945 CAATTGAGCTC-CTACACTAAATTTGCACC
1 CAATTGAGC-CACTACACCAAATCTGCACC
*
27394974 TAATTGAGCCA
1 CAATTGAGCCA
27394985 ATATCATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.03
29 33 0.94
30 1 0.03
ACGTcount: A:0.33, C:0.32, G:0.12, T:0.23
Consensus pattern (29 bp):
CAATTGAGCCACTACACCAAATCTGCACC
Found at i:27396080 original size:18 final size:19
Alignment explanation
Indices: 27396059--27396107 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
27396049 AGTTTAGACT
27396059 TTTTTTTATAATTTATAA-
1 TTTTTTTATAATTTATAAG
* *
27396077 TTTTTATATTATTTATAAG
1 TTTTTTTATAATTTATAAG
27396096 TTTTTTTTATAA
1 -TTTTTTTATAA
27396108 AATTTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 16 0.64
20 9 0.36
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTTTATAATTTATAAG
Found at i:27398096 original size:6 final size:6
Alignment explanation
Indices: 27398030--27398094 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
27398020 AAACTCTTCC
* * * *
27398030 TCCTCC TCCTCT TCCTCT TCGTCT TCCTCT TCTTCGT TCTGCTCT TCCACT
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTC-T TC--CTCT TCCTCT
*
27398081 TCCTCT TCGTCT TC
1 TCCTCT TCCTCT TC
27398095 GTTATCATCT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
6 40 0.83
7 3 0.06
8 3 0.06
9 2 0.04
ACGTcount: A:0.02, C:0.45, G:0.06, T:0.48
Consensus pattern (6 bp):
TCCTCT
Found at i:27399151 original size:18 final size:19
Alignment explanation
Indices: 27399110--27399151 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
27399100 TGTGGTTGTT
* *
27399110 ATAAATACTTTTTTAATTT
1 ATAAATACTTTTTAAATTG
27399129 A-AAATA-TTTTTAAATTG
1 ATAAATACTTTTTAAATTG
27399146 ATAAAT
1 ATAAAT
27399152 TCTAAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 9 0.45
19 1 0.05
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
ATAAATACTTTTTAAATTG
Found at i:27407683 original size:42 final size:42
Alignment explanation
Indices: 27407570--27407689 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 42
27407560 CTTTCTATGT
* * * * *
27407570 AGCTCTTACGAGCTTCTATTTAACTCATATGAGTTTCCGTTC
1 AGCTTTTACGAGCTTCTGTTTAACTCTTATGGGTTTCCGTTA
* *
27407612 AGCTCTTT-TGAGCTTTTGTTTAACTCTTATGGGTTTCCGTTA
1 AGCT-TTTACGAGCTTCTGTTTAACTCTTATGGGTTTCCGTTA
* *
27407654 AGCTTTTACGAGCTTCTGTTCAACCCTTATGGGTTT
1 AGCTTTTACGAGCTTCTGTTTAACTCTTATGGGTTT
27407690 TTGTTTAGCT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 3 0.05
42 60 0.92
43 2 0.03
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.44
Consensus pattern (42 bp):
AGCTTTTACGAGCTTCTGTTTAACTCTTATGGGTTTCCGTTA
Found at i:27407709 original size:42 final size:42
Alignment explanation
Indices: 27407570--27407715 Score: 121
Period size: 42 Copynumber: 3.5 Consensus size: 42
27407560 CTTTCTATGT
* * * * * * * *
27407570 AGCTCTTACGAGCTTCTATTTAACTCATATGAGTTTCCGTTC
1 AGCTCTCATGAGCTTCTGTTCAACCCTTATGGGTTTCCGTTA
** * * *
27407612 AGCTCTTTTGAGCTTTTGTTTAACTCTTATGGGTTTCCGTTA
1 AGCTCTCATGAGCTTCTGTTCAACCCTTATGGGTTTCCGTTA
* * * ** *
27407654 AGCTTTTACGAGCTTCTGTTCAACCCTTATGGGTTTTTGTTT
1 AGCTCTCATGAGCTTCTGTTCAACCCTTATGGGTTTCCGTTA
27407696 AGCTCTCATGAGCTTCTGTT
1 AGCTCTCATGAGCTTCTGTT
27407716 AACGATGTAC
Statistics
Matches: 85, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (42 bp):
AGCTCTCATGAGCTTCTGTTCAACCCTTATGGGTTTCCGTTA
Found at i:27415176 original size:40 final size:41
Alignment explanation
Indices: 27415123--27415205 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
27415113 GTTATTGTTA
*
27415123 TTAGTTTCAAAGTATACAA-TTTTTTTTATTGTATGTTATT
1 TTAGCTTCAAAGTATACAATTTTTTTTTATTGTATGTTATT
* *
27415163 TTAGCTTCAAAGTATATAATTTTTTTTTATTTTATGTTATT
1 TTAGCTTCAAAGTATACAATTTTTTTTTATTGTATGTTATT
27415204 TT
1 TT
27415206 TAAACGTACA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 17 0.44
41 22 0.56
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.60
Consensus pattern (41 bp):
TTAGCTTCAAAGTATACAATTTTTTTTTATTGTATGTTATT
Found at i:27433914 original size:21 final size:23
Alignment explanation
Indices: 27433871--27433915 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
27433861 AAAAATCTTA
*
27433871 AAAATATTTTTATATTTACATTT
1 AAAATATTTTTATATCTACATTT
*
27433894 AAAAT-TTTTTA-ATCTATATTT
1 AAAATATTTTTATATCTACATTT
27433915 A
1 A
27433916 CTTTTTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
AAAATATTTTTATATCTACATTT
Found at i:27434355 original size:27 final size:27
Alignment explanation
Indices: 27434304--27434356 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
27434294 CAATTGAAAT
* **
27434304 ATTTTTAAAAGGTTGATGGTTAAATTC
1 ATTTTTAAAAGGTTGAGGGACAAATTC
*
27434331 ATTTTTTAAAGGTTGAGGGACAAATT
1 ATTTTTAAAAGGTTGAGGGACAAATT
27434357 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.42
Consensus pattern (27 bp):
ATTTTTAAAAGGTTGAGGGACAAATTC
Found at i:27435934 original size:21 final size:22
Alignment explanation
Indices: 27435908--27435951 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
27435898 GTATGTCATT
27435908 AACATATAAAACC-AATATAGA
1 AACATATAAAACCAAATATAGA
27435929 AACATATAAAACCAAATATAGA
1 AACATATAAAACCAAATATAGA
27435951 A
1 A
27435952 CCTTACTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.64, C:0.14, G:0.05, T:0.18
Consensus pattern (22 bp):
AACATATAAAACCAAATATAGA
Found at i:27441420 original size:12 final size:12
Alignment explanation
Indices: 27441403--27441427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27441393 AAATCATTGT
27441403 AATATATGTAAA
1 AATATATGTAAA
27441415 AATATATGTAAA
1 AATATATGTAAA
27441427 A
1 A
27441428 CAGTTTTTCC
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
AATATATGTAAA
Found at i:27441538 original size:19 final size:19
Alignment explanation
Indices: 27441503--27441539 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27441493 TCCAAACATC
**
27441503 AGAAAAGTAAATTATTTTT
1 AGAAAAGTAAAACATTTTT
27441522 AGAAAAGTAAAACATTTT
1 AGAAAAGTAAAACATTTT
27441540 CAAGAAATTA
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:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (19 bp):
AGAAAAGTAAAACATTTTT
Found at i:27442175 original size:22 final size:22
Alignment explanation
Indices: 27442149--27442190 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
27442139 CATAAAATTA
27442149 AAAAAGAA-AAACGAATCAATCT
1 AAAAAGAATAAA-GAATCAATCT
*
27442171 AAAAATAATAAAGAATCAAT
1 AAAAAGAATAAAGAATCAAT
27442191 TTATTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (22 bp):
AAAAAGAATAAAGAATCAATCT
Found at i:27446112 original size:21 final size:20
Alignment explanation
Indices: 27446084--27446123 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
27446074 CATGTTTATT
* *
27446084 ATTATTAATTAAGTTAAAAA
1 ATTATTAAATAAATTAAAAA
27446104 ATTAGTTAAATAAATTAAAA
1 ATTA-TTAAATAAATTAAAA
27446124 TATGCTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTATTAAATAAATTAAAAA
Found at i:27450231 original size:37 final size:37
Alignment explanation
Indices: 27450188--27450296 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 37
27450178 ATTTTTCAGA
27450188 AATTAAATTAAGAGTTAGGAAATTCCTCGATTTTTCT
1 AATTAAATTAAGAGTTAGGAAATTCCTCGATTTTTCT
** *
27450225 AATTAAAATTAA-A---A-TCAA-TCCT--ATTTTTCAGA
1 AATT-AAATTAAGAGTTAGGAAATTCCTCGATTTTTC--T
*
27450257 AATTAAATTAAGAGTTAGGGAATTCCTCGATTTTTCT
1 AATTAAATTAAGAGTTAGGAAATTCCTCGATTTTTCT
27450294 AAT
1 AAT
27450297 CAAAGGAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 22
0.66 0.07 0.27
Matches are distributed among these distances:
30 7 0.13
31 7 0.13
32 9 0.16
33 2 0.04
34 1 0.02
35 1 0.02
36 2 0.04
37 12 0.22
38 7 0.13
39 7 0.13
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (37 bp):
AATTAAATTAAGAGTTAGGAAATTCCTCGATTTTTCT
Found at i:27450243 original size:69 final size:69
Alignment explanation
Indices: 27450160--27450296 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 69
27450150 CTCACAAATC
*
27450160 AAAATTACAATCAATCCTATTTTTCAGAAATTAAATTAAGAGTTAGGAAATTCCTCGATTTTTCT
1 AAAATTAAAATCAATCCTATTTTTCAGAAATTAAATTAAGAGTTAGGAAATTCCTCGATTTTTCT
27450225 AATT
66 AATT
*
27450229 AAAATTAAAATCAATCCTATTTTTCAGAAATTAAATTAAGAGTTAGGGAATTCCTCGATTTTTCT
1 AAAATTAAAATCAATCCTATTTTTCAGAAATTAAATTAAGAGTTAGGAAATTCCTCGATTTTTCT
27450294 AAT
66 AAT
27450297 CAAAGGAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (69 bp):
AAAATTAAAATCAATCCTATTTTTCAGAAATTAAATTAAGAGTTAGGAAATTCCTCGATTTTTCT
AATT
Found at i:27457505 original size:13 final size:13
Alignment explanation
Indices: 27457484--27457547 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
27457474 AGTTCTTCAT
27457484 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
27457497 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
*
27457510 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
* *
27457523 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
27457536 TGCTTTTGAAAA
1 TGCTTTTGAAAA
27457548 ATTTGGTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 3 0.07
13 35 0.85
14 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:27465253 original size:371 final size:371
Alignment explanation
Indices: 27464555--27465301 Score: 1138
Period size: 371 Copynumber: 2.0 Consensus size: 371
27464545 TGTAATTTAT
* *
27464555 AATAAATGAGGCCACTATATGAGCCTTCAAGGAGAAAACTTTAAACTCGAGGTGGATTACAAAGT
1 AATAAAGGAGGCCACTATAGGAGCCTTCAAGGAGAAAACTTTAAACTCGAGGTGGATTACAAAGT
* * *
27464620 TGCAATTTCTACCATGACCAAATATGTTGGTGAGTGTTAAAGTGGTAACAAAGATATAAATGGAG
66 CGCAATTTCTACCATGACCAAATATGTTGGTGAGTGTCAAAGCGGTAACAAAGATATAAATGGAG
* * *
27464685 GGTCAAGGTAGCATTGATGAAAAAGAAACAAAATTAGGAAATTTGAAAATATGAAGGTCCTTATA
131 GGTCAAGGTAGCATTGATGAAAAAGAAACAAAATTAGGAAATTTAAAAATATGAAAGTCCTCATA
* * *
27464750 CTTGCACAACTAACTCAAGATTATCACAAAATAGATTCCAAGCTTATTTGCAAATTAATAATCCC
196 CTTGCACAACTAACGCAAGATCATCACAAAATAGATTCCAAGCTTATTTGCAAATGAATAATCCC
* * * *
27464815 GTCGATCAAAGAGAATATAACAATTTTAGTATCATTACTAATAGTTGATATGTAGTCTCGATTCA
261 GTCGATCAAAGAAAATATAACAATTTCAGTATCATTACTAATAGTTGATATGTAGCCTAGATTCA
* *
27464880 AATGCTCCATCACATATTGAAAGGCATAGAAAACGAAGCTGAAGGC
326 AATACTCCATCACATATTGAAAGGCATAGAAAACAAAGCTGAAGGC
* * *
27464926 AATAAAGGAGGCCATTATAGGAGCTTTCAAGGAGAAAACTTTAAACTTTG-GGTGGATTACAAAG
1 AATAAAGGAGGCCACTATAGGAGCCTTCAAGGAGAAAACTTTAAAC-TCGAGGTGGATTACAAAG
* *
27464990 TCGTAATTTCTACCATGACCAAATATGTTGGTGAGTGTCAAAGCGGTAACGAAGATATAAATGGA
65 TCGCAATTTCTACCATGACCAAATATGTTGGTGAGTGTCAAAGCGGTAACAAAGATATAAATGGA
* *
27465055 GGGTCAAGGTAGGATTGATGAAAAAGAAACAAAATTGGGAAATTTAAAAATATGAAAGTCCTCAT
130 GGGTCAAGGTAGCATTGATGAAAAAGAAACAAAATTAGGAAATTTAAAAATATGAAAGTCCTCAT
*
27465120 ACTTGCACAACTAACGCGAGATCATCACAAAATAGATTCCAAGCTTATTTGCAAATGAATAATCC
195 ACTTGCACAACTAACGCAAGATCATCACAAAATAGATTCCAAGCTTATTTGCAAATGAATAATCC
* * * * * *
27465185 CGTTGGTTAGAGAAAATCTGACAATTTCAGTATCATTACTAATAGTTGATATGTAGCCCTAG-TT
260 CGTCGATCAAAGAAAATATAACAATTTCAGTATCATTACTAATAGTTGATATGTAG-CCTAGATT
* ** * *
27465249 CAAATATTCCATCACATATTGAAATTCATGGAAAGCAAAGCTGAAGGC
324 CAAATACTCCATCACATATTGAAAGGCATAGAAAACAAAGCTGAAGGC
27465297 AATAA
1 AATAA
27465302 GTGAATTGTT
Statistics
Matches: 338, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
371 333 0.99
372 5 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (371 bp):
AATAAAGGAGGCCACTATAGGAGCCTTCAAGGAGAAAACTTTAAACTCGAGGTGGATTACAAAGT
CGCAATTTCTACCATGACCAAATATGTTGGTGAGTGTCAAAGCGGTAACAAAGATATAAATGGAG
GGTCAAGGTAGCATTGATGAAAAAGAAACAAAATTAGGAAATTTAAAAATATGAAAGTCCTCATA
CTTGCACAACTAACGCAAGATCATCACAAAATAGATTCCAAGCTTATTTGCAAATGAATAATCCC
GTCGATCAAAGAAAATATAACAATTTCAGTATCATTACTAATAGTTGATATGTAGCCTAGATTCA
AATACTCCATCACATATTGAAAGGCATAGAAAACAAAGCTGAAGGC
Found at i:27467635 original size:63 final size:63
Alignment explanation
Indices: 27467528--27467646 Score: 166
Period size: 63 Copynumber: 1.9 Consensus size: 63
27467518 ACTAACCTCA
* * *
27467528 TTATTTTTACACAAACACCACACTGTGCACCACCATACCTTGCATCAACACCTTCTGCACCTG
1 TTATTTTTACACAAACACCACACTATGAACCACCATACCCTGCATCAACACCTTCTGCACCTG
* * ** *
27467591 TTATTTTTACACAAGCACCACACTATGAACTACTGTGCCCTGCATCAACACCTTCT
1 TTATTTTTACACAAACACCACACTATGAACCACCATACCCTGCATCAACACCTTCT
27467647 ACAGGTATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.29, C:0.34, G:0.08, T:0.29
Consensus pattern (63 bp):
TTATTTTTACACAAACACCACACTATGAACCACCATACCCTGCATCAACACCTTCTGCACCTG
Found at i:27473370 original size:18 final size:18
Alignment explanation
Indices: 27473347--27473383 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
27473337 TCCTTAAGAT
27473347 TACCATTAGTTTGAATAA
1 TACCATTAGTTTGAATAA
27473365 TACCATTAGTTTGAATAA
1 TACCATTAGTTTGAATAA
27473383 T
1 T
27473384 TGTATACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (18 bp):
TACCATTAGTTTGAATAA
Found at i:27473947 original size:30 final size:30
Alignment explanation
Indices: 27473911--27473973 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
27473901 ATTTATTTTA
27473911 TTGTTAATTTTGTAATTATTTTAAAGACAT
1 TTGTTAATTTTGTAATTATTTTAAAGACAT
* * *
27473941 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTAATTATTTTAAAGACAT
27473971 TTG
1 TTG
27473974 CTTATTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTAATTATTTTAAAGACAT
Found at i:27474972 original size:19 final size:21
Alignment explanation
Indices: 27474935--27474973 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
27474925 GATGGAATAT
27474935 ATATATGATGGAATGAAATGC
1 ATATATGATGGAATGAAATGC
*
27474956 ATATA-GATGGTAT-AAATG
1 ATATATGATGGAATGAAATG
27474974 TGATATGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.31
Consensus pattern (21 bp):
ATATATGATGGAATGAAATGC
Found at i:27483073 original size:25 final size:25
Alignment explanation
Indices: 27483045--27483249 Score: 116
Period size: 24 Copynumber: 8.2 Consensus size: 25
27483035 ATAAACAGGT
27483045 AGCTCAAGAGAGCCATTAATCGGGA
1 AGCTCAAGAGAGCCATTAATCGGGA
* * *
27483070 AGCTCATGTGAGCCATGTAA-CAGGA
1 AGCTCAAGAGAGCCAT-TAATCGGGA
*** **
27483095 AGCTCATTCGAGCTGTATAA-CGGGA
1 AGCTCAAGAGAGCCAT-TAATCGGGA
*
27483120 AGCTTATA-AGAGCCA-TAATCGGGA
1 AGCTCA-AGAGAGCCATTAATCGGGA
* * * *
27483144 AGTTCAAGTGAGCCAAT-GTCGGGA
1 AGCTCAAGAGAGCCATTAATCGGGA
* *
27483168 AGCTCCAGAGAGCCAAT-ATCGGGA
1 AGCTCAAGAGAGCCATTAATCGGGA
* * * *
27483192 AGCTCTAGAAAGCCAATTATTTGGGA
1 AGCTCAAGAGAGCC-ATTAATCGGGA
* * *
27483218 AGCTCATGAAAGAGCCTTTAATCCGGA
1 AGCTCA--AGAGAGCCATTAATCGGGA
27483245 AGCTC
1 AGCTC
27483250 CGAAAAGTCA
Statistics
Matches: 137, Mismatches: 34, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
23 4 0.03
24 53 0.39
25 49 0.36
26 13 0.09
27 12 0.09
28 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (25 bp):
AGCTCAAGAGAGCCATTAATCGGGA
Found at i:27486961 original size:21 final size:21
Alignment explanation
Indices: 27486935--27486985 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
27486925 TACGATTTAG
27486935 GGTTTAGGGGATAAGGGTTGT
1 GGTTTAGGGGATAAGGGTTGT
27486956 GGTTTAGGGGATAAGGGTTGT
1 GGTTTAGGGGATAAGGGTTGT
27486977 GGTTTAGGG
1 GGTTTAGGG
27486986 TCTAGGTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.00, G:0.49, T:0.33
Consensus pattern (21 bp):
GGTTTAGGGGATAAGGGTTGT
Found at i:27487319 original size:38 final size:39
Alignment explanation
Indices: 27487252--27487330 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 39
27487242 TTAAAATTAC
* *
27487252 GTAAAACGGCGCCGTTTGGCTAAAGGAATTTGAATTTTA
1 GTAAAACGGCGCCGTTTGGCCAAAAGAATTTGAATTTTA
27487291 GTAAAACGGCG-CGTTTGGCCAAAAGAATTTGAATTTTA
1 GTAAAACGGCGCCGTTTGGCCAAAAGAATTTGAATTTTA
27487329 GT
1 GT
27487331 GGTGTTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 27 0.71
39 11 0.29
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (39 bp):
GTAAAACGGCGCCGTTTGGCCAAAAGAATTTGAATTTTA
Found at i:27487703 original size:251 final size:250
Alignment explanation
Indices: 27487315--27487810 Score: 631
Period size: 251 Copynumber: 2.0 Consensus size: 250
27487305 TTGGCCAAAA
* * * * * *
27487315 GAATTTGAATTTTAGTGGTGTTTTTATTAAAAACGCCACTGAAGGTATGCTATAGTGGCATTTTA
1 GAATTTGAATTTTAGTGGCGTTTGTATGAAAAACGCCACAGAAGGTATACTATAGTGGCAGTTTA
* * *
27487380 TATTGAAACGCTGCAAATACATAAATGTTTCTCTGTACGAAAACGGCGTCGTTTTCTTAAATTAT
66 TA-TGAAACGCCGCAAATACATAAATGTTTCTCTGAACGAAAACGGCGTCGTTTTCTTAAATGAT
* * * *
27487445 TTGAACTCCTTACTGGCGTTTTTATTTAAAACGCCGCAAACTGTGATCTTTAGCGGCGTTT-GTT
130 TTGAACTCCTTACTGGCGTTTGTATTTAAAACGCCGC-AACTGTAAGCTTTAACGGCGTTTAG-T
* * *
27487509 ATGGAAATGCCACAAATGTGCATTACAAAATGTTCAGAACGTCACCGTTTCGTTACAT
193 ATGAAAACGCCACAAATGTGCATTACAAAATGTTCAAAACGTCACCGTTTCGTTACAT
*
27487567 GAATTTGAATTTTAGTGGCGTTTGTATGAAAAACGCCACAGAAGGTATACAGTAGTGGTGGC-GT
1 GAATTTGAATTTTAGTGGCGTTTGTATGAAAAACGCCACAGAAGGTATAC--TA-TAGTGGCAGT
* * * * * * *
27487631 TT-TA-GAAACGCCGCAAATCCGTATATGTTTTTGTGAATGAAAACGGCGTCGTTTTCTTGAATG
63 TTATATGAAACGCCGCAAATACATAAATGTTTCTCTGAACGAAAACGGCGTCGTTTTCTTAAATG
* ** *
27487694 ATTTGAACTCTTTTGTGGCGTTTGTATTTAAAACGCCGCAACTGTAAGCTTTAACGGCTTTTAGT
128 ATTTGAACTCCTTACTGGCGTTTGTATTTAAAACGCCGCAACTGTAAGCTTTAACGGCGTTTAGT
* * *
27487759 ATGAAAACGCCACAAATGTGTATTACAATATGTTCAAAACGTCGCCGTTTCG
193 ATGAAAACGCCACAAATGTGCATTACAAAATGTTCAAAACGTCACCGTTTCG
27487811 GTTGAGGAAC
Statistics
Matches: 209, Mismatches: 31, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
250 66 0.32
251 85 0.41
252 45 0.22
253 2 0.01
254 5 0.02
255 6 0.03
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (250 bp):
GAATTTGAATTTTAGTGGCGTTTGTATGAAAAACGCCACAGAAGGTATACTATAGTGGCAGTTTA
TATGAAACGCCGCAAATACATAAATGTTTCTCTGAACGAAAACGGCGTCGTTTTCTTAAATGATT
TGAACTCCTTACTGGCGTTTGTATTTAAAACGCCGCAACTGTAAGCTTTAACGGCGTTTAGTATG
AAAACGCCACAAATGTGCATTACAAAATGTTCAAAACGTCACCGTTTCGTTACAT
Found at i:27488517 original size:22 final size:22
Alignment explanation
Indices: 27488490--27488536 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
27488480 GTCTTTCTAC
27488490 TTAGGTTTAATCAGTATAAAAT
1 TTAGGTTTAATCAGTATAAAAT
27488512 TTAGGTTTAATCAGTATAAAAT
1 TTAGGTTTAATCAGTATAAAAT
27488534 TTA
1 TTA
27488537 AGAAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (22 bp):
TTAGGTTTAATCAGTATAAAAT
Found at i:27489946 original size:9 final size:9
Alignment explanation
Indices: 27489932--27490051 Score: 103
Period size: 9 Copynumber: 13.7 Consensus size: 9
27489922 NNNNNNNNNN
27489932 ATAACTTAC
1 ATAACTTAC
27489941 ATAACTTAC
1 ATAACTTAC
27489950 ATAACTTAC
1 ATAACTTAC
27489959 ATAACTTAC
1 ATAACTTAC
27489968 ATAA--TAC
1 ATAACTTAC
27489975 ATAACCTT-C
1 ATAA-CTTAC
*
27489984 CTAACTTAC
1 ATAACTTAC
* *
27489993 ATTA-TTGTC
1 ATAACTT-AC
27490002 -TAA--TAC
1 ATAACTTAC
27490008 ATAACTTAGTAC
1 ATAAC-T--TAC
27490020 ATAACTTAC
1 ATAACTTAC
*
27490029 ATAA-ATAC
1 ATAACTTAC
27490037 ATAACTTAC
1 ATAACTTAC
27490046 ATAACT
1 ATAACT
27490052 GGCGTTTTGA
Statistics
Matches: 91, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
6 1 0.01
7 11 0.12
8 14 0.15
9 55 0.60
10 1 0.01
11 1 0.01
12 8 0.09
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:27490039 original size:17 final size:17
Alignment explanation
Indices: 27490017--27490049 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
27490007 CATAACTTAG
27490017 TACATAACTTACATAAA
1 TACATAACTTACATAAA
27490034 TACATAACTTACATAA
1 TACATAACTTACATAA
27490050 CTGGCGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (17 bp):
TACATAACTTACATAAA
Found at i:27492899 original size:43 final size:42
Alignment explanation
Indices: 27492797--27493091 Score: 314
Period size: 42 Copynumber: 7.0 Consensus size: 42
27492787 GTTTGTGAAA
* * **
27492797 TAAGTGCCGCTAAAGAACACT-ACTTTTAGCGGCATTTTTGAAC
1 TAAGCGCCGCTAAAGAACA-TGACTTTTAGCGGCGTTTTT-TCC
* *
27492840 -AAGCGCCGCTAAAGAACATTACTTTTAGAGGCGTTTTATTCC
1 TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTT-TTCC
*
27492882 AAAGCGCCGCTAAAGAACATGA-TCTTTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCG-TTTTTTCC
** * * *
27492925 TAAGCGCCGCTAAAGAACATGAGATTTCGCGGAGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTCC
* *
27492967 TAAGCGCCGCTAAAGAACATGATCTTTT-GCGGCATTTTTTTC
1 TAAGCGCCGCTAAAGAACATGA-CTTTTAGCGGCGTTTTTTCC
*
27493009 TAAGCGCCGCTACAGAACATGA-TCTTTAGCGGCGTTTATTTCC
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTT-TTTCC
* *
27493052 TTAA-TGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTT
1 -TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTT
27493092 TGTGTAAGCG
Statistics
Matches: 219, Mismatches: 21, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
40 1 0.00
41 4 0.02
42 107 0.49
43 99 0.45
44 8 0.04
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTCC
Found at i:27493051 original size:127 final size:130
Alignment explanation
Indices: 27492840--27493110 Score: 363
Period size: 127 Copynumber: 2.1 Consensus size: 130
27492830 ATTTTTGAAC
* *
27492840 AAGCGCCGCTAAAGAACATTACTTTTAGAGGCGTTTTATTCCAAAGCGCCGCTAAAGAACATGAT
1 AAGCGCCGCTAAAGAACATGACTTTTAGAGGCATTTTATTCCAAAGCGCCGCTAAAGAACATGAT
* *
27492905 CTTTAGCGGCGTTTTTTTCC-TAAGCGCCGCTAAAGAACATGAGATTTCGCGGAG-TTTTTT-TC
66 CTTTAGCGGCGTTTATTTCCTTAA-CGCCGCTAAAGAACATGAGATTTAGCGGAGTTTTTTTGTC
27492967 T
130 T
* * * *
27492968 AAGCGCCGCTAAAGAACATGATCTTTT-GCGGCATTTT-TTTCTAAGCGCCGCTACAGAACATGA
1 AAGCGCCGCTAAAGAACATGA-CTTTTAGAGGCATTTTATTCCAAAGCGCCGCTAAAGAACATGA
* ** * *
27493031 TCTTTAGCGGCGTTTATTTCCTTAATGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTTGTG
65 TCTTTAGCGGCGTTTATTTCCTTAACGCCGCTAAAGAACATGAGATTTAGCGGAGTTTTTTTGTC
27493096 T
130 T
*
27493097 AAGCGCCGCAAAAG
1 AAGCGCCGCTAAAG
27493111 TTAGCGACGT
Statistics
Matches: 125, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
127 68 0.54
128 37 0.30
129 20 0.16
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (130 bp):
AAGCGCCGCTAAAGAACATGACTTTTAGAGGCATTTTATTCCAAAGCGCCGCTAAAGAACATGAT
CTTTAGCGGCGTTTATTTCCTTAACGCCGCTAAAGAACATGAGATTTAGCGGAGTTTTTTTGTCT
Found at i:27493092 original size:85 final size:83
Alignment explanation
Indices: 27492797--27493110 Score: 330
Period size: 85 Copynumber: 3.7 Consensus size: 83
27492787 GTTTGTGAAA
* * ** *
27492797 TAAGTGCCGCTAAAGAACACT-ACTTTTAGCGGCATTTTTGAAC-AAGCGCCGCTAAAGAACATT
1 TAAGCGCCGCTAAAGAACA-TGATTTTTAGCGGCATTTTT-TTCTAAGCGCCGCTAAAGAACATG
*
27492860 ACTTTTAGAGGCGTTTTATTCC
64 AC-TTTAGCGGCGTTTT-TTCC
* * *
27492882 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATGATTTTTAGCGGCATTTTTTT-CTAAGCGCCGCTAAAGAACATGA
* * * *
27492947 GATTTCGCGGAGTTTTTTTC
65 -CTTTAGCGGCGTTTTTTCC
*
27492967 TAAGCGCCGCTAAAGAACATGATCTTTT-GCGGCATTTTTTTCTAAGCGCCGCTACAGAACATGA
1 TAAGCGCCGCTAAAGAACATGAT-TTTTAGCGGCATTTTTTTCTAAGCGCCGCTAAAGAACATGA
27493031 TCTTTAGCGGCGTTTATTTCC
65 -CTTTAGCGGCGTTT-TTTCC
* * * *
27493052 TTAA-TGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTTGTGTAAGCGCCGCAAAAG
1 -TAAGCGCCGCTAAAGAACATGATTTTTAGCGGC-ATTTTTT-TCTAAGCGCCGCTAAAG
27493111 TTAGCGACGT
Statistics
Matches: 192, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
84 38 0.20
85 97 0.51
86 43 0.22
87 14 0.07
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (83 bp):
TAAGCGCCGCTAAAGAACATGATTTTTAGCGGCATTTTTTTCTAAGCGCCGCTAAAGAACATGAC
TTTAGCGGCGTTTTTTCC
Found at i:27497938 original size:18 final size:18
Alignment explanation
Indices: 27497894--27497930 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
27497884 TTTCATTGAT
27497894 AAAAACTTAATTGTTACA
1 AAAAACTTAATTGTTACA
27497912 AAAAACTTAATTGTTACA
1 AAAAACTTAATTGTTACA
27497930 A
1 A
27497931 GTTACTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAAACTTAATTGTTACA
Found at i:27499608 original size:21 final size:24
Alignment explanation
Indices: 27499584--27499638 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 24
27499574 TATATATATA
27499584 TAAAATAATACAT-TAT-GAAA-T
1 TAAAATAATACATATATAGAAACT
27499605 T-AAATAATA-ATATATAGGAAACT
1 TAAAATAATACATATATA-GAAACT
27499628 TAAAATAATAC
1 TAAAATAATAC
27499639 TACAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.07
20 11 0.39
21 1 0.04
22 4 0.14
23 2 0.07
24 8 0.29
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (24 bp):
TAAAATAATACATATATAGAAACT
Found at i:27500787 original size:16 final size:17
Alignment explanation
Indices: 27500768--27500799 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
27500758 GGTCAGATTA
27500768 GGTTTGGGTT-TAATTG
1 GGTTTGGGTTATAATTG
27500784 GGTTTGGGTTATAATT
1 GGTTTGGGTTATAATT
27500800 TTGGGCTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (17 bp):
GGTTTGGGTTATAATTG
Found at i:27501303 original size:50 final size:49
Alignment explanation
Indices: 27501240--27501610 Score: 230
Period size: 50 Copynumber: 7.4 Consensus size: 49
27501230 ACTGCAATGT
* * * * *
27501240 CGGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTTCACTACATCGC
1 CGGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTG-TTCACTGCATCGC
** ** * * * * ** *
27501290 CAAGGAAGTAAGATTTGCTATTGTAGCTTTAATCTTTTTAACCGCAAGGT
1 CGGGGAAGTAAGATTCACTGTTGTAGCTTTAATC-TGTTCACTGCATCGC
* * *
27501340 CGGGGAAGCAAGATTCACTGATGTGGCTTTAATCTGTTCCACTGCATCGC
1 CGGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTGTT-CACTGCATCGC
* * * * *
27501390 TTGGGG-AGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAAT-GT
1 -CGGGGAAGTAAGATTCACTGTTGTAGCTTTAATC-TGTTCACTGC-ATCGC
* * * * *
27501440 CGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGC
1 CGGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTGTT-CACTGCATCGC
* * * * *
27501490 CTAGGG-AGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAAT-GT
1 C-GGGGAAGTAAGATTCACTGTTGTAGCTTTAATC-TGTTCACTGC-ATCGC
** * * * *
27501540 CGGGGAAGCCAGATTCACCGATGTGGCTTTAATCTATTCCACTGCATCGC
1 CGGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTGTT-CACTGCATCGC
*
27501590 CTGGGG-AGTAAGATTCGCTGT
1 C-GGGGAAGTAAGATTCACTGT
27501611 AATTCTTCGG
Statistics
Matches: 233, Mismatches: 73, Indels: 30
0.69 0.22 0.09
Matches are distributed among these distances:
49 19 0.08
50 193 0.83
51 21 0.09
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (49 bp):
CGGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTGTTCACTGCATCGC
Found at i:27501353 original size:100 final size:100
Alignment explanation
Indices: 27501217--27501610 Score: 619
Period size: 100 Copynumber: 3.9 Consensus size: 100
27501207 TCGTTGTGAT
* * *
27501217 TTTAATCCTTTTAACTGCAATGTCGGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTT-CA
1 TTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTG-TTCCA
* * * * *
27501281 CTACATCGCCAAGGAAGTAAGATTTGCTATTGTAGC
65 CTGCATCGCCTAGGGAGTAAGATTCGCTGTTGTAGC
* * *
27501317 TTTAATCTTTTTAACCGCAAGGTCGGGGAAGCAAGATTCACTGATGTGGCTTTAATCTGTTCCAC
1 TTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCAC
* *
27501382 TGCATCGCTTGGGGAGTAAGATTCGCTGTTGTAGC
66 TGCATCGCCTAGGGAGTAAGATTCGCTGTTGTAGC
27501417 TTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCAC
1 TTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCAC
*
27501482 TGCACCGCCTAGGGAGTAAGATTCGCTGTTGTAGC
66 TGCATCGCCTAGGGAGTAAGATTCGCTGTTGTAGC
* *
27501517 TTTAATCTTTTTAACTGCAATGTCGGGGAAGCCAGATTCACCGATGTGGCTTTAATCTATTCCAC
1 TTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCAC
*
27501582 TGCATCGCCTGGGGAGTAAGATTCGCTGT
66 TGCATCGCCTAGGGAGTAAGATTCGCTGT
27501611 AATTCTTCGG
Statistics
Matches: 270, Mismatches: 23, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
99 2 0.01
100 268 0.99
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (100 bp):
TTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCAC
TGCATCGCCTAGGGAGTAAGATTCGCTGTTGTAGC
Found at i:27503124 original size:7 final size:7
Alignment explanation
Indices: 27503114--27503167 Score: 67
Period size: 7 Copynumber: 8.0 Consensus size: 7
27503104 TTAGCCTCTC
*
27503114 CATTTTC
1 CATTTTT
27503121 CATTTTT
1 CATTTTT
27503128 CA-TTTT
1 CATTTTT
27503134 CATTTTT
1 CATTTTT
* *
27503141 TA-TTCT
1 CATTTTT
27503147 CATTTTT
1 CATTTTT
27503154 CATTTTT
1 CATTTTT
27503161 CATTTTT
1 CATTTTT
27503168 TTAGAGTGCC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 10 0.25
7 30 0.75
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:27503139 original size:13 final size:13
Alignment explanation
Indices: 27503114--27503167 Score: 72
Period size: 13 Copynumber: 4.0 Consensus size: 13
27503104 TTAGCCTCTC
27503114 CATTTTCCATTTTT
1 CATTTT-CATTTTT
27503128 CATTTTCATTTTT
1 CATTTTCATTTTT
* *
27503141 TATTCTCATTTTT
1 CATTTTCATTTTT
27503154 CATTTTTCATTTTT
1 CA-TTTTCATTTTT
27503168 TTAGAGTGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 19 0.54
14 16 0.46
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
CATTTTCATTTTT
Found at i:27504063 original size:28 final size:28
Alignment explanation
Indices: 27504032--27504157 Score: 96
Period size: 30 Copynumber: 4.4 Consensus size: 28
27504022 TCTTTTCATA
27504032 TTTTATTTTGACTTTGATTGATTTCTCTT
1 TTTTATTTTGACTTTGATTGATTTCT-TT
**
27504061 TTTTACTTTTGACTTTGATTTTTTTCTTT
1 TTTTA-TTTTGACTTTGATTGATTTCTTT
* *
27504090 TCTTT-TTTTGATTTTGATTTTGATTT-TGAT
1 T-TTTATTTTGACTTTGA--TTGATTTCT-TT
* * ** *
27504120 TTTGATTTTGATTTTGATTTTTTTCGTT
1 TTTTATTTTGACTTTGATTGATTTCTTT
27504148 TTTT-TTTTGA
1 TTTTATTTTGA
27504158 ATCTGAACCC
Statistics
Matches: 78, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
27 6 0.08
28 20 0.26
29 11 0.14
30 41 0.53
ACGTcount: A:0.12, C:0.06, G:0.11, T:0.71
Consensus pattern (28 bp):
TTTTATTTTGACTTTGATTGATTTCTTT
Found at i:27504086 original size:58 final size:55
Alignment explanation
Indices: 27504032--27504157 Score: 137
Period size: 58 Copynumber: 2.2 Consensus size: 55
27504022 TCTTTTCATA
* * *
27504032 TTTTATTTTGACTTTGA-TTGATTTCTCTTTTTTACTTTTGACTTTGATTTTTTTCTT
1 TTTTTTTTTGACTTTGATTTGATTT-TCATTTTGA-TTTTGACTTTGATTTTTTTC-T
* * *
27504089 TTCTTTTTTTGATTTTGATTTTGATTTTGATTTTGATTTTGATTTTGATTTTTTTCGT
1 TT-TTTTTTTGACTTTGA-TTTGATTTTCATTTTGATTTTGACTTTGATTTTTTTC-T
27504147 TTTTTTTTTGA
1 TTTTTTTTTGA
27504158 ATCTGAACCC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 11 0.19
58 35 0.59
59 6 0.10
60 7 0.12
ACGTcount: A:0.12, C:0.06, G:0.11, T:0.71
Consensus pattern (55 bp):
TTTTTTTTTGACTTTGATTTGATTTTCATTTTGATTTTGACTTTGATTTTTTTCT
Found at i:27504104 original size:6 final size:6
Alignment explanation
Indices: 27504095--27504140 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
27504085 TCTTTTCTTT
27504095 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
27504141 TTTCGTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTTGA
Found at i:27508880 original size:21 final size:21
Alignment explanation
Indices: 27508828--27508882 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 21
27508818 TAGGCTCATA
*
27508828 TAAAATAATACATTATGAAAT
1 TAAAATAATACATTAGGAAAT
*
27508849 T-AAATAATAATATATAGGAAACT
1 TAAAATAAT-ACAT-TAGGAAA-T
27508872 TAAAATAATAC
1 TAAAATAATAC
27508883 TACATAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 7 0.26
21 4 0.15
22 6 0.22
23 3 0.11
24 7 0.26
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (21 bp):
TAAAATAATACATTAGGAAAT
Found at i:27510020 original size:16 final size:16
Alignment explanation
Indices: 27510001--27510038 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
27509991 GGGTTTAGTA
27510001 TTGGGTCAAATTAGGT
1 TTGGGTCAAATTAGGT
**
27510017 TTGGGTTTAATTAGGT
1 TTGGGTCAAATTAGGT
27510033 TTGGGT
1 TTGGGT
27510039 TATAATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.18, C:0.03, G:0.34, T:0.45
Consensus pattern (16 bp):
TTGGGTCAAATTAGGT
Found at i:27510039 original size:16 final size:17
Alignment explanation
Indices: 27510009--27510045 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
27509999 TATTGGGTCA
27510009 AATTAGGTTTGGGTT-T
1 AATTAGGTTTGGGTTAT
27510025 AATTAGGTTTGGGTTAT
1 AATTAGGTTTGGGTTAT
27510042 AATT
1 AATT
27510046 TTGGGCTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (17 bp):
AATTAGGTTTGGGTTAT
Found at i:27521699 original size:24 final size:24
Alignment explanation
Indices: 27521663--27521709 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
27521653 AAGAACCATT
27521663 TAACAGGAAGCTCATGAGAGCTAA
1 TAACAGGAAGCTCATGAGAGCTAA
* * * *
27521687 TAACGGGATGCTCTTTAGAGCTA
1 TAACAGGAAGCTCATGAGAGCTA
27521710 TGGTGTGTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (24 bp):
TAACAGGAAGCTCATGAGAGCTAA
Found at i:27527377 original size:12 final size:12
Alignment explanation
Indices: 27527360--27527387 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
27527350 AAAACAAAAG
27527360 TGATGAGAAGGA
1 TGATGAGAAGGA
27527372 TGATGAGAAGGA
1 TGATGAGAAGGA
27527384 TGAT
1 TGAT
27527388 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (12 bp):
TGATGAGAAGGA
Found at i:27529911 original size:38 final size:38
Alignment explanation
Indices: 27529869--27530027 Score: 318
Period size: 38 Copynumber: 4.2 Consensus size: 38
27529859 TATTGAAATT
27529869 TTGCATACATATAGGATAGAATCATTTAGTTTAATTAA
1 TTGCATACATATAGGATAGAATCATTTAGTTTAATTAA
27529907 TTGCATACATATAGGATAGAATCATTTAGTTTAATTAA
1 TTGCATACATATAGGATAGAATCATTTAGTTTAATTAA
27529945 TTGCATACATATAGGATAGAATCATTTAGTTTAATTAA
1 TTGCATACATATAGGATAGAATCATTTAGTTTAATTAA
27529983 TTGCATACATATAGGATAGAATCATTTAGTTTAATTAA
1 TTGCATACATATAGGATAGAATCATTTAGTTTAATTAA
27530021 TTGCATA
1 TTGCATA
27530028 AACCCCTTTA
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 121 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (38 bp):
TTGCATACATATAGGATAGAATCATTTAGTTTAATTAA
Found at i:27532689 original size:28 final size:28
Alignment explanation
Indices: 27532641--27532740 Score: 114
Period size: 28 Copynumber: 3.6 Consensus size: 28
27532631 CATTTATCAT
* * *
27532641 AAAGGCCTTCC-TTTCCTTAGATTACCAG
1 AAAGG-CTTCCATTTTCATAGATTACCAC
27532669 AAAGGCTTCCATTTTCATAGATTACCAC
1 AAAGGCTTCCATTTTCATAGATTACCAC
* *
27532697 AAAGGC-TCCTATTTTCATAGATTGCTAC
1 AAAGGCTTCC-ATTTTCATAGATTACCAC
*
27532725 AAACGCTTCCATTTTC
1 AAAGGCTTCCATTTTC
27532741 TACCGTGTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
27 8 0.13
28 52 0.83
29 3 0.05
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (28 bp):
AAAGGCTTCCATTTTCATAGATTACCAC
Found at i:27537076 original size:15 final size:16
Alignment explanation
Indices: 27537047--27537076 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27537037 TGCATTTCAT
27537047 TTGCATTTAGGTTAAC
1 TTGCATTTAGGTTAAC
27537063 TTGCATTT-GGTTAA
1 TTGCATTTAGGTTAA
27537077 TTAATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.47
Consensus pattern (16 bp):
TTGCATTTAGGTTAAC
Found at i:27539030 original size:234 final size:234
Alignment explanation
Indices: 27538621--27539080 Score: 875
Period size: 234 Copynumber: 2.0 Consensus size: 234
27538611 GCTTTCCTCT
*
27538621 TTGAAATTAGAATCTCATCACTAATCTTGATATAGCTTCCTCTTCTACTTCCAGTCGAGCTAACT
1 TTGAAATTAGAATCTCATCACTAATCTTGATATAGCTTCCTCTTCTACTACCAGTCGAGCTAACT
27538686 CTCTTATTGGTGATACATGACTTCCTTCTCACTCAAACCTTCATGACATGGAAATCTCATCTATT
66 CTCTTATTGGTGATACATGACTTCCTTCTCACTCAAACCTTCATGACATGGAAATCTCATCTATT
* *
27538751 CTAAAGAGAACTCGTGGCAAAGAGGTCACTACTACTTTATCCAAGAAATTAGTAGCAAAAAAAAA
131 CTAAAGAAAACTCGTGGCAAAGAGGTCACTACTACTTCATCCAAGAAATTAGTAGCAAAAAAAAA
27538816 CAAGGAAGAGGGTTAGAGGGAAGAGAGCACTTGGGGGTC
196 CAAGGAAGAGGGTTAGAGGGAAGAGAGCACTTGGGGGTC
*
27538855 TTGAAATTAGAATCTCATCACTAATCTTGATATAGCTTCCTCTTCTACTACCAGTTGAGCTAACT
1 TTGAAATTAGAATCTCATCACTAATCTTGATATAGCTTCCTCTTCTACTACCAGTCGAGCTAACT
*
27538920 CTCTTATTGGTGATACATGACTTCCTTCTCACTCAAATCTTCATGACATGGAAATCTCATCTATT
66 CTCTTATTGGTGATACATGACTTCCTTCTCACTCAAACCTTCATGACATGGAAATCTCATCTATT
27538985 CTAAAGAAAACTCGTGGCAAAGAGGTCACTACTACTTCATCCAAGAAATTAGTAGCAAAAAAAAA
131 CTAAAGAAAACTCGTGGCAAAGAGGTCACTACTACTTCATCCAAGAAATTAGTAGCAAAAAAAAA
27539050 CAAGGAAGAGGGTTAGAGGGAAGAGAGCACT
196 CAAGGAAGAGGGTTAGAGGGAAGAGAGCACT
27539081 CAGGAGTCAG
Statistics
Matches: 221, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
234 221 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (234 bp):
TTGAAATTAGAATCTCATCACTAATCTTGATATAGCTTCCTCTTCTACTACCAGTCGAGCTAACT
CTCTTATTGGTGATACATGACTTCCTTCTCACTCAAACCTTCATGACATGGAAATCTCATCTATT
CTAAAGAAAACTCGTGGCAAAGAGGTCACTACTACTTCATCCAAGAAATTAGTAGCAAAAAAAAA
CAAGGAAGAGGGTTAGAGGGAAGAGAGCACTTGGGGGTC
Found at i:27543526 original size:11 final size:11
Alignment explanation
Indices: 27543512--27543570 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
27543502 TAAAAAAAGT
27543512 ATTTTAAAAAA
1 ATTTTAAAAAA
27543523 ATTTT---AAA
1 ATTTTAAAAAA
27543531 A--TTAAAAAA
1 ATTTTAAAAAA
27543540 A--TTAAAAAA
1 ATTTTAAAAAA
27543549 TTATTTTAAAAAA
1 --ATTTTAAAAAA
27543562 ATTTTAAAA
1 ATTTTAAAA
27543571 TTTAAAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
6 2 0.05
8 4 0.10
9 12 0.29
11 15 0.37
13 8 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:27543548 original size:40 final size:41
Alignment explanation
Indices: 27543496--27543600 Score: 169
Period size: 39 Copynumber: 2.6 Consensus size: 41
27543486 AAATTAAAAT
27543496 AAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAA-TTAA
1 AAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAATTTAA
*
27543536 AAAAATT-AAAAAATTATTTTAAAAAAATTTTAAAATTTAA
1 AAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAATTTAA
* *
27543576 AAAATTTAATAAAAGTATTTTAAAA
1 AAAAATTAAAAAAAGTATTTTAAAA
27543601 TTTAAAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
39 27 0.46
40 17 0.29
41 15 0.25
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (41 bp):
AAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAATTTAA
Found at i:27543578 original size:30 final size:29
Alignment explanation
Indices: 27543553--27543610 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
27543543 AAAAAATTAT
27543553 TTTAA-AAAA-ATTTTAAAATTTAAAAAA
1 TTTAATAAAAGATTTTAAAATTTAAAAAA
27543580 TTTAATAAAAGTATTTTAAAATTTAAAAAA
1 TTTAATAAAAG-ATTTTAAAATTTAAAAAA
27543610 T
1 T
27543611 AAAAAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 5 0.18
28 4 0.14
30 19 0.68
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TTTAATAAAAGATTTTAAAATTTAAAAAA
Found at i:27562098 original size:42 final size:42
Alignment explanation
Indices: 27562034--27562165 Score: 178
Period size: 43 Copynumber: 3.1 Consensus size: 42
27562024 NNNNCATTAC
27562034 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATT-AATGAT
* * * *
27562077 GCGG-GGAATCAGCACATAGCAACC-CCTTTCACAGTTAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTT-ATA-TTAATGAT
27562119 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTAAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATT-AATGAT
27562162 ACGG
1 ACGG
27562166 ATTCACATAG
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
41 5 0.07
42 31 0.41
43 35 0.46
44 5 0.07
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (42 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTAATGAT
Found at i:27562339 original size:50 final size:50
Alignment explanation
Indices: 27562173--27562357 Score: 203
Period size: 51 Copynumber: 3.7 Consensus size: 50
27562163 CGGATTCACA
* * * *
27562173 TAGTAGCATGCACATAATACTACTCATGTGACCATCACTATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCA-TATCTGGTACACG
* * * * *
27562224 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGC-TATCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-C-CATCATATCTGGTACACG
* *
27562275 TAGTAGCCTGCACATAGTACTACACGTGCGACCTATCAT-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACC-ATCATATCTGGTACACG
* *
27562325 TAGTAGCCTACACATAGTACTACACACGTGACC
1 TAGTAGCCTGCACATAGTACTACACATGTGACC
27562358 GTCACTTTCA
Statistics
Matches: 110, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
50 41 0.37
51 66 0.60
52 1 0.01
53 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATCATATCTGGTACACG
Found at i:27562347 original size:101 final size:102
Alignment explanation
Indices: 27562171--27562355 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
27562161 TACGGATTCA
* * *
27562171 CATAGTAGCATGCACATAATACTACTCATGTGACCATCACTATCTGATACACGTAGTAGCCTGCA
1 CATAGTAGCATGCACATAATACTACACATGCGACCATCACTATCTGATACACGTAGTAGCCTACA
27562236 CATAGTACTACACACGTGATCGAAGCTATCTGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCTGGTACG
* * * *
27562273 CATAGTAGCCTGCACATAGTACTACACGTGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTAC
1 CATAGTAGCATGCACATAATACTACACATGCGACC-ATCACTATCTGATACACGTAGTAGCCTAC
27562336 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
27562356 CCGTCACTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 40 0.53
102 31 0.41
103 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (102 bp):
CATAGTAGCATGCACATAATACTACACATGCGACCATCACTATCTGATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCGAAGCTATCTGGTACG
Found at i:27562378 original size:101 final size:102
Alignment explanation
Indices: 27562167--27562389 Score: 254
Period size: 101 Copynumber: 2.2 Consensus size: 102
27562157 ATGATACGGA
* * *
27562167 TTCACATAGTAGCATGCACATAATACTACTCATGTGACCATCACTATCTGATACACGTAGTAGCC
1 TTCACATAGTAGCCTGCACATAATACTACACATGCGACCATCACTATCTGATACACGTAGTAGCC
* * **
27562232 TGCACATAGTACTACACACGTGATCGAAGCTATCTGG
66 TACACATAGTACTACACACGTGACCGAAGCTATCACG
* * * * *
27562269 TACGCATAGTAGCCTGCACATAGTACTACACGTGCGACCTATCA-T-TCTGGTACACGTAGTAGC
1 TTCACATAGTAGCCTGCACATAATACTACACATGCGACC-ATCACTATCTGATACACGTAGTAGC
* * *
27562332 CTACACATAGTACTACACACGTGACCGTCA-CTTTCACT
65 CTACACATAGTACTACACACGTGACCG-AAGCTATCACG
* *
27562370 TTCACATAGTGGCCTACACA
1 TTCACATAGTAGCCTGCACA
27562390 CAGTCCATGC
Statistics
Matches: 100, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
101 62 0.62
102 34 0.34
103 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (102 bp):
TTCACATAGTAGCCTGCACATAATACTACACATGCGACCATCACTATCTGATACACGTAGTAGCC
TACACATAGTACTACACACGTGACCGAAGCTATCACG
Found at i:27568141 original size:23 final size:23
Alignment explanation
Indices: 27568091--27568141 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
27568081 CATAAGTGCC
* *
27568091 ACACTGATATGTAGCCGAAGCTA
1 ACACTGATACGTAGCCGAAGATA
*
27568114 CCACTGATACGTAGCCGAAGATA
1 ACACTGATACGTAGCCGAAGATA
27568137 ACACT
1 ACACT
27568142 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (23 bp):
ACACTGATACGTAGCCGAAGATA
Found at i:27570190 original size:28 final size:28
Alignment explanation
Indices: 27570156--27570214 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
27570146 ATTTTCACTT
27570156 ATGAAATAATAACACGTAAAACTTTCAC
1 ATGAAATAATAACACGTAAAACTTTCAC
27570184 ATGAAATAATAACACGTAAAACTTTCAC
1 ATGAAATAATAACACGTAAAACTTTCAC
27570212 ATG
1 ATG
27570215 CTTTTCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.49, C:0.17, G:0.08, T:0.25
Consensus pattern (28 bp):
ATGAAATAATAACACGTAAAACTTTCAC
Found at i:27574188 original size:24 final size:24
Alignment explanation
Indices: 27574161--27574209 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
27574151 GAAACGAAAC
27574161 AGAAAGAAAATG-AAAATGAAAGAA
1 AGAAAGAAAA-GAAAAATGAAAGAA
27574185 AGAAAGAAAAGAAAAATGAAAGAA
1 AGAAAGAAAAGAAAAATGAAAGAA
27574209 A
1 A
27574210 TGAAGGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.06
Consensus pattern (24 bp):
AGAAAGAAAAGAAAAATGAAAGAA
Found at i:27574203 original size:30 final size:32
Alignment explanation
Indices: 27574130--27574205 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
27574120 ATGATAAAAT
* *
27574130 AAAGAATAAATAAAAAAGATAGAAACGAAACAG
1 AAAGAA-AAATGAAAAAGAAAGAAACGAAACAG
* *
27574163 AAAG-AAAATGAAAATGAAAGAAA-GAAAGA-
1 AAAGAAAAATGAAAAAGAAAGAAACGAAACAG
27574192 AAAGAAAAATGAAA
1 AAAGAAAAATGAAA
27574206 GAAATGAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 4 0.11
30 14 0.37
31 15 0.39
32 1 0.03
33 4 0.11
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.08
Consensus pattern (32 bp):
AAAGAAAAATGAAAAAGAAAGAAACGAAACAG
Found at i:27574210 original size:9 final size:9
Alignment explanation
Indices: 27574174--27574213 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
27574164 AAGAAAATGA
27574174 AAATGAAAG
1 AAATGAAAG
27574183 AAA-GAAAG
1 AAATGAAAG
*
27574191 AAAAG-AA-
1 AAATGAAAG
27574198 AAATGAAAG
1 AAATGAAAG
27574207 AAATGAA
1 AAATGAA
27574214 GGAGAAAGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
7 4 0.15
8 12 0.44
9 11 0.41
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.07
Consensus pattern (9 bp):
AAATGAAAG
Found at i:27574905 original size:24 final size:24
Alignment explanation
Indices: 27574873--27574930 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
27574863 GTGTTTTTCA
27574873 ATTGAAATTGATTG-ATTTAGTATGTG
1 ATTG-AATTGATTGAATTTA-TAT-TG
*
27574899 A-TGAATTTATTGAATTTATATTG
1 ATTGAATTGATTGAATTTATATTG
27574922 ATTGAATTG
1 ATTGAATTG
27574931 GTATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 3 0.11
24 17 0.61
25 7 0.25
26 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (24 bp):
ATTGAATTGATTGAATTTATATTG
Found at i:27575188 original size:37 final size:38
Alignment explanation
Indices: 27575088--27575190 Score: 100
Period size: 37 Copynumber: 2.7 Consensus size: 38
27575078 AGCTTCGAGT
**
27575088 CGATGAGACACTGGGTGTCAATTTACTACTTCAGATTAATT
1 CGATGAGACACTGGGTGTCAA-TT--TACTTCAGATTAAGC
* * * * * *
27575129 CAATGAGGCACTAGGTGCCAATTTACTTC-GGTTTAGC
1 CGATGAGACACTGGGTGTCAATTTACTTCAGATTAAGC
27575166 CGATGAGACACTGGGTGTCAATTTA
1 CGATGAGACACTGGGTGTCAATTTA
27575191 TTACTTTGAA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 25 0.50
38 6 0.12
40 2 0.04
41 17 0.34
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAATTTACTTCAGATTAAGC
Found at i:27580202 original size:13 final size:13
Alignment explanation
Indices: 27580184--27580208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27580174 TAAATGATAA
27580184 AAATTTTCACACG
1 AAATTTTCACACG
27580197 AAATTTTCACAC
1 AAATTTTCACAC
27580209 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:27591438 original size:16 final size:16
Alignment explanation
Indices: 27591417--27591449 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
27591407 TAAATCCCCA
27591417 ATCCAAAAACTAATTG
1 ATCCAAAAACTAATTG
27591433 ATCCAAAAACTAATTG
1 ATCCAAAAACTAATTG
27591449 A
1 A
27591450 CAACATGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.24
Consensus pattern (16 bp):
ATCCAAAAACTAATTG
Found at i:27599806 original size:20 final size:20
Alignment explanation
Indices: 27599772--27599813 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
27599762 AACTATTTAA
** *
27599772 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
27599792 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
27599812 AT
1 AT
27599814 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:27606665 original size:36 final size:35
Alignment explanation
Indices: 27606613--27606693 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 35
27606603 TTTTACCGAC
*
27606613 TGAACTTGATATTCAAATTAAGGTTTTTATGATGG
1 TGAACTTGATATTCAAATTAAAGTTTTTATGATGG
27606648 TGAACTTTGATATTCAAATTAAAGTTTTTATGATGG
1 TGAAC-TTGATATTCAAATTAAAGTTTTTATGATGG
27606684 TGTAA-TTGAT
1 TG-AACTTGAT
27606694 GGTCTGTTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 10 0.23
36 31 0.72
37 2 0.05
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (35 bp):
TGAACTTGATATTCAAATTAAAGTTTTTATGATGG
Found at i:27623125 original size:17 final size:17
Alignment explanation
Indices: 27623091--27623128 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
27623081 AATTATCAAC
*
27623091 AAATAATCTCAAATAAT
1 AAATAATCTCAAAGAAT
*
27623108 AAATAATCTCAAGGAAT
1 AAATAATCTCAAAGAAT
27623125 AAAT
1 AAAT
27623129 TCAAATTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (17 bp):
AAATAATCTCAAAGAAT
Found at i:27646859 original size:67 final size:67
Alignment explanation
Indices: 27646729--27646868 Score: 181
Period size: 67 Copynumber: 2.1 Consensus size: 67
27646719 CTAACCATGC
* ** * * * *
27646729 GTATGTAACTCATTTACTTTGATATAATTAGAGGCTCATGCTCTAAAGATGATCGAGCCCATAGT
1 GTATGTAACTCATTTACTTTGAAATAAGCAGAGACTCATGCTCTAAAGATGATCGAACACATAGC
27646794 TA
66 TA
* * *
27646796 GTATGTAACTCATTTGCTTTGAAATAAGCAGAGACTTATGCTCTAAAGATGATTGAACACATAGC
1 GTATGTAACTCATTTACTTTGAAATAAGCAGAGACTCATGCTCTAAAGATGATCGAACACATAGC
*
27646861 TG
66 TA
27646863 GTATGT
1 GTATGT
27646869 TGGGTACATG
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (67 bp):
GTATGTAACTCATTTACTTTGAAATAAGCAGAGACTCATGCTCTAAAGATGATCGAACACATAGC
TA
Found at i:27649383 original size:42 final size:42
Alignment explanation
Indices: 27649312--27649392 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
27649302 TCGTGTCCCA
* *
27649312 GCCCGTGTAACTTACTAACTTGAGACACATGACCGTATCTCT
1 GCCCATGTAACTCACTAACTTGAGACACATGACCGTATCTCT
*
27649354 GCCCATGTAACTCACTAACTT-AGGTCACATGACCGTATC
1 GCCCATGTAACTCACTAACTTGA-GACACATGACCGTATC
27649393 CCAGGCCGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (42 bp):
GCCCATGTAACTCACTAACTTGAGACACATGACCGTATCTCT
Found at i:27650209 original size:30 final size:30
Alignment explanation
Indices: 27650168--27650226 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
27650158 GAGTTCACAA
* *
27650168 GTTTTAGCACAT-TGCAATGATATTTCATAT
1 GTTTAAGCACATAT-CAATGATATTCCATAT
*
27650198 GTTTAAGCACATATCAATGTTATTCCATA
1 GTTTAAGCACATATCAATGATATTCCATA
27650227 AATATAGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (30 bp):
GTTTAAGCACATATCAATGATATTCCATAT
Found at i:27650353 original size:18 final size:19
Alignment explanation
Indices: 27650311--27650358 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
27650301 GATTCACATC
27650311 TCATTTCATCATCCCATATT
1 TCATTTC-TCATCCCATATT
*
27650331 TCATTTCTCATCTCATA-T
1 TCATTTCTCATCCCATATT
27650349 TCATTTCTCA
1 TCATTTCTCA
27650359 ACATTGCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 11 0.41
19 9 0.33
20 7 0.26
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (19 bp):
TCATTTCTCATCCCATATT
Found at i:27653172 original size:19 final size:19
Alignment explanation
Indices: 27653143--27653206 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 19
27653133 TAGAATATTT
27653143 AAATATTAAATTTTTATAAA
1 AAAT-TTAAATTTTTATAAA
*
27653163 AAATTTAAA-TATTA-AAA
1 AAATTTAAATTTTTATAAA
27653180 AAA--T--ATTTTTAT--A
1 AAATTTAAATTTTTATAAA
27653193 AAATTTAAATTTTT
1 AAATTTAAATTTTT
27653207 TTTATAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 15
0.68 0.04 0.28
Matches are distributed among these distances:
13 5 0.14
14 4 0.11
15 2 0.06
17 12 0.33
18 4 0.11
19 5 0.14
20 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTTAAATTTTTATAAA
Found at i:27659939 original size:14 final size:14
Alignment explanation
Indices: 27659922--27659952 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27659912 TTTATTTTTA
*
27659922 TTATCATTATTGTT
1 TTATCATTATTATT
27659936 TTATCATTATTATT
1 TTATCATTATTATT
27659950 TTA
1 TTA
27659953 ATTTGTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (14 bp):
TTATCATTATTATT
Found at i:27667519 original size:2 final size:2
Alignment explanation
Indices: 27667512--27667537 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27667502 ATTAAGTTTG
27667512 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
27667538 TAAGACTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27682021 original size:44 final size:44
Alignment explanation
Indices: 27681973--27682116 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 44
27681963 AGACACCAGC
27681973 CTTGCCTCTCTGGGTTGTAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCTCTGGGTTGTAGCGGAGCAGGTTAAAAATAGCAGAT
**** * * * ** * * * *
27682017 CTTGCCT-TCCTGCACCGACAGCGAAGCAGATCGAAGACACCA-AC
1 CTTGCCTCT-CTGGGTTG-TAGCGGAGCAGGTTAAAAATAGCAGAT
*
27682061 CTTGCCTCCCTGGGTTGTAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCTCTGGGTTGTAGCGGAGCAGGTTAAAAATAGCAGAT
*
27682105 CTTGCCTTTCTG
1 CTTGCCTCTCTG
27682117 CACCGACAGC
Statistics
Matches: 67, Mismatches: 29, Indels: 8
0.64 0.28 0.08
Matches are distributed among these distances:
43 17 0.25
44 34 0.51
45 16 0.24
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (44 bp):
CTTGCCTCTCTGGGTTGTAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:27682074 original size:88 final size:88
Alignment explanation
Indices: 27681925--27682138 Score: 401
Period size: 88 Copynumber: 2.4 Consensus size: 88
27681915 TGAAGATAAT
* *
27681925 AGATCTTGCCTTTCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCTCTGGGTTG
1 AGATCTTGCCTTTCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTTG
27681990 TAGCGGAGCAGGTTAAAAATAGC
66 TAGCGGAGCAGGTTAAAAATAGC
*
27682013 AGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTTG
1 AGATCTTGCCTTTCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTTG
27682078 TAGCGGAGCAGGTTAAAAATAGC
66 TAGCGGAGCAGGTTAAAAATAGC
27682101 AGATCTTGCCTTTCTGCACCGACAGCGAAGCAGATCGA
1 AGATCTTGCCTTTCTGCACCGACAGCGAAGCAGATCGA
27682139 TGACTCAGCC
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 122 1.00
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.21
Consensus pattern (88 bp):
AGATCTTGCCTTTCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTTG
TAGCGGAGCAGGTTAAAAATAGC
Found at i:27682214 original size:44 final size:43
Alignment explanation
Indices: 27682148--27682419 Score: 174
Period size: 44 Copynumber: 6.2 Consensus size: 43
27682138 ATGACTCAGC
* *
27682148 CCTATCTCCCTAGGCAGTAGTGGAATAGGTTTAAGTTTGTGAAT
1 CCTATCTCCCT-GGCAGTAGTGGAATAGGTTAAAGATTGTGAAT
* *
27682192 TCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGG-CAGTAGTGGAATAGGTTAAAGATTGTGAAT
* * **
27682236 CCTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAA-ATT-ACAGAT
1 CCTATCTCCCTG-GCAGTAGTGGAATAGGTT-AAAGATTGTGA-AT
* ** ** * ** **** *
27682280 CTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAG--TCCCCAG
1 CCTATCTCCCT-GGCAGTAGTGGAATAGGTTAAAGATTGTGAAT
* * *
27682322 CCTTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTATGAAT
1 CC-TATCTCCCTGG-CAGTAGTGGAATAGGTTAAAGATTGTGAAT
* * * *
27682367 CCTATCTCCCTGGTCAGCAGGGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGG-CAGTAGTGGAATAGGTTAAAGATTGTGAAT
*
27682411 CTTATCTCC
1 CCTATCTCC
27682420 TTAAAGTTGC
Statistics
Matches: 179, Mismatches: 38, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
42 3 0.02
43 31 0.17
44 137 0.77
45 8 0.04
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (43 bp):
CCTATCTCCCTGGCAGTAGTGGAATAGGTTAAAGATTGTGAAT
Found at i:27682463 original size:175 final size:175
Alignment explanation
Indices: 27682144--27682465 Score: 389
Period size: 175 Copynumber: 1.8 Consensus size: 175
27682134 ATCGATGACT
* * * * *
27682144 CAGCCCTATCTCCCTAGGCAGTAGTGGAATAGGTTTAAGTTTGTGAATTCTATCTCCCTGGTCAG
1 CAGCCCTATCTCCCTAGGCAGCAGTGGAATAGGTTGAAGATTATGAATCCTATCTCCCTGGTCAG
* * * * * * * **
27682209 CAGTGGAATAGGTTAAAGATTGTGAATCCTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATT
66 CAGGGGAATAGGTTAAAGATTGAGAATCCTATCTCCCTAAGCAGCAGTGGAATAGATTGAAAACC
* *
27682274 ACAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGTCCC
131 ACAAATCCTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGTCCC
*
27682319 CAGCCTTATCTCCCT-GGTCAGCAGTGGAATAGGTTGAAGATTATGAATCCTATCTCCCTGGTCA
1 CAGCCCTATCTCCCTAGG-CAGCAGTGGAATAGGTTGAAGATTATGAATCCTATCTCCCTGGTCA
* * * ** *
27682383 GCAGGGGAATAGGTTGAAGATTGAGAATCTTATCTCCTTAAAGTTGCAGTGGAATAGATT-AAAG
65 GCAGGGGAATAGGTTAAAGATTGAGAATCCTATCTCCCT-AAGCAGCAGTGGAATAGATTGAAAA
27682447 CCA-ATAATCCTATCTCCCT
129 CCACA-AATCCTATCTCCCT
27682466 GAAGTTGTAG
Statistics
Matches: 121, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
174 3 0.02
175 104 0.86
176 14 0.12
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (175 bp):
CAGCCCTATCTCCCTAGGCAGCAGTGGAATAGGTTGAAGATTATGAATCCTATCTCCCTGGTCAG
CAGGGGAATAGGTTAAAGATTGAGAATCCTATCTCCCTAAGCAGCAGTGGAATAGATTGAAAACC
ACAAATCCTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGTCCC
Found at i:27682595 original size:44 final size:45
Alignment explanation
Indices: 27682538--27682653 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 45
27682528 GTCGCATCTG
* *
27682538 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGACT-AAGAAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATGAACAAA
* * * * *
27682582 GTCTTATCCCCCTGAAATTACAGTGGGGCAGACTGAATGAACAAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATGAACAAA
* * *
27682627 -TCTTATCTCCTTAAAGTTGTAGTGGAG
1 GTCTTATCTCCCTGAAGTTGCAGTGGAG
27682654 TGGATTAGAA
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
44 52 0.91
45 5 0.09
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (45 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATGAACAAA
Found at i:27690514 original size:21 final size:21
Alignment explanation
Indices: 27690477--27690517 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27690467 TTAATCCAAA
27690477 TACAAAATAAAATTAAATAAT
1 TACAAAATAAAATTAAATAAT
*
27690498 TACAAGATATAAA-TAAATAA
1 TACAAAATA-AAATTAAATAA
27690518 ATAATGGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
TACAAAATAAAATTAAATAAT
Found at i:27693906 original size:19 final size:19
Alignment explanation
Indices: 27693884--27693923 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
27693874 AATTTAATGA
*
27693884 TTTTTTAAAATTTTT-AAT
1 TTTTTTTAAATTTTTAAAT
*
27693902 TTTTTTTGAATTTTTAAAT
1 TTTTTTTAAATTTTTAAAT
27693921 TTT
1 TTT
27693924 AAAAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTTTTTAAATTTTTAAAT
Found at i:27715454 original size:5 final size:5
Alignment explanation
Indices: 27715444--27715469 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
27715434 CTCATGACAA
27715444 AGATG AGATG AGATG AGATG AGATG A
1 AGATG AGATG AGATG AGATG AGATG A
27715470 TATGTCAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.19
Consensus pattern (5 bp):
AGATG
Found at i:27719099 original size:32 final size:32
Alignment explanation
Indices: 27719018--27719101 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
27719008 TATTGAAATT
*
27719018 AACTTGTTGGATTTTAAAATTATTATGTTTTA
1 AACTTGTTGGATTTTGAAATTATTATGTTTTA
*
27719050 AACTTGTTGGATTTTGAATTTATTATGTTTTA
1 AACTTGTTGGATTTTGAAATTATTATGTTTTA
** *
27719082 AGTTTGTTGGATATTGAAAT
1 AACTTGTTGGATTTTGAAAT
27719102 GATTGACAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (32 bp):
AACTTGTTGGATTTTGAAATTATTATGTTTTA
Found at i:27723664 original size:16 final size:16
Alignment explanation
Indices: 27723613--27723664 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
27723603 TGGTTCACTG
*
27723613 TAATGGAATAGGGCTA
1 TAATGGAATAGAGCTA
* * *
27723629 TAATTGAATAGAGTTG
1 TAATGGAATAGAGCTA
*
27723645 TAATGGAATATAGCTA
1 TAATGGAATAGAGCTA
27723661 TAAT
1 TAAT
27723665 CAGTAATTCA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (16 bp):
TAATGGAATAGAGCTA
Done.