Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 183 of 205
Found at i:54422359 original size:200 final size:201
Alignment explanation
Indices: 54421926--54422435 Score: 810
Period size: 200 Copynumber: 2.5 Consensus size: 201
54421916 TCGGGGAAGC
* * * *
54421926 AAGATTCGCTGTTGTGGCTTTAATATTTTTAACTGCAATGTCGAGGAAGCAAGATTCGCCGTTGT
1 AAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGT
*
54421991 GGCTTTAATCTGTTCCATTGCACTGCCTGGGAGAGTAAGATTCGTCGTTGTGACTTTATTCCATT
66 GGCTTTAATCTGTTCCATTGCACTGCCTGGGAGAGTAAGATTCGTCGTTGTGACTTTAATCCATT
*
54422056 TAACTGCAATGTTGGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
131 TAACTGCAATGTCGGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
54422121 AGAGGT
196 AGAGGT
* *
54422127 AAAATTTGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGT
1 AAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGT
* * *
54422192 GGCTTTAATCTGTTTCATTGCACTGCCTAGGAGAGTAAGATTCGTCGTTGTGAC-TTAATCCTTT
66 GGCTTTAATCTGTTCCATTGCACTGCCTGGGAGAGTAAGATTCGTCGTTGTGACTTTAATCCATT
* *
54422256 TAACTGCAATGTCGGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCATTGCACCGTCTG
131 TAACTGCAATGTCGGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
*
54422321 GGAGGT
196 AGAGGT
* * * *
54422327 AAGATTCGCTGCTGTAGCTTTCATCTTTTTAACCGCAATGTCAGGG-AGACAAGATTCACCGTTG
1 AAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAG-CAAGATTCGCCGTTG
* *
54422391 TGGCTTTAATCTGTTCCACTGCACCGCCTGGGAG-GTAAGATTCGT
65 TGGCTTTAATCTGTTCCATTGCACTGCCTGGGAGAGTAAGATTCGT
54422436 AATCTTCAAC
Statistics
Matches: 284, Mismatches: 24, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
199 13 0.05
200 160 0.56
201 111 0.39
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (201 bp):
AAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGT
GGCTTTAATCTGTTCCATTGCACTGCCTGGGAGAGTAAGATTCGTCGTTGTGACTTTAATCCATT
TAACTGCAATGTCGGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
AGAGGT
Found at i:54422684 original size:131 final size:131
Alignment explanation
Indices: 54422420--54423681 Score: 1984
Period size: 131 Copynumber: 9.8 Consensus size: 131
54422410 TGCACCGCCT
* *
54422420 GGGAGGTAAGAT-TCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCT
1 GGGAGATAAGATCT-GTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCT
* *
54422484 TAAATC-GTTTCCCTACTCCTGGGGAAGATAAGATTTGCCGTCTTCGATCTGCTTCACTATTGCT
65 TAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCT
54422548 TA
130 TA
*
54422550 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGTTGACCAGGGAGATAGGACTGGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
54422615 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
54422680 A
131 A
* * *
54422681 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTACTGACCAGGGAGATAGGAATAGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
** * * * *
54422746 AAATCTACTGCCCTACTTCTTGGGAAGATAAGATTCGCCGTTTTCGATCTGCTCCACTATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
54422811 A
131 A
54422812 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
* * *
54422877 AAATCTGTTTCCCTACTCCTAGGGAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
54422942 A
131 A
* *
54422943 AGGTGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
*
54423008 AAATCTGTTTCCCTACTCTTGGGGAAGATAAGATT---CG-C--CG---T-CT----T-TTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
54423058 A
131 A
* *
54423059 GGGAGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
* *
54423124 AAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
54423189 A
131 A
* * ** * *
54423190 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGC-GATCTGTAATCATAGGACTAGTGGCT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGA-GATAGGACTGGTGGCT
* * *
54423254 TAAATCTGCTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
65 TAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCT
54423319 TA
130 TA
54423321 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
* * *
54423386 AAATTTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTCGTCTTCGATCTTCTCCACTATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
54423451 A
131 A
*
54423452 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTTGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
* * *
54423517 AAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATTTGCTCCACAATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
54423582 A
131 A
* * *
54423583 GGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATTGATGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
*
54423648 AAATCTGCTTCCCTACTCCTGGGGAAGATAAGAT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGAT
54423682 CCGTAATCTT
Statistics
Matches: 1043, Mismatches: 70, Indels: 37
0.91 0.06 0.03
Matches are distributed among these distances:
116 101 0.10
117 1 0.00
119 2 0.00
120 1 0.00
121 2 0.00
122 3 0.00
125 2 0.00
126 2 0.00
127 1 0.00
128 2 0.00
130 71 0.07
131 850 0.81
132 5 0.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (131 bp):
GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
A
Found at i:54422690 original size:44 final size:45
Alignment explanation
Indices: 54422640--54422823 Score: 107
Period size: 44 Copynumber: 4.2 Consensus size: 45
54422630 CTCCTGGGGA
*
54422640 AGATAAGATTCGCCGTCTTCGATCTGCT-CCACTATTGCTTAGGG
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCCACTATTGCTTAGGG
*** * * * *
54422684 AGATAAGA-TCTGTAATCTTCAACCT-ATCCCACTACTGAC-CAGGG
1 AGATAAGATTC-GCCGTCTTCAATCTGCTCCCACTATTG-CTTAGGG
* * * * * * * *
54422728 AGATAGGAATAG-TGGCTTAAATCTACTGCC-CTACTT-CTT-GGG
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCCACTA-TTGCTTAGGG
* *
54422770 AAGATAAGATTCGCCGTTTTCGATCTGCT-CCACTATTGCTTAGGG
1 -AGATAAGATTCGCCGTCTTCAATCTGCTCCCACTATTGCTTAGGG
54422815 AGATAAGAT
1 AGATAAGAT
54422824 CTGTAATCTT
Statistics
Matches: 100, Mismatches: 28, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
42 4 0.04
43 26 0.26
44 65 0.65
45 5 0.05
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (45 bp):
AGATAAGATTCGCCGTCTTCAATCTGCTCCCACTATTGCTTAGGG
Found at i:54423140 original size:116 final size:116
Alignment explanation
Indices: 54422936--54423167 Score: 410
Period size: 116 Copynumber: 2.0 Consensus size: 116
54422926 TGCTCCACTA
* * *
54422936 TTGCTTAAGGTGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTG
1 TTGCTTAAGGAGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTA
* *
54423001 GTGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTT
66 GTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTT
*
54423052 TTGCTTAGGGAGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTA
1 TTGCTTAAGGAGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTA
54423117 GTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTT
66 GTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTT
54423168 CGATCTGCTC
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 110 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (116 bp):
TTGCTTAAGGAGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTA
GTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTT
Found at i:54423356 original size:44 final size:45
Alignment explanation
Indices: 54423308--54423487 Score: 99
Period size: 44 Copynumber: 4.1 Consensus size: 45
54423298 TCGATCTGCT
54423308 CCACTACTGCTTAGGGAGATAAGATCT-GTAATCTTCAACCTATC
1 CCACTACTGCTTAGGGAGATAAGATCTCGTAATCTTCAACCTATC
* * * * ** * ** * *
54423352 CCACTGCTGAC-CAGGGAGATAGGA-CTGGT-GGCTTAAATTTGTTT
1 CCACTACTG-CTTAGGGAGATAAGATCTCGTAATCTTCAACCT-ATC
* * ** * *
54423396 CC-CTACT-CCTGGGGAAGATAAGAT-TCGTCGTCTTCGATCT-TC
1 CCACTACTGCTTAGGG-AGATAAGATCTCGTAATCTTCAACCTATC
*
54423438 TCCACTATTGCTTAGGGAGATAAGATCT-GTAATCTTCAACCTATC
1 -CCACTACTGCTTAGGGAGATAAGATCTCGTAATCTTCAACCTATC
54423483 CCACT
1 CCACT
54423488 GCTGACCAGG
Statistics
Matches: 97, Mismatches: 27, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
41 1 0.01
42 4 0.04
43 24 0.25
44 59 0.61
45 9 0.09
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (45 bp):
CCACTACTGCTTAGGGAGATAAGATCTCGTAATCTTCAACCTATC
Found at i:54423630 original size:44 final size:44
Alignment explanation
Indices: 54423582--54423721 Score: 116
Period size: 44 Copynumber: 3.2 Consensus size: 44
54423572 ACAATTGCTT
54423582 AGGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACC
1 AGGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACC
* * * *
54423626 AGGGAGATAGGAT---TGATGGCTTAAATCTGCT-TCCCTACTCCTG---
1 AGGGAGATAAGATCCGTAAT--CTTCAA-C--CTATCCC-ACTGCTGACC
*
54423669 -GGGAAGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACC
1 AGGG-AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACC
54423713 AGGGAGATA
1 AGGGAGATA
54423722 GGACTAGTGG
Statistics
Matches: 72, Mismatches: 9, Indels: 30
0.65 0.08 0.27
Matches are distributed among these distances:
41 11 0.15
42 6 0.08
43 14 0.19
44 23 0.32
45 7 0.10
46 11 0.15
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (44 bp):
AGGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACC
Found at i:54423720 original size:218 final size:218
Alignment explanation
Indices: 54423455--54423899 Score: 737
Period size: 218 Copynumber: 2.0 Consensus size: 218
54423445 TTGCTTAGGG
* *
54423455 AGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* ** *
54423520 TCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATTTGCTCCACAATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACAATTGCTTAGG
* *
54423585 GAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATTGATGGCTTAA
131 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGATGGCTTAA
54423650 ATCTGCTTCCCTACTCCTGGGGA
196 ATCTGCTTCCCTACTCCTGGGGA
*
54423673 AGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* * *
54423738 TCTGTTTCCTTACTCCTGGGGAAGATAAGATTCGCCACCTTCTATCTGCTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACAATTGCTTAGG
* * *
54423803 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTTACTAGGGAGATAGGACTGGTGGCTTAA
131 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGATGGCTTAA
* *
54423868 ATCTGTTTCCCTACTTCTGGGGA
196 ATCTGCTTCCCTACTCCTGGGGA
54423891 AGATAAGAT
1 AGATAAGAT
54423900 TCACCGTCTT
Statistics
Matches: 210, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
218 210 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (218 bp):
AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACAATTGCTTAGG
GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGATGGCTTAA
ATCTGCTTCCCTACTCCTGGGGA
Found at i:54423733 original size:87 final size:87
Alignment explanation
Indices: 54423586--54423768 Score: 314
Period size: 87 Copynumber: 2.1 Consensus size: 87
54423576 TTGCTTAGGG
*
54423586 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATTGATGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATAGATGGCTTAAA
54423651 TCTGCTTCCCTACTCCTGGGGA
66 TCTGCTTCCCTACTCCTGGGGA
*
54423673 AGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAGGGAGATAGGACTAG-TGGCTTAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGA-TAGATGGCTTAA
* *
54423737 ATCTGTTTCCTTACTCCTGGGGA
65 ATCTGCTTCCCTACTCCTGGGGA
54423760 AGATAAGAT
1 AGATAAGAT
54423769 TCGCCACCTT
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
87 89 0.98
88 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (87 bp):
AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATAGATGGCTTAAA
TCTGCTTCCCTACTCCTGGGGA
Found at i:54423768 original size:349 final size:349
Alignment explanation
Indices: 54423324--54424030 Score: 1175
Period size: 349 Copynumber: 2.0 Consensus size: 349
54423314 CTGCTTAGGG
* *
54423324 AGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* * ** *
54423389 TTTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTCGTCTTCGATCTTCTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACTATTGCTTAGG
* * *
54423454 GAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAA
131 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAA
* *
54423519 ATCTGTTTCCCTAC-TCTTGGGGAAGATAAGATTCGCCGTCTTCGATTTGCTCCACAATTGCTTA
196 ATCTGTTTCCCTACTTC-TGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACAATTGCTTA
* *
54423583 GGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGA-TTGATGGCT
260 GGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAG-TGGCT
*
54423647 TAAATCTGCTTCCCTACTCCTGGGGA
324 TAAATCTGCTTCCCTACTCCTGGAGA
*
54423673 AGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* *
54423738 TCTGTTTCCTTACTCCTGGGGAAGATAAGATTCGCCACCTTCTATCTGCTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACTATTGCTTAGG
* *
54423803 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTTACTAGGGAGATAGGACTGGTGGCTTAA
131 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAA
*
54423868 ATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAG
196 ATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACAATTGCTTAG
* *
54423933 GGAGATAAGATCTGTGATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCTTA
261 GGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCTTA
54423998 AATCTGCTTCCCTACTCCTGGAGA
326 AATCTGCTTCCCTACTCCTGGAGA
54424022 AGATAAGAT
1 AGATAAGAT
54424031 TCGCCGTCTT
Statistics
Matches: 333, Mismatches: 23, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
349 329 0.99
350 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.29
Consensus pattern (349 bp):
AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACTATTGCTTAGG
GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAA
ATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACAATTGCTTAG
GGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCTTA
AATCTGCTTCCCTACTCCTGGAGA
Found at i:54423785 original size:131 final size:131
Alignment explanation
Indices: 54423673--54424384 Score: 1091
Period size: 131 Copynumber: 5.4 Consensus size: 131
54423663 CTCCTGGGGA
*
54423673 AGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* ** * *
54423738 TCTGTTTCCTTACTCCTGGGGAAGATAAGATTCGCCACCTTCTATCTGCTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCCTAGG
54423803 G
131 G
* * * *
54423804 AGATAAGATCCGTAATCTTCAACCCATCCCACTGCTTACTAGGGAGATAGGACTGGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* * *
54423869 TCTGTTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCCTAGG
54423934 G
131 G
* * *
54423935 AGATAAGATCTGTGATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* * * ** *
54424000 TCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATCACTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCCTAGG
54424065 G
131 G
* * * *
54424066 AGATAAGATCTGTAATCTTCAAGCTATCACACTGCTGACCAGGGAGATAGGACTGGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* * ** * * *
54424131 TCTGCTTCCCTACTCCTAGGGAAGATAAGATTCGTTGCCTTCGATCTGCTCCACTATTGCTTAGA
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCCTAGG
54424196 G
131 G
*
54424197 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* *
54424262 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCCTAGG
54424327 G
131 G
*
54424328 AGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGT
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGT
54424385 AGTCTTCCAC
Statistics
Matches: 530, Mismatches: 51, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
131 530 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (131 bp):
AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCCTAGG
G
Found at i:54423810 original size:262 final size:258
Alignment explanation
Indices: 54423542--54424336 Score: 761
Period size: 262 Copynumber: 3.0 Consensus size: 258
54423532 CTCTTGGGGA
** * * *
54423542 AGATAAGATTCGCCGTCTTCGATTTGCTCCACAATTGCT-TAGGGAGATAAGA-TCCGTAATCTT
1 AGATAAGATTCGCAATCTTC-A--TGCTCCAC-ACTGCTATAGGGAGATAAGACT-GGT-AGCTT
* *
54423605 CAACCTATCCCACTGCTGACCAGGG-AGATAGGATTGATGGCTTAAATCTGCTTCC-CTACTCCT
60 AAACCTATCCCACTGCTG-CCAGGGAAGATAAGATTGATGGCTTAAATCTGC-TCCACTACTCCT
* *
54423668 GGGGAAGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAGGGAGATAGGACTAGTGGC
123 GGGGAAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGC
* ** * *
54423733 TTAAATCTGTTTCCTTACTCCTGGGGAAGATAAGATTCGCCACCTTCTATCTGCTCCACTATTGC
188 TTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATTGC
54423798 TTAGGG
253 TTAGGG
* * ** * *
54423804 AGATAAGATCCGTAATCTTCAACCCATCC-CACTGCTTACTAGGGAGATAGGACTGGTGGCTTAA
1 AGATAAGATTCGCAATCTTC-ATGC-TCCACACTGC-TA-TAGGGAGATAAGACTGGTAGCTTAA
* * * * * * ** * *
54423868 ATCTGTTTCCCTACTTCTG---GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCT
62 A-C-CTATCCC-ACTGCTGCCAGGGAAGATAAGATTGA-TGGCTTAAATCTGCTCCACTACT-CC
* * *
54423930 TAGGG-AGATAAGATCTGTGATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGG
122 TGGGGAAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGG
* * **
54423994 CTTAAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATCA
187 CTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATTG
54424059 CTTAGGG
252 CTTAGGG
* * * * * *
54424066 AGATAAGA-TCTGTAATCTTCAAGCTATCACACTGCTGACCAGGGAGATAGGACTGGTGGCTTAA
1 AGATAAGATTC-GCAATCTTCATGCT-CCACACTGCT-A-TAGGGAGATAAGACTGGTAGCTTAA
* * * * * * ** * *
54424130 ATCTGCTTCC-CTACT-CCTAGGGAAGATAAGATTCGTTGCCTTCGATCTGCTCCACTATTGCT-
62 ACCT-ATCCCACTGCTGCC-AGGGAAGATAAGATT-GATGGCTTAAATCTGCTCCACTACTCCTG
** * *
54424192 TAGAGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGC
124 GGGA-AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGC
54424257 TTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATTGC
188 TTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATTGC
54424322 TTAGGG
253 TTAGGG
54424328 AGATAAGAT
1 AGATAAGAT
54424337 CTGTAATCTT
Statistics
Matches: 444, Mismatches: 64, Indels: 49
0.80 0.11 0.09
Matches are distributed among these distances:
259 8 0.02
260 9 0.02
261 30 0.07
262 380 0.86
263 11 0.02
264 6 0.01
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (258 bp):
AGATAAGATTCGCAATCTTCATGCTCCACACTGCTATAGGGAGATAAGACTGGTAGCTTAAACCT
ATCCCACTGCTGCCAGGGAAGATAAGATTGATGGCTTAAATCTGCTCCACTACTCCTGGGGAAGA
TAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCTTAAATCT
GTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATTGCTTAGGG
Found at i:54423880 original size:611 final size:611
Alignment explanation
Indices: 54423062--54424292 Score: 2011
Period size: 611 Copynumber: 2.0 Consensus size: 611
54423052 TTGCTTAGGG
* *
54423062 AGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
**
54423127 TCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGG
66 TCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACTACTGCTTAGG
* * *
54423192 GAGATAAGATCTGTAATCTTCAACCTATCCCACTGCGATCTGTAATCATAGGACTAGTGGCTTAA
131 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCGATCTGGAATCATAGGACTAGTGGCTTAA
*
54423257 ATCTGCTTCCCTAC-TCTTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTA
196 ATCTGCTTCCCTACTTC-TGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTA
* *
54423321 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
260 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCTT
* * * * **
54423386 AAATTTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTCGTCTTCGATCT-TCTCCACTATTGCT
325 AAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCTTCGATCTGT-TCCACTATCACT
* *
54423450 TAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTTGTGGC
389 TAGGGAGATAAGATCTGTAATCTTCAACCTATCACACTGCTGACCAGGGAGATAGGACTGGTGGC
* * * * *
54423515 TTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATTTGCTCCACAATTGC
454 TTAAATCTGCTTCCCTACTCCTAGGGAAGATAAGATTCGCCGCCTTCGATCTGCTCCACAATTGC
* *
54423580 TTAGGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATTGATGG
519 TTAGAGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGATGG
54423645 CTTAAATCTGCTTCCCTACTCCTGGGGA
584 CTTAAATCTGCTTCCCTACTCCTGGGGA
*
54423673 AGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* * * *
54423738 TCTGTTTCCTTACTCCTGGGGAAGATAAGATTCGCCACCTTCTATCTGCTCCACTATTGCTTAGG
66 TCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACTACTGCTTAGG
* * * *
54423803 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGC-TTACTAGGGA-GATAGGACTGGTGGCTT
131 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCGAT-CT-GGAATCATAGGACTAGTGGCTT
* *
54423866 AAATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTT
194 AAATCTGCTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTT
*
54423931 AGGGAGATAAGATCTGTGATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCT
259 AGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCT
54423996 TAAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATCACT
324 TAAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATCACT
*
54424061 TAGGGAGATAAGATCTGTAATCTTCAAGCTATCACACTGCTGACCAGGGAGATAGGACTGGTGGC
389 TAGGGAGATAAGATCTGTAATCTTCAACCTATCACACTGCTGACCAGGGAGATAGGACTGGTGGC
** *
54424126 TTAAATCTGCTTCCCTACTCCTAGGGAAGATAAGATTCGTTGCCTTCGATCTGCTCCACTATTGC
454 TTAAATCTGCTTCCCTACTCCTAGGGAAGATAAGATTCGCCGCCTTCGATCTGCTCCACAATTGC
*
54424191 TTAGAGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGG
519 TTAGAGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGATGG
*
54424256 CTTAAATCTGTTTCCCTACTCCTGGGGA
584 CTTAAATCTGCTTCCCTACTCCTGGGGA
54424284 AGATAAGAT
1 AGATAAGAT
54424293 TCGCCGTCTT
Statistics
Matches: 573, Mismatches: 43, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
610 1 0.00
611 567 0.99
612 5 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.29
Consensus pattern (611 bp):
AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
TCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACTACTGCTTAGG
GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCGATCTGGAATCATAGGACTAGTGGCTTAA
ATCTGCTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAG
GGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCTTA
AATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATCACTTA
GGGAGATAAGATCTGTAATCTTCAACCTATCACACTGCTGACCAGGGAGATAGGACTGGTGGCTT
AAATCTGCTTCCCTACTCCTAGGGAAGATAAGATTCGCCGCCTTCGATCTGCTCCACAATTGCTT
AGAGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGATGGCT
TAAATCTGCTTCCCTACTCCTGGGGA
Found at i:54424003 original size:480 final size:480
Alignment explanation
Indices: 54423170--54424161 Score: 1567
Period size: 480 Copynumber: 2.1 Consensus size: 480
54423160 GCCGTCTTCG
* * * *
54423170 ATCTGC-TCCACTACTGCTTAGGG-AGATAAGATCTGTAATCTTCAACCTATCCCACTGCGATCT
1 ATCTGCTTCC-CTACT-CCTAGGGAAGATAAGATCCGTAATCTTCAACCTATCCCACTGCGACCA
* * **
54423233 GTAATCATAGGACTAGTGGCTTAAATCTGCTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCT
64 GGAATCATAGGACTAGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCT
* *
54423298 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGAC
129 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGAC
* **
54423363 CAGGGAGATAGGACTGGTGGCTTAAATTTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTCGTC
194 CAGGGAGATAGGACTGGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACCGTC
*
54423428 TTCGATCTTCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGA
259 TTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGA
* * * * *
54423493 CCAGGGAGATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGT
324 CCAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGT
* ** *
54423558 CTTCGATTTGCTCCACAATTGCTTAGGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTG
389 CTTCGATCTGCTCCACAATCACTTAGGGAGATAAGATCCGTAATCTTCAACCTATCACACTGCTG
*
54423623 ACCAGGGAGATAGGATTGATGGCTTAA
454 ACCAGGGAGATAGGACTGATGGCTTAA
* *
54423650 ATCTGCTTCCCTACTCCTGGGGAAGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAG
1 ATCTGCTTCCCTACTCCTAGGGAAGATAAGATCCGTAATCTTCAACCTATCCCACTGC-GACCAG
* * * *
54423715 GGA-GATAGGACTAGTGGCTTAAATCTGTTTCCTTACTCCTGGGGAAGATAAGATTCGCCACCTT
65 GAATCATAGGACTAGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTT
* * * *
54423779 CTATCTGCTCCACTATTGCTTAGGGAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTTACT
130 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACC
*
54423844 AGGGAGATAGGACTGGTGGCTTAAATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCT
195 AGGGAGATAGGACTGGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACCGTCT
*
54423909 TCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGATCTTCAACCTATCCCACTGCTGAC
260 TCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGAC
54423974 CAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTC
325 CAGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTC
* * * *
54424039 TTCGATCTGTTCCACTATCACTTAGGGAGATAAGATCTGTAATCTTCAAGCTATCACACTGCTGA
390 TTCGATCTGCTCCACAATCACTTAGGGAGATAAGATCCGTAATCTTCAACCTATCACACTGCTGA
*
54424104 CCAGGGAGATAGGACTGGTGGCTTAA
455 CCAGGGAGATAGGACTGATGGCTTAA
54424130 ATCTGCTTCCCTACTCCTAGGGAAGATAAGAT
1 ATCTGCTTCCCTACTCCTAGGGAAGATAAGAT
54424162 TCGTTGCCTT
Statistics
Matches: 467, Mismatches: 42, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
479 5 0.01
480 454 0.97
481 8 0.02
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.29
Consensus pattern (480 bp):
ATCTGCTTCCCTACTCCTAGGGAAGATAAGATCCGTAATCTTCAACCTATCCCACTGCGACCAGG
AATCATAGGACTAGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTC
GATCTGCTCCACTACTGCTTAGGGAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCA
GGGAGATAGGACTGGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACCGTCTT
CGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACC
AGGGAGATAAGACTAGTGGCTTAAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCT
TCGATCTGCTCCACAATCACTTAGGGAGATAAGATCCGTAATCTTCAACCTATCACACTGCTGAC
CAGGGAGATAGGACTGATGGCTTAA
Found at i:54424415 original size:44 final size:43
Alignment explanation
Indices: 54424343--54424733 Score: 415
Period size: 44 Copynumber: 8.9 Consensus size: 43
54424333 AGATCTGTAA
* * ** *
54424343 TCTTCAACCTATCCCACTGCTGACCAGGGAGA-TAGGACTAGTAG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGA-ACTAGGACTA-CAG
* * * *
54424387 TCTTCCACCTATTACACTACTGGTCAGGGAACTAGGACTTGCGG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGAC-TACAG
* * * *
54424431 TCTTCCGCCTATTCCACTGCTGGTCAAGGAACTAGGACTTGCGG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGAC-TACAG
* ** *
54424475 TCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGTTTTACAA
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGG-ACTACAG
* * *
54424519 TCTTTCGCCTATTCCACTGCTGGTGAGGGAACTAGGACTTACAG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGAC-TACAG
** *
54424563 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGTTTTACAA
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGG-ACTACAG
*
54424607 TCTTTCACCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGAC-TACAG
* ** *
54424651 TCTTCCACCTATTCCACTGCTAGTCAGGGAACTAGGTTTTACAA
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGG-ACTACAG
* * *
54424695 TCTTTCGCCTATTCCACTACTGGTCAGGGAACTAGGACT
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGACT
54424734 TATCTTTGAT
Statistics
Matches: 295, Mismatches: 45, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
43 2 0.01
44 292 0.99
45 1 0.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.29
Consensus pattern (43 bp):
TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGACTACAG
Found at i:54424448 original size:88 final size:88
Alignment explanation
Indices: 54424350--54424735 Score: 560
Period size: 88 Copynumber: 4.4 Consensus size: 88
54424340 TAATCTTCAA
* ** * * *
54424350 CCTATCCCACTGCTGACCAGGGAGA-TAGGAC-TAGTAGTCTTCCACCTATTACACTACTGGTCA
1 CCTATTCCACTGCTGGTCAGGGA-ACTAGGACTTA-CAGTCTTCCACCTATTCCACTGCTGGTCA
** * ** *
54424413 GGGAACTAGGACTTGCGGTCTTCCG
64 GGGAACTAGGTTTTACAATCTTTCG
* * * *
54424438 CCTATTCCACTGCTGGTCAAGGAACTAGGACTTGCGGTCTTCCGCCTATTCCACTGCTGGTCAGG
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTCAGG
54424503 GAACTAGGTTTTACAATCTTTCG
66 GAACTAGGTTTTACAATCTTTCG
*
54424526 CCTATTCCACTGCTGGTGAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTCAGG
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTCAGG
*
54424591 GAACTAGGTTTTACAATCTTTCA
66 GAACTAGGTTTTACAATCTTTCG
*
54424614 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTAGTCAGG
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTCAGG
54424679 GAACTAGGTTTTACAATCTTTCG
66 GAACTAGGTTTTACAATCTTTCG
*
54424702 CCTATTCCACTACTGGTCAGGGAACTAGGACTTA
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTA
54424736 TCTTTGATCT
Statistics
Matches: 270, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
87 1 0.00
88 268 0.99
89 1 0.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (88 bp):
CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTCAGG
GAACTAGGTTTTACAATCTTTCG
Found at i:54424504 original size:132 final size:131
Alignment explanation
Indices: 54424341--54424735 Score: 477
Period size: 132 Copynumber: 3.0 Consensus size: 131
54424331 TAAGATCTGT
* * ** * *
54424341 AATCTTCAACCTATCCCACTGCTGACCAGGGAGA-TAGGACTAGTAGTCTTCCACCTATTACACT
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGA-ACTAGGACTA-CAGTCTTCCACCTATTCCACT
* * * *
54424405 ACTGGTCAGGGAACTAGGACTTGCGGTCTTCCGCCTATTCCACTGCTGGTCAAGGAACTAGGACT
64 GCTGGTCAGGGAACTAGGACTTACAGTCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACT
*
54424470 TGC
129 TAC
** * ** * * *
54424473 GGTCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGTTTTACAATCTTTCGCCTATTCCACTG
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGG-ACTACAGTCTTCCACCTATTCCACTG
* * **
54424538 CTGGTGAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGTTTT
65 CTGGTCAGGGAACTAGGACTTACAGTCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTT
54424603 AC
130 AC
*
54424605 AATCTTTCACCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTG
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGAC-TACAGTCTTCCACCTATTCCACTG
* ** * * *
54424670 CTAGTCAGGGAACTAGGTTTTACAATCTTTCGCCTATTCCACTACTGGTCAGGGAACTAGGACTT
65 CTGGTCAGGGAACTAGGACTTACAGTCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTT
54424735 A
130 A
54424736 TCTTTGATCT
Statistics
Matches: 218, Mismatches: 42, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
131 1 0.00
132 215 0.99
133 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (131 bp):
AATCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGACTACAGTCTTCCACCTATTCCACTGC
TGGTCAGGGAACTAGGACTTACAGTCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTA
C
Found at i:54426063 original size:15 final size:15
Alignment explanation
Indices: 54426029--54426062 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
54426019 AGCCTCTCTA
*
54426029 TTTTTACTTTTTCAT
1 TTTTTACTTTTTAAT
54426044 TTTTTA-TTTTTAAT
1 TTTTTACTTTTTAAT
54426058 TTTTT
1 TTTTT
54426063 TTGACTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTACTTTTTAAT
Found at i:54431925 original size:50 final size:50
Alignment explanation
Indices: 54431862--54432084 Score: 211
Period size: 50 Copynumber: 4.4 Consensus size: 50
54431852 TGGAAAGTAG
* *
54431862 GATTCGCTATTGTGG-TTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAA
1 GATTCGCTGTTGTGGCTTT-AATCTTTTTAACTGCAATGTCGAGGAAGCAA
*
54431912 GATTCGCTGTTGTGGCTTTAATATTTTTAACTGCAATGTCGAGGAAGCAA
1 GATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAA
* * ** * * * *
54431962 GATTCGCCGTTGTGGCTTTAATCTGTTCCATTGCACTGCCTG-GGAGAGTAA
1 GATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTC-GAGGA-AGCAA
* * ** *
54432013 GATTCG-TCGTTGTGACTTTATTCCATTTAACTGCAATGTTG-GGAAAGCAA
1 GATTCGCT-GTTGTGGCTTTAATCTTTTTAACTGCAATGTCGAGG-AAGCAA
* *
54432063 GATTCACCGTTGTGGCTTTAAT
1 GATTCGCTGTTGTGGCTTTAAT
54432085 TAGACCATTT
Statistics
Matches: 139, Mismatches: 28, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
50 102 0.73
51 37 0.27
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (50 bp):
GATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAA
Found at i:54442211 original size:77 final size:77
Alignment explanation
Indices: 54442084--54442315 Score: 455
Period size: 77 Copynumber: 3.0 Consensus size: 77
54442074 GTAGTTCTAG
*
54442084 CTGATAGGTGACAAGTCTGATGCCTTTTAGAATATAGTAAGGTCTAATGAACCTCGGACTCAACT
1 CTGATAGGTGACAAGTCTGATGCGTTTTAGAATATAGTAAGGTCTAATGAACCTCGGACTCAACT
54442149 TACCTTTACGCT
66 TACCTTTACGCT
54442161 CTGATAGGTGACAAGTCTGATGCGTTTTAGAATATAGTAAGGTCTAATGAACCTCGGACTCAACT
1 CTGATAGGTGACAAGTCTGATGCGTTTTAGAATATAGTAAGGTCTAATGAACCTCGGACTCAACT
54442226 TACCTTTACGCT
66 TACCTTTACGCT
54442238 CTGATAGGTGACAAGTCTGATGCGTTTTAGAATATAGTAAGGTCTAATGAACCTCGGACTCAACT
1 CTGATAGGTGACAAGTCTGATGCGTTTTAGAATATAGTAAGGTCTAATGAACCTCGGACTCAACT
54442303 TACCTTTACGCT
66 TACCTTTACGCT
54442315 C
1 C
54442316 AAACCAGAGA
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 154 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (77 bp):
CTGATAGGTGACAAGTCTGATGCGTTTTAGAATATAGTAAGGTCTAATGAACCTCGGACTCAACT
TACCTTTACGCT
Found at i:54443863 original size:34 final size:35
Alignment explanation
Indices: 54443825--54443891 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
54443815 TACCAGATTC
54443825 AGGCTATA-TAGAATAGGTGGCTGAGTCAAAACGG
1 AGGCTATACTAGAATAGGTGGCTGAGTCAAAACGG
54443859 AGGCTATACTAGAATAGGTGGCTGAGTCAAAAC
1 AGGCTATACTAGAATAGGTGGCTGAGTCAAAAC
54443892 AGACTTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 8 0.25
35 24 0.75
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (35 bp):
AGGCTATACTAGAATAGGTGGCTGAGTCAAAACGG
Found at i:54452733 original size:59 final size:60
Alignment explanation
Indices: 54452664--54452780 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 60
54452654 ATCACTTTAA
* * *
54452664 TATTAAATTAATATAATACTTATC-AAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTATCTAAGATAAACATTAAATTAAATTTAATATTAAATCT
* *
54452723 TATTAAATTAATAGAATATTTATCTATAAGATAAACATTAAATTAAATTTAATCTTAA
1 TATTAAATTAATAGAATACTTATC--TAAGATAAACATTAAATTAAATTTAATATTAA
54452781 GATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 22 0.44
62 28 0.56
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (60 bp):
TATTAAATTAATAGAATACTTATCTAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:54452773 original size:29 final size:31
Alignment explanation
Indices: 54452740--54452803 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
54452730 TTAATAGAAT
54452740 ATTT-ATCTATAAGATAA-ACATTAA-ATTAA
1 ATTTAATCT-TAAGATAACACATTAATATTAA
*
54452769 ATTTAATCTTAAGATAATCACTTTAATATTAA
1 ATTTAATCTTAAGATAA-CACATTAATATTAA
54452801 ATT
1 ATT
54452804 AATAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 12 0.40
30 4 0.13
31 6 0.20
32 8 0.27
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTTAATCTTAAGATAACACATTAATATTAA
Found at i:54452864 original size:68 final size:71
Alignment explanation
Indices: 54452723--54452867 Score: 163
Period size: 68 Copynumber: 2.1 Consensus size: 71
54452713 TATTAAATCT
* *
54452723 TATTAAATTAATAGAATATTTATCTATAAGATAAACATTAAATTAAATTTAATCTTAAGATAATC
1 TATTAAATTAATAAAATATTTA-CTATAAGATAAACATTAAATTAAATTTAATATTAAGATAATC
***
54452788 ACTTTAA
65 AAAATAA
** * *
54452795 TATTAAATTAATAAAATA-TTA-T-TAAGATAAGTATTAAATTTAATTTAATATTAAAGAT-ATT
1 TATTAAATTAATAAAATATTTACTATAAGATAAACATTAAATTAAATTTAATATT-AAGATAATC
54452856 AAAATAA
65 AAAATAA
54452863 TATTA
1 TATTA
54452868 TTTTTGGAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
68 37 0.59
69 6 0.10
71 3 0.05
72 17 0.27
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.41
Consensus pattern (71 bp):
TATTAAATTAATAAAATATTTACTATAAGATAAACATTAAATTAAATTTAATATTAAGATAATCA
AAATAA
Found at i:54456807 original size:10 final size:10
Alignment explanation
Indices: 54456792--54456820 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
54456782 TTCAATCGGT
54456792 GACTGGACTA
1 GACTGGACTA
54456802 GACTGGACTA
1 GACTGGACTA
54456812 GACTGGACT
1 GACTGGACT
54456821 GGTCGGGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (10 bp):
GACTGGACTA
Found at i:54457346 original size:11 final size:11
Alignment explanation
Indices: 54457332--54457361 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
54457322 AAAGAAATTA
54457332 TTTTAGAAAAT
1 TTTTAGAAAAT
54457343 TTTTCAGAAAAT
1 TTTT-AGAAAAT
54457355 TTTTAGA
1 TTTTAGA
54457362 GATATTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (11 bp):
TTTTAGAAAAT
Found at i:54462815 original size:40 final size:39
Alignment explanation
Indices: 54462770--54462906 Score: 123
Period size: 40 Copynumber: 3.4 Consensus size: 39
54462760 ACAAGAGAAT
* *
54462770 GTATGTGCAATCAGGGATACCGAAGTAAAAACAAAGTCA-
1 GTATGTGCATTCAGGG-TACCGAAGTAAAAACAAAGGCAC
* * * **
54462809 GCTATGTGCATTCAAAGGTATCGAAGTAGAAACAGGGGCAC
1 G-TATGTGCATTC-AGGGTACCGAAGTAAAAACAAAGGCAC
* * *
54462850 GTATGTGCATTCAGGGGTACCGAAGTACAAACAAGGGCAT
1 GTATGTGCATTCA-GGGTACCGAAGTAAAAACAAAGGCAC
* *
54462890 GCAAGTGCATTCAGGGT
1 GTATGTGCATTCAGGGT
54462907 CATTTCTTCA
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
39 6 0.08
40 70 0.88
41 4 0.05
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (39 bp):
GTATGTGCATTCAGGGTACCGAAGTAAAAACAAAGGCAC
Found at i:54468654 original size:18 final size:18
Alignment explanation
Indices: 54468633--54468672 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
54468623 AAATTGAATC
54468633 AAAACAT-AAAATTTAGGA
1 AAAACATAAAAATTT-GGA
54468651 AAAACATAGAAAATTTGGA
1 AAAACATA-AAAATTTGGA
54468670 AAA
1 AAA
54468673 CAGGGGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 6 0.30
20 7 0.35
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (18 bp):
AAAACATAAAAATTTGGA
Found at i:54469660 original size:40 final size:40
Alignment explanation
Indices: 54469554--54469718 Score: 154
Period size: 40 Copynumber: 4.2 Consensus size: 40
54469544 AATGTGTGTT
* * * * *
54469554 AAGGGTATCAAGGTACAAACAAGAGCACATATGTGCAATC
1 AAGGGTACCAAAGTACAAACAGGGGCACATATGTGCATTC
** * * * *
54469594 -AGGGATACTGAAGTACAAATAAGGGCACTTATGTGCATTT
1 AAGGG-TACCAAAGTACAAACAGGGGCACATATGTGCATTC
* *
54469634 AAGGGTACCAAAGTTCAAACAGGGGCACGTATGTGCATTC
1 AAGGGTACCAAAGTACAAACAGGGGCACATATGTGCATTC
* * * *
54469674 AGGGGTACCAATGTACAAATAGGGGCACATGTGTGCATTC
1 AAGGGTACCAAAGTACAAACAGGGGCACATATGTGCATTC
54469714 -AGGGT
1 AAGGGT
54469719 CATTTTCTTC
Statistics
Matches: 100, Mismatches: 23, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
39 8 0.08
40 88 0.88
41 4 0.04
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (40 bp):
AAGGGTACCAAAGTACAAACAGGGGCACATATGTGCATTC
Found at i:54469667 original size:80 final size:80
Alignment explanation
Indices: 54469552--54469712 Score: 198
Period size: 80 Copynumber: 2.0 Consensus size: 80
54469542 TGAATGTGTG
* * *
54469552 TTAAGGGTATCAAGGTACAAACAAGAGCACATATGTGCAATCAGGGATACTGAA-GTACAAATAA
1 TTAAGGGTACCAAAGTACAAACAAGAGCACATATGTGCAATCAGGGATAC-CAATGTACAAATAA
*
54469616 GGGCACTTATGTGCAT
65 GGGCACATATGTGCAT
* * * * * * *
54469632 TTAAGGGTACCAAAGTTCAAACAGGGGCACGTATGTGCATTCAGGGGTACCAATGTACAAATAGG
1 TTAAGGGTACCAAAGTACAAACAAGAGCACATATGTGCAATCAGGGATACCAATGTACAAATAAG
*
54469697 GGCACATGTGTGCAT
66 GGCACATATGTGCAT
54469712 T
1 T
54469713 CAGGGTCATT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
79 2 0.03
80 66 0.97
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (80 bp):
TTAAGGGTACCAAAGTACAAACAAGAGCACATATGTGCAATCAGGGATACCAATGTACAAATAAG
GGCACATATGTGCAT
Found at i:54474623 original size:15 final size:15
Alignment explanation
Indices: 54474605--54474643 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
54474595 AAATTTTAGT
54474605 AAATAAAAAATATAA
1 AAATAAAAAATATAA
** *
54474620 AAATATTAAATATCA
1 AAATAAAAAATATAA
54474635 AAATAAAAA
1 AAATAAAAA
54474644 TAATATAAAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAAAAATATAA
Found at i:54482520 original size:2 final size:2
Alignment explanation
Indices: 54482513--54482537 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54482503 CTATACACAA
54482513 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
54482538 TGTATGCTAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54483503 original size:103 final size:103
Alignment explanation
Indices: 54483360--54483568 Score: 316
Period size: 103 Copynumber: 2.0 Consensus size: 103
54483350 ACAATTACCC
54483360 GTATCATTGTTTAAATCAAGTATTTAGCATAAGAAGAGTTGTTTTAAGTACATATTAACTTAGTC
1 GTATCATTGTTTAAATCAAGTATTTAGCATAAGAAGAGTTGTTTTAAGTACATATTAACTTAGTC
*
54483425 TTTC-TATCTCTCATTT-CCCTTCGCTTTTGCATGCATT
66 TTTCATATCTCTC-TTTACCCTTCCCTTTTGCATGCATT
* *
54483462 GTATCATTGTTTAAATCAAAGTATTTAGCATAGGGAA-AGTTGTTTTAAGTACATATTAAGTTAG
1 GTATCATTGTTTAAATC-AAGTATTTAGCATA-AGAAGAGTTGTTTTAAGTACATATTAACTTAG
54483526 TCTTTCTATATATCTCTCTTTACCCTTCCCTTTTGCATGCATT
64 TCTTTC---ATATCTCTCTTTACCCTTCCCTTTTGCATGCATT
54483569 TCAACAGATA
Statistics
Matches: 97, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
102 17 0.18
103 46 0.47
104 3 0.03
106 3 0.03
107 28 0.29
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (103 bp):
GTATCATTGTTTAAATCAAGTATTTAGCATAAGAAGAGTTGTTTTAAGTACATATTAACTTAGTC
TTTCATATCTCTCTTTACCCTTCCCTTTTGCATGCATT
Found at i:54492256 original size:25 final size:26
Alignment explanation
Indices: 54492219--54492274 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
54492209 AACTTTTTAG
* *
54492219 TAATTATATAATTTTACATTTACAAA
1 TAATAATATAATTTGACATTTACAAA
* *
54492245 TAATAATA-AATTTGATATTTAGAAA
1 TAATAATATAATTTGACATTTACAAA
54492270 -AATAA
1 TAATAA
54492275 AATCTTTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 5 0.19
25 14 0.54
26 7 0.27
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (26 bp):
TAATAATATAATTTGACATTTACAAA
Found at i:54493555 original size:21 final size:21
Alignment explanation
Indices: 54493526--54493573 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
54493516 ATGACAATGT
54493526 AAATAAATAAATAA-ATGAATA
1 AAATAAATAAA-AATATGAATA
*
54493547 AAATGAATAAAAATATGAA-A
1 AAATAAATAAAAATATGAATA
*
54493567 ATATAAA
1 AAATAAA
54493574 AAGATACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATAAATAAAAATATGAATA
Found at i:54493667 original size:10 final size:10
Alignment explanation
Indices: 54493652--54493686 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
54493642 ATATGTATTA
54493652 AAATATATAT
1 AAATATATAT
54493662 AAATATATAT
1 AAATATATAT
*
54493672 AAAAATATAT
1 AAATATATAT
54493682 AAATA
1 AAATA
54493687 CACATACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATATATAT
Found at i:54493667 original size:22 final size:21
Alignment explanation
Indices: 54493632--54493705 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 21
54493622 GGGTATTTAG
* * *
54493632 ATATATGTAGATATGTATTAAA
1 ATATATATAAATATATA-TAAA
54493654 ATATATATAAATATATATAAA
1 ATATATATAAATATATATAAA
* *
54493675 A-ATATATAAATACACATACAA
1 ATATATATAAATATATATA-AA
*
54493696 ATATAAATAA
1 ATATATATAA
54493706 GTTACAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 15 0.34
21 8 0.18
22 21 0.48
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (21 bp):
ATATATATAAATATATATAAA
Found at i:54493669 original size:12 final size:12
Alignment explanation
Indices: 54493632--54493682 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
54493622 GGGTATTTAG
* *
54493632 ATATATGTAGAT
1 ATATATATAAAT
*
54493644 ATGTAT-TAAA-
1 ATATATATAAAT
54493654 ATATATATAAAT
1 ATATATATAAAT
*
54493666 ATATATAAAAAT
1 ATATATATAAAT
54493678 ATATA
1 ATATA
54493683 AATACACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 5 0.15
11 7 0.21
12 21 0.64
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:54493681 original size:20 final size:20
Alignment explanation
Indices: 54493650--54493700 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
54493640 AGATATGTAT
* *
54493650 TAAAATATATATAAATATATA
1 TAAAA-ATATATAAATACACA
54493671 TAAAAATATATAAATACACA
1 TAAAAATATATAAATACACA
*
54493691 TACAAATATA
1 TAAAAATATA
54493701 AATAAGTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAATATATAAATACACA
Found at i:54494174 original size:18 final size:18
Alignment explanation
Indices: 54494153--54494235 Score: 53
Period size: 18 Copynumber: 4.3 Consensus size: 18
54494143 TAAGAATAAT
54494153 AATAATAATAGTAGTAAA
1 AATAATAATAGTAGTAAA
* *
54494171 AATATATAA-AATA-AAAA
1 AATA-ATAATAGTAGTAAA
*
54494188 AATAATAGTGATAACAGTATTAAA
1 AATAATA---AT---AGTAGTAAA
*
54494212 CATAATAATAGTAGTAAA
1 AATAATAATAGTAGTAAA
54494230 AATAAT
1 AATAAT
54494236 GATAACATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 18
0.66 0.09 0.24
Matches are distributed among these distances:
16 3 0.06
17 7 0.14
18 20 0.41
19 5 0.10
21 2 0.04
23 3 0.06
24 9 0.18
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.28
Consensus pattern (18 bp):
AATAATAATAGTAGTAAA
Found at i:54495955 original size:47 final size:44
Alignment explanation
Indices: 54495805--54496048 Score: 203
Period size: 44 Copynumber: 5.6 Consensus size: 44
54495795 TTCTTTCGTT
* * * * *
54495805 TGCTCCACTGTAACTTCAGGGAGATAAGA-C--TGGATGTGATC
1 TGCTCTACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATC
*
54495846 TGCTCTACTGCAACTTTCAGAGAGATAAGATCTGTGGTTTTAATC
1 TGCTCTACTGCAAC-TTCAGGGAGATAAGATCTGTGGTTTTAATC
* * * * * * **
54495891 CGCTCCACTGTAACTTCAGGGAGATAGGATTTGTAGCTTTTTTTGTC
1 TGCTCTACTGCAACTTCAGGGAGATAAGATCTGT-G--GTTTTAATC
* * ***
54495938 TGCTCTACTGCAACTTCAGGGAGATAAGA-C-G-AGATGCGATC
1 TGCTCTACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATC
* *
54495979 TGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATC
* *
54496023 TGCTCCACTGTAACTTCAGGGAGATA
1 TGCTCTACTGCAACTTCAGGGAGATA
54496049 GGGCTAGTAA
Statistics
Matches: 156, Mismatches: 37, Indels: 17
0.74 0.18 0.08
Matches are distributed among these distances:
41 43 0.28
42 15 0.10
43 2 0.01
44 44 0.28
45 21 0.13
47 31 0.20
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (44 bp):
TGCTCTACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATC
Found at i:54496043 original size:132 final size:133
Alignment explanation
Indices: 54495805--54496050 Score: 424
Period size: 132 Copynumber: 1.9 Consensus size: 133
54495795 TTCTTTCGTT
* *
54495805 TGCTCCACTGTAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTTCAGAGAG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTCAGAGAG
*
54495870 ATAAGATCTGTGGTTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTGTAGCTTTTTTT
66 ATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTGTAGCTTTTTTT
54495935 GTC
131 GTC
*
54495938 TGCTCTACTGCAACTTCAGGGAGATAAGAC-GAGATGCGATCTGCTCTACTGCAAC-TTCAGAGA
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTG-GATGCGATCTGCTCTACTGCAACTTTCAGAGA
*
54496001 GATAAGATCTGTGATTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGG
65 GATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGG
54496051 GCTAGTAACT
Statistics
Matches: 107, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
132 57 0.53
133 50 0.47
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (133 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTTCAGAGAG
ATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTGTAGCTTTTTTT
GTC
Found at i:54496539 original size:46 final size:46
Alignment explanation
Indices: 54496356--54498240 Score: 2741
Period size: 46 Copynumber: 40.9 Consensus size: 46
54496346 TCGCTATCGG
* *
54496356 TATAGGAAGATAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * *
54496402 TACAGGAAGACAAAATCTGTTATATCTTTGATCTACTTCGCTGCCAAA
1 TATAGGAAGACAAGATCTG--CTATCTTTGATCTACTCCGCTGCCAAA
* * *
54496450 TACAGGAAGACAAGATCTGCTATATCTTCGATCTAATCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGC--TATCTTTGATCTACTCCGCTGCCAAA
* *
54496498 TATAGGAAGACAATATTTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54496544 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54496590 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54496636 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54496682 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54496728 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54496774 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54496820 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54496866 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54496912 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54496958 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54497004 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54497050 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
54497096 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * *
54497142 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACTACCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * *
54497188 TACAGGAAGACAAGATCTGCGATCTTTGATCTACTTCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * *
54497234 TACAGGAAGACAAGATCTGCTATCTTCGATCTAATCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
** * *
54497280 TATAATAAGACAATATTTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* *
54497326 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * * * *
54497372 TACAGGAAGACAAGATCTACTAT-TTTCGGTCTACTTCACTGCTAAA
1 TATAGGAAGACAAGATCTGCTATCTTT-GATCTACTCCGCTGCCAAA
* * **
54497418 TACAGGAAGACAAGATCTACTATCTTCAATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * *
54497464 TATAGGAAAACAAGATCTGCTATCTTCGATCGACTCCACTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * * * *
54497510 TACAAGAAGACAAGATCTGAC-ATCTTCGATCTATTTCACTGCCAAA
1 TATAGGAAGACAAGATCTG-CTATCTTTGATCTACTCCGCTGCCAAA
* * * *
54497556 TACAGGAAGATAAGATCTGCTATCTTTGATCTACTTCACTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
*
54497602 TATAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * *
54497648 TACAGGAAGACAAGATCTGCTAT-TTTCGGTCTACTTCGCTGCTAAA
1 TATAGGAAGACAAGATCTGCTATCTTT-GATCTACTCCGCTGCCAAA
* * **
54497694 TACAAGAAGACAAGATCTGCTATCTTCAATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * *
54497740 TATAGGAAGACAAGATCTCCTATCTTCGATCGACTCCACTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * * *
54497786 TACAGGAACACAAGATCTGCCATCTTCGATCTACTTCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * * *
54497832 TACAGGAACACAAGATCTGCCATCTTCGATCTACTTCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * * *
54497878 TACAGGAACACAAGATCTGCCATCTTCGATCTACTTCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * * *
54497924 TACAGGAACACAAGATCTGCCATCTTCGATCTACTTCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* **
54497970 TACAGGAAGACAAGATCTGCTATCTTCAATCTACTCCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * *
54498016 TATAGGAAGACAAGATCTACTATCTTCGATCGACTCCACTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * * * *
54498062 TACAGGAACACAAGATCTGCCATCTTCGATCTACTTCACTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * *
54498108 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* * * *
54498154 TACAGGAAGACAAGATCTACTATCTTCGATCTACTCCACTGCCAAA
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
* *
54498200 TACAGGAAGACAAGATCTGCTATCTTTGATCTATTCCGCTG
1 TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTG
54498241 TAATTTCTAA
Statistics
Matches: 1705, Mismatches: 124, Indels: 20
0.92 0.07 0.01
Matches are distributed among these distances:
45 5 0.00
46 1613 0.95
47 5 0.00
48 82 0.05
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (46 bp):
TATAGGAAGACAAGATCTGCTATCTTTGATCTACTCCGCTGCCAAA
Found at i:54499282 original size:108 final size:106
Alignment explanation
Indices: 54499111--54499429 Score: 356
Period size: 97 Copynumber: 3.1 Consensus size: 106
54499101 GAAAAATGCT
* * * * * * *
54499111 TGAAAAAGATTACCAAAATGGACAAGAAAG-AATTTTATTGAGAATAAGGCTCAAAATAAATAAA
1 TGAAAAAGATTATCACAATGGATAA-AATGAAATTTTATTGAGAACAAAGCTCAAAATGAATAAA
*
54499175 TTAATCAAGATATCAAATTTTGTTCAAATACGAACTGAATAAGA
65 TTAATCAAGATAGCAAATTTTG-TCAAATACGAA-TGAATAAGA
* * * * *
54499219 TGAAAAATATTATTACAATGGATAAGATGAAATTTTATTGAAAACAAAGCTCGAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATAAAT
54499284 TAATCAAGATAGCAAATTTTG-C---T---AA-G-ATAAGA
66 TAATCAAGATAGCAAATTTTGTCAAATACGAATGAATAAGA
* *
54499316 TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAGCACAGCTCAAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATAAAT
*
54499381 TAATTAAGATAGCAAATTTTG-CTAATATACGAAATGAATAAGA
66 TAATCAAGATAGCAAATTTTGTC-AA-ATACG-AATGAATAAGA
54499424 T-AAAAA
1 TGAAAAA
54499430 CAGGTGCCCC
Statistics
Matches: 178, Mismatches: 21, Indels: 25
0.79 0.09 0.11
Matches are distributed among these distances:
97 85 0.48
98 1 0.01
100 2 0.01
102 1 0.01
103 1 0.01
106 3 0.02
107 8 0.04
108 77 0.43
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.27
Consensus pattern (106 bp):
TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATAAAT
TAATCAAGATAGCAAATTTTGTCAAATACGAATGAATAAGA
Found at i:54499713 original size:5 final size:5
Alignment explanation
Indices: 54499694--54499749 Score: 64
Period size: 5 Copynumber: 11.8 Consensus size: 5
54499684 GGCCTCTCCT
* * *
54499694 TTTTC TTTT- TCTTC TTTTC TTTTC TTTTT TTTTC TTTTC -TTT- TTTCC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
54499741 TTTTC TTTT
1 TTTTC TTTT
54499750 TTCTGTTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
4 8 0.19
5 34 0.81
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:54499715 original size:20 final size:20
Alignment explanation
Indices: 54499692--54499765 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
54499682 TTGGCCTCTC
54499692 CTTTTTCTTTTTCTTCTTTT
1 CTTTTTCTTTTTCTTCTTTT
*
54499712 C-TTTTCTTTTTTTTTCTTTT
1 CTTTTTC-TTTTTCTTCTTTT
*
54499732 CTTTTTTCCTTTTCTT-TTTT
1 C-TTTTTCTTTTTCTTCTTTT
54499752 CTGTTCTTCTTTTT
1 CT-TT-TTCTTTTT
54499766 TTTTTTGGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
19 6 0.13
20 21 0.47
21 13 0.29
22 5 0.11
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (20 bp):
CTTTTTCTTTTTCTTCTTTT
Found at i:54499731 original size:28 final size:29
Alignment explanation
Indices: 54499693--54499770 Score: 97
Period size: 28 Copynumber: 2.6 Consensus size: 29
54499683 TGGCCTCTCC
54499693 TTTTTCTTTTTCTTCTTTT-CTTTTCTTTT
1 TTTTTCTTTTTCTT-TTTTCCTTTTCTTTT
54499722 TTTTTC-TTTTCTTTTTTCCTTTTCTTTT
1 TTTTTCTTTTTCTTTTTTCCTTTTCTTTT
*
54499750 TTCTGTTCTTCTTTTTTTTTT
1 TT-T-TTCTT-TTTCTTTTTT
54499771 TGGACATTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
27 4 0.09
28 19 0.44
29 7 0.16
30 3 0.07
31 1 0.02
32 9 0.21
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.82
Consensus pattern (29 bp):
TTTTTCTTTTTCTTTTTTCCTTTTCTTTT
Found at i:54504119 original size:221 final size:221
Alignment explanation
Indices: 54503736--54504154 Score: 793
Period size: 221 Copynumber: 1.9 Consensus size: 221
54503726 GAAGAGATTT
* *
54503736 AAAATACGATCCTTATTTTTTTAAAAGAAAATTTATATAAATCAAGTTACTCATTAATACTCTCT
1 AAAATACGATCCTTATTTTTTAAAAAGAAAATTTATATAAATCAAGTTACTCATTAAGACTCTCT
54503801 CATTTCAGAAAGAGAAAATGTCACACCCAATGCGTTAGGGCACAATATTTTACCTCTTCAGAAAT
66 CATTTCAGAAAGAGAAAATGTCACACCCAATGCGTTAGGGCACAATATTTTACCTCTTCAGAAAT
54503866 GAACTAGTCTAAAAACTTGCATAGTAAAATTTAAAAGGGTGTTCAATTGTTTAAATCATGTGAAA
131 GAACTAGTCTAAAAACTTGCATAGTAAAATTTAAAAGGGTGTTCAATTGTTTAAATCATGTGAAA
54503931 GAAGTTAGGGCACAATATTTTACCTC
196 GAAGTTAGGGCACAATATTTTACCTC
*
54503957 AAAATACGATCCTTATTTTTTAAAAAGAAAATTTATATAAATCAAGTTACTCGTTAAGACTCTCT
1 AAAATACGATCCTTATTTTTTAAAAAGAAAATTTATATAAATCAAGTTACTCATTAAGACTCTCT
* *
54504022 CATTTCAGAAAGAGAAAATGTCACACCTAATGCGTTAGGGCACGATATTTTACCTCTTCAGAAAT
66 CATTTCAGAAAGAGAAAATGTCACACCCAATGCGTTAGGGCACAATATTTTACCTCTTCAGAAAT
54504087 GAACTAGTCTAAAAACTTGCATAGTAAAATTTAAAAGGGTGTTCAATTGTTTAAATCATGTGAAA
131 GAACTAGTCTAAAAACTTGCATAGTAAAATTTAAAAGGGTGTTCAATTGTTTAAATCATGTGAAA
54504152 GAA
196 GAA
54504155 TTGCAACCCA
Statistics
Matches: 193, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
221 193 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (221 bp):
AAAATACGATCCTTATTTTTTAAAAAGAAAATTTATATAAATCAAGTTACTCATTAAGACTCTCT
CATTTCAGAAAGAGAAAATGTCACACCCAATGCGTTAGGGCACAATATTTTACCTCTTCAGAAAT
GAACTAGTCTAAAAACTTGCATAGTAAAATTTAAAAGGGTGTTCAATTGTTTAAATCATGTGAAA
GAAGTTAGGGCACAATATTTTACCTC
Found at i:54504760 original size:10 final size:10
Alignment explanation
Indices: 54504745--54504779 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
54504735 ATATGTATTA
54504745 AAATATATAT
1 AAATATATAT
54504755 AAATATATAT
1 AAATATATAT
*
54504765 AAAAATATAT
1 AAATATATAT
54504775 AAATA
1 AAATA
54504780 CACATACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATATATAT
Found at i:54504760 original size:22 final size:21
Alignment explanation
Indices: 54504725--54504798 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 21
54504715 GGGTATTTAG
* * *
54504725 ATATATGTAGATATGTATTAAA
1 ATATATATAAATATATA-TAAA
54504747 ATATATATAAATATATATAAA
1 ATATATATAAATATATATAAA
* *
54504768 A-ATATATAAATACACATACAA
1 ATATATATAAATATATATA-AA
*
54504789 ATATAAATAA
1 ATATATATAA
54504799 GTTACAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 15 0.34
21 8 0.18
22 21 0.48
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (21 bp):
ATATATATAAATATATATAAA
Found at i:54504762 original size:12 final size:12
Alignment explanation
Indices: 54504725--54504775 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
54504715 GGGTATTTAG
* *
54504725 ATATATGTAGAT
1 ATATATATAAAT
*
54504737 ATGTAT-TAAA-
1 ATATATATAAAT
54504747 ATATATATAAAT
1 ATATATATAAAT
*
54504759 ATATATAAAAAT
1 ATATATATAAAT
54504771 ATATA
1 ATATA
54504776 AATACACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 5 0.15
11 7 0.21
12 21 0.64
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:54504774 original size:20 final size:20
Alignment explanation
Indices: 54504743--54504793 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
54504733 AGATATGTAT
* *
54504743 TAAAATATATATAAATATATA
1 TAAAA-ATATATAAATACACA
54504764 TAAAAATATATAAATACACA
1 TAAAAATATATAAATACACA
*
54504784 TACAAATATA
1 TAAAAATATA
54504794 AATAAGTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAATATATAAATACACA
Found at i:54509241 original size:41 final size:41
Alignment explanation
Indices: 54509184--54509464 Score: 264
Period size: 41 Copynumber: 6.9 Consensus size: 41
54509174 ATTTTTAAAC
* *
54509184 CTTTAGTGGCGTTTTTATTTGAGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * *
54509225 CTTTAGCAGCGTTTTTAACTGAGCGCCGCTAAT-C-C-AAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * *
54509263 GGCATTTATCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
1 --C-TTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * * * *
54509307 CTTTAGTGGCGTTTTTATCTGAGCGCCACTAGTTCTTTGG-C
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGC-TCGGAT
* * * *
54509348 CTTTAGCAGCGTTTATCTCTAAGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * **
54509389 CTTTAGTGGCGTTTTTATCTGAGCGCCACTAATTCTCGGGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * *
54509430 CTTTAGCGGCGTTTATAGCTAAGCGCCGCTAATGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGC
54509465 ATTTACCTTT
Statistics
Matches: 187, Mismatches: 45, Indels: 16
0.75 0.18 0.06
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 5 0.03
41 171 0.91
42 5 0.03
43 1 0.01
44 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
Found at i:54509329 original size:82 final size:82
Alignment explanation
Indices: 54509183--54509486 Score: 369
Period size: 82 Copynumber: 3.7 Consensus size: 82
54509173 GATTTTTAAA
* * * * ** *
54509183 CCTTTAGTGGCGTTTTTATTTGAGCGCCGCTAATGCTCGGATCTTTAGCAGCGTTTTTAACTGAG
1 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAG
* * *
54509248 CGCCGCTAATCCAATGG
66 CGCCACTAATTCTATGG
* *
54509265 CATTTATCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAG
* *
54509330 CGCCACTAGTTCTTTGG
66 CGCCACTAATTCTATGG
* * *
54509347 CCTTTAGCAGCGTTTATCTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAG
**
54509412 CGCCACTAATTCTCGGG
66 CGCCACTAATTCTATGG
* ** *
54509429 CCTTTAGCGGCGTTTATAG-CTAAGCGCCGCTAATGCAT-TTACCTTTAGTGGCGTTTTT
1 CCTTTAGCGGCGTTT-TTGTCTAAGCGCCGCTAATGC-TCGGATCTTTAGTGGCGTTTTT
54509487 GCCGAAGCGC
Statistics
Matches: 191, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
82 190 0.99
83 1 0.01
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (82 bp):
CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAG
CGCCACTAATTCTATGG
Found at i:54509474 original size:123 final size:123
Alignment explanation
Indices: 54509273--54509503 Score: 268
Period size: 123 Copynumber: 1.9 Consensus size: 123
54509263 GGCATTTATC
* * * * * * *
54509273 GGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGTGGCGTTTTTATCTGAGCGCCACTA
1 GGCGTTTTTATCTAAGCGCCACTAATGCTCGGACCTTTAGCGGCGTTTATAGCTAAGCGCCACTA
* * * *
54509338 GTTCTTTGGCCTTTAGCAGCGTTTAT-CTCTAAGCGCCGCTAATGCTCGGATCTTTAGT
66 ATGCTTTGACCTTTAGCAGCGTTTATGC-CGAAGCGCCGCTAATGCTCGGATCTTTAGT
* * * *
54509396 GGCGTTTTTATCTGAGCGCCACTAATTCTCGGGCCTTTAGCGGCGTTTATAGCTAAGCGCCGCTA
1 GGCGTTTTTATCTAAGCGCCACTAATGCTCGGACCTTTAGCGGCGTTTATAGCTAAGCGCCACTA
** *
54509461 ATGCATTT-ACCTTTAGTGGCGTTTTTGCCGAAGCGCCGCTAAT
66 ATGC-TTTGACCTTTAGCAGCGTTTATGCCGAAGCGCCGCTAAT
54509504 AGTAATAAAA
Statistics
Matches: 88, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
123 84 0.95
124 4 0.05
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (123 bp):
GGCGTTTTTATCTAAGCGCCACTAATGCTCGGACCTTTAGCGGCGTTTATAGCTAAGCGCCACTA
ATGCTTTGACCTTTAGCAGCGTTTATGCCGAAGCGCCGCTAATGCTCGGATCTTTAGT
Found at i:54510044 original size:15 final size:15
Alignment explanation
Indices: 54510023--54510060 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
54510013 AATAAGGTTA
54510023 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
54510038 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
54510053 ATTTAGGG
1 ATTTAGGG
54510061 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:54510876 original size:21 final size:21
Alignment explanation
Indices: 54510850--54510891 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
54510840 TAATTATTAC
*
54510850 ATAATTTATAGTATTTGAAAT
1 ATAATTTATAATATTTGAAAT
54510871 ATAATTTATAATATTTGAAAT
1 ATAATTTATAATATTTGAAAT
54510892 TTTGAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (21 bp):
ATAATTTATAATATTTGAAAT
Found at i:54511223 original size:16 final size:18
Alignment explanation
Indices: 54511197--54511236 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
54511187 TGAAAGTTAC
*
54511197 AAAATTAGCA-TCATTTA
1 AAAATTAGCATTCATTCA
54511214 AAAATT-GCATTCATTCA
1 AAAATTAGCATTCATTCA
54511231 AAAATT
1 AAAATT
54511237 TAGAGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (18 bp):
AAAATTAGCATTCATTCA
Found at i:54511822 original size:20 final size:19
Alignment explanation
Indices: 54511795--54511852 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 19
54511785 AAAAATTCTA
54511795 TTTTTATTTTTAAAATGAT
1 TTTTTATTTTTAAAATGAT
*
54511814 TTTTCTATTATTTTAATATG-T
1 TTTT-TA-T-TTTTAAAATGAT
54511835 TTTTTATAATTTTAAAAT
1 TTTTTAT--TTTTAAAAT
54511853 TCTATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 5 0.15
20 13 0.39
21 6 0.18
22 9 0.27
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTATTTTTAAAATGAT
Found at i:54511860 original size:22 final size:21
Alignment explanation
Indices: 54511770--54511879 Score: 84
Period size: 22 Copynumber: 5.2 Consensus size: 21
54511760 ACTATTTTAA
54511770 TTTTTTATAATTTTTAAAAATTC
1 TTTTTTATAA-TTTT-AAAATTC
**
54511793 TATTTTTAT--TTTTAAAATGA
1 T-TTTTTATAATTTTAAAATTC
* * *
54511813 TTTTTCTATTATTTTAATA-TG
1 TTTTT-TATAATTTTAAAATTC
54511834 TTTTTTATAATTTTAAAATTC
1 TTTTTTATAATTTTAAAATTC
* *
54511855 TATTTTTAAAATTTTTAAATT-
1 T-TTTTTATAATTTTAAAATTC
54511876 TTTT
1 TTTT
54511880 ATGATTTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
19 4 0.06
20 23 0.32
21 12 0.17
22 24 0.34
23 1 0.01
24 7 0.10
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTTATAATTTTAAAATTC
Found at i:54511890 original size:62 final size:63
Alignment explanation
Indices: 54511770--54511891 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 63
54511760 ACTATTTTAA
*
54511770 TTTTTTATAATTTTTAAAAATTCTATTTTTATTTTTAAAATGATTTTTCTATTATTTTAATATG
1 TTTTTTATAATTTTTAAAAATTCTATTTTTATTTTTAAAAT-ATTTTTATATTATTTTAATATG
54511834 TTTTTTATAA-TTTT-AAAATTCTATTTTTAAAATTTTT-AAAT-TTTTTATGATT-TTTTAA
1 TTTTTTATAATTTTTAAAAATTCTATTTTT---ATTTTTAAAATATTTTTAT-ATTATTTTAA
54511892 ATAAATATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
62 26 0.49
63 7 0.13
64 14 0.26
65 6 0.11
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (63 bp):
TTTTTTATAATTTTTAAAAATTCTATTTTTATTTTTAAAATATTTTTATATTATTTTAATATG
Found at i:54511990 original size:30 final size:30
Alignment explanation
Indices: 54511950--54512020 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
54511940 AAAAGACAAT
* *
54511950 GGCTTGATTGATTGCTT-AAATTCGATTGAG
1 GGCTTAATTGAGTGCTTGAAATT-GATTGAG
*
54511980 GGCTTAATTGAGTGCTTGAACTTGATTGAG
1 GGCTTAATTGAGTGCTTGAAATTGATTGAG
*
54512010 GGCTCAATTGA
1 GGCTTAATTGA
54512021 ATGTTGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (30 bp):
GGCTTAATTGAGTGCTTGAAATTGATTGAG
Found at i:54521442 original size:497 final size:498
Alignment explanation
Indices: 54520497--54521486 Score: 1901
Period size: 497 Copynumber: 2.0 Consensus size: 498
54520487 CCCCCAAAAT
* *
54520497 AGCCATTTCATGATCCGTGCTTATGAGTAACGGACAGTGGTCTAAAAAGGAGTGTGGCAAATGAC
1 AGCCATTTCATGATCCGTGCTTATGAGTAACAGACAGTGGTCTAAAAAAGAGTGTGGCAAATGAC
*
54520562 GGATTCAGGTATTTAGAAACAAAGTCAACCATTTATCATTTGCGACCCCTTTGTCTATCTCTCCC
66 GGATTCAGGTATTTAGAAACAAAATCAACCATTTATCATTTGCGACCCCTTTGTCTATCTCTCCC
*
54520627 TTATGTTTGTCTTCGGCAAATTCCCTCTTTCTAATGTGAACCACTCTTCTAAATATCCCACATCC
131 TTATGTTTGTCTTCGGCAAATTCCCTCTTTCCAATGTGAACCACTCTTCTAAATATCCCACATCC
*
54520692 ATTAATTGACACTCTTCAAGGACATCTTGGAAAGCCTCCATTCTTCTCTCATCCCTTGGCATACC
196 ATTAATTGACACTCTTCAAGGACATCTTGGAAAGCCTCCATTCTTCTCTCATCCATTGGCATACC
54520757 TCCAGCCTTCTCAAAGGAATACATGATTTTATTGGAGTCTCCACACACCAACCAAGGAAAATTCC
261 TCCAGCCTTCTCAAAGGAATACATGATTTTATTGGAGTCTCCACACACCAACCAAGGAAAATTCC
54520822 AATTCTACCCTAGTCTCCGAAATAAGTTCCAAGAACCATTTCTATAACTTGCAAAATGTGCTCTA
326 AATTCTACCCTAGTCTCCGAAATAAGTTCCAAGAACCATTTCTATAACTTGCAAAATGTGCTCTA
54520887 TAAAACCCAGTGAATCTCTATTCCTTATCATCACTATCCTCTTTAACCAAAGCATTTAAATGATT
391 TAAAACCCAGTGAATCTCTATTCCTTATCATCACTATCCTCTTTAACCAAAGCATTTAAATGATT
54520952 TTTAGAAAAGCTCCTTAGACTAACAGTAACATCTCCTTAGAAA
456 TTTAGAAAAGCTCCTTAGACTAACAGTAACATCTCCTTAGAAA
* *
54520995 AGCCCTTTCGTGATCCGTGCTTATGAGTAACAGACAGTGGTCTAAAAAAGAGTGTGGCAAATGAC
1 AGCCATTTCATGATCCGTGCTTATGAGTAACAGACAGTGGTCTAAAAAAGAGTGTGGCAAATGAC
54521060 GGATTCAGGTATTTAGAAACAAAATCAACCATTTATCATTTGCGACCCCTTTGTCTATCTCTCCC
66 GGATTCAGGTATTTAGAAACAAAATCAACCATTTATCATTTGCGACCCCTTTGTCTATCTCTCCC
54521125 TTATGTTTGTCTTCGGCAAATTCCCTCTTTCCAATGTGAACCACTCTTCTAAATATCCCACATCC
131 TTATGTTTGTCTTCGGCAAATTCCCTCTTTCCAATGTGAACCACTCTTCTAAATATCCCACATCC
*
54521190 ATTAATTGACACTCTTCAAGGACATCTTGG-AAGCCTCCATTCTTCTCTCCTCCATTGGCATACC
196 ATTAATTGACACTCTTCAAGGACATCTTGGAAAGCCTCCATTCTTCTCTCATCCATTGGCATACC
54521254 TCCAGCCTTCTCAAAGGAATACATGATTTTATTGGAGTCTCCACACACCAACCAAGGAAAATTCC
261 TCCAGCCTTCTCAAAGGAATACATGATTTTATTGGAGTCTCCACACACCAACCAAGGAAAATTCC
54521319 AATTCTACCCTAGTCTCCGAAATAAGTTCCAAGAACCATTTCTATAACTTGCAAAATGTGCTCTA
326 AATTCTACCCTAGTCTCCGAAATAAGTTCCAAGAACCATTTCTATAACTTGCAAAATGTGCTCTA
54521384 TAAAACCCAGTGAATCTCTATTCCTTATCATCACTATCCTCTTTAACCAAAGCATTTAAATGATT
391 TAAAACCCAGTGAATCTCTATTCCTTATCATCACTATCCTCTTTAACCAAAGCATTTAAATGATT
54521449 TTTAGAAAAGCTCCTTAGACTAACAGTAACATCTCCTT
456 TTTAGAAAAGCTCCTTAGACTAACAGTAACATCTCCTT
54521487 TCCACACAAA
Statistics
Matches: 484, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
497 265 0.55
498 219 0.45
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (498 bp):
AGCCATTTCATGATCCGTGCTTATGAGTAACAGACAGTGGTCTAAAAAAGAGTGTGGCAAATGAC
GGATTCAGGTATTTAGAAACAAAATCAACCATTTATCATTTGCGACCCCTTTGTCTATCTCTCCC
TTATGTTTGTCTTCGGCAAATTCCCTCTTTCCAATGTGAACCACTCTTCTAAATATCCCACATCC
ATTAATTGACACTCTTCAAGGACATCTTGGAAAGCCTCCATTCTTCTCTCATCCATTGGCATACC
TCCAGCCTTCTCAAAGGAATACATGATTTTATTGGAGTCTCCACACACCAACCAAGGAAAATTCC
AATTCTACCCTAGTCTCCGAAATAAGTTCCAAGAACCATTTCTATAACTTGCAAAATGTGCTCTA
TAAAACCCAGTGAATCTCTATTCCTTATCATCACTATCCTCTTTAACCAAAGCATTTAAATGATT
TTTAGAAAAGCTCCTTAGACTAACAGTAACATCTCCTTAGAAA
Found at i:54525084 original size:18 final size:18
Alignment explanation
Indices: 54525056--54525098 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
54525046 TTTTTAATAT
*
54525056 AATATTTAAAAGAT-AAAA
1 AATAATTAAAA-ATCAAAA
*
54525074 ATTAATTAAAAATCAAAA
1 AATAATTAAAAATCAAAA
54525092 AATAATT
1 AATAATT
54525099 TTTTAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
AATAATTAAAAATCAAAA
Found at i:54526127 original size:93 final size:95
Alignment explanation
Indices: 54525999--54526232 Score: 253
Period size: 96 Copynumber: 2.5 Consensus size: 95
54525989 TTGTATTTGA
* * * *
54525999 GTAAACTTTCAGTTTTGGTCTCTCTGTTAAACTCGAATTTAAGATTTAA-ATTT-TATATCT-A-
1 GTAAAATTTCAGTTTTGATCCCTCTATTAAACTCGAATTTAAGATTTAATATTTATAT-TCTCAC
** * **
54526060 TTTTTTTTATTTTTTTCATTTCAATTATAATG
65 TCCTTTTT-TGTTTGACATTTCAATTATAATG
* * * *
54526092 GTAAAA-TTCTAGTTTTGATCCCTCTTTTAGACTCGAATTTAAAATTTAATATTTATATTTTCAC
1 GTAAAATTTC-AGTTTTGATCCCTCTATTAAACTCGAATTTAAGATTTAATATTTATATTCTCAC
54526156 GTCCTTTTTTGTTTGACATTTCAATTATAATG
65 -TCCTTTTTTGTTTGACATTTCAATTATAATG
* **
54526188 GTAAAATTTCAATTTTGATCCCTCTATTAAACTTAAATTTAAGAT
1 GTAAAATTTCAGTTTTGATCCCTCTATTAAACTCGAATTTAAGAT
54526233 GCAATCTTGT
Statistics
Matches: 116, Mismatches: 18, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
92 3 0.03
93 39 0.34
94 6 0.05
95 4 0.03
96 55 0.47
97 9 0.08
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (95 bp):
GTAAAATTTCAGTTTTGATCCCTCTATTAAACTCGAATTTAAGATTTAATATTTATATTCTCACT
CCTTTTTTGTTTGACATTTCAATTATAATG
Found at i:54527290 original size:55 final size:59
Alignment explanation
Indices: 54527224--54527337 Score: 182
Period size: 61 Copynumber: 2.0 Consensus size: 59
54527214 GATAAGACCA
54527224 TGTTGAGATTAATG-T-T-TA-TATATATATATGTATATGCCTTACAAGTAATAAAATC
1 TGTTGAGATTAATGTTATATATTATATATATATGTATATGCCTTACAAGTAATAAAATC
54527279 TGTTGAGATTAATGTTTATATATTTATATATATATGTATATGCCTTACAAGTAATAAAA
1 TGTTGAGATTAATG-TTATATA-TTATATATATATGTATATGCCTTACAAGTAATAAAA
54527338 GAGGTATGCC
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
55 14 0.26
57 1 0.02
58 1 0.02
59 2 0.04
61 35 0.66
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (59 bp):
TGTTGAGATTAATGTTATATATTATATATATATGTATATGCCTTACAAGTAATAAAATC
Found at i:54545838 original size:41 final size:40
Alignment explanation
Indices: 54545793--54545993 Score: 208
Period size: 41 Copynumber: 4.9 Consensus size: 40
54545783 ACACTAGTAT
* * *
54545793 GAAGCCTGCTAGGCTCAAAGCCTGATGTAACACATCGACAC
1 GAAGCCTGCTAGGCACAAAGCCTGATATAATACA-CGACAC
* * * *
54545834 GAAGCTTGTTAGGCACAAAGCTTGATATAATACATCGACAT
1 GAAGCCTGCTAGGCACAAAGCCTGATATAATACA-CGACAC
* * *
54545875 GCAA-CCCGCTAGGCACAAAGTCTGATATAATACACCAGCAC
1 G-AAGCCTGCTAGGCACAAAGCCTGATATAATACACGA-CAC
*
54545916 GAAGCCTGCTAGGCACAACA-CCTGATATAATACACAGGCAC
1 GAAGCCTGCTAGGCACAA-AGCCTGATATAATACAC-GACAC
* * *
54545957 GAAGCCTACTAGGCACAACGTCTGATATAATACACGA
1 GAAGCCTGCTAGGCACAAAGCCTGATATAATACACGA
54545994 AATCTAAAAT
Statistics
Matches: 132, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
40 5 0.04
41 124 0.94
42 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.18
Consensus pattern (40 bp):
GAAGCCTGCTAGGCACAAAGCCTGATATAATACACGACAC
Found at i:54553668 original size:16 final size:16
Alignment explanation
Indices: 54553647--54553688 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
54553637 AATTGGGTTG
*
54553647 AGAAAATTATTTAATT
1 AGAAAATTAATTAATT
54553663 AGAAAATTAATTAATT
1 AGAAAATTAATTAATT
54553679 --AAAATTAATT
1 AGAAAATTAATT
54553689 TCATAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 10 0.40
16 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
AGAAAATTAATTAATT
Found at i:54556433 original size:21 final size:21
Alignment explanation
Indices: 54556407--54556450 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
54556397 AGGATTAGAG
**
54556407 TTGGGAACATTATGTCCGACA
1 TTGGGAACAACATGTCCGACA
*
54556428 TTGGGAACAACATGTCTGACA
1 TTGGGAACAACATGTCCGACA
54556449 TT
1 TT
54556451 TTCCAATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (21 bp):
TTGGGAACAACATGTCCGACA
Found at i:54558894 original size:13 final size:13
Alignment explanation
Indices: 54558876--54558900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54558866 AAATAGATAT
54558876 TTATTATATTATA
1 TTATTATATTATA
54558889 TTATTATATTAT
1 TTATTATATTAT
54558901 TATTGTTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATATTATA
Found at i:54559020 original size:11 final size:11
Alignment explanation
Indices: 54558994--54559028 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
54558984 CGAAACAGGG
54558994 GAAAAGAAAGAA
1 GAAAAGAAA-AA
54559006 GAAAAGAAAAA
1 GAAAAGAAAAA
54559017 GAAAAGGAAAAA
1 GAAAA-GAAAAA
54559029 CTAGGGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:54559318 original size:19 final size:20
Alignment explanation
Indices: 54559294--54559331 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54559284 GCAAGAATTT
*
54559294 TGAAA-TTAGATATTTATGA
1 TGAAATTTAGATAGTTATGA
54559313 TGAAATTTAGATAGTTATG
1 TGAAATTTAGATAGTTATG
54559332 TCCAAGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (20 bp):
TGAAATTTAGATAGTTATGA
Found at i:54560216 original size:23 final size:23
Alignment explanation
Indices: 54560189--54560243 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
54560179 GGCTTTGCCA
54560189 ATCAGGCACTTTATGTATCGTAT
1 ATCAGGCACTTTATGTATCGTAT
*
54560212 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTATCGTAT
*
54560235 TTCAGGCAC
1 ATCAGGCAC
54560244 CTCGTATGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
ATCAGGCACTTTATGTATCGTAT
Found at i:54560274 original size:21 final size:22
Alignment explanation
Indices: 54560225--54560274 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
54560215 AGGCACTTTA
*
54560225 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAAGCACCTCG
* *
54560248 TATGTCGTA-TCAAGCACCTGG
1 TGTGTCGTATTCAAGCACCTCG
54560269 TGTGTC
1 TGTGTC
54560275 ATTTCAGGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.65
23 8 0.35
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (22 bp):
TGTGTCGTATTCAAGCACCTCG
Found at i:54560285 original size:21 final size:21
Alignment explanation
Indices: 54560233--54560285 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
54560223 TATGTGTCGT
54560233 ATTTCAGGCACCTCGTATGTC
1 ATTTCAGGCACCTCGTATGTC
* * * * *
54560254 GTATCAAGCACCTGGTGTGTC
1 ATTTCAGGCACCTCGTATGTC
54560275 ATTTCAGGCAC
1 ATTTCAGGCAC
54560286 TTATGTGTCG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (21 bp):
ATTTCAGGCACCTCGTATGTC
Found at i:54560565 original size:24 final size:24
Alignment explanation
Indices: 54560538--54560583 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
54560528 GATTTGAAAT
* *
54560538 TGAAATATATGAAATGGTTATTAA
1 TGAAATACATGAAATGGATATTAA
*
54560562 TGAAATGCATGAAATGGATATT
1 TGAAATACATGAAATGGATATT
54560584 GATATAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (24 bp):
TGAAATACATGAAATGGATATTAA
Found at i:54561318 original size:18 final size:18
Alignment explanation
Indices: 54561276--54561319 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
54561266 AAATATTATT
54561276 ATTTTTTAAATTATAGAA
1 ATTTTTTAAATTATAGAA
* *
54561294 ATATTTTAAATGT-TATAA
1 ATTTTTTAAAT-TATAGAA
54561312 ATTTTTTA
1 ATTTTTTA
54561320 CAAAATACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTTTTTAAATTATAGAA
Found at i:54574712 original size:44 final size:44
Alignment explanation
Indices: 54574638--54574728 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
54574628 GTAGGTCAAA
54574638 TAATATTAAAGTAACCTACACTAATAAGAGTTTAAG-TGGAAAAC
1 TAATATTAAAGTAACCTACACTAATAAGAGTTTAAGCTGG-AAAC
* * *
54574682 TAATATTAAAGTAACCTATATTAATCAGAGTTTAAGCTGGAAAC
1 TAATATTAAAGTAACCTACACTAATAAGAGTTTAAGCTGGAAAC
54574726 TAA
1 TAA
54574729 AAGTAGAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 40 0.93
45 3 0.07
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (44 bp):
TAATATTAAAGTAACCTACACTAATAAGAGTTTAAGCTGGAAAC
Found at i:54576671 original size:44 final size:44
Alignment explanation
Indices: 54576621--54576706 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
54576611 TTTGTAGGTC
54576621 AAATAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGAA
1 AAATAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGAA
* *
54576665 AAATAATATTAAAGTAATCTACACTAATCAGAGTTTAAGTGG
1 AAATAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGG
54576707 GGAACTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (44 bp):
AAATAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGAA
Found at i:54593873 original size:36 final size:36
Alignment explanation
Indices: 54593833--54593902 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
54593823 TGTCAAGATG
* *
54593833 AATATGAGGGTGTGTTGTTCATGCCATGTGATAGCA
1 AATATGAGGGTATGTTATTCATGCCATGTGATAGCA
54593869 AATATGAGGGTATGTTATTCATGCCATGTGATAG
1 AATATGAGGGTATGTTATTCATGCCATGTGATAG
54593903 TGATTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (36 bp):
AATATGAGGGTATGTTATTCATGCCATGTGATAGCA
Found at i:54594348 original size:23 final size:23
Alignment explanation
Indices: 54594322--54594369 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
54594312 TAATGTGTGT
*
54594322 TGTAA-TATATGTTTAAATATTCA
1 TGTAATTA-ATGTGTAAATATTCA
54594345 TGTAATTAATGTGTAAATATTCA
1 TGTAATTAATGTGTAAATATTCA
54594368 TG
1 TG
54594370 AAAGTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (23 bp):
TGTAATTAATGTGTAAATATTCA
Found at i:54617183 original size:27 final size:27
Alignment explanation
Indices: 54617161--54617327 Score: 170
Period size: 27 Copynumber: 6.5 Consensus size: 27
54617151 AAGGGTATAA
*
54617161 CGGTCATTTTACCCTATGGGGGTATTT
1 CGGTCATTCTACCCTATGGGGGTATTT
* *
54617188 CAGTCATTCTATCCTATGGGGGTATTT
1 CGGTCATTCTACCCTATGGGGGTATTT
*
54617215 TGGTCATTCTACCCTATGGGGGTATTT
1 CGGTCATTCTACCCTATGGGGGTATTT
** * *
54617242 CGACCATTTTACCTTATGGGGGTATTT
1 CGGTCATTCTACCCTATGGGGGTATTT
* *
54617269 TGGTTATT-T----TA---GGGTATTT
1 CGGTCATTCTACCCTATGGGGGTATTT
*
54617288 CGGTCATTTTACCCTATGGGGGTATTT
1 CGGTCATTCTACCCTATGGGGGTATTT
*
54617315 CGGTCATTTTACC
1 CGGTCATTCTACC
54617328 TATTTTGGAG
Statistics
Matches: 115, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
19 14 0.12
20 1 0.01
22 2 0.02
24 2 0.02
26 1 0.01
27 95 0.83
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (27 bp):
CGGTCATTCTACCCTATGGGGGTATTT
Found at i:54617285 original size:19 final size:19
Alignment explanation
Indices: 54617261--54617298 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
54617251 TACCTTATGG
* *
54617261 GGGTATTTTGGTTATTTTA
1 GGGTATTTCGGTCATTTTA
54617280 GGGTATTTCGGTCATTTTA
1 GGGTATTTCGGTCATTTTA
54617299 CCCTATGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.05, G:0.26, T:0.53
Consensus pattern (19 bp):
GGGTATTTCGGTCATTTTA
Found at i:54617306 original size:46 final size:46
Alignment explanation
Indices: 54617234--54617325 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
54617224 TACCCTATGG
* * *
54617234 GGGTATTTCGACCATTTTACCTTATGGGGGTATTTTGGTTATTTTA
1 GGGTATTTCGACCATTTTACCCTATGGGGGTATTTCGGTCATTTTA
**
54617280 GGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTA
1 GGGTATTTCGACCATTTTACCCTATGGGGGTATTTCGGTCATTTTA
54617326 CCTATTTTGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.16, C:0.13, G:0.25, T:0.46
Consensus pattern (46 bp):
GGGTATTTCGACCATTTTACCCTATGGGGGTATTTCGGTCATTTTA
Found at i:54619620 original size:34 final size:34
Alignment explanation
Indices: 54619577--54619645 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
54619567 ATTTAAACTT
54619577 TTAATTCTTAAATAAACCCAAGATTTCTTAATCA
1 TTAATTCTTAAATAAACCCAAGATTTCTTAATCA
54619611 TTAATTCTTAAATAAACCCAAGATTTCTTAATCA
1 TTAATTCTTAAATAAACCCAAGATTTCTTAATCA
54619645 T
1 T
54619646 ACATGATTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (34 bp):
TTAATTCTTAAATAAACCCAAGATTTCTTAATCA
Found at i:54627563 original size:28 final size:28
Alignment explanation
Indices: 54627532--54627588 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
54627522 ACATGCAATG
54627532 ACAGTCTGGGCCTGAGCCCTAAGCAGTA
1 ACAGTCTGGGCCTGAGCCCTAAGCAGTA
*
54627560 ACAGTCTGGGCCTTAGCCCTAAGCAGTA
1 ACAGTCTGGGCCTGAGCCCTAAGCAGTA
54627588 A
1 A
54627589 TAGTGTAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (28 bp):
ACAGTCTGGGCCTGAGCCCTAAGCAGTA
Found at i:54628056 original size:54 final size:54
Alignment explanation
Indices: 54627973--54628152 Score: 245
Period size: 54 Copynumber: 3.3 Consensus size: 54
54627963 TTGATTCCCA
** * * *
54627973 GGGGTATAACAGTTATTTTACCCTATGGGGGTATTTCGGTCATTCTATCCTTCG
1 GGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTATCCTTCG
* * * *
54628027 GGGGTATTTCAGTCATTTTACCCTTTGGGGGCATTTTGGTTATTTTACCCTTCG
1 GGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTATCCTTCG
54628081 GGGGTATTTC-GTTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTATCCTTCG
1 GGGGTATTTCAG-TCATTTTACCCTTTGGGGGTATTTCGGTCATTTTATCCTTCG
* *
54628135 AGGGTATTTCGGTCATTT
1 GGGGTATTTCAGTCATTT
54628153 GCCCATGAAT
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 108 0.98
55 1 0.01
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.43
Consensus pattern (54 bp):
GGGGTATTTCAGTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTATCCTTCG
Found at i:54628145 original size:27 final size:27
Alignment explanation
Indices: 54627987--54628152 Score: 217
Period size: 27 Copynumber: 6.1 Consensus size: 27
54627977 TATAACAGTT
54627987 ATTTTACCCTAT-GGGGGTATTTCGGTC
1 ATTTTACCCT-TCGGGGGTATTTCGGTC
* * *
54628014 ATTCTATCCTTCGGGGGTATTTCAGTC
1 ATTTTACCCTTCGGGGGTATTTCGGTC
* * * *
54628041 ATTTTACCCTTTGGGGGCATTTTGGTT
1 ATTTTACCCTTCGGGGGTATTTCGGTC
*
54628068 ATTTTACCCTTCGGGGGTATTTCGTTC
1 ATTTTACCCTTCGGGGGTATTTCGGTC
*
54628095 ATTTTACCCTTTGGGGGTATTTCGGTC
1 ATTTTACCCTTCGGGGGTATTTCGGTC
* *
54628122 ATTTTATCCTTCGAGGGTATTTCGGTC
1 ATTTTACCCTTCGGGGGTATTTCGGTC
54628149 ATTT
1 ATTT
54628153 GCCCATGAAT
Statistics
Matches: 118, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
26 1 0.01
27 117 0.99
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (27 bp):
ATTTTACCCTTCGGGGGTATTTCGGTC
Found at i:54628852 original size:15 final size:15
Alignment explanation
Indices: 54628834--54628866 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
54628824 GAAGAGGAAA
54628834 AGAAGAGAAAAGAAG
1 AGAAGAGAAAAGAAG
*
54628849 AGAAGAGATAAGAAG
1 AGAAGAGAAAAGAAG
54628864 AGA
1 AGA
54628867 GGATTTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (15 bp):
AGAAGAGAAAAGAAG
Found at i:54632906 original size:13 final size:13
Alignment explanation
Indices: 54632832--54632909 Score: 52
Period size: 13 Copynumber: 5.8 Consensus size: 13
54632822 TAGCCTTGCG
54632832 TCTTTCTTTCTCTT
1 TCTTTCTTT-TCTT
54632846 T-TTTCTTTCTCTT
1 TCTTTCTTT-TCTT
*
54632859 TCTTTGTTTTCGTT
1 TCTTTCTTTTC-TT
** **
54632873 TGGTT-TTGGCTT
1 TCTTTCTTTTCTT
54632885 TGGCTTTCTTTTCTT
1 T--CTTTCTTTTCTT
54632900 TCTTTCTTTT
1 TCTTTCTTTT
54632910 TATTTGTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
12 3 0.06
13 27 0.54
14 14 0.28
15 6 0.12
ACGTcount: A:0.00, C:0.19, G:0.10, T:0.71
Consensus pattern (13 bp):
TCTTTCTTTTCTT
Found at i:54634428 original size:28 final size:28
Alignment explanation
Indices: 54634396--54634451 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
54634386 TCTTTCCATG
54634396 ATGTGCATAACATTTCTCATATATTAGT
1 ATGTGCATAACATTTCTCATATATTAGT
54634424 ATGTGCATAACATTTCTCATATATTAGT
1 ATGTGCATAACATTTCTCATATATTAGT
54634452 GCACACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (28 bp):
ATGTGCATAACATTTCTCATATATTAGT
Found at i:54634460 original size:28 final size:28
Alignment explanation
Indices: 54634401--54634460 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
54634391 CCATGATGTG
****
54634401 CATAACATTTCTCATATATTAGTATGTG
1 CATAACATTTCTCATATATTAGTACACA
*
54634429 CATAACATTTCTCATATATTAGTGCACA
1 CATAACATTTCTCATATATTAGTACACA
54634457 CATA
1 CATA
54634461 TGTGCATTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (28 bp):
CATAACATTTCTCATATATTAGTACACA
Found at i:54640322 original size:24 final size:25
Alignment explanation
Indices: 54640276--54640323 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
54640266 AACTTAGGGT
54640276 CTCACGACACAATATTTAATTTAGGC
1 CTCACGACAC-ATATTTAATTTAGGC
*
54640302 CTCACGACAC-TATTTAGTTTAG
1 CTCACGACACATATTTAATTTAG
54640324 ACCCTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
26 10 0.48
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (25 bp):
CTCACGACACATATTTAATTTAGGC
Found at i:54643198 original size:6 final size:6
Alignment explanation
Indices: 54643187--54643219 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
54643177 AACGATCTAG
*
54643187 TTGATA TTGATA TTGATG TTGATA TTGATA TTG
1 TTGATA TTGATA TTGATA TTGATA TTGATA TTG
54643220 TGAGGATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (6 bp):
TTGATA
Found at i:54645728 original size:20 final size:20
Alignment explanation
Indices: 54645699--54645743 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
54645689 AGCACATGAA
54645699 TGGA-ACCCCAAATGCCCAC
1 TGGATACCCCAAATGCCCAC
54645718 TGGATACCCCAAATGCCCAC
1 TGGATACCCCAAATGCCCAC
54645738 TGGATA
1 TGGATA
54645744 ATCATTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.31, C:0.36, G:0.18, T:0.16
Consensus pattern (20 bp):
TGGATACCCCAAATGCCCAC
Found at i:54649506 original size:21 final size:22
Alignment explanation
Indices: 54649465--54649512 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
54649455 TAAATTTGAA
*
54649465 CATTTTAAGTTATAAGTATTTT
1 CATTTTAAGATATAAGTATTTT
*
54649487 CATTTTAA-ATATAA-TAATTT
1 CATTTTAAGATATAAGTATTTT
54649507 -ATTTTA
1 CATTTTA
54649513 TTTTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 5 0.21
21 5 0.21
22 8 0.33
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (22 bp):
CATTTTAAGATATAAGTATTTT
Found at i:54649667 original size:18 final size:20
Alignment explanation
Indices: 54649623--54649669 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
54649613 TTATTCTATG
*
54649623 ATATTATATGATTTAATGAT
1 ATATTATATGATTTAATAAT
* *
54649643 TTTTTAT-TG-TTTAATAAT
1 ATATTATATGATTTAATAAT
54649661 ATATTATAT
1 ATATTATAT
54649670 TGACAATTGA
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
18 13 0.62
19 3 0.14
20 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
ATATTATATGATTTAATAAT
Found at i:54651921 original size:18 final size:18
Alignment explanation
Indices: 54651863--54651923 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
54651853 AGTGTAGATG
*
54651863 AAAAAAATAATGATATTT
1 AAAATAATAATGATATTT
* * * *
54651881 GAAAT-AT-TTTATATATA
1 AAAATAATAATGATAT-TT
54651898 AAAATAATAATGATATTT
1 AAAATAATAATGATATTT
54651916 AAAATAAT
1 AAAATAAT
54651924 TATTTTATTT
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
16 5 0.16
17 7 0.23
18 14 0.45
19 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATAATAATGATATTT
Found at i:54652984 original size:79 final size:79
Alignment explanation
Indices: 54652888--54653045 Score: 262
Period size: 79 Copynumber: 2.0 Consensus size: 79
54652878 GCTAGTACGT
* * *
54652888 CTCTACGTTACTCTGTTGATGAAGAATGTGCAATATCTGAATATGTTGGATTGATGGTTACTGAT
1 CTCTACGTTACTCTGTTGATGAAGAATATACAATATCTGAATATGTTAGATTGATGGTTACTGAT
54652953 TCTAATTTATAACC
66 TCTAATTTATAACC
* *
54652967 CTCTACGTTACTCTGTTGATGAAGAATATACGATATCTGAATATGTTAGATTGATTGTTACTGAT
1 CTCTACGTTACTCTGTTGATGAAGAATATACAATATCTGAATATGTTAGATTGATGGTTACTGAT
*
54653032 TCTGATTTATAACC
66 TCTAATTTATAACC
54653046 GTGCATGTGA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (79 bp):
CTCTACGTTACTCTGTTGATGAAGAATATACAATATCTGAATATGTTAGATTGATGGTTACTGAT
TCTAATTTATAACC
Found at i:54653549 original size:25 final size:24
Alignment explanation
Indices: 54653515--54653601 Score: 111
Period size: 25 Copynumber: 3.5 Consensus size: 24
54653505 AACGTACATG
54653515 CTCTGCTCTGTTATGTTCAATTCTA
1 CTCTGCTCTGTTATGTT-AATTCTA
*
54653540 CTCTGCTCTGTTATGTTTAGTTCTA
1 CTCTGCTCTGTTATG-TTAATTCTA
** *
54653565 CTCTGCTCTACTATGTTATATTCTG
1 CTCTGCTCTGTTATGTTA-ATTCTA
54653590 CTCTGCTCTGTT
1 CTCTGCTCTGTT
54653602 CTATTCTCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
24 3 0.06
25 48 0.91
26 2 0.04
ACGTcount: A:0.13, C:0.24, G:0.14, T:0.49
Consensus pattern (24 bp):
CTCTGCTCTGTTATGTTAATTCTA
Found at i:54653591 original size:20 final size:20
Alignment explanation
Indices: 54653566--54653608 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
54653556 TTAGTTCTAC
54653566 TCTGCTCTACTATGTTATAT
1 TCTGCTCTACTATGTTATAT
* * *
54653586 TCTGCTCTGCTCTGTTCTAT
1 TCTGCTCTACTATGTTATAT
54653606 TCT
1 TCT
54653609 CTTATGTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.26, G:0.12, T:0.51
Consensus pattern (20 bp):
TCTGCTCTACTATGTTATAT
Found at i:54653599 original size:30 final size:30
Alignment explanation
Indices: 54653565--54653623 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
54653555 TTTAGTTCTA
*
54653565 CTCTGCTCTACTATGTTATATTCTGCTCTG
1 CTCTGCTCTACTATCTTATATTCTGCTCTG
* * * *
54653595 CTCTGTTCTATTCTCTTATGTTCTGCTCT
1 CTCTGCTCTACTATCTTATATTCTGCTCT
54653624 ATCCTGTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.10, C:0.27, G:0.12, T:0.51
Consensus pattern (30 bp):
CTCTGCTCTACTATCTTATATTCTGCTCTG
Found at i:54654607 original size:17 final size:16
Alignment explanation
Indices: 54654583--54654621 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
54654573 TTATGCACAC
54654583 TTTATTAATAATATAT
1 TTTATTAATAATATAT
*
54654599 TTGTATTAATAATGTAT
1 TT-TATTAATAATATAT
54654616 TTTATT
1 TTTATT
54654622 GAGTTGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTATTAATAATATAT
Found at i:54654918 original size:15 final size:15
Alignment explanation
Indices: 54654887--54654919 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
54654877 TTAGTAATAG
54654887 TTATATATTTTATTA
1 TTATATATTTTATTA
54654902 TTAT-TATTTTATGTA
1 TTATATATTTTAT-TA
54654917 TTA
1 TTA
54654920 GTAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTATATATTTTATTA
Found at i:54655760 original size:32 final size:33
Alignment explanation
Indices: 54655705--54655772 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
54655695 TTAAAGGCCC
*
54655705 AAATTTTTTTTTTACCAAATTTTAA-GAGACCTA
1 AAATTTTTTTTCTACCAAATTTTAAGGA-ACCTA
*
54655738 AAATTTTTTTTCT-CCAACTTTTAAGGAACCTA
1 AAATTTTTTTTCTACCAAATTTTAAGGAACCTA
54655770 AAA
1 AAA
54655773 CCTCATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 18 0.56
33 14 0.44
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (33 bp):
AAATTTTTTTTCTACCAAATTTTAAGGAACCTA
Found at i:54655883 original size:6 final size:6
Alignment explanation
Indices: 54655872--54655896 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54655862 ACTTCCAACT
54655872 CTCTCC CTCTCC CTCTCC CTCTCC C
1 CTCTCC CTCTCC CTCTCC CTCTCC C
54655897 AACCGTTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCTCC
Found at i:54662248 original size:22 final size:23
Alignment explanation
Indices: 54662205--54662250 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
54662195 TGTCAAGTAA
*
54662205 TTTTTTGTGGTGTGTTGGCTTAG
1 TTTTTTGTGGTGTGTTGCCTTAG
54662228 TTTTTTGT-GT-TGTTCGCCTTAG
1 TTTTTTGTGGTGTGTT-GCCTTAG
54662250 T
1 T
54662251 CTTGTGTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 9 0.43
23 8 0.38
ACGTcount: A:0.04, C:0.09, G:0.28, T:0.59
Consensus pattern (23 bp):
TTTTTTGTGGTGTGTTGCCTTAG
Found at i:54662547 original size:13 final size:13
Alignment explanation
Indices: 54662522--54662555 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
54662512 TTTTCTTTCA
54662522 TTTCTTT-TTGTT
1 TTTCTTTCTTGTT
54662534 TTTCTTTCTTGTT
1 TTTCTTTCTTGTT
*
54662547 TATCTTTCT
1 TTTCTTTCT
54662556 CTTTTTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (13 bp):
TTTCTTTCTTGTT
Found at i:54663671 original size:27 final size:27
Alignment explanation
Indices: 54663599--54663731 Score: 149
Period size: 27 Copynumber: 4.9 Consensus size: 27
54663589 TTGCTGACTA
* * *
54663599 AAATACCTTCGAAGGGTAAAATGGCTG
1 AAATACCCTCGAAGGGTAAAATGACCG
* ** *
54663626 AAATACCCTCAAATTGTAAAATGACCA
1 AAATACCCTCGAAGGGTAAAATGACCG
* *
54663653 AAATACCCTCGAAGGGTAAAATAATCG
1 AAATACCCTCGAAGGGTAAAATGACCG
* *
54663680 AAATACCCCCGAAGGGTAAAATGATCG
1 AAATACCCTCGAAGGGTAAAATGACCG
* *
54663707 AAATACCTTTGAAGGGTAAAATGAC
1 AAATACCCTCGAAGGGTAAAATGAC
54663732 TGTTATACCC
Statistics
Matches: 87, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 87 1.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATGACCG
Found at i:54663740 original size:54 final size:54
Alignment explanation
Indices: 54663593--54663742 Score: 167
Period size: 54 Copynumber: 2.8 Consensus size: 54
54663583 TTCTCTTTGC
* * * **
54663593 TGACTAAAATACCTTCGAAGGGTAAAATGGCTGAAATACCCTCAAATTGTAAAA
1 TGACCAAAATACCTTCGAAGGGTAAAATGACTGAAATACCCCCAAAGGGTAAAA
* * *
54663647 TGACCAAAATACCCTCGAAGGGTAAAAT-AATCGAAATACCCCCGAAGGGTAAAA
1 TGACCAAAATACCTTCGAAGGGTAAAATGACT-GAAATACCCCCAAAGGGTAAAA
* * * **
54663701 TGATCGAAATACCTTTGAAGGGTAAAATGACTGTTATACCCC
1 TGACCAAAATACCTTCGAAGGGTAAAATGACTGAAATACCCC
54663743 TAGGAATTGA
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 76 0.96
55 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (54 bp):
TGACCAAAATACCTTCGAAGGGTAAAATGACTGAAATACCCCCAAAGGGTAAAA
Found at i:54663935 original size:26 final size:26
Alignment explanation
Indices: 54663906--54664007 Score: 105
Period size: 26 Copynumber: 3.9 Consensus size: 26
54663896 TTGCCACAAA
*
54663906 TACTGTTATTGGCAGCTTTGCTGCGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* * * *
54663932 TACTGATACTGGCAGCTCTACTGGGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* * *
54663958 TACTGTTAGTGGCAGCTTTGTTGCAT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* * *
54663984 TACTATTACTGGTAGTTTTGCTGC
1 TACTGTTACTGGCAGCTTTGCTGC
54664008 AATATTAGTG
Statistics
Matches: 59, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCGT
Found at i:54664173 original size:28 final size:28
Alignment explanation
Indices: 54664135--54664236 Score: 105
Period size: 30 Copynumber: 3.5 Consensus size: 28
54664125 ATTTTAGGCT
*
54664135 TAAGGCTCACACTGTTACTGTATTGGGC
1 TAAGGCCCACACTGTTACTGTATTGGGC
54664163 TAAGGCCCACACTCTGTTACTGTATTGGGC
1 TAAGGCCCACA--CTGTTACTGTATTGGGC
* * * *
54664193 TATGGTCCACACACTGCTATTGTATAGGGC
1 TAAGG-CC-CACACTGTTACTGTATTGGGC
* *
54664223 TCAGGCCCAGACTG
1 TAAGGCCCACACTG
54664237 ATTCTGCATG
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
28 16 0.26
29 2 0.03
30 38 0.61
31 2 0.03
32 4 0.06
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (28 bp):
TAAGGCCCACACTGTTACTGTATTGGGC
Found at i:54664182 original size:30 final size:30
Alignment explanation
Indices: 54664142--54664231 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
54664132 GCTTAAGGCT
54664142 CACACTGTTACTGTATTGGGCTAAGGCCCA
1 CACACTGTTACTGTATTGGGCTAAGGCCCA
* * *
54664172 CACTCTGTTACTGTATTGGGCTATGGTCCA
1 CACACTGTTACTGTATTGGGCTAAGGCCCA
* * * *
54664202 CACACTGCTATTGTATAGGGCTCAGGCCCA
1 CACACTGTTACTGTATTGGGCTAAGGCCCA
54664232 GACTGATTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (30 bp):
CACACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:54666782 original size:43 final size:42
Alignment explanation
Indices: 54666655--54666770 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 42
54666645 AGCTCGTACA
* *
54666655 ATGCCATCGTCCCAGACGTGGTCTTATATGTAATCACATATCG
1 ATGCCA-CGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* *
54666698 ATGCCACTATCCCAGACAG-GGTCTTACACGTAATCAAATATCG
1 ATGCCAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
54666741 ATGCCGACGTCCCAGACGTGGTCTTACACG
1 ATGCC-ACGTCCCAGACGTGGTCTTACACG
54666771 AAAATACATA
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
42 2 0.03
43 59 0.92
44 3 0.05
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (42 bp):
ATGCCACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:54667716 original size:28 final size:28
Alignment explanation
Indices: 54667662--54667718 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
54667652 TATGTTTGTT
54667662 TTTATTATAAAAACTTTATAATATATTA
1 TTTATTATAAAAACTTTATAATATATTA
* *
54667690 TTTATTATTATAACCTTTATAAT-TATTA
1 TTTATTA-TAAAAACTTTATAATATATTA
54667718 T
1 T
54667719 AAAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTATTATAAAAACTTTATAATATATTA
Found at i:54671027 original size:21 final size:21
Alignment explanation
Indices: 54671003--54671106 Score: 115
Period size: 21 Copynumber: 5.0 Consensus size: 21
54670993 TTTGGGTGGA
*
54671003 TCAGCTCTTACGGGTTTCTGT
1 TCAGCTCTTACGAGTTTCTGT
*
54671024 TCAGCTCTTATGAGTTTCTGT
1 TCAGCTCTTACGAGTTTCTGT
*
54671045 TTAGCTCTTACGAGCTTT-TGT
1 TCAGCTCTTACGAG-TTTCTGT
* *
54671066 TCAGCT-TT-CAAGCTTCTGT
1 TCAGCTCTTACGAGTTTCTGT
* *
54671085 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTACGAGTTTCTGT
54671106 T
1 T
54671107 AATGATGTAC
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
18 2 0.03
19 12 0.17
20 4 0.06
21 49 0.70
22 3 0.04
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (21 bp):
TCAGCTCTTACGAGTTTCTGT
Found at i:54671094 original size:40 final size:41
Alignment explanation
Indices: 54671003--54671106 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 41
54670993 TTTGGGTGGA
* *
54671003 TCAGCTCTTACG-GGTTTCTGTTCAGCTCTTATGAGTTTCTGT
1 TCAGCTCTTACGAGCTTT-TGTTCAGCTCTTA-GAGCTTCTGT
*
54671045 TTAGCTCTTACGAGCTTTTGTTCAGCT-TTCA-AGCTTCTGT
1 TCAGCTCTTACGAGCTTTTGTTCAGCTCTT-AGAGCTTCTGT
* *
54671085 TCAGCTCTTATGAGCTTCTGTT
1 TCAGCTCTTACGAGCTTTTGTT
54671107 AATGATGTAC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
40 27 0.50
41 2 0.04
42 21 0.39
43 4 0.07
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (41 bp):
TCAGCTCTTACGAGCTTTTGTTCAGCTCTTAGAGCTTCTGT
Found at i:54671269 original size:21 final size:20
Alignment explanation
Indices: 54671243--54671290 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
54671233 TAGAAGTTAA
*
54671243 GAATGATAGGAAATTATCAGT
1 GAATGATAGGAAATTAACA-T
* *
54671264 GAATGAAAGGGAATTAACAT
1 GAATGATAGGAAATTAACAT
54671284 GAATGAT
1 GAATGAT
54671291 TTTATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.46, C:0.04, G:0.25, T:0.25
Consensus pattern (20 bp):
GAATGATAGGAAATTAACAT
Found at i:54678281 original size:39 final size:40
Alignment explanation
Indices: 54678186--54678447 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
54678176 TTGAATGATG
*
54678186 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
54678224 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
54678265 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
54678304 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
54678343 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
54678382 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
54678421 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
54678448 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:54685012 original size:39 final size:40
Alignment explanation
Indices: 54684917--54685258 Score: 443
Period size: 40 Copynumber: 8.7 Consensus size: 40
54684907 TTGAATGATG
*
54684917 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
54684955 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
54684996 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
54685035 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
54685074 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
54685113 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
54685153 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
54685193 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
54685232 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
54685259 AACGAGGAGC
Statistics
Matches: 283, Mismatches: 11, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
39 132 0.47
40 139 0.49
41 11 0.04
42 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:54688094 original size:30 final size:30
Alignment explanation
Indices: 54688050--54688109 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
54688040 ACTTAACAAG
*
54688050 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAAAAACAAAATTAA
* *
54688080 CAAATGTCTTTAAAATAAAAACAAAATTAA
1 CAAATGCCTCTAAAATAAAAACAAAATTAA
54688110 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAAAAACAAAATTAA
Done.