Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 176 of 210
Found at i:52553810 original size:9 final size:9
Alignment explanation
Indices: 52553791--52554060 Score: 155
Period size: 9 Copynumber: 29.3 Consensus size: 9
52553781 AAATGGACAC
52553791 AAATT-TAA
1 AAATTATAA
52553799 AAATTATAA
1 AAATTATAA
52553808 AAACTTATAA
1 AAA-TTATAA
*
52553818 ATATTATAA
1 AAATTATAA
52553827 AAA-TATAAA
1 AAATTAT-AA
*
52553836 AAATTA-AC
1 AAATTATAA
*
52553844 AAATCAT-A
1 AAATTATAA
*
52553852 AAATTTTATA
1 AAATTATA-A
52553862 AAATTAATAAAA
1 AAATT-AT--AA
*
52553874 AAATATTTACA
1 AAAT-TATA-A
** *
52553885 ATTTTATGA
1 AAATTATAA
*
52553894 AAATCAT-A
1 AAATTATAA
52553902 AAA-TATTAA
1 AAATTA-TAA
*
52553911 AAA-TATAT
1 AAATTATAA
52553919 AAATTAGTAA
1 AAATTA-TAA
*
52553929 AAAATATAA
1 AAATTATAA
52553938 AAACTTATAA
1 AAA-TTATAA
*
52553948 ATATTATAA
1 AAATTATAA
*
52553957 AAAATATAA
1 AAATTATAA
*
52553966 TAATTA-AA
1 AAATTATAA
**
52553974 ATTTTATAA
1 AAATTATAA
*
52553983 AAACATATAA
1 AAA-TTATAA
52553993 AAATTCATAA
1 AAATT-ATAA
52554003 AAACTTATAA
1 AAA-TTATAA
52554013 ATAA-TATAA
1 A-AATTATAA
*
52554022 AAATTCTAA
1 AAATTATAA
52554031 TAAATTATAA
1 -AAATTATAA
*
52554041 AAA-AATAA
1 AAATTATAA
52554049 AAATTATAA
1 AAATTATAA
52554058 AAA
1 AAA
52554061 CTCATTTACA
Statistics
Matches: 200, Mismatches: 37, Indels: 49
0.70 0.13 0.17
Matches are distributed among these distances:
7 1 0.00
8 43 0.22
9 79 0.40
10 61 0.31
11 8 0.04
12 6 0.03
13 2 0.01
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.33
Consensus pattern (9 bp):
AAATTATAA
Found at i:52553810 original size:10 final size:10
Alignment explanation
Indices: 52553797--52554060 Score: 93
Period size: 10 Copynumber: 27.4 Consensus size: 10
52553787 ACACAAATTT
52553797 AAAAATTATA
1 AAAAATTATA
*
52553807 AAAACTTAT-
1 AAAAATTATA
*
52553816 AAATATTAT-
1 AAAAATTATA
52553825 AAAAA-TATA
1 AAAAATTATA
52553834 AAAAA-T-TA
1 AAAAATTATA
* *
52553842 ACAAATCAT-
1 AAAAATTATA
*
52553851 -AAAATTTTA
1 AAAAATTATA
*
52553860 TAAAATTAATA
1 AAAAATT-ATA
* *
52553871 AAAAAATATT
1 AAAAATTATA
* * *
52553881 TACAATTTTA
1 AAAAATTATA
* *
52553891 TGAAAATCAT-
1 -AAAAATTATA
*
52553901 -AAAA-TATT
1 AAAAATTATA
52553909 AAAAA-TAT-
1 AAAAATTATA
*
52553917 ATAAATTAGTA
1 AAAAATTA-TA
52553928 AAAAA-TATA
1 AAAAATTATA
*
52553937 AAAACTTAT-
1 AAAAATTATA
*
52553946 AAATATTATA
1 AAAAATTATA
52553956 AAAAATATAATA
1 AAAAAT-T-ATA
52553968 ATTAAAATTTTATA
1 A--AAAA--TTATA
52553982 AAAACA-TAT-
1 AAAA-ATTATA
52553991 AAAAATTCATA
1 AAAAATT-ATA
*
52554002 AAAACTTATA
1 AAAAATTATA
*
52554012 AATAA-TAT-
1 AAAAATTATA
*
52554020 AAAAATTCTA
1 AAAAATTATA
*
52554030 ATAAATTATA
1 AAAAATTATA
52554040 AAAAA--AT-
1 AAAAATTATA
52554047 AAAAATTATA
1 AAAAATTATA
52554057 AAAA
1 AAAA
52554061 CTCATTTACA
Statistics
Matches: 188, Mismatches: 37, Indels: 58
0.66 0.13 0.20
Matches are distributed among these distances:
7 7 0.04
8 29 0.15
9 51 0.27
10 60 0.32
11 23 0.12
12 7 0.04
13 1 0.01
14 8 0.04
15 1 0.01
16 1 0.01
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (10 bp):
AAAAATTATA
Found at i:52554042 original size:130 final size:129
Alignment explanation
Indices: 52553791--52554060 Score: 284
Period size: 130 Copynumber: 2.1 Consensus size: 129
52553781 AAATGGACAC
*
52553791 AAATT-TAAAAATTATAAAAACTTATAAATATTATAAAAATATAAAAAATTAACAAATCATAAAA
1 AAATTATAAAAAATATAAAAACTTATAAATATTATAAAAATATAAAAAATTAACAAATCATAAAA
*** * ** * * *
52553855 TTTTATAAAATTAATAAAAAAATATTTACAATTTTATGAAAATCATAAAATATTAAAAATATAT
66 ACATATAAAATTAATAAAAAAATATATACAATAATATAAAAATCATAAAATATTAAAAAAATAA
* * *
52553919 AAATTAGTAAAAAATATAAAAACTTATAAATATTATAAAAA-ATATAATAATTAA-AATTTTATA
1 AAATTA-TAAAAAATATAAAAACTTATAAATATTATAAAAATATA-AAAAATTAACAA-ATCATA
* * *
52553982 AAAACATATAAAAATTCAT-AAAAACT-TATA-AATAATATAAAAATTCTAATAAATTA-TAAAA
63 AAAACATAT-AAAATTAATAAAAAAATATATACAATAATATAAAAA-TC--ATAAAATATTAAAA
52554043 AAATAA
124 AAATAA
52554049 AAATTATAAAAA
1 AAATTATAAAAA
52554061 CTCATTTACA
Statistics
Matches: 118, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
128 15 0.13
129 16 0.14
130 72 0.61
131 15 0.13
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.33
Consensus pattern (129 bp):
AAATTATAAAAAATATAAAAACTTATAAATATTATAAAAATATAAAAAATTAACAAATCATAAAA
ACATATAAAATTAATAAAAAAATATATACAATAATATAAAAATCATAAAATATTAAAAAAATAA
Found at i:52554494 original size:15 final size:16
Alignment explanation
Indices: 52554474--52554505 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
52554464 TAAAGAAAAC
52554474 ATTAAA-AAACTAATA
1 ATTAAATAAACTAATA
52554489 ATTAAATAAACTAATA
1 ATTAAATAAACTAATA
52554505 A
1 A
52554506 AAAAATTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (16 bp):
ATTAAATAAACTAATA
Found at i:52554646 original size:19 final size:18
Alignment explanation
Indices: 52554624--52554703 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 18
52554614 CAGTTTAATT
52554624 TTTTAATGATTTTTTATAA
1 TTTTAAT-ATTTTTTATAA
*
52554643 TTTT-ATATGTTTATATTAA
1 TTTTAATAT-TTTTTA-TAA
*
52554662 TTTTAATATTTTTGA-ATA
1 TTTTAATATTTTTTATA-A
*
52554680 TTTTTATGATTTTTTATAA
1 TTTTAAT-ATTTTTTATAA
*
52554699 GTTTA
1 TTTTA
52554704 GAAGAATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
17 3 0.06
18 14 0.29
19 26 0.54
20 5 0.10
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (18 bp):
TTTTAATATTTTTTATAA
Found at i:52554681 original size:10 final size:9
Alignment explanation
Indices: 52554617--52554685 Score: 52
Period size: 10 Copynumber: 7.4 Consensus size: 9
52554607 TCTGGTCCAG
52554617 TTTAAT-TT
1 TTTAATATT
52554625 TTTAATGATT
1 TTTAAT-ATT
* *
52554635 TTTTATAAT
1 TTTAATATT
52554644 TTT-ATATGT
1 TTTAATAT-T
* *
52554653 TTATATTAAT
1 TT-TAATATT
52554663 TTTAATATT
1 TTTAATATT
52554672 TTTGAATATT
1 TTT-AATATT
52554682 TTTA
1 TTTA
52554686 TGATTTTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
8 9 0.19
9 17 0.35
10 20 0.42
11 2 0.04
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTAATATT
Found at i:52555348 original size:43 final size:43
Alignment explanation
Indices: 52555281--52555559 Score: 330
Period size: 43 Copynumber: 6.3 Consensus size: 43
52555271 TTTTTGAAAT
52555281 AAACGCCGCTATAGACCA-TGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCAGT-ACCTTTAGCGGCGCTTTTCCCAC
* *
52555324 AAACGCCGCTAAAGACCAGTACCTTTAGCGGCGCTATT-CCAC
1 AAACGCCGCTATAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
52555366 AAACGCCGCTATAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
*
52555409 AAACGCCGCTATAGACCAATACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
* *
52555452 AAACGCCGCTATAGACCATGACCTATAGCGGTCTATAGCGGCGCTTTTTCCCGC
1 AAACGCCGCTATAGACCA-G-----TA-C---CTTTAGCGGCGC-TTTTCCCAC
* * * * *
52555506 AAACGCTGCTAAAGA-CAATGACCTTTAGCGGCGCTTTTCACAA
1 AAACGCCGCTATAGACCAGT-ACCTTTAGCGGCGCTTTTCCCAC
52555549 AAACGCCGCTA
1 AAACGCCGCTA
52555560 AAAACTTATC
Statistics
Matches: 206, Mismatches: 16, Indels: 28
0.82 0.06 0.11
Matches are distributed among these distances:
42 40 0.19
43 114 0.55
44 12 0.06
47 2 0.01
48 1 0.00
49 2 0.01
50 1 0.00
53 13 0.06
54 21 0.10
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTATAGACCAGTACCTTTAGCGGCGCTTTTCCCAC
Found at i:52555425 original size:85 final size:86
Alignment explanation
Indices: 52555281--52555559 Score: 348
Period size: 85 Copynumber: 3.1 Consensus size: 86
52555271 TTTTTGAAAT
*
52555281 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGTAC
1 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAATAC
52555346 CTTTAGCGGCGCTATT-CCAC
66 CTTTAGCGGCGCTATTCCCAC
*
52555366 AAACGCCGCTATAGACCA-GTACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCAATA
1 AAACGCCGCTATAGACCATG-ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAATA
*
52555430 CCTTTAGCGGCGCTTTTCCCAC
65 CCTTTAGCGGCGCTATTCCCAC
* *
52555452 AAACGCCGCTATAGACCATGACCTATAGCGGTCTATAGCGGCGCTTTTTCCCGCAAACGCTGCTA
1 AAACGCCGCTATAGACCATGA-C-----C--T-T-TAGCGGCGC-TTTTCCCACAAACGCCGCTA
* * *
52555517 AAGA-CAATGACCTTTAGCGGCGCTTTTCACAA
55 AAGACCAAT-ACCTTTAGCGGCGCTATTCCCAC
52555549 AAACGCCGCTA
1 AAACGCCGCTA
52555560 AAAACTTATC
Statistics
Matches: 171, Mismatches: 8, Indels: 18
0.87 0.04 0.09
Matches are distributed among these distances:
84 1 0.01
85 76 0.44
86 23 0.13
87 2 0.01
92 1 0.01
94 1 0.01
95 1 0.01
96 13 0.08
97 53 0.31
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (86 bp):
AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAATAC
CTTTAGCGGCGCTATTCCCAC
Found at i:52555510 original size:54 final size:53
Alignment explanation
Indices: 52555434--52555536 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 53
52555424 CCAATACCTT
* *
52555434 TAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCATGACCTATAGCGGTCTA
1 TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACAATGACCTATAGCGGTCTA
* * *
52555487 TAGCGGCGCTTTTTCCCGCAAACGCTGCTAAAGACAATGACCTTTAGCGG
1 TAGCGGCGC-TTTTCCCACAAACGCCGCTAAAGACAATGACCTATAGCGG
52555537 CGCTTTTCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 9 0.20
54 35 0.80
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.23
Consensus pattern (53 bp):
TAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACAATGACCTATAGCGGTCTA
Found at i:52555884 original size:43 final size:43
Alignment explanation
Indices: 52555836--52555930 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 43
52555826 ACATATGCAA
* * * *
52555836 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
52555879 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
52555922 GGTAATAAA
1 GGTAATAAA
52555931 GTATCCTGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:52561369 original size:19 final size:20
Alignment explanation
Indices: 52561343--52561388 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
52561333 ATAGAATTTT
52561343 AATT-AATA-TAAATAAACA
1 AATTAAATAGTAAATAAACA
* *
52561361 AATTAAATAGTAATTAGACA
1 AATTAAATAGTAAATAAACA
*
52561381 AATAAAAT
1 AATTAAAT
52561389 GTTTTTGCGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (20 bp):
AATTAAATAGTAAATAAACA
Found at i:52561456 original size:41 final size:41
Alignment explanation
Indices: 52561395--52561587 Score: 280
Period size: 41 Copynumber: 4.7 Consensus size: 41
52561385 AAATGTTTTT
*
52561395 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCTGAGCATTA
*
52561436 GCGACGCTTTTCCAAAAACGCCGCTAAAGACCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCTGAGCATTA
* *
52561477 GCGGCGC-TTCCCAGAAAACGCTGCTAAAGACCTGAGCATTA
1 GCGGCGCTTTTCCA-AAAACGCCGCTAAAGACCTGAGCATTA
* * *
52561518 GCGGCGCTTCTCCAAAAACGCCGCTAAAGACCCGAGAATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCTGAGCATTA
* **
52561559 GCGCCGCTTTTATAAAAACGCCGCTAAAG
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAG
52561588 CCCCGAAAGG
Statistics
Matches: 136, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 5 0.04
41 127 0.93
42 4 0.03
ACGTcount: A:0.31, C:0.30, G:0.22, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCTGAGCATTA
Found at i:52561862 original size:41 final size:41
Alignment explanation
Indices: 52561803--52561952 Score: 248
Period size: 41 Copynumber: 3.7 Consensus size: 41
52561793 NNNNNNNNNN
* * *
52561803 GCGGCGCTTTTCCAAAAATGCCGCTAAAGACCCGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGACCAGAGCATTA
*
52561844 GCGGCGCTTC-CCAGAAAATGCCGCTAAAGACCAGAGCATTA
1 GCGGCGCTTCTCCA-AAAACGCCGCTAAAGACCAGAGCATTA
52561885 GCGGCGCTTCTCCAAAAACGCCGCTAAAGACCAGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGACCAGAGCATTA
52561926 GCGGCGCTTCTCCAAAAACGCCGCTAA
1 GCGGCGCTTCTCCAAAAACGCCGCTAA
52561953 TGCTCGATTT
Statistics
Matches: 104, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
40 3 0.03
41 98 0.94
42 3 0.03
ACGTcount: A:0.30, C:0.31, G:0.23, T:0.16
Consensus pattern (41 bp):
GCGGCGCTTCTCCAAAAACGCCGCTAAAGACCAGAGCATTA
Found at i:52567771 original size:19 final size:19
Alignment explanation
Indices: 52567718--52567775 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
52567708 AAATTGACAC
52567718 AAATT-TAA-AAATTAT-A
1 AAATTCTAATAAATTATAA
*
52567734 AAA-TCTTATAAATAGTATAA
1 AAATTCTAATAAAT--TATAA
52567754 AAATTCTAATAAATTATAA
1 AAATTCTAATAAATTATAA
52567773 AAA
1 AAA
52567776 ATTATAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 1 0.03
16 5 0.15
17 4 0.12
19 11 0.32
20 4 0.12
21 9 0.26
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATTCTAATAAATTATAA
Found at i:52567777 original size:10 final size:10
Alignment explanation
Indices: 52567724--52567785 Score: 56
Period size: 10 Copynumber: 6.4 Consensus size: 10
52567714 ACACAAATTT
52567724 AAAAATTATA
1 AAAAATTATA
**
52567734 AAATCTTAT-
1 AAAAATTATA
* *
52567743 AAATAGTAT-
1 AAAAATTATA
*
52567752 AAAAATTCTA
1 AAAAATTATA
*
52567762 ATAAATTATA
1 AAAAATTATA
52567772 AAAAATTATA
1 AAAAATTATA
52567782 AAAA
1 AAAA
52567786 GTGATTTAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
9 13 0.32
10 28 0.68
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (10 bp):
AAAAATTATA
Found at i:52567782 original size:17 final size:17
Alignment explanation
Indices: 52567665--52567783 Score: 55
Period size: 17 Copynumber: 6.7 Consensus size: 17
52567655 AACAATGATT
* *
52567665 AAAAATCATAAAATATAA
1 AAAAATTATAAATTAT-A
52567683 AAAAATTA-AATATT-TA
1 AAAAATTATAA-ATTATA
* *
52567699 AAAGTATTA-AAATTGACA
1 AAA-AATTATAAATT-ATA
* * *
52567717 CAAATTTAAAAATTATA
1 AAAAATTATAAATTATA
**
52567734 AAATCTTATAAATAGTATA
1 AAAAATTATAAAT--TATA
*
52567753 AAAATTCTAATAAATTATA
1 AAAAAT-T-ATAAATTATA
52567772 AAAAATTATAAA
1 AAAAATTATAAA
52567784 AAGTGATTTA
Statistics
Matches: 77, Mismatches: 15, Indels: 19
0.69 0.14 0.17
Matches are distributed among these distances:
16 7 0.09
17 28 0.36
18 18 0.23
19 17 0.22
20 1 0.01
21 6 0.08
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (17 bp):
AAAAATTATAAATTATA
Found at i:52568664 original size:19 final size:19
Alignment explanation
Indices: 52568621--52568681 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
52568611 GCATTTTCTG
52568621 ATTA-TTTTATAATTTTTA
1 ATTATTTTTATAATTTTTA
* *
52568639 ATAATTTTTATGAGTTTTT-
1 ATTATTTTTAT-AATTTTTA
52568658 ATTA--TTTAT-ATTTTTA
1 ATTATTTTTATAATTTTTA
*
52568674 AATATTTT
1 ATTATTTT
52568682 GTGTGAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
15 5 0.15
16 3 0.09
17 5 0.15
18 5 0.15
19 9 0.27
20 6 0.18
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
ATTATTTTTATAATTTTTA
Found at i:52572337 original size:26 final size:25
Alignment explanation
Indices: 52572294--52572345 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
52572284 ATCCATCAAT
*
52572294 ATTATTAGTTCAATAAATTATATTAA
1 ATTATTAGTTCAA-AAAATATATTAA
*
52572320 ATTATTATGTT-AAAAAATATTTTAA
1 ATTATTA-GTTCAAAAAATATATTAA
52572345 A
1 A
52572346 AATATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 11 0.48
26 9 0.39
27 3 0.13
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
ATTATTAGTTCAAAAAATATATTAA
Found at i:52572612 original size:9 final size:9
Alignment explanation
Indices: 52572565--52572856 Score: 106
Period size: 10 Copynumber: 31.6 Consensus size: 9
52572555 AGGCGATAAG
52572565 AAAAA-TAT
1 AAAAATTAT
*
52572573 TAAAA-TAT
1 AAAAATTAT
*
52572581 TAAAATTGAT
1 AAAAATT-AT
*
52572591 ACAAATT-T
1 AAAAATTAT
52572599 AAAAATTAT
1 AAAAATTAT
52572608 AAAAACTTAT
1 AAAAA-TTAT
* *
52572618 AAATATTGT
1 AAAAATTAT
52572627 -AAAA-TAT
1 AAAAATTAT
52572634 AAAAA--AT
1 AAAAATTAT
*
52572641 AACAAATCAT
1 AA-AAATTAT
52572651 AAAAAATT-T
1 -AAAAATTAT
*
52572660 AAAATTTGAT
1 AAAAATT-AT
* *
52572670 GAACATTAT
1 AAAAATTAT
* *
52572679 AAAAGTCAT
1 AAAAATTAT
52572688 AAAATATT-T
1 AAAA-ATTAT
*
52572697 -AAAATGAT
1 AAAAATTAT
*
52572705 ATAAATTTAT
1 A-AAAATTAT
* *
52572715 AAAAAATAA
1 AAAAATTAT
52572724 AAATAACTTAT
1 AAA-AA-TTAT
*
52572735 AAATATTAT
1 AAAAATTAT
*
52572744 AAAAATAACT
1 AAAAATTA-T
52572754 AATAAATCTA-
1 AA-AAAT-TAT
*
52572764 ATAAATTAT
1 AAAAATTAT
52572773 AATAAAATTAATT
1 -A-AAAATT-A-T
* *
52572786 TAAAATAATT
1 AAAAATTA-T
*
52572796 AAAATTTTAT
1 AAAA-ATTAT
52572806 AAATAATTAT
1 AAA-AATTAT
52572816 AAATAA-TAT
1 AAA-AATTAT
*
52572825 -AAAATTCT
1 AAAAATTAT
52572833 AATAAATTAT
1 AA-AAATTAT
52572843 AAAAATTAT
1 AAAAATTAT
52572852 AAAAA
1 AAAAA
52572857 ATCATTTAAA
Statistics
Matches: 213, Mismatches: 41, Indels: 59
0.68 0.13 0.19
Matches are distributed among these distances:
7 10 0.05
8 45 0.21
9 61 0.29
10 70 0.33
11 24 0.11
12 2 0.01
13 1 0.00
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:52572717 original size:18 final size:19
Alignment explanation
Indices: 52572674--52572718 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
52572664 TTTGATGAAC
52572674 ATTATAAAAGTCATAAAAT
1 ATTATAAAAGTCATAAAAT
*
52572693 ATT-TAAAA-TGATATAAAT
1 ATTATAAAAGTCATA-AAAT
52572711 -TTATAAAA
1 ATTATAAAA
52572719 AATAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 6 0.26
18 14 0.61
19 3 0.13
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (19 bp):
ATTATAAAAGTCATAAAAT
Found at i:52572719 original size:28 final size:29
Alignment explanation
Indices: 52572704--52572848 Score: 72
Period size: 28 Copynumber: 4.9 Consensus size: 29
52572694 TTTAAAATGA
52572704 TATAAAT-TTATAAAAA-ATAAAAATAAC
1 TATAAATATTATAAAAATATAAAAATAAC
52572731 TTATAAATATTATAAAAATAACTAATAAAT--C
1 -TATAAATATTATAAAAAT-A-TAA-AAATAAC
* * * *
52572762 TAATAAATTATAATAAAATTAATTTAAAATAAT
1 T-ATAAA-TATTATAAAAAT-A-TAAAAATAAC
* *
52572795 TA-AAATTTTATAAATAAT-TATAAATAA-
1 TATAAATATTATAAA-AATATAAAAATAAC
*
52572822 TATAAA-ATTCTAATAAATTATAAAAAT
1 TATAAATATTATAA-AAA-TATAAAAAT
52572849 TATAAAAAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 27
0.69 0.10 0.21
Matches are distributed among these distances:
27 9 0.10
28 19 0.21
29 15 0.17
30 8 0.09
31 16 0.18
32 18 0.20
33 5 0.06
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (29 bp):
TATAAATATTATAAAAATATAAAAATAAC
Found at i:52572767 original size:22 final size:22
Alignment explanation
Indices: 52572719--52572768 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
52572709 ATTTATAAAA
*
52572719 AATAAAAATAACTTATAAATAT
1 AATAAAAATAACTAATAAATAT
* *
52572741 TATAAAAATAACTAATAAATCT
1 AATAAAAATAACTAATAAATAT
52572763 AATAAA
1 AATAAA
52572769 TTATAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (22 bp):
AATAAAAATAACTAATAAATAT
Found at i:52572811 original size:18 final size:18
Alignment explanation
Indices: 52572784--52572819 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
52572774 ATAAAATTAA
52572784 TTTAAAATAATTA-AAAT
1 TTTAAAATAATTATAAAT
52572801 TTTATAAATAATTATAAAT
1 TTTA-AAATAATTATAAAT
52572820 AATATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAAAATAATTATAAAT
Found at i:52572837 original size:20 final size:20
Alignment explanation
Indices: 52572814--52572873 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
52572804 ATAAATAATT
52572814 ATAAATAATATAAAATTCTA
1 ATAAATAATATAAAATTCTA
* *
52572834 ATAAATTATA-AAAATTATA
1 ATAAATAATATAAAATTCTA
* * * *
52572853 AAAAATCATTTAAACTTCTA
1 ATAAATAATATAAAATTCTA
52572873 A
1 A
52572874 AACTATAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAATAATATAAAATTCTA
Found at i:52572848 original size:29 final size:29
Alignment explanation
Indices: 52572689--52572858 Score: 88
Period size: 29 Copynumber: 5.8 Consensus size: 29
52572679 AAAAGTCATA
* *
52572689 AAAT-ATTTAAAATGATAT-AAATTT-AT
1 AAATAATTAAAAATAATATAAAATTTAAT
*
52572715 AAA-AAATAAAAATAACTTATAAATATTATAA-
1 AAATAATTAAAAATAA--TATAAA-ATT-TAAT
* *
52572746 AAATAACTAATAAAT-CTA-ATAAATTATAAT
1 AAATAATTAA-AAATAATATA-AAATT-TAAT
* *
52572776 AAAATTAATTTAAAATAAT-TAAAATTTTAT
1 -AAA-TAATTAAAAATAATATAAAATTTAAT
*
52572806 AAATAATTATAAATAATATAAAATTCTAAT
1 AAATAATTAAAAATAATATAAAATT-TAAT
* * *
52572836 AAATTA-TAAAAATTATAAAAAAT
1 AAATAATTAAAAATAATATAAAAT
52572859 CATTTAAACT
Statistics
Matches: 111, Mismatches: 16, Indels: 31
0.70 0.10 0.20
Matches are distributed among these distances:
26 11 0.10
28 15 0.14
29 34 0.31
30 18 0.16
31 16 0.14
32 13 0.12
33 4 0.04
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (29 bp):
AAATAATTAAAAATAATATAAAATTTAAT
Found at i:52572858 original size:19 final size:19
Alignment explanation
Indices: 52572593--52572858 Score: 80
Period size: 19 Copynumber: 14.2 Consensus size: 19
52572583 AAATTGATAC
52572593 AAATT-TAAAAATTATAAA
1 AAATTATAAAAATTATAAA
* * *
52572611 AACTTATAAATATTGT--A
1 AAATTATAAAAATTATAAA
*
52572628 AAA-TATAAAAA--ATAAC
1 AAATTATAAAAATTATAAA
*
52572644 AAATCATAAAAAATT-T-AA
1 AAATTAT-AAAAATTATAAA
* * *
52572662 AATTTGATGAACATTAT-AA
1 AAATT-ATAAAAATTATAAA
* *
52572681 AAGTCATAAAATATT-T--A
1 AAATTATAAAA-ATTATAAA
* *
52572698 AAATGATATAAATTTATAAA
1 AAATTATA-AAAATTATAAA
*
52572718 AAA-TAAAAATAACTTAT-AA
1 AAATTATAAA-AA-TTATAAA
* * *
52572737 ATATTATAAAAATAACTAAT
1 AAATTATAAAAATTA-TAAA
*
52572757 AAATCTA-ATAAATTATAATA
1 AAAT-TATAAAAATTATAA-A
* *
52572777 AAATTAATTTAAAATAATTAAA
1 AAATT-A-TAAAAATTA-TAAA
**
52572799 ATTTTATAAATAATTATAAA
1 AAATTATAAA-AATTATAAA
* * *
52572819 TAA-TAT-AAAATTCTAAT
1 AAATTATAAAAATTATAAA
52572836 AAATTATAAAAATTATAAA
1 AAATTATAAAAATTATAAA
52572855 AAAT
1 AAAT
52572859 CATTTAAACT
Statistics
Matches: 174, Mismatches: 46, Indels: 55
0.63 0.17 0.20
Matches are distributed among these distances:
14 1 0.01
16 10 0.06
17 23 0.13
18 36 0.21
19 50 0.29
20 35 0.20
21 7 0.04
22 9 0.05
23 3 0.02
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATTATAAAAATTATAAA
Found at i:52573414 original size:20 final size:19
Alignment explanation
Indices: 52573391--52573478 Score: 54
Period size: 20 Copynumber: 4.4 Consensus size: 19
52573381 TAGTTTAATT
52573391 TTTTAATGATTTTTTTATAA
1 TTTTAAT-ATTTTTTTATAA
* *
52573411 TTTT-ATATGTTTATATCAA
1 TTTTAATATTTTTTTAT-AA
* **
52573430 TTTTAATCTTTTTGAAT-A
1 TTTTAATATTTTTTTATAA
*
52573448 TGTTTTATGATTTTTTTATAA
1 T-TTTAAT-ATTTTTTTATAA
52573469 GTTTTTAATA
1 --TTTTAATA
52573479 ATTTATACAT
Statistics
Matches: 50, Mismatches: 11, Indels: 13
0.68 0.15 0.18
Matches are distributed among these distances:
18 10 0.20
19 13 0.26
20 19 0.38
21 2 0.04
22 5 0.10
23 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.62
Consensus pattern (19 bp):
TTTTAATATTTTTTTATAA
Found at i:52574674 original size:19 final size:19
Alignment explanation
Indices: 52574650--52574724 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
52574640 AATCTTCAAA
52574650 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
52574669 GATATGCGATCTTAGATAT
1 GATATGCAATCTTAGATAT
52574688 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
52574709 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
52574725 AGATATGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
21 18 0.35
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52574696 original size:21 final size:21
Alignment explanation
Indices: 52574651--52574713 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
52574641 ATCTTCAAAG
52574651 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
*
52574670 ATATGCGATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
52574691 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
52574712 AT
1 AT
52574714 GTAATCTTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 18 0.45
21 22 0.55
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:52574743 original size:23 final size:22
Alignment explanation
Indices: 52574663--52574747 Score: 72
Period size: 19 Copynumber: 4.0 Consensus size: 22
52574653 ATGCAATCTT
**
52574663 AGATATGATATGCGATCTTAG-
1 AGATATGATATGTAATCTTAGA
* *
52574684 ATATGAT-ATATGCAATCTT---
1 AGAT-ATGATATGTAATCTTAGA
52574703 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
52574725 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
52574748 GGTTTAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
21 14 0.26
22 10 0.19
23 13 0.25
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:52578966 original size:14 final size:14
Alignment explanation
Indices: 52578938--52578993 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
52578928 CCGGGGAGAA
*
52578938 AAGAAGGAAAGAAAG
1 AAGAA-GAAAAAAAG
*
52578953 GAGAAGAAAAAAAG
1 AAGAAGAAAAAAAG
*
52578967 AAGAAG-AAAGAAG
1 AAGAAGAAAAAAAG
52578980 AAAGAA-AAAAAAAG
1 -AAGAAGAAAAAAAG
52578994 GTATGTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
13 6 0.18
14 24 0.71
15 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AAGAAGAAAAAAAG
Found at i:52578973 original size:24 final size:27
Alignment explanation
Indices: 52578936--52578994 Score: 81
Period size: 25 Copynumber: 2.3 Consensus size: 27
52578926 CACCGGGGAG
*
52578936 AAAAGAAGGAAAGAAAGGAG-AAGAAA
1 AAAAGAAGGAAAGAAAGAAGAAAGAAA
52578962 AAAAGAA-G-AAGAAAGAAGAAAGAAA
1 AAAAGAAGGAAAGAAAGAAGAAAGAAA
52578987 AAAA-AAGG
1 AAAAGAAGG
52578995 TATGTATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 11 0.37
25 12 0.40
26 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (27 bp):
AAAAGAAGGAAAGAAAGAAGAAAGAAA
Found at i:52579341 original size:72 final size:72
Alignment explanation
Indices: 52579208--52579341 Score: 157
Period size: 73 Copynumber: 1.9 Consensus size: 72
52579198 GTGTATAGTA
* *** *
52579208 TTTTGTGAATTTTTATTAATGTAAAACTATTTTGTTAATTATTTTGTTAGTAATTTATGTTAATG
1 TTTTGTGAATTTTTAGTAATGTAAAACTATTTTAAAAAATATTTTGTTAGTAATTTATGTTAATG
52579273 TTTTGTG
66 TTTTGTG
* *
52579280 TTTTGTGATTTTTTTAGTAATGTAAAA-TATTTTAAAAAAATATTTT-TATAGTTATTT-TGTTA
1 TTTTGTGA-ATTTTTAGTAATGTAAAACTATTTT-AAAAAATATTTTGT-TAGTAATTTATGTTA
52579342 GTAATTTATG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
72 20 0.38
73 32 0.62
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.57
Consensus pattern (72 bp):
TTTTGTGAATTTTTAGTAATGTAAAACTATTTTAAAAAATATTTTGTTAGTAATTTATGTTAATG
TTTTGTG
Found at i:52579464 original size:98 final size:100
Alignment explanation
Indices: 52579277--52579619 Score: 435
Period size: 104 Copynumber: 3.4 Consensus size: 100
52579267 TTAATGTTTT
*
52579277 GTGTTTTGTGATTTTTTTAGTAATGTAAAATATTTTAAAAAAATATTTTTATAGTTATTTTGTTA
1 GTGTTTTGTGA-TTTTTTAGTAATGT-AAATTTTTTAAAAAAA-A-TTTTATAGTTATTTTGTTA
52579342 GTAATTTATGATTAGTTTATAAATTGTTAGTG-T-TTT-
62 GTAATTTATGATTAGTTTATAAATTGTTAGTGTTATTTA
* ** *
52579378 GTGTTTTGTGATTTATTAGTAATGTAAATTCTTTTTTAAAAAATGTTATAGTTATTTTGTTAGTA
1 GTGTTTTGTGATTTTTTAGTAATGTAAATT-TTTTAAAAAAAATTTTATAGTTATTTTGTTAGTA
*
52579443 ATTTATGATTA-TTTTTGAAATTGTTAGTGTTTAGTTTA
65 ATTTATGATTAGTTTAT-AAATTGTTAGTG-TTA-TTTA
* *
52579481 GGGTTTTGTGATTTTTTAGTAATGT-AATTTTTAAAAAAATAATTTTATAGTTATTTTGTTAGTA
1 GTGTTTTGTGATTTTTTAGTAATGTAAATTTTTTAAAAAA-AATTTTATAGTTATTTTGTTAGTA
*
52579545 AATTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTA
65 ATTTATGATTA-GTT-TATAAATTGTTAGTG-TTA-TTTA
* *
52579585 GTGTTTTGTGGTTTTTTATTAATGTAAATTTTTTA
1 GTGTTTTGTGATTTTTTAGTAATGTAAATTTTTTA
52579620 TAATGTAATT
Statistics
Matches: 212, Mismatches: 18, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
97 4 0.02
98 44 0.21
99 5 0.02
100 23 0.11
101 18 0.08
102 40 0.19
103 23 0.11
104 45 0.21
105 10 0.05
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.55
Consensus pattern (100 bp):
GTGTTTTGTGATTTTTTAGTAATGTAAATTTTTTAAAAAAAATTTTATAGTTATTTTGTTAGTAA
TTTATGATTAGTTTATAAATTGTTAGTGTTATTTA
Found at i:52579616 original size:15 final size:15
Alignment explanation
Indices: 52579598--52579635 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
52579588 TTTTGTGGTT
52579598 TTTTAT-TAATGTAAA
1 TTTTATATAATGT-AA
*
52579613 TTTTTTATAATGTAA
1 TTTTATATAATGTAA
52579628 TTTTATAT
1 TTTTATAT
52579636 GATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (15 bp):
TTTTATATAATGTAA
Found at i:52579623 original size:16 final size:16
Alignment explanation
Indices: 52579596--52579631 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
52579586 TGTTTTGTGG
52579596 TTTTTTATTAATGTAAA
1 TTTTTTATTAATGT-AA
52579613 TTTTTTA-TAATGTAA
1 TTTTTTATTAATGTAA
52579628 TTTT
1 TTTT
52579632 ATATGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 6 0.32
17 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TTTTTTATTAATGTAA
Found at i:52579641 original size:104 final size:103
Alignment explanation
Indices: 52579272--52579617 Score: 465
Period size: 98 Copynumber: 3.4 Consensus size: 103
52579262 TTATGTTAAT
* *
52579272 GTTTTGTGTTTTGTGATTTTTTTAGTAATGTAAAATATTTTAAAAAAATATTTTTATAGTTATTT
1 GTTTAGTGTTTTGTGA-TTTTTTAGTAATGT-AAAT-TTTTAAAAAAATAATTTTATAGTTATTT
52579337 TGTTAGTAATTTATGATTAGTTTATAAATTGTTAGTG--T-
63 TGTTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTA
* *** *
52579375 -TTT-GTGTTTTGTGATTTATTAGTAATGTAAATTCTTTTTTAAAA-AATGTTATAGTTATTTTG
1 GTTTAGTGTTTTGTGATTTTTTAGTAATGTAAATT-TTTAAAAAAATAATTTTATAGTTATTTTG
*
52579437 TTAGTAATTTATGATTA-TTTTTGAAATTGTTAGTGTTTA
65 TTAGTAATTTATGATTAGTTTAT-AAATTGTTAGTGTTTA
*
52579476 GTTTAGGGTTTTGTGATTTTTTAGTAATGT-AATTTTTAAAAAAATAATTTTATAGTTATTTTGT
1 GTTTAGTGTTTTGTGATTTTTTAGTAATGTAAATTTTTAAAAAAATAATTTTATAGTTATTTTGT
*
52579540 TAGTAAATTATGATTAGGTTATATAAATTGTTAGTGTTTA
66 TAGTAATTTATGATTA-GTT-TATAAATTGTTAGTGTTTA
* *
52579580 GTTTAGTGTTTTGTGGTTTTTTATTAATGTAAATTTTT
1 GTTTAGTGTTTTGTGATTTTTTAGTAATGTAAATTTTT
52579618 TATAATGTAA
Statistics
Matches: 213, Mismatches: 18, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
97 4 0.02
98 46 0.22
99 11 0.05
100 14 0.07
101 18 0.08
102 43 0.20
103 23 0.11
104 45 0.21
105 9 0.04
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (103 bp):
GTTTAGTGTTTTGTGATTTTTTAGTAATGTAAATTTTTAAAAAAATAATTTTATAGTTATTTTGT
TAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTA
Found at i:52584050 original size:43 final size:40
Alignment explanation
Indices: 52583989--52584126 Score: 130
Period size: 43 Copynumber: 3.5 Consensus size: 40
52583979 AGTGATTCGA
52583989 GGAATCAACACTTAGCAACCCTTTTCACATTCAACGATACGGT
1 GGAATCAACACTTAGCAACCC-TTTCACATT-AA-GATACGGT
52584032 GGAATCAACACTTAGCAACCAC---CA-A-TAA-AT-CGG-
1 GGAATCAACACTTAGCAACC-CTTTCACATTAAGATACGGT
* *
52584065 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACAGT
1 GGAATCAACACTTAGCAA-CCCTTTCACA-TTAAGATACGGT
* *
52584107 GGGATCAGCACTTAGCAACC
1 GGAATCAACACTTAGCAACC
52584127 ACCAATGAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 24
0.75 0.03 0.22
Matches are distributed among these distances:
33 18 0.22
34 5 0.06
35 2 0.02
36 2 0.02
37 3 0.04
38 1 0.01
39 4 0.05
40 4 0.05
41 4 0.05
42 17 0.21
43 20 0.25
44 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.22
Consensus pattern (40 bp):
GGAATCAACACTTAGCAACCCTTTCACATTAAGATACGGT
Found at i:52584077 original size:33 final size:33
Alignment explanation
Indices: 52584032--52584261 Score: 186
Period size: 33 Copynumber: 6.6 Consensus size: 33
52584022 ACGATACGGT
*
52584032 GGAATCAACACTTAGCAACCACCAATAAATCGG
1 GGAATCAGCACTTAGCAACCACCAATAAATCGG
*
52584065 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACAGTG
1 GGAATCAGCACTTAGCAACCAC---CA-A--TAA-AT-C-G-G
*
52584108 GG-ATCAGCACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATAAATCGG
*
52584140 GGAATCAGCACTTAGCAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATAAATCGG
*
52584167 GGAATCAGCACTTAGCAACCCCCTTCACATTTAGAATACGG
1 GGAATCAGCACTTAGCAA-CCAC--CA-A--TA-AAT-CGG
*
52584208 TGGAATCAGCACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATAAATCGG
52584242 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
52584262 CCCTTCATAT
Statistics
Matches: 163, Mismatches: 8, Indels: 52
0.73 0.04 0.23
Matches are distributed among these distances:
27 21 0.13
28 2 0.01
29 1 0.01
30 1 0.01
31 1 0.01
32 5 0.03
33 58 0.36
34 4 0.02
35 5 0.03
36 6 0.04
37 1 0.01
38 2 0.01
39 7 0.04
40 3 0.02
41 6 0.04
42 37 0.23
43 3 0.02
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATAAATCGG
Found at i:52584078 original size:76 final size:75
Alignment explanation
Indices: 52583952--52584163 Score: 316
Period size: 76 Copynumber: 2.8 Consensus size: 75
52583942 TATCCGTTAT
* * * * * *
52583952 CGGTGGATTCAGCACTTAGCAACCACCAGTGATTCGAGGAATCAACACTTAGCAACCCTTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
52584017 ATTCAACGATA
66 ATTCAA-GATA
* *
52584028 CGGTGGAATCAACACTTAGCAACCACCAATAAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
52584093 ATTTAAGATA
66 ATTCAAGATA
* *
52584103 CAGTGGGATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
52584164 GGGGGAATCA
Statistics
Matches: 123, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 61 0.50
76 62 0.50
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTCAAGATA
Found at i:52584139 original size:75 final size:76
Alignment explanation
Indices: 52583954--52584163 Score: 314
Period size: 75 Copynumber: 2.8 Consensus size: 76
52583944 TCCGTTATCG
* * * * * *
52583954 GTGGATTCAGCACTTAGCAACCACCAGTGATTCGAGGAATCAACACTTAGCAACCCTTTTCACAT
1 GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCACAT
*
52584019 TCAACGATACG
66 TCAACGATACA
* *
52584030 GTGGAATCAACACTTAGCAACCACCAATAAATCGGGGAATCAGCACTTAGCAACCCCTTTCACAT
1 GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCACAT
*
52584095 TTAA-GATACA
66 TCAACGATACA
*
52584105 GTGGGATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
1 GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
52584164 GGGGGAATCA
Statistics
Matches: 121, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
75 61 0.50
76 60 0.50
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (76 bp):
GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCACAT
TCAACGATACA
Found at i:52584183 original size:102 final size:102
Alignment explanation
Indices: 52584063--52584263 Score: 359
Period size: 102 Copynumber: 2.0 Consensus size: 102
52584053 CCAATAAATC
* *
52584063 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTA-AGATACAGTGGGATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAGA-ATACAGTGGAATCAGCACTTAGCAACC
52584127 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
65 ACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
*
52584165 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAGAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAGAATACAGTGGAATCAGCACTTAGCAACCA
52584230 CCAATGAATCGGGGAATCAGCACTTAGCAACCCC
66 CCAATGAATCGGGGAATCAGCACTTAGCAACCCC
52584264 CTTCATATTC
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
102 94 0.99
103 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.19
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAGAATACAGTGGAATCAGCACTTAGCAACCA
CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:52585398 original size:23 final size:23
Alignment explanation
Indices: 52585372--52585429 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
52585362 CCACATGCGA
*
52585372 CTTTTATACCCCTGTTCGTATGG
1 CTTTTATACCCCTGTCCGTATGG
** * *
52585395 CTTTTATGTCTCTGTCCGTGTGG
1 CTTTTATACCCCTGTCCGTATGG
52585418 CTTTTATACCCC
1 CTTTTATACCCC
52585430 AATAGTAAGT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.10, C:0.28, G:0.17, T:0.45
Consensus pattern (23 bp):
CTTTTATACCCCTGTCCGTATGG
Found at i:52586805 original size:77 final size:75
Alignment explanation
Indices: 52586655--52586800 Score: 206
Period size: 74 Copynumber: 1.9 Consensus size: 75
52586645 CATATTTGTA
* * * *
52586655 TAATGACTTTTTTTCCATTTAAGTATTAATTTTATGGGTTTTTTTTGCAATTTAAATAGTCAACT
1 TAATGACTTTTTTGCCATTTAAGTATTAATTTTA-GGGTATTTTTTGCAATTTAAATAATAAACT
52586720 TTGTATTTATG
65 TTGTATTTATG
* *
52586731 TAATGACTTTTTTGCTATTTCAATTATTAATTTTA-GG-ATTTTTTGCAATTTAAATAATAAACT
1 TAATGACTTTTTTGCCATTT-AAGTATTAATTTTAGGGTATTTTTTGCAATTTAAATAATAAACT
52586794 TTGTATT
65 TTGTATT
52586801 ATTTACATAA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
74 30 0.48
75 2 0.03
76 18 0.29
77 13 0.21
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (75 bp):
TAATGACTTTTTTGCCATTTAAGTATTAATTTTAGGGTATTTTTTGCAATTTAAATAATAAACTT
TGTATTTATG
Found at i:52592092 original size:71 final size:71
Alignment explanation
Indices: 52592008--52592142 Score: 252
Period size: 71 Copynumber: 1.9 Consensus size: 71
52591998 TATCCAATCG
52592008 AATTTCATATACATGACCATTACACAATACACATACATACAATTCAATTCAAACATATAAATATG
1 AATTTCATATACATGACCATTACACAATACACATACATACAATTCAATTCAAACATATAAATATG
52592073 TGATCA
66 TGATCA
* *
52592079 AATTTCATATACATGACCATTGCACAATACACATACATATAATTCAATTCAAACATATAAATAT
1 AATTTCATATACATGACCATTACACAATACACATACATACAATTCAATTCAAACATATAAATAT
52592143 ACAATTCAGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.30
Consensus pattern (71 bp):
AATTTCATATACATGACCATTACACAATACACATACATACAATTCAATTCAAACATATAAATATG
TGATCA
Found at i:52592312 original size:21 final size:21
Alignment explanation
Indices: 52592273--52592312 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52592263 TTTAGCTCAA
* *
52592273 TTTAATACAATTTATATTGAT
1 TTTAATACAATTCACATTGAT
*
52592294 TTTAATTCAATTCACATTG
1 TTTAATACAATTCACATTG
52592313 TAATAACCCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTAATACAATTCACATTGAT
Found at i:52592361 original size:12 final size:12
Alignment explanation
Indices: 52592344--52592376 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
52592334 CCCAAATCAG
52592344 AAATAAATAA-AT
1 AAATAAA-AATAT
52592356 AAATAAAAATAT
1 AAATAAAAATAT
52592368 AAATAAAAA
1 AAATAAAAA
52592377 CAAAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.10
12 18 0.90
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAATAAAAATAT
Found at i:52592618 original size:26 final size:25
Alignment explanation
Indices: 52592582--52592661 Score: 99
Period size: 25 Copynumber: 3.1 Consensus size: 25
52592572 ATAAAATACA
*
52592582 TCTTTACATTCATTTTTGAGCCAA-TAT
1 TCTTT-CATTC-TTTTTGA-ACAATTAT
*
52592609 TCTTTCATTCTTTTTGAATAATTAT
1 TCTTTCATTCTTTTTGAACAATTAT
*
52592634 TCTTTCATTCTTTTTGAATAATTAT
1 TCTTTCATTCTTTTTGAACAATTAT
52592659 TCT
1 TCT
52592662 GAAAGAATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
24 2 0.04
25 38 0.76
26 5 0.10
27 5 0.10
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (25 bp):
TCTTTCATTCTTTTTGAACAATTAT
Found at i:52592634 original size:25 final size:25
Alignment explanation
Indices: 52592606--52592661 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
52592596 TTTGAGCCAA
52592606 TATTCTTTCATTCTTTTTGAATAAT
1 TATTCTTTCATTCTTTTTGAATAAT
52592631 TATTCTTTCATTCTTTTTGAATAAT
1 TATTCTTTCATTCTTTTTGAATAAT
52592656 TATTCT
1 TATTCT
52592662 GAAAGAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.23, C:0.12, G:0.04, T:0.61
Consensus pattern (25 bp):
TATTCTTTCATTCTTTTTGAATAAT
Found at i:52594372 original size:48 final size:45
Alignment explanation
Indices: 52594292--52594388 Score: 140
Period size: 48 Copynumber: 2.1 Consensus size: 45
52594282 GATCAAGGTG
*
52594292 AAAACCCGCAAAGGGCGCCTTGATTCCTAAAAAAAAAAGACCAAAGTA
1 AAAACCCGCAAAGGGCGCCTTGAGTCC-AAAAAAAAAA-ACCAAAG-A
* *
52594340 AAAACCCGCAAAGGGCGCTTTGAGTCCAAAAAAATAAACCAAAGA
1 AAAACCCGCAAAGGGCGCCTTGAGTCCAAAAAAAAAAACCAAAGA
52594385 AAAA
1 AAAA
52594389 GAAAATAGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 5 0.11
46 7 0.15
47 9 0.20
48 25 0.54
ACGTcount: A:0.51, C:0.22, G:0.16, T:0.11
Consensus pattern (45 bp):
AAAACCCGCAAAGGGCGCCTTGAGTCCAAAAAAAAAAACCAAAGA
Found at i:52595767 original size:45 final size:45
Alignment explanation
Indices: 52595718--52596219 Score: 428
Period size: 45 Copynumber: 11.3 Consensus size: 45
52595708 GTTGCAGTGG
* * * *
52595718 AGCAGGTTAAAGATAGCATATCTTGCTTTCCTGTACTGACGGCGA
1 AGCAGATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGA
* * * * * *
52595763 AGCAGATCGAAGACACCA-ACCTTGCCTTCCTGTACTGACAGCGG
1 AGCAGATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGA
*
52595807 AGCAGATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGA
1 AGCAGATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGA
* ** * * * * *
52595852 AACAGATCAAAGACA-CTAG-CCTTGCCTTTCTGTACTGACAGCGG
1 AGCAGATTGAAGATAGC-AGATCTTGCCTTCCTGTACTGACGGCGA
* * *
52595896 AGCAGACTGAAGATAGGAGATCTTGCCTTCCTGTACTGATGGCGA
1 AGCAGATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGA
* * * * ** *
52595941 AGCAGATCGAAGATACCAG-CCTTGCCTTCCTGTACTAATAGCGG
1 AGCAGATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGA
* * *
52595985 AGCAGACTGAAGATAGCAGATGC-TGCCTTCCTGTACTAACGGTGA
1 AGCAGATTGAAGATAGCAGAT-CTTGCCTTCCTGTACTGACGGCGA
* * * * * * *
52596030 AGCAGATCGAAAACACCAG-CCTTGCCTTCCTGTTCTGACAGC-A
1 AGCAGATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGA
* * *
52596073 GAGCAAACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGACGA
1 -AGCAGATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGA
* * * * * * * *
52596119 AGCAGATCGAAAACACCAG-CCTTG-CTTCCTGTACTAACAGCGG
1 AGCAGATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGA
* * *
52596162 AGCAGACTGAATATAGCAAATCTTGCCTTCCTGTACTGACGGCGA
1 AGCAGATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGA
*
52596207 AGCAGATCGAAGA
1 AGCAGATTGAAGA
52596220 AACCAGCTTT
Statistics
Matches: 349, Mismatches: 96, Indels: 24
0.74 0.20 0.05
Matches are distributed among these distances:
43 30 0.09
44 144 0.41
45 173 0.50
46 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.23
Consensus pattern (45 bp):
AGCAGATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGA
Found at i:52595830 original size:89 final size:89
Alignment explanation
Indices: 52595638--52596233 Score: 756
Period size: 89 Copynumber: 6.7 Consensus size: 89
52595628 AACAGATCAG
* * * ** * *
52595638 TGAAGATAGTAGATCTTGCCTTCTTGTA-TCGACAGCGAAGCAGATTAAAAACA-AAGCCTTGCC
1 TGAAGATAGCAGATCTTGCCTTCCTGTACT-GACGGCGAAGCAGATCGAAGACACCAGCCTTGCC
* * **
52595701 TCCCTCGGT--TG-CAGTGGAGCAGGT
65 TTCCT--GTACTGACAGCGGAGCAGAC
* * * *
52595725 TAAAGATAGCATATCTTGCTTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAACCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
52595790 TCCTGTACTGACAGCGGAGCAGAT
66 TCCTGTACTGACAGCGGAGCAGAC
* * * *
52595814 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAACAGATCAAAGACACTAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
52595879 TTCTGTACTGACAGCGGAGCAGAC
66 TCCTGTACTGACAGCGGAGCAGAC
* * *
52595903 TGAAGATAGGAGATCTTGCCTTCCTGTACTGATGGCGAAGCAGATCGAAGATACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
52595968 TCCTGTACTAATAGCGGAGCAGAC
66 TCCTGTACTGACAGCGGAGCAGAC
* * *
52595992 TGAAGATAGCAGATGC-TGCCTTCCTGTACTAACGGTGAAGCAGATCGAAAACACCAGCCTTGCC
1 TGAAGATAGCAGAT-CTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCC
* * *
52596056 TTCCTGTTCTGACAGCAGAGCAAAC
65 TTCCTGTACTGACAGCGGAGCAGAC
* *
52596081 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGACGAAGCAGATCGAAAACACCAGCCTTG-CT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
52596145 TCCTGTACTAACAGCGGAGCAGAC
66 TCCTGTACTGACAGCGGAGCAGAC
* * * *
52596169 TGAATATAGCAAATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGAAACCAGCTTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCT
52596234 CTTGGGTTGT
Statistics
Matches: 443, Mismatches: 58, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
86 2 0.00
87 42 0.09
88 94 0.21
89 304 0.69
90 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.23
Consensus pattern (89 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCT
TCCTGTACTGACAGCGGAGCAGAC
Found at i:52596533 original size:132 final size:132
Alignment explanation
Indices: 52596296--52597360 Score: 1289
Period size: 132 Copynumber: 8.1 Consensus size: 132
52596286 GACAGCGAAA
* *
52596296 CAGATCAAAGATGGCAGATCTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGACAGATCTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* * *
52596361 TATCTCTCTAGGTAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
66 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
52596426 AG
131 AG
* * *
52596428 CAGATCGAAGATGACGGATCTTACCTCCTTGAGGTTATAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGACAGATCTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* *
52596493 TATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGA
66 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
52596558 AG
131 AG
* * * *
52596560 TAGATCGAAGATGGCAGATTTTACCTCTCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGACAGATCTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
*
52596625 TATCT-CCTCGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTTCCTAAGCAGTAGTG
66 TATCTCCCT-GGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTG
52596689 GAG
130 GAG
* * * * * * *
52596692 CAGACCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTATATTGAAGTCAGTAATTC
1 CAGATCGAAGATGACAGATCTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* *
52596757 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTATAGATCTGATCTCCCTAAGCAGTAGTGG
66 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
52596822 AG
131 AG
* * * *
52596824 CAGATCGAAGATGGCAGATTTTACCTCCTTGAGGTTACAGTGGAGTACATTGAAGCCAGTAGTTC
1 CAGATCGAAGATGACAGATCTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* * *
52596889 TATCTCTCTGAGCAGTAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
66 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
52596954 AG
131 AG
* * * * *
52596956 CAGATCGAAGAT-AGCAGATTTTACCTCCCTGAGGTCATAGTGGAGTACATTGAAGCTAATAATT
1 CAGATCGAAGATGA-CAGATCTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATT
* * *
52597020 CTATCTCCCTGGGCAACAGTGGAATAGATTGGAA-ATTACAGATCTTATCTCCCTAAGCAGTTGC
65 CTATCTCCCTGGGCAGCAGTGGAATAGATT-GAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
52597084 GGAG
129 GGAG
* * * * * * * *
52597088 CAGATCGAAGA-CAGC-GAATCTTATCTTCCC-CAGG--AGTAG-GGAAGCAGATTTAAGCCA-C
1 CAGATCGAAGATGA-CAG-ATCTTA-CCTCCCTGAGGTTA-CAGTGG-AGTACATTGAAGCCAGT
* * * * * * * * *
52597146 AAGTCCTATCTCCTTGGTCATCAATAGAATAGATTGAAAATTACGGATCTTATCTCCCCAAGCAG
61 AA-TTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAG
52597211 TAGTGGAG
125 TAGTGGAG
* * * * * *
52597219 CAGATCGAAGACGAC-GAATCTTATCCTCCCT-AGG--AGTAG-GGAAGCATATTTAAGCCA-CA
1 CAGATCGAAGATGACAG-ATCTTA-CCTCCCTGAGGTTA-CAGTGG-AGTACATTGAAGCCAGTA
* * *
52597278 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGATTGAAAATTACAGATCTTATCTCCCTAAGCAGT
62 A-TTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
*
52597343 AGTAGAG
126 AGTGGAG
*
52597350 CAAATCGAAGA
1 CAGATCGAAGA
52597361 CGATGAATCT
Statistics
Matches: 836, Mismatches: 84, Indels: 27
0.88 0.09 0.03
Matches are distributed among these distances:
130 8 0.01
131 202 0.24
132 615 0.74
133 11 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (132 bp):
CAGATCGAAGATGACAGATCTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
AG
Found at i:52597609 original size:50 final size:49
Alignment explanation
Indices: 52597534--52597846 Score: 275
Period size: 50 Copynumber: 6.3 Consensus size: 49
52597524 GGAGTAGGTT
* * * *
52597534 GAATCTTACTTCCCAGGCGGTGCAGTAGAATAGATTGAAGCCACAACGGC
1 GAATCTTACTTCCCAGACAGTGCAGTA-AAAAGATTAAAGCCACAACGGC
* * * *
52597584 GAATCTTACTTCCCTGACATTGCAGTTAAAAATATTAAAGCCACAACAGC
1 GAATCTTACTTCCCAGACAGTGCAG-TAAAAAGATTAAAGCCACAACGGC
* * * ** *
52597634 GAATCTTACTTCCCAGGCGGTGCAGTGGAGCAGATTAAAGCCACAATGGC
1 GAATCTTACTTCCCAGACAGTGCAGT-AAAAAGATTAAAGCCACAACGGC
* * * * * * *
52597684 GAATCTTGCTTCCCCGACATTGAAATTAAAAAGATTAAAGCCACAAAGGT
1 GAATCTTACTTCCCAGACAGTG-CAGTAAAAAGATTAAAGCCACAACGGC
* * * * *
52597734 GAATCTTACTTCCCAGGCAGTGCAGTGGAACATATTGAAGCCACAACGGC
1 GAATCTTACTTCCCAGACAGTGCAGT-AAAAAGATTAAAGCCACAACGGC
* * * * * * *
52597784 GAATCTTACTTCTCTGACATTACAATTAAATAGATTGAAGCCACAACGGC
1 GAATCTTACTTCCCAGACAGTGC-AGTAAAAAGATTAAAGCCACAACGGC
52597834 GAATCTTACTTCC
1 GAATCTTACTTCC
52597847 TTAGTGGTGC
Statistics
Matches: 206, Mismatches: 52, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
49 3 0.01
50 197 0.96
51 6 0.03
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (49 bp):
GAATCTTACTTCCCAGACAGTGCAGTAAAAAGATTAAAGCCACAACGGC
Found at i:52597713 original size:100 final size:100
Alignment explanation
Indices: 52597534--52597873 Score: 452
Period size: 100 Copynumber: 3.4 Consensus size: 100
52597524 GGAGTAGGTT
* *
52597534 GAATCTTACTTCCCAGGCGGTGCAGTAGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCT
1 GAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCT
* * *
52597599 GACATTGCAGTTAAAAATATTAAAGCCACAACAGC
66 GACATTGAAATTAAAAAGATTAAAGCCACAACAGC
* * * * *
52597634 GAATCTTACTTCCCAGGCGGTGCAGTGGAGCAGATTAAAGCCACAATGGCGAATCTTGCTTCCCC
1 GAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCT
*
52597699 GACATTGAAATTAAAAAGATTAAAGCCACAA-AGGT
66 GACATTGAAATTAAAAAGATTAAAGCCACAACA-GC
* * *
52597734 GAATCTTACTTCCCAGGCAGTGCAGTGGAACATATTGAAGCCACAACGGCGAATCTTACTTCTCT
1 GAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCT
* * *
52597799 GACATT-ACAATTAAATAGATTGAAGCCACAACGGC
66 GACATTGA-AATTAAAAAGATTAAAGCCACAACAGC
* * *
52597834 GAATCTTACTTCCTTA-GTGGTGCAGTGAAACAGATTGAAG
1 GAATCTTACTTCC-CAGGCGGTGCAGTGGAACAGATTGAAG
52597874 TTATGACGAC
Statistics
Matches: 208, Mismatches: 28, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
99 2 0.01
100 205 0.99
101 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (100 bp):
GAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCT
GACATTGAAATTAAAAAGATTAAAGCCACAACAGC
Found at i:52597819 original size:150 final size:150
Alignment explanation
Indices: 52597565--52597846 Score: 339
Period size: 150 Copynumber: 1.9 Consensus size: 150
52597555 GCAGTAGAAT
* * * * *
52597565 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGACATTGCAGTTAAAAATATTAAAGCCACAA
1 AGATTAAAGCCACAAAGGCGAATCTTACTTCCCAGACAGTGCAGTGAAAAATATTAAAGCCACAA
* * * * * * * *
52597630 CAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAGCAGATTAAAGCCACAATGGCGAATCTTGCTT
66 CAGCGAATCTTACTTCCCAGACAGTACAATGAAACAGATTAAAGCCACAACGGCGAATCTTACTT
52597695 CCCCGACATTGAAATTAAAA
131 CCCCGACATTGAAATTAAAA
* * * * *
52597715 AGATTAAAGCCACAAAGGTGAATCTTACTTCCCAGGCAGTGCAGTGGAACATATTGAAGCCACAA
1 AGATTAAAGCCACAAAGGCGAATCTTACTTCCCAGACAGTGCAGTGAAAAATATTAAAGCCACAA
* * * * * * *
52597780 CGGCGAATCTTACTTCTCTGACATTACAATTAAATAGATTGAAGCCACAACGGCGAATCTTACTT
66 CAGCGAATCTTACTTCCCAGACAGTACAATGAAACAGATTAAAGCCACAACGGCGAATCTTACTT
52597845 CC
131 CC
52597847 TTAGTGGTGC
Statistics
Matches: 107, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
150 107 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (150 bp):
AGATTAAAGCCACAAAGGCGAATCTTACTTCCCAGACAGTGCAGTGAAAAATATTAAAGCCACAA
CAGCGAATCTTACTTCCCAGACAGTACAATGAAACAGATTAAAGCCACAACGGCGAATCTTACTT
CCCCGACATTGAAATTAAAA
Found at i:52597889 original size:200 final size:200
Alignment explanation
Indices: 52597533--52597905 Score: 505
Period size: 200 Copynumber: 1.9 Consensus size: 200
52597523 TGGAGTAGGT
* *
52597533 TGAATCTTACTTCCCAGGCGGTGCAGTAGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCC
1 TGAATCTTACTTCCCAGGCAGTGCAGTAGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCC
* * * *
52597598 TGACATTGCAGTTAAAAATATTAAAGCCACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGGA
66 TGACATTACAATTAAAAAGATTAAAGCCACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGAA
* * * *
52597663 GCAGATTAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGAAATTAAAAAGATTAAAGCCAC
131 ACAGATTAAAGCCACAACGACGAATCTCGCTTCCCCGACATTGAAATTAAAAAGATTAAAGCCAC
52597728 AAAGG
196 AAAGG
* * *
52597733 TGAATCTTACTTCCCAGGCAGTGCAGTGGAACATATTGAAGCCACAACGGCGAATCTTACTTCTC
1 TGAATCTTACTTCCCAGGCAGTGCAGTAGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCC
* * * * *
52597798 TGACATTACAATTAAATAGATTGAAGCCACAACGGCGAATCTTACTTCCTTA-GTGGTGCAGTGA
66 TGACATTACAATTAAAAAGATTAAAGCCACAACAGCGAATCTTACTTCC-CAGGCGGTGCAGTGA
* ** ** * *
52597862 AACAGATTGAAGTTATGACGACGAATCTCGTTTTCCCGACATTG
130 AACAGATTAAAGCCACAACGACGAATCTCGCTTCCCCGACATTG
52597906 TAGATTGAAG
Statistics
Matches: 147, Mismatches: 25, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
200 146 0.99
201 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (200 bp):
TGAATCTTACTTCCCAGGCAGTGCAGTAGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCC
TGACATTACAATTAAAAAGATTAAAGCCACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGAA
ACAGATTAAAGCCACAACGACGAATCTCGCTTCCCCGACATTGAAATTAAAAAGATTAAAGCCAC
AAAGG
Found at i:52598415 original size:18 final size:20
Alignment explanation
Indices: 52598384--52598421 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
52598374 CAAATCAGAA
52598384 ATAAATAAATAAACAAAAAT
1 ATAAATAAATAAACAAAAAT
52598404 ATAAAT-AA-AAACAAAAAT
1 ATAAATAAATAAACAAAAAT
52598422 TATTAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
ATAAATAAATAAACAAAAAT
Found at i:52599577 original size:15 final size:15
Alignment explanation
Indices: 52599557--52599587 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52599547 ATTAGCTTAG
*
52599557 TATTTTTAATATGTT
1 TATTTTTAATAAGTT
52599572 TATTTTTAATAAGTT
1 TATTTTTAATAAGTT
52599587 T
1 T
52599588 TAAGTATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TATTTTTAATAAGTT
Found at i:52602259 original size:20 final size:19
Alignment explanation
Indices: 52602207--52602270 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
52602197 AAAAATACAA
*
52602207 ATTTTAGAATTTTTATAAA-T
1 ATTTTA-AA-TTTTAAAAATT
52602227 ATTTTAAATTTTAAAAATT
1 ATTTTAAATTTTAAAAATT
*
52602246 ATTTTCATATTTTAAAAATT
1 ATTTT-AAATTTTAAAAATT
52602266 ATTTT
1 ATTTT
52602271 GATTATTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.20
19 8 0.20
20 24 0.60
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTAAATTTTAAAAATT
Found at i:52603236 original size:6 final size:6
Alignment explanation
Indices: 52603225--52603253 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
52603215 TAATTTTATA
52603225 ATTAGT ATTAGT ATTAGT ATTAGT ATTAG
1 ATTAGT ATTAGT ATTAGT ATTAGT ATTAG
52603254 AGCTTTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (6 bp):
ATTAGT
Found at i:52615296 original size:21 final size:21
Alignment explanation
Indices: 52615272--52615313 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52615262 TTTATAGATG
*
52615272 CCTCTGTTCTCTATTGAAAAT
1 CCTCTATTCTCTATTGAAAAT
* *
52615293 CCTCTATTTTCTTTTGAAAAT
1 CCTCTATTCTCTATTGAAAAT
52615314 AAATAGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (21 bp):
CCTCTATTCTCTATTGAAAAT
Found at i:52623752 original size:21 final size:21
Alignment explanation
Indices: 52623714--52623753 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52623704 AGTCAGTTAA
* * *
52623714 AGTAGTCAGTTTGTTGTTAGT
1 AGTAGGCAGTTAGCTGTTAGT
52623735 AGTAGGCAGTTAGCTGTTA
1 AGTAGGCAGTTAGCTGTTA
52623754 ACGTTAGTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (21 bp):
AGTAGGCAGTTAGCTGTTAGT
Found at i:52624071 original size:15 final size:15
Alignment explanation
Indices: 52624051--52624081 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
52624041 GATAACATTT
52624051 GGCTAGATGAGTTTA
1 GGCTAGATGAGTTTA
52624066 GGCTAGATGAGTTTA
1 GGCTAGATGAGTTTA
52624081 G
1 G
52624082 TTACTCATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.35, T:0.32
Consensus pattern (15 bp):
GGCTAGATGAGTTTA
Found at i:52625569 original size:8 final size:8
Alignment explanation
Indices: 52625556--52625593 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
52625546 AAACTTCCTA
52625556 GGTTTAAT
1 GGTTTAAT
52625564 GGTTTAAT
1 GGTTTAAT
52625572 GGTTTAAT
1 GGTTTAAT
*
52625580 AG-TTAAT
1 GGTTTAAT
52625587 GTGTTTA
1 G-GTTTA
52625594 TCATTTCAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 5 0.19
8 18 0.69
9 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (8 bp):
GGTTTAAT
Found at i:52631363 original size:19 final size:19
Alignment explanation
Indices: 52631330--52631368 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
52631320 AAAGTTACTC
*
52631330 AAATTATTATCTTA-TAAA
1 AAATTATTATATTATTAAA
52631348 AAATTAATTATATTATTAAA
1 AAATT-ATTATATTATTAAA
52631368 A
1 A
52631369 TTTTAACAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTATTATATTATTAAA
Found at i:52639887 original size:18 final size:18
Alignment explanation
Indices: 52639855--52639904 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
52639845 ATGTAAACTT
* *
52639855 TAAAAATTGTA-AAAATA
1 TAAAAATTATATAAAAAA
52639872 TAAAAATTATATAAAAAA
1 TAAAAATTATATAAAAAA
52639890 TAAAGAATATATATA
1 TAAA-AAT-TATATA
52639905 TATATACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 10 0.36
18 9 0.32
19 3 0.11
20 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (18 bp):
TAAAAATTATATAAAAAA
Found at i:52639890 original size:20 final size:20
Alignment explanation
Indices: 52639865--52639904 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
52639855 TAAAAATTGT
52639865 AAAAATATAAAAAT-TATATA
1 AAAAATA-AAAAATATATATA
*
52639885 AAAAATAAAGAATATATATA
1 AAAAATAAAAAATATATATA
52639905 TATATACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAAATAAAAAATATATATA
Found at i:52640179 original size:20 final size:20
Alignment explanation
Indices: 52640154--52640191 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
52640144 AGTGACAAAA
52640154 CAGTCACTCAACTTTCAATT
1 CAGTCACTCAACTTTCAATT
*
52640174 CAGTCACTCAAGTTTCAA
1 CAGTCACTCAACTTTCAA
52640192 AAAATAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.08, T:0.32
Consensus pattern (20 bp):
CAGTCACTCAACTTTCAATT
Found at i:52641214 original size:38 final size:38
Alignment explanation
Indices: 52641169--52641242 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
52641159 ATAACAGAAA
*
52641169 ATGTTAATGAGTGACTGATTTGTAACTTTTTGATAACG
1 ATGTTAATGAGTGACTGATTTGTAACTTTTCGATAACG
* *
52641207 ATGTTAATGGGTGACTGATTTGTCACTTTTCGATAA
1 ATGTTAATGAGTGACTGATTTGTAACTTTTCGATAA
52641243 TATTAGTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (38 bp):
ATGTTAATGAGTGACTGATTTGTAACTTTTCGATAACG
Found at i:52642215 original size:37 final size:37
Alignment explanation
Indices: 52642172--52642282 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
52642162 AAGTAAATGT
* *
52642172 AAGCACATAATTTGACTTTAAGTACTGCTGTAATAGC
1 AAGCACATAATTTGACTTCAAGTACTACTGTAATAGC
*
52642209 AAGCACATAATTTGACTTCAAGTACTATTGTAATAGC
1 AAGCACATAATTTGACTTCAAGTACTACTGTAATAGC
*
52642246 AAGCACATAATTTGACTTCAAGTACTACGGTAATAGC
1 AAGCACATAATTTGACTTCAAGTACTACTGTAATAGC
52642283 CCCATTTTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (37 bp):
AAGCACATAATTTGACTTCAAGTACTACTGTAATAGC
Found at i:52644191 original size:16 final size:16
Alignment explanation
Indices: 52644157--52644199 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
52644147 AATTGAAAGG
*
52644157 AATAT-ATATATGTGTA
1 AATATGATA-ATGTGCA
*
52644173 AATGTGATAATGTGCA
1 AATATGATAATGTGCA
52644189 AATATGATAAT
1 AATATGATAAT
52644200 AGGATATTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.37
Consensus pattern (16 bp):
AATATGATAATGTGCA
Found at i:52645420 original size:17 final size:18
Alignment explanation
Indices: 52645400--52645433 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52645390 TTTTGTGACA
52645400 TCTTATT-TTGGTTTTTC
1 TCTTATTGTTGGTTTTTC
*
52645417 TCTTTTTGTTGGTTTTT
1 TCTTATTGTTGGTTTTT
52645434 TAAACTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.03, C:0.09, G:0.15, T:0.74
Consensus pattern (18 bp):
TCTTATTGTTGGTTTTTC
Found at i:52656790 original size:17 final size:19
Alignment explanation
Indices: 52656754--52656792 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
52656744 GTTTAATATG
52656754 AATAATATATAAAATCTAA
1 AATAATATATAAAATCTAA
*
52656773 AATAA-ATA-AAAATGTAA
1 AATAATATATAAAATCTAA
52656790 AAT
1 AAT
52656793 TTGCTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 3 0.16
19 5 0.26
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (19 bp):
AATAATATATAAAATCTAA
Found at i:52663074 original size:17 final size:18
Alignment explanation
Indices: 52663049--52663082 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52663039 AAACATATTA
*
52663049 AATTAAAATTTAAAATAT
1 AATTAAAATTGAAAATAT
52663067 AATT-AAATTGAAAATA
1 AATTAAAATTGAAAATA
52663083 AACATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AATTAAAATTGAAAATAT
Found at i:52668162 original size:20 final size:17
Alignment explanation
Indices: 52668133--52668172 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
52668123 ATTTATTTTT
52668133 TATAATTTAAAAAATAAAA
1 TATAATTT--AAAATAAAA
52668152 TATATATTTAAAATAAAA
1 TATA-ATTTAAAATAAAA
52668170 TAT
1 TAT
52668173 TTTTTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 12 0.60
19 4 0.20
20 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAATTTAAAATAAAA
Found at i:52669325 original size:17 final size:17
Alignment explanation
Indices: 52669303--52669337 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
52669293 ACCCAGATCA
52669303 ATCAAGAGCAGCCTATG
1 ATCAAGAGCAGCCTATG
52669320 ATCAAGAGCAGCCTATG
1 ATCAAGAGCAGCCTATG
52669337 A
1 A
52669338 CAAAACACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (17 bp):
ATCAAGAGCAGCCTATG
Found at i:52677256 original size:19 final size:19
Alignment explanation
Indices: 52677209--52677258 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
52677199 TTTTAACCAT
** **
52677209 ATTTTAAATAATTTTAATG
1 ATTTTAAATTTTTTTAAAA
*
52677228 ATTTTTAATTTTTTTAAAA
1 ATTTTAAATTTTTTTAAAA
52677247 ATTTTAAATTTT
1 ATTTTAAATTTT
52677259 AAAATATTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTAAATTTTTTTAAAA
Found at i:52682758 original size:16 final size:16
Alignment explanation
Indices: 52682734--52682767 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52682724 GTATATTTGG
52682734 ATGGAATATTTATAAT
1 ATGGAATATTTATAAT
* *
52682750 ATGGTATATTTATCAT
1 ATGGAATATTTATAAT
52682766 AT
1 AT
52682768 TAGTCCATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (16 bp):
ATGGAATATTTATAAT
Found at i:52688560 original size:16 final size:16
Alignment explanation
Indices: 52688539--52688608 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
52688529 TTTGGTTCGC
52688539 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
* *
52688555 TGTAATGAAATATAGG
1 TGTAATGGAATAGAGG
*
52688571 TGTAATGGAACAGAGG
1 TGTAATGGAATAGAGG
*
52688587 TGTAATGGAATAAAGG
1 TGTAATGGAATAGAGG
*
52688603 CGTAAT
1 TGTAAT
52688609 AGTAATTCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.40, C:0.03, G:0.31, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:52697099 original size:79 final size:80
Alignment explanation
Indices: 52697008--52697165 Score: 255
Period size: 81 Copynumber: 2.0 Consensus size: 80
52696998 AAATCATTTC
* *
52697008 ATAGAAATTATATATATTCTGACTTTA-GTTTAATTGATTCAAATAGTAAGTACTAAGAGGTGGT
1 ATAGAAATTATATATATTCTGAATTTACGCTTAATTGATTCAAATAGTAAGTACTAAGAGGTGGT
52697072 ATTAATTAAATTTTG
66 ATTAATTAAATTTTG
* *
52697087 ATAGAAATTATATATATTCTGAATTTAGCGCTTAATTGATTCAAATAGTAAGTATTAAGAGGTTG
1 ATAGAAATTATATATATTCTGAATTTA-CGCTTAATTGATTCAAATAGTAAGTACTAAGAGGTGG
*
52697152 TATTGATTAAATTT
65 TATTAATTAAATTT
52697166 GGGATTCAAC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
79 26 0.36
81 46 0.64
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (80 bp):
ATAGAAATTATATATATTCTGAATTTACGCTTAATTGATTCAAATAGTAAGTACTAAGAGGTGGT
ATTAATTAAATTTTG
Found at i:52697253 original size:24 final size:24
Alignment explanation
Indices: 52697226--52697278 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
52697216 TATTATATTT
52697226 ATAAACTGTTTATTTTTAAAAATA-
1 ATAAACTGTTTA-TTTTAAAAATAG
** *
52697250 ATAATGTGTTTATTTTAAATATAG
1 ATAAACTGTTTATTTTAAAAATAG
52697274 ATAAA
1 ATAAA
52697279 GTATAATTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (24 bp):
ATAAACTGTTTATTTTAAAAATAG
Found at i:52704186 original size:17 final size:17
Alignment explanation
Indices: 52704166--52704231 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 17
52704156 AAAATGAAAT
52704166 AAAAAATAAAAAAAAGA
1 AAAAAATAAAAAAAAGA
* *
52704183 AAAAAAGATGAAAAAAGA
1 AAAAAATA-AAAAAAAGA
*
52704201 AAATTAATGAAAAAAGAA-A
1 AAA-AAAT-AAAAAA-AAGA
*
52704220 ATAAAATAAAAA
1 AAAAAATAAAAA
52704232 TGAGTGAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 12 0.32
18 14 0.37
19 9 0.24
20 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (17 bp):
AAAAAATAAAAAAAAGA
Found at i:52705755 original size:134 final size:134
Alignment explanation
Indices: 52705523--52706052 Score: 818
Period size: 134 Copynumber: 4.0 Consensus size: 134
52705513 TGAAGATAAT
*
52705523 AGATCTTGCC-TCCTTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAC
1 AGATCTTGCCTTCC-TGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAC
* *
52705587 TACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTAAAG
65 TACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
52705652 ATTGC
130 ATTGC
* **
52705657 AGATCTTGCCTTCCTGTATTTGGCAGCGAAACAGATCGAAGATGGCAGATTTTACCTCATTGACT
1 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGACT
52705722 ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
66 ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
52705787 TTGC
131 TTGC
*
52705791 AGATCTTGCCTTTCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGACT
1 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGACT
52705856 ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
66 ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
**
52705921 TAAC
131 TTGC
* * * * * * *
52705925 AGATCTTGCCCTCCTGCA-TCGTCAGCGAGGCAGATC-AGATATGGCAGATTTTACCTCTCTGAC
1 AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGA-AGATGGCAGATTTTACCTCCCTGAC
* * * * *
52705988 TACAGTGGAGTACATTGAAGTCGATAATTCTATCTCCCTG--GTTAGCAGTTGAATAGATTGAAG
65 TACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAG
52706051 AT
130 AT
52706053 CAAAGATGGC
Statistics
Matches: 369, Mismatches: 25, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
131 22 0.06
132 1 0.00
133 76 0.21
134 267 0.72
135 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (134 bp):
AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGACT
ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGA
TTGC
Found at i:52706068 original size:93 final size:94
Alignment explanation
Indices: 52705956--52706141 Score: 241
Period size: 95 Copynumber: 2.0 Consensus size: 94
52705946 TCAGCGAGGC
* * *
52705956 AGATCAGATATGGCAGATTTTACCT-CTCT-GACTACAGTGGAGTACATTGAAGTCGATAATTCT
1 AGATCAAAGATGGCAGATTTTACCTCCT-TAGACTACAGTGGAGTACATTGAAGCCGATAATTCT
* ** *
52706019 ATCTCCCTGGTTAGCAGTTGAATAGATTGA
65 ATCCCCCTGGGCAGCAGTGGAATAGATTGA
* * * *
52706049 AGATCAAAGATGGCGGATTTTACCTCCTTGAGATTACAGTGGAGTACATTGAAGCCGGTAGTTCT
1 AGATCAAAGATGGCAGATTTTACCTCCTT-AGACTACAGTGGAGTACATTGAAGCCGATAATTCT
52706114 ATCCCCCTGGGCAGCAGTGGAATAGATT
65 ATCCCCCTGGGCAGCAGTGGAATAGATT
52706142 TAAAACCACA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
93 23 0.29
94 2 0.03
95 54 0.68
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (94 bp):
AGATCAAAGATGGCAGATTTTACCTCCTTAGACTACAGTGGAGTACATTGAAGCCGATAATTCTA
TCCCCCTGGGCAGCAGTGGAATAGATTGA
Found at i:52713913 original size:18 final size:18
Alignment explanation
Indices: 52713890--52713924 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
52713880 TCCACGTCAT
52713890 GACGATGAAGGTACTCCC
1 GACGATGAAGGTACTCCC
52713908 GACGATGAAGGTACTCC
1 GACGATGAAGGTACTCC
52713925 ACGTTGCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.17
Consensus pattern (18 bp):
GACGATGAAGGTACTCCC
Found at i:52717713 original size:31 final size:30
Alignment explanation
Indices: 52717675--52717758 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 30
52717665 CTACTTCCAA
** **
52717675 GGTCACTCAATTATTAGTAAGTATACACTTT
1 GGTCACTCAATTATTAAAAAGT-TACAAATT
52717706 GGTCACTCAATT-TTAAAAAGTTACAAATT
1 GGTCACTCAATTATTAAAAAGTTACAAATT
* **
52717735 GGTCACTGAATTATTCGAAAGTTA
1 GGTCACTCAATTATTAAAAAGTTA
52717759 TCTTTTAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 17 0.38
30 16 0.36
31 12 0.27
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (30 bp):
GGTCACTCAATTATTAAAAAGTTACAAATT
Found at i:52717740 original size:29 final size:31
Alignment explanation
Indices: 52717675--52717749 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
52717665 CTACTTCCAA
** **
52717675 GGTCACTCAATTATTAGTAAGTATACACTTT
1 GGTCACTCAATTATTAAAAAGTATACAAATT
52717706 GGTCACTCAATT-TTAAAAAGT-TACAAATT
1 GGTCACTCAATTATTAAAAAGTATACAAATT
*
52717735 GGTCACTGAATTATT
1 GGTCACTCAATTATT
52717750 CGAAAGTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 17 0.45
30 9 0.24
31 12 0.32
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (31 bp):
GGTCACTCAATTATTAAAAAGTATACAAATT
Found at i:52721582 original size:60 final size:60
Alignment explanation
Indices: 52721498--52721617 Score: 181
Period size: 61 Copynumber: 2.0 Consensus size: 60
52721488 CATATAGAGA
*
52721498 AATGGGTATGGGGTTATGATCTTCC-AAGAACCTG-TAAATACATGGAAATCTTGAAAAGT
1 AATGGGTATGGGGTTATGATCTTCCAAAG-ACCCGCTAAATACATGGAAATCTTGAAAAGT
* *
52721557 AATGGGTATGGGTTTTATGATCTTCCAAAGACCCGCTAAATACATGGAAATCTTGGAAAGT
1 AATGGGTATGGG-GTTATGATCTTCCAAAGACCCGCTAAATACATGGAAATCTTGAAAAGT
52721618 GAACATACCT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
59 12 0.22
60 16 0.29
61 27 0.49
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (60 bp):
AATGGGTATGGGGTTATGATCTTCCAAAGACCCGCTAAATACATGGAAATCTTGAAAAGT
Found at i:52724443 original size:18 final size:18
Alignment explanation
Indices: 52724407--52724459 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
52724397 TTTTTAATTA
*
52724407 AAAAATTATAATAAGTATT
1 AAAAATTATAA-AAATATT
52724426 AAAAATTATAAAAATATT
1 AAAAATTATAAAAATATT
* *
52724444 AAATATTAAAAAAATA
1 AAAAATTATAAAAATA
52724460 AAATATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
18 20 0.65
19 11 0.35
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAAATTATAAAAATATT
Found at i:52724453 original size:16 final size:16
Alignment explanation
Indices: 52724425--52724470 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
52724415 TAATAAGTAT
52724425 TAAAA-ATTATAAAAATA
1 TAAAATATTA-AAAAA-A
*
52724442 TTAAATATTAAAAAAA
1 TAAAATATTAAAAAAA
52724458 TAAAATATTAAAA
1 TAAAATATTAAAA
52724471 TTGATACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 13 0.50
17 9 0.35
18 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAATATTAAAAAAA
Found at i:52725171 original size:16 final size:17
Alignment explanation
Indices: 52725140--52725172 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
52725130 ATTGTTTACT
52725140 AAGTATTATATGATATA
1 AAGTATTATATGATATA
*
52725157 AAGTATT-TTTGATATA
1 AAGTATTATATGATATA
52725173 GTTAGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (17 bp):
AAGTATTATATGATATA
Found at i:52728799 original size:43 final size:43
Alignment explanation
Indices: 52728554--52728906 Score: 415
Period size: 43 Copynumber: 8.3 Consensus size: 43
52728544 AAAAAAAACA
* * *** * *
52728554 CCGCTAAAAGTCATGATTTATAGCGGCGTTTCTCCCAAAATCG
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCG
* * * *
52728597 CCGCTAAAAGTCATGATCTATAACAG-ATTTGTGGGAAAAGCG
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCG
52728639 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCG
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCG
* *
52728682 CCGTTAAAAGTCATGATCTATAGCGGCATTTGTGGGAGAAGCG
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCG
* *
52728725 CTGCTCAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCG
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCG
* * *
52728768 CCGCTAAAGGTCATGATCTATAGCGGCGTTTGAGGGAAAAGCG
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCG
* * *
52728811 TCGCTAAAGGTCATGATCTATAGCGGTGTTTGTGGTG-GAAGCG
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGG-GAGAAGCG
* * * * * * * *
52728854 CCGCTAAAGGTCCTGACCTTTAGCGGCGTTT-TTGTAAAAGCA
1 CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCG
52728896 CCGCTAAAAGT
1 CCGCTAAAAGT
52728907 TAGCAACGTT
Statistics
Matches: 269, Mismatches: 38, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
42 50 0.19
43 218 0.81
44 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (43 bp):
CCGCTAAAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCG
Found at i:52732270 original size:3 final size:3
Alignment explanation
Indices: 52732262--52732286 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52732252 TTATTTTTTG
52732262 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
52732287 TATTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:52738283 original size:18 final size:18
Alignment explanation
Indices: 52738255--52738303 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
52738245 AAATAAAAAA
* *
52738255 AATATTTTGAAAATGAAT
1 AATAATTTGAAAATAAAT
*
52738273 AATGATTTGAAAATAAAT
1 AATAATTTGAAAATAAAT
52738291 AATAATTTGAAAA
1 AATAATTTGAAAA
52738304 CGAACGACGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (18 bp):
AATAATTTGAAAATAAAT
Found at i:52738657 original size:25 final size:25
Alignment explanation
Indices: 52738629--52738695 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
52738619 AACTGTCCTT
* *
52738629 GATAGTATATCCTGAAACTGCTATA
1 GATAGTATATACTGAAACTACTATA
*
52738654 GATAGTATATACTGAGACTACTATA
1 GATAGTATATACTGAAACTACTATA
52738679 GATAG-ACTATACTGAAA
1 GATAGTA-TATACTGAAA
52738696 ACACTTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (25 bp):
GATAGTATATACTGAAACTACTATA
Found at i:52752878 original size:2 final size:2
Alignment explanation
Indices: 52752871--52752916 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
52752861 AGATTTTAAC
52752871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52752913 AT AT
1 AT AT
52752917 TTATGACAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52755416 original size:31 final size:31
Alignment explanation
Indices: 52755381--52755447 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
52755371 TTTAACAGCT
*
52755381 GGTGACCAGAAAAGAAAATTTCGAATAATTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
*
52755412 GGTGACCAGAAAAGAAAATCTCGAATAGTTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
52755443 GGTGA
1 GGTGA
52755448 TCATTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (31 bp):
GGTGACCAGAAAAGAAAATCTCGAATAATTG
Found at i:52756927 original size:2 final size:2
Alignment explanation
Indices: 52756920--52756951 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52756910 AGATTTTAAC
52756920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52756952 TTATGACAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52759466 original size:31 final size:31
Alignment explanation
Indices: 52759410--52759476 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
52759400 TTTAACAGCT
*
52759410 GGTGACCAGAAAAGAAAAATTTGAATAATTG
1 GGTGACCAGAAAAGAAAAATATGAATAATTG
* *
52759441 GGTGACCAGAAAAG-AAAATCATGAATAGTTT
1 GGTGACCAGAAAAGAAAAAT-ATGAATAATTG
52759472 GGTGA
1 GGTGA
52759477 TCATTTTGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.22
Consensus pattern (31 bp):
GGTGACCAGAAAAGAAAAATATGAATAATTG
Found at i:52767961 original size:2 final size:2
Alignment explanation
Indices: 52767954--52767985 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52767944 GTGAAATTGC
52767954 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
52767986 AAGCTAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52771100 original size:31 final size:31
Alignment explanation
Indices: 52771065--52771131 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
52771055 TTTAACAGCT
*
52771065 GGTGACCAGAAAAGAAAATTTCGAATAATTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
*
52771096 GGTGACCAGAAAAGAAAATCTCGAATAGTTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
52771127 GGTGA
1 GGTGA
52771132 TCATTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (31 bp):
GGTGACCAGAAAAGAAAATCTCGAATAATTG
Found at i:52797071 original size:31 final size:31
Alignment explanation
Indices: 52797036--52797102 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
52797026 TTTAACAGCT
*
52797036 GGTGACCAGAAAAGAAAATTTCGAATAATTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
*
52797067 GGTGACCAGAAAAGAAAATCTCGAATAGTTG
1 GGTGACCAGAAAAGAAAATCTCGAATAATTG
52797098 GGTGA
1 GGTGA
52797103 TCATTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (31 bp):
GGTGACCAGAAAAGAAAATCTCGAATAATTG
Found at i:52821801 original size:18 final size:19
Alignment explanation
Indices: 52821762--52821802 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
52821752 ATTATTTGGA
52821762 TATTGTATAAATCTTATTT
1 TATTGTATAAATCTTATTT
52821781 TATTGT-TAAAT-TTATTAT
1 TATTGTATAAATCTTATT-T
52821799 TATT
1 TATT
52821803 TTAGAGGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 10 0.48
19 6 0.29
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (19 bp):
TATTGTATAAATCTTATTT
Found at i:52825145 original size:42 final size:42
Alignment explanation
Indices: 52825063--52825192 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
52825053 CTCTAACTCA
* * * * * *
52825063 TATGAGTTTCCGTTCAACCCTAATGGGTTTCTGTTTAGCTCT
1 TATGAGCTTCCGTTTAACCCTTATAGGTTTCCGTTCAGCTCT
* *
52825105 TTTGAGCTTCTGTTTAACCCTTATAGGTTTCCGTTCAGCTCT
1 TATGAGCTTCCGTTTAACCCTTATAGGTTTCCGTTCAGCTCT
* * *
52825147 TATGAGCTTCCGTTTAACCCTTAT-GAGTTTCTGTTTAGCACT
1 TATGAGCTTCCGTTTAACCCTTATAG-GTTTCCGTTCAGCTCT
52825189 TATG
1 TATG
52825193 CGTTTCTATT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
41 1 0.01
42 73 0.99
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.44
Consensus pattern (42 bp):
TATGAGCTTCCGTTTAACCCTTATAGGTTTCCGTTCAGCTCT
Found at i:52825197 original size:21 final size:21
Alignment explanation
Indices: 52825063--52825199 Score: 105
Period size: 21 Copynumber: 6.5 Consensus size: 21
52825053 CTCTAACTCA
* * *
52825063 TATGAGTTTCCGTTCAACCCT
1 TATGAGTTTCTGTTTAGCCCT
* * *
52825084 AATGGGTTTCTGTTTAGCTCT
1 TATGAGTTTCTGTTTAGCCCT
* * *
52825105 TTTGAGCTTCTGTTTAACCCT
1 TATGAGTTTCTGTTTAGCCCT
* * *
52825126 TAT-AGGTTTCCGTTCAGCTCT
1 TATGA-GTTTCTGTTTAGCCCT
* * *
52825147 TATGAGCTTCCGTTTAACCCT
1 TATGAGTTTCTGTTTAGCCCT
*
52825168 TATGAGTTTCTGTTTAGCACT
1 TATGAGTTTCTGTTTAGCCCT
*
52825189 TATGCGTTTCT
1 TATGAGTTTCT
52825200 ATTCAGCCTT
Statistics
Matches: 87, Mismatches: 27, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
20 1 0.01
21 85 0.98
22 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.45
Consensus pattern (21 bp):
TATGAGTTTCTGTTTAGCCCT
Found at i:52825716 original size:21 final size:21
Alignment explanation
Indices: 52825690--52825729 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52825680 CAAAACAGGT
*
52825690 TTTTAGCGGCGTTTTTTAGTA
1 TTTTAGCGGCGCTTTTTAGTA
52825711 TTTTAGCGGCGCTTTTTAG
1 TTTTAGCGGCGCTTTTTAG
52825730 CGCCACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (21 bp):
TTTTAGCGGCGCTTTTTAGTA
Found at i:52825823 original size:30 final size:30
Alignment explanation
Indices: 52825787--52825857 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
52825777 CGCTATTGAC
52825787 AACGTCGCTAAGGTTTGCGGCATTTCTATA
1 AACGTCGCTAAGGTTTGCGGCATTTCTATA
52825817 AACGTCGCTAAGGTTTGCGGCATTTCTATA
1 AACGTCGCTAAGGTTTGCGGCATTTCTATA
*
52825847 AACGCCGCTAA
1 AACGTCGCTAA
52825858 AGGTCATGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (30 bp):
AACGTCGCTAAGGTTTGCGGCATTTCTATA
Found at i:52825899 original size:43 final size:43
Alignment explanation
Indices: 52825846--52825937 Score: 132
Period size: 43 Copynumber: 2.1 Consensus size: 43
52825836 GCATTTCTAT
* * *
52825846 AAACGCCGCTAAAGGTCATG-TTCTTTAGCGGCGCTTATCCCAC
1 AAACGTCGCTAAAGGTCATGACT-TTTAGCAGCGCTTATCCCAC
*
52825889 AAACGTCGCTAAAGGTCATGACTTTTAGCAGCGCTTTTCCCAC
1 AAACGTCGCTAAAGGTCATGACTTTTAGCAGCGCTTATCCCAC
52825932 AAACGT
1 AAACGT
52825938 TGCTTTTACA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 43 0.98
44 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (43 bp):
AAACGTCGCTAAAGGTCATGACTTTTAGCAGCGCTTATCCCAC
Found at i:52826072 original size:44 final size:43
Alignment explanation
Indices: 52825949--52826085 Score: 177
Period size: 43 Copynumber: 3.2 Consensus size: 43
52825939 GCTTTTACAC
* *
52825949 AAACGCCGCTATAAATCATGACTTTTAGCGGCGCTTTTATC-AC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTT-TCTAT
52825992 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCTAT
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCTAT
* * * ** *
52826035 AAACGCTGCTATTGTTTGGTGACTTTTAGCGGTGCTTTTTCTAT
1 AAACGCCGCTATAG-ATCATGACTTTTAGCGGCGCTTTTTCTAT
52826079 AAACGCC
1 AAACGCC
52826086 ACTAATTTTG
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
42 2 0.02
43 50 0.60
44 31 0.37
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (43 bp):
AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCTAT
Found at i:52828388 original size:9 final size:9
Alignment explanation
Indices: 52828374--52828802 Score: 268
Period size: 9 Copynumber: 48.2 Consensus size: 9
52828364 TATATTTATG
52828374 TATGTAAGT
1 TATGTAAGT
52828383 TATGT-A-T
1 TATGTAAGT
*
52828390 TATGTTAGT
1 TATGTAAGT
*
52828399 AATGTAAGT
1 TATGTAAGT
*
52828408 TGTGT-A-T
1 TATGTAAGT
52828415 TATGTAAGT
1 TATGTAAGT
52828424 TATGTAAGT
1 TATGTAAGT
*
52828433 TGTGTAAGT
1 TATGTAAGT
*
52828442 TCTGT-A-T
1 TATGTAAGT
52828449 TATGTAAGT
1 TATGTAAGT
52828458 TATGTAAGT
1 TATGTAAGT
*
52828467 TGTG-AA-T
1 TATGTAAGT
*
52828474 TATGTAATT
1 TATGTAAGT
52828483 TATGTAA-T
1 TATGTAAGT
52828491 TCATGT-A-T
1 T-ATGTAAGT
*
52828499 TATGGAAGT
1 TATGTAAGT
52828508 TATGTAAGT
1 TATGTAAGT
*
52828517 AATGT-A-T
1 TATGTAAGT
*
52828524 TATGTCAGT
1 TATGTAAGT
52828533 TATGT-A-T
1 TATGTAAGT
52828540 TATGTAAGT
1 TATGTAAGT
52828549 TATGT-A-T
1 TATGTAAGT
52828556 TATGTAAGTT
1 TATGTAAG-T
52828566 TATGTAAGT
1 TATGTAAGT
*
52828575 TATGTAAAT
1 TATGTAAGT
* *
52828584 TATATAATT
1 TATGTAAGT
* *
52828593 TATGAAATT
1 TATGTAAGT
* *
52828602 TGATCTTTAAAT
1 T-A--TGTAAGT
52828614 TATGTAAGT
1 TATGTAAGT
*
52828623 TATGTAAAT
1 TATGTAAGT
52828632 TATGTAAGT
1 TATGTAAGT
* * *
52828641 TAAGAAATT
1 TATGTAAGT
* *
52828650 TGATCTTTAAAT
1 T-A--TGTAAGT
52828662 TATGTAAGT
1 TATGTAAGT
*
52828671 CT-TGTAACT
1 -TATGTAAGT
52828680 TATGTAAGT
1 TATGTAAGT
* *
52828689 TATGAAATT
1 TATGTAAGT
* *
52828698 TGATTTTTAAAT
1 T-A--TGTAAGT
52828710 TATGTAAGT
1 TATGTAAGT
*
52828719 TATGTAAAT
1 TATGTAAGT
52828728 TATGTAAGT
1 TATGTAAGT
* *
52828737 TATGAAATT
1 TATGTAAGT
* *
52828746 TGATCTTTAAAT
1 T-A--TGTAAGT
52828758 TATGTAAGT
1 TATGTAAGT
52828767 TATGT-A-T
1 TATGTAAGT
*
52828774 TATGTAATT
1 TATGTAAGT
*
52828783 TATGTAAAT
1 TATGTAAGT
52828792 TATGTAAGT
1 TATGTAAGT
52828801 TA
1 TA
52828803 AAATATTTGA
Statistics
Matches: 331, Mismatches: 55, Indels: 68
0.73 0.12 0.15
Matches are distributed among these distances:
7 46 0.14
8 25 0.08
9 223 0.67
10 14 0.04
11 4 0.01
12 19 0.06
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (9 bp):
TATGTAAGT
Found at i:52828403 original size:16 final size:16
Alignment explanation
Indices: 52828400--52828564 Score: 87
Period size: 16 Copynumber: 10.5 Consensus size: 16
52828390 TATGTTAGTA
**
52828400 ATGTAAGTTGTGTATT
1 ATGTAAGTAATGTATT
*
52828416 ATGTAAGTTATGTAAGTT
1 ATGTAAGTAATGT-A-TT
* **
52828434 GTGTAAGTTCTGTATT
1 ATGTAAGTAATGTATT
* *
52828450 ATGTAAGTTATGTAAGT
1 ATGTAAGTAATGT-ATT
*
52828467 -TGTGAA-TTATGTAATTT
1 ATGT-AAGTAATGT-A-TT
* *
52828484 ATGTAATTCATGTATT
1 ATGTAAGTAATGTATT
52828500 ATG---G-AA-GT-T-
1 ATGTAAGTAATGTATT
52828509 ATGTAAGTAATGTATT
1 ATGTAAGTAATGTATT
* *
52828525 ATGTCAGTTATGTATT
1 ATGTAAGTAATGTATT
*
52828541 ATGTAAGTTATGTATT
1 ATGTAAGTAATGTATT
52828557 ATGTAAGT
1 ATGTAAGT
52828565 TTATGTAAGT
Statistics
Matches: 122, Mismatches: 13, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
9 3 0.02
10 1 0.01
11 2 0.02
12 2 0.02
13 2 0.02
14 2 0.02
15 1 0.01
16 78 0.64
17 10 0.08
18 21 0.17
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (16 bp):
ATGTAAGTAATGTATT
Found at i:52828548 original size:32 final size:35
Alignment explanation
Indices: 52828400--52828581 Score: 153
Period size: 34 Copynumber: 5.2 Consensus size: 35
52828390 TATGTTAGTA
**
52828400 ATGTAAGTTGTGTATTATGTAAG-TTATGTAAGTT
1 ATGTAAGTAATGTATTATGTAAGTTTATGTAAGTT
* **
52828434 GTGTAAGTTCTGTATTATGTAAG-TTATGTAAGTT
1 ATGTAAGTAATGTATTATGTAAGTTTATGTAAGTT
* * *
52828468 GTG-AA-TTATGTAATTTATGTAATTCATGTATTATGGAAGTT
1 ATGTAAGTAATGT-A-TTATGT-A---A-GT-TTATGTAAGTT
*
52828509 ATGTAAGTAATGTATTATGTCAG-TTATGT-A-TT
1 ATGTAAGTAATGTATTATGTAAGTTTATGTAAGTT
*
52828541 ATGTAAGTTATGTATTATGTAAGTTTATGTAAGTT
1 ATGTAAGTAATGTATTATGTAAGTTTATGTAAGTT
52828576 ATGTAA
1 ATGTAA
52828582 ATTATATAAT
Statistics
Matches: 124, Mismatches: 10, Indels: 27
0.77 0.06 0.17
Matches are distributed among these distances:
32 28 0.23
33 10 0.08
34 47 0.38
35 9 0.07
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
41 18 0.15
42 3 0.02
43 5 0.04
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.47
Consensus pattern (35 bp):
ATGTAAGTAATGTATTATGTAAGTTTATGTAAGTT
Found at i:52828571 original size:26 final size:25
Alignment explanation
Indices: 52828374--52828797 Score: 230
Period size: 25 Copynumber: 17.0 Consensus size: 25
52828364 TATATTTATG
52828374 TATGTAAGTTATGT-A-TTATGTTAGT
1 TATGTAAGTTATGTAAGTTATG-TA-T
* *
52828399 AATGTAAGTTGTGT-A-TTATGTAAGT
1 TATGTAAGTTATGTAAGTTATGT-A-T
* *
52828424 TATGTAAGTTGTGTAAGTTCTGTAT
1 TATGTAAGTTATGTAAGTTATGTAT
* *
52828449 TATGTAAGTTATGTAAGTTGTGAAT
1 TATGTAAGTTATGTAAGTTATGTAT
*
52828474 TATGTAATTTATGTAA-TTCATGTAT
1 TATGTAAGTTATGTAAGTT-ATGTAT
* *
52828499 TATGGAAGTTATGTAAGTAATGTAT
1 TATGTAAGTTATGTAAGTTATGTAT
*
52828524 TATGTCAGTTATGT-A-TTATGTAAGT
1 TATGTAAGTTATGTAAGTTATGT-A-T
52828549 TATGT-A-TTATGTAAGTTTATGTAAGT
1 TATGTAAGTTATGTAAG-TTATGT-A-T
* * * *
52828575 TATGTAAATTATATAATTTATGAAATT
1 TATGTAAGTTATGTAAGTTATG-TA-T
* *
52828602 TGATCTTTAAATTATGTAAGTTATGTAAAT
1 T-A--TGTAAGTTATGTAAGTTATGT--AT
* *
52828632 TATGTAAGTTAAG-AAATT-TG-AT
1 TATGTAAGTTATGTAAGTTATGTAT
*
52828654 CT-T-TAAATTATGTAAGTCT-TGTAACT
1 -TATGTAAGTTATGTAAGT-TATGT-A-T
*
52828680 TATGTAAGTTATG-AAATT-TG-AT
1 TATGTAAGTTATGTAAGTTATGTAT
* *
52828702 T-TTTAAATTATGTAAGTTATGTAAAT
1 TATGTAAGTTATGTAAGTTATGT--AT
*
52828728 TATGTAAGTTATG-AAATT-TG-AT
1 TATGTAAGTTATGTAAGTTATGTAT
*
52828750 CT-T-TAAATTATGTAAGTTATGTAT
1 -TATGTAAGTTATGTAAGTTATGTAT
* *
52828774 TATGTAATTTATGTAAATTATGTA
1 TATGTAAGTTATGTAAGTTATGTA
52828798 AGTTAAAATA
Statistics
Matches: 318, Mismatches: 43, Indels: 76
0.73 0.10 0.17
Matches are distributed among these distances:
21 24 0.08
22 19 0.06
23 22 0.07
24 10 0.03
25 141 0.44
26 34 0.11
27 39 0.12
28 8 0.03
29 1 0.00
30 19 0.06
31 1 0.00
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (25 bp):
TATGTAAGTTATGTAAGTTATGTAT
Found at i:52828622 original size:48 final size:48
Alignment explanation
Indices: 52828565--52828792 Score: 363
Period size: 48 Copynumber: 4.8 Consensus size: 48
52828555 TTATGTAAGT
* *
52828565 TTATGTAAGTTATGTAAATTATATAATTTATGAAATTTGATCTTTAAA
1 TTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTTAAA
*
52828613 TTATGTAAGTTATGTAAATTATGTAAGTTAAGAAATTTGATCTTTAAA
1 TTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTTAAA
* *
52828661 TTATGTAAGTCT-TGTAACTTATGTAAGTTATGAAATTTGATTTTTAAA
1 TTATGTAAGT-TATGTAAATTATGTAAGTTATGAAATTTGATCTTTAAA
52828709 TTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTTAAA
1 TTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTTAAA
*
52828757 TTATGTAAGTTATGT--ATTATGTAATTTATGTAAATT
1 TTATGTAAGTTATGTAAATTATGTAAGTTATG-AAATT
52828793 ATGTAAGTTA
Statistics
Matches: 168, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
46 14 0.08
47 6 0.04
48 147 0.88
49 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (48 bp):
TTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGATCTTTAAA
Found at i:52828757 original size:30 final size:30
Alignment explanation
Indices: 52828723--52828833 Score: 109
Period size: 30 Copynumber: 3.6 Consensus size: 30
52828713 GTAAGTTATG
52828723 TAAATTATGTAAGTTATGAAATTTGATCTT
1 TAAATTATGTAAGTTATGAAATTTGATCTT
* *
52828753 TAAATTATGTAAGTTATG-TATTATGTAATTTAT
1 TAAATTATGTAAGTTATGAAATT-TG--ATCT-T
* *
52828786 GTAAATTATGTAAGTTA-AAATATTTGATGTT
1 -TAAATTATGTAAGTTATGAA-ATTTGATCTT
*
52828817 TGAATTATGTAAGTTAT
1 TAAATTATGTAAGTTAT
52828834 ATAAATTATG
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
29 3 0.04
30 35 0.52
31 1 0.01
32 6 0.09
33 1 0.01
34 18 0.27
35 3 0.04
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.48
Consensus pattern (30 bp):
TAAATTATGTAAGTTATGAAATTTGATCTT
Found at i:52828786 original size:64 final size:65
Alignment explanation
Indices: 52828707--52828857 Score: 218
Period size: 64 Copynumber: 2.3 Consensus size: 65
52828697 TTGATTTTTA
* *
52828707 AATTATGTAAGTTATGTAAATTATGTAAGTTATGAA-ATTTGATCTTTAAATTATGTAAGTTATG
1 AATTATGTAAGTTATGTAAATTATGTAAGTTA-AAATATTTGATCTTTAAATTATGTAAGTTATA
52828771 T
65 T
* * *
52828772 -ATTATGTAATTTATGTAAATTATGTAAGTTAAAATATTTGATGTTTGAATTATGTAAGTTATAT
1 AATTATGTAAGTTATGTAAATTATGTAAGTTAAAATATTTGATCTTTAAATTATGTAAGTTATAT
52828836 AAATTATGTAAGTTATG-AAATT
1 -AATTATGTAAGTTATGTAAATT
52828858 TTATCTTTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
63 2 0.03
64 56 0.73
65 5 0.06
66 14 0.18
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.46
Consensus pattern (65 bp):
AATTATGTAAGTTATGTAAATTATGTAAGTTAAAATATTTGATCTTTAAATTATGTAAGTTATAT
Found at i:52828804 original size:48 final size:50
Alignment explanation
Indices: 52828374--52828850 Score: 313
Period size: 48 Copynumber: 9.9 Consensus size: 50
52828364 TATATTTATG
* * * * *
52828374 TATGTAAGTTATGT-ATTATGTTAGTAATGTAAGTTGTGTATTA-TGTAAGT
1 TATGTAAGTTATGTAATTATGTAAGTTATGTAAATTATGTA-TAGT-TAAAT
* * * *
52828424 TATGTAAGTTGTGTAAGTTCTGT-A-TTATGTAAGTTATGTA-AGTTGTGAAT
1 TATGTAAGTTATGTAA-TTATGTAAGTTATGTAAATTATGTATAG-T-TAAAT
* * *
52828474 TATGTAATTTATGTAATTCATGT-A-TTATGGAAGTTATGTA-AG-TAATGTAT
1 TATGTAAGTTATGTAATT-ATGTAAGTTATGTAAATTATGTATAGTTAA---AT
*
52828524 TATGTCAGTTATGT-ATTATGTAAGTTATGT--ATTATGTA-AG-T---T
1 TATGTAAGTTATGTAATTATGTAAGTTATGTAAATTATGTATAGTTAAAT
* * **
52828566 TATGTAAGTTATGTAAATTATATAATTTATG-AAATT-TG-ATCTTTAAAT
1 TATGTAAGTTATGT-AATTATGTAAGTTATGTAAATTATGTATAGTTAAAT
* **
52828614 TATGTAAGTTATGTAAATTATGTAAGTTAAG-AAATT-TG-ATCTTTAAAT
1 TATGTAAGTTATGT-AATTATGTAAGTTATGTAAATTATGTATAGTTAAAT
**
52828662 TATGTAAGTCT-TGTAACTTATGTAAGTTATG-AAATT-TG-ATTTTTAAAT
1 TATGTAAGT-TATGTAA-TTATGTAAGTTATGTAAATTATGTATAGTTAAAT
**
52828710 TATGTAAGTTATGTAAATTATGTAAGTTATG-AAATT-TG-ATCTTTAAAT
1 TATGTAAGTTATGT-AATTATGTAAGTTATGTAAATTATGTATAGTTAAAT
* *
52828758 TATGTAAGTTATGT-ATTATGTAATTTATGTAAATTATGTA-AGTTAAAA
1 TATGTAAGTTATGTAATTATGTAAGTTATGTAAATTATGTATAGTTAAAT
* * *
52828806 TATTTGATGTT-TG-AATTATGTAAGTTATATAAATTATGTA-AGTTA
1 TATGT-AAGTTATGTAATTATGTAAGTTATGTAAATTATGTATAGTTA
52828851 TGAAATTTTA
Statistics
Matches: 365, Mismatches: 34, Indels: 58
0.80 0.07 0.13
Matches are distributed among these distances:
42 14 0.04
43 1 0.00
44 15 0.04
45 4 0.01
46 14 0.04
47 10 0.03
48 200 0.55
49 14 0.04
50 86 0.24
51 2 0.01
52 5 0.01
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.47
Consensus pattern (50 bp):
TATGTAAGTTATGTAATTATGTAAGTTATGTAAATTATGTATAGTTAAAT
Found at i:52828811 original size:112 final size:112
Alignment explanation
Indices: 52828660--52828879 Score: 345
Period size: 112 Copynumber: 2.0 Consensus size: 112
52828650 TGATCTTTAA
* * * *
52828660 ATTATGTAAGTCTTGTAACTTATGTAAGTTATGAAATTTGATTTTTAAATTATGTAAGTTATGTA
1 ATTATGTAAGTCTTGTAAATTATGTAAGTTATAAAATTTGATGTTTAAATTATGTAAGTTATATA
52828725 AATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTTATGT
66 AATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTTATGT
* *
52828772 ATTATGTAA-TTTATGTAAATTATGTAAGTTA-AAATATTTGATGTTTGAATTATGTAAGTTATA
1 ATTATGTAAGTCT-TGTAAATTATGTAAGTTATAAA-ATTTGATGTTTAAATTATGTAAGTTATA
*
52828835 TAAATTATGTAAGTTATGAAATTTTATCTTTAAATTATGTAAGTT
64 TAAATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTT
52828880 TATTAAGCGA
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
111 4 0.04
112 95 0.96
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (112 bp):
ATTATGTAAGTCTTGTAAATTATGTAAGTTATAAAATTTGATGTTTAAATTATGTAAGTTATATA
AATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTTATGT
Found at i:52828871 original size:48 final size:48
Alignment explanation
Indices: 52828772--52828879 Score: 148
Period size: 48 Copynumber: 2.2 Consensus size: 48
52828762 TAAGTTATGT
* * * *
52828772 ATTATGTAATTTATGTAAATTATGTAAGTTAAAATATTTGATGTTTGA
1 ATTATGTAAGTTATATAAATTATGTAAGTTAAAATATTTGATCTTTAA
52828820 ATTATGTAAGTTATATAAATTATGTAAGTTATGAAAT-TTT-ATCTTTAA
1 ATTATGTAAGTTATATAAATTATGTAAGTTA--AAATATTTGATCTTTAA
52828868 ATTATGTAAGTT
1 ATTATGTAAGTT
52828880 TATTAAGCGA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
48 47 0.87
49 3 0.06
50 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (48 bp):
ATTATGTAAGTTATATAAATTATGTAAGTTAAAATATTTGATCTTTAA
Done.