Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 171 of 182
Found at i:52217354 original size:115 final size:114
Alignment explanation
Indices: 52217018--52217467 Score: 392
Period size: 115 Copynumber: 3.9 Consensus size: 114
52217008 TAGTCTGATT
* ** * * * *
52217018 TTTTAGTGGCGTTTTTACTAAAATGCCGCAAAACGAGTTA--TATTAGTGGTGTTTCTACAAAAA
1 TTTTAGTGGCGTTTTTACAAAAACACCGCAAAA-G-GTTATGTGTTAGTGGCGTTTTTA-TAAAA
* * ** * * **
52217081 ATGCCGCAATTATGTTTTTTGTCTTT-TTCAAACGTTGTCATTTTTATCTAGG
63 ACGCCGCAATTATGTTATAAGTGTTTGCT-AAACGTTGTCATTTTTATCTACA
* * * * * * ***
52217133 TTTTCAGTGGCGTTTTTGCCAAAACGCCGCAAAA--TGATGTGTTAGTGGCATTTTCA-GGTAAC
1 TTTT-AGTGGCGTTTTTACAAAAACACCGCAAAAGGTTATGTGTTAGTGGCGTTTTTATAAAAAC
* * *
52217195 GCCGCAATTATGTTATTAGTCTTTTG-TAAACGTTGTCGTTTTTATCTACA
65 GCCGCAATTATGTTATAAGT-GTTTGCTAAACGTTGTCATTTTTATCTACA
* * *
52217245 TTATTAGTGGCATTTTTACAAAAACACCGCAAAAGGTTATGTGGTAGTGGCGTTTTTATAAAAAT
1 TT-TTAGTGGCGTTTTTACAAAAACACCGCAAAAGGTTATGTGTTAGTGGCGTTTTTATAAAAAC
*
52217310 GCCGCAATTATGTTATAAGTGTTCGCTAAACGTTGTCATTTTTATCTACGA
65 GCCGCAATTATGTTATAAGTGTTTGCTAAACGTTGTCATTTTTATCTAC-A
* * ** * * * *
52217361 TTTTAGTGGCGTTTGTACTAAAACACCGGTAAAGGATATGTTTTAGTGGCGTCTTTATTATAAAC
1 TTTTAGTGGCGTTTTTACAAAAACACCGCAAAAGGTTATGTGTTAGTGGCGTTTTTA-TAAAAAC
* * *
52217426 GCCGCAAATATGTTTTAAGTGTTTGCTAAACGTTGTCGTTTT
65 GCCGCAATTATGTTATAAGTGTTTGCTAAACGTTGTCATTTT
52217468 CTATATGGGA
Statistics
Matches: 273, Mismatches: 50, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
112 69 0.25
113 6 0.02
114 33 0.12
115 93 0.34
116 72 0.26
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (114 bp):
TTTTAGTGGCGTTTTTACAAAAACACCGCAAAAGGTTATGTGTTAGTGGCGTTTTTATAAAAACG
CCGCAATTATGTTATAAGTGTTTGCTAAACGTTGTCATTTTTATCTACA
Found at i:52218999 original size:20 final size:20
Alignment explanation
Indices: 52218961--52218999 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52218951 TTCGGTTTGT
* *
52218961 GGTTTGTAAACTATGAATTG
1 GGTTTCTAAACTATCAATTG
*
52218981 GGTTTCTAAACTTTCAATT
1 GGTTTCTAAACTATCAATT
52219000 TATGGTTTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (20 bp):
GGTTTCTAAACTATCAATTG
Found at i:52219329 original size:9 final size:9
Alignment explanation
Indices: 52219304--52219944 Score: 637
Period size: 9 Copynumber: 74.4 Consensus size: 9
52219294 TAATAACATA
*
52219304 ATAACTAAC
1 ATAACTTAC
52219313 ATAA--TAC
1 ATAACTTAC
*
52219320 ATAACCTAC
1 ATAACTTAC
52219329 ATAACTTAC
1 ATAACTTAC
52219338 ATAACTTAC
1 ATAACTTAC
* *
52219347 ATAAATTAA
1 ATAACTTAC
52219356 ATAACTTAC
1 ATAACTTAC
52219365 ATAACTTAC
1 ATAACTTAC
52219374 ATAACTTAC
1 ATAACTTAC
52219383 ATAACTTAC
1 ATAACTTAC
52219392 ATAACTTAC
1 ATAACTTAC
52219401 ATAACTTAC
1 ATAACTTAC
* *
52219410 ATAAATTAA
1 ATAACTTAC
52219419 ATAACTTAC
1 ATAACTTAC
52219428 ATAACTTAC
1 ATAACTTAC
*
52219437 ATAACTTAA
1 ATAACTTAC
52219446 ATAACTTAC
1 ATAACTTAC
52219455 ATAA--TAC
1 ATAACTTAC
*
52219462 ATAACCCT-C
1 ATAA-CTTAC
*
52219471 CTAACTTAC
1 ATAACTTAC
* *
52219480 ATTATTTAC
1 ATAACTTAC
52219489 ATAA--TAC
1 ATAACTTAC
** *
52219496 ATTGCCTAC
1 ATAACTTAC
52219505 ATAACTTAC
1 ATAACTTAC
52219514 ATAACTTAC
1 ATAACTTAC
* *
52219523 ATAAATTAA
1 ATAACTTAC
*
52219532 ATAACTTGC
1 ATAACTTAC
52219541 ATAACTTAC
1 ATAACTTAC
52219550 ATAACTTAC
1 ATAACTTAC
52219559 ATAACTTAC
1 ATAACTTAC
* *
52219568 ATAAATTAA
1 ATAACTTAC
*
52219577 ATAACTTGC
1 ATAACTTAC
52219586 ATAACTTAC
1 ATAACTTAC
52219595 ATAACTTAC
1 ATAACTTAC
52219604 ATAAC-T--
1 ATAACTTAC
52219610 -T-ACTTAC
1 ATAACTTAC
52219617 ATAACTTAC
1 ATAACTTAC
52219626 ATAACTTAC
1 ATAACTTAC
* *
52219635 ATAAATTAA
1 ATAACTTAC
52219644 ATAACTTAC
1 ATAACTTAC
52219653 ATAACTTAC
1 ATAACTTAC
*
52219662 ATAACTTAA
1 ATAACTTAC
52219671 ATAACTTAC
1 ATAACTTAC
52219680 ATAA--TAC
1 ATAACTTAC
*
52219687 ATAACCCT-C
1 ATAA-CTTAC
*
52219696 CTAACTTAC
1 ATAACTTAC
* *
52219705 ATTATTTAC
1 ATAACTTAC
52219714 ATAA--TAC
1 ATAACTTAC
**
52219721 ATTGCTTAC
1 ATAACTTAC
52219730 ATAACTTAC
1 ATAACTTAC
52219739 ATAACTTAC
1 ATAACTTAC
* *
52219748 ATAAATTAA
1 ATAACTTAC
52219757 ATAACTTAC
1 ATAACTTAC
52219766 ATAACTTAC
1 ATAACTTAC
52219775 ATAACTTAC
1 ATAACTTAC
* *
52219784 ATAAATTAA
1 ATAACTTAC
52219793 ATAACTTAC
1 ATAACTTAC
*
52219802 ATAA--TAT
1 ATAACTTAC
52219809 ATAACCTT-C
1 ATAA-CTTAC
*
52219818 TTAACTTAC
1 ATAACTTAC
*
52219827 ATTA--TAC
1 ATAACTTAC
*
52219834 ACAACTTAC
1 ATAACTTAC
52219843 ATAA-TTA-
1 ATAACTTAC
*
52219850 AT-ATTATAC
1 ATAACT-TAC
*
52219859 ACAACTTAC
1 ATAACTTAC
52219868 ATAA--TAC
1 ATAACTTAC
*
52219875 ATTACTTAC
1 ATAACTTAC
*
52219884 ATTACTTAC
1 ATAACTTAC
52219893 ATAACTTAC
1 ATAACTTAC
*
52219902 ATTACTTAC
1 ATAACTTAC
52219911 ATAA--TAC
1 ATAACTTAC
52219918 ATAA--TAC
1 ATAACTTAC
52219925 ATAA--TAC
1 ATAACTTAC
52219932 ATAACTTAC
1 ATAACTTAC
52219941 ATAA
1 ATAA
52219945 TACATAAAAA
Statistics
Matches: 525, Mismatches: 74, Indels: 66
0.79 0.11 0.10
Matches are distributed among these distances:
4 2 0.00
5 2 0.00
6 1 0.00
7 71 0.14
8 14 0.03
9 430 0.82
10 5 0.01
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:52219616 original size:13 final size:13
Alignment explanation
Indices: 52219598--52219625 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52219588 AACTTACATA
52219598 ACTTACATAACTT
1 ACTTACATAACTT
52219611 ACTTACATAACTT
1 ACTTACATAACTT
52219624 AC
1 AC
52219626 ATAACTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (13 bp):
ACTTACATAACTT
Found at i:52219617 original size:22 final size:22
Alignment explanation
Indices: 52219589--52219634 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
52219579 AACTTGCATA
52219589 ACTTACATAACTTACATAACTT
1 ACTTACATAACTTACATAACTT
52219611 ACTTACATAACTTACATAACTT
1 ACTTACATAACTTACATAACTT
52219633 AC
1 AC
52219635 ATAAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (22 bp):
ACTTACATAACTTACATAACTT
Found at i:52219920 original size:7 final size:7
Alignment explanation
Indices: 52219908--52219951 Score: 70
Period size: 7 Copynumber: 6.0 Consensus size: 7
52219898 TTACATTACT
52219908 TACATAA
1 TACATAA
52219915 TACATAA
1 TACATAA
52219922 TACATAA
1 TACATAA
52219929 TACATAA
1 TACATAA
52219936 CTTACATAA
1 --TACATAA
52219945 TACATAA
1 TACATAA
52219952 AAATATATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 28 0.80
9 7 0.20
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (7 bp):
TACATAA
Found at i:52219939 original size:30 final size:31
Alignment explanation
Indices: 52219890--52219978 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 31
52219880 TTACATTACT
*
52219890 TACATAACTTACATTACTTACATAATACAT-AA
1 TACATAA--TACATAACTTACATAATACATAAA
52219922 TACATAATACATAACTTACATAATACATAAAAA
1 TACATAATACATAACTTACATAATACAT--AAA
* *
52219955 TATATCATATCATAACTTACATAA
1 TACATAATA-CATAACTTACATAA
52219979 CTCATTTATG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
30 20 0.40
32 7 0.14
33 9 0.18
34 14 0.28
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.33
Consensus pattern (31 bp):
TACATAATACATAACTTACATAATACATAAA
Found at i:52225242 original size:66 final size:66
Alignment explanation
Indices: 52225108--52225242 Score: 200
Period size: 66 Copynumber: 2.0 Consensus size: 66
52225098 GACCACAGTT
* * * *
52225108 GAGGTTCAAAGGAAATATGAAGAACTCTAGCTACAACTTAAAGCAGAGGCAGCAGTGAGGGAATC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCAGCAGTGAGAGAAGC
52225173 A
66 A
* *
52225174 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGGCA-TCGAGAGAAG
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCAGCAGT-GAGAGAAG
52225238 CA
65 CA
52225240 GAG
1 GAG
52225243 AAGAGCAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
65 1 0.02
66 61 0.98
ACGTcount: A:0.41, C:0.16, G:0.27, T:0.16
Consensus pattern (66 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCAGCAGTGAGAGAAGC
A
Found at i:52225682 original size:43 final size:41
Alignment explanation
Indices: 52225594--52225853 Score: 200
Period size: 42 Copynumber: 6.2 Consensus size: 41
52225584 GTTCTATAAA
* * *
52225594 GGCGTTTGTGAAGAGAGCGCCGCTAAAGAACAT-TTCTTTTTGC
1 GGCGTTT-T-AAGAAAGCGCCGCTAAAGAACATGATC-TTTAGC
*
52225637 GGCGTTTGTAAAGAAAGCGCCGCTAAAGAACATGATCTCTAGC
1 GGCGTTT-T-AAGAAAGCGCCGCTAAAGAACATGATCTTTAGC
* **
52225680 GGCGTTTTTACCAAGCGCCGCTAAAGAACATGATCTTTAGC
1 GGCGTTTTAAGAAAGCGCCGCTAAAGAACATGATCTTTAGC
* **** *
52225721 AGCGTTTTTCTTTAAGCGCCGCTAAAGAACATGATCTTTAGT
1 GGCG-TTTTAAGAAAGCGCCGCTAAAGAACATGATCTTTAGC
* ***** * *
52225763 GACGTCTTTTTTTTAGCCCCGCTAAAGAACATGACCTTTAGC
1 GGCGT-TTTAAGAAAGCGCCGCTAAAGAACATGATCTTTAGC
** * *
52225805 GGCGTTTTTTCG-AAGCGTCGCTAAAGAACATGACCTTTAGC
1 GGCG-TTTTAAGAAAGCGCCGCTAAAGAACATGATCTTTAGC
*
52225846 AGCGTTTT
1 GGCGTTTT
52225854 TTCTGTAAAC
Statistics
Matches: 184, Mismatches: 29, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
40 4 0.02
41 62 0.34
42 73 0.40
43 43 0.23
44 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (41 bp):
GGCGTTTTAAGAAAGCGCCGCTAAAGAACATGATCTTTAGC
Found at i:52225708 original size:41 final size:41
Alignment explanation
Indices: 52225651--52225857 Score: 261
Period size: 41 Copynumber: 5.0 Consensus size: 41
52225641 TTTGTAAAGA
* * *
52225651 AAGCGCCGCTAAAGAACATGATCTCTAGCGGCGTTTTTACC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCT
* *
52225692 AAGCGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTTCTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-TCT
* * *
52225734 AAGCGCCGCTAAAGAACATGATCTTTAGTGACGTCTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTCT
* * * *
52225776 TAGCCCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTCG
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCT
* * *
52225817 AAGCGTCGCTAAAGAACATGACCTTTAGCAGCGTTTTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCT
52225858 GTAAACGCTG
Statistics
Matches: 144, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
41 77 0.53
42 63 0.44
43 4 0.03
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCT
Found at i:52226597 original size:43 final size:43
Alignment explanation
Indices: 52226517--52226748 Score: 234
Period size: 43 Copynumber: 5.4 Consensus size: 43
52226507 ATAGACCACG
* * * * *
52226517 AACGCTGCTAAAGATCATGACCTTTAGCGACGTTTTTCAAACA
1 AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCACACA
* * * *
52226560 AATGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACA
1 AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCACACA
* * **
52226603 AATGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTGTCACA
1 AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCACACA
* *
52226646 AACGCCGCTAAAGAACATGAACTTTAGCGGCGCTTTTTATCACA
1 AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCA-CACA
* * * * * ** *
52226690 AACGCCGCTATAGAACA-AACCTTTAGCGACACTTCTCGTAAA
1 AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCACACA
52226732 AACGCCGCTAAA-AACAT
1 AACGCCGCTAAAGAACAT
52226749 ATCATGCAAA
Statistics
Matches: 160, Mismatches: 27, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
41 4 0.03
42 13 0.08
43 123 0.77
44 20 0.12
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCACACA
Found at i:52226812 original size:22 final size:21
Alignment explanation
Indices: 52226762--52226812 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
52226752 ATGCAAAAAA
52226762 ATTATTTTAATCAAATAATAT
1 ATTATTTTAATCAAATAATAT
*
52226783 -TTATTTTTATGAT-AAATATTAT
1 ATTA-TTTTA--ATCAAATAATAT
52226805 ATTATTTT
1 ATTATTTT
52226813 TTATTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 12 0.48
23 5 0.20
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTATTTTAATCAAATAATAT
Found at i:52234380 original size:19 final size:19
Alignment explanation
Indices: 52234338--52234380 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
52234328 TGGTCTATTT
*
52234338 AGTTTGTCGTTTACTTTGC
1 AGTTTGTCGGTTACTTTGC
* * *
52234357 TGTTTGTTGGTTACTTTTC
1 AGTTTGTCGGTTACTTTGC
52234376 AGTTT
1 AGTTT
52234381 CATTTTCTTG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (19 bp):
AGTTTGTCGGTTACTTTGC
Found at i:52234707 original size:22 final size:22
Alignment explanation
Indices: 52234680--52234731 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
52234670 ATCACTAACT
52234680 CTTAACCTCTAAGCT-CTAACCC
1 CTTAACCTCTAA-CTACTAACCC
*
52234702 CTTAACCCCTAACTACTAACCC
1 CTTAACCTCTAACTACTAACCC
*
52234724 CTAAACCT
1 CTTAACCT
52234732 TATTTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.31, C:0.42, G:0.02, T:0.25
Consensus pattern (22 bp):
CTTAACCTCTAACTACTAACCC
Found at i:52234963 original size:14 final size:15
Alignment explanation
Indices: 52234946--52234974 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52234936 AAACCAGAAC
52234946 CCCTAA-TCCATAAT
1 CCCTAATTCCATAAT
52234960 CCCTAATTCCATAAT
1 CCCTAATTCCATAAT
52234975 ATATAAACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (15 bp):
CCCTAATTCCATAAT
Found at i:52235439 original size:41 final size:41
Alignment explanation
Indices: 52235387--52235529 Score: 241
Period size: 41 Copynumber: 3.5 Consensus size: 41
52235377 CGGCACTTTT
* *
52235387 CAAAAACGCCGCTAAAGCACTGAGCATTAGCGGCGCTTTTC
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTC
*
52235428 CAAAATCGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTC
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTC
*
52235469 CAAAAACGCCGCTAAAGCCCGGAGCATTAGCGGCGCTTCTC
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTC
*
52235510 TAAAAACGCCGCTAAAGCCC
1 CAAAAACGCCGCTAAAGCCC
52235530 CGAAAGGTCA
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.29, C:0.33, G:0.22, T:0.17
Consensus pattern (41 bp):
CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCTC
Found at i:52235689 original size:40 final size:40
Alignment explanation
Indices: 52235645--52235723 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
52235635 GTGCTTTCCT
*
52235645 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTTTTG
1 TAAAGCGACGCTAATGCTCGATCTTTAGCGGCGTTTTTTG
*
52235685 TAAAGCGACGCTAATGCTCGATTTTTAGCGGCGTTTTTT
1 TAAAGCGACGCTAATGCTCGATCTTTAGCGGCGTTTTTT
52235724 ATCCAAGCGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (40 bp):
TAAAGCGACGCTAATGCTCGATCTTTAGCGGCGTTTTTTG
Found at i:52238832 original size:29 final size:29
Alignment explanation
Indices: 52238780--52238836 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
52238770 GTAGTTCCGG
* *
52238780 TGGTTTATCCATAAATTTGGGAGTTCTAA
1 TGGTTTATCCACAAATTTGAGAGTTCTAA
52238809 TGGTTTATCCACAAATATT-AGAGTTCTA
1 TGGTTTATCCACAAAT-TTGAGAGTTCTA
52238837 GCGGTATAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (29 bp):
TGGTTTATCCACAAATTTGAGAGTTCTAA
Found at i:52251880 original size:20 final size:21
Alignment explanation
Indices: 52251852--52251898 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
52251842 CAAGAGATGC
52251852 AATTATCATT-ATCACTCAAT
1 AATTATCATTCATCACTCAAT
*
52251872 AATTTTCATTCATCACTCAAT
1 AATTATCATTCATCACTCAAT
52251893 AATTAT
1 AATTAT
52251899 TTTCCAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTATCATTCATCACTCAAT
Found at i:52266685 original size:18 final size:19
Alignment explanation
Indices: 52266652--52266687 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52266642 TTCACTTCGA
*
52266652 TTTTTTCTTCTATTGTTTT
1 TTTTTTCATCTATTGTTTT
52266671 TTTTTTCATCT-TTGTTT
1 TTTTTTCATCTATTGTTT
52266688 CATACCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.06, C:0.11, G:0.06, T:0.78
Consensus pattern (19 bp):
TTTTTTCATCTATTGTTTT
Found at i:52267292 original size:3 final size:3
Alignment explanation
Indices: 52267284--52267315 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
52267274 TTATGTACTC
*
52267284 TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
52267316 GCCACGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:52267866 original size:24 final size:25
Alignment explanation
Indices: 52267839--52267914 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 25
52267829 ACATAGGTAC
52267839 ATATTTTA-ATTTACATACATATAT
1 ATATTTTATATTTACATACATATAT
* * * * *
52267863 ATA-TGTATATATACATTCTTACAT
1 ATATTTTATATTTACATACATATAT
52267887 ATATTTTTATATTT-CATA-ATATAT
1 ATA-TTTTATATTTACATACATATAT
52267911 ATAT
1 ATAT
52267915 GCACATATTC
Statistics
Matches: 39, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
23 4 0.10
24 25 0.64
25 3 0.08
26 7 0.18
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.51
Consensus pattern (25 bp):
ATATTTTATATTTACATACATATAT
Found at i:52271706 original size:3 final size:3
Alignment explanation
Indices: 52271691--52271732 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
52271681 TTTGCTATTC
* * *
52271691 TAT TAT TAA TAT TAT TAT TAT T-C TAT TAT TAA TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
52271733 TACTTATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:52271714 original size:23 final size:23
Alignment explanation
Indices: 52271686--52271732 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
52271676 GATTATTTGC
52271686 TATTCTATTATTAATATTATTAT
1 TATTCTATTATTAATATTATTAT
52271709 TATTCTATTATTAATATTATTAT
1 TATTCTATTATTAATATTATTAT
52271732 T
1 T
52271733 TACTTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTCTATTATTAATATTATTAT
Found at i:52271740 original size:23 final size:23
Alignment explanation
Indices: 52271689--52271740 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
52271679 TATTTGCTAT
*
52271689 TCTATTATTAATATTATTATTAT
1 TCTATTATTAATATTATTATTAC
52271712 TCTATTATTAATATTATTATTTAC
1 TCTATTATTAATATTATTA-TTAC
52271736 T-TATT
1 TCTATT
52271741 TATATCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.62
Consensus pattern (23 bp):
TCTATTATTAATATTATTATTAC
Found at i:52288088 original size:3 final size:3
Alignment explanation
Indices: 52288082--52288118 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
52288072 GTAAAAAAAC
52288082 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
52288119 GGAGATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52292021 original size:16 final size:17
Alignment explanation
Indices: 52291986--52292030 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
52291976 GCTATTCTGG
52291986 ACAGTTATTCTTCGAACA
1 ACAGTTATTCTTC-AACA
*
52292004 ACAGTTGTTCTT-AACA
1 ACAGTTATTCTTCAACA
*
52292020 ACAATTATTCT
1 ACAGTTATTCT
52292031 AAATAAGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
18 11 0.46
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (17 bp):
ACAGTTATTCTTCAACA
Found at i:52292866 original size:21 final size:22
Alignment explanation
Indices: 52292829--52292869 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
52292819 TCGATACATA
52292829 TTTTAAATGGATCTATTTTTTC
1 TTTTAAATGGATCTATTTTTTC
52292851 TTTT-AATGAGAT-TATTTTT
1 TTTTAAATG-GATCTATTTTT
52292870 CACTTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.61
Consensus pattern (22 bp):
TTTTAAATGGATCTATTTTTTC
Found at i:52299602 original size:21 final size:22
Alignment explanation
Indices: 52299573--52299613 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
52299563 GAACGAAAAA
52299573 TAAAGAGAAAAAAAAAGAAAGT
1 TAAAGAGAAAAAAAAAGAAAGT
* *
52299595 TAAA-AGAACATAAAAGAAA
1 TAAAGAGAAAAAAAAAGAAA
52299614 AAAATCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.73, C:0.02, G:0.15, T:0.10
Consensus pattern (22 bp):
TAAAGAGAAAAAAAAAGAAAGT
Found at i:52310158 original size:9 final size:9
Alignment explanation
Indices: 52310147--52310240 Score: 152
Period size: 9 Copynumber: 10.4 Consensus size: 9
52310137 TTTGGTTAAA
*
52310147 AATTAACCA
1 AATTAACCG
52310156 AATTAACCG
1 AATTAACCG
52310165 AATTAACCG
1 AATTAACCG
*
52310174 AATTACCCG
1 AATTAACCG
52310183 AATTAACCG
1 AATTAACCG
52310192 AATTAACCG
1 AATTAACCG
*
52310201 AATTACCCG
1 AATTAACCG
52310210 AATTAACCG
1 AATTAACCG
52310219 AATTAACCG
1 AATTAACCG
*
52310228 AATTAACCA
1 AATTAACCG
52310237 AATT
1 AATT
52310241 GAATCACTAC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 79 1.00
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:52311133 original size:14 final size:14
Alignment explanation
Indices: 52311114--52311140 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52311104 AAAAATTAAA
52311114 TAAAATAAAAATAT
1 TAAAATAAAAATAT
52311128 TAAAATAAAAATA
1 TAAAATAAAAATA
52311141 AAAAATGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAAATAAAAATAT
Found at i:52313114 original size:44 final size:42
Alignment explanation
Indices: 52313055--52313152 Score: 124
Period size: 44 Copynumber: 2.3 Consensus size: 42
52313045 ATACGTGATA
* * * * *
52313055 TCGTATAAGATCATGTTTGGGACGTTGGCATCGATTTAAGATT
1 TCGTGTAAGACCATGTTTGGGACATTAGCATCG-TATAAGATT
*
52313098 TACGTGTAAGACCATGTTTGGGACATTAGCATCGTATATGATT
1 T-CGTGTAAGACCATGTTTGGGACATTAGCATCGTATAAGATT
52313141 TCGTGTAAGACC
1 TCGTGTAAGACC
52313153 CTATCTGGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 11 0.23
43 9 0.19
44 28 0.58
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (42 bp):
TCGTGTAAGACCATGTTTGGGACATTAGCATCGTATAAGATT
Found at i:52313162 original size:42 final size:43
Alignment explanation
Indices: 52313094--52313174 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 43
52313084 ATCGATTTAA
* * *
52313094 GATTTACGTGTAAGACCATGTTTGGGACATTAGCATCGTATAT
1 GATTTACGTGTAAGACCATATCTGGGACAGTAGCATCGTATAT
* *
52313137 GATTT-CGTGTAAGACCCTATCTGGGACAGTGGCATCGT
1 GATTTACGTGTAAGACCATATCTGGGACAGTAGCATCGT
52313175 TATTTGAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
42 28 0.85
43 5 0.15
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
GATTTACGTGTAAGACCATATCTGGGACAGTAGCATCGTATAT
Found at i:52320134 original size:20 final size:21
Alignment explanation
Indices: 52320106--52320146 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52320096 ATTTTTTCAC
52320106 ATAAAAAAT-ATTTAAAATAA
1 ATAAAAAATAATTTAAAATAA
* *
52320126 ATAATAAATAATTTGAAATAA
1 ATAAAAAATAATTTAAAATAA
52320147 TTATTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAAAAAATAATTTAAAATAA
Found at i:52320795 original size:9 final size:9
Alignment explanation
Indices: 52320765--52320835 Score: 56
Period size: 9 Copynumber: 7.7 Consensus size: 9
52320755 TAATTTGTTC
52320765 ATTTTTAATA
1 ATTTTT-ATA
*
52320775 A-TTTTAGAA
1 ATTTTTA-TA
52320784 ATTTTTATA
1 ATTTTTATA
*
52320793 ATTCTTAATA
1 ATT-TTTATA
*
52320803 ATATTTA-A
1 ATTTTTATA
52320811 ATTTTCTATA
1 ATTTT-TATA
*
52320821 GTTTTTATA
1 ATTTTTATA
52320830 ATTTTT
1 ATTTTT
52320836 TAAAAAACCA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
8 6 0.12
9 24 0.50
10 18 0.38
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (9 bp):
ATTTTTATA
Found at i:52320801 original size:28 final size:26
Alignment explanation
Indices: 52320767--52320834 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
52320757 ATTTGTTCAT
52320767 TTTTAATAATTTTAGAAATTTT-TATAA
1 TTTTAATAATTTT--AAATTTTCTATAA
*
52320794 TTCTTAATAATATTTAAATTTTCTATAG
1 TT-TTAATAAT-TTTAAATTTTCTATAA
*
52320822 TTTTTATAATTTT
1 TTTTAATAATTTT
52320835 TTAAAAAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
26 3 0.08
27 16 0.44
28 14 0.39
29 3 0.08
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (26 bp):
TTTTAATAATTTTAAATTTTCTATAA
Found at i:52320838 original size:28 final size:27
Alignment explanation
Indices: 52320765--52320839 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
52320755 TAATTTGTTC
**
52320765 ATTTTTAATAATTTTAGAAATTTTTATA
1 ATTTTT-ATAATTTTTTAAATTTTTATA
* *
52320793 ATTCTTAATAA-TATTTAAATTTTCTATA
1 ATT-TTTATAATTTTTTAAATTTT-TATA
*
52320821 GTTTTTATAATTTTTTAAA
1 ATTTTTATAATTTTTTAAA
52320840 AAACCATGTC
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
27 15 0.41
28 20 0.54
29 2 0.05
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (27 bp):
ATTTTTATAATTTTTTAAATTTTTATA
Found at i:52322907 original size:25 final size:25
Alignment explanation
Indices: 52322876--52323030 Score: 129
Period size: 25 Copynumber: 6.3 Consensus size: 25
52322866 GCCCTCTTTC
*
52322876 GAGCCATATAACAGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGT
* * *
52322901 GAGCCATGTAATGGGAAGCTTATGT
1 GAGCCATATAACGGGAAGCTCATGT
* ** *
52322926 GAGCCATGTAACGGGAAGCTCCGGA
1 GAGCCATATAACGGGAAGCTCATGT
**
52322951 GAGCCAT-TAACGGGAAGCTCATAC
1 GAGCCATATAACGGGAAGCTCATGT
* * *
52322975 GAGCCA-ATAACGGGAAGGTTTAAGT
1 GAGCCATATAACGGGAA-GCTCATGT
* *
52323000 GAGCCAGTAT--CGGGAAGCTCAGGA
1 GAGCCA-TATAACGGGAAGCTCATGT
52323024 GAGCCAT
1 GAGCCAT
52323031 TAATCGATAA
Statistics
Matches: 104, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
23 1 0.01
24 38 0.37
25 63 0.61
27 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.31, T:0.18
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGT
Found at i:52323028 original size:73 final size:74
Alignment explanation
Indices: 52322876--52323033 Score: 203
Period size: 73 Copynumber: 2.1 Consensus size: 74
52322866 GCCCTCTTTC
** * * *
52322876 GAGCCATATAACAGGAAGCTCATGTGAGCCATGTAATGGGAAGCTTATGTGAGCCATGTAACGGG
1 GAGCCAT-TAACAGGAAGCTCATACGAGCCATATAACGGGAAGCTTAAGTGAGCCATGTAACGGG
*
52322941 AAGCTCCGGA
65 AAGCTCAGGA
* * *
52322951 GAGCCATTAACGGGAAGCTCATACGAGCCA-ATAACGGGAAGGTTTAAGTGAGCCA-GTATCGGG
1 GAGCCATTAACAGGAAGCTCATACGAGCCATATAACGGGAA-GCTTAAGTGAGCCATGTAACGGG
52323014 AAGCTCAGGA
65 AAGCTCAGGA
52323024 GAGCCATTAA
1 GAGCCATTAA
52323034 TCGATAAGTT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
73 34 0.47
74 32 0.44
75 7 0.10
ACGTcount: A:0.32, C:0.19, G:0.30, T:0.18
Consensus pattern (74 bp):
GAGCCATTAACAGGAAGCTCATACGAGCCATATAACGGGAAGCTTAAGTGAGCCATGTAACGGGA
AGCTCAGGA
Found at i:52323592 original size:10 final size:11
Alignment explanation
Indices: 52323570--52323598 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
52323560 GAATTAAATA
52323570 TCAATTCATAT
1 TCAATTCATAT
52323581 TCAATTCA-AT
1 TCAATTCATAT
52323591 TCAATTCA
1 TCAATTCA
52323599 CACCTTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (11 bp):
TCAATTCATAT
Found at i:52331291 original size:20 final size:20
Alignment explanation
Indices: 52331266--52331303 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52331256 AGGTAAACTT
52331266 TTCATATATTTATAATTTAA
1 TTCATATATTTATAATTTAA
* *
52331286 TTCATATGTTTTTAATTT
1 TTCATATATTTATAATTT
52331304 TAGAAATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (20 bp):
TTCATATATTTATAATTTAA
Found at i:52337431 original size:19 final size:18
Alignment explanation
Indices: 52337389--52337430 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
52337379 GTATCACTTC
**
52337389 TAAAAAGCACTTTTAGTA
1 TAAAAAGCACTTTTAACA
52337407 TAAAAAGCACTTTTAACA
1 TAAAAAGCACTTTTAACA
52337425 TAAAAA
1 TAAAAA
52337431 AAATATTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (18 bp):
TAAAAAGCACTTTTAACA
Found at i:52340171 original size:25 final size:26
Alignment explanation
Indices: 52340130--52340189 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
52340120 TTTAAAGTAC
* *
52340130 TTTTAAAATAATTTTTTTATTTTTTTA
1 TTTTAAAATAATTTTTTT-TATGTTTA
52340157 TTTTAAAATAA-TTTTTTTATGTTTA
1 TTTTAAAATAATTTTTTTTATGTTTA
52340182 TTTTAAAA
1 TTTTAAAA
52340190 ATGGGCTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 14 0.45
26 6 0.19
27 11 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTAAAATAATTTTTTTTATGTTTA
Found at i:52340191 original size:26 final size:26
Alignment explanation
Indices: 52340130--52340189 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 26
52340120 TTTAAAGTAC
*
52340130 TTTTAAAATAATTTTTTTATTTTTTTA
1 TTTTAAAATAATTTTTTTA-TTGTTTA
52340157 TTTTAAAATAATTTTTTTA-TGTTTA
1 TTTTAAAATAATTTTTTTATTGTTTA
52340182 TTTTAAAA
1 TTTTAAAA
52340190 ATGGGCTGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 13 0.41
27 19 0.59
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTAAAATAATTTTTTTATTGTTTA
Found at i:52341595 original size:26 final size:26
Alignment explanation
Indices: 52341563--52341628 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
52341553 AAACTAAAGC
*
52341563 AAATAAAATAAAAATTAGAAAGTA-AA
1 AAATAAAATAAAAATCA-AAAGTATAA
* * *
52341589 AATTAAACTAAAAA-CAAAATTATAA
1 AAATAAAATAAAAATCAAAAGTATAA
52341614 AAATAAAATAAAAAT
1 AAATAAAATAAAAAT
52341629 GGCTAAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 5 0.16
25 15 0.47
26 12 0.38
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (26 bp):
AAATAAAATAAAAATCAAAAGTATAA
Found at i:52344937 original size:23 final size:24
Alignment explanation
Indices: 52344910--52344962 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
52344900 TTATCAATTC
*
52344910 AAATATTATAA-TAAAATTTTTTT
1 AAATATTATAATTAAAATATTTTT
52344933 AAATA--ATAATTAAAATATTTTT
1 AAATATTATAATTAAAATATTTTT
52344955 AACATATT
1 AA-ATATT
52344963 CAGCATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 4 0.16
22 13 0.52
23 8 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATATTATAATTAAAATATTTTT
Found at i:52353219 original size:87 final size:87
Alignment explanation
Indices: 52353025--52353586 Score: 672
Period size: 87 Copynumber: 6.5 Consensus size: 87
52353015 ATGGAATAAA
* * * * *
52353025 GGCGGGAATAAAACCCGAAACAAATTTTATTTAATTTTAATTTCTCGTTTGGCAA-AAAATAAAA
1 GGCGAGAATAAAACCCGAAACAGATTTTATTTAATTTTAATTACTCTTTTGGAAACAAAATAAAA
*
52353089 AATGGAATAAAATCTATTGAAC
66 AATGGAATAAAATCTGTTGAAC
* * * * *
52353111 AGCGAGAATAAAACCTGAAACATATTTTATTTAATTTTAATTTCTCTTTTGGCAACAAAATAAAA
1 GGCGAGAATAAAACCCGAAACAGATTTTATTTAATTTTAATTACTCTTTTGGAAACAAAATAAAA
* * *
52353176 AATGGAATAAAGTCTATTTAAC
66 AATGGAATAAAATCTGTTGAAC
* * *
52353198 GGCGAGAATAAAACCCAAAACAGATTTTATTTAATTTTAATTTCTCGTTT-GACAACAAAATAAA
1 GGCGAGAATAAAACCCGAAACAGATTTTATTTAATTTTAATTACTCTTTTGGA-AACAAAATAAA
52353262 AAATGGAATAAAATCTGTTGAAC
65 AAATGGAATAAAATCTGTTGAAC
* * *
52353285 GGCGGGAATAAAACCCAAAATAGATTTTATTTAATTTTAA-TACT-TGTTTGGAAACAAAATAAA
1 GGCGAGAATAAAACCCGAAACAGATTTTATTTAATTTTAATTACTCT-TTTGGAAACAAAAT-AA
*
52353348 AAAATAGAATAAAATCTGTTGAAC
64 AAAATGGAATAAAATCTGTTGAAC
* * * * * * *
52353372 GAC-AGGAATAAACCCCGAAATAGATTTTATTTTAGTTTAA-TACTCATTTGGAAACAAAAGAAA
1 GGCGA-GAATAAAACCCGAAACAGATTTTATTTAATTTTAATTACTCTTTTGGAAACAAAA-TAA
52353435 AAAATGGAATAAAATCTGTTGAAC
64 AAAATGGAATAAAATCTGTTGAAC
* * * * *
52353459 GGGGGGAATAAATCTCGAAATAGAGTTTTATTTAATTTTAA-TACT-TGTTTGGAAACAAAATAA
1 GGCGAGAATAAAACCCGAAACAGA-TTTTATTTAATTTTAATTACTCT-TTTGGAAACAAAATAA
* *
52353522 AATATGAAATAAAATCTGTTGAAC
64 AAAATGGAATAAAATCTGTTGAAC
**
52353546 GGCGAGAATAAATGCCGAAACAGATTTTATTTAATTTTAAT
1 GGCGAGAATAAAACCCGAAACAGATTTTATTTAATTTTAAT
52353587 ATTTATTTTC
Statistics
Matches: 418, Mismatches: 46, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
86 81 0.19
87 306 0.73
88 31 0.07
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.31
Consensus pattern (87 bp):
GGCGAGAATAAAACCCGAAACAGATTTTATTTAATTTTAATTACTCTTTTGGAAACAAAATAAAA
AATGGAATAAAATCTGTTGAAC
Found at i:52353518 original size:261 final size:259
Alignment explanation
Indices: 52352850--52353587 Score: 732
Period size: 261 Copynumber: 2.9 Consensus size: 259
52352840 ATCAAGATCT
* * * * ** *
52352850 AATAAAATCTGTTAAAC-GACGAGAATAAATCTCGAAACAGA--TTATTCGA-TTTAATT-CTAA
1 AATAAAATCTATTGAACAG-CGAGAATAAAACCCGAAACAGATTTTATTTAAGTTTAATTACTCA
* ** * * * * * *
52352910 TTTAGAAAC-AAAATTAAAATTGAATAAATTCTATTAAACGGCGAGATTAAATCCCAGAACAGAT
65 TTTGGAAACAAAAAAAAAAATGGAATAAAATCTATTGAACGGCGAGAATAAAACCCAAAACAGAT
* * *
52352974 TTTATTTAATTTAAATTTCTCGTTTAGA-AA-AAAATAAAAAAATGGAAT---A-------AA-G
130 TTTATTTAATTTTAATTACTCGTTT-GACAACAAAAT-AAAAAATGAAATAAAATCTGTTGAACG
* * *
52353026 GCGGGAATAAAACCCGAAACAAATTTTATTTAATTTTAATTTCTCGTTTGGCAAAAAATAAAAAA
193 GCGGGAATAAAACCCGAAACAGATTTTATTTAATTTTAA-TACTCGTTTGGAAAAAAATAAAAAA
*
52353091 TGG
257 TAG
* * * * *
52353094 AATAAAATCTATTGAACAGCGAGAATAAAACCTGAAACATATTTTATTTAATTTTAATTTCTCTT
1 AATAAAATCTATTGAACAGCGAGAATAAAACCCGAAACAGATTTTATTTAAGTTTAATTACTCAT
* * * *
52353159 TTGGCAACAAAATAAAAAATGGAATAAAGTCTATTTAACGGCGAGAATAAAACCCAAAACAGATT
66 TTGGAAACAAAAAAAAAAATGGAATAAAATCTATTGAACGGCGAGAATAAAACCCAAAACAGATT
* *
52353224 TTATTTAATTTTAATTTCTCGTTTGACAACAAAATAAAAAATGGAATAAAATCTGTTGAACGGCG
131 TTATTTAATTTTAATTACTCGTTTGACAACAAAATAAAAAATGAAATAAAATCTGTTGAACGGCG
* * *
52353289 GGAATAAAACCCAAAATAGATTTTATTTAATTTTAATACTTGTTTGGAAACAAAATAAAAAAATA
196 GGAATAAAACCCGAAACAGATTTTATTTAATTTTAATACTCGTTTGGAAA-AAAAT-AAAAAATA
52353354 G
259 G
* * * *
52353355 AATAAAATCTGTTGAAC-GAC-AGGAATAAACCCCGAAATAGATTTTATTTTAGTTTAA-TACTC
1 AATAAAATCTATTGAACAG-CGA-GAATAAAACCCGAAACAGATTTTATTTAAGTTTAATTACTC
* * * * * * *
52353417 ATTTGGAAACAAAAGAAAAAAATGGAATAAAATCTGTTGAACGGGGGGAATAAATCTCGAAATAG
64 ATTTGGAAACAAAA-AAAAAAATGGAATAAAATCTATTGAACGGCGAGAATAAAACCCAAAACAG
* *
52353482 AGTTTTATTTAATTTTAA-TACTTGTTTGGA-AACAAAATAAAATATGAAATAAAATCTGTTGAA
128 A-TTTTATTTAATTTTAATTACTCGTTT-GACAACAAAATAAAAAATGAAATAAAATCTGTTGAA
* **
52353545 CGGCGAGAATAAATGCCGAAACAGATTTTATTTAATTTTAATA
191 CGGCGGGAATAAAACCCGAAACAGATTTTATTTAATTTTAATA
52353588 TTTATTTTCA
Statistics
Matches: 410, Mismatches: 58, Indels: 35
0.82 0.12 0.07
Matches are distributed among these distances:
244 33 0.08
245 1 0.00
246 6 0.01
247 7 0.02
248 11 0.03
249 84 0.20
250 5 0.01
252 1 0.00
259 13 0.03
260 60 0.15
261 171 0.42
262 18 0.04
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.31
Consensus pattern (259 bp):
AATAAAATCTATTGAACAGCGAGAATAAAACCCGAAACAGATTTTATTTAAGTTTAATTACTCAT
TTGGAAACAAAAAAAAAAATGGAATAAAATCTATTGAACGGCGAGAATAAAACCCAAAACAGATT
TTATTTAATTTTAATTACTCGTTTGACAACAAAATAAAAAATGAAATAAAATCTGTTGAACGGCG
GGAATAAAACCCGAAACAGATTTTATTTAATTTTAATACTCGTTTGGAAAAAAATAAAAAATAG
Found at i:52353739 original size:22 final size:22
Alignment explanation
Indices: 52353712--52353753 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
52353702 TTAGCGAACA
*
52353712 AAATATATAAATATAAATAAGC
1 AAATATATAAATAAAAATAAGC
* *
52353734 AAATATTTATATAAAAATAA
1 AAATATATAAATAAAAATAA
52353754 AATATAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATATATAAATAAAAATAAGC
Found at i:52354236 original size:20 final size:20
Alignment explanation
Indices: 52354213--52354254 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
52354203 TTAAATCTAT
*
52354213 TTGATTAAAATCAAATCAAA
1 TTGATTAAAATCAAATAAAA
*
52354233 TTGATTAGAATCAAATAAAA
1 TTGATTAAAATCAAATAAAA
52354253 TT
1 TT
52354255 AGGATACGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (20 bp):
TTGATTAAAATCAAATAAAA
Found at i:52361990 original size:23 final size:23
Alignment explanation
Indices: 52361943--52361991 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
52361933 ACCTACTTTC
* * * *
52361943 TTACTGTAGTAATTTTTGGGGTA
1 TTACAGTAGTAATTTTCGAGATA
52361966 TTACAGTAGTAATTTTCGAGATA
1 TTACAGTAGTAATTTTCGAGATA
52361989 TTA
1 TTA
52361992 TAAGATACGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGAGATA
Found at i:52367931 original size:5 final size:5
Alignment explanation
Indices: 52367923--52367966 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
52367913 TTTTTATAAT
52367923 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT
52367967 TTTTCATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:52370216 original size:10 final size:10
Alignment explanation
Indices: 52370201--52370302 Score: 84
Period size: 10 Copynumber: 10.4 Consensus size: 10
52370191 GGCATGTGGA
52370201 AAAAAATTAT
1 AAAAAATTAT
52370211 AAAAAA-TA-
1 AAAAAATTAT
*
52370219 AAAAAAATAT
1 AAAAAATTAT
52370229 AAAAAATTAT
1 AAAAAATTAT
* **
52370239 TAAATTTTAAT
1 AAAAAATT-AT
52370250 AAAAAATTAT
1 AAAAAATTAT
*
52370260 TAAAAATTAT
1 AAAAAATTAT
**
52370270 AAAATTTTAT
1 AAAAAATTAT
*
52370280 -AAAAATCAT
1 AAAAAATTAT
* *
52370289 AACAAATTCT
1 AAAAAATTAT
52370299 AAAA
1 AAAA
52370303 TGCATCAAAA
Statistics
Matches: 70, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
8 6 0.09
9 10 0.14
10 47 0.67
11 7 0.10
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:52370223 original size:18 final size:18
Alignment explanation
Indices: 52370200--52370235 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
52370190 TGGCATGTGG
*
52370200 AAAAAAATTATAAAAAAT
1 AAAAAAAATATAAAAAAT
52370218 AAAAAAAATATAAAAAAT
1 AAAAAAAATATAAAAAAT
52370236 TATTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAAAAAATATAAAAAAT
Found at i:52370254 original size:30 final size:30
Alignment explanation
Indices: 52370201--52370303 Score: 104
Period size: 31 Copynumber: 3.5 Consensus size: 30
52370191 GGCATGTGGA
** *
52370201 AAAAAATTATAAAA-AATA-AAAAAAATAT
1 AAAAAATTATAAAATTTTATAAAAAATTAT
*
52370229 AAAAAATTATTAAATTTTAATAAAAAATTAT
1 AAAAAATTATAAAATTTT-ATAAAAAATTAT
* *
52370260 TAAAAATTATAAAATTTTAT-AAAAATCAT
1 AAAAAATTATAAAATTTTATAAAAAATTAT
* *
52370289 AACAAATTCTAAAAT
1 AAAAAATTATAAAAT
52370304 GCATCAAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
28 13 0.21
29 21 0.34
30 3 0.05
31 25 0.40
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAAAATTATAAAATTTTATAAAAAATTAT
Found at i:52370588 original size:9 final size:9
Alignment explanation
Indices: 52370576--52370736 Score: 62
Period size: 9 Copynumber: 17.2 Consensus size: 9
52370566 TTTCTATATA
52370576 TTTTATAAT
1 TTTTATAAT
52370585 TTTT-TACACT
1 TTTTATA-A-T
*
52370595 TTTTATAAAA
1 TTTTAT-AAT
* *
52370605 TTTTACAGT
1 TTTTATAAT
52370614 TTTTAT-AT
1 TTTTATAAT
* *
52370622 TTTTTTACGAG
1 TTTTATA--AT
52370633 TTTTATAATTT
1 TTTTATAA--T
*
52370644 TTTTCTAA-
1 TTTTATAAT
*
52370652 TTTTAAATAT
1 TTTTATA-AT
52370662 TTTTATAA-
1 TTTTATAAT
*
52370670 TTTTATTAAAA
1 TTTTA-T-AAT
* *
52370681 TTTAACAAT
1 TTTTATAAT
52370690 TTTTATAAT
1 TTTTATAAT
*
52370699 TTTTATAAC
1 TTTTATAAT
*
52370708 TTTTATTGAT
1 TTTTA-TAAT
*
52370718 TTTTAT-TT
1 TTTTATAAT
*
52370726 TTTTATCAT
1 TTTTATAAT
52370735 TT
1 TT
52370737 CTCTGTCACA
Statistics
Matches: 112, Mismatches: 24, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
8 25 0.22
9 41 0.37
10 25 0.22
11 20 0.18
12 1 0.01
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:52370655 original size:28 final size:28
Alignment explanation
Indices: 52370624--52370702 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 28
52370614 TTTTATATTT
* * **
52370624 TTTTACGAGTTTTATAATTTTTTTCTAA
1 TTTTACAATTTTTATAATTTTTTTAAAA
* *
52370652 TTTTAAATATTTTTATAATTTTATTAAAA
1 TTTTACA-ATTTTTATAATTTTTTTAAAA
*
52370681 TTTAACAATTTTTATAATTTTT
1 TTTTACAATTTTTATAATTTTT
52370703 ATAACTTTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 19 0.46
29 22 0.54
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTTACAATTTTTATAATTTTTTTAAAA
Found at i:52370663 original size:20 final size:21
Alignment explanation
Indices: 52370618--52370665 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
52370608 TACAGTTTTT
* *
52370618 ATATTTTTTTACGAGTTTTAT
1 ATATTTTTTTACGAATTTTAA
*
52370639 A-ATTTTTTT-CTAATTTTAA
1 ATATTTTTTTACGAATTTTAA
52370658 ATATTTTT
1 ATATTTTT
52370666 ATAATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 8 0.35
20 14 0.61
21 1 0.04
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (21 bp):
ATATTTTTTTACGAATTTTAA
Found at i:52370702 original size:29 final size:30
Alignment explanation
Indices: 52370633--52370704 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 30
52370623 TTTTTACGAG
* *
52370633 TTTTATAATTTTT-TTCTAATTTTAAATAT
1 TTTTATAATTTTTATTCAAAATTTAAATAT
52370662 TTTTATAA-TTTTATT-AAAATTTAACA-AT
1 TTTTATAATTTTTATTCAAAATTTAA-ATAT
52370690 TTTTATAATTTTTAT
1 TTTTATAATTTTTAT
52370705 AACTTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 21 0.55
29 17 0.45
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTATAATTTTTATTCAAAATTTAAATAT
Found at i:52370703 original size:19 final size:19
Alignment explanation
Indices: 52370576--52370702 Score: 98
Period size: 19 Copynumber: 6.7 Consensus size: 19
52370566 TTTCTATATA
*
52370576 TTTTATAATTTTTTACACT
1 TTTTATAATTTTTTACAAT
** *
52370595 TTTTATAAAATTTTACAGT
1 TTTTATAATTTTTTACAAT
* * *
52370614 TTTTATATTTTTTTACGAG
1 TTTTATAATTTTTTACAAT
*
52370633 TTTTATAATTTTTTTCTAA-
1 TTTTATAATTTTTTAC-AAT
*
52370652 TTTTA-AATATTTTTATAA-
1 TTTTATAAT-TTTTTACAAT
** *
52370670 TTTTATTAAAATTTAACAAT
1 TTTTA-TAATTTTTTACAAT
52370690 TTTTATAATTTTT
1 TTTTATAATTTTT
52370703 ATAACTTTTA
Statistics
Matches: 83, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
18 10 0.12
19 65 0.78
20 8 0.10
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:52376618 original size:10 final size:11
Alignment explanation
Indices: 52376603--52376651 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 11
52376593 CAACCCAATT
52376603 TTTATTTTT-C
1 TTTATTTTTAC
*
52376613 TTTATTTTTAT
1 TTTATTTTTAC
52376624 TTTA-TTTTA-
1 TTTATTTTTAC
52376633 -TTATTTATTAC
1 TTTATTT-TTAC
52376644 TTTATTTT
1 TTTATTTT
52376652 ATTTGGATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
8 3 0.09
9 2 0.06
10 17 0.52
11 5 0.15
12 6 0.18
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTATTTTTAC
Found at i:52376621 original size:16 final size:16
Alignment explanation
Indices: 52376600--52376655 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 16
52376590 AGGCAACCCA
52376600 ATTTTTATTTT-TCTTT
1 ATTTTTATTTTAT-TTT
52376616 ATTTTTATTTTATTTT
1 ATTTTTATTTTATTTT
52376632 ATTATTTATTACTTTATTTT
1 ATT-TTTA-T--TTTATTTT
52376652 ATTT
1 ATTT
52376656 GGATATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 17 0.49
17 5 0.14
18 1 0.03
19 1 0.03
20 11 0.31
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTTATTTTATTTT
Found at i:52376647 original size:20 final size:19
Alignment explanation
Indices: 52376614--52376654 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
52376604 TTATTTTTCT
*
52376614 TTATTTTTATTTTATTTTA
1 TTATTTTTACTTTATTTTA
52376633 TTATTTATTACTTTATTTTA
1 TTATTT-TTACTTTATTTTA
52376653 TT
1 TT
52376655 TGGATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (19 bp):
TTATTTTTACTTTATTTTA
Found at i:52376829 original size:19 final size:19
Alignment explanation
Indices: 52376805--52376851 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
52376795 AAATATGCAT
52376805 CCAAACACCTACCCTATAG
1 CCAAACACCTACCCTATAG
*
52376824 CCAAACACCTACCTTATAG
1 CCAAACACCTACCCTATAG
52376843 CCAAACACC
1 CCAAACACC
52376852 CTTTCTTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.43, G:0.04, T:0.15
Consensus pattern (19 bp):
CCAAACACCTACCCTATAG
Found at i:52378008 original size:109 final size:111
Alignment explanation
Indices: 52377817--52378019 Score: 311
Period size: 109 Copynumber: 1.8 Consensus size: 111
52377807 CAAAAAAATT
* **
52377817 TTAGGAATACGTTGGGCTAATTAACTGGGGTAGGGTGATTGGTTGTCATCTCTCCTCGCGTCAAA
1 TTAGGAATACGTTGGGCTAAGTAACCAGGGTAGGGTGATTGGTTGTCATCTCTCCTCGCGTCAAA
52377882 AGGTTCAATATATTCTTAAG-AAA-AAAATATATAAATATAATAAA
66 AGGTTCAATATATTCTTAAGCAAAGAAAATATATAAATATAATAAA
* * * * * *
52377926 TTAGGAGTATGTTGGGCTGAGTAACCAGGGTGGGGTGATTGGTTGTCATTTCTCTTCGCGTCAAA
1 TTAGGAATACGTTGGGCTAAGTAACCAGGGTAGGGTGATTGGTTGTCATCTCTCCTCGCGTCAAA
52377991 AGGTTCAATATATTCTTAAGCAAAGAAAA
66 AGGTTCAATATATTCTTAAGCAAAGAAAA
52378020 ACATAAAAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
109 76 0.92
110 3 0.04
111 4 0.05
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (111 bp):
TTAGGAATACGTTGGGCTAAGTAACCAGGGTAGGGTGATTGGTTGTCATCTCTCCTCGCGTCAAA
AGGTTCAATATATTCTTAAGCAAAGAAAATATATAAATATAATAAA
Found at i:52381271 original size:10 final size:11
Alignment explanation
Indices: 52381248--52381273 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52381238 TTTAAAAACC
52381248 TTTTATTTATT
1 TTTTATTTATT
52381259 TTTTATTTATT
1 TTTTATTTATT
52381270 TTTT
1 TTTT
52381274 TCCTTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:52382520 original size:2 final size:2
Alignment explanation
Indices: 52382513--52382539 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52382503 AGGAGGAAAA
52382513 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
52382540 AAAGACAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52385513 original size:20 final size:20
Alignment explanation
Indices: 52385488--52385526 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
52385478 TGTTGAGCTT
*
52385488 ATTAATGAGTAATTTATATA
1 ATTAATGAATAATTTATATA
52385508 ATTAATGAATAATTTATAT
1 ATTAATGAATAATTTATAT
52385527 TTGAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
ATTAATGAATAATTTATATA
Found at i:52387250 original size:7 final size:7
Alignment explanation
Indices: 52387238--52387263 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52387228 AAACAGTTAT
52387238 AAAATCC
1 AAAATCC
52387245 AAAATCC
1 AAAATCC
52387252 AAAATCC
1 AAAATCC
52387259 AAAAT
1 AAAAT
52387264 TAAATAGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATCC
Found at i:52392208 original size:23 final size:23
Alignment explanation
Indices: 52392164--52392209 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
52392154 GGATAGTTAT
* *
52392164 ATATCAGGAAGTTCAAGCGAGCC
1 ATATCAGGAAGCTCAAGAGAGCC
52392187 ATATCAGGAAGCTCATA-AGAGCC
1 ATATCAGGAAGCTCA-AGAGAGCC
52392210 TTATATTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (23 bp):
ATATCAGGAAGCTCAAGAGAGCC
Found at i:52401633 original size:164 final size:164
Alignment explanation
Indices: 52401362--52401664 Score: 588
Period size: 164 Copynumber: 1.8 Consensus size: 164
52401352 ATAGATTTCA
*
52401362 TCTTCCCTAGGTATCTAGGGAATTTAGTTCATAATCCTGAATAGAAATATCTCAAAGTCAAAATA
1 TCTTCCCTAGGTATCTAGGGAATTTAGTTCATAATCCTGAATAGAAATATCTCAAAATCAAAATA
*
52401427 ACCACAATATATAAAGAAACTCAATAAAACTTCGAAAGAAATTAAAAGGAGATCTTTGATCTTAA
66 ACCACAATATACAAAGAAACTCAATAAAACTTCGAAAGAAATTAAAAGGAGATCTTTGATCTTAA
52401492 TGGAGATTCGCTTTCGAGTTGATTCCGATGGTGT
131 TGGAGATTCGCTTTCGAGTTGATTCCGATGGTGT
52401526 TCTTCCCTAGGTATCTAGGGAATTTAGTTCATAATCCTGAATAGAAATATCTCAAAATCAAAATA
1 TCTTCCCTAGGTATCTAGGGAATTTAGTTCATAATCCTGAATAGAAATATCTCAAAATCAAAATA
52401591 ACCACAATATACAAAGAAACTCAATAAAACTTCGAAAGAAATTAAAAGGAGATCTTTGATCTTAA
66 ACCACAATATACAAAGAAACTCAATAAAACTTCGAAAGAAATTAAAAGGAGATCTTTGATCTTAA
52401656 TGGAGATTC
131 TGGAGATTC
52401665 CCCTTTATGT
Statistics
Matches: 137, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 137 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (164 bp):
TCTTCCCTAGGTATCTAGGGAATTTAGTTCATAATCCTGAATAGAAATATCTCAAAATCAAAATA
ACCACAATATACAAAGAAACTCAATAAAACTTCGAAAGAAATTAAAAGGAGATCTTTGATCTTAA
TGGAGATTCGCTTTCGAGTTGATTCCGATGGTGT
Found at i:52406325 original size:7 final size:7
Alignment explanation
Indices: 52406288--52406382 Score: 54
Period size: 7 Copynumber: 13.7 Consensus size: 7
52406278 TGGTTTACTA
52406288 GTTTAGG
1 GTTTAGG
52406295 GTTT-GG
1 GTTTAGG
*
52406301 GTTTATG
1 GTTTAGG
*
52406308 GTTAAAGGG
1 GTT-TA-GG
52406317 GTTTAGG
1 GTTTAGG
*
52406324 G-TGATGG
1 GTTTA-GG
*
52406331 GTTT-GA
1 GTTTAGG
*
52406337 GTTTAAG
1 GTTTAGG
52406344 GTTT-GG
1 GTTTAGG
*
52406350 GCTTAGG
1 GTTTAGG
*
52406357 ATTTAGG
1 GTTTAGG
*
52406364 GTTTAGT
1 GTTTAGG
*
52406371 GTTTATG
1 GTTTAGG
52406378 GTTTA
1 GTTTA
52406383 ATATTTAGGG
Statistics
Matches: 64, Mismatches: 17, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
6 17 0.27
7 40 0.62
8 3 0.05
9 4 0.06
ACGTcount: A:0.17, C:0.01, G:0.38, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:52406375 original size:14 final size:14
Alignment explanation
Indices: 52406358--52406438 Score: 58
Period size: 14 Copynumber: 5.8 Consensus size: 14
52406348 GGGCTTAGGA
52406358 TTTAGGGTTTAGTG
1 TTTAGGGTTTAGTG
* * *
52406372 TTTATGGTTTAATA
1 TTTAGGGTTTAGTG
*
52406386 TTTAGGGTTGT-GTC
1 TTTAGGGTT-TAGTG
*
52406400 TTTAAGGTTTAGTG
1 TTTAGGGTTTAGTG
* *
52406414 ATTAGGCTTTTA-TG
1 TTTAGG-GTTTAGTG
*
52406428 TTTATGGTTTA
1 TTTAGGGTTTA
52406439 TGGTTTGAGA
Statistics
Matches: 50, Mismatches: 14, Indels: 7
0.70 0.20 0.10
Matches are distributed among these distances:
13 5 0.10
14 40 0.80
15 5 0.10
ACGTcount: A:0.19, C:0.02, G:0.26, T:0.53
Consensus pattern (14 bp):
TTTAGGGTTTAGTG
Found at i:52406393 original size:28 final size:29
Alignment explanation
Indices: 52406356--52406438 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 29
52406346 TTGGGCTTAG
52406356 GATTTAGGGTTTAGTGTTTATGGTTTAAT
1 GATTTAGGGTTTAGTGTTTATGGTTTAAT
* * *
52406385 -ATTTAGGGTTGT-GTCTTTAAGGTTTAGT
1 GATTTAGGGTT-TAGTGTTTATGGTTTAAT
*
52406413 GA-TTAGGCTTTTA-TGTTTATGGTTTA
1 GATTTAGG-GTTTAGTGTTTATGGTTTA
52406439 TGGTTTGAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
28 40 0.91
29 4 0.09
ACGTcount: A:0.19, C:0.02, G:0.27, T:0.52
Consensus pattern (29 bp):
GATTTAGGGTTTAGTGTTTATGGTTTAAT
Found at i:52406674 original size:7 final size:7
Alignment explanation
Indices: 52406651--52406744 Score: 52
Period size: 7 Copynumber: 13.6 Consensus size: 7
52406641 TGATTTTAGA
*
52406651 TTTAAGG
1 TTTATGG
*
52406658 TTAATGG
1 TTTATGG
52406665 TTTATGG
1 TTTATGG
52406672 TTTA-GG
1 TTTATGG
*
52406678 TTTAGGG
1 TTTATGG
*
52406685 TTGATGG
1 TTTATGG
52406692 -TTATGTG
1 TTTATG-G
*
52406699 ATTGA-GG
1 -TTTATGG
52406706 TTTTATGG
1 -TTTATGG
*
52406714 TTTATTG
1 TTTATGG
*
52406721 TTTATTG
1 TTTATGG
*
52406728 TTTA-AG
1 TTTATGG
*
52406734 TTTAGGG
1 TTTATGG
52406741 TTTA
1 TTTA
52406745 AGTGTTTAGG
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
6 15 0.22
7 49 0.71
8 3 0.04
9 2 0.03
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (7 bp):
TTTATGG
Found at i:52406678 original size:20 final size:20
Alignment explanation
Indices: 52406655--52406693 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52406645 TTTAGATTTA
* *
52406655 AGGTTAATGGTTTATGGTTT
1 AGGTTAAGGGTTGATGGTTT
*
52406675 AGGTTTAGGGTTGATGGTT
1 AGGTTAAGGGTTGATGGTT
52406694 ATGTGATTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (20 bp):
AGGTTAAGGGTTGATGGTTT
Found at i:52406852 original size:20 final size:20
Alignment explanation
Indices: 52406823--52406860 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52406813 TAAATTTATG
* *
52406823 GTTTATAGTTTTATGTTTAA
1 GTTTAGAGTTTTAGGTTTAA
52406843 GTTTAGAGTTTTAGGTTT
1 GTTTAGAGTTTTAGGTTT
52406861 TATGTTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.58
Consensus pattern (20 bp):
GTTTAGAGTTTTAGGTTTAA
Found at i:52406889 original size:28 final size:27
Alignment explanation
Indices: 52406831--52406890 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
52406821 TGGTTTATAG
** *
52406831 TTTTATGTTTAAGTTTAGAGTTTTAGG
1 TTTTATGTTTAAGTTTAGAGTTCGAGA
* *
52406858 TTTTATGTTTTAGATTTAGGGTTCGAGA
1 TTTTATGTTTAAG-TTTAGAGTTCGAGA
52406886 TTTTA
1 TTTTA
52406891 GATTTAAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.55
Consensus pattern (27 bp):
TTTTATGTTTAAGTTTAGAGTTCGAGA
Found at i:52406918 original size:7 final size:7
Alignment explanation
Indices: 52406906--52406931 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52406896 AAAGTTCATG
52406906 GTTTAAT
1 GTTTAAT
52406913 GTTTAAT
1 GTTTAAT
52406920 GTTTAAT
1 GTTTAAT
52406927 GTTTA
1 GTTTA
52406932 GAATTCAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTTTAAT
Found at i:52407627 original size:28 final size:28
Alignment explanation
Indices: 52407582--52407646 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
52407572 TGTGTTTAAG
* *
52407582 TTTAGGGTTTATGGTTTTAAT-TTAATTA
1 TTTAGGGTTTATGATTTTAATCTT-ATGA
*
52407610 TTTAGGGTTTGA-GATTTTAGTCTTATGA
1 TTTAGGGTTT-ATGATTTTAATCTTATGA
52407638 TTTAGGGTT
1 TTTAGGGTT
52407647 ATGGGTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.22, C:0.02, G:0.23, T:0.54
Consensus pattern (28 bp):
TTTAGGGTTTATGATTTTAATCTTATGA
Found at i:52407662 original size:19 final size:19
Alignment explanation
Indices: 52407638--52407674 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
52407628 AGTCTTATGA
52407638 TTTAGGGTTATG-GGTTCAG
1 TTTAGGGTT-TGTGGTTCAG
52407657 TTTAGGGTTTGTGGTTCA
1 TTTAGGGTTTGTGGTTCA
52407675 AGTTCTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.14, C:0.05, G:0.35, T:0.46
Consensus pattern (19 bp):
TTTAGGGTTTGTGGTTCAG
Found at i:52407849 original size:21 final size:22
Alignment explanation
Indices: 52407825--52407877 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
52407815 ATGTGTTCGA
52407825 GTTTAGGGTTTC-A-ATTTCTAG
1 GTTTAGGGTTTCGAGA-TTCTAG
*
52407846 GTTTTGGG-TTCGAGATTCTAG
1 GTTTAGGGTTTCGAGATTCTAG
*
52407867 GTTTAGTGTTT
1 GTTTAGGGTTT
52407878 GTGGTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.12
21 20 0.77
22 3 0.12
ACGTcount: A:0.15, C:0.08, G:0.28, T:0.49
Consensus pattern (22 bp):
GTTTAGGGTTTCGAGATTCTAG
Found at i:52408186 original size:14 final size:14
Alignment explanation
Indices: 52408167--52408196 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52408157 CCCAAAACCG
*
52408167 AATCTTGAACCTTA
1 AATCTTAAACCTTA
52408181 AATCTTAAACCTTA
1 AATCTTAAACCTTA
52408195 AA
1 AA
52408197 CTTTAGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.33
Consensus pattern (14 bp):
AATCTTAAACCTTA
Found at i:52408222 original size:14 final size:14
Alignment explanation
Indices: 52408203--52408247 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
52408193 TAAACTTTAG
52408203 GGTTTAGGGTTCAA
1 GGTTTAGGGTTCAA
* *
52408217 GGTTTAAGGTTCAT
1 GGTTTAGGGTTCAA
*
52408231 GGTTT-GAGTTCAA
1 GGTTTAGGGTTCAA
52408244 GGTT
1 GGTT
52408248 CAGGATTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (14 bp):
GGTTTAGGGTTCAA
Found at i:52412576 original size:26 final size:26
Alignment explanation
Indices: 52412543--52412595 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
52412533 AGCTTCTCAA
52412543 AGAATAATTT-AGGTCAATTTAACCTC
1 AGAATAATTTGA-GTCAATTTAACCTC
* *
52412569 AGAATAATTTGAGTTAGTTTAACCTC
1 AGAATAATTTGAGTCAATTTAACCTC
52412595 A
1 A
52412596 AATTGTGGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (26 bp):
AGAATAATTTGAGTCAATTTAACCTC
Found at i:52414073 original size:31 final size:32
Alignment explanation
Indices: 52414013--52414093 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
52414003 TTCGAGCTCT
***
52414013 AATCATTTTAAATTTTGGTTATTTAGAATT-A
1 AATCATTTTAAATTTAAATTATTTAGAATTCA
* *
52414044 AATCATTTTAAATTTAAATTGTTTTGAATTCA
1 AATCATTTTAAATTTAAATTATTTAGAATTCA
*
52414076 AATCAATTTTAAGTTTAA
1 AATC-ATTTTAAATTTAA
52414094 GTTGAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 25 0.60
32 5 0.12
33 12 0.29
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49
Consensus pattern (32 bp):
AATCATTTTAAATTTAAATTATTTAGAATTCA
Found at i:52416980 original size:9 final size:9
Alignment explanation
Indices: 52416966--52417019 Score: 56
Period size: 9 Copynumber: 5.7 Consensus size: 9
52416956 TGGTTTAAGG
52416966 TTTTTTATA
1 TTTTTTATA
52416975 TTTTTTA-A
1 TTTTTTATA
52416983 GTTTTTTCTATA
1 --TTTTT-TATA
52416995 TTTTTTATA
1 TTTTTTATA
*
52417004 CTTTTTATA
1 TTTTTTATA
52417013 CTTTTTT
1 -TTTTTT
52417020 GACTTGTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 1 0.03
9 19 0.50
10 15 0.39
11 2 0.05
12 1 0.03
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTTTATA
Found at i:52416983 original size:19 final size:20
Alignment explanation
Indices: 52416959--52417001 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
52416949 GGGTTTATGG
52416959 TTTAAGGTTTTT-TATATTT
1 TTTAAGGTTTTTCTATATTT
*
52416978 TTTAAGTTTTTTCTATATTT
1 TTTAAGGTTTTTCTATATTT
52416998 TTTA
1 TTTA
52417002 TACTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70
Consensus pattern (20 bp):
TTTAAGGTTTTTCTATATTT
Found at i:52417008 original size:20 final size:19
Alignment explanation
Indices: 52416959--52417019 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
52416949 GGGTTTATGG
*
52416959 TTTAAGGTTTTTTATATTT
1 TTTAAGCTTTTTTATATTT
*
52416978 TTTAAGTTTTTTCTATATTT
1 TTTAAGCTTTTT-TATATTT
52416998 TTTATA-C-TTTTTATACTTT
1 TTTA-AGCTTTTTTATA-TTT
52417017 TTT
1 TTT
52417020 GACTTGTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 4 0.11
19 21 0.57
20 11 0.30
21 1 0.03
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTAAGCTTTTTTATATTT
Found at i:52421609 original size:50 final size:50
Alignment explanation
Indices: 52421550--52421724 Score: 145
Period size: 50 Copynumber: 3.5 Consensus size: 50
52421540 ACAATTAAAA
52421550 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAAT
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAAT
* * * * *** * * * * **** *
52421600 AGATTGAAGCTACGACAGCGGGTCTGGTTTCCCT-GATATTGCAATTAAAG
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTACAGCGGAAT
* *
52421650 AGATTGAAGTCACAACGGTGGATCTTACTTCCTTAGCAGTACAGCGGAAT
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAAT
* * *
52421700 AGATTGAAGCTACGACGGCAGATCT
1 AGATTGAAGCCACAACGGCGGATCT
52421725 GGTTTCCCTG
Statistics
Matches: 84, Mismatches: 39, Indels: 4
0.66 0.31 0.03
Matches are distributed among these distances:
49 1 0.01
50 82 0.98
51 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAAT
Found at i:52421816 original size:100 final size:100
Alignment explanation
Indices: 52421541--52421817 Score: 394
Period size: 100 Copynumber: 2.8 Consensus size: 100
52421531 GAGCGGGTTA
*
52421541 CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
1 CAATTAAAAAGATTGAAGCCACAACGTCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
* * *
52421606 AAGCTACGACAGCGGGTCTGGTTTCCCTGATATTG
66 AAGCTACGACGGCAGATCTGGTTTCCCTGATATTG
* *
52421641 CAATTAAAGAGATTGAAGTCACAACGGT-GGATCTTACTTCCTTAGCAGTACAGCGGAATAGATT
1 CAATTAAAAAGATTGAAGCCACAAC-GTCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATT
*
52421705 GAAGCTACGACGGCAGATCTGGTTTCCCTGATATTT
65 GAAGCTACGACGGCAGATCTGGTTTCCCTGATATTG
* * * ** * * *
52421741 CAATTAAAAAGATTGAAGCCACAATGTCGAATCTTACTTCCTTGGTGGTATAGTGGAACAGATTG
1 CAATTAAAAAGATTGAAGCCACAACGTCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
*
52421806 ATGCTACGACGG
66 AAGCTACGACGG
52421818 TGAATCTTGT
Statistics
Matches: 157, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
99 2 0.01
100 154 0.98
101 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (100 bp):
CAATTAAAAAGATTGAAGCCACAACGTCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
AAGCTACGACGGCAGATCTGGTTTCCCTGATATTG
Found at i:52421830 original size:100 final size:99
Alignment explanation
Indices: 52421541--52421858 Score: 381
Period size: 100 Copynumber: 3.2 Consensus size: 99
52421531 GAGCGGGTTA
*
52421541 CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
1 CAATTAAAAAGATTGAAGCCACAACGTCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
* *
52421606 AAGCTACGACAGCGG-GTCTGGTTTCCCTGATATTG
66 AAGCTACGAC-G-GGAATCTGGTTTCCCTGATATTT
* *
52421641 CAATTAAAGAGATTGAAGTCACAACGGT-GGATCTTACTTCCTTAGCAGTACAGCGGAATAGATT
1 CAATTAAAAAGATTGAAGCCACAAC-GTCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATT
*
52421705 GAAGCTACGACGGCAGATCTGGTTTCCCTGATATTT
65 GAAGCTACGACGGGA-ATCTGGTTTCCCTGATATTT
* * * ** * * *
52421741 CAATTAAAAAGATTGAAGCCACAATGTCGAATCTTACTTCCTTGGTGGTATAGTGGAACAGATTG
1 CAATTAAAAAGATTGAAGCCACAACGTCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
* * * *
52421806 ATGCTACGACGGTGAATCTTGTTTCCCCGACA-TT
66 AAGCTACGACGG-GAATCTGGTTTCCCTGATATTT
* *
52421840 CTAGTTAAACAGATTGAAG
1 C-AATTAAAAAGATTGAAG
52421859 ATGGCGAATC
Statistics
Matches: 189, Mismatches: 23, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
98 1 0.01
99 6 0.03
100 180 0.95
101 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (99 bp):
CAATTAAAAAGATTGAAGCCACAACGTCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
AAGCTACGACGGGAATCTGGTTTCCCTGATATTT
Found at i:52424521 original size:50 final size:50
Alignment explanation
Indices: 52424462--52424636 Score: 145
Period size: 50 Copynumber: 3.5 Consensus size: 50
52424452 ACAATTAAAA
52424462 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAAT
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAAT
* * * * *** * * * * **** *
52424512 AGATTGAAGCTACGACAGCGGGTCTGGTTTCCCT-GATATTGCAATTAAAG
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTACAGCGGAAT
* *
52424562 AGATTGAAGTCACAACGGTGGATCTTACTTCCTTAGCAGTACAGCGGAAT
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAAT
* * *
52424612 AGATTGAAGCTACGACGGCAGATCT
1 AGATTGAAGCCACAACGGCGGATCT
52424637 GGTTTATTAG
Statistics
Matches: 84, Mismatches: 39, Indels: 4
0.66 0.31 0.03
Matches are distributed among these distances:
49 1 0.01
50 82 0.98
51 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAAT
Found at i:52424820 original size:50 final size:50
Alignment explanation
Indices: 52424761--52425029 Score: 191
Period size: 50 Copynumber: 5.4 Consensus size: 50
52424751 AAAAGTAAAA
*
52424761 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGTATTACAGCGGAAT
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGTATTACAGCGAAAT
* * * *** * * *** *
52424811 AGATTGAAGCTACGACAGCGGATCTGGTTTCCCT-GATATTGCAATTAAAG
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-TATTACAGCGAAAT
* * * *
52424861 ATATTGAAGCCACAACAGCGGATCTTACTTCCTTAGCAGTACAGCGAAAT
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGTATTACAGCGAAAT
* * * *** * * *** *
52424911 AGATTGAAGCTACGACGGCAGATCTGGTTTCCAT-GATATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-TATTACAGCGAAAT
* * * *
52424961 AGATTGAAGCCACAGCGGCGGATCTTACTTCCTTAGCAGTACAGCGGAAT
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGTATTACAGCGAAAT
* *
52425011 AGATTGAAGCTACGACGGC
1 AGATTGAAGCCACAACGGC
52425030 AAGATTGAAG
Statistics
Matches: 153, Mismatches: 62, Indels: 8
0.69 0.28 0.04
Matches are distributed among these distances:
49 2 0.01
50 149 0.97
51 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGTATTACAGCGAAAT
Found at i:52424886 original size:299 final size:298
Alignment explanation
Indices: 52424344--52424940 Score: 1068
Period size: 299 Copynumber: 2.0 Consensus size: 298
52424334 CATCCTAATC
* *
52424344 ATTAGGCATAATTAGGCTCATAAAGTGAGTCATATAGGTTATGTTCCACAGAGAGCAGATCGGTG
1 ATTAGGCATAATTAGGCTCATAAAGTGAGTCATACAGGTCATGTTCCACAGAGAGCAGATCGGTG
* * *
52424409 AAATCATAAAGCCTTGTCTCCCTGGGTAACAATGGAGCGGGTTACAATTAAAAAGATTGAAGCCA
66 AAATCATAAAGCCTTGTCTCCCTGAGTAACAATGGAGCGGGTTAAAAGTAAAAAGATTGAAGCCA
*
52424474 CAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTGAAGCTACGACAGCGGGTCTGG
131 CAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTGAAGCTACGACAGCGGATCTGG
* * *
52424539 TTTCCCTGATATTGCAATTAAAGAGATTGAAGTCACAACGGTGGATCTTACTTCCTTAGCAGTAC
196 TTTCCCTGATATTGCAATTAAAGAGATTGAAGCCACAACAGCGGATCTTACTTCCTTAGCAGTAC
*
52424604 AGCGGAATAGATTGAAGCTACGACGGCAGATCTGGTTT
261 AGCGAAATAGATTGAAGCTACGACGGCAGATCTGGTTT
52424642 ATTAGGCATAATTAGGCTCATAAAGTGAGTCATACAGGTCATGTTCCACAGAGAGCAGATCGGTG
1 ATTAGGCATAATTAGGCTCATAAAGTGAGTCATACAGGTCATGTTCCACAGAGAGCAGATCGGTG
52424707 AAATCATAAAGCCTTGTCTCCCTGAGTAACAATGGAGCGGGTTGAAAAGTAAAAAGATTGAAGCC
66 AAATCATAAAGCCTTGTCTCCCTGAGTAACAATGGAGCGGGTT-AAAAGTAAAAAGATTGAAGCC
* *
52424772 ACAACGGCGGATCTTACTTCCTTAGTATTACAGCGGAATAGATTGAAGCTACGACAGCGGATCTG
130 ACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTGAAGCTACGACAGCGGATCTG
*
52424837 GTTTCCCTGATATTGCAATTAAAGATATTGAAGCCACAACAGCGGATCTTACTTCCTTAGCAGTA
195 GTTTCCCTGATATTGCAATTAAAGAGATTGAAGCCACAACAGCGGATCTTACTTCCTTAGCAGTA
52424902 CAGCGAAATAGATTGAAGCTACGACGGCAGATCTGGTTT
260 CAGCGAAATAGATTGAAGCTACGACGGCAGATCTGGTTT
52424941 CCATGATATT
Statistics
Matches: 285, Mismatches: 13, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
298 105 0.37
299 180 0.63
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (298 bp):
ATTAGGCATAATTAGGCTCATAAAGTGAGTCATACAGGTCATGTTCCACAGAGAGCAGATCGGTG
AAATCATAAAGCCTTGTCTCCCTGAGTAACAATGGAGCGGGTTAAAAGTAAAAAGATTGAAGCCA
CAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTGAAGCTACGACAGCGGATCTGG
TTTCCCTGATATTGCAATTAAAGAGATTGAAGCCACAACAGCGGATCTTACTTCCTTAGCAGTAC
AGCGAAATAGATTGAAGCTACGACGGCAGATCTGGTTT
Found at i:52425027 original size:100 final size:100
Alignment explanation
Indices: 52424453--52425030 Score: 490
Period size: 100 Copynumber: 5.8 Consensus size: 100
52424443 GAGCGGGTTA
52424453 CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
1 CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
* * * *
52424518 AAGCTACGACAGCGGGTCTGGTTTCCCTGATATTG
66 AAGCTACGACGGCAGATCTGGTTTCCATGATATTG
* * *
52424553 CAATTAAAGAGATTGAAGTCACAACGGTGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
1 CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
** *
52424618 AAGCTACGACGGCAGATCTGGTTTATTAGGCATAATTAGG
66 AAGCTACGACGGCAGATCTGGTTT-CCATG-AT-ATT--G
* * * * * * * * * * *
52424658 C--TCATAAAG--TG-AGTCA-TAC--AGG-TCAT-GTTCC--A-CAG-AGAGCAG-ATCG-GTG
1 CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
* * * * * ** * **
52424707 AAATCATA--AAGCCTTGTCTCCCTGAGTAACAATGGAGCGGGTTG
66 -AAGC-TACGACGGC-AG-AT--CTG-GTTTCCAT-GA---TATTG
* * * *
52424751 AAAAGTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGTATTACAGCGGAATAGATT
1 -CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATT
* * *
52424816 GAAGCTACGACAGCGGATCTGGTTTCCCTGATATTG
65 GAAGCTACGACGGCAGATCTGGTTTCCATGATATTG
* * * *
52424852 CAATTAAAGATATTGAAGCCACAACAGCGGATCTTACTTCCTTAGCAGTACAGCGAAATAGATTG
1 CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
52424917 AAGCTACGACGGCAGATCTGGTTTCCATGATATTG
66 AAGCTACGACGGCAGATCTGGTTTCCATGATATTG
*
52424952 CAATTAAAAAGATTGAAGCCACAGCGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
1 CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
52425017 AAGCTACGACGGCA
66 AAGCTACGACGGCA
52425031 AGATTGAAGC
Statistics
Matches: 367, Mismatches: 76, Indels: 70
0.72 0.15 0.14
Matches are distributed among these distances:
89 5 0.01
90 7 0.02
91 8 0.02
92 3 0.01
93 7 0.02
94 3 0.01
95 6 0.02
96 8 0.02
97 2 0.01
98 2 0.01
99 6 0.02
100 253 0.69
101 6 0.02
102 4 0.01
103 11 0.03
104 6 0.02
105 6 0.02
106 4 0.01
107 1 0.00
108 8 0.02
109 7 0.02
110 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (100 bp):
CAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTG
AAGCTACGACGGCAGATCTGGTTTCCATGATATTG
Found at i:52425048 original size:20 final size:20
Alignment explanation
Indices: 52425011--52425049 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52425001 ACAGCGGAAT
* *
52425011 AGATTGAAGCTACGACGGCA
1 AGATTGAAGCCACAACGGCA
52425031 AGATTGAAGCCACAACGGC
1 AGATTGAAGCCACAACGGC
52425050 GGAACTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.23, G:0.28, T:0.13
Consensus pattern (20 bp):
AGATTGAAGCCACAACGGCA
Found at i:52425085 original size:70 final size:70
Alignment explanation
Indices: 52424960--52425099 Score: 226
Period size: 70 Copynumber: 2.0 Consensus size: 70
52424950 TGCAATTAAA
* * * *
52424960 AAGATTGAAGCCACAGCGGCGGATCTTACTTCCTTAGCAGTACAGCGGAATAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGGAACTTACTTCCTTAGCAGTACAACGGAACAGATTGAAGCTACG
52425025 ACGGC
66 ACGGC
* *
52425030 AAGATTGAAGCCACAACGGCGGAACTTACTTCCTTAGCAGTGCAATGGAACAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGGAACTTACTTCCTTAGCAGTACAACGGAACAGATTGAAGCTACG
52425095 ACGGC
66 ACGGC
52425100 GGATCTGGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.19
Consensus pattern (70 bp):
AAGATTGAAGCCACAACGGCGGAACTTACTTCCTTAGCAGTACAACGGAACAGATTGAAGCTACG
ACGGC
Found at i:52425124 original size:50 final size:50
Alignment explanation
Indices: 52425070--52425340 Score: 254
Period size: 50 Copynumber: 5.4 Consensus size: 50
52425060 TCCTTAGCAG
* *
52425070 TGCAATGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TGCAATGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACAT
** * * * *** * * *
52425120 TGCAATTAAAAAGATTGAAGCTACAACGGCAGATCTTACTTCCTTAGCAG
1 TGCAATGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACAT
*
52425170 TGCAATGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAATAT
1 TGCAATGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACAT
** * * * *** ** *
52425220 TGCAATTAAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCAG
1 TGCAA-TGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACAT
** * *
52425271 TGCGGTGGAACAGATTGAAGCTACGACGGCGGATCTAGTTTCCCCAACAT
1 TGCAATGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACAT
* *
52425321 TGCAATTGAACAAATTGAAG
1 TGCAATGGAACAGATTGAAG
52425341 ATTACAGATC
Statistics
Matches: 165, Mismatches: 55, Indels: 2
0.74 0.25 0.01
Matches are distributed among these distances:
50 129 0.78
51 36 0.22
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (50 bp):
TGCAATGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACAT
Found at i:52425157 original size:170 final size:170
Alignment explanation
Indices: 52424863--52425199 Score: 530
Period size: 170 Copynumber: 2.0 Consensus size: 170
52424853 AATTAAAGAT
* * *
52424863 ATTGAAGCCACAACAGCGGATCTTACTTCCTTAGCAGTACAGCGAAATAGATTGAAGCTACGACG
1 ATTGAAGCCACAACAGCGGAACTTACTTCCTTAGCAGTACAACGAAACAGATTGAAGCTACGACG
* *
52424928 GCAGATCTGGTTTCCATGATATTGCAATTAAAAAGATTGAAGCCACAGCGGCGGATCTTACTTCC
66 GCAGATCTGGTTTCCATGATATTGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCC
* *
52424993 TTAGCAGTACAGCGGAATAGATTGAAGCTACGACGGCAAG
131 TTAGCAGTACAACGGAACAGATTGAAGCTACGACGGCAAG
* * * *
52425033 ATTGAAGCCACAACGGCGGAACTTACTTCCTTAGCAGTGCAATGGAACAGATTGAAGCTACGACG
1 ATTGAAGCCACAACAGCGGAACTTACTTCCTTAGCAGTACAACGAAACAGATTGAAGCTACGACG
* * *
52425098 GCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCTACAACGGCAGATCTTACTTCC
66 GCAGATCTGGTTTCCATGATATTGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCC
* *
52425163 TTAGCAGTGCAATGGAACAGATTGAAGCTACGACGGC
131 TTAGCAGTACAACGGAACAGATTGAAGCTACGACGGC
52425200 GGATCTGGTT
Statistics
Matches: 151, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
170 151 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (170 bp):
ATTGAAGCCACAACAGCGGAACTTACTTCCTTAGCAGTACAACGAAACAGATTGAAGCTACGACG
GCAGATCTGGTTTCCATGATATTGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCC
TTAGCAGTACAACGGAACAGATTGAAGCTACGACGGCAAG
Found at i:52425203 original size:100 final size:101
Alignment explanation
Indices: 52425030--52425340 Score: 491
Period size: 100 Copynumber: 3.1 Consensus size: 101
52425020 CTACGACGGC
*
52425030 AAGATTGAAGCCACAACGGCGGAACTTACTTCCTTAGCAGTGCAATGGAACAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGGAACAGATTGAAGCTACG
*
52425095 ACGGCGGATCTGGTTTCCCTGATATTGCAATT-AAA
66 ACGGCGGATCTGGTTTCCCTAATATTGCAATTAAAA
* *
52425130 AAGATTGAAGCTACAACGGCAGATCTTACTTCCTTAGCAGTGCAATGGAACAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGGAACAGATTGAAGCTACG
52425195 ACGGCGGATCTGGTTTCCCTAATATTGCAATTAAAA
66 ACGGCGGATCTGGTTTCCCTAATATTGCAATTAAAA
* * **
52425231 AAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCAGTGCGGTGGAACAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGGAACAGATTGAAGCTACG
* * * * *
52425296 ACGGCGGATCTAGTTTCCCCAACATTGCAATTGAAC
66 ACGGCGGATCTGGTTTCCCTAATATTGCAATTAAAA
52425332 AA-ATTGAAG
1 AAGATTGAAG
52425341 ATTACAGATC
Statistics
Matches: 195, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
100 100 0.51
101 95 0.49
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (101 bp):
AAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGGAACAGATTGAAGCTACG
ACGGCGGATCTGGTTTCCCTAATATTGCAATTAAAA
Found at i:52425714 original size:44 final size:42
Alignment explanation
Indices: 52425570--52425719 Score: 117
Period size: 44 Copynumber: 3.4 Consensus size: 42
52425560 ATACAAGTCT
* * *
52425570 TATCTCCCTGAAGTTGCAGTAGAGCAGACAAAACTAATCAATCC
1 TATCTCCTTGAAGTTGCAGTGGAGCAGAC-AAA-TAACCAATCC
* ** * *
52425614 TATCTCCTTGAAGTTGCAATGGAGTGGATTAAA-ACCGCAGAT-C
1 TATCTCCTTGAAGTTGCAGTGGAGCAGA-CAAATAAC-CA-ATCC
*
52425657 TCAT-TTCTCTGAAGTTGCAGTGGAGCAGACAGAAGTAACCAATCC
1 T-ATCTCCT-TGAAGTTGCAGTGGAGCAGACA-AA-TAACCAATCC
52425702 TATCTCCTTGAAGTTGCA
1 TATCTCCTTGAAGTTGCA
52425720 ATGGTGTGGA
Statistics
Matches: 81, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
42 1 0.01
43 8 0.10
44 63 0.78
45 7 0.09
46 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (42 bp):
TATCTCCTTGAAGTTGCAGTGGAGCAGACAAATAACCAATCC
Found at i:52425790 original size:88 final size:87
Alignment explanation
Indices: 52425571--52425771 Score: 296
Period size: 88 Copynumber: 2.3 Consensus size: 87
52425561 TACAAGTCTT
* * * *
52425571 ATCTCCCTGAAGTTGCAGTAGAGCAGACAAAACTAATCAATCCTATCTCCTTGAAGTTGCAATGG
1 ATCTCTCTGAAGTTGCAGTAGAGCAGACAGAAGTAACCAATCCTATCTCCTTGAAGTTGCAATGG
*
52425636 AGTGGATTAAAACCGCAGATCTC
66 AGTGGATCAAAACCGCAGA-CTC
* *
52425659 ATTTCTCTGAAGTTGCAGTGGAGCAGACAGAAGTAACCAATCCTATCTCCTTGAAGTTGCAATGG
1 ATCTCTCTGAAGTTGCAGTAGAGCAGACAGAAGTAACCAATCCTATCTCCTTGAAGTTGCAATGG
* *
52425724 TGTGGATCAAAACTGCAGA-TC
66 AGTGGATCAAAACCGCAGACTC
*
52425745 ATCTCTCTGGAGTTGCAGTAGAGCAGA
1 ATCTCTCTGAAGTTGCAGTAGAGCAGA
52425772 TCGCATCAAG
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 26 0.26
88 75 0.74
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (87 bp):
ATCTCTCTGAAGTTGCAGTAGAGCAGACAGAAGTAACCAATCCTATCTCCTTGAAGTTGCAATGG
AGTGGATCAAAACCGCAGACTC
Found at i:52427439 original size:18 final size:18
Alignment explanation
Indices: 52427406--52427442 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
52427396 ATCTTTTTAT
52427406 CCTTCATATTTTTATATA
1 CCTTCATATTTTTATATA
52427424 CCTT-ATATTTTATATATA
1 CCTTCATATTTT-TATATA
52427442 C
1 C
52427443 GTATTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (18 bp):
CCTTCATATTTTTATATA
Found at i:52432472 original size:16 final size:16
Alignment explanation
Indices: 52432435--52432472 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
52432425 GCTCTAATCG
* *
52432435 TTTTAAATTTAGATTA
1 TTTTAAAGTTAAATTA
52432451 -TTTAAAGTTAAATTA
1 TTTTAAAGTTAAATTA
52432466 TTTTAAA
1 TTTTAAA
52432473 ATTATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
TTTTAAAGTTAAATTA
Found at i:52433374 original size:26 final size:28
Alignment explanation
Indices: 52433341--52433395 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
52433331 TAATGTAATG
52433341 ATTTTCAT-TATGATTTAATAT-AATAT
1 ATTTTCATATATGATTTAATATAAATAT
* *
52433367 ATTTTCATATATTATTTAATTTAAATAT
1 ATTTTCATATATGATTTAATATAAATAT
52433395 A
1 A
52433396 ATATAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.32
27 11 0.44
28 6 0.24
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (28 bp):
ATTTTCATATATGATTTAATATAAATAT
Found at i:52433929 original size:34 final size:34
Alignment explanation
Indices: 52433890--52433958 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
52433880 GTGGTTTATT
52433890 AGTCAAGTGTTTATTTTCTCAAAGAATAACTTAG
1 AGTCAAGTGTTTATTTTCTCAAAGAATAACTTAG
52433924 AGTCAAGTGTTTATTTTCTCAAAGAATAACTTAG
1 AGTCAAGTGTTTATTTTCTCAAAGAATAACTTAG
52433958 A
1 A
52433959 TTTGATTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (34 bp):
AGTCAAGTGTTTATTTTCTCAAAGAATAACTTAG
Found at i:52439555 original size:30 final size:30
Alignment explanation
Indices: 52439521--52439577 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
52439511 CGAGCTTTGA
52439521 GGCAAAAGTGTAAATATGCAAAAGTTTAGG
1 GGCAAAAGTGTAAATATGCAAAAGTTTAGG
* * * *
52439551 GGCAAAATTGTAATTTTGCCAAAGTTT
1 GGCAAAAGTGTAAATATGCAAAAGTTT
52439578 GAGTCAAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (30 bp):
GGCAAAAGTGTAAATATGCAAAAGTTTAGG
Found at i:52440219 original size:38 final size:37
Alignment explanation
Indices: 52440177--52440249 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
52440167 ATGTGTGGAA
* *
52440177 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
52440215 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
52440250 ATAATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:52442604 original size:15 final size:16
Alignment explanation
Indices: 52442579--52442608 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52442569 CCTAACTTGA
52442579 AGTTGAAAAAAAAATT
1 AGTTGAAAAAAAAATT
52442595 AGTT-AAAAAAAAAT
1 AGTTGAAAAAAAAAT
52442609 CATTTTTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (16 bp):
AGTTGAAAAAAAAATT
Found at i:52449599 original size:15 final size:14
Alignment explanation
Indices: 52449574--52449604 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
52449564 GAAACAAGAA
52449574 ATCTGTTTGATTTG
1 ATCTGTTTGATTTG
52449588 ATCTGATTTGATTTG
1 ATCTG-TTTGATTTG
52449603 AT
1 AT
52449605 TTTCTTTCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.55
Consensus pattern (14 bp):
ATCTGTTTGATTTG
Found at i:52456246 original size:18 final size:18
Alignment explanation
Indices: 52456219--52456257 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
52456209 TTCAGTTCCC
52456219 TTTTTCCTTTTTCCTTTT
1 TTTTTCCTTTTTCCTTTT
* *
52456237 TTTTTTCTTTTTTCTTTT
1 TTTTTCCTTTTTCCTTTT
52456255 TTT
1 TTT
52456258 AATGGAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTCCTTTTTCCTTTT
Found at i:52461176 original size:2 final size:2
Alignment explanation
Indices: 52461171--52461197 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52461161 ATATATATAT
52461171 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
52461198 ATGCACATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52462075 original size:209 final size:209
Alignment explanation
Indices: 52461715--52462140 Score: 843
Period size: 209 Copynumber: 2.0 Consensus size: 209
52461705 CTTTCTTTTT
52461715 TAAAAAATGGTCTGCTAGGGTTTCTTCAAAATTTTCTTTCTGCGCCGTCGCTCGTCGGCCTTTTG
1 TAAAAAATGGTCTGCTAGGGTTTCTTCAAAATTTTCTTTCTGCGCCGTCGCTCGTCGGCCTTTTG
52461780 AACCGGATCTCCGATTACGGCGGAGATAGTAGCAAACGGCGGCCCGAACACAGAGGTAAACTCCT
66 AACCGGATCTCCGATTACGGCGGAGATAGTAGCAAACGGCGGCCCGAACACAGAGGTAAACTCCT
52461845 CTTCGCTCTCTTCTCTTTATAAATCAACAATAAACATGAAAAAATAATGAACACTGGAAGAAAAA
131 CTTCGCTCTCTTCTCTTTATAAATCAACAATAAACATGAAAAAATAATGAACACTGGAAGAAAAA
52461910 GACCTTTATATTCA
196 GACCTTTATATTCA
52461924 TAAAAAATGGTCTGCTAGGGTTTCTTCAAAATTTTCTTTCTGCGCCGTCGCTCGTCGGCCTTTTG
1 TAAAAAATGGTCTGCTAGGGTTTCTTCAAAATTTTCTTTCTGCGCCGTCGCTCGTCGGCCTTTTG
52461989 AACCGGATCTCCGATTACGGCGGAGATAGTAGCAAACGGCGGCCCGAACACAGAGGTAAACTCCT
66 AACCGGATCTCCGATTACGGCGGAGATAGTAGCAAACGGCGGCCCGAACACAGAGGTAAACTCCT
52462054 CTTCGCTCTCTTCTCTTTATAAATCAACAATAAACATGAAAAAATAATGAACACTGGAAGAAAAA
131 CTTCGCTCTCTTCTCTTTATAAATCAACAATAAACATGAAAAAATAATGAACACTGGAAGAAAAA
52462119 GACCTTTATATTCA
196 GACCTTTATATTCA
*
52462133 AAAAAAAT
1 TAAAAAAT
52462141 TTGTATCTTT
Statistics
Matches: 216, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 216 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (209 bp):
TAAAAAATGGTCTGCTAGGGTTTCTTCAAAATTTTCTTTCTGCGCCGTCGCTCGTCGGCCTTTTG
AACCGGATCTCCGATTACGGCGGAGATAGTAGCAAACGGCGGCCCGAACACAGAGGTAAACTCCT
CTTCGCTCTCTTCTCTTTATAAATCAACAATAAACATGAAAAAATAATGAACACTGGAAGAAAAA
GACCTTTATATTCA
Found at i:52462868 original size:50 final size:50
Alignment explanation
Indices: 52462809--52463480 Score: 405
Period size: 50 Copynumber: 13.4 Consensus size: 50
52462799 GATAAGACTT
* * *
52462809 GTAGCTTCAATTTGTTCAACTGCAATGTTGGGGAAACCAGATCCGCCGTC
1 GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
* * * * *** *
52462859 GTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCGCCGTT
1 GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
* * * * * * *
52462909 GTGGTTTCAATCTTTTTAACTGTAATATCAGGGAAACCAGATCTGCCGTC
1 GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
* * * * *** *
52462959 GTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCGCCGTT
1 GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
* * * * * * *
52463009 GTGGTTTCAATCTTTTTAACTGTAATATCAGGGAAACCAGATCTGCCGTC
1 GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
* * * * *** *
52463059 GTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCGCCGTT
1 GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
* * * * * * *
52463109 GTGGTTTCAATCTTTTTAACTGTAATATCAGGGAAACCAGATCTGCCGTC
1 GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
* * * * *** *
52463159 GTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCGCCGTT
1 GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
* * * * * * *
52463209 GTGGTTTCAATCTTTTTAACTGTAATATCAGGGAAACCAGATCTGCCGTC
1 GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
* * * * * **** * ***
52463259 GTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAGGTAAGATCTGAAATC
1 GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
* * * **
52463309 TTTA-CTTCAATTTGTTCAACTGCAATGTGGGGGAAACCAGATCCGCCGTC
1 -GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
* * * * *** *
52463359 GTAGCTTCAATCTGTTCCACCG-CATCGTCAGGGAAGTAAGATCCGTCGAT-
1 GTAGCTTCAATCTGTTCAACTGTAAT-GTTAGGGAAACCAGATCCGCCG-TC
* * * * * * * *
52463409 GTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTT
1 GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
* *
52463459 GTAGCTTCAATCTATTCCACTG
1 GTAGCTTCAATCTGTTCAACTG
52463481 CACTGTTAAG
Statistics
Matches: 438, Mismatches: 178, Indels: 12
0.70 0.28 0.02
Matches are distributed among these distances:
49 5 0.01
50 428 0.98
51 5 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (50 bp):
GTAGCTTCAATCTGTTCAACTGTAATGTTAGGGAAACCAGATCCGCCGTC
Found at i:52463182 original size:200 final size:200
Alignment explanation
Indices: 52462839--52463787 Score: 1304
Period size: 200 Copynumber: 4.8 Consensus size: 200
52462829 TGCAATGTTG
52462839 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
52462904 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAA
66 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAA
* *
52462969 TCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGGTTTCAATCTTTTTAACTGTAA
131 TCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAACTGTAA
52463034 TATCA
196 TATCA
*
52463039 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
52463104 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAA
66 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAA
* *
52463169 TCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGGTTTCAATCTTTTTAACTGTAA
131 TCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAACTGTAA
52463234 TATCA
196 TATCA
* * * *
52463239 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAGGTAAGATCTG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
*** *** * * * ** *
52463304 AAATCT-TTACTTCAAT-TTGTTCAACTGCAATGTGGGGGAAACCAGATCCGCCGTCGTAGCTTC
66 CCGT-TGTGGTTTCAATCTT-TTTAACTGTAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTC
* * * * *
52463367 AATCTGTTCCACCGCA-T-CGTCAGGGAAGTAAGATCCGTCGATGTGGCTTCAATCTTTTTAATT
129 AATCTGTTCCACTGCACTGC-T-AAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAACT
*
52463430 GCAATATCA
192 GTAATATCA
* * * *
52463439 GGGAAACCAGATCCGCCGTTGTAGCTTCAATCTATTCCACTGCACTGTTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
* * * *********** *
52463504 CCATTGTGGCTTCTATC-------CT-T--T-T---NNNNNNNNNNNCCGCCGTCGTAGCTTCAA
66 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAA
*
52463555 TCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGTAA
131 TCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAACTGTAA
52463620 TATCA
196 TATCA
52463625 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
52463690 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAA
66 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAA
*
52463755 TCTGTTCCACTGCACTGCTAAGGAGGTAAGATC
131 TCTGTTCCACTGCACTGCTAAGGAAGTAAGATC
52463788 TGAAATCTTT
Statistics
Matches: 655, Mismatches: 72, Indels: 44
0.85 0.09 0.06
Matches are distributed among these distances:
186 153 0.23
187 2 0.00
188 1 0.00
189 1 0.00
190 1 0.00
193 4 0.01
194 1 0.00
196 1 0.00
197 1 0.00
198 1 0.00
199 5 0.01
200 483 0.74
201 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.30
Consensus pattern (200 bp):
GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAA
TCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAACTGTAA
TATCA
Found at i:52463516 original size:100 final size:100
Alignment explanation
Indices: 52462839--52463512 Score: 1014
Period size: 100 Copynumber: 6.7 Consensus size: 100
52462829 TGCAATGTTG
*
52462839 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
52462904 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCA
66 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCA
52462939 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
52463004 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCA
66 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCA
52463039 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
52463104 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCA
66 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCA
52463139 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
52463204 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCA
66 CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCA
* * *
52463239 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAGGTAAGATCTG
1 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
*** *** * * * **
52463304 AAATCT-TTACTTCAAT-TTGTTCAACTGCAATGTGG
66 CCGT-TGTGGTTTCAATCTT-TTTAACTGTAATATCA
* * * *
52463339 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCA-T-CGTCAGGGAAGTAAGATC
1 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGC-T-AAGGAAGTAAGATC
* * * * *
52463402 CGTCGATGTGGCTTCAATCTTTTTAATTGCAATATCA
64 CGCCGTTGTGGTTTCAATCTTTTTAACTGTAATATCA
* * * * *
52463439 GGGAAACCAGATCCGCCGTTGTAGCTTCAATCTATTCCACTGCACTGTTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
*
52463504 CCATTGTGG
66 CCGTTGTGG
52463513 CTTCTATCCT
Statistics
Matches: 527, Mismatches: 39, Indels: 16
0.91 0.07 0.03
Matches are distributed among these distances:
98 1 0.00
99 5 0.01
100 516 0.98
101 5 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (100 bp):
GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCG
CCGTTGTGGTTTCAATCTTTTTAACTGTAATATCA
Found at i:52463710 original size:100 final size:100
Alignment explanation
Indices: 52463537--52463787 Score: 457
Period size: 100 Copynumber: 2.5 Consensus size: 100
52463527 NNNNNNNNNN
52463537 CCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTT
1 CCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTT
*
52463602 CAATCTTTTTAATTGTAATATCAGGGAAACCAGAT
66 CAATCTTTTTAACTGTAATATCAGGGAAACCAGAT
* *
52463637 CCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGGTTT
1 CCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTT
52463702 CAATCTTTTTAACTGTAATATCAGGGAAACCAGAT
66 CAATCTTTTTAACTGTAATATCAGGGAAACCAGAT
* *
52463737 CTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAGGTAAGATC
1 CCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATC
52463788 TGAAATCTTT
Statistics
Matches: 145, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 145 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (100 bp):
CCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTT
CAATCTTTTTAACTGTAATATCAGGGAAACCAGAT
Found at i:52463789 original size:50 final size:50
Alignment explanation
Indices: 52463537--52463787 Score: 195
Period size: 50 Copynumber: 5.0 Consensus size: 50
52463527 NNNNNNNNNN
* *
52463537 CCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGAT
1 CCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAGGTAAGAT
* * * ** * * * * **
52463587 CCGCCGTTGTGGCTTCAATCTTTTTAATTGTAAT-ATCAGG-GAAACCAGAT
1 CCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAGGTA--AGAT
*
52463637 CCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAAGTAAGAT
1 CCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAGGTAAGAT
* * * * ** * * * **
52463687 CCGCCGTTGTGGTTTCAATCTTTTTAACTGTAAT-ATCAGG-GAAACCAGAT
1 CCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAGGTA--AGAT
* *
52463737 CTGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAGGTAAGAT
1 CCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAGGTAAGAT
52463787 C
1 C
52463788 TGAAATCTTT
Statistics
Matches: 143, Mismatches: 50, Indels: 16
0.68 0.24 0.08
Matches are distributed among these distances:
48 2 0.01
49 8 0.06
50 122 0.85
51 8 0.06
52 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (50 bp):
CCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAGGTAAGAT
Found at i:52463953 original size:132 final size:132
Alignment explanation
Indices: 52463782--52465730 Score: 2785
Period size: 132 Copynumber: 14.9 Consensus size: 132
52463772 CTAAGGAGGT
* *
52463782 AAGATCTGAAATCTTTAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
* * *
52463847 CTCCACTGCAACTACAGGGAAGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
52463912 AC
131 AC
* *
52463914 AAGATCTGAAATCTTCAATCTATTCCGCTACTGTTCAGGGAAGTAGAATTACTGGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
* * * *
52463979 CTCCACTGTAACCATAAGAAGGTAAAATCTGCCATCTTTGATCTACTCCACTACTGCTTAGGGAG
66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
52464044 AC
131 AC
*
52464046 AAGATCTGAAATCCTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
* * * * *
52464111 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATATTTGATCTGATTCGCTACTGCTTAGGGAA
66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
52464176 AC
131 AC
*
52464178 AAGATCTGAAATCTTCAATCTATTCTGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
* * *
52464243 CTCCACTGCAACTACAGGGAAGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
52464308 AC
131 AC
* *
52464310 AAGATCTGAAATCTTCAATCTATTCCGCTACTGTTCAGGGAAGTAGAATTACTGGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
* * * *
52464375 CTCCACTGTAACCATAAGAAGGTAAAATCTGCCATCTTTGATCTACTCCACTACTGCTTAGGGAG
66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
52464440 AC
131 AC
*
52464442 AAGATCTGAAATCCTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
* * * * *
52464507 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATATTTGATCTGATTCGCTACTGCTTAGGGAA
66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
52464572 AC
131 AC
*
52464574 AAGATCTGAAATCTTCAATCTATTCTGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
* * * *
52464639 CTCTACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCTACTACCGGTTAGGGAG
66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
52464704 AC
131 AC
* * * * *
52464706 AATATCTGAAATCTTCAATCTATTCTGCTACTATCCAGAGAAGTAGAATTACTGGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
* * * *
52464771 CTCCACTGTAACCATAGGGAGGTAAAATCTGCCATATTTGATCTGCTCCGCTACTGCTTAGGGAA
66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
52464836 AC
131 AC
* ** *
52464838 AAGATCTGAAATCTTCAATCTATTCCGCTGTTGTCCAGAAAAGTAGAATTACTAGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
52464903 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
52464968 AC
131 AC
* * * * *
52464970 AAGATCTGAAATCTTGAATCTATTCTGCTGCTATCTAGAGAAGTAGAATTACTGGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
*
52465035 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCGTCTTTGATCTGCTTCGCTATCTA-TGC--AG
66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGC-TC-C-A-CTACTGCTTAG
*
52465097 GAAGAC
127 GGAGAC
** * * *
52465103 AAGATCCAAAATCTTCAGTCTATTCCACTGCTGCCCAGGG-AGATAGAATTACTGGCTTCAATGT
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAG-TAGAATTACTGGCTTCAATGT
* * * * * * * *
52465167 ACTTCACTGTAACCTCAGGGAGGTAAAATCTGCCGTCTTTGATATGCTTCGCTA-T-C-TATGCA
65 ACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGA
52465229 GA-
130 GAC
* * * *
52465231 AAGA-C---AA-----GA-CTATTCCACTGCTGCCCAGGG-AGATAGAATTGCTGGCTTCAATGT
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAG-TAGAATTACTGGCTTCAATGT
* * * *
52465285 ACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTATTGCTTAGGGA
65 ACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGA
52465350 GAC
130 GAC
* * * *
52465353 AAGATCTGAAATCTTCAATATATTCTGCTGCTATCCAGAGAAGTAGAATTACTGGCTTCAATGTA
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
* *
52465418 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATATTTGATTTGCTCCACTACTGCTTAGGGAG
66 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
52465483 AC
131 AC
* * *
52465485 AAGATCTGAAATCCTCAATCTATTCCACTGCTG-CCTAGGG-AGATAAAATTACTGGCTTCAATG
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCC-AGGGAAG-TAGAATTACTGGCTTCAATG
* *
52465548 TACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATATTTGATTTGCTCCACTACTGCTTAGGG
64 TACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGG
52465613 AGAC
129 AGAC
* * *
52465617 AAGATCTGAAATCCTCAATCTATTCCACTGCTG-CCTAGGG-AGATAAAATTACTGGCTTCAATG
1 AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCC-AGGGAAG-TAGAATTACTGGCTTCAATG
*
52465680 TACTCCACTGTAACCACAGGGAGGTAAAAT-TCGTCATCTTTGATCTGCTCC
64 TACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCATCTTTGATCTGCTCC
52465731 GCTGTCTATG
Statistics
Matches: 1642, Mismatches: 151, Indels: 48
0.89 0.08 0.03
Matches are distributed among these distances:
118 91 0.06
119 1 0.00
120 1 0.00
121 6 0.00
122 4 0.00
123 1 0.00
124 2 0.00
126 2 0.00
127 1 0.00
128 5 0.00
129 9 0.01
131 7 0.00
132 1398 0.85
133 106 0.06
134 1 0.00
135 4 0.00
136 3 0.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (132 bp):
AAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTA
CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
AC
Done.