Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 186 of 190
Found at i:55414125 original size:60 final size:60
Alignment explanation
Indices: 55413984--55414126 Score: 155
Period size: 60 Copynumber: 2.4 Consensus size: 60
55413974 GTAGTCACAC
* ** * * * *
55413984 AACTATTAGTAAATAATTTTTTTGATCATTCAACTATGAAAAGTTATAAAATGGTGATCT
1 AACTATTCGTAAATTTTTTTTTTGATCATTCAACTATGAAAAGTCACAAAATGGTCATCA
* * *
55414044 AACTATTCGTAAATTTATTTTTTGGTCA-TCTAACTATGGAAAGTCACAAAATGGTCATCA
1 AACTATTCGTAAATTTTTTTTTTGATCATTC-AACTATGAAAAGTCACAAAATGGTCATCA
**
55414104 AACTATTCG-ATTTTTTTTTTTTG
1 AACTATTCGTAAATTTTTTTTTTG
55414127 TCACCAATTG
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 13 0.19
60 56 0.81
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (60 bp):
AACTATTCGTAAATTTTTTTTTTGATCATTCAACTATGAAAAGTCACAAAATGGTCATCA
Found at i:55419770 original size:5 final size:5
Alignment explanation
Indices: 55419760--55419786 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
55419750 TTGCTTAAGT
55419760 ATTAG ATTAG ATTAG ATTAG ATTAG AT
1 ATTAG ATTAG ATTAG ATTAG ATTAG AT
55419787 ATCAAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTAG
Found at i:55421170 original size:6 final size:6
Alignment explanation
Indices: 55421159--55421187 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
55421149 TAAAAGCTAA
55421159 ATCGCC ATCGCC ATCGCC ATCGCC ATCGC
1 ATCGCC ATCGCC ATCGCC ATCGCC ATCGC
55421188 ATACGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.48, G:0.17, T:0.17
Consensus pattern (6 bp):
ATCGCC
Found at i:55421897 original size:30 final size:30
Alignment explanation
Indices: 55421833--55421900 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 30
55421823 ATTAATAATT
*
55421833 TATA-AAAATTAGATCAAATTAAAATTTCA
1 TATATAAAATTAGATCAAAATAAAATTTCA
*
55421862 T-TATAAAATTATA-CAAAATAAAATTT-A
1 TATATAAAATTAGATCAAAATAAAATTTCA
*
55421889 TATATATAATTA
1 TATATAAAATTA
55421901 CGCATTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 2 0.06
28 23 0.68
29 9 0.26
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (30 bp):
TATATAAAATTAGATCAAAATAAAATTTCA
Found at i:55424645 original size:25 final size:25
Alignment explanation
Indices: 55424611--55424660 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
55424601 CATATTCCAC
55424611 CACCTACTTAAAAATAACAAATTAA
1 CACCTACTTAAAAATAACAAATTAA
*
55424636 CACCTACTTAAAAATAATAAATTAA
1 CACCTACTTAAAAATAACAAATTAA
55424661 TCTCGTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (25 bp):
CACCTACTTAAAAATAACAAATTAA
Found at i:55431721 original size:2 final size:2
Alignment explanation
Indices: 55431714--55431738 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55431704 AAATGGCTTC
55431714 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
55431739 GGACCAGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55433795 original size:7 final size:7
Alignment explanation
Indices: 55433783--55433809 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
55433773 TTGTAGATTA
55433783 TTTATAT
1 TTTATAT
55433790 TTTATAT
1 TTTATAT
55433797 TTTATAT
1 TTTATAT
55433804 TTTATA
1 TTTATA
55433810 AAATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTATAT
Found at i:55434679 original size:52 final size:52
Alignment explanation
Indices: 55434620--55434886 Score: 228
Period size: 52 Copynumber: 5.1 Consensus size: 52
55434610 TTTTTAAGTT
* * * *
55434620 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATATATA
1 TATATATATAATTATTATCTTTATGATCTATATATTTATTAACTTATATATA
* * *
55434672 TATATATGTACATATATATATTATACTTTCT-ATAC-ATAT-TTTA-TAATTTCTATATA
1 TATATA--T--ATA-AT-TATTAT-CTTTATGAT-CTATATATTTATTAACTTATATATA
* *
55434728 TATATATATAATCATTATCTTTATGATCTATATATTTATTACCTTATATATA
1 TATATATATAATTATTATCTTTATGATCTATATATTTATTAACTTATATATA
* * * *
55434780 TGTACGTATAT-ATATATTATACTTTCT-ATAC-ATAT-TTTA-TAATTTCTATATA
1 TATA--TATATAAT-TATTAT-CTTTATGAT-CTATATATTTATTAACTTATATATA
*
55434832 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATA
1 TATATATATAATTATTATCTTTATGATCTATATATTTATTAACTTATATATA
55434884 TAT
1 TAT
55434887 GTACGTATAT
Statistics
Matches: 170, Mismatches: 23, Indels: 44
0.72 0.10 0.19
Matches are distributed among these distances:
49 12 0.07
50 27 0.16
51 12 0.07
52 49 0.29
53 6 0.04
54 18 0.11
55 6 0.04
56 18 0.11
57 6 0.04
58 12 0.07
59 4 0.02
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (52 bp):
TATATATATAATTATTATCTTTATGATCTATATATTTATTAACTTATATATA
Found at i:55434710 original size:20 final size:20
Alignment explanation
Indices: 55434687--55434841 Score: 68
Period size: 20 Copynumber: 7.5 Consensus size: 20
55434677 ATGTACATAT
55434687 ATATATTATACTTTCTATAC
1 ATATATTATACTTTCTATAC
* * *
55434707 ATATTTTATAATTTCTATAT
1 ATATATTATACTTTCTATAC
* *
55434727 ATATATATATAATCATTATCTTTATG
1 ATATAT-TAT-A-C-TT-TCTATA-C
* *
55434753 ATCTA-TATA-TTTAT-TAC
1 ATATATTATACTTTCTATAC
* * *
55434770 CT-TATATATA-TGTACGTATAT
1 ATATAT-TATACT-TTC-TATAC
55434791 ATATATTATACTTTCTATAC
1 ATATATTATACTTTCTATAC
* * *
55434811 ATATTTTATAATTTCTATAT
1 ATATATTATACTTTCTATAC
55434831 ATATATATATA
1 ATATAT-TATA
55434842 ATCATTATCT
Statistics
Matches: 100, Mismatches: 21, Indels: 27
0.68 0.14 0.18
Matches are distributed among these distances:
16 2 0.02
17 1 0.01
18 7 0.07
19 3 0.03
20 51 0.51
21 16 0.16
22 5 0.05
23 1 0.01
24 5 0.05
25 5 0.05
26 4 0.04
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATATTATACTTTCTATAC
Found at i:55434733 original size:56 final size:54
Alignment explanation
Indices: 55434666--55434942 Score: 238
Period size: 54 Copynumber: 5.2 Consensus size: 54
55434656 TATTACCTTA
55434666 TATATATATATATGTACATATATATATTATACTTTCTATACATATTTTATAATTTC
1 TATATATATATATGTA-ATATATATATTATACTTTCTAT-CATATTTTATAATTTC
* * * * **
55434722 TATATATATATATATAATCAT-TATCTT-TA-TGATCTAT-ATA-TTTATTACCT-
1 TATATATATATATGTAAT-ATATATATTATACT-TTCTATCATATTTTATAATTTC
* *
55434772 TATATATATGTACGT-ATATATATATTATACTTTCTATACATATTTTATAATTTC
1 TATATATATATATGTAATATATATATTATACTTTCTAT-CATATTTTATAATTTC
* * * * *
55434826 TATATATATATATATAATCAT-TATCTT-TA-TGATCTAT-ATA-TTTATTAACTTA
1 TATATATATATATGTAAT-ATATATATTATACT-TTCTATCATATTTTA-TAATTTC
* *
55434878 TATATATATGTACGT-ATATATATATTATACTTTCTATCCATATTTTATAATTTC
1 TATATATATATATGTAATATATATATTATACTTTCTAT-CATATTTTATAATTTC
*
55434932 TATATGTATAT
1 TATATATATAT
55434943 TTTTCTTTAT
Statistics
Matches: 172, Mismatches: 30, Indels: 40
0.71 0.12 0.17
Matches are distributed among these distances:
48 2 0.01
49 7 0.04
50 21 0.12
51 19 0.11
52 33 0.19
53 10 0.06
54 43 0.25
55 18 0.10
56 19 0.11
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (54 bp):
TATATATATATATGTAATATATATATTATACTTTCTATCATATTTTATAATTTC
Found at i:55434737 original size:50 final size:49
Alignment explanation
Indices: 55434672--55434942 Score: 244
Period size: 50 Copynumber: 5.2 Consensus size: 49
55434662 CTTATATATA
* *
55434672 TATATATGTACATATATATATTATACTTTCTATACATATTTTATAATTTC
1 TATATATATATATATATATATTATACTTTCTAT-CATATTTTATAATTTC
* ** *
55434722 TATATATATATATATA-ATCATTAT-CTTTATGATCTATATATTTATTACCTTA
1 TATATATATATATATATAT-ATTATACTTTCT-ATC-ATAT-TTTA-TAATTTC
*
55434774 TATATATGTACGTATATATATATTATACTTTCTATACATATTTTATAATTTC
1 TATATATATA--TATATATATATTATACTTTCTAT-CATATTTTATAATTTC
* *
55434826 TATATATATATATATA-ATCATTAT-CTTTATGATCTATATATTTATTAACTTATA
1 TATATATATATATATATAT-ATTATACTTTCT-ATC-ATAT-TTTA-TAA-TT-TC
*
55434880 TATATATGTACGTATATATATATTATACTTTCTATCCATATTTTATAATTTC
1 TATATATATA--TATATATATATTATACTTTCTAT-CATATTTTATAATTTC
*
55434932 TATATGTATAT
1 TATATATATAT
55434943 TTTTCTTTAT
Statistics
Matches: 180, Mismatches: 19, Indels: 44
0.74 0.08 0.18
Matches are distributed among these distances:
49 16 0.09
50 43 0.24
51 8 0.04
52 38 0.21
53 8 0.04
54 30 0.17
55 12 0.07
56 17 0.09
57 8 0.04
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (49 bp):
TATATATATATATATATATATTATACTTTCTATCATATTTTATAATTTC
Found at i:55434745 original size:108 final size:106
Alignment explanation
Indices: 55434620--55434942 Score: 533
Period size: 104 Copynumber: 3.0 Consensus size: 106
55434610 TTTTTAAGTT
* * * * * *
55434620 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATATATATATATATGTACAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTACCTTATATATATATGTACGT--AT
55434685 ATATATATTATACTTTCTATACATATTTTATAATTTCTATATA
64 ATATATATTATACTTTCTATACATATTTTATAATTTCTATATA
55434728 TATATATATAATCATTATCTTTATGATCTATATATTTATTACC-T-TATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTACCTTATATATATATGTACGTATAT
55434791 ATATATTATACTTTCTATACATATTTTATAATTTCTATATA
66 ATATATTATACTTTCTATACATATTTTATAATTTCTATATA
*
55434832 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTACCTTATATATATATGTACGTATAT
* *
55434897 ATATATTATACTTTCTATCCATATTTTATAATTTCTATATG
66 ATATATTATACTTTCTATACATATTTTATAATTTCTATATA
55434938 TATAT
1 TATAT
55434943 TTTTCTTTAT
Statistics
Matches: 204, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
104 87 0.43
105 1 0.00
106 76 0.37
107 1 0.00
108 39 0.19
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (106 bp):
TATATATATAATCATTATCTTTATGATCTATATATTTATTACCTTATATATATATGTACGTATAT
ATATATTATACTTTCTATACATATTTTATAATTTCTATATA
Found at i:55434758 original size:54 final size:51
Alignment explanation
Indices: 55434700--55434942 Score: 182
Period size: 52 Copynumber: 4.6 Consensus size: 51
55434690 TATTATACTT
55434700 TCTATACATATTTTATAATTTCTATATATATATATATAATCATTATCTTTATGA
1 TCTAT-CATATTTTATAATTTCTATATATATATATATAAT-ATTATCTTTAT-A
** * * *
55434754 TCTAT-ATA-TTTATTACCTTATATATATGTACGTATATATATATTATACTTTCTA
1 TCTATCATATTTTA-TAATTTCTATATATATA--TATATA-ATATTAT-CTTTATA
55434808 --TA-CATATTTTATAATTTCTATATATATATATATAATCATTATCTTTATGA
1 TCTATCATATTTTATAATTTCTATATATATATATATAAT-ATTATCTTTAT-A
* * *
55434858 TCTAT-ATA-TTTATTAACTTATATATATATGTACGTATATATATATTATACTTTCTA
1 TCTATCATATTTTA-TAA-TT-TCTATATATATA--TATATA-ATATTAT-CTTTATA
*
55434914 TC---CATATTTTATAATTTCTATATGTATAT
1 TCTATCATATTTTATAATTTCTATATATATAT
55434943 TTTTCTTTAT
Statistics
Matches: 152, Mismatches: 16, Indels: 46
0.71 0.07 0.21
Matches are distributed among these distances:
49 7 0.05
50 13 0.09
51 8 0.05
52 51 0.34
53 8 0.05
54 33 0.22
55 11 0.07
56 14 0.09
57 7 0.05
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.52
Consensus pattern (51 bp):
TCTATCATATTTTATAATTTCTATATATATATATATAATATTATCTTTATA
Found at i:55434881 original size:16 final size:16
Alignment explanation
Indices: 55434860--55434909 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
55434850 CTTTATGATC
*
55434860 TATATATTTATTAACT
1 TATATATATATTAACT
*
55434876 TATATATATATGT-ACG
1 TATATATATAT-TAACT
55434892 TATATATATATTATACT
1 TATATATATATTA-ACT
55434909 T
1 T
55434910 TCTATCCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 1 0.04
16 23 0.82
17 4 0.14
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (16 bp):
TATATATATATTAACT
Found at i:55434920 original size:20 final size:20
Alignment explanation
Indices: 55434897--55434934 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55434887 GTACGTATAT
*
55434897 ATATATTATACTTTCTATCC
1 ATATATTATAATTTCTATCC
*
55434917 ATATTTTATAATTTCTAT
1 ATATATTATAATTTCTAT
55434935 ATGTATATTT
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:0.13, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATTATAATTTCTATCC
Found at i:55434995 original size:23 final size:21
Alignment explanation
Indices: 55434971--55435013 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
55434961 ATGTATTATA
55434971 TATATAAATTTTATATTTTTT
1 TATATAAATTTTATATTTTTT
55434992 TATATAAATTTTATATTTTTT
1 TATATAAATTTTATATTTTTT
55435013 T
1 T
55435014 CCATAATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATATAAATTTTATATTTTTT
Found at i:55435019 original size:21 final size:21
Alignment explanation
Indices: 55434974--55435019 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
55434964 TATTATATAT
*
55434974 ATAAATTTTATATTTTTTTAT
1 ATAAATTTTATATTTTTTTAC
*
55434995 ATAAATTTTATATTTTTTTCC
1 ATAAATTTTATATTTTTTTAC
55435016 ATAA
1 ATAA
55435020 TTTCAATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
ATAAATTTTATATTTTTTTAC
Found at i:55444430 original size:19 final size:20
Alignment explanation
Indices: 55444387--55444432 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
55444377 AAAAATAATT
55444387 TAAAATTATTAAAATATTCA
1 TAAAATTATTAAAATATTCA
*
55444407 AAAAATTA-TAAAA-ATGTCA
1 TAAAATTATTAAAATAT-TCA
55444426 TAAAATT
1 TAAAATT
55444433 CAAAACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.61
20 7 0.30
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAAATTATTAAAATATTCA
Found at i:55445843 original size:24 final size:24
Alignment explanation
Indices: 55445797--55445843 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
55445787 TAACTGGAAC
* *
55445797 AAAAATTCAAGCATCAAATTGAAA
1 AAAAATTCAAACATCAAAGTGAAA
* *
55445821 AAAAATTCAAATATTAAAGTGAA
1 AAAAATTCAAACATCAAAGTGAA
55445844 CATTAAAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (24 bp):
AAAAATTCAAACATCAAAGTGAAA
Found at i:55462029 original size:20 final size:20
Alignment explanation
Indices: 55462004--55462061 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
55461994 ATAAAATATA
55462004 AAAAAAT-CTAAAAAATTTTC
1 AAAAAATAC-AAAAAATTTTC
* *
55462024 AAAAAATACCATAAAGTTTTC
1 AAAAAATA-CAAAAAATTTTC
* *
55462045 CAAAAATGCAAAAAATT
1 AAAAAATACAAAAAATT
55462062 CTAAAATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 14 0.47
21 15 0.50
22 1 0.03
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAAAATACAAAAAATTTTC
Found at i:55463777 original size:55 final size:55
Alignment explanation
Indices: 55463703--55463813 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
55463693 AAAATCCAAT
55463703 TATGAACCCAGTTTTCCAAGCCTATTCCTAGTGCAGGTGGAGAGCTCCAAAGGGA
1 TATGAACCCAGTTTTCCAAGCCTATTCCTAGTGCAGGTGGAGAGCTCCAAAGGGA
55463758 TATGAACCCAGTTTTCCAAGCCTATTCCTAGTGCAGGTGGAGAGCTCCAAAGGGA
1 TATGAACCCAGTTTTCCAAGCCTATTCCTAGTGCAGGTGGAGAGCTCCAAAGGGA
55463813 T
1 T
55463814 CGCATTGATC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.24
Consensus pattern (55 bp):
TATGAACCCAGTTTTCCAAGCCTATTCCTAGTGCAGGTGGAGAGCTCCAAAGGGA
Found at i:55464859 original size:2 final size:2
Alignment explanation
Indices: 55464852--55464886 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
55464842 ATATTATAAA
55464852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55464887 GGATGTACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55473410 original size:12 final size:12
Alignment explanation
Indices: 55473391--55473421 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
55473381 TAATAATAAA
55473391 TATTTTATTTTT
1 TATTTTATTTTT
*
55473403 TTTTTTATTTTT
1 TATTTTATTTTT
55473415 TATTTTA
1 TATTTTA
55473422 AAATACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TATTTTATTTTT
Found at i:55473439 original size:26 final size:26
Alignment explanation
Indices: 55473410--55473460 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
55473400 TTTTTTTTTA
55473410 TTTTTT-ATTTTAAAATACTTTTTAAT
1 TTTTTTAATTTTAAAATA-TTTTTAAT
55473436 TTTTTTAATTTTAAAATATTTTTAA
1 TTTTTTAATTTTAAAATATTTTTAA
55473461 AATACTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTTTAATTTTAAAATATTTTTAAT
Found at i:55473460 original size:11 final size:11
Alignment explanation
Indices: 55473444--55473483 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
55473434 ATTTTTTTAA
55473444 TTTTAAAATAT
1 TTTTAAAATAT
55473455 TTTTAAAATACT
1 TTTTAAAATA-T
* *
55473467 TTGTAAAATTT
1 TTTTAAAATAT
55473478 TTTTAA
1 TTTTAA
55473484 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:55473492 original size:40 final size:37
Alignment explanation
Indices: 55473415--55473508 Score: 134
Period size: 40 Copynumber: 2.5 Consensus size: 37
55473405 TTTTATTTTT
* *
55473415 TATTTTAAAATACTTTTTAATTTTTTTAATTTTAAAA
1 TATTTTAAAATACTTTTAAATTTTTTTAATTTAAAAA
55473452 TATTTTTAAAATACTTTGTAAAATTTTTTTAATTTAAAAA
1 TA-TTTTAAAATACTTT-T-AAATTTTTTTAATTTAAAAA
*
55473492 TATTTTAAAATAATTTT
1 TATTTTAAAATACTTTT
55473509 TTTATTTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
37 2 0.04
38 15 0.29
39 14 0.27
40 20 0.39
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (37 bp):
TATTTTAAAATACTTTTAAATTTTTTTAATTTAAAAA
Found at i:55473508 original size:29 final size:29
Alignment explanation
Indices: 55473459--55473519 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
55473449 AAATATTTTT
55473459 AAAATACTTTGTAAAATTTTTTTAATTTA
1 AAAATACTTTGTAAAATTTTTTTAATTTA
* ** *
55473488 AAAATATTTTAAAATAATTTTTTTATTTTA
1 AAAATACTTTGTAA-AATTTTTTTAATTTA
55473518 AA
1 AA
55473520 TAATTTTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
AAAATACTTTGTAAAATTTTTTTAATTTA
Found at i:55473522 original size:18 final size:19
Alignment explanation
Indices: 55473492--55473527 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
55473482 AATTTAAAAA
55473492 TATTTTAAAATAATTTTTT
1 TATTTTAAAATAATTTTTT
55473511 TATTTT-AAATAATTTTT
1 TATTTTAAAATAATTTTT
55473528 GGTTGGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTTAAAATAATTTTTT
Found at i:55474105 original size:18 final size:18
Alignment explanation
Indices: 55474084--55474118 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55474074 TAAAACATTA
55474084 TAAAATAAAAAAATTAAT
1 TAAAATAAAAAAATTAAT
* *
55474102 TAAAATGATAAAATTAA
1 TAAAATAAAAAAATTAA
55474119 AGTTTTGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
TAAAATAAAAAAATTAAT
Found at i:55481834 original size:41 final size:37
Alignment explanation
Indices: 55481780--55481914 Score: 119
Period size: 40 Copynumber: 3.5 Consensus size: 37
55481770 GACTTCGATT
*
55481780 CGATGAGACACTGGGTGTCAATTTACTACTTCAGATTAATT
1 CGATGAGACACTGGGTGTCAA-TTA-TACTTC-GATT-ATC
* * * * *
55481821 CGATGAGGCACTGGATGCCAATT-TACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAATTATACTTC-GATTATC
*
55481858 CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
1 CGATGAGACACTGGGTGTC-AATTA-TACTTCG-ATTATC
*
55481898 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
55481915 CCAAACTGGT
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
37 17 0.22
38 13 0.17
39 1 0.01
40 27 0.36
41 18 0.24
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (37 bp):
CGATGAGACACTGGGTGTCAATTATACTTCGATTATC
Found at i:55484115 original size:8 final size:8
Alignment explanation
Indices: 55484112--55484142 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
55484102 TATATTGTTA
55484112 TATTATAT
1 TATTATAT
55484120 TATTATAT
1 TATTATAT
55484128 TATTATAT
1 TATTATAT
55484136 TATTATA
1 TATTATA
55484143 ATAAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTATAT
Found at i:55484250 original size:26 final size:27
Alignment explanation
Indices: 55484195--55484251 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
55484185 AACAGAGAGC
* *
55484195 AAAACGAAAACAGGGGAGAAAGGAAAG
1 AAAAAGAAAACAGGGAAGAAAGGAAAG
*
55484222 AAAAAGAAAA-AGGGAAGGAAA-GAAGG
1 AAAAAGAAAACAGGGAA-GAAAGGAAAG
55484248 AAAA
1 AAAA
55484252 TTTGGGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.65, C:0.04, G:0.32, T:0.00
Consensus pattern (27 bp):
AAAAAGAAAACAGGGAAGAAAGGAAAG
Found at i:55485443 original size:41 final size:37
Alignment explanation
Indices: 55485395--55485494 Score: 92
Period size: 41 Copynumber: 2.6 Consensus size: 37
55485385 TCGACCTCGA
55485395 GTCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA-AC--TTACTTCGGATAG
* ** ** * *
55485435 ATTCGATGAGGTACTGGGTACCAACTTACTTCGGCTTG
1 -GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
*
55485473 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
55485495 CTTTATTGCT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
37 16 0.35
38 11 0.24
40 2 0.04
41 17 0.37
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (37 bp):
GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
Found at i:55490329 original size:12 final size:12
Alignment explanation
Indices: 55490314--55490338 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55490304 AATTGAGCCG
55490314 TAAATATTTTTA
1 TAAATATTTTTA
55490326 TAAATATTTTTA
1 TAAATATTTTTA
55490338 T
1 T
55490339 GAACGTCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAATATTTTTA
Found at i:55494488 original size:21 final size:21
Alignment explanation
Indices: 55494464--55494509 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
55494454 TTAAGTGTTA
55494464 TAATTCATTGCTTCTTAATTG
1 TAATTCATTGCTTCTTAATTG
55494485 TAATTCATTGCTTCTTAATTG
1 TAATTCATTGCTTCTTAATTG
55494506 -AATT
1 TAATT
55494510 TGATTCTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (21 bp):
TAATTCATTGCTTCTTAATTG
Found at i:55498683 original size:17 final size:17
Alignment explanation
Indices: 55498654--55498695 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
55498644 AAAGCCCGTT
*
55498654 TATAATGTTTTATATTA
1 TATAATTTTTTATATTA
*
55498671 TATTATTTTTTATATTA
1 TATAATTTTTTATATTA
55498688 TATAATTT
1 TATAATTT
55498696 ATAACATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:55499531 original size:19 final size:20
Alignment explanation
Indices: 55499509--55499547 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
55499499 ATTTAGTTCA
55499509 TTTTATTT-TATTTTTCTTG
1 TTTTATTTATATTTTTCTTG
55499528 TTTTATTTAATATTTTTCTT
1 TTTTATTT-ATATTTTTCTT
55499548 TTTCCGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTTATTTATATTTTTCTTG
Found at i:55510091 original size:21 final size:22
Alignment explanation
Indices: 55510067--55510108 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
55510057 CTCGAGGGTC
* *
55510067 AAAGTGATA-AAAATTAAAATT
1 AAAGTGACAGAAAATAAAAATT
55510088 AAAGTGACAGAAAATAAAAAT
1 AAAGTGACAGAAAATAAAAAT
55510109 AAACATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.21
Consensus pattern (22 bp):
AAAGTGACAGAAAATAAAAATT
Found at i:55510111 original size:21 final size:21
Alignment explanation
Indices: 55510067--55510111 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
55510057 CTCGAGGGTC
* *
55510067 AAAGTGATAAAAATTAAAATT
1 AAAGTGACAAAAATTAAAAAT
55510088 AAAGTGACAGAAAA-TAAAAAT
1 AAAGTGACA-AAAATTAAAAAT
55510109 AAA
1 AAA
55510112 CATTAAAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (21 bp):
AAAGTGACAAAAATTAAAAAT
Found at i:55511913 original size:2 final size:2
Alignment explanation
Indices: 55511866--55511899 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55511856 NNNNNNNAGT
55511866 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55511900 AATGAGATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55513690 original size:26 final size:26
Alignment explanation
Indices: 55513645--55513699 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
55513635 AAAACTTTTA
* *
55513645 TATTAAAAATTAAATTAATTTATT-T
1 TATTAAAAATTAAATAAATTAATTAT
*
55513670 TATTAAAAAATTATATAAATTAATTAT
1 TATT-AAAAATTAAATAAATTAATTAT
55513697 TAT
1 TAT
55513700 ACGTTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.16
26 17 0.68
27 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATTAAAAATTAAATAAATTAATTAT
Found at i:55516545 original size:13 final size:13
Alignment explanation
Indices: 55516527--55516551 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55516517 TTTTATGAGT
55516527 TTTTAATTTTAAA
1 TTTTAATTTTAAA
55516540 TTTTAATTTTAA
1 TTTTAATTTTAA
55516552 GAACACAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTAATTTTAAA
Found at i:55519920 original size:6 final size:6
Alignment explanation
Indices: 55519909--55519934 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
55519899 ATTTGATGTT
55519909 ATTTTC ATTTTC ATTTTC ATTTTC AT
1 ATTTTC ATTTTC ATTTTC ATTTTC AT
55519935 CCCCTATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTC
Found at i:55520425 original size:12 final size:12
Alignment explanation
Indices: 55520405--55520527 Score: 149
Period size: 12 Copynumber: 10.2 Consensus size: 12
55520395 AGGACCTGCT
55520405 AAAGAAGAAAAG
1 AAAGAAGAAAAG
*
55520417 AAAGTAGAAAA-
1 AAAGAAGAAAAG
55520428 AAAGGAAGAAAAG
1 AAA-GAAGAAAAG
*
55520441 AAAGAGGAAAAG
1 AAAGAAGAAAAG
* *
55520453 AAAGAGGAGAAG
1 AAAGAAGAAAAG
*
55520465 AAAGAAGAGAAG
1 AAAGAAGAAAAG
* *
55520477 AAGGAAGAGAAG
1 AAAGAAGAAAAG
*
55520489 AAAGAGGAAAAG
1 AAAGAAGAAAAG
55520501 AAAGAAGAAAAG
1 AAAGAAGAAAAG
*
55520513 AAGGAAGAAAAG
1 AAAGAAGAAAAG
55520525 AAA
1 AAA
55520528 TAAATTAAAA
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
11 3 0.03
12 91 0.94
13 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (12 bp):
AAAGAAGAAAAG
Found at i:55522103 original size:28 final size:28
Alignment explanation
Indices: 55522046--55522104 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
55522036 CAATCATTAT
** *
55522046 ATTATTTTTATAATTAAATAAATTCTTA
1 ATTATTTTTATAATTAAATAAACCCCTA
*
55522074 ATTATTTTTGTAATTAAATAAACCCCTA
1 ATTATTTTTATAATTAAATAAACCCCTA
55522102 ATT
1 ATT
55522105 TATTATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (28 bp):
ATTATTTTTATAATTAAATAAACCCCTA
Found at i:55534978 original size:156 final size:155
Alignment explanation
Indices: 55534526--55534992 Score: 630
Period size: 156 Copynumber: 3.0 Consensus size: 155
55534516 TCAAGACTAT
* *
55534526 GTCACAATTCAATGATCTTGCTTTTTTCTTGAATCCCCAGAAAAGTAGCGCTAGAGAAAATGCTG
1 GTCACAAGTCAATGATCTTGATTTTTTCTTGAATCCCCAGAAAAGTAGCGCTAGAG-AAATGCTG
* * * * * *
55534591 GACCTGAGGCCATGTCGTCCAATCCAAAGGCTGAATTACCGAATGTTTCATCTGGTCGTTCAGTT
65 GACCTGCGGCCATGTCATTCAACCCAAAGGCTGAATTACCCAATGTTTCATCTGGTCATTCAGTT
* *
55534656 GAAGCATGTGAATCCGCTGGTCTACA
130 GAAGCATGTGCATCCACTGGTCTACA
* * ** *
55534682 GTCACATGTCAATGGTCCAGATTTTTTCTTGAATCCCCAGAAAAGTAGTGCTAGAGAAGATGCTG
1 GTCACAAGTCAATGATCTTGATTTTTTCTTGAATCCCCAGAAAAGTAGCGCTAGAGAA-ATGCTG
* * * * * *
55534747 CACCTGCGGCCAGGTCTTTTAACCGAAAGGCTGAATCACCCAATGGTTT-ATCTGGTCATTCAGT
65 GACCTGCGGCCATGTCATTCAACCCAAAGGCTGAATTACCCAAT-GTTTCATCTGGTCATTCAGT
* * *
55534811 TGAAGCATGTGCTTACACTGGTCTACC
129 TGAAGCATGTGCATCCACTGGTCTACA
* *
55534838 GTTACAAGTCAATGATCTTGATTTTTTCTTGAATCCCCAGAAAAGTAGCACTAGAGATAATGCTG
1 GTCACAAGTCAATGATCTTGATTTTTTCTTGAATCCCCAGAAAAGTAGCGCTAGAGA-AATGCTG
*
55534903 GACCTGCGGCCATGTCATTCAACCCAAGGGCTGAATTACCCAATGTTTCATCTGGTCATTCAGTT
65 GACCTGCGGCCATGTCATTCAACCCAAAGGCTGAATTACCCAATGTTTCATCTGGTCATTCAGTT
* *
55534968 GAAGCATGTGCGTCCACGGGTCTAC
130 GAAGCATGTGCATCCACTGGTCTAC
55534993 TATTGCAGCA
Statistics
Matches: 267, Mismatches: 40, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
155 6 0.02
156 256 0.96
157 5 0.02
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (155 bp):
GTCACAAGTCAATGATCTTGATTTTTTCTTGAATCCCCAGAAAAGTAGCGCTAGAGAAATGCTGG
ACCTGCGGCCATGTCATTCAACCCAAAGGCTGAATTACCCAATGTTTCATCTGGTCATTCAGTTG
AAGCATGTGCATCCACTGGTCTACA
Found at i:55556069 original size:4 final size:4
Alignment explanation
Indices: 55556060--55556109 Score: 100
Period size: 4 Copynumber: 12.5 Consensus size: 4
55556050 TCATTAGTTC
55556060 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
55556108 CA
1 CA
55556110 GTGTTGTTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:55581579 original size:122 final size:124
Alignment explanation
Indices: 55581384--55581610 Score: 316
Period size: 122 Copynumber: 1.8 Consensus size: 124
55581374 TTAGTTTTTC
* * * *
55581384 TCTTTAAGCTTCTTTGTGTTTTTTTGAGTTTGATAGTTTATTAAAATTTGGTGTATAATGTCAAA
1 TCTTTAAGCTTCTTTGTGTCTTCTTGAGTTTGATAGTTTATTAAAACTTGCTGTATAATGTCAAA
* *
55581449 AGGCAATCAACTAGCATAGTTTTAGAGTAAATTGCATTGTTTGTTAAAATTTTTCATAT
66 AGGCAATCAACCAGCATAGTTCTAGAGTAAATTGCATTGTTTGTTAAAATTTTTCATAT
* *
55581508 TCTTTAAGCTTCTTTGTG-CTTCTT-AGTTTGGTAGTTTATT-AAACTTGCTTTATAATGTCAGA
1 TCTTTAAGCTTCTTTGTGTCTTCTTGAGTTTGATAGTTTATTAAAACTTGCTGTATAATGTCA-A
* * * *
55581570 ACGGTAATCAACCAGCGTAGTTCTAGAGTAATTTGCATTGT
65 AAGGCAATCAACCAGCATAGTTCTAGAGTAAATTGCATTGT
55581611 AAGTGGCTAA
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
121 17 0.19
122 51 0.57
123 4 0.04
124 18 0.20
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (124 bp):
TCTTTAAGCTTCTTTGTGTCTTCTTGAGTTTGATAGTTTATTAAAACTTGCTGTATAATGTCAAA
AGGCAATCAACCAGCATAGTTCTAGAGTAAATTGCATTGTTTGTTAAAATTTTTCATAT
Found at i:55583723 original size:31 final size:29
Alignment explanation
Indices: 55583686--55583751 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
55583676 TAAAATTGAC
*
55583686 TATTAAAATAA-AATTTAAATATTAATTAATT
1 TATTAAAATAATAAATT--ATATTAA-TAATT
55583717 TATTAAAAATAATAAATTATATTAATAATT
1 TATT-AAAATAATAAATTATATTAATAATT
55583747 TATTA
1 TATTA
55583752 TATGACTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 1 0.03
30 9 0.28
31 11 0.34
32 7 0.22
33 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TATTAAAATAATAAATTATATTAATAATT
Found at i:55583751 original size:16 final size:16
Alignment explanation
Indices: 55583704--55583754 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
55583694 TAAAATTTAA
55583704 ATATTAATTAATTTATT
1 ATATTAA-TAATTTATT
* **
55583721 A-A-AAATAATAAATT
1 ATATTAATAATTTATT
55583735 ATATTAATAATTTATT
1 ATATTAATAATTTATT
55583751 ATAT
1 ATAT
55583755 GACTAAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
14 8 0.31
15 3 0.12
16 14 0.54
17 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:55583847 original size:10 final size:9
Alignment explanation
Indices: 55583818--55583843 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55583808 ATTTTATATT
55583818 AATATTTTA
1 AATATTTTA
55583827 AATATTTTA
1 AATATTTTA
55583836 AATATTTT
1 AATATTTT
55583844 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTA
Found at i:55583926 original size:25 final size:25
Alignment explanation
Indices: 55583898--55583947 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
55583888 TTGATTTAAG
*
55583898 TTAATTTTTATATAAAAGTAAAATT
1 TTAATTTTTAAATAAAAGTAAAATT
55583923 TTAATTTTTAAATAAAAGTAAAATT
1 TTAATTTTTAAATAAAAGTAAAATT
55583948 ATCTATTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
TTAATTTTTAAATAAAAGTAAAATT
Found at i:55591677 original size:15 final size:14
Alignment explanation
Indices: 55591653--55591682 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
55591643 CAGAATTTAG
55591653 AAAAAAAAAAAGAA
1 AAAAAAAAAAAGAA
55591667 AAAAAAGAAAAAGAA
1 AAAAAA-AAAAAGAA
55591682 A
1 A
55591683 GGAAGACTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:55592492 original size:33 final size:35
Alignment explanation
Indices: 55592454--55592551 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 35
55592444 ATGGTTATAT
55592454 TTAAATATTTAAAATATAATTCATATATT-C-TAA
1 TTAAATATTTAAAATATAATTCATATATTACTTAA
* *
55592487 TTAAAT-TTTATAA-ATAATTAATATTTATTACTTAA
1 TTAAATATTTAAAATATAATTCATA--TATTACTTAA
*
55592522 --AAATATTTAAAATTTATATTTCATATATTA
1 TTAAATATTTAAAA--TATAATTCATATATTA
55592552 AAATATTAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 9 0.17
32 6 0.12
33 14 0.27
34 7 0.13
35 8 0.15
37 8 0.15
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTCATATATTACTTAA
Found at i:55592541 original size:30 final size:30
Alignment explanation
Indices: 55592502--55592558 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
55592492 TTTTATAAAT
55592502 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
55592532 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
55592559 AACAAGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:55592746 original size:13 final size:13
Alignment explanation
Indices: 55592730--55592754 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55592720 TTTAAACCAA
55592730 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
55592743 ACTTTTCAAAAG
1 ACTTTTCAAAAG
55592755 CATTGCCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:55599341 original size:29 final size:28
Alignment explanation
Indices: 55599272--55599341 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
55599262 AAGCTGTAAG
*
55599272 TAAAAAA-AATAATTATTTTATAATTTT
1 TAAAAAAGGATAATTATTTTATAATTTT
* ** *
55599299 TATAATTGGATAATTATTTATCTAATTTT
1 TAAAAAAGGATAATTATTT-TATAATTTT
*
55599328 TAAAAAAGGTTAAT
1 TAAAAAAGGATAAT
55599342 GAGTAAAATT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
27 4 0.12
28 10 0.31
29 18 0.56
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (28 bp):
TAAAAAAGGATAATTATTTTATAATTTT
Found at i:55605884 original size:12 final size:12
Alignment explanation
Indices: 55605867--55605891 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55605857 CAGCAGAAAG
55605867 GAGTGAAGAGAA
1 GAGTGAAGAGAA
55605879 GAGTGAAGAGAA
1 GAGTGAAGAGAA
55605891 G
1 G
55605892 GCATTTCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGTGAAGAGAA
Found at i:55616140 original size:92 final size:92
Alignment explanation
Indices: 55615983--55616169 Score: 356
Period size: 92 Copynumber: 2.0 Consensus size: 92
55615973 TCATACAGTC
55615983 AAGAACATGTTTTAGCTTGTATTGATTGCTTGGTTGGGATATATTGGTGTACGTGAATGTTGAGT
1 AAGAACATGTTTTAGCTTGTATTGATTGCTTGGTTGGGATATATTGGTGTACGTGAATGTTGAGT
55616048 ACAGATTAATGTCAAAATGCGTGAGAA
66 ACAGATTAATGTCAAAATGCGTGAGAA
*
55616075 AAGAACATGTTTTAGCTTGTATTGATTGCTTGGTTGGGATATATTGGTGTATGTGAATGTTGAGT
1 AAGAACATGTTTTAGCTTGTATTGATTGCTTGGTTGGGATATATTGGTGTACGTGAATGTTGAGT
*
55616140 ACAGGTTAATGTCAAAATGCGTGAGAA
66 ACAGATTAATGTCAAAATGCGTGAGAA
55616167 AAG
1 AAG
55616170 TGGCCTTAAA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.29, C:0.07, G:0.28, T:0.36
Consensus pattern (92 bp):
AAGAACATGTTTTAGCTTGTATTGATTGCTTGGTTGGGATATATTGGTGTACGTGAATGTTGAGT
ACAGATTAATGTCAAAATGCGTGAGAA
Found at i:55616908 original size:5 final size:5
Alignment explanation
Indices: 55616879--55616917 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
55616869 TAAATTTAAC
* *
55616879 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
55616918 CATCTTAGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:55620155 original size:22 final size:22
Alignment explanation
Indices: 55620060--55620157 Score: 124
Period size: 22 Copynumber: 4.5 Consensus size: 22
55620050 TATGCAAAAG
* *
55620060 TCTCATGTTTAACGAACTAAAC
1 TCTCATGTTTAACGTACTAAGC
* **
55620082 CCTCATGGCTAACGTACTAAGC
1 TCTCATGTTTAACGTACTAAGC
**
55620104 TCTCATGGCTAACGTACTAAGC
1 TCTCATGTTTAACGTACTAAGC
*
55620126 TCTCATGTTTCACGTACTAAGC
1 TCTCATGTTTAACGTACTAAGC
55620148 TCTCATGTTT
1 TCTCATGTTT
55620158 GAACAATAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 67 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.33
Consensus pattern (22 bp):
TCTCATGTTTAACGTACTAAGC
Found at i:55620941 original size:13 final size:13
Alignment explanation
Indices: 55620923--55620947 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55620913 CTCCAGGATA
55620923 TAAATACACCCCC
1 TAAATACACCCCC
55620936 TAAATACACCCC
1 TAAATACACCCC
55620948 TCTCAATGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.44, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAATACACCCCC
Found at i:55625232 original size:273 final size:273
Alignment explanation
Indices: 55624745--55625291 Score: 1085
Period size: 273 Copynumber: 2.0 Consensus size: 273
55624735 TAGGGAGACC
55624745 AAAAATGGTTTTACATACATGATCTATTACAAGCATTTCCTAAGAAAAGTCAAAGATACTCTGTA
1 AAAAATGGTTTTACATACATGATCTATTACAAGCATTTCCTAAGAAAAGTCAAAGATACTCTGTA
55624810 TATGCTGCAAGTGGAAGGCTAAAAATTTCGGTCAGCTGACAACCTCGAACCAATGGAGTTGATGA
66 TATGCTGCAAGTGGAAGGCTAAAAATTTCGGTCAGCTGACAACCTCGAACCAATGGAGTTGATGA
55624875 CTTTAACAATAGTAAAGGAGGCTATGTAGAAGTCAGCATTTTGTTTGAACAGATTACTTATATAA
131 CTTTAACAATAGTAAAGGAGGCTATGTAGAAGTCAGCATTTTGTTTGAACAGATTACTTATATAA
*
55624940 ATTAAAATTTATTTATCACATTTCACACTAGATCAAAATTAATATATAATTTTAAGATTTATGTT
196 ATTAAAATTTATTTATCACATTTCACACTAGATCAAAATCAATATATAATTTTAAGATTTATGTT
55625005 GTTAAATGAATAA
261 GTTAAATGAATAA
55625018 AAAAATGGTTTTACATACATGATCTATTACAAGCATTTCCTAAGAAAAGTCAAAGATACTCTGTA
1 AAAAATGGTTTTACATACATGATCTATTACAAGCATTTCCTAAGAAAAGTCAAAGATACTCTGTA
55625083 TATGCTGCAAGTGGAAGGCTAAAAATTTCGGTCAGCTGACAACCTCGAACCAATGGAGTTGATGA
66 TATGCTGCAAGTGGAAGGCTAAAAATTTCGGTCAGCTGACAACCTCGAACCAATGGAGTTGATGA
55625148 CTTTAACAATAGTAAAGGAGGCTATGTAGAAGTCAGCATTTTGTTTGAACAGATTACTTATATAA
131 CTTTAACAATAGTAAAGGAGGCTATGTAGAAGTCAGCATTTTGTTTGAACAGATTACTTATATAA
55625213 ATTAAAATTTATTTATCACATTTCACACTAGATCAAAATCAATATATAATTTTAAGATTTATGTT
196 ATTAAAATTTATTTATCACATTTCACACTAGATCAAAATCAATATATAATTTTAAGATTTATGTT
55625278 GTTAAATGAATAA
261 GTTAAATGAATAA
55625291 A
1 A
55625292 TTATTATTGA
Statistics
Matches: 273, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
273 273 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (273 bp):
AAAAATGGTTTTACATACATGATCTATTACAAGCATTTCCTAAGAAAAGTCAAAGATACTCTGTA
TATGCTGCAAGTGGAAGGCTAAAAATTTCGGTCAGCTGACAACCTCGAACCAATGGAGTTGATGA
CTTTAACAATAGTAAAGGAGGCTATGTAGAAGTCAGCATTTTGTTTGAACAGATTACTTATATAA
ATTAAAATTTATTTATCACATTTCACACTAGATCAAAATCAATATATAATTTTAAGATTTATGTT
GTTAAATGAATAA
Found at i:55630785 original size:25 final size:25
Alignment explanation
Indices: 55630753--55630816 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
55630743 GGAGTTTAGC
* *
55630753 GTGCTCTCTGATTATTAGCATGTCA
1 GTGCTCTCTGATTACTAGCACGTCA
*
55630778 GTGTTCTCTGATTACTAGCACGTCA
1 GTGCTCTCTGATTACTAGCACGTCA
55630803 GTGCTCTCTGATTA
1 GTGCTCTCTGATTA
55630817 ATTATATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (25 bp):
GTGCTCTCTGATTACTAGCACGTCA
Found at i:55640653 original size:4 final size:4
Alignment explanation
Indices: 55640646--55640673 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
55640636 CATAACAAAC
55640646 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
55640674 TTCTGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:55640933 original size:31 final size:32
Alignment explanation
Indices: 55640884--55640943 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
55640874 AGTTATAACG
*
55640884 TTTTAGGTAATTTCTATTTTAG-TCACTCATA
1 TTTTAGATAATTTCTATTTTAGATCACTCATA
* * *
55640915 TTTTAGATTATTTTTATTTTTGATCACTC
1 TTTTAGATAATTTCTATTTTAGATCACTC
55640944 TCTATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 18 0.75
32 6 0.25
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.57
Consensus pattern (32 bp):
TTTTAGATAATTTCTATTTTAGATCACTCATA
Found at i:55641153 original size:20 final size:20
Alignment explanation
Indices: 55641091--55641151 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
55641081 AATTTGATCC
55641091 TTAAACACATATAATTAAA-
1 TTAAACACATATAATTAAAT
* * *
55641110 -TATA-A-TTATAATTATAT
1 TTAAACACATATAATTAAAT
55641127 TTAAACACATATAATTAAAT
1 TTAAACACATATAATTAAAT
55641147 CTTAA
1 -TTAA
55641152 CAAACTTGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
16 9 0.29
17 1 0.03
18 6 0.19
19 1 0.03
20 10 0.32
21 4 0.13
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAAACACATATAATTAAAT
Found at i:55641304 original size:31 final size:29
Alignment explanation
Indices: 55641266--55641335 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
55641256 ATCCCAAAAT
*
55641266 TATACATGAACTATGGTTTAATATGCAATTG
1 TATACATGAACTATGATTT--TATGCAATTG
* *
55641297 TATACATGAACTTTGATTTTATGCAATTT
1 TATACATGAACTATGATTTTATGCAATTG
55641326 TATACATGAA
1 TATACATGAA
55641336 AAATTGATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 19 0.53
31 17 0.47
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (29 bp):
TATACATGAACTATGATTTTATGCAATTG
Found at i:55649821 original size:29 final size:28
Alignment explanation
Indices: 55649767--55649831 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
55649757 TGTAATTTTC
*
55649767 TAATATTTATGTTATAAAATACACATATA
1 TAATATTTATGTAATAAAATACACATA-A
* *
55649796 TAATTTTTATGTAATATAAAT-TACATAA
1 TAATATTTATGTAATA-AAATACACATAA
55649824 TAAATATT
1 T-AATATT
55649832 ACGATTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 2 0.07
29 24 0.80
30 4 0.13
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (28 bp):
TAATATTTATGTAATAAAATACACATAA
Found at i:55654435 original size:16 final size:15
Alignment explanation
Indices: 55654396--55654436 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
55654386 TTTTCTCCTA
55654396 TTTTGTTTCTATTCT
1 TTTTGTTTCTATTCT
* *
55654411 GTTTCTTTCTATTTCT
1 TTTTGTTTCTA-TTCT
55654427 TTTTGTTTCT
1 TTTTGTTTCT
55654437 TTTATTTAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.73
Consensus pattern (15 bp):
TTTTGTTTCTATTCT
Found at i:55654471 original size:7 final size:7
Alignment explanation
Indices: 55654459--55654524 Score: 53
Period size: 7 Copynumber: 8.6 Consensus size: 7
55654449 ATTTACTTAT
55654459 TATAATA
1 TATAATA
55654466 TATAATA
1 TATAATA
55654473 TAATATATA
1 T-ATA-ATA
55654482 TACTTAATA
1 TA--TAATA
*
55654491 -ATTAAGA
1 TA-TAATA
55654498 TATAATA
1 TATAATA
55654505 TTATAATA
1 -TATAATA
55654513 TTATAATA
1 -TATAATA
55654521 TATA
1 TATA
55654525 TTTTAACTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
7 21 0.41
8 21 0.41
9 7 0.14
10 2 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (7 bp):
TATAATA
Found at i:55654486 original size:30 final size:31
Alignment explanation
Indices: 55654446--55654524 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 31
55654436 TTTTATTTAG
*
55654446 TATATTTACTTATTATAATATATA-ATATAA
1 TATATATACTTATTATAATATATAGATATAA
55654476 TATATATACTTA--ATAAT-TA-AGATATAA
1 TATATATACTTATTATAATATATAGATATAA
*
55654503 TAT-TATA-ATATTATAATATATA
1 TATATATACTTATTATAATATATA
55654525 TTTTAACTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
25 2 0.05
26 5 0.12
27 16 0.38
28 7 0.17
29 1 0.02
30 11 0.26
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (31 bp):
TATATATACTTATTATAATATATAGATATAA
Found at i:55654511 original size:8 final size:8
Alignment explanation
Indices: 55654456--55654521 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
55654446 TATATTTACT
55654456 TATTATAA
1 TATTATAA
55654464 TA-TATAA
1 TATTATAA
*
55654471 TATAAT-A
1 TATTATAA
55654478 TATATACTTAA
1 TAT-TA--TAA
*
55654489 TAAT-TAA
1 TATTATAA
*
55654496 GA-TATAA
1 TATTATAA
55654503 TATTATAA
1 TATTATAA
55654511 TATTATAA
1 TATTATAA
55654519 TAT
1 TAT
55654522 ATATTTTAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
6 1 0.02
7 19 0.41
8 21 0.46
10 2 0.04
11 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (8 bp):
TATTATAA
Found at i:55656944 original size:13 final size:13
Alignment explanation
Indices: 55656926--55656963 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
55656916 AGTTCTTTAT
*
55656926 TGCTTTTGAGAAG
1 TGCTTTTGAGAAC
*
55656939 TGCTTTTCAGAAC
1 TGCTTTTGAGAAC
55656952 TGCTTTTGAGAA
1 TGCTTTTGAGAA
55656964 ATTTGATTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAC
Found at i:55657577 original size:22 final size:21
Alignment explanation
Indices: 55657552--55657595 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
55657542 AAGCATATGA
*
55657552 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
55657574 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
55657595 A
1 A
55657596 CTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:55657620 original size:38 final size:38
Alignment explanation
Indices: 55657576--55657655 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
55657566 TATTCAATAA
55657576 ATGATTTGGTTAATACAATACTTATATTTGATAAGCAT
1 ATGATTTGGTTAATACAATACTTATATTTGATAAGCAT
*
55657614 ATGATTTGGTTAATACAATACTTATCTTTGATAAGCAT
1 ATGATTTGGTTAATACAATACTTATATTTGATAAGCAT
55657652 ATGA
1 ATGA
55657656 AAATGAAAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (38 bp):
ATGATTTGGTTAATACAATACTTATATTTGATAAGCAT
Found at i:55658580 original size:18 final size:20
Alignment explanation
Indices: 55658557--55658596 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
55658547 TACTTGTATT
*
55658557 TTCATTTTTAT-TTATT-TA
1 TTCATTATTATATTATTATA
55658575 TTCATTATTATATTATTATA
1 TTCATTATTATATTATTATA
55658595 TT
1 TT
55658597 ATACTATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCATTATTATATTATTATA
Found at i:55658591 original size:3 final size:3
Alignment explanation
Indices: 55658572--55658639 Score: 52
Period size: 3 Copynumber: 22.7 Consensus size: 3
55658562 TTTTATTTAT
* *
55658572 TTA TTCA TTA TTA -TA TTA TTA -TA TTA -TA CTA TTA GTTC TGTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA
* *
55658617 TTA TTA TTA TTA TAA CTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
55658640 TACTCATTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
2 6 0.12
3 39 0.75
4 7 0.13
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:55659378 original size:72 final size:70
Alignment explanation
Indices: 55659261--55659403 Score: 196
Period size: 72 Copynumber: 2.0 Consensus size: 70
55659251 TCTTTTCAAA
* * * *
55659261 CTCAAGTATTAAACGATCTCGGGAATCAAGAAGAGATCATGTCCTAACTTACTGGGCGTGATCCC
1 CTCAAGTATTAAACGATCTCAGGAATCAAGAAAAGACCATGTCCTAACTTACTGGGCATGAT--C
55659326 CTTTTTT
64 CTTTTTT
* * * *
55659333 CTCAAGTTTTAAACGATCTCAGGAATTAAGAAAAGACCGTGTCCTAACTTACTGGTCATGATCCT
1 CTCAAGTATTAAACGATCTCAGGAATCAAGAAAAGACCATGTCCTAACTTACTGGGCATGATCCT
55659398 TTTTT
66 TTTTT
55659403 C
1 C
55659404 AAATCCGAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
70 9 0.14
72 54 0.86
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (70 bp):
CTCAAGTATTAAACGATCTCAGGAATCAAGAAAAGACCATGTCCTAACTTACTGGGCATGATCCT
TTTTT
Found at i:55669107 original size:41 final size:40
Alignment explanation
Indices: 55669028--55669104 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
55669018 AAAAATATTT
*
55669028 ATATTAAAAAACACTACCATAAATATAATAAATATTTTATC
1 ATATTAAAAAACACGA-CATAAATATAATAAATATTTTATC
55669069 ATATTAAAAAACACGA-ATAAATATAATAAATATTTT
1 ATATTAAAAAACACGACATAAATATAATAAATATTTT
55669105 TTAAATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 20 0.57
41 15 0.43
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (40 bp):
ATATTAAAAAACACGACATAAATATAATAAATATTTTATC
Found at i:55675154 original size:2 final size:2
Alignment explanation
Indices: 55675147--55675174 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55675137 AACTGGTAGA
55675147 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55675175 GGCTGCAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55676439 original size:20 final size:20
Alignment explanation
Indices: 55676414--55676454 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
55676404 CTGTGAGGAA
55676414 GCTATTCAGCTTTCTTGGAT
1 GCTATTCAGCTTTCTTGGAT
55676434 GCTATTCAGCTTTCTTGGAT
1 GCTATTCAGCTTTCTTGGAT
55676454 G
1 G
55676455 GTTTAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.44
Consensus pattern (20 bp):
GCTATTCAGCTTTCTTGGAT
Found at i:55678655 original size:18 final size:19
Alignment explanation
Indices: 55678615--55678655 Score: 50
Period size: 17 Copynumber: 2.2 Consensus size: 19
55678605 TTTATTTAGA
*
55678615 TATTGTATAATTTTTATTT
1 TATTGTATAATTTTTATTC
55678634 TATTGT-TAA-TTTTATTAC
1 TATTGTATAATTTTTATT-C
55678652 TATT
1 TATT
55678656 TTAGAAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 7 0.35
18 7 0.35
19 6 0.30
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (19 bp):
TATTGTATAATTTTTATTC
Found at i:55683249 original size:25 final size:23
Alignment explanation
Indices: 55683221--55683286 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 23
55683211 ATTTTTAAAA
55683221 AACTATAAAAATATAAATTCTATT
1 AACTATAAAAAT-TAAATTCTATT
*
55683245 CAACTGAT-GAAATTAAATTTCTATT
1 -AACT-ATAAAAATTAAA-TTCTATT
*
55683270 -ATTATAAAAATTAAATT
1 AACTATAAAAATTAAATT
55683287 TTAATTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
22 4 0.11
23 10 0.29
24 4 0.11
25 15 0.43
26 2 0.06
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (23 bp):
AACTATAAAAATTAAATTCTATT
Found at i:55683524 original size:3 final size:3
Alignment explanation
Indices: 55683516--55683544 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
55683506 TCCATTAACC
55683516 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
55683545 CTCTCTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:55691795 original size:21 final size:21
Alignment explanation
Indices: 55691771--55691810 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
55691761 TCTTTTATCA
55691771 AAAGTAAAGAGATTAATTTGC
1 AAAGTAAAGAGATTAATTTGC
55691792 AAAGTAAAGAGATTAATTT
1 AAAGTAAAGAGATTAATTT
55691811 ACTCATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (21 bp):
AAAGTAAAGAGATTAATTTGC
Found at i:55702199 original size:20 final size:20
Alignment explanation
Indices: 55702154--55702199 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
55702144 CCTTTGATGA
55702154 TAAA-AAAAAAATCAATTTT
1 TAAATAAAAAAATCAATTTT
** *
55702173 TGTATAAAAAATTCAATTTT
1 TAAATAAAAAAATCAATTTT
55702193 TAAATAA
1 TAAATAA
55702200 TCTATACTCT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAATAAAAAAATCAATTTT
Found at i:55703016 original size:19 final size:21
Alignment explanation
Indices: 55702978--55703017 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55702968 AGTTTTTAAC
55702978 AACAGAAATAGATGGAATTTA
1 AACAGAAATAGATGGAATTTA
*
55702999 AACATAAAT-GAT-GAATTTA
1 AACAGAAATAGATGGAATTTA
55703018 CTCTTTGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.28
Consensus pattern (21 bp):
AACAGAAATAGATGGAATTTA
Found at i:55704992 original size:30 final size:32
Alignment explanation
Indices: 55704951--55705015 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
55704941 AACTTAACAA
55704951 TTAAGTAACTTAAATA-AAAAAATTAAATAGT
1 TTAAGTAACTTAAATAGAAAAAATTAAATAGT
***
55704982 TTAA-TAACTTAAATAGAAATTTTTAAATAGT
1 TTAAGTAACTTAAATAGAAAAAATTAAATAGT
55705013 TTA
1 TTA
55705016 GTGACCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.38
Consensus pattern (32 bp):
TTAAGTAACTTAAATAGAAAAAATTAAATAGT
Found at i:55705011 original size:31 final size:30
Alignment explanation
Indices: 55704951--55705034 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
55704941 AACTTAACAA
***
55704951 TTAAGTAACTTAAATAAAAAAATTAAATAGT
1 TTAA-TAACTTAAATAAAATTTTTAAATAGT
55704982 TTAATAACTTAAATAGAAATTTTTAAATAGT
1 TTAATAACTTAAATA-AAATTTTTAAATAGT
* * *
55705013 TTAGTGACCTAAATATAAATTT
1 TTAATAACTTAAATA-AAATTT
55705035 ATTATTAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 11 0.24
31 34 0.76
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (30 bp):
TTAATAACTTAAATAAAATTTTTAAATAGT
Found at i:55708143 original size:16 final size:15
Alignment explanation
Indices: 55708123--55708159 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
55708113 GTATTTTGGT
55708123 TTTATAATTATTTTA
1 TTTATAATTATTTTA
*
55708138 TATTATAATTTTTTTA
1 T-TTATAATTATTTTA
55708154 TTTATA
1 TTTATA
55708160 TAATAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATAATTATTTTA
Found at i:55725655 original size:10 final size:10
Alignment explanation
Indices: 55725640--55725664 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55725630 ATACAAGGGC
55725640 ATATATAAAT
1 ATATATAAAT
55725650 ATATATAAAT
1 ATATATAAAT
55725660 ATATA
1 ATATA
55725665 GATTGTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATATAAAT
Found at i:55726435 original size:22 final size:22
Alignment explanation
Indices: 55726407--55726452 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
55726397 AAAATAATCT
* * *
55726407 AAAAAATGTATAAATTTTAAAA
1 AAAAAATCTAAAAATTTCAAAA
55726429 AAAAAATCTAAAAATTTCAAAA
1 AAAAAATCTAAAAATTTCAAAA
55726451 AA
1 AA
55726453 CAATACGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAAATCTAAAAATTTCAAAA
Found at i:55740456 original size:6 final size:6
Alignment explanation
Indices: 55740442--55740505 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
55740432 TATACAGCCA
* * * * *
55740442 GAGCTG GAGCAG GAGCAG GAGCGG GAGCTG GAGCTG GAGCGG GAGC-G
1 GAGCAG GAGCAG GAGCAG GAGCAG GAGCAG GAGCAG GAGCAG GAGCAG
*
55740489 GAAGCGG GAGCAG GAGC
1 G-AGCAG GAGCAG GAGC
55740506 TGGGGCAGTC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
5 2 0.04
6 47 0.92
7 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.55, T:0.05
Consensus pattern (6 bp):
GAGCAG
Found at i:55740468 original size:18 final size:17
Alignment explanation
Indices: 55740442--55740505 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
55740432 TATACAGCCA
*
55740442 GAGCTGGAGCAGGAGCAG
1 GAGCGGGAGC-GGAGCAG
*
55740460 GAGCGGGAGCTGGAGCTG
1 GAGCGGGAGC-GGAGCAG
*
55740478 GAGCGGGAGCGGAAGCGG
1 GAGCGGGAGCGG-AGCAG
*
55740496 GAGCAGGAGC
1 GAGCGGGAGC
55740506 TGGGGCAGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
17 2 0.05
18 38 0.95
ACGTcount: A:0.23, C:0.17, G:0.55, T:0.05
Consensus pattern (17 bp):
GAGCGGGAGCGGAGCAG
Found at i:55740513 original size:12 final size:12
Alignment explanation
Indices: 55740442--55740513 Score: 74
Period size: 12 Copynumber: 6.0 Consensus size: 12
55740432 TATACAGCCA
55740442 GAGCTGGAGCAG
1 GAGCTGGAGCAG
* *
55740454 GAGCAGGAGCGG
1 GAGCTGGAGCAG
*
55740466 GAGCTGGAGCTG
1 GAGCTGGAGCAG
*
55740478 GAGCGGGAGC-G
1 GAGCTGGAGCAG
*
55740489 GAAGCGGGAGCAG
1 G-AGCTGGAGCAG
*
55740502 GAGCTGGGGCAG
1 GAGCTGGAGCAG
55740514 TCATCACTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
11 2 0.04
12 47 0.92
13 2 0.04
ACGTcount: A:0.22, C:0.17, G:0.56, T:0.06
Consensus pattern (12 bp):
GAGCTGGAGCAG
Found at i:55741504 original size:24 final size:24
Alignment explanation
Indices: 55741477--55741522 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
55741467 TGTAACCAGG
*
55741477 ATTCAGGCTAGGGTAAGAGCTGTT
1 ATTCAGACTAGGGTAAGAGCTGTT
55741501 ATTCAGACTAGGGTAAGAGCTG
1 ATTCAGACTAGGGTAAGAGCTG
55741523 CTACTGCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.33, T:0.26
Consensus pattern (24 bp):
ATTCAGACTAGGGTAAGAGCTGTT
Found at i:55741611 original size:72 final size:72
Alignment explanation
Indices: 55741491--55741710 Score: 359
Period size: 72 Copynumber: 3.1 Consensus size: 72
55741481 AGGCTAGGGT
* *
55741491 AAGAGCTGTTATTCAGACTAGGGTAAGAGCTGCTACTGCTTCCGAAGAGCCCATTACCCAATGTA
1 AAGAGCTGCTATTCAGACTAGGGTAAGAGCTGCTACTGCTTCCAAAGAGCCCATTACCCAATGTA
*
55741556 GCACCCG
66 GAACCCG
* * * * *
55741563 AAGAGCTGCTATTGAGACTAGGGTGAGACCTGCTACTGCTTCCAAAGAGCCCATTAACCACTGTA
1 AAGAGCTGCTATTCAGACTAGGGTAAGAGCTGCTACTGCTTCCAAAGAGCCCATTACCCAATGTA
55741628 GAACCCG
66 GAACCCG
*
55741635 AAGAGCTGCTATTCAGACTAGGGTAAGAGCTGCTACCGCTTCCAAAGAGCCCATTACCCAATGTA
1 AAGAGCTGCTATTCAGACTAGGGTAAGAGCTGCTACTGCTTCCAAAGAGCCCATTACCCAATGTA
55741700 GAACCCG
66 GAACCCG
55741707 AAGA
1 AAGA
55741711 ATGAAAGCCA
Statistics
Matches: 134, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 134 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.20
Consensus pattern (72 bp):
AAGAGCTGCTATTCAGACTAGGGTAAGAGCTGCTACTGCTTCCAAAGAGCCCATTACCCAATGTA
GAACCCG
Found at i:55741907 original size:6 final size:6
Alignment explanation
Indices: 55741873--55741906 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
55741863 ACGAACTCGA
*
55741873 TCCAAT TCCAAT TCCAAT TCCAAT TCCATT TCCA
1 TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TCCA
55741907 TATCCCACGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (6 bp):
TCCAAT
Found at i:55747862 original size:38 final size:38
Alignment explanation
Indices: 55747819--55747891 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
55747809 TAATGAGAAA
55747819 GAAAAATAAAACACGCAAAAATTTTACATGGAAACAAT
1 GAAAAATAAAACACGCAAAAATTTTACATGGAAACAAT
55747857 GAAAAATAAAACACGCAAAAATTTTACATGGAAAC
1 GAAAAATAAAACACGCAAAAATTTTACATGGAAAC
55747892 CTTTTCGGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.58, C:0.14, G:0.11, T:0.18
Consensus pattern (38 bp):
GAAAAATAAAACACGCAAAAATTTTACATGGAAACAAT
Found at i:55748091 original size:50 final size:50
Alignment explanation
Indices: 55748007--55748106 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
55747997 ACTTTATTCT
* *
55748007 AATCAATGTCAAATAAAAGAAGAGTGGTTATATATGGAT-TCTACTTGTGC
1 AATCAATGTCAAATAAAAGAAAAGTAGTTATATATGGATCT-TACTTGTGC
*
55748057 AATCAATGTCAAATAAAAGAAAAGTAGTTCTATATGGATCTTACTTGTGC
1 AATCAATGTCAAATAAAAGAAAAGTAGTTATATATGGATCTTACTTGTGC
55748107 TACTTGATCT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 45 0.98
51 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (50 bp):
AATCAATGTCAAATAAAAGAAAAGTAGTTATATATGGATCTTACTTGTGC
Found at i:55749140 original size:27 final size:28
Alignment explanation
Indices: 55749096--55749159 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 28
55749086 GGCCCATTTT
* *
55749096 TATTTT-AAATTTAAAAATTAAAAATA-
1 TATTTTAAAATTAAAAAATTAAAAAAAG
55749122 TATTTTAAAATTAAAAAATTAAAAAAAG
1 TATTTTAAAATTAAAAAATTAAAAAAAG
55749150 TATTTTAAAA
1 TATTTTAAAA
55749160 ATATTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 6 0.18
27 18 0.53
28 10 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (28 bp):
TATTTTAAAATTAAAAAATTAAAAAAAG
Found at i:55749197 original size:36 final size:37
Alignment explanation
Indices: 55749121--55749254 Score: 202
Period size: 36 Copynumber: 3.6 Consensus size: 37
55749111 AATTAAAAAT
55749121 ATATTTTAAAATTAAAAAATTAAAAAAAGTATTTTAAAA
1 ATATTTTAAAATTAAAAAATT-AAAAAAGTATTTT-AAA
55749160 ATATTTTAAAATT-AAAAATTAAAAAAGTATTTTAAA
1 ATATTTTAAAATTAAAAAATTAAAAAAGTATTTTAAA
* *
55749196 ATATTTTAAATTTAAAAAATT-AAAAAGTA-TGTAAA
1 ATATTTTAAAATTAAAAAATTAAAAAAGTATTTTAAA
*
55749231 ATATTTTAAAATTAAAAAAATAAA
1 ATATTTTAAAATTAAAAAATTAAA
55749255 TATATTTATT
Statistics
Matches: 89, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
35 24 0.27
36 25 0.28
37 20 0.22
38 7 0.08
39 13 0.15
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (37 bp):
ATATTTTAAAATTAAAAAATTAAAAAAGTATTTTAAA
Found at i:55749211 original size:16 final size:16
Alignment explanation
Indices: 55749190--55749247 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
55749180 AAAAAAGTAT
55749190 TTTAAAATATTTTAAA
1 TTTAAAATATTTTAAA
* **
55749206 TTTAAAAAATTAAAAA
1 TTTAAAATATTTTAAA
55749222 GTATGTAAAATATTTTAAA
1 -T-T-TAAAATATTTTAAA
*
55749241 ATTAAAA
1 TTTAAAA
55749248 AAATAAATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
16 18 0.56
17 2 0.06
18 1 0.03
19 11 0.34
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
TTTAAAATATTTTAAA
Found at i:55763767 original size:23 final size:24
Alignment explanation
Indices: 55763722--55763767 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
55763712 GATTAAAGTT
*
55763722 ATGGATAAAATTTGGTTTTAAATA
1 ATGGATAAAATTTGGTTTGAAATA
**
55763746 ATGGATAAGGTTT-GTTTGAAAT
1 ATGGATAAAATTTGGTTTGAAAT
55763768 TTTTAAATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (24 bp):
ATGGATAAAATTTGGTTTGAAATA
Found at i:55764839 original size:18 final size:17
Alignment explanation
Indices: 55764808--55764842 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55764798 AACTTTTAAA
*
55764808 TTTTTTAAATTTTAATT
1 TTTTTTAAAATTTAATT
55764825 TTTTTTAAAAATTTAATT
1 TTTTTT-AAAATTTAATT
55764843 ACTTTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTTAAAATTTAATT
Found at i:55772320 original size:43 final size:43
Alignment explanation
Indices: 55772259--55772431 Score: 337
Period size: 43 Copynumber: 4.0 Consensus size: 43
55772249 CTTGAATAAG
*
55772259 AATACGCATCAAAGTTCAAAACCCTCAACTTTATTACATATAC
1 AATACGCATCAAAGTTCAAAACCATCAACTTTATTACATATAC
55772302 AATACGCATCAAAGTTCAAAACCATCAACTTTATTACATATAC
1 AATACGCATCAAAGTTCAAAACCATCAACTTTATTACATATAC
55772345 AATACGCATCAAAGTTCAAAACCATCAACTTTATTACATATAC
1 AATACGCATCAAAGTTCAAAACCATCAACTTTATTACATATAC
55772388 AATACGCATCAAAGTTCAAAACCATCAACTTTATTACATATAC
1 AATACGCATCAAAGTTCAAAACCATCAACTTTATTACATATAC
55772431 A
1 A
55772432 GTCGAAGTTT
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 129 1.00
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.28
Consensus pattern (43 bp):
AATACGCATCAAAGTTCAAAACCATCAACTTTATTACATATAC
Found at i:55774471 original size:16 final size:16
Alignment explanation
Indices: 55774450--55774482 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55774440 TTAATCCAAC
55774450 ACCTAATATTAAACAA
1 ACCTAATATTAAACAA
55774466 ACCTAATATTAAACAA
1 ACCTAATATTAAACAA
55774482 A
1 A
55774483 TTATGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (16 bp):
ACCTAATATTAAACAA
Found at i:55775919 original size:16 final size:16
Alignment explanation
Indices: 55775898--55775932 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
55775888 TGCAAGGCTC
*
55775898 ACAAGTATAGTGCGGA
1 ACAAGTATAATGCGGA
55775914 ACAAGTATAATGCGGA
1 ACAAGTATAATGCGGA
55775930 ACA
1 ACA
55775933 TTGATTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.17
Consensus pattern (16 bp):
ACAAGTATAATGCGGA
Found at i:55776499 original size:2 final size:2
Alignment explanation
Indices: 55776492--55776526 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
55776482 AACTAGCTGC
55776492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55776527 GAAGTATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55777515 original size:20 final size:20
Alignment explanation
Indices: 55777490--55777529 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
55777480 TACTAACAGT
55777490 TACGTGGCACTACAAGACGA
1 TACGTGGCACTACAAGACGA
55777510 TACGTGGCACTACAAGACGA
1 TACGTGGCACTACAAGACGA
55777530 GGGATGACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (20 bp):
TACGTGGCACTACAAGACGA
Found at i:55783954 original size:19 final size:21
Alignment explanation
Indices: 55783922--55783961 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
55783912 AGAACTTTAA
*
55783922 TTTAATATATAAAAATTAAAT
1 TTTAATATATAAAAATAAAAT
55783943 TTTAA-ATA-AAAAATAAAAT
1 TTTAATATATAAAAATAAAAT
55783962 ATAATTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAATATATAAAAATAAAAT
Found at i:55785746 original size:43 final size:43
Alignment explanation
Indices: 55785667--55785749 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
55785657 AAAGATAGTT
* *
55785667 ATACTTTAACTGACAACCATTAAAAATATTAAAATAAATAGCA
1 ATACCTTAACTGACAACCATTAAAAAGATTAAAATAAATAGCA
* * *
55785710 ATACCTTAACTGATAACCATTAGAAAGATTATAATAAATA
1 ATACCTTAACTGACAACCATTAAAAAGATTAAAATAAATA
55785750 ATTACTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (43 bp):
ATACCTTAACTGACAACCATTAAAAAGATTAAAATAAATAGCA
Found at i:55792116 original size:14 final size:14
Alignment explanation
Indices: 55792093--55792132 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
55792083 ACAGAAAAAT
*
55792093 AAAACATTTT-CTA
1 AAAACATTTTACGA
55792106 AAAATCATTTTACGA
1 AAAA-CATTTTACGA
55792121 AAAACATTTTAC
1 AAAACATTTTAC
55792133 TGGCAATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 14 0.58
15 6 0.25
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (14 bp):
AAAACATTTTACGA
Found at i:55794958 original size:41 final size:43
Alignment explanation
Indices: 55794904--55794989 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 43
55794894 GGACATAAAT
55794904 CGCTCCCTCAAGGGCACG-T-TTTGCTACCACATAAGCGCTCC
1 CGCTCCCTCAAGGGCACGTTATTTGCTACCACATAAGCGCTCC
* *
55794945 CGCTCCCTTAAGGGCACGTTAATTTGCTGCCACATAAGCGCTCC
1 CGCTCCCTCAAGGGCACGTT-ATTTGCTACCACATAAGCGCTCC
55794989 C
1 C
55794990 CTGGGGACGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
41 17 0.43
42 1 0.03
44 22 0.55
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (43 bp):
CGCTCCCTCAAGGGCACGTTATTTGCTACCACATAAGCGCTCC
Found at i:55795651 original size:125 final size:124
Alignment explanation
Indices: 55795261--55795671 Score: 633
Period size: 124 Copynumber: 3.3 Consensus size: 124
55795251 ATTTATTAAG
** * * * *
55795261 GAAATCGCTCCCACGCAGATGCGTTTTTGATACAGTAGGTCCTGAAAATATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* * *
55795326 GTTTATGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATAAGAAAAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATAAGAAGAATTTTT
** * * *
55795385 GAAATAACTCCCACGTGGACGCGCTTTTGCTACAGTAAGTCTTGAAAAAATAATTTCAAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
*
55795450 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATTAGAAGAATTTTT
66 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATAAGAAGAATTTTT
* * * *
55795509 GAAATCGCTTCCACGTGGATGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAA
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
*
55795574 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
66 GTTTCTGAGCAAATAGTAT-AAAAACGCTTCAAGCAGGATGCTTTATAAGAAGAATTTTT
55795634 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
55795672 CATGTTTGGG
Statistics
Matches: 259, Mismatches: 27, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
124 184 0.71
125 75 0.29
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (124 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATAAGAAGAATTTTT
Found at i:55800279 original size:13 final size:13
Alignment explanation
Indices: 55800261--55800290 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
55800251 NNNNCAAACT
55800261 CAATTACCCAACC
1 CAATTACCCAACC
55800274 CAATTACCCAACC
1 CAATTACCCAACC
55800287 CAAT
1 CAAT
55800291 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:55800918 original size:48 final size:48
Alignment explanation
Indices: 55800819--55800943 Score: 214
Period size: 48 Copynumber: 2.6 Consensus size: 48
55800809 TAAGAATATT
55800819 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATC-AATAATATCAAAATATTCAAAATA
*
55800868 AACTATTTTGTATTTTATTACATCAATAATATCAAAATATTCAAATTA
1 AACTATTTTGTATTTTATTACATCAATAATATCAAAATATTCAAAATA
* *
55800916 AACTATTTTGTATTCTATTACATTAATA
1 AACTATTTTGTATTTTATTACATCAATA
55800944 TAAACTATTT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
48 49 0.67
49 24 0.33
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (48 bp):
AACTATTTTGTATTTTATTACATCAATAATATCAAAATATTCAAAATA
Found at i:55801865 original size:16 final size:16
Alignment explanation
Indices: 55801787--55801868 Score: 55
Period size: 16 Copynumber: 5.2 Consensus size: 16
55801777 TTATATTATT
55801787 AGAA-AAAAGAAATGAA
1 AGAAGAAAAGAAA-GAA
*
55801803 A-AAG-AAAGAAACAAA
1 AGAAGAAAAGAAA-GAA
* * *
55801818 AGCA-AAAAGAAACAG
1 AGAAGAAAAGAAAGAA
* * *
55801833 AGAAGGAAGGAAGGAA
1 AGAAGAAAAGAAAGAA
55801849 AGAAGAAAAGAAAGAA
1 AGAAGAAAAGAAAGAA
55801865 AGAA
1 AGAA
55801869 AAGGGAAAAT
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
15 16 0.33
16 32 0.67
ACGTcount: A:0.71, C:0.04, G:0.24, T:0.01
Consensus pattern (16 bp):
AGAAGAAAAGAAAGAA
Found at i:55802207 original size:13 final size:13
Alignment explanation
Indices: 55802189--55802215 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55802179 GTTAAATGTG
55802189 AGTTTGGTAGGAA
1 AGTTTGGTAGGAA
55802202 AGTTTGGTAGGAA
1 AGTTTGGTAGGAA
55802215 A
1 A
55802216 TTAAGTAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (13 bp):
AGTTTGGTAGGAA
Done.