Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 181 of 187
Found at i:55307554 original size:26 final size:26
Alignment explanation
Indices: 55307505--55307557 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
55307495 ACACACTAAA
* *
55307505 ATTATTAATTTTATACTACGAATAAT
1 ATTAATAATTTTATACTACAAATAAT
55307531 ATTAATAATTTTATACT-CAAAATAAT
1 ATTAATAATTTTATACTAC-AAATAAT
55307557 A
1 A
55307558 CACACTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAATAATTTTATACTACAAATAAT
Found at i:55307741 original size:3 final size:3
Alignment explanation
Indices: 55307733--55307776 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
55307723 TCTTCATACT
55307733 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
55307777 TAATAATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:55307781 original size:3 final size:3
Alignment explanation
Indices: 55307775--55307809 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
55307765 CAACAACAAC
55307775 AAT AAT AAT AAT AAT AAT AAT AAT AAT AACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
55307810 CTTTTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:55307879 original size:19 final size:21
Alignment explanation
Indices: 55307855--55307893 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
55307845 ACTAAAACAA
*
55307855 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
55307874 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
55307894 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:55308063 original size:27 final size:27
Alignment explanation
Indices: 55308025--55308100 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
55308015 ATAATACGAG
55308025 TGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** *
55308052 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
55308079 TGGTGCCGCCAATATCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
55308101 GTGACCAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:55308185 original size:27 final size:27
Alignment explanation
Indices: 55308150--55308224 Score: 116
Period size: 27 Copynumber: 2.7 Consensus size: 27
55308140 TTTTTTGTTT
55308150 TTTTGATATATTTTGGTAAATAAAAAAA
1 TTTT-ATATATTTTGGTAAATAAAAAAA
55308178 TTTTATATATTTTGGTAAATAAAAAAA
1 TTTTATATATTTTGGTAAATAAAAAAA
*
55308205 -GTTATAATATTTTGGTAAAT
1 TTTTAT-ATATTTTGGTAAAT
55308225 TTTTATTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
26 4 0.09
27 37 0.82
28 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (27 bp):
TTTTATATATTTTGGTAAATAAAAAAA
Found at i:55314446 original size:18 final size:18
Alignment explanation
Indices: 55314423--55314463 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
55314413 GAATTGTGCA
*
55314423 AACCCATATATGAATGTG
1 AACCCATATATGAATGCG
* *
55314441 AACCCATGTATGCATGCG
1 AACCCATATATGAATGCG
55314459 AACCC
1 AACCC
55314464 TATTAAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (18 bp):
AACCCATATATGAATGCG
Found at i:55316868 original size:6 final size:6
Alignment explanation
Indices: 55316769--55316850 Score: 148
Period size: 6 Copynumber: 13.8 Consensus size: 6
55316759 ACAACCTATT
55316769 AAAAT- AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
*
55316816 AAAATC AAAATC AAAATC AAAATC AAAATT AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
55316851 AAGGATGAAA
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
5 5 0.07
6 70 0.93
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATC
Found at i:55326824 original size:17 final size:18
Alignment explanation
Indices: 55326791--55326824 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55326781 TTGATTCTAC
*
55326791 ATTAAAATAAGTTCATAA
1 ATTAAAATAAATTCATAA
55326809 ATTAAAA-AAATTCATA
1 ATTAAAATAAATTCATA
55326825 CTTCAACCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (18 bp):
ATTAAAATAAATTCATAA
Found at i:55327677 original size:11 final size:11
Alignment explanation
Indices: 55327641--55327699 Score: 77
Period size: 11 Copynumber: 5.4 Consensus size: 11
55327631 TAAATCCTTT
*
55327641 CTCTC-AATTT
1 CTCTCAAATTC
55327651 CTCTCCAATATT-
1 CTCT-CAA-ATTC
55327663 CTCTCAAATTC
1 CTCTCAAATTC
55327674 CTCTCAAATTC
1 CTCTCAAATTC
55327685 CTCTCAAATTC
1 CTCTCAAATTC
55327696 CTCT
1 CTCT
55327700 TAAAAAAGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.16
11 30 0.67
12 5 0.11
13 3 0.07
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.41
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:55328178 original size:41 final size:41
Alignment explanation
Indices: 55328112--55328193 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
55328102 GTGGAGACTC
* *
55328112 GAGATGCATACATTCCATCTTCCATGTGGAGAGTGTACTAT
1 GAGACGCACACATTCCATCTTCCATGTGGAGAGTGTACTAT
55328153 GAGACGCACACATTCCATCTTCCATGTGGAGAGTGTACTAT
1 GAGACGCACACATTCCATCTTCCATGTGGAGAGTGTACTAT
55328194 CACTTTGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (41 bp):
GAGACGCACACATTCCATCTTCCATGTGGAGAGTGTACTAT
Found at i:55330065 original size:35 final size:34
Alignment explanation
Indices: 55329981--55330077 Score: 124
Period size: 34 Copynumber: 2.8 Consensus size: 34
55329971 ATTTTGAATA
*
55329981 TTTTGATATTATTTGATGTAATAAAATAGAAATTC
1 TTTT-ATATTATTTAATGTAATAAAATAGAAATTC
*
55330016 TTATATATTATTTAATGTAATAAAATAGAAAATTAC
1 TTTTATATTATTTAATGTAATAAAATAG-AAATT-C
*
55330052 TTTTATATT-TTTAATATAATAGAAAT
1 TTTTATATTATTTAATGTAATA-AAAT
55330078 TCTTTTAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
34 23 0.42
35 19 0.35
36 13 0.24
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (34 bp):
TTTTATATTATTTAATGTAATAAAATAGAAATTC
Found at i:55333498 original size:103 final size:103
Alignment explanation
Indices: 55333362--55333834 Score: 437
Period size: 95 Copynumber: 4.7 Consensus size: 103
55333352 CACGTGGGAG
* * * * * * * *
55333362 TTTTTTTTAAATTAACAAATAATTTAATTAAGTAACCCTAAACCCCAAACCCTAATTTATTTGAG
1 TTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAAT
*
55333427 TTTTCTTTAAAAA-CGTTAAACACTAAACCCTAATCTAA
66 TTTTCTTTAAAAACCCTT-AACACTAAACCCTAATCTAA
*
55333465 TTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAAACCCTAATTTATTTAAT
1 TTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAAT
*
55333530 TTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAA
66 TTTTCTTTAAAAACCCTTAACACTAAACCCTAATCTAA
* * *
55333568 TTTTGTT-AAATTTATAATTAAATTACTCAAGTAACCCT-------AAACCCTAATTTATTTGAT
1 TTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAAT
* * * *
55333625 TTTTCCTTAAAAACCCTTAACACTAAACCTTAATTTGA
66 TTTTCTTTAAAAACCCTTAACACTAAACCCTAATCTAA
* * *
55333663 --TTTTTAAAATTTTTTAATTAATTTACTCAAGTAA-GCT------TAAACCCTAATTTAATTTA
1 TTTTTTTAAAA-TTTATAATTAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTT-ATTTA
* *** * *
55333719 TTTTTTCTTTAAAAATTATAAACACGAAACCCTAATCTAA
64 ATTTTTCTTTAAAAACCCTTAACACTAAACCCTAATCTAA
** * * * * * ** *
55333759 -TTTTAAAAAATTT-TAATTAATTTAATTAAGAAACTCTAAACCCTAATTCCTTATTTATTTAAT
1 TTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAA-
55333822 TTTTTCTTTAAAA
65 TTTTTCTTTAAAA
55333835 CCATAAACCT
Statistics
Matches: 314, Mismatches: 42, Indels: 29
0.82 0.11 0.08
Matches are distributed among these distances:
93 4 0.01
94 5 0.02
95 104 0.33
96 39 0.12
97 7 0.02
101 5 0.02
102 53 0.17
103 94 0.30
104 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.41
Consensus pattern (103 bp):
TTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAAT
TTTTCTTTAAAAACCCTTAACACTAAACCCTAATCTAA
Found at i:55333556 original size:43 final size:43
Alignment explanation
Indices: 55333498--55333665 Score: 138
Period size: 43 Copynumber: 3.7 Consensus size: 43
55333488 TTACTCAAGT
* *
55333498 AACCCTAAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAA
1 AACCCTTAACACTAAACCCTAATTTATTTAATTTTTCCTTAAA
* * **
55333541 AACCCTTAACACTAAACCCTAATCTAATTTTGTTAAATTTATAATTAAA
1 AACCCTTAACACTAAACCCTAA--T--TTAT-TT-AATTTTTCCTTAAA
* ** * *
55333590 TTACTCAAGTAACCCTAAACCCTAATTTATTTGATTTTTCCTTAAA
1 -AAC-C-CTTAACACTAAACCCTAATTTATTTAATTTTTCCTTAAA
*
55333636 AACCCTTAACACTAAACCTTAATTTGATTT
1 AACCCTTAACACTAAACCCTAATTT-ATTT
55333666 TTAAAATTTT
Statistics
Matches: 95, Mismatches: 20, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
43 37 0.39
44 5 0.05
45 3 0.03
46 10 0.11
47 5 0.05
48 5 0.05
49 11 0.12
50 3 0.03
51 1 0.01
52 15 0.16
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (43 bp):
AACCCTTAACACTAAACCCTAATTTATTTAATTTTTCCTTAAA
Found at i:55333643 original size:95 final size:94
Alignment explanation
Indices: 55333402--55333806 Score: 438
Period size: 95 Copynumber: 4.2 Consensus size: 94
55333392 AGTAACCCTA
* * * *
55333402 AACCCCAAACCCTAATTTATTTGAGTTTTCTTTAAAAA-CGTTAAACACTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTT-AACACTAAACCCTAATCTAA-
55333466 TTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCT
64 -TTTTTAAAATTTATAATTAATTTACTCAAG------T
*
55333504 AAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAAT
1 -AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAAT
* *
55333569 TTTGTTAAATTTATAATTAAATTACTCAAGT
65 TTT-TAAAATTTATAATTAATTTACTCAAGT
* * *
55333600 AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCTTAATTTGATT
1 AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAATT
*
55333665 TTTAAAATTTTTTAATTAATTTACTCAAGT
66 TTTAAAA-TTTATAATTAATTTACTCAAGT
* * * *** * *
55333695 AAGCTTAAACCCTAATTTAATTT-ATTTTTTCTTTAAAAATTATAAACACGAAACCCTAATCTAA
1 AACCCTAAACCCTAATTT-ATTTGA-TTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAA
* * * *
55333759 TTTTAAAAAATTT-TAATTAATTTAATTAAGA
64 TTTT-TAAAATTTATAATTAATTTACTCAAGT
*
55333790 AACTCTAAACCCTAATT
1 AACCCTAAACCCTAATT
55333807 CCTTATTTAT
Statistics
Matches: 264, Mismatches: 32, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
94 4 0.02
95 129 0.49
96 42 0.16
97 4 0.02
101 4 0.02
102 24 0.09
103 54 0.20
104 3 0.01
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.40
Consensus pattern (94 bp):
AACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAATT
TTTAAAATTTATAATTAATTTACTCAAGT
Found at i:55338904 original size:29 final size:27
Alignment explanation
Indices: 55338871--55338955 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 27
55338861 GTATAGGGAT
55338871 GCACCGAAGTGCAATAACAGAACAGAGTA
1 GCACC-AAGTGC-ATAACAGAACAGAGTA
** *
55338900 GCACCAGAGTGCCATGTCAGAACAGAATA
1 GCACCA-AGTG-CATAACAGAACAGAGTA
*
55338929 GCACTCAAGTGCTTAATCAGAACAGAG
1 GCAC-CAAGTGCATAA-CAGAACAGAG
55338956 CGACACTGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.14
Consensus pattern (27 bp):
GCACCAAGTGCATAACAGAACAGAGTA
Found at i:55341714 original size:2 final size:2
Alignment explanation
Indices: 55341709--55341740 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
55341699 ATATATATAT
*
55341709 AG AG AG AG AG AG AG AG AG AG AG TG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
55341741 TGAGTGAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
AG
Found at i:55341741 original size:10 final size:10
Alignment explanation
Indices: 55341712--55341744 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
55341702 TATATATAGA
*
55341712 GAGAGAGAGA
1 GAGAGAGAGT
55341722 GAGAGAGAGT
1 GAGAGAGAGT
55341732 GAGAGAGAGT
1 GAGAGAGAGT
55341742 GAG
1 GAG
55341745 TGAGCAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.52, T:0.06
Consensus pattern (10 bp):
GAGAGAGAGT
Found at i:55341745 original size:14 final size:14
Alignment explanation
Indices: 55341709--55341748 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
55341699 ATATATATAT
*
55341709 AGAGAGAGAGAGAG
1 AGAGAGAGTGAGAG
55341723 AGAGAGAGTGAGAG
1 AGAGAGAGTGAGAG
*
55341737 AGAGTGAGTGAG
1 AGAGAGAGTGAG
55341749 CAGCTAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.50, T:0.07
Consensus pattern (14 bp):
AGAGAGAGTGAGAG
Found at i:55343392 original size:27 final size:27
Alignment explanation
Indices: 55343345--55343398 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
55343335 CATTCAATTA
*
55343345 TTTATATTTTTCATATTTTTATAGTAT
1 TTTATATTTTTCATATTTTTAAAGTAT
55343372 TTTA-ATTTATTCA-ATATTTTAAAGTAT
1 TTTATATTT-TTCATAT-TTTTAAAGTAT
55343399 AAAATTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTATATTTTTCATATTTTTAAAGTAT
Found at i:55350815 original size:15 final size:13
Alignment explanation
Indices: 55350780--55350805 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55350770 AATATCCTTC
55350780 GTGACTGGAATTT
1 GTGACTGGAATTT
55350793 GTGACTGGAATTT
1 GTGACTGGAATTT
55350806 TTAAGACTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (13 bp):
GTGACTGGAATTT
Found at i:55351327 original size:27 final size:27
Alignment explanation
Indices: 55351290--55351367 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
55351280 CATAACATAG
*
55351290 ACACATTAAGTTAGTATCAAACTAGAC
1 ACACATCAAGTTAGTATCAAACTAGAC
55351317 ACACATCAAGTTAGTATCAAACTAGAC
1 ACACATCAAGTTAGTATCAAACTAGAC
55351344 ACACATCAAGTTAGTATCAAACTA
1 ACACATCAAGTTAGTATCAAACTA
55351368 CTCTACTTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.24
Consensus pattern (27 bp):
ACACATCAAGTTAGTATCAAACTAGAC
Found at i:55366416 original size:16 final size:16
Alignment explanation
Indices: 55366395--55366426 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55366385 ATTTTGTTGC
*
55366395 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
55366411 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
55366427 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:55366712 original size:51 final size:50
Alignment explanation
Indices: 55366650--55366845 Score: 236
Period size: 51 Copynumber: 3.9 Consensus size: 50
55366640 GATACCGATT
* *
55366650 CACATAATAGCCTGCACATAGTACTACACATGTGACCATCACTGTCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACT-TCCGGTA
** *
55366701 CATGTAGTAGCCTGCACATAGTACTACACATGTGATCGA--AGCTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATCA-CT-TCCGGTA
* * * *
55366752 CGCATAGTAGCCTGCACATTGTACTACACATGCGACCTATCA-TTCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTTCCGGTA
*
55366802 CACATAGTAGCCTACACATAGTACTACACATGTGACCATCACTT
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTT
55366846 TCAGTTTATC
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
49 4 0.03
50 43 0.35
51 72 0.59
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTTCCGGTA
Found at i:55366830 original size:12 final size:13
Alignment explanation
Indices: 55366800--55366832 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
55366790 ATCATTCTGG
55366800 TACACATAGTAGCC
1 TACACATAGTA-CC
55366814 TACACATAGTA-C
1 TACACATAGTACC
55366826 TACACAT
1 TACACAT
55366833 GTGACCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (13 bp):
TACACATAGTACC
Found at i:55366833 original size:101 final size:102
Alignment explanation
Indices: 55366652--55366836 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 102
55366642 TACCGATTCA
* ** *
55366652 CATAATAGCCTGCACATAGTACTACACATGTGACCATCACTGTCCGATACATGTAGTAGCCTGCA
1 CATAATAGCCTGCACATAGTACTACACATGCGACCATCACTGTCCGATACACATAGTAGCCTACA
55366717 CATAGTACTACACATGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACATGTGATCGAAGCTATCCGGTACG
* * * *
55366754 CATAGTAGCCTGCACATTGTACTACACATGCGACCTATCA-T-TCTGGTACACATAGTAGCCTAC
1 CATAATAGCCTGCACATAGTACTACACATGCGACC-ATCACTGTCCGATACACATAGTAGCCTAC
55366817 ACATAGTACTACACATGTGA
65 ACATAGTACTACACATGTGA
55366837 CCATCACTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
101 37 0.50
102 33 0.45
103 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (102 bp):
CATAATAGCCTGCACATAGTACTACACATGCGACCATCACTGTCCGATACACATAGTAGCCTACA
CATAGTACTACACATGTGATCGAAGCTATCCGGTACG
Found at i:55377780 original size:9 final size:9
Alignment explanation
Indices: 55377768--55377819 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
55377758 TATTAAAAAC
55377768 GAGAGACTT
1 GAGAGACTT
55377777 GAGAGACTT
1 GAGAGACTT
**
55377786 GAGAGGGTTT
1 GAGA-GACTT
55377796 GAGAGAAC-T
1 GAGAG-ACTT
*
55377805 GAGAGAGTT
1 GAGAGACTT
55377814 GAGAGA
1 GAGAGA
55377820 AGGATATGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
8 1 0.03
9 27 0.77
10 7 0.20
ACGTcount: A:0.35, C:0.06, G:0.40, T:0.19
Consensus pattern (9 bp):
GAGAGACTT
Found at i:55377799 original size:19 final size:17
Alignment explanation
Indices: 55377768--55377819 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
55377758 TATTAAAAAC
*
55377768 GAGAGACTTGAGAGACTT
1 GAGAGAGTTGAGAGAC-T
*
55377786 GAGAGGGTTTGAGAGAACT
1 GAGAGAG-TTGAGAG-ACT
55377805 GAGAGAGTTGAGAGA
1 GAGAGAGTTGAGAGA
55377820 AGGATATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 1 0.03
18 12 0.41
19 14 0.48
20 2 0.07
ACGTcount: A:0.35, C:0.06, G:0.40, T:0.19
Consensus pattern (17 bp):
GAGAGAGTTGAGAGACT
Found at i:55379731 original size:14 final size:14
Alignment explanation
Indices: 55379714--55379740 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55379704 TGAAGAGATG
55379714 TGTGTGAAATGAGT
1 TGTGTGAAATGAGT
55379728 TGTGTGAAATGAG
1 TGTGTGAAATGAG
55379741 GAAGGGAAGA
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:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (14 bp):
TGTGTGAAATGAGT
Found at i:55380263 original size:27 final size:28
Alignment explanation
Indices: 55380210--55380263 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
55380200 AAAAATAATT
*
55380210 AAAATTAAATATGTTAATAATTTAAGTG
1 AAAATTAAATATGTTAATAATTAAAGTG
* *
55380238 AAAATTAATTAT-TTTATAATTAAAGT
1 AAAATTAAATATGTTAATAATTAAAGT
55380264 ATGAATTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (28 bp):
AAAATTAAATATGTTAATAATTAAAGTG
Found at i:55380469 original size:14 final size:15
Alignment explanation
Indices: 55380450--55380478 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55380440 GCCAAAAGAC
55380450 ATCTTCTAAC-CACA
1 ATCTTCTAACACACA
55380464 ATCTTCTAACACACA
1 ATCTTCTAACACACA
55380479 TACACCCGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (15 bp):
ATCTTCTAACACACA
Found at i:55381730 original size:14 final size:14
Alignment explanation
Indices: 55381713--55381739 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55381703 TGAAGAGATG
55381713 TGTGTGAAATGAGT
1 TGTGTGAAATGAGT
55381727 TGTGTGAAATGAG
1 TGTGTGAAATGAG
55381740 GAAGGGAAGA
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:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (14 bp):
TGTGTGAAATGAGT
Found at i:55382262 original size:27 final size:28
Alignment explanation
Indices: 55382209--55382262 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
55382199 AAAAATAATT
*
55382209 AAAATTAAATATGTTAATAATTTAAGTG
1 AAAATTAAATATGTTAATAATTAAAGTG
* *
55382237 AAAATTAATTAT-TTTATAATTAAAGT
1 AAAATTAAATATGTTAATAATTAAAGT
55382263 ATGAATTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (28 bp):
AAAATTAAATATGTTAATAATTAAAGTG
Found at i:55382468 original size:14 final size:15
Alignment explanation
Indices: 55382449--55382477 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55382439 GCCAAAAGAC
55382449 ATCTTCTAAC-CACA
1 ATCTTCTAACACACA
55382463 ATCTTCTAACACACA
1 ATCTTCTAACACACA
55382478 TACACCCGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (15 bp):
ATCTTCTAACACACA
Found at i:55383948 original size:14 final size:14
Alignment explanation
Indices: 55383931--55383957 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55383921 TGAAGAGATG
55383931 TGTGTGAAATGAGT
1 TGTGTGAAATGAGT
55383945 TGTGTGAAATGAG
1 TGTGTGAAATGAG
55383958 GAAGGGAAGA
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:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (14 bp):
TGTGTGAAATGAGT
Found at i:55384480 original size:27 final size:28
Alignment explanation
Indices: 55384427--55384480 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
55384417 AAAAATAATT
*
55384427 AAAATTAAATATGTTAATAATTTAAGTG
1 AAAATTAAATATGTTAATAATTAAAGTG
* *
55384455 AAAATTAATTAT-TTTATAATTAAAGT
1 AAAATTAAATATGTTAATAATTAAAGT
55384481 ATGAATTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (28 bp):
AAAATTAAATATGTTAATAATTAAAGTG
Found at i:55384686 original size:14 final size:15
Alignment explanation
Indices: 55384667--55384695 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55384657 GCCAAAAGAC
55384667 ATCTTCTAAC-CACA
1 ATCTTCTAACACACA
55384681 ATCTTCTAACACACA
1 ATCTTCTAACACACA
55384696 TACACCCGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (15 bp):
ATCTTCTAACACACA
Found at i:55387172 original size:21 final size:22
Alignment explanation
Indices: 55387129--55387181 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
55387119 GGGAGAGCAC
*
55387129 TAAATTAATTCTAATTTAAACA-
1 TAAA-TAAATCTAATTTAAACAT
55387151 TAAATAAATCTAA-TTAATACAT
1 TAAATAAATCTAATTTAA-ACAT
*
55387173 TAATTAAAT
1 TAAATAAAT
55387182 TATAGTACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 11 0.41
22 12 0.44
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATAAATCTAATTTAAACAT
Found at i:55392848 original size:25 final size:25
Alignment explanation
Indices: 55392811--55392884 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
55392801 AGGTCATGAG
** *
55392811 AGCTTACTAATTCTCAGCTCGTATA
1 AGCTTACCGATTCACAGCTCGTATA
* *
55392836 AGCTTACCGATTCACAACTCGTGA-G
1 AGCTTACCGATTCACAGCTCGT-ATA
*
55392861 AGCATACCGATTCACAGCTCGTAT
1 AGCTTACCGATTCACAGCTCGTAT
55392885 GAGCATACAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 1 0.03
25 38 0.95
26 1 0.03
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (25 bp):
AGCTTACCGATTCACAGCTCGTATA
Found at i:55392888 original size:25 final size:25
Alignment explanation
Indices: 55392820--55392892 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
55392810 GAGCTTACTA
* * *
55392820 ATTCTCAGCTCGTATAAGCTTACCG
1 ATTCACAGCTCGTATGAGCATACCG
*
55392845 ATTCACAACTCGTGA-GAGCATACCG
1 ATTCACAGCTCGT-ATGAGCATACCG
55392870 ATTCACAGCTCGTATGAGCATAC
1 ATTCACAGCTCGTATGAGCATAC
55392893 ATGTACAAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 1 0.02
25 39 0.95
26 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (25 bp):
ATTCACAGCTCGTATGAGCATACCG
Found at i:55396260 original size:115 final size:115
Alignment explanation
Indices: 55396058--55396287 Score: 399
Period size: 115 Copynumber: 2.0 Consensus size: 115
55396048 CAATAGTGGA
*
55396058 ATTCATAGTCCAAGTCATGGGTAAATGATATCCTCTCATTGGTATTACATGGTTGATGAAAAGTA
1 ATTCATAGCCCAAGTCATGGGTAAATGATATCCTCTCATTGGTATTACATGGTTGATGAAAAGTA
*
55396123 AACAGAGGTAAAATTGGGATGAGAAAATTATTTAATATAAACATTGAAGT
66 AACAGAGGTAAAATTGGGATGAGAAAATTATTTAATATAAACATTAAAGT
* *
55396173 ATTCATAGCCCGAGTCATGGGTAAATGATATCCTTTCATTGGTATTACATGGTTGATGAAAAGTA
1 ATTCATAGCCCAAGTCATGGGTAAATGATATCCTCTCATTGGTATTACATGGTTGATGAAAAGTA
*
55396238 AA-TGAAGGTAAAATTGGGATGAGAAAATTATTTAATATAAACATTAAAGT
66 AACAG-AGGTAAAATTGGGATGAGAAAATTATTTAATATAAACATTAAAGT
55396288 TTATTTTGGG
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
114 1 0.01
115 108 0.99
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (115 bp):
ATTCATAGCCCAAGTCATGGGTAAATGATATCCTCTCATTGGTATTACATGGTTGATGAAAAGTA
AACAGAGGTAAAATTGGGATGAGAAAATTATTTAATATAAACATTAAAGT
Found at i:55400565 original size:15 final size:15
Alignment explanation
Indices: 55400543--55400580 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
55400533 TTATATATAT
*
55400543 ATTGAATTTTGATTCA
1 ATTGAATTTTAATT-A
55400559 A-TGAATTTTAATTA
1 ATTGAATTTTAATTA
55400573 ATTGAATT
1 ATTGAATT
55400581 AATTGTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 17 0.85
16 1 0.05
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50
Consensus pattern (15 bp):
ATTGAATTTTAATTA
Found at i:55404500 original size:35 final size:35
Alignment explanation
Indices: 55404459--55404530 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
55404449 TAATTGATTT
* *
55404459 AGCTTTGACAATTGGAGTTCCCGAACAGTCATTGA
1 AGCTTTGACAATTGAAGTTCCCAAACAGTCATTGA
*
55404494 AGCTTTGACAATTGAAGTTCCCAAATAGTCATTGA
1 AGCTTTGACAATTGAAGTTCCCAAACAGTCATTGA
55404529 AG
1 AG
55404531 TGGACTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (35 bp):
AGCTTTGACAATTGAAGTTCCCAAACAGTCATTGA
Found at i:55414809 original size:25 final size:25
Alignment explanation
Indices: 55414775--55414847 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
55414765 AGGGTTATCG
*
55414775 ATTTATAGCTCGAGAGAGCATACTA
1 ATTTATAGCTCGAGAGAGCATACAA
*
55414800 ATTTATAGCTCGAGAAAGCATACAA
1 ATTTATAGCTCGAGAGAGCATACAA
*
55414825 ATTTATAGCTCGTGAGAGCATAC
1 ATTTATAGCTCGAGAGAGCATAC
55414848 GGATCTTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.27
Consensus pattern (25 bp):
ATTTATAGCTCGAGAGAGCATACAA
Found at i:55416304 original size:20 final size:20
Alignment explanation
Indices: 55416267--55416304 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55416257 TGCAGTGTTG
*
55416267 AAAAATTCTACTATTTTTTA
1 AAAAATTCTACTAGTTTTTA
55416287 AAAAATTCT-CTGAGTTTT
1 AAAAATTCTACT-AGTTTT
55416305 CGATATAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (20 bp):
AAAAATTCTACTAGTTTTTA
Found at i:55432273 original size:20 final size:20
Alignment explanation
Indices: 55432225--55432265 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
55432215 AAATATCTTG
55432225 ATTTGATTTGATTTCAATCA
1 ATTTGATTTGATTTCAATCA
*
55432245 ATTTGATTTGATTTTAATCA
1 ATTTGATTTGATTTCAATCA
55432265 A
1 A
55432266 ATTTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (20 bp):
ATTTGATTTGATTTCAATCA
Found at i:55433055 original size:82 final size:82
Alignment explanation
Indices: 55432969--55433175 Score: 299
Period size: 82 Copynumber: 2.5 Consensus size: 82
55432959 ATTCATTCCA
* * * *
55432969 TTCAACAGATTTTATTCCATTTTGATTTTGTTTCCAAACGAGAATTAATTGTATAATTCTATTTC
1 TTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGAATTAAATGGATAATTCTATTTC
*
55433034 -GAGATTTATTCTCGCCG
66 AG-GATTTATTCCCGCCG
* * * *
55433051 TTCAACATATTTTATTCTATTTTGATTTTGTTTCTAAACAATAATTAAATGGATAATTCTGTTTC
1 TTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGAATTAAATGGATAATTCTATTTC
55433116 AGGATTTATTCCCGCCG
66 AGGATTTATTCCCGCCG
* *
55433133 TTTAACATATTTTATTCGATTTTGATTTTGTTTCCAAACAAGA
1 TTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGA
55433176 CATAATTAAG
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 110 0.99
83 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.46
Consensus pattern (82 bp):
TTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGAATTAAATGGATAATTCTATTTC
AGGATTTATTCCCGCCG
Found at i:55433190 original size:82 final size:81
Alignment explanation
Indices: 55432948--55433203 Score: 284
Period size: 82 Copynumber: 3.1 Consensus size: 81
55432938 ATAAAATCTG
* ** * * *
55432948 TTTCGGGATTTATTCATTCCATTCAACAGATTTTATTCCATTTTGATTTTGTTTCCAAACGAGAA
1 TTTCAGGATTTATTCACGCCGTTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGAA
55433013 TTAATT-GTATAATTCTA
66 TTAATTAG--TAATTCTA
* * * *
55433030 TTTC-GAGATTTATTCTCGCCGTTCAACATATTTTATTCTATTTTGATTTTGTTTCTAAACAATA
1 TTTCAG-GATTTATTCACGCCGTTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGA
* * *
55433094 ATTAAATGGATAATTCTG
65 ATTAATTAG-TAATTCTA
* * *
55433112 TTTCAGGATTTATTCCCGCCGTTTAACATATTTTATTCGATTTTGATTTTGTTTCCAAACAAGAC
1 TTTCAGGATTTATTCACGCCGTTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGA-
*
55433177 A-TAATTAAGTAATTGTA
65 ATTAATT-AGTAATTCTA
55433194 TTTCAGGATT
1 TTTCAGGATT
55433204 CAATCCTGTC
Statistics
Matches: 149, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
81 1 0.01
82 144 0.97
83 4 0.03
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (81 bp):
TTTCAGGATTTATTCACGCCGTTCAACATATTTTATTCCATTTTGATTTTGTTTCCAAACAAGAA
TTAATTAGTAATTCTA
Found at i:55435772 original size:81 final size:82
Alignment explanation
Indices: 55435420--55435791 Score: 374
Period size: 82 Copynumber: 4.5 Consensus size: 82
55435410 AAAAAAATAA
* * **
55435420 AATTGAATAAAATCTATTTCGAGACTTATTCCTTCCGTTCAACAGATTTTATTCCATTTTGATTT
1 AATTGAAT-AATTCTATTTCGAGATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGATTT
* * ** * *
55435485 TTTTTCAAAATGATAACT
65 TGTTTCCAAACAAGAATT
* *
55435503 AATTGAATAATTCTATTTCGGGGTTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGATTTT
1 AATTGAATAATTCTATTTCGAGATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGATTTT
*
55435568 GTTTCCAAACTAGAATT
66 GTTTCCAAACAAGAATT
* * * * * * *
55435585 AATTGTATAATTCTACTTCTAGATTTATTCTCGCCGCTCAACATATTTTATTCTATTTTGATTTT
1 AATTGAATAATTCTATTTCGAGATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGATTTT
*
55435650 GTTTCCAAACAATAATT
66 GTTTCCAAACAAGAATT
* * * * * * * * *
55435667 AAATGAATAATTTTTTTTAG-GATTTATTCCCGCCATTTAACAAATTTTATTCGATTTTCATTTT
1 AATTGAATAATTCTATTTCGAGATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGATTTT
*
55435731 -TTTCCAAACAAGATTT
66 GTTTCCAAACAAGAATT
* * * *
55435747 AATTAAATAATTTTATTTTC-AGATTTGA-TCCTGCCGGTCAACAGA
1 AATTGAATAATTCTA-TTTCGAGATTT-ATTCCCGCCGTTCAACAGA
55435792 ATTGATTCTG
Statistics
Matches: 238, Mismatches: 48, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
80 26 0.11
81 57 0.24
82 147 0.62
83 8 0.03
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.45
Consensus pattern (82 bp):
AATTGAATAATTCTATTTCGAGATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTGATTTT
GTTTCCAAACAAGAATT
Found at i:55440325 original size:20 final size:20
Alignment explanation
Indices: 55440300--55440348 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
55440290 AAATATCTTG
55440300 ATTTGATTTGATTCTAATCA
1 ATTTGATTTGATTCTAATCA
* *
55440320 ATTTGATTTGATTTTATTCA
1 ATTTGATTTGATTCTAATCA
*
55440340 AATTGATTT
1 ATTTGATTT
55440349 AAAAGCTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (20 bp):
ATTTGATTTGATTCTAATCA
Found at i:55443342 original size:27 final size:28
Alignment explanation
Indices: 55443308--55443477 Score: 131
Period size: 27 Copynumber: 6.3 Consensus size: 28
55443298 TACCCCTGAA
55443308 GGTAAAATGACCGAAATACCCTCAGT-G
1 GGTAAAATGACCGAAATACCCTCAGTAG
*
55443335 GGTAAAATGATCGAAATACCCTC-G-ATG
1 GGTAAAATGACCGAAATACCCTCAGTA-G
* * * *
55443362 GGTAATATGATCGTAATACCCT-TGTAG
1 GGTAAAATGACCGAAATACCCTCAGTAG
* * * *
55443389 GGTAAAATGACTGTAATGCCC-CTGTAG
1 GGTAAAATGACCGAAATACCCTCAGTAG
* *
55443416 GGTAAAATGACCGTAATGCCC-CAGTAG
1 GGTAAAATGACCGAAATACCCTCAGTAG
* * *
55443443 GGTAACATAACC-ATAATACCCT-TGTAG
1 GGTAAAATGACCGA-AATACCCTCAGTAG
*
55443470 AGTAAAAT
1 GGTAAAAT
55443478 AATTGTCATG
Statistics
Matches: 120, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.01
27 118 0.98
28 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (28 bp):
GGTAAAATGACCGAAATACCCTCAGTAG
Found at i:55443420 original size:81 final size:81
Alignment explanation
Indices: 55443308--55443477 Score: 184
Period size: 81 Copynumber: 2.1 Consensus size: 81
55443298 TACCCCTGAA
* * *
55443308 GGTAAAATGACCGAAATACCCTCAGTGGGTAAAATGATCGAAATACCCTC-G-ATGGGTAATATG
1 GGTAAAATGACCGAAATACCCTCAGTGGGTAAAATGACCGAAATACCC-CAGTA-GGGTAACATA
* *
55443371 ATCGTAATACCCTTGTAG
64 ACCATAATACCCTTGTAG
* * * * * *
55443389 GGTAAAATGACTGTAATGCCC-CTGTAGGGTAAAATGACCGTAATGCCCCAGTAGGGTAACATAA
1 GGTAAAATGACCGAAATACCCTCAGT-GGGTAAAATGACCGAAATACCCCAGTAGGGTAACATAA
55443453 CCATAATACCCTTGTAG
65 CCATAATACCCTTGTAG
*
55443470 AGTAAAAT
1 GGTAAAAT
55443478 AATTGTCATG
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
80 4 0.05
81 69 0.93
82 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (81 bp):
GGTAAAATGACCGAAATACCCTCAGTGGGTAAAATGACCGAAATACCCCAGTAGGGTAACATAAC
CATAATACCCTTGTAG
Found at i:55443469 original size:54 final size:54
Alignment explanation
Indices: 55443308--55443477 Score: 148
Period size: 54 Copynumber: 3.1 Consensus size: 54
55443298 TACCCCTGAA
* * * *
55443308 GGTAAAATGACCGAAATACCCTCAGT-GGGTAAAATGATCGA-AATACCCTCG-ATG
1 GGTAAAATGACCGTAATACCC-CAGTAGGGTAAAAT-AACCATAATACCCTTGTA-G
* * ** * ** * *
55443362 GGTAATATGATCGTAATACCCTTGTAGGGTAAAATGACTGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATACCCCAGTAGGGTAAAATAACCATAATACCCTTGTAG
* *
55443416 GGTAAAATGACCGTAATGCCCCAGTAGGGTAACATAACCATAATACCCTTGTAG
1 GGTAAAATGACCGTAATACCCCAGTAGGGTAAAATAACCATAATACCCTTGTAG
*
55443470 AGTAAAAT
1 GGTAAAAT
55443478 AATTGTCATG
Statistics
Matches: 89, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
53 3 0.03
54 85 0.96
55 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (54 bp):
GGTAAAATGACCGTAATACCCCAGTAGGGTAAAATAACCATAATACCCTTGTAG
Found at i:55443562 original size:23 final size:24
Alignment explanation
Indices: 55443526--55443592 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
55443516 CCTCGAAGTC
* *
55443526 AAATGATTGTTTTGTCTGTGGTT-
1 AAATGACTGATTTGTCTGTGGTTG
*
55443549 AAATGACTGATTTGTCTGTGTTTG
1 AAATGACTGATTTGTCTGTGGTTG
**
55443573 GTATGACTGATTTGTCTGTG
1 AAATGACTGATTTGTCTGTG
55443593 ATTTGAATGG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.18, C:0.07, G:0.27, T:0.48
Consensus pattern (24 bp):
AAATGACTGATTTGTCTGTGGTTG
Found at i:55443606 original size:24 final size:23
Alignment explanation
Indices: 55443527--55443608 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 23
55443517 CTCGAAGTCA
* * * *
55443527 AATGATTGTTTTGTCTGTGGTTA
1 AATGACTGATTTGTCTGTGTTTG
55443550 AATGACTGATTTGTCTGTGTTTGG
1 AATGACTGATTTGTCTGTGTTT-G
*
55443574 TATGACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTG-TTTG
*
55443598 AATGGCTGATT
1 AATGACTGATT
55443609 CTGAGCATGG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
23 19 0.38
24 28 0.56
25 3 0.06
ACGTcount: A:0.18, C:0.07, G:0.27, T:0.48
Consensus pattern (23 bp):
AATGACTGATTTGTCTGTGTTTG
Found at i:55443881 original size:64 final size:64
Alignment explanation
Indices: 55443780--55443926 Score: 240
Period size: 64 Copynumber: 2.3 Consensus size: 64
55443770 TTTACTGCGA
55443780 TGCTACTGATGGCTTTGTGTCGATCATATTACCATTACTAATGGTTGTGTGCCGATCATATCAC
1 TGCTACTGATGGCTTTGTGTCGATCATATTACCATTACTAATGGTTGTGTGCCGATCATATCAC
* * **
55443844 TGCTACTGAAGGCTTTGTGTCGATCATGTTACCATTACTGGTGGTTGTGTGCCGATCATATCAC
1 TGCTACTGATGGCTTTGTGTCGATCATATTACCATTACTAATGGTTGTGTGCCGATCATATCAC
* *
55443908 TACTACTGATGGCTCTGTG
1 TGCTACTGATGGCTTTGTG
55443927 CCAATCACAT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 76 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTGTCGATCATATTACCATTACTAATGGTTGTGTGCCGATCATATCAC
Found at i:55443915 original size:32 final size:32
Alignment explanation
Indices: 55443782--55443933 Score: 128
Period size: 32 Copynumber: 4.8 Consensus size: 32
55443772 TACTGCGATG
* * *
55443782 CTACTGATGGCTT-TGTGTCGATCATATTACCA
1 CTACTGATGG-TTGTGTGCCGATCATATCACTA
* * *
55443814 TTACTAATGGTTGTGTGCCGATCATATCACTG
1 CTACTGATGGTTGTGTGCCGATCATATCACTA
* * * * *
55443846 CTACTGAAGGCTT-TGTGTCGATCATGTTACCA
1 CTACTGATGG-TTGTGTGCCGATCATATCACTA
* *
55443878 TTACTGGTGGTTGTGTGCCGATCATATCACTA
1 CTACTGATGGTTGTGTGCCGATCATATCACTA
* * *
55443910 CTACTGATGGCTCTGTGCCAATCA
1 CTACTGATGGTTGTGTGCCGATCA
55443934 CATTACTGTA
Statistics
Matches: 91, Mismatches: 26, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
31 4 0.04
32 85 0.93
33 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (32 bp):
CTACTGATGGTTGTGTGCCGATCATATCACTA
Found at i:55443970 original size:22 final size:22
Alignment explanation
Indices: 55443945--55443991 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
55443935 ATTACTGTAC
* * * *
55443945 TTATGGCTTGTAGTTATTCTGT
1 TTATAGCTTATAGCTATCCTGT
55443967 TTATAGCTTATAGCTATCCTGT
1 TTATAGCTTATAGCTATCCTGT
55443989 TTA
1 TTA
55443992 CGACTCTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.13, G:0.17, T:0.51
Consensus pattern (22 bp):
TTATAGCTTATAGCTATCCTGT
Found at i:55444032 original size:26 final size:26
Alignment explanation
Indices: 55444003--55444056 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
55443993 GACTCTTAGC
* *
55444003 CATTCTGACTACTGCCAGCTCTGCTG
1 CATTATGACTACTGCCAGCTATGCTG
* *
55444029 CATTATTACTACTGGCAGCTATGCTG
1 CATTATGACTACTGCCAGCTATGCTG
55444055 CA
1 CA
55444057 ATATTGGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.30, G:0.19, T:0.31
Consensus pattern (26 bp):
CATTATGACTACTGCCAGCTATGCTG
Found at i:55444061 original size:26 final size:26
Alignment explanation
Indices: 55444010--55444061 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
55444000 AGCCATTCTG
* *
55444010 ACTACTGCCAGCTCTGCTGCATTATT
1 ACTACTGCCAGCTATGCTGCAATATT
*
55444036 ACTACTGGCAGCTATGCTGCAATATT
1 ACTACTGCCAGCTATGCTGCAATATT
55444062 GGTGTGAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (26 bp):
ACTACTGCCAGCTATGCTGCAATATT
Found at i:55444832 original size:20 final size:20
Alignment explanation
Indices: 55444803--55444864 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
55444793 GGTGTTACAA
*
55444803 CATTACTGGCAGCTTATCTG
1 CATTATTGGCAGCTTATCTG
* *
55444823 CATTATTGGCAGTTTATTTG
1 CATTATTGGCAGCTTATCTG
* *
55444843 CATTATTGACAGCTTGTCTG
1 CATTATTGGCAGCTTATCTG
55444863 CA
1 CA
55444865 CTGCTGGCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
CATTATTGGCAGCTTATCTG
Found at i:55444873 original size:40 final size:40
Alignment explanation
Indices: 55444803--55444930 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 40
55444793 GGTGTTACAA
* * * * * *
55444803 CATTACTGGCAGCTTATCTGCATTATTGGCAGTTTATTTG
1 CATTACTGACAGCTTGTCTGCACTACTGGCAATTTATCTG
* * *
55444843 CATTATTGACAGCTTGTCTGCACTGCTGGCAATTTATCTA
1 CATTACTGACAGCTTGTCTGCACTACTGGCAATTTATCTG
** *
55444883 CATTACTGGTAGCTTGTCTGTACTACTGGCAATTTATCTG
1 CATTACTGACAGCTTGTCTGCACTACTGGCAATTTATCTG
*
55444923 CATCACTG
1 CATTACTG
55444931 GTGGCTTGTC
Statistics
Matches: 72, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (40 bp):
CATTACTGACAGCTTGTCTGCACTACTGGCAATTTATCTG
Found at i:55444931 original size:40 final size:40
Alignment explanation
Indices: 55444853--55444940 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
55444843 CATTATTGAC
* *
55444853 AGCTTGTCTGCACTGCTGGCAATTTATCTACATTACTGGT
1 AGCTTGTCTGCACTACTGGCAATTTATCTACATCACTGGT
* *
55444893 AGCTTGTCTGTACTACTGGCAATTTATCTGCATCACTGGT
1 AGCTTGTCTGCACTACTGGCAATTTATCTACATCACTGGT
*
55444933 GGCTTGTC
1 AGCTTGTC
55444941 CATAAATTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.38
Consensus pattern (40 bp):
AGCTTGTCTGCACTACTGGCAATTTATCTACATCACTGGT
Found at i:55449427 original size:41 final size:41
Alignment explanation
Indices: 55449382--55449538 Score: 172
Period size: 41 Copynumber: 3.8 Consensus size: 41
55449372 GCTTATTAAA
* * *
55449382 ATACACAGGCATAAAGCCTTCTAGGCACAAAGCCAGATATG
1 ATACACCGGCATAAAGCCTGCTAGGCACAAAGCCTGATATG
** *
55449423 ATACACCGGCACGAAGCCTGCTAGGCATAAAGCCTGATATG
1 ATACACCGGCATAAAGCCTGCTAGGCACAAAGCCTGATATG
* * * * *
55449464 GTACACCGGCATGAAGCCTGTTAGGCATAAAGCCTGTTAT-
1 ATACACCGGCATAAAGCCTGCTAGGCACAAAGCCTGATATG
* * *
55449504 AGTTCACCGACATAAAGCCTGCTAGGAACAAAGCC
1 A-TACACCGGCATAAAGCCTGCTAGGCACAAAGCC
55449539 CGAGTATCAT
Statistics
Matches: 98, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
41 98 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.18
Consensus pattern (41 bp):
ATACACCGGCATAAAGCCTGCTAGGCACAAAGCCTGATATG
Found at i:55449496 original size:16 final size:16
Alignment explanation
Indices: 55449471--55449502 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55449461 ATGGTACACC
*
55449471 GGCATGAAGCCTGTTA
1 GGCATAAAGCCTGTTA
55449487 GGCATAAAGCCTGTTA
1 GGCATAAAGCCTGTTA
55449503 TAGTTCACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (16 bp):
GGCATAAAGCCTGTTA
Found at i:55452811 original size:22 final size:22
Alignment explanation
Indices: 55452771--55452812 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55452761 AAAGTTAAAT
55452771 ATAAAATAATTTAATATAATGA
1 ATAAAATAATTTAATATAATGA
*
55452793 ATAAATTATATTTAA-ATAAT
1 ATAAAATA-ATTTAATATAAT
55452813 TTAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAAAATAATTTAATATAATGA
Found at i:55452847 original size:33 final size:32
Alignment explanation
Indices: 55452778--55452866 Score: 126
Period size: 33 Copynumber: 2.8 Consensus size: 32
55452768 AATATAAAAT
* * *
55452778 AATTTAATATAATGAATAAAT-TATATTTAAAT
1 AATTTAATATAATG-ATACATAAATATTTAAAC
55452810 AATTTAATATAATGATACATGAAATATTTAAAC
1 AATTTAATATAATGATACAT-AAATATTTAAAC
55452843 AATTTAATATAATGATACATAAAT
1 AATTTAATATAATGATACATAAAT
55452867 TAGAAACTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 5 0.10
32 18 0.35
33 29 0.56
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.39
Consensus pattern (32 bp):
AATTTAATATAATGATACATAAATATTTAAAC
Found at i:55453464 original size:19 final size:20
Alignment explanation
Indices: 55453440--55453503 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 20
55453430 TAAATGTTGA
*
55453440 AATTTTTATAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
55453459 AA-TTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
* * *
55453478 AATTTTTGAAATTTAATTT-
1 AATTTTTAAAAATTATTTTG
55453497 AATTTTT
1 AATTTTT
55453504 TTGTAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.21
19 18 0.46
20 13 0.33
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:55458536 original size:12 final size:11
Alignment explanation
Indices: 55458508--55458543 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
55458498 AGCAACCTCC
55458508 CCCCTATTGTA
1 CCCCTATTGTA
55458519 CCCCTATTGTA
1 CCCCTATTGTA
55458530 CCACCTATTGTA
1 CC-CCTATTGTA
55458542 CC
1 CC
55458544 TCCGGTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.19, C:0.39, G:0.08, T:0.33
Consensus pattern (11 bp):
CCCCTATTGTA
Found at i:55469401 original size:9 final size:9
Alignment explanation
Indices: 55469380--55469420 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
55469370 ATGTAAGAAT
55469380 TAAAAATTCA
1 TAAAAATT-A
55469390 TAAAAATTA
1 TAAAAATTA
55469399 TAAAAATTA
1 TAAAAATTA
*
55469408 T-AAATTTA
1 TAAAAATTA
55469416 TAAAA
1 TAAAA
55469421 TCCTTTCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.24
9 14 0.48
10 8 0.28
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:55469416 original size:17 final size:19
Alignment explanation
Indices: 55469380--55469420 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
55469370 ATGTAAGAAT
55469380 TAAAAATTCATAAAAATTA
1 TAAAAATTCATAAAAATTA
*
55469399 TAAAAATT-AT-AAATTTA
1 TAAAAATTCATAAAAATTA
55469416 TAAAA
1 TAAAA
55469421 TCCTTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.52
18 2 0.10
19 8 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAAATTCATAAAAATTA
Found at i:55471306 original size:19 final size:19
Alignment explanation
Indices: 55471282--55471335 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
55471272 AATCATATAT
55471282 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
55471301 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
55471320 TTTAAGATTGCATATC
1 TCTAAGATTGCATATC
55471336 CTTGAAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:55471333 original size:38 final size:41
Alignment explanation
Indices: 55471259--55471335 Score: 115
Period size: 38 Copynumber: 1.9 Consensus size: 41
55471249 AAATTAAATC
55471259 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCA-ATATTCTAAGATTGCATATCATA
*
55471301 TCTAAGATTAC-ATATC-ATATT-TAAGATTGCATATC
1 TCTAAGATTACAAAATCAATATTCTAAGATTGCATATC
55471336 CTTGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 14 0.41
39 5 0.15
41 4 0.12
42 11 0.32
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (41 bp):
TCTAAGATTACAAAATCAATATTCTAAGATTGCATATCATA
Found at i:55472106 original size:101 final size:101
Alignment explanation
Indices: 55471935--55472420 Score: 726
Period size: 101 Copynumber: 4.8 Consensus size: 101
55471925 CCATCTTTAG
* * * *
55471935 TCTTTTAAATTGTAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAACCTGTTCCACTACAC
1 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
* *
55472000 CGCCAGGGAAGTAAAATTTACCGTTTGCCGCTTTAA
66 CGCCAGGGAAGTAAAATTCACCGTTTGCCGCTTCAA
* *
55472036 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTATTCCGCTACAC
1 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
* *
55472101 TGCCAGGGAAGTAAAATTCACCGTTTGCGGCTTCAA
66 CGCCAGGGAAGTAAAATTCACCGTTTGCCGCTTCAA
* *
55472137 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCTGTCGTAGCTTTAATCTGTTCCACTACAC
1 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
* **
55472202 CGCTAGGGAAGTAAAATTTGCCGTTT-CCGGCTTCAA
66 CGCCAGGGAAGTAAAATTCACCGTTTGCC-GCTTCAA
* * *
55472238 TCTTTTTAATTGCAATGCTAGGGAAACGAGATTCGCCGTCATAGCTTCAATCTGTTCCACTACAC
1 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
** *
55472303 CGCCAGGGAAGTAAAATTCGTCG-TTGCGGCTTCAA
66 CGCCAGGGAAGTAAAATTCACCGTTTGCCGCTTCAA
*
55472338 TCTTTTTAATTGCAATGTTGGGGAAACTAGATTCGCCGTCG-AGCTTCAATCTGTTCCACTACAC
1 TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
* *
55472402 CGCCAGGGGAGTAAGATTC
66 CGCCAGGGAAGTAAAATTC
55472421 GTTGTTGCGG
Statistics
Matches: 349, Mismatches: 34, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
99 40 0.11
100 47 0.13
101 262 0.75
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (101 bp):
TCTTTTTAATTGCAATGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
CGCCAGGGAAGTAAAATTCACCGTTTGCCGCTTCAA
Found at i:55472161 original size:51 final size:51
Alignment explanation
Indices: 55472005--55472161 Score: 118
Period size: 51 Copynumber: 3.1 Consensus size: 51
55471995 TACACCGCCA
* * *
55472005 GGGAAGTAAAATTTACCGTTTGCCGCTTTAATCTTTTTAATTGCAATGTTG
1 GGGAAGTAAAATTCACCGTTTGCAGCTTCAATCTTTTTAATTGCAATGTTG
*** * * * * * **** * * ***
55472056 GGGAAACGAGATTCGCCG-TCGTAGCTTCAATCTATTCCGCTACACTGCCA
1 GGGAAGTAAAATTCACCGTTTGCAGCTTCAATCTTTTTAATTGCAATGTTG
*
55472106 GGGAAGTAAAATTCACCGTTTGCGGCTTCAATCTTTTTAATTGCAATGTTG
1 GGGAAGTAAAATTCACCGTTTGCAGCTTCAATCTTTTTAATTGCAATGTTG
55472157 GGGAA
1 GGGAA
55472162 ACGAGATTCG
Statistics
Matches: 67, Mismatches: 38, Indels: 2
0.63 0.36 0.02
Matches are distributed among these distances:
50 31 0.46
51 36 0.54
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (51 bp):
GGGAAGTAAAATTCACCGTTTGCAGCTTCAATCTTTTTAATTGCAATGTTG
Found at i:55472276 original size:51 final size:50
Alignment explanation
Indices: 55472020--55472389 Score: 142
Period size: 50 Copynumber: 7.4 Consensus size: 50
55472010 GTAAAATTTA
* * * *
55472020 CCGTTTGCCGCTTTAATCTTTTTAATTGCAATGTTGGGGAAACGAGATTCG
1 CCGTTT-CGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
* **** * * * *** * *
55472071 CCG--TCGTAGCTTCAATCTATTCCGCTACACTGCCAGGGAAGTAAAATTCA
1 CCGTTTCG--GCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
* *
55472121 CCGTTTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGAAACGAGATTCG
1 CCGTTT-CGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
* * * ** * * ** *** * *
55472172 -C-TGTCGTAGCTTTAATCTGTTCCACTACACCGCTAGGGAAGTAAAATTTG
1 CCGTTTCG--GCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
55472222 CCGTTTCCGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
1 CCGTTT-CGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
* * * ** * * ** * *** *
55472273 CCGTCAT-AGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAAATTCG
1 CCGT-TTCGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
* * * * *
55472323 TCGTTGCGGCTTCAATCTTTTTAATTGCAATGTTGGGGAAACTAGATTCG
1 CCGTTTCGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
55472373 CCG--TCGAGCTTCAATCT
1 CCGTTTCG-GCTTCAATCT
55472390 GTTCCACTAC
Statistics
Matches: 210, Mismatches: 96, Indels: 28
0.63 0.29 0.08
Matches are distributed among these distances:
48 5 0.02
49 13 0.06
50 120 0.57
51 64 0.30
52 4 0.02
53 4 0.02
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (50 bp):
CCGTTTCGGCTTCAATCTTTTTAATTGCAATGCTAGGGAAACGAGATTCG
Found at i:55472419 original size:49 final size:49
Alignment explanation
Indices: 55472266--55472421 Score: 120
Period size: 50 Copynumber: 3.1 Consensus size: 49
55472256 TAGGGAAACG
* *
55472266 AGATTCGCCGTCATAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTA
1 AGATTCGCCGTC-GAGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTA
* * * ** * * ** ** *
55472316 AAATTCGTCGTTGCG-GCTTCAATCTTTTTAATTGCAATG-TTGGGGA-AA
1 AGATTCGCCG-T-CGAGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTA
55472364 CTAGATTCGCCGTCGAGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTA
1 --AGATTCGCCGTCGAGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTA
55472415 AGATTCG
1 AGATTCG
55472422 TTGTTGCGGC
Statistics
Matches: 73, Mismatches: 26, Indels: 15
0.64 0.23 0.13
Matches are distributed among these distances:
48 3 0.04
49 29 0.40
50 38 0.52
51 2 0.03
52 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (49 bp):
AGATTCGCCGTCGAGCTTCAATCTGTTCCACTACACCGCCAGGGGAGTA
Found at i:55472803 original size:44 final size:44
Alignment explanation
Indices: 55472754--55472963 Score: 244
Period size: 44 Copynumber: 5.0 Consensus size: 44
55472744 GAAGTAAGAT
* *
55472754 TCACAATCTTCAACCTATTCCACTACTAACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
55472798 TCACAATCTTCAACCTATTCCACTGCTGACCA-GGAGATAGG--
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
*
55472839 -----A--TTC-ACCTATTCCACTGCTGACCAGGGAGATAGGAT
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
* * * *
55472875 TTACAATTTTCAAACTATTCCACTACTGACCAGGGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
* * * *
55472919 TTACAATTTTCAACCTATTCCATTGCTGACCAGTGAGATAGGAC
1 TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
55472963 T
1 T
55472964 AGGGTCATCG
Statistics
Matches: 146, Mismatches: 9, Indels: 22
0.82 0.05 0.12
Matches are distributed among these distances:
33 20 0.14
34 12 0.08
36 1 0.01
41 1 0.01
43 12 0.08
44 100 0.68
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27
Consensus pattern (44 bp):
TCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGAC
Found at i:55472852 original size:33 final size:34
Alignment explanation
Indices: 55472810--55472875 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
55472800 ACAATCTTCA
55472810 ACCTATTCCACTGCTGACCA-GGAGATAGGATTC
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
55472843 ACCTATTCCACTGCTGACCAGGGAGATAGGATT
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATT
55472876 TACAATTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 20 0.62
34 12 0.38
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (34 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
Found at i:55472893 original size:77 final size:78
Alignment explanation
Indices: 55472766--55472917 Score: 234
Period size: 77 Copynumber: 2.0 Consensus size: 78
55472756 ACAATCTTCA
* *
55472766 ACCTATTCCACTACTAACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACCA-
1 ACCTATTCCACTACTAACCAGGGAGATAGGACTCACAATCTTCAAACTATTCCACTACTGACCAG
55472830 GGAGATAGGATTC
66 GGAGATAGGATTC
* * * * *
55472843 ACCTATTCCACTGCTGACCAGGGAGATAGGATTTACAATTTTCAAACTATTCCACTACTGACCAG
1 ACCTATTCCACTACTAACCAGGGAGATAGGACTCACAATCTTCAAACTATTCCACTACTGACCAG
55472908 GGAGATAGGA
66 GGAGATAGGA
55472918 CTTACAATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
77 57 0.85
78 10 0.15
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (78 bp):
ACCTATTCCACTACTAACCAGGGAGATAGGACTCACAATCTTCAAACTATTCCACTACTGACCAG
GGAGATAGGATTC
Found at i:55474358 original size:16 final size:17
Alignment explanation
Indices: 55474318--55474364 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
55474308 CCTTGGCCTC
*
55474318 TCTTTTTCCTCTTATTCTT
1 TCTTTTT-CT-TTTTTCTT
55474337 TCTTTTTCTTTTTTCTT
1 TCTTTTTCTTTTTTCTT
55474354 T-TTTTTCTTTT
1 TCTTTTTCTTTT
55474365 CCTTTTTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 10 0.37
17 8 0.30
18 2 0.07
19 7 0.26
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (17 bp):
TCTTTTTCTTTTTTCTT
Found at i:55479534 original size:19 final size:19
Alignment explanation
Indices: 55479510--55479601 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
55479500 AATCATATCT
55479510 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
55479529 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
55479548 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
55479567 TCTAATATTACATATCATA
1 TCTAAGATTGCATATCATA
55479586 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
55479602 CTTGAAGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:55479559 original size:38 final size:38
Alignment explanation
Indices: 55479487--55479601 Score: 176
Period size: 38 Copynumber: 2.9 Consensus size: 38
55479477 AAATTAAATC
*
55479487 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
55479529 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
*
55479567 TCTAATATTACATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
55479602 CTTGAAGATT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
38 53 0.75
41 7 0.10
42 11 0.15
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:55479805 original size:16 final size:16
Alignment explanation
Indices: 55479779--55479811 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
55479769 TGTATATTAA
55479779 AGTTTTTTT-AATTTT
1 AGTTTTTTTAAATTTT
55479794 AGTTTTTATTAAATTTT
1 AGTTTTT-TTAAATTTT
55479811 A
1 A
55479812 ATGAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
AGTTTTTTTAAATTTT
Found at i:55485716 original size:16 final size:17
Alignment explanation
Indices: 55485685--55485718 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
55485675 ATTAGAAATG
*
55485685 AATAATTTATATATAAA
1 AATAAATTATATATAAA
55485702 AATAAATTA-ATATAAA
1 AATAAATTATATATAAA
55485718 A
1 A
55485719 TTATGTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAAATTATATATAAA
Found at i:55487226 original size:15 final size:15
Alignment explanation
Indices: 55487208--55487269 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
55487198 AAGGTTTTTG
* *
55487208 AATTATTATTTAATT
1 AATTATAATTAAATT
55487223 AATTATAATTAAATT
1 AATTATAATTAAATT
55487238 -ATTA-AAGTTAAA--
1 AATTATAA-TTAAATT
* *
55487250 AAATAGAATTAAATT
1 AATTATAATTAAATT
55487265 AATTA
1 AATTA
55487270 GTTATTGTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
13 10 0.26
14 11 0.29
15 17 0.45
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
AATTATAATTAAATT
Found at i:55488412 original size:50 final size:50
Alignment explanation
Indices: 55488331--55488456 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 50
55488321 CTCGCCACTT
* *
55488331 AGGCTTTCCAAATTATACACCACATAGGCCTTTCAGAAAACTAGACACAA
1 AGGCTTTCCAAATTATATACCACATAAGCCTTTCAGAAAACTAGACACAA
* * * ** * * *
55488381 AGGTTTTCCAAATAATATACCACATAAGCCTTTTAGGTATCTCGCCACAA
1 AGGCTTTCCAAATTATATACCACATAAGCCTTTCAGAAAACTAGACACAA
*
55488431 AGGCTTTCCAAATTATATGCCACATA
1 AGGCTTTCCAAATTATATACCACATA
55488457 GGCACCACAT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.27
Consensus pattern (50 bp):
AGGCTTTCCAAATTATATACCACATAAGCCTTTCAGAAAACTAGACACAA
Found at i:55489447 original size:25 final size:26
Alignment explanation
Indices: 55489393--55489448 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
55489383 TAGCTTAATG
*
55489393 AAGAAGAATAGAACATTTAGGTTAGA
1 AAGAAGAATAGAACATTGAGGTTAGA
*
55489419 AAGAAGAACTAGAACGTTGA-G-TAGA
1 AAGAAGAA-TAGAACATTGAGGTTAGA
55489444 AAGAA
1 AAGAA
55489449 AAACCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 9 0.33
26 9 0.33
27 9 0.33
ACGTcount: A:0.52, C:0.05, G:0.25, T:0.18
Consensus pattern (26 bp):
AAGAAGAATAGAACATTGAGGTTAGA
Found at i:55490752 original size:28 final size:28
Alignment explanation
Indices: 55490695--55490752 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
55490685 AGCTACAGAA
* *
55490695 GCTTTCCTTCTAGAGTCTCTCCATAGAG
1 GCTTTCCTTCTAGAGTCTCTCCACAAAG
55490723 GCTTTCCTTCTAGAGTCT-TGCCACAAAG
1 GCTTTCCTTCTAGAGTCTCT-CCACAAAG
55490751 GC
1 GC
55490753 ATCCTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (28 bp):
GCTTTCCTTCTAGAGTCTCTCCACAAAG
Found at i:55490773 original size:29 final size:29
Alignment explanation
Indices: 55490742--55490925 Score: 170
Period size: 29 Copynumber: 6.3 Consensus size: 29
55490732 CTAGAGTCTT
*
55490742 GCCACAAAGGCATCCTTTTAATAGAGATT
1 GCCACAAAGGCATCCTTTTAATAGAGATA
* *
55490771 GCCACAAAGGCTTCCTTTTAATAAAGATA
1 GCCACAAAGGCATCCTTTTAATAGAGATA
* * * *
55490800 GCCACAAAGACTTCCTTTTAACAAAGATA
1 GCCACAAAGGCATCCTTTTAATAGAGATA
**
55490829 GCCACAAAGGTGTCCTTTTAATAGAGATA
1 GCCACAAAGGCATCCTTTTAATAGAGATA
* ** * *
55490858 GCCACAAATGTGTCCTTTTAATCAGATATT
1 GCCACAAAGGCATCCTTTTAAT-AGAGATA
* * ** *
55490888 GTCATAAAGAAATCTTTTTAATCAGAGATA
1 GCCACAAAGGCATCCTTTTAAT-AGAGATA
*
55490918 CCCACAAA
1 GCCACAAA
55490926 AGCTTTCTTT
Statistics
Matches: 129, Mismatches: 25, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
29 98 0.76
30 31 0.24
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (29 bp):
GCCACAAAGGCATCCTTTTAATAGAGATA
Found at i:55490905 original size:87 final size:89
Alignment explanation
Indices: 55490742--55490925 Score: 207
Period size: 87 Copynumber: 2.1 Consensus size: 89
55490732 CTAGAGTCTT
*
55490742 GCCACAAAGGCATCCTTTTAATAGAGATTGCCACAAAGGCTTCCTTTTAATAAAGATAGCCACAA
1 GCCACAAAGGCATCCTTTTAATAGAGATAGCCACAAAGGCTTCCTTTTAATAAAGATAGCCACAA
**
55490807 AGACTTCC-TTTTAA-CAAAGATA
66 AGAAATCCTTTTTAATCAAAGATA
** * * *
55490829 GCCACAAAGGTGTCCTTTTAATAGAGATAGCCACAAATG-TGTCCTTTTAAT-CAGATATTGTCA
1 GCCACAAAGGCATCCTTTTAATAGAGATAGCCACAAAGGCT-TCCTTTTAATAAAGATA--GCCA
* *
55490892 TAAAGAAAT-CTTTTTAATCAGAGATA
63 CAAAGAAATCCTTTTTAATCAAAGATA
*
55490918 CCCACAAA
1 GCCACAAA
55490926 AGCTTTCTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
86 6 0.07
87 46 0.57
88 15 0.19
89 14 0.17
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (89 bp):
GCCACAAAGGCATCCTTTTAATAGAGATAGCCACAAAGGCTTCCTTTTAATAAAGATAGCCACAA
AGAAATCCTTTTTAATCAAAGATA
Found at i:55500227 original size:15 final size:15
Alignment explanation
Indices: 55500209--55500242 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
55500199 AAAATAATAA
55500209 AAAAGGAAATAAATG
1 AAAAGGAAATAAATG
*
55500224 AAAAGTAAATAAATG
1 AAAAGGAAATAAATG
55500239 AAAA
1 AAAA
55500243 AAACAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
AAAAGGAAATAAATG
Found at i:55505502 original size:17 final size:17
Alignment explanation
Indices: 55505480--55505512 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
55505470 CGATTTGAGA
55505480 TGTGGAATTAAATTAGG
1 TGTGGAATTAAATTAGG
55505497 TGTGGAATTAAATTAG
1 TGTGGAATTAAATTAG
55505513 CTTGATCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (17 bp):
TGTGGAATTAAATTAGG
Found at i:55513950 original size:29 final size:29
Alignment explanation
Indices: 55513887--55513956 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
55513877 TCATCGACAA
55513887 ATGAAAAGGGATAGCTTCAGCTATCGAGT
1 ATGAAAAGGGATAGCTTCAGCTATCGAGT
*
55513916 ACGAAAAGGGATAGCTTCAGCTATCGA-T
1 ATGAAAAGGGATAGCTTCAGCTATCGAGT
*
55513944 GATGAAAAAGGAT
1 -ATGAAAAGGGAT
55513957 GGTGATAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 1 0.03
29 36 0.97
ACGTcount: A:0.39, C:0.13, G:0.27, T:0.21
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCAGCTATCGAGT
Found at i:55513977 original size:29 final size:30
Alignment explanation
Indices: 55513945--55514017 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 30
55513935 GCTATCGATG
*
55513945 ATGAAAAAGGATGGTGATAACCATC-AACA
1 ATGAAAAGGGATGGTGATAACCATCGAACA
*
55513974 ATGAAAAGGGATGGTGATGACCATCGAACA
1 ATGAAAAGGGATGGTGATAACCATCGAACA
55514004 ATGAAAAGGGATGG
1 ATGAAAAGGGATGG
55514018 CTTCGACTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 23 0.56
30 18 0.44
ACGTcount: A:0.44, C:0.11, G:0.29, T:0.16
Consensus pattern (30 bp):
ATGAAAAGGGATGGTGATAACCATCGAACA
Found at i:55514030 original size:30 final size:30
Alignment explanation
Indices: 55513887--55514135 Score: 122
Period size: 30 Copynumber: 8.4 Consensus size: 30
55513877 TCATCGACAA
*
55513887 ATGAAAAGGGATAGCTTC-AGCTATCG-AGT
1 ATGAAAAGGGATAGCTTCGA-CTATCGAACT
*
55513916 ACGAAAAGGGATAGCTTC-AGCTATCG-A-T
1 ATGAAAAGGGATAGCTTCGA-CTATCGAACT
* * * * *
55513944 GATGAAAAAGGAT-GGTGAT-AACCATC-AACA
1 -ATGAAAAGGGATAGCT--TCGACTATCGAACT
* * *
55513974 ATGAAAAGGGAT-GGTGAT-GACCATCGAACA
1 ATGAAAAGGGATAGCT--TCGACTATCGAACT
* *
55514004 ATGAAAAGGGATGGCTTCGACTATCGATCT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
* * * * * * *
55514034 GTGGAAAGAGATAGCTCCGGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
* * *
55514064 ATGAAAAGGGATAGCTTCGGCTGTCGAAGT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
* * * *
55514094 ATGAAAAGGGATAACTTCGATTATCAAATT
1 ATGAAAAGGGATAGCTTCGACTATCGAACT
*
55514124 ATGAAAAAGGAT
1 ATGAAAAGGGAT
55514136 GTATCAACAT
Statistics
Matches: 176, Mismatches: 35, Indels: 17
0.77 0.15 0.07
Matches are distributed among these distances:
28 3 0.02
29 65 0.37
30 106 0.60
31 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGACTATCGAACT
Found at i:55514906 original size:43 final size:42
Alignment explanation
Indices: 55514858--55514984 Score: 106
Period size: 43 Copynumber: 3.1 Consensus size: 42
55514848 TGGTATAAAC
55514858 TTGGTTAAGTATGAGTTTAACAATTGACCAATTTGTGTTTATA
1 TTGGTTAAGTAT-AGTTTAACAATTGACCAATTTGTGTTTATA
* * *** * * *
55514901 TTGGTT-GGTA-A----AACAAATGGTAAATATG-GTATAAA
1 TTGGTTAAGTATAGTTTAACAATTGACCAATTTGTGTTTATA
55514936 CTTGGTTAAGTATTAGTTTAACAATTGACCAATTTGTGTTTATA
1 -TTGGTTAAGTA-TAGTTTAACAATTGACCAATTTGTGTTTATA
55514980 TTGGT
1 TTGGT
55514985 ACATGTTTTA
Statistics
Matches: 59, Mismatches: 16, Indels: 18
0.63 0.17 0.19
Matches are distributed among these distances:
35 5 0.08
36 18 0.31
37 3 0.05
39 1 0.02
40 1 0.02
42 3 0.05
43 23 0.39
44 5 0.08
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (42 bp):
TTGGTTAAGTATAGTTTAACAATTGACCAATTTGTGTTTATA
Found at i:55514954 original size:79 final size:80
Alignment explanation
Indices: 55514821--55514984 Score: 303
Period size: 79 Copynumber: 2.1 Consensus size: 80
55514811 TGGTATGTTT
55514821 TTGGTTAGTAAAACAAATGGTACAATATGGTATAAACTTGGTTAAGTATGAGTTTAACAATTGAC
1 TTGGTTAGTAAAACAAATGGTACAATATGGTATAAACTTGGTTAAGTATGAGTTTAACAATTGAC
55514886 CAATTTGTGTTTATA
66 CAATTTGTGTTTATA
* *
55514901 TTGGTTGGTAAAACAAATGGTA-AATATGGTATAAACTTGGTTAAGTATTAGTTTAACAATTGAC
1 TTGGTTAGTAAAACAAATGGTACAATATGGTATAAACTTGGTTAAGTATGAGTTTAACAATTGAC
55514965 CAATTTGTGTTTATA
66 CAATTTGTGTTTATA
55514980 TTGGT
1 TTGGT
55514985 ACATGTTTTA
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
79 61 0.74
80 21 0.26
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.39
Consensus pattern (80 bp):
TTGGTTAGTAAAACAAATGGTACAATATGGTATAAACTTGGTTAAGTATGAGTTTAACAATTGAC
CAATTTGTGTTTATA
Found at i:55521304 original size:29 final size:29
Alignment explanation
Indices: 55521239--55521308 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
55521229 TCATCGACGA
* *
55521239 ATGAAAAGGGATAGCTTTGGCTATCGAAT
1 ATGAAAAGGGATAACTTCGGCTATCGAAT
* * * *
55521268 ACGGAAAGGGATAACTTCGGCTATTGATT
1 ATGAAAAGGGATAACTTCGGCTATCGAAT
*
55521297 GTGAAAAGGGAT
1 ATGAAAAGGGAT
55521309 GGTGATGACC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.26
Consensus pattern (29 bp):
ATGAAAAGGGATAACTTCGGCTATCGAAT
Found at i:55521368 original size:30 final size:30
Alignment explanation
Indices: 55521298--55521487 Score: 161
Period size: 30 Copynumber: 6.4 Consensus size: 30
55521288 CTATTGATTG
* *
55521298 TGAAAAGGGATGGTGATGACCATC-AACAA
1 TGAAAAGGGATGGTGACGACCATCGAACTA
* *
55521327 AGAATAGGGATGGTGACGACCATCGAACTA
1 TGAAAAGGGATGGTGACGACCATCGAACTA
** ** *
55521357 TGAAAAGGGATGGCT-TTGAATATCGATCTA
1 TGAAAAGGGATGG-TGACGACCATCGAACTA
* * * * * *
55521387 TGAAAAGGGATAGCT-TCGGCTATCAAATTA
1 TGAAAAGGGAT-GGTGACGACCATCGAACTA
*
55521417 TGAAAAGGGATGGTGACGACCATCGAACAA
1 TGAAAAGGGATGGTGACGACCATCGAACTA
* * * *
55521447 TGAAAAGGGATGGTGACAACCGTCAAATTA
1 TGAAAAGGGATGGTGACGACCATCGAACTA
55521477 TGAAAAGGGAT
1 TGAAAAGGGAT
55521488 AGGTTTGGCT
Statistics
Matches: 127, Mismatches: 30, Indels: 7
0.77 0.18 0.04
Matches are distributed among these distances:
29 23 0.18
30 102 0.80
31 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (30 bp):
TGAAAAGGGATGGTGACGACCATCGAACTA
Found at i:55521473 original size:60 final size:60
Alignment explanation
Indices: 55521298--55521487 Score: 197
Period size: 60 Copynumber: 3.2 Consensus size: 60
55521288 CTATTGATTG
* * * *
55521298 TGAAAAGGGATGGTGATGACCATC-AACAAAGAATAGGGATGGTGACGACCATCGAACTA
1 TGAAAAGGGATGGTGATGACCATCGAACAATGAAAAGGGATGGTGACGACCATCAAATTA
* ** * * * * * *
55521357 TGAAAAGGGATGGCT-TTGAATATCGATCTATGAAAAGGGATAGCT-TCGGCTATCAAATTA
1 TGAAAAGGGATGG-TGATGACCATCGAACAATGAAAAGGGAT-GGTGACGACCATCAAATTA
* * *
55521417 TGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGTGACAACCGTCAAATTA
1 TGAAAAGGGATGGTGATGACCATCGAACAATGAAAAGGGATGGTGACGACCATCAAATTA
55521477 TGAAAAGGGAT
1 TGAAAAGGGAT
55521488 AGGTTTGGCT
Statistics
Matches: 101, Mismatches: 25, Indels: 9
0.75 0.19 0.07
Matches are distributed among these distances:
59 22 0.22
60 77 0.76
61 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (60 bp):
TGAAAAGGGATGGTGATGACCATCGAACAATGAAAAGGGATGGTGACGACCATCAAATTA
Found at i:55521479 original size:90 final size:90
Alignment explanation
Indices: 55521332--55521517 Score: 232
Period size: 90 Copynumber: 2.1 Consensus size: 90
55521322 AACAAAGAAT
* *** * *
55521332 AGGGATGGTGACGACCATCGAACTATGAAAAGGGATGGCTTTGAATATCGATCTATGAAAAGGGA
1 AGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCTGACAACATCAATCTATGAAAAGGGA
*
55521397 TAGCTTCGGCTATCAAATTATGAAA
66 TAGCTTCGGCTATCAAACTATGAAA
*
55521422 AGGGATGGTGACGACCATCGAACAATGAAAAGGGATGG-TGACAACCGTCAAAT-TATGAAAAGG
1 AGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCTGACAA-CATC-AATCTATGAAAAGG
* * * *
55521485 GATAGGTTTGGCTGTCGAACTATGAAA
64 GATAGCTTCGGCTATCAAACTATGAAA
55521512 AGGGAT
1 AGGGAT
55521518 AACTTTGATT
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
89 3 0.04
90 77 0.94
91 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.29, T:0.22
Consensus pattern (90 bp):
AGGGATGGTGACGACCATCGAACAATGAAAAGGGATGGCTGACAACATCAATCTATGAAAAGGGA
TAGCTTCGGCTATCAAACTATGAAA
Found at i:55521518 original size:30 final size:29
Alignment explanation
Indices: 55521298--55521517 Score: 129
Period size: 30 Copynumber: 7.4 Consensus size: 29
55521288 CTATTGATTG
* *
55521298 TGAAAAGGGATGGTGAT-GACCATC-AACAA
1 TGAAAAGGGATGGT--TCGACTATCGAACTA
* * * *
55521327 AGAATAGGGATGGTGACGACCATCGAACTA
1 TGAAAAGGGATGGT-TCGACTATCGAACTA
* * *
55521357 TGAAAAGGGATGGCTTTGAATATCGATCTA
1 TGAAAAGGGATGG-TTCGACTATCGAACTA
* * * *
55521387 TGAAAAGGGATAGCTTCGGCTATCAAATTA
1 TGAAAAGGGAT-GGTTCGACTATCGAACTA
* * *
55521417 TGAAAAGGGATGGTGACGACCATCGAACAA
1 TGAAAAGGGATGGT-TCGACTATCGAACTA
* * ** * *
55521447 TGAAAAGGGATGGTGACAACCGTCAAATTA
1 TGAAAAGGGATGGT-TCGACTATCGAACTA
* * *
55521477 TGAAAAGGGATAGGTTTGGCTGTCGAACTA
1 TGAAAAGGGAT-GGTTCGACTATCGAACTA
55521507 TGAAAAGGGAT
1 TGAAAAGGGAT
55521518 AACTTTGATT
Statistics
Matches: 147, Mismatches: 38, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
29 21 0.14
30 121 0.82
31 5 0.03
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.21
Consensus pattern (29 bp):
TGAAAAGGGATGGTTCGACTATCGAACTA
Found at i:55526115 original size:150 final size:150
Alignment explanation
Indices: 55525844--55526144 Score: 530
Period size: 150 Copynumber: 2.0 Consensus size: 150
55525834 AGAATGTGAT
* *
55525844 TGGTGTACCACCTGGATACAATCAACCAATGCTGCGGCAAAATGTGTAACAAAGCTTGTCATCTT
1 TGGTGTACCACCTGCATACAATCAACCAATGCTGCGGCAAAATGTGCAACAAAGCTTGTCATCTT
** *
55525909 CAACATCATTTATGGAAGCTCTCTTAAAGGAGTATATGGCTAAGAATGATGTAATTATTCAGAGC
66 CAACATCAACTATAGAAGCTCTCTTAAAGGAGTATATGGCTAAGAATGATGTAATTATTCAGAGC
55525974 CAGGTAGCTTTCTTAAGAGC
131 CAGGTAGCTTTCTTAAGAGC
* * *
55525994 TGGTGTACCACTTGCATACAGTCAACCAATGCTGCGGCAAAATGTGCAACAAAGTTTGTCATCTT
1 TGGTGTACCACCTGCATACAATCAACCAATGCTGCGGCAAAATGTGCAACAAAGCTTGTCATCTT
55526059 CAACATCAACTATAGAAGCTCTCTTAAAGGAGTATATGGCTAAGAATGATGTAATTATTCAGAGC
66 CAACATCAACTATAGAAGCTCTCTTAAAGGAGTATATGGCTAAGAATGATGTAATTATTCAGAGC
55526124 CAGGTAGCTTTCTTAAGAGC
131 CAGGTAGCTTTCTTAAGAGC
55526144 T
1 T
55526145 CTAGAGAATC
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 143 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (150 bp):
TGGTGTACCACCTGCATACAATCAACCAATGCTGCGGCAAAATGTGCAACAAAGCTTGTCATCTT
CAACATCAACTATAGAAGCTCTCTTAAAGGAGTATATGGCTAAGAATGATGTAATTATTCAGAGC
CAGGTAGCTTTCTTAAGAGC
Found at i:55542531 original size:28 final size:28
Alignment explanation
Indices: 55542499--55542743 Score: 375
Period size: 28 Copynumber: 8.8 Consensus size: 28
55542489 AACAGTATTG
*
55542499 TGTGGGCCTTAGCCCAATACAGCAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
* *
55542527 TGTGGGCCCTAGCCTAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
* *
55542555 TATGGGTCTTAGCCCAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
55542583 TGTGGGCCTTAGCCCAAAACA-TCAACAA
1 TGTGGGCCTTAGCCCAATACAGT-AACAA
*
55542611 TGTGGGCCTTAGCCCAATACAATAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
55542639 TGTGGGCTTTAGCCCAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
**
55542667 TGTGGGCCTTAGCCCAATACAACAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
55542695 TGTGGGCCTTAGCCCAAAACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
55542723 TGTGGGCCTTAGCCCAATACA
1 TGTGGGCCTTAGCCCAATACA
55542744 ATATCGGTAT
Statistics
Matches: 195, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
27 1 0.01
28 193 0.99
29 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGTAACAA
Found at i:55542968 original size:27 final size:27
Alignment explanation
Indices: 55542930--55543001 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
55542920 GGGACCCGTG
55542930 GGGGTAATTCGGTTATTTTATCCTATA
1 GGGGTAATTCGGTTATTTTATCCTATA
*
55542957 GGGGTAATTCGGTTATTTTATCCTGTA
1 GGGGTAATTCGGTTATTTTATCCTATA
*
55542984 GGGGTAATTCGGTCATTT
1 GGGGTAATTCGGTTATTT
55543002 ACTGACCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.43
Consensus pattern (27 bp):
GGGGTAATTCGGTTATTTTATCCTATA
Found at i:55549996 original size:23 final size:22
Alignment explanation
Indices: 55549944--55549996 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
55549934 TCCACGTCTT
*
55549944 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
55549966 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
55549989 TTTCTTTT
1 TTTCTTTT
55549997 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:55559075 original size:37 final size:35
Alignment explanation
Indices: 55559012--55559080 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 35
55559002 ATTCCAACAA
*
55559012 TAATATTATTTTAATAGTTTAATATTAAATTTAATC
1 TAATATTATCTTAATAGTTTAATATT-AATTTAATC
*
55559048 TAATACTTATCTTAATAGTATT-TTATTAATTTA
1 TAATA-TTATCTTAATAGT-TTAATATTAATTTA
55559081 TTATTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 11 0.38
37 16 0.55
38 2 0.07
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (35 bp):
TAATATTATCTTAATAGTTTAATATTAATTTAATC
Found at i:55559214 original size:59 final size:62
Alignment explanation
Indices: 55559098--55559214 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 62
55559088 ATTGATTATC
* * * * *
55559098 TTAAAATTAAATTTCATTTAATGTTTATCTTGTAGATAAACATTCTATTATTTTAATAAGAT
1 TTAAAATTAAATTTAATCTAATATTTATCTTGTAGATAAACATTATATTAATTTAATAAGAT
* *
55559160 TTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATA
1 TTAAAATTAAATTTAATCTAATATTTATCTTGTAGATAAACATTATATTAATTTAATA
55559215 TTAAATTGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 21 0.44
60 1 0.02
61 1 0.02
62 25 0.52
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (62 bp):
TTAAAATTAAATTTAATCTAATATTTATCTTGTAGATAAACATTATATTAATTTAATAAGAT
Found at i:55561216 original size:50 final size:50
Alignment explanation
Indices: 55561105--55561352 Score: 207
Period size: 50 Copynumber: 4.9 Consensus size: 50
55561095 ATTTGGGTAA
* *
55561105 AGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATTATTGAGATTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ATCGAG---ATG
* **
55561161 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCATCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
* ** * * * * *
55561211 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCAATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
* * * *
55561261 AGA-ACTCTCATGTAAGACCATATCTGGGATATGGCATTGGTAGTAC-A-A-G
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-T-CGAGATG
* * *
55561310 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
55561353 GTTATTATCA
Statistics
Matches: 159, Mismatches: 29, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
48 1 0.01
49 35 0.22
50 78 0.49
51 1 0.01
52 1 0.01
53 5 0.03
56 38 0.24
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
Found at i:55564315 original size:40 final size:38
Alignment explanation
Indices: 55564221--55564319 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 38
55564211 GAAATCCTTG
*
55564221 TTATAATTATTGTAATTAT-AATTTAGGATCAAATATTA
1 TTATAATTA-TGTAATTATAAATTTAGGATCAAACATTA
* ** *
55564259 TTATAATTACTATAATTATAAATTTTTTGCTCAAACATTA
1 TTATAATTA-TGTAATTATAAA-TTTAGGATCAAACATTA
55564299 TTATAATTATGGTAATTATAA
1 TTATAATTAT-GTAATTATAA
55564320 CTATTATATT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
38 17 0.33
39 3 0.06
40 31 0.61
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.47
Consensus pattern (38 bp):
TTATAATTATGTAATTATAAATTTAGGATCAAACATTA
Found at i:55567130 original size:31 final size:31
Alignment explanation
Indices: 55567093--55567154 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
55567083 AGATAATTTT
55567093 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
55567124 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
55567155 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:55572876 original size:31 final size:31
Alignment explanation
Indices: 55572839--55572899 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
55572829 AGATAATTTT
55572839 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
55572870 AAAGAGTTTTATTAGGATTCAATTACTCTT
1 AAAGAGTTTTATTAGGATTCAATTACTCTT
55572900 TTAATTTGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.43
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:55574826 original size:11 final size:11
Alignment explanation
Indices: 55574810--55574834 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55574800 TTTTGAGTAA
55574810 TTTGGTTAAGT
1 TTTGGTTAAGT
55574821 TTTGGTTAAGT
1 TTTGGTTAAGT
55574832 TTT
1 TTT
55574835 ATAATGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (11 bp):
TTTGGTTAAGT
Found at i:55577950 original size:17 final size:17
Alignment explanation
Indices: 55577928--55577962 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
55577918 TTAGCAGTCA
*
55577928 ATCGTGAGGCTGGAATT
1 ATCGTGAGACTGGAATT
55577945 ATCGTGAGACTGGAATT
1 ATCGTGAGACTGGAATT
55577962 A
1 A
55577963 ACATTCGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (17 bp):
ATCGTGAGACTGGAATT
Found at i:55589118 original size:25 final size:25
Alignment explanation
Indices: 55589011--55589134 Score: 153
Period size: 25 Copynumber: 5.0 Consensus size: 25
55589001 CGAATACTTC
55589011 ATAGCTCATGAGAGCATA-CTGATTT
1 ATAGCTCATGAGAGCATATC-GATTT
*
55589036 ATAGCTCATGAGAGCATACCGATTT
1 ATAGCTCATGAGAGCATATCGATTT
* *
55589061 ATAGCTCATGAGAGGATATTGATTT
1 ATAGCTCATGAGAGCATATCGATTT
* * *
55589086 ATAGCTCGTGGGAGCATATCGATCT
1 ATAGCTCATGAGAGCATATCGATTT
*
55589111 ATAGCTCGA-GTGAGCATATCGATT
1 ATAGCTC-ATGAGAGCATATCGATT
55589135 CACAGCTCCT
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
25 85 0.99
26 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (25 bp):
ATAGCTCATGAGAGCATATCGATTT
Found at i:55589141 original size:25 final size:25
Alignment explanation
Indices: 55589088--55589142 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
55589078 ATTGATTTAT
* *
55589088 AGCTCGTGGGAGCATATCGATCTAT
1 AGCTCGAGGGAGCATATCGATCTAC
*
55589113 AGCTCGAGTGAGCATATCGAT-TCAC
1 AGCTCGAGGGAGCATATCGATCT-AC
55589138 AGCTC
1 AGCTC
55589143 CTATGAGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (25 bp):
AGCTCGAGGGAGCATATCGATCTAC
Found at i:55605330 original size:22 final size:22
Alignment explanation
Indices: 55605282--55605333 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
55605272 TACTTCATGG
* * *
55605282 AGTGTGAACACATTTATGTTTT
1 AGTGTGAACACACTTAAGTGTT
55605304 AGTGTGAACA-ACTTAAGTGTT
1 AGTGTGAACACACTTAAGTGTT
55605325 AGGTGTGAA
1 A-GTGTGAA
55605334 TGTGTTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.37
Consensus pattern (22 bp):
AGTGTGAACACACTTAAGTGTT
Found at i:55624387 original size:29 final size:29
Alignment explanation
Indices: 55624355--55624414 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
55624345 ATATTAGTTG
55624355 TTATTTAAAAGTATTTTGTTAAGTGATTT
1 TTATTTAAAAGTATTTTGTTAAGTGATTT
55624384 TTATTTAAAAGTATTTTGTTAAGTGATTT
1 TTATTTAAAAGTATTTTGTTAAGTGATTT
55624413 TT
1 TT
55624415 GATAAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (29 bp):
TTATTTAAAAGTATTTTGTTAAGTGATTT
Found at i:55633569 original size:15 final size:15
Alignment explanation
Indices: 55633546--55633607 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
55633536 CGAATAAAAT
55633546 TTTAAATTTTTATAA
1 TTTAAATTTTTATAA
*
55633561 TTTATATTTTTATAA
1 TTTAAATTTTTATAA
* *
55633576 TTTTAAAGTATTA-AA
1 -TTTAAATTTTTATAA
*
55633591 -TTAAAATTTTATAA
1 TTTAAATTTTTATAA
55633605 TTT
1 TTT
55633608 TAGAATGAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 18 0.47
16 9 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTAAATTTTTATAA
Done.