Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 181 of 199
Found at i:52379663 original size:2 final size:2
Alignment explanation
Indices: 52379656--52379680 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52379646 TGAAATATTT
52379656 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 T
52379681 TTATTTAGGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52380491 original size:22 final size:24
Alignment explanation
Indices: 52380466--52380513 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
52380456 TTTTACTTTT
52380466 AATAAATAAATATA-TAAA-TAAA
1 AATAAATAAATATACTAAACTAAA
*
52380488 AATAAATTAATATACTAAACTAAA
1 AATAAATAAATATACTAAACTAAA
52380512 AA
1 AA
52380514 AATTATTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.57
23 4 0.17
24 6 0.26
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (24 bp):
AATAAATAAATATACTAAACTAAA
Found at i:52380545 original size:29 final size:30
Alignment explanation
Indices: 52380508--52380569 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
52380498 TATACTAAAC
*
52380508 TAAAAAAAT-TATTCTTATTTACTTCAAAA
1 TAAAAAAATATAATCTTATTTACTTCAAAA
*
52380537 TAAAAAAATATAATCTTATTTGCTTCAAAA
1 TAAAAAAATATAATCTTATTTACTTCAAAA
52380567 TAA
1 TAA
52380570 CAAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.39
Consensus pattern (30 bp):
TAAAAAAATATAATCTTATTTACTTCAAAA
Found at i:52380889 original size:2 final size:2
Alignment explanation
Indices: 52380884--52380916 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
52380874 CTAAAAAATT
*
52380884 TA TA TA TA TA TA TA TA TA TA TG TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52380917 AAGAAGCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52386718 original size:22 final size:19
Alignment explanation
Indices: 52386697--52386741 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
52386687 GCAATAAAAT
* *
52386697 AATAACAACATAATAGTGA
1 AATAATAACAAAATAGTGA
**
52386716 AATTGTAACAAAATAGTGA
1 AATAATAACAAAATAGTGA
52386735 AATAATA
1 AATAATA
52386742 GGAAGAAAAT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.58, C:0.07, G:0.11, T:0.24
Consensus pattern (19 bp):
AATAATAACAAAATAGTGA
Found at i:52387941 original size:58 final size:55
Alignment explanation
Indices: 52387868--52387976 Score: 157
Period size: 58 Copynumber: 1.9 Consensus size: 55
52387858 TTATTATTAA
*
52387868 ATTTTAATAAAATTATTATTGAAA-ATAATTTAATAAAAATAATAAATAATTTAACCAT
1 ATTTTAACAAAATTATTATT-AAATATAATTTAATAAAAA-AAT--ATAATTTAACCAT
*
52387926 ATTTTAACATAATTATTATTAAATATAATTTAATAAAAAAATATAATTTAA
1 ATTTTAACAAAATTATTATTAAATATAATTTAATAAAAAAATATAATTTAA
52387977 TAACATTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
55 9 0.19
57 6 0.12
58 33 0.69
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (55 bp):
ATTTTAACAAAATTATTATTAAATATAATTTAATAAAAAAATATAATTTAACCAT
Found at i:52388192 original size:22 final size:22
Alignment explanation
Indices: 52388167--52388222 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
52388157 ATAACTTGAG
52388167 AATTATATTAAGAATG-TTATTA
1 AATTATATTAAGAA-GATTATTA
*
52388189 AATTATATTTAATAAGATTATTA
1 AATTATA-TTAAGAAGATTATTA
52388212 AGATTAT-TTAA
1 A-ATTATATTAA
52388223 AAGTAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 12 0.40
23 13 0.43
24 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (22 bp):
AATTATATTAAGAAGATTATTA
Found at i:52389617 original size:57 final size:59
Alignment explanation
Indices: 52389524--52389670 Score: 192
Period size: 57 Copynumber: 2.5 Consensus size: 59
52389514 ACTCTAATTC
* * * *
52389524 GGATTACCCGTCTGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATGTC-A-A
1 GGATCACCCGTCCGGGCTAGATCC-TTTTCCACATATTCTTCGGGAGGGCTATATCGATA
52389582 -GATCACCCGTCCGGGCTAGATCCTTTTCACACATATTCTTCGGGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTC-CACATATTCTTCGGGAGGGCTATATC--GATA
*
52389643 GGATCACCCGTCCAGGCTAGATCCTTTT
1 GGATCACCCGTCCGGGCTAGATCCTTTT
52389671 TACCGTCAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
56 5 0.06
57 45 0.58
60 1 0.01
61 1 0.01
62 26 0.33
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (59 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
Found at i:52395844 original size:22 final size:22
Alignment explanation
Indices: 52395819--52395861 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52395809 CAAAACAGGA
* *
52395819 AAAATACGTATATGTATATATT
1 AAAACACGTATATATATATATT
*
52395841 AAAACACTTATATATATATAT
1 AAAACACGTATATATATATAT
52395862 ATAATATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (22 bp):
AAAACACGTATATATATATATT
Found at i:52397866 original size:10 final size:11
Alignment explanation
Indices: 52397854--52397883 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
52397844 ATTTTATACG
52397854 AAATAAAACGA
1 AAATAAAACGA
52397865 AAATAAAA-GA
1 AAATAAAACGA
52397875 AAATAAAAC
1 AAATAAAAC
52397884 ACATATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (11 bp):
AAATAAAACGA
Found at i:52400673 original size:15 final size:17
Alignment explanation
Indices: 52400640--52400677 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
52400630 TTTTCATAAA
52400640 TATATACTTATATACTT
1 TATATACTTATATACTT
*
52400657 TATAT-CTTATTTA-TT
1 TATATACTTATATACTT
52400672 TATATA
1 TATATA
52400678 TCCTTGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 7 0.37
17 5 0.26
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATACTTATATACTT
Found at i:52410827 original size:45 final size:45
Alignment explanation
Indices: 52410762--52410926 Score: 177
Period size: 45 Copynumber: 3.6 Consensus size: 45
52410752 GCATTTAAAA
* *
52410762 AGATTGAAGCTACAATAGCGGATCTTACTAGTGATGCGGTGGAGC
1 AGATTGAAGCTACAACAGCGGATCTTACTAGTGATGCAGTGGAGC
** * ** **
52410807 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCATTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTAC-T-AGTG--A-TGCAGTGGAGC
* *
52410857 AGATTGAAGCTACAACAGCGGATCTTATTAGTGATGCAGCGGAGC
1 AGATTGAAGCTACAACAGCGGATCTTACTAGTGATGCAGTGGAGC
*
52410902 AGATTGAAGCTACAACAGCGAATCT
1 AGATTGAAGCTACAACAGCGGATCT
52410927 CACTTCCCCG
Statistics
Matches: 96, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
45 56 0.58
46 2 0.02
47 2 0.02
48 2 0.02
49 2 0.02
50 32 0.33
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (45 bp):
AGATTGAAGCTACAACAGCGGATCTTACTAGTGATGCAGTGGAGC
Found at i:52410869 original size:50 final size:50
Alignment explanation
Indices: 52410726--52410883 Score: 200
Period size: 50 Copynumber: 3.3 Consensus size: 50
52410716 TCCTGCACTG
52410726 ACAGCGGATCTTACTTCCCTGACATTGCATTTAAAAAGATTGAAGCTACA
1 ACAGCGGATCTTACTTCCCTGACATTGCATTTAAAAAGATTGAAGCTACA
* ** ** ** **
52410776 ATAGCGGATCTTAC-T-AGTG--A-TGCGGTGGAGCAGATTGAAGCTACA
1 ACAGCGGATCTTACTTCCCTGACATTGCATTTAAAAAGATTGAAGCTACA
52410821 ACAGCGGATCTTACTTCCCTGACATTGCATTTAAAAAGATTGAAGCTACA
1 ACAGCGGATCTTACTTCCCTGACATTGCATTTAAAAAGATTGAAGCTACA
52410871 ACAGCGGATCTTA
1 ACAGCGGATCTTA
52410884 TTAGTGATGC
Statistics
Matches: 85, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
45 32 0.38
46 2 0.02
47 2 0.02
48 2 0.02
49 2 0.02
50 45 0.53
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (50 bp):
ACAGCGGATCTTACTTCCCTGACATTGCATTTAAAAAGATTGAAGCTACA
Found at i:52411030 original size:48 final size:48
Alignment explanation
Indices: 52410958--52411128 Score: 146
Period size: 48 Copynumber: 3.5 Consensus size: 48
52410948 TAAAAGATCA
* * * *
52410958 AAGCCACAGCGGCTAATCTCACTTCTGGCGATGTAGCGGAGCAGATTG
1 AAGCTACAACGGCGAATCTCACTTCTGGCGATGTAGTGGAGCAGATTG
* ** * * ** ** *
52411006 AAACTACAACGGCGAATCTCACTTC-CCCGACATTGCAATTTAAAAGATCG
1 AAGCTACAACGGCGAATCTCACTTCTGGCG--A-TGTAGTGGAGCAGATTG
* * *
52411056 AAGCCACAGCGGCGAATCTTACTTCTGGCGATGTAGTGGAGCAGATTG
1 AAGCTACAACGGCGAATCTCACTTCTGGCGATGTAGTGGAGCAGATTG
*
52411104 AAGCTACAACAGCGAATCTCACTTC
1 AAGCTACAACGGCGAATCTCACTTC
52411129 CCCGACATTG
Statistics
Matches: 88, Mismatches: 31, Indels: 8
0.69 0.24 0.06
Matches are distributed among these distances:
47 2 0.02
48 52 0.59
49 2 0.02
50 30 0.34
51 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.22
Consensus pattern (48 bp):
AAGCTACAACGGCGAATCTCACTTCTGGCGATGTAGTGGAGCAGATTG
Found at i:52411200 original size:99 final size:98
Alignment explanation
Indices: 52410726--52411303 Score: 668
Period size: 98 Copynumber: 5.9 Consensus size: 98
52410716 TCCTGCACTG
* * * * * ** *
52410726 ACAGCGGATCTTACTTCCCTGACATTGC-ATTTAAAAAGATTGAAGCTACAATAGCGGATCTTA-
1 ACAGCGAATCTCACTTCCCCGACATTGCAATTT-AAAAGATCGAAGCCACAACGGCGAATCTTAC
* * * *
52410789 --CTAGTGATGCGGTGGAGCAGATTGAAGCTACA
65 TTCTGGCGATGCAGCGGAGCAGATTGAAGCTACA
* * * * * * *
52410821 ACAGCGGATCTTACTTCCCTGACATTGC-ATTTAAAAAGATTGAAGCTACAACAGCGGATCTTA-
1 ACAGCGAATCTCACTTCCCCGACATTGCAATTT-AAAAGATCGAAGCCACAACGGCGAATCTTAC
* *
52410884 -T-TAGTGATGCAGCGGAGCAGATTGAAGCTACA
65 TTCTGGCGATGCAGCGGAGCAGATTGAAGCTACA
* * * * *
52410916 ACAGCGAATCTCACTTCCCCGACACTGCAATTTAAAAGATCAAAGCCACAGCGGCTAATCTCACT
1 ACAGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACT
* *
52410981 TCTGGCGATGTAGCGGAGCAGATTGAAACTACA
66 TCTGGCGATGCAGCGGAGCAGATTGAAGCTACA
* *
52411014 ACGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCGAAGCCACAGCGGCGAATCTTACT
1 ACAGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACT
* *
52411079 TCTGGCGATGTAGTGGAGCAGATTGAAGCTACA
66 TCTGGCGATGCAGCGGAGCAGATTGAAGCTACA
* *
52411112 ACAGCGAATCTCACTTCCCCGACATTGCAAATTTAAAAGATCGAAGCCACAACGGTGAATCTTAT
1 ACAGCGAATCTCACTTCCCCGACATTGC-AATTTAAAAGATCGAAGCCACAACGGCGAATCTTAC
* * * *
52411177 TTTTGGCGATGCAGTGGAACAGATTGAAACTACA
65 TTCTGGCGATGCAGCGGAGCAGATTGAAGCTACA
** *
52411211 ATGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCGAAGCCACAACAGCGAATCTTACT
1 ACAGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACT
* * *
52411276 TCCAGGCGACGCAGCGGAACAGATTGAA
66 T-CTGGCGATGCAGCGGAGCAGATTGAA
52411304 ACCTCTACGG
Statistics
Matches: 433, Mismatches: 43, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
95 137 0.32
96 4 0.01
97 1 0.00
98 180 0.42
99 111 0.26
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (98 bp):
ACAGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACT
TCTGGCGATGCAGCGGAGCAGATTGAAGCTACA
Found at i:52411209 original size:197 final size:196
Alignment explanation
Indices: 52410794--52411303 Score: 697
Period size: 197 Copynumber: 2.6 Consensus size: 196
52410784 TCTTACTAGT
* * * * * *
52410794 GATGCGGTGGAGCAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGC-ATTTAAAAA
1 GATGCAGTGGAGCAGATTGAAACTACAACGGCGAATCTCACTTCCCCGACATTGCAATTT-AAAA
* * * *
52410858 GATTGAAGCTACAACAGCGGATCTTA--T-TAGTGATGCAGCGGAGCAGATTGAAGCTACAACAG
65 GATCGAAGCCACAACAGCGAATCTTACTTCTAGCGATGCAGCGGAGCAGATTGAAGCTACAACAG
*
52410920 CGAATCTCACTTCCCCGACACTGCAATTTAAAAGATCAAAGCCACAGCGGCTAATCTCACTTCTG
130 CGAATCTCACTTCCCCGACACTGCAATTTAAAAGATCAAAGCCACAACGGCTAATCTCACTTCTG
52410985 GC
195 GC
* *
52410987 GATGTAGCGGAGCAGATTGAAACTACAACGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAG
1 GATGCAGTGGAGCAGATTGAAACTACAACGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAG
* * * * *
52411052 ATCGAAGCCACAGCGGCGAATCTTACTTCTGGCGATGTAGTGGAGCAGATTGAAGCTACAACAGC
66 ATCGAAGCCACAACAGCGAATCTTACTTCTAGCGATGCAGCGGAGCAGATTGAAGCTACAACAGC
* * * * *
52411117 GAATCTCACTTCCCCGACATTGCAAATTTAAAAGATCGAAGCCACAACGG-TGAATCTTATTTTT
131 GAATCTCACTTCCCCGACACTGC-AATTTAAAAGATCAAAGCCACAACGGCT-AATCTCACTTCT
52411181 GGC
194 GGC
* *
52411184 GATGCAGTGGAACAGATTGAAACTACAATGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAG
1 GATGCAGTGGAGCAGATTGAAACTACAACGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAG
* * *
52411249 ATCGAAGCCACAACAGCGAATCTTACTTCCAGGCGACGCAGCGGAACAGATTGAA
66 ATCGAAGCCACAACAGCGAATCTTACTTCTA-GCGATGCAGCGGAGCAGATTGAA
52411304 ACCTCTACGG
Statistics
Matches: 275, Mismatches: 35, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
193 72 0.26
194 4 0.01
195 1 0.00
196 55 0.20
197 124 0.45
198 19 0.07
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (196 bp):
GATGCAGTGGAGCAGATTGAAACTACAACGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAG
ATCGAAGCCACAACAGCGAATCTTACTTCTAGCGATGCAGCGGAGCAGATTGAAGCTACAACAGC
GAATCTCACTTCCCCGACACTGCAATTTAAAAGATCAAAGCCACAACGGCTAATCTCACTTCTGG
C
Found at i:52418263 original size:15 final size:17
Alignment explanation
Indices: 52418230--52418267 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
52418220 TTTTCATAAA
52418230 TATATACTTATATACTT
1 TATATACTTATATACTT
*
52418247 TATAT-CTTATTTA-TT
1 TATATACTTATATACTT
52418262 TATATA
1 TATATA
52418268 TCCTTGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 7 0.37
17 5 0.26
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATACTTATATACTT
Found at i:52420197 original size:40 final size:41
Alignment explanation
Indices: 52420129--52420205 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 41
52420119 GTTGATGGAA
* *
52420129 AATATAAATTGTGATTATTATGCATTTAAAAATAATAATTT
1 AATAAAAATTGTGATTATTATACATTTAAAAATAATAATTT
**
52420170 AATAAAAATTGTGA-TATTATATTTTTAAAAATAATA
1 AATAAAAATTGTGATTATTATACATTTAAAAATAATA
52420206 TAATTTAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 19 0.59
41 13 0.41
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.43
Consensus pattern (41 bp):
AATAAAAATTGTGATTATTATACATTTAAAAATAATAATTT
Found at i:52422808 original size:18 final size:18
Alignment explanation
Indices: 52422785--52422832 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
52422775 GATTTTTTTA
52422785 TTTTATAATTT-AATAGAT
1 TTTTATAATTTGAATA-AT
52422803 TTTTATAAATTTGAATAAT
1 TTTTAT-AATTTGAATAAT
* *
52422822 CTTTATGATTT
1 TTTTATAATTT
52422833 CATTATTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 10 0.38
19 12 0.46
20 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTTATAATTTGAATAAT
Found at i:52422883 original size:21 final size:21
Alignment explanation
Indices: 52422857--52422896 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52422847 TTTAAAGTTT
52422857 TATATTTTTTGGAATTTTTAA
1 TATATTTTTTGGAATTTTTAA
*
52422878 TATATTTTTTTGAATTTTT
1 TATATTTTTTGGAATTTTT
52422897 TTCATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
TATATTTTTTGGAATTTTTAA
Found at i:52433781 original size:23 final size:24
Alignment explanation
Indices: 52433755--52433801 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
52433745 TAAAGATTAA
52433755 AAAAATGAAAAAATA-TAAAAAAT
1 AAAAATGAAAAAATATTAAAAAAT
* *
52433778 AAAAATTAAAAATTATTAAAAAAT
1 AAAAATGAAAAAATATTAAAAAAT
52433802 TTACGTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (24 bp):
AAAAATGAAAAAATATTAAAAAAT
Found at i:52434738 original size:18 final size:18
Alignment explanation
Indices: 52434715--52434757 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
52434705 TATTTGTACA
52434715 TTTTATG-ATTTTAAATAT
1 TTTTATGTATTTTAAAT-T
*
52434733 TTTTATTGTTTTTTAAATT
1 TTTTA-TGTATTTTAAATT
52434752 TTTTAT
1 TTTTAT
52434758 TTTTAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.27
19 8 0.36
20 8 0.36
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTATGTATTTTAAATT
Found at i:52434767 original size:18 final size:19
Alignment explanation
Indices: 52434726--52434769 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
52434716 TTTATGATTT
**
52434726 TAAATATTTTTATTGTTTTT
1 TAAAT-TTTTTATTGTTTAA
52434746 TAAATTTTTTATT-TTTAA
1 TAAATTTTTTATTGTTTAA
52434764 TAAATT
1 TAAATT
52434770 CAATTCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 8 0.36
20 5 0.23
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TAAATTTTTTATTGTTTAA
Found at i:52435195 original size:8 final size:7
Alignment explanation
Indices: 52435168--52435193 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52435158 GACACATCAT
52435168 AAAAATA
1 AAAAATA
52435175 AAAAATA
1 AAAAATA
52435182 AAAAATA
1 AAAAATA
52435189 AAAAA
1 AAAAA
52435194 ATTGCTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:52436237 original size:6 final size:6
Alignment explanation
Indices: 52436228--52436253 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52436218 GGAACTTGAA
52436228 CTGGAT CTGGAT CTGGAT CTGGAT CT
1 CTGGAT CTGGAT CTGGAT CTGGAT CT
52436254 CTCTCTCTTT
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:0.15, C:0.19, G:0.31, T:0.35
Consensus pattern (6 bp):
CTGGAT
Found at i:52437556 original size:41 final size:41
Alignment explanation
Indices: 52437506--52437584 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
52437496 TCCAAACTGA
52437506 TCTAAATGCAGGCTAGCCTGCATTTTCTTTCTTTCTTTCTT
1 TCTAAATGCAGGCTAGCCTGCATTTTCTTTCTTTCTTTCTT
52437547 TCTAAATGCAGGCTAGCCTGCATTTTCTTTCTTTCTTT
1 TCTAAATGCAGGCTAGCCTGCATTTTCTTTCTTTCTTT
52437585 TTAAAGCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.15, C:0.24, G:0.13, T:0.48
Consensus pattern (41 bp):
TCTAAATGCAGGCTAGCCTGCATTTTCTTTCTTTCTTTCTT
Found at i:52445933 original size:23 final size:23
Alignment explanation
Indices: 52445903--52445950 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
52445893 TCAGGTGGTT
52445903 CGGCCTATGGACAACTTTATTGA
1 CGGCCTATGGACAACTTTATTGA
52445926 CGGCCTATGGACAACTTTATTGA
1 CGGCCTATGGACAACTTTATTGA
52445949 CG
1 CG
52445951 ACTGACCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (23 bp):
CGGCCTATGGACAACTTTATTGA
Found at i:52446759 original size:22 final size:22
Alignment explanation
Indices: 52446713--52446753 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
52446703 TCGAAGAAAT
52446713 TTAATTAAAAATTTTAAAAAAA
1 TTAATTAAAAATTTTAAAAAAA
52446735 TTAATT-AAAATTTTAAAAA
1 TTAATTAAAAATTTTAAAAA
52446754 TTATTATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAATTAAAAATTTTAAAAAAA
Found at i:52461160 original size:18 final size:17
Alignment explanation
Indices: 52461129--52461177 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
52461119 CTCATTGTTC
52461129 TTTCTTTTTCCTTTCTG
1 TTTCTTTTTCCTTTCTG
* *
52461146 TTTCGTTTTTTCTTTCTA
1 TTTC-TTTTTCCTTTCTG
*
52461164 CTTCTTTTT-CTTTC
1 TTTCTTTTTCCTTTC
52461178 ATTATTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 14 0.50
ACGTcount: A:0.02, C:0.22, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTCTTTTTCCTTTCTG
Found at i:52477836 original size:21 final size:22
Alignment explanation
Indices: 52477810--52477852 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
52477800 TTTTTATAAT
*
52477810 TTTTAAAA-AATTAAATTAAAA
1 TTTTAAAATAATTAAATAAAAA
*
52477831 TTTTAAAATATTTAAATAAAAA
1 TTTTAAAATAATTAAATAAAAA
52477853 AATTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAATTAAATAAAAA
Found at i:52479926 original size:12 final size:12
Alignment explanation
Indices: 52479909--52479933 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52479899 TAGGGTCAAG
52479909 TCTTCTTCTTTT
1 TCTTCTTCTTTT
52479921 TCTTCTTCTTTT
1 TCTTCTTCTTTT
52479933 T
1 T
52479934 GTCAAAAAAA
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTCTTCTTTT
Found at i:52482749 original size:18 final size:18
Alignment explanation
Indices: 52482722--52482763 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
52482712 CTTATTTAAT
*
52482722 AATA-TTTTTATTTCAAA
1 AATATTTTTTATTCCAAA
*
52482739 CATATTTTTTATTCCAAA
1 AATATTTTTTATTCCAAA
52482757 AATATTT
1 AATATTT
52482764 ATAAGAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (18 bp):
AATATTTTTTATTCCAAA
Found at i:52486768 original size:311 final size:311
Alignment explanation
Indices: 52486198--52486776 Score: 820
Period size: 311 Copynumber: 1.9 Consensus size: 311
52486188 ATTTAGAATT
* *** *
52486198 TATATGTGTTTAAAAATAATATATAATAAACAATATGTGTATGGTTTGAAACTAATTAATCATGA
1 TATATGTGTTTAAAAATAACATATAATAAACAATAAACGTATGGTTTGAAACTAATTAATCATAA
* * * * *
52486263 TAACACATTAAATATATACAATATTAAAATAAAAAAATAGAATAATTTGTGAGAAAATATTAAAT
66 TAACAAATTAAATATATACAATATTAAAATAAAAAAATAGAATAAATTATAAGAAAACA-TAAAT
* ** * *
52486328 GTAAACACACGAATATGTCATATTAACAACACAAAATGCATTACAATTATTTATCATGATGTTGT
130 GTAAACACACAAATACATCATATAAACAACACAAAATGCACTACAATTATTTATCATGATGTTGT
* * * * *
52486393 CATCAATTGTGAGTTAGTGTTGAGTTGACATATGGCACCAACTCAATTAACAATATTATTAATAT
195 CATCAATTGTAAATTAGTGTTAAGTTGACATATGACACCAACTCAATTAACAACATTATTAATAT
52486458 ATA-AATTCTATCACACATGTATGCGTGCGGAAACCGCGAATTTATAACACA
260 ATACAATTCTATCACACATGTATGCGTGCGGAAACCGCGAATTTATAACACA
*
52486509 TATATGTGTTTAAAAATAACGTATAATAAACAATAAAACGTATGGTTTGAAACTAATTAATCATA
1 TATATGTGTTTAAAAATAACATATAATAAACAAT-AAACGTATGGTTTGAAACTAATTAATCATA
* * *
52486574 ATAACAAATTAAATATGTACAGTATTAAAATAAAAAAATAGATTAAATTATAAGTAAAACA-AAA
65 ATAACAAATTAAATATATACAATATTAAAATAAAAAAATAGAATAAATTATAAG-AAAACATAAA
* * * * * *
52486638 TTTAAACACATAAATACATCATATAAACGATACTAAATGCACTACAATTATTTATCATGATTTTG
129 TGTAAACACACAAATACATCATATAAACAACACAAAATGCACTACAATTATTTATCATGATGTTG
* * *
52486703 TCATCAATTGTAAATTAGTGTTAAGTTGACTTATGACATCAACTCAATTAACAACATTGTTAATA
194 TCATCAATTGTAAATTAGTGTTAAGTTGACATATGACACCAACTCAATTAACAACATTATTAATA
52486768 TATACAATT
259 TATACAATT
52486777 GATGAAGATA
Statistics
Matches: 232, Mismatches: 33, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
311 150 0.65
312 77 0.33
313 5 0.02
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (311 bp):
TATATGTGTTTAAAAATAACATATAATAAACAATAAACGTATGGTTTGAAACTAATTAATCATAA
TAACAAATTAAATATATACAATATTAAAATAAAAAAATAGAATAAATTATAAGAAAACATAAATG
TAAACACACAAATACATCATATAAACAACACAAAATGCACTACAATTATTTATCATGATGTTGTC
ATCAATTGTAAATTAGTGTTAAGTTGACATATGACACCAACTCAATTAACAACATTATTAATATA
TACAATTCTATCACACATGTATGCGTGCGGAAACCGCGAATTTATAACACA
Found at i:52497329 original size:19 final size:18
Alignment explanation
Indices: 52497293--52497332 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52497283 TTTCCACTCG
*
52497293 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
52497311 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
52497330 TTT
1 TTT
52497333 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:52500673 original size:13 final size:13
Alignment explanation
Indices: 52500655--52500703 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
52500645 TAGTTTCTCG
52500655 AAAAAAAACTTGA
1 AAAAAAAACTTGA
* **
52500668 AAAAAAAATTTTT
1 AAAAAAAACTTGA
52500681 AAAAAAAA-TTCGA
1 AAAAAAAACTT-GA
52500694 AAAAAAAACT
1 AAAAAAAACT
52500704 AGTTCCCATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 2 0.07
13 26 0.90
14 1 0.03
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.20
Consensus pattern (13 bp):
AAAAAAAACTTGA
Found at i:52500771 original size:19 final size:19
Alignment explanation
Indices: 52500746--52500783 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
52500736 AAGTTGTGAA
*
52500746 AAAAAAAATTTTTAAAAAAG
1 AAAAAAAA-TTTGAAAAAAG
52500766 AAAAAAAATTTGAAAAAA
1 AAAAAAAATTTGAAAAAA
52500784 AAATTGTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAAAAAATTTGAAAAAAG
Found at i:52500780 original size:12 final size:13
Alignment explanation
Indices: 52500765--52500799 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
52500755 TTTTAAAAAA
52500765 GAAAAAAAATT-T
1 GAAAAAAAATTGT
52500777 GAAAAAAAAATTGT
1 G-AAAAAAAATTGT
52500791 GAAAAAAAA
1 GAAAAAAAA
52500800 AGAGAGCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 18 0.86
14 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (13 bp):
GAAAAAAAATTGT
Found at i:52500782 original size:20 final size:20
Alignment explanation
Indices: 52500746--52500784 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52500736 AAGTTGTGAA
**
52500746 AAAAAAAATTTTTAAAAAAG
1 AAAAAAAATTTGAAAAAAAG
52500766 AAAAAAAATTTGAAAAAAA
1 AAAAAAAATTTGAAAAAAA
52500785 AATTGTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAAAAAATTTGAAAAAAAG
Found at i:52500783 original size:14 final size:14
Alignment explanation
Indices: 52500766--52500800 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
52500756 TTTAAAAAAG
52500766 AAAAAAAATT-TGA
1 AAAAAAAATTGTGA
52500779 AAAAAAAATTGTGA
1 AAAAAAAATTGTGA
52500793 AAAAAAAA
1 AAAAAAAA
52500801 GAGAGCTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (14 bp):
AAAAAAAATTGTGA
Found at i:52521952 original size:29 final size:29
Alignment explanation
Indices: 52521915--52521987 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
52521905 TTAGATATTA
* *
52521915 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
52521944 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
52521973 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
52521988 ACTAATACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:52535883 original size:14 final size:15
Alignment explanation
Indices: 52535856--52535885 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
52535846 AATACTTAGA
52535856 AAATCATAAATTTAT
1 AAATCATAAATTTAT
52535871 AAATCAT-AATTTAT
1 AAATCATAAATTTAT
52535885 A
1 A
52535886 GTTTATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATCATAAATTTAT
Found at i:52536391 original size:20 final size:20
Alignment explanation
Indices: 52536344--52536418 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
52536334 TCAGACAAAT
*
52536344 TGCCAGTAATGTGGACAAG-
1 TGCCAGTAATGTAGACAAGC
52536363 T-CACTAGTAATGTAGACAAGC
1 TGC-C-AGTAATGTAGACAAGC
* * *
52536384 TGCCAGTATTGTGGACAAAC
1 TGCCAGTAATGTAGACAAGC
*
52536404 TACCAGTAATGTAGA
1 TGCCAGTAATGTAGA
52536419 TAAATTGCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 39 0.87
21 2 0.04
22 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (20 bp):
TGCCAGTAATGTAGACAAGC
Found at i:52549048 original size:10 final size:10
Alignment explanation
Indices: 52549034--52549091 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
52549024 CAGCTCCGAC
52549034 CAGCTCAATT
1 CAGCTCAATT
* *
52549044 GAGCTCATTT
1 CAGCTCAATT
52549054 CAGCTCAA-T
1 CAGCTCAATT
52549063 CAAGCTCAATT
1 C-AGCTCAATT
*
52549074 TAGCTACAATT
1 CAGCT-CAATT
52549085 CAGCTCA
1 CAGCTCA
52549092 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:52554292 original size:21 final size:22
Alignment explanation
Indices: 52554263--52554313 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
52554253 TCTCTCTCGC
*
52554263 TTTCCTTTTCGCCTTTTTCA-T
1 TTTCATTTTCGCCTTTTTCACT
**
52554284 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCGCCTTTTTCACT
52554306 TTT-ATTTT
1 TTTCATTTT
52554314 TCCCTTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCGCCTTTTTCACT
Found at i:52557904 original size:11 final size:11
Alignment explanation
Indices: 52557869--52557921 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
52557859 TTTGAACCAT
*
52557869 TACCAATT-CG
1 TACCAATTCCA
*
52557879 TACCAAATACCA
1 TACC-AATTCCA
52557891 TACCAATTCCA
1 TACCAATTCCA
*
52557902 TACC-ATTTCA
1 TACCAATTCCA
52557912 TACCAATTCC
1 TACCAATTCC
52557922 CAAATACCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 13 0.37
11 17 0.49
12 5 0.14
ACGTcount: A:0.36, C:0.34, G:0.02, T:0.28
Consensus pattern (11 bp):
TACCAATTCCA
Found at i:52559284 original size:21 final size:19
Alignment explanation
Indices: 52559241--52559285 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
52559231 GAGCTCAAAT
* *
52559241 GAGCTGAAATGAGTTCATG
1 GAGCTGAAATGAGCTAATG
52559260 GAGCTGGAAATGAGCTAATTG
1 GAGCT-GAAATGAGCTAA-TG
52559281 GAGCT
1 GAGCT
52559286 CAATGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.24
Consensus pattern (19 bp):
GAGCTGAAATGAGCTAATG
Found at i:52566068 original size:22 final size:22
Alignment explanation
Indices: 52566011--52566070 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
52566001 TTTGGTATTT
* *
52566011 GGGAATTGGTATGAAACGGTAA
1 GGGATTTGGTACGAAACGGTAA
** *
52566033 GGGATTTGAAACGAAATGGTAA
1 GGGATTTGGTACGAAACGGTAA
*
52566055 TGGATTTGGTACGAAA
1 GGGATTTGGTACGAAA
52566071 ATGGAAATAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.05, G:0.33, T:0.25
Consensus pattern (22 bp):
GGGATTTGGTACGAAACGGTAA
Found at i:52572784 original size:21 final size:21
Alignment explanation
Indices: 52572739--52572801 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
52572729 TTTGAACCAT
* *
52572739 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
52572761 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
*
52572782 TACCATTTCGTACTAATTCC
1 TACCATTTCGTACCAATTCC
52572802 CAAATACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 24 0.67
22 12 0.33
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:52588134 original size:22 final size:22
Alignment explanation
Indices: 52588103--52588167 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
52588093 ACCTTTTTGA
52588103 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCGTACCAAAT
*
52588126 ACCATACC-ATCTCGTACCAACT
1 ACCATACCAAT-TCGTACCAAAT
* *
52588148 TCCATACCATTTCGTACCAA
1 ACCATACCAATTCGTACCAA
52588168 TTCCTAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.05
22 30 0.81
23 5 0.14
ACGTcount: A:0.34, C:0.35, G:0.05, T:0.26
Consensus pattern (22 bp):
ACCATACCAATTCGTACCAAAT
Found at i:52594083 original size:45 final size:43
Alignment explanation
Indices: 52594018--52594184 Score: 181
Period size: 45 Copynumber: 3.7 Consensus size: 43
52594008 GTTGAAAAAC
*
52594018 GAGTAAGACCATAGTGGAAAGACACAATGGCATCACGATTCAAA
1 GAGTAAGACCATAGT-GAAAGACACTATGGCATCACGATTCAAA
** * *
52594062 TGAGTAAGACCATAGCTGAAAGACGTTATGACATCACAATTCAAA
1 -GAGTAAGACCATAG-TGAAAGACACTATGGCATCACGATTCAAA
* *
52594107 CGAGTAAGACCATAGATGAAAGACACTATAGCATCATGATTCAAA
1 -GAGTAAGACCATAG-TGAAAGACACTATGGCATCACGATTCAAA
* * *
52594152 CATGTAAGACAATAGTTGAAAGAAACTATGGCA
1 GA-GTAAGACCATAG-TGAAAGACACTATGGCA
52594185 AGATGAAAGA
Statistics
Matches: 102, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
44 1 0.01
45 100 0.98
46 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.20
Consensus pattern (43 bp):
GAGTAAGACCATAGTGAAAGACACTATGGCATCACGATTCAAA
Found at i:52602736 original size:32 final size:32
Alignment explanation
Indices: 52602694--52602768 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
52602684 AAAGATGCAA
* *
52602694 ACTTTAATTAACATG-AGAATTACATAATGCATG
1 ACTTTAATTAA-ATGCAGAA-CACAAAATGCATG
52602727 ACTTT-ATTAAATGCAGAACACAAAATGCATG
1 ACTTTAATTAAATGCAGAACACAAAATGCATG
*
52602758 AC-ATAATTAAA
1 ACTTTAATTAAA
52602769 AGATGTAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 1 0.03
31 22 0.59
32 9 0.24
33 5 0.14
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (32 bp):
ACTTTAATTAAATGCAGAACACAAAATGCATG
Found at i:52606688 original size:25 final size:25
Alignment explanation
Indices: 52606618--52606690 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
52606608 TGCTTATACG
* * * *
52606618 AGCTATGAATCTGTATGCTCACATG
1 AGCTATAAATCGGTATGCTCTCATA
*
52606643 AGCTATAAATTGGTATGCTCTCATA
1 AGCTATAAATCGGTATGCTCTCATA
* *
52606668 AGCTGTAAATCGGTATACTCTCA
1 AGCTATAAATCGGTATGCTCTCA
52606691 CGAGTTATGG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (25 bp):
AGCTATAAATCGGTATGCTCTCATA
Found at i:52612588 original size:11 final size:11
Alignment explanation
Indices: 52612572--52612612 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
52612562 CTCGAGGCCC
*
52612572 TAGAAATACCT
1 TAGAAACACCT
52612583 TAGAAACACCT
1 TAGAAACACCT
52612594 TAGAAACACCT
1 TAGAAACACCT
52612605 TAGAAACA
1 TAGAAACA
52612613 ATTCAGGACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.20
Consensus pattern (11 bp):
TAGAAACACCT
Found at i:52613608 original size:14 final size:15
Alignment explanation
Indices: 52613589--52613617 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52613579 TACATATTAA
52613589 CATATCAATC-TCAT
1 CATATCAATCATCAT
52613603 CATATCAATCATCAT
1 CATATCAATCATCAT
52613618 AATAATCACA
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:0.28, G:0.00, T:0.34
Consensus pattern (15 bp):
CATATCAATCATCAT
Found at i:52614406 original size:54 final size:54
Alignment explanation
Indices: 52614288--52614397 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
52614278 ACTTACTTGG
* * *
52614288 TATCCTTATTTACCGATTTTTACCGATCTCTGTGAATACACTCGTATTCACACA
1 TATCCTTATTTACCGATTTTTACCAATCTCTATGAATACACTCATATTCACACA
* * *
52614342 TATCCTTATTTATCGATTTTTACTAATCTCTATGAATACGCTCATATTCACACA
1 TATCCTTATTTACCGATTTTTACCAATCTCTATGAATACACTCATATTCACACA
52614396 TA
1 TA
52614398 CTTATATTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (54 bp):
TATCCTTATTTACCGATTTTTACCAATCTCTATGAATACACTCATATTCACACA
Found at i:52614472 original size:21 final size:21
Alignment explanation
Indices: 52614443--52614482 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52614433 TATTTAAAAT
* *
52614443 ATCACTATTATTTATTATTTA
1 ATCAATATTATTAATTATTTA
52614464 ATCAATATTATTAATTATT
1 ATCAATATTATTAATTATT
52614483 ATCAAGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
ATCAATATTATTAATTATTTA
Found at i:52616770 original size:36 final size:35
Alignment explanation
Indices: 52616719--52616846 Score: 143
Period size: 35 Copynumber: 3.6 Consensus size: 35
52616709 AGTACATCGT
*
52616719 CAATCCAACCAAAACACACCAGATGCTCATAAGAGC
1 CAATCCAACCGAAACACACCA-ATGCTCATAAGAGC
*
52616755 CAATCCAACTGAAACACACCAATGCTCATAAGAGC
1 CAATCCAACCGAAACACACCAATGCTCATAAGAGC
* * *
52616790 TAATACC-TCCGGAACACACCAATGCTCATAAGAGC
1 CAAT-CCAACCGAAACACACCAATGCTCATAAGAGC
* * *
52616825 TAGTTC-ACTCGAAACACACCAA
1 CAATCCAAC-CGAAACACACCAA
52616847 ATAGAGAGTA
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.03
35 57 0.71
36 21 0.26
ACGTcount: A:0.41, C:0.32, G:0.12, T:0.15
Consensus pattern (35 bp):
CAATCCAACCGAAACACACCAATGCTCATAAGAGC
Found at i:52618591 original size:27 final size:27
Alignment explanation
Indices: 52618561--52618651 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
52618551 CTCTATAATT
* *
52618561 CGCCATAAAGGCGTTCTTTTCATATTC
1 CGCCACAAAGGCGTTCTTTTCATATTA
*
52618588 CGCCACAAAGG-GTTTTCTTTCATATTA
1 CGCCACAAAGGCGTTCT-TTTCATATTA
* *
52618615 CGCCACAAAGTCTTTC-TTTCATATTA
1 CGCCACAAAGGCGTTCTTTTCATATTA
*
52618641 TGCCACAAAGG
1 CGCCACAAAGG
52618652 TTATCATTAC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
26 23 0.43
27 29 0.54
28 2 0.04
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.34
Consensus pattern (27 bp):
CGCCACAAAGGCGTTCTTTTCATATTA
Found at i:52618637 original size:26 final size:25
Alignment explanation
Indices: 52618578--52618650 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 25
52618568 AAGGCGTTCT
*
52618578 TTTCATATTCCGCCACAAAGGGTTTTC
1 TTTCATATTACGCCACAAA--GTTTTC
52618605 TTTCATATTACGCCACAAAGTCTTTC
1 TTTCATATTACGCCACAAAGT-TTTC
*
52618631 TTTCATATTATGCCACAAAG
1 TTTCATATTACGCCACAAAG
52618651 GTTATCATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
25 2 0.05
26 23 0.53
27 18 0.42
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (25 bp):
TTTCATATTACGCCACAAAGTTTTC
Found at i:52632165 original size:18 final size:18
Alignment explanation
Indices: 52632144--52632179 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
52632134 AAGATAAAAT
52632144 TCTATAATATTAAATGTC
1 TCTATAATATTAAATGTC
*
52632162 TCTATTATATTAAATGTC
1 TCTATAATATTAAATGTC
52632180 ATATATAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (18 bp):
TCTATAATATTAAATGTC
Found at i:52632380 original size:10 final size:11
Alignment explanation
Indices: 52632353--52632393 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
52632343 CATACAATAC
52632353 TTATTATTAAA
1 TTATTATTAAA
52632364 -TATT-TATAAA
1 TTATTAT-TAAA
52632374 TTATTATTAAA
1 TTATTATTAAA
*
52632385 TTAATATTA
1 TTATTATTA
52632394 TTAAGAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 1 0.04
10 8 0.31
11 16 0.62
12 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTATTATTAAA
Found at i:52635084 original size:2 final size:2
Alignment explanation
Indices: 52635077--52635119 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
52635067 GAAGATTGGT
52635077 TA TA TA TA 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 TA TA TA TA
52635119 T
1 T
52635120 GGGTGAGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52636475 original size:20 final size:20
Alignment explanation
Indices: 52636450--52636498 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
52636440 AGCTAATTGC
52636450 TTGTATTTAGGTACATTT-AG
1 TTGTATTTAGG-ACATTTCAG
*
52636470 TTGTATTTTAGGACATTTCAT
1 TTGTA-TTTAGGACATTTCAG
52636491 TTGTATTT
1 TTGTATTT
52636499 TCTCATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.55
Consensus pattern (20 bp):
TTGTATTTAGGACATTTCAG
Found at i:52636481 original size:21 final size:21
Alignment explanation
Indices: 52636450--52636499 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
52636440 AGCTAATTGC
52636450 TTGTA-TTTAGGTACATTT-AG
1 TTGTATTTTAGG-ACATTTCAG
*
52636470 TTGTATTTTAGGACATTTCAT
1 TTGTATTTTAGGACATTTCAG
52636491 TTGTATTTT
1 TTGTATTTT
52636500 CTCATCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.56
Consensus pattern (21 bp):
TTGTATTTTAGGACATTTCAG
Found at i:52646509 original size:12 final size:12
Alignment explanation
Indices: 52646492--52646521 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
52646482 AGAGAGAAAG
52646492 AAAAAAATTGAA
1 AAAAAAATTGAA
52646504 AAAAAAATTGAA
1 AAAAAAATTGAA
52646516 AAAAAA
1 AAAAAA
52646522 GAGAAGAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:52646521 original size:56 final size:55
Alignment explanation
Indices: 52646416--52646520 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 55
52646406 GTATTGGATT
** *
52646416 AAAAAAAAAGAAAGAAAATCGAAAAAAATTTCAAAAAAAAGTGGAAAAAATCGAGC
1 AAAAAAAAAGAAAGAAAA-CGAAAAAAATTGAAAAAAAAAGTGAAAAAAATCGAGC
* *
52646472 AAAAAAAAAGAGAGAGAAA-GAAAAAAATTGAAAAAAAAATTGAAAAAAA
1 AAAAAAAAAGAAAGA-AAACGAAAAAAATTGAAAAAAAAAGTGAAAAAAA
52646521 AGAGAAGAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
55 26 0.60
56 14 0.33
57 3 0.07
ACGTcount: A:0.72, C:0.04, G:0.14, T:0.10
Consensus pattern (55 bp):
AAAAAAAAAGAAAGAAAACGAAAAAAATTGAAAAAAAAAGTGAAAAAAATCGAGC
Found at i:52656079 original size:18 final size:17
Alignment explanation
Indices: 52656058--52656102 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
52656048 GAGTGACGAG
52656058 AGAAAAAGAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
52656076 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
52656094 AGAGAAAAA
1 AGA-AAAAA
52656103 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:52656107 original size:18 final size:18
Alignment explanation
Indices: 52656056--52656107 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
52656046 AAGAGTGACG
*
52656056 AGAGAAAAAGAAACTGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
52656076 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
52656094 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
52656108 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:52672428 original size:17 final size:16
Alignment explanation
Indices: 52672387--52672430 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
52672377 CTCACAAGAC
52672387 TTTTCACTTCATTTTT
1 TTTTCACTTCATTTTT
52672403 TTTAT-ACTTCGATTTTT
1 TTT-TCACTTC-ATTTTT
52672420 TTTTCACTTCA
1 TTTTCACTTCA
52672431 AATACAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.16, C:0.18, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTTCACTTCATTTTT
Found at i:52676204 original size:21 final size:21
Alignment explanation
Indices: 52676180--52676227 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
52676170 AAAGAAGAAG
52676180 AAATTCA-AAAAAAAATCAAAA
1 AAATTCATAAAAAAAA-CAAAA
* *
52676201 AAATTGATTAAAAAAACAAAA
1 AAATTCATAAAAAAAACAAAA
52676222 AAATTC
1 AAATTC
52676228 GAAGTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.19
Consensus pattern (21 bp):
AAATTCATAAAAAAAACAAAA
Found at i:52686026 original size:33 final size:33
Alignment explanation
Indices: 52685984--52686139 Score: 99
Period size: 33 Copynumber: 4.6 Consensus size: 33
52685974 AAAATACGGT
52685984 GGAATCAGCACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
** *
52686017 GGAATCAGCACACAGCAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
52686044 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC---CA-A--T-GAAT-CGG
* *
52686086 TGGAATCAGCACTTAGCAACCACTAATGAATAGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
**
52686120 GGAATCAGCACACAGCAACC
1 GGAATCAGCACTTAGCAACC
52686140 CCTTTATATG
Statistics
Matches: 95, Mismatches: 12, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
27 19 0.20
28 2 0.02
29 1 0.01
30 1 0.01
32 3 0.03
33 36 0.38
34 2 0.02
35 3 0.03
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
41 1 0.01
42 5 0.05
43 18 0.19
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:52686122 original size:103 final size:103
Alignment explanation
Indices: 52685774--52686143 Score: 580
Period size: 104 Copynumber: 3.6 Consensus size: 103
52685764 TAACCGTTAT
* * * * *
52685774 CGGTGGATTCCGCACTTAGCAACCACCAATGAATCGGGGAATTAGCACACTGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTTGGGG
* * *
52685839 GAATCAGCACTTAGCAACCCCC-TTCACATTTCAGATG
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* * * ** *
52685876 CGGTTGAATCAGCACTTAGCAACCATCAATGAATAGGGGAATTAGCACTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTTGGGG
52685941 GAATCAGCACTTAGCAACCCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAA-CCCCCTTTCACATTTAAAATA
*
52685980 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTTGGGG
52686045 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
*
52686083 CGGTGGAATCAGCACTTAGCAACCACTAATGAATAGGGGAATCAGCACACAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTT
52686144 TATATGCAAT
Statistics
Matches: 245, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
102 73 0.30
103 85 0.35
104 87 0.36
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTTGGGG
GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
Found at i:52697068 original size:10 final size:10
Alignment explanation
Indices: 52697053--52697114 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
52697043 TTTGAACCAT
*
52697053 TACCAATTCG
1 TACCAATTCA
*
52697063 TACCAAATACCA
1 TACC-AAT-TCA
*
52697075 TACCATTTCA
1 TACCAATTCA
52697085 TACCAATTCCA
1 TACCAATT-CA
* *
52697096 TACCATTTCG
1 TACCAATTCA
52697106 TACCAATTC
1 TACCAATTC
52697115 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:52697098 original size:21 final size:21
Alignment explanation
Indices: 52697053--52697115 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
52697043 TTTGAACCAT
* *
52697053 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
52697075 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
52697096 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
52697116 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:52698197 original size:72 final size:73
Alignment explanation
Indices: 52698062--52698209 Score: 201
Period size: 72 Copynumber: 2.0 Consensus size: 73
52698052 GCAGGTACAT
* *
52698062 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTAATGAGTGCAT
1 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAATGAGTGCAT
52698127 GGGACTTG
66 GGGACTTG
* * * * * *
52698135 GGACGGCATTTAAAGATAAA-GTTGCTGTTGTA-TTTTCCCAACCAGCCGAATTTAGTGTGTGCA
1 GGACGGCATTTAAAGA-AAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAATGAGTGCA
52698198 TGGGACTTG
65 TGGGACTTG
52698207 GGA
1 GGA
52698210 TAGCATTAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
72 38 0.58
73 25 0.38
74 3 0.05
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (73 bp):
GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAATGAGTGCAT
GGGACTTG
Found at i:52701137 original size:20 final size:20
Alignment explanation
Indices: 52701112--52701157 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
52701102 AATGAGCTAG
52701112 TGAGCTAATAACGAGCTC-AA
1 TGAGCTAA-AACGAGCTCGAA
**
52701132 TGAGCTAAATTGAGCTCGAA
1 TGAGCTAAAACGAGCTCGAA
52701152 TGAGCT
1 TGAGCT
52701158 GAATCAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (20 bp):
TGAGCTAAAACGAGCTCGAA
Found at i:52747974 original size:23 final size:24
Alignment explanation
Indices: 52747943--52747992 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
52747933 CTAAGAGTGG
*
52747943 TAAAGTAAA-TAAAAAAGTAAATAA
1 TAAAGTAAAGGAAAAAA-TAAATAA
*
52747967 TAAA-TAAAGGAAAATATAAATAA
1 TAAAGTAAAGGAAAAAATAAATAA
52747990 TAA
1 TAA
52747993 TAATCAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (24 bp):
TAAAGTAAAGGAAAAAATAAATAA
Found at i:52752739 original size:27 final size:27
Alignment explanation
Indices: 52752700--52753059 Score: 400
Period size: 27 Copynumber: 13.3 Consensus size: 27
52752690 AATGGGCCTC
* *
52752700 TAAAATGATCGAAATACCCTTGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
*
52752727 TAAAATGACCGAAATACCCTCAAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
52752754 TAAAATTACCAAAATACCCTCAAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
*
52752781 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
52752808 TAAAATGACCGGAATACCCCCAAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
52752835 TAAAATGACCAAAATACCCCCGAATGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * * *
52752862 TAAAATGATCGGAATACCCCCAAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * * *
52752889 TAACATGACCAAAATACCCTTGAAAGG
1 TAAAATGACCGAAATACCCTCGAAGGG
52752916 TAAAATGACCGAAATACCC-CTGAAGGG
1 TAAAATGACCGAAATACCCTC-GAAGGG
* ** *
52752943 TTAAATGATTGAAATACCCTCGATGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* **
52752970 TAAAATTACCGAAATAGGCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* **
52752997 TAAAATGACCGAAAAACCCTTAAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
*
52753024 TAAAATGATCGAAATACCCTC-ATAGGG
1 TAAAATGACCGAAATACCCTCGA-AGGG
52753051 TAAAATGAC
1 TAAAATGAC
52753060 TGTTATACCC
Statistics
Matches: 275, Mismatches: 55, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
26 1 0.00
27 273 0.99
28 1 0.00
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.18
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCGAAGGG
Found at i:52753270 original size:26 final size:26
Alignment explanation
Indices: 52753240--52753315 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
52753230 CAAACATTGT
52753240 TACTGGCAGATTTGCTGCGTTACTGA
1 TACTGGCAGATTTGCTGCGTTACTGA
* * * **
52753266 TACTGGCAGCTCTGCTGCATTACTTT
1 TACTGGCAGATTTGCTGCGTTACTGA
* *
52753292 TATTGGCA-ACTTTGTTGCGTTACT
1 TACTGGCAGA-TTTGCTGCGTTACT
52753316 ATTACTAGCA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.39
Consensus pattern (26 bp):
TACTGGCAGATTTGCTGCGTTACTGA
Found at i:52753877 original size:29 final size:29
Alignment explanation
Indices: 52753840--52753912 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
52753830 TTAGATATTA
* *
52753840 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
52753869 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
52753898 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
52753913 ACTAATACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:52759182 original size:29 final size:29
Alignment explanation
Indices: 52759140--52759197 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
52759130 TCGTAGAAGA
* * *
52759140 GGTGGAGAACTTATTTGTTGAGAGTTCGT
1 GGTGAAGAAATTATTCGTTGAGAGTTCGT
52759169 GGTGAAGAAATTATTCGTTGAGAGTTCGT
1 GGTGAAGAAATTATTCGTTGAGAGTTCGT
52759198 ATCAAGGTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.07, G:0.33, T:0.36
Consensus pattern (29 bp):
GGTGAAGAAATTATTCGTTGAGAGTTCGT
Found at i:52759707 original size:20 final size:20
Alignment explanation
Indices: 52759679--52759716 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52759669 GGGTTTAGGG
*
52759679 TTTATAAATATTGATAAAAC
1 TTTAGAAATATTGATAAAAC
*
52759699 TTTAGAAATATTGTTAAA
1 TTTAGAAATATTGATAAA
52759717 TCCTTAGATA
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:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (20 bp):
TTTAGAAATATTGATAAAAC
Found at i:52759723 original size:20 final size:20
Alignment explanation
Indices: 52759684--52759774 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
52759674 TAGGGTTTAT
* * *
52759684 AAATATTGATAAAACTTTAG
1 AAATATTGGTAAATCCTTAG
*
52759704 AAATATTGTTAAATCCTTAG
1 AAATATTGGTAAATCCTTAG
* * *
52759724 ATATTTTGGT-AGT-CTTAG
1 AAATATTGGTAAATCCTTAG
*
52759742 AAATATTGGTAAGTCCTTA-
1 AAATATTGGTAAATCCTTAG
*
52759761 AATATTTTGGTAAA
1 AA-ATATTGGTAAA
52759775 AGTTTTTCCT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
18 13 0.23
19 7 0.12
20 37 0.65
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (20 bp):
AAATATTGGTAAATCCTTAG
Found at i:52759740 original size:18 final size:19
Alignment explanation
Indices: 52759717--52759772 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
52759707 TATTGTTAAA
52759717 TCCTTAGATATTTTGGTAG
1 TCCTTAGATATTTTGGTAG
* *
52759736 T-CTTAGAAATATTGGTAAG
1 TCCTTAGATATTTTGGT-AG
*
52759755 TCCTTAAATATTTTGGTA
1 TCCTTAGATATTTTGGTA
52759773 AAAGTTTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 13 0.43
19 5 0.17
20 12 0.40
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.45
Consensus pattern (19 bp):
TCCTTAGATATTTTGGTAG
Found at i:52759742 original size:38 final size:38
Alignment explanation
Indices: 52759700--52759772 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
52759690 TGATAAAACT
* *
52759700 TTAGAAATATTGTTAAATCCTTAGATATTTTGGTAGTC
1 TTAGAAATATTGGTAAATCCTTAAATATTTTGGTAGTC
*
52759738 TTAGAAATATTGGTAAGTCCTTAAATATTTTGGTA
1 TTAGAAATATTGGTAAATCCTTAAATATTTTGGTA
52759773 AAAGTTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (38 bp):
TTAGAAATATTGGTAAATCCTTAAATATTTTGGTAGTC
Found at i:52760511 original size:36 final size:36
Alignment explanation
Indices: 52760464--52760536 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
52760454 TCCATCATGG
*
52760464 GTCAAAATATATATATCACTTGTCAGTCAACCTTGT
1 GTCAAAATATATATATCACTTGCCAGTCAACCTTGT
* * *
52760500 GTCAATATATATATATCAGTTGCCGGTCAACCTTGT
1 GTCAAAATATATATATCACTTGCCAGTCAACCTTGT
52760536 G
1 G
52760537 CATTTGTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (36 bp):
GTCAAAATATATATATCACTTGCCAGTCAACCTTGT
Found at i:52760675 original size:20 final size:20
Alignment explanation
Indices: 52760642--52760680 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52760632 AAAAACTTTA
*
52760642 AAATCAACTTGAAATTAAAG
1 AAATCAACTAGAAATTAAAG
*
52760662 AAATCGACTAGAAATTAAA
1 AAATCAACTAGAAATTAAA
52760681 AGCTCAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (20 bp):
AAATCAACTAGAAATTAAAG
Found at i:52770332 original size:36 final size:37
Alignment explanation
Indices: 52770287--52770361 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 37
52770277 ATATGGATGT
* * *
52770287 TAATTTAAAAATAGTATATAATAACA-ATGAAATTTA
1 TAATTTAAAAATAATAAATAATAACATATGAAATATA
*
52770323 TAATTTAAAATTAATAAATAATAACATATGAAATATA
1 TAATTTAAAAATAATAAATAATAACATATGAAATATA
52770360 TA
1 TA
52770362 CAATATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
36 23 0.68
37 11 0.32
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (37 bp):
TAATTTAAAAATAATAAATAATAACATATGAAATATA
Found at i:52780583 original size:16 final size:17
Alignment explanation
Indices: 52780551--52780590 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
52780541 TTAATTGAGA
*
52780551 AATTAATTTAGTTAAAT
1 AATTAATTGAGTTAAAT
52780568 AATTAATTGA-TTAAAT
1 AATTAATTGAGTTAAAT
*
52780584 AAATAAT
1 AATTAAT
52780591 ATTTTGGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
AATTAATTGAGTTAAAT
Found at i:52785677 original size:23 final size:23
Alignment explanation
Indices: 52785651--52785698 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
52785641 AATCAGCTTC
*
52785651 TTTAATAC-ACCTATTAGGACCCA
1 TTTAA-ACGACCTATTAGGACACA
*
52785674 TTTAAACGACTTATTAGGACACA
1 TTTAAACGACCTATTAGGACACA
52785697 TT
1 TT
52785699 AATCATACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.33
Consensus pattern (23 bp):
TTTAAACGACCTATTAGGACACA
Found at i:52790374 original size:16 final size:16
Alignment explanation
Indices: 52790353--52790383 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52790343 ATTTTGTTGC
*
52790353 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
52790369 TAATTTCACTTTTTC
1 TAATTTCACTTTTTC
52790384 CCTTTCAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:52790585 original size:46 final size:43
Alignment explanation
Indices: 52790508--52790606 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 43
52790498 AAAAATAACA
* *
52790508 GATACACGGTGGATTCAGCACACAGCGACCACCCTTTGTAATCAAT
1 GATAC-CGGTGGATTCAGCACACAGCAACCA-CC-TTATAATCAAT
* *
52790554 GATATCCGGTGGGATT-AGCACATAGCAACCACCTTATAATTAAT
1 GATA-CCGGT-GGATTCAGCACACAGCAACCACCTTATAATCAAT
52790598 GATACCGGT
1 GATACCGGT
52790607 TCATATAGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.11
44 13 0.28
45 2 0.04
46 21 0.45
47 6 0.13
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (43 bp):
GATACCGGTGGATTCAGCACACAGCAACCACCTTATAATCAAT
Found at i:52790670 original size:51 final size:51
Alignment explanation
Indices: 52790612--52790802 Score: 192
Period size: 51 Copynumber: 3.8 Consensus size: 51
52790602 CCGGTTCATA
* * * *
52790612 TAGTAGCCTGCACATAGTAATACACATGTGACCATCACTATCCGATAAACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* ** * * * * *
52790663 TAGTAGCCTACATGTAGTACTATATACGTGATCGA--AGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACACG
* * *
52790714 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
52790764 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
52790803 TTCACTTTCA
Statistics
Matches: 109, Mismatches: 25, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
49 4 0.04
50 42 0.39
51 60 0.55
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
Found at i:52796631 original size:26 final size:26
Alignment explanation
Indices: 52796602--52796653 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
52796592 ATATAATTTC
52796602 CAAATCATGTATC-TATATATCATGTA
1 CAAATCAT-TATCATATATATCATGTA
* *
52796628 CAAATCATTTTCATATATCTCATGTA
1 CAAATCATTATCATATATATCATGTA
52796654 AATACCTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (26 bp):
CAAATCATTATCATATATATCATGTA
Found at i:52796855 original size:25 final size:25
Alignment explanation
Indices: 52796810--52796883 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
52796800 ACGAGCTGTA
* *
52796810 AACGGTAAGCTCCT-CTGAGCTGAAT
1 AACGGTAAGCTCATAC-AAGCTGAAT
*
52796835 AACGGTAAGCTCATACAAGCTGAGT
1 AACGGTAAGCTCATACAAGCTGAAT
* *
52796860 ATCGGTAAGCTTATA-AGAGCTGAA
1 AACGGTAAGCTCATACA-AGCTGAA
52796884 ATCGATAACC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 1 0.02
25 39 0.95
26 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (25 bp):
AACGGTAAGCTCATACAAGCTGAAT
Found at i:52806992 original size:36 final size:36
Alignment explanation
Indices: 52806952--52807025 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
52806942 ACAAAAATAA
*
52806952 AAGAATGAAAAAGAGAGTGAAAAGAAAATCGAGAAG
1 AAGAATGAAAAAGAGAGTAAAAAGAAAATCGAGAAG
52806988 AAGAATGAAAAAGAGAGTAAAAAGAAAATCGAGAAG
1 AAGAATGAAAAAGAGAGTAAAAAGAAAATCGAGAAG
52807024 AA
1 AA
52807026 AGAAAAACCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.64, C:0.03, G:0.26, T:0.08
Consensus pattern (36 bp):
AAGAATGAAAAAGAGAGTAAAAAGAAAATCGAGAAG
Found at i:52807003 original size:18 final size:19
Alignment explanation
Indices: 52806952--52807004 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
52806942 ACAAAAATAA
*
52806952 AAGAATGAAAAAGAGAGTG
1 AAGAATGAAAAAGAGAGAG
*
52806971 AA-AA-GAAAATCGAGA-AG
1 AAGAATGAAAA-AGAGAGAG
52806988 AAGAATGAAAAAGAGAG
1 AAGAATGAAAAAGAGAG
52807005 TAAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
17 8 0.30
18 12 0.44
19 7 0.26
ACGTcount: A:0.62, C:0.02, G:0.28, T:0.08
Consensus pattern (19 bp):
AAGAATGAAAAAGAGAGAG
Found at i:52807021 original size:18 final size:18
Alignment explanation
Indices: 52806964--52807021 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
52806954 GAATGAAAAA
*
52806964 GAGAGTGAAAAGAAAATC
1 GAGAGTAAAAAGAAAATC
* *
52806982 GAGAAG-AAGAATGAAAA-A
1 GAG-AGTAA-AAAGAAAATC
52807000 GAGAGTAAAAAGAAAATC
1 GAGAGTAAAAAGAAAATC
52807018 GAGA
1 GAGA
52807022 AGAAAGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
17 9 0.29
18 13 0.42
19 9 0.29
ACGTcount: A:0.60, C:0.03, G:0.28, T:0.09
Consensus pattern (18 bp):
GAGAGTAAAAAGAAAATC
Found at i:52807027 original size:16 final size:16
Alignment explanation
Indices: 52806972--52807031 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 16
52806962 AAGAGAGTGA
52806972 AAAGAAAATCGAGAAG
1 AAAGAAAATCGAGAAG
* *
52806988 AAGAATGAAAA-AGAGAGTAA
1 -A-AA-GAAAATCGAGA--AG
52807008 AAAGAAAATCGAGAAG
1 AAAGAAAATCGAGAAG
52807024 AAAGAAAA
1 AAAGAAAA
52807032 ACCATTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
16 9 0.26
17 6 0.18
18 12 0.35
19 6 0.18
20 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (16 bp):
AAAGAAAATCGAGAAG
Found at i:52811569 original size:26 final size:26
Alignment explanation
Indices: 52811508--52811609 Score: 152
Period size: 26 Copynumber: 3.9 Consensus size: 26
52811498 GATGTCCCTG
* *
52811508 TGTTTATTG-CCCTGGCGAACTACTTCA
1 TGTTTATTGTCCC-GGTGAACTAC-CCA
52811535 TGTTTATTGTCCCGGTGAACTACCCA
1 TGTTTATTGTCCCGGTGAACTACCCA
*
52811561 TGTTTATTGTCCCGGTGAACTACCCG
1 TGTTTATTGTCCCGGTGAACTACCCA
52811587 TGTTTATTGTCCCGGTGAACTAC
1 TGTTTATTGTCCCGGTGAACTAC
52811610 ACTGATAACC
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
26 50 0.70
27 18 0.25
28 3 0.04
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (26 bp):
TGTTTATTGTCCCGGTGAACTACCCA
Found at i:52812839 original size:21 final size:22
Alignment explanation
Indices: 52812810--52812850 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
52812800 AATGTTATGA
* *
52812810 AAAATTTAA-TAAAATAAAATT
1 AAAAGTTAATTAAAACAAAATT
52812831 AAAAGTTAATTAAAACAAAA
1 AAAAGTTAATTAAAACAAAA
52812851 AGATGTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAGTTAATTAAAACAAAATT
Found at i:52821459 original size:19 final size:19
Alignment explanation
Indices: 52821428--52821465 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
52821418 TAAAAATAGG
*
52821428 TAAATAATATTTTGGAAAA
1 TAAATAATATTTTAGAAAA
52821447 TAAA-AATATTTTTAGAAAA
1 TAAATAATA-TTTTAGAAAA
52821466 AATAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (19 bp):
TAAATAATATTTTAGAAAA
Found at i:52825370 original size:23 final size:23
Alignment explanation
Indices: 52825344--52825393 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
52825334 TATGCAGAAT
* *
52825344 GGAAAATTCATAGTTGCACAAAA
1 GGAAAAGTCATAGCTGCACAAAA
*
52825367 GGAAAAGTCATAGCTGCACGAAA
1 GGAAAAGTCATAGCTGCACAAAA
52825390 GGAA
1 GGAA
52825394 TTACCAGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.16
Consensus pattern (23 bp):
GGAAAAGTCATAGCTGCACAAAA
Found at i:52826625 original size:29 final size:30
Alignment explanation
Indices: 52826569--52826629 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
52826559 ATTTTTGAGC
*
52826569 TTTGGGACAAAAATGTAATTATGCAAAAGT
1 TTTGGGACAAAAATATAATTATGCAAAAGT
* *
52826599 TTTGGGAC-AAAATCATAATTTTGAAAAAGT
1 TTTGGGACAAAAAT-ATAATTATGCAAAAGT
52826629 T
1 T
52826630 GAATCGAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.33
Consensus pattern (30 bp):
TTTGGGACAAAAATATAATTATGCAAAAGT
Found at i:52827158 original size:51 final size:51
Alignment explanation
Indices: 52827098--52827437 Score: 356
Period size: 51 Copynumber: 6.7 Consensus size: 51
52827088 TATCGATGAA
* * *
52827098 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* * * * *
52827149 CACGTGTGTAGTACTAAGTAAAGGCTACAATGTGTACCGATAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATATTGGT
* * *
52827200 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGA-TGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATTGGT
* * *
52827251 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TATTGGT
* * * * *
52827302 CATGTGTATAGTACTATGTGAAGGCTAATACGTGAACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA-TTGGT
* *
52827352 CACGTGTGTAGTACTATGTGAAGGAC-ACTACGTGAACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGG-CTACTACGTGTACCGATAAATA-TTGGT
*
52827402 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
52827438 TCGAATGATA
Statistics
Matches: 243, Mismatches: 35, Indels: 23
0.81 0.12 0.08
Matches are distributed among these distances:
49 1 0.00
50 85 0.35
51 155 0.64
52 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
Found at i:52827275 original size:102 final size:102
Alignment explanation
Indices: 52827098--52827441 Score: 437
Period size: 102 Copynumber: 3.4 Consensus size: 102
52827088 TATCGATGAA
* *
52827098 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACGTGTGTAGTAC
* *
52827163 TAAGTAAAGGCTACAATGTGTACCGATAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGATAAGCTTTGGT
* * *
52827200 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACGTGTGTAGTAC
*
52827265 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGATAAGCTTTGGT
* * * * * *
52827302 CATGTGTATAGTACTATGTGAAGGCTAATACGTGAACCG-TAAA-ACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACGTGTGTAGTA
* * * * *
52827365 CTATGTGAAGGAC-ACTACGTGAACCG-TAAAAC-TTGAT
65 CTAAGTGAAGG-CTACTATGTGTACCGAT-AAGCTTTGGT
* *
52827402 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
52827442 ATGATAAAAG
Statistics
Matches: 211, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
100 37 0.18
101 43 0.20
102 131 0.62
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACGTGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGATAAGCTTTGGT
Found at i:52827747 original size:22 final size:22
Alignment explanation
Indices: 52827717--52827759 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
52827707 ACACCAAAAC
*
52827717 AGGCTTTTAGAGGCGCTTTTTT
1 AGGCCTTTAGAGGCGCTTTTTT
*
52827739 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGAGGCGCTTTTT
52827760 AGCACCGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.19, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGAGGCGCTTTTTT
Found at i:52827897 original size:43 final size:43
Alignment explanation
Indices: 52827831--52828009 Score: 162
Period size: 43 Copynumber: 4.2 Consensus size: 43
52827821 GCGTCGCTAA
** * * *
52827831 CTTTAGCGGCGCTTTCCCCACAAACGCCTCTAAAGACCAAGAC
1 CTTTAGCGATGCTTTACCCACAAACGCCTCTATAGACCATGAC
* ** **
52827874 CTTTAGCGATGCTTTACCTACAAACGCCTCTATAGGTCATGGT
1 CTTTAGCGATGCTTTACCCACAAACGCCTCTATAGACCATGAC
* * *
52827917 CTATAGCGATGCTTTTCCCACAAACG-CTGCTATATACCATGAC
1 CTTTAGCGATGCTTTACCCACAAACGCCT-CTATAGACCATGAC
** ** * * *
52827960 CTTTAGCGGCGCTTTTGCCACAAACACCGCTATAGACCATGAT
1 CTTTAGCGATGCTTTACCCACAAACGCCTCTATAGACCATGAC
52828003 CTTTAGC
1 CTTTAGC
52828010 AGCACTTTTA
Statistics
Matches: 108, Mismatches: 26, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
42 2 0.02
43 105 0.97
44 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.27
Consensus pattern (43 bp):
CTTTAGCGATGCTTTACCCACAAACGCCTCTATAGACCATGAC
Found at i:52827983 original size:86 final size:82
Alignment explanation
Indices: 52827841--52828075 Score: 220
Period size: 86 Copynumber: 2.8 Consensus size: 82
52827831 CTTTAGCGGC
* ** * *
52827841 GCTTTCCCCACAAACGCCT-CTAAAGACCAAGACCTTTAGCGATGCTTTACCTACAAACGCCTCT
1 GCTTTTCCCACAAACG-CTGCTAAAGACC-AGACCTTTAGCGGCGCTTTTCC-ACAAACGCCGCT
** *
52827905 ATAGGTCATGGTCTATAGCGA
63 ATAGACCATGATCTATAGC-A
* * *
52827926 TGCTTTTCCCACAAACGCTGCTATATACCATGACCTTTAGCGGCGCTTTTGCCACAAACACCGCT
1 -GCTTTTCCCACAAACGCTGCTAAAGACCA-GACCTTTAGCGGCGCTTTT-CCACAAACGCCGCT
*
52827991 ATAGACCATGATCTTTAGCA
63 ATAGACCATGATCTATAGCA
** * * * *
52828011 GCACTTTTATCACAAACGCTGCTAAAGAACAAACCTTTAGCGGCGCTTCTCCAAAAACGCCGCTA
1 G--CTTTTCCCACAAACGCTGCTAAAGACCAGACCTTTAGCGGCGCTTTTCCACAAACGCCGCTA
52828076 AAAACTTAAC
Statistics
Matches: 123, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
84 14 0.11
85 21 0.17
86 86 0.70
87 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.25
Consensus pattern (82 bp):
GCTTTTCCCACAAACGCTGCTAAAGACCAGACCTTTAGCGGCGCTTTTCCACAAACGCCGCTATA
GACCATGATCTATAGCA
Found at i:52828018 original size:43 final size:43
Alignment explanation
Indices: 52827928--52828027 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
52827918 TATAGCGATG
* * * * * *
52827928 CTTTTCCCACAAACGCTGCTATATACCATGACCTTTAGCGGCG
1 CTTTTACCACAAACACCGCTATAGACCATGACCTTTAGCAGCA
* *
52827971 CTTTTGCCACAAACACCGCTATAGACCATGATCTTTAGCAGCA
1 CTTTTACCACAAACACCGCTATAGACCATGACCTTTAGCAGCA
*
52828014 CTTTTATCACAAAC
1 CTTTTACCACAAAC
52828028 GCTGCTAAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (43 bp):
CTTTTACCACAAACACCGCTATAGACCATGACCTTTAGCAGCA
Found at i:52838671 original size:13 final size:13
Alignment explanation
Indices: 52838653--52838678 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52838643 TATGGTCTAC
52838653 AATTTCGAGAAAA
1 AATTTCGAGAAAA
52838666 AATTTCGAGAAAA
1 AATTTCGAGAAAA
52838679 TTTCGTTCGA
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:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
AATTTCGAGAAAA
Found at i:52840196 original size:22 final size:22
Alignment explanation
Indices: 52840166--52840208 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52840156 ACACCAAAAC
* *
52840166 AGGCTTTTAGAGGCGCTTTTTT
1 AGGCCTTTAGAGGCACTTTTTT
*
52840188 AGGCCTTTAGCGGCACTTTTT
1 AGGCCTTTAGAGGCACTTTTT
52840209 AGCACCGCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGAGGCACTTTTTT
Found at i:52840344 original size:43 final size:43
Alignment explanation
Indices: 52840280--52840422 Score: 187
Period size: 43 Copynumber: 3.3 Consensus size: 43
52840270 GCGTCGCTAA
* * ** *
52840280 CTTTAGCGGTGCTTTCCCCACAAACGTCGCTATAGGTCATGGT
1 CTTTAGCGGCGCTTTTCCCACAAACGTCGCTATAGACCATGAT
* * *
52840323 CTATAGCGGCGCTTTTCCCACAAACGTTGCTATAGACCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGTCGCTATAGACCATGAT
* **
52840366 CTTTAGCGGCGCATTTCCCACAAACACCGCTATAGACCATGAT
1 CTTTAGCGGCGCTTTTCCCACAAACGTCGCTATAGACCATGAT
52840409 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
52840423 CTCCAAAATC
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 85 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGTCGCTATAGACCATGAT
Found at i:52845124 original size:38 final size:40
Alignment explanation
Indices: 52845073--52845169 Score: 121
Period size: 38 Copynumber: 2.5 Consensus size: 40
52845063 TGGGCTTAGG
52845073 TTTTTTGCGGCGTTTTTTGGAAAAAG-CCACTAATGCTC-
1 TTTTTTGCGGCGTTTTTTGGAAAAAGACCACTAATGCTCA
* *
52845111 TTTTTTGTGGCG-TTTTT-GAAAAAGCACCGCTAATGCTCGA
1 TTTTTTGCGGCGTTTTTTGGAAAAAG-ACCACTAATGCTC-A
*
52845151 TTTTTAGCGGCGTTTTTTG
1 TTTTTTGCGGCGTTTTTTG
52845170 TCCAAACAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
36 7 0.14
37 5 0.10
38 22 0.45
40 10 0.20
41 5 0.10
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (40 bp):
TTTTTTGCGGCGTTTTTTGGAAAAAGACCACTAATGCTCA
Found at i:52856823 original size:102 final size:101
Alignment explanation
Indices: 52856646--52856988 Score: 417
Period size: 102 Copynumber: 3.4 Consensus size: 101
52856636 TATCGATGAA
* * * *
52856646 CACGTGTGTAGTATTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGCCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
* *
52856711 TAAGTGAAGGCTACAATGTGTGCC-AATAAGCTTTGGT
66 TAAGT-AAGGCTACTATGTGTACCGAA-AAGCTTTGGT
* *
52856748 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
52856813 TAAGTAAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGT-AAGGCTACTATGTGTACCGAAAAGCTTTGGT
* * * **
52856850 CACGTGTGTAGTACTATGTGAAGGCTACTTCGTGAACCG-TAAA-ACTTTATCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTGTAGTA
* * * ** * *
52856913 CTATGTGAGGCCACTACATGAACCGTAAAA-C-TTGAT
65 CTAAGTAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
*
52856949 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
52856989 ATGATAAAAG
Statistics
Matches: 213, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
99 40 0.19
100 15 0.07
101 28 0.13
102 128 0.60
103 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTAAGGCTACTATGTGTACCGAAAAGCTTTGGT
Found at i:52856951 original size:49 final size:50
Alignment explanation
Indices: 52856646--52856982 Score: 288
Period size: 51 Copynumber: 6.7 Consensus size: 50
52856636 TATCGATGAA
* * * * * **
52856646 CACGTGTGTAGTATTGTGTGAAGGCTACTACGTGTATCGATAAATA-ATGGC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGAT
* * * * ** *
52856697 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTGCC--AATAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAA-AA-C-TTGAT
* * *** *
52856748 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGAT
* * * * * *
52856799 CACATGTGTAGTACTAAGTAAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGAT
* *
52856850 CACGTGTGTAGTACTATGTGAAGGCTACTTCGTGAACCGTAAAACTTTAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
* * *
52856900 CACATGTGTAGTACTATGTG-AGGCCACTACATGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
52856949 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
52856983 TATCGAATGA
Statistics
Matches: 228, Mismatches: 47, Indels: 23
0.77 0.16 0.08
Matches are distributed among these distances:
48 3 0.01
49 48 0.21
50 33 0.14
51 137 0.60
52 4 0.02
53 1 0.00
54 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
Found at i:52860293 original size:30 final size:30
Alignment explanation
Indices: 52860257--52860313 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
52860247 CCTAGACCCA
* *
52860257 ACTTGCATTGAACCTTCGGAATAAATGTGT
1 ACTTGCATCGAACCTTCAGAATAAATGTGT
52860287 ACTTGCATCGAACCTTCAGAATAAATG
1 ACTTGCATCGAACCTTCAGAATAAATG
52860314 CGTCCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (30 bp):
ACTTGCATCGAACCTTCAGAATAAATGTGT
Found at i:52867024 original size:20 final size:21
Alignment explanation
Indices: 52867001--52867039 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
52866991 TAAATTTCAA
*
52867001 TTTAACCCAAAA-TATTTATT
1 TTTAACCAAAAATTATTTATT
*
52867021 TTTAGCCAAAAATTATTTA
1 TTTAACCAAAAATTATTTA
52867040 AAACCATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.44
Consensus pattern (21 bp):
TTTAACCAAAAATTATTTATT
Found at i:52867080 original size:19 final size:19
Alignment explanation
Indices: 52867056--52867095 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
52867046 TAAAATTAAT
52867056 TTTTCTAAAAATATT-TTTA
1 TTTTCT-AAAATATTATTTA
*
52867075 TTTTCTAGAATATTATTTA
1 TTTTCTAAAATATTATTTA
52867094 TT
1 TT
52867096 AATTTTTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTTCTAAAATATTATTTA
Found at i:52868430 original size:27 final size:28
Alignment explanation
Indices: 52868370--52868423 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
52868360 AAAAATAATT
*
52868370 AAAATTAAATATTTTAATAATTTAAGTG
1 AAAATTAAATATTTTAATAATTAAAGTG
*
52868398 AAAATTAATTATTTT-ATAATTAAAGT
1 AAAATTAAATATTTTAATAATTAAAGT
52868424 ATGAATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (28 bp):
AAAATTAAATATTTTAATAATTAAAGTG
Done.