Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold185
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: 1073966
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 182459 characters in sequence are not A, C, G, or T
File 3 of 7
Found at i:203526 original size:13 final size:13
Alignment explanation
Indices: 203508--203532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
203498 CATAAAGTGT
203508 TGTATCGATACAA
1 TGTATCGATACAA
203521 TGTATCGATACA
1 TGTATCGATACA
203533 TGTTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:203612 original size:13 final size:13
Alignment explanation
Indices: 203594--203618 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
203584 ATCACTTAAA
203594 TGTATCGATACAT
1 TGTATCGATACAT
203607 TGTATCGATACA
1 TGTATCGATACA
203619 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:203683 original size:52 final size:52
Alignment explanation
Indices: 203627--203807 Score: 317
Period size: 52 Copynumber: 3.5 Consensus size: 52
203617 CACTGATCTT
* * *
203627 TGTATCGATACATGCAGGCAAATTTGTCCAAATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
203679 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
203731 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
203783 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
203808 TCATATTTCG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 124 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:208068 original size:78 final size:79
Alignment explanation
Indices: 207870--208198 Score: 353
Period size: 78 Copynumber: 4.2 Consensus size: 79
207860 CTACCATTAG
* * * ** * * *
207870 GGATACTACAAGCCCGTTATTTTTGAAAGGATACTCCAACTATGGTTTTATTTTTAAAATACCAA
1 GGATACTCCAACCCCGTTATTTTCGAAAGGATACTCCAACCCTGATTTTATTTTCAAAACACCAA
207935 TTTTTCACAATCGA
66 TTTTTCACAATCGA
* * * *
207949 GGATACTCCAACCTCATTATTTTCGAGAGGATACTCCAACCCTGATTTTATTTTCAGAACACCAA
1 GGATACTCCAACCCCGTTATTTTCGAAAGGATACTCCAACCCTGATTTTATTTTCAAAACACCAA
208014 TTTTTCACAATC-A
66 TTTTTCACAATCGA
** * * *
208027 GGATACTCCAACCCCGTTATTTTCGAAAAAATACTCAAACCCT-AGTTTTATTTCCACAACA-CA
1 GGATACTCCAACCCCGTTATTTTCGAAAGGATACTCCAACCCTGA-TTTTATTTTCAAAACACCA
*
208090 GATTTTTCACAATCAA
65 -ATTTTTCACAATCGA
* * * * * **
208106 GAATACTCCAACCCCG-TATTTTCGAAGGGATATTCCAACTC-GACTTTATTTTCAAAACACTGA
1 GGATACTCCAACCCCGTTATTTTCGAAAGGATACTCCAACCCTGATTTTATTTTCAAAACACCAA
* * *
208169 TTTTCCATAATCGG
66 TTTTTCACAATCGA
208183 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
208199 ATTTTATTTT
Statistics
Matches: 208, Mismatches: 37, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
77 42 0.20
78 85 0.41
79 81 0.39
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (79 bp):
GGATACTCCAACCCCGTTATTTTCGAAAGGATACTCCAACCCTGATTTTATTTTCAAAACACCAA
TTTTTCACAATCGA
Found at i:208204 original size:128 final size:130
Alignment explanation
Indices: 208072--208328 Score: 285
Period size: 128 Copynumber: 2.0 Consensus size: 130
208062 CAAACCCTAG
* *
208072 TTTTATTTCCACAACAC-AGATTTTTCACAATCAAGAATACTCCAACCCCG-TATTT-TCGA-AG
1 TTTTATTTCCAAAACACTA-AATTTTCACAATCAAGAATACTCCAACCCCGTTATTTCT-GAGA-
* * * * *
208133 GGATATTCCAACTC-GA-CTTTATTTTCAAAACA-CTGATTTTCCATAATCGGGGATACTCCAAC
63 GAATACTCCAAC-CGGATCTTTATTTTCAAAACATC-GATTTTCCACAATCAGAGATACTCCAAC
208195 CCCGA
126 CCCGA
* * ** *
208200 TTTTATTTTCAAAACACTAAATTTTCACTATTGAGGATACTCCAACCCCGTTATTTCTGAGAGAA
1 TTTTATTTCCAAAACACTAAATTTTCACAATCAAGAATACTCCAACCCCGTTATTTCTGAGAGAA
* *
208265 TACTCCAACCGTGATTTTTATTTTCAAAACATCGATTTTTCACAATCAGAGATACTCCAACCCC
66 TACTCCAACCG-GATCTTTATTTTCAAAACATCGATTTTCCACAATCAGAGATACTCCAACCCC
208329 ATTATTTTCG
Statistics
Matches: 107, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
128 42 0.39
129 18 0.17
130 4 0.04
131 42 0.39
132 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (130 bp):
TTTTATTTCCAAAACACTAAATTTTCACAATCAAGAATACTCCAACCCCGTTATTTCTGAGAGAA
TACTCCAACCGGATCTTTATTTTCAAAACATCGATTTTCCACAATCAGAGATACTCCAACCCCGA
Found at i:208212 original size:51 final size:51
Alignment explanation
Indices: 208132--208249 Score: 143
Period size: 51 Copynumber: 2.3 Consensus size: 51
208122 TATTTTCGAA
* * *
208132 GGGATATTCCAA-CTCGACTTTATTTTCAAAACACT-GATTTTC-CATAATCG
1 GGGATACTCCAACCCCGACTTTATTTTCAAAACACTAAATTTTCAC-T-ATCG
* *
208182 GGGATACTCCAACCCCGATTTTATTTTCAAAACACTAAATTTTCACTATTG
1 GGGATACTCCAACCCCGACTTTATTTTCAAAACACTAAATTTTCACTATCG
*
208233 AGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
208250 TTATTTCTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 11 0.19
51 40 0.68
52 7 0.12
53 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACCCCGACTTTATTTTCAAAACACTAAATTTTCACTATCG
Found at i:208426 original size:158 final size:158
Alignment explanation
Indices: 208183--208551 Score: 388
Period size: 158 Copynumber: 2.3 Consensus size: 158
208173 CCATAATCGG
* * * *
208183 GGATACTCCAACCCCGATTTTATTTTCAAAACA-CTAAATTTTCACTATTGAGGATACTCCAACC
1 GGATACACCAACCCCGGTTTTATTTTCAAAACATC-AATTTTTCACTATCG-GGATACTCCAACC
** *
208247 CCGTTATTTCTGAGAGAATACTCCAA-CCGTGATTTTTATTT-TCAAAACATCGATTTTTCACAA
64 CCGTTATTTCTGAGAGAATACTCCAACCCCAG-TTTTTATTTCT-AAAACACCGATTTTTCACAA
* ** * *
208310 TCAGAGATACTCCAACCCCATTATTTTCGAGA
127 TCAGAGATACTCCAACCCCACTATTCCCAAAA
* * * * *
208342 GGATACACTAACCTCGGTTTTATTTTCAAAATATCAATTTTTCACTATCGGGATACTTCAACCCT
1 GGATACACCAACCCCGGTTTTATTTTCAAAACATCAATTTTTCACTATCGGGATACTCCAACCCC
* * *
208407 GTTA-TTCTCGA-AGGGATACTCTAACCCCAGTTTTTATTTCTAGAACACCGATTTTTCACAATC
66 GTTATTTCT-GAGA-GAATACTCCAACCCCAGTTTTTATTTCTAAAACACCGATTTTTCACAATC
* * * *
208470 GGGGATACTCTAACCCCGCTATTCCCAAAA
129 AGAGATACTCCAACCCCACTATTCCCAAAA
* * * * *
208500 GGATGCTCCAACCCCGGTTTTATTTTTAAAACATCGATTTTTCACCATCGGG
1 GGATACACCAACCCCGGTTTTATTTTCAAAACATCAATTTTTCACTATCGGG
208552 GAATGTACTC
Statistics
Matches: 173, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
157 5 0.03
158 122 0.71
159 45 0.26
160 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (158 bp):
GGATACACCAACCCCGGTTTTATTTTCAAAACATCAATTTTTCACTATCGGGATACTCCAACCCC
GTTATTTCTGAGAGAATACTCCAACCCCAGTTTTTATTTCTAAAACACCGATTTTTCACAATCAG
AGATACTCCAACCCCACTATTCCCAAAA
Found at i:208442 original size:79 final size:77
Alignment explanation
Indices: 208182--208551 Score: 323
Period size: 80 Copynumber: 4.7 Consensus size: 77
208172 TCCATAATCG
* * * * *
208182 GGGATACTCCAACCCCGATTTTATTTTCAAAACA-CTAAATTTTCACTATTGAGGATACTCCAAC
1 GGGATACTCCAACCCCGGTTTTATTTTCAAAACATC-GATTTTTCACAATCG-GGATACTCCAAC
208246 CCCGTTATT-TCTGA
64 CCCGTTATTCTC-GA
* ** * *
208260 GAGAATACTCCAACCGTGATTTTTATTTTCAAAACATCGATTTTTCACAATCAGAGATACTCCAA
1 G-GGATACTCCAACCCCG-GTTTTATTTTCAAAACATCGATTTTTCACAATC-GGGATACTCCAA
* *
208325 CCCCATTATTTTCGA
63 CCCCGTTATTCTCGA
* * * * * * *
208340 GAGGATACACTAACCTCGGTTTTATTTTCAAAATATCAATTTTTCACTATCGGGATACTTCAACC
1 G-GGATACTCCAACCCCGGTTTTATTTTCAAAACATCGATTTTTCACAATCGGGATACTCCAACC
*
208405 CTGTTATTCTCGAA
65 CCGTTATTCTCG-A
* * * * *
208419 GGGATACTCTAACCCCAGTTTT-TATTTCTAGAACACCGATTTTTCACAATCGGGGATACTCTAA
1 GGGATACTCCAACCCCGGTTTTAT-TTTC-AAAACATCGATTTTTCACAATC-GGGATACTCCAA
* * *
208483 CCCCGCTATTCCCAAA
63 CCCCGTTATTCTC-GA
* * * *
208499 AGGATGCTCCAACCCCGGTTTTATTTTTAAAACATCGATTTTTCACCATCGGG
1 GGGATACTCCAACCCCGGTTTTATTTTCAAAACATCGATTTTTCACAATCGGG
208552 GAATGTACTC
Statistics
Matches: 235, Mismatches: 46, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
77 1 0.00
78 47 0.20
79 80 0.34
80 102 0.43
81 5 0.02
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (77 bp):
GGGATACTCCAACCCCGGTTTTATTTTCAAAACATCGATTTTTCACAATCGGGATACTCCAACCC
CGTTATTCTCGA
Found at i:210910 original size:8 final size:8
Alignment explanation
Indices: 210897--210967 Score: 51
Period size: 8 Copynumber: 8.9 Consensus size: 8
210887 ATTTAATAAG
210897 TTATATAT
1 TTATATAT
210905 TTATATTAT
1 TTATA-TAT
210914 ATTAATATAT
1 -TT-ATATAT
210924 TT-TATTAT
1 TTATA-TAT
*
210932 TT-TATAA
1 TTATATAT
210939 TTATAT-T
1 TTATATAT
* *
210946 TAAAATAT
1 TTATATAT
210954 TT-TATAT
1 TTATATAT
210961 TTATATA
1 TTATATA
210968 AATTTAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
7 16 0.32
8 21 0.42
9 5 0.10
10 5 0.10
11 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATAT
Found at i:210932 original size:21 final size:20
Alignment explanation
Indices: 210892--210946 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
210882 TTTAAATTTA
210892 ATAAGTTATATATTTATATTAT
1 ATAA-TTATAT-TTTATATTAT
*
210914 ATTAA-TATATTTTATTATTTT
1 A-TAATTATATTTTA-TATTAT
210935 ATAATTATATTT
1 ATAATTATATTT
210947 AAAATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 7 0.24
21 18 0.62
22 1 0.03
23 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATAATTATATTTTATATTAT
Found at i:210956 original size:30 final size:27
Alignment explanation
Indices: 210900--210997 Score: 103
Period size: 26 Copynumber: 3.6 Consensus size: 27
210890 TAATAAGTTA
*
210900 TATATTTATATTATA-TTAATATATTT
1 TATATTTATATTATATTTAAAATATTT
210926 TATTATTTTATAATTATATTTAAAATATTT
1 TA-TA-TTTAT-ATTATATTTAAAATATTT
*
210956 TATATTTATA-TAAATTTAAAATA-TT
1 TATATTTATATTATATTTAAAATATTT
* *
210981 AATAATTTATATGATAT
1 TAT-ATTTATATTATAT
210998 AAATTTTAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
25 4 0.07
26 21 0.34
27 6 0.10
28 10 0.16
29 8 0.13
30 12 0.20
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (27 bp):
TATATTTATATTATATTTAAAATATTT
Found at i:210973 original size:16 final size:15
Alignment explanation
Indices: 210875--210992 Score: 61
Period size: 15 Copynumber: 7.9 Consensus size: 15
210865 ATTTTATTAA
* *
210875 TATATTATTTAAATT
1 TATATAATTTATATT
*
210890 TA-ATAAGTTATATAT
1 TATATAATTTATAT-T
210905 T-TAT-A-TTATATT
1 TATATAATTTATATT
* *
210917 AATATATTTTATTATT
1 TATATAATTTA-TATT
210933 T-TATAA-TTATATT
1 TATATAATTTATATT
* *
210946 TAAAATATTTTATATT
1 T-ATATAATTTATATT
*
210962 TATATAAATTTAAAATAT
1 TATAT-AATTT-ATAT-T
210980 TA-ATAATTTATAT
1 TATATAATTTATAT
210993 GATATAAATT
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
12 1 0.01
13 14 0.18
14 12 0.15
15 22 0.28
16 21 0.27
17 5 0.06
18 3 0.04
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (15 bp):
TATATAATTTATATT
Found at i:210988 original size:26 final size:26
Alignment explanation
Indices: 210869--210992 Score: 85
Period size: 26 Copynumber: 4.6 Consensus size: 26
210859 TTTTATATTT
*
210869 TATTA-ATATATTATTTAAATTTAATAA
1 TATTATATAT-TTATATAAATTTAA-AA
* * *
210896 -GTTATATATTTATAT-TATATTAATA
1 TATTATATATTTATATAAAT-TTAAAA
* *
210921 TATTTTATTATTTTATAATTATATTTAAAA
1 TATTATA-TA-TTTAT-A-TAAATTTAAAA
*
210951 TATTTTATATTTATATAAATTTAAAA
1 TATTATATATTTATATAAATTTAAAA
210977 TATTA-ATAATTTATAT
1 TATTATAT-ATTTATAT
210993 GATATAAATT
Statistics
Matches: 79, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
25 5 0.06
26 38 0.48
27 7 0.09
28 10 0.13
29 3 0.04
30 13 0.16
31 3 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
TATTATATATTTATATAAATTTAAAA
Found at i:210991 original size:32 final size:32
Alignment explanation
Indices: 210949--211016 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
210939 TTATATTTAA
* *
210949 AATATTTTATATTTATATAAA-TTTAAAATATT
1 AATAATTTATA-TGATATAAATTTTAAAATATT
210981 AATAATTTATATGATATAAATTTTAAAATATT
1 AATAATTTATATGATATAAATTTTAAAATATT
211013 AATA
1 AATA
211017 TATAATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
AATAATTTATATGATATAAATTTTAAAATATT
Found at i:211672 original size:11 final size:11
Alignment explanation
Indices: 211647--211690 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
211637 TTTGATTTTT
*
211647 TAAATAAA-AA
1 TAAATAAATTA
211657 TAAATAAATTA
1 TAAATAAATTA
211668 TAAATAAATTAA
1 TAAATAAATT-A
*
211680 AAAATAAATTA
1 TAAATAAATTA
211691 ATAATTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 8 0.27
11 12 0.40
12 10 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAATAAATTA
Found at i:211686 original size:12 final size:12
Alignment explanation
Indices: 211658--211691 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
211648 AAATAAAAAT
*
211658 AAATAAATT-AT
1 AAATAAATTAAA
211669 AAATAAATTAAA
1 AAATAAATTAAA
211681 AAATAAATTAA
1 AAATAAATTAA
211692 TAATTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATAAATTAAA
Found at i:213820 original size:79 final size:77
Alignment explanation
Indices: 213703--214063 Score: 268
Period size: 79 Copynumber: 4.6 Consensus size: 77
213693 TTATTTATAT
* * * * * *
213703 TTTTATTTCTAAAATACCGA-TTTTCTACCATTAGGGATACTACAAGCCCGTTATTTTTGAAAGG
1 TTTTATTTTTAAAATACCAATTTTTC-ACAATCA-GGATACTCCAA-CCCGTTATTTTCGAAAGG
* *
213767 ATACTCCAACTATGG
63 ATACTCCAACCATGA
* *
213782 TTTTATTTTTAAAATACCAATTTTTCACAATCGAGGATACTCCAACCTCATTATTTTCGAGAGGA
1 TTTTATTTTTAAAATACCAATTTTTCACAATC-AGGATACTCCAACC-CGTTATTTTCGAAAGGA
*
213847 TACTCCAACCCTGA
64 TACTCCAACCATGA
* * * **
213861 TTTTATTTTCAGAACACCAATTTTTCACAATCAGGATACTCCAACCCCGTTATTTTCGAAAAAAT
1 TTTTATTTTTAAAATACCAATTTTTCACAATCAGGATACTCCAA-CCCGTTATTTTCGAAAGGAT
* *
213926 ACTCAAACCCT-A
65 ACTCCAACCATGA
** * * *
213938 GTTTTATTTCCACAACA-CAGATTTTTCACAATCAAGAATACTCCAACCTCG-TATTTTCG-AAG
1 -TTTTATTTTTAAAATACCA-ATTTTTCACAATC-AGGATACTCCAACC-CGTTATTTTCGAAAG
*
214000 AGATATTCCAA-C-TCGA
62 -GATACTCCAACCAT-GA
* * * ** * * *
214016 CTTTATTTTCAAAACACTGATTTTCCATAATCGGGGATACTCCAACCC
1 TTTTATTTTTAAAATACCAATTTTTCACAATC-AGGATACTCCAACCC
214064 CGATTTTATT
Statistics
Matches: 234, Mismatches: 36, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
76 2 0.01
77 42 0.18
78 83 0.35
79 101 0.43
80 6 0.03
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (77 bp):
TTTTATTTTTAAAATACCAATTTTTCACAATCAGGATACTCCAACCCGTTATTTTCGAAAGGATA
CTCCAACCATGA
Found at i:213935 original size:78 final size:79
Alignment explanation
Indices: 213737--214065 Score: 335
Period size: 78 Copynumber: 4.2 Consensus size: 79
213727 CTACCATTAG
* * * * ** * * *
213737 GGATACTACAAGCCCGTTATTTTTGAAAGGATACTCCAACTATGGTTTTATTTTTAAAATACCAA
1 GGATACTCCAACCCCGTTATTTTCGAAAAGATACTCCAACCCTGATTTTATTTTCAAAACACCAA
213802 TTTTTCACAATCGA
66 TTTTTCACAATCGA
* * * * *
213816 GGATACTCCAACCTCATTATTTTCGAGAGGATACTCCAACCCTGATTTTATTTTCAGAACACCAA
1 GGATACTCCAACCCCGTTATTTTCGAAAAGATACTCCAACCCTGATTTTATTTTCAAAACACCAA
213881 TTTTTCACAATC-A
66 TTTTTCACAATCGA
* * * *
213894 GGATACTCCAACCCCGTTATTTTCGAAAAAATACTCAAACCCT-AGTTTTATTTCCACAACA-CA
1 GGATACTCCAACCCCGTTATTTTCGAAAAGATACTCCAACCCTGA-TTTTATTTTCAAAACACCA
*
213957 GATTTTTCACAATCAA
65 -ATTTTTCACAATCGA
* * * * * * **
213973 GAATACTCCAACCTCG-TATTTTCGAAGAGATATTCCAACTC-GACTTTATTTTCAAAACACTGA
1 GGATACTCCAACCCCGTTATTTTCGAAAAGATACTCCAACCCTGATTTTATTTTCAAAACACCAA
* * *
214036 TTTTCCATAATCGG
66 TTTTTCACAATCGA
214050 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
214066 ATTTTATTTT
Statistics
Matches: 207, Mismatches: 38, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
77 41 0.20
78 86 0.42
79 80 0.39
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (79 bp):
GGATACTCCAACCCCGTTATTTTCGAAAAGATACTCCAACCCTGATTTTATTTTCAAAACACCAA
TTTTTCACAATCGA
Found at i:214071 original size:128 final size:130
Alignment explanation
Indices: 213939--214195 Score: 312
Period size: 131 Copynumber: 2.0 Consensus size: 130
213929 CAAACCCTAG
* * *
213939 TTTTATTTCCACAACAC-AGATTTTTCACAATCAAGAATACTCCAACCTCG-TATTT-TCGA-AG
1 TTTTATTTCCAAAACACTA-AATTTTCACAATCAAGAATACTCCAACCCCGTTATTTCT-GAGAG
* * *
214000 AGATATTCCAACTC-GA-CTTTATTTTCAAAACA-CTGATTTTCCATAATCGGGGATACTCCAAC
64 A-ATACTCCAAC-CGGATCTTTATTTTCAAAACATC-GATTTTCCACAATCGGAGATACTCCAAC
214062 CCCGA
126 CCCGA
* * * *
214067 TTTTATTTTCAAAACACTAAATTTTCACTATCGAGGATACTCCAACCCCGTTATTTCTGAGAGAA
1 TTTTATTTCCAAAACACTAAATTTTCACAATCAAGAATACTCCAACCCCGTTATTTCTGAGAGAA
*
214132 TACTCCAACCGTGATTTTTATTTTCAAAACATCGATTTTCCACAATCGGAGATACTCCAACCCC
66 TACTCCAACCG-GATCTTTATTTTCAAAACATCGATTTTCCACAATCGGAGATACTCCAACCCC
214196 ATTATTTTCG
Statistics
Matches: 110, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
128 42 0.38
129 17 0.15
130 6 0.05
131 44 0.40
132 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.33
Consensus pattern (130 bp):
TTTTATTTCCAAAACACTAAATTTTCACAATCAAGAATACTCCAACCCCGTTATTTCTGAGAGAA
TACTCCAACCGGATCTTTATTTTCAAAACATCGATTTTCCACAATCGGAGATACTCCAACCCCGA
Found at i:214081 original size:51 final size:51
Alignment explanation
Indices: 214017--214116 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
214007 CCAACTCGAC
* *
214017 TTTATTTTCAAAACACT-GATTTTC-CATAATCGGGGATACTCCAACCCCGAT
1 TTTATTTTCAAAACACTAAATTTTCAC-T-ATCGAGGATACTCCAACCCCGAT
214068 TTTATTTTCAAAACACTAAATTTTCACTATCGAGGATACTCCAACCCCG
1 TTTATTTTCAAAACACTAAATTTTCACTATCGAGGATACTCCAACCCCG
214117 TTATTTCTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
51 37 0.82
52 7 0.16
53 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (51 bp):
TTTATTTTCAAAACACTAAATTTTCACTATCGAGGATACTCCAACCCCGAT
Found at i:214188 original size:80 final size:80
Alignment explanation
Indices: 214050--214417 Score: 292
Period size: 79 Copynumber: 4.6 Consensus size: 80
214040 CCATAATCGG
* *
214050 GGATACTCCAACCCCGA-TTTTATTTTCAAAACA-CTAAATTTTCACTATC-GAGGATACTCCAA
1 GGATACTCCAA-CCCGATTTTTATTTTCAAAACATC-AATTTTTCACAATCGGA-GATACTCCAA
214112 CCCCGTTATTTCT-GAGA
63 CCCCGTTATTTCTCGAGA
* * * *
214129 GAATACTCCAACCGTGATTTTTATTTTCAAAACATCGATTTTCCACAATCGGAGATACTCCAACC
1 GGATACTCCAACC-CGATTTTTATTTTCAAAACATCAATTTTTCACAATCGGAGATACTCCAACC
*
214194 CCATTATTT-TCGAGA
65 CCGTTATTTCTCGAGA
* * * * * *
214209 GGATACACTAACCTCG-GTTTTATTTTCAAAATATCAATTTTTCACTATCGG-GATACTTCAACC
1 GGATACTCCAACC-CGATTTTTATTTTCAAAACATCAATTTTTCACAATCGGAGATACTCCAACC
*
214272 CTGTTA-TTCTCGA-A
65 CCGTTATTTCTCGAGA
* * * * * * *
214286 GGGATACTCTAACCCCAGTTTTTA-TTTCTAGAACACCGATTTTTCACAATCGGGGATACTCTAA
1 -GGATACTCCAACCCGA-TTTTTATTTTC-AAAACATCAATTTTTCACAATCGGAGATACTCCAA
* * * *
214350 CCCCGCTA-TTCCCAAAA
63 CCCCGTTATTTCTCGAGA
* * * * * *
214367 AGATGCTCCAACCCCG-GTTTTATTTTTAAAACATCGATTTTTCACCATCGG
1 GGATACTCCAA-CCCGATTTTTATTTTCAAAACATCAATTTTTCACAATCGG
214418 GGAATGTACT
Statistics
Matches: 232, Mismatches: 43, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
77 4 0.02
78 37 0.16
79 93 0.40
80 91 0.39
81 7 0.03
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (80 bp):
GGATACTCCAACCCGATTTTTATTTTCAAAACATCAATTTTTCACAATCGGAGATACTCCAACCC
CGTTATTTCTCGAGA
Found at i:214249 original size:79 final size:79
Alignment explanation
Indices: 214050--214417 Score: 291
Period size: 80 Copynumber: 4.6 Consensus size: 79
214040 CCATAATCGG
* * * * *
214050 GGATACTCCAACCCCGATTTTATTTTCAAAACA-CTAAATTTTCACTATC-GAGGATACTCCAAC
1 GGATACTCTAACCTCGGTTTTATTTTCAAAACATC-AATTTTTCACAATCGGA-GATACTCCAAC
214113 CCCGTTA-TTTCTGAGA
64 CCCGTTATTTTC-GAGA
* * * * *
214129 GAATACTCCAACCGT-GATTTTTATTTTCAAAACATCGATTTTCCACAATCGGAGATACTCCAAC
1 GGATACTCTAACC-TCG-GTTTTATTTTCAAAACATCAATTTTTCACAATCGGAGATACTCCAAC
*
214193 CCCATTATTTTCGAGA
64 CCCGTTATTTTCGAGA
* * * *
214209 GGATACACTAACCTCGGTTTTATTTTCAAAATATCAATTTTTCACTATCGG-GATACTTCAACCC
1 GGATACTCTAACCTCGGTTTTATTTTCAAAACATCAATTTTTCACAATCGGAGATACTCCAACCC
* *
214273 TGTTATTCTCGA-A
66 CGTTATTTTCGAGA
* * * * * * *
214286 GGGATACTCTAACCCCAGTTTT-TATTTCTAGAACACCGATTTTTCACAATCGGGGATACTCTAA
1 -GGATACTCTAACCTCGGTTTTAT-TTTC-AAAACATCAATTTTTCACAATCGGAGATACTCCAA
* ** * *
214350 CCCCGCTATTCCCAAAA
63 CCCCGTTATTTTCGAGA
* * * * * * *
214367 AGATGCTCCAACCCCGGTTTTATTTTTAAAACATCGATTTTTCACCATCGG
1 GGATACTCTAACCTCGGTTTTATTTTCAAAACATCAATTTTTCACAATCGG
214418 GGAATGTACT
Statistics
Matches: 235, Mismatches: 42, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
77 2 0.01
78 43 0.18
79 84 0.36
80 97 0.41
81 9 0.04
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (79 bp):
GGATACTCTAACCTCGGTTTTATTTTCAAAACATCAATTTTTCACAATCGGAGATACTCCAACCC
CGTTATTTTCGAGA
Found at i:214385 original size:158 final size:158
Alignment explanation
Indices: 214051--214418 Score: 395
Period size: 158 Copynumber: 2.3 Consensus size: 158
214041 CATAATCGGG
* *
214051 GATACTCCAACCCCGATTTTATTTTCAAAACA-CTAAATTTTCACTATCGAGGATACTCCAACCC
1 GATACTCCAACCCCGGTTTTATTTTCAAAACATC-AATTTTTCACTATCG-GGATACTCCAACCC
** *
214115 CGTTATTTCTGAGAGAATACTCCAACCGTGATTTTTATTTTCAAAACATCGATTTTCCACAATCG
64 CGTTATTTCTGAGAGAATACTCCAACCCAGATTTTTATTTTCAAAACACCGATTTTCCACAATCG
* ** * * *
214180 GAGATACTCCAACCCCATTATTTTCGAGAG
129 GAGATACTCCAACCCCACTATTCCCAAAAA
* * * * * *
214210 GATACACTAACCTCGGTTTTATTTTCAAAATATCAATTTTTCACTATCGGGATACTTCAACCCTG
1 GATACTCCAACCCCGGTTTTATTTTCAAAACATCAATTTTTCACTATCGGGATACTCCAACCCCG
* * * *
214275 TTA-TTCTCGA-AGGGATACTCTAACCCCAG-TTTTTA-TTTCTAGAACACCGATTTTTCACAAT
66 TTATTTCT-GAGA-GAATACTCCAA-CCCAGATTTTTATTTTC-AAAACACCGATTTTCCACAAT
* * *
214336 CGGGGATACTCTAACCCCGCTATTCCCAAAAA
127 CGGAGATACTCCAACCCCACTATTCCCAAAAA
* * * *
214368 GATGCTCCAACCCCGGTTTTATTTTTAAAACATCGATTTTTCACCATCGGG
1 GATACTCCAACCCCGGTTTTATTTTCAAAACATCAATTTTTCACTATCGGG
214419 GAATGTACTC
Statistics
Matches: 172, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
157 9 0.05
158 118 0.69
159 44 0.26
160 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (158 bp):
GATACTCCAACCCCGGTTTTATTTTCAAAACATCAATTTTTCACTATCGGGATACTCCAACCCCG
TTATTTCTGAGAGAATACTCCAACCCAGATTTTTATTTTCAAAACACCGATTTTCCACAATCGGA
GATACTCCAACCCCACTATTCCCAAAAA
Found at i:216778 original size:8 final size:8
Alignment explanation
Indices: 216765--216835 Score: 51
Period size: 8 Copynumber: 8.9 Consensus size: 8
216755 ATTTAATAAG
216765 TTATATAT
1 TTATATAT
216773 TTATATTAT
1 TTATA-TAT
216782 ATTAATATAT
1 -TT-ATATAT
216792 TT-TATTAT
1 TTATA-TAT
*
216800 TT-TATAA
1 TTATATAT
216807 TTATAT-T
1 TTATATAT
* *
216814 TAAAATAT
1 TTATATAT
216822 TT-TATAT
1 TTATATAT
216829 TTATATA
1 TTATATA
216836 AATTTAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
7 16 0.32
8 21 0.42
9 5 0.10
10 5 0.10
11 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATAT
Found at i:216800 original size:21 final size:20
Alignment explanation
Indices: 216760--216814 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
216750 TTTAAATTTA
216760 ATAAGTTATATATTTATATTAT
1 ATAA-TTATAT-TTTATATTAT
*
216782 ATTAA-TATATTTTATTATTTT
1 A-TAATTATATTTTA-TATTAT
216803 ATAATTATATTT
1 ATAATTATATTT
216815 AAAATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 7 0.24
21 18 0.62
22 1 0.03
23 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATAATTATATTTTATATTAT
Found at i:216824 original size:30 final size:27
Alignment explanation
Indices: 216768--216865 Score: 103
Period size: 26 Copynumber: 3.6 Consensus size: 27
216758 TAATAAGTTA
*
216768 TATATTTATATTATA-TTAATATATTT
1 TATATTTATATTATATTTAAAATATTT
216794 TATTATTTTATAATTATATTTAAAATATTT
1 TA-TA-TTTAT-ATTATATTTAAAATATTT
*
216824 TATATTTATA-TAAATTTAAAATA-TT
1 TATATTTATATTATATTTAAAATATTT
* *
216849 AATAATTTATATGATAT
1 TAT-ATTTATATTATAT
216866 AAATTTTAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
25 4 0.07
26 21 0.34
27 6 0.10
28 10 0.16
29 8 0.13
30 12 0.20
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (27 bp):
TATATTTATATTATATTTAAAATATTT
Found at i:216841 original size:16 final size:15
Alignment explanation
Indices: 216743--216860 Score: 61
Period size: 15 Copynumber: 7.9 Consensus size: 15
216733 ATTTTATTAA
* *
216743 TATATTATTTAAATT
1 TATATAATTTATATT
*
216758 TA-ATAAGTTATATAT
1 TATATAATTTATAT-T
216773 T-TAT-A-TTATATT
1 TATATAATTTATATT
* *
216785 AATATATTTTATTATT
1 TATATAATTTA-TATT
216801 T-TATAA-TTATATT
1 TATATAATTTATATT
* *
216814 TAAAATATTTTATATT
1 T-ATATAATTTATATT
*
216830 TATATAAATTTAAAATAT
1 TATAT-AATTT-ATAT-T
216848 TA-ATAATTTATAT
1 TATATAATTTATAT
216861 GATATAAATT
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
12 1 0.01
13 14 0.18
14 12 0.15
15 22 0.28
16 21 0.27
17 5 0.06
18 3 0.04
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (15 bp):
TATATAATTTATATT
Found at i:216856 original size:26 final size:26
Alignment explanation
Indices: 216737--216860 Score: 85
Period size: 26 Copynumber: 4.6 Consensus size: 26
216727 TTTTATATTT
*
216737 TATTA-ATATATTATTTAAATTTAATAA
1 TATTATATAT-TTATATAAATTTAA-AA
* * *
216764 -GTTATATATTTATAT-TATATTAATA
1 TATTATATATTTATATAAAT-TTAAAA
* *
216789 TATTTTATTATTTTATAATTATATTTAAAA
1 TATTATA-TA-TTTAT-A-TAAATTTAAAA
*
216819 TATTTTATATTTATATAAATTTAAAA
1 TATTATATATTTATATAAATTTAAAA
216845 TATTA-ATAATTTATAT
1 TATTATAT-ATTTATAT
216861 GATATAAATT
Statistics
Matches: 79, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
25 5 0.06
26 38 0.48
27 7 0.09
28 10 0.13
29 3 0.04
30 13 0.16
31 3 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
TATTATATATTTATATAAATTTAAAA
Found at i:216859 original size:32 final size:32
Alignment explanation
Indices: 216817--216884 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
216807 TTATATTTAA
* *
216817 AATATTTTATATTTATATAAA-TTTAAAATATT
1 AATAATTTATA-TGATATAAATTTTAAAATATT
216849 AATAATTTATATGATATAAATTTTAAAATATT
1 AATAATTTATATGATATAAATTTTAAAATATT
216881 AATA
1 AATA
216885 TATAATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
AATAATTTATATGATATAAATTTTAAAATATT
Found at i:217527 original size:15 final size:15
Alignment explanation
Indices: 217509--217554 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
217499 TTTTGATTTT
217509 TTAAATAAAAATAAA
1 TTAAATAAAAATAAA
* *
217524 TTAATTATAAATAAA
1 TTAAATAAAAATAAA
217539 TT--A-AAAAATAAA
1 TTAAATAAAAATAAA
217551 TTAA
1 TTAA
217555 CAATTTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
12 10 0.40
15 15 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAATAAAAATAAA
Found at i:218074 original size:17 final size:17
Alignment explanation
Indices: 218036--218096 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
218026 ATGATGATAT
*
218036 TTTATTATATTTAA-AATG
1 TTTA-TATATTTAATAA-A
218054 TTTATATATTTAATAAA
1 TTTATATATTTAATAAA
* *
218071 TTTAAATAAATTAAT-AA
1 TTTATAT-ATTTAATAAA
218088 TTTATATAT
1 TTTATATAT
218097 ACCTATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
16 1 0.03
17 23 0.64
18 12 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTATATATTTAATAAA
Found at i:218339 original size:2 final size:2
Alignment explanation
Indices: 218334--218366 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
218324 TCCCGCCACA
*
218334 CT CT CT CT CT CT CT CT CT CT CT CC CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
218367 CCCCACCCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:221235 original size:13 final size:13
Alignment explanation
Indices: 221205--221241 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
221195 TATGAACATT
221205 TTAAAATTTA-T-
1 TTAAAATTTATTA
*
221216 GTAAAATTTATTA
1 TTAAAATTTATTA
221229 TTAAAATTTATTA
1 TTAAAATTTATTA
221242 AAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 9 0.41
12 1 0.05
13 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (13 bp):
TTAAAATTTATTA
Found at i:221252 original size:20 final size:19
Alignment explanation
Indices: 221227--221292 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
221217 TAAAATTTAT
221227 TATTAAAATTTATTAAAAAA
1 TATTAAAATTTA-TAAAAAA
*
221247 TATTAAAGTTTATAAAAAA
1 TATTAAAATTTATAAAAAA
* * * *
221266 AATTAATATGTATATAAAA
1 TATTAAAATTTATAAAAAA
221285 TATATAAA
1 TAT-TAAA
221293 CCAAACACAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 23 0.62
20 14 0.38
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TATTAAAATTTATAAAAAA
Found at i:222004 original size:18 final size:18
Alignment explanation
Indices: 221968--222009 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
221958 AAAGATATAA
*
221968 AGGAAAAATGAAGAAAAG
1 AGGAAAAATAAAGAAAAG
221986 AGGAAAAA-AAAGAAGAAG
1 AGGAAAAATAAAGAA-AAG
*
222004 AAGAAA
1 AGGAAA
222010 GCTTTGTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (18 bp):
AGGAAAAATAAAGAAAAG
Found at i:222635 original size:13 final size:13
Alignment explanation
Indices: 222617--222641 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
222607 CATAAAGTGT
222617 TGTATCGATACAA
1 TGTATCGATACAA
222630 TGTATCGATACA
1 TGTATCGATACA
222642 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:222723 original size:13 final size:13
Alignment explanation
Indices: 222705--222732 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
222695 ATCACTTAAA
222705 TGTATCGATACAT
1 TGTATCGATACAT
222718 TGTATCGATACAT
1 TGTATCGATACAT
222731 TG
1 TG
222733 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:222782 original size:52 final size:51
Alignment explanation
Indices: 222718--222866 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
222708 ATCGATACAT
** *
222718 TGTATCGATACATTGATCTTTGTATCGATACATGCAGGAAAATTTGCCAAGA
1 TGTATCGATACATT-ATCAATGTATCGATACATGCAGGCAAATTTGCCAAGA
* *
222770 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATTAT-CAATGTATCGATACATGCAGGCAAATTTGCCAAGA
*
222822 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATTA-TCAATGTATCGATACATGCAGGCAAATTT
222867 TCATATTTCG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.97
53 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (51 bp):
TGTATCGATACATTATCAATGTATCGATACATGCAGGCAAATTTGCCAAGA
Found at i:227522 original size:13 final size:14
Alignment explanation
Indices: 227506--227534 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
227496 TTAAAAACAA
227506 AAAT-TAATTTTTT
1 AAATATAATTTTTT
227519 AAATATAATTTTTT
1 AAATATAATTTTTT
227533 AA
1 AA
227535 TTTTTATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AAATATAATTTTTT
Found at i:227984 original size:7 final size:7
Alignment explanation
Indices: 227972--228019 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
227962 AAGTTAAATA
227972 TTTTAAT
1 TTTTAAT
227979 TTTTAAT
1 TTTTAAT
227986 TTTTAA-
1 TTTTAAT
* *
227992 ATATAATT
1 TTTTAA-T
228000 TTTTAAT
1 TTTTAAT
228007 TTTTATAT
1 TTTTA-AT
228015 TTTTA
1 TTTTA
228020 GATATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
6 4 0.12
7 19 0.56
8 11 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTAAT
Found at i:228024 original size:29 final size:30
Alignment explanation
Indices: 227972--228034 Score: 94
Period size: 28 Copynumber: 2.1 Consensus size: 30
227962 AAGTTAAATA
227972 TTTTAATTTTTAATTTTTAAATATA-AT-T
1 TTTTAATTTTTAATTTTTAAATATATATAT
*
228000 TTTTAATTTTTATATTTTTAGATATATATAT
1 TTTTAATTTTTA-ATTTTTAAATATATATAT
228031 TTTT
1 TTTT
228035 TAAAAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 12 0.39
29 12 0.39
30 2 0.06
31 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (30 bp):
TTTTAATTTTTAATTTTTAAATATATATAT
Found at i:228296 original size:453 final size:459
Alignment explanation
Indices: 227509--228384 Score: 1125
Period size: 453 Copynumber: 1.9 Consensus size: 459
227499 AAAACAAAAA
227509 TTAATTTTTTAAATATAATTTTTTAATTTTTATACTTTTAGTATATATATATTTTTAAAAATAGA
1 TTAATTTTTTAAATATAATTTTTTAATTTTTATACTTTTAGTATATATATATTTTTAAAAATAGA
* * * *
227574 TAATAATTTAAAAATTATAATTTTAAATTCTTTTATATTTTTAAAATAATTTTTTCTTTTCGAAA
66 T-ATAATTTAAAAATTATAATTTTAAATACCTTTATATTTTTAAAATAA-TTCTTCTTTTCAAAA
227639 AATAAAATTTACAAAAAAAAAAATGAATGTTGCCACATGCCATCACCTAATTAGTCAATGCCAAA
129 AATAAAATTT------AAAAAAA-GAA--TTGCCACATGCCATCACCTAATTAGTCAATGCCAAA
* * *
227704 TCACTACCGATATTTATAGTATTAAATATTATGCAATTTGATTACATAAGTACCATATTGAACAT
185 TCACTACCGATATTTATAATATTAAATATTATACAATTTGATTACATAAGTACCACATTGAACAT
* * * * *
227769 TTTTTAAAATACAAATACTACATTGATAAATTTGATAAACTTACAAGATTACTTATAATATCATA
250 TTTTTAAAATACAAATACCACATTAACAAATTTGATAAACTTAAAAAATTACTTATAATATCATA
* * * *
227834 CTGAATATAAATATGATATCCGAAACTTA-TCTATTATACATCAAAGTCATATTTTTAATTAATA
315 CTGAATATAAATATCATATCCAAAACTTACT-TATTATACATCAAAATCATATTTCTAATTAATA
*
227898 TTTAATTCAAAGGTATTATAATATATTTATACATATAATTTATATCATTATAACCCTGTGTTTTA
379 TTTAATTCAAAGATATTAT-A-ATATTTATACATATAATTTATATCATTATAACCCTGTGTTTTA
227963 AGTTAAATATTTTAATTT
442 AGTTAAATATTTTAATTT
* *
227981 TTAA-TTTTTAAATATAATTTTTTAATTTTTATATTTTTAG-ATATATATATTTTTTAAAA-A-A
1 TTAATTTTTTAAATATAATTTTTTAATTTTTATACTTTTAGTATATATATATTTTTAAAAATAGA
*
228042 T-TAGATTTAGAAATTATAATTTTAAATACCTTTAT-TTTTTAAAATAA-TCTT-TTTTCAAAAA
66 TATA-ATTTAAAAATTATAATTTTAAATACCTTTATATTTTTAAAATAATTCTTCTTTTCAAAAA
* * *
228103 ATAAAATTT-AAAAAA-AA-TGCCACATGCCATCACCTAATTAGTCAATGCCACATCACTATCTA
130 ATAAAATTTAAAAAAAGAATTGCCACATGCCATCACCTAATTAGTCAATGCCAAATCACTACCGA
* * * * ** *
228165 TATTTATAATGTTACGTATTTATATATAATTTGATTGTATAAGTACTACATTGAACA-TTTTTAA
195 TATTTATAATATTA--AATAT-TATACAATTTGATTACATAAGTACCACATTGAACATTTTTTAA
** ** *
228229 AATGA-AAATACCGTATTAACAAATTTGATAAA-TTATAAAAATTACTTATAATATCATTTTTAA
257 AAT-ACAAATACCACATTAACAAATTTGATAAACTTA-AAAAATTACTTATAATATCATACTGAA
** *
228292 TATAAATATCATATTTAAAACTTACTTGTTATACATCAAAATCATATTTCTAATTAATATTTAAT
320 TATAAATATCATATCCAAAACTTACTTATTATACATCAAAATCATATTTCTAATTAATATTTAAT
228357 TCAAAGATATTATAATATTTATACATAT
385 TCAAAGATATTATAATATTTATACATAT
228385 TTTTTTCATC
Statistics
Matches: 359, Mismatches: 38, Indels: 35
0.83 0.09 0.08
Matches are distributed among these distances:
451 68 0.19
452 4 0.01
453 125 0.35
454 33 0.09
456 6 0.02
463 18 0.05
464 3 0.01
466 14 0.04
467 28 0.08
468 2 0.01
469 1 0.00
470 18 0.05
471 35 0.10
472 4 0.01
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.43
Consensus pattern (459 bp):
TTAATTTTTTAAATATAATTTTTTAATTTTTATACTTTTAGTATATATATATTTTTAAAAATAGA
TATAATTTAAAAATTATAATTTTAAATACCTTTATATTTTTAAAATAATTCTTCTTTTCAAAAAA
TAAAATTTAAAAAAAGAATTGCCACATGCCATCACCTAATTAGTCAATGCCAAATCACTACCGAT
ATTTATAATATTAAATATTATACAATTTGATTACATAAGTACCACATTGAACATTTTTTAAAATA
CAAATACCACATTAACAAATTTGATAAACTTAAAAAATTACTTATAATATCATACTGAATATAAA
TATCATATCCAAAACTTACTTATTATACATCAAAATCATATTTCTAATTAATATTTAATTCAAAG
ATATTATAATATTTATACATATAATTTATATCATTATAACCCTGTGTTTTAAGTTAAATATTTTA
ATTT
Found at i:228643 original size:2 final size:2
Alignment explanation
Indices: 228638--228683 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
228628 TTCAAAAAAT
*
228638 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
228681 TA T
1 TA T
228684 TGCAAACTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:229507 original size:2 final size:2
Alignment explanation
Indices: 229500--229546 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
229490 AATTTGGAAA
229500 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
229542 AG AG A
1 AG AG A
229547 AGAAAAGATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:232644 original size:3 final size:3
Alignment explanation
Indices: 232636--232669 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
232626 AAATTTTCTG
232636 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
232670 CTTGTTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:245201 original size:45 final size:45
Alignment explanation
Indices: 245135--245221 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
245125 TTTGTTATTT
*
245135 TTTTAATTCGGTTTGGGTTTAAGTTTATATAGATTTTTAGTTAGA
1 TTTTAATTCGGTTTGGATTTAAGTTTATATAGATTTTTAGTTAGA
*
245180 TTTTAATTGGGTTTGGATTTAAGTTTATATAGATTTTTAGTT
1 TTTTAATTCGGTTTGGATTTAAGTTTATATAGATTTTTAGTT
245222 TGTATTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.24, C:0.01, G:0.20, T:0.55
Consensus pattern (45 bp):
TTTTAATTCGGTTTGGATTTAAGTTTATATAGATTTTTAGTTAGA
Found at i:245246 original size:45 final size:45
Alignment explanation
Indices: 245152--245251 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
245142 TCGGTTTGGG
* * * *
245152 TTTAAGTTTATATAGATTTTTAGTTAGATTTTAATTGGGTTTGGA
1 TTTAAGTTTATATAGATTTTTAGTTAGATATTAAATGGGCTTGAA
*
245197 TTTAAGTTTATATAGATTTTTAGTTTG-TATTAAATGGGCTT-AA
1 TTTAAGTTTATATAGATTTTTAGTTAGATATTAAATGGGCTTGAA
245240 CTTTTAAGTTTA
1 --TTTAAGTTTA
245252 ATTTATATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 1 0.02
44 11 0.23
45 36 0.75
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (45 bp):
TTTAAGTTTATATAGATTTTTAGTTAGATATTAAATGGGCTTGAA
Found at i:247040 original size:21 final size:20
Alignment explanation
Indices: 247015--247054 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
247005 AAAATATGTT
*
247015 TGAGAAAGAAAATTTTTTGAA
1 TGAG-AAGAAAAGTTTTTGAA
*
247036 TGAGACGAAAAGTTTTTGA
1 TGAGAAGAAAAGTTTTTGA
247055 TTTTTTGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.33
Consensus pattern (20 bp):
TGAGAAGAAAAGTTTTTGAA
Found at i:248359 original size:11 final size:10
Alignment explanation
Indices: 248295--248345 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
248285 ATAATAAAAG
248295 TTAATTAATT
1 TTAATTAATT
248305 TTAAAATT-ATT
1 TT--AATTAATT
248316 TTAATTAATAT
1 TTAATTAAT-T
*
248327 TAAATTAAATT
1 TTAATT-AATT
248338 TTAATTAA
1 TTAATTAA
248346 ATTACATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
9 4 0.12
10 6 0.18
11 17 0.50
12 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTAATTAATT
Found at i:248359 original size:22 final size:22
Alignment explanation
Indices: 248295--248349 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
248285 ATAATAAAAG
*
248295 TTAATTAATTTTAAAATT--ATT
1 TTAATTAATATT-AAATTAAATT
248316 TTAATTAATATTAAATTAAATT
1 TTAATTAATATTAAATTAAATT
248338 TTAATTAA-ATTA
1 TTAATTAATATTA
248350 CATTTTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 5 0.16
21 15 0.48
22 11 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTAATATTAAATTAAATT
Found at i:248367 original size:16 final size:16
Alignment explanation
Indices: 248325--248373 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
248315 TTTAATTAAT
*
248325 ATTAAATTAAATTTTA
1 ATTAAATTACATTTTA
248341 ATTAAATTACATTTTA
1 ATTAAATTACATTTTA
*
248357 ATTCAAA-TACATATTA
1 ATT-AAATTACATTTTA
248373 A
1 A
248374 ATATTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 27 0.90
17 3 0.10
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAATTACATTTTA
Found at i:256954 original size:51 final size:49
Alignment explanation
Indices: 256872--257043 Score: 146
Period size: 51 Copynumber: 3.4 Consensus size: 49
256862 TCTCAGAAAT
* * * * * * *
256872 AACGAGGTTGAAGTATCCTCGATTGTAGAAAATCGATATTTTGAAAATAA
1 AACGGGGTTGGAGTATCCCCAATGGTGGAAAAT-GATGTTTTGAAAATAA
* * ** * *
256922 AATCGGGATTGGAGTATCTCTGATGGTGGAAAATTAGTGTTTTGGAAATAA
1 AA-CGGGGTTGGAGTATCCCCAATGGTGGAAAATGA-TGTTTTGAAAATAA
* * *
256973 AACCGGGGTTGGAGTATCCCCAATTGTGCAAAATTGGTGTTTTGAAAATAA
1 AA-CGGGGTTGGAGTATCCCCAATGGTGGAAAA-TGATGTTTTGAAAATAA
257024 AACTGGGGTTGGAGTATCCC
1 AAC-GGGGTTGGAGTATCCC
257044 TTCAGAAATA
Statistics
Matches: 97, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
50 4 0.04
51 92 0.95
52 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (49 bp):
AACGGGGTTGGAGTATCCCCAATGGTGGAAAATGATGTTTTGAAAATAA
Found at i:257068 original size:79 final size:79
Alignment explanation
Indices: 256977--257279 Score: 344
Period size: 79 Copynumber: 3.8 Consensus size: 79
256967 AAATAAAACC
* * * * * *
256977 GGGGTTGGAGTATCCCCAATTGTGCAAAATTGGTGTTTTGAAAATAAAACTGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTAGAGTATC
257042 CCTTCAGAAATAAT
66 CCTTCAGAAATAAT
* * * * * *
257056 AGGGTTGGAGTATCCCCGATTGTGGAAAATCGATATTTT-AGAAATAAAA-TCGAGGTTGGAGTA
1 GGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGA-AAATAAAACT-GGGGTTAGAGTA
257119 TCCC-TCAGAAATAAT
64 TCCCTTCAGAAATAAT
* * * *
257134 GGGGTTGGAGTATCTCCGATTATGAAAAATCGATGTTTTGGAAATAAAACTGGGGTTAAAGTATT
1 GGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTAGAGTATC
* * *
257199 TCTT-TGAAAATAAC
66 CCTTCAG-AAATAAT
* * * *
257213 GGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAAAAATAAAACCGGGGTTAGAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTAGAGTATC
257278 CC
66 CC
257280 CTCGAAAATA
Statistics
Matches: 189, Mismatches: 29, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
78 67 0.35
79 122 0.65
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTAGAGTATC
CCTTCAGAAATAAT
Found at i:257086 original size:181 final size:181
Alignment explanation
Indices: 256780--257120 Score: 458
Period size: 181 Copynumber: 1.9 Consensus size: 181
256770 AAATTTAATA
* * * *
256780 TTTTGGAGATAAAAACGGGGTTGGATTATCCTCGATTGTGAAAAATCGATGTTCTAGAAATAAAA
1 TTTTGGAAATAAAAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTTCTAGAAATAAAA
* * * *
256845 CTGATGTTGGAGTATTCTCTCAGAAATAACGAGGTTGAAGTATCCTCGATTGTAGAAAATCGATA
66 CTGAGGTTGGAGTATCCTCTCAGAAATAAAGAGGTTGAAGTATCCCCGATTGTAGAAAATCGATA
256910 TTTT-GAAAATAAAATCG-GGATTGGAGTATCTCTGATGGTGGAAAATTAGTG
131 TTTTAG-AAATAAAATCGAGG-TTGGAGTATCTCTGATGGTGGAAAATTAGTG
* * * * *
256961 TTTTGGAAATAAAACCGGGGTTGGAGTATCCCCAATTGTGCAAAATTGGTGTT-TTGAAAATAAA
1 TTTTGGAAATAAAAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTTCTAG-AAATAAA
* * *
257025 ACTGGGGTTGGAGTATCC-CTTCAGAAATAATAG-GGTTGGAGTATCCCCGATTGTGGAAAATCG
65 ACTGAGGTTGGAGTATCCTC-TCAGAAATAA-AGAGGTTGAAGTATCCCCGATTGTAGAAAATCG
257088 ATATTTTAGAAATAAAATCGAGGTTGGAGTATC
128 ATATTTTAGAAATAAAATCGAGGTTGGAGTATC
257121 CCTCAGAAAT
Statistics
Matches: 139, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
180 3 0.02
181 132 0.95
182 4 0.03
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (181 bp):
TTTTGGAAATAAAAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTTCTAGAAATAAAA
CTGAGGTTGGAGTATCCTCTCAGAAATAAAGAGGTTGAAGTATCCCCGATTGTAGAAAATCGATA
TTTTAGAAATAAAATCGAGGTTGGAGTATCTCTGATGGTGGAAAATTAGTG
Found at i:257275 original size:157 final size:157
Alignment explanation
Indices: 256977--257279 Score: 383
Period size: 157 Copynumber: 1.9 Consensus size: 157
256967 AAATAAAACC
* * * * **
256977 GGGGTTGGAGTATCCCCAATTGTGCAAAATTGGTGTTTTGAAAATAAAACTGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTAAAGTATC
* * * * *
257042 CCTTCAGAAATAATAGGGTTGGAGTATCCCCGATTGTGGAAAATCGATATTTTAGAAATAAAATC
66 CCTTCAGAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTAAAAATAAAACC
*
257107 GAGGTTGGAGTATCCCTCAGAAATAAT
131 GAGGTTAGAGTATCCCTCAGAAATAAT
* * * *
257134 GGGGTTGGAGTATCTCCGATTATGAAAAATCGATGTTTTGGAAATAAAACTGGGGTTAAAGTATT
1 GGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTAAAGTATC
* * * * * *
257199 TCTT-TGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAAAAATAAAAC
66 CCTTCAG-AAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTAAAAATAAAAC
*
257263 CGGGGTTAGAGTATCCC
130 CGAGGTTAGAGTATCCC
257280 CTCGAAAATA
Statistics
Matches: 122, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
156 1 0.01
157 121 0.99
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (157 bp):
GGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGAAAATAAAACTGGGGTTAAAGTATC
CCTTCAGAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTAAAAATAAAACC
GAGGTTAGAGTATCCCTCAGAAATAAT
Found at i:259214 original size:50 final size:50
Alignment explanation
Indices: 259151--259294 Score: 193
Period size: 50 Copynumber: 2.9 Consensus size: 50
259141 GAAATGGTTA
* * *
259151 AAAATGCCTGAATGTATCGATACATTGAGA-AATGTATCGATACATCTGGGT
1 AAAAT-CCAGAATGTATCGATACAATGA-ACAATGTATCGATACATCTAGGT
* *
259202 AAAA-CTCAGAATGTATCGATATAATAAACAATGTATCGATACATCTAGGT
1 AAAATC-CAGAATGTATCGATACAATGAACAATGTATCGATACATCTAGGT
*
259252 AAAATCCAGAATGTATCGATACAATGAAGAATGTATCGATACA
1 AAAATCCAGAATGTATCGATACAATGAACAATGTATCGATACA
259295 AATTGTGAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
49 2 0.02
50 75 0.91
51 5 0.06
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (50 bp):
AAAATCCAGAATGTATCGATACAATGAACAATGTATCGATACATCTAGGT
Found at i:260433 original size:27 final size:26
Alignment explanation
Indices: 260396--260452 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
260386 GGCATTTTTT
260396 CCTTTTAAGTCCATC-ACTCTGTGGCA
1 CCTTTTAAGTCCA-CAACTCTGTGGCA
260422 CCTTTATAAGTCCACAACTCTGTGGCA
1 CCTTT-TAAGTCCACAACTCTGTGGCA
260449 CCTT
1 CCTT
260453 GTTTCTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.21, C:0.32, G:0.14, T:0.33
Consensus pattern (26 bp):
CCTTTTAAGTCCACAACTCTGTGGCA
Found at i:260480 original size:33 final size:32
Alignment explanation
Indices: 260370--262102 Score: 1151
Period size: 33 Copynumber: 54.8 Consensus size: 32
260360 CTTTTTTGAA
* *
260370 AAGTCCACAACTCTGTGGCA-TTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTT-CTTTT
* *
260402 AAGTCCATC-ACTCTGTGGCACC----T-TTAT
1 AAGTCCA-CAACTCCGTGGCACCTTTTTCTTTT
*
260429 AAGTCCACAACTCTGTGGCACCTTGTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTT
* * * **
260462 AAGCCCACAACTCCGTGGCATCTTTTCCTTCA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
260494 AAGTCCACAATTTCATGGCACCTTGTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTT
* *
260527 AAGTCCACAACTCCGTGGCATCTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
*
260559 AAGTCCATAACTCCGTGGCACC-----CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * * * *
260586 TAGTCTACAACTCTGTGACACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTT
* * * **
260619 AAGTCCACAACTTCGTTGCCCCTTTTTCCTTCA
1 AAGTCCACAACTCCGTGGCACCTTTTT-CTTTT
* * *
260652 AAATCCACAACTCCGTAGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTT
*
260685 AAGTCCACAACTCCGTGG----TTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
*
260713 AAGTCCACAACTCCGTGG----TTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
260741 AAGTCCACAACTCCGTGGCA-C----TCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * * *
260768 AAATCCACAACTCCGTGGTACCTTATCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
260800 AAGTCCACAACTCCGTGGCA-C----TC-TTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
260826 AAGTCCACAACTCTGTGGTACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTT
* * *
260859 AAGTTCACAACTCTGTGGCACCTTTTTTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * * ** *
260891 GAGTCCATAATTCTATAGCACC-TTTTCTTCTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTT-TT
* * * * **
260923 AAAGCCCATAACTCCGTGGTA-TTTTTTCCTTCA
1 -AAGTCCACAACTCCGTGGCACCTTTTT-CTTTT
* *
260956 AAGTCCACAACTCCATGGCACCTTGTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
260988 GAAGTCCACAACTCCATGGCATCTTATTCTTTTT
1 -AAGTCCACAACTCCGTGGCACCTTTTTC-TTTT
261022 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
261054 CAAAGTCCACAACTCTGTAGCACCTTGTTCCTTTT
1 --AAGTCCACAACTCCGTGGCACCTT-TTTCTTTT
* * * *
261089 AAGTCTACAACTCTGTGGCATCTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
** *
261121 AAGTCCATTACTCCGTGGTACC----T-TTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* *
261148 AAGTCCACAACTCTGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTT
* * * *
261181 AATTCCACAACTCCCTGGCACATTTTTTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* *
261213 CAAAGTCCACAACTCCGTGGGACCTTATTCTTTTT
1 --AAGTCCACAACTCCGTGGCACCTTTTTC-TTTT
** * *
261248 AAGTCCACAACTTTGTGGCA-CATTTTCTTCTCA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTT-T-T
* * * * * **
261281 AAGCCCATAACTCTGTGGCATCTTTTCCTTCA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
261313 AAGTCCACAACTCTGTGGTACCTTGTTCATTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTC-TTTT
* *
261346 AAGTCCACAACTCTGTGGTACCTTTTTCTTCTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTT-TT
* * * * * *
261379 AAAGCCCATAACTTCATGGCATCTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
261412 AAGTCCAAAACTCCATGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTT
*
261445 AAGTCCACAACTCCGTGGCACCTTTTTCTTCTCA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTT-T-T
* * *
261479 AAGCCCACAACTCCGTGGCATCTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
261511 AAGTCCATAACTTCGTGACACC-----CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * * * * *
261538 AAGTCTATAACTTCATGGCACTTTTTTCTTCTCA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTT-T-T
* ** * * **
261572 AAGCCCACAACTCCGTGATATCTTTTCCTTCA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* *
261604 AAGTCCACAACTCCGTGGTACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTT
* *** * *
261637 AAGTCCACAATTTTATGGCACTTTTTTCTTTA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * ** * * *
261669 AAGCCCATAACTCTATGGCATCTTTTCCTTTA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
*
261701 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTT
* *
261734 AAGTCCACAACTCTGTGGCACATTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
261766 CAAAGCCCACAACTCCGTGCCA-TTTTTTCCTTTT
1 --AAGTCCACAACTCCGTGGCACCTTTTT-CTTTT
* *
261800 AAGTCCACAACTTCATGGCACC-----CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* *
261827 AAGTCCACAACTCTGTGGCACCTCTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* *
261859 CAAAGCCCACAACTCCGTGGCATCTTTTT-TTTT
1 --AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
*
261892 AAGT---CAACTCCGTGGCA-CTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTT
* * * * **
261921 AAGTCCATAACTCCATGGAACATTTTCTCTTCA
1 AAGTCCACAACTCCGTGGCACCTTTT-TCTTTT
* * *
261954 AAGCCCACAACTTCGTGGCA-TTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTT-CTTTT
* *
261986 AAGTCCACCACTCCATGGCACC----T-TTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* *
262013 AAGTCCACAACTCCATGGCACCTTGTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
*
262045 AAAGTCCACAACTCTGTGGCACC-TTTTCTTTTT
1 -AAGTCCACAACTCCGTGGCACCTTTTTC-TTTT
* * *
262078 AAAGCCCATAACTCCATGGCACCTT
1 -AAGTCCACAACTCCGTGGCACCTT
262103 CCTCTAAAGC
Statistics
Matches: 1344, Mismatches: 259, Indels: 194
0.75 0.14 0.11
Matches are distributed among these distances:
26 22 0.02
27 167 0.12
28 70 0.05
29 12 0.01
31 14 0.01
32 392 0.29
33 481 0.36
34 175 0.13
35 11 0.01
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.37
Consensus pattern (32 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
Found at i:260513 original size:65 final size:64
Alignment explanation
Indices: 260370--262102 Score: 1232
Period size: 65 Copynumber: 27.4 Consensus size: 64
260360 CTTTTTTGAA
* * * *
260370 AAGTCCACAACTCTGTGGCA-TTTTTTCCTTTTAAGTCCATC-ACTCTGTGGCACC---T--TTA
1 AAGTCCACAACTCCGTGGCACCTTTTT-CTTTTAAGTCCA-CAACTCCGTGGCACCTTTTCCTTT
260428 T
64 T
* * * **
260429 AAGTCCACAACTCTGTGGCACCTTGTTTCTTTTAAGCCCACAACTCCGTGGCATCTTTTCCTTCA
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * * *
260494 AAGTCCACAATTTCATGGCACCTTGTTTCTTTTAAGTCCACAACTCCGTGGCATCTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * * * *
260559 AAGTCCATAACTCCGTGGCACC-----CTTTTTAGTCTACAACTCTGTGACACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* * * ** * *
260619 AAGTCCACAACTTCGTTGCCCCTTTTTCCTTCAAAATCCACAACTCCGTAGCACCTTGTTCCTTT
1 AAGTCCACAACTCCGTGGCACCTTTTT-CTTTTAAGTCCACAACTCCGTGGCACCTT-TTCCTTT
260684 T
64 T
*
260685 AAGTCCACAACTCCGTGG----TTTTCCTTTTAAGTCCACAACTCCGTGG----TTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * *
260741 AAGTCCACAACTCCGTGGCA-C----TCTTTTAAATCCACAACTCCGTGGTACCTTATCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* *
260800 AAGTCCACAACTCCGTGGCA-C----TC-TTTAAGTCCACAACTCTGTGGTACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* * * * * * ** *
260859 AAGTTCACAACTCTGTGGCACCTTTTTTTTTTGAGTCCATAATTCTATAGCACCTTTT-CTTCTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTCCTT-TT
* * * * ** *
260923 AAAGCCCATAACTCCGTGGTA-TTTTTTCCTTCAAAGTCCACAACTCCATGGCACCTTGTT-CTT
1 -AAGTCCACAACTCCGTGGCACCTTTTT-CTTTTAAGTCCACAACTCCGTGGCACCTT-TTCCTT
260986 TT
63 TT
* * * *
260988 GAAGTCCACAACTCCATGGCATCTTATTCTTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTT
1 -AAGTCCACAACTCCGTGGCACCTTTTTC-TTTTAAGTCCACAACTCCGTGGCACCTTTTCCTTT
261053 T
64 T
* * * * * *
261054 CAAAGTCCACAACTCTGTAGCACCTTGTTCCTTTTAAGTCTACAACTCTGTGGCATCTTTTCCTT
1 --AAGTCCACAACTCCGTGGCACCTT-TTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTCCTT
261119 TT
63 TT
** * *
261121 AAGTCCATTACTCCGTGGTACC----T-TTTTAAGTCCACAACTCTGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* * * * * *
261181 AATTCCACAACTCCCTGGCACATTTTTTTTTTCAAAGTCCACAACTCCGTGGGACCTTATTCTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT--AAGTCCACAACTCCGTGGCACCTT-TTCCTT
261246 TT
63 TT
** * * * * * * *
261248 AAGTCCACAACTTTGTGGCA-CATTTTCTTCTCAAAGCCCATAACTCTGTGGCATCTTTTCCTTC
1 AAGTCCACAACTCCGTGGCACCTTTTTCTT-T-TAAGTCCACAACTCCGTGGCACCTTTTCCTTT
*
261312 A
64 T
* * * * * *
261313 AAGTCCACAACTCTGTGGTACCTTGTTCATTTTAAGTCCACAACTCTGTGGTACCTTTTTCTTCT
1 AAGTCCACAACTCCGTGGCACCTTTTTC-TTTTAAGTCCACAACTCCGTGGCACCTTTTCCTT-T
261378 T
64 T
* * * * * * * *
261379 AAAGCCCATAACTTCATGGCATCTTTTCCTTTTAAGTCCAAAACTCCATGGCACCTTGTTCCTTT
1 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTT-TTCCTTT
261444 T
64 T
* * *
261445 AAGTCCACAACTCCGTGGCACCTTTTTCTTCTCAAAGCCCACAACTCCGTGGCATCTTTTCCTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTT-T-TAAGTCCACAACTCCGTGGCACCTTTTCCTTT
261510 T
64 T
* * * * * * * * *
261511 AAGTCCATAACTTCGTGACACC-----CTTTTAAGTCTATAACTTCATGGCACTTTTTTCTTCTC
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTCCTT-T-
*
261571 A
64 T
* ** * * ** *
261572 AAGCCCACAACTCCGTGATATCTTTTCCTTCAAAGTCCACAACTCCGTGGTACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTT-TTCCTTTT
* *** * * * * ** * *
261637 AAGTCCACAATTTTATGGCACTTTTTTCTTTAAAGCCCATAACTCTATGGCATCTTTTCCTTTA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * * *
261701 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACATTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * * * *
261766 CAAAGCCCACAACTCCGTGCCA-TTTTTTCCTTTTAAGTCCACAACTTCATGGCA-C----CCTT
1 --AAGTCCACAACTCCGTGGCACCTTTTT-CTTTTAAGTCCACAACTCCGTGGCACCTTTTCCTT
261825 TT
63 TT
* * * * *
261827 AAGTCCACAACTCTGTGGCACCTCTTTCTTTTCAAAGCCCACAACTCCGTGGCATCTTTT-TTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT--AAGTCCACAACTCCGTGGCACCTTTTCCTTT
261891 T
64 T
* * * * * *
261892 AAGT---CAACTCCGTGGCA-CTTGTTCCTTTTAAGTCCATAACTCCATGGAACATTTTCTCTTC
1 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTC-CTTT
*
261953 A
64 T
* * * * *
261954 AAGCCCACAACTTCGTGGCA-TTTTTTCCTTTTAAGTCCACCACTCCATGGCACC---T--TTTT
1 AAGTCCACAACTCCGTGGCACCTTTTT-CTTTTAAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * * *
262013 AAGTCCACAACTCCATGGCACCTTGTTCTTTTAAAGTCCACAACTCTGTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT-AAGTCCACAACTCCGTGGCACCTTTTCCTTTT
* * *
262078 AAAGCCCATAACTCCATGGCACCTT
1 -AAGTCCACAACTCCGTGGCACCTT
262103 CCTCTAAAGC
Statistics
Matches: 1312, Mismatches: 272, Indels: 173
0.75 0.15 0.10
Matches are distributed among these distances:
55 22 0.02
56 26 0.02
57 2 0.00
58 25 0.02
59 196 0.15
60 124 0.09
61 66 0.05
62 30 0.02
63 5 0.00
64 39 0.03
65 370 0.28
66 238 0.18
67 167 0.13
68 2 0.00
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.37
Consensus pattern (64 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTCCTTTT
Found at i:260597 original size:27 final size:27
Alignment explanation
Indices: 260522--260607 Score: 73
Period size: 32 Copynumber: 3.0 Consensus size: 27
260512 CACCTTGTTT
*
260522 CTTTTAAGTCCACAACTCCGTGGCATCTTTTC
1 CTTTTAAGTCCACAACTCCGTGACA-C----C
* *
260554 CTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGACACC
* * *
260581 CTTTTTAGTCTACAACTCTGTGACACC
1 CTTTTAAGTCCACAACTCCGTGACACC
260608 TTGTTCCTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
27 23 0.48
31 1 0.02
32 24 0.50
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.35
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGACACC
Found at i:261445 original size:99 final size:98
Alignment explanation
Indices: 260370--262102 Score: 1349
Period size: 99 Copynumber: 18.2 Consensus size: 98
260360 CTTTTTTGAA
* * * *
260370 AAGTCCACAACTCTGTGGCA-TTTTTTCCTTTTAAGTCCATC-ACTCTGTGGCACC----T-TTA
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCA-CAACTCTGTGGCACCTTTTTCTTT
* * * *
260428 T-AAGTCCACAACTCTGTGGCACCTTGTTTCTTTT
65 TAAAGCCCACAACTCCGTGGCATCTT-TTCCTTTT
* * ** * *
260462 AAGCCCACAACTCCGTGGCATCTT-TTCCTTCAAAGTCCACAA-TTTCATGGCACCTTGTTTCTT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCT-GTGGCACCTT-TTTCTT
*
260525 TT-AAGTCCACAACTCCGTGGCATCTTTTCCTTTT
64 TTAAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
* * * * *
260559 AAGTCCATAACTCCGTGGCA-C-----CCTTTTTAGTCTACAACTCTGTGACACCTTGTTCCTTT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTT-TTTCTTT
* * * ** **
260618 T-AAGTCCACAACTTCGTTGCCCCTTTTTCCTTCA
65 TAAAGCCCACAACTCCGTGGCATC-TTTTCCTTTT
* * * *
260652 AAATCCACAACTCCGTAGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGG----TTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
*
260713 -AAGTCCACAACTCCGTGG----TTTTCCTTTT
66 AAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
* * * * *
260741 AAGTCCACAACTCCGTGGCA-C----T-CTTTTAAATCCACAACTCCGTGGTACCTTATCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
*
260800 -AAGTCCACAACTCCGTGGCA-C---T-C-TTT
66 AAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
* * *
260826 AAGTCCACAACTCTGTGGTACCTTGTTCCTTTTAAGTTCACAACTCTGTGGCACCTTTTT-TTTT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
** * * * ** * *
260890 TGAGTCCATAATTCTATAGCACCTTTT-CTTCTT
66 AAAGCCCACAACTCCGTGGCATCTTTTCCTT-TT
* * * * * ** ** *
260923 AAAGCCCATAACTCCGTGGTA-TTTTTTCCTTCAAAGTCCACAACTCCATGGCACCTTGTTCTTT
1 -AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTT
* * * *
260987 TGAAGTCCACAACTCCATGGCATCTTATTCTTTTT
65 TAAAGCCCACAACTCCGTGGCATCTT-TTCCTTTT
* * *
261022 AAGTCCACAACTCCGTGGCACCTT-TTTCTTTTCAAAGTCCACAACTCTGTAGCACCTTGTTCCT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT--AAGTCCACAACTCTGTGGCACCTT-TTTCT
* * *
261086 TTT-AAGTCTACAACTCTGTGGCATCTTTTCCTTTT
63 TTTAAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
** * *
261121 AAGTCCATTACTCCGTGGTACC----T--TTTTAAGTCCACAACTCTGTGGCACCTTGTTCCTTT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTT-TTTCTTT
** * **
261180 T-AATTCCACAACTCCCTGGCA-CATTTTTTTTTT
65 TAAAGCCCACAACTCCGTGGCATC-TTTTCCTTTT
* * * * *
261213 CAAAGTCCACAACTCCGTGGGACCTTATTCTTTTTAAGTCCACAACTTTGTGGCA-CATTTTCTT
1 --AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTT
* * * **
261277 CTCAAAGCCCATAACTCTGTGGCATCTTTTCCTTCA
64 -TTAAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
* * * *
261313 AAGTCCACAACTCTGTGGTACCTTGTTCATTTTAAGTCCACAACTCTGTGGTACCTTTTTCTTCT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTT-T
* * *
261378 TAAAGCCCATAACTTCATGGCATCTTTTCCTTTT
65 TAAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
* * *
261412 AAGTCCAAAACTCCATGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTCT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTT-T
*
261477 CAAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
65 TAAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
* * * * * * *
261511 AAGTCCATAACTTCGTGACA-C-----CCTTTTAAGTCTATAACT-TCATGGCACTTTTTTCTTC
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCT-GTGGCACCTTTTTCTT-
* ** **
261569 TCAAAGCCCACAACTCCGTGATATCTTTTCCTTCA
64 TTAAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
* * * * *
261604 AAGTCCACAACTCCGTGGTACCTTGTTCCTTTTAAGTCCACAATTTTATGGCACTTTTTTC-TTT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* ** *
261668 AAAGCCCATAACTCTATGGCATCTTTTCCTTTA
66 AAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
*
261701 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACATTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* *
261766 CAAAGCCCACAACTCCGTGCCATTTTTTCCTTTT
66 -AAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
* * *
261800 AAGTCCACAACTTCATGGCA-C-----CCTTTTAAGTCCACAACTCTGTGGCACCTCTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
*
261859 CAAAGCCCACAACTCCGTGGCATCTTTT-TTTTT
66 -AAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
* ** * *
261892 AAGT---CAACTCCGTGGCA-CTTGTTCCTTTTAAGTCCATAACTCCATGG-AACATTTTCTCTT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCT-TT
* * *
261952 CAAAGCCCACAACTTCGTGGCATTTTTTCCTTTT
65 TAAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
* * ** *
261986 AAGTCCACCACTCCATGGCACC----T--TTTTAAGTCCACAACTCCATGGCACCTTGTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* * * *
262045 AAAGTCCACAACTCTGTGGCACCTTTTCTTTTT
66 AAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
* * *
262078 AAAGCCCATAACTCCATGGCACCTT
1 -AAGTCCACAACTCCGTGGCACCTT
262103 CCTCTAAAGC
Statistics
Matches: 1344, Mismatches: 214, Indels: 163
0.78 0.12 0.09
Matches are distributed among these distances:
83 22 0.02
84 1 0.00
85 21 0.02
86 2 0.00
87 28 0.02
88 1 0.00
89 38 0.03
90 5 0.00
91 44 0.03
92 200 0.15
93 227 0.17
94 81 0.06
95 4 0.00
96 3 0.00
97 154 0.11
98 146 0.11
99 271 0.20
100 89 0.07
101 7 0.01
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.37
Consensus pattern (98 bp):
AAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
AAAGCCCACAACTCCGTGGCATCTTTTCCTTTT
Found at i:261598 original size:126 final size:126
Alignment explanation
Indices: 260422--262009 Score: 433
Period size: 126 Copynumber: 12.5 Consensus size: 126
260412 CTCTGTGGCA
* * * ** *
260422 CCTTTATAAGTCCACAACTCTGTGGCACCTTGTTT-CTTTTAAGCCCACAACTCCGTGGCATCTT
1 CCTTTA-AAGCCCACAACTCCGTGACACCTT-TTTCCTTCAAAGCCCACAACTCCGTGGCACCTT
** * * * * * * *
260486 -TTCCTTCAAAGTCCACAATTTCATGGCACCTTGTTTCTTTTAAGTCCACAACTCCGTGGCATCT
64 GTTCCTTTTAAGTCCATAACTTCGTGACACC------CTTTTAAGTCCAAAACTCCATGGCACCT
260550 T-TT
123 TGTT
* * * * * * * * *
260553 CCTTTTAAGTCCATAACTCCGTGGCACC-CTTT--TT---AGTCTACAACTCTGTGACACCTTGT
1 CCTTTAAAGCCCACAACTCCGTGACACCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTTGT
* * * * *
260612 TCCTTTTAAGTCCACAACTTCGTTG-C-CCCTTTTTCCTTCAAAATCCACAACTCCGTAGCACCT
66 TCCTTTTAAGTCCATAACTTCG-TGACACCC---TT--TT--AAGTCCAAAACTCCATGGCACCT
260675 TGTT
123 TGTT
* * * ** *
260679 CCTTTTAAGTCCACAACTCCGTG-----GTTTTCCTTTTAAGTCCACAACTCCGTGG----TT-T
1 CCTTTAAAGCCCACAACTCCGTGACACCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTTGT
* * * * * * * * *
260734 TCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTAAATCCACAACTCCGTGGTACCTT-AT
66 TCCTTTTAAGTCCATAACTTCGTGACACCCTTTTAAGTCCAAAACTCCATGGCACCTTGTT
* * * * * * *
260794 CCTTTTAAGTCCACAACTCCGTGGCA-C----T-CTT-TAAGTCCACAACTCTGTGGTACCTTGT
1 CCTTTAAAGCCCACAACTCCGTGACACCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTTGT
* * * * * * * * *
260852 TCCTTTTAAGTTCACAAC-TCTGTGGCACCTTTTTTTTTTGAGTCCATAATTCTATAGCACCTT-
66 TCCTTTTAAGTCCATAACTTC-GTGACACC-----CTTTTAAGTCCAAAACTCCATGGCACCTTG
260915 TT
125 TT
* * ** * * *
260917 CTTCTTAAAGCCCATAACTCCGTGGTA-TTTTTTCCTTCAAAGTCCACAACTCCATGGCACCTTG
1 CCT-TTAAAGCCCACAACTCCGTGACACCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTTG
* * * * * * *
260981 TT-CTTTTGAAGTCCACAACTCCATGGCATCTTATTCTTTTTAAGTCCACAACTCCGTGGCACCT
65 TTCCTTTT-AAGTCCATAACTTCGT-G-A-C--A-CCCTTTTAAGTCCAAAACTCCATGGCACCT
*
261045 TTTT
123 TGTT
* * * * ** * * * *
261049 CTTTTCAAAGTCCACAACTCTGT-AGCACCTTGTTCCTTTTAAGTCTACAACTCTGTGGCATCTT
1 CCTTT-AAAGCCCACAACTCCGTGA-CACCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTT
* * ** * * **
261113 -TTCCTTTTAAGTCCATTACTCCGTGGTACCTTTTTAAGTCCACAACTCTGTGGCACCTTGTT
64 GTTCCTTTTAAGTCCATAACTTCGTGACACCCTTTTAAGTCCAAAACTCCATGGCACCTTGTT
* ** * * * ** * * *
261175 CCTTTTAATTCCACAACTCCCTGGCACATTTTTTTTTTCAAAGTCCACAACTCCGTGGGACCTTA
1 CCTTTAAAGCCCACAACTCCGTGACAC-CTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTTG
* * * ** * * * ** *
261240 TTCTTTTTAAGTCCACAACTTTGTGGCACATTTTCTTCTCAAAGCCCATAACTCTGTGGCATCTT
65 TTCCTTTTAAGTCCATAACTTCGT-G-ACA--CCCTT-T-TAAGTCCAAAACTCCATGGCACCTT
261305 -TT
124 GTT
* * * ** * * ** * * *
261307 CCTTCAAAGTCCACAACTCTGTGGTACCTTGTTCATTTTAAGTCCACAACTCTGTGGTACCTT-T
1 CCTTTAAAGCCCACAACTCCGTGACACCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTTGT
* * * *
261371 TTCTTCTTAAAGCCCATAACTTCATGGCATCTTTTCCTTTTAAGTCCAAAACTCCATGGCACCTT
66 TCCTT-TT-AAGTCCATAACTTCGTGACA-C----CCTTTTAAGTCCAAAACTCCATGGCACCTT
261436 GTT
124 GTT
* * * * *
261439 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTCTCAAAGCCCACAACTCCGTGGCATCTT-
1 CCTTTAAAGCCCACAACTCCGTGACACCTTTTTCCT-TCAAAGCCCACAACTCCGTGGCACCTTG
* * * *
261503 TTCCTTTTAAGTCCATAACTTCGTGACACCCTTTTAAGTCTATAACTTCATGGCA-CTTTTT
65 TTCCTTTTAAGTCCATAACTTCGTGACACCCTTTTAAGTCCAAAACTCCATGGCACCTTGTT
* * * * *
261564 TCTTCTCAAAGCCCACAACTCCGTGATATC-TTTTCCTTCAAAGTCCACAACTCCGTGGTACCTT
1 CCTT-T-AAAGCCCACAACTCCGTGACACCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTT
* * ** * * * * * * *
261628 GTTCCTTTTAAGTCCACAATTTTATGGCACTTTTTTCTTTAAAGCCCATAACTCTATGGCATCTT
64 GTTCCTTTTAAGTCCATAACTTCGTGACAC-----CCTTTTAAGTCCAAAACTCCATGGCACCTT
261693 -TT
124 GTT
* * * ** * * *
261695 CCTTTAAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACATT-T
1 CCTTTAAAGCCCACAACTCCGTGACACCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTTGT
* * * * * * * *
261759 TTCTTTTCAAAGCCCACAACTCCGTGCCATTTTTTCCTTTTAAGTCCACAACTTCATGGCA-C--
66 TCCTTTT--AAGTCCATAACTTCGTGACA-----CCCTTTTAAGTCCAAAACTCCATGGCACCTT
261821 ---
124 GTT
* * * * * * *
261821 CCTTTTAAGTCCACAACTCTGTGGCACCTCTTTCTTTTCAAAGCCCACAACTCCGTGGCATCTT-
1 CCTTTAAAGCCCACAACTCCGTGACACCTTTTTC-CTTCAAAGCCCACAACTCCGTGGCACCTTG
* * * * * *
261885 TT-TTTTTAAGT-C--AACTCCGTGGCACTTGTTCCTTTTAAGTCCATAACTCCATGGAACATT-
65 TTCCTTTTAAGTCCATAACTTCGTGACAC-----CCTTTTAAGTCCAAAACTCCATGGCACCTTG
261945 TT
125 TT
* * * * ** * * *
261947 CTCTTCAAAGCCCACAACTTCGTGGCA-TTTTTTCCTTTTAAGTCCACCACTCCATGGCACCTT
1 C-CTTTAAAGCCCACAACTCCGTGACACCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTT
262010 TTTAAGTCCA
Statistics
Matches: 1118, Mismatches: 240, Indels: 204
0.72 0.15 0.13
Matches are distributed among these distances:
113 18 0.02
114 3 0.00
115 25 0.02
116 22 0.02
117 3 0.00
118 28 0.03
120 2 0.00
121 38 0.03
122 26 0.02
123 30 0.03
124 44 0.04
125 111 0.10
126 181 0.16
127 98 0.09
128 5 0.00
129 36 0.03
130 92 0.08
131 161 0.14
132 109 0.10
133 84 0.08
135 1 0.00
136 1 0.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (126 bp):
CCTTTAAAGCCCACAACTCCGTGACACCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTTGT
TCCTTTTAAGTCCATAACTTCGTGACACCCTTTTAAGTCCAAAACTCCATGGCACCTTGTT
Found at i:261899 original size:28 final size:29
Alignment explanation
Indices: 261868--261925 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
261858 TCAAAGCCCA
*
261868 CAACTCCGTGGCATCTT-TT-TTTTTAAGT
1 CAACTCCGTGGCA-CTTGTTCCTTTTAAGT
261896 CAACTCCGTGGCACTTGTTCCTTTTAAGT
1 CAACTCCGTGGCACTTGTTCCTTTTAAGT
261925 C
1 C
261926 CATAACTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 3 0.11
28 15 0.56
29 9 0.33
ACGTcount: A:0.17, C:0.26, G:0.16, T:0.41
Consensus pattern (29 bp):
CAACTCCGTGGCACTTGTTCCTTTTAAGT
Found at i:262017 original size:27 final size:27
Alignment explanation
Indices: 261982--262036 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
261972 CATTTTTTCC
*
261982 TTTTAAGTCCACCACTCCATGGCACCT
1 TTTTAAGTCCACAACTCCATGGCACCT
262009 TTTTAAGTCCACAACTCCATGGCACCT
1 TTTTAAGTCCACAACTCCATGGCACCT
262036 T
1 T
262037 GTTCTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.35, G:0.11, T:0.31
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCATGGCACCT
Found at i:262316 original size:32 final size:32
Alignment explanation
Indices: 262232--262457 Score: 244
Period size: 32 Copynumber: 7.0 Consensus size: 32
262222 TAAGTGGAGA
* *
262232 AACCTTCTTCAAAGCCCATACAAGTTGGTGGC
1 AACCCTCTTCAAAGCCCACACAAGTTGGTGGC
*
262264 AATCCTCTTCAAAAGCCCACACAAGTCT-GTGGC
1 AACCCTCTTC-AAAGCCCACACAAGT-TGGTGGC
*
262297 AGCCCTCTTCAAAGCCCACACAAGTTGGTGGC
1 AACCCTCTTCAAAGCCCACACAAGTTGGTGGC
* * * *
262329 AATCCTTCTT-AAAACCCACATAAGTTAGTGGC
1 AA-CCCTCTTCAAAGCCCACACAAGTTGGTGGC
262361 AACCCT-TTCAAAAGCCCACACAAGTTGGTGGC
1 AACCCTCTTC-AAAGCCCACACAAGTTGGTGGC
* * * **
262393 AACCTTTTTTAAAGCCCACACAAGTCAGTGGC
1 AACCCTCTTCAAAGCCCACACAAGTTGGTGGC
* *
262425 GACCCT-TTCAAAAGACCACACAAGTTGGTGGC
1 AACCCTCTTC-AAAGCCCACACAAGTTGGTGGC
262457 A
1 A
262458 TCTTTTTCTA
Statistics
Matches: 161, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
30 2 0.01
31 6 0.04
32 117 0.73
33 35 0.22
34 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (32 bp):
AACCCTCTTCAAAGCCCACACAAGTTGGTGGC
Found at i:262379 original size:64 final size:64
Alignment explanation
Indices: 262242--262457 Score: 287
Period size: 64 Copynumber: 3.4 Consensus size: 64
262232 AACCTTCTTC
* *
262242 AAAGCCCATACAAGTTGGTGGCAATCC-TCTTCAAAAGCCCACACAAGTCT-GTGGCAGCCCTCT
1 AAAGCCCACACAAGTTGGTGGCAATCCTTCTT-AAAA-CCCACACAAGT-TAGTGGCAACCCT-T
262305 TC-
62 TCA
*
262307 AAAGCCCACACAAGTTGGTGGCAATCCTTCTTAAAACCCACATAAGTTAGTGGCAACCCTTTCA
1 AAAGCCCACACAAGTTGGTGGCAATCCTTCTTAAAACCCACACAAGTTAGTGGCAACCCTTTCA
* * * *
262371 AAAGCCCACACAAGTTGGTGGCAA-CCTTTTTTAAAGCCCACACAAGTCAGTGGCGACCCTTTCA
1 AAAGCCCACACAAGTTGGTGGCAATCC-TTCTTAAAACCCACACAAGTTAGTGGCAACCCTTTCA
*
262435 AAAGACCACACAAGTTGGTGGCA
1 AAAGCCCACACAAGTTGGTGGCA
262458 TCTTTTTCTA
Statistics
Matches: 138, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
63 6 0.04
64 98 0.71
65 30 0.22
66 4 0.03
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (64 bp):
AAAGCCCACACAAGTTGGTGGCAATCCTTCTTAAAACCCACACAAGTTAGTGGCAACCCTTTCA
Found at i:262604 original size:43 final size:43
Alignment explanation
Indices: 262556--262892 Score: 127
Period size: 43 Copynumber: 7.2 Consensus size: 43
262546 TGCCTTTGTT
* * ** **
262556 CATCTTTAAGTCTAATGTCGCTGGCTTTGAATCAGTGTATTGG
1 CATCTTTAAGTCCAATATCGCTAACTTTGAATCAGCATATTGG
*
262599 CATCTTTAAGTCCAATATCGCTAACTTTGAATTAGCATATTGG
1 CATCTTTAAGTCCAATATCGCTAACTTTGAATCAGCATATTGG
* ** * *
262642 CATCTTTACCACCTTTAAGTTCAATATCGCTGGCTTGGAATTAGCATATTGGTGCCTTTG
1 CA----T-----CTTTAAGTCCAATATCGCTAACTTTGAATCAGCATA-T--TG-----G
* ** * *
262702 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATCTTGG
1 -CATCTTTAAGTCCAATATCGCTAACTTTGAATCAGCATATTGG
* * * * *
262746 CACCTTTAAGTCGAATATCGCTAGCCTTGAATCAGCATATTAG
1 CATCTTTAAGTCCAATATCGCTAACTTTGAATCAGCATATTGG
* ** * *
262789 CACCTTTACCACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG
1 CA----T----C-TTTAAGTCCAATATCGCTAACTTTGAATCAGCATATTGG
* ** *
262841 CA-CTTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGG
1 CATC-TTTAAGTCCAATATCGCTAACTTTGAATCAGCATATTGG
*
262884 CATTTTTAA
1 CATCTTTAA
262893 CATTCTTAAA
Statistics
Matches: 233, Mismatches: 33, Indels: 56
0.72 0.10 0.17
Matches are distributed among these distances:
43 122 0.52
44 1 0.00
47 1 0.00
49 2 0.01
51 2 0.01
52 98 0.42
53 1 0.00
55 2 0.01
57 1 0.00
60 1 0.00
61 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (43 bp):
CATCTTTAAGTCCAATATCGCTAACTTTGAATCAGCATATTGG
Found at i:262683 original size:52 final size:51
Alignment explanation
Indices: 262602--262848 Score: 197
Period size: 52 Copynumber: 4.9 Consensus size: 51
262592 GTATTGGCAT
** *
262602 CTTTAAGTCCAATATCGCTAACTTTGAATTAGCATATTGGCATCTTTACCAC
1 CTTTAAGTCCAATATCGCTGGC-TTGAATTAGCATATTGGCACCTTTACCAC
* ** ** *
262654 CTTTAAGTTCAATATCGCTGGCTTGGAATTAGCATATTGGTGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCTT-GAATTAGCATATTGGCACCTTTACCAC
* * *
262706 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATCTTGG---------CAC
1 CTTTAAGTCCAATATCGCTGG-CTTGAATTAGCATATTGGCACCTTTACCAC
* * * *
262749 CTTTAAGTCGAATATCGCTAGCCTTGAATCAGCATATTAGCACCTTTACCAC
1 CTTTAAGTCCAATATCGCT-GGCTTGAATTAGCATATTGGCACCTTTACCAC
* * * * *
262801 TTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTTA
1 CTTTAAGTCCAATATCGCTGG-CTTGAATTAGCATATTGGCACCTTTA
262849 AGTCCAATAT
Statistics
Matches: 156, Mismatches: 26, Indels: 26
0.75 0.12 0.12
Matches are distributed among these distances:
43 35 0.22
44 1 0.01
51 3 0.02
52 114 0.73
53 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (51 bp):
CTTTAAGTCCAATATCGCTGGCTTGAATTAGCATATTGGCACCTTTACCAC
Found at i:262750 original size:95 final size:92
Alignment explanation
Indices: 262651--262937 Score: 303
Period size: 95 Copynumber: 3.0 Consensus size: 92
262641 GCATCTTTAC
* *
262651 CACCTTTAAGTTCAATATCGCTGGCTTGGAATTAGCATATTGGTGCCTTTGTCATCTTTAAGTCC
1 CACCTTTAAGTTCAATATCGCTGGCTT-GAATCAGCATATT-G-GCCTTTATCATCTTTAAGTCC
262716 AATGTCGCTGGCCTTGAATCAGCATCTTGG
63 AATGTCGCTGGCCTTGAATCAGCATCTTGG
* * *
262746 CACCTTTAAG-TCGAATATCGCTAGCCTTGAATCAGCATATTAGCACCTTTACCA-CTTTTAAGT
1 CACCTTTAAGTTC-AATATCGCT-GGCTTGAATCAGCATATT-G-GCCTTTATCATC-TTTAAGT
262809 CCAATGTCGCTGGCCTTGAATCAGCA-CATTGG
61 CCAATGTCGCTGGCCTTGAATCAGCATC-TTGG
* * * * * **
262841 CACTTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATTTTTAACAT-TCTTAAACC
1 CACCTTTAAGTTCAATATCGCTGG-CTTGAATCAGCATATTGGC--CTTTATCATCT-TTAAGTC
* *
262905 CAATGTCGTTGGCCTTGAATCAGCATATTGG
62 CAATGTCGCTGGCCTTGAATCAGCATCTTGG
262936 CA
1 CA
262938 TTTTTAACAT
Statistics
Matches: 163, Mismatches: 18, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
93 1 0.01
94 7 0.04
95 150 0.92
96 5 0.03
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (92 bp):
CACCTTTAAGTTCAATATCGCTGGCTTGAATCAGCATATTGGCCTTTATCATCTTTAAGTCCAAT
GTCGCTGGCCTTGAATCAGCATCTTGG
Found at i:262757 original size:147 final size:148
Alignment explanation
Indices: 262504--262840 Score: 444
Period size: 147 Copynumber: 2.3 Consensus size: 148
262494 GTACATTGGT
** * * * * *
262504 ACCTTTAAGTTTAATATTGTTGACCTTAAATCAGCATATTGGTGCCTTTGTTCATCTTTAAGTCT
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTTCATCTTTAAGTCC
* ** * * *
262569 AATGTCGCTGGCTTTGAATCAGTGTATTGGCATCTTTAAGTCCAATATCGCTAACTTTGAATTAG
66 AATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATCGCTAACCTTGAATCAG
* *
262634 CATATTGGCATCTTTACC
131 CATATTAGCACCTTTACC
* *
262652 ACCTTTAAGTTCAATATCGCTGG-CTTGGAATTAGCATATTGGTGCCTTTG-TCATCTTTAAGTC
1 ACCTTTAAGTCCAATATCGCTGGCCTT-GAATCAGCATATTGGTGCCTTTGTTCATCTTTAAGTC
* * *
262715 CAATGTCGCTGGCCTTGAATCAGCATCTTGGCACCTTTAAGTCGAATATCGCTAGCCTTGAATCA
65 CAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATCGCTAACCTTGAATCA
262780 GCATATTAGCACCTTTACC
130 GCATATTAGCACCTTTACC
* * *
262799 ACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
262841 CACTTTTAAG
Statistics
Matches: 164, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
147 121 0.74
148 43 0.26
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.36
Consensus pattern (148 bp):
ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTTCATCTTTAAGTCC
AATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATCGCTAACCTTGAATCAG
CATATTAGCACCTTTACC
Found at i:262930 original size:52 final size:52
Alignment explanation
Indices: 262862--263091 Score: 252
Period size: 52 Copynumber: 4.4 Consensus size: 52
262852 CCAATATCGT
* *
262862 TGGCCTTGAATCAGCATATTGGCATTTTTAACATTCTTAAACCCAATGTCGT
1 TGGCCTTGAATCAGCATATTGGCATTTTTAACATTCTTAAACCTAATGTCGC
*
262914 TGGCCTTGAATCAGCATATTGGCATTTTTAACATTCTTAAGCCTAATGTCGC
1 TGGCCTTGAATCAGCATATTGGCATTTTTAACATTCTTAAACCTAATGTCGC
* * * * ** ** *
262966 TAGCCTTGAATCAGCACATTGGCAGTCTTCTCA-TCTTCAAGTCTAATGTCAC
1 TGGCCTTGAATCAGCATATTGGCATTTTTAACATTCTT-AAACCTAATGTCGC
* * * *
263018 TGG-CTGTGAATCAGCACATTGACATTCTTT-GCATT-TTAAAGCCTAATATCGC
1 TGGCCT-TGAATCAGCATATTGGCATT-TTTAACATTCTTAAA-CCTAATGTCGC
263070 TGGCCTTGAATCAGCATATTGG
1 TGGCCTTGAATCAGCATATTGG
263092 TGCATTTCTC
Statistics
Matches: 150, Mismatches: 22, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
51 8 0.05
52 137 0.91
53 5 0.03
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (52 bp):
TGGCCTTGAATCAGCATATTGGCATTTTTAACATTCTTAAACCTAATGTCGC
Found at i:262943 original size:95 final size:95
Alignment explanation
Indices: 262714--262944 Score: 320
Period size: 95 Copynumber: 2.4 Consensus size: 95
262704 ATCTTTAAGT
* * *
262714 CCAATGTCGCTGGCCTTGAATCAGCATCTTGGCACCTTTAAGTCGAATATCGCTAGCCTTGAATC
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTAAGTCCAATATCGCTAGCCTTGAATC
* **
262779 AGCATATTAGCACCTTTACCACTTTTAAGT
66 AGCATATTAGCACCTTTAACACTTTTAAAC
* * *
262809 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTTAAGTCCAATATCGTTGGCCTTGAATC
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTAAGTCCAATATCGCTAGCCTTGAATC
* **
262874 AGCATATTGGCATTTTTAACA-TTCTTAAAC
66 AGCATATTAGCACCTTTAACACTT-TTAAAC
* *
262904 CCAATGTCGTTGGCCTTGAATCAGCATATTGGCATTTTTAA
1 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTAA
262945 CATTCTTAAG
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
94 2 0.02
95 118 0.98
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (95 bp):
CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTAAGTCCAATATCGCTAGCCTTGAATC
AGCATATTAGCACCTTTAACACTTTTAAAC
Found at i:263101 original size:104 final size:101
Alignment explanation
Indices: 262846--263106 Score: 269
Period size: 104 Copynumber: 2.5 Consensus size: 101
262836 ATTGGCACTT
* *
262846 TTAAGTCC-AATATCGTTGGCCTTGAATCAGCATATTGGCATTTTTAACATTCTTAAACCCAATG
1 TTAAG-CCTAATATCGCTGGCCTTGAATCAGCATATTGGCATTTCT--CA-TCTTAAACCCAATG
** * *
262910 TCGTTGGCCTTGAATCAGCATATTGGCATTTTTAACATTC
62 TCACTGGCCTTGAATCAGCACATTGACATTTTTAACATTC
* * * ** *
262950 TTAAGCCTAATGTCGCTAGCCTTGAATCAGCACATTGGCAGTCTTCTCATCTTCAAGTCTAATGT
1 TTAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCA-T-TTCTCATCTT-AAACCCAATGT
*
263015 CACTGG-CTGTGAATCAGCACATTGACATTCTTT-GCATT-
63 CACTGGCCT-TGAATCAGCACATTGACATT-TTTAACATTC
263053 TTAAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGTGCATTTCTCATCTT
1 TT-AAGCCTAATATCGCTGGCCTTGAATCAGCATATT-G-GCATTTCTCATCTT
263107 TATCATCTTC
Statistics
Matches: 132, Mismatches: 16, Indels: 18
0.80 0.10 0.11
Matches are distributed among these distances:
103 10 0.08
104 110 0.83
105 6 0.05
106 6 0.05
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (101 bp):
TTAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCATTTCTCATCTTAAACCCAATGTCAC
TGGCCTTGAATCAGCACATTGACATTTTTAACATTC
Found at i:263910 original size:27 final size:27
Alignment explanation
Indices: 263872--263924 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
263862 TTTTACGCAG
*
263872 ATGTATCGATACATTA-TACAATGTATA
1 ATGTATCAATACATTATTA-AATGTATA
263899 ATGTATCAATACATTATTAAATGTAT
1 ATGTATCAATACATTATTAAATGTAT
263925 TGATACATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (27 bp):
ATGTATCAATACATTATTAAATGTATA
Found at i:268155 original size:69 final size:68
Alignment explanation
Indices: 268027--268223 Score: 270
Period size: 69 Copynumber: 2.9 Consensus size: 68
268017 TTTTGTCTCA
* * *
268027 AAGTCCACGACTCAGTGGCATCCTTGTTCCTTTTAAGTCTACAACTCCATGGCATCCTTGTTCCT
1 AAGTCCACAACTCAGTGGCATCCTTGTTCCTTTTAAGTCCACAACTCCGTGGCATCCTTGTTCCT
268092 TTT
66 TTT
*
268095 AAGTCCACAACTCTGTGGCATCCTTGTTCCTTTTTAAGTCCACAACTCCGTGGCATCCTTGTTCC
1 AAGTCCACAACTCAGTGGCATCCTTGTTCC-TTTTAAGTCCACAACTCCGTGGCATCCTTGTTCC
268160 TTTT
65 TTTT
* * * * * *
268164 AAGTCCATAACTCCGTGGCA-CTCTTTTTCCCTTTTAAGTCCACAATTTCGTGGCACCCTT
1 AAGTCCACAACTCAGTGGCATC-CTTGTT-CCTTTTAAGTCCACAACTCCGTGGCATCCTT
268224 TTAAGTCTAC
Statistics
Matches: 116, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
68 29 0.25
69 85 0.73
70 2 0.02
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (68 bp):
AAGTCCACAACTCAGTGGCATCCTTGTTCCTTTTAAGTCCACAACTCCGTGGCATCCTTGTTCCT
TTT
Found at i:268216 original size:35 final size:34
Alignment explanation
Indices: 268027--268258 Score: 275
Period size: 34 Copynumber: 7.0 Consensus size: 34
268017 TTTTGTCTCA
* *
268027 AAGTCCACGACTCAGTGGCATCCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTGTTCCTTTT
* *
268061 AAGTCTACAACTCCATGGCATCCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTGTTCCTTTT
*
268095 AAGTCCACAACTCTGTGGCATCCTTGTTCCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTGTTCC-TTTT
268130 AAGTCCACAACTCCGTGGCATCCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTGTTCCTTTT
* *
268164 AAGTCCATAACTCCGTGGCA-CTCTTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCATC-CTTGTT-CCTTTT
* *
268199 AAGTCCACAATTTCGTGGCA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTGTTCCTTTT
* *
268226 AAGTCTACAACTCCGTGGCAT-CTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTGTTCCTTTT
268259 CAAAAGCCCA
Statistics
Matches: 173, Mismatches: 16, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
27 23 0.13
28 1 0.01
33 8 0.05
34 85 0.49
35 56 0.32
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.38
Consensus pattern (34 bp):
AAGTCCACAACTCCGTGGCATCCTTGTTCCTTTT
Found at i:268252 original size:27 final size:27
Alignment explanation
Indices: 268192--268245 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
268182 CACTCTTTTT
* *
268192 CCCTTTTAAGTCCACAATTTCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
*
268219 CCCTTTTAAGTCTACAACTCCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
268246 TCTTTTTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.31
Consensus pattern (27 bp):
CCCTTTTAAGTCCACAACTCCGTGGCA
Found at i:268401 original size:43 final size:43
Alignment explanation
Indices: 268338--268653 Score: 362
Period size: 43 Copynumber: 7.0 Consensus size: 43
268328 GCACCTTTAT
*
268338 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
268381 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C
268428 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
268473 CTTTAAGTCCAATGTCGTTGGCCTTGAATCAACACATTGGCATTTAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC----AC
268520 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
268563 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
268606 CTTTATCTCTAAGTCCAATGTAGTTGCCCTTAAATCAGCACATTGGCA
1 C----T-T-TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
268654 TTCTTTTCAT
Statistics
Matches: 233, Mismatches: 24, Indels: 26
0.82 0.08 0.09
Matches are distributed among these distances:
43 118 0.51
45 1 0.00
47 41 0.18
48 1 0.00
49 72 0.31
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:268447 original size:92 final size:92
Alignment explanation
Indices: 268290--268653 Score: 597
Period size: 92 Copynumber: 4.0 Consensus size: 92
268280 GGCATCTTCT
* * *
268290 TTTAAGCCCAATATCGTTGACCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
*
268355 CTGGCCTTGAATCAACACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
*
268382 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
268447 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * * *
268474 TTTAAGTCCAATGTCGTTGGCCTTGAATCAACACATTGGCA--TTTATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
268537 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
*
268564 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTCTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
* * *
268629 TTGCCCTTAAATCAGCACATTGGCA
66 CTGGCCTTGAATCAGCACATTGGCA
268654 TTCTTTTCAT
Statistics
Matches: 252, Mismatches: 18, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
90 85 0.34
92 167 0.66
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACC
Found at i:268531 original size:182 final size:183
Alignment explanation
Indices: 268290--268653 Score: 613
Period size: 182 Copynumber: 2.0 Consensus size: 183
268280 GGCATCTTCT
* *
268290 TTTAAGCCCAATATCGTTGACCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
1 TTTAAGCCCAATATCGTTGACCTTGAATCAACACATTGGCA-CTTTATCTTTAAGTCCAATGTAG
268355 CTGGCCTTGAATCAACACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
65 CTGGCCTTGAATCAACACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
* * *
268420 GCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
130 GCACCTTCATCTCTAAGTCCAATGTAGCTGCCCTTAAATCAGCACATTGGCACC
* * *
268474 TTTAAGTCCAATGTCGTTGGCCTTGAATCAACACATTGGCA-TTTATCTTTAAGTCCAATGTAGC
1 TTTAAGCCCAATATCGTTGACCTTGAATCAACACATTGGCACTTTATCTTTAAGTCCAATGTAGC
*
268538 TGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
66 TGGCCTTGAATCAACACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
* *
268603 CACCTTTATCTCTAAGTCCAATGTAGTTGCCCTTAAATCAGCACATTGGCA
131 CACCTTCATCTCTAAGTCCAATGTAGCTGCCCTTAAATCAGCACATTGGCA
268654 TTCTTTTCAT
Statistics
Matches: 169, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
182 133 0.79
184 36 0.21
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (183 bp):
TTTAAGCCCAATATCGTTGACCTTGAATCAACACATTGGCACTTTATCTTTAAGTCCAATGTAGC
TGGCCTTGAATCAACACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
CACCTTCATCTCTAAGTCCAATGTAGCTGCCCTTAAATCAGCACATTGGCACC
Found at i:268747 original size:53 final size:52
Alignment explanation
Indices: 268638--268747 Score: 132
Period size: 53 Copynumber: 2.1 Consensus size: 52
268628 GTTGCCCTTA
* * * *
268638 AATCAGCACATTGGCATTCTTTTCATCTTCAAGACTAATGTCGCTGATCGTG
1 AATCAGCACATTGACATTCTTTTCATCTTCAAGACCAATATCGCTGACCGTG
* * *
268690 AATCAGCACATTGACATTCTTTCTCATCTTTAA-ACCCAATATCGTTGGCCGTG
1 AATCAGCACATTGACATTCTTT-TCATCTTCAAGA-CCAATATCGCTGACCGTG
268743 AATCA
1 AATCA
268748 ACGTATTGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
52 22 0.45
53 27 0.55
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.34
Consensus pattern (52 bp):
AATCAGCACATTGACATTCTTTTCATCTTCAAGACCAATATCGCTGACCGTG
Found at i:269504 original size:13 final size:13
Alignment explanation
Indices: 269486--269510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
269476 ATTACTCAAA
269486 TGTATCGATACAT
1 TGTATCGATACAT
269499 TGTATCGATACA
1 TGTATCGATACA
269511 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:273919 original size:18 final size:19
Alignment explanation
Indices: 273896--273950 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
273886 AAAATCACTC
*
273896 AAAACAAATGTTAACA-CA
1 AAAACAAATGTTAACATAA
*
273914 AAAACAAATTTTAAACATAA
1 AAAACAAATGTT-AACATAA
273934 AAACACAAATGTTAACA
1 AAA-ACAAATGTTAACA
273951 GAAACAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 11 0.35
19 4 0.13
20 8 0.26
21 8 0.26
ACGTcount: A:0.62, C:0.15, G:0.04, T:0.20
Consensus pattern (19 bp):
AAAACAAATGTTAACATAA
Found at i:274872 original size:21 final size:21
Alignment explanation
Indices: 274846--274902 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
274836 TACTTGCAAC
*
274846 TCATTTCTTTTC-TTCTCTAAT
1 TCATTTATTTTCTTTC-CTAAT
274867 TCATTTATTTTCTTTCCTAAT
1 TCATTTATTTTCTTTCCTAAT
* *
274888 TCACTTAATTTCTTT
1 TCATTTATTTTCTTT
274903 TTAAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (21 bp):
TCATTTATTTTCTTTCCTAAT
Found at i:276991 original size:72 final size:72
Alignment explanation
Indices: 276874--277028 Score: 238
Period size: 72 Copynumber: 2.2 Consensus size: 72
276864 CACACTCTTC
* * * *
276874 TGTATCGATACAATTTATAATATATCGATACATGCATTTGAAATTATAGCCGTTTATAGTCGTTA
1 TGTATCGATACAATTCATAATATATCAATACATGCATTTGAAATTATAGCCATTTATAGCCGTTA
276939 GGCTCAA
66 GGCTCAA
* * * *
276946 TGTATCAATACAATTCATAATGTATCAATACATGCATTTGAAATTATAGCTATTTATAGCCGTTG
1 TGTATCGATACAATTCATAATATATCAATACATGCATTTGAAATTATAGCCATTTATAGCCGTTA
277011 GGCTCAA
66 GGCTCAA
277018 TGTATCGATAC
1 TGTATCGATAC
277029 TAGGTGATGA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (72 bp):
TGTATCGATACAATTCATAATATATCAATACATGCATTTGAAATTATAGCCATTTATAGCCGTTA
GGCTCAA
Found at i:277098 original size:13 final size:13
Alignment explanation
Indices: 277080--277104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277070 CTACAGTTTT
277080 ATGTATCGATACA
1 ATGTATCGATACA
277093 ATGTATCGATAC
1 ATGTATCGATAC
277105 TAAGTAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:278645 original size:25 final size:25
Alignment explanation
Indices: 278597--278653 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
278587 ACATTGATAT
278597 AAATATT--AAATTTTTAATTATTA
1 AAATATTAAAAATTTTTAATTATTA
*
278620 AAATATTAAAAATTATTT-ATTTTTA
1 AAATATTAAAAATT-TTTAATTATTA
*
278645 AAAAATTAA
1 AAATATTAA
278654 TATTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 7 0.24
25 19 0.66
26 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATATTAAAAATTTTTAATTATTA
Found at i:278743 original size:97 final size:96
Alignment explanation
Indices: 278629--278961 Score: 273
Period size: 97 Copynumber: 3.3 Consensus size: 96
278619 AAAATATTAA
* *
278629 AAATTATTTATTTTTAAAAAATTAATAT-TTTAAATAGTAATATTTTAATCATGATATTTAATAC
1 AAATTATTTATTATTAAAAAATTAATATATTTAAATAGTAATATTTTAATAAT-ATATTTAATA-
*
278693 TAAAATATTACATTAATATTAAATACTTAAAAT
64 TAAAATATTATATTAATATTAAATACTTAAAAT
* * * * *
278726 AAATTATTTATTATTAAAATATTAAT-TATATAAATATTATTATTTTTATTTAAATATTATTTTA
1 AAATTATTTATTATTAAAAAATTAATATATTTAAATAGTAATA-TTTTA-AT-AATA-TA-TTT-
* * * * *
278790 CAATTTTTAAGTAGTAATATTGATA-TAAATA-TTAAAAT
60 -AA-TATAAAATA-TTATATTAATATTAAATACTTAAAAT
* * * *
278828 TAA-TATTTAAATATTAACAATTATTAATTTAATATTAAAATAGTAATATTTTAATAATAATATT
1 AAATTATTT-ATTATTAA-AA-AATTAA--T-ATATTTAAATAGTAATATTTTAATAAT-ATATT
*
278892 TAGTGATAAAATATTATATTAATATTAAATACTTAAAAT
59 TAAT-ATAAAATATTATATTAATATTAAATACTTAAAAT
278931 AATATTATTTATTATT-AAAAATTAATTATAT
1 AA-ATTATTTATTATTAAAAAATTAA-TATAT
278962 GAAATTTTAA
Statistics
Matches: 184, Mismatches: 29, Indels: 44
0.72 0.11 0.17
Matches are distributed among these distances:
96 1 0.01
97 35 0.19
98 5 0.03
99 6 0.03
100 6 0.03
101 23 0.12
102 30 0.16
103 24 0.13
104 24 0.13
105 10 0.05
106 3 0.02
107 5 0.03
108 12 0.07
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (96 bp):
AAATTATTTATTATTAAAAAATTAATATATTTAAATAGTAATATTTTAATAATATATTTAATATA
AAATATTATATTAATATTAAATACTTAAAAT
Found at i:278747 original size:36 final size:35
Alignment explanation
Indices: 278707--278784 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 35
278697 ATATTACATT
278707 AATATTAAATACT-TAAA-ATAAATTATTTATTATTAA
1 AATATTAAATA-TATAAATAT-AATTATTT-TTATTAA
* * *
278743 AATATTAATTATATAAATATTATTATTTTTATTTA
1 AATATTAAATATATAAATATAATTATTTTTATTAA
278778 AATATTA
1 AATATTA
278785 TTTTACAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 14 0.38
36 21 0.57
37 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (35 bp):
AATATTAAATATATAAATATAATTATTTTTATTAA
Found at i:278861 original size:21 final size:20
Alignment explanation
Indices: 278815--278936 Score: 83
Period size: 21 Copynumber: 6.0 Consensus size: 20
278805 AATATTGATA
278815 TAAATATTAAAATTAATATT
1 TAAATATTAAAATTAATATT
*
278835 TAAATATTAACAATTATTAATT
1 TAAATATTAA-AATTAAT-ATT
278857 T-AATATTAAAATAGTAATATT
1 TAAATATTAAAAT--TAATATT
* * * *
278878 TTAATAATAATATTTAGTGA-T
1 TAAATATTAA-AATTAAT-ATT
* *
278899 AAAATATT-ATATTAATA-T
1 TAAATATTAAAATTAATATT
278917 TAAATACTTAAAA-TAATATT
1 TAAATA-TTAAAATTAATATT
278937 ATTTATTATT
Statistics
Matches: 79, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
18 7 0.09
19 11 0.14
20 17 0.22
21 27 0.34
22 15 0.19
23 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TAAATATTAAAATTAATATT
Found at i:278905 original size:43 final size:41
Alignment explanation
Indices: 278810--278922 Score: 104
Period size: 43 Copynumber: 2.7 Consensus size: 41
278800 GTAGTAATAT
* *
278810 TGATATAAATATTAAAATTAATATTTAAATATTAACAATTAT
1 TGATA-AAATATTAAAATTAATATTTAAATAATAACAATTAG
* ** * * *
278852 TAATTTAATATTAAAATAGTAATATTTTAATAATAATATTTAG
1 TGATAAAATATTAAAAT--TAATATTTAAATAATAACAATTAG
*
278895 TGATAAAATATT-ATATTAATA-TTAAATA
1 TGATAAAATATTAAAATTAATATTTAAATA
278923 CTTAAAATAA
Statistics
Matches: 56, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
39 6 0.11
40 5 0.09
41 11 0.20
42 6 0.11
43 28 0.50
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (41 bp):
TGATAAAATATTAAAATTAATATTTAAATAATAACAATTAG
Found at i:279054 original size:22 final size:25
Alignment explanation
Indices: 279004--279055 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
278994 ATGTTATTTC
279004 TATTAATATTTCTATACTCTAAAAA
1 TATTAATATTTCTATACTCTAAAAA
279029 TATTAAT-TTT-TATA-T-TAAAAA
1 TATTAATATTTCTATACTCTAAAAA
279050 TTATTA
1 -TATTA
279056 TTAAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.23
22 6 0.23
23 4 0.15
24 3 0.12
25 7 0.27
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTAATATTTCTATACTCTAAAAA
Found at i:279101 original size:11 final size:14
Alignment explanation
Indices: 279065--279117 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
279055 ATTAAATATT
*
279065 TATAAAATATAATTTA
1 TATAAAA-AT-ATTCA
279081 TATAAAAATATT-A
1 TATAAAAATATTCA
279094 T-T-AAAATATTCA
1 TATAAAAATATTCA
279106 TATAAAAATATT
1 TATAAAAATATT
279118 TTCAACAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
11 8 0.24
12 3 0.09
13 3 0.09
14 11 0.32
15 2 0.06
16 7 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
TATAAAAATATTCA
Found at i:279115 original size:14 final size:13
Alignment explanation
Indices: 279038--279117 Score: 64
Period size: 11 Copynumber: 6.2 Consensus size: 13
279028 ATATTAATTT
279038 TTATATTAAAAATTA
1 TTATA-TAAAAA-TA
279053 TTAT-T--AAATA
1 TTATATAAAAATA
279063 TT-TATAAAATATAA
1 TTATATAAAA-AT-A
279077 TTTATATAAAAATA
1 -TTATATAAAAATA
279091 TTAT-T-AAAATA
1 TTATATAAAAATA
279102 TTCATATAAAAATA
1 TT-ATATAAAAATA
279116 TT
1 TT
279118 TTCAACAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 21
0.72 0.00 0.28
Matches are distributed among these distances:
9 1 0.02
10 5 0.09
11 11 0.20
12 5 0.09
13 8 0.15
14 10 0.18
15 8 0.15
16 7 0.13
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (13 bp):
TTATATAAAAATA
Found at i:279283 original size:16 final size:16
Alignment explanation
Indices: 279245--279285 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
279235 ATTAATAATT
279245 TATTATT-AAAATCTA
1 TATTATTAAAAATCTA
* *
279260 -AATATTAAAAATTTA
1 TATTATTAAAAATCTA
279275 TATTATTAAAA
1 TATTATTAAAA
279286 TAATTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.24
15 7 0.33
16 9 0.43
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TATTATTAAAAATCTA
Found at i:279285 original size:15 final size:15
Alignment explanation
Indices: 279245--279286 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
279235 ATTAATAATT
279245 TATTATTAAAATCTA
1 TATTATTAAAATCTA
* *
279260 -AATATTAAAAATTTA
1 TATTATT-AAAATCTA
279275 TATTATTAAAAT
1 TATTATTAAAAT
279287 AATTTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 5 0.23
15 12 0.55
16 5 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTATTAAAATCTA
Found at i:283050 original size:3 final size:3
Alignment explanation
Indices: 283042--283074 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
283032 CCCGACCCTG
283042 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
283075 AGGCACAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:283391 original size:6 final size:6
Alignment explanation
Indices: 283380--283406 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
283370 CTTCTCTCGA
283380 CGCCTC CGCCTC CGCCTC CGCCTC CGC
1 CGCCTC CGCCTC CGCCTC CGCCTC CGC
283407 AAAACCCGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.67, G:0.19, T:0.15
Consensus pattern (6 bp):
CGCCTC
Found at i:285517 original size:15 final size:15
Alignment explanation
Indices: 285485--285527 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
285475 TTCAATTAAT
285485 TTAAATTTGAAATAAC
1 TTAAATTT-AAATAAC
*
285501 TTAAATTTAAATGAC
1 TTAAATTTAAATAAC
285516 TTGAAACTTTAA
1 TT-AAA-TTTAA
285528 TTCAAAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 11 0.46
17 5 0.21
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
TTAAATTTAAATAAC
Found at i:286828 original size:174 final size:174
Alignment explanation
Indices: 286523--286875 Score: 530
Period size: 174 Copynumber: 2.0 Consensus size: 174
286513 TTTTTACGGG
* * *
286523 TTGTTTAAAAAGTATTATATATTTATATAAATTTTAATACATTCATAAGTCTATTATATAGATAT
1 TTGTTTAAAAAATATTATATATTTATATAAATTTTAATAAATTCATAAGTCTATTATATAAATAT
* *
286588 TGATAAGGTCATATATCTATATTATATTTGTGTTATTTTTGTGTTATGTCATATTTTTGGTAATA
66 TGATAAGGTCATATATCTATATTATATTTGTGTTATTTTTGTATTATGTCATATTTTTGATAATA
* * *
286653 TTTTAGTTATTTTTCATATTATATTTGTGTCATCTAATAATATA
131 TTTTAATTATTTTTCATATTATATTTGTGCCATATAATAATATA
*
286697 TTGTTTAAAAAATATTATATATTTATATAAATTTTGATAAATTCATAAGTCTATTATATAAATAT
1 TTGTTTAAAAAATATTATATATTTATATAAATTTTAATAAATTCATAAGTCTATTATATAAATAT
* * * *
286762 TGATAAGGTCATATATTTATATTGTGTTTGTGTTATTTTT-TATATCATGTCGTATTTTT-ATAA
66 TGATAAGGTCATATATCTATATTATATTTGTGTTATTTTTGTAT-T-ATGTCATATTTTTGATAA
* * *
286825 TATTTTAATTATTTTTCATGTTATGTTTGTGCCATATAATAATATC
129 TATTTTAATTATTTTTCATATTATATTTGTGCCATATAATAATATA
286871 TTGTT
1 TTGTT
286876 CAAAGTCGCT
Statistics
Matches: 161, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
173 2 0.01
174 147 0.91
175 12 0.07
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53
Consensus pattern (174 bp):
TTGTTTAAAAAATATTATATATTTATATAAATTTTAATAAATTCATAAGTCTATTATATAAATAT
TGATAAGGTCATATATCTATATTATATTTGTGTTATTTTTGTATTATGTCATATTTTTGATAATA
TTTTAATTATTTTTCATATTATATTTGTGCCATATAATAATATA
Found at i:287911 original size:16 final size:16
Alignment explanation
Indices: 287890--287922 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
287880 ATACATAACG
287890 TTATAATAATAAATTA
1 TTATAATAATAAATTA
*
287906 TTATAATATTAAATTA
1 TTATAATAATAAATTA
287922 T
1 T
287923 GTGATATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATAATAATAAATTA
Found at i:288378 original size:16 final size:16
Alignment explanation
Indices: 288357--288411 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
288347 AACTTGATAG
* *
288357 AAATTTGAAATATTTT
1 AAATTTAAAATAATTT
288373 AAATTTAAAATAATTT
1 AAATTTAAAATAATTT
*
288389 AAACTTAAAATTAATTT
1 AAATTTAAAA-TAATTT
288406 AAATTT
1 AAATTT
288412 TTTTAAATCC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 23 0.68
17 11 0.32
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATTTAAAATAATTT
Found at i:290758 original size:2 final size:2
Alignment explanation
Indices: 290751--290784 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
290741 AATTAGAAAG
290751 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
290785 AATCCAGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:292001 original size:28 final size:29
Alignment explanation
Indices: 291951--292013 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
291941 ATATATTTAG
* * *
291951 TTTTAAACAATTAAATTTTAGATAAATTC
1 TTTTAAACAATTAAAGTTAAGATAAATTA
* *
291980 TTTTAAA-ATTTAAAGTTAAGATAAGTTA
1 TTTTAAACAATTAAAGTTAAGATAAATTA
292008 TTTTAA
1 TTTTAA
292014 TTAATAGTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (29 bp):
TTTTAAACAATTAAAGTTAAGATAAATTA
Found at i:292071 original size:22 final size:23
Alignment explanation
Indices: 292043--292091 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
292033 TAATATTTTT
*
292043 ATATAAAT-TTAATTATAAAAA-A
1 ATATAAATATT-ACTATAAAAATA
292065 ATATAAATATTACTATAAAAATA
1 ATATAAATATTACTATAAAAATA
292088 ATAT
1 ATAT
292092 TTTAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATAAATATTACTATAAAAATA
Found at i:292333 original size:11 final size:11
Alignment explanation
Indices: 292276--292394 Score: 66
Period size: 11 Copynumber: 10.7 Consensus size: 11
292266 GCATTAATTT
292276 TAAAAATAATA
1 TAAAAATAATA
* *
292287 TAAAATACAAAA
1 TAAAA-ATAATA
*
292299 TAAACATAATA
1 TAAAAATAATA
**
292310 TATTCAATAAATA
1 TA-AAAAT-AATA
292323 TAAAAATAATA
1 TAAAAATAATA
*
292334 T--AATTAAT-
1 TAAAAATAATA
* * *
292342 TTAATATAATT
1 TAAAAATAATA
*
292353 TAAACATAATA
1 TAAAAATAATA
292364 T-AAAATAAATA
1 TAAAAAT-AATA
*
292375 AAAAAATAATA
1 TAAAAATAATA
292386 TAATAAATA
1 TAA-AAATA
292395 TAATTTAAAT
Statistics
Matches: 80, Mismatches: 19, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
8 1 0.01
9 6 0.08
10 9 0.11
11 35 0.44
12 23 0.29
13 6 0.08
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:292366 original size:5 final size:5
Alignment explanation
Indices: 292315--292398 Score: 54
Period size: 5 Copynumber: 17.6 Consensus size: 5
292305 TAATATATTC
* * * *
292315 AATA- AATAT AAAAAT AATAT AAT-T AATTT AATAT AATTT AAACAT AATAT
1 AATAT AATAT -AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT
* *
292365 AAAAT AA-AT AA-A- AAAAT AATAT AATA- AATAT AAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT
292399 TTAAATGACA
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
3 2 0.03
4 18 0.28
5 37 0.58
6 7 0.11
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (5 bp):
AATAT
Found at i:293017 original size:31 final size:29
Alignment explanation
Indices: 292983--293071 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 29
292973 GTTTTATTAA
292983 AATTATTTTTAAAATATTTTATATTTATAT
1 AATTA-TTTTAAAATATTTTATATTTATAT
*
293013 AA--ATTTTAATATA-TTTATAATTTATATT
1 AATTATTTTAAAATATTTTAT-ATTTATA-T
* *
293041 ATATAATTTTAAAATATTTATAAATTTATAT
1 A-ATTATTTTAAAATATTT-TATATTTATAT
293072 CGTATTTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
26 5 0.10
27 16 0.33
28 3 0.06
29 1 0.02
30 2 0.04
31 11 0.22
32 9 0.18
33 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
AATTATTTTAAAATATTTTATATTTATAT
Found at i:293019 original size:27 final size:28
Alignment explanation
Indices: 292989--293071 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 28
292979 TTAAAATTAT
292989 TTTTAAAATATTTTATATTTATATA-AA
1 TTTTAAAATATTTTATATTTATATATAA
*
293016 TTTTAATATA-TTTATAATTTATATTATATAA
1 TTTTAAAATATTTTAT-A-TT-TA-TATATAA
*
293047 TTTTAAAATATTTATAAATTTATAT
1 TTTTAAAATATTT-TATATTTATAT
293072 CGTATTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
26 5 0.11
27 10 0.22
28 2 0.04
29 5 0.11
30 6 0.13
31 13 0.28
32 3 0.07
33 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTAAAATATTTTATATTTATATATAA
Found at i:293024 original size:18 final size:16
Alignment explanation
Indices: 292998--293071 Score: 64
Period size: 17 Copynumber: 4.6 Consensus size: 16
292988 TTTTTAAAAT
292998 ATTTTATAT-TTATATAA
1 ATTTTATATATT-TAT-A
293015 ATTTTAATATATTTATA
1 ATTTT-ATATATTTATA
*
293032 A-TTTATAT-TATATA
1 ATTTTATATATTTATA
*
293046 ATTTTAAAATATTTATA
1 ATTTT-ATATATTTATA
*
293063 AATTTATAT
1 ATTTTATAT
293072 CGTATTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.13
15 7 0.15
16 9 0.19
17 16 0.34
18 7 0.15
19 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTATATATTTATA
Found at i:293046 original size:32 final size:32
Alignment explanation
Indices: 293000--293071 Score: 110
Period size: 31 Copynumber: 2.2 Consensus size: 32
292990 TTTAAAATAT
*
293000 TTTATATTTATATAAATTTTAATATATTTAT-AA
1 TTTATA-TTATAT-AATTTTAAAATATTTATAAA
293033 TTTATATTATATAATTTTAAAATATTTATAAA
1 TTTATATTATATAATTTTAAAATATTTATAAA
293065 TTTATAT
1 TTTATAT
293072 CGTATTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 16 0.43
32 15 0.41
33 6 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TTTATATTATATAATTTTAAAATATTTATAAA
Found at i:293221 original size:61 final size:61
Alignment explanation
Indices: 293151--293273 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 61
293141 TCAATATAAA
* * * *
293151 TATGATTAATGTAAAAATAAAAATTATATATGAGATAATAATTTTGATTTATTAATTTAAT
1 TATGATTAATATAAAAATAAAAATAATATATGAGATAATAATTTTGACTCATTAATTTAAT
* **
293212 TATGATTAATATAAAAATAAAAATAATGTATGAGATGGTAATTTTGACTCATTAATTTAAT
1 TATGATTAATATAAAAATAAAAATAATATATGAGATAATAATTTTGACTCATTAATTTAAT
293273 T
1 T
293274 CTCATAAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (61 bp):
TATGATTAATATAAAAATAAAAATAATATATGAGATAATAATTTTGACTCATTAATTTAAT
Found at i:294445 original size:21 final size:22
Alignment explanation
Indices: 294404--294450 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
294394 TACTTTCGGA
294404 TTAAATTATTATTTAAAATTTT
1 TTAAATTATTATTTAAAATTTT
*
294426 TTAAATTTTTATTT-AAATTTT
1 TTAAATTATTATTTAAAATTTT
294447 TTAA
1 TTAA
294451 GTAAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTAAATTATTATTTAAAATTTT
Found at i:294449 original size:13 final size:12
Alignment explanation
Indices: 294404--294447 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
294394 TACTTTCGGA
*
294404 TTAAATTATTAT
1 TTAAATTTTTAT
*
294416 TTAAA-ATTT-T
1 TTAAATTTTTAT
294426 TTAAATTTTTAT
1 TTAAATTTTTAT
294438 TTAAATTTTT
1 TTAAATTTTT
294448 TAAGTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 6 0.22
11 5 0.19
12 16 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTAAATTTTTAT
Found at i:294495 original size:20 final size:20
Alignment explanation
Indices: 294436--294483 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
294426 TTAAATTTTT
**
294436 ATTTAAATTT-TTTAAGTAA
1 ATTTAAATTTATTTATTTAA
294455 ATTTAAATTTATTTATTTAA
1 ATTTAAATTTATTTATTTAA
294475 ATTTAAATT
1 ATTTAAATT
294484 ATTCTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTAAATTTATTTATTTAA
Found at i:294537 original size:19 final size:19
Alignment explanation
Indices: 294513--294549 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
294503 AATATTAAAA
294513 ATTTTAT-ATTAATATTTAT
1 ATTTTATAATTAA-ATTTAT
294532 ATTTTATAATTAAATTTA
1 ATTTTATAATTAAATTTA
294550 AATAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTATAATTAAATTTAT
Found at i:295106 original size:15 final size:16
Alignment explanation
Indices: 295079--295109 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
295069 ATTAATATGT
295079 TTAGACAATGAATTAA
1 TTAGACAATGAATTAA
295095 TTAGAC-ATGAATTAA
1 TTAGACAATGAATTAA
295110 AAAAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (16 bp):
TTAGACAATGAATTAA
Found at i:295278 original size:19 final size:20
Alignment explanation
Indices: 295240--295284 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
295230 CATCACGATC
*
295240 ATAATTTTTTTAAATTTAT-
1 ATAATTTTTTTAAATATATA
295259 ATAATTTTTTTACAA-ATATA
1 ATAATTTTTTTA-AATATATA
295279 ATAATT
1 ATAATT
295285 ATAATTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAATTTTTTTAAATATATA
Found at i:297007 original size:20 final size:20
Alignment explanation
Indices: 296984--297023 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
296974 TATTTTTATT
296984 TAAAT-TTAATTATAAAAATA
1 TAAATATTAA-TATAAAAATA
297004 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
297024 ATTTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATATTAATATAAAAATA
Found at i:299174 original size:48 final size:48
Alignment explanation
Indices: 299089--299183 Score: 113
Period size: 48 Copynumber: 2.0 Consensus size: 48
299079 TGGCATGAGT
* * *
299089 GTCACGAACTTATTTACATAGACCTGAAGTAGCTTGGGATG-ATGAAAC
1 GTCACGAACTCATTTACACAGACCTGAAATAGCTTGGGA-GAATGAAAC
* *
299137 GTCACGAACTCATTTACACA-ATCTTGAAATAGTTTGGGAGAATGAAA
1 GTCACGAACTCATTTACACAGA-CCTGAAATAGCTTGGGAGAATGAAA
299184 TAGCCTGTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
47 2 0.05
48 38 0.95
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (48 bp):
GTCACGAACTCATTTACACAGACCTGAAATAGCTTGGGAGAATGAAAC
Done.