Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 160 of 310
Found at i:52444337 original size:33 final size:33
Alignment explanation
Indices: 52444277--52444417 Score: 167
Period size: 33 Copynumber: 4.2 Consensus size: 33
52444267 TTCAACCAAA
* * *
52444277 CACACCAGATGCTCACT-CAAGCCAATCCACCCAT
1 CACACCA-ATGCTCA-TAAAAGCTAATCCAACCAT
* *
52444311 CGCACCAATGGTCATAAAAGCTAATCCAACCAT
1 CACACCAATGCTCATAAAAGCTAATCCAACCAT
* *
52444344 CACACCAATGCTCATAAGAGCTAAACCAACCAT
1 CACACCAATGCTCATAAAAGCTAATCCAACCAT
* *
52444377 CACACCAATGCTCATAAGAGCTAATCCAACCAA
1 CACACCAATGCTCATAAAAGCTAATCCAACCAT
*
52444410 AACACCAA
1 CACACCAA
52444418 ATAGAGAGTA
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
32 1 0.01
33 87 0.93
34 6 0.06
ACGTcount: A:0.40, C:0.35, G:0.09, T:0.15
Consensus pattern (33 bp):
CACACCAATGCTCATAAAAGCTAATCCAACCAT
Found at i:52448087 original size:38 final size:38
Alignment explanation
Indices: 52447887--52448088 Score: 262
Period size: 38 Copynumber: 5.3 Consensus size: 38
52447877 GGATCAAAGG
* * * *
52447887 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* *
52447925 CCC-GATTATAATACCAGCACGAAGCCTGCAGGATTTAA
1 CCCGGA-TATATTACCAGCACGAAGCCTGCGGGATTTAA
*
52447963 CCTGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * **
52448001 CCCGGATATAATACCACCATTAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * *
52448039 CCCAGATATATTACAAGCATGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
52448077 CCCGGATATATT
1 CCCGGATATATT
52448089 TTTCGATAAA
Statistics
Matches: 144, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
37 1 0.01
38 141 0.98
39 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (38 bp):
CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
Found at i:52453468 original size:38 final size:38
Alignment explanation
Indices: 52453268--52453469 Score: 244
Period size: 38 Copynumber: 5.3 Consensus size: 38
52453258 GGATCAAAGG
* * * *
52453268 CCCGAATATAATACCAACACTAGGCCTGCGGGATTTAA
1 CCCGAATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * * *
52453306 CCCGATTATAATACCAGCACGAATCCTGCAGGATTTAA
1 CCCGAATATATTACCAGCACGAAGCCTGCGGGATTTAA
* *
52453344 CCTGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGAATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * * *
52453382 CCCGGATATAATACCACCATGAAGCCTGCGGGATTTAA
1 CCCGAATATATTACCAGCACGAAGCCTGCGGGATTTAA
* *
52453420 CCC-AGATATATTACAAGCATGAAGCCTGCGGGATTTAA
1 CCCGA-ATATATTACCAGCACGAAGCCTGCGGGATTTAA
52453458 CCCGAATATATT
1 CCCGAATATATT
52453470 TTTCAATAAA
Statistics
Matches: 142, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
38 141 0.99
39 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (38 bp):
CCCGAATATATTACCAGCACGAAGCCTGCGGGATTTAA
Found at i:52453776 original size:138 final size:138
Alignment explanation
Indices: 52453589--52453862 Score: 512
Period size: 138 Copynumber: 2.0 Consensus size: 138
52453579 AGGGTTTAAT
* * *
52453589 TTCACATTGGAACACATGTCTTAGTACATCAGTTAATAGTATCAAATTCGACTAGAGCTGCTAGT
1 TTCACATTGGAACACATATCTTAGTACATCACTTAATAGTATCAAATTCGACTAGAGATGCTAGT
52453654 CACATACGGCTCATAACTTAAATTTAATGTTCATTCGACACAAAGAACATATGTATATTTTCACT
66 CACATACGGCTCATAACTTAAATTTAATGTTCATTCGACACAAAGAACATATGTATATTTTCACT
52453719 GAAGCATC
131 GAAGCATC
*
52453727 TTCACATTGGAACACATATCTTAGTACATCACTTAATAGTATCAAATTCGACTAGATATGCTAGT
1 TTCACATTGGAACACATATCTTAGTACATCACTTAATAGTATCAAATTCGACTAGAGATGCTAGT
52453792 CACATACGGCTCATAACTTAAATTTAATGTTCATTCGACACAAAGAACATATGTATATTTTCACT
66 CACATACGGCTCATAACTTAAATTTAATGTTCATTCGACACAAAGAACATATGTATATTTTCACT
52453857 GAAGCA
131 GAAGCA
52453863 CCATCTCAAT
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 132 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (138 bp):
TTCACATTGGAACACATATCTTAGTACATCACTTAATAGTATCAAATTCGACTAGAGATGCTAGT
CACATACGGCTCATAACTTAAATTTAATGTTCATTCGACACAAAGAACATATGTATATTTTCACT
GAAGCATC
Found at i:52458952 original size:38 final size:38
Alignment explanation
Indices: 52458757--52458951 Score: 259
Period size: 38 Copynumber: 5.1 Consensus size: 38
52458747 AAAGGCTCGA
*
52458757 ATATAATACCAGCACT-AGGCCTGCGGGATTTAACCC-G
1 ATATAATACCAGCA-TGAAGCCTGCGGGATTTAACCCGG
* * **
52458794 ATTATAATACCAGCACGATGCCTGTAGGATTTAACCCGG
1 A-TATAATACCAGCATGAAGCCTGCGGGATTTAACCCGG
* * * *
52458833 ATTTATTACCAACACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCATGAAGCCTGCGGGATTTAACCCGG
*
52458871 ATATAATACCACCATGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCATGAAGCCTGCGGGATTTAACCCGG
*
52458909 ATATATTACCAGCATGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCATGAAGCCTGCGGGATTTAACCCGG
52458947 ATATA
1 ATATA
52458952 TATTTCGATA
Statistics
Matches: 139, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
37 1 0.01
38 136 0.98
39 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (38 bp):
ATATAATACCAGCATGAAGCCTGCGGGATTTAACCCGG
Found at i:52464388 original size:23 final size:23
Alignment explanation
Indices: 52464362--52464407 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
52464352 GTATTATTGG
* *
52464362 ACCAAAGTGCCAGTAACATAAGT
1 ACCAAAGTACCAGTAACAAAAGT
*
52464385 ACCAAAGTACTAGTAACAAAAGT
1 ACCAAAGTACCAGTAACAAAAGT
52464408 CTCCTATTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (23 bp):
ACCAAAGTACCAGTAACAAAAGT
Found at i:52464717 original size:30 final size:30
Alignment explanation
Indices: 52464681--52464740 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
52464671 ATAGAGACTC
*
52464681 TGATAAAGCATTGTAATCACCCCTTTTGAT
1 TGATAAAGCATTGTAATCACCCATTTTGAT
*
52464711 TGATAAAGCATTGTAATCAGCCATTTTGAT
1 TGATAAAGCATTGTAATCACCCATTTTGAT
52464741 CAATAAAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (30 bp):
TGATAAAGCATTGTAATCACCCATTTTGAT
Found at i:52464747 original size:30 final size:30
Alignment explanation
Indices: 52464683--52464748 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
52464673 AGAGACTCTG
* **
52464683 ATAAAGCATTGTAATCACCCCTTTTGATTG
1 ATAAAGCATTGTAATCACCCATTTTGATCA
*
52464713 ATAAAGCATTGTAATCAGCCATTTTGATCA
1 ATAAAGCATTGTAATCACCCATTTTGATCA
52464743 ATAAAG
1 ATAAAG
52464749 TATATCCTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (30 bp):
ATAAAGCATTGTAATCACCCATTTTGATCA
Found at i:52466645 original size:43 final size:43
Alignment explanation
Indices: 52466444--52466634 Score: 271
Period size: 43 Copynumber: 4.4 Consensus size: 43
52466434 CGAGATTACA
** **
52466444 TGTAAGACCATGTCTGGGACATTGTTAT--TGTATTTTGATTATG
1 TGTAAGACCATGTCTGGGACATTGGCATCAT-TA-TACGATTATG
52466487 TGTAAGACCATGTCTGGGACATTGGCATCATTATACGATTATG
1 TGTAAGACCATGTCTGGGACATTGGCATCATTATACGATTATG
52466530 TGTAAGACCATGTCTGGGACATTGGCATCATTATACGATTATG
1 TGTAAGACCATGTCTGGGACATTGGCATCATTATACGATTATG
*
52466573 TGTAAGACCATGTCTGGGACATTGGCATCGTTA-ATCGATTATG
1 TGTAAGACCATGTCTGGGACATTGGCATCATTATA-CGATTATG
* *
52466616 TGTAAGACCCTCTCTGGGA
1 TGTAAGACCATGTCTGGGA
52466635 TAGTAGCATC
Statistics
Matches: 138, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
42 1 0.01
43 134 0.97
44 2 0.01
45 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.35
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCATTATACGATTATG
Found at i:52466664 original size:86 final size:86
Alignment explanation
Indices: 52466488--52466685 Score: 231
Period size: 86 Copynumber: 2.3 Consensus size: 86
52466478 TTGATTATGT
* *
52466488 GTAAGACCATGTCTGGGACATTGGCATCATTATACGATTATGTGTAAGACCATGTCTGGGACATT
1 GTAAGACCATGTCTGGGACATTGGCATCATTATACGATTATGTGTAAGACCATCTCTGGGACAGT
* * ***
52466553 GGCATCATTATACGATTATGT
66 AGCATCATTATACGATAACAA
* * *
52466574 GTAAGACCATGTCTGGGACATTGGCATCGTTA-ATCGATTATGTGTAAGACCCTCTCTGGGATAG
1 GTAAGACCATGTCTGGGACATTGGCATCATTATA-CGATTATGTGTAAGACCATCTCTGGGACAG
**
52466638 TAGCATCGA-TATGTGATAACAA
65 TAGCATC-ATTATACGATAACAA
* *
52466660 GTAAGACCATATCTGGGA-TTTGGCAT
1 GTAAGACCATGTCTGGGACATTGGCAT
52466686 TGTACAAGCT
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
85 8 0.08
86 87 0.91
87 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (86 bp):
GTAAGACCATGTCTGGGACATTGGCATCATTATACGATTATGTGTAAGACCATCTCTGGGACAGT
AGCATCATTATACGATAACAA
Found at i:52469651 original size:47 final size:45
Alignment explanation
Indices: 52469582--52469747 Score: 172
Period size: 49 Copynumber: 3.6 Consensus size: 45
52469572 GGGATAAGAA
* * *
52469582 GCCATGTCCTAGATAGGTCTTACACTGACTAGCACATCAAAGTTGAT
1 GCCATGTCCCAGACAGGTCTTACACTGACTA-CACATC-AAGCTGAT
* * * * *
52469629 GCCATGTCCCAGATAGGTCTTACACTGACTTCCATATATCGAGGCTAAT
1 GCCATGTCCCAGACAGGTCTTACACTGAC-T--ACACATC-AAGCTGAT
* *
52469678 GCCATGTCCCAGACAGGTCTTACACTGAC-ACACAACAAGCTGAC
1 GCCATGTCCCAGACAGGTCTTACACTGACTACACATCAAGCTGAT
*
52469722 GCCATGTCACAGACAGGTCTTACACT
1 GCCATGTCCCAGACAGGTCTTACACT
52469748 AGCTTGTATA
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
44 30 0.30
45 4 0.04
47 28 0.28
48 1 0.01
49 37 0.37
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (45 bp):
GCCATGTCCCAGACAGGTCTTACACTGACTACACATCAAGCTGAT
Found at i:52469696 original size:49 final size:49
Alignment explanation
Indices: 52469582--52469889 Score: 221
Period size: 48 Copynumber: 6.5 Consensus size: 49
52469572 GGGATAAGAA
* * * * * * **
52469582 GCCATGTCCTAGATAGGTCTTACACTGACTAGC--ACATCAAAGTTGAT
1 GCCATGTCCCAGACAGGTCTTACACTGACTTGCATATATCGAGGCCGAT
* * **
52469629 GCCATGTCCCAGATAGGTCTTACACTGACTTCCATATATCGAGGCTAAT
1 GCCATGTCCCAGACAGGTCTTACACTGACTTGCATATATCGAGGCCGAT
* * * * *
52469678 GCCATGTCCCAGACAGGTCTTACACTGAC--ACACA-A-C-AAGCTGAC
1 GCCATGTCCCAGACAGGTCTTACACTGACTTGCATATATCGAGGCCGAT
* * *
52469722 GCCATGTCACAGACAGGTCTTACACT-AGCTTGTATATCTCGAGGCCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGA-CTTGCATATATCGAGGCCGAT
* * * * * *
52469771 G-CATGTCCCAGACATGTCTTACATTGGCTTGTATATCTTGAGGCCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGACTTGCATATATCGAGGCCGAT
* * *
52469819 G-CATGTCCCAGACATGTCTTACACTGGCTCT-CATA-AT-GTGGCCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGACT-TGCATATATCGAGGCCGAT
* *
52469865 -TCATGTCCCAGACATGTCTTACACT
1 GCCATGTCCCAGACAGGTCTTACACT
52469890 AGAACACATA
Statistics
Matches: 219, Mismatches: 31, Indels: 23
0.80 0.11 0.08
Matches are distributed among these distances:
43 1 0.00
44 31 0.14
45 1 0.00
46 35 0.16
47 34 0.16
48 73 0.33
49 44 0.20
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (49 bp):
GCCATGTCCCAGACAGGTCTTACACTGACTTGCATATATCGAGGCCGAT
Found at i:52469764 original size:93 final size:96
Alignment explanation
Indices: 52469582--52469793 Score: 263
Period size: 93 Copynumber: 2.2 Consensus size: 96
52469572 GGGATAAGAA
* * * * * * *
52469582 GCCATGTCCTAGATAGGTCTTACACTGACTAGCACATCAAAGTTGATGCCATGTCCCAGATAGGT
1 GCCATGTCCCAGACAGGTCTTACACTGACTAGCACAACAAAGCTGACGCCATGTCACAGACAGGT
*
52469647 CTTACACTGACTTCCATATATCGAGGCTAAT
66 CTTACACTGACTTCCATATATCGAGGCCAAT
52469678 GCCATGTCCCAGACAGGTCTTACACTGAC-A-CACAAC-AAGCTGACGCCATGTCACAGACAGGT
1 GCCATGTCCCAGACAGGTCTTACACTGACTAGCACAACAAAGCTGACGCCATGTCACAGACAGGT
** * *
52469740 CTTACACT-AGCTTGTATATCTCGAGGCCGAT
66 CTTACACTGA-CTTCCATATATCGAGGCCAAT
*
52469771 G-CATGTCCCAGACATGTCTTACA
1 GCCATGTCCCAGACAGGTCTTACA
52469794 TTGGCTTGTA
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
92 22 0.22
93 47 0.46
94 5 0.05
95 1 0.01
96 27 0.26
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (96 bp):
GCCATGTCCCAGACAGGTCTTACACTGACTAGCACAACAAAGCTGACGCCATGTCACAGACAGGT
CTTACACTGACTTCCATATATCGAGGCCAAT
Found at i:52470504 original size:20 final size:18
Alignment explanation
Indices: 52470467--52470517 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
52470457 CTATAGCAAC
52470467 TCACAATTT-CAATTATT
1 TCACAATTTACAATTATT
52470484 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
*
52470504 TTACAACTTTACAA
1 TCACAA-TTTACAA
52470518 AATAGCCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 4 0.14
20 16 0.55
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:52471095 original size:17 final size:17
Alignment explanation
Indices: 52471073--52471108 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
52471063 AGCATGAAAT
52471073 CACTAAATTTATTCCAC
1 CACTAAATTTATTCCAC
*
52471090 CACTAAATTTATTTCAC
1 CACTAAATTTATTCCAC
52471107 CA
1 CA
52471109 AAATTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (17 bp):
CACTAAATTTATTCCAC
Found at i:52472428 original size:16 final size:15
Alignment explanation
Indices: 52472386--52472430 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
52472376 GTTATGTAAC
52472386 AAGAAAACCAAG-TA
1 AAGAAAACCAAGATA
*
52472400 AAGAAATCCAAGATA
1 AAGAAAACCAAGATA
*
52472415 GAGAAAACCCAAGATA
1 AAGAAAA-CCAAGATA
52472431 CGATACTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 11 0.42
15 7 0.27
16 8 0.31
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.09
Consensus pattern (15 bp):
AAGAAAACCAAGATA
Found at i:52473556 original size:40 final size:40
Alignment explanation
Indices: 52473501--52473636 Score: 184
Period size: 40 Copynumber: 3.4 Consensus size: 40
52473491 TTTAGATAAA
* *
52473501 AAAAAAGCCACTATAGATAGAGCATTAGTGGCGCTTTTTG
1 AAAAACGCCACTATAGATCGAGCATTAGTGGCGCTTTTTG
*
52473541 AAAAACACCACTATAGATCGAGCATTAGTGGCGCTTTTTG
1 AAAAACGCCACTATAGATCGAGCATTAGTGGCGCTTTTTG
* * * *
52473581 AAAAATGTCACTATAGATCGAGCATTAGCGGTGCTTTTT-
1 AAAAACGCCACTATAGATCGAGCATTAGTGGCGCTTTTTG
*
52473620 AAAGAACGCCGCTATAG
1 AAA-AACGCCACTATAG
52473637 GTCAACCATT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 3 0.04
40 81 0.96
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (40 bp):
AAAAACGCCACTATAGATCGAGCATTAGTGGCGCTTTTTG
Found at i:52473665 original size:80 final size:80
Alignment explanation
Indices: 52473509--52473667 Score: 180
Period size: 80 Copynumber: 2.0 Consensus size: 80
52473499 AAAAAAAAGC
* * *
52473509 CACTATAGATAGAGCATTAGTGGCGCTTTTTGAAAAACACCACTATAGATCGAGCATTAGTGGCG
1 CACTATAGATAGAGCATTAGCGGCGCTTTTTGAAAAACACCACTATAGATCAACCATTAGTGGCG
**
52473574 CTTTTTGAAAAATGT
66 CTTCATGAAAAATGT
* * * * *
52473589 CACTATAGATCGAGCATTAGCGGTGCTTTTT-AAAGAACGCCGCTATAGGTCAACCATTAGCT-G
1 CACTATAGATAGAGCATTAGCGGCGCTTTTTGAAA-AACACCACTATAGATCAACCATTAG-TGG
52473652 CGCATTCAT-AAAAATG
64 CGC-TTCATGAAAAATG
52473668 CTGCAAAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
79 3 0.05
80 59 0.89
81 4 0.06
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (80 bp):
CACTATAGATAGAGCATTAGCGGCGCTTTTTGAAAAACACCACTATAGATCAACCATTAGTGGCG
CTTCATGAAAAATGT
Found at i:52473886 original size:40 final size:40
Alignment explanation
Indices: 52473842--52473922 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
52473832 ATAGGTTGAC
*
52473842 CATTACCGGTG-TCTTTTGAAAAACGCCACTATAAATCGAG
1 CATTACCGGTGCT-TTTTGAAAAACACCACTATAAATCGAG
** * * *
52473882 CATTAGTGGTGCTTTTTGAAAAGCACTACTATAGATCGAG
1 CATTACCGGTGCTTTTTGAAAAACACCACTATAAATCGAG
52473922 C
1 C
52473923 TTTAGCAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (40 bp):
CATTACCGGTGCTTTTTGAAAAACACCACTATAAATCGAG
Found at i:52474135 original size:27 final size:28
Alignment explanation
Indices: 52474097--52474155 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
52474087 ATATTTGTTC
*
52474097 AAAATGAAAAAAATTAAAATACTATGAA
1 AAAATGAAAAAAATTAAAAAACTATGAA
52474125 AAAAT-AAAAAAATTAAAAAACTATGAA
1 AAAATGAAAAAAATTAAAAAACTATGAA
52474152 AAAA
1 AAAA
52474156 ATAATTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (28 bp):
AAAATGAAAAAAATTAAAAAACTATGAA
Found at i:52475858 original size:28 final size:28
Alignment explanation
Indices: 52475826--52475895 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
52475816 AATGAGATTG
52475826 GCACTAAGTGTGCGAGTTT-AAT-TGTATA
1 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
*
52475854 GCACTAAGTGTGCGAGTTTGACTATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
52475882 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
52475896 GACTTACTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:52495209 original size:40 final size:40
Alignment explanation
Indices: 52495027--52495249 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
52495017 TCCTCGTTCA
* * * * *
52495027 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
52495066 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52495106 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
52495146 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
52495186 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
52495226 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
52495250 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:52495258 original size:41 final size:41
Alignment explanation
Indices: 52495181--52495258 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
52495171 TTAGTATCTC
* * *
52495181 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
52495222 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
52495259 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:52500025 original size:13 final size:13
Alignment explanation
Indices: 52500007--52500031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52499997 GATATAAATT
52500007 CACAAAAAATAAA
1 CACAAAAAATAAA
52500020 CACAAAAAATAA
1 CACAAAAAATAA
52500032 TTTTAAAATA
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:0.76, C:0.16, G:0.00, T:0.08
Consensus pattern (13 bp):
CACAAAAAATAAA
Found at i:52503088 original size:101 final size:99
Alignment explanation
Indices: 52502905--52503088 Score: 233
Period size: 101 Copynumber: 1.8 Consensus size: 99
52502895 CTGGTACGCA
* * * * *
52502905 TAGTAGCTTGCACTTAGTACTACACATGCGACCAATTATCCGGTCCACGTAGTAGCCTACACTTA
1 TAGTAGCCTCCACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTACACTTA
* *
52502970 GTACTGCACACGTGACCTAACCATTTGATACACG
66 GTACTACACACGCGACCTAACCATTTGATACACG
* * * * *
52503004 TAGTAGCCTCCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTCCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACATAGTAGCCTACACT
*
52503069 TAGTACTACACATGCGACCT
64 TAGTACTACACACGCGACCT
52503089 CACAATAGAT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
99 27 0.39
100 3 0.04
101 40 0.57
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTCCACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTACACTTA
GTACTACACACGCGACCTAACCATTTGATACACG
Found at i:52508750 original size:50 final size:49
Alignment explanation
Indices: 52508632--52508754 Score: 156
Period size: 50 Copynumber: 2.5 Consensus size: 49
52508622 CTGGTACGCA
* * ** * *
52508632 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTCCACG
1 TAGTAGCCTGCACTTAGTACTACAAAAGCGACCAACCATCCGATACACG
* **
52508681 TAGTAGCCTGCACTTAGTACTACAAAAGTGACCTAACCATTTGATACACG
1 TAGTAGCCTGCACTTAGTACTACAAAAGCGACC-AACCATCCGATACACG
52508731 TAGTAGCCTGCACTTAGTACTACA
1 TAGTAGCCTGCACTTAGTACTACA
52508755 CACGTGATCG
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
49 30 0.47
50 34 0.53
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACAAAAGCGACCAACCATCCGATACACG
Found at i:52508815 original size:101 final size:98
Alignment explanation
Indices: 52508632--52508815 Score: 244
Period size: 101 Copynumber: 1.8 Consensus size: 98
52508622 CTGGTACGCA
* * *
52508632 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTCCACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCAGGT-CACGTAGTACCCTGCACTTA
*
52508697 GTACTACAAAAGTGACCTAACCATTTGATACACG
65 GTACTACAAAAGCGACCTAACCATTTGATACACG
* *
52508731 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGT-ACGTATAGTACCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCAGGTCACG--TAGTACCCTGCAC
* *
52508795 TTAGTACTACACATGCGACCT
62 TTAGTACTACAAAAGCGACCT
52508816 CACAATAGAT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
99 32 0.44
100 3 0.04
101 38 0.52
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCAGGTCACGTAGTACCCTGCACTTAG
TACTACAAAAGCGACCTAACCATTTGATACACG
Found at i:52514451 original size:50 final size:48
Alignment explanation
Indices: 52514338--52514513 Score: 199
Period size: 50 Copynumber: 3.5 Consensus size: 48
52514328 CTGGTACGCA
* * *
52514338 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCGA-TACACG
* **
52514387 TAGTAGCCTCCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATC-GATACACG
* * * *
52514437 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATC-GATACACG
*
52514488 TAGTAGCCTACACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
52514514 TGCGACCTCA
Statistics
Matches: 108, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
49 30 0.28
50 43 0.40
51 35 0.32
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (48 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCGATACACG
Found at i:52514521 original size:101 final size:99
Alignment explanation
Indices: 52514338--52514521 Score: 260
Period size: 101 Copynumber: 1.8 Consensus size: 99
52514328 CTGGTACGCA
* * *
52514338 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAGTAGCCTCCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCAGTACACATAGTAGCCTACACTTA
*
52514403 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGCGACCTAACCATCTGATACACG
* * ** *
52514437 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTACACT
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCAGTACACATAGTAGCCTACACT
*
52514502 TAGTACTACACATGCGACCT
64 TAGTACTACACACGCGACCT
52514522 CACAATAGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 29 0.40
100 3 0.04
101 41 0.56
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCAGTACACATAGTAGCCTACACTTA
GTACTACACACGCGACCTAACCATCTGATACACG
Found at i:52519950 original size:11 final size:11
Alignment explanation
Indices: 52519934--52519967 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
52519924 GTGTTCAATA
52519934 CAAATATTTCT
1 CAAATATTTCT
52519945 CAAATATTTCT
1 CAAATATTTCT
52519956 CAAATATTTCT
1 CAAATATTTCT
52519967 C
1 C
52519968 GACAGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (11 bp):
CAAATATTTCT
Found at i:52535684 original size:34 final size:34
Alignment explanation
Indices: 52535646--52535727 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
52535636 CAAAATGATC
* *
52535646 TGGGCCTTAGCCCATATA-AGT-CGCAATATTAGTG
1 TGGGCCTTAGCCCAT-TACAATAC-CAATATCAGTG
* * *
52535680 TGGGCCCTAGCCTATTACAATACCAGTATCAGTG
1 TGGGCCTTAGCCCATTACAATACCAATATCAGTG
52535714 TGGGCCTTAGCCCA
1 TGGGCCTTAGCCCA
52535728 ATTCAGTACA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
33 2 0.05
34 36 0.92
35 1 0.03
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (34 bp):
TGGGCCTTAGCCCATTACAATACCAATATCAGTG
Found at i:52543562 original size:50 final size:49
Alignment explanation
Indices: 52543494--52543623 Score: 188
Period size: 50 Copynumber: 2.6 Consensus size: 49
52543484 AAAACTGTGA
* **
52543494 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGTGAGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATGGT-AGG
* *
52543544 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGTTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATGGTAGG
* *
52543593 TCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTA
52543624 TGCGTACTAG
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
49 31 0.42
50 42 0.58
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (49 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATGGTAGG
Found at i:52546500 original size:28 final size:28
Alignment explanation
Indices: 52546422--52546503 Score: 146
Period size: 28 Copynumber: 2.9 Consensus size: 28
52546412 GCTTAGTAAT
* *
52546422 CTCGTACCAAAAACATCAATAGGATAAG
1 CTCGTACCAAAAACATCAACAGTATAAG
52546450 CTCGTACCAAAAACATCAACAGTATAAG
1 CTCGTACCAAAAACATCAACAGTATAAG
52546478 CTCGTACCAAAAACATCAACAGTATA
1 CTCGTACCAAAAACATCAACAGTATA
52546504 TAAAATATGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.18
Consensus pattern (28 bp):
CTCGTACCAAAAACATCAACAGTATAAG
Found at i:52553721 original size:26 final size:26
Alignment explanation
Indices: 52553692--52553770 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 26
52553682 TTCAAAAGCT
*
52553692 TAGTAATCTTGTACCAAAAACATCAA
1 TAGTAAACTTGTACCAAAAACATCAA
*
52553718 TAGTATAAACTCGTACCAAAAACATCAA
1 TAG--TAAACTTGTACCAAAAACATCAA
* *
52553746 CAGTATAAGTTCGTACCAAAAACAT
1 TAGTA-AACTT-GTACCAAAAACAT
52553771 TGACAGTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 5 0.11
27 3 0.07
28 36 0.82
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (26 bp):
TAGTAAACTTGTACCAAAAACATCAA
Found at i:52553734 original size:28 final size:28
Alignment explanation
Indices: 52553702--52553780 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 28
52553692 TAGTAATCTT
*
52553702 GTACCAAAAACATCAATAGTATAAACTC
1 GTACCAAAAACATCAACAGTATAAACTC
**
52553730 GTACCAAAAACATCAACAGTATAAGTTC
1 GTACCAAAAACATCAACAGTATAAACTC
**
52553758 GTACCAAAAACATTGACAGTATA
1 GTACCAAAAACATCAACAGTATA
52553781 TAAAATATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.22
Consensus pattern (28 bp):
GTACCAAAAACATCAACAGTATAAACTC
Found at i:52559831 original size:18 final size:18
Alignment explanation
Indices: 52559810--52559848 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
52559800 TCAGAACTAG
*
52559810 AATCAAAATTAGAATCAA
1 AATCAAAATCAGAATCAA
*
52559828 AATCATAATCAGAATCAA
1 AATCAAAATCAGAATCAA
52559846 AAT
1 AAT
52559849 TAGGTGACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.23
Consensus pattern (18 bp):
AATCAAAATCAGAATCAA
Found at i:52559869 original size:31 final size:31
Alignment explanation
Indices: 52559828--52559904 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
52559818 TTAGAATCAA
* * *
52559828 AATCATAATCAGAATCAAAATTAGGTGACAG
1 AATCAAAATCAGAATCAAAATCAGGTAACAG
**
52559859 AATCAAAATCAGAATCAGTATCAGGTAACAG
1 AATCAAAATCAGAATCAAAATCAGGTAACAG
52559890 AATCAAAATCAGAAT
1 AATCAAAATCAGAAT
52559905 GGGAATGCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.21
Consensus pattern (31 bp):
AATCAAAATCAGAATCAAAATCAGGTAACAG
Found at i:52559901 original size:19 final size:19
Alignment explanation
Indices: 52559820--52559881 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 19
52559810 AATCAAAATT
52559820 AGAATCAAAATCA-TAATC
1 AGAATCAAAATCAGTAATC
* *
52559838 AGAATCAAAATTAGGTGA-C
1 AGAATCAAAATCA-GTAATC
52559857 AGAATCAAAATCAG-AATC
1 AGAATCAAAATCAGTAATC
*
52559875 AGTATCA
1 AGAATCA
52559882 GGTAACAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
17 1 0.03
18 20 0.56
19 13 0.36
20 2 0.06
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.21
Consensus pattern (19 bp):
AGAATCAAAATCAGTAATC
Found at i:52560354 original size:27 final size:27
Alignment explanation
Indices: 52560336--52560440 Score: 149
Period size: 27 Copynumber: 3.9 Consensus size: 27
52560326 GGTATCTCGA
* *
52560336 TAATTCCACCCTACAAGGGTATTTCAG
1 TAATTCTACCCTACAGGGGTATTTCAG
*
52560363 TAATTCTACCCTGCAGGGGTATTTTC-G
1 TAATTCTACCCTACAGGGGTA-TTTCAG
*
52560390 TAATTCTATCCTACAGGGGTATTTCAG
1 TAATTCTACCCTACAGGGGTATTTCAG
*
52560417 TAATTTTACCCTACAGGGGTATTT
1 TAATTCTACCCTACAGGGGTATTT
52560441 TGGTAATTTC
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 4 0.06
27 61 0.88
28 4 0.06
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (27 bp):
TAATTCTACCCTACAGGGGTATTTCAG
Found at i:52560403 original size:54 final size:54
Alignment explanation
Indices: 52560336--52560448 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
52560326 GGTATCTCGA
*
52560336 TAATTCCACCCTACAAGGGTATTTCAGTAATTCTACCCTGCAGGGGTATTTTCG
1 TAATTCCACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTTCG
* * * * *
52560390 TAATTCTATCCTACAGGGGTATTTCAGTAATTTTACCCTACAGGGGTATTTTGG
1 TAATTCCACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTTCG
52560444 TAATT
1 TAATT
52560449 TCACAAATCA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (54 bp):
TAATTCCACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTTCG
Found at i:52560446 original size:27 final size:27
Alignment explanation
Indices: 52560311--52560478 Score: 142
Period size: 27 Copynumber: 6.2 Consensus size: 27
52560301 ACACCCTAGC
* * * *
52560311 ATTTTACCCCACAAGGGTATCTCGATA
1 ATTTTACCCTACAGGGGTATTTCGGTA
** * *
52560338 ATTCCACCCTACAAGGGTATTTCAGTA
1 ATTTTACCCTACAGGGGTATTTCGGTA
* *
52560365 ATTCTACCCTGCAGGGGTATTTTC-GTA
1 ATTTTACCCTACAGGGGTA-TTTCGGTA
* * *
52560392 ATTCTATCCTACAGGGGTATTTCAGTA
1 ATTTTACCCTACAGGGGTATTTCGGTA
*
52560419 ATTTTACCCTACAGGGGTATTTTGGTA
1 ATTTTACCCTACAGGGGTATTTCGGTA
* ** *
52560446 ATTTCA-CAAATCAGGGGTATTTTGGTA
1 ATTTTACCCTA-CAGGGGTATTTCGGTA
52560473 ATTTTA
1 ATTTTA
52560479 TTGATCGAGG
Statistics
Matches: 119, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
26 6 0.05
27 109 0.92
28 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (27 bp):
ATTTTACCCTACAGGGGTATTTCGGTA
Found at i:52560461 original size:54 final size:54
Alignment explanation
Indices: 52560352--52560478 Score: 159
Period size: 54 Copynumber: 2.4 Consensus size: 54
52560342 CACCCTACAA
* * **
52560352 GGGTATTTCAGTAATTCTACCCTGCAGGGGTATTTTCGTAATTCTATCCTACAG
1 GGGTATTTCAGTAATTTTACCCTACAGGGGTATTTTCGTAATTCTATCAAACAG
*
52560406 GGGTATTTCAGTAATTTTACCCTACAGGGGTATTTTGGTAATT-TCA-CAAATCAG
1 GGGTATTTCAGTAATTTTACCCTACAGGGGTATTTTCGTAATTCT-ATCAAA-CAG
**
52560460 GGGTATTTTGGTAATTTTA
1 GGGTATTTCAGTAATTTTA
52560479 TTGATCGAGG
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
53 3 0.05
54 61 0.95
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.39
Consensus pattern (54 bp):
GGGTATTTCAGTAATTTTACCCTACAGGGGTATTTTCGTAATTCTATCAAACAG
Found at i:52560490 original size:27 final size:27
Alignment explanation
Indices: 52560376--52560531 Score: 102
Period size: 27 Copynumber: 5.8 Consensus size: 27
52560366 TTCTACCCTG
* * **
52560376 CAGGGGTATTTTCGTAATTCTATCCTA-
1 CAGGGGTATTTTGGTAATTTTA-CAAAT
** **
52560403 CAGGGGTATTTCAGTAATTTTAC-CCT
1 CAGGGGTATTTTGGTAATTTTACAAAT
*
52560429 ACAGGGGTATTTTGGTAATTTCACAAAT
1 -CAGGGGTATTTTGGTAATTTTACAAAT
***
52560457 CAGGGGTATTTTGGTAATTTTATTGAT
1 CAGGGGTATTTTGGTAATTTTACAAAT
** *
52560484 C-GAGGGTATTTTGGTAATTTTGTAAAC
1 CAG-GGGTATTTTGGTAATTTTACAAAT
** *
52560511 CAATGGTATTTTAGTAATTTT
1 CAGGGGTATTTTGGTAATTTT
52560532 GTAAATCGAG
Statistics
Matches: 103, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
26 2 0.02
27 100 0.97
28 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTACAAAT
Found at i:52560545 original size:27 final size:27
Alignment explanation
Indices: 52560433--52560826 Score: 177
Period size: 27 Copynumber: 14.6 Consensus size: 27
52560423 TACCCTACAG
* * *
52560433 GGGTATTTTGGTAATTTCACAAATC-A
1 GGGTATTTTAGTAATTTTATAAATCGA
* **
52560459 GGGGTATTTTGGTAATTTTATTGATCGA
1 -GGGTATTTTAGTAATTTTATAAATCGA
* * * *
52560487 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTAGTAATTTTATAAATCGA
* *
52560514 TGGTATTTTAGTAATTTTGTAAATCGA
1 GGGTATTTTAGTAATTTTATAAATCGA
*** * * *
52560541 GGGTAAAATAGTAATTCTGTCAATCGA
1 GGGTATTTTAGTAATTTTATAAATCGA
*** * * * *
52560568 GGGTAAAATGGTAATTCTGTAAATTGA
1 GGGTATTTTAGTAATTTTATAAATCGA
*** *
52560595 GGGTAAAATAGTAATTTTATAAATCGC
1 GGGTATTTTAGTAATTTTATAAATCGA
*** * * *
52560622 GGGTAAAATAATAATTCTATAAATCAA
1 GGGTATTTTAGTAATTTTATAAATCGA
* **** * *
52560649 GTGTAAAACAGTAATTTTGTAATTCGA
1 GGGTATTTTAGTAATTTTATAAATCGA
* * *
52560676 GGGTACTTT-GATAATTTTACAAGTCGA
1 GGGTATTTTAG-TAATTTTATAAATCGA
* **
52560703 GGGTATTTCAGTAATTTTGCAAA-CTGA
1 GGGTATTTTAGTAATTTTATAAATC-GA
* *
52560730 GGGTATTTTGGTAATTTTACAAATCGA
1 GGGTATTTTAGTAATTTTATAAATCGA
* ** *
52560757 GGATATTTGGGTAATTTTATAAA-CCA
1 GGGTATTTTAGTAATTTTATAAATCGA
* * * * *
52560783 GAGGTACTTTGGTAATTTTA-CAACCGG
1 G-GGTATTTTAGTAATTTTATAAATCGA
*
52560810 GGGTATTTCAGTAATTT
1 GGGTATTTTAGTAATTT
52560827 AGTAAACTAA
Statistics
Matches: 294, Mismatches: 66, Indels: 15
0.78 0.18 0.04
Matches are distributed among these distances:
26 20 0.07
27 271 0.92
28 3 0.01
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (27 bp):
GGGTATTTTAGTAATTTTATAAATCGA
Found at i:52560694 original size:81 final size:81
Alignment explanation
Indices: 52560522--52560680 Score: 212
Period size: 81 Copynumber: 2.0 Consensus size: 81
52560512 AATGGTATTT
* * * * * **
52560522 TAGTAATTTTGTAAATCGAGGGTAAAATAGTAATTCTGTCAATCGAGGGTAAAATGGTAATTCTG
1 TAGTAATTTTATAAATCGAGGGTAAAATAATAATTCTATAAATCAAGGGTAAAACAGTAATTCTG
52560587 TAAATTGAGGGTAAAA
66 TAAATTGAGGGTAAAA
* * *
52560603 TAGTAATTTTATAAATCGCGGGTAAAATAATAATTCTATAAATCAAGTGTAAAACAGTAATTTTG
1 TAGTAATTTTATAAATCGAGGGTAAAATAATAATTCTATAAATCAAGGGTAAAACAGTAATTCTG
52560668 T-AATTCGAGGGTA
66 TAAATT-GAGGGTA
52560681 CTTTGATAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
80 4 0.06
81 63 0.94
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (81 bp):
TAGTAATTTTATAAATCGAGGGTAAAATAATAATTCTATAAATCAAGGGTAAAACAGTAATTCTG
TAAATTGAGGGTAAAA
Found at i:52560707 original size:81 final size:81
Alignment explanation
Indices: 52560522--52560707 Score: 196
Period size: 81 Copynumber: 2.3 Consensus size: 81
52560512 AATGGTATTT
** * * * * **
52560522 TAGTAATTTTGTAAATCGAGGGTAAAATAGTAATTCTGTCAATCGAGGGTAAAATGGTAATTCTG
1 TAGTAATTTTACAAATCGAGGGTAAAATAATAATTCTATAAATCAAGGGTAAAACAGTAATTCTG
52560587 TAAATTGAGGGTAAAA
66 TAAATTGAGGGTAAAA
* * * *
52560603 TAGTAATTTTATAAATCGCGGGTAAAATAATAATTCTATAAATCAAGTGTAAAACAGTAATTTTG
1 TAGTAATTTTACAAATCGAGGGTAAAATAATAATTCTATAAATCAAGGGTAAAACAGTAATTCTG
**
52560668 T-AATTCGAGGGT-ACT
66 TAAATT-GAGGGTAAAA
* *
52560683 TTGATAATTTTACAAGTCGAGGGTA
1 TAG-TAATTTTACAAATCGAGGGTA
52560708 TTTCAGTAAT
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
80 7 0.08
81 80 0.92
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (81 bp):
TAGTAATTTTACAAATCGAGGGTAAAATAATAATTCTATAAATCAAGGGTAAAACAGTAATTCTG
TAAATTGAGGGTAAAA
Found at i:52570129 original size:23 final size:23
Alignment explanation
Indices: 52570103--52570178 Score: 127
Period size: 23 Copynumber: 3.3 Consensus size: 23
52570093 CCTCACACGT
52570103 CCGTGTGGAGGCAATGCACACAC
1 CCGTGTGGAGGCAATGCACACAC
*
52570126 CCGTGTGGAGGCAATGCACACGC
1 CCGTGTGGAGGCAATGCACACAC
52570149 CCGTGTGGAGGCAATGCACACGA-
1 CCGTGTGGAGGCAATGCACAC-AC
52570172 CCGTGTG
1 CCGTGTG
52570179 CATTGGGACA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.22, C:0.29, G:0.34, T:0.14
Consensus pattern (23 bp):
CCGTGTGGAGGCAATGCACACAC
Found at i:52575095 original size:40 final size:40
Alignment explanation
Indices: 52575006--52575348 Score: 484
Period size: 40 Copynumber: 8.7 Consensus size: 40
52574996 TTGAATGATG
* *
52575006 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
52575045 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
52575085 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
52575124 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
52575163 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
52575203 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
52575243 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
52575283 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
52575324 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
52575349 AACGAGGAGC
Statistics
Matches: 285, Mismatches: 12, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
39 92 0.32
40 183 0.64
41 10 0.04
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:52576383 original size:38 final size:38
Alignment explanation
Indices: 52576332--52576408 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
52576322 TATGTATAGT
52576332 TTCCTCTCTGAGTCTAGTTTCTACAGAAACAAACGGCA
1 TTCCTCTCTGAGTCTAGTTTCTACAGAAACAAACGGCA
*
52576370 TTCCTCTCTGAGTCTAGTTTCTATAGAAACAAACGGCA
1 TTCCTCTCTGAGTCTAGTTTCTACAGAAACAAACGGCA
52576408 T
1 T
52576409 CAGTATTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (38 bp):
TTCCTCTCTGAGTCTAGTTTCTACAGAAACAAACGGCA
Found at i:52583277 original size:79 final size:81
Alignment explanation
Indices: 52583137--52583321 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
52583127 TTGAATGATG
* *
52583137 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
52583201 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * * **
52583216 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCTGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
52583278 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* * *
52583296 ACTGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
52583322 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 55 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:52583328 original size:40 final size:40
Alignment explanation
Indices: 52583140--52583321 Score: 201
Period size: 40 Copynumber: 4.6 Consensus size: 40
52583130 AATGATGTCC
* * * * *
52583140 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCT
* * * *
52583180 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCT
52583220 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCT
* *
52583259 GGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA-CT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCT
*
52583299 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
52583322 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 34 0.28
40 77 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCT
Found at i:52583343 original size:79 final size:79
Alignment explanation
Indices: 52583190--52583354 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 79
52583180 GGACTAAGAT
* * **
52583190 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
* *
52583255 ATCTGGGTTAAGTC
66 ATCTCGGTTAAATC
* * *
52583269 CCGAAGGCAATTGTGCGAGTTACT-ATAACTGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
52583332 TATATC-CGGTTAAATT
63 TAAATCTCGGTTAAATC
52583348 CCGAAGG
1 CCGAAGG
52583355 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCTCGGTTAAATC
Found at i:52585393 original size:768 final size:768
Alignment explanation
Indices: 52583917--52585396 Score: 2326
Period size: 768 Copynumber: 1.9 Consensus size: 768
52583907 CATTTGGTAT
* *
52583917 GGATATGGTTATTGAGAGGTGTGGATAGGCTTGACAAGGATTGGCCATGGGAATGGTTAATCACT
1 GGATATGGTTATTGAGAGGTGTGGATAGGCTTAACAAGGATTGGCCATGGGAATGGCTAATCACT
52583982 ATCATAAATTGTGCTACTTATGCAAAAAGGGCTAGTTGAATCATGGAAACTATGAAATAGGTAAA
66 ATCATAAATTGTGCTACTTATGCAAAAAGGGCTAGTTGAATCATGGAAACTATGAAATAGGTAAA
* *
52584047 GTCTATCTTAAAGGCAGATGCTGACAGCAGCAGTGATGTAGATTTGGAAATTCACTAAAAATAGT
131 GTCTACCTTAAAGGCAGATGCTGACAGCAGCAGTGATGTAGATTTGGAAAATCACTAAAAATAGT
* * *
52584112 AGGAATGGAATTAAATAGTGAATAAATTATTTAAACGAACCTTGCTGAATGTATTTTCATAGAAA
196 AGGAATGGAATTAAATAGTGAATAAATTATGTAAACGAACCTTGATGAATCTATTTTCATAGAAA
* *
52584177 AGTAACGAAACAATCATACGGACAGTATGTTAGGAGATATTCAGGTTCTTGTGAGACAGAGCCAG
261 AGTAACGAAACAATCATACGGACAGTATGTTAAGAGATATTCAGGTTCTCGTGAGACAGAGCCAG
52584242 AACGGTTTCTGGATTTCCTGTTCCGACTTTGGAAATTCATTATAAACTAACCAGAGAGAATTAGG
326 AACGGTTTCTGGATTTCCTGTTCCGACTTTGGAAATTCATTATAAACTAACCAGAGAGAATTAGG
* * * *
52584307 AGTCAAGCCATATATGTATAGATTCCCCTCTGAGTCTATTTTCTATATAAATAAACGGCATCAGT
391 AGTCAAGCCATATATGTATAGATTCACCTCTGAGTCTAGTTTCTATAGAAACAAACGGCATCAGT
* *
52584372 ATTGAAGCTCTGTACAGGGAGATATCCAAGTCGTAATGCACAAAGGTCAGGGTAGTCAATCCCTG
456 ATTGAAGCTCTGTACAGGGAGATATCCAAATCGTAATGCACAAAGGTCAGGGTAGTCAATCCCTA
* * * ** *
52584437 TAACATGGGAGACTTTGACTAATAAACTGTACTAATTGGCCTGACCAAAAACTCTAGGAAAAAAT
521 TAACAGGGGAGAATTTAACTAATAAACTGTACTAATTGGCCCAACCAAAAACTCTAGAAAAAAAT
* **
52584502 ATGTAGATGGAAATATGAGTCTAGTTTCAGGGAAAATTTACGGGACTGGATTCCGAGTTTCTGAA
586 ATGTAGATGGAAATATGAGTCTAGTTTCAGGGAAAAATTACGAAACTGGATTCCGAGTTTCTGAA
* * * *
52584567 CTCAAGATATGATTTTTAAAGTGACTATTACGCAGATTGGCAGTGTCTGGAAAATTTTTAAAGTT
651 CTCAAGATATGATTTTTAAAGTGACTATGACGCAGATTGCCACTGCCTGGAAAATTTTTAAAGTT
52584632 TGTTAACACCTCGTGTTCGACTCCGGTGACGGTCTCGGGTTCGGGGTGTTACA
716 TGTTAACACCTCGTGTTCGACTCCGGTGACGGTCTCGGGTTCGGGGTGTTACA
*
52584685 GGATATGGTTATTGAGAGGTGTGGATATGCTTAACAAGGATTGGCCATGGGAATGGCTAATCACT
1 GGATATGGTTATTGAGAGGTGTGGATAGGCTTAACAAGGATTGGCCATGGGAATGGCTAATCACT
* * *
52584750 ATCATAATTTGTGCTATTTATGCTAAAAGGGCTAGTTGAATCATGGAAACTATGAAATAGGTAAA
66 ATCATAAATTGTGCTACTTATGCAAAAAGGGCTAGTTGAATCATGGAAACTATGAAATAGGTAAA
* *
52584815 GTCTACCTTAAAGGGAGATGCTGACAGCAGCAGTGATGTAGATTTGGAAAATCACTAAAACTAGT
131 GTCTACCTTAAAGGCAGATGCTGACAGCAGCAGTGATGTAGATTTGGAAAATCACTAAAAATAGT
*
52584880 AGGAATGGAATTAAATAGTGAATAAATTATGTAAACGAACCTTGATGAATCTATTTTCATAGGAA
196 AGGAATGGAATTAAATAGTGAATAAATTATGTAAACGAACCTTGATGAATCTATTTTCATAGAAA
* * * *
52584945 AGTAACGAAACGATCATATGGACTGTATGTTAAGAGATATTCAGGTTCTCGTGAGACAGGGCCAG
261 AGTAACGAAACAATCATACGGACAGTATGTTAAGAGATATTCAGGTTCTCGTGAGACAGAGCCAG
* * *
52585010 AACGGTTTCTGGA-TTCTCTGTTCCGACTTTGGAAATTCATTATATATTAACCAGAGATAATTAG
326 AACGGTTTCTGGATTTC-CTGTTCCGACTTTGGAAATTCATTATAAACTAACCAGAGAGAATTAG
** *
52585074 GAGTCATTCCATATATGTATAGATTCATCTCTGAGTCTAGTTTCTATAGAAACAAACGGCATCAG
390 GAGTCAAGCCATATATGTATAGATTCACCTCTGAGTCTAGTTTCTATAGAAACAAACGGCATCAG
** ** * *
52585139 TATTGAAGCTCTGTGGAGGGAGATATCCAAATCGTAATGCATGAAGGTCAGTGTAGTCGCA-CCC
455 TATTGAAGCTCTGTACAGGGAGATATCCAAATCGTAATGCACAAAGGTCAGGGTAGTC-AATCCC
* *
52585203 TATAACAGGGGAGAATTTAACTAATAAACTGTACTAATTGGCCCAACCGAAAATTCTAGAAAAAA
519 TATAACAGGGGAGAATTTAACTAATAAACTGTACTAATTGGCCCAACCAAAAACTCTAGAAAAAA
* * *
52585268 ATATGTAGATGGGAATATGAGTCTAGTTTCAGGGAAAAATTACGAAACT-GATTTTCGAG-TTGT
584 ATATGTAGATGGAAATATGAGTCTAGTTTCAGGGAAAAATTACGAAACTGGA-TTCCGAGTTTCT
**
52585331 GAAACTCAAGATATGATTTTTAGGGTGAC-AGTGACGCAG-TTAGCCAACTGCCTGG-AAATTTT
648 G-AACTCAAGATATGATTTTTAAAGTGACTA-TGACGCAGATT-GCC-ACTGCCTGGAAAATTTT
52585393 TAAA
709 TAAA
52585397 ATGGACTGCG
Statistics
Matches: 647, Mismatches: 58, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
767 12 0.02
768 627 0.97
769 8 0.01
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (768 bp):
GGATATGGTTATTGAGAGGTGTGGATAGGCTTAACAAGGATTGGCCATGGGAATGGCTAATCACT
ATCATAAATTGTGCTACTTATGCAAAAAGGGCTAGTTGAATCATGGAAACTATGAAATAGGTAAA
GTCTACCTTAAAGGCAGATGCTGACAGCAGCAGTGATGTAGATTTGGAAAATCACTAAAAATAGT
AGGAATGGAATTAAATAGTGAATAAATTATGTAAACGAACCTTGATGAATCTATTTTCATAGAAA
AGTAACGAAACAATCATACGGACAGTATGTTAAGAGATATTCAGGTTCTCGTGAGACAGAGCCAG
AACGGTTTCTGGATTTCCTGTTCCGACTTTGGAAATTCATTATAAACTAACCAGAGAGAATTAGG
AGTCAAGCCATATATGTATAGATTCACCTCTGAGTCTAGTTTCTATAGAAACAAACGGCATCAGT
ATTGAAGCTCTGTACAGGGAGATATCCAAATCGTAATGCACAAAGGTCAGGGTAGTCAATCCCTA
TAACAGGGGAGAATTTAACTAATAAACTGTACTAATTGGCCCAACCAAAAACTCTAGAAAAAAAT
ATGTAGATGGAAATATGAGTCTAGTTTCAGGGAAAAATTACGAAACTGGATTCCGAGTTTCTGAA
CTCAAGATATGATTTTTAAAGTGACTATGACGCAGATTGCCACTGCCTGGAAAATTTTTAAAGTT
TGTTAACACCTCGTGTTCGACTCCGGTGACGGTCTCGGGTTCGGGGTGTTACA
Found at i:52589854 original size:10 final size:10
Alignment explanation
Indices: 52589819--52589860 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
52589809 GAACAGATGT
52589819 TTTGGTATGA
1 TTTGGTATGA
*
52589829 TTTTGGTTTAGA
1 -TTTGGTAT-GA
52589841 TTTGGTATGA
1 TTTGGTATGA
52589851 TTTGGT-TGA
1 TTTGGTATGA
52589860 T
1 T
52589861 GAGTTGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 4 0.14
10 8 0.29
11 14 0.50
12 2 0.07
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.55
Consensus pattern (10 bp):
TTTGGTATGA
Found at i:52591869 original size:47 final size:44
Alignment explanation
Indices: 52591801--52592064 Score: 194
Period size: 47 Copynumber: 5.6 Consensus size: 44
52591791 TTTGTGAACT
*
52591801 AGTGTAAGACATGTCTAGGACATGCATCAGCCACATT-ATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-G--ACATTGATGAGAGCC
* * *
52591847 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGATGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACATT--GATGAGAGCC
* ** * *
52591895 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGAC-A-TTGATGAGAGCC
*
52591941 AGTGTAAGACAATGTCTGGTACATGGCATCGAC-TTGA-GATATGAGCC
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCGACATTGATG--A-GAGCC
* *
52591988 AGTGTAAGACCGTGTCTGGGACATGGCATCGACATGAGAT-ATGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACAT-TGATGA-GAGCC
* *
52592035 ATTGTAAGACTGTGTCTGGGACATGGCATC
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATC
52592065 AGCACCTTAC
Statistics
Matches: 181, Mismatches: 20, Indels: 33
0.77 0.09 0.14
Matches are distributed among these distances:
44 1 0.01
45 6 0.03
46 36 0.20
47 105 0.58
48 31 0.17
49 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACATTGATGAGAGCC
Found at i:52591965 original size:94 final size:92
Alignment explanation
Indices: 52591799--52592064 Score: 295
Period size: 94 Copynumber: 2.8 Consensus size: 92
52591789 TGTTTGTGAA
* * * * * *
52591799 CTAGTGTAAGACATGTCTAGGACATGCATCAGCCAC-ATTATGAGAGCCAGTGTAAGACCATGTT
1 CTAGTGTAAGACATGTCTGGGACATGCATC-GGCACGA-GATGATAGCCAGTGTAAGACAATGTC
*
52591863 TGGGACATGGCATCGGCATTGAGATGA-GAG
64 TGGGACATGGCATCGAC-TTGAGAT-ATGAG
*
52591893 CTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGATAGTCAGTGTAAGACAATGTCT
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGC-ACGAGATGATAGCCAGTGTAAGACAATGTCT
*
52591958 GGTACATGGCATCGACTTGAGATATGAG
65 GGGACATGGCATCGACTTGAGATATGAG
* * * * * **
52591986 CCAGTGTAAGACCGTGTCTGGGACATGGCATCGACATGAGAT-ATGAGCCATTGTAAGACTGTGT
1 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACGAGATGAT-AGCCAGTGTAAGACAATGT
52592050 CTGGGACATGGCATC
63 CTGGGACATGGCATC
52592065 AGCACCTTAC
Statistics
Matches: 148, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
92 1 0.01
93 24 0.16
94 115 0.78
95 8 0.05
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (92 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCGGCACGAGATGATAGCCAGTGTAAGACAATGTCTG
GGACATGGCATCGACTTGAGATATGAG
Found at i:52593616 original size:55 final size:56
Alignment explanation
Indices: 52593539--52593662 Score: 162
Period size: 55 Copynumber: 2.2 Consensus size: 56
52593529 TAGCCTGTGT
* * ** * *
52593539 ACAACACTGACTT-TAGGGCACGGCCATGATGCACGCCTGTGTGGCCTACTCGTGG
1 ACAATACTGACTTATAGGACACGGCCATGACACACGCCCGTGTGGCCTACCCGTGG
* *
52593594 ACAATACTGACTTATA-GACACGGCTATGGCACACGCCCGTGTGGCCTACCCGTGG
1 ACAATACTGACTTATAGGACACGGCCATGACACACGCCCGTGTGGCCTACCCGTGG
52593649 ACAATACTGACTTA
1 ACAATACTGACTTA
52593663 AAAGTTTAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
55 58 0.97
56 2 0.03
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (56 bp):
ACAATACTGACTTATAGGACACGGCCATGACACACGCCCGTGTGGCCTACCCGTGG
Found at i:52599124 original size:40 final size:40
Alignment explanation
Indices: 52599087--52599351 Score: 358
Period size: 40 Copynumber: 6.7 Consensus size: 40
52599077 GCTACTCGTT
* *
52599087 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
52599127 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
52599167 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
52599207 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
52599247 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
52599286 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
52599327 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
52599352 CATCATTCAA
Statistics
Matches: 205, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
38 2 0.01
39 33 0.16
40 157 0.77
41 13 0.06
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:52599342 original size:119 final size:121
Alignment explanation
Indices: 52599087--52599351 Score: 369
Period size: 119 Copynumber: 2.2 Consensus size: 121
52599077 GCTACTCGTT
* *
52599087 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* * *
52599151 GATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 GAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA
* *
52599207 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* ** * *
52599270 GAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
66 GAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCA
52599327 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52599352 CATCATTCAA
Statistics
Matches: 129, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
118 3 0.02
119 68 0.53
120 56 0.43
121 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (121 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
GAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA
Found at i:52600997 original size:61 final size:61
Alignment explanation
Indices: 52600902--52601026 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 61
52600892 GCCGAATCGA
52600902 GACTGTTCGAAAATATATGAGGTAAGTTTTAAGAAGTTAAATATAAATAATATTCGATAAT
1 GACTGTTCGAAAATATATGAGGTAAGTTTTAAGAAGTTAAATATAAATAATATTCGATAAT
*
52600963 GACTGTTCGAAAATATTTGAGGTAAGTTTTAAGAAGTTAAATATAAATAATATTCGATAAT
1 GACTGTTCGAAAATATATGAGGTAAGTTTTAAGAAGTTAAATATAAATAATATTCGATAAT
52601024 GAC
1 GAC
52601027 ATGACAGATT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (61 bp):
GACTGTTCGAAAATATATGAGGTAAGTTTTAAGAAGTTAAATATAAATAATATTCGATAAT
Found at i:52601365 original size:45 final size:45
Alignment explanation
Indices: 52601301--52601433 Score: 230
Period size: 45 Copynumber: 3.0 Consensus size: 45
52601291 TATCGTACAG
*
52601301 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
52601346 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * *
52601391 TACTATTTGGGCCTTCGAGCCTAGCAAGCTATAATGCCGGTGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
52601434 AATGATATCG
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 84 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:52610433 original size:56 final size:56
Alignment explanation
Indices: 52610342--52610464 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
52610332 GAGATTGGCG
* * *
52610342 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
52610399 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
52610454 CTGAGTGTGCG
1 CTAAGTGTGCG
52610465 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:52610451 original size:27 final size:28
Alignment explanation
Indices: 52610342--52610464 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
52610332 GAGATTGGCG
* * * *
52610342 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
52610371 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
52610399 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
52610427 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
52610454 CTGAGTGTGCG
1 CTAAGTGTGCG
52610465 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:52610475 original size:27 final size:27
Alignment explanation
Indices: 52610367--52610477 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
52610357 TAAATTGTAC
* * *
52610367 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
52610395 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
52610423 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
52610450 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
52610477 A
1 A
52610478 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:52612971 original size:27 final size:27
Alignment explanation
Indices: 52612932--52613023 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
52612922 GGAAGCGTCT
*
52612932 TGGTGGCTATGCCACAATTATCTGATC
1 TGGTGGCTCTGCCACAATTATCTGATC
*
52612959 TGGTGGCTCTGCCACATATT-TCTGTTC
1 TGGTGGCTCTGCCACA-ATTATCTGATC
* * *
52612986 TGGTGGTTCTACCACGATTATCTGTATC
1 TGGTGGCTCTGCCACAATTATCTG-ATC
*
52613014 TGGTGACTCT
1 TGGTGGCTCT
52613024 TTTACATTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
26 3 0.06
27 38 0.70
28 13 0.24
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (27 bp):
TGGTGGCTCTGCCACAATTATCTGATC
Found at i:52620815 original size:27 final size:26
Alignment explanation
Indices: 52620756--52620865 Score: 123
Period size: 27 Copynumber: 4.1 Consensus size: 26
52620746 GGAAGCGTCT
* *
52620756 TGGTGGCTATGCCACAATTA-CTGATC
1 TGGTGGCTCTGCCAC-ATTATCTGTTC
*
52620782 TGGTGGCTCTGCCACATATTTCTGTTC
1 TGGTGGCTCTGCCACAT-TATCTGTTC
52620809 TGGTGGCTCTGCCACGATTATCTGTATC
1 TGGTGGCTCTGCCAC-ATTATCTGT-TC
* * *
52620837 TAGTGACTCTGTCACATTATCTGTTC
1 TGGTGGCTCTGCCACATTATCTGTTC
52620863 TGG
1 TGG
52620866 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.03
26 19 0.26
27 35 0.49
28 16 0.22
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
TGGTGGCTCTGCCACATTATCTGTTC
Found at i:52631291 original size:27 final size:27
Alignment explanation
Indices: 52631261--52631438 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
52631251 ATATTGAGTC
* * * *
52631261 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
52631288 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
52631315 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
52631343 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
52631370 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
52631397 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
52631424 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52631439 GTACAATTCA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:52631400 original size:82 final size:81
Alignment explanation
Indices: 52631282--52631437 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
52631272 TGCTATATAA
* *
52631282 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
52631347 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
52631364 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
52631428 CACTTAGTGC
65 CACTTAGTGC
52631438 TGTACAATTC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:52631450 original size:82 final size:83
Alignment explanation
Indices: 52631261--52631450 Score: 221
Period size: 82 Copynumber: 2.3 Consensus size: 83
52631251 ATATTGAGTC
* * * * *
52631261 CGCACACTCAGTGCTATATAA-TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTA
1 CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
*
52631325 GTGCTACATAGTCAAACT
66 GTGCAACATAGTCAAACT
* * **
52631343 CGCACACTTAGTGCCG--C-ATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACAC
1 CGCACACTTAGTGCTGTACAAT--TCAATTCGCACACTTAGTGCTA-CATAATCAAATCGCACAC
52631404 TTAGTGCAACATAGTCAAA-T
63 TTAGTGCAACATAGTCAAACT
52631424 CGCACACTTAGTGCTGTACAATTCAAT
1 CGCACACTTAGTGCTGTACAATTCAAT
52631451 CCCGCGCACT
Statistics
Matches: 90, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
79 1 0.01
81 17 0.19
82 69 0.77
83 1 0.01
84 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (83 bp):
CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
GTGCAACATAGTCAAACT
Found at i:52635468 original size:26 final size:26
Alignment explanation
Indices: 52635439--52635488 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
52635429 TACGTTACAA
52635439 TAAAAGAAAACATTCAATATTTCAAT
1 TAAAAGAAAACATTCAATATTTCAAT
****
52635465 TAAATTCTAACATTCAATATTTCA
1 TAAAAGAAAACATTCAATATTTCA
52635489 GTTTAATTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (26 bp):
TAAAAGAAAACATTCAATATTTCAAT
Found at i:52637568 original size:300 final size:299
Alignment explanation
Indices: 52637020--52637618 Score: 1108
Period size: 300 Copynumber: 2.0 Consensus size: 299
52637010 AAATAAAGAC
*
52637020 AAAAGAGCAATTTTGGCCCTTTACGTCTGGTAACCGTTTTTTAGCTTTAGCAATCCTATATCCTT
1 AAAAGAACAATTTTGGCCCTTTACGTCTGGTAACCGTTTTTTAGCTTTAGCAATCCTATATCCTT
52637085 AAGCAGACGGAGATGGTGAATCGATCAATGCAAGGCAATTATTCCATGTCTGAATGCTCTTAGCT
66 AAGCAGACGGAGATGGTGAATCGATCAATGCAAGGCAATTATTCCATGTCTGAATGCTCTTAGCT
*
52637150 ATAATTGTCGCTGGGTTTAGGTCTTTGAATAGAGGATTTTCAACAGTCCTCTTTACTAATGCTGA
131 ATAATTGTCGCTGGGTTTAGGTCTTTGAATAGAGGATTTTCAACAGTCCTCTTTACAAATGCTGA
* *
52637215 GTGGCAAAATTTTCCCAACACAACAAGTTCGCCGCAACACTTGTTAGAAATACTCCCTATATTGA
196 GTGGCAAAATTTTCCCAACACAACAAGTTCACCGCAACACTTGTTAGAAATACTCCCTATATTAA
52637280 AAATACTCATGAAAGCTTCTAGAACACAGGGCAAACCCA
261 AAATACTCATGAAAGCTTCTAGAACACAGGGCAAACCCA
*
52637319 AAAAGAACAATTTTGGCCTTTTACGTCTGGTAACCGTTTTTTTAGCTTTAGCAATCCTATATCCT
1 AAAAGAACAATTTTGGCCCTTTACGTCTGGTAACCG-TTTTTTAGCTTTAGCAATCCTATATCCT
52637384 TAAGCAGACGGAGATGGTGAATCGATCAATGCAAGGCAATTATTCCATGTCTGAATGCTCTTAGC
65 TAAGCAGACGGAGATGGTGAATCGATCAATGCAAGGCAATTATTCCATGTCTGAATGCTCTTAGC
*
52637449 TATAATTGTCGCTGGGTTTAGGTCTTTGAATAGAGGATTTTCAAGAGTCCTCTTTACAAATGCTG
130 TATAATTGTCGCTGGGTTTAGGTCTTTGAATAGAGGATTTTCAACAGTCCTCTTTACAAATGCTG
* *
52637514 AGTGGCAAACTTTTCCCAACACAACAAGTTCACCGCAACACTTGTTAGAAATACTCCCTGTATTA
195 AGTGGCAAAATTTTCCCAACACAACAAGTTCACCGCAACACTTGTTAGAAATACTCCCTATATTA
*
52637579 AAAATACTCGTGAAAGCTTCTAGAACACAGGGCAAACCCA
260 AAAATACTCATGAAAGCTTCTAGAACACAGGGCAAACCCA
52637619 TTTTAGTTTC
Statistics
Matches: 290, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
299 34 0.12
300 256 0.88
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (299 bp):
AAAAGAACAATTTTGGCCCTTTACGTCTGGTAACCGTTTTTTAGCTTTAGCAATCCTATATCCTT
AAGCAGACGGAGATGGTGAATCGATCAATGCAAGGCAATTATTCCATGTCTGAATGCTCTTAGCT
ATAATTGTCGCTGGGTTTAGGTCTTTGAATAGAGGATTTTCAACAGTCCTCTTTACAAATGCTGA
GTGGCAAAATTTTCCCAACACAACAAGTTCACCGCAACACTTGTTAGAAATACTCCCTATATTAA
AAATACTCATGAAAGCTTCTAGAACACAGGGCAAACCCA
Found at i:52637915 original size:26 final size:26
Alignment explanation
Indices: 52637868--52637917 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
52637858 AATAAAAGAA
*
52637868 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAAGTTAATTCT
*
52637894 AACATTCAATATTTCAGGTTAATT
1 AACATTCAATATTTCAAGTTAATT
52637918 AGCATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (26 bp):
AACATTCAATATTTCAAGTTAATTCT
Found at i:52642135 original size:20 final size:20
Alignment explanation
Indices: 52642110--52642149 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
52642100 TGTTGATAGC
52642110 AGCAAAAGATAAAGGAGAGA
1 AGCAAAAGATAAAGGAGAGA
52642130 AGCAAAAGATAAAGGAGAGA
1 AGCAAAAGATAAAGGAGAGA
52642150 TAAGAAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.30, T:0.05
Consensus pattern (20 bp):
AGCAAAAGATAAAGGAGAGA
Found at i:52646922 original size:26 final size:26
Alignment explanation
Indices: 52646892--52646942 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
52646882 AATAAAAGAA
*
52646892 AACATTGAATATTTCTA-TTTAATTAT
1 AACATTCAATATTTC-AGTTTAATTAT
52646918 AACATTCAATATTTCAGTTTAATTA
1 AACATTCAATATTTCAGTTTAATTA
52646943 GCATTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTAT
Found at i:52655012 original size:5 final size:5
Alignment explanation
Indices: 52655002--52655033 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
52654992 TTGTGTGTTC
52655002 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
52655034 TCACATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:52655016 original size:9 final size:9
Alignment explanation
Indices: 52655002--52655032 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
52654992 TTGTGTGTTC
52655002 TTTATTTTA
1 TTTATTTTA
52655011 TTTATTTTA
1 TTTATTTTA
52655020 TTTTATTTTA
1 -TTTATTTTA
52655030 TTT
1 TTT
52655033 TTCACATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:52657819 original size:67 final size:63
Alignment explanation
Indices: 52657702--52657824 Score: 165
Period size: 67 Copynumber: 1.9 Consensus size: 63
52657692 TACTTTAACA
* *
52657702 ATTTATGCAAATATAATATAGAAAATGATAAATAACTACATAAATTACATAATATACATTATC
1 ATTTATGCAAATATAATATAGAAAATAATAAATAACAACATAAATTACATAATATACATTATC
* * *
52657765 ATTTCATGCAGATATAATCATAGAAAATAATGAATATAGCAATATAAATTACATAATATA
1 ATTT-ATGCAAATATAAT-ATAGAAAATAAT-AA-ATAACAACATAAATTACATAATATA
52657825 TATACAATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 4 0.08
64 12 0.24
65 11 0.22
66 2 0.04
67 22 0.43
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (63 bp):
ATTTATGCAAATATAATATAGAAAATAATAAATAACAACATAAATTACATAATATACATTATC
Found at i:52657845 original size:71 final size:64
Alignment explanation
Indices: 52657702--52657852 Score: 162
Period size: 71 Copynumber: 2.3 Consensus size: 64
52657692 TACTTTAACA
* * *
52657702 ATTT-ATGCAAATATAATATAGAAAATGATAAATAACTACATAAATTACATAATATACATTATC
1 ATTTCATGCAAATATAATATAGAAAATAATAAATAACAACATAAATTACATAATATACATAATC
* * *
52657765 ATTTCATGCAGATATAATCATAGAAAATAATGAATATAGCAATATAAATTACATAATATATATAC
1 ATTTCATGCAAATATAAT-ATAGAAAATAAT-AA-ATAACAACATAAATTAC---ATA-ATATAC
52657830 AATAAT-
59 -ATAATC
52657836 ATTTCATGCAAATATAA
1 ATTTCATGCAAATATAA
52657853 CTTAAAATAA
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
63 4 0.06
64 12 0.17
65 11 0.15
66 2 0.03
67 14 0.19
70 3 0.04
71 22 0.31
72 4 0.06
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (64 bp):
ATTTCATGCAAATATAATATAGAAAATAATAAATAACAACATAAATTACATAATATACATAATC
Found at i:52658143 original size:7 final size:7
Alignment explanation
Indices: 52658127--52658228 Score: 54
Period size: 7 Copynumber: 15.1 Consensus size: 7
52658117 GAAACGATTA
52658127 ATAT-AT
1 ATATAAT
52658133 ATATAAT
1 ATATAAT
52658140 ATATAAT
1 ATATAAT
52658147 ATATAAT
1 ATATAAT
*
52658154 A-A-AAG
1 ATATAAT
*
52658159 CTATAA-
1 ATATAAT
*
52658165 ATAAAAT
1 ATATAAT
*
52658172 ATATAAA
1 ATATAAT
52658179 ATATAAAT
1 ATAT-AAT
* *
52658187 AACATGAT
1 -ATATAAT
*
52658195 AAATAAT
1 ATATAAT
*
52658202 ACATAA-
1 ATATAAT
*
52658208 ATA-AAA
1 ATATAAT
*
52658214 ATATTAT
1 ATATAAT
52658221 ATATAAT
1 ATATAAT
52658228 A
1 A
52658229 ATTTTACATG
Statistics
Matches: 72, Mismatches: 16, Indels: 15
0.70 0.16 0.15
Matches are distributed among these distances:
5 4 0.06
6 15 0.21
7 46 0.64
8 4 0.06
9 3 0.04
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (7 bp):
ATATAAT
Found at i:52658173 original size:23 final size:22
Alignment explanation
Indices: 52658142--52658213 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
52658132 TATATAATAT
*
52658142 ATAATATATAATAAAAGCTATAA
1 ATAAAATATAATAAAA-CTATAA
52658165 ATAAAATAT-ATAAAA-TATAA
1 ATAAAATATAATAAAACTATAA
* *
52658185 ATAACATGATAAATAATAC-ATAA
1 ATAAAAT-AT-AATAAAACTATAA
52658208 ATAAAA
1 ATAAAA
52658214 ATATTATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 11 0.27
21 2 0.05
22 6 0.15
23 22 0.54
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (22 bp):
ATAAAATATAATAAAACTATAA
Found at i:52658223 original size:47 final size:51
Alignment explanation
Indices: 52658161--52658280 Score: 128
Period size: 49 Copynumber: 2.4 Consensus size: 51
52658151 AATAAAAGCT
*
52658161 ATAAATAAAATATATAAAATATAAATAACATG-ATAAATAATA-CATAAATA
1 ATAAATAATATATATAAAATATAAATAACATGTATAAATAATATCATAAA-A
* * *
52658211 A-AAATATTATATATAATAAT-T---TTACATGTATAAATAATATTTATAAAA
1 ATAAATAATATATATAA-AATATAAATAACATGTATAAATAATA-TCATAAAA
52658259 ATAAATAATATATATAAAATAT
1 ATAAATAATATATATAAAATAT
52658281 TTAAAATAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
46 6 0.10
47 10 0.17
48 5 0.08
49 34 0.58
50 4 0.07
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (51 bp):
ATAAATAATATATATAAAATATAAATAACATGTATAAATAATATCATAAAA
Found at i:52658226 original size:15 final size:15
Alignment explanation
Indices: 52658208--52658320 Score: 61
Period size: 15 Copynumber: 7.3 Consensus size: 15
52658198 TAATACATAA
52658208 ATAAAAATATTATAT
1 ATAAAAATATTATAT
* * *
52658223 ATAATAATTTTACAT
1 ATAAAAATATTATAT
* * * *
52658238 GTATAAATAATATTT
1 ATAAAAATATTATAT
*
52658253 ATAAAAATAAATAATAT
1 ATAAAAAT--ATTATAT
*
52658270 ATATAAAATATT-TAAA
1 ATA-AAAATATTAT-AT
52658286 ATAAATAA-ATTATAT
1 ATAAA-AATATTATAT
*
52658301 AT-AAAATGTATATAT
1 ATAAAAATAT-TATAT
52658316 ATAAA
1 ATAAA
52658321 GATTAAAATT
Statistics
Matches: 70, Mismatches: 19, Indels: 17
0.66 0.18 0.16
Matches are distributed among these distances:
13 2 0.03
14 3 0.04
15 42 0.60
16 11 0.16
17 7 0.10
18 5 0.07
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (15 bp):
ATAAAAATATTATAT
Found at i:52658262 original size:19 final size:19
Alignment explanation
Indices: 52658240--52658277 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
52658230 TTTTACATGT
*
52658240 ATAAATAATATTTATAAAA
1 ATAAATAATATATATAAAA
52658259 ATAAATAATATATATAAAA
1 ATAAATAATATATATAAAA
52658278 TATTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAATAATATATATAAAA
Found at i:52658295 original size:31 final size:28
Alignment explanation
Indices: 52658246--52658307 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 28
52658236 ATGTATAAAT
*
52658246 AATATTTATAAAAATAAATAATATATATAA
1 AATATTTAAAAAAATAAAT--TATATATAA
52658276 AATATTTAAAATAAATAAATTATATATAA
1 AATATTTAAAA-AAATAAATTATATATAA
52658305 AAT
1 AAT
52658308 GTATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 12 0.40
30 10 0.33
31 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AATATTTAAAAAAATAAATTATATATAA
Found at i:52659902 original size:90 final size:90
Alignment explanation
Indices: 52659749--52660104 Score: 466
Period size: 90 Copynumber: 4.0 Consensus size: 90
52659739 AATATTCTTA
** * * *
52659749 ATCTGCTCCTTGTCAAATACAGAGACGCCAAATCTGTCATCTTCGATTTGCTTCGATGCAAACAC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
* *
52659814 ACGAATGTCGGAT-TCGTTATCTTTG
66 ACGAATGTCAGATCT-GCTATCTTTG
* * * *
52659839 ATCTGCTCCCCGTCTAATACAAAGAGGCCAAACCTGTCATTTTCGATCTGCTTCGATGTAAACAC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
*
52659904 ATGAATGTCAGATCTGCTATCTTTG
66 ACGAATGTCAGATCTGCTATCTTTG
*
52659929 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
* * *
52659994 ACGGATGTTAGATCTGCTATCTTCG
66 ACGAATGTCAGATCTGCTATCTTTG
* * ** * *
52660019 ATCTGCTCCCCGTCTAATATAGAGACGCCAAATCTGTCATCTTCGATTTG-TTCCCTGTCAAGAC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
*
52660083 A-GAGATGTCAAATCTGCTATCT
66 ACGA-ATGTCAGATCTGCTATCT
52660105 ACATTGTCCC
Statistics
Matches: 234, Mismatches: 30, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
88 1 0.00
89 27 0.12
90 205 0.88
91 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (90 bp):
ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACAC
ACGAATGTCAGATCTGCTATCTTTG
Found at i:52660054 original size:45 final size:45
Alignment explanation
Indices: 52659831--52660104 Score: 181
Period size: 45 Copynumber: 6.1 Consensus size: 45
52659821 TCGGATTCGT
* * * *
52659831 TATCTTTGATCTGCTCCCCGTCTAATACAAAGAGGCCAAACCTG-
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGC
* * * * * *
52659875 TCATTTTCGATCTGCT--TCGATGTAA-ACACATGAATGTCAGATCTGC
1 T-ATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ATGCCAAATCTGC
*
52659921 TATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTG-
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGC
* * * ** *
52659965 TCATCTTCGATCTGCT--TCGATGTAA-ACACACGGATGTTAGATCTGC
1 T-ATCTTCGATCTGCTCCCCG-TCTAATACAGA--GATGCCAAATCTGC
* *
52660011 TATCTTCGATCTGCTCCCCGTCTAATATAGAGACGCCAAATCTG-
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGC
* * * * *
52660055 TCATCTTCGATTTGTTCCCTGTC-AAGACAGAGATGTCAAATCTGC
1 T-ATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGC
52660100 TATCT
1 TATCT
52660105 ACATTGTCCC
Statistics
Matches: 174, Mismatches: 38, Indels: 36
0.70 0.15 0.15
Matches are distributed among these distances:
43 12 0.07
44 33 0.19
45 107 0.61
46 11 0.06
47 11 0.06
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (45 bp):
TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGC
Found at i:52665436 original size:35 final size:34
Alignment explanation
Indices: 52665390--52665459 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 34
52665380 CTGCTCCTGC
52665390 TGAATGTATCCAAGGCCTCCCCAACAGGCAATTG
1 TGAATGTATCCAAGGCCTCCCCAACAGGCAATTG
* *
52665424 NTGAATGTATCCAAGGCTTCCTCAACAGGCAATTG
1 -TGAATGTATCCAAGGCCTCCCCAACAGGCAATTG
52665459 T
1 T
52665460 AAGAGGGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 1 0.03
35 32 0.97
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.24
Consensus pattern (34 bp):
TGAATGTATCCAAGGCCTCCCCAACAGGCAATTG
Found at i:52668008 original size:40 final size:40
Alignment explanation
Indices: 52667953--52668134 Score: 314
Period size: 40 Copynumber: 4.6 Consensus size: 40
52667943 TATTCGAATG
52667953 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
52667993 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
52668033 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
52668073 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
52668113 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
52668135 TACTTGGGTT
Statistics
Matches: 137, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
39 14 0.10
40 121 0.88
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:52687729 original size:39 final size:40
Alignment explanation
Indices: 52687628--52687729 Score: 120
Period size: 40 Copynumber: 2.6 Consensus size: 40
52687618 TATTCGAATG
* * * *
52687628 ATATCCGGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAATCCCGAAGGAATTTGTGCGAGTGACT
52687668 ATATCCGGGCTAAGA-CCCGAAGGAATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAA-ATCCCGAAGGAATTTGTGCGAG-TGACT
*
52687708 ATAT-CTGGCTAAATCCCGAAGG
1 ATATCCGGGCTAAATCCCGAAGG
52687730 TAAGACTCGG
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
38 1 0.02
39 15 0.28
40 36 0.67
41 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAATCCCGAAGGAATTTGTGCGAGTGACT
Found at i:52694353 original size:15 final size:15
Alignment explanation
Indices: 52694333--52694364 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
52694323 GAACATATAT
52694333 AAAATATAAGTAAAA
1 AAAATATAAGTAAAA
*
52694348 AAAATATAATTAAAA
1 AAAATATAAGTAAAA
52694363 AA
1 AA
52694365 TATTGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (15 bp):
AAAATATAAGTAAAA
Found at i:52698327 original size:261 final size:261
Alignment explanation
Indices: 52697854--52698374 Score: 871
Period size: 261 Copynumber: 2.0 Consensus size: 261
52697844 CCAGTTTGGT
* **
52697854 TATTATCTTCTTCGTTCTAGGTTAAATTTTTAGGTGTAAGCGTTCTGGCCCAATTTTTTTAAAAT
1 TATTATCTTCTTCGTTCTACGTTAAATTTTTAGGTGTAAGCGTTCTGGCCCAATTTTACTAAAAT
*
52697919 ATGAATGAAACCTTTTAGTGGAATAAGTAACAGAGCTTGGAAAATGAAAAATTCTATTAGAGAGT
66 ATGAATGAAACCTTTCAGTGGAATAAGTAACAGAGCTTGGAAAATGAAAAATTCTATTAGAGAGT
* * *
52697984 GAAATTGGAAACAACAAATGATGTTTCATTTTTGTAACTCTCGTCGGTATATCCCAAATAATGAA
131 GAAATTGGAAACAACAAATGACGTTTCATTTTTATAACTCTCGTAGGTATATCCCAAATAATGAA
* * *
52698049 TAGGATTTAGTTTTTATACAAATTGATCCTTTTTTAGTAGGGAAAATGTGAGGCATACGTCGCCG
196 TAGGATTTAGGTTTTATACAAATTGATCCTTGTTTAGTAAGGAAAATGTGAGGCATACGTCGCCG
52698114 G
261 G
* * *
52698115 TATTGTCTTCTTCGTTCTACGTTAAATTTTTAGGTGTAAGCGTTCTTGCCCAATTTTACTGAAAT
1 TATTATCTTCTTCGTTCTACGTTAAATTTTTAGGTGTAAGCGTTCTGGCCCAATTTTACTAAAAT
* * *
52698180 ATGAATGAAAGCTTTCAGTGGAATAAGTAATAGAGCTTGGAAAATGAATAATTCTATTAGAGAGT
66 ATGAATGAAACCTTTCAGTGGAATAAGTAACAGAGCTTGGAAAATGAAAAATTCTATTAGAGAGT
*
52698245 GAAATTGGAAACAACAAATGACGTTTCATTTTTATAACTCTCGTAGGTATTTCCCAAATAATGAA
131 GAAATTGGAAACAACAAATGACGTTTCATTTTTATAACTCTCGTAGGTATATCCCAAATAATGAA
* *
52698310 TAGGATTTAGGTTTTATATAAATTGATCCTTGTTTAGTAAGGAAAATGTGAGGCGTACGTCGCCG
196 TAGGATTTAGGTTTTATACAAATTGATCCTTGTTTAGTAAGGAAAATGTGAGGCATACGTCGCCG
52698375 ACATATTTGG
Statistics
Matches: 241, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
261 241 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (261 bp):
TATTATCTTCTTCGTTCTACGTTAAATTTTTAGGTGTAAGCGTTCTGGCCCAATTTTACTAAAAT
ATGAATGAAACCTTTCAGTGGAATAAGTAACAGAGCTTGGAAAATGAAAAATTCTATTAGAGAGT
GAAATTGGAAACAACAAATGACGTTTCATTTTTATAACTCTCGTAGGTATATCCCAAATAATGAA
TAGGATTTAGGTTTTATACAAATTGATCCTTGTTTAGTAAGGAAAATGTGAGGCATACGTCGCCG
G
Found at i:52699613 original size:26 final size:26
Alignment explanation
Indices: 52699584--52699633 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
52699574 AATAAAAGAA
52699584 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
52699610 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
52699634 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:52701115 original size:19 final size:19
Alignment explanation
Indices: 52701091--52701152 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
52701081 AATCTTTAAG
52701091 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
52701110 GATATGCAATCTTTGATAT
1 GATATGCAATCTTAGATAT
52701129 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
52701150 GAT
1 GAT
52701153 CTTGTAATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 31 0.79
21 8 0.21
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52706299 original size:225 final size:225
Alignment explanation
Indices: 52705908--52706347 Score: 790
Period size: 225 Copynumber: 2.0 Consensus size: 225
52705898 CAAGGATCTT
* * * *
52705908 CTGACAATGTGCTACATGGTACTGTCATTGGCAACAAAGTATGCCATCCAAAGAATAATGATTTT
1 CTGACAATGTGCTACATGGTACTGTCATTGACAACAAAGTATGCCATCCAAAAAACAACGATTTT
*
52705973 TACCTTGGTACCCATGCTGGAATGATTGGAATCACGAGGCAGACCCACTATCATGTTTTCTTAGA
66 TACCTTGGTACCCATGCTGGAATGATTGGAATCACGAGGCAGACCCACTATCATGTTCTCTTAGA
* * *
52706038 CCAGGCTGGGTTTTCGGCTGATGATCTATAAGAGTTTGTTCATTCTCTGTCCTATATGTATCAAA
131 CCAGGCTGGATTTTCGGCTGATGATCTACAAGAGTTTGTTCATTCTCTATCCTATATGTATCAAA
52706103 GGAGCACCACAACCATATTTTTCGTGGCTC
196 GGAGCACCACAACCATATTTTTCGTGGCTC
52706133 CTGACAATGTGCTACATGGTACTGTCATTGACAACAAAGTATGCCATCCAAAAAACAACGATTTT
1 CTGACAATGTGCTACATGGTACTGTCATTGACAACAAAGTATGCCATCCAAAAAACAACGATTTT
52706198 TACCTTGGTACCCATGCTGGAATGATTGGAATCACGAGGCAGACCCACTATCATGTTCTCTTAGA
66 TACCTTGGTACCCATGCTGGAATGATTGGAATCACGAGGCAGACCCACTATCATGTTCTCTTAGA
*
52706263 CCAGGCTGGATTTTCGGCTGATGATCTGCAAGAGTTTGTTCATTCTCTATCCTATATGTATCAAA
131 CCAGGCTGGATTTTCGGCTGATGATCTACAAGAGTTTGTTCATTCTCTATCCTATATGTATCAAA
*
52706328 GGAGCACCACAGCCATATTT
196 GGAGCACCACAACCATATTT
52706348 GTTGTGTCTC
Statistics
Matches: 205, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
225 205 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (225 bp):
CTGACAATGTGCTACATGGTACTGTCATTGACAACAAAGTATGCCATCCAAAAAACAACGATTTT
TACCTTGGTACCCATGCTGGAATGATTGGAATCACGAGGCAGACCCACTATCATGTTCTCTTAGA
CCAGGCTGGATTTTCGGCTGATGATCTACAAGAGTTTGTTCATTCTCTATCCTATATGTATCAAA
GGAGCACCACAACCATATTTTTCGTGGCTC
Found at i:52707012 original size:7 final size:7
Alignment explanation
Indices: 52706995--52707051 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
52706985 CTATTTCAAA
52706995 AAAAAATG
1 AAAAAA-G
52707003 AAAAAAG
1 AAAAAAG
* *
52707010 AAAATAT
1 AAAAAAG
*
52707017 AAAGAGAAA
1 AAA-A-AAG
52707026 AAAAAAG
1 AAAAAAG
52707033 -AAAAAG
1 AAAAAAG
52707039 AAAAAAG
1 AAAAAAG
52707046 AAAAAA
1 AAAAAA
52707052 TAGAGAGGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
6 6 0.15
7 23 0.56
8 8 0.20
9 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:52707013 original size:13 final size:12
Alignment explanation
Indices: 52706992--52707049 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
52706982 CTTCTATTTC
52706992 AAAAA-AAAATGA
1 AAAAAGAAAAT-A
52707004 AAAAAGAAAAT-
1 AAAAAGAAAATA
*
52707015 ATAAAGAGAAA-A
1 AAAAAGA-AAATA
*
52707027 AAAAAGAAAAAGA
1 AAAAAG-AAAATA
52707040 AAAAAGAAAA
1 AAAAAGAAAA
52707050 AATAGAGAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 13 0.33
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (12 bp):
AAAAAGAAAATA
Found at i:52707026 original size:18 final size:18
Alignment explanation
Indices: 52706992--52707049 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
52706982 CTTCTATTTC
52706992 AAAA-AAAAATGAAAAAAG
1 AAAAGAAAAA-GAAAAAAG
* *
52707010 AAAATATAAAGAGAAAAA-
1 AAAAGAAAAAGA-AAAAAG
52707028 AAAAGAAAAAGAAAAAAG
1 AAAAGAAAAAGAAAAAAG
52707046 AAAA
1 AAAA
52707050 AATAGAGAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.15
18 20 0.59
19 9 0.26
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAAAG
Found at i:52707047 original size:23 final size:23
Alignment explanation
Indices: 52707003--52707051 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
52706993 AAAAAAAATG
* *
52707003 AAAAAAGAAAATATAAAGAGAAA
1 AAAAAAGAAAATAAAAAAAGAAA
52707026 AAAAAAGAAAA-AGAAAAAAGAAA
1 AAAAAAGAAAATA-AAAAAAGAAA
52707049 AAA
1 AAA
52707052 TAGAGAGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (23 bp):
AAAAAAGAAAATAAAAAAAGAAA
Found at i:52707050 original size:13 final size:12
Alignment explanation
Indices: 52707003--52707051 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
52706993 AAAAAAAATG
52707003 AAAAAAG-AAAA
1 AAAAAAGAAAAA
* * *
52707014 TATAAAGAGAAA
1 AAAAAAGAAAAA
52707026 AAAAAAGAAAAA
1 AAAAAAGAAAAA
52707038 GAAAAAAGAAAAA
1 -AAAAAAGAAAAA
52707051 A
1 A
52707052 TAGAGAGGCC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
11 5 0.17
12 13 0.43
13 12 0.40
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:52708142 original size:43 final size:42
Alignment explanation
Indices: 52708009--52708232 Score: 144
Period size: 43 Copynumber: 5.3 Consensus size: 42
52707999 TGCCTTAATC
* *
52708009 CCCTAAGCAGTAGGATAACAGGTTAAATTTACAGATTTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTT-CAGATCTTATCT
* * * * * * *
52708052 CCCTACGCAGTAGTGG-AGCTGATCGAAGA-CTC-G-CCTTAATC-
1 CCCTAAGCAGTAG-GGTAACAGGT-TAA-ATTTCAGATCTT-ATCT
52708093 CCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTT-CAGATCTTATCT
* * * * *
52708136 CCCTAAGCAGTAGTGG-AGCAGATCGAAGA-CTC-G-CCTTAATC-
1 CCCTAAGCAGTAG-GGTAACAGGT-TAA-ATTTCAGATCTT-ATCT
*
52708177 CCCTAAGCAATAGGGTAACAGGTTAAATTTGCAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTTAAATTT-CAGATCTTATCT
52708220 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
52708233 TGGAGTAGAT
Statistics
Matches: 133, Mismatches: 28, Indels: 40
0.66 0.14 0.20
Matches are distributed among these distances:
39 2 0.02
40 10 0.08
41 40 0.30
42 16 0.12
43 54 0.41
44 9 0.07
45 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (42 bp):
CCCTAAGCAGTAGGGTAACAGGTTAAATTTCAGATCTTATCT
Found at i:52708146 original size:84 final size:84
Alignment explanation
Indices: 52708000--52708273 Score: 469
Period size: 84 Copynumber: 3.3 Consensus size: 84
52707990 AAAATTCAGT
* * * *
52708000 GCCTTAATCCCCTAAGCAGTAGGATAACAGGTTAAATTTACAGATTTTATCTCCCTACGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
52708065 TGGAGCTGATCGAAGACTC
66 TGGAGCTGATCGAAGACTC
52708084 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
*
52708149 TGGAGCAGATCGAAGACTC
66 TGGAGCTGATCGAAGACTC
*
52708168 GCCTTAATCCCCTAAGCAATAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
52708233 TGGAG-TAGATCGAAGACTC
66 TGGAGCT-GATCGAAGACTC
*
52708252 GCTTTAATCCCCTAAGCAGTAG
1 GCCTTAATCCCCTAAGCAGTAG
52708274 TGGAGTAGAT
Statistics
Matches: 180, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
84 180 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (84 bp):
GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAG
TGGAGCTGATCGAAGACTC
Found at i:52708289 original size:125 final size:125
Alignment explanation
Indices: 52708136--52708398 Score: 427
Period size: 125 Copynumber: 2.1 Consensus size: 125
52708126 GATCTTATCT
*
52708136 CCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAATAGGGTAACAGGTT
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAACAATAGGGTAACAGGTT
* * *
52708201 AAATTTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACTCGCTTTAATC
66 AAATTTGCAGAACTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATC
* * * **
52708261 CCCTAAGCAGTAGTGGAGTAGATCGAAGACTCGCCTTAATCTCTTAAACGGTAGGGTAACAGGTT
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAACAATAGGGTAACAGGTT
*
52708326 AAATTTGTAGAACTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATC
66 AAATTTGCAGAACTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATC
*
52708386 CCCTAAGTAGTAG
1 CCCTAAGCAGTAG
52708399 GGTAACAGGT
Statistics
Matches: 127, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 127 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (125 bp):
CCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAACAATAGGGTAACAGGTT
AAATTTGCAGAACTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTCGCCTTAATC
Found at i:52709590 original size:41 final size:41
Alignment explanation
Indices: 52709541--52709678 Score: 113
Period size: 41 Copynumber: 3.3 Consensus size: 41
52709531 GATCTTATCT
52709541 CCCTAAGCAGTAGTGGAGCAGATCGAAGACT-CACCTTAATC
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGCACCTTAATC
* * * * * *
52709582 CCCTAAGCAATAG-GGTAACAGGTC-AAAATTGTGGATCTT-ATC
1 CCCTAAGCAGTAGTGG-AGCAGATCGAAGA---TGCACCTTAATC
* * *
52709624 TCCCTAAGTAGTAGTGGAGCAGATCGAAGATGCGCCTTAACC
1 -CCCTAAGCAGTAGTGGAGCAGATCGAAGATGCACCTTAATC
52709666 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
52709679 GGTAACAGGT
Statistics
Matches: 72, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
40 5 0.07
41 35 0.49
42 6 0.08
43 21 0.29
44 5 0.07
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (41 bp):
CCCTAAGCAGTAGTGGAGCAGATCGAAGATGCACCTTAATC
Found at i:52709619 original size:84 final size:84
Alignment explanation
Indices: 52709461--52709688 Score: 307
Period size: 84 Copynumber: 2.7 Consensus size: 84
52709451 TGGGGTGTTA
* *
52709461 CAGTAGCGGAGCAGATCGACGACGACTCGCCTTAATCCCCTAAGCAA-ATGGGTAACAGGTTAAA
1 CAGTAGTGGAGCAGATCGA--A-GACTCGCCTTAATCCCCTAAGCAATA-GGGTAACAGGTCAAA
*
52709525 TTTACAGATCTTATCTCCCTAAG
62 ATTACAGATCTTATCTCCCTAAG
* *
52709548 CAGTAGTGGAGCAGATCGAAGACTCACCTTAATCCCCTAAGCAATAGGGTAACAGGTCAAAATTG
1 CAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAATAGGGTAACAGGTCAAAATTA
**
52709613 TGGATCTTATCTCCCTAAG
66 CAGATCTTATCTCCCTAAG
* * *
52709632 TAGTAGTGGAGCAGATCGAAGA-TGCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGT
1 CAGTAGTGGAGCAGATCGAAGACT-CGCCTTAATCCCCTAAGCAATAGGGTAACAGGT
52709689 TAAAGTATAG
Statistics
Matches: 128, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
83 1 0.01
84 107 0.84
85 2 0.02
87 18 0.14
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.22
Consensus pattern (84 bp):
CAGTAGTGGAGCAGATCGAAGACTCGCCTTAATCCCCTAAGCAATAGGGTAACAGGTCAAAATTA
CAGATCTTATCTCCCTAAG
Found at i:52709960 original size:87 final size:87
Alignment explanation
Indices: 52709695--52709968 Score: 229
Period size: 87 Copynumber: 3.1 Consensus size: 87
52709685 AGGTTAAAGT
** * * *
52709695 ATAGCAGATCTGGCCTTCAGGTGTTCACGCTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTCTCACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
* * *
52709760 TTACAAGGATCAAATCGAAGAC
66 TTACAGGGAACAGATCGAAGAC
* * ** * *
52709782 ATAGCAGATCTGACTTTTGGATGTTCTCACATCAAAGCAGATCCAAGATAATAGATCTGGCATCT
1 ATAGCAGATCTAACCTTCAGATGTTCTCAC-T-GAAGCAGATCCAAG---AT-GATTTGGCAT-T
* * ** *
52709847 CCATAT-TCGAC-GGAGAGCAGAT-----AC
59 -CTTGTGTTTACAGG-GAACAGATCGAAGAC
* *
52709871 ATAGCAGATCTAACCTTCAGATGTTTTTACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTCTCACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
52709936 TTACAGGGAACAGATCGAAGAC
66 TTACAGGGAACAGATCGAAGAC
52709958 ATAGCAGATCT
1 ATAGCAGATCT
52709969 GACATTCCTG
Statistics
Matches: 142, Mismatches: 29, Indels: 32
0.70 0.14 0.16
Matches are distributed among these distances:
81 3 0.02
82 11 0.08
83 11 0.08
84 2 0.01
87 49 0.35
88 2 0.01
89 39 0.27
92 2 0.01
93 10 0.07
94 10 0.07
95 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (87 bp):
ATAGCAGATCTAACCTTCAGATGTTCTCACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
TTACAGGGAACAGATCGAAGAC
Found at i:52710580 original size:19 final size:19
Alignment explanation
Indices: 52710556--52710616 Score: 104
Period size: 19 Copynumber: 3.1 Consensus size: 19
52710546 ATCTTTAAAT
52710556 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
52710575 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
52710594 ATATGCAATCTTGAAGATATG
1 ATATGCAATCTT--AGATATG
52710615 AT
1 AT
52710617 CTTGTAATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 31 0.77
21 9 0.22
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:52712840 original size:26 final size:26
Alignment explanation
Indices: 52712811--52712861 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
52712801 AATAAAAGAA
*
52712811 AACATTCAATATTTCTA-TTTAATTAT
1 AACATTCAACATTTC-AGTTTAATTAT
52712837 AACATTCAACATTTCAGTTTAATTA
1 AACATTCAACATTTCAGTTTAATTA
52712862 GTATTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (26 bp):
AACATTCAACATTTCAGTTTAATTAT
Found at i:52715296 original size:26 final size:26
Alignment explanation
Indices: 52715267--52715318 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
52715257 AATAAAAGAA
52715267 AACATTCAATATTTCAATTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
*
52715293 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
52715319 CATTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTAG
Found at i:52717464 original size:26 final size:26
Alignment explanation
Indices: 52717435--52717488 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
52717425 AATAAAAGAA
52717435 AACATTCAATATTTCAATTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
* *
52717461 AACATTCAATATTTTAGTTTAATTAG
1 AACATTCAATATTTCAATTTAATTAG
52717487 AA
1 AA
52717489 TTAATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTAG
Found at i:52719582 original size:26 final size:26
Alignment explanation
Indices: 52719553--52719602 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
52719543 AATAAAAGAA
52719553 AACATTCAATATTTCAATTTAATTCT
1 AACATTCAATATTTCAATTTAATTCT
*
52719579 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAATTTAATT
52719603 AGCATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
AACATTCAATATTTCAATTTAATTCT
Found at i:52720418 original size:299 final size:299
Alignment explanation
Indices: 52719863--52720459 Score: 1059
Period size: 299 Copynumber: 2.0 Consensus size: 299
52719853 GACAAGCACA
* *
52719863 CATATTTGTGATGCGTACCATCCTATTTTTCTAATTTTTTGAAGTTGTGTATGCACATGATATGT
1 CATATTCGTGATGCGTACCATCCTATTTTTCTAATTTTTTGAAGTTGTGCATGCACATGATATGT
* *
52719928 TGATGGTTAAAAATTCACATGCATCTCAAAATTGAATGAGCTATACCAGATTCCCCTAACAATGA
66 TAACGGTTAAAAATTCACATGCATCTCAAAATTGAATGAGCTATACCAGATTCCCCTAACAATGA
52719993 TATGTTTATACCACAATGTAGAAATAATTATGCAAAGCATAAAATCTTATAACCTTGTTGTTGTT
131 TATGTTTATACCACAATGTAGAAATAATTATGCAAAGCATAAAATCTTATAACCTTGTTGTTGTT
** * * *
52720058 AAAAAGTTTTTATCACACTTATCATATTTGTAAAATGTAAAATTGCAACTAAATGATTGACATTC
196 AAAAAAATTTTATCACACTTATCATATATGTAAAATGGAAAATGGCAACTAAATGATTGACATTC
* *
52720123 GAAATTAATTCATCAACAATATTTCACGTTCTGATATTT
261 AAAATTAATTCATCAACAATATTTCACGTTCTAATATTT
* * *
52720162 CATATTCGTTATGCGTTCCATCCTATTTTTCTAATTTTTTGAAGTTGTGCATGCACATGTTATGT
1 CATATTCGTGATGCGTACCATCCTATTTTTCTAATTTTTTGAAGTTGTGCATGCACATGATATGT
52720227 TAACGGTTAAAAATTCACATGCATCTCAAAATTGAATGAGCTATACCAGATTCCCCTAACAATGA
66 TAACGGTTAAAAATTCACATGCATCTCAAAATTGAATGAGCTATACCAGATTCCCCTAACAATGA
52720292 TATGTTTATACCACAATGTAGAAATAATTATGCAAAGCATAAAATCTTATAACCTTGTTGTTGTT
131 TATGTTTATACCACAATGTAGAAATAATTATGCAAAGCATAAAATCTTATAACCTTGTTGTTGTT
52720357 AAAAAAATTTTATCACACTTATCATATATGTAAAATGGAAAATGGCAACTAAATGATTGACATTC
196 AAAAAAATTTTATCACACTTATCATATATGTAAAATGGAAAATGGCAACTAAATGATTGACATTC
*
52720422 AAAATTAATTTATCAACAATATTTCACGTTCTAATATT
261 AAAATTAATTCATCAACAATATTTCACGTTCTAATATT
52720460 AAGTCGATGT
Statistics
Matches: 283, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
299 283 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (299 bp):
CATATTCGTGATGCGTACCATCCTATTTTTCTAATTTTTTGAAGTTGTGCATGCACATGATATGT
TAACGGTTAAAAATTCACATGCATCTCAAAATTGAATGAGCTATACCAGATTCCCCTAACAATGA
TATGTTTATACCACAATGTAGAAATAATTATGCAAAGCATAAAATCTTATAACCTTGTTGTTGTT
AAAAAAATTTTATCACACTTATCATATATGTAAAATGGAAAATGGCAACTAAATGATTGACATTC
AAAATTAATTCATCAACAATATTTCACGTTCTAATATTT
Found at i:52735267 original size:9 final size:9
Alignment explanation
Indices: 52735253--52735326 Score: 67
Period size: 9 Copynumber: 7.6 Consensus size: 9
52735243 CCATGATCTT
52735253 GTATGTAAA
1 GTATGTAAA
52735262 GTATGTAAA
1 GTATGTAAA
*
52735271 GTATGTTTTAA
1 GTATG--TAAA
*
52735282 GTATGTTTTAA
1 GTATG--TAAA
52735293 GTATGTAAA
1 GTATGTAAA
*
52735302 GTATGTTTTAA
1 GTATG--TAAA
52735313 GTATGTAAA
1 GTATGTAAA
52735322 GTATG
1 GTATG
52735327 AGGTTACCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
9 30 0.53
11 27 0.47
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (9 bp):
GTATGTAAA
Found at i:52735285 original size:11 final size:11
Alignment explanation
Indices: 52735269--52735318 Score: 77
Period size: 11 Copynumber: 4.7 Consensus size: 11
52735259 AAAGTATGTA
52735269 AAGTATGTTTT
1 AAGTATGTTTT
52735280 AAGTATGTTTT
1 AAGTATGTTTT
*
52735291 AAGTATG--TA
1 AAGTATGTTTT
52735300 AAGTATGTTTT
1 AAGTATGTTTT
52735311 AAGTATGT
1 AAGTATGT
52735319 AAAGTATGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 8 0.23
11 27 0.77
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (11 bp):
AAGTATGTTTT
Found at i:52735285 original size:20 final size:20
Alignment explanation
Indices: 52735253--52735326 Score: 98
Period size: 20 Copynumber: 3.7 Consensus size: 20
52735243 CCATGATCTT
*
52735253 GTATGTAAAGTATG--TAAA
1 GTATGTAAAGTATGTTTTAA
*
52735271 GTATGTTTTAAGTATGTTTTAA
1 GTATG--TAAAGTATGTTTTAA
52735293 GTATGTAAAGTATGTTTTAA
1 GTATGTAAAGTATGTTTTAA
52735313 GTATGTAAAGTATG
1 GTATGTAAAGTATG
52735327 AGGTTACCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
18 5 0.10
20 36 0.73
22 8 0.16
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (20 bp):
GTATGTAAAGTATGTTTTAA
Found at i:52735298 original size:31 final size:31
Alignment explanation
Indices: 52735260--52735318 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
52735250 CTTGTATGTA
52735260 AAGTATGTAAAGTATGTTTTAAGTATGTTTT
1 AAGTATGTAAAGTATGTTTTAAGTATGTTTT
52735291 AAGTATGTAAAGTATGTTTTAAGTATGT
1 AAGTATGTAAAGTATGTTTTAAGTATGT
52735319 AAAGTATGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (31 bp):
AAGTATGTAAAGTATGTTTTAAGTATGTTTT
Found at i:52739550 original size:16 final size:16
Alignment explanation
Indices: 52739526--52739559 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
52739516 TTGGATTGAG
*
52739526 AAAATTAATTAATTAA
1 AAAAATAATTAATTAA
52739542 AAAAATAATTAATTAA
1 AAAAATAATTAATTAA
52739558 AA
1 AA
52739560 TTAATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATAATTAATTAA
Found at i:52754470 original size:43 final size:41
Alignment explanation
Indices: 52754361--52754471 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 41
52754351 TGTTCTCGTT
* *
52754361 TAAGACCAGGTCTGGGACGTTGGCATCGATATGTGATTCGTG
1 TAAGACCA-GTCTGGGACGTTGGCATCGACATGTGATTCATG
*
52754403 TAAGATCCTA-TCTGGGATAG-TGGCATCGACATGTGATTACATG
1 TAAGA-CC-AGTCTGGGA-CGTTGGCATCGACATGTGATT-CATG
*
52754446 TAAGACCACGTTTGGGACGTTGGCAT
1 TAAGACCA-GTCTGGGACGTTGGCAT
52754472 TGTACGATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
41 1 0.02
42 32 0.56
43 23 0.40
44 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (41 bp):
TAAGACCAGTCTGGGACGTTGGCATCGACATGTGATTCATG
Found at i:52756314 original size:40 final size:40
Alignment explanation
Indices: 52756131--52756300 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 40
52756121 TCCTCGTTCA
* * * * * *
52756131 AATGCCTTCGGGACATAGCCCTGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
52756170 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52756210 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
52756250 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
52756290 AAGGCCTTCGG
1 AATGCCTTCGG
52756301 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 33 0.28
40 85 0.72
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:52756337 original size:80 final size:79
Alignment explanation
Indices: 52756167--52756353 Score: 205
Period size: 80 Copynumber: 2.3 Consensus size: 79
52756157 TAGTAACTCA
* * *
52756167 CACAATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCG
1 CACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCG
* *
52756232 GATTTAATAACTCG
66 GATATAATAACTAG
** * **
52756246 CACGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTC
1 CAC-AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACC
* **
52756310 CGGATATATTCGCTTAG
64 CGGATATAATAAC-TAG
* *
52756327 CACAAAGCCTTCGGGACTTAGCCCGGA
1 CACAATGCCTTCGGGACTTAACCCGGA
52756354 CAGCATTCAA
Statistics
Matches: 90, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
79 6 0.07
80 79 0.88
81 5 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
CACAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCG
GATATAATAACTAG
Found at i:52761451 original size:49 final size:49
Alignment explanation
Indices: 52761391--52761518 Score: 141
Period size: 49 Copynumber: 2.6 Consensus size: 49
52761381 ACATTAGAAT
* * * *
52761391 CGATGTCATGTCCCAGAAAGATCTTACACTGACTTTCATATATCGAGGC
1 CGATGCCATGTCCCAGAAAGGTCTTACACTGACTCTCATATATCGAGAC
* * * * *
52761440 CGATGCTATGTCCCA-AACAGGTCTTACACTGGCTCTCATTTATCGATAT
1 CGATGCCATGTCCCAGAA-AGGTCTTACACTGACTCTCATATATCGAGAC
* *
52761489 TGATGCCATGTCCCAGACAGGTCTTACACT
1 CGATGCCATGTCCCAGAAAGGTCTTACACT
52761519 AGCTTGTATA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 2 0.03
49 62 0.95
50 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (49 bp):
CGATGCCATGTCCCAGAAAGGTCTTACACTGACTCTCATATATCGAGAC
Done.