Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 37 of 161
Found at i:11271021 original size:40 final size:39
Alignment explanation
Indices: 11270957--11271089 Score: 108
Period size: 40 Copynumber: 3.4 Consensus size: 39
11270947 TATTGAATCT
* * * * *
11270957 ACTGAAACGTATGCGCTTTTGAGCCATACTTACTGATCCC
1 ACTGAAA-GTATGCTCTATCGAGCCATACCTAATGATCCC
* * * *
11270997 ACTGAAATGTGTG-TACTATCGAGCCTTACCTAATGATTCT
1 ACTGAAA-GTATGCT-CTATCGAGCCATACCTAATGATCCC
* * *
11271037 ACTGAAAGTATGCTTTATCGAGCCATACCTAATGATTCT
1 ACTGAAAGTATGCTCTATCGAGCCATACCTAATGATCCC
*
11271076 ATTGAAAGTA-GCTC
1 ACTGAAAGTATGCTC
11271090 AAACGAGCAA
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
38 3 0.04
39 36 0.47
40 37 0.49
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (39 bp):
ACTGAAAGTATGCTCTATCGAGCCATACCTAATGATCCC
Found at i:11271845 original size:29 final size:28
Alignment explanation
Indices: 11271791--11271888 Score: 81
Period size: 29 Copynumber: 3.4 Consensus size: 28
11271781 CACACGGCCT
* * *
11271791 AGGACTCGGGCTATCACATAGT-TGTGTA
1 AGGACACGGGCTATCACAGACTGTGTG-A
11271819 GAGGACACGGGCTATCACACGACTGTGTGA
1 -AGGACACGGGCTATCACA-GACTGTGTGA
* * *
11271849 AGCACACAGGCTATCACATGACCGTGTGA
1 AGGACACGGGCTATCACA-GACTGTGTGA
* *
11271878 AGCATACGGGC
1 AGGACACGGGC
11271889 ATATGACCAG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
29 51 0.88
30 3 0.05
31 4 0.07
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.19
Consensus pattern (28 bp):
AGGACACGGGCTATCACAGACTGTGTGA
Found at i:11273467 original size:50 final size:50
Alignment explanation
Indices: 11273392--11273491 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
11273382 AGTGTAAGTA
11273392 AAGATTATTTTGGGTCGTAAAAACCCTTCTCCTAATGATTCCTTAATATG
1 AAGATTATTTTGGGTCGTAAAAACCCTTCTCCTAATGATTCCTTAATATG
*
11273442 AAGATTATTTTGGGTCGTAAAAACCCTTCTCCTAGTGATTCCTTAATATG
1 AAGATTATTTTGGGTCGTAAAAACCCTTCTCCTAATGATTCCTTAATATG
11273492 GTCGAATGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (50 bp):
AAGATTATTTTGGGTCGTAAAAACCCTTCTCCTAATGATTCCTTAATATG
Found at i:11277890 original size:50 final size:50
Alignment explanation
Indices: 11277778--11278074 Score: 283
Period size: 50 Copynumber: 5.8 Consensus size: 50
11277768 ATTTGGGTAA
* *
11277778 AGAGATCCCATGTAAAACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
11277834 AGAGGTCCCATGCAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
11277884 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGACACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
11277934 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
11277984 AGAATTCCCATGTAAGACCATATCTGGGATATGACATTGGTA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * * *
11278033 AAACATTCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
11278075 TGTTATTATC
Statistics
Matches: 204, Mismatches: 36, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
48 1 0.00
49 36 0.18
50 124 0.61
53 3 0.01
55 2 0.01
56 38 0.19
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:11279840 original size:50 final size:50
Alignment explanation
Indices: 11279728--11280024 Score: 283
Period size: 50 Copynumber: 5.8 Consensus size: 50
11279718 ATTTGGGTAA
* *
11279728 AGAGATCCCATGTAAAACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
11279784 AGAGGTCCCATGCAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
11279834 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGACACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
11279884 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
11279934 AGAATTCCCATGTAAGACCATATCTGGGATATGACATTGGTA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * * *
11279983 AAACATTCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
11280025 TGTTATTATC
Statistics
Matches: 204, Mismatches: 36, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
48 1 0.00
49 36 0.18
50 124 0.61
53 3 0.01
55 2 0.01
56 38 0.19
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:11283075 original size:51 final size:50
Alignment explanation
Indices: 11282903--11283238 Score: 356
Period size: 51 Copynumber: 6.6 Consensus size: 50
11282893 ATTCGATACG
* *
11282903 CGTAGTAGCCTTCACATAGTACTGCACACGTGATCAAG-TTTTACGGTTCA
1 CGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTT-CGGTTCA
* *
11282953 CGTAGTAGCCTTCACATAGTACTACACACGTGATCAAG-TTTTACGGTTTA
1 CGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTT-CGGTTCA
* *
11283003 CGTAGTAGCCTTCACATAGTACTGCACACGTGACCAAAGCTTTTCGGTACA
1 CGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGGTTCA
* * * * * *
11283054 CATAGTATCCTTCACTTAGTACTACACATGTGACC-ATCATTTATCGATTCA
1 CGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TTT-TCGGTTCA
* * * * *
11283105 CGTAATAGCCTTCACACAGTACTGCACACGTGATCAAAGCTTTTCGGTACA
1 CGTAGTAGCCTTCACATAGTACTACACACGTGA-CCAAGCTTTTCGGTTCA
* * * * * *
11283156 CATAGTATCCTTCACTTAGTACTACACATGTGACC-ATCATTTATCGATTCA
1 CGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TTT-TCGGTTCA
*
11283207 CGTAGTAGCCTTCACACAGTACTACACACGTG
1 CGTAGTAGCCTTCACATAGTACTACACACGTG
11283239 TTCATCGATA
Statistics
Matches: 237, Mismatches: 41, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
49 4 0.02
50 88 0.37
51 135 0.57
52 8 0.03
53 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (50 bp):
CGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTTCGGTTCA
Found at i:11283135 original size:102 final size:102
Alignment explanation
Indices: 11282903--11283238 Score: 498
Period size: 102 Copynumber: 3.3 Consensus size: 102
11282893 ATTCGATACG
* * * *
11282903 CGTAGTAGCCTTCACATAGTACTGCACACGTGATC-AAG-TTTTACGGTTCACGTAGTAGCCTTC
1 CGTAGTAGCCTTCACACAGTACTGCACACGTGATCAAAGCTTTT-CGGTACACATAGTATCCTTC
* * * *** * *
11282966 ACATAGTACTACACACGTGATCAAGTTTTA-CGGTTTA
65 ACTTAGTACTACACATGTGACCATCATTTATCGATTCA
* *
11283003 CGTAGTAGCCTTCACATAGTACTGCACACGTGACCAAAGCTTTTCGGTACACATAGTATCCTTCA
1 CGTAGTAGCCTTCACACAGTACTGCACACGTGATCAAAGCTTTTCGGTACACATAGTATCCTTCA
11283068 CTTAGTACTACACATGTGACCATCATTTATCGATTCA
66 CTTAGTACTACACATGTGACCATCATTTATCGATTCA
*
11283105 CGTAATAGCCTTCACACAGTACTGCACACGTGATCAAAGCTTTTCGGTACACATAGTATCCTTCA
1 CGTAGTAGCCTTCACACAGTACTGCACACGTGATCAAAGCTTTTCGGTACACATAGTATCCTTCA
11283170 CTTAGTACTACACATGTGACCATCATTTATCGATTCA
66 CTTAGTACTACACATGTGACCATCATTTATCGATTCA
*
11283207 CGTAGTAGCCTTCACACAGTACTACACACGTG
1 CGTAGTAGCCTTCACACAGTACTGCACACGTG
11283239 TTCATCGATA
Statistics
Matches: 216, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
100 34 0.16
101 44 0.20
102 138 0.64
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (102 bp):
CGTAGTAGCCTTCACACAGTACTGCACACGTGATCAAAGCTTTTCGGTACACATAGTATCCTTCA
CTTAGTACTACACATGTGACCATCATTTATCGATTCA
Found at i:11283309 original size:69 final size:69
Alignment explanation
Indices: 11283198--11283335 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
11283188 ACCATCATTT
*
11283198 ATCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGTTCATCGATACCTTATTCAAATCT
1 ATCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGTTCATCGATACCTTATTCAAATCT
11283263 TTAC
66 TTAC
11283267 ATCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGTTCATCGATACCTTATTCAAATCT
1 ATCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGTTCATCGATACCTTATTCAAATCT
11283332 TTAC
66 TTAC
11283336 CATTCCGACA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.31
Consensus pattern (69 bp):
ATCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGTTCATCGATACCTTATTCAAATCT
TTAC
Found at i:11293918 original size:11 final size:11
Alignment explanation
Indices: 11293888--11293925 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
11293878 TTATAAACAC
11293888 TTTTATTATCAA
1 TTTTATTAT-AA
11293900 TTTT-TTATAA
1 TTTTATTATAA
*
11293910 TTTTATTATTA
1 TTTTATTATAA
11293921 TTTTA
1 TTTTA
11293926 CTATGTCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 6 0.25
11 14 0.58
12 4 0.17
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTATTATAA
Found at i:11300437 original size:25 final size:24
Alignment explanation
Indices: 11300405--11300453 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
11300395 AATTCACAAC
11300405 TTTAAGATCTTCCAATTTTCTTTA
1 TTTAAGATCTTCCAATTTTCTTTA
11300429 TTTACAGATCTTCCAATTTTCTTTA
1 TTTA-AGATCTTCCAATTTTCTTTA
11300454 AATTTTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.24, C:0.18, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTAAGATCTTCCAATTTTCTTTA
Found at i:11310691 original size:15 final size:15
Alignment explanation
Indices: 11310671--11310699 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11310661 GGTGTCATTC
11310671 GTATACATAGTATTT
1 GTATACATAGTATTT
11310686 GTATACATAGTATT
1 GTATACATAGTATT
11310700 AATAATATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (15 bp):
GTATACATAGTATTT
Found at i:11313807 original size:134 final size:134
Alignment explanation
Indices: 11313567--11313834 Score: 536
Period size: 134 Copynumber: 2.0 Consensus size: 134
11313557 ACAGTTGATG
11313567 AGGTTTATGATTCTTTAACCTCGTATGATAAGATGAAACATCTTGTGGTTAAAATTGACTCTTAG
1 AGGTTTATGATTCTTTAACCTCGTATGATAAGATGAAACATCTTGTGGTTAAAATTGACTCTTAG
11313632 GGATAGGTCTCATTGTTCGTGGAAGACAAGATCAGAATGCTGATGATGATCGTGGAAGGATACAG
66 GGATAGGTCTCATTGTTCGTGGAAGACAAGATCAGAATGCTGATGATGATCGTGGAAGGATACAG
11313697 GATT
131 GATT
11313701 AGGTTTATGATTCTTTAACCTCGTATGATAAGATGAAACATCTTGTGGTTAAAATTGACTCTTAG
1 AGGTTTATGATTCTTTAACCTCGTATGATAAGATGAAACATCTTGTGGTTAAAATTGACTCTTAG
11313766 GGATAGGTCTCATTGTTCGTGGAAGACAAGATCAGAATGCTGATGATGATCGTGGAAGGATACAG
66 GGATAGGTCTCATTGTTCGTGGAAGACAAGATCAGAATGCTGATGATGATCGTGGAAGGATACAG
11313831 GATT
131 GATT
11313835 GGAATCCTCG
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 134 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (134 bp):
AGGTTTATGATTCTTTAACCTCGTATGATAAGATGAAACATCTTGTGGTTAAAATTGACTCTTAG
GGATAGGTCTCATTGTTCGTGGAAGACAAGATCAGAATGCTGATGATGATCGTGGAAGGATACAG
GATT
Found at i:11320341 original size:17 final size:17
Alignment explanation
Indices: 11320319--11320354 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
11320309 TTCTTTCTTG
11320319 CTTCTCTACTTCTGTTC
1 CTTCTCTACTTCTGTTC
11320336 CTTCTCTACTTCTGTTC
1 CTTCTCTACTTCTGTTC
11320353 CT
1 CT
11320355 GTTTATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.06, C:0.36, G:0.06, T:0.53
Consensus pattern (17 bp):
CTTCTCTACTTCTGTTC
Found at i:11320628 original size:15 final size:16
Alignment explanation
Indices: 11320592--11320635 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
11320582 GGACTAGACT
11320592 TTTATTTGTTTTTGTTG
1 TTTATTTGTTTTTG-TG
11320609 TTTATTTGTTTTTG-G
1 TTTATTTGTTTTTGTG
11320624 TTTATTTGTTTT
1 TTTATTTGTTTT
11320636 GTTTTGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 13 0.48
17 14 0.52
ACGTcount: A:0.07, C:0.00, G:0.16, T:0.77
Consensus pattern (16 bp):
TTTATTTGTTTTTGTG
Found at i:11324115 original size:2 final size:2
Alignment explanation
Indices: 11324108--11324143 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11324098 TAGCAGTAAC
11324108 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
11324144 AAATAAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:11340675 original size:41 final size:42
Alignment explanation
Indices: 11340586--11340675 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 42
11340576 ATTTAAAAAC
11340586 ATAAAAACAAATATTAAAACAAGAAACAAATAAAAAATGATA
1 ATAAAAACAAATATTAAAACAAGAAACAAATAAAAAATGATA
* * * * * *
11340628 CT-AAAACAATTCTTAAAACAATACACAAATTAAAAAT-ATA
1 ATAAAAACAAATATTAAAACAAGAAACAAATAAAAAATGATA
11340668 ATAAAAAC
1 ATAAAAAC
11340676 TAGTTATATT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
40 4 0.10
41 35 0.88
42 1 0.03
ACGTcount: A:0.67, C:0.11, G:0.02, T:0.20
Consensus pattern (42 bp):
ATAAAAACAAATATTAAAACAAGAAACAAATAAAAAATGATA
Found at i:11340846 original size:11 final size:10
Alignment explanation
Indices: 11340830--11340912 Score: 67
Period size: 11 Copynumber: 7.5 Consensus size: 10
11340820 AAAGTAGCAC
11340830 CAAAACAACA
1 CAAAACAACA
11340840 TCAAAACAACA
1 -CAAAACAACA
* *
11340851 CCAAACAGCA
1 CAAAACAACA
11340861 TCAAAACAACA
1 -CAAAACAACA
*
11340872 CAAAAAACAGCA
1 C--AAAACAACA
11340884 TCACAAACAACA
1 -CA-AAACAACA
11340896 CTAAAACAACA
1 C-AAAACAACA
11340907 CCAAAA
1 -CAAAA
11340913 ACCTGCAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
10 9 0.15
11 32 0.54
12 17 0.29
13 1 0.02
ACGTcount: A:0.63, C:0.30, G:0.02, T:0.05
Consensus pattern (10 bp):
CAAAACAACA
Found at i:11340862 original size:21 final size:21
Alignment explanation
Indices: 11340827--11340896 Score: 86
Period size: 21 Copynumber: 3.1 Consensus size: 21
11340817 ACAAAAGTAG
*
11340827 CACCAAAACAACATCAAAACAA
1 CACC-AAACAGCATCAAAACAA
11340849 CACCAAACAGCATCAAAACAA
1 CACCAAACAGCATCAAAACAA
*
11340870 CACAAAAAACAGCATCACAAACAA
1 CAC--CAAACAGCATCA-AAACAA
11340894 CAC
1 CAC
11340897 TAAAACAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.44
22 4 0.09
23 11 0.26
24 9 0.21
ACGTcount: A:0.60, C:0.33, G:0.03, T:0.04
Consensus pattern (21 bp):
CACCAAACAGCATCAAAACAA
Found at i:11340911 original size:21 final size:21
Alignment explanation
Indices: 11340830--11340912 Score: 94
Period size: 23 Copynumber: 3.8 Consensus size: 21
11340820 AAAGTAGCAC
11340830 CAAAACAACATCAAAACAACA
1 CAAAACAACATCAAAACAACA
* *
11340851 CCAAACAGCATCAAAACAACA
1 CAAAACAACATCAAAACAACA
*
11340872 CAAAAAACAGCATCACAAACAACA
1 C--AAAACAACATCA-AAACAACA
*
11340896 CTAAAACAACACCAAAA
1 C-AAAACAACATCAAAA
11340913 ACCTGCAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
21 20 0.38
22 3 0.06
23 21 0.40
24 9 0.17
ACGTcount: A:0.63, C:0.30, G:0.02, T:0.05
Consensus pattern (21 bp):
CAAAACAACATCAAAACAACA
Found at i:11352696 original size:23 final size:22
Alignment explanation
Indices: 11352664--11352726 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
11352654 CCCGTCCCGT
*
11352664 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
11352688 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
11352710 TTCTTATTAAAATTAAA
1 TTTTTATTAAAATTAAA
11352727 TGTTATCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 17 0.46
23 15 0.41
24 5 0.14
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:11352720 original size:16 final size:16
Alignment explanation
Indices: 11352699--11352755 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
11352689 TTTTATTAAA
* *
11352699 ATTAAAACTAATTCTT
1 ATTAAAATTAATTGTT
*
11352715 ATTAAAATTAAATGTT
1 ATTAAAATTAATTGTT
*
11352731 ATCAAAATTAATTGTT
1 ATTAAAATTAATTGTT
11352747 ATTAAAATT
1 ATTAAAATT
11352756 GTATCAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:11352921 original size:40 final size:36
Alignment explanation
Indices: 11352870--11352968 Score: 110
Period size: 40 Copynumber: 2.6 Consensus size: 36
11352860 AAATTATATC
11352870 AAATTATTAATTATTAATTGTTACTAACATTTTGTTAGTA
1 AAATTATTAATTATTAATTGTTA-TAA-A--TTGTTAGTA
* * *
11352910 AAATTATTAATTGTGAATTG-TATTAATTGTTAGTA
1 AAATTATTAATTATTAATTGTTATAAATTGTTAGTA
*
11352945 AAATTATCAAATTATTAATTGTTA
1 AAATTAT-TAATTATTAATTGTTA
11352969 ATTGTATTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
35 16 0.31
36 10 0.20
37 3 0.06
38 2 0.04
39 2 0.04
40 18 0.35
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (36 bp):
AAATTATTAATTATTAATTGTTATAAATTGTTAGTA
Found at i:11352978 original size:16 final size:16
Alignment explanation
Indices: 11352914--11352980 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 16
11352904 TTAGTAAAAT
*
11352914 TATTAATTGTGAATTG
1 TATTAATTGTTAATTG
11352930 TATTAATTGTT-A--G
1 TATTAATTGTTAATTG
* * * *
11352943 TA-AAATTATCAAAT-
1 TATTAATTGTTAATTG
11352957 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
11352973 TATTAATT
1 TATTAATT
11352981 CTTATAACAA
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
12 5 0.13
13 4 0.11
14 2 0.05
15 9 0.24
16 18 0.47
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.51
Consensus pattern (16 bp):
TATTAATTGTTAATTG
Found at i:11353047 original size:22 final size:22
Alignment explanation
Indices: 11353022--11353068 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
11353012 AAACTTAAAA
* *
11353022 TAAAACTAAAACTAGTATAT-TT
1 TAAAAATAAAAATA-TATATATT
11353044 TAAAAATAAAAATATATATATT
1 TAAAAATAAAAATATATATATT
11353066 TAA
1 TAA
11353069 TATATTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAAAATAAAAATATATATATT
Found at i:11353848 original size:21 final size:22
Alignment explanation
Indices: 11353805--11353850 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
11353795 AAAATTAAGT
*
11353805 TAGGATGTGTATTTGAATTTTA
1 TAGGATGTGAATTTGAATTTTA
11353827 TAGGAT-TGAATTT-AATTATTA
1 TAGGATGTGAATTTGAATT-TTA
11353848 TAG
1 TAG
11353851 ATCAAGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 12 0.55
22 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (22 bp):
TAGGATGTGAATTTGAATTTTA
Found at i:11356856 original size:40 final size:40
Alignment explanation
Indices: 11356794--11356911 Score: 150
Period size: 40 Copynumber: 3.0 Consensus size: 40
11356784 CGTCAGATAG
* * *
11356794 ACCG-AACACACCAGACAAAAGCTCATAAGAGTTGATCCA
1 ACCGAAACACACCAAACAGAAGCTCATAAGAGCTGATCCA
* *
11356833 ACCGAAATACACCAAACAGAAGCTCATAAGAGCTGGTCCA
1 ACCGAAACACACCAAACAGAAGCTCATAAGAGCTGATCCA
* **
11356873 CCCGAAACATGCC-AACAGAAGCTCATAAGAGCTGATCCA
1 ACCGAAACACACCAAACAGAAGCTCATAAGAGCTGATCCA
11356912 CTCGAATCAT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 29 0.43
40 39 0.57
ACGTcount: A:0.42, C:0.29, G:0.17, T:0.13
Consensus pattern (40 bp):
ACCGAAACACACCAAACAGAAGCTCATAAGAGCTGATCCA
Found at i:11356901 original size:39 final size:39
Alignment explanation
Indices: 11356812--11356932 Score: 143
Period size: 40 Copynumber: 3.1 Consensus size: 39
11356802 CACCAGACAA
* * * **
11356812 AAGCTCATAAGAGTTGATCCAACCGAAATACACCAAACAG
1 AAGCTCATAAGAGCTGATCCACCCGAAACATGCC-AACAG
*
11356852 AAGCTCATAAGAGCTGGTCCACCCGAAACATGCCAACAG
1 AAGCTCATAAGAGCTGATCCACCCGAAACATGCCAACAG
* * *
11356891 AAGCTCATAAGAGCTGATCCACTCGAATCATGTCAAACAG
1 AAGCTCATAAGAGCTGATCCACCCGAAACATG-CCAACAG
11356931 AA
1 AA
11356933 AGTATAACGC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
39 34 0.49
40 36 0.51
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.16
Consensus pattern (39 bp):
AAGCTCATAAGAGCTGATCCACCCGAAACATGCCAACAG
Found at i:11357878 original size:21 final size:19
Alignment explanation
Indices: 11357854--11357901 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
11357844 CCATTATGTT
11357854 TTCTTATATTTTAACCTTTTA
1 TTCTTATATTTTAA--TTTTA
*
11357875 TTCTTTTATTTTAATTTTA
1 TTCTTATATTTTAATTTTA
11357894 TTACTTAT
1 TT-CTTAT
11357902 TTTAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.29
20 4 0.17
21 13 0.54
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (19 bp):
TTCTTATATTTTAATTTTA
Found at i:11358720 original size:20 final size:20
Alignment explanation
Indices: 11358695--11358732 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11358685 GTTTGTACGG
11358695 GATTGCACTTCGGTGCCTCT
1 GATTGCACTTCGGTGCCTCT
*
11358715 GATTGCACTTTGGTGCCT
1 GATTGCACTTCGGTGCCT
11358733 TTGTTAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.26, G:0.26, T:0.37
Consensus pattern (20 bp):
GATTGCACTTCGGTGCCTCT
Found at i:11379693 original size:123 final size:123
Alignment explanation
Indices: 11379347--11379672 Score: 589
Period size: 123 Copynumber: 2.7 Consensus size: 123
11379337 TAATTTCGAG
** * *
11379347 TTGACGTTTCTGATAAAATAGTATAAAATCGCTTCTAGCATGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
11379412 AAATCGCGGCCTCGTCAGTGCACTTTTGCTACAGTAAGTCATGTAAGAAATAATTTTT
66 AAATCGCGGCCTCGTCAGTGCACTTTTGCTACAGTAAGTCATGTAAGAAATAATTTTT
11379470 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
11379535 AAATCGCGGCCTCGTCAGTGCACTTTTGCTACAGTAAGTCATGTAAGAAATAATTTTT
66 AAATCGCGGCCTCGTCAGTGCACTTTTGCTACAGTAAGTCATGTAAGAAATAATTTTT
*
11379593 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTA
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* *
11379658 AAACCGCGCCCTCGT
66 AAATCGCGGCCTCGT
11379673 GGACGCGCTT
Statistics
Matches: 196, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 196 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGGCCTCGTCAGTGCACTTTTGCTACAGTAAGTCATGTAAGAAATAATTTTT
Found at i:11382270 original size:61 final size:61
Alignment explanation
Indices: 11382205--11382388 Score: 151
Period size: 61 Copynumber: 3.1 Consensus size: 61
11382195 CAAATCTAAC
11382205 ATTATGTGAATGTAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAA
1 ATTATGTGAATGTAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAA
* ** * * *
11382266 ATTATGTAAAAT-TATTATT-TGTTAGTACCAATCAAAA---CATT--T--TT--TCAAATCTA-
1 ATTATGT-GAATGTAAAATTAT-TAAGT--CAA--AAAATTGTATTAATGGTTAGTAAAAT-TAT
*
11382319 -AC
59 CAA
11382321 ATTATGTGAATGTAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAA
1 ATTATGTGAATGTAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAA
11382382 ATTATGT
1 ATTATGT
11382389 AAAATTATTA
Statistics
Matches: 89, Mismatches: 14, Indels: 40
0.62 0.10 0.28
Matches are distributed among these distances:
51 4 0.04
53 3 0.03
54 6 0.07
55 17 0.19
56 7 0.08
57 2 0.02
58 4 0.04
59 2 0.02
60 7 0.08
61 24 0.27
62 6 0.07
63 3 0.03
65 4 0.04
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (61 bp):
ATTATGTGAATGTAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAA
Found at i:11382275 original size:55 final size:55
Alignment explanation
Indices: 11382214--11382398 Score: 144
Period size: 55 Copynumber: 3.3 Consensus size: 55
11382204 CATTATGTGA
11382214 ATGTAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATT
1 ATGTAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATT
* * ** * ** ** * * *
11382269 ATGTAAAATTATTATTTGTTAGTACCAA-T-CAAAACAT--TTTTTCAAATCTAACATTATGT
1 ATGTAAAATTATTA--AGTCA--AAAAATTGTATTA-ATGGTTAGTAAAAT-TATCA-AAT-T
11382328 GAATGTAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATT
1 --ATGTAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATT
11382385 ATGTAAAATTATTA
1 ATGTAAAATTATTA
11382399 TTTGTTAGTA
Statistics
Matches: 92, Mismatches: 24, Indels: 28
0.64 0.17 0.19
Matches are distributed among these distances:
55 28 0.30
56 7 0.08
57 13 0.14
58 10 0.11
59 13 0.14
60 7 0.08
61 14 0.15
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (55 bp):
ATGTAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATT
Found at i:11382315 original size:116 final size:116
Alignment explanation
Indices: 11382107--11382440 Score: 623
Period size: 116 Copynumber: 2.9 Consensus size: 116
11382097 TGATAAATTG
* *
11382107 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
*
11382172 TAGTACCAGTCAAAATATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
11382223 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
* *
11382288 TAGTACCAATCAAAACATTTTTTCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
11382339 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
11382404 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTA
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTA
11382441 CGTTAAGGTT
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 211 1.00
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.39
Consensus pattern (116 bp):
TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
Found at i:11382477 original size:22 final size:20
Alignment explanation
Indices: 11382442--11382481 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
11382432 CTAACATTAC
11382442 GTTAAGGTTAGGGTTTTTGA
1 GTTAAGGTTAGGGTTTTTGA
11382462 GTTAAGGGTTTAGGGTTTTT
1 GTTAA-GG-TTAGGGTTTTT
11382482 AATTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.47
Consensus pattern (20 bp):
GTTAAGGTTAGGGTTTTTGA
Found at i:11382555 original size:52 final size:52
Alignment explanation
Indices: 11382466--11383069 Score: 621
Period size: 52 Copynumber: 11.1 Consensus size: 52
11382456 TTTTGAGTTA
*
11382466 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTAAGTT
1 AGGG-TTAGGGTTTTTAATT-AA--A--TTAG-GTTAGGGTTTTTAATTAAATTAGGTT
* *
11382525 AGGGTTTGAGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT
* * * *
11382577 AAGGTTAGGGTTTTTAAGTT-AA-GAGTTTAGAGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT
*
11382628 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGTTT
1 AGGGTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAATTAGGTT
* *
11382686 AAGGTTAGGGTTTTTAAGTT-AA--GGGTTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAA-TTAAATTAGG-TTAGGGTTTTTAATTAAATTAGGTT
* *
11382737 AGAGTTAGGGTTTTTAATTAAATTACGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT
11382789 AGGGTTTTTAATTAGGGTTTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGG-------TTAGGG--TTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT
* *
11382850 AAGGTTAGGGTTTTTAAGTT-AA--GGGTTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAA-TTAAATTAGG-TTAGGGTTTTTAATTAAATTAGGTT
* *
11382901 AGAGTTAGGGTTTTTAATTAAATTACGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT
* *
11382953 AGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGGTTAGGGTTTTTAATTAAATTAAGTT
1 AGGGTTAGGGTTTTTAATTAA---A--TTA--GGTTAGGGTTTTTAATTAAATTAGGTT
* * * ****
11383012 AGGGTTAGGGTTTTTAATTAATTTAGGTTACGATTTAGGGTTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT
11383064 AGGGTT
1 AGGGTT
11383070 TTTATTACAT
Statistics
Matches: 468, Mismatches: 42, Indels: 77
0.80 0.07 0.13
Matches are distributed among these distances:
50 10 0.02
51 125 0.27
52 149 0.32
53 10 0.02
54 10 0.02
55 3 0.01
57 7 0.01
58 53 0.11
59 57 0.12
61 44 0.09
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (52 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT
Found at i:11382597 original size:132 final size:132
Alignment explanation
Indices: 11382437--11383003 Score: 604
Period size: 132 Copynumber: 4.2 Consensus size: 132
11382427 CAAATCTAAC
* *
11382437 ATTACGTTAAGGTTAGGGTTTTTGAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTT
1 ATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTT
* *
11382502 AGGGTTTTTAATTAAATTAAGTTAGGGTTTGAGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT
66 AGGGTTTTTAATTAAATTAGGTTAGGGTTTGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT
11382567 AA
131 AA
* * *
11382569 ATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGAGTTTAGAGTTTTTAATTAAATTAGGTTAGGGTT
1 ATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTT
* * * ****
11382634 AGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGTTTAAGG-TTAGGGTT
66 AGGGTTTTTAATTAAATTAGGTTAGGGTTTGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT
11382698 --
131 AA
* * *
11382698 TTTAAGTTAAGGGTTTAGGGTTTTTAA-TTAAATTAGGTTAGAGTTAGGGTTTTTAATT-AA--A
1 ATTAGGTTAA-GG-TTAGGGTTTTTAAGTT--A--AGG---G-TTTAGGGTTTTTAATTAAATTA
*
11382759 --TTA-CGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAGGGTTTTTTTAATTAAAT
56 GGTTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGG----T--TT-GGG--TTTTTAATTAAAT
11382821 TAGGTTAGGGTTTTTAATTAA
112 TAGGTTAGGGTTTTTAATTAA
11382842 ATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTT
1 ATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTT
* * ** *
11382907 AGGGTTTTTAATTAAATTACGTTAGGGTTT---TTAATTAAATTAGGTTAGGGTTAGGGTTTGTA
66 AGGGTTTTTAATTAAATTAGGTTAGGGTTTGGGTT--TTTAATTAAATTA-GGTTAGGGTTTTTA
11382969 ATTAA
128 ATTAA
* *
11382974 TTTAGGTTAGGGGTTAGGGTTTTTAA-TTAA
1 ATTAGGTTA-AGGTTAGGGTTTTTAAGTTAA
11383004 ATTAAGTTAG
Statistics
Matches: 364, Mismatches: 38, Indels: 66
0.78 0.08 0.14
Matches are distributed among these distances:
129 10 0.03
130 4 0.01
131 27 0.07
132 172 0.47
133 18 0.05
134 2 0.01
135 18 0.05
136 4 0.01
137 4 0.01
138 16 0.04
139 6 0.02
140 3 0.01
141 51 0.14
142 17 0.05
143 4 0.01
144 8 0.02
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.46
Consensus pattern (132 bp):
ATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTT
AGGGTTTTTAATTAAATTAGGTTAGGGTTTGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT
AA
Found at i:11382611 original size:22 final size:20
Alignment explanation
Indices: 11382574--11382619 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
11382564 ATTAAATTAG
*
11382574 GTTAAGGTTAGGGTTTTTAA
1 GTTAAGGTTAGAGTTTTTAA
11382594 GTTAAGAGTTTAGAGTTTTTAA
1 GTTAAG-G-TTAGAGTTTTTAA
11382616 -TTAA
1 GTTAA
11382620 ATTAGGTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 5 0.22
22 12 0.52
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (20 bp):
GTTAAGGTTAGAGTTTTTAA
Found at i:11382669 original size:80 final size:79
Alignment explanation
Indices: 11382552--11383004 Score: 385
Period size: 80 Copynumber: 5.6 Consensus size: 79
11382542 TTAAATTAGG
*
11382552 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAAGAGTTTAGAGTTTTTAAT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAA-TTAA-AGTTTAGAGTTTTTAAT
11382617 TAAATTAGGTTAGGG-
64 TAAATTAGGTTAGGGT
* ****
11382632 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGTTTA-AGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT-AA--AGTTTAGAGTTTTTAA
* *
11382696 TT--TTTAAGTTAAGGGT
63 TTAAATTAGGTT-AGGGT
* * *
11382712 TTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTACGTTAGGGTTTTTAA
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAGT---TTAGAGTTTTTAA
11382777 TTAAATTAGGTTAGGGTTTTT
63 TTAAATTAGGTTAGGG----T
** *
11382798 AATTAGGGTTTTT--TT-AATTAAATTA-GGTTAGGGTTTTTAATTAAA--TTAG-GTTAAGGTT
1 --TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAGTTTAGAGTT---TTT
* * *
11382856 AGGGTT--TTTAAGTTAAGGGT
61 A--ATTAAATTAGGTT-AGGGT
* * *
11382876 TTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTACGTTAGGGTTTTTAA
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAGT---TTAGAGTTTTTAA
11382941 TTAAATTAGGTTAGGG-
63 TTAAATTAGGTTAGGGT
* *
11382957 TTAGGGTTTGTAATTAATTTAGGTTAGGGGTTAGGGTTTTTAATTAAA
1 TTAGGGTTTTTAATTAAATTAGGTTA-GGGTTAGGGTTTTTAATTAAA
11383005 TTAAGTTAGG
Statistics
Matches: 302, Mismatches: 36, Indels: 68
0.74 0.09 0.17
Matches are distributed among these distances:
76 11 0.04
77 2 0.01
78 12 0.04
79 20 0.07
80 114 0.38
81 46 0.15
82 32 0.11
83 17 0.06
84 19 0.06
85 12 0.04
86 6 0.02
88 11 0.04
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (79 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAGTTTAGAGTTTTTAATTA
AATTAGGTTAGGGT
Found at i:11382691 original size:35 final size:29
Alignment explanation
Indices: 11382466--11383041 Score: 378
Period size: 29 Copynumber: 21.0 Consensus size: 29
11382456 TTTTGAGTTA
11382466 AGGGTTTAGGGTTTTTAATTAAATTAGGTT
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTT
* *
11382496 AGAGTTAGGGTTTTTAATTAAATTAAGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
11382525 AGGGTTTGAGTTTTTAATT-AA--A--TT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
11382549 A-GGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
11382577 AAGGTTAGGGTTTTTAAGTT--A--A-G--
1 AGGGTTAGGGTTTTTAA-TTAAATTAGGTT
* *
11382600 A-GTTTAGAGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
11382628 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
11382657 AGGGTTAGGGTTTTTAATTAAATTAGTTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
11382686 AAGGTTAGGGTTTTTAAGTT-AA--GGGTTT
1 AGGGTTAGGGTTTTTAA-TTAAATTAGG-TT
*
11382714 AGGGTT----TTTAATTAAATT--A-G--GTT
1 AGGGTTAGGGTTT--TT-AATTAAATTAGGTT
*
11382737 AGAGTTAGGGTTTTTAATT-AA--A--TT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
11382761 A-CGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
**
11382789 AGGGTTTTTAATTAGGGTTTTT--TT-AATTAAATT
1 AGGG-------TTAGGGTTTTTAATTAAATTAGGTT
11382822 A-GGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
11382850 AAGGTTAGGGTTTTTAAGTT-AA--GGGTTT
1 AGGGTTAGGGTTTTTAA-TTAAATTAGG-TT
*
11382878 AGGGTT----TTTAATTAAATT--A-G--GTT
1 AGGGTTAGGGTTT--TT-AATTAAATTAGGTT
*
11382901 AGAGTTAGGGTTTTTAATT-AA--A--TT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
11382925 A-CGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
11382953 AGGGTTAGGGTTTGTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
11382982 AGGGGTTAGGGTTTTTAATTAAATTAAGTT
1 A-GGGTTAGGGTTTTTAATTAAATTAGGTT
*
11383012 AGGGTTAGGGTTTTTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
11383041 A
1 A
11383042 CGATTTAGGG
Statistics
Matches: 448, Mismatches: 35, Indels: 127
0.73 0.06 0.21
Matches are distributed among these distances:
21 2 0.00
22 13 0.03
23 63 0.14
24 31 0.07
25 21 0.05
26 14 0.03
27 15 0.03
28 35 0.08
29 196 0.44
30 35 0.08
32 2 0.00
33 8 0.02
34 2 0.00
36 11 0.02
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.46
Consensus pattern (29 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTT
Found at i:11382744 original size:29 final size:29
Alignment explanation
Indices: 11382712--11382790 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 29
11382702 AGTTAAGGGT
11382712 TTAGGGTTTTTAATTAAATTAGGTTAGAG
1 TTAGGGTTTTTAATTAAATTAGGTTAGAG
*
11382741 TTAGGGTTTTTAATT-AA--A--TTA-CG
1 TTAGGGTTTTTAATTAAATTAGGTTAGAG
11382764 TTAGGGTTTTTAATTAAATTAGGTTAG
1 TTAGGGTTTTTAATTAAATTAGGTTAG
11382791 GGTTTTTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
23 16 0.37
24 5 0.12
26 2 0.05
28 5 0.12
29 15 0.35
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.47
Consensus pattern (29 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGAG
Found at i:11382785 original size:18 final size:21
Alignment explanation
Indices: 11382741--11382802 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 21
11382731 TAGGTTAGAG
11382741 TTAGGGTTTTTAATTAAATTAC
1 TTAGGGTTTTTAATTAAA-TAC
*
11382763 GTTAGGGTTTTTAATTAAATTAGG
1 -TTAGGGTTTTTAATTAAA-TA-C
11382787 TTAGGGTTTTTAATTA
1 TTAGGGTTTTTAATTA
11382803 GGGTTTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.50
Consensus pattern (21 bp):
TTAGGGTTTTTAATTAAATAC
Found at i:11382882 original size:22 final size:20
Alignment explanation
Indices: 11382847--11382892 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
11382837 ATTAAATTAG
11382847 GTTAAGGTTAGGGTTTTTAA
1 GTTAAGGTTAGGGTTTTTAA
11382867 GTTAAGGGTTTAGGGTTTTTAA
1 GTTAA-GG-TTAGGGTTTTTAA
11382889 -TTAA
1 GTTAA
11382893 ATTAGGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 5 0.21
21 6 0.25
22 13 0.54
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (20 bp):
GTTAAGGTTAGGGTTTTTAA
Found at i:11382950 original size:18 final size:21
Alignment explanation
Indices: 11382905--11382946 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
11382895 TAGGTTAGAG
11382905 TTAGGGTTTTTAATTAAATTAC
1 TTAGGGTTTTTAATTAAA-TAC
11382927 GTTAGGGTTTTTAATTAAAT
1 -TTAGGGTTTTTAATTAAAT
11382947 TAGGTTAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (21 bp):
TTAGGGTTTTTAATTAAATAC
Found at i:11383097 original size:25 final size:25
Alignment explanation
Indices: 11383069--11383180 Score: 105
Period size: 25 Copynumber: 4.7 Consensus size: 25
11383059 AGGTTAGGGT
11383069 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
11383094 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * * *
11383117 --AAATAAC-TC-GA-AAACTTTTTA
1 TTTTATTACATCAAATAAAC-TTCTA
11383138 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
11383163 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
11383181 TATCAAAATA
Statistics
Matches: 67, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
19 3 0.04
20 3 0.04
21 6 0.09
23 6 0.09
24 6 0.09
25 39 0.58
26 4 0.06
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:11383174 original size:69 final size:69
Alignment explanation
Indices: 11383069--11383223 Score: 253
Period size: 69 Copynumber: 2.3 Consensus size: 69
11383059 AGGTTAGGGT
11383069 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC-TCGAAAACT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTTC-AAAA-T
11383133 TTT-TA
64 TTTCTA
11383138 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTTCAAAATTT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTTCAAAATTT
11383203 TCTA
66 TCTA
* *
11383207 TTTT-GTACATAAAATAA
1 TTTTATTACATCAAATAA
11383224 TATCAAAATA
Statistics
Matches: 82, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
68 15 0.18
69 65 0.79
70 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (69 bp):
TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTTCAAAATTT
TCTA
Found at i:11383222 original size:43 final size:42
Alignment explanation
Indices: 11383158--11383241 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 42
11383148 TCAAATAAAC
* *
11383158 TTCTATTTTATTACATCAAATAATATCAAAATAACTTCAAAATT
1 TTCTATTTTAGTACATAAAATAATATCAAAAT-A-TTCAAAATT
11383202 TTCTATTTT-GTACATAAAATAATATCAAAATATTCAAAAT
1 TTCTATTTTAGTACATAAAATAATATCAAAATATTCAAAAT
11383242 ATTTGTACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 8 0.21
42 1 0.03
43 20 0.53
44 9 0.24
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.40
Consensus pattern (42 bp):
TTCTATTTTAGTACATAAAATAATATCAAAATATTCAAAATT
Found at i:11385888 original size:46 final size:46
Alignment explanation
Indices: 11385827--11385997 Score: 270
Period size: 46 Copynumber: 3.6 Consensus size: 46
11385817 TTTGAGTACT
11385827 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
11385873 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTA
11385919 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
11385971 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
11385998 GCTACACTTA
Statistics
Matches: 116, Mismatches: 3, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
46 72 0.62
52 44 0.38
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:11385953 original size:52 final size:52
Alignment explanation
Indices: 11385879--11385997 Score: 193
Period size: 52 Copynumber: 2.2 Consensus size: 52
11385869 CTTATCTGAT
*
11385879 CAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
*
11385932 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
*
11385984 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
11385998 GCTACACTTA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
52 44 0.71
53 18 0.29
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
Found at i:11386007 original size:37 final size:37
Alignment explanation
Indices: 11385960--11386069 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
11385950 TGATAGCTTC
*
11385960 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
11385997 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
11386034 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
11386069 G
1 G
11386070 ATCATACGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:11387128 original size:72 final size:72
Alignment explanation
Indices: 11387011--11387151 Score: 212
Period size: 72 Copynumber: 2.0 Consensus size: 72
11387001 GTCTGGTGCA
* * **
11387011 GCTCCACGGTTGCGTAGTTGACCAACACGACTTTCACGTGCCAAGC-TTGTGGATTTTGTAAAAA
1 GCTCCACGGTTGCATAGTTGACCAACACCACTTTCACGTGCCAAGCGTT-CAGATTTTGTAAAAA
11387075 CTCTTAGG
65 CTCTTAGG
* *
11387083 GCTCCACGGTTGCATAGTTGATCAACACCACTTTCGCGTGCCAAGCGTTCAGATTTTGTAAAAAC
1 GCTCCACGGTTGCATAGTTGACCAACACCACTTTCACGTGCCAAGCGTTCAGATTTTGTAAAAAC
11387148 TCTT
66 TCTT
11387152 TCGGGATTAC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
72 60 0.97
73 2 0.03
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (72 bp):
GCTCCACGGTTGCATAGTTGACCAACACCACTTTCACGTGCCAAGCGTTCAGATTTTGTAAAAAC
TCTTAGG
Found at i:11387247 original size:7 final size:7
Alignment explanation
Indices: 11387237--11387261 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11387227 TTATATACAT
11387237 AATACTA
1 AATACTA
11387244 AATACTA
1 AATACTA
11387251 AATACTA
1 AATACTA
11387258 AATA
1 AATA
11387262 TCAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:11387818 original size:265 final size:263
Alignment explanation
Indices: 11387334--11387859 Score: 878
Period size: 265 Copynumber: 2.0 Consensus size: 263
11387324 CGTTGGTCCA
* *
11387334 ATAGAAGCCGTATATCTTCAAGAGAGGTCGGTAATCGACGATAACTTGCCGGATGGTTCCACCTA
1 ATAGAAGCCGTATATCTTCAAGACAGGACGGTAATCGACGATAACTTGCCGGATGGTTCCACCTA
11387399 ATTAAATAAATTTTTAGCATACTTTTATTCTTACAAAATCTACATAATAATTCTAAAATGTAATA
66 ATTAAATAAATTTTTAGCATACTTTTATTCTTACAAAATCTACATAATAATTCTAAAATGTAATA
* *
11387464 TAAAATTTACCTCGTTGCGAGTGGGAATGTTTATGGGTGGGTCACTCGAGGACGTAGAAATGGAA
131 TAAAATTTACCTCGTTACGAGTGGGAATGTATATGGGTGGGTCACTCGAGGACGTAGAAATGGAA
*
11387529 AGCGAAACTGTGCCCATGATTGCAGTAGTAACAGGCAACCTCCGATGGTTGCTCTCCTCGGTCGC
196 AGCGAAACCGTGCCCATGATTGCAGTAGTAACAGGCAACCTCCGATGGTTGCTCTCCTCGGTCGC
11387594 GAC
261 GAC
*
11387597 ATAGAAGCCGTATATCTTCAAGTTCA-GACGGTAATCGA-GCATAACTTGCCGGATGGTTCCACC
1 ATAGAAGCCGTATATCTTCAAG-ACAGGACGGTAATCGACG-ATAACTTGCCGGATGGTTCCACC
* *
11387660 TAATTAAATAAATTTTTAGCATACTTTTATTTTTA-AAAATCTACATAATAATTGTAAAATGTAA
64 TAATTAAATAAATTTTTAGCATACTTTTATTCTTACAAAATCTACATAATAATTCTAAAATGT-A
* *
11387724 TATAATAAAATTTACCTCGTTATGAGTGGGAATGTATATGGGTGGTTCACTCGAGGACGTAGAAA
128 -AT-ATAAAATTTACCTCGTTACGAGTGGGAATGTATATGGGTGGGTCACTCGAGGACGTAGAAA
* *
11387789 TGGAAAGCGAAACCGTGCCCATGATTGCAGTAGTGACAGGCAACCTCCGATGTTTGCTCTCCTCG
191 TGGAAAGCGAAACCGTGCCCATGATTGCAGTAGTAACAGGCAACCTCCGATGGTTGCTCTCCTCG
11387854 GTCGCG
256 GTCGCG
11387860 TCGCCCCACA
Statistics
Matches: 246, Mismatches: 12, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
262 27 0.11
263 91 0.37
264 3 0.01
265 125 0.51
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (263 bp):
ATAGAAGCCGTATATCTTCAAGACAGGACGGTAATCGACGATAACTTGCCGGATGGTTCCACCTA
ATTAAATAAATTTTTAGCATACTTTTATTCTTACAAAATCTACATAATAATTCTAAAATGTAATA
TAAAATTTACCTCGTTACGAGTGGGAATGTATATGGGTGGGTCACTCGAGGACGTAGAAATGGAA
AGCGAAACCGTGCCCATGATTGCAGTAGTAACAGGCAACCTCCGATGGTTGCTCTCCTCGGTCGC
GAC
Found at i:11388735 original size:22 final size:22
Alignment explanation
Indices: 11388710--11388762 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
11388700 TATGGATTTA
11388710 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
11388732 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
11388754 AGAGGAATT
1 AGA-GAATT
11388763 GAGAGGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 25 0.83
23 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:11388779 original size:12 final size:11
Alignment explanation
Indices: 11388723--11388779 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
11388713 GAATTTTGGA
11388723 AGGAAATTGAG
1 AGGAAATTGAG
*
11388734 A-GAATTTTG-G
1 AGGAA-ATTGAG
11388744 AAGGAAATTGAG
1 -AGGAAATTGAG
11388756 AGG-AATTGAG
1 AGGAAATTGAG
11388766 AGGAAATATGAG
1 AGGAAAT-TGAG
11388778 AG
1 AG
11388780 AGGATTTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 14 0.37
11 14 0.37
12 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:11390681 original size:26 final size:26
Alignment explanation
Indices: 11390645--11390720 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
11390635 ATATATTTTC
*
11390645 TCAAAATTTTACCAGGGGTAAAATTA
1 TCAAAATTTTACCAGGGGTAAAATCA
* * *
11390671 TCAAAATTTTATCAAGTGTAAAATCA
1 TCAAAATTTTACCAGGGGTAAAATCA
* **
11390697 TCAAAATTTTGCTGGGGGTAAAAT
1 TCAAAATTTTACCAGGGGTAAAAT
11390721 AGGGATGAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTACCAGGGGTAAAATCA
Found at i:11392857 original size:24 final size:24
Alignment explanation
Indices: 11392830--11392892 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
11392820 CAGCTCAAAA
*
11392830 GAGCGTCCCATTATTAGCTCTCAT
1 GAGCATCCCATTATTAGCTCTCAT
* * *
11392854 GAGCATCCTAATATTTGGCTCTCAT
1 GAGCATCCCATTA-TTAGCTCTCAT
* *
11392879 GAGCTTCCCGTTAT
1 GAGCATCCCATTAT
11392893 ATGGTTCTTG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 11 0.37
25 19 0.63
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (24 bp):
GAGCATCCCATTATTAGCTCTCAT
Found at i:11393013 original size:25 final size:24
Alignment explanation
Indices: 11392985--11393075 Score: 78
Period size: 25 Copynumber: 3.5 Consensus size: 24
11392975 CAACTCTTTG
*
11392985 GAGCGTCCTGATATAAGGCTCTTCT
1 GAGCTTCC-GATATAAGGCTCTTCT
11393010 GAGCTTCCCGAT-TAAAGGCTCTTTCAT
1 GAGCTT-CCGATAT-AAGGCTC-TTC-T
*
11393037 GAGCTTCCGA-ATTAATGGCTCTTCG
1 GAGCTTCCGATA-TAA-GGCTCTTCT
11393062 GAGCTTCCAGATAT
1 GAGCTTCC-GATAT
11393076 TGGCTCGCTT
Statistics
Matches: 55, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
24 1 0.02
25 23 0.42
26 17 0.31
27 14 0.25
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (24 bp):
GAGCTTCCGATATAAGGCTCTTCT
Found at i:11393044 original size:27 final size:26
Alignment explanation
Indices: 11392999--11393069 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 26
11392989 GTCCTGATAT
11392999 AAGGCTC-TTCTGAGCTTCCCG-ATTA
1 AAGGCTCTTTCTGAGCTT-CCGAATTA
11393024 AAGGCTCTTTCATGAGCTTCCGAATTA
1 AAGGCTCTTTC-TGAGCTTCCGAATTA
* *
11393051 ATGGCTC-TTCGGAGCTTCC
1 AAGGCTCTTTCTGAGCTTCC
11393070 AGATATTGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 15 0.37
26 9 0.22
27 17 0.41
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (26 bp):
AAGGCTCTTTCTGAGCTTCCGAATTA
Found at i:11399493 original size:122 final size:121
Alignment explanation
Indices: 11399270--11399502 Score: 261
Period size: 122 Copynumber: 1.9 Consensus size: 121
11399260 GATTCCCTCA
* * * *
11399270 AAATAACACTTCTTGCTTAGTAAAATAAATGGGCTTTTTATAAATTCACAATTGAGTTGGGACTC
1 AAATAACACTTCTTGCTTAGTAAAATAAATGGGCTTTTTATAAATTCACAACTGAGCTGGAACCC
* * ** ** *
11399335 AATTAATGGATGACATCAACTTAGTCAAAAGGATTATATATAGTATAGATACTCTAG
66 AATTAATGAATGACACCAACACAGTCAAAAACATTATA-ATAATATAGATACTCTAG
* * * *
11399392 AAATAATACTTGTTGCTTTGTAAAATAAATGTG-TTTTTAGTAAATTCACAACTGAGCTGGAACC
1 AAATAACACTTCTTGCTTAGTAAAATAAATGGGCTTTTTA-TAAATTCACAACTGAGCTGGAACC
* * * * *
11399456 CAGTTGATGAATGGCACCAACACATTTAAAAACATTATAATAATATA
65 CAATTAATGAATGACACCAACACAGTCAAAAACATTATAATAATATA
11399503 AATATAAACT
Statistics
Matches: 90, Mismatches: 20, Indels: 3
0.80 0.18 0.03
Matches are distributed among these distances:
121 13 0.14
122 77 0.86
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (121 bp):
AAATAACACTTCTTGCTTAGTAAAATAAATGGGCTTTTTATAAATTCACAACTGAGCTGGAACCC
AATTAATGAATGACACCAACACAGTCAAAAACATTATAATAATATAGATACTCTAG
Found at i:11400657 original size:122 final size:122
Alignment explanation
Indices: 11400435--11400658 Score: 260
Period size: 122 Copynumber: 1.8 Consensus size: 122
11400425 CTACTGCTAC
* * * *
11400435 CTTGAGGACTTCTACCGCAACAAGTCAAAACAGTAGCCAAGGTTTAGCCTCTCCCACATTTCTAC
1 CTTGAGGACTTCTACCGCAACAAGTCAAAACAGTAGCCAAAGTTCAGCATCCCCCACATTTCTAC
** *
11400500 CAAAACTCTGATGGCTTCTATTGATACAAGTTGAAACTACTAGAATTCTACTTATAT
66 CAAAACTCTGATGGCTTCTATCAATACAAGATGAAACTACTAGAATTCTACTTATAT
* * * * *
11400557 CTTGAGGACTTCTATCGTAACAAGTTAAGATAGTAGCCAAAGTTCAGCATCCCCTGCAC-TTT-T
1 CTTGAGGACTTCTACCGCAACAAGTCAAAACAGTAGCCAAAGTTCAGCATCCCC--CACATTTCT
11400620 A-CAAATACTCTGATTGG-TTCTATCAATACCAA-ATGAAAC
64 ACCAAA-ACTCTGA-TGGCTTCTATCAATA-CAAGATGAAAC
11400659 CCTCAGCGTT
Statistics
Matches: 85, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
121 4 0.05
122 69 0.81
123 9 0.11
124 3 0.04
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (122 bp):
CTTGAGGACTTCTACCGCAACAAGTCAAAACAGTAGCCAAAGTTCAGCATCCCCCACATTTCTAC
CAAAACTCTGATGGCTTCTATCAATACAAGATGAAACTACTAGAATTCTACTTATAT
Found at i:11409794 original size:108 final size:107
Alignment explanation
Indices: 11409646--11409886 Score: 269
Period size: 108 Copynumber: 2.3 Consensus size: 107
11409636 AACCATATAA
* ***
11409646 TTTT-AATAATTTT-TTATTTA-AATTCCAAAATGAATATAGACAAATGGGTGTCCAAAT-TCAA
1 TTTTAAATAATTTTATT-TTTATAATTTCAAAATGAATATAGACAAACAAGTGTCC-AATCTCAA
* *
11409707 ATGAACTTAAACAACCATTTGTCCT-GTTAATCCG-TATACTTATT
64 ATGAACTTAAACAACCATTTAT-CTAGTTAAT-CGTTATACTCATT
* *
11409751 TTTTAAATAATTTTGATTTTTATAATTTCAAAATGAATCTAGACAAACAAGTGTTCAATCTCAAA
1 TTTTAAATAATTTT-ATTTTTATAATTTCAAAATGAATATAGACAAACAAGTGTCCAATCTCAAA
* *
11409816 TGAACTTAAACAACTATTTATCTAGTTAATTGTTATACTCATT
65 TGAACTTAAACAACCATTTATCTAGTTAATCGTTATACTCATT
* * *
11409859 TTTAAAATAATATTAATTTTTTTAATTT
1 TTTTAAATAAT-TTTATTTTTATAATTT
11409887 GTTTCTAACA
Statistics
Matches: 115, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
105 4 0.03
106 9 0.08
107 10 0.09
108 90 0.78
109 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (107 bp):
TTTTAAATAATTTTATTTTTATAATTTCAAAATGAATATAGACAAACAAGTGTCCAATCTCAAAT
GAACTTAAACAACCATTTATCTAGTTAATCGTTATACTCATT
Found at i:11412915 original size:42 final size:41
Alignment explanation
Indices: 11412843--11412928 Score: 145
Period size: 42 Copynumber: 2.1 Consensus size: 41
11412833 TACCAGAAGT
*
11412843 AACCACATGATGACATTATCAGCAGTGATTGATAACAGAGA
1 AACCACATGATGACATTATCAGCAGCGATTGATAACAGAGA
*
11412884 AACCCCATGATGACATTTATCAGCAGCGATTGATAACAGAGA
1 AACCACATGATGACA-TTATCAGCAGCGATTGATAACAGAGA
11412926 AAC
1 AAC
11412929 ACTGCCTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
41 14 0.33
42 28 0.67
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (41 bp):
AACCACATGATGACATTATCAGCAGCGATTGATAACAGAGA
Found at i:11416928 original size:21 final size:21
Alignment explanation
Indices: 11416902--11416955 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
11416892 TGGGGCAACC
11416902 TGTTGAGTTGGGGTA-CTCTCT
1 TGTTGAGTTGGGGTAGC-CTCT
* *
11416923 TGTTGATTTGGGGTAGCCTGT
1 TGTTGAGTTGGGGTAGCCTCT
*
11416944 TGCTGAGTTGGG
1 TGTTGAGTTGGG
11416956 ACATCAACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.09, C:0.11, G:0.39, T:0.41
Consensus pattern (21 bp):
TGTTGAGTTGGGGTAGCCTCT
Found at i:11417657 original size:28 final size:28
Alignment explanation
Indices: 11417615--11417677 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
11417605 CACATACACC
* *
11417615 TAAAAAAACAGTCACTACATGCATATTA
1 TAAAAAAACACTCACCACATGCATATTA
* *
11417643 TAAAAAAATACTCACCGCATGCATATTA
1 TAAAAAAACACTCACCACATGCATATTA
11417671 -AAAAAAA
1 TAAAAAAA
11417678 GTCAACACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 7 0.23
28 24 0.77
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.22
Consensus pattern (28 bp):
TAAAAAAACACTCACCACATGCATATTA
Found at i:11419419 original size:15 final size:15
Alignment explanation
Indices: 11419387--11419432 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
11419377 TTATCCTATT
**
11419387 AGACACATCACTTTC
1 AGACACATCACTACC
**
11419402 AGATGCATCACTACC
1 AGACACATCACTACC
11419417 AGACACATCACTACC
1 AGACACATCACTACC
11419432 A
1 A
11419433 AACATTTCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.37, C:0.35, G:0.09, T:0.20
Consensus pattern (15 bp):
AGACACATCACTACC
Found at i:11419901 original size:12 final size:12
Alignment explanation
Indices: 11419880--11419922 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
11419870 ACTTTAATAA
*
11419880 CCAAACCAAAAT
1 CCAAATCAAAAT
11419892 CCAAATCAAAAT
1 CCAAATCAAAAT
* *
11419904 CAAAATCTAAAT
1 CCAAATCAAAAT
*
11419916 CTAAATC
1 CCAAATC
11419923 GAGATCGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.19
Consensus pattern (12 bp):
CCAAATCAAAAT
Found at i:11419903 original size:6 final size:6
Alignment explanation
Indices: 11419886--11419953 Score: 55
Period size: 6 Copynumber: 11.3 Consensus size: 6
11419876 ATAACCAAAC
* * * * * *
11419886 CAAAAT CCAAAT CAAAAT CAAAAT CTAAAT CTAAAT CGAGAT CGAAAT
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT
** *
11419934 TGAAAT CAAAAT TAAAAT CA
1 CAAAAT CAAAAT CAAAAT CA
11419954 GAATGAGTGA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.22
Consensus pattern (6 bp):
CAAAAT
Found at i:11419986 original size:12 final size:12
Alignment explanation
Indices: 11419969--11420029 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
11419959 AGTGAGTGTT
*
11419969 TCAAAATTGAAA
1 TCAAAATCGAAA
11419981 TCAAAATCGAAA
1 TCAAAATCGAAA
* * *
11419993 TCGAAGTCAAAA
1 TCAAAATCGAAA
* *
11420005 TTAGAATCGAAA
1 TCAAAATCGAAA
*
11420017 TCAAAATTGAAA
1 TCAAAATCGAAA
11420029 T
1 T
11420030 TGAAATAACC
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.23
Consensus pattern (12 bp):
TCAAAATCGAAA
Found at i:11420002 original size:18 final size:17
Alignment explanation
Indices: 11419972--11420035 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
11419962 GAGTGTTTCA
*
11419972 AAATTGAAATCAAAATCG
1 AAATCGAAATCAAAAT-G
* *
11419990 AAATCGAAGTCAAAATT
1 AAATCGAAATCAAAATG
11420007 AGAATCGAAATCAAAATTG
1 A-AATCGAAATCAAAA-TG
*
11420026 AAATTGAAAT
1 AAATCGAAAT
11420036 AACCCTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
17 1 0.03
18 35 0.92
19 2 0.05
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.23
Consensus pattern (17 bp):
AAATCGAAATCAAAATG
Found at i:11421827 original size:31 final size:31
Alignment explanation
Indices: 11421790--11421853 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
11421780 TAAATATGAG
11421790 GTATTGACTAAATTGTAAGAAAGTGAAAAGT
1 GTATTGACTAAATTGTAAGAAAGTGAAAAGT
*
11421821 GTATTGACTAGATTGTAAGAAAGTGAAAAGT
1 GTATTGACTAAATTGTAAGAAAGTGAAAAGT
11421852 GT
1 GT
11421854 TGGGATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.30
Consensus pattern (31 bp):
GTATTGACTAAATTGTAAGAAAGTGAAAAGT
Found at i:11423521 original size:15 final size:15
Alignment explanation
Indices: 11423492--11423526 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
11423482 AACTCTATTT
11423492 TAATT-ATATTAAGA
1 TAATTAATATTAAGA
*
11423506 TAATTAATATTGAGA
1 TAATTAATATTAAGA
11423521 TAATTA
1 TAATTA
11423527 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:11424396 original size:9 final size:8
Alignment explanation
Indices: 11424379--11424403 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11424369 TTTAATTCTA
11424379 TTATTTTT
1 TTATTTTT
11424387 TTATTTTT
1 TTATTTTT
11424395 TTATTTTT
1 TTATTTTT
11424403 T
1 T
11424404 CAGGAACGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:11427489 original size:7 final size:7
Alignment explanation
Indices: 11427473--11427558 Score: 63
Period size: 7 Copynumber: 11.9 Consensus size: 7
11427463 CAACCCAATT
11427473 TTTATT-
1 TTTATTA
11427479 TTTATTA
1 TTTATTA
11427486 TTTATTA
1 TTTATTA
11427493 TTT-TT-
1 TTTATTA
* *
11427498 TCT-TTC
1 TTTATTA
11427504 TTTACTTTA
1 TTTA--TTA
11427513 TTTATTA
1 TTTATTA
11427520 CTTTATTA
1 -TTTATTA
11427528 TTTTATTTTA
1 -TTTA--TTA
11427538 TTTTATTA
1 -TTTATTA
11427546 TTTATTA
1 TTTATTA
11427553 TTTATT
1 TTTATT
11427559 TGGATATTAA
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
5 4 0.06
6 10 0.15
7 26 0.38
8 14 0.21
9 6 0.09
10 8 0.12
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTATTA
Found at i:11427516 original size:4 final size:4
Alignment explanation
Indices: 11427473--11427559 Score: 51
Period size: 4 Copynumber: 21.8 Consensus size: 4
11427463 CAACCCAATT
* * *
11427473 TTTA TTTT TATTA TTTA -TTA TTT- TTTC TTTC TTTA CTTTA TTTA -TTA
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA
11427520 CTTTA -TTA TTTTA TTTTA TTT- TATTA TTTA -TTA TTTA TTT
1 -TTTA TTTA -TTTA -TTTA TTTA T-TTA TTTA TTTA TTTA TTT
11427560 GGATATTAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 22
0.73 0.03 0.23
Matches are distributed among these distances:
3 16 0.23
4 34 0.49
5 19 0.28
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:11427538 original size:25 final size:24
Alignment explanation
Indices: 11427504--11427559 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
11427494 TTTTTCTTTC
*
11427504 TTTACTTTA-TTTATTACTTTATTA
1 TTTATTTTATTTTATTA-TTTATTA
11427528 TTTTATTTTATTTTATTATTTATTA
1 -TTTATTTTATTTTATTATTTATTA
11427553 TTTATTT
1 TTTATTT
11427560 GGATATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 7 0.24
25 15 0.52
26 7 0.24
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTATTTTATTTTATTATTTATTA
Found at i:11430454 original size:27 final size:27
Alignment explanation
Indices: 11430424--11430483 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
11430414 GCGCATAATA
*
11430424 ATAGTGACACTTTAGTGCAACTT-AGTG
1 ATAGTGACACTTCAGTGCAA-TTCAGTG
*
11430451 ATAGTAACACTTCAGTGCAATTCAGTG
1 ATAGTGACACTTCAGTGCAATTCAGTG
11430478 ATAGTG
1 ATAGTG
11430484 GCTCTTCGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (27 bp):
ATAGTGACACTTCAGTGCAATTCAGTG
Found at i:11440876 original size:23 final size:22
Alignment explanation
Indices: 11440831--11440876 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
11440821 ATTTTCAAGT
11440831 ATATATTCAATTCAATTCCACAC
1 ATATATTCAATTCAATT-CACAC
11440854 ATATATTCATTATTCAATT-ACAC
1 ATATATTCA--ATTCAATTCACAC
11440877 TTAATCGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 13 0.62
25 8 0.38
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATATTCAATTCAATTCACAC
Found at i:11441001 original size:23 final size:23
Alignment explanation
Indices: 11440975--11441095 Score: 190
Period size: 23 Copynumber: 5.3 Consensus size: 23
11440965 ATAAGTGCCA
*
11440975 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
11440998 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
11441021 CATTGATAA-GTAGCCGAAGCTAC
1 CACTGA-AATGTAGCCGAAGCTAC
*
11441044 CACAGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
11441067 CACTAAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
11441090 CACTGA
1 CACTGA
11441096 TCAATAACAC
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
22 2 0.02
23 85 0.96
24 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:11446740 original size:18 final size:18
Alignment explanation
Indices: 11446717--11446753 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
11446707 CTTCAGTTGA
11446717 GATCAATTATCGAGACAT
1 GATCAATTATCGAGACAT
11446735 GATCAATTATCGAGACAT
1 GATCAATTATCGAGACAT
11446753 G
1 G
11446754 GACTACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (18 bp):
GATCAATTATCGAGACAT
Found at i:11447100 original size:19 final size:19
Alignment explanation
Indices: 11447076--11447151 Score: 82
Period size: 19 Copynumber: 3.9 Consensus size: 19
11447066 ACCTTATATG
*
11447076 CCAAGATACACTTGGTGTA
1 CCAAGATACACTTTGTGTA
** *
11447095 CCAAGATATGCTTTGTG-C
1 CCAAGATACACTTTGTGTA
*
11447113 CCTAAGATGCAGCTTTGTGTA
1 CC-AAGATACA-CTTTGTGTA
11447134 CCAAGATACACTTTGTGT
1 CCAAGATACACTTTGTGT
11447152 GATAGTGATG
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
18 2 0.04
19 27 0.60
20 14 0.31
21 2 0.04
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (19 bp):
CCAAGATACACTTTGTGTA
Found at i:11449710 original size:17 final size:17
Alignment explanation
Indices: 11449688--11449737 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
11449678 ATTGAAAGTC
11449688 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
11449705 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
*
11449722 AAAGATATGGATATCA
1 AAAGATATGGGTATCA
11449738 AAATCTGGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:11455391 original size:30 final size:30
Alignment explanation
Indices: 11455348--11455418 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
11455338 TTGATAAATG
* *
11455348 AACTTTGATTTGGTGCAATTATATACATGA
1 AACTTTAATTTGGTGCAAATATATACATGA
* * * * *
11455378 AATTTTTATTTGGTTCAAATGTATATATGA
1 AACTTTAATTTGGTGCAAATATATACATGA
11455408 AACTTTAATTT
1 AACTTTAATTT
11455419 TGATTCAATC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (30 bp):
AACTTTAATTTGGTGCAAATATATACATGA
Found at i:11455588 original size:30 final size:29
Alignment explanation
Indices: 11455563--11455643 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
11455553 TAATTGGATC
*
11455563 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATC-AAAGTTCATGTATAAAATTGCACA
* * *
11455593 AAATCAAAGTTCATGTCTAAAATTTCATA
1 AAATCAAAGTTCATGTATAAAATTGCACA
* *
11455622 TTAAATTAAAGTTCATATATAA
1 --AAATCAAAGTTCATGTATAA
11455644 TTAATTTGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 20 0.48
30 5 0.12
31 17 0.40
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATAAAATTGCACA
Found at i:11463755 original size:3 final size:3
Alignment explanation
Indices: 11463747--11463781 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
11463737 TGACACTGTT
11463747 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
11463782 ATGTTCCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:11469563 original size:15 final size:15
Alignment explanation
Indices: 11469543--11469577 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
11469533 CTTACCGAGC
11469543 TCTTTGACTTCAAAT
1 TCTTTGACTTCAAAT
11469558 TCTTTGACTTCAAAT
1 TCTTTGACTTCAAAT
11469573 TCTTT
1 TCTTT
11469578 TAAATTCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (15 bp):
TCTTTGACTTCAAAT
Found at i:11470609 original size:24 final size:24
Alignment explanation
Indices: 11470582--11470641 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
11470572 TTGGTAGGCA
11470582 AGGACTGAGTGTTTGGCTG-GACAG
1 AGGACTGAGTGTTTGGCTGCG-CAG
*
11470606 AGGATTGAGTGTTTGGCTGCGCAG
1 AGGACTGAGTGTTTGGCTGCGCAG
*
11470630 AGAACTGAGTGT
1 AGGACTGAGTGT
11470642 GAGTGTTTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.22, C:0.12, G:0.40, T:0.27
Consensus pattern (24 bp):
AGGACTGAGTGTTTGGCTGCGCAG
Found at i:11482137 original size:410 final size:408
Alignment explanation
Indices: 11481379--11482191 Score: 1461
Period size: 410 Copynumber: 2.0 Consensus size: 408
11481369 TCAGTCATCA
*
11481379 TTGCCTTTTGGATAATTACAAGAATGGTTTCTTTCATGGGATTGCAAATTTTAGTTAATTACAGT
1 TTGCCTTTTGGATAATTACAAGAATGATTTCTTTCATGGGATTGCAAATTTTAGTTAATTACAGT
11481444 TTATAGTTGTAATATAAGTTTTGTTAATTGTTTTATATTTTGGATATATATTTAAAAAATACAGA
66 TTATAGTTGTAATATAAGTTTTGTTAATTGTTTTATATTTTGGATATATATTTAAAAAATACAGA
* *
11481509 AAAATTCACTTGTAATAAGACCAAAATGAAAATGGATGATGTTCTGTGAGAAAGTGTTGGTAATT
131 AAAATTCACTTATAATAAGACCAAAATGAAAATGGATGATGTTCTGTGAGAAAGTATTGGTAATT
* *
11481574 TAGTTATTTAATGGGTAATGTGTTCACGGAGTTAGGGGAATAAGTTTATTGCCAATATCCAAGCT
196 TAGTTATTTAATGGGTAATGTGTTCACGGAGTTAGCGGAATAAGTTTACTGCCAATATCCAAGCT
11481639 TAATTATAATGTTCTTCTAAAGCTTTATGCCAAAATCCTTTTCGTAAACGCATCTGTATTATTGG
261 TAATTATAATGTTCTTCTAAAGCTTTATGCCAAAATCCTTTTCGTAAACGCATCTGTATTATTGG
11481704 TTTTATTCTCAATCCATACGGTGGTTTGATCTAATGAGCTTTTCCACTCAGCTTGGAATCAAGAG
326 TTTTATTCTCAATCCATACGGTGGTTTGATCTAATGAGCTTTTCCACTCAGCTTGGAATCAAGAG
11481769 ATACAAACAAGTTTATAG
391 ATACAAACAAGTTTATAG
*
11481787 TTGCCTTTTGGATAATTA-ACAGAATGATTTCTTTCATGGGATTGCAAGTTTTAGTTAATTACAG
1 TTGCCTTTTGGATAATTACA-AGAATGATTTCTTTCATGGGATTGCAAATTTTAGTTAATTACAG
11481851 TTTATAGTTGTAATAT-AGATTTTGTTAATTGTTTTATATTTTGGATATATATTTTAAAAAATAC
65 TTTATAGTTGTAATATAAG-TTTTGTTAATTGTTTTATATTTTGGATATATA-TTTAAAAAATAC
* * *
11481915 AGAAAAATTTACTTATAATAAGACCAAAAATGAAAATGGATGGTGTTCTGTGAG-AGGTATTGGT
128 AGAAAAATTCACTTATAATAAGACC-AAAATGAAAATGGATGATGTTCTGTGAGAAAGTATTGGT
*
11481979 AATTTAGTTATTTAATGGGTAATGTGTTCACGGAGTTAGCGGAGTAAAGTTTACTGCCAATATCC
192 AATTTAGTTATTTAATGGGTAATGTGTTCACGGAGTTAGCGGAAT-AAGTTTACTGCCAATATCC
*
11482044 AAGCTTAATTATAATGTTCTTCTAAAGCTTTATGCCAAAATCCTTTTTGTAAACGCATCTGTATT
256 AAGCTTAATTATAATGTTCTTCTAAAGCTTTATGCCAAAATCCTTTTCGTAAACGCATCTGTATT
11482109 ATTGGTTTTATTCTCAATCCATACGGTGGTTTGATCTAATGAGCTTTTCCACTCAGCTTGGAATC
321 ATTGGTTTTATTCTCAATCCATACGGTGGTTTGATCTAATGAGCTTTTCCACTCAGCTTGGAATC
11482174 AAGAGATACAAACAAGTT
386 AAGAGATACAAACAAGTT
11482192 ATGCTCCATC
Statistics
Matches: 389, Mismatches: 11, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
407 3 0.01
408 108 0.28
409 86 0.22
410 192 0.49
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (408 bp):
TTGCCTTTTGGATAATTACAAGAATGATTTCTTTCATGGGATTGCAAATTTTAGTTAATTACAGT
TTATAGTTGTAATATAAGTTTTGTTAATTGTTTTATATTTTGGATATATATTTAAAAAATACAGA
AAAATTCACTTATAATAAGACCAAAATGAAAATGGATGATGTTCTGTGAGAAAGTATTGGTAATT
TAGTTATTTAATGGGTAATGTGTTCACGGAGTTAGCGGAATAAGTTTACTGCCAATATCCAAGCT
TAATTATAATGTTCTTCTAAAGCTTTATGCCAAAATCCTTTTCGTAAACGCATCTGTATTATTGG
TTTTATTCTCAATCCATACGGTGGTTTGATCTAATGAGCTTTTCCACTCAGCTTGGAATCAAGAG
ATACAAACAAGTTTATAG
Found at i:11488188 original size:20 final size:20
Alignment explanation
Indices: 11488144--11488260 Score: 64
Period size: 19 Copynumber: 5.8 Consensus size: 20
11488134 AAATTATAAA
*
11488144 AAAAAATTCAAAATTATTT-T
1 AAAAAATTTAAAA-TATTTAT
*
11488164 CAAAAATTTAAAATATTTAT
1 AAAAAATTTAAAATATTTAT
* *
11488184 AAAAATATTAAAATTTATATTTTTT
1 AAAAA-ATTTAAA---ATA-TTTAT
*
11488209 AAAAAA--TACAAATA-ATAT
1 AAAAAATTTA-AAATATTTAT
* * *
11488227 ATAAAATTTTAAAT-TTTAA
1 AAAAAATTTAAAATATTTAT
11488246 AAAAAATTTAAAATA
1 AAAAAATTTAAAATA
11488261 ATAATTTTGG
Statistics
Matches: 72, Mismatches: 14, Indels: 22
0.67 0.13 0.20
Matches are distributed among these distances:
18 7 0.10
19 23 0.32
20 20 0.28
21 6 0.08
22 1 0.01
23 2 0.03
24 4 0.06
25 9 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATTTAAAATATTTAT
Found at i:11488202 original size:18 final size:19
Alignment explanation
Indices: 11488145--11488197 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
11488135 AATTATAAAA
*
11488145 AAAAATTCAAAATTATTT-T
1 AAAAATTTAAAA-TATTTAT
11488164 CAAAAATTTAAAATATTTAT
1 -AAAAATTTAAAATATTTAT
11488184 AAAAATATTAAAAT
1 AAAAAT-TTAAAAT
11488198 TTATATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:11489113 original size:7 final size:7
Alignment explanation
Indices: 11489101--11489127 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
11489091 AAAAAGTCAA
11489101 TGAAATG
1 TGAAATG
11489108 TGAAATG
1 TGAAATG
11489115 TGAAATG
1 TGAAATG
11489122 TGAAAT
1 TGAAAT
11489128 CAATTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (7 bp):
TGAAATG
Found at i:11491468 original size:41 final size:41
Alignment explanation
Indices: 11491406--11491555 Score: 255
Period size: 41 Copynumber: 3.6 Consensus size: 41
11491396 GACTATACGT
* *
11491406 CTAGCAGGCTAAGTGCTGGTGATCTGAATCATGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
11491447 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
11491488 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
11491529 CTAGCAGGCTAAGTGCCGGTGAATCTG
1 CTAGCAGGCTAAGTGCCGGTG-ATCTG
11491556 TTAAATTAAG
Statistics
Matches: 104, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 99 0.95
42 5 0.05
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:11506394 original size:7 final size:7
Alignment explanation
Indices: 11506375--11506405 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
11506365 AACAAAAGCG
11506375 AATATAT
1 AATATAT
11506382 -ATATAT
1 AATATAT
11506388 AATATAT
1 AATATAT
11506395 AATATAT
1 AATATAT
11506402 AATA
1 AATA
11506406 CAAGCCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATAT
Found at i:11514588 original size:123 final size:123
Alignment explanation
Indices: 11514369--11514609 Score: 482
Period size: 123 Copynumber: 2.0 Consensus size: 123
11514359 AGTAAAAGGG
11514369 TTCCTTAAATCTGATTGCTTGAGCAAAGACAGCAGACCCATGTTTGCTCTCCAGGAAACAGTACA
1 TTCCTTAAATCTGATTGCTTGAGCAAAGACAGCAGACCCATGTTTGCTCTCCAGGAAACAGTACA
11514434 AGTTTACCTTAATTAAATCAATGTTTTAGCACATCCCATTGATGACTTCAGCTGCTAC
66 AGTTTACCTTAATTAAATCAATGTTTTAGCACATCCCATTGATGACTTCAGCTGCTAC
11514492 TTCCTTAAATCTGATTGCTTGAGCAAAGACAGCAGACCCATGTTTGCTCTCCAGGAAACAGTACA
1 TTCCTTAAATCTGATTGCTTGAGCAAAGACAGCAGACCCATGTTTGCTCTCCAGGAAACAGTACA
11514557 AGTTTACCTTAATTAAATCAATGTTTTAGCACATCCCATTGATGACTTCAGCT
66 AGTTTACCTTAATTAAATCAATGTTTTAGCACATCCCATTGATGACTTCAGCT
11514610 CTGCTGCCCT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 118 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.31
Consensus pattern (123 bp):
TTCCTTAAATCTGATTGCTTGAGCAAAGACAGCAGACCCATGTTTGCTCTCCAGGAAACAGTACA
AGTTTACCTTAATTAAATCAATGTTTTAGCACATCCCATTGATGACTTCAGCTGCTAC
Found at i:11514673 original size:66 final size:66
Alignment explanation
Indices: 11514591--11514741 Score: 302
Period size: 66 Copynumber: 2.3 Consensus size: 66
11514581 TTTAGCACAT
11514591 CCCATTGATGACTTCAGCTCTGCTGCCCTAAAATATTCCAACCCCTTTTATTTTATTAACTCAAC
1 CCCATTGATGACTTCAGCTCTGCTGCCCTAAAATATTCCAACCCCTTTTATTTTATTAACTCAAC
11514656 C
66 C
11514657 CCCATTGATGACTTCAGCTCTGCTGCCCTAAAATATTCCAACCCCTTTTATTTTATTAACTCAAC
1 CCCATTGATGACTTCAGCTCTGCTGCCCTAAAATATTCCAACCCCTTTTATTTTATTAACTCAAC
11514722 C
66 C
11514723 CCCATTGATGACTTCAGCT
1 CCCATTGATGACTTCAGCT
11514742 GCTACTCATT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 85 1.00
ACGTcount: A:0.25, C:0.32, G:0.09, T:0.34
Consensus pattern (66 bp):
CCCATTGATGACTTCAGCTCTGCTGCCCTAAAATATTCCAACCCCTTTTATTTTATTAACTCAAC
C
Found at i:11520450 original size:20 final size:20
Alignment explanation
Indices: 11520409--11520450 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
11520399 ATACTACCCA
* *
11520409 TTGAATCAAAATGCGGAAAT
1 TTGAATCAAAATCCGAAAAT
11520429 TTGAA-CAAAATCCGAAATAT
1 TTGAATCAAAATCCGAAA-AT
11520449 TT
1 TT
11520451 ATGCAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (20 bp):
TTGAATCAAAATCCGAAAAT
Found at i:11521036 original size:25 final size:23
Alignment explanation
Indices: 11520997--11521048 Score: 61
Period size: 26 Copynumber: 2.2 Consensus size: 23
11520987 TTAAAAATTC
*
11520997 AAAATATATTTAAAAGTT-AAGA
1 AAAATATATTTAAAAATTAAAGA
11521019 AAAATTATATTTACAAAAATTAAAGA
1 AAAA-TATATTT--AAAAATTAAAGA
11521045 AAAA
1 AAAA
11521049 AACAACCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 4 0.16
23 7 0.28
25 6 0.24
26 8 0.32
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (23 bp):
AAAATATATTTAAAAATTAAAGA
Found at i:11528981 original size:19 final size:20
Alignment explanation
Indices: 11528936--11528984 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
11528926 TTGAAAGTTG
11528936 TTATTAAAAAATATAAAATA
1 TTATTAAAAAATATAAAATA
* *
11528956 TTTTTAAAAAAT-TATAGA-A
1 TTATTAAAAAATATA-AAATA
11528975 TTATTAAAAA
1 TTATTAAAAA
11528985 TTCCAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TTATTAAAAAATATAAAATA
Found at i:11529090 original size:18 final size:20
Alignment explanation
Indices: 11529052--11529092 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
11529042 ACTGATTATT
*
11529052 AAAAAGTTATAAGAATCATA
1 AAAAAATTATAAGAATCATA
11529072 AAAAAATTATAA-AAT-ATA
1 AAAAAATTATAAGAATCATA
11529090 AAA
1 AAA
11529093 TTCAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 3 0.15
20 11 0.55
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.24
Consensus pattern (20 bp):
AAAAAATTATAAGAATCATA
Found at i:11533953 original size:19 final size:19
Alignment explanation
Indices: 11533926--11533962 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11533916 TATCGAATAT
11533926 TGCCATTATTTTCATTTGC
1 TGCCATTATTTTCATTTGC
*
11533945 TGCCTTTATTTTCATTTG
1 TGCCATTATTTTCATTTG
11533963 TTAGAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.19, G:0.11, T:0.57
Consensus pattern (19 bp):
TGCCATTATTTTCATTTGC
Found at i:11534917 original size:3 final size:3
Alignment explanation
Indices: 11534909--11534966 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
11534899 AACTAATACA
* * * * * *
11534909 AAT AAT AAT ACT AAT AAT TAT AGT AAC ATT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
11534957 AAT AAA AAT A
1 AAT AAT AAT A
11534967 GTTAAGTAAT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11538832 original size:21 final size:21
Alignment explanation
Indices: 11538806--11538942 Score: 96
Period size: 21 Copynumber: 6.5 Consensus size: 21
11538796 CCTAAGGCTG
11538806 AACAGAAGCTCATAAGAGTTA
1 AACAGAAGCTCATAAGAGTTA
* * * *
11538827 AACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGTTA
** * * *
11538848 AATGGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGTTA
* * *
11538869 AACGGAAACTCATAAGGGTTA
1 AACAGAAGCTCATAAGAGTTA
* * *
11538890 AATAGAAGCTCA-ATAGAGCTG
1 AACAGAAGCTCATA-AGAGTTA
* * *
11538911 AACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGTTA
11538932 AACAGAAGCTC
1 AACAGAAGCTC
11538943 GCGAGAGCTG
Statistics
Matches: 83, Mismatches: 31, Indels: 4
0.70 0.26 0.03
Matches are distributed among these distances:
20 1 0.01
21 81 0.98
22 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGTTA
Found at i:11538950 original size:42 final size:42
Alignment explanation
Indices: 11538806--11538956 Score: 144
Period size: 42 Copynumber: 3.6 Consensus size: 42
11538796 CCTAAGGCTG
* * * * * *
11538806 AACAGAAGCTC-ATAAGAGTTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCGA-AAGAGCTGAACGGAAACTCATAAGAGTTA
** * *
11538848 AATGGAAGCTCGTAAGAGCTGAACGGAAACTCATAAGGGTTA
1 AACAGAAGCTCGAAAGAGCTGAACGGAAACTCATAAGAGTTA
* *
11538890 AATAGAAGCTC-AATAGAGCTGAACGGAAACTCATATGAGTTA
1 AACAGAAGCTCGAA-AGAGCTGAACGGAAACTCATAAGAGTTA
**
11538932 AACAGAAGCTCGCGAGAGCTGAACG
1 AACAGAAGCTCGAAAGAGCTGAACG
11538957 AAAAGTAAAC
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
41 1 0.01
42 90 0.99
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCGAAAGAGCTGAACGGAAACTCATAAGAGTTA
Found at i:11540946 original size:19 final size:21
Alignment explanation
Indices: 11540916--11540956 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
11540906 CTGCTTTCAC
*
11540916 TTGCTAACAAA-TCAAACATT
1 TTGCTAACAAATTCAAAAATT
11540936 TTGCT-ACAAATTCAAAAATT
1 TTGCTAACAAATTCAAAAATT
11540956 T
1 T
11540957 CCCGTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (21 bp):
TTGCTAACAAATTCAAAAATT
Found at i:11547483 original size:144 final size:144
Alignment explanation
Indices: 11547223--11547506 Score: 505
Period size: 144 Copynumber: 2.0 Consensus size: 144
11547213 GTCTAAATTG
* *
11547223 AGGTAAGGGTATAAGTATAACAATAATATATGATAAGGTTAGCTGCACATTTAGAGTTTAAGGTT
1 AGGTAAGGATATAAGTATAACAATAATATACGATAAGGTTAGCTGCACATTTAGAGTTTAAGGTT
* **
11547288 GCGTATCATTAATATACAAATGTACATTATAGTGGCATAGTTGTATATACTATATAGGGTTACAC
66 ACGTATCATTAATATACAAATGTACATTATAGTAACATAGTTGTATATACTATATAGGGTTACAC
11547353 ATTATTACTATATA
131 ATTATTACTATATA
* *
11547367 AGGTAAGGATATAAGTATAACAATAATATACGATAAGGTTAGTTGCACATTTAGGGTTTAAGGTT
1 AGGTAAGGATATAAGTATAACAATAATATACGATAAGGTTAGCTGCACATTTAGAGTTTAAGGTT
11547432 ACGTATCATTAATATACAAATGTACATTATAGTAACATAGTTGTATATACTATATAGGGTTACAC
66 ACGTATCATTAATATACAAATGTACATTATAGTAACATAGTTGTATATACTATATAGGGTTACAC
11547497 ATTATTACTA
131 ATTATTACTA
11547507 ATCTACCTTA
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
144 133 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35
Consensus pattern (144 bp):
AGGTAAGGATATAAGTATAACAATAATATACGATAAGGTTAGCTGCACATTTAGAGTTTAAGGTT
ACGTATCATTAATATACAAATGTACATTATAGTAACATAGTTGTATATACTATATAGGGTTACAC
ATTATTACTATATA
Found at i:11549357 original size:77 final size:77
Alignment explanation
Indices: 11549230--11549384 Score: 292
Period size: 77 Copynumber: 2.0 Consensus size: 77
11549220 CAACCTTGCT
*
11549230 TTAAATTTATCAATGGTTCCATCGACCTTCATTTTCTTTTTGAAGATCCATTTATAACCTATTGG
1 TTAAATTTATCAATGGTTCCATCGACCTTCATTTTCTTTTTGAAGATCCATTTACAACCTATTGG
11549295 TTTGAAACCTGG
66 TTTGAAACCTGG
11549307 TTAAATTTATCAATGGTTCCATCGACCTTCATTTTCTTTTTGAAGATCCATTTACAACCTATTGG
1 TTAAATTTATCAATGGTTCCATCGACCTTCATTTTCTTTTTGAAGATCCATTTACAACCTATTGG
*
11549372 TTTGGAACCTGG
66 TTTGAAACCTGG
11549384 T
1 T
11549385 GGAAGATCAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.43
Consensus pattern (77 bp):
TTAAATTTATCAATGGTTCCATCGACCTTCATTTTCTTTTTGAAGATCCATTTACAACCTATTGG
TTTGAAACCTGG
Found at i:11550883 original size:19 final size:19
Alignment explanation
Indices: 11550859--11550912 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
11550849 AATTTTCAAG
11550859 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
11550878 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11550897 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
11550913 AGATATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:11550901 original size:38 final size:40
Alignment explanation
Indices: 11550859--11550935 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
11550849 AATTTTCAAG
11550859 GATATGCAATCTT-AGATATGA-TATGTAATCTTAGATAT
1 GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
*
11550897 GATATGCAATCTTAGAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTT--AAGATATGATTATGTAATCTTAGA
11550936 GATTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 13 0.38
41 8 0.24
42 13 0.38
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (40 bp):
GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
Found at i:11551165 original size:23 final size:23
Alignment explanation
Indices: 11551121--11551165 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
11551111 TCTTATTTTG
* *
11551121 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
11551144 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
11551166 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:11551394 original size:6 final size:6
Alignment explanation
Indices: 11551384--11551423 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
11551374 TCTTGTATCA
* *
11551384 TTATTA TTATTT ATATTT TTATTT TTATTT TTATTT TTAT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTAT
11551424 ATTCATGCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:11551975 original size:13 final size:12
Alignment explanation
Indices: 11551939--11551988 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
11551929 TCATGGATTA
11551939 TTGTTT-TTT-T
1 TTGTTTATTTAT
* *
11551949 TTGTATATTAAT
1 TTGTTTATTTAT
11551961 TTCGTTTATTTAT
1 TT-GTTTATTTAT
11551974 TTGTTTATATTAT
1 TTGTTTAT-TTAT
11551987 TT
1 TT
11551989 ATATGCCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 5 0.16
11 2 0.06
12 9 0.28
13 16 0.50
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.72
Consensus pattern (12 bp):
TTGTTTATTTAT
Found at i:11561511 original size:24 final size:25
Alignment explanation
Indices: 11561472--11561518 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
11561462 TTAATTTAAT
*
11561472 CTATTAAAAATTATAAAAATATAAA
1 CTATTAAAAATAATAAAAATATAAA
*
11561497 CTATT-AAAATAATAAAATTATA
1 CTATTAAAAATAATAAAAATATA
11561519 TTTTTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (25 bp):
CTATTAAAAATAATAAAAATATAAA
Found at i:11570616 original size:8 final size:8
Alignment explanation
Indices: 11570603--11570627 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11570593 CACCAAGATC
11570603 TGAATATT
1 TGAATATT
11570611 TGAATATT
1 TGAATATT
11570619 TGAATATT
1 TGAATATT
11570627 T
1 T
11570628 CCTTATAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TGAATATT
Found at i:11576329 original size:55 final size:55
Alignment explanation
Indices: 11576239--11576352 Score: 194
Period size: 55 Copynumber: 2.1 Consensus size: 55
11576229 ATTGCCACCT
*
11576239 TAAT-CTTTTAATCTTTATCAAATAAATCAGGATTAGATGTGGCAGCTAGTTGAC
1 TAATGCTTTTAATCTTTATCAAATAAATCAGAATTAGATGTGGCAGCTAGTTGAC
*
11576293 TAATGCTTTTAATCTTTATCAAATAAATCAGAATTAGATGTGGCAGTTAGTTGAC
1 TAATGCTTTTAATCTTTATCAAATAAATCAGAATTAGATGTGGCAGCTAGTTGAC
*
11576348 CAATG
1 TAATG
11576353 GTCAATGATA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 4 0.07
55 52 0.93
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (55 bp):
TAATGCTTTTAATCTTTATCAAATAAATCAGAATTAGATGTGGCAGCTAGTTGAC
Found at i:11576869 original size:21 final size:20
Alignment explanation
Indices: 11576829--11576869 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
11576819 TTCTTAACCT
**
11576829 TAATGGTATTTTTTTTCTAC
1 TAATGGTATTTTTTCCCTAC
11576849 NTAATGGTATTTTTTCCCTAC
1 -TAATGGTATTTTTTCCCTAC
11576870 ATTCCTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.54
Consensus pattern (20 bp):
TAATGGTATTTTTTCCCTAC
Found at i:11577674 original size:16 final size:17
Alignment explanation
Indices: 11577644--11577679 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
11577634 AAGAAGGTTG
11577644 AAAATAATTCAAAATTA
1 AAAATAATTCAAAATTA
*
11577661 AAAATAA-TCGAAATTA
1 AAAATAATTCAAAATTA
11577677 AAA
1 AAA
11577680 TAGGAGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAATAATTCAAAATTA
Found at i:11579433 original size:19 final size:20
Alignment explanation
Indices: 11579401--11579445 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
11579391 TTTTAAATTT
* *
11579401 TTTTTTATAATTTTTCTATAA
1 TTTTTTAT-ATTTTTATAAAA
11579422 TTTTTTAT-TTTTTATAAAA
1 TTTTTTATATTTTTATAAAA
11579441 TTTTT
1 TTTTT
11579446 ACTGTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTTATATTTTTATAAAA
Found at i:11587377 original size:17 final size:17
Alignment explanation
Indices: 11587357--11587389 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11587347 CCATTTTTTA
11587357 AAAAATATTAA-TATATT
1 AAAAA-ATTAATTATATT
11587374 AAAAAATTAATTATAT
1 AAAAAATTAATTATAT
11587390 AATTTTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAAATTAATTATATT
Found at i:11589426 original size:22 final size:22
Alignment explanation
Indices: 11589398--11589439 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
11589388 AAATTGATAT
11589398 AAACTTATTAAA-ATTATAAAAA
1 AAACTTA-TAAATATTATAAAAA
11589420 AAACTTATAAATATTATAAA
1 AAACTTATAAATATTATAAA
11589440 TTTAGTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AAACTTATAAATATTATAAAAA
Found at i:11589554 original size:10 final size:11
Alignment explanation
Indices: 11589527--11589555 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
11589517 ATATAAACTT
11589527 ATAAAAAAGTC
1 ATAAAAAAGTC
11589538 ATAAAAAAGTC
1 ATAAAAAAGTC
11589549 ATAAAAA
1 ATAAAAA
11589556 CTTGAAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (11 bp):
ATAAAAAAGTC
Found at i:11589982 original size:9 final size:9
Alignment explanation
Indices: 11589966--11590055 Score: 72
Period size: 9 Copynumber: 9.4 Consensus size: 9
11589956 TTTTATGATT
11589966 TTTTTATAA
1 TTTTTATAA
*
11589975 TTTGTATAA
1 TTTTTATAA
* *
11589984 GTTTATATCA
1 -TTTTTATAA
*
11589994 TTTTAATAA
1 TTTTTATAA
*
11590003 TTTTTATGAT
1 TTTTTAT-AA
11590013 TTTTATATAA
1 TTTT-TATAA
*
11590023 TTTTAATAA
1 TTTTTATAA
11590032 TTTTTATATA
1 TTTTTATA-A
*
11590042 ATTTTATATA
1 TTTTTATA-A
11590052 TTTT
1 TTTT
11590056 AATATGTGTC
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
9 31 0.48
10 30 0.47
11 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Done.