Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 53 of 93
Found at i:20308327 original size:18 final size:18
Alignment explanation
Indices: 20308306--20308364 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
20308296 TCTCTTTTTC
20308306 TTCCTTTCTTTCTTTCCT
1 TTCCTTTCTTTCTTTCCT
20308324 TTCCTTTCTTT-TTT-C-
1 TTCCTTTCTTTCTTTCCT
*
20308339 TT-CTTTCTATCCTTTCCT
1 TTCCTTTCT-TTCTTTCCT
20308357 TTCTCTTT
1 TTC-CTTT
20308365 TCTTCTTGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
17 4 0.12
18 13 0.38
20 4 0.12
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.68
Consensus pattern (18 bp):
TTCCTTTCTTTCTTTCCT
Found at i:20308339 original size:33 final size:34
Alignment explanation
Indices: 20308300--20308364 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
20308290 CTTTTCTCTC
*
20308300 TTTTTCTTCCTTTCT-TTCTTTCCTTTC-CTTTCT
1 TTTTTCTT-CTTTCTATCCTTTCCTTTCTCTTTCT
20308333 TTTTTCTTCTTTCTATCCTTTCCTTTCTCTTT
1 TTTTTCTTCTTTCTATCCTTTCCTTTCTCTTT
20308365 TCTTCTTGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 6 0.21
33 19 0.66
34 4 0.14
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (34 bp):
TTTTTCTTCTTTCTATCCTTTCCTTTCTCTTTCT
Found at i:20308343 original size:28 final size:28
Alignment explanation
Indices: 20308311--20308371 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
20308301 TTTTCTTCCT
* *
20308311 TTCTTTCTTTCCTTTCCTTTCTTTTTTC
1 TTCTTTCTATCCTTTCCTTTCTCTTTTC
20308339 TTCTTTCTATCCTTTCCTTTCTCTTTTC
1 TTCTTTCTATCCTTTCCTTTCTCTTTTC
20308367 TTCTT
1 TTCTT
20308372 GGTTATGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (28 bp):
TTCTTTCTATCCTTTCCTTTCTCTTTTC
Found at i:20311483 original size:72 final size:72
Alignment explanation
Indices: 20311363--20311523 Score: 250
Period size: 72 Copynumber: 2.2 Consensus size: 72
20311353 CCCGAGAGTT
* * * ** *
20311363 TCTCGCTGCAACGAGAACCAGGCCAATGTAACCCCCCCCAACTTGAGAGTTTCTCGTTGCAATGC
1 TCTCGTTGCAGCGAGAACCAAGCCAATGTAACCCCCCCCAACCCGAGAGTTTCTCGCTGCAATGC
20311428 AAATGAA
66 AAATGAA
*
20311435 TCTCGTTGCAGCGAGAACCAAGCCAATGTAACCCCCCTCAACCCGAGAGTTTCTCGCTGCAATGC
1 TCTCGTTGCAGCGAGAACCAAGCCAATGTAACCCCCCCCAACCCGAGAGTTTCTCGCTGCAATGC
20311500 AAATGAA
66 AAATGAA
*
20311507 TCTCGTTGCAGCTAGAA
1 TCTCGTTGCAGCGAGAA
20311524 ACAAAGCAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 81 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (72 bp):
TCTCGTTGCAGCGAGAACCAAGCCAATGTAACCCCCCCCAACCCGAGAGTTTCTCGCTGCAATGC
AAATGAA
Found at i:20320263 original size:42 final size:41
Alignment explanation
Indices: 20320211--20320291 Score: 117
Period size: 42 Copynumber: 2.0 Consensus size: 41
20320201 GTGGACTCGG
* *
20320211 CTATGTGCGAGTAGGAGTGTGCATAAGCCGATGATGACCCGA
1 CTATATGCGAGTAGGAGTGCGCATAAGCCGA-GATGACCCGA
* *
20320253 CTATATGCGAGTGGGAGTGCGTATAAGCCGAGATGACCC
1 CTATATGCGAGTAGGAGTGCGCATAAGCCGAGATGACCC
20320292 AGCCATGTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 8 0.23
42 27 0.77
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (41 bp):
CTATATGCGAGTAGGAGTGCGCATAAGCCGAGATGACCCGA
Found at i:20320310 original size:42 final size:42
Alignment explanation
Indices: 20320216--20320314 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
20320206 CTCGGCTATG
* * *
20320216 TGCGAGTAGGAGTGTGCATAAGCCGATGATGACCCGACTATA
1 TGCGAGTGGGAGTGCGCATAAGCCGATGATGACCCGACCATA
* *
20320258 TGCGAGTGGGAGTGCGTATAAGCCGA-GATGACCC-AGCCATG
1 TGCGAGTGGGAGTGCGCATAAGCCGATGATGACCCGA-CCATA
*
20320299 TGCTAGTTGGGAGTGC
1 TGCGAG-TGGGAGTGC
20320315 ACATGAGTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
40 1 0.02
41 16 0.33
42 32 0.65
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.21
Consensus pattern (42 bp):
TGCGAGTGGGAGTGCGCATAAGCCGATGATGACCCGACCATA
Found at i:20331128 original size:26 final size:26
Alignment explanation
Indices: 20331099--20331185 Score: 156
Period size: 26 Copynumber: 3.3 Consensus size: 26
20331089 ACCATATACC
*
20331099 CATCGTCATCATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
20331125 CATCATCATCATGCACACCTTCCCAT
1 CATCATCATCATGCACACCATCCCAT
20331151 CATCATCATCATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
20331177 CATCATCAT
1 CATCATCAT
20331186 TCTCAGCTCA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 58 1.00
ACGTcount: A:0.29, C:0.41, G:0.05, T:0.25
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:20331248 original size:43 final size:43
Alignment explanation
Indices: 20331195--20331356 Score: 198
Period size: 43 Copynumber: 3.8 Consensus size: 43
20331185 TTCTCAGCTC
** **
20331195 ATGCGCACTCCCTACTCGCACATGTCTAGGTCATCATCGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCATCGGGTT
* *
20331238 ATGCGTACTCCCTACTCGCACATAACCGGGTCATCACCGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCATCGGGTT
* * ***
20331281 ATGCGCACTCTCTACTCACACATAACCGGGTCATCATCTACTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCATCGGGTT
* * *
20331324 ATGCGTACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
20331357 ATATCATTAC
Statistics
Matches: 101, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCATCGGGTT
Found at i:20331314 original size:86 final size:86
Alignment explanation
Indices: 20331195--20331356 Score: 225
Period size: 86 Copynumber: 1.9 Consensus size: 86
20331185 TTCTCAGCTC
* ** * **
20331195 ATGCGCACTCCCTACTCGCACATGTCTAGGTCATCATCGGGTTATGCGTACTCCCTACTCGCACA
1 ATGCGCACTCCCTACTCACACATAACCAGGTCATCATCGACTTATGCGTACTCCCTACTCGCACA
*
20331260 TAACCGGGTCATCACCGGGTT
66 TAACCGAGTCATCACCGGGTT
* * *
20331281 ATGCGCACTCTCTACTCACACATAACCGGGTCATCATCTACTTATGCGTACTCCCTACTCGCACA
1 ATGCGCACTCCCTACTCACACATAACCAGGTCATCATCGACTTATGCGTACTCCCTACTCGCACA
*
20331346 TAGCCGAGTCA
66 TAACCGAGTCA
20331357 ATATCATTAC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 65 1.00
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (86 bp):
ATGCGCACTCCCTACTCACACATAACCAGGTCATCATCGACTTATGCGTACTCCCTACTCGCACA
TAACCGAGTCATCACCGGGTT
Found at i:20331388 original size:2 final size:2
Alignment explanation
Indices: 20331381--20331413 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20331371 CAATGTATTC
20331381 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20331414 CANNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20336979 original size:11 final size:12
Alignment explanation
Indices: 20336963--20337004 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
20336953 AACCAGCAAC
20336963 AAGAACAAAGA-
1 AAGAACAAAGAG
20336974 AAGAACAAA-AG
1 AAGAACAAAGAG
*
20336985 AAGAACAAAGGG
1 AAGAACAAAGAG
*
20336997 AAAAACAA
1 AAGAACAA
20337005 GAAAACCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 1 0.04
11 18 0.67
12 8 0.30
ACGTcount: A:0.71, C:0.10, G:0.19, T:0.00
Consensus pattern (12 bp):
AAGAACAAAGAG
Found at i:20338045 original size:42 final size:42
Alignment explanation
Indices: 20337980--20338060 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
20337970 GTTGATTTGA
20337980 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* *
20338022 ACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGTTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTG
20338061 TTGCCCCCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.35, T:0.22
Consensus pattern (42 bp):
ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
Found at i:20338331 original size:26 final size:26
Alignment explanation
Indices: 20338295--20338356 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
20338285 TTGCATATGA
20338295 GATGATGATGATGGGATGATGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
20338321 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
20338347 GTTGATGATG
1 GATGATGATG
20338357 GGTATATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.40, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGATGTGCAT
Found at i:20343824 original size:21 final size:22
Alignment explanation
Indices: 20343787--20343829 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
20343777 TTTTTCAGTT
*
20343787 TTAATTCAAATCATGTTATTAA
1 TTAATTCAAAGCATGTTATTAA
*
20343809 TTAATT-AAAGCATGTTTTTAA
1 TTAATTCAAAGCATGTTATTAA
20343830 AAGGTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (22 bp):
TTAATTCAAAGCATGTTATTAA
Found at i:20351813 original size:20 final size:21
Alignment explanation
Indices: 20351788--20351829 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
20351778 TAGTCTATGG
*
20351788 AATTGAATTTG-TTAATTTAA
1 AATTGAATATGATTAATTTAA
*
20351808 AATTGAATATGATTCATTTAA
1 AATTGAATATGATTAATTTAA
20351829 A
1 A
20351830 TTAATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (21 bp):
AATTGAATATGATTAATTTAA
Found at i:20368527 original size:20 final size:20
Alignment explanation
Indices: 20368501--20368546 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
20368491 AATCTTACCT
* *
20368501 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
20368522 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
20368543 TTTT
1 TTTT
20368547 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:20368548 original size:22 final size:22
Alignment explanation
Indices: 20368506--20368546 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20368496 TACCTTTTTT
*
20368506 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
20368528 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
20368547 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:20375054 original size:37 final size:37
Alignment explanation
Indices: 20374984--20375102 Score: 159
Period size: 37 Copynumber: 3.2 Consensus size: 37
20374974 TATATACATA
*
20374984 CATCGTCATCATGTGTGCACTCCTTACTCGCACAC-T
1 CATCATCATCATGTGTGCACTCCTTACTCGCACACTT
* * * * *
20375020 CTATTATCATCATGTGTGTATTCCCTACTAGCACACTT
1 C-ATCATCATCATGTGTGCACTCCTTACTCGCACACTT
20375058 CATCATCATCATGTGTGCACTCCTTACTCGCACACTT
1 CATCATCATCATGTGTGCACTCCTTACTCGCACACTT
*
20375095 CAACATCA
1 CATCATCA
20375103 CCACCCAACA
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
36 1 0.01
37 66 0.96
38 2 0.03
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.33
Consensus pattern (37 bp):
CATCATCATCATGTGTGCACTCCTTACTCGCACACTT
Found at i:20383909 original size:38 final size:39
Alignment explanation
Indices: 20383867--20383969 Score: 111
Period size: 38 Copynumber: 2.6 Consensus size: 39
20383857 ATATTGTCCG
* *
20383867 TGTGCACAATGTGGGGGGATGTACACGATGGCATT-AAC-
1 TGTGCACAATGTGGGGGGATGCACACGATGAC-TTCAACA
** * *
20383905 TGTGCATGATGTGGGGGGATGCACGCGATGACTTCAGCTA
1 TGTGCACAATGTGGGGGGATGCACACGATGACTTCAAC-A
*
20383945 TGTGCACAATGTAGGGGGATGCACA
1 TGTGCACAATGTGGGGGGATGCACA
20383970 TGAGCTAGGT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
37 2 0.04
38 29 0.56
40 21 0.40
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.23
Consensus pattern (39 bp):
TGTGCACAATGTGGGGGGATGCACACGATGACTTCAACA
Found at i:20386849 original size:24 final size:24
Alignment explanation
Indices: 20386817--20386875 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
20386807 TGAAAATAAT
20386817 GAAAAATAAAAGGATAACGTAGTG
1 GAAAAATAAAAGGATAACGTAGTG
20386841 GAAAAATAAAAGGATAACGTAGTG
1 GAAAAATAAAAGGATAACGTAGTG
*
20386865 AAAAAATAAAA
1 GAAAAATAAAA
20386876 ATAGATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.61, C:0.03, G:0.20, T:0.15
Consensus pattern (24 bp):
GAAAAATAAAAGGATAACGTAGTG
Found at i:20394871 original size:19 final size:19
Alignment explanation
Indices: 20394830--20394872 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
20394820 AATGAGGGTG
*
20394830 GTGAGATTATATAATCCCG
1 GTGAGATTATATAATCCCA
*
20394849 GTGAGATTATATAATCTCA
1 GTGAGATTATATAATCCCA
20394868 GTGAG
1 GTGAG
20394873 TAAACAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (19 bp):
GTGAGATTATATAATCCCA
Found at i:20401080 original size:11 final size:11
Alignment explanation
Indices: 20401064--20401091 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20401054 CACTGTAGTT
20401064 TTTAAAACAAC
1 TTTAAAACAAC
20401075 TTTAAAACAAC
1 TTTAAAACAAC
20401086 TTTAAA
1 TTTAAA
20401092 CCCAAAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (11 bp):
TTTAAAACAAC
Found at i:20404910 original size:13 final size:13
Alignment explanation
Indices: 20404892--20404916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20404882 TTTCAAAAAA
20404892 TTTATAAAATCAT
1 TTTATAAAATCAT
20404905 TTTATAAAATCA
1 TTTATAAAATCA
20404917 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:20409628 original size:19 final size:19
Alignment explanation
Indices: 20409604--20409641 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
20409594 ACTTCTAAAC
20409604 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
*
20409623 CTCAAATCATACTGCAATA
1 CTCAAATCATACTCCAATA
20409642 AGTCAAATGG
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:0.42, C:0.29, G:0.03, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:20411758 original size:40 final size:40
Alignment explanation
Indices: 20411703--20411805 Score: 111
Period size: 38 Copynumber: 2.6 Consensus size: 40
20411693 ACCCGACTCA
* * *
20411703 TGTGCATCTCCCCACATCGTGCACATAGCCGGAGCCATCG
1 TGTGCATCACCCCACATCGTGCACATAACCAGAGCCATCG
* * * *
20411743 TGTGCATCACCCCACATTGTG--CATAATCAGTGCCATTG
1 TGTGCATCACCCCACATCGTGCACATAACCAGAGCCATCG
* *
20411781 TGTACATCCCCCCACATCGTGCACA
1 TGTGCATCACCCCACATCGTGCACA
20411806 CGGGCACTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
38 30 0.59
40 21 0.41
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (40 bp):
TGTGCATCACCCCACATCGTGCACATAACCAGAGCCATCG
Found at i:20417272 original size:60 final size:60
Alignment explanation
Indices: 20417179--20417324 Score: 184
Period size: 60 Copynumber: 2.4 Consensus size: 60
20417169 TAGGAGACCA
* * * * * * *
20417179 AAACAGAAGGTTTTTCGCTGCAGCGAGATTCAATCTCGCTGCAGCAAAATTATAACCCAT
1 AAACAGAAAGTTTCTCGCTGCAGCGAAATTCAATCTCACTGCAACAAAATTACAACCCAG
* * ** *
20417239 AAACAGAATGTTTCTCGCTGCAGGGAAATTCAATCTCACTGCAATGAAATTGCAACCCAG
1 AAACAGAAAGTTTCTCGCTGCAGCGAAATTCAATCTCACTGCAACAAAATTACAACCCAG
20417299 AAACAGAAAGTTTCTCGCTGCAGCGA
1 AAACAGAAAGTTTCTCGCTGCAGCGA
20417325 GAAGCTACAG
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (60 bp):
AAACAGAAAGTTTCTCGCTGCAGCGAAATTCAATCTCACTGCAACAAAATTACAACCCAG
Found at i:20417710 original size:43 final size:43
Alignment explanation
Indices: 20417663--20417769 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 43
20417653 CCAACTCATT
* ** * **
20417663 CGCACTCCCTACTCGCACATGGCTAGGTCATCAC-CGGGTTATG
1 CGCACTCCCTACTCACACATAACCAGGTCATC-CTCGACTTATG
*
20417706 CGCACTCCCTACTCACACATAACCGGGTCATCCTCGACTTATG
1 CGCACTCCCTACTCACACATAACCAGGTCATCCTCGACTTATG
20417749 CGCACTCCCTACTCACACATA
1 CGCACTCCCTACTCACACATA
20417770 GCTGAGTCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.02
43 55 0.98
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.22
Consensus pattern (43 bp):
CGCACTCCCTACTCACACATAACCAGGTCATCCTCGACTTATG
Found at i:20427831 original size:24 final size:24
Alignment explanation
Indices: 20427811--20427871 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
20427801 TAAAGTTTTT
*
20427811 TTTTAATTATTTTAAATAGTTTAG
1 TTTTAATTATTTTAAATAGTTTAA
*
20427835 TTTTAATTATTTTAAGTAGTTTAA
1 TTTTAATTATTTTAAATAGTTTAA
*
20427859 TTTTAGTTATTTT
1 TTTTAATTATTTT
20427872 GGTTAAGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (24 bp):
TTTTAATTATTTTAAATAGTTTAA
Found at i:20441813 original size:19 final size:19
Alignment explanation
Indices: 20441789--20441886 Score: 56
Period size: 19 Copynumber: 5.1 Consensus size: 19
20441779 TGCCCGTGTG
20441789 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
20441808 CACGATG-GCACTGATTGTG
1 CACGATGTGGGGGGA-TGTA
*
20441827 CACGATGT-GGGGGATGCA
1 CACGATGTGGGGGGATGTA
* * ** *
20441845 CATGATGGTGCCGGCTATGTG
1 CACGAT-GTG-GGGGGATGTA
20441866 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
20441885 CA
1 CA
20441887 TGAGCCGGGA
Statistics
Matches: 52, Mismatches: 22, Indels: 10
0.62 0.26 0.12
Matches are distributed among these distances:
18 10 0.19
19 29 0.56
20 3 0.06
21 10 0.19
ACGTcount: A:0.20, C:0.16, G:0.41, T:0.22
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:20444607 original size:55 final size:55
Alignment explanation
Indices: 20444548--20444752 Score: 313
Period size: 55 Copynumber: 3.7 Consensus size: 55
20444538 TGATGATGGG
** *
20444548 TGATTCCAGCTATGTGCAATGTGGGAGTGCACATGAGCTAATGACCGGTGGATGA
1 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGA
*
20444603 TGATTCCAGCTATGTGC-GTCGTGGCAGTGCACATGAGCTGATGACCGGTGGATGA
1 TGATTCCAGCTATGTGCGGT-GTGGGAGTGCACATGAGCTGATGACCGGTGGATGA
* * **
20444658 TGATTCCAGCTATGTGTGGTGTGGAAGTGCACATGAGCTGATGACTAGTGGATGA
1 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGA
*
20444713 TGATTCCAGCTATGTGGGGTGTGGGAGTGCACATGAGCTG
1 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
20444753 TTGAGCCGAT
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
54 1 0.01
55 136 0.98
56 2 0.01
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.27
Consensus pattern (55 bp):
TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGACCGGTGGATGA
Found at i:20448093 original size:13 final size:13
Alignment explanation
Indices: 20448075--20448099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20448065 GGAGAAATTG
20448075 TGATTTTATAAAA
1 TGATTTTATAAAA
20448088 TGATTTTATAAA
1 TGATTTTATAAA
20448100 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:20461482 original size:9 final size:9
Alignment explanation
Indices: 20461468--20461501 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
20461458 AGGAAAAACC
20461468 TTTGAGCGT
1 TTTGAGCGT
20461477 TTTGAGCGT
1 TTTGAGCGT
* *
20461486 TTTAAGCAT
1 TTTGAGCGT
20461495 TTTGAGC
1 TTTGAGC
20461502 ATTGATAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.44
Consensus pattern (9 bp):
TTTGAGCGT
Found at i:20461755 original size:59 final size:59
Alignment explanation
Indices: 20461684--20461799 Score: 160
Period size: 59 Copynumber: 2.0 Consensus size: 59
20461674 GGGCCATGTG
** *
20461684 TGACTAGTTTTAGGCATTAGGTTTAAGGGCTTTGGGCATTGCGTGACTTATGGTTTGCA
1 TGACTAGTTTTAGGCATTAGGTTTAAGGGCTTTAAGCATTGCGTGACTTAAGGTTTGCA
* * * * *
20461743 TGACTAGTTTTAGGCATTGGGTTTAGGGGTTTTAAGCATTTCTTGACTTAAGGTTTG
1 TGACTAGTTTTAGGCATTAGGTTTAAGGGCTTTAAGCATTGCGTGACTTAAGGTTTG
20461800 AGTGATTGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.41
Consensus pattern (59 bp):
TGACTAGTTTTAGGCATTAGGTTTAAGGGCTTTAAGCATTGCGTGACTTAAGGTTTGCA
Found at i:20461934 original size:45 final size:45
Alignment explanation
Indices: 20461854--20461941 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
20461844 GCGTGATTGG
* * * * *
20461854 TTGATAGGGCATTGCGTGATTGGTTTTAAATCATTACGTGACTAA
1 TTGATAGGGCATTGCATGAATAGTTATAAAGCATTACGTGACTAA
*
20461899 TTGATAGGGCATTGCATGAATAGTTGAT-AAGCATTATGTGACT
1 TTGATAGGGCATTGCATGAATAGTT-ATAAAGCATTACGTGACT
20461942 GGCTTTTAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
45 35 0.97
46 1 0.03
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.36
Consensus pattern (45 bp):
TTGATAGGGCATTGCATGAATAGTTATAAAGCATTACGTGACTAA
Found at i:20462149 original size:22 final size:22
Alignment explanation
Indices: 20462117--20462163 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
20462107 AGGCATTACA
* *
20462117 TGATTGGTTTTTAGACTTTGCG
1 TGATTGATTTTTAGACATTGCG
*
20462139 TGATTGATTTTTAGGCATTGCG
1 TGATTGATTTTTAGACATTGCG
20462161 TGA
1 TGA
20462164 CTAGTTGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.09, G:0.28, T:0.47
Consensus pattern (22 bp):
TGATTGATTTTTAGACATTGCG
Found at i:20462186 original size:23 final size:22
Alignment explanation
Indices: 20462150--20462213 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
20462140 GATTGATTTT
*
20462150 TAGGCATTGCGTGACTAGTTGA
1 TAGGCATTACGTGACTAGTTGA
* **
20462172 TAGGGCATTATGTGACTAGTTTT
1 TA-GGCATTACGTGACTAGTTGA
20462195 TAGGCATTACGTGAC-AGTT
1 TAGGCATTACGTGACTAGTT
20462214 TTCTAGTCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.11
22 14 0.39
23 18 0.50
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.36
Consensus pattern (22 bp):
TAGGCATTACGTGACTAGTTGA
Found at i:20462197 original size:112 final size:112
Alignment explanation
Indices: 20461975--20462202 Score: 235
Period size: 112 Copynumber: 2.0 Consensus size: 112
20461965 ATTTGTAAGG
* * * *
20461975 CATTGCATGACTGGTTGAGAGGGCATTGCATGACTAGCTTATAGTCATTTCGTGATCGATTTGTA
1 CATTGCATGACTGCTTGAGAAGGCATTACATGACTAGCTTATAGACATTTCGTGATCGATTTGTA
** * * *
20462040 GGGCATTACGTGACTAATTTTTAGGCATTGTATGATTGGTGTTTAGA
66 GGGCATTACGTGACTAATTGATAGGCATTATATGACTAGTGTTTAGA
* * * * * * *
20462087 CATTGCATGACTGCTTGATAAGGCATTACATGATTGGTTTTTAGAC-TTTGCGTGATTGATTTTT
1 CATTGCATGACTGCTTGAGAAGGCATTACATGACTAGCTTATAGACATTT-CGTGATCGATTTGT
* * * * *
20462151 A-GGCATTGCGTGACTAGTTGATAGGGCATTATGTGACTAGTTTTTAGG
65 AGGGCATTACGTGACTAATTGATA-GGCATTATATGACTAGTGTTTAGA
20462199 CATT
1 CATT
20462203 ACGTGACAGT
Statistics
Matches: 93, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
111 21 0.23
112 72 0.77
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39
Consensus pattern (112 bp):
CATTGCATGACTGCTTGAGAAGGCATTACATGACTAGCTTATAGACATTTCGTGATCGATTTGTA
GGGCATTACGTGACTAATTGATAGGCATTATATGACTAGTGTTTAGA
Found at i:20462208 original size:67 final size:67
Alignment explanation
Indices: 20462038--20462208 Score: 191
Period size: 67 Copynumber: 2.6 Consensus size: 67
20462028 GATCGATTTG
* ** *
20462038 TAGGGCATTACGTGACTAATTTTTAGGCATTGTATGATTGGTGTTTAGACATTGCATGACTGCTT
1 TAGGGCATTACGTGACTAGTTTTTAGGCATTGCGTGATTGATGTTTAGACATTGCATGACTGCTT
20462103 GA
66 GA
* * * * * * * * *
20462105 TAAGGCATTACATGATTGGTTTTTAGACTTTGCGTGATTGATTTTTAGGCATTGCGTGACTAG-T
1 TAGGGCATTACGTGACTAGTTTTTAGGCATTGCGTGATTGATGTTTAGACATTGCATGACT-GCT
20462169 TGA
65 TGA
* *
20462172 TAGGGCATTATGTGACTAGTTTTTAGGCATTACGTGA
1 TAGGGCATTACGTGACTAGTTTTTAGGCATTGCGTGA
20462209 CAGTTTTCTA
Statistics
Matches: 82, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
67 81 0.99
68 1 0.01
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (67 bp):
TAGGGCATTACGTGACTAGTTTTTAGGCATTGCGTGATTGATGTTTAGACATTGCATGACTGCTT
GA
Found at i:20462224 original size:22 final size:22
Alignment explanation
Indices: 20462146--20462224 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
20462136 GCGTGATTGA
*
20462146 TTTTTAGGCATTGCGTGACTAG
1 TTTTTAGGCATTACGTGACTAG
** *
20462168 TTGATAGGGCATTATGTGACTAG
1 TTTTTA-GGCATTACGTGACTAG
20462191 TTTTTAGGCATTACGTGAC-AG
1 TTTTTAGGCATTACGTGACTAG
*
20462212 TTTTCTAGTCATT
1 TTTT-TAGGCATT
20462225 GCTTGGATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
21 6 0.13
22 23 0.49
23 18 0.38
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.42
Consensus pattern (22 bp):
TTTTTAGGCATTACGTGACTAG
Found at i:20465670 original size:43 final size:43
Alignment explanation
Indices: 20465623--20465706 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
20465613 TAAGCATTGC
** * *
20465623 GTGACCCCACATCTGGGATTGCATTGCGTGAATTAGGCATTCT
1 GTGACCCCACATCCAGCATTGCATTACGTGAATTAGGCATTCT
*
20465666 GTGACCCCACATCCAGCATTGCATTACGTGACTTAGGCATT
1 GTGACCCCACATCCAGCATTGCATTACGTGAATTAGGCATT
20465707 GTGTAACAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (43 bp):
GTGACCCCACATCCAGCATTGCATTACGTGAATTAGGCATTCT
Found at i:20465808 original size:20 final size:20
Alignment explanation
Indices: 20465775--20465831 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
20465765 TCTGGCTAAA
*
20465775 CACT-TCTATAGATAGATTG
1 CACTATCTATCGATAGATTG
20465794 CACTATCTATCGATAGATTG
1 CACTATCTATCGATAGATTG
20465814 CACTATCTATCGATAGAT
1 CACTATCTATCGATAGAT
20465832 GAGGTCTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 4 0.11
20 32 0.89
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (20 bp):
CACTATCTATCGATAGATTG
Found at i:20468598 original size:21 final size:20
Alignment explanation
Indices: 20468555--20468599 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
20468545 TGTCATTAAG
* **
20468555 CTATTGATAGATAAGTTCAT
1 CTATTGATAAATAAGAACAT
20468575 CTATTGATAAATAAAGAACAT
1 CTATTGATAAAT-AAGAACAT
20468596 CTAT
1 CTAT
20468600 CGACAATTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (20 bp):
CTATTGATAAATAAGAACAT
Found at i:20474018 original size:40 final size:40
Alignment explanation
Indices: 20473942--20474020 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
20473932 TGGCTAGTTT
**
20473942 TTCACCTTAGTAGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTAGGGTTTTCAACCTCACCAAGATTGGTGA
*
20473982 TTCACCTTAGTGGGGTTTTCAACCTCACCACA-ATTGGTG
1 TTCACCTTAGTAGGGTTTTCAACCTCACCA-AGATTGGTG
20474021 TCTTTCATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (40 bp):
TTCACCTTAGTAGGGTTTTCAACCTCACCAAGATTGGTGA
Found at i:20478921 original size:40 final size:40
Alignment explanation
Indices: 20478863--20478938 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
20478853 CTATTTTTTT
*
20478863 ACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGATTC
1 ACCTTAGTGGGGTCTTCAACCTTGCCAAGATTGGTGATTC
*
20478903 ACCTTAGTGGGGTCTTCAACCTTGCCATGATTGGTG
1 ACCTTAGTGGGGTCTTCAACCTTGCCAAGATTGGTG
20478939 TCTTTCATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.34
Consensus pattern (40 bp):
ACCTTAGTGGGGTCTTCAACCTTGCCAAGATTGGTGATTC
Found at i:20478971 original size:19 final size:20
Alignment explanation
Indices: 20478935--20478972 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20478925 TGCCATGATT
*
20478935 GGTGTCTTTCATAACACCTA
1 GGTGTCTTTCACAACACCTA
20478955 GGTGTCTTT-ACAACACCT
1 GGTGTCTTTCACAACACCT
20478973 CGGCGTCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (20 bp):
GGTGTCTTTCACAACACCTA
Found at i:20479617 original size:21 final size:21
Alignment explanation
Indices: 20479589--20479670 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
20479579 CGCAATACTT
20479589 CAGTCACACAATGCCTAAAAC
1 CAGTCACACAATGCCTAAAAC
** * *
20479610 TGGTCACATAATTCCTAAAAAC
1 CAGTCACACAATGCCT-AAAAC
* *
20479632 CAATCACACAATGCTTAAAAC
1 CAGTCACACAATGCCTAAAAC
* *
20479653 CAGTCATATAATGCCTAA
1 CAGTCACACAATGCCTAA
20479671 GTTTCAAAGA
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
21 31 0.67
22 15 0.33
ACGTcount: A:0.43, C:0.27, G:0.09, T:0.22
Consensus pattern (21 bp):
CAGTCACACAATGCCTAAAAC
Found at i:20484881 original size:124 final size:124
Alignment explanation
Indices: 20484661--20484893 Score: 346
Period size: 124 Copynumber: 1.9 Consensus size: 124
20484651 ACCTTAGAAG
* *
20484661 TGGCAATATGGCTTAATTGAAGGGAGCAATTATGGACTATGCACTGTAATCTTTTTTTCCTTCTG
1 TGGCAATATGGCTCAATTGAAGGGAGCAATTATGGACTATACACTGTAATCTTTTTTTCCTTCTG
*
20484726 ATTAGTTTTGTCCCACTAGGTTTTTTTGGCTTAAAATTTTTAATGAGGTAGTCCACAAA
66 ATGAGTTTTGTCCCACTAGGTTTTTTTGGCTTAAAATTTTTAATGAGGTAGTCCACAAA
* *
20484785 TGGCAATATGGCTCAATTGAAGGGGAGCAATTATGGACTATACACTGTATTC-TTTTTTCTTTCT
1 TGGCAATATGGCTCAATTGAA-GGGAGCAATTATGGACTATACACTGTAATCTTTTTTTCCTTCT
* **
20484849 GATCGA-TTGTTGTCTCACT-GGTTTTTTTGGCTTAAGGTTTTTAAT
65 GAT-GAGTT-TTGTCCCACTAGGTTTTTTTGGCTTAAAATTTTTAAT
20484894 AAAGTAATAT
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
124 60 0.61
125 38 0.39
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (124 bp):
TGGCAATATGGCTCAATTGAAGGGAGCAATTATGGACTATACACTGTAATCTTTTTTTCCTTCTG
ATGAGTTTTGTCCCACTAGGTTTTTTTGGCTTAAAATTTTTAATGAGGTAGTCCACAAA
Found at i:20485864 original size:94 final size:92
Alignment explanation
Indices: 20485721--20486041 Score: 444
Period size: 94 Copynumber: 3.4 Consensus size: 92
20485711 ATAGCACCAC
* * * * *
20485721 TCAGAGTTGGTGAGACGCCATAGAGGGAATCTATGAGACCCCGGAGTTAAGAGTTGGTGACACGC
1 TCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACACC-AAGTTAAGAGTTGGTGACACG-
* *
20485786 CATGGTGGGAATCTGTGACACGACAGCGT
64 CATGGAGGGAATCTGTGACACGCCAGCGT
*
20485815 TCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACACCAATGTTAAGAGTTGGTGACACAA
1 TCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACACCAA-GTTAAGAGTTGGTGACAC-G
* *
20485880 CATGGAGGGAATCTGTGACATGCCAGCAT
64 CATGGAGGGAATCTGTGACACGCCAGCGT
* * *
20485909 TTAGAGTTGGTGAGACGCCATGGAGGGAATTTGTGACACACTAGAGTTAAGAGTTGGTGACACAG
1 TCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACACCA-AGTTAAGAGTTGGTGACAC-G
*
20485974 CATGGAGGGAATTTGTGACACGCCAGCGT
64 CATGGAGGGAATCTGTGACACGCCAGCGT
* *
20486003 TCAGAGTTCGTGAGACCCCATGGAGGGAATCTGTGACAC
1 TCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACAC
20486042 GCCATGGAGG
Statistics
Matches: 203, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
93 1 0.00
94 201 0.99
95 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.33, T:0.21
Consensus pattern (92 bp):
TCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACACCAAGTTAAGAGTTGGTGACACGCA
TGGAGGGAATCTGTGACACGCCAGCGT
Found at i:20486038 original size:23 final size:23
Alignment explanation
Indices: 20486012--20486064 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
20486002 TTCAGAGTTC
*
20486012 GTGAGACCCCATGGAGGGAATCT
1 GTGACACCCCATGGAGGGAATCT
*
20486035 GTGACACGCCATGGAGGGAATCT
1 GTGACACCCCATGGAGGGAATCT
*
20486058 ATGACAC
1 GTGACAC
20486065 GCCAACGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.32, T:0.17
Consensus pattern (23 bp):
GTGACACCCCATGGAGGGAATCT
Found at i:20486040 original size:70 final size:70
Alignment explanation
Indices: 20485965--20486115 Score: 241
Period size: 70 Copynumber: 2.2 Consensus size: 70
20485955 TTAAGAGTTG
* * *
20485965 GTGACACAG-CATGGAGGGAATTTGTGACACGCCAGCGTTCAGAGTTCGTGAGACCCCATGGAGG
1 GTGACAC-GCCATGGAGGGAATCTATGACACGCCAACGTTCAGAGTTCGTGAGACCCCATGGAGG
20486029 GAATCT
65 GAATCT
*
20486035 GTGACACGCCATGGAGGGAATCTATGACACGCCAACGTTCAGAGTTCGTGAGACGCCATGGAGGG
1 GTGACACGCCATGGAGGGAATCTATGACACGCCAACGTTCAGAGTTCGTGAGACCCCATGGAGGG
20486100 AATCT
66 AATCT
*
20486105 GTGACATGCCA
1 GTGACACGCCA
20486116 AAGTTCAAAG
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
69 1 0.01
70 74 0.99
ACGTcount: A:0.26, C:0.23, G:0.32, T:0.19
Consensus pattern (70 bp):
GTGACACGCCATGGAGGGAATCTATGACACGCCAACGTTCAGAGTTCGTGAGACCCCATGGAGGG
AATCT
Found at i:20486042 original size:47 final size:47
Alignment explanation
Indices: 20485723--20486045 Score: 378
Period size: 47 Copynumber: 6.9 Consensus size: 47
20485713 AGCACCACTC
* * * * * *
20485723 AGAGTTGGTGAGACGCCATAGAGGGAATCTATGAGACCCCGGAGTTA
1 AGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACGCCAGCGTTA
* * * *
20485770 AGAGTTGGTGACACGCCATGGTGGGAATCTGTGACACGACAGCGTTC
1 AGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACGCCAGCGTTA
* **
20485817 AGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACACCAATGTTA
1 AGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACGCCAGCGTTA
* ** * * *
20485864 AGAGTTGGTGACACAACATGGAGGGAATCTGTGACATGCCAGCATTT
1 AGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACGCCAGCGTTA
* * * *
20485911 AGAGTTGGTGAGACGCCATGGAGGGAATTTGTGACACACTAGAGTTA
1 AGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACGCCAGCGTTA
* * *
20485958 AGAGTTGGTGACACAG-CATGGAGGGAATTTGTGACACGCCAGCGTTC
1 AGAGTTGGTGAGAC-GCCATGGAGGGAATCTGTGACACGCCAGCGTTA
* *
20486005 AGAGTTCGTGAGACCCCATGGAGGGAATCTGTGACACGCCA
1 AGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACGCCA
20486046 TGGAGGGAAT
Statistics
Matches: 229, Mismatches: 45, Indels: 4
0.82 0.16 0.01
Matches are distributed among these distances:
47 228 1.00
48 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.33, T:0.21
Consensus pattern (47 bp):
AGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACGCCAGCGTTA
Found at i:20486065 original size:23 final size:23
Alignment explanation
Indices: 20486020--20486068 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
20486010 TCGTGAGACC
*
20486020 CCATGGAGGGAATCTGTGACACG
1 CCATGGAGGGAATCTATGACACG
20486043 CCATGGAGGGAATCTATGACACG
1 CCATGGAGGGAATCTATGACACG
20486066 CCA
1 CCA
20486069 ACGTTCAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.31, T:0.16
Consensus pattern (23 bp):
CCATGGAGGGAATCTATGACACG
Found at i:20486080 original size:117 final size:117
Alignment explanation
Indices: 20485918--20486160 Score: 301
Period size: 117 Copynumber: 2.1 Consensus size: 117
20485908 TTTAGAGTTG
* * * * *
20485918 GTGAGACGCCATGGAGGGAATTTGTGACACACTAGAGTTAAGAGTTGGTGACACAG-CATGGAGG
1 GTGACACGCCATGGAGGGAATCTATGACACACCAGAGTTAAGAGTTCGTGACAC-GCCATGGAGG
* ** * * * *
20485982 GAATTTGTGACACGCCAGCGTTCAGAGTTCGTGAGACCCCATGGAGGGAATCT
65 GAATCTGTGACACGCCAAAGTTCAAAGTTAGTGACACCCCATGGAGGGAAGCT
* * *
20486035 GTGACACGCCATGGAGGGAATCTATGACACGCCA-ACGTTCAGAGTTCGTGAGACGCCATGGAGG
1 GTGACACGCCATGGAGGGAATCTATGACACACCAGA-GTTAAGAGTTCGTGACACGCCATGGAGG
* *
20486099 GAATCTGTGACATGCCAAAGTTCAAAGTTAGTGACACGCCATGGAGGGAAGCT
65 GAATCTGTGACACGCCAAAGTTCAAAGTTAGTGACACCCCATGGAGGGAAGCT
20486152 GTGACACGC
1 GTGACACGC
20486161 TAAAGTTCAG
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
116 2 0.02
117 105 0.98
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (117 bp):
GTGACACGCCATGGAGGGAATCTATGACACACCAGAGTTAAGAGTTCGTGACACGCCATGGAGGG
AATCTGTGACACGCCAAAGTTCAAAGTTAGTGACACCCCATGGAGGGAAGCT
Found at i:20486090 original size:164 final size:164
Alignment explanation
Indices: 20485871--20486179 Score: 406
Period size: 164 Copynumber: 1.9 Consensus size: 164
20485861 TTAAGAGTTG
* * * * *
20485871 GTGACACAACATGGAGGGAATCTGTGACATGCCAGCATTTAGAGTTGGTGAGACGCCATGGAGGG
1 GTGACACAACATGGAGGGAATCTATGACACGCCAACATTCAGAGTTCGTGAGACGCCATGGAGGG
* * * * **
20485936 AATTTGTGACACACTAGAGTT-AAGAGTTGGTGACACAG-CATGGAGGGAATTTGTGACACGCCA
66 AATCTGTGACACACCAAAGTTCAA-AGTTAGTGACAC-GCCATGGAGGGAAGCTGTGACACGCCA
**
20485999 GCGTTCAGAGTTCGTGAGACCCCATGGAGGGAATCT
129 AAGTTCAGAGTTCGTGAGACCCCATGGAGGGAATCT
** *
20486035 GTGACACGCCATGGAGGGAATCTATGACACGCCAACGTTCAGAGTTCGTGAGACGCCATGGAGGG
1 GTGACACAACATGGAGGGAATCTATGACACGCCAACATTCAGAGTTCGTGAGACGCCATGGAGGG
** *
20486100 AATCTGTGACATGCCAAAGTTCAAAGTTAGTGACACGCCATGGAGGGAAGCTGTGACACGCTAAA
66 AATCTGTGACACACCAAAGTTCAAAGTTAGTGACACGCCATGGAGGGAAGCTGTGACACGCCAAA
*
20486165 GTTCAGAGTTGGTGA
131 GTTCAGAGTTCGTGA
20486180 CATGCCATGG
Statistics
Matches: 123, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
163 1 0.01
164 120 0.98
165 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.21
Consensus pattern (164 bp):
GTGACACAACATGGAGGGAATCTATGACACGCCAACATTCAGAGTTCGTGAGACGCCATGGAGGG
AATCTGTGACACACCAAAGTTCAAAGTTAGTGACACGCCATGGAGGGAAGCTGTGACACGCCAAA
GTTCAGAGTTCGTGAGACCCCATGGAGGGAATCT
Found at i:20486091 original size:47 final size:47
Alignment explanation
Indices: 20486035--20486189 Score: 220
Period size: 47 Copynumber: 3.3 Consensus size: 47
20486025 GAGGGAATCT
* * *
20486035 GTGACACGCCATGGAGGGAATCTATGACACGCCAACGTTCAGAGTTC
1 GTGACACGCCATGGAGGGAATCTGTGACACGCCAAAGTTCAGAGTTA
* * *
20486082 GTGAGACGCCATGGAGGGAATCTGTGACATGCCAAAGTTCAAAGTTA
1 GTGACACGCCATGGAGGGAATCTGTGACACGCCAAAGTTCAGAGTTA
* * *
20486129 GTGACACGCCATGGAGGGAAGCTGTGACACGCTAAAGTTCAGAGTTG
1 GTGACACGCCATGGAGGGAATCTGTGACACGCCAAAGTTCAGAGTTA
*
20486176 GTGACATGCCATGG
1 GTGACACGCCATGG
20486190 TCATCGTTTA
Statistics
Matches: 95, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 95 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.20
Consensus pattern (47 bp):
GTGACACGCCATGGAGGGAATCTGTGACACGCCAAAGTTCAGAGTTA
Found at i:20486158 original size:23 final size:23
Alignment explanation
Indices: 20486020--20486160 Score: 77
Period size: 23 Copynumber: 6.0 Consensus size: 23
20486010 TCGTGAGACC
*
20486020 CCATGGAGGGAATCTGTGACACG
1 CCATGGAGGGAAGCTGTGACACG
* *
20486043 CCATGGAGGGAATCTATGACACG
1 CCATGGAGGGAAGCTGTGACACG
** *** * *
20486066 CCAACG-TTCAGAGTTCGTGAGACG
1 CCATGGAGGGA-AGCT-GTGACACG
* *
20486090 CCATGGAGGGAATCTGTGACATG
1 CCATGGAGGGAAGCTGTGACACG
** **** *
20486113 CCAAAGTTCAAAGTTAGTGACACG
1 CCATGGAGGGAAGCT-GTGACACG
20486137 CCATGGAGGGAAGCTGTGACACG
1 CCATGGAGGGAAGCTGTGACACG
20486160 C
1 C
20486161 TAAAGTTCAG
Statistics
Matches: 79, Mismatches: 35, Indels: 8
0.65 0.29 0.07
Matches are distributed among these distances:
22 1 0.01
23 50 0.63
24 27 0.34
25 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.18
Consensus pattern (23 bp):
CCATGGAGGGAAGCTGTGACACG
Found at i:20486742 original size:31 final size:31
Alignment explanation
Indices: 20486696--20486961 Score: 284
Period size: 31 Copynumber: 8.6 Consensus size: 31
20486686 AGTTAGTTAT
20486696 TGGCGTGTGACAGCATTTTACTTGATATGCA
1 TGGCGTGTGACAGCATTTTACTTGATATGCA
* *
20486727 TGGCATGTGATAGCATTTTACTTGATATGCA
1 TGGCGTGTGACAGCATTTTACTTGATATGCA
* *
20486758 TGGCGTCTGATAGCATTTTACTTGATATGCA
1 TGGCGTGTGACAGCATTTTACTTGATATGCA
* * * *
20486789 TGGCGTGTCACAACATTTTACTTGTTATGGA
1 TGGCGTGTGACAGCATTTTACTTGATATGCA
* *
20486820 TGGCATGTGATAGCATTTTACTTGATATGCA
1 TGGCGTGTGACAGCATTTTACTTGATATGCA
* * * * *
20486851 TGGCGTGTCACAACGTTTAACTTGTTATGCA
1 TGGCGTGTGACAGCATTTTACTTGATATGCA
* *
20486882 TGGCGTGTCACAACATTTTACTTGCA-ATGCA
1 TGGCGTGTGACAGCATTTTACTTG-ATATGCA
* * * * *
20486913 TGGCATGTCACAACATTTTGCTT-ACAGTGCA
1 TGGCGTGTGACAGCATTTTACTTGATA-TGCA
* *
20486944 TGGCGTGTCACAACATTT
1 TGGCGTGTGACAGCATTT
20486962 ATTCCTTATT
Statistics
Matches: 203, Mismatches: 29, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
29 1 0.00
30 1 0.00
31 201 0.99
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (31 bp):
TGGCGTGTGACAGCATTTTACTTGATATGCA
Found at i:20486773 original size:62 final size:62
Alignment explanation
Indices: 20486696--20486931 Score: 321
Period size: 62 Copynumber: 3.8 Consensus size: 62
20486686 AGTTAGTTAT
* * * *
20486696 TGGCGTGTGACAGCATTTTACTTGATATGCATGGCATGTGATAGCATTTTACTTGATATGCA
1 TGGCGTGTGACAGCATTTTACTTGATATGCATGGCATGTCACAACATTTTACTTGTTATGCA
* * * *
20486758 TGGCGTCTGATAGCATTTTACTTGATATGCATGGCGTGTCACAACATTTTACTTGTTATGGA
1 TGGCGTGTGACAGCATTTTACTTGATATGCATGGCATGTCACAACATTTTACTTGTTATGCA
* * * * *
20486820 TGGCATGTGATAGCATTTTACTTGATATGCATGGCGTGTCACAACGTTTAACTTGTTATGCA
1 TGGCGTGTGACAGCATTTTACTTGATATGCATGGCATGTCACAACATTTTACTTGTTATGCA
* *
20486882 TGGCGTGTCACAACATTTTACTTGCA-ATGCATGGCATGTCACAACATTTT
1 TGGCGTGTGACAGCATTTTACTTG-ATATGCATGGCATGTCACAACATTTT
20486932 GCTTACAGTG
Statistics
Matches: 153, Mismatches: 20, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
62 152 0.99
63 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (62 bp):
TGGCGTGTGACAGCATTTTACTTGATATGCATGGCATGTCACAACATTTTACTTGTTATGCA
Found at i:20486855 original size:93 final size:93
Alignment explanation
Indices: 20486696--20486962 Score: 349
Period size: 93 Copynumber: 2.9 Consensus size: 93
20486686 AGTTAGTTAT
* *
20486696 TGGCGTGTGACAGCATTTTACTTGATATGCATGGCATGTGATAGCATTTTACTTGATATGCATGG
1 TGGCGTGTCACAACATTTTACTTGATATGCATGGCATGTGATAGCATTTTACTTGATATGCATGG
* * * *
20486761 CGTCTGATAGCATTTTACTTGATATGCA
66 CGTCTCACAACATTTAACTTGATATGCA
* *
20486789 TGGCGTGTCACAACATTTTACTTGTTATGGATGGCATGTGATAGCATTTTACTTGATATGCATGG
1 TGGCGTGTCACAACATTTTACTTGATATGCATGGCATGTGATAGCATTTTACTTGATATGCATGG
* * *
20486854 CGTGTCACAACGTTTAACTTGTTATGCA
66 CGTCTCACAACATTTAACTTGATATGCA
* * * * *
20486882 TGGCGTGTCACAACATTTTACTTGCA-ATGCATGGCATGTCACAACATTTTGCTT-ACAGTGCAT
1 TGGCGTGTCACAACATTTTACTTG-ATATGCATGGCATGTGATAGCATTTTACTTGATA-TGCAT
*
20486945 GGCGTGTCACAACATTTA
64 GGCGTCTCACAACATTTA
20486963 TTCCTTATTT
Statistics
Matches: 153, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
92 2 0.01
93 151 0.99
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (93 bp):
TGGCGTGTCACAACATTTTACTTGATATGCATGGCATGTGATAGCATTTTACTTGATATGCATGG
CGTCTCACAACATTTAACTTGATATGCA
Found at i:20486944 original size:62 final size:62
Alignment explanation
Indices: 20486696--20486961 Score: 320
Period size: 62 Copynumber: 4.3 Consensus size: 62
20486686 AGTTAGTTAT
* * *
20486696 TGGCGTGTGACAGCATTTTACTTGATATGCATGGCATGTGATAGCATTTTACTTGATATGCA
1 TGGCGTGTGACAGCATTTTACTTGATATGCATGGCATGTCACAACATTTTACTTGATATGCA
* * * * *
20486758 TGGCGTCTGATAGCATTTTACTTGATATGCATGGCGTGTCACAACATTTTACTTGTTATGGA
1 TGGCGTGTGACAGCATTTTACTTGATATGCATGGCATGTCACAACATTTTACTTGATATGCA
* * * * * *
20486820 TGGCATGTGATAGCATTTTACTTGATATGCATGGCGTGTCACAACGTTTAACTTGTTATGCA
1 TGGCGTGTGACAGCATTTTACTTGATATGCATGGCATGTCACAACATTTTACTTGATATGCA
* * * *
20486882 TGGCGTGTCACAACATTTTACTTGCA-ATGCATGGCATGTCACAACATTTTGCTT-ACAGTGCA
1 TGGCGTGTGACAGCATTTTACTTG-ATATGCATGGCATGTCACAACATTTTACTTGATA-TGCA
* *
20486944 TGGCGTGTCACAACATTT
1 TGGCGTGTGACAGCATTT
20486962 ATTCCTTATT
Statistics
Matches: 179, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
61 1 0.01
62 177 0.99
63 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (62 bp):
TGGCGTGTGACAGCATTTTACTTGATATGCATGGCATGTCACAACATTTTACTTGATATGCA
Found at i:20489345 original size:31 final size:31
Alignment explanation
Indices: 20489304--20489632 Score: 336
Period size: 31 Copynumber: 10.6 Consensus size: 31
20489294 TCAACCTTAA
* *
20489304 CGTGTGACAACATTTGACTTGATATGCATGG
1 CGTGTCACAACATTTTACTTGATATGCATGG
* *
20489335 CGTGTCACAACATTTTACTTGTTATTCATGG
1 CGTGTCACAACATTTTACTTGATATGCATGG
* * * *
20489366 CGTGTCACAACGTTTGATTTTATATGCATGG
1 CGTGTCACAACATTTTACTTGATATGCATGG
* * * * ** * * *
20489397 TGTGTCAGAATATTTTGCTTCTTATCCTTAG
1 CGTGTCACAACATTTTACTTGATATGCATGG
* * * * *
20489428 CGTGTCATAATAATTTACTTGTTATGGATGG
1 CGTGTCACAACATTTTACTTGATATGCATGG
* * *
20489459 CGTGTCACAACGTTTAACTTGTTATGCATGG
1 CGTGTCACAACATTTTACTTGATATGCATGG
* * *
20489490 TGTGTCACAACATTTTACTTGTTTTGCATGG
1 CGTGTCACAACATTTTACTTGATATGCATGG
* ***
20489521 CGTGTGACAACATTTTACTTGATATGCACAA
1 CGTGTCACAACATTTTACTTGATATGCATGG
*
20489552 CGTGTCACAACATTTTACTT-ATTTTGCATGG
1 CGTGTCACAACATTTTACTTGA-TATGCATGG
*
20489583 CGTGTGACAACATTTTACTTGATATGCATGG
1 CGTGTCACAACATTTTACTTGATATGCATGG
20489614 CGTGTCACAACATTTTACT
1 CGTGTCACAACATTTTACT
20489633 GTTTATGGTT
Statistics
Matches: 240, Mismatches: 56, Indels: 4
0.80 0.19 0.01
Matches are distributed among these distances:
30 1 0.00
31 238 0.99
32 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.39
Consensus pattern (31 bp):
CGTGTCACAACATTTTACTTGATATGCATGG
Found at i:20492668 original size:55 final size:54
Alignment explanation
Indices: 20492574--20492759 Score: 212
Period size: 55 Copynumber: 3.4 Consensus size: 54
20492564 TCGTTAAACC
* *
20492574 AACAGCAGTGACACGCTAAAAACCCAAAAAACCATTTAACCCACGACACGCTAGG
1 AACAGCCGTGACACGCTAAAAACCCAAAAAA-CAGTTAACCCACGACACGCTAGG
* ** * *
20492629 AGCAGCCGTGACACG-TCAAAAACCCATAAATTCAGTTAACCCACGACACACCAGG
1 AACAGCCGTGACACGCT-AAAAACCCA-AAAAACAGTTAACCCACGACACGCTAGG
* * *
20492684 AACAACCGTGACACGCTAACAACCCAAAAAACTAGTTAACCCACAACACGCTAGG
1 AACAGCCGTGACACGCTAAAAACCCAAAAAAC-AGTTAACCCACGACACGCTAGG
* * *
20492739 AATAACCGTGACACACTAAAA
1 AACAGCCGTGACACGCTAAAA
20492760 TAACTTTAAC
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
54 5 0.05
55 100 0.92
56 4 0.04
ACGTcount: A:0.43, C:0.31, G:0.14, T:0.12
Consensus pattern (54 bp):
AACAGCCGTGACACGCTAAAAACCCAAAAAACAGTTAACCCACGACACGCTAGG
Found at i:20493521 original size:22 final size:22
Alignment explanation
Indices: 20493473--20493523 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
20493463 TATATGAATT
20493473 ATTATT-TTATATATAAATTAA
1 ATTATTATTATATATAAATTAA
* ** *
20493494 AATATTATTATATATTCATTTA
1 ATTATTATTATATATAAATTAA
20493516 ATTATTAT
1 ATTATTAT
20493524 ATGAATTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTATTATTATATATAAATTAA
Found at i:20504829 original size:18 final size:18
Alignment explanation
Indices: 20504788--20504834 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
20504778 AGGAAACAAG
*
20504788 ACATAAATCATAGATTTAT
1 ACATAAA-CATACATTTAT
*
20504807 A-ATAAACATACATTTTT
1 ACATAAACATACATTTAT
*
20504824 ACATAATCATA
1 ACATAAACATA
20504835 ACTTTCTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.42
18 13 0.54
19 1 0.04
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (18 bp):
ACATAAACATACATTTAT
Found at i:20507528 original size:17 final size:17
Alignment explanation
Indices: 20507508--20507556 Score: 89
Period size: 18 Copynumber: 2.8 Consensus size: 17
20507498 TATTTTGAAT
20507508 TTTTCTTTTGTTCAACA
1 TTTTCTTTTGTTCAACA
20507525 TTTTCTTTTGTTCAAACA
1 TTTTCTTTTGTTC-AACA
20507543 TTTTCTTTTGTTCA
1 TTTTCTTTTGTTCA
20507557 TAATCTCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 14 0.45
18 17 0.55
ACGTcount: A:0.16, C:0.16, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTTCTTTTGTTCAACA
Found at i:20517567 original size:2 final size:2
Alignment explanation
Indices: 20517560--20517592 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
20517550 ATGATGGATG
*
20517560 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20517593 GGATATGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20522514 original size:20 final size:20
Alignment explanation
Indices: 20522488--20522533 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
20522478 AATCTTACCT
* *
20522488 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
20522509 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
20522530 TTTT
1 TTTT
20522534 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:20522535 original size:22 final size:22
Alignment explanation
Indices: 20522493--20522533 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20522483 TACCTTTTTT
*
20522493 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
20522515 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
20522534 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:20522602 original size:11 final size:11
Alignment explanation
Indices: 20522547--20522596 Score: 70
Period size: 11 Copynumber: 4.8 Consensus size: 11
20522537 ACCTAGGGTT
20522547 TTTGTTCTT-C
1 TTTGTTCTTCC
20522557 -TT-TTCTTCC
1 TTTGTTCTTCC
*
20522566 TTTGTTCCTCC
1 TTTGTTCTTCC
20522577 TTTGTTCTTCC
1 TTTGTTCTTCC
20522588 TTTGTTCTT
1 TTTGTTCTT
20522597 GTTTTGGTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 5 0.14
9 3 0.09
10 2 0.06
11 25 0.71
ACGTcount: A:0.00, C:0.26, G:0.08, T:0.66
Consensus pattern (11 bp):
TTTGTTCTTCC
Found at i:20531587 original size:34 final size:34
Alignment explanation
Indices: 20531491--20531579 Score: 151
Period size: 34 Copynumber: 2.6 Consensus size: 34
20531481 AAAGTTGAGC
*
20531491 TGTTTGCTGCCAATTTGTGAAAAAAAATTAGAGT
1 TGTTTGCTGCCAATTTGTGCAAAAAAATTAGAGT
**
20531525 TGTTTGCAACCAATTTGTGCAAAAAAATTAGAGT
1 TGTTTGCTGCCAATTTGTGCAAAAAAATTAGAGT
20531559 TGTTTGCTGCCAATTTGTGCA
1 TGTTTGCTGCCAATTTGTGCA
20531580 GGAAAATTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (34 bp):
TGTTTGCTGCCAATTTGTGCAAAAAAATTAGAGT
Found at i:20531741 original size:16 final size:17
Alignment explanation
Indices: 20531720--20531757 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
20531710 CGTGGAAGAG
20531720 AGAAAAAG-AAAGAAAA
1 AGAAAAAGAAAAGAAAA
*
20531736 AG-AAAAGAAAAGAAAT
1 AGAAAAAGAAAAGAAAA
20531752 AGAAAA
1 AGAAAA
20531758 TAAATGGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.26
16 11 0.58
17 3 0.16
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AGAAAAAGAAAAGAAAA
Found at i:20535617 original size:36 final size:34
Alignment explanation
Indices: 20535546--20535634 Score: 92
Period size: 36 Copynumber: 2.6 Consensus size: 34
20535536 CTCAACTCAG
* * * *
20535546 CTCATGTGCACTCTCACACCTCACATAGCTGATATC
1 CTCATGTGCACTCCCACACCGCACATAGAT-A-ATA
20535582 CTCATGTGCACTCCCACACCGCACAT-GATAAATA
1 CTCATGTGCACTCCCACACCGCACATAGAT-AATA
*
20535616 -TCATGTACACTCCCACACC
1 CTCATGTGCACTCCCACACC
20535635 ACATCATCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 18 0.38
34 2 0.04
35 3 0.06
36 24 0.51
ACGTcount: A:0.28, C:0.38, G:0.10, T:0.24
Consensus pattern (34 bp):
CTCATGTGCACTCCCACACCGCACATAGATAATA
Found at i:20535658 original size:31 final size:31
Alignment explanation
Indices: 20535587--20535668 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
20535577 ATATCCTCAT
* * *
20535587 GTGCACTCCCACACCGCACATGATAAATATCAT
1 GTGCACTCCCACA-C-CACATCATAAACATCAC
* * *
20535620 GTACACTCCCACACCACATCATCACCATCAC
1 GTGCACTCCCACACCACATCATAAACATCAC
20535651 GTGCACTCCCACACCACA
1 GTGCACTCCCACACCACA
20535669 CATGCATGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 29 0.69
32 1 0.02
33 12 0.29
ACGTcount: A:0.32, C:0.43, G:0.09, T:0.17
Consensus pattern (31 bp):
GTGCACTCCCACACCACATCATAAACATCAC
Found at i:20536774 original size:35 final size:36
Alignment explanation
Indices: 20536696--20536822 Score: 120
Period size: 35 Copynumber: 3.5 Consensus size: 36
20536686 TCTCACTAGC
*
20536696 TCATGTGCACTTC-CACACCGCACATA-GC-TAGAATCA
1 TCATGTGCAC-TCACACATCGCACA-AGGCATAG-ATCA
* *
20536732 TCCTGTGCACTCACACATCGCACAAGGCA-ATATCA
1 TCATGTGCACTCACACATCGCACAAGGCATAGATCA
*
20536767 TCATGTGCACT-ACCACATCGCACATGGCATAGATCA
1 TCATGTGCACTCA-CACATCGCACAAGGCATAGATCA
20536803 TCAACGTGTGCACTCACACA
1 TC-A--TGTGCACTCACACA
20536823 GCACACCACT
Statistics
Matches: 76, Mismatches: 6, Indels: 15
0.78 0.06 0.15
Matches are distributed among these distances:
34 1 0.01
35 32 0.42
36 29 0.38
37 1 0.01
39 12 0.16
40 1 0.01
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (36 bp):
TCATGTGCACTCACACATCGCACAAGGCATAGATCA
Found at i:20536855 original size:52 final size:52
Alignment explanation
Indices: 20536785--20536993 Score: 337
Period size: 52 Copynumber: 4.0 Consensus size: 52
20536775 ACTACCACAT
* **
20536785 CGCACATGGCATAGATCATCAACGTGTGCACTCACACAGCACACCACTATCA
1 CGCACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCA
* *
20536837 CGCACATGGCATATATCATCAGTGTGTGCACTTACATAGCACACCACTATCA
1 CGCACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCA
* * *
20536889 CACATATGGCATATATCATCAGTGTGTGCACTCACACAGCACATCACTATCA
1 CGCACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCA
*
20536941 CGCACATGGCATATATCATCAGTGTGTGCACTCACACAGCACATCACTATCA
1 CGCACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCA
20536993 C
1 C
20536994 TGTCACGTGC
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 145 1.00
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (52 bp):
CGCACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCA
Found at i:20542489 original size:42 final size:43
Alignment explanation
Indices: 20542389--20542519 Score: 156
Period size: 43 Copynumber: 3.1 Consensus size: 43
20542379 CACCATCCCA
* * * ** *
20542389 TCATCATCAGCTCAAGTGCACTCCCTACTCGCACATGGCTGGG
1 TCATCATCGGCTTATGTGCACTCCCTACTCGCACATAACCGGG
* *
20542432 TCATCACCGGGTTATGTGCACTCCCTACTCGCA-ATAACCGGG
1 TCATCATCGGCTTATGTGCACTCCCTACTCGCACATAACCGGG
* * *
20542474 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGAG
1 TCATCATCGGCTTATGTGCACTCCCTACTCGCACATAACCGGG
20542517 TCA
1 TCA
20542520 ATATCATTAC
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 36 0.49
43 38 0.51
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.24
Consensus pattern (43 bp):
TCATCATCGGCTTATGTGCACTCCCTACTCGCACATAACCGGG
Found at i:20543326 original size:12 final size:12
Alignment explanation
Indices: 20543309--20543340 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
20543299 GTGAGATGGA
20543309 AGAAGAAGAAAG
1 AGAAGAAGAAAG
20543321 AGAAGAAGAAAG
1 AGAAGAAGAAAG
20543333 AGAAGAAG
1 AGAAGAAG
20543341 TTGTTGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
AGAAGAAGAAAG
Found at i:20546700 original size:2 final size:2
Alignment explanation
Indices: 20546690--20546724 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
20546680 ACATATTTAC
*
20546690 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20546725 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20549906 original size:2 final size:2
Alignment explanation
Indices: 20549899--20549944 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
20549889 ATGTATACAT
* *
20549899 TA TA TA TA TA TA TA TA TA -A TG TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20549940 TA TA T
1 TA TA T
20549945 TTTTTTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20556188 original size:47 final size:47
Alignment explanation
Indices: 20556132--20556231 Score: 191
Period size: 47 Copynumber: 2.1 Consensus size: 47
20556122 ATCAACATGG
20556132 CTTATGAATTTTTTAAAAATTTTGGGTCATGCCAAAATCATTTTCATA
1 CTTA-GAATTTTTTAAAAATTTTGGGTCATGCCAAAATCATTTTCATA
20556180 CTTAGAATTTTTTAAAAATTTTGGGTCATGCCAAAATCATTTTCATA
1 CTTAGAATTTTTTAAAAATTTTGGGTCATGCCAAAATCATTTTCATA
20556227 CTTAG
1 CTTAG
20556232 TTATTAGGGA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 48 0.92
48 4 0.08
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (47 bp):
CTTAGAATTTTTTAAAAATTTTGGGTCATGCCAAAATCATTTTCATA
Found at i:20558700 original size:69 final size:74
Alignment explanation
Indices: 20558612--20558797 Score: 211
Period size: 79 Copynumber: 2.5 Consensus size: 74
20558602 ATCACATAAC
* * *
20558612 TTTAGGAATATCTTCTAAAGTAGGAAACTATTTCCTATG-AATTT-T-T-C-AAATTAAAATACT
1 TTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCCTATGTAATTTATATCCAAAATTAAAATACT
20558672 ATCCTTAAT
66 ATCCTTAAT
* **
20558681 TTTAGGAATTTCTTTTAAAGTAGGAAACAATTTTCTATGTTTTTTATGAATCACCCAAAATTAAA
1 TTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCCTATGTAATTTAT--AT---CCAAAATTAAA
*
20558746 ATTCTATCCTTAAT
61 ATACTATCCTTAAT
* *
20558760 TTTAGGAATTGCTTTTAAAGTAGGCAACAATTTCCTAT
1 TTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCCTAT
20558798 TTTTTTATGA
Statistics
Matches: 97, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
69 35 0.36
70 3 0.03
71 1 0.01
74 1 0.01
78 1 0.01
79 56 0.58
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (74 bp):
TTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCCTATGTAATTTATATCCAAAATTAAAATACT
ATCCTTAAT
Found at i:20558790 original size:79 final size:78
Alignment explanation
Indices: 20558659--20558826 Score: 291
Period size: 79 Copynumber: 2.1 Consensus size: 78
20558649 TGAATTTTTC
* *
20558659 AAATTAAAATACTATCCTTAATTTTAGGAATTTCTTTTAAAGTAGGAAACAATTTTCTATGTTTT
1 AAATTAAAATACTATCCTTAATTTTAGGAATTGCTTTTAAAGTAGGAAACAATTTCCTAT-TTTT
20558724 TTATGAATCACCCA
65 TTATGAATCACCCA
* *
20558738 AAATTAAAATTCTATCCTTAATTTTAGGAATTGCTTTTAAAGTAGGCAACAATTTCCTATTTTTT
1 AAATTAAAATACTATCCTTAATTTTAGGAATTGCTTTTAAAGTAGGAAACAATTTCCTATTTTTT
20558803 TATGAATCACCCA
66 TATGAATCACCCA
20558816 AAATTAAAATA
1 AAATTAAAATA
20558827 AATGGTATTT
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
78 28 0.33
79 56 0.67
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (78 bp):
AAATTAAAATACTATCCTTAATTTTAGGAATTGCTTTTAAAGTAGGAAACAATTTCCTATTTTTT
TATGAATCACCCA
Found at i:20582848 original size:2 final size:2
Alignment explanation
Indices: 20582829--20582867 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
20582819 TAAACAGCGC
*
20582829 AG AG CG AG AG AG CA- AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG A
20582868 AGTGGAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.05, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20583565 original size:2 final size:2
Alignment explanation
Indices: 20583558--20583655 Score: 128
Period size: 2 Copynumber: 49.5 Consensus size: 2
20583548 AGCAACAGGC
* * *
20583558 TA TA TA TA AA TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20583600 TA TA TA TA TNA AA TA -A TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20583641 TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA T
20583656 GTGTGGAATA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
1 2 0.02
2 80 0.96
3 1 0.01
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:20586326 original size:22 final size:22
Alignment explanation
Indices: 20586308--20586360 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
20586298 AAGTAAGCAT
* *
20586308 TCATTATTTAGTTATTAAGATA
1 TCATGATTCAGTTATTAAGATA
20586330 TCATGATTCAGTTATTAAGATA
1 TCATGATTCAGTTATTAAGATA
20586352 TCATGATTC
1 TCATGATTC
20586361 TATTGAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (22 bp):
TCATGATTCAGTTATTAAGATA
Found at i:20586369 original size:19 final size:20
Alignment explanation
Indices: 20586320--20586371 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
20586310 ATTATTTAGT
20586320 TATTAAGATATCATGATTCA
1 TATTAAGATATCATGATTCA
20586340 GTTATTAAGATATCATGATTC-
1 --TATTAAGATATCATGATTCA
*
20586361 TATTGAGATAT
1 TATTAAGATAT
20586372 TAAAATACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 10 0.34
22 19 0.66
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (20 bp):
TATTAAGATATCATGATTCA
Found at i:20587371 original size:28 final size:28
Alignment explanation
Indices: 20587330--20587530 Score: 197
Period size: 28 Copynumber: 7.0 Consensus size: 28
20587320 TGGTAACTTT
*
20587330 AACATGATTTGTCTTAATTTAGACAAGAT
1 AACATG-TTTGTCTTAATTTAGACAAGAA
20587359 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
20587387 AACATGTTTTGTCATAATTTAGACAAGAA
1 AACATG-TTTGTCTTAATTTAGACAAGAA
* * * *
20587416 AATATATTTGTCTTAATTAAGATAAGAAAA
1 AACATGTTTGTCTTAATTTAGACAAG--AA
* * *
20587446 ATACAT-TTTGTTTTAATCTAGATAAGAA
1 A-ACATGTTTGTCTTAATTTAGACAAGAA
* * * *
20587474 AACATATTTGTCTCAATTTAGATAAGAT
1 AACATGTTTGTCTTAATTTAGACAAGAA
* *
20587502 AACATGTTTTATCTTAATTAAAGACAAGA
1 AACATG-TTTGTCTTAATT-TAGACAAGA
20587531 GTTGTCTTAA
Statistics
Matches: 145, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
27 4 0.03
28 70 0.48
29 41 0.28
30 27 0.19
31 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:20587426 original size:57 final size:57
Alignment explanation
Indices: 20587330--20587530 Score: 233
Period size: 57 Copynumber: 3.5 Consensus size: 57
20587320 TGGTAACTTT
* * * *
20587330 AACATGATTTGTCTTAATTTAGACAAGATAACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGATAAGAA
* * *
20587387 AACATGTTTTGTCATAATTTAGACAAGAAAATATATTTGTCTTAATTAAGATAAGAA
1 AACATGTTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGATAAGAA
* * * * * *
20587444 AA-ATACATTTTGTTTTAATCTAGATAAGAAAACATATTTGTCTCAATTTAGATAAGAT
1 AACAT--GTTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGATAAGAA
* *
20587502 AACATGTTTTATCTTAATTAAAGACAAGA
1 AACATGTTTTGTCTTAATT-TAGACAAGA
20587531 GTTGTCTTAA
Statistics
Matches: 118, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
56 2 0.02
57 62 0.53
58 52 0.44
59 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (57 bp):
AACATGTTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGATAAGAA
Found at i:20590512 original size:73 final size:73
Alignment explanation
Indices: 20590426--20590632 Score: 271
Period size: 73 Copynumber: 2.9 Consensus size: 73
20590416 GAAGATGGCC
20590426 AGTTCAGAAACAGAACCAACTTAATCAACTAAGAGATATTGTTAGTCGACTAA-ATGCTTACTGC
1 AGTTCAGAAACAGAACCAACTTAATCAACTAAGAGATATTGTTAGTCGACTAAGA-GCTTACTGC
*
20590490 CAGAAGTCG
65 CAGAAATCG
* * *
20590499 AGTTCAAAAACAGAACCGACTTAATCAACTAAGAGGA-ATCGTTAGTCGACTAAGAGCTTACTGC
1 AGTTCAGAAACAGAACCAACTTAATCAACTAAGA-GATATTGTTAGTCGACTAAGAGCTTACTGC
*
20590563 CCGAAATCG
65 CAGAAATCG
* * * *
20590572 GGTTCAGAGACA-AATCAACTTAATCAACTAAGA-AGTA-TGTTAGTCGACTAAGAGCTCACTG
1 AGTTCAGAAACAGAACCAACTTAATCAACTAAGAGA-TATTGTTAGTCGACTAAGAGCTTACTG
20590633 TTTGCAACTG
Statistics
Matches: 118, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
70 1 0.01
71 22 0.19
72 20 0.17
73 72 0.61
74 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (73 bp):
AGTTCAGAAACAGAACCAACTTAATCAACTAAGAGATATTGTTAGTCGACTAAGAGCTTACTGCC
AGAAATCG
Found at i:20590687 original size:73 final size:72
Alignment explanation
Indices: 20590429--20590707 Score: 221
Period size: 73 Copynumber: 3.8 Consensus size: 72
20590419 GATGGCCAGT
* * *
20590429 TCAGAAACAGAACCAACTTAATCAACTAAG-AG-ATATTGTTAGTCGACTAA-ATGCTTACTG-C
1 TCAGAGACAGAATCAACTTAATCAACTAAGAAGCA-A--GTTAGTCGACTAAGA-GCTCACTGTC
* * *
20590490 CAGAAGTCGAGT
62 C-GAAATCGGGG
* * * * * * *
20590502 TCAAAAACAGAACCGACTTAATCAACTAAG-AGGAATCGTTAGTCGACTAAGAGCTTACTGCCCG
1 TCAGAGACAGAATCAACTTAATCAACTAAGAAGCAA--GTTAGTCGACTAAGAGCTCACTGTCCG
*
20590566 AAATCGGGT
64 AAATCGGGG
* * ** *
20590575 TCAGAGACA-AATCAACTTAATCAACTAAGAAGTATGTTAGTCGACTAAGAGCTCACTGTTTGCA
1 TCAGAGACAGAATCAACTTAATCAACTAAGAAGCAAGTTAGTCGACTAAGAGCTCACTGTCCGAA
20590639 A-CTGGGG
66 ATC-GGGG
* * * *
20590646 TCAGAAGACAGAATCAACTTAATCGACTAAGAAGCAAGTTAGTCAACTACGAGCTCTCTGTC
1 TCAG-AGACAGAATCAACTTAATCAACTAAGAAGCAAGTTAGTCGACTAAGAGCTCACTGTC
20590708 TGCCACCTCG
Statistics
Matches: 175, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
70 1 0.01
71 32 0.18
72 23 0.13
73 115 0.66
74 4 0.02
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (72 bp):
TCAGAGACAGAATCAACTTAATCAACTAAGAAGCAAGTTAGTCGACTAAGAGCTCACTGTCCGAA
ATCGGGG
Found at i:20591210 original size:10 final size:10
Alignment explanation
Indices: 20591180--20591281 Score: 50
Period size: 10 Copynumber: 9.9 Consensus size: 10
20591170 ATGTAATTAT
20591180 TTATTTTATTA
1 TTATTTT-TTA
* *
20591191 TAATTTTTTTG
1 TTA-TTTTTTA
20591202 TTATTTTTTA
1 TTATTTTTTA
*
20591212 TTA-TTTTCA
1 TTATTTTTTA
20591221 TT-TTATTTTA
1 TTATT-TTTTA
* *
20591231 TTCTTTCTTA
1 TTATTTTTTA
*
20591241 TCATATTTTTA
1 TTAT-TTTTTA
20591252 TTTATTTTAATTA
1 -TTATTTT--TTA
*
20591265 TTA-TTATTA
1 TTATTTTTTA
20591274 -TATTTTTT
1 TTATTTTTT
20591282 TATCTTACAT
Statistics
Matches: 69, Mismatches: 13, Indels: 20
0.68 0.13 0.20
Matches are distributed among these distances:
8 2 0.03
9 15 0.22
10 21 0.30
11 18 0.26
12 10 0.14
13 3 0.04
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.73
Consensus pattern (10 bp):
TTATTTTTTA
Found at i:20591226 original size:21 final size:21
Alignment explanation
Indices: 20591179--20591232 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
20591169 AATGTAATTA
*
20591179 TTTATTTTATTATAATTTTTT
1 TTTATTTTATTATAATTTTAT
*
20591200 TGTTATTTT-TTATTATTTTCAT
1 T-TTATTTTATTATAATTTT-AT
20591222 TTTATTTTATT
1 TTTATTTTATT
20591233 CTTTCTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTATTTTATTATAATTTTAT
Found at i:20592802 original size:22 final size:22
Alignment explanation
Indices: 20592757--20592803 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
20592747 TTGTGTATTT
* *
20592757 TTTTTTTACATATTTTTTTTGA
1 TTTTTTTACATATTTTTGTGGA
**
20592779 TTTTTTTGTATATTTTTGTGGA
1 TTTTTTTACATATTTTTGTGGA
20592801 TTT
1 TTT
20592804 GTGGTTGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.15, C:0.02, G:0.11, T:0.72
Consensus pattern (22 bp):
TTTTTTTACATATTTTTGTGGA
Found at i:20593006 original size:12 final size:12
Alignment explanation
Indices: 20592989--20593013 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20592979 TCATTCATCA
20592989 TCATTCATTTTT
1 TCATTCATTTTT
20593001 TCATTCATTTTT
1 TCATTCATTTTT
20593013 T
1 T
20593014 TAAAATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (12 bp):
TCATTCATTTTT
Found at i:20593182 original size:17 final size:16
Alignment explanation
Indices: 20593159--20593232 Score: 78
Period size: 17 Copynumber: 4.6 Consensus size: 16
20593149 CTCTTACCAA
*
20593159 GTTTTTTTTTTGGTTT
1 GTTTTTTTTTTTGTTT
*
20593175 GTTTTTTTGTTTTTTTT
1 GTTTTTTT-TTTTGTTT
**
20593192 GTTTTGTTTTGCTGTTT
1 GTTTT-TTTTTTTGTTT
*
20593209 GTTTTTTTTTTT-TGT
1 GTTTTTTTTTTTGTTT
20593224 GTTTTTTTT
1 GTTTTTTTT
20593233 AAATGAGACT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
15 11 0.23
16 13 0.27
17 21 0.44
18 3 0.06
ACGTcount: A:0.00, C:0.01, G:0.16, T:0.82
Consensus pattern (16 bp):
GTTTTTTTTTTTGTTT
Found at i:20593190 original size:22 final size:21
Alignment explanation
Indices: 20593162--20593232 Score: 74
Period size: 22 Copynumber: 3.4 Consensus size: 21
20593152 TTACCAAGTT
*
20593162 TTTTTTTTGGTTTGTTTTTTTG
1 TTTTTTTT-GTTTGTTTTTCTG
*
20593184 TTTTTTTTGTTTTGTTTTGCTG
1 TTTTTTTTG-TTTGTTTTTCTG
* *
20593206 TTTGTTTT-TTT-TTTTTGTG
1 TTTTTTTTGTTTGTTTTTCTG
20593225 TTTTTTTT
1 TTTTTTTT
20593233 AAATGAGACT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
19 13 0.31
20 3 0.07
21 1 0.02
22 25 0.60
ACGTcount: A:0.00, C:0.01, G:0.15, T:0.83
Consensus pattern (21 bp):
TTTTTTTTGTTTGTTTTTCTG
Found at i:20593218 original size:30 final size:31
Alignment explanation
Indices: 20593174--20593232 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
20593164 TTTTTTGGTT
20593174 TGTTTTTTTGTTTTTTTTGT-TTTGTTTTGC
1 TGTTTTTTTGTTTTTTTTGTGTTTGTTTTGC
*
20593204 TGTTTGTTTT-TTTTTTTTGTGTTTTTTTT
1 TGTTT-TTTTGTTTTTTTTGTGTTTGTTTT
20593233 AAATGAGACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (31 bp):
TGTTTTTTTGTTTTTTTTGTGTTTGTTTTGC
Found at i:20593231 original size:13 final size:13
Alignment explanation
Indices: 20593159--20593232 Score: 73
Period size: 13 Copynumber: 5.7 Consensus size: 13
20593149 CTCTTACCAA
20593159 GTTTTTTTTTTG-
1 GTTTTTTTTTTGT
20593171 GTTTGTTTTTTTGT
1 GTTT-TTTTTTTGT
20593185 -TTTTTTTGTTT-T
1 GTTTTTTT-TTTGT
* *
20593197 GTTTTGCTGTTTGT
1 GTTTT-TTTTTTGT
*
20593211 TTTTTTTTTTTGT
1 GTTTTTTTTTTGT
20593224 GTTTTTTTT
1 GTTTTTTTT
20593233 AAATGAGACT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
12 9 0.18
13 35 0.70
14 6 0.12
ACGTcount: A:0.00, C:0.01, G:0.16, T:0.82
Consensus pattern (13 bp):
GTTTTTTTTTTGT
Found at i:20593281 original size:37 final size:37
Alignment explanation
Indices: 20593228--20593713 Score: 520
Period size: 37 Copynumber: 13.1 Consensus size: 37
20593218 TTTTGTGTTT
* **
20593228 TTTTTAAATGAGACTCCTCAAAGTTGAGGCAACGAAAC
1 TTTTAAAATGA-ACTCCTCAAAACTGAGGCAACGAAAC
* * *
20593266 TTTTAAAATGAACTCCTCAAAATTGAGGCTACAAAAC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
** * *
20593303 TTTTAAAAATGAACTCCTCAAAGTTGAGGTAACAAAAC
1 TTTT-AAAATGAACTCCTCAAAACTGAGGCAACGAAAC
* *
20593341 TTTTAAAATGAACTCCTCAAAACTAAGGCAACGAGAC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
* *
20593378 TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGAC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
*** *
20593415 -TTTAAGAATGAACTCCTCAAAACT---GCGTTG--CC
1 TTTTAA-AATGAACTCCTCAAAACTGAGGCAACGAAAC
* *
20593447 TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGAC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
* *
20593484 TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGAC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
* *
20593521 -TTTGAAATGAACTCCTCAAAACTGAGGCAACCAAAGC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAAA-C
* *
20593558 TTTTAAAAATGAACTCCTCAAAGCTGAGGCAAC-ATATC
1 TTTT-AAAATGAACTCCTCAAAACTGAGGCAACGA-AAC
* *
20593596 TTTAAAAATGAATTCCTCAAAACTGAGGCAACGAAAGC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAAA-C
** * *
20593634 TTTTAAAAATGAACTCCTCAAAGTTGAGGCAACGTATC
1 TTTT-AAAATGAACTCCTCAAAACTGAGGCAACGAAAC
* * *
20593672 TTTAAAAATGAATTTCTCAAAACTGAGGCAACGAAAC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
20593709 ATTTT
1 -TTTT
20593714 TTCCTTTTTT
Statistics
Matches: 382, Mismatches: 50, Indels: 32
0.82 0.11 0.07
Matches are distributed among these distances:
32 19 0.05
33 4 0.01
34 3 0.01
35 3 0.01
36 35 0.09
37 200 0.52
38 64 0.17
39 54 0.14
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (37 bp):
TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
Found at i:20593616 original size:112 final size:113
Alignment explanation
Indices: 20593233--20593705 Score: 556
Period size: 112 Copynumber: 4.3 Consensus size: 113
20593223 TGTTTTTTTT
** * * * *
20593233 AAATGAGACTCCTCAAAGTTGAGGCAACGAAACTTTTAAAATGAACTCCTCAAAATTGAGGCTAC
1 AAATGA-ACTCCTCAAAACTGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAAC
* ** * *
20593298 AAAACTTTTAAAAATGAACTCCTCAAAGTTGAGGTAACAAAACTTTT-A
65 GAAACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACAAAGCTTTTAA
*
20593346 AAATGAACTCCTCAAAACTAAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAACG
1 AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAACG
* * *** *
20593411 AGAC-TTTAAGAATGAACTCCTCAAAACT---G---CGTTGCCTTTAA
66 AAACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACAAAGCTTTTAA
20593452 AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAACG
1 AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAACG
* *
20593517 AGAC-TTT-GAAATGAACTCCTCAAAACTGAGGCAACCAAAGCTTTTAA
66 AAACTTTTAAAAATGAACTCCTCAAAACTGAGGCAA-CAAAGCTTTTAA
* * *
20593564 AAATGAACTCCTCAAAGCTGAGGCAAC-ATATCTTTAAAAATGAATTCCTCAAAACTGAGGCAAC
1 AAATGAACTCCTCAAAACTGAGGCAACGAGA-CTTTAAAAATGAACTCCTCAAAACTGAGGCAAC
** ** *
20593628 GAAAGCTTTTAAAAATGAACTCCTCAAAGTTGAGGCAACGTATC-TTTAA
65 GAAA-CTTTTAAAAATGAACTCCTCAAAACTGAGGCAACAAAGCTTTTAA
* *
20593677 AAATGAATTTCTCAAAACTGAGGCAACGA
1 AAATGAACTCCTCAAAACTGAGGCAACGA
20593706 AACATTTTTT
Statistics
Matches: 310, Mismatches: 37, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
105 23 0.07
106 72 0.23
108 2 0.01
111 23 0.07
112 123 0.40
113 36 0.12
114 7 0.02
115 24 0.08
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (113 bp):
AAATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAACG
AAACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACAAAGCTTTTAA
Found at i:20593618 original size:218 final size:221
Alignment explanation
Indices: 20593233--20593655 Score: 606
Period size: 218 Copynumber: 1.9 Consensus size: 221
20593223 TGTTTTTTTT
** * * *
20593233 AAATGAGACTCCTCAAAGTTGAGGCAACGAAACTTTTAAAATGAACTCCTCAAAATTGAGGCTAC
1 AAATGAGACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAACTGAGGCAAC
** *
20593298 AAAACTTTTAAAAATGAACTCCTCAAAGTTGAGGTAACAAAACTTTTAAAATGAACTCCTCAAAA
66 AAAACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACAAAACTTTTAAAATGAACTCCTCAAAA
* *
20593363 CTAAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGA-C-TTTAAGAATGA
131 CTAAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAGCTTTTAAAAATGA
20593426 ACTCCTCAAAACTGCGTTGCCTTTAA
196 ACTCCTCAAAACTGCGTTGCCTTTAA
*
20593452 AAATGA-ACTCCTCAAAACTGAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAAC
1 AAATGAGACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAACTGAGGCAAC
* * * *
20593516 GAGAC-TTT-GAAATGAACTCCTCAAAACTGAGGCAACCAAAGCTTTTAAAAATGAACTCCTCAA
66 AAAACTTTTAAAAATGAACTCCTCAAAACTGAGGCAA-CAAAACTTTT-AAAATGAACTCCTCAA
* * * *
20593579 AGCTGAGGCAAC-ATATCTTTAAAAATGAATTCCTCAAAACTGAGGCAACGAAAGCTTTTAAAAA
129 AACTAAGGCAACGAGA-CTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAGCTTTTAAAAA
20593643 TGAACTCCTCAAA
193 TGAACTCCTCAAA
20593656 GTTGAGGCAA
Statistics
Matches: 180, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
216 23 0.13
217 14 0.08
218 116 0.64
219 7 0.04
220 20 0.11
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (221 bp):
AAATGAGACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAACTGAGGCAAC
AAAACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACAAAACTTTTAAAATGAACTCCTCAAAA
CTAAGGCAACGAGACTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAGCTTTTAAAAATGA
ACTCCTCAAAACTGCGTTGCCTTTAA
Found at i:20605961 original size:55 final size:53
Alignment explanation
Indices: 20605883--20605990 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 53
20605873 TTTCTGTTAT
20605883 TTATTTATTTTATTATTATCATGTATATTGCATTTTCACAAATTAATTATTTA
1 TTATTTATTTTATTATTATCATGTATATTGCATTTTCACAAATTAATTATTTA
20605936 NTTATTTATTTTTATTATTATCATGTATATTGCATTTTCACAAATTAATTATTTA
1 -TTATTTA-TTTTATTATTATCATGTATATTGCATTTTCACAAATTAATTATTTA
20605991 CCATATATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 7 0.13
55 46 0.87
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.56
Consensus pattern (53 bp):
TTATTTATTTTATTATTATCATGTATATTGCATTTTCACAAATTAATTATTTA
Found at i:20605973 original size:25 final size:25
Alignment explanation
Indices: 20605889--20605973 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 25
20605879 TTATTTATTT
20605889 ATTTTATTATTATCATGTATATTGC
1 ATTTTATTATTATCATGTATATTGC
** * * *
20605914 ATTTTCACAAATTAATTATTTANTTATT-T
1 ATTTT-A-TTATT-ATCATGTA--TATTGC
20605943 ATTTTTATTATTATCATGTATATTGC
1 A-TTTTATTATTATCATGTATATTGC
20605969 ATTTT
1 ATTTT
20605974 CACAAATTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 13 0.30
26 2 0.05
27 9 0.21
28 9 0.21
29 2 0.05
30 8 0.19
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.58
Consensus pattern (25 bp):
ATTTTATTATTATCATGTATATTGC
Found at i:20606000 original size:54 final size:55
Alignment explanation
Indices: 20605890--20606010 Score: 181
Period size: 55 Copynumber: 2.2 Consensus size: 55
20605880 TATTTATTTA
*** *
20605890 TTTTATTATTATCATGTATATTGCATTTTCACAAATTAATTATTTANTTATTTAT
1 TTTTATTATTATCATGTATATTGCATTTTCACAAATTAATTATTTAACCATATAT
20605945 TTTTATTATTATCATGTATATTGCATTTTCACAAATTAATTATTT-ACCATATAT
1 TTTTATTATTATCATGTATATTGCATTTTCACAAATTAATTATTTAACCATATAT
**
20605999 TTGAATTATTAT
1 TTTTATTATTAT
20606011 TATTATTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
54 15 0.25
55 45 0.75
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.55
Consensus pattern (55 bp):
TTTTATTATTATCATGTATATTGCATTTTCACAAATTAATTATTTAACCATATAT
Found at i:20607553 original size:12 final size:12
Alignment explanation
Indices: 20607536--20607560 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20607526 TCATTCATCA
20607536 TCATTCATTTTT
1 TCATTCATTTTT
20607548 TCATTCATTTTT
1 TCATTCATTTTT
20607560 T
1 T
20607561 TAAATCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (12 bp):
TCATTCATTTTT
Found at i:20611977 original size:91 final size:91
Alignment explanation
Indices: 20611865--20612057 Score: 287
Period size: 91 Copynumber: 2.1 Consensus size: 91
20611855 AGAAGAGCTG
* *
20611865 GAAGAGCTTTCCTATGATGATGATGAAAAATTGGCTCTTGTTGCAAGAAAATTCAGAAAGCTAAT
1 GAAGAGCTTTCCGATGATGATGATGAAAAATTGGCTCTGGTTGCAAGAAAATTCAGAAAGCTAAT
20611930 GAGCAAAAGAAACCAAAGGCTAACTA
66 GAGCAAAAGAAACCAAAGGCTAACTA
* * *
20611956 GAAGAGCTTTCCGGTGATGATGATGAAGAATTGGCTCTGGTTGCAAGAAAATTCAGAAAGTTAAT
1 GAAGAGCTTTCCGATGATGATGATGAAAAATTGGCTCTGGTTGCAAGAAAATTCAGAAAGCTAAT
* ** * *
20612021 GAGCAGAAGAAGTCGAAGGCTAGCTA
66 GAGCAAAAGAAACCAAAGGCTAACTA
*
20612047 GAAGAGGTTTC
1 GAAGAGCTTTC
20612058 AGGAAAGACC
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (91 bp):
GAAGAGCTTTCCGATGATGATGATGAAAAATTGGCTCTGGTTGCAAGAAAATTCAGAAAGCTAAT
GAGCAAAAGAAACCAAAGGCTAACTA
Found at i:20621130 original size:36 final size:36
Alignment explanation
Indices: 20621023--20621226 Score: 193
Period size: 36 Copynumber: 5.7 Consensus size: 36
20621013 TAACCGTGCG
* * * * **
20621023 TGTGCGGTGTGGGAGTGCACAAGACGGT-GATGGTA
1 TGTGCGGTGTGGGAGTGCACATGATGATATATGCCA
20621058 GTGTGCGGTGTGGGAGTGCACATGCTGATGATATATGCCA
1 -TGTGCGGTGTGGGAGTGCACA---TGATGATATATGCCA
* * * *
20621098 TGTGTGGTGTCGAAGTGCACATGATGATATATGTCA
1 TGTGCGGTGTGGGAGTGCACATGATGATATATGCCA
* *
20621134 TGTGCGGTGTGGGCGTGCACATGAT-A-CT-TGCCA
1 TGTGCGGTGTGGGAGTGCACATGATGATATATGCCA
* *
20621167 TGTGCGGTGTGGGAGTGCACATGACGATAT-TAGCTA
1 TGTGCGGTGTGGGAGTGCACATGATGATATAT-GCCA
*
20621203 TGTGCAGTGTGGGAGTGCACATGA
1 TGTGCGGTGTGGGAGTGCACATGA
20621227 GCTGAGTTGA
Statistics
Matches: 140, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
33 27 0.19
34 2 0.01
35 3 0.02
36 82 0.59
39 22 0.16
40 4 0.03
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.27
Consensus pattern (36 bp):
TGTGCGGTGTGGGAGTGCACATGATGATATATGCCA
Found at i:20621176 original size:69 final size:69
Alignment explanation
Indices: 20621085--20621226 Score: 182
Period size: 69 Copynumber: 2.1 Consensus size: 69
20621075 GCACATGCTG
* * * *
20621085 ATGATATATGCCATGTGTGGTGTCGAAGTGCACATGATGATA-TATG-TCATGTGCGGTGTGGGC
1 ATGATATATGCCATGTGCGGTGTCGAAGTGCACATGACGATATTA-GCT-ATGTGCAGTGTGGGA
20621148 GTGCAC
64 GTGCAC
* *
20621154 ATGATACT-TGCCATGTGCGGTGTGGGAGTGCACATGACGATATTAGCTATGTGCAGTGTGGGAG
1 ATGATA-TATGCCATGTGCGGTGTCGAAGTGCACATGACGATATTAGCTATGTGCAGTGTGGGAG
20621218 TGCAC
65 TGCAC
20621223 ATGA
1 ATGA
20621227 GCTGAGTTGA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
69 60 0.94
70 4 0.06
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.29
Consensus pattern (69 bp):
ATGATATATGCCATGTGCGGTGTCGAAGTGCACATGACGATATTAGCTATGTGCAGTGTGGGAGT
GCAC
Found at i:20623507 original size:2 final size:2
Alignment explanation
Indices: 20623500--20623559 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
20623490 NNNNNNNNNN
20623500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20623542 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
20623560 CAACATAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20627574 original size:2 final size:2
Alignment explanation
Indices: 20627567--20627593 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20627557 TATAACGTAC
20627567 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20627594 CATACATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20627690 original size:37 final size:37
Alignment explanation
Indices: 20627643--20627724 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
20627633 AATGCAATAT
*
20627643 CATCATCATGTGTGCACTCTCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
*
20627680 CATCATCATGTTTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
20627717 CATCATCA
1 CATCATCA
20627725 CACAACATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.26, C:0.37, G:0.09, T:0.29
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:20631935 original size:18 final size:17
Alignment explanation
Indices: 20631897--20631947 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
20631887 GCTAGAGCTG
*
20631897 AAAAAAAAAGAAGAAGA-
1 AAAAGAAAAGAAGAA-AT
*
20631914 AAAAGACAAGAGAGAAAT
1 AAAAGAAAAGA-AGAAAT
20631932 AAAAGAAAAGAAGAAA
1 AAAAGAAAAGAAGAAA
20631948 AACATTGCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAGAAGAAAT
Found at i:20638502 original size:40 final size:39
Alignment explanation
Indices: 20638401--20638509 Score: 148
Period size: 38 Copynumber: 2.8 Consensus size: 39
20638391 ATAGTGATAG
*
20638401 TGCTTGTGTGCACGATGTAGGGGGATGCACACGATGGCAC
1 TGCTT-TGTGCACGATGTAGGGGGATGCACACGATGACAC
** * *
20638441 T-AATTGTGCACGATGTGGGGGGATGCACACGATGACTCC
1 TGCTTTGTGCACGATGTAGGGGGATGCACACGATGAC-AC
20638480 TGCTTTGTGCACGATGTAGGGGGATGCACA
1 TGCTTTGTGCACGATGTAGGGGGATGCACA
20638510 TGAGCTGGGT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 30 0.51
39 3 0.05
40 26 0.44
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (39 bp):
TGCTTTGTGCACGATGTAGGGGGATGCACACGATGACAC
Found at i:20638562 original size:10 final size:10
Alignment explanation
Indices: 20638547--20638571 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20638537 GGTGTTTATC
20638547 TATGTATATA
1 TATGTATATA
20638557 TATGTATATA
1 TATGTATATA
20638567 TATGT
1 TATGT
20638572 TTATGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (10 bp):
TATGTATATA
Found at i:20638919 original size:21 final size:21
Alignment explanation
Indices: 20638893--20638955 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
20638883 TTGGCCACTT
20638893 GAATCTAGCTGCAGCGAGAAA
1 GAATCTAGCTGCAGCGAGAAA
20638914 GAATCTAGCTGCAGCGAGAAA
1 GAATCTAGCTGCAGCGAGAAA
* *
20638935 GAATCTCGCTGCAACGAGAAA
1 GAATCTAGCTGCAGCGAGAAA
20638956 CTTTATGTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.38, C:0.21, G:0.27, T:0.14
Consensus pattern (21 bp):
GAATCTAGCTGCAGCGAGAAA
Found at i:20655080 original size:29 final size:29
Alignment explanation
Indices: 20655016--20655073 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
20655006 CTTCTGTGTG
20655016 AAAGAGAAAATTGCTTGTGAAACAATTTT
1 AAAGAGAAAATTGCTTGTGAAACAATTTT
20655045 AAAGAGAAAATTGCTTGTGAAACAATTTT
1 AAAGAGAAAATTGCTTGTGAAACAATTTT
20655074 TTAGAGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (29 bp):
AAAGAGAAAATTGCTTGTGAAACAATTTT
Found at i:20664754 original size:21 final size:19
Alignment explanation
Indices: 20664730--20664770 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
20664720 TAATTTTAAA
20664730 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
20664751 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
20664770 A
1 A
20664771 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:20667051 original size:15 final size:15
Alignment explanation
Indices: 20667031--20667062 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
20667021 TCTAAAGGGT
20667031 AAACTAAGCTTATGA
1 AAACTAAGCTTATGA
20667046 AAACTAAGCTTATGA
1 AAACTAAGCTTATGA
20667061 AA
1 AA
20667063 GCTTAGGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (15 bp):
AAACTAAGCTTATGA
Found at i:20668765 original size:25 final size:25
Alignment explanation
Indices: 20668737--20668819 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
20668727 CATAGCCGGA
20668737 CATCCCATCTCACCCAGCTCATGTG
1 CATCCCATCTCACCCAGCTCATGTG
* * * ** * *
20668762 CATCCCACCACATCGTGCACATAATCGG
1 CATCCCATCTCACCCAGCTCAT-GT--G
20668790 ACATCCCATCTCACCCAGCTCATGTG
1 -CATCCCATCTCACCCAGCTCATGTG
20668816 CATC
1 CATC
20668820 ACACCACATT
Statistics
Matches: 40, Mismatches: 14, Indels: 8
0.65 0.23 0.13
Matches are distributed among these distances:
25 20 0.50
26 2 0.05
28 2 0.05
29 16 0.40
ACGTcount: A:0.24, C:0.42, G:0.12, T:0.22
Consensus pattern (25 bp):
CATCCCATCTCACCCAGCTCATGTG
Found at i:20668769 original size:54 final size:54
Alignment explanation
Indices: 20668687--20668840 Score: 263
Period size: 54 Copynumber: 2.9 Consensus size: 54
20668677 CACAATCATT
*
20668687 CCATCTCACCTAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATC
1 CCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATC
**
20668741 CCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAATCGGACATC
1 CCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATC
* *
20668795 CCATCTCACCCAGCTCATGTGCATCACACCACATTGTGCACATAGC
1 CCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGC
20668841 TGGATAGTAT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.25, C:0.40, G:0.14, T:0.21
Consensus pattern (54 bp):
CCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATC
Done.