Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 106 of 167
Found at i:35269957 original size:24 final size:24
Alignment explanation
Indices: 35269930--35269977 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
35269920 TCGCCTTGGC
*
35269930 CTCTCCTTTGCTTTTCTTTTCTTT
1 CTCTCCTTTGCTTTTCTCTTCTTT
** *
35269954 CTCTTTTTTGTTTTTCTCTTCTTT
1 CTCTCCTTTGCTTTTCTCTTCTTT
35269978 TTCTTTTTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.00, C:0.25, G:0.04, T:0.71
Consensus pattern (24 bp):
CTCTCCTTTGCTTTTCTCTTCTTT
Found at i:35269969 original size:15 final size:15
Alignment explanation
Indices: 35269951--35270014 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 15
35269941 TTTTCTTTTC
*
35269951 TTTCTCTTTTTTGTT
1 TTTCTCTTTTTTCTT
35269966 TTTCTCTTCTTTTTCTT
1 TTTCTC-T-TTTTTCTT
*
35269983 TTTC-CTTTTTTCTC
1 TTTCTCTTTTTTCTT
*
35269997 TTTCAT-TTTTCTCTT
1 TTTC-TCTTTTTTCTT
35270012 TTT
1 TTT
35270015 TTTTGTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 11 0.27
15 17 0.41
16 2 0.05
17 11 0.27
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTCTCTTTTTTCTT
Found at i:35269981 original size:6 final size:6
Alignment explanation
Indices: 35269941--35270024 Score: 57
Period size: 6 Copynumber: 13.7 Consensus size: 6
35269931 TCTCCTTTGC
* * *
35269941 TTTTC- TTTTCT TTCTCTT TTTTGT TTTTC- TCTTCT TTTTCT TTTTCCTT
1 TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT TTTT-C-T
* *
35269990 TTTTCT CTTTCAT TTTTCT CTTTT-T TTTTGT TTTT
1 TTTTCT TTTTC-T TTTTCT -TTTTCT TTTTCT TTTT
35270025 GAAAGTGAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
5 13 0.21
6 30 0.48
7 15 0.24
8 5 0.08
ACGTcount: A:0.01, C:0.18, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:35269982 original size:24 final size:23
Alignment explanation
Indices: 35269941--35270018 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 23
35269931 TCTCCTTTGC
* *
35269941 TTTTCTTTTCTTTCTCTTTTTTGT
1 TTTTCTCTTCTTTTTCTTTTTT-T
35269965 TTTTCTCTTCTTTTTCTTTTTCCTT
1 TTTTCTCTTCTTTTTCTTTTT--TT
*
35269990 TTTTCTCTTTCATTTTTCTCTTTTT
1 TTTTCTC-TTC-TTTTTCTTTTTTT
35270015 TTTT
1 TTTT
35270019 GTTTTTGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 19 0.40
25 14 0.30
26 4 0.09
27 10 0.21
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (23 bp):
TTTTCTCTTCTTTTTCTTTTTTT
Found at i:35269998 original size:16 final size:17
Alignment explanation
Indices: 35269958--35269999 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
35269948 TTCTTTCTCT
*
35269958 TTTTTGTTTTTCTCTTC
1 TTTTTCTTTTTCTCTTC
35269975 TTTTTCTTTTTC-CTT-
1 TTTTTCTTTTTCTCTTC
35269990 TTTTCTCTTT
1 TTTT-TCTTT
35270000 CATTTTTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 11 0.48
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTCTCTTC
Found at i:35270018 original size:13 final size:13
Alignment explanation
Indices: 35269946--35270018 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
35269936 TTTGCTTTTC
*
35269946 TTTTCTTTCTCTT
1 TTTTTTTTCTCTT
*
35269959 TTTTGTTTT-TCTC
1 TTTT-TTTTCTCTT
*
35269972 TTCTTTTTCT-TT
1 TTTTTTTTCTCTT
35269984 TTCCTTTTTTCTCTT
1 TT--TTTTTTCTCTT
**
35269999 TCATTTTTCTCTT
1 TTTTTTTTCTCTT
35270012 TTTTTTT
1 TTTTTTT
35270019 GTTTTTGAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
12 7 0.15
13 26 0.57
14 10 0.22
15 3 0.07
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (13 bp):
TTTTTTTTCTCTT
Found at i:35272637 original size:21 final size:21
Alignment explanation
Indices: 35272611--35272654 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
35272601 GCTGGCTCAT
*
35272611 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
*
35272632 CATGTTTTTCTGGGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
35272653 CA
1 CA
35272655 ATTGATCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCCAG
Found at i:35276406 original size:13 final size:12
Alignment explanation
Indices: 35276387--35276427 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
35276377 AACCATATAT
*
35276387 AAATAATAAATA
1 AAATAATTAATA
35276399 ATAATAATTAATA
1 A-AATAATTAATA
35276412 GAAATAATTAATA
1 -AAATAATTAATA
35276425 AAA
1 AAA
35276428 CAACAGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 4 0.15
13 21 0.81
14 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (12 bp):
AAATAATTAATA
Found at i:35276749 original size:14 final size:14
Alignment explanation
Indices: 35276730--35276760 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35276720 ATATATTTAC
*
35276730 ATAATAAATATATA
1 ATAATAAATAAATA
35276744 ATAATAAATAAATA
1 ATAATAAATAAATA
35276758 ATA
1 ATA
35276761 TAATAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATAAATAAATA
Found at i:35276761 original size:19 final size:18
Alignment explanation
Indices: 35276732--35276768 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
35276722 ATATTTACAT
35276732 AATAAATATATAATAATA
1 AATAAATATATAATAATA
35276750 AATAAATAATATAATAATA
1 AATAAAT-ATATAATAATA
35276769 TGAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATATAATAATA
Found at i:35276820 original size:63 final size:63
Alignment explanation
Indices: 35276743--35276875 Score: 161
Period size: 62 Copynumber: 2.2 Consensus size: 63
35276733 ATAAATATAT
* * *
35276743 AATAATAAATAAA-TAATATAATAAT-ATGAAACAT-AA-CTCAAATTAATTAAATTAATAG-AA
1 AATAATAAA-AAACAAATATAAAAATAATGAAA-ATAAAGCTCAAATTAATTAAATTAACAGTAA
* *
35276803 AATAATAAAAAACAAATATAAAAATAATGAGAATAAAGCTCAAATTAATTAATTTAACAGTAA
1 AATAATAAAAAACAAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAA
35276866 AATAA-AAAAA
1 AATAATAAAAA
35276876 TAAAAAAGGG
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
59 3 0.05
60 21 0.33
61 7 0.11
62 25 0.40
63 7 0.11
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (63 bp):
AATAATAAAAAACAAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAA
Found at i:35276821 original size:60 final size:62
Alignment explanation
Indices: 35276743--35276881 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 62
35276733 ATAAATATAT
* * *
35276743 AATAATAAATAAATAATATAATAAT-ATGAAACAT-AA-CTCAAATTAATTAAATTAATAG-AA
1 AATAATAAA-AAAAAATATAAAAATAATGAAA-ATAAAGCTCAAATTAATTAAATTAACAGTAA
* *
35276803 AATAATAAAAAACAAATATAAAAATAATGAGAATAAAGCTCAAATTAATTAATTTAACAGTAA
1 AATAATAAAAAA-AAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAA
*
35276866 AATAAAAAAATAAAAA
1 AATAATAAAA-AAAAA
35276882 AGGGGTTAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
59 3 0.04
60 21 0.31
61 7 0.10
62 20 0.30
63 14 0.21
64 2 0.03
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.26
Consensus pattern (62 bp):
AATAATAAAAAAAAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAA
Found at i:35277171 original size:18 final size:18
Alignment explanation
Indices: 35277148--35277183 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35277138 ATAACAAGTA
*
35277148 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
35277166 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
35277184 ATGGTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.58, T:0.25
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:35277199 original size:29 final size:29
Alignment explanation
Indices: 35277199--35277265 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
35277189 TTAGTAGGGT
35277199 GTAGGGGTGATGGAAGTAGTGGATGGTTTA
1 GTAG-GGTGATGGAAGTAGTGGATGGTTTA
**
35277229 GTAGGGTGATGGATTTAGTGG-TCGGTTTA
1 GTAGGGTGATGGAAGTAGTGGAT-GGTTTA
*
35277258 GTGGGGTG
1 GTAGGGTG
35277266 TTTAATTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 28 0.85
30 4 0.12
ACGTcount: A:0.18, C:0.01, G:0.48, T:0.33
Consensus pattern (29 bp):
GTAGGGTGATGGAAGTAGTGGATGGTTTA
Found at i:35277218 original size:37 final size:37
Alignment explanation
Indices: 35277165--35277236 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
35277155 GGAGTTAGTG
*
35277165 GGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGTGTA
1 GGGGTGATGGAAGTAGTGGATGGTTTAGTAGGGTGTA
35277202 GGGGTGATGGAAGTAGTGGATGGTTTAGTAGGGTG
1 GGGGTGATGGAAGTAGTGGATGGTTTAGTAGGGTG
35277237 ATGGATTTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.19, C:0.00, G:0.51, T:0.29
Consensus pattern (37 bp):
GGGGTGATGGAAGTAGTGGATGGTTTAGTAGGGTGTA
Found at i:35280122 original size:15 final size:13
Alignment explanation
Indices: 35280093--35280119 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35280083 GCTCGGCAAG
35280093 GACACGCCCGTGT
1 GACACGCCCGTGT
35280106 GACACGCCCGTGT
1 GACACGCCCGTGT
35280119 G
1 G
35280120 TGATTACTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:35286495 original size:111 final size:111
Alignment explanation
Indices: 35286301--35286521 Score: 343
Period size: 111 Copynumber: 2.0 Consensus size: 111
35286291 TTATGCAAAT
*
35286301 TATGTGACCATTTTCCTTAAAGTAAAAATGAATGTCAATTGTATGTCAAACTTTTTATTTTGGCC
1 TATGTGACCATTTTCCTTAAAGTAAAAATGAATGTCAATTATATGTCAAACTTTTTATTTTGGCC
**
35286366 TCAAATTTGAAATAACTTTTATTAAGGGGAGCAATTATTCAAAAAC
66 TCAAATTCAAAATAACTTTTATTAAGGGGAGCAATTATTCAAAAAC
* * * *
35286412 TATGTGACCATTTTTCTTGAAGTAAAAATGAATGTCAATTATATGTCCATCTTTTTATTTTGGCC
1 TATGTGACCATTTTCCTTAAAGTAAAAATGAATGTCAATTATATGTCAAACTTTTTATTTTGGCC
* * * *
35286477 TTAAATTCAAAATGACTTTTATTAATGGGAGTAATTATTCAAAAA
66 TCAAATTCAAAATAACTTTTATTAAGGGGAGCAATTATTCAAAAA
35286522 GAAATTTACC
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
111 99 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (111 bp):
TATGTGACCATTTTCCTTAAAGTAAAAATGAATGTCAATTATATGTCAAACTTTTTATTTTGGCC
TCAAATTCAAAATAACTTTTATTAAGGGGAGCAATTATTCAAAAAC
Found at i:35288004 original size:19 final size:20
Alignment explanation
Indices: 35287980--35288017 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
35287970 GGTACCACCA
35287980 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
35287999 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
35288018 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:35288384 original size:46 final size:45
Alignment explanation
Indices: 35288291--35288376 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
35288281 TACATCTCAC
* *
35288291 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGA-ATGCGCAACCATAAGT
*
35288337 GAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
1 GAACTCGGACTCAACTCAACGAGTTCGGAATGCGCAACCAT
35288377 CCTAGTGACA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 9 0.24
46 28 0.76
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGAATGCGCAACCATAAGT
Found at i:35288822 original size:30 final size:30
Alignment explanation
Indices: 35288788--35288847 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
35288778 ATTTAATACG
35288788 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
35288818 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
35288848 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:35297979 original size:19 final size:20
Alignment explanation
Indices: 35297955--35297992 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
35297945 GGTATCACCA
35297955 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
35297974 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
35297993 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:35298329 original size:93 final size:93
Alignment explanation
Indices: 35298221--35298390 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 93
35298211 CGCCCCTAAG
* *
35298221 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
35298286 GCGAGTTCGGATTCCTAGTTACATCTCA
66 ACGAGTTCGGATTCCTAGTTACATCTCA
*
35298314 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
35298379 ACGAGTTCGGAT
66 ACGAGTTCGGAT
35298391 GCTCAACCAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
TGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATTCCTAGTTACATCTCA
Found at i:35298389 original size:46 final size:46
Alignment explanation
Indices: 35298217--35298389 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
35298207 AACCCGCCCC
* * *
35298217 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
35298263 TAAGTGAACTCGGACTCAACTCAGCGAGTTCGG--ATTC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--TCCA
*
35298309 TCTCA-TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
35298356 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
35298390 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 2 0.02
46 64 0.58
47 31 0.28
48 2 0.02
49 5 0.05
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:35298846 original size:30 final size:30
Alignment explanation
Indices: 35298812--35298871 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
35298802 ATTTAATACG
35298812 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
35298842 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
35298872 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:35300478 original size:30 final size:30
Alignment explanation
Indices: 35300444--35300507 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 30
35300434 TTTAATTAAT
35300444 GAAAAGTTGTATTTT-GAAAGGAAAAAAA-AG
1 GAAAAGTTGTATTTTGGAAA--AAAAAAAGAG
35300474 GAAAAGTTGTATTTTGGAAAAAAAAAAGAG
1 GAAAAGTTGTATTTTGGAAAAAAAAAAGAG
35300504 GAAA
1 GAAA
35300508 GAAAGAAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 7 0.22
30 21 0.66
31 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.22
Consensus pattern (30 bp):
GAAAAGTTGTATTTTGGAAAAAAAAAAGAG
Found at i:35303232 original size:17 final size:17
Alignment explanation
Indices: 35303210--35303257 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
35303200 CCCCGCCCGA
35303210 TTTTAATATTAAATTAT
1 TTTTAATATTAAATTAT
* ***
35303227 TTTTAAAATTTTTTTAT
1 TTTTAATATTAAATTAT
*
35303244 TTTTAATTTTAAAT
1 TTTTAATATTAAAT
35303258 AACTTTAGTA
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAATATTAAATTAT
Found at i:35303476 original size:19 final size:20
Alignment explanation
Indices: 35303448--35303486 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
35303438 TCCCATTTTT
35303448 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
*
35303467 TATTTGTTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
35303487 ATGTATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:35303504 original size:25 final size:23
Alignment explanation
Indices: 35303467--35303512 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
35303457 TTTGTTTTAA
*
35303467 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
35303490 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
35303513 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:35305134 original size:171 final size:171
Alignment explanation
Indices: 35304846--35305188 Score: 616
Period size: 171 Copynumber: 2.0 Consensus size: 171
35304836 TATATTTATC
35304846 AATAATTTAATTTATTTATTATATTTTATTTTTAAAATTATTAAAAATAAAATAAAAATATTTAA
1 AATAATTTAATTTATTTATTATATTTTATTTTTAAAATTATTAAAAATAAAATAAAAATATTTAA
*
35304911 GAAACAAATTATTAAAAATTAATTTAAAATATTAAAATCACGCATAAACAAATATGATACAATTA
66 GAAACAAATTATTAAAAATTAATTTAAAATATCAAAATCACGCATAAACAAATATGATACAATTA
35304976 TGTAAACC-ATATTAATCAAAATGCGCTGAAACACACATAAA
131 TGTAAACCAATATTAATCAAAATGCGCTGAAACACACA-AAA
*
35305017 AATAATTTAATTTATTTATTATATTTTATTTTTAAAATTATTAAAAATAAAATAAAAATTTTTAA
1 AATAATTTAATTTATTTATTATATTTTATTTTTAAAATTATTAAAAATAAAATAAAAATATTTAA
* * * *
35305082 GACATAAATTATTAAAAATTAATTTAAAATATCAAAATCACGTATCAACAAATATGATACAATTA
66 GAAACAAATTATTAAAAATTAATTTAAAATATCAAAATCACGCATAAACAAATATGATACAATTA
35305147 TGTAAACCAATATTAATCAAAATGCGCTGAAACACACAAAA
131 TGTAAACCAATATTAATCAAAATGCGCTGAAACACACAAAA
35305188 A
1 A
35305189 TTTGAGTTAA
Statistics
Matches: 165, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
171 136 0.82
172 29 0.18
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.35
Consensus pattern (171 bp):
AATAATTTAATTTATTTATTATATTTTATTTTTAAAATTATTAAAAATAAAATAAAAATATTTAA
GAAACAAATTATTAAAAATTAATTTAAAATATCAAAATCACGCATAAACAAATATGATACAATTA
TGTAAACCAATATTAATCAAAATGCGCTGAAACACACAAAA
Found at i:35305438 original size:17 final size:17
Alignment explanation
Indices: 35305418--35305451 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35305408 TATTTTTTAA
*
35305418 AATTTATTTTCGAATAT
1 AATTTATTTTCAAATAT
*
35305435 AATTTTTTTTCAAATAT
1 AATTTATTTTCAAATAT
35305452 TAAAAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (17 bp):
AATTTATTTTCAAATAT
Found at i:35308946 original size:36 final size:36
Alignment explanation
Indices: 35308905--35308976 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
35308895 ATAAAGAGAG
*
35308905 AAAGGATGGAATGGCTATAAAAAGCCATTAGCTATT
1 AAAGGATGGAATGGCTATAAAAAGCCATCAGCTATT
35308941 AAAGGATGGAATGGCTATAAAAAGCCATCAGCTATT
1 AAAGGATGGAATGGCTATAAAAAGCCATCAGCTATT
35308977 GTGTTCTCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (36 bp):
AAAGGATGGAATGGCTATAAAAAGCCATCAGCTATT
Found at i:35311237 original size:61 final size:61
Alignment explanation
Indices: 35311142--35311259 Score: 236
Period size: 61 Copynumber: 1.9 Consensus size: 61
35311132 TAGCATGTGC
35311142 CTAGGTGTGTGTATTAAGGTTGAATGTGAAGAGACTTAAATGTGAAACTCAATGTTTACTG
1 CTAGGTGTGTGTATTAAGGTTGAATGTGAAGAGACTTAAATGTGAAACTCAATGTTTACTG
35311203 CTAGGTGTGTGTATTAAGGTTGAATGTGAAGAGACTTAAATGTGAAACTCAATGTTT
1 CTAGGTGTGTGTATTAAGGTTGAATGTGAAGAGACTTAAATGTGAAACTCAATGTTT
35311260 GCTTAAATTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (61 bp):
CTAGGTGTGTGTATTAAGGTTGAATGTGAAGAGACTTAAATGTGAAACTCAATGTTTACTG
Found at i:35313155 original size:43 final size:43
Alignment explanation
Indices: 35313041--35313158 Score: 166
Period size: 43 Copynumber: 2.7 Consensus size: 43
35313031 ATTACCGAGG
* *
35313041 TGAGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTTA
1 TGAGATTACATGTAAGACCATGTCTGGGATATTGGCATCGATA
*
35313084 T-ATGATTTCATGTAAGACCATGTCTGGGATATTGGCATCGATA
1 TGA-GATTACATGTAAGACCATGTCTGGGATATTGGCATCGATA
* * *
35313127 TGAGATAACATGTAAGACCATATTTGGGATAT
1 TGAGATTACATGTAAGACCATGTCTGGGATAT
35313159 GACATTGTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.02
43 64 0.97
44 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.32
Consensus pattern (43 bp):
TGAGATTACATGTAAGACCATGTCTGGGATATTGGCATCGATA
Found at i:35318410 original size:59 final size:59
Alignment explanation
Indices: 35318343--35318462 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 59
35318333 GAATAAGTCT
35318343 TTGAGAAAGTATTGTTGTGGATATAGCATTACTCAATTTAGCCATAAAGAGAAGTTGGG
1 TTGAGAAAGTATTGTTGTGGATATAGCATTACTCAATTTAGCCATAAAGAGAAGTTGGG
* *
35318402 TTGAGAAAGTATTGTTGTGGATATAGCATTTCTCAATTTAGCCATAAATAGAAGTTGGG
1 TTGAGAAAGTATTGTTGTGGATATAGCATTACTCAATTTAGCCATAAAGAGAAGTTGGG
35318461 TT
1 TT
35318463 TGCGATTTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (59 bp):
TTGAGAAAGTATTGTTGTGGATATAGCATTACTCAATTTAGCCATAAAGAGAAGTTGGG
Found at i:35320106 original size:31 final size:31
Alignment explanation
Indices: 35320063--35320171 Score: 191
Period size: 31 Copynumber: 3.5 Consensus size: 31
35320053 TTAACGGTTG
*
35320063 CTGGGCCAAAGCCTTTTCATAAATCATATCA
1 CTGGGCCGAAGCCTTTTCATAAATCATATCA
*
35320094 CTGGGCTGAAGCCTTTTCATAAATCATATCA
1 CTGGGCCGAAGCCTTTTCATAAATCATATCA
*
35320125 CTGGGCCGAAGCCTTTTCATAAATCATTTCA
1 CTGGGCCGAAGCCTTTTCATAAATCATATCA
35320156 CTGGGCCGAAGCCTTT
1 CTGGGCCGAAGCCTTT
35320172 ACTGTAAACG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (31 bp):
CTGGGCCGAAGCCTTTTCATAAATCATATCA
Found at i:35320246 original size:42 final size:42
Alignment explanation
Indices: 35320195--35320286 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
35320185 TGGCCCATAG
* ** *
35320195 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
* *
35320237 GCCTATTTCAATATCATATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
35320279 GCCCATTT
1 GCCCATTT
35320287 GGGGAGACTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:35320509 original size:26 final size:26
Alignment explanation
Indices: 35320424--35320554 Score: 171
Period size: 26 Copynumber: 5.2 Consensus size: 26
35320414 GGCCTAGACT
35320424 CTTTT-AAT-AACTGGGGCA-AAGCC
1 CTTTTCAATAAACTGGGGCATAAGCC
** * *
35320447 CTTTTCGGTAAATTGGGGCA-AAACC
1 CTTTTCAATAAACTGGGGCATAAGCC
35320472 CTTTTCAATAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCATAAGCC
***
35320498 CTTTTTGGTAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCATAAGCC
35320524 CTTTTCAATAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCATAAGCC
35320550 CTTTT
1 CTTTT
35320555 GCACTTCCTC
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
23 5 0.05
24 1 0.01
25 30 0.33
26 55 0.60
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (26 bp):
CTTTTCAATAAACTGGGGCATAAGCC
Found at i:35320544 original size:52 final size:51
Alignment explanation
Indices: 35320424--35320554 Score: 205
Period size: 52 Copynumber: 2.6 Consensus size: 51
35320414 GGCCTAGACT
*
35320424 CTTTT-AAT-AACTGGGGCA-AAGCCCTTTTCGGTAAATTGGGGCAAAACC
1 CTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAAAACC
* *
35320472 CTTTTCAATAAACTGGGGCATAAGCCCTTTTTGGTAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCA-AAACC
35320524 CTTTTCAATAAACTGGGGCATAAGCCCTTTT
1 CTTTTCAATAAACTGGGGCATAAGCCCTTTT
35320555 GCACTTCCTC
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
48 5 0.07
49 3 0.04
50 10 0.13
51 23 0.30
52 35 0.46
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (51 bp):
CTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAAAACC
Found at i:35320629 original size:20 final size:20
Alignment explanation
Indices: 35320604--35320670 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
35320594 TTATGAATAC
35320604 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
35320624 ATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
*
35320644 ATCATGTGCATATCATATCA-
1 ATCATGTGCATTTCATA-CAT
35320664 ATCATGT
1 ATCATGT
35320671 ATATCATATC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:35321205 original size:27 final size:29
Alignment explanation
Indices: 35321147--35321209 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
35321137 TATACCCAAT
35321147 GGTATTTCTATAATTTTTAGAAAGTCAAG
1 GGTATTTCTATAATTTTTAGAAAGTCAAG
* *
35321176 GGTATTTCTGT-ATTTTT-GTAAA-TCAGG
1 GGTATTTCTATAATTTTTAG-AAAGTCAAG
35321203 GGTATTT
1 GGTATTT
35321210 TGGCAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 12 0.39
28 9 0.29
29 10 0.32
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (29 bp):
GGTATTTCTATAATTTTTAGAAAGTCAAG
Found at i:35321225 original size:27 final size:27
Alignment explanation
Indices: 35321200--35321358 Score: 142
Period size: 27 Copynumber: 5.9 Consensus size: 27
35321190 TTTGTAAATC
*
35321200 AGGGGTATTTTGGCAATTTTACAAA-T
1 AGGGGTATTTTGGTAATTTTACAAACT
* * *
35321226 TGAGGGTATTTCGGTAATTTCACAAACT
1 AG-GGGTATTTTGGTAATTTTACAAACT
*** *
35321254 AATAGTATTTCGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
*
35321281 AGGGGTATTTTGGTAATTGTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
* * * *
35321308 AGGGATTTTTTGGTAATTCTATCATAC-
1 AGGGGTATTTTGGTAATTTTA-CAAACT
** *
35321335 AGGGGTATTTCAGTAATTTCACAA
1 AGGGGTATTTTGGTAATTTTACAA
35321359 TTGAGGGTAA
Statistics
Matches: 105, Mismatches: 25, Indels: 6
0.77 0.18 0.04
Matches are distributed among these distances:
26 3 0.03
27 97 0.92
28 5 0.05
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACT
Found at i:35321376 original size:26 final size:26
Alignment explanation
Indices: 35321347--35321405 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
35321337 GGGTATTTCA
35321347 GTAATTT-CACAATTGAGGGTAAAACG
1 GTAATTTGCA-AATTGAGGGTAAAACG
* *
35321373 GTAATTTTGTAAATTGAGGGTAAAATG
1 GTAA-TTTGCAAATTGAGGGTAAAACG
35321400 GTAATT
1 GTAATT
35321406 CTGTANNNNN
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 6 0.21
27 22 0.76
28 1 0.03
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (26 bp):
GTAATTTGCAAATTGAGGGTAAAACG
Found at i:35321387 original size:27 final size:27
Alignment explanation
Indices: 35321357--35321410 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
35321347 GTAATTTCAC
*
35321357 AATTGAGGGTAAAACGGTAATTTTGTA
1 AATTGAGGGTAAAACGGTAATTCTGTA
*
35321384 AATTGAGGGTAAAATGGTAATTCTGTA
1 AATTGAGGGTAAAACGGTAATTCTGTA
35321411 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (27 bp):
AATTGAGGGTAAAACGGTAATTCTGTA
Found at i:35326654 original size:43 final size:44
Alignment explanation
Indices: 35326606--35326770 Score: 133
Period size: 43 Copynumber: 3.8 Consensus size: 44
35326596 ATCGAGATGA
*
35326606 GATTACATGTAAGACCATATCTGGGACATTGGCATTGCA-CTGT
1 GATTACATGTAAGACCATATCTGGGACATTGGCATTGCATATGT
* * * ** * *
35326649 GATTACGTGTAAGACCATGTTTATGACATTGACA-T-CATTATAT
1 GATTACATGTAAGACCATATCTGGGACATTGGCATTGCA-TATGT
* * * * * *
35326692 GATTCCGTGTAAGACCATGTCTGGGACATTAGCATCG-ATATGA
1 GATTACATGTAAGACCATATCTGGGACATTGGCATTGCATATGT
* * *
35326735 GATAACATGTAAGACCATATTTGGGATA-TGGCATTG
1 GATTACATGTAAGACCATATCTGGGACATTGGCATTG
35326771 TATGAGCTTT
Statistics
Matches: 93, Mismatches: 25, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
41 2 0.02
42 7 0.08
43 83 0.89
44 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (44 bp):
GATTACATGTAAGACCATATCTGGGACATTGGCATTGCATATGT
Found at i:35332488 original size:21 final size:22
Alignment explanation
Indices: 35332464--35332511 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
35332454 GTAGGGGTCT
35332464 ACACGCCCATATGGAGGT-CAC
1 ACACGCCCATATGGAGGTGCAC
* *
35332485 ACACGCCTATGTGGAGGTGGCAC
1 ACACGCCCATATGGAGGT-GCAC
35332508 ACAC
1 ACAC
35332512 ACGTGTGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.70
23 7 0.30
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (22 bp):
ACACGCCCATATGGAGGTGCAC
Found at i:35348658 original size:42 final size:42
Alignment explanation
Indices: 35348539--35348689 Score: 135
Period size: 42 Copynumber: 3.6 Consensus size: 42
35348529 TACCGTACCA
* * * ** * *
35348539 ATGCCATATCTCAAATATAGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACATAGTCTCATATCG
* * * * *
35348581 TTGCCAATAGCCCAGGTATGGTCTTGCACGA-AGTCTTATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACAC-ATAGTCTCATATCG
35348624 ATGCCATATCCCAGATATGGTCTTACACATAGTCTCATA-CTG
1 ATGCCATATCCCAGATATGGTCTTACACATAGTCTCATATC-G
* *
35348666 AAGCCATATCTCAGATATGGTCTT
1 ATGCCATATCCCAGATATGGTCTT
35348690 TGTAACAGCC
Statistics
Matches: 86, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
41 2 0.02
42 55 0.64
43 29 0.34
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACATAGTCTCATATCG
Found at i:35349937 original size:42 final size:43
Alignment explanation
Indices: 35349891--35350001 Score: 102
Period size: 43 Copynumber: 2.6 Consensus size: 43
35349881 GTATGGAATT
*
35349891 GATATGTGATTTCATGTAAGACCAT-GTCTAAGAC-AT-GGCATC
1 GATATGTGATATCATGTAAGACCATAGT-T-AGACTATCGGCATC
* * * * *
35349933 GATATGAGACATCGTGTAAGACCATAGTTGGCCTATCGGCATC
1 GATATGTGATATCATGTAAGACCATAGTTAGACTATCGGCATC
* **
35349976 GATATGTGCTCCCATGTAAGACCATA
1 GATATGTGATATCATGTAAGACCATA
35350002 TCTGGGATCT
Statistics
Matches: 54, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
41 2 0.04
42 24 0.44
43 28 0.52
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (43 bp):
GATATGTGATATCATGTAAGACCATAGTTAGACTATCGGCATC
Found at i:35353410 original size:48 final size:48
Alignment explanation
Indices: 35353355--35353590 Score: 230
Period size: 48 Copynumber: 4.9 Consensus size: 48
35353345 GGTGAATTGT
* *
35353355 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGA-GGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACATATC-ATGGC
* * * *
35353403 CGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAAT-GT
1 CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACATATC-ATGGC
* * *
35353451 AGATGCCATG-TCCTAGACATGGTCTTACACTGGCTCTCAT-TACATTGC
1 CGATGCCATGTTCC-AGACATGGTCTTACACTGGCTCACATAT-CATGGC
* * * * * *
35353499 TGATGTCATGTTCCAAACATGATCTTACACTGGCTCTCATAAT-ATGGT
1 CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACAT-ATCATGGC
* * *
35353547 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCA
1 CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACATATCA
35353591 CCCAAATGTC
Statistics
Matches: 153, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
47 7 0.05
48 142 0.93
49 3 0.02
50 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACATATCATGGC
Found at i:35361214 original size:37 final size:37
Alignment explanation
Indices: 35361155--35361263 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
35361145 AGCTCAGACG
* *
35361155 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
35361192 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
35361229 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
35361264 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:35361550 original size:50 final size:50
Alignment explanation
Indices: 35361426--35361558 Score: 223
Period size: 50 Copynumber: 2.7 Consensus size: 50
35361416 TTCACACTAG
*
35361426 CCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATTGA
1 CCATTCGGCTTTACCACATATGCATATCTCATATATATATTTCACATTGA
*
35361476 CCAGTCGGCTTTACCACATATGCATATCTCATATATATATTTCACATTGA
1 CCATTCGGCTTTACCACATATGCATATCTCATATATATATTTCACATTGA
* *
35361526 CCATTCGGCTTTACCACATGTGCATGT-TCATAT
1 CCATTCGGCTTTACCACATATGCATATCTCATAT
35361559 TCACCACATT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 6 0.08
50 72 0.92
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.37
Consensus pattern (50 bp):
CCATTCGGCTTTACCACATATGCATATCTCATATATATATTTCACATTGA
Found at i:35361575 original size:45 final size:47
Alignment explanation
Indices: 35361518--35361632 Score: 153
Period size: 47 Copynumber: 2.5 Consensus size: 47
35361508 ATATATATTT
* * * * *
35361518 CACATTGACCATTCGGCTTTA-C-CACATGTGCATGTTCATATTCAC
1 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCAC
* *
35361563 CACATTGGCCATTCGACCTTATCACACATATGCATGCTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCAC
35361610 CACATTGGCCATTCGGCCTTATC
1 CACATTGGCCATTCGGCCTTATC
35361633 TCATATATAC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 18 0.30
46 1 0.02
47 41 0.68
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.31
Consensus pattern (47 bp):
CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCAC
Found at i:35361651 original size:47 final size:47
Alignment explanation
Indices: 35361552--35361661 Score: 139
Period size: 47 Copynumber: 2.3 Consensus size: 47
35361542 CATGTGCATG
* * * **
35361552 TTCATATTCACCACATTGGCCATTCGACCTTATCACACATATGCATG
1 TTCACATTCATCACATTGGCCATTCGACCTTATCACACATATACACA
* * * *
35361599 CTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATACACA
1 TTCACATTCATCACATTGGCCATTCGACCTTATCACACATATACACA
35361646 TTCACATTCATCACAT
1 TTCACATTCATCACAT
35361662 AAAATCCTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
TTCACATTCATCACATTGGCCATTCGACCTTATCACACATATACACA
Found at i:35365481 original size:21 final size:21
Alignment explanation
Indices: 35365452--35365501 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
35365442 CAGGCCAAAT
*
35365452 TATGTGAGCCTATTAATATCA
1 TATGCGAGCCTATTAATATCA
*
35365473 TATGCGAGCCTATTAATATTA
1 TATGCGAGCCTATTAATATCA
*
35365494 CATGCGAG
1 TATGCGAG
35365502 TCAAATTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (21 bp):
TATGCGAGCCTATTAATATCA
Found at i:35365704 original size:29 final size:28
Alignment explanation
Indices: 35365638--35365705 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
35365628 TGTACATGCA
* * *
35365638 AACCCTAGGTGCAACCCTTACTTGCGTG
1 AACCCTAAGTGCAACCCCTACTTGCGCG
* *
35365666 AACCCTAAGTGCTACCCCTACTTGTGCG
1 AACCCTAAGTGCAACCCCTACTTGCGCG
35365694 AACCCTTAAGTG
1 AACCC-TAAGTG
35365706 TGCGAGAGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 28 0.82
29 6 0.18
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
AACCCTAAGTGCAACCCCTACTTGCGCG
Found at i:35380797 original size:42 final size:43
Alignment explanation
Indices: 35380676--35380798 Score: 162
Period size: 43 Copynumber: 2.9 Consensus size: 43
35380666 TACCATACTA
*
35380676 ATGCCATATCCCAGATATGGTCTTACATGTAATCT-AGTATCT
1 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCAGTATCG
* * * *
35380718 ATGCCAATAGCCTAGCTATGGTCTTACACG-AAGTCTCA-TATCG
1 ATGCC-ATATCCCAGATATGGTCTTACATGTAA-TCTCAGTATCG
35380761 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCAG
1 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCAG
35380799 AAACCCTAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
42 32 0.48
43 34 0.51
44 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (43 bp):
ATGCCATATCCCAGATATGGTCTTACATGTAATCTCAGTATCG
Found at i:35383420 original size:42 final size:43
Alignment explanation
Indices: 35383373--35383483 Score: 118
Period size: 43 Copynumber: 2.6 Consensus size: 43
35383363 GTTTTACGTA
* * * * *
35383373 TAAGACCATGTTTGGGACATTGGCTTCG-TATATGATTTCGTG
1 TAAGACCATGTCTGGGACATTGGCATCGATATATAATTACATG
* * *
35383415 TAAGACTC-TGTCTGGGACAGTGGCATCGATGTTTAATTACATG
1 TAAGAC-CATGTCTGGGACATTGGCATCGATATATAATTACATG
*
35383458 TAAGACCACGTCTGGGACATTGGCAT
1 TAAGACCATGTCTGGGACATTGGCAT
35383484 TGTATTTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 24 0.43
43 32 0.57
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACATTGGCATCGATATATAATTACATG
Found at i:35384123 original size:22 final size:26
Alignment explanation
Indices: 35384075--35384136 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 26
35384065 ATGAGATTAC
35384075 ATGATTTATTGATTATACGTTTAGGT
1 ATGATTTATTGATTATACGTTTAGGT
*
35384101 ATGATTT-TTG-TTA-A-GTTTTGGT
1 ATGATTTATTGATTATACGTTTAGGT
*
35384123 ATGAATTGATTGAT
1 ATG-ATTTATTGAT
35384137 GAATTGAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 10 0.32
23 4 0.13
24 6 0.19
25 4 0.13
26 7 0.23
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.52
Consensus pattern (26 bp):
ATGATTTATTGATTATACGTTTAGGT
Found at i:35384481 original size:12 final size:12
Alignment explanation
Indices: 35384464--35384494 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
35384454 GGCACACAGG
35384464 CGTGTGGTCGGC
1 CGTGTGGTCGGC
35384476 CGTGTGGTCGGC
1 CGTGTGGTCGGC
35384488 CGTGTGG
1 CGTGTGG
35384495 CCAAGTCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.52, T:0.26
Consensus pattern (12 bp):
CGTGTGGTCGGC
Found at i:35395503 original size:19 final size:19
Alignment explanation
Indices: 35395470--35395511 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
35395460 TATATGTATG
*
35395470 TTTATATTTTAATTTATTA
1 TTTATATTTTAATTTAATA
35395489 TTTAT-TTTTAGATTTAATA
1 TTTATATTTTA-ATTTAATA
35395508 TTTA
1 TTTA
35395512 AGATTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTATATTTTAATTTAATA
Found at i:35395579 original size:22 final size:22
Alignment explanation
Indices: 35395551--35395621 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
35395541 TTTGTGTTAA
35395551 AGTTTTAGAGATAGATTATGAT
1 AGTTTTAGAGATAGATTATGAT
*
35395573 AGTTTTA-ATG-TATG-TGT-T-AA
1 AGTTTTAGA-GATA-GAT-TATGAT
35395593 AGTTTTAGAGATAGATTATGAT
1 AGTTTTAGAGATAGATTATGAT
*
35395615 GGTTTTA
1 AGTTTTA
35395622 ATGTATGTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
20 11 0.29
21 10 0.26
22 17 0.45
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (22 bp):
AGTTTTAGAGATAGATTATGAT
Found at i:35395598 original size:42 final size:42
Alignment explanation
Indices: 35395543--35395629 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
35395533 AAATTGTATT
35395543 TGTGTTAAAGTTTTAGAGATAGATTATGATAGTTTTAATGTA
1 TGTGTTAAAGTTTTAGAGATAGATTATGATAGTTTTAATGTA
*
35395585 TGTGTTAAAGTTTTAGAGATAGATTATGATGGTTTTAATGTA
1 TGTGTTAAAGTTTTAGAGATAGATTATGATAGTTTTAATGTA
35395627 TGT
1 TGT
35395630 TCTTTTTAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (42 bp):
TGTGTTAAAGTTTTAGAGATAGATTATGATAGTTTTAATGTA
Found at i:35397940 original size:19 final size:19
Alignment explanation
Indices: 35397907--35397948 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
35397897 TATATGTATG
*
35397907 TTTATATTTTAATTTATTA
1 TTTATATTTTAATTTAATA
35397926 TTTAT-TTTTAGATTTAATA
1 TTTATATTTTA-ATTTAATA
35397945 TTTA
1 TTTA
35397949 AGATTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTATATTTTAATTTAATA
Found at i:35398016 original size:22 final size:22
Alignment explanation
Indices: 35397988--35398058 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
35397978 TTTGTGTTAA
35397988 AGTTTTAGAGATAGATTATGAT
1 AGTTTTAGAGATAGATTATGAT
*
35398010 AGTTTTA-ATG-TATG-TGT-T-AA
1 AGTTTTAGA-GATA-GAT-TATGAT
35398030 AGTTTTAGAGATAGATTATGAT
1 AGTTTTAGAGATAGATTATGAT
*
35398052 GGTTTTA
1 AGTTTTA
35398059 ATGTATGTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
20 11 0.29
21 10 0.26
22 17 0.45
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (22 bp):
AGTTTTAGAGATAGATTATGAT
Found at i:35398035 original size:42 final size:42
Alignment explanation
Indices: 35397980--35398066 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
35397970 AAATTGTATT
35397980 TGTGTTAAAGTTTTAGAGATAGATTATGATAGTTTTAATGTA
1 TGTGTTAAAGTTTTAGAGATAGATTATGATAGTTTTAATGTA
*
35398022 TGTGTTAAAGTTTTAGAGATAGATTATGATGGTTTTAATGTA
1 TGTGTTAAAGTTTTAGAGATAGATTATGATAGTTTTAATGTA
35398064 TGT
1 TGT
35398067 TCTTTTTAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (42 bp):
TGTGTTAAAGTTTTAGAGATAGATTATGATAGTTTTAATGTA
Found at i:35413422 original size:47 final size:47
Alignment explanation
Indices: 35413345--35413566 Score: 201
Period size: 47 Copynumber: 4.8 Consensus size: 47
35413335 ATGGGTTATT
*
35413345 ATGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACATTGAGACG
1 ATGAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGAC-TTGAGACG
* *
35413394 A-GAGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCTTCGAGACG
1 ATGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTT-GAGACG
* * * * * *
35413440 -TAAGCCAGTGTAAGA-CATG-CTTAGGACATGTAT-TAGC-T-ACAAG
1 ATGAGCCAGTGTAAGACCATGTC-TGGGACATGCATCGA-CTTGAGACG
* * *
35413483 ATGTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGA-T
1 ATGAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGACTTGAGACG
*
35413530 ATGAGCCAGTGTAAGACCATGTCTGAGACATAGCATC
1 ATGAGCCAGTGTAAGACCATGTCTGGGACAT-GCATC
35413567 AGCATTCGAC
Statistics
Matches: 139, Mismatches: 23, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
43 3 0.02
44 12 0.09
45 15 0.11
46 45 0.32
47 48 0.35
48 15 0.11
49 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (47 bp):
ATGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTTGAGACG
Found at i:35413450 original size:46 final size:48
Alignment explanation
Indices: 35413348--35413575 Score: 188
Period size: 46 Copynumber: 4.9 Consensus size: 48
35413338 GGTTATTATG
* *
35413348 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACATT-GAGACG-A
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTCGAGACGTA
*
35413395 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTTCGAGACGTA
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGACGTA
* * ** * * *
35413442 AGCCAGTGTAAGA-CATG-CTTAGGACAT-GTATTAGCTACAAGATGT-
1 AGCCAGTGTAAGACCATGTC-TGGGACATGGCATCGGCTTCGAGACGTA
* * ** *
35413487 -GTCAGTGTAAGACCATGTCTGGGACATGGCATCGACTT-GAGATATG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGACGTA
* * *
35413533 AGCCAGTGTAAGACCATGTCTGAGACATAGCATCAGCATTCGA
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTCGA
35413576 CCCCATGTTT
Statistics
Matches: 145, Mismatches: 25, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
44 11 0.08
45 19 0.13
46 54 0.37
47 45 0.31
48 14 0.10
49 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (48 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGACGTA
Found at i:35416017 original size:21 final size:21
Alignment explanation
Indices: 35415993--35416034 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
35415983 AAATAAGTTC
*
35415993 GTGTAACTCGAAGTAAACTTT
1 GTGTAACTCGAAGAAAACTTT
35416014 GTGTAACTCGAAGAAAACTTT
1 GTGTAACTCGAAGAAAACTTT
35416035 AAATATACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (21 bp):
GTGTAACTCGAAGAAAACTTT
Found at i:35421598 original size:32 final size:32
Alignment explanation
Indices: 35421561--35421621 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
35421551 CAAGACAAAG
35421561 CATATTCCCAATTGGACTTGATAGACAATGAA
1 CATATTCCCAATTGGACTTGATAGACAATGAA
35421593 CATATTCCCAATTGGACTTGATAGACAAT
1 CATATTCCCAATTGGACTTGATAGACAAT
35421622 ATATTAATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (32 bp):
CATATTCCCAATTGGACTTGATAGACAATGAA
Found at i:35426059 original size:31 final size:30
Alignment explanation
Indices: 35425988--35426061 Score: 114
Period size: 31 Copynumber: 2.5 Consensus size: 30
35425978 GATTTCTAAC
35425988 AGCTTTTTTTT-TTCTCGTTTTGTTAAACA
1 AGCTTTTTTTTCTTCTCGTTTTGTTAAACA
* *
35426017 AACTCTTTTTTCTATCTCGTTTTGTTAAACA
1 AGCTTTTTTTTCT-TCTCGTTTTGTTAAACA
35426048 AGCTTTTTTTTCTT
1 AGCTTTTTTTTCTT
35426062 TTGTTCTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 9 0.23
30 2 0.05
31 28 0.72
ACGTcount: A:0.18, C:0.16, G:0.08, T:0.58
Consensus pattern (30 bp):
AGCTTTTTTTTCTTCTCGTTTTGTTAAACA
Found at i:35432639 original size:10 final size:10
Alignment explanation
Indices: 35432624--35432653 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
35432614 GAAAGGAGAT
35432624 AAGGCACAGC
1 AAGGCACAGC
35432634 AAGGCACAGC
1 AAGGCACAGC
*
35432644 AAAGCACAGC
1 AAGGCACAGC
35432654 CCACAGCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.30, G:0.27, T:0.00
Consensus pattern (10 bp):
AAGGCACAGC
Found at i:35433246 original size:18 final size:18
Alignment explanation
Indices: 35433215--35433262 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
35433205 ACACCCATTT
*
35433215 AAAT-TAAAATTTAAAAA
1 AAATATAAAAATTAAAAA
*
35433232 AAATATAAAAATTAAAAT
1 AAATATAAAAATTAAAAA
* *
35433250 ACATAAAAAAATT
1 AAATATAAAAATT
35433263 TTGATTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATATAAAAATTAAAAA
Found at i:35438110 original size:29 final size:28
Alignment explanation
Indices: 35438046--35438111 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
35438036 AGTGGGTCTA
35438046 CTAATTTTTTTTTTGAAAATCTCTTTTT
1 CTAATTTTTTTTTTGAAAATCTCTTTTT
** *
35438074 CTTTTTTTTTCTTTTTATAAA-CTCTTTTT
1 CTAATTTTTT-TTTTGA-AAATCTCTTTTT
35438103 CTAATTTTT
1 CTAATTTTT
35438112 ATTTATGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 8 0.26
29 20 0.65
30 3 0.10
ACGTcount: A:0.18, C:0.12, G:0.02, T:0.68
Consensus pattern (28 bp):
CTAATTTTTTTTTTGAAAATCTCTTTTT
Found at i:35442094 original size:20 final size:20
Alignment explanation
Indices: 35442069--35442106 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
35442059 TTTCAATTTT
35442069 ATTTGATGTTATATTTCATC
1 ATTTGATGTTATATTTCATC
35442089 ATTTGATGTTATATTTCA
1 ATTTGATGTTATATTTCA
35442107 GTTTCAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (20 bp):
ATTTGATGTTATATTTCATC
Found at i:35456141 original size:13 final size:15
Alignment explanation
Indices: 35456112--35456143 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
35456102 GGGAAAGGTT
35456112 GATTCAGAGGTAAGA
1 GATTCAGAGGTAAGA
35456127 GATTC-GAGG-AAGA
1 GATTCAGAGGTAAGA
35456140 GATT
1 GATT
35456144 GATAAGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.38, C:0.06, G:0.34, T:0.22
Consensus pattern (15 bp):
GATTCAGAGGTAAGA
Found at i:35461231 original size:41 final size:41
Alignment explanation
Indices: 35461099--35461281 Score: 160
Period size: 40 Copynumber: 4.4 Consensus size: 41
35461089 GATATGTTTT
* * *
35461099 GCACTTAGTGTGCG-TATCGAGATAGCTTCGGCTATATAAA
1 GCACTTAGTGTGCGAGATTGAGATAGCTTCGGCTATATAAG
*
35461139 GCACTTAGTGCGCGA-ATTG-GAATAGCTTCGGCTATATATATG
1 GCACTTAGTGTGCGAGATTGAG-ATAGCTTCGGCTATATA-A-G
* *
35461181 GCACTTAGTGTGCGAGATTGAGACAGCTTCGGCTACGA-AAG
1 GCACTTAGTGTGCGAGATTGAGATAGCTTCGGCTA-TATAAG
* * * * **
35461222 GCACTTAGTGTACGAGATT-ATAATAGCTTCAGCTATGCTTTG
1 GCACTTAGTGTGCGAGATTGA-GATAGCTTCGGCTAT-ATAAG
*
35461264 GCACTTAGTGTGTGAGAT
1 GCACTTAGTGTGCGAGAT
35461282 ATCGAGTATT
Statistics
Matches: 117, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
39 1 0.01
40 34 0.29
41 31 0.26
42 32 0.27
43 17 0.15
44 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (41 bp):
GCACTTAGTGTGCGAGATTGAGATAGCTTCGGCTATATAAG
Found at i:35461266 original size:83 final size:81
Alignment explanation
Indices: 35461091--35461281 Score: 206
Period size: 83 Copynumber: 2.3 Consensus size: 81
35461081 ATGAACCGGA
* * * * *
35461091 TATGTTTTGCACTTAGTGTGCG-TATCGAGATAGCTTCGGCTATATAAAGCACTTAGTGCGCGAA
1 TATGTTTGGCACTTAGTGTGCGAGATCGAGACAGCTTCGGCTAGATAAAGCACTTAGTGCACGAA
* *
35461155 TTGGAATAGCTTCGGC
66 TTAGAATAGCTTCAGC
* * * *
35461171 TATATATATGGCACTTAGTGTGCGAGATTGAGACAGCTTCGGCTACGA-AAGGCACTTAGTGTAC
1 TATGT-T-TGGCACTTAGTGTGCGAGATCGAGACAGCTTCGGCTA-GATAAAGCACTTAGTGCAC
*
35461235 GAGATTATAATAGCTTCAGC
63 GA-ATTAGAATAGCTTCAGC
*
35461255 TATGCTTTGGCACTTAGTGTGTGAGAT
1 TATG-TTTGGCACTTAGTGTGCGAGAT
35461282 ATCGAGTATT
Statistics
Matches: 91, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
80 4 0.04
81 1 0.01
82 15 0.16
83 51 0.56
84 19 0.21
85 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (81 bp):
TATGTTTGGCACTTAGTGTGCGAGATCGAGACAGCTTCGGCTAGATAAAGCACTTAGTGCACGAA
TTAGAATAGCTTCAGC
Found at i:35465039 original size:120 final size:120
Alignment explanation
Indices: 35464826--35465065 Score: 471
Period size: 120 Copynumber: 2.0 Consensus size: 120
35464816 ATAAAACCTT
35464826 GCCATGAATATCCACTAACTATTAAAATGGTCTAATTACCATCTAAGTCCATTCACTTTAAAGTT
1 GCCATGAATATCCACTAACTATTAAAATGGTCTAATTACCATCTAAGTCCATTCACTTTAAAGTT
35464891 TCATAGCCATTTGACTTTTTTAACTAATGGAAACCTACTTTTAAACTTTTTACGA
66 TCATAGCCATTTGACTTTTTTAACTAATGGAAACCTACTTTTAAACTTTTTACGA
35464946 GCCATGAATATCCACTAACTATTAAAATGGTCTAATTACCATCTAAGTCCATTCACTTTAAAGTT
1 GCCATGAATATCCACTAACTATTAAAATGGTCTAATTACCATCTAAGTCCATTCACTTTAAAGTT
*
35465011 TCATAGCCATTTGACTTTTTTAACTAATGGAAACCTACTTTTACACTTTTTACGA
66 TCATAGCCATTTGACTTTTTTAACTAATGGAAACCTACTTTTAAACTTTTTACGA
35465066 TTTTGTCCTT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (120 bp):
GCCATGAATATCCACTAACTATTAAAATGGTCTAATTACCATCTAAGTCCATTCACTTTAAAGTT
TCATAGCCATTTGACTTTTTTAACTAATGGAAACCTACTTTTAAACTTTTTACGA
Found at i:35465600 original size:20 final size:20
Alignment explanation
Indices: 35465555--35465600 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
35465545 ATTTAGCCAT
* *
35465555 TTTTTTTATTTTTATTTTCA
1 TTTTTTTATTTTTAATTTAA
* *
35465575 TATTTTTGTTTTTAATTTAA
1 TTTTTTTATTTTTAATTTAA
35465595 TTTTTT
1 TTTTTT
35465601 CATTCTAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTTTTATTTTTAATTTAA
Found at i:35466883 original size:213 final size:213
Alignment explanation
Indices: 35466516--35466944 Score: 655
Period size: 213 Copynumber: 2.0 Consensus size: 213
35466506 GGTGTTTTTA
* * * *
35466516 ATATGGATGCAGTTGCTATGTTGGCATGTCAGGTAGAAGCATTGAATAAAAAAATTGATGGTTTG
1 ATATGGATGCAGTTGCTATGTTGGCAAGTCAGGTAGAAGCACTAAAGAAAAAAATTGATGGTTTG
* *
35466581 AGTTGCAATAATACGATGAATCCAGTAATGCAATGTGATGCAACTGGACCAGGGATGATCAATCC
66 AGTTGCAATAATACGATGAATCCAATAATGCAATGTGACGCAACTGGACCAGGGATGATCAATCC
* * * *
35466646 AGAATGTTTTCCCTTCGATTCTAACATGGAGCATGAGCAAGTCAACTTTATGGGTAATAATTCTA
131 AGAAGGTTTACCCTTCGATTCTAACATGGAGCATGAACAAGTCAACTTTATGGATAATAATTCTA
* *
35466711 GATCGCAAAATAACCCTT
196 GACCGCAAAATAACCCCT
* *
35466729 ATATGGATGCAGTTGTTATGTTGGCAAGTCAGGTA-AAGGTACTAAAGAAAAAAATTGATGGTTT
1 ATATGGATGCAGTTGCTATGTTGGCAAGTCAGGTAGAA-GCACTAAAGAAAAAAATTGATGGTTT
* *
35466793 GAGTTGCAATAATACGATGAATCCAATAATGCAATGTGACGCAACTGGAGCGGGGATGATCAATC
65 GAGTTGCAATAATACGATGAATCCAATAATGCAATGTGACGCAACTGGACCAGGGATGATCAATC
* *
35466858 CCGAAGGTTTACCCTTC-AGTTCTAACATGGAGTATGAACAAGTCAACTTTATGGATAATAATTC
130 CAGAAGGTTTACCCTTCGA-TTCTAACATGGAGCATGAACAAGTCAACTTTATGGATAATAATTC
*
35466922 TAGACCTCAAAATAACCCCT
194 TAGACCGCAAAATAACCCCT
35466942 ATA
1 ATA
35466945 GCAATAACTA
Statistics
Matches: 195, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
212 3 0.02
213 192 0.98
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (213 bp):
ATATGGATGCAGTTGCTATGTTGGCAAGTCAGGTAGAAGCACTAAAGAAAAAAATTGATGGTTTG
AGTTGCAATAATACGATGAATCCAATAATGCAATGTGACGCAACTGGACCAGGGATGATCAATCC
AGAAGGTTTACCCTTCGATTCTAACATGGAGCATGAACAAGTCAACTTTATGGATAATAATTCTA
GACCGCAAAATAACCCCT
Found at i:35469627 original size:21 final size:21
Alignment explanation
Indices: 35469582--35469630 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
35469572 TTAACTTTTT
* **
35469582 TTATTAGTGTTGTTACTGTTT
1 TTATTAGTGTTGTTACTCTCA
*
35469603 TTATTAGTGTTGTTATTCTCA
1 TTATTAGTGTTGTTACTCTCA
35469624 TTATTAG
1 TTATTAG
35469631 GTTTATTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.06, G:0.16, T:0.59
Consensus pattern (21 bp):
TTATTAGTGTTGTTACTCTCA
Found at i:35472216 original size:14 final size:14
Alignment explanation
Indices: 35472188--35472235 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
35472178 TTCTTGTTCT
35472188 AAAAAAAAG-AAGA
1 AAAAAAAAGAAAGA
* *
35472201 AAGAACAAGAAAGA
1 AAAAAAAAGAAAGA
35472215 AAAAAAAAGAAAGGA
1 AAAAAAAAGAAA-GA
35472230 AAAAAA
1 AAAAAA
35472236 TTGATTGAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 7 0.24
14 14 0.48
15 8 0.28
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAGA
Found at i:35480082 original size:49 final size:50
Alignment explanation
Indices: 35480021--35480135 Score: 153
Period size: 49 Copynumber: 2.3 Consensus size: 50
35480011 CTGGTATGCA
* **
35480021 TAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAACAGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTCAACA-TCTAATACACG
* * *
35480070 TAGTAGCTTGCACTTAGTACTACACACGTGACCTCACCATCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTCAACATCTAATACACG
35480120 TAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTA
35480136 AACATGCTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
49 28 0.49
50 25 0.44
51 4 0.07
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCTCAACATCTAATACACG
Found at i:35491023 original size:27 final size:27
Alignment explanation
Indices: 35490993--35491046 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
35490983 ACATACAACC
35490993 CATGTAAT-AGTAATTTAACATTCAATT
1 CATGTAATGA-TAATTTAACATTCAATT
**
35491020 CATGTAATGATAATTTGCCATTCAATT
1 CATGTAATGATAATTTAACATTCAATT
35491047 TCACTTGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (27 bp):
CATGTAATGATAATTTAACATTCAATT
Found at i:35499961 original size:22 final size:22
Alignment explanation
Indices: 35499936--35499980 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
35499926 TTGAGAAGTG
35499936 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
35499958 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
35499980 T
1 T
35499981 CTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:35507991 original size:17 final size:18
Alignment explanation
Indices: 35507969--35508003 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35507959 TGCGATAACA
*
35507969 TTCTATT-TTCATATTCT
1 TTCTATTATTCAAATTCT
35507986 TTCTATTATTCAAATTCT
1 TTCTATTATTCAAATTCT
35508004 AGCTAAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (18 bp):
TTCTATTATTCAAATTCT
Found at i:35510815 original size:48 final size:48
Alignment explanation
Indices: 35510744--35510969 Score: 287
Period size: 48 Copynumber: 4.7 Consensus size: 48
35510734 GAGTTACACG
35510744 GGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT
1 GGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT
35510792 GGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT
1 GGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT
* ** * * * * *
35510840 GGCCAATAACATGTCCTAAACATGGTCTTACACTAGCACACATATCAATGT
1 GGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC--AT-AATGT
* * * *
35510891 ---CAATGCCATGTCCTAGGCATGATCTTACACTGGCTCTCATAATGT
1 GGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT
*
35510936 GGCCGATGCCATGTCCCAAACATGGTCTTACACT
1 GGCCGATGCCATGTCCCAGACATGGTCTTACACT
35510970 AGCACACATA
Statistics
Matches: 151, Mismatches: 21, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
45 5 0.03
46 2 0.01
48 137 0.91
50 2 0.01
51 5 0.03
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (48 bp):
GGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT
Found at i:35511470 original size:20 final size:18
Alignment explanation
Indices: 35511434--35511472 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
35511424 TTATAGAACC
*
35511434 TCACAATTTTCAATTATT
1 TCACAATTTACAATTATT
35511452 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
35511472 T
1 T
35511473 TATAAACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:35513784 original size:19 final size:19
Alignment explanation
Indices: 35513757--35513801 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
35513747 CAAATCATTA
*
35513757 TCATATCATCTCAAGATTT
1 TCATATCATCTCAAGAATT
* *
35513776 TCATGTCATGTCAAGAATT
1 TCATATCATCTCAAGAATT
35513795 TCATATC
1 TCATATC
35513802 CGTTGAATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (19 bp):
TCATATCATCTCAAGAATT
Found at i:35514661 original size:20 final size:20
Alignment explanation
Indices: 35514632--35514676 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
35514622 AGCACATGTA
*
35514632 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTAGAAATT
* *
35514652 TTCATCAAATTTTATAAATT
1 TTCATAAAATTTTAGAAATT
35514672 TTCAT
1 TTCAT
35514677 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (20 bp):
TTCATAAAATTTTAGAAATT
Found at i:35524216 original size:19 final size:20
Alignment explanation
Indices: 35524192--35524229 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
35524182 TAATATCATC
*
35524192 TCAAGATTTTCATG-CCATG
1 TCAAGAGTTTCATGTCCATG
35524211 TCAAGAGTTTCATGTCCAT
1 TCAAGAGTTTCATGTCCAT
35524230 TGAATCATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (20 bp):
TCAAGAGTTTCATGTCCATG
Found at i:35527909 original size:38 final size:38
Alignment explanation
Indices: 35527865--35527942 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
35527855 AAATTAAGTA
*
35527865 CATACATAACTCAAACCTATCATTCACTCTCAATTATC
1 CATACATAACTCAAACCTATCACTCACTCTCAATTATC
*
35527903 CATACATAACTCAAACCTATCACTCACTCTCAATTTTC
1 CATACATAACTCAAACCTATCACTCACTCTCAATTATC
35527941 CA
1 CA
35527943 CCAAATGACC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (38 bp):
CATACATAACTCAAACCTATCACTCACTCTCAATTATC
Found at i:35533645 original size:43 final size:43
Alignment explanation
Indices: 35533584--35533676 Score: 177
Period size: 43 Copynumber: 2.2 Consensus size: 43
35533574 CAAGATATCA
*
35533584 AAAAAGTATATTGACTGTGAATCGTTAGTTTCATATTATGTTG
1 AAAAACTATATTGACTGTGAATCGTTAGTTTCATATTATGTTG
35533627 AAAAACTATATTGACTGTGAATCGTTAGTTTCATATTATGTTG
1 AAAAACTATATTGACTGTGAATCGTTAGTTTCATATTATGTTG
35533670 AAAAACT
1 AAAAACT
35533677 CATTTTTATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (43 bp):
AAAAACTATATTGACTGTGAATCGTTAGTTTCATATTATGTTG
Found at i:35540464 original size:9 final size:9
Alignment explanation
Indices: 35540450--35540506 Score: 62
Period size: 9 Copynumber: 6.3 Consensus size: 9
35540440 CAAATCTAAC
*
35540450 TCTCTCTAT
1 TCTCTCAAT
35540459 TCTCTCTAA-
1 TCTCTC-AAT
*
35540468 ACTCTCAAT
1 TCTCTCAAT
*
35540477 TCTCTCAAC
1 TCTCTCAAT
*
35540486 TCTCTCACT
1 TCTCTCAAT
35540495 TCTCTCAAT
1 TCTCTCAAT
35540504 TCT
1 TCT
35540507 TACAATTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 2 0.05
9 36 0.92
10 1 0.03
ACGTcount: A:0.19, C:0.37, G:0.00, T:0.44
Consensus pattern (9 bp):
TCTCTCAAT
Found at i:35544514 original size:29 final size:29
Alignment explanation
Indices: 35544482--35544565 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 29
35544472 GGGTCTAACG
35544482 GGCCATATAAATGTGATTTGGGCCTAATA
1 GGCCATATAAATGTGATTTGGGCCTAATA
* * *
35544511 GGCCATATACAGGTGATTT-GGCCTAATG
1 GGCCATATAAATGTGATTTGGGCCTAATA
* * *
35544539 GGCCATATGAATATGA-TTGGGCTTAAT
1 GGCCATATAAATGTGATTTGGGCCTAAT
35544566 GAGCTAGATA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 2 0.04
28 27 0.59
29 17 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (29 bp):
GGCCATATAAATGTGATTTGGGCCTAATA
Found at i:35544542 original size:28 final size:29
Alignment explanation
Indices: 35544471--35544546 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
35544461 ATGAATGTGC
* * *
35544471 TGGGTCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAAGGTGATT
* *
35544500 TGGGCCTAATAGGCCATATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAAGGTGATT
35544529 T-GGCCTAATGGGCCATAT
1 TGGGCCTAATGGGCCATAT
35544547 GAATATGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 16 0.39
29 25 0.61
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAAGGTGATT
Found at i:35545773 original size:21 final size:21
Alignment explanation
Indices: 35545749--35545794 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
35545739 GTAACTTGGT
35545749 CACACGGGCA-TGTGTCTCCTC
1 CACACGGG-AGTGTGTCTCCTC
* *
35545770 CACATGGGAGTTTGTCTCCTC
1 CACACGGGAGTGTGTCTCCTC
35545791 CACA
1 CACA
35545795 TAGGTGTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.17, C:0.35, G:0.22, T:0.26
Consensus pattern (21 bp):
CACACGGGAGTGTGTCTCCTC
Found at i:35546504 original size:21 final size:20
Alignment explanation
Indices: 35546468--35546508 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
35546458 CTAAATATAC
35546468 GTCTGTTTGTCAGAACATTTT
1 GTCTGTTTGTCAGAAC-TTTT
35546489 GTCTGTTTGT-ATGAACTTTT
1 GTCTGTTTGTCA-GAACTTTT
35546509 AGTGATTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.17, C:0.12, G:0.20, T:0.51
Consensus pattern (20 bp):
GTCTGTTTGTCAGAACTTTT
Found at i:35548269 original size:16 final size:16
Alignment explanation
Indices: 35548241--35548279 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
35548231 CCTATAAGTA
35548241 TTTTTTATATTTATTT
1 TTTTTTATATTTATTT
35548257 TTTTGTTAT-TTTATTT
1 TTTT-TTATATTTATTT
*
35548273 TATTTTA
1 TTTTTTA
35548280 AAAAGGGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 14 0.67
17 4 0.19
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTTATATTTATTT
Found at i:35549492 original size:21 final size:20
Alignment explanation
Indices: 35549459--35549497 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
35549449 AATATACGTT
35549459 TGTTTGTCAGAACATTTTGTC
1 TGTTTGTCAGAAC-TTTTGTC
**
35549480 TGTTTGTGTGAACTTTTG
1 TGTTTGTCAGAACTTTTG
35549498 GTTATTGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.15, C:0.10, G:0.23, T:0.51
Consensus pattern (20 bp):
TGTTTGTCAGAACTTTTGTC
Found at i:35551221 original size:23 final size:25
Alignment explanation
Indices: 35551176--35551228 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
35551166 TTTCACTCTT
* *
35551176 AAAATCCTAACTCTTAATTCCTAAA
1 AAAATCCTAACTCCTAATACCTAAA
*
35551201 AAAATCCTAAC-CCTAA-ACCTAAC
1 AAAATCCTAACTCCTAATACCTAAA
35551224 AAAAT
1 AAAAT
35551229 TAAAAAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 10 0.40
24 4 0.16
25 11 0.44
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (25 bp):
AAAATCCTAACTCCTAATACCTAAA
Found at i:35551689 original size:15 final size:15
Alignment explanation
Indices: 35551641--35551690 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
35551631 TCATTTAATT
35551641 TTTAATAATATAA-AA
1 TTTAATAATA-AATAA
* * *
35551656 TTTAA-ATTCAATTA
1 TTTAATAATAAATAA
35551670 TTTAATAATAAATAA
1 TTTAATAATAAATAA
35551685 TTTAAT
1 TTTAAT
35551691 TTGATTCAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 17 0.63
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAATAATAAATAA
Found at i:35553323 original size:231 final size:231
Alignment explanation
Indices: 35552920--35553381 Score: 915
Period size: 231 Copynumber: 2.0 Consensus size: 231
35552910 AAATGTGAAG
35552920 CTTAGGTAAGCAGATATTAGTGTGTTGGTTGATCCATGAATGTTCAAAATCCAAGCTCTACGTTG
1 CTTAGGTAAGCAGATATTAGTGTGTTGGTTGATCCATGAATGTTCAAAATCCAAGCTCTACGTTG
35552985 AAGCAAACCTTGGGCGACTGTTTGGCGAGTCAATTTAGGGTTGTTGATCCATCATTTCGATCAAG
66 AAGCAAACCTTGGGCGACTGTTTGGCGAGTCAATTTAGGGTTGTTGATCCATCATTTCGATCAAG
*
35553050 TTGAGAAAGAACCCTATCTACGCTTCTTTCATTTTATTGTAATATTTTAGGTTTTTTCAATTTGT
131 TTGAGAAACAACCCTATCTACGCTTCTTTCATTTTATTGTAATATTTTAGGTTTTTTCAATTTGT
35553115 AAAAGATTGGCCATTGGTTCAATCTATTCAACCGTA
196 AAAAGATTGGCCATTGGTTCAATCTATTCAACCGTA
35553151 CTTAGGTAAGCAGATATTAGTGTGTTGGTTGATCCATGAATGTTCAAAATCCAAGCTCTACGTTG
1 CTTAGGTAAGCAGATATTAGTGTGTTGGTTGATCCATGAATGTTCAAAATCCAAGCTCTACGTTG
35553216 AAGCAAACCTTGGGCGACTGTTTGGCGAGTCAATTTAGGGTTGTTGATCCATCATTTCGATCAAG
66 AAGCAAACCTTGGGCGACTGTTTGGCGAGTCAATTTAGGGTTGTTGATCCATCATTTCGATCAAG
35553281 TTGAGAAACAACCCTATCTACGCTTCTTTCATTTTATTGTAATATTTTAGGTTTTTTCAATTTGT
131 TTGAGAAACAACCCTATCTACGCTTCTTTCATTTTATTGTAATATTTTAGGTTTTTTCAATTTGT
35553346 AAAAGATTGGCCATTGGTTCAATCTATTCAACCGTA
196 AAAAGATTGGCCATTGGTTCAATCTATTCAACCGTA
35553382 AATTTATATT
Statistics
Matches: 230, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 230 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (231 bp):
CTTAGGTAAGCAGATATTAGTGTGTTGGTTGATCCATGAATGTTCAAAATCCAAGCTCTACGTTG
AAGCAAACCTTGGGCGACTGTTTGGCGAGTCAATTTAGGGTTGTTGATCCATCATTTCGATCAAG
TTGAGAAACAACCCTATCTACGCTTCTTTCATTTTATTGTAATATTTTAGGTTTTTTCAATTTGT
AAAAGATTGGCCATTGGTTCAATCTATTCAACCGTA
Found at i:35553446 original size:17 final size:18
Alignment explanation
Indices: 35553424--35553457 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
35553414 CGATTATGAC
35553424 CTTTTTTTTT-CTTTTTT
1 CTTTTTTTTTACTTTTTT
35553441 CTTTTTTTTTACTTTTT
1 CTTTTTTTTTACTTTTT
35553458 CATTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (18 bp):
CTTTTTTTTTACTTTTTT
Found at i:35554138 original size:24 final size:24
Alignment explanation
Indices: 35554107--35554162 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
35554097 TAAATAATGT
35554107 AAGTTTAATGGCTAAAATAAGCAG
1 AAGTTTAATGGCTAAAATAAGCAG
*
35554131 AAGTTTAATGGCTAAAATAGGCAG
1 AAGTTTAATGGCTAAAATAAGCAG
*
35554155 AAATTTAA
1 AAGTTTAA
35554163 ATAGAGGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (24 bp):
AAGTTTAATGGCTAAAATAAGCAG
Found at i:35554803 original size:15 final size:14
Alignment explanation
Indices: 35554783--35554821 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
35554773 AACAATAAAA
35554783 AAAATATCAAAAACT
1 AAAATAT-AAAAACT
*
35554798 AAAATATAAAAATT
1 AAAATATAAAAACT
35554812 AAAAT-TAAAA
1 AAAATATAAAA
35554822 TTTAATCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.22
14 11 0.48
15 7 0.30
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATATAAAAACT
Found at i:35558578 original size:208 final size:212
Alignment explanation
Indices: 35558213--35558692 Score: 815
Period size: 208 Copynumber: 2.3 Consensus size: 212
35558203 TTAATTTTAA
*
35558213 TAATGCATACTTCATCTGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAA
1 TAATGCATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAA
35558278 TAAAATTATAAAACAATATGTTATTTGAAAAATAACTATTATTATAATGAGATACATGTTTTATT
66 TAAAATTATAAAACAATATGTTATTTGAAAAATAACTATTATTATAATGAGATACATGTTTTATT
35558343 AGGTATAAGTATTTAAAATTTTGTTTTTGTAATGTAATACATGCG-TATATA-TATATA-A-AAT
131 AGGTATAAGTATTTAAAATTTTGTTTTTGTAATGTAATACATGCGATATATATTATATATATAAT
* *
35558404 CATATTAGTGAATCTGC
196 CATATTACTGAACCTGC
* *
35558421 TAATGCGTACTTCATCCGGATAAAGTATGCATTATCAAAATTAAATTAAAATATTAAATAAGAAA
1 TAATGCATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAA
35558486 TAAAATTATAAAACAATATGTTATTTGAAAAATAACTATTATTATAATGAGATACATGTTTTATT
66 TAAAATTATAAAACAATATGTTATTTGAAAAATAACTATTATTATAATGAGATACATGTTTTATT
* *
35558551 AGGTATAAGTATTTAAAATTTTGTTTTTGTAATGTGATGCATGCGTAAATATATATATTATATAT
131 AGGTATAAGTATTTAAAATTTTGTTTTTGTAATGTAATACATGCG-----ATATATATTATATAT
35558616 ATAATCATATTACTGAACCTGC
191 ATAATCATATTACTGAACCTGC
*
35558638 TAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATT
1 TAATGCATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATT
35558693 TTTTAAAAAC
Statistics
Matches: 253, Mismatches: 10, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
208 170 0.67
214 6 0.02
215 6 0.02
216 1 0.00
217 70 0.28
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.39
Consensus pattern (212 bp):
TAATGCATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAA
TAAAATTATAAAACAATATGTTATTTGAAAAATAACTATTATTATAATGAGATACATGTTTTATT
AGGTATAAGTATTTAAAATTTTGTTTTTGTAATGTAATACATGCGATATATATTATATATATAAT
CATATTACTGAACCTGC
Found at i:35560987 original size:39 final size:40
Alignment explanation
Indices: 35560865--35561087 Score: 248
Period size: 39 Copynumber: 5.7 Consensus size: 40
35560855 GCTCCTCGTT
* *
35560865 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
35560905 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
35560945 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGAA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
35560984 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
35561023 CAAATGCCTTC-GGATCTTAGTCCGGATATT-TTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
35561064 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
35561088 CATCATTCAA
Statistics
Matches: 163, Mismatches: 12, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
38 2 0.01
39 87 0.53
40 63 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:35561048 original size:118 final size:119
Alignment explanation
Indices: 35560865--35561087 Score: 280
Period size: 118 Copynumber: 1.9 Consensus size: 119
35560855 GCTCCTCGTT
*
35560865 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
*
35560930 AT-TTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGAA
66 ATATT-GTAACTTAGCAC-AA-GCCTTCGGGACTTAGCCCGGAATTAGTATCTCGAA
* **
35560984 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
* *
35561045 CGGATATTTTCACTTAGCACAAGCCTTCGGGACTTAGCCCGGA
63 CGGATATTGTAACTTAGCACAAGCCTTCGGGACTTAGCCCGGA
35561088 CATCATTCAA
Statistics
Matches: 91, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
117 15 0.16
118 55 0.60
119 21 0.23
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATTGTAACTTAGCACAAGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGAA
Found at i:35561071 original size:78 final size:79
Alignment explanation
Indices: 35560865--35561087 Score: 226
Period size: 79 Copynumber: 2.8 Consensus size: 79
35560855 GCTCCTCGTT
* * * * *
35560865 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTAGAACAAATGCCTTCGGGACTTAGCCC
*
35560928 GGATTTAGTAACTCGCA
63 GGAATTAGTAACTCGCA
*
35560945 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGAACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTAGAACAAATGCCTTCGGGACTTAGCCCGGA
*
35561009 ATTAGTATCTCGCA
66 ATTAGTAACTCGCA
* * * *
35561023 CAAATGCCTTCGGATCTTAGTCCGGATATT-TTCA-CTTAGCAC-AA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TAGAACAAATGCCTTCGGGACTTAGCC
35561084 CGGA
62 CGGA
35561088 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 46 0.37
79 56 0.45
80 23 0.18
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTAGAACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:35566551 original size:45 final size:45
Alignment explanation
Indices: 35566384--35566643 Score: 248
Period size: 45 Copynumber: 5.9 Consensus size: 45
35566374 ATACCATACA
* * * *
35566384 ATGCCAACGTCCCAGACGTGGTCTTAAATG--CT-ACCTCATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACAT-ATATCG
** *
35566427 ATGCC-ACTGTCCCAGACAAGGTCTTACACG-AATC-GA-ATA-CG
1 ATGCCAAC-GTCCCAGACGTGGTCTTACACGAAATCACATATATCG
*** * * * * * *
35566468 AAATCGATGTCCTAGACATGGTCTTACACGTAACCACATATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACATATATCG
* *
35566513 ATGCTAACGTCCCAAACGTGGTCTTACACGAAATCACATATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACATATATCG
* * *
35566558 ATGCCAACGTCCCAGACATAGTCTTACATGAAATCACATATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACATATATCG
*
35566603 ATGCCAACGTCCCAGACGTGGTCTTACACAAAATCACATAT
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACATAT
35566644 CGAAATCCTA
Statistics
Matches: 174, Mismatches: 35, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
41 24 0.14
42 9 0.05
43 24 0.14
44 4 0.02
45 113 0.65
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (45 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCACATATATCG
Found at i:35568114 original size:30 final size:30
Alignment explanation
Indices: 35568078--35568138 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
35568068 TTCCCGAGCC
35568078 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
35568108 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
35568138 T
1 T
35568139 GTATTAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:35568610 original size:47 final size:46
Alignment explanation
Indices: 35568554--35568689 Score: 204
Period size: 47 Copynumber: 2.9 Consensus size: 46
35568544 TAGGATGGTT
*
35568554 GAACATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGT
1 GAACATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
*
35568600 GAA-ATGTCCGAACTCGTTGAGTTGAGTCGGAGTTCACTTATGGATGC
1 GAACA--TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
*
35568647 GAACA-CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGA
1 GAACATCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGA
35568690 CGGGTTACAT
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
45 5 0.06
46 34 0.41
47 42 0.51
48 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (46 bp):
GAACATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:35573719 original size:24 final size:24
Alignment explanation
Indices: 35573663--35573749 Score: 77
Period size: 24 Copynumber: 3.5 Consensus size: 24
35573653 TAGCTCATAT
* * *
35573663 GAGCTTACTGATATATCAACTCGTAA
1 GAGCTTACT-AT-TCTCAACTCATTA
*
35573689 GATCTTACTATTCTCAACTCATTA
1 GAGCTTACTATTCTCAACTCATTA
* * *
35573713 GAGCTTACTGTT-TCTAGCTCAATA
1 GAGCTTACTATTCTC-AACTCATTA
35573737 GAGCTTACTATTC
1 GAGCTTACTATTC
35573750 ATTAGCTTAG
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
23 2 0.04
24 38 0.76
25 2 0.04
26 8 0.16
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (24 bp):
GAGCTTACTATTCTCAACTCATTA
Found at i:35580696 original size:34 final size:34
Alignment explanation
Indices: 35580644--35580710 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
35580634 TCGGAAAATA
*
35580644 TTAAATTCTGTTTGAATGATGAATTTTAATGGAG
1 TTAAATTCCGTTTGAATGATGAATTTTAATGGAG
* *
35580678 TTAAGTTCCGTTTGAATGATGAATTTTGATGGA
1 TTAAATTCCGTTTGAATGATGAATTTTAATGGA
35580711 TATATGTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.43
Consensus pattern (34 bp):
TTAAATTCCGTTTGAATGATGAATTTTAATGGAG
Found at i:35581690 original size:22 final size:22
Alignment explanation
Indices: 35581662--35581705 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
35581652 ACTCATTTTG
35581662 GTATAATGGCATGTATAGGCTA
1 GTATAATGGCATGTATAGGCTA
35581684 GTATAATGGCATGTATAGGCTA
1 GTATAATGGCATGTATAGGCTA
35581706 ACTTTACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (22 bp):
GTATAATGGCATGTATAGGCTA
Found at i:35585102 original size:46 final size:46
Alignment explanation
Indices: 35585035--35585209 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
35585025 TGTAACCCGC
35585035 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCACAT
*
35585081 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC--A-GGC--GTTCACAT
* * * *
35585131 CTC-T---CGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCACAT
*
35585174 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAG
35585210 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 7, Indels: 25
0.77 0.05 0.18
Matches are distributed among these distances:
42 3 0.03
43 6 0.06
44 1 0.01
46 60 0.55
47 26 0.24
48 1 0.01
49 2 0.02
50 6 0.06
51 4 0.04
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCACAT
Found at i:35585155 original size:93 final size:93
Alignment explanation
Indices: 35585043--35585213 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
35585033 GCCCATAAGT
*
35585043 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCACATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
*
35585107 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCAGATGCCTAGTTACATCTCTC
* *
35585136 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
35585201 CGAGTTCAGATGC
66 CGAGCTCAGATGC
35585214 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCAGATGCCTAGTTACATCTCTC
Found at i:35585229 original size:46 final size:45
Alignment explanation
Indices: 35585040--35585229 Score: 147
Period size: 46 Copynumber: 4.1 Consensus size: 45
35585030 CCCGCCCATA
** *
35585040 AGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTC-ACATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGCTCAGATGCTCAACATCC-T
*
35585085 AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGC-CTAGTTACATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGCTCAGATGCTC-A---ACATC-CT
* * * *** *
35585135 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGCTCAGATGCTCAACATCC-T
*
35585178 AAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGCTCAGATGCTCAA-CATCCT
35585225 AGTGA
1 AGTGA
35585230 CATGTCACTT
Statistics
Matches: 115, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
42 1 0.01
43 5 0.04
45 1 0.01
46 66 0.57
47 29 0.25
48 6 0.05
50 6 0.05
51 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGCTCAGATGCTCAACATCCT
Found at i:35591734 original size:30 final size:30
Alignment explanation
Indices: 35591700--35591760 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
35591690 TACTTAACTC
35591700 AAACTTTGGCAGAATTACAATTTTGCCCCT
1 AAACTTTGGCAGAATTACAATTTTGCCCCT
* * * *
35591730 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAGAATTACAATTTTGCCCCT
35591760 A
1 A
35591761 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (30 bp):
AAACTTTGGCAGAATTACAATTTTGCCCCT
Found at i:35596622 original size:17 final size:16
Alignment explanation
Indices: 35596568--35596629 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 16
35596558 TCCATCCATG
** *
35596568 CATGTATCTTAAAATA
1 CATGTATCTTCCAATT
* *
35596584 CATGAATCTTTCAATT
1 CATGTATCTTCCAATT
35596600 CAATGTATCTTCCAAGTT
1 C-ATGTATCTTCCAA-TT
35596618 CATGTATCTTCC
1 CATGTATCTTCC
35596630 CTTTTGATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 13 0.34
17 22 0.58
18 3 0.08
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (16 bp):
CATGTATCTTCCAATT
Done.