Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 104 of 182
Found at i:33943251 original size:4 final size:4
Alignment explanation
Indices: 33943244--33943294 Score: 77
Period size: 4 Copynumber: 12.8 Consensus size: 4
33943234 TTCTTCCTTC
*
33943244 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT
33943292 TTC
1 TTC
33943295 CTTCAATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 3 0.07
4 37 0.86
5 3 0.07
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:33943264 original size:33 final size:33
Alignment explanation
Indices: 33943210--33943298 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 33
33943200 AAGTGGTCCC
* *
33943210 CTTCTTCTCCTTC-TTCCTTCTTCCTTCTTCCTT
1 CTTCTT-TCTTTCTTTCTTTCTTCCTTCTTCCTT
* *
33943243 CTTCTTTCTTTCTTTCTTTCTTTC-T-TTCTTT
1 CTTCTTTCTTTCTTTCTTTCTTCCTTCTTCCTT
*
33943274 C-TCTTT-TTTCTTTCTTTTTTCCTTC
1 CTTCTTTCTTTCTTTCTTTCTTCCTTC
33943299 AATTTTCATT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
29 14 0.30
30 6 0.13
31 6 0.13
32 6 0.13
33 15 0.32
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (33 bp):
CTTCTTTCTTTCTTTCTTTCTTCCTTCTTCCTT
Found at i:33944150 original size:14 final size:15
Alignment explanation
Indices: 33944121--33944158 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
33944111 AAATATATTT
33944121 TTTTAATAATTTTAAA
1 TTTTAA-AATTTTAAA
33944137 TTTTAAAA-TTTAAA
1 TTTTAAAATTTTAAA
*
33944151 TTATAAAA
1 TTTTAAAA
33944159 AATTATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 2 0.10
16 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTAAAATTTTAAA
Found at i:33946057 original size:30 final size:31
Alignment explanation
Indices: 33946023--33946113 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 31
33946013 TGGGAGTTTT
*
33946023 GGGGAGTAAAA-TTTTGAGGGAAAATAAATA
1 GGGGAGTAAAAGTTTTGAGGGAAAATAAAGA
*
33946053 GGGGAGTAAAAGTTTT-AGGGAGAAAGT-GAGA
1 GGGGAGTAAAAGTTTTGAGGGA-AAA-TAAAGA
33946084 GGGAGAGTAAAAGTTTTG-GAGGAAAATAAA
1 GGG-GAGTAAAAGTTTTGAG-GGAAAATAAA
33946114 AAATTTTAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
30 16 0.31
31 13 0.25
32 19 0.37
33 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (31 bp):
GGGGAGTAAAAGTTTTGAGGGAAAATAAAGA
Found at i:33946344 original size:9 final size:9
Alignment explanation
Indices: 33946330--33946357 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
33946320 TATATTTTGA
33946330 TATTCGAAT
1 TATTCGAAT
33946339 TATTCGAAT
1 TATTCGAAT
33946348 TATTCGAAT
1 TATTCGAAT
33946357 T
1 T
33946358 CTAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:33948297 original size:73 final size:73
Alignment explanation
Indices: 33948123--33948350 Score: 249
Period size: 73 Copynumber: 3.1 Consensus size: 73
33948113 CCGTGAGTTG
* * * *
33948123 GACCGTGTGACCATACTGTCTTAAGAATTCAAAAACAGTGAGTTACACGGCCTGGACACACGGGC
1 GACCGTGTGAACATACTGTTTTAAGAAATAAAAAACAGTGAGTTACACGGCCTGGACACACGGGC
33948188 GTGTGCCA
66 GTGTGCCA
* ** ** * * * *
33948196 TACCGTGTGGGCATACTGTTGGATGAAATAAAAAACAGAGAGTTACATGGCCTGGGCACACGGGC
1 GACCGTGTGAACATACTGTTTTAAGAAATAAAAAACAGTGAGTTACACGGCCTGGACACACGGGC
33948261 GTGTGCCA
66 GTGTGCCA
* * * * * * * * *
33948269 GACCGTGTGAATATATTGTTTTAAGAAATTAGAAACAGTGAGTTACACGACTTGAACTCACGGGT
1 GACCGTGTGAACATACTGTTTTAAGAAATAAAAAACAGTGAGTTACACGGCCTGGACACACGGGC
33948334 GTGTGCCA
66 GTGTGCCA
*
33948342 CACCGTGTG
1 GACCGTGTG
33948351 TCCCACATGG
Statistics
Matches: 124, Mismatches: 31, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
73 124 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (73 bp):
GACCGTGTGAACATACTGTTTTAAGAAATAAAAAACAGTGAGTTACACGGCCTGGACACACGGGC
GTGTGCCA
Found at i:33950544 original size:19 final size:19
Alignment explanation
Indices: 33950522--33950563 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
33950512 AATAGTTAAA
33950522 AAAAATCAAAACTTTGTTT
1 AAAAATCAAAACTTTGTTT
** *
33950541 AAAAATTTAAACTTTTTTT
1 AAAAATCAAAACTTTGTTT
33950560 AAAA
1 AAAA
33950564 TCACTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAAATCAAAACTTTGTTT
Found at i:33950655 original size:150 final size:144
Alignment explanation
Indices: 33950455--33950841 Score: 524
Period size: 150 Copynumber: 2.6 Consensus size: 144
33950445 AATCAAAAGT
* * *
33950455 TTTCT-TTTATTAAAACAAAATCACTATTTTACTTAAAAATCAAAATTTTTATTTCAAAATAGTT
1 TTTCTCTTT-TTAAAA-AAAATCACTATTTTACTTAAAATTC-AAACTTTTATTTCGAAATAGTT
* *
33950519 AAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTTTAAAATCACTAAAAAATAAATTTTT
63 AAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTTTAAAATAAATAAAAAATAAATTTTT
*
33950584 ATTTTTTAAAAATCTAAAC
128 A--TTTTAAAAATATAAAC
** * *
33950603 TTTCTTTCTTTTTTAATGAAAATCACTACTTTACTTATAAATTCAAACTTTTATTTCGAAATAAT
1 TTTC--TC-TTTTTAAAAAAAATCACTATTTTACTTA-AAATTCAAACTTTTATTTCGAAATAGT
* * *
33950668 TAAAAAAAATCAAAATTTTGTTTAAAAATTTAAACTTTTTTTGAAATAAATAGAAAATAAATTTT
62 TAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTTTAAAATAAATAAAAAATAAATTTT
33950733 TATTTTAAAAATATAAAC
127 TATTTTAAAAATATAAAC
* * *
33950751 TTTCTCTTTTTAAAAAAAATTACTATTTTACTTAAAAATCCAAACCTTTATTTCGAAATAGTTAA
1 TTTCTCTTTTTAAAAAAAATCACTATTTTACTT-AAAATTCAAACTTTTATTTCGAAATAGTTAA
*
33950816 AAAAAATCAAAACTTTATTTAAAAAT
65 AAAAAATCAAAACTTTGTTTAAAAAT
33950842 GACTAAAAAA
Statistics
Matches: 211, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
145 74 0.35
146 3 0.01
148 23 0.11
150 99 0.47
151 9 0.04
152 3 0.01
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (144 bp):
TTTCTCTTTTTAAAAAAAATCACTATTTTACTTAAAATTCAAACTTTTATTTCGAAATAGTTAAA
AAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTTTAAAATAAATAAAAAATAAATTTTTATT
TTAAAAATATAAAC
Found at i:33950697 original size:52 final size:50
Alignment explanation
Indices: 33950463--33950841 Score: 153
Period size: 52 Copynumber: 7.6 Consensus size: 50
33950453 GTTTTCTTTT
** * * *
33950463 ATTAAAACAAAATCACTATTTTACTTAAAAA-TCAAAATTTTTATTTCAAAATA
1 ATTAAAA-AAAATCAAAATTTTATTTAAAAATTC-AAACTTTT-TTT-GAAATA
* * * * * *
33950516 GTTAAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTTTAAAATC
1 ATTAAAAAAAATCAAAATTTTATTTAAAAATTCAAACTTTTTTTGAAATA
* * * ** *
33950566 ACT--AAAAAAT-AAATTTTTATTTTTTAAAAA-TCTAAACTTTCTTT--CTTT
1 ATTAAAAAAAATCAAAATTTTA---TTTAAAAATTC-AAACTTTTTTTGAAATA
* ** ** * * *
33950614 TTTAATGAAAATCACTACTTTACTTATAAATTCAAACTTTTATTTCGAAATA
1 ATTAAAAAAAATCAAAATTTTATTTAAAAATTCAAACTTTT-TTT-GAAATA
* *
33950666 ATTAAAAAAAATCAAAATTTTGTTTAAAAATTTAAACTTTTTTTGAAATA
1 ATTAAAAAAAATCAAAATTTTATTTAAAAATTCAAACTTTTTTTGAAATA
* * * *
33950716 A--ATAGAAAAT-AAATTTTTATTTTAAAAATAT-AAACTTTCTCTT----T-
1 ATTAAAAAAAATCAAAATTTTA-TTTAAAAAT-TCAAACTTT-TTTTGAAATA
* ** * * *
33950760 -TTAAAAAAAATTACTATTTTACTTAAAAATCCAAACCTTTATTTCGAAATA
1 ATTAAAAAAAATCAAAATTTTATTTAAAAATTCAAA-CTTT-TTTTGAAATA
* *
33950811 GTTAAAAAAAATCAAAACTTTATTTAAAAAT
1 ATTAAAAAAAATCAAAATTTTATTTAAAAAT
33950842 GACTAAAAAA
Statistics
Matches: 236, Mismatches: 63, Indels: 55
0.67 0.18 0.16
Matches are distributed among these distances:
45 19 0.08
46 12 0.05
47 13 0.06
48 45 0.19
49 10 0.04
50 37 0.16
51 11 0.05
52 82 0.35
53 7 0.03
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.41
Consensus pattern (50 bp):
ATTAAAAAAAATCAAAATTTTATTTAAAAATTCAAACTTTTTTTGAAATA
Found at i:33951745 original size:16 final size:17
Alignment explanation
Indices: 33951713--33951745 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
33951703 CCTTCATATA
33951713 CAATGAAGAAATAAATG
1 CAATGAAGAAATAAATG
*
33951730 CAATGAA-AAGTAAATG
1 CAATGAAGAAATAAATG
33951746 GACCTCCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.58, C:0.06, G:0.18, T:0.18
Consensus pattern (17 bp):
CAATGAAGAAATAAATG
Found at i:33951783 original size:42 final size:42
Alignment explanation
Indices: 33951724--33951908 Score: 239
Period size: 42 Copynumber: 4.4 Consensus size: 42
33951714 AATGAAGAAA
33951724 TAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTC
1 TAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTC
* * * *
33951766 TAAATGCAATGAAAAGTAAATGGGCTTCCACACCTGGGCTTT
1 TAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTC
* *
33951808 TAAATGCAATGAAAAGTAAAT-GAGCTTCCATA-CTCGGGCCTC
1 TAAATGCAATGAAAAGTAAATGGA-CCTCCACACCT-GGGCCTC
* * * *
33951850 TAAATGTAATGAAAAGTAAATAGACCTTCACACCTGGGTCTC
1 TAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTC
*
33951892 TAAATGCGATGAAAAGT
1 TAAATGCAATGAAAAGT
33951909 CACTCCTAGG
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
41 3 0.02
42 117 0.94
43 4 0.03
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (42 bp):
TAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTC
Found at i:33951865 original size:84 final size:84
Alignment explanation
Indices: 33951724--33952134 Score: 271
Period size: 84 Copynumber: 4.7 Consensus size: 84
33951714 AATGAAGAAA
33951724 TAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAAT-G
1 TAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAATAG
** *
33951788 GGCTTCCACACCTGGG-CTTT
66 ACCTT-CACACCTGGGTC-TC
* * *
33951808 TAAATGCAATGAAAAGTAAAT-GAGCTTCCATA-CTCGGGCCTCTAAATGTAATGAAAAGTAAAT
1 TAAATGCAATGAAAAGTAAATGGA-CCTCCACACCT-GGGCCTCTAAATGCAATGAAAAGTAAAT
33951871 AGACCTTCACACCTGGGTCTC
64 AGACCTTCACACCTGGGTCTC
* ** * * *
33951892 TAAATGCGATGAAAAGTCACTCCTAGG-CCTCTA-A-ATGAGATGAACCTCCACACATGGGCCTC
1 TAAATGCAATGAAAAGT-A--AAT-GGACCTCCACACCTG-G--G--CCTCTA-A-AT--G---C
* * * * *
33951954 TAAACGTGATGAAAAGTAAATGGACCTCCACACTTGAGCCTC
50 ---A----ATGAAAAGTAAATAGACCTTCACACCTGGGTCTC
* * * * *
33951996 TAAATGCAATGAAAAGTATATAGACCTCCACACCTGGGTCTCTAAATGTAATGAAAAGTAAATGG
1 TAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAATAG
* *
33952061 A-CTTCCACACTTGGGCCTC
66 ACCTT-CACACCTGGGTCTC
* * *
33952080 TAAATGTAATGAAAAGTAAATGGACCTCCACACCTAGACCTCTAAATGCAATGAA
1 TAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
33952135 TGCTTTCCTT
Statistics
Matches: 258, Mismatches: 37, Indels: 64
0.72 0.10 0.18
Matches are distributed among these distances:
83 6 0.02
84 158 0.61
85 7 0.03
86 3 0.01
87 5 0.02
88 2 0.01
89 1 0.00
90 5 0.02
91 1 0.00
92 2 0.01
94 2 0.01
96 2 0.01
97 1 0.00
98 4 0.02
100 3 0.01
101 6 0.02
102 2 0.01
103 3 0.01
104 45 0.17
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (84 bp):
TAAATGCAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAATAG
ACCTTCACACCTGGGTCTC
Found at i:33951995 original size:42 final size:42
Alignment explanation
Indices: 33951935--33952134 Score: 274
Period size: 42 Copynumber: 4.8 Consensus size: 42
33951925 AATGAGATGA
* * *
33951935 ACCTCCACACATGGGCCTCTAAACGTGATGAAAAGTAAATGG
1 ACCTCCACACCTGGGCCTCTAAATGTAATGAAAAGTAAATGG
* * * * *
33951977 ACCTCCACACTTGAGCCTCTAAATGCAATGAAAAGTATATAG
1 ACCTCCACACCTGGGCCTCTAAATGTAATGAAAAGTAAATGG
*
33952019 ACCTCCACACCTGGGTCTCTAAATGTAATGAAAAGTAAATGG
1 ACCTCCACACCTGGGCCTCTAAATGTAATGAAAAGTAAATGG
* *
33952061 ACTTCCACACTTGGGCCTCTAAATGTAATGAAAAGTAAATGG
1 ACCTCCACACCTGGGCCTCTAAATGTAATGAAAAGTAAATGG
* * *
33952103 ACCTCCACACCTAGACCTCTAAATGCAATGAA
1 ACCTCCACACCTGGGCCTCTAAATGTAATGAA
33952135 TGCTTTCCTT
Statistics
Matches: 137, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 137 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (42 bp):
ACCTCCACACCTGGGCCTCTAAATGTAATGAAAAGTAAATGG
Found at i:33952083 original size:188 final size:188
Alignment explanation
Indices: 33951747--33952096 Score: 481
Period size: 188 Copynumber: 1.9 Consensus size: 188
33951737 AAGTAAATGG
* * * * * * *
33951747 ACCTCCACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGGGCTTCCACACCTGGGCTTTTAAA
1 ACCTCCACACATGGGCCTCTAAACGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAA
* *
33951812 TGCAATGAAAAGTAAATGAGCTTCCATACTCGGGCCTCTAAATGTAATGAAAAGTAAATAGACCT
66 TGCAATGAAAAGTAAATGAGCCTCCACACTCGGGCCTCTAAATGTAATGAAAAGTAAATAGACCT
* *
33951877 TCACACCTGGGTCTCTAAATGCGATGAAAAGTCACTCCTAGGCCTCTAAATGAGATGA
131 TCACACCTGGGCCTCTAAATGCAATGAAAAGTCACTCCTAGGCCTCTAAATGAGATGA
** *
33951935 ACCTCCACACATGGGCCTCTAAACGTGATGAAAAGTAAATGGACCTCCACACTTGAGCCTCTAAA
1 ACCTCCACACATGGGCCTCTAAACGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAA
* * *
33952000 TGCAATGAAAAGTATAT-AGACCTCCACAC-CTGGGTCTCTAAATGTAATGAAAAGTAAATGGA-
66 TGCAATGAAAAGTAAATGAG-CCTCCACACTC-GGGCCTCTAAATGTAATGAAAAGTAAATAGAC
* *
33952062 CTTCCACACTTGGGCCTCTAAATGTAATGAAAAGT
129 CTT-CACACCTGGGCCTCTAAATGCAATGAAAAGT
33952097 AAATGGACCT
Statistics
Matches: 140, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
187 6 0.04
188 134 0.96
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (188 bp):
ACCTCCACACATGGGCCTCTAAACGCAATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAA
TGCAATGAAAAGTAAATGAGCCTCCACACTCGGGCCTCTAAATGTAATGAAAAGTAAATAGACCT
TCACACCTGGGCCTCTAAATGCAATGAAAAGTCACTCCTAGGCCTCTAAATGAGATGA
Found at i:33952564 original size:20 final size:18
Alignment explanation
Indices: 33952535--33952579 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
33952525 GCTCTCTCTA
*
33952535 TTTTTCTTCTTTTTCATTGT
1 TTTTTTTTCTTTTT--TTGT
33952555 TTTTTTTTCTTTTTTTGT
1 TTTTTTTTCTTTTTTTGT
33952573 TTTTTTT
1 TTTTTTT
33952580 CTAATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 11 0.46
20 13 0.54
ACGTcount: A:0.02, C:0.09, G:0.04, T:0.84
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTTGT
Found at i:33953140 original size:8 final size:9
Alignment explanation
Indices: 33953112--33953141 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
33953102 TTACTCCTTC
33953112 TATTTCTTT
1 TATTTCTTT
33953121 TATTTCTTT
1 TATTTCTTT
33953130 TATTT-TTT
1 TATTTCTTT
33953138 TATT
1 TATT
33953142 CGTTTTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (9 bp):
TATTTCTTT
Found at i:33963265 original size:21 final size:21
Alignment explanation
Indices: 33963239--33963280 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
33963229 GATTAAATAT
33963239 GACATCCATAGAGATGCGTTC
1 GACATCCATAGAGATGCGTTC
*
33963260 GACATCCATAGGGATGCGTTC
1 GACATCCATAGAGATGCGTTC
33963281 CCCTTTAAAA
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:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (21 bp):
GACATCCATAGAGATGCGTTC
Found at i:33965607 original size:52 final size:52
Alignment explanation
Indices: 33965542--33965646 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 52
33965532 TTTTTTAATG
** *
33965542 AAAATCACTACTTTACTTAAAAATTCAAACTTTTAT-TTTAAAATAATTAAAA
1 AAAATCAAAACTTTACTTAAAAATTCAAACTTTT-TCTTTAAAATAACTAAAA
** *
33965594 AAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAA
1 AAAATCAAAACTTTACTTAAAAATTCAAACTTTTTCTTTAAAATAACTAAAA
33965646 A
1 A
33965647 CAGATTTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
51 1 0.02
52 45 0.98
ACGTcount: A:0.50, C:0.10, G:0.01, T:0.38
Consensus pattern (52 bp):
AAAATCAAAACTTTACTTAAAAATTCAAACTTTTTCTTTAAAATAACTAAAA
Found at i:33965731 original size:145 final size:146
Alignment explanation
Indices: 33965398--33965896 Score: 699
Period size: 144 Copynumber: 3.4 Consensus size: 146
33965388 TTTCTTTTAC
* * *
33965398 AAAATCACTATTTTACTTTAAAATCAAAACTTTTATCTT-GAAATAGTTAAAAAAAATCAAAATT
1 AAAATCACTATTTTACTTAAAAATCAAAACTTTTAT-TTCGAAATAATTAAAAAAAATCAAAACT
* * * * *
33965462 TTGTTTAAAAATTTAAATTTTTTCTTTAAAATCACTAAAAAATATATTTTTATTTTTAAAAATCT
65 TTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATAT
33965527 AAAC-TT-TTTTT-AAT
130 AAACTTTCTTTTTAAAT
* **
33965541 GAAAATCACTACTTTACTTAAAAATTC-AAACTTTTATTTTAAAATAATTAAAAAAAATCAAAAC
1 -AAAATCACTATTTTACTTAAAAA-TCAAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAAC
*
33965605 TTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAACAGATTTTTA-TATTAAAAATA
64 TTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATA
33965668 TAAACTTTCTCTTTTAAAT
129 TAAACTTTCT-TTTTAAAT
* *
33965687 AAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
* *
33965751 TGTTTAAAAATTTAAACTTTTTATTTAAAATAACTAAAAAACAGAATTTTATTTTTAAAAATATA
66 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATA
* *
33965816 AACTCTCTTTTTTAAAG
131 AACTTTC-TTTTTAAAT
* * *
33965833 AAAATCACTATTTTTCTTAAAAATCAAAATTTTTATTTCGAAATTATTAAAAAAAAATCAAAAC
1 AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAATT-AAAAAAAATCAAAAC
33965897 GTTTCTCAAA
Statistics
Matches: 318, Mismatches: 25, Indels: 20
0.88 0.07 0.06
Matches are distributed among these distances:
142 14 0.04
143 17 0.05
144 140 0.44
145 61 0.19
146 71 0.22
147 1 0.00
148 14 0.04
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (146 bp):
AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATA
AACTTTCTTTTTAAAT
Found at i:33966398 original size:13 final size:12
Alignment explanation
Indices: 33966366--33966392 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33966356 TTGACAAGCC
33966366 AAAAAAGAAAAA
1 AAAAAAGAAAAA
33966378 AAAAAAGAAAAA
1 AAAAAAGAAAAA
33966390 AAA
1 AAA
33966393 CCAAGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:33973687 original size:48 final size:48
Alignment explanation
Indices: 33973608--33973719 Score: 163
Period size: 48 Copynumber: 2.4 Consensus size: 48
33973598 TGCAATTTGG
** *
33973608 ATTTTATTAA-TTTGGCCCACTGTTACTGTATGCTAAACCCAATTTTC
1 ATTTTATTAACTTCAGCCCACTGTTACTGTATGATAAACCCAATTTTC
* *
33973655 ATTTTATTAACTTCAGCCCATTGTTATTGTATGATAAACCCAATTTTC
1 ATTTTATTAACTTCAGCCCACTGTTACTGTATGATAAACCCAATTTTC
*
33973703 TTTTTATTAACTTCAGC
1 ATTTTATTAACTTCAGC
33973720 TAATCTTTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 10 0.17
48 48 0.83
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.45
Consensus pattern (48 bp):
ATTTTATTAACTTCAGCCCACTGTTACTGTATGATAAACCCAATTTTC
Found at i:33982813 original size:9 final size:9
Alignment explanation
Indices: 33982799--33982825 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
33982789 TCGAGTCCTT
33982799 CCGTAGTTA
1 CCGTAGTTA
33982808 CCGTAGTTA
1 CCGTAGTTA
33982817 CCGTAGTTA
1 CCGTAGTTA
33982826 TTATGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (9 bp):
CCGTAGTTA
Found at i:33985182 original size:16 final size:16
Alignment explanation
Indices: 33985144--33985182 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
33985134 CAATTAGTCC
33985144 AAAAAAA-ATTTCTAT
1 AAAAAAATATTTCTAT
* *
33985159 CAAAAAATATTTTTAT
1 AAAAAAATATTTCTAT
33985175 AAAAAAAT
1 AAAAAAAT
33985183 CCAATTCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAAAATATTTCTAT
Found at i:33986483 original size:7 final size:7
Alignment explanation
Indices: 33986457--33986533 Score: 73
Period size: 7 Copynumber: 11.0 Consensus size: 7
33986447 GGATTCGATT
33986457 TTAAACC
1 TTAAACC
* *
33986464 CTAAGCC
1 TTAAACC
*
33986471 TTAAACT
1 TTAAACC
33986478 TTAAACC
1 TTAAACC
*
33986485 TTAAACA
1 TTAAACC
*
33986492 TAAAACC
1 TTAAACC
*
33986499 CTAAACC
1 TTAAACC
*
33986506 TTAAACG
1 TTAAACC
*
33986513 TGAAACC
1 TTAAACC
33986520 TTAAACC
1 TTAAACC
*
33986527 CTAAACC
1 TTAAACC
33986534 ATATATGATG
Statistics
Matches: 53, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 53 1.00
ACGTcount: A:0.44, C:0.29, G:0.04, T:0.23
Consensus pattern (7 bp):
TTAAACC
Found at i:33989936 original size:43 final size:43
Alignment explanation
Indices: 33989873--33989974 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 43
33989863 AACTGCACAA
* *
33989873 TTAATAACATGTCAAGATATTAACAATAATCAAGTAATATAAT
1 TTAATAACATGCCAAGATATTAACAAGAATCAAGTAATATAAT
* **
33989916 TTAATAACATGCCACA-ATATTAACACGGGTCAAGTAATATAAT
1 TTAATAACATGCCA-AGATATTAACAAGAATCAAGTAATATAAT
*
33989959 TTAATAACATGTCAAG
1 TTAATAACATGCCAAG
33989975 GAATATCATA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
42 1 0.02
43 49 0.96
44 1 0.02
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (43 bp):
TTAATAACATGCCAAGATATTAACAAGAATCAAGTAATATAAT
Found at i:33991356 original size:19 final size:18
Alignment explanation
Indices: 33991328--33991372 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
33991318 TACTACTAAC
33991328 AAAATAAAATTACAATAAA
1 AAAATAAAATTA-AATAAA
*
33991347 AAAATTAAATTAAATAAA
1 AAAATAAAATTAAATAAA
33991365 ACAAATAA
1 A-AAATAA
33991373 CTTATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAATAAAATTAAATAAA
Found at i:33991360 original size:14 final size:15
Alignment explanation
Indices: 33991329--33991365 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
33991319 ACTACTAACA
33991329 AAATAAAATTACAAT
1 AAATAAAATTACAAT
33991344 AAA-AAAATTA-AATT
1 AAATAAAATTACAA-T
33991358 AAATAAAA
1 AAATAAAA
33991366 CAAATAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.10
14 11 0.55
15 7 0.35
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAAATTACAAT
Found at i:33991608 original size:3 final size:3
Alignment explanation
Indices: 33991600--33991666 Score: 71
Period size: 3 Copynumber: 20.3 Consensus size: 3
33991590 TAAAATAACA
*
33991600 TTC TTC TTC TTC TTC TTC TTC TTC TTC TGC TTTC TTTC TTTC TTTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC -TTC -TTC -TTC TTC
33991649 TTTC TTTC TTC TTC TTC T
1 -TTC -TTC TTC TTC TTC T
33991667 CTCGTAGCTG
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 39 0.65
4 21 0.35
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:33991620 original size:15 final size:17
Alignment explanation
Indices: 33991603--33991666 Score: 87
Period size: 19 Copynumber: 3.8 Consensus size: 17
33991593 AATAACATTC
33991603 TTCTTCTTCTTC-TTC-
1 TTCTTCTTCTTCTTTCT
*
33991618 TTCTTCTTCTGCTTTCT
1 TTCTTCTTCTTCTTTCT
33991635 TTCTTTCTTTCTTCTTTCT
1 TTC-TTC-TTCTTCTTTCT
33991654 TTCTTCTTCTTCT
1 TTCTTCTTCTTCT
33991667 CTCGTAGCTG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
15 11 0.26
16 3 0.07
17 10 0.23
18 6 0.14
19 13 0.30
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.69
Consensus pattern (17 bp):
TTCTTCTTCTTCTTTCT
Found at i:33991638 original size:4 final size:4
Alignment explanation
Indices: 33991629--33991658 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
33991619 TCTTCTTCTG
33991629 CTTT CTTT CTTT CTTT C-TT CTTT CTTT CTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
33991659 CTTCTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:33991978 original size:25 final size:24
Alignment explanation
Indices: 33991949--33992004 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
33991939 TTAATCTACT
*
33991949 AAATAAAAA-AAATTAATAGCAAATC
1 AAATAAAAATAAATTAA-A-CAAAAC
33991974 AAATAAAAATTAAATTAAACAAAAC
1 AAATAAAAA-TAAATTAAACAAAAC
33991999 AAATAA
1 AAATAA
33992005 CTTATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 20 0.71
26 1 0.04
27 7 0.25
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (24 bp):
AAATAAAAATAAATTAAACAAAAC
Found at i:33992254 original size:17 final size:17
Alignment explanation
Indices: 33992232--33992284 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
33992222 AAATAACATT
33992232 TTTCTTCTTCTTCTTTC
1 TTTCTTCTTCTTCTTTC
*
33992249 TTTCTTTTTCTTTCTTTC
1 TTTCTTCTTC-TTCTTTC
33992267 TTTCCTTTCCTTCTTCTT
1 TTT-C-TT-CTTCTTCTT
33992285 CTCTCGTAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 9 0.30
18 10 0.33
19 1 0.03
20 7 0.23
21 3 0.10
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTCTTCTTCTTCTTTC
Found at i:33992259 original size:14 final size:14
Alignment explanation
Indices: 33992232--33992269 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
33992222 AAATAACATT
*
33992232 TTTC-TTCTTCTTC
1 TTTCTTTCTTTTTC
33992245 TTTCTTTCTTTTTC
1 TTTCTTTCTTTTTC
33992259 TTTCTTTCTTT
1 TTTCTTTCTTT
33992270 CCTTTCCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTTTCTTTTTC
Found at i:33993052 original size:632 final size:630
Alignment explanation
Indices: 33991346--33993121 Score: 2608
Period size: 632 Copynumber: 2.8 Consensus size: 630
33991336 ATTACAATAA
*
33991346 AAAAATTAAATTAAATAAAACAAATAACTTATAATAATAATTACTAAACAAAATATAACTTTAAA
1 AAAAATTAAATTAAACAAAACAAATAACTTATAATAATAATTACTAAACAAAATATAACTTTAAA
* * *
33991411 TTAACAATAAAACATTTACATTTACCTTTATTTTAGCTTTTAACTCTTTTAATC-ACCTACTAAA
66 TTAACAATAAAACATTTACATTTACCTTTCTTTTAGCTTTTATCTCCTTTAATCAACCTACTAAA
* *
33991475 CAAATAAAATTATAATAACAAATCAATCACATT-AA-A-T--CATTAAAACTAAAAACTAAATAA
131 TAAAT-AAATTATAATAACAAATCAATCACATTAAACATTAAAATTAAAACTAAAAACTAAATAA
*
33991535 TTACTACTACTACAAACAAATTAAATAAATTTAAAAATATAATAAACACACAAAATAAAATAACA
195 TTACTACTACTACTAACAAATTAAATAAATTTAAAAATATAATAAACACACAAAATAAAATAACA
* *
33991600 TTCTTCTTCTTCTTCTTCTTCTTCTTCTGCTTTCTTTCTTTCTTTC-TTCTTTCTTTCTTCTTCT
260 -TCTTCTTCTTCTTCTTCCTCTTCTT-T-CTTTCTTTCTTTCTTTCTTTCCTTC-TTCTTCTTCT
33991664 TCTCTCGTAGCTGCCCAAACACAAAACCACAATACCCTATTTTTTTACCTTTCTTTTTTAACCCA
321 TCTCTCGTAGCTGCCCAAACACAAAACCACAATACCCTATTTTTTTACCTTTCTTTTTTAACCCA
* * *
33991729 TTGGTCTTCCTCCCTCTTTTATAACCAAAAAACCCACCCAATTTTATTTCCCCTTAACCCTCAAC
386 TTGGTCTTCCTCCCTCTTTTATAACAAAAAAACCCACCCAATTTAATTTCCCC-TAACCCCCAAC
* * * * *
33991794 CAAATCTGTCTCCCAAACCCCCACACACAAACACACAGGCCACTCGAGGCGTGCCACAAGTCCTA
450 CGAATCTGCCTCCCAAACCCCCACACACAAACACACGGGCCACTCGAGGCGTGCCACGAGTCCCA
* ** *
33991859 AAAACCCTCAATGCCGCCACTTAGAATGGCACCTTTGGTGCCACCACTCAACATGGCACATTTCT
515 AAAACCCTCAATGCCACCACTTAGAATGGCA-C-AAGGTGCCACCACTCAACATGACACATTTCT
*
33991924 TCCTCTCCTCTTAATTTAATCTACTAAATAAAAAAAATTAATAGCAAATCAAAT
578 TCCTCTCCTCTTAATTTAATCTACTAAAT-AAAAAAATTAATAACAAATCAAAT
33991978 AAAAATTAAATTAAACAAAACAAATAAC-T-T-ATAATAATTACTAAACAAAATATAACTTTAAA
1 AAAAATTAAATTAAACAAAACAAATAACTTATAATAATAATTACTAAACAAAATATAACTTTAAA
33992040 TTAACAATAAAACATTTACATTTACCTTTCTTTTAGCTTTTATCTCCTTTAATCAACCTACTAAA
66 TTAACAATAAAACATTTACATTTACCTTTCTTTTAGCTTTTATCTCCTTTAATCAACCTACTAAA
*
33992105 TAAATAAAATTATAATAACAAATCAATCACATTAAAACATTAAAA-T-----TAAAAATTAAATA
131 TAAAT-AAATTATAATAACAAATCAATCACATT-AAACATTAAAATTAAAACTAAAAACTAAATA
* * *
33992164 ATTAATGCTACTACTAACAAATTAAATAAATTTAAAAATACAATAAACACACAAAATAAAATAAC
194 ATTACTACTACTACTAACAAATTAAATAAATTTAAAAATATAATAAACACACAAAATAAAATAAC
*
33992229 AT-TT-TTCTTCTTCTT-CT-TTCTTTC-TT-TTTCTTTCTTTCTTTCCTT-TCCTTCTTCTTCT
259 ATCTTCTTCTTCTTCTTCCTCTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCTTCTTCTTCTTCT
* * *
33992287 CTCGTAGCTGCCCTAACACAAAACCACAATACTCTATTTTTTTTACCTTTCTTTTTTAACCAATT
324 CTCGTAGCTGCCCAAACACAAAACCACAATACCCTA-TTTTTTTACCTTTCTTTTTTAACCCATT
33992352 GGTCTTCCTCCCTCTTTTATAACAAAAAAACCCACCCAATTTAATTTTCCCCTAACCCCCAACCG
388 GGTCTTCCTCCCTCTTTTATAACAAAAAAACCCACCCAATTTAA-TTTCCCCTAACCCCCAACCG
* * * *
33992417 AATCTGCCTCCCAAATCCCCACACACAAACACATGGGCCACTCGAGACATGCCACGAGTCCCAAA
452 AATCTGCCTCCCAAACCCCCACACACAAACACACGGGCCACTCGAGGCGTGCCACGAGTCCCAAA
* ** * * *
33992482 AATCCTCGGTGTCACCACTTAGAAT-G-A-AAGGTGCCACCACTCAACATGACACCTTTCTTTCT
517 AACCCTCAATGCCACCACTTAGAATGGCACAAGGTGCCACCACTCAACATGACACATTTCTTCCT
33992544 CTCCTCTT-ATTTAATCTACTAAAT-AAAAAATTAATAACAAATCAAAT
582 CTCCTCTTAATTTAATCTACTAAATAAAAAAATTAATAACAAATCAAAT
33992591 AAAAATTAAATTAAAACAAAACAAATAACTTATAATAATAATTACTAAACAAAATATAACTTTAA
1 AAAAATTAAATT-AAACAAAACAAATAACTTATAATAATAATTACTAAACAAAATATAACTTTAA
* * *
33992656 ATTAATAATAAAACATTTACATTTACCTTTCTTTTAGCTTTTATCTCCTTTAACCAACC-ATTAA
65 ATTAACAATAAAACATTTACATTTACCTTTCTTTTAGCTTTTATCTCCTTTAATCAACCTACTAA
*
33992720 ATAAAT-AATTATAATAACAAATCAACCACATTAAACATTAAAATTAAAACTAAAAACTAAATAA
130 ATAAATAAATTATAATAACAAATCAATCACATTAAACATTAAAATTAAAACTAAAAACTAAATAA
*
33992784 TTACTATTACTACTAACAAATTAAATAAATTTAAAAATATAAATAAACACACAAAAAAAATAAAA
195 TTACTACTACTACTAACAAATTAAATAAATTTAAAAATAT-AATAAACACAC----AAAATAAAA
*
33992849 TAACATCTTCTTCTTCTTCTTCCTCTGCTTTCTTTCTTTCTTTCTTTCATTTCCTTCTTCTTCTT
255 TAACATCTTCTTCTTCTTCTTCCTCTTCTTTCTTTCTTTCTTTCTTTC-TTTCCTTCTTCTTCTT
* *
33992914 CTTCTCTCGTAG-TCGTCCAAACACAAAACCACAATACCCTATTTTTTTACCTTTCTTTTTCAAC
319 CTTCTCTCGTAGCT-GCCCAAACACAAAACCACAATACCCTATTTTTTTACCTTTCTTTTTTAAC
* * * * * *
33992978 CCATTGGTC-ACCTTCCCTATTTTATACAAAAAAAAATCCATCCAATTTAACTTCCACCTAACCC
383 CCATTGGTCTTCC-TCCCTCTTTTATA-ACAAAAAAACCCACCCAATTTAATTTCC-CCTAACCC
* *
33993042 CCAACCGAATCTGCCTCCCAAACCCCCACACACAAACACACGGGCCACTCAAGGCGTGCCACGTG
445 CCAACCGAATCTGCCTCCCAAACCCCCACACACAAACACACGGGCCACTCGAGGCGTGCCACGAG
33993107 TCCCAAAAACCCTCA
510 TCCCAAAAACCCTCA
33993122 GTGCTGCCAC
Statistics
Matches: 1037, Mismatches: 70, Indels: 74
0.88 0.06 0.06
Matches are distributed among these distances:
613 45 0.04
614 42 0.04
615 17 0.02
616 49 0.05
617 88 0.08
619 50 0.05
620 58 0.06
621 169 0.16
622 14 0.01
623 1 0.00
624 16 0.02
625 7 0.01
626 12 0.01
627 13 0.01
628 8 0.01
629 86 0.08
630 131 0.13
631 55 0.05
632 172 0.17
633 1 0.00
634 1 0.00
635 1 0.00
636 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (630 bp):
AAAAATTAAATTAAACAAAACAAATAACTTATAATAATAATTACTAAACAAAATATAACTTTAAA
TTAACAATAAAACATTTACATTTACCTTTCTTTTAGCTTTTATCTCCTTTAATCAACCTACTAAA
TAAATAAATTATAATAACAAATCAATCACATTAAACATTAAAATTAAAACTAAAAACTAAATAAT
TACTACTACTACTAACAAATTAAATAAATTTAAAAATATAATAAACACACAAAATAAAATAACAT
CTTCTTCTTCTTCTTCCTCTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCTTCTTCTTCTTCTCT
CGTAGCTGCCCAAACACAAAACCACAATACCCTATTTTTTTACCTTTCTTTTTTAACCCATTGGT
CTTCCTCCCTCTTTTATAACAAAAAAACCCACCCAATTTAATTTCCCCTAACCCCCAACCGAATC
TGCCTCCCAAACCCCCACACACAAACACACGGGCCACTCGAGGCGTGCCACGAGTCCCAAAAACC
CTCAATGCCACCACTTAGAATGGCACAAGGTGCCACCACTCAACATGACACATTTCTTCCTCTCC
TCTTAATTTAATCTACTAAATAAAAAAATTAATAACAAATCAAAT
Found at i:33994305 original size:17 final size:16
Alignment explanation
Indices: 33994287--33994346 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 16
33994277 AATAACTTTA
33994287 AAAATAAATTTAAAAT
1 AAAATAAATTTAAAAT
***
33994303 AAAAATAAACACACAAAGT
1 -AAAATAAATTTA-AAA-T
33994322 AAAATAAATTTTAAAAT
1 AAAATAAA-TTTAAAAT
33994339 AAAATAAA
1 AAAATAAA
33994347 ATAATCTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 18 0.53
18 14 0.41
19 2 0.06
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAATAAATTTAAAAT
Found at i:33994682 original size:757 final size:745
Alignment explanation
Indices: 33993122--33997276 Score: 4351
Period size: 757 Copynumber: 5.5 Consensus size: 745
33993112 AAAACCCTCA
* * * * *
33993122 GTGCTGCCACTCAACTTGGCACCACCCATTTGTTAGGTA--TTTTTATCCTATTCTCGTATTTAT
1 GTGCCGCCACTCAACATGGCACCACCCATGTGTCAGGTATTTTTTTATCCCATTCTCGTATTTAT
* * * * *
33993185 TTGTCTGATTTGTACTGTATCTATACAAAATAGTACCGCCACTCAAGTTGGCACCATCATTATTT
66 TTGTCTGATTTGTACTGTATGTATACAAAGTGGTGCCGCCACTCAAGTTGGCACCACCATTATTT
*
33993250 TATATATATATATTTTTATTTTT--TATAT--ATATAATAAAAAATTAAAAAAATCAATGTCAGA
131 TATATAT-T-T-TTTTT-TTTTTAATATATAAATATAAT-AAAAATTAAAAAAATCAGTGTCAGA
* * * *
33993311 ATACCCCTTAGTGCTGCCGATTAAGTACCCCCTCC-CCCTCGAAAACATACCATTTTGGTAATTA
191 ATACCCCTTGGTGCCGCCGATTAAGTA--CCCTCCACCC-CAAAAACATA-CATTTTGATAATTA
* * * * * *
33993375 AT-GGGTGAAAAATACTATTTTGGTAGATAAATAATTA-TCTCTATTAATTTGATAAAAAAACTC
252 ATGGGGTG-GAGATACCATTTTGGTAGATAAATAATTATTTTGTATTAATTTGATAAAAAACCTC
* *
33993438 CTTTAATCAACC-ACTAAACAAATAAAATTATAATAACAAATCAATCACTTTAACCATTAAAATT
316 CTTTAATCAACCTACTAAACAAATAAAATTATAATAACAAATCAATCACATTAAACATTAAAATT
33993502 AAAAACTAAATAATTACTACTACTAACAAATTAAATAACTTTAAAAATAAATTTAAAATTAAAAT
381 AAAAACTAAATAATTACTACTACTAACAAATTAAATAACTTTAAAAATAAATTTAAAATTAAAAT
*
33993567 AAACACACAAAGT---A-AAA---TAAAAT-AACT-T--TC---TTCTCCTTC---TTTC----T
446 AAACACACAAA-TAAAATAAATTTTAAAATAAAATATAATCTTATTCTCCTTCTTTTTTCTTTGT
* * *
33993611 TTCCTTTCCTTCTTCTTCTTCTC-CCGTAGCTGCCCAAACACAAAACCAAAATCCTTTATTTTTT
510 TTCCTTTCCTTCTTCTTCTTCTCTCC-TAACTGCCCAAACACAAAACTACAA-----TA--TTTT
* * *
33993675 TTTACATTTCTTTTTCAACCCATTGGTCCCCCCTCTCTTTTTTATAACCAAAAATCCCACCCAAT
567 TTTACCTTTCTTTTTCAACCCATTGGT-CCCCCTCTCTCTTTTATAACCAAAAAACCCACCCAAT
* * * * *
33993740 TTAATTTCTCCCTAACCCCCAATCGAATCTGCCTCTCC-AACCCCTCCACACATACGGGCCACTC
631 TTAATTTC-CCCTAA-CCCCAACCGAATCTGCCTC-CCAAACCCC-CC-CACACACAGGTCACTT
33993804 GAGGCATGCCACGTGTCCCAAAAACCCTCGGTGCCGCCACTTAGAATGGCACCTTTG
691 G-GGCATGCCACGTGTCCC-AAAACCCTCGGTGCCGCCACTTAGAATGGCACCTTTG
* * *
33993861 GTGCCGCCACTCAACATGACACCACCCATGTGTCAGGTATTTTTTTTATCTCATTCTTGTATTTA
1 GTGCCGCCACTCAACATGGCACCACCCATGTGTCAGGTA-TTTTTTTATCCCATTCTCGTATTTA
* * *
33993926 TTTG-CTTGATTTGTATTGTATGTATACAAAGTGGTGCTGCCACTCAAGTTGACACCACCATTA-
65 TTTGTC-TGATTTGTACTGTATGTATACAAAGTGGTGCCGCCACTCAAGTTGGCACCACCATTAT
*
33993989 TTTATAT-TTTTTTTTTTTTTAATATATAAATATAATAAAAAATTTAAAAAAATCAGTGCCAGAA
129 TTTATATATTTTTTTTTTTTTAATATATAAATATAAT-AAAAA-TTAAAAAAATCAGTGTCAGAA
* * * *
33994053 TACCCCTTGGTGTCGTCGATTAAGTGCCCTCCATCCCCAAAAACATATCATTTTAATAATTAATG
192 TACCCCTTGGTGCCGCCGATTAAGTACCCTCCA-CCCCAAAAACATA-CATTTTGATAATTAATG
* *
33994118 GGGTGGAGATACCATTTTGGTAAATAAATAATTAGTTTGTATTAATTT-AGTAAAAAATCCTCCT
255 GGGTGGAGATACCATTTTGGTAGATAAATAATTATTTTGTATTAATTTGA-TAAAAAA-CCTCCT
* * *
33994182 TTAATCAACCAATTAAACAAATAAAATTAAAATAACAAATCAATCACATTAAA-ATTAAAATTAA
318 TTAATCAACCTACTAAACAAATAAAATTATAATAACAAATCAATCACATTAAACATTAAAATTAA
* *
33994246 AAACTCAATAATTACTACTACTAACAAATTAAATAACTTTAAAAATAAATTTAAAATAAAAATAA
383 AAACTAAATAATTACTACTACTAACAAATTAAATAACTTTAAAAATAAATTTAAAATTAAAATAA
*
33994311 ACACACAAAGTAAAATAAATTTTAAAATAAAATAAAATAATCTTATTCTCCTTCTTTTTTCTTTA
448 ACACACAAA-TAAAATAAATTTTAAAATAAAAT---ATAATCTTATTCTCCTTCTTTTTTCTTTG
** *
33994376 TTTGTTTTCCTTCTTCTTCTTCTCTCCTAACTGCCCAAGCACAAAACTACAATA-TTTTTTACCT
509 TTTCCTTTCCTTCTTCTTCTTCTCTCCTAACTGCCCAAACACAAAACTACAATATTTTTTTACCT
*
33994440 TT-TTTTTCAACCCATTAGTTCCCCCTCTCTCTTTTATAACCAAAAAACCCACCCAATTTAATTT
574 TTCTTTTTCAACCCATT-GGTCCCCCTCTCTCTTTTATAACCAAAAAACCCACCCAATTTAATTT
* * ** * * ** *
33994504 TCCCTATCCCCAACAAAATTTGCCTCCCAAACCCTCCCTCCCACACATAGACCACTTGGGATATG
638 CCCCTAACCCCAACCGAATCTGCCTCCCAAA--C-CCC-CCCACACACAGGTCACTTGGG-CATG
* *
33994569 CCATGTGTCCCAAAACCCTTCGATGCCGCCACTTA-ATATGGCACCTTTG
698 CCACGTGTCCCAAAACCC-TCGGTGCCGCCACTTAGA-ATGGCACCTTTG
* * ** *
33994618 GTGCTGCCACTCAACATGGCACCACCCATGTGTTAGGTATTTTTTTTATTTCATTTTCGTATTTA
1 GTGCCGCCACTCAACATGGCACCACCCATGTGTCAGGTA-TTTTTTTATCCCATTCTCGTATTTA
* *
33994683 TTTGTCTGATTTGTACTGTATGTATAGAAAGTGGTGTCGCCACTCAAGTTGGCACCACCATTATT
65 TTTGTCTGATTTGTACTGTATGTATACAAAGTGGTGCCGCCACTCAAGTTGGCACCACCATTATT
*
33994748 TTATATATTTTTTTATTTTTTTATATATAAATATAAT-AAAATT-AAAAAATCAGTGTCAGAATA
130 TTATATATTTTTTT-TTTTTTAATATATAAATATAATAAAAATTAAAAAAATCAGTGTCAGAATA
** * * * * *
33994811 CCCCTTGGTATCGACGATTAAGTACCTTTCCACACCAAAAAATATACCATTTTGATAATTAATTG
194 CCCCTTGGTGCCGCCGATTAAGTACC-CTCCAC-CCCAAAAACATA-CATTTTGATAATTAATGG
* * * * * *
33994876 GGTGGGGATATCATTTTGATATATAAATAATTATTTTGTATTAATTTGGTAAAAGAAATTCTCCT
256 GGTGGAGATACCATTTTGGTAGATAAATAATTATTTTGTATTAATTTGAT-AAA-AAA-CCTCCT
*
33994941 TTAATCAACCTACTAAACAAATAAAATTATAATAACAAATTAATCACATTAAACATTAAAATTAA
318 TTAATCAACCTACTAAACAAATAAAATTATAATAACAAATCAATCACATTAAACATTAAAATTAA
* *
33995006 AAACTAAATAATTACAACAACTACTAACAAATTAAATAACATTAAAAATAAATTTAAAATTAAAA
383 AAACTAAATAATT---ACTACTACTAACAAATTAAATAACTTTAAAAATAAATTTAAAATTAAAA
* **** **** * ** **
33995071 TAAACA-ACAAATAAAATAACCTTCTTCTGCTTCTTCCTTTGCTTCTTCCTTTATTTCTTTTTTC
445 TAAACACACAAATAAAATAA--AT-TT-T--AAAATAAAAT--ATAAT-C-TTA-TTC-TCCTTC
* * *
33995135 TCTTTGTTCTTTCTTTCCTTTCCTTTTTCTTCTTCTTTTCCCGTAACTGCCCAAACACAAAATCA
498 T-TTT-TTCTTTGTTTCCTTTCCTTCTTCTTCTTC-TCT-CC-TAACTGCCCAAACACAAAA-C-
* * * * *
33995200 AAATACCATATTTTTTTA-CATTC-TTTTCAATCCATTGGTCCCCCTCACTCATTTATAACCAAA
556 ---TACAATATTTTTTTACCTTTCTTTTTCAACCCATTGGTCCCCCTCTCTCTTTTATAACCAAA
* * * * *
33995263 AAATCCACCCAATTTAATTTCCCCCAAACCCCAACCGAATCTGGCTCACAAA-CTCCCCACACAC
618 AAACCCACCCAATTTAATTT-CCCCTAACCCCAACCGAATCTGCCTCCCAAACCCCCCCACACAC
* * * * * * *
33995327 AGGTCACTTGAGGCGTGCCACATGTCCCAAATACTCTAGGTACAGGCACTTAGAATGGCACCTTT
682 AGGTCACTTG-GGCATGCCACGTGTCCCAAA-ACCCTCGGTGCCGCCACTTAGAATGGCACCTTT
33995392 G
745 G
* * * * ** *
33995393 GTGCCACCACTCAACACGGCACCAACCATGTGTTAGGTATTTTTTTTATCTAATTCTTGTATTTT
1 GTGCCGCCACTCAACATGGCACCACCCATGTGTCAGGTA-TTTTTTTATCCCATTCTCGTA-TTT
* * * *
33995458 ATTTGTCTGATTTGTACTGTATGCATGCAAAGTGGTACCGTCACTCAAGTTGGCACCACCATTAT
64 ATTTGTCTGATTTGTACTGTATGTATACAAAGTGGTGCCGCCACTCAAGTTGGCACCACCATTAT
** *
33995523 TTTATAT-TTTTTAATTTTTTAATATATAAATATAATAAAAATT---GAAA--A-----AGAATA
129 TTTATATATTTTTTTTTTTTTAATATATAAATATAATAAAAATTAAAAAAATCAGTGTCAGAATA
* * *
33995577 CCCCTTGATGCCGCCGATTAAGTACCCTCCACACCAAAAAACATACTATTTTGGTAATTAATGGG
194 CCCCTTGGTGCCGCCGATTAAGTACCCTCCAC-CCCAAAAACATAC-ATTTTGATAATTAATGGG
* *
33995642 GTGGAGAGATACCATTTTGGTAGATAAAAAATT-TTTTGAATTAATTTGATAAAAAA-CTCCTTT
257 GT-G-GAGATACCATTTTGGTAGATAAATAATTATTTTGTATTAATTTGATAAAAAACCTCCTTT
* * * * * *
33995705 AATCAACCAAATAAAAAAATAAAATTATAATAACAAATTAATCCCATTAAATATTAAAATTAAAA
320 AATCAACCTACTAAACAAATAAAATTATAATAACAAATCAATCACATTAAACATTAAAATTAAAA
*
33995770 ACTAAATAATTACTACTATTACTAACAAATTAAATAACTCTAAAAATAAATTTAAAATTAAAATA
385 ACTAAATAATTACTAC---TACTAACAAATTAAATAACTTTAAAAATAAATTTAAAATTAAAATA
* * *
33995835 AACACACAATATAAAATAAATTTTAAAATAAAATAAAATAACATTCTTCTCTTTCTTTCTTTCTT
447 AACACACAA-ATAAAATAAATTTTAAAATAAAATATAAT--C-TTATTCTCCTTCTTT-TTTCTT
* * * *
33995900 TGTTTCCTTTCCTTCTTCTTCTTCTTTCGTAGCTGCCCAAATACAAAA-TCACAATACCCTATTT
507 TGTTTCCTTTCCTTCTTCTTCTTCTCTCCTAACTGCCCAAACACAAAACT-AC-A-A---TATTT
* * * * *
33995964 TTTTACCTTTCTTTTTCTACTCATTTGTCTCCCTTCCCTCTTTTATAA--AAAAAACCCACCCAA
566 TTTTACCTTTCTTTTTCAACCCATTGGTC-CCCCTCTCTCTTTTATAACCAAAAAACCCACCCAA
* * * * *
33996027 TTTAATTTCCCCTTAACCTCCAACCAAATCTGACT-CCTAA-CCCCCCACACACGGGTCAATTGG
630 TTTAATTTCCCC-TAACC-CCAACCGAATCTGCCTCCCAAACCCCCCCACACACAGGTCACTT-G
* * * * *
33996090 GGCGTACCACGTGTCCCAAAAACTCTCAGTGCCGCCACTTAGAATGTCACCTTTG
692 GGCATGCCACGTGTCCC-AAAACCCTCGGTGCCGCCACTTAGAATGGCACCTTTG
*
33996145 GTGCCGCCACTCAACATTGCACCACCCATGTGTCAGGTA-TTTTTTATCCCATTCTCGTATTTAT
1 GTGCCGCCACTCAACATGGCACCACCCATGTGTCAGGTATTTTTTTATCCCATTCTCGTATTTAT
* * * * * ** *
33996209 TTATCTGATTTGTACAGTATGTATATAAAGTGGTGCC-TCACTTAAGTTGGCATGACTATTA-TT
66 TTGTCTGATTTGTACTGTATGTATACAAAGTGGTGCCGCCACTCAAGTTGGCACCACCATTATTT
* * * *
33996272 T-TATATTATTTTATTTTTAATATATAAATATAATAAAAAATTTAAAAAAAATCAATGTGAGAAT
131 TATATATTTTTTTTTTTTTAATATATAAATATAAT-AAAAA-TT-AAAAAAATCAGTGTCAGAAT
* * * * *
33996336 ACCCCTTGATGCCGCCGATTAAGTACTCTCTACCCCCAAAACATACAATTTT-ATAATTAATAGG
193 ACCCCTTGGTGCCGCCGATTAAGTACCCTCCACCCCAAAAACATAC-ATTTTGATAATTAATGGG
* * *
33996400 ATGGAGATACCATTTTGGTAGATAAATAATTAATTTGTATTAATTTGATAAAAAACCCTTCTTTA
257 GTGGAGATACCATTTTGGTAGATAAATAATTATTTTGTATTAATTTGATAAAAAA-CCTCCTTTA
*
33996465 ATCAACCTACTAAACAAATAAAATTATAATAATAAATCAATCACATT----A--AAAATT--AAA
321 ATCAACCTACTAAACAAATAAAATTATAATAACAAATCAATCACATTAAACATTAAAATTAAAAA
* * * * *
33996522 -T-AATTACTACTACTACCAACAAATTCAATATA-TTTAAAAATGAATTTAAAATTAAAATAAAC
386 CTAAATAATTACTACTACTAACAAATTAAATA-ACTTTAAAAATAAATTTAAAATTAAAATAAAC
* * *
33996584 ACAC-------A-AAA---TAAAATAAAATA-AA-CTTCTCCTTCTTCTTTATTTCTTTGTTTCC
450 ACACAAATAAAATAAATTTTAAAATAAAATATAATCTTATTCTCCTTCTTT-TTTCTTTGTTTCC
*
33996636 TTTCCTTCTTCTTC-T-TCTCCTGAAGCTGCCCAAACACAAAACCACAATACACTTTTTTTTTTA
514 TTTCCTTCTTCTTCTTCTCTCCT-AA-CTGCCCAAACACAAAACTACAAT--A----TTTTTTTA
*
33996699 CCTTTCTTTTTCAACCCATTGGTCCCCCATC-CTCTTTTATAACCAAAAAAAATCCACCCAATTT
571 CCTTTCTTTTTCAACCCATTGGTCCCCC-TCTCTCTTTTATAACC--AAAAAACCCACCCAATTT
* *
33996763 AATTTCCCCTAACCCCCAACCGAATCTGCCTCCCAAA--CCCCC-CACACGGGTCACTCGGGGCA
633 AATTTCCCCTAA-CCCCAACCGAATCTGCCTCCCAAACCCCCCCACACACAGGTCACT-TGGGCA
* *
33996825 TGCCACGTGTCCCAAAAACCCTCGGTGCCTCCACTTAGAATTGCCACCTTTG
696 TGCCACGTGTCCC-AAAACCCTCGGTGCCGCCACTTAGAA-TGGCACCTTTG
* * * *
33996877 GTGTCGGCACTCAACATGGCACCACCCATGTGTCAGGTATTTTTTAATCCCATTCTCATATTTAT
1 GTGCCGCCACTCAACATGGCACCACCCATGTGTCAGGTATTTTTTTATCCCATTCTCGTATTTAT
* *
33996942 TTGTCTGATTTGTACTGTAAGTATA-AAAGTGGTGCAGCCACTCAAGTTGGCACCACCATTA-TT
66 TTGTCTGATTTGTACTGTATGTATACAAAGTGGTGCCGCCACTCAAGTTGGCACCACCATTATTT
* * * *
33997005 T-TATATTTTTATATTTTTAATATATAAATATAATAAAAATTAAAAAAATCAGTGCCAGAATACT
131 TATATATTTTTTTTTTTTTAATATATAAATATAATAAAAATTAAAAAAATCAGTGTCAGAATACC
*
33997069 CCTTGGTGCCGCCGATTAAGTACCCTCCA-CCCAAAAACATACCATTTTGGTAATTAATGGGGTG
196 CCTTGGTGCCGCCGATTAAGTACCCTCCACCCCAAAAACATA-CATTTTGATAATTAATGGGGTG
* *
33997133 GAGATACCATTTTGGTAGATAAATAATTATTTTGTATTAATTTGGTAAAAAACCCTCCTTTAATT
260 GAGATACCATTTTGGTAGATAAATAATTATTTTGTATTAATTTGATAAAAAA-CCTCCTTTAATC
* * *
33997198 AATCTACTAAACAAATAAAATAATAATAACAAATCAATTACATTAAACATTAAAATTAAAAACTA
324 AACCTACTAAACAAATAAAATTATAATAACAAATCAATCACATTAAACATTAAAATTAAAAACTA
33997263 AATAATTACTACTA
389 AATAATTACTACTA
33997277 TTGAAATCAT
Statistics
Matches: 2902, Mismatches: 351, Indels: 325
0.81 0.10 0.09
Matches are distributed among these distances:
724 1 0.00
726 1 0.00
727 5 0.00
728 3 0.00
729 86 0.03
730 191 0.07
731 54 0.02
732 83 0.03
733 132 0.05
734 13 0.00
736 11 0.00
737 8 0.00
738 10 0.00
739 42 0.01
740 75 0.03
741 74 0.03
742 173 0.06
743 38 0.01
745 2 0.00
746 55 0.02
747 29 0.01
748 26 0.01
749 54 0.02
750 21 0.01
751 34 0.01
752 129 0.04
753 43 0.01
754 47 0.02
755 26 0.01
756 91 0.03
757 324 0.11
758 47 0.02
759 142 0.05
760 81 0.03
761 12 0.00
762 136 0.05
763 57 0.02
764 15 0.01
765 39 0.01
766 89 0.03
767 28 0.01
768 3 0.00
769 3 0.00
770 5 0.00
771 4 0.00
772 25 0.01
773 5 0.00
774 23 0.01
775 135 0.05
776 78 0.03
779 43 0.01
780 44 0.02
781 7 0.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (745 bp):
GTGCCGCCACTCAACATGGCACCACCCATGTGTCAGGTATTTTTTTATCCCATTCTCGTATTTAT
TTGTCTGATTTGTACTGTATGTATACAAAGTGGTGCCGCCACTCAAGTTGGCACCACCATTATTT
TATATATTTTTTTTTTTTTAATATATAAATATAATAAAAATTAAAAAAATCAGTGTCAGAATACC
CCTTGGTGCCGCCGATTAAGTACCCTCCACCCCAAAAACATACATTTTGATAATTAATGGGGTGG
AGATACCATTTTGGTAGATAAATAATTATTTTGTATTAATTTGATAAAAAACCTCCTTTAATCAA
CCTACTAAACAAATAAAATTATAATAACAAATCAATCACATTAAACATTAAAATTAAAAACTAAA
TAATTACTACTACTAACAAATTAAATAACTTTAAAAATAAATTTAAAATTAAAATAAACACACAA
ATAAAATAAATTTTAAAATAAAATATAATCTTATTCTCCTTCTTTTTTCTTTGTTTCCTTTCCTT
CTTCTTCTTCTCTCCTAACTGCCCAAACACAAAACTACAATATTTTTTTACCTTTCTTTTTCAAC
CCATTGGTCCCCCTCTCTCTTTTATAACCAAAAAACCCACCCAATTTAATTTCCCCTAACCCCAA
CCGAATCTGCCTCCCAAACCCCCCCACACACAGGTCACTTGGGCATGCCACGTGTCCCAAAACCC
TCGGTGCCGCCACTTAGAATGGCACCTTTG
Found at i:33995072 original size:57 final size:55
Alignment explanation
Indices: 33994973--33995080 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 55
33994963 AAAATTATAA
* *
33994973 TAACAAATTAATCACATTAAACATTAAAATTAAAAACTAAATAATTACAACAACTAC
1 TAACAAATTAATAACATTAAACAATAAAATTAAAAACTAAATAA--ACAACAACTAC
* *
33995030 TAACAAATTAAATAACATTAAA-AAT-AAATTTAAAATTAAAATAAACAACAA
1 TAACAAATT-AATAACATTAAACAATAAAATTAAAAACT-AAATAAACAACAA
33995081 ATAAAATAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
55 7 0.16
56 10 0.22
57 17 0.38
58 11 0.24
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (55 bp):
TAACAAATTAATAACATTAAACAATAAAATTAAAAACTAAATAAACAACAACTAC
Found at i:33995113 original size:12 final size:12
Alignment explanation
Indices: 33995098--33995122 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33995088 AACCTTCTTC
33995098 TGCTTCTTCCTT
1 TGCTTCTTCCTT
33995110 TGCTTCTTCCTT
1 TGCTTCTTCCTT
33995122 T
1 T
33995123 ATTTCTTTTT
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:0.00, C:0.32, G:0.08, T:0.60
Consensus pattern (12 bp):
TGCTTCTTCCTT
Found at i:33995140 original size:29 final size:29
Alignment explanation
Indices: 33995107--33995164 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
33995097 CTGCTTCTTC
*
33995107 CTTTGCTTCTTCCTTT-ATTTCTTTTTTCT
1 CTTTG-TTCTTCCTTTCATTTCCTTTTTCT
* *
33995136 CTTTGTTCTTTCTTTCCTTTCCTTTTTCT
1 CTTTGTTCTTCCTTTCATTTCCTTTTTCT
33995165 TCTTCTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.02, C:0.26, G:0.03, T:0.69
Consensus pattern (29 bp):
CTTTGTTCTTCCTTTCATTTCCTTTTTCT
Found at i:33995832 original size:17 final size:17
Alignment explanation
Indices: 33995812--33995871 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
33995802 AATAACTCTA
33995812 AAAATAAATTTAAAATT
1 AAAATAAATTTAAAATT
*** *
33995829 AAAATAAACACACAATAT
1 AAAATAAATTTAAAAT-T
33995847 AAAATAAATTTTAAAA-T
1 AAAATAAA-TTTAAAATT
33995864 AAAATAAA
1 AAAATAAA
33995872 ATAACATTCT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 21 0.64
18 9 0.27
19 3 0.09
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAAATTTAAAATT
Found at i:34001245 original size:14 final size:13
Alignment explanation
Indices: 34001213--34001248 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
34001203 TTAGGTGTTT
34001213 TTTTATTT-TTTA
1 TTTTATTTATTTA
34001225 TTTTATTTATTTA
1 TTTTATTTATTTA
34001238 TTTATATTTAT
1 TTT-TATTTAT
34001249 AAATAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.36
13 7 0.32
14 7 0.32
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:34003612 original size:83 final size:82
Alignment explanation
Indices: 34003539--34003703 Score: 294
Period size: 83 Copynumber: 2.0 Consensus size: 82
34003529 ATTCTACCTT
* *
34003539 GTAAAGTGGGTTGGACGGTAATGGTTTGGAATTATTAAGGGAAAATTTATTAGTTAAAAGGGAAA
1 GTAAAGTGGGTTGGACAGTAATGGTTTGGAATTATTAAGGGAAAATTTATTAGTTAAAAAGG-AA
34003604 AAATGGTAAATAAACAAA
65 AAATGGTAAATAAACAAA
*
34003622 GTAAAGTGGGTTGGACAGTAATGGTTTGGAATTATTAAGGGAAAATTTATTAGTTAAAAAGGTAA
1 GTAAAGTGGGTTGGACAGTAATGGTTTGGAATTATTAAGGGAAAATTTATTAGTTAAAAAGGAAA
34003687 AATGGTAAATAAACAAA
66 AATGGTAAATAAACAAA
34003704 ACCTAATATG
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
82 19 0.24
83 60 0.76
ACGTcount: A:0.44, C:0.02, G:0.25, T:0.28
Consensus pattern (82 bp):
GTAAAGTGGGTTGGACAGTAATGGTTTGGAATTATTAAGGGAAAATTTATTAGTTAAAAAGGAAA
AATGGTAAATAAACAAA
Found at i:34004883 original size:193 final size:195
Alignment explanation
Indices: 34004545--34004989 Score: 515
Period size: 193 Copynumber: 2.3 Consensus size: 195
34004535 TGAAACGACA
* * * **
34004545 CGATGGTTGAGGTATCACATGTGTTGCGAATCCTCGATAGCTCGTGTGAGTAGCATCGTGAGTTG
1 CGATGGCTGAGGTACCACATGTGTTGCGAATCCTCGACAGCTCGTGTGAGTAGCATCGTGAGTCA
* * * * * *
34004610 AGAAATGAGTAAAGAATCCAAGAATGGATTATAGGCCCTGCGATGGCTGAGATTTATGCATAAGT
66 AAAAAAGAGTAAAGAATCCAAGAATGGATTACAAGCCCTACGATGGCTGAGACTTATGCATAAGT
** *
34004675 GCATATTCTCGACAGCTCGTGTGAGCAGCATCATCAGGGAACAGTTATATGCACAGATACCGTAT
131 GCATACACCCGACAGCTCGTGTGAGCAGCATCATCAGGGAACAGTTATATGCACAGATACCGTAT
* * *
34004740 CGATGGCTGAGGTACCGCATGTGTTGC-AAGTTCTCGACAGCTTGTGTGAGTAGCATCGTGAGTC
1 CGATGGCTGAGGTACCACATGTGTTGCGAA-TCCTCGACAGCTCGTGTGAGTAGCATCGTGAGTC
* *
34004804 AAAAAAAGA-T-ATGAATCCTAGAATGGATTACAAGCCCTACGATGGCT-AGGACTTATGCATAA
65 AAAAAAAGAGTAAAGAATCCAAGAATGGATTACAAGCCCTACGATGGCTGA-GACTTATGCATAA
* * * * * *
34004866 GTGCATACACCCGACAGCTCGTGTGAGCAGCATCGTTA-GGAGGCAATTATATAG-ACAAACACC
129 GTGCATACACCCGACAGCTCGTGTGAGCAGCATCATCAGGGA-ACAGTTATAT-GCACAGATACC
* *
34004929 GCAC
192 GTAT
* * * * * *
34004933 CAATGGCTGGGGTACCACATATGTTGCGAGTCGTCGACAGCTCGTGTGAGCAGCATC
1 CGATGGCTGAGGTACCACATGTGTTGCGAATCCTCGACAGCTCGTGTGAGTAGCATC
34004990 AGGTACTGGT
Statistics
Matches: 209, Mismatches: 36, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
192 4 0.02
193 140 0.67
194 5 0.02
195 60 0.29
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (195 bp):
CGATGGCTGAGGTACCACATGTGTTGCGAATCCTCGACAGCTCGTGTGAGTAGCATCGTGAGTCA
AAAAAAGAGTAAAGAATCCAAGAATGGATTACAAGCCCTACGATGGCTGAGACTTATGCATAAGT
GCATACACCCGACAGCTCGTGTGAGCAGCATCATCAGGGAACAGTTATATGCACAGATACCGTAT
Found at i:34007175 original size:41 final size:41
Alignment explanation
Indices: 34007088--34007315 Score: 258
Period size: 41 Copynumber: 5.5 Consensus size: 41
34007078 TTATGCTCTT
* * * * * *
34007088 TCGAGTCATAAGTCTTCCTTTAACCATATTCTCATTCTCAAC
1 TCGAGACATGAGTCTTCC-TTAATCAAAATCTCATTCTCATC
* *
34007130 TCGAGATATGAGTCTTCCTTAATCAAAATCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
* *
34007171 TCGAGACATGAGTCTTCCTTATTCAAAATCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
* *
34007212 TCGAGACATGAGTCTTTCTTATTCAAAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
* ** * *
34007253 TCGAGACATGAGTCTTCCATTTATACAATTTCTCATGCTCAGC
1 TCGAGACATGAGTCTTCC-TTAAT-CAAAATCTCATTCTCATC
* *
34007296 CCGAGACAAGAGTCTTCCTT
1 TCGAGACATGAGTCTTCCTT
34007316 TTTATACACC
Statistics
Matches: 163, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
41 113 0.69
42 20 0.12
43 30 0.18
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATC
Found at i:34008029 original size:7 final size:7
Alignment explanation
Indices: 34008017--34008042 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
34008007 GTGTCGTGTG
34008017 AAGAAGA
1 AAGAAGA
34008024 AAGAAGA
1 AAGAAGA
34008031 AAGAAGA
1 AAGAAGA
34008038 AAGAA
1 AAGAA
34008043 AATGGGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:34008168 original size:20 final size:21
Alignment explanation
Indices: 34008125--34008168 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
34008115 ACTTTCATCA
* *
34008125 TTAAGCTTTAATTAAACATTT
1 TTAACCTTTAATTAAACATAT
*
34008146 TTAACCTTT-ATTAAACCTAT
1 TTAACCTTTAATTAAACATAT
34008166 TTA
1 TTA
34008169 TAATCAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAACCTTTAATTAAACATAT
Found at i:34011964 original size:8 final size:9
Alignment explanation
Indices: 34011942--34011982 Score: 73
Period size: 9 Copynumber: 4.6 Consensus size: 9
34011932 CTTATTTATA
34011942 TAAAAAATT
1 TAAAAAATT
34011951 TAAAAAATT
1 TAAAAAATT
34011960 TAAAAAATT
1 TAAAAAATT
*
34011969 TAAAAACTT
1 TAAAAAATT
34011978 TAAAA
1 TAAAA
34011983 TTAACTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (9 bp):
TAAAAAATT
Found at i:34012199 original size:9 final size:9
Alignment explanation
Indices: 34012182--34012212 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34012172 TGAAGAAATC
*
34012182 TTGAGAGAA
1 TTGAAAGAA
34012191 TTGAAAGAA
1 TTGAAAGAA
34012200 TTGAAAGAA
1 TTGAAAGAA
34012209 TTGA
1 TTGA
34012213 GAGATTGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (9 bp):
TTGAAAGAA
Found at i:34028085 original size:39 final size:38
Alignment explanation
Indices: 34028042--34028228 Score: 106
Period size: 39 Copynumber: 4.8 Consensus size: 38
34028032 TCATGGGGCG
*
34028042 GATCATAGTCATCCGATCTTTTACCCCGAGCTTGAGGTA
1 GATCATA-TCATCCGATCTTTTACCCCGAGCTTGAGGCA
* * * * * *
34028081 GATCACCATCAGCCAATCTCTTACCCCGACCTTGGGGCA
1 GATCA-TATCATCCGATCTTTTACCCCGAGCTTGAGGCA
** * *
34028120 GATTGTAACCATCCGATCTTTTACCCCGAGCCT-AGGGCA
1 GATCAT-ATCATCCGATCTTTTACCCCGAGCTTGA-GGCA
* * * * * * * *
34028159 GATCACCATCAACCAATCTCTTACCTCAAGCCTGGGGCA
1 GATCA-TATCATCCGATCTTTTACCCCGAGCTTGAGGCA
** * *
34028198 GATTGTAACCATCCGATCCTTTACCCCGAGC
1 GATCAT-ATCATCCGATCTTTTACCCCGAGC
34028229 CTAGGGCAGA
Statistics
Matches: 105, Mismatches: 37, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
39 104 0.99
40 1 0.01
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (38 bp):
GATCATATCATCCGATCTTTTACCCCGAGCTTGAGGCA
Found at i:34028133 original size:78 final size:78
Alignment explanation
Indices: 34028051--34028239 Score: 292
Period size: 78 Copynumber: 2.4 Consensus size: 78
34028041 GGATCATAGT
* * * *
34028051 CATCCGATCTTTTACCCCGAG-CTTGAGGTAGATCACCATCAGCCAATCTCTTACCCCGA-CCTT
1 CATCCGATCTTTTACCCCGAGCCTAG-GGCAGATCACCATCAACCAATCTCTTACCCCAAGCC-T
34028114 GGGGCAGATTGTAAC
64 GGGGCAGATTGTAAC
*
34028129 CATCCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAACCAATCTCTTACCTCAAGCCTGG
1 CATCCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAACCAATCTCTTACCCCAAGCCTGG
34028194 GGCAGATTGTAAC
66 GGCAGATTGTAAC
*
34028207 CATCCGATCCTTTACCCCGAGCCTAGGGCAGAT
1 CATCCGATCTTTTACCCCGAGCCTAGGGCAGAT
34028240 TGTAGCCATC
Statistics
Matches: 103, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
78 98 0.95
79 5 0.05
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (78 bp):
CATCCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAACCAATCTCTTACCCCAAGCCTGG
GGCAGATTGTAAC
Found at i:34028230 original size:39 final size:39
Alignment explanation
Indices: 34028101--34028254 Score: 159
Period size: 39 Copynumber: 3.9 Consensus size: 39
34028091 AGCCAATCTC
* *
34028101 TTACCCCGA-CCTTGGGGCAGATTGTAACCATCCGATCTT
1 TTACCCCGAGCC-TAGGGCAGATTGTAACCATCCGATCCT
**** * * *
34028140 TTACCCCGAGCCTAGGGCAGATCACCATCAACCAAT-CT
1 TTACCCCGAGCCTAGGGCAGATTGTAACCATCCGATCCT
* * *
34028178 CTTACCTCAAGCCTGGGGCAGATTGTAACCATCCGATCCT
1 -TTACCCCGAGCCTAGGGCAGATTGTAACCATCCGATCCT
*
34028218 TTACCCCGAGCCTAGGGCAGATTGTAGCCATCCGATC
1 TTACCCCGAGCCTAGGGCAGATTGTAACCATCCGATC
34028255 TTGTAACATC
Statistics
Matches: 89, Mismatches: 23, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
38 1 0.01
39 84 0.94
40 4 0.04
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.23
Consensus pattern (39 bp):
TTACCCCGAGCCTAGGGCAGATTGTAACCATCCGATCCT
Found at i:34030104 original size:6 final size:6
Alignment explanation
Indices: 34030093--34030137 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
34030083 TGATCAAAAT
* * *
34030093 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
34030138 TATGAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:34031453 original size:78 final size:78
Alignment explanation
Indices: 34031321--34031870 Score: 607
Period size: 78 Copynumber: 7.1 Consensus size: 78
34031311 GGGTGTTACA
* * * * ** * *
34031321 GATCTTTTA-CCCGAGTCTGGGGTAGATTAGTATCAGCCAATCTCTTACCACGAGCTTGGGGCAG
1 GATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAG
*
34031385 ATTGCAGTCATCC
66 ATTGCAGCCATCC
* *
34031398 GATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGTCAATCTCTTACCTCGAGCCTGGGGCAG
1 GATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAG
*
34031463 ATTACAGCCATCC
66 ATTGCAGCCATCC
** * * * * *
34031476 GATCTTTTACCCCAAGCCTAAGGCAGATCACTATCAGCCAATCTCTTACCCTGAGCTTGAGGCAA
1 GATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAG
34031541 ATTGCAGCCATCC
66 ATTGCAGCCATCC
** * * *
34031554 GATCTTTTACCCTGAGCCTGAGGCAGATCACCATTAGCCAATCTCTTACCCCGAGCCTGGGGTAG
1 GATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAG
* *
34031619 ATTGTAGCCATTC
66 ATTGCAGCCATCC
* * * * *
34031632 GATCTTTTACCTCAAGCTTGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCTTGGGACAG
1 GATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAG
* **
34031697 ATTGCAACCATTT
66 ATTGCAGCCATCC
* * * *
34031710 GATCTTTTACCCCGATCATGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAG
1 GATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAG
*
34031775 ATTGCAGCCATTC
66 ATTGCAGCCATCC
** * * * ** * * * * **
34031788 GATCTTTTACCCTGATCATGAGGCAGATCACTGTCAACTAATCTCTTACCCCGCGACAAGGGCAG
1 GATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAG
*
34031853 ATTGCAACCATCC
66 ATTGCAGCCATCC
*
34031866 AATCT
1 GATCT
34031871 CTTAAATAAA
Statistics
Matches: 404, Mismatches: 68, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
77 9 0.02
78 395 0.98
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25
Consensus pattern (78 bp):
GATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAG
ATTGCAGCCATCC
Found at i:34031798 original size:39 final size:38
Alignment explanation
Indices: 34031360--34031799 Score: 232
Period size: 39 Copynumber: 11.3 Consensus size: 38
34031350 GTATCAGCCA
* * * *
34031360 ATCTCTTACCACGAGCTTGGGGCAGATTGCAGTCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCA-CCATTCG
* * *
34031399 ATCTTTTACCCCAAGCCTGGGGCAGA-T-CACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCACCAT---TCG
* * *
34031438 ATCTCTTACCTCGAGCCTGGGGCAGATTACAGCCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCA-CCATTCG
* * ** ** * ** *
34031477 ATCTTTTACCCCAAGCCTAAGGCAGATCACTATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGC-ACCATTCG
* * * * *
34031516 ATCTCTTACCCTGAGCTTGAGGCAAATTGCAGCCATCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCA-CCATTCG
* * * *
34031555 ATCTTTTACCCTGAGCCTGAGGCAGA-T-CACCATTAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCACCATT---CG
* *
34031594 ATCTCTTACCCCGAGCCTGGGGTAGATTGTAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCA-CCATTCG
* * * * * *
34031633 ATCTTTTACCTCAAGCTTGGGGCAGA-T-CACCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCACCAT---TCG
* * *
34031672 ATCTCTTACCCCGAGCTTGGGACAGATTGCAACCATTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGC-ACCATTCG
* * *
34031711 ATCTTTTACCCCGATCATGGGGCAGA-T-CACCA-TCAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGCACCATTC-G
*
34031747 CCAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATTCG
1 ---ATCTCTTACCCCGAGCCTGGGGCAGATTGCA-CCATTCG
*
34031789 ATCTTTTACCC
1 ATCTCTTACCC
34031800 TGATCATGAG
Statistics
Matches: 305, Mismatches: 68, Indels: 56
0.71 0.16 0.13
Matches are distributed among these distances:
35 1 0.00
36 16 0.05
37 6 0.02
38 5 0.02
39 246 0.81
40 5 0.02
41 6 0.02
42 18 0.06
43 2 0.01
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTGCACCATTCG
Found at i:34032326 original size:208 final size:207
Alignment explanation
Indices: 34031948--34032457 Score: 716
Period size: 208 Copynumber: 2.4 Consensus size: 207
34031938 TCATAAGGAA
* * *
34031948 AAGTGAAAATTCAAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGTTGAAGCGATAAAGTGG
1 AAGTGAAACTTC-AAACCCCATCTTCCTGATGAGATACAAAGAAGTGGTCGAAGCAATAAAGTGG
* *
34032013 TCATCTTCCTGACGAGATGCAGAGAAGTGAACCAAGTTCGTCTTCCTAATGAGATACAAAGAAGT
65 TCATCTTCCTGACGAGATGCAGAGAAGTGAACCAAATCCGTCTTCCTAATGAGATACAAAGAAGT
* * *
34032078 GGATTAAAACAATGAAGCGGTAATCTTTCTGATAAGATACAGAGAAGTAGACAAATTCAATGAAA
130 GGATTAAAACAATGAAGCGGTAATCTTCCTAATAAGATACAGAGAAGTACACAAATTCAATGAAA
* *
34032143 CGAAGCTCAATGT
195 CGAAACTCAATGC
* * *
34032156 GAG-GAAACTTCTAAACCCCATCTTCCTGATGAGATACAGAGAAATGAGTCGAAGCAATAAAGTG
1 AAGTGAAACTTC-AAACCCCATCTTCCTGATGAGATACAAAGAAGTG-GTCGAAGCAATAAAGTG
* *
34032220 GTCATCTTCCTGACGAGATGCAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAG
64 GTCATCTTCCTGACGAGATGCAGAGAAGTGAACCAAATCCGTCTTCCTAATGAGATACAAAGAAG
* * *
34032285 TGGATTAAAACAATGAAGCGGTCATCTTCCTAATGAGATACAGAGAAGTACACCAATTCAATGAA
129 TGGATTAAAACAATGAAGCGGTAATCTTCCTAATAAGATACAGAGAAGTACACAAATTCAATGAA
* *
34032350 GCGAAACTTAATGC
194 ACGAAACTCAATGC
* * * * *
34032364 AAGTGAAACTTCAAACCCCTATCTTCCTAATGAGATATAAAGAAGTGGGTCGAAGTAATGAAGCG
1 AAGTGAAACTTCAAACCCC-ATCTTCCTGATGAGATACAAAGAAGT-GGTCGAAGCAATAAAGTG
* **
34032429 GTCATCTTCCTGATGAGATATAGAGAAGT
64 GTCATCTTCCTGACGAGATGCAGAGAAGT
34032458 AGACCAAGAG
Statistics
Matches: 266, Mismatches: 32, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
207 39 0.15
208 156 0.59
209 70 0.26
210 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (207 bp):
AAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGTCGAAGCAATAAAGTGGT
CATCTTCCTGACGAGATGCAGAGAAGTGAACCAAATCCGTCTTCCTAATGAGATACAAAGAAGTG
GATTAAAACAATGAAGCGGTAATCTTCCTAATAAGATACAGAGAAGTACACAAATTCAATGAAAC
GAAACTCAATGC
Found at i:34032340 original size:85 final size:85
Alignment explanation
Indices: 34032176--34032333 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 85
34032166 CTAAACCCCA
* * * * *
34032176 TCTTCCTGATGAGATACAGAGAAATGAGTCGAAGCAATAAAGTGGTCATCTTCCTGACGAGATGC
1 TCTTCCTGATGAGATACAGAGAAATGAGTCAAAACAATAAAGCGGTCATCTTCCTAACGAGATAC
34032241 AGAGAAGTGAACCAAATCCG
66 AGAGAAGTGAACCAAATCCG
* * * *
34032261 TCTTCCTGATGAGATACAGAGAAGTG-GATTAAAACAATGAAGCGGTCATCTTCCTAATGAGATA
1 TCTTCCTGATGAGATACAGAGAAATGAG-TCAAAACAATAAAGCGGTCATCTTCCTAACGAGATA
34032325 CAGAGAAGT
65 CAGAGAAGT
34032334 ACACCAATTC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 1 0.02
85 62 0.98
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAATGAGTCAAAACAATAAAGCGGTCATCTTCCTAACGAGATAC
AGAGAAGTGAACCAAATCCG
Found at i:34032347 original size:48 final size:48
Alignment explanation
Indices: 34032261--34032352 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
34032251 ACCAAATCCG
* ** **
34032261 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAAGCGGTCA
1 TCTTCCTAATGAGATACAGAGAAGTACACCAAAACAATGAAGCGGTCA
**
34032309 TCTTCCTAATGAGATACAGAGAAGTACACCAATTCAATGAAGCG
1 TCTTCCTAATGAGATACAGAGAAGTACACCAAAACAATGAAGCG
34032353 AAACTTAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (48 bp):
TCTTCCTAATGAGATACAGAGAAGTACACCAAAACAATGAAGCGGTCA
Found at i:34032919 original size:16 final size:16
Alignment explanation
Indices: 34032898--34032934 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
34032888 TTTAAAATGT
34032898 CCAATTACAGTTAAGC
1 CCAATTACAGTTAAGC
*
34032914 CCAATTATAGTTAAGC
1 CCAATTACAGTTAAGC
34032930 CCAAT
1 CCAAT
34032935 AAGCCCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (16 bp):
CCAATTACAGTTAAGC
Found at i:34034357 original size:29 final size:30
Alignment explanation
Indices: 34034301--34034810 Score: 388
Period size: 30 Copynumber: 17.3 Consensus size: 30
34034291 TCTAATAGGT
* * * *
34034301 CCCT-AAACTTTTCAAAAATCATATTTTGA
1 CCCTCAAACTTCTCAAAAATTACATTTTAA
** * *
34034330 CCCTCAAACTTCTCAAAAATTTTATTTGAC
1 CCCTCAAACTTCTCAAAAATTACATTTTAA
* * *
34034360 CCCT-AAAATTTTCGAAAATTACATTTTAA
1 CCCTCAAACTTCTCAAAAATTACATTTTAA
* * * *
34034389 CCC-CTAAATTTTTCCAAAATTACATTTTTA
1 CCCTC-AAACTTCTCAAAAATTACATTTTAA
* *
34034419 CCC-CTAAACTTCTCCAAAATTATATTTTAA
1 CCCTC-AAACTTCTCAAAAATTACATTTTAA
**
34034449 CCC-CTAAACTTCTTC-AAAATTATGTTTTAA
1 CCCTC-AAACTTC-TCAAAAATTACATTTTAA
* * * * * *
34034479 CTCTAAAACTTTTCCAAAATTATATTTTGA
1 CCCTCAAACTTCTCAAAAATTACATTTTAA
*
34034509 CCCTTAAACTTCTCAAAAA-TACATTTTAA
1 CCCTCAAACTTCTCAAAAATTACATTTTAA
* *
34034538 CCCT-AAACTTCTCAAAAATCACATTTTGA
1 CCCTCAAACTTCTCAAAAATTACATTTTAA
* * *
34034567 -CCTCGAACTT-TCCAAAAATCACATTTTGA
1 CCCTCAAACTTCT-CAAAAATTACATTTTAA
* * * *
34034596 -TCTCGAACTTCTCAAAAATCACATCTTAA
1 CCCTCAAACTTCTCAAAAATTACATTTTAA
*
34034625 CCCT-AAACTTCTCAAAAATCACATTTTAA
1 CCCTCAAACTTCTCAAAAATTACATTTTAA
* * *
34034654 CCCTCAAACTT-TCCAAAAATCATATTTTGA
1 CCCTCAAACTTCT-CAAAAATTACATTTTAA
* * *
34034684 -CCTCAAATTTCTCAAAAATCACATTTTGA
1 CCCTCAAACTTCTCAAAAATTACATTTTAA
* * *
34034713 -TCTCGAACTT-TCCAAAAATAACATTTTAA
1 CCCTCAAACTTCT-CAAAAATTACATTTTAA
* * *
34034742 CCCCCGAACTTCTCAAAAATCACATTTTAA
1 CCCTCAAACTTCTCAAAAATTACATTTTAA
* *
34034772 CCCTTAAACTTCTCAAAAATTACATTTTGA
1 CCCTCAAACTTCTCAAAAATTACATTTTAA
34034802 CCCT-AAACT
1 CCCTCAAACT
34034811 CTCCAAACTA
Statistics
Matches: 406, Mismatches: 58, Indels: 34
0.82 0.12 0.07
Matches are distributed among these distances:
28 19 0.05
29 173 0.43
30 211 0.52
31 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
CCCTCAAACTTCTCAAAAATTACATTTTAA
Found at i:34034492 original size:90 final size:90
Alignment explanation
Indices: 34034301--34034810 Score: 345
Period size: 88 Copynumber: 5.8 Consensus size: 90
34034291 TCTAATAGGT
* * * * *
34034301 CCCTAAACTTTTCAAAAATCATATTTTGA-CCCTCAAACTTCTCAAAAATTTTA-TTTGACCCCT
1 CCCTAAACTTTTCCAAAATTATATTTTGACCCCT-AAACTTCTCCAAAATTATATTTTAACCCCT
*
34034364 AAAATT-TTCGAAAATTACATTTTAAC
65 AAACTTCTTC-AAAATTACATTTTAAC
* * *
34034390 CCCTAAATTTTTCCAAAATTACATTTTTACCCCTAAACTTCTCCAAAATTATATTTTAACCCCTA
1 CCCTAAACTTTTCCAAAATTATATTTTGACCCCTAAACTTCTCCAAAATTATATTTTAACCCCTA
**
34034455 AACTTCTTCAAAATTATGTTTTAA-
66 AACTTCTTCAAAATTACATTTTAAC
* * * *
34034479 CTCTAAAACTTTTCCAAAATTATATTTTGACCCTTAAACTTCT-CAAAAATACATTTTAA-CCCT
1 CCCT-AAACTTTTCCAAAATTATATTTTGACCCCTAAACTTCTCCAAAATTATATTTTAACCCCT
* *
34034542 AAACTTC-TCAAAAATCACATTTTGAC
65 AAACTTCTTC-AAAATTACATTTTAAC
* * * * * * * * * * *
34034568 CTC-GAAC-TTTCCAAAAATCACATTTTGATCTC-GAACTTCTCAAAAATCACATCTTAA-CCCT
1 CCCTAAACTTTTCC-AAAATTATATTTTGACCCCTAAACTTCTCCAAAATTATATTTTAACCCCT
*
34034629 AAACTTC-TCAAAAATCACATTTTAA-
65 AAACTTCTTC-AAAATTACATTTTAAC
* * * * * * * * *
34034654 CCCTCAAAC-TTTCCAAAAATCATATTTTGACCTC-AAATTTCTCAAAAATCACATTTTGATCTC
1 CCCT-AAACTTTTCC-AAAATTATATTTTGACCCCTAAACTTCTCCAAAATTATATTTTAACCCC
* * *
34034717 -GAACTT-TCCAAAAATAACATTTTAAC
64 TAAACTTCTTC-AAAATTACATTTTAAC
** * * * * * * * * *
34034743 CCCCGAACTTCTCAAAAATCACATTTTAACCCTTAAACTTCTCAAAAATTACATTTTGA-CCCTA
1 CCCTAAACTTTTCCAAAATTATATTTTGACCCCTAAACTTCTCCAAAATTATATTTTAACCCCTA
34034807 AACT
66 AACT
34034811 CTCCAAACTA
Statistics
Matches: 347, Mismatches: 58, Indels: 32
0.79 0.13 0.07
Matches are distributed among these distances:
86 14 0.04
87 59 0.17
88 110 0.32
89 96 0.28
90 65 0.19
91 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (90 bp):
CCCTAAACTTTTCCAAAATTATATTTTGACCCCTAAACTTCTCCAAAATTATATTTTAACCCCTA
AACTTCTTCAAAATTACATTTTAAC
Found at i:34034696 original size:59 final size:60
Alignment explanation
Indices: 34034301--34034810 Score: 367
Period size: 59 Copynumber: 8.7 Consensus size: 60
34034291 TCTAATAGGT
* * *** * *
34034301 CCCT-AAACTTTTCAAAAATCATATTTTGACC-CTCAAACTTCTCAAAAATTTTATTTGAC
1 CCCTCAAACTTTCCAAAAATCACATTTTGACCTCT-AAACTTCTCAAAAATCACATTTTAA
* * * * * * * * * * *
34034360 CCCT-AAAATTTTCGAAAATTACATTTTAACCCCTAAATTTTTCCAAAATTACATTTTTA
1 CCCTCAAACTTTCCAAAAATCACATTTTGACCTCTAAACTTCTCAAAAATCACATTTTAA
* * * * * **
34034419 CCC-CTAAACTTCTCC-AAAATTATATTTTAACCCCTAAACTTCTTC-AAAATTATGTTTTAA
1 CCCTC-AAACTT-TCCAAAAATCACATTTTGACCTCTAAACTTC-TCAAAAATCACATTTTAA
* * * *
34034479 CTCTAAAACTTTTCC-AAAATTATATTTTGACC-CTTAAACTTCTCAAAAAT-ACATTTTAA
1 CCCTCAAAC-TTTCCAAAAATCACATTTTGACCTC-TAAACTTCTCAAAAATCACATTTTAA
* *
34034538 CCCT-AAAC-TTCTCAAAAATCACATTTTGACCTC-GAACTT-TCCAAAAATCACATTTTGA
1 CCCTCAAACTTTC-CAAAAATCACATTTTGACCTCTAAACTTCT-CAAAAATCACATTTTAA
* * * *
34034596 -TCTCGAAC-TTCTCAAAAATCACATCTTAACC-CTAAACTTCTCAAAAATCACATTTTAA
1 CCCTCAAACTTTC-CAAAAATCACATTTTGACCTCTAAACTTCTCAAAAATCACATTTTAA
* * *
34034654 CCCTCAAACTTTCCAAAAATCATATTTTGACCTC-AAATTTCTCAAAAATCACATTTTGA
1 CCCTCAAACTTTCCAAAAATCACATTTTGACCTCTAAACTTCTCAAAAATCACATTTTAA
* * * * * **
34034713 -TCTCGAACTTTCCAAAAATAACATTTTAACCCCCGAACTTCTCAAAAATCACATTTTAA
1 CCCTCAAACTTTCCAAAAATCACATTTTGACCTCTAAACTTCTCAAAAATCACATTTTAA
* *
34034772 CCCTTAAAC-TTCTCAAAAATTACATTTTGACC-CTAAACT
1 CCCTCAAACTTTC-CAAAAATCACATTTTGACCTCTAAACT
34034811 CTCCAAACTA
Statistics
Matches: 368, Mismatches: 60, Indels: 46
0.78 0.13 0.10
Matches are distributed among these distances:
56 4 0.01
57 16 0.04
58 99 0.27
59 136 0.37
60 107 0.29
61 6 0.02
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (60 bp):
CCCTCAAACTTTCCAAAAATCACATTTTGACCTCTAAACTTCTCAAAAATCACATTTTAA
Found at i:34036561 original size:84 final size:84
Alignment explanation
Indices: 34036444--34036598 Score: 211
Period size: 84 Copynumber: 1.8 Consensus size: 84
34036434 GTCTTTGAAA
** * * * *
34036444 AAAGATAGCCACAAAGGTGTCATCAAACAAAGATAGCCACAAAGGCGTCCTTAAGCAAATATAGC
1 AAAGATAGCCACAAAGGCATCATCAAACAAAGATAACCACAAAGGCATCCTTAAGCAAAGATAAC
34036509 CATAAAGGCGTCCTCAAGC
66 CATAAAGGCGTCCTCAAGC
* * * * *
34036528 AAAGATAGCTACAAAGGCATCCTTAAGCAAAGATAACCATAAAGGCATCCTTAAGCAAAGATAAC
1 AAAGATAGCCACAAAGGCATCATCAAACAAAGATAACCACAAAGGCATCCTTAAGCAAAGATAAC
34036593 CATAAA
66 CATAAA
34036599 AACCATCAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 60 1.00
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (84 bp):
AAAGATAGCCACAAAGGCATCATCAAACAAAGATAACCACAAAGGCATCCTTAAGCAAAGATAAC
CATAAAGGCGTCCTCAAGC
Found at i:34036574 original size:28 final size:28
Alignment explanation
Indices: 34036418--34036598 Score: 175
Period size: 28 Copynumber: 6.5 Consensus size: 28
34036408 CTTTTGACAT
* * * *
34036418 AGATAGCCATAGAGGCGTCTTTGAA-AAA
1 AGATAGCCATAAAGGCATCCTT-AAGCAA
* ** * * *
34036446 AGATAGCCACAAAGGTGTCATCAAACAA
1 AGATAGCCATAAAGGCATCCTTAAGCAA
* *
34036474 AGATAGCCACAAAGGCGTCCTTAAGCAA
1 AGATAGCCATAAAGGCATCCTTAAGCAA
* * *
34036502 ATATAGCCATAAAGGCGTCCTCAAGCAA
1 AGATAGCCATAAAGGCATCCTTAAGCAA
* *
34036530 AGATAGCTACAAAGGCATCCTTAAGCAA
1 AGATAGCCATAAAGGCATCCTTAAGCAA
*
34036558 AGATAACCATAAAGGCATCCTTAAGCAA
1 AGATAGCCATAAAGGCATCCTTAAGCAA
*
34036586 AGATAACCATAAA
1 AGATAGCCATAAA
34036599 AACCATCAAT
Statistics
Matches: 131, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
27 2 0.02
28 129 0.98
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (28 bp):
AGATAGCCATAAAGGCATCCTTAAGCAA
Found at i:34038062 original size:22 final size:23
Alignment explanation
Indices: 34038034--34038077 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
34038024 TCCTCTACAT
34038034 CACCTTGATATT-C-CCCTTATTC
1 CACCTTG-TATTCCTCCCTTATTC
34038056 CACCTTGTATTCCTCCCTTATT
1 CACCTTGTATTCCTCCCTTATT
34038078 ATACTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 8 0.40
ACGTcount: A:0.16, C:0.36, G:0.05, T:0.43
Consensus pattern (23 bp):
CACCTTGTATTCCTCCCTTATTC
Found at i:34043596 original size:26 final size:26
Alignment explanation
Indices: 34043548--34043598 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
34043538 TTGTTATTAA
* * * *
34043548 ATTTTAATAAGATTATTATTAAATAT
1 ATTTTAATAAAAATAATAATAAATAT
34043574 ATTTTAATAAAAATAATAATAAATA
1 ATTTTAATAAAAATAATAATAAATA
34043599 CTTTAATCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTTTAATAAAAATAATAATAAATAT
Found at i:34043624 original size:61 final size:58
Alignment explanation
Indices: 34043559--34043693 Score: 166
Period size: 61 Copynumber: 2.3 Consensus size: 58
34043549 TTTTAATAAG
* * *
34043559 ATTATTATTAAATATATTTTAATAAAAATAATAATAAATACTTTAATCATATT-TTAACATA
1 ATTATTATTAAATATATTTTAAT-AAAATAAT-AT--ATAATTTAATAACATTCTTAACATA
* * *
34043620 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATATATTTTAATAAAATAATATATAATTTAATAACATTCTTAACATA
34043678 ATTATTATTAAA-ATAT
1 ATTATTATTAAATATAT
34043694 GAATTAAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 15 0.23
58 19 0.29
59 2 0.03
60 8 0.12
61 21 0.32
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAATATATTTTAATAAAATAATATATAATTTAATAACATTCTTAACATA
Found at i:34043761 original size:21 final size:23
Alignment explanation
Indices: 34043696--34043760 Score: 105
Period size: 23 Copynumber: 2.8 Consensus size: 23
34043686 TAAAATATGA
*
34043696 ATTAAAAAATTATAATATATAAT
1 ATTAAAAAATAATAATATATAAT
34043719 ATTAAAAAATAATAATATATAAT
1 ATTAAAAAATAATAATATATAAT
34043742 ATTATAAAAATAAT-ATATA
1 ATTA-AAAAATAATAATATA
34043761 ACCTACATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 31 0.77
24 9 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTAAAAAATAATAATATATAAT
Found at i:34050078 original size:23 final size:24
Alignment explanation
Indices: 34050039--34050084 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
34050029 GTGAAAAAGA
*
34050039 ACAAAACAAAAATGAGT-AGAAAT
1 ACAAAACAAAAAAGAGTAAGAAAT
34050062 ACAAAA-AAGAAAAGAGTAAGAAA
1 ACAAAACAA-AAAAGAGTAAGAAA
34050085 AAGTGTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 13 0.65
24 5 0.25
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.09
Consensus pattern (24 bp):
ACAAAACAAAAAAGAGTAAGAAAT
Found at i:34057102 original size:9 final size:9
Alignment explanation
Indices: 34057090--34057167 Score: 50
Period size: 9 Copynumber: 8.7 Consensus size: 9
34057080 AAATTACCCA
34057090 AATTAATCG
1 AATTAATCG
* *
34057099 AATTACTGG
1 AATTAATCG
**
34057108 AATTACCCG
1 AATTAATCG
*
34057117 AATTACTCG
1 AATTAATCG
*
34057126 AATTAACCG
1 AATTAATCG
*
34057135 AATTAA-CAA
1 AATTAATC-G
*
34057144 AATTAATTG
1 AATTAATCG
**
34057153 AATTACCCG
1 AATTAATCG
34057162 AATTAA
1 AATTAA
34057168 AGTATTAAAT
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
8 1 0.02
9 52 0.98
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTAATCG
Found at i:34057104 original size:18 final size:18
Alignment explanation
Indices: 34057081--34057167 Score: 75
Period size: 18 Copynumber: 4.8 Consensus size: 18
34057071 TTCGCATGAA
* *
34057081 AATTACCCAAATTAATCG
1 AATTACCCGAATTAACCG
** *
34057099 AATTACTGGAATTACCCG
1 AATTACCCGAATTAACCG
*
34057117 AATTACTCGAATTAACCG
1 AATTACCCGAATTAACCG
* ** **
34057135 AATTAACAAAATTAATTG
1 AATTACCCGAATTAACCG
34057153 AATTACCCGAATTAA
1 AATTACCCGAATTAA
34057168 AGTATTAAAT
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:34057137 original size:27 final size:27
Alignment explanation
Indices: 34057081--34057166 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
34057071 TTCGCATGAA
*
34057081 AATTACCCAAATTAATCGAATT-ACTGG
1 AATTACCCAAATTAATCGAATTAAC-CG
* *
34057108 AATTACCCGAATTACTCGAATTAACCG
1 AATTACCCAAATTAATCGAATTAACCG
* * * *
34057135 AATTAACAAAATTAATTGAATTACCCG
1 AATTACCCAAATTAATCGAATTAACCG
34057162 AATTA
1 AATTA
34057167 AAGTATTAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 47 0.96
28 2 0.04
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (27 bp):
AATTACCCAAATTAATCGAATTAACCG
Found at i:34061033 original size:22 final size:22
Alignment explanation
Indices: 34061006--34061052 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
34060996 TTCAGTTATC
34061006 CGGCCGATTAATCGACTTCGGT
1 CGGCCGATTAATCGACTTCGGT
34061028 CGGCCGATTAATCGACTTCGGT
1 CGGCCGATTAATCGACTTCGGT
34061050 CGG
1 CGG
34061053 TTAACCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.26
Consensus pattern (22 bp):
CGGCCGATTAATCGACTTCGGT
Found at i:34078052 original size:28 final size:26
Alignment explanation
Indices: 34077983--34078039 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
34077973 TGTCCACTTC
* *
34077983 TCCCAAATTAGTACTTATGATTTTTTG
1 TCCCAAATTGGTAC-CATGATTTTTTG
34078010 TCCCAAATTGGTACCATGATTTTTT-
1 TCCCAAATTGGTACCATGATTTTTTG
34078035 TCCCA
1 TCCCA
34078040 CTATATTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 5 0.18
26 10 0.36
27 13 0.46
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.44
Consensus pattern (26 bp):
TCCCAAATTGGTACCATGATTTTTTG
Found at i:34078360 original size:36 final size:35
Alignment explanation
Indices: 34078317--34078439 Score: 92
Period size: 36 Copynumber: 3.5 Consensus size: 35
34078307 CTACACTAAA
34078317 TCTTTCTTCTGTCAAAAACCCCCAAAACTTCTTCTT
1 TCTTTCTTCTGTCAAAAACCCCCAAAA-TTCTTCTT
* * *
34078353 TCTTTCTTCTATC--AACCCCCCAAAATT-TTCCTC
1 TCTTTCTTCTGTCAAAAACCCCCAAAATTCTT-CTT
* * ** *
34078386 ACTTTCTCATCAT-CCAATCACCACCAAAATTTCTTCTT
1 TCTTTCT--TC-TGTCAAAAACCCCCAAAA-TTCTTCTT
34078424 TCTTTCTTCTGTCAAA
1 TCTTTCTTCTGTCAAA
34078440 TTTTAAAATT
Statistics
Matches: 65, Mismatches: 13, Indels: 18
0.68 0.14 0.19
Matches are distributed among these distances:
32 2 0.03
33 10 0.15
34 11 0.17
35 4 0.06
36 18 0.28
37 8 0.12
38 10 0.15
39 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.02, T:0.40
Consensus pattern (35 bp):
TCTTTCTTCTGTCAAAAACCCCCAAAATTCTTCTT
Found at i:34078455 original size:135 final size:134
Alignment explanation
Indices: 34078218--34078461 Score: 350
Period size: 135 Copynumber: 1.8 Consensus size: 134
34078208 TCTACGTTCA
*
34078218 TCTTTTTCTATCAAACCCCCTTCAAAATTCCCTCATTTTCTCTCCATCCAATCACCACCAAAATT
1 TCTTTTTCTATCAAACCCCC-TCAAAATTCCCTCACTTTCTCTCCATCCAATCACCACCAAAATT
* *
34078283 TCTTTTTCTTTCTTATGTCAAATTCTACACTAAATCTTTCTTCTGTCAAAAACCCCCAAAACTTC
65 TCTTTTTCTTTCTTATGTCAAATTCTAAAATAAATCTTTCTTCTGTCAAAAACCCCCAAAACTTC
34078348 TTCTT
130 TTCTT
*
34078353 TCTTTCTTCTATC-AACCCCC-CAAAATTTTCCTCACTTTCTCAT-CATCCAATCACCACCAAAA
1 TCTTT-TTCTATCAAACCCCCTCAAAA-TTCCCTCACTTTCTC-TCCATCCAATCACCACCAAAA
* * **
34078415 TTTCTTCTTTCTTTCTTCTGTCAAATTTTAAAATTCATCTTTCTTCT
63 TTTCTT-TTTCTTTCTTATGTCAAATTCTAAAATAAATCTTTCTTCT
34078462 TGTTTCTTCT
Statistics
Matches: 97, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
133 5 0.05
134 38 0.39
135 47 0.48
136 7 0.07
ACGTcount: A:0.25, C:0.32, G:0.01, T:0.42
Consensus pattern (134 bp):
TCTTTTTCTATCAAACCCCCTCAAAATTCCCTCACTTTCTCTCCATCCAATCACCACCAAAATTT
CTTTTTCTTTCTTATGTCAAATTCTAAAATAAATCTTTCTTCTGTCAAAAACCCCCAAAACTTCT
TCTT
Found at i:34080991 original size:128 final size:129
Alignment explanation
Indices: 34080763--34081076 Score: 522
Period size: 128 Copynumber: 2.4 Consensus size: 129
34080753 GACCTAATCA
* * * * *
34080763 AATCTTTTTACGCGAATTGAGATGACAAACCCAGCACCTCGACCCGATTACTCAATTTGAATAAT
1 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTTGAATAAG
** *
34080828 TTGTTAACTTATTTTTCAAGGTAGCCTGGTTAGTGGAGTGTAACAAGCTTTGGTTCGTCACTC-
66 TTGTTAACTTATTTTTCAAGGTAGCCCAGTTAGTGGAGTGTAACAAGATTTGGTTCGTCACTCG
*
34080891 AATCTTTTTACGCGAATGGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTTGAATAAG
1 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTTGAATAAG
*
34080956 TTGTTAACTTATTTTTCAAGGTAGCCCAGTTAGTGGAGTGTAACAAGATTTGGTTTGTCACTCG
66 TTGTTAACTTATTTTTCAAGGTAGCCCAGTTAGTGGAGTGTAACAAGATTTGGTTCGTCACTCG
*
34081020 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCAGTTACTCAATT
1 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATT
34081077 CGGTCACATT
Statistics
Matches: 173, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
128 118 0.68
129 55 0.32
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (129 bp):
AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTTGAATAAG
TTGTTAACTTATTTTTCAAGGTAGCCCAGTTAGTGGAGTGTAACAAGATTTGGTTCGTCACTCG
Found at i:34089941 original size:16 final size:17
Alignment explanation
Indices: 34089906--34089944 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
34089896 GGGTTTAGAC
*
34089906 ATAAAACATCAAACTAAA
1 ATAAAACA-CAAAATAAA
34089924 ATAAAACA-AAAATAAA
1 ATAAAACACAAAATAAA
34089940 ATAAA
1 ATAAA
34089945 TTAAGTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
18 8 0.40
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.15
Consensus pattern (17 bp):
ATAAAACACAAAATAAA
Found at i:34091338 original size:6 final size:6
Alignment explanation
Indices: 34091327--34091369 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
34091317 AAGCAACCCT
*
34091327 GAAAAA GAAAAA GAAAAA GACAAATA CAAAAA G-AAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GA-AAA-A GAAAAA GAAAAA GAAAAA
34091370 AAAGAAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.16
6 19 0.59
7 6 0.19
8 2 0.06
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:34092531 original size:11 final size:11
Alignment explanation
Indices: 34092515--34092539 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34092505 AATATGCCAC
34092515 AAACTAAATCA
1 AAACTAAATCA
34092526 AAACTAAATCA
1 AAACTAAATCA
34092537 AAA
1 AAA
34092540 TAACCCACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (11 bp):
AAACTAAATCA
Found at i:34098384 original size:24 final size:24
Alignment explanation
Indices: 34098352--34098458 Score: 135
Period size: 24 Copynumber: 4.5 Consensus size: 24
34098342 TTAAACTCTG
* * *
34098352 TCTGTGCTCATAAGAGCTAAACAT
1 TCTGGGCTCGTAAGAGCTAATCAT
34098376 TCTGGGCTCGTAAGAGCTAATCAT
1 TCTGGGCTCGTAAGAGCTAATCAT
*
34098400 TGT-GGCTTCGTAAGAGCTAATCAT
1 TCTGGGC-TCGTAAGAGCTAATCAT
* *
34098424 TGTGGGCTCGTAATAGCTAATCAT
1 TCTGGGCTCGTAAGAGCTAATCAT
*
34098448 TCTAGGCTCGT
1 TCTGGGCTCGT
34098459 GTTGGCTAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
23 3 0.04
24 68 0.92
25 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAATCAT
Found at i:34102881 original size:23 final size:24
Alignment explanation
Indices: 34102844--34102901 Score: 109
Period size: 23 Copynumber: 2.5 Consensus size: 24
34102834 TTAAACTCTG
34102844 TCTGGGCTCGTAAGAGCTAATCAT
1 TCTGGGCTCGTAAGAGCTAATCAT
34102868 TCTGGGC-CGTAAGAGCTAATCAT
1 TCTGGGCTCGTAAGAGCTAATCAT
34102891 TCTGGGCTCGT
1 TCTGGGCTCGT
34102902 GTTGGCTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 23 0.70
24 10 0.30
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAATCAT
Found at i:34111536 original size:17 final size:18
Alignment explanation
Indices: 34111498--34111539 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
34111488 ATAGGTCAAT
* *
34111498 TCGGGTTCGGTCAATGGG
1 TCGGGTTCGATCAATCGG
34111516 TCGGGTTCGATCAA-CGG
1 TCGGGTTCGATCAATCGG
34111533 TCGGGTT
1 TCGGGTT
34111540 AGGTTCAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.12, C:0.19, G:0.40, T:0.29
Consensus pattern (18 bp):
TCGGGTTCGATCAATCGG
Found at i:34114575 original size:21 final size:21
Alignment explanation
Indices: 34114549--34114612 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
34114539 TACCTTTTTA
*
34114549 AAGTTAAAAGTCAAAACCATT
1 AAGTTAAAAGGCAAAACCATT
*
34114570 AAGTTAAAAGGCAAAATCATT
1 AAGTTAAAAGGCAAAACCATT
34114591 AAGTTAAAAGGCAAAACCATT
1 AAGTTAAAAGGCAAAACCATT
34114612 A
1 A
34114613 TATTGTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.22
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACCATT
Found at i:34127215 original size:13 final size:14
Alignment explanation
Indices: 34127190--34127219 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
34127180 TGAAACCTAA
34127190 AGAAAAGAAAAAAG
1 AGAAAAGAAAAAAG
34127204 AGAAAA-AAAAAAG
1 AGAAAAGAAAAAAG
34127217 AGA
1 AGA
34127220 GGTCCAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AGAAAAGAAAAAAG
Found at i:34128170 original size:42 final size:42
Alignment explanation
Indices: 34128110--34128612 Score: 489
Period size: 42 Copynumber: 12.1 Consensus size: 42
34128100 TGAAATTACA
* *
34128110 GAAGACACCATCCAATCTCTTACCCCAACCACGGGGCAAATT
1 GAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATT
* * * * *
34128152 GAAGATACCATTCGATCTCTTACCCTAACCATGAGGCAGATT
1 GAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATT
* * * *
34128194 AAAGACACCTTCCAATCTCTTACCCTAATCATGGGGCAGATT
1 GAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATT
* * * *
34128236 GAAGACACCATCCAATCTCATACCCTAACCATGAGGCAAATT
1 GAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATT
* * * *
34128278 GAAGATACCATCCAATCTCTTACCCTAACCACGGGGTAGATT
1 GAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATT
* * * ** * *
34128320 GAAGACACCATTCGACCTCTTACCCCAACCATGAAGCGGGTT
1 GAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATT
* * *
34128362 GAAGACACCATCCAATCTCTTACTCCAACCACGGAGCAGATT
1 GAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATT
* * * * *
34128404 AAAGACACCATTCGATCTCTTACCCCAACCACGGGGTAGATT
1 GAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATT
*
34128446 GAAGACACCATCCGATCTCTTACCCCAACCATGGGGCAGATT
1 GAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATT
* *** * *
34128488 GAAG--ACCTTTTGATCTTTTACCCCAACCATGAGGCAGATT
1 GAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATT
* * * *
34128528 GAAG--ATCGTCCAATCTCTTACCCCGACCATGGGGCATATT
1 GAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATT
* * * * * *
34128568 G-AG-GACCATCCGATCTTTTACCCTAACTA-GAGGACAGATT
1 GAAGACACCATCCAATCTCTTACCCCAACCATG-GGGCAGATT
34128608 GAAGA
1 GAAGA
34128613 TCATCCGTTC
Statistics
Matches: 379, Mismatches: 78, Indels: 8
0.82 0.17 0.02
Matches are distributed among these distances:
39 3 0.01
40 89 0.23
41 2 0.01
42 285 0.75
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (42 bp):
GAAGACACCATCCAATCTCTTACCCCAACCATGGGGCAGATT
Found at i:34128254 original size:84 final size:84
Alignment explanation
Indices: 34128110--34128612 Score: 579
Period size: 84 Copynumber: 6.1 Consensus size: 84
34128100 TGAAATTACA
* *
34128110 GAAGACACCATCCAATCTCTTACCCCAACCACGGGGCAAATTGAAGATACCATTCGATCTCTTAC
1 GAAGACACCATCCAATCTCTTACCCCAACCACGGGGCAGATTGAAGACACCATTCGATCTCTTAC
*
34128175 CCTAACCATGAGGCAGATT
66 CCCAACCATGAGGCAGATT
* * * * * * * *
34128194 AAAGACACCTTCCAATCTCTTACCCTAATCATGGGGCAGATTGAAGACACCATCCAATCTCATAC
1 GAAGACACCATCCAATCTCTTACCCCAACCACGGGGCAGATTGAAGACACCATTCGATCTCTTAC
* *
34128259 CCTAACCATGAGGCAAATT
66 CCCAACCATGAGGCAGATT
* * * *
34128278 GAAGATACCATCCAATCTCTTACCCTAACCACGGGGTAGATTGAAGACACCATTCGACCTCTTAC
1 GAAGACACCATCCAATCTCTTACCCCAACCACGGGGCAGATTGAAGACACCATTCGATCTCTTAC
* * *
34128343 CCCAACCATGAAGCGGGTT
66 CCCAACCATGAGGCAGATT
* * *
34128362 GAAGACACCATCCAATCTCTTACTCCAACCACGGAGCAGATTAAAGACACCATTCGATCTCTTAC
1 GAAGACACCATCCAATCTCTTACCCCAACCACGGGGCAGATTGAAGACACCATTCGATCTCTTAC
* * *
34128427 CCCAACCACGGGGTAGATT
66 CCCAACCATGAGGCAGATT
* * * * *
34128446 GAAGACACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAG--ACCTTTTGATCTTTTAC
1 GAAGACACCATCCAATCTCTTACCCCAACCACGGGGCAGATTGAAGACACCATTCGATCTCTTAC
34128509 CCCAACCATGAGGCAGATT
66 CCCAACCATGAGGCAGATT
* * * * * * * *
34128528 GAAG--ATCGTCCAATCTCTTACCCCGACCATGGGGCATATTG-AG-GACCATCCGATCTTTTAC
1 GAAGACACCATCCAATCTCTTACCCCAACCACGGGGCAGATTGAAGACACCATTCGATCTCTTAC
* *
34128589 CCTAACTA-GAGGACAGATT
66 CCCAACCATGAGG-CAGATT
34128608 GAAGA
1 GAAGA
34128613 TCATCCGTTC
Statistics
Matches: 356, Mismatches: 60, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
79 6 0.02
80 62 0.17
82 34 0.10
84 254 0.71
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (84 bp):
GAAGACACCATCCAATCTCTTACCCCAACCACGGGGCAGATTGAAGACACCATTCGATCTCTTAC
CCCAACCATGAGGCAGATT
Found at i:34128618 original size:40 final size:41
Alignment explanation
Indices: 34128116--34128730 Score: 373
Period size: 42 Copynumber: 15.0 Consensus size: 41
34128106 TACAGAAGAC
* * * *
34128116 ACCATCCAATCTCTTACCCCAACCACG-GGGCAAATTGAAG
1 ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* * * *
34128156 ATACCATTCGATCTCTTACCCTAACCATGA-GGCAGATTAAAG
1 --ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* * * * *
34128198 ACACCTTCCAATCTCTTACCCTAATCATG-GGGCAGATTGAAG
1 --ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* ** * *
34128240 ACACCATCCAATCTCATACCCTAACCATGA-GGCAAATTGAAG
1 --ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* * * * *
34128282 ATACCATCCAATCTCTTACCCTAACCACG-GGGTAGATTGAAG
1 --ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* * * * * *
34128324 ACACCATTCGACCTCTTACCCCAACCATGA-AGCGGGTTGAAG
1 --ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* * * * * *
34128366 ACACCATCCAATCTCTTACTCCAACCACG-GAGCAGATTAAAG
1 --ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* * * *
34128408 ACACCATTCGATCTCTTACCCCAACCACG-GGGTAGATTGAAG
1 --ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
*
34128450 ACACCATCCGATCTCTTACCCCAACCATG-GGGCAGATTGAAG
1 --ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* **
34128492 ACCTTTTGATCTTTTACCCCAACCATGA-GGCAGATTGAAG
1 ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* * * * * * *
34128532 ATCGTCCAATCTCTTACCCCGACCATG-GGGCATATTGAGG
1 ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* * *
34128572 ACCATCCGATCTTTTACCCTAACTA-GAGGACAGATTGAAG
1 ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* * * * *
34128612 ATCATCCGTTCTTTTACCCTAACTA-GAGGGTAGATTGAAG
1 ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* * * *
34128652 ACCACCCGATCTTTTACCCTAACCA-GAGGGTAAATTGAAG
1 ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
* * *
34128692 -CCATCC-AGTCTTTTACCCCATCCA-GAAGGTAGATTGAAG
1 ACCATCCGA-TCTTTTACCCCAACCATGAGGGCAGATTGAAG
34128731 TATGAAAGCG
Statistics
Matches: 478, Mismatches: 85, Indels: 23
0.82 0.15 0.04
Matches are distributed among these distances:
38 1 0.00
39 33 0.07
40 164 0.34
42 280 0.59
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (41 bp):
ACCATCCGATCTTTTACCCCAACCATGAGGGCAGATTGAAG
Found at i:34128629 original size:80 final size:79
Alignment explanation
Indices: 34128118--34128680 Score: 428
Period size: 84 Copynumber: 6.8 Consensus size: 79
34128108 CAGAAGACAC
* * * * *
34128118 CATCCAATCTCTTACCCCAACCACGGGGCAAATTGAAGATACCATTCGATCTCTTACCCTAACCA
1 CATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAG--ACCATCCGATCTTTTACCCTAACCA
*
34128183 TGAGGCAGATTAAAGA-
64 -GAGGCAGATTGAAGAT
* * * * **
34128199 CACCTTCCAATCTCTTACCCTAATCATGGGGCAGATTGAAGACACCATCCAATCTCATACCCTAA
1 CA---TCCGATCTCTTACCCCAACCATGGGGCAGATTGAAG--ACCATCCGATCTTTTACCCTAA
*
34128264 CCATGAGGCAAATTGAAGAT
61 CCA-GAGGCAGATTGAAGAT
* * * * * * * *
34128284 ACCATCCAATCTCTTACCCTAACCACGGGGTAGATTGAAGACACCATTCGACCTCTTACCCCAAC
1 --CATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAG--ACCATCCGATCTTTTACCCTAAC
* * * *
34128349 CATGAAGCGGGTTGAAGACAC
62 CA-GAGGCAGATTGAAG--AT
* * * * * * * *
34128370 CATCCAATCTCTTACTCCAACCACGGAGCAGATTAAAGACACCATTCGATCTCTTACCCCAACCA
1 CATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAG--ACCATCCGATCTTTTACCCTAACCA
* * *
34128435 CGGGGTAGATTGAAGACAC
64 -GAGGCAGATTGAAG--AT
* ** *
34128454 CATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGACCTTTTGATCTTTTACCCCAACCATG
1 CATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGACCATCCGATCTTTTACCCTAACCA-G
34128519 AGGCAGATTGAAGAT
65 AGGCAGATTGAAGAT
* * * * * *
34128534 CGTCCAATCTCTTACCCCGACCATGGGGCATATTGAGGACCATCCGATCTTTTACCCTAACTAGA
1 CATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGACCATCCGATCTTTTACCCTAACCAGA
34128599 GGACAGATTGAAGAT
66 GG-CAGATTGAAGAT
* * * * * *
34128614 CATCCGTTCTTTTACCCTAACTA-GAGGGTAGATTGAAGACCACCCGATCTTTTACCCTAACCAG
1 CATCCGATCTCTTACCCCAACCATG-GGGCAGATTGAAGACCATCCGATCTTTTACCCTAACCAG
34128678 AGG
65 AGG
34128681 GTAAATTGAA
Statistics
Matches: 403, Mismatches: 69, Indels: 21
0.82 0.14 0.04
Matches are distributed among these distances:
79 5 0.01
80 119 0.30
81 2 0.00
82 34 0.08
84 240 0.60
86 1 0.00
87 2 0.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (79 bp):
CATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAGACCATCCGATCTTTTACCCTAACCAGA
GGCAGATTGAAGAT
Found at i:34128669 original size:120 final size:122
Alignment explanation
Indices: 34128116--34128676 Score: 416
Period size: 126 Copynumber: 4.5 Consensus size: 122
34128106 TACAGAAGAC
* * * * * ** *
34128116 ACCATCCAATCTCTTACCCCAACCACGGGGCAAATTGAAGATACCATTCGATCTCTTACCCTAAC
1 ACCATCCGATCTTTTACCCCAACCATGAGGCAGATTGAAG--ACCACCCGATCTCTTACCCCAAC
* * * * * * * *
34128181 CATGAGGCAGATTAAAGACACCTTCCAATCTCTTACCCTAATCATGGGGCAGATTGAAG
64 CACGGGGCAGATTGAAGACACCATCCGATCTCTTACCCCAACCATGGGACAGATTGAAG
* ** * * * * *
34128240 ACACCATCCAATCTCATACCCTAACCATGAGGCAAATTGAAGATACCATCCAATCTCTTACCCTA
1 --ACCATCCGATCTTTTACCCCAACCATGAGGCAGATTGAAG--ACCACCCGATCTCTTACCCCA
* * * * * *
34128305 ACCACGGGGTAGATTGAAGACACCATTCGACCTCTTACCCCAACCAT-GAAGCGGGTTGAAG
62 ACCACGGGGCAGATTGAAGACACCATCCGATCTCTTACCCCAACCATGGGA-CAGATTGAAG
* * * * *
34128366 ACACCATCCAATCTCTTACTCCAACCACG-GAGCAGATTAAAGA-CACCATTCGATCTCTTACCC
1 --ACCATCCGATCTTTTACCCCAACCATGAG-GCAGATTGAAGACCACC---CGATCTCTTACCC
* *
34128429 CAACCACGGGGTAGATTGAAGACACCATCCGATCTCTTACCCCAACCATGGGGCAGATTGAAG
60 CAACCACGGGGCAGATTGAAGACACCATCCGATCTCTTACCCCAACCATGGGACAGATTGAAG
* ** * ** * *
34128492 ACCTTTTGATCTTTTACCCCAACCATGAGGCAGATTGAAGATCGTCCAATCTCTTACCCCGACCA
1 ACCATCCGATCTTTTACCCCAACCATGAGGCAGATTGAAGACCACCCGATCTCTTACCCCAACCA
* * * * * *
34128557 TGGGGCATATTG-AG-GACCATCCGATCTTTTACCCTAACTA-GAGGACAGATTGAAG
66 CGGGGCAGATTGAAGACACCATCCGATCTCTTACCCCAACCATG-GGACAGATTGAAG
* * * * * * *
34128612 ATCATCCGTTCTTTTACCCTAACTA-GAGGGTAGATTGAAGACCACCCGATCTTTTACCCTAACC
1 ACCATCCGATCTTTTACCCCAACCATGA-GGCAGATTGAAGACCACCCGATCTCTTACCCCAACC
34128676 A
65 A
34128677 GAGGGTAAAT
Statistics
Matches: 355, Mismatches: 70, Indels: 26
0.79 0.16 0.06
Matches are distributed among these distances:
119 3 0.01
120 81 0.23
121 2 0.01
122 26 0.07
123 3 0.01
124 32 0.09
125 5 0.01
126 202 0.57
127 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (122 bp):
ACCATCCGATCTTTTACCCCAACCATGAGGCAGATTGAAGACCACCCGATCTCTTACCCCAACCA
CGGGGCAGATTGAAGACACCATCCGATCTCTTACCCCAACCATGGGACAGATTGAAG
Found at i:34128689 original size:80 final size:79
Alignment explanation
Indices: 34128499--34128730 Score: 209
Period size: 80 Copynumber: 2.9 Consensus size: 79
34128489 AAGACCTTTT
* * * * * * * *
34128499 GATCTTTTACCCCAACCATGAGG-CAGATTGAAGATCGTCCAATCTCTTACCCCGACCATG-GGG
1 GATCTTTTACCCTAACCA-GAGGACAAATTGAAG-CCATCCAGTCTTTTACCCCAACCA-GAAGG
* * * *
34128562 CATATTGAGGACCATCC
63 TAGATTGAAGACCACCC
* * * * * *
34128579 GATCTTTTACCCTAACTAGAGGACAGATTGAAGATCATCC-GTTCTTTTACCCTAACTAGAGGGT
1 GATCTTTTACCCTAACCAGAGGACAAATTGAAG-CCATCCAG-TCTTTTACCCCAACCAGAAGGT
34128643 AGATTGAAGACCACCC
64 AGATTGAAGACCACCC
** *
34128659 GATCTTTTACCCTAACCAGAGGGTAAATTGAAGCCATCCAGTCTTTTACCCCATCCAGAAGGTAG
1 GATCTTTTACCCTAACCAGAGGACAAATTGAAGCCATCCAGTCTTTTACCCCAACCAGAAGGTAG
34128724 ATTGAAG
66 ATTGAAG
34128731 TATGAAAGCG
Statistics
Matches: 127, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
79 37 0.29
80 90 0.71
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (79 bp):
GATCTTTTACCCTAACCAGAGGACAAATTGAAGCCATCCAGTCTTTTACCCCAACCAGAAGGTAG
ATTGAAGACCACCC
Found at i:34128717 original size:39 final size:40
Alignment explanation
Indices: 34128417--34128730 Score: 189
Period size: 40 Copynumber: 7.8 Consensus size: 40
34128407 GACACCATTC
* *
34128417 GATCTCTTACCCCAACCACG-GGGTAGATTGAAGA-CACCA
1 GATCTTTTACCCTAACCA-GAGGGTAGATTGAAGACCACCA
* * * ****
34128456 TCCGATCTCTTACCCCAACCATG-GGGCAGATTGAAGACCTTTT
1 ---GATCTTTTACCCTAACCA-GAGGGTAGATTGAAGACCACCA
* * **
34128499 GATCTTTTACCCCAACCATGA-GGCAGATTGAAGATCGTCCA
1 GATCTTTTACCCTAACCA-GAGGGTAGATTGAAGA-CCACCA
* ** * * *
34128540 -ATCTCTTACCCCGACCATG-GGGCATATTGAGGACCATCC-
1 GATCTTTTACCCTAACCA-GAGGGTAGATTGAAGACCA-CCA
* ** *
34128579 GATCTTTTACCCTAACTAGAGGACAGATTGAAGATCATCC-
1 GATCTTTTACCCTAACCAGAGGGTAGATTGAAGACCA-CCA
* * *
34128619 GTTCTTTTACCCTAACTAGAGGGTAGATTGAAGACCACCC
1 GATCTTTTACCCTAACCAGAGGGTAGATTGAAGACCACCA
*
34128659 GATCTTTTACCCTAACCAGAGGGTAAATTGAAG-CCATCCA
1 GATCTTTTACCCTAACCAGAGGGTAGATTGAAGACCA-CCA
* * *
34128699 G-TCTTTTACCCCATCCAGAAGGTAGATTGAAG
1 GATCTTTTACCCTAACCAGAGGGTAGATTGAAG
34128731 TATGAAAGCG
Statistics
Matches: 226, Mismatches: 37, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
39 34 0.15
40 157 0.69
41 2 0.01
42 32 0.14
43 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (40 bp):
GATCTTTTACCCTAACCAGAGGGTAGATTGAAGACCACCA
Found at i:34133199 original size:24 final size:24
Alignment explanation
Indices: 34133165--34133224 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
34133155 AAAAGTCAAT
* * *
34133165 AGTCAATAGTCAATGGGTCGGGTC
1 AGTCAACAGTCAATAGGTCAGGTC
34133189 AGTCAACAGTCAATAGGTCAGGTC
1 AGTCAACAGTCAATAGGTCAGGTC
34133213 AGTCAACTAGTC
1 AGTCAAC-AGTC
34133225 GGGTCGATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (24 bp):
AGTCAACAGTCAATAGGTCAGGTC
Found at i:34135294 original size:58 final size:58
Alignment explanation
Indices: 34135187--34135306 Score: 136
Period size: 58 Copynumber: 2.1 Consensus size: 58
34135177 TTTTAAATTT
* * *
34135187 TTTTAGAATTGGAACTAAATTGATAAATTTTATAAATGTTAAAGTTAAATTTATTCAA
1 TTTTAGAATTGGAACTAAATTGATAAATTTTATAAATATTAAAGCTAAATTTATTAAA
* * ** *
34135245 TTTTAGAATTTGAATTAAAATT-A-AAATTTTATAAATATTGAGGGCTAAATTTGTTAAA
1 TTTTAGAATTGGAACT-AAATTGATAAATTTTATAAATATT-AAAGCTAAATTTATTAAA
34135303 TTTT
1 TTTT
34135307 TTATATTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
57 15 0.29
58 32 0.62
59 5 0.10
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (58 bp):
TTTTAGAATTGGAACTAAATTGATAAATTTTATAAATATTAAAGCTAAATTTATTAAA
Found at i:34138146 original size:27 final size:29
Alignment explanation
Indices: 34138096--34138152 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
34138086 ATGATTCAAA
*
34138096 ATTTTTTTTAACAATTTTTAAAGGATCTT
1 ATTTTTTTTAACAATTTTTAAAGGAACTT
**
34138125 ATTTTTTTTTCCAA-TTTT-AAGGAACTT
1 ATTTTTTTTAACAATTTTTAAAGGAACTT
34138152 A
1 A
34138153 AAACTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.36
28 4 0.16
29 12 0.48
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (29 bp):
ATTTTTTTTAACAATTTTTAAAGGAACTT
Found at i:34138940 original size:26 final size:26
Alignment explanation
Indices: 34138897--34138947 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
34138887 TCATTTCTCT
34138897 CTCTATATAAATACATATATGATTAC
1 CTCTATATAAATACATATATGATTAC
** *
34138923 CTCTATATTTATATATATATGATTA
1 CTCTATATAAATACATATATGATTA
34138948 TAGTATAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (26 bp):
CTCTATATAAATACATATATGATTAC
Found at i:34139525 original size:20 final size:20
Alignment explanation
Indices: 34139495--34139539 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
34139485 AGATAACTTT
34139495 TTTTTTAGAAATATATAAGAA
1 TTTTTTAGAAATATATAA-AA
* *
34139516 TTTTTT-GAAATTTATTAAA
1 TTTTTTAGAAATATATAAAA
34139535 TTTTT
1 TTTTT
34139540 AATATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 9 0.41
21 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTTTTAGAAATATATAAAA
Found at i:34139985 original size:69 final size:68
Alignment explanation
Indices: 34139873--34140213 Score: 448
Period size: 69 Copynumber: 4.9 Consensus size: 68
34139863 AGCTGAAAGG
* * * *
34139873 ATTTTCCCCCAATGGTAACTAACGGCTACTTTTTTCAACGGCTATTTAATTAGCCGTTGGACCCC
1 ATTTT-CCCCAACGGTAACTAACGACTACTTTCTCCAACGGCTATTTAATTAGCCGTTGGACCCC
34139938 AAGC
65 AAGC
* * **
34139942 ATTTTCTCCCAACGGTAACTAATGACTACTTTCTCCAATGGCTATTTAATTAGTTGTTGGACCCC
1 ATTTTC-CCCAACGGTAACTAACGACTACTTTCTCCAACGGCTATTTAATTAGCCGTTGGACCCC
34140007 AAGC
65 AAGC
*
34140011 ATTTTCCCCCAACGGTAACTAACGACTACTTTCTCCAACGGCTATTTAATTAGCCGTTGGACTCC
1 ATTTT-CCCCAACGGTAACTAACGACTACTTTCTCCAACGGCTATTTAATTAGCCGTTGGACCCC
34140076 AAGC
65 AAGC
* * * * * * *
34140080 GTTTTCCTCCAACAGTAAATAACAACTACTTTCTCCAACGGCTAATTAAATAGCCATTGGACCCC
1 ATTTTCC-CCAACGGTAACTAACGACTACTTTCTCCAACGGCTATTTAATTAGCCGTTGGACCCC
*
34140145 AAGT
65 AAGC
* * * *
34140149 GTTTTCCCTGAACGGTAACTAACGACTACTTTCTCCAACGACTATTTAATTAGCCATTGGACCCC
1 ATTTTCCC-CAACGGTAACTAACGACTACTTTCTCCAACGGCTATTTAATTAGCCGTTGGACCCC
34140214 TCACCCCCAA
Statistics
Matches: 239, Mismatches: 29, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
68 4 0.02
69 234 0.98
70 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (68 bp):
ATTTTCCCCAACGGTAACTAACGACTACTTTCTCCAACGGCTATTTAATTAGCCGTTGGACCCCA
AGC
Found at i:34140291 original size:11 final size:11
Alignment explanation
Indices: 34140277--34140336 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 11
34140267 TTCAATTCAA
*
34140277 TCTCAACTCTC
1 TCTCAAATCTC
*
34140288 TCTCACA-CT-
1 TCTCAAATCTC
34140297 -CTCAAATCTC
1 TCTCAAATCTC
*
34140307 TCTCAAATTTC
1 TCTCAAATCTC
*
34140318 TCTCAATTCTC
1 TCTCAAATCTC
*
34140329 TCTTAAAT
1 TCTCAAAT
34140337 TATCACTCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
8 5 0.13
9 2 0.05
10 2 0.05
11 29 0.76
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTCAAATCTC
Found at i:34140321 original size:13 final size:11
Alignment explanation
Indices: 34140295--34140336 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
34140285 CTCTCTCACA
34140295 CTCTCAAATCT
1 CTCTCAAATCT
*
34140306 CTCTCAAATTT
1 CTCTCAAATCT
*
34140317 CTCTCAATTCT
1 CTCTCAAATCT
*
34140328 CTCTTAAAT
1 CTCTCAAAT
34140337 TATCACTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (11 bp):
CTCTCAAATCT
Found at i:34140323 original size:22 final size:23
Alignment explanation
Indices: 34140295--34140348 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
34140285 CTCTCTCACA
34140295 CTCTCAAATCTCTCTCAAATT-T
1 CTCTCAAATCTCTCTCAAATTAT
* *
34140317 CTCTCAATTCTCTCTTAAATTAT
1 CTCTCAAATCTCTCTCAAATTAT
*
34140340 CACTCAAAT
1 CTCTCAAAT
34140349 TTATTTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (23 bp):
CTCTCAAATCTCTCTCAAATTAT
Found at i:34145009 original size:23 final size:25
Alignment explanation
Indices: 34144983--34145028 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
34144973 CCAATTAAGA
34144983 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
34145006 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
34145029 TGGATCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:34146158 original size:21 final size:22
Alignment explanation
Indices: 34146127--34146167 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
34146117 CATACTTTTT
34146127 AAACCATAAACCCTAACCCTAA
1 AAACCATAAACCCTAACCCTAA
34146149 AAACCA-AAACCCTAACCCT
1 AAACCATAAACCCTAACCCT
34146168 TCCAACTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.49, C:0.39, G:0.00, T:0.12
Consensus pattern (22 bp):
AAACCATAAACCCTAACCCTAA
Found at i:34151283 original size:13 final size:12
Alignment explanation
Indices: 34151265--34151299 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
34151255 TCAAGAAAAC
34151265 TCTCTATGTAAG
1 TCTCTATGTAAG
34151277 TTCTCTATGATAAG
1 -TCTCTATG-TAAG
34151291 TCTCTATGT
1 TCTCTATGT
34151300 GTGGTCCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 16 0.76
14 4 0.19
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (12 bp):
TCTCTATGTAAG
Found at i:34154512 original size:21 final size:22
Alignment explanation
Indices: 34154468--34154541 Score: 84
Period size: 21 Copynumber: 3.5 Consensus size: 22
34154458 AGTGCAGACC
* *
34154468 TCTACCAATACAAGTGA-TAGT
1 TCTACCGATACAAGTGACTACT
34154489 TCTACCGATACAAGTGACT-CT
1 TCTACCGATACAAGTGACTACT
*
34154510 TCTACCGAAACAAGT--CTTACT
1 TCTACCGATACAAGTGAC-TACT
34154531 TCTACCGATAC
1 TCTACCGATAC
34154542 TAAAAACTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 43 0.93
22 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.28
Consensus pattern (22 bp):
TCTACCGATACAAGTGACTACT
Found at i:34155351 original size:52 final size:52
Alignment explanation
Indices: 34155307--34155505 Score: 308
Period size: 52 Copynumber: 3.8 Consensus size: 52
34155297 TCACAGTCCA
* * * *
34155307 TAAAGGATTCACATACTCACGATGACATGTAGTCATCGGACCTCATAATGCG
1 TAAAGGATTCATATACTCACGATGACACGTAGTCATCGAACCTCATAATCCG
* * *
34155359 TAATGGATTCATATACTCACGATGACACGTAGTCATCAAACCTCATAATCTG
1 TAAAGGATTCATATACTCACGATGACACGTAGTCATCGAACCTCATAATCCG
* * *
34155411 TAAAGGATTCATATACTCACGATGACATGTGGTCATCGAACCTCATACTCCG
1 TAAAGGATTCATATACTCACGATGACACGTAGTCATCGAACCTCATAATCCG
34155463 TAAAGGATTCATATACTCACGATGACACGTAGTCATCGAACCT
1 TAAAGGATTCATATACTCACGATGACACGTAGTCATCGAACCT
34155506 TTTTACATTT
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 132 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (52 bp):
TAAAGGATTCATATACTCACGATGACACGTAGTCATCGAACCTCATAATCCG
Found at i:34156761 original size:18 final size:18
Alignment explanation
Indices: 34156738--34156780 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
34156728 TTTTCAGTTG
34156738 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
34156756 TAATTAATTAAAATTATT
1 TAATTAATTAAAATTATT
34156774 TAATTAA
1 TAATTAA
34156781 AAATTTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:34157571 original size:21 final size:19
Alignment explanation
Indices: 34157537--34157592 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
34157527 AAAAACAAAA
* *
34157537 AAAACATAT-AAATATTTT
1 AAAATATATAAAATAATTT
34157555 CAAAATATATAATAATAAATTT
1 -AAAATATATAA-AAT-AATTT
34157577 AAAATATATAAAATAA
1 AAAATATATAAAATAA
34157593 AAAATTATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 10 0.31
20 4 0.12
21 14 0.44
22 4 0.12
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATATATAAAATAATTT
Found at i:34157597 original size:23 final size:21
Alignment explanation
Indices: 34157556--34157598 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
34157546 AAATATTTTC
*
34157556 AAAATATATAATAATAAATTT
1 AAAATATATAATAAAAAATTT
34157577 AAAATATATAAAATAAAAAATT
1 AAAATATAT--AATAAAAAATT
34157599 ATTGTTGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
23 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATATATAATAAAAAATTT
Found at i:34159374 original size:18 final size:18
Alignment explanation
Indices: 34159351--34159393 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
34159341 GTTCAAGGTG
34159351 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
34159369 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
34159387 TAATTAA
1 TAATTAA
34159394 AAATCTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:34159758 original size:25 final size:24
Alignment explanation
Indices: 34159729--34159797 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
34159719 TTTTCATATA
* *
34159729 AATTTTTGAAATTTTTATAATTTTT
1 AATTTTTAAAATTTGTA-AATTTTT
*
34159754 AATTTTTTTACAA-TTGTAAATTTTT
1 AA--TTTTTAAAATTTGTAAATTTTT
34159779 AATTTTTAAAATATTGTAA
1 AATTTTTAAAAT-TTGTAA
34159798 TGTTAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
23 8 0.22
25 17 0.47
26 4 0.11
27 7 0.19
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (24 bp):
AATTTTTAAAATTTGTAAATTTTT
Found at i:34159761 original size:18 final size:18
Alignment explanation
Indices: 34159740--34159778 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
34159730 ATTTTTGAAA
* * *
34159740 TTTTTATAATTTTTAATT
1 TTTTTACAATTGTAAATT
34159758 TTTTTACAATTGTAAATT
1 TTTTTACAATTGTAAATT
34159776 TTT
1 TTT
34159779 AATTTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTTACAATTGTAAATT
Found at i:34161418 original size:20 final size:20
Alignment explanation
Indices: 34161366--34161424 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
34161356 ATTACTTTAG
**
34161366 TAATTTTT-TATTTTTGTTT
1 TAATTTTTCTATTTTTAATT
*
34161385 TAATATTTGC-ATTTTTAATT
1 TAAT-TTTTCTATTTTTAATT
34161405 TAATTTTTCTA-TTTTAATT
1 TAATTTTTCTATTTTTAATT
34161424 T
1 T
34161425 TTCCATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (20 bp):
TAATTTTTCTATTTTTAATT
Found at i:34161422 original size:14 final size:14
Alignment explanation
Indices: 34161403--34161434 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
34161393 GCATTTTTAA
*
34161403 TTTAATTTTTCTAT
1 TTTAATTTTTCCAT
34161417 TTTAATTTTTCCAT
1 TTTAATTTTTCCAT
34161431 TTTA
1 TTTA
34161435 TTTGTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTAATTTTTCCAT
Found at i:34162780 original size:42 final size:42
Alignment explanation
Indices: 34162728--34162848 Score: 170
Period size: 42 Copynumber: 2.9 Consensus size: 42
34162718 AATGAGATAG
*
34162728 CTTTTAAAAATCAACAAGCATCAATTCATGGCCTTGAGACAA
1 CTTTGAAAAATCAACAAGCATCAATTCATGGCCTTGAGACAA
* * * *
34162770 CTTTGAAAAATCAGCAACCATCAATTCATGGTCTTGAGATAA
1 CTTTGAAAAATCAACAAGCATCAATTCATGGCCTTGAGACAA
* * *
34162812 CTGTGAAAAATTAACAAGCATCATTTCATGGCCTTGA
1 CTTTGAAAAATCAACAAGCATCAATTCATGGCCTTGA
34162849 AAATCAAATC
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (42 bp):
CTTTGAAAAATCAACAAGCATCAATTCATGGCCTTGAGACAA
Found at i:34167493 original size:75 final size:75
Alignment explanation
Indices: 34167335--34167494 Score: 198
Period size: 75 Copynumber: 2.1 Consensus size: 75
34167325 AGGTACATGA
* * *
34167335 CCTGGACACACAGGCATGTGCCAGACCGTGTGACCACAGGGCAATATTTTTATTTTACTTCGAAA
1 CCTGGACACACAAGCATGTGCCAGACCGTGTGACCACAGGGCAATAATTTTATTTTAATTCGAAA
* *
34167400 TGATACACGG
66 TGACACACAG
* * *
34167410 CCTAGACACACAAGCATGTGTCAGACCGTGTGACCACTA-GGCAATAATTTTGTTTTAATTC-AA
1 CCTGGACACACAAGCATGTGCCAGACCGTGTGACCAC-AGGGCAATAATTTTATTTTAATTCGAA
* *
34167473 TGTGGCACACAG
65 -ATGACACACAG
34167485 CCTGGACACA
1 CCTGGACACA
34167495 TGGGCGTGTT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
74 2 0.03
75 69 0.96
76 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (75 bp):
CCTGGACACACAAGCATGTGCCAGACCGTGTGACCACAGGGCAATAATTTTATTTTAATTCGAAA
TGACACACAG
Found at i:34168110 original size:20 final size:20
Alignment explanation
Indices: 34168085--34168126 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
34168075 ACCTCTCCCT
*
34168085 TTTCAATTTTTTTATTTTTA
1 TTTCAATTTCTTTATTTTTA
34168105 TTTCAATTTCTTTATTTTTA
1 TTTCAATTTCTTTATTTTTA
34168125 TT
1 TT
34168127 AGTATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTCAATTTCTTTATTTTTA
Found at i:34168188 original size:3 final size:3
Alignment explanation
Indices: 34168116--34168257 Score: 70
Period size: 3 Copynumber: 48.7 Consensus size: 3
34168106 TTCAATTTCT
* * * *
34168116 TTA TTT TTA TTA GTA TTAA TTA TT- TGTA TTT TTA TT- TTA -TG TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* * *
34168160 TT- TTA TTA TTCC TTG TT- TTA TT- TTA TTA TCA TTA TTA TTTA TT-
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* * *
34168203 TTA TT- TTA TTT TTA TT- TTA GTTA TTA TTA TTA TTG TGA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
34168246 CTTA TTA TTA TT
1 -TTA TTA TTA TT
34168258 TGCTCATTTC
Statistics
Matches: 105, Mismatches: 18, Indels: 32
0.68 0.12 0.21
Matches are distributed among these distances:
2 17 0.16
3 73 0.70
4 15 0.14
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:34168202 original size:41 final size:37
Alignment explanation
Indices: 34168135--34168236 Score: 107
Period size: 41 Copynumber: 2.6 Consensus size: 37
34168125 TTAGTATTAA
* *
34168135 TTATTTGTATTTTTATT-TTATGTTATTTTATTATTCCTTGTT
1 TTATTT-TATTATTATTATTAT-TTATTTTATT-TT--AT-TT
*
34168177 TTATTTTATTATCATTATTATTTATTTTATTTTATTT
1 TTATTTTATTATTATTATTATTTATTTTATTTTATTT
34168214 TTATTTTAGTTATTATTATTATT
1 TTATTTTA-TTATTATTATTATT
34168237 GTGATATTAC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
37 10 0.19
38 14 0.26
40 2 0.04
41 18 0.33
42 10 0.19
ACGTcount: A:0.22, C:0.03, G:0.04, T:0.72
Consensus pattern (37 bp):
TTATTTTATTATTATTATTATTTATTTTATTTTATTT
Found at i:34168203 original size:4 final size:5
Alignment explanation
Indices: 34168135--34168236 Score: 66
Period size: 5 Copynumber: 19.0 Consensus size: 5
34168125 TTAGTATTAA
* *
34168135 TTATT TGTATTT TTATT TTATG TTATT TTA-- TTATT CCTTGTT TTATT
1 TTATT T-TA-TT TTATT TTATT TTATT TTATT TTATT --TTATT TTATT
*
34168182 TTATT ATCATT ATTA-T TTATT TTATT TTATTT TTATT TTAGTT ATTATT
1 TTATT -TTATT -TTATT TTATT TTATT TTA-TT TTATT TTA-TT -TTATT
34168231 ATTATT
1 -TTATT
34168237 GTGATATTAC
Statistics
Matches: 80, Mismatches: 6, Indels: 21
0.75 0.06 0.20
Matches are distributed among these distances:
3 3 0.04
4 3 0.04
5 38 0.47
6 26 0.32
7 10 0.12
ACGTcount: A:0.22, C:0.03, G:0.04, T:0.72
Consensus pattern (5 bp):
TTATT
Found at i:34168204 original size:26 final size:24
Alignment explanation
Indices: 34168085--34168220 Score: 84
Period size: 26 Copynumber: 5.5 Consensus size: 24
34168075 ACCTCTCCCT
*
34168085 TTTCAATT-TTTTTATTTTTATTTCAA
1 TTTC-ATTATTTTTA-TTTTATTT-TA
* *
34168111 TTTCTTTATTTTTATTAGTATTAATTA
1 TTTCATTATTTTTATT-TTATT--TTA
* *
34168138 TTT--GTATTTTTATTTTATGTTA
1 TTTCATTATTTTTATTTTATTTTA
* * *
34168160 TTTTATTATTCCTTGTTTTATTTTA
1 TTTCATTATT-TTTATTTTATTTTA
34168185 TTATCATTATTATTTATTTTATTTTA
1 TT-TCATTATT-TTTATTTTATTTTA
34168211 TTT--TTATTTT
1 TTTCATTATTTT
34168221 AGTTATTATT
Statistics
Matches: 88, Mismatches: 14, Indels: 20
0.72 0.11 0.16
Matches are distributed among these distances:
22 8 0.09
23 5 0.06
24 7 0.08
25 28 0.32
26 35 0.40
27 4 0.05
28 1 0.01
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.71
Consensus pattern (24 bp):
TTTCATTATTTTTATTTTATTTTA
Done.