Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 30 of 54
Found at i:12495357 original size:16 final size:16
Alignment explanation
Indices: 12495327--12495356 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12495317 CTAAAATTTA
12495327 GATTTTGATTCTTTTG
1 GATTTTGATTCTTTTG
12495343 GATTTTGATT-TTTT
1 GATTTTGATTCTTTT
12495357 TTATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (16 bp):
GATTTTGATTCTTTTG
Found at i:12497129 original size:32 final size:31
Alignment explanation
Indices: 12497040--12497129 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
12497030 CATTTTGATG
*
12497040 ACATGGCACCTACATGATGACATGACATGCC
1 ACATGGCACCTACATGATGACATGGCATGCC
* * * * **
12497071 ACATGGCATCGACGTGATTATGTGGCAGTGCC
1 ACATGGCACCTACATGATGACATGGCA-TGCC
12497103 ACATGGCA-CTACTATGATGACATGGCA
1 ACATGGCACCTAC-ATGATGACATGGCA
12497130 CTGACATATT
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
31 23 0.51
32 22 0.49
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (31 bp):
ACATGGCACCTACATGATGACATGGCATGCC
Found at i:12497142 original size:19 final size:18
Alignment explanation
Indices: 12497103--12497145 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
12497093 TGGCAGTGCC
12497103 ACATGGCACTACTATGATG
1 ACATGGCACTACTAT-ATG
12497122 ACATGGCACTGAC-ATATTG
1 ACATGGCACT-ACTATA-TG
12497141 ACATG
1 ACATG
12497146 TCAATGCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.05
19 19 0.86
20 2 0.09
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (18 bp):
ACATGGCACTACTATATG
Found at i:12498425 original size:17 final size:16
Alignment explanation
Indices: 12498400--12498438 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
12498390 AAAATATTTA
*
12498400 TATATATTTTTTAACAC
1 TATAAATTTTTT-ACAC
12498417 TATAAATTTTTTACAC
1 TATAAATTTTTTACAC
12498433 T-TAAAT
1 TATAAAT
12498439 ATTTGACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 5 0.24
17 11 0.52
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (16 bp):
TATAAATTTTTTACAC
Found at i:12498442 original size:17 final size:18
Alignment explanation
Indices: 12498398--12498442 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
12498388 AGAAAATATT
12498398 TATATATATTTTTTAACAC
1 TATA-ATATTTTTTAACAC
12498417 TATAA-ATTTTTT-ACAC
1 TATAATATTTTTTAACAC
12498433 T-TAAATATTT
1 TAT-AATATTT
12498443 GACTTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 7 0.29
17 11 0.46
18 1 0.04
19 4 0.17
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (18 bp):
TATAATATTTTTTAACAC
Found at i:12501107 original size:10 final size:10
Alignment explanation
Indices: 12501088--12501131 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
12501078 TTATTCAATA
*
12501088 TTTTTATTCT
1 TTTTTTTTCT
12501098 TTTTTTTTCT
1 TTTTTTTTCT
**
12501108 TTAATTTTCT
1 TTTTTTTTCT
*
12501118 TTTTATTTCT
1 TTTTTTTTCT
12501128 TTTT
1 TTTT
12501132 AGATTTTCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:12511055 original size:2 final size:2
Alignment explanation
Indices: 12511048--12511077 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12511038 TATATTTTTC
12511048 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12511078 TTTTAGCAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:12513338 original size:32 final size:32
Alignment explanation
Indices: 12513293--12513371 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
12513283 AAGATGAATG
* *
12513293 CAAGCACATAAGCAAAAAAGGCACAAAGGCTT
1 CAAGCACACAAGCAAAAAAGGCACAAAGCCTT
* * *
12513325 CAGGCACACAAGCACATAAGGCACAAAGCCTT
1 CAAGCACACAAGCAAAAAAGGCACAAAGCCTT
12513357 CAAGCACACAAGCAA
1 CAAGCACACAAGCAA
12513372 GCAAGATATG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
CAAGCACACAAGCAAAAAAGGCACAAAGCCTT
Found at i:12516924 original size:2 final size:2
Alignment explanation
Indices: 12516914--12516947 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
12516904 TATAACACAC
* *
12516914 AT AT CT AT AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12516948 CCATCACCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12517047 original size:42 final size:42
Alignment explanation
Indices: 12516995--12517176 Score: 222
Period size: 42 Copynumber: 4.3 Consensus size: 42
12516985 TATGCATTCT
* * * *
12516995 CACTAGCACATGGCTAGGTTAGCATCGGCTTATGCGCACTCC
1 CACTCGCACATAGCTGGGTCAGCATCGGCTTATGCGCACTCC
*
12517037 TACTCGCACATAG-TCGGGTCAGCATCGGCTTATGCGCACTCC
1 CACTCGCACATAGCT-GGGTCAGCATCGGCTTATGCGCACTCC
* * * *
12517079 CCCTCGCACATAGCCGGGTCAGCATCTGTTTATGCGCACTCC
1 CACTCGCACATAGCTGGGTCAGCATCGGCTTATGCGCACTCC
* * *
12517121 CCCTCGCACATAGCTGAGTCAGCATCGGCTTATGCACACTCC
1 CACTCGCACATAGCTGGGTCAGCATCGGCTTATGCGCACTCC
* *
12517163 TACTCACACATAGC
1 CACTCGCACATAGC
12517177 CGAGTCAATA
Statistics
Matches: 120, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
41 1 0.01
42 119 0.99
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (42 bp):
CACTCGCACATAGCTGGGTCAGCATCGGCTTATGCGCACTCC
Found at i:12517182 original size:42 final size:42
Alignment explanation
Indices: 12517015--12517183 Score: 230
Period size: 42 Copynumber: 4.0 Consensus size: 42
12517005 TGGCTAGGTT
* * *
12517015 AGCATCGGCTTATGCGCACTCCTACTCGCACATAGTCGGGTC
1 AGCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGAGTC
* *
12517057 AGCATCGGCTTATGCGCACTCCCCCTCGCACATAGCCGGGTC
1 AGCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGAGTC
* * * *
12517099 AGCATCTGTTTATGCGCACTCCCCCTCGCACATAGCTGAGTC
1 AGCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGAGTC
* * *
12517141 AGCATCGGCTTATGCACACTCCTACTCACACATAGCCGAGTC
1 AGCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGAGTC
12517183 A
1 A
12517184 ATATCATTAC
Statistics
Matches: 113, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 113 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.22
Consensus pattern (42 bp):
AGCATCGGCTTATGCGCACTCCCACTCGCACATAGCCGAGTC
Found at i:12520858 original size:38 final size:39
Alignment explanation
Indices: 12520769--12520870 Score: 136
Period size: 38 Copynumber: 2.6 Consensus size: 39
12520759 CACACCCAGT
*
12520769 TCATGTGCATCCCCCCACATCATGCACATAGTCGGAGTCA
1 TCATGTGCATCCCCCCACATCATGCACA-AGTCGAAGTCA
* *
12520809 TCGTGTGCATCCCCCCACATCGTGCAC-AGTC-AATGTCA
1 TCATGTGCATCCCCCCACATCATGCACAAGTCGAA-GTCA
*
12520847 TCATGTACATCCCCCCACATCATG
1 TCATGTGCATCCCCCCACATCATG
12520871 AACACGGGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
37 1 0.02
38 29 0.53
40 25 0.45
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.24
Consensus pattern (39 bp):
TCATGTGCATCCCCCCACATCATGCACAAGTCGAAGTCA
Found at i:12520931 original size:70 final size:70
Alignment explanation
Indices: 12520848--12521016 Score: 284
Period size: 70 Copynumber: 2.4 Consensus size: 70
12520838 TCAATGTCAT
* *
12520848 CATGTACATCCCCCCACATCATGAACACGGGCACTATCATCATCCACCTCCCTCACCACGCCATC
1 CATGTGCATCCCCCCACATCATGAACACAGGCACTATCATCATCCACCTCCCTCACCACGCCATC
*
12520913 ACTGG
66 ACCGG
*
12520918 CATGTGCATCCCCCCACATCATGCACACAGGCACTATCATCATCCACCTCCCTCACCACGCCATC
1 CATGTGCATCCCCCCACATCATGAACACAGGCACTATCATCATCCACCTCCCTCACCACGCCATC
12520983 ACCGG
66 ACCGG
* *
12520988 CATGTGCATCCCCCCACATCGTGCACACA
1 CATGTGCATCCCCCCACATCATGAACACA
12521017 CACGGTTATA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 94 1.00
ACGTcount: A:0.25, C:0.46, G:0.12, T:0.18
Consensus pattern (70 bp):
CATGTGCATCCCCCCACATCATGAACACAGGCACTATCATCATCCACCTCCCTCACCACGCCATC
ACCGG
Found at i:12521500 original size:14 final size:14
Alignment explanation
Indices: 12521481--12521510 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12521471 CTCAACTACA
12521481 ACATTCACAAGTCT
1 ACATTCACAAGTCT
12521495 ACATTCACAAGTCT
1 ACATTCACAAGTCT
12521509 AC
1 AC
12521511 TTACTAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.27
Consensus pattern (14 bp):
ACATTCACAAGTCT
Found at i:12521865 original size:19 final size:19
Alignment explanation
Indices: 12521841--12521885 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
12521831 GGAGGAAGAA
12521841 GAAGAAGCTGCTAAAAATT
1 GAAGAAGCTGCTAAAAATT
*
12521860 GAAGAAACTGCTAAAAATT
1 GAAGAAGCTGCTAAAAATT
12521879 GAAGAAG
1 GAAGAAG
12521886 ATATTTATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.51, C:0.09, G:0.22, T:0.18
Consensus pattern (19 bp):
GAAGAAGCTGCTAAAAATT
Found at i:12525221 original size:13 final size:13
Alignment explanation
Indices: 12525203--12525227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12525193 TTCCAGAAAA
12525203 TTTATAAAATCAT
1 TTTATAAAATCAT
12525216 TTTATAAAATCA
1 TTTATAAAATCA
12525228 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:12530978 original size:26 final size:27
Alignment explanation
Indices: 12530938--12530989 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
12530928 ATGTAATCAT
* * *
12530938 TTAAAAGTAAGTTAAAATAGATTTGTC
1 TTAAAAGTAAATTAAAACAGACTTGTC
12530965 TTAAAA-TAAATTAAAACAGACTTGT
1 TTAAAAGTAAATTAAAACAGACTTGT
12530990 GAGTAAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.35
Consensus pattern (27 bp):
TTAAAAGTAAATTAAAACAGACTTGTC
Found at i:12532858 original size:27 final size:29
Alignment explanation
Indices: 12532830--12532887 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
12532820 ATGCATACAA
* *
12532830 ATATTTTATTTGTCTTTATTAAGATAAAT
1 ATATATTATATGTCTTTATTAAGATAAAT
12532859 ATATAACTTATATGTCTTTATTAAGATAA
1 ATAT-A-TTATATGTCTTTATTAAGATAA
12532888 CTAGATGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.16
31 21 0.84
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (29 bp):
ATATATTATATGTCTTTATTAAGATAAAT
Found at i:12538706 original size:3 final size:3
Alignment explanation
Indices: 12538698--12538757 Score: 63
Period size: 3 Copynumber: 20.7 Consensus size: 3
12538688 CCTCTTGTAT
* *
12538698 TTA TTA TTA TT- TAA TT- TTA TTA TTA TTA TTA TTA TTA -TA TTTC
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
12538741 TTA TTA TTA CTA TTA TT
1 TTA TTA TTA TTA TTA TT
12538758 TTTTTTTGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.11
3 41 0.87
4 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12542498 original size:7 final size:7
Alignment explanation
Indices: 12542488--12542527 Score: 71
Period size: 7 Copynumber: 5.6 Consensus size: 7
12542478 GGAGGTTGAG
12542488 AAAATGT
1 AAAATGT
12542495 AAAATGT
1 AAAATGT
12542502 AAAATGT
1 AAAATGT
12542509 AAAATGT
1 AAAATGT
12542516 AAAATGT
1 AAAATGT
12542523 CAAAA
1 -AAAA
12542528 AGGCACTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 28 0.88
8 4 0.12
ACGTcount: A:0.60, C:0.03, G:0.12, T:0.25
Consensus pattern (7 bp):
AAAATGT
Found at i:12543884 original size:17 final size:18
Alignment explanation
Indices: 12543862--12543900 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
12543852 AACAAGGAAG
12543862 GGAACAAGCATACCAT-A
1 GGAACAAGCATACCATAA
12543879 GGAACAAGCATACCATAA
1 GGAACAAGCATACCATAA
12543897 GGAA
1 GGAA
12543901 TGTTTAACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.10
Consensus pattern (18 bp):
GGAACAAGCATACCATAA
Found at i:12544369 original size:39 final size:39
Alignment explanation
Indices: 12544321--12544395 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
12544311 CAGCGAGATT
* * *
12544321 CAGCGAAATTGTAACCTAGAAATAGAAAGTTTCTCGCTG
1 CAGCAAAATTGTAACCCAGAAACAGAAAGTTTCTCGCTG
12544360 CAGCAAAATTGTAACCCAGAAACAGAAAGTTTCTCG
1 CAGCAAAATTGTAACCCAGAAACAGAAAGTTTCTCG
12544396 TTTCAGCGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (39 bp):
CAGCAAAATTGTAACCCAGAAACAGAAAGTTTCTCGCTG
Found at i:12544467 original size:22 final size:22
Alignment explanation
Indices: 12544439--12544495 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
12544429 GCTACAGTGT
12544439 CATTCTCGCTGCAGCGAAAATG
1 CATTCTCGCTGCAGCGAAAATG
12544461 CATTCTCGCTGCAGCGAAAATG
1 CATTCTCGCTGCAGCGAAAATG
12544483 CATTCTCGCTGCA
1 CATTCTCGCTGCA
12544496 ACAAGTTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (22 bp):
CATTCTCGCTGCAGCGAAAATG
Found at i:12544828 original size:26 final size:23
Alignment explanation
Indices: 12544767--12544826 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
12544757 TATGCGTATA
*
12544767 CCCATCATCATCATGCACACCAT
1 CCCATCATCATCATACACACCAT
12544790 CCCATCATCATCATACACACCAT
1 CCCATCATCATCATACACACCAT
**
12544813 CATATCATCATCAT
1 CCCATCATCATCAT
12544827 CACCAGCTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.40, G:0.02, T:0.25
Consensus pattern (23 bp):
CCCATCATCATCATACACACCAT
Found at i:12545727 original size:3 final size:3
Alignment explanation
Indices: 12545719--12545745 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12545709 AACGTGAAAG
12545719 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
12545746 CAAGCTACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12546695 original size:13 final size:14
Alignment explanation
Indices: 12546669--12546698 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
12546659 TTTAATTAAA
12546669 TTATATTCTAATAT
1 TTATATTCTAATAT
12546683 TTATATT-TAATAT
1 TTATATTCTAATAT
12546696 TTA
1 TTA
12546699 ATAGTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATATTCTAATAT
Found at i:12548874 original size:22 final size:21
Alignment explanation
Indices: 12548835--12548889 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
12548825 AATGAAAAGA
* * *
12548835 TTAAAATATTTTTTTTATTAAT
1 TTAAAAAATTATTATTA-TAAT
*
12548857 TTAAAAAATTATTATTATATT
1 TTAAAAAATTATTATTATAAT
*
12548878 TTTAAAAATTAT
1 TTAAAAAATTAT
12548890 AAAAATAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAAAAATTATTATTATAAT
Found at i:12551728 original size:53 final size:54
Alignment explanation
Indices: 12551637--12551747 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 54
12551627 ATCATTCATA
* * *
12551637 AAAACAAAAAAATAAAGAAAAAAAATTAGGATTGATGTAACCATAAAGAAAAAC
1 AAAACAAAAAAATAAAGAAAAAAAATTAAGACTAATGTAACCATAAAGAAAAAC
* ** *
12551691 AAAAC-AAAAAATAAAGAACAAAGTTTAAGACTAATGTAACCATAAAGAAAAGC
1 AAAACAAAAAAATAAAGAAAAAAAATTAAGACTAATGTAACCATAAAGAAAAAC
12551744 AAAA
1 AAAA
12551748 GGTCATATTG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 45 0.90
54 5 0.10
ACGTcount: A:0.66, C:0.09, G:0.11, T:0.14
Consensus pattern (54 bp):
AAAACAAAAAAATAAAGAAAAAAAATTAAGACTAATGTAACCATAAAGAAAAAC
Found at i:12553363 original size:12 final size:12
Alignment explanation
Indices: 12553341--12553386 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
12553331 TTTTATTTTT
12553341 TTTAT-TTTATA
1 TTTATATTTATA
12553352 TTTCA-ATTTATA
1 TTT-ATATTTATA
12553364 TTTATATTTATA
1 TTTATATTTATA
*
12553376 TTTATTTTTAT
1 TTTATATTTAT
12553387 TTTTTTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
11 4 0.13
12 27 0.87
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATATTTATA
Found at i:12553369 original size:18 final size:17
Alignment explanation
Indices: 12553330--12553388 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
12553320 GCCTCACTCA
12553330 ATTTTAT-TTT-T-TTT
1 ATTTTATATTTATATTT
12553344 ATTTTATATTTCA-ATTT
1 ATTTTATATTT-ATATTT
12553361 ATATTTATATTTATATTT
1 AT-TTTATATTTATATTT
12553379 ATTTT-TATTT
1 ATTTTATATTT
12553389 TTTTCATTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 7 0.18
15 3 0.08
16 5 0.13
17 9 0.23
18 15 0.38
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTATATTTATATTT
Found at i:12555393 original size:23 final size:23
Alignment explanation
Indices: 12555351--12555395 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12555341 TGTTAACTTT
** *
12555351 TAATGATTTGTATGATGTGTTGC
1 TAATGATTTGTACAAAGTGTTGC
12555374 TAATGATTTGTACAAAGTGTTG
1 TAATGATTTGTACAAAGTGTTG
12555396 ATATACCAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.04, G:0.24, T:0.44
Consensus pattern (23 bp):
TAATGATTTGTACAAAGTGTTGC
Found at i:12555585 original size:26 final size:28
Alignment explanation
Indices: 12555554--12555609 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
12555544 GCCATTTTCT
*
12555554 AAATATT-T-GTTACATAGCATGTTGGG
1 AAATATTATCGTTACACAGCATGTTGGG
* *
12555580 AAATATTATCGTTATACATCATGTTGGG
1 AAATATTATCGTTACACAGCATGTTGGG
12555608 AA
1 AA
12555610 TTTTGATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.28
27 1 0.04
28 17 0.68
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38
Consensus pattern (28 bp):
AAATATTATCGTTACACAGCATGTTGGG
Found at i:12555713 original size:55 final size:54
Alignment explanation
Indices: 12555639--12555933 Score: 276
Period size: 55 Copynumber: 5.4 Consensus size: 54
12555629 AGGAAAAAAT
* *
12555639 GTTGTTA-ACGCCATGTTGAAAAATGTAGTT-TTACATTCCATGTTCAAAAATTTA
1 GTTGTTACACGCCATGTTG-AAAATTTAGTTGTTACATT-CATGTTGAAAAATTTA
* * * ** *
12555693 ATTGTTACATGTCATGTTGAAAATTTAGTTGTTACAAGCCATGTTG-AAGATTTA
1 GTTGTTACACGCCATGTTGAAAATTTAGTTGTTAC-ATTCATGTTGAAAAATTTA
* * * *
12555747 GTTATTACAAGCCATGTTGAAAATTTAGTTGTTACACGTCATATTGAAAAATTTA
1 GTTGTTACACGCCATGTTGAAAATTTAGTTGTTACA-TTCATGTTGAAAAATTTA
* *
12555802 TTTGTTACACGCCATGTTGAAAATTTAGTTGTTACACATT-ATGTTGAAAAATGTA
1 GTTGTTACACGCCATGTTGAAAATTTAGTTGTT--ACATTCATGTTGAAAAATTTA
** * * * * *
12555857 GTTGTTACACGTTATGTTGAAGATTTTGTCGTTATACGTCATGTTG-AAAATTTA
1 GTTGTTACACGCCATGTTGAAAATTTAGTTGTTACA-TTCATGTTGAAAAATTTA
* * *
12555911 GTTGTTATATGCCATGATGAAAA
1 GTTGTTACACGCCATGTTGAAAA
12555934 ATTTGTTACA
Statistics
Matches: 196, Mismatches: 36, Indels: 18
0.78 0.14 0.07
Matches are distributed among these distances:
53 3 0.02
54 86 0.44
55 102 0.52
56 2 0.01
57 3 0.02
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (54 bp):
GTTGTTACACGCCATGTTGAAAATTTAGTTGTTACATTCATGTTGAAAAATTTA
Found at i:12555740 original size:82 final size:82
Alignment explanation
Indices: 12555639--12555937 Score: 343
Period size: 82 Copynumber: 3.7 Consensus size: 82
12555629 AGGAAAAAAT
* * * *
12555639 GTTGTTA-ACGCCATGTTGAAAAATGTAGTT-TTACATTCCATGTTCAAAAATTTAATTGTTACA
1 GTTGTTACACGCCATGTTG-AAAATTTAGTTGTTACATGCCATGTTGAAAAATTTAGTTGTTACA
*
12555702 TGTCATGTTGAAAATTTA
65 CGTCATGTTGAAAATTTA
* * * *
12555720 GTTGTTACAAGCCATGTTGAAGATTTAGTTATTACAAGCCATGTTG-AAAATTTAGTTGTTACAC
1 GTTGTTACACGCCATGTTGAAAATTTAGTTGTTACATGCCATGTTGAAAAATTTAGTTGTTACAC
*
12555784 GTCATATTGAAAAATTTA
66 GTCATGTTG-AAAATTTA
* **** *
12555802 TTTGTTACACGCCATGTTGAAAATTTAGTTGTTACACATTATGTTGAAAAATGTAGTTGTTACAC
1 GTTGTTACACGCCATGTTGAAAATTTAGTTGTTACATGCCATGTTGAAAAATTTAGTTGTTACAC
* * *
12555867 GTTATGTTGAAGATTTT
66 GTCATGTTGAAAATTTA
* * * * *
12555884 GTCGTTATACGTCATGTTGAAAATTTAGTTGTTATATGCCATGATGAAAAATTT
1 GTTGTTACACGCCATGTTGAAAATTTAGTTGTTACATGCCATGTTGAAAAATTT
12555938 GTTACACGCC
Statistics
Matches: 181, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
81 40 0.22
82 117 0.65
83 24 0.13
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.40
Consensus pattern (82 bp):
GTTGTTACACGCCATGTTGAAAATTTAGTTGTTACATGCCATGTTGAAAAATTTAGTTGTTACAC
GTCATGTTGAAAATTTA
Found at i:12555926 original size:27 final size:27
Alignment explanation
Indices: 12555639--12555948 Score: 288
Period size: 27 Copynumber: 11.5 Consensus size: 27
12555629 AGGAAAAAAT
*
12555639 GTTGTTA-ACGCCATGTTGAAAAATGTA
1 GTTGTTACACGCCATGTTG-AAAATTTA
** *
12555666 GTT-TTACATTCCATGTTCAAAAATTTA
1 GTTGTTACACGCCATGTT-GAAAATTTA
* * *
12555693 ATTGTTACATGTCATGTTGAAAATTTA
1 GTTGTTACACGCCATGTTGAAAATTTA
* *
12555720 GTTGTTACAAGCCATGTTGAAGATTTA
1 GTTGTTACACGCCATGTTGAAAATTTA
* *
12555747 GTTATTACAAGCCATGTTGAAAATTTA
1 GTTGTTACACGCCATGTTGAAAATTTA
* *
12555774 GTTGTTACACGTCATATTGAAAAATTTA
1 GTTGTTACACGCCATGTTG-AAAATTTA
*
12555802 TTTGTTACACGCCATGTTGAAAATTTA
1 GTTGTTACACGCCATGTTGAAAATTTA
*** *
12555829 GTTGTTACACATTATGTTGAAAAATGTA
1 GTTGTTACACGCCATGTTG-AAAATTTA
** * *
12555857 GTTGTTACACGTTATGTTGAAGATTTT
1 GTTGTTACACGCCATGTTGAAAATTTA
* * *
12555884 GTCGTTATACGTCATGTTGAAAATTTA
1 GTTGTTACACGCCATGTTGAAAATTTA
* * *
12555911 GTTGTTATATGCCATGATGAAAA---A
1 GTTGTTACACGCCATGTTGAAAATTTA
*
12555935 TTTGTTACACGCCA
1 GTTGTTACACGCCA
12555949 CGTCATAATT
Statistics
Matches: 236, Mismatches: 42, Indels: 13
0.81 0.14 0.04
Matches are distributed among these distances:
24 12 0.05
26 3 0.01
27 160 0.68
28 61 0.26
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (27 bp):
GTTGTTACACGCCATGTTGAAAATTTA
Found at i:12559113 original size:42 final size:41
Alignment explanation
Indices: 12559054--12559180 Score: 182
Period size: 42 Copynumber: 3.0 Consensus size: 41
12559044 GTAATGATAT
*
12559054 TGACCCAGCTATGTGCGAGTAAGAGTGTGCATAAGCCGATGC
1 TGACCCA-CTATGTGCGAGTAGGAGTGTGCATAAGCCGATGC
* * *
12559096 TGACCCGACTATGTGCGAATGGGAGTGCGCATAAGCCGATGC
1 TGACCC-ACTATGTGCGAGTAGGAGTGTGCATAAGCCGATGC
*
12559138 TGACCCAACTATGTGCAAGTAGGAGTGTGCATAAGCCGATGC
1 TGACCC-ACTATGTGCGAGTAGGAGTGTGCATAAGCCGATGC
12559180 T
1 T
12559181 AATCTAGCCA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
42 74 0.99
43 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (41 bp):
TGACCCACTATGTGCGAGTAGGAGTGTGCATAAGCCGATGC
Found at i:12559204 original size:84 final size:84
Alignment explanation
Indices: 12559054--12559207 Score: 202
Period size: 84 Copynumber: 1.8 Consensus size: 84
12559044 GTAATGATAT
* * * * * *
12559054 TGACCCAGCTATGTGCGAGTAAGAGTGTGCATAAGCCGATGCTGACCCGACTATGTGCGAATGGG
1 TGACCCAACTATGTGCAAGTAAGAGTGTGCATAAGCCGATGCTAACCAGACCATGTGCGAAGGGG
12559119 AGTGCGCATAAGCCGATGC
66 AGTGCGCATAAGCCGATGC
* * * *
12559138 TGACCCAACTATGTGCAAGTAGGAGTGTGCATAAGCCGATGCTAATCTAG-CCATGTGCTAGGGG
1 TGACCCAACTATGTGCAAGTAAGAGTGTGCATAAGCCGATGCTAA-CCAGACCATGTGCGAAGGG
12559202 GAGTGC
65 GAGTGC
12559208 ATATGAGCTG
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
84 57 0.97
85 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.21
Consensus pattern (84 bp):
TGACCCAACTATGTGCAAGTAAGAGTGTGCATAAGCCGATGCTAACCAGACCATGTGCGAAGGGG
AGTGCGCATAAGCCGATGC
Found at i:12559753 original size:19 final size:19
Alignment explanation
Indices: 12559729--12559768 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12559719 AGGGTTTAGA
* *
12559729 GAGAAATCCTCGGCTAGTT
1 GAGAAACCCTCGGCCAGTT
*
12559748 GAGAAACCCTTGGCCAGTT
1 GAGAAACCCTCGGCCAGTT
12559767 GA
1 GA
12559769 TAATTGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.23
Consensus pattern (19 bp):
GAGAAACCCTCGGCCAGTT
Found at i:12564029 original size:3 final size:3
Alignment explanation
Indices: 12564023--12564096 Score: 71
Period size: 3 Copynumber: 24.7 Consensus size: 3
12564013 TTATTGTTGT
* * * *
12564023 TTA TTA TTA -TA TTC TTAA TTA TTG TTA TTA TTA TTT TTG TTCA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TT-A TTA
*
12564069 CT- TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12564097 TATTTTAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
2 3 0.05
3 51 0.88
4 4 0.07
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12564054 original size:9 final size:9
Alignment explanation
Indices: 12564007--12564096 Score: 50
Period size: 9 Copynumber: 10.6 Consensus size: 9
12563997 TTATCATTTT
12564007 TTATTGTTA
1 TTATTGTTA
*
12564016 TTGTTG-T-
1 TTATTGTTA
*
12564023 TTATTATTA
1 TTATTGTTA
*
12564032 -TATTCTTAA
1 TTATTGTT-A
12564041 TTATTGTTA
1 TTATTGTTA
12564050 TTA---TTA
1 TTATTGTTA
*
12564056 TTTTTGTTCA
1 TTATTGTT-A
*
12564066 TTACT-TTA
1 TTATTGTTA
*
12564074 TTATTATTA
1 TTATTGTTA
*
12564083 TTATTATTA
1 TTATTGTTA
12564092 TTATT
1 TTATT
12564097 TATTTTAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
6 5 0.08
7 4 0.06
8 13 0.21
9 31 0.49
10 10 0.16
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (9 bp):
TTATTGTTA
Found at i:12565296 original size:19 final size:19
Alignment explanation
Indices: 12565274--12565310 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12565264 TTTCATACTT
* *
12565274 TTATTTTTTGTTTTTTTTA
1 TTATATTTTATTTTTTTTA
12565293 TTATATTTTATTTTTTTT
1 TTATATTTTATTTTTTTT
12565311 GAAATAGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.84
Consensus pattern (19 bp):
TTATATTTTATTTTTTTTA
Found at i:12572835 original size:21 final size:19
Alignment explanation
Indices: 12572799--12572839 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
12572789 ACATGTTGAG
12572799 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
12572818 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
12572839 T
1 T
12572840 GTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:12583713 original size:6 final size:6
Alignment explanation
Indices: 12583702--12583726 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12583692 ATAAAGGAAA
12583702 TTAATT TTAATT TTAATT TTAATT T
1 TTAATT TTAATT TTAATT TTAATT T
12583727 CCAAGGACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTAATT
Found at i:12585432 original size:180 final size:179
Alignment explanation
Indices: 12585076--12585547 Score: 515
Period size: 180 Copynumber: 2.6 Consensus size: 179
12585066 GCAAGCCACT
* * * * * * *
12585076 GTTTTGAATTTTTTTGACAGCCAAAAACATTTTCTAAAATCATGGAAAATTAATATGGAATTTTT
1 GTTTTGAATATTTTTGACAGCCAAAAACATCTCCTAAAATCCTGAAAAATTATTATGGAATATTT
* * *
12585141 CCATAAGTTATCTATCAAGGA-AAATTTAATTGGAAATTAAATTCCTGATTTTATGCTGCCAAAT
66 CCATAAGTTATCTATC-AGGATAAATTTTATTGG-AATTAAATTCCTAATTTTATGCTGCCAAAG
* * ** * *
12585205 AATTTCAAAAGGAAGACAAAACCGAAACTGCCTCTGTAGATAAAGGTCATG
129 AATTTCAAAAGGAACACAAAACCGAAACTGCCCCTACAGAGAAAGGTCACG
** * **
12585256 GTTTTGAATATTTTTGACAGCCAAAAAGGTCTCCTAAAATCCTGAAAAAATATTATGGAATAGAT
1 GTTTTGAATATTTTTGACAGCCAAAAACATCTCCTAAAATCCTGAAAAATTATTATGGAATATTT
*
12585321 CCATAAGTTATCTATCAGGATAAATTTTATTAGGAATTAAATTCCTAATTTT-TGGT-CACAAAG
66 CCATAAGTTATCTATCAGGATAAATTTTATT-GGAATTAAATTCCTAATTTTATGCTGC-CAAAG
** * ***
12585384 AATTTCAAAAGTGCTCA-AAAACTGTTTCTGCCACCTACAGAGAAAGGTCACG
129 AATTTCAAAAG-GAACACAAAACCGAAACTGCC-CCTACAGAGAAAGGTCACG
* * * * * *
12585436 GTTTTTGAA-GTTTTTGA-ATGCCCAAATCACCTCCTAAAATCCGGAAAAATTATTCTGGAATAT
1 G-TTTTGAATATTTTTGACA-GCCAAAAACATCTCCTAAAATCCTGAAAAATTATTATGGAATAT
*
12585499 TTCCATGAGTTATCTATCAGGATAAATTTTATTGGAATTAAATTCCTAA
64 TTCCATAAGTTATCTATCAGGATAAATTTTATTGGAATTAAATTCCTAA
12585548 AGATACACTA
Statistics
Matches: 245, Mismatches: 40, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
178 1 0.00
179 50 0.20
180 185 0.76
181 9 0.04
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (179 bp):
GTTTTGAATATTTTTGACAGCCAAAAACATCTCCTAAAATCCTGAAAAATTATTATGGAATATTT
CCATAAGTTATCTATCAGGATAAATTTTATTGGAATTAAATTCCTAATTTTATGCTGCCAAAGAA
TTTCAAAAGGAACACAAAACCGAAACTGCCCCTACAGAGAAAGGTCACG
Found at i:12586895 original size:58 final size:57
Alignment explanation
Indices: 12586805--12586914 Score: 184
Period size: 58 Copynumber: 1.9 Consensus size: 57
12586795 CAAATTAGTT
*
12586805 TGCATGTGATAGATTTATTTTATGCAATTTAATAAATGTTATGCAATGCAAAGTAATA
1 TGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCTATGC-ATGCAAAGTAATA
**
12586863 TGCATGTGATAGATTTATTTTATGTGATTTAATAAATGCTATGCATGCAAAG
1 TGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCTATGCATGCAAAG
12586915 ATGAGACCCT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
57 8 0.16
58 41 0.84
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (57 bp):
TGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCTATGCATGCAAAGTAATA
Found at i:12588788 original size:34 final size:34
Alignment explanation
Indices: 12588722--12588789 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
12588712 AACCACTTTG
*
12588722 GGTTTTAGTTGAGCCCGTGAAAAACTAGTGTAAA
1 GGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAA
* ** * *
12588756 GGTTTTGGTTGAGCTTGTGAAAAGCCATTGTAAA
1 GGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAA
12588790 AGCTTGGTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.29, C:0.10, G:0.28, T:0.32
Consensus pattern (34 bp):
GGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAA
Found at i:12597964 original size:19 final size:19
Alignment explanation
Indices: 12597940--12597977 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12597930 ATTTTTCAAC
12597940 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
12597959 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
12597978 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:12605803 original size:2 final size:2
Alignment explanation
Indices: 12605796--12605829 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12605786 AATGGATTAC
*
12605796 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12605830 GTAAGGTCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12609395 original size:9 final size:9
Alignment explanation
Indices: 12609378--12609411 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
12609368 TGTTTTTAAG
12609378 TTTTATTAT
1 TTTTATTAT
*
12609387 TTTTGTTAT
1 TTTTATTAT
12609396 TTTTATTAT
1 TTTTATTAT
*
12609405 TATTATT
1 TTTTATT
12609412 TATACAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTTATTAT
Found at i:12611612 original size:15 final size:15
Alignment explanation
Indices: 12611568--12611615 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
12611558 TTTCCACAGA
*
12611568 TTTCCAACGAAAAAT
1 TTTCCAACAAAAAAT
**
12611583 TTTCC--CACCAAAT
1 TTTCCAACAAAAAAT
12611596 TTTCCAACAAAAAAT
1 TTTCCAACAAAAAAT
12611611 TTTCC
1 TTTCC
12611616 GTTGGAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 10 0.38
15 16 0.62
ACGTcount: A:0.40, C:0.27, G:0.02, T:0.31
Consensus pattern (15 bp):
TTTCCAACAAAAAAT
Found at i:12615164 original size:2 final size:2
Alignment explanation
Indices: 12615157--12615203 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
12615147 NNNNNNNNNN
12615157 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12615199 TA TA T
1 TA TA T
12615204 GAGTTAATAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12615346 original size:32 final size:34
Alignment explanation
Indices: 12615310--12615374 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
12615300 ATACAACTTT
12615310 ATGTATATGAGTT-A-ATATATATGTTTACATAC
1 ATGTATATGAGTTAATATATATATGTTTACATAC
12615342 ATGTATATGAGTTAATATATATATGTTTACATA
1 ATGTATATGAGTTAATATATATATGTTTACATA
12615375 TAACTTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
33 1 0.03
34 17 0.55
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (34 bp):
ATGTATATGAGTTAATATATATATGTTTACATAC
Found at i:12619080 original size:35 final size:34
Alignment explanation
Indices: 12619035--12619230 Score: 170
Period size: 35 Copynumber: 5.8 Consensus size: 34
12619025 TTAGTTGTTG
* *
12619035 GGTTTTGGTTGATCTCGTGAAAAACCATTGTTGTA
1 GGTTGTGGTTGAGC-CGTGAAAAACCATTGTTGTA
* * * *
12619070 GATTGTGGTTGAGCCTTTGAAAAATCACT-TTG--
1 GGTTGTGGTTGAGCC-GTGAAAAACCATTGTTGTA
* *
12619102 GGTTTTGGTTGAGCCCGTGAAAAACCATCGTTGTA
1 GGTTGTGGTTGAG-CCGTGAAAAACCATTGTTGTA
* * *
12619137 GGTTGTGGTTAAGCCTTTGAAAAACCACT-TTG--
1 GGTTGTGGTTGAGCC-GTGAAAAACCATTGTTGTA
* *
12619169 GGTTTTGGTTGAGCTTGTGAAAAACCATTGTTGTA
1 GGTTGTGGTTGAGC-CGTGAAAAACCATTGTTGTA
*
12619204 GGTTGTGGTTGAGCCTTTGAAAAACCA
1 GGTTGTGGTTGAGCC-GTGAAAAACCA
12619231 CTTTGGGTTT
Statistics
Matches: 125, Mismatches: 25, Indels: 22
0.73 0.15 0.13
Matches are distributed among these distances:
32 43 0.34
33 8 0.06
34 9 0.07
35 65 0.52
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (34 bp):
GGTTGTGGTTGAGCCGTGAAAAACCATTGTTGTA
Found at i:12619116 original size:32 final size:32
Alignment explanation
Indices: 12619075--12619245 Score: 200
Period size: 32 Copynumber: 5.2 Consensus size: 32
12619065 TTGTAGATTG
*
12619075 TGGTTGAGCCTTTGAAAAATCACTTTGGGTTT
1 TGGTTGAGCCTTTGAAAAACCACTTTGGGTTT
** * *
12619107 TGGTTGAGCCCGTGAAAAACCATCGTTGTAGGTTG
1 TGGTTGAGCCTTTGAAAAACCA-C-TT-TGGGTTT
*
12619142 TGGTTAAGCCTTTGAAAAACCACTTTGGGTTT
1 TGGTTGAGCCTTTGAAAAACCACTTTGGGTTT
* *
12619174 TGGTTGAG-CTTGTGAAAAACCATTGTTGTAGGTTG
1 TGGTTGAGCCTT-TGAAAAACCACT-TTG--GGTTT
12619209 TGGTTGAGCCTTTGAAAAACCACTTTGGGTTT
1 TGGTTGAGCCTTTGAAAAACCACTTTGGGTTT
12619241 TGGTT
1 TGGTT
12619246 AATTTCGGTA
Statistics
Matches: 116, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
31 3 0.03
32 51 0.44
33 6 0.05
34 6 0.05
35 47 0.41
36 3 0.03
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.37
Consensus pattern (32 bp):
TGGTTGAGCCTTTGAAAAACCACTTTGGGTTT
Found at i:12619143 original size:67 final size:67
Alignment explanation
Indices: 12619032--12619245 Score: 365
Period size: 67 Copynumber: 3.2 Consensus size: 67
12619022 AAGTTAGTTG
* * *
12619032 TTGGGTTTTGGTTGATCTCGTGAAAAACCATTGTTGTAGATTGTGGTTGAGCCTTTGAAAAATCA
1 TTGGGTTTTGGTTGAGCTCGTGAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTTTGAAAAACCA
12619097 CT
66 CT
* * *
12619099 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATCGTTGTAGGTTGTGGTTAAGCCTTTGAAAAACCA
1 TTGGGTTTTGGTTGAGCTCGTGAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTTTGAAAAACCA
12619164 CT
66 CT
*
12619166 TTGGGTTTTGGTTGAGCTTGTGAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTTTGAAAAACCA
1 TTGGGTTTTGGTTGAGCTCGTGAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTTTGAAAAACCA
12619231 CT
66 CT
12619233 TTGGGTTTTGGTT
1 TTGGGTTTTGGTT
12619246 AATTTCGGTA
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 137 1.00
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.38
Consensus pattern (67 bp):
TTGGGTTTTGGTTGAGCTCGTGAAAAACCATTGTTGTAGGTTGTGGTTGAGCCTTTGAAAAACCA
CT
Found at i:12622681 original size:28 final size:27
Alignment explanation
Indices: 12622645--12622697 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
12622635 ATATCCTGGT
*
12622645 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
12622672 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
12622698 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:12622765 original size:20 final size:20
Alignment explanation
Indices: 12622742--12622787 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
12622732 CTTCTAAACC
12622742 TCAAATCATACT-TCAATAAG
1 TCAAATCATACTCT-AATAAG
*
12622762 TCAAATTATACTCTAATAAG
1 TCAAATCATACTCTAATAAG
12622782 TCAAAT
1 TCAAAT
12622788 GGGGTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (20 bp):
TCAAATCATACTCTAATAAG
Found at i:12628180 original size:22 final size:22
Alignment explanation
Indices: 12628137--12628180 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12628127 TTTAAAACAA
* *
12628137 CTTTAAAACTAAAAACTTTGAT
1 CTTTAAAACCAAAAACTCTGAT
*
12628159 CTTTAAAACCAAAAGCTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
12628181 ACCAATCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTGAT
Found at i:12630718 original size:28 final size:27
Alignment explanation
Indices: 12630682--12630734 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
12630672 ATATCCTGGT
*
12630682 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
12630709 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
12630735 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:12630802 original size:20 final size:20
Alignment explanation
Indices: 12630779--12630824 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
12630769 CTTCTAAACC
12630779 TCAAATCATACT-TCAATAAG
1 TCAAATCATACTCT-AATAAG
*
12630799 TCAAATTATACTCTAATAAG
1 TCAAATCATACTCTAATAAG
12630819 TCAAAT
1 TCAAAT
12630825 GGGGTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (20 bp):
TCAAATCATACTCTAATAAG
Found at i:12639037 original size:19 final size:19
Alignment explanation
Indices: 12639013--12639050 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12639003 ACTTCTCAAC
*
12639013 CTCAAATCATACTCTAATA
1 CTCAAATCATACTCCAATA
*
12639032 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
12639051 AGTCAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:12645768 original size:46 final size:46
Alignment explanation
Indices: 12645718--12645814 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
12645708 GTAAAATAGA
12645718 ACAATTCATACAATTTATAAAACACAGCCCAGCCAGTCATGCCAAC
1 ACAATTCATACAATTTATAAAACACAGCCCAGCCAGTCATGCCAAC
*
12645764 ACAATTCATACAATTTATAAAACACATCCCAGCCAGTCATGCCAAC
1 ACAATTCATACAATTTATAAAACACAGCCCAGCCAGTCATGCCAAC
12645810 ACAAT
1 ACAAT
12645815 AACATAAGCC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.42, C:0.30, G:0.07, T:0.21
Consensus pattern (46 bp):
ACAATTCATACAATTTATAAAACACAGCCCAGCCAGTCATGCCAAC
Found at i:12651542 original size:11 final size:12
Alignment explanation
Indices: 12651526--12651559 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
12651516 ATATGGCCTG
12651526 CCAAAGGAA-AA
1 CCAAAGGAAGAA
12651537 CCAAAGGAAGAA
1 CCAAAGGAAGAA
12651549 -CAAAGGAAGAA
1 CCAAAGGAAGAA
12651560 AAGAAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 20 0.91
12 2 0.09
ACGTcount: A:0.62, C:0.15, G:0.24, T:0.00
Consensus pattern (12 bp):
CCAAAGGAAGAA
Found at i:12654168 original size:60 final size:60
Alignment explanation
Indices: 12654075--12654228 Score: 200
Period size: 60 Copynumber: 2.6 Consensus size: 60
12654065 TAGGAGACCA
* ** * * * *
12654075 AAACAGAAGGTTTTTCGTTGCAACGAGATTGAATCTCGCTGCAGCGAAATTGTAGCTCAG
1 AAACAGAAAGTTCCTCGCTGCAACGAGATTGAATCTCGCTGCAGCGAAATTGCAACCCAG
* * *
12654135 AAACAGAATGTTCCTTGCTGCAGCGAGATTGAATCTCGCTGCAGCGAAATTGCAACCCAG
1 AAACAGAAAGTTCCTCGCTGCAACGAGATTGAATCTCGCTGCAGCGAAATTGCAACCCAG
* *
12654195 AAACAGAAAGTTTCTCGCTGCAACGAGAATGAAT
1 AAACAGAAAGTTCCTCGCTGCAACGAGATTGAAT
12654229 TTTGCTGTAG
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 80 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (60 bp):
AAACAGAAAGTTCCTCGCTGCAACGAGATTGAATCTCGCTGCAGCGAAATTGCAACCCAG
Found at i:12657203 original size:18 final size:19
Alignment explanation
Indices: 12657175--12657222 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
12657165 GTTACGAGTG
*
12657175 AAAAGAATATTTTA-GAAT
1 AAAATAATATTTTATGAAT
*
12657193 AAAATATTATTTTATGAAT
1 AAAATAATATTTTATGAAT
12657212 AAAATAATATT
1 AAAATAATATT
12657223 AAAATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATGAAT
Found at i:12660057 original size:2 final size:2
Alignment explanation
Indices: 12660052--12660084 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12660042 ATTGTGTGTG
12660052 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12660085 TATTGATCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12660135 original size:2 final size:2
Alignment explanation
Indices: 12660130--12660162 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12660120 CCATTGTGTG
12660130 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12660163 TTATGATCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12660175 original size:78 final size:79
Alignment explanation
Indices: 12660032--12660188 Score: 282
Period size: 80 Copynumber: 2.0 Consensus size: 79
12660022 ACTTGGAAAT
*
12660032 TTTAGACTCCATTGTGTGTGTATATATATATATATATATATATATATATATATTATTGATCACAT
1 TTTAGACTCCATTGTGTGTATATATATATATATATATATATATATATATATATTATTGATCACAT
12660097 GATTTAAAAATTGC
66 GATTTAAAAATTGC
12660111 NTTTAGACTCCATTGTGTGTATATATATATATATATATATATATATATATAT-TTA-TGATCACA
1 -TTTAGACTCCATTGTGTGTATATATATATATATATATATATATATATATATATTATTGATCACA
12660174 TGATTTAAAAATTGC
65 TGATTTAAAAATTGC
12660189 ATTGTTTCAT
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
78 23 0.30
79 3 0.04
80 50 0.66
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (79 bp):
TTTAGACTCCATTGTGTGTATATATATATATATATATATATATATATATATATTATTGATCACAT
GATTTAAAAATTGC
Found at i:12663018 original size:19 final size:19
Alignment explanation
Indices: 12662981--12663018 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12662971 CCATTTAACT
* *
12662981 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATCTGAG
12663000 TATTGGAGTATAATCTGAG
1 TATTGGAGTATAATCTGAG
12663019 GGCTTGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.39
Consensus pattern (19 bp):
TATTGGAGTATAATCTGAG
Found at i:12667709 original size:18 final size:18
Alignment explanation
Indices: 12667686--12667724 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12667676 CTACTATCGT
* *
12667686 TGTTTCCACTGCTGTTTC
1 TGTTTCCACTACTGTCTC
12667704 TGTTTCCACTACTGTCTC
1 TGTTTCCACTACTGTCTC
12667722 TGT
1 TGT
12667725 CCCTACTGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.28, G:0.15, T:0.49
Consensus pattern (18 bp):
TGTTTCCACTACTGTCTC
Found at i:12668323 original size:20 final size:20
Alignment explanation
Indices: 12668298--12668343 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
12668288 TTTTGGCCTC
12668298 ATTTGACTTAATGGAGTATA
1 ATTTGACTTAATGGAGTATA
* *
12668318 ATTTGACTTATTGGAGTATG
1 ATTTGACTTAATGGAGTATA
12668338 ATTTGA
1 ATTTGA
12668344 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.43
Consensus pattern (20 bp):
ATTTGACTTAATGGAGTATA
Found at i:12668419 original size:28 final size:27
Alignment explanation
Indices: 12668388--12668440 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
12668378 TTTAGAGTAT
*
12668388 AGGGGTAAAATGGTAATTTTGCCACCCA
1 AGGGGCAAAATGGTAATTTT-CCACCCA
*
12668416 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
12668441 ACCAGGACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCCA
Found at i:12689449 original size:19 final size:19
Alignment explanation
Indices: 12689425--12689462 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12689415 CCATTTGACT
*
12689425 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
12689444 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
12689463 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:12699861 original size:25 final size:25
Alignment explanation
Indices: 12699826--12699873 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
12699816 TGGGTCAGCC
12699826 CATTTTTTAATTTT-TAAAAAAAAT
1 CATTTTTTAATTTTATAAAAAAAAT
*
12699850 CATTTTTATAATTTTATAATAAAA
1 CATTTTT-TAATTTTATAAAAAAA
12699874 TTATTTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 7 0.33
26 7 0.33
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
CATTTTTTAATTTTATAAAAAAAAT
Found at i:12699864 original size:24 final size:25
Alignment explanation
Indices: 12699826--12699880 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
12699816 TGGGTCAGCC
12699826 CATTTTTTAATTTTTA-AAAAAAAT
1 CATTTTTTAATTTTTATAAAAAAAT
*
12699850 CATTTTTATAA-TTTTATAATAAAAT
1 CATTTTT-TAATTTTTATAAAAAAAT
*
12699875 TATTTT
1 CATTTT
12699881 ATGATTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
CATTTTTTAATTTTTATAAAAAAAT
Found at i:12699881 original size:24 final size:24
Alignment explanation
Indices: 12699826--12699887 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
12699816 TGGGTCAGCC
*
12699826 CATTTTTTAATTTTTAAAAAAAAT
1 CATTTTATAATTTTTAAAAAAAAT
*
12699850 CATTTTTATAA-TTTTATAATAAAAT
1 CA-TTTTATAATTTTTA-AAAAAAAT
* *
12699875 TATTTTATGATTT
1 CATTTTATAATTT
12699888 AATTTATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 14 0.45
25 17 0.55
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (24 bp):
CATTTTATAATTTTTAAAAAAAAT
Found at i:12700008 original size:22 final size:22
Alignment explanation
Indices: 12699965--12700016 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
12699955 AATATTATTG
**
12699965 ATAATTAAATTATTAATCTTAT
1 ATAATTAAATTATTAAAATTAT
12699987 ATAATTAAA-TATATAAAATTAT
1 ATAATTAAATTAT-TAAAATTAT
12700009 -TAAATTAA
1 AT-AATTAA
12700017 TTAAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATTAAATTATTAAAATTAT
Found at i:12701597 original size:25 final size:27
Alignment explanation
Indices: 12701569--12701618 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
12701559 AGTTAGGTAA
12701569 AAATAATAA-TA-AAAATAAAATATAT
1 AAATAATAATTATAAAATAAAATATAT
*
12701594 AAATAATAATTATGAAATAAAATAT
1 AAATAATAATTATAAAATAAAATAT
12701619 TTGGTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 2 0.09
27 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (27 bp):
AAATAATAATTATAAAATAAAATATAT
Found at i:12704212 original size:243 final size:241
Alignment explanation
Indices: 12703775--12704256 Score: 883
Period size: 243 Copynumber: 2.0 Consensus size: 241
12703765 ACCACTAGCA
*
12703775 CAAAGCCAATGCTACCACATCGTATGTGGATTCAATCCATCTAGCAATCGTGTCTGCATGTAGAC
1 CAAAGCAAATGCTACCACATCGTATGTGGATTCAATCCATCTAGCAATCGTGTCTGCATGTAGAC
12703840 TTGCTTGTGCACTTCAATGTGGTTAATTATTTTTATCTATCTTCGTGATGTCCATGCATCACATC
66 TTGCTTGTGCACTTCAATGTGGTTAATTATTTTTATCTATCTTCGTGATGTCCATGCATCACATC
**
12703905 ATGTCATATTACTATATCTAGATCCAATGAGACCCAAGTTCTGCTTGTATGGCTCCATTGTTACA
131 ATGTCATATTACTATATCTAGATCCAATGAGACCCAAGTTCTGCTAATATGGCTCCATTGTTACA
*
12703970 TTAACAATGTTCAAAACCTTTTATTAGTTCCATGGACTAACGATTT
196 TTAAAAATGTTCAAAACCTTTTATTAGTTCCATGGACTAACGATTT
* *
12704016 NCAAAGCAAATTGCTACCTCATCGTATGTGGGTTCAATCCATCTAGCAATCGTGTCTGCATGTAG
1 -CAAAGCAAA-TGCTACCACATCGTATGTGGATTCAATCCATCTAGCAATCGTGTCTGCATGTAG
12704081 ACTTGCTTGTGCACTTCAATGTGGTTAATTATTTTTATCTATCTTCGTGATGTCCATGCATCACA
64 ACTTGCTTGTGCACTTCAATGTGGTTAATTATTTTTATCTATCTTCGTGATGTCCATGCATCACA
*
12704146 TCATGTCATATTACTATATCTAGATTCAATGAGACCCAAGTTCTGCTAATATGGCTCCATTGTTA
129 TCATGTCATATTACTATATCTAGATCCAATGAGACCCAAGTTCTGCTAATATGGCTCCATTGTTA
12704211 CATTAAAAATGTTCAAAACCTTTTATTAGTTCCATGGACTAACGAT
194 CATTAAAAATGTTCAAAACCTTTTATTAGTTCCATGGACTAACGAT
12704257 CTAAGTATGT
Statistics
Matches: 232, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
242 8 0.03
243 224 0.97
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (241 bp):
CAAAGCAAATGCTACCACATCGTATGTGGATTCAATCCATCTAGCAATCGTGTCTGCATGTAGAC
TTGCTTGTGCACTTCAATGTGGTTAATTATTTTTATCTATCTTCGTGATGTCCATGCATCACATC
ATGTCATATTACTATATCTAGATCCAATGAGACCCAAGTTCTGCTAATATGGCTCCATTGTTACA
TTAAAAATGTTCAAAACCTTTTATTAGTTCCATGGACTAACGATTT
Found at i:12704527 original size:22 final size:22
Alignment explanation
Indices: 12704499--12704544 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
12704489 CTAACCTCAT
12704499 TTTGTCTATGAGATAAATACAC
1 TTTGTCTATGAGATAAATACAC
12704521 TTTGTCTATGAGATAAATACAC
1 TTTGTCTATGAGATAAATACAC
12704543 TT
1 TT
12704545 GTACATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (22 bp):
TTTGTCTATGAGATAAATACAC
Found at i:12706273 original size:60 final size:60
Alignment explanation
Indices: 12706193--12706377 Score: 228
Period size: 60 Copynumber: 3.1 Consensus size: 60
12706183 CTCTCAGACA
* * *
12706193 TCTTCACCTACTCGTGGGAACTGCCCACACCACCATATATAAATCGGGGCTTCAATTCCC
1 TCTTTACCTACTCGTGGGAACTGCCCACGCCACCATATATAAATCGGGGCTTCAAGTCCC
* * * * ** * *
12706253 TTTTTACCTACTTGTGGGAACTGCCCACGTCACTATATATAAATCAAGGCTTTAGGTCCC
1 TCTTTACCTACTCGTGGGAACTGCCCACGCCACCATATATAAATCGGGGCTTCAAGTCCC
* *
12706313 TCTTTACCTACTCGTGGGAACTACCCACGCCAACCA-ATATAAATCGGGGCTTCAGGTCCC
1 TCTTTACCTACTCGTGGGAACTGCCCACGCC-ACCATATATAAATCGGGGCTTCAAGTCCC
*
12706373 CCTTT
1 TCTTT
12706378 TTAAATCAAA
Statistics
Matches: 104, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
60 101 0.97
61 3 0.03
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.28
Consensus pattern (60 bp):
TCTTTACCTACTCGTGGGAACTGCCCACGCCACCATATATAAATCGGGGCTTCAAGTCCC
Found at i:12706751 original size:2 final size:2
Alignment explanation
Indices: 12706744--12706777 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
12706734 AACCATGTAG
12706744 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12706778 AAGAGAAACG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12707282 original size:68 final size:69
Alignment explanation
Indices: 12707116--12707293 Score: 241
Period size: 69 Copynumber: 2.6 Consensus size: 69
12707106 GGCACCGTCG
* *
12707116 CTACTTCCTCTCTCTTTCTTCTTCTTTTTCTTTCTTCTTCCTTCCCTCTCATTCTTCTCCTCGAC
1 CTACTCCCTCTCTCTTTCTTCTTCTTTTTCTTTTTTCTTCCTTCCCTCTCATTCTTCTCCTCGAC
*
12707181 GCTA
66 GCCA
* * * *
12707185 CTACTCTCTCTCTCTTTCTTCTTCATTTTCTTTTTTCTTCCTTCCCTTTC-TTCTTCTCCTTGAC
1 CTACTCCCTCTCTCTTTCTTCTTCTTTTTCTTTTTTCTTCCTTCCCTCTCATTCTTCTCCTCGAC
*
12707249 GCCG
66 GCCA
* *
12707253 CTGCTCCCTCTCTCTTTCTTTTTCTTTTTCTCTTTCTTCTT
1 CTACTCCCTCTCTCTTTCTTCTTCTTTTTCT-TTT-TTCTT
12707294 TCTTTTTCTT
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
68 42 0.44
69 48 0.51
70 5 0.05
ACGTcount: A:0.04, C:0.37, G:0.03, T:0.56
Consensus pattern (69 bp):
CTACTCCCTCTCTCTTTCTTCTTCTTTTTCTTTTTTCTTCCTTCCCTCTCATTCTTCTCCTCGAC
GCCA
Found at i:12707304 original size:10 final size:10
Alignment explanation
Indices: 12707273--12707332 Score: 70
Period size: 10 Copynumber: 6.1 Consensus size: 10
12707263 TCTCTTTCTT
12707273 TTTCTTTTTC
1 TTTCTTTTTC
12707283 --TCTTTCTTC
1 TTTCTTT-TTC
12707292 TTTCTTTTTC
1 TTTCTTTTTC
12707302 TTTCTTTTTC
1 TTTCTTTTTC
* *
12707312 CTTCCTTTTC
1 TTTCTTTTTC
*
12707322 TTTCTTCTTC
1 TTTCTTTTTC
12707332 T
1 T
12707333 CAAGCCGCTG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
8 5 0.12
9 3 0.07
10 29 0.69
11 5 0.12
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:12707311 original size:6 final size:6
Alignment explanation
Indices: 12707267--12707304 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
12707257 TCCCTCTCTC
*
12707267 TTTCTT TTTCTT TTTCTC TTTCTT CTTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT -TTTCTT TTTCTT T
12707305 CTTTTTCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:12707313 original size:87 final size:84
Alignment explanation
Indices: 12707195--12707393 Score: 222
Period size: 87 Copynumber: 2.3 Consensus size: 84
12707185 CTACTCTCTC
* *
12707195 TCTCTTTCTTCTTCATTTTCTTTTTTCTTCCTTCCCTTTC-TTCTTCTCCTTGACGCCGCTGCTC
1 TCTCTTTCTTCTTCATTTTCTTTTTTCTTCCTTCCCTTTCTTTCTTCTCC-TCAAGCCGCTGCT-
*
12707259 CCTCTCTCTTTCTTTTTCTTTT
64 -CTCTCTCTTTCTTTTTCTTCT
* * *
12707281 TCTCTTTCTTCTTTCTTTTTCTTTCTTT-TTCCTTCCTTTTCTTTCTTCTTCTCAAGCCGCTGCT
1 TCTCTTTCTTC-TTCATTTTCTTT-TTTCTTCCTTCCCTTTCTTTCTTCTCCTCAAGCCGCTGCT
* *
12707345 CTTTCTCTTTTTTTTTCTTCT
64 CTCTCTCTTTCTTTTTCTTCT
* * *
12707366 TCTCTCTCCTTTCTTCCTTGTCTTTTTT
1 TCTCT-TTC-TTCTTCATTTTCTTTTTT
12707394 TGGCCAGGCC
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
85 26 0.27
86 23 0.24
87 37 0.38
88 11 0.11
ACGTcount: A:0.02, C:0.32, G:0.04, T:0.62
Consensus pattern (84 bp):
TCTCTTTCTTCTTCATTTTCTTTTTTCTTCCTTCCCTTTCTTTCTTCTCCTCAAGCCGCTGCTCT
CTCTCTTTCTTTTTCTTCT
Found at i:12707425 original size:12 final size:12
Alignment explanation
Indices: 12707408--12707469 Score: 63
Period size: 12 Copynumber: 5.0 Consensus size: 12
12707398 CAGGCCCCCA
12707408 TTTTCTTCTTCT
1 TTTTCTTCTTCT
12707420 TTTTCTTCTTTCT
1 TTTTCTTC-TTCT
12707433 TTTCTCTTC-TCTT
1 TTT-TCTTCTTC-T
*
12707446 TTTTCTTTTTCT
1 TTTTCTTCTTCT
* *
12707458 TTCTCTTTTTCT
1 TTTTCTTCTTCT
12707470 CTTCACATGC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 26 0.59
13 13 0.30
14 5 0.11
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTCTTCT
Found at i:12707433 original size:19 final size:18
Alignment explanation
Indices: 12707408--12707473 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 18
12707398 CAGGCCCCCA
*
12707408 TTTTCTTCTTCTTTTTCT
1 TTTTCTTCTTCTTTCTCT
12707426 TCTTTCTT-TTCTCTTCTCTT
1 T-TTTCTTCTTCT-TTCTC-T
*
12707446 TTTTCTTTTTCTTTCTCT
1 TTTTCTTCTTCTTTCTCT
12707464 TTTTC-TCTTC
1 TTTTCTTCTTC
12707474 ACATGCCAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
17 4 0.10
18 11 0.26
19 21 0.50
20 6 0.14
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTCTTCTTCTTTCTCT
Found at i:12707448 original size:26 final size:24
Alignment explanation
Indices: 12707411--12707469 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
12707401 GCCCCCATTT
12707411 TCTTCTTCTTTTTCTTCTTTCTTTTC
1 TCTTCTTCTTTTTCTT-TTTC-TTTC
12707437 TCTTC-TCTTTTTTCTTTTTCTTTC
1 TCTTCTTC-TTTTTCTTTTTCTTTC
*
12707461 TCTTTTTCT
1 TCTTCTTCT
12707470 CTTCACATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 9 0.30
25 8 0.27
26 13 0.43
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (24 bp):
TCTTCTTCTTTTTCTTTTTCTTTC
Found at i:12714289 original size:16 final size:16
Alignment explanation
Indices: 12714268--12714298 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12714258 ACTCCCTCTC
12714268 TCTTTCTTCTTCTTTT
1 TCTTTCTTCTTCTTTT
12714284 TCTTTCTTCTTCTTT
1 TCTTTCTTCTTCTTT
12714299 CCCTTTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TCTTTCTTCTTCTTTT
Found at i:12714304 original size:16 final size:16
Alignment explanation
Indices: 12714269--12714311 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
12714259 CTCCCTCTCT
**
12714269 CTTTCTTCTTCTTTTT
1 CTTTCTTCTTCTTTCC
12714285 CTTTCTTCTTCTTTCC
1 CTTTCTTCTTCTTTCC
12714301 CTTTCCTTCTT
1 CTTT-CTTCTT
12714312 TTCTTCGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
CTTTCTTCTTCTTTCC
Found at i:12714327 original size:69 final size:69
Alignment explanation
Indices: 12714199--12714384 Score: 245
Period size: 69 Copynumber: 2.7 Consensus size: 69
12714189 TTGCTCTCTA
* *
12714199 TCTCTTTCTTCTTC-TTTTCTTTCTTC-TCTCTCCCTCTTCTTCTTTTCCTTGACATCACTACTC
1 TCTCTTTCTTCTTCTTTTTCTTTCTTCTTCTTTCCCTCTTCTTCTTTTCCTTGACACCACTACTC
12714262 CCTC
66 CCTC
12714266 TCTCTTTCTTCTTCTTTTTCTTTCTTCTTCTTTCCCT-TTCCTTCTTTT-CTTCGACACCACTAC
1 TCTCTTTCTTCTTCTTTTTCTTTCTTCTTCTTTCCCTCTT-CTTCTTTTCCTT-GACACCACTAC
*
12714329 TCCCTT
64 TCCCTC
* **
12714335 TCTCTTTCTTCTTCTTTTTATTTTTCTTCTTCTTTTTCTCTTTCTTCTTT
1 TCTCTTTCTTCTTC-TTTT-TCTTTCTTCTTCTTTCCCTC-TTCTTCTTT
12714385 CTTTTTCTTT
Statistics
Matches: 105, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
67 14 0.13
68 17 0.16
69 45 0.43
70 4 0.04
71 16 0.15
72 7 0.07
73 2 0.02
ACGTcount: A:0.05, C:0.34, G:0.01, T:0.60
Consensus pattern (69 bp):
TCTCTTTCTTCTTCTTTTTCTTTCTTCTTCTTTCCCTCTTCTTCTTTTCCTTGACACCACTACTC
CCTC
Found at i:12714362 original size:18 final size:18
Alignment explanation
Indices: 12714333--12714401 Score: 93
Period size: 18 Copynumber: 3.7 Consensus size: 18
12714323 CACTACTCCC
*
12714333 TTTCTCTTTCTTCTTCTT
1 TTTCTTTTTCTTCTTCTT
*
12714351 TTTATTTTTCTTCTTCTT
1 TTTCTTTTTCTTCTTCTT
*
12714369 TTTCTCTTTCTTCTTTCTT
1 TTTCTTTTTCTTC-TTCTT
12714388 TTTCTTTCTTCTTC
1 TTTCTTT-TTCTTC
12714402 CTTCCCTCTC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
18 27 0.61
19 11 0.25
20 6 0.14
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTCTTTTTCTTCTTCTT
Found at i:12714414 original size:106 final size:107
Alignment explanation
Indices: 12714266--12714471 Score: 317
Period size: 106 Copynumber: 1.9 Consensus size: 107
12714256 CTACTCCCTC
* * * *
12714266 TCTCTTTCTTCTTCTTTTTCTTTCTTCTTCTTTCCCTTTCCTTCTTTTCTTCGACACCACTACTC
1 TCTCTTTCTTCTTCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCGACACCACTACTC
12714331 CCTTTCTCTTTCTTCT-TCTTTTTATTT-TTCTTCTTCTTTT
66 CCTTTCTCTTTCTTCTCTCTTTTTATTTCTTCTTCTTCTTTT
* *
12714371 TCTCTTTCTTCTTTCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCGACTCCACTGCT
1 TCTCTTTCTTC-TTCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCGACACCACTACT
* *
12714436 CCCTTTCTTTTTCTTCTCTCTTTTTCTTTCTTCTTC
65 CCCTTTCTCTTTCTTCTCTCTTTTTATTTCTTCTTC
12714472 CTTCCCTCTC
Statistics
Matches: 90, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
105 11 0.12
106 63 0.70
107 10 0.11
108 6 0.07
ACGTcount: A:0.03, C:0.34, G:0.01, T:0.61
Consensus pattern (107 bp):
TCTCTTTCTTCTTCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCGACACCACTACTC
CCTTTCTCTTTCTTCTCTCTTTTTATTTCTTCTTCTTCTTTT
Found at i:12714443 original size:70 final size:70
Alignment explanation
Indices: 12714369--12714531 Score: 240
Period size: 70 Copynumber: 2.3 Consensus size: 70
12714359 TCTTCTTCTT
*
12714369 TTTCTCTTTCTTCTTTCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCGAC-TCCACT
1 TTTCTCTTTCTTCTTTCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCAACGT-CACT
*
12714433 GCTCCC
65 ACTCCC
* * **
12714439 TTTCTTTTTCTTCTCTCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCAACGTCGTTA
1 TTTCTCTTTCTTCTTTCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCAACGTCACTA
12714504 CTCCC
66 CTCCC
*
12714509 TCTCTCTTTCTTC-TTCTTTTTCT
1 TTTCTCTTTCTTCTTTCTTTTTCT
12714532 CTTTCTTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
69 9 0.11
70 73 0.88
71 1 0.01
ACGTcount: A:0.03, C:0.39, G:0.02, T:0.56
Consensus pattern (70 bp):
TTTCTCTTTCTTCTTTCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCAACGTCACTA
CTCCC
Found at i:12714508 original size:176 final size:173
Alignment explanation
Indices: 12714199--12714550 Score: 458
Period size: 176 Copynumber: 2.0 Consensus size: 173
12714189 TTGCTCTCTA
* * *
12714199 TCTCTTTCTTCTTCTTTTCTTTCTTCTCTCTCCCTCTTCTTCTTTTCCTTGACATCACTACTCCC
1 TCTCTTTCTTCTTCTTTTCTTTCTTCTCTCTCCCTCTCCTTCTTCTCCTCGACATCACTACTCCC
* * * * *
12714264 TCTCTCTTTCTTCTTCTTTTTCTTTCTTCTTCTTTCCCTTTCCTTCTTTTCTTCGACACCACTAC
66 TCTCTCTTTCTTCTTCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCAACACCACTAC
* *
12714329 TCCCTTTCTCTTTCTTCTTCTTTTTATTTTTC-TTCTTCTTTT
131 TCCCTCTCTCTTTCTTCTTCTTTTTATCTTTCTTTCTTCTTTT
*
12714371 TCTCTTTCTTCTTTCTTTTTCTTTCTTCT-TCCTTCCCTCTCCTTCTTCTCCTCGAC-TCCACTG
1 TCTCTTTCTTC-TTC-TTTTCTTTCTTCTCT-C-TCCCTCTCCTTCTTCTCCTCGACAT-CACTA
* * **
12714434 CTCCCTTTCTTTTTCTTCTCTCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCAACGT
61 CTCCCTCTCTCTTTCTTCT-TCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCAACAC
** * *
12714499 CGTTACTCCCTCTCTCTTTCTTCTTCTTTTTCTCTTTCTTTTTTCTTTT
125 CACTACTCCCTCTCTCTTTCTTCTTCTTTTTATCTTTCTTTCTTCTTTT
12714548 TCT
1 TCT
12714551 TTCTTGTCTT
Statistics
Matches: 154, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
172 11 0.07
173 4 0.03
174 15 0.10
175 41 0.27
176 71 0.46
177 12 0.08
ACGTcount: A:0.04, C:0.36, G:0.02, T:0.59
Consensus pattern (173 bp):
TCTCTTTCTTCTTCTTTTCTTTCTTCTCTCTCCCTCTCCTTCTTCTCCTCGACATCACTACTCCC
TCTCTCTTTCTTCTTCTTTTTCTTTCTTCTTCCTTCCCTCTCCTTCTTCTCCTCAACACCACTAC
TCCCTCTCTCTTTCTTCTTCTTTTTATCTTTCTTTCTTCTTTT
Found at i:12714533 original size:22 final size:23
Alignment explanation
Indices: 12714508--12714554 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
12714498 TCGTTACTCC
12714508 CTCTCTCTTTCTTCTTCTT-TTT
1 CTCTCTCTTTCTTCTTCTTCTTT
* * *
12714530 CTCTTTCTTTTTTCTTTTTCTTT
1 CTCTCTCTTTCTTCTTCTTCTTT
12714553 CT
1 CT
12714555 TGTCTTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (23 bp):
CTCTCTCTTTCTTCTTCTTCTTT
Found at i:12714674 original size:12 final size:12
Alignment explanation
Indices: 12714657--12714718 Score: 56
Period size: 12 Copynumber: 5.0 Consensus size: 12
12714647 CAGCCCCCCC
12714657 TTTTCTTTTTCT
1 TTTTCTTTTTCT
12714669 TTTTCTTCTTTC-
1 TTTTCTT-TTTCT
*
12714681 TTTTCTCTTCTCT
1 TTTTCT-TTTTCT
12714694 TTTGTCTTTTTCCT
1 TTT-TCTTTTT-CT
*
12714708 TCTT-TTTTTCT
1 TTTTCTTTTTCT
12714719 CTTCACATGC
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
11 2 0.05
12 21 0.50
13 12 0.29
14 7 0.17
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:12714691 original size:14 final size:13
Alignment explanation
Indices: 12714657--12714691 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
12714647 CAGCCCCCCC
12714657 TTTTCTT-TTTCT
1 TTTTCTTCTTTCT
12714669 TTTTCTTCTTTCT
1 TTTTCTTCTTTCT
12714682 TTTCTCTTCT
1 TTT-TCTTCT
12714692 CTTTTGTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.33
13 8 0.38
14 6 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCTTCTTTCT
Found at i:12714694 original size:19 final size:18
Alignment explanation
Indices: 12714657--12714718 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
12714647 CAGCCCCCCC
*
12714657 TTTTCTTTTTCTTTTTCT
1 TTTTCTTTTTCTTTCTCT
12714675 TCTTTC-TTTTCTCTTCTCT
1 T-TTTCTTTTTCT-TTCTCT
* *
12714694 TTTGTCTTTTTCCTTCTTT
1 TTT-TCTTTTTCTTTCTCT
12714713 TTTTCT
1 TTTTCT
12714719 CTTCACATGC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 12 0.32
19 20 0.54
20 5 0.14
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTTCTTTCTCT
Found at i:12714703 original size:32 final size:31
Alignment explanation
Indices: 12714660--12714722 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
12714650 CCCCCCCTTT
12714660 TCTTTTTCTTTTT-CTTCTTTCTTTTCTCTTC
1 TCTTTTTCTTTTTCCTTCTTT-TTTTCTCTTC
12714691 TCTTTTGTCTTTTTCCTTCTTTTTTTCTCTTC
1 TCTTTT-TCTTTTTCCTTCTTTTTTTCTCTTC
12714723 ACATGCTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 6 0.20
32 17 0.57
33 7 0.23
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (31 bp):
TCTTTTTCTTTTTCCTTCTTTTTTTCTCTTC
Found at i:12715998 original size:58 final size:58
Alignment explanation
Indices: 12715913--12716025 Score: 199
Period size: 58 Copynumber: 1.9 Consensus size: 58
12715903 CATCTTTACA
*
12715913 TGCATAGCATTTATTAAATCGTATAAAATAAATCTATCACATGCATACTACTTTGCAT
1 TGCATAGCATTTATTAAATCGTATAAAATAAATCTATCACATGCAAACTACTTTGCAT
* *
12715971 TGCATAGCGTTTATTAAATTGTATAAAATAAATCTATCACATGCAAACTACTTTG
1 TGCATAGCATTTATTAAATCGTATAAAATAAATCTATCACATGCAAACTACTTTG
12716026 GATGATTATA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (58 bp):
TGCATAGCATTTATTAAATCGTATAAAATAAATCTATCACATGCAAACTACTTTGCAT
Found at i:12725563 original size:27 final size:29
Alignment explanation
Indices: 12725526--12725584 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
12725516 GGACAAATGT
*
12725526 CCTGGTGGTGG-AAAATTACAATTTTGCC
1 CCTGGTGGTGGTAAAATTACAATTTTACC
*
12725554 CCTGG-GGTGGTAAAATTACCATTTTACC
1 CCTGGTGGTGGTAAAATTACAATTTTACC
12725582 CCT
1 CCT
12725585 ATACTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (29 bp):
CCTGGTGGTGGTAAAATTACAATTTTACC
Found at i:12725652 original size:19 final size:19
Alignment explanation
Indices: 12725628--12725665 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12725618 ACTTCTAAAC
*
12725628 CTCAAATCGTACTCCAATA
1 CTCAAATCATACTCCAATA
12725647 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
12725666 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.32, G:0.03, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:12731048 original size:22 final size:22
Alignment explanation
Indices: 12731005--12731048 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12730995 TTTAAAACCA
* *
12731005 CTTTAAAACTAAAAACTTTGAT
1 CTTTAAAACCAAAAACTCTGAT
*
12731027 CTTTAAAACCAAAAGCTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
12731049 ACCAATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTGAT
Found at i:12735915 original size:18 final size:19
Alignment explanation
Indices: 12735874--12735917 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
12735864 CATTTCACGC
* *
12735874 ATTCATGCATGTGACATAT
1 ATTCATTCATATGACATAT
*
12735893 TTTCATTCATATG-CATAT
1 ATTCATTCATATGACATAT
12735911 ATTCATT
1 ATTCATT
12735918 TCATGTTTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (19 bp):
ATTCATTCATATGACATAT
Found at i:12737869 original size:13 final size:13
Alignment explanation
Indices: 12737851--12737875 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12737841 GGAAAATTTG
12737851 TGATTTTATAAAA
1 TGATTTTATAAAA
12737864 TGATTTTATAAA
1 TGATTTTATAAA
12737876 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:12740641 original size:81 final size:81
Alignment explanation
Indices: 12740486--12740650 Score: 226
Period size: 81 Copynumber: 2.0 Consensus size: 81
12740476 CGGGAGTGTG
*
12740486 GATGATGAGATTGCCTATGTGCGCGATGTGGGGGGAGCACATGATGGCATTAGTTATGCACAATG
1 GATGATGAGATTGCCTATGTGCGCAATGTGGGGGGAGCACATGATGGCATTAGTTATGCACAATG
* *
12740551 TGGGGGTGCACACGAT
66 AGGGAGTGCACACGAT
* * ***
12740567 GATGATGATATATGCC-ATGTGCGCAATGTGGGGGGAGCACATGATGGCATTAGTTGTGTGTGAA
1 GATGATGAGAT-TGCCTATGTGCGCAATGTGGGGGGAGCACATGATGGCATTAGTTATG-CACAA
12740631 T-AGGGAGTGCACACGAT
64 TGAGGGAGTGCACACGAT
12740648 GAT
1 GAT
12740651 ATTGAAATGT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
81 67 0.91
82 7 0.09
ACGTcount: A:0.25, C:0.13, G:0.36, T:0.25
Consensus pattern (81 bp):
GATGATGAGATTGCCTATGTGCGCAATGTGGGGGGAGCACATGATGGCATTAGTTATGCACAATG
AGGGAGTGCACACGAT
Found at i:12740708 original size:35 final size:35
Alignment explanation
Indices: 12740620--12740712 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 35
12740610 ATGGCATTAG
12740620 TTGTGTGTGAATAGGGAGTGCACACGATGATATTGAA
1 TTGTGTGTG--TAGGGAGTGCACACGATGATATTGAA
* * * * * **
12740657 ATGTGCGAGTAAGGAGTGCACATGATGATATTGCC
1 TTGTGTGTGTAGGGAGTGCACACGATGATATTGAA
12740692 TTGTGTGTGTAGGGAGTGCAC
1 TTGTGTGTGTAGGGAGTGCAC
12740713 CTTGGCTGAG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
35 39 0.87
37 6 0.13
ACGTcount: A:0.26, C:0.11, G:0.34, T:0.29
Consensus pattern (35 bp):
TTGTGTGTGTAGGGAGTGCACACGATGATATTGAA
Found at i:12745546 original size:19 final size:18
Alignment explanation
Indices: 12745505--12745550 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
12745495 AGTTATGAAG
*
12745505 AAAAGAAGAAACAAAAAA
1 AAAATAAGAAACAAAAAA
12745523 AAAATAAGAAA-AAAGAAA
1 AAAATAAGAAACAAA-AAA
12745541 AGAAATAAGA
1 A-AAATAAGA
12745551 GAGTAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 14 0.56
19 8 0.32
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (18 bp):
AAAATAAGAAACAAAAAA
Found at i:12747692 original size:21 final size:22
Alignment explanation
Indices: 12747667--12747719 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
12747657 CCTTCTCTTA
*
12747667 TAAAACCTCCAAGTACA-TCTC
1 TAAAACCTCCAAGAACATTCTC
* * *
12747688 TAAAACTTGCAAGAATATTCTC
1 TAAAACCTCCAAGAACATTCTC
12747710 TAAAACCTCC
1 TAAAACCTCC
12747720 GGGTATATTC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.40, C:0.28, G:0.06, T:0.26
Consensus pattern (22 bp):
TAAAACCTCCAAGAACATTCTC
Found at i:12747737 original size:21 final size:21
Alignment explanation
Indices: 12747702--12747818 Score: 99
Period size: 21 Copynumber: 5.3 Consensus size: 21
12747692 ACTTGCAAGA
12747702 ATATTCTCTAAAACCTCCGGGT
1 ATATTCTC-AAAACCTCCGGGT
*
12747724 ATATTCTCAAAACCTCTGGGT
1 ATATTCTCAAAACCTCCGGGT
* * *
12747745 ATATTCTTATAAAGCCTCTGGGA
1 ATATTCTCA-AAA-CCTCCGGGT
* * *
12747768 AAATCTTTACAAAACCTCCAGGT
1 ATAT-TCT-CAAAACCTCCGGGT
* *
12747791 ATATTCTTAAAACCTTCGGGT
1 ATATTCTCAAAACCTCCGGGT
*
12747812 AAATTCT
1 ATATTCT
12747819 TATAAAACCT
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
21 37 0.49
22 13 0.17
23 20 0.26
24 5 0.07
25 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (21 bp):
ATATTCTCAAAACCTCCGGGT
Found at i:12747836 original size:23 final size:23
Alignment explanation
Indices: 12747710--12747836 Score: 102
Period size: 23 Copynumber: 5.7 Consensus size: 23
12747700 GAATATTCTC
*
12747710 TAAAACCTCCGGGTATATTC-T-
1 TAAAACCTCCGGGTAAATTCTTA
* * *
12747731 CAAAACCTCTGGGTATATTCTTA
1 TAAAACCTCCGGGTAAATTCTTA
* * *
12747754 TAAAGCCTCTGGG-AAAATCTTTA
1 TAAAACCTCCGGGTAAATTC-TTA
* * *
12747777 CAAAACCTCCAGGTATATTC-T-
1 TAAAACCTCCGGGTAAATTCTTA
*
12747798 TAAAACCTTCGGGTAAATTCTTA
1 TAAAACCTCCGGGTAAATTCTTA
*
12747821 TAAAACCTCCGAGTAA
1 TAAAACCTCCGGGTAA
12747837 CTAGCATCAA
Statistics
Matches: 82, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 34 0.41
22 7 0.09
23 37 0.45
24 4 0.05
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (23 bp):
TAAAACCTCCGGGTAAATTCTTA
Found at i:12747934 original size:101 final size:101
Alignment explanation
Indices: 12747822--12748207 Score: 314
Period size: 101 Copynumber: 3.8 Consensus size: 101
12747812 AAATTCTTAT
* *** * *
12747822 AAAACCTCCGAGTAACTAGCATCAAGATTTTTTTAAAGTTACGTAGCCTCGTTTAAAGACGACG-
1 AAAACCTCCGAGTAATTATTTTCAGGATTTTTTTAAAGTTACGTAACCTCGTTTAAAGACGA-GA
* * *
12747886 AGCAA-CTTTTCTTATAAAA-TTGTCGGGTATATTCTCC
65 AGCAATC-TTTCTTATAAAACCTCT-GGGAATATTCTCC
* * * * *
12747923 AAAACCTCCGAGTAATTATTTTTAGGATTTCTTTAAAGTTATGTAACCTCGTTTAGAGATGAGAA
1 AAAACCTCCGAGTAATTATTTTCAGGATTTTTTTAAAGTTACGTAACCTCGTTTAAAGACGAGAA
12747988 GCAATCTTTCTTATAAAACCTCTGGGAATATTCTCC
66 GCAATCTTTCTTATAAAACCTCTGGGAATATTCTCC
* *** * * * *
12748024 AAAACCTCCTG-GTAATTATTTTCAGGATTTTTTTAAAGTTACATAGTTTCATTTAGAGATGAGG
1 AAAACCTCC-GAGTAATTATTTTCAGGATTTTTTTAAAGTTACGTAACCTCGTTTAAAGACGAGA
* * *** * *
12748088 AGCAATCTTTTTTATACAACCTCCAAGTATA-TCGCC
65 AGCAATCTTTCTTATAAAACCTCTGGGAATATTCTCC
* * * * * * * * * * *
12748124 AAAACTTCCGGGCAATTAGTTTCAAGATTTCTTTAAAGCTACGTAACCTCATTTAGAGATGAGGA
1 AAAACCTCCGAGTAATTATTTTCAGGATTTTTTTAAAGTTACGTAACCTCGTTTAAAGACGAGAA
* *
12748189 GTAACCTCTTCTTATAAAA
66 GCAATCT-TTCTTATAAAA
12748208 ACTCCGAGTA
Statistics
Matches: 235, Mismatches: 44, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
99 1 0.00
100 63 0.27
101 167 0.71
102 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (101 bp):
AAAACCTCCGAGTAATTATTTTCAGGATTTTTTTAAAGTTACGTAACCTCGTTTAAAGACGAGAA
GCAATCTTTCTTATAAAACCTCTGGGAATATTCTCC
Found at i:12748246 original size:21 final size:21
Alignment explanation
Indices: 12748204--12748264 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
12748194 CTCTTCTTAT
* * *
12748204 AAAAACTCCGAGTATATTTTC
1 AAAACCTCCGAGTACATCTTC
* *
12748225 AACACCTCCGGGTACATCTTC
1 AAAACCTCCGAGTACATCTTC
*
12748246 AAAACCTCTGAGTACATCT
1 AAAACCTCCGAGTACATCT
12748265 CTAAGACTTC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (21 bp):
AAAACCTCCGAGTACATCTTC
Found at i:12748381 original size:50 final size:48
Alignment explanation
Indices: 12748291--12748397 Score: 153
Period size: 50 Copynumber: 2.1 Consensus size: 48
12748281 ATCATTTATT
*
12748291 TTTTTAAAGTTGTGGAGCCTTCATGAGAGGAGTTGTTTATTTTTCAAATTG
1 TTTTT-AAGTTGTGGAGCCTTAAT-AGAGGAGTTGTTTATTTTTC-AATTG
12748342 ATTTTTAAGTTGTGGAGCCTTAA-ATGAGGAGTTGTTTATTTTTCAATTG
1 -TTTTTAAGTTGTGGAGCCTTAATA-GAGGAGTTGTTTATTTTTCAATTG
12748391 TTTTTAA
1 TTTTTAA
12748398 AAAGTGGTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
48 7 0.13
49 6 0.11
50 19 0.36
51 16 0.30
52 5 0.09
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (48 bp):
TTTTTAAGTTGTGGAGCCTTAATAGAGGAGTTGTTTATTTTTCAATTG
Found at i:12748419 original size:52 final size:50
Alignment explanation
Indices: 12748317--12748431 Score: 144
Period size: 52 Copynumber: 2.3 Consensus size: 50
12748307 GCCTTCATGA
* *
12748317 GAGGAGTTGTTTATTTTTCAAATTGATTTTTAAGTTGTGGAGCCTTAAAT
1 GAGGAGTTGTTTATTTTTCAAATTGATTTTTAAGTGGTGAAGCCTTAAAT
*
12748367 GAGGAGTTGTTTATTTTTC-AATTG-TTTTTAAAAAGTGGTTTAAGCCTTAAAT
1 GAGGAGTTGTTTATTTTTCAAATTGATTTTT---AAGTGG-TGAAGCCTTAAAT
*
12748419 GAAGAGTTGTTTA
1 GAGGAGTTGTTTA
12748432 ACCAAGTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
48 5 0.09
49 5 0.09
50 19 0.33
51 5 0.09
52 23 0.40
ACGTcount: A:0.28, C:0.05, G:0.22, T:0.45
Consensus pattern (50 bp):
GAGGAGTTGTTTATTTTTCAAATTGATTTTTAAGTGGTGAAGCCTTAAAT
Found at i:12761338 original size:19 final size:19
Alignment explanation
Indices: 12761314--12761353 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
12761304 GATCTTCTTA
*
12761314 CTCCCTTTAAATACTTTCT
1 CTCCCTCTAAATACTTTCT
12761333 CTCCCTCTAAATACTTTCT
1 CTCCCTCTAAATACTTTCT
12761352 CT
1 CT
12761354 TATATTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.45
Consensus pattern (19 bp):
CTCCCTCTAAATACTTTCT
Found at i:12768993 original size:21 final size:21
Alignment explanation
Indices: 12768955--12768994 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12768945 CATAAAATTG
* *
12768955 AAAGTAAATATGTTTATATTT
1 AAAGTAAATATATATATATTT
*
12768976 AAAGTACATATATATATAT
1 AAAGTAAATATATATATAT
12768995 ATATACAACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAGTAAATATATATATATTT
Found at i:12774482 original size:2 final size:2
Alignment explanation
Indices: 12774475--12774506 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12774465 ATAAAATGAA
12774475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12774507 GGAAAAGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.