Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 114 of 185
Found at i:35711959 original size:40 final size:40
Alignment explanation
Indices: 35711904--35711998 Score: 190
Period size: 40 Copynumber: 2.4 Consensus size: 40
35711894 TTGATGTTGT
35711904 GATGGGCTAAGGCCCTACTGCATATTTGATACTGTACTGA
1 GATGGGCTAAGGCCCTACTGCATATTTGATACTGTACTGA
35711944 GATGGGCTAAGGCCCTACTGCATATTTGATACTGTACTGA
1 GATGGGCTAAGGCCCTACTGCATATTTGATACTGTACTGA
35711984 GATGGGCTAAGGCCC
1 GATGGGCTAAGGCCC
35711999 AAACTGTTAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
GATGGGCTAAGGCCCTACTGCATATTTGATACTGTACTGA
Found at i:35720696 original size:43 final size:43
Alignment explanation
Indices: 35720643--35721032 Score: 496
Period size: 43 Copynumber: 9.1 Consensus size: 43
35720633 TTCTAAAAAT
* * *
35720643 GCCGCTAAAGATCAAGACCTTTAGCGGCGCTTTTCCCATAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAAC
* *
35720686 GCCGCTAAAGACCAAGACCTTTAACGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAAC
* * * *
35720729 GCCGCTAAAGACCAAGACCTTTAGCAGCACTTTTCCCACAAAT
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAAC
* * *
35720772 GCCGCTAAAAACCAAAACCTTTAGCGGCGCTTATACCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAAC
* *
35720815 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATCCCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAAC
* *
35720858 GCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTACCAAAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAAC
* * *
35720901 GCTGCTAAAGACCAAGACCTTTAGCTGCG-TTTTATCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAAC
* ** * *
35720943 GCCGCTATAGACCGTGACCTTTAGCGGCGCTTTTATCGCAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAAC
* * * * * *
35720986 GCCGCTAAAGAACAA-ACCTTTAGCAGCGATTCTAGCAAAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAAC
35721028 GCCGC
1 GCCGC
35721033 CAAAAACATA
Statistics
Matches: 304, Mismatches: 42, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
42 61 0.20
43 243 0.80
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.20
Consensus pattern (43 bp):
GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAAC
Found at i:35721810 original size:23 final size:23
Alignment explanation
Indices: 35721760--35721811 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
35721750 GTTAGGTGTC
* *
35721760 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
35721783 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
35721806 AGTATG
1 AGTATG
35721812 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:35725425 original size:10 final size:10
Alignment explanation
Indices: 35725379--35725437 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
35725369 AAAATAAAAG
35725379 TTAAAATCTTT
1 TTAAAATC-TT
*
35725390 TTTAAAT-TT
1 TTAAAATCTT
**
35725399 TTAAAAAATT
1 TTAAAATCTT
35725409 TTAAAATCTT
1 TTAAAATCTT
35725419 TTAAAATTCATT
1 TTAAAA-TC-TT
35725431 TTAAAAT
1 TTAAAAT
35725438 TTTAAATCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 7 0.17
10 16 0.40
11 9 0.22
12 8 0.20
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (10 bp):
TTAAAATCTT
Found at i:35725434 original size:12 final size:12
Alignment explanation
Indices: 35725406--35725438 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
35725396 TTTTTAAAAA
35725406 ATTTTAAAA-TC
1 ATTTTAAAATTC
35725417 -TTTTAAAATTC
1 ATTTTAAAATTC
35725428 ATTTTAAAATT
1 ATTTTAAAATT
35725439 TTAAATCACG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 2 0.10
12 10 0.50
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTTAAAATTC
Found at i:35726223 original size:21 final size:20
Alignment explanation
Indices: 35726173--35726224 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
35726163 CTAACTCGAC
35726173 CCCAAATCTCTAAACCTTAAA
1 CCCAAA-CTCTAAACCTTAAA
* *
35726194 CCTCTAACTCTAAACCTCTAAT
1 CC-CAAACTCTAAACCT-TAAA
35726216 CCCAAACTC
1 CCCAAACTC
35726225 ATAACCCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.37, C:0.38, G:0.00, T:0.25
Consensus pattern (20 bp):
CCCAAACTCTAAACCTTAAA
Found at i:35727081 original size:41 final size:41
Alignment explanation
Indices: 35727049--35727310 Score: 418
Period size: 41 Copynumber: 6.4 Consensus size: 41
35727039 GCGCTTTACC
35727049 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
1 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
* * ** *
35727090 AAAAAACGCAGCTAAAGGTCTGCCCATTAGCGGCTTTTCTTT
1 -AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
* *
35727132 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTATTT
1 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
*
35727173 AAAAACGCCGCTAAAGGTCTGCACATT-GCGGCGCTTCTTG
1 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
* *
35727213 AAAAACGCCGCTAAAGGTCTGCGCATTAGCAGTGCTTCTTG
1 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
35727254 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
1 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
35727295 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
35727311 ACCCACAAGG
Statistics
Matches: 201, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
40 37 0.18
41 128 0.64
42 36 0.18
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
Found at i:35727258 original size:81 final size:82
Alignment explanation
Indices: 35727049--35727310 Score: 418
Period size: 81 Copynumber: 3.2 Consensus size: 82
35727039 GCGCTTTACC
* *
35727049 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTGAAAAAACGCAGCTAAAGGTCTGCC
1 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG-AAAAACGCCGCTAAAGGTCTGCA
** *
35727114 CATTAGCGGCTTTTCTTT
65 CATTAGCGGCGCTTCTTG
* *
35727132 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTATTTAAAAACGCCGCTAAAGGTCTGCAC
1 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTGAAAAACGCCGCTAAAGGTCTGCAC
35727197 ATT-GCGGCGCTTCTTG
66 ATTAGCGGCGCTTCTTG
* * *
35727213 AAAAACGCCGCTAAAGGTCTGCGCATTAGCAGTGCTTCTTGAAAAACGCCGCTAAAGGTCTGCGC
1 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTGAAAAACGCCGCTAAAGGTCTGCAC
35727278 ATTAGCGGCGCTTCTTG
66 ATTAGCGGCGCTTCTTG
35727295 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
35727311 ACCCACAAGG
Statistics
Matches: 166, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
81 73 0.44
82 54 0.33
83 39 0.23
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (82 bp):
AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTGAAAAACGCCGCTAAAGGTCTGCAC
ATTAGCGGCGCTTCTTG
Found at i:35727258 original size:122 final size:123
Alignment explanation
Indices: 35727049--35727310 Score: 422
Period size: 122 Copynumber: 2.1 Consensus size: 123
35727039 GCGCTTTACC
*
35727049 AAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTGAAAAAACGCAGCTAAAGGTCTGCC
1 AAAAACGCCGCTAAAGGTCTGCACATTAGCGGCGCTTCTTGAAAAAACGCAGCTAAAGGTCTGCC
* *
35727114 CATTAGCGGCTTTTCTTTAAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTATTT
66 CATTAGCGGC-TTTCTTGAAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTATTG
* *
35727173 AAAAACGCCGCTAAAGGTCTGCACATT-GCGGCGCTTCTTG-AAAAACGCCGCTAAAGGTCTGCG
1 AAAAACGCCGCTAAAGGTCTGCACATTAGCGGCGCTTCTTGAAAAAACGCAGCTAAAGGTCTGCC
*
35727236 CATTAGCAGTGC-TTCTTGAAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCTTG
66 CATTAGC-G-GCTTTCTTGAAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTATTG
35727295 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
35727311 ACCCACAAGG
Statistics
Matches: 130, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
122 88 0.68
123 14 0.11
124 28 0.22
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (123 bp):
AAAAACGCCGCTAAAGGTCTGCACATTAGCGGCGCTTCTTGAAAAAACGCAGCTAAAGGTCTGCC
CATTAGCGGCTTTCTTGAAAAACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTATTG
Found at i:35728550 original size:21 final size:21
Alignment explanation
Indices: 35728524--35728563 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35728514 AATTAGACAC
*
35728524 TTTCATATTTA-ACCATTAATT
1 TTTCAT-TTTACACAATTAATT
35728545 TTTCATTTTACACAATTAA
1 TTTCATTTTACACAATTAA
35728564 GCCATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTCATTTTACACAATTAATT
Found at i:35728571 original size:18 final size:18
Alignment explanation
Indices: 35728548--35728583 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
35728538 ATTAATTTTT
35728548 CATTTTA-CACAATTAAGC
1 CATTTTATCA-AATTAAGC
35728566 CATTTTATCAAATTAAGC
1 CATTTTATCAAATTAAGC
35728584 ACCCAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (18 bp):
CATTTTATCAAATTAAGC
Found at i:35734883 original size:20 final size:22
Alignment explanation
Indices: 35734853--35734893 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
35734843 AATAATTCAA
35734853 TAAATTTAAAAATTA-GATAAT
1 TAAATTTAAAAATTAGGATAAT
*
35734874 TAAA-TTAAAATTTAGGATAA
1 TAAATTTAAAAATTAGGATAA
35734894 AAATTGGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
TAAATTTAAAAATTAGGATAAT
Found at i:35735571 original size:30 final size:30
Alignment explanation
Indices: 35735537--35735598 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
35735527 GCTTTTTGAA
*
35735537 AATATTTACAAAAAGAGGCATCT-AATTTTT
1 AATATTTACAAAAAGA-GCAACTAAATTTTT
35735567 AATATTTACAAAAAGAGCAACTAAATTTTT
1 AATATTTACAAAAAGAGCAACTAAATTTTT
35735597 AA
1 AA
35735599 AAATAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGCAACTAAATTTTT
Found at i:35746275 original size:38 final size:38
Alignment explanation
Indices: 35746224--35746329 Score: 142
Period size: 38 Copynumber: 2.8 Consensus size: 38
35746214 ATTAGCCACA
* * * *
35746224 AAGCCTGCTAGGCA-AGAAGCCCGAATAACACTGGTATT
1 AAGCCTGCTAGGCACA-AAGCCCAAATAACACTAGCACT
* *
35746262 AAGCCTACTAGGCACAAAGCCTAAATAACACTAGCACT
1 AAGCCTGCTAGGCACAAAGCCCAAATAACACTAGCACT
35746300 AAGCCTGCTAGGCACAAAGCCCAAATAACA
1 AAGCCTGCTAGGCACAAAGCCCAAATAACA
35746330 ATATAATTCA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
38 58 0.98
39 1 0.02
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.15
Consensus pattern (38 bp):
AAGCCTGCTAGGCACAAAGCCCAAATAACACTAGCACT
Found at i:35760172 original size:40 final size:40
Alignment explanation
Indices: 35760123--35760238 Score: 160
Period size: 40 Copynumber: 2.9 Consensus size: 40
35760113 AAAAATATTG
* *
35760123 CTATAGATCGAGCATTAACGGCGCTTTTTGAGAAACGCCA
1 CTATTGATCGAGCATTAGCGGCGCTTTTTGAGAAACGCCA
* * *
35760163 CTATTGATCGAGCATTAGCGGCGCTTCTTGAGAAACTCCG
1 CTATTGATCGAGCATTAGCGGCGCTTTTTGAGAAACGCCA
** *
35760203 CTATTGATCGAGCATTAGTTGCGCTTTTTGAAAAAC
1 CTATTGATCGAGCATTAGCGGCGCTTTTTGAGAAAC
35760239 AGCAAAAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (40 bp):
CTATTGATCGAGCATTAGCGGCGCTTTTTGAGAAACGCCA
Found at i:35763663 original size:15 final size:14
Alignment explanation
Indices: 35763643--35763691 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
35763633 ACTATTTTAA
35763643 GGTTTATGGATTAT
1 GGTTTATGGATTAT
35763657 GGGTTTA-GAGATTAT
1 -GGTTTATG-GATTAT
* *
35763672 GATTTATGGTTTAT
1 GGTTTATGGATTAT
35763686 GGTTTA
1 GGTTTA
35763692 AGGGTTGGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:35763758 original size:86 final size:85
Alignment explanation
Indices: 35763613--35763799 Score: 338
Period size: 86 Copynumber: 2.2 Consensus size: 85
35763603 TTATAGTTTA
35763613 GGGTTTAAGGTTTAGGAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATGATTTA
1 GGGTTTAA-GTTTAGGAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATGATTTA
35763678 TGGTTTATGGTTTAAGGGTTG
65 TGGTTTATGGTTTAAGGGTTG
*
35763699 GGGTTTGAAGTTTAGGAGTTGCTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATGATTTA
1 GGGTTT-AAGTTTAGGAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATGATTTA
35763764 TGGTTTATGGTTTAAGGGTTG
65 TGGTTTATGGTTTAAGGGTTG
35763785 GGGTTTAAAGTTTAG
1 GGGTTT-AAGTTTAG
35763800 AGGTTATGGG
Statistics
Matches: 98, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
86 96 0.98
87 2 0.02
ACGTcount: A:0.23, C:0.01, G:0.31, T:0.45
Consensus pattern (85 bp):
GGGTTTAAGTTTAGGAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATGATTTAT
GGTTTATGGTTTAAGGGTTG
Found at i:35763770 original size:7 final size:7
Alignment explanation
Indices: 35763724--35763854 Score: 52
Period size: 7 Copynumber: 18.6 Consensus size: 7
35763714 GAGTTGCTAT
*
35763724 TTTAAGG
1 TTTATGG
35763731 TTTATGG
1 TTTATGG
*
35763738 ATTATGGG
1 TTTAT-GG
35763746 TTTA-GAG
1 TTTATG-G
* *
35763753 ATTATGA
1 TTTATGG
35763760 TTTATGG
1 TTTATGG
35763767 TTTATGG
1 TTTATGG
*
35763774 TTTAAGG
1 TTTATGG
* **
35763781 GTTGGGG
1 TTTATGG
**
35763788 TTTAAAG
1 TTTATGG
35763795 TTTA-GAG
1 TTTATG-G
*
35763802 GTTATGG
1 TTTATGG
*
35763809 GTTATGG
1 TTTATGG
* *
35763816 GTTAGGGG
1 TTTA-TGG
*
35763824 TTTAGGG
1 TTTATGG
35763831 TTTATGG
1 TTTATGG
* *
35763838 TTCATGT
1 TTTATGG
35763845 TTTAT-G
1 TTTATGG
35763851 TTTA
1 TTTA
35763855 GGGGATAGAG
Statistics
Matches: 94, Mismatches: 24, Indels: 13
0.72 0.18 0.10
Matches are distributed among these distances:
6 5 0.05
7 77 0.82
8 12 0.13
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.47
Consensus pattern (7 bp):
TTTATGG
Found at i:35763789 original size:21 final size:21
Alignment explanation
Indices: 35763765--35763839 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
35763755 TATGATTTAT
*
35763765 GGTTTATGGTTTAAGGGTTGG
1 GGTTTATGGTTTAAGGGTTAG
**
35763786 GGTTTAAAGTTT-AGAGGTTATG
1 GGTTTATGGTTTAAG-GGTTA-G
* *
35763808 GG-TTATGGGTTAGGGGTTTAG
1 GGTTTATGGTTTAAGGG-TTAG
35763829 GGTTTATGGTT
1 GGTTTATGGTT
35763840 CATGTTTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
20 2 0.05
21 25 0.61
22 14 0.34
ACGTcount: A:0.17, C:0.00, G:0.40, T:0.43
Consensus pattern (21 bp):
GGTTTATGGTTTAAGGGTTAG
Found at i:35767021 original size:13 final size:13
Alignment explanation
Indices: 35767003--35767028 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35766993 TGCACTTTTA
35767003 AACATAAAACATT
1 AACATAAAACATT
35767016 AACATAAAACATT
1 AACATAAAACATT
35767029 TTTTGTATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
AACATAAAACATT
Found at i:35769128 original size:43 final size:43
Alignment explanation
Indices: 35769097--35769238 Score: 230
Period size: 43 Copynumber: 3.3 Consensus size: 43
35769087 GTACGGTACT
35769097 TTTAGTGGCGTTTGTGATAAAAACGCCGCTAAAGGTCATGTTC
1 TTTAGTGGCGTTTGTGATAAAAACGCCGCTAAAGGTCATGTTC
* * *
35769140 TTTAGCGGCATTTGTGATAAAAATGCCGCTAAAGGTCATGTTC
1 TTTAGTGGCGTTTGTGATAAAAACGCCGCTAAAGGTCATGTTC
* * *
35769183 TTTAGTGGCGTTTGTGATAAAAGCGCCACTAATGGTCATGTTC
1 TTTAGTGGCGTTTGTGATAAAAACGCCGCTAAAGGTCATGTTC
35769226 TTTAGTGGCGTTT
1 TTTAGTGGCGTTT
35769239 TTCCACATAA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 90 1.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.35
Consensus pattern (43 bp):
TTTAGTGGCGTTTGTGATAAAAACGCCGCTAAAGGTCATGTTC
Found at i:35771120 original size:25 final size:25
Alignment explanation
Indices: 35771089--35771170 Score: 101
Period size: 25 Copynumber: 3.3 Consensus size: 25
35771079 AGCTCTCTCT
35771089 TGAGCCATATAACGGGAAGCTCATA
1 TGAGCCATATAACGGGAAGCTCATA
* * * *
35771114 TGAGCCATTTAATGGGAAGCTTATC
1 TGAGCCATATAACGGGAAGCTCATA
**
35771139 TGAGCTGTATAACGGGAAGCTCATA
1 TGAGCCATATAACGGGAAGCTCATA
*
35771164 AGAGCCA
1 TGAGCCA
35771171 CAATCAAGAA
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (25 bp):
TGAGCCATATAACGGGAAGCTCATA
Found at i:35771349 original size:25 final size:25
Alignment explanation
Indices: 35771190--35771350 Score: 77
Period size: 25 Copynumber: 6.5 Consensus size: 25
35771180 AGCTCATGCA
* * *
35771190 AGCCA-ATAACGGGTAGCTCCGAAA
1 AGCCATATATCGGGAAGCTCCGAAG
* * *
35771214 AGCCAT-TAATCAGGAAGCTCCGGAT
1 AGCCATAT-ATCGGGAAGCTCCGAAG
* *
35771239 AGCCATATATCGAGAAG-TTC-AAGTG
1 AGCCATATATCGGGAAGCTCCGAA--G
*
35771264 AGCC--ATATCGGGAAGCTCCGGAG
1 AGCCATATATCGGGAAGCTCCGAAG
* * **
35771287 ATCCAT-TAATCAGGAAGCTCATAATG
1 AGCCATAT-ATCGGGAAGCTCCGAA-G
* *
35771313 AGCC-TTTAATCGGGAAGCTTCGAAG
1 AGCCATAT-ATCGGGAAGCTCCGAAG
35771338 AGCCATATATCGG
1 AGCCATATATCGG
35771351 AGCGCTCATA
Statistics
Matches: 100, Mismatches: 24, Indels: 25
0.67 0.16 0.17
Matches are distributed among these distances:
23 15 0.15
24 11 0.11
25 53 0.53
26 21 0.21
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (25 bp):
AGCCATATATCGGGAAGCTCCGAAG
Found at i:35771858 original size:5 final size:5
Alignment explanation
Indices: 35771829--35771867 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
35771819 TAAATTTAGC
* *
35771829 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
35771868 CATCTTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:35779147 original size:24 final size:23
Alignment explanation
Indices: 35779050--35779139 Score: 72
Period size: 25 Copynumber: 3.7 Consensus size: 23
35779040 CTCGAGCCAT
* *
35779050 ATAATGGGAAGCACATATGAGCC
1 ATAATGGGAAGCTCATAAGAGCC
* ** * *
35779073 ATGTAATGGGAAGCTTATCCGGGCTGT
1 A--TAATGGGAAGCTCATAAGAGC--C
35779100 ATAATGGGAAGCTCATAAGAGCC
1 ATAATGGGAAGCTCATAAGAGCC
35779123 ATAATGAGGAAGCTCAT
1 ATAATG-GGAAGCTCAT
35779140 GTGAGCCAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
23 7 0.14
24 10 0.20
25 33 0.65
27 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (23 bp):
ATAATGGGAAGCTCATAAGAGCC
Found at i:35779258 original size:25 final size:25
Alignment explanation
Indices: 35779221--35779284 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
35779211 CAAGCGAGCC
* *
35779221 ATATCGGGAAGCTCCGGAGAGCCAT
1 ATATCAGGAAGCTCCGAAGAGCCAT
*
35779246 -TAATCAGGAAGCTCCGAAGAGCTAT
1 AT-ATCAGGAAGCTCCGAAGAGCCAT
*
35779271 ATATCAGGACGCTC
1 ATATCAGGAAGCTC
35779285 ATAAGAGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 1 0.03
25 31 0.94
26 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (25 bp):
ATATCAGGAAGCTCCGAAGAGCCAT
Found at i:35785320 original size:6 final size:6
Alignment explanation
Indices: 35785309--35785335 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
35785299 TCCTCAAACA
35785309 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
35785336 CAATTAAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:35792010 original size:4 final size:4
Alignment explanation
Indices: 35791996--35792052 Score: 105
Period size: 4 Copynumber: 14.2 Consensus size: 4
35791986 CTAATAATCT
*
35791996 AACA CACA AACA AACA AACA AACA AACA AACA AACA AACA AACA AACA
1 AACA AACA AACA AACA AACA AACA AACA AACA AACA AACA AACA AACA
35792044 AACA AACA A
1 AACA AACA A
35792053 GGGTGTGAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:35798048 original size:27 final size:25
Alignment explanation
Indices: 35798018--35798067 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
35798008 AATAACTTAA
* *
35798018 TAAGTTGTAGTGATTGAGAAGAAGAAC
1 TAAGTTGCAATGA-TGAGAA-AAGAAC
35798045 TAAGTTGCAATGATGAGAAAAGA
1 TAAGTTGCAATGATGAGAAAAGA
35798068 GAAATTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 6 0.29
27 11 0.52
ACGTcount: A:0.44, C:0.04, G:0.28, T:0.24
Consensus pattern (25 bp):
TAAGTTGCAATGATGAGAAAAGAAC
Found at i:35802069 original size:18 final size:18
Alignment explanation
Indices: 35802042--35802127 Score: 61
Period size: 18 Copynumber: 4.7 Consensus size: 18
35802032 TAGAATTTTC
35802042 AAAAATTATAAAAAAATAT
1 AAAAA-TATAAAAAAATAT
*
35802061 AAAAATATAAAAATAT-T
1 AAAAATATAAAAAAATAT
* * *
35802078 AAAAAT-TACATTAACATTT
1 AAAAATATA-A-AAAAATAT
*
35802097 AAAATTAT-AAAAAATATT
1 AAAAATATAAAAAAATA-T
*
35802115 TAAAATATAAAAA
1 AAAAATATAAAAA
35802128 TATAAAATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
16 2 0.04
17 12 0.23
18 22 0.42
19 15 0.29
20 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATATAAAAAAATAT
Found at i:35802072 original size:7 final size:8
Alignment explanation
Indices: 35802053--35802154 Score: 71
Period size: 8 Copynumber: 11.6 Consensus size: 8
35802043 AAAATTATAA
35802053 AAAAATAT
1 AAAAATAT
35802061 AAAAATAT
1 AAAAATAT
35802069 AAAAATATT
1 AAAAATA-T
35802078 AAAAAT-T
1 AAAAATAT
*
35802085 ACATTAACATTT
1 A-A--AA-ATAT
*
35802097 AAAATTAT
1 AAAAATAT
35802105 AAAAAATATT
1 -AAAAATA-T
*
35802115 TAAAATAT
1 AAAAATAT
35802123 AAAAATAT
1 AAAAATAT
*
35802131 AAAATATTGT
1 AAAA-A-TAT
35802141 AAAAAGTAT
1 AAAAA-TAT
35802150 AAAAA
1 AAAAA
35802155 CAGAAAATAA
Statistics
Matches: 76, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
7 2 0.03
8 30 0.39
9 30 0.39
10 9 0.12
11 3 0.04
12 2 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (8 bp):
AAAAATAT
Found at i:35802653 original size:21 final size:20
Alignment explanation
Indices: 35802627--35802705 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
35802617 TTTTCAATAT
35802627 TTTATAGTTTTTAAATATTTC
1 TTTATA-TTTTTAAATATTTC
*
35802648 TTTATAATTTTATAAT-TTTC
1 TTTATATTTTTA-AATATTTC
*
35802668 TATTA-ATTTTT-AATAATT-
1 T-TTATATTTTTAAATATTTC
*
35802686 TTTATGATTTTTAAACATTT
1 TTTAT-ATTTTTAAATATTT
35802706 TAAAAAGAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
17 3 0.06
18 4 0.09
19 8 0.17
20 20 0.43
21 12 0.26
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTATATTTTTAAATATTTC
Found at i:35802686 original size:10 final size:10
Alignment explanation
Indices: 35802601--35802699 Score: 52
Period size: 10 Copynumber: 10.3 Consensus size: 10
35802591 ACTTTTTTAA
*
35802601 TAATATTTTT
1 TAATAATTTT
35802611 TAA-ACATTTT
1 TAATA-ATTTT
*
35802621 CAAT-A-TTT
1 TAATAATTTT
*
35802629 T-ATAGTTTT
1 TAATAATTTT
35802638 TAA-ATATTTCT
1 TAATA-ATTT-T
*
35802649 TTATAA-TTT
1 TAATAATTTT
35802658 T-ATAATTTT
1 TAATAATTTT
*
35802667 CTATTAATTTT
1 -TAATAATTTT
35802678 TAATAATTTT
1 TAATAATTTT
*
35802688 T-ATGATTTT
1 TAATAATTTT
35802697 TAA
1 TAA
35802700 ACATTTTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 24
0.67 0.09 0.24
Matches are distributed among these distances:
7 2 0.03
8 7 0.10
9 20 0.29
10 27 0.40
11 11 0.16
12 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (10 bp):
TAATAATTTT
Found at i:35802695 original size:9 final size:9
Alignment explanation
Indices: 35802648--35802698 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
35802638 TAAATATTTC
35802648 TTTATAA-T
1 TTTATAATT
35802656 TTTATAATT
1 TTTATAATT
35802665 TTCTATTAATT
1 TT-TA-TAATT
35802676 TTTAATAATT
1 TTT-ATAATT
*
35802686 TTTATGATT
1 TTTATAATT
35802695 TTTA
1 TTTA
35802699 AACATTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 7 0.18
9 12 0.32
10 11 0.29
11 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTATAATT
Found at i:35802705 original size:29 final size:27
Alignment explanation
Indices: 35802584--35802706 Score: 87
Period size: 29 Copynumber: 4.5 Consensus size: 27
35802574 ATTTTAGTTT
* *
35802584 TTTTTATACTTTTTTAATAA---TAT-
1 TTTTTAAACATTTTTAATAATTTTATA
*
35802607 TTTTTAAACATTTTCAAT-ATTTTATA
1 TTTTTAAACATTTTTAATAATTTTATA
* *
35802633 GTTTTTAAATATTTCTTTATAATTTTATAA
1 -TTTTTAAACATTT-TTAATAATTTTAT-A
*
35802663 TTTTCTATTA-ATTTTTAATAATTTTTATGA
1 TTTT-TA-AACATTTTTAATAA-TTTTAT-A
35802693 TTTTTAAACATTTT
1 TTTTTAAACATTTT
35802707 AAAAAGAATG
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
22 1 0.01
23 15 0.19
25 3 0.04
27 12 0.15
28 4 0.05
29 24 0.31
30 18 0.23
31 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTTAAACATTTTTAATAATTTTATA
Found at i:35814297 original size:17 final size:19
Alignment explanation
Indices: 35814277--35814311 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
35814267 GGCCCAAGTA
35814277 CTAATT-AGTTT-ATTTTC
1 CTAATTCAGTTTAATTTTC
35814294 CTAATTCAGTTTAATTTT
1 CTAATTCAGTTTAATTTT
35814312 TTAGTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (19 bp):
CTAATTCAGTTTAATTTTC
Found at i:35816032 original size:21 final size:20
Alignment explanation
Indices: 35816006--35816044 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
35815996 AGGGATTTAT
35816006 TTGTGAAATGTGTAAAATACA
1 TTGTGAAAT-TGTAAAATACA
*
35816027 TTGTGAAATTGTGAAATA
1 TTGTGAAATTGTAAAATA
35816045 ATGAATTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGTGAAATTGTAAAATACA
Found at i:35824423 original size:29 final size:28
Alignment explanation
Indices: 35824381--35824550 Score: 198
Period size: 29 Copynumber: 5.9 Consensus size: 28
35824371 GTATCGACGC
35824381 CCATCGAATATGAAAAGGGATGGTGGTGA
1 CCATCGAATATGAAAAGGGATGGT-GTGA
* *
35824410 CCATCGAGTATGAAAAGGGATGGTAGCGA
1 CCATCGAATATGAAAAGGGATGGT-GTGA
*
35824439 CCATCGAATAATGAAAAGGGATGGCTTTGA
1 CCATCGAAT-ATGAAAAGGGATGG-TGTGA
* **
35824469 CCATCGAATATGAAAAGGGTTGGTGACAA
1 CCATCGAATATGAAAAGGGATGGTG-TGA
35824498 CCATCGAATATGAAAAGGGATGGCT-TCGA
1 CCATCGAATATGAAAAGGGATGG-TGT-GA
* *
35824527 CCATCGAATATAAAAATGGATGGT
1 CCATCGAATATGAAAAGGGATGGT
35824551 TCTGACAATC
Statistics
Matches: 121, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
28 2 0.02
29 92 0.76
30 26 0.21
31 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (28 bp):
CCATCGAATATGAAAAGGGATGGTGTGA
Found at i:35824462 original size:59 final size:57
Alignment explanation
Indices: 35824381--35824550 Score: 227
Period size: 59 Copynumber: 2.9 Consensus size: 57
35824371 GTATCGACGC
* *
35824381 CCATCGAATATGAAAAGGGATGG-TGGTGACCATCGAGTATGAAAAGGGATGGT-AGCGA
1 CCATCGAATATGAAAAGGGATGGCT--TGACCATCGAATATGAAAAGGGATGGTGA-CAA
*
35824439 CCATCGAATAATGAAAAGGGATGGCTTTGACCATCGAATATGAAAAGGGTTGGTGACAA
1 CCATCGAAT-ATGAAAAGGGATGGC-TTGACCATCGAATATGAAAAGGGATGGTGACAA
* *
35824498 CCATCGAATATGAAAAGGGATGGCTTCGACCATCGAATATAAAAATGGATGGT
1 CCATCGAATATGAAAAGGGATGGCTT-GACCATCGAATATGAAAAGGGATGGT
35824551 TCTGACAATC
Statistics
Matches: 101, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
57 2 0.02
58 47 0.47
59 50 0.50
60 1 0.01
61 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (57 bp):
CCATCGAATATGAAAAGGGATGGCTTGACCATCGAATATGAAAAGGGATGGTGACAA
Found at i:35824530 original size:88 final size:87
Alignment explanation
Indices: 35824381--35824549 Score: 241
Period size: 88 Copynumber: 1.9 Consensus size: 87
35824371 GTATCGACGC
*** *
35824381 CCATCGAATATGAAAAGGGATGGTGGTGACCATCGAGTATGAAAAGGGATGGTAGCGACCATCGA
1 CCATCGAATATGAAAAGGGATGGTGACAACCATCGAATATGAAAAGGGATGGTAGCGACCATCGA
*
35824446 ATAATGAAAAGGGATGGCTTTGA
66 AT-ATAAAAAGGGATGGCTTTGA
* *
35824469 CCATCGAATATGAAAAGGGTTGGTGACAACCATCGAATATGAAAAGGGATGGCT-TCGACCATCG
1 CCATCGAATATGAAAAGGGATGGTGACAACCATCGAATATGAAAAGGGATGG-TAGCGACCATCG
*
35824533 AATATAAAAATGGATGG
65 AATATAAAAAGGGATGG
35824550 TTCTGACAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
87 12 0.17
88 59 0.82
89 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.21
Consensus pattern (87 bp):
CCATCGAATATGAAAAGGGATGGTGACAACCATCGAATATGAAAAGGGATGGTAGCGACCATCGA
ATATAAAAAGGGATGGCTTTGA
Found at i:35837201 original size:15 final size:15
Alignment explanation
Indices: 35837181--35837211 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35837171 AAAACAACAT
35837181 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
35837196 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
35837211 A
1 A
35837212 CTTACATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:35840574 original size:15 final size:16
Alignment explanation
Indices: 35840556--35840585 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35840546 TCCCTTCTTG
35840556 ACCACGACC-TTTTCC
1 ACCACGACCATTTTCC
35840571 ACCACGACCATTTTC
1 ACCACGACCATTTTC
35840586 TCGATCTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.43, G:0.07, T:0.27
Consensus pattern (16 bp):
ACCACGACCATTTTCC
Found at i:35864833 original size:15 final size:15
Alignment explanation
Indices: 35864796--35864853 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
35864786 ATTTCTAAGA
*
35864796 AAATAAAA-ATAAAAC
1 AAATAAAAGA-AAAAG
*
35864811 AACTAAAAGCAAAAAG
1 AAATAAAAG-AAAAAG
35864827 AAA-AAAAGAAAAAG
1 AAATAAAAGAAAAAG
*
35864841 AAATAAAATAAAA
1 AAATAAAAGAAAA
35864854 TCAATGATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 9 0.25
15 20 0.56
16 6 0.17
17 1 0.03
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.09
Consensus pattern (15 bp):
AAATAAAAGAAAAAG
Found at i:35865818 original size:23 final size:24
Alignment explanation
Indices: 35865775--35865820 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
35865765 ATATCAGATA
*
35865775 AGTAGAAGAAACAGGATAGACAAT
1 AGTAGAAGAAACAGGAGAGACAAT
35865799 AGTA-AAGAAAACA-GAGAGACAA
1 AGTAGAAG-AAACAGGAGAGACAA
35865821 ATCGAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.59, C:0.09, G:0.24, T:0.09
Consensus pattern (24 bp):
AGTAGAAGAAACAGGAGAGACAAT
Found at i:35866197 original size:5 final size:5
Alignment explanation
Indices: 35866175--35866233 Score: 54
Period size: 5 Copynumber: 12.2 Consensus size: 5
35866165 GAAAATTATT
* *
35866175 AATAA AA-AG AAT-A AATAA AATAA TAA-GA AATATA AATAA AAT-A AATAA
1 AATAA AATAA AATAA AATAA AATAA -AATAA AATA-A AATAA AATAA AATAA
35866223 AATAA AATAA A
1 AATAA AATAA A
35866234 CAAAAGAGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
4 12 0.27
5 25 0.57
6 7 0.16
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:35866238 original size:9 final size:9
Alignment explanation
Indices: 35866175--35866233 Score: 57
Period size: 9 Copynumber: 6.1 Consensus size: 9
35866165 GAAAATTATT
35866175 AATAAA-AA
1 AATAAATAA
35866183 GAATAAATAA
1 -AATAAATAA
*
35866193 AATAATAAGAA
1 AAT-A-AATAA
35866204 ATATAAATAA
1 A-ATAAATAA
35866214 AATAAATAA
1 AATAAATAA
35866223 AATAAAATAA
1 AAT-AAATAA
35866233 A
1 A
35866234 CAAAAGAGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
9 20 0.47
10 15 0.35
11 6 0.14
12 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.20
Consensus pattern (9 bp):
AATAAATAA
Found at i:35869946 original size:91 final size:91
Alignment explanation
Indices: 35869782--35869947 Score: 226
Period size: 91 Copynumber: 1.8 Consensus size: 91
35869772 CTTTAACACT
** * * *
35869782 TCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACATATCAATTAACAACATTTATA
1 TCAATTTACAGCAACTAAACACTTCAATTTGCAGCACTTAAACATATCAATTAACAACACTTAAA
*
35869847 CACGTCAATTACAGCGATAAAACATC
66 CACCTCAATTACAGCGATAAAACATC
* ** *
35869873 TCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACT-TCAATTTGCAGCACTTAA
1 TCAATTTACAGCAACTAAACACTTCAATTTGCAGCACTTAAACA-TATCAATTAACAACACTTAA
35869937 ACACCTCAATT
65 ACACCTCAATT
35869948 TATAGCATTT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
91 63 0.98
92 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.30
Consensus pattern (91 bp):
TCAATTTACAGCAACTAAACACTTCAATTTGCAGCACTTAAACATATCAATTAACAACACTTAAA
CACCTCAATTACAGCGATAAAACATC
Found at i:35870032 original size:160 final size:160
Alignment explanation
Indices: 35869768--35870111 Score: 571
Period size: 160 Copynumber: 2.1 Consensus size: 160
35869758 AATGGAAAGT
* * * *
35869768 AGCACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACATATCAAT
1 AGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAACATATAAAT
* *
35869833 TAACAACATTTATACACGTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAACACTTC
66 TAACAACATTTATACACCTCAATTACAGAGATAAAACATCTCAATTTCCAGCAACTAAACACTTC
*
35869898 AATTTGCAGCACTTAAACACTTCAATTTGC
131 AATTTGCAGCACTTAAACACTTCAATTTAC
* *
35869928 AGCACTTAAACACCTCAATTTATAGCATTTAAACACTTAAATTTGCAGCACTTAAACATATAAAT
1 AGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAACATATAAAT
*
35869993 TAACAACATTTATACACCTCAATTACAGAGATAAAACATCTCAATTTCCAGCAACTAAATACTTC
66 TAACAACATTTATACACCTCAATTACAGAGATAAAACATCTCAATTTCCAGCAACTAAACACTTC
35870058 AATTTGCAGCACTTAAACACTTCAATTTAC
131 AATTTGCAGCACTTAAACACTTCAATTTAC
* * *
35870088 AACATTTAAACACTTAAATTTACA
1 AGCACTTAAACACTTCAATTTACA
35870112 AATCCACCAT
Statistics
Matches: 169, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
160 169 1.00
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.31
Consensus pattern (160 bp):
AGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAACATATAAAT
TAACAACATTTATACACCTCAATTACAGAGATAAAACATCTCAATTTCCAGCAACTAAACACTTC
AATTTGCAGCACTTAAACACTTCAATTTAC
Found at i:35870112 original size:23 final size:23
Alignment explanation
Indices: 35869768--35870111 Score: 249
Period size: 23 Copynumber: 15.0 Consensus size: 23
35869758 AATGGAAAGT
35869768 AGCACTTT-AACACTTCAATTTAC
1 AGCA-TTTAAACACTTCAATTTAC
*
35869791 AGCATTTAAACACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
35869814 AGCACTTT-AACA-TATCAATTAAC
1 AGCA-TTTAAACACT-TCAATTTAC
* * *
35869837 AACATTTATACACGTCAA-TTAC
1 AGCATTTAAACACTTCAATTTAC
* *
35869859 AGCGA-TAAAACA-TCTCAATTTCC
1 AGC-ATTTAAACACT-TCAATTTAC
** *
35869882 AGCAACTAAACACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
* *
35869905 AGCACTTAAACACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
* * *
35869928 AGCACTTAAACACCTCAATTTAT
1 AGCATTTAAACACTTCAATTTAC
* *
35869951 AGCATTTAAACACTTAAATTTGC
1 AGCATTTAAACACTTCAATTTAC
* * *
35869974 AGCACTTAAACA-TATAAATTAAC
1 AGCATTTAAACACT-TCAATTTAC
* * *
35869997 AACATTTATACACCTCAA-TTAC
1 AGCATTTAAACACTTCAATTTAC
** *
35870019 AG-AGATAAA-ACATCTCAATTTCC
1 AGCATTTAAACAC-T-TCAATTTAC
** * *
35870042 AGCAACTAAATACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
35870065 AGCACTTAAACACTTCAATTTAC
1 AGCATTTAAACACTTCAATTTAC
* *
35870088 AACATTTAAACACTTAAATTTAC
1 AGCATTTAAACACTTCAATTTAC
35870111 A
1 A
35870112 AATCCACCAT
Statistics
Matches: 254, Mismatches: 50, Indels: 34
0.75 0.15 0.10
Matches are distributed among these distances:
20 2 0.01
21 4 0.02
22 31 0.12
23 205 0.81
24 10 0.04
25 2 0.01
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.31
Consensus pattern (23 bp):
AGCATTTAAACACTTCAATTTAC
Found at i:35872763 original size:23 final size:24
Alignment explanation
Indices: 35872730--35872780 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
35872720 AACCGATTAG
35872730 TGTTCAAATTTTAGGCTTT-TGGT
1 TGTTCAAATTTTAGGCTTTCTGGT
* *
35872753 TGTTCATATTTTAGGTTTTCTGGT
1 TGTTCAAATTTTAGGCTTTCTGGT
35872777 TGTT
1 TGTT
35872781 ACTTTCGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.14, C:0.08, G:0.22, T:0.57
Consensus pattern (24 bp):
TGTTCAAATTTTAGGCTTTCTGGT
Found at i:35873404 original size:24 final size:24
Alignment explanation
Indices: 35873377--35873424 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35873367 GCATGTTTGG
35873377 TTGGGTGTATTGGCATAGCCAATA
1 TTGGGTGTATTGGCATAGCCAATA
35873401 TTGGGTGTATTGGCATAGCCAATA
1 TTGGGTGTATTGGCATAGCCAATA
35873425 CACCCCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.33
Consensus pattern (24 bp):
TTGGGTGTATTGGCATAGCCAATA
Found at i:35876870 original size:66 final size:66
Alignment explanation
Indices: 35876764--35876894 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
35876754 CAAAAGGTTT
* *
35876764 TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTATGAGTATAATTTGAACCCAAAT
1 TGGTAGTGTTGGCATTGGCATTAATAAAAATTTGAGCTTACTATGAATATAATTTGAACCCAAAT
35876829 G
66 G
* *
35876830 TGGTAGTGTTGGCATTGGCATTAATAAAAATTTGAGCTTACTATGAATCTAATTTGAACTCAAAT
1 TGGTAGTGTTGGCATTGGCATTAATAAAAATTTGAGCTTACTATGAATATAATTTGAACCCAAAT
35876895 CATATTTGCG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.36
Consensus pattern (66 bp):
TGGTAGTGTTGGCATTGGCATTAATAAAAATTTGAGCTTACTATGAATATAATTTGAACCCAAAT
G
Found at i:35877205 original size:47 final size:47
Alignment explanation
Indices: 35877146--35877292 Score: 146
Period size: 47 Copynumber: 3.2 Consensus size: 47
35877136 TTATATAAGA
* *
35877146 ATATTTATTATTAAGAATTTTTTGAAATTATATATCATTATTAAATT
1 ATATTTAATATTAAGAATTTTTTGAAATTATATATAATTATTAAATT
35877193 ATATTTAATATT---AATTATTTT-AAATTATATA-AATTCATATAAGA--
1 ATATTTAATATTAAGAATT-TTTTGAAATTATATATAATT-AT-TAA-ATT
* * * * *
35877237 AAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATT
1 ATATTTAATATTAAGAATTTTTTGAAATTATATATAATTATTAAATT
35877284 ATATTTAAT
1 ATATTTAAT
35877293 TAAAATATAA
Statistics
Matches: 80, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
43 3 0.04
44 25 0.31
45 8 0.10
46 7 0.09
47 34 0.43
48 3 0.04
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (47 bp):
ATATTTAATATTAAGAATTTTTTGAAATTATATATAATTATTAAATT
Found at i:35877257 original size:44 final size:43
Alignment explanation
Indices: 35877132--35877258 Score: 123
Period size: 44 Copynumber: 2.8 Consensus size: 43
35877122 ATGATTTTAG
35877132 TAAATTATATAAGAATATTTATTATTAAGAATTTTTTGAAATTATA
1 TAAATTATATAAGAATATTTATTATTAAGAA--TTTT-AAATTATA
* * **
35877178 TATCATTAT-TAA-ATTATATTTAATATTAATTATTTTAAATTATA
1 TA-AATTATATAAGA--ATATTTATTATTAAGAATTTTAAATTATA
* *
35877222 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTA
1 TAAATT-ATATAAGAATATTTATTATTAAGAATTTTA
35877259 TGAAATTATA
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
43 3 0.05
44 29 0.45
45 8 0.12
46 6 0.09
47 19 0.29
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (43 bp):
TAAATTATATAAGAATATTTATTATTAAGAATTTTAAATTATA
Found at i:35877463 original size:120 final size:118
Alignment explanation
Indices: 35877355--35878217 Score: 1537
Period size: 120 Copynumber: 7.2 Consensus size: 118
35877345 TTTTCAAGTT
*
35877355 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
35877420 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT--A
*
35877475 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
35877540 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT--A
35877595 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
35877660 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT--A
35877715 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
35877780 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT--A
35877835 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
35877900 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT--A
35877955 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
35878020 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT--A
35878075 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
35878140 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATT--A
35878195 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
35878218 TAAATATGAT
Statistics
Matches: 735, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 735 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (118 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTA
Found at i:35878074 original size:18 final size:17
Alignment explanation
Indices: 35878046--35878080 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35878036 ATTATTAAGA
*
35878046 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
35878063 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
35878081 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:35878194 original size:18 final size:17
Alignment explanation
Indices: 35878166--35878200 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35878156 ATTATTAAGA
*
35878166 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
35878183 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
35878201 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:35878430 original size:44 final size:45
Alignment explanation
Indices: 35878365--35878455 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
35878355 ACCTCTATTC
* * *
35878365 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
35878409 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
35878454 CA
1 CA
35878456 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:35878457 original size:16 final size:16
Alignment explanation
Indices: 35878436--35878504 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
35878426 GATTAGCTAT
35878436 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
35878452 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
35878469 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
35878485 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
35878501 TACA
1 TACA
35878505 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:35878478 original size:33 final size:32
Alignment explanation
Indices: 35878436--35878504 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
35878426 GATTAGCTAT
35878436 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
35878469 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
35878501 TACA
1 TACA
35878505 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:35880060 original size:41 final size:41
Alignment explanation
Indices: 35880015--35880214 Score: 238
Period size: 41 Copynumber: 4.9 Consensus size: 41
35880005 AAATGTTTTT
* *
35880015 GCGGCGCTTTTTTAAAAACGCCGCTAAAGTCCCGAGCATTA
1 GCGGCGCTTTTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
** * * *
35880056 GCGGCGCTTCCTGGAAAACGTCGCTAAAGCCCCAAGCATTA
1 GCGGCGCTTTTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
* *
35880097 GCGGCGCTTCTTGAAAAACGCCACTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
* ** *
35880138 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * *
35880179 GTGGTGCTTTTTTAAAAAACGCCACTAAAGCCCCGA
1 GCGGCGC-TTTTTGAAAAACGCCGCTAAAGCCCCGA
35880215 AAGGTAGAAA
Statistics
Matches: 133, Mismatches: 25, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
41 110 0.83
42 23 0.17
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTTTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
Found at i:35895306 original size:42 final size:42
Alignment explanation
Indices: 35895234--35895409 Score: 153
Period size: 42 Copynumber: 4.2 Consensus size: 42
35895224 GGCAAGTATA
* * * * *
35895234 TGCATCATCGGATAAA-CTGAAATAACTATACTGGTACATAAG
1 TGCATCATCGAATAAATC-GAAACAAATATACTAGCACATAAG
* * *
35895276 TGCACCATCGAATAAATCGAATCAAATATACTAGCACGTAAG
1 TGCATCATCGAATAAATCGAAACAAATATACTAGCACATAAG
* * *
35895318 TGCATCAT-TAGATAAA-CCAAAAAAATATACTAGCACATAAG
1 TGCATCATCGA-ATAAATCGAAACAAATATACTAGCACATAAG
* * * * *
35895359 TGCAT-ATTTGGATAAATCGAAGCAAATATACTGGCACGTAAG
1 TGCATCA-TCGAATAAATCGAAACAAATATACTAGCACATAAG
35895401 TGCATCATC
1 TGCATCATC
35895410 AACTACACCA
Statistics
Matches: 106, Mismatches: 22, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
40 1 0.01
41 33 0.31
42 70 0.66
43 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (42 bp):
TGCATCATCGAATAAATCGAAACAAATATACTAGCACATAAG
Found at i:35895352 original size:41 final size:42
Alignment explanation
Indices: 35895299--35895408 Score: 143
Period size: 41 Copynumber: 2.6 Consensus size: 42
35895289 AAATCGAATC
35895299 AAATATACTAGCACGTAAGTGCATCATTAGATAAA-CCAAAA
1 AAATATACTAGCACGTAAGTGCATCATTAGATAAATCCAAAA
* * * **
35895340 AAATATACTAGCACATAAGTGCAT-ATTTGGATAAATCGAAGC
1 AAATATACTAGCACGTAAGTGCATCA-TTAGATAAATCCAAAA
*
35895382 AAATATACTGGCACGTAAGTGCATCAT
1 AAATATACTAGCACGTAAGTGCATCAT
35895409 CAACTACACC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
40 1 0.02
41 31 0.53
42 26 0.44
43 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (42 bp):
AAATATACTAGCACGTAAGTGCATCATTAGATAAATCCAAAA
Found at i:35904225 original size:49 final size:49
Alignment explanation
Indices: 35904153--35904247 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
35904143 GTAGTCAATA
* * * *
35904153 TGCCAATCTAGTTAGCAATTAACATGCCCTACTAATGGCCAATCATCTC
1 TGCCAACCTAGTTACCAACTAACATGCCCTACCAATGGCCAATCATCTC
*
35904202 TGCCAACCTAGTTACCAACTAACATGCCCTACCAATGGCCCATCAT
1 TGCCAACCTAGTTACCAACTAACATGCCCTACCAATGGCCAATCAT
35904248 ATCGAGTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.31, C:0.33, G:0.12, T:0.25
Consensus pattern (49 bp):
TGCCAACCTAGTTACCAACTAACATGCCCTACCAATGGCCAATCATCTC
Found at i:35912757 original size:13 final size:12
Alignment explanation
Indices: 35912699--35912758 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 12
35912689 TAGTTAAAAA
35912699 ATATTGAAATTAT
1 ATATT-AAATTAT
35912712 ATATTAAATT-T
1 ATATTAAATTAT
*
35912723 ATATTAATATTTTAA
1 ATATTAA-A--TTAT
*
35912738 ATTTTAAATTTAT
1 ATATTAAA-TTAT
35912751 ATATTAAA
1 ATATTAAA
35912759 CTTGTATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 8 0.21
12 6 0.15
13 16 0.41
14 3 0.08
15 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
ATATTAAATTAT
Found at i:35913663 original size:23 final size:22
Alignment explanation
Indices: 35913619--35913663 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
35913609 ATTTAAAAAT
35913619 TATTTTATATTAATATTTTATA
1 TATTTTATATTAATATTTTATA
35913641 TATTTTATAATTAA-A-TTTATA
1 TATTTTAT-ATTAATATTTTATA
35913662 TA
1 TA
35913664 AATTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.36
22 9 0.41
23 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTATATTAATATTTTATA
Found at i:35924307 original size:8 final size:8
Alignment explanation
Indices: 35924272--35924306 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
35924262 GTGAATCGGC
35924272 AAAAGCCG
1 AAAAGCCG
35924280 AAAAGCCG
1 AAAAGCCG
35924288 AAAAGCCG
1 AAAAGCCG
35924296 AAAAGCC-
1 AAAAGCCG
35924303 AAAA
1 AAAA
35924307 ATACGGCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.15
8 23 0.85
ACGTcount: A:0.57, C:0.23, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAGCCG
Found at i:35924575 original size:27 final size:27
Alignment explanation
Indices: 35924543--35924609 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
35924533 AAAGGTTGTT
35924543 AAATGATCGTAATACCCCTATAAGGTA
1 AAATGATCGTAATACCCCTATAAGGTA
*
35924570 AAATGATCGAAATACCCCTATAAGGTA
1 AAATGATCGTAATACCCCTATAAGGTA
*
35924597 AAATGACCGTAAT
1 AAATGATCGTAAT
35924610 GCCCTTGAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (27 bp):
AAATGATCGTAATACCCCTATAAGGTA
Found at i:35926437 original size:46 final size:46
Alignment explanation
Indices: 35926370--35926461 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
35926360 AGGGCCTCCA
35926370 TGATATTTTTACTGGATTTACACAAGTATTAGTAAATTACTTTTTT
1 TGATATTTTTACTGGATTTACACAAGTATTAGTAAATTACTTTTTT
35926416 TGATATTTTTACTGGATTTACACAAGTATTAGTAAATTACTTTTTT
1 TGATATTTTTACTGGATTTACACAAGTATTAGTAAATTACTTTTTT
35926462 ATCATCAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (46 bp):
TGATATTTTTACTGGATTTACACAAGTATTAGTAAATTACTTTTTT
Found at i:35926762 original size:16 final size:17
Alignment explanation
Indices: 35926731--35926763 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35926721 TAAATTTTAT
*
35926731 TGAAAATATACCAAAAA
1 TGAAAACATACCAAAAA
35926748 TGAAAACAT-CCAAAAA
1 TGAAAACATACCAAAAA
35926764 CTTGATATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.64, C:0.15, G:0.06, T:0.15
Consensus pattern (17 bp):
TGAAAACATACCAAAAA
Found at i:35927910 original size:153 final size:153
Alignment explanation
Indices: 35927632--35927938 Score: 596
Period size: 153 Copynumber: 2.0 Consensus size: 153
35927622 TTTTTAAATT
35927632 AATACTAAATTGACACAATATATAAATGTTAAAAACTAAATTTATAATTGAGCCGATTTTTAAAG
1 AATACTAAATTGACACAATATATAAATGTTAAAAACTAAATTTATAATTGAGCCGATTTTTAAAG
35927697 TTGCCATGTCATCTTTTCATTATCCATTTAATGACTGGTGATCAAAATAGAAAAATCAAATAGTT
66 TTGCCATGTCATCTTTTCATTATCCATTTAATGACTGGTGATCAAAATAGAAAAATCAAATAGTT
35927762 ATTTTGTAACTTTCCATAGTTGG
131 ATTTTGTAACTTTCCATAGTTGG
* *
35927785 AATACTAAATTTACACAATATATAAATGTTAAAAATTAAATTTATAATTGAGCCGATTTTTAAAG
1 AATACTAAATTGACACAATATATAAATGTTAAAAACTAAATTTATAATTGAGCCGATTTTTAAAG
35927850 TTGCCATGTCATCTTTTCATTATCCATTTAATGACTGGTGATCAAAATAGAAAAATCAAATAGTT
66 TTGCCATGTCATCTTTTCATTATCCATTTAATGACTGGTGATCAAAATAGAAAAATCAAATAGTT
35927915 ATTTTGTAACTTTCCATAGTTGG
131 ATTTTGTAACTTTCCATAGTTGG
35927938 A
1 A
35927939 TGAAGAAAAA
Statistics
Matches: 152, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 152 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (153 bp):
AATACTAAATTGACACAATATATAAATGTTAAAAACTAAATTTATAATTGAGCCGATTTTTAAAG
TTGCCATGTCATCTTTTCATTATCCATTTAATGACTGGTGATCAAAATAGAAAAATCAAATAGTT
ATTTTGTAACTTTCCATAGTTGG
Found at i:35928509 original size:17 final size:17
Alignment explanation
Indices: 35928476--35928514 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
35928466 TATAATGTAT
*
35928476 ATTATTAATTTTGGTTA
1 ATTATTAATTTTAGTTA
35928493 ATTAGTTAA-TTTAGTTA
1 ATTA-TTAATTTTAGTTA
35928510 ATTAT
1 ATTAT
35928515 AATAAGTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 15 0.75
18 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (17 bp):
ATTATTAATTTTAGTTA
Found at i:35933050 original size:40 final size:40
Alignment explanation
Indices: 35933004--35933079 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
35932994 TTATGAAAGA
35933004 AAAATAATAAAAGAAAAGGGTTTATTACAAATAAAATAAT
1 AAAATAATAAAAGAAAAGGGTTTATTACAAATAAAATAAT
35933044 AAAATAATAAAAGAAAAGGGTTTATTACAAATAAAA
1 AAAATAATAAAAGAAAAGGGTTTATTACAAATAAAA
35933080 GGGTTTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.24
Consensus pattern (40 bp):
AAAATAATAAAAGAAAAGGGTTTATTACAAATAAAATAAT
Found at i:35933081 original size:19 final size:19
Alignment explanation
Indices: 35933057--35933094 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
35933047 ATAATAAAAG
35933057 AAAAGGGTTTATTACAAAT
1 AAAAGGGTTTATTACAAAT
35933076 AAAAGGGTTTATTACAAAT
1 AAAAGGGTTTATTACAAAT
35933095 CTAATCGAGG
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:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (19 bp):
AAAAGGGTTTATTACAAAT
Found at i:35938046 original size:23 final size:23
Alignment explanation
Indices: 35937989--35938064 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
35937979 TTAAGCACCG
* * *
35937989 AAATTGAAGTGCTTAAATCCTAT
1 AAATTGAAGTGTTTAAATACTGT
*
35938012 AAATTGAAGTGTTTAACTACTGT
1 AAATTGAAGTGTTTAAATACTGT
** *
35938035 AAATTGAAGTGTTTAGTTACTGA
1 AAATTGAAGTGTTTAAATACTGT
35938058 AAATTGA
1 AAATTGA
35938065 GATGTTTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (23 bp):
AAATTGAAGTGTTTAAATACTGT
Found at i:35938120 original size:23 final size:24
Alignment explanation
Indices: 35938094--35938155 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
35938084 TGAGGTGTAT
35938094 AAGTGTTATTAA-TTG-GGATTTTA
1 AAGTGTTA-TAAGTTGAGGATTTTA
*
35938117 AAGTGTTATAAGTTGAGGTTTTTA
1 AAGTGTTATAAGTTGAGGATTTTA
* *
35938141 AA-TGTTGTAAATTGA
1 AAGTGTTATAAGTTGA
35938156 AGTGTTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 3 0.09
23 22 0.65
24 9 0.26
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (24 bp):
AAGTGTTATAAGTTGAGGATTTTA
Found at i:35939481 original size:25 final size:23
Alignment explanation
Indices: 35939452--35939527 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 23
35939442 AAAACTAGAT
35939452 AGCATTTTCACACCAAAATTTGGAC
1 AGCA-TTTCACA-CAAAATTTGGAC
* *
35939477 AGCATAT-ATACAAAATTTGGAC
1 AGCATTTCACACAAAATTTGGAC
*
35939499 TGCATTTCTACATCAAAATTT-GAC
1 AGCATTTC-ACA-CAAAATTTGGAC
35939523 AGCAT
1 AGCAT
35939528 ATGCATATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
22 17 0.40
23 2 0.05
24 11 0.26
25 12 0.29
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (23 bp):
AGCATTTCACACAAAATTTGGAC
Found at i:35939491 original size:22 final size:23
Alignment explanation
Indices: 35939465--35939580 Score: 89
Period size: 22 Copynumber: 5.0 Consensus size: 23
35939455 ATTTTCACAC
*
35939465 CAAAATTTGGACAGCATATATA-
1 CAAAATTTGGACAGCATATACAT
* *
35939487 CAAAATTTGGACTGCATTTCTACAT
1 CAAAATTTGGACAGCA--TATACAT
*
35939512 CAAAATTT-GACAGCATATGCAT
1 CAAAATTTGGACAGCATATACAT
* *
35939534 -ATATAA-TTGGACTGCATTTGTACAT
1 CA-A-AATTTGGACAGCA--TATACAT
35939559 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
35939581 TCATTTACTC
Statistics
Matches: 73, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
21 1 0.01
22 29 0.40
23 8 0.11
24 18 0.25
25 16 0.22
26 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (23 bp):
CAAAATTTGGACAGCATATACAT
Found at i:35939516 original size:47 final size:45
Alignment explanation
Indices: 35939435--35939577 Score: 164
Period size: 47 Copynumber: 3.1 Consensus size: 45
35939425 GAACAACATT
* * *
35939435 TATATACAAAACTAGA-TAGCATTT-TCACACCAAAATTTGGACAGCA
1 TATATACAAAATTGGACT-GCATTTCT-ACATCAAAATTT-GACAGCA
35939481 TATATACAAAATTTGGACTGCATTTCTACATCAAAATTTGACAGCA
1 TATATACAAAA-TTGGACTGCATTTCTACATCAAAATTTGACAGCA
* * *
35939527 TATGCATATATAATTGGACTGCATTTGTACATCAAAATTTGACAGCA
1 TAT--ATACAAAATTGGACTGCATTTCTACATCAAAATTTGACAGCA
35939574 TATA
1 TATA
35939578 CATTCATTTA
Statistics
Matches: 86, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
45 1 0.01
46 21 0.24
47 56 0.65
48 8 0.09
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (45 bp):
TATATACAAAATTGGACTGCATTTCTACATCAAAATTTGACAGCA
Found at i:35939565 original size:24 final size:24
Alignment explanation
Indices: 35939452--35939574 Score: 83
Period size: 24 Copynumber: 5.2 Consensus size: 24
35939442 AAAACTAGAT
*
35939452 AGCATTT-TCACACCAAAATTTGGAC
1 AGCATTTGT-ACATCAAAA-TTGGAC
* * *
35939477 AGCATATATACA--AAATTTGGAC
1 AGCATTTGTACATCAAAATTGGAC
* * *
35939499 TGCATTTCTACATCAAAATTTGAC
1 AGCATTTGTACATCAAAATTGGAC
* * * *
35939523 AGCATATGCATAT-ATAATTGGAC
1 AGCATTTGTACATCAAAATTGGAC
* *
35939546 TGCATTTGTACATCAAAATTTGAC
1 AGCATTTGTACATCAAAATTGGAC
35939570 AGCAT
1 AGCAT
35939575 ATACATTCAT
Statistics
Matches: 73, Mismatches: 21, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
22 15 0.21
23 20 0.27
24 28 0.38
25 9 0.12
26 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (24 bp):
AGCATTTGTACATCAAAATTGGAC
Found at i:35939837 original size:14 final size:15
Alignment explanation
Indices: 35939799--35939847 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
35939789 TCACCATGCA
* *
35939799 CATATATATACATTAC
1 CATATAAATAC-TAAC
35939815 CATATAAATACTAAC
1 CATATAAATACTAAC
35939830 CATA-AAATACTAATC
1 CATATAAATACTAA-C
35939845 CAT
1 CAT
35939848 GATTAAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 9 0.30
15 11 0.37
16 10 0.33
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (15 bp):
CATATAAATACTAAC
Found at i:35940561 original size:43 final size:43
Alignment explanation
Indices: 35940501--35940623 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
35940491 TACAATGCCA
* * * * *
35940501 ACGTCCTAGATGTGGTCTTACATGTAATCACATATCGATG-CC
1 ACGTCCCAGACGTGGTCTTACACGAAAACACATATCGATGTCC
*
35940543 ACTGTCCCAGACAG-GGTCTTACACGAAAACACA-AGTCGATGTCG
1 AC-GTCCCAGAC-GTGGTCTTACACGAAAACACATA-TCGATGTCC
35940587 ACGTCCCAGACGTGGTCTTACACGAAAACACATATCG
1 ACGTCCCAGACGTGGTCTTACACGAAAACACATATCG
35940624 GAGTCCTATG
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
42 4 0.06
43 60 0.87
44 5 0.07
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (43 bp):
ACGTCCCAGACGTGGTCTTACACGAAAACACATATCGATGTCC
Found at i:35947161 original size:22 final size:23
Alignment explanation
Indices: 35947135--35947438 Score: 188
Period size: 22 Copynumber: 13.0 Consensus size: 23
35947125 ATTTGCACAC
*
35947135 CAAAATTTGGACAGCATATATA-
1 CAAAATTTGGACAGCATATACAT
*
35947157 CAAAATTTGGACTGCATTTATACAT
1 CAAAATTTGGACAGCA--TATACAT
*
35947182 CAAAATTT-GACAGCATATGCAT
1 CAAAATTTGGACAGCATATACAT
*
35947204 -ATATAA-TTGGACTGCATTTATACAT
1 CA-A-AATTTGGACAGCA--TATACAT
35947229 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* * *
35947251 -AAATAATTGGACTGCATTTGTACAT
1 CAAA-ATTTGGACAGCA--TATACAT
35947276 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* * *
35947298 ACATAA-TTGGACTGCATTTGTACAT
1 -CAAAATTTGGACAGCA--TATACAT
35947323 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
*
35947345 -ATATAA-TTGGACTGCATTTATACAT
1 CA-A-AATTTGGACAGCA--TATACAT
*
35947370 CAAAATTT-GATAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* *
35947392 -ATATAA-TTGGACTGCATTTGTACAT
1 CA-A-AATTTGGACAGCA--TATACAT
*
35947417 CAAAATTT-GACATCATATACAT
1 CAAAATTTGGACAGCATATACAT
35947439 TCATTTACTC
Statistics
Matches: 220, Mismatches: 28, Indels: 68
0.70 0.09 0.22
Matches are distributed among these distances:
21 6 0.03
22 67 0.30
23 39 0.18
24 49 0.22
25 53 0.24
26 6 0.03
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (23 bp):
CAAAATTTGGACAGCATATACAT
Found at i:35947435 original size:47 final size:47
Alignment explanation
Indices: 35947123--35947438 Score: 492
Period size: 47 Copynumber: 6.7 Consensus size: 47
35947113 AAACTAGATA
* * * *
35947123 GCATTTGCACACCAAAATTTGGACAGCATAT--ATACAAAATTTGGACT
1 GCATTTGTACATCAAAATTT-GACAGCATATACATATATAA-TTGGACT
* *
35947170 GCATTTATACATCAAAATTTGACAGCATATGCATATATAATTGGACT
1 GCATTTGTACATCAAAATTTGACAGCATATACATATATAATTGGACT
* *
35947217 GCATTTATACATCAAAATTTGACAGCATATACATAAATAATTGGACT
1 GCATTTGTACATCAAAATTTGACAGCATATACATATATAATTGGACT
*
35947264 GCATTTGTACATCAAAATTTGACAGCATATACATACATAATTGGACT
1 GCATTTGTACATCAAAATTTGACAGCATATACATATATAATTGGACT
35947311 GCATTTGTACATCAAAATTTGACAGCATATACATATATAATTGGACT
1 GCATTTGTACATCAAAATTTGACAGCATATACATATATAATTGGACT
* *
35947358 GCATTTATACATCAAAATTTGATAGCATATACATATATAATTGGACT
1 GCATTTGTACATCAAAATTTGACAGCATATACATATATAATTGGACT
*
35947405 GCATTTGTACATCAAAATTTGACATCATATACAT
1 GCATTTGTACATCAAAATTTGACAGCATATACAT
35947439 TCATTTACTC
Statistics
Matches: 252, Mismatches: 15, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
46 10 0.04
47 236 0.94
48 6 0.02
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (47 bp):
GCATTTGTACATCAAAATTTGACAGCATATACATATATAATTGGACT
Found at i:35947697 original size:14 final size:15
Alignment explanation
Indices: 35947673--35947707 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
35947663 TATATACATT
35947673 ACCATATAAATACTA
1 ACCATATAAATACTA
35947688 ACCATA-AAATACTA
1 ACCATATAAATACTA
35947702 ATCCAT
1 A-CCAT
35947708 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:35948364 original size:43 final size:43
Alignment explanation
Indices: 35948294--35948400 Score: 130
Period size: 43 Copynumber: 2.5 Consensus size: 43
35948284 CTTCATAGAT
* * *
35948294 GTGGTCTTACATGTAATCACATA-TCGATG-CCACTGTCCCAGAC
1 GTGGTCTTACACGAAAACACA-AGTCGATGTCCAC-GTCCCAGAC
*
35948337 AG-GGTCTTACACGAAAACACAAGTCGATGTCGACGTCCCAGAC
1 -GTGGTCTTACACGAAAACACAAGTCGATGTCCACGTCCCAGAC
35948380 GTGGTCTTACACGAAAACACA
1 GTGGTCTTACACGAAAACACA
35948401 TATCAGAGTC
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.04
43 50 0.89
44 4 0.07
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (43 bp):
GTGGTCTTACACGAAAACACAAGTCGATGTCCACGTCCCAGAC
Found at i:35953191 original size:75 final size:75
Alignment explanation
Indices: 35953102--35953311 Score: 291
Period size: 75 Copynumber: 2.8 Consensus size: 75
35953092 TTGATCTACC
** *
35953102 ATACTTAAATTATAAATTTATTTATTAAATCTAGATTATTAAATTATAAGTTGAGCTTTACGT-A
1 ATACTTAAATTATAAATTTAACTATTAAATCTA-AATATTAAATTATAAGTTGAGCTTTACGTCA
35953166 GACAT-TTTTAA
65 -ACATCTTTTAA
*
35953177 ATACTTAAATTATAAATTTAACTATTAAATATTAAATATTAAATTATAAGTTGAGCTTTACGTCA
1 ATACTTAAATTATAAATTTAACTATTAAAT-CTAAATATTAAATTATAAGTTGAGCTTTACGTCA
*
35953242 ACATCTTTTTA
65 ACATCTTTTAA
* * *
35953253 ATATTTAAATTATAAA-TTAACTATTAAACCTAAAATATTAAATTTTAAGTTGAGCTTTA
1 ATACTTAAATTATAAATTTAACTATTAAATCT-AAATATTAAATTATAAGTTGAGCTTTA
35953312 TATTAATATT
Statistics
Matches: 122, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
74 1 0.01
75 98 0.80
76 23 0.19
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (75 bp):
ATACTTAAATTATAAATTTAACTATTAAATCTAAATATTAAATTATAAGTTGAGCTTTACGTCAA
CATCTTTTAA
Found at i:35953204 original size:7 final size:7
Alignment explanation
Indices: 35953173--35953220 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
35953163 GTAGACATTT
35953173 TTAAATA
1 TTAAATA
35953180 CTTAAAT-
1 -TTAAATA
35953187 TATAAAT-
1 T-TAAATA
*
35953194 TTAACTA
1 TTAAATA
35953201 TTAAATA
1 TTAAATA
35953208 TTAAATA
1 TTAAATA
35953215 TTAAAT
1 TTAAAT
35953221 TATAAGTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
6 5 0.14
7 25 0.69
8 6 0.17
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (7 bp):
TTAAATA
Found at i:35955801 original size:23 final size:23
Alignment explanation
Indices: 35955775--35955825 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
35955765 ATTGATATTC
*
35955775 TGATCTGTATCGTTCTAGG-TATA
1 TGATCTGTATCATTCT-GGTTATA
* *
35955798 TGATTTGTTTCATTCTGGTTATA
1 TGATCTGTATCATTCTGGTTATA
35955821 TGATC
1 TGATC
35955826 ACTATTAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.49
Consensus pattern (23 bp):
TGATCTGTATCATTCTGGTTATA
Found at i:35961388 original size:11 final size:11
Alignment explanation
Indices: 35961372--35961438 Score: 63
Period size: 12 Copynumber: 6.4 Consensus size: 11
35961362 TAAAAATTAA
35961372 AAAAATATTTT
1 AAAAATATTTT
35961383 AAAAATATTTT
1 AAAAATATTTT
35961394 --AAA-A--TT
1 AAAAATATTTT
* *
35961400 AAAAAAAATTT
1 AAAAATATTTT
35961411 AAAAAGTATTTT
1 AAAAA-TATTTT
35961423 AAAAAGTATTTT
1 AAAAA-TATTTT
35961435 AAAA
1 AAAA
35961439 TTAAAAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
6 2 0.04
8 4 0.08
9 4 0.08
11 18 0.38
12 20 0.42
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:35961489 original size:44 final size:43
Alignment explanation
Indices: 35961370--35961497 Score: 176
Period size: 43 Copynumber: 3.1 Consensus size: 43
35961360 TTTAAAAATT
*
35961370 AAAAAAA-TATTTTAAAAA-TATTTTAAAATT-AAAAA-AAAT
1 AAAAAAAGTATTTTAAAAAGTATTTTAAAATTAAAAAATAAAA
**
35961409 TTAAAAAGTATTTTAAAAAGTATTTTAAAATTAAAAAATAATAA
1 AAAAAAAGTATTTTAAAAAGTATTTTAAAATTAAAAAATAA-AA
*
35961453 AAAAAAAGTATTTTAAAAA-TATTTTAAAATTAAAAAATTAAA
1 AAAAAAAGTATTTTAAAAAGTATTTTAAAATTAAAAAATAAAA
35961495 AAA
1 AAA
35961498 TAAATATATT
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
39 5 0.06
40 11 0.14
41 12 0.15
42 10 0.13
43 22 0.28
44 18 0.23
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (43 bp):
AAAAAAAGTATTTTAAAAAGTATTTTAAAATTAAAAAATAAAA
Found at i:35961508 original size:43 final size:43
Alignment explanation
Indices: 35961370--35961509 Score: 173
Period size: 41 Copynumber: 3.3 Consensus size: 43
35961360 TTTAAAAATT
**
35961370 AAAAAAATATTTTAAAAA-TATTTTAAAATTAAAAAA-A-ATT
1 AAAAAAATATTTTAAAAAGTATTTTAAAATTAAAAAATATAAA
* *
35961410 TAAAAAGTATTTTAAAAAGTATTTTAAAATTAAAAAATAATAAA
1 AAAAAAATATTTTAAAAAGTATTTTAAAATTAAAAAAT-ATAAA
*
35961454 AAAAAAGTATTTTAAAAA-TATTTTAAAATTAAAAAAT-TAAA
1 AAAAAAATATTTTAAAAAGTATTTTAAAATTAAAAAATATAAA
*
35961495 AAATAAATATATTTA
1 AAAAAAATAT-TTTA
35961510 TTATACCAGG
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
40 16 0.18
41 30 0.34
42 4 0.05
43 20 0.23
44 18 0.20
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (43 bp):
AAAAAAATATTTTAAAAAGTATTTTAAAATTAAAAAATATAAA
Found at i:35962560 original size:23 final size:23
Alignment explanation
Indices: 35962534--35962584 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
35962524 GTTGATATTT
35962534 TGATCTGTTGTGTTCTAGG-TATA
1 TGATCTGTTGTGTTCT-GGTTATA
*
35962557 TGATCTGTTTTGTTCTGGTTATA
1 TGATCTGTTGTGTTCTGGTTATA
35962580 TGATC
1 TGATC
35962585 GCTATTAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.16, C:0.10, G:0.24, T:0.51
Consensus pattern (23 bp):
TGATCTGTTGTGTTCTGGTTATA
Found at i:35963277 original size:24 final size:24
Alignment explanation
Indices: 35963249--35963301 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
35963239 ATTTGTAGGT
* *
35963249 TAAATAAATTATGCTAATAAATGC
1 TAAATAAATTATACTAATAAATAC
*
35963273 TAAATATATTATACTAATAAATAC
1 TAAATAAATTATACTAATAAATAC
35963297 TAAAT
1 TAAAT
35963302 CTTGTAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.36
Consensus pattern (24 bp):
TAAATAAATTATACTAATAAATAC
Found at i:35965198 original size:24 final size:24
Alignment explanation
Indices: 35965165--35965216 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
35965155 TTCGCAGGTC
* *
35965165 AAATAAATTATACTAATAAATGCT
1 AAATAAATTATACTAAAAAATACT
* *
35965189 AAATATATTATATTAAAAAATACT
1 AAATAAATTATACTAAAAAATACT
35965213 AAAT
1 AAAT
35965217 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAAAAAATACT
Found at i:35971982 original size:26 final size:26
Alignment explanation
Indices: 35971946--35972007 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
35971936 CTTGTAAGTG
*
35971946 TTCTGAAACTGATACATGCTATGATA
1 TTCTGAAACTGATACACGCTATGATA
* * *
35971972 TTCTGAAACTGGTATACGTTATGATA
1 TTCTGAAACTGATACACGCTATGATA
*
35971998 TTTTGAAACT
1 TTCTGAAACT
35972008 ACTGTAGATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (26 bp):
TTCTGAAACTGATACACGCTATGATA
Found at i:35981095 original size:30 final size:31
Alignment explanation
Indices: 35981010--35981095 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 31
35981000 GTGATTGAAT
* *
35981010 TGTGATCGATTACAGGGTATGAA-ATACAAA
1 TGTGAACGATTACAGGGTATGAATATGCAAA
* **
35981040 TGTGACCGATTACAAAGTATG-ATATGCAAA
1 TGTGAACGATTACAGGGTATGAATATGCAAA
*
35981070 TGTGAATGA-TACAGGGTATGAATATG
1 TGTGAACGATTACAGGGTATGAATATG
35981096 TTAAGAAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 10 0.22
30 36 0.78
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.28
Consensus pattern (31 bp):
TGTGAACGATTACAGGGTATGAATATGCAAA
Found at i:35985015 original size:27 final size:27
Alignment explanation
Indices: 35984975--35985127 Score: 143
Period size: 27 Copynumber: 5.7 Consensus size: 27
35984965 AATGGGACAC
*
35984975 AAATTACCGAAATACACCT-ATAGGGTA
1 AAATTACCGAAATACCCCTGA-AGGGTA
* *
35985002 ATATTATCGAAATA-CCCTCGAAGGGTA
1 AAATTACCGAAATACCCCT-GAAGGGTA
***
35985029 AAATTATTAAAATACCCCT-ATAGGGTA
1 AAATTACCGAAATACCCCTGA-AGGGTA
35985056 AAATTACCGAAATACCCCTGAAGGGTA
1 AAATTACCGAAATACCCCTGAAGGGTA
* * *
35985083 AAATGACCAAAATATCCCC-GAAAGGTA
1 AAATTACCGAAATA-CCCCTGAAGGGTA
* *
35985110 AAATGACCAAAATACCCC
1 AAATTACCGAAATACCCC
35985128 ATAGGGTAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
26 8 0.07
27 90 0.83
28 10 0.09
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.21
Consensus pattern (27 bp):
AAATTACCGAAATACCCCTGAAGGGTA
Found at i:35985067 original size:54 final size:54
Alignment explanation
Indices: 35984975--35985127 Score: 166
Period size: 54 Copynumber: 2.8 Consensus size: 54
35984965 AATGGGACAC
* * * * *
35984975 AAATTACCGAAATACACCTATAGGGTAATATTATCGAAATA-CCCTCGAAGGGTA
1 AAATGACCAAAATACCCCTATAGGGTAAAATTACCGAAATACCCCT-GAAGGGTA
* **
35985029 AAATTATTAAAATACCCCTATAGGGTAAAATTACCGAAATACCCCTGAAGGGTA
1 AAATGACCAAAATACCCCTATAGGGTAAAATTACCGAAATACCCCTGAAGGGTA
* * * *
35985083 AAATGACCAAAATATCCCCGA-AAGGTAAAATGACCAAAATACCCC
1 AAATGACCAAAATA-CCCCTATAGGGTAAAATTACCGAAATACCCC
35985128 ATAGGGTAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 75 0.89
55 9 0.11
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.21
Consensus pattern (54 bp):
AAATGACCAAAATACCCCTATAGGGTAAAATTACCGAAATACCCCTGAAGGGTA
Found at i:35985110 original size:81 final size:80
Alignment explanation
Indices: 35984975--35985137 Score: 204
Period size: 81 Copynumber: 2.0 Consensus size: 80
35984965 AATGGGACAC
* * * * * * **
35984975 AAATTACCGAAATACACCTATAGGGTAATATTATCGAAATACCCTCGAAGGGTAAAATTATTAAA
1 AAATTACCGAAATACACCTATAGGGTAAAATGACCAAAATACCCTCGAAAGGTAAAATGACCAAA
35985040 ATACCCCTATAGGGTA
66 ATACCCC-ATAGGGTA
*
35985056 AAATTACCGAAATACCCCTGA-AGGGTAAAATGACCAAAATATCCC-CGAAAGGTAAAATGACCA
1 AAATTACCGAAATACACCT-ATAGGGTAAAATGACCAAAATA-CCCTCGAAAGGTAAAATGACCA
35985119 AAATACCCCATAGGGTA
64 AAATACCCCATAGGGTA
35985136 AA
1 AA
35985138 CTGACTGATA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
80 10 0.14
81 57 0.80
82 4 0.06
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (80 bp):
AAATTACCGAAATACACCTATAGGGTAAAATGACCAAAATACCCTCGAAAGGTAAAATGACCAAA
ATACCCCATAGGGTA
Found at i:35985356 original size:26 final size:26
Alignment explanation
Indices: 35985321--35985419 Score: 117
Period size: 26 Copynumber: 3.8 Consensus size: 26
35985311 CCACAAATAC
*
35985321 TGTTACTGGCAGCTTTGCTGCATTAT
1 TGTTACTGGCAACTTTGCTGCATTAT
* * *
35985347 TGTTATTGGCAACTTTGCTGCGTTAC
1 TGTTACTGGCAACTTTGCTGCATTAT
* * * *
35985373 TGTTACTGGCAGCTCTGTTGCACTAT
1 TGTTACTGGCAACTTTGCTGCATTAT
*
35985399 TATTACTGGCAACTTTGCTGC
1 TGTTACTGGCAACTTTGCTGC
35985420 GATATTGGTG
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 58 1.00
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.40
Consensus pattern (26 bp):
TGTTACTGGCAACTTTGCTGCATTAT
Found at i:35985385 original size:52 final size:52
Alignment explanation
Indices: 35985318--35985420 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
35985308 TTGCCACAAA
* * * *
35985318 TACTGTTACTGGCAGCTTTGCTGCATTATTGTTATTGGCAACTTTGCTGCGT
1 TACTGTTACTGGCAGCTCTGCTGCACTATTATTACTGGCAACTTTGCTGCGT
*
35985370 TACTGTTACTGGCAGCTCTGTTGCACTATTATTACTGGCAACTTTGCTGCG
1 TACTGTTACTGGCAGCTCTGCTGCACTATTATTACTGGCAACTTTGCTGCG
35985421 ATATTGGTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (52 bp):
TACTGTTACTGGCAGCTCTGCTGCACTATTATTACTGGCAACTTTGCTGCGT
Found at i:35985573 original size:28 final size:28
Alignment explanation
Indices: 35985531--35985625 Score: 138
Period size: 28 Copynumber: 3.4 Consensus size: 28
35985521 ATTGTATTGT
*
35985531 TTACTGTATTGGGCTAAGGCCCACGCTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
* *
35985559 TTACTGTATTAGGCTAAGGCCCACACTA
1 TTACTGTATTGGGCTAAGGCCCACACTG
*
35985587 TTACTGTAATGGGCTAAGGCCCACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
35985615 -TACTGATATTG
1 TTACTG-TATTG
35985626 TATAGGGCTT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 5 0.08
28 54 0.92
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.29
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTG
Found at i:35987297 original size:55 final size:54
Alignment explanation
Indices: 35987218--35987326 Score: 132
Period size: 55 Copynumber: 2.0 Consensus size: 54
35987208 TAGAGACATT
* * * *
35987218 CTTTTTATCAAAGATTGCCACAAAG-GCTTCCGTTTAACAGAGATCGCCACAAAAG
1 CTTTTTATCAAAGACTACCACAAAGAACTT-C-TTTAACAGAGATAGCCACAAAAG
35987273 CTTTGTTATCAAA-ACTACCACAAAGACACTTCTTTAACAGAGATAGCCACAAAA
1 CTTT-TTATCAAAGACTACCACAAAGA-ACTTCTTTAACAGAGATAGCCACAAAA
35987327 ACATCTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
55 35 0.74
56 9 0.19
57 3 0.06
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.25
Consensus pattern (54 bp):
CTTTTTATCAAAGACTACCACAAAGAACTTCTTTAACAGAGATAGCCACAAAAG
Found at i:35987378 original size:26 final size:26
Alignment explanation
Indices: 35987311--35987378 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
35987301 CTTCTTTAAC
* *
35987311 AGAGATAGCCACAAAAACATCTTTTT
1 AGAGATAGCCACAAAGACATCCTTTT
*
35987337 AGAGATAGCTACAAAGACATCCTTTT
1 AGAGATAGCCACAAAGACATCCTTTT
35987363 AGAGATAGCCACAAAG
1 AGAGATAGCCACAAAG
35987379 GCTTACTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (26 bp):
AGAGATAGCCACAAAGACATCCTTTT
Found at i:36005900 original size:42 final size:42
Alignment explanation
Indices: 36005848--36005931 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
36005838 CACAAATACT
* *
36005848 AAAAAACCTAGCTCTCAAACCTAAGTAAGTCGGCTTACTAGC
1 AAAAAACCTAGCTCTCAAACCTAAGTAAGTCGACTCACTAGC
36005890 AAAAAACCTAGCTCTCAAACCTAAGTAAGTCGACTCACTAGC
1 AAAAAACCTAGCTCTCAAACCTAAGTAAGTCGACTCACTAGC
36005932 GTCCCCAGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.20
Consensus pattern (42 bp):
AAAAAACCTAGCTCTCAAACCTAAGTAAGTCGACTCACTAGC
Found at i:36009326 original size:14 final size:14
Alignment explanation
Indices: 36009307--36009334 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36009297 TAAATTTATT
36009307 AATGAATTATTAAA
1 AATGAATTATTAAA
36009321 AATGAATTATTAAA
1 AATGAATTATTAAA
36009335 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:36018252 original size:26 final size:25
Alignment explanation
Indices: 36018202--36018268 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
36018192 CATTTCGACC
*
36018202 CACAGCTCGTGTGAGTAGGCTTATTT
1 CACAGCTCGTGTGAG-AGGCCTATTT
36018228 CACAGCTCGTGTGA-ACGGACCTATTT
1 CACAGCTCGTGTGAGA-GG-CCTATTT
* *
36018254 CATAACTCGTGTGAG
1 CACAGCTCGTGTGAG
36018269 CAATGATGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 1 0.03
25 2 0.06
26 32 0.91
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (25 bp):
CACAGCTCGTGTGAGAGGCCTATTT
Found at i:36020701 original size:27 final size:27
Alignment explanation
Indices: 36020684--36020964 Score: 323
Period size: 27 Copynumber: 10.4 Consensus size: 27
36020674 GGGTATAACA
*
36020684 GTCATTTTACCCTATAGGAGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* * *
36020711 ATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
* ** *
36020738 GTCATTTTACACTACGGGGGAATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
36020765 GTAATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
**
36020792 GTCATTTTACCCTATAAAGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* * *
36020819 ATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
*
36020846 GTTATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
36020873 ATCATTTTACCCAAT-GAGGGTATTTCG
1 GTCATTTTACCCTATAG-GGGTATTTCG
* *
36020900 ATCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
* **
36020927 GTCATTTTATCCTAT-GAGGGTATTTTA
1 GTCATTTTACCCTATAG-GGGTATTTCG
36020954 GTCATTTTACC
1 GTCATTTTACC
36020965 TATTTTGGGG
Statistics
Matches: 214, Mismatches: 37, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
26 2 0.01
27 211 0.99
28 1 0.00
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTCG
Found at i:36020731 original size:54 final size:54
Alignment explanation
Indices: 36020684--36020964 Score: 382
Period size: 54 Copynumber: 5.2 Consensus size: 54
36020674 GGGTATAACA
*
36020684 GTCATTTTACCCTATAGGAGTATTTCGATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTG
* ** * * * *
36020738 GTCATTTTACACTACGGGGGAATTTCGGTAATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTG
**
36020792 GTCATTTTACCCTATAAAGGTATTTCGATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTG
* * * *
36020846 GTTATTTTACCCTATAGGGGTATTTCGATCATTTTACCCAATGAGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTG
* * * * * *
36020900 ATCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCCTATGAGGGTATTTTA
1 GTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTG
36020954 GTCATTTTACC
1 GTCATTTTACC
36020965 TATTTTGGGG
Statistics
Matches: 195, Mismatches: 32, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 195 1.00
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.42
Consensus pattern (54 bp):
GTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTG
Found at i:36020797 original size:81 final size:81
Alignment explanation
Indices: 36020687--36020964 Score: 371
Period size: 81 Copynumber: 3.4 Consensus size: 81
36020677 TATAACAGTC
* * * * *
36020687 ATTTTACCCTATAGGAGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACACTA
1 ATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTA
* *
36020752 CGGGGGAATTTCGGTA
66 TGGGGGTATTTCGGTA
* * * *
36020768 ATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATAAAGGTATTTCGATCATTTTACCCTA
1 ATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTA
* *
36020833 TGGGGGTATTTTGGTT
66 TGGGGGTATTTCGGTA
*
36020849 ATTTTACCCTATAGGGGTATTTCGATCATTTTACCCAATGAGGGTATTTCGATCATTTTACCCTA
1 ATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTA
*
36020914 TGGGGGTATTTCGGTC
66 TGGGGGTATTTCGGTA
* *
36020930 ATTTTATCCTAT-GAGGGTATTT-TAGTCATTTTACC
1 ATTTTACCCTATAG-GGGTATTTCGA-TCATTTTACC
36020965 TATTTTGGGG
Statistics
Matches: 173, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
80 2 0.01
81 171 0.99
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (81 bp):
ATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTA
TGGGGGTATTTCGGTA
Found at i:36035765 original size:42 final size:42
Alignment explanation
Indices: 36035705--36035883 Score: 268
Period size: 42 Copynumber: 4.3 Consensus size: 42
36035695 AAGGGAAGCA
* * * * *
36035705 TTCATTGCATTTAAAGGCCCAGCTGTGGAGGTCCGTTTACCT
1 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
*
36035747 TTCATTGCATTTAGAGGCCCAGGGGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
*
36035789 TTCATTACATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
* * *
36035831 TTCATTACATTTAGAGGCCTAGGTGTAGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
36035873 TTCATTGCATT
1 TTCATTGCATT
36035884 GTATATGAAG
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 126 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
Found at i:36037618 original size:15 final size:15
Alignment explanation
Indices: 36037598--36037627 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36037588 TGAGAAGGAC
36037598 AAGAAAGAATATGCT
1 AAGAAAGAATATGCT
*
36037613 AAGAAAGAATCTGCT
1 AAGAAAGAATATGCT
36037628 CGAAACATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.20
Consensus pattern (15 bp):
AAGAAAGAATATGCT
Found at i:36041074 original size:36 final size:36
Alignment explanation
Indices: 36041021--36041099 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
36041011 CCATGCCATA
36041021 TCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCGG
1 TCCCA-ACATGGTCTTAC-ATGGGACCTCTCATCTCGG
*
36041058 TGCCAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TCCCAACATGGTCTTACATGGGACCTCTCATCTCGG
36041094 TCCCAA
1 TCCCAA
36041100 TGCCATGTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
35 1 0.03
36 34 0.87
37 4 0.10
ACGTcount: A:0.20, C:0.33, G:0.22, T:0.25
Consensus pattern (36 bp):
TCCCAACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:36041122 original size:86 final size:87
Alignment explanation
Indices: 36040976--36041146 Score: 267
Period size: 86 Copynumber: 2.0 Consensus size: 87
36040966 CATGTCCTAG
**
36040976 ACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATATCCCAGACATGGTCTTACGA
1 ACATGGTCTTACATGGGATCCTCTCATATCGGTGCCCATGCCATATCCCAGACATGGTCTTAC-A
36041041 -GGGACCTCTCATCTCGGTGCCA
65 TGGGACCTCTCATCTCGGTGCCA
* *
36041063 ACATGGTCTTACATGGGA-CCTCTCATCTCGGT-CCCAATGCCATGTCCCAGACATGGTCTTACA
1 ACATGGTCTTACATGGGATCCTCTCATATCGGTGCCC-ATGCCATATCCCAGACATGGTCTTACA
36041126 TGGGACCTCTCATCTCGGTGC
65 TGGGACCTCTCATCTCGGTGC
36041147 TAATTCCATG
Statistics
Matches: 78, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
85 4 0.05
86 56 0.72
87 18 0.23
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.27
Consensus pattern (87 bp):
ACATGGTCTTACATGGGATCCTCTCATATCGGTGCCCATGCCATATCCCAGACATGGTCTTACAT
GGGACCTCTCATCTCGGTGCCA
Found at i:36041213 original size:56 final size:50
Alignment explanation
Indices: 36041063--36041241 Score: 250
Period size: 50 Copynumber: 3.5 Consensus size: 50
36041053 CTCGGTGCCA
*
36041063 ACATGGTCTTACATGGGACCTCTCATCTCGGTCCCAATGCCATGTCCCAG
1 ACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAG
* *
36041113 ACATGGTCTTACATGGGACCTCTCATCTCGGTGCTAATTCCATGTCCCAG
1 ACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAG
**
36041163 ACATAATCTTACATGGGACCTCTCATGATCTCAAGGATGCCAATGCCATGTCCCAG
1 ACATGGTCTTACATGGGACCTCTC---ATCTC--GG-TGCCAATGCCATGTCCCAG
*
36041219 ACATGGTCTTACATGGGATCTCT
1 ACATGGTCTTACATGGGACCTCT
36041242 TTACCCAAAT
Statistics
Matches: 113, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
50 69 0.61
53 5 0.04
55 2 0.02
56 37 0.33
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (50 bp):
ACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAG
Found at i:36047018 original size:21 final size:22
Alignment explanation
Indices: 36046981--36047030 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
36046971 TTTGATCTTT
* *
36046981 AAGAAAAGTTGTGATTTTTTAA
1 AAGAAAACTTGTGATTTTCTAA
36047003 AAGAAAACTT-TGATTTTCTAA
1 AAGAAAACTTGTGATTTTCTAA
*
36047024 AAAAAAA
1 AAGAAAA
36047031 AGGGATTCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.34
Consensus pattern (22 bp):
AAGAAAACTTGTGATTTTCTAA
Found at i:36052084 original size:8 final size:8
Alignment explanation
Indices: 36052065--36052095 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
36052055 CTCCCTTGAG
36052065 AGATTAGTT
1 AGATT-GTT
36052074 AGATTGTT
1 AGATTGTT
36052082 AGATTGTT
1 AGATTGTT
36052090 AGATTG
1 AGATTG
36052096 CACGGGTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (8 bp):
AGATTGTT
Found at i:36056285 original size:29 final size:29
Alignment explanation
Indices: 36056239--36056409 Score: 150
Period size: 29 Copynumber: 5.9 Consensus size: 29
36056229 TGGGTTAAAT
*
36056239 GATGGTCGTAACCGTCCCTTTTCATATTC
1 GATGGTCGTAACCATCCCTTTTCATATTC
* * *
36056268 GATGGTCGTCACCATCCCTTTTCATAATA
1 GATGGTCGTAACCATCCCTTTTCATATTC
* * * *
36056297 AATAGCCG-AAGCTATCCCTTTTCATATTC
1 GATGGTCGTAA-CCATCCCTTTTCATATTC
* ** * *
36056326 GATAG-CCAAAGCTATTCCTTTTCATATTC
1 GATGGTCGTAA-CCATCCCTTTTCATATTC
* *
36056355 GATGGTTGTCACCATCCCTTTTCATAGTT-
1 GATGGTCGTAACCATCCCTTTTCATA-TTC
*
36056384 GATGGTCGTCACCATCCCTTTTCATA
1 GATGGTCGTAACCATCCCTTTTCATA
36056410 ATTGATAGCC
Statistics
Matches: 116, Mismatches: 22, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
28 2 0.02
29 111 0.96
30 3 0.03
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (29 bp):
GATGGTCGTAACCATCCCTTTTCATATTC
Found at i:36056401 original size:87 final size:87
Alignment explanation
Indices: 36056253--36056444 Score: 262
Period size: 87 Copynumber: 2.2 Consensus size: 87
36056243 GTCGTAACCG
*
36056253 TCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAATAAATAGCCGAAGCTATCCCTTT
1 TCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAATAAATAGCCGAAGCCATCCCTTT
36056318 TCAT-ATTCGATAGCCAAAGCTA
66 TCATAATT-GATAGCCAAAGCTA
* * * ** * * *
36056340 TTCCTTTTCATATTCGATGGTTGTCACCATCCCTTTTCATAGTTGATGGTCGTCA-CCATCCCTT
1 TCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAATAAATAGCCG-AAGCCATCCCTT
36056404 TTCATAATTGATAGCCAAAGCTA
65 TTCATAATTGATAGCCAAAGCTA
*
36056427 TCCCATTTCATATTCGAT
1 TCCCTTTTCATATTCGAT
36056445 AATCGAAGCT
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
87 88 0.96
88 4 0.04
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.38
Consensus pattern (87 bp):
TCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAATAAATAGCCGAAGCCATCCCTTT
TCATAATTGATAGCCAAAGCTA
Done.