Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 175 of 235
Found at i:59380413 original size:24 final size:23
Alignment explanation
Indices: 59380386--59380442 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
59380376 GAGCCATGAT
59380386 CGGTAAGCTCT-TCTTGAACTGAAA
1 CGGTAAGCTCTATC--GAACTGAAA
* *
59380410 CGGTAAACTCTATCGAGCTGAAA
1 CGGTAAGCTCTATCGAACTGAAA
59380433 CGGTAAGCTC
1 CGGTAAGCTC
59380443 CAATGAGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.59
24 10 0.34
25 2 0.07
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (23 bp):
CGGTAAGCTCTATCGAACTGAAA
Found at i:59380450 original size:23 final size:24
Alignment explanation
Indices: 59380404--59380466 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
59380394 TCTTCTTGAA
* *
59380404 CTGAAACGGTAAACT-CTATCGAG
1 CTGAAACGGTAAGCTCCAATCGAG
59380427 CTGAAACGGTAAGCTCCAAT-GAG
1 CTGAAACGGTAAGCTCCAATCGAG
* *
59380450 CTAAAAACAGTAAGCTC
1 CT-GAAACGGTAAGCTC
59380467 TTACGAGCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 19 0.56
24 15 0.44
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (24 bp):
CTGAAACGGTAAGCTCCAATCGAG
Found at i:59380474 original size:24 final size:26
Alignment explanation
Indices: 59380447--59380501 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
59380437 AAGCTCCAAT
*
59380447 GAGCTAA-A-AACAGTAAGCTCTTAC
1 GAGCTAATATAACAGTAAGCTCATAC
* *
59380471 GAGCTAATATATCTGTAAGCTCATAC
1 GAGCTAATATAACAGTAAGCTCATAC
59380497 GAGCT
1 GAGCT
59380502 GTGGTGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 7 0.27
25 1 0.04
26 18 0.69
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (26 bp):
GAGCTAATATAACAGTAAGCTCATAC
Found at i:59383869 original size:16 final size:16
Alignment explanation
Indices: 59383837--59383870 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
59383827 TATTTTATTA
59383837 TTTACATTTTAACCAT
1 TTTACATTTTAACCAT
59383853 TTTACCATTTTAA-CAT
1 TTTA-CATTTTAACCAT
59383869 TT
1 TT
59383871 AATAATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTACATTTTAACCAT
Found at i:59389129 original size:23 final size:23
Alignment explanation
Indices: 59389103--59389336 Score: 276
Period size: 23 Copynumber: 10.2 Consensus size: 23
59389093 GCTACATTTC
*
59389103 AGTGGTAGCTTCGACTACAATAT
1 AGTGGTAGCTTCGGCTACAATAT
* *
59389126 AGTGGTAGCTTTGGCTAC-ATCT
1 AGTGGTAGCTTCGGCTACAATAT
* *
59389148 CAGTGGTAGCTTCAGCTACAATAC
1 -AGTGGTAGCTTCGGCTACAATAT
*
59389172 AGTGGTAGCTTCTGCTACAATAT
1 AGTGGTAGCTTCGGCTACAATAT
* *
59389195 AGTGGTAGCTTCAGCTACAATAC
1 AGTGGTAGCTTCGGCTACAATAT
* *
59389218 AGTGGTAGCTTTGGCTAC-ATCT
1 AGTGGTAGCTTCGGCTACAATAT
59389240 CAGTGGTAGCTTCGGCTACAATAT
1 -AGTGGTAGCTTCGGCTACAATAT
*
59389264 AGTGGTAGCTTCGGCTAC-ATCT
1 AGTGGTAGCTTCGGCTACAATAT
**
59389286 CAGTGGTAGCTTCGGCTACGTTAT
1 -AGTGGTAGCTTCGGCTACAATAT
* * *
59389310 AGTGATAGCTTCGGCTATATTAT
1 AGTGGTAGCTTCGGCTACAATAT
59389333 AGTG
1 AGTG
59389337 TAGTACTTTG
Statistics
Matches: 182, Mismatches: 23, Indels: 12
0.84 0.11 0.06
Matches are distributed among these distances:
22 8 0.04
23 167 0.92
24 7 0.04
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACAATAT
Found at i:59389159 original size:46 final size:46
Alignment explanation
Indices: 59389092--59389326 Score: 307
Period size: 46 Copynumber: 5.1 Consensus size: 46
59389082 GGAATCTATA
*
59389092 GGCTACATTTCAGTGGTAGCTTCGACTACAATATAGTGGTAGCTTT
1 GGCTACATCTCAGTGGTAGCTTCGACTACAATATAGTGGTAGCTTT
*
59389138 GGCTACATCTCAGTGGTAGCTTC-AGCTACAATACAGTGGTAGCTTCT
1 GGCTACATCTCAGTGGTAGCTTCGA-CTACAATATAGTGGTAGCTT-T
* *
59389185 -GCTACAATAT-AGTGGTAGCTTC-AGCTACAATACAGTGGTAGCTTT
1 GGCTAC-ATCTCAGTGGTAGCTTCGA-CTACAATATAGTGGTAGCTTT
* *
59389230 GGCTACATCTCAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTC
1 GGCTACATCTCAGTGGTAGCTTCGACTACAATATAGTGGTAGCTTT
* ** * *
59389276 GGCTACATCTCAGTGGTAGCTTCGGCTACGTTATAGTGATAGCTTC
1 GGCTACATCTCAGTGGTAGCTTCGACTACAATATAGTGGTAGCTTT
59389322 GGCTA
1 GGCTA
59389327 TATTATAGTG
Statistics
Matches: 173, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
45 5 0.03
46 164 0.95
47 4 0.02
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.31
Consensus pattern (46 bp):
GGCTACATCTCAGTGGTAGCTTCGACTACAATATAGTGGTAGCTTT
Found at i:59389204 original size:69 final size:69
Alignment explanation
Indices: 59389092--59389336 Score: 314
Period size: 69 Copynumber: 3.6 Consensus size: 69
59389082 GGAATCTATA
* * * *
59389092 GGCTACATTTCAGTGGTAGCTTCGACTACAATATAGTGGTAGCTTTGGCTACATCTCAGTGGTAG
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTACATCTCAGTGGTAG
59389157 CTTC
66 CTTC
* * * *
59389161 AGCTACAATACAGTGGTAGCTTCTGCTACAATATAGTGGTAGCTTCAGCTACAAT-ACAGTGGTA
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTAC-ATCTCAGTGGTA
*
59389225 GCTTT
65 GCTTC
*
59389230 GGCTAC-ATCTCAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTACATCTCAGTGGTA
1 GGCTACAAT-ACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTACATCTCAGTGGTA
59389294 GCTTC
65 GCTTC
** * * * *
59389299 GGCTACGTTATAGTGATAGCTTCGGCTATATTATAGTG
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTG
59389337 TAGTACTTTG
Statistics
Matches: 151, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
68 4 0.03
69 144 0.95
70 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (69 bp):
GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTACATCTCAGTGGTAG
CTTC
Found at i:59395494 original size:23 final size:23
Alignment explanation
Indices: 59395468--59395710 Score: 294
Period size: 23 Copynumber: 10.6 Consensus size: 23
59395458 GCTACATTTC
*
59395468 AGTGGTAGCTCCGGCTACAATAT
1 AGTGGTAGCTTCGGCTACAATAT
* *
59395491 AGTGGTAGCTTTGGCTAC-ATCT
1 AGTGGTAGCTTCGGCTACAATAT
* *
59395513 CAGTGGTAGCTTCGTCTACAATAC
1 -AGTGGTAGCTTCGGCTACAATAT
*
59395537 AGTGGTAGCTTCGGCTAGAATAT
1 AGTGGTAGCTTCGGCTACAATAT
*
59395560 AGTGGTAGCTTCGGCTACAATAC
1 AGTGGTAGCTTCGGCTACAATAT
* *
59395583 AGTGGTAGCTTTGGCTAC-ATCTT
1 AGTGGTAGCTTCGGCTACAAT-AT
*
59395606 AGTGGTAGCTTCGGCTACAATAC
1 AGTGGTAGCTTCGGCTACAATAT
*
59395629 AGTGGTAGCTTCGGCTAC-ATCT
1 AGTGGTAGCTTCGGCTACAATAT
*
59395651 CAGTGGTAGCTTCGGCTACAATAC
1 -AGTGGTAGCTTCGGCTACAATAT
**
59395675 AGTGGTAGCTTCGGCTACGTTAT
1 AGTGGTAGCTTCGGCTACAATAT
* *
59395698 AGTGATTGCTTCG
1 AGTGGTAGCTTCG
59395711 ACTATATTAC
Statistics
Matches: 187, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
22 7 0.04
23 174 0.93
24 6 0.03
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACAATAT
Found at i:59395532 original size:46 final size:46
Alignment explanation
Indices: 59395457--59395692 Score: 375
Period size: 46 Copynumber: 5.1 Consensus size: 46
59395447 GGAATCTATG
* * * *
59395457 GGCTACATTTCAGTGGTAGCTCCGGCTACAATATAGTGGTAGCTTT
1 GGCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTC
*
59395503 GGCTACATCTCAGTGGTAGCTTCGTCTACAATACAGTGGTAGCTTC
1 GGCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTC
* * *
59395549 GGCTAGAATAT-AGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTT
1 GGCTA-CATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTC
*
59395595 GGCTACATCTTAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTC
1 GGCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTC
59395641 GGCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTC
1 GGCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTC
59395687 GGCTAC
1 GGCTAC
59395693 GTTATAGTGA
Statistics
Matches: 175, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 3 0.02
46 169 0.97
47 3 0.02
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (46 bp):
GGCTACATCTCAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTC
Found at i:59395570 original size:69 final size:69
Alignment explanation
Indices: 59395457--59395710 Score: 343
Period size: 69 Copynumber: 3.7 Consensus size: 69
59395447 GGAATCTATG
* * * *
59395457 GGCTACATTTCAGTGGTAGCTCCGGCTACAATATAGTGGTAGCTTTGGCTACATCTCAGTGGTAG
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTACATCTCAGTGGTAG
59395522 CTTC
66 CTTC
* * *
59395526 GTCTACAATACAGTGGTAGCTTCGGCTAGAATATAGTGGTAGCTTCGGCTACAAT-ACAGTGGTA
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTAC-ATCTCAGTGGTA
*
59395590 GCTTT
65 GCTTC
*
59395595 GGCTAC-AT-CTTAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTCGGCTACATCTCAGTGGT
1 GGCTACAATAC--AGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTACATCTCAGTGGT
59395658 AGCTTC
64 AGCTTC
** * *
59395664 GGCTACAATACAGTGGTAGCTTCGGCTACGTTATAGTGATTGCTTCG
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCG
59395711 ACTATATTAC
Statistics
Matches: 161, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
67 1 0.01
68 4 0.02
69 151 0.94
70 4 0.02
71 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (69 bp):
GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTACATCTCAGTGGTAG
CTTC
Found at i:59397115 original size:40 final size:40
Alignment explanation
Indices: 59397044--59397218 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 40
59397034 ACCCAAGTAT
*
59397044 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
59397083 CTTCGGGTCCTAGCCCGGATACAGCAAGTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
59397123 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * *
59397163 CTTCGGGTCTTAGCCCGG-T-TATC-ATTTGATACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCG-CACAAATGC
59397201 CTTCGGGTCTTAGCCCGG
1 CTTCGGGTCTTAGCCCGG
59397219 TTATCATCTG
Statistics
Matches: 122, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
37 3 0.02
38 30 0.25
39 11 0.09
40 78 0.64
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:59405415 original size:40 final size:40
Alignment explanation
Indices: 59405356--59405452 Score: 144
Period size: 40 Copynumber: 2.5 Consensus size: 40
59405346 ACCCAAGTAT
*
59405356 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCACACAAATGC
* *
59405395 CTTCGGGTCTTGGCCCGGATATAGCAACTCACACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCACACAAATGC
59405435 CTTCGGGTCTTAGCCCGG
1 CTTCGGGTCTTAGCCCGG
59405453 TTATCATCTG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.02
39 10 0.19
40 41 0.79
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCACACAAATGC
Found at i:59410699 original size:41 final size:42
Alignment explanation
Indices: 59410642--59410732 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
59410632 AGCTACAAGG
* * *
59410642 GACACACAGTCGTGTCACCTGGCCGTGTGT-CACACGGTTGA
1 GACACACAGCCGTGTCACCCGGCCGTGTATACACACGGTTGA
*
59410683 GACACACAGCCGTGTCACCCGGTCGTGTATCACACACGGTTGA
1 GACACACAGCCGTGTCACCCGGCCGTGTAT-ACACACGGTTGA
59410726 GACACAC
1 GACACAC
59410733 GCTCATGTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 26 0.59
43 18 0.41
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (42 bp):
GACACACAGCCGTGTCACCCGGCCGTGTATACACACGGTTGA
Found at i:59411420 original size:24 final size:24
Alignment explanation
Indices: 59411384--59411454 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
59411374 CTGTCAGGAG
*
59411384 AGGATTTAAGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
59411408 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
59411432 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
59411455 GGAAATCTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.37, C:0.01, G:0.37, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:59412906 original size:27 final size:27
Alignment explanation
Indices: 59412866--59412977 Score: 120
Period size: 27 Copynumber: 4.1 Consensus size: 27
59412856 AGGAAGCGTC
*
59412866 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
59412893 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
* *
59412920 ATGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * * *
59412948 CTAGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
59412974 CTGG
1 CTGG
59412978 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 7 0.10
27 48 0.68
28 16 0.23
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:59412972 original size:54 final size:54
Alignment explanation
Indices: 59412867--59412973 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
59412857 GGAAGCGTCC
* * *
59412867 TGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTTA
1 TGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATATATCTGTTA
* * *
59412921 TGGTGGCTCTGCCACGATTATCTGTATCTAGTGACTCTGTCACAT-TATCTGTT
1 TGGTGGCTATGCCACAATTATCTG-ATCTAGTGACTCTGCCACATATATCTGTT
59412974 CTGGCAGCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 29 0.63
55 17 0.37
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.38
Consensus pattern (54 bp):
TGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATATATCTGTTA
Found at i:59417499 original size:52 final size:51
Alignment explanation
Indices: 59417426--59417529 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 51
59417416 ATTACTTCAG
* * **
59417426 GTCGTGTTCGAGTCTATTAGAATGGCACGGGCGTGTGCTATACCCGTGTGA
1 GTCGTGTTCGAGTCTACTAGAATGACACGACCGTGTGCTATACCCGTGTGA
* * * * *
59417477 GTCGTGCTTCGATTCTGCTAGAATGACACGACCGTGTGGTCTGCCCGTGTGA
1 GTCGTG-TTCGAGTCTACTAGAATGACACGACCGTGTGCTATACCCGTGTGA
59417529 G
1 G
59417530 GAAGTCCAGG
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
51 6 0.14
52 37 0.86
ACGTcount: A:0.16, C:0.22, G:0.33, T:0.29
Consensus pattern (51 bp):
GTCGTGTTCGAGTCTACTAGAATGACACGACCGTGTGCTATACCCGTGTGA
Found at i:59419498 original size:21 final size:22
Alignment explanation
Indices: 59419453--59419499 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
59419443 AGCAGGGCTC
**
59419453 ACACGCCCGTGTAGTCCTAGGG
1 ACACGCCCGTGTAACCCTAGGG
59419475 ACACGCCCGTGTAACCCT-GGG
1 ACACGCCCGTGTAACCCTAGGG
59419496 ACAC
1 ACAC
59419500 CCCCTTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.15
Consensus pattern (22 bp):
ACACGCCCGTGTAACCCTAGGG
Found at i:59422596 original size:24 final size:24
Alignment explanation
Indices: 59422520--59422599 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
59422510 TCCTATAAAT
* *
59422520 GTATGCTCACACGAGCTGTAAATCG
1 GTATGCTCTCACGAGCTAT-AATCG
* **
59422545 GTATGCTCTCACGGGCTATACCCG
1 GTATGCTCTCACGAGCTATAATCG
*
59422569 GTATGCTCTCACGAGCTATAATCA
1 GTATGCTCTCACGAGCTATAATCG
59422593 GTATGCT
1 GTATGCT
59422600 TTCATGAGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 30 0.65
25 16 0.35
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (24 bp):
GTATGCTCTCACGAGCTATAATCG
Found at i:59447646 original size:16 final size:16
Alignment explanation
Indices: 59447625--59447695 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
59447615 GTTTGGTTCA
*
59447625 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
59447641 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
* *
59447657 CTGTAATGAAACAGAG
1 CTGTAATGGAATAGAG
59447673 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
59447689 CTGTAAT
1 CTGTAAT
59447696 CAGTAATTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.27
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:59447739 original size:46 final size:44
Alignment explanation
Indices: 59447677--59447770 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
59447667 ACAGAGCTGT
* *
59447677 AATGGAATAGAGCTGTAATCAGTAATTCA-ATTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAT-AGT-ATTCATA-TATTTGGTTGAATGG
*
59447723 AATGGAATAGAACTGTAATAGTATTCTTATATTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCATATATTTGGTTGAATGG
59447767 AATG
1 AATG
59447771 ATATTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
44 22 0.50
45 4 0.09
46 18 0.41
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATATATTTGGTTGAATGG
Found at i:59447955 original size:58 final size:58
Alignment explanation
Indices: 59447876--59447997 Score: 174
Period size: 58 Copynumber: 2.1 Consensus size: 58
59447866 TTTTAATAAG
* * *
59447876 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATCATATT-TTTACATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAACAATTTAATAATATTCTTAACATA
* * *
59447934 ATTATTATTAAATATAATTTAATAAAATAATATACAATTTAATAATATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAACAATTTAATAATATTCTTAACATA
59447992 ATTATT
1 ATTATT
59447998 TATGAATTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 23 0.40
58 34 0.60
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAACAATTTAATAATATTCTTAACATA
Found at i:59451629 original size:17 final size:18
Alignment explanation
Indices: 59451607--59451640 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59451597 TAACTAGACC
59451607 AATGATG-GGTTTGTTCA
1 AATGATGTGGTTTGTTCA
*
59451624 AATGATGTGTTTTGTTC
1 AATGATGTGGTTTGTTC
59451641 CATACGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.06, G:0.26, T:0.47
Consensus pattern (18 bp):
AATGATGTGGTTTGTTCA
Found at i:59451775 original size:20 final size:20
Alignment explanation
Indices: 59451752--59451793 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
59451742 AATCTTATCA
59451752 ATCTTTTTATTAAATTATTT
1 ATCTTTTTATTAAATTATTT
59451772 ATCTTTTTATTAAATTATTT
1 ATCTTTTTATTAAATTATTT
59451792 AT
1 AT
59451794 GTCAGATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
ATCTTTTTATTAAATTATTT
Found at i:59469500 original size:46 final size:46
Alignment explanation
Indices: 59469433--59469607 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
59469423 TGTAACCCGC
* *
59469433 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
59469479 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
59469529 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
59469572 CCATAAGTGAACTCGGACTCAACTTAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
59469608 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 59 0.56
47 27 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:59469569 original size:93 final size:93
Alignment explanation
Indices: 59469440--59469611 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
59469430 CGCCCATAAG
* * * *
59469440 CGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
59469505 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
59469533 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTTA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
59469598 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
59469612 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:59469627 original size:46 final size:44
Alignment explanation
Indices: 59469484--59469627 Score: 123
Period size: 46 Copynumber: 3.1 Consensus size: 44
59469474 CGCATCCATA
59469484 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * * *
59469531 CA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTC-G-GATGC-CAACCATCT
*
59469577 AGTGAACTCGGACTCAACTTAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
59469623 AGTGA
1 AGTGA
59469628 CATGTCACTT
Statistics
Matches: 77, Mismatches: 12, Indels: 16
0.73 0.11 0.15
Matches are distributed among these distances:
44 9 0.12
45 2 0.03
46 30 0.39
47 29 0.38
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:59474657 original size:13 final size:13
Alignment explanation
Indices: 59474639--59474665 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59474629 GCTCGGCAGG
59474639 GACACGCCCGTGT
1 GACACGCCCGTGT
59474652 GACACGCCCGTGT
1 GACACGCCCGTGT
59474665 G
1 G
59474666 CGATTTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:59487625 original size:6 final size:6
Alignment explanation
Indices: 59487614--59487651 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
59487604 ATTTTATTTG
59487614 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC- TTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTT
59487652 ATGTTTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:59487664 original size:12 final size:12
Alignment explanation
Indices: 59487648--59487695 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
59487638 TTTTCTTTTC
59487648 TTTTATGTTTAT
1 TTTTATGTTTAT
* *
59487660 GTTTATGTCTAT
1 TTTTATGTTTAT
59487672 TTTTAGTTGTTTTAT
1 TTTTA--TG-TTTAT
59487687 TTTTATGTT
1 TTTTATGTT
59487696 CTTAGACTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 16 0.55
13 2 0.07
14 2 0.07
15 9 0.31
ACGTcount: A:0.15, C:0.02, G:0.12, T:0.71
Consensus pattern (12 bp):
TTTTATGTTTAT
Found at i:59489552 original size:30 final size:30
Alignment explanation
Indices: 59489518--59489605 Score: 124
Period size: 30 Copynumber: 2.9 Consensus size: 30
59489508 CTGGGCATTT
*
59489518 CCACACGAGCTGGACACATGCACTTGTGTG
1 CCACACGAGCTGGACACATGCCCTTGTGTG
*
59489548 CCACACGGGCTGGACACATGCCCTTGTGTG
1 CCACACGAGCTGGACACATGCCCTTGTGTG
* *
59489578 CCACA-TAGGCTGCACACATGCCCTTGTG
1 CCACACGA-GCTGGACACATGCCCTTGTG
59489606 CCAACCCGTG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.20
Consensus pattern (30 bp):
CCACACGAGCTGGACACATGCCCTTGTGTG
Found at i:59490252 original size:26 final size:26
Alignment explanation
Indices: 59490216--59490268 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
59490206 GAAAGATATT
59490216 TCAAATAATCAAACTAGAGTCAGTTG
1 TCAAATAATCAAACTAGAGTCAGTTG
59490242 TCAAATAATCAAACTAGAGTCAGTTG
1 TCAAATAATCAAACTAGAGTCAGTTG
59490268 T
1 T
59490269 TCTTACTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (26 bp):
TCAAATAATCAAACTAGAGTCAGTTG
Found at i:59491949 original size:27 final size:27
Alignment explanation
Indices: 59491891--59491948 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
59491881 ATGAATTTTC
*
59491891 TCAAAATTTTA-CTAGGGTTAAAATCT
1 TCAAAATTTTATCTAGGGGTAAAATCT
59491917 TCAAAATTTTATC-AGGGGTAAAAT-T
1 TCAAAATTTTATCTAGGGGTAAAATCT
59491942 GTCAAAA
1 -TCAAAA
59491949 AATTTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 1 0.03
26 27 0.93
27 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (27 bp):
TCAAAATTTTATCTAGGGGTAAAATCT
Found at i:59502200 original size:46 final size:46
Alignment explanation
Indices: 59502147--59502412 Score: 149
Period size: 46 Copynumber: 5.7 Consensus size: 46
59502137 TTGTGAGCTA
59502147 GTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATGAGAGCCT
1 GTGTAAGACCATGTCTGGGACATGGCATCGG-C-CATTATGAGAGCCT
* * *
59502193 GTGTAAGACCATGTCTGTGACATGGCATCGG-CATTGA-CACGAGTGCT
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCCATT-ATGA-GAG-CCT
* * * * *
59502240 AGTGTAAGA-CATGTCTAGGACAT-GCATCGGCC-TCGA-GACATAAGTCA
1 -GTGTAAGACCATGTCTGGGACATGGCATCGGCCAT-TATG--A-GAGCCT
* * * * * *
59502287 ATGTAAGA-CATGTCTGGGACAT-GCATCGGCTATGA-GATGTGTCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCCATTATGA-GAGCCT
** * *
59502331 GCATAAGACCATGTATGGGACATGGCATCGGCACAGATATGCTAGAGCCT
1 GTGTAAGACCATGTCTGGGACATGGCATCGGC-CA-TTATG--AGAGCCT
*
59502381 GTGTAAGACCATGTTTGGGACATGGCATCGGC
1 GTGTAAGACCATGTCTGGGACATGGCATCGGC
59502413 ACCTTACCCC
Statistics
Matches: 173, Mismatches: 29, Indels: 32
0.74 0.12 0.14
Matches are distributed among these distances:
44 11 0.06
45 18 0.10
46 60 0.35
47 31 0.18
48 19 0.11
49 1 0.01
50 32 0.18
51 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (46 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCCATTATGAGAGCCT
Found at i:59502253 original size:47 final size:43
Alignment explanation
Indices: 59502143--59502270 Score: 125
Period size: 47 Copynumber: 2.8 Consensus size: 43
59502133 GCTATTGTGA
*
59502143 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAG
1 GCTAGTGTAAGACATGTCT-GGACATGCATCGG---CATTATCAGAG
*
59502190 CCT-GTGTAAGACCATGTCTGTGACATGGCATCGGCATTGA-CACGAG
1 GCTAGTGTAAGA-CATGTCTG-GACAT-GCATCGGCATT-ATCA-GAG
59502236 TGCTAGTGTAAGACATGTCTAGGACATGCATCGGC
1 -GCTAGTGTAAGACATGTCT-GGACATGCATCGGC
59502271 CTCGAGACAT
Statistics
Matches: 70, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
45 5 0.07
46 21 0.30
47 28 0.40
48 16 0.23
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (43 bp):
GCTAGTGTAAGACATGTCTGGACATGCATCGGCATTATCAGAG
Found at i:59505147 original size:39 final size:38
Alignment explanation
Indices: 59505066--59505300 Score: 245
Period size: 39 Copynumber: 6.0 Consensus size: 38
59505056 CAAATCCAAT
* * *
59505066 CACCACCACAAAGCATGCTGGACTTTAAGCCCGGATATAA
1 CACCAGCACAAAGCCTGCGGGAC-TT-AGCCCGGATATAA
*
59505106 TACCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATAA
1 CACCAGCACAAAGCCTGCGGGAC-TTAGCCCGGATATAA
* *
59505145 TACCAGCATAAAGCCTGCGGGACTTTAGCCCGGATATAA
1 CACCAGCACAAAGCCTGCGGGAC-TTAGCCCGGATATAA
* * * * * *
59505184 CACCGGCACGAATGCCTTCGGGGCTTAACCCAGATATAA
1 CACCAGCAC-AAAGCCTGCGGGACTTAGCCCGGATATAA
* * *
59505223 CACCAGCATGAATGCCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCA-CAAAGCCTGCGGGACTTAGCCCGGATATAA
* * *
59505262 CACCAGCACGAATGCCTTCGGGACTTAGCCCGAATATAA
1 CACCAGCAC-AAAGCCTGCGGGACTTAGCCCGGATATAA
59505301 TTCTCCATTA
Statistics
Matches: 172, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 139 0.81
40 33 0.19
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.19
Consensus pattern (38 bp):
CACCAGCACAAAGCCTGCGGGACTTAGCCCGGATATAA
Found at i:59505220 original size:78 final size:78
Alignment explanation
Indices: 59505075--59505301 Score: 289
Period size: 78 Copynumber: 2.9 Consensus size: 78
59505065 TCACCACCAC
* * * * *
59505075 AAAGCATGCTGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTGCGGGACTTTAGCCCGG
1 AAAGCCTGCGGGACTTT-AGCCCGGATATAACACCAGCACGAATGCCTTCGGGAC-TTAGCCC-G
59505139 ATATAATACCAGCAT-
63 ATATAATACCAGCATG
* * *
59505154 AAAGCCTGCGGGACTTTAGCCCGGATATAACACCGGCACGAATGCCTTCGGGGCTTAACCCAGAT
1 AAAGCCTGCGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCC-GAT
*
59505219 ATAACACCAGCATG
65 ATAATACCAGCATG
* *
59505233 AATGCCTTCGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGAAT
1 AAAGCCTGCGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCG-AT
59505297 ATAAT
65 ATAAT
59505302 TCTCCATTAT
Statistics
Matches: 129, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
77 1 0.01
78 90 0.70
79 38 0.29
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.20
Consensus pattern (78 bp):
AAAGCCTGCGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGATA
TAATACCAGCATG
Found at i:59505826 original size:110 final size:110
Alignment explanation
Indices: 59505633--59505852 Score: 431
Period size: 110 Copynumber: 2.0 Consensus size: 110
59505623 TGTGGATAGG
*
59505633 CTACTCGATTGCTTTCTCCTTTCCCCTATCTGATTTAGTTCCTCTTTGCTCTTGAGCTTTAAATT
1 CTACTCGATTGCTTTCCCCTTTCCCCTATCTGATTTAGTTCCTCTTTGCTCTTGAGCTTTAAATT
59505698 TAAACAAATGAATTTGTTTAATTACTTACTCAACTTTAATTCTAT
66 TAAACAAATGAATTTGTTTAATTACTTACTCAACTTTAATTCTAT
59505743 CTACTCGATTGCTTTCCCCTTTCCCCTATCTGATTTAGTTCCTCTTTGCTCTTGAGCTTTAAATT
1 CTACTCGATTGCTTTCCCCTTTCCCCTATCTGATTTAGTTCCTCTTTGCTCTTGAGCTTTAAATT
59505808 TAAACAAATGAATTTGTTTAATTACTTACTCAACTTTAATTCTAT
66 TAAACAAATGAATTTGTTTAATTACTTACTCAACTTTAATTCTAT
59505853 AATAGTCACA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (110 bp):
CTACTCGATTGCTTTCCCCTTTCCCCTATCTGATTTAGTTCCTCTTTGCTCTTGAGCTTTAAATT
TAAACAAATGAATTTGTTTAATTACTTACTCAACTTTAATTCTAT
Found at i:59518545 original size:27 final size:27
Alignment explanation
Indices: 59518514--59518691 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
59518504 TAAATTGTAC
59518514 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
59518541 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
59518567 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
59518595 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
59518623 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
59518650 AGCACTAAGTGTGTGAGTTGACTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
59518677 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
59518692 GACTCAATAT
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:59518682 original size:82 final size:81
Alignment explanation
Indices: 59518511--59518691 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
59518501 GATTAAATTG
* *
59518511 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
59518576 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
59518592 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* * *
59518656 AAGTGTGTGAGTTGACTA
64 AAGTGTGCGAATTGACCA
* *
59518674 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
59518692 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:59525301 original size:56 final size:56
Alignment explanation
Indices: 59525215--59525390 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
59525205 ACAAGGAATG
59525215 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
59525271 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
59525327 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
59525383 ATGGGCAA
1 ATGGGCAA
59525391 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:59533595 original size:17 final size:17
Alignment explanation
Indices: 59533573--59533638 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
59533563 TTATTTATCA
*
59533573 TTATTCTTAGTATTATT
1 TTATTCTTATTATTATT
59533590 TTATTCCCTTATTATTATT
1 TTATT--CTTATTATTATT
59533609 GTT-TTCTTATTATT-TT
1 -TTATTCTTATTATTATT
*
59533625 TTAGTCATTATTAT
1 TTATTC-TTATTAT
59533639 GAGTTTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
15 2 0.05
16 4 0.10
17 21 0.50
19 13 0.31
20 2 0.05
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (17 bp):
TTATTCTTATTATTATT
Found at i:59533909 original size:24 final size:24
Alignment explanation
Indices: 59533877--59533931 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
59533867 AGTTAACTTT
*
59533877 TCTTGTTAATATGTTTCTTTCTAG
1 TCTTATTAATATGTTTCTTTCTAG
59533901 TCTTATTAATATGTTTCTTTCTAG
1 TCTTATTAATATGTTTCTTTCTAG
59533925 TCTTATT
1 TCTTATT
59533932 GGTCATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.60
Consensus pattern (24 bp):
TCTTATTAATATGTTTCTTTCTAG
Found at i:59535314 original size:6 final size:6
Alignment explanation
Indices: 59535303--59535354 Score: 61
Period size: 6 Copynumber: 8.5 Consensus size: 6
59535293 AGTCCAATTA
* *
59535303 TTTTAT TTTTAT TTTTAT TTTTAT TTTCAT GTTTAT TTTGT-T TTTCTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT TTT-TAT
59535352 TTT
1 TTT
59535355 GAACTTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
6 34 0.87
7 5 0.13
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:59536261 original size:27 final size:27
Alignment explanation
Indices: 59536231--59536317 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 27
59536221 TTTGATTTGG
59536231 TTAGTTGCCTAACTATTTTCTTTTATT
1 TTAGTTGCCTAACTATTTTCTTTTATT
* ** * * *
59536258 TTAGTGGTGTAA-TTTTTTCTTATTGTGG
1 TTAGTTGCCTAACTATTTTCTT-TTAT-T
59536286 TTAGTTGCCTAACTATTTTCTTTTATT
1 TTAGTTGCCTAACTATTTTCTTTTATT
59536313 TTAGT
1 TTAGT
59536318 GGTGTAATTT
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
26 8 0.18
27 17 0.38
28 12 0.27
29 8 0.18
ACGTcount: A:0.17, C:0.10, G:0.14, T:0.59
Consensus pattern (27 bp):
TTAGTTGCCTAACTATTTTCTTTTATT
Found at i:59536273 original size:24 final size:24
Alignment explanation
Indices: 59536245--59536336 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 24
59536235 TTGCCTAACT
59536245 ATTTTCTTTTATTTTAGTGGTGTA
1 ATTTTCTTTTATTTTAGTGGTGTA
* **
59536269 ATTTT-TTCTTATTGTGGTTAGTTGCCTAA
1 ATTTTCTT-TTA-T-T--TTAGTGGTGT-A
59536298 CTATTTTCTTTTATTTTAGTGGTGTA
1 --ATTTTCTTTTATTTTAGTGGTGTA
*
59536324 ATTTTCTCTTATT
1 ATTTTCTTTTATT
59536337 GTACATTCAT
Statistics
Matches: 52, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
23 2 0.04
24 20 0.38
25 1 0.02
26 2 0.04
27 7 0.13
28 7 0.13
29 2 0.04
30 1 0.02
31 8 0.15
32 2 0.04
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.61
Consensus pattern (24 bp):
ATTTTCTTTTATTTTAGTGGTGTA
Found at i:59536289 original size:55 final size:55
Alignment explanation
Indices: 59536228--59536338 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
59536218 GGATTTGATT
*
59536228 TGGTTAGTTGCCTAACTATTTTCTTTTATTTTAGTGGTGTAATTTTTTCTTATTG
1 TGGTTAGTTGCCTAACTATTTTCTTTTATTTTAGTGGTGTAATTTTCTCTTATTG
59536283 TGGTTAGTTGCCTAACTATTTTCTTTTATTTTAGTGGTGTAATTTTCTCTTATTG
1 TGGTTAGTTGCCTAACTATTTTCTTTTATTTTAGTGGTGTAATTTTCTCTTATTG
59536338 T
1 T
59536339 ACATTCATTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.58
Consensus pattern (55 bp):
TGGTTAGTTGCCTAACTATTTTCTTTTATTTTAGTGGTGTAATTTTCTCTTATTG
Found at i:59545286 original size:27 final size:27
Alignment explanation
Indices: 59545256--59545719 Score: 594
Period size: 27 Copynumber: 17.2 Consensus size: 27
59545246 AAAGTACTCC
59545256 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
59545283 CGATTTATAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
59545310 CGATTTTTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
59545337 CGATTTACAGAATTAACGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
59545364 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
59545391 C-AGTTTATAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
59545418 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
59545445 C-AGTTTACAGAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
59545472 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
59545499 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * * *
59545526 TGATTTATAGAATTACTGGTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
59545553 C-AGTTTACAAAATTATCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
59545580 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
59545607 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * * *
59545634 TGATTTATAGAATTACTGGTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
59545661 C-AGTTTACAAAATTATCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
59545688 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
59545715 TGATT
1 CGATT
59545720 GTGAAATTAC
Statistics
Matches: 378, Mismatches: 51, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.01
27 370 0.98
28 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.40
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:59545401 original size:108 final size:108
Alignment explanation
Indices: 59545256--59545719 Score: 682
Period size: 108 Copynumber: 4.3 Consensus size: 108
59545246 AAAGTACTCC
* * *
59545256 CGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTTTAAA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGA
* *
59545321 ATTACCGTTTTACCCTC-GATTTACAGAATTAACGTTTTACCCT
66 ATTACCGGTTTACCCTCAG-TTTACAAAATTAACGTTTTACCCT
* * *
59545364 CGATTTACAGAATTACCGTTTTACCCTC-AGTTTATAGAATTACTATTTTACCCTCGATTTACAG
1 CGATTTACAGAATTACCGTTTTACCCTCGA-TTTATAAAATTACCATTTTACCCTCGATTTATAG
** *
59545428 AATTACCATTTTACCCTCAGTTTACAGAATT-ACTGTTTTACCCT
65 AATTACCGGTTTACCCTCAGTTTACAAAATTAAC-GTTTTACCCT
* * *
59545472 CGATTTACAGAATTACCGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCTTGATTTATAGA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGA
* *
59545537 ATTACTGGTTTACCCTCAGTTTACAAAATTATCGTTTTACCCT
66 ATTACCGGTTTACCCTCAGTTTACAAAATTAACGTTTTACCCT
* * *
59545580 CGATTTACAGAATTACCGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCTTGATTTATAGA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGA
* *
59545645 ATTACTGGTTTACCCTCAGTTTACAAAATTATCGTTTTACCCT
66 ATTACCGGTTTACCCTCAGTTTACAAAATTAACGTTTTACCCT
*
59545688 CGATTTACAGAATTACCGTTTTACCCTTGATT
1 CGATTTACAGAATTACCGTTTTACCCTCGATT
59545720 GTGAAATTAC
Statistics
Matches: 334, Mismatches: 17, Indels: 10
0.93 0.05 0.03
Matches are distributed among these distances:
107 3 0.01
108 328 0.98
109 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.40
Consensus pattern (108 bp):
CGATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGA
ATTACCGGTTTACCCTCAGTTTACAAAATTAACGTTTTACCCT
Found at i:59545754 original size:27 final size:27
Alignment explanation
Indices: 59545724--59545892 Score: 212
Period size: 27 Copynumber: 6.3 Consensus size: 27
59545714 TTGATTGTGA
* *
59545724 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
59545751 AATTTCCGAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
59545778 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
59545805 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
59545832 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
59545859 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
59545886 AATTACC
1 AATTACC
59545893 ATTTTGCCCC
Statistics
Matches: 122, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 122 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:59546129 original size:27 final size:26
Alignment explanation
Indices: 59546091--59546173 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
59546081 CGGAGGAAGC
*
59546091 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
59546118 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
59546144 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
59546171 GTT
1 GTT
59546174 GACCGATCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:59546293 original size:22 final size:22
Alignment explanation
Indices: 59546261--59546319 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
59546251 CCCGTTATTA
*
59546261 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
59546283 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
59546305 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
59546320 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:59546539 original size:27 final size:27
Alignment explanation
Indices: 59546484--59546558 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
59546474 TAGGTGGGTT
* **
59546484 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGAATC
59546511 TGCCACAATATCTGTATCTGGTGAATC
1 TGCCACAATATCTGTATCTGGTGAATC
* * *
59546538 TGTCACGATATCTAT-TCTGGT
1 TGCCACAATATCTGTATCTGGT
59546559 AGCCATGCTG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.15
27 34 0.83
28 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGAATC
Found at i:59546684 original size:6 final size:6
Alignment explanation
Indices: 59546675--59546804 Score: 81
Period size: 6 Copynumber: 21.3 Consensus size: 6
59546665 TTGCATTCAC
* * * *
59546675 ATTCTG ATTCTG ATTCTG -TCACGTA ATTCTG ATTCTG -TCACGTA ATTCTG
1 ATTCTG ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG AT-TC-TG ATTCTG
*
59546725 ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG
1 ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG
* * * *
59546773 ATTCTG ATTCTC ATTTTG GTTCTA ATTCTG AT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT
59546805 AATGTTTCTT
Statistics
Matches: 94, Mismatches: 18, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
5 7 0.07
6 77 0.82
7 7 0.07
8 3 0.03
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:59546705 original size:19 final size:19
Alignment explanation
Indices: 59546681--59546748 Score: 104
Period size: 19 Copynumber: 3.6 Consensus size: 19
59546671 TCACATTCTG
59546681 ATTCTGATTCTGTCACGTA
1 ATTCTGATTCTGTCACGTA
59546700 ATTCTGATTCTGTCACGTA
1 ATTCTGATTCTGTCACGTA
*
59546719 ATTCTGATTCTGTTAC-TA
1 ATTCTGATTCTGTCACGTA
59546737 ATAT-TGATTCTG
1 AT-TCTGATTCTG
59546749 ATTCTGATTC
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
18 12 0.26
19 35 0.74
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.46
Consensus pattern (19 bp):
ATTCTGATTCTGTCACGTA
Found at i:59546754 original size:30 final size:30
Alignment explanation
Indices: 59546719--59546804 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
59546709 CTGTCACGTA
59546719 ATTCTGATTCTGTTACTAATAT-TGATTCTG
1 ATTCTGATTCTGTTACTAAT-TCTGATTCTG
*
59546749 ATTCTGATTCTGTTACTGATTCTGATTCTG
1 ATTCTGATTCTGTTACTAATTCTGATTCTG
* *
59546779 ATTCTCATTTTGGTT-CTAATTCTGAT
1 ATTCTGATTCT-GTTACTAATTCTGAT
59546805 AATGTTTCTT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.02
30 46 0.92
31 3 0.06
ACGTcount: A:0.20, C:0.15, G:0.14, T:0.51
Consensus pattern (30 bp):
ATTCTGATTCTGTTACTAATTCTGATTCTG
Found at i:59546813 original size:18 final size:17
Alignment explanation
Indices: 59546792--59546825 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
59546782 CTCATTTTGG
59546792 TTCTAATTCTGATAATGT
1 TTCTAATTCTG-TAATGT
*
59546810 TTCTTATTCTGTAATG
1 TTCTAATTCTGTAATG
59546826 GGCTAAGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (17 bp):
TTCTAATTCTGTAATGT
Found at i:59548651 original size:25 final size:25
Alignment explanation
Indices: 59548617--59548669 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
59548607 GTGTATGCTA
*
59548617 CATTGAGATTGTCAAGTAAAGAAAC
1 CATTGAGATTGTCAAGCAAAGAAAC
*
59548642 CATTGAGATTGTCAAGCGAAGAAAC
1 CATTGAGATTGTCAAGCAAAGAAAC
59548667 CAT
1 CAT
59548670 GTGACAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.23
Consensus pattern (25 bp):
CATTGAGATTGTCAAGCAAAGAAAC
Found at i:59550465 original size:53 final size:53
Alignment explanation
Indices: 59550358--59550465 Score: 117
Period size: 53 Copynumber: 2.0 Consensus size: 53
59550348 CTTTCTCACT
* *
59550358 TATTATTTGAGAATGGACACAGCATTTTAATTACCCTAACATATTTTTAGTCA
1 TATTATTTGAGAATGGACACAGCATTTTAATTACCCTAACATATTCTCAGTCA
* * * * * * ** *
59550411 TATTCTTTGAGAATTGCCTCAGCATTTTCATTTCCCTAGGATATTCTCATTCA
1 TATTATTTGAGAATGGACACAGCATTTTAATTACCCTAACATATTCTCAGTCA
59550464 TA
1 TA
59550466 GTTGATTTCA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.42
Consensus pattern (53 bp):
TATTATTTGAGAATGGACACAGCATTTTAATTACCCTAACATATTCTCAGTCA
Found at i:59560849 original size:38 final size:38
Alignment explanation
Indices: 59560805--59560881 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
59560795 ATTACAGCCA
*
59560805 GTTACTATACCGGAGTGGAAATGGGAAAGAGTTACAAT
1 GTTACTATACCAGAGTGGAAATGGGAAAGAGTTACAAT
*
59560843 GTTACTATACCAGAGTGGAAATGTGAAAGAGTTACAAT
1 GTTACTATACCAGAGTGGAAATGGGAAAGAGTTACAAT
59560881 G
1 G
59560882 GATTTTGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (38 bp):
GTTACTATACCAGAGTGGAAATGGGAAAGAGTTACAAT
Found at i:59564287 original size:24 final size:25
Alignment explanation
Indices: 59564260--59564311 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
59564250 TCCTAGCCTC
59564260 TTTTAATAAC-TAGGGCAAAGCCCT
1 TTTTAATAACTTAGGGCAAAGCCCT
** *
59564284 TTTTGGTAACTTGGGGCAAAGCCCT
1 TTTTAATAACTTAGGGCAAAGCCCT
59564309 TTT
1 TTT
59564312 CGCACTTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (25 bp):
TTTTAATAACTTAGGGCAAAGCCCT
Found at i:59564545 original size:27 final size:27
Alignment explanation
Indices: 59564515--59564871 Score: 326
Period size: 27 Copynumber: 13.3 Consensus size: 27
59564505 GAGGCAGAAT
* * * *
59564515 GGTAATTTTACCCCACAAGGTTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
59564542 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
59564569 GATATTTCTACCGTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
59564596 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
59564623 GGTAATTCTACCCTATAGGGGCATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * * *
59564650 AGTAATTCTACCTTATAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
59564677 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
59564704 GGTAATTCTACCTTA-TAGGAGTATTTT
1 GGTAATTCTACCCTACAAGG-GTATTTC
*
59564731 AGTAATTCTACCCTAC-AGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * *
59564757 GATAATTCTACCTTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
59564784 AGTAATTCTACCCTACATGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
59564811 AGTAATTCTACCCTACAGGGGTATTTTC
1 GGTAATTCTACCCTACAAGGGTA-TTTC
* ** *
59564839 -GTAATTTTA-CAAACCAAGGGTATTTT
1 GGTAATTCTACCCTA-CAAGGGTATTTC
59564865 GGTAATT
1 GGTAATT
59564872 TTACAAACTA
Statistics
Matches: 277, Mismatches: 47, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
26 25 0.09
27 248 0.90
28 4 0.01
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:59564587 original size:54 final size:55
Alignment explanation
Indices: 59564516--59564836 Score: 377
Period size: 54 Copynumber: 5.9 Consensus size: 55
59564506 AGGCAGAATG
* * * * *
59564516 GTAATTTTACCCCACAAGGTTATCTCGGTAATTCTACCCTACAGGGGTATTTCGA
1 GTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGA
* *
59564571 -TATTTCTACCGTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCG-
1 GTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGA
* * * * * *
59564624 GTAATTCTACCCTATAGGGGCATTTCAGTAATTCTACCTTATAGGGGTATTT-TA
1 GTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGA
* * * * * * *
59564678 GTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCTTATAGGAGTATTT-TA
1 GTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGA
* *
59564732 GTAATTCTACCCTAC-AGGGTATTTC-GATAATTCTACCTTATAGGGGTATTTC-A
1 GTAATTCTACCCTACAAGGGTATTTCAG-TAATTCTACCCTACAGGGGTATTTCGA
*
59564785 GTAATTCTACCCTACATGGGTATTTCAGTAATTCTACCCTACAGGGGTATTT
1 GTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTT
59564837 TCGTAATTTT
Statistics
Matches: 236, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
52 1 0.00
53 48 0.20
54 186 0.79
55 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (55 bp):
GTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGA
Found at i:59564659 original size:81 final size:80
Alignment explanation
Indices: 59564516--59564844 Score: 392
Period size: 81 Copynumber: 4.1 Consensus size: 80
59564506 AGGCAGAATG
* * * * * *
59564516 GTAATTTTACCCCACAAGGTTATCTCGGTAATTCTACCCTACAGGGGTATTTC-GATATTTCTAC
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAG-TAATTCTAC
*
59564580 CGTACAAGGGTATTTC
65 CCTACAAGGGTATTTC
* *
59564596 AGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAGGGGCATTTCAGTAATTCTAC
1 -GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTAC
* * * *
59564661 CTTATAGGGGTATTTTA
65 CCTACAAGGGTA-TTTC
* * * * *
59564678 GTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCTTATAGGAGTATTTTAGTAATTCTACC
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACC
59564743 CTAC-AGGGTATTTC
66 CTACAAGGGTATTTC
* * * *
59564757 GATAATTCTACCTTATAGGGGTATTTCAGTAATTCTACCCTACATGGGTATTTCAGTAATTCTAC
1 G-TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTAC
*
59564822 CCTACAGGGGTATTTTC
65 CCTACAAGGGTA-TTTC
59564839 GTAATT
1 GTAATT
59564845 TTACAAACCA
Statistics
Matches: 214, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
79 4 0.02
80 66 0.31
81 135 0.63
82 9 0.04
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (80 bp):
GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACC
CTACAAGGGTATTTC
Found at i:59564872 original size:27 final size:27
Alignment explanation
Indices: 59564829--59564896 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
59564819 TACCCTACAG
*
59564829 GGGTATTTTCGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
59564856 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAA
59564883 GGGTATTTTGGTAA
1 GGGTATTTTGGTAA
59564897 CTTTGGTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:59567630 original size:33 final size:33
Alignment explanation
Indices: 59567557--59567634 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
59567547 GGGAGTATAT
* *
59567557 GTGTAAGACCATAGCTAGGCTATGGCATCCTGA
1 GTGTAAGACCATAGCTAGGATATGGCATACTGA
* *
59567590 -TGATAAGACCATATCTGGGATATGGCACTAC-GA
1 GTG-TAAGACCATAGCTAGGATATGGCA-TACTGA
59567623 GTGTAAGACCAT
1 GTGTAAGACCAT
59567635 GGCTGCGCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 2 0.05
33 32 0.84
34 4 0.11
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (33 bp):
GTGTAAGACCATAGCTAGGATATGGCATACTGA
Found at i:59567815 original size:45 final size:45
Alignment explanation
Indices: 59567697--59567805 Score: 164
Period size: 45 Copynumber: 2.4 Consensus size: 45
59567687 TCCAGAAAGG
*
59567697 AGTAAGACCATAGATGAAAGACGCTATGGCATCGCGATTCAGACA
1 AGTAAGACCATAGATGAAAGACGCTATGGCATCACGATTCAGACA
* * *
59567742 AGTAAGACCATAGCTGAAAGACGTTATGGCATCACGATTCAGATA
1 AGTAAGACCATAGATGAAAGACGCTATGGCATCACGATTCAGACA
* *
59567787 TGTAAGACCATAGTTGAAA
1 AGTAAGACCATAGATGAAA
59567806 TATACTATGG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (45 bp):
AGTAAGACCATAGATGAAAGACGCTATGGCATCACGATTCAGACA
Found at i:59567849 original size:46 final size:45
Alignment explanation
Indices: 59567789--59567993 Score: 284
Period size: 46 Copynumber: 4.5 Consensus size: 45
59567779 TTCAGATATG
* * * * * *
59567789 TAAGACCATAGTTGAAATATACTATGGTAATATGACGAGATATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAC-AGAAATGAA
*
59567835 TAAGACCATGGTTGAAAGATACCATGGGAACATGACAGAAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAG-AAATGAA
*
59567881 TAAGACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAG-AAATGAA
* *
59567927 TAAGACCATGGTTGAAAGATTCCATAGCAACATGACAGGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAATGAA
59567973 TAAGACCATGGTTGAAAGATA
1 TAAGACCATGGTTGAAAGATA
59567994 GAAATGAACA
Statistics
Matches: 145, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
45 2 0.01
46 142 0.98
47 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.21
Consensus pattern (45 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAATGAA
Found at i:59568007 original size:29 final size:29
Alignment explanation
Indices: 59567965--59568020 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
59567955 AACATGACAG
* *
59567965 GAAATGAATAAGACCATGGTTGAAAGATA
1 GAAATGAACAAGACCATAGTTGAAAGATA
*
59567994 GAAATGAACAAGACCATAGTTGGAAGA
1 GAAATGAACAAGACCATAGTTGAAAGA
59568021 CATTATGGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (29 bp):
GAAATGAACAAGACCATAGTTGAAAGATA
Found at i:59570726 original size:31 final size:31
Alignment explanation
Indices: 59570689--59570747 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
59570679 GTAAATACTC
**
59570689 AAAATTTAAAGGGTTAA-AGTGTAAATATGAA
1 AAAATTT-AAGGACTAATAGTGTAAATATGAA
59570720 AAAATTTAAGGACTAATAGTGTAAATAT
1 AAAATTTAAGGACTAATAGTGTAAATAT
59570748 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.31
Consensus pattern (31 bp):
AAAATTTAAGGACTAATAGTGTAAATATGAA
Found at i:59571001 original size:11 final size:11
Alignment explanation
Indices: 59570987--59571031 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
59570977 AGATAAATAT
59570987 TATTTTATTAA
1 TATTTTATTAA
*
59570998 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
59571011 TATTTTATTAT
1 TATTTTATTAA
59571022 TATTTTATTA
1 TATTTTATTA
59571032 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:59572787 original size:200 final size:200
Alignment explanation
Indices: 59572444--59572846 Score: 770
Period size: 200 Copynumber: 2.0 Consensus size: 200
59572434 GTTGAAATTT
59572444 CATGATTATTTGTTAAATTAGGAATGATATAATGTATTATTTCATATGTTTGCAATTGAATTATG
1 CATGATTATTTGTTAAATTAGGAATGATATAATGTATTATTTCATATGTTTGCAATTGAATTATG
* *
59572509 AATATTTTTAAATTATGGAAATTAGATCAGAAGTTCAAATTGAGCAGAACGCTGAATTGAATATG
66 AATATTTTTAAATTATGGAAATCAGATCAAAAGTTCAAATTGAGCAGAACGCTGAATTGAATATG
59572574 ATCGTTTAGTGATCAGTGATGAATTGACAGATAAGACCATGGCTGGGTCATGGCAATATATGTGT
131 ATCGTTTAGTGATCAGTGATGAATTGACAGATAAGACCATGGCTGGGTCATGGCAATATATGTGT
*
59572639 AATAC
196 AAGAC
59572644 CATGATTATTTGTTAAATTAGGAATGATATAATGTATTATTTCATATGTTTGCAATTGAATTATG
1 CATGATTATTTGTTAAATTAGGAATGATATAATGTATTATTTCATATGTTTGCAATTGAATTATG
*
59572709 AATATTTTTAAATTATGGAAATCGGATCAAAAGTTCAAATTGAGCAGAACGCTGAATTGAATATG
66 AATATTTTTAAATTATGGAAATCAGATCAAAAGTTCAAATTGAGCAGAACGCTGAATTGAATATG
59572774 ATCGTTTAGTGATCAGTGATGAATTGACAGATAAGACCATGGCTGGGTCATGGCAATATATGTGT
131 ATCGTTTAGTGATCAGTGATGAATTGACAGATAAGACCATGGCTGGGTCATGGCAATATATGTGT
59572839 AAGAC
196 AAGAC
59572844 CAT
1 CAT
59572847 AGCTAGTTAT
Statistics
Matches: 199, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 199 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.35
Consensus pattern (200 bp):
CATGATTATTTGTTAAATTAGGAATGATATAATGTATTATTTCATATGTTTGCAATTGAATTATG
AATATTTTTAAATTATGGAAATCAGATCAAAAGTTCAAATTGAGCAGAACGCTGAATTGAATATG
ATCGTTTAGTGATCAGTGATGAATTGACAGATAAGACCATGGCTGGGTCATGGCAATATATGTGT
AAGAC
Found at i:59573019 original size:45 final size:45
Alignment explanation
Indices: 59572970--59573093 Score: 162
Period size: 45 Copynumber: 2.8 Consensus size: 45
59572960 CATACCATAA
* *
59572970 ACGAGTAAGACCATAGTTAAAAGACACTATGGCATTGA-GATTCAG
1 ACGAGTAAGACCATAGTTGAAAGACACTATGGCA-TCACGATTCAG
**
59573015 ACGAGTAAGACCATAGTTGAAAGACGTTATGGCATCACGATTCAG
1 ACGAGTAAGACCATAGTTGAAAGACACTATGGCATCACGATTCAG
* *
59573060 A-TATGTAAGACCATAGTTGAAAGATACTATGGCA
1 ACGA-GTAAGACCATAGTTGAAAGACACTATGGCA
59573094 ATGTGACGAG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
44 3 0.04
45 66 0.96
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (45 bp):
ACGAGTAAGACCATAGTTGAAAGACACTATGGCATCACGATTCAG
Found at i:59573177 original size:45 final size:47
Alignment explanation
Indices: 59573065--59573222 Score: 243
Period size: 46 Copynumber: 3.4 Consensus size: 47
59573055 TTCAGATATG
* * **
59573065 TAAGACCATAGTTGAAAGATACTATGGCAATGTGAC-GAGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAGAAATGAA
*
59573111 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA-AAACGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAGAAATGAA
59573157 TAAGACCATGGTTG-AAGATACCATGGCAACATGACA-AGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAGAAATGAA
59573202 TAAGACCATGGTTGAAAGATA
1 TAAGACCATGGTTGAAAGATA
59573223 GAAATGAATA
Statistics
Matches: 103, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
44 1 0.01
45 42 0.41
46 58 0.56
47 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (47 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAGAAATGAA
Found at i:59573225 original size:29 final size:29
Alignment explanation
Indices: 59573193--59573249 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
59573183 CAACATGACA
*
59573193 AGAAATGAATAAGACCATGGTTGAAAGAT
1 AGAAATGAATAAGACCATAGTTGAAAGAT
* *
59573222 AGAAATGAATAATACCATAGTTGGAAGA
1 AGAAATGAATAAGACCATAGTTGAAAGA
59573250 CACTATGGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.49, C:0.07, G:0.23, T:0.21
Consensus pattern (29 bp):
AGAAATGAATAAGACCATAGTTGAAAGAT
Found at i:59580088 original size:12 final size:13
Alignment explanation
Indices: 59580060--59580092 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
59580050 TTATTTCTTT
59580060 TTCTCCATCTACC
1 TTCTCCATCTACC
*
59580073 TTCTCC-TCTTCC
1 TTCTCCATCTACC
59580085 TTCTCCAT
1 TTCTCCAT
59580093 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:59580906 original size:16 final size:15
Alignment explanation
Indices: 59580880--59580910 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
59580870 GCTAGATCGG
59580880 CAAAAGCCGAAAAGC
1 CAAAAGCCGAAAAGC
59580895 CAAAATGCCGAAAAGC
1 CAAAA-GCCGAAAAGC
59580911 TGGTATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.26, G:0.19, T:0.03
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:59581191 original size:28 final size:28
Alignment explanation
Indices: 59581159--59581223 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
59581149 ATTTACTAGA
*
59581159 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
59581187 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
59581215 ATACCCCTA
1 ATACCCCTA
59581224 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:59581370 original size:28 final size:27
Alignment explanation
Indices: 59581329--59581408 Score: 90
Period size: 27 Copynumber: 2.9 Consensus size: 27
59581319 AGGAAGCGTC
59581329 CTGGTGGCTA-TGCCACAAATTATCTATT
1 CTGGTGGC-ACTGCCACAAA-TATCTATT
* ** *
59581357 CTGGTGGCCCTGCCACGTATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTATT
59581384 CTGGTGGCACTGCCACAAAATATCT
1 CTGGTGGCACTGCCAC-AAATATCT
59581409 GTATCTGGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
27 22 0.51
28 21 0.49
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTATT
Found at i:59582507 original size:11 final size:10
Alignment explanation
Indices: 59582479--59582512 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
59582469 AGCCTGTAAG
59582479 TATTCTGAAT
1 TATTCTGAAT
*
59582489 TTTTCTGAAT
1 TATTCTGAAT
59582499 ATATTCTGAAT
1 -TATTCTGAAT
59582510 TAT
1 TAT
59582513 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:59587922 original size:12 final size:13
Alignment explanation
Indices: 59587894--59587926 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
59587884 TTATTTCTTT
59587894 TTCTCCATCTACC
1 TTCTCCATCTACC
*
59587907 TTCTCC-TCTTCC
1 TTCTCCATCTACC
59587919 TTCTCCAT
1 TTCTCCAT
59587927 AGCCTAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:59589025 original size:28 final size:28
Alignment explanation
Indices: 59588993--59589057 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
59588983 ATTTACTAGA
* *
59588993 ATACCCCTATGTATGCACAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* **
59589021 ATACCCCTATGTGTGCAAAATGACGTTT
1 ATACCCCTATGTATGCAAAATGACCATT
59589049 ATACCCCTA
1 ATACCCCTA
59589058 GGGTTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:59589204 original size:28 final size:27
Alignment explanation
Indices: 59589163--59589252 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 27
59589153 AGGAAGTGTC
*
59589163 CTGGTGGCTA-TGCCACAAATTATCTATT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* **
59589191 CTGGTGGCCCTGCCACGTATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
59589218 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
59589247 CTGGTG
1 CTGGTG
59589253 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 22 0.42
28 23 0.44
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:59589221 original size:27 final size:28
Alignment explanation
Indices: 59589163--59589252 Score: 103
Period size: 27 Copynumber: 3.2 Consensus size: 28
59589153 AGGAAGTGTC
* *
59589163 CTGGTGGCTA-TGCCACAAATTATCTATT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
59589191 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
59589218 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
59589247 CTGGTG
1 CTGGTG
59589253 ACTCTGTCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 22 0.43
28 22 0.43
29 7 0.14
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:59589263 original size:29 final size:28
Alignment explanation
Indices: 59589173--59589263 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
59589163 CTGGTGGCTA
* * * *
59589173 TGCCACAAATTATCTATTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
59589201 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
59589228 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
59589257 TGTCACA
1 TGCCACA
59589264 TTTTCTGTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
27 22 0.43
28 14 0.27
29 15 0.29
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:59589271 original size:55 final size:56
Alignment explanation
Indices: 59589163--59589277 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 56
59589153 AGGAAGTGTC
* * *
59589163 CTGGTGGCTATGCCACAAATTATCTATTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTATTCTGGTGACCCTGCCACATATATCTGTAT
* * * *
59589218 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTAT-TCTGGTGACCCTGCCACATATATCTGTAT
59589274 CTGG
1 CTGG
59589278 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.58
56 20 0.40
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTATTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:59599016 original size:29 final size:29
Alignment explanation
Indices: 59598956--59599065 Score: 118
Period size: 29 Copynumber: 3.9 Consensus size: 29
59598946 TACCTGTATC
* * * * *
59598956 TGGCCCATTAAG-CCTAATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTTACA
*
59598984 TGGCCCATTAGGCCCACATCAC-TTGTACA
1 TGGCCCATTAGGCCCAAATCACATT-TACA
*
59599013 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTACA
*
59599042 TGGCCCATTAGGCCC-AGTCACATT
1 TGGCCCATTAGGCCCAAATCACATT
59599066 CATATTCATG
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.30
29 47 0.67
30 2 0.03
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTACA
Found at i:59601816 original size:37 final size:37
Alignment explanation
Indices: 59601757--59601865 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
59601747 AGCTCAGACG
* *
59601757 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
59601794 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
59601831 TAATCTCCACACGTAGTCATCGGGTCTTATCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
59601866 ATATATTTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:59602076 original size:56 final size:56
Alignment explanation
Indices: 59602014--59602121 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 56
59602004 CATCGCCTAC
*
59602014 ATATTTCACACTAG-CCATTC-GACTTTACCACATATACATATCTCATATATATATAT
1 ATATTTCACA-TAGACCATTCAG-CTTTACCACATATACATATCTCATACATATATAT
* *
59602070 ATATTTCACATTGACCATTCAGCTTTACCACATATACATTTCTCATACATAT
1 ATATTTCACATAGACCATTCAGCTTTACCACATATACATATCTCATACATAT
59602122 TTCACATTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
55 2 0.04
56 44 0.94
57 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (56 bp):
ATATTTCACATAGACCATTCAGCTTTACCACATATACATATCTCATACATATATAT
Found at i:59602186 original size:47 final size:47
Alignment explanation
Indices: 59602123--59602363 Score: 356
Period size: 47 Copynumber: 5.1 Consensus size: 47
59602113 CATACATATT
* * * * *
59602123 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGCTCACATTCA
* *
59602170 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGCTCACATTCA
59602217 TCACATTGGCCATTCGGCCTTATCACATATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGCTCACATTCA
* *
59602264 TCACATTGGCCATTCGACCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGCTCACATTCA
* * ***
59602311 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGCTCACATTCA
59602358 TCACAT
1 TCACAT
59602364 AAAATCCTAA
Statistics
Matches: 178, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 178 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGCTCACATTCA
Found at i:59602291 original size:22 final size:22
Alignment explanation
Indices: 59602216--59602334 Score: 66
Period size: 22 Copynumber: 5.1 Consensus size: 22
59602206 GCTCACATTC
*
59602216 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGACCTT
* *
59602238 ATCACATATATG-CATGCTC-ACATT
1 ATCACAT-T-GGCCAT--TCGACCTT
59602262 CATCACATTGGCCATTCGACCTT
1 -ATCACATTGGCCATTCGACCTT
* *
59602285 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGACCTT
*
59602309 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGACCTT
59602332 ATC
1 ATC
59602335 TCATATATAC
Statistics
Matches: 73, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
22 22 0.30
23 16 0.22
24 16 0.22
25 19 0.26
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGACCTT
Found at i:59607622 original size:29 final size:29
Alignment explanation
Indices: 59607559--59607666 Score: 121
Period size: 29 Copynumber: 3.8 Consensus size: 29
59607549 TTCACATACC
* ** *
59607559 TGTATCTGGCCCATTAAACCC-AATCATA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* *
59607587 T-TCATATGGCCCATTAGGCCTAAATCACC
1 TGT-ATATGGCCCATTAGGCCCAAATCACA
*
59607616 TGTATATGGCCCATTAGGCCCAAATCATA
1 TGTATATGGCCCATTAGGCCCAAATCACA
*
59607645 TTTATATGGCCCATTAGGCCCA
1 TGTATATGGCCCATTAGGCCCA
59607667 GTCATATTCA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.01
28 15 0.22
29 50 0.75
30 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCACA
Found at i:59607626 original size:57 final size:58
Alignment explanation
Indices: 59607556--59607664 Score: 175
Period size: 58 Copynumber: 1.9 Consensus size: 58
59607546 AATTTCACAT
*
59607556 ACCTGTATCTGGCCCATTAAACCC-AATCATATTCATATGGCCCATTAGGCCTAAATC
1 ACCTGTATATGGCCCATTAAACCCAAATCATATTCATATGGCCCATTAGGCCTAAATC
** *
59607613 ACCTGTATATGGCCCATTAGGCCCAAATCATATTTATATGGCCCATTAGGCC
1 ACCTGTATATGGCCCATTAAACCCAAATCATATTCATATGGCCCATTAGGCC
59607665 CAGTCATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 21 0.45
58 26 0.55
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (58 bp):
ACCTGTATATGGCCCATTAAACCCAAATCATATTCATATGGCCCATTAGGCCTAAATC
Found at i:59607769 original size:18 final size:19
Alignment explanation
Indices: 59607746--59607781 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
59607736 ATGGGCACAA
59607746 TAGCCCA-TCGGGCCCATT
1 TAGCCCATTCGGGCCCATT
*
59607764 TAGCCCATTCTGGCCCAT
1 TAGCCCATTCGGGCCCAT
59607782 ATGGCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.17, C:0.39, G:0.19, T:0.25
Consensus pattern (19 bp):
TAGCCCATTCGGGCCCATT
Found at i:59611236 original size:77 final size:77
Alignment explanation
Indices: 59611109--59611262 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 77
59611099 TATAACCATA
*
59611109 AGTATGATTTATGCTTGTTATGTTACTCATGGTTAAAATGATTTGGCTATGCTTCATGTAAAAAT
1 AGTATGATTTATGCTTGTTATGTTACTCATGGTTAAAATGATTCGGCTATGCTTCATGTAAAAAT
59611174 AAAATATACATG
66 AAAATATACATG
*
59611186 AGTATGATTTATGCTTGTTATGTTACTCATGGTTAAAATGATTCGGCTATGCTTTATGTAAAAAT
1 AGTATGATTTATGCTTGTTATGTTACTCATGGTTAAAATGATTCGGCTATGCTTCATGTAAAAAT
59611251 AAAATATACATG
66 AAAATATACATG
59611263 TGAATTCGGA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (77 bp):
AGTATGATTTATGCTTGTTATGTTACTCATGGTTAAAATGATTCGGCTATGCTTCATGTAAAAAT
AAAATATACATG
Found at i:59612198 original size:39 final size:40
Alignment explanation
Indices: 59612144--59612241 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 40
59612134 GATGATAACT
* * *
59612144 GGGCTAAGTCTCGAAGGTATCTGCGCTAGTGACT-AATCC
1 GGGCTAAGTCCCGAAGGCATCTGCGCGAGTGACTAAATCC
* * *
59612183 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATCTGCGCGAGTGACTAAATCC
59612223 GGGCTAAGTCCCGAAGGCA
1 GGGCTAAGTCCCGAAGGCA
59612242 ATTGTTCGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 28 0.54
40 24 0.46
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.22
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATCTGCGCGAGTGACTAAATCC
Found at i:59612231 original size:40 final size:39
Alignment explanation
Indices: 59612144--59612292 Score: 165
Period size: 40 Copynumber: 3.8 Consensus size: 39
59612134 GATGATAACT
* * * * * *
59612144 GGGCTAAGTCTCGAAGGTATCTGCGCTAGTGACTAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATCC
59612183 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AATCC
* *
59612223 GGGCTAAGTCCCGAAGGCAATTGTTCGAGTTACTCTAA-CC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA--CTAATCC
* * *
59612263 GGGCTATGTCCTGAAGGCATTTGAGCGAGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT
59612293 AGCTATATCC
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
39 28 0.30
40 62 0.66
41 2 0.02
42 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATCC
Found at i:59613999 original size:65 final size:65
Alignment explanation
Indices: 59613918--59614047 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
59613908 CGAATGATGA
59613918 GGCTAAGCAAGCTTTTTATAGCGTGATGAATGATTGGTTCAACCAATACATTCGAACTAATATGG
1 GGCTAAGCAAGCTTTTTATAGCGTGATGAATGATTGGTTCAACCAATACATTCGAACTAATATGG
*
59613983 GGCTAGGCAAGCTTTTTATAGCGTGATGAATGATTGGTTCAACCAATACATTCGAACTAATATGG
1 GGCTAAGCAAGCTTTTTATAGCGTGATGAATGATTGGTTCAACCAATACATTCGAACTAATATGG
59614048 CTGTTCCACA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (65 bp):
GGCTAAGCAAGCTTTTTATAGCGTGATGAATGATTGGTTCAACCAATACATTCGAACTAATATGG
Found at i:59617635 original size:429 final size:421
Alignment explanation
Indices: 59616799--59617586 Score: 1063
Period size: 429 Copynumber: 1.8 Consensus size: 421
59616789 GAAGCCTGAA
* * *
59616799 TGTGACAGCCCTAAAGTGACCCTAGTCGGAAAGCGGTTTCGGGACCGCTAAACCGAGTCACCAAA
1 TGTGACACCCCTAAAGTGACCCTAGTCGGAAAGCGATTTCGGGACCGCTAAACCGAGTAACCAAA
* *
59616864 TTATTTGAATATGATATTTATTGTCTAAAATATGTGATTATGAATGTGTGAAAGTTTTAAGCTTC
66 TTATTTGAACATGATATTTATTGTCT-AAATA---GATTA-GAATGTGTGAAAATTTTAAGCTTC
59616929 GATTTAGTAAATTGCATGTGAATTTAGTCAATAGGACTTATGTGTGACACTTTTGAAATGTGATA
126 GATTTAGTAAATTGCATGTGAATTTAGTCAATAGGACTTATGTGTGACACTTTTGAAATGTGATA
* * * * *
59616994 GGTTAATCTATAAGGATCTATTAGTGCATGTAATCATAGGGGTGGACTTGCATGTCAATTTCCCC
191 GATAAAACTATAAGGACCTATTAGTGCATGTAA-CAAAGGGGTGGACTTGCATGTCAATTTCCCC
*
59617059 CATTTAATTACTAGTGGCCGGCCGTGACAAAGGGTGATGGGCAAAACATGTCATAGACATGTTAT
255 C--TCAATTACTAGTGGCCGGCCGTGACAAAGGGTGATGGGCAAAACATGTCATAGACATGTTAT
* * *
59617124 GTTGGTGCATCATGGGAGAAACAACAAAATAAAAAGTTAGTAATAAAGAAATGGAAAAAGGAAAA
318 GTTGGTGCATCATGGGAGAAACAACAAAATAAAAAGTGAGCAATAAAGAAATAGAAAAAGGAAAA
59617189 TGATGAAAGAAAAAAAAAGGGATCATCATTCATGTTCTT
383 TGATGAAAGAAAAAAAAAGGGATCATCATTCATGTTCTT
** *
59617228 TGTGACACCCCTAATTTGACCCTAGTCGGAAAGCGATTTCGGGACTGCTAAACCGAGTAACCAAA
1 TGTGACACCCCTAAAGTGACCCTAGTCGGAAAGCGATTTCGGGACCGCTAAACCGAGTAACCAAA
59617293 TTATTTGAACATGATATTTATTGTCT-AA-A-A-TA-AATGTGTGAAAATTTTAAGCTTCGATTT
66 TTATTTGAACATGATATTTATTGTCTAAATAGATTAGAATGTGTGAAAATTTTAAGCTTCGATTT
* *
59617353 AGTAAATTTCATGTGAATTTAGTCAATAGGACTTATGTGTGACATTTTTGAAATGTGATAGATCA
131 AGTAAATTGCATGTGAATTTAGTCAATAGGACTTATGTGTGACACTTTTGAAATGTGATAGAT-A
59617418 AAAC-ATAAGGACCTATTAGTGCATGTTGAA-AAAGGGG-GGACTTGCATGTCAATTTTCCCCC-
195 AAACTATAAGGACCTATTAGTGCATG-T-AACAAAGGGGTGGACTTGCATGTCAA-TTTCCCCCT
* *
59617479 CCATCTAGTAGTGGCCGGCCATGACATTAGGATGGACAAAGGGTGATGGGCAAAACATGTCATAG
257 CAAT-TACTAGTGGCCGG-C----C-----G-T-GACAAAGGGTGATGGGCAAAACATGTCATAG
* * *
59617544 ACATGTTCTGTTGGTGCGTCATGGGAGGAAACAATAAAATAAA
309 ACATGTTATGTTGGTGCATCATGGGA-GAAACAACAAAATAAA
59617587 GAGCATGGGC
Statistics
Matches: 320, Mismatches: 21, Indels: 35
0.85 0.06 0.09
Matches are distributed among these distances:
416 2 0.01
417 12 0.04
418 16 0.05
419 121 0.38
420 4 0.01
421 4 0.01
422 2 0.01
426 1 0.00
427 3 0.01
428 1 0.00
429 139 0.43
430 15 0.05
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (421 bp):
TGTGACACCCCTAAAGTGACCCTAGTCGGAAAGCGATTTCGGGACCGCTAAACCGAGTAACCAAA
TTATTTGAACATGATATTTATTGTCTAAATAGATTAGAATGTGTGAAAATTTTAAGCTTCGATTT
AGTAAATTGCATGTGAATTTAGTCAATAGGACTTATGTGTGACACTTTTGAAATGTGATAGATAA
AACTATAAGGACCTATTAGTGCATGTAACAAAGGGGTGGACTTGCATGTCAATTTCCCCCTCAAT
TACTAGTGGCCGGCCGTGACAAAGGGTGATGGGCAAAACATGTCATAGACATGTTATGTTGGTGC
ATCATGGGAGAAACAACAAAATAAAAAGTGAGCAATAAAGAAATAGAAAAAGGAAAATGATGAAA
GAAAAAAAAAGGGATCATCATTCATGTTCTT
Found at i:59619713 original size:47 final size:47
Alignment explanation
Indices: 59619655--59619955 Score: 476
Period size: 47 Copynumber: 6.4 Consensus size: 47
59619645 CAGCCAAGAC
59619655 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
59619702 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
59619749 AGTGTATGTATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
59619796 AGTGTATATATGTAATAAGGCCTAATGGACGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
59619843 AGTGTATATATGTGGTAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
59619890 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
59619937 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
59619956 TCCCGAAGGG
Statistics
Matches: 233, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 233 1.00
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:59620130 original size:37 final size:37
Alignment explanation
Indices: 59620074--59620152 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
59620064 CCGAGCTCTA
* *
59620074 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
* *
59620111 AAGACCCGATAACTTCGTGTGGAGATTATGTCCTGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
59620148 AAGAC
1 AAGAC
59620153 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:59622861 original size:40 final size:40
Alignment explanation
Indices: 59622767--59622991 Score: 290
Period size: 40 Copynumber: 5.6 Consensus size: 40
59622757 TATTCGAATG
* * *
59622767 ATATCCGAGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT
* * * *
59622808 ATAACCGGACTAAGATCCGAAGGCATTCGTGCTAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
* *
59622848 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* *
59622888 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
59622928 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
*
59622968 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
59622992 CTTGTGCAAG
Statistics
Matches: 160, Mismatches: 22, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 130 0.81
41 29 0.18
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:59628987 original size:37 final size:37
Alignment explanation
Indices: 59628937--59629015 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
59628927 TTATTACGAA
* * *
59628937 GTCTTACCAGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCAGGACAAAATCCCCACACGAAGTCATCGG
* *
59628974 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCAGGACAAAATCCCCACACGAAGTCATCGG
59629011 GTCTT
1 GTCTT
59629016 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCAGGACAAAATCCCCACACGAAGTCATCGG
Found at i:59629212 original size:47 final size:47
Alignment explanation
Indices: 59629187--59630202 Score: 1944
Period size: 47 Copynumber: 21.6 Consensus size: 47
59629177 CGGCCCTGTC
* **
59629187 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTACC
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629234 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629281 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629328 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629375 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629422 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629469 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629516 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629563 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629610 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629657 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629704 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629751 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629798 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629845 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629892 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629939 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59629986 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
59630033 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
*
59630080 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATC
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
* *
59630127 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
* *
59630174 ACATATATGCA-TGTTCACATCCATCACAT
1 ACATATATACACT-TTCACATTCATCACAT
59630203 AGAATCCTAA
Statistics
Matches: 961, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
46 1 0.00
47 960 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (47 bp):
ACATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATT
Found at i:59632179 original size:132 final size:132
Alignment explanation
Indices: 59631942--59632951 Score: 1741
Period size: 132 Copynumber: 7.7 Consensus size: 132
59631932 GGCTGTCACA
* ** *
59631942 CCCTAAGTAGTAGTGGAGCAGATCAAAGATAACAAATCTTATCTTTCGAAGATAGTGGGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
59632007 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTAT
66 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTAT
59632072 CT
131 CT
* * *
59632074 CCCTAATCAGTAGTAGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAACAG
1 CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
59632139 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTAT
66 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTAT
59632204 CT
131 CT
* *
59632206 CCTTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAA
1 CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* *
59632271 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGGATTAGGTTGAAGATTGTAGATCTTAT
66 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTAT
59632336 CT
131 CT
* *
59632338 CCTTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAA
1 CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* *
59632403 ATTTAAGCCACCAAGCCTTGTCTTCCTGAGCAGCGGCGGAGTAGGTTGAAGATTGTAGATCTTAT
66 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTAT
59632468 CT
131 CT
* *
59632470 CCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCGAAGATAGTGGGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* *
59632535 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGCAGGTTGAAAATTGTAGATCTTAT
66 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTAT
*
59632600 AT
131 CT
* *
59632602 CCCTAAGCAGTAGGGGAGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* * *
59632667 ATTTAAGCCAGCAAGCCTTGTCTTCCTGAGCAGCGGCGGAGTAGGTTGAAGATTGTAGATCTTAT
66 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTAT
59632732 CT
131 CT
* *
59632734 CCTTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAA
1 CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
* *
59632799 ATTTAAGCCACCAAGCCTTGTCTTCCTGAGCAGCGGCGGAGTAGGTTGAAGATTGTAGATCTTAT
66 ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTAT
59632864 CT
131 CT
*
59632866 CCTTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
1 CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
*
59632931 ATTTAAGCCAGCAAGCCTTGT
66 ATTTAAGCCACCAAGCCTTGT
59632952 GATACGACCA
Statistics
Matches: 834, Mismatches: 44, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 834 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (132 bp):
CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
ATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTAT
CT
Found at i:59632511 original size:44 final size:44
Alignment explanation
Indices: 59632461--59632909 Score: 124
Period size: 44 Copynumber: 10.2 Consensus size: 44
59632451 AAGATTGTAG
*
59632461 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
** * ** ****
59632505 ATCTTATCTTTCGAAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATCAAAGATGGCAA
** * * * * * * * * *
59632549 GCCTTGTCTCCCTGAGCAGCAGCGGAGCAGGTTGAAA-ATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCA-GATCAAAGATGGCAA
* * *
59632593 ATCTTATATCCCTAAGCAGTAGGGGAGCAGATCGAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
* ** ***
59632637 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCAGCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGATGGCAA
** * * * ** * * * ** * * *
59632681 GCCTTGTCTTCCTGAGCAGCGGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
*
59632725 ATCTTATCTCCTTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
* * ** ****
59632769 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCAAAGATGGCAA
** * * * ** * * * ** * * *
59632813 GCCTTGTCTTCCTGAGCAGCGGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
*
59632857 ATCTTATCTCCTTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
59632901 ATCTTATCT
1 ATCTTATCT
59632910 TTCCAAGATA
Statistics
Matches: 267, Mismatches: 120, Indels: 36
0.63 0.28 0.09
Matches are distributed among these distances:
42 11 0.04
43 21 0.08
44 213 0.80
45 18 0.07
46 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAA
Found at i:59634749 original size:25 final size:24
Alignment explanation
Indices: 59634717--59634771 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
59634707 ACGTTATTGT
*
59634717 AAAAAAATAAAAAAAAAAACTTGAA
1 AAAAAAATAAAAAAAAAAA-TTCAA
**
59634742 AAAAAAATTCAAAAAAAAATTCAA
1 AAAAAAATAAAAAAAAAAATTCAA
59634766 AAAAAA
1 AAAAAA
59634772 GTTTGTATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.13
Consensus pattern (24 bp):
AAAAAAATAAAAAAAAAAATTCAA
Found at i:59634856 original size:27 final size:27
Alignment explanation
Indices: 59634809--59634880 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
59634799 TGTATTTAGT
** *
59634809 ATTGAAGAAAAAAATAAAAAAAAATTCGGA
1 ATTGAA-AAAAAAAAGAAAA-AAATT-GAA
59634839 ATT-AAAAAAAAAAGAAAAAAATTGAA
1 ATTGAAAAAAAAAAGAAAAAAATTGAA
59634865 ATTGAAAAAAAAAAGA
1 ATTGAAAAAAAAAAGA
59634881 GTGATTGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 5 0.13
27 17 0.45
28 11 0.29
29 2 0.05
30 3 0.08
ACGTcount: A:0.72, C:0.01, G:0.11, T:0.15
Consensus pattern (27 bp):
ATTGAAAAAAAAAAGAAAAAAATTGAA
Found at i:59635860 original size:12 final size:12
Alignment explanation
Indices: 59635843--59635916 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
59635833 AGTGAAAAGC
59635843 AAAAAGAGATTG
1 AAAAAGAGATTG
*
59635855 AAAAAGAAATTG
1 AAAAAGAGATTG
59635867 AAAAAGA-A--G
1 AAAAAGAGATTG
*
59635876 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
59635891 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
59635903 AAAGAGAGCTTG
1 AAAAAGAGATTG
59635915 AA
1 AA
59635917 CAGAAATTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
9 7 0.14
11 2 0.04
12 32 0.64
13 2 0.04
15 7 0.14
ACGTcount: A:0.62, C:0.01, G:0.24, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:59637251 original size:20 final size:20
Alignment explanation
Indices: 59637226--59637280 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
59637216 TGTGGTTCAA
*
59637226 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
59637246 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
59637266 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
59637281 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:59640263 original size:188 final size:188
Alignment explanation
Indices: 59639946--59640322 Score: 709
Period size: 188 Copynumber: 2.0 Consensus size: 188
59639936 CAAGGGCGAA
*
59639946 TCATAATTTCACATTGCATGGATGGTGGAGTCTCCAAAGCTGCTCATTAAAGCTTCCCAGACTTT
1 TCATAATTTCACATTGCATGGACGGTGGAGTCTCCAAAGCTGCTCATTAAAGCTTCCCAGACTTT
*
59640011 TCAGCTAATCAAGTAAATTTTAATAGCTCATCAAATTGTTGGCCGAACTTAGCTTGTCCCATTCA
66 TCAGCTAATCAAGCAAATTTTAATAGCTCATCAAATTGTTGGCCGAACTTAGCTTGTCCCATTCA
59640076 GCTCCCAATGTAGCTCATTACTTTCCAGCTAATTCCAAGGCCTCTAAAAGCTGGCTGT
131 GCTCCCAATGTAGCTCATTACTTTCCAGCTAATTCCAAGGCCTCTAAAAGCTGGCTGT
*
59640134 TCATAATTTCACATTGCATGGCCGGTGGAGTCTCCAAAGCTGCTCATTAAAGCTTCCCAGACTTT
1 TCATAATTTCACATTGCATGGACGGTGGAGTCTCCAAAGCTGCTCATTAAAGCTTCCCAGACTTT
59640199 TCAGCTAATCAAGCAAATTTTAATAGCTCATCAAATTGTTGGCCGAACTTAGCTTGTCCCATTCA
66 TCAGCTAATCAAGCAAATTTTAATAGCTCATCAAATTGTTGGCCGAACTTAGCTTGTCCCATTCA
* *
59640264 GCTCCCAATGTAGCTCATTACTTTCCAGCTGATTCCAAGGCCTCTAGAAGCTGGCTGT
131 GCTCCCAATGTAGCTCATTACTTTCCAGCTAATTCCAAGGCCTCTAAAAGCTGGCTGT
59640322 T
1 T
59640323 GACGATGCCA
Statistics
Matches: 184, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
188 184 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (188 bp):
TCATAATTTCACATTGCATGGACGGTGGAGTCTCCAAAGCTGCTCATTAAAGCTTCCCAGACTTT
TCAGCTAATCAAGCAAATTTTAATAGCTCATCAAATTGTTGGCCGAACTTAGCTTGTCCCATTCA
GCTCCCAATGTAGCTCATTACTTTCCAGCTAATTCCAAGGCCTCTAAAAGCTGGCTGT
Found at i:59641048 original size:44 final size:44
Alignment explanation
Indices: 59641000--59641448 Score: 162
Period size: 44 Copynumber: 10.2 Consensus size: 44
59640990 AAGATTGTAG
** *
59641000 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGCAA
* * * **
59641044 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTGCAA
** * * * * * ** * * * *
59641088 GCCTTGTCTCCATGAGCAGCAGCGGATTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGCAA
** *
59641132 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGCAA
* * * **
59641176 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTGCAA
** * * * * * * * * * * *
59641220 GCCTTGTGTCCCTGAGCAGCAGCGAAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGCAA
* **
59641264 ATCTTATATCCCTAAGCAGTAGTGGAGCAGATCAAAGACTGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGCAA
* * * **
59641308 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACTGCAA
** * * * * * * * * *
59641352 GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGCAA
* * *
59641396 ATCTTATATCCCTAAGCAGTAGGGGAGCAGATCGAAGAC-GACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTG-CAA
59641440 ATCTTATCT
1 ATCTTATCT
59641449 TTCCAAGATA
Statistics
Matches: 270, Mismatches: 116, Indels: 38
0.64 0.27 0.09
Matches are distributed among these distances:
42 12 0.04
43 18 0.07
44 217 0.80
45 17 0.06
46 6 0.02
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACTGCAA
Found at i:59641530 original size:44 final size:44
Alignment explanation
Indices: 59641482--59641566 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
59641472 TTAAGCCAGC
*
59641482 AAGTCTTATCGT-CCTGAAGTTGCAGTGGAGCAGATTAAAGCTAT
1 AAGTCTTATC-TCCCTGAAGTTACAGTGGAGCAGATTAAAGCTAT
* * *
59641526 AAGTCTTTTCTCCCTGAAGTTACAGTGGAGTAGATTGAAGC
1 AAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGC
59641567 ATGAATTCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (44 bp):
AAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTAT
Found at i:59641540 original size:132 final size:132
Alignment explanation
Indices: 59640957--59641484 Score: 930
Period size: 132 Copynumber: 4.0 Consensus size: 132
59640947 GGTCACATCA
* *
59640957 CCTTGTCTCCCTGAGTAGCAGCGGAGGAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
59641022 TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
66 TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
59641087 AG
131 AG
* *
59641089 CCTTGTCTCCATGAGCAGCAGCGGATTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
59641154 TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
66 TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
59641219 AG
131 AG
* * *
59641221 CCTTGTGTCCCTGAGCAGCAGCGAAGTAGGTTGAAGATTGTAGATCTTATATCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
*
59641286 TGGAGCAGATCAAAGACTGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
66 TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
59641351 AG
131 AG
*
59641353 CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATATCCCTAAGCAGTAG
1 CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
* * * * *
59641418 GGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAAGCCAGCA
66 TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
59641483 AG
131 AG
59641485 TCTTATCGTC
Statistics
Matches: 378, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 378 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCA
AG
Found at i:59641797 original size:19 final size:19
Alignment explanation
Indices: 59641769--59641832 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
59641759 AATTTTCGAG
*
59641769 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
59641788 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
*
59641807 GATATATGTAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
59641828 GATAT
1 GATAT
59641833 ATACAATCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 22 0.56
21 17 0.44
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:59641851 original size:19 final size:21
Alignment explanation
Indices: 59641770--59641845 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
59641760 ATTTTCGAGG
59641770 ATATACAATCTTAGATATG--
1 ATATACAATCTTAGATATGAT
* *
59641789 ATATGCAATCCTAGATATGAT
1 ATATACAATCTTAGATATGAT
**
59641810 ATATGTAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
59641831 ATATACAATCTTAGA
1 ATATACAATCTTAGA
59641846 AGATATGATT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
19 17 0.35
21 32 0.65
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:59641881 original size:21 final size:23
Alignment explanation
Indices: 59641837--59641881 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
59641827 TGATATATAC
*
59641837 AATCTTAGAAGATATGATTTTGT
1 AATCTTAGAAGATATGAATTTGT
*
59641860 AATCTTA-AAGAT-TTAATTTGT
1 AATCTTAGAAGATATGAATTTGT
59641881 A
1 A
59641882 GATACCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 7 0.35
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (23 bp):
AATCTTAGAAGATATGAATTTGT
Found at i:59642310 original size:3 final size:3
Alignment explanation
Indices: 59642302--59642341 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
59642292 ATTAATTTTG
*
59642302 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
59642342 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:59642310 original size:15 final size:15
Alignment explanation
Indices: 59642286--59642340 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
59642276 GTTTTTAGTC
59642286 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
59642300 TGTTATTATTATTTT
1 TATTATTATTAATTT
59642315 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
59642329 ATATTATTATTA
1 -TATTATTATTA
59642341 TACCTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 24 0.75
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:59642317 original size:12 final size:12
Alignment explanation
Indices: 59642288--59642339 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
59642278 TTTTAGTCTA
59642288 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
59642300 TGTTATTATTAT
1 TTTTATTATTAT
59642312 TTTTATTATTAT
1 TTTTATTATTAT
59642324 ATTATATATTATTAT
1 -TT-T-TATTATTAT
59642339 T
1 T
59642340 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Done.