Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 74 of 226
Found at i:27612634 original size:96 final size:96
Alignment explanation
Indices: 27612513--27612723 Score: 291
Period size: 96 Copynumber: 2.2 Consensus size: 96
27612503 TGTTCCACTG
* * * * *
27612513 CAACTTCA-GAGAGATAAGATTTGTAACTTGTAGCTTTAATTTTTTCCACTGCAACTTTAGAGAA
1 CAACTTCAGGGGA-ATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGAAACTTCAGAGAA
27612577 ATAAGATTCACTATCTTTAATTTG-CCCTACAA
65 ATAAGATTCACTATCTTTAATTTGTCCC-ACAA
*
27612609 CAACTTCAGGGGAATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAAA
1 CAACTTCAGGGGAATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGAAACTTCAGAGAAA
* * **
27612674 TAAGATTCGCTATCTTTAATTTGTTCCACTG
66 TAAGATTCACTATCTTTAATTTGTCCCACAA
*
27612705 CAACTTCAGGGAAATAAGA
1 CAACTTCAGGGGAATAAGA
27612724 CCTGTAGCTT
Statistics
Matches: 102, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
96 97 0.95
97 5 0.05
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (96 bp):
CAACTTCAGGGGAATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGAAACTTCAGAGAAA
TAAGATTCACTATCTTTAATTTGTCCCACAA
Found at i:27612668 original size:51 final size:51
Alignment explanation
Indices: 27612440--27613020 Score: 234
Period size: 51 Copynumber: 11.8 Consensus size: 51
27612430 AATAAGATTA
* * * * *
27612440 GTAGCTTCAATCTGCTCCACT-ACAACTTTC-GAGAGATAAGATTTGTAACTA
1 GTAGCTTTAATCTGTTCCACTGA-AAC-TTCAGGGAAATAAGATTTGTAACTT
* * * *
27612491 GTAGATTTAATCTGTTCCACTGCAACTTCAGAGAGATAAGATTTGTAACTT
1 GTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAAATAAGATTTGTAACTT
* * * * * *
27612542 GTAGCTTTAATTTTTTCCACTGCAACTTTAGAGAAATAAGA--T-TCAC--
1 GTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAAATAAGATTTGTAACTT
* * * * *
27612588 -TATCTTTAATTTG-CCCTAC-AACAACTTCAGGGGAATAAGATTTGTAACTT
1 GTAGCTTTAATCTGTTCC-ACTGA-AACTTCAGGGAAATAAGATTTGTAACTT
*
27612638 GTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAAATAAGATTCG---C--
1 GTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAAATAAGATTTGTAACTT
* * * *
27612684 -TATCTTTAATTTGTTCCACTGCAACTTCAGGGAAAT-A-A---G--ACCT
1 GTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAAATAAGATTTGTAACTT
* ** * *
27612727 GTAGCTTTAATATACTCCACTGCAACTTCA-AGAAGATAAGA----T---TT
1 GTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAA-ATAAGATTTGTAACTT
* ** * * * * *
27612771 GTAGCTTCAATCTACTCTACCGCAACTTCAAGGAGATAAGATTTG-----T
1 GTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAAATAAGATTTGTAACTT
* *
27612817 G--GCTTTAATCTGCTCCACTGTAACTTCAAGGG-AATAAGATTTGTAACTT
1 GTAGCTTTAATCTGTTCCACTGAAACTTC-AGGGAAATAAGATTTGTAACTT
** * * * ** *
27612866 ACAGCTTTAATCTATTCCACTGCAACTTCAGAGAAATAAGATAAGGGAAATAAGATTT
1 GTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAAATAAGAT--TTG---T-A-ACTT
* * ** *
27612924 ACTATCTTTAATC-GGCCCACTGTAACTTCAGGGAAATAAGATTTGTAATAACTT
1 -GTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAAATAAGATTTG---TAACTT
* *
27612978 GTAGCTTTAATCTGTTCCACTGCAACTTTAGGGAAATAAGATT
1 GTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAAATAAGATT
27613021 CGCTATCTTT
Statistics
Matches: 413, Mismatches: 74, Indels: 83
0.72 0.13 0.15
Matches are distributed among these distances:
40 1 0.00
41 1 0.00
43 4 0.01
44 94 0.23
45 67 0.16
46 3 0.01
47 1 0.00
48 7 0.02
49 2 0.00
50 6 0.01
51 141 0.34
52 3 0.01
53 11 0.03
54 29 0.07
55 1 0.00
56 5 0.01
57 1 0.00
58 27 0.07
59 9 0.02
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (51 bp):
GTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAAATAAGATTTGTAACTT
Found at i:27612750 original size:44 final size:44
Alignment explanation
Indices: 27612636--27613155 Score: 299
Period size: 44 Copynumber: 11.1 Consensus size: 44
27612626 GATTTGTAAC
* *
27612636 TTGTAGCTTTAATCTGTTCCACTGAAACTTCAGGGAAATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* * * * *
27612680 TCGCTATCTTTAATTTGTTCCACTGCAACTTCAGGGAAATAAGAC
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* * * *
27612725 CTGTAGCTTTAATATACTCCACTGCAACTTCA-AGAAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAA-ATAAGAT
* * * * * *
27612769 TTGTAGCTTCAATCTACTCTACCGCAACTTCAAGGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* *
27612813 TTGTGGCTTTAATCTGCTCCACTGTAACTTCAAGGG-AATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTC-AGGGAAATAAGAT
** *
27612857 TTGTAACTTACAGCTTTAATCTATTCCACTGCAACTTCAGAGAAATAAGAT
1 TTG-----T--AGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
** * *
27612908 AAGGGAAATAAGATTTACTATCTTTAATCGGC-CCACTGTAACTTCAGGGAAATAAGATTTGTAA
1 --TTG---T-AGCTTTA--ATC-----T--GCTCCACTGCAACTTCAGGGAAAT-A-A---G--A
27612972 T
44 T
* *
27612973 AACTTGTAGCTTTAATCTGTTCCACTGCAACTTTAGGGAAATAAGAT
1 ---TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* * * * * *
27613020 TCGCTATCTTTAATCTGCCCCACTGTAACTTCAGGGAGATAAGAC
1 TTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* * * *
27613065 TTGTAGCTTCAATCTACTCCACTGTAACTTCAGGGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
* * * * * *
27613109 TTGTGGTTTTAATCTACTCCATTGCAAATTCAGGGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
27613153 TTG
1 TTG
27613156 CCACGATGAC
Statistics
Matches: 373, Mismatches: 70, Indels: 66
0.73 0.14 0.13
Matches are distributed among these distances:
43 3 0.01
44 181 0.49
45 79 0.21
47 2 0.01
49 2 0.01
50 9 0.02
51 33 0.09
52 4 0.01
53 3 0.01
54 19 0.05
55 1 0.00
57 1 0.00
58 19 0.05
59 1 0.00
60 4 0.01
62 6 0.02
63 2 0.01
65 2 0.01
66 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (44 bp):
TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
Found at i:27613015 original size:112 final size:110
Alignment explanation
Indices: 27612819--27613019 Score: 298
Period size: 112 Copynumber: 1.8 Consensus size: 110
27612809 AGATTTGTGG
*
27612819 CTTTAATCTGCTCCACTGTAACTTCAAGGGAATAAGATTTGTAACTTACAGCTTTAATCTATTCC
1 CTTTAATCGGCTCCACTGTAACTTCAAGGGAATAAGATTTGTAACTTACAGCTTTAATCTATTCC
27612884 ACTGCAACTTCAGAGAAATAAGATAAGGGAAATAAGATTTACTAT
66 ACTGCAACTTCAGAGAAATAAGATAAGGGAAATAAGATTTACTAT
** *
27612929 CTTTAATCGGC-CCACTGTAACTTC-AGGGAAATAAGATTTGTAATAACTTGTAGCTTTAATCTG
1 CTTTAATCGGCTCCACTGTAACTTCAAGGG-AATAAGATTTG---TAACTTACAGCTTTAATCTA
* *
27612992 TTCCACTGCAACTTTAGGGAAATAAGAT
62 TTCCACTGCAACTTCAGAGAAATAAGAT
27613020 TCGCTATCTT
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
108 4 0.05
109 24 0.30
110 10 0.12
112 43 0.53
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (110 bp):
CTTTAATCGGCTCCACTGTAACTTCAAGGGAATAAGATTTGTAACTTACAGCTTTAATCTATTCC
ACTGCAACTTCAGAGAAATAAGATAAGGGAAATAAGATTTACTAT
Found at i:27621673 original size:25 final size:26
Alignment explanation
Indices: 27621645--27621713 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 26
27621635 CGGACTCACC
27621645 ACAGCTCGTATGAGCTTA-TCGATT-T
1 ACAGCTCGTATGAGCTTACT-GATTCT
*
27621670 ACAGCTCGTAAGAGCTTACTGATTCT
1 ACAGCTCGTATGAGCTTACTGATTCT
* *
27621696 -CAGCTCTTATAAGCTTAC
1 ACAGCTCGTATGAGCTTAC
27621714 CGTTATTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Consensus pattern (26 bp):
ACAGCTCGTATGAGCTTACTGATTCT
Found at i:27623053 original size:10 final size:10
Alignment explanation
Indices: 27623039--27623078 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
27623029 ACTAGGGACT
**
27623039 TTATGATTAT
1 TTATGATTGG
27623049 TTATGATTGG
1 TTATGATTGG
27623059 TTATGATTGG
1 TTATGATTGG
27623069 TTATGATTGG
1 TTATGATTGG
27623079 AATATGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (10 bp):
TTATGATTGG
Found at i:27623865 original size:19 final size:20
Alignment explanation
Indices: 27623841--27623878 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
27623831 TTATAAAACT
*
27623841 TAATGCATATG-ATGAAATA
1 TAATGCAGATGAATGAAATA
27623860 TAATGCAGATGAATGAAAT
1 TAATGCAGATGAATGAAAT
27623879 GAATGCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.29
Consensus pattern (20 bp):
TAATGCAGATGAATGAAATA
Found at i:27623883 original size:19 final size:19
Alignment explanation
Indices: 27623842--27623885 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
27623832 TATAAAACTT
* *
27623842 AATGCATATGATGAAATAT
1 AATGCAGATGATGAAATAG
27623861 AATGCAGATGAATGAAAT-G
1 AATGCAGATG-ATGAAATAG
27623880 AATGCA
1 AATGCA
27623886 AAAAGAGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (19 bp):
AATGCAGATGATGAAATAG
Found at i:27625857 original size:16 final size:15
Alignment explanation
Indices: 27625817--27625862 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
27625807 TTTTATGAAC
27625817 TTTTTAT-ATTTTTT
1 TTTTTATAATTTTTT
27625831 TTAATTT-TAATTTTTT
1 TT--TTTATAATTTTTT
27625847 ATTTTTATAATTTTTT
1 -TTTTTATAATTTTTT
27625863 GAACTACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.07
15 4 0.15
16 19 0.70
17 2 0.07
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTATAATTTTTT
Found at i:27626325 original size:22 final size:24
Alignment explanation
Indices: 27626300--27626360 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 24
27626290 GCCCGACCCG
*
27626300 TTTTTAATTAAAATTAAAA-TTAT
1 TTTTTAATTAAAATTAAAACTAAT
27626323 TTTTTAA-TAAAATTAAAACTAA-
1 TTTTTAATTAAAATTAAAACTAAT
*
27626345 TTGTT-ATTAAAATTAA
1 TTTTTAATTAAAATTAA
27626361 TTATTAGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 1 0.03
22 24 0.71
23 9 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTTTAATTAAAATTAAAACTAAT
Found at i:27626373 original size:16 final size:16
Alignment explanation
Indices: 27626336--27626375 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
27626326 TTAATAAAAT
* * *
27626336 TAAAACTAATTGTTAT
1 TAAAATTAATTATTAG
27626352 TAAAATTAATTATTAG
1 TAAAATTAATTATTAG
27626368 TAAAATTA
1 TAAAATTA
27626376 TCAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTATTAG
Found at i:27626481 original size:9 final size:9
Alignment explanation
Indices: 27626448--27626475 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
27626438 TTTATCAAAT
27626448 TATTAATTG
1 TATTAATTG
27626457 TATTAATTG
1 TATTAATTG
27626466 TATTAATTG
1 TATTAATTG
27626475 T
1 T
27626476 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:27626486 original size:68 final size:68
Alignment explanation
Indices: 27626363--27626543 Score: 339
Period size: 68 Copynumber: 2.7 Consensus size: 68
27626353 AAAATTAATT
*
27626363 ATTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACAT
1 ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
27626426 TTG
66 TTG
27626429 ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
1 ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
27626494 TTG
66 TTG
27626497 ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGT
1 ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGT
27626544 ATTAATTGTT
Statistics
Matches: 112, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 27 0.24
68 85 0.76
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.48
Consensus pattern (68 bp):
ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACAT
TTG
Found at i:27626528 original size:9 final size:9
Alignment explanation
Indices: 27626516--27626552 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
27626506 TTTATCAAAT
27626516 TATTAATTG
1 TATTAATTG
27626525 TATTAATTG
1 TATTAATTG
27626534 TATTAATTG
1 TATTAATTG
27626543 TATTAATTG
1 TATTAATTG
27626552 T
1 T
27626553 TGTAACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:27626689 original size:22 final size:24
Alignment explanation
Indices: 27626649--27626692 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
27626639 AAATAAACTT
27626649 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
27626673 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
27626693 AATATTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:27633013 original size:19 final size:21
Alignment explanation
Indices: 27632978--27633017 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
27632968 GTATTGCTTT
27632978 TTATTTTTAATATTAATATAA
1 TTATTTTTAATATTAATATAA
27632999 TTATTTTT-A-ATTAATATAA
1 TTATTTTTAATATTAATATAA
27633018 ATATAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 1 0.05
21 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTTTTAATATTAATATAA
Found at i:27633034 original size:6 final size:6
Alignment explanation
Indices: 27633011--27633036 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27633001 ATTTTTAATT
27633011 AATATA AATATA AATATA AATATA AA
1 AATATA AATATA AATATA AATATA AA
27633037 ATTAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:27642308 original size:11 final size:11
Alignment explanation
Indices: 27642294--27642323 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
27642284 TTATCAGAAG
27642294 TTTCAAAAATC
1 TTTCAAAAATC
*
27642305 TTTCAATAATC
1 TTTCAAAAATC
27642316 TTTCAAAA
1 TTTCAAAA
27642324 GTTTTAGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (11 bp):
TTTCAAAAATC
Found at i:27646588 original size:28 final size:26
Alignment explanation
Indices: 27646530--27646599 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
27646520 GAGCGAGCCC
* *
27646530 CTATGTGCGAACCCTATAGACAGACC
1 CTATGTGCGAACCCTATAGACAAACA
* *
27646556 CTATGTGTGAACCTTATAGAAACAAACA
1 CTATGTGCGAACCCTATAG--ACAAACA
* *
27646584 CTATGCGCAAACCCTA
1 CTATGTGCGAACCCTA
27646600 CTTGTGCGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
26 17 0.50
28 17 0.50
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (26 bp):
CTATGTGCGAACCCTATAGACAAACA
Found at i:27648049 original size:18 final size:19
Alignment explanation
Indices: 27648022--27648057 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
27648012 AAATATTATA
27648022 TTTAAATTT-ATTTTTAAT
1 TTTAAATTTAATTTTTAAT
*
27648040 TTTAATTTTAATTTTTAA
1 TTTAAATTTAATTTTTAA
27648058 AAATATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTAAATTTAATTTTTAAT
Found at i:27650857 original size:21 final size:21
Alignment explanation
Indices: 27650810--27650852 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 21
27650800 TATGTAATAT
27650810 AACATATAATATATAATAAGTA
1 AACATATAATATATAATAAG-A
27650832 AACATATATATATATATATAA
1 AACATATA-ATATATA-ATAA
27650853 AACATCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 8 0.42
23 7 0.37
24 4 0.21
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (21 bp):
AACATATAATATATAATAAGA
Found at i:27652065 original size:8 final size:8
Alignment explanation
Indices: 27652052--27652101 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
27652042 ATAATAAGAG
27652052 AAATAATA
1 AAATAATA
27652060 AAATAATA
1 AAATAATA
*
27652068 AGAACACACTA
1 A-AATA-A-TA
27652079 AAA-AATA
1 AAATAATA
27652086 AAA-AATA
1 AAATAATA
27652093 AAATAATA
1 AAATAATA
27652101 A
1 A
27652102 TGACAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
7 12 0.32
8 15 0.41
9 4 0.11
10 3 0.08
11 3 0.08
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.18
Consensus pattern (8 bp):
AAATAATA
Found at i:27652094 original size:33 final size:31
Alignment explanation
Indices: 27652056--27652121 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
27652046 TAAGAGAAAT
27652056 AATAAAATAATAA-GAACACACTAAAAAATAAAA
1 AATAAAATAATAATG-ACA-A-TAAAAAATAAAA
*
27652089 AATAAAATAATAATGACAATAATAAATAAAA
1 AATAAAATAATAATGACAATAAAAAATAAAA
27652120 AA
1 AA
27652122 AATGCACCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 13 0.42
32 1 0.03
33 16 0.52
34 1 0.03
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (31 bp):
AATAAAATAATAATGACAATAAAAAATAAAA
Found at i:27652132 original size:24 final size:24
Alignment explanation
Indices: 27652082--27652137 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
27652072 CACACTAAAA
27652082 AATAAAAAATAAAATAATAATGAC
1 AATAAAAAATAAAATAATAATGAC
*
27652106 AATAATAAATAAAA-AA-AATGCACC
1 AATAAAAAATAAAATAATAATG-A-C
27652130 AATAAAAA
1 AATAAAAA
27652138 GCATATACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.14
23 3 0.11
24 21 0.75
ACGTcount: A:0.71, C:0.07, G:0.04, T:0.18
Consensus pattern (24 bp):
AATAAAAAATAAAATAATAATGAC
Found at i:27652303 original size:4 final size:4
Alignment explanation
Indices: 27652294--27652437 Score: 73
Period size: 4 Copynumber: 35.5 Consensus size: 4
27652284 ATGAAGGAAT
**
27652294 AATA AATA AATA AATA AACG AATA AA-A GAATTAA AATA AA-A AAGTA
1 AATA AATA AATA AATA AATA AATA AATA -AA-T-A AATA AATA AA-TA
* * * * * * *
27652340 AATA AGTG AAT- AATA TATA AATA AATA AGTA AATG AGTA AATA AATG
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * * *
27652387 AATAA AATA AA-A GGAAT- AATG AATA AATA AATA AGTA AATA GATG AATA
1 AAT-A AATA AATA --AATA AATA AATA AATA AATA AATA AATA AATA AATA
27652436 AA
1 AA
27652438 AGAATTAAAA
Statistics
Matches: 104, Mismatches: 24, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
3 11 0.11
4 81 0.78
5 9 0.09
6 2 0.02
7 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.10, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:27652351 original size:57 final size:56
Alignment explanation
Indices: 27652282--27652455 Score: 167
Period size: 57 Copynumber: 3.0 Consensus size: 56
27652272 AAATATTAAA
*
27652282 AAATGAAG-GAATAATAAATAAATAAATAAACGAATAAAAGAATTAAAATAAAAAAG
1 AAAT-AAGTGAATAATAAATAAATAAATAAATGAATAAAAGAATTAAAATAAAAAAG
* * *
27652338 TAAATAAGTGAATAATATATAAATAAATAAGTAAATGAGTAAATA-AATGAATAA-AATAAAAG
1 -AAATAAGTG---AATA-ATAAATAAATAAATAAATGAATAAA-AGAATTAA-AATAA-AAAAG
* * *
27652400 GAATAA-TGAATAAATAAATAAGTAAATAGATGAATAAAAGAATTAAAATAAAAAAG
1 AAATAAGTGAAT-AATAAATAAATAAATAAATGAATAAAAGAATTAAAATAAAAAAG
27652456 GACTTAATTG
Statistics
Matches: 96, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
56 11 0.11
57 36 0.38
58 1 0.01
60 6 0.06
61 34 0.35
62 8 0.08
ACGTcount: A:0.66, C:0.01, G:0.11, T:0.22
Consensus pattern (56 bp):
AAATAAGTGAATAATAAATAAATAAATAAATGAATAAAAGAATTAAAATAAAAAAG
Found at i:27652406 original size:53 final size:54
Alignment explanation
Indices: 27652347--27652452 Score: 155
Period size: 53 Copynumber: 2.0 Consensus size: 54
27652337 GTAAATAAGT
*
27652347 GAATAAT-ATATAAATAAATAAGTAAAT-GAGTAAATAAATGAA-TAAAATAAAAG
1 GAATAATGA-ATAAATAAATAAGTAAATAGA-TAAATAAAAGAATTAAAATAAAAG
*
27652400 GAATAATGAATAAATAAATAAGTAAATAGATGAATAAAAGAATTAAAATAAAA
1 GAATAATGAATAAATAAATAAGTAAATAGATAAATAAAAGAATTAAAATAAAA
27652453 AAGGACTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
53 35 0.73
54 13 0.27
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (54 bp):
GAATAATGAATAAATAAATAAGTAAATAGATAAATAAAAGAATTAAAATAAAAG
Found at i:27653299 original size:14 final size:13
Alignment explanation
Indices: 27653263--27653303 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
27653253 TCGAAAATGC
27653263 TTGTATTC-TTTT
1 TTGTATTCTTTTT
27653275 TTG-ATTACTTTTT
1 TTGTATT-CTTTTT
27653288 TTGTATATCTTTTT
1 TTGTAT-TCTTTTT
27653302 TT
1 TT
27653304 TCTATTCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 3 0.12
12 4 0.16
13 7 0.28
14 10 0.40
15 1 0.04
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.73
Consensus pattern (13 bp):
TTGTATTCTTTTT
Found at i:27659535 original size:46 final size:46
Alignment explanation
Indices: 27659468--27659669 Score: 359
Period size: 46 Copynumber: 4.4 Consensus size: 46
27659458 TGATCAGTGA
* *
27659468 CAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTACCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
27659514 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
27659560 CAAGTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
27659606 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGGTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
27659652 CACGTGACAAAGTGATAA
1 CAAGTGACAAAGTGATAA
27659670 ATGTAATCAA
Statistics
Matches: 150, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 150 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:27665083 original size:14 final size:15
Alignment explanation
Indices: 27665064--27665108 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
27665054 TTTAAAAATA
27665064 TATAATATT-TATTG
1 TATAATATTATATTG
27665078 TATAAT-TTATATTG
1 TATAATATTATATTG
27665092 TA-AATATATATAATTG
1 TATAATAT-TAT-ATTG
27665108 T
1 T
27665109 GATTTAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.19
14 14 0.52
15 3 0.11
16 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
TATAATATTATATTG
Found at i:27665299 original size:44 final size:43
Alignment explanation
Indices: 27665250--27665335 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 43
27665240 GTTGACATAA
* *
27665250 AATAG-AATTTGTGATAATTATACGTTTAACAATAATTATAATTC
1 AATAGAAATTT-TGATAATTACACATTTAA-AATAATTATAATTC
27665294 AATAGAAATTTTGATAATTACACATTTAAAATAATTATAATT
1 AATAGAAATTTTGATAATTACACATTTAAAATAATTATAATT
27665336 TTCATTTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
43 13 0.33
44 21 0.54
45 5 0.13
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.41
Consensus pattern (43 bp):
AATAGAAATTTTGATAATTACACATTTAAAATAATTATAATTC
Found at i:27669036 original size:9 final size:9
Alignment explanation
Indices: 27669022--27669052 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
27669012 GTTAAACGAA
27669022 TCGAGTTAT
1 TCGAGTTAT
*
27669031 TCGAGTTAA
1 TCGAGTTAT
27669040 TCGAGTTAT
1 TCGAGTTAT
27669049 TCGA
1 TCGA
27669053 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:27669124 original size:9 final size:9
Alignment explanation
Indices: 27669105--27669141 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
27669095 TGAGTTTTCA
*
27669105 AATTTGAAT
1 AATTCGAAT
*
27669114 AACTCGAAT
1 AATTCGAAT
27669123 AATTCGAAT
1 AATTCGAAT
27669132 AATTCGAAT
1 AATTCGAAT
27669141 A
1 A
27669142 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:27670176 original size:5 final size:5
Alignment explanation
Indices: 27670166--27670191 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
27670156 CTCGAAAATT
27670166 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
27670192 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:27676191 original size:13 final size:14
Alignment explanation
Indices: 27676173--27676206 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
27676163 CCATCTTTAC
27676173 TTTTAATTTCT-TT
1 TTTTAATTTCTATT
*
27676186 TTTTAATTTTTATT
1 TTTTAATTTCTATT
27676200 TTTTAAT
1 TTTTAAT
27676207 GTTGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTAATTTCTATT
Found at i:27687285 original size:40 final size:39
Alignment explanation
Indices: 27687207--27687330 Score: 158
Period size: 41 Copynumber: 3.0 Consensus size: 39
27687197 ACCAAAAATT
27687207 TATTTTAAAAATTAAAATAAAAATTAAAAAATGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAA-GTATTTTAAAAA
27687251 TATTTTAAAATTAAACAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAA-AAAATTAAAAAAGTATTTTAAAAA
* *
27687291 AATTTTAAAATTTAAAAAATTTGAAAAAAGTATTTTAAAA
1 TATTTTAAAA-TTAAAAAAATT-AAAAAAGTATTTTAAAA
27687331 TTAAAAAAAT
Statistics
Matches: 75, Mismatches: 2, Indels: 9
0.87 0.02 0.10
Matches are distributed among these distances:
40 27 0.36
41 36 0.48
43 6 0.08
44 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:27687308 original size:30 final size:29
Alignment explanation
Indices: 27687267--27687340 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
27687257 AAAATTAAAC
*
27687267 AAAATTAAAAAAGTATTTTAAAAAA-ATTTT
1 AAAATTAAAAAA--ATTTGAAAAAAGATTTT
*
27687297 AAAATTTAAAAAATTTGAAAAAAGTATTTT
1 AAAATTAAAAAAATTTGAAAAAAG-ATTTT
27687327 AAAATTAAAAAAAT
1 AAAATTAAAAAAAT
27687341 AAAAAATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 10 0.26
30 29 0.74
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAATTAAAAAAATTTGAAAAAAGATTTT
Found at i:27689691 original size:13 final size:14
Alignment explanation
Indices: 27689664--27689694 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
27689654 ATGAGATGAG
27689664 AATATTATCTTAAA
1 AATATTATCTTAAA
27689678 AATATTAT-TTAAA
1 AATATTATCTTAAA
27689691 AATA
1 AATA
27689695 AAATAAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AATATTATCTTAAA
Found at i:27693891 original size:2 final size:2
Alignment explanation
Indices: 27693884--27693922 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
27693874 AAGGGCAATA
27693884 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27693923 AAATCTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27695253 original size:49 final size:48
Alignment explanation
Indices: 27695169--27695265 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 48
27695159 TTTCTTTGCT
* *
27695169 TAAAAACGCCTAAGACAGCCTAACTCGCAATGATAACGGATTCAACAG
1 TAAAAACACCTAAGACAGCCTAACTCGCAATGATAAAGGATTCAACAG
* *
27695217 TAAAAACACCTAAGTCAGCTTAATCTCGCAATGATAAAGGATTCAACAG
1 TAAAAACACCTAAGACAGCCTAA-CTCGCAATGATAAAGGATTCAACAG
27695266 AATTCCCTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 20 0.45
49 24 0.55
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (48 bp):
TAAAAACACCTAAGACAGCCTAACTCGCAATGATAAAGGATTCAACAG
Found at i:27695499 original size:36 final size:36
Alignment explanation
Indices: 27695459--27695529 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
27695449 ATCAAGGGCT
*
27695459 ACAATTAAAAGTTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
*
27695495 ACAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
27695530 TTACATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:27695500 original size:19 final size:19
Alignment explanation
Indices: 27695476--27695529 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
27695466 AAAGTTGTAT
27695476 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
27695495 ACAATTAGAA-GCT--GTAT
1 ACAATTAGAACTCTAAG-AC
27695512 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
27695530 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 4 0.14
19 11 0.39
20 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:27695517 original size:17 final size:17
Alignment explanation
Indices: 27695458--27695521 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
27695448 CATCAAGGGC
* *
27695458 TACAATTAAAAGTTGTA
1 TACAATTAGAAGCTGTA
*
27695475 TACAATTAGAA-CTCTAAGA
1 TACAATTAGAAGCTGT---A
*
27695494 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
27695511 TACAATTAGAA
1 TACAATTAGAA
27695522 CTCTAAGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 2 0.05
17 21 0.57
19 11 0.30
20 3 0.08
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:27700885 original size:24 final size:25
Alignment explanation
Indices: 27700858--27700905 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
27700848 TTTAAATAAA
* *
27700858 TAAATAAATTTATTTATTT-TATAT
1 TAAATAAATATAATTATTTGTATAT
27700882 TAAATAAATATAATTATTTGTATA
1 TAAATAAATATAATTATTTGTATA
27700906 CGTAATATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAAATAAATATAATTATTTGTATAT
Found at i:27706259 original size:98 final size:99
Alignment explanation
Indices: 27706081--27706286 Score: 353
Period size: 98 Copynumber: 2.1 Consensus size: 99
27706071 GCATCTACCA
* * * *
27706081 AAATTATCTAAAGATATCCACTTGTTGGAAAAATTAGCCTGTATTTCTTTTAGAAATGTAAGAGA
1 AAATCATCTAAAGATATCCACTTGTTGGAAAAATGAGCCCGTATTTCTTTCAGAAATGTAAGAGA
27706146 TTCAATCTCAACTTTTGTTAATGAGGTTATTAAT
66 TTCAATCTCAACTTTTGTTAATGAGGTTATTAAT
27706180 AAATCATC-AAAGATATCCACTTGTTGGAAAAATG-GACCCGTATTTCTTTCAGAAATGTAAGAG
1 AAATCATCTAAAGATATCCACTTGTTGGAAAAATGAG-CCCGTATTTCTTTCAGAAATGTAAGAG
27706243 ATTCAATCTCAACTTTTGTTAATGAGGTTATTAAT
65 ATTCAATCTCAACTTTTGTTAATGAGGTTATTAAT
27706278 AAATCATCT
1 AAATCATCT
27706287 TCTTTGAGAA
Statistics
Matches: 101, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
97 1 0.01
98 93 0.92
99 7 0.07
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (99 bp):
AAATCATCTAAAGATATCCACTTGTTGGAAAAATGAGCCCGTATTTCTTTCAGAAATGTAAGAGA
TTCAATCTCAACTTTTGTTAATGAGGTTATTAAT
Found at i:27712332 original size:18 final size:18
Alignment explanation
Indices: 27712309--27712346 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
27712299 CTCAGAAAAT
*
27712309 GATACATATAAGAGTTAG
1 GATACATATAAGAGCTAG
27712327 GATACATATAAGAGCTAG
1 GATACATATAAGAGCTAG
27712345 GA
1 GA
27712347 AACGCACCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.08, G:0.24, T:0.24
Consensus pattern (18 bp):
GATACATATAAGAGCTAG
Found at i:27713007 original size:7 final size:7
Alignment explanation
Indices: 27712997--27713022 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27712987 TTATATACAT
27712997 AATACTA
1 AATACTA
27713004 AATACTA
1 AATACTA
27713011 AATACTA
1 AATACTA
27713018 AATAC
1 AATAC
27713023 CAATCAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:27713216 original size:20 final size:20
Alignment explanation
Indices: 27713191--27713228 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27713181 TTTATTTTTA
27713191 AAAATCT-ATATAATAATTGT
1 AAAATCTAATATAA-AATTGT
27713211 AAAATCTAATATAAAATT
1 AAAATCTAATATAAAATT
27713229 TACCTCGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAATCTAATATAAAATTGT
Found at i:27714264 original size:12 final size:12
Alignment explanation
Indices: 27714222--27714267 Score: 62
Period size: 11 Copynumber: 4.0 Consensus size: 12
27714212 GGATTTTACA
27714222 GAAATTTG-GAAG
1 GAAATTTGAG-AG
27714234 G-AATTTGAGAG
1 GAAATTTGAGAG
27714245 GAAA-TTGAGAG
1 GAAATTTGAGAG
27714256 GAAATTTGAGAG
1 GAAATTTGAGAG
27714268 AGGATTAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (12 bp):
GAAATTTGAGAG
Found at i:27742194 original size:21 final size:20
Alignment explanation
Indices: 27742170--27742208 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
27742160 AAAGATTCTC
27742170 GAAAGCAATTCTGATTAAGAT
1 GAAAGCAATT-TGATTAAGAT
* *
27742191 GAAAGTAGTTTGATTAAG
1 GAAAGCAATTTGATTAAG
27742209 CTTTTTAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (20 bp):
GAAAGCAATTTGATTAAGAT
Found at i:27743467 original size:2 final size:2
Alignment explanation
Indices: 27743460--27743506 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
27743450 TGGAACGTTT
27743460 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27743502 TA TA T
1 TA TA T
27743507 GTTTATACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27744991 original size:3 final size:3
Alignment explanation
Indices: 27744983--27745031 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
27744973 ATCAATCTAA
*
27744983 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27745031 T
1 T
27745032 CACTCATTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:27747788 original size:19 final size:19
Alignment explanation
Indices: 27747764--27747810 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
27747754 AACGTCTCTT
*
27747764 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
27747783 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
27747802 TATGCATTA
1 TTTGCATTA
27747811 GATTTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:27749923 original size:9 final size:9
Alignment explanation
Indices: 27749909--27749964 Score: 64
Period size: 8 Copynumber: 6.3 Consensus size: 9
27749899 TTCAGACTAA
27749909 AAAAAAATC
1 AAAAAAATC
*
27749918 AAAAAAATTTA
1 AAAAAAA--TC
27749929 AAAAAAATC
1 AAAAAAATC
27749938 -AAAAAAT-
1 AAAAAAATC
27749945 AAAAAAAT-
1 AAAAAAATC
27749953 AAAAAAATC
1 AAAAAAATC
27749962 AAA
1 AAA
27749965 GTCAAAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 22 0.54
9 11 0.27
11 8 0.20
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAAAATC
Found at i:27749923 original size:10 final size:10
Alignment explanation
Indices: 27749908--27749943 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
27749898 GTTCAGACTA
27749908 AAAAAAAATC
1 AAAAAAAATC
* *
27749918 AAAAAAATTT
1 AAAAAAAATC
27749928 AAAAAAAATC
1 AAAAAAAATC
27749938 AAAAAA
1 AAAAAA
27749944 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:27749951 original size:20 final size:20
Alignment explanation
Indices: 27749907--27749951 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
27749897 AGTTCAGACT
*
27749907 AAAAAAAAATCAAAAAAATT
1 AAAAAAAAATCAAAAAAATA
*
27749927 TAAAAAAAATC-AAAAAATA
1 AAAAAAAAATCAAAAAAATA
27749946 AAAAAA
1 AAAAAA
27749952 TAAAAAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.82, C:0.04, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAAAAAAATCAAAAAAATA
Found at i:27750812 original size:21 final size:23
Alignment explanation
Indices: 27750786--27750835 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
27750776 ATTTTGGGTC
*
27750786 AAAAAAATG-ATGATG-AAAATG
1 AAAAAAATGAATAATGAAAAATG
27750807 AAAAAAATGAATAATGAAAAAATG
1 AAAAAAATGAATAATG-AAAAATG
27750831 AAAAA
1 AAAAA
27750836 GTAAAAATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 9 0.36
22 5 0.20
24 11 0.44
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (23 bp):
AAAAAAATGAATAATGAAAAATG
Found at i:27750824 original size:16 final size:14
Alignment explanation
Indices: 27750798--27750844 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
27750788 AAAAATGATG
27750798 ATGAAAATGAAAAAA
1 ATGAAAATG-AAAAA
27750813 ATGAATAATGAAAAA
1 ATGAA-AATGAAAAA
* *
27750828 ATGAAAAAGTAAAA
1 ATGAAAATGAAAAA
27750842 ATG
1 ATG
27750845 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 10 0.34
15 15 0.52
16 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (14 bp):
ATGAAAATGAAAAA
Found at i:27761150 original size:18 final size:18
Alignment explanation
Indices: 27761114--27761153 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
27761104 GCAAATGTTC
*
27761114 TTTCATTCTTTACGTTTT
1 TTTCATTCTTTACGATTT
27761132 TTTCATTCTTT-CAGATTT
1 TTTCATTCTTTAC-GATTT
27761150 TTTC
1 TTTC
27761154 TGCCAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.12, C:0.17, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTCATTCTTTACGATTT
Found at i:27764045 original size:50 final size:50
Alignment explanation
Indices: 27763638--27764023 Score: 229
Period size: 50 Copynumber: 7.7 Consensus size: 50
27763628 NNNNNNNNNN
* * *** * * * *
27763638 AAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAGTGCAGTAG
1 AAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-CATTGCAATTG
* * * *
27763688 AACAGATTGAAGCTACGACGGTGGATCTGGTTTCCCTGATATTGCAATTA
1 AAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCAATTG
* * *** * * * *
27763738 AAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAGTGCAGTGG
1 AAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-CATTGCAATTG
* * * *
27763788 AACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATATTGCAATTA
1 AAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCAATTG
* * *** * ** *
27763838 AAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCAGCGCAATGG
1 AAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-CATTGCAATTG
* * * * ** * *
27763888 AATAGATTGAAACTACGACAGCGGATCTAGTTTTTCGGACATTGCAATTA
1 AAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCAATTG
* * *** ** ** *
27763938 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACGGTGCGGTGG
1 AAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCAATTG
* *
27763988 GATAGATTGAAGCTACGACGGCGGATCTGGTTTCCC
1 AAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCC
27764024 CAATATTGCA
Statistics
Matches: 240, Mismatches: 91, Indels: 10
0.70 0.27 0.03
Matches are distributed among these distances:
49 8 0.03
50 222 0.93
51 10 0.04
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (50 bp):
AAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACATTGCAATTG
Found at i:27764045 original size:100 final size:100
Alignment explanation
Indices: 27763638--27764033 Score: 596
Period size: 100 Copynumber: 4.0 Consensus size: 100
27763628 NNNNNNNNNN
*
27763638 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTAGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
*
27763703 CGACGGTGGATCTGGTTTCCCTGATATTGCAATTA
66 CGACGGCGGATCTGGTTTCCCTGATATTGCAATTA
27763738 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
*
27763803 CGACGGCAGATCTGGTTTCCCTGATATTGCAATTA
66 CGACGGCGGATCTGGTTTCCCTGATATTGCAATTA
* * * *
27763838 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGCGCAATGGAATAGATTGAAACTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
* * ** * *
27763903 CGACAGCGGATCTAGTTTTTCGGACATTGCAATTA
66 CGACGGCGGATCTGGTTTCCCTGATATTGCAATTA
* * * * *
27763938 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCT-GACGGTGCGGTGGGATAGATTGAAGCT
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCT
**
27764002 ACGACGGCGGATCTGGTTTCCCCAATATTGCA
65 ACGACGGCGGATCTGGTTTCCCTGATATTGCA
27764034 GTTGAATAGA
Statistics
Matches: 267, Mismatches: 28, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
99 1 0.00
100 266 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
CGACGGCGGATCTGGTTTCCCTGATATTGCAATTA
Found at i:27764244 original size:44 final size:44
Alignment explanation
Indices: 27764040--27764245 Score: 114
Period size: 44 Copynumber: 4.7 Consensus size: 44
27764030 TGCAGTTGAA
* ** *
27764040 TAGATTAAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAG
1 TAGATCAAAGATGGCAGATTTTATCTCCCTAAGCAGTAGTGGAG
* * * *
27764084 CAGATCAAAGATGGCGGATTTTACCTCCCTATG--GTTACAGTGGAG
1 TAGATCAAAGATGGCAGATTTTATCTCCCTAAGCAG-T--AGTGGAG
* ** *** * * ** * *
27764129 TACATTGAAGCCAGTA-ATTCTATCTCCCTCGGCAGCAGTGGAA
1 TAGATCAAAGATGGCAGATTTTATCTCCCTAAGCAGTAGTGGAG
* ** * *
27764172 TAGATTGAAA-ATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAG
1 TAGA-TCAAAGATGGCAGATTTTATCTCCCTAAGCAGTAGTGGAG
*
27764216 TAGATCAAAGATGGCAGATTTTACCTCCCT
1 TAGATCAAAGATGGCAGATTTTATCTCCCT
27764246 GTGGTTATAG
Statistics
Matches: 110, Mismatches: 44, Indels: 16
0.65 0.26 0.09
Matches are distributed among these distances:
42 1 0.01
43 15 0.14
44 79 0.72
45 14 0.13
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (44 bp):
TAGATCAAAGATGGCAGATTTTATCTCCCTAAGCAGTAGTGGAG
Found at i:27764578 original size:132 final size:132
Alignment explanation
Indices: 27764031--27764598 Score: 838
Period size: 132 Copynumber: 4.3 Consensus size: 132
27764021 CCCCAATATT
* * *
27764031 GCAGTTGAATAGATTAAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
1 GCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
* *
27764096 GGCGGATTTTACCTCCCT-ATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTCG
66 GGCAGATTTTACCTCCCTGA-GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGG
27764160 GCA
130 GCA
* *
27764163 GCAGTGGAATAGATTGAAAATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGTAGATCAAAGAT
1 GCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
* *
27764228 GGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGG
66 GGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGG
27764292 GCA
130 GCA
* * * *
27764295 TCAGTGGAATAGATTGAAGATTTCAAATCTTGTCTCCCTAAGCAGTAGTGAACCAGATCAAAGAT
1 GCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
* *
27764360 GG-TGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGG
66 GGCAG-ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGG
27764424 GCA
130 GCA
* *
27764427 GCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGGAGCATATCAAAGAT
1 GCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
* * * *
27764492 GGTAGATTTTACCTCGCGGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCGGGG
66 GGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGG
27764557 CA
131 CA
* ** ** *
27764559 ACAGTGGAATAGACAGAAGAAATCA-ATCTTATCTCCCTAA
1 GCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAA
27764599 AGTTGCAGTG
Statistics
Matches: 396, Mismatches: 35, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
131 15 0.04
132 379 0.96
133 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
GCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
GGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGG
CA
Found at i:27776094 original size:30 final size:30
Alignment explanation
Indices: 27776060--27776118 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
27776050 CTTAACAAGC
*
27776060 AAATGCCTCTAAAATAATAACAAATTTAAT
1 AAATGCCTCTAAAATAATAACAAAATTAAT
* * *
27776090 AAATGCTTTTAAAATGATAACAAAATTAA
1 AAATGCCTCTAAAATAATAACAAAATTAA
27776119 CAATAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAT
Found at i:27779460 original size:25 final size:25
Alignment explanation
Indices: 27779420--27779469 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
27779410 GTTGTTAATT
*
27779420 AGAGTTTAAGT-GGAAAACTAAAAAC
1 AGAGTTTAAGTAGAAAAAC-AAAAAC
*
27779445 AGAGTTTAATTAGAAAAACAAAAAC
1 AGAGTTTAAGTAGAAAAACAAAAAC
27779470 CAAATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (25 bp):
AGAGTTTAAGTAGAAAAACAAAAAC
Found at i:27791421 original size:18 final size:18
Alignment explanation
Indices: 27791389--27791425 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
27791379 AAATTTTAAA
27791389 TTAATTAATTCGAGTTAT
1 TTAATTAATTCGAGTTAT
27791407 TTAAGTTAATT-GAGTTAT
1 TTAA-TTAATTCGAGTTAT
27791425 T
1 T
27791426 CGAATAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (18 bp):
TTAATTAATTCGAGTTAT
Found at i:27791677 original size:21 final size:21
Alignment explanation
Indices: 27791637--27791677 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27791627 CCCCCTTTTA
* * *
27791637 ATCACCACCGTCCATTTTCCC
1 ATCACAACCGTCAATGTTCCC
27791658 ATCACAACCGTCAATGTTCC
1 ATCACAACCGTCAATGTTCC
27791678 TCTTCACTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.41, G:0.07, T:0.27
Consensus pattern (21 bp):
ATCACAACCGTCAATGTTCCC
Found at i:27804958 original size:58 final size:58
Alignment explanation
Indices: 27804881--27804997 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
27804871 GCCAATTGGA
27804881 ATACTGTAAATGATTACGCACACTGAAATAGAGAAAAGAATCAAGAAAAAGAAAAAGG
1 ATACTGTAAATGATTACGCACACTGAAATAGAGAAAAGAATCAAGAAAAAGAAAAAGG
27804939 ATACTGTAAATGATTACGCACACTGAAATAGAGAAAAGAATCAAGAAAAAGAAAAAGG
1 ATACTGTAAATGATTACGCACACTGAAATAGAGAAAAGAATCAAGAAAAAGAAAAAGG
27804997 A
1 A
27804998 AATCAGGCTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.56, C:0.10, G:0.19, T:0.15
Consensus pattern (58 bp):
ATACTGTAAATGATTACGCACACTGAAATAGAGAAAAGAATCAAGAAAAAGAAAAAGG
Found at i:27818395 original size:2 final size:2
Alignment explanation
Indices: 27818388--27818412 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27818378 TCTCAAACTG
27818388 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
27818413 GTAGCATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27822461 original size:17 final size:19
Alignment explanation
Indices: 27822439--27822475 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
27822429 CCTATTTATC
27822439 TTATAC-CTTA-ATATATA
1 TTATACGCTTATATATATA
27822456 TTATACGCTTATATATATA
1 TTATACGCTTATATATATA
27822475 T
1 T
27822476 ATTGAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (19 bp):
TTATACGCTTATATATATA
Found at i:27823813 original size:34 final size:35
Alignment explanation
Indices: 27823755--27823821 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
27823745 CAAACACCAA
27823755 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
27823790 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
27823822 TATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:27824107 original size:23 final size:24
Alignment explanation
Indices: 27824073--27824118 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
27824063 TATTTTTTTC
27824073 TTTTTTCTTTTCAT-TTAAAATTG
1 TTTTTTCTTTTCATATTAAAATTG
*
27824096 TTTTTT-TATTTCATATTATAATT
1 TTTTTTCT-TTTCATATTAAAATT
27824119 TTTAAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 12 0.60
24 7 0.35
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTTTCTTTTCATATTAAAATTG
Found at i:27825240 original size:12 final size:10
Alignment explanation
Indices: 27825214--27825260 Score: 58
Period size: 10 Copynumber: 4.4 Consensus size: 10
27825204 AACTAAATCC
27825214 TTTCTCTCAA
1 TTTCTCTCAA
27825224 TTTCTCTCTAA
1 TTTCTCTC-AA
27825235 TATTCTCTCAAA
1 T-TTCTCTC-AA
*
27825247 TTCCTCTCAA
1 TTTCTCTCAA
27825257 TTTC
1 TTTC
27825261 CTATTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 13 0.41
11 9 0.28
12 10 0.31
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.49
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:27825313 original size:28 final size:27
Alignment explanation
Indices: 27825264--27825321 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
27825254 CAATTTCCTA
*
27825264 TTTAAAAAAGCTTTAATTTTTTAATTATT
1 TTTAAAAAAGCTTTAATATTTT-ATT-TT
*
27825293 TTTAAAAAAGTTTTAA-ATTTTATTTT
1 TTTAAAAAAGCTTTAATATTTTATTTT
27825319 TTT
1 TTT
27825322 GAATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 5 0.19
27 3 0.11
28 4 0.15
29 15 0.56
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (27 bp):
TTTAAAAAAGCTTTAATATTTTATTTT
Found at i:27826441 original size:7 final size:7
Alignment explanation
Indices: 27826429--27826454 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
27826419 TAGTCGATTG
27826429 GTATTTA
1 GTATTTA
27826436 GTATTTA
1 GTATTTA
27826443 GTATTTA
1 GTATTTA
27826450 GTATT
1 GTATT
27826455 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:27827576 original size:111 final size:111
Alignment explanation
Indices: 27827378--27827599 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 111
27827368 ATTCTATACT
*
27827378 GCTACCAAACATGGGTTGTTCCGTGTTTTGTAACCCACTAATCGAGTGTCGGGTAGGGGTCGTGT
1 GCTACCAAACATGGGTTGTTCCGTGTTTTGTAACCCACTAATCGAGTGTCGGGCAGGGGTCGTGT
* *
27827443 ATGCCTCTCGAACAGCAGTCGCAAGTGCATCATTTGGCGATATAAA
66 ATACCTCTCGAACAGCAATCGCAAGTGCATCATTTGGCGATATAAA
27827489 GCTACCAAACATGGGTTGTTCCGTGTTTTGTAACCCACTAATCGAGTGTCGGGCAGGGGTCGTGT
1 GCTACCAAACATGGGTTGTTCCGTGTTTTGTAACCCACTAATCGAGTGTCGGGCAGGGGTCGTGT
27827554 ATACCTCTCGAACAGCAATCGCAAGTGCATCATTTGGCGATATAAA
66 ATACCTCTCGAACAGCAATCGCAAGTGCATCATTTGGCGATATAAA
27827600 TTGTACATAT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (111 bp):
GCTACCAAACATGGGTTGTTCCGTGTTTTGTAACCCACTAATCGAGTGTCGGGCAGGGGTCGTGT
ATACCTCTCGAACAGCAATCGCAAGTGCATCATTTGGCGATATAAA
Found at i:27828241 original size:126 final size:125
Alignment explanation
Indices: 27828016--27828547 Score: 766
Period size: 126 Copynumber: 4.3 Consensus size: 125
27828006 GACCAAACAA
* *
27828016 GAGCTACTGGAGCAAAAGCGGGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
1 GAGCTACTGTAGCAAAAGC-GGTCCACATGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
* * * * *
27828081 ATGCTTAAAGCGTTTTTAACACTATTTGCTCAGAAACATCTACTCAAAATTATTTTTTCAG
65 CTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAG
* *
27828142 GAGCTACTGTAGCAAAAGCGGATCCATATGGGAGCTTCTTTCAGTACTTTTGTTGACAAAGCATC
1 GAGCTACTGTAGCAAAAGCGG-TCCACATGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
27828207 CTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAG
65 CTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAG
*
27828268 GAGCTACTGTAGC---A-C-G------TGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCC
1 GAGCTACTGTAGCAAAAGCGGTCCACATGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCC
* *
27828322 TGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTAGTTTTTCAG
66 TGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAG
* * *
27828382 GAGCTACTGTAGCAAAAGCGCGTCAACATGAGAGCTTCTTTCAGTACTTTTGCTGACAATGCATC
1 GAGCTACTGTAGCAAAAGCG-GTCCACATGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
* *
27828447 CTGTTTAAAGCATTTTTGACACTATTTACTCAGAAACGTCTTA-TCGAAATTATTTTTT-AG
65 CTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTC-TACTCGAAATTATTTTTTCAG
*
27828507 GAGCTACTGTAGCAAAAGCGAGTCCACGTGGGAGCTTCTTT
1 GAGCTACTGTAGCAAAAGCG-GTCCACATGGGAGCTTCTTT
27828548 AAATTAACAA
Statistics
Matches: 370, Mismatches: 22, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
114 107 0.29
117 1 0.00
118 1 0.00
120 1 0.00
121 1 0.00
122 1 0.00
123 1 0.00
125 41 0.11
126 214 0.58
127 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (125 bp):
GAGCTACTGTAGCAAAAGCGGTCCACATGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCC
TGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAG
Found at i:27828378 original size:114 final size:115
Alignment explanation
Indices: 27828173--27828520 Score: 504
Period size: 114 Copynumber: 2.9 Consensus size: 115
27828163 ATCCATATGG
*
27828173 GAGCTTCTTTCAGTACTTTTGTTGACAAAGCATCCTGCTTAAAGCATTTTTGACACTATTTGCTC
1 GAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCTGCTTAAAGCATTTTTGACACTATTTGCTC
27828238 AGAAACGTCTACTCGAAATTATTTTTTCAGGAGCTACTGTAGCA-CG-TGA
66 AGAAACGTCTACTCGAAATTA-TTTTTCAGGAGCTACTGTAGCAGCGATGA
*
27828287 GAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCTGCTTAAAGCGTTTTTGACACTATTTGCTC
1 GAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCTGCTTAAAGCATTTTTGACACTATTTGCTC
27828352 AGAAACGTCTACTCGAAATTAGTTTTTCAGGAGCTACTGTAGCAAAAGCGCGTCAACATGA
66 AGAAACGTCTACTCGAAATTA-TTTTTCAGGAGCTACTGTAGC---A--GCG-----ATGA
* * *
27828413 GAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCTGTTTAAAGCATTTTTGACACTATTTACTC
1 GAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCTGCTTAAAGCATTTTTGACACTATTTGCTC
*
27828478 AGAAACGTCTTA-TCGAAATTATTTTTTAGGAGCTACTGTAGCA
66 AGAAACGTC-TACTCGAAATTATTTTTCAGGAGCTACTGTAGCA
27828521 AAAGCGAGTC
Statistics
Matches: 213, Mismatches: 8, Indels: 18
0.89 0.03 0.08
Matches are distributed among these distances:
114 105 0.49
117 1 0.00
120 2 0.01
122 1 0.00
125 20 0.09
126 82 0.38
127 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (115 bp):
GAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCTGCTTAAAGCATTTTTGACACTATTTGCTC
AGAAACGTCTACTCGAAATTATTTTTCAGGAGCTACTGTAGCAGCGATGA
Found at i:27828470 original size:240 final size:239
Alignment explanation
Indices: 27828040--27828520 Score: 804
Period size: 240 Copynumber: 2.0 Consensus size: 239
27828030 AAAGCGGGTC
*
27828040 CACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCATGCTTAAAGCGTTTTTAACACTA
1 CACGTGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCATGCTTAAAGCGTTTTTAACACTA
* * *
27828105 TTTGCTCAGAAACATCTACTCAAAATTATTTTTTCAGGAGCTACTGTAGCAAAAGCGGATCCATA
66 TTTGCTCAGAAACATCTACTCAAAATTAGTTTTTCAGGAGCTACTGTAGCAAAAGCGGATCAACA
* * *
27828170 TGGGAGCTTCTTTCAGTACTTTTGTTGACAAAGCATCCTGCTTAAAGCATTTTTGACACTATTTG
131 TGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCTGCTTAAAGCATTTTTGACACTATTTA
27828235 CTCAGAAACGTC-TACTCGAAATTATTTTTTCAGGAGCTACTGTAG
196 CTCAGAAACGTCTTA-TCGAAATTATTTTTT-AGGAGCTACTGTAG
* *
27828280 CACGTGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCTGCTTAAAGCGTTTTTGACACTA
1 CACGTGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCATGCTTAAAGCGTTTTTAACACTA
* *
27828345 TTTGCTCAGAAACGTCTACTCGAAATTAGTTTTTCAGGAGCTACTGTAGCAAAAGCGCG-TCAAC
66 TTTGCTCAGAAACATCTACTCAAAATTAGTTTTTCAGGAGCTACTGTAGCAAAAGCG-GATCAAC
* *
27828409 ATGAGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCTGTTTAAAGCATTTTTGACACTATTT
130 ATGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCTGCTTAAAGCATTTTTGACACTATTT
27828474 ACTCAGAAACGTCTTATCGAAATTATTTTTTAGGAGCTACTGTAG
195 ACTCAGAAACGTCTTATCGAAATTATTTTTTAGGAGCTACTGTAG
27828519 CA
1 CA
27828521 AAAGCGAGTC
Statistics
Matches: 226, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
239 16 0.07
240 207 0.92
241 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (239 bp):
CACGTGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCATGCTTAAAGCGTTTTTAACACTA
TTTGCTCAGAAACATCTACTCAAAATTAGTTTTTCAGGAGCTACTGTAGCAAAAGCGGATCAACA
TGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCTGCTTAAAGCATTTTTGACACTATTTA
CTCAGAAACGTCTTATCGAAATTATTTTTTAGGAGCTACTGTAG
Found at i:27828889 original size:95 final size:96
Alignment explanation
Indices: 27828576--27828974 Score: 464
Period size: 97 Copynumber: 4.2 Consensus size: 96
27828566 ATTAACCCTA
* * * * * *
27828576 AACCCCAAACTCTAATTTATTTGAGTTTTTACTTAAAAACTCTAAACCCTAAACTCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGA-TTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAAT
* *
27828641 TTTTTAAAAATTTATAATTAATTTACTCAAGT
65 TTTTTAAAAAATTATAATTAAATTACTCAAGT
* * * *
27828673 AACCTTAAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATCTAATT
1 AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAA-T
* *
27828738 TTTTTTAAAAATTTTAATTAAATTACTCAAGT
65 TTTTTAAAAAATTATAATTAAATTACTCAAGT
* * *
27828770 AACCTTAAACCGC-AATTTATTTGATTTTTTCTTAAAAACCCTTAACACTAAACCCTGATCTAA-
1 AACCCTAAACC-CTAATTTATTTGATTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAAT
** *
27828833 TTTTTAAAATTTTTTAATTAAATTACTCAAGT
65 TTTTTAAAAAATTATAATTAAATTACTCAAGT
* * * *
27828865 AACCCTAAACCCTAATTTAATTGATTTTTTCTTTAAAAACCATAAACACGAAA-CCTAATCCAA-
1 AACCCTAAACCCTAATTTATTTGATTTTTTC-TTAAAAACCCTAAACACTAAACCCTAATCTAAT
* * * ** *
27828928 TTTTAAAAAAATTATAATTAATTTAATTGAGA
65 TTTTTAAAAAATTATAATTAAATTACTCAAGT
27828960 AACCCTAAACCCTAA
1 AACCCTAAACCCTAA
27828975 ACCCTTATTT
Statistics
Matches: 263, Mismatches: 35, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
94 1 0.00
95 102 0.39
96 52 0.20
97 107 0.41
98 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.38
Consensus pattern (96 bp):
AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATT
TTTTAAAAAATTATAATTAAATTACTCAAGT
Found at i:27832151 original size:89 final size:89
Alignment explanation
Indices: 27831995--27833018 Score: 1377
Period size: 89 Copynumber: 11.5 Consensus size: 89
27831985 GCGAAACCAT
* * * *
27831995 AGATCTAGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACCAGTCTTGCCTTCCTGTAGTG
1 AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTG
**
27832060 ACAGTAGAGCAGACTGAAGATAGC
66 ACAGCGGAGCAGACTGAAGATAGC
* * *
27832084 AGATCTTGCCTTCCTGTACTGACGGTAAAACAGATCGAAGACACCAACCTTGCCTTCCTGTACTG
1 AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTG
*
27832149 ACAACGGAGCAGACTGAAGATAGC
66 ACAGCGGAGCAGACTGAAGATAGC
* * * * * *
27832173 AGATCTTGCCTTCCTATAGTGACGGTAAAGTAAATCGAAGACACTAGCCTTGCCTTCCTGTACTG
1 AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTG
* *
27832238 ACAGCGGAGCAAACTGAAGATAGT
66 ACAGCGGAGCAGACTGAAGATAGC
* * * * *
27832262 AAATTTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGTCTTGCCTTCTTGTATTG
1 AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTG
* *
27832327 ACAGCGAAGCAGACAGAAGATAGC
66 ACAGCGGAGCAGACTGAAGATAGC
* *
27832351 AGATCTTGCCTTCCTGTACTGA-GGTGAAGCAGATCGAAGACACCAGCTTTGCCTTTCTGTACTG
1 AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTG
*
27832415 ACAGCGGAGCAGACTGAAGATAGT
66 ACAGCGGAGCAGACTGAAGATAGC
* * * *
27832439 AGATCTTACCTTCCGGTACTGACGATGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTG
1 AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTG
** * * *
27832504 ACAGTAGAGTAGA-TTACAAATAGC
66 ACAGCGGAGCAGACTGA-AGATAGC
** * * *
27832528 AGATCTTGCCTTCCTGTACTGACGACGAAGCAGATTGAAGACACTAACCTTGCCTTCCTGTACTG
1 AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTG
27832593 ACAGCGGAGCAGACTGAAGATAGC
66 ACAGCGGAGCAGACTGAAGATAGC
* * * *
27832617 AAATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAATACACTAGCCTTGCCTTCTTGTACTG
1 AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTG
* *
27832682 ACAGCAGAGCAGACTGAAGGTAGC
66 ACAGCGGAGCAGACTGAAGATAGC
* * * * *
27832706 AGATCTTGCCTTCCTGTACTAACGGCGAAGTAGATCAAAGACACCAGCCTTGTCTTCCTGTACTG
1 AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTG
*
27832771 ACAGCGGAGCAGACTGAAGATAGA
66 ACAGCGGAGCAGACTGAAGATAGC
* * * * * *
27832795 AAATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACTAACCTTACCTTCCTGTACTC
1 AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTG
* *
27832860 ACAACGGAGCAGACTGAAGATAGT
66 ACAGCGGAGCAGACTGAAGATAGC
* * * *
27832884 AGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAAACACCAGCCTTGCCTTCCTATAATG
1 AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTG
* *
27832949 ACAACGGAGCATACTGAAGATAGC
66 ACAGCGGAGCAGACTGAAGATAGC
* * * *
27832973 AGATCTTGCATTCCTATACTGACGGCGAAGCAAATCGAAGACACCA
1 AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCA
27833019 TAGTTTGCAA
Statistics
Matches: 815, Mismatches: 117, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
88 80 0.10
89 733 0.90
90 2 0.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (89 bp):
AGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTG
ACAGCGGAGCAGACTGAAGATAGC
Found at i:27832301 original size:178 final size:178
Alignment explanation
Indices: 27831995--27833625 Score: 1790
Period size: 178 Copynumber: 9.2 Consensus size: 178
27831985 GCGAAACCAT
* * * *
27831995 AGATCTAGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACCAGTCTTGCCTTCCTGTAGTG
1 AGATCTTGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTG
** * *
27832060 ACAGTAGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTAAAACAGATCGAAGA
66 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGA
* *
27832125 CACCAACCTTGCCTTCCTGTACTGACAACGGAGCAGACTGAAGATAGC
131 CACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGC
* * * *
27832173 AGATCTTGCCTTCCTATAGTGACGGTAAAGTAAATCGAAGACACTAGCCTTGCCTTCCTGTACTG
1 AGATCTTGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTG
* * * *
27832238 ACAGCGGAGCAAACTGAAGATAGTAAATTTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGA
66 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGA
* * * * *
27832303 CACCAGTCTTGCCTTCTTGTATTGACAGCGAAGCAGACAGAAGATAGC
131 CACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGC
* * * *
27832351 AGATCTTGCCTTCCTGTACTGA-GGTGAAGCAGATCGAAGACACCAGCTTTGCCTTTCTGTACTG
1 AGATCTTGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTG
* * * *
27832415 ACAGCGGAGCAGACTGAAGATAGTAGATCTTACCTTCCGGTACTGACGATGAAGCAGATCGAAGA
66 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGA
* ** * * *
27832480 CACTAGCCTTGCCTTCCTGTACTGACAGTAGAGTAGA-TTACAAATAGC
131 CACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGA-AGATAGC
* ** * *
27832528 AGATCTTGCCTTCCTGTACTGACGACGAAGCAGATTGAAGACACTAACCTTGCCTTCCTGTACTG
1 AGATCTTGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTG
* *
27832593 ACAGCGGAGCAGACTGAAGATAGCAAATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAATA
66 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGA
* * * *
27832658 CACTAGCCTTGCCTTCTTGTACTGACAGCAGAGCAGACTGAAGGTAGC
131 CACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGC
* * * * * * *
27832706 AGATCTTGCCTTCCTGTACTAACGGCGAAGTAGATCAAAGACACCAGCCTTGTCTTCCTGTACTG
1 AGATCTTGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTG
* * *
27832771 ACAGCGGAGCAGACTGAAGATAGAAAATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGA
66 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGA
* * * * * *
27832836 CACTAACCTTACCTTCCTGTACTCACAACGGAGCAGACTGAAGATAGT
131 CACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGC
* * * * * *
27832884 AGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAAACACCAGCCTTGCCTTCCTATAATG
1 AGATCTTGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTG
* * * * * *
27832949 ACAACGGAGCATACTGAAGATAGCAGATCTTGCATTCCTATACTGACGGCGAAGCAAATCGAAGA
66 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGA
* * ** *** ** * * *
27833014 CACCA---TAG--TT--TGCAACAAAGCAGTTAAAAAGATTGAAGCTCCAAC
131 CACCAGCCTTGCCTTCCTG-TACTGA-CAGCGGAGCAGACTGAAGAT--AGC
* * * * **
27833059 AATGAATCTT-ACTTCCCTA-AGCAGTA--GTGGAGCAGATCGAAG--A-T-G--GTG-AAT-CT
1 -A-G-ATCTTGCCTT-CCTATA-CTG-ACGGTGAAGCAGATCGAAGACACTAGCCTTGCCTTCCT
** * * * * *
27833112 -TATCTTTC--C-AAG-ATAGTGGAGA-AGCAGAT-TTAAGCCTTCTTGTACTGA-GGTGAAGCA
60 GTA-CTGACAGCGGAGCAGACTGAAGATAGCAGATCTT--GCCTTCCTGTACTGACGGTGAAGCA
* * *
27833169 GATCGAAGACACCAGCTTTGCCTTCCTGTACTGACAGTGGAGCAGACTGAAGATAGT
122 GATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGC
* ** * * * *
27833226 AAATCTTGCCTTCCGGTACTGACGATGAAGCAGATCGAAGACACTAGTCTTACTTTCCTGTACTG
1 AGATCTTGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTG
* * * *
27833291 ACAGCGGAGCAGATTAAAGATAGCAGATCTTGCCTTCCTGCACTGACGGCGAAGCAGATCGAAGA
66 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGA
* *
27833356 CACCAACTTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGC
131 CACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGC
* *
27833404 AAATCTTGCCTTCCTATACTGACGGTGAAGCAGATCGAATACACTAGCCTTGCCTTCCTGTACTG
1 AGATCTTGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTG
* * *
27833469 ATAGCAGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGA
66 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGA
* * *
27833534 TACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCATACTGAAGATACC
131 CACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGC
* *
27833582 AGATCTTGCATTCCTATACTGACGGCGAAGCAGATCGAAGACAC
1 AGATCTTGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACAC
27833626 CATAGTTTGC
Statistics
Matches: 1215, Mismatches: 195, Indels: 86
0.81 0.13 0.06
Matches are distributed among these distances:
163 3 0.00
164 37 0.03
165 38 0.03
166 3 0.00
167 5 0.00
168 3 0.00
169 21 0.02
170 4 0.00
171 7 0.01
172 4 0.00
173 20 0.02
174 2 0.00
175 4 0.00
176 4 0.00
177 190 0.16
178 865 0.71
179 5 0.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (178 bp):
AGATCTTGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTG
ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGA
CACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGC
Found at i:27832803 original size:267 final size:267
Alignment explanation
Indices: 27831997--27833627 Score: 1792
Period size: 267 Copynumber: 6.2 Consensus size: 267
27831987 GAAACCATAG
* * * ** *
27831997 ATCTAGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACCAGTCTTGCCTTCCTGTAGTGAC
1 ATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAACCTTGCCTTCCTGTACTGAC
** * *
27832062 AGTAGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTAAAACAGATCGAAGACA
66 AGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACA
* * * *
27832127 CCAACCTTGCCTTCCTGTACTGACAACGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTATAG
131 CCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTAC
** * * * *
27832192 TGACGGTAAAGTAAATCGAAGACACTAGCCTTGCCTTCCTGTACTGACAGCGGAGCAAACTGAAG
196 TGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAG
*
27832257 ATAGTAA
261 ATAGCAA
* * ** * *
27832264 ATTTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGTCTTGCCTTCTTGTATTGAC
1 ATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAACCTTGCCTTCCTGTACTGAC
* *
27832329 AGCGAAGCAGACAGAAGATAGCAGATCTTGCCTTCCTGTACTGA-GGTGAAGCAGATCGAAGACA
66 AGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACA
* * * * *
27832393 CCAGCTTTGCCTTTCTGTACTGACAGCGGAGCAGACTGAAGATAGTAGATCTTACCTTCCGGTAC
131 CCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTAC
** * ** * *
27832458 TGACGATGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTGACAGTAGAGTAGA-TTACA
196 TGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGA-A
* *
27832522 AATAGCAG
260 GATAGCAA
* * *
27832530 ATCTTGCCTTCCTGTACTGACGACGAAGCAGATTGAAGACACTAACCTTGCCTTCCTGTACTGAC
1 ATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAACCTTGCCTTCCTGTACTGAC
* *
27832595 AGCGGAGCAGACTGAAGATAGCAAATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAATACA
66 AGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACA
* * * *
27832660 CTAGCCTTGCCTTCTTGTACTGACAGCAGAGCAGACTGAAGGTAGCAGATCTTGCCTTCCTGTAC
131 CCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTAC
* * * *
27832725 TAACGGCGAAGTAGATCAAAGACACCAGCCTTGTCTTCCTGTACTGACAGCGGAGCAGACTGAAG
196 TGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAG
*
27832790 ATAGAAA
261 ATAGCAA
* * *
27832797 ATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACTAACCTTACCTTCCTGTACTCAC
1 ATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAACCTTGCCTTCCTGTACTGAC
* * * *
27832862 AACGGAGCAGACTGAAGATAGTAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAAACA
66 AGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACA
* * * * * *
27832927 CCAGCCTTGCCTTCCTATAATGACAACGGAGCATACTGAAGATAGCAGATCTTGCATTCCTATAC
131 CCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTAC
* * * ** *** ** *
27832992 TGACGGCGAAGCAAATCGAAGACACCA---TAG--TT--TGCAACAAAGCAGTTAAAAAGATTGA
196 TGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTG-TACTGA-CAGCGGAGCAGACTGA
* *
27833050 AGCTCCAACAATGA
259 AGAT--AGC-A--A
* * * **** * *
27833064 ATCTT-ACTTCCCT-AAGCAGTA-GTG-G-AGCAGATCGAAGATGGTGAATCTT---AT-CT-T-
1 ATCTTGCCTT-CCTGTA-CTG-ACG-GCGAAGCAGATCGAAGA-CACCAACCTTGCCTTCCTGTA
* * * * *
27833118 -T--C--C-AAG-ATAGTGGAGA-AGCAGAT-TTAAGCCTTCTTGTACTGA-GGTGAAGCAGATC
61 CTGACAGCGGAGCAGACTGAAGATAGCAGATCTT--GCCTTCCTGTACTGACGGTGAAGCAGATC
* * * *
27833173 GAAGACACCAGCTTTGCCTTCCTGTACTGACAGTGGAGCAGACTGAAGATAGTAAATCTTGCCTT
124 GAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTT
* ** * * * *
27833238 CCGGTACTGACGATGAAGCAGATCGAAGACACTAGTCTTACTTTCCTGTACTGACAGCGGAGCAG
189 CCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAG
* * *
27833303 ATTAAAGATAGCAG
254 ACTGAAGATAGCAA
* *
27833317 ATCTTGCCTTCCTGCACTGACGGCGAAGCAGATCGAAGACACCAACTTTGCCTTCCTGTACTGAC
1 ATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAACCTTGCCTTCCTGTACTGAC
* * *
27833382 AGCGGAGCAGACTGAAGATAGCAAATCTTGCCTTCCTATACTGACGGTGAAGCAGATCGAATACA
66 AGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACA
* * *
27833447 CTAGCCTTGCCTTCCTGTACTGATAGCAGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTAC
131 CCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTAC
* *
27833512 TGACGGCGAAGCAGATCGAAGATACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCATACTGAAG
196 TGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAG
* *
27833577 ATACCAG
261 ATAGCAA
* *
27833584 ATCTTGCATTCCTATACTGACGGCGAAGCAGATCGAAGACACCA
1 ATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCA
27833628 TAGTTTGCAA
Statistics
Matches: 1129, Mismatches: 190, Indels: 90
0.80 0.13 0.06
Matches are distributed among these distances:
252 4 0.00
253 117 0.10
254 38 0.03
255 3 0.00
256 5 0.00
257 2 0.00
258 17 0.02
259 3 0.00
260 6 0.01
261 3 0.00
262 17 0.02
263 2 0.00
264 5 0.00
265 5 0.00
266 265 0.23
267 631 0.56
268 6 0.01
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (267 bp):
ATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAACCTTGCCTTCCTGTACTGAC
AGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACA
CCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTAC
TGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAG
ATAGCAA
Found at i:27833300 original size:89 final size:89
Alignment explanation
Indices: 27833145--27833627 Score: 689
Period size: 89 Copynumber: 5.4 Consensus size: 89
27833135 GCAGATTTAA
* * * *
27833145 GCCTTCTTGTACTGA-GGTGAAGCAGATCGAAGACACCAGCTTTGCCTTCCTGTACTGACAGTGG
1 GCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGG
* *
27833209 AGCAGACTGAAGATAGTAAATCTT
66 AGCAGACTGAAGATAGCAGATCTT
* ** * * * *
27833233 GCCTTCCGGTACTGACGATGAAGCAGATCGAAGACACTAGTCTTACTTTCCTGTACTGACAGCGG
1 GCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGG
* *
27833298 AGCAGATTAAAGATAGCAGATCTT
66 AGCAGACTGAAGATAGCAGATCTT
* * *
27833322 GCCTTCCTGCACTGACGGCGAAGCAGATCGAAGACACCAACTTTGCCTTCCTGTACTGACAGCGG
1 GCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGG
*
27833387 AGCAGACTGAAGATAGCAAATCTT
66 AGCAGACTGAAGATAGCAGATCTT
* * * * * *
27833411 GCCTTCCTATACTGACGGTGAAGCAGATCGAATACACTAGCCTTGCCTTCCTGTACTGATAGCAG
1 GCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGG
27833476 AGCAGACTGAAGATAGCAGATCTT
66 AGCAGACTGAAGATAGCAGATCTT
*
27833500 GCCTTCCTGTACTGACGGCGAAGCAGATCGAAGATACCAGCCTTGCCTTCCTGTACTGACAGCGG
1 GCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGG
* *
27833565 AGCATACTGAAGATACCAGATCTT
66 AGCAGACTGAAGATAGCAGATCTT
* *
27833589 GCATTCCTATACTGACGGCGAAGCAGATCGAAGACACCA
1 GCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCA
27833628 TAGTTTGCAA
Statistics
Matches: 346, Mismatches: 48, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
88 13 0.04
89 333 0.96
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (89 bp):
GCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAGCGG
AGCAGACTGAAGATAGCAGATCTT
Found at i:27833604 original size:45 final size:44
Alignment explanation
Indices: 27831995--27833018 Score: 687
Period size: 44 Copynumber: 23.0 Consensus size: 44
27831985 GCGAAACCAT
* * * * *
27831995 AGATCTAGCCTTCCTATACTGACGGTGAAGCAGATCGAAGACACC
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGAT-GAAGATACC
* * *
27832040 AG-TCTTGCCTTCCTGTAGTGACAG-TAGAGCAGACTGAAGATAGC
1 AGATCTTGCCTTCCTGTACTGACAGCGA-AGCAGA-TGAAGATACC
* ** * *
27832084 AGATCTTGCCTTCCTGTACTGACGGTAAAACAGATCGAAGACACC
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGAT-GAAGATACC
* * * *
27832129 A-ACCTTGCCTTCCTGTACTGACAACGGAGCAGACTGAAGATAGC
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA-TGAAGATACC
* * * ** * * * *
27832173 AGATCTTGCCTTCCTATAGTGACGGTAAAGTAAATCGAAGACACT
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGAT-GAAGATACC
* * * **
27832218 AG-CCTTGCCTTCCTGTACTGACAGCGGAGCAAACTGAAGATAGT
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA-TGAAGATACC
* * * * *
27832262 AAATTTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACC
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGAT-GAAGATACC
* * * *
27832307 AG-TCTTGCCTTCTTGTATTGACAGCGAAGCAGACAGAAGATAGC
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA-TGAAGATACC
* * *
27832351 AGATCTTGCCTTCCTGTACTGA-GGTGAAGCAGATCGAAGACACC
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGAT-GAAGATACC
* * * **
27832395 AGCT-TTGCCTTTCTGTACTGACAGCGGAGCAGACTGAAGATAGT
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA-TGAAGATACC
* * * * *
27832439 AGATCTTACCTTCCGGTACTGAC-GATGAAGCAGATCGAAGACACT
1 AGATCTTGCCTTCCTGTACTGACAG-CGAAGCAGAT-GAAGATACC
* * * * * *
27832484 AG-CCTTGCCTTCCTGTACTGACAG-TAGAGTAGATTACAAATAGC
1 AGATCTTGCCTTCCTGTACTGACAGCGA-AGCAGATGA-AGATACC
* *
27832528 AGATCTTGCCTTCCTGTACTGAC-GACGAAGCAGATTGAAGACACT
1 AGATCTTGCCTTCCTGTACTGACAG-CGAAGCAGA-TGAAGATACC
* * *
27832573 A-ACCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGC
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA-TGAAGATACC
* * * * * *
27832617 AAATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAATACACT
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGAT-GAAGATACC
* * * *
27832662 AG-CCTTGCCTTCTTGTACTGACAGC-AGAGCAGACTGAAGGTAGC
1 AGATCTTGCCTTCCTGTACTGACAGCGA-AGCAGA-TGAAGATACC
* * * * *
27832706 AGATCTTGCCTTCCTGTACTAACGGCGAAGTAGATCAAAGACACC
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGAT-GAAGATACC
* * * **
27832751 AG-CCTTGTCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGA
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA-TGAAGATACC
* * * *
27832795 AAATCTTGCCTTCCTGTACTGACGGCGAAGCAGATCGAAGACACT
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGAT-GAAGATACC
* * * * * **
27832840 A-ACCTTACCTTCCTGTACTCACAACGGAGCAGACTGAAGATAGT
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA-TGAAGATACC
* * *
27832884 AGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAAACACC
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGAT-GAAGATACC
* * * * * * *
27832929 AG-CCTTGCCTTCCTATAATGACAACGGAGCATACTGAAGATAGC
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA-TGAAGATACC
* * * * *
27832973 AGATCTTGCATTCCTATACTGACGGCGAAGCAAATCGAAGACACC
1 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGAT-GAAGATACC
27833018 A
1 A
27833019 TAGTTTGCAA
Statistics
Matches: 743, Mismatches: 193, Indels: 86
0.73 0.19 0.08
Matches are distributed among these distances:
43 20 0.03
44 371 0.50
45 347 0.47
46 5 0.01
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (44 bp):
AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATGAAGATACC
Found at i:27833842 original size:132 final size:132
Alignment explanation
Indices: 27833681--27834169 Score: 762
Period size: 132 Copynumber: 3.7 Consensus size: 132
27833671 GAATCTTACT
*
27833681 TCCCTAAGCAGTAGTGGAGCAGATCGAAGATGCTGAATCTTATCTTCCCAAGATAGTGGAGAAGC
1 TCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGC
* * * * * * *
27833746 GGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTTGAGTGGGTTGACGATTGCAGATTCTA
66 AGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATTCTG
27833811 TC
131 TC
* * *
27833813 TCCCTAAGTAGTAGTAGAGCAGATCGAAGATGGTGAATATTATCTTCCCAAGATAGTGGAGAAGC
1 TCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGC
* *
27833878 AGATTTAAGCCATTAGTCATATCTCCCTCAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATTCTG
66 AGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATTCTG
27833943 TC
131 TC
* * * * *
27833945 TCCCGAAGCAGTAGTGGAGCAGATCGAAAATGGTTAATCTTATCTTCCCAATATAGTGGAGATGC
1 TCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGC
*
27834010 AGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTAAAGATTGCAGATTCTG
66 AGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATTCTG
27834075 TC
131 TC
* * *
27834077 TCCCTAAGCAGTATTGGAGCAGATCGAAGATGGTGAATCTTATATTCCCAAGATAGTAGAGAAGC
1 TCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGC
* *
27834142 ATATTTAAGCCATTAGTCTTATCTCCCT
66 AGATTTAAGCCATTAGTCCTATCTCCCT
27834170 GAAGTTGTAG
Statistics
Matches: 323, Mismatches: 34, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 323 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
TCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAAGC
AGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATTCTG
TC
Found at i:27836390 original size:70 final size:70
Alignment explanation
Indices: 27836277--27836416 Score: 199
Period size: 70 Copynumber: 2.0 Consensus size: 70
27836267 TATTTTCAAA
* * * *
27836277 CTCAATTTTTAAACGATCTCGAGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATGATCAT
1 CTCAAGTTTTAAACGATCTCGAGAAATAAAAAAAGATCGTGTCCTAACTTACTGGGCATGATCAT
27836342 TTTTT
66 TTTTT
* * ** *
27836347 CTCAAGTTTTAAACGATCTCGGGAAATAAAAAAAGATTGTGTCCTAACTTACTGGGTGTGATCCT
1 CTCAAGTTTTAAACGATCTCGAGAAATAAAAAAAGATCGTGTCCTAACTTACTGGGCATGATCAT
27836412 TTTTT
66 TTTTT
27836417 AAATCCGAGA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (70 bp):
CTCAAGTTTTAAACGATCTCGAGAAATAAAAAAAGATCGTGTCCTAACTTACTGGGCATGATCAT
TTTTT
Found at i:27838831 original size:20 final size:20
Alignment explanation
Indices: 27838806--27838843 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27838796 AAAATTAATA
27838806 AAATAAAA-AAATTGTAATTC
1 AAATAAAAGAAATT-TAATTC
27838826 AAATAAAAGAAATTTAAT
1 AAATAAAAGAAATTTAAT
27838844 AGTAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
AAATAAAAGAAATTTAATTC
Found at i:27840158 original size:30 final size:29
Alignment explanation
Indices: 27840023--27840159 Score: 120
Period size: 29 Copynumber: 4.7 Consensus size: 29
27840013 AAAATTCAAA
* *
27840023 AAAATTACATTTTAACTCCTAAACTTTTC
1 AAAATTACATTTTAGCCCCTAAACTTTTC
* *
27840052 AAAATTCCATTTTAACCCCT-AACTTTTTC
1 AAAATTACATTTTAGCCCCTAAAC-TTTTC
*
27840081 AAAATTTACATCTT-GACCCCTAATA-TTTT-
1 AAAA-TTACATTTTAG-CCCCTAA-ACTTTTC
**
27840110 ATAAATTACATTCAAGCCCCTAAACTTTCTC
1 A-AAATTACATTTTAGCCCCTAAACTTT-TC
*
27840141 AAAATTATATTTTAGCCCC
1 AAAATTACATTTTAGCCCC
27840160 ATATTTTCCT
Statistics
Matches: 87, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
28 4 0.05
29 44 0.51
30 36 0.41
31 2 0.02
32 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (29 bp):
AAAATTACATTTTAGCCCCTAAACTTTTC
Found at i:27840423 original size:11 final size:11
Alignment explanation
Indices: 27840404--27840435 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
27840394 AACGCAAAAA
27840404 AAAAAAACAGC
1 AAAAAAACAGC
*
27840415 AAAAGAACAGC
1 AAAAAAACAGC
27840426 AAAAAAACAG
1 AAAAAAACAG
27840436 AGAGCAGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.72, C:0.16, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAACAGC
Found at i:27840775 original size:15 final size:15
Alignment explanation
Indices: 27840755--27840790 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
27840745 AGGAAAGTAA
27840755 AAAGAAGAAAAATAG
1 AAAGAAGAAAAATAG
27840770 AAAGAAGAAAAATAG
1 AAAGAAGAAAAATAG
27840785 AAAGAA
1 AAAGAA
27840791 AAATTGAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (15 bp):
AAAGAAGAAAAATAG
Found at i:27840789 original size:12 final size:12
Alignment explanation
Indices: 27840747--27840818 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
27840737 AAGAAGAGAG
*
27840747 GAAAGTAAAA-A
1 GAAAGAAAAATA
27840758 G-AAGAAAAATA
1 GAAAGAAAAATA
27840769 GAAAGAAGAAAAATA
1 G--A-AAGAAAAATA
*
27840784 GAAAGAAAAATT
1 GAAAGAAAAATA
* *
27840796 GAAGGAAAAAAAA
1 GAAAG-AAAAATA
27840809 GAAAGAAAAA
1 GAAAGAAAAA
27840819 AAAGGAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
10 7 0.14
11 3 0.06
12 18 0.37
13 10 0.20
15 11 0.22
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (12 bp):
GAAAGAAAAATA
Found at i:27840790 original size:27 final size:25
Alignment explanation
Indices: 27840753--27840818 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
27840743 AGAGGAAAGT
27840753 AAAAAG-AAGAAAAATAGAAAGAAGA
1 AAAAAGAAAGAAAAATAGAAAGAA-A
* *
27840778 AAAATAGAAAGAAAAATTGAAGGAAA
1 AAAA-AGAAAGAAAAATAGAAAGAAA
27840804 AAAAAGAAAGAAAAA
1 AAAAAGAAAGAAAAA
27840819 AAAGGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 15 0.41
26 7 0.19
27 15 0.41
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (25 bp):
AAAAAGAAAGAAAAATAGAAAGAAA
Found at i:27840987 original size:23 final size:23
Alignment explanation
Indices: 27840943--27840987 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
27840933 AAAAAAAAAA
*
27840943 CAAAAAACAGCAGGCCTACAGCC
1 CAAAAAACAGCAGGCCCACAGCC
27840966 CAAAAAA-AGCAGGCCCAGCAGC
1 CAAAAAACAGCAGGCCCA-CAGC
27840988 AGGCCACAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.44, C:0.33, G:0.20, T:0.02
Consensus pattern (23 bp):
CAAAAAACAGCAGGCCCACAGCC
Found at i:27841640 original size:17 final size:17
Alignment explanation
Indices: 27841614--27841915 Score: 171
Period size: 17 Copynumber: 16.5 Consensus size: 17
27841604 CGATACCTCT
27841614 TTTC-AAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
*
27841630 TTTCAAAAATTTTTCATG
1 TTTCAAAAA-TTTTCGTG
*
27841648 TTTTCAAAAAATTTATTGTG
1 -TTTC-AAAAATTT-TCGTG
27841668 TTT-AAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
* *
27841684 TTTCAAGAATTTTCGTATT
1 TTTCAAAAATTTTCG--TG
* *
27841703 TTTAAAAAATTCTCGTG
1 TTTCAAAAATTTTCGTG
* * *
27841720 TTT-AAAACTTTTTGCG
1 TTTCAAAAATTTTCGTG
27841736 TTATCAAAAAAAATTTTCGTG
1 TT-TC---AAAAATTTTCGTG
* *
27841757 TTTCAAAAAATTTCGGG
1 TTTCAAAAATTTTCGTG
* *
27841774 TTTTCAAAAAAAAATTTCGGG
1 -TTTC---AAAAATTTTCGTG
*
27841795 TTTCAAAAAATTTCGTG
1 TTTCAAAAATTTTCGTG
*
27841812 TTTTCAAAAAAAATTTCGTG
1 -TTTC--AAAAATTTTCGTG
*
27841832 TTTCAAAGAA-TTTCATG
1 TTTCAAA-AATTTTCGTG
* *
27841849 TTTTCAAAAAACAATGTTCTTG
1 -TTTC---AAA-AATTTTCGTG
*
27841871 TTTAAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
*
27841888 TTTTCAAACAAATTTCGTG
1 -TTTCAAA-AATTTTCGTG
27841907 TTTCAAAAA
1 TTTCAAAAA
27841916 GAAATTCTCG
Statistics
Matches: 229, Mismatches: 29, Indels: 55
0.73 0.09 0.18
Matches are distributed among these distances:
16 22 0.10
17 69 0.30
18 37 0.16
19 36 0.16
20 27 0.12
21 33 0.14
22 5 0.02
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (17 bp):
TTTCAAAAATTTTCGTG
Found at i:27841649 original size:18 final size:18
Alignment explanation
Indices: 27841614--27841915 Score: 128
Period size: 18 Copynumber: 16.5 Consensus size: 18
27841604 CGATACCTCT
27841614 TTTC-AAAA-TTTTCGTG
1 TTTCAAAAATTTTTCGTG
*
27841630 TTTCAAAAATTTTTCATG
1 TTTCAAAAATTTTTCGTG
27841648 TTTTCAAAAAATTTATT-GTG
1 -TTTC-AAAAATTT-TTCGTG
27841668 TTT-AAAAA-TTTTCGTG
1 TTTCAAAAATTTTTCGTG
* *
27841684 TTTCAAGAA-TTTTCGTAT
1 TTTCAAAAATTTTTCGT-G
* * *
27841702 TTTTAAAAAATTCTCGTG
1 TTTCAAAAATTTTTCGTG
*
27841720 TTT-AAAACTTTTTGCGT-
1 TTTCAAAAATTTTT-CGTG
* *
27841737 TATCAAAAAAAATTTTCGTG
1 TTTC--AAAAATTTTTCGTG
* *
27841757 TTTCAAAAA-ATTTCGGG
1 TTTCAAAAATTTTTCGTG
** *
27841774 TTTTCAAAAAAAAATTTCGGG
1 -TTTC--AAAAATTTTTCGTG
*
27841795 TTTCAAAAA-ATTTCGTG
1 TTTCAAAAATTTTTCGTG
**
27841812 TTTTCAAAAAAAATTTCGTG
1 -TTTC-AAAAATTTTTCGTG
*
27841832 TTTCAAAGAA--TTTCATG
1 TTTCAAA-AATTTTTCGTG
* * *
27841849 TTTTCAAAAAACAATGTTCTTG
1 -TTTC--AAAA-ATTTTTCGTG
*
27841871 TTT-AAAAAATTTTCGTG
1 TTTCAAAAATTTTTCGTG
*
27841888 TTTTCAAACAA-ATTTCGTG
1 -TTTCAAA-AATTTTTCGTG
27841907 TTTCAAAAA
1 TTTCAAAAA
27841916 GAAATTCTCG
Statistics
Matches: 231, Mismatches: 24, Indels: 61
0.73 0.08 0.19
Matches are distributed among these distances:
15 2 0.01
16 12 0.05
17 58 0.25
18 59 0.26
19 38 0.16
20 44 0.19
21 13 0.06
22 5 0.02
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (18 bp):
TTTCAAAAATTTTTCGTG
Found at i:27841747 original size:21 final size:20
Alignment explanation
Indices: 27841723--27841838 Score: 84
Period size: 20 Copynumber: 6.0 Consensus size: 20
27841713 TCTCGTGTTT
* *
27841723 AAAACTTTTTGCGTTATCAAA
1 AAAAATTTTCGCGTT-TCAAA
*
27841744 AAAAATTTTCGTGTTTC--A
1 AAAAATTTTCGCGTTTCAAA
*
27841762 AAAAA-TTTCGGGTTTTCAAA
1 AAAAATTTTCGCG-TTTCAAA
* *
27841782 AAAAAATTTCGGGTTTC--A
1 AAAAATTTTCGCGTTTCAAA
*
27841800 AAAAA-TTTCGTGTTTTCAAA
1 AAAAATTTTCGCG-TTTCAAA
*
27841820 AAAAA-TTTCGTGTTTCAAA
1 AAAAATTTTCGCGTTTCAAA
27841839 GAATTTCATG
Statistics
Matches: 83, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
17 12 0.14
18 20 0.24
19 7 0.08
20 25 0.30
21 19 0.23
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (20 bp):
AAAAATTTTCGCGTTTCAAA
Found at i:27841781 original size:38 final size:38
Alignment explanation
Indices: 27841671--27841915 Score: 261
Period size: 38 Copynumber: 6.6 Consensus size: 38
27841661 TATTGTGTTT
* * * *
27841671 AAAAATTTTCGTGTTTCAAGAATTTTCGTATTTT--TA
1 AAAAATTTTCGTGTTTCAAAAAATTTCGTGTTTTCAAA
* ** * * *
27841707 AAAAATTCTCGTGTTT-AAAACTTTTTGCGTTATCAAA
1 AAAAATTTTCGTGTTTCAAAAAATTTCGTGTTTTCAAA
*
27841744 AAAAATTTTCGTGTTTCAAAAAATTTCGGGTTTTCAAA
1 AAAAATTTTCGTGTTTCAAAAAATTTCGTGTTTTCAAA
* *
27841782 AAAAAATTTCGGGTTTCAAAAAATTTCGTGTTTTCAAA
1 AAAAATTTTCGTGTTTCAAAAAATTTCGTGTTTTCAAA
* *
27841820 AAAAA-TTTCGTGTTTCAAAGAATTTCATGTTTTCAAA
1 AAAAATTTTCGTGTTTCAAAAAATTTCGTGTTTTCAAA
* *
27841857 AAACAATGTTCTTGTTT-AAAAAATTTTCGTGTTTTC-AA
1 AAA-AATTTTCGTGTTTCAAAAAA-TTTCGTGTTTTCAAA
*
27841895 ACAAA-TTTCGTGTTTCAAAAA
1 AAAAATTTTCGTGTTTCAAAAA
27841916 GAAATTCTCG
Statistics
Matches: 175, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
35 11 0.06
36 23 0.13
37 55 0.31
38 67 0.38
39 19 0.11
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (38 bp):
AAAAATTTTCGTGTTTCAAAAAATTTCGTGTTTTCAAA
Found at i:27841835 original size:75 final size:76
Alignment explanation
Indices: 27841739--27841915 Score: 252
Period size: 75 Copynumber: 2.3 Consensus size: 76
27841729 TTTTGCGTTA
*
27841739 TCAAAAAAAATTTTCGTGTTTCAAAAAATTTCGGGTTTTCAAAAAAAAAT-TTCGGGTTTCAAAA
1 TCAAAAAAAA-TTTCGTGTTTCAAAAAATTTCAGGTTTTCAAAAAAAAATGTTCGGGTTT-AAAA
27841803 AA-TTTCGTGTTT
64 AATTTTCGTGTTT
* * * **
27841815 TCAAAAAAAATTTCGTGTTTCAAAGAATTTCATGTTTTCAAAAAACAATGTTCTTGTTTAAAAAA
1 TCAAAAAAAATTTCGTGTTTCAAAAAATTTCAGGTTTTCAAAAAAAAATGTTCGGGTTTAAAAAA
27841880 TTTTCGTGTTT
66 TTTTCGTGTTT
*
27841891 TC-AAACAAATTTCGTGTTTCAAAAA
1 TCAAAAAAAATTTCGTGTTTCAAAAA
27841916 GAAATTCTCG
Statistics
Matches: 91, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
75 62 0.68
76 29 0.32
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (76 bp):
TCAAAAAAAATTTCGTGTTTCAAAAAATTTCAGGTTTTCAAAAAAAAATGTTCGGGTTTAAAAAA
TTTTCGTGTTT
Found at i:27841935 original size:20 final size:20
Alignment explanation
Indices: 27841739--27841936 Score: 65
Period size: 20 Copynumber: 10.3 Consensus size: 20
27841729 TTTTGCGTTA
*
27841739 TCAAAAA-AAATTTTCGTGTT
1 TCAAAAAGAAA-TTTCGTGGT
27841759 TC--AAA-AAATTTCG-GGTTT
1 TCAAAAAGAAATTTCGTGG--T
*
27841777 TCAAAAAAAAATTTCG-GGTT
1 TCAAAAAGAAATTTCGTGG-T
*
27841797 TC--AAA-AAATTTCGTGTTT
1 TCAAAAAGAAATTTCGTG-GT
*
27841815 TCAAAAA-AAATTTCGTGTT
1 TCAAAAAGAAATTTCGTGGT
* *
27841834 TC--AAAG-AATTTCATGTTT
1 TCAAAAAGAAATTTCGTG-GT
*
27841852 TCAAAAA-ACAATGTTC-TTGT
1 TCAAAAAGA-AAT-TTCGTGGT
* * *
27841872 T-TAAAA-AATTTTCGTGTTT
1 TCAAAAAGAAATTTCGTG-GT
* *
27841891 TC--AAACAAATTTCGTGTT
1 TCAAAAAGAAATTTCGTGGT
27841909 TCAAAAAGAAATTCTCGTGGT
1 TCAAAAAGAAATT-TCGTGGT
27841930 TCAAAAA
1 TCAAAAA
27841937 TTTCCGTATT
Statistics
Matches: 143, Mismatches: 12, Indels: 45
0.71 0.06 0.22
Matches are distributed among these distances:
16 1 0.01
17 27 0.19
18 30 0.21
19 20 0.14
20 35 0.24
21 27 0.19
22 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (20 bp):
TCAAAAAGAAATTTCGTGGT
Found at i:27847575 original size:13 final size:13
Alignment explanation
Indices: 27847557--27847589 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
27847547 ATTATGCCTA
27847557 AAAAAAACAAAAC
1 AAAAAAACAAAAC
27847570 AAAAAAACAAAAC
1 AAAAAAACAAAAC
27847583 AAAAAAA
1 AAAAAAA
27847590 AAAGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:27847583 original size:18 final size:16
Alignment explanation
Indices: 27847556--27847598 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 16
27847546 TATTATGCCT
27847556 AAAAAAAACAAAACAAA
1 AAAAAAAACAAAA-AAA
27847573 AAAACAAAACAAAAAAA
1 AAAA-AAAACAAAAAAA
27847590 AAAGAAAAA
1 AAA-AAAAA
27847599 ACAAGATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAAAAA
Found at i:27847599 original size:11 final size:12
Alignment explanation
Indices: 27847558--27847602 Score: 65
Period size: 13 Copynumber: 3.8 Consensus size: 12
27847548 TTATGCCTAA
27847558 AAAAAACAAAAC
1 AAAAAACAAAAC
27847570 AAAAAAACAAAAC
1 -AAAAAACAAAAC
*
27847583 AAAAAA-AAAAG
1 AAAAAACAAAAC
27847594 AAAAAACAA
1 AAAAAACAA
27847603 GATGAAAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 10 0.33
12 8 0.27
13 12 0.40
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAC
Found at i:27847599 original size:18 final size:18
Alignment explanation
Indices: 27847556--27847602 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
27847546 TATTATGCCT
27847556 AAAAAAAACAAAACAAAA
1 AAAAAAAACAAAACAAAA
*
27847574 AAACAAAACAAAA-AAAA
1 AAAAAAAACAAAACAAAA
27847591 AAGAAAAAACAA
1 AA-AAAAAACAA
27847603 GATGAAAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAAAAACAAAACAAAA
Found at i:27848649 original size:80 final size:76
Alignment explanation
Indices: 27848471--27849481 Score: 1023
Period size: 75 Copynumber: 13.0 Consensus size: 76
27848461 TTTTTTTTTT
* * * *
27848471 AAATCAACTCATAATGC-AGGAGGTGAGTTGAGCCTCGGGGCACATGCCGAGGTATTTCTCAATT
1 AAATCAACTCATATTGCGA-GAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAAATT
*
27848535 TCTGTTTTTTTAA
65 TCTG-TTTTTCAA
* *
27848548 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCGGGTCACATACCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA--T-TTTTAAA
27848613 TTTCTGTTTTTCAAA
63 TTTCTGTTTTTC-AA
*
27848628 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGAC-CATGCCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA--T-TTTTAAA
*
27848691 TTTATGTTTTTCAA
63 TTTCTGTTTTTCAA
* * * **
27848705 AAATCAACTCATAATGCGAAAAGTGAGTTGAGCCTCGGGTCAC--GTTGAGGTATTTTT-AATTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAAATTT
*
27848767 CTGTTTTTTAAAAAAA
66 CTG-TTTTT----CAA
* * * *
27848783 ATCATCATCAACTCATAATGCGAGAGGTGAGTTGAACCTCGGGTCAC--GCCGAGGTAGTTTTCA
1 A--A--ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAA
* *
27848846 ATTGCTTTTTTTCAA
62 ATTTCTGTTTTTCAA
* * * * * **
27848861 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCGCAAGCTGAGGTA-TTTTACGTTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAAATTT
27848925 CTGTTTTTCAA
66 CTGTTTTTCAA
* * *
27848936 AAATCAACTCATATTGCTAGAGGTGAGCTGAGCCTCGGGTCACATGCCGAGGTA-TTTTCAATTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAAATTT
*
27849000 ATGTTTTTCAA
66 CTGTTTTTCAA
* * *
27849011 AAATCAACTCATATTGCGAGAGTTGAGTTGAGCCTCGGGTCAC--GCTGAGGTATTTTTTAATTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAAATTT
27849074 CTGTTTTTTCAA
66 CTG-TTTTTCAA
* * *
27849086 AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCAC--GCTGAGGTATTTTTAAATTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAAATTT
27849149 CTGTTTTTTGCAA
66 CTG-TTTTT-CAA
* * * * * *
27849162 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCATTGAGTCA-A-GTCGAGGTATTTTTCAATTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAAATTT
* **
27849225 TTACTTTTCAAAAAAAAAA
66 CTGTTTTTC--------AA
*
27849244 TCAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAAGTATTTCTTTTA
1 --AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA--T-TTTTA
27849309 AATTTCTGTTTTTCAA
61 AATTTCTGTTTTTCAA
*
27849325 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCATGCCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA--T-TTTTAAA
*
27849390 TTTATGTTTTTGCAA
63 TTTCTGTTTTT-CAA
* * * * * *
27849405 AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTTGAGTCA-A-GTCGAGGTATTTTTCAATTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAAATTT
* **
27849468 TTACTTTTCAA
66 CTGTTTTTCAA
27849479 AAA
1 AAA
27849482 AAAAAAACAA
Statistics
Matches: 802, Mismatches: 93, Indels: 81
0.82 0.10 0.08
Matches are distributed among these distances:
73 15 0.02
74 65 0.08
75 215 0.27
76 67 0.08
77 90 0.11
78 51 0.06
79 84 0.10
80 89 0.11
81 2 0.00
82 56 0.07
83 6 0.01
84 38 0.05
85 1 0.00
86 7 0.01
88 1 0.00
89 15 0.02
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (76 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTAAATTT
CTGTTTTTCAA
Found at i:27849516 original size:173 final size:173
Alignment explanation
Indices: 27849325--27849640 Score: 510
Period size: 173 Copynumber: 1.8 Consensus size: 173
27849315 TGTTTTTCAA
*
27849325 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCATGCCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTCTTTTAAA
* * * *
27849390 TTTATGTTTTTG-CAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTTGAGTCAAG-TCGA
66 TTTATGTTTTCGAAAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGTCTCGAGTCAAGCT-GA
27849453 GGTATTTTTCAATTTTTACTTTTCAAAAAAAAAAAACAAAAAATC
130 GGTA-TTTTCAATTTTTACTTTTCAAAAAAAAAAAACAAAAAATC
* *
27849498 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGTCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTCTTTTAAA
* * *
27849563 TTTTTGTTTTCGAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGTCTCGAGTCATGCTGAG
66 TTTATGTTTTCGAAAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGTCTCGAGTCAAGCTGAG
27849628 GTATTTTCAATTT
131 GTATTTTCAATTT
27849641 CTGTTTGTCA
Statistics
Matches: 131, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
173 82 0.63
174 48 0.37
175 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (173 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTCTTTTAAA
TTTATGTTTTCGAAAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGTCTCGAGTCAAGCTGAG
GTATTTTCAATTTTTACTTTTCAAAAAAAAAAAACAAAAAATC
Found at i:27849579 original size:93 final size:90
Alignment explanation
Indices: 27849405--27849581 Score: 221
Period size: 93 Copynumber: 1.9 Consensus size: 90
27849395 GTTTTTGCAA
* *
27849405 AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTTGAGTCAAGTCGAGGTATTTTTCAATTTTT
1 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGAGTCAAGTCGAGGTATTTTTAAATTTTT
27849470 ACTTTTCAAAAAAAAAAAACAAAAAATC
66 ACTTTTC---AAAAAAAAACAAAAAATC
* *
27849498 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGTCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGAGTCA-A-GTCGAGGTA--T-TTTTAAA
* *
27849563 TTTTT-GTTTTCGAAAAAAA
61 TTTTTACTTTTCAAAAAAAA
27849582 TCAACTCATA
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
93 39 0.53
94 8 0.11
95 9 0.12
97 6 0.08
98 11 0.15
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (90 bp):
AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGAGTCAAGTCGAGGTATTTTTAAATTTTT
ACTTTTCAAAAAAAAACAAAAAATC
Found at i:27849785 original size:77 final size:77
Alignment explanation
Indices: 27849498--27849787 Score: 281
Period size: 77 Copynumber: 3.8 Consensus size: 77
27849488 ACAAAAAATC
* * * *
27849498 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGTCGAGGTATTTCTTTTAAA
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGTCGCATTTCGAGGTA-TT-TTTCAAA
*
27849563 TTTT-TGTTTTCGAAAA
64 TTTTGTTTTTTC---AA
* * * *
27849579 AAATCAACTCATAATGCGAGAGGTGAGTTGAGTCTCGAGT--CA-TGCTGAGGTA-TTTTC-AAT
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGTCGCATTTC-GAGGTATTTTTCAAAT
*
27849639 TTCTG-TTTGTCAA
65 TT-TGTTTTTTCAA
* * ***
27849652 AAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTTGGATCGCACACCGAGGTATTTTTCAAATT
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGTCGCATTTCGAGGTATTTTTCAAATT
27849717 TTGTTTTTTCAA
66 TTGTTTTTTCAA
* * * *
27849729 AGATCAACTCATAATCCGAGAGGTGAGTTGAG-CTTCGGGTTGCATTTCGAGCTATTTTT
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTT-GGGTCGCATTTCGAGGTATTTTT
27849788 GATTTCTGTT
Statistics
Matches: 173, Mismatches: 26, Indels: 24
0.78 0.12 0.11
Matches are distributed among these distances:
73 37 0.21
75 13 0.08
76 19 0.11
77 59 0.34
78 1 0.01
79 8 0.05
81 36 0.21
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (77 bp):
AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGTCGCATTTCGAGGTATTTTTCAAATT
TTGTTTTTTCAA
Found at i:27850042 original size:29 final size:29
Alignment explanation
Indices: 27849973--27850051 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
27849963 AAAAATTCAA
27849973 AAAATTACATTTTAGCCCCTAAACTTTCTC
1 AAAATTACATTTTAGCCCC-AAACTTTCTC
* *
27850003 AAAATTACATTTTAGCCCCATATTTTC-C
1 AAAATTACATTTTAGCCCCAAACTTTCTC
* *
27850031 TAAAATTGCATTTTTGCCCCA
1 -AAAATTACATTTTAGCCCCA
27850052 GAAACTTTGC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.02
29 24 0.55
30 19 0.43
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATTACATTTTAGCCCCAAACTTTCTC
Found at i:27850628 original size:11 final size:11
Alignment explanation
Indices: 27850612--27850685 Score: 69
Period size: 11 Copynumber: 6.4 Consensus size: 11
27850602 AGAGGAAAGT
27850612 AAAAAGAAGAA
1 AAAAAGAAGAA
27850623 AAAAAGAAAGAA
1 AAAAAG-AAGAA
27850635 CAAAAATTGAAAGAA
1 -AAAAA--G-AAGAA
*
27850650 AAATAGAAGAA
1 AAAAAGAAGAA
*
27850661 AAAAAAAAGAA
1 AAAAAGAAGAA
*
27850672 AGAAAGAA-AA
1 AAAAAGAAGAA
27850682 AAAA
1 AAAA
27850686 GGAAAAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
10 5 0.09
11 26 0.49
12 6 0.11
13 5 0.09
14 4 0.08
15 7 0.13
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.04
Consensus pattern (11 bp):
AAAAAGAAGAA
Found at i:27850634 original size:15 final size:14
Alignment explanation
Indices: 27850614--27850700 Score: 77
Period size: 15 Copynumber: 5.9 Consensus size: 14
27850604 AGGAAAGTAA
27850614 AAAGAAGAAAAAAAG
1 AAAGAA-AAAAAAAG
**
27850629 AAAGAACAAAAATTG
1 AAAGAA-AAAAAAAG
*
27850644 AAAGAAAAATAGAAG
1 AAAGAAAAA-AAAAG
*
27850659 AAAAAAAAAAGAAAG
1 AAAGAAAAAA-AAAG
*
27850674 AAAGAAAAAAAAGG
1 AAAGAAAAAAAAAG
27850688 AAA-AAATAAAAAA
1 AAAGAAA-AAAAAA
27850701 TAAAATAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
13 3 0.05
14 15 0.26
15 40 0.69
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.05
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:27850659 original size:26 final size:27
Alignment explanation
Indices: 27850612--27850698 Score: 88
Period size: 26 Copynumber: 3.2 Consensus size: 27
27850602 AGAGGAAAGT
*
27850612 AAAAAG-AAGAAAAAAAGAAAGAACAA
1 AAAAAGAAAGAAAAAAAGAAAGAAAAA
** *
27850638 AAATTGAAAGAAAAATAG-AAGAAAAA
1 AAAAAGAAAGAAAAAAAGAAAGAAAAA
*
27850664 AAAAAGAAAGAAAGAAAAAAAAGGAAAAA
1 AAAAAGAAAGAAA-AAAAGAAA-GAAAAA
27850693 ATAAAA
1 A-AAAA
27850699 AATAAAATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
26 22 0.46
27 13 0.27
28 2 0.04
29 7 0.15
30 4 0.08
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.05
Consensus pattern (27 bp):
AAAAAGAAAGAAAAAAAGAAAGAAAAA
Found at i:27850695 original size:41 final size:40
Alignment explanation
Indices: 27850615--27850692 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 40
27850605 GGAAAGTAAA
* *
27850615 AAGAAGAAAAAAAGAAAGAACAAAAATTGAAAGAAAAATAG
1 AAGAAAAAAAAAAGAAAGAACAAAAA-TAAAAGAAAAATAG
27850656 AAGAAAAAAAAAAGAAAGAA-AGAAAA-AAAAGGAAAAA
1 AAGAAAAAAAAAAGAAAGAACA-AAAATAAAA-GAAAAA
27850693 ATAAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
39 3 0.09
40 7 0.21
41 23 0.70
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.04
Consensus pattern (40 bp):
AAGAAAAAAAAAAGAAAGAACAAAAATAAAAGAAAAATAG
Found at i:27850873 original size:24 final size:23
Alignment explanation
Indices: 27850828--27850873 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
27850818 AAAAAAAAAA
* *
27850828 CAAAAAACAGCAGGCCTACAGCC
1 CAAAAAAAAGCAGGCCCACAGCC
27850851 CAAAAAAAAGCAGGCCCAGCAGC
1 CAAAAAAAAGCAGGCCCA-CAGC
27850874 AGGCCACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.46, C:0.33, G:0.20, T:0.02
Consensus pattern (23 bp):
CAAAAAAAAGCAGGCCCACAGCC
Found at i:27851569 original size:36 final size:35
Alignment explanation
Indices: 27851494--27851699 Score: 134
Period size: 36 Copynumber: 5.6 Consensus size: 35
27851484 ACCTCTTTTC
* *
27851494 AAAATTTTCGTGTTTTCAAAAAATTTATTG-TGTTT-A
1 AAAATTTTCGTG-TTTC-AAAAATTT-TCGTTTTTTAA
*
27851530 AAAATTTTCGTGTTTCAAGAATTTTCGTATTTTTAA
1 AAAATTTTCGTGTTTCAAAAATTTTCGT-TTTTTAA
* ***
27851566 AAAATTATCGTGTTT-AAAAATTTTTGCGTTATCAAAA
1 AAAATTTTCGTGTTTCAAAAA-TTTT-CGTT-TTTTAA
**
27851603 AAAATTTTCGTGTTTCAAAAATTTTCGGGTTTTCAAAAAA
1 AAAATTTTCGTGTTTCAAAAATTTTC--GTTTT---TTAA
* *
27851643 AAAAATTTCGTGTTTCAAAAAATTTT-GTGTTTTCAA
1 AAAATTTTCGTGTTTC-AAAAATTTTCGT-TTTTTAA
*
27851679 ACAAA-TTTCGTGTTTAAAAAA
1 A-AAATTTTCGTGTTTCAAAAA
27851700 GAAATTCTCG
Statistics
Matches: 141, Mismatches: 14, Indels: 31
0.76 0.08 0.17
Matches are distributed among these distances:
33 2 0.01
34 7 0.05
35 17 0.12
36 46 0.33
37 28 0.20
38 10 0.07
39 3 0.02
40 19 0.13
41 9 0.06
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (35 bp):
AAAATTTTCGTGTTTCAAAAATTTTCGTTTTTTAA
Found at i:27851579 original size:52 final size:52
Alignment explanation
Indices: 27851490--27851589 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
27851480 CGATACCTCT
* *
27851490 TTTCAAAATTTTCGTGTTTTCAAAAAATTTATTGTGTTTAAAAATTTTCGTG
1 TTTCAAAATTTTCGTATTTTCAAAAAATTTATCGTGTTTAAAAATTTTCGTG
*
27851542 TTTCAAGAATTTTCGTATTTTTAAAAAA-TTATCGTGTTTAAAAATTTT
1 TTTCAA-AATTTTCGTATTTTCAAAAAATTTATCGTGTTTAAAAATTTT
27851590 TGCGTTATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 25 0.57
53 19 0.43
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (52 bp):
TTTCAAAATTTTCGTATTTTCAAAAAATTTATCGTGTTTAAAAATTTTCGTG
Found at i:27851606 original size:21 final size:20
Alignment explanation
Indices: 27851581--27851664 Score: 66
Period size: 21 Copynumber: 4.2 Consensus size: 20
27851571 TATCGTGTTT
*
27851581 AAAAATTTTTGCGTTATCAAA
1 AAAAATTTTCGCGTT-TCAAA
*
27851602 AAAAATTTTCGTGTTTC---
1 AAAAATTTTCGCGTTTCAAA
*
27851619 AAAAATTTTCGGGTTTTCAAAAA
1 AAAAATTTTCGCG-TTTC--AAA
* *
27851642 AAAAAATTTCGTGTTTCAAA
1 AAAAATTTTCGCGTTTCAAA
27851662 AAA
1 AAA
27851665 TTTTGTGTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
17 12 0.23
18 4 0.08
20 8 0.15
21 13 0.25
22 4 0.08
23 11 0.21
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.37
Consensus pattern (20 bp):
AAAAATTTTCGCGTTTCAAA
Found at i:27851646 original size:23 final size:22
Alignment explanation
Indices: 27851619--27851664 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
27851609 TTCGTGTTTC
*
27851619 AAAAATTTTCGGGTTTTCAAAAA
1 AAAAAATTTCGGG-TTTCAAAAA
*
27851642 AAAAAATTTCGTGTTTCAAAAA
1 AAAAAATTTCGGGTTTCAAAAA
27851664 A
1 A
27851665 TTTTGTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.33
Consensus pattern (22 bp):
AAAAAATTTCGGGTTTCAAAAA
Found at i:27851654 original size:40 final size:39
Alignment explanation
Indices: 27851564--27851679 Score: 139
Period size: 40 Copynumber: 2.9 Consensus size: 39
27851554 TCGTATTTTT
*
27851564 AAAAAATTATCGTGTTT-AAAAATTTTTGCGTTATC--AAA
1 AAAAAATT-TCGTGTTTCAAAAA-TTTTGCGTTTTCAAAAA
* *
27851602 AAAAATTTTCGTGTTTCAAAAATTTTCGGGTTTTCAAAAA
1 AAAAAATTTCGTGTTTCAAAAATTTT-GCGTTTTCAAAAA
*
27851642 AAAAAATTTCGTGTTTCAAAAAATTTTGTGTTTTCAAA
1 AAAAAATTTCGTGTTTC-AAAAATTTTGCGTTTTCAAA
27851680 CAAATTTCGT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
37 12 0.18
38 18 0.26
40 29 0.43
41 9 0.13
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.41
Consensus pattern (39 bp):
AAAAAATTTCGTGTTTCAAAAATTTTGCGTTTTCAAAAA
Found at i:27851664 original size:17 final size:17
Alignment explanation
Indices: 27851490--27851699 Score: 122
Period size: 17 Copynumber: 11.6 Consensus size: 17
27851480 CGATACCTCT
*
27851490 TTTC-AAAATTTTCGTG
1 TTTCAAAAAATTTCGTG
*
27851506 TTTTCAAAAAATTTATTGTG
1 -TTTCAAAAAA-TT-TCGTG
*
27851526 TTT-AAAAATTTTCGTG
1 TTTCAAAAAATTTCGTG
* * *
27851542 TTTCAAGAATTTTCGTAT
1 TTTCAAAAAATTTCGT-G
*
27851560 TTTTAAAAAATTATCGTG
1 TTTCAAAAAATT-TCGTG
* * *
27851578 TTT-AAAAATTTTTGCG
1 TTTCAAAAAATTTCGTG
27851594 TTATCAAAAAAAATTTTCGTG
1 TT-TC--AAAAAA-TTTCGTG
* *
27851615 TTTCAAAAATTTTCGGG
1 TTTCAAAAAATTTCGTG
27851632 TTTTCAAAAAAAAAAATTTCGTG
1 -TTTC-----AAAAAATTTCGTG
*
27851655 TTTCAAAAAATTTTGTG
1 TTTCAAAAAATTTCGTG
27851672 TTTTCAAACAAATTTCGTG
1 -TTTCAAA-AAATTTCGTG
27851691 TTT-AAAAAA
1 TTTCAAAAAA
27851700 GAAATTCTCG
Statistics
Matches: 152, Mismatches: 22, Indels: 39
0.71 0.10 0.18
Matches are distributed among these distances:
16 15 0.10
17 46 0.30
18 40 0.26
19 18 0.12
20 11 0.07
21 7 0.05
22 4 0.03
23 11 0.07
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (17 bp):
TTTCAAAAAATTTCGTG
Done.