Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 17 of 172
Found at i:5456666 original size:19 final size:20
Alignment explanation
Indices: 5456613--5456667 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
5456603 AAAGTTGTAC
*
5456613 ATAAAAATTTATAAAAAGTTA
1 ATAAAAA-TAATAAAAAGTTA
* *
5456634 ATAAAAGTATTAAAAAGTT-
1 ATAAAAATAATAAAAAGTTA
5456653 ATAAAAATAATAAAA
1 ATAAAAATAATAAAA
5456668 TATATATAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 13 0.45
20 10 0.34
21 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
ATAAAAATAATAAAAAGTTA
Found at i:5457031 original size:18 final size:19
Alignment explanation
Indices: 5457010--5457047 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
5457000 TTTTATAAAA
*
5457010 TTTAATATTTTTATT-TTT
1 TTTAATAATTTTATTATTT
5457028 TTTAATAATTTTATTATTT
1 TTTAATAATTTTATTATTT
5457047 T
1 T
5457048 GTTACTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTAATAATTTTATTATTT
Found at i:5457514 original size:27 final size:27
Alignment explanation
Indices: 5457483--5457535 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
5457473 AGAAAAAAGA
5457483 ACTTTGATTCAATCCCTAATATCCTTG
1 ACTTTGATTCAATCCCTAATATCCTTG
5457510 ACTTTGATTCAATCCCTAATATCCTT
1 ACTTTGATTCAATCCCTAATATCCTT
5457536 ACATTATCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (27 bp):
ACTTTGATTCAATCCCTAATATCCTTG
Found at i:5467267 original size:2 final size:2
Alignment explanation
Indices: 5467260--5467284 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5467250 GACCAGCTGT
5467260 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5467285 TGGTGGTTAC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5473607 original size:25 final size:25
Alignment explanation
Indices: 5473579--5473632 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
5473569 GGCTGGACCA
* *
5473579 AACCGGTTGGGTCATCACTGGCCTG
1 AACCGATTGGGTCATCACAGGCCTG
**
5473604 AACCGATTGGGTTGTCACAGGCCTG
1 AACCGATTGGGTCATCACAGGCCTG
5473629 AACC
1 AACC
5473633 TAACCAGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.22
Consensus pattern (25 bp):
AACCGATTGGGTCATCACAGGCCTG
Found at i:5473928 original size:23 final size:23
Alignment explanation
Indices: 5473859--5473928 Score: 54
Period size: 24 Copynumber: 3.0 Consensus size: 23
5473849 TATTTTAATA
* *
5473859 AATTTAATATTAAATTAAATTTATT
1 AATTTAATATTAAAGT-GA-TTATT
* *
5473884 -ATTT-ATATTGATAGTGTTTTATT
1 AATTTAATATT-AAAGTG-ATTATT
5473907 AATTTAATATTAAAGTGATTAT
1 AATTTAATATTAAAGTGATTAT
5473929 GTTAATATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
23 14 0.40
24 16 0.46
25 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (23 bp):
AATTTAATATTAAAGTGATTATT
Found at i:5476819 original size:17 final size:17
Alignment explanation
Indices: 5476782--5476819 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5476772 TAGAATTGGG
*
5476782 TTAAGAAAATTATTTAA
1 TTAAGAAAATTAATTAA
*
5476799 TTAAGAAAATTAATTAT
1 TTAAGAAAATTAATTAA
5476816 TTAA
1 TTAA
5476820 ATTAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TTAAGAAAATTAATTAA
Found at i:5478095 original size:130 final size:130
Alignment explanation
Indices: 5477861--5478211 Score: 364
Period size: 130 Copynumber: 2.7 Consensus size: 130
5477851 AATTTTGAAG
* * * * * *
5477861 GGATATTTGATTATTTTAAAC-AATCGGGAAATTGCTACCCAACACGTTAGGGCATGATCCCGCG
1 GGATATTCGATTATTTTGAACAAAT-GCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCG
* * * * * * * * *
5477925 AATTGCCAAATATTACATATCGCCTTCGTTTTAGAGATTTTAAAAGACACGAGCAAAATTTTAAA
65 AATTGCCAAACATCAAATATCACCTTCATTTAAGAGATTTTAAAAAACACGAACAAAATTTCAAA
5477990 A
130 A
* * * *
5477991 TGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGACACAATTCCACGA
1 GGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGA
* * * * ** *
5478056 ATTGCCAAACATCAAATCTCATCTTCATTTAAG-GAATTTTAAAAAATATGAATGAAATTTCGAA
66 ATTGCCAAACATCAAATATCACCTTCATTTAAGAG-ATTTTAAAAAACACGAACAAAATTTCAAA
*
5478120 G
130 A
* * *
5478121 GGAAATTCGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGA
1 GGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGA
* * * *
5478186 ATCGCCGAACATCAAATTTCGCCTTC
66 ATTGCCAAACATCAAATATCACCTTC
5478212 GTTTTGAAGA
Statistics
Matches: 180, Mismatches: 39, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
129 1 0.01
130 176 0.98
131 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (130 bp):
GGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGA
ATTGCCAAACATCAAATATCACCTTCATTTAAGAGATTTTAAAAAACACGAACAAAATTTCAAAA
Found at i:5479013 original size:344 final size:344
Alignment explanation
Indices: 5478386--5479076 Score: 1382
Period size: 344 Copynumber: 2.0 Consensus size: 344
5478376 TAATAATTAA
5478386 AAAATAGCTAACCTAAAAGCGTAATCCGATGGCAATAATGTGTGGAGAATAATAATCATACCAGG
1 AAAATAGCTAACCTAAAAGCGTAATCCGATGGCAATAATGTGTGGAGAATAATAATCATACCAGG
5478451 ACAAAGATGATAATATAACAACCATTCAAGCAAAACAATACATACTATAACATGCCACAATAATA
66 ACAAAGATGATAATATAACAACCATTCAAGCAAAACAATACATACTATAACATGCCACAATAATA
5478516 TACAACACATGATATAGAATAACCAATACAAGATATAAAAATAATATAGCAATTAGAAACCAATG
131 TACAACACATGATATAGAATAACCAATACAAGATATAAAAATAATATAGCAATTAGAAACCAATG
5478581 CGCTATAAAATGATTCTAAAATAATAACGAATAAATGGACCTATATTTATGTTGACAAATTTTCA
196 CGCTATAAAATGATTCTAAAATAATAACGAATAAATGGACCTATATTTATGTTGACAAATTTTCA
5478646 TGAAAGCCATAGATAGCTATATGATTTTTTTTGAACATATATTATAGAATGAAAATTTGAATCAA
261 TGAAAGCCATAGATAGCTATATGATTTTTTTTGAACATATATTATAGAATGAAAATTTGAATCAA
5478711 ATTGCATGTAAAATGTTTT
326 ATTGCATGTAAAATGTTTT
5478730 AAAATAGCTAACCTAAAAGCGTAATCCGATGGCAATAATGTGTGGAGAATAATAATCATACCAGG
1 AAAATAGCTAACCTAAAAGCGTAATCCGATGGCAATAATGTGTGGAGAATAATAATCATACCAGG
5478795 ACAAAGATGATAATATAACAACCATTCAAGCAAAACAATACATACTATAACATGCCACAATAATA
66 ACAAAGATGATAATATAACAACCATTCAAGCAAAACAATACATACTATAACATGCCACAATAATA
5478860 TACAACACATGATATAGAATAACCAATACAAGATATAAAAATAATATAGCAATTAGAAACCAATG
131 TACAACACATGATATAGAATAACCAATACAAGATATAAAAATAATATAGCAATTAGAAACCAATG
5478925 CGCTATAAAATGATTCTAAAATAATAACGAATAAATGGACCTATATTTATGTTGACAAATTTTCA
196 CGCTATAAAATGATTCTAAAATAATAACGAATAAATGGACCTATATTTATGTTGACAAATTTTCA
5478990 TGAAAGCCATAGATAGCTATATGATTTTTTTTGAACATATATTATAGAATGAAAATTTGAATCAA
261 TGAAAGCCATAGATAGCTATATGATTTTTTTTGAACATATATTATAGAATGAAAATTTGAATCAA
5479055 ATTGCATGTAAAATGTTTT
326 ATTGCATGTAAAATGTTTT
5479074 AAA
1 AAA
5479077 CATGAATTTA
Statistics
Matches: 347, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
344 347 1.00
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (344 bp):
AAAATAGCTAACCTAAAAGCGTAATCCGATGGCAATAATGTGTGGAGAATAATAATCATACCAGG
ACAAAGATGATAATATAACAACCATTCAAGCAAAACAATACATACTATAACATGCCACAATAATA
TACAACACATGATATAGAATAACCAATACAAGATATAAAAATAATATAGCAATTAGAAACCAATG
CGCTATAAAATGATTCTAAAATAATAACGAATAAATGGACCTATATTTATGTTGACAAATTTTCA
TGAAAGCCATAGATAGCTATATGATTTTTTTTGAACATATATTATAGAATGAAAATTTGAATCAA
ATTGCATGTAAAATGTTTT
Found at i:5480676 original size:21 final size:20
Alignment explanation
Indices: 5480643--5480688 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5480633 CCTTTGCTAT
* *
5480643 TTTGCTGTTGTTTGTTTGTA
1 TTTGCTGTCGTTTGTATGTA
*
5480663 TTTGCTGTACGTTTGTATGTT
1 TTTGCTGT-CGTTTGTATGTA
5480684 TTTGC
1 TTTGC
5480689 AGGTACAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.07, C:0.09, G:0.24, T:0.61
Consensus pattern (20 bp):
TTTGCTGTCGTTTGTATGTA
Found at i:5481323 original size:28 final size:30
Alignment explanation
Indices: 5481273--5481329 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
5481263 CAATTTTTTA
*
5481273 AATATTTATATTATAATAATATATAATATT
1 AATATATATATTATAATAATATATAATATT
*
5481303 AATATATAT-TTATAA-ATTATATAATAT
1 AATATATATATTATAATAATATATAATAT
5481330 ATAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.44
29 6 0.24
30 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
AATATATATATTATAATAATATATAATATT
Found at i:5481337 original size:18 final size:18
Alignment explanation
Indices: 5481282--5481337 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
5481272 AAATATTTAT
*
5481282 ATTATAATAATATAT-AAT
1 ATTAT-ATAATATATAAAA
* *
5481300 ATTA-ATATATATTTATAA
1 ATTATATA-ATATATAAAA
5481318 ATTATATAATATATAAAA
1 ATTATATAATATATAAAA
5481336 AT
1 AT
5481338 AAAAAATTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 3 0.10
17 5 0.17
18 19 0.63
19 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTATATAATATATAAAA
Found at i:5483625 original size:20 final size:20
Alignment explanation
Indices: 5483580--5483626 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
5483570 TTAAATCAAG
5483580 TTTAAAATTATTATATTAAT
1 TTTAAAATTATTATATTAAT
** *
5483600 AATAAAATT-TTAATTTTAAT
1 TTTAAAATTATT-ATATTAAT
5483620 TTTAAAA
1 TTTAAAA
5483627 AATATTATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAAATTATTATATTAAT
Found at i:5483806 original size:13 final size:13
Alignment explanation
Indices: 5483788--5483812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5483778 GGGTATAGTA
5483788 AAATATTTAAAAT
1 AAATATTTAAAAT
5483801 AAATATTTAAAA
1 AAATATTTAAAA
5483813 AAAAGACACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATATTTAAAAT
Found at i:5484242 original size:17 final size:18
Alignment explanation
Indices: 5484216--5484259 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
5484206 ATTAAGTTTA
* *
5484216 TATAAGATATTA-ATTGT
1 TATAAAATATTATATTAT
*
5484233 TATAAAATATTATCTTAT
1 TATAAAATATTATATTAT
5484251 TATAAAATA
1 TATAAAATA
5484260 AATTTTGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (18 bp):
TATAAAATATTATATTAT
Found at i:5500015 original size:175 final size:179
Alignment explanation
Indices: 5499710--5500061 Score: 489
Period size: 175 Copynumber: 2.0 Consensus size: 179
5499700 CACTTGCCCC
* * * *
5499710 TTTGTTGATTACCAATCAAATAAGCAATTAGTAGAAGTTTTCATCAACATTATTGAACTTTATAT
1 TTTGTTGATTACCAATCAAATAAGCAATTAGTAGAAGTGTTCATCAAAATTATCGAAATTTATAT
* * * *
5499775 TGTGATGGAGGGGCATTGGAAATGGCCTATGTCTTAATGGAATATCACATCTGGTAGTAACTTTG
66 TGAGATGAAGGGGCATTGAAAATGGCC-ATGTCTTAATGGAATATCACATCAGGTAGTAACTTTG
5499840 CCACAAATTAAAATTAATCTCAT-AATAAGGCGCAACCTATAATTCACCA
130 CCACAAATTAAAATTAATCTCATAAATAAGGCGCAACCTATAATTCACCA
* *
5499889 TTTGTTGATTACCAATTAAATAAGCAATTAGT-GGAG-GTTCATCAAAATTATCGAAATTTATAT
1 TTTGTTGATTACCAATCAAATAAGCAATTAGTAGAAGTGTTCATCAAAATTATCGAAATTTATAT
* * *
5499952 TGAGATGAAGGGGTATTGAAAAATGG-C-TGTCTTAATGGAATATCACTTCAGTTAGTAACTTTG
66 TGAGATGAAGGGGCATTG-AAAATGGCCATGTCTTAATGGAATATCACATCAGGTAGTAACTTTG
* * * * *
5500015 CCACAGATTAAAATTGATCTCATAAATAAGGTGCAGCTTATAATTCA
130 CCACAAATTAAAATTAATCTCATAAATAAGGCGCAACCTATAATTCA
5500062 TCATAACAAT
Statistics
Matches: 153, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
175 54 0.35
176 20 0.13
177 39 0.25
178 9 0.06
179 31 0.20
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (179 bp):
TTTGTTGATTACCAATCAAATAAGCAATTAGTAGAAGTGTTCATCAAAATTATCGAAATTTATAT
TGAGATGAAGGGGCATTGAAAATGGCCATGTCTTAATGGAATATCACATCAGGTAGTAACTTTGC
CACAAATTAAAATTAATCTCATAAATAAGGCGCAACCTATAATTCACCA
Found at i:5500392 original size:17 final size:16
Alignment explanation
Indices: 5500370--5500413 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
5500360 AACGAAAAAA
*
5500370 GAAGAAGAAAGACAATG
1 GAAGAAGAAAGAC-AGG
*
5500387 GAAGAAGGAAAGGCAGG
1 GAAGAA-GAAAGACAGG
5500404 GAAGAAGAAA
1 GAAGAAGAAA
5500414 AACCGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.17
17 14 0.58
18 6 0.25
ACGTcount: A:0.57, C:0.05, G:0.36, T:0.02
Consensus pattern (16 bp):
GAAGAAGAAAGACAGG
Found at i:5503526 original size:3 final size:3
Alignment explanation
Indices: 5503518--5503547 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5503508 CTAATACTAG
5503518 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5503548 TGGCCAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5504346 original size:46 final size:46
Alignment explanation
Indices: 5504278--5504373 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
5504268 GGGTCTTGGC
*
5504278 TTTATTGAGTAGGGGATAGCATAAGTTCTTTGAGCTGAATCAACAT
1 TTTATTGAGTAGGGGATAGCATAAATTCTTTGAGCTGAATCAACAT
* * * *
5504324 TTTATTGTGTAGGGGTTTGCATAAATTCTTTGAGCTTAATCAACAT
1 TTTATTGAGTAGGGGATAGCATAAATTCTTTGAGCTGAATCAACAT
5504370 TTTA
1 TTTA
5504374 ATCTAGCTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (46 bp):
TTTATTGAGTAGGGGATAGCATAAATTCTTTGAGCTGAATCAACAT
Found at i:5505322 original size:31 final size:30
Alignment explanation
Indices: 5505214--5505322 Score: 89
Period size: 31 Copynumber: 3.6 Consensus size: 30
5505204 AAACGTAAAA
* *
5505214 CAAGTTTAGGTATTAAATTAAGAAAAAGTGT
1 CAAGTTTAGGTACTAAATTAAGAAAAAG-AT
* *
5505245 CAATTTTAGGTATTAAATTAA-AATAAA-A-
1 CAAGTTTAGGTACTAAATTAAGAA-AAAGAT
* * ** *
5505273 AAAGCTTAAATACCAAATTAAGAAAAAGCAT
1 CAAGTTTAGGTACTAAATTAAGAAAAAG-AT
5505304 CAAGTTTAGGTACTAAATT
1 CAAGTTTAGGTACTAAATT
5505323 GAGACAATAT
Statistics
Matches: 59, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
28 17 0.29
29 2 0.03
30 3 0.05
31 37 0.63
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (30 bp):
CAAGTTTAGGTACTAAATTAAGAAAAAGAT
Found at i:5508029 original size:12 final size:12
Alignment explanation
Indices: 5508012--5508053 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
5508002 TATGAAAATA
*
5508012 CATGTGGATTGC
1 CATGTGGGTTGC
5508024 CATGTGGGTTGC
1 CATGTGGGTTGC
*
5508036 CATGTGGGCTGC
1 CATGTGGGTTGC
5508048 CATGTG
1 CATGTG
5508054 ATGATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.12, C:0.19, G:0.38, T:0.31
Consensus pattern (12 bp):
CATGTGGGTTGC
Found at i:5510011 original size:10 final size:9
Alignment explanation
Indices: 5509977--5510022 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
5509967 TTATTTTTTG
*
5509977 AATTTTGAA
1 AATTTTTAA
5509986 AATTTTCTAA
1 AATTTT-TAA
*
5509996 TATTTTTAA
1 AATTTTTAA
5510005 AATTTTTAA
1 AATTTTTAA
5510014 AATTATTTA
1 AATT-TTTA
5510023 TTGACGTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 21 0.66
10 11 0.34
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (9 bp):
AATTTTTAA
Found at i:5510022 original size:19 final size:19
Alignment explanation
Indices: 5509977--5510022 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5509967 TTATTTTTTG
*
5509977 AATTTTGAAAATTTTCTAA
1 AATTTTTAAAATTTTCTAA
*
5509996 TATTTTTAAAATTTT-TAA
1 AATTTTTAAAATTTTCTAA
5510014 AATTATTTA
1 AATT-TTTA
5510023 TTGACGTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
AATTTTTAAAATTTTCTAA
Found at i:5530914 original size:22 final size:22
Alignment explanation
Indices: 5530889--5530934 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5530879 AAATATGAAT
5530889 ATTATTCC-AATTCAATAATTTA
1 ATTA-TCCTAATTCAATAATTTA
**
5530911 ATTATCCTTTTTCAATAATTTA
1 ATTATCCTAATTCAATAATTTA
5530933 AT
1 AT
5530935 ATACATCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTATCCTAATTCAATAATTTA
Found at i:5536757 original size:13 final size:13
Alignment explanation
Indices: 5536741--5536765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5536731 GAAATTTTTA
5536741 GCTTTTCAAAAGT
1 GCTTTTCAAAAGT
5536754 GCTTTTCAAAAG
1 GCTTTTCAAAAG
5536766 CACTTCTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GCTTTTCAAAAGT
Found at i:5537240 original size:13 final size:13
Alignment explanation
Indices: 5537224--5537284 Score: 86
Period size: 13 Copynumber: 4.7 Consensus size: 13
5537214 ACCAAATTTT
5537224 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
5537237 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* *
5537250 TCCACAGCACTTC
1 TCAAAAGCACTTC
*
5537263 TCAAAAGCACTTT
1 TCAAAAGCACTTC
5537276 TCAAAAGCA
1 TCAAAAGCA
5537285 TTGCCAAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.38, C:0.30, G:0.08, T:0.25
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:5537284 original size:26 final size:26
Alignment explanation
Indices: 5537221--5537284 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
5537211 TAAACCAAAT
5537221 TTTTCAAAAGCACTTCTCAAAAGCAC
1 TTTTCAAAAGCACTTCTCAAAAGCAC
* *
5537247 TTTTCCACAGCACTTCTCAAAAGCAC
1 TTTTCAAAAGCACTTCTCAAAAGCAC
5537273 TTTTCAAAAGCA
1 TTTTCAAAAGCA
5537285 TTGCCAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (26 bp):
TTTTCAAAAGCACTTCTCAAAAGCAC
Found at i:5537338 original size:33 final size:33
Alignment explanation
Indices: 5537301--5537366 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
5537291 AACTAGCCCT
5537301 AAAAGTACTAAGCCCAATGGAGGGCATTGATAA
1 AAAAGTACTAAGCCCAATGGAGGGCATTGATAA
5537334 AAAAGTACTAAGCCCAATGGAGGGCATTGATAA
1 AAAAGTACTAAGCCCAATGGAGGGCATTGATAA
5537367 CATATATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.18
Consensus pattern (33 bp):
AAAAGTACTAAGCCCAATGGAGGGCATTGATAA
Found at i:5549335 original size:77 final size:77
Alignment explanation
Indices: 5549208--5549361 Score: 299
Period size: 77 Copynumber: 2.0 Consensus size: 77
5549198 CAGCATGGTT
5549208 GAAGCTAATAATCTTGAACTCAAGCATGGATGGCAGATTGAATCCTTAGACCTAGCCAACAGAAC
1 GAAGCTAATAATCTTGAACTCAAGCATGGATGGCAGATTGAATCCTTAGACCTAGCCAACAGAAC
5549273 AACCCCAATTTC
66 AACCCCAATTTC
*
5549285 GAAGCTAATAATCTTGAGCTCAAGCATGGATGGCAGATTGAATCCTTAGACCTAGCCAACAGAAC
1 GAAGCTAATAATCTTGAACTCAAGCATGGATGGCAGATTGAATCCTTAGACCTAGCCAACAGAAC
5549350 AACCCCAATTTC
66 AACCCCAATTTC
5549362 AAACCGTCTA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.22
Consensus pattern (77 bp):
GAAGCTAATAATCTTGAACTCAAGCATGGATGGCAGATTGAATCCTTAGACCTAGCCAACAGAAC
AACCCCAATTTC
Found at i:5552153 original size:22 final size:20
Alignment explanation
Indices: 5552120--5552159 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
5552110 CCTTATTTTA
5552120 TAATTAAATTAAATTTAATT
1 TAATTAAATTAAATTTAATT
5552140 TAATTAATATTTAAATTTAA
1 TAATTAA-A-TTAAATTTAA
5552160 CTCAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATTAAATTAAATTTAATT
Found at i:5556969 original size:124 final size:124
Alignment explanation
Indices: 5556749--5556996 Score: 451
Period size: 124 Copynumber: 2.0 Consensus size: 124
5556739 TCTACCAAGC
5556749 AAAGCCTTAATGATTGAGAATAATCAAATTGATTAATGGTAAATAGAATTATACACTTCAAATTT
1 AAAGCCTTAATGATTGAGAATAATCAAATTGATTAATGGTAAATAGAATTATACACTTCAAATTT
*
5556814 CCATCTTATATAAAATATTAATGCATAAAATATTAATCTCAATGTTTTTTAAACCGGAT
66 CCATCCTATATAAAATATTAATGCATAAAATATTAATCTCAATGTTTTTTAAACCGGAT
* * * *
5556873 AAAGCCTTAGTGATTGGGAATAATCAAATTGATTGATGGTACATAGAATTATACACTTCAAATTT
1 AAAGCCTTAATGATTGAGAATAATCAAATTGATTAATGGTAAATAGAATTATACACTTCAAATTT
5556938 CCATCCTATATAAAATATTAATGCATAAAATATTAATCTCAATGTTTTTTAAACCGGAT
66 CCATCCTATATAAAATATTAATGCATAAAATATTAATCTCAATGTTTTTTAAACCGGAT
5556997 TGGTGGCCGA
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 119 1.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (124 bp):
AAAGCCTTAATGATTGAGAATAATCAAATTGATTAATGGTAAATAGAATTATACACTTCAAATTT
CCATCCTATATAAAATATTAATGCATAAAATATTAATCTCAATGTTTTTTAAACCGGAT
Found at i:5557393 original size:2 final size:2
Alignment explanation
Indices: 5557386--5557453 Score: 82
Period size: 2 Copynumber: 34.0 Consensus size: 2
5557376 AACACGTCTA
* * * *
5557386 TC TC TC TC TC TT TC TT TT TC TC TC TC TC TC TC TC TC TC TC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
5557428 TC TC TT TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
5557454 CCAAAATTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (2 bp):
TC
Found at i:5563438 original size:24 final size:24
Alignment explanation
Indices: 5563411--5563462 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5563401 TCTCTAGAAG
*
5563411 ATTTAATATTCATTAGTATAATAT
1 ATTTAACATTCATTAGTATAATAT
* *
5563435 ATTTAACATTTATTAGTATAATTT
1 ATTTAACATTCATTAGTATAATAT
5563459 ATTT
1 ATTT
5563463 GACCTACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (24 bp):
ATTTAACATTCATTAGTATAATAT
Found at i:5567351 original size:16 final size:15
Alignment explanation
Indices: 5567330--5567372 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
5567320 CAAATCATCA
5567330 AACTTTTATTTTTTTT
1 AACTTTT-TTTTTTTT
5567346 AACTTTTTTTTATTTT
1 AACTTTTTTTT-TTTT
5567362 --CTTTTTTTTTT
1 AACTTTTTTTTTT
5567373 GAATTATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.08
14 9 0.35
15 4 0.15
16 11 0.42
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (15 bp):
AACTTTTTTTTTTTT
Found at i:5574813 original size:35 final size:35
Alignment explanation
Indices: 5574767--5574837 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
5574757 ACGTCAGATC
5574767 AGCGTCGTGCCCACGACTCCAGCCGTGACAGAATA
1 AGCGTCGTGCCCACGACTCCAGCCGTGACAGAATA
*
5574802 AGCGTCGTGCCCACGGCTCCAGCCGTGACAGAATA
1 AGCGTCGTGCCCACGACTCCAGCCGTGACAGAATA
5574837 A
1 A
5574838 AAAGAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.25, C:0.34, G:0.27, T:0.14
Consensus pattern (35 bp):
AGCGTCGTGCCCACGACTCCAGCCGTGACAGAATA
Found at i:5575591 original size:10 final size:10
Alignment explanation
Indices: 5575563--5575662 Score: 60
Period size: 10 Copynumber: 9.4 Consensus size: 10
5575553 ATCATCAAAC
*
5575563 TTTTATTTTT
1 TTTTCTTTTT
*
5575573 TTTAACTTTTT
1 TTT-TCTTTTT
*
5575584 TTTTC-TTTC
1 TTTTCTTTTT
5575593 TTTTCTTTTT
1 TTTTCTTTTT
5575603 TTTTCGAATTATTT
1 TTTTC---TT-TTT
5575617 CTTCTTCTTTTT
1 -TT-TTCTTTTT
* *
5575629 TGTTGTTTTT
1 TTTTCTTTTT
5575639 TTTTGC-TTTT
1 TTTT-CTTTTT
*
5575649 TTGTCTTTTT
1 TTTTCTTTTT
5575659 TTTT
1 TTTT
5575663 GTGGAACATG
Statistics
Matches: 69, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
9 9 0.13
10 36 0.52
11 9 0.13
12 3 0.04
13 4 0.06
14 3 0.04
15 2 0.03
16 3 0.04
ACGTcount: A:0.06, C:0.10, G:0.05, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:5590594 original size:9 final size:9
Alignment explanation
Indices: 5590575--5590674 Score: 71
Period size: 9 Copynumber: 10.9 Consensus size: 9
5590565 ATTAAAAATC
5590575 ATAAAATTTT
1 ATAAAA-TTT
5590585 ATAAAATTT
1 ATAAAATTT
5590594 AT-AAATTT
1 ATAAAATTT
*
5590602 ATAAAAATT
1 ATAAAATTT
*
5590611 ATAAAA--A
1 ATAAAATTT
5590618 ATAAAATTT
1 ATAAAATTT
**
5590627 ATAAAAAGT
1 ATAAAATTT
*
5590636 ATTAGAAATTA
1 A-TA-AAATTT
* *
5590647 ATAAATAATC
1 ATAAA-ATTT
5590657 ATAAAATTTT
1 ATAAAA-TTT
5590667 ATAAAATT
1 ATAAAATT
5590675 AAGGGTAAAC
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
7 6 0.08
8 8 0.11
9 29 0.41
10 24 0.34
11 4 0.06
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (9 bp):
ATAAAATTT
Found at i:5590604 original size:17 final size:17
Alignment explanation
Indices: 5590582--5590631 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
5590572 ATCATAAAAT
5590582 TTTATAAAATTTATAAA
1 TTTATAAAATTTATAAA
*
5590599 TTTATAAAAATTATAAA
1 TTTATAAAATTTATAAA
**
5590616 -AAATAAAATTTATAAA
1 TTTATAAAATTTATAAA
5590632 AAGTATTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTATAAAATTTATAAA
Found at i:5590623 original size:16 final size:16
Alignment explanation
Indices: 5590602--5590633 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5590592 TTATAAATTT
5590602 ATAAAAATTATAAAAA
1 ATAAAAATTATAAAAA
*
5590618 ATAAAATTTATAAAAA
1 ATAAAAATTATAAAAA
5590634 GTATTAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAAAATTATAAAAA
Found at i:5594254 original size:144 final size:144
Alignment explanation
Indices: 5593981--5594245 Score: 341
Period size: 144 Copynumber: 1.8 Consensus size: 144
5593971 TACGCAGACA
* ** * * * * *
5593981 CCTTAGAGAAGAGAGATTTCTGAACGAGTCTGGCAAGGCTTCTATTTCATGAAACCCCCACATAG
1 CCTTAAAGAAGAGAGATTTCCCAACCACTCTGGAAAGGCTTCTATTCCATGAAACCCCAACATAG
* * * * * *
5594046 TCAAATCTTCAAGGGCAGTGGGGAGTTGGAGTTGGTGAGGAAGACTCTTTAGCTTTCCAAAACCA
66 TCAAATCTTCAAGGGCAGAGAGGAATTGAAGTTGGGGAGGAAGACTCTTAAGCTTTCCAAAACCA
5594111 CTTAAATATAGATG
131 CTTAAATATAGATG
* * * * *
5594125 CCTTAAAGAAGAGAGATTTCCCAACCACTCTGGAAAGGCTTCTATTCCTTGAAACTCTAATATCG
1 CCTTAAAGAAGAGAGATTTCCCAACCACTCTGGAAAGGCTTCTATTCCATGAAACCCCAACATAG
* *
5594190 TCAATTCTTCAAGGGCAGAGAGGAATTGAAGTTGGGGGGGAAGACTCTTAAGCTTT
66 TCAAATCTTCAAGGGCAGAGAGGAATTGAAGTTGGGGAGGAAGACTCTTAAGCTTT
5594246 TCCCAACCAG
Statistics
Matches: 100, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
144 100 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (144 bp):
CCTTAAAGAAGAGAGATTTCCCAACCACTCTGGAAAGGCTTCTATTCCATGAAACCCCAACATAG
TCAAATCTTCAAGGGCAGAGAGGAATTGAAGTTGGGGAGGAAGACTCTTAAGCTTTCCAAAACCA
CTTAAATATAGATG
Found at i:5594975 original size:210 final size:209
Alignment explanation
Indices: 5594613--5595285 Score: 997
Period size: 210 Copynumber: 3.2 Consensus size: 209
5594603 GGAAAACTCG
*
5594613 CCAATTCCTTGCAGCTATCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATCTGGAATC
1 CCAATTCGTTGCAGCTATCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATCTGGAATC
* * *
5594678 CAACTTAAATTAGAACAAAGATATAGATCTAATTCTTTAAGATAAGTGGAGGTAGATAATCCGTC
66 AAACTTAAATTAGAACAAAGATATAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTC
* *
5594743 TCCGATCTTGCTCATATTTTTGCAACTGGAAATTCTAAGCTTTTCAAGAGATGAACATCTTCCTG
131 TCCGATCTTGCTTATATTTTTGCAACTGGAAATTCTAAGCTTTTCAAGAGATGAACATCTTCCAG
5594808 TTATGGGAAGAACTT
196 TTAT-GGAAGAACTT
*
5594823 CCAATTCGTTGCAGCTATCAATTGATAGATTTTGAAGAGAGGAAAATCCTTCCAAATCTGGAATC
1 CCAATTCGTTGCAGCTATCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATCTGGAATC
*
5594888 AAACTTAAATTAGAACAAAGATATAGATATAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTC
66 AAACTTAAATTAGAACAAAGATATAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTC
*
5594953 TCCGATCTTGCTTATATTTTTGCAACTGGAAATTCTAAGCTTTTCAATAGATGAACATCTTCCAG
131 TCCGATCTTGCTTATATTTTTGCAACTGGAAATTCTAAGCTTTTCAAGAGATGAACATCTTCCAG
5595018 TTATTGGAAGAACTT
196 TTA-TGGAAGAACTT
* * * ** * *
5595033 CCAATTCATTGCACCTATTAATTGACAGGCTCTGAAGAGAGGAAAATCCTTCCAAATTTGGAATC
1 CCAATTCGTTGCAGCTATCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATCTGGAATC
* * ** * * * *
5595098 GAACTTAAATTAGGACAATTATATAGACCTAATTCTTTGAGACAAGCGCAGGCAGATAATCCGTC
66 AAACTTAAATTAGAACAAAGATATAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTC
* *** * *
5595163 TCCAATCTTGCTTA-ATTTTTCGCAACCAAAAATGCTAAGCTTTTCAAGAGATGAACACCTTCCA
131 TCCGATCTTGCTTATATTTTT-GCAACTGGAAATTCTAAGCTTTTCAAGAGATGAACATCTTCCA
* *
5595227 GGTAATGAAAGAACTT
195 -GTTATGGAAGAACTT
* *
5595243 CTAATTCGTTGCAACTATCAATTGACAGATTTTGAAGAGAGGA
1 CCAATTCGTTGCAGCTATCAATTGACAGATTTTGAAGAGAGGA
5595286 GGTAAATAAT
Statistics
Matches: 418, Mismatches: 42, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
209 6 0.01
210 408 0.98
211 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (209 bp):
CCAATTCGTTGCAGCTATCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATCTGGAATC
AAACTTAAATTAGAACAAAGATATAGATCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTC
TCCGATCTTGCTTATATTTTTGCAACTGGAAATTCTAAGCTTTTCAAGAGATGAACATCTTCCAG
TTATGGAAGAACTT
Found at i:5595404 original size:138 final size:138
Alignment explanation
Indices: 5595153--5595421 Score: 387
Period size: 138 Copynumber: 1.9 Consensus size: 138
5595143 GCGCAGGCAG
*
5595153 ATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAACCAAAAATGCTAAGCTTTTCAAGAGATGAA
1 ATAATCCATCTCCAATCTTGCTTAATTTTTCGCAACCAAAAATGCTAAGCTTTTCAAGAGATGAA
* *
5595218 CACCTTCCAGGTAATGAAAGAACTTCTAATTCGTTGCAACTATCAATTGACAG-ATTTTGAAGAG
66 CACCTTCCAGGTAACGAAAGAACTTCAAATTCGTTGCAACTATCAATTGACAGAATTTT-AAGAG
5595282 AGGAGGTAA
130 AGGAGGTAA
* ***
5595291 ATAATCCATCTCCGATCTTGCTTAATTTTTCGCAACTGGAAATGCTAAGCTTTTCAAGAGATGAA
1 ATAATCCATCTCCAATCTTGCTTAATTTTTCGCAACCAAAAATGCTAAGCTTTTCAAGAGATGAA
* * * * * * * *
5595356 CATCTTCCTGTTACCGGAAGAACTTCAAATTTGTTGCAGCTATTAATTGACAGAATTTTAAGAGA
66 CACCTTCCAGGTAACGAAAGAACTTCAAATTCGTTGCAACTATCAATTGACAGAATTTTAAGAGA
5595421 G
131 G
5595422 AAACATCCTT
Statistics
Matches: 115, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
138 110 0.96
139 5 0.04
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (138 bp):
ATAATCCATCTCCAATCTTGCTTAATTTTTCGCAACCAAAAATGCTAAGCTTTTCAAGAGATGAA
CACCTTCCAGGTAACGAAAGAACTTCAAATTCGTTGCAACTATCAATTGACAGAATTTTAAGAGA
GGAGGTAA
Found at i:5595589 original size:348 final size:348
Alignment explanation
Indices: 5594935--5595633 Score: 1021
Period size: 348 Copynumber: 2.0 Consensus size: 348
5594925 TGAGACAAGT
* * *
5594935 GGAGGTAGATAATCCGTCTCCGATCTTGCTTATATTTTTGCAACTGGAAATTCTAAGCTTTTCAA
1 GGAGGTAAATAATCCATCTCCGATCTTGCTTATATTTTTGCAACTGGAAATGCTAAGCTTTTCAA
* ** * **
5595000 TAGATGAACATCTTCCAGTTATTGGAAGAACTTCCAATTCATTGCACCTATTAATTGACAGGCTC
66 GAGATGAACATCTTCCAGTTACCGGAAGAACTTCAAATTCATTGCACCTATTAATTGACAGAATC
* * * * *
5595065 TGAAGAGAGGAAAATCCTTCCAAATTTGGAATCGAACTTAAATTAGGACAATTATATAGACCTAA
131 TGAAGAGAGGAAAATCCTTCCAAATCTGGAATCGAACTTAAATTAGAACAATGACATAGACATAA
* *
5595130 TTCTTTGAGACAAGCGCAGGCAGATAATCCGTCTCCAATCTTGCTTAATTTTTCGCAACCAAAAA
196 TTCTTTGAGACAAGCGCAGGCAAATAATCCGTCTCCAATCTTGCTTAATTTTTCACAACCAAAAA
* * *
5595195 TGCTAAGCTTTTCAAGAGATGAACACCTTCCAGGTAATGAAAGAACTTCTAATTCGTTGCAACTA
261 TCCTAAGCTTTTCAAGAGATGAACACCTTCCAGGTAATGAAAGAACTTCCAATTCCTTGCAACTA
5595260 TCAATTGACAGATTTTGAAGAGA
326 TCAATTGACAGATTTTGAAGAGA
5595283 GGAGGTAAATAATCCATCTCCGATCTTGCTTA-ATTTTTCGCAACTGGAAATGCTAAGCTTTTCA
1 GGAGGTAAATAATCCATCTCCGATCTTGCTTATATTTTT-GCAACTGGAAATGCTAAGCTTTTCA
* ** *
5595347 AGAGATGAACATCTTCCTGTTACCGGAAGAACTTCAAATTTGTTGCAGCTATTAATTGACAGAAT
65 AGAGATGAACATCTTCCAGTTACCGGAAGAACTTCAAATTCATTGCACCTATTAATTGACAGAAT
* * *
5595412 TTTAAGAGA-GAAACATCCTTCCAAATCTGGAATCGAACTTAAATTAGAACAATGACATAGATAT
130 CTGAAGAGAGGAAA-ATCCTTCCAAATCTGGAATCGAACTTAAATTAGAACAATGACATAGACAT
* * * *
5595476 AATTCTTTGAGACAAGTGGA-GCTAAATAATCCGTCTCCGATCTTGCTTAATTTTTCACAACCCA
194 AATTCTTTGAGACAAGCGCAGGC-AAATAATCCGTCTCCAATCTTGCTTAATTTTTCACAACCAA
* *
5595540 AAATCCTAAGCTTTTCAAGAGATGAACAACC-TCC-GGTTATAGGAAGAACTTCCAATTCCTTGC
258 AAATCCTAAGCTTTTCAAGAGATGAAC-ACCTTCCAGGTAAT-GAAAGAACTTCCAATTCCTTGC
*
5595603 AGCTATCAATTGACAGATTTTGAAGAGA
321 AACTATCAATTGACAGATTTTGAAGAGA
5595631 GGA
1 GGA
5595634 AAATCCTTCC
Statistics
Matches: 313, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
347 17 0.05
348 293 0.94
349 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (348 bp):
GGAGGTAAATAATCCATCTCCGATCTTGCTTATATTTTTGCAACTGGAAATGCTAAGCTTTTCAA
GAGATGAACATCTTCCAGTTACCGGAAGAACTTCAAATTCATTGCACCTATTAATTGACAGAATC
TGAAGAGAGGAAAATCCTTCCAAATCTGGAATCGAACTTAAATTAGAACAATGACATAGACATAA
TTCTTTGAGACAAGCGCAGGCAAATAATCCGTCTCCAATCTTGCTTAATTTTTCACAACCAAAAA
TCCTAAGCTTTTCAAGAGATGAACACCTTCCAGGTAATGAAAGAACTTCCAATTCCTTGCAACTA
TCAATTGACAGATTTTGAAGAGA
Found at i:5595663 original size:210 final size:210
Alignment explanation
Indices: 5595283--5595674 Score: 581
Period size: 210 Copynumber: 1.9 Consensus size: 210
5595273 TTTGAAGAGA
* * *** *
5595283 GGAGGTAAATAATCCATCTCCGATCTTGCTTAATTTTTCGCAACTGGAAATGCTAAGCTTTTCAA
1 GGAGCTAAATAATCCATCTCCGATCTTGCTTAATTTTTCACAACCCAAAATCCTAAGCTTTTCAA
* * * * ** *
5595348 GAGATGAACATCTTCCTGTTACCGGAAGAACTTCAAATTTGTTGCAGCTATTAATTGACAGAATT
66 GAGATGAACAACCTCCGGTTACAGGAAGAACTTCAAATTCCTTGCAGCTATCAATTGACAGAATT
* *
5595413 TTAAGAGAGAAACATCCTTCCAAATCTGGAATCGAACTTAAATTAGAACAATGACATAGATATAA
131 TTAAGAGAGAAACATCCTTCCAAATCCGGAATCCAACTTAAATTAGAACAATGACATAGATATAA
5595478 TTCTTTGAGACAAGT
196 TTCTTTGAGACAAGT
*
5595493 GGAGCTAAATAATCCGTCTCCGATCTTGCTTAATTTTTCACAACCCAAAATCCTAAGCTTTTCAA
1 GGAGCTAAATAATCCATCTCCGATCTTGCTTAATTTTTCACAACCCAAAATCCTAAGCTTTTCAA
* *
5595558 GAGATGAACAACCTCCGGTTATAGGAAGAACTTCCAATTCCTTGCAGCTATCAATTGACAG-ATT
66 GAGATGAACAACCTCCGGTTACAGGAAGAACTTCAAATTCCTTGCAGCTATCAATTGACAGAATT
*
5595622 TTGAAGAGAGGAAA-ATCCTTCCAAATCCGGAATCCAACTTAAATTAGGACAAT
131 TT-AAGAGA-GAAACATCCTTCCAAATCCGGAATCCAACTTAAATTAGAACAAT
5595675 CTTTTAAATC
Statistics
Matches: 161, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
209 5 0.03
210 152 0.94
211 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (210 bp):
GGAGCTAAATAATCCATCTCCGATCTTGCTTAATTTTTCACAACCCAAAATCCTAAGCTTTTCAA
GAGATGAACAACCTCCGGTTACAGGAAGAACTTCAAATTCCTTGCAGCTATCAATTGACAGAATT
TTAAGAGAGAAACATCCTTCCAAATCCGGAATCCAACTTAAATTAGAACAATGACATAGATATAA
TTCTTTGAGACAAGT
Found at i:5595763 original size:210 final size:210
Alignment explanation
Indices: 5595299--5595777 Score: 554
Period size: 210 Copynumber: 2.3 Consensus size: 210
5595289 AAATAATCCA
* * * * *
5595299 TCTCCGATCTTGCTTAATTTTTCGCAACTGGAAATGCTAAGCTTTTCAAGAGATGAACATCTTCC
1 TCTCCGATCTTGCTTAATTTTTCACACCTGGAAACGCTAAGCTTTTCAAGAGATGAACAACCTCC
* * ** *
5595364 TGTTACCGGAAGAACTTCAAATTTGTTGCAGCTATTAATTGACAGAATTTTAAGAGAGAAACATC
66 GGTTACAGGAAGAACTTCAAATTCCTTGCAGCTATCAATTGACAGAATTTTAAGAGAGAAACATC
* * * * * *
5595429 CTTCCAAATCTGGAATCGAACTTAAATTAGAACAATGACATAGATATAATTCTTTGAGACAAGTG
131 CTTCCAAATCCGGAATCCAACTTAAATTAGAACAATCACATAAATATAATTCCTTGAGACAAATG
* *
5595494 GAGCTAAATAATCCG
196 GAGCTAAACAACCCG
**
5595509 TCTCCGATCTTGCTTAATTTTTCACAACC-CAAAATC-CTAAGCTTTTCAAGAGATGAACAACCT
1 TCTCCGATCTTGCTTAATTTTTCAC-ACCTGGAAA-CGCTAAGCTTTTCAAGAGATGAACAACCT
* *
5595572 CCGGTTATAGGAAGAACTTCCAATTCCTTGCAGCTATCAATTGACAG-ATTTTGAAGAGAGGAAA
64 CCGGTTACAGGAAGAACTTCAAATTCCTTGCAGCTATCAATTGACAGAATTTT-AAGAGA-GAAA
* *** * *
5595636 -ATCCTTCCAAATCCGGAATCCAACTTAAATTAGGACAATCTTTTAAATCTAATTCCTTGAGATA
127 CATCCTTCCAAATCCGGAATCCAACTTAAATTAGAACAATCACATAAATATAATTCCTTGAGACA
* ** *
5595700 AATGGAGGTTGACAGCCCG
192 AATGGAGCTAAACAACCCG
* * * *
5595719 TCTCTGATCTTGCTTAATGTTTT-ACACCTGGAAACGCGAAGCTTTTTAAGAGAGGAACA
1 TCTCCGATCTTGCTTAAT-TTTTCACACCTGGAAACGCTAAGCTTTTCAAGAGATGAACA
5595778 TTGCCCCGTT
Statistics
Matches: 224, Mismatches: 38, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
209 9 0.04
210 205 0.92
211 10 0.04
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (210 bp):
TCTCCGATCTTGCTTAATTTTTCACACCTGGAAACGCTAAGCTTTTCAAGAGATGAACAACCTCC
GGTTACAGGAAGAACTTCAAATTCCTTGCAGCTATCAATTGACAGAATTTTAAGAGAGAAACATC
CTTCCAAATCCGGAATCCAACTTAAATTAGAACAATCACATAAATATAATTCCTTGAGACAAATG
GAGCTAAACAACCCG
Found at i:5597439 original size:24 final size:24
Alignment explanation
Indices: 5597407--5597455 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5597397 GAGGCCATCA
5597407 ATGCTCGTTCTTTAATTATGGACC
1 ATGCTCGTTCTTTAATTATGGACC
5597431 ATGCTCGTTCTTTAATTATGGACC
1 ATGCTCGTTCTTTAATTATGGACC
5597455 A
1 A
5597456 GCATTCTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.41
Consensus pattern (24 bp):
ATGCTCGTTCTTTAATTATGGACC
Found at i:5599425 original size:19 final size:20
Alignment explanation
Indices: 5599403--5599447 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
5599393 TTTAGTATCA
*
5599403 TTTTTTTATTTGTTTCT-TG
1 TTTTTATATTTGTTTCTATG
* *
5599422 TTTTAATATTTGTTTTTATG
1 TTTTTATATTTGTTTCTATG
5599442 TTTTTA
1 TTTTTA
5599448 AATGTATTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.13, C:0.02, G:0.09, T:0.76
Consensus pattern (20 bp):
TTTTTATATTTGTTTCTATG
Found at i:5599484 original size:13 final size:13
Alignment explanation
Indices: 5599466--5599505 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5599456 TGATTTATTA
5599466 TATTTAAAAAAAT
1 TATTTAAAAAAAT
*
5599479 TATTTAATAAAAT
1 TATTTAAAAAAAT
* *
5599492 AAGTTAAAAAAAT
1 TATTTAAAAAAAT
5599505 T
1 T
5599506 TAATATGGGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
TATTTAAAAAAAT
Found at i:5600549 original size:169 final size:166
Alignment explanation
Indices: 5600254--5600594 Score: 432
Period size: 169 Copynumber: 2.0 Consensus size: 166
5600244 TCGCCTGCAA
* * * *
5600254 TTTTTTCCCTCCCATCAACCATTTCTTTATTTCTTCTTCTCATTCACTGCACGTCTTCTCTCGTT
1 TTTTTCCCCTCCCATCAACCATTTCTTGATTTCTTCTTCTCATTCACTACACGTCTTCTCTAGTT
* * *
5600319 TCAATTTACAGATCTATATTGTGGGTATCTTTGTTATCTTCACAAGTTGTAATGGACAGATGACG
66 TCAATTTACAGATCTATATTGTAGGCATCTTTGTTATCTTCACAAGTTGTAATAGACAGATGAC-
*
5600384 GTGCATGTCATTCGCTAAAACTTCACCGGTCACCAATAG
130 G-GC-TGTCATTCGCTAAAACTCCACCGGTCACCAATAG
* * * * * *
5600423 TTTTTCCCCTCCTATTAACCATTTCTTGCTTTCTTCTTCTCATTTACTACTCGTCTTCTCTATTT
1 TTTTTCCCCTCCCATCAACCATTTCTTGATTTCTTCTTCTCATTCACTACACGTCTTCTCTAGTT
* * * * *
5600488 TC-ATCTTGCAGATCTATTTTGTAGGCATTTTTGTTGTCTTCACAAGTTGTGATAGACAGATGAC
66 TCAAT-TTACAGATCTATATTGTAGGCATCTTTGTTATCTTCACAAGTTGTAATAGACAGATGAC
** **
5600552 GGCTGTTGTTCGCTAAAACTCCGTCGGTCACCAATAG
130 GGCTGTCATTCGCTAAAACTCCACCGGTCACCAATAG
5600589 TTTTTC
1 TTTTTC
5600595 TTGGAAAGTG
Statistics
Matches: 148, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
166 35 0.24
167 2 0.01
168 3 0.02
169 108 0.73
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (166 bp):
TTTTTCCCCTCCCATCAACCATTTCTTGATTTCTTCTTCTCATTCACTACACGTCTTCTCTAGTT
TCAATTTACAGATCTATATTGTAGGCATCTTTGTTATCTTCACAAGTTGTAATAGACAGATGACG
GCTGTCATTCGCTAAAACTCCACCGGTCACCAATAG
Found at i:5602342 original size:20 final size:20
Alignment explanation
Indices: 5602304--5602343 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
5602294 AATTACATTC
5602304 AATTAAATAATAATTCAAAGA
1 AATTAAATAAT-ATTCAAAGA
5602325 AATTAAATTAAT-TTCAAAG
1 AATTAAA-TAATATTCAAAG
5602344 TCATTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
AATTAAATAATATTCAAAGA
Found at i:5618404 original size:13 final size:13
Alignment explanation
Indices: 5618386--5618424 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
5618376 TTTTAGTTAC
5618386 TAATAATATATTA
1 TAATAATATATTA
*
5618399 TAATAATTTATTTA
1 TAATAATATA-TTA
5618413 TATATAATATAT
1 TA-ATAATATAT
5618425 AAATATCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 6 0.27
15 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAATAATATATTA
Found at i:5619074 original size:77 final size:77
Alignment explanation
Indices: 5618944--5619120 Score: 234
Period size: 77 Copynumber: 2.3 Consensus size: 77
5618934 AGTGATACGT
* * * *
5618944 TGAATTGG-TATCGAGCCATGATATTAGCACTTCGGGTGCGTATATTACCGATTTGGCTTC-GGA
1 TGAATTGGCT-TCGGGCCATGATATCAACACTTCGGGTGCGTATATTACCGATTTGACTTCAGG-
5619007 CCATGCATATCGGA
64 CCATGCATATCGGA
* **
5619021 TGAATTGGCTTCGGGCCATGATATCAACACTTCGGGTGTGTATATTATTGATTTGACTTCAGGCC
1 TGAATTGGCTTCGGGCCATGATATCAACACTTCGGGTGCGTATATTACCGATTTGACTTCAGGCC
*
5619086 ATGCATATTGGA
66 ATGCATATCGGA
5619098 T-AATTTGGCTTCGGGCCATGATA
1 TGAA-TTGGCTTCGGGCCATGATA
5619121 ATAGTTCATC
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
76 2 0.02
77 84 0.94
78 3 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (77 bp):
TGAATTGGCTTCGGGCCATGATATCAACACTTCGGGTGCGTATATTACCGATTTGACTTCAGGCC
ATGCATATCGGA
Found at i:5621326 original size:29 final size:30
Alignment explanation
Indices: 5621267--5621324 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5621257 TCCGAGCCTT
*
5621267 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
5621297 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
5621325 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:5621554 original size:13 final size:13
Alignment explanation
Indices: 5621536--5621567 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5621526 TTTCCAGCAA
5621536 TTATGAATTTATT
1 TTATGAATTTATT
5621549 TTATGAATTTATT
1 TTATGAATTTATT
*
5621562 TGATGA
1 TTATGA
5621568 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:5621775 original size:50 final size:50
Alignment explanation
Indices: 5621662--5621903 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
5621652 ATTTGGGTAA
* * *
5621662 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
5621718 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
5621768 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
5621818 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
5621868 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
5621904 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:5621851 original size:100 final size:103
Alignment explanation
Indices: 5621662--5621911 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
5621652 ATTTGGGTAA
5621662 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
5621727 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
5621768 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
5621830 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
5621868 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
5621912 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:5631425 original size:26 final size:26
Alignment explanation
Indices: 5631396--5631448 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
5631386 TCAAACATGC
5631396 ATTTAGGTTAATTTAAC-CCTAGGGGT
1 ATTTAGG-TAATTTAACTCCTAGGGGT
* *
5631422 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAGGTAATTTAACTCCTAGGGGT
5631448 A
1 A
5631449 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.40
Consensus pattern (26 bp):
ATTTAGGTAATTTAACTCCTAGGGGT
Found at i:5634920 original size:14 final size:15
Alignment explanation
Indices: 5634901--5634929 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5634891 TAGTTTTACT
5634901 AAAGT-ACTAAAGTA
1 AAAGTAACTAAAGTA
5634915 AAAGTAACTAAAGTA
1 AAAGTAACTAAAGTA
5634930 CAGTTAACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.21
Consensus pattern (15 bp):
AAAGTAACTAAAGTA
Found at i:5635801 original size:34 final size:34
Alignment explanation
Indices: 5635751--5635874 Score: 133
Period size: 34 Copynumber: 3.6 Consensus size: 34
5635741 ACATATACAA
* * * *
5635751 ATATCATATCAGAATGTCACATTACTAGAAACAT
1 ATATCAGATCAAAATGTCATATTTCTAGAAACAT
*
5635785 ATATCAGATCAAAATGTCATATTTCCAGAAACAT
1 ATATCAGATCAAAATGTCATATTTCTAGAAACAT
* * * *
5635819 ATA-CTAGATTAGAATGTCATATTTTTAGAAGCAT
1 ATATC-AGATCAAAATGTCATATTTCTAGAAACAT
* *
5635853 ATTTCATATCAAAATGTCATAT
1 ATATCAGATCAAAATGTCATAT
5635875 CATATCAGAA
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
33 1 0.01
34 72 0.97
35 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (34 bp):
ATATCAGATCAAAATGTCATATTTCTAGAAACAT
Found at i:5639647 original size:16 final size:17
Alignment explanation
Indices: 5639626--5639660 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5639616 TGATATTTGG
5639626 ATGATTAAAAT-TTTTT
1 ATGATTAAAATATTTTT
*
5639642 ATGATTAAATTATTTTT
1 ATGATTAAAATATTTTT
5639659 AT
1 AT
5639661 TAAATATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
ATGATTAAAATATTTTT
Found at i:5643747 original size:47 final size:47
Alignment explanation
Indices: 5643499--5643870 Score: 226
Period size: 47 Copynumber: 7.9 Consensus size: 47
5643489 TGGGTTAAGT
* * *
5643499 TGCCGATGCCATGTCCCAGGCATGGTCTTACACTGGCTA-TCTTCATCGA
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGC-ACTCATC-TCTA
* * * * * *
5643548 GGCCGATGCCATGTCCCAGACATAGTCTTACACTAGCTCTCGTGTATA
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCACTCATCTCTA
* * ** *
5643596 CGTGCTGATG-CATGTCCCAGACATGTCTTACACTAGCACGAAGCT-TA
1 --TGCCGATGCCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTA
* * **
5643643 -GTCTATG-CATGTCCCAGACACATCTTACACTGGCTA-TCATCATCGT-
1 TGCCGATGCCATGTCCCAGACATGTCTTACACTGGC-ACTCATC-TC-TA
* * *
5643689 GGCCAAT-CCATGTCCCAGACATGTCTTACACTGGCACTCCTCTCTA
1 TGCCGATGCCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTA
* * * *
5643735 TGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTA-TGATAATGT-
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGC-ACTCAT-CTCTA
* * * * ** * ** *
5643783 GGCTGATG-CATGTCCTAGACATGTATTACACTATCCCTTGTCTCAA
1 TGCCGATGCCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTA
*
5643829 TGCCGATGCCATGTCCCAGACATGATCTTACACTGGCTCTCA
1 TGCCGATGCCATGTCCCAGACATG-TCTTACACTGGCACTCA
5643871 CATAACCCAA
Statistics
Matches: 246, Mismatches: 58, Indels: 39
0.72 0.17 0.11
Matches are distributed among these distances:
44 30 0.12
45 4 0.02
46 26 0.11
47 78 0.32
48 49 0.20
49 53 0.22
50 6 0.02
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (47 bp):
TGCCGATGCCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTA
Found at i:5643797 original size:94 final size:94
Alignment explanation
Indices: 5643503--5643866 Score: 319
Period size: 94 Copynumber: 3.9 Consensus size: 94
5643493 TTAAGTTGCC
* * * * *
5643503 GATGCCATGTCCCAGGCATGGTCTTACACTGGCTA-TCTTCATCGAGGCCGATGCCATGTCCCAG
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGC-ACTCATC-TCTATGCCGATGCCATGTCCCAG
* * * *
5643567 ACAT-AGTCTTACACTAGCTCTCGTGTATACGT-GCT
62 ACATGA-TCTTACACTGGCTAT-G-ATA-ATGTGGCT
** * * *
5643602 GATGCATGTCCCAGACATGTCTTACACTAGCACGAAGCT-TA-GTCTATG-CATGTCCCAGACA-
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAGACAT
* * * *
5643663 CATCTTACACTGGCTATCATCATCGTGGCC
66 GATCTTACACTGGCTATGATAAT-GTGGCT
* * * * *
5643693 AATCCATGTCCCAGACATGTCTTACACTGGCACTCCTCTCTATGCCGATGCCATGTCCTAGACAT
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAGACAT
*
5643758 GGTCTTACACTGGCTATGATAATGTGGCT
66 GATCTTACACTGGCTATGATAATGTGGCT
* * * * ** *
5643787 GATGCATGTCCTAGACATGTATTACACTATCCCTTGTCTCAATGCCGATGCCATGTCCCAGACAT
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAGACAT
5643852 GATCTTACACTGGCT
66 GATCTTACACTGGCT
5643867 CTCACATAAC
Statistics
Matches: 214, Mismatches: 43, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
89 1 0.00
90 3 0.01
91 34 0.16
92 15 0.07
93 19 0.09
94 90 0.42
95 20 0.09
96 2 0.01
97 13 0.06
98 13 0.06
99 4 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (94 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCTATGCCGATGCCATGTCCCAGACAT
GATCTTACACTGGCTATGATAATGTGGCT
Found at i:5643812 original size:141 final size:141
Alignment explanation
Indices: 5643503--5643814 Score: 339
Period size: 141 Copynumber: 2.2 Consensus size: 141
5643493 TTAAGTTGCC
* * *
5643503 GATGCCATGTCCCAGGCATGGTCTTACACTGGCTATCTTCATCGAGGCCGATGCCATGTCCCAGA
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCATCATCGAGGCCAATGCCATGTCCCAGA
* * * *
5643568 CATAGTCTTACACTAGCTCTCGTGTATACGTGCTGATGCATGTCCCAGACATGTCTTACACTAGC
64 CATAGTCTTACACTAGCACTCCTCTATAC-TGCCGATGCATGTCCCAGACATGTCTTACACTAGC
* *
5643633 ACGAAGCTTAGTCT
128 ACGAAGATTAGGCT
** *
5643647 -ATGCATGTCCCAGACACATCTTACACTGGCTATCATCATCGTGGCCAAT-CCATGTCCCAGACA
1 GATGCATGTCCCAGACATGTCTTACACTGGCTATCATCATCGAGGCCAATGCCATGTCCCAGACA
* * * *
5643710 T-GTCTTACACTGGCACTCCTCTCTA-TGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCT
66 TAGTCTTACACTAGCACTCCTCTATACTGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGC-
*
5643773 ATGATA-ATGT-GGCT
128 ACGA-AGAT-TAGGCT
* *
5643787 GATGCATGTCCTAGACATGTATTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
5643815 ATCCCTTGTC
Statistics
Matches: 141, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
137 7 0.05
138 13 0.09
139 31 0.22
140 22 0.16
141 53 0.38
142 12 0.09
143 3 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (141 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTATCATCATCGAGGCCAATGCCATGTCCCAGACA
TAGTCTTACACTAGCACTCCTCTATACTGCCGATGCATGTCCCAGACATGTCTTACACTAGCACG
AAGATTAGGCT
Found at i:5649863 original size:59 final size:62
Alignment explanation
Indices: 5649747--5649863 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 62
5649737 AAGTGATATC
* * * * *
5649747 TTAATATTAAATTTAATTTAATGTTTATTTTGTAGATAAATATTTTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATTCTGTAGATAAATATTATATTAATTTAATAAGAT
5649809 TTAATATTAAATTTAATCTAATATTTA-TCT-T-GATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATTCTGTAGATAAATATTATATTAATTTAATA
5649864 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 22 0.44
60 1 0.02
61 2 0.04
62 25 0.50
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (62 bp):
TTAATATTAAATTTAATCTAATATTTATTCTGTAGATAAATATTATATTAATTTAATAAGAT
Found at i:5650022 original size:26 final size:26
Alignment explanation
Indices: 5649972--5650021 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
5649962 AGTTGTAGAG
5649972 AGAAAATTCTCTAAAGAGATTTTTTC
1 AGAAAATTCTCTAAAGAGATTTTTTC
* *
5649998 AGAAAATT-TCTAGAGATATTTTTT
1 AGAAAATTCTCTAAAGAGATTTTTT
5650022 TAATTTACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTTTTTC
Found at i:5650691 original size:15 final size:15
Alignment explanation
Indices: 5650671--5650700 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5650661 TTCACTATTA
*
5650671 TGTCTTTTATATTTT
1 TGTCTTTCATATTTT
5650686 TGTCTTTCATATTTT
1 TGTCTTTCATATTTT
5650701 GCATAAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
TGTCTTTCATATTTT
Found at i:5652424 original size:62 final size:59
Alignment explanation
Indices: 5652358--5652475 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 59
5652348 AGGTGATTAT
* *
5652358 TTTAATATTAAATTTAATTTAATATTAATCTTGTAGATAAACATTCTATTAATTTAATAAGA
1 TTTAATATTAAATTTAATGTAATATTAATC-T-T-GATAAACATTATATTAATTTAATAAGA
* * *
5652420 TTTAATTTTAAATTTAATGTAATATTTATCTTGATAAATATTATATTAATTTAATA
1 TTTAATATTAAATTTAATGTAATATTAATCTTGATAAACATTATATTAATTTAATA
5652476 TTAAAGTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
59 22 0.43
60 1 0.02
61 1 0.02
62 27 0.53
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.50
Consensus pattern (59 bp):
TTTAATATTAAATTTAATGTAATATTAATCTTGATAAACATTATATTAATTTAATAAGA
Found at i:5654033 original size:10 final size:10
Alignment explanation
Indices: 5653995--5654036 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
5653985 TTTCAATTAG
* *
5653995 TTTCTAATAG
1 TTTCTAAAAT
*
5654005 TTTATAAAAT
1 TTTCTAAAAT
5654015 TTTCT-AAAT
1 TTTCTAAAAT
5654024 TTTCTAAAAT
1 TTTCTAAAAT
5654034 TTT
1 TTT
5654037 ATGATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (10 bp):
TTTCTAAAAT
Found at i:5654033 original size:19 final size:20
Alignment explanation
Indices: 5653995--5654036 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
5653985 TTTCAATTAG
5653995 TTTCTAATAGTTTATAAAAT
1 TTTCTAATAGTTTATAAAAT
* *
5654015 TTTCTAA-ATTTTCTAAAAT
1 TTTCTAATAGTTTATAAAAT
5654034 TTT
1 TTT
5654037 ATGATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTCTAATAGTTTATAAAAT
Found at i:5654078 original size:30 final size:28
Alignment explanation
Indices: 5654024--5654079 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
5654014 TTTTCTAAAT
* *
5654024 TTTCTAAAATTTTATGATTTTAAATTAA
1 TTTCTAAAATTTTATAAATTTAAATTAA
5654052 TTTCTAATAATTGTTATAAATTTAAATT
1 TTTCTAA-AATT-TTATAAATTTAAATT
5654080 TTTTTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 4 0.17
30 13 0.54
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (28 bp):
TTTCTAAAATTTTATAAATTTAAATTAA
Found at i:5654101 original size:30 final size:29
Alignment explanation
Indices: 5654067--5654144 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
5654057 AATAATTGTT
* *
5654067 ATAAATTTAAATTTTTTTTTATGATTTTAA
1 ATAAATTTAAA-TATTTTTTATAATTTTAA
* **
5654097 ATAAATTTCTAATATTTTTTATAATTTTTT
1 ATAAATTT-AAATATTTTTTATAATTTTAA
*
5654127 ATAAATTTATAAAATTTT
1 ATAAATTTA-AATATTTT
5654145 ATTCTTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 37 0.95
31 2 0.05
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (29 bp):
ATAAATTTAAATATTTTTTATAATTTTAA
Found at i:5654203 original size:108 final size:106
Alignment explanation
Indices: 5653995--5654201 Score: 272
Period size: 108 Copynumber: 1.9 Consensus size: 106
5653985 TTTCAATTAG
* *
5653995 TTTCTAATAGTTTATAAAATTTTCTAAATTTTCTAAAATTTTATGATTTTAAATTAATTTCTAAT
1 TTTCTAATAGTTTATAAAATTTTCTAAAATTTATAAAATTTTATGATTTTAAATTAATTTCTAAT
5654060 AATTGTTATAAATTTAAATTTTTTTTTATGATTTTAAATAAA
66 AATTGTTATAAATTT-AATTTTTTTTTATGATTTTAAATAAA
* * * * ** * *
5654102 TTTCTAATATTTTTTATAATTTTTTATAAATTTATAAAATTTTATTCTTTTTAATTAGTTTCTAA
1 TTTCTAATAGTTTATAAAATTTTCTA-AAATTTATAAAATTTTATGATTTTAAATTAATTTCTAA
* *
5654167 TAATTTTTATAAAATTT-ATTTTTTTTTATGTTTTT
65 TAATTGTTAT-AAATTTAATTTTTTTTTATGATTTT
5654202 TATACTTCTA
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
107 39 0.45
108 41 0.48
109 6 0.07
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (106 bp):
TTTCTAATAGTTTATAAAATTTTCTAAAATTTATAAAATTTTATGATTTTAAATTAATTTCTAAT
AATTGTTATAAATTTAATTTTTTTTTATGATTTTAAATAAA
Found at i:5654918 original size:24 final size:24
Alignment explanation
Indices: 5654891--5654944 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
5654881 ATTTTAACAT
* *
5654891 AAAAATATAAATTTCTGTTAATGA
1 AAAAAGATAAATTTCGGTTAATGA
* * *
5654915 AAAAGGGTAAATTTCGGTTAATGG
1 AAAAAGATAAATTTCGGTTAATGA
5654939 AAAAAG
1 AAAAAG
5654945 TTTGGTTGTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.19, T:0.30
Consensus pattern (24 bp):
AAAAAGATAAATTTCGGTTAATGA
Found at i:5660321 original size:22 final size:22
Alignment explanation
Indices: 5660296--5660340 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5660286 TTTAATAAAA
5660296 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
5660318 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
5660340 A
1 A
5660341 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:5664203 original size:22 final size:22
Alignment explanation
Indices: 5664178--5664222 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5664168 TTTAATAAAA
5664178 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
5664200 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
5664222 A
1 A
5664223 CACTTAGAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:5667201 original size:20 final size:20
Alignment explanation
Indices: 5667157--5667201 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5667147 GTTTGTGAAA
* *
5667157 ACATATGTGTATACATGCCT
1 ACATACGTGTATACATGCAT
* *
5667177 GCATACGTGTATGCATGCAT
1 ACATACGTGTATACATGCAT
5667197 ACATA
1 ACATA
5667202 TCCACAAATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (20 bp):
ACATACGTGTATACATGCAT
Found at i:5669282 original size:28 final size:28
Alignment explanation
Indices: 5669249--5669305 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
5669239 ACTATGCATC
5669249 CTTATCCTTTAGGATTTACAATAATTAT
1 CTTATCCTTTAGGATTTACAATAATTAT
5669277 CTTATCCTTTAGGATTTACAATAATTAT
1 CTTATCCTTTAGGATTTACAATAATTAT
5669305 C
1 C
5669306 CTGGTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.46
Consensus pattern (28 bp):
CTTATCCTTTAGGATTTACAATAATTAT
Found at i:5670072 original size:95 final size:95
Alignment explanation
Indices: 5669909--5670097 Score: 342
Period size: 95 Copynumber: 2.0 Consensus size: 95
5669899 TTGACTTCTC
*
5669909 TGTATTAGTCCAGAAGATTATTTGAGTTTTTTAGCATTCTCTTTATGTCTTGAGAAATATCCAAA
1 TGTATTAGTCCAGAAGATTATTTGAGTTTTTTAGCATTCGCTTTATGTCTTGAGAAATATCCAAA
*
5669974 TTGAGATAATACACTAAATATATTTGTTTT
66 TTGAGATAAGACACTAAATATATTTGTTTT
* *
5670004 TGTATTAGTCTAGAAGATTATTTGAGTTTTTTAGCATTCGCTTTATGTCTTGAGAGATATCCAAA
1 TGTATTAGTCCAGAAGATTATTTGAGTTTTTTAGCATTCGCTTTATGTCTTGAGAAATATCCAAA
5670069 TTGAGATAAGACACTAAATATATTTGTTT
66 TTGAGATAAGACACTAAATATATTTGTTT
5670098 GGTCAAGATT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.43
Consensus pattern (95 bp):
TGTATTAGTCCAGAAGATTATTTGAGTTTTTTAGCATTCGCTTTATGTCTTGAGAAATATCCAAA
TTGAGATAAGACACTAAATATATTTGTTTT
Found at i:5674423 original size:40 final size:40
Alignment explanation
Indices: 5674378--5674793 Score: 417
Period size: 40 Copynumber: 10.7 Consensus size: 40
5674368 GTGCTTATGA
* * *
5674378 TTGTAC-TCTGGTACCCCCGAATGCACATATGTGCTCCTAT
1 TTGTACTTC-GGTACCCCTGAATGCACATACGTGCTCCTGT
* * *
5674418 TTGTACTTCGGTACCCTTGAACGCATATACGTGCTCCT-T
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCTCCTGT
*
5674457 TTGTACTTCGGTACCACCTGAATGCACATACATGCTCCTGT
1 TTGTACTTCGGTACC-CCTGAATGCACATACGTGCTCCTGT
* * * *
5674498 TTGTACTTCGATACCCCTGAATGCAAAAAAGTGCTCCTGT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCTCCTGT
* * *
5674538 TTGTACTTCAGTACCCCTAAATACACATACGTGCTCCTGT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCTCCTGT
* * * *
5674578 TTGTACTTCGGTACCCTTGAACGCACATGCGTGCTCCTAT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCTCCTGT
* *
5674618 TTGTACTTTGGAACCCCTGAATGCACATACGTGCTCCTGT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCTCCTGT
** *
5674658 TTGTACTTCAATACCGCTGAATG--CATA---GCT--TGT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCTCCTGT
* *
5674691 TTGTACTTTGGTACCCCTGAATGCACATACATGCTCC---
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCTCCTGT
* * * * *
5674728 TTATACTTCGGTA-CCTTAAAATGCACATACGTACTCCTAT
1 TTGTACTTCGGTACCCCT-GAATGCACATACGTGCTCCTGT
** *
5674768 TTGTACTTCAATACCCTTGAATGCAC
1 TTGTACTTCGGTACCCCTGAATGCAC
5674794 TTGAGTGCCT
Statistics
Matches: 308, Mismatches: 53, Indels: 30
0.79 0.14 0.08
Matches are distributed among these distances:
33 22 0.07
35 7 0.02
36 3 0.01
37 27 0.09
38 7 0.02
39 16 0.05
40 205 0.67
41 21 0.07
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (40 bp):
TTGTACTTCGGTACCCCTGAATGCACATACGTGCTCCTGT
Found at i:5675998 original size:17 final size:17
Alignment explanation
Indices: 5675976--5676013 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
5675966 GTGTTACAAA
5675976 ATGTTTCTTGGATTATT
1 ATGTTTCTTGGATTATT
5675993 ATGTTTCTTGGATTATT
1 ATGTTTCTTGGATTATT
5676010 ATGT
1 ATGT
5676014 AATAGTCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.05, G:0.18, T:0.58
Consensus pattern (17 bp):
ATGTTTCTTGGATTATT
Found at i:5676986 original size:62 final size:57
Alignment explanation
Indices: 5676874--5677005 Score: 156
Period size: 62 Copynumber: 2.2 Consensus size: 57
5676864 ATCACTTTAA
* * * *
5676874 TATTAAATTAATATAATATTTATTAAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAA-C
* * *
5676932 TTATTAAAATAATAGAATGTTTATCTACAAGATAAACATTAAATTTAATTTAATATTAGAC
1 -TATTAAAATAATAGAATATTTAT-T--AAGATAAACATTAAATTAAATTTAATATTAAAC
5676993 TATTAAAATAATA
1 TATTAAAATAATA
5677006 TTATTTTTGG
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 20 0.32
60 14 0.22
61 1 0.02
62 28 0.44
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.42
Consensus pattern (57 bp):
TATTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAAC
Found at i:5677513 original size:13 final size:13
Alignment explanation
Indices: 5677495--5677520 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5677485 TATTTCAAGA
5677495 AAATTCTTTAATT
1 AAATTCTTTAATT
5677508 AAATTCTTTAATT
1 AAATTCTTTAATT
5677521 GAACAATTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
AAATTCTTTAATT
Found at i:5678620 original size:16 final size:16
Alignment explanation
Indices: 5678599--5678629 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5678589 CTATGCACAC
*
5678599 AAAATATAAAAGACAA
1 AAAATACAAAAGACAA
5678615 AAAATACAAAAGACA
1 AAAATACAAAAGACA
5678630 TAATAGTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAA
Found at i:5682668 original size:131 final size:131
Alignment explanation
Indices: 5682434--5682694 Score: 468
Period size: 131 Copynumber: 2.0 Consensus size: 131
5682424 TTGCAACCCA
* *
5682434 CAAACAGATTACTTGATATGAGTCCAAATCACCAAAAATTAAGTCCAAACTATCTCCAATCATTC
1 CAAACAGATTACTTGATATAAGTCCAAATCACCAAAAATTAAGTCCAAACTATCTCCAATCATCC
* *
5682499 CATAACATTTCTAAACATTTTTAGAACTTAAAATATATCAAAAGATCATTCAAAAATGTCATATA
66 CATAACATTTCTAAACATTTCTAGAACTTAAAATATATCAAAAGATCATTCAAAAATATCATATA
5682564 G
131 G
* *
5682565 CAAACATATTACTTGATATAAGTCCAAATCACCAAAAATTTAGTCCAAACTATCTCCAATCATCC
1 CAAACAGATTACTTGATATAAGTCCAAATCACCAAAAATTAAGTCCAAACTATCTCCAATCATCC
5682630 CATAACATTTCTAAACATTTCTAGAACTTAAAATATATCAAAAGATCATTCAAAAATATCATATA
66 CATAACATTTCTAAACATTTCTAGAACTTAAAATATATCAAAAGATCATTCAAAAATATCATATA
5682695 ACACACAATT
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 124 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (131 bp):
CAAACAGATTACTTGATATAAGTCCAAATCACCAAAAATTAAGTCCAAACTATCTCCAATCATCC
CATAACATTTCTAAACATTTCTAGAACTTAAAATATATCAAAAGATCATTCAAAAATATCATATA
G
Found at i:5686715 original size:86 final size:86
Alignment explanation
Indices: 5686570--5686732 Score: 265
Period size: 86 Copynumber: 1.9 Consensus size: 86
5686560 AAATAAAAAC
* * *
5686570 TGAAAATACCTCAATGTGTCTCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAA
1 TGAAAATACCTCAATGTATCTCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAA
5686635 ACAGAAATTAAAGACAGAAAT
66 ACAGAAATTAAAGACAGAAAT
* *
5686656 TGAAATTACCTCAGTGTATC-CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAA
1 TGAAAATACCTCAATGTATCTC-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAA
5686720 AACAGAAATTAAA
65 AACAGAAATTAAA
5686733 AGGCTCAACT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
85 1 0.01
86 70 0.99
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (86 bp):
TGAAAATACCTCAATGTATCTCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAA
ACAGAAATTAAAGACAGAAAT
Found at i:5686742 original size:54 final size:54
Alignment explanation
Indices: 5686679--5686786 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
5686669 GTGTATCCTG
5686679 AGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAAACAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAAACAGAAATTAAA
*
5686733 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAAACAGAAATTAAA
5686787 GACAGAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (54 bp):
AGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAAACAGAAATTAAA
Found at i:5687029 original size:54 final size:54
Alignment explanation
Indices: 5686947--5687050 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
5686937 ATGTGTCTCG
* *
5686947 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAATAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
5687001 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAT
5687051 GAAATTACCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (54 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
Found at i:5687115 original size:126 final size:127
Alignment explanation
Indices: 5686648--5687427 Score: 1104
Period size: 126 Copynumber: 6.1 Consensus size: 127
5686638 GAAATTAAAG
*
5686648 ACAGAAATTGAAATTACCTCAGTGTATCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATT
1 ACAGAAACTGAAATTACCTCAGTGTATCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATT
5686713 TTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
66 TTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
5686775 ACAGAAATTAAAGACAGAAATTGAAATTACCTCAGTGTATCCTGAGGCTCAACTCACCTCTCGCA
1 ACAG------AA-AC------TGAAATTACCTCAGTGTATCCTGAGGCTCAACTCACCTCTCGCA
*
5686840 ATATAAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATAAGTTGA
53 ATATAAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGA
5686905 TTTTTTGAAAA
118 -TTTTTGAAAA
* * * * * *
5686916 ATAAAAACTGAAAATACCTCAATGTGT-CTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 ACAGAAACTGAAATTACCTCAGTGTATCCT-GAGGCTCAACTCACCTCTCGCAATATAAGTTGAT
* *
5686980 TTTTTAAAAATAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
65 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
* *
5687043 ACAGAAA-TGAAATTACCTCAGCGTATCCTGAGGCTCAACTCACCTTTCGCAATATAAGTTGATT
1 ACAGAAACTGAAATTACCTCAGTGTATCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATT
5687107 TTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
66 TTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
* * *
5687169 ACAGAAA-TGAAATTAACTCAGCGTATCCTGAGGCTCAACTCACCTTTCGCAATATAAGTTGATT
1 ACAGAAACTGAAATTACCTCAGTGTATCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATT
* * *
5687233 TTTGAAAAACAGAAATTAAAAGGCTCAACTCACATCTCGCAATATAAGTTGATTTTTGAAAC
66 TTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
* * * * *
5687295 ATAAAAACTGAAAATACCTCCA-TGTGT-CTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 ACAGAAACTGAAATTACCT-CAGTGTATCCT-GAGGCTCAACTCACCTCTCGCAATATAAGTTGA
* * * * * *
5687358 TTTTTGAAAAATAGAAATTAAAATGCTCAACTCACTTCTCGCAATATGAGTCGATTTCTG-AGA
64 TTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
5687421 ACAGAAA
1 ACAGAAA
5687428 ACATCAAAAT
Statistics
Matches: 591, Mismatches: 43, Indels: 39
0.88 0.06 0.06
Matches are distributed among these distances:
126 243 0.41
127 120 0.20
128 101 0.17
133 2 0.00
134 3 0.01
135 2 0.00
140 108 0.18
141 12 0.02
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (127 bp):
ACAGAAACTGAAATTACCTCAGTGTATCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATT
TTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
Found at i:5687137 original size:54 final size:54
Alignment explanation
Indices: 5687073--5687176 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
5687063 GCGTATCCTG
*
5687073 AGGCTCAACTCACCTTTCGCAATATAAGTTGATTTTTGAAAAACAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAAACAGAAATTAAA
*
5687127 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAT
1 AGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAAACAGAAAT
5687177 GAAATTAACT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (54 bp):
AGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAAACAGAAATTAAA
Found at i:5703188 original size:106 final size:105
Alignment explanation
Indices: 5702886--5703192 Score: 508
Period size: 105 Copynumber: 2.9 Consensus size: 105
5702876 CCTTAGATAC
** *
5702886 ATCTTAATTTTAGTTTTGAGACTTTAGGCAATAAGTAACTAACCAACCTAACTTAAATGATTAGT
1 ATCTTAATTTT--TTTTGAGACTTTAGGCAATAAGCGACTAACCAACCTAACTCAAATGATTAGT
*
5702951 GGCAACTCTACTCATATGGGTTCTATGTCTAGCTTAAGGAAT
64 GGCGACTCTACTCATATGGGTTCTATGTCTAGCTTAAGGAAT
5702993 ATCTTAATTTATTTTTGAGACTTTAGGCAATAA-CGACTAACCAACCTAACTCAAATGATTAGTG
1 ATCTTAATTT-TTTTTGAGACTTTAGGCAATAAGCGACTAACCAACCTAACTCAAATGATTAGTG
*
5703057 GCGACTCTACTCATATGGATTCTATGTCTAGCTTAAGGAAT
65 GCGACTCTACTCATATGGGTTCTATGTCTAGCTTAAGGAAT
* *
5703098 ATCTTAATTTGTTTTTGAGACTTTAGGCAATAAGCGACTAACCAACCTAACTCAAATTATTAGCG
1 ATCTTAATTT-TTTTTGAGACTTTAGGCAATAAGCGACTAACCAACCTAACTCAAATGATTAGTG
5703163 GCGACTCTACTCATATGGGTTCTATGTCTA
65 GCGACTCTACTCATATGGGTTCTATGTCTA
5703193 ACTTGTTAAG
Statistics
Matches: 189, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
105 99 0.52
106 79 0.42
107 10 0.05
108 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (105 bp):
ATCTTAATTTTTTTTGAGACTTTAGGCAATAAGCGACTAACCAACCTAACTCAAATGATTAGTGG
CGACTCTACTCATATGGGTTCTATGTCTAGCTTAAGGAAT
Found at i:5709841 original size:14 final size:14
Alignment explanation
Indices: 5709822--5709869 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
5709812 AATCATTAAA
5709822 TTATTTGAAAGTTT
1 TTATTTGAAAGTTT
*
5709836 TTATTT-AAA-TTAAA
1 TTATTTGAAAGTT--T
5709850 TTATTTGAAAGTTT
1 TTATTTGAAAGTTT
5709864 TTATTT
1 TTATTT
5709870 AAATCACTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 2 0.07
13 3 0.11
14 18 0.64
15 3 0.11
16 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (14 bp):
TTATTTGAAAGTTT
Found at i:5709854 original size:28 final size:28
Alignment explanation
Indices: 5709816--5709873 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
5709806 TAATTTAATC
5709816 ATTAAATTATTTGAAAGTTTTTATTTAA
1 ATTAAATTATTTGAAAGTTTTTATTTAA
5709844 ATTAAATTATTTGAAAGTTTTTATTTAA
1 ATTAAATTATTTGAAAGTTTTTATTTAA
5709872 AT
1 AT
5709874 CACTGAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (28 bp):
ATTAAATTATTTGAAAGTTTTTATTTAA
Found at i:5716944 original size:54 final size:54
Alignment explanation
Indices: 5716878--5716985 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
5716868 TATTGTAGGC
*
5716878 GTTTAGCTATTGTCAACTAAGGTTCCGACACATAAAGCATATGTTTCGGAACTT
1 GTTTAGCTATTGTCAACTAAGGTTCCAACACATAAAGCATATGTTTCGGAACTT
5716932 GTTTAGCTATTGTCAACTAAGGTTCCAACACATAAAGCATATGTTTCGGAACTT
1 GTTTAGCTATTGTCAACTAAGGTTCCAACACATAAAGCATATGTTTCGGAACTT
5716986 ATATCCTTGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (54 bp):
GTTTAGCTATTGTCAACTAAGGTTCCAACACATAAAGCATATGTTTCGGAACTT
Found at i:5719662 original size:19 final size:19
Alignment explanation
Indices: 5719638--5719675 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5719628 TTTTTTTTAC
5719638 AAAATTAT-TAAGATTTCTT
1 AAAATTATCTAA-ATTTCTT
*
5719657 AAAATTTTCTAAATTTCTT
1 AAAATTATCTAAATTTCTT
5719676 TGAAAGTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (19 bp):
AAAATTATCTAAATTTCTT
Found at i:5726381 original size:23 final size:23
Alignment explanation
Indices: 5726350--5726439 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 23
5726340 GGCTTTGCCG
*
5726350 ATCAAGCACTTTATGTGTCATAT
1 ATCAGGCACTTTATGTGTCATAT
*
5726373 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCATAT
* * * **
5726396 TTTAGGCACCTCGTGTGTCAT-T
1 ATCAGGCACTTTATGTGTCATAT
* *
5726418 -TTAGGCAC-TTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCATAT
5726439 A
1 A
5726440 CTAATCATGT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
20 8 0.15
21 9 0.17
22 1 0.02
23 36 0.67
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCATAT
Found at i:5731042 original size:21 final size:22
Alignment explanation
Indices: 5731008--5731048 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5730998 AATAAAAGCT
5731008 TTCAATGAAAATTTT-TAATAG
1 TTCAATGAAAATTTTGTAATAG
**
5731029 TTCAATGATCATTTTGTAAT
1 TTCAATGAAAATTTTGTAAT
5731049 TTTTTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (22 bp):
TTCAATGAAAATTTTGTAATAG
Found at i:5733092 original size:17 final size:16
Alignment explanation
Indices: 5733070--5733102 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
5733060 AAAAATTGTG
5733070 ATAATTATACATTTAAA
1 ATAATTATA-ATTTAAA
5733087 ATAATTATAATTTAAA
1 ATAATTATAATTTAAA
5733103 CTGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATTATAATTTAAA
Found at i:5735537 original size:16 final size:15
Alignment explanation
Indices: 5735499--5735538 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
5735489 GTGCCCCACT
*
5735499 TACTCTTTGGAAGCA
1 TACTCCTTGGAAGCA
5735514 TACTCCTTGGAAGCA
1 TACTCCTTGGAAGCA
5735529 TACCTCCTTG
1 TA-CTCCTTG
5735539 ACTTAACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.33
Consensus pattern (15 bp):
TACTCCTTGGAAGCA
Found at i:5737247 original size:15 final size:15
Alignment explanation
Indices: 5737223--5737257 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
5737213 ATCAATTTTA
5737223 AAAAATTATAAATTAT
1 AAAAATTATAAA-TAT
5737239 AAAAA-TATAAATAT
1 AAAAATTATAAATAT
5737253 AAAAA
1 AAAAA
5737258 ATTCAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
15 6 0.32
16 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATTATAAATAT
Found at i:5737258 original size:15 final size:14
Alignment explanation
Indices: 5737220--5737259 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 14
5737210 TATATCAATT
5737220 TTAAAAAATTATAAA
1 TTAAAAAA-TATAAA
5737235 TTATAAAAATATAAA
1 TTA-AAAAATATAAA
5737250 TATAAAAAAT
1 T-TAAAAAAT
5737260 TCAGAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAAAATATAAA
Found at i:5738179 original size:14 final size:15
Alignment explanation
Indices: 5738157--5738189 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5738147 ACAAAAAAAT
5738157 TTAAAATTAT-TTTA
1 TTAAAATTATCTTTA
*
5738171 TTAATATTATCTTTA
1 TTAAAATTATCTTTA
5738186 TTAA
1 TTAA
5738190 CACTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAAATTATCTTTA
Found at i:5738599 original size:9 final size:9
Alignment explanation
Indices: 5738577--5738645 Score: 57
Period size: 9 Copynumber: 7.0 Consensus size: 9
5738567 ATTATTTTAT
5738577 TTTTTTAAA
1 TTTTTTAAA
* *
5738586 ATTTTTAAC
1 TTTTTTAAA
5738595 TTTTTTATATA
1 TTTTTTA-A-A
5738606 TTTTTTAAGAA
1 TTTTTT-A-AA
*
5738617 TTTTTTAAT
1 TTTTTTAAA
5738626 TTCTTTTATAA
1 TT-TTTTA-AA
5738637 TTTTTTAAA
1 TTTTTTAAA
5738646 AAACATAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
9 18 0.38
10 12 0.25
11 16 0.33
12 2 0.04
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:5738610 original size:30 final size:32
Alignment explanation
Indices: 5738574--5738647 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
5738564 ATTATTATTT
5738574 TATTTTTTTAAAA-TTTTTAACTT-TTTTATA
1 TATTTTTTTAAAATTTTTTAACTTCTTTTATA
*
5738604 TA-TTTTTTAAGAATTTTTTAATTTCTTTTATA
1 TATTTTTTTAA-AATTTTTTAACTTCTTTTATA
*
5738636 -ATTTTTTAAAAA
1 TATTTTTTTAAAA
5738648 ACATAATTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 8 0.21
30 4 0.11
31 12 0.32
32 14 0.37
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (32 bp):
TATTTTTTTAAAATTTTTTAACTTCTTTTATA
Found at i:5738622 original size:31 final size:29
Alignment explanation
Indices: 5738577--5738646 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 29
5738567 ATTATTTTAT
5738577 TTTTTTAAAATTTTTAACTT-TTTTATATA
1 TTTTTTAAAATTTTTAACTTCTTTTATA-A
*
5738606 TTTTTTAAGAATTTTTTAATTTCTTTTATAA
1 TTTTTTAA-AA-TTTTTAACTTCTTTTATAA
5738637 TTTTTTAAAA
1 TTTTTTAAAA
5738647 AACATAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 8 0.22
30 4 0.11
31 18 0.49
32 7 0.19
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (29 bp):
TTTTTTAAAATTTTTAACTTCTTTTATAA
Found at i:5741090 original size:27 final size:27
Alignment explanation
Indices: 5741030--5741084 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
5741020 AATTCAAGAG
5741030 ATAGACACCGTTTTCTCATAAAGTTGT
1 ATAGACACCGTTTTCTCATAAAGTTGT
*
5741057 ATAGACACCGTTTTCTTATAAAGTTGT
1 ATAGACACCGTTTTCTCATAAAGTTGT
5741084 A
1 A
5741085 CTGACATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (27 bp):
ATAGACACCGTTTTCTCATAAAGTTGT
Found at i:5745503 original size:386 final size:387
Alignment explanation
Indices: 5744751--5745518 Score: 1520
Period size: 386 Copynumber: 2.0 Consensus size: 387
5744741 TCCAAGCCCC
5744751 GTTTTTAATGATCTTTACGTTTTTTAAGTCCCGGTAGCTCGATAAAGCTTATGCTAGCAATAATT
1 GTTTTTAATGATCTTTACGTTTTTTAAGTCCCGGTAGCTCGATAAAGCTTATGCTAGCAATAATT
5744816 TAAGTTAGGAATCAAATTTGGAAAAATACCCATAGGTGAAATTTGTGTATTTTGATGTTTTATGA
66 TAAGTTAGGAATCAAATTTGGAAAAATACCCATAGGTGAAATTTGTGTATTTTGATGTTTTATGA
5744881 TGGAATATGAGGCTTTAAATTATGTTAGACAACTTGTGCTACTTGGTTTTAAGTGAAAACGAGTA
131 TGGAATATGAGGCTTTAAATTATGTTAGACAACTTGTGCTACTTGGTTTTAAGTGAAAACGAGTA
5744946 AAAAGGCTTAATCGGTAAAAATACCTAATAGTCATAAGTACATGTTAGTGTGTGAATTTGATGTT
196 AAAAGGCTTAATCGGTAAAAATACCTAATAGTCATAAGTACATGTTAGTGTGTGAATTTGATGTT
5745011 GTCATAGAAGGGAAAAATGATCAGTATGTCATAAAACATAAGAAAATAGGATGAAGTTTAATTTA
261 GTCATAGAAGGGAAAAATGATCAGTATGTCATAAAACATAAGAAAATAGGATGAAGTTTAATTTA
5745076 CGAGCCTTGGGGCAAAAGTGCAAATATGTGAAAGTTTAGGGGCAAAAATGTGATTTTGCCAT
326 CGAGCCTTGGGGCAAAAGTGCAAATATGTGAAAGTTTAGGGGCAAAAATGTGATTTTGCCAT
*
5745138 GTTTTTAATGATCTTTACGTTTTTTAAGTCCTGGTAGC-CGATAAAGCTTATGCTAGCAATAATT
1 GTTTTTAATGATCTTTACGTTTTTTAAGTCCCGGTAGCTCGATAAAGCTTATGCTAGCAATAATT
5745202 TAAGTTAGGAATCAAATTTGGAAAAATACCCATAGGTGAAATTTGTGTATTTTGATGTTTTATGA
66 TAAGTTAGGAATCAAATTTGGAAAAATACCCATAGGTGAAATTTGTGTATTTTGATGTTTTATGA
5745267 TGGAATATGAGGCTTTAAATTATGTTAGACAACTTGTGCTACTTGGTTTTAAGTGAAAACGAGTA
131 TGGAATATGAGGCTTTAAATTATGTTAGACAACTTGTGCTACTTGGTTTTAAGTGAAAACGAGTA
5745332 AAAAGGCTTAATCGGTAAAAATACCTAATAGTCATAAGTACATGTTAGTGTGTGAATTTGATGTT
196 AAAAGGCTTAATCGGTAAAAATACCTAATAGTCATAAGTACATGTTAGTGTGTGAATTTGATGTT
5745397 GTCATAGAAGGGAAAAATGATCAGTATGTCATAAAACATAAGAAAATAGGATGAAGTTTAATTTA
261 GTCATAGAAGGGAAAAATGATCAGTATGTCATAAAACATAAGAAAATAGGATGAAGTTTAATTTA
5745462 CGAGCCTTGGGGCAAAAGTGCAAATATGTGAAAGTTTAGGGGCAAAAATGTGATTTT
326 CGAGCCTTGGGGCAAAAGTGCAAATATGTGAAAGTTTAGGGGCAAAAATGTGATTTT
5745519 TCCAAAGTTT
Statistics
Matches: 380, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
386 343 0.90
387 37 0.10
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.34
Consensus pattern (387 bp):
GTTTTTAATGATCTTTACGTTTTTTAAGTCCCGGTAGCTCGATAAAGCTTATGCTAGCAATAATT
TAAGTTAGGAATCAAATTTGGAAAAATACCCATAGGTGAAATTTGTGTATTTTGATGTTTTATGA
TGGAATATGAGGCTTTAAATTATGTTAGACAACTTGTGCTACTTGGTTTTAAGTGAAAACGAGTA
AAAAGGCTTAATCGGTAAAAATACCTAATAGTCATAAGTACATGTTAGTGTGTGAATTTGATGTT
GTCATAGAAGGGAAAAATGATCAGTATGTCATAAAACATAAGAAAATAGGATGAAGTTTAATTTA
CGAGCCTTGGGGCAAAAGTGCAAATATGTGAAAGTTTAGGGGCAAAAATGTGATTTTGCCAT
Found at i:5745919 original size:46 final size:44
Alignment explanation
Indices: 5745860--5745974 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
5745850 ACAGGACAGA
* *
5745860 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
5745906 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
5745950 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
5745975 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:5745955 original size:44 final size:45
Alignment explanation
Indices: 5745860--5745993 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
5745850 ACAGGACAGA
* *
5745860 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
5745906 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
5745950 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
5745994 CAGGGTATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:5747145 original size:31 final size:29
Alignment explanation
Indices: 5747107--5747176 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
5747097 ATCCCAAAAC
*
5747107 TATACATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTATGATTT--TGTGCAATTG
* * *
5747138 TATACATGAGCTTTGATTTTGTGCAATTT
1 TATACATGAACTATGATTTTGTGCAATTG
*
5747167 TGTACATGAA
1 TATACATGAA
5747177 ATTTTGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 17 0.52
31 16 0.48
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (29 bp):
TATACATGAACTATGATTTTGTGCAATTG
Found at i:5747412 original size:29 final size:29
Alignment explanation
Indices: 5747344--5747438 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 29
5747334 AATCTTCTAC
* * * *
5747344 TATACAATTGAATCACAATTAGAATTTCACG
1 TATACAATTGCATTA-AATTA-AAGTTCATG
* *
5747375 TGTATAATTGCATTAAATTAAAGTTCATG
1 TATACAATTGCATTAAATTAAAGTTCATG
5747404 TATACAATTGCACATTAAATTAAAGTTCATG
1 TATACAATTG--CATTAAATTAAAGTTCATG
5747435 TATA
1 TATA
5747439 ATTTTGAGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.28
30 5 0.09
31 34 0.63
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.37
Consensus pattern (29 bp):
TATACAATTGCATTAAATTAAAGTTCATG
Found at i:5759668 original size:45 final size:45
Alignment explanation
Indices: 5759604--5759693 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
5759594 TTTAACTAAG
*
5759604 TACAAAAATACTTACAGGATC-GATCCTAGAGACTCGGTGAACCAC
1 TACAAAAATACTTACAGGATCGGA-CCTAGAGACTCGGTAAACCAC
* *
5759649 TACAAAAATACTTATAGGATCGGAGCTAGAGACTCGGTAAACCAC
1 TACAAAAATACTTACAGGATCGGACCTAGAGACTCGGTAAACCAC
5759694 ATTCTCAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 39 0.95
46 2 0.05
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (45 bp):
TACAAAAATACTTACAGGATCGGACCTAGAGACTCGGTAAACCAC
Found at i:5761544 original size:12 final size:12
Alignment explanation
Indices: 5761514--5761566 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
5761504 AATTTGTGTA
* *
5761514 TTGTTTTAAGAA
1 TTGTTTTAATAT
5761526 TTGTTTTAATAT
1 TTGTTTTAATAT
5761538 TAT-TTTT--TAT
1 T-TGTTTTAATAT
5761548 TTGTTTTAATAT
1 TTGTTTTAATAT
5761560 TTGTTTT
1 TTGTTTT
5761567 TATGTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
9 1 0.03
10 8 0.23
12 25 0.71
13 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:5761554 original size:22 final size:22
Alignment explanation
Indices: 5761526--5761577 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
5761516 GTTTTAAGAA
5761526 TTGTTTTAATATTAT-TTTTTAT
1 TTGTTTTAATATT-TGTTTTTAT
5761548 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTGTTTTTAT
*
5761570 GT-TTTTAA
1 TTGTTTTAA
5761578 ACGTATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (22 bp):
TTGTTTTAATATTTGTTTTTAT
Found at i:5762092 original size:20 final size:20
Alignment explanation
Indices: 5762069--5762106 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5762059 AAAATCTTTA
5762069 TGAAAGTTTTTAAATTTTGT
1 TGAAAGTTTTTAAATTTTGT
**
5762089 TGAATTTTTTTAAATTTT
1 TGAAAGTTTTTAAATTTT
5762107 TTATGAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (20 bp):
TGAAAGTTTTTAAATTTTGT
Found at i:5762107 original size:10 final size:10
Alignment explanation
Indices: 5762075--5762108 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5762065 TTTATGAAAG
5762075 TTTTTAAATT
1 TTTTTAAATT
* *
5762085 TTGTTGAATT
1 TTTTTAAATT
5762095 TTTTTAAATT
1 TTTTTAAATT
5762105 TTTT
1 TTTT
5762109 ATGAAATGTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:5763697 original size:17 final size:17
Alignment explanation
Indices: 5763645--5763713 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 17
5763635 TTGGGTTTTA
* *
5763645 CTTTTTTCCTTC-TCAT
1 CTTTTCTCCTTCATCTT
5763661 C-TTTCT-CTTCATC-T
1 CTTTTCTCCTTCATCTT
5763675 -TTTTCTCCTT-ATGCTT
1 CTTTTCTCCTTCAT-CTT
*
5763691 CTTTTCTTCTTCATCTT
1 CTTTTCTCCTTCATCTT
5763708 CTTTTC
1 CTTTTC
5763714 ATCTTCTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
14 12 0.27
15 10 0.23
16 2 0.05
17 18 0.41
18 2 0.05
ACGTcount: A:0.06, C:0.30, G:0.01, T:0.62
Consensus pattern (17 bp):
CTTTTCTCCTTCATCTT
Found at i:5763714 original size:11 final size:11
Alignment explanation
Indices: 5763694--5763723 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
5763684 TATGCTTCTT
5763694 TTCTTCTTCATC
1 TTCTT-TTCATC
5763706 TTCTTTTCATC
1 TTCTTTTCATC
5763717 TTCTTTT
1 TTCTTTT
5763724 ACCACTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (11 bp):
TTCTTTTCATC
Found at i:5767353 original size:15 final size:16
Alignment explanation
Indices: 5767330--5767362 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5767320 AGAACATAGA
*
5767330 AATACATGAATG-CAT
1 AATAAATGAATGTCAT
5767345 AATAAATGAATGTCAT
1 AATAAATGAATGTCAT
5767361 AA
1 AA
5767363 ACAGTTCCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (16 bp):
AATAAATGAATGTCAT
Found at i:5783262 original size:43 final size:43
Alignment explanation
Indices: 5783199--5783284 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
5783189 ATTATAAGTC
*
5783199 TAAAAGTGCTCATTTTGTTAGTGCCTCTAAAGACAACAACTTA
1 TAAAAGTGCTCATTTGGTTAGTGCCTCTAAAGACAACAACTTA
*
5783242 TAAAAGTGCTTATTTGGTTAGTGCCTCTAAAGACAACAACTTA
1 TAAAAGTGCTCATTTGGTTAGTGCCTCTAAAGACAACAACTTA
5783285 CATTCTAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (43 bp):
TAAAAGTGCTCATTTGGTTAGTGCCTCTAAAGACAACAACTTA
Found at i:5784578 original size:19 final size:19
Alignment explanation
Indices: 5784531--5784609 Score: 108
Period size: 19 Copynumber: 4.2 Consensus size: 19
5784521 AATCTTTAAG
5784531 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
5784550 GATA--CAATCTTAGACAT
1 GATATGCAATCTTAGATAT
*
5784567 GATATGCAATCTTCGATAT
1 GATATGCAATCTTAGATAT
5784586 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
5784607 GAT
1 GAT
5784610 CTTGTAATCT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
17 16 0.31
19 28 0.54
21 8 0.15
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Done.