Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 59 of 279
Found at i:19718363 original size:16 final size:16
Alignment explanation
Indices: 19718344--19718377 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
19718334 TGGAAAAGAC
19718344 TAATTTTGAGGGTTTT
1 TAATTTTGAGGGTTTT
19718360 TAATTTTGAGGGTTTT
1 TAATTTTGAGGGTTTT
19718376 TA
1 TA
19718378 GGCATTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.56
Consensus pattern (16 bp):
TAATTTTGAGGGTTTT
Found at i:19719475 original size:12 final size:12
Alignment explanation
Indices: 19719458--19719509 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
19719448 TTTAATATTA
19719458 TTATTTATTAAT
1 TTATTTATTAAT
* *
19719470 TTATTTTTTCATT
1 TTATTTATT-AAT
*
19719483 TTATTT-TTATT
1 TTATTTATTAAT
19719494 ATTATTTATTAAT
1 -TTATTTATTAAT
19719507 TTA
1 TTA
19719510 CTTTTTCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.09
12 19 0.56
13 12 0.35
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTTATTAAT
Found at i:19719503 original size:37 final size:38
Alignment explanation
Indices: 19719441--19719516 Score: 127
Period size: 37 Copynumber: 2.0 Consensus size: 38
19719431 TTGCAAATTA
*
19719441 ATTTTATTTTAATATTATTATTTATTAATTTATTTTTTC
1 ATTTTATTTT-ATATTATTATTTATTAATTTACTTTTTC
19719480 ATTTTATTTT-TATTATTATTTATTAATTTACTTTTTC
1 ATTTTATTTTATATTATTATTTATTAATTTACTTTTTC
19719517 TTTCTCTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 26 0.72
39 10 0.28
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (38 bp):
ATTTTATTTTATATTATTATTTATTAATTTACTTTTTC
Found at i:19722960 original size:11 final size:11
Alignment explanation
Indices: 19722946--19723794 Score: 1698
Period size: 11 Copynumber: 77.2 Consensus size: 11
19722936 GTTTTTATAG
19722946 AAGATTTATTA
1 AAGATTTATTA
19722957 AAGATTTATTA
1 AAGATTTATTA
19722968 AAGATTTATTA
1 AAGATTTATTA
19722979 AAGATTTATTA
1 AAGATTTATTA
19722990 AAGATTTATTA
1 AAGATTTATTA
19723001 AAGATTTATTA
1 AAGATTTATTA
19723012 AAGATTTATTA
1 AAGATTTATTA
19723023 AAGATTTATTA
1 AAGATTTATTA
19723034 AAGATTTATTA
1 AAGATTTATTA
19723045 AAGATTTATTA
1 AAGATTTATTA
19723056 AAGATTTATTA
1 AAGATTTATTA
19723067 AAGATTTATTA
1 AAGATTTATTA
19723078 AAGATTTATTA
1 AAGATTTATTA
19723089 AAGATTTATTA
1 AAGATTTATTA
19723100 AAGATTTATTA
1 AAGATTTATTA
19723111 AAGATTTATTA
1 AAGATTTATTA
19723122 AAGATTTATTA
1 AAGATTTATTA
19723133 AAGATTTATTA
1 AAGATTTATTA
19723144 AAGATTTATTA
1 AAGATTTATTA
19723155 AAGATTTATTA
1 AAGATTTATTA
19723166 AAGATTTATTA
1 AAGATTTATTA
19723177 AAGATTTATTA
1 AAGATTTATTA
19723188 AAGATTTATTA
1 AAGATTTATTA
19723199 AAGATTTATTA
1 AAGATTTATTA
19723210 AAGATTTATTA
1 AAGATTTATTA
19723221 AAGATTTATTA
1 AAGATTTATTA
19723232 AAGATTTATTA
1 AAGATTTATTA
19723243 AAGATTTATTA
1 AAGATTTATTA
19723254 AAGATTTATTA
1 AAGATTTATTA
19723265 AAGATTTATTA
1 AAGATTTATTA
19723276 AAGATTTATTA
1 AAGATTTATTA
19723287 AAGATTTATTA
1 AAGATTTATTA
19723298 AAGATTTATTA
1 AAGATTTATTA
19723309 AAGATTTATTA
1 AAGATTTATTA
19723320 AAGATTTATTA
1 AAGATTTATTA
19723331 AAGATTTATTA
1 AAGATTTATTA
19723342 AAGATTTATTA
1 AAGATTTATTA
19723353 AAGATTTATTA
1 AAGATTTATTA
19723364 AAGATTTATTA
1 AAGATTTATTA
19723375 AAGATTTATTA
1 AAGATTTATTA
19723386 AAGATTTATTA
1 AAGATTTATTA
19723397 AAGATTTATTA
1 AAGATTTATTA
19723408 AAGATTTATTA
1 AAGATTTATTA
19723419 AAGATTTATTA
1 AAGATTTATTA
19723430 AAGATTTATTA
1 AAGATTTATTA
19723441 AAGATTTATTA
1 AAGATTTATTA
19723452 AAGATTTATTA
1 AAGATTTATTA
19723463 AAGATTTATTA
1 AAGATTTATTA
19723474 AAGATTTATTA
1 AAGATTTATTA
19723485 AAGATTTATTA
1 AAGATTTATTA
19723496 AAGATTTATTA
1 AAGATTTATTA
19723507 AAGATTTATTA
1 AAGATTTATTA
19723518 AAGATTTATTA
1 AAGATTTATTA
19723529 AAGATTTATTA
1 AAGATTTATTA
19723540 AAGATTTATTA
1 AAGATTTATTA
19723551 AAGATTTATTA
1 AAGATTTATTA
19723562 AAGATTTATTA
1 AAGATTTATTA
19723573 AAGATTTATTA
1 AAGATTTATTA
19723584 AAGATTTATTA
1 AAGATTTATTA
19723595 AAGATTTATTA
1 AAGATTTATTA
19723606 AAGATTTATTA
1 AAGATTTATTA
19723617 AAGATTTATTA
1 AAGATTTATTA
19723628 AAGATTTATTA
1 AAGATTTATTA
19723639 AAGATTTATTA
1 AAGATTTATTA
19723650 AAGATTTATTA
1 AAGATTTATTA
19723661 AAGATTTATTA
1 AAGATTTATTA
19723672 AAGATTTATTA
1 AAGATTTATTA
19723683 AAGATTTATTA
1 AAGATTTATTA
19723694 AAGATTTATTA
1 AAGATTTATTA
19723705 AAGATTTATTA
1 AAGATTTATTA
19723716 AAGATTTATTA
1 AAGATTTATTA
19723727 AAGATTTATTA
1 AAGATTTATTA
19723738 AAGATTTATTA
1 AAGATTTATTA
19723749 AAGATTTATTA
1 AAGATTTATTA
19723760 AAGATTTATTA
1 AAGATTTATTA
19723771 AAGATTTATTA
1 AAGATTTATTA
19723782 AAGATTTATTA
1 AAGATTTATTA
19723793 AA
1 AA
19723795 TAGCTAAGCC
Statistics
Matches: 838, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 838 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (11 bp):
AAGATTTATTA
Found at i:19729275 original size:25 final size:25
Alignment explanation
Indices: 19729241--19729290 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
19729231 CCGTATAACA
* * *
19729241 TAAAAATGACCGTTTTGCCCCTAGG
1 TAAAAATGACCATTATACCCCTAGG
19729266 TAAAAATGACCATTATACCCCTAGG
1 TAAAAATGACCATTATACCCCTAGG
19729291 GGTTATGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (25 bp):
TAAAAATGACCATTATACCCCTAGG
Found at i:19729374 original size:11 final size:11
Alignment explanation
Indices: 19729338--19729393 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
19729328 CATGGTATGT
19729338 ATGATATGCAC
1 ATGATATGCAC
* *
19729349 ATGACATG--T
1 ATGATATGCAC
19729358 ATGATATGCAC
1 ATGATATGCAC
*
19729369 ATGATATG--T
1 ATGATATGCAC
19729378 ATGATATGCAC
1 ATGATATGCAC
19729389 ATGAT
1 ATGAT
19729394 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:19729393 original size:20 final size:20
Alignment explanation
Indices: 19729327--19729393 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
19729317 ATTTTAATAA
*
19729327 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
19729347 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
19729367 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
19729387 ACATGAT
1 ACATGAT
19729394 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:19729504 original size:24 final size:24
Alignment explanation
Indices: 19729443--19729523 Score: 110
Period size: 24 Copynumber: 3.4 Consensus size: 24
19729433 GAGGAAGTGA
19729443 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
19729467 -AAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
19729490 AAAAGGGATTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
19729514 CAAAGAGGCT
1 AAAAG-GGCT
19729524 AGGCTTCCAG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
23 22 0.45
24 24 0.49
25 3 0.06
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:19729762 original size:7 final size:7
Alignment explanation
Indices: 19729750--19729777 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
19729740 GGCCCAGTGT
19729750 TATGAAA
1 TATGAAA
19729757 TATGAAA
1 TATGAAA
19729764 TATGAAA
1 TATGAAA
19729771 TATGAAA
1 TATGAAA
19729778 AGGGCTACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (7 bp):
TATGAAA
Found at i:19738182 original size:40 final size:40
Alignment explanation
Indices: 19738134--19738281 Score: 244
Period size: 40 Copynumber: 3.7 Consensus size: 40
19738124 GCTACTCACT
19738134 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
19738174 CAATTGCCTTCGGGACTTGGCCCAGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
19738214 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
19738254 CAAATGCCTTCGGG-CTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
19738282 CAATCCGAAT
Statistics
Matches: 99, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 13 0.13
40 86 0.87
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:19743075 original size:40 final size:39
Alignment explanation
Indices: 19742977--19743239 Score: 269
Period size: 40 Copynumber: 6.6 Consensus size: 39
19742967 TCCTCGTTCA
* * * *
19742977 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
19743016 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
19743055 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
19743095 GAATGCCTTCGGGATTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
19743135 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
19743175 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
19743216 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
19743240 CAGCATTCAA
Statistics
Matches: 195, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
39 40 0.21
40 143 0.73
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:19743248 original size:41 final size:41
Alignment explanation
Indices: 19743171--19743248 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
19743161 TTTGTATCTC
* * *
19743171 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
19743212 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
19743249 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:19744491 original size:103 final size:100
Alignment explanation
Indices: 19744300--19744502 Score: 379
Period size: 103 Copynumber: 2.0 Consensus size: 100
19744290 CTTCTCCTCT
19744300 CTTTTCTTTAGCTCACGGCAATGGGGGGGGAAAGAATCAACTACTCACTTTTTTTTTTGTGTAAT
1 CTTTTCTTTAGCTCACGGCAATGGGGGGGGAAAGAATCAACTACTCACTTTTTTTTTTGTGTAAT
19744365 CATCATACTCCTTTTCATTATTTAATTTCCATGCC
66 CATCATACTCCTTTTCATTATTTAATTTCCATGCC
19744400 CTTTTCTTTAGCTCACGGCAATGGGGGGGGAAAAAGAATCAACTACTCACTTTTTTTTTTTGTGT
1 CTTTTCTTTAGCTCACGGCAATGGGGGGGG--AAAGAATCAACTACTCAC-TTTTTTTTTTGTGT
19744465 AATCATCATACTCCTTTTCATTATTTAATTTCCATGCC
63 AATCATCATACTCCTTTTCATTATTTAATTTCCATGCC
19744503 TATTATTTTA
Statistics
Matches: 100, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
100 30 0.30
102 18 0.18
103 52 0.52
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (100 bp):
CTTTTCTTTAGCTCACGGCAATGGGGGGGGAAAGAATCAACTACTCACTTTTTTTTTTGTGTAAT
CATCATACTCCTTTTCATTATTTAATTTCCATGCC
Found at i:19745652 original size:42 final size:44
Alignment explanation
Indices: 19745580--19745774 Score: 171
Period size: 48 Copynumber: 4.2 Consensus size: 44
19745570 TAATCCAACT
*
19745580 ATGGTCTTACA-GAAGTCACATATC-G-ATGCCATGTCCCAGAC
1 ATGGTCTTACACGAAATCACATATCAGCATGCCATGTCCCAGAC
*
19745621 ATGGTCTTACACGAAATCACATATCGATGCCAATGCCATGTCCCATAC
1 ATGGTCTTACACGAAATCACATATC-A-G-C-ATGCCATGTCCCAGAC
** *
19745669 ATGGTCTTACACGGGATCATATATCGATGCCAATGCCATGTCCCAGAC
1 ATGGTCTTACACGAAATCACATATC-A-G-C-ATGCCATGTCCCAGAC
* ** * *
19745717 ATGGTCTTACATGGGATCACATATCGATGAAATGTCATGTCCCAGAC
1 ATGGTCTTACACGAAATCACATATC-A-G-CATGCCATGTCCCAGAC
*
19745764 ATTGTCTTACA
1 ATGGTCTTACA
19745775 AGGGATCACA
Statistics
Matches: 135, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
41 11 0.08
42 12 0.09
45 1 0.01
47 25 0.19
48 86 0.64
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (44 bp):
ATGGTCTTACACGAAATCACATATCAGCATGCCATGTCCCAGAC
Found at i:19745774 original size:47 final size:48
Alignment explanation
Indices: 19745605--19745784 Score: 272
Period size: 48 Copynumber: 3.8 Consensus size: 48
19745595 TCACATATCG
**
19745605 ATGCCATGTCCCAGACATGGTCTTACACGAAATCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACGGGATCACATATCGATGCCA
* *
19745653 ATGCCATGTCCCATACATGGTCTTACACGGGATCATATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACGGGATCACATATCGATGCCA
* *
19745701 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATG-AA
1 ATGCCATGTCCCAGACATGGTCTTACACGGGATCACATATCGATGCCA
* * *
19745748 ATGTCATGTCCCAGACATTGTCTTACAAGGGATCACA
1 ATGCCATGTCCCAGACATGGTCTTACACGGGATCACA
19745785 ATGCCATAGC
Statistics
Matches: 121, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 35 0.29
48 86 0.71
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACGGGATCACATATCGATGCCA
Found at i:19745808 original size:37 final size:37
Alignment explanation
Indices: 19745767--19745848 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
19745757 CCCAGACATT
*
19745767 GTCTTACAAGGGATCACAATGCCATAGCCCAGCTATG
1 GTCTTACAAGGCATCACAATGCCATAGCCCAGCTATG
* * * *
19745804 GTCTTACATGTCATTACGATGCCATAGCCCAGCTATG
1 GTCTTACAAGGCATCACAATGCCATAGCCCAGCTATG
*
19745841 GTGTTACA
1 GTCTTACA
19745849 CGTACTCAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (37 bp):
GTCTTACAAGGCATCACAATGCCATAGCCCAGCTATG
Found at i:19748825 original size:30 final size:30
Alignment explanation
Indices: 19748791--19748851 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
19748781 GTATGTGCAC
*
19748791 TATCAATCACAATGGGTTATAAACAATTAT
1 TATCAATCACAATGGGTAATAAACAATTAT
*
19748821 TATCAATCATAATGGGTAATAAACAATTAT
1 TATCAATCACAATGGGTAATAAACAATTAT
19748851 T
1 T
19748852 TCCACAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.34
Consensus pattern (30 bp):
TATCAATCACAATGGGTAATAAACAATTAT
Found at i:19755898 original size:40 final size:39
Alignment explanation
Indices: 19755851--19755974 Score: 169
Period size: 40 Copynumber: 3.1 Consensus size: 39
19755841 CGGGCTTTAA
*
19755851 CCGGATATAGCCACTCGCTCAAATGCCTTCGGGACTTAGC
1 CCGGATATAG-CACTCGCACAAATGCCTTCGGGACTTAGC
* *
19755891 CCGGATATAGTAGTTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGCA-CTCGCACAAATGCCTTCGGGACTTAGC
*
19755931 CCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAG-CACTCGCACAAATGCCTTCGGGACTTAGC
19755971 CCGG
1 CCGG
19755975 TTATCATCCG
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
39 2 0.03
40 72 0.96
41 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (39 bp):
CCGGATATAGCACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:19757384 original size:249 final size:250
Alignment explanation
Indices: 19756946--19757444 Score: 964
Period size: 249 Copynumber: 2.0 Consensus size: 250
19756936 ATGACATCAA
19756946 CACAAGTCCACCTTAGCCGAAACTTAACTCATCTTCATGCTTCATCACCACAACATCAAACACCA
1 CACAAGTCCACCTTAGCCGAAACTTAACTCATCTTCATGCTTCATCACCACAACATCAAACACCA
19757011 ATCAAGAAGACAACACCCATGGCCGAATATCATCTCCATCTCATAGCAAAGATTTAAACCATGGG
66 ATCAAGAAGACAACACCCATGGCCGAATATCATCTCCATCTCATAGCAAAGATTTAAACCATGGG
19757076 CTAGGTAGAACTCAAGCTAACAACTAAAAACATGCATGAATCTCATGGAACAACATCAACATACC
131 CTAGGTAGAACTCAAGCTAACAACTAAAAACATGCATGAATCTCATGGAACAACATCAACATACC
*
19757141 TTAGTCTAGTGAACCACCATAGCCGATTTTCTCCAAGATCTTTCCCTTCT-TTTC
196 TTAGTCTAGTGAACCACCATAGCCGATTTTCTCCAAGATCTTTCCCCTCTCTTTC
19757195 CACAAGTCCACCTTAGCCGAAACTTAACTCATCTTCATGCTTCATCACCACAACATCAAACACCA
1 CACAAGTCCACCTTAGCCGAAACTTAACTCATCTTCATGCTTCATCACCACAACATCAAACACCA
19757260 ATCAAGAAGACAACACCCATGGCCGAATATCATCTCCATCTCATAGCAAAGATTTAAACCATGGG
66 ATCAAGAAGACAACACCCATGGCCGAATATCATCTCCATCTCATAGCAAAGATTTAAACCATGGG
*
19757325 CTAGGTAGAACTCAAGCTAACAACTAAAAATATGCATGAATCTCATGGAACAACATCAACATACC
131 CTAGGTAGAACTCAAGCTAACAACTAAAAACATGCATGAATCTCATGGAACAACATCAACATACC
*
19757390 TTAGTCTAGTGAACCACCATAGCCGATTTTCTCCAAGCTCTTTCCCCTCTCTTTC
196 TTAGTCTAGTGAACCACCATAGCCGATTTTCTCCAAGATCTTTCCCCTCTCTTTC
19757445 TTTATTCTAT
Statistics
Matches: 246, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
249 242 0.98
250 4 0.02
ACGTcount: A:0.35, C:0.30, G:0.11, T:0.24
Consensus pattern (250 bp):
CACAAGTCCACCTTAGCCGAAACTTAACTCATCTTCATGCTTCATCACCACAACATCAAACACCA
ATCAAGAAGACAACACCCATGGCCGAATATCATCTCCATCTCATAGCAAAGATTTAAACCATGGG
CTAGGTAGAACTCAAGCTAACAACTAAAAACATGCATGAATCTCATGGAACAACATCAACATACC
TTAGTCTAGTGAACCACCATAGCCGATTTTCTCCAAGATCTTTCCCCTCTCTTTC
Found at i:19757523 original size:48 final size:48
Alignment explanation
Indices: 19757441--19757547 Score: 146
Period size: 48 Copynumber: 2.2 Consensus size: 48
19757431 TTCCCCTCTC
* *
19757441 TTTCTTTATTCTATTCGGCCAAGTTCACAACATGAGAACTTTTTTT-TT
1 TTTCTTTCTTCTATTCGGCCAAGTTAACAACATGAGAA-TTTTTTTCTT
*
19757489 TTTCTTTCTTCTATTCGGCCAA-TTGAACAGCATGAGAATTTTTTTCTT
1 TTTCTTTCTTCTATTCGGCCAAGTT-AACAACATGAGAATTTTTTTCTT
*
19757537 TTTTTTTCTTC
1 TTTCTTTCTTC
19757548 ATCATTTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
47 9 0.17
48 44 0.83
ACGTcount: A:0.20, C:0.19, G:0.10, T:0.51
Consensus pattern (48 bp):
TTTCTTTCTTCTATTCGGCCAAGTTAACAACATGAGAATTTTTTTCTT
Found at i:19759064 original size:49 final size:50
Alignment explanation
Indices: 19758993--19759218 Score: 262
Period size: 49 Copynumber: 4.6 Consensus size: 50
19758983 TGATCTATTG
* * * *
19758993 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATTA
1 TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA
* * *
19759043 TT-GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAA
1 TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA
* * * * * * * **
19759092 CTTCGATCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTATCAGATGG
1 -TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA
*
19759143 TTAGGTCG--TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAA
1 TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA
19759191 TT-GGTCGCATGTGTAGTACTAAGTGCAG
1 TTAGGTCGCATGTGTAGTACTAAGTGCAG
19759219 TGATCTTTAC
Statistics
Matches: 146, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
47 5 0.03
48 36 0.25
49 59 0.40
50 9 0.06
51 37 0.25
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA
Found at i:19759230 original size:99 final size:99
Alignment explanation
Indices: 19758998--19759230 Score: 246
Period size: 99 Copynumber: 2.3 Consensus size: 99
19758988 TATTGTTAGG
* * *
19758998 TCACGTGTGTAGTACTAAGTGCAG-G-CTACTACGTGTATCGGATTATTGGTCGCATGTGTAGTA
1 TCACATGTGTAGTACTAAGTGCAGTGACT--TACGTGTATCAGATGATTGGTCG-ATGTGTAGTA
** *
19759061 CTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGA
63 CTAAGTGCAGGCTACTACACGTACCGGATAACTTCGA
* *
19759098 TCACGTGTGTAGTACTAAGTGCAAGCT-AC-TACGTGTATCAGATGGTTAGGTCG-TGTGTAGTA
1 TCACATGTGTAGTACTAAGTGC-AG-TGACTTACGTGTATCAGATGATT-GGTCGATGTGTAGTA
* *
19759160 CTAAGTGCAGGCTACTACATGTACCGGATAA-TT-GG
63 CTAAGTGCAGGCTACTACACGTACCGGATAACTTCGA
*
19759195 TCGCATGTGTAGTACTAAGTGCAGTGATCTTTACGT
1 TCACATGTGTAGTACTAAGTGCAGTGA-C-TTACGT
19759231 TTTCGGAGTC
Statistics
Matches: 114, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
95 1 0.01
96 3 0.03
97 22 0.19
98 2 0.02
99 41 0.36
100 37 0.32
101 7 0.06
103 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (99 bp):
TCACATGTGTAGTACTAAGTGCAGTGACTTACGTGTATCAGATGATTGGTCGATGTGTAGTACTA
AGTGCAGGCTACTACACGTACCGGATAACTTCGA
Found at i:19766076 original size:49 final size:50
Alignment explanation
Indices: 19766015--19766236 Score: 227
Period size: 49 Copynumber: 4.5 Consensus size: 50
19766005 CAAGGTCACG
* * *
19766015 TGTGTAGTACTAAGTGCAGGCCACTACGTGTGCCGGATTATT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTAGGTCGCA
* * * * * * * *
19766064 TGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TTAGGTCGCA
* * **
19766115 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCG--
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTAGGTCGCA
* * * *
19766163 TGTGTAGTAATAAGTGAAGGCTACTACATGTACTGGATAATT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTAGGTCGCA
*
19766212 TGTGTAGTACTAAGTGCAAGCTACT
1 TGTGTAGTACTAAGTGCAGGCTACT
19766237 GTGCGTACTA
Statistics
Matches: 138, Mismatches: 31, Indels: 8
0.78 0.18 0.05
Matches are distributed among these distances:
47 5 0.04
48 34 0.25
49 55 0.40
50 7 0.05
51 37 0.27
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTAGGTCGCA
Found at i:19768713 original size:29 final size:28
Alignment explanation
Indices: 19768681--19768736 Score: 103
Period size: 29 Copynumber: 2.0 Consensus size: 28
19768671 AAGATAAACC
19768681 GATTTGGCTTCGGGCCATGCATATCAGTT
1 GATTTGGCTTCGGGCCATG-ATATCAGTT
19768710 GATTTGGCTTCGGGCCATGATATCAGT
1 GATTTGGCTTCGGGCCATGATATCAGT
19768737 ATTTCGGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.34
Consensus pattern (28 bp):
GATTTGGCTTCGGGCCATGATATCAGTT
Found at i:19770147 original size:21 final size:21
Alignment explanation
Indices: 19770121--19770161 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19770111 CATTAAATTA
* * *
19770121 ATATATGTTATAATATAATAT
1 ATATATATCATAAAATAATAT
19770142 ATATATATCATAAAATAATA
1 ATATATATCATAAAATAATA
19770162 ATAAGCCATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATATATCATAAAATAATAT
Found at i:19771287 original size:56 final size:56
Alignment explanation
Indices: 19771194--19771404 Score: 289
Period size: 56 Copynumber: 3.8 Consensus size: 56
19771184 GAAGAATATG
* *
19771194 TGGCATCGATATGTGACTT-TGATATATGTGTGCGAGTAAGACCACGTTTAATACAT
1 TGGCATCGATATGTGA-TTCTGATATATGTGTACGAGTAAGACCACGTTTAATACGT
* * * * *
19771250 TGACATCGATATGTGATTCCGATATATGTGTATGAGTAAGTCCACGTTTAATATGT
1 TGGCATCGATATGTGATTCTGATATATGTGTACGAGTAAGACCACGTTTAATACGT
* * * *
19771306 TGGCATCAATATGTGATTCTGATATATGTGTGCGAGTAAGTCCACGTTTCATACGT
1 TGGCATCGATATGTGATTCTGATATATGTGTACGAGTAAGACCACGTTTAATACGT
* *
19771362 TGGCATCGATATGTGATTCTGATATGTGTTTACGAGTAAGACC
1 TGGCATCGATATGTGATTCTGATATATGTGTACGAGTAAGACC
19771405 CAATCTAGGA
Statistics
Matches: 135, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
55 2 0.01
56 133 0.99
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (56 bp):
TGGCATCGATATGTGATTCTGATATATGTGTACGAGTAAGACCACGTTTAATACGT
Found at i:19771422 original size:112 final size:111
Alignment explanation
Indices: 19771188--19771435 Score: 322
Period size: 112 Copynumber: 2.2 Consensus size: 111
19771178 TACCTGGAAG
19771188 AATATGTGGCATCGATATGTGACTTTGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGA
1 AATATGTGGCATCGATATGTGACTTTGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGA
* * * *
19771253 CATCGATATGTGATTCCGATATATGTGTATGAGTAAGTCCACGTTT
66 CATCGATATGTGATTCCGATATATGTGTACGAGTAAGCCCACATCT
* * * *
19771299 AATATGTTGGCATCAATATGTGA-TTCTGATATATGTGTGCGAGTAAGTCCACGTTTCATACGTT
1 AATATG-TGGCATCGATATGTGACTT-TGATATATGTGTGCGAGTAAGACCACGTTTAATACATT
* * * *
19771363 GGCATCGATATGTGATTCTGATATGTGTTTACGAGTAAGACCCA-ATCT
64 GACATCGATATGTGATTCCGATATATGTGTACGAGTAAG-CCCACATCT
19771411 AGGATA-GTGGCATCGATATGTGACT
1 A--ATATGTGGCATCGATATGTGACT
19771436 AAATGTAAGT
Statistics
Matches: 118, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
111 8 0.07
112 102 0.86
113 5 0.04
114 3 0.03
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (111 bp):
AATATGTGGCATCGATATGTGACTTTGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGA
CATCGATATGTGATTCCGATATATGTGTACGAGTAAGCCCACATCT
Found at i:19781897 original size:40 final size:40
Alignment explanation
Indices: 19781801--19782061 Score: 253
Period size: 40 Copynumber: 6.5 Consensus size: 40
19781791 CTCGTTCAAT
* * * *
19781801 TGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AA
1 TGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAA
* ** *
19781840 TGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAA
*
19781880 TGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAA
* * *
19781920 GGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCACAAA
* * *
19781960 TGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCCCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCACAAA
** * * * *
19782000 TGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAA
1 TGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACAAA
*
19782041 -GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGACTTAACCCGGA
19782062 CAGCATTCAA
Statistics
Matches: 192, Mismatches: 24, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
39 37 0.19
40 141 0.73
41 14 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAA
Found at i:19788579 original size:35 final size:35
Alignment explanation
Indices: 19788539--19788606 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
19788529 TTTTCCCTGA
19788539 AACTAGACTCATATCCCCACCTATGTATTTTTTGC
1 AACTAGACTCATATCCCCACCTATGTATTTTTTGC
* *
19788574 AACTAGACTCATGTTCCCACCTATGTATTTTTT
1 AACTAGACTCATATCCCCACCTATGTATTTTTT
19788607 TCTAGAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.26, G:0.09, T:0.40
Consensus pattern (35 bp):
AACTAGACTCATATCCCCACCTATGTATTTTTTGC
Found at i:19788954 original size:51 final size:51
Alignment explanation
Indices: 19788894--19788997 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
19788884 AATATCTCTT
19788894 TCTGTACTGTTCCTATAATTGTTTCGTTACTTCCATATGAAAGTAGATTCA
1 TCTGTACTGTTCCTATAATTGTTTCGTTACTTCCATATGAAAGTAGATTCA
* *
19788945 TCTGTACTGTTCCTTTAATTGTTTCGTTACTTCCATATGAAATTAGATTCA
1 TCTGTACTGTTCCTATAATTGTTTCGTTACTTCCATATGAAAGTAGATTCA
19788996 TC
1 TC
19788998 AAGGTTCGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (51 bp):
TCTGTACTGTTCCTATAATTGTTTCGTTACTTCCATATGAAAGTAGATTCA
Found at i:19789939 original size:40 final size:40
Alignment explanation
Indices: 19789848--19790017 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 40
19789838 TCCTCGTTCA
* * * *
19789848 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACACG
* * * *
19789887 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACACG
*
19789927 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCACACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACACG
* * * * *
19789967 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACACG
*
19790007 AAGGCCTTCGG
1 AATGCCTTCGG
19790018 ATCTTAGTCC
Statistics
Matches: 110, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 32 0.29
40 78 0.71
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACACG
Found at i:19789949 original size:79 final size:80
Alignment explanation
Indices: 19789846--19790017 Score: 229
Period size: 80 Copynumber: 2.2 Consensus size: 80
19789836 GCTCCTCGTT
* * * * *
19789846 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-CATGCCTTCGGGACGTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGG
19789910 ATTTAACAACTCGCA
66 ATTTAACAACTCGCA
* * *
19789925 CGAATGCCTTCGGGACTTAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGG
** *
19789990 ATTTAGTATCTCGCA
66 ATTTAACAACTCGCA
*
19790005 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
19790018 ATCTTAGTCC
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
79 36 0.46
80 43 0.54
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (80 bp):
CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGG
ATTTAACAACTCGCA
Found at i:19794780 original size:76 final size:76
Alignment explanation
Indices: 19794654--19794875 Score: 390
Period size: 76 Copynumber: 2.9 Consensus size: 76
19794644 CGGTTAATCA
** **
19794654 ATCGGTTAACTAAATTTTTTTAGTCCGGGGTCGGTTAATTATTTTTTGATTTTTCAGTTAACGGT
1 ATCGGTTAACCGAATTTTTTCGGTCCGGGGTCGGTTAATTATTTTTTGATTTTTCAGTTAACGGT
19794719 TAATTCGATCG
66 TAATTCGATCG
19794730 ATCGGTTAACCGAATTTTTTCGGTCCGGGGTCGGTTAATTATTTTTTGATTTTTCAGTTAACGGT
1 ATCGGTTAACCGAATTTTTTCGGTCCGGGGTCGGTTAATTATTTTTTGATTTTTCAGTTAACGGT
19794795 TAATTCGATCG
66 TAATTCGATCG
* *
19794806 ATCGGTTAACCGAATTTTTTCGGTCCGGGGTCGGTTAATTATTTTTTGATTTTTCGGTTAACAGT
1 ATCGGTTAACCGAATTTTTTCGGTCCGGGGTCGGTTAATTATTTTTTGATTTTTCAGTTAACGGT
19794871 TAATT
66 TAATT
19794876 TGGTTTGAAA
Statistics
Matches: 140, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 140 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (76 bp):
ATCGGTTAACCGAATTTTTTCGGTCCGGGGTCGGTTAATTATTTTTTGATTTTTCAGTTAACGGT
TAATTCGATCG
Found at i:19795991 original size:57 final size:57
Alignment explanation
Indices: 19795828--19796102 Score: 253
Period size: 56 Copynumber: 5.0 Consensus size: 57
19795818 TTACTGTTTG
* * * *
19795828 CATGCTATCATAAATTGAATTAAA---GTTGTTTGAGTGTTTCAAATTGAGCATATT
1 CATGCTGTCCTAAATTGAATTAAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATTTT
* * * * *
19795882 CATACTATCTTAAATTGAA-TCAAGCTGTTGTTTTAGTGTTTCAAATTGAGCATTTT
1 CATGCTGTCCTAAATTGAATTAAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATTTT
* * ** *
19795938 CATGTTGTCCTAAATTGAATTAAAGTTGGTGTTTTAGTGTAACAAATTAAGCATTTT
1 CATGCTGTCCTAAATTGAATTAAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATTTT
* * ** * *
19795995 CATTCTGTCTTAAATTTCATT-AAGTTGTTG-TTTAATGTTTCAAATTGAGTATTATT
1 CATGCTGTCCTAAATTGAATTAAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATT-TT
* * * * *
19796051 -ATGCTGTCCTAAATTAAATTAAAG-TGTTGCTTCA-TGTCTCAAATTAAGCATT
1 CATGCTGTCCTAAATTGAATTAAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATT
19796103 ATTGTGCTAT
Statistics
Matches: 180, Mismatches: 34, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
53 3 0.02
54 17 0.09
55 54 0.30
56 59 0.33
57 47 0.26
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.44
Consensus pattern (57 bp):
CATGCTGTCCTAAATTGAATTAAAGTTGTTGTTTTAGTGTTTCAAATTGAGCATTTT
Found at i:19796007 original size:113 final size:110
Alignment explanation
Indices: 19795829--19796101 Score: 291
Period size: 113 Copynumber: 2.5 Consensus size: 110
19795819 TACTGTTTGC
* * ** *
19795829 ATGCTATCATAAATTGAATTAAAG-TTGTTTGAGTGTTTCAAATTGAGCATATTCATACTATCTT
1 ATGCTGTCCTAAATTGAATTAAAGTTTGTTTGAGTGTAACAAATTAAGCATATTCATACTATCTT
*
19795893 AAATTGAATCAAGCTGTTGTTTTAGTGTTTCAAATTGAGCATT-TT
66 AAATTGAATCAAGCTGTTG-TTTAATGTTTCAAATTGAGCATTATT
* * * * *
19795938 CATGTTGTCCTAAATTGAATTAAAGTTGGTGTTTTAGTGTAACAAATTAAGCATTTTCATTCTGT
1 -ATGCTGTCCTAAATTGAATTAAAGTT--TGTTTGAGTGTAACAAATTAAGCATATTCATACTAT
** * * *
19796003 CTTAAATTTCATTAAGTTGTTGTTTAATGTTTCAAATTGAGTATTATT
63 CTTAAATTGAATCAAGCTGTTGTTTAATGTTTCAAATTGAGCATTATT
* * * **
19796051 ATGCTGTCCTAAATTAAATTAAAGTGTTGCTTCA-TGTCTCAAATTAAGCAT
1 ATGCTGTCCTAAATTGAATTAAAGT-TTGTTTGAGTGTAACAAATTAAGCAT
19796102 TATTGTGCTA
Statistics
Matches: 136, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
110 36 0.26
111 6 0.04
112 44 0.32
113 50 0.37
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.44
Consensus pattern (110 bp):
ATGCTGTCCTAAATTGAATTAAAGTTTGTTTGAGTGTAACAAATTAAGCATATTCATACTATCTT
AAATTGAATCAAGCTGTTGTTTAATGTTTCAAATTGAGCATTATT
Found at i:19796058 original size:55 final size:57
Alignment explanation
Indices: 19795828--19796105 Score: 252
Period size: 55 Copynumber: 5.0 Consensus size: 57
19795818 TTACTGTTTG
* * *
19795828 CATGCTATCATAAATTGAATTAAAGTTG-T-TTGAGTGTTTCAAATTGAGCA-TATT
1 CATGCTGTCCTAAATTGAATTAAAGTTGTTGTTTAGTGTTTCAAATTGAGCATTATT
* * * * *
19795882 CATACTATCTTAAATTGAA-TCAAGCTGTTGTTTTAGTGTTTCAAATTGAGCATT-TT
1 CATGCTGTCCTAAATTGAATTAAAGTTGTTG-TTTAGTGTTTCAAATTGAGCATTATT
* * ** *
19795938 CATGTTGTCCTAAATTGAATTAAAGTTGGTGTTTTAGTGTAACAAATTAAGCATT-TT
1 CATGCTGTCCTAAATTGAATTAAAGTTGTTG-TTTAGTGTTTCAAATTGAGCATTATT
* * ** * *
19795995 CATTCTGTCTTAAATTTCATT-AAGTTGTTGTTTAATGTTTCAAATTGAGTATTATT
1 CATGCTGTCCTAAATTGAATTAAAGTTGTTGTTTAGTGTTTCAAATTGAGCATTATT
* * * *
19796051 -ATGCTGTCCTAAATTAAATTAAAG-TGTTGCTTCA-TGTCTCAAATTAAGCATTATT
1 CATGCTGTCCTAAATTGAATTAAAGTTGTTG-TTTAGTGTTTCAAATTGAGCATTATT
19796106 GTGCTATTGA
Statistics
Matches: 182, Mismatches: 34, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
53 6 0.03
54 18 0.10
55 57 0.31
56 53 0.29
57 48 0.26
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.44
Consensus pattern (57 bp):
CATGCTGTCCTAAATTGAATTAAAGTTGTTGTTTAGTGTTTCAAATTGAGCATTATT
Found at i:19798898 original size:9 final size:9
Alignment explanation
Indices: 19798881--19798911 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19798871 GTAGTGATTC
19798881 AATTCGGTT
1 AATTCGGTT
*
19798890 AATTTGGTT
1 AATTCGGTT
19798899 AATTCGGTT
1 AATTCGGTT
19798908 AATT
1 AATT
19798912 TTTAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (9 bp):
AATTCGGTT
Found at i:19803549 original size:29 final size:29
Alignment explanation
Indices: 19803516--19803571 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
19803506 ATAACCAAAC
*
19803516 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
19803545 CTACATAAACTTCATATCCATAAACCC
1 CTACAAAAACTTCATATCCATAAACCC
19803572 TTCTTTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:19803568 original size:15 final size:15
Alignment explanation
Indices: 19803522--19803569 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
19803512 AAACCTACAA
*
19803522 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
19803537 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
19803551 AAACTTCATATCCAT
1 AAACTTCATATCCAT
19803566 AAAC
1 AAAC
19803570 CCTTCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:19804297 original size:30 final size:28
Alignment explanation
Indices: 19804261--19804316 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
19804251 AAACAAAAAA
* *
19804261 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
19804291 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
19804317 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:19807584 original size:29 final size:29
Alignment explanation
Indices: 19807551--19807610 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
19807541 ATAACCAAAC
*
19807551 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
19807580 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
19807609 CT
1 CT
19807611 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:19807603 original size:15 final size:15
Alignment explanation
Indices: 19807557--19807604 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
19807547 AAACCTACAA
*
19807557 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
19807572 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
19807586 AAACTTCATATCCAT
1 AAACTTCATATCCAT
19807601 AAAC
1 AAAC
19807605 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:19813757 original size:57 final size:56
Alignment explanation
Indices: 19813662--19813803 Score: 196
Period size: 57 Copynumber: 2.5 Consensus size: 56
19813652 TACATTTTAC
*
19813662 AATA-GGATTACCAGTCCAGGCTAAATCCTATCCATAGCATATGCTCTAGAGAGCTT
1 AATATGGATTACCA-TCCGGGCTAAATCCTATCCATAGCATATGCTCTAGAGAGCTT
**
19813718 AATATGGATTACTCATCCGGGCTAAATCCTATCTGTAGCATATGCTCTAGAGAGCTT
1 AATATGGATTAC-CATCCGGGCTAAATCCTATCCATAGCATATGCTCTAGAGAGCTT
* * *
19813775 AATATGAATTACCCGTCCGAGCTAAATCC
1 AATATGGATTA-CCATCCGGGCTAAATCC
19813804 AATTTACAGC
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
56 4 0.05
57 70 0.91
58 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (56 bp):
AATATGGATTACCATCCGGGCTAAATCCTATCCATAGCATATGCTCTAGAGAGCTT
Found at i:19813832 original size:57 final size:57
Alignment explanation
Indices: 19813681--19813859 Score: 180
Period size: 57 Copynumber: 3.1 Consensus size: 57
19813671 ACCAGTCCAG
* * * * * * *
19813681 GCTAAATCCTATCCATAGCATATGCTCTAGAGAGCTTAATATGGATTACTCATCCGG
1 GCTAAATCCAATCTACAGCATAAGCTCTAGAGAGCTTAATATGAATTACCCATCCGA
* ** * *
19813738 GCTAAATCCTATCTGTAGCATATGCTCTAGAGAGCTTAATATGAATTACCCGTCCGA
1 GCTAAATCCAATCTACAGCATAAGCTCTAGAGAGCTTAATATGAATTACCCATCCGA
* * * * *
19813795 GCTAAATCCAATTTACAGCCTAAGCTCAAGAGGGCTTAA-ATTAGAATTACCCATCCGT
1 GCTAAATCCAATCTACAGCATAAGCTCTAGAGAGCTTAATA-T-GAATTACCCATCCGA
19813853 GCTAAAT
1 GCTAAAT
19813860 TCTATCTGCA
Statistics
Matches: 104, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
56 1 0.01
57 83 0.80
58 20 0.19
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (57 bp):
GCTAAATCCAATCTACAGCATAAGCTCTAGAGAGCTTAATATGAATTACCCATCCGA
Found at i:19817724 original size:14 final size:14
Alignment explanation
Indices: 19817705--19817733 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19817695 GTAACATCCT
19817705 ATTTACTATCAAAG
1 ATTTACTATCAAAG
19817719 ATTTACTATCAAAG
1 ATTTACTATCAAAG
19817733 A
1 A
19817734 AGCGTAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (14 bp):
ATTTACTATCAAAG
Found at i:19822820 original size:43 final size:42
Alignment explanation
Indices: 19822743--19822887 Score: 123
Period size: 43 Copynumber: 3.4 Consensus size: 42
19822733 GATTACAACC
* * *
19822743 AAGACCATCTCTGGGACATTCGCATTGTATTATGATTAAGTGT
1 AAGACCATGTCTGGGACATTGGCATCGTA-TATGATTAAGTGT
* * * *
19822786 AAGACCATGTGTTGGACATTGGCATCGTTATATGAATT-CGTAT
1 AAGACCATGTCTGGGACATTGGCATCG-TATATG-ATTAAGTGT
* * * *
19822829 AAGACCCTGTCTGGGACAGTGGCATCGATATGTGA-TAACATGT
1 AAGACCATGTCTGGGACATTGGCATCG-TATATGATTAA-GTGT
*
19822872 AAGACCATATCTGGGA
1 AAGACCATGTCTGGGA
19822888 TAAGGCATTG
Statistics
Matches: 80, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 73 0.91
44 5 0.06
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (42 bp):
AAGACCATGTCTGGGACATTGGCATCGTATATGATTAAGTGT
Found at i:19827274 original size:64 final size:64
Alignment explanation
Indices: 19827169--19827376 Score: 197
Period size: 67 Copynumber: 3.2 Consensus size: 64
19827159 CATCATGTGT
* *
19827169 ACAAGAAAGCTACGAGACATTATAATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTACGAG--A-TA-AATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATG
19827234 TAG
62 TAG
* * * * * * * *
19827237 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACAATGT
1 ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGT
19827302 AG
63 AG
* * *
19827304 ACAAGAGAGCTACGAGATAAACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-G
1 ACAAGAGAGCTACGAGATAAA-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG
19827366 TACAAGAGAGC
1 -ACAAGAGAGC
19827377 CGAACTATAT
Statistics
Matches: 114, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
62 1 0.01
63 18 0.16
64 25 0.22
65 2 0.02
66 22 0.19
67 30 0.26
68 16 0.14
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATAAATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG
Found at i:19827710 original size:28 final size:28
Alignment explanation
Indices: 19827670--19827802 Score: 96
Period size: 28 Copynumber: 4.8 Consensus size: 28
19827660 CCAAACGAAC
* * *
19827670 GGCACTTAGTGTGCGAAGTAT-TGAGGAT
1 GGCACTTAGTGTGCGAAGCATCCGA-AAT
19827698 GGCACTTAGTGTGC-AAGACATCCGAAAT
1 GGCACTTAGTGTGCGAAG-CATCCGAAAT
* ** * * *
19827726 GACAC--AGTGTATGAAGTAT-TGATGAT
1 GGCACTTAGTGTGCGAAGCATCCGA-AAT
* *
19827752 GACACTTAGTGTGCGAAACATCCGAAAT
1 GGCACTTAGTGTGCGAAGCATCCGAAAT
*
19827780 GGCACTTAGTGTGCGAAACATCC
1 GGCACTTAGTGTGCGAAGCATCC
19827803 AGTATAGCAC
Statistics
Matches: 82, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
25 2 0.02
26 14 0.17
27 6 0.07
28 56 0.68
29 4 0.05
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (28 bp):
GGCACTTAGTGTGCGAAGCATCCGAAAT
Found at i:19827812 original size:28 final size:28
Alignment explanation
Indices: 19827754--19827829 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 28
19827744 TTGATGATGA
*
19827754 CACTTAGTGTGCGAAACATCCGAAATGG
1 CACTTAGTGTGCGAAACATCCGAAATAG
*
19827782 CACTTAGTGTGCGAAACATCC-AGTATAG
1 CACTTAGTGTGCGAAACATCCGA-AATAG
*
19827810 CACTTAGCGTGC-AAGACATC
1 CACTTAGTGTGCGAA-ACATC
19827830 GATTGTGCAG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 3 0.07
28 40 0.93
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (28 bp):
CACTTAGTGTGCGAAACATCCGAAATAG
Found at i:19831438 original size:14 final size:15
Alignment explanation
Indices: 19831410--19831438 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19831400 CTCTTTCAAG
19831410 GACAAGAATAATCCA
1 GACAAGAATAATCCA
19831425 GACAAGAA-AATCCA
1 GACAAGAATAATCCA
19831439 TATTAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.21, G:0.14, T:0.10
Consensus pattern (15 bp):
GACAAGAATAATCCA
Found at i:19832107 original size:15 final size:15
Alignment explanation
Indices: 19832087--19832130 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
19832077 AAAGCCCAGA
*
19832087 ATAAAGAATTCCAAG
1 ATAAAGAAATCCAAG
*
19832102 ATAAAGAAATCCATG
1 ATAAAGAAATCCAAG
*
19832117 ATAAGGAAATCCAA
1 ATAAAGAAATCCAA
19832131 ATTACAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.18
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:19848312 original size:19 final size:20
Alignment explanation
Indices: 19848288--19848331 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
19848278 AATGTTTCAA
*
19848288 TGAAT-AAAATAGTTAATTT
1 TGAATAAAAAAAGTTAATTT
*
19848307 TGAATAAAAAAATTTAATTT
1 TGAATAAAAAAAGTTAATTT
19848327 TGAAT
1 TGAAT
19848332 GTATATAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (20 bp):
TGAATAAAAAAAGTTAATTT
Found at i:19849126 original size:41 final size:41
Alignment explanation
Indices: 19849069--19849147 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
19849059 TTTTAAAGCT
*
19849069 TACTTTGTCTGTTCTTTCCCTCTTTTATAGATTATCTAGCC
1 TACTTTGTCTGTTCTTTCCCTATTTTATAGATTATCTAGCC
* *
19849110 TACTTTGTGTGTTCTTTTCCTATTTTATAGATTATCTA
1 TACTTTGTCTGTTCTTTCCCTATTTTATAGATTATCTA
19849148 AGCTAGCTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.16, C:0.19, G:0.10, T:0.54
Consensus pattern (41 bp):
TACTTTGTCTGTTCTTTCCCTATTTTATAGATTATCTAGCC
Found at i:19856356 original size:10 final size:10
Alignment explanation
Indices: 19856341--19856421 Score: 76
Period size: 10 Copynumber: 7.9 Consensus size: 10
19856331 AATTTTAGCT
19856341 TTTATCTTTA
1 TTTATCTTTA
*
19856351 TTTATC-CTA
1 TTTATCTTTA
*
19856360 GCTTTTATATTTA
1 ---TTTATCTTTA
*
19856373 TTTATCGTTA
1 TTTATCTTTA
19856383 TTTATCTTTA
1 TTTATCTTTA
*
19856393 ATTATCTTTA
1 TTTATCTTTA
19856403 TTTAT-TTGTA
1 TTTATCTT-TA
19856413 TTTATCTTT
1 TTTATCTTT
19856422 TAGAATTTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
9 4 0.07
10 44 0.77
11 2 0.04
12 5 0.09
13 2 0.04
ACGTcount: A:0.21, C:0.10, G:0.04, T:0.65
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:19856364 original size:22 final size:22
Alignment explanation
Indices: 19856336--19856378 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
19856326 GATTTAATTT
*
19856336 TAGCTTTTATCTTTATTTATCC
1 TAGCTTTTATATTTATTTATCC
19856358 TAGCTTTTATATTTATTTATC
1 TAGCTTTTATATTTATTTATC
19856379 GTTATTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (22 bp):
TAGCTTTTATATTTATTTATCC
Found at i:19858024 original size:40 final size:40
Alignment explanation
Indices: 19857963--19858140 Score: 218
Period size: 40 Copynumber: 4.5 Consensus size: 40
19857953 AAGCCAAGTA
* * * *
19857963 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
19858002 CCTTCGGGACATAGACCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
19858042 CCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
19858082 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
19858122 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
19858141 TTATCATCCG
Statistics
Matches: 124, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
39 13 0.10
40 111 0.90
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:19865358 original size:14 final size:14
Alignment explanation
Indices: 19865341--19865369 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19865331 TTTTTTTCGA
19865341 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
19865355 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
19865369 T
1 T
19865370 CTTCTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTGAATT
Found at i:19877853 original size:21 final size:21
Alignment explanation
Indices: 19877827--19877901 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
19877817 CATATAAGAG
19877827 TATAATAAAATATTAAAAATA
1 TATAATAAAATATTAAAAATA
*
19877848 TATAATTGAAA-ATTAAAAAT-
1 TATAA-TAAAATATTAAAAATA
* *
19877868 TAATTATATAAATA--ATAAATA
1 T-ATAATA-AAATATTAAAAATA
19877889 T-TAATAAAATATT
1 TATAATAAAATATT
19877902 TATCTCTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 15
0.68 0.08 0.24
Matches are distributed among these distances:
18 5 0.12
19 4 0.10
20 7 0.17
21 21 0.50
22 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (21 bp):
TATAATAAAATATTAAAAATA
Found at i:19878190 original size:63 final size:63
Alignment explanation
Indices: 19878117--19878244 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
19878107 TGCGGAAGAA
*
19878117 AGAATCAAATAAAATATGAAAAAGAAGATTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
1 AGAATCAAATAAAATATGAAAAAGAAGACTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
19878180 AGAATCAAATAAAATATGAAAAAGAAGACTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
1 AGAATCAAATAAAATATGAAAAAGAAGACTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
19878243 AG
1 AG
19878245 TTGGCGAGAG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.24
Consensus pattern (63 bp):
AGAATCAAATAAAATATGAAAAAGAAGACTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
Found at i:19878437 original size:3 final size:3
Alignment explanation
Indices: 19878429--19878479 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
19878419 CCCAATTTGG
19878429 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
19878477 CTT
1 CTT
19878480 TCACTTTCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:19887278 original size:48 final size:48
Alignment explanation
Indices: 19887191--19887314 Score: 117
Period size: 48 Copynumber: 2.6 Consensus size: 48
19887181 ATTCCACAAA
* * * * *
19887191 AATATTATTTTAATAGTTTAATATTTTATTTTATTTAATACTTA-TCTG
1 AATATTATTTTATTAATTTAATA-TTAATTTAATCTAATACTTATTCTG
* *
19887239 AATATTATTTTATTAATTTAATATTAACTTTAATCTAATATTTATTTTG
1 AATATTATTTTATTAATTTAATATTAA-TTTAATCTAATACTTATTCTG
* * *
19887288 -TTAACTATTATATTAATTTAATATTAA
1 AAT-ATTATTTTATTAATTTAATATTAA
19887315 AGTGATTATG
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
47 3 0.05
48 35 0.56
49 25 0.40
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.56
Consensus pattern (48 bp):
AATATTATTTTATTAATTTAATATTAATTTAATCTAATACTTATTCTG
Found at i:19887308 original size:37 final size:37
Alignment explanation
Indices: 19887234--19887309 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
19887224 TTTAATACTT
19887234 ATCTGAATATTATTTTATTAATTTAATATTAACTTTA
1 ATCTGAATATTATTTTATTAATTTAATATTAACTTTA
*
19887271 ATCT-AATATTTATTTTGTTAACTATT-ATATTAA-TTTA
1 ATCTGAATA-TTATTTTATTAA-T-TTAATATTAACTTTA
19887308 AT
1 AT
19887310 ATTAAAGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 4 0.11
37 21 0.60
38 8 0.23
39 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (37 bp):
ATCTGAATATTATTTTATTAATTTAATATTAACTTTA
Found at i:19890051 original size:33 final size:33
Alignment explanation
Indices: 19890013--19890075 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
19890003 AGTTTAGATC
*
19890013 ATTTCATATCATAACTTTACTCATATTAATTGG
1 ATTTCATATCAGAACTTTACTCATATTAATTGG
19890046 ATTTCATATCAGAACTTTACTCATATTAAT
1 ATTTCATATCAGAACTTTACTCATATTAAT
19890076 CGGAATATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (33 bp):
ATTTCATATCAGAACTTTACTCATATTAATTGG
Found at i:19904074 original size:21 final size:22
Alignment explanation
Indices: 19904035--19904075 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19904025 GTCGAATCGT
19904035 CACACAGGCGTGTTGCCCCTCC
1 CACACAGGCGTGTTGCCCCTCC
*
19904057 CACACGGGCGTG-TGCCCCT
1 CACACAGGCGTGTTGCCCCT
19904076 ATGTCTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.12, C:0.44, G:0.27, T:0.17
Consensus pattern (22 bp):
CACACAGGCGTGTTGCCCCTCC
Found at i:19905729 original size:20 final size:20
Alignment explanation
Indices: 19905700--19905744 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
19905690 AGCACATGTA
*
19905700 TTCATAAAATTTCATAATTT
1 TTCATAAAATTTCATAACTT
* *
19905720 TTCATCAAATTTTATAACTT
1 TTCATAAAATTTCATAACTT
19905740 TTCAT
1 TTCAT
19905745 TTTAGTCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (20 bp):
TTCATAAAATTTCATAACTT
Found at i:19913931 original size:25 final size:26
Alignment explanation
Indices: 19913897--19913952 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
19913887 TTCTCTCACC
* * *
19913897 AAAAACGACTTATTTTCCTAA-TTAA
1 AAAAACGACTTATATGCCAAATTTAA
*
19913922 AAAAATGACTTATATGCCAAATTTAA
1 AAAAACGACTTATATGCCAAATTTAA
19913948 AAAAA
1 AAAAA
19913953 AAGGCATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.30
Consensus pattern (26 bp):
AAAAACGACTTATATGCCAAATTTAA
Found at i:19915517 original size:9 final size:9
Alignment explanation
Indices: 19915503--19915629 Score: 50
Period size: 10 Copynumber: 13.7 Consensus size: 9
19915493 GTCACATGTG
19915503 ATAAAAATT
1 ATAAAAATT
19915512 ATAAAAA--
1 ATAAAAATT
*
19915519 AT-AAAATCA
1 ATAAAAAT-T
19915528 ATAAAAATT
1 ATAAAAATT
*
19915537 AT-TAAATGT
1 ATAAAAAT-T
*
19915546 -TAATAAAAT
1 ATAA-AAATT
19915555 ATAAAAAATTT
1 AT-AAAAA-TT
19915566 ATAAAAATCGT
1 ATAAAAAT--T
19915577 A-AAAAATAT
1 ATAAAAAT-T
*
19915586 AAAAAAATT
1 ATAAAAATT
* * *
19915595 GTAAGATTT
1 ATAAAAATT
*
19915604 ATAAAAATC
1 ATAAAAATT
19915613 ATAGAAAAGTT
1 ATA-AAAA-TT
19915624 ATAAAA
1 ATAAAA
19915630 TGCATCAAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 29
0.67 0.11 0.22
Matches are distributed among these distances:
6 4 0.05
7 2 0.02
8 5 0.06
9 30 0.34
10 36 0.41
11 11 0.12
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (9 bp):
ATAAAAATT
Found at i:19915579 original size:20 final size:20
Alignment explanation
Indices: 19915556--19915629 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
19915546 TAATAAAATA
19915556 TAAAAAATTTATAAAAATCG
1 TAAAAAATTTATAAAAATCG
* * *
19915576 TAAAAAATATAAAAAAATTG
1 TAAAAAATTTATAAAAATCG
* *
19915596 T--AAGATTTATAAAAATCA
1 TAAAAAATTTATAAAAATCG
* *
19915614 TAGAAAAGTTATAAAA
1 TAAAAAATTTATAAAA
19915630 TGCATCAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
18 13 0.31
20 29 0.69
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (20 bp):
TAAAAAATTTATAAAAATCG
Found at i:19915865 original size:10 final size:9
Alignment explanation
Indices: 19915854--19915939 Score: 52
Period size: 9 Copynumber: 9.4 Consensus size: 9
19915844 TTCTTTTCAT
19915854 TTTTTATAA
1 TTTTTATAA
*
19915863 TTTTGTATGA
1 TTTT-TATAA
*
19915873 -CTTTATAAA
1 TTTTTAT-AA
*
19915882 ATTTTATAA
1 TTTTTATAA
19915891 TTTTTAT-A
1 TTTTTATAA
19915899 TTTTTAT-A
1 TTTTTATAA
**
19915907 TATTTTACCA
1 T-TTTTATAA
*
19915917 TTTTTATGA
1 TTTTTATAA
*
19915926 TTTTATAAAA
1 TTTT-TATAA
19915936 TTTT
1 TTTT
19915940 ACATTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
8 13 0.21
9 30 0.49
10 18 0.30
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:19915919 original size:26 final size:26
Alignment explanation
Indices: 19915862--19915947 Score: 95
Period size: 26 Copynumber: 3.2 Consensus size: 26
19915852 ATTTTTTATA
* *
19915862 ATTTTGTATGACTTTATAAAATTTTATA
1 ATTTT-TATGATTTTATAAAATTTTA-C
*
19915890 ATTTTTAT-ATTTT-TATATATTTTACC
1 ATTTTTATGATTTTATA-AAATTTTA-C
19915916 ATTTTTATGATTTTATAAAATTTTAC
1 ATTTTTATGATTTTATAAAATTTTAC
19915942 ATTTTT
1 ATTTTT
19915948 TTTTCTAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
25 2 0.04
26 26 0.52
27 15 0.30
28 7 0.14
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.60
Consensus pattern (26 bp):
ATTTTTATGATTTTATAAAATTTTAC
Found at i:19915939 original size:18 final size:18
Alignment explanation
Indices: 19915855--19915940 Score: 63
Period size: 18 Copynumber: 4.8 Consensus size: 18
19915845 TCTTTTCATT
19915855 TTTTAT-AATTTTGTATGA
1 TTTTATAAATTTT-TATGA
* * *
19915873 CTTTATAAAATTTTATAA
1 TTTTATAAATTTTTATGA
*
19915891 TTTT-TATATTTTTAT-A
1 TTTTATAAATTTTTATGA
*
19915907 TATTT-TACCATTTTTATGA
1 T-TTTATA-AATTTTTATGA
*
19915926 TTTTATAAAATTTTA
1 TTTTATAAATTTTTA
19915941 CATTTTTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
16 2 0.04
17 14 0.26
18 29 0.54
19 9 0.17
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTATAAATTTTTATGA
Found at i:19919512 original size:23 final size:23
Alignment explanation
Indices: 19919486--19919556 Score: 133
Period size: 23 Copynumber: 3.0 Consensus size: 23
19919476 TTAAGGTAGC
19919486 TAAGGGTTAAATTAGCGACGGTA
1 TAAGGGTTAAATTAGCGACGGTA
19919509 TAAGGGTTAAATTAGCGACGGTA
1 TAAGGGTTAAATTAGCGACGGTA
19919532 TTAAGGGTTAAATTAGCGACGGTA
1 -TAAGGGTTAAATTAGCGACGGTA
19919556 T
1 T
19919557 TAAACGGTAC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
23 24 0.51
24 23 0.49
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (23 bp):
TAAGGGTTAAATTAGCGACGGTA
Found at i:19919572 original size:24 final size:24
Alignment explanation
Indices: 19919486--19919559 Score: 141
Period size: 24 Copynumber: 3.1 Consensus size: 24
19919476 TTAAGGTAGC
19919486 TAAGGGTTAAATTAGCGACGGTA-
1 TAAGGGTTAAATTAGCGACGGTAT
19919509 TAAGGGTTAAATTAGCGACGGTAT
1 TAAGGGTTAAATTAGCGACGGTAT
19919533 TAAGGGTTAAATTAGCGACGGTAT
1 TAAGGGTTAAATTAGCGACGGTAT
19919557 TAA
1 TAA
19919560 ACGGTACATT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 23 0.46
24 27 0.54
ACGTcount: A:0.35, C:0.08, G:0.28, T:0.28
Consensus pattern (24 bp):
TAAGGGTTAAATTAGCGACGGTAT
Found at i:19920358 original size:31 final size:30
Alignment explanation
Indices: 19920301--19920359 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
19920291 GTAAGTACTC
* * * *
19920301 AAAATTTGAGGGATTAAAGTGTAAATATGA
1 AAAAGTTGAAGGACTAAAGTGAAAATATGA
19920331 AAAAGTTGAAGGACTAATAGTGAAAATAT
1 AAAAGTTGAAGGACTAA-AGTGAAAATAT
19920360 TTTAATGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.49, C:0.02, G:0.22, T:0.27
Consensus pattern (30 bp):
AAAAGTTGAAGGACTAAAGTGAAAATATGA
Found at i:19920598 original size:8 final size:8
Alignment explanation
Indices: 19920587--19920618 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
19920577 TTTAATAAGA
19920587 TATTTTAT
1 TATTTTAT
19920595 TA-TTTAT
1 TATTTTAT
19920602 TATTTTAT
1 TATTTTAT
19920610 TATTTTAT
1 TATTTTAT
19920618 T
1 T
19920619 TAGCCTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTTTAT
Found at i:19924243 original size:20 final size:20
Alignment explanation
Indices: 19924204--19924244 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19924194 AGGAACTATC
* * *
19924204 CTAGAATTAGGGGATTACAA
1 CTAGAATTAGAGAATCACAA
19924224 CTAGAATTAGAGAATCACAA
1 CTAGAATTAGAGAATCACAA
19924244 C
1 C
19924245 AAATTATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.22
Consensus pattern (20 bp):
CTAGAATTAGAGAATCACAA
Found at i:19931438 original size:28 final size:28
Alignment explanation
Indices: 19931400--19931476 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
19931390 AATCAAATAT
* * *
19931400 GGCACTCAGTGTACGAAATATTGAGAAA
1 GGCACTTAGTGTGCGAGATATTGAGAAA
*
19931428 GGCACTTAGTGTGCGAGATATTGAGAAT
1 GGCACTTAGTGTGCGAGATATTGAGAAA
*
19931456 GACACTTAGTGTGCGAGATAT
1 GGCACTTAGTGTGCGAGATAT
19931477 CAAATGATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (28 bp):
GGCACTTAGTGTGCGAGATATTGAGAAA
Found at i:19931916 original size:25 final size:25
Alignment explanation
Indices: 19931866--19931916 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
19931856 AAGGTAAGTA
*
19931866 TATGTGCAAAGAATATATTGTGATG
1 TATGTGCAAAGAATATATGGTGATG
* *
19931891 TATGTGGAAATGAA-ATATGGTTATG
1 TATGTGCAAA-GAATATATGGTGATG
19931916 T
1 T
19931917 GCCAATGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.37
Consensus pattern (25 bp):
TATGTGCAAAGAATATATGGTGATG
Found at i:19935938 original size:22 final size:20
Alignment explanation
Indices: 19935894--19935940 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
19935884 ATTTTTTTAA
* *
19935894 ATTTTTAATATTTAACTGTT
1 ATTTTTAATAATAAACTGTT
19935914 ATTTTTAATGAATAAACATGTT
1 ATTTTTAAT-AATAAAC-TGTT
19935936 ATTTT
1 ATTTT
19935941 CAAATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 5 0.22
22 9 0.39
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (20 bp):
ATTTTTAATAATAAACTGTT
Found at i:19937597 original size:104 final size:104
Alignment explanation
Indices: 19937413--19937614 Score: 287
Period size: 104 Copynumber: 1.9 Consensus size: 104
19937403 TGAGTCACAT
* * * * *
19937413 GGCCTGGGCACACGCACGTGTCCCTGGCCGTATGGTCTTAAATCATAAATAGTGAGTTACACGGC
1 GGCCTGGGCACACACACATGTCCCTGGCCGTATCGTCCTAAATCATAAACAGTGAGTTACACGGC
** * *
19937478 CTGGACACATGCCCATGTCCTTGCCTGTGTGGCTCAAAC
66 CTGGACACACACCCATGTCCTTACCCGTGTGGCTCAAAC
** * *
19937517 GGCCTGGGCACACACTTATGTCCCTGGCTGTGTCGTCCTAAATCATAAACAGTGAGTTACACGGC
1 GGCCTGGGCACACACACATGTCCCTGGCCGTATCGTCCTAAATCATAAACAGTGAGTTACACGGC
19937582 CTGGACACACACCCATGTCCTTACCCGTGTGGC
66 CTGGACACACACCCATGTCCTTACCCGTGTGGC
19937615 GTCGACAGCC
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
104 85 1.00
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.24
Consensus pattern (104 bp):
GGCCTGGGCACACACACATGTCCCTGGCCGTATCGTCCTAAATCATAAACAGTGAGTTACACGGC
CTGGACACACACCCATGTCCTTACCCGTGTGGCTCAAAC
Found at i:19938889 original size:26 final size:22
Alignment explanation
Indices: 19938840--19938884 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
19938830 CAAATCTAAG
19938840 TAGAAATATTTATTTTATTATT
1 TAGAAATATTTATTTTATTATT
19938862 TAGAAATATTTATTTTATTATT
1 TAGAAATATTTATTTTATTATT
19938884 T
1 T
19938885 CTTTAACGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TAGAAATATTTATTTTATTATT
Found at i:19941314 original size:42 final size:42
Alignment explanation
Indices: 19941255--19941374 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 42
19941245 GGGTTAGTTG
*
19941255 AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATATA
1 AGATTACGTGTAAGACCATATCTGGGATATGGCATCAATATA
* * * * *
19941297 AGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCAATTTG
1 AGATTACGTGTAAGACCATATCTGGGATA-TGGCATCAATATA
** *
19941340 AGATCCCATGTAAGACCATATCTGGGATATGGCAT
1 AGATTACGTGTAAGACCATATCTGGGATATGGCAT
19941375 TGGTATGGTA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
42 32 0.48
43 34 0.52
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (42 bp):
AGATTACGTGTAAGACCATATCTGGGATATGGCATCAATATA
Found at i:19943247 original size:28 final size:29
Alignment explanation
Indices: 19943196--19943250 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
19943186 ACAGGGGTTT
*
19943196 TCACACGGCCAAGTACACGTCTGTGTCCC
1 TCACACGGCCAAGTACACGCCTGTGTCCC
* *
19943225 TCACATGGCCTAG-ACACGCCTGTGTC
1 TCACACGGCCAAGTACACGCCTGTGTC
19943251 ATCGCCCGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.20, C:0.36, G:0.22, T:0.22
Consensus pattern (29 bp):
TCACACGGCCAAGTACACGCCTGTGTCCC
Found at i:19950109 original size:55 final size:54
Alignment explanation
Indices: 19950022--19950276 Score: 242
Period size: 55 Copynumber: 4.8 Consensus size: 54
19950012 ATTAGGGTTT
* *
19950022 AAGGGTACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAAGGC
* * * * * *
19950077 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAAGGC
* * *
19950132 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAAGGC
* *
19950185 CAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
* * * *
19950234 AATGATACCATGTAAGACCATGACAAGTCATGG-AAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
19950277 GTACCCGTGT
Statistics
Matches: 168, Mismatches: 24, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
48 2 0.01
49 36 0.21
52 6 0.04
53 41 0.24
54 11 0.07
55 68 0.40
56 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
Found at i:19950489 original size:16 final size:16
Alignment explanation
Indices: 19950468--19950498 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19950458 ATAAATTTGA
19950468 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
19950484 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
19950499 ATTGAAGAAG
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:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:19952343 original size:42 final size:42
Alignment explanation
Indices: 19952223--19952367 Score: 146
Period size: 42 Copynumber: 3.5 Consensus size: 42
19952213 AAACAGTGAG
* * *
19952223 TCACATGGCCTGGGCACACACCCATGTCCTTGCCCGTGTGGC
1 TCACACGGCCTAGGCACACACCCATGTCCTTGCTCGTGTGGC
* * * * * * *
19952265 TTACATGGCTTGGGCATACGCACATGTCCTTGCTCGTGTGGC
1 TCACACGGCCTAGGCACACACCCATGTCCTTGCTCGTGTGGC
* * * * *
19952307 TCACACGGCCTAGGCACACACCCATCTTCTTACTCGTATGAC
1 TCACACGGCCTAGGCACACACCCATGTCCTTGCTCGTGTGGC
*
19952349 TCACACGACCTAGGCACAC
1 TCACACGGCCTAGGCACAC
19952368 GCCTATATTC
Statistics
Matches: 84, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.19, C:0.35, G:0.22, T:0.23
Consensus pattern (42 bp):
TCACACGGCCTAGGCACACACCCATGTCCTTGCTCGTGTGGC
Found at i:19953921 original size:22 final size:23
Alignment explanation
Indices: 19953896--19953949 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
19953886 AACATAATGA
*
19953896 TATATATATAATATATTT-TTAT
1 TATATATATAACATATTTATTAT
*
19953918 TATATA-ATTACATATTTATTAT
1 TATATATATAACATATTTATTAT
* *
19953940 TTTATTTATA
1 TATATATATA
19953950 TAAATAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 9 0.36
22 14 0.56
23 2 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATATATAACATATTTATTAT
Found at i:19953937 original size:19 final size:18
Alignment explanation
Indices: 19953900--19953939 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
19953890 TAATGATATA
* *
19953900 TATATAATATATTTTTAT
1 TATATAATACATATTTAT
19953918 TATATAATTACATATTTAT
1 TATATAA-TACATATTTAT
19953937 TAT
1 TAT
19953940 TTTATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATAATACATATTTAT
Found at i:19954327 original size:21 final size:21
Alignment explanation
Indices: 19954301--19954342 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
19954291 TTTTGTCTAC
19954301 TTATTTTACATATA-ATTAATT
1 TTATTTTA-ATATATATTAATT
19954322 TTATTTTAATATATATTAATT
1 TTATTTTAATATATATTAATT
19954343 ATTTACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATTTTAATATATATTAATT
Found at i:19955559 original size:18 final size:18
Alignment explanation
Indices: 19955532--19955571 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
19955522 TAGTTATACC
19955532 TCTACGTCTACTA-CTACA
1 TCTACGTCTA-TATCTACA
*
19955550 TCTACTTCTATATCTACA
1 TCTACGTCTATATCTACA
19955568 TCTA
1 TCTA
19955572 TGTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.28, C:0.30, G:0.03, T:0.40
Consensus pattern (18 bp):
TCTACGTCTATATCTACA
Found at i:19957667 original size:20 final size:20
Alignment explanation
Indices: 19957639--19957676 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19957629 TAGGAAATTA
19957639 TGTGATCTGAGCTCATGAGT
1 TGTGATCTGAGCTCATGAGT
*
19957659 TGTGGTCTGAGCTCATGA
1 TGTGATCTGAGCTCATGA
19957677 TATATGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (20 bp):
TGTGATCTGAGCTCATGAGT
Found at i:19960531 original size:28 final size:28
Alignment explanation
Indices: 19960491--19960549 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
19960481 GTTCAGCTAC
19960491 ATATATGGCTAATAAATGCAATATTCTA
1 ATATATGGCTAATAAATGCAATATTCTA
* *
19960519 ATATATGGCTAATAAATGCATTTTTCTA
1 ATATATGGCTAATAAATGCAATATTCTA
19960547 ATA
1 ATA
19960550 AATGTTAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (28 bp):
ATATATGGCTAATAAATGCAATATTCTA
Found at i:19964674 original size:20 final size:19
Alignment explanation
Indices: 19964651--19964697 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
19964641 TATTTCTTAA
19964651 AATTAAAACTCAATTCTACC
1 AATTAAAACTCAATTC-ACC
* *
19964671 AATTCAAAACTCCATTCAGC
1 AATT-AAAACTCAATTCACC
19964691 AATTAAA
1 AATTAAA
19964698 CATGAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (19 bp):
AATTAAAACTCAATTCACC
Found at i:19969490 original size:67 final size:67
Alignment explanation
Indices: 19969403--19969671 Score: 529
Period size: 67 Copynumber: 4.0 Consensus size: 67
19969393 TGCACCTAAA
19969403 TTGTTGCAAAATAGAATGCTCAGTATCGAGACATGGGTATGAGACACGGTCGTGTCTCTCAGCCG
1 TTGTTGCAAAATAGAATGCTCAGTATCGAGACATGGGTATGAGACACGGTCGTGTCTCTCAGCCG
19969468 TG
66 TG
19969470 TTGTTGCAAAATAGAATGCTCAGTATCGAGACATGGGTATGAGACACGGTCGTGTCTCTCAGCCG
1 TTGTTGCAAAATAGAATGCTCAGTATCGAGACATGGGTATGAGACACGGTCGTGTCTCTCAGCCG
19969535 TG
66 TG
19969537 TTGTTGCAAAATAGAATGCTCAGTATCGAGACATGGGTATGAGACACGGTCGTGTCTCTCAGCCG
1 TTGTTGCAAAATAGAATGCTCAGTATCGAGACATGGGTATGAGACACGGTCGTGTCTCTCAGCCG
19969602 TG
66 TG
*
19969604 TTGTTGCAAAATAGAATGCTCAGTATCGAGACATGGGTATGAGACACGGTCGTGTCTCTCAGCTG
1 TTGTTGCAAAATAGAATGCTCAGTATCGAGACATGGGTATGAGACACGGTCGTGTCTCTCAGCCG
19969669 TG
66 TG
19969671 T
1 T
19969672 GAAGGACACG
Statistics
Matches: 201, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 201 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (67 bp):
TTGTTGCAAAATAGAATGCTCAGTATCGAGACATGGGTATGAGACACGGTCGTGTCTCTCAGCCG
TG
Found at i:19972485 original size:21 final size:22
Alignment explanation
Indices: 19972433--19972485 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
19972423 AAATAAAGTC
*
19972433 CATGTA-CAGATATCATCATCT
1 CATGTATCATATATCATCATCT
* *
19972454 CATGTTTTCATATATCAT-ATGT
1 CATG-TATCATATATCATCATCT
19972476 CATGTATCAT
1 CATGTATCAT
19972486 CATTTACTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.35
22 8 0.31
23 9 0.35
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (22 bp):
CATGTATCATATATCATCATCT
Found at i:19979931 original size:68 final size:64
Alignment explanation
Indices: 19979866--19980073 Score: 197
Period size: 67 Copynumber: 3.2 Consensus size: 64
19979856 CATCATGTGT
*
19979866 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGA-TAT-ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
19979931 TAG
62 TAG
* * * * * * *
19979934 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTTCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGT
19979999 AG
63 AG
* * * * *
19980001 ACAAGAGAGCTACGAGATAAACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-G
1 ACAAGAGAGCTACGAGATATA-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
19980063 TACAAGAGAGC
1 -ACAAGAGAGC
19980074 CGAACTATAT
Statistics
Matches: 116, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.16
64 21 0.18
65 11 0.09
66 18 0.16
67 31 0.27
68 15 0.13
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
Found at i:19985240 original size:25 final size:25
Alignment explanation
Indices: 19985210--19985262 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
19985200 TGAAACTTTG
*
19985210 TTCTTTCCCTAATCTCAATTTGTAT
1 TTCTTTCCCTAATCTAAATTTGTAT
*
19985235 TTCTTTCCCTAATTTAAATTTGTAT
1 TTCTTTCCCTAATCTAAATTTGTAT
19985260 TTC
1 TTC
19985263 GCCTTTCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.55
Consensus pattern (25 bp):
TTCTTTCCCTAATCTAAATTTGTAT
Found at i:19987184 original size:23 final size:24
Alignment explanation
Indices: 19987158--19987209 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
19987148 CCGTGAAATC
*
19987158 CTGTACAT-GTATGCTCACACGAG
1 CTGTACATCGTATGCTCACACAAG
*
19987181 CTGTAGATCGGTATGCTCACACAAG
1 CTGTACATC-GTATGCTCACACAAG
19987206 CTGT
1 CTGT
19987210 GGGTCAGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
25 18 0.72
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (24 bp):
CTGTACATCGTATGCTCACACAAG
Found at i:19994091 original size:40 final size:40
Alignment explanation
Indices: 19994021--19994198 Score: 227
Period size: 40 Copynumber: 4.5 Consensus size: 40
19994011 AAGCCAAGTA
* * *
19994021 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
19994060 CCTTCGGGATTTAGCCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
19994100 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * **
19994140 CCTTCGGGACTTAGCCCAGA-ACTAGTCACTAGCGTAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
19994180 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
19994199 TTATCATCCA
Statistics
Matches: 125, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
39 15 0.12
40 110 0.88
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:20002063 original size:40 final size:40
Alignment explanation
Indices: 20002001--20002138 Score: 167
Period size: 40 Copynumber: 3.5 Consensus size: 40
20001991 AAGCCAAGTA
* *
20002001 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCTCAAATG
*
20002040 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCTCAAATG
* * *
20002080 CCTTCGGGACTTAGCCCAGA-ACTAGTCACTAGCGT-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGC-TCAAATG
20002120 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
20002139 TTATCATCCA
Statistics
Matches: 87, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
39 14 0.16
40 73 0.84
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCTCAAATG
Found at i:20005936 original size:31 final size:31
Alignment explanation
Indices: 20005889--20005953 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
20005879 TACACAAAGA
*
20005889 CTTATCATAGAAAGCTCACATAGGGAGCTTG
1 CTTATCACAGAAAGCTCACATAGGGAGCTTG
*
20005920 CTTATCACAGAGAGCTCACATAGGGAGCTTG
1 CTTATCACAGAAAGCTCACATAGGGAGCTTG
20005951 CTT
1 CTT
20005954 GAAACACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (31 bp):
CTTATCACAGAAAGCTCACATAGGGAGCTTG
Found at i:20006103 original size:27 final size:26
Alignment explanation
Indices: 20006062--20006117 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
20006052 GCACATGTAA
* *
20006062 AACATATCTTTAAAATCATAGCTTAAG
1 AACATATCTTGAAAAT-AGAGCTTAAG
*
20006089 AACATATCTTGAAAATAGAGTTTAAG
1 AACATATCTTGAAAATAGAGCTTAAG
20006115 AAC
1 AAC
20006118 TTGAAAACAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.30
Consensus pattern (26 bp):
AACATATCTTGAAAATAGAGCTTAAG
Found at i:20006783 original size:27 final size:27
Alignment explanation
Indices: 20006727--20006784 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
20006717 TTACTTAGGA
* * *
20006727 AACCCTAGCTCGCCAAATACACTGGTG
1 AACCCTAGCTCGCCAAACACACTAGCG
*
20006754 AACCCTAGCTCAG-CAAACATACTAGCG
1 AACCCTAGCTC-GCCAAACACACTAGCG
20006781 AACC
1 AACC
20006785 TACATGCAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.34, C:0.34, G:0.16, T:0.16
Consensus pattern (27 bp):
AACCCTAGCTCGCCAAACACACTAGCG
Found at i:20007116 original size:62 final size:64
Alignment explanation
Indices: 20007041--20007163 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 64
20007031 AAGGCTTCTA
20007041 AAAGTCCTATTTATAT-ACCTAATTTCATGTGAAAATATGA-AAAAA-ATCCCTAGAATAATAAG
1 AAAGTCCTATTTATATGA-CTAATTTCATGTGAAAATATGACAAAAACATCCCTAGAATAATAAG
* * *
20007103 AAAGTCCTATTTATATGATTAATTTCGTGTGAAAATGTGACAAAAACATCCCTAGAATAAT
1 AAAGTCCTATTTATATGACTAATTTCATGTGAAAATATGACAAAAACATCCCTAGAATAAT
20007164 CAGAGTTAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
62 35 0.64
63 6 0.11
64 14 0.25
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (64 bp):
AAAGTCCTATTTATATGACTAATTTCATGTGAAAATATGACAAAAACATCCCTAGAATAATAAG
Found at i:20008860 original size:30 final size:30
Alignment explanation
Indices: 20008826--20008892 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
20008816 GATGATTTTT
* *
20008826 ATATTTATCATGTTGATAATTTATTGAATG
1 ATATTTATAATGTTGATAATTTATTGAATA
*
20008856 ATATTTATAATGTTTATAATTTATTGAATA
1 ATATTTATAATGTTGATAATTTATTGAATA
20008886 ATATTTA
1 ATATTTA
20008893 AGAGTAGCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.52
Consensus pattern (30 bp):
ATATTTATAATGTTGATAATTTATTGAATA
Found at i:20010168 original size:46 final size:46
Alignment explanation
Indices: 20010116--20010212 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
20010106 CTTTTAAAAC
20010116 ACTTGTATTTAATTGTAATGAATGTGCATAATCGAGTAATTGATAT
1 ACTTGTATTTAATTGTAATGAATGTGCATAATCGAGTAATTGATAT
*
20010162 ACTTGTATTTAATTGTAATGAATGTGCATAATTGAGTAATTGATAT
1 ACTTGTATTTAATTGTAATGAATGTGCATAATCGAGTAATTGATAT
20010208 ACTTG
1 ACTTG
20010213 GAATATTAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (46 bp):
ACTTGTATTTAATTGTAATGAATGTGCATAATCGAGTAATTGATAT
Found at i:20010410 original size:24 final size:27
Alignment explanation
Indices: 20010347--20010415 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 27
20010337 TGACTCACCG
20010347 CAGCTCGTATGAGCTTA-TCGATATAT
1 CAGCTCGTATGAGCTTACTCGATATAT
* * *
20010373 TAGCTCGTAAGAGCTTACT-G-T-TCT
1 CAGCTCGTATGAGCTTACTCGATATAT
20010397 CAGCTCGTATGAGCTTACT
1 CAGCTCGTATGAGCTTACT
20010416 AATTCAACTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 19 0.51
25 1 0.03
26 16 0.43
27 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (27 bp):
CAGCTCGTATGAGCTTACTCGATATAT
Found at i:20010487 original size:26 final size:26
Alignment explanation
Indices: 20010453--20010513 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
20010443 CAGCTCAATA
*
20010453 AAGCTTACTGTCAATCAGCTCAGGAG
1 AAGCTTACTGTCAATCAGCTCAGAAG
* * *
20010479 GAGCTTACTGTCTATTAGCTCAGAAG
1 AAGCTTACTGTCAATCAGCTCAGAAG
20010505 AAGCTTACT
1 AAGCTTACT
20010514 ATTCATAGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (26 bp):
AAGCTTACTGTCAATCAGCTCAGAAG
Found at i:20011657 original size:66 final size:65
Alignment explanation
Indices: 20011533--20011677 Score: 157
Period size: 66 Copynumber: 2.2 Consensus size: 65
20011523 ACACGGTCTC
* *
20011533 ACACACGGGTGTGTGACAGGCCGTGTGGTACAAGTCAGTATACCCCCTATTTGGCACACGACCTA
1 ACACACGGGCGTGTGACAGGCCGTGTGGCACAAGTCAGTATACCCCCTATTTGGCACACGACCTA
* * * * * * * *
20011598 ACACATGGGCGTGTGACTTGGCCGTGTTGCATAAGTCAGTATACTCTCTAGTTT-TCACACGGCC
1 ACACACGGGCGTGTGAC-AGGCCGTGTGGCACAAGTCAGTATACCCCCTA-TTTGGCACACGACC
*
20011662 TG
64 TA
*
20011664 GCACACGGGCGTGT
1 ACACACGGGCGTGT
20011678 CTTCGGCCAT
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
65 15 0.23
66 47 0.72
67 3 0.05
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (65 bp):
ACACACGGGCGTGTGACAGGCCGTGTGGCACAAGTCAGTATACCCCCTATTTGGCACACGACCTA
Found at i:20012991 original size:25 final size:25
Alignment explanation
Indices: 20012943--20012993 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
20012933 ATGAAAGTAC
**
20012943 CTTCACTATTAAACAATCGCAGATG
1 CTTCACTATTAAACAATCAAAGATG
20012968 CTTCACTATTAAACAATCAAAGATG
1 CTTCACTATTAAACAATCAAAGATG
20012993 C
1 C
20012994 AAATGCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (25 bp):
CTTCACTATTAAACAATCAAAGATG
Found at i:20024653 original size:4 final size:4
Alignment explanation
Indices: 20024640--20024681 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
20024630 TAAATAAACA
* * *
20024640 AATG AGTG AATG AATG AATG GATG AATG AATG AATG ATTG AA
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AA
20024682 ATTAGGGCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (4 bp):
AATG
Found at i:20029707 original size:40 final size:40
Alignment explanation
Indices: 20029663--20029865 Score: 193
Period size: 40 Copynumber: 5.1 Consensus size: 40
20029653 CGGGATTTAA
* *
20029663 CCGGATATAGCT-ACTCGCTCGAATGCCTTCAGGACATAGC
1 CCGGATATAG-TAACTCGCACGAATGCCTTCGGGACATAGC
* *
20029703 CCGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGACATAGC
* * *
20029743 CCGGACATAATAACTCGCACGGATGCCTTCGGGA-ATTAGC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGACA-TAGC
* * * *
20029783 CCGGGTATAATAACTCACAC-AATTGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACGAA-TGCCTTCGGGACATAGC
* * *
20029822 CCGGA-ATTAGTCACTAC-CACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACT-CGCACGAATGCCTTCGGGACATAGC
20029862 CCGG
1 CCGG
20029866 TTATCATCTG
Statistics
Matches: 138, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
38 1 0.01
39 29 0.21
40 108 0.78
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.22
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACGAATGCCTTCGGGACATAGC
Found at i:20029861 original size:79 final size:80
Alignment explanation
Indices: 20029675--20029865 Score: 219
Period size: 80 Copynumber: 2.4 Consensus size: 80
20029665 GGATATAGCT
* * * * * *
20029675 ACTCGCTCGAATGCCTTCAGGACATAGCCCGGATATAGTAACTCGCACCAATGCCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCACACCAATGCCTTCGGGACTT
20029740 AGCCCGGACATAATA
66 AGCCCGGACATAATA
** * *
20029755 ACTCGCACGGATGCCTTCGGGAATTAGCCCGGGTATAATAACTCACA-CAATTGCCTTCGGG-CT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCACACCAA-TGCCTTCGGGACT
* *
20029818 TAGCCCGGA-ATTAGTC
65 TAGCCCGGACA-TAATA
20029834 ACTAC-CACAAATGCCTTCGGGACTTAGCCCGG
1 ACT-CGCACAAATGCCTTCGGGACTTAGCCCGG
20029866 TTATCATCTG
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
78 1 0.01
79 44 0.46
80 50 0.53
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.22
Consensus pattern (80 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCACACCAATGCCTTCGGGACTT
AGCCCGGACATAATA
Found at i:20038736 original size:40 final size:40
Alignment explanation
Indices: 20038676--20038859 Score: 214
Period size: 40 Copynumber: 4.6 Consensus size: 40
20038666 TATTCGAATG
* *
20038676 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGTTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
20038716 ATATCCGGACTAAGATCCGAAGGCATTTGTGCAAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* *
20038756 ATATCCGGGCTAAGA-CTCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATC-CGAAGGCATTTATGCTAGTGACT
*
20038796 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* *
20038836 ATATCCGAGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
20038860 CTTGTGCGAG
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 2 0.02
40 118 0.95
41 4 0.03
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:20038809 original size:80 final size:80
Alignment explanation
Indices: 20038676--20038859 Score: 237
Period size: 80 Copynumber: 2.3 Consensus size: 80
20038666 TATTCGAATG
* * * *
20038676 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGTTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC
* *
20038740 ATTTGTGCAAGTTG-CT
65 ATTTATGCAAG-TGACC
* * *
20038756 ATATCCGGGCTAAGACTCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
*
20038821 TTTATGCTAGTGACC
66 TTTATGCAAGTGACC
*
20038836 ATATCCGAGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
20038860 CTTGTGCGAG
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
79 3 0.03
80 87 0.97
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
TTTATGCAAGTGACC
Found at i:20041017 original size:29 final size:29
Alignment explanation
Indices: 20040942--20041037 Score: 124
Period size: 28 Copynumber: 3.3 Consensus size: 29
20040932 AAGTCTACAT
* *
20040942 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
20040970 TCATTTATATGGCCCATTAGGCCCCAAATC
1 ACATTCATATGGCCCATTAGG-CCCAAATC
*
20041000 ACATTCATATGG-CTATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
20041028 ACATTCATAT
1 ACATTCATAT
20041038 ACATACTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
28 35 0.59
29 10 0.17
30 14 0.24
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:20042844 original size:16 final size:16
Alignment explanation
Indices: 20042825--20042855 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20042815 CTTCTTCACT
20042825 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
20042841 TACTTACTTACTTAA
1 TACTCACTTACTTAA
20042856 TCAAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:20042861 original size:20 final size:20
Alignment explanation
Indices: 20042822--20042861 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20042812 AAACTTCTTC
* *
20042822 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
20042842 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
20042862 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:20043246 original size:108 final size:110
Alignment explanation
Indices: 20043093--20043290 Score: 319
Period size: 108 Copynumber: 1.8 Consensus size: 110
20043083 ATCCTTTTGA
* * *
20043093 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTAGCCTTGCCTTATGAA-CTCACCAA-
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATAGCCTTGCCTTAGGAACCTCACCAAT
20043156 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
66 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* ** *
20043201 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGGAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATAGCCTTGCCTTAGGAACCTCACCAAT
20043266 TGCCATGCCTTGGCATGGTCTTACA
66 TGCCATGCCTTGGCATGGTCTTACA
20043291 CGGTATCCTT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 49 0.60
109 7 0.09
110 25 0.31
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATAGCCTTGCCTTAGGAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:20043300 original size:55 final size:54
Alignment explanation
Indices: 20043046--20043300 Score: 258
Period size: 55 Copynumber: 4.8 Consensus size: 54
20043036 ACATGGGTAC
* * * *
20043046 CTTACC-ATTTCCATGACTTGTCATGGTCTTACATGGTATCCTT---TT-GAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGGAA
* * *
20043095 CTTACC-ATTGCCATGTCTTGACATGGTCTTACATGGTAGCCTTGCCTTATGAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGGAA
* * * *
20043148 CTCACCAA-TGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCC-T-TAGGAA
* * * *
20043203 CTTATCAA-TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGGAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGGAA
* *
20043256 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACACGGTATCCTT
1 -CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTT
20043301 AAACCATAAT
Statistics
Matches: 169, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
49 39 0.23
52 4 0.02
53 44 0.26
54 10 0.06
55 70 0.41
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (54 bp):
CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGGAA
Done.