Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 69 of 202
Found at i:20387589 original size:3 final size:3
Alignment explanation
Indices: 20387581--20387619 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
20387571 ATTAATCTTG
*
20387581 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA
20387620 CCATGTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:20392404 original size:2 final size:2
Alignment explanation
Indices: 20392391--20392420 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20392381 TAATTAACAA
*
20392391 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20392421 TAGAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20392980 original size:29 final size:29
Alignment explanation
Indices: 20392948--20393006 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
20392938 TAAAAATTTA
20392948 AAAAATTA-TAAAAACTATT-TTTAAAAAAT
1 AAAAATTATTAAAAA--ATTATTTAAAAAAT
20392977 AAAAATTATTAAAAAATTATTTAAAAAAT
1 AAAAATTATTAAAAAATTATTTAAAAAAT
20393006 A
1 A
20393007 TTTTTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 3 0.11
29 19 0.68
30 6 0.21
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAAATTATTAAAAAATTATTTAAAAAAT
Found at i:20392989 original size:40 final size:39
Alignment explanation
Indices: 20392926--20393012 Score: 113
Period size: 38 Copynumber: 2.2 Consensus size: 39
20392916 CATTTAATTA
** *
20392926 ATTTTTAAAATTTAAAAATTTAAAAAATTA-TAAAAACT
1 ATTTTTAAAAAATAAAAATTTAAAAAATTATTAAAAAAT
20392964 ATTTTTAAAAAATAAAAATTATTAAAAAATTATTTAAAAAAT
1 ATTTTTAAAAAATAAAAA-T-TTAAAAAATTA-TTAAAAAAT
20393006 ATTTTTA
1 ATTTTTA
20393013 TATTTTAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 16 0.38
39 1 0.02
40 11 0.26
42 14 0.33
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (39 bp):
ATTTTTAAAAAATAAAAATTTAAAAAATTATTAAAAAAT
Found at i:20392993 original size:11 final size:12
Alignment explanation
Indices: 20392977--20393009 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
20392967 TTTAAAAAAT
20392977 AAAAATTA-TTA
1 AAAAATTATTTA
20392988 AAAAATTATTTA
1 AAAAATTATTTA
20393000 AAAAA-TATTT
1 AAAAATTATTT
20393010 TTATATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAAATTATTTA
Found at i:20393347 original size:20 final size:20
Alignment explanation
Indices: 20393310--20393347 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20393300 AGAATAAACT
*
20393310 TTTACCAAAATATTTAAAGA
1 TTTACCAAAATATCTAAAGA
20393330 TTTACCAATAAT-TCTAAA
1 TTTACCAA-AATATCTAAA
20393348 ATCATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (20 bp):
TTTACCAAAATATCTAAAGA
Found at i:20408625 original size:16 final size:14
Alignment explanation
Indices: 20408584--20408644 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 14
20408574 ATAATAATAA
*
20408584 AAAAAGAAATAAAAG
1 AAAAAGAAA-CAAAG
20408599 AAAAAGAAACAAAG
1 AAAAAGAAACAAAG
20408613 AACAAACGAAACAGGAAG
1 AA-AAA-GAAACA--AAG
*
20408631 AAAAAGAAAAAAAG
1 AAAAAGAAACAAAG
20408645 GGGAACAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 9 0.22
15 12 0.30
16 11 0.28
17 3 0.08
18 5 0.12
ACGTcount: A:0.75, C:0.07, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAAAGAAACAAAG
Found at i:20410230 original size:2 final size:2
Alignment explanation
Indices: 20410223--20410261 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
20410213 ATTGGTTGGT
*
20410223 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20410262 GTGTTTATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20416242 original size:33 final size:32
Alignment explanation
Indices: 20416185--20416247 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
20416175 TATAATAATC
*
20416185 AAACAAAGAAATAAAAGAAAAAAATAGAAAAAA
1 AAACAAAGAAACAAAAGAAAAAAATA-AAAAAA
*
20416218 AAACAAAG-AACAAACGAAAGAAAATAAAAA
1 AAACAAAGAAACAAAAGAAA-AAAATAAAAA
20416248 GGCGAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.79, C:0.06, G:0.10, T:0.05
Consensus pattern (32 bp):
AAACAAAGAAACAAAAGAAAAAAATAAAAAAA
Found at i:20416415 original size:24 final size:24
Alignment explanation
Indices: 20416383--20416431 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
20416373 GTCAAAATTT
20416383 TAGAAATTATTAAGTTTTTAAGTG
1 TAGAAATTATTAAGTTTTTAAGTG
20416407 TAGAAATTATTAAGTTTTTAAGTG
1 TAGAAATTATTAAGTTTTTAAGTG
20416431 T
1 T
20416432 TTTTTTTGTT
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:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (24 bp):
TAGAAATTATTAAGTTTTTAAGTG
Found at i:20418876 original size:18 final size:17
Alignment explanation
Indices: 20418853--20418888 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
20418843 TCAATTTTCA
20418853 AATTCAAAAAACTCGAAT
1 AATTCAAAAAACT-GAAT
*
20418871 AATTCAAATAACTGAAT
1 AATTCAAAAAACTGAAT
20418888 A
1 A
20418889 CCAAACTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (17 bp):
AATTCAAAAAACTGAAT
Found at i:20419206 original size:329 final size:330
Alignment explanation
Indices: 20418618--20419276 Score: 1194
Period size: 329 Copynumber: 2.0 Consensus size: 330
20418608 TACTTTTAGG
*
20418618 AAATCTCCTCGATGAGATCCACGTGAGAATCCTACCTTGGGGTGGTTAAATTTTCATGTCATCAC
1 AAATCTCCTCGATGAGATCCACGTGAGAATCCTACCTTGGGGTAGTTAAATTTTCATGTCATCAC
*
20418683 AAGAGACCATTAATAAATGACGTAGGTAGAAGTAAGCAAAATTTAATTCGATTCAAAAAATTGAG
66 AAGAGACCATTAATAAATGACGTAGGTAGAACTAAGCAAAATTTAATTCGATTCAAAAAATTGAG
*
20418748 AAAAAGAAGTTCACATTTCAAATTATTTGAATTGATTTAATCGAGTTAATCGAGTCAACTCGATA
131 AAAAAGAAGTTCACATTTCAAATTATTCGAATTGATTTAATCGAGTTAATCGAGTCAACTCGATA
*
20418813 TTGTTTTCTAATTTTGAGTTCGAGTCAAGTTCAATTTTCAAATTCAAAAAACTCGAATAATTCAA
196 TTGTTTTCAAATTTTGAGTTCGAGTCAAGTTCAATTTTCAAATTCAAAAAACTCGAATAATTCAA
*
20418878 ATAACTGAATACCAAACTACCCCTTCTCCCCCACGCCCCTATTCTTTTCAAAAAAAATTTTACTT
261 ATAACTGAATACCAAACTACCCCTTCTCCCCCACGCCCCTATTCTTTTCAAAAAAAAATTTACTT
20418943 TCCCT
326 TCCCT
20418948 AAATCTCCTCGATGAGATCCACGTGAGAATCCTACCTTGGGGTAGTTAAATTTTCATGTCATCAC
1 AAATCTCCTCGATGAGATCCACGTGAGAATCCTACCTTGGGGTAGTTAAATTTTCATGTCATCAC
* *
20419013 AAGAGACCATTAATAAATGACGTAGGTAGAACTGAGTAAAA-TTAATTCGATTCAAAAAATTGAG
66 AAGAGACCATTAATAAATGACGTAGGTAGAACTAAGCAAAATTTAATTCGATTCAAAAAATTGAG
* *
20419077 AAAAAGAAGTTCACATTTCAAATTATTCGAATTGATTTAATTGAGTTAATCGAGTCAGCTCGATA
131 AAAAAGAAGTTCACATTTCAAATTATTCGAATTGATTTAATCGAGTTAATCGAGTCAACTCGATA
* * *
20419142 TTGTTTTCAAATTTTGAGTTCGAGTCAAGTTCAATTTTCGAATTCAAAAAATTCGACTAATTCAA
196 TTGTTTTCAAATTTTGAGTTCGAGTCAAGTTCAATTTTCAAATTCAAAAAACTCGAATAATTCAA
*
20419207 ATAACTGACTACCAAACTACCCCTTCTCCCCCACGCCCCTATTCTTTTCAAAAAAAAATTTACTT
261 ATAACTGAATACCAAACTACCCCTTCTCCCCCACGCCCCTATTCTTTTCAAAAAAAAATTTACTT
20419272 TCCCT
326 TCCCT
20419277 CCCTCTTTTA
Statistics
Matches: 316, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
329 214 0.68
330 102 0.32
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (330 bp):
AAATCTCCTCGATGAGATCCACGTGAGAATCCTACCTTGGGGTAGTTAAATTTTCATGTCATCAC
AAGAGACCATTAATAAATGACGTAGGTAGAACTAAGCAAAATTTAATTCGATTCAAAAAATTGAG
AAAAAGAAGTTCACATTTCAAATTATTCGAATTGATTTAATCGAGTTAATCGAGTCAACTCGATA
TTGTTTTCAAATTTTGAGTTCGAGTCAAGTTCAATTTTCAAATTCAAAAAACTCGAATAATTCAA
ATAACTGAATACCAAACTACCCCTTCTCCCCCACGCCCCTATTCTTTTCAAAAAAAAATTTACTT
TCCCT
Found at i:20419389 original size:32 final size:32
Alignment explanation
Indices: 20419311--20419391 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 32
20419301 AAATCCCCAC
*
20419311 AAATATTTTATTTCCCCCTCCTTTACCCTAAA
1 AAATCTTTTATTTCCCCCTCCTTTACCCTAAA
*
20419343 AAATC-TTTACTTTCCTTCC-CCTTTACTCC-AAA
1 AAATCTTTTA-TTTCC-CCCTCCTTTAC-CCTAAA
20419375 AAATCTTTTATTTCCCC
1 AAATCTTTTATTTCCCC
20419392 ATTTACCCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
31 5 0.12
32 29 0.69
33 8 0.19
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (32 bp):
AAATCTTTTATTTCCCCCTCCTTTACCCTAAA
Found at i:20424091 original size:106 final size:106
Alignment explanation
Indices: 20423906--20424116 Score: 298
Period size: 106 Copynumber: 2.0 Consensus size: 106
20423896 TTTCTAAATA
* *
20423906 AGGCAATATTTCGCGTTTAGAAAATCGAGAAAATGTGCCCTAACGTGTCGGGTTCCGACTTCTTG
1 AGGCAATATTTCGCGTTTAGAAAATCGAGAAAACGTGCCCTAACGTGTCGGGTTCCGACTTCTCG
* * * *
20423971 TTTGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAGTG
66 TTCGACCAAATAGCCAAATACCCTCTTAAAACTTCAAAGTG
* * * * *
20424012 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGAT-GGGTTTCGATTTCTC
1 AGGCAATATTTCGCGTTTAGAAAATCGAGAAAACGTGCCCTAACGTG-TCGGGTTCCGACTTCTC
*
20424076 GTTCGACTAAATAGCCAAATACCCTCTTAAAACTTCAAAGT
65 GTTCGACCAAATAGCCAAATACCCTCTTAAAACTTCAAAGT
20424117 ATGGTTTCAT
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
106 91 0.99
107 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (106 bp):
AGGCAATATTTCGCGTTTAGAAAATCGAGAAAACGTGCCCTAACGTGTCGGGTTCCGACTTCTCG
TTCGACCAAATAGCCAAATACCCTCTTAAAACTTCAAAGTG
Found at i:20425036 original size:3 final size:3
Alignment explanation
Indices: 20425028--20425053 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20425018 CCAAGAAGGG
20425028 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
20425054 TGGTGATGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:20429564 original size:13 final size:14
Alignment explanation
Indices: 20429546--20429575 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
20429536 CCTAAACCTT
20429546 GAATCCCAAA-CCC
1 GAATCCCAAATCCC
20429559 GAATCCCAAATCCC
1 GAATCCCAAATCCC
20429573 GAA
1 GAA
20429576 CTTGAATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.40, C:0.40, G:0.10, T:0.10
Consensus pattern (14 bp):
GAATCCCAAATCCC
Found at i:20430919 original size:44 final size:45
Alignment explanation
Indices: 20430833--20430922 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
20430823 TTTGGTTCGC
* * *
20430833 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
20430878 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
20430922 T
1 T
20430923 AGAATAGAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.38
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:20430939 original size:39 final size:43
Alignment explanation
Indices: 20430843--20430946 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 43
20430833 TGTATTGGAT
20430843 TAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAATGTAATGGAA
1 TAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA-GTAA-GGAA
* ***
20430888 TAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA-T-A-GAA
1 TAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAAGTAAGGAA
20430927 TAGAGGTGTAATAGCATAAT
1 TAGAGGTGTAATAGC-TAAT
20430947 GGAAAAAACT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
39 16 0.31
41 5 0.10
42 1 0.02
44 17 0.33
45 13 0.25
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.34
Consensus pattern (43 bp):
TAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAAGTAAGGAA
Found at i:20432053 original size:3 final size:3
Alignment explanation
Indices: 20432047--20432094 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
20432037 TTTGTTGTTG
20432047 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20432095 CTATATATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20453640 original size:45 final size:43
Alignment explanation
Indices: 20453575--20453670 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
20453565 TGAATACAAA
* ** *
20453575 AGATCTTGTCTTCCTATACTGGTGGTGAAGTAGATCCAAGAAAAC
1 AGATCTTGTCTTCATATACTGG-CATGAAGTAGATCAAAG-AAAC
*
20453620 AGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGAAAC
1 AGATCTTGTCTTCATATACTGGCATGAAGTAGATCAAAGAAAC
20453663 AGATCTTG
1 AGATCTTG
20453671 CCTCCCTAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 12 0.26
44 14 0.30
45 20 0.43
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (43 bp):
AGATCTTGTCTTCATATACTGGCATGAAGTAGATCAAAGAAAC
Found at i:20453958 original size:89 final size:89
Alignment explanation
Indices: 20453789--20454231 Score: 478
Period size: 89 Copynumber: 5.0 Consensus size: 89
20453779 ATCAATCGGA
* * *
20453789 AAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCC
1 AAAA-CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCT
* *
20453854 ATACTGGTGGCGAAGTAGATCGAAG
65 ATACTGGTCGTGAAGTAGATCGAAG
* *
20453879 AAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCCTGTCTTCCTA
1 AAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTA
* * *
20453944 TATTGGTAGTGAAGTGGATCGAAG
66 TACTGGTCGTGAAGTAGATCGAAG
** * * * *
20453968 -ATGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAATATAGCAGATCTTGTCTTCCCA
1 AAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTA
* *
20454032 TACTGGTGGCGAAGTAGATCGAAG
66 TACTGGTCGTGAAGTAGATCGAAG
* * * * * * * * * * *
20454056 AGAGCAAATCTTATCTTCATGTATTGGCGTGAAGTAGATTGAAGAAAACAGATCTTGTCGTCATG
1 AAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTA
*
20454121 TACTGG-CGTGAAGTAGATCAAAG
66 TACTGGTCGTGAAGTAGATCGAAG
* *** * * * * *
20454144 ATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGGTCTTGTCTTCAT
1 AAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCT
* *
20454209 GTATTGG-CGTGAAGTAGATCGAA
65 ATACTGGTCGTGAAGTAGATCGAA
20454232 TATCGCAGAT
Statistics
Matches: 300, Mismatches: 51, Indels: 5
0.84 0.14 0.01
Matches are distributed among these distances:
88 109 0.36
89 187 0.62
90 4 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (89 bp):
AAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTA
TACTGGTCGTGAAGTAGATCGAAG
Found at i:20453999 original size:177 final size:177
Alignment explanation
Indices: 20453792--20454161 Score: 517
Period size: 177 Copynumber: 2.1 Consensus size: 177
20453782 AATCGGAAAA
*
20453792 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATA
* *
20453857 CTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAA
66 CTGGTGGCGAAGTAGATCGAAGAAAACAAATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAA
* * * * * * *
20453922 GATAGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGAT
131 GAAAACAGATCCTGTCGTCATATACTGG-AGTGAAGTAGATCAAAGAT
* * * *
20453970 -GCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAATATAGCAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATA
* * * **
20454034 CTGGTGGCGAAGTAGATCGAAGAGAGCAAATCTTATCTTCATGTATTGGCGTGAAGTAGATTGAA
66 CTGGTGGCGAAGTAGATCGAAGAAAACAAATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAA
* * *
20454099 GAAAACAGATCTTGTCGTCATGTACTGGCGTGAAGTAGATCAAAGAT
131 GAAAACAGATCCTGTCGTCATATACTGGAGTGAAGTAGATCAAAGAT
*
20454146 AACAGATCTTGTCTTC
1 AGCAGATCTTGTCTTC
20454162 CCATACTGGT
Statistics
Matches: 168, Mismatches: 23, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
176 16 0.10
177 152 0.90
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (177 bp):
AGCAGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATA
CTGGTGGCGAAGTAGATCGAAGAAAACAAATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAA
GAAAACAGATCCTGTCGTCATATACTGGAGTGAAGTAGATCAAAGAT
Found at i:20454046 original size:133 final size:132
Alignment explanation
Indices: 20453790--20454248 Score: 533
Period size: 133 Copynumber: 3.4 Consensus size: 132
20453780 TCAATCGGAA
* * * ***
20453790 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT-GCAGATCTTGTCTTCATG
* * * * *** * *
20453855 TACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC
65 TACTAG-CGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
*
20453919 AAAG
129 GAAG
* * * * * *
20453923 ATAGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCATG
1 AAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATGCAGATCTTGTCTTCATG
* * *
20453988 TATTAGCGTGAAGTAGATCGAATATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
65 TACTAGCGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
20454053 AAG
130 AAG
* * * * ** *
20454056 AGAGCAAATCTTATCTTCATGTATTGGCGTGAAGTAGATTGAAGAAAACAGATCTTGTCGTCATG
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-ATGCAGATCTTGTCTTCATG
* *
20454121 TACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
65 TACTAGCGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
20454186 AAG
130 AAG
* * *
20454189 AAAGCAGGTCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAATATCGCAGATCTGGTCT
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT-GCAGATCTTGTCT
20454249 CTCTGAAGTT
Statistics
Matches: 270, Mismatches: 52, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
132 51 0.19
133 203 0.75
134 16 0.06
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (132 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATGCAGATCTTGTCTTCATGT
ACTAGCGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
AG
Found at i:20454111 original size:39 final size:39
Alignment explanation
Indices: 20454068--20454155 Score: 95
Period size: 44 Copynumber: 2.1 Consensus size: 39
20454058 AGCAAATCTT
* **
20454068 ATCTTCATGTATTGGCGTGAAGTAGATTGAAGAAAACAG
1 ATCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAG
*
20454107 ATCTTGTCGTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG
1 ATC---T--TCATGTACTGGCGTGAAGTAGATCAAAGAAAACAG
20454151 ATCTT
1 ATCTT
20454156 GTCTTCCCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
39 4 0.10
41 1 0.03
42 1 0.03
44 34 0.85
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30
Consensus pattern (39 bp):
ATCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAG
Found at i:20454241 original size:89 final size:89
Alignment explanation
Indices: 20454086--20454248 Score: 236
Period size: 89 Copynumber: 1.8 Consensus size: 89
20454076 GTATTGGCGT
*
20454086 GAAGTAGATTGAAGAAAACAGATCTTGTCGTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG
1 GAAGTAGATCGAAGAAAACAGATCTTGTCGTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG
*
20454151 ATCTTGTCTTCCCATACTGGTGGC
66 ATCTGGTCTTCCCATACTGGTGGC
* * * * * * **
20454175 GAAGTAGATCGAAGAAAGCAGGTCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAATATCGCAG
1 GAAGTAGATCGAAGAAAACAGATCTTGTCGTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG
20454240 ATCTGGTCT
66 ATCTGGTCT
20454249 CTCTGAAGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
89 64 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (89 bp):
GAAGTAGATCGAAGAAAACAGATCTTGTCGTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG
ATCTGGTCTTCCCATACTGGTGGC
Found at i:20455662 original size:3 final size:3
Alignment explanation
Indices: 20455656--20455712 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
20455646 TTTATTGTTG
20455656 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20455704 TTA TTA TTA
1 TTA TTA TTA
20455713 CTATATATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20457071 original size:16 final size:16
Alignment explanation
Indices: 20457034--20457088 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
20457024 TTAATCATAT
*
20457034 TTAAACATA-ATTATAA
1 TTAAA-ATATATTTTAA
20457050 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
20457065 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
20457083 -TAAAAT
1 TTAAAAT
20457089 TCTTATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:20457081 original size:18 final size:18
Alignment explanation
Indices: 20457040--20457088 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
20457030 ATATTTAAAC
20457040 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
20457058 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
20457074 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
20457089 TCTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:20462138 original size:12 final size:11
Alignment explanation
Indices: 20462098--20462135 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
20462088 ATAATGAGAT
20462098 TATTAAAAAAA
1 TATTAAAAAAA
20462109 TA-T-AAAAAA
1 TATTAAAAAAA
20462118 TATTAATAAAAA
1 TATTAA-AAAAA
20462130 TATTAA
1 TATTAA
20462136 TAATGTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.33
10 2 0.08
11 3 0.12
12 11 0.46
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TATTAAAAAAA
Found at i:20465093 original size:25 final size:26
Alignment explanation
Indices: 20465055--20465112 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
20465045 AAATTTAGTA
*
20465055 GTAAAATGGATAAAA-TTTACCAGGG
1 GTAAAATCGATAAAATTTTACCAGGG
* **
20465080 GTAAAATCGTTAAAATTTTATTAGGG
1 GTAAAATCGATAAAATTTTACCAGGG
20465106 GTAAAAT
1 GTAAAAT
20465113 AGGGATGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (26 bp):
GTAAAATCGATAAAATTTTACCAGGG
Found at i:20470542 original size:25 final size:26
Alignment explanation
Indices: 20470496--20470559 Score: 103
Period size: 25 Copynumber: 2.5 Consensus size: 26
20470486 ACATATTTTC
20470496 TCAAAATTTTACTCGGGGTAAAATCG
1 TCAAAATTTTACTCGGGGTAAAATCG
*
20470522 TCAAAATTTTA-TCGGGGTAAAATTG
1 TCAAAATTTTACTCGGGGTAAAATCG
*
20470547 TTAAAATTTTACT
1 TCAAAATTTTACT
20470560 GGGACTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 23 0.66
26 12 0.34
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (26 bp):
TCAAAATTTTACTCGGGGTAAAATCG
Found at i:20471703 original size:36 final size:36
Alignment explanation
Indices: 20471658--20471886 Score: 234
Period size: 35 Copynumber: 6.4 Consensus size: 36
20471648 GCTGAGTTTT
*
20471658 AAAGAGTTGGGATAGACCATTCTATGCCAACCTTAAA
1 AAAG-GTTGGGATAGACCAGTCTATGCCAACCTTAAA
* *
20471695 AAAGGTTGGGATAGACCCA-TCTAAGGCAA-CTTAAA
1 AAAGGTTGGGATAGA-CCAGTCTATGCCAACCTTAAA
* * *
20471730 AAAGTTTGGGATAAACCATTCTATGCCAACCTTAAA
1 AAAGGTTGGGATAGACCAGTCTATGCCAACCTTAAA
* * ** **
20471766 AAAGGTTGGGATAGACCCGTCTAAGGTAA-CTTTTA
1 AAAGGTTGGGATAGACCAGTCTATGCCAACCTTAAA
*
20471801 AAAGGTTGGGATAGACTAGTCTATGCCAACCTT-AA
1 AAAGGTTGGGATAGACCAGTCTATGCCAACCTTAAA
* * * * *
20471836 AAAGGTTGGGATAGACCCGTCTAAGGCAA-ATTTAA
1 AAAGGTTGGGATAGACCAGTCTATGCCAACCTTAAA
*
20471871 AAAGGTTGGAATAGAC
1 AAAGGTTGGGATAGAC
20471887 TTTATCTGCG
Statistics
Matches: 160, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
34 5 0.03
35 98 0.61
36 50 0.31
37 7 0.04
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (36 bp):
AAAGGTTGGGATAGACCAGTCTATGCCAACCTTAAA
Found at i:20471748 original size:71 final size:71
Alignment explanation
Indices: 20471658--20471886 Score: 352
Period size: 71 Copynumber: 3.2 Consensus size: 71
20471648 GCTGAGTTTT
*
20471658 AAAGAGTTGGGATAGACCATTCTATGCCAACCTTAAAAAAGGTTGGGATAGACCCATCTAAGGCA
1 AAAG-GTTGGGATAGACCATTCTATGCCAACCTTAAAAAAGGTTGGGATAGACCCGTCTAAGGCA
*
20471723 ACTTAAA
65 ACTTTAA
* * *
20471730 AAAGTTTGGGATAAACCATTCTATGCCAACCTTAAAAAAGGTTGGGATAGACCCGTCTAAGGTAA
1 AAAGGTTGGGATAGACCATTCTATGCCAACCTTAAAAAAGGTTGGGATAGACCCGTCTAAGGCAA
*
20471795 CTTTTA
66 CTTTAA
* *
20471801 AAAGGTTGGGATAGACTAGTCTATGCCAACCTT-AAAAAGGTTGGGATAGACCCGTCTAAGGCAA
1 AAAGGTTGGGATAGACCATTCTATGCCAACCTTAAAAAAGGTTGGGATAGACCCGTCTAAGGCAA
*
20471865 ATTTAA
66 CTTTAA
*
20471871 AAAGGTTGGAATAGAC
1 AAAGGTTGGGATAGAC
20471887 TTTATCTGCG
Statistics
Matches: 143, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
70 49 0.34
71 90 0.63
72 4 0.03
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (71 bp):
AAAGGTTGGGATAGACCATTCTATGCCAACCTTAAAAAAGGTTGGGATAGACCCGTCTAAGGCAA
CTTTAA
Found at i:20473886 original size:17 final size:18
Alignment explanation
Indices: 20473864--20473897 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20473854 AAATGGTTTC
*
20473864 GTTATAA-ATTTTTTAAG
1 GTTATAATATTTATTAAG
20473881 GTTATAATATTTATTAA
1 GTTATAATATTTATTAA
20473898 TTTTTAGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
GTTATAATATTTATTAAG
Found at i:20474231 original size:126 final size:126
Alignment explanation
Indices: 20473996--20474238 Score: 319
Period size: 126 Copynumber: 1.9 Consensus size: 126
20473986 AGTCAACATT
* * * * * *
20473996 GTGTTGGACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGGCATCCATATCTCAGCCCTTATACA
1 GTGTTGCAAAAAGCCGAATCTTATTTAAGTGTTGCCTTAGGCATCCATATCACAACACTTATACA
* *
20474061 AAGAGTTGGCCTAAGTGTATGTCGACAAGTCTATCCCAACACTTAGGAAAGTGTCGGCTTA
66 AAGAGTTGGCCTAAGTGTATGTCGACAAGTCTATCCAAACACTTAAGAAAGTGTCGGCTTA
* * * *
20474122 GTGTTGCAAAAAGTCGAATCTTATTTAAGTGTTGCCTTAGGCGTGCATTTCACAACACTTATACA
1 GTGTTGCAAAAAGCCGAATCTTATTTAAGTGTTGCCTTAGGCATCCATATCACAACACTTATACA
* * *
20474187 AAGAGTTGG-CTAAAGTGTATGTC-AGGAAGTCTATTCAAATACTTAAGAAAGT
66 AAGAGTTGGCCT-AAGTGTATGTCGA-CAAGTCTATCCAAACACTTAAGAAAGT
20474239 TTCAGGCCAA
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
125 3 0.03
126 97 0.97
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (126 bp):
GTGTTGCAAAAAGCCGAATCTTATTTAAGTGTTGCCTTAGGCATCCATATCACAACACTTATACA
AAGAGTTGGCCTAAGTGTATGTCGACAAGTCTATCCAAACACTTAAGAAAGTGTCGGCTTA
Found at i:20474408 original size:139 final size:139
Alignment explanation
Indices: 20474108--20474528 Score: 492
Period size: 139 Copynumber: 3.1 Consensus size: 139
20474098 AACACTTAGG
* * * * * *
20474108 AAAGTGTCGGCTTAGTGTTGCAAAAAGTCGAATCTTATTTAAGTGTTGCCTTAGGCGTGCATTTC
1 AAAGTGTCGACATAGTGTTGGAAAAAGTCGACTCTTATTTAAGTGTTGCCTTAGGCATGCATATC
* * * * * * * *
20474173 ACAACACTTATACAAAGAGTTGGCTAAAGTGTATGTCAGGAAGTCTATTCAAATACTTAAGAAAG
66 -CAACCCTTATACAAAGACTTGGCCAAAGTGTATGTCAGCAAGTCTATCCCAACACTTAGGAAAG
* *
20474238 TTTCAGGCCA
130 TGTCAGCCCA
* * * * * *
20474248 AAAGTTTCAACATAGTATTGGACAAAGTCGACTCTTATTTGAGTGTTGCCTTACGCATGCATATC
1 AAAGTGTCGACATAGTGTTGGAAAAAGTCGACTCTTATTTAAGTGTTGCCTTAGGCATGCATAT-
* *
20474313 CCAACCCTTATACAAAGACTT-GCCAAAGTGTATGTCTGCAAATCTATCCCAACACTTAGGAAAG
65 CCAACCCTTATACAAAGACTTGGCCAAAGTGTATGTCAGCAAGTCTATCCCAACACTTAGGAAAG
20474377 TGTCAGCCCA
130 TGTCAGCCCA
* * *
20474387 AAAGTGTCGACATAATGTTGGATAAAGACGACTCTTATTTAAGTGTTGCCTTAGGCATGCATAT-
1 AAAGTGTCGACATAGTGTTGGAAAAAGTCGACTCTTATTTAAGTGTTGCCTTAGGCATGCATATC
* * * *
20474451 ---CCCTTATACAAAGACTTGGCCAAAGCGTATGTCCGTAAGTCTATCCCAACACTTAGGAAACT
66 CAACCCTTATACAAAGACTTGGCCAAAGTGTATGTCAGCAAGTCTATCCCAACACTTAGGAAAGT
* *
20474513 GTCGGCTCA
131 GTCAGCCCA
20474522 AAAGTGT
1 AAAGTGT
20474529 TGTCTTAGGA
Statistics
Matches: 240, Mismatches: 39, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
134 17 0.07
135 53 0.22
139 99 0.41
140 70 0.29
141 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (139 bp):
AAAGTGTCGACATAGTGTTGGAAAAAGTCGACTCTTATTTAAGTGTTGCCTTAGGCATGCATATC
CAACCCTTATACAAAGACTTGGCCAAAGTGTATGTCAGCAAGTCTATCCCAACACTTAGGAAAGT
GTCAGCCCA
Found at i:20478130 original size:35 final size:35
Alignment explanation
Indices: 20478091--20478241 Score: 176
Period size: 35 Copynumber: 4.3 Consensus size: 35
20478081 CTCCCTATTT
* * * * *
20478091 TGGTGTGTTTCGGTTCGATTATCTCTTCTAAGCAC
1 TGGTGTGTTTCGGATGGATTAGCTCTTTTGAGCAC
* * * *
20478126 TGGTGTGTTTTGGATGGATTATCTCTTTTGTGCAT
1 TGGTGTGTTTCGGATGGATTAGCTCTTTTGAGCAC
* *
20478161 TGGTGTGTTTAGGATGGATTAGCTCTTTTGAGCAT
1 TGGTGTGTTTCGGATGGATTAGCTCTTTTGAGCAC
* *
20478196 TGGTGTGTTTCAGATGGATTAGCTCTTATGAGCATC
1 TGGTGTGTTTCGGATGGATTAGCTCTTTTGAGCA-C
20478232 TGGTGTGTTT
1 TGGTGTGTTT
20478242 GGTTGGAATA
Statistics
Matches: 101, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 91 0.90
36 10 0.10
ACGTcount: A:0.15, C:0.12, G:0.28, T:0.45
Consensus pattern (35 bp):
TGGTGTGTTTCGGATGGATTAGCTCTTTTGAGCAC
Found at i:20480538 original size:140 final size:139
Alignment explanation
Indices: 20480249--20480598 Score: 551
Period size: 140 Copynumber: 2.5 Consensus size: 139
20480239 ATTTTTATTC
* * ** * * * * *
20480249 TTTCCAAAAGAATATTAACTTCCACGTATTTTATATTTTGACCGAAATTAATTAATATAACTATT
1 TTTCAAAAAGAATATTAATTTCCTTGTTTTTTATATTTTGACCAAAATTAACTAATATAATTGTT
*
20480314 TATCTTAATAAATTCGACAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAG
66 TATATTAATAAATTCGACAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAG
20480379 TTATATTTT
131 TTATATTTT
*
20480388 TTTCTAAAAGAATATTAATTTCCTTGTTTTTTATATTTTGACCAAAATTAACTAATATAATTGTT
1 TTTCAAAAAGAATATTAATTTCCTTGTTTTTTATATTTTGACCAAAATTAACTAATATAATTGTT
*
20480453 TATATTAATAAATTTGGTA-AAAATATATA-ATATTAATATTTTGTATGAATCAAATTCATATAT
66 TATATTAATAAA-TTCG-ACAAAATATATACA-ATTAATATTTTGTATGAATCAAATTCATATAT
20480516 TAGTTATATTTT
128 TAGTTATATTTT
20480528 TTTCAAAAAGAATATTAATTTCCTTGTTTTTTATATTTTGACCAAAATTAACTAATATAATTGTT
1 TTTCAAAAAGAATATTAATTTCCTTGTTTTTTATATTTTGACCAAAATTAACTAATATAATTGTT
20480593 TATATT
66 TATATT
20480599 CTTTCCAAAA
Statistics
Matches: 196, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
139 68 0.35
140 127 0.65
141 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (139 bp):
TTTCAAAAAGAATATTAATTTCCTTGTTTTTTATATTTTGACCAAAATTAACTAATATAATTGTT
TATATTAATAAATTCGACAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATATTAG
TTATATTTT
Found at i:20486613 original size:16 final size:16
Alignment explanation
Indices: 20486592--20486626 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20486582 ATATAGATCC
*
20486592 TAATTTTAGTTATTTT
1 TAATTTTAGTTAATTT
*
20486608 TAATTTTATTTAATTT
1 TAATTTTAGTTAATTT
20486624 TAA
1 TAA
20486627 GTTAGTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TAATTTTAGTTAATTT
Found at i:20505781 original size:20 final size:20
Alignment explanation
Indices: 20505756--20505800 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
20505746 GAATATATAA
20505756 TTTTAATTTGGC-TGATTTAT
1 TTTTAATTT-GCTTGATTTAT
*
20505776 TTTTAATTTGCTTTATTTAT
1 TTTTAATTTGCTTGATTTAT
20505796 TTTTA
1 TTTTA
20505801 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.20, C:0.04, G:0.09, T:0.67
Consensus pattern (20 bp):
TTTTAATTTGCTTGATTTAT
Found at i:20520696 original size:17 final size:18
Alignment explanation
Indices: 20520671--20520704 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20520661 CAGATTGGAC
20520671 GTGTAGG-CCACACGAGT
1 GTGTAGGCCCACACGAGT
*
20520688 GTGTGGGCCCACACGAG
1 GTGTAGGCCCACACGAG
20520705 CATTCCACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (18 bp):
GTGTAGGCCCACACGAGT
Found at i:20521277 original size:13 final size:13
Alignment explanation
Indices: 20521261--20521306 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
20521251 GGGGGTAGGA
20521261 TTCTGTATATCTG
1 TTCTGTATATCTG
*
20521274 TTCTGTTTATCTG
1 TTCTGTATATCTG
20521287 ATTCTG-ATATCTG
1 -TTCTGTATATCTG
20521300 TATCTGT
1 T-TCTGT
20521307 TATGGGCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 1 0.04
13 22 0.79
14 5 0.18
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
TTCTGTATATCTG
Found at i:20523897 original size:18 final size:16
Alignment explanation
Indices: 20523866--20523902 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
20523856 CCCTTGCTGA
20523866 TCATTCCACTCATCCC
1 TCATTCCACTCATCCC
20523882 TCATTCACATCTCATCCC
1 TCATTC-CA-CTCATCCC
20523900 TCA
1 TCA
20523903 CATTCTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 2 0.11
18 11 0.58
ACGTcount: A:0.22, C:0.46, G:0.00, T:0.32
Consensus pattern (16 bp):
TCATTCCACTCATCCC
Found at i:20531911 original size:22 final size:22
Alignment explanation
Indices: 20531885--20531937 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
20531875 CCTAAAAATC
20531885 AATTTGAAAACAATTAGGGACT
1 AATTTGAAAACAATTAGGGACT
*
20531907 AATTTGAAAATAATTAGGGACT
1 AATTTGAAAACAATTAGGGACT
20531929 AATTTGAAA
1 AATTTGAAA
20531938 TGAAATAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (22 bp):
AATTTGAAAACAATTAGGGACT
Found at i:20541935 original size:15 final size:15
Alignment explanation
Indices: 20541915--20541943 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20541905 ACTAGCTCTC
20541915 TTTTTTTTTCACAAT
1 TTTTTTTTTCACAAT
20541930 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
20541944 CTTGATATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTTTTTCACAAT
Found at i:20542018 original size:13 final size:13
Alignment explanation
Indices: 20541979--20542018 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
20541969 AATGGAAACT
*
20541979 AGTTTTTTTTTTG
1 AGTTTTTTTTTCG
*
20541992 A-ATTTTTTTTCG
1 AGTTTTTTTTTCG
20542004 AGTTTTTTTTTCG
1 AGTTTTTTTTTCG
20542017 AG
1 AG
20542019 AAACTACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.12, C:0.05, G:0.15, T:0.68
Consensus pattern (13 bp):
AGTTTTTTTTTCG
Found at i:20550783 original size:2 final size:2
Alignment explanation
Indices: 20550776--20550808 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20550766 GAATGCCAAG
20550776 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20550809 TACATCATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20553326 original size:6 final size:6
Alignment explanation
Indices: 20553315--20553339 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20553305 GATATTATAA
20553315 TAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT T
20553340 TTAAAAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:20555119 original size:16 final size:16
Alignment explanation
Indices: 20555100--20555141 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
20555090 TAGGTAAAAT
20555100 AAAATATTTTATGTTA
1 AAAATATTTTATGTTA
* *
20555116 AAAATATTCTATTTTA
1 AAAATATTTTATGTTA
20555132 AAAATTATTT
1 AAAA-TATTT
20555142 AATAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (16 bp):
AAAATATTTTATGTTA
Found at i:20555312 original size:20 final size:20
Alignment explanation
Indices: 20555275--20555315 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
20555265 TCTTCATAAT
**
20555275 AATATTAATTATTTTTTAAA
1 AATATTAATTATAATTTAAA
20555295 AATATTAATTATAATTTAAA
1 AATATTAATTATAATTTAAA
20555315 A
1 A
20555316 GAATGAGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTAATTATAATTTAAA
Found at i:20569718 original size:18 final size:19
Alignment explanation
Indices: 20569695--20569736 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
20569685 TGTAGAAGGA
*
20569695 TGAAATTGA-GATCAATTT
1 TGAAATTGAGGATCAAATT
*
20569713 TGAAATTGAGGCTCAAATT
1 TGAAATTGAGGATCAAATT
20569732 TGAAA
1 TGAAA
20569737 GTTATAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (19 bp):
TGAAATTGAGGATCAAATT
Found at i:20574276 original size:22 final size:24
Alignment explanation
Indices: 20574244--20574293 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
20574234 ATCATGAAGA
20574244 TAAATATTGTTTATC-TTA-ATATT
1 TAAATATTG-TTATCATTAGATATT
*
20574267 TAAAT-TTGTTATCATTAGATTTT
1 TAAATATTGTTATCATTAGATATT
20574290 TAAA
1 TAAA
20574294 ATTATCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 6 0.25
23 13 0.54
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (24 bp):
TAAATATTGTTATCATTAGATATT
Found at i:20575575 original size:22 final size:21
Alignment explanation
Indices: 20575539--20575584 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
20575529 AATTTAAACT
20575539 AAAAATGTATCAAACTTAATATA
1 AAAAATGTATCAAAC-T-ATATA
*
20575562 AAAAATTTAT-AAACTATATA
1 AAAAATGTATCAAACTATATA
20575582 AAA
1 AAA
20575585 GAAATTAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 1 0.05
22 4 0.18
23 9 0.41
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAATGTATCAAACTATATA
Found at i:20576544 original size:36 final size:36
Alignment explanation
Indices: 20576503--20576573 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
20576493 GATTATTTAA
*
20576503 TCTTAGAGTTCTAATTGTATACTGCTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
*
20576539 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTAT
20576574 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
Found at i:20581634 original size:17 final size:16
Alignment explanation
Indices: 20581610--20581663 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
20581600 TTAATCTTAG
20581610 AGTTCTAATTGTATAC
1 AGTTCTAATTGTATAC
* *
20581626 AGCTTCTAATTATGTCTTAG
1 AG-TTCTAA-T-TGT-ATAC
20581646 AGTTCTAATTGTATAC
1 AGTTCTAATTGTATAC
20581662 AG
1 AG
20581664 GTTTTAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 6 0.20
17 9 0.30
18 2 0.07
19 9 0.30
20 4 0.13
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (16 bp):
AGTTCTAATTGTATAC
Found at i:20581645 original size:36 final size:36
Alignment explanation
Indices: 20581604--20581674 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
20581594 GATTATTTAA
20581604 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
* *
20581640 TCTTAGAGTTCTAATTGTATACAGGTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTAT
20581675 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
Found at i:20581653 original size:19 final size:18
Alignment explanation
Indices: 20581604--20581655 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
20581594 GATTATTTAA
20581604 TCTTAGAGTTCTAA-TTG
1 TCTTAGAGTTCTAATTTG
* *
20581621 T-ATACAGCTTCTAATTATG
1 TCTTAGAG-TTCTAATT-TG
20581640 TCTTAGAGTTCTAATT
1 TCTTAGAGTTCTAATT
20581656 GTATACAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 1 0.04
19 11 0.41
20 4 0.15
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (18 bp):
TCTTAGAGTTCTAATTTG
Found at i:20588803 original size:54 final size:54
Alignment explanation
Indices: 20588744--20588852 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
20588734 TTCATGTTAG
* *
20588744 TTTTCAATCCACATATTATTATGAATATGCCACAAATACACTAATTATGCCAAA
1 TTTTCAATCCACATATCATTATGAATATGCCACAAATACACCAATTATGCCAAA
20588798 TTTTCAATCCACATATCATTATGAATATGCCACAAATACACCAATTATGCCAAA
1 TTTTCAATCCACATATCATTATGAATATGCCACAAATACACCAATTATGCCAAA
20588852 T
1 T
20588853 GAATCAACTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (54 bp):
TTTTCAATCCACATATCATTATGAATATGCCACAAATACACCAATTATGCCAAA
Found at i:20590912 original size:2 final size:2
Alignment explanation
Indices: 20590900--20590960 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
20590890 AAACATTTTA
*
20590900 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20590942 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
20590961 ACACTTAGTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20592650 original size:17 final size:18
Alignment explanation
Indices: 20592623--20592657 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
20592613 TGACTGCAGA
20592623 GTGGTTTTTTTTTTAATT
1 GTGGTTTTTTTTTTAATT
20592641 GTGG-TTTTTTTTTAATT
1 GTGGTTTTTTTTTTAATT
20592658 TTAAAATGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.11, C:0.00, G:0.17, T:0.71
Consensus pattern (18 bp):
GTGGTTTTTTTTTTAATT
Found at i:20596428 original size:27 final size:27
Alignment explanation
Indices: 20596393--20596446 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
20596383 AGTACAAAGT
20596393 TCACCCCTAA-CAGAAGAGCACAAAGGC
1 TCACCCCTAATCAGAA-AGCACAAAGGC
* * *
20596420 TCACTCCTAATCAGCAAGCCCAAAGGC
1 TCACCCCTAATCAGAAAGCACAAAGGC
20596447 CGAACAAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.37, C:0.35, G:0.17, T:0.11
Consensus pattern (27 bp):
TCACCCCTAATCAGAAAGCACAAAGGC
Found at i:20600715 original size:642 final size:641
Alignment explanation
Indices: 20599456--20601169 Score: 2572
Period size: 668 Copynumber: 2.6 Consensus size: 641
20599446 CAGCAGAGCT
* * * *
20599456 TATTTCGATCCAGTTTTTATTTC--TT-TTTTTATTAAATATATGTATAGTTTTGTTCTCATTCG
1 TATTTCGATCCAGTCTTTATTTCTGTTCTTTTTATTATATATATGTATATTTTTGTTCTCGTTCG
* *
20599518 ATCTTGTGATTTAAATAAATATTTTATATTACCGTTTATTTTACTAACGTGTGTGCAAGACCATA
66 ATCTTGTGATTTAAATAAATATTTTATATTACTGTTTATTTTACTAACGTGTGTGCAAGATCATA
* **
20599583 TTCACTCCAATTTAAAGCCAAATTTGATTTTCCTTTCCGTTTTCACCATTTATGACTCATTTGCT
131 TTCACTTCAATTTAAAGCCAAATTTGATTTTCCTTTCCGTTTTCACCATTTATGACTCATTCCCT
* *
20599648 CAATTAGGTCTTGCTAATTTCCCATTTTCCTAAGCTTTTGCTACTTTTAGTGGGATTTAGCTCAA
196 CAATTAGGTCTTGTTAATTTCCCATTTTCCTAAGCTTTTGCTACTTTTAGTGGGATTTAGCTTAA
* *
20599713 GAATCGCATTTAAAATTTGGGAAAAGAACTAAGTT-TTTTAGCTTTATGAAATTCAATGCAATGA
261 GAATCACATTTAAAATTTGGAAAAAGAACTAAGTTCTTTTAGCTTTATGAAATTCAATGCAATGA
*
20599777 AGTGTTTTCACTATTTCAAGGACAAGTTTTGAAGCAAGGGCAAAATATTAGCCTCAGAATTAAAA
326 AGTGTTTTCACTATTTCAAGGACAAGTTTTGAAGCAAGGG-AAAATATTAGCCTCAGAATTGAAA
* * *
20599842 GAATGAATGAACGAAATCAAAGGAACATTCAAAGGCATTTTTCAAACTGTTTTTGGTGATAGCCG
390 GAATGAATGAACGAAATCAAAGGAACATTCAAAGGCATTTTTCAAACTATTTTCGGTGATAGACG
* * *
20599907 AAGGCAAGACTATTGTTCGTTGATCACTGTAGCCGTGCTACTACCGTGCTCATCTTGTTGTTGTG
455 AAGGCAAGACTACTGTTCGTTGATCACTGCAGCCGTGCTACTACCGTGCTCATCTTGTTGTTGTA
**
20599972 TCCTAAGAGACAATCGACCAACGTTTCTCCAGCACCAAAGGAGCGGTCGAATCTATCTTAAGGAA
520 TCCTAAGAGACAATCGACCAACGTTTCTCCAGCACCAAAGGAGCGACCGAATCTATCTTAAGGAA
* * *
20600037 ACTGTGAAAATAGGCCTCAACTACCAATCCGTTTTTCCTGCCTACGTACGAGTATAA
585 ACTATGAAAATAGGCCTCAACTACCAATCCGTTTTTCCTACCTACCTACGAGTATAA
*
20600094 TATTTCGATCCAGTCTTTCTTTCTGTTCTTTTTATTATATATATGTATATTTTTGTTCTCGTTCG
1 TATTTCGATCCAGTCTTTATTTCTGTTCTTTTTATTATATATATGTATATTTTTGTTCTCGTTCG
20600159 ATCTTGTGATTTAAATAAATATTTTATATTACTGTTTATTTTACTAACGTGTGTGCAAGATCATA
66 ATCTTGTGATTTAAATAAATATTTTATATTACTGTTTATTTTACTAACGTGTGTGCAAGATCATA
*
20600224 TTCACTTCAATTTAAAGCCAAATTTGATTTTCCTTTCCATTTTCACCATTTATGACTCATTCCCT
131 TTCACTTCAATTTAAAGCCAAATTTGATTTTCCTTTCCGTTTTCACCATTTATGACTCATTCCCT
* *
20600289 CGATTAGGTCTTGTTAATTTCCCATTTTCCTAAGCTTTTGCTACTTTTAGTGGGATTTAACTTAA
196 CAATTAGGTCTTGTTAATTTCCCATTTTCCTAAGCTTTTGCTACTTTTAGTGGGATTTAGCTTAA
* * * * * *
20600354 GAATCATATTTAAAATTTGGTACAAGAATTGAGTTCTTTTAGCTTTATGAAATTCAATGTAATGA
261 GAATCACATTTAAAATTTGGAAAAAGAACTAAGTTCTTTTAGCTTTATGAAATTCAATGCAATGA
*
20600419 AGTGTTTTCACTATTTCAAGGACAAGTTTTGAAGCAAAGGAAAACTATTAGCCTCAGAATTGAAA
326 AGTGTTTTCACTATTTCAAGGACAAGTTTTGAAGCAAGGGAAAA-TATTAGCCTCAGAATTGAAA
* *
20600484 GAATGAATGAAGGAAATCAAAGGAACATTCAAAGGCATTTTTCAAACTATTTTCGGTGATAGATG
390 GAATGAATGAACGAAATCAAAGGAACATTCAAAGGCATTTTTCAAACTATTTTCGGTGATAGACG
* * **
20600549 AAGGCAAGGCTACTGTTCGTTGATCACTGCAGTCGTGCTACTGTCGTGCTCATCTTGTTGTTGTA
455 AAGGCAAGACTACTGTTCGTTGATCACTGCAGCCGTGCTACTACCGTGCTCATCTTGTTGTTGTA
* ** * * *
20600614 TCTTGGGAGACAATCGACCAATGTTTCTCCAGCACCAAAGGAGTGACCGAATCTGTCTTAAGGAA
520 TCCTAAGAGACAATCGACCAACGTTTCTCCAGCACCAAAGGAGCGACCGAATCTATCTTAAGGAA
* * * *
20600679 ACTATGAAAATAGGCCTCAACTATCAGTCTGTTTTTCCTACCTACCTATGAGTATAA
585 ACTATGAAAATAGGCCTCAACTACCAATCCGTTTTTCCTACCTACCTACGAGTATAA
*
20600736 TATTTCGATCTAGTCTTTATTTCTGTTCTTTATTTTAATTATTATTATTATTATTATTATTATTA
1 TATTTCGATCCAGTCTTTATTTCTGTTC-----------------------T-TT-TTATTA-TA
* * *
20600801 TATATGTATATTTTTGTTCTCGTTCGATCTTGTGATTTAAATAAATATTTTTTATTATTTTTTAT
40 TATATGTATATTTTTGTTCTCGTTCGATCTTGTGATTTAAATAAATATTTTATATTACTGTTTAT
* * *
20600866 TTTACTAACATGTGTGCAAGATCATATTCACTTAAATTTAAAGCCAAATTTGATTTTCCTTTCTG
105 TTTACTAACGTGTGTGCAAGATCATATTCACTTCAATTTAAAGCCAAATTTGATTTTCCTTTCCG
* *
20600931 TTTTCACCATTTATGACTCATTCCCTCAATTAGGTCCTGTTAATTTCCCATTTTTCTAAGCTTTT
170 TTTTCACCATTTATGACTCATTCCCTCAATTAGGTCTTGTTAATTTCCCATTTTCCTAAGCTTTT
*
20600996 GCTACTTTTAGTGGGATTTAGCTTAAGAATCACATTTAAAATTTGGAAAAAGAACCAAGTTCTTT
235 GCTACTTTTAGTGGGATTTAGCTTAAGAATCACATTTAAAATTTGGAAAAAGAACTAAGTTCTTT
20601061 TAGCTTTATGAAATTCAATGCAATGAAGTGTTTTCACTATTTCAAGGACAAGTTTTGAAGCAAGG
300 TAGCTTTATGAAATTCAATGCAATGAAGTGTTTTCACTATTTCAAGGACAAGTTTTGAAGCAAGG
*
20601126 GAAAAATATTAGCCTCAGAATTGAAAGAATGAAGGAACGAAATC
365 G-AAAATATTAGCCTCAGAATTGAAAGAATGAATGAACGAAATC
20601170 TGTTAGAGTT
Statistics
Matches: 970, Mismatches: 74, Indels: 34
0.90 0.07 0.03
Matches are distributed among these distances:
638 21 0.02
640 2 0.00
641 252 0.26
642 337 0.35
665 1 0.00
666 2 0.00
667 6 0.01
668 345 0.36
669 4 0.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.39
Consensus pattern (641 bp):
TATTTCGATCCAGTCTTTATTTCTGTTCTTTTTATTATATATATGTATATTTTTGTTCTCGTTCG
ATCTTGTGATTTAAATAAATATTTTATATTACTGTTTATTTTACTAACGTGTGTGCAAGATCATA
TTCACTTCAATTTAAAGCCAAATTTGATTTTCCTTTCCGTTTTCACCATTTATGACTCATTCCCT
CAATTAGGTCTTGTTAATTTCCCATTTTCCTAAGCTTTTGCTACTTTTAGTGGGATTTAGCTTAA
GAATCACATTTAAAATTTGGAAAAAGAACTAAGTTCTTTTAGCTTTATGAAATTCAATGCAATGA
AGTGTTTTCACTATTTCAAGGACAAGTTTTGAAGCAAGGGAAAATATTAGCCTCAGAATTGAAAG
AATGAATGAACGAAATCAAAGGAACATTCAAAGGCATTTTTCAAACTATTTTCGGTGATAGACGA
AGGCAAGACTACTGTTCGTTGATCACTGCAGCCGTGCTACTACCGTGCTCATCTTGTTGTTGTAT
CCTAAGAGACAATCGACCAACGTTTCTCCAGCACCAAAGGAGCGACCGAATCTATCTTAAGGAAA
CTATGAAAATAGGCCTCAACTACCAATCCGTTTTTCCTACCTACCTACGAGTATAA
Found at i:20600781 original size:3 final size:3
Alignment explanation
Indices: 20600773--20600801 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20600763 CTTTATTTTA
20600773 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
20600802 ATATGTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:20604878 original size:14 final size:14
Alignment explanation
Indices: 20604841--20604878 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
20604831 TTGTTACAAA
*
20604841 AACTTTTCTTCTTT
1 AACTTTTCTTCTCT
20604855 AACGTTTTCTTCTCT
1 AAC-TTTTCTTCTCT
20604870 AACTTTTCT
1 AACTTTTCT
20604879 ATTTTCCCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.58
Consensus pattern (14 bp):
AACTTTTCTTCTCT
Found at i:20606995 original size:25 final size:25
Alignment explanation
Indices: 20606963--20607018 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
20606953 GCAATCTAAC
20606963 AATCTCAACAATATACAACTTTGCT
1 AATCTCAACAATATACAACTTTGCT
*
20606988 AATCTCAACAATATACAACTTTGTT
1 AATCTCAACAATATACAACTTTGCT
20607013 AATCTC
1 AATCTC
20607019 TTAAGTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (25 bp):
AATCTCAACAATATACAACTTTGCT
Found at i:20616174 original size:21 final size:21
Alignment explanation
Indices: 20616148--20616192 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
20616138 ACTTAATTTT
20616148 AAAAC-TAAGTACTAAATACCA
1 AAAACTTAAGTA-TAAATACCA
* *
20616169 AAAACTTAATTATAAATACTA
1 AAAACTTAAGTATAAATACCA
20616190 AAA
1 AAA
20616193 TGTCTAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAACTTAAGTATAAATACCA
Found at i:20625275 original size:32 final size:31
Alignment explanation
Indices: 20625230--20625325 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
20625220 CTTAGATAAT
20625230 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
20625261 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
20625293 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
20625324 TT
1 TT
20625326 GTAATTTCCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:20625936 original size:25 final size:24
Alignment explanation
Indices: 20625873--20625936 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
20625863 CTTATTCTTT
*
20625873 AAAAAA-AACAAAAAAGCGCAAAA
1 AAAAAAGAAAAAAAAAGCGCAAAA
* **
20625896 AAAAAAGTGAGTAAAAAGCGCAAAAA
1 AAAAAAG-AAAAAAAAAGCGC-AAAA
20625922 AAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
20625937 GCAAAAAGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
23 6 0.19
25 15 0.47
26 11 0.34
ACGTcount: A:0.77, C:0.08, G:0.12, T:0.03
Consensus pattern (24 bp):
AAAAAAGAAAAAAAAAGCGCAAAA
Found at i:20625957 original size:17 final size:16
Alignment explanation
Indices: 20625923--20625966 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
20625913 GCGCAAAAAA
20625923 AAAAAGAAAAAAAAGC
1 AAAAAGAAAAAAAAGC
**
20625939 AAAAAGCAAAAAAGCGC
1 AAAAAG-AAAAAAAAGC
20625956 AAAAA-AAAAAA
1 AAAAAGAAAAAA
20625967 GTTGCCTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 6 0.24
17 13 0.52
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGC
Found at i:20631625 original size:31 final size:31
Alignment explanation
Indices: 20631589--20631683 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
20631579 CTTAGATAAT
20631589 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
20631620 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
*
20631651 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
20631682 TT
1 TT
20631684 GTAATTTCCC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:20632270 original size:25 final size:25
Alignment explanation
Indices: 20632237--20632324 Score: 158
Period size: 25 Copynumber: 3.5 Consensus size: 25
20632227 TAGCTCTCAT
20632237 GAGCTTCCCGTTATATGGTTATTGC
1 GAGCTTCCCGTTATATGGTTATTGC
20632262 GAGCTTCCCGTTATATGGTTATTGC
1 GAGCTTCCCGTTATATGGTTATTGC
*
20632287 GAGTTTCCCGTTATATGGTTATTGC
1 GAGCTTCCCGTTATATGGTTATTGC
*
20632312 GAGCTTCCTGTTA
1 GAGCTTCCCGTTA
20632325 ATAGCTCTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGTTATTGC
Found at i:20632427 original size:25 final size:24
Alignment explanation
Indices: 20632405--20632487 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 24
20632395 GTCCCGATAT
*
20632405 ATGGCTCTTTGGAGCTTCTCGATTA
1 ATGGCTCTTCGGAGCTTC-CGATTA
*
20632430 AAGGCTCTTCGTGAGCTTCCCGATTA
1 ATGGCTCTTCG-GAGCTT-CCGATTA
*
20632456 ATGGCTCTCCGGAGCTTCCTG-TTA
1 ATGGCTCTTCGGAGCTTCC-GATTA
20632480 TATGGCTC
1 -ATGGCTC
20632488 ACATGAGCTT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
24 5 0.10
25 23 0.46
26 21 0.42
27 1 0.02
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (24 bp):
ATGGCTCTTCGGAGCTTCCGATTA
Found at i:20632453 original size:26 final size:25
Alignment explanation
Indices: 20632407--20632474 Score: 91
Period size: 26 Copynumber: 2.7 Consensus size: 25
20632397 CCCGATATAT
* *
20632407 GGCTCTTTGGAGCTTCTCGATTAAA
1 GGCTCTTCGGAGCTTCCCGATTAAA
*
20632432 GGCTCTTCGTGAGCTTCCCGATTAAT
1 GGCTCTTCG-GAGCTTCCCGATTAAA
*
20632458 GGCTCTCCGGAGCTTCC
1 GGCTCTTCGGAGCTTCC
20632475 TGTTATATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 16 0.42
26 22 0.58
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.32
Consensus pattern (25 bp):
GGCTCTTCGGAGCTTCCCGATTAAA
Found at i:20632495 original size:25 final size:26
Alignment explanation
Indices: 20632441--20632534 Score: 97
Period size: 25 Copynumber: 3.7 Consensus size: 26
20632431 AGGCTCTTCG
* *
20632441 TGAGCTTCCCGATTA-ATGGCTCTCC
1 TGAGCTTCCCGATTATATGGCTCACA
* *
20632466 GGAGCTTCCTG-TTATATGGCTCACA
1 TGAGCTTCCCGATTATATGGCTCACA
20632491 TGAGCTTCCC-ATTATATGGCTCGA-A
1 TGAGCTTCCCGATTATATGGCTC-ACA
* *
20632516 AGAGCTTCCCGTTTATATG
1 TGAGCTTCCCGATTATATG
20632535 CTCGTATGAG
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
24 3 0.05
25 46 0.81
26 8 0.14
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (26 bp):
TGAGCTTCCCGATTATATGGCTCACA
Found at i:20632545 original size:25 final size:25
Alignment explanation
Indices: 20632441--20632545 Score: 90
Period size: 25 Copynumber: 4.2 Consensus size: 25
20632431 AGGCTCTTCG
***
20632441 TGAGCTTCCCGATTA-ATGGCTCTCC
1 TGAGCTTCCCG-TTATATGGCTCGAA
* *
20632466 GGAGCTTCCTGTTATATGGCTC-ACA
1 TGAGCTTCCCGTTATATGGCTCGA-A
*
20632491 TGAGCTTCCCATTATATGGCTCGAA
1 TGAGCTTCCCGTTATATGGCTCGAA
* *
20632516 AGAGCTTCCCGTTTATAT-GCTCGTA
1 TGAGCTTCCCG-TTATATGGCTCGAA
20632541 TGAGC
1 TGAGC
20632546 ATTCTCGAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
24 3 0.05
25 55 0.85
26 7 0.11
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (25 bp):
TGAGCTTCCCGTTATATGGCTCGAA
Found at i:20634551 original size:17 final size:17
Alignment explanation
Indices: 20634481--20634555 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 17
20634471 AGAACTCACA
* *
20634481 GGTGAGCTCTCAAGTTT
1 GGTGAGCTCACAATTTT
* * * *
20634498 GGTAAGCTTACAGTCTT
1 GGTGAGCTCACAATTTT
*
20634515 GGTGAGCTCACATTTTTT
1 GGTGAGCTCACA-ATTTT
20634533 GGTGAGCTCACAATTTT
1 GGTGAGCTCACAATTTT
20634550 GGTGAG
1 GGTGAG
20634556 TTCGCAGTTC
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
17 31 0.67
18 15 0.33
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (17 bp):
GGTGAGCTCACAATTTT
Found at i:20639354 original size:47 final size:47
Alignment explanation
Indices: 20639289--20639382 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
20639279 ATATATGCAC
* *
20639289 CAACTTGAGAGAGTGTGTTGAAATATGTAAAACCTATATATTTTGGG
1 CAACTTGAGAGAGGGTGTTGAAATATGTAAAACCCATATATTTTGGG
* *
20639336 CAACTTGAGGGAGGGTGTTGAAATATGTGAAACCCATATATTTTGGG
1 CAACTTGAGAGAGGGTGTTGAAATATGTAAAACCCATATATTTTGGG
20639383 GATATATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.32
Consensus pattern (47 bp):
CAACTTGAGAGAGGGTGTTGAAATATGTAAAACCCATATATTTTGGG
Found at i:20641408 original size:21 final size:21
Alignment explanation
Indices: 20641382--20641423 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20641372 GTGGAAAAGG
20641382 TTAGAAACTCTTTATGTGACT
1 TTAGAAACTCTTTATGTGACT
20641403 TTAGAAACTCTTTATGTGACT
1 TTAGAAACTCTTTATGTGACT
20641424 AAGTCTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (21 bp):
TTAGAAACTCTTTATGTGACT
Found at i:20646168 original size:16 final size:16
Alignment explanation
Indices: 20646138--20646167 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20646128 TAAATGTAAC
20646138 ATATAATATGAAAAAT
1 ATATAATATGAAAAAT
20646154 ATATAATA-GAAAAA
1 ATATAATATGAAAAA
20646168 ACTAAACAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (16 bp):
ATATAATATGAAAAAT
Found at i:20647873 original size:6 final size:6
Alignment explanation
Indices: 20647859--20647890 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
20647849 ATTTCCACTG
*
20647859 CCTCCA CCTCTA CCTCTA CCTCTA CCTCTA CC
1 CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CC
20647891 GCCACCAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.56, G:0.00, T:0.28
Consensus pattern (6 bp):
CCTCTA
Found at i:20649919 original size:16 final size:17
Alignment explanation
Indices: 20649900--20649941 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
20649890 ATAAGTTTTT
20649900 ATTTTAAAAATAT-ATA
1 ATTTTAAAAATATAATA
20649916 ATTTAATAAAAATATAATA
1 ATTT--TAAAAATATAATA
20649935 ACTTTTA
1 A-TTTTA
20649942 CATCAAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.18
18 11 0.50
19 4 0.18
20 3 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTTAAAAATATAATA
Found at i:20656317 original size:97 final size:97
Alignment explanation
Indices: 20656176--20656607 Score: 613
Period size: 97 Copynumber: 4.6 Consensus size: 97
20656166 GTTTTAGGAT
* * ** *
20656176 TTTTAGAT-TTTAGGG-TTTTAAGGAAAAAAAT-AAATAAATAAGGGTTTAGGGTTTTTTTAAGT
1 TTTTAG-TGTTTAGGGTTTTTAAGG-AAAAAATCAAATAAATTAGGGTTT-GGGGTTACTTGAGT
20656238 AAATTAATTATAAA-TTTTAAAAAATTAGATTAGG
63 AAATTAATTATAAATTTTTAAAAAATTAGATTAGG
* *
20656272 TTTTAGTGTTTAGGGTTCTTAAGGAGAAAATCAAATAAATTAGGGTTTGGGGTTACTTGAGTAAA
1 TTTTAGTGTTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTGGGGTTACTTGAGTAAA
20656337 TTAATTATAAATTTTTAAAAAATTAGATTAGG
66 TTAATTATAAATTTTTAAAAAATTAGATTAGG
* *
20656369 GTTTAGTGTTTAGGGTTTTTAA-GAAAAAATTCAAATAAATTAGGGTTTAGGGTTACTTGAGTAA
1 TTTTAGTGTTTAGGGTTTTTAAGGAAAAAA-TCAAATAAATTAGGGTTTGGGGTTACTTGAGTAA
20656433 ATTAATTATAAATTTTTAAAAAATTAGATTAGG
65 ATTAATTATAAATTTTTAAAAAATTAGATTAGG
* *
20656466 GTTTAGTTTTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTGGGGTTACTTGAGTAAA
1 TTTTAGTGTTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTGGGGTTACTTGAGTAAA
20656531 TTAATTATAAATTTTTAAAAAATTAGATTA-G
66 TTAATTATAAATTTTTAAAAAATTAGATTAGG
**
20656562 ----A--GTTTAGGACTTTTAAGG--AAAATCAAATAAATTAGGGTTTGGGGTT
1 TTTTAGTGTTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTGGGGTT
20656608 TAGGGTTACT
Statistics
Matches: 314, Mismatches: 16, Indels: 20
0.90 0.05 0.06
Matches are distributed among these distances:
88 28 0.09
90 14 0.04
92 1 0.00
95 1 0.00
96 50 0.16
97 213 0.68
98 7 0.02
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.40
Consensus pattern (97 bp):
TTTTAGTGTTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTGGGGTTACTTGAGTAAA
TTAATTATAAATTTTTAAAAAATTAGATTAGG
Found at i:20656872 original size:126 final size:126
Alignment explanation
Indices: 20656644--20657058 Score: 670
Period size: 126 Copynumber: 3.3 Consensus size: 126
20656634 TAATTTAAAA
*
20656644 AAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGTTT
1 AAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGTTCTTAAAAAAATAATTTTGAGAAGACGTTT
* *
20656709 CTGAGCAAATAGTGTCAAAAACTCTTTGAGCAGGATGCATTGTCAGCACAAGTACTGAAAG
66 CTGAGCAAATAGTGTCAAAAACTCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
* *
20656770 AAGCTCCCATGTGGACGCTCTTTTGCTAAAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGTTT
1 AAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGTTCTTAAAAAAATAATTTTGAGAAGACGTTT
* *
20656835 CTGAGCAAATAGTGTCAAAAACTCTTTAAGCAAGATGCATTGTCAGCAAAAGTACTGAAAT
66 CTGAGCAAATAGTGTCAAAAACTCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
* * *
20656896 AAGCTCTCACGTGGACGCTCTTTTGCTACAGTAGTT-TCTAAAAAAATAATTTTGAGAAGATGTT
1 AAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGTTCT-TAAAAAAATAATTTTGAGAAGACGTT
* * * * * *
20656960 TCTGAGCAAATAGAGTGAAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTAAAAG
65 TCTGAGCAAATAGTGTCAAAAACTCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
20657022 AAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGTTC
1 AAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGTTC
20657059 CTATTTGGCC
Statistics
Matches: 265, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
125 1 0.00
126 264 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (126 bp):
AAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGTTCTTAAAAAAATAATTTTGAGAAGACGTTT
CTGAGCAAATAGTGTCAAAAACTCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
Found at i:20660764 original size:30 final size:30
Alignment explanation
Indices: 20660730--20660786 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
20660720 TGCTGGGCCT
20660730 GGTGATTGTGTGGCCGCTATTGATGGGTCG
1 GGTGATTGTGTGGCCGCTATTGATGGGTCG
* *
20660760 GGTGATTGTGTGGGCGCTGTTGATGGG
1 GGTGATTGTGTGGCCGCTATTGATGGG
20660787 CCTGCATCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.09, C:0.11, G:0.47, T:0.33
Consensus pattern (30 bp):
GGTGATTGTGTGGCCGCTATTGATGGGTCG
Found at i:20662383 original size:11 final size:11
Alignment explanation
Indices: 20662369--20662401 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
20662359 CTTGGAGATG
*
20662369 AATTTGAGAGA
1 AATTTGAAAGA
20662380 AATTTGAAAGA
1 AATTTGAAAGA
20662391 AATTTGAAAGA
1 AATTTGAAAGA
20662402 TTGAAGATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (11 bp):
AATTTGAAAGA
Found at i:20664580 original size:30 final size:30
Alignment explanation
Indices: 20664544--20664600 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
20664534 ATGATACAAG
*
20664544 CCCATCAACGGCGCCCACACAATCACCCGA
1 CCCATCAACAGCGCCCACACAATCACCCGA
* *
20664574 CCCATCAACAGCGCCCATACATTCACC
1 CCCATCAACAGCGCCCACACAATCACC
20664601 AGGCCCAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.49, G:0.11, T:0.11
Consensus pattern (30 bp):
CCCATCAACAGCGCCCACACAATCACCCGA
Found at i:20668741 original size:94 final size:94
Alignment explanation
Indices: 20668480--20668868 Score: 595
Period size: 94 Copynumber: 4.1 Consensus size: 94
20668470 AACGCTAAAC
* *
20668480 CCCAAACCCTAATTTATTTGATTTTTTCTTAAAAATCCTAAACACTAAACCCTAATCTAATTTTT
1 CCCAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAA--TTT
20668545 TTTAAAATTTATAATTAATTTACTCAAGTAA
64 TTTAAAATTTATAATTAATTTACTCAAGTAA
*
20668576 CCCCAAACCTTAATTTATTTGATTTTTCCTTAAAAACCCTAAAC-CTTAAACCCTAATCTAAATT
1 -CCCAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAAACAC-TAAACCCTAATCT-AATT
20668640 TTTTAAAA-TTATAATTAATTTACTCAAGTAA
63 TTTTAAAATTTATAATTAATTTACTCAAGTAA
*
20668671 CCCAAACCCTAATTTATTTGATTTTATCCTTAAGAACCCTAAACACTAAACCCTAATCTAATTTT
1 CCCAAACCCTAATTTATTTGATTTT-TCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTT
20668736 TTAAAATTTATAATTAATTTACTCAAGTAA
65 TTAAAATTTATAATTAATTTACTCAAGTAA
* * *
20668766 CCTTAAACCCTAATTTATTT-ATTTTTCCTTAAAAACCATAAACAGTAAACCCTAATCTAATTTT
1 CC-CAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTT
* * *
20668830 TTAAAATTTATAATTAATTTAATTAAGAAA
65 TTAAAATTTATAATTAATTTACTCAAGTAA
20668860 CCCTAAACC
1 CCC-AAACC
20668869 TTAAACCCTT
Statistics
Matches: 272, Mismatches: 13, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
94 106 0.39
95 83 0.31
96 28 0.10
97 53 0.19
98 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.39
Consensus pattern (94 bp):
CCCAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTT
TAAAATTTATAATTAATTTACTCAAGTAA
Found at i:20668754 original size:190 final size:189
Alignment explanation
Indices: 20668480--20668868 Score: 611
Period size: 189 Copynumber: 2.0 Consensus size: 189
20668470 AACGCTAAAC
* *
20668480 CCCAAACCCTAATTTATTTGATTTTTTCTTAAAAATCCTAAACACTAAACCCTAATCTAATTTTT
1 CCCAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAA-TTTT
*
20668545 TTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCTTAATTTATTTGATTTTTCCTTAAA
65 TTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTT-ATTTTTCCTTAAA
* ** * *
20668610 AACCCTAAACCTTAAACCCTAATCTAAATTTTTTAAAA-TTATAATTAATTTACTCAAGTAA
129 AACCATAAACAGTAAACCCTAATCT-AATTTTTTAAAATTTATAATTAATTTAATCAAGAAA
*
20668671 CCCAAACCCTAATTTATTTGATTTTATCCTTAAGAACCCTAAACACTAAACCCTAATCTAA-TTT
1 CCCAAACCCTAATTTATTTGATTTT-TCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTT
**
20668735 TTTAAAATTTATAATTAATTTACTCAAGTAACCTTAAACCCTAATTTATTTATTTTTCCTTAAAA
65 TTTAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTATTTTTCCTTAAAA
*
20668800 ACCATAAACAGTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTAATTAAGAAA
130 ACCATAAACAGTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTAATCAAGAAA
20668860 CCCTAAACC
1 CCC-AAACC
20668869 TTAAACCCTT
Statistics
Matches: 183, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
188 12 0.07
189 58 0.32
190 56 0.31
191 25 0.14
192 32 0.17
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.39
Consensus pattern (189 bp):
CCCAAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTT
TTAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAATTTATTTATTTTTCCTTAAAAA
CCATAAACAGTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTAATCAAGAAA
Found at i:20671522 original size:36 final size:36
Alignment explanation
Indices: 20671482--20671613 Score: 147
Period size: 36 Copynumber: 3.4 Consensus size: 36
20671472 TTTCATTCAT
20671482 TCAGATAAGTGTAGTATTTATCACTTTGTCACTTGA
1 TCAGATAAGTGTAGTATTTATCACTTTGTCACTTGA
*
20671518 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGA
1 TCAGATAAGTGTAG-T--A--T-----TTATCACTTTGTCACTTGA
* *
20671564 TCAGATAAGTGTAGCACTTATCACTTTGTCACTTGA
1 TCAGATAAGTGTAGTATTTATCACTTTGTCACTTGA
20671600 TCAGATAAGTGTAG
1 TCAGATAAGTGTAG
20671614 CTAAAGCTAC
Statistics
Matches: 82, Mismatches: 4, Indels: 20
0.77 0.04 0.19
Matches are distributed among these distances:
36 46 0.56
37 1 0.01
39 1 0.01
41 1 0.01
43 1 0.01
46 32 0.39
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (36 bp):
TCAGATAAGTGTAGTATTTATCACTTTGTCACTTGA
Found at i:20671566 original size:46 final size:46
Alignment explanation
Indices: 20671499--20671650 Score: 198
Period size: 46 Copynumber: 3.5 Consensus size: 46
20671489 AGTGTAGTAT
20671499 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
20671545 TTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG----CAC
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
20671581 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAA
1 TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
20671627 TTATCACTTTATCTCTTGATCAGA
1 TTATCACTTTGTCACTTGATCAGA
20671651 AGTACTCAAA
Statistics
Matches: 91, Mismatches: 5, Indels: 20
0.78 0.04 0.17
Matches are distributed among these distances:
36 29 0.32
38 2 0.02
39 1 0.01
40 3 0.03
42 3 0.03
43 1 0.01
44 2 0.02
46 50 0.55
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.36
Consensus pattern (46 bp):
TTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:20671619 original size:82 final size:82
Alignment explanation
Indices: 20671482--20671650 Score: 302
Period size: 82 Copynumber: 2.1 Consensus size: 82
20671472 TTTCATTCAT
* * *
20671482 TCAGATAAGTGTAGTATTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 TCAGATAAGTGTAGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAATT
*
20671547 ATCACTTTGTCTCTTGA
66 ATCACTTTATCTCTTGA
20671564 TCAGATAAGTGTAGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAATT
1 TCAGATAAGTGTAGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAATT
20671629 ATCACTTTATCTCTTGA
66 ATCACTTTATCTCTTGA
20671646 TCAGA
1 TCAGA
20671651 AGTACTCAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (82 bp):
TCAGATAAGTGTAGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAATT
ATCACTTTATCTCTTGA
Found at i:20678466 original size:10 final size:10
Alignment explanation
Indices: 20678451--20678482 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
20678441 CAAGTGGGTT
20678451 AGCTTGCAAC
1 AGCTTGCAAC
20678461 AGCTTGCAAC
1 AGCTTGCAAC
20678471 AGCTTGCAAC
1 AGCTTGCAAC
20678481 AG
1 AG
20678483 AACTTAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (10 bp):
AGCTTGCAAC
Found at i:20683241 original size:12 final size:12
Alignment explanation
Indices: 20683226--20683252 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20683216 GGCTGTGTGC
20683226 TAGGCTATGTAA
1 TAGGCTATGTAA
20683238 TAGGCTATGTAA
1 TAGGCTATGTAA
20683250 TAG
1 TAG
20683253 CCTGACTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (12 bp):
TAGGCTATGTAA
Found at i:20686082 original size:15 final size:16
Alignment explanation
Indices: 20686062--20686091 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20686052 TGGCAACTAA
20686062 TATATAAT-TATATTT
1 TATATAATATATATTT
20686077 TATATAATATATATT
1 TATATAATATATATT
20686092 AATTGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:20687976 original size:20 final size:20
Alignment explanation
Indices: 20687951--20687991 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
20687941 TCGAGGAGGG
20687951 AACGAGG-TGATTCAAGCAAA
1 AACGAGGATGA-TCAAGCAAA
*
20687971 AACGAGGATGATGAAGCAAA
1 AACGAGGATGATCAAGCAAA
20687991 A
1 A
20687992 GATGGGTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.49, C:0.12, G:0.27, T:0.12
Consensus pattern (20 bp):
AACGAGGATGATCAAGCAAA
Found at i:20694054 original size:16 final size:16
Alignment explanation
Indices: 20694035--20694065 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20694025 CTTAGGTTCA
*
20694035 CAAACAGATAGGCTCG
1 CAAACAAATAGGCTCG
20694051 CAAACAAATAGGCTC
1 CAAACAAATAGGCTC
20694066 TCATACATAT
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:0.26, G:0.19, T:0.13
Consensus pattern (16 bp):
CAAACAAATAGGCTCG
Found at i:20694196 original size:21 final size:21
Alignment explanation
Indices: 20694172--20694211 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20694162 GTAATATAGA
*
20694172 AGGGTTCGTACACATTTTAAT
1 AGGGTTCGCACACATTTTAAT
*
20694193 AGGGTTCGCATACATTTTA
1 AGGGTTCGCACACATTTTA
20694212 TTCAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (21 bp):
AGGGTTCGCACACATTTTAAT
Found at i:20694941 original size:6 final size:6
Alignment explanation
Indices: 20694930--20694961 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
20694920 AAACCCAATT
20694930 ATTTTA ATTTTA ATTTTA A-TTT- ATTTTA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTT
20694962 CTACAACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 1 0.04
5 6 0.25
6 17 0.71
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
ATTTTA
Found at i:20698340 original size:9 final size:9
Alignment explanation
Indices: 20698326--20698362 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20698316 TATAGTTTGA
20698326 TATTCGAAT
1 TATTCGAAT
20698335 TATTCGAAT
1 TATTCGAAT
*
20698344 TATTCGAGT
1 TATTCGAAT
20698353 TATTCGAAT
1 TATTCGAAT
20698362 T
1 T
20698363 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:20699154 original size:46 final size:45
Alignment explanation
Indices: 20699072--20699266 Score: 169
Period size: 46 Copynumber: 4.2 Consensus size: 45
20699062 TTTATCATGT
* * * *
20699072 TTGAAGTGTTAAAAGTGTTGCATATTGAAGTATTTAAATGTTGTGAA
1 TTGAAGTGTT--AAGTGCTGCAAATTGAAGTGTTTAAATGTTGTAAA
*
20699119 TTGAAGTGTTAGTGTGCTGCAAATTGAAGTGTTTAAATGTTGTAAA
1 TTGAAGTGTTA-AGTGCTGCAAATTGAAGTGTTTAAATGTTGTAAA
* * ** * *
20699165 TTGAAGTGTTTTAAGTACTGCAAATTGAATTGTTTAGTTGCTGAAAA
1 TTGAAGTG--TTAAGTGCTGCAAATTGAAGTGTTTAAATGTTGTAAA
* * * * *
20699212 TTG-AGATGTTTTATTGCTG-TAATTGAGGTGTATAAATGTTGTAAA
1 TTGAAG-TG-TTAAGTGCTGCAAATTGAAGTGTTTAAATGTTGTAAA
20699257 TTGAAGTGTT
1 TTGAAGTGTT
20699267 TTATTGCTGA
Statistics
Matches: 120, Mismatches: 23, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
44 2 0.02
45 24 0.20
46 49 0.41
47 42 0.35
48 3 0.03
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.42
Consensus pattern (45 bp):
TTGAAGTGTTAAGTGCTGCAAATTGAAGTGTTTAAATGTTGTAAA
Found at i:20699172 original size:23 final size:23
Alignment explanation
Indices: 20699072--20699267 Score: 132
Period size: 23 Copynumber: 8.5 Consensus size: 23
20699062 TTTATCATGT
* * *
20699072 TTGAAGTGTTAAAAGTGTTGCATA
1 TTGAAGTGTTTAAA-TGTTGTAAA
* *
20699096 TTGAAGTATTTAAATGTTGTGAA
1 TTGAAGTGTTTAAATGTTGTAAA
* *
20699119 TTGAAGTG-TT-AGTGTGCTGCAAA
1 TTGAAGTGTTTAAATGT--TGTAAA
20699142 TTGAAGTGTTTAAATGTTGTAAA
1 TTGAAGTGTTTAAATGTTGTAAA
* *
20699165 TTGAAGTGTTTTAA-GTACTGCAAA
1 TTGAAGTGTTTAAATGT--TGTAAA
* ** * *
20699189 TTGAATTGTTTAGTTGCTGAAAA
1 TTGAAGTGTTTAAATGTTGTAAA
* * *
20699212 TTG-AGATGTTTTATTGCTGT-AA
1 TTGAAG-TGTTTAAATGTTGTAAA
* *
20699234 TTGAGGTGTATAAATGTTGTAAA
1 TTGAAGTGTTTAAATGTTGTAAA
20699257 TTGAAGTGTTT
1 TTGAAGTGTTT
20699268 TATTGCTGAA
Statistics
Matches: 132, Mismatches: 30, Indels: 21
0.72 0.16 0.11
Matches are distributed among these distances:
21 4 0.03
22 20 0.15
23 74 0.56
24 29 0.22
25 5 0.04
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.42
Consensus pattern (23 bp):
TTGAAGTGTTTAAATGTTGTAAA
Found at i:20699178 original size:70 final size:68
Alignment explanation
Indices: 20699072--20699282 Score: 196
Period size: 70 Copynumber: 3.0 Consensus size: 68
20699062 TTTATCATGT
* * * * *
20699072 TTGAAGTGTTAAAAGTGTTGCATATTGAAGTATTTAAATGTTGTGAATTGAAGTGTTAGTGTGCT
1 TTGAAGTGTTTAAA-TGTTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAGT-TGCT
*
20699137 GCAAA
64 GAAAA
* * *
20699142 TTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTTAA-GTACTGCAAATTGAATTGTTTAGTTGC
1 TTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTAAATGT--TGTAAATTGAAGTG-TTAGTTGC
20699206 TGAAAA
63 TGAAAA
* * * * *
20699212 TTG-AGATGTTTTATTGCTGT-AATTGAGGTGTATAAATGTTGTAAATTGAAGTGTTTTA-TTGC
1 TTGAAG-TGTTTAAATGTTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTG--TTAGTTGC
20699274 TGAAAA
63 TGAAAA
20699280 TTG
1 TTG
20699283 GATGGTATAA
Statistics
Matches: 118, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
68 27 0.23
69 38 0.32
70 48 0.41
71 5 0.04
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.42
Consensus pattern (68 bp):
TTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAGTTGCTGA
AAA
Found at i:20699213 original size:47 final size:47
Alignment explanation
Indices: 20699135--20699224 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
20699125 TGTTAGTGTG
* *
20699135 CTGCAAATTGAAGTGTTTAAATGTTGTAAATTGA-AGTGTTTTAAGTA
1 CTGCAAATTGAAGTGTTTAAATGCTGAAAATTGAGA-TGTTTTAAGTA
* **
20699182 CTGCAAATTGAATTGTTTAGTTGCTGAAAATTGAGATGTTTTA
1 CTGCAAATTGAAGTGTTTAAATGCTGAAAATTGAGATGTTTTA
20699225 TTGCTGTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
47 36 0.97
48 1 0.03
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (47 bp):
CTGCAAATTGAAGTGTTTAAATGCTGAAAATTGAGATGTTTTAAGTA
Found at i:20699238 original size:22 final size:23
Alignment explanation
Indices: 20699133--20699286 Score: 79
Period size: 23 Copynumber: 6.7 Consensus size: 23
20699123 AGTGTTAGTG
* * *
20699133 TGCTGCAAATTGA-AGTGTTTAAA
1 TGCTGTAAATTGAGA-TGTTTTAT
* *
20699156 TGTTGTAAATTGA-AGTGTTTTAAG
1 TGCTGTAAATTGAGA-TGTTTT-AT
* *
20699180 TACTGCAAATTGA-AT-TGTTTAGT
1 TGCTGTAAATTGAGATGT-TTTA-T
*
20699203 TGCTGAAAATTGAGATGTTTTAT
1 TGCTGTAAATTGAGATGTTTTAT
* * * *
20699226 TGCTGT-AATTGAGGTGTATAAA
1 TGCTGTAAATTGAGATGTTTTAT
*
20699248 TGTTGTAAATTGA-AGTGTTTTAT
1 TGCTGTAAATTGAGA-TGTTTTAT
*
20699271 TGCTGAAAATTG-GATG
1 TGCTGTAAATTGAGATG
20699287 GTATAATGAC
Statistics
Matches: 101, Mismatches: 22, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
22 21 0.21
23 61 0.60
24 18 0.18
25 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.42
Consensus pattern (23 bp):
TGCTGTAAATTGAGATGTTTTAT
Found at i:20699897 original size:45 final size:44
Alignment explanation
Indices: 20699814--20699909 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 44
20699804 ATTACAACAT
*
20699814 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTACATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
*
20699858 CATTACATTCAACCAAACA-ATTGAATTACTATTACAGTTCTATTC
1 CATTACATTCAACCAAACACA-AGAA-TACTATTACAGTTCTATTC
20699903 CATTACA
1 CATTACA
20699910 GCTCTATTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.44
45 26 0.54
ACGTcount: A:0.39, C:0.25, G:0.04, T:0.32
Consensus pattern (44 bp):
CATTACATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:20699909 original size:16 final size:16
Alignment explanation
Indices: 20699888--20699927 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
20699878 TTGAATTACT
* *
20699888 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCA
20699904 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
20699920 ATTACAGC
1 ATTACAGC
20699928 GAACCAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:20702269 original size:45 final size:47
Alignment explanation
Indices: 20702218--20702315 Score: 137
Period size: 48 Copynumber: 2.1 Consensus size: 47
20702208 GAAGATGCTT
20702218 TTTCATC-A-AATAATAATGAAAGCTTCAAAGGTGATTGAAAACGCG
1 TTTCATCAATAATAATAATGAAAGCTTCAAAGGTGATTGAAAACGCG
* * * *
20702263 TTTCATCGAATAATAATAATGAATGCTTCAGAGGTGCTTGAAAACGTG
1 TTTCATC-AATAATAATAATGAAAGCTTCAAAGGTGATTGAAAACGCG
20702311 TTTCA
1 TTTCA
20702316 GCAGATATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
45 7 0.15
47 1 0.02
48 38 0.83
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (47 bp):
TTTCATCAATAATAATAATGAAAGCTTCAAAGGTGATTGAAAACGCG
Found at i:20708963 original size:14 final size:14
Alignment explanation
Indices: 20708944--20708973 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20708934 ATTCAATAGA
20708944 ACTAAAATGATTAT
1 ACTAAAATGATTAT
*
20708958 ACTAAAGTGATTAT
1 ACTAAAATGATTAT
20708972 AC
1 AC
20708974 ATAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (14 bp):
ACTAAAATGATTAT
Found at i:20710643 original size:38 final size:38
Alignment explanation
Indices: 20710601--20710676 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
20710591 TCAATACACA
20710601 GCATGTAATTCACTTACCAAAACTTACCAATTGTACAT
1 GCATGTAATTCACTTACCAAAACTTACCAATTGTACAT
*
20710639 GCATGTAATTCACTTGCCAAAACTTACCAATTGTACAT
1 GCATGTAATTCACTTACCAAAACTTACCAATTGTACAT
20710677 ATAATCAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.32
Consensus pattern (38 bp):
GCATGTAATTCACTTACCAAAACTTACCAATTGTACAT
Found at i:20711541 original size:25 final size:25
Alignment explanation
Indices: 20711482--20711590 Score: 107
Period size: 25 Copynumber: 4.4 Consensus size: 25
20711472 AGCTCTAAAC
* *
20711482 CGGTATGCTCTTACGAGCT-A-TAA
1 CGGTAAGCTCATACGAGCTGAGTAA
*
20711505 TCGATAAGCTCATACGAGCTGAGTAA
1 -CGGTAAGCTCATACGAGCTGAGTAA
* * * *
20711531 CTGTAAGCTCATGCGAGTTGAATAA
1 CGGTAAGCTCATACGAGCTGAGTAA
*
20711556 CGGTAAGCTCATACAAGCTGAG-AA
1 CGGTAAGCTCATACGAGCTGAGTAA
20711580 TCGGTAAGCTC
1 -CGGTAAGCTC
20711591 TCACGAGTTG
Statistics
Matches: 69, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
24 18 0.26
25 48 0.70
26 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (25 bp):
CGGTAAGCTCATACGAGCTGAGTAA
Found at i:20729795 original size:25 final size:25
Alignment explanation
Indices: 20729754--20729848 Score: 122
Period size: 25 Copynumber: 3.8 Consensus size: 25
20729744 TATGCTCATA
*
20729754 TGAGCTGTA-AACGGTAAGCTCCTC
1 TGAGCTGAATAACGGTAAGCTCCTC
* *
20729778 TAAGCTAAATAACGGTAAGCTCCT-
1 TGAGCTGAATAACGGTAAGCTCCTC
20729802 TCGAGCTGAATAACGGTAAGCTCCTC
1 T-GAGCTGAATAACGGTAAGCTCCTC
* *
20729828 CGAGCTGAATAATGGTAAGCT
1 TGAGCTGAATAACGGTAAGCT
20729849 TACACAAGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
24 7 0.11
25 54 0.89
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (25 bp):
TGAGCTGAATAACGGTAAGCTCCTC
Found at i:20729859 original size:50 final size:50
Alignment explanation
Indices: 20729763--20729859 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 50
20729753 ATGAGCTGTA
* * * *
20729763 AACGGTAAGCTCCTCTAAGCTAAATAACGGTAAGCTCCTTCGAGCTGAAT
1 AACGGTAAGCTCCTCCAAGCTAAATAACGGTAAGCTACTACAAGCTGAAT
* * *
20729813 AACGGTAAGCTCCTCCGAGCTGAATAATGGTAAGCTTAC-ACAAGCTG
1 AACGGTAAGCTCCTCCAAGCTAAATAACGGTAAGC-TACTACAAGCTG
20729860 GGTATAGGTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 37 0.95
51 2 0.05
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (50 bp):
AACGGTAAGCTCCTCCAAGCTAAATAACGGTAAGCTACTACAAGCTGAAT
Found at i:20741103 original size:82 final size:82
Alignment explanation
Indices: 20740966--20741126 Score: 295
Period size: 82 Copynumber: 2.0 Consensus size: 82
20740956 TAAGACATGA
*
20740966 AAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTATTT
1 AAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATT
20741031 GTATATATTTTACCAGG
66 GTATATATTTTACCAGG
* *
20741048 AAATTAATATTCTTTTGGAAAGAATATAATTAATATTTGAATTTGATTCATACAAATTATTAATT
1 AAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATT
20741113 GTATATATTTTACC
66 GTATATATTTTACC
20741127 GAATTTAGTA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (82 bp):
AAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATT
GTATATATTTTACCAGG
Found at i:20748382 original size:70 final size:70
Alignment explanation
Indices: 20748292--20748428 Score: 256
Period size: 70 Copynumber: 2.0 Consensus size: 70
20748282 GAAGTTTCAT
* *
20748292 TAAAATTTTTGGAGTGGTTTTAAAGTATTATATTTTTTTGATAAATAATATCTCACTGAAATTTA
1 TAAAATTTATGGAATGGTTTTAAAGTATTATATTTTTTTGATAAATAATATCTCACTGAAATTTA
20748357 TACGC
66 TACGC
20748362 TAAAATTTATGGAATGGTTTTAAAGTATTATATTTTTTTGATAAATAATATCTCACTGAAATTTA
1 TAAAATTTATGGAATGGTTTTAAAGTATTATATTTTTTTGATAAATAATATCTCACTGAAATTTA
20748427 TA
66 TA
20748429 TGCCATTTAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (70 bp):
TAAAATTTATGGAATGGTTTTAAAGTATTATATTTTTTTGATAAATAATATCTCACTGAAATTTA
TACGC
Found at i:20751184 original size:37 final size:37
Alignment explanation
Indices: 20751143--20751218 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
20751133 CTGAGAAAAG
*
20751143 TATATTTTCTGGGTCATGTTATCTATATTAATGGCAT
1 TATATTTTCTGGGTCATGTTATCTACATTAATGGCAT
20751180 TATATTTTCTGGGTCATGTTATCTACATTAATGGCAT
1 TATATTTTCTGGGTCATGTTATCTACATTAATGGCAT
20751217 TA
1 TA
20751219 AAGTAGATCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (37 bp):
TATATTTTCTGGGTCATGTTATCTACATTAATGGCAT
Found at i:20753060 original size:4 final size:4
Alignment explanation
Indices: 20753051--20753087 Score: 65
Period size: 4 Copynumber: 9.0 Consensus size: 4
20753041 AGTAAAAGAT
20753051 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA TATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA -ATTA
20753088 TGAGATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
ATTA
Found at i:20753233 original size:10 final size:10
Alignment explanation
Indices: 20753218--20753263 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
20753208 AACATAAAGT
20753218 AAATGAAATA
1 AAATGAAATA
20753228 AAATGAAATA
1 AAATGAAATA
20753238 AAA-GAAA-A
1 AAATGAAATA
20753246 CAAATGAAATA
1 -AAATGAAATA
20753257 AAA-GAAA
1 AAATGAAA
20753264 GAAAGAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 1 0.03
9 11 0.33
10 20 0.61
11 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (10 bp):
AAATGAAATA
Found at i:20754099 original size:14 final size:14
Alignment explanation
Indices: 20754082--20754111 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20754072 TTGATAGGGA
20754082 GAAAATATTTTCCG
1 GAAAATATTTTCCG
20754096 GAAAATATTTTCCG
1 GAAAATATTTTCCG
20754110 GA
1 GA
20754112 TTTCCCGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (14 bp):
GAAAATATTTTCCG
Found at i:20754316 original size:14 final size:14
Alignment explanation
Indices: 20754297--20754326 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20754287 AACGATTGCA
20754297 GCCTCATCATCTCT
1 GCCTCATCATCTCT
*
20754311 GCCTCATCTTCTCT
1 GCCTCATCATCTCT
20754325 GC
1 GC
20754327 TAGTTCACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.43, G:0.10, T:0.37
Consensus pattern (14 bp):
GCCTCATCATCTCT
Found at i:20754974 original size:16 final size:16
Alignment explanation
Indices: 20754949--20754980 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20754939 ACTAAAGTGC
*
20754949 TTATTTTGCAAATCGA
1 TTATTCTGCAAATCGA
20754965 TTATTCTGCAAATCGA
1 TTATTCTGCAAATCGA
20754981 CAACAAATCT
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:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (16 bp):
TTATTCTGCAAATCGA
Done.