Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 154 of 187
Found at i:45784253 original size:45 final size:45
Alignment explanation
Indices: 45784190--45784339 Score: 248
Period size: 45 Copynumber: 3.3 Consensus size: 45
45784180 ATAACGGTAG
* *
45784190 CAGTAACA-TGAACAGTAACAGTATTCAACACACAAAGTGCTGAAT
1 CAGTAACAGT-AACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* *
45784235 CTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
45784280 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
45784325 CAGTAACAGTAACAG
1 CAGTAACAGTAACAG
45784340 AAGTTGGCAC
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 97 0.99
46 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
Found at i:45785772 original size:12 final size:12
Alignment explanation
Indices: 45785755--45785788 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
45785745 AAAACCCTAA
45785755 TTTTTCCTTTTC
1 TTTTTCCTTTTC
45785767 TTTTT-CTTTTC
1 TTTTTCCTTTTC
45785778 TTCTTTCCTTT
1 TT-TTTCCTTT
45785789 CCCCTGTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 8 0.40
13 4 0.20
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCCTTTTC
Found at i:45789550 original size:44 final size:46
Alignment explanation
Indices: 45789500--45789589 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
45789490 AGCTATTCCC
**
45789500 TTCAACCAAACACAAT-AAT-ACT-ATTACAGTTCTATTCCATTACA
1 TTCAACCAAACA-AATGAATCACTGATTACAACTCTATTCCATTACA
*
45789544 TTCAACCAAACAATTGAATCACTGATTACAACTCTATTCCATTACA
1 TTCAACCAAACAAATGAATCACTGATTACAACTCTATTCCATTACA
45789590 GCCCTATTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
43 2 0.05
44 15 0.38
45 3 0.08
46 20 0.50
ACGTcount: A:0.40, C:0.26, G:0.03, T:0.31
Consensus pattern (46 bp):
TTCAACCAAACAAATGAATCACTGATTACAACTCTATTCCATTACA
Found at i:45789589 original size:16 final size:16
Alignment explanation
Indices: 45789568--45789618 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
45789558 TGAATCACTG
*
45789568 ATTACAACTCTATTCC
1 ATTACAACACTATTCC
* *
45789584 ATTACAGCCCTATTCC
1 ATTACAACACTATTCC
*
45789600 ATTACAACAGTATTCC
1 ATTACAACACTATTCC
45789616 ATT
1 ATT
45789619 CCAATGAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACAACACTATTCC
Found at i:45793290 original size:166 final size:166
Alignment explanation
Indices: 45793061--45793389 Score: 541
Period size: 166 Copynumber: 2.0 Consensus size: 166
45793051 TTTTAACCAA
* * * * *
45793061 TTTTATATTTAAAACTAGGTTTCATGCATATTTAAGCATAATCATAAGTTTGTTCAGTTTCAAAC
1 TTTTATATTAAAAACCAGGTTTAATGCATATTTAAGCATAATCATAAATTTGTCCAGTTTCAAAC
45793126 ATTTTTGCATGTAATGCAAACTAAAACCAACCAAAAATAACCCACGCCACAATCCAAATAAATTA
66 ATTTTTGCATGTAATGCAAACTAAAACCAACCAAAAATAACCCACGCCACAATCCAAATAAATTA
*
45793191 TTACAATCCCCAAATAAAAATTGATAAATTAAATTT
131 TTACAACCCCCAAATAAAAATTGATAAATTAAATTT
*
45793227 TTTTGTATTAAAAACCAGGTTTAATGCATATTTAAGCATAATCATAAATTTGTCCAGTTTCAAAC
1 TTTTATATTAAAAACCAGGTTTAATGCATATTTAAGCATAATCATAAATTTGTCCAGTTTCAAAC
* * * *
45793292 GTTTTTGCATGTAATGCAAACTAAAACCAACCAAAAATAACTCATGCCACAATCCAAATAATTTA
66 ATTTTTGCATGTAATGCAAACTAAAACCAACCAAAAATAACCCACGCCACAATCCAAATAAATTA
* *
45793357 TTACAGCCCCCAAATAGAAATTGATAAATTAAA
131 TTACAACCCCCAAATAAAAATTGATAAATTAAA
45793390 GTAAAAATAC
Statistics
Matches: 150, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
166 150 1.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.32
Consensus pattern (166 bp):
TTTTATATTAAAAACCAGGTTTAATGCATATTTAAGCATAATCATAAATTTGTCCAGTTTCAAAC
ATTTTTGCATGTAATGCAAACTAAAACCAACCAAAAATAACCCACGCCACAATCCAAATAAATTA
TTACAACCCCCAAATAAAAATTGATAAATTAAATTT
Found at i:45796537 original size:32 final size:32
Alignment explanation
Indices: 45796465--45796544 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 32
45796455 ATATATAGTA
* *
45796465 AAAAATTAAAATATATATTTTAGACATGATATT
1 AAAAATTAAAATAAATAATTTAGA-ATGATATT
45796498 AAAAATTAAAA-AAATAATTTAG-ATGATATTT
1 AAAAATTAAAATAAATAATTTAGAATGATA-TT
45796529 AAATAATTAAATATAA
1 AAA-AATTAAA-ATAA
45796545 TATAGCAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 6 0.15
31 5 0.12
32 16 0.39
33 12 0.29
34 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.36
Consensus pattern (32 bp):
AAAAATTAAAATAAATAATTTAGAATGATATT
Found at i:45796545 original size:30 final size:30
Alignment explanation
Indices: 45796465--45796545 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 30
45796455 ATATATAGTA
45796465 AAAAATTAAAATATATATTTTAGACATGATATT
1 AAAAATTAAAATATA-A-TTTAGA-ATGATATT
*
45796498 AAAAATTAAAAAAATAATTTAG-ATGATATTT
1 AAAAATT-AAAATATAATTTAGAATGATA-TT
45796529 AAATAATT-AAATATAAT
1 AAA-AATTAAAATATAAT
45796546 ATAGCAAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
30 14 0.33
31 5 0.12
32 9 0.21
33 8 0.19
34 7 0.16
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAAATTAAAATATAATTTAGAATGATATT
Found at i:45796978 original size:11 final size:9
Alignment explanation
Indices: 45796954--45797021 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 9
45796944 TTAAAAGTTC
45796954 AAAAATTAT
1 AAAAATTAT
45796963 AAAAATTATTT
1 AAAAATTA--T
*
45796974 AAAAA-AAT
1 AAAAATTAT
*
45796982 AAAAAATCATT
1 -AAAAATTA-T
*
45796993 AAAAAAGTAT
1 -AAAAATTAT
45797003 AAAAATTAT
1 AAAAATTAT
45797012 AAAAA-TAT
1 AAAAATTAT
45797020 AA
1 AA
45797022 TTTTTAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
8 6 0.12
9 26 0.53
10 3 0.06
11 14 0.29
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:45796986 original size:20 final size:21
Alignment explanation
Indices: 45796954--45797011 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 21
45796944 TTAAAAGTTC
*
45796954 AAAAATTATAAAAATTATTTA
1 AAAAAATATAAAAATTATTTA
*
45796975 AAAAAATA-AAAAATCA-TTA
1 AAAAAATATAAAAATTATTTA
*
45796994 AAAAAGTATAAAAATTAT
1 AAAAAATATAAAAATTAT
45797012 AAAAATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 10 0.32
20 14 0.45
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAAATATAAAAATTATTTA
Found at i:45797014 original size:19 final size:20
Alignment explanation
Indices: 45796954--45797016 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 20
45796944 TTAAAAGTTC
*
45796954 AAAAATTATAAAAATTATTTA
1 AAAAAATATAAAAATTA-TTA
*
45796975 AAAAAATA-AAAAATCATTA
1 AAAAAATATAAAAATTATTA
*
45796994 AAAAAGTATAAAAATTA-TA
1 AAAAAATATAAAAATTATTA
45797013 AAAA
1 AAAA
45797017 TATAATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.43
20 14 0.38
21 7 0.19
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAAATATAAAAATTATTA
Found at i:45797841 original size:20 final size:20
Alignment explanation
Indices: 45797818--45797855 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
45797808 ACAAAAATAC
45797818 AAAAAAATTCAAAAACAGAA
1 AAAAAAATTCAAAAACAGAA
*
45797838 AAAACAATTCAAAAACAG
1 AAAAAAATTCAAAAACAG
45797856 TAAAGAATAT
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:0.71, C:0.13, G:0.05, T:0.11
Consensus pattern (20 bp):
AAAAAAATTCAAAAACAGAA
Found at i:45798754 original size:28 final size:27
Alignment explanation
Indices: 45798722--45798779 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
45798712 TATCTATATA
* *
45798722 TTTTTAATAAT-TTTATTTTTATGATACT
1 TTTTTAA-AATATTTATGTATAT-ATACT
*
45798750 TTTTTTAAATATTTATGTATATATACT
1 TTTTTAAAATATTTATGTATATATACT
45798777 TTT
1 TTT
45798780 GTGCTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (27 bp):
TTTTTAAAATATTTATGTATATATACT
Found at i:45804566 original size:20 final size:21
Alignment explanation
Indices: 45804532--45804597 Score: 89
Period size: 20 Copynumber: 3.1 Consensus size: 21
45804522 AAACTACTAG
*
45804532 AAATATGTGGATAAATCACCA
1 AAATATGTAGATAAATCACCA
*
45804553 AAAT-TGTAGATAAATTACCA
1 AAATATGTAGATAAATCACCA
*
45804573 GAAATATGTGGATAAATCACCA
1 -AAATATGTAGATAAATCACCA
45804595 AAA
1 AAA
45804598 ATGCAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.36
21 11 0.28
22 14 0.36
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (21 bp):
AAATATGTAGATAAATCACCA
Found at i:45804576 original size:42 final size:42
Alignment explanation
Indices: 45804515--45804619 Score: 165
Period size: 42 Copynumber: 2.5 Consensus size: 42
45804505 CACCAGTATT
* *
45804515 TGCAAATAAACTACTAGAAATATGTGGATAAATCACCAAAAT
1 TGCAAATAAACTACCAGAAATATGTGGATAAATCACCAAAAA
* * *
45804557 TGTAGATAAATTACCAGAAATATGTGGATAAATCACCAAAAA
1 TGCAAATAAACTACCAGAAATATGTGGATAAATCACCAAAAA
45804599 TGCAAATAAACTACCAGAAAT
1 TGCAAATAAACTACCAGAAAT
45804620 TTTCTCCTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.23
Consensus pattern (42 bp):
TGCAAATAAACTACCAGAAATATGTGGATAAATCACCAAAAA
Found at i:45804587 original size:22 final size:22
Alignment explanation
Indices: 45804530--45804599 Score: 99
Period size: 22 Copynumber: 3.3 Consensus size: 22
45804520 ATAAACTACT
45804530 AGAAATATGTGGATAAATCACC
1 AGAAATATGTGGATAAATCACC
* *
45804552 A-AAAT-TGTAGATAAATTACC
1 AGAAATATGTGGATAAATCACC
45804572 AGAAATATGTGGATAAATCACC
1 AGAAATATGTGGATAAATCACC
*
45804594 AAAAAT
1 AGAAAT
45804600 GCAAATAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 14 0.34
21 8 0.20
22 19 0.46
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.24
Consensus pattern (22 bp):
AGAAATATGTGGATAAATCACC
Found at i:45810405 original size:10 final size:10
Alignment explanation
Indices: 45810375--45810412 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
45810365 TAAATAAATC
*
45810375 AAAAGAAAAAG
1 AAAAG-AAAGG
45810386 AAAA-AAAGG
1 AAAAGAAAGG
45810395 AAAAGAAAGG
1 AAAAGAAAGG
45810405 AAAAGAAA
1 AAAAGAAA
45810413 AAGAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 8 0.32
10 13 0.52
11 4 0.16
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAGAAAGG
Found at i:45814384 original size:29 final size:28
Alignment explanation
Indices: 45814333--45814389 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
45814323 TAAAAACCAT
* *
45814333 GTTCTTTAGCGGCGCTTACAAAAAACGC
1 GTTCTTTAGCGGCGCTCAAAAAAAACGC
45814361 GTTCTTTAGCGGCGCTCAGAAAAAAACGC
1 GTTCTTTAGCGGCGCTCA-AAAAAAACGC
45814390 TGCTAAAGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (28 bp):
GTTCTTTAGCGGCGCTCAAAAAAAACGC
Found at i:45814441 original size:43 final size:43
Alignment explanation
Indices: 45814361--45814585 Score: 341
Period size: 42 Copynumber: 5.3 Consensus size: 43
45814351 CAAAAAACGC
*
45814361 GTTCTTTAGCGGCGCTCAG-AAAAAAACG-CTGCTAAAGACCAT
1 GTTCTTTAGCGGCGCTTAGAAAAAAAACGCCT-CTAAAGACCAT
*
45814403 GTTCTTTAGCGGCGCTTAGAAAAAAAACGCCTCTAAAGACCGT
1 GTTCTTTAGCGGCGCTTAGAAAAAAAACGCCTCTAAAGACCAT
* *
45814446 GTTCTTTAGCGGCACTTAGAAAAAAAACGCCTCTAAAGACCGT
1 GTTCTTTAGCGGCGCTTAGAAAAAAAACGCCTCTAAAGACCAT
*
45814489 GTTCTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGACCAT
1 GTTCTTTAGCGGCGCTTAGAAAAAAAACGCCTCTAAAGACCAT
* * *
45814531 GTTCGTTAGCGGCGCTTA-AGAAAAAACGCCGCTAAAGACCAT
1 GTTCTTTAGCGGCGCTTAGAAAAAAAACGCCTCTAAAGACCAT
45814573 GTTCTTTAGCGGC
1 GTTCTTTAGCGGC
45814586 ATTTATTCTT
Statistics
Matches: 171, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
42 90 0.53
43 79 0.46
44 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (43 bp):
GTTCTTTAGCGGCGCTTAGAAAAAAAACGCCTCTAAAGACCAT
Found at i:45814610 original size:42 final size:42
Alignment explanation
Indices: 45814381--45814586 Score: 252
Period size: 43 Copynumber: 4.9 Consensus size: 42
45814371 GGCGCTCAGA
* * * *
45814381 AAAAAACGCTGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAAACGCCGCTAAAGACCATGTTCGTTAGCGGCACTTA-AG
* * * *
45814424 AAAAAACGCCTCTAAAGACCGTGTTCTTTAGCGGCACTTAGAA
1 AAAAAACGCCGCTAAAGACCATGTTCGTTAGCGGCACTTA-AG
* * * *
45814467 AAAAAACGCCTCTAAAGACCGTGTTCTTTAGCGGCGCTT-AG
1 AAAAAACGCCGCTAAAGACCATGTTCGTTAGCGGCACTTAAG
*
45814508 AAAAAAACGCCGCTAAAGACCATGTTCGTTAGCGGCGCTTAAG
1 -AAAAAACGCCGCTAAAGACCATGTTCGTTAGCGGCACTTAAG
*
45814551 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCA
1 AAAAAACGCCGCTAAAGACCATGTTCGTTAGCGGCA
45814587 TTTATTCTTA
Statistics
Matches: 150, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
41 1 0.01
42 70 0.47
43 79 0.53
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGACCATGTTCGTTAGCGGCACTTAAG
Found at i:45815018 original size:21 final size:21
Alignment explanation
Indices: 45814992--45815037 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
45814982 TTTTGGTCTG
45814992 CTCTGCTTCCCTCGCTG-CGGC
1 CTCTGCTTCCCTCGCTGTC-GC
45815013 CTCTGCTTCCCTCGCTGTCGC
1 CTCTGCTTCCCTCGCTGTCGC
45815034 CTCT
1 CTCT
45815038 ACTTTAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.00, C:0.48, G:0.20, T:0.33
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGTCGC
Found at i:45820598 original size:9 final size:9
Alignment explanation
Indices: 45820584--45820668 Score: 88
Period size: 9 Copynumber: 9.9 Consensus size: 9
45820574 AAGTTATACA
45820584 TTATGTAAG
1 TTATGTAAG
45820593 TTATGTAAG
1 TTATGTAAG
45820602 TTATGTAAG
1 TTATGTAAG
45820611 TTATGTAAG
1 TTATGTAAG
*
45820620 TTGTGT-A-
1 TTATGTAAG
* *
45820627 TTATGAAAC
1 TTATGTAAG
45820636 TTATGTAAG
1 TTATGTAAG
**
45820645 TTGCGTAAG
1 TTATGTAAG
*
45820654 TTGTGT-A-
1 TTATGTAAG
45820661 TTATGTAA
1 TTATGTAA
45820669 CTTACCCTTG
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
7 9 0.14
8 4 0.06
9 51 0.80
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:45820621 original size:43 final size:43
Alignment explanation
Indices: 45820573--45820660 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
45820563 GATTTAGGAA
* * *
45820573 TAAGTTATACATTATGTAAGTTATGTAAGTTATGTAAGTTATG
1 TAAGTTATACATTATGAAACTTATGTAAGTTACGTAAGTTATG
* ** * *
45820616 TAAGTTGTGTATTATGAAACTTATGTAAGTTGCGTAAGTTGTG
1 TAAGTTATACATTATGAAACTTATGTAAGTTACGTAAGTTATG
45820659 TA
1 TA
45820661 TTATGTAACT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (43 bp):
TAAGTTATACATTATGAAACTTATGTAAGTTACGTAAGTTATG
Found at i:45820631 original size:34 final size:34
Alignment explanation
Indices: 45820593--45820672 Score: 124
Period size: 34 Copynumber: 2.4 Consensus size: 34
45820583 ATTATGTAAG
* *
45820593 TTATGTAAGTTATGTAAGTTATGTAAGTTGTGTA
1 TTATGTAACTTATGTAAGTTACGTAAGTTGTGTA
* *
45820627 TTATGAAACTTATGTAAGTTGCGTAAGTTGTGTA
1 TTATGTAACTTATGTAAGTTACGTAAGTTGTGTA
45820661 TTATGTAACTTA
1 TTATGTAACTTA
45820673 CCCTTGACAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (34 bp):
TTATGTAACTTATGTAAGTTACGTAAGTTGTGTA
Found at i:45820639 original size:25 final size:27
Alignment explanation
Indices: 45820584--45820655 Score: 94
Period size: 25 Copynumber: 2.7 Consensus size: 27
45820574 AAGTTATACA
* * *
45820584 TTATGTAAGTTATGTAAGTTATGTAAG
1 TTATGTAAGTTGTGTAAGTTATGAAAC
45820611 TTATGTAAGTTGTGT-A-TTATGAAAC
1 TTATGTAAGTTGTGTAAGTTATGAAAC
*
45820636 TTATGTAAGTTGCGTAAGTT
1 TTATGTAAGTTGTGTAAGTT
45820656 GTGTATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 21 0.54
26 2 0.05
27 16 0.41
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (27 bp):
TTATGTAAGTTGTGTAAGTTATGAAAC
Found at i:45820756 original size:16 final size:16
Alignment explanation
Indices: 45820735--45820780 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
45820725 TTATTTACAC
*
45820735 ATGTAAGTTATGTCTT
1 ATGTAAGTTATGTATT
*
45820751 ATGTAAGTTGTGTATT
1 ATGTAAGTTATGTATT
* *
45820767 ATGAAACTTATGTA
1 ATGTAAGTTATGTA
45820781 AGTTGCATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (16 bp):
ATGTAAGTTATGTATT
Found at i:45820786 original size:138 final size:136
Alignment explanation
Indices: 45820595--45820955 Score: 569
Period size: 138 Copynumber: 2.6 Consensus size: 136
45820585 TATGTAAGTT
*
45820595 ATGTAAGTTATGTAAGTTATGTAAGTTGTGTATTATGAAACTTATGTAAGTTGCGTAAGTTGTGT
1 ATGTAAGTTATGT--CTTATGTAAGTTGTGTATTATGAAACTTATGTAAGTTGCGTAAGTTGTGT
* *
45820660 ATTATGTAACTTACCCTTGACAAATTCATCCAAGAATGGTCCATTTAAGTTATGTAAGTTCTGTA
64 ATTATGTAACTTACCCTTGACAAATTCATCCAAGAATGAT--ATGTAAGTTATGTAAGTTCTGTA
45820725 TTATTTACAC
127 TTATTTACAC
*
45820735 ATGTAAGTTATGTCTTATGTAAGTTGTGTATTATGAAACTTATGTAAGTTGCATAAGTTGTGTAT
1 ATGTAAGTTATGTCTTATGTAAGTTGTGTATTATGAAACTTATGTAAGTTGCGTAAGTTGTGTAT
45820800 TATGTAACTTACCCTTGACAAATTCATCCAAGAATGATATGTAAGTTATGTAAGTTCTGTATTAT
66 TATGTAACTTACCCTTGACAAATTCATCCAAGAATGATATGTAAGTTATGTAAGTTCTGTATTAT
45820865 TTACAC
131 TTACAC
45820871 ATGTAAGTTATGTCTTATGTAAGTTGTGTAAGTTGTGTATTATGAAACTTATGTAAGTTGCGTAA
1 ATGTAAGTTATGTC---T-T-A----TGTAAGTTGTGTATTATGAAACTTATGTAAGTTGCGTAA
45820936 GTTGTGTATTATGTAACTTA
57 GTTGTGTATTATGTAACTTA
45820956 TTTAATTTAT
Statistics
Matches: 207, Mismatches: 5, Indels: 13
0.92 0.02 0.06
Matches are distributed among these distances:
136 46 0.22
138 87 0.42
139 1 0.00
140 14 0.07
141 1 0.00
145 58 0.28
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (136 bp):
ATGTAAGTTATGTCTTATGTAAGTTGTGTATTATGAAACTTATGTAAGTTGCGTAAGTTGTGTAT
TATGTAACTTACCCTTGACAAATTCATCCAAGAATGATATGTAAGTTATGTAAGTTCTGTATTAT
TTACAC
Found at i:45820851 original size:9 final size:9
Alignment explanation
Indices: 45820837--45821031 Score: 74
Period size: 9 Copynumber: 22.8 Consensus size: 9
45820827 CCAAGAATGA
45820837 TATGTAAGT
1 TATGTAAGT
45820846 TATGTAAGT
1 TATGTAAGT
*
45820855 TCTGT-A-T
1 TATGTAAGT
*
45820862 TATTTACA--
1 TATGTA-AGT
*
45820870 CATGTAAGT
1 TATGTAAGT
*
45820879 TATGT--CT
1 TATGTAAGT
45820886 TATGTAAGT
1 TATGTAAGT
*
45820895 TGTGTAAGT
1 TATGTAAGT
*
45820904 TGTGT-A-T
1 TATGTAAGT
* *
45820911 TATGAAACT
1 TATGTAAGT
45820920 TATGTAAGT
1 TATGTAAGT
**
45820929 TGCGTAAGT
1 TATGTAAGT
*
45820938 TGTGT-A-T
1 TATGTAAGT
*
45820945 TATGTAACT
1 TATGTAAGT
* *
45820954 TATTTAATT
1 TATGTAAGT
* *
45820963 TATGTAGGG
1 TATGTAAGT
*
45820972 TATGATTTA-T
1 TATG--TAAGT
*
45820982 TATGTAACT
1 TATGTAAGT
* *
45820991 TATTTAATT
1 TATGTAAGT
* *
45821000 TATGTAGGG
1 TATGTAAGT
45821009 TATGTAAGT
1 TATGTAAGT
45821018 TATGT--GT
1 TATGTAAGT
45821025 TATGTAA
1 TATGTAA
45821032 ATGAATATAT
Statistics
Matches: 136, Mismatches: 35, Indels: 30
0.68 0.17 0.15
Matches are distributed among these distances:
7 27 0.20
8 11 0.08
9 93 0.68
10 4 0.03
11 1 0.01
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (9 bp):
TATGTAAGT
Found at i:45820922 original size:34 final size:34
Alignment explanation
Indices: 45820884--45820956 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
45820874 TAAGTTATGT
*
45820884 CTTATGTAAGTTGTGTAAGTTGTGTATTATGAAA
1 CTTATGTAAGTTGCGTAAGTTGTGTATTATGAAA
*
45820918 CTTATGTAAGTTGCGTAAGTTGTGTATTATGTAA
1 CTTATGTAAGTTGCGTAAGTTGTGTATTATGAAA
45820952 CTTAT
1 CTTAT
45820957 TTAATTTATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.45
Consensus pattern (34 bp):
CTTATGTAAGTTGCGTAAGTTGTGTATTATGAAA
Found at i:45820930 original size:25 final size:25
Alignment explanation
Indices: 45820845--45820930 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 25
45820835 GATATGTAAG
* * *
45820845 TTATGTAAGTTCTGTATTATTTACAC
1 TTATGTAAGTTGTGTATTA-TGAAAC
* * * *
45820871 --ATGTAAGTTATGTCTTATGTAAG
1 TTATGTAAGTTGTGTATTATGAAAC
*
45820894 TTGTGTAAGTTGTGTATTATGAAAC
1 TTATGTAAGTTGTGTATTATGAAAC
45820919 TTATGTAAGTTG
1 TTATGTAAGTTG
45820931 CGTAAGTTGT
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
23 2 0.04
24 15 0.33
25 29 0.63
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.47
Consensus pattern (25 bp):
TTATGTAAGTTGTGTATTATGAAAC
Found at i:45820985 original size:37 final size:37
Alignment explanation
Indices: 45820942--45821012 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
45820932 GTAAGTTGTG
45820942 TATTATGTAACTTATTTAATTTATGTAGGGTATGATT
1 TATTATGTAACTTATTTAATTTATGTAGGGTATGATT
45820979 TATTATGTAACTTATTTAATTTATGTAGGGTATG
1 TATTATGTAACTTATTTAATTTATGTAGGGTATG
45821013 TAAGTTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.51
Consensus pattern (37 bp):
TATTATGTAACTTATTTAATTTATGTAGGGTATGATT
Found at i:45821581 original size:212 final size:212
Alignment explanation
Indices: 45821028--45821805 Score: 1457
Period size: 212 Copynumber: 3.7 Consensus size: 212
45821018 TATGTGTTAT
*
45821028 GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTATCAATTTATTATT
1 GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
*
45821093 AATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATCTTCCACTTAATTAT
66 AATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATCTTCCACTGAATTAT
45821158 TCGTGGAGAGGTATATGTGTACAAAATTGACAACAAAATATGTTTAAATATTATTAATAAAATCT
131 TCGTGGAGAGGTATATGTGTACAAAATTGACAACAAAATATGTTTAAATATTATTAATAAAAT-T
*
45821223 GAAATATAGCTTACATAC
195 TAAATATAGCTTACATAC
45821241 GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
1 GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
*
45821306 AATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATCTTCCATTGAATTAT
66 AATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATCTTCCACTGAATTAT
45821371 TCGTGGAGAGGTATATGTGTACAAAATTGACAACAAAATATGTTTAAATATTATTAATAAAATTT
131 TCGTGGAGAGGTATATGTGTACAAAATTGACAACAAAATATGTTTAAATATTATTAATAAAATTT
45821436 AAATATAGCTTACATAC
196 AAATATAGCTTACATAC
*
45821453 GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAACTTATTATT
1 GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
45821518 AATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATCTTCCACTGAATTAT
66 AATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATCTTCCACTGAATTAT
45821583 TCGTGGAGAGGTATATGTGTACAAAATTGACAACAAAATATGTTTAAATATTATTAATAAAATTT
131 TCGTGGAGAGGTATATGTGTACAAAATTGACAACAAAATATGTTTAAATATTATTAATAAAATTT
45821648 AAATATAGCTTACATAC
196 AAATATAGCTTACATAC
*
45821665 GTAAATGAATATATGTATAATATTAAAAATATGGTAATACTTATTTAAGTTGTCAATTTATTATT
1 GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
* * *
45821730 AATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTTACCGGTCCACTGAATTA
66 AATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATC-TTCCACTGAATTA
45821795 TTCGTGGAGAG
130 TTCGTGGAGAG
45821806 TGAATATACA
Statistics
Matches: 553, Mismatches: 11, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
212 340 0.61
213 213 0.39
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (212 bp):
GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
AATAAAATTTAAATATAGCTTACATAAGCAATCTTTGCTTTTAAACTAATCTTCCACTGAATTAT
TCGTGGAGAGGTATATGTGTACAAAATTGACAACAAAATATGTTTAAATATTATTAATAAAATTT
AAATATAGCTTACATAC
Found at i:45825739 original size:36 final size:34
Alignment explanation
Indices: 45825652--45825739 Score: 88
Period size: 36 Copynumber: 2.5 Consensus size: 34
45825642 ATATAGGCAT
* * *
45825652 ATATATTATATA-TTATATATATAATGACCATAG
1 ATATATTATATATTTATATATATAAAGACCACAC
* *
45825685 ATGTATGTATTTATTTTATATATATAACAAGACCACAC
1 ATATAT-TATATA-TTTATATATAT-A-AAGACCACAC
45825723 ATATATTATATATTTAT
1 ATATATTATATATTTAT
45825740 CGAGATGCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
33 5 0.12
34 5 0.12
36 15 0.35
37 6 0.14
38 12 0.28
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (34 bp):
ATATATTATATATTTATATATATAAAGACCACAC
Found at i:45829880 original size:18 final size:18
Alignment explanation
Indices: 45829857--45829932 Score: 134
Period size: 18 Copynumber: 4.2 Consensus size: 18
45829847 TTTGGTTAAA
*
45829857 AATTACCCGATTTAACCG
1 AATTACCCGAATTAACCG
45829875 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
*
45829893 GATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
45829911 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
45829929 AATT
1 AATT
45829933 GAATCACTAC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:45829884 original size:9 final size:9
Alignment explanation
Indices: 45829857--45829932 Score: 98
Period size: 9 Copynumber: 8.4 Consensus size: 9
45829847 TTTGGTTAAA
*
45829857 AATTACCCG
1 AATTAACCG
*
45829866 ATTTAACCG
1 AATTAACCG
*
45829875 AATTACCCG
1 AATTAACCG
45829884 AATTAACCG
1 AATTAACCG
* *
45829893 GATTACCCG
1 AATTAACCG
45829902 AATTAACCG
1 AATTAACCG
*
45829911 AATTACCCG
1 AATTAACCG
45829920 AATTAACCG
1 AATTAACCG
45829929 AATT
1 AATT
45829933 GAATCACTAC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 56 1.00
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:45829982 original size:13 final size:13
Alignment explanation
Indices: 45829964--45830006 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
45829954 ATTTTTAGAC
*
45829964 TTTTAGACTTTAG
1 TTTTAGATTTTAG
45829977 TTTTAG-TTTTAG
1 TTTTAGATTTTAG
* *
45829989 CTTTAGATTTTAT
1 TTTTAGATTTTAG
45830002 TTTTA
1 TTTTA
45830007 TTTATTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.63
Consensus pattern (13 bp):
TTTTAGATTTTAG
Found at i:45829988 original size:19 final size:19
Alignment explanation
Indices: 45829964--45830006 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
45829954 ATTTTTAGAC
45829964 TTTTAGACTTTAG-TTTTAG
1 TTTTAG-CTTTAGATTTTAG
*
45829983 TTTTAGCTTTAGATTTTAT
1 TTTTAGCTTTAGATTTTAG
45830002 TTTTA
1 TTTTA
45830007 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.63
Consensus pattern (19 bp):
TTTTAGCTTTAGATTTTAG
Found at i:45829995 original size:25 final size:27
Alignment explanation
Indices: 45829956--45830006 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
45829946 ATTAAATTAT
45829956 TTTTAGACTTTTAGACTTTAGTTTTAG
1 TTTTAGACTTTTAGACTTTAGTTTTAG
* *
45829983 TTTTAG-C-TTTAGATTTTATTTTTA
1 TTTTAGACTTTTAGACTTTAGTTTTA
45830007 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 1 0.05
27 6 0.27
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.61
Consensus pattern (27 bp):
TTTTAGACTTTTAGACTTTAGTTTTAG
Found at i:45832590 original size:15 final size:15
Alignment explanation
Indices: 45832572--45832601 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45832562 TCTATTTTTT
45832572 TTATATCAATTTGAG
1 TTATATCAATTTGAG
*
45832587 TTATATCGATTTGAG
1 TTATATCAATTTGAG
45832602 CTTGAAAGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (15 bp):
TTATATCAATTTGAG
Found at i:45836913 original size:16 final size:16
Alignment explanation
Indices: 45836892--45836967 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 16
45836882 ATCATTTTCA
45836892 ATATTATTATTTATGC
1 ATATTATTATTTATGC
*
45836908 ATATTAGTA-TTATG-
1 ATATTATTATTTATGC
45836922 AT-TTATTA-TTATGAC
1 ATATTATTATTTATG-C
* *
45836937 ACTTTTAAATTTTATTATGC
1 A-TATT--ATTAT-TTATGC
45836957 ATATTATTATT
1 ATATTATTATT
45836968 ATATTATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
13 10 0.21
14 2 0.04
15 6 0.13
16 10 0.21
17 6 0.13
19 6 0.13
20 2 0.04
21 5 0.11
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (16 bp):
ATATTATTATTTATGC
Found at i:45836931 original size:13 final size:14
Alignment explanation
Indices: 45836892--45836935 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
45836882 ATCATTTTCA
45836892 ATATTATTATTTATG
1 ATATTATTA-TTATG
*
45836907 CATATTAGTATTATG
1 -ATATTATTATTATG
45836922 AT-TTATTATTATG
1 ATATTATTATTATG
45836935 A
1 A
45836936 CACTTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 11 0.42
14 2 0.08
15 5 0.19
16 8 0.31
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (14 bp):
ATATTATTATTATG
Found at i:45837413 original size:29 final size:29
Alignment explanation
Indices: 45837373--45837431 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
45837363 GAATAAAAAC
*
45837373 TATATTTTTTATTTTTAAAATATACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
45837402 TATATTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
45837431 T
1 T
45837432 TTAAAACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAATACACTACA
Found at i:45837956 original size:111 final size:112
Alignment explanation
Indices: 45837724--45838056 Score: 489
Period size: 111 Copynumber: 3.0 Consensus size: 112
45837714 CCGCTAACAA
* *
45837724 TAAGCATTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAATCCAAAACGACGCAGTTTTGT
1 TAAGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGAC-CAGTTTTG-
**
45837789 A-AGCTTTCGGGGATTTAGTAGCGTTTTTAAGAAAGCGCCGCTAATGCTC
64 AGAGCTTTCGGGGATTTAGCGGCGTTTTTAA-AAAGCGCCGCTAATGCTC
45837838 TAAGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGA-C-GTTTTGAG
1 TAAGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACCAGTTTTGAG
*
45837901 AGCTTTCAGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGCTC
66 AGCTTTCGGGGATTTAGCGGCGTTTTTAA-AAAGCGCCGCTAATGCTC
* *
45837949 -AGGGCTTTAGCGGC-ATTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTG
1 TA-AGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGAC-CAGTTTTG
* *
45838012 TGAGCTTT-GGGGATTTAGCGGCGTTTTTAAGAAGCGCCGCTAATG
64 AGAGCTTTCGGGGATTTAGCGGCGTTTTTAAAAAGCGCCGCTAATG
45838057 NNNNNNNNNN
Statistics
Matches: 203, Mismatches: 11, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
110 40 0.20
111 75 0.37
112 23 0.11
113 13 0.06
114 52 0.26
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (112 bp):
TAAGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACCAGTTTTGAG
AGCTTTCGGGGATTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTC
Found at i:45838647 original size:17 final size:17
Alignment explanation
Indices: 45838616--45838659 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
45838606 TAGGGAGTAT
45838616 TTATGGATT--TAGGGA
1 TTATGGATTAATAGGGA
45838631 TTATGGATTAATAGGGA
1 TTATGGATTAATAGGGA
*
45838648 TTATGGTTTAAT
1 TTATGGATTAAT
45838660 TAAGGGTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 9 0.35
17 17 0.65
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (17 bp):
TTATGGATTAATAGGGA
Found at i:45839537 original size:47 final size:47
Alignment explanation
Indices: 45839478--45839579 Score: 159
Period size: 47 Copynumber: 2.1 Consensus size: 47
45839468 GAAAATGAAA
* * *
45839478 TAAAAACACTAAACTTTTTGATTTTATCTAATTTTTAAAAATATTACT
1 TAAAAA-ACTAAAATTTTTAATTTTATCTAATTTTTAAAAATATAACT
*
45839526 TAAAAAACTAAAATTTTTAATTTTATCTAATTTTTATAAATATAACT
1 TAAAAAACTAAAATTTTTAATTTTATCTAATTTTTAAAAATATAACT
45839573 TAAAAAA
1 TAAAAAA
45839580 ATCTATGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 44 0.88
48 6 0.12
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (47 bp):
TAAAAAACTAAAATTTTTAATTTTATCTAATTTTTAAAAATATAACT
Found at i:45843505 original size:15 final size:15
Alignment explanation
Indices: 45843485--45843514 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45843475 GAGTTGAAAG
45843485 TGAAGAAGAAGATGA
1 TGAAGAAGAAGATGA
*
45843500 TGAAGATGAAGATGA
1 TGAAGAAGAAGATGA
45843515 AGATAATCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (15 bp):
TGAAGAAGAAGATGA
Found at i:45843773 original size:16 final size:16
Alignment explanation
Indices: 45843749--45843782 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
45843739 TAATACTAAT
*
45843749 TAATTTTTGATATTAA
1 TAATGTTTGATATTAA
*
45843765 TAATGTTTGATTTTAA
1 TAATGTTTGATATTAA
45843781 TA
1 TA
45843783 TTTAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
TAATGTTTGATATTAA
Found at i:45843944 original size:43 final size:44
Alignment explanation
Indices: 45843837--45843958 Score: 140
Period size: 43 Copynumber: 2.8 Consensus size: 44
45843827 ATGGTGTTTT
* * ** *
45843837 TAGCGGCGTTTGTAATCAAAGCATCGCTAAAGGTCTTTGATCTA
1 TAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCTTTGAGCTA
* * *
45843881 TAGCGGTGTTTGTGGTAAAAGTGCCGCTAAAGGTC-TTGAGCTA
1 TAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCTTTGAGCTA
*
45843924 TAGCGGCGTTTGTTAG-AAAAGCGTCGCTAAAGGTC
1 TAGCGGCGTTTG-TAGTAAAAGCGCCGCTAAAGGTC
45843959 ATGACCTTGG
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 35 0.54
44 30 0.46
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (44 bp):
TAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCTTTGAGCTA
Found at i:45846140 original size:5 final size:5
Alignment explanation
Indices: 45846132--45846179 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
45846122 CGAACAAATA
* *
45846132 ATTCG ATTCG ATTCG ATTCG ATCTCT ATCTC- ACTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG AT-TCG AT-TCG ATTCG ATTCG ATTCG AT
45846180 AAAACTTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
4 2 0.05
5 29 0.76
6 7 0.18
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.40
Consensus pattern (5 bp):
ATTCG
Found at i:45846252 original size:5 final size:5
Alignment explanation
Indices: 45846242--45846267 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
45846232 CTCGAAAATT
45846242 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
45846268 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:45848426 original size:13 final size:13
Alignment explanation
Indices: 45848408--45848435 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
45848398 TCCAAACCTA
45848408 TACATACCAAATT
1 TACATACCAAATT
45848421 TACATACCAAATT
1 TACATACCAAATT
45848434 TA
1 TA
45848436 ACAGCACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.32
Consensus pattern (13 bp):
TACATACCAAATT
Found at i:45848532 original size:24 final size:22
Alignment explanation
Indices: 45848426--45848730 Score: 108
Period size: 24 Copynumber: 13.2 Consensus size: 22
45848416 AAATTTACAT
*
45848426 ACCAAATTTAACAGCACTTTTAC
1 ACCAAATTTAACAGCA-TTATAC
45848449 ACCATAAAATTTAACAGCATATATAC
1 ACC---AAATTTAACAGCAT-TATAC
** *
45848475 AGTAAA--TAGGCAGCA-TATAC
1 ACCAAATTTA-ACAGCATTATAC
*
45848495 ATACCAAATTTAACAGCACTTTTAC
1 --ACCAAATTTAACAGCA-TTATAC
*
45848520 ACCAAAATTTAACAACATATATAC
1 ACC-AAATTTAACAGCAT-TATAC
* *
45848544 AGCAAA--TAGGCAGCA-TATAC
1 ACCAAATTTA-ACAGCATTATAC
* *
45848564 ATACCAAATTTAACAACACTTTTAC
1 --ACCAAATTTAACAGCA-TTATAC
45848589 ACCAAAATTTAACAGCATATATAC
1 ACC-AAATTTAACAGCAT-TATAC
* ** *
45848613 AACAAA-TTGGCAACA-TATAC
1 ACCAAATTTAACAGCATTATAC
* * *
45848633 ATACCAAATTGAGCAGCATTTTTAC
1 --ACCAAATTTAACAGCA-TTATAC
*
45848658 ACCAAAATTTATCAGCATATATAC
1 ACC-AAATTTAACAGCAT-TATAC
* ***
45848682 AACAAA-TGGGCAGCA-TATAC
1 ACCAAATTTAACAGCATTATAC
*
45848702 ATACCAAATTTAACAGCACTTTTAC
1 --ACCAAATTTAACAGCA-TTATAC
45848727 ACCA
1 ACCA
45848731 TAAGATTATA
Statistics
Matches: 208, Mismatches: 40, Indels: 68
0.66 0.13 0.22
Matches are distributed among these distances:
20 20 0.10
21 4 0.02
22 40 0.19
23 52 0.25
24 57 0.27
25 17 0.08
26 18 0.09
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.26
Consensus pattern (22 bp):
ACCAAATTTAACAGCATTATAC
Found at i:45848561 original size:69 final size:69
Alignment explanation
Indices: 45848421--45848730 Score: 494
Period size: 69 Copynumber: 4.5 Consensus size: 69
45848411 ATACCAAATT
**
45848421 TACATACCAAATTTAACAGCACTTTTACACCATAAAATTTAACAGCATATATACAGTAAATAGGC
1 TACATACCAAATTTAACAGCACTTTTACACC--AAAATTTAACAGCATATATACAACAAATAGGC
45848486 AGCATA
64 AGCATA
* *
45848492 TACATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAACATATATACAGCAAATAGGCAG
1 TACATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAG
45848557 CATA
66 CATA
* * *
45848561 TACATACCAAATTTAACAACACTTTTACACCAAAATTTAACAGCATATATACAACAAATTGGCAA
1 TACATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAG
45848626 CATA
66 CATA
* * * * *
45848630 TACATACCAAATTGAGCAGCATTTTTACACCAAAATTTATCAGCATATATACAACAAATGGGCAG
1 TACATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAG
45848695 CATA
66 CATA
45848699 TACATACCAAATTTAACAGCACTTTTACACCA
1 TACATACCAAATTTAACAGCACTTTTACACCA
45848731 TAAGATTATA
Statistics
Matches: 222, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
69 191 0.86
71 31 0.14
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.26
Consensus pattern (69 bp):
TACATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAG
CATA
Found at i:45848698 original size:22 final size:23
Alignment explanation
Indices: 45848601--45848700 Score: 87
Period size: 22 Copynumber: 4.4 Consensus size: 23
45848591 CAAAATTTAA
45848601 CAGCATATATACAACAAATTG-G
1 CAGCATATATACAACAAATTGAG
* * * *
45848623 CAACATATACATACCAAATTGAG
1 CAGCATATATACAACAAATTGAG
* * * * *
45848646 CAGCATTTTTACACCAAAATTTAT
1 CAGCATATATACAAC-AAATTGAG
*
45848670 CAGCATATATACAACAAA-TGGG
1 CAGCATATATACAACAAATTGAG
45848692 CAGCATATA
1 CAGCATATA
45848701 CATACCAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
22 27 0.46
23 14 0.24
24 18 0.31
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (23 bp):
CAGCATATATACAACAAATTGAG
Found at i:45848719 original size:45 final size:46
Alignment explanation
Indices: 45848518--45848716 Score: 154
Period size: 45 Copynumber: 4.3 Consensus size: 46
45848508 CAGCACTTTT
* *
45848518 ACACCAAAATTTAACAACATATATACAGCAAATAG-GCAGCATATAC
1 ACACC-AAATTTAACAACATATATACACCAAATTGAGCAGCATATAC
* * * * *
45848564 ATACCAAATTTAACAACACT-TTTACACCAAAATTTAACAGCATATAT
1 ACACCAAATTTAACAACA-TATATACACC-AAATTGAGCAGCATATAC
* ** * * * **
45848611 ACAACAAA-TTGGCAACATATACATACCAAATTGAGCAGCATTTTT
1 ACACCAAATTTAACAACATATATACACCAAATTGAGCAGCATATAC
* * * *
45848656 ACACCAAAATTTATCAGCATATATACAACAAA-TGGGCAGCATATAC
1 ACACC-AAATTTAACAACATATATACACCAAATTGAGCAGCATATAC
*
45848702 ATACCAAATTTAACA
1 ACACCAAATTTAACA
45848717 GCACTTTTAC
Statistics
Matches: 116, Mismatches: 31, Indels: 13
0.73 0.19 0.08
Matches are distributed among these distances:
45 47 0.41
46 38 0.33
47 31 0.27
ACGTcount: A:0.47, C:0.21, G:0.08, T:0.25
Consensus pattern (46 bp):
ACACCAAATTTAACAACATATATACACCAAATTGAGCAGCATATAC
Found at i:45848937 original size:69 final size:69
Alignment explanation
Indices: 45848855--45849355 Score: 921
Period size: 69 Copynumber: 7.3 Consensus size: 69
45848845 GGACAGCTTT
* * *
45848855 TATATACAACAAATGGGTAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
1 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
45848920 AGCA
66 AGCA
45848924 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
1 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
45848989 AGCA
66 AGCA
*
45848993 TATATACAGTAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
1 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
45849058 AGCA
66 AGCA
* * *
45849062 TATATACAACAAATGGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAT
1 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
45849127 AGCA
66 AGCA
*
45849131 TATATACAGCAAATAGGCAACATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
1 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
45849196 AGCA
66 AGCA
45849200 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
1 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
45849265 AGCA
66 AGCA
*
45849269 TATATACAGTAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
1 TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
45849334 AGCA
66 AGCA
45849338 TATATACAGCAAATAGGC
1 TATATACAGCAAATAGGC
45849356 TTAAATATAA
Statistics
Matches: 417, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 417 1.00
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.25
Consensus pattern (69 bp):
TATATACAGCAAATAGGCAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAAC
AGCA
Found at i:45850160 original size:41 final size:41
Alignment explanation
Indices: 45850115--45850271 Score: 215
Period size: 41 Copynumber: 3.8 Consensus size: 41
45850105 TTGTATAAAA
* * * * *
45850115 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* * *
45850156 CACCGGCACAAAGCCTACTAGACATAAAGTCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
*
45850197 CACCGGCACAGAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* *
45850238 CACCGGCATAAAGCTTGCTAGGCATAAAGCCTGA
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGA
45850272 ACTTACAAAA
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 101 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:45850686 original size:28 final size:30
Alignment explanation
Indices: 45850647--45850705 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 30
45850637 TTTTATTATA
45850647 TTAATATATTTAATTT-ATAA-AACTAACC
1 TTAATATATTTAATTTAATAATAACTAACC
*
45850675 TTAATGAT-TTTACTTTAATAATTAACTAACC
1 TTAAT-ATATTTAATTTAATAA-TAACTAACC
45850706 ATGTCCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 12 0.46
29 6 0.23
31 8 0.31
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (30 bp):
TTAATATATTTAATTTAATAATAACTAACC
Found at i:45858045 original size:26 final size:27
Alignment explanation
Indices: 45858016--45858068 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
45858006 ATGATCGTAA
45858016 TGCCCCTAGAGGGTAAATAACT-ATTT
1 TGCCCCTAGAGGGTAAATAACTGATTT
* * *
45858042 TGCCCCTCGTGGGTAAATGACTGATTT
1 TGCCCCTAGAGGGTAAATAACTGATTT
45858069 GTGCTATGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (27 bp):
TGCCCCTAGAGGGTAAATAACTGATTT
Found at i:45858451 original size:34 final size:35
Alignment explanation
Indices: 45858402--45858482 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
45858392 CATTGCATAT
* * *
45858402 ACTGATCCTGATACTG-TAATGGGCTAAGGCCCAC
1 ACTGATACTGTTACTGTTAAAGGGCTAAGGCCCAC
* * *
45858436 ACTGATACTGTTACTGTTAAAGGGCTTAGGCCTAG
1 ACTGATACTGTTACTGTTAAAGGGCTAAGGCCCAC
*
45858471 ACTGATTCTGTT
1 ACTGATACTGTT
45858483 TCTATAATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 14 0.36
35 25 0.64
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (35 bp):
ACTGATACTGTTACTGTTAAAGGGCTAAGGCCCAC
Found at i:45859403 original size:25 final size:25
Alignment explanation
Indices: 45859351--45859437 Score: 81
Period size: 25 Copynumber: 3.4 Consensus size: 25
45859341 AAAGTAAAAG
* *
45859351 AGAAAGAAATAG--AAAAAGAATGAG
1 AGAAAGAAA-AGAAAAAAAGAAGGAA
* *
45859375 AGAAAGAAACA-AAACAGAGAAGGAA
1 AGAAAGAAA-AGAAAAAAAGAAGGAA
45859400 AGAAAGAAAAGAAAAAAAGAAGGAA
1 AGAAAGAAAAGAAAAAAAGAAGGAA
45859425 AGAAGGAGAAAAG
1 AGAA--AGAAAAG
45859438 TTCGGGTTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
24 11 0.22
25 33 0.65
27 7 0.14
ACGTcount: A:0.69, C:0.02, G:0.26, T:0.02
Consensus pattern (25 bp):
AGAAAGAAAAGAAAAAAAGAAGGAA
Found at i:45860341 original size:41 final size:38
Alignment explanation
Indices: 45860296--45860402 Score: 101
Period size: 37 Copynumber: 2.8 Consensus size: 38
45860286 ACTTCGATTT
*
45860296 GATGAGACATTGGGTGTCAATTTATTACTACGGATTAATTC
1 GATGAGACATTGGGTGTCAATTTATTACT--GGATTAA-CC
* * * * *
45860337 GATGAGGCACTAGGTGCCAATTTACTT--TGGTTTAACC
1 GATGAGACATTGGGTGTCAATTTA-TTACTGGATTAACC
*
45860374 GATGAGATATTGGGTGTCAATTTATTACT
1 GATGAGACATTGGGTGTCAATTTATTACT
45860403 TTGAATTATT
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
36 2 0.04
37 20 0.38
38 7 0.13
40 1 0.02
41 20 0.38
42 2 0.04
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (38 bp):
GATGAGACATTGGGTGTCAATTTATTACTGGATTAACC
Found at i:45866543 original size:44 final size:44
Alignment explanation
Indices: 45866480--45866760 Score: 168
Period size: 44 Copynumber: 6.1 Consensus size: 44
45866470 CATCGTGGCC
45866480 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAGGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-GCTACA
* * * * ***
45866524 AATCTTATCTCCCTGAAGTTACAGTAGAGCAAATTGAAGATGTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* * * * * *
45866568 AATCTTATTTCCTTGAAGTTACATTGGAACAGATTAAAGCTACAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC-----A
** * ***
45866617 CGAATCTTATCTCCCTGAAAATGCAGTGGAGCAGATTGAAGATGTG
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* ** * *
45866663 AATCTTATTTCTTTGAAGTTGCAGTGGAACAGATTAAAGTGACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T----TG--AAGCTACA
** * *
45866714 AATCTTATCTCCCTGAAGTTGCAGTATAGTAGATTGAAGCAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
45866758 AAT
1 AAT
45866761 TCTACACCTC
Statistics
Matches: 173, Mismatches: 49, Indels: 30
0.69 0.19 0.12
Matches are distributed among these distances:
44 103 0.60
45 3 0.02
46 2 0.01
49 2 0.01
50 1 0.01
51 62 0.36
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
Found at i:45866737 original size:95 final size:95
Alignment explanation
Indices: 45866520--45866752 Score: 351
Period size: 95 Copynumber: 2.5 Consensus size: 95
45866510 AGATTAAGGC
* *
45866520 TACAAATCTTATCTCCCTGAAGTTACAGTAGAGCAAATTGAAGATGTGAATCTTATTTCCTTGAA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATGTGAATCTTATTTCCTTGAA
*
45866585 GTTACATTGGAACAGATTAAAGCTACAAGT
66 GTTACAGTGGAACAGATTAAAGCTACAAGT
* ** * *
45866615 TACGAATCTTATCTCCCTGAAAATGCAGTGGAGCAGATTGAAGATGTGAATCTTATTTCTTTGAA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATGTGAATCTTATTTCCTTGAA
*
45866680 GTTGCAGTGGAACAGATTAAAG-TGACAAGT
66 GTTACAGTGGAACAGATTAAAGCT-ACAAGT
* *
45866710 TACAAATCTTATCTCCCTGAAGTTGCAGTATAGTAGATTGAAG
1 TACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAG
45866753 CAACAAATTC
Statistics
Matches: 122, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
94 1 0.01
95 121 0.99
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (95 bp):
TACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATGTGAATCTTATTTCCTTGAA
GTTACAGTGGAACAGATTAAAGCTACAAGT
Found at i:45866775 original size:95 final size:95
Alignment explanation
Indices: 45866520--45866784 Score: 232
Period size: 95 Copynumber: 2.8 Consensus size: 95
45866510 AGATTAAGGC
** * * *** **
45866520 TACAAATCTTATCTCCCTGAAGTTACAGTAGAGCAAATTGAAGATGTGAATCTTATTTCCT-TGA
1 TACAAATCTTATCTCCCTGAAAATGCAGTAGAGCAGATTGAAGATACAAATCTTA-CACCTCTGA
*
45866584 AGTTACATTGGAACAGATTAAAGCTACAAGT
65 AGTTACAGTGGAACAGATTAAAGCTACAAGT
* * *** *** *
45866615 TACGAATCTTATCTCCCTGAAAATGCAGTGGAGCAGATTGAAGATGTGAATCTTATTTCTTTGAA
1 TACAAATCTTATCTCCCTGAAAATGCAGTAGAGCAGATTGAAGATACAAATCTTACACCTCTGAA
*
45866680 GTTGCAGTGGAACAGATTAAAG-TGACAAGT
66 GTTACAGTGGAACAGATTAAAGCT-ACAAGT
** * *
45866710 TACAAATCTTATCTCCCTGAAGTTGCAGTATAGTAGATTGAAGCA-ACAAAT-TCTACACCTCTG
1 TACAAATCTTATCTCCCTGAAAATGCAGTAGAGCAGATTGAAG-ATACAAATCT-TACACCTCTG
* *
45866773 AAGCTAGAGTGG
64 AAGTTACAGTGG
45866785 GTTAGAATGA
Statistics
Matches: 141, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
94 6 0.04
95 134 0.95
96 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (95 bp):
TACAAATCTTATCTCCCTGAAAATGCAGTAGAGCAGATTGAAGATACAAATCTTACACCTCTGAA
GTTACAGTGGAACAGATTAAAGCTACAAGT
Found at i:45868455 original size:3 final size:3
Alignment explanation
Indices: 45868442--45868502 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
45868432 AAAAAATTAG
* * * *
45868442 ATT ATTT ATT ATT ATT GTT ATT ACT ATT GTT ATT ATT ATC ATT -TT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
45868487 CATT ATT ATT ATT ATT
1 -ATT ATT ATT ATT ATT
45868503 TACGCATATT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 5 0.11
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:45874205 original size:21 final size:22
Alignment explanation
Indices: 45874160--45874205 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
45874150 CTGTTTGTGA
*
45874160 AACCTAGTGTGATTTTCTAGTAT
1 AACCTAGTGTAATTTTCTAG-AT
*
45874183 AACCTTGTGTAATTTTCTA-AT
1 AACCTAGTGTAATTTTCTAGAT
45874204 AA
1 AA
45874206 ATAATTTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
23 17 0.81
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (22 bp):
AACCTAGTGTAATTTTCTAGAT
Found at i:45880936 original size:21 final size:21
Alignment explanation
Indices: 45880886--45880938 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
45880876 GGGACAGATT
*
45880886 GAATATATATAATTAAGGTTC
1 GAATATTTATAATTAAGGTTC
* *
45880907 AAATAATTTGTAATTAA-GTTCC
1 GAAT-ATTTATAATTAAGGTT-C
45880929 GAATATTTAT
1 GAATATTTAT
45880939 CTGTTAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (21 bp):
GAATATTTATAATTAAGGTTC
Found at i:45882396 original size:50 final size:50
Alignment explanation
Indices: 45882282--45882524 Score: 387
Period size: 50 Copynumber: 4.8 Consensus size: 50
45882272 GATAATAACA
* * *
45882282 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGCTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
45882333 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
45882383 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
45882433 TGCCAATGCGATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
45882483 TGCCAATGGCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
45882525 TTACCCAAAT
Statistics
Matches: 176, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 143 0.81
51 33 0.19
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:45882640 original size:13 final size:13
Alignment explanation
Indices: 45882619--45882649 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
45882609 GCTTAGATCA
*
45882619 TCATCAAATAAAT
1 TCATAAAATAAAT
45882632 TCATAAAATAAAT
1 TCATAAAATAAAT
45882645 TCATA
1 TCATA
45882650 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:45885356 original size:38 final size:38
Alignment explanation
Indices: 45885308--45885408 Score: 159
Period size: 38 Copynumber: 2.7 Consensus size: 38
45885298 TCCTTCTAGC
*
45885308 TTTTGCCGATTTTCTCCCTCTGTTT-TTTATCTTTTCTT
1 TTTTGCCGATTTGCTCCCTCTGTTTATTT-TCTTTTCTT
*
45885346 TTTTGCCGATTTGCTCTCTCTGTTTATTTTCTTTTCTT
1 TTTTGCCGATTTGCTCCCTCTGTTTATTTTCTTTTCTT
*
45885384 TTCTGCCGATTTGCTCCCTCTGTTT
1 TTTTGCCGATTTGCTCCCTCTGTTT
45885409 CCCCTTTTCT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 55 0.95
39 3 0.05
ACGTcount: A:0.05, C:0.25, G:0.11, T:0.59
Consensus pattern (38 bp):
TTTTGCCGATTTGCTCCCTCTGTTTATTTTCTTTTCTT
Found at i:45893785 original size:16 final size:16
Alignment explanation
Indices: 45893764--45893809 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
45893754 TTGATTTGCT
45893764 ATTACACCTCTATTAC
1 ATTACACCTCTATTAC
*
45893780 ATTACACCTCTATTCC
1 ATTACACCTCTATTAC
*
45893796 ATTACGCCTCTATT
1 ATTACACCTCTATT
45893810 TCAATACAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTAC
Found at i:45899818 original size:2 final size:2
Alignment explanation
Indices: 45899811--45899835 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45899801 TTTAATCATG
45899811 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
45899836 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45900666 original size:132 final size:132
Alignment explanation
Indices: 45900423--45901348 Score: 1570
Period size: 132 Copynumber: 7.0 Consensus size: 132
45900413 GGTTGTCAGC
*
45900423 TACAAACTTCATTTAGCCCTGCACCTCAAGGCAATATCTCAACTTCAAATGGCTATTTTGGAAGT
1 TACAAACTTCATTTAGCCCTGCACCTCAAGGCAATATCTCAACTTCAAATGGCTATTCTGGAAGT
* * * *
45900488 TCACCACATCAGGAAACTTTGGCTGCAGCTGCTGCCTACACAGACTGGCTTGTTGATGAAGATCT
66 TCACCACATCAGGAAACTTCGGCTGCAGCTGCTGCCGACACGGACTGGCCTGTTGATGAAGATCT
45900553 TA
131 TA
*
45900555 TACAAACTTCATTTAGCCCTGCACCTCAAGGCAATACCTCAACTTCAAATGGCTATTCTGGAAGT
1 TACAAACTTCATTTAGCCCTGCACCTCAAGGCAATATCTCAACTTCAAATGGCTATTCTGGAAGT
* * *
45900620 TCACCACATCAGGAAACTTCAGCTGCAGCTGCTGCCGTCACGGACTGGCTTGTTGATGAAGATCT
66 TCACCACATCAGGAAACTTCGGCTGCAGCTGCTGCCGACACGGACTGGCCTGTTGATGAAGATCT
45900685 TA
131 TA
45900687 TACAAACTTCATTTAGCCCTGCACCTCAAGGCAATA---CAACTTCAAATGGCTATTCTGGAAGT
1 TACAAACTTCATTTAGCCCTGCACCTCAAGGCAATATCTCAACTTCAAATGGCTATTCTGGAAGT
* * *
45900749 TCACCACATCAGGAAACTTTGGCTGCAGCTGCTGCCGACATGGACTGGCCTGTTGATGAGGATCT
66 TCACCACATCAGGAAACTTCGGCTGCAGCTGCTGCCGACACGGACTGGCCTGTTGATGAAGATCT
45900814 TA
131 TA
* * *
45900816 TACAAACTTCATTTAGCCCTGCATCTCAAGGCAATATCTCAACTTCAAATGGCTACTCCGGAAGT
1 TACAAACTTCATTTAGCCCTGCACCTCAAGGCAATATCTCAACTTCAAATGGCTATTCTGGAAGT
45900881 TCACCACATCAGGAAACTTCGGCTGCAGCTGCTGCCGACACGGACTGGCCTGTTGATGAAGATCT
66 TCACCACATCAGGAAACTTCGGCTGCAGCTGCTGCCGACACGGACTGGCCTGTTGATGAAGATCT
45900946 TA
131 TA
* * *
45900948 TACAAACTTCATTTAGCCCTTCACCTAAAGGCAATATCTCAACTTCTAATGGCTATTCTGGAAGT
1 TACAAACTTCATTTAGCCCTGCACCTCAAGGCAATATCTCAACTTCAAATGGCTATTCTGGAAGT
* *
45901013 TCACCACATCAGGAAACTTCGGCTGCAGCTGCTGCCGACATGGACTGGCCTGTTGATGAGGATCT
66 TCACCACATCAGGAAACTTCGGCTGCAGCTGCTGCCGACACGGACTGGCCTGTTGATGAAGATCT
45901078 TA
131 TA
* *
45901080 TACAAACTCCATTTAGCCCTGCACCTCAAGGCAATATCTCAACTTCAAATGGCTATTCCGGAAGT
1 TACAAACTTCATTTAGCCCTGCACCTCAAGGCAATATCTCAACTTCAAATGGCTATTCTGGAAGT
*
45901145 TCACCACATCAGGAAACTTCGGCTGCAGCTGCAGCCGACACGGACTGGCCTGTTGATGAAGATCT
66 TCACCACATCAGGAAACTTCGGCTGCAGCTGCTGCCGACACGGACTGGCCTGTTGATGAAGATCT
45901210 TA
131 TA
* * *
45901212 TACAAACTTCATTTAGCCCTGCACCTAAAGGCAATATCTCAACTTCTAATGGCTATTCTGCAAGT
1 TACAAACTTCATTTAGCCCTGCACCTCAAGGCAATATCTCAACTTCAAATGGCTATTCTGGAAGT
* **
45901277 TCACCACATCAGGAAACTTCGGCTGCAGCTGCTGCCAACATTGACTGGCCTGTTGATGAAGATCT
66 TCACCACATCAGGAAACTTCGGCTGCAGCTGCTGCCGACACGGACTGGCCTGTTGATGAAGATCT
45901342 TA
131 TA
45901344 TACAA
1 TACAA
45901349 GCTTTCTTTA
Statistics
Matches: 747, Mismatches: 44, Indels: 6
0.94 0.06 0.01
Matches are distributed among these distances:
129 122 0.16
132 625 0.84
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (132 bp):
TACAAACTTCATTTAGCCCTGCACCTCAAGGCAATATCTCAACTTCAAATGGCTATTCTGGAAGT
TCACCACATCAGGAAACTTCGGCTGCAGCTGCTGCCGACACGGACTGGCCTGTTGATGAAGATCT
TA
Found at i:45902131 original size:19 final size:19
Alignment explanation
Indices: 45902098--45902134 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
45902088 TTTTCTAATT
**
45902098 TTTAATTTCTTTAATTTTA
1 TTTAATTTCCATAATTTTA
45902117 TTTAATTTCCATAATTTT
1 TTTAATTTCCATAATTTT
45902135 TAAAAAAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTAATTTCCATAATTTTA
Found at i:45903118 original size:14 final size:14
Alignment explanation
Indices: 45903099--45903149 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
45903089 GTAAGAGTCA
*
45903099 TTTAATAATATATT
1 TTTAATATTATATT
*
45903113 TTTAATATTATTTT
1 TTTAATATTATATT
45903127 TTTAATTATTATATT
1 TTTAA-TATTATATT
*
45903142 TTTGATAT
1 TTTAATAT
45903150 AAAATATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
TTTAATATTATATT
Found at i:45904287 original size:24 final size:24
Alignment explanation
Indices: 45904239--45904288 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
45904229 TGGAAGAACA
*
45904239 AGATAAAGATGAAGACAATGTTGG
1 AGATAAAGATGAAGACAATGATGG
*
45904263 AGATGAAGATGAAGATCAA-GATGG
1 AGATAAAGATGAAGA-CAATGATGG
45904287 AG
1 AG
45904289 GTGGAGGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.46, C:0.04, G:0.32, T:0.18
Consensus pattern (24 bp):
AGATAAAGATGAAGACAATGATGG
Found at i:45904681 original size:75 final size:74
Alignment explanation
Indices: 45904535--45904866 Score: 390
Period size: 75 Copynumber: 4.5 Consensus size: 74
45904525 TTTTTTTATT
* * * * * *
45904535 TCAATAATATAGTTATTTACAACCTACGAAAAAATGAAAAAATTTGTTTGTATTTTATTCTATTT
1 TCAATAATATACTTATTTACAATCTACAAAAAAATGAAAAAAGTTGTTTGTATTGTATTCTATTG
*
45904600 TATTTTAGA
66 TATTTTACA
* * *
45904609 TCAATAATATATTTATTTACAATCTACAAAAAAATGAAAAAAAGTTGTTTGTATTATACTCTATT
1 TCAATAATATACTTATTTACAATCTACAAAAAAATG-AAAAAAGTTGTTTGTATTGTATTCTATT
45904674 GTATTTTACA
65 GTATTTTACA
* * * *
45904684 TCAATAATGTACTTATTTACAAAT-TACAAAAAATTGAAAAAA-TTGTCTGTATTGT-TTGTATT
1 TCAATAATATACTTATTTAC-AATCTACAAAAAAATGAAAAAAGTTGTTTGTATTGTATTCTATT
45904746 GTATTTTACA
65 GTATTTTACA
* * * *
45904756 TTAATAACATACTTATTTACAATTTACGAAAAAATG-AAAAAGTTGTTTGTATTGTATTCTATTG
1 TCAATAATATACTTATTTACAATCTACAAAAAAATGAAAAAAGTTGTTTGTATTGTATTCTATTG
*
45904820 CATTTTTACA
66 TA-TTTTACA
* **
45904830 T---TAATATACTTATTTACAATGTACCCAAAAATGAAAA
1 TCAATAATATACTTATTTACAATCTACAAAAAAATGAAAA
45904867 GTCATGAAAA
Statistics
Matches: 224, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
71 36 0.16
72 57 0.25
73 19 0.08
74 47 0.21
75 62 0.28
76 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (74 bp):
TCAATAATATACTTATTTACAATCTACAAAAAAATGAAAAAAGTTGTTTGTATTGTATTCTATTG
TATTTTACA
Found at i:45905038 original size:34 final size:34
Alignment explanation
Indices: 45904995--45905063 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
45904985 GCTTACTATG
45904995 CCTTAGGTTCCTACAATAACTACATAACCTTGGT
1 CCTTAGGTTCCTACAATAACTACATAACCTTGGT
45905029 CCTTAGGTTCCTACAATAACTACATAACCTTGGT
1 CCTTAGGTTCCTACAATAACTACATAACCTTGGT
45905063 C
1 C
45905064 AGTCTATCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.32
Consensus pattern (34 bp):
CCTTAGGTTCCTACAATAACTACATAACCTTGGT
Found at i:45905877 original size:15 final size:15
Alignment explanation
Indices: 45905839--45905880 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
45905829 ATATTCATGA
45905839 ATGAAAATAATGTAT
1 ATGAAAATAATGTAT
*
45905854 ATGTTAAATAATG-AT
1 ATG-AAAATAATGTAT
45905869 ATAGAAAATAAT
1 AT-GAAAATAAT
45905881 ATTTACTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (15 bp):
ATGAAAATAATGTAT
Found at i:45907157 original size:25 final size:25
Alignment explanation
Indices: 45907125--45907174 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
45907115 AAGACTCGAA
45907125 AACGGAAATAATCAACTTAAACCCT
1 AACGGAAATAATCAACTTAAACCCT
45907150 AACGGAAATAATCAACTTAAACCCT
1 AACGGAAATAATCAACTTAAACCCT
45907175 GAGGCCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.08, T:0.20
Consensus pattern (25 bp):
AACGGAAATAATCAACTTAAACCCT
Found at i:45923779 original size:917 final size:915
Alignment explanation
Indices: 45921616--45926255 Score: 4348
Period size: 918 Copynumber: 5.0 Consensus size: 915
45921606 GGAGGTGGTC
* * * *
45921616 AGTTTGCTACTCTTTAAGTTTTCTTGCATAAAAATCTCAACTTTCTCATTTCTCTCAAG-TTATA
1 AGTTTTCTGCTCTTTAAGTTTTCTTGCATAAAAATCTCAACTTTCACATTTTTCTCAAGCTT-TA
* ** *
45921680 C-TT--TAA-TG-GTTGTTTT-GTTTTCCATGTCCATTTCTTTTACTTTGAGCATGAGTAGCTAA
65 CTTTAATAACTGCTTTGTTTTCCATTTCCATGTCCATTTCTTTTACTTTGAGCATGAGTAGTTAA
* * *
45921739 ACCTCAAGGGAGGTTGGTTGATGGAGATGTGGGTAAACTAAAATCTTTGGACAAATGACTAAATC
130 ACCTCAAGGAAGGTTGGTTGATGGAGATATGGGTAAACTAAAACCTTT-G------G-----A-C
* * * * * *
45921804 ATAATAAATTATTATAAATCGAATAGACCTGAGAACTTAGGTAGTGACTCCCCTAAGAGAATATT
182 ---A-AAA-GA--ATAAATCGAATAGACCTTAGAACATAGGTAGTGAC-ACCCTAAGGGAATATC
** *** * * * * *
45921869 TAGGTAAGTGAGACTGGAAGGTAATGTTTTCGTGCACC-GATTCATTAGTCTCAGG-CTAGCTAG
239 TAGACAAGTGAGACCAAAAGGTAATCTTGTCATGCACCTG-TTCATTAGTCTC-GGATTAACTAG
* * * * * * * *
45921932 TGAGATGGGAAGATAAATCGTAGCTAATTCGTTTAAGTCGGTAAAATTGAGATTGAAAGATAAAT
302 TGAGATCGAAAGATAAATCGTAGATAATTCGTCTAAGTCGATAAAATTGAGATCGGAAGATAAAA
* * * * *
45921997 TGGAGTCACTTAGTAATTTACACGATTTAAGTCCCTTATTTAAGGATCGGTGAACCAAATCAAAG
367 TGGAGCCACTTAGTAATTTACACGATTTAAGTCCCTTGTTTGAGGATCGGTGAACCACATCGAAG
* *
45922062 TCAACTAACCACCATTAGTTATTTATTGGATAGTCCC-TTAGTTTTACATTCTTTGCAATTTAGT
432 TCAACCAACCACCATTAGTTATTTATTGGATAGTCCCATT--TTTTACATTATTTGCAATTTAGT
** * *
45922126 CCTTAGAGTAGCATATCTAATTTTCGAGCAATATTTTCTTGTTATGAATCGTTGTACTATAAAAT
495 CCTTAGAGTAGCATATCTAATTTTCTTGCAATATTTTCTTGTTATGAATTGTCGTACTATAAAAT
** ** * * * ** * ** *
45922191 CATAGTAGT-GTTTACTTAGACTATATTATGTATGCTAGATATTTCTCAATCGTCACCTTTTTTA
560 TGTAGTAGTAG-CCACTTAGACTCTATTATGTATGCTAGTTATTGCTCAATCACCATCTCCTTTG
* * * * * * *
45922255 GGTTTGACCTCTTGGAACACTTCGTGTTCCATCAGAACTATAAATATTACAACTGACTTATATGC
624 GGTTTAACC-CTTGGAATACTTTGTGTTCCATCGGAACTATAAATATTACAAATGACCTATACGC
* ** * * *
45922320 TTGCAGTAAAACCAGGCTTTAAAAAATTGTTTTATAAGTTCGTTGGTTTAATGTGCATATGTGAA
688 TTGCAGTAAAACCAGGCTTTAAAAAATTGTTTTATAAGTT-TTTTTTTTAATGCGCACATGCGAA
* * * * ** * * *
45922385 GCTGGTCAACTACCCCATGTTTAC-AATCCCGATGGACTCTATATGCTACTATAATCGAGCTATG
752 GCCGGTCAACTACCCCATATTTACTATTCCTGGCGGACTCCATATGCTGCCATAATCGAGCTATG
* * * *
45922449 CTTTTACACAATATACCCCATGTTTAACGTCCTTGCGGACTACTCCGTGCTTACTGTC-CTGGCG
817 GTTTTACACAATATACCCCATGTTTAACGTCCTGGCGGACTACT-CATGTTTACTGTCTC-GGCG
* * * *
45922513 GACTATACCAGG-TGTCATAGTCGAGCCATGGTCTTA
880 GACTATA-CTGGTTGCCATAGTAGAGCCATGGTATTA
* * *
45922549 AGTTTTTTGCTCTTCAAGTTTTCTTGCATAAAAATCTCAACTTTCACATTTTTTCTCAAGCTATA
1 AGTTTTCTGCTCTTTAAGTTTTCTTGCATAAAAATCTCAACTTTCACA-TTTTTCTCAAGCTTTA
* * * * *
45922614 CTTTAATGACTGCTTTGTTTTCAATTTCCATGTCTATTTCTTTTATTTTCAGCATGAGTAGTTAA
65 CTTTAATAACTGCTTTGTTTTCCATTTCCATGTCCATTTCTTTTACTTTGAGCATGAGTAGTTAA
* * * *
45922679 ACCTAAAGGAAGATTGGTTGATAGAGATATGGGCAAACTAAAACCTTTGGA-AAAAGGAATAAAT
130 ACCTCAAGGAAGGTTGGTTGATGGAGATATGGGTAAACTAAAACCTTTGGACAAAA-GAATAAAT
* * * ** * *
45922743 CGAATACACCTTAGAACGTAGATAGTGATGCCTCTAAGGGTATATCTAGACAAGTGAGACCAGAA
194 CGAATAGACCTTAGAACATAGGTAGTGACACC-CTAAGGGAATATCTAGACAAGTGAGACCAAAA
* * * ** * * *
45922808 GGTAATGTTGTCATGCACCTGTTCATTAGTCCCGAATTAACCGGTTAAATCGAAAGATAAATTGT
258 GGTAATCTTGTCATGCACCTGTTCATTAGTCTCGGATTAACTAGTGAGATCGAAAGATAAATCGT
* * * * *
45922873 AGATAATTCATCTAAGTCAGA-AAATTTGATATCAGAAGATAAAATTGAGCCA--TACTGTAATT
323 AGATAATTCGTCTAAGTC-GATAAAATTGAGATCGGAAGATAAAATGGAGCCACTTA--GTAATT
* * * * * *
45922935 TGCGCAATTTAGGTCCTTTGCTTGAGGATCGGTGAACCACATCGAAGTCAACCAACCACCATTAG
385 TACACGATTTAAGTCCCTTGTTTGAGGATCGGTGAACCACATCGAAGTCAACCAACCACCATTAG
*
45923000 TTATTTATTGGATAGTCCCATTTTTTACATTTTTTTGCAATTTAGTCCTTAGAGTAGCATATCTA
450 TTATTTATTGGATAGTCCCATTTTTTACA-TTATTTGCAATTTAGTCCTTAGAGTAGCATATCTA
* * * * *
45923065 CTTTTCTTCCAATATTTTCTTGTTATGAATTTTCATACTATAAAACCTT-T-GTAGTTGCCACTT
514 ATTTTCTTGCAATATTTTCTTGTTATGAATTGTCGTACTATAAAA--TTGTAGTAGTAGCCACTT
* * * *
45923128 AGACTCTATTGTGTATGTTAGTCATTGCTCAATAACCATCTCCTTTGGGTTTAACCCTTGGAATA
577 AGACTCTATTATGTATGCTAGTTATTGCTCAATCACCATCTCCTTTGGGTTTAACCCTTGGAATA
* * * * * *
45923193 ATTCGTTTTCCATTGGAACTATAAATTTTACAAATGACCTATACGCTTGTAGTAAAACC-GAGCT
642 CTTTGTGTTCCATCGGAACTATAAATATTACAAATGACCTATACGCTTGCAGTAAAACCAG-GCT
* * * * * ** *
45923257 TTAAAAAATTATTTTATAAGTTATTTTCTTTAATGTGCACATGCGAAGCCAGTCAACAACTTCGT
706 TTAAAAAATTGTTTTATAAGTT-TTTTTTTTAATGCGCACATGCGAAGCCGGTCAACTACCCCAT
* * * * * * * *
45923322 ATTTACTATTTC-GGTGGACTCCATATGCTGCTATAATTGAGCTATGATCTTACCCAATATGCCC
770 ATTTACTATTCCTGGCGGACTCCATATGCTGCCATAATCGAGCTATGGTTTTACACAATATACCC
* * * * *
45923386 TATATTTAACGTCCTGGCGGACTACCTCGTGTTTACTGTCTCGGCGAACTATACTGGTTGTCATA
835 CATGTTTAACGTCCTGGCGGACTA-CTCATGTTTACTGTCTCGGCGGACTATACTGGTTGCCATA
** *
45923451 GCCGAGCGATGGTATTA
899 GTAGAGCCATGGTATTA
* * * *
45923468 A-TTTTCTGCTCTTTAAGTTTTCTTCCATAGAAATCTCAACTTTCATATTTTTCTTAAGCTTTAC
1 AGTTTTCTGCTCTTTAAGTTTTCTTGCATAAAAATCTCAACTTTCACATTTTTCTCAAGCTTTAC
* *
45923532 TTTAATAACTGTTTTGTTTTCCATTTCCATGTCCATTTCTTTTTCTTTGAGCATGAGTAGTTAAA
66 TTTAATAACTGCTTTGTTTTCCATTTCCATGTCCATTTCTTTTACTTTGAGCATGAGTAGTTAAA
* * * * *
45923597 CCTCAAGGAAGGTTGGTTGATGGAAATGTGGGTGAAA-TAAAACCTTCGGACAAAAGACTAAATT
131 CCTCAAGGAAGGTTGGTTGATGGAGATATGGGT-AAACTAAAACCTTTGGACAAAAGAATAAATC
* *
45923661 GAATAAACCTTAGAACATAGGTAGTGACACCCATAAGTGAATATCTAGACAAGTGAGACCAAAAG
195 GAATAGACCTTAGAACATAGGTAGTGACACCC-TAAGGGAATATCTAGACAAGTGAGACCAAAAG
* * *
45923726 GTAATCTTGTCATGCA-CTCGTTTATTAGTCTCGGATTAATTAGTGAGATCGAAAGATAAATCAT
259 GTAATCTTGTCATGCACCT-GTTCATTAGTCTCGGATTAACTAGTGAGATCGAAAGATAAATCGT
* * * * * * *
45923790 AGCTAATTCGTTTAAGTCGATAAAATTGAGATTGAAAGATAAAATGGAGTCACCTAGTAATTTAT
323 AGATAATTCGTCTAAGTCGATAAAATTGAGATCGGAAGATAAAATGGAGCCACTTAGTAATTTAC
* * * * * *
45923855 ACGATTTAATTCCTTTTTTTGAGGATCGGTGAACCACATCAAATTCAACCAACCACCATTAATTA
388 ACGATTTAAGTCCCTTGTTTGAGGATCGGTGAACCACATCGAAGTCAACCAACCACCATTAGTTA
* * *
45923920 TTTATTGGATA--CCCTCTTAGTTTTACATTATTTGCAATTAAGTCCTCAGAGTAGCATATCTAA
453 TTTATTGGATAGTCCC-ATT--TTTTACATTATTTGCAATTTAGTCCTTAGAGTAGCATATCTAA
* * *
45923983 TTTTCTTGCAATATTTTCTTATTATGAATTGTCGTACTATAAAATTGTAGTAGGAGCCACTTAAA
515 TTTTCTTGCAATATTTTCTTGTTATGAATTGTCGTACTATAAAATTGTAGTAGTAGCCACTTAGA
*
45924048 CTCTATTATGTATGCTAGTTATTGCTCAATCACCATCTCCTTTGGGTTCAACCCCTTGGAATACT
580 CTCTATTATGTATGCTAGTTATTGCTCAATCACCATCTCCTTTGGGTTTAA-CCCTTGGAATACT
* * * ***
45924113 TTATGTTCCATCGGAACTATAAATATTACAATTGACCTATATGCTTATTGTAAAACCAGGCTTT-
644 TTGTGTTCCATCGGAACTATAAATATTACAAATGACCTATACGCTTGCAGTAAAACCAGGCTTTA
* * * * * * * *
45924177 -AAATTTTTTTTATAAGTTTGTTTTTTTAATACGTAGATACGAAGCCGGTCAACTACCCCTTGTT
709 AAAAATTGTTTTATAAGTTT-TTTTTTTAATGCGCACATGCGAAGCCGGTCAACTACCCCATATT
* * * *
45924241 TA-TTTTCCTGGCAGACTCCATATGTTGCCATAA-CTGAGCTATGGTTTTACACAATATACCTCA
773 TACTATTCCTGGCGGACTCCATATGCTGCCATAATC-GAGCTATGGTTTTACACAATATACCCCA
* *
45924304 TGTTTAACGTCTTGATGAACTACTTCATGCTTACTGTATCGGTAAACTACCTCATATTTACTATC
837 TGTTTAA---C-----G---T-C--C-TG------G---CGG---ACTA-CTCATGTTTACTGTC
* * * *
45924369 TCAGTGGACTATATTGGTTGCCATAGAAGAGCCATGGTATTA
874 TCGGCGGACTATACTGGTTGCCATAGTAGAGCCATGGTATTA
* * * *
45924411 AGTTTTCTTCTCTTTAAGTTTTCTTGCATAAAACTCGCAACATTCACATTTTTCTCAAGCTTTAC
1 AGTTTTCTGCTCTTTAAGTTTTCTTGCATAAAAATCTCAACTTTCACATTTTTCTCAAGCTTTAC
* * * * *
45924476 TTTAATAGCTGCATTGTTTTCCATTTCTATGTCCTTTTCTTTTACTTTGAGCATGAGTAGCTAAA
66 TTTAATAACTGCTTTGTTTTCCATTTCCATGTCCATTTCTTTTACTTTGAGCATGAGTAGTTAAA
* * * * * * *
45924541 CTTCAAGGAAGGTTGGTTGATTGATATATGGGTAAACTAAAACATTTGGACAAAGGACTAAATCA
131 CCTCAAGGAAGGTTGGTTGATGGAGATATGGGTAAACTAAAACCTTTGGACAAAAGAATAAATCG
* * * * * * *
45924606 AATAGACCTTAGAACCTAGGTAGCGACGCCCTAAGGGAATATTTAGGCAAGTGAGACTAAAAGGC
196 AATAGACCTTAGAACATAGGTAGTGACACCCTAAGGGAATATCTAGACAAGTGAGACCAAAAGGT
* *
45924671 AATCTTTTCATGCACCTGTTCATTAGTAC-CAGATTAACTAGTGAGATC-AGAAGATAAAATCGT
261 AATCTTGTCATGCACCTGTTCATTAGT-CTCGGATTAACTAGTGAGATCGA-AAGAT-AAATCGT
* * * * *
45924734 AGCTCATTCGTCCAAGTCGATAAAATTGAGATTGGAAGATAAAATGGAGTCACTTAGTAATTTAC
323 AGATAATTCGTCTAAGTCGATAAAATTGAGATCGGAAGATAAAATGGAGCCACTTAGTAATTTAC
* *
45924799 ACGATTTAAGTCCCTTGTTTGAGGATCGGTGAAACACATCGAATTCAACCAACCACCATTAGTTA
388 ACGATTTAAGTCCCTTGTTTGAGGATCGGTGAACCACATCGAAGTCAACCAACCACCATTAGTTA
* * * * * *
45924864 TATATTAGATAGTCCCTTATTTTTACACTATTTACAATTTAGTCCTTAGAGTAGCATATCTAATA
453 TTTATTGGATAGTCCCAT-TTTTTACATTATTTGCAATTTAGTCCTTAGAGTAGCATATCTAATT
** * *
45924929 TTCTTGTTATATTTTCTTGTTATGAATTGTCATACTATAAAATTGTAGTAGAAGCCACTTAGACT
517 TTCTTGCAATATTTTCTTGTTATGAATTGTCGTACTATAAAATTGTAGTAGTAGCCACTTAGACT
* * ** ** *
45924994 CTATTGTGTATGATAGTTATTGCTCAATGTCCATCTCCTTTGGGATCGACCCCTTGGAATACTTT
582 CTATTATGTATGCTAGTTATTGCTCAATCACCATCTCCTTTGGG-TTTAACCCTTGGAATACTTT
* * * *
45925059 GTGTTCTATTGGAACTATAAATATTACAAATGACCTATACGCTTGCAGTATAACCAGGCTTTACA
646 GTGTTCCATCGGAACTATAAATATTACAAATGACCTATACGCTTGCAGTAAAACCAGGCTTTAAA
* ** *
45925124 AAATTGTTTTATAAGTTTTTTGTTTTAATGCACACATATGAAGCCGGTCAACTACCCCATACTTA
711 AAATTGTTTTATAAGTTTTTT-TTTTAATGCGCACATGCGAAGCCGGTCAACTACCCCATATTTA
* * * * *
45925189 CTA-TCCTGGCGGACTCTATATGCTGCCATAGTCGAGTTATGGTATTACATAATATACCCCATGT
775 CTATTCCTGGCGGACTCCATATGCTGCCATAATCGAGCTATGGTTTTACACAATATACCCCATGT
* * * * *
45925253 TTAATGTCTTGGCGAACTACTCTATGCTTACTATCCTGACAAACGTATTTATTGTCCCAATGGAC
840 TTAACGTCCTGGCGGACTACTC-ATG-TT--TA--CTGTC--TCG--------G---C---GGAC
*
45925318 TATACTGGTTGCCATAGTAGAGCCATGGTCTTA
883 TATACTGGTTGCCATAGTAGAGCCATGGTATTA
* ** * * * * *
45925351 ATTTTTCTTTTCATTAAGTTTTCTTGCATAAAAATCTCAAATTTTACATTTTTCTTAAGTTTTAC
1 AGTTTTCTGCTCTTTAAGTTTTCTTGCATAAAAATCTCAACTTTCACATTTTTCTCAAGCTTTAC
*** * *
45925416 TTTAATGGTTGCTTTGTTTTCCA-TT-C-TGT-CATTTTCTTTAACTTTAAGCATGAGTA-TCTA
66 TTTAATAACTGCTTTGTTTTCCATTTCCATGTCCA-TTTCTTTTACTTTGAGCATGAGTAGT-TA
** * * *
45925476 AACCTCAAAAAAGGTTGGTTGATGGAGATGTAGGTAAACTAAAACCTTTGGACAAAGGAATAAAT
129 AACCTCAAGGAAGGTTGGTTGATGGAGATATGGGTAAACTAAAACCTTTGGACAAAAGAATAAAT
* * * *
45925541 TGAATAGACCTTAGAACTTAGGTAGTGA-AGCCCCTAAGGGAATATTTAGGCAAGTGAGACCAAA
194 CGAATAGACCTTAGAACATAGGTAGTGACA--CCCTAAGGGAATATCTAGACAAGTGAGACCAAA
* * * *
45925605 ACGTAATATTGTCATCCA-C----C--T-GT-TC------A-T--T-AGATCGAAAGATGAATCG
257 AGGTAATCTTGTCATGCACCTGTTCATTAGTCTCGGATTAACTAGTGAGATCGAAAGATAAATCG
* *
45925651 TAGATAATTCGTCTAAGTCGGTAAAATTGAGATCGGAAGAAAAAATGGAGCCACTTAGTAATTTA
322 TAGATAATTCGTCTAAGTCGATAAAATTGAGATCGGAAGATAAAATGGAGCCACTTAGTAATTTA
* * * *
45925716 CGCGATTTAAGTCCCTTGTTTGAGCATCGGTGAACCACATTGAAGTCAACCAACCATCATTAGTT
387 CACGATTTAAGTCCCTTGTTTGAGGATCGGTGAACCACATCGAAGTCAACCAACCACCATTAGTT
* * * *
45925781 ATTTATTGGATAGT-CTATTATTTTTACATTCTTTACAATTTAGTACTTAGAGTAGCATATCTAA
452 ATTTATTGGATAGTCCCA-T-TTTTTACATTATTTGCAATTTAGTCCTTAGAGTAGCATATCTAA
* * * **
45925845 TTTTCTTGCAATATTTTATTATTATGAATTATCGTACTATAAAATTGTCTTAGTAGCCACTTA-A
515 TTTTCTTGCAATATTTTCTTGTTATGAATTGTCGTACTATAAAATTGTAGTAGTAGCCACTTAGA
* * * * * * *
45925909 TCTCAATTATATATGCTAGTTATTGCGCAATCGCCATCTACTTTGGGTTTGACCCCTTGAAATAC
580 -CTCTATTATGTATGCTAGTTATTGCTCAATCACCATCTCCTTTGGGTTT-AACCCTTGGAATAC
* * * *
45925974 TTTGTGTTCCATCGGAACTATAAATATTACAACTGACCTATACGCTTACAGTAAAATC-GAACTT
643 TTTGTGTTCCATCGGAACTATAAATATTACAAATGACCTATACGCTTGCAGTAAAACCAG-GCTT
* * * * ** * *
45926038 TAAAAAATTGTTTTATAGGTTTGTTGTTTTCATGCGCACATGCGAAGCTGGTCAACTACATCGTG
707 TAAAAAATTGTTTTATAAGTTT-TTTTTTTAATGCGCACATGCGAAGCCGGTCAACTACCCCATA
* *** * * * * * * *
45926103 TTTATTA-TCCTGATAGACTTCATATGTTGTCATAGTCGACCTATAGTCTTACACAATATACCCC
771 TTTACTATTCCTGGCGGACTCCATATGCTGCCATAATCGAGCTATGGTTTTACACAATATACCCC
* * * * * * * * * *
45926167 AAGTTTAACGTCCTAGCGGATTACTCCGTGCTTACTGTCCCGGCAGACTATACTAGTTGTCATAA
836 ATGTTTAACGTCCTGGCGGACTACT-CATGTTTACTGTCTCGGCGGACTATACTGGTTGCCATAG
* * *
45926232 TTGAGACATGGTCTTA
900 TAGAGCCATGGTATTA
45926248 AGTTTTCT
1 AGTTTTCT
45926256 TCTTTGTAAC
Statistics
Matches: 3078, Mismatches: 512, Indels: 270
0.80 0.13 0.07
Matches are distributed among these distances:
897 38 0.01
900 1 0.00
903 1 0.00
911 2 0.00
913 4 0.00
915 12 0.00
916 106 0.03
917 473 0.15
918 586 0.19
919 260 0.08
920 352 0.11
921 6 0.00
922 10 0.00
923 2 0.00
924 4 0.00
925 1 0.00
926 1 0.00
927 1 0.00
928 2 0.00
929 1 0.00
930 3 0.00
931 5 0.00
933 45 0.01
934 15 0.00
935 4 0.00
936 1 0.00
937 111 0.04
938 48 0.02
939 10 0.00
940 190 0.06
942 1 0.00
943 128 0.04
944 535 0.17
945 6 0.00
946 111 0.04
947 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (915 bp):
AGTTTTCTGCTCTTTAAGTTTTCTTGCATAAAAATCTCAACTTTCACATTTTTCTCAAGCTTTAC
TTTAATAACTGCTTTGTTTTCCATTTCCATGTCCATTTCTTTTACTTTGAGCATGAGTAGTTAAA
CCTCAAGGAAGGTTGGTTGATGGAGATATGGGTAAACTAAAACCTTTGGACAAAAGAATAAATCG
AATAGACCTTAGAACATAGGTAGTGACACCCTAAGGGAATATCTAGACAAGTGAGACCAAAAGGT
AATCTTGTCATGCACCTGTTCATTAGTCTCGGATTAACTAGTGAGATCGAAAGATAAATCGTAGA
TAATTCGTCTAAGTCGATAAAATTGAGATCGGAAGATAAAATGGAGCCACTTAGTAATTTACACG
ATTTAAGTCCCTTGTTTGAGGATCGGTGAACCACATCGAAGTCAACCAACCACCATTAGTTATTT
ATTGGATAGTCCCATTTTTTACATTATTTGCAATTTAGTCCTTAGAGTAGCATATCTAATTTTCT
TGCAATATTTTCTTGTTATGAATTGTCGTACTATAAAATTGTAGTAGTAGCCACTTAGACTCTAT
TATGTATGCTAGTTATTGCTCAATCACCATCTCCTTTGGGTTTAACCCTTGGAATACTTTGTGTT
CCATCGGAACTATAAATATTACAAATGACCTATACGCTTGCAGTAAAACCAGGCTTTAAAAAATT
GTTTTATAAGTTTTTTTTTTAATGCGCACATGCGAAGCCGGTCAACTACCCCATATTTACTATTC
CTGGCGGACTCCATATGCTGCCATAATCGAGCTATGGTTTTACACAATATACCCCATGTTTAACG
TCCTGGCGGACTACTCATGTTTACTGTCTCGGCGGACTATACTGGTTGCCATAGTAGAGCCATGG
TATTA
Found at i:45934906 original size:18 final size:19
Alignment explanation
Indices: 45934878--45934914 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
45934868 TTATTCCCAG
*
45934878 TTCCATCTTCGTTCTCAAC
1 TTCCATCTTCGTTATCAAC
45934897 TTCC-TCTTCGTTATCAAC
1 TTCCATCTTCGTTATCAAC
45934915 CATAGTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.16, C:0.35, G:0.05, T:0.43
Consensus pattern (19 bp):
TTCCATCTTCGTTATCAAC
Found at i:45937387 original size:31 final size:26
Alignment explanation
Indices: 45937322--45937386 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
45937312 ATTGTAGATA
*
45937322 AATATTATATTAATTTAATAATATTT
1 AATATTAAATTAATTTAATAATATTT
*
45937348 AATATTAAATTAAATTTAATTATA-TT
1 AATATTAAATT-AATTTAATAATATTT
45937374 AAT-TTAATATTAA
1 AATATTAA-ATTAA
45937387 AGTGATTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 6 0.17
26 18 0.51
27 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AATATTAAATTAATTTAATAATATTT
Found at i:45937532 original size:25 final size:27
Alignment explanation
Indices: 45937493--45937542 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
45937483 TTGTAGAGAG
45937493 AAAATTCTCTAGAGAAATTATTTTAGA
1 AAAATTCTCTAGAGAAATTATTTTAGA
* *
45937520 AAAATT-T-TAGAGATATTTTTTTA
1 AAAATTCTCTAGAGAAATTATTTTA
45937543 TTTATAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 1 0.05
27 6 0.29
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (27 bp):
AAAATTCTCTAGAGAAATTATTTTAGA
Found at i:45943188 original size:18 final size:19
Alignment explanation
Indices: 45943165--45943205 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
45943155 TTCGCAATTT
45943165 ATTTTTATTATTT-TA-AAA
1 ATTTTTA-TATTTATATAAA
45943183 ATTTTTATATTTATATAAA
1 ATTTTTATATTTATATAAA
45943202 ATTT
1 ATTT
45943206 CAAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 9 0.43
19 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTTATATTTATATAAA
Found at i:45943230 original size:20 final size:21
Alignment explanation
Indices: 45943197--45943236 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
45943187 TTATATTTAT
45943197 ATAAAATTTCAAAA-AAAAAC
1 ATAAAATTTCAAAATAAAAAC
45943217 ATAAAA-TTCTAAAATAAAAA
1 ATAAAATTTC-AAAATAAAAA
45943237 AAAACTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 10 0.56
21 5 0.28
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (21 bp):
ATAAAATTTCAAAATAAAAAC
Found at i:45943680 original size:16 final size:16
Alignment explanation
Indices: 45943655--45943694 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
45943645 TTCGTTCGCT
*
45943655 GTAATAGAATAGATGC
1 GTAATAGAATAGAGGC
*
45943671 GTAATGGAATAGAGGC
1 GTAATAGAATAGAGGC
45943687 GTAATAGA
1 GTAATAGA
45943695 TAATTCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.30, T:0.23
Consensus pattern (16 bp):
GTAATAGAATAGAGGC
Found at i:45943767 original size:44 final size:47
Alignment explanation
Indices: 45943671--45943768 Score: 132
Period size: 44 Copynumber: 2.2 Consensus size: 47
45943661 GAATAGATGC
* * *
45943671 GTAATGGAATAGAGGCGTAATAGATAATTCTTTTGTTTGGTTGAATA
1 GTAATAGAATAGAGGCGTAATAGATAACTCTTATGTTTGGTTGAATA
*
45943718 G-AATAGAATAGAGGTGTAATAG-T-ACTCTTATGTTTGGTTGAAT-
1 GTAATAGAATAGAGGCGTAATAGATAACTCTTATGTTTGGTTGAATA
45943761 GTAATAGA
1 GTAATAGA
45943769 GCTGTAATAG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
43 1 0.02
44 24 0.52
45 1 0.02
46 19 0.41
47 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.37
Consensus pattern (47 bp):
GTAATAGAATAGAGGCGTAATAGATAACTCTTATGTTTGGTTGAATA
Found at i:45943971 original size:15 final size:16
Alignment explanation
Indices: 45943951--45943980 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
45943941 ATATATAATT
45943951 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
45943966 TAATAAATATTCTTA
1 TAATAAATATTCTTA
45943981 TATGGATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:45944163 original size:102 final size:102
Alignment explanation
Indices: 45943943--45944161 Score: 368
Period size: 102 Copynumber: 2.2 Consensus size: 102
45943933 TAATAAAAAT
* *
45943943 ATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGGATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATAATAAATATTATTATATGAATTTACTAAAATCATAATATAT
45944008 AATACTATAAAATATAATTTAAAATAATTATTATTAA
66 AATACTATAAAATATAATTTAAAATAATTATTATTAA
*
45944045 ATATAATTTAATAAAATTCTTAATAATAAATATTATTATATGAATTTACTAAAATCATAATATGT
1 ATATAATTTAATAAAATTCTTAATAATAAATATTATTATATGAATTTACTAAAATCATAATATAT
* * * *
45944110 AATACTATAAAATATAGTTT-AATTAGTTTTTATTAA
66 AATACTATAAAATATAATTTAAAATAATTATTATTAA
45944146 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
45944162 ATATATAATT
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 29 0.26
102 81 0.74
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (102 bp):
ATATAATTTAATAAAATTCTTAATAATAAATATTATTATATGAATTTACTAAAATCATAATATAT
AATACTATAAAATATAATTTAAAATAATTATTATTAA
Found at i:45944340 original size:18 final size:18
Alignment explanation
Indices: 45944317--45944351 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
45944307 TTTTTATTAA
45944317 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
45944335 ATATAATTTAATAAAAA
1 ATATAATTTAATAAAAA
45944352 ATTTAGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:45944411 original size:44 final size:44
Alignment explanation
Indices: 45944361--45944502 Score: 148
Period size: 44 Copynumber: 3.2 Consensus size: 44
45944351 AATTTAGTAA
*
45944361 TAAATATTCTTATATGAATTTGTACAATTTAAAATAATTATTAT
1 TAAATATTCTTATATGAATTTGTATAATTTAAAATAATTATTAT
* * * *
45944405 TAAATATAAT-TTA-AT-AATAATATATAATTTCATAA-AATTCTTAAT
1 TAAATAT--TCTTATATGAAT-TTGTATAATTT-AAAATAATTATT-AT
45944450 AGTAAATATTCTTATATGAATTTGTATAATTTAAAATAATTATTAT
1 --TAAATATTCTTATATGAATTTGTATAATTTAAAATAATTATTAT
45944496 TAAATAT
1 TAAATAT
45944503 AATTTAATAA
Statistics
Matches: 78, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
43 3 0.04
44 30 0.38
45 9 0.12
46 9 0.12
47 24 0.31
48 3 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (44 bp):
TAAATATTCTTATATGAATTTGTATAATTTAAAATAATTATTAT
Found at i:45944456 original size:47 final size:45
Alignment explanation
Indices: 45944405--45944549 Score: 138
Period size: 47 Copynumber: 3.2 Consensus size: 45
45944395 TAATTATTAT
45944405 TAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATA
1 TAAATATAATTTAATAAT-ATATATAATTTCATAAAATTCTTAATA
* * * *
45944451 GTAAATAT--TCTTATATGAATTTGTATAATTT-AAAATAATTATT-AT-
1 -TAAATATAAT-TTA-AT-AATATATATAATTTCATAA-AATTCTTAATA
*
45944496 TAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTACTAA
1 TAAATATAATTTAATAAT-ATATATAATTTCATAAAATTCTTAAT-A
45944543 TAAATAT
1 TAAATAT
45944550 TCTTATATGA
Statistics
Matches: 78, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
43 3 0.04
44 24 0.31
45 8 0.10
46 9 0.12
47 31 0.40
48 3 0.04
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (45 bp):
TAAATATAATTTAATAATATATATAATTTCATAAAATTCTTAATA
Found at i:45944462 original size:91 final size:91
Alignment explanation
Indices: 45944310--45944563 Score: 420
Period size: 91 Copynumber: 2.8 Consensus size: 91
45944300 TAATTAGTTT
* * * *
45944310 TTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAAAT-TTAGTAATAAATATTCTTAT
1 TTATTAAATATAATTTAATAATAATATATAATTTCAT-AAAATTCTTAATAATAAATATTCTTAT
45944374 ATGAATTTGTACAATTTAAAATAATTA
65 ATGAATTTGTACAATTTAAAATAATTA
*
45944401 TTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATAGTAAATATTCTTATA
1 TTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATAATAAATATTCTTATA
*
45944466 TGAATTTGTATAATTTAAAATAATTA
66 TGAATTTGTACAATTTAAAATAATTA
* *
45944492 TTATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTACTAATAAATATTCTTATA
1 TTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATAATAAATATTCTTATA
45944557 TGAATTT
66 TGAATTT
45944564 ACTAAAATCA
Statistics
Matches: 153, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
90 5 0.03
91 148 0.97
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (91 bp):
TTATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATAATAAATATTCTTATA
TGAATTTGTACAATTTAAAATAATTA
Found at i:45945051 original size:10 final size:10
Alignment explanation
Indices: 45945036--45945066 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
45945026 GATACCATCA
45945036 AGAAACATAC
1 AGAAACATAC
45945046 AGAAACATAC
1 AGAAACATAC
*
45945056 AGAGACATAC
1 AGAAACATAC
45945066 A
1 A
45945067 AAATATAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.58, C:0.19, G:0.13, T:0.10
Consensus pattern (10 bp):
AGAAACATAC
Found at i:45945103 original size:27 final size:25
Alignment explanation
Indices: 45945048--45945138 Score: 112
Period size: 25 Copynumber: 3.6 Consensus size: 25
45945038 AAACATACAG
*
45945048 AAACATACAGAGACATACAA-AATAT
1 AAACATACAGAAACATA-AAGAATAT
* *
45945073 AAACATACAAAAACGTAAATTGAATAT
1 AAACATACAGAAACATAAA--GAATAT
*
45945100 AAACATACAGAAACATACAGAATAT
1 AAACATACAGAAACATAAAGAATAT
45945125 AAACATACAGAAAC
1 AAACATACAGAAAC
45945139 CATTTCCAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
24 2 0.04
25 34 0.60
27 21 0.37
ACGTcount: A:0.60, C:0.15, G:0.08, T:0.16
Consensus pattern (25 bp):
AAACATACAGAAACATAAAGAATAT
Found at i:45960626 original size:6 final size:6
Alignment explanation
Indices: 45960599--45960676 Score: 50
Period size: 6 Copynumber: 12.5 Consensus size: 6
45960589 AGTTTATTTG
* * * * * *
45960599 TTTTCT TTTTAA TTTTAA TTTTATT TTTTAT GTTTAT GTTTAT TTTTCT
1 TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTTTAT
*
45960648 TTTTAAT TGTTT-T GTTTTAG TTTTAT TTT
1 TTTT-AT T-TTTAT -TTTTAT TTTTAT TTT
45960677 CTTGTACTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
6 47 0.81
7 8 0.14
8 3 0.05
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:45960634 original size:25 final size:25
Alignment explanation
Indices: 45960610--45960676 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
45960600 TTTCTTTTTA
*
45960610 ATTTTAATTTTATTTTTTA-TGTTT
1 ATTTTAATTTTATTTTTAATTGTTT
* *
45960634 ATGTTTATTTTTCTTTTTAATTGTTTT
1 AT-TTTAATTTTATTTTTAATTG-TTT
* *
45960661 GTTTTAGTTTTATTTT
1 ATTTTAATTTTATTTT
45960677 CTTGTACTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 2 0.06
25 14 0.41
26 14 0.41
27 4 0.12
ACGTcount: A:0.16, C:0.01, G:0.07, T:0.75
Consensus pattern (25 bp):
ATTTTAATTTTATTTTTAATTGTTT
Found at i:45963171 original size:13 final size:13
Alignment explanation
Indices: 45963153--45963177 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45963143 TTAATCAACA
45963153 TAAAGTCAGTTGC
1 TAAAGTCAGTTGC
45963166 TAAAGTCAGTTG
1 TAAAGTCAGTTG
45963178 TTCTTACTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (13 bp):
TAAAGTCAGTTGC
Found at i:45967083 original size:42 final size:42
Alignment explanation
Indices: 45967036--45967133 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
45967026 TCTTAGATGT
* *
45967036 GGTCTTACATGTAATCAAATAACGATGCCATTGTCC-AGATAG
1 GGTCTTACATGTAATCAAAT-ACGATGCCAATGTCCTAGACAG
* *
45967078 GGTCTTACATGTAATCATATACGATGCCAATGTCCTAGACAT
1 GGTCTTACATGTAATCAAATACGATGCCAATGTCCTAGACAG
*
45967120 GGTCTTACACGTAA
1 GGTCTTACATGTAA
45967134 ATCTCAAATC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 14 0.28
42 36 0.72
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (42 bp):
GGTCTTACATGTAATCAAATACGATGCCAATGTCCTAGACAG
Found at i:45968959 original size:21 final size:20
Alignment explanation
Indices: 45968909--45968964 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
45968899 TCTTTGCAAA
*
45968909 ATAAGAGTATCGATAATTATT
1 ATAA-AGTATCGATAATTATG
* * *
45968930 TTAAGGTATCGATACTTTATG
1 ATAAAGTATCGATA-ATTATG
45968951 ATAAAGTAT-GATAA
1 ATAAAGTATCGATAA
45968965 AGTATCAATA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (20 bp):
ATAAAGTATCGATAATTATG
Found at i:45984447 original size:35 final size:35
Alignment explanation
Indices: 45984401--45984468 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
45984391 AAGATAATTC
45984401 AAATTTAAAATAAAGTAGCACTTATCGACATTTTT
1 AAATTTAAAATAAAGTAGCACTTATCGACATTTTT
45984436 AAATTTAAAATAAAGTAGCACTTATCGACATTT
1 AAATTTAAAATAAAGTAGCACTTATCGACATTT
45984469 CCCCAATCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (35 bp):
AAATTTAAAATAAAGTAGCACTTATCGACATTTTT
Found at i:45987643 original size:19 final size:19
Alignment explanation
Indices: 45987615--45987651 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
45987605 GACAGATTTC
*
45987615 TTTTGATTTTTTGATTTTA
1 TTTTGATTTTTTCATTTTA
*
45987634 TTTTGTTTTTTTCATTTT
1 TTTTGATTTTTTCATTTT
45987652 TGGCTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.03, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTTGATTTTTTCATTTTA
Found at i:45993158 original size:6 final size:6
Alignment explanation
Indices: 45993119--45993157 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
45993109 ATCCAAAAAA
* *
45993119 AAAATC AAAATC AAAATC AAAGTC AAAATG AAAAT- AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
45993158 AAGAGAGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.69, C:0.10, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:45995487 original size:129 final size:129
Alignment explanation
Indices: 45995283--45995835 Score: 903
Period size: 129 Copynumber: 4.3 Consensus size: 129
45995273 CCTGACCAGT
*
45995283 AGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTGAGCAATAGCGGAGCAGATCAAAGACG
1 AGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACG
* *
45995348 GCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGTCACAAGTCCTATATCCCTGGCCAGC
66 GCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGC
* **
45995412 AGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAGATA
1 AGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACG
* * *
45995477 GTGAATCTTATCTTCAAGTGTAAGGAAGTAGATTTAAGCCACAAGTCTTATATCCCTGGTCAGC
66 GCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGC
* *
45995541 AGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAAG-T
1 AGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATC-AAAGAC
* *
45995605 GGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGC
65 GGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGC
* *
45995670 AGTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCTAAGCAATAGTGGAGTAGATCAAAGACG
1 AGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACG
* *
45995734 GCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCTTATATTCCTGGTCAGC
66 GCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGC
* * *
45995798 AGTGGAATAGGTTGGGAAATTACAAATCCTCTCTCCCT
1 AGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCT
45995836 GAAGTTGTAG
Statistics
Matches: 393, Mismatches: 28, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
127 4 0.01
128 115 0.29
129 270 0.69
130 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (129 bp):
AGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACG
GCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGC
Found at i:45995873 original size:257 final size:258
Alignment explanation
Indices: 45995283--45995875 Score: 861
Period size: 257 Copynumber: 2.3 Consensus size: 258
45995273 CCTGACCAGT
* * * * *
45995283 AGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTGAGCAATAGCGGAGCAGATC-AAAG-A
1 AGTGGAATAGGTTGGGAAATTACAAATCCTCTCTCCCTAAGCAGTAGCGGAGCAGATCGAAAGTA
* * * *
45995346 CGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGTCACAAGTCCTATATCCCTGGCCAG
66 --ACAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGCCAG
*
45995411 CAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAGAT
129 CAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAGAC
* *
45995476 AGTGAATCTTATCTTCAAGTGTAAGGAAGTAGATTTAAGCCACAAGTCTTATATCCCTGGTCAGC
194 AGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCTTATATCCCTGGTCAGC
* * * *
45995541 AGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAAGTG
1 AGTGGAATAGGTTGGGAAATTACAAATCCTCTCTCCCTAAGCAGTAGCGGAGCAGATCGAAAGTA
* *
45995606 GCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCA
66 ACAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGCCAGCA
** * *
45995671 GTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCTAAGCAATAGTGGAGTAGATCAAAGACGG
131 GTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAGACAG
*
45995735 CGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCTTATATTCCTGGTCAGC
196 CGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCTTATATCCCTGGTCAGC
** * * *
45995798 AGTGGAATAGGTTGGGAAATTACAAATCCTCTCTCCCTGAAGTTGTAGTGGAGCAGGT-TAAAGT
1 AGTGGAATAGGTTGGGAAATTACAAATCCTCTCTCCCT-AAGCAGTAGCGGAGCAGATCGAAAGT
* *
45995862 AATAGATCTTATCT
65 AACAAATCTTATCT
45995876 CTCTAAAGTT
Statistics
Matches: 305, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
257 157 0.51
258 144 0.47
259 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (258 bp):
AGTGGAATAGGTTGGGAAATTACAAATCCTCTCTCCCTAAGCAGTAGCGGAGCAGATCGAAAGTA
ACAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGCCAGCA
GTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAGACAG
CGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCTTATATCCCTGGTCAGC
Found at i:45995957 original size:44 final size:44
Alignment explanation
Indices: 45995905--45996027 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
45995895 TGGATCGCAT
* *
45995905 CAAGTCTTATCTCCGTGAGGTTACAGTGGAGCAGACTG-AGAAAA
1 CAAGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAG-AAA
* * * * * *
45995949 CAAGTCTTATCCCCCTGAAGTCACAGTGGGGTAGACCGAAGAAG
1 CAAGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAAA
* *
45995993 CAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGA
1 CAAGTCTTATCTCCCTGAGGTTACAGTGGAGCAGA
45996028 TTGAACTCAA
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
44 61 0.97
45 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (44 bp):
CAAGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAAA
Found at i:45996048 original size:44 final size:44
Alignment explanation
Indices: 45995996--45996116 Score: 156
Period size: 44 Copynumber: 2.8 Consensus size: 44
45995986 GAAGAAGCAA
* *
45995996 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAACTCAATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAACT-AATAG
* *
45996040 ATAC-TATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTAATAG
1 AT-CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAACTAATAG
* *
45996084 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
45996117 CGCATCAAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
43 5 0.07
44 61 0.91
45 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAACTAATAG
Found at i:45997584 original size:11 final size:11
Alignment explanation
Indices: 45997568--45997593 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
45997558 TTTGATTATT
45997568 ATATTTTTAAA
1 ATATTTTTAAA
45997579 ATATTTTTAAA
1 ATATTTTTAAA
45997590 ATAT
1 ATAT
45997594 GACAATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATATTTTTAAA
Found at i:46004227 original size:32 final size:32
Alignment explanation
Indices: 46004166--46004273 Score: 146
Period size: 32 Copynumber: 3.4 Consensus size: 32
46004156 GAATGGCTAC
* * *
46004166 AAGCCATAAGTA-CAGTATTATGATTGGCACA
1 AAGCCATCAGTAGTAGTAATATGATTGGCACA
*
46004197 AAGCCATCAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAGTAGTAATATGATTGGCACA
* *
46004229 AAGCCATCAGTAATGGTAATATGATTGGCACA
1 AAGCCATCAGTAGTAGTAATATGATTGGCACA
*
46004261 AAGTCATCAGTAG
1 AAGCCATCAGTAG
46004274 CATCGCAGCA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
31 11 0.16
32 56 0.84
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (32 bp):
AAGCCATCAGTAGTAGTAATATGATTGGCACA
Found at i:46004325 original size:25 final size:26
Alignment explanation
Indices: 46004279--46004327 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
46004269 AGTAGCATCG
*
46004279 CAGCAAGGCTGCCAGTAACAGTATCA
1 CAGCAAAGCTGCCAGTAACAGTATCA
46004305 CAGCAAAGCTG-CAGTAACAGTAT
1 CAGCAAAGCTGCCAGTAACAGTAT
46004328 ATGTGGCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (26 bp):
CAGCAAAGCTGCCAGTAACAGTATCA
Found at i:46004359 original size:27 final size:27
Alignment explanation
Indices: 46004316--46004379 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
46004306 AGCAAAGCTG
46004316 CAGTAACAGTATATGTGGCCA-AGCCAC
1 CAGTAACAGTATATGTGG-CAGAGCCAC
*
46004343 CAGTAATAGTGAT-TGTGGCAGAGCCAC
1 CAGTAACAGT-ATATGTGGCAGAGCCAC
46004370 CAGT-ACAGTA
1 CAGTAACAGTA
46004380 CTTCCTCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 1 0.03
26 6 0.18
27 24 0.73
28 2 0.06
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (27 bp):
CAGTAACAGTATATGTGGCAGAGCCAC
Found at i:46004597 original size:24 final size:24
Alignment explanation
Indices: 46004455--46004600 Score: 175
Period size: 24 Copynumber: 6.1 Consensus size: 24
46004445 TCCGTCATAC
** **
46004455 AAATCACAGACAAATTTGTCATAC
1 AAATCACAGACAAATCAGTCATTT
* *
46004479 CAATAACAGACAAATCAGTCATTT
1 AAATCACAGACAAATCAGTCATTT
46004503 AAATCACAGACAAATCAGTCATTT
1 AAATCACAGACAAATCAGTCATTT
*
46004527 AAATCACAAACAAATCAGTCATTT
1 AAATCACAGACAAATCAGTCATTT
* * * *
46004551 ACATCTCGGACAAATCAATCATTT
1 AAATCACAGACAAATCAGTCATTT
* *
46004575 ACATCACAGACAAATCAATCATTT
1 AAATCACAGACAAATCAGTCATTT
46004599 AA
1 AA
46004601 CCTCAAGGGG
Statistics
Matches: 105, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 105 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.25
Consensus pattern (24 bp):
AAATCACAGACAAATCAGTCATTT
Found at i:46004647 original size:26 final size:26
Alignment explanation
Indices: 46004618--46004758 Score: 115
Period size: 27 Copynumber: 5.3 Consensus size: 26
46004608 GGGTAAAATA
*
46004618 GTCATTTACCCT-CTAGGATCATTACG
1 GTCATTTACCCTAC-AGGAGCATTACG
*
46004644 GTCATTTTACCCTACAGGGGCATTACG
1 GTCA-TTTACCCTACAGGAGCATTACG
* *
46004671 GTTATTTCACCCTACAAGG-GCATTAAG
1 GTCATTT-ACCCTAC-AGGAGCATTACG
* * * **
46004698 ATCATTTTACCCTATAGGGGCATTATA
1 GTCA-TTTACCCTACAGGAGCATTACG
*
46004725 GTCATTTTACCCTACAGGGGCATTACG
1 GTCA-TTTACCCTACAGGAGCATTACG
*
46004752 GTTATTT
1 GTCATTT
46004759 TACAAATATT
Statistics
Matches: 95, Mismatches: 14, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
26 13 0.14
27 75 0.79
28 7 0.07
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (26 bp):
GTCATTTACCCTACAGGAGCATTACG
Found at i:46004656 original size:27 final size:27
Alignment explanation
Indices: 46004637--46004761 Score: 169
Period size: 27 Copynumber: 4.6 Consensus size: 27
46004627 CCTCTAGGAT
46004637 CATTACGGTCATTTTACCCTACAGGGG
1 CATTACGGTCATTTTACCCTACAGGGG
* * *
46004664 CATTACGGTTATTTCACCCTACAAGGG
1 CATTACGGTCATTTTACCCTACAGGGG
* * *
46004691 CATTAAGATCATTTTACCCTATAGGGG
1 CATTACGGTCATTTTACCCTACAGGGG
**
46004718 CATTATAGTCATTTTACCCTACAGGGG
1 CATTACGGTCATTTTACCCTACAGGGG
*
46004745 CATTACGGTTATTTTAC
1 CATTACGGTCATTTTAC
46004762 AAATATTGGT
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (27 bp):
CATTACGGTCATTTTACCCTACAGGGG
Found at i:46005134 original size:17 final size:17
Alignment explanation
Indices: 46005112--46005153 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
46005102 TTATCTGTGT
46005112 GGCCCACAAGCCCACTA
1 GGCCCACAAGCCCACTA
* *
46005129 GGCCCATAAGCCCACTG
1 GGCCCACAAGCCCACTA
46005146 GGCCCACA
1 GGCCCACA
46005154 CAACCCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.26, C:0.45, G:0.21, T:0.07
Consensus pattern (17 bp):
GGCCCACAAGCCCACTA
Found at i:46011402 original size:33 final size:33
Alignment explanation
Indices: 46011346--46011459 Score: 147
Period size: 33 Copynumber: 3.4 Consensus size: 33
46011336 CATTTTCAGC
* * * *
46011346 CCAACCAAACACACTAGATGCTCACACGAGCCAAT
1 CCAACC-AACACACCA-ATGCTCATAAGAGCTAAT
**
46011381 CCCTCCAACACACCAATGCTCATAAGAGCTAAT
1 CCAACCAACACACCAATGCTCATAAGAGCTAAT
*
46011414 CCAACCAACACACCAATACTCATAAGAGCTAAT
1 CCAACCAACACACCAATGCTCATAAGAGCTAAT
46011447 CCAACCAACACAC
1 CCAACCAACACAC
46011460 TAAACAGAGT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
33 58 0.83
34 8 0.11
35 4 0.06
ACGTcount: A:0.41, C:0.38, G:0.08, T:0.13
Consensus pattern (33 bp):
CCAACCAACACACCAATGCTCATAAGAGCTAAT
Found at i:46012409 original size:21 final size:21
Alignment explanation
Indices: 46012383--46012424 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
46012373 AAAGTTACCA
46012383 TGTTTTAATTT-CACTTTAATT
1 TGTTTTAATTTCCA-TTTAATT
46012404 TGTTTTAATTTCCATTTAATT
1 TGTTTTAATTTCCATTTAATT
46012425 ATAAAATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.62
Consensus pattern (21 bp):
TGTTTTAATTTCCATTTAATT
Found at i:46023771 original size:17 final size:19
Alignment explanation
Indices: 46023749--46023794 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
46023739 CGAGCAAACC
*
46023749 AATAAGAAAATAAA-A-AA
1 AATAAGAAAAGAAATACAA
46023766 AATAAGATAAAGAAATACAA
1 AATAAGA-AAAGAAATACAA
46023786 AAT-AGAAAA
1 AATAAGAAAA
46023795 AAACTGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.28
18 9 0.36
19 4 0.16
20 5 0.20
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.13
Consensus pattern (19 bp):
AATAAGAAAAGAAATACAA
Found at i:46024444 original size:20 final size:19
Alignment explanation
Indices: 46024412--46024451 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
46024402 ATGTGGACCA
46024412 CCTTTTTTTAATT-TTTTT
1 CCTTTTTTTAATTCTTTTT
46024430 CCTTTTTTTCGAATTCTTTTT
1 CCTTTTTTT--AATTCTTTTT
46024451 C
1 C
46024452 AAATCTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
20 4 0.21
21 6 0.32
ACGTcount: A:0.10, C:0.17, G:0.03, T:0.70
Consensus pattern (19 bp):
CCTTTTTTTAATTCTTTTT
Done.