Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007895.1 Hibiscus syriacus cultivar Beakdansim tig00110280_pilon, whole genome shotgun sequence
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: 561701
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 3
Found at i:383860 original size:59 final size:60
Alignment explanation
Indices: 383791--383939 Score: 228
Period size: 59 Copynumber: 2.5 Consensus size: 60
383781 TACTTTATTG
*
383791 AGTCCCTTGACTATTAAGAGTTATAAAATGATCCCCGACTATAGGAAATTG-CTTTCTTT
1 AGTCCCTTGACTATTAAGAGTTACAAAATGATCCCCGACTATAGGAAATTGTCTTTCTTT
* *
383850 AGTCCCTTGACTATTAAGAGTTACAAAATGATCCTCGACTATAGGAAATTGTTTTTCTTT
1 AGTCCCTTGACTATTAAGAGTTACAAAATGATCCCCGACTATAGGAAATTGTCTTTCTTT
** * *
383910 AGTCCCTCAACTATCAAAAGTTACAAAATG
1 AGTCCCTTGACTATTAAGAGTTACAAAATG
383940 GTCACCCAAC
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 49 0.60
60 33 0.40
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (60 bp):
AGTCCCTTGACTATTAAGAGTTACAAAATGATCCCCGACTATAGGAAATTGTCTTTCTTT
Found at i:384311 original size:20 final size:20
Alignment explanation
Indices: 384286--384332 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
384276 ACCATTTATG
384286 TACTTTACCCATTAAACATA
1 TACTTTACCCATTAAACATA
384306 TACTTTACCCATTAAACATA
1 TACTTTACCCATTAAACATA
384326 TACTTTA
1 TACTTTA
384333 ACGGATCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (20 bp):
TACTTTACCCATTAAACATA
Found at i:387719 original size:32 final size:32
Alignment explanation
Indices: 387660--387721 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
387650 ATTTTTCTCA
*
387660 GTCCATGGTGTTTTTTCGGTTGCCCTCCCGGT
1 GTCCATGGTGTTTTTTCGGGTGCCCTCCCGGT
*
387692 GTCCATGGTGTTTTCTT-GGGTGTCCTCCCG
1 GTCCATGGTGTTTT-TTCGGGTGCCCTCCCG
387722 ATTCTCTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 25 0.93
33 2 0.07
ACGTcount: A:0.03, C:0.27, G:0.29, T:0.40
Consensus pattern (32 bp):
GTCCATGGTGTTTTTTCGGGTGCCCTCCCGGT
Found at i:389819 original size:29 final size:28
Alignment explanation
Indices: 389757--389820 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
389747 ATCACATATT
* *
389757 TAAACCCTAAACTTTAAATTCTAAATCA
1 TAAACCCTAAACTTGAAATACTAAATCA
*
389785 TAAAACCCTAAACTTGAAGTACTTAAATTC-
1 T-AAACCCTAAACTTGAAATAC-TAAA-TCA
389815 TAAACC
1 TAAACC
389821 ATATATGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.03
29 22 0.73
30 5 0.17
31 2 0.07
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (28 bp):
TAAACCCTAAACTTGAAATACTAAATCA
Found at i:390758 original size:36 final size:36
Alignment explanation
Indices: 390696--390768 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
390686 CGGGCCTGAT
* *
390696 TCGGGTTGGGTTAAGGGTATACATTTTCAGGTCGGG
1 TCGGGTTGGGTGAAGGATATACATTTTCAGGTCGGG
*
390732 TCGGGTT-GGTGAAGGATATACAATTTTCGGGTCGGG
1 TCGGGTTGGGTGAAGGATATAC-ATTTTCAGGTCGGG
390768 T
1 T
390769 TGGTCCAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 12 0.36
36 21 0.64
ACGTcount: A:0.18, C:0.11, G:0.38, T:0.33
Consensus pattern (36 bp):
TCGGGTTGGGTGAAGGATATACATTTTCAGGTCGGG
Found at i:391158 original size:82 final size:83
Alignment explanation
Indices: 391013--391191 Score: 310
Period size: 82 Copynumber: 2.2 Consensus size: 83
391003 AATAAAAATT
**
391013 ATAAT-TTAGTCACTCAATTAAAATATTAATTATAAAGAATTTATTCATCGTTAAATTTAAAA-A
1 ATAATATTAGTCTTTCAATTAAAATATTAATTATAAAGAATTTATTCATCGTTAAATTTAAAACA
391076 CATGTTCAACATAACATA
66 CATGTTCAACATAACATA
391094 ATAATATTAGTCTTTCAATTAAAATATTAATTATAAAGAATTTATTCTATCGTTAAATTTAAAAC
1 ATAATATTAGTCTTTCAATTAAAATATTAATTATAAAGAATTTATTC-ATCGTTAAATTTAAAAC
391159 ACATGTTCAACATAACATA
65 ACATGTTCAACATAACATA
391178 ATAATA-TAGTCTTT
1 ATAATATTAGTCTTT
391192 AAAAGTGATA
Statistics
Matches: 93, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
81 5 0.05
82 39 0.42
83 24 0.26
84 25 0.27
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (83 bp):
ATAATATTAGTCTTTCAATTAAAATATTAATTATAAAGAATTTATTCATCGTTAAATTTAAAACA
CATGTTCAACATAACATA
Found at i:391733 original size:27 final size:29
Alignment explanation
Indices: 391703--391764 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
391693 CACAAATCGG
*
391703 TCACTAATGTTAT-TTT-TTACAAAATGA
1 TCACTAAAGTTATCTTTGTTACAAAATGA
*
391730 TCACTAAAGTTATCGTTTGTTACAAAATGG
1 TCACTAAAGTTATC-TTTGTTACAAAATGA
391760 TCACT
1 TCACT
391765 CAACGTTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 12 0.40
29 3 0.10
30 15 0.50
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (29 bp):
TCACTAAAGTTATCTTTGTTACAAAATGA
Found at i:392872 original size:3 final size:3
Alignment explanation
Indices: 392866--392921 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
392856 GGAGGAGGAC
392866 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
392914 GAA GAA GA
1 GAA GAA GA
392922 GTTAAACATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:399127 original size:31 final size:31
Alignment explanation
Indices: 399092--399176 Score: 109
Period size: 31 Copynumber: 2.6 Consensus size: 31
399082 CTTTATTTTG
399092 TTCGGGTCGGGTCGGGTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTAAGTGTGATA
399123 TTCGGGTCGAGTTGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTC-----GGGTCGGG-TTTTTAAGTGTGATA
399160 -TCGGGTCGGGTCGGGTT
1 TTCGGGTCGGGTCGGGTT
399177 CGGGTTTAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
30 2 0.04
31 16 0.33
36 15 0.31
37 15 0.31
ACGTcount: A:0.11, C:0.11, G:0.41, T:0.38
Consensus pattern (31 bp):
TTCGGGTCGGGTCGGGTTTTTAAGTGTGATA
Found at i:399157 original size:37 final size:36
Alignment explanation
Indices: 399097--399183 Score: 131
Period size: 36 Copynumber: 2.4 Consensus size: 36
399087 TTTTGTTCGG
399097 GTCGGGTCGGG-TTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTGTGATA-TCGGGTCGA
* *
399133 GTTGGGTCGGGTTTTTTAAGTGTGATATCGGGTCGG
1 GTCGGGTCGGGTTTTTTAAGTGTGATATCGGGTCGA
399169 GTCGGGTTCGGGTTT
1 GTCGGG-TCGGGTTT
399184 AGGGTGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 23 0.50
37 23 0.50
ACGTcount: A:0.10, C:0.10, G:0.41, T:0.38
Consensus pattern (36 bp):
GTCGGGTCGGGTTTTTTAAGTGTGATATCGGGTCGA
Found at i:399739 original size:18 final size:18
Alignment explanation
Indices: 399702--399748 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
399692 TATGGAATTG
*
399702 GATTCTAATT-CTTGACA
1 GATTCCAATTCCTTGACA
*
399719 GATTCCAATTCCTTTACA
1 GATTCCAATTCCTTGACA
399737 GATTCCAATTCC
1 GATTCCAATTCC
399749 CTCAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.38
Consensus pattern (18 bp):
GATTCCAATTCCTTGACA
Found at i:399803 original size:2 final size:2
Alignment explanation
Indices: 399796--399830 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
399786 GAATGTTTGC
399796 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
399831 TGAAGTTCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:403345 original size:28 final size:28
Alignment explanation
Indices: 403313--403368 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
403303 CACCCGAACA
403313 ACGAATCAATGTAACGAAGTATGTTATT
1 ACGAATCAATGTAACGAAGTATGTTATT
403341 ACGAATCAATGTAACGAAGTATGTTATT
1 ACGAATCAATGTAACGAAGTATGTTATT
403369 TACTTTAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (28 bp):
ACGAATCAATGTAACGAAGTATGTTATT
Found at i:404982 original size:131 final size:131
Alignment explanation
Indices: 404748--405010 Score: 526
Period size: 131 Copynumber: 2.0 Consensus size: 131
404738 GACTAGCTAC
404748 TACGTCGAACAATATTTATGATCCAGGTTTAGCCGAGCTACATAGCCTTGCTGTAGCTGTTAATC
1 TACGTCGAACAATATTTATGATCCAGGTTTAGCCGAGCTACATAGCCTTGCTGTAGCTGTTAATC
404813 TGGCTTTGGAGGAGGGATGCAGGACAATTCTATCATGGTAGTCAAGCTGTACAACAATGCGAGTG
66 TGGCTTTGGAGGAGGGATGCAGGACAATTCTATCATGGTAGTCAAGCTGTACAACAATGCGAGTG
404878 G
131 G
404879 TACGTCGAACAATATTTATGATCCAGGTTTAGCCGAGCTACATAGCCTTGCTGTAGCTGTTAATC
1 TACGTCGAACAATATTTATGATCCAGGTTTAGCCGAGCTACATAGCCTTGCTGTAGCTGTTAATC
404944 TGGCTTTGGAGGAGGGATGCAGGACAATTCTATCATGGTAGTCAAGCTGTACAACAATGCGAGTG
66 TGGCTTTGGAGGAGGGATGCAGGACAATTCTATCATGGTAGTCAAGCTGTACAACAATGCGAGTG
405009 G
131 G
405010 T
1 T
405011 GCGGATTCCA
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 132 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (131 bp):
TACGTCGAACAATATTTATGATCCAGGTTTAGCCGAGCTACATAGCCTTGCTGTAGCTGTTAATC
TGGCTTTGGAGGAGGGATGCAGGACAATTCTATCATGGTAGTCAAGCTGTACAACAATGCGAGTG
G
Found at i:406046 original size:24 final size:24
Alignment explanation
Indices: 406016--406071 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
406006 TAGAAGTTCG
406016 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
406040 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
406064 ATTGAAGC
1 ATTGAAGC
406072 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:411841 original size:2 final size:2
Alignment explanation
Indices: 411834--411861 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
411824 CCATCCATCC
411834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
411862 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:412206 original size:17 final size:17
Alignment explanation
Indices: 412157--412206 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
412147 TTGTTCATGT
412157 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
412174 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
412188 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
412205 TT
1 TT
412207 AGAAGAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:413086 original size:10 final size:10
Alignment explanation
Indices: 413073--413121 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
413063 ATAAATATAA
413073 AAAAATAAAG
1 AAAAATAAAG
413083 AAAAATAAAG
1 AAAAATAAAG
* *
413093 AAAAAGAAGG
1 AAAAATAAAG
*
413103 AAAACATATA-
1 AAAA-ATAAAG
413113 AAAAATAAA
1 AAAAATAAA
413122 ACAAGTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 4 0.12
10 26 0.81
11 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAATAAAG
Found at i:413155 original size:2 final size:2
Alignment explanation
Indices: 413150--413234 Score: 83
Period size: 2 Copynumber: 45.0 Consensus size: 2
413140 AATAAAAAAT
* *
413150 TA TA TA TA TA TA TA TA TA TA TA AA T- TA -A TA -A AA T- TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* *
413189 -A TA AA AA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
413229 TA TA TA
1 TA TA TA
413235 ATCTAAAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
1 6 0.08
2 64 0.90
3 1 0.01
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (2 bp):
TA
Found at i:413613 original size:37 final size:37
Alignment explanation
Indices: 413563--413667 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
413553 GTGCTTGTGG
* * *
413563 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
413600 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
413637 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
413668 GACGAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:414716 original size:106 final size:105
Alignment explanation
Indices: 414398--415561 Score: 1662
Period size: 106 Copynumber: 11.0 Consensus size: 105
414388 GCATTGTTCT
* * * ***
414398 GAGTCCAATATCCTCCGTCGTGATGTTGAAATTGGCTCTGGAAGCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGGAAATTGTTTGTTGACAA
* * * * *
414463 ACAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
414504 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T-GAAA-T-TTTGTTGACAAT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTGTTTGTTGACAAC
* * *
414564 CAGTC-GCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
414605 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
* *
414669 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
414710 GAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG-AAATTGTTTGTTGACAA
*
414775 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
414816 GAGTCCAATATACTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTGTTGACAA
414881 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
414922 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
* * *
414987 CTAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
415028 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
415093 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
415134 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAATTGTTTGTTGACAA
* *
415199 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
415240 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
415305 CCAGCGGTCCCTTCGTTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTG
*
415347 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAATTGTTTGTTGACAA
* *
415412 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTTTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
415453 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG-AAATTGTTTGTTGACAA
* * * *
415517 CCAGTC-GTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCTT
65 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
415558 GAGT
1 GAGT
415562 GGCACGATAT
Statistics
Matches: 966, Mismatches: 74, Indels: 37
0.90 0.07 0.03
Matches are distributed among these distances:
100 79 0.08
101 6 0.01
102 5 0.01
104 4 0.00
105 56 0.06
106 712 0.74
107 104 0.11
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:416405 original size:22 final size:22
Alignment explanation
Indices: 416379--416477 Score: 180
Period size: 22 Copynumber: 4.5 Consensus size: 22
416369 TTATGTTTGG
416379 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
416401 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
416423 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
416445 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
416467 TCAACGGTTTG
1 TCAAAGGTTTG
416478 ATGGGGTAGC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:417150 original size:13 final size:12
Alignment explanation
Indices: 417120--417183 Score: 58
Period size: 13 Copynumber: 5.2 Consensus size: 12
417110 TTTCTTTCAG
417120 TTTTTGTTCTTT
1 TTTTTGTTCTTT
417132 CTTTTTGTTCTTT
1 -TTTTTGTTCTTT
* *
417145 TGTTTTTTTCCTT
1 T-TTTTGTTCTTT
**
417158 TTTTCCTTCTTT
1 TTTTTGTTCTTT
417170 TCTTTT-TTCTTT
1 T-TTTTGTTCTTT
417182 TT
1 TT
417184 GCCCTTTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
11 1 0.02
12 17 0.40
13 25 0.58
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (12 bp):
TTTTTGTTCTTT
Found at i:417189 original size:24 final size:25
Alignment explanation
Indices: 417139--417189 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
417129 TTTCTTTTTG
* *
417139 TTCTTTTGTTTTTTTCCTTTTTTCC
1 TTCTTTTGCTTTTTTCCTTTTTCCC
417164 TTCTTTT-CTTTTTT-CTTTTTGCCC
1 TTCTTTTGCTTTTTTCCTTTTT-CCC
417188 TT
1 TT
417190 TTTGTTCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.26
24 10 0.43
25 7 0.30
ACGTcount: A:0.00, C:0.22, G:0.04, T:0.75
Consensus pattern (25 bp):
TTCTTTTGCTTTTTTCCTTTTTCCC
Found at i:420302 original size:10 final size:10
Alignment explanation
Indices: 420287--420335 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
420277 AATAAATATA
420287 AAAAATAAAG
1 AAAAATAAAG
420297 AAAAATAAAG
1 AAAAATAAAG
* *
420307 AAAAAGAAGG
1 AAAAATAAAG
*
420317 AAAACATATA-
1 AAAA-ATAAAG
420327 AAAAATAAA
1 AAAAATAAA
420336 ACAAGTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 4 0.12
10 26 0.81
11 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAATAAAG
Found at i:420358 original size:9 final size:9
Alignment explanation
Indices: 420274--420362 Score: 54
Period size: 9 Copynumber: 9.1 Consensus size: 9
420264 AAATAGTAAG
*
420274 TAAAATAAA
1 TAAAAAAAA
*
420283 TATAAAAAA
1 TAAAAAAAA
420292 TAAAGAAAAA
1 TAAA-AAAAA
420302 TAAAGAAAAA
1 TAAA-AAAAA
* *
420312 GAAGGAAAACA
1 TAA--AAAAAA
*
420323 TATAAAAAA
1 TAAAAAAAA
420332 TAAAACAAGTAA
1 TAAAA-AA--AA
420344 -ATAAAAAAA
1 TA-AAAAAAA
420353 TAAAAAAAA
1 TAAAAAAAA
420362 T
1 T
420363 TATATATATA
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
9 29 0.46
10 20 0.32
11 8 0.13
12 6 0.10
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:420360 original size:30 final size:28
Alignment explanation
Indices: 420277--420362 Score: 75
Period size: 30 Copynumber: 2.9 Consensus size: 28
420267 TAGTAAGTAA
*
420277 AATAAATATAAAAAATAAAGAAAAATAAAG
1 AATAAATA-AAAAAATAAA-AAAAATAAAC
* *
420307 AA-AAAGAAGGAAAACATATAAAAAATAAAAC
1 AATAAATAA--AAAA-ATAAAAAAAAT-AAAC
420338 AAGTAAATAAAAAAATAAAAAAAAT
1 AA-TAAATAAAAAAATAAAAAAAAT
420363 TATATATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
28 1 0.02
29 4 0.09
30 22 0.49
31 13 0.29
33 5 0.11
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (28 bp):
AATAAATAAAAAAATAAAAAAAATAAAC
Found at i:420368 original size:2 final size:2
Alignment explanation
Indices: 420363--420417 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
420353 TAAAAAAAAT
* * *
420363 TA TA TA TA TA TA TA TA TA TA -A TA AA TA AA TA -A TA GTA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
420404 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
420418 AATTAATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (2 bp):
TA
Found at i:420386 original size:39 final size:38
Alignment explanation
Indices: 420343--420477 Score: 146
Period size: 39 Copynumber: 3.4 Consensus size: 38
420333 AAAACAAGTA
420343 AATAAAAAAATAAAAAAAATTATATATATATATATATAT
1 AATAAAAAAATAAAAAAAA-TATATATATATATATATAT
* ** *
420382 AATAAATAAATAATAGTAAATATATATATATATATAAATT
1 AATAAAAAAATAA-AAAAAATATATATATATATATATA-T
** *
420422 AATAAAATTGATAATAAAAATA-ATATATATATATATAT
1 AATAAAA-AAATAAAAAAAATATATATATATATATATAT
420460 AATCTAAAAAAATAAAAA
1 AA--TAAAAAAATAAAAA
420478 TATATACTAA
Statistics
Matches: 77, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
38 3 0.04
39 49 0.64
40 21 0.27
41 4 0.05
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (38 bp):
AATAAAAAAATAAAAAAAATATATATATATATATATAT
Found at i:420436 original size:41 final size:40
Alignment explanation
Indices: 420343--420479 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 40
420333 AAAACAAGTA
* *
420343 AATAAAA-AAATAAAAAAAAT-TATATATATATATATATAT
1 AATAAAATAAATAATAAAAATATATATATATATATAAAT-T
*
420382 AAT-AAATAAATAATAGTAAATATATATATATATATAAATT
1 AATAAAATAAATAATA-AAAATATATATATATATATAAATT
**
420422 AATAAAATTGATAATAAAAATAATATATATATATATATAATCT
1 AATAAAATAAATAATAAAAAT-ATATATATATATATA-AAT-T
*
420465 AAAAAAATAAA-AATA
1 AATAAAATAAATAATA
420480 TATACTAAAG
Statistics
Matches: 82, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.04
39 10 0.12
40 12 0.15
41 41 0.50
42 7 0.09
43 9 0.11
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (40 bp):
AATAAAATAAATAATAAAAATATATATATATATATAAATT
Found at i:420830 original size:37 final size:37
Alignment explanation
Indices: 420789--420893 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
420779 GTGCTTGTGG
* *
420789 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * *
420826 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* *
420863 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
420894 GACGAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:422373 original size:30 final size:30
Alignment explanation
Indices: 422337--422397 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
422327 ATGCCCTACA
*
422337 CTTCACATTTTAGTACTTTTTAACTAAATT
1 CTTCACATTTTAGTACCTTTTAACTAAATT
422367 CTTCACATTTTAGTACCTTTTAACTAAATT
1 CTTCACATTTTAGTACCTTTTAACTAAATT
422397 C
1 C
422398 ATTAAGTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.48
Consensus pattern (30 bp):
CTTCACATTTTAGTACCTTTTAACTAAATT
Found at i:425136 original size:20 final size:20
Alignment explanation
Indices: 425111--425170 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
425101 TATGGGTTCA
*
425111 AATATCGATACTAGATGAAT
1 AATATCGATACTGGATGAAT
*
425131 AATATCGATACTGGATGAAC
1 AATATCGATACTGGATGAAT
*
425151 AATATCGAAACTGGATGAAT
1 AATATCGATACTGGATGAAT
425171 TGGGACAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AATATCGATACTGGATGAAT
Found at i:426985 original size:14 final size:14
Alignment explanation
Indices: 426966--427027 Score: 70
Period size: 15 Copynumber: 4.2 Consensus size: 14
426956 TTATATAAAA
426966 ATGTGATATAAGCT
1 ATGTGATATAAGCT
* *
426980 ATGTGATAATGATCT
1 ATGTGAT-ATAAGCT
*
426995 ATGTGATTATATGTCT
1 ATGTGA-TATAAG-CT
427011 ATGTGATATAAGCT
1 ATGTGATATAAGCT
427025 ATG
1 ATG
427028 CGAAATGTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.31
15 18 0.46
16 9 0.23
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.40
Consensus pattern (14 bp):
ATGTGATATAAGCT
Found at i:427170 original size:23 final size:23
Alignment explanation
Indices: 427110--427172 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
427100 TTGAGGGTTC
* *
427110 TACGCGGTCATTTGAGACAATTT
1 TACGCGGTCATTCGGGACAATTT
* * *
427133 TATGTGGTCATTCGGGACATTTT
1 TACGCGGTCATTCGGGACAATTT
427156 TACGCGGTCATTCGGGA
1 TACGCGGTCATTCGGGA
427173 TAATACTATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (23 bp):
TACGCGGTCATTCGGGACAATTT
Found at i:427183 original size:46 final size:46
Alignment explanation
Indices: 427110--427200 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
427100 TTGAGGGTTC
* **
427110 TACGCGGTCATTTGAGACAATTTTATGTGGTCATTCGGGACATTTT
1 TACGCGGTCATTCGAGACAATACTATGTGGTCATTCGGGACATTTT
* * * *
427156 TACGCGGTCATTCGGGATAATACTATGTGGTCCTTCGGGATATTT
1 TACGCGGTCATTCGAGACAATACTATGTGGTCATTCGGGACATTT
427201 CTATGTGGCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.37
Consensus pattern (46 bp):
TACGCGGTCATTCGAGACAATACTATGTGGTCATTCGGGACATTTT
Found at i:427187 original size:23 final size:23
Alignment explanation
Indices: 427129--427216 Score: 90
Period size: 23 Copynumber: 3.9 Consensus size: 23
427119 ATTTGAGACA
*
427129 ATTT-TATGTGGTCATTCGGGAC
1 ATTTCTATGTGGTCATTCGGGAT
* * *
427151 ATTTTTACGCGGTCATTCGGGAT
1 ATTTCTATGTGGTCATTCGGGAT
* * *
427174 AATACTATGTGGTCCTTCGGGAT
1 ATTTCTATGTGGTCATTCGGGAT
427197 ATTTCTATGTGG-CACTTCGG
1 ATTTCTATGTGGTCA-TTCGG
427217 TACAATTTCT
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
22 5 0.10
23 47 0.90
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (23 bp):
ATTTCTATGTGGTCATTCGGGAT
Found at i:428502 original size:3 final size:3
Alignment explanation
Indices: 428496--428520 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
428486 GTTACATGTG
428496 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
428521 CTTATGAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:443861 original size:23 final size:23
Alignment explanation
Indices: 443835--443889 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
443825 AACGATTGAG
*
443835 AAAGA-AAACAAAAAACGTGTTAC
1 AAAGACAAA-AAAAAACGTGTCAC
* *
443858 AAAGACATATAAAAACGTGTCAC
1 AAAGACAAAAAAAAACGTGTCAC
*
443881 AAAGGCAAA
1 AAAGACAAA
443890 TTATTCTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.13
Consensus pattern (23 bp):
AAAGACAAAAAAAAACGTGTCAC
Found at i:445176 original size:21 final size:22
Alignment explanation
Indices: 445143--445183 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
445133 GGTTAAAATA
445143 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
445165 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
445184 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:445866 original size:19 final size:19
Alignment explanation
Indices: 445810--445872 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
445800 CTATTTAAAC
**
445810 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
445830 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
445850 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
445869 TAAA
1 TAAA
445873 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:445900 original size:64 final size:69
Alignment explanation
Indices: 445775--445972 Score: 219
Period size: 64 Copynumber: 2.8 Consensus size: 69
445765 TAAAACATCT
* * *
445775 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC----CTAAAAAAT-AATATAA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATAAAAAATAAAAATAA
*
445834 TATTC
65 TATCC
445839 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGTTAAAATATAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGAT--A---AAAA-ATAAA
445904 AATAATATCC
60 AATAATATCC
* * *
445914 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAAAATAA
445973 TGTTTAAAAT
Statistics
Matches: 114, Mismatches: 7, Indels: 20
0.81 0.05 0.14
Matches are distributed among these distances:
63 5 0.04
64 36 0.32
68 1 0.01
70 5 0.04
71 3 0.03
73 4 0.04
74 3 0.03
75 28 0.25
76 29 0.25
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.29
Consensus pattern (69 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAAAATAAAAATAAT
ATCC
Found at i:445982 original size:76 final size:75
Alignment explanation
Indices: 445830--445993 Score: 231
Period size: 76 Copynumber: 2.2 Consensus size: 75
445820 AAAAAATAAT
* * *
445830 ATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGTTA
1 ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
445895 AAATATAAAA
66 AAATATAAAA
*
445905 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1 ATAATATCCTAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
* * *
445969 ATAATGTTTAAA
65 AAAAT-ATAAAA
*
445981 ATATTATCCTAAA
1 ATAATATCCTAAA
445994 TTTGAGTTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 31 0.39
76 48 0.61
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.30
Consensus pattern (75 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
AAATATAAAA
Found at i:451249 original size:22 final size:21
Alignment explanation
Indices: 451224--451266 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
451214 TAGGTTGATT
*
451224 TTAAAATATACACATATAAATA
1 TTAAAATATAAACATA-AAATA
* *
451246 TTAAGATTTAAACATAAAATA
1 TTAAAATATAAACATAAAATA
451267 ATACCAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAATATAAACATAAAATA
Found at i:459755 original size:31 final size:30
Alignment explanation
Indices: 459719--459798 Score: 105
Period size: 26 Copynumber: 2.7 Consensus size: 30
459709 TTAAGATCGC
459719 GAGTTTTGGAGTCGAGTCGAGCTTCATTTCA
1 GAGTTTT-GAGTCGAGTCGAGCTTCATTTCA
*
459750 GAG-TTT---TCGAGTCGAGTTTCATTTCA
1 GAGTTTTGAGTCGAGTCGAGCTTCATTTCA
459776 GAGTTTTCGAGTCGAGTCGAGCT
1 GAGTTTT-GAGTCGAGTCGAGCT
459799 CAGCAATACT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
26 22 0.52
27 3 0.07
30 3 0.07
31 14 0.33
ACGTcount: A:0.19, C:0.16, G:0.29, T:0.36
Consensus pattern (30 bp):
GAGTTTTGAGTCGAGTCGAGCTTCATTTCA
Found at i:459792 original size:26 final size:26
Alignment explanation
Indices: 459730--459792 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
459720 AGTTTTGGAG
*
459730 TCGAGTCGAGCTTCATTTCAGAGTTT
1 TCGAGTCGAGTTTCATTTCAGAGTTT
459756 TCGAGTCGAGTTTCATTTCAGAGTTT
1 TCGAGTCGAGTTTCATTTCAGAGTTT
459782 TCGAGTCGAGT
1 TCGAGTCGAGT
459793 CGAGCTCAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (26 bp):
TCGAGTCGAGTTTCATTTCAGAGTTT
Found at i:461389 original size:22 final size:23
Alignment explanation
Indices: 461364--461444 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 23
461354 ACACAATAAA
461364 TAATATTATTTATCATAAAAT-T
1 TAATATTATTTATCATAAAATAT
*
461386 TAATATTA-TTATTTATAAAATAT
1 TAATATTATTTA-TCATAAAATAT
* *
461409 TAAAATAATTTATTTATTATTAAATAT
1 T--AAT-A-TTATTTATCATAAAATAT
*
461436 TAATTTTAT
1 TAATATTAT
461445 ATTTTTATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
21 3 0.06
22 16 0.33
23 6 0.12
25 6 0.12
26 1 0.02
27 14 0.29
28 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (23 bp):
TAATATTATTTATCATAAAATAT
Found at i:461415 original size:25 final size:25
Alignment explanation
Indices: 461360--461425 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
461350 TTAAACACAA
461360 TAAATAATATTATTTATCATAAAAT
1 TAAATAATATTATTTATCATAAAAT
* *
461385 TTAATATTATTATTTAT-A-AAATAT
1 TAAATAATATTATTTATCATAAA-AT
461409 TAAAATAAT-TTATTTAT
1 T-AAATAATATTATTTAT
461426 TATTAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 3 0.09
24 12 0.34
25 20 0.57
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAATAATATTATTTATCATAAAAT
Found at i:461612 original size:19 final size:19
Alignment explanation
Indices: 461544--461612 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
461534 TTAAATATCT
461544 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
461563 TTATTAGATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
461582 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
461602 TTATTAATAAT
1 TTATTAATAAT
461613 TTAATAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 8 0.20
19 18 0.44
20 8 0.20
22 7 0.17
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:461664 original size:24 final size:23
Alignment explanation
Indices: 461575--461686 Score: 57
Period size: 27 Copynumber: 4.5 Consensus size: 23
461565 ATTAGATTAA
461575 TATT-AAATATATAAATAATATTAT
1 TATTAAAATA-ATAAATAATA-TAT
* *
461599 TCATTATTAATAATTTAATAATAATAT
1 T-ATTA-AAATAA-TAAATAAT-ATAT
461626 T-TCTACGAAATTAATAAATAATATAAT
1 TAT-TA--AAA-TAATAAATAATAT-AT
* ** *
461653 TTTTAAAATAATTTATTATATAT
1 TATTAAAATAATAAATAATATAT
461676 TATTAAAATAA
1 TATTAAAATAA
461687 AACTATAATA
Statistics
Matches: 69, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
23 12 0.17
24 11 0.16
25 7 0.10
26 5 0.07
27 29 0.42
28 5 0.07
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.46
Consensus pattern (23 bp):
TATTAAAATAATAAATAATATAT
Found at i:461697 original size:24 final size:23
Alignment explanation
Indices: 461643--461702 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
461633 AAATTAATAA
* **
461643 ATAATATAATTTTTAAAATAATTT
1 ATAATAT-ATTATTAAAATAAACT
*
461667 ATTATATATTATTAAAATAAAACT
1 ATAATATATTATTAAAAT-AAACT
*
461691 ATAATATCTTAT
1 ATAATATATTAT
461703 ATTATTATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATATATTATTAAAATAAACT
Found at i:461756 original size:22 final size:23
Alignment explanation
Indices: 461728--461774 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
461718 TTGATTATTT
461728 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
461750 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
461773 TA
1 TA
461775 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:461779 original size:22 final size:22
Alignment explanation
Indices: 461736--461779 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
461726 TTTATTATAA
*
461736 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
461758 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
461780 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:462515 original size:22 final size:22
Alignment explanation
Indices: 462462--462515 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
462452 TTTTTAATAA
*
462462 TTCTATC-TCTATAACACGTTT
1 TTCTATCTTTTATAACACGTTT
* * * *
462483 TTGTATGTTTTATGACATGTTT
1 TTCTATCTTTTATAACACGTTT
462505 TTCTATCTTTT
1 TTCTATCTTTT
462516 GGCACGTTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.19, C:0.15, G:0.09, T:0.57
Consensus pattern (22 bp):
TTCTATCTTTTATAACACGTTT
Found at i:463074 original size:58 final size:58
Alignment explanation
Indices: 462999--463116 Score: 200
Period size: 58 Copynumber: 2.0 Consensus size: 58
462989 CTCAAAGAAC
* *
462999 AACAATAATTTCTTTATCACTGAAGTCATTTAATTTAAGTAAAAATATATACCATTTT
1 AACAATAATTTCTTTATCACCGAAGTCATTTAATTTAAGTAAAAATATATACCAATTT
* *
463057 AACATTAATTTCTTTATCACCGAAGTCATTTGATTTAAGTAAAAATATATACCAATTT
1 AACAATAATTTCTTTATCACCGAAGTCATTTAATTTAAGTAAAAATATATACCAATTT
463115 AA
1 AA
463117 AGTTAGTTGG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.40
Consensus pattern (58 bp):
AACAATAATTTCTTTATCACCGAAGTCATTTAATTTAAGTAAAAATATATACCAATTT
Found at i:463704 original size:2 final size:2
Alignment explanation
Indices: 463699--463727 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
463689 TATATGTTAT
463699 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
463728 GCTTTAGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:475574 original size:14 final size:14
Alignment explanation
Indices: 475557--475595 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
475547 TAGAAAATTT
475557 AATTTATTTTACGA
1 AATTTATTTTACGA
*
475571 AATTTATTTTCCGA
1 AATTTATTTTACGA
*
475585 AATCTATTTTA
1 AATTTATTTTA
475596 TGTGAACCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (14 bp):
AATTTATTTTACGA
Found at i:475723 original size:32 final size:32
Alignment explanation
Indices: 475675--475743 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
475665 CCGTGTCCTG
* *
475675 ACCCGGATGTTACGGGTACCTGGTAATCTGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
* *
475707 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
475739 ACCCG
1 ACCCG
475744 ATACCCGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.25
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGGTAATCGGGT
Found at i:475739 original size:15 final size:15
Alignment explanation
Indices: 475687--475743 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
475677 CCGGATGTTA
*
475687 CGGGTACCTGGTAAT
1 CGGGTACCCGGTAAT
* **
475702 CTGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
475718 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
475734 CGGGTACCCG
1 CGGGTACCCG
475744 ATACCCGATT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 19 0.58
16 4 0.12
17 10 0.30
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:477282 original size:9 final size:9
Alignment explanation
Indices: 477268--477298 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
477258 TGTGAAGTAT
477268 AAAAAAATA
1 AAAAAAATA
477277 AAAAAAATA
1 AAAAAAATA
477286 AAAAAAATA
1 AAAAAAATA
477295 AAAA
1 AAAA
477299 CTAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:478076 original size:60 final size:60
Alignment explanation
Indices: 477982--478118 Score: 211
Period size: 60 Copynumber: 2.3 Consensus size: 60
477972 CTTTGCAATG
*
477982 AAAGTTACAAAATGATCCCTTAACTATAGAGAGTTGCTTTGTTGAGTCCCTTAACTATTA
1 AAAGTTACAAAATGATCCCTTAACTATAGAGAGTTGCTTTGTTGAGTCCCTCAACTATTA
*** * * *
478042 AAAGTTACAAAATGATCCCTTGTTTATAGGGAGTTGTTTTGTTGAGTCCCTCGACTATTA
1 AAAGTTACAAAATGATCCCTTAACTATAGAGAGTTGCTTTGTTGAGTCCCTCAACTATTA
478102 AAAGTTACAAAATGATC
1 AAAGTTACAAAATGATC
478119 GCTCGACTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (60 bp):
AAAGTTACAAAATGATCCCTTAACTATAGAGAGTTGCTTTGTTGAGTCCCTCAACTATTA
Found at i:482287 original size:16 final size:16
Alignment explanation
Indices: 482266--482296 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
482256 TCCCTCTTTT
482266 ATATTTATTACTATAA
1 ATATTTATTACTATAA
*
482282 ATATTTATTATTATA
1 ATATTTATTACTATA
482297 TTATTTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTTATTACTATAA
Found at i:482677 original size:44 final size:42
Alignment explanation
Indices: 482618--482705 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 42
482608 TCGGGCCGGG
482618 TATATATATTTAAATTAAATATATAAATATTATATATATATA
1 TATATATATTTAAATTAAATATATAAATATTATATATATATA
* *
482660 TATATATTAATTTAAATTAAATTTATTAATATTATATATATATA
1 TATATA-T-ATTTAAATTAAATATATAAATATTATATATATATA
482704 TA
1 TA
482706 ATAATTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 6 0.14
43 1 0.02
44 35 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (42 bp):
TATATATATTTAAATTAAATATATAAATATTATATATATATA
Found at i:485340 original size:21 final size:21
Alignment explanation
Indices: 485314--485354 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
485304 TAAAAGTTAT
*
485314 GTGGTTATAGTTTAGTGTTTA
1 GTGGTTATAGTTTAGGGTTTA
*
485335 GTGGTTTTAGTTTAGGGTTT
1 GTGGTTATAGTTTAGGGTTT
485355 TAAGTTAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.32, T:0.54
Consensus pattern (21 bp):
GTGGTTATAGTTTAGGGTTTA
Found at i:486524 original size:16 final size:16
Alignment explanation
Indices: 486500--486560 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
486490 AATAAATAAC
486500 ACGAACATAAACGAAA
1 ACGAACATAAACGAAA
*
486516 ACAAACATAAACGAAA
1 ACGAACATAAACGAAA
*
486532 ACGAACATAAACGAAC
1 ACGAACATAAACGAAA
486548 ACGAACATAAACG
1 ACGAACATAAACG
486561 TTGGAGACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.61, C:0.21, G:0.11, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAA
Found at i:487675 original size:24 final size:24
Alignment explanation
Indices: 487640--487690 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
487630 GATTGGTTTA
487640 AACATAAATGAACGAACATAAACG
1 AACATAAATGAACGAACATAAACG
* * *
487664 AACATAACTGAATGAACATAACCG
1 AACATAAATGAACGAACATAAACG
487688 AAC
1 AAC
487691 GTTCACGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.14
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:488833 original size:23 final size:21
Alignment explanation
Indices: 488799--488841 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
488789 TGTAACTAAT
488799 ATTTTATTTTAAATAATTTAC
1 ATTTTATTTTAAATAATTTAC
*
488820 ATTTGTATCTTTAACTAATTTA
1 ATTT-TAT-TTTAAATAATTTA
488842 TAATTACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTATTTTAAATAATTTAC
Found at i:494316 original size:110 final size:110
Alignment explanation
Indices: 494123--494342 Score: 431
Period size: 110 Copynumber: 2.0 Consensus size: 110
494113 CCATTTTATA
494123 GCCTATGCATCTAGGACGCTAGACACGACTCAACAAAATTACTCGACCATGAAAAAGAACTCTTT
1 GCCTATGCATCTAGGACGCTAGACACGACTCAACAAAATTACTCGACCATGAAAAAGAACTCTTT
494188 GCCATTATTTTTACTTTGGATAAATATTGTTCTTATCTACTTGGT
66 GCCATTATTTTTACTTTGGATAAATATTGTTCTTATCTACTTGGT
*
494233 GCCTATGCATCTAGGACGCTAGACACGACTCAACGAAATTACTCGACCATGAAAAAGAACTCTTT
1 GCCTATGCATCTAGGACGCTAGACACGACTCAACAAAATTACTCGACCATGAAAAAGAACTCTTT
494298 GCCATTATTTTTACTTTGGATAAATATTGTTCTTATCTACTTGGT
66 GCCATTATTTTTACTTTGGATAAATATTGTTCTTATCTACTTGGT
494343 ACTAATATTA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (110 bp):
GCCTATGCATCTAGGACGCTAGACACGACTCAACAAAATTACTCGACCATGAAAAAGAACTCTTT
GCCATTATTTTTACTTTGGATAAATATTGTTCTTATCTACTTGGT
Found at i:503603 original size:24 final size:24
Alignment explanation
Indices: 503576--503685 Score: 102
Period size: 24 Copynumber: 4.6 Consensus size: 24
503566 GTAAACGTAG
*
503576 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
503600 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
503624 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
503647 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
*
503671 A-ATTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
503686 TAAAATATTT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 16 0.23
24 50 0.71
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:503607 original size:12 final size:12
Alignment explanation
Indices: 503580--503671 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
503570 ACGTAGATAT
* *
503580 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
503592 CAGAATTCATAT
1 CAGAATTCAGAA
503604 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
503616 CAGAATCCAGAT
1 CAGAATTCAGAA
503628 CAGAA-TCAGAA
1 CAGAATTCAGAA
503639 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
503653 C-GTA-TCAGAA
1 CAGAATTCAGAA
503663 CAGAATTCA
1 CAGAATTCA
503672 ATTCGGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:503659 original size:47 final size:48
Alignment explanation
Indices: 503578--503668 Score: 125
Period size: 47 Copynumber: 1.9 Consensus size: 48
503568 AAACGTAGAT
*
503578 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
*
503626 ATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCA--TAACAGATATCAGAACAGAAT
503669 TCAATTCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
47 30 0.77
48 6 0.15
49 3 0.08
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
Found at i:504785 original size:18 final size:18
Alignment explanation
Indices: 504764--504798 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
504754 TGCCATCCGG
*
504764 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
504782 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
504799 GTCCTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:508244 original size:24 final size:24
Alignment explanation
Indices: 508217--508326 Score: 111
Period size: 24 Copynumber: 4.6 Consensus size: 24
508207 GTAAACGGAG
*
508217 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
508241 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
508265 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
508288 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
508312 A-ATTCAGAAATCAGA
1 ATA-TCAGAAATCAGA
508327 TAAAATATTT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 16 0.23
24 50 0.71
25 2 0.03
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:508248 original size:12 final size:12
Alignment explanation
Indices: 508221--508312 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
508211 ACGGAGATAT
* *
508221 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
508233 CAGAATTCATAT
1 CAGAATTCAGAA
508245 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
508257 CAGAATCCAGAT
1 CAGAATTCAGAA
508269 CAGAA-TCAGAA
1 CAGAATTCAGAA
508280 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
508294 C-GTA-TCAGAA
1 CAGAATTCAGAA
508304 CAGAATTCA
1 CAGAATTCA
508313 ATTCAGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:508300 original size:47 final size:47
Alignment explanation
Indices: 508219--508326 Score: 132
Period size: 47 Copynumber: 2.3 Consensus size: 47
508209 AAACGGAGAT
* *
508219 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCATAACAGATATCAGAACAGAATCCA
*
508266 GATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCA--TAACAGATATCAGAACAGAATCCA
508313 ATTCAGAAATCAGA
1 A-TCAGAAATCAGA
508327 TAAAATATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
46 1 0.02
47 36 0.68
48 13 0.25
49 3 0.06
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCATAACAGATATCAGAACAGAATCCA
Found at i:510773 original size:13 final size:13
Alignment explanation
Indices: 510755--510797 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
510745 GCCGGTCAAC
510755 GGTCAACAGGTCG
1 GGTCAACAGGTCG
*
510768 GGTCAACGGGTCG
1 GGTCAACAGGTCG
510781 GGTCAACAGGTCG
1 GGTCAACAGGTCG
510794 GGTC
1 GGTC
510798 GGGTAAACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:510795 original size:18 final size:18
Alignment explanation
Indices: 510774--510819 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
510764 GTCGGGTCAA
*
510774 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTAAACAGGT
*
510792 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACAGGT
510810 CGGGTCGGGT
1 CGGGTCGGGT
510820 TGTAACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.20, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACAGGT
Found at i:510808 original size:13 final size:13
Alignment explanation
Indices: 510763--510814 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
510753 ACGGTCAACA
*
510763 GGTCGGGTCAACG
1 GGTCGGGTAAACG
510776 GGTCGGGTCAACAGGTCG
1 GGTCGGGT-AA-A---CG
510794 GGTCGGGTAAACG
1 GGTCGGGTAAACG
510807 GGTCGGGT
1 GGTCGGGT
510815 CGGGTTGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
13 18 0.55
14 1 0.03
15 1 0.03
16 1 0.03
17 2 0.06
18 10 0.30
ACGTcount: A:0.15, C:0.19, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCGGGTAAACG
Found at i:514838 original size:23 final size:23
Alignment explanation
Indices: 514785--514853 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
514775 ACATTTTATA
* * *
514785 TGGCACTTCGGTGCAAATCTACG
1 TGGCACTTCAGTGCAATTATACG
* **
514808 CGATACTTCAGTGCAATTATACG
1 TGGCACTTCAGTGCAATTATACG
*
514831 TGGCACTT-AGGTGCATTTATACG
1 TGGCACTTCA-GTGCAATTATACG
514854 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (23 bp):
TGGCACTTCAGTGCAATTATACG
Found at i:518296 original size:24 final size:20
Alignment explanation
Indices: 518263--518322 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 20
518253 AAATGCAATT
518263 AATGCATCGATGCACATGTTAAGG
1 AATGCATCGATGCAC-TG-T-A-G
* *
518287 GATGCATCGATACACTGTAG
1 AATGCATCGATGCACTGTAG
518307 AATGCATCGATGCACT
1 AATGCATCGATGCACT
518323 TCAAGGGGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 15 0.47
21 1 0.03
22 1 0.03
23 2 0.06
24 13 0.41
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (20 bp):
AATGCATCGATGCACTGTAG
Found at i:521801 original size:19 final size:20
Alignment explanation
Indices: 521779--521819 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
521769 CAAAATCTTG
*
521779 TTTTTA-TTGATTTAATTTA
1 TTTTTATTTGATTCAATTTA
*
521798 -TTTTATTTTATTCAATTTA
1 TTTTTATTTGATTCAATTTA
521817 TTT
1 TTT
521820 AATTATTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
18 5 0.28
19 11 0.61
20 2 0.11
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTATTTGATTCAATTTA
Found at i:525163 original size:165 final size:167
Alignment explanation
Indices: 524891--525222 Score: 634
Period size: 165 Copynumber: 2.0 Consensus size: 167
524881 TCTCTTTACT
524891 AAGGGTCTATCTTAACATCCCTTTGCCTGAGAGAATTGCTTGGTACAACTACAAGATCCTAGGCA
1 AAGGGTCTATCTTAACATCCCTTTGCCTGAGAGAATTGCTTGGTACAACTACAAGATCCTAGGCA
524956 TCAAGTTGATTGTTAAGGGTACCCCTCCACCTGCACCTAAGAAAGGCCAAAGT-G-GTCCTGTTT
66 TCAAGTTGATTGTTAAGGGTACCCCTCCACCTGCACCTAAGAAAGGCCAAAGTGGTGTCCTG-TT
525019 TGTTTGTAACCATAGAACGGTTTTAGACCC-GTTGTGA
130 TGTTTGTAACCATAGAACGGTTTTAGACCCGGTTGTGA
525056 AAGGGTCTATCTTAACATCCCTTTGCCTGAGAGAATTGCTTGGTACAACTACAAGATCCTAGGCA
1 AAGGGTCTATCTTAACATCCCTTTGCCTGAGAGAATTGCTTGGTACAACTACAAGATCCTAGGCA
525121 TCAAGTTGATTGTTAAGGGTACCCCTCCACCTGCACCTAAGAAAGGCCAAAGTGGTGTCCTGTTT
66 TCAAGTTGATTGTTAAGGGTACCCCTCCACCTGCACCTAAGAAAGGCCAAAGTGGTGTCCTGTTT
525186 GTTTGTAACCATAGAACGGTTTTAGACCCGGTTGTGA
131 GTTTGTAACCATAGAACGGTTTTAGACCCGGTTGTGA
525223 CGGCGGTCGC
Statistics
Matches: 164, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
165 118 0.72
166 33 0.20
167 13 0.08
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (167 bp):
AAGGGTCTATCTTAACATCCCTTTGCCTGAGAGAATTGCTTGGTACAACTACAAGATCCTAGGCA
TCAAGTTGATTGTTAAGGGTACCCCTCCACCTGCACCTAAGAAAGGCCAAAGTGGTGTCCTGTTT
GTTTGTAACCATAGAACGGTTTTAGACCCGGTTGTGA
Found at i:527451 original size:21 final size:21
Alignment explanation
Indices: 527427--527485 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
527417 ATTATCCAAT
* *
527427 AAACTTGACATCGATAGCAAC
1 AAACTTGACATCCATAACAAC
*
527448 AAACTTAACATCCATAACAAC
1 AAACTTGACATCCATAACAAC
* *
527469 TAACTTGAAATCCATAA
1 AAACTTGACATCCATAA
527486 TAATAAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (21 bp):
AAACTTGACATCCATAACAAC
Found at i:527734 original size:10 final size:10
Alignment explanation
Indices: 527719--527754 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
527709 AATATAACTT
527719 GTTCATGTTC
1 GTTCATGTTC
*
527729 GTTCATGTTT
1 GTTCATGTTC
527739 GTTCATGTTC
1 GTTCATGTTC
*
527749 ATTCAT
1 GTTCAT
527755 TTAAATGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.53
Consensus pattern (10 bp):
GTTCATGTTC
Found at i:527742 original size:20 final size:20
Alignment explanation
Indices: 527717--527754 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
527707 GGAATATAAC
*
527717 TTGTTCATGTTCGTTCATGT
1 TTGTTCATGTTCATTCATGT
527737 TTGTTCATGTTCATTCAT
1 TTGTTCATGTTCATTCAT
527755 TTAAATGATA
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:0.13, C:0.16, G:0.16, T:0.55
Consensus pattern (20 bp):
TTGTTCATGTTCATTCATGT
Found at i:527823 original size:23 final size:23
Alignment explanation
Indices: 527762--527829 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 23
527752 CATTTAAATG
*
527762 ATAAACGAACGTAAACGAACACA
1 ATAAATGAACGTAAACGAACACA
* *
527785 A-ACGAATGAACATAAACGAACATA
1 ATA--AATGAACGTAAACGAACACA
527809 ATAAATGAACGTAAACGAACA
1 ATAAATGAACGTAAACGAACA
527830 ACACAAACAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
22 1 0.03
23 18 0.47
24 18 0.47
25 1 0.03
ACGTcount: A:0.57, C:0.18, G:0.13, T:0.12
Consensus pattern (23 bp):
ATAAATGAACGTAAACGAACACA
Found at i:528112 original size:14 final size:14
Alignment explanation
Indices: 528093--528121 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
528083 GTCATCTGTT
528093 CGAACATAAATGAA
1 CGAACATAAATGAA
528107 CGAACATAAATGAA
1 CGAACATAAATGAA
528121 C
1 C
528122 AAAAATGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:530061 original size:22 final size:22
Alignment explanation
Indices: 530036--530082 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
530026 TCACTCTCTA
*
530036 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCCCATATC
*
530058 CGGCGACATCTGTCCCCATATC
1 CGGCGACATCCGTCCCCATATC
530080 CGG
1 CGG
530083 TGACCCCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.45, G:0.21, T:0.19
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATATC
Found at i:530521 original size:20 final size:20
Alignment explanation
Indices: 530471--530521 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
530461 TCACAACACG
*
530471 ATTTTAGTTTCGCATTGCGA
1 ATTTAAGTTTCGCATTGCGA
* * **
530491 ATTTCATTTTCGTGTTGCGA
1 ATTTAAGTTTCGCATTGCGA
530511 ATTTAAGTTTC
1 ATTTAAGTTTC
530522 AAAAACTACT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.49
Consensus pattern (20 bp):
ATTTAAGTTTCGCATTGCGA
Found at i:532069 original size:42 final size:42
Alignment explanation
Indices: 532010--532108 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
532000 CCCCCCACTT
* *
532010 CGAGAGCCATCACCTGATCGAGCCGATTCTACAGC-TCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACA-CATCAACAC
* *
532052 CGAGAGACATCACCTGATCGAGTCGATTATACACATCAACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACATCAACAC
532094 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
532109 ATTCCATCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.02
42 50 0.98
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.17
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACATCAACAC
Found at i:532266 original size:21 final size:21
Alignment explanation
Indices: 532223--532272 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
532213 GTTAGGAGAG
* *
532223 TTACGTGATGAGGTAAGTGCT
1 TTACGTGATGAGGTAACTACT
* *
532244 TTGCGTGATGAGGTCACTACT
1 TTACGTGATGAGGTAACTACT
532265 TTACGTGA
1 TTACGTGA
532273 CGATAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTAACTACT
Found at i:532707 original size:21 final size:21
Alignment explanation
Indices: 532679--532755 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
532669 GATTCATCTG
532679 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
532700 TTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
532721 TCATCATTCAAGAGGCCCCT-
1 TCATCGTTCAAGAGGCCCCTC
*
532741 TCCACCGTTCAAGAG
1 T-CATCGTTCAAGAG
532756 CCCGATTCAC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 1 0.02
21 49 0.98
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:534266 original size:20 final size:20
Alignment explanation
Indices: 534241--534315 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
534231 CCACCTTTAA
* *
534241 GAAAATGAAATTCGCAATGC
1 GAAAATCAAATTCGCAACGC
534261 GAAAATCAAATTCGCAACGC
1 GAAAATCAAATTCGCAACGC
* *
534281 GAAAGTCAAATTCGTAACGC
1 GAAAATCAAATTCGCAACGC
*
534301 GAAAGTCAAATTCGC
1 GAAAATCAAATTCGC
534316 GTTGGCGGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.19
Consensus pattern (20 bp):
GAAAATCAAATTCGCAACGC
Found at i:534383 original size:20 final size:20
Alignment explanation
Indices: 534345--534405 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
534335 GTCAAATTCA
* *
534345 CGTTGCGATTTTTATTTTCG
1 CGTTGCGAATTTGATTTTCG
534365 CG-TGTCGAATTTGATTTTCG
1 CGTTG-CGAATTTGATTTTCG
*
534385 CGTTGCGAATTTGACTTTCG
1 CGTTGCGAATTTGATTTTCG
534405 C
1 C
534406 AACAATCGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.13, C:0.18, G:0.23, T:0.46
Consensus pattern (20 bp):
CGTTGCGAATTTGATTTTCG
Found at i:534447 original size:49 final size:49
Alignment explanation
Indices: 534370--534493 Score: 185
Period size: 49 Copynumber: 2.5 Consensus size: 49
534360 TTTCGCGTGT
* *
534370 CGAATTTGATTTTCGCGTTGCGAATTTGACTTTCGCAACAATCGCAATG
1 CGAATTTGACTTTCGCGTTGCGAATTTGACTTTCGCAACAATCGCAACG
** * *
534419 CGAATTTGACTTTCGCGTTTTGATTTTGACTTTTGCAACAATCGCAACG
1 CGAATTTGACTTTCGCGTTGCGAATTTGACTTTCGCAACAATCGCAACG
*
534468 CGAATTTGACTTTCGCATTGCGAATT
1 CGAATTTGACTTTCGCGTTGCGAATT
534494 CAAGGGAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (49 bp):
CGAATTTGACTTTCGCGTTGCGAATTTGACTTTCGCAACAATCGCAACG
Found at i:537010 original size:24 final size:24
Alignment explanation
Indices: 536976--537030 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
536966 CTGAAATATC
536976 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
537000 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
537024 AT-AAAAT
1 ATCAAAAT
537031 TTCGAATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:537043 original size:24 final size:24
Alignment explanation
Indices: 536979--537043 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 24
536969 AAATATCATC
* *
536979 AAAA-TCCGAGTATTGACCAAGAT
1 AAAAGTCCGAATACTGACCAAGAT
* * *
537002 CAAAGTCCGAGTATTGACCAAGAT
1 AAAAGTCCGAATACTGACCAAGAT
* *
537026 AAAATTTCGAATACTGAC
1 AAAAGTCCGAATACTGAC
537044 TAGTACTCAC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (24 bp):
AAAAGTCCGAATACTGACCAAGAT
Found at i:537975 original size:20 final size:20
Alignment explanation
Indices: 537950--538117 Score: 89
Period size: 20 Copynumber: 8.3 Consensus size: 20
537940 ATAAAAGCTA
537950 TTGCGAAATTAAAATTCGTG
1 TTGCGAAATTAAAATTCGTG
*
537970 TTGCG-AATTCGAAAA-TCGAG
1 TTGCGAAATT--AAAATTCGTG
**
537990 TTGCGAAAACAAAATTCGTG
1 TTGCGAAATTAAAATTCGTG
* * *
538010 TTGCG-ATTTAGAAAATCTTG
1 TTGCGAAATTA-AAATTCGTG
** *
538030 TTGCGAAAAGGAAACTT-GTG
1 TTGCG-AAATTAAAATTCGTG
* *
538050 TTGCGAAA-AAGAAATTCGCG
1 TTGCGAAATTA-AAATTCGTG
*
538070 TTGCG-AATTCAGAAA-TCGAG
1 TTGCGAAATT-A-AAATTCGTG
* *
538090 TTGCGAATTTGAAATTCCGTG
1 TTGCGAAATTAAAATT-CGTG
538111 TTGCGAA
1 TTGCGAA
538118 TTTGGAAATC
Statistics
Matches: 111, Mismatches: 23, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
18 1 0.01
19 22 0.20
20 59 0.53
21 27 0.24
22 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (20 bp):
TTGCGAAATTAAAATTCGTG
Found at i:537996 original size:40 final size:40
Alignment explanation
Indices: 537950--538262 Score: 142
Period size: 40 Copynumber: 7.7 Consensus size: 40
537940 ATAAAAGCTA
* *
537950 TTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAG
1 TTGCGAAATTAAAATTCGTGTTGCGAATTAGAAAATCGTG
** * *
537990 TTGCGAAAACAAAATTCGTGTTGCGATTTAGAAAATCTTG
1 TTGCGAAATTAAAATTCGTGTTGCGAATTAGAAAATCGTG
** * ** * *
538030 TTGCGAAAAGGAAACTT-GTGTTGCGAAAAAGAAATTCGCG
1 TTGCG-AAATTAAAATTCGTGTTGCGAATTAGAAAATCGTG
* * *
538070 TTGCG-AATTCAGAAA-TCGAGTTGCGAATTTGAAATTCCGTG
1 TTGCGAAATT-A-AAATTCGTGTTGCGAATTAGAAAAT-CGTG
* * ** * *
538111 TTGCGAATTTGGAAA-TCAAGTTGCGAATTTGGAAAATCGCG
1 TTGCGAAATT-AAAATTCGTGTTGCGAA-TTAGAAAATCGTG
* * *
538152 TTGCGAGAA--AGAAATTCGCGTTGC-AATTGCAGAAACT-GAG
1 TTGCGA-AATTA-AAATTCGTGTTGCGAATT--AGAAAATCGTG
* * *
538192 TTGCG-AATCTGGGAAATTCGTGTTGCGAATTTGGAAA-CTGTG
1 TTGCGAAAT-T--AAAATTCGTGTTGCGAATTAGAAAATC-GTG
** * *
538234 TTGCGAAATTGGAGTTCGCGTTGCGAATT
1 TTGCGAAATTAAAATTCGTGTTGCGAATT
538263 TGTTGGTCAT
Statistics
Matches: 206, Mismatches: 46, Indels: 42
0.70 0.16 0.14
Matches are distributed among these distances:
38 4 0.02
39 4 0.02
40 106 0.51
41 54 0.26
42 31 0.15
43 7 0.03
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (40 bp):
TTGCGAAATTAAAATTCGTGTTGCGAATTAGAAAATCGTG
Found at i:538032 original size:60 final size:60
Alignment explanation
Indices: 537965--538117 Score: 157
Period size: 60 Copynumber: 2.5 Consensus size: 60
537955 AAATTAAAAT
* * *
537965 TCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAACA-AAATTCGTGTTGCG-ATTTAGAAAA
1 TCGTGTTGCGAATTCGAAAATCGTGTTGCGAAAA-AGAAATTCGCGTTGCGAATTCAG-AAA
* *** * *
538025 TCTTGTTGCGAAAAGGAAACTTGTGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAA
1 TCGTGTTGCGAATTCGAAAATCGTGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAA
* * *
538085 TCGAGTTGCGAATTTGAAATTCCGTGTTGCGAA
1 TCGTGTTGCGAATTCGAAAAT-CGTGTTGCGAA
538118 TTTGGAAATC
Statistics
Matches: 74, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
59 1 0.01
60 58 0.78
61 15 0.20
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (60 bp):
TCGTGTTGCGAATTCGAAAATCGTGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAA
Found at i:538126 original size:41 final size:40
Alignment explanation
Indices: 538060--538157 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 40
538050 TTGCGAAAAA
*
538060 GAAATTCGCGTTGCGAATTCAGAAATCGAGTTGCGAATTT
1 GAAATTCGCGTTGCGAATTCAGAAATCAAGTTGCGAATTT
* **
538100 GAAATTCCGTGTTGCGAATTTGGAAATCAAGTTGCGAATTT
1 GAAATT-CGCGTTGCGAATTCAGAAATCAAGTTGCGAATTT
*
538141 GGAAAATCGCGTTGCGA
1 -GAAATTCGCGTTGCGA
538158 GAAAGAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
40 6 0.12
41 39 0.78
42 5 0.10
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (40 bp):
GAAATTCGCGTTGCGAATTCAGAAATCAAGTTGCGAATTT
Found at i:538135 original size:20 final size:20
Alignment explanation
Indices: 538069--538264 Score: 109
Period size: 20 Copynumber: 9.6 Consensus size: 20
538059 AGAAATTCGC
**
538069 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATTTGGAAATCGA
*
538089 GTTGCGAATTT-GAAATTCCGT
1 GTTGCGAATTTGGAAA-T-CGA
*
538110 GTTGCGAATTTGGAAATCAA
1 GTTGCGAATTTGGAAATCGA
*
538130 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAATTTGG-AAATCGA
** *
538151 GTTGCGAGA--AAGAAATTCGC
1 GTTGCGA-ATTTGGAAA-TCGA
538171 GTTGC-AA-TTGCAGAAA-CTGA
1 GTTGCGAATTTG--GAAATC-GA
* *
538191 GTTGCGAATCTGGGAAATTCGT
1 GTTGCGAAT-TTGGAAA-TCGA
*
538213 GTTGCGAATTTGGAAA-CTGT
1 GTTGCGAATTTGGAAATC-GA
* ** *
538233 GTTGCGAAATTGGAGTTCGC
1 GTTGCGAATTTGGAAATCGA
538253 GTTGCGAATTTG
1 GTTGCGAATTTG
538265 TTGGTCATTT
Statistics
Matches: 140, Mismatches: 19, Indels: 34
0.73 0.10 0.18
Matches are distributed among these distances:
18 1 0.01
19 10 0.07
20 68 0.49
21 43 0.31
22 15 0.11
23 3 0.02
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (20 bp):
GTTGCGAATTTGGAAATCGA
Found at i:538216 original size:22 final size:20
Alignment explanation
Indices: 538183--538245 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
538173 TGCAATTGCA
*
538183 GAAACTGAGTTGCGAATCTGG
1 GAAACTGTGTTGCGAAT-TGG
* *
538204 GAAATTCGTGTTGCGAATTTG
1 GAAACT-GTGTTGCGAATTGG
538225 GAAACTGTGTTGCGAAATTGG
1 GAAACTGTGTTGCG-AATTGG
538246 AGTTCGCGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.23
21 17 0.49
22 10 0.29
ACGTcount: A:0.27, C:0.11, G:0.32, T:0.30
Consensus pattern (20 bp):
GAAACTGTGTTGCGAATTGG
Found at i:538253 original size:102 final size:102
Alignment explanation
Indices: 537961--538260 Score: 303
Period size: 102 Copynumber: 3.0 Consensus size: 102
537951 TGCGAAATTA
* **** *
537961 AAATTCGTGTTGCGAATTC-GAAAATCGAGTTGCGAAAACAAAATT-CGTGTTGCG-ATTTAGAA
1 AAATTCGCGTTGCGAATTCAG-AAATCGAGTTGCGAATTGGAAATTCCGTGTTGCGAATTT-GGA
** * * * *
538023 AATCTTGTTGCGAAA-AGGAAACTTGTGTTGCGAAAAAG
64 AATCAAGTTGCGAAATTGGAAAATCGCGTTGCGAAAAAG
*
538061 AAATTCGCGTTGCGAATTCAGAAATCGAGTTGCGAATTTGAAATTCCGTGTTGCGAATTTGGAAA
1 AAATTCGCGTTGCGAATTCAGAAATCGAGTTGCGAATTGGAAATTCCGTGTTGCGAATTTGGAAA
* *
538126 TCAAGTTGCGAATTTGGAAAATCGCGTTGCGAGAAAG
66 TCAAGTTGCGAAATTGGAAAATCGCGTTGCGAAAAAG
538163 AAATTCGCGTTGC-AATTGCAGAAA-CTGAGTTGCGAATCTGGGAAATT-CGTGTTGCGAATTTG
1 AAATTCGCGTTGCGAATT-CAGAAATC-GAGTTGCGAAT-T-GGAAATTCCGTGTTGCGAATTTG
** **
538225 GAAA-CTGTGTTGCGAAATTGG-AGTTCGCGTTGCGAA
62 GAAATC-AAGTTGCGAAATTGGAAAATCGCGTTGCGAA
538261 TTTGTTGGTC
Statistics
Matches: 170, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
100 38 0.22
101 29 0.17
102 65 0.38
103 32 0.19
104 6 0.04
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (102 bp):
AAATTCGCGTTGCGAATTCAGAAATCGAGTTGCGAATTGGAAATTCCGTGTTGCGAATTTGGAAA
TCAAGTTGCGAAATTGGAAAATCGCGTTGCGAAAAAG
Found at i:551756 original size:21 final size:20
Alignment explanation
Indices: 551730--551785 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
551720 CTTAGTACAG
*
551730 AGGGTATCGGTATTCCTATAA
1 AGGGTATCGGTACTCCTAT-A
*
551751 AGGGTATCGGTACTCGTATA
1 AGGGTATCGGTACTCCTATA
*
551771 AGGAGTATCAGTACT
1 AGG-GTATCGGTACT
551786 ACCTTTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (20 bp):
AGGGTATCGGTACTCCTATA
Found at i:558353 original size:48 final size:49
Alignment explanation
Indices: 558274--558367 Score: 111
Period size: 48 Copynumber: 1.9 Consensus size: 49
558264 GTTATTTTCC
* ** *
558274 AGTTCGGGTCAATATCGGATCGGTTG-CTTTTTGGATCAGGTCAATATCG
1 AGTTCGGGTCAATATCAGATCAATTGATTTTTTGG-TCAGGTCAATATCG
* *
558323 AGTT-GGGTTAATATCAGATCAATTGATTTTTTGGTCGGGTCAATA
1 AGTTCGGGTCAATATCAGATCAATTGATTTTTTGGTCAGGTCAATA
558368 CAGGATCGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
48 27 0.71
49 11 0.29
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (49 bp):
AGTTCGGGTCAATATCAGATCAATTGATTTTTTGGTCAGGTCAATATCG
Found at i:558392 original size:32 final size:31
Alignment explanation
Indices: 558327--558416 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 31
558317 ATATCGAGTT
* * * *
558327 GGGTTAATATCAGATCAATTGATTTTTTGGTC
1 GGGTCAATATCGGATCGATTGA-TTTTGGGTC
558359 GGGTCAATA-CAGGATCGATTAGATTTTGGGTC
1 GGGTCAATATC-GGATCGATT-GATTTTGGGTC
*
558391 GGGTCAATATCGGATCGGTTGATTTT
1 GGGTCAATATCGGATCGATTGATTTT
558417 CGGTTTAGGT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
31 7 0.14
32 40 0.80
33 3 0.06
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.38
Consensus pattern (31 bp):
GGGTCAATATCGGATCGATTGATTTTGGGTC
Found at i:559211 original size:16 final size:16
Alignment explanation
Indices: 559128--559249 Score: 66
Period size: 16 Copynumber: 7.6 Consensus size: 16
559118 TTTCGGGTTT
* *
559128 GGTTAAATTCAGTTCG
1 GGTTAATTTCGGTTCG
* * * *
559144 AGTTACTTTTGGATCG
1 GGTTAATTTCGGTTCG
559160 GGTTAAAATTT-GGTTCG
1 GGTT--AATTTCGGTTCG
** * *
559177 GGTTGCTTTCAGCTCG
1 GGTTAATTTCGGTTCG
*
559193 GGTTAATTTCGGTTTG
1 GGTTAATTTCGGTTCG
** **
559209 GGTTGTTTTTTGTTCG
1 GGTTAATTTCGGTTCG
*
559225 GGTTAATTTCGGTTCT
1 GGTTAATTTCGGTTCG
*
559241 GGTTGATTT
1 GGTTAATTT
559250 TTATTTCGCT
Statistics
Matches: 74, Mismatches: 29, Indels: 6
0.68 0.27 0.06
Matches are distributed among these distances:
15 3 0.04
16 58 0.78
17 9 0.12
18 4 0.05
ACGTcount: A:0.14, C:0.11, G:0.29, T:0.47
Consensus pattern (16 bp):
GGTTAATTTCGGTTCG
Found at i:559226 original size:32 final size:32
Alignment explanation
Indices: 559190--559251 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
559180 TGCTTTCAGC
*
559190 TCGGGTTAATTTCGGTT-TGGGTTGTTTTTTGT
1 TCGGGTTAATTTCGGTTCT-GGTTGATTTTTGT
559222 TCGGGTTAATTTCGGTTCTGGTTGATTTTT
1 TCGGGTTAATTTCGGTTCTGGTTGATTTTT
559252 ATTTCGCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.08, C:0.08, G:0.29, T:0.55
Consensus pattern (32 bp):
TCGGGTTAATTTCGGTTCTGGTTGATTTTTGT
Found at i:559539 original size:20 final size:20
Alignment explanation
Indices: 559468--559541 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 20
559458 ATTAAATAAT
559468 TATTTATATATATTTATAAAAA
1 TATTTATA-ATA-TTATAAAAA
*
559490 T-TTATATTAAATTATTCTAAAAGTA
1 TATT-TA-T-AA-TATTATAAAA--A
559515 TATTTATAATATTATAAAAA
1 TATTTATAATATTATAAAAA
559535 TATTTAT
1 TATTTAT
559542 TTAATTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
20 8 0.19
21 2 0.05
22 12 0.28
23 11 0.26
24 4 0.09
25 4 0.09
26 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (20 bp):
TATTTATAATATTATAAAAA
Found at i:559574 original size:19 final size:19
Alignment explanation
Indices: 559552--559607 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 19
559542 TTAATTTTTA
559552 AAATCATATTATTTATTTG
1 AAATCATATTATTTATTTG
559571 AAATGACATTGATTATTTATTTG
1 AAAT--CA-T-ATTATTTATTTG
*
559594 AAATAATATTATTT
1 AAATCATATTATTT
559608 TTAAATTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 11 0.34
20 1 0.03
21 3 0.09
22 1 0.03
23 16 0.50
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (19 bp):
AAATCATATTATTTATTTG
Found at i:559635 original size:18 final size:18
Alignment explanation
Indices: 559584--559637 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
559574 TGACATTGAT
*
559584 TATTT-ATTTGAAATA-A
1 TATTTAATTTTAAATATA
*
559600 TA-TTATTTTTAAATTATA
1 TATTTAATTTTAAA-TATA
559618 TATTTAATTTTAAATATA
1 TATTTAATTTTAAATATA
559636 TA
1 TA
559638 CATAGCTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 2 0.06
16 8 0.26
17 2 0.06
18 9 0.29
19 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TATTTAATTTTAAATATA
Found at i:561554 original size:2 final size:2
Alignment explanation
Indices: 561547--561698 Score: 142
Period size: 2 Copynumber: 80.5 Consensus size: 2
561537 TCCAATGATG
*
561547 CT CT CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
561589 CT CT CT CT C- CC CT CT CT CT C- CT CT CT C- CT CT C- CT C- CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * * * *
561626 CC CT C- CT CT CT C- CT C- CC CT CT CT CT CT CC CT CC CC CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
561665 CT CC CT CT CT C- CT CT CT CC CT CT CT CC CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
561699 CTC
Statistics
Matches: 125, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
1 9 0.07
2 116 0.93
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (2 bp):
CT
Done.