Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006565.1 Hibiscus syriacus cultivar Beakdansim tig00016066_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: 1014065
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:287509 original size:23 final size:23
Alignment explanation
Indices: 287459--287503 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
287449 TGCCTATTTT
* *
287459 ATTATATAAGCGCTACCTATTAC
1 ATTATAAAAGCGCTACCTAATAC
*
287482 ATTATAAAAGCGCTGCCTAATA
1 ATTATAAAAGCGCTACCTAATA
287504 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (23 bp):
ATTATAAAAGCGCTACCTAATAC
Found at i:289683 original size:54 final size:54
Alignment explanation
Indices: 289598--289933 Score: 455
Period size: 54 Copynumber: 6.2 Consensus size: 54
289588 CCATGTGTAC
* * *
289598 TATAGTCACTAAGTTTGCAACCCAC-AGAATTCATCATATGTTGATGAACAACAG
1 TATAGGCACTAAGTGTGCAAACCACGA-AATTCATCATATGTTGATGAACAACAG
* *
289652 TATAGGCACTAAGTGTGCAAACCAC-ATAATTCATCATATGTTGATGAATAACCG
1 TATAGGCACTAAGTGTGCAAACCACGA-AATTCATCATATGTTGATGAACAACAG
* *
289706 TATAGGCACTAAGTGTGGAAACCACGAAATTCATCATATGTTGATAAACAACTA-
1 TATAGGCACTAAGTGTGCAAACCACGAAATTCATCATATGTTGATGAACAAC-AG
* * *
289760 TATAGGTACTAAGTGTACAAACCACGAAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAAACCACGAAATTCATCATATGTTGATGAACAACAG
* * * *
289814 TATAGGCACTAAGAGTGCAGACCAACGGAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAAACC-ACGAAATTCATCATATGTTGATGAACAACAG
* *
289869 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGACGAACAACTA-
1 TATAGGCACTAAGTGTGCAAACCACGAAATTCATCATATGTTGATGAACAAC-AG
289923 TATAGGCACTA
1 TATAGGCACTA
289934 TACCACAGAA
Statistics
Matches: 251, Mismatches: 26, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
54 200 0.80
55 51 0.20
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAAACCACGAAATTCATCATATGTTGATGAACAACAG
Found at i:295703 original size:54 final size:53
Alignment explanation
Indices: 295642--295985 Score: 377
Period size: 54 Copynumber: 6.4 Consensus size: 53
295632 CTATGTGTAC
* *
295642 TATAGGCACTAAGTGTGCAACCCATGAAATTCATTATATATTGATGAACAACTG
1 TATAGGCACTAAGTGTGCAACCCA-GAAATTCATCATATATTGATGAACAACCG
* * * * *
295696 TATAGGCACTAAGTGTGGAAACCACATAATTCATCATATATTGATGAATAATCG
1 TATAGGCACTAAGTGTGCAACCCAGA-AATTCATCATATATTGATGAACAACCG
* *
295750 TATAGGCACTAAGTGTGCAAACCACAG-AATTCATCATATGTTGATGAACCACCG
1 TATAGGCACTAAGTGTGC-AACC-CAGAAATTCATCATATATTGATGAACAACCG
* * * * * *
295804 TATAGGTACTGAGTGTGCAACCAAGGAATTCATCATATGTTGATGAACAATCG
1 TATAGGCACTAAGTGTGCAACCCAGAAATTCATCATATATTGATGAACAACCG
* * * * *
295857 TATAGGCACTAAGTGTGTAAACCCACAAAATTAATAATATATTGATGAGCAACCG
1 TATAGGCACTAAGTGTG-CAACCCA-GAAATTCATCATATATTGATGAACAACCG
* * * *
295912 TATAGGAACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCA
1 TATAGGCACTAAGTGTGCAACCCAGA-AATTCATCATATATTGATGAACAACCG
*
295966 TATATGCACTATA-TGTGCAA
1 TATAGGCACTA-AGTGTGCAA
295986 AGCACATAAT
Statistics
Matches: 242, Mismatches: 40, Indels: 16
0.81 0.13 0.05
Matches are distributed among these distances:
52 2 0.01
53 46 0.19
54 150 0.62
55 42 0.17
56 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (53 bp):
TATAGGCACTAAGTGTGCAACCCAGAAATTCATCATATATTGATGAACAACCG
Found at i:295925 original size:162 final size:162
Alignment explanation
Indices: 295642--295985 Score: 478
Period size: 162 Copynumber: 2.1 Consensus size: 162
295632 CTATGTGTAC
* *
295642 TATAGGCACTAAGTGTGCAACCCATGAAATTCATTATATATTGATGAACAACTGTATAGGCACTA
1 TATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATATTGATGAACAACTGTATAGGCACTA
* * * * * *
295707 AGTGTGGAAACCACATAATTCATCATATATTGATGAATAATCGTATAGGCACTAAGTGTGCAAAC
66 AGTGTGGAAACCACAAAATTAATAATATATTGATGAACAACCGTATAGGAACTAAGTGTGCAAAC
* *
295772 CACAGAATTCATCATATGTTGATGAACCACCG
131 CACAGAATTCATCATATGTTGATGAACAACCA
* * * *
295804 TATAGGTACTGAGTGTGCAA-CCAAGGAATTCATCATATGTTGATGAACAA-TCGTATAGGCACT
1 TATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATATTGATGAACAACT-GTATAGGCACT
* *
295867 AAGTGTGTAAACCCACAAAATTAATAATATATTGATGAGCAACCGTATAGGAACTAAGTGTGCAA
65 AAGTGTGGAAA-CCACAAAATTAATAATATATTGATGAACAACCGTATAGGAACTAAGTGTGCAA
*
295932 CCCACAGAATTCATCATATGTTGATGAACAACCA
129 ACCACAGAATTCATCATATGTTGATGAACAACCA
*
295966 TATATGCACTATA-TGTGCAA
1 TATAGGCACTA-AGTGTGCAA
295986 AGCACATAAT
Statistics
Matches: 159, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
160 1 0.01
161 47 0.30
162 110 0.69
163 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (162 bp):
TATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATATTGATGAACAACTGTATAGGCACTA
AGTGTGGAAACCACAAAATTAATAATATATTGATGAACAACCGTATAGGAACTAAGTGTGCAAAC
CACAGAATTCATCATATGTTGATGAACAACCA
Found at i:301603 original size:16 final size:16
Alignment explanation
Indices: 301584--301616 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
301574 TTTTTTAATA
301584 TATTT-TAATCATTATT
1 TATTTGTAAT-ATTATT
301600 TATTTGTAATATTATT
1 TATTTGTAATATTATT
301616 T
1 T
301617 TGTTATTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (16 bp):
TATTTGTAATATTATT
Found at i:310364 original size:75 final size:75
Alignment explanation
Indices: 310241--310405 Score: 233
Period size: 75 Copynumber: 2.2 Consensus size: 75
310231 AATGATGGAA
* * * * *
310241 CATGCTGAAAGCTCATTTTATTCATGATCAGGAATGTTGACACATTTTGAACGTTTGTATTAGCT
1 CATGCTGAAAGCCCATTTCAATCATGATCAAGAATGTTGACACATTTTGAACGTTTGTATTAGCC
310306 AATGTCGGGG
66 AATGTCGGGG
* *
310316 CATGCTGAAAGCCCCTTTCAATCA-GAATCAAGAATGTTGACACATTTTGAATGTTTGTATTAGC
1 CATGCTGAAAGCCCATTTCAATCATG-ATCAAGAATGTTGACACATTTTGAACGTTTGTATTAGC
*
310380 CAATGTTGGGG
65 CAATGTCGGGG
*
310391 CATGCTGAAGGCCCA
1 CATGCTGAAAGCCCA
310406 CATCGTCATA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
74 1 0.01
75 78 0.99
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (75 bp):
CATGCTGAAAGCCCATTTCAATCATGATCAAGAATGTTGACACATTTTGAACGTTTGTATTAGCC
AATGTCGGGG
Found at i:312525 original size:46 final size:46
Alignment explanation
Indices: 312457--312811 Score: 541
Period size: 46 Copynumber: 7.7 Consensus size: 46
312447 CTATTTCCTA
*
312457 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* *
312503 CATCTGTAAGCCCTTCAATGCTTGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * * *
312548 CATCTGTAAGCTCTTCAATGCTTGATGTTTTCAAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* *
312594 CATCTGTAAGACCTTCAGTGCATGATGTTTTGAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * *
312640 CATCTGTAAGTCCTTCAGTGCATGATATTTTCAAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * *
312686 CATCTGTAAGTCCTTTAATGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * *
312732 CATCTGTAAGTCTTTCAGTGCATGATGTTTTCAAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
312778 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
312812 TATTTCCATC
Statistics
Matches: 285, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 44 0.15
46 241 0.85
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (46 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
Found at i:312957 original size:15 final size:15
Alignment explanation
Indices: 312939--312971 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
312929 CATTTTAAAT
*
312939 TTAAATTTATTATTA
1 TTAAAATTATTATTA
312954 TTAAAATTATTATTA
1 TTAAAATTATTATTA
312969 TTA
1 TTA
312972 TTAAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAAATTATTATTA
Found at i:314522 original size:22 final size:24
Alignment explanation
Indices: 314481--314527 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
314471 ATTAGTCACA
*
314481 TAAATATATATATTTTTATTTATT
1 TAAATATATATATCTTTATTTATT
314505 TAAATA-ATA-ATCTTTATTTATT
1 TAAATATATATATCTTTATTTATT
314527 T
1 T
314528 TCAATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
23 3 0.14
24 6 0.27
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TAAATATATATATCTTTATTTATT
Found at i:315437 original size:47 final size:47
Alignment explanation
Indices: 315370--315806 Score: 658
Period size: 47 Copynumber: 9.3 Consensus size: 47
315360 TCTTTCAAGT
* *
315370 ATCCGTTCATGCATTTTTAATTATGGCATCCTTTCATGCCTTAATGT
1 ATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGC
** * *
315417 ATCATTTCATGCATTTTTAATTATGCCATCCTTTCATGCCTTAATGC
1 ATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGC
* * * *
315464 ATCTGTTCATTCATTTTTTTAGTTTTGGCATCCTTTAATGCCTTAATGC
1 ATCCGTTCATGCA--TTTTTAGTTATGGCATCCTTTCATGCCTTAATGC
* *
315513 ATCCGTTCGTGTATTTTTAGTTATGGCATCCTTTCATGCCTTAATGC
1 ATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGC
** *
315560 ATCTTTTCATGCATTTTTAGTTATGGCATCTTTTCATGCCTTAATGC
1 ATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGC
*
315607 ATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAATGC
1 ATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGC
*
315654 ATCCGTTCATGCATTTTTAGTTATAGCATCCTTTCATGCCTTAATGC
1 ATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGC
* * *
315701 ATTCGTTCATGCATTTTTAGTTATGACATCCTTTCATACCTTAATGC
1 ATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGC
*
315748 ATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAATGC
1 ATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGC
*
315795 ATCCTTTCATGC
1 ATCCGTTCATGC
315807 CTTAATGCAT
Statistics
Matches: 352, Mismatches: 36, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
47 313 0.89
49 39 0.11
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.45
Consensus pattern (47 bp):
ATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGC
Found at i:315567 original size:20 final size:20
Alignment explanation
Indices: 315538--315609 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 20
315528 TTTAGTTATG
*
315538 GCATCCTTTCATGCCTTAAT
1 GCATCTTTTCATGCCTTAAT
*
315558 GCATCTTTTCATGCATTTTTAGTTAT
1 GCATCTTTTCATGC---CTTA---AT
315584 GGCATCTTTTCATGCCTTAAT
1 -GCATCTTTTCATGCCTTAAT
315605 GCATC
1 GCATC
315610 CGTTCATGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
20 18 0.43
21 2 0.05
23 3 0.07
24 3 0.07
26 2 0.05
27 14 0.33
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.44
Consensus pattern (20 bp):
GCATCTTTTCATGCCTTAAT
Found at i:315757 original size:114 final size:112
Alignment explanation
Indices: 315679--315918 Score: 381
Period size: 114 Copynumber: 2.1 Consensus size: 112
315669 TTTAGTTATA
*
315679 GCATCCTTTCATGCCTTAATGCATTCGTTCATGCATTTTTAGTTATGACATCCTTTCATACCTTA
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCCTTTCATACCTTA
*
315744 ATGCATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAAT
66 ATGCATCCGTTCATGCATTTTCAGTTATGGCAT-ATTTCATG-CTTAAT
* * *
315793 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCCTTTCATACCTTA
* *
315858 ATGCATCCTTTCATGCATTTTTAGTTATGGCATACTTTCATGCCTTAAT
66 ATGCATCCGTTCATGCATTTTCAGTTATGGCATA-TTTCATG-CTTAAT
315907 GCATCCTTTCAT
1 GCATCCTTTCAT
315919 TCATTTTTAT
Statistics
Matches: 120, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
113 1 0.01
114 119 0.99
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (112 bp):
GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGACATCCTTTCATACCTTA
ATGCATCCGTTCATGCATTTTCAGTTATGGCATATTTCATGCTTAAT
Found at i:315805 original size:161 final size:161
Alignment explanation
Indices: 315632--315927 Score: 502
Period size: 161 Copynumber: 1.8 Consensus size: 161
315622 TTTAGTTATG
315632 GCATCATTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATAGCATCCTTTCATGCCTTA
1 GCATCATTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATAGCATCCTTTCATGCCTTA
* *
315697 ATGCATTCGTTCATGCATTTTTAGTTATGACATCCTTTCATACCTTAATGCATCCGTTCATGCAT
66 ATGCATCCGTTCATGCATTTTTAGTTATGACATACTTTCATACCTTAATGCATCCGTTCATGCAT
315762 TTTTAGTTATGGCATCATTTCATGCCTTAAT
131 TTTTAGTTATGGCATCATTTCATGCCTTAAT
* * *
315793 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
1 GCATCATTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATAGCATCCTTTCATGCCTTA
* * * * *
315858 ATGCATCCTTTCATGCATTTTTAGTTATGGCATACTTTCATGCCTTAATGCATCCTTTCATTCAT
66 ATGCATCCGTTCATGCATTTTTAGTTATGACATACTTTCATACCTTAATGCATCCGTTCATGCAT
315923 TTTTA
131 TTTTA
315928 TTTAATCCGT
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
161 125 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (161 bp):
GCATCATTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATAGCATCCTTTCATGCCTTA
ATGCATCCGTTCATGCATTTTTAGTTATGACATACTTTCATACCTTAATGCATCCGTTCATGCAT
TTTTAGTTATGGCATCATTTCATGCCTTAAT
Found at i:315844 original size:47 final size:47
Alignment explanation
Indices: 315793--315927 Score: 252
Period size: 47 Copynumber: 2.9 Consensus size: 47
315783 ATGCCTTAAT
315793 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
315840 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
* *
315887 GCATACTTTCATGCCTTAATGCATCCTTTCATTCATTTTTA
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTA
315928 TTTAATCCGT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 86 1.00
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.45
Consensus pattern (47 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
Found at i:315872 original size:67 final size:67
Alignment explanation
Indices: 315727--315873 Score: 267
Period size: 67 Copynumber: 2.2 Consensus size: 67
315717 TTAGTTATGA
*
315727 CATCCTTTCATACCTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAA
1 CATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAA
315792 TG
66 TG
* *
315794 CATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAA
1 CATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAA
315859 TG
66 TG
315861 CATCCTTTCATGC
1 CATCCTTTCATGC
315874 ATTTTTAGTT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 77 1.00
ACGTcount: A:0.20, C:0.26, G:0.12, T:0.42
Consensus pattern (67 bp):
CATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAA
TG
Found at i:318636 original size:32 final size:32
Alignment explanation
Indices: 318595--318659 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
318585 AACACTTTCT
318595 TTCTTTCCATCTCATTTCATACCCGTTGAAGG
1 TTCTTTCCATCTCATTTCATACCCGTTGAAGG
318627 TTCTTTCCATCTCATTTCATACCCGTTGAAGG
1 TTCTTTCCATCTCATTTCATACCCGTTGAAGG
318659 T
1 T
318660 ACCTAGAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.28, G:0.12, T:0.42
Consensus pattern (32 bp):
TTCTTTCCATCTCATTTCATACCCGTTGAAGG
Found at i:328411 original size:63 final size:63
Alignment explanation
Indices: 328312--328437 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
328302 TTGCTAAAAG
328312 GGGTAAACTTCATTTTGGCTCCCTCTGTATTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTATTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
*
328375 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTATTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
328438 TAATTCCCTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (63 bp):
GGGTAAACTTCATTTTGGCTCCCTCTGTATTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
Found at i:328872 original size:236 final size:236
Alignment explanation
Indices: 328605--329076 Score: 887
Period size: 237 Copynumber: 2.0 Consensus size: 236
328595 TAGTTTATAT
328605 ATATATATACATTACCTATTTCCTTTTATTACATGCTATTTTA-T-TATATATATTACTCATA-T
1 ATATATATACATTACCTATTTCCTTTTATTACATGCTATTTTATTATATATATATTACTCATATT
328667 TTTTTTCATTTTCTTTGTTTTTATATTTTTTATTTATGTATATTTTTATTTACCTATCTATTTAT
66 TTTTTTCATTTTCTTTGTTTTTATATTTTTTATTTATGTATATTTTTATTTACCTATCTATTTAT
*
328732 ATTTTTTTCTTTTTTATTTGAATTTTCGTATTTTTCCTTGTAAATTTTATTCGTATTTCATTCTT
131 A-TTTTTT-TTCTTTATTTGAATTTTCGTATTTTTCCTTGTAAATTTTATTCGTATTTCATTCTT
328797 AATTTTTGTGTACATTATACTTTCTTTATTTCGTTTGTTCGCC
194 AATTTTTGTGTACATTATACTTTCTTTATTTCGTTTGTTCGCC
328840 ATATATATACATTACCTATTTTCCTTTTATTACATGCTATTTTATTATATATATATTACTCATAT
1 ATATATATACATTACCTA-TTTCCTTTTATTACATGCTATTTTATTATATATATATTACTCATAT
328905 TTTTTTTCATTTTCTTTGTTTTTATATTTTTTATTTATGTATATTTTTATTTACCTATCTATTTA
65 TTTTTTTCATTTTCTTTGTTTTTATATTTTTTATTTATGTATATTTTTATTTACCTATCTATTTA
328970 TATTTTTTTTCTTTATTTGAATTTTCGTATTTTTCCTTGTAAATTTTATTCGTATTTCATTCTTA
130 TATTTTTTTTCTTTATTTGAATTTTCGTATTTTTCCTTGTAAATTTTATTCGTATTTCATTCTTA
329035 ATTTTTGTGTACATTATACTTTCTTTATTTCGTTTGTTCGCC
195 ATTTTTGTGTACATTATACTTTCTTTATTTCGTTTGTTCGCC
329077 TTATTTTTAT
Statistics
Matches: 232, Mismatches: 1, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
235 18 0.08
236 25 0.11
237 99 0.43
238 23 0.10
239 67 0.29
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.62
Consensus pattern (236 bp):
ATATATATACATTACCTATTTCCTTTTATTACATGCTATTTTATTATATATATATTACTCATATT
TTTTTTCATTTTCTTTGTTTTTATATTTTTTATTTATGTATATTTTTATTTACCTATCTATTTAT
ATTTTTTTTCTTTATTTGAATTTTCGTATTTTTCCTTGTAAATTTTATTCGTATTTCATTCTTAA
TTTTTGTGTACATTATACTTTCTTTATTTCGTTTGTTCGCC
Found at i:339481 original size:6 final size:6
Alignment explanation
Indices: 339467--339501 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
339457 TCCTAAGTTG
339467 AAAAA- AAAAAC AAAAAAC AAAAAC AAAAAC AAAAA
1 AAAAAC AAAAAC -AAAAAC AAAAAC AAAAAC AAAAA
339502 GAGAAGAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.18
6 17 0.61
7 6 0.21
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:340526 original size:105 final size:105
Alignment explanation
Indices: 340343--340953 Score: 974
Period size: 105 Copynumber: 5.9 Consensus size: 105
340333 TTTTACCCAT
*
340343 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
340408 AAGGGACCACTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
340448 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
340513 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
*
340553 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
340618 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
* *
340658 AGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
340723 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATTCAG
* *
340764 AGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
340829 AAGGGACCGCTGGTTGTCAA-TAA-A-----CAATTTC--
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
* ***
340860 --CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
340923 AAGGGACCGCTGGTTCTCAACAAACAATTTC
66 AAGGGACCGCTGGTTGTCAACAAAC-ATTTC
340954 CCAGTCCCAG
Statistics
Matches: 477, Mismatches: 21, Indels: 20
0.92 0.04 0.04
Matches are distributed among these distances:
94 78 0.16
95 2 0.00
97 1 0.00
98 7 0.01
103 1 0.00
105 294 0.62
106 94 0.20
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
Found at i:340927 original size:94 final size:94
Alignment explanation
Indices: 340660--340956 Score: 378
Period size: 94 Copynumber: 3.0 Consensus size: 94
340650 AAATTCAGAG
* * * * *
340660 CCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAA
1 CCAATTTCAACGTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAA
*
340725 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 GGGACCGCTGGTTCTCAAC--A-AA-----CAATTTC
*
340762 AGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 ----CCAATTTCAACGTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGA
* *
340827 CGAAGGGACCGCTGGTTGTCAATAAACAATTTC
62 CGAAGGGACCGCTGGTTCTCAACAAACAATTTC
* **
340860 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACGTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAA
340925 GGGACCGCTGGTTCTCAACAAACAATTTC
66 GGGACCGCTGGTTCTCAACAAACAATTTC
340954 CCA
1 CCA
340957 GTCCCAGAAT
Statistics
Matches: 180, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
94 91 0.51
98 7 0.04
103 2 0.01
104 1 0.01
106 79 0.44
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (94 bp):
CCAATTTCAACGTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTCTCAACAAACAATTTC
Found at i:342578 original size:63 final size:62
Alignment explanation
Indices: 342468--342592 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 62
342458 TTGCTAAAAG
342468 GGGTAAACTTCATTTTGGCTCCTCTGTATTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCTCTGTATTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
*
342530 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCT-CCTCTGTATTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
342593 TAATTCCCTT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 20 0.33
63 41 0.67
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (62 bp):
GGGTAAACTTCATTTTGGCTCCTCTGTATTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
Found at i:343027 original size:238 final size:235
Alignment explanation
Indices: 342762--343234 Score: 910
Period size: 238 Copynumber: 2.0 Consensus size: 235
342752 TAGTTTATAT
342762 ATATATATACATTACCTATTTTCCTTTTATTACATGCTATTTTATTATATATATATTACTCATAT
1 ATATATATACATTACCTATTTTCCTTTTATTACATGCTATTTTATTATATATATATTACTCATAT
342827 TTTTTTCATTTTCTTTGTTTTTATATTTTTTATTTATGTATATTTTTATTTACCTATCTATTTAT
66 TTTTTTCATTTTCTTTGTTTTTATATTTTTTATTTATGTATATTTTTATTTACCTATCTATTTAT
342892 ATTTTTTTCTTTTTTATTTGAATTTTCGTATTTTTCCTTGTAAATTTTATTCGTATTTCATTCTT
131 ATTTTTTTC---TTTATTTGAATTTTCGTATTTTTCCTTGTAAATTTTATTCGTATTTCATTCTT
*
342957 AATTTTTTTGTACATTATACTTTCTTTATTTCGTTTGTTCGCC
193 AATTTTTGTGTACATTATACTTTCTTTATTTCGTTTGTTCGCC
343000 ATATATATACATTACCTATTTTCCTTTTATTACATGCTATTTTATTATATATATATTACTCATAT
1 ATATATATACATTACCTATTTTCCTTTTATTACATGCTATTTTATTATATATATATTACTCATAT
343065 TTTTTTCATTTTCTTTGTTTTTATATTTTTTATTTATGTATATTTTTATTTACCTATCTATTTAT
66 TTTTTTCATTTTCTTTGTTTTTATATTTTTTATTTATGTATATTTTTATTTACCTATCTATTTAT
343130 ATTTTTTTCTTTATTTGAATTTTCGTATTTTTCCTTGTAAATTTTATTCGTATTTCATTCTTAAT
131 ATTTTTTTCTTTATTTGAATTTTCGTATTTTTCCTTGTAAATTTTATTCGTATTTCATTCTTAAT
343195 TTTTGTGTACATTATACTTTCTTTATTTCGTTTGTTCGCC
196 TTTTGTGTACATTATACTTTCTTTATTTCGTTTGTTCGCC
343235 TTATTTTTAT
Statistics
Matches: 234, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
235 95 0.41
238 139 0.59
ACGTcount: A:0.22, C:0.12, G:0.05, T:0.62
Consensus pattern (235 bp):
ATATATATACATTACCTATTTTCCTTTTATTACATGCTATTTTATTATATATATATTACTCATAT
TTTTTTCATTTTCTTTGTTTTTATATTTTTTATTTATGTATATTTTTATTTACCTATCTATTTAT
ATTTTTTTCTTTATTTGAATTTTCGTATTTTTCCTTGTAAATTTTATTCGTATTTCATTCTTAAT
TTTTGTGTACATTATACTTTCTTTATTTCGTTTGTTCGCC
Found at i:344918 original size:23 final size:23
Alignment explanation
Indices: 344892--344935 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
344882 AGTGGCATAA
* *
344892 TTACAGTTAAACATAATCATCTT
1 TTACAGCTAAACATAAACATCTT
344915 TTACAGCTAAACATAAACATC
1 TTACAGCTAAACATAAACATC
344936 AGTGTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (23 bp):
TTACAGCTAAACATAAACATCTT
Found at i:348427 original size:22 final size:22
Alignment explanation
Indices: 348397--348442 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
348387 CTTTGATTAA
*
348397 ACGTTGACTTTGACCAGAATTG
1 ACGTCGACTTTGACCAGAATTG
* *
348419 ACGTCGACTTTGACTAGCATTG
1 ACGTCGACTTTGACCAGAATTG
348441 AC
1 AC
348443 TTTGACCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (22 bp):
ACGTCGACTTTGACCAGAATTG
Found at i:350868 original size:16 final size:16
Alignment explanation
Indices: 350847--350880 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
350837 TTTCACTGTC
350847 AAATAAATTTATCCTT
1 AAATAAATTTATCCTT
350863 AAATAAATTTATCCTT
1 AAATAAATTTATCCTT
350879 AA
1 AA
350881 TCTCATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATAAATTTATCCTT
Found at i:351712 original size:24 final size:24
Alignment explanation
Indices: 351655--351712 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
351645 TAGCATTTTA
*
351655 AAAAATAAA-ACTTAAAATAAAAT
1 AAAAATAAAGACTTAAAAGAAAAT
* *
351678 AAAAATGAAGACTTGAAAAGAGAAT
1 AAAAATAAAGACTT-AAAAGAAAAT
351703 -AAAATAAAGA
1 AAAAATAAAGA
351713 ACTTTATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 8 0.28
24 13 0.45
25 8 0.28
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.17
Consensus pattern (24 bp):
AAAAATAAAGACTTAAAAGAAAAT
Found at i:358114 original size:25 final size:25
Alignment explanation
Indices: 358078--358132 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
358068 TAGCATTTTT
*
358078 TAAAAAATAAAACTT-AATATAAAA
1 TAAAAAATAAAACTTGAAAATAAAA
358102 TAAAAAATGAAAACTTGAAAATAAAA
1 TAAAAAAT-AAAACTTGAAAATAAAA
*
358128 GAAAA
1 TAAAA
358133 GAAAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 8 0.30
25 7 0.26
26 12 0.44
ACGTcount: A:0.71, C:0.04, G:0.05, T:0.20
Consensus pattern (25 bp):
TAAAAAATAAAACTTGAAAATAAAA
Found at i:364438 original size:24 final size:24
Alignment explanation
Indices: 364405--364461 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
364395 TAGCATTTTA
*
364405 AAAAATAAAACTT-AAAATAAAAT
1 AAAAATAAAACTTGAAAAGAAAAT
364428 AAAAATGAAAACTTGAAAAGAAAAT
1 AAAAAT-AAAACTTGAAAAGAAAAT
364453 -AAAATAAAA
1 AAAAATAAAA
364462 GAAAGAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 10 0.32
24 12 0.39
25 9 0.29
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.18
Consensus pattern (24 bp):
AAAAATAAAACTTGAAAAGAAAAT
Found at i:370984 original size:24 final size:24
Alignment explanation
Indices: 370951--371002 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
370941 TAGCATTTTA
* *
370951 AAAAATAAAACTT-AAAATAAAAT
1 AAAAATAAAACTTGAAAAGAAAAG
370974 AAAAATGAAAACTTGAAAAGAAAAG
1 AAAAAT-AAAACTTGAAAAGAAAAG
370999 AAAA
1 AAAA
371003 GAAAAGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.24
24 7 0.28
25 12 0.48
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (24 bp):
AAAAATAAAACTTGAAAAGAAAAG
Found at i:377499 original size:12 final size:12
Alignment explanation
Indices: 377482--377523 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
377472 ACTTAGCATT
377482 TTAAAATAAAAC
1 TTAAAATAAAAC
377494 TTAAAATAAAA-
1 TTAAAATAAAAC
377505 -TAAAATGAAAAC
1 TTAAAAT-AAAAC
377517 TTGAAAA
1 TT-AAAA
377524 GAGAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 6 0.23
11 4 0.15
12 11 0.42
13 1 0.04
14 4 0.15
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (12 bp):
TTAAAATAAAAC
Found at i:377532 original size:23 final size:22
Alignment explanation
Indices: 377483--377534 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
377473 CTTAGCATTT
*
377483 TAAAATAAAACTTAAAATAAAA
1 TAAAATAAAACTTAAAAGAAAA
377505 TAAAATGAAAACTTGAAAAGAGAAA
1 TAAAAT-AAAACTT-AAAAGA-AAA
*
377530 AAAAA
1 TAAAA
377535 AGAACCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
23 7 0.28
24 5 0.20
25 7 0.28
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.17
Consensus pattern (22 bp):
TAAAATAAAACTTAAAAGAAAA
Found at i:381495 original size:34 final size:35
Alignment explanation
Indices: 381455--381534 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
381445 CAACATAGTC
* *
381455 ATCAATTACATT-TAAACCCCAAAATCCAAAATGCT
1 ATCAATTACATTCTAAACCCCAAAATCAAAAAT-AT
* * *
381490 -TCAATTATATTCTAAACCTCAAATTCAAAAATAT
1 ATCAATTACATTCTAAACCCCAAAATCAAAAATAT
381524 ATCAATTACAT
1 ATCAATTACAT
381535 GCCCAACCCC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
34 11 0.30
35 26 0.70
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.31
Consensus pattern (35 bp):
ATCAATTACATTCTAAACCCCAAAATCAAAAATAT
Found at i:381961 original size:153 final size:146
Alignment explanation
Indices: 381704--381999 Score: 457
Period size: 153 Copynumber: 2.0 Consensus size: 146
381694 AAATACTCAA
* * *
381704 TTCAATTTATAAAATAGTTGATTCGGAATTTTTTCTATTTGAGTTTAAAATTTAAATCAAGTCGA
1 TTCAATTTATAAAATAGTTGACTCGAAATTTTTTCTACTTGAGTTTAAAATTTAAATCAAGTCGA
* *
381769 ATTGAATTGAATTTTTGAGTTTATGTTTAAATTTAATTATAAATATTTATCATATTATAATATTA
66 ATTGAATTGAATTTTTGAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATATTA
*
381834 TTAGATTTTAATTCAG
131 TTAGATTCTAATTCAG
381850 TTCAATTTATAAAATAGTTGACTCGAAATTTTTTCTACTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAATTTATAAAATAGTTGACTCGAAATTTTTTCTACTTGAG-TT-TAAAATTTAAATCAAGTC
*
381915 AAATTGAATTGAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTAT
64 -----GAATTGAATTGAATTTTTGAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTAT
*
381980 AATATTATTTGATTCTAATT
124 AATATTATTAGATTCTAATT
382000 TAAATTGTTT
Statistics
Matches: 135, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
146 40 0.30
147 2 0.01
148 18 0.13
153 75 0.56
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (146 bp):
TTCAATTTATAAAATAGTTGACTCGAAATTTTTTCTACTTGAGTTTAAAATTTAAATCAAGTCGA
ATTGAATTGAATTTTTGAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATATTA
TTAGATTCTAATTCAG
Found at i:382530 original size:36 final size:35
Alignment explanation
Indices: 382482--382578 Score: 133
Period size: 35 Copynumber: 2.7 Consensus size: 35
382472 AATGAATTAT
*
382482 GAATTTGGGGTTT-GTCATGTAATTGAAGTATTTTTG
1 GAATTTGGGGTTTAG-AATGTAATTGAAGTA-TTTTG
*
382518 GAATTTGAGGTTTAGAATGTAATTGAAGTATTTTG
1 GAATTTGGGGTTTAGAATGTAATTGAAGTATTTTG
* *
382553 GAATTTGGGGTTTATAATATAATTGA
1 GAATTTGGGGTTTAGAATGTAATTGA
382579 TGATTGTGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
35 28 0.51
36 26 0.47
37 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.44
Consensus pattern (35 bp):
GAATTTGGGGTTTAGAATGTAATTGAAGTATTTTG
Found at i:387348 original size:14 final size:15
Alignment explanation
Indices: 387319--387394 Score: 59
Period size: 15 Copynumber: 5.3 Consensus size: 15
387309 AAAATAGTTA
387319 AATAATATATTTTAT
1 AATAATATATTTTAT
387334 AATAATATA-TTTAT
1 AATAATATATTTTAT
* * **
387348 AATTATTTATTAAAT
1 AATAATATATTTTAT
** * *
387363 TTTAA-ATA-ATTAA
1 AATAATATATTTTAT
387376 AATAATATATTTTAT
1 AATAATATATTTTAT
387391 AATA
1 AATA
387395 TTTTACTGTA
Statistics
Matches: 42, Mismatches: 16, Indels: 6
0.66 0.25 0.09
Matches are distributed among these distances:
13 4 0.10
14 17 0.40
15 21 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:395023 original size:23 final size:22
Alignment explanation
Indices: 394990--395050 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
394980 TTCTGCGCTA
*
394990 GGTATCGATACCCCCTTTGCATG
1 GGTATCGATACCCCC-TTGAATG
* *
395013 GGTATCAATACCATCCTTGAATG
1 GGTATCGATACC-CCCTTGAATG
395036 GGTATCGATACCCCC
1 GGTATCGATACCCCC
395051 CATGAGGGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 2 0.06
23 28 0.88
24 2 0.06
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (22 bp):
GGTATCGATACCCCCTTGAATG
Found at i:395549 original size:13 final size:13
Alignment explanation
Indices: 395524--395564 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
395514 TGAAAACTAC
395524 ACATTGATTTTCAA
1 ACATTG-TTTTCAA
395538 ACATTGTTTTCAA
1 ACATTGTTTTCAA
*
395551 ACATAGTTTTCAA
1 ACATTGTTTTCAA
395564 A
1 A
395565 ATTTGCCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
ACATTGTTTTCAA
Found at i:407588 original size:17 final size:16
Alignment explanation
Indices: 407551--407588 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
407541 TTGATGTGAC
407551 ATAA-ATATTAAATAA
1 ATAATATATTAAATAA
407566 ATTAATATATTATAATAA
1 A-TAATATATTA-AATAA
407584 ATAAT
1 ATAAT
407589 CACGTCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.05
16 3 0.15
17 10 0.50
18 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATATATTAAATAA
Found at i:408826 original size:191 final size:191
Alignment explanation
Indices: 408502--408882 Score: 744
Period size: 191 Copynumber: 2.0 Consensus size: 191
408492 CAATGGTGAA
408502 AACCATTACGAAGGTATAACTTCTCACTCTCACTTAAATGAGAAGAGCGATGTTTTAGCTAATTT
1 AACCATTACGAAGGTATAACTTCTCACTCTCACTTAAATGAGAAGAGCGATGTTTTAGCTAATTT
*
408567 CATGATAATGCAAGTGCACAATGTGTGAGGAAAAGCGAAAAACACAATCAAACAACACAAAGCTG
66 CATGATAATGCAAGTGCACAATGTGTGAGGAAAAGCGAAAAACACAATCAAACAACACAAAACTG
408632 AGTTCTCAATTCCCTTAAAATTATTGAATCTAAAAAAATAAAAAACCCAATTATTTAGTAT
131 AGTTCTCAATTCCCTTAAAATTATTGAATCTAAAAAAATAAAAAACCCAATTATTTAGTAT
408693 AACCATTACGAAGGTATAACTTCTCACTCTCACTTAAATGAGAAGAGCGATGTTTTAGCTAATTT
1 AACCATTACGAAGGTATAACTTCTCACTCTCACTTAAATGAGAAGAGCGATGTTTTAGCTAATTT
*
408758 CATGATAATGCAAGTGCACAATGTGTGAGGAAAAGCGAAAAACACAATCAAGCAACACAAAACTG
66 CATGATAATGCAAGTGCACAATGTGTGAGGAAAAGCGAAAAACACAATCAAACAACACAAAACTG
408823 AGTTCTCAATTCCCTTAAAATTATTGAATCTAAAAAAATAAAAAACCCAATTATTTAGTA
131 AGTTCTCAATTCCCTTAAAATTATTGAATCTAAAAAAATAAAAAACCCAATTATTTAGTA
408883 ATTAATCAAA
Statistics
Matches: 188, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
191 188 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.27
Consensus pattern (191 bp):
AACCATTACGAAGGTATAACTTCTCACTCTCACTTAAATGAGAAGAGCGATGTTTTAGCTAATTT
CATGATAATGCAAGTGCACAATGTGTGAGGAAAAGCGAAAAACACAATCAAACAACACAAAACTG
AGTTCTCAATTCCCTTAAAATTATTGAATCTAAAAAAATAAAAAACCCAATTATTTAGTAT
Found at i:412255 original size:10 final size:9
Alignment explanation
Indices: 412224--412257 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
412214 TGTGCATCTA
412224 TTTTAAAAT
1 TTTTAAAAT
412233 TTTTAAAAT
1 TTTTAAAAT
412242 TTTTAAAAT
1 TTTTAAAAT
412251 ATTTTAA
1 -TTTTAA
412258 GGAAAAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:423714 original size:20 final size:22
Alignment explanation
Indices: 423690--423759 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 22
423680 ATATCTAGAG
423690 TTAATTAAATATATT-TTTTAA
1 TTAATTAAATATATTATTTTAA
*
423711 -TAATCCTGAATAT-TTAATTTTAA
1 TTAAT--TAAATATATT-ATTTTAA
*
423734 TTAATTAAATATA-GA-TTTAA
1 TTAATTAAATATATTATTTTAA
423754 TTAATT
1 TTAATT
423760 TGAAATAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
20 15 0.38
21 3 0.08
22 12 0.30
23 6 0.15
24 4 0.10
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (22 bp):
TTAATTAAATATATTATTTTAA
Found at i:426241 original size:18 final size:18
Alignment explanation
Indices: 426218--426294 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
426208 CAACGGTCAA
426218 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
426236 CGGGTCGAGTCAA-----
1 CGGGTCGGGTCAACGGGT
*
426249 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
426267 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
426285 CGGGTCGGGT
1 CGGGTCGGGT
426295 TGTGTTCGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.22
18 39 0.78
ACGTcount: A:0.13, C:0.21, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:426251 original size:31 final size:31
Alignment explanation
Indices: 426213--426290 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
426203 CCGGTCAACG
426213 GTCAACGGGTCGGGTCAACGGGTCGGGTCGA
1 GTCAACGGGTCGGGTCAACGGGTCGGGTCGA
* *
426244 GTCAACGGGTCGGGTAAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTCAACGGGTCGGGTCGA
426275 GTCAACGGGTCGGGTC
1 GTCAACGGGTCGGGTC
426291 GGGTTGTGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.15, C:0.22, G:0.46, T:0.17
Consensus pattern (31 bp):
GTCAACGGGTCGGGTCAACGGGTCGGGTCGA
Found at i:426290 original size:13 final size:13
Alignment explanation
Indices: 426212--426272 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 13
426202 GCCGGTCAAC
426212 GGTCAACGGGTCG
1 GGTCAACGGGTCG
426225 GGTCAACGGGTCGGG
1 GGTCAACGGGTC--G
426240 TCGAGTCAACGGGTCG
1 --G-GTCAACGGGTCG
*
426256 GGTAAACGGGTCG
1 GGTCAACGGGTCG
426269 GGTC
1 GGTC
426273 GGGTCAACGG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 26 0.63
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 11 0.27
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:428463 original size:24 final size:24
Alignment explanation
Indices: 428436--428535 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
428426 GATATAAAAA
*
428436 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
428460 ATCATAACAGAATCCAGATTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* * *
428484 ATCAGAACATATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
428508 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
428532 ATCA
1 ATCA
428536 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:428535 original size:48 final size:48
Alignment explanation
Indices: 428434--428537 Score: 136
Period size: 48 Copynumber: 2.2 Consensus size: 48
428424 GAGATATAAA
* * * *
428434 AAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAGATTAG
1 AAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAAATCAG
* * * *
428482 GAATCAGAACATATTTCAGATCAGATGTCAAAACAGAATTCAAATCAG
1 AAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAAATCAG
428530 AAATCAGA
1 AAATCAGA
428538 TAAAATATTC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.22
Consensus pattern (48 bp):
AAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAAATCAG
Found at i:431017 original size:7 final size:7
Alignment explanation
Indices: 431005--431035 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
430995 GGTCAACGCT
431005 GGTCAAC
1 GGTCAAC
431012 GGTCAAC
1 GGTCAAC
431019 GGGTCAAC
1 -GGTCAAC
431027 GGTCAAC
1 GGTCAAC
431034 GG
1 GG
431036 GTCGGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:431025 original size:8 final size:8
Alignment explanation
Indices: 430995--431051 Score: 61
Period size: 8 Copynumber: 7.5 Consensus size: 8
430985 AGTCAATAGT
430995 GGTCAACG
1 GGTCAACG
431003 CTGGTCAAC-
1 --GGTCAACG
431012 GGTCAACG
1 GGTCAACG
431020 GGTCAAC-
1 GGTCAACG
431027 GGTCAACG
1 GGTCAACG
431035 GGT---CG
1 GGTCAACG
431040 GGTCAACG
1 GGTCAACG
431048 GGTC
1 GGTC
431052 GGGTCGGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 16 0.38
10 7 0.17
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:431025 original size:15 final size:15
Alignment explanation
Indices: 430995--431051 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
430985 AGTCAATAGT
430995 GGTCAACGCTGGTCAAC
1 GGTCAACG--GGTCAAC
431012 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
*
431027 GGTCAACGGGTC--G
1 GGTCAACGGGTCAAC
431040 GGTCAACGGGTC
1 GGTCAACGGGTC
431052 GGGTCGGGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
13 12 0.31
15 19 0.49
17 8 0.21
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:431045 original size:13 final size:13
Alignment explanation
Indices: 431012--431056 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
431002 GCTGGTCAAC
*
431012 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
431027 GGTCAACGGGTCG
1 GGTCAACGGGTCG
431040 GGTCAACGGGTCG
1 GGTCAACGGGTCG
431053 GGTC
1 GGTC
431057 GGGTTGTCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:443430 original size:15 final size:15
Alignment explanation
Indices: 443409--443461 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
443399 CAAAATACTT
443409 AACTTTTGAAAATTA
1 AACTTTTGAAAATTA
* ** **
443424 CACTTTTGGTACCTA
1 AACTTTTGAAAATTA
443439 AACTTTTGAAAATTA
1 AACTTTTGAAAATTA
*
443454 TACTTTTG
1 AACTTTTG
443462 GTACCCAAAC
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (15 bp):
AACTTTTGAAAATTA
Found at i:443445 original size:30 final size:30
Alignment explanation
Indices: 443409--443502 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
443399 CAAAATACTT
443409 AACTTTTGAAAATTACACTTTTGGTACCTA
1 AACTTTTGAAAATTACACTTTTGGTACCTA
* *
443439 AACTTTTGAAAATTATACTTTTGGTACCCA
1 AACTTTTGAAAATTACACTTTTGGTACCTA
* * *
443469 AACATTTGAAAATTATC-CCTTTGGTCCCTA
1 AACTTTTGAAAATTA-CACTTTTGGTACCTA
443499 AACT
1 AACT
443503 GTTCCAAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (30 bp):
AACTTTTGAAAATTACACTTTTGGTACCTA
Found at i:453390 original size:21 final size:21
Alignment explanation
Indices: 453365--453428 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
453355 TTCGTCCTAC
453365 TAGGATTCAAACTCCTAAAAA
1 TAGGATTCAAACTCCTAAAAA
* ** *
453386 TAGGA-T-AAAAT--T-TTAC
1 TAGGATTCAAACTCCTAAAAA
453402 TAGGATTCAAACTCCTAAAAA
1 TAGGATTCAAACTCCTAAAAA
453423 TAGGAT
1 TAGGAT
453429 AGAGTTCTAC
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
16 6 0.20
17 2 0.07
18 4 0.13
19 4 0.13
20 2 0.07
21 12 0.40
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.28
Consensus pattern (21 bp):
TAGGATTCAAACTCCTAAAAA
Found at i:453412 original size:37 final size:37
Alignment explanation
Indices: 453361--453465 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
453351 CCTTTTCGTC
453361 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
453398 TTACTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
453435 CTACTATGATTTAAAATCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
453466 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:453916 original size:10 final size:10
Alignment explanation
Indices: 453903--453953 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
453893 ATACGTATAT
453903 TTTTTATTTA
1 TTTTTATTTA
*
453913 TTTTTATTCA
1 TTTTTATTTA
453923 TTTTTATTTA
1 TTTTTATTTA
**
453933 TTAATA-TTA
1 TTTTTATTTA
453942 TTTATTATTTA
1 TTT-TTATTTA
453953 T
1 T
453954 ATATATATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 5 0.15
10 24 0.73
11 4 0.12
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:453958 original size:2 final size:2
Alignment explanation
Indices: 453951--453983 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
453941 ATTTATTATT
453951 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
453984 TTAAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:453959 original size:20 final size:20
Alignment explanation
Indices: 453900--453986 Score: 72
Period size: 20 Copynumber: 4.3 Consensus size: 20
453890 TATATACGTA
* * *
453900 TATTTTTTATTTATTTTTAT
1 TATTTATTATTTATATATAT
453920 TCATTT-TTATTTAT-TAATAT
1 T-ATTTATTATTTATAT-ATAT
453940 TATTTATTATTTATATATA-
1 TATTTATTATTTATATATAT
* *
453959 TATATATATATATATATATAT
1 TATTTAT-TATTTATATATAT
453980 ATATTTA
1 -TATTTA
453987 AATATTTTAC
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
19 11 0.20
20 35 0.62
21 5 0.09
22 5 0.09
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTATTATTTATATATAT
Found at i:454309 original size:16 final size:16
Alignment explanation
Indices: 454290--454330 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
454280 CATTTATTTA
*
454290 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
454306 TTTATTT-TTTTTACT
1 TTTATTTATTTTTACT
454321 TATT-TTTATT
1 T-TTATTTATT
454331 CTTCAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:458784 original size:29 final size:28
Alignment explanation
Indices: 458752--458816 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
458742 AATCAAGAAC
*
458752 AAAAAAGAAA-AGAAGCAAAAAAACAAAGA
1 AAAAAAGAAACAAAAG--AAAAAACAAAGA
*
458781 AAAAAGAGAAACAAAAGAAAAAAGAAAGA
1 AAAAA-AGAAACAAAAGAAAAAACAAAGA
458810 ATAAAAA
1 A-AAAAA
458817 TCAAAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
29 18 0.58
30 9 0.29
31 4 0.13
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.02
Consensus pattern (28 bp):
AAAAAAGAAACAAAAGAAAAAACAAAGA
Found at i:458792 original size:17 final size:18
Alignment explanation
Indices: 458772--458805 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
458762 AGAAGCAAAA
458772 AAAC-AAAGAAAAAAGAG
1 AAACAAAAGAAAAAAGAG
458789 AAACAAAAGAAAAAAGA
1 AAACAAAAGAAAAAAGA
458806 AAGAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (18 bp):
AAACAAAAGAAAAAAGAG
Found at i:458795 original size:25 final size:26
Alignment explanation
Indices: 458749--458827 Score: 78
Period size: 25 Copynumber: 3.1 Consensus size: 26
458739 TCCAATCAAG
*
458749 AACAAA-AAAGAAAAGAAGCAAAA-A
1 AACAAAGAAAGAAAAGAAACAAAAGA
458773 AACAAAGAAA-AAAGAGAAACAAAAGA
1 AACAAAGAAAGAAA-AGAAACAAAAGA
458799 AA-AAAGAAAGAATAA-AAATCAAAAAGA
1 AACAAAGAAAGAA-AAGAAA-C-AAAAGA
458826 AA
1 AA
458828 AAGGGACAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
24 9 0.19
25 22 0.47
26 7 0.15
27 9 0.19
ACGTcount: A:0.78, C:0.06, G:0.13, T:0.03
Consensus pattern (26 bp):
AACAAAGAAAGAAAAGAAACAAAAGA
Found at i:458802 original size:30 final size:31
Alignment explanation
Indices: 458746--458816 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
458736 AGATCCAATC
*
458746 AAGAACAAAAAAGAAAAGAAGCAAAAAAACA
1 AAGAACAAAAAAGAAAAAAAGCAAAAAAACA
* *
458777 AAGAA-AAAAGAGAAACAAAAG--AAAAAAGA
1 AAGAACAAAAAAGAAA-AAAAGCAAAAAAACA
*
458806 AAGAATAAAAA
1 AAGAACAAAAA
458817 TCAAAAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 12 0.35
30 13 0.38
31 9 0.26
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (31 bp):
AAGAACAAAAAAGAAAAAAAGCAAAAAAACA
Found at i:458816 original size:20 final size:19
Alignment explanation
Indices: 458752--458827 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 19
458742 AATCAAGAAC
458752 AAAAAAGAAAAGAAGCAAA-A
1 AAAAAAGAAAA-AAG-AAAGA
458772 AAACAAAGAAAAAAG--AGA
1 AAA-AAAGAAAAAAGAAAGA
458790 AACAAAAGAAAAAAGAAAGA
1 AA-AAAAGAAAAAAGAAAGA
**
458810 ATAAAAATCAAAAAGAAA
1 A-AAAAAGAAAAAAGAAA
458828 AAGGGACAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
17 1 0.02
18 14 0.29
19 1 0.02
20 23 0.48
21 9 0.19
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (19 bp):
AAAAAAGAAAAAAGAAAGA
Found at i:459686 original size:24 final size:24
Alignment explanation
Indices: 459659--459721 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
459649 GGGACAATAT
459659 TTTCAAAACTTTTAATTAAACATC
1 TTTCAAAACTTTTAATTAAACATC
* *
459683 TTTCAAAACTCTTGATTAAACATC
1 TTTCAAAACTTTTAATTAAACATC
*
459707 TTTCGAAACTCTTTA
1 TTTCAAAACT-TTTA
459722 TTGATATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (24 bp):
TTTCAAAACTTTTAATTAAACATC
Found at i:460399 original size:106 final size:106
Alignment explanation
Indices: 460212--461297 Score: 1635
Period size: 106 Copynumber: 10.3 Consensus size: 106
460202 AATTTGCTCG
* * *
460212 AGAGCCAATTTCAACTTTAC-GACGAAGGATATTGGACTCCAGACCACGCAAGTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
* * * *
460276 ACGAAGGGACCGTTGGTTGTCAAAAAATAATTTCCTAATTTC
65 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
* * * *
460318 AAAGCCAAATTCAACTTCACAGCGTAGGATATTGGACTCAAGACAATGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
460383 CGAAGGGACCGCTGGTTG-CAATAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
* *
460423 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
* * *
460488 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
* * * *
460529 AGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTCCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
* * *
460594 CAAAGGGACCACTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
* * *
460635 AGAGCCAATTTCAACTTCACATCGAAAGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
*
460700 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
*
460741 AGAGCCAATTTCAACTTTACAGCGAAGGATATTGGACT-ACAGACAACGCAAGTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA-AGACAACGCAAGTTCAACTTCACG
* * * *
460805 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTT
65 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
* * * *
460847 AGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCCAGACAATGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
*
460912 CGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCAA-TTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
* *
460952 AGAGCCAATTTCAACTTCACAGC-ATAAGATATAGGACTCAAGACAACGCAAGTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACAGCGA-AGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
* *
461016 ACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCCAATTTC
65 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
* * * * * *
461058 AGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGGACCCAAGACAACACAAGCTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
*
461123 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
* *
461164 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
*
461229 CGAAGGGACCTCTGGTTGTCAATAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
461270 AGAGCCAATTTCAACTTCAC-GACGAAGG
1 AGAGCCAATTTCAACTTCACAG-CGAAGG
461298 GAATCGTGCA
Statistics
Matches: 889, Mismatches: 83, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
104 1 0.00
105 192 0.22
106 694 0.78
107 2 0.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
Found at i:460998 original size:423 final size:423
Alignment explanation
Indices: 460212--461297 Score: 1685
Period size: 423 Copynumber: 2.6 Consensus size: 423
460202 AATTTGCTCG
* * *
460212 AGAGCCAATTTCAACTTTACGACGAAGGATATTGGACTCCAGACCACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCAC-ACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
* * * * *
460277 CGAAGGGACCGTTGGTTGTCAAAAAATAATTTCCTAATTTCAAAGCCAAATTCAACTTCACAGCG
65 CGAAGGGACCGCTGGTTGTCAAAAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCG
* *
460342 TAGGATATTGGACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG-CAATA
130 AAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
* *
460406 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATG
195 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCCAGACAATG
*
460471 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
260 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
460536 ATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTCCAACTTCACGACAAAGGG
325 ATTTCAACTTCACAACGAAAGATATAGGACTCAAGACAACGCAAGTCCAACTTCACGACAAAGGG
*
460601 ACCACTGGTTGTCAACAAACAATTTCCCAATTTC
390 ACCACTGGTTGTCAACAAACAACTTCCCAATTTC
* *
460635 AGAGCCAATTTCAACTTCACATCGAAAGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGA
1 AGAGCCAATTTCAACTTCACA-CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
* * *
460700 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTTACAGCG
65 CGAAGGGACCGCTGGTTGTCAAAAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCG
*
460765 AAGGATATTGGACT-ACAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
130 AAGGATATTGGACTCA-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
* * *
460829 AAACAACTTCTCAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCCAGACAAT
194 AAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCCAGACAAT
* * *
460894 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCAA-TTCAGAGCC
259 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
* * *
460958 AATTTCAACTTCACAGC-ATAAGATATAGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAG
324 AATTTCAACTTCACAACGA-AAGATATAGGACTCAAGACAACGCAAGTCCAACTTCACGACAAAG
** *
461022 GGACCGTTGGTTGTCAATAAACAACTTCCCAATTTC
388 GGACCACTGGTTGTCAACAAACAACTTCCCAATTTC
* * * * * *
461058 AGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGGACCCAAGACAACACAAGCTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACA-CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
* *
461123 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACG
65 CGAAGGGACCGCTGGTTGTCAAAAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCG
* *
461188 AAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCTCTGGTTGTCAATA
130 AAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
*
461253 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACGACGAAGG
195 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
461298 GAATCGTGCA
Statistics
Matches: 603, Mismatches: 55, Indels: 10
0.90 0.08 0.01
Matches are distributed among these distances:
422 3 0.00
423 486 0.81
424 114 0.19
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (423 bp):
AGAGCCAATTTCAACTTCACACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAC
GAAGGGACCGCTGGTTGTCAAAAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGA
AGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
ACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCCAGACAATGC
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAA
TTTCAACTTCACAACGAAAGATATAGGACTCAAGACAACGCAAGTCCAACTTCACGACAAAGGGA
CCACTGGTTGTCAACAAACAACTTCCCAATTTC
Found at i:461210 original size:529 final size:529
Alignment explanation
Indices: 460212--461297 Score: 1752
Period size: 529 Copynumber: 2.1 Consensus size: 529
460202 AATTTGCTCG
* *
460212 AGAGCCAATTTCAACTTTACGACGAAGGATATTGGACTCCAGACCACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTTACGACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACGA
* * * *
460277 CGAAGGGACCGTTGGTTGTCAAAAAATAATTTCCTAATTTCAAAGCCAAATTCAACTTCACAGCG
66 CGAAGGGACCGCTGGTTGTCAAAAAACAACTTCCTAATTTCAAAGCCAAATTCAACTTCACAACG
* *
460342 TAGGATATTGGACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGCAATAA
131 AAGGATATTGAACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGCAATAA
* * * *
460407 ACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGC
196 ACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATAGGACTCAAGACAACGC
*
460472 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAA
261 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAA
* * *
460537 TTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTCCAACTTCACGACAAAGGGA
326 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTCCAACTTCACAACAAAGGGA
*
460602 CCACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAAGATAT
391 CCACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAAGATAT
*
460667 TGGACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTT
456 TGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTT
460732 CCCAATTTC
521 CCCAATTTC
460741 AGAGCCAATTTCAACTTTAC-AGCGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
1 AGAGCCAATTTCAACTTTACGA-CGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
* * * *
460805 ACGAAGGGACCGCTGGTTGTCAACAAACAACTT-CTCAATTTTAGAGCCAATTTCAACTTCACAA
65 ACGAAGGGACCGCTGGTTGTCAAAAAACAACTTCCT-AATTTCAAAGCCAAATTCAACTTCACAA
*
460869 CGAAGGATATTGAACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
129 CGAAGGATATTGAACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG-CAA
*
460934 TAAATAATTTCCCAA-TTCAGAGCCAATTTCAACTTCACAGC-ATAAGATATAGGACTCAAGACA
193 TAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGA-AAGATATAGGACTCAAGACA
* *
460997 ACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
257 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAG
* * * *
461062 CCAATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAG-CTCAACTTCACAACG
322 CCAATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACACAAGTC-CAACTTCACAACA
*
461125 AAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAA
385 AAGGGACCACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAA
* * *
461190 GGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCTCTGGTTGTCAATAAA
450 AGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAA
*
461255 CAATTTCCCAATTTC
515 CAACTTCCCAATTTC
*
461270 AGAGCCAATTTCAACTTCACGACGAAGG
1 AGAGCCAATTTCAACTTTACGACGAAGG
461298 GAATCGTGCA
Statistics
Matches: 514, Mismatches: 36, Indels: 14
0.91 0.06 0.02
Matches are distributed among these distances:
528 7 0.01
529 489 0.95
530 18 0.04
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (529 bp):
AGAGCCAATTTCAACTTTACGACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAAAAAACAACTTCCTAATTTCAAAGCCAAATTCAACTTCACAACG
AAGGATATTGAACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGCAATAA
ACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATAGGACTCAAGACAACGC
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAA
TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTCCAACTTCACAACAAAGGGA
CCACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAAGATAT
TGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTT
CCCAATTTC
Found at i:461973 original size:37 final size:37
Alignment explanation
Indices: 461920--462024 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
461910 CCTTTTCGTC
461920 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
461957 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
461994 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
462025 CCACAAGCAC
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:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:462855 original size:2 final size:2
Alignment explanation
Indices: 462848--462880 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
462838 TTTTACTCAT
462848 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
462881 TTAATATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:462898 original size:4 final size:4
Alignment explanation
Indices: 462885--462933 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
462875 ATATATTTAA
* * *
462885 TATT TCATT TATT TATT TATT TATT TATT T-TT TTTT TTTT TTTT TATT
1 TATT T-ATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
462933 T
1 T
462934 TATTCTTCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
3 3 0.07
4 35 0.83
5 4 0.10
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (4 bp):
TATT
Found at i:462934 original size:8 final size:8
Alignment explanation
Indices: 462892--462964 Score: 51
Period size: 8 Copynumber: 9.2 Consensus size: 8
462882 TAATATTTCA
*
462892 TTTATTTA
1 TTTATTTT
*
462900 TTTATTTA
1 TTTATTTT
462908 TTTATTTT
1 TTTATTTT
462916 TTT-TTTT
1 TTTATTTT
*
462923 TTTTTTTAT
1 TTTATTT-T
*
462932 TTTA-TTC
1 TTTATTTT
*
462939 TTCATTTT
1 TTTATTTT
* *
462947 TTCATTTA
1 TTTATTTT
*
462955 TTCATTTT
1 TTTATTTT
462963 TT
1 TT
462965 CCCTCTAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
7 10 0.18
8 41 0.75
9 4 0.07
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTATTTT
Found at i:462934 original size:12 final size:12
Alignment explanation
Indices: 462892--462948 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
462882 TAATATTTCA
* *
462892 TTTATTTATTTA
1 TTTATTTTTTTT
*
462904 TTTATTTATTTT
1 TTTATTTTTTTT
462916 TTT-TTTTTTTT
1 TTTATTTTTTTT
* *
462927 TTTATTTTATTC
1 TTTATTTTTTTT
*
462939 TTCATTTTTT
1 TTTATTTTTT
462949 CATTTATTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 10 0.26
12 28 0.74
ACGTcount: A:0.14, C:0.04, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTATTTTTTTT
Found at i:463389 original size:19 final size:19
Alignment explanation
Indices: 463365--463401 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
463355 TAAACTTTTT
463365 TTATTTGAATTGATTTTAA
1 TTATTTGAATTGATTTTAA
* *
463384 TTATTTGATTTTATTTTA
1 TTATTTGAATTGATTTTA
463402 TTTTCATATT
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:0.00, G:0.08, T:0.65
Consensus pattern (19 bp):
TTATTTGAATTGATTTTAA
Found at i:463473 original size:19 final size:20
Alignment explanation
Indices: 463444--463483 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
463434 TAATGATTAT
463444 TTTAGTTTTTATATTTTTAA
1 TTTAGTTTTTATATTTTTAA
*
463464 TTTA-TTTTTATTTTTTTAA
1 TTTAGTTTTTATATTTTTAA
463483 T
1 T
463484 ATTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (20 bp):
TTTAGTTTTTATATTTTTAA
Found at i:463486 original size:17 final size:18
Alignment explanation
Indices: 463449--463494 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
463439 ATTATTTTAG
*
463449 TTTTTATATTTTTAATTTA
1 TTTTTATTTTTTTAA-TTA
463468 TTTTTATTTTTTTAA-TA
1 TTTTTATTTTTTTAATTA
463485 TTTTT-TTTTT
1 TTTTTATTTTT
463495 GCTTGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 5 0.19
17 7 0.27
19 14 0.54
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTATTTTTTTAATTA
Found at i:463719 original size:19 final size:19
Alignment explanation
Indices: 463695--463734 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
463685 CTCCCATCCA
*
463695 CTTTCATCTTCTTTTAACT
1 CTTTCATCTTCTTTGAACT
463714 CTTTCATCTTCTTTGAACT
1 CTTTCATCTTCTTTGAACT
463733 CT
1 CT
463735 AATTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.28, G:0.03, T:0.55
Consensus pattern (19 bp):
CTTTCATCTTCTTTGAACT
Found at i:466761 original size:20 final size:21
Alignment explanation
Indices: 466712--466765 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
466702 ACACTGAAGT
466712 GGGTATCGATACCATAGAAGAG
1 GGGTATCGATACCATAG-AGAG
** *
466734 AAGTATCGATATCATAG-GAG
1 GGGTATCGATACCATAGAGAG
466754 GGGTATCGATAC
1 GGGTATCGATAC
466766 TATTCAATCT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 12 0.46
22 14 0.54
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (21 bp):
GGGTATCGATACCATAGAGAG
Found at i:467235 original size:54 final size:54
Alignment explanation
Indices: 467066--467608 Score: 736
Period size: 54 Copynumber: 10.1 Consensus size: 54
467056 GTTTAATGTA
* * *
467066 TATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCATATCGTCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
* * *
467120 TATGTGTGCAACCCACGT-ATT--TCATGAGTTTGTGATTTACCGTATCGACAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
* *
467171 TATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATCGGCTC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
* * * *
467225 CATGTATGCAACCCACGTAAATCATAATGAGTTTGTGAATTACCATATCGGCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
*
467279 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATGGGCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
* * * *
467333 TATGTGTACAATCCAC-AAATTCATAATGAG-TCGTGAATTACCGTATCGGCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
* * *
467385 TATGTATGCAACCCACGTAATTAATAATGAGTTTGTGAATTACCGTATCGGTAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
* * * * *
467439 TATGTGTTCAACCCACGTAATTTATAATGAGTTTATGAATTACCATATCGACAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
* * * * *
467493 TATGTGTGCAACCCACATAATTCATAATAAGTTTGTGAATTACCGTATTGACAA
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
* * * **
467547 TATATGTGCAACCCACGTAATTCATAATGAGATTGTGAATTACCTTATCAACAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
467601 TATGTGTG
1 TATGTGTG
467609 TAAAAACCAT
Statistics
Matches: 427, Mismatches: 57, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
51 43 0.10
52 36 0.08
53 28 0.07
54 320 0.75
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (54 bp):
TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
Found at i:467434 original size:214 final size:215
Alignment explanation
Indices: 467066--467605 Score: 755
Period size: 214 Copynumber: 2.5 Consensus size: 215
467056 GTTTAATGTA
* *
467066 TATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCATATCGTCACTATGTGTGCAA
1 TATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAA
** * * * * *
467131 CCCACGTATT--TCATGAGTTTGTGATTTACCGTATCGACACTATGTGTGCAACCCACATAATTC
66 CCCACAAATTCATAATGAGATTGTGAATTACCGTATCGACACTATGTATGCAACCCACATAATTA
467194 ATAATGAGTTTGTGAATTACCGTATCGGCT-CCATGTATGCAACCCACGTAAATCATAATGAGTT
131 ATAATGAGTTTGTGAATTACCGTATCGG-TACCATGTATGCAACCCACGTAAATCATAATGAGTT
* *
467258 TGTGAATTACCATATCGGCAC
195 TATGAATTACCATATCGACAC
* * * *
467279 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATGGGCACTATGTGTACAA
1 TATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAA
* * * *
467344 TCCACAAATTCATAATGAG-TCGTGAATTACCGTATCGGCACTATGTATGCAACCCACGTAATTA
66 CCCACAAATTCATAATGAGATTGTGAATTACCGTATCGACACTATGTATGCAACCCACATAATTA
* * * * *
467408 ATAATGAGTTTGTGAATTACCGTATCGGTACTATGTGTTCAACCCACGTAATTTATAATGAGTTT
131 ATAATGAGTTTGTGAATTACCGTATCGGTACCATGTATGCAACCCACGTAAATCATAATGAGTTT
467473 ATGAATTACCATATCGACAC
196 ATGAATTACCATATCGACAC
* * * *
467493 TATGTGTGCAACCCACATAATTCATAATAAGTTTGTGAATTACCGTATTGACAATATATGTGCAA
1 TATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAA
* * *
467558 CCCACGTAATTCATAATGAGATTGTGAATTACCTTATCAACACTATGT
66 CCCAC-AAATTCATAATGAGATTGTGAATTACCGTATCGACACTATGT
467606 GTGTAAAAAC
Statistics
Matches: 287, Mismatches: 35, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
213 68 0.24
214 177 0.62
215 19 0.07
216 23 0.08
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (215 bp):
TATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTGCAA
CCCACAAATTCATAATGAGATTGTGAATTACCGTATCGACACTATGTATGCAACCCACATAATTA
ATAATGAGTTTGTGAATTACCGTATCGGTACCATGTATGCAACCCACGTAAATCATAATGAGTTT
ATGAATTACCATATCGACAC
Found at i:474782 original size:54 final size:54
Alignment explanation
Indices: 474694--477734 Score: 2250
Period size: 54 Copynumber: 56.2 Consensus size: 54
474684 TTTGTTTAAT
* *
474694 GCAC-ATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCATATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * *
474747 ACACTATATGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCATATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* *
474801 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACCATATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
** *
474855 GCACTATGTGTGCAACCCATATAATTCATAATGAGTTTGTGAATTACCGTATCT
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * *
474909 ACACTATGTGTGGAACCCACGTAATTCATAATGAGTTTGGGAATTACCATATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * **
474963 ACACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTATTGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * * *
475017 GCAATATGTGTGCAACCTACATAATTCATAATGAGTTTGTGAATTACTGTATCA
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* ** * * *
475071 GCACTACGTGTGCAACCCACACAATTTATAATGAGTTTTTGAATTACCGTATGG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * ** *
475125 GCACTATGTGTGCAATCCACGAAATTCATAATGAGTTCATGAATTACCGCATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* *
475179 GCACTACGTGTGCAACCCATGTAATTCATAATGAGTTTGTGAATTACCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
** *** * * * *
475233 ATACTATGTGTGCAACCCATAAAATTAATAATAAGTTTTTGAATTACCGTATGG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * * *
475287 GTATTATGTGTGCAACCCACGTAATTTATAATGAGTTTGTGAATTATCGTATCT
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
** *
475341 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACTATATCA
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* *
475395 GCACTATGTGTGCAAGCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
** * * *
475449 ATACTATGTGTACAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATGG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * *
475503 GCACTACGTGTGCAACCCACGTAATTCATAATGAGTTTCTGAATTACCGTGTCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * *
475557 GCACTATGTGTACAACCCAGGTAATTCATAATGAGTTTGTGAATTACCATATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * *
475611 ACACTATGTGTGCAACCCACGTAATTTATAATGAGTTTTTGAATTACAGTAT-G
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * * ** *
475664 TGCACTAT-TGTGTAATCCACGAAATTTATAATGAGTTCACT-ACTTACCGTATCG
1 -GCACTATGTGTGCAACCCACGTAATTCATAATGAGTT-TGTGAATTACCGTATCG
* * * * *
475718 ACCCTATATGTGTAACCCACATAATT-AGTAATGAGTTTGTGAATTACCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCA-TAATGAGTTTGTGAATTACCGTATCG
* * * * *
475772 GCACTATGTGTTCAATCCC-CATAATTCATAATGTGTTTGTGAATTATCGTAGCG
1 GCACTATGTGTGCAA-CCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* *
475826 GCACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCGTAACG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * *
475880 ACAATATGTGTGCAACCCACGTAA-TCATAATGAGTTTGTGAATTACCTTATCA
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * * * ** * **
475933 GCATTATGTGTGCAAAAACCATGAAATTTATAATGAG-TTGAAATATTCAATTCGTATTTT
1 GCACTATGTGTGC--AACCCACGTAATTCATAATGAGTTTGTGA-ATT--A-CCGTA-TCG
* * ** * ** ** * * *
475993 G-A-TA-GTTATG-ATA--CAC-TTATGTTTTAATTTCACCTCAT-TATTA--TTATGCC
1 GCACTATG-TGTGCA-ACCCACGTAAT-TCATAA--TGAGTTTGTGAATTACCGTAT-CG
* * * ** ** * * * * * *
476043 TCAATAAT-TGAT--TACTTAGCGTGTGTTGATTACACG-GGTAG-GTATTAGAGCG-AGT-G
1 GCACT-ATGTG-TGCAACCCA-CGT-AATTCA-TA-ATGAGTTTGTGAATT--ACCGTA-TCG
* * * * ** * * * * * * *
476099 G-AGTAAGGAGTGCAGCTGAC--ATTGTCAATTAA-G-GGTCGCCTCATCAGTAACTGTA-AG
1 GCACT-ATGTGTGCAACCCACGTAAT-TC-A-TAATGAGTTTG--TGA--A-TTACCGTATCG
** * * ***** * * ** ** * *
476156 ATAGCTATGTCTACTTTTGATGTTATT-A-GCTG-GCATGT-AA-TAGACTTAT--
1 GCA-CTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTA-CCGTATCG
* * * * * * * *
476205 G-A-TAATGCTCTG-AA---AAGTATTTGACTTATGA-TGATGTAATATTTA--ATAT-G
1 GCACT-ATG-TGTGCAACCCACGTAATTCA-TAATGAGT-TTGTGA-A-TTACCGTATCG
* * * ** ***** ** * * *
476255 TTCGA-AATTTAAG-ATTTTTC-TACA-T-ATAAAAAGTTAGTGAACATTTTAACGTTAT-T
1 -GC-ACTATGTGTGCAACCCACGTA-ATTCATAATGAGTTTGTG-A-A--TTACCG-TATCG
** * * *** ** * * * ** * *
476311 AAATTAAAATGTTTGATGAATAGAAACAAAATT-TTACTG-GTTT-TCCAAAAACGGAAT-G
1 GCACT---ATG--TG-TGCA-ACCCACGTAATTCATAATGAGTTTGT-GAATTACCGTATCG
** ** * ** * * * * ******
476369 TTTTAAAAGTTTTGTG--ACATATGTGACTT-ATGTACG-GAAACAAAATTTTACCGTATCG
1 --GCACTA--TGTGTGCAACCCACGT-AATTCAT-AATGAGTTTGTGAA--TTACCGTATCG
* * * *
476427 ACACTATGTGTGCAACCCACGTAATTAATAATAAGTTTGTGAATTACCGTATGG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* **
476481 GCAATATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATAT
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * *
476535 GCACTATGTGTGCAACCCACGTAATTCTTAATGAGTTTGTGAAGTACCGTTTCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * * *
476589 ACACTATGTGTGTAACCCACGTAATTCATAATGAGTTAGTAAATTACCGTATTG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * *
476643 GCACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACCATATGG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * **
476697 GCACTACGTGTGCAACCCACATAATTCATAATAAGTTCATGAATTACCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * *
476751 GCACTATGTGTGCAACCCATGTAATTCATAATGAGTTTGTGAATTATCATATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * *
476805 TCACTATATATGCAACCCACGTAATTCATAAAGAGTTTGTGAATTACCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* *
476859 GCACTATGTGTGCAACCCACGTAATTCATAATGAATTTGTGAATTACCGTATTG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * *
476913 GCACTATGTGTGCAACCCACATAATTCATACTGAGTTTGTGAATTACCATATGG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * *
476967 GCACTACGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTATCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* *
477021 GCACTATGTGTGAAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATGG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * * *
477075 GCACTATATGTGTAATCCACGAAATTCATAATGAGTTCGTGAATTACCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * *
477129 GCACTATGTGTACAACCCATGTAATTCATAATGAGTTTGTGATTTACCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * *
477183 GCACTATGTGTGTAACTCACGTAATTCATAATGAGTTAGTGAATTATCGTAT-G
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
** *
477236 TGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTATAGTGTCG
1 -GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * *
477291 GCACTATGTGTTCAACCCACATAATTCTTAATGAGTTTGTGAATTACCGTATTG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * *
477345 GCACTATGTGTGCAACCCACGTAATTTATAATGAGTTTGTGAATTACTGTATCA
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * * * * *
477399 ACACTATATATGCAAGCCATGTAATTCATAATAAGTTTGTGAATTATCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * * *
477453 ACACTATGTGTGCAACCCACGTAATTTATAATCAGTTTGTGAATTACTGTATCA
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * * * * *
477507 ACACTATATATGCAAGCCATGTAATTCATAATAAATTTGTGAATTACCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* *
477561 ACACTATGTGTGCAACCCACGTAATTTATAATGAGTTTGTGAATTACCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * *
477615 GC-CTATGTGTGCAACCCACATAATTCATAATAAGTTTGTGAATTACCTTATTG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* * * *
477668 GCACCATGTGTGCAAGCCACGTAATTCAAAATGAGTTTATGAATTACCGTATCG
1 GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
* *
477722 ACACTATATGTGC
1 GCACTATGTGTGC
477735 GAAAACCATA
Statistics
Matches: 2387, Mismatches: 484, Indels: 233
0.77 0.16 0.08
Matches are distributed among these distances:
44 5 0.00
45 1 0.00
46 1 0.00
47 5 0.00
48 8 0.00
49 6 0.00
50 5 0.00
51 11 0.00
52 10 0.00
53 159 0.07
54 2024 0.85
55 40 0.02
56 42 0.02
57 19 0.01
58 22 0.01
59 10 0.00
60 5 0.00
61 2 0.00
62 3 0.00
63 5 0.00
64 4 0.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (54 bp):
GCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATCG
Found at i:487821 original size:21 final size:21
Alignment explanation
Indices: 487795--487868 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
487785 GTTTCCAGAT
* *
487795 TCGCAACGAGAACATCGACTA
1 TCGCAACGCGAACTTCGACTA
487816 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
487837 TCGCAATGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
487858 TCGCAATGCGA
1 TCGCAACGCGA
487869 TTTTCCAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:487888 original size:19 final size:19
Alignment explanation
Indices: 487872--488061 Score: 132
Period size: 21 Copynumber: 9.3 Consensus size: 19
487862 AATGCGATTT
*
487872 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
487891 TCTAAGTTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
487912 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
487931 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
487954 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
487973 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
487996 TCCAAGTTCATTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
488015 -CCGAAGTTCGCGTTGCGATTTAT
1 TCC-AAGTT--CGTTGCGA--TAG
*
488038 TCTGAA-TTCGTTGCGATAG
1 TC-CAAGTTCGTTGCGATAG
488057 TCCAA
1 TCCAA
488062 AATCGCAACG
Statistics
Matches: 135, Mismatches: 19, Indels: 35
0.71 0.10 0.19
Matches are distributed among these distances:
18 4 0.03
19 43 0.32
21 64 0.47
23 21 0.16
24 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:487906 original size:21 final size:21
Alignment explanation
Indices: 487880--488033 Score: 151
Period size: 21 Copynumber: 7.4 Consensus size: 21
487870 TTTCCAAATT
*
487880 CGTTGCGATAGTCTAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
487901 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
*
487920 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
487941 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
487962 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
487983 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
488004 CATTGCGATAG-CCGAAGTTCG
1 CGTTGCGATAGTCC-AAGTTCG
488025 CGTTGCGAT
1 CGTTGCGAT
488034 TTATTCTGAA
Statistics
Matches: 109, Mismatches: 13, Indels: 22
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.02
19 33 0.30
21 57 0.52
23 17 0.16
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:487971 original size:42 final size:42
Alignment explanation
Indices: 487864--488058 Score: 290
Period size: 42 Copynumber: 4.7 Consensus size: 42
487854 ACTATCGCAA
*
487864 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCTAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* *
487904 TGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
487944 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* * *
487986 TGCGATTTATTCCAAGTTCATTGCGATAGCCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
**
488028 TGCGATTTATTCTGAATTCGTTGCGATAGTC
1 TGCGATTTATTCCAAATTCGTTGCGATAGTC
488059 CAAAATCGCA
Statistics
Matches: 139, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.01
40 40 0.29
42 98 0.71
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:488956 original size:21 final size:19
Alignment explanation
Indices: 488917--489031 Score: 77
Period size: 19 Copynumber: 5.6 Consensus size: 19
488907 ACCAGTCGTT
* *
488917 ACGATTTTGGACTATCGCA
1 ACGAATTTGGAATATCGCA
488936 ACGAATTTGGAATAAATCGCA
1 ACGAATTTGGAAT--ATCGCA
* *
488957 ATGCGAACTTGGACTATCGCA
1 A--CGAATTTGGAATATCGCA
* *
488978 ACGAATTTGTAATAAATTGCA
1 ACGAATTTGGAAT--ATCGCA
* *
488999 ACGCGAACTTGGACTATCGCA
1 A--CGAATTTGGAATATCGCA
*
489020 ACAAATTTGGAA
1 ACGAATTTGGAA
489032 AATTACAACG
Statistics
Matches: 73, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
19 28 0.38
21 26 0.36
23 19 0.26
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (19 bp):
ACGAATTTGGAATATCGCA
Found at i:488982 original size:42 final size:42
Alignment explanation
Indices: 488923--489062 Score: 194
Period size: 42 Copynumber: 3.4 Consensus size: 42
488913 CGTTACGATT
*
488923 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
488965 TTGGACTATCGCAACGAATTTGTAATAAATTGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* ** *
489007 TTGGACTATCGCAACAAATTTGG-A-AAATTACAACGCCAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
489047 TTCGACTATCGCAACG
1 TTGGACTATCGCAACG
489063 CGAACTTGGA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 28 0.31
41 1 0.01
42 60 0.67
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:489086 original size:21 final size:20
Alignment explanation
Indices: 488923--489087 Score: 102
Period size: 21 Copynumber: 8.0 Consensus size: 20
488913 CGTTACGATT
*
488923 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
488942 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
488965 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
* * *
488984 TTGTAATAAATTGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* *
489007 TTGGACTATCGCAA-CAAAT
1 TTGGACTATCGCAAGCGAAC
** ** *
489026 TTGGAAAATTACAACGCCAAC
1 TTGGACTATCGCAA-GCGAAC
*
489047 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA-GCGAAC
489068 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA-GCGAA
489088 TACGTAAATC
Statistics
Matches: 109, Mismatches: 27, Indels: 18
0.71 0.18 0.12
Matches are distributed among these distances:
19 28 0.26
21 62 0.57
23 19 0.17
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:489128 original size:21 final size:21
Alignment explanation
Indices: 489102--489148 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
489092 TAAATCGCAA
489102 TGCGATAGTCGAAGTTTGCGT
1 TGCGATAGTCGAAGTTTGCGT
*
489123 TGCGATAGTCGAAGTTTTCGT
1 TGCGATAGTCGAAGTTTGCGT
489144 TGCGA
1 TGCGA
489149 ATCTAGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.15, G:0.32, T:0.34
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTTGCGT
Found at i:490836 original size:5 final size:5
Alignment explanation
Indices: 490822--490853 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
490812 CCGCCGCCGC
490822 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
490854 GGTCGTGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.38
Consensus pattern (5 bp):
CGTCT
Found at i:490861 original size:6 final size:6
Alignment explanation
Indices: 490850--490886 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
490840 TCGTCTCGTC
490850 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
490887 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:491051 original size:20 final size:20
Alignment explanation
Indices: 491026--491073 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
491016 TAGACTATCG
491026 CAACGCGAAATGAAAAATCA
1 CAACGCGAAATGAAAAATCA
*
491046 CAACGCGAAATGAAAAATCG
1 CAACGCGAAATGAAAAATCA
491066 CAACGCGA
1 CAACGCGA
491074 TTTTCAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.50, C:0.23, G:0.19, T:0.08
Consensus pattern (20 bp):
CAACGCGAAATGAAAAATCA
Found at i:491088 original size:21 final size:21
Alignment explanation
Indices: 491062--491135 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
491052 GAAATGAAAA
491062 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
491083 ATCGCAACGCGAAATAGAA-A
1 ATCGCAACGCGATTTTCAACT
* *
491103 ATCGTAATGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
491124 ATCGCAACGCGA
1 ATCGCAACGCGA
491136 AATGCAACGC
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:491104 original size:41 final size:41
Alignment explanation
Indices: 491046--491139 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
491036 TGAAAAATCA
491046 CAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTATCG
1 CAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTATCG
* *
491087 CAACGCGAAAT-AGAAAATCGTAATGCGATTTTCAACTATCG
1 CAACGCGAAATGA-AAAATCGCAACGCGATTTTCAACTATCG
491128 CAACGCGAAATG
1 CAACGCGAAATG
491140 CAACGCGAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
40 1 0.02
41 48 0.98
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (41 bp):
CAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTATCG
Found at i:495894 original size:2 final size:2
Alignment explanation
Indices: 495887--495961 Score: 82
Period size: 2 Copynumber: 38.0 Consensus size: 2
495877 TACTAATAAT
* * * *
495887 TA TA TA TA TA TA TA TA TA TA TA TA TT TA AA TCA -A TA TA TT TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
*
495929 TA T- TA GA 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
495962 ATTATTTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
1 2 0.03
2 59 0.95
3 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:495980 original size:16 final size:18
Alignment explanation
Indices: 495961--495995 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
495951 ATATATATAT
495961 AATTA-TTTA-AAAATTA
1 AATTATTTTATAAAATTA
495977 AATTATTTTATAAAATTA
1 AATTATTTTATAAAATTA
495995 A
1 A
495996 TAATAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 4 0.24
18 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTATTTTATAAAATTA
Found at i:496005 original size:19 final size:19
Alignment explanation
Indices: 495959--496006 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
495949 ATATATATAT
*
495959 ATAATTATTTA-AAAATTA
1 ATAATAATTTATAAAATTA
* *
495977 A-ATTATTTTATAAAATTA
1 ATAATAATTTATAAAATTA
495995 ATAATAATTTAT
1 ATAATAATTTAT
496007 GTTGAACTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
17 6 0.26
18 9 0.39
19 8 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAATAATTTATAAAATTA
Found at i:502571 original size:84 final size:84
Alignment explanation
Indices: 502416--504068 Score: 1905
Period size: 84 Copynumber: 19.8 Consensus size: 84
502406 AAACTATCAT
* * * * * *
502416 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAGC-CAAGACCTTCGAGTTCGATTACACTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
502480 CTCAAAGGCACATCATTTG
66 CTCAAAGGCACATCATTTG
*
502499 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
502564 CTCAAAGGCACATCATTTG
66 CTCAAAGGCACATCATTTG
* * * * * * * * *
502583 CAGCATAGCTCAAGGCAAGAAGGGCTATTTGCCACCAAAAGACATTCGAGTTCAATTACACTAAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
* *
502648 CTCCAAGGCATATCATTTG
66 CTCAAAGGCACATCATTTG
* * * * * * *
502667 CAGCATAACTCAAGGCTAGAATGGTTATCTACCAACCAAAGACCTTCGAGTTCGAATATGCTCAT
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
*
502732 CTCCAAGGCACATCATTTG
66 CTCAAAGGCACATCATTTG
* * * * * **
502751 CAGCATAGCTCAAGGCAAGAAGGGCTATTTGCCAATAAAAGACCTTCGAGTTCGAATACGAACAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
*
502816 CTCAAAGGCATATCATTTG
66 CTCAAAGGCACATCATTTG
* * * * * *
502835 TAGCATAACACAAGGCCAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACACTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
*
502900 CTCCAAGGCACATCATTTG
66 CTCAAAGGCACATCATTTG
* * * * *
502919 CAGTATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
* * * *
502984 CTCAAAGGCATAACTTTTA
66 CTCAAAGGCACATCATTTG
* * * * * *
503003 CAGCACAACTCAAGTCTAGAAGGCTTATCTGCTAATAAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
*
503068 CTCCAAGGCACATCATTTG
66 CTCAAAGGCACATCATTTG
* * * * * * * *
503087 CAACATAGCTCAAGGCAAGAAGTGCTATTTGCCAATAAAAGATCTTCGAGTTCGACTCCGCTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
* *
503152 TTCCAAA-GCACATCATTTA
66 CT-CAAAGGCACATCATTTG
*
503171 CAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
*
503236 CTCCAAGGCACATCATTTG
66 CTCAAAGGCACATCATTTG
* * * * *
503255 TAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAATGACCTTCGAGTTCAACTACGCTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
*
503320 CTCCAAGGCACATCATTTG
66 CTCAAAGGCACATCATTTG
* * * * *
503339 TAACATAGCTCAAGGAAAGAAGGGTTATTCTTCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
1 CAGCATAACTCAAGGCAAGAAGGGTTA-TCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
*
503404 GCTCTAAGGCACATCATTTG
65 GCTCAAAGGCACATCATTTG
** * * * * * *
503424 CAATATAACTCAAGGCTAGAAGGGTTATCTGCCAGCAAAAAACCTTCGAGTTTGATTACACTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
*
503489 CTCAAAGGCACAACATTTG
66 CTCAAAGGCACATCATTTG
* * * *
503508 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGCTAACAAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
*
503573 CTCCAAGGCACATCATTTG
66 CTCAAAGGCACATCATTTG
* * * * *
503592 CAGTATAACTCAAGGCTAGAAGAGTTATCTGCCAATAAAAGACCTTCGAGTTCAACTACGCTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
* *
503657 CTCCAAGGCACATCATTTA
66 CTCAAAGGCACATCATTTG
** * * * *
503676 CAATATAGCTCAAGGAAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
** *
503741 CTCAAAGGTGCATCATTTA
66 CTCAAAGGCACATCATTTG
* * * * **
503760 CAACATAACTCAAGGCTAGAAGGGTTATCTG-C--C-AAAGACCTTCGAGTTCGATTACACTTTG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
*
503821 CTCAAAGGCACATTATTTG
66 CTCAAAGGCACATCATTTG
* * ** * * * *
503840 CAACATAACTCAAGGTAAGAACAGCTATCTG-C--C-AAAGGCCTTCGAGTTCGATTACACTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
*
503901 CTCAGAGGCACATCATTTG
66 CTCAAAGGCACATCATTTG
* * * *
503920 CAGCATAACTCAAGGCTAGAAGGGTTATCTG-C--C-AAAGACCTTCGGGTTCGATTACACTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
* *
503981 CTCCAAGGCACATCATTTA
66 CTCAAAGGCACATCATTTG
** * * * * * * *
504000 CAGCATAGTTAAAGGCAAGAAGGGCTATCTGTCAAC-AAATACCTTCGAGTTCGATTTCGTTCAG
1 CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
504064 CTCAA
66 CTCAA
504069 TCAACCACAT
Statistics
Matches: 1339, Mismatches: 224, Indels: 14
0.85 0.14 0.01
Matches are distributed among these distances:
80 204 0.15
81 2 0.00
83 65 0.05
84 990 0.74
85 78 0.06
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (84 bp):
CAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
CTCAAAGGCACATCATTTG
Found at i:504499 original size:37 final size:37
Alignment explanation
Indices: 504436--504890 Score: 453
Period size: 37 Copynumber: 12.1 Consensus size: 37
504426 TGCAAATGGT
*
504436 TTTTGAAAATACGTATATAATATATAGTTTTTAAAAACA
1 TTTTGAAAATA--TATATAATATATAGTTTTTTAAAACA
504475 TTTTGAAAATATATATAATATATAG-TTTTTAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTTAAAACA
*
504511 TTTTTGAAAACT-TATATAATATATAG-TTTTTAAAATA
1 -TTTTGAAAA-TATATATAATATATAGTTTTTTAAAACA
*
504548 TTTTAGAAAATATATATAATATATAGTTTTTTAAATCA
1 TTTT-GAAAATATATATAATATATAGTTTTTTAAAACA
* *
504586 TTTTGAAAACT-TATATAATATAAAGTTTTTTAAAATA
1 TTTTGAAAA-TATATATAATATATAGTTTTTTAAAACA
* *
504623 TTTTTGAAACT-TATATAATATATAG-TTTTGAAAACA
1 -TTTTGAAAATATATATAATATATAGTTTTTTAAAACA
* * **
504659 TTTTGAAAACCTTTATATATTATATAGATTTTAAAAAACA
1 TTTTGAAAA--TATATATAATATATAG-TTTTTTAAAACA
* * *
504699 TTTTGAAAACCTTTATATATTATATAGTTTTTAAAAAACA
1 TTTTGAAAA--TATATATAATATATAGTTTTT-TAAAACA
*
504739 TTTTG-AAA-ATATATAATATATATTTTTTTAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTTAAAACA
* * *
504774 TTTTTACAAATATATATATTATATAATTTTTTTAAAACA
1 TTTTGA-AAATATATATAATATAT-AGTTTTTTAAAACA
* * * *
504813 TTTTTGAAAACATATATGATATA-AATGTTTTAAAACA
1 -TTTTGAAAATATATATAATATATAGTTTTTTAAAACA
* * * *
504850 TTTTGGAAATTTATATATTATAT-GTTTTTTGAAAATA
1 TTTTGAAAATATATATAATATATAGTTTTTT-AAAACA
504887 TTTT
1 TTTT
504891 TTGTTATTAT
Statistics
Matches: 360, Mismatches: 36, Indels: 42
0.82 0.08 0.10
Matches are distributed among these distances:
35 18 0.05
36 63 0.17
37 133 0.37
38 48 0.13
39 45 0.12
40 53 0.15
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTTAAAACA
Found at i:504751 original size:34 final size:34
Alignment explanation
Indices: 504673--504792 Score: 100
Period size: 40 Copynumber: 3.3 Consensus size: 34
504663 GAAAACCTTT
* *
504673 ATATATTATATAGATTTTAAAAAACATTTTGAAAA
1 ATATATTATATA-TTTTTAAAAAACATTTTGACAA
504708 CCTTTATATATTATATAGTTTTTAAAAAACATTTTGA-AA
1 -----ATATATTATATA-TTTTTAAAAAACATTTTGACAA
** *
504747 ATATATAATATATATTTTTTTAAAACATTTTTACAA
1 ATATAT--TATATATTTTTAAAAAACATTTTGACAA
504783 ATATA-TATAT
1 ATATATTATAT
504793 TATATAATTT
Statistics
Matches: 73, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
33 5 0.07
34 6 0.08
35 16 0.22
36 13 0.18
39 2 0.03
40 31 0.42
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (34 bp):
ATATATTATATATTTTTAAAAAACATTTTGACAA
Found at i:504941 original size:18 final size:17
Alignment explanation
Indices: 504895--504934 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
504885 TATTTTTTGT
504895 TATTATTTATTATTATTTC
1 TATTA-TTATTATT-TTTC
*
504914 TATTATTATTATTTTTT
1 TATTATTATTATTTTTC
504931 TATT
1 TATT
504935 CCTTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTATTATTATTTTTC
Found at i:504957 original size:7 final size:7
Alignment explanation
Indices: 504897--504959 Score: 54
Period size: 7 Copynumber: 8.3 Consensus size: 7
504887 TTTTTTGTTA
*
504897 TTATTTA
1 TTATTTT
504904 TTATTATT
1 TTATT-TT
504912 TCTATTATT
1 T-TATT-TT
504921 ATTATTTTT
1 -TTA-TTTT
**
504930 TTATTCC
1 TTATTTT
504937 TTATTTT
1 TTATTTT
504944 TTATTTT
1 TTATTTT
504951 TTATTTT
1 TTATTTT
504958 TT
1 TT
504960 CTGTCCAGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
7 28 0.60
8 5 0.11
9 11 0.23
10 3 0.06
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (7 bp):
TTATTTT
Found at i:506205 original size:23 final size:23
Alignment explanation
Indices: 506145--506209 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
506135 TCATTTATTT
*
506145 ATTTATTATTATTATTATTTTTAA
1 ATTTATTATT-TTATTATTCTTAA
* *
506169 ATTT-TTCTCCTTATT-TTCCTTAA
1 ATTTATTAT-TTTATTATT-CTTAA
506192 ATTTATTATTTTATTATT
1 ATTTATTATTTTATTATT
506210 TTCATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
22 2 0.06
23 21 0.66
24 9 0.28
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTATTATTTTATTATTCTTAA
Found at i:514632 original size:64 final size:65
Alignment explanation
Indices: 514537--514662 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 65
514527 GATTCGATAA
*
514537 CCAAATCTATCAATGACTCCCTCAACTCATTGAGGCTTCATCTTCAAAGTATTCCTGTCATGGCT
1 CCAAATCTATCAATGACTCCCTCAACTCATTGAGGCTTCATCTTCAAAGTATTCCTCTCATGGCT
* *
514602 CCAAATCTATCGATGACT-CCTCAACTCATTGAGGTTTCATCTTCAAAGTATTCCTCTCATG
1 CCAAATCTATCAATGACTCCCTCAACTCATTGAGGCTTCATCTTCAAAGTATTCCTCTCATG
514663 ACTCACAACA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
64 41 0.71
65 17 0.29
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (65 bp):
CCAAATCTATCAATGACTCCCTCAACTCATTGAGGCTTCATCTTCAAAGTATTCCTCTCATGGCT
Found at i:527870 original size:42 final size:42
Alignment explanation
Indices: 527823--528155 Score: 199
Period size: 42 Copynumber: 7.7 Consensus size: 42
527813 TCGCACTTAG
* *
527823 TAAATCCTTTGAGTCATCAATAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTTGAGTCATCAGTAAGTCTTTCGAGCATGATGAT
* * * * *
527865 TAAATCCTTAGGGCCATCAGTAAGTATTTTGAGCATGATGAT
1 TAAATCCTTTGAGTCATCAGTAAGTCTTTCGAGCATGATGAT
* * * ** * * *
527907 TAAATCCTTAGGGTAATTTGTAAGCCTTCACGGAAG-A-GTAGTGAAG
1 TAAATCCTTTGAGTCATCAGTAAGTCTT-TC-G-AGCATG-A-TG-AT
* * * *
527953 CAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGAT
1 TAAATCC-T--TTGAGT--CATCAGTAAGTCTTTCGAGCATGATGAT
*
528000 TAAATCC-TTCAGGTCATCAGTAAGTCTTTCGAGCATGATGAT
1 TAAATCCTTTGA-GTCATCAGTAAGTCTTTCGAGCATGATGAT
* * * * *
528042 TAAATCATTCGGGCCATCATTAAGTCTTTCGAGCATGATGAT
1 TAAATCCTTTGAGTCATCAGTAAGTCTTTCGAGCATGATGAT
* *** * * *
528084 TAAATCATTTGAGTCATTTTTGAGTCTTTCGAGCAAGAT-AA
1 TAAATCCTTTGAGTCATCAGTAAGTCTTTCGAGCATGATGAT
* * *
528125 TAAATCCTTCGGGTCATCCA-TAAGTCCTTCG
1 TAAATCCTTTGAGTCAT-CAGTAAGTCTTTCG
528156 GGTAGGATGT
Statistics
Matches: 222, Mismatches: 53, Indels: 33
0.72 0.17 0.11
Matches are distributed among these distances:
41 24 0.11
42 151 0.68
43 4 0.02
44 5 0.02
45 4 0.02
46 6 0.03
47 7 0.03
48 4 0.02
49 5 0.02
50 2 0.01
51 10 0.05
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (42 bp):
TAAATCCTTTGAGTCATCAGTAAGTCTTTCGAGCATGATGAT
Found at i:527976 original size:13 final size:13
Alignment explanation
Indices: 527958--527982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
527948 TGAAGCAAAC
527958 CCATCAGTAAGTG
1 CCATCAGTAAGTG
527971 CCATCAGTAAGT
1 CCATCAGTAAGT
527983 CTTTCGAGCA
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:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:528085 original size:22 final size:22
Alignment explanation
Indices: 527978--528086 Score: 91
Period size: 22 Copynumber: 5.1 Consensus size: 22
527968 GTGCCATCAG
527978 TAAGTCTTTCGAGCATGATGAT
1 TAAGTCTTTCGAGCATGATGAT
* * * * * *
528000 TAAATCCTTC-AG-GTCATCAG
1 TAAGTCTTTCGAGCATGATGAT
528020 TAAGTCTTTCGAGCATGATGAT
1 TAAGTCTTTCGAGCATGATGAT
* * * * *
528042 TAAATCATTCGGGC--CATCAT
1 TAAGTCTTTCGAGCATGATGAT
528062 TAAGTCTTTCGAGCATGATGAT
1 TAAGTCTTTCGAGCATGATGAT
528084 TAA
1 TAA
528087 ATCATTTGAG
Statistics
Matches: 61, Mismatches: 22, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
20 27 0.44
21 4 0.07
22 30 0.49
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (22 bp):
TAAGTCTTTCGAGCATGATGAT
Found at i:528111 original size:84 final size:82
Alignment explanation
Indices: 527970--528155 Score: 221
Period size: 84 Copynumber: 2.2 Consensus size: 82
527960 ATCAGTAAGT
527970 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCAGTAAGTCTTTCGAGCA
1 GCCATCA-TAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCAGTAAGTCTTTCGAGCA
* *
528035 TGATGATTAAATCATTCGG
65 AGAT-AATAAATCATTCGG
* * *** *
528054 GCCATCATTAAGTCTTTCGAGCATGATGATTAAATCATT-TGAGTCATTTTTGAGTCTTTCGAGC
1 GCCATCA-TAAGTCTTTCGAGCATGATGATTAAATCCTTCAG-GTCATCAGTAAGTCTTTCGAGC
*
528118 AAGATAATAAATCCTTCGG
64 AAGATAATAAATCATTCGG
* *
528137 GTCATCCATAAGTCCTTCG
1 GCCAT-CATAAGTCTTTCG
528156 GGTAGGATGT
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
83 27 0.31
84 61 0.69
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (82 bp):
GCCATCATAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCAGTAAGTCTTTCGAGCAA
GATAATAAATCATTCGG
Found at i:528643 original size:53 final size:53
Alignment explanation
Indices: 528577--529050 Score: 590
Period size: 53 Copynumber: 8.9 Consensus size: 53
528567 AGAATTACAC
* *
528577 CAGAAAATTGTTCGAGTTCTAATCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * * * *
528630 CAGAATATCGTTCGAGTTCTACTCCCTGAAGCAAGAGGGATCAAACCCATAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * * *
528683 CAGAAGATTATTCGAGTTCTACGCTCCATTAAGCAAGTGGGAGCGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCTA--CTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* **
528738 CAGAAGATCGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAA
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * ***
528791 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACTCATTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
528844 TAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGA
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
528897 CAGAAGATTATTCGAGTTATACTCCCTAAAGCAAGAGGGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
** *
528950 CAGAAGATTGTTCGAGTTCTAC-CCCTTGAAATAAGAGGGAGCGAACCTGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCC-TGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
529003 CAGAAGATTATTCGAGTTATACTCCTTGAAGCAAGAAGGAGCGAACCC
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC
529051 ACTGGTCGAA
Statistics
Matches: 361, Mismatches: 56, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
52 3 0.01
53 311 0.86
54 2 0.01
55 45 0.12
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.21
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:533492 original size:65 final size:65
Alignment explanation
Indices: 533411--533711 Score: 426
Period size: 65 Copynumber: 4.6 Consensus size: 65
533401 TATCATATAG
* * * *
533411 TCACTCTACCTCATGCACCACAAAGGTACATGAGTCATATGAATGGTTTGTATAGTATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAATGGTCTGTACAATATTCAATTA
*
533476 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGGTCT-TACAATATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAATGGTCTGTACAATATTCAATTA
* * * * *
533540 TCACTCCACCTCATGCACCACAAAAGTGCATGAGTCATATGAGTAGTCTATACAATATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAATGGTCTGTACAATATTCAATTA
* * *
533605 TCACTCCACCTTATGCACTACAAAGGTACATGAGTCATAT-AAGTGGTCTGTACATTATTCAATT
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAA-TGGTCTGTACAATATTCAATT
533669 A
65 A
* * * *
533670 TCACACCACCTCATGCACTATAGAGGTACATGAGTCATATGA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGA
533712 GTGATCAGTG
Statistics
Matches: 213, Mismatches: 20, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
64 60 0.28
65 152 0.71
66 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (65 bp):
TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAATGGTCTGTACAATATTCAATTA
Found at i:533641 original size:129 final size:130
Alignment explanation
Indices: 533411--533713 Score: 446
Period size: 129 Copynumber: 2.3 Consensus size: 130
533401 TATCATATAG
* * * * * * *
533411 TCACTCTACCTCATGCACCACAAAGGTACATGAGTCATATGAATGGTTTGTATAGTATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTAGTCTATACAATATTCAATTA
*
533476 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGGTCT-TACAATATTCAATTA
66 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATAAGTGGTCTGTACAATATTCAATTA
* *
533540 TCACTCCACCTCATGCACCACAAAAGTGCATGAGTCATATGAGTAGTCTATACAATATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTAGTCTATACAATATTCAATTA
* * *
533605 TCACTCCACCTTATGCACTACAAAGGTACATGAGTCATATAAGTGGTCTGTACATTATTCAATTA
66 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATAAGTGGTCTGTACAATATTCAATTA
* * * *
533670 TCACACCACCTCATGCACTATAGAGGTACATGAGTCATATGAGT
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGT
533714 GATCAGTGTC
Statistics
Matches: 154, Mismatches: 19, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
129 102 0.66
130 52 0.34
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (130 bp):
TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTAGTCTATACAATATTCAATTA
TCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATAAGTGGTCTGTACAATATTCAATTA
Found at i:534619 original size:29 final size:29
Alignment explanation
Indices: 534577--534634 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
534567 AAACCCACAA
*
534577 CTTATATAATTTAT-AATTTAGTCTTCAAT
1 CTTATATAATTTATAAATTTA-ACTTCAAT
534606 CTTA-ATAATTTTATAAATTTAACTTCAAT
1 CTTATATAA-TTTATAAATTTAACTTCAAT
534635 TCAAGCTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.15
29 16 0.62
30 6 0.23
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (29 bp):
CTTATATAATTTATAAATTTAACTTCAAT
Found at i:540142 original size:20 final size:20
Alignment explanation
Indices: 540105--540143 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
540095 AGATTGAGTG
* * *
540105 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
540125 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
540144 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:540351 original size:23 final size:21
Alignment explanation
Indices: 540299--540379 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
540289 CCAGAACCCC
* *
540299 AGGGGGTATCGATTCCCCT-A
1 AGGGGGAATCGGTTCCCCTCA
*
540319 TGTGGGGAATCGGTTCCCCTTCAA
1 AG-GGGGAATCGGTTCCCC-TC-A
540343 AGGGGGAATCGGTT-CCCTCA
1 AGGGGGAATCGGTTCCCCTCA
* *
540363 AGGGGGGATCGATTCCC
1 AGGGGGAATCGGTTCCC
540380 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 14 0.28
21 18 0.36
22 4 0.08
23 12 0.24
24 2 0.04
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.23
Consensus pattern (21 bp):
AGGGGGAATCGGTTCCCCTCA
Found at i:540367 original size:20 final size:21
Alignment explanation
Indices: 540322--540381 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
540312 TCCCCTATGT
540322 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGGTT-CCC-TCAAAG
540345 GGGGAATCGGTTCCCTC-AAG
1 GGGGAATCGGTTCCCTCAAAG
* *
540365 GGGGGATCGATTCCCTC
1 GGGGAATCGGTTCCCTC
540382 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.18, C:0.27, G:0.33, T:0.22
Consensus pattern (21 bp):
GGGGAATCGGTTCCCTCAAAG
Found at i:561562 original size:18 final size:20
Alignment explanation
Indices: 561529--561572 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
561519 TTAAATCCCT
561529 ATATTTATTAAATAAA-ATA
1 ATATTTATTAAATAAATATA
*
561548 ATATTT-TTCAATAAATATA
1 ATATTTATTAAATAAATATA
*
561567 TTATTT
1 ATATTT
561573 CGGGTCAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTTATTAAATAAATATA
Found at i:566986 original size:2 final size:2
Alignment explanation
Indices: 566979--567024 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
566969 TGCTCATTAA
*
566979 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
567021 AT AT
1 AT AT
567025 GTACACACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:569515 original size:77 final size:79
Alignment explanation
Indices: 569427--569585 Score: 218
Period size: 77 Copynumber: 2.0 Consensus size: 79
569417 TTCGAATTAA
*
569427 TTAAACTCTTATTTAATTAATTC-AAATTAAATATCCATTA-AATACTTATAATCT-GAATTACA
1 TTAAACTCTTATTTAATT-ATTCTAAATTAAATATCCATTACAAGACTTATAAT-TAGAATTACA
569489 CTC-TTTAATGTTTAT
64 CTCTTTTAATGTTTAT
* * * * *
569504 TTAAACTCTTATTTAATTATTCTGAATTAAATATCCATTACAAGAGTTGTAATTAGAATTGCATT
1 TTAAACTCTTATTTAATTATTCTAAATTAAATATCCATTACAAGACTTATAATTAGAATTACACT
569569 CTTTTAATGTTTAT
66 CTTTTAATGTTTAT
569583 TTA
1 TTA
569586 CTATATTCGG
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
76 4 0.06
77 35 0.49
78 18 0.25
79 15 0.21
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (79 bp):
TTAAACTCTTATTTAATTATTCTAAATTAAATATCCATTACAAGACTTATAATTAGAATTACACT
CTTTTAATGTTTAT
Found at i:571678 original size:2 final size:2
Alignment explanation
Indices: 571671--571710 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
571661 ATATAATTAA
571671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
571711 TTAGGGTGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:575707 original size:43 final size:43
Alignment explanation
Indices: 575483--575700 Score: 314
Period size: 43 Copynumber: 5.1 Consensus size: 43
575473 TGGTAACAAA
* *** * *
575483 AAACGTCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* *
575526 AAACGCCGCAATAGGTGTTGATATTTGGTGGC-TTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
*
575568 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
575611 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTGTCC-AC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTT-TCCAAC
* *
575654 AAACGCCGCAATAGGTCTTGATATTTAGCGGCGTTTTTCCTAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
575697 AAAC
1 AAAC
575701 ATCGCAAAAG
Statistics
Matches: 159, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
42 41 0.26
43 115 0.72
44 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
Done.