Thanks Pierre! Actually, I'm more interested in http://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/nestedRepeats.txt.gz!
Which repeats are present in soft-masked sequence?
1 answer
Under http://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/, you can find simpleRepeat.txt.gz (and the schema in simpleRepeat.sql)
585 chr1 6480 6509 trf 3 9.7 3 100 0 58 68 31 0 0 0.89 AAC
585 chr1 6811 6856 trf 2 22.5 2 100 0 90 51 0 48 0 1 AG
585 chr1 7006 7048 trf 2 21 2 100 0 84 50 50 0 0 1 CA
585 chr1 7590 7709 trf 14 8.8 14 81 7 102 33 48 16 0 1.52 GCACACACACGCAC
585 chr1 7591 7670 trf 4 19.8 4 92 0 68 36 50 12 0 1.41 CACA
585 chr1 7591 7719 trf 10 12.8 10 79 6 98 34 48 15 1 1.55 CACACACGCA
585 chr1 7593 7682 trf 18 5.1 18 87 4 101 33 50 15 0 1.45 CACACACACGCACGCACG
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Pierre Lindenbaum
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