Example for output from COILS

Sequence: GCN4_YEAST (SWISS-PROT)

Coils output appended by default

OUTPUT

Note 1: comments marked by "## COMMENT: "

Note 2: to surpress a prediction of COILED coil regions use in the input the keyword no coils

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--- COILS HEADER: SUMMARY

COILS version 2.2: R.B. Russell, A.N. Lupas, 1999
using MTK matrix.
weights: a,d=2.5 and b,c,e,f,g=1.0

For the threshold of 5 ( probability > 0.5):
>prot

window size = 14        14  residues in coiled coil domain
window size = 21        35  residues in coiled coil domain
window size = 28        42  residues in coiled coil domain

               .    :    .    :    .    :    .    :    .    5
seq        MSEYQPSLFALNPMGFSPLDGSKSTNENVSASTSTAKPMVGQLIFDKFIK
frame-14   abcdefgabcdefgbabcabcdefgabcdefgefgfgfgaabcdefgabc
frame-21   abcdefaabcdabababcabcabcdefgabcdefgabcdefgdefgcdef
frame-28   abcdefgabcdefgabcdabcdefgabcdefgabcdefgabcdefgabcd
prob-14    --------------------------------------------------
prob-21    --------------------------------------------------
prob-28    --------------------------------------------------
               .    :    .    :    .    :    .    :    .    10
seq        TEEDPIIKQDTPSNLDFDFALPQTATAPDAKTVLPIPELDDAVVESFFSS
frame-14   defgdefgbcdefgabcdefgbcdefgefgeabcdabcabcdefgabcde
frame-21   gabcdefgabcdefgbcdefgbcdefggeabcdefgabcdefaabcdefg
frame-28   efgcdefgbcdefgabcdefgbcdefgbcabcdefabcabcdefgabcde
prob-14    --------------------------------------------------
prob-21    --------------------------------------------------
prob-28    --------------------------------------------------
               .    :    .    :    .    :    .    :    .    15
seq        STDSTPMFEYENLEDNSKEWTSLFDNDIPVTTDDVSLADKAIESTEEVSL
frame-14   fgabcdabcabcdefgabcdefgefggabaabcaabcdefgabcdefgef
frame-21   ababcdefgabcdefgabcdefgabcdabcdefgabcdefgabcdefgef
frame-28   fgabcdefgabcdefgabcdabcdefgabcdefgabcdefgabcdefgbc
prob-14    ---------11111111111111---------------------------
prob-21    --------------------------------------------------
prob-28    --------------------------------------------------
               .    :    .    :    .    :    .    :    .    20
seq        VPSNLEVSTTSFLPTPVLEDAKLTQTRKVKKPNSVVKKSHHVGKDDESRL
frame-14   gdefgefgefgfgaabcabcdefgabcdefgdefgabcdefgabcdefga
frame-21   gabcdefgefgfgaabcabcdefgabcdefgabcdabcdefgabcdefga
frame-28   defgabcdefgdefabcabcdabcdefgabcdefgabcdefgabcdefga
prob-14    --------------------------------------------------
prob-21    --------------------------------------------------
prob-28    --------------------------------------------------
               .    :    .    :    .    :    .    :    .    25
seq        DHLGVVAYNRKQRSIPLSPIVPESSDPAALKRARNTEAARRSRARKLQRM
frame-14   bcdefgabcdefgcdefgeabcabcdaabcdefgabcdefgfabcdefga
frame-21   bcdefgabcdefgggfggaabcdeababcabcdefabcdefgabcdefga
frame-28   bcdefgabcdefgfgefgbabcabcdeaabcdabcabcdefgabcdefga
prob-14    ------------------------------------------22222229
prob-21    -----------------------------------222222299999999
prob-28    -----------------------------------999999999999999
               .    :    .    :    .    :    .    :    .    30
seq        KQLEDKVEELLSKNYHLENEVARLKKLVGER
frame-14   bcdefgabcdefgabcdefgabcdefgefgg
frame-21   bcdefgabcdefgabcdefgabcdefgefgg
frame-28   bcdefgabcdefgabcdefgabcdefgefgg
prob-14    999999999999944444441111111----
prob-21    999999999999999999998888888----
prob-28    999999999999999999999999999----
// End
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