Table 4

The Stemloc grammar, part 3 pf 3: emissions.

L

R

(L R)


xyLoopMatch

baseSubstitution [A, B]

yLoopIns

baseIndel [B]

xLoopDel

baseIndel [A]

xyLBulgeMatch

baseSubstitution [A, B]

yLBulgeIns

baseIndel [B]

xLBulgeDel

baseIndel [A]

xyRBulgeMatch

baseSubstitution [C, D]

yRbulgeIns

baseIndel [D]

xRBulgeDel

baseIndel [C]

xyLRBulgeMatch

baseSubstitution [A, B]

yLRBulgeIns

baseIndel [B]

xLRBulgeDel

baseIndel [A]

xyStemMatch

basepairSubstitution [AC, BD]

yStemIns

basepairIndel [BD]

xStemDel

basepairIndel [AC]


Holmes BMC Bioinformatics 2005 6:73   doi:10.1186/1471-2105-6-73

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