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Table 17 Score selection. W m (W ms ) is the score for matching (mismatching) bases. Other notations are given in the text.

From: Splign: algorithms for computing spliced alignments with identification of paralogs

Alignment A Alignment B Conditions
a consensus intron and no indels a non-consensus intron and no indels Δ 1 1 < W c W n c W m W m s < Δ 1 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaeuiLdq0aaSbaaSqaaiabigdaXaqabaGccqGHsislcqaIXaqmcqGH8aapjuaGdaWcaaqaaiabdEfaxnaaBaaabaGaem4yamgabeaacqGHsislcqWGxbWvdaWgaaqaaiabd6gaUjabdogaJbqabaaabaGaem4vaC1aaSbaaeaacqWGTbqBaeqaaiabgkHiTiabdEfaxnaaBaaabaGaemyBa0Maem4CamhabeaaaaGccqGH8aapcqqHuoardaWgaaWcbaGaeGymaedabeaaaaa@44E2@
a consensus intron and an indel a non-consensus intron and no indels Δ 2 + W m W m W m s 1 < W c W n c + W g + W s W m W m s < Δ 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=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@579F@
two consensus introns and no indels a non-consensus intron and no indels Δ 3 1 < 2 W c W n c W m W m s < Δ 3 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaeuiLdq0aaSbaaSqaaiabiodaZaqabaGccqGHsislcqaIXaqmcqGH8aapjuaGdaWcaaqaaiabikdaYiabdEfaxnaaBaaabaGaem4yamgabeaacqGHsislcqWGxbWvdaWgaaqaaiabd6gaUjabdogaJbqabaaabaGaem4vaC1aaSbaaeaacqWGTbqBaeqaaiabgkHiTiabdEfaxnaaBaaabaGaemyBa0Maem4CamhabeaaaaGccqGH8aapcqqHuoardaWgaaWcbaGaeG4mamdabeaaaaa@45DC@
a consensus intron and no indels two consensus introns and no indels Δ 4 1 < W c W m W m s < Δ 4 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaeuiLdq0aaSbaaSqaaiabisda0aqabaGccqGHsislcqaIXaqmcqGH8aapjuaGdaWcaaqaaiabgkHiTiabdEfaxnaaBaaabaGaem4yamgabeaaaeaacqWGxbWvdaWgaaqaaiabd2gaTbqabaGaeyOeI0Iaem4vaC1aaSbaaeaacqWGTbqBcqWGZbWCaeqaaaaakiabgYda8iabfs5aenaaBaaaleaacqaI0aanaeqaaaaa@40E2@
two consensus introns and no indels a non-consensus intron and an indel Δ 5 1 < 2 W c W n c W g W s W m W m s < Δ 5 W m W m W m s MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=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@5956@
a consensus intron and no indels two consensus introns and an indel Δ 6 + W m W m W m s 1 < W g + W s W c W m W m s < Δ 6 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaeuiLdq0aaSbaaSqaaiabiAda2aqabaGccqGHRaWkjuaGdaWcaaqaaiabdEfaxnaaBaaabaGaemyBa0gabeaaaeaacqWGxbWvdaWgaaqaaiabd2gaTbqabaGaeyOeI0Iaem4vaC1aaSbaaeaacqWGTbqBcqWGZbWCaeqaaaaacqGHsislcqaIXaqmcqGH8aapdaWcaaqaaiabdEfaxnaaBaaabaGaem4zaCgabeaacqGHRaWkcqWGxbWvdaWgaaqaaiabdohaZbqabaGaeyOeI0Iaem4vaC1aaSbaaeaacqWGJbWyaeqaaaqaaiabdEfaxnaaBaaabaGaemyBa0gabeaacqGHsislcqWGxbWvdaWgaaqaaiabd2gaTjabdohaZbqabaaaaiabgYda8iabfs5aenaaBaaabaGaeGOnaydabeaaaaa@52AC@