| Scoring Example |
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| RHYPGDFSPA |
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| ARFPADFTAE |
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| 0114044101 = 16
points |
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| -RHYPGDFSPA- |
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| ARF-PADFT-AE |
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| -41-40441-4- = 18 points |
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| The “-” above represents -1 |
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| • | Are
there other alignments |
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| that
give the same score or a |
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| higher
score? |
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| • | Can
we resolve these |
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| questions
without having to |
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| look
at all possible |
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| alignments? |
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| CS409 - Spring
2000 |
| 12 |