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| The sequence parameter options specify how to represent the sequence if the reference is specified (refFile option). If the reference is not specified or seqOrig is specified, no modifications are made to the sequence. If the reference and seqBases is specified, any matches between the sequence and the reference are represented in the sequence as the appropriate base. If the reference and seqEquals is specified, any matches between the sequence and the reference are represented in the sequence as '='. | | The sequence parameter options specify how to represent the sequence if the reference is specified (refFile option). If the reference is not specified or seqOrig is specified, no modifications are made to the sequence. If the reference and seqBases is specified, any matches between the sequence and the reference are represented in the sequence as the appropriate base. If the reference and seqEquals is specified, any matches between the sequence and the reference are represented in the sequence as '='. |
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− | ==== Example ==== | + | ==== Examples ==== |
− | ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS | + | ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS |
− | Sequence: AATAA CTAGA T AGGG | + | Sequence: AATAA CTAGA T AGGG |
− | Reference: TAACCCTA ACCCT A | + | Reference: TAACCCTA ACCCT A |
− | Sequence with Orig: AATAACTAGATAGGG | + | Sequence with Orig: AATAACTAGATAGGG |
− | Sequence with Bases: AATAACTAGATAGGG | + | Sequence with Bases: AATAACTAGATAGGG |
− | Sequence with Equals: AA======G===GGG | + | Sequence with Equals: AA======G===GGG |
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− | ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS | + | ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS |
− | Sequence: AATGA CTGGA T AGGG | + | Sequence: AATGA CTGGA T AGGG |
− | Reference: TAACCCTA ACCCT A | + | Reference: TAACCCTA ACCCT A |
− | Sequence with Orig: AATGACTGGATAGGG | + | Sequence with Orig: AATGACTGGATAGGG |
− | Sequence with Bases: AATGACTGGATAGGG | + | Sequence with Bases: AATGACTGGATAGGG |
− | Sequence with Equals: AA=G===GG===GGG | + | Sequence with Equals: AA=G===GG===GGG |
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− | ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS | + | ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS |
− | Sequence: AAT=A CT=GA T AGGG | + | Sequence: AAT=A CT=GA T AGGG |
− | Reference: TAACCCTA ACCCT A | + | Reference: TAACCCTA ACCCT A |
− | Sequence with Orig: AAT=ACT=GATAGGG | + | Sequence with Orig: AAT=ACT=GATAGGG |
− | Sequence with Bases: AATGACTGGATAGGG | + | Sequence with Bases: AATGACTGGATAGGG |
− | Sequence with Equals: AA======G===GGG | + | Sequence with Equals: AA======G===GGG |
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− | ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS | + | ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS |
− | Sequence: AA=== ===G= = =GGG | + | Sequence: AA=== ===G= = =GGG |
− | Reference: TAACCCTA ACCCT A | + | Reference: TAACCCTA ACCCT A |
− | Sequence with Orig: AA======G===GGG | + | Sequence with Orig: AA======G===GGG |
− | Sequence with Bases: AATAACTAGATAGGG | + | Sequence with Bases: AATAACTAGATAGGG |
− | Sequence with Equals: AA======G===GGG | + | Sequence with Equals: AA======G===GGG |
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| === Parameters === | | === Parameters === |