[Reincarnate]

I think maybe I am not clear how you are supposed to be scoring stuff

is this right?

seq1: --ATGTTAT
seq2: ATCGTAGTA
score: -45

seq1: -A-TGTTAT
seq2: ATCGTAGTA
score: -45

seq1: -AT-GTTAT
seq2: ATCGTAGTA
score: -50

seq1: -ATG-TTAT
seq2: ATCGTAGTA
score: -25

seq1: -ATGT-TAT
seq2: ATCGTAGTA
score: 0

seq1: -ATGTT-AT
seq2: ATCGTAGTA
score: 0

seq1: -ATGTTA-T
seq2: ATCGTAGTA
score: -5

seq1: -ATGTTAT-
seq2: ATCGTAGTA
score: 20

seq1: A--TGTTAT
seq2: ATCGTAGTA
score: -20

seq1: A-T-GTTAT
seq2: ATCGTAGTA
score: -25

seq1: A-TG-TTAT
seq2: ATCGTAGTA
score: 0

seq1: A-TGT-TAT
seq2: ATCGTAGTA
score: 25

seq1: A-TGTT-AT
seq2: ATCGTAGTA
score: 25

seq1: A-TGTTA-T
seq2: ATCGTAGTA
score: 20

seq1: A-TGTTAT-
seq2: ATCGTAGTA
score: 45

seq1: AT--GTTAT
seq2: ATCGTAGTA
score: 5

seq1: AT-G-TTAT
seq2: ATCGTAGTA
score: 30

seq1: AT-GT-TAT
seq2: ATCGTAGTA
score: 55

seq1: AT-GTT-AT
seq2: ATCGTAGTA
score: 55

seq1: AT-GTTA-T
seq2: ATCGTAGTA
score: 50

seq1: AT-GTTAT-
seq2: ATCGTAGTA
score: 75

seq1: ATG--TTAT
seq2: ATCGTAGTA
score: 5

seq1: ATG-T-TAT
seq2: ATCGTAGTA
score: 30

seq1: ATG-TT-AT
seq2: ATCGTAGTA
score: 30

seq1: ATG-TTA-T
seq2: ATCGTAGTA
score: 25

seq1: ATG-TTAT-
seq2: ATCGTAGTA
score: 50

seq1: ATGT--TAT
seq2: ATCGTAGTA
score: 5

seq1: ATGT-T-AT
seq2: ATCGTAGTA
score: 5

seq1: ATGT-TA-T
seq2: ATCGTAGTA
score: 0

seq1: ATGT-TAT-
seq2: ATCGTAGTA
score: 25

seq1: ATGTT--AT
seq2: ATCGTAGTA
score: 30

seq1: ATGTT-A-T
seq2: ATCGTAGTA
score: 25

seq1: ATGTT-AT-
seq2: ATCGTAGTA
score: 50

seq1: ATGTTA--T
seq2: ATCGTAGTA
score: 55

seq1: ATGTTA-T-
seq2: ATCGTAGTA
score: 80

seq1: ATGTTAT--
seq2: ATCGTAGTA
score: 55

max score 80?

score: +matrix[base1][base2] if base1 and base2 match (e.g. "AA"), -matrix[base1][base2] if they don't match (e.g. "GC"), and -5 if we have a gap (e.g. "T-")

Wait you can insert gaps in both sequences, or just the shorter of the two?

(I also don't want to waste your time if I am going off-track with all this -- feel free to ignore if you're on a tight deadline)