Reference sequence TACATTCACAGAATGAT Fragments AT ACT GAA AG

Reference sequence: TACATTCACAGAATGAT Fragments: AT ACT GAA AGATT TCACTGA TAGATT TTCACT GAATG AGATT a) Align the set of mini-fragments above. ACCTACATTCGACAGAATGAT TC-ACTGA ACCTAG ACT GAA TAGATT AATGAT TTC-ACT AAT GAT AGA TTC TGAATG AGA TT GAATG ATTC-ACT ACCTAG AATGAT TGAATG ATT CACT

Solution

OH I GOT YOUR POINT, Actually the dashes are Guanine residues ... u just have to see reads aligned to reference... i will tell u how to read overlaps ... look vertically along all nucleoties u will see A in1st column c in 2nd and 3rd column ... two times T in 4th column vertically and 4 times A in 5th column .... when all else is aligned then the dash is possibly G as seen from the reference sequence .... it is like u imagine reference and read sequences as a table / grid .... then look vertically from all colums and see overlapping read nucleotide .... instead of overalpping reads we finally write just one continious nucleotide in reference ...

one more point sometimed u see reference and read not matching in nucleotide ... that could be sequencing error ... we have to see if our alignment satisfies the majority of read alignments or not .....if it does about 90% of times we consider it proper alignment and where ever there is a mismatch with reference sequence that could be because of possible SNP single nucleotide polymorphism or a mutation compared to reference genome ......

HOPE IT HELPS U TO UNDERSTAND IT and if i still didnt get your point what u wanted to know feel free to contact me as many times as u want i would be glad to answer my level best ..... Regards