seqs length in align.seqs command

Commands in mothur
1

Dear all,
I am wondering about my alignment. In the beginning, all my seqs have a length of 301 bp. After the alignment, the length is shorter. Why is that? Am I worried within reason?
Summary before align.seqs:
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 301 301 0 3 1
2.5%-tile: 1 301 301 0 4 12392
25%-tile: 1 301 301 0 4 123916
Median: 1 301 301 0 4 247832
75%-tile: 1 301 301 0 5 371747
97.5%-tile: 1 301 301 0 5 483271
Maximum: 1 301 301 2 13 495662
Mean: 1 301 301 1.00875e-005 4.27215

of unique seqs: 80227

total # of seqs: 495662

Summary after align.seqs:
Start End NBases Ambigs Polymer NumSeqs
Minimum: 0 0 0 0 1 1
2.5%-tile: 1043 5425 281 0 4 2006
25%-tile: 1043 5428 281 0 4 20057
Median: 1043 5461 281 0 4 40114
75%-tile: 1043 6106 281 0 5 60171
97.5%-tile: 1043 6333 282 0 5 78222
Maximum: 25318 25318 301 2 13 80227
Mean: 1140.69 5741.85 279.618 3.73939e-005 4.49485

of Seqs: 80227

thanks a lot for your help,
Maraike

2

I suspect your sequences include the 8f/27f primer. The reference alignment does not contain it since it is always primer sequence (unless it’s coming form a genome sequence). Since the alignment starts at 1044, you’ll lose anything that starts before there.

Pat

3

Yeah, that the primer. Okay, great to know. Thanks a lot!