about screen.seqs

Commands in mothur
1

Hello,

I have some problem to select the optimal end or start point in screen.seqs. After doing the alignment with Silva reference, I got the summary showed in below :
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1044 1130 27 0 2 1
2.5%-tile: 1044 1463 46 0 3 1487
25%-tile: 6428 15647 64 0 4 14866
Median: 13861 23443 117 0 4 29732
75%-tile: 32661 35424 222 0 4 44598
97.5%-tile: 42630 43116 422 0 5 57977
Maximum: 43020 43116 519 0 7 59463
Mean: 17939.5 23935.7 157.178 0 4.05686

of Seqs: 59463

I think there is less overlap of sequences with each other. I’m not sure what is the optimal end or start point which I should to use. Please suggest me.
Thank you very much

2

What are these data? We need some context. The first thing that comes to mind is that your sequences might need to be flipped in the trim.seqs or align.seqs steps. Do you know what direction your sequences were sequenced in? Did you use the flip=T option in trim.seqs?