usearch -ublast reads.fastq -db proteins.fa -evalue 0.01 -userout
hits.txt
-userfields query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits
| query | Query sequence label. | |
| target | Target sequenc label. | |
| clusternr | Cluster number. | |
| evalue | E-value. | |
| id | Fractional identity. | |
| mid | Fraction of letter pairs that match. | |
| pctpv | Percent positives (substitution score > 0). | |
| pctgaps | Percent gap columns. | |
| pairs | Number of letter pair columns. | |
| gaps | Number of gapped columns. | |
| qlo | 0-based start position of alignment in query sequence. | |
| qhi | 0-based end position of alignment in query sequence. | |
| tlo | 0-based start position of alignment in target sequence. | |
| thi | 0-based end position of alignment in target sequence. | |
| pv | Number of positive columns (substitution score > 0). | |
| ql | Query sequence length. | |
| tl | Target sequence length. | |
| qs | Query segment length. | |
| ts | Target segment length. | |
| alnlen | Number of alignment columns. | |
| opens | Number of gap opens. | |
| exts | Number of gap extensions (does not include gap opens). | |
| raw | Raw alignment score. | |
| bits | Bit score. | |
| aln | Alignment as string M=letter pair, D=delete (gap in query), I=insert (gap in target). | |
| caln | Compressed alignment (see uc file format). | |
| qseq | Full-length query sequence. | |
| tseq | Full-length target sequence. | |
| qstrand | Query strand. | |
| tstrand | Target strand. | |
| qrow | Aligned query segment with gaps. | |
| trow | Aligned target segment with gaps. | |
| qrowdots | Aligned query segment with gaps and dots for matched positions. | |
| trowdots | Aligned target segment with gaps and dots for matched positions. | |
| qframe | Query frame (-3 to +3). | |
| tframe | Target frame (-3 to +3). | |
| mism | Number of mismatches. | |
| ids | Number of columns with matching letters. | |
| qcov | Fraction of query sequence covered by alignment. | |
| tcov | Fraction of target sequence covered by alignment. | |
| diffs | Number of differences (gaps + mismatches). | |
| abskew | Abundance skew. | |
| qlor | 0-based query start coordinate. | |
| qhir | 0-based query end coordinate. | |
| tlor | 0-based target start coordinate. | |
| thir | 0-based target end coordinate. | |
| orflo | Start coordinate of query ORF in nt sequence. | |
| orfhi | End coordinate of query ORF in nt sequence. | |
| orfframe | Frame of query ORF. |