• $SUBCMD$
Generated: $TIME$
$JOB_NAME$
$COMMAND$
| Version | $VERSION$ |
| Subcommand | $SUBCMD$ |
| Input | $INPUT$ |
| Output | $OUTPUT$ |
| Ksizes | $KSIZES$ |
| Max Period | $MAX_PERIOD$ |
| Rolling Window Size | $ROLLING_WINDOW_SIZE$ |
| Min Smoothness Score | $MIN_SMOOTHNESS_SCORE$ |
| Alignment Parameters | $ALIGNMENT_PARAMETERS$ |
| Min Alignment Score | $MIN_ALIGNMENT_SCORE$ |
| Min Copy Number | $MIN_COPY_NUMBER$ |
| Total Running Time | $TOTAL_RUNNING_TIME$ |
Raw TRs
enomic regions with a smoothness score above the threshold. Regions are merged if they share the same motif period and are separated by less than 2 * ksize.
Polished TRs
Refined regions whose boundaries have been extended from the raw TRs. Neighboring regions with similar motifs are combined if adding the downstream sequence increases the confidence score.
Final TRs
Tandem repeats that remain after filtering based on alignment scores and are output.
| Number of Raw TRs | $NUMBER_OF_RAW_TRS$ |
| Number of Polished TRs | $NUMBER_OF_POLISHED_TRS$ |
| Number of Final TRs | $NUMBER_OF_FINAL_TRS$ |
The smoothness score shows how evenly spaced the motifs are in a genomic region. Regions with regular, uniform spacing get higher scores.
TR fraction panel shows the abundance of tandem repeats within each genomic window. Median TR length panel shows the median length of overlapped TRs overlapped with the specific window. Median motif length panel shows the median motif length of overlapped TRs overlapped with the specific window.
Entropy measures the nucleotide composition complexity within a tandem repeat. It is calculated from the nucleotide composition of the repeat. e.g., (A)n's entropy is 0, (ACTG)n's entropy is 1.