Chained pairwise alignments between this assembly and the hub's reference, cs10. A chain is an ordered series of gapless aligned blocks; gaps between blocks may be on either or both sequences.
Blocks are drawn as boxes joined by lines across gaps: a single line marks a gap in one sequence, a double line gaps in both. On cs10 the chains to every assembly sit in the Pairwise chains super-track, one track per assembly; on every other assembly a single track shows its chain to cs10. Click a block to see the aligned region in the other assembly.
Each assembly was aligned to cs10 (CBDRx, GCF_900626175.2) in Galaxy with UCSC's pairwise recipe: seeds and ungapped extension in KegAlign on a GPU, gapped extension in LASTZ, then axtChain, chainAntiRepeat, chainMergeSort, chainPreNet, chainNet and netSyntenic, using a substitution matrix derived from Cannabis haplotype pairs. Before alignment every assembly's depositor masking was removed and replaced by the union of four repeat detectors (WindowMasker, DustMasker, tantan and FasTAN), so all assemblies were masked alike. The track shows the chains UCSC itself turns into a chain track (the over.chain of doBlastzChainNet.pl: netChainSubset over the net, then chainStitchId), converted with chainToBigChain; on the other assembly it is the same chain swapped with chainSwap.
Every track file is a bigBed or bigWig under this hub's directory, named by the track's bigDataUrl, and can be read with UCSC's bigBedToBed and bigWigToBedGraph or downloaded directly.
Alignment pipeline by the HighGen project in Galaxy; UCSC kent utilities for chaining and display.
Contact: rcb112@psu.edu
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. PNAS 2003;100:11484-11489.
Harris RS. Improved pairwise alignment of genomic DNA. PhD thesis, The Pennsylvania State University, 2007.
Gulhan et al. KegAlign: optimizing pairwise alignments with diagonal partitioning. 2025.