Upcoming Ensembl Platform Transition

This is the final release of its kind on this website.

In summer 2026, this site will bring you to the new Ensembl platform currently at beta.ensembl.org.
Please bookmark this archive to retain access to the current site, tools and functionality until they are available on the new platform -> jun2026.archive.ensembl.org

 
Ensembl Home
More ▼
Search »
In this section
Related content

Human vs Greater bamboo lemur LastZ results

Human (Homo sapiens, GRCh38) and Greater bamboo lemur (Prolemur simus, Prosim_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 96. Human was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterHumanGreater bamboo lemur
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 2,014,256 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Human

Uncovered: 1,312,622,606 out of 3,099,750,718
Covered: 1,787,128,112 out of 3,099,750,718

Uncovered: 1,284,235 out of 38,571,754
Matches: 32,937,987 out of 38,571,754
Mismatches: 4,020,790 out of 38,571,754
Insertions: 328,742 out of 38,571,754
Identity over aligned base-pairs: 88.3%

Greater bamboo lemur

Uncovered: 755,234,491 out of 2,411,593,676
Covered: 1,656,359,185 out of 2,411,593,676

Uncovered: 1,088,868 out of 32,178,253
Matches: 28,173,654 out of 32,178,253
Mismatches: 2,808,892 out of 32,178,253
Insertions: 106,839 out of 32,178,253
Identity over aligned base-pairs: 90.6%

Block size distribution

Size range All 2,014,256 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
74,718
507.2 kb
10 bp - 100 bp
286,418
13.4 Mb
30,201
2.0 Mb
100 bp - 1 kb
1,051,944
461.3 Mb
109,926
37.8 Mb
1 kb - 10 kb
598,929
1.3 Gb
30,651
74.9 Mb
10 kb - 100 kb
2,238
30.0 Mb
2,735
75.2 Mb
100 kb - 1 Mb
9
1.0 Mb
1,074
413.4 Mb
1 Mb - 10 Mb
508
1.2 Gb
10 Mb - 100 Mb
2
25.1 Mb