[maker-devel] Repeat annotation by Maker2

[Quanwei Zhang]

Hello:

We want to summarize the statistical information of repeats for the genome
annotated by  Maker2. But we are not clear what does the annotation mean.
Would you explain? Many thanks!

Let me take this example
CasCan_contig_16053    repeatmasker    match    35887    35996    423
+    .
ID=CasCan_contig_16053:hit:51261:1.3.0.0;Name=species:Charlie4z|genus:DNA%2FhAT-Charlie;Target=species:Charlie4z|genus:DNA%2FhAT-Charlie
48 161 +

(1) "35887" and "35996" are the start and end position of the "match" in
this contig, and so for this repeat element it covers 35996-35887+1 (i.e.,
110bp) in the contig. Right?
(2) What does the "Name=species" (and "Target=species") mean?
(3) "genus" show the type of repeat element, right? Then what does "%" mean
in "DNA%2FhAT-Charlie" ?
(4) what does "48" and "161" mean? Are they the coordinates of the "match"
in the repeat element?



Examples:
CasCan_contig_16053    repeatmasker    match    35887    35996    423
+    .
ID=CasCan_contig_16053:hit:51261:1.3.0.0;Name=species:Charlie4z|genus:DNA%2FhAT-Charlie;Target=species:Charlie4z|genus:DNA%2FhAT-Charlie
48 161 +
CasCan_contig_16053    repeatmasker    match_part    35887    35996
423    +    .
ID=CasCan_contig_16053:hsp:120045:1.3.0.0;Parent=CasCan_contig_16053:hit:51261:1.3.0.0;Target=species:Charlie4z|genus:DNA%252FhAT-Charlie
48 161 +
CasCan_contig_16053    repeatmasker    match    36842    37881    2546
+    .
ID=CasCan_contig_16053:hit:51262:1.3.0.0;Name=species:L1MC1_EC|genus:LINE%2FL1;Target=species:L1MC1_EC|genus:LINE%2FL1
5384 6062 +
CasCan_contig_16053    repeatmasker    match_part    36842    37881
2546    +    .
ID=CasCan_contig_16053:hsp:120046:1.3.0.0;Parent=CasCan_contig_16053:hit:51262:1.3.0.0;Target=species:L1MC1_EC|genus:LINE%252FL1
5384 6062 +


Best
Quanwei
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