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MAL7 MAL7.remapped No telomere present at the left-end. A GC plateau (arrowed) is characteristic due to the terminal 7 bp repeat (not shown). Files: MAL7.embl.

Published byDayna Chase Modified over 8 years ago

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Presentation on theme: "MAL7 MAL7.remapped No telomere present at the left-end. A GC plateau (arrowed) is characteristic due to the terminal 7 bp repeat (not shown). Files: MAL7.embl."— Presentation transcript:

1 MAL7 MAL7.remapped No telomere present at the left-end. A GC plateau (arrowed) is characteristic due to the terminal 7 bp repeat (not shown). Files: MAL7.embl ; MAL7.embl.remapped; MAL7.remapped.fasta.V.MAL7.fasta.crunch Directory: /nfs/disk222/yeastpub/analysis/pathogen/malaria/ annotation/Plasmodium/falciparum/geneDB/chr7 Missing left hand telomere

2 gap MAL7 The gap is probably where the two telomere ends meet back to back. MAL7.remapped

3 The regions that probably belong to right and left telomeres are marked up on the gene line in green in MAL7.remapped. Good hits to the right telomere of MAL7.embl Hits the right telomere but inverted

4 Good hits to the right telomere, left section inverted. Hits overlap suggesting repeats are causing problems

5 These two regions have hits in both the right and the left teleomeres but hits are strongest to the right telomere. Again probably highly repetitive regions. Both are inverted.

6 Positioning of 7 bp tandem repeats which are characteristic of the terminal part of the telomere support this hypothesis. To view them read MAL7.remapped.7bp.repeats.Sco65 as and entry into MAL7.remapped. (Sco 65 is to show a 65 score cutoff). This cutoff will affect the percentage identitiy within the repeat consensus.

7 There are 21 bp repeats in this region. The file is MAL7.remapped.21bp.repeats.Sco200 and can be read as an entry into act. Also the MAL7.remapped.21bp.repeats.Sco800 gives a better idea as it only selects more well conserved repeats.

8 The layout of telomeres and subtelomeres in Plasmodium falciparum, characterised elements RepeatOther namestypeUnit size Presence Terminal repeatTandem7 ALL 14 bp repeatTARE-1, SB-1Tandem14 Most TARE-2Tandem135 Most TARE-3692-bp, 0.5Kb repeat Tandem692 Almost All TARE-4Tandem/inverted Most TARE-512-bp repeatTandem12 Most 17-bp repeatTandem17 ? 23/28 bp repeatTandem23/28 ? Rep11Tandem11 ? Rep20Rep2, 21-bp repeat, TARE-6, SB-3 Tandem21 ALL This is not to scale just to give an approximate idea of the layout of the telomere. These repeat elements are not always present. Those with thick outline are always present. Can compare to the layout of other finished chromosomes. MAL13 has repeat units annotated. There are files which show the positions of 14, 135, 21(rep20) and 12 bp repeats in MAL7.remapped. /nfs/disk222/yeastpub/analysis/pathogen/malaria/annotation/Plasmodium/falciparum/geneDB/chr7 Rep11 seems to be absent as does 17-bp repeat. The locations of the 7, 135 and 21 bp repeats seems to suggest that the region around 1387 kb (in remapped) are the telomere termini fused.

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