Zoomsa region genome alignments

Region name Flank Location
on Pf3D7_v3		 Aligned regions FASTA MAFFT
zoomsa		 SPOA
zoomsa		 Kmer sharing
k=31		 Kmer sharing
k=50		 ODGI
Pfsa1 ±±20kb Pf3D7_02_v3
611140-651240>
focus:631190		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
Pfsa2 ±±20kb Pf3D7_02_v3
794238-834338>
focus:814288		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
Pfsa3 ±±20kb Pf3D7_11_v3
1037985-1078085>
focus:1058035		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
SNRPF ±±20kb Pf3D7_11_v3
1034338-1074438>
focus:1054388		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
Pfsa4 ±±20kb Pf3D7_04_v3
1101422-1141522>
focus:1121472		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
CRT ±±20kb Pf3D7_07_v3
383568-423668>
focus:403618		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
AAT1 ±±20kb Pf3D7_06_v3
1195158-1235258>
focus:1215208		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
CSP ±±20kb Pf3D7_03_v3
202078-242178>
focus:222128		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
Annie_chr1_region ±±20kb Pf3D7_01_v3
537190-577290>
focus:557240		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
Annie_chr5_region ±±20kb Pf3D7_05_v3
176368-216468>
focus:196418		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
Annie_chr12_region ±±20kb Pf3D7_12_v3
152206-192306>
focus:172256		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
PTP7 ±±20kb Pf3D7_03_v3
76426-116526>
focus:96476		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
EBA175 ±±20kb Pf3D7_07_v3
1339950-1380050>
focus:1360000		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
CLAG3.1-3.2 ±±20kb Pf3D7_03_v3
111061-151161>
focus:131111		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
CLAG3.2 ±±20kb Pf3D7_03_v3
120010-160110>
focus:140060		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
Pfsa2B ±±20kb Pf3D7_02_v3
805307-845407>
focus:825357		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
FIKK3 ±±20kb Pf3D7_03_v3
59795-99895>
focus:79845		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
near_SR25 ±±20kb Pf3D7_07_v3
594370-634470>
focus:614420		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
REX2 ±±20kb Pf3D7_09_v3
1408825-1448925>
focus:1428875		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
REX2-v2 ±±20kb Pf3D7_09_v3
1407497-1447597>
focus:1427547		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
REX2-start ±±20kb Pf3D7_09_v3
1406102-1446202>
focus:1426152		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
K13 ±±20kb Pf3D7_13_v3
1706188-1746288>
focus:1726238		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
MDR1 ±±20kb Pf3D7_05_v3
939475-979575>
focus:959525		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
MSP2 ±±20kb Pf3D7_02_v3
253196-293296>
focus:273246		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
PMI ±±20kb Pf3D7_14_v3
269146-309246>
focus:289196		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
PMIII ±±20kb Pf3D7_14_v3
277842-317942>
focus:297892		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
AMA1 ±±20kb Pf3D7_11_v3
1274781-1314881>
focus:1294831		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
DHFR ±±20kb Pf3D7_04_v3
728931-769031>
focus:748981		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d
DHPS ±±20kb Pf3D7_08_v3
529426-569526>
focus:549476		 aligned
regions (paf)		 ±20000bp mafft
zoomsa		 spoa alignment
zoomsa		 (full region)
10kb
5kb
2kb 		(full region)
10kb
5kb
2kb 		1d
2d