Table S1,,,,,,,,
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Full list of non-telomeric Putative Quadruplex Sequences (PQS) in the Plasmodium falciparum 3D7 genome.,,,,,,,,
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Chromosome,Location,PQS Length,PQS,Type,Gene ID,Strand,Distance,Annotation
1,28063,30,GGGTTAAGGGTATACATTTAGGGGTTAGGG,Ups,PFA0005w,same,-1670,var group B1T
1_RC,618320,30,GGGTTAAGGGTATAACTTTAGGGGTTAGGG,Ups,PFA0765c ,same,-1707,var group B1T
1_RC,413595,18,GGGAAGGGAAGGGAAGGG,Down,PFA0515w,same,272,"phosphatidylinositol-4-phosphate 5-kinase, putative"
2_RC,925279,30,GGGTTAAGGGTATAACTTTAGGGGTTAGGG,Ups,PFB1055c,same,-1631,var group B1T
3,6270,28,GGGCGTTTTTGGGCAGGGAAAACATGGG,Down,PFC0002c,same,1000,hypothetical protein
3,31989,30,GGGTTAAGGGTATAACTTTAGGGGTTAGGG,ups,PFC0005w,same,-1652,var group B1T
3_RC,1036592,30,GGGTTAAGGGTATAACTTTAGGGGTTAGGG,ups,PFC1120c,same,-1668,var groupB1T
3_RC,219831,21,GGGGGGGGAGGGGTAAAGGGG,ups,PFC0210c,same,-600,circumsporozoite protein
4,56009,15,GGGGGGTTGGGTGGG,In,PFD0020c,opposite,/,var group A
4,954664,31,GGGGTTGTTGAGGGTGGGTGTATCACTAGGG,In,PFD1000c,opposite,/,var group C
4,966563,30,GGGTTGTTGAGGGTGGGTGTATCACTAGGG,In,PFD1005c ,opposite,/,var group B1C
4,1163198,26,GGGATGTGTACGGGTAAGGGTCAGGG,In,PFD1235w,same,/,var group A1ST
4_RC,1185482,30,GGGTTAAGGGTATAACGTTAAGGGTTAGGG,Ups,PFD1245c,same,-1632,var group B1T
5,1028916,25,GGGGGGATATTCAAGGGGTTGAGGG,In,PFE1240w,same,/,"hypothetical protein, conserved."
5,1134887,20,GGGGGGGGGGGGGGAAGGGG,Ups,PFE1335c,opposite,-38,ubiquitin carboxyl-terminal hydrolase
5_RC,348719,31,GGGTAATGAAAAGGGGGGATAATCCTATGGG,In,PFE0420c,same,/,"guanidine nucleotide exchanfe factor, put."
6,91361,15,GGGGGGGGGGATGGG,Ups,PFF0100w,same,-1200,put ATP dependent RNA helicase
6_RC,1384241,30,GGGTTAAGGGTATAACTTTAGGGGTTAGGG,Ups,PFF1595c ,same,-1631,var group B1T
6_RC,10854,33,GGGTTCATCGGAAGGGAGGGGTTCTACCTCGGG,In,PFF0010w,opposite,/,var group B2ST
7,29016,30,GGGTTAAGGGTATAACTTTAGGGGTTAGGG,Ups,MAL7P1.212,same,-1657,var group B1T
7,759886,33,GGGATAGAGATAGGGATAGGGAGAGAGATAGGG,In,PF07_0066,same,/,"hypothetical protein, conserved"
7_RC,"1,483,196",30,GGGTTAAGGGTATAACTTTAGGGGTTAGGG,Ups,MAL7P1.187,same,-1586,var group B1T
8,20715,30,GGGTTAAGGGTATAACTTTAGGGGTTAGGG,Ups,PF08_0142,same,-1654,var group B1T
8,32738,27,GGGGGGGGTTGTACGGGTGGAGGCGGG,In,Pf08_0141,opposite,/,var groupA1ST
8,1277340,20,GGGTGTGGGGGGTACTAGGG,Ups,MAL8a_5.8s,same,-3735,rRNA encoding
8,1280299,28,GGGTTAGGGTTTAATATTAGGGTTAGGG,Ups,MAL8a_5.8s,same,-799,rRNA encoding
8,1280337,28,GGGTTAGGGTTTAATATTAGGGTTAGGG,Ups,MAL8a_5.8s,same,-761,rRNA encoding
8,1280375,28,GGGTTAGGGTTTAATATTAGGGTTAGGG,Ups,MAL8a_5.8s,same,-723,rRNA encoding
8,1280419,24,GGGTTCAGGGTTTAGGGTTTAGGG,Ups,MAL8a_5.8s,same,-656,rRNA encoding
8,1280465,23,GGGTTAGGGTTTAGGGTATAGGG,Ups,MAL8a_5.8s,same,-610,rRNA encoding
8,1352281,26,GGGATGTGTACGGGTAAGGGTCAGGG,In,MAL8P1.207,same,/,var group A1ST
8,1393835,26,GGGGGGTCCGGCTTCGGGGGCAGGGG,In,MAL8P1.220,opposite,/,var group B1T
8,1395843,30,GGGTCGTTGGGTTCAAGGGTACCACTAGGG,In,MAL8P1.221,opposite,/,var group B1T
8_RC,1412853,28,GGGCGTTTTTGGGTAGGGAAAACATGGG,In,MAL8P1.330,same,/,"hypothetical protein, conserved"
8_RC,1400996,30,GGGTTAAGGGTATACATTTAGGGGTTAGGG,Ups,MAL8P1.220,same,-1762,var group B1T
8_RC,1388790,24,GGGAGGGCTTGTTCCGGGAATGGG,In,MAL8P1.219,same,/,Rifin
8_RC,145999,22,GGGAAAATTTTGGGGGGTTGGG,Ups,PF08_0132,opposite,-1211,"glutamate dehydrogenase, putative"
8_RC,47973,33,GGGTGGTGGGGGTATCACTAGGGGCTGAGGGGG,In,PF08_0140,opposite,/,var group B1SST 
8_RC,46792,25,GGGCTGTCGGGTGGTGGGTTTAGGG,In,PF08_0140,opposite,/,var group B1SST 
9,18452,30,GGGTTAAGGGTATAACTTTAGGGGTTAGGG,Ups,PFI0005w,same,-1628,var group B1T
9,1498042,28,GGGGGGTTTTGGTTGTGGGGTTTCGGGG,In,PFI1830c,opposite,/,var group B1T
9_RC,1349719,18,GGGGGGGAGGGTTTAGGG,Ups,PFI1665w,opposite,-60,uncharacterised trophozoite protein
9_RC,23803,30,GGGTTGTTGAGGGTGGGTGTATCACTAGGG,In,PFI0005w,opposite,/,var group B1T
10,768185,20,GGGGGGGAAGGGAGGTAGGG,In,PF10_0184,opposite,/,hypothetical protein
10,1257838,29,GGGGATTGGGTTGATGGGAAAATGCAGGG,In,PF10_0306,same,/,MORN repeat containing pro
10,1646314,30,GGGAAGAGGAGCCGGGGGTGATGGGTTGGG,In,PF10_0406,opposite,/,var group B1T
10_RC,1651590,30,GGGTTAAGGGTATAACGTTAAGGGTTAGGG,Ups,PF10_0406 ,same,-1643,var group B1T
10_RC,565972,25,GGGAAATGGGGGGTCCAAATATGGG,In,PF10_0263,opposite,/,hypothetical protein
11,22548,30,GGGTTAAGGGTATAACTTTAGGGGTTAGGG,Ups,PF11_0007,same,-1612,var groupB1T
11,934696,14,GGGGGGGGGGGGGG,Ups,PF11_0247,same,-1387,hypothetical protein
11,969496,18,GGGAAGGGAAGGGAAGGG,Down,PF11_0256,same,800,pyruvate dehydrogenase
12,985239,25,GGGGTTGGGTTAGGGTCTATGAGGG,Down,PFL1165w,same,900,"hypothetical protein, conserved"
12,1360358,14,GGGGGGGTGGGGGG,Down,PFL1595w,same,800,"hypothetical protein, conserved"
12,1593645,22,GGGGGGGAAGGGGAATGTAGGG,In,PFL1960c,opposite,/,"hypothetical protein, conserved"
12,1989020,22,GGGGGGAGTTGAAATGGGAGGG,In,PFL2330w,same,/,"hypothetical protein, conserved"
12_RC,2215641,31,GGGACGAACAGGGGGAACTCCAGGGACAGGG,In,PFL2625w,opposite,/,Rifin
12_RC,775872,30,GGGTTAAGGGTATAACGTTAAGGGTTAGGG,Ups,PFL0935c,same,-1682,var group B1C
12_RC,21963,31,GGGTGGTAAGTAGGGTTGGGGTTCTTGTGGG,In,PFL0005w,opposite,/,var group B1T
13_RC,2866206,30,GGGTTAAGGGTATAACTTTAGGGGTTAGGG,Ups,MAL13P1.356,same,-1656,var group B1T
13_RC,458846,27,GGGGGGGGGAGGGGGAAAATATTTGGG,Ups,PF13_0056,opposite,-317,"hypothetical protein, conserved."
13_RC,360355,14,GGGTGGGGGGGGGG,Ups,PF13_0043,opposite,-17,"CCAAT-binding transcription factor, putative."
13_RC,81687,14,GGGGGGGGGGGGGG,Ups,PF13_0073,opposite,-1200,"hypothetical protein, conserved."
14,2864587,24,GGGAAAAGGGAAAAGGGAAAAGGG,Down,PF14_0665,same,120,hypothetical protein
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"Type: PQS can be found upstream, downstream or in the gene sequence itself.",,,,,,,,
Gene ID: closest gene or the gene itself if PQS found in the gene.,,,,,,,,
Strand: whether the PQS if found on the same or the opposite strand of the closest gene.,,,,,,,,
Distance: number of nucleotides to the closest gene (upstream or downstream),,,,,,,,
Annotation: according to PlasmoDB 5.4 and Kraemer et al 2007.,,,,,,,,
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Abbreviations:,,,,,,,,
Ups = upstream,,,,,,,,
Down = downstream,,,,,,,,
In = Inside (i.e. PQS in the gene sequence itself),,,,,,,,
RC = Reverse Complement,,,,,,,,