P-values for our candidates, using the center, leftmost and rightmost
nucleotides, respectively, against different datasets.
We check overlap with EST exons. Due to the size of the EST data we
only tested for the center nucleotide.
Also P-values for EvoFold and RNAz candidates against TARs and Transfrags.

NB Observed is observed - 0.5 which gives more accrate results for a normal approximation to the binomial distribution. 

#Overlap with the center nucleotide of our candidate regions

GC-bin	Data		P				N		Expected	Observed	P-value    

0-35	EvoFold		0.0368474697637113		380		14		13.5		0.5543692
0-35	IPS		0.0622772395389268		380		23		24.5		0.4296842
0-35	Introns		0.59408703019382		380		225		217.5		0.8056972
0-35	lRNA		0.00986785164032337		380		3		4.5		0.3485097
0-35	RNAz		0.00758581687168245		380		2		19.5		4.4028e-23
0-35	sRNA		0.000449955972050047		380		0		0.5		0.2130555
0-35	TAR/Trans	0.00827015851137147		380		3		2.5		0.6420818
0-35	3' UTR		0.0237229475395418		380		9		9.5		0.435031
0-35	5' UTR		0.0825451488080199		380		31		23.5		0.9287466
0-35	EST		0.0884252186076416		380		33		29.5		0.7706829

35-40	EvoFold		0.0185948828000197		742		13		11.5		0.7337946
35-40	IPS		0.0822770314605995		742		61		70.5		0.1033721
35-40	Introns		0.603446775325765		742		447		435.5		0.8211816
35-40	lRNA		0.028723127714712		742		21		19.5		0.6548269
35-40	RNAz		0.0130586738520769		742		9		36.5		2.165124e-18
35-40	sRNA		0.00134039354091779		742		0		-0.5		0.9331475
35-40	TAR/Trans	0.0138940579512649		742		10		7.5		0.810873
35-40	3' UTR		0.0258333514648137		742		19		12.5		0.9386033
35-40	5' UTR		0.0758550519839084		742		56		39.5		0.990024
35-40	EST		0.0992274844231498		742		73		68.5		0.7355008

40-45	EvoFold		0.015023488270873		1216		18		27.5		0.01476913
40-45	IPS		0.0816833733281526		1216		99		129.5		0.0007907817
40-45	Introns		0.59567989247258		1216		724		745.5		0.1082173
40-45	lRNA		0.0631957055736491		1216		76		78.5		0.422719
40-45	RNAz		0.0183742703516376		1216		22		74.5		4.144812e-29
40-45	sRNA		0.00313288118898289		1216		3		9.5		0.001750013
40-45	TAR/Trans	0.0254504906383218		1216		30		34.5		0.2588754
40-45	3' UTR		0.0158461753112731		1216		19		17.5		0.6577073
40-45	5' UTR		0.0684647937195627		1216		83		82.5		0.5340788
40-45	EST		0.124175714834437		1216		150		148.5		0.5859702

45-50	EvoFold		0.0144888546986504		1377		19		39.5		5.200663e-06
45-50	IPS		0.0792714514719713		1377		109		162.5		5.161756e-08
45-50	Introns		0.593362696424032		1377		817		809.5		0.6608479
45-50	lRNA		0.12457080010346		1377		171		203.5		0.004546047
45-50	RNAz		0.0352520134320206		1377		48		123.5		3.19726e-28
45-50	sRNA		0.00661595938081083		1377		9		10.5		0.3220422
45-50	TAR/Trans	0.0447479569232639		1377		61		59.5		0.6087483
45-50	3' UTR		0.0150328352280012		1377		20		26.5		0.0994941
45-50	5' UTR		0.0672897985863917		1377		92		95.5		0.379915
45-50	EST		0.134324652619518		1377		184		189.5		0.3600274

50-100	EvoFold		0.0256948214148296		2866		73		110.5		6.762957e-06
50-100	IPS		0.069935545863517		2866		200		358.5		2.698889e-31
50-100	Introns		0.566541772478354		2866		1623		1674.5		0.02777643
50-100	lRNA		0.318573252885253		2866		913		922.5		0.352112
50-100	RNAz		0.0783100079657742		2866		224		415.5		1.427620e-40
50-100	sRNA		0.0377407150894226		2866		108		129.5		0.01825289
50-100	TAR/Trans	0.140769581141706		2866		403		438.5		0.02986645
50-100	3' UTR		0.00991094139644389		2866		28		19.5		0.9534386
50-100	5' UTR		0.0799078424398979		2866		229		300.5		4.229063e-07
50-100	EST		0.198338938492992		2866		568		567.5		0.5175502

All	EvoFold		0.0227020371025908		6581		149		204.5		2.560458e-06
All	IPS		0.0746646081771721		6581		491		747.5		1.538689e-33
All	Introns		0.590083805320177		6581		3883		3884.5		0.4884179
All	lRNA		0.110965650973104		6581		730		1230.5		4.083539e-86
All	RNAz		0.0308988906465482		6581		203		671.5		3.724094e-244
All	sRNA		0.0104082547917727		6581		68		151.5		3.329378e-24
All	TAR/Trans	0.0479990799943952		6581		315		544.5		5.463049e-40
All	3' UTR		0.0181027004653495		6581		119		87.5		0.9982768
All	5' UTR		0.0753234999668134		6581		495		543.5		0.01279192
All	EST		0.129505423239452		6581		852		1005.5		9.252039e-09


#Overlap with the leftmost nucleotide of our candidate regions

GC-bin	Data		P				N		Expected	Observed	P-value    

0-35	EvoFold		0.0368474697637113		380		14		14.5		0.4460696
0-35	IPS		0.0622772395389268		380		23		24.5		0.4296842
0-35	Introns		0.59408703019382		380		225		217.5		0.8056972
0-35	lRNA		0.00986785164032337		380		3		4.5		0.3485097
0-35	RNAz		0.00758581687168245		380		2		15.5		4.331074e-14
0-35	sRNA		0.000449955972050047		380		0		-0.5		0.947711
0-35	TAR/Trans	0.00827015851137147		380		3		1.5		0.8239361
0-35	3' UTR		0.0237229475395418		380		9		9.5		0.435031
0-35	5' UTR		0.0825451488080199		380		31		23.5		0.9287466

35-40	EvoFold		0.0185948828000197		742		13		10.5		0.8148963
35-40	IPS		0.0822770314605995		742		61		63.5		0.3716916
35-40	Introns		0.603446775325765		742		447		435.5		0.8211816
35-40	lRNA		0.028723127714712		742		21		19.5		0.6548269
35-40	RNAz		0.0130586738520769		742		9		31.5		8.761318e-13
35-40	sRNA		0.00134039354091779		742		0		0.5		0.6901418
35-40	TAR/Trans	0.0138940579512649		742		10		5.5		0.9342718
35-40	3' UTR		0.0258333514648137		742		19		12.5		0.9386033
35-40	5' UTR		0.0758550519839084		742		56		39.5		0.990024

40-45	EvoFold		0.015023488270873		1216		18		24.5		0.07091576
40-45	IPS		0.0816833733281526		1216		99		133.5		0.0001730450
40-45	Introns		0.59567989247258		1216		724		745.5		0.1082173
40-45	lRNA		0.0631957055736491		1216		76		75.5		0.5630223
40-45	RNAz		0.0183742703516376		1216		22		55.5		7.211379e-13
40-45	sRNA		0.00313288118898289		1216		3		3.5		0.5631113
40-45	TAR/Trans	0.0254504906383218		1216		30		36.5		0.1560097
40-45	3' UTR		0.0158461753112731		1216		19		18.5		0.5700801
40-45	5' UTR		0.0684647937195627		1216		83		82.5		0.5340788

45-50	EvoFold		0.0144888546986504		1377		19		26.5		0.06985168
45-50	IPS		0.0792714514719713		1377		109		135.5		0.004298080
45-50	Introns		0.593362696424032		1377		817		809.5		0.6608479
45-50	lRNA		0.12457080010346		1377		171		176.5		0.3426473
45-50	RNAz		0.0352520134320206		1377		48		93.5		2.522027e-11
45-50	sRNA		0.00661595938081083		1377		9		8.5		0.5803662
45-50	TAR/Trans	0.0447479569232639		1377		61		64.5		0.3535861
45-50	3' UTR		0.0150328352280012		1377		20		27.5		0.06604606
45-50	5' UTR		0.0672897985863917		1377		92		95.5		0.379915

50-100	EvoFold		0.0256948214148296		2866		73		88.5		0.03970103
50-100	IPS		0.069935545863517		2866		200		316.5		9.41943e-18
50-100	Introns		0.566541772478354		2866		1623		1670.5		0.03888697
50-100	lRNA		0.318573252885253		2866		913		936.5		0.1733781
50-100	RNAz		0.0783100079657742		2866		224		341.5		1.98928e-16
50-100	sRNA		0.0377407150894226		2866		108		135.5		0.003688114
50-100	TAR/Trans	0.140769581141706		2866		403		449.5		0.006688592
50-100	3' UTR		0.00991094139644389		2866		28		19.5		0.9534386
50-100	5' UTR		0.0799078424398979		2866		229		302.5		2.071500e-07

All	EvoFold		0.0227020371025908		6581		149		166.5		0.07853696
All	IPS		0.0746646081771721		6581		491		675.5		2.928953e-18
All	Introns		0.590083805320177		6581		3883		3880.5		0.5283886
All	lRNA		0.110965650973104		6581		730		1214.5		7.824722e-81
All	RNAz		0.0308988906465482		6581		203		539.5		5.059307e-127
All	sRNA		0.0104082547917727		6581		68		149.5		3.833109e-23
All	TAR/Trans	0.0479990799943952		6581		315		559.5		3.936973e-45
All	3' UTR		0.0181027004653495		6581		119		89.5		0.9969273
All	5' UTR		0.0753234999668134		6581		495		545.5		0.01001227


#Overlap with the rightmost nucleotide of our candidate regions

GC-bin	Data		P				N		Expected	Observed	P-value    

0-35	EvoFold		0.0368474697637113		380		14		16.5		0.2481860
0-35	IPS		0.0622772395389268		380		23		19.5		0.81171
0-35	Introns		0.59408703019382		380		225		217.5		0.8056972
0-35	lRNA		0.00986785164032337		380		3		5.5		0.1818528
0-35	RNAz		0.00758581687168245		380		2		10.5		3.33947e-06
0-35	sRNA		0.000449955972050047		380		0		-0.5		0.947711
0-35	TAR/Trans	0.00827015851137147		380		3		1.5		0.8239361
0-35	3' UTR		0.0237229475395418		380		9		9.5		0.435031
0-35	5' UTR		0.0825451488080199		380		31		23.5		0.9287466

35-40	EvoFold		0.0185948828000197		742		13		13.5		0.5322077
35-40	IPS		0.0822770314605995		742		61		74.5		0.03617062
35-40	Introns		0.603446775325765		742		447		435.5		0.8211816
35-40	lRNA		0.028723127714712		742		21		20.5		0.5708717
35-40	RNAz		0.0130586738520769		742		9		29.5		7.461728e-11
35-40	sRNA		0.00134039354091779		742		0		-0.5		0.9331475
35-40	TAR/Trans	0.0138940579512649		742		10		9.5		0.6001949
35-40	3' UTR		0.0258333514648137		742		19		12.5		0.9386033
35-40	5' UTR		0.0758550519839084		742		56		39.5		0.990024

40-45	EvoFold		0.015023488270873		1216		18		27.5		0.01476913
40-45	IPS		0.0816833733281526		1216		99		122.5		0.007625858
40-45	Introns		0.59567989247258		1216		724		745.5		0.1082173
40-45	lRNA		0.0631957055736491		1216		76		90.5		0.05378
40-45	RNAz		0.0183742703516376		1216		22		57.5		3.025208e-14
40-45	sRNA		0.00313288118898289		1216		3		4.5		0.3615623
40-45	TAR/Trans	0.0254504906383218		1216		30		33.5		0.3210633
40-45	3' UTR		0.0158461753112731		1216		19		17.5		0.6577073
40-45	5' UTR		0.0684647937195627		1216		83		82.5		0.5340788

45-50	EvoFold		0.0144888546986504		1377		19		33.5		0.001123289
45-50	IPS		0.0792714514719713		1377		109		153.5		4.862623e-06
45-50	Introns		0.593362696424032		1377		817		809.5		0.6608479
45-50	lRNA		0.12457080010346		1377		171		188.5		0.08310217
45-50	RNAz		0.0352520134320206		1377		48		115.5		6.56531e-23
45-50	sRNA		0.00661595938081083		1377		9		7.5		0.7037593
45-50	TAR/Trans	0.0447479569232639		1377		61		54.5		0.8232372
45-50	3' UTR		0.0150328352280012		1377		20		26.5		0.0994941
45-50	5' UTR		0.0672897985863917		1377		92		96.5		0.3397035

50-100	EvoFold		0.0256948214148296		2866		73		83.5		0.1222361
50-100	IPS		0.069935545863517		2866		200		321.5		3.758997e-19
50-100	Introns		0.566541772478354		2866		1623		1675.5		0.02545599
50-100	lRNA		0.318573252885253		2866		913		946.5		0.08982874
50-100	RNAz		0.0783100079657742		2866		224		359.5		2.979574e-21
50-100	sRNA		0.0377407150894226		2866		108		136.5		0.002739932
50-100	TAR/Trans	0.140769581141706		2866		403		447.5		0.008987146
50-100	3' UTR		0.00991094139644389		2866		28		20.5		0.9319644
50-100	5' UTR		0.0799078424398979		2866		229		299.5		6.001158e-07

All	EvoFold		0.0227020371025908		6581		149		176.5		0.01246267
All	IPS		0.0746646081771721		6581		491		693.5		1.278277e-21
All	Introns		0.590083805320177		6581		3883		3885.5		0.4784278
All	lRNA		0.110965650973104		6581		730		1253.5		5.227358e-94
All	RNAz		0.0308988906465482		6581		203		574.5		2.411384e-154
All	sRNA		0.0104082547917727		6581		68		149.5		3.833109e-23
All	TAR/Trans	0.0479990799943952		6581		315		548.5		2.499002e-41
All	3' UTR		0.0181027004653495		6581		119		88.5		0.9976898
All	5' UTR		0.0753234999668134		6581		495		543.5		0.01279192


P-values for RNAz and EvoFold candidates that are completely within our MAF input blocks (against TARs and Transfrags)

EvoFold:

GC-bin	Data		P				N		Expected	Observed	P-value    

0-35	TAR/Trans	0.00827015851137147		361		2		2.5		0.6110923
35-40	TAR/Trans	0.0138940579512649		201		2		3.5		0.3349766
40-45	TAR/Trans	0.0254504906383218		168		4		2.5		0.8078177
45-50	TAR/Trans	0.0447479569232639		120		5		8.5		0.0834692
50-100	TAR/Trans	0.140769581141706		351		49		50.5		0.4335793
All	TAR/Trans	0.0479990799943952		1201		57		69.5		0.05479704
     
RNAz:

GC-bin	Data		P				N		Expected	Observed	P-value    

0-35	TAR/Trans	0.00827015851137147		76		0		0.5		0.5646615
35-40	TAR/Trans	0.0138940579512649		146		2		0.5		0.860094
40-45	TAR/Trans	0.0254504906383218		169		4		7.5		0.05909241
45-50	TAR/Trans	0.0447479569232639		224		10		9.5		0.5671776
50-100	TAR/Trans	0.140769581141706		757		106		107.5		0.4609792
All	TAR/Trans	0.0479990799943952		1372		65		127.5		3.441691e-15


