Novel porcine repetitive elements

BMC Genomics

Table 1 Count numbers for novel porcine repetitive elements

Repeat name	length	GC content	BLAST hits to SSGI ¹	BLAST hits to BAC-ends ²	count number regular ³	count number irregular ⁴	BLAST hits to Bovine Genome ⁵
MPRE2	111	0.40	66	528	513		1000
MPRE3	411	0.51	25	392		324	57
MPRE6	255	0.55	15	392		342	0
MPRE11	76	0.33	888	8876	8040		1599
MPRE12	199	0.47	26	272		123	1051
MPRE14	234	0.57	29	292	306		1157
MPRE15	912	0.50	56	520	592	452	1475
MPRE16	276	0.46	379	4688	5051	4035	1260
MPRE17	870	0.29	5	89		75	1002
MPRE19	125	0.34	30	577	550		534
MPRE21	595	0.48	16	189		201	1604
MPRE22	166	0.46	6	83	81		0
MPRE26	324	0.50	75	475	479		1054
MPRE28	140	0.64	27	700	648		0
MPRE38	176	0.35	610	7567	7110	5806	1417
MPRE42	220	0.39	160	2350	2425		1050
MPRE44	55	0.40	22	560	551		6
MPRE49	221	0.50	3	52		50	6
MPRE50	136	0.35	40	907	871		0
MPRE51	71	0.49	17	140	112		110
MPRE52	341	0.30	28	457	703	362	643
MPRE54	326	0.46	17	121	125		62
MPRE55	161	0.52	39	247	244		1075
MPRE58	196	0.41	4	98		98	1034
MPRE59	123	0.27	207	1830	1723		1431
MPRE60	151	0.40	13	98	90		0
MPRE61	1059	0.37	2	31		41	10

¹ The number of BLAST hits, at least half as long as the repeat element, found within the TIGR Sus scrofa Gene Index version 11, which contains 104,328 entries and 70.0 MB. ² The number of similar BLAST hits to the Sanger archive of BAC-ends that has 275,595 entries totaling 335.9 MB. ^3,4 The regular and irregular columns give the number of BLAST hits across the repeat element, again using the Sanger data. The regular values are the average of the middle 90% of the repeat element while the irregular values are the minimum value within the middle 80% of the repeat element. ⁵ The number of BLAST hits, including those less than half the length of the repeat element, found within the whole Bovine genome (build AAFCO2).

ISSN: 1471-2164