1. Repeat_TotalInfo##.txt (including elements < 3000bp from CpG islands)

ID	16 (just temp ID)
------------------------------
Name	AluSp	
Family	Alu
Category	SINE 
Chromosome	chr1
Orientation	+
Divergence	103
Genostart	16653
Genoend	16925
---------- Available in genome browser as the results of RepeatMasker program
Count_A	70
Count_C	69
Count_G	86
Count_T	47
Interval	272
CpG	13
TpG	19
CpA	22
Distance_CpGisland	1673
Substitution	11.07
----------- For each repeat sequences, (di)nucleotide frequencies were calculated with
----------- Distance from CpGislands (bp) and Substitution level (Jukes-Cantor model from divergence)


2. Alu Pair Information

PrevID	1 (just temp ID)
---------------------------
PairOrient	Inverted
Identity Perc	84.76
Align Length	105
Real Inverval	524
------------- Inverted/Direct determined from the orientation
------------- Identity Perc [= sequence homology (%)] & Alignable region length (bp) determined from BLAST result (bl2seq.exe)
------------- Real Intervals between alignable regions were recalculated as the distance between alignable regions
Ccount1	72
Gcount1	89
Interval1	313
CpGcount1	11
Ccount2	79
Gcount2	69
Interval2	294
CpGcount2	4
Chr1	chr1
Start1	92838
End2	93772
-------------- Nucleotide freq. of two Alu elements and genomic coordinates