Understanding the output of "FEELnc_classifier.pl"

[simang5c]

Hi,

I would just like to understand the output of "FEELnc_classifier.pl". The parameter passed for the identification of lncRNA interaction is:
"#Minimal window size : 1000
#Maximal window size : 1000"

However in the output we see that some distance is as long as 66670, 8293 etc which are way beyond 1000 maximal window size. I just want to understand why the tool considers those gene/transcript which are so far away :

cat {INPUT}_classes.txt
isBest lncRNA_gene lncRNA_transcript partnerRNA_gene partnerRNA_transcript direction type distance subtype location
1 XLOC_090743 TCONS_00232056 ENSCAFG00000013346 ENSCAFT00000021186 antisense intergenic 377 divergent upstream
1 XLOC_090720 TCONS_00231943 ENSCAFG00000026373 ENSCAFT00000040656 sense intergenic 66670 same_strand upstream
1 XLOC_090678 TCONS_00231794 ENSCAFG00000010781 ENSCAFT00000017151 antisense genic 0 nested intronic
0 XLOC_090678 TCONS_00231794 ENSCAFG00000010794 ENSCAFT00000017171 sense intergenic 8293 same_strand upstream
0 XLOC_090678 TCONS_00231794 ENSCAFG00000010781 ENSCAFT00000017154 antisense genic 0 overlapping intronic
1 XLOC_090878 TCONS_00232599 ENSCAFG00000009675 ENSCAFT00000015370 sense intergenic 19181 same_strand upstream
1 XLOC_090974 TCONS_00232971 ENSCAFG00000010842 ENSCAFT00000017240 sense intergenic 85066 same_strand downstream
1 XLOC_090620 TCONS_00231531 ENSCAFG00000009999 ENSCAFT00000015918 antisense genic 0 overlapping exonic
0 XLOC_090620 TCONS_00231531 ENSCAFG00000009970 ENSCAFT00000015870 antisense intergenic 516 divergent upstream