Possible inconsistency in "position in repeat (left)" column in .out file #369
Description
Hello,
thank you for developing and maintaining this tool!
I thought I understood the meaning of the "position in repeat (left)" column in the .out file, but I found a case that made me doubt it.
In the first row, the repeat MLT1E1A maps from position 1 to 172 of its consensus sequence, leaving out 388 bases (as indicated in the next column). From this, I would infer that the consensus should be 172 + 388 = 560 bp long.
However, in the third row, another fragment of the same repeat (same repID) maps from 173 to 666, leaving out 14 bases — which instead suggests a consensus length of 680 bp (matching the length reported in Dfam).
Could you please clarify how "position in repeat (left)" is computed in such cases?
Thanks!