BLAT-Based Comparative Analysis for Transposable Elements: BLATCAT

Table 3

Description of the Censor attributes.

Attribute	Description
Name	Column Name contains locus names of submitted query sequences (first column) and Repbase library sequences (fourth column). Repbase names are hyperlinked to their sequences.
From/To	Column From/To contains beginning/ending of positions of fragment on corresponding sequence.
Class	This is class/subclass of repeat as specified in repeat annotation.
Dir	Values in column Dir indicate orientation (“d” for direct and “c” for complementary) of repeat fragment—columns 4–6.
Sim	Column Sim contains value of similarity between 2 aligned fragments.
Pos	Column Pos is roughly the ratio of positives to alignment length.
Mn : Ts	Column Mm : Ts is a ratio of mismatches to transitions in nucleotide alignment. The closer this number is to 1 the more likely is that mutations are evolutionary.
Score	This column contains the alignment score obtained from blast.