I am using Blat to map long contigs to annotated transcripts. But Blat does not report all feasible hits exhaustively. For example, there is a transcript T with length 2280. If I aligned all contigs to it, Blat reports one hit with range [770, 2280]:

Transcript T:   ===============================================================
Hit (contig A):                           -------------------------------------
                                          ^770                                ^2280
               |<-    missing region    <-|

But if I truncate the transcript (keep the first 770 bases only) and blat again, there is an exact hit: 770 matches, 0 mismatch, 0 gap.

Partial T:      ==========================
Hit (contig B): --------------------------
                ^0                       ^770                                                      
                |<-    An exact hit    <-|

Somehow Blat does not report Contig B at first (The missing region). This is not what I want.

I do not want to use Blast, because my program is all using Blat format.

I tried the options -fine and -oneOff=1 to do the same mapping, but the results are the same.

Does anybody know how to enforce exhaustive searching using Blat? Or any script to convert blastn results to PSL format? Thanks.