The "stitch-maf-blocks" report that I get 763,251 sequences. After I download the result, the number of the sequences is actually 988,610 sequences. This number is equal to the every segments in the exon not the number of lines of bed file.
I have used this tools for several times. This situation is not found before. Every time, the number of found sequences reported is equal to the number of bed file' lines,which may contain several exons for a line.
Tool name: Stitch MAF blocks
Tool version: 1.0.1
Tool ID: Interval_Maf_Merged_Fasta2