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Loaded ra/good.txt in 2.922000 seconds
Loaded genome in 0.113000 seconds
Making introns
Done making introns
Writing introns gff
Wrote 106720 introns: 53832 + 52888 - 0 ?
6063 consensus mismatches, 268 nonconsensus mismatches on strand
Making exons
Made 562971 exons
Done making 381906 exons after removing dupes
Looking for alt genes with overlapping introns
Really weird i:9383165-9383864!
Really weird i:15068634-15074677!
Really weird i:15068476-15069158!
Really weird i:15068797-15076102!
Really weird i:15069141-15073390!
Really weird i:15068687-15074425!
Really weird i:15068620-15074549!
Really weird i:15069141-15074325!
Really weird i:15068600-15074063!
Really weird i:15070144-15075248!
Really weird i:15070141-15070945!
Really weird i:15070496-15075416!
Really weird i:15070571-15071350!
Really weird i:15070563-15071350!
Really weird i:15070610-15077660!
Really weird i:15070613-15071295!
Really weird i:15071054-15071707!
Really weird i:15071488-15075015!
Really weird i:15071388-15071873!
Really weird i:15071716-15076352!
Really weird i:15071826-15078250!
Really weird i:15071641-15076381!
Really weird i:15071552-15077745!
Really weird i:15072345-15075314!
Really weird i:15072436-15073783!
Really weird i:15072879-15075413!
Really weird i:15072877-15075009!
Really weird i:15072911-15075337!
Really weird i:15073230-15074230!
Really weird i:15073280-15075099!
Really weird i:15073318-15074426!
Really weird i:15074021-15074991!
Really weird i:15073837-15074636!
Really weird i:15073844-15074598!
Really weird i:15073614-15074501!
Really weird i:15073741-15074409!
Really weird i:15074004-15075249!
Really weird i:15074054-15074693!
Really weird i:15074072-15075350!
Really weird i:15073920-15075209!
Really weird i:15074342-15075067!
Really weird i:15074384-15075225!
Really weird i:15074562-15075213!
Really weird i:15075046-15076385!
Really weird i:15075184-15075954!
Really weird i:15075141-15075766!
Really weird i:15075672-15076354!
Really weird i:15075527-15076336!
Really weird i:15077768-15078547!
Really weird i:15077760-15078547!
Really weird i:15077810-15078492!
Really weird ii:8787679-8788108!
Really weird ii:8787678-8788247!
Really weird ii:8787678-8788016!
Really weird ii:12602054-12603551!
Really weird iv:4191702-4192122!
Really weird iv:7363882-7365076!
Really weird v:6175575-6176180!
Really weird v:6175222-6176385!
Really weird v:11793260-11794267!
Really weird v:14110447-14112609!
Really weird v:14110426-14112747!
Really weird v:14110417-14112748!
Really weird v:17649214-17650019!
Really weird v:18234216-18235398!
Really weird v:18234205-18235492!
Really weird x:16921096-16922499!
Really weird x:16922003-16923080!
1996 genes with overlapping introns
Looking for alt genes with overlapping exon/introns
3694 Alt spliced genes: 1551 with skipped introns, 895 with skipped exons,
1010 with alt 5' ends 995 with alt 3' ends
Wrote 3694 alt genes