[U41181.est12.alu.upf@am75281 Tpseudo]$ genewise -pep -pretty -cdna -gff SelM.fa SelMTpseudoextret1.fa
Find start end points: [49,9002][115,9206] Score 10418
Recovering alignment: Alignment recoveredExplicit read offone 76%

genewise output
Score 30.06 bits over entire alignment
Scores as bits over a synchronous coding model

Warning: The bits scores is not probablistically correct for single seqs
See WWW help for more info

Information
	Name gi|209487133|gb|AAFD02000028.1|:subseq(10000,12000) is longer
than allowed name block (15). Truncating

SPP00000113_1.0   50 LNRLKEVKAFVTE--DIQLYHNLVMKHLPGADPELVLLSRNYQELERIP 
                     LNRL E+K+F+ +   + LY N+ +  + G    L +      ELE+I  
                     LNRLPELKSFLKDLNGVDLYKNVEVHFISGKRAVLTIFEGG-RELEKIT 
gi|209487133|gb 9001 caaccgtattcagcagggctaagggctaagaaggtaatggg agtgaaa 
                     tagtcatacttaatagtataaatatattggagcttcttagg gataatc 
                     ctggtagagttgtgtcattcgtagttcatcagggggatgaa gggggcg 


SPP00000113_1.0   97 LSQMT-RDEINALVQELGFYR                             
                     LS    +++++ L  E GF +                             
                     LSDYNDKEKLHTLFAEKGFVK                             
gi|209487133|gb 9145 tagtagagatcattggagtga                             
                     tgaaaaaaatacttcaagtta                             
                     gttctcggggttgtaggatgg                             


//
>gi|209487133|gb|AAFD02000028.1|:subseq(10000,12000).pep
LNRLPELKSFLKDLNGVDLYKNVEVHFISGKRAVLTIFEGGRELEKITLSDYNDKEKLHT
LFAEKGFVK
//
>gi|209487133|gb|AAFD02000028.1|:subseq(10000,12000).[9001:9207].sp
CTCAATAGGCTGCCTGAATTGAAATCGTTTCTTAAGGATCTGAATGGCGTAGATCTTTAC
AAGAATGTAGAGGTTCATTTCATAAGTGGCAAAAGGGCGGTGTTGACGATATTTGAGGGA
GGAAGGGAGTTGGAGAAGATCACGTTGAGTGATTACAATGACAAGGAGAAGTTGCATACT
TTGTTTGCAGAGAAGGGATTTGTGAAG
//
gi|209487133|gb|AAFD02000028.1|:subseq(10000,12000)	GeneWise	match	9001	9207	31.06	+	.	gi|209487133|gb|AAFD02000028.1|:subseq(10000,12000)-genewise-prediction-1
gi|209487133|gb|AAFD02000028.1|:subseq(10000,12000)	GeneWise	cds	9001	9207	0.00	+	0	gi|209487133|gb|AAFD02000028.1|:subseq(10000,12000)-genewise-prediction-1
//

