U63741@luke:~> genewise -pep -pretty -cdna -gff seqaahsx/GPx5.hs.fa Gpx5hs.subseq
Find start end points: [27,38408][220,44909] Score 113825
Recovering alignment: Alignment recovered] Explicit read offe 71%

genewise output
Score 328.43 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 GL193897.1:subseq(369358,55000) is longer than allowed name
block (15). Truncating

SPP00000008_1.0   28 MKMDCHKDEKGTIYDYEAIALNKNEYVSFKQYVGKHILFVNVATYCGLT 
                     ++MDC+K   GTIY+Y A+ LN  EY+ FK Y GKH+LFVNVATY GLT 
                     FQMDCYKGVTGTIYEYGALTLNDEEYIQFKHYAGKHVLFVNVATYXGLT 
GL193897.1:subs38407 tcagttaggagaatgtggcacagggtactactggacgctgaggattgta 
                     tatagaagtcgctaaagctctaaaaatataaacgaattttatccaggtc 
                     cggtccggggccctgtgcccctcggctgcgccgcgccctccgcccacga 


SPP00000008_1.0   77 AQYP                          LNALQEELKPYGLVVLGFP 
                     AQYP                          LNAL +ELKP+G+VVLGFP 
                     AQYP          E:E[gaa]        LNALHQELKPFGVVVLGFP 
GL193897.1:subs38554 gctcGGTAAGAG  Intron 1   CAGAAcagcccgcactggggcgtc 
                     caac <1-----[38567:42847]-1>  tactaaatactgttttgtc 
                     tgta                          gtaacggcgtttccggctc 


SPP00000008_1.0  101 CNQFGKQEPGDNKEILPGL                          YVRP 
                     CNQFGKQEPG N EIL GL                          YVRP 
                     CNQFGKQEPGKNSEILSGL           K:K[aag]       YVRP 
GL193897.1:subs42907 tactgacgcgaatgactgcAAGTGAGTG  Intron 2   CAGGtgcc 
                     gaatgaaacgaacattcgt  <2-----[42966:43414]-2> atgc 
                     ccataaaaaagcagcttgc                          tgta 


SPP00000008_1.0  125 GGGFVPSFQLFEKGDVNGEKEQKVFSFLK                     
                     GGGFVP+FQLFEKGDVNGEKEQKVF+FLK                     
                     GGGFVPNFQLFEKGDVNGEKEQKVFTFLK                     
GL193897.1:subs43428 gggtgcatcctgagggaggagcagtatcaGTGAGTG  Intron 3    
                     gggttcatattaagatagaaaaattctta<0-----[43515:44706] 
                     ttctccttgctgagtgtaaaaggcttcgg                     


SPP00000008_1.0  154    HSCPHPSEILGTFKSISWDPVKVHDIRWNFEKFLVGPDGIPVMRWS 
                        +SCP  S++LG+   + W+P+KVHDIRWNFEKFLVGPDG+PVMRW  
                        NSCPPTSDLLGSSNQLFWEPMKVHDIRWNFEKFLVGPDGVPVMRWF 
GL193897.1:subs44704 CAGattccatgctgttaccttgcaagcgactatgatcggcgggcgactt 
                     -0>acgccccattgccaattgactataatggataatttgcagtcttggt 
                        ccctactctgcaacaccggcggcccccgctggcgggtcactcgcgc 


SPP00000008_1.0  200 HRATVSSVKTDILAYLKQFKTK                            
                     H+A VS+VK+DIL YLKQFKT+                            
                     HKAPVSTVKSDILEYLKQFKTE                            
GL193897.1:subs44845 cagcgaagatgacgtcactaag                            
                     aacctgctacattaataataca                            
                     cgtcccgcgaccggcgagcacg                            


//
Making a E in phase 1 intron
Making a K in phase 2 intron
>GL193897.1:subseq(369358,55000).pep
FQMDCYKGVTGTIYEYGALTLNDEEYIQFKHYAGKHVLFVNVATYXGLTAQYPELNALHQ
ELKPFGVVVLGFPCNQFGKQEPGKNSEILSGLKYVRPGGGFVPNFQLFEKGDVNGEKEQK
VFTFLKNSCPPTSDLLGSSNQLFWEPMKVHDIRWNFEKFLVGPDGVPVMRWFHKAPVSTV
KSDILEYLKQFKTE
//
>GL193897.1:subseq(369358,55000).[38407:44910].sp
TTCCAGATGGATTGCTACAAGGGGGTGACGGGCACCATCTATGAGTATGGGGCCCTCACC
CTCAATGACGAGGAGTACATTCAGTTCAAGCACTACGCGGGCAAGCACGTCCTCTTTGTC
AACGTGGCCACCTACTGAGGCTTGACAGCTCAGTATCCAGAACTGAATGCACTACACCAG
GAGCTCAAGCCTTTTGGTGTCGTCGTGCTGGGCTTTCCCTGCAACCAATTTGGAAAACAA
GAACCAGGAAAGAACTCAGAGATCCTTTCTGGGCTCAAGTATGTGCGTCCAGGTGGTGGC
TTTGTCCCCAATTTTCAGCTCTTTGAGAAAGGGGATGTGAATGGAGAAAAAGAACAGAAG
GTCTTTACTTTCCTGAAGAACTCCTGCCCTCCAACCTCTGACCTTTTGGGCTCATCAAAC
CAACTCTTCTGGGAGCCCATGAAGGTCCACGACATCCGCTGGAACTTTGAGAAGTTCCTG
GTGGGGCCTGACGGAGTCCCTGTCATGCGCTGGTTCCACAAGGCTCCCGTCAGCACGGTC
AAGTCAGACATCCTGGAGTACCTGAAACAGTTCAAAACCGAG
//
GL193897.1:subseq(369358,55000)	GeneWise	match	38407	44910	328.43	+	.	GL193897.1:subseq(369358,55000)-genewise-prediction-1
GL193897.1:subseq(369358,55000)	GeneWise	cds	38407	38566	0.00	+	0	GL193897.1:subseq(369358,55000)-genewise-prediction-1
GL193897.1:subseq(369358,55000)	GeneWise	intron	38567	42847	0.00	+	.	GL193897.1:subseq(369358,55000)-genewise-prediction-1
GL193897.1:subseq(369358,55000)	GeneWise	cds	42848	42965	0.00	+	2	GL193897.1:subseq(369358,55000)-genewise-prediction-1
GL193897.1:subseq(369358,55000)	GeneWise	intron	42966	43414	0.00	+	.	GL193897.1:subseq(369358,55000)-genewise-prediction-1
GL193897.1:subseq(369358,55000)	GeneWise	cds	43415	43514	0.00	+	1	GL193897.1:subseq(369358,55000)-genewise-prediction-1
GL193897.1:subseq(369358,55000)	GeneWise	intron	43515	44706	0.00	+	.	GL193897.1:subseq(369358,55000)-genewise-prediction-1
GL193897.1:subseq(369358,55000)	GeneWise	cds	44707	44910	0.00	+	0	GL193897.1:subseq(369358,55000)-genewise-prediction-1