C4 Alignment:
------------
         Query: SPP00000124_2.0 # Protein # Selenoprotein W1 (SelW1) # Human (Homo sapiens)
        Target: gi|397461887|gb|JH733614.1|:subseq(500000,100000) Alligator mississippiensis unplaced genomic scaffold scaffold-4174, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 246
   Query range: 0 -> 87
  Target range: 42828 -> 47895

     1 : MetAlaLeuAlaValArgValValTyr{Cy}  >>>> Target Intron 1 >>>>   :    10
         |||!.!:!!  !|||!:!|||:!!|||{||}           1282 bp           
         MetValValLysValLysValLeuTyr{Cy}++                         ++
 42829 : ATGGTTGTCAAGGTCAAGGTGCTGTAT{TG}gt.........................ag : 44138

    11 : {s}GlyAlaUnkGlyTyrLysSerLys  >>>> Target Intron 2 >>>>  TyrL :    20
         {|}|||::!   ||||||  !||||||            508 bp           |||!
         {s}GlySer***GlyTyrGlySerLys++                         ++TyrA
 44139 : {C}GGGAGCTGAGGCTATGGGTCCAAGgt.........................agTATC : 44676

    21 : euGlnLeuLysLysLysLeuGluAspGluPheProGlyArgLeuAspIle  >>>> Tar :    37
          !||||||::!  !:!!||||||..!..!|||||||||!:!|||!!:|||          
         rgGlnLeuArgLeuGluLeuGluSerArgPheProGlyLysLeuGluIle++        
 44677 : GACAGCTCCGGCTGGAACTCGAAAGCAGGTTCCCAGGCAAGCTGGAGATAgt........ : 44729

    38 : get Intron 3 >>>>  CysGlyGluGlyThrProGlnAlaThrGlyPhePheGluVa :    50
           959 bp            !!.!!|||||||||! !:!!|||||||||!::||||||||
                          ++SerSerGluGlyThrArgGluAlaThrGlyTrpPheGluVa
 44730 : .................agAGCAGTGAGGGGACTCGTGAGGCCACAGGATGGTTTGAAGT : 45725

    51 : lMetValAlaGlyLysLeuIleHisSerLysLys  >>>> Target Intron 4 >>> :    62
         |   |||!.!|||||||||:!:||||||||||||           2057 bp        
         lSerValGlyGlyLysLeuValHisSerLysLys++                        
 45726 : GTCAGTCGGAGGCAAGCTGGTGCATTCTAAAAAGgt........................ : 45763

    63 : >  LysGlyAspGlyTyrValAspThrGluSerLysPheLeuLysLeuValAlaAlaIle :    80
            !!.|||||||||!:!||||||  !.!...!|||.!!  !|||:!! !!.!!||||||
          ++AsnGlyAspGlyPheValAspAspAsnAspLysLeuAspLysIlePheThrAlaIle
 45764 : .agAATGGCGATGGCTTTGTGGATGACAACGACAAGCTTGACAAGATCTTTACGGCCATC : 47872

    81 : LysAlaAlaLeuAlaGlnGly :    87
         |||! !||||||||| !!|||
         LysGluAlaLeuAla***Gly
 47873 : AAAGAGGCTCTGGCATAGGGA : 47895

vulgar: SPP00000124_2.0 0 87 . gi|397461887|gb|JH733614.1|:subseq(500000,100000) 42828 47895 + 246 M 9 27 S 0 2 5 0 2 I 0 1278 3 0 2 S 1 1 M 8 24 5 0 2 I 0 504 3 0 2 M 18 54 5 0 2 I 0 955 3 0 2 M 25 75 5 0 2 I 0 2053 3 0 2 M 26 78
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-15
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	gene	42829	47895	246	+	.	gene_id 1 ; sequence SPP00000124_2.0 ; gene_orientation +
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	cds	42829	42857	.	+	.	
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	exon	42829	42857	.	+	.	insertions 0 ; deletions 0
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	splice5	42858	42859	.	+	.	intron_id 1 ; splice_site "GT"
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	intron	42858	44139	.	+	.	intron_id 1
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	splice3	44138	44139	.	+	.	intron_id 0 ; splice_site "AG"
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	cds	44140	44164	.	+	.	
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	exon	44140	44164	.	+	.	insertions 0 ; deletions 0
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	splice5	44165	44166	.	+	.	intron_id 2 ; splice_site "GT"
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	intron	44165	44672	.	+	.	intron_id 2
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	splice3	44671	44672	.	+	.	intron_id 1 ; splice_site "AG"
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	cds	44673	44726	.	+	.	
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	exon	44673	44726	.	+	.	insertions 0 ; deletions 0
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	splice5	44727	44728	.	+	.	intron_id 3 ; splice_site "GT"
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	intron	44727	45685	.	+	.	intron_id 3
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	splice3	45684	45685	.	+	.	intron_id 2 ; splice_site "AG"
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	cds	45686	45760	.	+	.	
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	exon	45686	45760	.	+	.	insertions 0 ; deletions 0
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	splice5	45761	45762	.	+	.	intron_id 4 ; splice_site "GT"
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	intron	45761	47817	.	+	.	intron_id 4
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	splice3	47816	47817	.	+	.	intron_id 3 ; splice_site "AG"
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	cds	47818	47895	.	+	.	
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	exon	47818	47895	.	+	.	insertions 0 ; deletions 0
gi|397461887|gb|JH733614.1|:subseq(500000,100000)	exonerate:protein2genome:local	similarity	42829	47895	246	+	.	alignment_id 1 ; Query SPP00000124_2.0 ; Align 42829 1 27 ; Align 44141 11 24 ; Align 44673 19 54 ; Align 45686 37 75 ; Align 47818 62 78
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis