Command line: [exonerate -m p2g --showtargetgff -q ../Sel.human/SELR1.fa -t gi|397459852|gb|JH735649.1|subseq.fa -E]
Hostname: [ws101060]

** (process:3151): WARNING **: Exhaustively generating suboptimal alignments will be VERY SLOW

C4 Alignment:
------------
         Query: SPP00000087_2.0 # Protein # Methionine-R-sufoxide reductase 1 (SelR1) # Human (Homo sapiens)
        Target: gi|397459852|gb|JH735649.1|:subseq(240000,100000) Alligator mississippiensis unplaced genomic scaffold scaffold-7522, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 425
   Query range: 0 -> 115
  Target range: 57913 -> 70497

     1 : MetSerPheCysSerPhePheGlyGlyGluValPheGlnAsnHisPheGluPro{G}  > :    19
         ||||||||||||:!!|||  !|||!.!|||  !!:!   ..!! !|||!!:|||{|}   
         MetSerPheCysAlaPheArgGlyAlaGluArgTyrAlaGlyLeuPheAspPro{G}++ 
 57914 : ATGTCCTTCTGCGCCTTCCGCGGCGCCGAGCGCTACGCCGGCCTCTTCGACCCG{G}gt. : 57971

    20 : >>> Target Intron 1 >>>>  {ly}ValTyrValCysAlaLysCysGlyTyrGlu :    29
                 1340 bp           {||}:!!|||||||||:!!|||||||||||||||
                                 ++{ly}IleTyrValCysSerLysCysGlyTyrGlu
 57972 : ........................ag{GC}ATCTACGTGTGCTCCAAGTGCGGCTACGAG : 59338

    30 : LeuPheSerSerArgSerLysTyrAlaHisSerSerProTrpProAlaPheThrGluThr :    49
         ||||||||||||!:!:!!|||!:!! !|||||||||||||||||||||||||||:!!|||
         LeuPheSerSerGlnAlaLysPheGluHisSerSerProTrpProAlaPheThrLysThr
 59339 : CTCTTCTCCAGCCAGGCCAAGTTCGAGCACTCGTCGCCGTGGCCAGCGTTCACCAAGACG : 59398

    50 : IleHisAlaAspSerValAlaLysArgProGluHisAsnArgSerGluAlaLeuLys  > :    69
         :!!|||||||||||||||:!!|||  !  !|||      ||| !!!  .!!||||||   
         ValHisAlaAspSerValSerLysTyrGluGlu------ArgProGlyThrLeuLys++ 
 59399 : GTCCATGCCGACAGCGTGTCCAAGTACGAGGAG------CGTCCGGGCACCCTGAAGgt. : 59454

    70 : >>> Target Intron 2 >>>>  ValSerCysGlyLysCysGlyAsnGlyLeuGlyH :    80
                  124 bp           ||||||||||||||||||||||||||||||||||
                                 ++ValSerCysGlyLysCysGlyAsnGlyLeuGlyH
 59455 : ........................agGTATCGTGCGGCAAGTGCGGCAATGGCCTGGGCC : 59609

    81 : isGluPheLeuAsnAspGlyProLysProGlyGlnSerArgPheUnkIlePheSerSerS :   100
         ||||||||||||||||||||||||||  !|||||||||||||||   |||||||||||||
         isGluPheLeuAsnAspGlyProLysLysGlyGlnSerArgPhe***IlePheSerSerS
 59610 : ACGAGTTCCTCAACGACGGGCCGAAGAAGGGGCAGTCCCGCTTCTGAATATTCAGCAGCT : 59669

   101 : erLeuLysPheValProLys{G}  >>>> Target Intron 3 >>>>  {ly}LysG :   109
         |||||||||||:!!||||||{|}           10781 bp          {||}||||
         erLeuLysPheIleProLys{G}++                         -+{ly}LysG
 59670 : CGCTGAAGTTCATCCCCAAA{G}gt.........................tg{GG}AAAG : 70477

   110 : luThrSerAlaSerGlnGly :   115
         ||.!!..!  !|||||||||
         luAlaAspArgSerGlnGly
 70478 : AAGCTGATCGCTCCCAGGGT : 70497

vulgar: SPP00000087_2.0 0 115 . gi|397459852|gb|JH735649.1|:subseq(240000,100000) 57913 70497 + 425 M 18 54 S 0 1 5 0 2 I 0 1336 3 0 2 S 1 2 M 41 123 G 2 0 M 6 18 5 0 2 I 0 120 3 0 2 M 38 114 S 0 1 5 0 2 I 0 10777 3 0 2 S 1 2 M 8 24
# --- 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|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	gene	57914	70497	425	+	.	gene_id 1 ; sequence SPP00000087_2.0 ; gene_orientation +
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	cds	57914	57968	.	+	.	
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	exon	57914	57968	.	+	.	insertions 0 ; deletions 0
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	splice5	57969	57970	.	+	.	intron_id 1 ; splice_site "GT"
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	intron	57969	59308	.	+	.	intron_id 1
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	splice3	59307	59308	.	+	.	intron_id 0 ; splice_site "AG"
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	cds	59309	59451	.	+	.	
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	exon	59309	59451	.	+	.	insertions 0 ; deletions 2
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	splice5	59452	59453	.	+	.	intron_id 2 ; splice_site "GT"
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	intron	59452	59575	.	+	.	intron_id 2
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	splice3	59574	59575	.	+	.	intron_id 1 ; splice_site "AG"
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	cds	59576	59690	.	+	.	
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	exon	59576	59690	.	+	.	insertions 0 ; deletions 0
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	splice5	59691	59692	.	+	.	intron_id 3 ; splice_site "GT"
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	intron	59691	70471	.	+	.	intron_id 3
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	splice3	70470	70471	.	+	.	intron_id 2 ; splice_site "TG"
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	cds	70472	70497	.	+	.	
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	exon	70472	70497	.	+	.	insertions 0 ; deletions 0
gi|397459852|gb|JH735649.1|:subseq(240000,100000)	exonerate:protein2genome:local	similarity	57914	70497	425	+	.	alignment_id 1 ; Query SPP00000087_2.0 ; Align 57914 1 54 ; Align 59311 20 123 ; Align 59434 63 18 ; Align 59576 69 114 ; Align 70474 108 24
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis