Command line: [exonerate -m p2g --showtargetgff -q ./proteins/SPP02.fa -t ./subsequences/SPP02_1_genomic.fa_exonerate.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP02 tRNA selenocysteine 1-associated protein 1 [Homo sapiens]
        Target: gi|357434040|gb|JH378323.1|:subseq(1,328368) Saimiri boliviensis boliviensis unplaced genomic scaffold scaffold00219, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1490
   Query range: 0 -> 287
  Target range: 143010 -> 114115

      1 : MetAlaAlaSerLeuTrpMetGlyAsp  >>>> Target Intron 1 >>>>  Le :     10
          |||||||||||||||||||||||||||            499 bp           ||
          MetAlaAlaSerLeuTrpMetGlyAsp++                         ++Le
 143010 : ATGGCGGCCAGCCTGTGGATGGGAGACgt.........................agCT : 142484

     11 : uGluProTyrMetAspGluAsnPheIleSerArgAlaPheAlaThrMetGlyGluThr :     29
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          uGluProTyrMetAspGluAsnPheIleSerArgAlaPheAlaThrMetGlyGluThr
 142483 : GGAACCCTACATGGATGAGAACTTCATCTCCAGAGCCTTCGCCACCATGGGGGAGACT : 142427

     30 : ValMetSerValLysIleIleArgAsnArgLeuThr{Gl}  >>>> Target Intr :     42
          ||||||||||||||||||||||||||||||||||||{||}           10873 b
          ValMetSerValLysIleIleArgAsnArgLeuThr{Gl}++                
 142426 : GTAATGAGCGTCAAAATTATCCGAAACCGCCTCACC{GG}gt................ : 142384

     43 : on 2 >>>>  {y}IleProAlaGlyTyrCysPheValGluPheAlaAspLeuAlaTh :     57
          p          {|}||||||||||||||||||||||||||||||||||||||||||||
                   ++{y}IleProAlaGlyTyrCysPheValGluPheAlaAspLeuAlaTh
 142383 : .........ag{G}ATCCCAGCTGGCTACTGCTTTGTAGAATTCGCAGATTTGGCCAC : 131470

     58 : rAlaGluLysCysLeuHisLysIleAsnGlyLysProLeuProGlyAlaThrPro  > :     76
          |||||||||||||||||||||||||||||||||||||||||||||||||||||||   
          rAlaGluLysCysLeuHisLysIleAsnGlyLysProLeuProGlyAlaThrPro++ 
 131469 : AGCTGAGAAGTGTTTGCATAAAATTAATGGGAAACCCCTTCCAGGAGCCACACCTgt. : 131411

     77 : >>> Target Intron 3 >>>>  AlaLysArgPheLysLeuAsnTyrAlaThrTy :     86
                   627 bp           ||||||||||||||||||||||||||||||||
                                  ++AlaLysArgPheLysLeuAsnTyrAlaThrTy
 131410 : ........................agGCGAAACGTTTTAAACTGAACTATGCCACTTA : 130756

     87 : rGlyLysGlnProAspAsn{Se}  >>>> Target Intron 4 >>>>  {r}Pro :     94
          |||||||||||||||||||{||}           3373 bp           {|}|||
          rGlyLysGlnProAspAsn{Se}++                         ++{r}Pro
 130755 : TGGGAAACAACCAGATAAC{AG}gt.........................ag{C}CCT : 127359

     95 : GluTyrSerLeuPheValGlyAspLeuThrProAspValAspAspGlyMetLeuTyrG :    114
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          GluTyrSerLeuPheValGlyAspLeuThrProAspValAspAspGlyMetLeuTyrG
 127358 : GAGTATTCCCTCTTTGTGGGGGACCTGACCCCAGACGTGGATGATGGCATGCTGTATG : 127299

    115 : luPhePheValLysValTyrProSerCysArgGlyGlyLysValValLeuAspGlnTh :    133
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          luPhePheValLysValTyrProSerCysArgGlyGlyLysValValLeuAspGlnTh
 127298 : AATTCTTCGTCAAAGTCTATCCCTCCTGTCGGGGAGGCAAGGTGGTTTTGGACCAGAC : 127242

    134 : rGlyValSer{Ly}  >>>> Target Intron 5 >>>>  {s}GlyTyrGlyPhe :    141
          ||||||||||{||}           3592 bp           {|}||||||||||||
          rGlyValSer{Ly}++                         ++{s}GlyTyrGlyPhe
 127241 : AGGCGTGTCT{AA}gt.........................ag{G}GGTTATGGTTTT : 123626

    142 : ValLysPheThrAspGluLeuGluGlnLysArgAlaLeuThrGluCysGlnGlyAlaV :    161
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          ValLysPheThrAspGluLeuGluGlnLysArgAlaLeuThrGluCysGlnGlyAlaV
 123625 : GTGAAATTCACAGATGAACTGGAACAGAAACGAGCCCTGACGGAGTGCCAGGGAGCAG : 123566

    162 : alGlyLeuGlySerLysProValArgLeuSerValAlaIleProLys{Al}  >>>>  :    177
          |||||||||||||||||||||||||||||||||||||||||||||||{||}       
          alGlyLeuGlySerLysProValArgLeuSerValAlaIleProLys{Al}++     
 123565 : TGGGACTGGGGTCTAAACCTGTGCGGCTGAGCGTGGCAATCCCTAAA{GC}gt..... : 123514

    178 : Target Intron 6 >>>>  {a}SerArgValLysProValGluTyrSerGlnMet :    188
              4265 bp           {|}|||||||||||||||||||||||||||||||||
                              ++{a}SerArgValLysProValGluTyrSerGlnMet
 123513 : ....................ag{G}AGCCGTGTAAAGCCAGTGGAATATAGTCAGATG : 119220

    189 : TyrSerTyrSerTyrAsnGlnTyrTyrGlnGlnTyrGlnAsnTyrTyrAlaGlnTrpG :    208
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          TyrSerTyrSerTyrAsnGlnTyrTyrGlnGlnTyrGlnAsnTyrTyrAlaGlnTrpG
 119219 : TACAGTTATAGCTACAACCAGTATTACCAGCAGTACCAGAACTACTATGCTCAGTGGG : 119160

    209 : lyTyrAspGlnAsnThrGlySerTyrSerTyrSerTyrProGlnTyrGlyTyrThrGl :    227
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          lyTyrAspGlnAsnThrGlySerTyrSerTyrSerTyrProGlnTyrGlyTyrThrGl
 119159 : GCTATGACCAGAACACAGGCAGCTACAGCTACAGTTACCCCCAGTATGGCTATACTCA : 119103

    228 : nSerThrMetGln  >>>> Target Intron 7 >>>>  ThrTyrGluGluValG :    237
          |||||||||||||            527 bp           ||||||||||||||||
          nSerThrMetGln++                         ++ThrTyrGluGluValG
 119102 : GAGCACCATGCAGgt.........................agACATATGAAGAAGTTG : 118546

    238 : lyAspAspAlaLeuGlu{A}  >>>> Target Intron 8 >>>>  {sp}ProMe :    245
          |||||||||||||||||{|}           4278 bp           {||}|||||
          lyAspAspAlaLeuGlu{A}++                         ++{sp}ProMe
 118545 : GAGATGATGCATTGGAA{G}gt.........................ag{AC}CCCAT : 114244

    246 : tProGlnLeuAspValThrGluAlaAsnLysGluPheMetGluGlnSerGluGluLeu :    264
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          tProGlnLeuAspValThrGluAlaAsnLysGluPheMetGluGlnSerGluGluLeu
 114243 : GCCACAGCTGGATGTGACTGAGGCCAACAAGGAGTTCATGGAACAGAGTGAGGAGCTG : 114187

    265 : TyrAspAlaLeuMetAspCysHisTrpGlnProLeuAspThrValSerSerGluIleP :    284
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          TyrAspAlaLeuMetAspCysHisTrpGlnProLeuAspThrValSerSerGluIleP
 114186 : TATGACGCTCTGATGGACTGTCACTGGCAGCCCCTGGACACAGTGTCTTCAGAGATCC : 114127

    285 : roAlaMetMet :    287
          |||||||||||
          roAlaMetMet
 114126 : CTGCCATGATG : 114116

vulgar: SPP02 0 287 . gi|357434040|gb|JH378323.1|:subseq(1,328368) 143010 114115 - 1490 M 9 27 5 0 2 I 0 495 3 0 2 M 32 96 S 0 2 5 0 2 I 0 10869 3 0 2 S 1 1 M 33 99 5 0 2 I 0 623 3 0 2 M 17 51 S 0 2 5 0 2 I 0 3369 3 0 2 S 1 1 M 43 129 S 0 2 5 0 2 I 0 3588 3 0 2 S 1 1 M 39 117 S 0 2 5 0 2 I 0 4261 3 0 2 S 1 1 M 54 162 5 0 2 I 0 523 3 0 2 M 11 33 S 0 1 5 0 2 I 0 4274 3 0 2 S 1 2 M 44 132
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2012-12-04
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	gene	114116	143010	1490	-	.	gene_id 1 ; sequence SPP02 ; gene_orientation +
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	cds	142984	143010	.	-	.	
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	exon	142984	143010	.	-	.	insertions 0 ; deletions 0
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice5	142982	142983	.	-	.	intron_id 1 ; splice_site "GT"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	intron	142485	142983	.	-	.	intron_id 1
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice3	142485	142486	.	-	.	intron_id 0 ; splice_site "AG"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	cds	142387	142484	.	-	.	
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	exon	142387	142484	.	-	.	insertions 0 ; deletions 0
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice5	142385	142386	.	-	.	intron_id 2 ; splice_site "GT"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	intron	131514	142386	.	-	.	intron_id 2
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice3	131514	131515	.	-	.	intron_id 1 ; splice_site "AG"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	cds	131414	131513	.	-	.	
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	exon	131414	131513	.	-	.	insertions 0 ; deletions 0
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice5	131412	131413	.	-	.	intron_id 3 ; splice_site "GT"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	intron	130787	131413	.	-	.	intron_id 3
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice3	130787	130788	.	-	.	intron_id 2 ; splice_site "AG"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	cds	130734	130786	.	-	.	
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	exon	130734	130786	.	-	.	insertions 0 ; deletions 0
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice5	130732	130733	.	-	.	intron_id 4 ; splice_site "GT"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	intron	127361	130733	.	-	.	intron_id 4
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice3	127361	127362	.	-	.	intron_id 3 ; splice_site "AG"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	cds	127229	127360	.	-	.	
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	exon	127229	127360	.	-	.	insertions 0 ; deletions 0
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice5	127227	127228	.	-	.	intron_id 5 ; splice_site "GT"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	intron	123637	127228	.	-	.	intron_id 5
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice3	123637	123638	.	-	.	intron_id 4 ; splice_site "AG"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	cds	123517	123636	.	-	.	
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	exon	123517	123636	.	-	.	insertions 0 ; deletions 0
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice5	123515	123516	.	-	.	intron_id 6 ; splice_site "GT"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	intron	119252	123516	.	-	.	intron_id 6
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice3	119252	119253	.	-	.	intron_id 5 ; splice_site "AG"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	cds	119089	119251	.	-	.	
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	exon	119089	119251	.	-	.	insertions 0 ; deletions 0
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice5	119087	119088	.	-	.	intron_id 7 ; splice_site "GT"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	intron	118562	119088	.	-	.	intron_id 7
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice3	118562	118563	.	-	.	intron_id 6 ; splice_site "AG"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	cds	118528	118561	.	-	.	
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	exon	118528	118561	.	-	.	insertions 0 ; deletions 0
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice5	118526	118527	.	-	.	intron_id 8 ; splice_site "GT"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	intron	114250	118527	.	-	.	intron_id 8
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	splice3	114250	114251	.	-	.	intron_id 7 ; splice_site "AG"
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	cds	114116	114249	.	-	.	
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	exon	114116	114249	.	-	.	insertions 0 ; deletions 0
gi|357434040|gb|JH378323.1|:subseq(1,328368)	exonerate:protein2genome:local	similarity	114116	143010	1490	-	.	alignment_id 1 ; Query SPP02 ; Align 143011 1 27 ; Align 142485 10 96 ; Align 131513 43 99 ; Align 130787 76 51 ; Align 127360 94 129 ; Align 123636 138 117 ; Align 119251 178 162 ; Align 118562 232 33 ; Align 114248 244 132
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis