Command line: [exonerate -m p2g --showtargetgff -q MsrA.aa.fa -t MrsA_JSZB01006427.1.subseq.da]
Hostname: [ws116040u]

C4 Alignment:
------------
         Query: SPP00000044_2.0 # Protein # Methionine sulfoxide reductase A (MsrA) # Human 
        Target: JSZB01006427.1:subseq(69765,135570) Manis javanica isolate MP_PG03-UM SCAFFOLD7353, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 606
   Query range: 111 -> 234
  Target range: 125532 -> 2

    112 : LysThrGlyHisAlaGluValValArgValValTyrGlnProGluHisMetSerPheG :    131
          |||||||||||||||||||||||||||||||||!:!||||||||||||!!:|||||||
          LysThrGlyHisAlaGluValValArgValValPheGlnProGluHisIleSerPheG
 125532 : AAAACTGGCCACGCAGAGGTAGTCCGAGTGGTGTTCCAGCCAGAACACATCAGCTTTG : 125475

    132 : luGluLeuLeuLysValPheTrpGluAsnHisAspProThrGln{G}  >>>> Targ :    146
          ||||||||||||||||||||||||||||||||||||||||||||{|}           
          luGluLeuLeuLysValPheTrpGluAsnHisAspProThrGln{G}++         
 125474 : AGGAGCTGCTGAAGGTCTTCTGGGAGAATCATGACCCGACCCAA{G}gt......... : 125427

    147 : et Intron 1 >>>>  {ly}MetArgGlnGlyAsnAspHisGlyThrGlnTyrArg :    158
          26908 bp          {||}||||||||||||||||||||||||:!!|||||||||
                          ++{ly}MetArgGlnGlyAsnAspHisGlySerGlnTyrArg
 125426 : ................ag{GC}ATGCGCCAAGGCAATGACCACGGCTCGCAGTACCGC :  98486

    159 : SerAlaIleTyrProThrSerAlaLysGlnMetGluAlaAlaLeuSerSerLysGluA :    178
          ||||||||||||||||||||||||:!!!!.:!!||||||||||||!.!|||! !|||:
          SerAlaIleTyrProThrSerAlaGluHisLeuGluAlaAlaLeuLysSerThrGluA
  98485 : TCGGCCATCTATCCGACCTCCGCCGAGCACCTGGAGGCAGCCCTGAAGTCCACAGAGG :  98426

    179 : snTyrGlnLys  >>>> Target Intron 2 >>>>  ValLeuSerGluHisGly :    187
          !!|||||||||           98253 bp          ||||||||||||||||||
          spTyrGlnLys++                         ++ValLeuSerGluHisGly
  98425 : ACTACCAGAAGgt.........................agGTTCTTTCAGAGCATGGC :    146

    188 : PheGlyProIleThrThrAspIleArgGluGlyGlnThrPheTyrTyrAlaGluAspT :    207
          !:!||||||||||||||||||:!!|||||||||||| !!|||||||||||||||||||
          TyrGlyProIleThrThrAspValArgGluGlyGlnProPheTyrTyrAlaGluAspT
    145 : TATGGCCCGATCACAACCGACGTCCGGGAGGGGCAGCCCTTCTACTACGCAGAGGATT :     86

    208 : yrHisGlnGlnTyrLeuSerLysAsnProAsnGlyTyrCysGlyLeuGlyGlyThrGl :    226
          |||||||||||||||||||||||||||||:!!||||||||||||||||||||||||||
          yrHisGlnGlnTyrLeuSerLysAsnProAspGlyTyrCysGlyLeuGlyGlyThrGl
     85 : ACCACCAGCAGTACCTGAGCAAGAACCCCGACGGATACTGCGGCCTTGGGGGCACTGG :     29

    227 : yValSerCysProValGlyIleLys :    234
          |||||||||||||:!:|||||||||
          yValSerCysProLeuGlyIleLys
     28 : AGTGTCTTGTCCATTgggtattaaa :      3

vulgar: SPP00000044_2.0 111 234 . JSZB01006427.1:subseq(69765,135570) 125532 2 - 606 M 34 102 S 0 1 5 0 2 I 0 26904 3 0 2 S 1 2 M 35 105 5 0 2 I 0 98249 3 0 2 M 53 159
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2016-11-11
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	gene	3	125532	606	-	.	gene_id 1 ; sequence SPP00000044_2.0 ; gene_orientation +
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	cds	125430	125532	.	-	.	
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	exon	125430	125532	.	-	.	insertions 0 ; deletions 0
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	splice5	125428	125429	.	-	.	intron_id 1 ; splice_site "GT"
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	intron	98522	125429	.	-	.	intron_id 1
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	splice3	98522	98523	.	-	.	intron_id 0 ; splice_site "AG"
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	cds	98415	98521	.	-	.	
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	exon	98415	98521	.	-	.	insertions 0 ; deletions 0
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	splice5	98413	98414	.	-	.	intron_id 2 ; splice_site "GT"
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	intron	162	98414	.	-	.	intron_id 2
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	splice3	162	163	.	-	.	intron_id 1 ; splice_site "AG"
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	cds	3	161	.	-	.	
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	exon	3	161	.	-	.	insertions 0 ; deletions 0
JSZB01006427.1:subseq(69765,135570)	exonerate:protein2genome:local	similarity	3	125532	606	-	.	alignment_id 1 ; Query SPP00000044_2.0 ; Align 125533 112 102 ; Align 98520 147 105 ; Align 162 182 159
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis