Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/MM.SBP2.1.fa.x.fa -t 3B.fastasub.dir/1.MM.SBP2.1.fa.x.fa]
Hostname: [ws116063]

C4 Alignment:
------------
         Query: SPP00001557_2.0 # Protein # SECIS binding protein 2 (SBP2) # Mouse (Mus musculus)
        Target: gi|398924730|gb|JH767728.1|:subseq(30580663,142843) Ceratotherium simum simum unplaced genomic scaffold scaffold00006, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 4426
   Query range: 0 -> 1021
  Target range: 92843 -> 49999

     1 : LysAsnValLysLeuSerAlaGluValGluProPheValProGlnLysLysAsnLeuAsp :    20
         ||||||||||||||||||||||||||||||||||||:!!|||||||||||||||! !|||
         LysAsnValLysLeuSerAlaGluValGluProPheIleProGlnLysLysAsnProAsp
 92843 : AAGAATGTCAAGCTGTCAGCTGAGGTAGAGCCATTTATTCCCCAGAAGAAGAATCCTGAT : 92786

    21 : AlaPheValLeuProMetAlaLeuProSerAspAsnGlySerValSerGlyValGluPro :    40
         .!!|||:!!:!!|||||||||||||||!:!|||||||||!:!||||||||||||||||||
         ThrPheMetIleProMetAlaLeuProAsnAspAsnGlyAsnValSerGlyValGluPro
 92785 : ACATTTATGATCCCTATGGCACTCCCAAATGATAATGGCAATGTTTCTGGTGTAGAACCA : 92726

    41 : ThrProIleProSerTyrLeuIleThrCysTyrProPheValGlnGluAsnGlnSerAsn :    60
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         ThrProIleProSerTyrLeuIleThrCysTyrProPheValGlnGluAsnGlnSerAsn
 92725 : ACTCCAATTCCCAGTTACCTGATTACTTGTTATCCATTTGTGCAGGAAAACCAGTCCAAT : 92666

    61 : {Ar}  >>>> Target Intron 1 >>>>  {g}GlnPheProLeuTyrAsnAsnAsp :    69
         {||}           2225 bp           {|}||||||||||||||||||||||||
         {Ar}++                         ++{g}GlnPheProLeuTyrAsnAsnAsp
 92665 : {AG}gt.........................ag{A}CAGTTTCCATTATATAACAATGAC : 90414

    70 : IleArgTrpGlnGlnProSerProSerProThrGlyProTyrLeuAlaTyrProIleIle :    89
         ||||||||||||||||||!:!|||!:!|||.!!|||||||||||||||||||||||||||
         IleArgTrpGlnGlnProAsnProAsnProAlaGlyProTyrLeuAlaTyrProIleIle
 90413 : ATACGATGGCAACAGCCCAATCCAAACCCTGCTGGACCATACCTTGCCTACCCCATTATA : 90354

    90 : SerAlaGlnProProValSerThrGluTyrThrTyrTyrGlnLeuMetProAlaProCys :   109
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         SerAlaGlnProProValSerThrGluTyrThrTyrTyrGlnLeuMetProAlaProCys
 90353 : TCTGCTCAGCCACCTGTTTCTACAGAGTATACATATTATCAGCTGATGCCAGCACCGTGT : 90294

   110 : AlaGlnValMetGlyPheTyrHisProPheProThrProTyrSerSerThrPheGlnAla :   129
         |||||||||||||||||||||||||||||||||||||||||||||!:!||||||||||||
         AlaGlnValMetGlyPheTyrHisProPheProThrProTyrSerAsnThrPheGlnAla
 90293 : GCCCAAGTTATGGGTTTCTATCATCCTTTTCCTACACCTTACTCCAACACCTTTCAGGCT : 90234

   130 : AlaAsnThrValAsnAlaIleSerThrGluCysThrGluArgProAsnGlnLeuGlyGln :   149
         |||||||||||||||.!!|||!!!||||||||||||||||||||||||||||||||||||
         AlaAsnThrValAsnThrIleThrThrGluCysThrGluArgProAsnGlnLeuGlyGln
 90233 : GCAAATACTGTGAATACTATAACCACAGAATGCACTGAGCGTCCAAATCAGCTTGGACAG : 90174

   150 : AlaPheProLeuSerSerHisArgSerArgAsnGlyAsnArgGlyProValValProLys :   169
         !.!||||||||||||||||||||||||||||||.!!||||||||||||||||||||||||
         ValPheProLeuSerSerHisArgSerArgAsnSerAsnArgGlyProValValProLys
 90173 : GTCTTCCCATTGTCCAGTCATCGAAGCAGAAATAGTAACAGAGGGCCAGTGGTACCAAAA : 90114

   170 :   >>>> Target Intron 2 >>>>  ProGlnLeuLeuGlnGlnHisIleLysAsnL :   180
                    1876 bp           ! !||||||||||||||||||||||||!:!|
         ++                         ++GlnGlnLeuLeuGlnGlnHisIleLysSerL
 90113 : gt.........................agCAACAACTTTTACAACAGCACATAAAAAGCA : 88205

   181 : ysArgProGlnValLysAsnValAlaThrGlnLysGluThrSerAlaThrGlyProAspS :   200
         ||||||||  !||||||||||||||||||||||||||||||!:!|||:!!|||||||||!
         ysArgProLeuValLysAsnValAlaThrGlnLysGluThrAsnAlaSerGlyProAspA
 88204 : AACGGCCATTGGTGAAAAATGTAGCTACTCAGAAAGAGACAAATGCATCAGGTCCTGATA : 88145

   201 : erArgSerLysIleValLeuLeuValAspAlaSerGlnGlnThr{A}  >>>> Target :   215
         :!||||||||||||||||||||||||||||||||||||||||||{|}           42
         snArgSerLysIleValLeuLeuValAspAlaSerGlnGlnThr{A}++           
 88144 : ATCGATCAAAAATTGTGCTTCTGGTAGATGCTTCACAGCAAACA{G}gt........... : 88097

   216 :  Intron 3 >>>>  {sp}PheProSerAspIleAlaAsnLysSerLeuSerGluSerT :   229
         87 bp           {||}|||||||||||||||||||||||||||||||||||||||:
                       ++{sp}PheProSerAspIleAlaAsnLysSerLeuSerGluSerS
 88096 : ..............ag{AT}TTCCCATCAGACATCGCCAACAAGTCTCTCTCGGAGAGCT : 83771

   230 : hrAlaThrMetLeuTrpLysAlaLysGlyArgArgArgArgAlaSerHisProAlaValG :   249
         !!||||||||||||||||||:!!||||||||||||||||||||||||||||||.!!!.!|
         erAlaThrMetLeuTrpLysSerLysGlyArgArgArgArgAlaSerHisProThrAlaG
 83770 : CTGCCACAATGCTTTGGAAATCCAAAGGCAGGAGGAGAAGAGCATCCCACCCTACTGCGG : 83711

   250 : luSerSerSerGluGlnGlyAlaSerGluAlaAspIleAspSerAspSerGlyTyrCysS :   269
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         luSerSerSerGluGlnGlyAlaSerGluAlaAspIleAspSerAspSerGlyTyrCysS
 83710 : AATCCTCTAGTGAGCAGGGGGCTAGTGAAGCTGACATTGACAGTGATAGTGGCTACTGCA : 83651

   270 : erProLysHis<->AsnAsnGlnSerAlaProGlyAlaLeuArgAspProAlaSerGlyT :   288
         |||||||||||   ||||||||| !!||| !!||||||||||||:!!|||! !|||||||
         erProLysHisSerAsnAsnGlnProAlaAlaGlyAlaLeuArgAsnProAspSerGlyT
 83650 : GTCCCAAGCACAGCAACAACCAGCCCGCAGCAGGGGCTTTGAGAAATCCTGATTCTGGCA : 83591

   289 : hrMetAsnValArgTyrLeu{S}  >>>> Target Intron 4 >>>>  {er}ValS :   297
         ||!!:|||||| !! !!:!!{ }            851 bp           { !}|||!
         hrIleAsnValCysAsnMet{V}-+                         +-{al}ValT
 83590 : CCATAAATGTATGTAACATG{G}ct.........................at{TT}GTTA : 82713

   298 : erSerGlyValAsnTrpProLysValThrCysGlnAlaThrGlnLysArgProTrpMetG :   317
         !!.!!|||||||||||| !!!!.||||||||||||||||||||||||!:!||||||||||
         hrGlyGlyValAsnTrpSerAsnValThrCysGlnAlaThrGlnLysLysProTrpMetG
 82712 : CAGGTGGTGTAAATTGGTCCAATGTAACTTGCCAGGCAACTCAGAAAAAACCTTGGATGG : 82653

   318 : luLysAsnGlnAlaPheSerArgGlyGlyArgGlnThrGluGlnArgAsnAsnLeuGln  :   337
         |||||||||||  !|||||||||||||||||||||||||||||||||||||||! !||| 
         luLysAsnGlnIlePheSerArgGlyGlyArgGlnThrGluGlnArgAsnAsnSerGln+
 82652 : AAAAAAATCAGATATTTTCTAGAGGTGGAAGGCAGACTGAACAAAGAAATAATTCACAGg : 82593

   338 :  >>>> Target Intron 5 >>>>  ValGlyPheArgCysArgGlyHisSerThrSe :   347
                   6138 bp           ||||||||||||||||||||||||||||||||
         +                         ++ValGlyPheArgCysArgGlyHisSerThrSe
 82592 : t.........................agGTTGGATTCAGATGCCGAGGACATAGTACTTC : 76425

   348 : rSerGluArgArgGlnAsnLeuGlnLysArgGlnAspAsnLysHisLeuAsnSerThrGl :   367
         |||||||||||||||||||||||||||||||||||||||||||!!.|||||| !!!:!||
         rSerGluArgArgGlnAsnLeuGlnLysArgGlnAspAsnLysGlnLeuAsnProSerGl
 76424 : CTCTGAAAGAAGACAGAATTTGCAAAAGCGACAAGATAATAAGCAGTTAAACCCCAGTCA : 76365

   368 : nSerHisArgSerAspProAsnSerGluSerLeuTyrPheGlu  >>>> Target Int :   382
         ||||||||||.!!||||||||||||||||||||||||||||||           1734 b
         nSerHisArgGlyAspProAsnSerGluSerLeuTyrPheGlu++               
 76364 : ATCTCATAGAGGCGACCCAAATTCTGAGTCTTTATATTTTGAGgt............... : 76318

   383 : ron 6 >>>>  AspGluAspGlyPheGlnGluLeuSerGluAsnGlyAsnSerLysAsp :   397
         p           |||||||||||||||!:!||||||!:!||||||||||||:!!||||||
                   ++AspGluAspGlyPheArgGluLeuAsnGluAsnGlyAsnAlaLysAsp
 76317 : ..........agGATGAAGATGGATTTCGAGAACTAAATGAGAATGGAAATGCTAAGGAT : 74541

   398 : GluAsnIleGlnGlnLysLeuSerSerLysVal  >>>> Target Intron 7 >>>> :   409
         |||||||||||||||||||||||||||||||||            791 bp         
         GluAsnIleGlnGlnLysLeuSerSerLysVal++                         
 74540 : GAGAATATTCAACAGAAACTTTCTTCAAAAGTAgt......................... : 74503

   410 :   LeuAspAspLeuProGluAsnSerProIleAsnIleValGlnThrProIleProIleT :   428
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         ++LeuAspAspLeuProGluAsnSerProIleAsnIleValGlnThrProIleProIleT
 74502 : agTTGGATGATTTACCTGAAAACTCACCAATCAACATAGTTCAGACTCCAATTCCCATTA : 73657

   429 : hrThrSerValProLysArgAlaLysSerGlnLysLysLysAlaLeuAlaAlaAlaLeuA :   448
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         hrThrSerValProLysArgAlaLysSerGlnLysLysLysAlaLeuAlaAlaAlaLeuA
 73656 : CAACCTCAGTTCCTAAACGTGCAAAAAGTCAGAAGAAGAAAGCTTTAGCAGCAGCTCTTG : 73597

   449 : laThrAlaGlnGluTyrSerGluIleSerMetGluGlnLysLysLeuGln  >>>> Tar :   465
         ||||||||||||||||||||||||||||||||||||||||||||||||||          
         laThrAlaGlnGluTyrSerGluIleSerMetGluGlnLysLysLeuGln++        
 73596 : CCACAGCTCAAGAATATTCAGAAATAAGTATGGAGCAAAAAAAATTACAGgt........ : 73544

   466 : get Intron 8 >>>>  GluAlaLeuSerLysAlaAlaGlyLysLysThrLysThrPr :   478
           137 bp           ||||||||||||||||||||||||||||||!.!||||||||
                          ++GluAlaLeuSerLysAlaAlaGlyLysLysAsnLysThrPr
 73543 : .................agGAAGCTTTATCAAAGGCAGCTGGAAAAAAGAATAAAACCCC : 73370

   479 : oValGlnLeuAspLeuGlyAspMetLeuAlaAlaLeuGluLysGlnGlnGlnAlaMetLy :   498
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         oValGlnLeuAspLeuGlyAspMetLeuAlaAlaLeuGluLysGlnGlnGlnAlaMetLy
 73369 : TGTGCAGCTAGATTTGGGGGATATGTTAGCAGCTCTGGAAAAACAACAACAAGCAATGAA : 73310

   499 : sAlaArgGlnIleThrAsnThrArgProLeuAlaHisPro{V}  >>>> Target Int :   512
         |||||||||||||||||||||||||||||||:!!:!! !!{|}           3504 b
         sAlaArgGlnIleThrAsnThrArgProLeuSerTyrThr{V}++               
 73309 : AGCACGGCAAATTACTAATACCAGACCACTGTCATATACA{G}gt............... : 73265

   513 : ron 9 >>>>  {al}ValThrThrAlaThrPheHisThrLysAspSer<->AsnArgLy :   526
         p           {||}||||||.!!|||:!!||||||||||||||||||   ||||||||
                   ++{al}ValThrAlaAlaSerPheHisThrLysAspSerThrAsnArgLy
 73264 : ..........ag{TG}GTCACTGCAGCTTCTTTTCACACTAAAGACTCTACTAACAGAAA : 69719

   527 : sThrLeuAlaLysSerGlnProCysValThrSerPheAsnSerLeuAspIleThrSerSe :   546
         | !!|||.!!|||||||||||||||:!!||||||||||||||||||||||||.!!|||||
         sProLeuThrLysSerGlnProCysLeuThrSerPheAsnSerLeuAspIleAlaSerSe
 69718 : ACCTTTAACCAAAAGTCAGCCCTGTTTGACATCCTTTAATTCTTTGGACATTGCTTCCTC : 69659

   547 : rLysAlaLysLysGlyLysGluLysGluIleAlaLysLeuLysArgProThrAlaLeuLy :   566
         ||||.!!|||||||||||||||||||||||||||||||||||||||||||||||||||||
         rLysThrLysLysGlyLysGluLysGluIleAlaLysLeuLysArgProThrAlaLeuLy
 69658 : TAAAACGAAAAAAGGAAAAGAGAAGGAAATTGCAAAACTAAAACGACCCACAGCACTTAA : 69599

   567 : sLys  >>>> Target Intron 10 >>>>  ValIleLeuLysGluArgGluGluLy :   576
         ||||            810 bp            ||||||||||||||||||||||||||
         sLys++                          ++ValIleLeuLysGluArgGluGluLy
 69598 : AAAGgt..........................agGTTATTTTGAAAGAAAGAGAGGAAAA : 68759

   577 : sLysGlyArgLeuIleValGluHisSerValLeuGlyAlaGluGluProThrGluThrHi :   596
         |||||||||||||! !|||!!:|||!:!:!!||||||:!!|||||||||..!|||! !||
         sLysGlyArgLeuThrValAspHisAsnLeuLeuGlySerGluGluProValGluMetHi
 68758 : GAAGGGCCGGTTAACTGTGGACCACAATCTTTTGGGATCTGAGGAACCAGTAGAAATGCA : 68699

   597 : sLeuAspLeuThrAsnAspLeuProGlnGluThrValSerGlnGlu{A}  >>>> Targ :   612
         |||||||!!!! !:!!||||||! !||||||! !||||||||||||{|}           
         sLeuAspPheIleAspAspLeuGlnGlnGluIleValSerGlnGlu{A}++         
 68698 : CTTAGATTTTATTGATGACTTGCAGCAGGAGATTGTTTCCCAGGAA{G}gt......... : 68648

   613 : et Intron 11 >>>>  {sp}AlaGlyLeuSerMetProSerAspAlaSerLeuSerP :   625
          1596 bp           {||}.!!|||||||||||||||||||||.!!||||||||||
                          ++{sp}ThrGlyLeuSerMetProSerAspThrSerLeuSerP
 68647 : .................ag{AT}ACTGGACTGAGCATGCCCAGTGATACTTCGCTCTCTC : 67016

   626 : roAlaSerGlnAsnSerProTyrCysMetThrProValSerGlnGlySerProAlaSerS :   645
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         roAlaSerGlnAsnSerProTyrCysMetThrProValSerGlnGlySerProAlaSerS
 67015 : CAGCAAGTCAGAACTCTCCATACTGTATGACACCTGTGTCACAAGGCTCTCCGGCTAGTT : 66956

   646 : erGlyIleGlySerProMetAlaSerSerThrIleThrLysIleHisSerLysArgPheA :   665
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         erGlyIleGlySerProMetAlaSerSerThrIleThrLysIleHisSerLysArgPheA
 66955 : CCGGGATAGGCAGTCCAATGGCATCTTCGACAATAACCAAAATCCACAGCAAAAGATTTA : 66896

   666 : rg{Gl}  >>>> Target Intron 12 >>>>  {u}TyrCysAsnGlnValLeuSer :   673
         ||{||}            2010 bp           {|}||||||||||||||||||!!!
         rg{Gl}++                          ++{u}TyrCysAsnGlnValLeuCys
 66895 : GA{GA}gt..........................ag{G}TATTGTAATCAGGTTCTTTGT : 64862

   674 : LysGluIleAspGluCysValThrLeuLeuLeuGlnGluLeuValSerPheGlnGluArg :   693
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         LysGluIleAspGluCysValThrLeuLeuLeuGlnGluLeuValSerPheGlnGluArg
 64861 : AAAGAGATTGATGAGTGTGTGACTCTTCTTCTCCAAGAGCTCGTCAGTTTCCAGGAACGC : 64802

   694 : IleTyrGlnLysAspProValArgAlaLysAlaArgArgArgLeuValMetGlyLeuArg :   713
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         IleTyrGlnLysAspProValArgAlaLysAlaArgArgArgLeuValMetGlyLeuArg
 64801 : ATCTACCAAAAGGATCCTGTCAGAGCAAAAGCGAGGAGACGGCTGGTTATGGGTCTAAGG : 64742

   714 : GluValThrLysHisMetLysLeuAsnLysIleLysCysValIleIleSerProAsnCys :   733
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         GluValThrLysHisMetLysLeuAsnLysIleLysCysValIleIleSerProAsnCys
 64741 : GAGGTTACCAAACATATGAAGCTAAACAAGATCAAGTGTGTTATAATTTCTCCAAACTGT : 64682

   734 : GluLysIleGlnSerLys{G}  >>>> Target Intron 13 >>>>  {ly}GlyLe :   742
         ||||||||||||||||||{|}            1206 bp           {||}|||||
         GluLysIleGlnSerLys{G}++                          ++{ly}GlyLe
 64681 : GAAAAAATCCAGTCAAAG{G}gt..........................ag{GT}GGCCT : 63449

   743 : uAspGluAlaLeuTyrAsnValIleAlaMetAlaArgGluGlnGluIleProPheValPh :   762
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         uAspGluAlaLeuTyrAsnValIleAlaMetAlaArgGluGlnGluIleProPheValPh
 63448 : GGATGAGGCTCTCTATAATGTTATAGCCATGGCACGGGAACAAGAAATTCCTTTTGTGTT : 63389

   763 : eAlaLeuGlyArgLysAlaLeuGlyArgCysValAsnLysLeuValProValSerValVa :   782
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         eAlaLeuGlyArgLysAlaLeuGlyArgCysValAsnLysLeuValProValSerValVa
 63388 : TGCCCTTGGAAGAAAAGCTCTAGGACGCTGTGTGAACAAGCTGGTTCCTGTTAGTGTAGT : 63329

   783 : lGlyIlePheAsnTyrPheGlyAlaGlu  >>>> Target Intron 14 >>>>  Se :   792
         ||||||||||||||||||||||||||||            5492 bp           ||
         lGlyIlePheAsnTyrPheGlyAlaGlu++                          ++Se
 63328 : GGGAATCTTCAACTACTTTGGTGCTGAGgt..........................agAG : 57807

   793 : rLeuPheAsnArgLeuValGluLeuThrGluGluAlaArgLysAlaTyrLysAspMetVa :   812
         ||||||||||!:!|||||||||||||||||||||||||||||||||||||||||||||||
         rLeuPheAsnLysLeuValGluLeuThrGluGluAlaArgLysAlaTyrLysAspMetVa
 57806 : TCTGTTTAACAAGTTAGTAGAACTCACTGAGGAAGCCAGGAAGGCATATAAGGATATGGT : 57747

   813 : lAlaAlaThrGluGlnGluGlnAlaGluGluAlaLeuArgSerValLysThrValProHi :   832
         |||||||! !|||||||||||||||||||||||||||!:!!:!!.!|||! !||||||||
         lAlaAlaMetGluGlnGluGlnAlaGluGluAlaLeuLysAsnAlaLysLysValProHi
 57746 : TGCAGCAATGGAACAAGAGCAGGCCGAGGAAGCCTTGAAGAACGCGAAGAAGGTGCCACA : 57687

   833 : sHisMetGlyHisSerArgAsnProSerAlaAlaSerAlaIleSerPheCysSerValIl :   852
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         sHisMetGlyHisSerArgAsnProSerAlaAlaSerAlaIleSerPheCysSerValIl
 57686 : CCACATGGGGCATTCTCGGAATCCCTCTGCAGCAAGTGCCATTTCTTTCTGCAGTGTTAT : 57627

   853 : eSerGluProIleSerGluValAsnGluLysGluTyr{G}  >>>> Target Intron :   865
         |||||||||||||||||||||||||||||||||||||{|}            7109 bp 
         eSerGluProIleSerGluValAsnGluLysGluTyr{G}++                  
 57626 : TTCTGAACCCATCTCTGAAGTCAATGAAAAGGAATAT{G}gt.................. : 57585

   866 :  15 >>>>  {lu}ThrAsnTrpArgSerMetValGluThrSerAspGlyLeuGluProS :   881
                   {||}||||||||||||!:!||||||||||||||||||||||||||| !!|
                 ++{lu}ThrAsnTrpArgAsnMetValGluThrSerAspGlyLeuGluThrS
 57584 : ........ag{AA}ACAAATTGGAGAAACATGGTGGAAACTTCAGATGGACTGGAAACAT : 50431

   882 : erGluMetGluLysAlaAlaProCysThrHisSerProProGluLysProSerArgLeuA :   901
         |||||!  |||!:!! !!.! !!|||! !|||||| !! !!|||||||||.!!!:!||| 
         erGluAsnGluArgGluValSerCysLysHisSerAlaSerGluLysProGlyLysLeuP
 50430 : CAGAAAATGAGAGAGAGGTTTCCTGTAAGCACAGCGCATCTGAAAAACCCGGTAAACTTC : 50371

   902 : laLeuAspThrSerLeuValGlyLysGlnLeuProLeu<->AlaAlaGlySerIleThrS :   920
         !!!!!|||.!!:!!! !||||||||||||! ! !!|||   ||||||||||||! !||||
         roPheAspAlaAlaProValGlyLysGlnProSerLeuValAlaAlaGlySerThrThrS
 50370 : CATTTGACGCAGCCCCTGTTGGTAAGCAGCCATCGTTAGTGGCTGCAGGCAGTACTACCT : 50311

   921 : erAlaProSerGlnGlyLysProThr<->GlyAspLysAspGluLeuLysProAspAspL :   939
         ||||| !!!:!!  |||||| !!|||   .!!||||||!!:|||:!!|||||||||||||
         erAlaThrAsnProGlyLysSerThrValSerAspLysGluGluValLysProAspAspL
 50310 : CAGCTACAAACCCTGGGAAATCGACAGTGAGCGATAAAGAGGAAGTGAAGCCAGATGACC : 50251

   940 : euGluTrpAlaSerGlnGlnSerThrGluThrGlySerLeuAspGlySerCysArgAspL :   959
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         euGluTrpAlaSerGlnGlnSerThrGluThrGlySerLeuAspGlySerCysArgAspL
 50250 : TGGAATGGGCCTCTCAGCAGAGTACAGAGACCGGCTCTTTGGATGGCAGTTGCCGAGATC : 50191

   960 : euLeuAsnSerSerIleThrSerThrThrSerThrLeuValProGlyMetLeuGluGluG :   979
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         euLeuAsnSerSerIleThrSerThrThrSerThrLeuValProGlyMetLeuGluGluG
 50190 : TTTTGAATTCCTCCATCACCAGCACCACCAGCACTCTCGTACCTGGCATGCTTGAAGAAG : 50131

   980 : luGluAspGlu<->GluGluGluGluGluAspTyrSerHisGluProThrAlaGluGluV :   998
         ||!!:||||||   |||||||||||||||||||||!!!|||||||||! !:!!! !||||
         luAspAspGluAspGluGluGluGluGluAspTyrThrHisGluProIleSerValGluV
 50130 : AGGATGATGAAGATGAGGAGGAGGAAGAAGATTATACTCATGAACCCATATCTGTAGAAG : 50071

   999 : alGlnLeuAsnSerArgIleGluSerTrpValSerGluThrGlnArgThrMetGluThrL :  1018
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         alGlnLeuAsnSerArgIleGluSerTrpValSerGluThrGlnArgThrMetGluThrL
 50070 : TACAGCTTAATAGTAGAATTGAGTCTTGGGTTTCTGAGACCCAGAGAACGATGGAAACTC : 50011

  1019 : euGlnLeuGly :  1021
         |||||||||||
         euGlnLeuGly
 50010 : TGCAGCTTGGA : 50000

vulgar: SPP00001557_2.0 0 1021 . gi|398924730|gb|JH767728.1|:subseq(30580663,142843) 92843 49999 - 4426 M 60 180 S 0 2 5 0 2 I 0 2221 3 0 2 S 1 1 M 108 324 5 0 2 I 0 1872 3 0 2 M 45 135 S 0 1 5 0 2 I 0 4283 3 0 2 S 1 2 M 57 171 G 0 3 M 22 66 S 0 1 5 0 2 I 0 847 3 0 2 S 1 2 M 41 123 5 0 2 I 0 6134 3 0 2 M 45 135 5 0 2 I 0 1730 3 0 2 M 27 81 5 0 2 I 0 787 3 0 2 M 56 168 5 0 2 I 0 133 3 0 2 M 47 141 S 0 1 5 0 2 I 0 3500 3 0 2 S 1 2 M 11 33 G 0 3 M 44 132 5 0 2 I 0 806 3 0 2 M 44 132 S 0 1 5 0 2 I 0 1592 3 0 2 S 1 2 M 53 159 S 0 2 5 0 2 I 0 2006 3 0 2 S 1 1 M 73 219 S 0 1 5 0 2 I 0 1202 3 0 2 S 1 2 M 51 153 5 0 2 I 0 5488 3 0 2 M 73 219 S 0 1 5 0 2 I 0 7105 3 0 2 S 1 2 M 48 144 G 0 3 M 15 45 G 0 3 M 54 162 G 0 3 M 39 117
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-26
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	gene	50000	92843	4426	-	.	gene_id 1 ; sequence SPP00001557_2.0 ; gene_orientation +
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	92662	92843	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	92662	92843	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	92660	92661	.	-	.	intron_id 1 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	90437	92661	.	-	.	intron_id 1
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	90437	90438	.	-	.	intron_id 0 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	90112	90436	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	90112	90436	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	90110	90111	.	-	.	intron_id 2 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	88236	90111	.	-	.	intron_id 2
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	88236	88237	.	-	.	intron_id 1 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	88100	88235	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	88100	88235	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	88098	88099	.	-	.	intron_id 3 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	83813	88099	.	-	.	intron_id 3
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	83813	83814	.	-	.	intron_id 2 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	83570	83812	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	83570	83812	.	-	.	insertions 3 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	83568	83569	.	-	.	intron_id 4 ; splice_site "CT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	82719	83569	.	-	.	intron_id 4
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	82719	82720	.	-	.	intron_id 3 ; splice_site "AT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	82594	82718	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	82594	82718	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	82592	82593	.	-	.	intron_id 5 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	76456	82593	.	-	.	intron_id 5
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	76456	76457	.	-	.	intron_id 4 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	76321	76455	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	76321	76455	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	76319	76320	.	-	.	intron_id 6 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	74587	76320	.	-	.	intron_id 6
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	74587	74588	.	-	.	intron_id 5 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	74506	74586	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	74506	74586	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	74504	74505	.	-	.	intron_id 7 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	73715	74505	.	-	.	intron_id 7
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	73715	73716	.	-	.	intron_id 6 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	73547	73714	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	73547	73714	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	73545	73546	.	-	.	intron_id 8 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	73410	73546	.	-	.	intron_id 8
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	73410	73411	.	-	.	intron_id 7 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	73268	73409	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	73268	73409	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	73266	73267	.	-	.	intron_id 9 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	69764	73267	.	-	.	intron_id 9
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	69764	69765	.	-	.	intron_id 8 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	69594	69763	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	69594	69763	.	-	.	insertions 3 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	69592	69593	.	-	.	intron_id 10 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	68784	69593	.	-	.	intron_id 10
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	68784	68785	.	-	.	intron_id 9 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	68651	68783	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	68651	68783	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	68649	68650	.	-	.	intron_id 11 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	67055	68650	.	-	.	intron_id 11
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	67055	67056	.	-	.	intron_id 10 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	66892	67054	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	66892	67054	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	66890	66891	.	-	.	intron_id 12 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	64882	66891	.	-	.	intron_id 12
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	64882	64883	.	-	.	intron_id 11 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	64661	64881	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	64661	64881	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	64659	64660	.	-	.	intron_id 13 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	63455	64660	.	-	.	intron_id 13
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	63455	63456	.	-	.	intron_id 12 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	63300	63454	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	63300	63454	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	63298	63299	.	-	.	intron_id 14 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	57808	63299	.	-	.	intron_id 14
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	57808	57809	.	-	.	intron_id 13 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	57588	57807	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	57588	57807	.	-	.	insertions 0 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice5	57586	57587	.	-	.	intron_id 15 ; splice_site "GT"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	intron	50479	57587	.	-	.	intron_id 15
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	splice3	50479	50480	.	-	.	intron_id 14 ; splice_site "AG"
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	cds	50000	50478	.	-	.	
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	exon	50000	50478	.	-	.	insertions 9 ; deletions 0
gi|398924730|gb|JH767728.1|:subseq(30580663,142843)	exonerate:protein2genome:local	similarity	50000	92843	4426	-	.	alignment_id 1 ; Query SPP00001557_2.0 ; Align 92844 1 180 ; Align 90436 62 324 ; Align 88236 170 135 ; Align 83811 216 171 ; Align 83637 273 66 ; Align 82717 296 123 ; Align 76456 337 135 ; Align 74587 382 81 ; Align 73715 409 168 ; Align 73410 465 141 ; Align 69762 513 33 ; Align 69726 524 132 ; Align 68784 568 132 ; Align 67053 613 159 ; Align 64881 667 219 ; Align 63453 741 153 ; Align 57808 792 219 ; Align 50477 866 144 ; Align 50330 914 45 ; Align 50282 929 162 ; Align 50117 983 117
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis




Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/MM.SBP2.1.fa.x.fa -t 3B.fastasub.dir/2.MM.SBP2.1.fa.x.fa]
Hostname: [ws116063]

C4 Alignment:
------------
         Query: SPP00001557_2.0 # Protein # SECIS binding protein 2 (SBP2) # Mouse (Mus musculus)
        Target: gi|398923423|gb|JH767747.1|:subseq(16258547,119598) Ceratotherium simum simum unplaced genomic scaffold scaffold00025, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 495
   Query range: 651 -> 791
  Target range: 62317 -> 69598

   652 : AlaSerSerThrIleThrLysIleHisSerLysArgPheArg{Gl}  >>>> Target  :   666
         !.!|||:!!.!!  ! !!!:!|||||||||::!|||||||||{!!}            69
         GlySerAlaAlaCysProArgIleHisSerArgArgPheArg{As}++            
 62318 : GGCAGTGCCGCCTGCCCCAGGATCCACAGCCGGAGATTCAGG{GA}gt............ : 62364

   667 : Intron 1 >>>>  {u}TyrCysAsnGlnValLeuSerLysGluIleAspGluCysVal :   680
         6 bp           {:}||||||!:!|||:!!||||||||||||:!:|||!  ||||||
                      ++{p}TyrCysSerGlnIleLeuSerLysGluValAspAlaCysVal
 62365 : .............ag{T}TACTGCAGCCAGATACTCAGTAAAGAAGTGGACGCCTGTGTT : 63098

   681 : ThrLeuLeuLeuGlnGluLeuValSerPheGlnGluArgIleTyrGlnLysAspProVal :   700
         |||  !||||||:!!||||||||| !!||||||!!:|||!!:||||||||||||||||||
         ThrAspLeuLeuLysGluLeuValArgPheGlnAspArgMetTyrGlnLysAspProVal
 63099 : ACGGACCTGCTGAAAGAGCTGGTCCGTTTCCAAGACCGCATGTACCAGAAAGATCCAGTC : 63158

   701 : ArgAlaLysAlaArgArgArgLeuValMetGlyLeuArgGluValThrLysHisMetLys :   720
         !:!|||!:!.!!!:!||||||||||||:!!|||||||||||||||  !||||||:!!|||
         LysAlaArgThrLysArgArgLeuValLeuGlyLeuArgGluValLeuLysHisLeuLys
 63159 : AAGGCCAGGACCAAGCGCCGGCTCGTGTTGGGGCTGAGGGAGGTCCTCAAGCACCTGAAG : 63218

   721 : LeuAsnLysIleLysCysValIleIleSerProAsnCysGluLysIleGlnSerLys{G} :   740
         |||!..|||:!:||||||:!!||||||||||||||||||||||||||||||||||||{|}
         LeuArgLysLeuLysCysIleIleIleSerProAsnCysGluLysIleGlnSerLys{G}
 63219 : CTCAGGAAGCTGAAGTGCATCATCATCTCTCCCAACTGCGAGAAAATCCAGTCGAAA{G} : 63278

   741 :   >>>> Target Intron 2 >>>>  {ly}GlyLeuAspGluAlaLeuTyrAsnVal :   749
                    6165 bp           {||}|||||||||!!:.!!|||:!!!.!:!!
         ++                         ++{ly}GlyLeuAspAspThrLeuHisThrIle
 63279 : gt.........................ag{GT}GGGCTGGATGACACCCTGCACACCATC : 69470

   750 : IleAlaMetAlaArgGluGlnGluIleProPheValPheAlaLeuGlyArgLysAlaLeu :   769
         |||! !   ||| !!||||||.!.||||||! !||||||||||||..!||||||||||||
         IleAspTyrAlaCysGluGlnAsnIleProCysValPheAlaLeuAsnArgLysAlaLeu
 69471 : ATTGATTACGCCTGTGAGCAGAACATTCCCTGTGTGTTTGCACTCAACCGCAAAGCTCTG : 69530

   770 : GlyArgCysValAsnLysLeuValProValSerValValGlyIlePheAsnTyrPheGly :   789
         |||||| !!:!!||||||  !|||||||||||||||||||||||||||!:!|||  !|||
         GlyArgSerLeuAsnLysAlaValProValSerValValGlyIlePheSerTyrAspGly
 69531 : GGGCGCAGTCTGAACAAAGCCGTTCCTGTCAGCGTGGTGGGGATCTTCAGCTACGATGGA : 69590

   790 : AlaGlu :   791
         |||:!!
         AlaGln
 69591 : GCCCAG : 69598

vulgar: SPP00001557_2.0 651 791 . gi|398923423|gb|JH767747.1|:subseq(16258547,119598) 62317 69598 + 495 M 14 42 S 0 2 5 0 2 I 0 692 3 0 2 S 1 1 M 73 219 S 0 1 5 0 2 I 0 6161 3 0 2 S 1 2 M 51 153
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-26
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	gene	62318	69598	495	+	.	gene_id 1 ; sequence SPP00001557_2.0 ; gene_orientation +
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	cds	62318	62361	.	+	.	
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	exon	62318	62361	.	+	.	insertions 0 ; deletions 0
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	splice5	62362	62363	.	+	.	intron_id 1 ; splice_site "GT"
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	intron	62362	63057	.	+	.	intron_id 1
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	splice3	63056	63057	.	+	.	intron_id 0 ; splice_site "AG"
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	cds	63058	63278	.	+	.	
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	exon	63058	63278	.	+	.	insertions 0 ; deletions 0
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	splice5	63279	63280	.	+	.	intron_id 2 ; splice_site "GT"
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	intron	63279	69443	.	+	.	intron_id 2
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	splice3	69442	69443	.	+	.	intron_id 1 ; splice_site "AG"
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	cds	69444	69598	.	+	.	
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	exon	69444	69598	.	+	.	insertions 0 ; deletions 0
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	similarity	62318	69598	495	+	.	alignment_id 1 ; Query SPP00001557_2.0 ; Align 62318 652 42 ; Align 63059 667 219 ; Align 69446 741 153
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00001557_2.0 # Protein # SECIS binding protein 2 (SBP2) # Mouse (Mus musculus)
        Target: gi|398923423|gb|JH767747.1|:subseq(16258547,119598) Ceratotherium simum simum unplaced genomic scaffold scaffold00025, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 191
   Query range: 468 -> 586
  Target range: 49999 -> 60626

   469 : LysAlaAlaGlyLysLysThrLysThrProValGlnLeuAspLeuGlyAspMetLeuAla :   488
         |||  !::!|||||||||!:!:!!||||||||||||||||||||||||!  ||||||.!!
         LysAsnSerGlyLysLysSerGlnThrProValGlnLeuAspLeuGlyGlyMetLeuThr
 50000 : AAAAATAGTGGAAAGAAGAGCCAAACTCCAGTACAGTTGGATTTGGGGGGAATGCTGACA : 50057

   489 : AlaLeuGluLysGlnGlnGlnAlaMetLysAlaArgGlnIleThrAsnThrArgProLeu :   508
         ||||||||||||:!!|||!!.:!!..!!!.|||!:!|||         :!!!:!|||:!!
         AlaLeuGluLysLysGlnHisSerGlnAsnAlaLysGln------ProSerLysProVal
 50058 : GCACTGGAGAAGAAGCAGCACTCCCAGAATGCAAAGCAG------CCGTCCAAACCGGTG : 50111

   509 : AlaHisPro{V}  >>>> Target Intron 1 >>>>  {al}ValThrThrAlaThr :   517
         !.!  ! !!{|}           9635 bp           {||}! !.!!..! !!..!
         ValPheSer{V}++                         ++{al}GlyAlaValProVal
 50112 : GTGTTCTCA{G}gt.........................ag{TC}GGGGCCGTGCCAGTC : 59773

   518 : PheHisThrLysAspSerAsnArgLysThrLeuAlaLysSerGlnProCysValThrSer :   537
         .!!  !! !:!!! !!!!::: !!|||! !  !  !:::! !...  !     !||| !!
         LeuSerLysGluAlaThrSerGlyLysLysGlyHisArgPheSerGluValLysThrPro
 59774 : CTCTCCAAAGAGGCCACGTCAGGGAAGAAGGGCCACCGCTTCAGCGAAGTGAAGACCCCG : 59833

   538 : PheAsnSerLeuAspIleThrSerSerLysAlaLysLysGlyLysGluLysGluIleAla :   557
           !||| !!||||||  !!:!:!! !!  !  !||||||||||||:!!!:!|||:!! !!
         HisAsnProLeuAspSerSerAlaProLeuMetLysLysGlyLysGlnArgGluValPro
 59834 : CACAACCCCCTGGACTCCAGTGCCCCCCTGATGAAGAAGGGAAAGCAGAGGGAGGTCCCC : 59893

   558 : LysLeuLysArgProThrAlaLeuLysLys  >>>> Target Intron 2 >>>>  V :   568
         |||  !|||!:!||||||:!!|||||||||            644 bp           :
         LysAlaLysLysProThrSerLeuLysLys++                         ++I
 59894 : AAAGCCAAGAAGCCAACCTCGTTGAAGAAGgt.........................agA : 60570

   569 : alIleLeuLysGluArgGluGluLysLysGlyArgLeuIleValGluHisSerVal :   586
         !!|||||||||||||||:!!|||!:!|||  !!:!! !:!!  !|||:!!:!!:!!
         leIleLeuLysGluArgGlnGluArgLysGlnGlnArgLeuGlnGluAsnAlaMet
 60571 : TTATTTTGAAAGAACGTCAGGAGAGAAAGCAGCAGCGTCTCCAGGAAAATGCCATG : 60626

vulgar: SPP00001557_2.0 468 586 . gi|398923423|gb|JH767747.1|:subseq(16258547,119598) 49999 60626 + 191 M 33 99 G 2 0 M 8 24 S 0 1 5 0 2 I 0 9631 3 0 2 S 1 2 M 55 165 5 0 2 I 0 640 3 0 2 M 19 57
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-26
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	gene	50000	60626	191	+	.	gene_id 2 ; sequence SPP00001557_2.0 ; gene_orientation +
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	cds	50000	50123	.	+	.	
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	exon	50000	50123	.	+	.	insertions 0 ; deletions 2
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	splice5	50124	50125	.	+	.	intron_id 1 ; splice_site "GT"
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	intron	50124	59758	.	+	.	intron_id 1
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	splice3	59757	59758	.	+	.	intron_id 0 ; splice_site "AG"
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	cds	59759	59925	.	+	.	
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	exon	59759	59925	.	+	.	insertions 0 ; deletions 0
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	splice5	59926	59927	.	+	.	intron_id 2 ; splice_site "GT"
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	intron	59926	60569	.	+	.	intron_id 2
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	splice3	60568	60569	.	+	.	intron_id 1 ; splice_site "AG"
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	cds	60570	60626	.	+	.	
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	exon	60570	60626	.	+	.	insertions 0 ; deletions 0
gi|398923423|gb|JH767747.1|:subseq(16258547,119598)	exonerate:protein2genome:local	similarity	50000	60626	191	+	.	alignment_id 2 ; Query SPP00001557_2.0 ; Align 50000 469 99 ; Align 50099 504 24 ; Align 59761 513 165 ; Align 60570 568 57
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis


