Command line: [exonerate -m p2g --showtargetgff -q PmarinusNCBI.aa.fa -t cromPmarinus.fa]
Hostname: [ws101133.aulescm.upf.edu]

C4 Alignment:
------------
         Query: gi|239878374|gb|EER05138.1| thioredoxin reductase 1, cytoplasmic, putative [Perkinsus marinus ATCC 50983]
        Target: gi|126302086|gb|AAXJ01000419.1| Perkinsus marinus ATCC 50983 strain ATCC 50983 gcontig_1104296604260, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 2500
   Query range: 0 -> 495
  Target range: 3047 -> 1296

    1 : MetProAspProAlaGluSerValTyrAspTrpAspLeuPheValIleGlyGlyGlySerGl :   21
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        MetProAspProAlaGluSerValTyrAspTrpAspLeuPheValIleGlyGlyGlySerGl
 3047 : ATGCCCGATCCCGCTGAGTCTGTCTATGACTGGGATCTATTCGTAATTGGAGGGGGATCAGG : 2987

   22 : yGlyLeuAlaAlaAlaLysThrAlaAlaAlaLeuGlyAlaArgValAlaLeuAlaAspPheV :   42
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        yGlyLeuAlaAlaAlaLysThrAlaAlaAlaLeuGlyAlaArgValAlaLeuAlaAspPheV
 2986 : CGGCCTCGCAGCTGCCAAGACCGCCGCTGCTCTCGGTGCCCGAGTTGCACTAGCTGATTTCG : 2924

   43 : alLysProSerProGln{G}  >>>> Target Intron 1 >>>>  {ly}ThrThrTrp :   51
        |||||||||||||||||{|}            47 bp            {||}|||||||||
        alLysProSerProGln{G}++                         ++{ly}ThrThrTrp
 2923 : TCAAGCCTAGTCCGCAG{G}gt.........................ag{GT}ACAACATGG : 2850

   52 : GlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuLeuHisMetSerAl :   72
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        GlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuLeuHisMetSerAl
 2849 : GGATTGGGTGGCACATGTGTTAACGTTGGATGCATTCCCAAGAAGCTCCTCCACATGTCTGC : 2787

   73 : aHisThrAlaGluThrAla  >>>> Target Intron 2 >>>>  GlyAspSerAlaGl :   83
        |||||||||||||||||||            51 bp            ||||||||||||||
        aHisThrAlaGluThrAla++                         ++GlyAspSerAlaGl
 2786 : TCACACAGCAGAGACTGCGgt.........................agGGTGACAGTGCTGG : 2703

   84 : yLeuGlyTrpGluLeuThrAlaSerHisAsnTrpGluAlaMetIleGlnAsnValThrThrT :  104
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        yLeuGlyTrpGluLeuThrAlaSerHisAsnTrpGluAlaMetIleGlnAsnValThrThrT
 2702 : CTTGGGATGGGAGCTGACAGCGTCTCACAATTGGGAGGCTATGATACAAAATGTAACTACCT : 2640

  105 : yrIleSerSerLeuAsnTrpGlyTyrLysSerGluLeuArgSerThrAsnVal{Ly}  >>> :  122
        |||||||||||||||||||||||||||||||||||||||||||||||||||||{||}     
        yrIleSerSerLeuAsnTrpGlyTyrLysSerGluLeuArgSerThrAsnVal{Ly}++   
 2639 : ACATCAGCTCTCTTAATTGGGGTTACAAGTCTGAGCTCCGCTCTACCAACGTC{AA}gt... : 2582

  123 : > Target Intron 3 >>>>  {s}TyrPheAsnSerPheAlaThrPheIleAspArgAs :  134
               46 bp            {|}|||||||||||||||||||||||||||||||||||
                              ++{s}TyrPheAsnSerPheAlaThrPheIleAspArgAs
 2581 : ......................ag{A}TATTTCAATTCCTTTGCAACGTTTATCGATCGGAA : 2504

  135 : nThrLeuLysLeuThrAspLysArgGlyLysGluSerIleValThrAla{Ar}  >>>> Ta :  151
        |||||||||||||||||||||||||||||||||||||||||||||||||{||}         
        nThrLeuLysLeuThrAspLysArgGlyLysGluSerIleValThrAla{Ar}++       
 2503 : TACTCTCAAGCTCACTGACAAAAGAGGAAAGGAGTCGATTGTCACTGCA{AG}gt....... : 2449

  152 : rget Intron 4 >>>>  {g}TyrIleLeuIleAlaThrGlyGlyArgProAsnLeuGly :  164
           40 bp            {|}|||||||||||||||||||||||||||||||||||||||
                          ++{g}TyrIleLeuIleAlaThrGlyGlyArgProAsnLeuGly
 2448 : ..................ag{G}TACATACTGATAGCGACAGGTGGTCGCCCTAATCTAGGA : 2374

  165 : GlyTyrProGlyAlaGlyGluCysCysIleThrSerAspAspIlePheArgArgLysAlaPr :  185
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        GlyTyrProGlyAlaGlyGluCysCysIleThrSerAspAspIlePheArgArgLysAlaPr
 2373 : GGCTATCCTGGTGCAGGAGAGTGCTGCATTACCAGTGATGATATCTTCCGACGCAAGGCACC : 2311

  186 : oProGlyLysThrLeuValValGlyAla{Se}  >>>> Target Intron 5 >>>>  { :  195
        ||||||||||||||||||||||||||||{||}            41 bp            {
        oProGlyLysThrLeuValValGlyAla{Se}++                         ++{
 2310 : ACCTGGGAAAACTCTAGTGGTGGGGGCC{AG}gt.........................ag{ : 2238

  196 : r}TyrIleAlaLeuGluCysAlaGlyPheIleAlaGlyPheGlyTyrAspThrThrValMet :  215
        |}||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        r}TyrIleAlaLeuGluCysAlaGlyPheIleAlaGlyPheGlyTyrAspThrThrValMet
 2237 : T}TACATTGCCTTGGAATGTGCTGGCTTCATAGCGGGCTTTGGGTATGATACCACAGTCATG : 2180

  216 : ValArgSerIleLeuLeuArgGlyPheAspGlnAspMetAlaGlnArgIleGlyLysTyrMe :  236
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        ValArgSerIleLeuLeuArgGlyPheAspGlnAspMetAlaGlnArgIleGlyLysTyrMe
 2179 : GTGCGTTCTATATTACTCCGAGGCTTCGACCAAGATATGGCCCAACGCATAGGAAAGTATAT : 2117

  237 : tGluLeuHisGlyThrLysPhe  >>>> Target Intron 6 >>>>  ValHisGluMe :  247
        ||||||||||||||||||||||            41 bp            |||||||||||
        tGluLeuHisGlyThrLysPhe++                         ++ValHisGluMe
 2116 : GGAACTACATGGCACTAAATTCgt.........................agGTGCATGAGAT : 2043

  248 : tIleProThrLysPheGluLysThrGluAspGlyLysValArgValTyrAlaLysSerSerS :  268
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        tIleProThrLysPheGluLysThrGluAspGlyLysValArgValTyrAlaLysSerSerS
 2042 : GATTCCGACTAAATTCGAGAAGACTGAAGATGGCAAAGTCAGAGTCTATGCCAAGTCGTCAT : 1980

  269 : erAspThrMetSerAspAlaAspSerGluPheGlyValPheAspThrValLeuMetAlaVal :  288
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        erAspThrMetSerAspAlaAspSerGluPheGlyValPheAspThrValLeuMetAlaVal
 1979 : CTGATACTATGTCTGATGCTGACAGCGAGTTCGGTGTTTTCGACACAGTGCTGATGGCTGTT : 1920

  289 : GlyArgThrGlyCysAlaGlyTrpLeuSerLeuAspAsnAlaGlyValHisTyrAsnProAs :  309
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        GlyArgThrGlyCysAlaGlyTrpLeuSerLeuAspAsnAlaGlyValHisTyrAsnProAs
 1919 : GGTCGTACTGGTTGTGCTGGCTGGCTTTCCTTGGACAACGCTGGAGTTCATTATAATCCTGA : 1857

  310 : pLysGlyLysIleProValAspLysPheGluMetThrAsnIleAspAsnIleTyrAlaIleG :  330
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        pLysGlyLysIleProValAspLysPheGluMetThrAsnIleAspAsnIleTyrAlaIleG
 1856 : TAAGGGGAAGATACCTGTTGATAAGTTCGAGATGACCAACATTGATAACATCTATGCCATAG : 1794

  331 : lyAspValValGluGlyMetLeuGluLeuThrProValAlaIleGlnSerGlyLysMetLeu :  350
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        lyAspValValGluGlyMetLeuGluLeuThrProValAlaIleGlnSerGlyLysMetLeu
 1793 : GGGATGTTGTCGAGGGCATGCTAGAGCTTACTCCAGTCGCTATACAGTCAGGGAAAATGCTG : 1734

  351 : AlaAlaArgLeuPheGlyGlyAlaSerArgLeuMetAspTyrHisAsnValProThrThrVa :  371
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        AlaAlaArgLeuPheGlyGlyAlaSerArgLeuMetAspTyrHisAsnValProThrThrVa
 1733 : GCTGCAAGGCTATTCGGTGGGGCATCTAGACTCATGGACTACCACAACGTGCCTACTACTGT : 1671

  372 : lPheThrProIleGluTyrGlySerValGlySerSerGluGluAsnAlaLysGluGluTyrG :  392
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        lPheThrProIleGluTyrGlySerValGlySerSerGluGluAsnAlaLysGluGluTyrG
 1670 : ATTTACACCAATCGAATACGGATCTGTTGGGTCAAGTGAGGAGAATGCTAAGGAGGAATATG : 1608

  393 : lyAspAspLeuIleValTyrHisSerPhePheLysProLeuLeuTrpAlaLeuAsnLysAsp :  412
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        lyAspAspLeuIleValTyrHisSerPhePheLysProLeuLeuTrpAlaLeuAsnLysAsp
 1607 : GCGATGATTTGATCGTGTACCACTCCTTCTTCAAACCTTTGTTATGGGCACTCAATAAGGAT : 1548

  413 : ArgGlyAspAlaAspCysTyrMetLysValLeuCysGluAsnLysGlyAspLysLysValVa :  433
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        ArgGlyAspAlaAspCysTyrMetLysValLeuCysGluAsnLysGlyAspLysLysValVa
 1547 : CGCGGTGATGCCGATTGTTATATGAAAGTCCTATGCGAAAATAAAGGTGATAAGAAGGTAGT : 1485

  434 : lGlyIleHisIleLeuGlyProAspAlaGlyGluMetIleGlnGlyLeuAlaValAlaMetL :  454
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        lGlyIleHisIleLeuGlyProAspAlaGlyGluMetIleGlnGlyLeuAlaValAlaMetL
 1484 : GGGTATACACATACTAGGTCCTGATGCTGGGGAGATGATACAGGGTTTAGCAGTAGCTATGA : 1422

  455 : ysAlaGlyCysThrLysAlaAsnLeuAspAspThrValGlyIleHisProThrCysAlaGlu :  474
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        ysAlaGlyCysThrLysAlaAsnLeuAspAspThrValGlyIleHisProThrCysAlaGlu
 1421 : AGGCTGGCTGTACAAAGGCGAACCTCGACGATACTGTTGGTATTCATCCCACTTGTGCTGAG : 1362

  475 : ThrPheThrThrLeuThrGlnIleLysGluAspGlyGlnAspAlaThrValGlyGlySerCy :  495
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        ThrPheThrThrLeuThrGlnIleLysGluAspGlyGlnAspAlaThrValGlyGlySerCy
 1361 : ACCTTCACCACTTTAACGCAAATCAAAGAGGATGGGCAGGATGCAACAGTTGGAGGTAGCTG : 1299

  496 : s :  495
        |
        s
 1298 : C : 1297

vulgar: gi|239878374|gb|EER05138.1| 0 495 . gi|126302086|gb|AAXJ01000419.1| 3047 1296 - 2500 M 47 141 S 0 1 5 0 2 I 0 43 3 0 2 S 1 2 M 30 90 5 0 2 I 0 47 3 0 2 M 43 129 S 0 2 5 0 2 I 0 42 3 0 2 S 1 1 M 28 84 S 0 2 5 0 2 I 0 36 3 0 2 S 1 1 M 43 129 S 0 2 5 0 2 I 0 37 3 0 2 S 1 1 M 48 144 5 0 2 I 0 37 3 0 2 M 252 756
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-11
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	gene	1297	3047	2500	-	.	gene_id 1 ; sequence gi|239878374|gb|EER05138.1| ; gene_orientation +
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	cds	2906	3047	.	-	.	
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	exon	2906	3047	.	-	.	insertions 0 ; deletions 0
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	splice5	2904	2905	.	-	.	intron_id 1 ; splice_site "GT"
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	intron	2859	2905	.	-	.	intron_id 1
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	splice3	2859	2860	.	-	.	intron_id 0 ; splice_site "AG"
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	cds	2767	2858	.	-	.	
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	exon	2767	2858	.	-	.	insertions 0 ; deletions 0
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	splice5	2765	2766	.	-	.	intron_id 2 ; splice_site "GT"
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	intron	2716	2766	.	-	.	intron_id 2
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	splice3	2716	2717	.	-	.	intron_id 1 ; splice_site "AG"
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	cds	2585	2715	.	-	.	
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	exon	2585	2715	.	-	.	insertions 0 ; deletions 0
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	splice5	2583	2584	.	-	.	intron_id 3 ; splice_site "GT"
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	intron	2539	2584	.	-	.	intron_id 3
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	splice3	2539	2540	.	-	.	intron_id 2 ; splice_site "AG"
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	cds	2452	2538	.	-	.	
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	exon	2452	2538	.	-	.	insertions 0 ; deletions 0
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	splice5	2450	2451	.	-	.	intron_id 4 ; splice_site "GT"
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	intron	2412	2451	.	-	.	intron_id 4
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	splice3	2412	2413	.	-	.	intron_id 3 ; splice_site "AG"
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	cds	2280	2411	.	-	.	
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	exon	2280	2411	.	-	.	insertions 0 ; deletions 0
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	splice5	2278	2279	.	-	.	intron_id 5 ; splice_site "GT"
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	intron	2239	2279	.	-	.	intron_id 5
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	splice3	2239	2240	.	-	.	intron_id 4 ; splice_site "AG"
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	cds	2094	2238	.	-	.	
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	exon	2094	2238	.	-	.	insertions 0 ; deletions 0
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	splice5	2092	2093	.	-	.	intron_id 6 ; splice_site "GT"
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	intron	2053	2093	.	-	.	intron_id 6
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	splice3	2053	2054	.	-	.	intron_id 5 ; splice_site "AG"
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	cds	1297	2052	.	-	.	
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	exon	1297	2052	.	-	.	insertions 0 ; deletions 0
gi|126302086|gb|AAXJ01000419.1|	exonerate:protein2genome:local	similarity	1297	3047	2500	-	.	alignment_id 1 ; Query gi|239878374|gb|EER05138.1| ; Align 3048 1 141 ; Align 2857 49 90 ; Align 2716 79 129 ; Align 2538 123 84 ; Align 2411 152 129 ; Align 2238 196 144 ; Align 2053 244 756
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
