Command line: [exonerate -m genome2genome ../intron.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
Hostname: [blackbriar]

C4 Alignment:
------------
         Query: sacCer3_dna range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none:[revcomp]
        Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
         Model: genome2genome
     Raw score: 2641
   Query range: 529 -> 0
  Target range: 1319997 -> 1319468

     529 :                           TGG                            :     474
           ATCCCTTATCTCTTTATCTTGTTGCCTrpTTCTCTTTTCCCTTTAAATGGAGATTA
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
           ATCCCTTATCTCTTTATCTTGTTGCCTrpTTCTCTTTTCCCTTTAAATGGAGATTA
 1319997 :                           TGG                            : 1319942

     473 : CAAACTAGCGAAACTGCAGAAAAGGAAAGCCTCCAAAACTACTGCCAGGGTAAAAA :     418
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319941 : CAAACTAGCGAAACTGCAGAAAAGGAAAGCCTCCAAAACTACTGCCAGGGTAAAAA : 1319886

     417 : GTGAAACTGGGAAACGACATAAAGAAGAGCAAATTAAAACCAAAATGAGCGATGAA :     362
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319885 : GTGAAACTGGGAAACGACATAAAGAAGAGCAAATTAAAACCAAAATGAGCGATGAA : 1319830

     361 : AATAAGAGTACGCGTATGTCAGTTAATCTCAGTCACAATTTTGTGACTTTCAATAC :     306
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319829 : AATAAGAGTACGCGTATGTCAGTTAATCTCAGTCACAATTTTGTGACTTTCAATAC : 1319774

     305 : AATTTTTCTTTACTAACTCGAGGAAGAGTGAGGTTTTCTTCCATGAATTGCAGCTA :     250
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319773 : AATTTTTCTTTACTAACTCGAGGAAGAGTGAGGTTTTCTTCCATGAATTGCAGCTA : 1319718

     249 : TTGTTAAGGCGTCTGACATAGTATGTAATTGTGCCATGATATACATGTTTTGTGTG :     194
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319717 : TTGTTAAGGCGTCTGACATAGTATGTAATTGTGCCATGATATACATGTTTTGTGTG : 1319662

     193 : TGTACATTTGAATATATATATTTACTAACAAGGAGAAAACTTAGACCGACAAGCTG :     138
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319661 : TGTACATTTGAATATATATATTTACTAACAAGGAGAAAACTTAGACCGACAAGCTG : 1319606

     137 : AAAGAGGATATTTTAACCATCAGTAAAGATGCTCTGGACAAGTACCAGTTGGAAAG :      82
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319605 : AAAGAGGATATTTTAACCATCAGTAAAGATGCTCTGGACAAGTACCAGTTGGAAAG : 1319550

      81 : AGACATTGCTGGGACGGTAAAGAAGCAATTGGATGTCAAATACGGCAATACCTGGC :      26
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319549 : AGACATTGCTGGGACGGTAAAGAAGCAATTGGATGTCAAATACGGCAATACCTGGC : 1319494

      25 : ATGTGATTGTCGGAAAGAACTTTGG :       1
           |||||||||||||||||||||||||
 1319493 : ATGTGATTGTCGGAAAGAACTTTGG : 1319469


C4 Alignment:
------------
         Query: sacCer3_dna range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none
        Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence
         Model: genome2genome
     Raw score: 2641
   Query range: 0 -> 529
  Target range: 1319468 -> 1319997

       1 : CCAAAGTTCTTTCCGACAATCACATGCCAGGTATTGCCGTATTTGACATCCAATTG :      56
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319469 : CCAAAGTTCTTTCCGACAATCACATGCCAGGTATTGCCGTATTTGACATCCAATTG : 1319524

      57 :                                   TGG                    :     112
           CTTCTTTACCGTCCCAGCAATGTCTCTTTCCAACTrpTACTTGTCCAGAGCATCTT
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
           CTTCTTTACCGTCCCAGCAATGTCTCTTTCCAACTrpTACTTGTCCAGAGCATCTT
 1319525 :                                   TGG                    : 1319580

     113 : TACTGATGGTTAAAATATCCTCTTTCAGCTTGTCGGTCTAAGTTTTCTCCTTGTTA :     168
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319581 : TACTGATGGTTAAAATATCCTCTTTCAGCTTGTCGGTCTAAGTTTTCTCCTTGTTA : 1319636

     169 : GTAAATATATATATTCAAATGTACACACACAAAACATGTATATCATGGCACAATTA :     224
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319637 : GTAAATATATATATTCAAATGTACACACACAAAACATGTATATCATGGCACAATTA : 1319692

     225 : CATACTATGTCAGACGCCTTAACAATAGCTGCAATTCATGGAAGAAAACCTCACTC :     280
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319693 : CATACTATGTCAGACGCCTTAACAATAGCTGCAATTCATGGAAGAAAACCTCACTC : 1319748

     281 : TTCCTCGAGTTAGTAAAGAAAAATTGTATTGAAAGTCACAAAATTGTGACTGAGAT :     336
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319749 : TTCCTCGAGTTAGTAAAGAAAAATTGTATTGAAAGTCACAAAATTGTGACTGAGAT : 1319804

     337 : TAACTGACATACGCGTACTCTTATTTTCATCGCTCATTTTGGTTTTAATTTGCTCT :     392
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319805 : TAACTGACATACGCGTACTCTTATTTTCATCGCTCATTTTGGTTTTAATTTGCTCT : 1319860

     393 : TCTTTATGTCGTTTCCCAGTTTCACTTTTTACCCTGGCAGTAGTTTTGGAGGCTTT :     448
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319861 : TCTTTATGTCGTTTCCCAGTTTCACTTTTTACCCTGGCAGTAGTTTTGGAGGCTTT : 1319916

     449 : CCTTTTCTGCAGTTTCGCTAGTTTGTAATCTCCATTTAAAGGGAAAAGAGAACCAG :     504
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319917 : CCTTTTCTGCAGTTTCGCTAGTTTGTAATCTCCATTTAAAGGGAAAAGAGAACCAG : 1319972

     505 : GCAACAAGATAAAGAGATAAGGGAT :     529
           |||||||||||||||||||||||||
 1319973 : GCAACAAGATAAAGAGATAAGGGAT : 1319997


C4 Alignment:
------------
         Query: sacCer3_dna range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none:[revcomp]
        Target: gi|330443489|ref|NC_001135.5| Saccharomyces cerevisiae S288c chromosome III, complete sequence
         Model: genome2genome
     Raw score: 267
   Query range: 491 -> 162
  Target range: 23668 -> 115569

    491 : CCCTTTAAATGGAGATTACAAACTAGCGA  >>>> Target Intron 1 >>>>   :    462
          ||  | ||| | |||  ||||| |  | |++         8983 bp         +-
  23669 : CCGCTGAAAGGAAGAGAACAAAGTTACAAgt.........................aa :  32679

    461 : AACTGCAGAAAAGGAAAGCCTCCAAAACTACT--GC-CAGGGTAAAAAGTGA  >>>> :    413
          |||||||||||||    |  ||   ||| |||  ||  ||||||| ||  ||-+    
  32680 : AACTGCAGAAAAGACTGGTATCTTGAACGACTTGGCGAAGGGTAAGAAAAGAat.... :  32735

    412 :  Target Intron 2 >>>>  AACTGGGAA--ACG-ACAT-AAAGAAGAGCAAATT :    383
               9555 bp         +-||| || ||   || || | |||||||||||||| 
  32736 : .....................atAAC-GGTAATCTCGAACTTCAAAGAAGAGCAAATG :  42321

    382 :    {A}                             {CC}AAA                 :    358
          AAA{T}  >>>> Target Intron 3 >>>>  {hr}LysATGAGCGATGAAAATA
          || { }++         55423 bp        ++{  } !  |||  ||||||||||
          AAC{L}gt.........................ag{eu}AspTTGAATGATGAAAATA
  42322 :    {C}                             {TG}GAT                 :  97769

    357 : AGAGTACGCGTATGTCAGTTAATCTCAGTCACAATTTTGTGACTTTCAATACAAT  > :    302
          |||| |    | | | ||| |   ||||| |  || | ||     |||||| | |+- 
  97770 : AGAGAA---ATTTATTAGTCATATTCAGTGATTATGTGGTTTTCATCAATATACTgg. :  97824

    301 : >>> Target Intron 4 >>>>  TTTTCTTTACTAAC-TCGAGGAAGAGTGAGGT :    272
                  17598 bp        ++| ||    || | | |  |||||| |||| | 
  97825 : ........................agTCTTGAAGACCAGCATGTAGGAAG-GTGATGA : 115450

    271 : TTTCTTCC---ATGAATTGCAGCTATTG---T-TAAGGCGTCTGAC-ATAGTATGTAA :    222
          | |  |||   |  ||||| |  |||||   | |||      |||| ||| ||   ||
 115451 : TATGCTCCGTAAATAATTGGAAATATTGAGATATAATAACGATGACAATACTA-ACAA : 115507

    221 : TTGTGCCA--TGATATACATGTTTTGTGTGTGTACATTTGAATATATATATTTAC-TA :    167
            ||   |  |||  | |     |||  ||| |   |||||||||||||   | | ||
 115508 : AAGTAATAGGTGAGCTCCGCCAATTGATTGTTTTGTTTTGAATATATATTGATGCTTA : 115565

    166 : ACAA :    163
          ||||
 115566 : ACAA : 115569


C4 Alignment:
------------
         Query: sacCer3_dna range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none:[revcomp]
        Target: gi|330443667|ref|NC_001143.9| Saccharomyces cerevisiae S288c chromosome XI, complete sequence:[revcomp]
         Model: genome2genome
     Raw score: 267
   Query range: 529 -> 78
  Target range: 641760 -> 71883

    529 : ATCCCTTATCTCTTTATCTTGTTGCCTGGTTCTCTTTTCCCTTTAAATGGAGATTACA :    472
          ||||||||||||||       |||  |||||   ||||  || |  ||     || ||
 641760 : ATCCCTTATCTCTTCTAAAGATTGTGTGGTT---TTTT--CTATGCATATTTTTTCCA : 641708

    471 :                           ga                        ag     :    385
          A---ACTAGCGAA-ACTGCAGAAAAG+->>>> Joint Intron 1 >>>>++CAAA
          |    || || ||  || || | |||     61 bp // 154295 bp     ||| 
          ACCTTCTTGCCAATTCTTCA-ACAAG-+>>>> Joint Intron 1 >>>>++CAAT
 641707 :                           tt                        ag     : 487384

    384 : TTAAAACCAAAATGAGCGATGAAAATAAGAGTACGCGTATGTCAGTTAATC-TCAGTC :    328
          |||| ||||| ||||||||||     |||| | |   |||| | ||||| | ||| | 
 487383 : TTAACACCAAGATGAGCGATG-----AAGA-TTC---TATG-CTGTTAAACTTCACTA : 487336

    327 :         gt                        ga                       :    263
          ACAATTTT++>>>> Joint Intron 2 >>>>--GGAAGAGTGAGGTTTTCTTCCA
           ||||        35 bp // 101120 bp     |||| |   |  || | | | |
          CCAATGAG+->>>> Joint Intron 2 >>>>++GGAACATAAAAATTCTGTCCTA
 487335 :         ga                        ag                       : 386186

    262 :                                              TGCCATGATATAC :    206
          T-GAATTGCAGCTATTGTTAAGGCGTCTGACATAGTATGTAATTGCysHisAspIleH
          |  || | ||   |||| ||  || ||  | || || |||| |||  ! ! .!.||+ 
          TCAAAATTCAATAATTG-TACAGCTTC-CA-ATTGTGTGTACTTGValLysGlnIleG
 386185 :                                              GTCAAACAAATCG : 386131

    205 : ATGTT{TT}  >>>> Target Intron 1 >>>>  {G}TGTGTGTACATT      :    182
          isVal{Le}                             {u}CysValTyrIleTG-AA
               {::}          177446 bp          {:}   !  !::   || ||
          lyHis{Il}++                         ++{e}LysGlyPhe***TGAAA
 386130 : GACAC{AT}gt.........................ag{C}AAAGGATTTTGA      : 208660

    181 :                     ga                        ag           :    105
          TATATATATTTACTAACAAG+->>>> Joint Intron 3 >>>>++TAAAGATGCT
          |||||||||||||| | |       47 bp // 136722 bp      ||||||  |
          TATATATATTTACTTAGAGT++>>>> Joint Intron 3 >>>>++AAAAGATTTT
 208659 :                     gt                        ag           :  71908

    104 : CTGGACAAGTACCAGTTGGAAAGAGA :     79
          ||  || | |  ||||||||||||||
  71907 : CT--ACGACTTGCAGTTGGAAAGAGA :  71884

-- completed exonerate analysis
