Command line: [exonerate -m est2genome ../scer_cad1.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
Hostname: [blackbriar]

C4 Alignment:
------------
         Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
        Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
         Model: est2genome
     Raw score: 6150
   Query range: 0 -> 1230
  Target range: 1319275 -> 1318045

       1 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA :      56
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319275 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAA : 1319220

      57 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA :     112
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319219 : GCAAATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTGGGCAGACCAGGCA : 1319164

     113 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT :     168
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319163 : GAAAAAGGATTGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGAATAGGGCAGCT : 1319108

     169 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT :     224
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319107 : CAACGAGCGTTCCGAGATAGGAAAGAAGCCAAAATGAAGAGTTTGCAAGAGAGGGT : 1319052

     225 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT :     280
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1319051 : AGAGTTACTAGAACAGAAAGATGCGCAGAATAAGACTACCACGGACTTTTTACTAT : 1318996

     281 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT :     336
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318995 : GTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGAT : 1318940

     337 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA :     392
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318939 : GATGAAAGAATATTAGCCTTCCTCGATGATCTGCAAGAACAACAGAAAAGGGAAAA : 1318884

     393 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA :     448
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318883 : CGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCAAAGGAATTGCCATCGCCTA : 1318828

     449 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA :     504
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318827 : ATTCAGATGAAAACATGACTGTGAACACAAGTATAGAAGTACAGCCGCACACTCAA : 1318772

     505 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA :     560
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318771 : GAGAATGAGAAAGTTATGTGGAACATAGGCTCATGGAACGCTCCCAGTTTAACCAA : 1318716

     561 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA :     616
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318715 : TTCGTGGGATTCTCCCCCCGGAAATCGAACAGGTGCCGTTACCATCGGTGACGAAA : 1318660

     617 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA :     672
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318659 : GTATTAATGGTAGTGAAATGCCAGATTTCAGTCTCGATCTTGTCTCCAATGATAGA : 1318604

     673 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC :     728
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318603 : CAGACTGGTCTAGAAGCTTTAGATTACGACATTCATAACTACTTTCCTCAGCACTC : 1318548

     729 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC :     784
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318547 : TGAACGCCTGACCGCTGAAAAAATAGATACGTCAGCATGTCAATGTGAAATTGACC : 1318492

     785 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC :     840
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318491 : AAAAGTATCTTCCATACGAGACAGAAGATGATACTTTATTCCCCAGCGTGCTTCCC : 1318436

     841 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA :     896
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318435 : CTTGCTGTAGGGAGCCAGTGTAATAATATTTGCAACCGCAAGTGTATCGGGACCAA : 1318380

     897 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC :     952
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318379 : ACCATGTTCAAATAAGGAGATCAAATGCGACTTAATAACAAGCCACCTGTTGAATC : 1318324

     953 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA :    1008
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318323 : AGAAATCTCTAGCTTCGGTGCTTCCGGTGGCTGCTTCTCATACTAAAACAATTCGA : 1318268

    1009 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC :    1064
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318267 : ACCCAATCTGAAGCAATTGAACACATTAGCAGCGCCATATCGAATGGAAAAGCGTC : 1318212

    1065 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA :    1120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318211 : TTGCTACCACATTCTCGAAGAGATCTCCTCCCTACCAAAATATTCATCGTTGGACA : 1318156

    1121 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA :    1176
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318155 : TAGATGATTTATGCAGCGAATTAATAATCAAGGCAAAATGTACAGATGACTGCAAA : 1318100

    1177 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG :    1230
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||
 1318099 : ATAGTAGTCAAAGCTCGCGACTTACAGAGTGCTCTGGTTAGACAGCTCCTGTAG : 1318046


C4 Alignment:
------------
         Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
        Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence
         Model: est2genome
     Raw score: 439
   Query range: 0 -> 346
  Target range: 85010 -> 473201

      1 : ATGGGCAATATCCTTCGGAAAGGTCAGCAAATATATTTAGCAGGTGACATGAAGAAGC :     58
          ||||  ||  | ||||   | ||||||  |||| | | | ||||    ||||||||||
  85011 : ATGGTGAACCT-CTTCAAGACGGTCAG--AATA-A-TCAACAGG----ATGAAGAAGC :  85059

     59 : AAATGTT  >>>> Target Intron 1 >>>>  GCTA-AATAAAGATGGAACACC :     86
          ||| | |++        168908 bp        -+|| |  |||  || | |  |||
  85060 : AAAAGATgt.........................tgGCGAGGATAGCGA-GCA--ACC : 253993

     87 : TAAGAGGAAGGTGGGCAGACCAGGCAGAAA-AAGGATT--GACTCTGAAGCTAAGAGT :    141
           |||| |||||   ||| | |  ||| |||  | ||||  ||  ||||| |||||   
 253994 : GAAGAAGAAGGGTAGCAAAACTAGCAAAAAGCAAGATTTGGATCCTGAAACTAAGCAG : 254051

    142 : AGGAGGACTGCCCAGAATAGGGCAGCTCAACGAGCGTTCCGAGATAGGAAAGAAGCCA :    199
          | |||||||||||| ||| |||| |||||| |||| ||  | ||  | || ||    |
 254052 : AAGAGGACTGCCCAAAATCGGGCCGCTCAAAGAGCTTTTAGGGAACGTAAGGAGAGGA : 254109

    200 : AAATGAAGAGTTTGCAAGAGAGGGTA  >>>> Target Intron 2 >>>>  GAG :    228
          | ||||||   ||| |  ||| ||||--         96824 bp        -+| |
 254110 : AGATGAAGGAATTGGAGAAGAAGGTAca.........................tgGGG : 350962

    229 : TTACTAGAACA--GAAAGATGCGCAGAATA--AGACTACCACGGACTT-TTTACTATG :    281
          | | || | ||      |||| |  |||||   ||  |||||   |||  |||  |||
 350963 : TGATTATATCATTTCTGGATGAG--GAATACCTGAAGACCAC--TCTTCATTAAAATG : 351016

    282 : TTCTTTAAAAAGTTTACTGTCGGAAAT-TACAAAATATAG  >>>> Target Intr :    321
          ||||||||||| | | || | ||| || | | |    |||-+        122118 b
 351017 : TTCTTTAAAAA-TATTCTTTTGGATATATTCTA---CTAGtt................ : 351055

    322 : on 3 >>>>  AGCTAAGAATTCTGATGATG-----AAAGAA :    346
          p        ++|   |||||||||||| |||     ||||||
 351056 : .........agATGGAAGAATTCTGATAATGCTGTAAAAGAA : 473201


C4 Alignment:
------------
         Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
        Target: gi|330443688|ref|NC_001145.3| Saccharomyces cerevisiae S288c chromosome XIII, complete sequence:[revcomp]
         Model: est2genome
     Raw score: 263
   Query range: 25 -> 406
  Target range: 130198 -> 11338

     26 : AGCAAATATATTTA-GCAGGTGACATGAAGAAGCAAATGTTGCTAA-ATAAAGATG-- :     80
          | |||| |||   | ||||   | | || |||| | |  ||  |||  |  || ||  
 130198 : ACCAAAGATAACAAGGCAG--AAAAAGAGGAAGAAGAAATTAATAAGGTTGAGGTGAC : 130143

     81 : ----GAACACCTAAGAGGAAGGTGGGCAGACCAGGCAGAAAAAGGATTGACTCTGAAG :    133
              ||| | | |||   |||    |   || |||||||||||| |  ||    ||| 
 130142 : CCCAGAAGAGCCAAGCAAAAGCATAGATAACAAGGCAGAAAAAGAA--GAAGAAGAAA : 130087

    134 : CTAAGA--GTAGGAG-GACTGCCCAGAATAGGGCAGCTCAACGAGCGTTCCGA  <<< :    184
           ||| |  || | || |||  ||||||  ||   |||  || ||   ||| ||++   
 130086 : TTAATAAGGTTGAAGTGAC--CCCAGAGGAGCCAAGCAAAAAGA---TTCGGAct... : 130036

    185 : < Target Intron 1 <<<<  GATAGGAAAGAAG-CCAAAATGAAGAGTTTGCAA :    216
                9357 bp         -+| ||   |||||| |||| | ||||| |    ||
 130035 : ......................tcG-TATTGAAGAAGTCCAAGAAGAAGA-TGAAGAA : 120650

    217 : GA-GAGGGTAGAGTTACTAGAACAGAAAGATG-CGCAG  <<<< Target Intron :    253
          ||  | | | |||  |  ||||||  |||| |  | ||--        109125 bp 
 120649 : GATAATGATGGAG-AAGAAGAACAAGAAGAAGAAGAAGaa.................. : 120610

    254 :  2 <<<<  AATAAGACTACCACGGACTTTTTACTATGTTCTTTAAAAAGTTTACTGT :    301
                 ++|||||||  | ||| |    |||| | |  | | ||     || | |||
 120609 : .......acAATAAGAGCAACACAG----TTTA-TCTTATATGTA-----TTCAATGT :  11449

    302 : CGGAAATTACAAAATATAGAGCT--AAGA--ATTCTGATGATGAAAGAATATTAGCCT :    355
             | ||| |||||||||||| |  || |  ||||  |  ||  || ||  ||  |||
  11448 : -ATAGATTTCAAAATATAGAGTTTAAATATCATTCAAAATATTCAATAAATTTTTCCT :  11392

    356 : TCCTCGA-TGA-TCTGCAAGAACAACAGAAAAGGGAAAACGAAAAAGGAACAA :    406
          |     | | |  |  | | || |  | || ||  ||||||||  ||  ||||
  11391 : TTGAAAATTTAGGCCACTAAAAAATTATAAGAGCCAAAACGAAGTAGATACAA :  11339

-- completed exonerate analysis
