Command line: [exonerate -m affine:local ../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: affine:local:dna2dna
     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: affine:local:dna2dna
     Raw score: 359
   Query range: 83 -> 552
  Target range: 253990 -> 254474

     84 : ACCTAAGAGGAAGGTGGGCAGACCAGGCAGAAAA-AGGATT--GACTCTGAAGCTAAG :    138
          ||| |||| |||||   ||| | |  ||| |||  | ||||  ||  ||||| |||||
 253991 : ACCGAAGAAGAAGGGTAGCAAAACTAGCAAAAAGCAAGATTTGGATCCTGAAACTAAG : 254048

    139 : AGTAGGAGGACTGCCCAGAATAGGGCAGCTCAACGAGCGTTCCGAGATAGGAAAGAAG :    196
             | |||||||||||| ||| |||| |||||| |||| ||  | ||  | || ||  
 254049 : CAGAAGAGGACTGCCCAAAATCGGGCCGCTCAAAGAGCTTTTAGGGAACGTAAGGAGA : 254106

    197 : CCAAAATGAAGAGTTTGCAAGAGAGGGT--AGAGTTACTAGAACAGAAAGATGC-GCA :    251
            || ||||||   ||| |  ||| |||  | ||||  ||| | || |    || |||
 254107 : GGAAGATGAAGGAATTGGAGAAGAAGGTACAAAGTT--TAG-AGAGTATTCAGCAGCA : 254161

    252 : GAATAAGACTACCACGGACTTTTTACTATGTTC-TTTAAAAAGTTTACTGTCGGAAAT :    308
           ||| | | |   |   |||||||     |  |  ||||  | | |  ||   ||  |
 254162 : AAATGA-AGTGGAAGCTACTTTTTTGAGGGACCAGTTAATCACTCTGGTGAATGAGTT : 254218

    309 : TACAAAATAT-----AGAGCTAAGAATT--CTGATGA-TGAAAGAATA-TTAGCCTTC :    357
           | |||||||     ||||  ||||| |  || |  | ||   ||||| |||||    
 254219 : AAAAAAATATAGACCAGAGACAAGAAATGACTCAAAAGTGCTGGAATATTTAGCAAGG : 254276

    358 : CTCGA---TGATCTGCA-AGAACAACAGAAAAGGGAAA--AC-GAAAAAG-GA-ACAA :    406
          |  ||   | || ||||     ||| | | || |  ||  || | || || ||  |||
 254277 : CGAGATCCTAATTTGCATTTTTCAAAAAATAACGTTAACCACAGCAATAGCGAGCCAA : 254334

    407 : GT-ACAGCAGTTAGCAAGGCTG-CA---AAGGAATTGCCATCGCCTAATTCAGATGAA :    459
           | ||| ||     ||| | || ||   ||| || ||   |   | ||   |||||||
 254335 : TTGACA-CA---CCCAATGATGACATACAAGAAAATG--TTAAACAAA---AGATGAA : 254383

    460 : -AACATGACTGTGAACA-CAAGTATAGAAGTACAGCCGCACACTCAAGAGAATGAGAA :    515
             || |  | | || | |   |  | ||  ||| |  ||    ||| ||  | | ||
 254384 : TTTCACG--TTTCAATATCCGCTTGATAACGACAACGACAACGACAACAG--TAAAAA : 254437

    516 : AGTTATGTGGAACA--TAGGCTCATGGAACGCTCCCAGT :    552
           ||   | | ||||  ||   |||   || | ||| |||
 254438 : TGT--GGGGAAACAATTACCTTCACCAAATGATCCAAGT : 254474


C4 Alignment:
------------
         Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
        Target: gi|330443715|ref|NC_001146.8| Saccharomyces cerevisiae S288c chromosome XIV, complete sequence
         Model: affine:local:dna2dna
     Raw score: 219
   Query range: 60 -> 517
  Target range: 454073 -> 454531

     61 : ATGTTGCTAAATAAAGATGGAACACCTAAGAGGAAGGTG-GGCAGACCAGGCAGAAAA :    117
          ||| || || || | |||||   |   |||| ||    | || |||  | | | |  |
 454074 : ATGATGATATATTA-GATGGGG-ATG-AAGATGAGCCAGAGGAAGAGGATGAAAATGA : 454128

    118 : AGGAT-TGACTCTGAAGCTAAGAGTAGGAGGACTGCCCAGA--ATAGGG-CAGCTCA- :    171
          |||   ||||   |||| ||    || ||   | | |  ||  | |  | | | | | 
 454129 : AGGCGATGACGAAGAAGATACT--TATGACAGCGGTCTTGATGAAACTGACCGTTTAG : 454184

    172 : ACGAGCGTTCCGAGATAGGAA-AGA-AGCCAAAATGAAGA-GTTTGCAAGA-GAGGGT :    224
          | ||  || | || || |    ||| |||||  |  |||  | ||  |||  ||    
 454185 : AAGAAGGT-CGGAAATTGATTCAGATAGCCATTACAAAGTTGCTTCAAAGTCGAATAA : 454241

    225 : AGAGTTACTAGAAC-AGAAAGATGCGCAGAATAA--GACTACCACGGACTTTTTACTA :    279
           |  ||  ||  |  ||||| | ||  | |||||  |||||  ||     || ||| |
 454242 : TGGCTTCTTATCATGAGAAACAGGCAGATAATAACAGACTAAAAC-----TTCTACAA : 454294

    280 : TGTTCTTTAAAAAGTTTACTGTCGGAAATTACAAAATATAGAGCTAAGAATTCTGATG :    337
           |  ||  || |||   |  |   ||||  | | ||   |||   || ||  | ||  
 454295 : -GAACTAGAAGAAGAAAAAAGAAAGAAAAGAGAGAAGGAAGA---AAAAAAGCAGAAA : 454348

    338 : ATGAAAGAATATTAGCCTTCCTCGATGAT-CTGCAAGA---A-CAACAGAAAAGGGAA :    390
          |  | |||| |  ||        || ||  |||||| |   | | | |||  | | ||
 454349 : AAAAGAGAAAAAGAGAAAGAAAAGAAGAGGCTGCAACAGTTAGCTAAAGAGGAAGAAA : 454406

    391 : AACGAAAAAGGAACAAGTACAGCAGTTAGCAAGGCTGCA-AAGGAATTGCCATCGCCT :    447
          |||||||||||   ||| | || |   || ||||||  | ||||||||   |  || |
 454407 : AACGAAAAAGG--GAAGAAGAGAA---AGAAAGGCTAAAGAAGGAATTAGAAGAGCGT : 454459

    448 : -AATTCAGATGAAAACATG-ACTGTGAACACAAG-TATAGAAGTACAGCCGCACACTC :    502
           || | ||| ||  | | |  |   | | | | | |  |||||   | | | | |   
 454460 : GAAATGAGAAGACGAGAGGCTCAAAGGAAAAAGGTTGAAGAAGCCAAACGGAAGAAAG : 454517

    503 : AAGAGAATGAGAAAG :    517
          | ||| | |||||||
 454518 : ACGAGGA-GAGAAAG : 454531

-- completed exonerate analysis
