Command line: [exonerate -m est2genome comb.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar yes --showvulgar yes]
Hostname: [blackbriar]

C4 Alignment:
------------
         Query: gi|296142823|ref|NM_001178508.1| Saccharomyces cerevisiae S288c Cdc28p (CDC28) mRNA, complete cds
        Target: gi|330443482|ref|NC_001134.8| Saccharomyces cerevisiae S288c chromosome II, complete sequence
         Model: est2genome
     Raw score: 4485
   Query range: 0 -> 897
  Target range: 560077 -> 560974

      1 : ATGAGCGGTGAATTAGCAAATTACAAAAGACTTGAGAAAGTCGGTGAAGGTACATACG :     58
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560078 : ATGAGCGGTGAATTAGCAAATTACAAAAGACTTGAGAAAGTCGGTGAAGGTACATACG : 560135

     59 : GTGTTGTTTATAAAGCGTTAGACTTAAGACCTGGCCAAGGTCAAAGAGTAGTCGCATT :    116
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560136 : GTGTTGTTTATAAAGCGTTAGACTTAAGACCTGGCCAAGGTCAAAGAGTAGTCGCATT : 560193

    117 : GAAGAAAATAAGACTAGAGAGTGAAGACGAGGGTGTTCCCAGTACAGCCATCAGAGAA :    174
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560194 : GAAGAAAATAAGACTAGAGAGTGAAGACGAGGGTGTTCCCAGTACAGCCATCAGAGAA : 560251

    175 : ATCTCATTATTGAAGGAATTAAAAGACGATAATATTGTCAGATTATACGATATTGTTC :    232
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560252 : ATCTCATTATTGAAGGAATTAAAAGACGATAATATTGTCAGATTATACGATATTGTTC : 560309

    233 : ACTCTGATGCACACAAGCTATATCTTGTTTTTGAGTTCCTCGATTTGGACCTGAAAAG :    290
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560310 : ACTCTGATGCACACAAGCTATATCTTGTTTTTGAGTTCCTCGATTTGGACCTGAAAAG : 560367

    291 : ATATATGGAGGGTATTCCAAAGGACCAACCGTTAGGAGCTGATATTGTTAAGAAGTTT :    348
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560368 : ATATATGGAGGGTATTCCAAAGGACCAACCGTTAGGAGCTGATATTGTTAAGAAGTTT : 560425

    349 : ATGATGCAACTTTGTAAGGGTATTGCATACTGCCACTCACACCGTATTCTGCATCGTG :    406
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560426 : ATGATGCAACTTTGTAAGGGTATTGCATACTGCCACTCACACCGTATTCTGCATCGTG : 560483

    407 : ATTTAAAACCGCAGAACTTATTGATTAACAAAGATGGGAATCTAAAACTAGGTGATTT :    464
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560484 : ATTTAAAACCGCAGAACTTATTGATTAACAAAGATGGGAATCTAAAACTAGGTGATTT : 560541

    465 : TGGCTTAGCGCGTGCTTTTGGTGTTCCGTTGAGAGCTTACACACATGAAATTGTTACT :    522
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560542 : TGGCTTAGCGCGTGCTTTTGGTGTTCCGTTGAGAGCTTACACACATGAAATTGTTACT : 560599

    523 : CTATGGTATAGAGCTCCGGAGGTATTACTGGGTGGAAAACAATATAGTACAGGTGTCG :    580
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560600 : CTATGGTATAGAGCTCCGGAGGTATTACTGGGTGGAAAACAATATAGTACAGGTGTCG : 560657

    581 : ATACATGGTCCATCGGCTGTATATTTGCCGAAATGTGTAACAGGAAACCAATCTTCAG :    638
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560658 : ATACATGGTCCATCGGCTGTATATTTGCCGAAATGTGTAACAGGAAACCAATCTTCAG : 560715

    639 : TGGCGATAGTGAGATCGATCAGATTTTCAAGATATTCAGAGTATTGGGAACGCCGAAT :    696
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560716 : TGGCGATAGTGAGATCGATCAGATTTTCAAGATATTCAGAGTATTGGGAACGCCGAAT : 560773

    697 : GAAGCTATATGGCCAGATATTGTCTACTTGCCTGATTTCAAGCCAAGCTTTCCTCAAT :    754
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560774 : GAAGCTATATGGCCAGATATTGTCTACTTGCCTGATTTCAAGCCAAGCTTTCCTCAAT : 560831

    755 : GGCGCAGAAAAGACCTATCACAAGTGGTACCAAGTCTAGATCCACGCGGTATTGATTT :    812
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560832 : GGCGCAGAAAAGACCTATCACAAGTGGTACCAAGTCTAGATCCACGCGGTATTGATTT : 560889

    813 : GTTGGACAAACTCCTCGCGTATGACCCTATTAACCGGATTAGCGCCAGAAGAGCAGCC :    870
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 560890 : GTTGGACAAACTCCTCGCGTATGACCCTATTAACCGGATTAGCGCCAGAAGAGCAGCC : 560947

    871 : ATCCACCCCTACTTCCAAGAATCATAA :    897
          |||||||||||||||||||||||||||
 560948 : ATCCACCCCTACTTCCAAGAATCATAA : 560974

cigar: gi|296142823|ref|NM_001178508.1| 0 897 + gi|330443482|ref|NC_001134.8| 560077 560974 + 4485  M 897
vulgar: gi|296142823|ref|NM_001178508.1| 0 897 + gi|330443482|ref|NC_001134.8| 560077 560974 + 4485 M 897 897

C4 Alignment:
------------
         Query: gi|296142823|ref|NM_001178508.1| Saccharomyces cerevisiae S288c Cdc28p (CDC28) mRNA, complete cds
        Target: gi|330443753|ref|NC_001148.4| Saccharomyces cerevisiae S288c chromosome XVI, complete sequence:[revcomp]
         Model: est2genome
     Raw score: 941
   Query range: 2 -> 896
  Target range: 492933 -> 492033

      3 : GAGCGGTGAATTAGCAAATTACAAAAGACTTGAGAAAGTCGGTGAAGGTACATACGGT :     60
          ||||  |  || | || |||  |  ||  | || ||  | ||  | ||||| || |  
 492933 : GAGC--TCTATGAACAGATTTAAGCAG-TTAGAAAAGCTTGGCAATGGTACGTATGCC : 492879

     61 : GTTGTTTATAAAGCGTTAGACTTAAGACCTGGCCAAGGTCAAAGAGTAGTCGCATTGA :    118
             || || || |   |  ||  || |||    || ||  | |   | || ||  |||
 492878 : ACAGTGTACAAGGGACTGAAC--AAAACC---ACAGGGGTATA---T-GTTGCCCTGA : 492830

    119 : AGAAAATAAGACTAGAGAGTGAAGACGAGGGTGTTCCCAGTACAGCCATCAGAGAAAT :    176
          |  |  ||| ||| ||   |  ||| || |||   |||  ||| |||||| | || ||
 492829 : AAGAGGTAAAACTGGA---TTCAGAGGAAGGTACACCCTCTACGGCCATCCGTGAGAT : 492775

    177 : CTCATTATTGAAGGAATTAAAAGACGATAATATTGTCAGATTATACGATATTGTTCAC :    234
          |||  || |||| ||||| ||| | || || ||||| ||| | || ||  || |||||
 492774 : CTCCCTAATGAAAGAATTGAAACATGAGAACATTGTTAGACTTTATGACGTTATTCAC : 492717

    235 : TCTGATGCACACAAGCTATATCTTGTTTTTGAGTTCCTCGATTTGGACCTGAAAAGAT :    292
           | || | | ||||| |   | | |||||||| ||| | ||    ||  | || | ||
 492716 : ACAGA-G-A-ACAAGTTGACTTTGGTTTTTGAATTCATGGACAACGATTTAAAGAAAT : 492662

    293 : ATATGGA---GGGTATTCCAAAGG-ACCA-ACCGTTAGGAGCT-GA--TA---TTG-T :    338
          | |||||     | |  ||   || | || |||   ||| ||| ||  ||   ||| |
 492661 : ACATGGATTCCCGCA--CCGTGGGCAACACACCAAGAGG-GCTAGAACTAAACTTGGT : 492607

    339 : TAAGAAGTTTATGATGCAACT-TTGTAAGGGTATTGCATACTGCCACTCACACCGTAT :    395
          |||  | ||   |  ||||||  || |||||  | || |  |||||   | ||   ||
 492606 : TAAATACTTCCAGTGGCAACTACTGCAAGGG-CTGGCCTTTTGCCATGAAAACAAGAT : 492550

    396 : TCTGCATCGTGATTTAAAACCGCAGAACTTATTGATTAACAA-AGATGGGAATCTAAA :    452
          ||| || |||||||||||||| || ||| |||| || ||||| ||| ||  |  | ||
 492549 : TCTCCACCGTGATTTAAAACCTCAAAACCTATTAATCAACAAGAGA-GGCCAGTTGAA : 492493

    453 : ACTAGGTGATTTTGGCTTAGCGCGTGCTTTTGGTGTTCCGTTGAGAGCTTACACACAT :    510
          | | |||||||| ||  | || |||||||| ||| ||||| | |   | |   ||   
 492492 : ATTGGGTGATTTCGGTCTGGCCCGTGCTTTCGGTATTCCGGTCAACACATTTTCAAGC : 492435

    511 : GAAATTGTTACTCTATGGTATAGAGCTCCGGAGGTATTACTGGGTGGAAAACAATATA :    568
          ||| | || ||  | |||||  | ||||| || ||  || |||||   |     ||  
 492434 : GAAGTCGTAACGTTGTGGTACCGTGCTCCTGATGTGCTAATGGGTTCTAGGACGTACT : 492377

    569 : GTACAGGTGTCGATACATGGTCCATCGGCTGTATATTTGCCGAAATGTGTAACAGG-A :    625
            |||    | |||| ||||||    || || ||  |||| ||||||  |||| || |
 492376 : CCACATCCATTGATATATGGTCGTGTGGGTGCATTCTTGCGGAAATG-ATAACGGGTA : 492320

    626 : AACCAATCTTCAGTGGCGATAGTGAGATCGATCAGATTTTCAAGATATTCAGAGTATT :    683
          | ||  | ||   ||||   |  ||    || ||  |      ||| |||    |  |
 492319 : AGCCTTTGTTTCCTGGCACCAACGACGAAGAACAACTGAAATTGATCTTCGACATCAT : 492262

    684 : GGGAACGCCGAATGAAGCTATATGGCCAGATATTGTCTACTTGCCTGATTTCAAGCCA :    741
          ||| || || |||||  |  |||||||   | |     | || ||  | | ||| |||
 492261 : GGGCACTCCTAATGAGTCCCTATGGCCCAGTGTAACAAAGTTACCCAAATACAACCCA : 492204

    742 : AGCTTTCCTCAATGGCGCAGAAAAGACCTATCACAAG---TGGTACCA-AGTC--TAG :    793
          |   | |  ||| | |    || |||||||   ||||   ||  |||| |  |   ||
 492203 : AATATCCAGCAACGACCACCAAGAGACCTACGTCAAGTATTGCAACCACACACCAAAG : 492146

    794 : ATCCAC--G-CGGTA------TTGATTTGTTGGACAAACTCCTCGCGTATGACCCTAT :    842
          | || |  | ||| |      | ||||| ||  ||  |||| |      | | ||   
 492145 : AACCGCTAGACGGGAATCTCATGGATTTCTTACACGGACTCTTGCAACTTAATCCGGA : 492088

    843 : TAACCGGATTAGCGCC-AGAAGAGCAGCCATCCACCCCTACTTCCAAGAATCATA :    896
          ||   || | |||||| || ||      ||| ||||| |  ||   ||| |  ||
 492087 : TATGAGGCTGAGCGCCAAGCAGGCTCTGCAT-CACCCTTGGTTTGCAGAGTACTA : 492034

cigar: gi|296142823|ref|NM_001178508.1| 2 896 + gi|330443753|ref|NC_001148.4| 492933 492033 - 941  M 4 I 2 M 21 I 1 M 51 I 2 M 6 I 3 M 11 I 3 M 1 I 1 M 26 I 3 M 102 I 1 M 1 I 1 M 1 I 1 M 55 D 3 M 5 I 2 M 7 D 1 M 4 D 1 M 9 I 1 M 3 D 1 M 2 D 2 M 2 D 3 M 3 D 1 M 22 D 1 M 9 I 1 M 68 D 1 M 3 I 1 M 174 I 1 M 8 D 1 M 154 D 3 M 8 D 1 M 4 D 2 M 9 D 2 M 1 D 1 M 5 D 6 M 53 D 1 M 14 I 1 M 23
vulgar: gi|296142823|ref|NM_001178508.1| 2 896 + gi|330443753|ref|NC_001148.4| 492933 492033 - 941 M 4 4 G 2 0 M 21 21 G 1 0 M 51 51 G 2 0 M 6 6 G 3 0 M 11 11 G 3 0 M 1 1 G 1 0 M 26 26 G 3 0 M 102 102 G 1 0 M 1 1 G 1 0 M 1 1 G 1 0 M 55 55 G 0 3 M 5 5 G 2 0 M 7 7 G 0 1 M 4 4 G 0 1 M 9 9 G 1 0 M 3 3 G 0 1 M 2 2 G 0 2 M 2 2 G 0 3 M 3 3 G 0 1 M 22 22 G 0 1 M 9 9 G 1 0 M 68 68 G 0 1 M 3 3 G 1 0 M 174 174 G 1 0 M 8 8 G 0 1 M 154 154 G 0 3 M 8 8 G 0 1 M 4 4 G 0 2 M 9 9 G 0 2 M 1 1 G 0 1 M 5 5 G 0 6 M 53 53 G 0 1 M 14 14 G 1 0 M 23 23

C4 Alignment:
------------
         Query: gi|296142823|ref|NM_001178508.1| Saccharomyces cerevisiae S288c Cdc28p (CDC28) mRNA, complete cds
        Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence
         Model: est2genome
     Raw score: 651
   Query range: 34 -> 721
  Target range: 267809 -> 300717

     35 : AGAAAGTCGGTGAAGGTACATACGGTGTTGTTTATAAAGCGTTAGACTTAAGAC---- :     89
          ||||||| ||||| ||||| || |  ||||||||    | ||| |  | || ||    
 267810 : AGAAAGTTGGTGAGGGTACTTATGCGGTTGTTTA-CTTGGGTT-G--TCAACACTCTA : 267863

     90 : CTGGCCAAGGTCAAAGAGTAGTCGCATTGAAGAAAATAAGACTAGAGAGTGAAGACGA :    146
          ||||  |||   ||||| |  |   ||| | || |  || ||    || |  | | ||
 267864 : CTGG--AAG---AAAGATTGCT---ATTAAGGAGATCAAAACATCCGAATTTA-AAGA : 267912

    147 : GGGTGTTCCCAGTACAGCCATCAGAGAAATCTCATTA--TTGAAGGAAT-TAAAAGAC :    201
           ||| |    |   |||| ||| | ||| | | | ||  |  ||| |||  |  |  |
 267913 : TGGTTTAGATATGTCAGCTATCCGTGAAGT-TAAGTACCTCCAAGAAATGCAGCATCC : 267969

    202 : GATAAT-ATTGTCAGATTATACGATATTGTTCACTCTGATGCACACAAGCTATATCTT :    258
          ||   | || |    | || || |||||  |  || | |||   | ||  || |||| 
 267970 : GAACGTCATAGAACTAATAGAC-ATATTTATGGCT-T-ATG---ATAATTTAAATCTC : 268021

    259 : GTTTTTGAGTTCCTCGATTTGGACCTGAAAAGATATATGGAGGGTATTCCAAAGGAC- :    316
          ||| | ||||||||        |||  ||  ||| ||  |  |||| |  ||| ||| 
 268022 : GTTCTGGAGTTCCT--------ACC--AACTGATCTAGAGGTGGTAAT--AAAAGACA : 268067

    317 : ---CA--ACCGTT---AGGAGCTGATATT--GTTA-AGAAGTTTATGATGCAACTTTG :    362
             ||  || |||   |  ||| ||||||  |  |  || | |||||     ||||||
 268068 : AATCAATACTGTTTACACCAGCAGATATTAAGGCATGGATGCTTATG-----ACTTTG : 268120

    363 : TAAGGGTATTGCAT-ACTGCCACTCACACCGTATTCTGCATCGTGATTTAAAACCGCA :    419
            ||||   || || | ||||||  | |    ||| ||||  | ||| | |||||  |
 268121 : --AGGGGCGTGTATCATTGCCACAGAAATTTCATTTTGCACAGGGATCTGAAACCAAA : 268176

    420 : GAACTTATTGATTAACA-AAGATGGGAATCTAAAACTAGGTGATTTTGGCTTAGCGCG :    476
           || ||||| |||  ||   |||||  |  ||||| |||  ||||| ||  ||||  |
 268177 : CAATTTATT-ATTTTCACCTGATGGCCAGATAAAAGTAGCAGATTTCGGTCTAGCAAG : 268233

    477 : TGCTTTTGGTGTTCC-GTTGAGAGCTTACACACATGAAA--TTGTTACTCTATGGTAT :    531
           ||  |    |  ||   |||||   |||  ||| | ||  | || ||   |||||||
 268234 : GGCGATACCGGCCCCACATGAGA---TACTGACAAGTAACGTCGTAACAAGATGGTAT : 268288

    532 : AGAGCTCCGGAGGTATTACTGGGTGGAAAACAATATAGTACAGGTGTCGATACATGGT :    589
          ||||| || ||  | ||  | || |  ||||| || |   | | | | ||||  ||||
 268289 : AGAGCGCCAGAATTGTTGTTTGGAGCTAAACATTACACATCGGCTATTGATATCTGGT : 268346

    590 : CCATCGGCTGTATATTTGCCGAAAT-GTGTAACAGGAAACCAATCTTCAGTGGCGATA :    646
          |  | |||  |||||| || ||| |  ||  | |||| |||    ||    ||  | |
 268347 : CAGTAGGCGTTATATTCGCGGAATTAATGCTA-AGGATACCTTATTTACCAGGACAGA : 268403

    647 : GTGAGATCGATCAGATTTTCAAG--ATATTCAGAGTATTGGGAACGC  <<<< Targ :    692
           |||  ||||||| |  |  |||  |  ||||| |  || || || |++         
 268404 : ATGATGTCGATCAAA--TGGAAGTAACGTTCAGGGCCTTAGGGACACct......... : 268451

    693 : et Intron 1 <<<<  CGAATGAAGCTA-TATGGCCAGATATTGTCT :    721
          32238 bp        +-| ||   || ||  ||||||||||||| |||
 268452 : ................aaCAAACCGAGATAGAATGGCCAGATATTCTCT : 300717

cigar: gi|296142823|ref|NM_001178508.1| 34 721 + gi|330443520|ref|NC_001136.10| 267809 300717 + 651  M 34 I 1 M 8 I 1 M 1 I 2 M 7 D 4 M 4 I 2 M 3 I 3 M 10 I 3 M 28 I 1 M 34 I 1 M 6 D 2 M 10 D 1 M 14 D 1 M 15 I 1 M 12 I 1 M 1 I 1 M 3 I 3 M 28 I 8 M 3 I 2 M 21 I 2 M 7 D 4 M 2 D 2 M 6 D 3 M 13 D 2 M 4 D 1 M 11 I 5 M 6 I 2 M 12 D 1 M 52 I 1 M 7 D 1 M 55 D 1 M 7 I 3 M 13 D 2 M 100 D 1 M 6 I 1 M 40 I 2 M 6 D 2 M 22 D 32238 M 12 D 1 M 18
vulgar: gi|296142823|ref|NM_001178508.1| 34 721 + gi|330443520|ref|NC_001136.10| 267809 300717 + 651 M 34 34 G 1 0 M 8 8 G 1 0 M 1 1 G 2 0 M 7 7 G 0 4 M 4 4 G 2 0 M 3 3 G 3 0 M 10 10 G 3 0 M 28 28 G 1 0 M 34 34 G 1 0 M 6 6 G 0 2 M 10 10 G 0 1 M 14 14 G 0 1 M 15 15 G 1 0 M 12 12 G 1 0 M 1 1 G 1 0 M 3 3 G 3 0 M 28 28 G 8 0 M 3 3 G 2 0 M 21 21 G 2 0 M 7 7 G 0 4 M 2 2 G 0 2 M 6 6 G 0 3 M 13 13 G 0 2 M 4 4 G 0 1 M 11 11 G 5 0 M 6 6 G 2 0 M 12 12 G 0 1 M 52 52 G 1 0 M 7 7 G 0 1 M 55 55 G 0 1 M 7 7 G 3 0 M 13 13 G 0 2 M 100 100 G 0 1 M 6 6 G 1 0 M 40 40 G 2 0 M 6 6 G 0 2 M 22 22 3 0 2 I 0 32234 5 0 2 M 12 12 G 0 1 M 18 18

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

cigar: gi|296143771|ref|NM_001180731.1| 0 1230 + gi|330443520|ref|NC_001136.10| 1319275 1318045 - 6150  M 1230
vulgar: gi|296143771|ref|NM_001180731.1| 0 1230 + gi|330443520|ref|NC_001136.10| 1319275 1318045 - 6150 M 1230 1230

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

cigar: gi|296143771|ref|NM_001180731.1| 0 346 + gi|330443688|ref|NC_001145.3| 85010 473201 + 439  M 11 I 1 M 15 I 2 M 4 I 1 M 1 I 1 M 8 I 4 M 17 D 168908 M 4 D 1 M 8 I 1 M 3 I 2 M 33 D 1 M 7 D 2 M 102 D 96824 M 14 D 2 M 10 I 2 M 5 D 2 M 10 I 2 M 4 D 1 M 20 I 1 M 15 D 1 M 5 I 3 M 4 D 122118 M 20 D 5 M 6
vulgar: gi|296143771|ref|NM_001180731.1| 0 346 + gi|330443688|ref|NC_001145.3| 85010 473201 + 439 M 11 11 G 1 0 M 15 15 G 2 0 M 4 4 G 1 0 M 1 1 G 1 0 M 8 8 G 4 0 M 17 17 5 0 2 I 0 168904 3 0 2 M 4 4 G 0 1 M 8 8 G 1 0 M 3 3 G 2 0 M 33 33 G 0 1 M 7 7 G 0 2 M 102 102 5 0 2 I 0 96820 3 0 2 M 14 14 G 0 2 M 10 10 G 2 0 M 5 5 G 0 2 M 10 10 G 2 0 M 4 4 G 0 1 M 20 20 G 1 0 M 15 15 G 0 1 M 5 5 G 3 0 M 4 4 5 0 2 I 0 122114 3 0 2 M 20 20 G 0 5 M 6 6

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

cigar: gi|296143771|ref|NM_001180731.1| 25 406 + gi|330443688|ref|NC_001145.3| 130198 11338 - 263  M 14 D 1 M 4 I 2 M 25 D 1 M 9 D 6 M 42 I 2 M 16 D 2 M 7 D 1 M 3 I 2 M 23 I 3 M 6 D 9357 M 1 I 1 M 11 D 1 M 12 I 1 M 9 D 1 M 10 I 1 M 18 D 1 M 5 D 109125 M 16 I 4 M 4 I 1 M 11 I 5 M 8 I 1 M 22 D 2 M 4 D 2 M 34 D 1 M 3 D 1 M 41
vulgar: gi|296143771|ref|NM_001180731.1| 25 406 + gi|330443688|ref|NC_001145.3| 130198 11338 - 263 M 14 14 G 0 1 M 4 4 G 2 0 M 25 25 G 0 1 M 9 9 G 0 6 M 42 42 G 2 0 M 16 16 G 0 2 M 7 7 G 0 1 M 3 3 G 2 0 M 23 23 G 3 0 M 6 6 3 0 2 I 0 9353 5 0 2 M 1 1 G 1 0 M 11 11 G 0 1 M 12 12 G 1 0 M 9 9 G 0 1 M 10 10 G 1 0 M 18 18 G 0 1 M 5 5 3 0 2 I 0 109121 5 0 2 M 16 16 G 4 0 M 4 4 G 1 0 M 11 11 G 5 0 M 8 8 G 1 0 M 22 22 G 0 2 M 4 4 G 0 2 M 34 34 G 0 1 M 3 3 G 0 1 M 41 41
-- completed exonerate analysis
