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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
|
