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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
|
