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Command line: [exonerate -m genome2genome ../intron.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3 --showcigar no --showvulgar no]
Hostname: [blackbriar]
C4 Alignment:
------------
Query: sacCer3_dna range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none:[revcomp]
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
Model: genome2genome
Raw score: 2641
Query range: 529 -> 0
Target range: 1319997 -> 1319468
529 : TGG : 474
ATCCCTTATCTCTTTATCTTGTTGCCTrpTTCTCTTTTCCCTTTAAATGGAGATTA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ATCCCTTATCTCTTTATCTTGTTGCCTrpTTCTCTTTTCCCTTTAAATGGAGATTA
1319997 : TGG : 1319942
473 : CAAACTAGCGAAACTGCAGAAAAGGAAAGCCTCCAAAACTACTGCCAGGGTAAAAA : 418
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319941 : CAAACTAGCGAAACTGCAGAAAAGGAAAGCCTCCAAAACTACTGCCAGGGTAAAAA : 1319886
417 : GTGAAACTGGGAAACGACATAAAGAAGAGCAAATTAAAACCAAAATGAGCGATGAA : 362
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319885 : GTGAAACTGGGAAACGACATAAAGAAGAGCAAATTAAAACCAAAATGAGCGATGAA : 1319830
361 : AATAAGAGTACGCGTATGTCAGTTAATCTCAGTCACAATTTTGTGACTTTCAATAC : 306
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319829 : AATAAGAGTACGCGTATGTCAGTTAATCTCAGTCACAATTTTGTGACTTTCAATAC : 1319774
305 : AATTTTTCTTTACTAACTCGAGGAAGAGTGAGGTTTTCTTCCATGAATTGCAGCTA : 250
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319773 : AATTTTTCTTTACTAACTCGAGGAAGAGTGAGGTTTTCTTCCATGAATTGCAGCTA : 1319718
249 : TTGTTAAGGCGTCTGACATAGTATGTAATTGTGCCATGATATACATGTTTTGTGTG : 194
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319717 : TTGTTAAGGCGTCTGACATAGTATGTAATTGTGCCATGATATACATGTTTTGTGTG : 1319662
193 : TGTACATTTGAATATATATATTTACTAACAAGGAGAAAACTTAGACCGACAAGCTG : 138
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319661 : TGTACATTTGAATATATATATTTACTAACAAGGAGAAAACTTAGACCGACAAGCTG : 1319606
137 : AAAGAGGATATTTTAACCATCAGTAAAGATGCTCTGGACAAGTACCAGTTGGAAAG : 82
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319605 : AAAGAGGATATTTTAACCATCAGTAAAGATGCTCTGGACAAGTACCAGTTGGAAAG : 1319550
81 : AGACATTGCTGGGACGGTAAAGAAGCAATTGGATGTCAAATACGGCAATACCTGGC : 26
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319549 : AGACATTGCTGGGACGGTAAAGAAGCAATTGGATGTCAAATACGGCAATACCTGGC : 1319494
25 : ATGTGATTGTCGGAAAGAACTTTGG : 1
|||||||||||||||||||||||||
1319493 : ATGTGATTGTCGGAAAGAACTTTGG : 1319469
C4 Alignment:
------------
Query: sacCer3_dna range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none
Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence
Model: genome2genome
Raw score: 2641
Query range: 0 -> 529
Target range: 1319468 -> 1319997
1 : CCAAAGTTCTTTCCGACAATCACATGCCAGGTATTGCCGTATTTGACATCCAATTG : 56
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319469 : CCAAAGTTCTTTCCGACAATCACATGCCAGGTATTGCCGTATTTGACATCCAATTG : 1319524
57 : TGG : 112
CTTCTTTACCGTCCCAGCAATGTCTCTTTCCAACTrpTACTTGTCCAGAGCATCTT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTTCTTTACCGTCCCAGCAATGTCTCTTTCCAACTrpTACTTGTCCAGAGCATCTT
1319525 : TGG : 1319580
113 : TACTGATGGTTAAAATATCCTCTTTCAGCTTGTCGGTCTAAGTTTTCTCCTTGTTA : 168
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319581 : TACTGATGGTTAAAATATCCTCTTTCAGCTTGTCGGTCTAAGTTTTCTCCTTGTTA : 1319636
169 : GTAAATATATATATTCAAATGTACACACACAAAACATGTATATCATGGCACAATTA : 224
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319637 : GTAAATATATATATTCAAATGTACACACACAAAACATGTATATCATGGCACAATTA : 1319692
225 : CATACTATGTCAGACGCCTTAACAATAGCTGCAATTCATGGAAGAAAACCTCACTC : 280
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319693 : CATACTATGTCAGACGCCTTAACAATAGCTGCAATTCATGGAAGAAAACCTCACTC : 1319748
281 : TTCCTCGAGTTAGTAAAGAAAAATTGTATTGAAAGTCACAAAATTGTGACTGAGAT : 336
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319749 : TTCCTCGAGTTAGTAAAGAAAAATTGTATTGAAAGTCACAAAATTGTGACTGAGAT : 1319804
337 : TAACTGACATACGCGTACTCTTATTTTCATCGCTCATTTTGGTTTTAATTTGCTCT : 392
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319805 : TAACTGACATACGCGTACTCTTATTTTCATCGCTCATTTTGGTTTTAATTTGCTCT : 1319860
393 : TCTTTATGTCGTTTCCCAGTTTCACTTTTTACCCTGGCAGTAGTTTTGGAGGCTTT : 448
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319861 : TCTTTATGTCGTTTCCCAGTTTCACTTTTTACCCTGGCAGTAGTTTTGGAGGCTTT : 1319916
449 : CCTTTTCTGCAGTTTCGCTAGTTTGTAATCTCCATTTAAAGGGAAAAGAGAACCAG : 504
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1319917 : CCTTTTCTGCAGTTTCGCTAGTTTGTAATCTCCATTTAAAGGGAAAAGAGAACCAG : 1319972
505 : GCAACAAGATAAAGAGATAAGGGAT : 529
|||||||||||||||||||||||||
1319973 : GCAACAAGATAAAGAGATAAGGGAT : 1319997
C4 Alignment:
------------
Query: sacCer3_dna range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none:[revcomp]
Target: gi|330443489|ref|NC_001135.5| Saccharomyces cerevisiae S288c chromosome III, complete sequence
Model: genome2genome
Raw score: 267
Query range: 491 -> 162
Target range: 23668 -> 115569
491 : CCCTTTAAATGGAGATTACAAACTAGCGA >>>> Target Intron 1 >>>> : 462
|| | ||| | ||| ||||| | | |++ 8983 bp +-
23669 : CCGCTGAAAGGAAGAGAACAAAGTTACAAgt.........................aa : 32679
461 : AACTGCAGAAAAGGAAAGCCTCCAAAACTACT--GC-CAGGGTAAAAAGTGA >>>> : 413
||||||||||||| | || ||| ||| || ||||||| || ||-+
32680 : AACTGCAGAAAAGACTGGTATCTTGAACGACTTGGCGAAGGGTAAGAAAAGAat.... : 32735
412 : Target Intron 2 >>>> AACTGGGAA--ACG-ACAT-AAAGAAGAGCAAATT : 383
9555 bp +-||| || || || || | ||||||||||||||
32736 : .....................atAAC-GGTAATCTCGAACTTCAAAGAAGAGCAAATG : 42321
382 : {A} {CC}AAA : 358
AAA{T} >>>> Target Intron 3 >>>> {hr}LysATGAGCGATGAAAATA
|| { }++ 55423 bp ++{ } ! ||| ||||||||||
AAC{L}gt.........................ag{eu}AspTTGAATGATGAAAATA
42322 : {C} {TG}GAT : 97769
357 : AGAGTACGCGTATGTCAGTTAATCTCAGTCACAATTTTGTGACTTTCAATACAAT > : 302
|||| | | | | ||| | ||||| | || | || |||||| | |+-
97770 : AGAGAA---ATTTATTAGTCATATTCAGTGATTATGTGGTTTTCATCAATATACTgg. : 97824
301 : >>> Target Intron 4 >>>> TTTTCTTTACTAAC-TCGAGGAAGAGTGAGGT : 272
17598 bp ++| || || | | | |||||| |||| |
97825 : ........................agTCTTGAAGACCAGCATGTAGGAAG-GTGATGA : 115450
271 : TTTCTTCC---ATGAATTGCAGCTATTG---T-TAAGGCGTCTGAC-ATAGTATGTAA : 222
| | ||| | ||||| | ||||| | ||| |||| ||| || ||
115451 : TATGCTCCGTAAATAATTGGAAATATTGAGATATAATAACGATGACAATACTA-ACAA : 115507
221 : TTGTGCCA--TGATATACATGTTTTGTGTGTGTACATTTGAATATATATATTTAC-TA : 167
|| | ||| | | ||| ||| | ||||||||||||| | | ||
115508 : AAGTAATAGGTGAGCTCCGCCAATTGATTGTTTTGTTTTGAATATATATTGATGCTTA : 115565
166 : ACAA : 163
||||
115566 : ACAA : 115569
C4 Alignment:
------------
Query: sacCer3_dna range=chrIV:1319469-1319997 5'pad=0 3'pad=0 strand=+ repeatMasking=none:[revcomp]
Target: gi|330443667|ref|NC_001143.9| Saccharomyces cerevisiae S288c chromosome XI, complete sequence:[revcomp]
Model: genome2genome
Raw score: 267
Query range: 529 -> 78
Target range: 641760 -> 71883
529 : ATCCCTTATCTCTTTATCTTGTTGCCTGGTTCTCTTTTCCCTTTAAATGGAGATTACA : 472
|||||||||||||| ||| ||||| |||| || | || || ||
641760 : ATCCCTTATCTCTTCTAAAGATTGTGTGGTT---TTTT--CTATGCATATTTTTTCCA : 641708
471 : ga ag : 385
A---ACTAGCGAA-ACTGCAGAAAAG+->>>> Joint Intron 1 >>>>++CAAA
| || || || || || | ||| 61 bp // 154295 bp |||
ACCTTCTTGCCAATTCTTCA-ACAAG-+>>>> Joint Intron 1 >>>>++CAAT
641707 : tt ag : 487384
384 : TTAAAACCAAAATGAGCGATGAAAATAAGAGTACGCGTATGTCAGTTAATC-TCAGTC : 328
|||| ||||| |||||||||| |||| | | |||| | ||||| | ||| |
487383 : TTAACACCAAGATGAGCGATG-----AAGA-TTC---TATG-CTGTTAAACTTCACTA : 487336
327 : gt ga : 263
ACAATTTT++>>>> Joint Intron 2 >>>>--GGAAGAGTGAGGTTTTCTTCCA
|||| 35 bp // 101120 bp |||| | | || | | | |
CCAATGAG+->>>> Joint Intron 2 >>>>++GGAACATAAAAATTCTGTCCTA
487335 : ga ag : 386186
262 : TGCCATGATATAC : 206
T-GAATTGCAGCTATTGTTAAGGCGTCTGACATAGTATGTAATTGCysHisAspIleH
| || | || |||| || || || | || || |||| ||| ! ! .!.||+
TCAAAATTCAATAATTG-TACAGCTTC-CA-ATTGTGTGTACTTGValLysGlnIleG
386185 : GTCAAACAAATCG : 386131
205 : ATGTT{TT} >>>> Target Intron 1 >>>> {G}TGTGTGTACATT : 182
isVal{Le} {u}CysValTyrIleTG-AA
{::} 177446 bp {:} ! !:: || ||
lyHis{Il}++ ++{e}LysGlyPhe***TGAAA
386130 : GACAC{AT}gt.........................ag{C}AAAGGATTTTGA : 208660
181 : ga ag : 105
TATATATATTTACTAACAAG+->>>> Joint Intron 3 >>>>++TAAAGATGCT
|||||||||||||| | | 47 bp // 136722 bp |||||| |
TATATATATTTACTTAGAGT++>>>> Joint Intron 3 >>>>++AAAAGATTTT
208659 : gt ag : 71908
104 : CTGGACAAGTACCAGTTGGAAAGAGA : 79
|| || | | ||||||||||||||
71907 : CT--ACGACTTGCAGTTGGAAAGAGA : 71884
-- completed exonerate analysis
|
