Locus 1812

Sequence ID	3L_DroMel_CAF1
Location	5,083,690 – 5,083,841
Length	151
Max. P	0.813716

overview

Window 1

Location	5,083,690 – 5,083,801
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.13
Mean single sequence MFE	-30.24
Consensus MFE	-22.36
Energy contribution	-22.68
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-2.02
Structure conservation index	0.74
SVM decision value	0.66
SVM RNA-class probability	0.813716
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5083690 111 - 23771897
AAGA-CAGCGUA-------GAGAGAAGAGAGAAAUGCAGAUUGCAUGUCCUGGCAACAGGAUGCACCCGUCCCAGUCAUGCAUUAAUAACAACCCCAU-CUCCAGCAAACAAUCCCAGCC
....-..((...-------((((.........(((((((((((...((((((....))))))((....))..))))).)))))).............)-)))..)).............. ( -25.05)
>DroSec_CAF1 289909 109 - 1
AAGA-CAGCGAG---------GAGAAGAGGGAAAUGCAGAUUGCAUGUCCUGGCAACAGGAUGCACCCGCCCCAGUCAUGCAUUAACAACAACGCCAU-CUCCAGCAAACAAUCCCAGCC
....-..((..(---------((((....((.(((((((((((...((((((....))))))((....))..))))).))))))..........)).)-)))).)).............. ( -31.30)
>DroSim_CAF1 311210 109 - 1
AAGA-CAGCGAA---------GAGAAGAGGGAAAUGCAGAUUGCAUGUCCUGGCAACAGGAUGCACCCGCCCCAGUCAUGCAUUAACAACAACGCCAU-CUCCAGCAAACAAUCCCAGCC
....-.......---------.......(((((((((((((((...((((((....))))))((....))..))))).)))))).........((...-.....))......)))).... ( -29.80)
>DroYak_CAF1 301464 120 - 1
AAAAGCAGCGAGAGGCUGACUGAAAUGAGAGAAAUGCAGAUUGUAUGUCCUGGCAACAGGAUGCAUUCGCCCCAGUCAUGCAUUAACAACAACCCCAUACCCCAGCAAACAAUCGCAGCC
....((.((((...((((.((......))...(((((((((((...((((((....))))))((....))..))))).))))))..................))))......)))).)). ( -34.80)
>consensus
AAGA_CAGCGAA_________GAGAAGAGAGAAAUGCAGAUUGCAUGUCCUGGCAACAGGAUGCACCCGCCCCAGUCAUGCAUUAACAACAACCCCAU_CUCCAGCAAACAAUCCCAGCC
............................(((((((((((((((...((((((....))))))((....))..))))).))))))....................(....)..)))).... (-22.36 = -22.68 +   0.31)

alignment

secondary structure

dotplot

Window 2

Location	5,083,729 – 5,083,841
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.63
Mean single sequence MFE	-33.72
Consensus MFE	-27.48
Energy contribution	-27.10
Covariance contribution	-0.38
Combinations/Pair	1.12
Mean z-score	-1.36
Structure conservation index	0.81
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5083729 112 - 23771897
UUUGGCAAAAGUUGCCUACGAUCUUUUCGGACUACAAACGAAGA-CAGCGUA-------GAGAGAAGAGAGAAAUGCAGAUUGCAUGUCCUGGCAACAGGAUGCACCCGUCCCAGUCAUG
..((((....((((((.....(((((((...((((.........-....)))-------)...)))))))((.((((.....)))).))..)))))).(((((....)))))..)))).. ( -32.92)
>DroSec_CAF1 289948 110 - 1
UUUGGCAAAAGUUGCCUACGAUCUUUUCGGACUACAAACGAAGA-CAGCGAG---------GAGAAGAGGGAAAUGCAGAUUGCAUGUCCUGGCAACAGGAUGCACCCGCCCCAGUCAUG
...(((........(((.((...((((((.........))))))-...))))---------)......(((..((((.....))))((((((....))))))...))))))......... ( -34.40)
>DroSim_CAF1 311249 110 - 1
UUUGGCAAAAGUUGCCUACGAUCUUUUCGGACUACAAACGAAGA-CAGCGAA---------GAGAAGAGGGAAAUGCAGAUUGCAUGUCCUGGCAACAGGAUGCACCCGCCCCAGUCAUG
...(((....((((((.....((((((((...............-...))))---------))))...((((.((((.....)))).)))))))))).((......)))))......... ( -32.97)
>DroYak_CAF1 301504 120 - 1
UUUGGCAAAAGUUGCCUACGAUCUCUUCGGACUACAAGCGAAAAGCAGCGAGAGGCUGACUGAAAUGAGAGAAAUGCAGAUUGUAUGUCCUGGCAACAGGAUGCAUUCGCCCCAGUCAUG
...((((.....))))..(((.....)))((((....(((((.((((((.....)))).))............((((.....))))((((((....))))))...)))))...))))... ( -34.60)
>consensus
UUUGGCAAAAGUUGCCUACGAUCUUUUCGGACUACAAACGAAGA_CAGCGAA_________GAGAAGAGAGAAAUGCAGAUUGCAUGUCCUGGCAACAGGAUGCACCCGCCCCAGUCAUG
...((((.....))))..(((.....)))((((.....((........))..................(((..((((.....))))((((((....))))))...))).....))))... (-27.48 = -27.10 +  -0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:16 2006