Locus 4393

Sequence ID	X_DroMel_CAF1
Location	11,564,885 – 11,565,033
Length	148
Max. P	0.790984

overview

Window 5

Location	11,564,885 – 11,564,993
Length	108
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	75.35
Mean single sequence MFE	-31.62
Consensus MFE	-19.12
Energy contribution	-19.90
Covariance contribution	0.78
Combinations/Pair	1.06
Mean z-score	-1.56
Structure conservation index	0.60
SVM decision value	0.59
SVM RNA-class probability	0.790984
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11564885 108 - 22224390
CCAACAUCUCCAACUGCAGCAGCUGGAGGCAAACAAUCGCUUCCAGGAGGUCUUUGCCACGGCCACCAUCAUUCAGGCACAUCCGCAUCCCCAUCCACAUCCCAGGGA
.....((((((....((....))(((((((........)))))))))))))...(((....(((...........)))......)))((((.............)))) ( -26.62)
>DroVir_CAF1 9973 108 - 1
GCAACAUCUACAGCUGCAGCAGCUGGAGGCGAGCAAUCGCUUCCAGGAGGUGUUCGCCACGGCCACCAUUAUACAGGCACAUCCACAUCCGCAUCCGCACUUGCGUGA
(((((((((...((....))..((((((((((....)))))))))).))))))).))(((((((...........)))............((....)).....)))). ( -39.00)
>DroPse_CAF1 8245 102 - 1
ACAGCACCUCCAGCUCCAACAGCUGGAGGCGAGUAACCGCUUCCAGGAGAUCUUCGCCACGGCCACCAUCAUUCAGGCGCAUCCGCAUCCCAA------UCCCCGGGA
...((..((((((((.....))))(((((((......))))))).)))).....((((.................)))).....)).((((..------.....)))) ( -32.23)
>DroGri_CAF1 10164 96 - 1
GCAACAUCUACAGCUCCAGCAGCUGGAGGCGAGCAAUCGUUUCCAGGAGGUAUUUGCCACCGCCACCAUAAUACAGGCGCAUCCGCAU------------UCACGCGA
((((.((((...((....))..((((((((((....)))))))))).))))..))))...((((...........))))....(((..------------....))). ( -30.70)
>DroWil_CAF1 29929 96 - 1
ACAGCAUCUGCAAUUGAAGCAACUGGAUGCGAGCAAUCGUUUCCAAGAGGUUUUUGCCACGGCCACCAUAAUUCAGGCGCAUCCCCA------GUCGCUU------GA
...((....(((...(((((..(((((.((((....)))).))).))..))))))))....)).........((((((((.......------).)))))------)) ( -26.40)
>DroMoj_CAF1 9994 96 - 1
GCAGCAUCUGCAGCUGCAGCAGCUGGAGGCAAGCAAUCGCUUCCAGGAGGUGUUCGCCACGGCCACCAUCUACCAGGCGCAUCAGCAA------------CCACGUGA
(((((((((.((((((...)))))((((((........)))))).).))))))).))(((((((...........)))((....))..------------...)))). ( -34.80)
>consensus
GCAACAUCUACAGCUGCAGCAGCUGGAGGCGAGCAAUCGCUUCCAGGAGGUCUUCGCCACGGCCACCAUCAUUCAGGCGCAUCCGCAU___________UCCACGGGA
......................((((((((((....))))))))))..(((....)))...(((...........))).............................. (-19.12 = -19.90 +   0.78)

alignment

secondary structure

dotplot

Window 6

Location	11,564,913 – 11,565,033
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.89
Mean single sequence MFE	-41.26
Consensus MFE	-25.99
Energy contribution	-27.27
Covariance contribution	1.28
Combinations/Pair	1.13
Mean z-score	-2.39
Structure conservation index	0.63
SVM decision value	0.58
SVM RNA-class probability	0.788137
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11564913 120 - 22224390
UCAGCCACAUGCAACAGCAGCGCCAGCAACUGCUGCAGCGCCAACAUCUCCAACUGCAGCAGCUGGAGGCAAACAAUCGCUUCCAGGAGGUCUUUGCCACGGCCACCAUCAUUCAGGCAC
...(((...(((....)))(.(((.(((((((((((((...............)))))))))((((((((........)))))))).......))))...))))...........))).. ( -43.16)
>DroVir_CAF1 10001 120 - 1
UGAACCAUUUGCAAAUGCAGCGCCAGCAGUUCCUGCAGAAGCAACAUCUACAGCUGCAGCAGCUGGAGGCGAGCAAUCGCUUCCAGGAGGUGUUCGCCACGGCCACCAUUAUACAGGCAC
....((..((((...((((((....((((...))))(((.......)))...))))))))))((((((((((....))))))))))..((((..((...))..))))........))... ( -44.30)
>DroPse_CAF1 8267 120 - 1
AUAACCACCUGCAACAGCAGCGCCAGCAGUUCCUGCAGAAACAGCACCUCCAGCUCCAACAGCUGGAGGCGAGUAACCGCUUCCAGGAGAUCUUCGCCACGGCCACCAUCAUUCAGGCGC
.........(((....)))(((((.((((...)))).(((.......((((((((.....))))(((((((......))))))).))))......((....))........))).))))) ( -39.70)
>DroGri_CAF1 10180 120 - 1
UAAAUCGUUUGCAGCUGCAACGCCAGCAGUUCCUUGCGAAGCAACAUCUACAGCUCCAGCAGCUGGAGGCGAGCAAUCGUUUCCAGGAGGUAUUUGCCACCGCCACCAUAAUACAGGCGC
....((((..(.((((((.......)))))).)..)))).((((.((((...((....))..((((((((((....)))))))))).))))..))))...((((...........)))). ( -40.40)
>DroWil_CAF1 29945 120 - 1
UCAAUCAUUUGCAACAGCAGCACCAGCAGUUUUUGCACAAACAGCAUCUGCAAUUGAAGCAACUGGAUGCGAGCAAUCGUUUCCAAGAGGUUUUUGCCACGGCCACCAUAAUUCAGGCGC
.........(((....)))((.((.((((....(((.......))).))))...((((.....((((.((((....)))).))))...(((....((....)).)))....)))))).)) ( -31.30)
>DroMoj_CAF1 10010 120 - 1
UGAACCACUUGCAAAUGCAGCGCCAGCAGUUCCUGCAGAAGCAGCAUCUGCAGCUGCAGCAGCUGGAGGCAAGCAAUCGCUUCCAGGAGGUGUUCGCCACGGCCACCAUCUACCAGGCGC
.........(((....)))(((((...((((.((((((..((((...))))..)))))).))))((((((........)))))).(((((((...((....))...))))).)).))))) ( -48.70)
>consensus
UCAACCACUUGCAACAGCAGCGCCAGCAGUUCCUGCAGAAGCAACAUCUACAGCUGCAGCAGCUGGAGGCGAGCAAUCGCUUCCAGGAGGUCUUCGCCACGGCCACCAUCAUUCAGGCGC
.........(((....)))(((((......(((((...............(((((.....)))))(((((((....))))))))))))(((....((....)).)))........))))) (-25.99 = -27.27 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:53 2006