Locus 7536

Sequence ID	3R_DroMel_CAF1
Location	20,167,189 – 20,167,318
Length	129
Max. P	0.671430

overview

Window 3

Location	20,167,189 – 20,167,289
Length	100
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	74.28
Mean single sequence MFE	-33.33
Consensus MFE	-18.48
Energy contribution	-18.48
Covariance contribution	0.00
Combinations/Pair	1.29
Mean z-score	-1.58
Structure conservation index	0.55
SVM decision value	0.29
SVM RNA-class probability	0.671430
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20167189 100 + 27905053
GCCGUCAGCCAAUCAGAGGCCACCGCGGCAUCUGCGCUCGUCCUCGGCGGAAGUAAAUAAAAGCGGAUGUCCUGGCUGGACAGGACAUCAUUCGAGUGCU
(((((..(((.......)))....)))))....(((((((......((....))...........(((((((((......)))))))))...))))))). ( -42.50)
>DroVir_CAF1 8895 96 + 1
----UGGACCAAUGGCAGGCUUGCAUUUGGUCUGUGUGCGUGCUCAGCGGAAGUAAAUAAAAGCUGAUGUCCUGUCAAGGCAGACCAUCAUUCGAGUGCC
----.(((((((..((......))..)))))))......(..(((.((....))..........(((((..((((....))))..)))))...)))..). ( -32.60)
>DroGri_CAF1 10110 97 + 1
---GCCAGCCAAUCGAAUGCUGGCACUAUGUCUGUGUGCGUUCUCAGCGGAAGUAAAUAAAAGCUGAUGUCCUGCCACAGCAGAGCAUCAUUCGAGUGCC
---((((((.........))))))...............((.(((.((....))..........(((((..((((....))))..)))))...))).)). ( -30.30)
>DroSec_CAF1 7941 100 + 1
CCCGUCAGCCAAUCAGAGGCCACCGCGGAAUCUGCGCUCGUCCUCGGCGGAAGUAAAUAAAAGCGGAUGUCCUGGCUGAACAGGACAUCAUUCGAGUGCU
.((((..(((.......)))....)))).....(((((((......((....))...........(((((((((......)))))))))...))))))). ( -38.80)
>DroWil_CAF1 8356 98 + 1
--CAACGACCAAUCAGAAGCUUGCCAUUUGUCUGUGCGCGUCCACAACGGAAGUGAAUAAAAGCUGAUGUCCUGUCGUUAGAGGACAUCAUUCGAGUGCU
--...(((.........((((((((((......))).)).......((....))......)))))((((((((........))))))))..)))...... ( -25.10)
>DroAna_CAF1 7911 100 + 1
UCAGCCAGCCAAUCGCAGGCCAUCGUGUCUUCUGGGCUCUUCCUCGACGGAAGUAAAUAAAAGCGGAUGUCCUGUGCAGGCAGGACAUCAUUCAAGUUCU
...((.((((....(.((((......)))).)..))))(((((.....))))).........)).((((((((((....))))))))))........... ( -30.70)
>consensus
__CGUCAGCCAAUCAGAGGCCAGCGCGUCGUCUGUGCGCGUCCUCAGCGGAAGUAAAUAAAAGCGGAUGUCCUGUCAAGACAGGACAUCAUUCGAGUGCU
.................................((((.((......((....))...........(((((((((......)))))))))...)).)))). (-18.48 = -18.48 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	20,167,209 – 20,167,318
Length	109
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	75.37
Mean single sequence MFE	-32.97
Consensus MFE	-20.44
Energy contribution	-21.05
Covariance contribution	0.61
Combinations/Pair	1.22
Mean z-score	-1.32
Structure conservation index	0.62
SVM decision value	0.16
SVM RNA-class probability	0.612402
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20167209 109 + 27905053
CACCGCGGCAUCUGCGCUCGUCCUCGGCGGAAGUAAAUAAAAGCGGAUGUCCUGGCUGGACAGGACAUCAUUCGAGUGCUUGCGUUCAACAAGUCC-AGCAAACAGAGCA
....((((...))))(((((..((((((....))...........(((((((((......)))))))))...))))..)((((.............-.))))...)))). ( -38.74)
>DroVir_CAF1 8911 107 + 1
UUGCAUUUGGUCUGUGUGCGUGCUCAGCGGAAGUAAAUAAAAGCUGAUGUCCUGUCAAGGCAGACCAUCAUUCGAGUGCCUGCGUUCAACAAGUUC-AAUUCUAUCA--G
(((.(((((...((..((((..(((.((....))..........(((((..((((....))))..)))))...)))..)..)))..)).))))).)-))........--. ( -28.40)
>DroGri_CAF1 10127 109 + 1
UGGCACUAUGUCUGUGUGCGUUCUCAGCGGAAGUAAAUAAAAGCUGAUGUCCUGCCACAGCAGAGCAUCAUUCGAGUGCCUGCGUUCAACAAGUUC-AAUUCAAGGAACA
.((((((..........((.......((....))........))(((((..((((....))))..)))))....))))))............((((-........)))). ( -30.06)
>DroSec_CAF1 7961 109 + 1
CACCGCGGAAUCUGCGCUCGUCCUCGGCGGAAGUAAAUAAAAGCGGAUGUCCUGGCUGAACAGGACAUCAUUCGAGUGCUUGCGUUCAACAAGUCC-AGCAAACAGAGCA
....((((...))))(((((..((((((....))...........(((((((((......)))))))))...))))..)((((.............-.))))...)))). ( -38.74)
>DroWil_CAF1 8374 107 + 1
UUGCCAUUUGUCUGUGCGCGUCCACAACGGAAGUGAAUAAAAGCUGAUGUCCUGUCGUUAGAGGACAUCAUUCGAGUGCUUGCGUUCAACAAGUU---ACAGUCAGUGCU
(((..((((((.((.(((((..(((.((....))..........(((((((((........))))))))).....)))..))))).)))))))).---.)))........ ( -32.00)
>DroAna_CAF1 7931 110 + 1
CAUCGUGUCUUCUGGGCUCUUCCUCGACGGAAGUAAAUAAAAGCGGAUGUCCUGUGCAGGCAGGACAUCAUUCAAGUUCUUGCGUUCAACAAGUUCAAGUAACUAGUGCA
......(((.....))).(((((.....))))).........(((((((((((((....)))))))))).....((((((((..((.....))..)))).))))..))). ( -29.90)
>consensus
CAGCGCGUCGUCUGUGCGCGUCCUCAGCGGAAGUAAAUAAAAGCGGAUGUCCUGUCAAGACAGGACAUCAUUCGAGUGCUUGCGUUCAACAAGUUC_AACAAACAGAGCA
..............(((..(..(((.((....))...........(((((((((......)))))))))....)))..)..))).......................... (-20.44 = -21.05 +   0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:16 2006