Locus 137

Sequence ID	X_DroMel_CAF1
Location	525,453 – 525,599
Length	146
Max. P	0.987905

overview

Window 4

Location	525,453 – 525,573
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.00
Mean single sequence MFE	-35.26
Consensus MFE	-31.46
Energy contribution	-32.06
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.10
Structure conservation index	0.89
SVM decision value	2.10
SVM RNA-class probability	0.987905
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 525453 120 - 22224390
GAAAACCGCGCGCCAACCGAAAAAUUUGUUUGCAGUUUUGGCUUGGCAGCGUGGAAAUGGAAAUGCAUUUGACCACGUCAGAAAACGUGAAAGAAGCUAACAAGGAUAACCGGGGCAGAG
.....(((((((((((((((((...(((....))))))))).))))).))))))(((((......)))))...(((((......)))))......(((.....((....))..))).... ( -34.90)
>DroSec_CAF1 11938 119 - 1
GA-AACCGCGCGCCAACCGAAAAAUUUGUUUGCAGUUUUGGCUUGGCAGCGUGGAAAUGGAAAUGCAUUUGACCACGUCAGAAAACGUGAAAGAAGCUAACAAGGAUAACCGGGGCAGAG
..-..(((((((((((((((((...(((....))))))))).))))).))))))(((((......)))))...(((((......)))))......(((.....((....))..))).... ( -34.90)
>DroSim_CAF1 12262 120 - 1
GAAAACCGCGCGCCAACCGAAAAAUUUGUUUGCAGUUUUGGCUUGGCAGCGUGGAAAUGGAAAUGCAUUUGACCACGUCAGAAAACGUGAAAGAAGCUAACAAGGAUAACCGGGGCAGAG
.....(((((((((((((((((...(((....))))))))).))))).))))))(((((......)))))...(((((......)))))......(((.....((....))..))).... ( -34.90)
>DroEre_CAF1 17022 120 - 1
GAAAACCGCGCGCCAACCGAAAAAUUUGUUUGCAGUUUUGGCUUGGCAGCGUGGAAAUGGAAAUGCAUUUGACCACGUCAGAAAACGUGAAAGAAGCUAACAAGGAUAACCGGGGCAGAG
.....(((((((((((((((((...(((....))))))))).))))).))))))(((((......)))))...(((((......)))))......(((.....((....))..))).... ( -34.90)
>DroYak_CAF1 10776 120 - 1
GGAAACCGCGCGCCAAGCGAAAAAUUUGUUUGGAGUUUUGGCUUGGCAGCGUGGAAAUGGAAAUGCAUUUGACCACGUCAGGAAACGUGAAAGAAGCUAACAAGAAUAACCGGGGCAGAG
((...(((((((((((((..(((((((.....))))))).))))))).))))))..........((.(((...(((((......)))))...)))))............))......... ( -36.70)
>consensus
GAAAACCGCGCGCCAACCGAAAAAUUUGUUUGCAGUUUUGGCUUGGCAGCGUGGAAAUGGAAAUGCAUUUGACCACGUCAGAAAACGUGAAAGAAGCUAACAAGGAUAACCGGGGCAGAG
.....(((((((((((((((((...(((....))))))))).))))).))))))(((((......)))))...(((((......)))))......(((.....((....))..))).... (-31.46 = -32.06 +   0.60)

alignment

secondary structure

dotplot

Window 5

Location	525,493 – 525,599
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.23
Mean single sequence MFE	-37.48
Consensus MFE	-30.82
Energy contribution	-31.18
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.96
Structure conservation index	0.82
SVM decision value	1.43
SVM RNA-class probability	0.953028
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 525493 106 - 22224390
UGCC--------------CGGCGGUUCGCCUACUUUGGUUGAAAACCGCGCGCCAACCGAAAAAUUUGUUUGCAGUUUUGGCUUGGCAGCGUGGAAAUGGAAAUGCAUUUGACCACGUCA
....--------------.((((...)))).....(((((.....(((((((((((((((((...(((....))))))))).))))).))))))(((((......))))))))))..... ( -35.60)
>DroSec_CAF1 11978 105 - 1
UGCC--------------CGGCGGUUCGCCUACUUUGGUUGA-AACCGCGCGCCAACCGAAAAAUUUGUUUGCAGUUUUGGCUUGGCAGCGUGGAAAUGGAAAUGCAUUUGACCACGUCA
.((.--------------..((((((((((......)).)).-))))))))(((((((((((...(((....))))))))).))))).(((((((((((......)))))..)))))).. ( -35.80)
>DroSim_CAF1 12302 106 - 1
UGCC--------------CGGCGGUUCGCCUACUUUGGUUGAAAACCGCGCGCCAACCGAAAAAUUUGUUUGCAGUUUUGGCUUGGCAGCGUGGAAAUGGAAAUGCAUUUGACCACGUCA
....--------------.((((...)))).....(((((.....(((((((((((((((((...(((....))))))))).))))).))))))(((((......))))))))))..... ( -35.60)
>DroEre_CAF1 17062 99 - 1
---------------------UGGUUCGCCUACUUUGGUUGAAAACCGCGCGCCAACCGAAAAAUUUGUUUGCAGUUUUGGCUUGGCAGCGUGGAAAUGGAAAUGCAUUUGACCACGUCA
---------------------.((....)).....(((((.....(((((((((((((((((...(((....))))))))).))))).))))))(((((......))))))))))..... ( -31.80)
>DroYak_CAF1 10816 120 - 1
UGGCAGGUGGCAGGUGGACGGUGGUUCGCCUACUUUGGUUGGAAACCGCGCGCCAAGCGAAAAAUUUGUUUGGAGUUUUGGCUUGGCAGCGUGGAAAUGGAAAUGCAUUUGACCACGUCA
.(((....((.((((((((....)))))))).)).((((..((..(((((((((((((..(((((((.....))))))).))))))).))))))..((....))...))..)))).))). ( -48.60)
>consensus
UGCC______________CGGCGGUUCGCCUACUUUGGUUGAAAACCGCGCGCCAACCGAAAAAUUUGUUUGCAGUUUUGGCUUGGCAGCGUGGAAAUGGAAAUGCAUUUGACCACGUCA
....................((((((.(((......)))....))))))..(((((((((((...(((....))))))))).))))).(((((((((((......)))))..)))))).. (-30.82 = -31.18 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:56 2006