Locus 1752

Sequence ID	3R_DroMel_CAF1
Location	5,055,751 – 5,055,851
Length	100
Max. P	0.786223

overview

Window 8

Location	5,055,751 – 5,055,851
Length	100
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	83.79
Mean single sequence MFE	-19.11
Consensus MFE	-10.46
Energy contribution	-13.66
Covariance contribution	3.20
Combinations/Pair	1.00
Mean z-score	-2.64
Structure conservation index	0.55
SVM decision value	0.57
SVM RNA-class probability	0.786223
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5055751 100 + 27905053
---AGAAACCCCAAGAACAACAACAACAAGUUUGCGAAAACUCUCUUUUGCACAACUUUACUUUACCUCCAGCCAGGAGGUCUUUAUUUUGUUACUAUUAUUC
---..........(((((((.......((((((((((((......))))))).)))))......((((((.....)))))).......))))).))....... ( -20.10)
>DroSec_CAF1 162039 100 + 1
---AGAAACCCCGAGAACAACAACAACAAGUUUGCGAAAACUCUCUUUUGCACAACUUUAGUUUACCUCCUGCCAGGAGGUCCUUACUUUGUUACUAUUAUUC
---..........(((((((.......((((((((((((......))))))).))))).(((..((((((.....))))))....)))))))).))....... ( -21.00)
>DroSim_CAF1 167809 100 + 1
---GGAAACCCCGAGAACAACAACAACAAGUUUGCGAAAACUCUCUUUUGCACAACUUUACUUUACCUCCUGCCAGGAGGUCCUUAUUUUGUUACUAUUAUUC
---((.....)).(((((((.......((((((((((((......))))))).)))))......((((((.....)))))).......))))).))....... ( -21.30)
>DroEre_CAF1 164651 80 + 1
---AGAAAACCCAAGAAAAACAAG--------------AACUCUCUUUUGCAGAACUUUAC------UCCUGCCAGGAGGUCCUUAUUUUGUUACUCUUAUUC
---.........((((..((((((--------------(((.(((((..((((........------..)))).))))))).....)))))))..)))).... ( -14.80)
>DroYak_CAF1 168648 103 + 1
CCAAGAAAACCAUAGAACAACAACAACAAGUUUGCUAUAACUCUCUUUUGCACAACUUUACUUUACCUCCUGCUAGGAGGUCCUUAUUUUGUUGCUAUUACUC
...........((((..((((((....((((((((..............))).)))))......((((((.....)))))).......))))))))))..... ( -18.34)
>consensus
___AGAAACCCCAAGAACAACAACAACAAGUUUGCGAAAACUCUCUUUUGCACAACUUUACUUUACCUCCUGCCAGGAGGUCCUUAUUUUGUUACUAUUAUUC
..................(((((....((((((((((((......))))))).)))))......((((((.....)))))).......))))).......... (-10.46 = -13.66 +   3.20)

alignment

secondary structure

dotplot

Window 9

Location	5,055,751 – 5,055,851
Length	100
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	83.79
Mean single sequence MFE	-25.96
Consensus MFE	-16.00
Energy contribution	-18.12
Covariance contribution	2.12
Combinations/Pair	1.08
Mean z-score	-2.29
Structure conservation index	0.62
SVM decision value	0.55
SVM RNA-class probability	0.779617
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5055751 100 - 27905053
GAAUAAUAGUAACAAAAUAAAGACCUCCUGGCUGGAGGUAAAGUAAAGUUGUGCAAAAGAGAGUUUUCGCAAACUUGUUGUUGUUGUUCUUGGGGUUUCU---
(((((((((((((.........((((((.....))))))......(((((.(((.((((....)))).)))))))))))))))))))))...........--- ( -26.20)
>DroSec_CAF1 162039 100 - 1
GAAUAAUAGUAACAAAGUAAGGACCUCCUGGCAGGAGGUAAACUAAAGUUGUGCAAAAGAGAGUUUUCGCAAACUUGUUGUUGUUGUUCUCGGGGUUUCU---
(((((((((((((((.((.((.((((((.....))))))...))....(((((.((((.....))))))))))))))))))))))))))...........--- ( -27.10)
>DroSim_CAF1 167809 100 - 1
GAAUAAUAGUAACAAAAUAAGGACCUCCUGGCAGGAGGUAAAGUAAAGUUGUGCAAAAGAGAGUUUUCGCAAACUUGUUGUUGUUGUUCUCGGGGUUUCC---
(((((((((((((.........((((((.....))))))......(((((.(((.((((....)))).)))))))))))))))))))))...........--- ( -25.90)
>DroEre_CAF1 164651 80 - 1
GAAUAAGAGUAACAAAAUAAGGACCUCCUGGCAGGA------GUAAAGUUCUGCAAAAGAGAGUU--------------CUUGUUUUUCUUGGGUUUUCU---
((((..(((....((((((((((((((...((((((------......))))))....))).)))--------------)))))))).)))..))))...--- ( -23.30)
>DroYak_CAF1 168648 103 - 1
GAGUAAUAGCAACAAAAUAAGGACCUCCUAGCAGGAGGUAAAGUAAAGUUGUGCAAAAGAGAGUUAUAGCAAACUUGUUGUUGUUGUUCUAUGGUUUUCUUGG
(((((((((((((((.......((((((.....))))))........(((((((........).))))))....))))))))))))))).............. ( -27.30)
>consensus
GAAUAAUAGUAACAAAAUAAGGACCUCCUGGCAGGAGGUAAAGUAAAGUUGUGCAAAAGAGAGUUUUCGCAAACUUGUUGUUGUUGUUCUCGGGGUUUCU___
(((((((((((((((.......((((((.....))))))...(((......)))....................))))))))))))))).............. (-16.00 = -18.12 +   2.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:26 2006