Locus 7435

Sequence ID	3R_DroMel_CAF1
Location	19,801,675 – 19,801,782
Length	107
Max. P	0.994648

overview

Window 1

Location	19,801,675 – 19,801,782
Length	107
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	50.97
Mean single sequence MFE	-23.45
Consensus MFE	-13.24
Energy contribution	-14.05
Covariance contribution	0.81
Combinations/Pair	1.38
Mean z-score	-2.92
Structure conservation index	0.56
SVM decision value	2.50
SVM RNA-class probability	0.994648
Prediction	RNA
WARNING	Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19801675 107 + 27905053
UACUCGGAAGGAUAUGUAUUAAAU----AUAUGUAAGA---CAGAAAAUAGCAUUUAAAACGAAAUAAGCAUUUUUAA---AAAGA---ACUCAUUUAAUGCACAUUUUUCCGAAUGUAA
(((((((((((((.((((((((((----...((.....---))((((((.((((((......))))..))))))))..---.....---....)))))))))).))))))))))..))). ( -22.50)
>DroEre_CAF1 32637 89 + 1
UCCUCGGAAGAAUAUGUAUUACAUCUAAAUG--UA-----------------------AAUGAAUUAACCUAUUUUGA---GGAGA---AACGAUUUAAUGCACAUUUUUCUGAACGUAA
...((((((((((.(((((((.(((..(((.--..-----------------------.....)))..(((......)---))...---...))).))))))).))))))))))...... ( -19.90)
>DroYak_CAF1 32744 94 + 1
UCCUCGGAAGAUUAUGUAUUAAAUAUAUAUAGUUG-----------------------AGAUAAUGAACCUUUUUUAAAAAAGAGA---UAUAGUUUAAUGCACAUUUUUCCGAGCGUAA
..(((((((((...((((((((((.(((((.(((.-----------------------(.....).)))((((((....)))))))---))))))))))))))...)))))))))..... ( -25.00)
>DroAna_CAF1 34052 106 + 1
CACUCGAAAAAGU-UCCAGUAAUUACUUAGGCUUAAGGAUUCAGAGCUUGGC-UUAGAAGCUUC------UUGUAUUG---GAAGGCUAACUUACUCGAUA---ACUUUUUCGAAUGCAU
((.((((((((((-((.(((((....((((((((.........)))))))).-((((...((((------(......)---)))).)))).))))).))..---)))))))))).))... ( -26.40)
>consensus
UACUCGGAAGAAUAUGUAUUAAAUAUAUAUA_UUA_______________________AACGAAUUAACCUUUUUUAA___AAAGA___AAUAAUUUAAUGCACAUUUUUCCGAACGUAA
...((((((((((.(((((((((((...................................................................))))))))))).))))))))))...... (-13.24 = -14.05 +   0.81)

alignment

secondary structure

dotplot

Window 2

Location	19,801,675 – 19,801,782
Length	107
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	50.97
Mean single sequence MFE	-19.05
Consensus MFE	-8.64
Energy contribution	-10.57
Covariance contribution	1.94
Combinations/Pair	1.24
Mean z-score	-1.94
Structure conservation index	0.45
SVM decision value	1.86
SVM RNA-class probability	0.980422
Prediction	RNA
WARNING	Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19801675 107 - 27905053
UUACAUUCGGAAAAAUGUGCAUUAAAUGAGU---UCUUU---UUAAAAAUGCUUAUUUCGUUUUAAAUGCUAUUUUCUG---UCUUACAUAU----AUUUAAUACAUAUCCUUCCGAGUA
....((((((((..(((((.(((((((((((---....(---((((((............))))))).)))......((---.....))..)----))))))).)))))..)))))))). ( -19.30)
>DroEre_CAF1 32637 89 - 1
UUACGUUCAGAAAAAUGUGCAUUAAAUCGUU---UCUCC---UCAAAAUAGGUUAAUUCAUU-----------------------UA--CAUUUAGAUGUAAUACAUAUUCUUCCGAGGA
.....(((.(((.((((((.((((.......---...((---(......)))......((((-----------------------((--....)))))))))).)))))).))).))).. ( -11.70)
>DroYak_CAF1 32744 94 - 1
UUACGCUCGGAAAAAUGUGCAUUAAACUAUA---UCUCUUUUUUAAAAAAGGUUCAUUAUCU-----------------------CAACUAUAUAUAUUUAAUACAUAAUCUUCCGAGGA
.....(((((((.(.((((.((((((.((((---(..(((((....)))))(((........-----------------------.)))...))))))))))).)))).).))))))).. ( -16.30)
>DroAna_CAF1 34052 106 - 1
AUGCAUUCGAAAAAGU---UAUCGAGUAAGUUAGCCUUC---CAAUACAA------GAAGCUUCUAA-GCCAAGCUCUGAAUCCUUAAGCCUAAGUAAUUACUGGA-ACUUUUUCGAGUG
...(((((((((((((---..((.(((((.((((.(((.---.......(------((.((((....-...)))))))........))).))))....))))).))-))))))))))))) ( -28.89)
>consensus
UUACAUUCGGAAAAAUGUGCAUUAAAUAAGU___UCUCC___UUAAAAAAGGUUAAUUAGCU_______________________UAA_CAUAUAUAUUUAAUACAUAUUCUUCCGAGGA
.....(((((((.((((((.((((((((...................................................................)))))))).)))))).))))))).. ( -8.64 = -10.57 +   1.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:57 2006