Locus 522

Sequence ID	3R_DroMel_CAF1
Location	1,916,975 – 1,917,095
Length	120
Max. P	0.868621

overview

Window 4

Location	1,916,975 – 1,917,095
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.92
Mean single sequence MFE	-24.25
Consensus MFE	-19.31
Energy contribution	-20.50
Covariance contribution	1.19
Combinations/Pair	1.06
Mean z-score	-1.38
Structure conservation index	0.80
SVM decision value	-0.03
SVM RNA-class probability	0.516890
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1916975 120 + 27905053
AAACCAACAGCUGGUCCUUGGAACCAAAACUUUAAAAUGGGUUUGGCAAUUACGAAUCAAAUUACAAAAGUUGUAAAUUUAAAAUAGGUUCGUGUAUUUCGACUUCAAGGUAAACAAAUG
..((((.....))))(((((((.(((((.(((......))))))))....((((((((((((((((.....))).)))))......)))))))).........))))))).......... ( -22.10)
>DroSec_CAF1 75375 120 + 1
AAGCCAACAGCUGGUCCUUGGAACCAAAACUUUAAAAUAGGUUUGGCAAUUACGAAUCAAAUUACCAAAGUUUUAAAUUUUAAAGAGGUUCGUGUAUUUUGACUUCAAGGAAAACAACUG
.......(((.((.(((((((((((....(((((((((((.(((((.((((........)))).))))).))....))))))))).)))))((........))..))))))...)).))) ( -27.40)
>DroSim_CAF1 76151 120 + 1
AAGCCAACAGCUGGUCCUUGGAACCAAAACUUUAAAAUAGGUUUGGCAAUUACGAAUCAAAUUACCAAAGUUUUAAAUUUUAAAGAGGUUCGUGUAUUUUGACUUCAAGGAAAACAAGUG
.........((((.(((((((((((....(((((((((((.(((((.((((........)))).))))).))....))))))))).)))))((........))..))))))...).))). ( -25.10)
>DroEre_CAF1 77329 109 + 1
AAGCCAACAUCUGGUGCUUGGCACCGAAACUUUAAAAUAGGUUUGGCAAUUACGAAUCAAAUUACCAAAGUUGUAAAUUUGAAUGAGGUGCGUAUAUUUCGACUACAAG-----------
..((((.....)))).(((((((((.....((((((((((.(((((.((((........)))).))))).))))...))))))...)))))((........))..))))----------- ( -22.40)
>consensus
AAGCCAACAGCUGGUCCUUGGAACCAAAACUUUAAAAUAGGUUUGGCAAUUACGAAUCAAAUUACCAAAGUUGUAAAUUUUAAAGAGGUUCGUGUAUUUCGACUUCAAGGAAAACAA_UG
..((((.....))))((((((((((....(((((((((.((((((.......))))))...((((.......))))))))))))).)))))((........))..))))).......... (-19.31 = -20.50 +   1.19)

alignment

secondary structure

dotplot

Window 5

Location	1,916,975 – 1,917,095
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.92
Mean single sequence MFE	-25.68
Consensus MFE	-20.17
Energy contribution	-21.30
Covariance contribution	1.13
Combinations/Pair	1.03
Mean z-score	-2.01
Structure conservation index	0.79
SVM decision value	0.86
SVM RNA-class probability	0.868621
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1916975 120 - 27905053
CAUUUGUUUACCUUGAAGUCGAAAUACACGAACCUAUUUUAAAUUUACAACUUUUGUAAUUUGAUUCGUAAUUGCCAAACCCAUUUUAAAGUUUUGGUUCCAAGGACCAGCUGUUGGUUU
..........(((((..((......))..(((((.((((((((........(((.((((((........)))))).))).....))))))))...))))))))))(((((...))))).. ( -19.62)
>DroSec_CAF1 75375 120 - 1
CAGUUGUUUUCCUUGAAGUCAAAAUACACGAACCUCUUUAAAAUUUAAAACUUUGGUAAUUUGAUUCGUAAUUGCCAAACCUAUUUUAAAGUUUUGGUUCCAAGGACCAGCUGUUGGCUU
((((((...((((((..((......))..(((((.(((((((((.......((((((((((........))))))))))...)))))))))....))))))))))).))))))....... ( -33.50)
>DroSim_CAF1 76151 120 - 1
CACUUGUUUUCCUUGAAGUCAAAAUACACGAACCUCUUUAAAAUUUAAAACUUUGGUAAUUUGAUUCGUAAUUGCCAAACCUAUUUUAAAGUUUUGGUUCCAAGGACCAGCUGUUGGCUU
.........((((((..((......))..(((((.(((((((((.......((((((((((........))))))))))...)))))))))....)))))))))))..(((.....))). ( -28.70)
>DroEre_CAF1 77329 109 - 1
-----------CUUGUAGUCGAAAUAUACGCACCUCAUUCAAAUUUACAACUUUGGUAAUUUGAUUCGUAAUUGCCAAACCUAUUUUAAAGUUUCGGUGCCAAGCACCAGAUGUUGGCUU
-----------..((..((((.......)).))..))..........((((((((((((((........))))))))))...........((((.(((((...))))))))))))).... ( -20.90)
>consensus
CA_UUGUUUUCCUUGAAGUCAAAAUACACGAACCUCUUUAAAAUUUAAAACUUUGGUAAUUUGAUUCGUAAUUGCCAAACCUAUUUUAAAGUUUUGGUUCCAAGGACCAGCUGUUGGCUU
..........(((((..((........))(((((.(((((((((.......((((((((((........))))))))))...)))))))))....)))))))))).((((...))))... (-20.17 = -21.30 +   1.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:10 2006