Locus 7658

Sequence ID	X_DroMel_CAF1
Location	19,073,949 – 19,074,102
Length	153
Max. P	0.928898

overview

Window 0

Location	19,073,949 – 19,074,062
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.26
Mean single sequence MFE	-27.13
Consensus MFE	-16.55
Energy contribution	-18.05
Covariance contribution	1.50
Combinations/Pair	1.15
Mean z-score	-2.18
Structure conservation index	0.61
SVM decision value	0.86
SVM RNA-class probability	0.867701
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19073949 113 - 22224390
UGUUGUUUCAAUACGAAAUACGCUAUGUGUAUUCGUGACUUAGUUAUGAGAAAUUGUCAAAUAAGUUAC-------GAGCGACGUGCAAAUUUAAUAUUUCUGUAACUUUUAAACAACCA
.(((((((.(((((((((((.......(((((((((((((((...(..(....)..)....))))))))-------)).....))))).......)))))).)))...)).))))))).. ( -25.34)
>DroSec_CAF1 25547 103 - 1
UGUUGUUUCAAUGCGAUAUACGAUUUGUGUAUCCGUGACUUAGUUAUGACAAAUUGUCAAAUGAGUUAC-------GAGCGACGUGCAAAUGUCAUAUUUCUGUAACUUU----------
....(((.((..(((((((((.....)))))))(((((((((....((((.....))))..))))))))-------).))(((((....))))).......)).)))...---------- ( -29.20)
>DroSim_CAF1 27467 103 - 1
UGUUGUUUCAAUACGAUAUACGAUUUGUGUAUCCGUGACUUAGUUAUGACAAAUUGUCAAAUGAGUUAC-------GAGCGACGUGCAAAUGUCAUAUUUCUGUAACUUU----------
.(((..........(((((((.....)))))))(((((((((....((((.....))))..))))))))-------))))(((((....)))))................---------- ( -26.50)
>DroYak_CAF1 28033 117 - 1
UGUU---CUAAUACGAAAUAAUUGUUGCUUAUCCGUGACUUAGUUAUGACAAAUUGUCGAAUGAGUUACGAGCUACGAGCGACGUGCAAAUGUCAUGAUUCUGUAACUUCGAAACAUCGA
....---................(((((..((((((((((((....((((.....))))..))))))))).((.....))(((((....)))))..)))...))))).((((....)))) ( -27.50)
>consensus
UGUUGUUUCAAUACGAAAUACGAUUUGUGUAUCCGUGACUUAGUUAUGACAAAUUGUCAAAUGAGUUAC_______GAGCGACGUGCAAAUGUCAUAUUUCUGUAACUUU__________
.(((((((......(((((((.....))))))).((((((((....((((.....))))..)))))))).......)))))))..................................... (-16.55 = -18.05 +   1.50)

alignment

secondary structure

dotplot

Window 1

Location	19,073,989 – 19,074,102
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.98
Mean single sequence MFE	-28.66
Consensus MFE	-18.65
Energy contribution	-20.03
Covariance contribution	1.38
Combinations/Pair	1.19
Mean z-score	-2.54
Structure conservation index	0.65
SVM decision value	1.19
SVM RNA-class probability	0.928898
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19073989 113 - 22224390
CAAAUUAAGGUUUAGUGAAACAACGAGAAAAUGGGAAACAUGUUGUUUCAAUACGAAAUACGCUAUGUGUAUUCGUGACUUAGUUAUGAGAAAUUGUCAAAUAAGUUAC-------GAGC
.........((....((((((((((........(....).))))))))))..))...((((((...))))))((((((((((...(..(....)..)....))))))))-------)).. ( -27.20)
>DroSec_CAF1 25577 113 - 1
AAAAUUAAAGUUUACUGAAACAACGCGAGAAUGGGAAACAUGUUGUUUCAAUGCGAUAUACGAUUUGUGUAUCCGUGACUUAGUUAUGACAAAUUGUCAAAUGAGUUAC-------GAGC
...............((((((((((........(....).))))))))))..(((((((((.....)))))))(((((((((....((((.....))))..))))))))-------).)) ( -31.50)
>DroSim_CAF1 27497 113 - 1
AAAAUUAAGGUUUAGUGAAACAACGCGAGAAUGGGAAACAUGUUGUUUCAAUACGAUAUACGAUUUGUGUAUCCGUGACUUAGUUAUGACAAAUUGUCAAAUGAGUUAC-------GAGC
.........((....((((((((((........(....).))))))))))..))(((((((.....)))))))(((((((((....((((.....))))..))))))))-------)... ( -31.70)
>DroYak_CAF1 28073 117 - 1
GGAAUUAAAGUUUAGUGAAGCAAUGCGAAACUGGCAAACAUGUU---CUAAUACGAAAUAAUUGUUGCUUAUCCGUGACUUAGUUAUGACAAAUUGUCGAAUGAGUUACGAGCUACGAGC
(((((......(((((...((...))...))))).......)))---))............((((.(((....(((((((((....((((.....))))..)))))))))))).)))).. ( -24.22)
>consensus
AAAAUUAAAGUUUAGUGAAACAACGCGAAAAUGGGAAACAUGUUGUUUCAAUACGAAAUACGAUUUGUGUAUCCGUGACUUAGUUAUGACAAAUUGUCAAAUGAGUUAC_______GAGC
.........((....((((((((((........(....).))))))))))..))(((((((.....))))))).((((((((....((((.....))))..))))))))........... (-18.65 = -20.03 +   1.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:44:30 2006