Locus 115

Sequence ID	3L_DroMel_CAF1
Location	382,727 – 382,870
Length	143
Max. P	0.934045

overview

Window 4

Location	382,727 – 382,833
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.68
Mean single sequence MFE	-27.28
Consensus MFE	-18.70
Energy contribution	-19.78
Covariance contribution	1.08
Combinations/Pair	1.12
Mean z-score	-1.94
Structure conservation index	0.69
SVM decision value	0.37
SVM RNA-class probability	0.709633
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 382727 106 - 23771897
AAAAACUUUUUAGCUAAUGAAAGUCAAACUACUUUCGUU-------------GCUGGU-GGCAUCUUUCAAUUAGAAAACAUGCUUGGCUAAGUAGGAAAACUCUAAAGGGACAAGGACA
.....((.((((((((((((((((......)))))))))-------------......-(((((.((((.....))))..))))).))))))).)).....(((....)))......... ( -21.80)
>DroSec_CAF1 36821 119 - 1
AAAAACUUUUUAGCUAAUGAAAGUCAAACUACUUUCGUUGGCAGUCGCACAUGCUGGU-GGCAUCUUUCAAUUAGAAAACAUGCUUGGCUAAGUAGGAAAACUCUAAAGGGACAUGGGCA
............((((((((((((......))))))))))))....((.((((.((((-(((((.((((.....))))..)))))..))))..........(((....))).)))).)). ( -30.40)
>DroSim_CAF1 37575 119 - 1
AAAAACUUUUUAGCUAAUGAAAGUCAAACUACUUUCGUUGGCAGUCGCACAUGCUGGU-GGCAUCUUUCAAUUAGAAAACCUGCUUGGCUAAGUAGGAAAACUCUAAAGGGACAUGGGCA
............((((((((((((......)))))))))))).........((((.((-(...((((.....((((...(((((((....))))))).....))))))))..))).)))) ( -33.50)
>DroEre_CAF1 40248 101 - 1
AAAAACUUUUUAGCUAAUGGAAGUCAAACUACUUUCGUUGGC------------UGGU-GGCAUCUUUCAAUUAGAAAAUCCGCUUGGCUAAGUAGGAAAACUCUAAAGGGA------CA
.........(((((((((((((((......))))))))))))------------))).-.......(((..(((((...(((((((....)))).)))....)))))..)))------.. ( -24.70)
>DroYak_CAF1 38788 107 - 1
AAAAACUUUUUAGCUAAUGGAAGUCAAACUACU-GCAUUGGC------------AGUCCCACAUCUUUUAAUUAGAAAAUCUGCUUGGCUAAGUAGGAAAACUCUAAAGGGACAAGGACA
.....((((...(((((((..(((......)))-.)))))))------------.(((((...(((.......)))...(((((((....)))))))...........)))))))))... ( -26.00)
>consensus
AAAAACUUUUUAGCUAAUGAAAGUCAAACUACUUUCGUUGGC__________GCUGGU_GGCAUCUUUCAAUUAGAAAACCUGCUUGGCUAAGUAGGAAAACUCUAAAGGGACAAGGACA
.....(((((((((((((((((((......)))))))))))).....................................(((((((....))))))).......)))))))......... (-18.70 = -19.78 +   1.08)

alignment

secondary structure

dotplot

Window 5

Location	382,767 – 382,870
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.70
Mean single sequence MFE	-28.15
Consensus MFE	-15.12
Energy contribution	-16.64
Covariance contribution	1.52
Combinations/Pair	1.24
Mean z-score	-2.51
Structure conservation index	0.54
SVM decision value	1.23
SVM RNA-class probability	0.934045
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 382767 103 - 23771897
--CCCCAGCAUCUAC-UUGUUCUGCGUUUAAGUAGGCAUGAAAAACUUUUUAGCUAAUGAAAGUCAAACUACUUUCGUU-------------GCUGGU-GGCAUCUUUCAAUUAGAAAAC
--(((((((..((((-(((.........)))))))((.(((((....))))))).(((((((((......)))))))))-------------))))).-))....((((.....)))).. ( -25.90)
>DroSec_CAF1 36861 116 - 1
--CCCCAGCAUCUAC-UUGCUCUGUGUUUAAGUAGGCAUGAAAAACUUUUUAGCUAAUGAAAGUCAAACUACUUUCGUUGGCAGUCGCACAUGCUGGU-GGCAUCUUUCAAUUAGAAAAC
--(((((((((((((-((((.....))..))))))((.(((((....)))))((((((((((((......))))))))))))....))..))))))).-))....((((.....)))).. ( -35.30)
>DroSim_CAF1 37615 117 - 1
--CCACAGCAUCUAUUUUGCUCUGUGUUUAAGUAGGCAUGAAAAACUUUUUAGCUAAUGAAAGUCAAACUACUUUCGUUGGCAGUCGCACAUGCUGGU-GGCAUCUUUCAAUUAGAAAAC
--(((((((((((((((.((.....))..))))))((.(((((....)))))((((((((((((......))))))))))))....))..))))).))-))....((((.....)))).. ( -31.80)
>DroEre_CAF1 40282 106 - 1
CUCCCCGCCAUUUGC-UUGCCCAGUGUUUAUGUAGGCAUAAAAAACUUUUUAGCUAAUGGAAGUCAAACUACUUUCGUUGGC------------UGGU-GGCAUCUUUCAAUUAGAAAAU
......(((((.(((-((((...........)))))))............((((((((((((((......))))))))))))------------))))-)))...((((.....)))).. ( -30.70)
>DroYak_CAF1 38828 106 - 1
GUCCCCAGCAUUUCC-UUGCUUAUUGUUUAAUUAGGCAUAAAAAACUUUUUAGCUAAUGGAAGUCAAACUACU-GCAUUGGC------------AGUCCCACAUCUUUUAAUUAGAAAAU
......((((.....-.)))).....(((((((((((.(((((....))))))))....((((.......(((-((....))------------))).......)))))))))))).... ( -17.04)
>consensus
__CCCCAGCAUCUAC_UUGCUCUGUGUUUAAGUAGGCAUGAAAAACUUUUUAGCUAAUGAAAGUCAAACUACUUUCGUUGGC__________GCUGGU_GGCAUCUUUCAAUUAGAAAAC
....(((((........((((.............))))..............((((((((((((......))))))))))))..........)))))........((((.....)))).. (-15.12 = -16.64 +   1.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:53 2006