Locus 5396

Sequence ID	3L_DroMel_CAF1
Location	14,810,704 – 14,810,840
Length	136
Max. P	0.956936

overview

Window 7

Location	14,810,704 – 14,810,800
Length	96
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	94.32
Mean single sequence MFE	-25.97
Consensus MFE	-21.46
Energy contribution	-21.86
Covariance contribution	0.40
Combinations/Pair	1.09
Mean z-score	-1.98
Structure conservation index	0.83
SVM decision value	1.47
SVM RNA-class probability	0.956936
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14810704 96 - 23771897
UGUAAGCCCCCCCCCCUCAUAAAUUGCAUUAAUAUGCAAGGG-GAGUUUUGGGGCUAGGGUAAAUUAUGCCAUGACAUCAGCAAGUAGAACAACAAA
(((.((((((.((((((.......(((((....)))))))))-).)....))))))..((((.....)))).........))).............. ( -26.41)
>DroSec_CAF1 45932 94 - 1
UGUCAGUCCC--CCCCUCAUAAAUUGCAUUAAUAUGCAAGGG-GAGUUUUGGGGCUAGGGUAAAUUAUGCCAGGACAUCAGCAAGUAGAACAACAAA
((((((((((--(((((.......(((((....)))))))))-)......))))))..((((.....))))..)))).................... ( -26.21)
>DroSim_CAF1 38880 94 - 1
UGUCAGUCCC--CCCCUCAUAAAUUGCAUUAAUAUGCAAGGG-GAGUUUUGGGGCUAGGGUAAAUUAUGCCAGGACAUCAGCAAGUAGAACAACAAA
((((((((((--(((((.......(((((....)))))))))-)......))))))..((((.....))))..)))).................... ( -26.21)
>DroEre_CAF1 45312 93 - 1
UGUCAGUCCC---CCCUCAUAAAUUGCAUUAAUAUGCAAGGG-GGUUUUUGGGGCCAGGGUAAAUUAUGCCAGGACAUCAGCAAGUAGAACAACAAA
((((.(((((---(((((.....((((((....)))))))))-)).....)))))...((((.....))))..)))).................... ( -25.20)
>DroYak_CAF1 48840 93 - 1
UGUCAGUCCC----CCUCAUAAAUUGCAUUAAUAUGCAAGGGGGGUUUUCGGGGCUAGGGUAAAUUAUGCCAGGACAUCAGCAAGUAGAACAACAAA
((((((((((----((((.....((((((....))))))..)))).....))))))..((((.....))))..)))).................... ( -25.80)
>consensus
UGUCAGUCCC__CCCCUCAUAAAUUGCAUUAAUAUGCAAGGG_GAGUUUUGGGGCUAGGGUAAAUUAUGCCAGGACAUCAGCAAGUAGAACAACAAA
((((((((((.....(((.....((((((....))))))....)))....))))))..((((.....))))..)))).................... (-21.46 = -21.86 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	14,810,741 – 14,810,840
Length	99
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	94.09
Mean single sequence MFE	-32.17
Consensus MFE	-25.37
Energy contribution	-25.45
Covariance contribution	0.08
Combinations/Pair	1.04
Mean z-score	-1.69
Structure conservation index	0.79
SVM decision value	0.32
SVM RNA-class probability	0.685853
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14810741 99 - 23771897
GCCGGGGAAUCCUUAGCUUAGGGAAAUGAAGCAACGCUUUUGUAAGCCCCCCCCCCUCAUAAAUUGCAUUAAUAUGCAAGGG-GAGUUUUGGGGCUAGGG
(((((((..((((((...))))))...........((((....)))))))).(((((.......(((((....)))))))))-)........)))..... ( -31.31)
>DroSec_CAF1 45969 97 - 1
GCCGGGGAAUCCUUAGCUUAGGGAAAUGAAGCAACGCUUUUGUCAGUCCC--CCCCUCAUAAAUUGCAUUAAUAUGCAAGGG-GAGUUUUGGGGCUAGGG
..........(((((((((.((((...(((((...)))))......))))--(((((.......(((((....)))))))))-).......))))))))) ( -31.71)
>DroSim_CAF1 38917 97 - 1
GCCGGGGAAUCCUUAGCUUAGGGAAAUGAAGCAACGCUUUUGUCAGUCCC--CCCCUCAUAAAUUGCAUUAAUAUGCAAGGG-GAGUUUUGGGGCUAGGG
..........(((((((((.((((...(((((...)))))......))))--(((((.......(((((....)))))))))-).......))))))))) ( -31.71)
>DroEre_CAF1 45349 96 - 1
GCCAGGGAAUCCUUGGCUUAGGGAAAUGAAGCAACGCUUUUGUCAGUCCC---CCCUCAUAAAUUGCAUUAAUAUGCAAGGG-GGUUUUUGGGGCCAGGG
..........(((((((((.((((...(((((...)))))......))))---(((((.....((((((....)))))))))-))......))))))))) ( -33.40)
>DroYak_CAF1 48877 96 - 1
GCCGGGGAAUCCUUAGCUUAGGGAAAUGAAGCAACGCUUUUGUCAGUCCC----CCUCAUAAAUUGCAUUAAUAUGCAAGGGGGGUUUUCGGGGCUAGGG
..........(((((((((..(((((((((((...))))).......(((----(((.......(((((....))))))))))))))))).))))))))) ( -32.71)
>consensus
GCCGGGGAAUCCUUAGCUUAGGGAAAUGAAGCAACGCUUUUGUCAGUCCC__CCCCUCAUAAAUUGCAUUAAUAUGCAAGGG_GAGUUUUGGGGCUAGGG
..........(((((((((.((((...(((((...)))))......))))...((((.......(((((....))))))))).........))))))))) (-25.37 = -25.45 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:17 2006