Locus 876

Sequence ID	2L_DroMel_CAF1
Location	2,499,360 – 2,499,462
Length	102
Max. P	0.954989

overview

Window 8

Location	2,499,360 – 2,499,462
Length	102
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	86.03
Mean single sequence MFE	-34.30
Consensus MFE	-24.10
Energy contribution	-25.10
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.70
SVM decision value	0.06
SVM RNA-class probability	0.565403
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2499360 102 + 22407834
GAAUUUGUUACGAUUUCGCAGCAGCAGCUACAGGAGAAGGAGGAACAGGAGGAGGAGGAAUGCCAGUCGGAAAUGGCGCAGGAGUCCUGCUCCAGGAGCUCC
...((((((.(..((((..(((....)))......))))..).)))))).((((.((((...((.((((....))))...))..)))).))))......... ( -27.50)
>DroSec_CAF1 78291 90 + 1
GAAUUUGUUACGAUUUCGCAGCAGCAGCUGCAGGAGG------------AGGAGUAGGAGUGCCAGUCGGAAAUGGCGCAGGAGUCCUGCUCCAGGAGCUCC
(((.(((...))).)))(((((....))))).((((.------------.(((((((((((((((........)))))).....))))))))).....)))) ( -36.80)
>DroSim_CAF1 81674 96 + 1
GAAUUUGUUACGAUUUCGCAGCAGCAGCUGCAGGAGGAGGAG------GAGGAGUAGGAGUGCCAGUCGGAAAUGGCGCAGGAGUCCUGCUCCAGGAGCUCC
(((.(((...))).)))(((((....)))))....((((...------..(((((((((((((((........)))))).....))))))))).....)))) ( -38.00)
>DroYak_CAF1 81728 94 + 1
GAAUUUGUUACGAUUUCGCAGCAGCAGCAGGAGGAG---UGG-----UGAAGUGGAGCAGUGCCAGUCGGAAAUGGCGCUGGAGUCCUGCGCCAGGACCUCC
....(((((.((....)).))))).....(((((..---(((-----((....(((.((((((((........))))))))...)))..)))))...))))) ( -34.90)
>consensus
GAAUUUGUUACGAUUUCGCAGCAGCAGCUGCAGGAGG__GAG______GAGGAGGAGGAGUGCCAGUCGGAAAUGGCGCAGGAGUCCUGCUCCAGGAGCUCC
(((.(((...))).)))(((((....)))))............................((((((........)))))).(((((((((...))))).)))) (-24.10 = -25.10 +   1.00)

alignment

secondary structure

dotplot

Window 9

Location	2,499,360 – 2,499,462
Length	102
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	86.03
Mean single sequence MFE	-29.93
Consensus MFE	-23.94
Energy contribution	-24.50
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-2.33
Structure conservation index	0.80
SVM decision value	1.45
SVM RNA-class probability	0.954989
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2499360 102 - 22407834
GGAGCUCCUGGAGCAGGACUCCUGCGCCAUUUCCGACUGGCAUUCCUCCUCCUCCUGUUCCUCCUUCUCCUGUAGCUGCUGCUGCGAAAUCGUAACAAAUUC
((((.....((((((((((....).((((........))))...........))))))))).....))))((((((....))))))................ ( -31.40)
>DroSec_CAF1 78291 90 - 1
GGAGCUCCUGGAGCAGGACUCCUGCGCCAUUUCCGACUGGCACUCCUACUCCU------------CCUCCUGCAGCUGCUGCUGCGAAAUCGUAACAAAUUC
((((.....((((((((...)))))((((........))))..))).....))------------))...((((((....))))))................ ( -30.50)
>DroSim_CAF1 81674 96 - 1
GGAGCUCCUGGAGCAGGACUCCUGCGCCAUUUCCGACUGGCACUCCUACUCCUC------CUCCUCCUCCUGCAGCUGCUGCUGCGAAAUCGUAACAAAUUC
((((.....((((((((...)))))((((........))))..))).....)))------).........((((((....))))))................ ( -30.50)
>DroYak_CAF1 81728 94 - 1
GGAGGUCCUGGCGCAGGACUCCAGCGCCAUUUCCGACUGGCACUGCUCCACUUCA-----CCA---CUCCUCCUGCUGCUGCUGCGAAAUCGUAACAAAUUC
(((((...(((.(.((.....(((.((((........)))).))).....)).).-----)))---..))))).((....))((((....))))........ ( -27.30)
>consensus
GGAGCUCCUGGAGCAGGACUCCUGCGCCAUUUCCGACUGGCACUCCUACUCCUC______CUC__CCUCCUGCAGCUGCUGCUGCGAAAUCGUAACAAAUUC
((((.(((((...)))))))))(((((((........)))).............................((((((....)))))).....)))........ (-23.94 = -24.50 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:44 2006