Locus 4000

Sequence ID 3L_DroMel_CAF1
Location 11,654,544 – 11,654,649
Length 105
Max. P 0.567019
window6233

overview

Window 3

Location 11,654,544 – 11,654,649
Length 105
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 89.02
Mean single sequence MFE -39.44
Consensus MFE -28.55
Energy contribution -29.43
Covariance contribution 0.88
Combinations/Pair 1.08
Mean z-score -1.72
Structure conservation index 0.72
SVM decision value 0.07
SVM RNA-class probability 0.567019
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11654544 105 - 23771897
UGAACACCCACGGGCGUCCAGCCUGCAGAGUUGCCUGAA-----------UGGCUCGGAAAAGCCCAGUCGCUCAAAGGGUGGGAAACUACUCCGCGGAAACUCCUCCUGAACUUG
...........((((.(((((((..(((......)))..-----------.)))).)))...))))......(((..((((((....)))).))..(((......))))))..... ( -36.20)
>DroSec_CAF1 28717 105 - 1
UGAACACCCACGGGCGUCCAGCCUGCAGAGUUGCCUGAA-----------UGGCUCGGAAAAGCCCAUUCGCUCGAAGGGUGGGAAACUACUCCGCGGAAACUCCACCUGAGCUUG
...........((((.(((((((..(((......)))..-----------.)))).)))...))))....(((((..((((((....))))))..)((.....))....))))... ( -41.70)
>DroSim_CAF1 29674 105 - 1
UGAACACCCACGGGCGUCCAGCCUGCAGAGUUGCCUGAA-----------UGGCUCGGAAAAGCCCAGUCGCUCGAAGGGUGGGAAACUACUCCGCGGAAACUCCACCUGAGCUUG
...........((((.(((((((..(((......)))..-----------.)))).)))...))))....(((((..((((((....))))))..)((.....))....))))... ( -41.70)
>DroEre_CAF1 27865 104 - 1
UGAACACCCACGG-CUAUCAGCCUGGGGAGUUGCAUGAA-----------UUGCUCGGAAAAGCCCAGUGGCUCGUAGGGUGGGAAACUACUCCGCGGAAACUCCAUCUGAGCUUG
(((((.((((.((-(.....)))))))..))).))....-----------..(((((((..((((....))))((..((((((....))))))..)).........)))))))... ( -42.20)
>DroYak_CAF1 29861 115 - 1
UGAACACCCACGG-CGUCCAGCCUGAAGAGUUGCCUGAGUUAAAAAAAAAUGGCUCGGAAAAGCCCAGUCGCUGGGAGGGUGGGAAACUACUCCGCGGAAACUCCACCUGAGCUUG
........((.((-(.....)))))..(((((((((((((((........)))))))).....(((((...))))).((((((....)))).))))((.....)).....))))). ( -35.40)
>consensus
UGAACACCCACGGGCGUCCAGCCUGCAGAGUUGCCUGAA___________UGGCUCGGAAAAGCCCAGUCGCUCGAAGGGUGGGAAACUACUCCGCGGAAACUCCACCUGAGCUUG
...........((((.(((((((............................)))).)))...))))....(((((..((((((....)))).))..((.....))...)))))... (-28.55 = -29.43 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:05 2006