Locus 2977

Sequence ID 3R_DroMel_CAF1
Location 7,957,046 – 7,957,166
Length 120
Max. P 0.726505
window4792 window4793

overview

Window 2

Location 7,957,046 – 7,957,166
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.89
Mean single sequence MFE -40.11
Consensus MFE -37.59
Energy contribution -36.93
Covariance contribution -0.66
Combinations/Pair 1.09
Mean z-score -1.39
Structure conservation index 0.94
SVM decision value 0.27
SVM RNA-class probability 0.663255
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7957046 120 + 27905053
GUCGGGUGUUUUGGCGGGUGACCUUCACAUGCCCGGAUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGGCCAUCUUUUUUUGCCU
...(((((...((((((....))......((((((((((((((........))))..(((((((((.....)))))))))(((.......)))))))))))))))))........))))) ( -46.40)
>DroSec_CAF1 23450 112 + 1
GUAAUGUUUUUUGGCGGACGACUUUCACCUGCUCGGAUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGGUCAUCUUU--------
((..((((....))))....))......(((((((((((((((........))))..(((((((((.....)))))))))(((.......))))))))))))))........-------- ( -33.80)
>DroSim_CAF1 23682 120 + 1
GCAAUGUUUUUUGGCGGACGACUUUCACCUGCCCGGAUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGGCCAUCUUUUUUUGAUU
.(((.......(((((((.....)))...((((((((((((((........))))..(((((((((.....)))))))))(((.......))))))))))))))))).......)))... ( -40.14)
>consensus
GUAAUGUUUUUUGGCGGACGACUUUCACCUGCCCGGAUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGGCCAUCUUUUUUUG__U
...........(((((((.....)))...((((((((((((((........))))..(((((((((.....)))))))))(((.......)))))))))))))))))............. (-37.59 = -36.93 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 7,957,046 – 7,957,166
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.89
Mean single sequence MFE -34.87
Consensus MFE -30.34
Energy contribution -30.90
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -1.91
Structure conservation index 0.87
SVM decision value 0.41
SVM RNA-class probability 0.726505
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7957046 120 - 27905053
AGGCAAAAAAAGAUGGCCGCCCGAACAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUAUCCGGGCAUGUGAAGGUCACCCGCCAAAACACCCGAC
.(((..............(((((..(((((.......))))).....((((((.....)))))).((((........))))....)))))..(((.....)))..)))............ ( -37.00)
>DroSec_CAF1 23450 112 - 1
--------AAAGAUGACCGCCCGAACAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUAUCCGAGCAGGUGAAAGUCGUCCGCCAAAAAACAUUAC
--------...((((((((((....(((((.......)))))....(((((((............((((........)))).)))))))..))))...))))))................ ( -30.52)
>DroSim_CAF1 23682 120 - 1
AAUCAAAAAAAGAUGGCCGCCCGAACAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUAUCCGGGCAGGUGAAAGUCGUCCGCCAAAAAACAUUGC
.............((((.(((((..(((((.......))))).....((((((.....)))))).((((........))))....))))).((((.....)).))))))........... ( -37.10)
>consensus
A__CAAAAAAAGAUGGCCGCCCGAACAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUAUCCGGGCAGGUGAAAGUCGUCCGCCAAAAAACAUUAC
...........((((((..(((.....)))(((((...((((((...((((((.....)))))).((((........))))..)))))))))))....))))))................ (-30.34 = -30.90 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:16 2006