Locus 2065

Sequence ID 3R_DroMel_CAF1
Location 5,875,586 – 5,875,690
Length 104
Max. P 0.550199
window3374

overview

Window 4

Location 5,875,586 – 5,875,690
Length 104
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 76.61
Mean single sequence MFE -40.43
Consensus MFE -20.91
Energy contribution -20.88
Covariance contribution -0.02
Combinations/Pair 1.38
Mean z-score -1.72
Structure conservation index 0.52
SVM decision value 0.03
SVM RNA-class probability 0.550199
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5875586 104 + 27905053
GACAACUUCCUACAGCGAGUGCGUAGCAUGGUCUUUAGCCAGGAGCGACGGCGCAGUCGCACAAGCGAGGAAACGAGCCAGG---AGG---CUGCCGAGCAG-------CCCGUUGA
..((((.((((...((((.(((((.((.((((.....))))...))....))))).))))....((..(....)..)).)))---)((---((((...))))-------)).)))). ( -45.10)
>DroGri_CAF1 8867 107 + 1
GAGAACUUCUUGCAGCGGGUGCGUAGCAUGGUCUUUAGCCAGGAUCGAGUGCGUGGCCGCGAAAGCGAUGAGGCCAACCUGGAUG------C----GGGCAAUGUUGUCGAUGAGGA
((.(((((((((((.(((((((...)).(((((((..((((.(........).))))(((....)))..))))))))))))..))------)----))).)).))).))........ ( -39.50)
>DroSim_CAF1 21937 107 + 1
GACAACUUCCUACAGCGAGUGCGUAGCAUGGUCUUUAGCCAGGAGCGACGACGCAGUCGCACAAGCGAGGAAACGAGCCAGGAGGAGG---CUGCCGAGGAG-------CCCGAUGA
.....((((((...((((.(((((.((.((((.....))))...))....))))).))))....((..(....)..)).)))))).((---((.(....)))-------))...... ( -41.00)
>DroEre_CAF1 22734 104 + 1
GACAACUUCCUACAGCGAGUGCGUAGUAUGGUCUUCAGCCAGGAGCGACGACGCAGUCGCACAAGCGAGGAAACUAGCCAGGAGG------AUGUCGAGCAG-------CCCGAAGA
((((.((((((...((((.(((((.((.((.((((.....)))).)))).))))).))))....((.((....)).)).))))))------.))))......-------........ ( -40.10)
>DroYak_CAF1 6357 110 + 1
GACAACUUCCUACAGCGUGUGCGUAGCAUUGUCUUCAGCCAGGAGCGACGACGCAGUCGCACAAGCGAGGAAACGAGCCAGGAGGCUGCCGAUGCCGAGCAG-------CCCAAUGA
......(((((...((.((((((..((.((((((((......))).))))).))...)))))).)).)))))......((...((((((((....)).))))-------))...)). ( -41.70)
>DroAna_CAF1 6518 104 + 1
GACAACUUCCUGCAACGGGUGCGCAGCAUGGUAUUCAGCCAGGAGAGGCGGCGCAGUCGCACUAGCGACGAUACCAGCCAAGAUG------GAGGAGAGCAA-------GCGGAGGA
.....(((((.((...((.(((((.((.((((.....))))......)).)))))(((((....)))))....))..((.....)------)..........-------))))))). ( -35.20)
>consensus
GACAACUUCCUACAGCGAGUGCGUAGCAUGGUCUUCAGCCAGGAGCGACGACGCAGUCGCACAAGCGAGGAAACGAGCCAGGAGG______CUGCCGAGCAG_______CCCGAUGA
.....((((((...((((.(((((.((.((((.....))))...))....))))).))))...)).))))............................................... (-20.91 = -20.88 +  -0.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:27 2006