Locus 8393

Sequence ID 3R_DroMel_CAF1
Location 22,360,827 – 22,360,931
Length 104
Max. P 0.529499
window13519

overview

Window 9

Location 22,360,827 – 22,360,931
Length 104
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.13
Mean single sequence MFE -25.23
Consensus MFE -18.31
Energy contribution -18.12
Covariance contribution -0.19
Combinations/Pair 1.07
Mean z-score -1.45
Structure conservation index 0.73
SVM decision value -0.01
SVM RNA-class probability 0.529499
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22360827 104 + 27905053
------CACGCAGCGUCGUCGAAAAU---------AUCGCGAAUUUACAAGCGCCGGCAAAAAUUUACUAGAGAAAUCCGCCCGCAAUUACACAGAGCGACGCAGCAAACACGUCCAAA-
------...((.((((((((......---------...((..........))((.(((((....))....((....)).))).)).........)).)))))).)).............- ( -22.40)
>DroSim_CAF1 72524 113 + 1
------CACGCAGUGUCGGCGAAAAUAUCGCAAAUAUCGCGAAUUUACAAGCGCCGGCAAAAAUUUACUCGAGAAAUCCGCCCGCAAUUGCACAGAGCGACGCAGCAAACACGUCCAAA-
------...((((((((((((.((((.((((.......)))))))).....)))))))............((....))........))))).....(.((((.........)))))...- ( -26.90)
>DroEre_CAF1 71017 111 + 1
------CACACAGCGUCGUCGAAAA--UCGCA-AUAUCGCGAAUUUACAAGCGCCGGCAAAAAUUUACUCGACAAAUCCGCCCGCAAGUGCACAGAGCGACGCAGCAAACACGUCCAAAC
------......((((((((((...--((((.-.....))))........((....))..........)))))......((.(....).)).......)))))................. ( -27.60)
>DroYak_CAF1 70603 120 + 1
UAAGCGAACACAGCGUCGUCAAAAAUAUCGCAAAUAUCGCGAAUUUACAAGCGCCGGCAAAAAUUUACUCGACAAAUCCGCCCGCAAUUGCACAGAGCGACGCAGCAAACACGUCCAAAC
...(((....).((((((((.......((((.......)))).....(((..((.(((.....................))).))..)))....)).)))))).)).............. ( -24.00)
>consensus
______CACACAGCGUCGUCGAAAAU_UCGCA_AUAUCGCGAAUUUACAAGCGCCGGCAAAAAUUUACUCGACAAAUCCGCCCGCAAUUGCACAGAGCGACGCAGCAAACACGUCCAAA_
............((((((.(..................((..........))((.(((.....................))).))...........)))))))................. (-18.31 = -18.12 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:26 2006