Locus 1729

Sequence ID 3R_DroMel_CAF1
Location 4,971,776 – 4,971,883
Length 107
Max. P 0.500000
window2842

overview

Window 2

Location 4,971,776 – 4,971,883
Length 107
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 70.24
Mean single sequence MFE -18.02
Consensus MFE -9.19
Energy contribution -8.88
Covariance contribution -0.30
Combinations/Pair 1.25
Mean z-score -1.44
Structure conservation index 0.51
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4971776 107 + 27905053
GAUCGC-CCCCCGCACAGCAGUUUGCCAUUUUCCCGGGAAACGCAUUUCGCCGCAAAUCGUUUUCCAACCCACCUCCC--ACC-------AACCAUCGCCACGAAAUGCUCUAA-AAU
....((-.....))......((((.((........)).))))((((((((..((........................--...-------.......))..)))))))).....-... ( -17.28)
>DroPse_CAF1 117394 82 + 1
GCCCC--CCUUGGGGAUGGGGUUUGCCAUUUCCGAGGGAAAUGCAUUUUCCAGCAAAUUGUUUCC---------------------------------CCUCGAAUCGCACAAA-AAU
((..(--((((((..((((......))))..)))))))...(((........)))..........---------------------------------.........)).....-... ( -25.70)
>DroSec_CAF1 78624 111 + 1
GAUCU--CCCACGCACAGCAGUUUGCCAUUUUCCCGGGAAACGCAUUUCGCCGCAAAUCGUUUUCCAACCCACCUCCC--CCCA---CCAAACCCUUGCCACGAAAUGCUCUAAAAAU
.....--.............((((.((........)).))))((((((((..((((...((((...............--....---..))))..))))..))))))))......... ( -19.70)
>DroSim_CAF1 80443 92 + 1
GAUCC--CACCCGCACAGCAGUUUGCCAUUUUCCCGGGAAACGCAUUUCGCCGCAAAUCGUUUUCCAACCCAACUCCC--C----------------------AACUGCUCUAAAAAU
.....--.........(((((((............((((((((.((((......))))))))))))............--.----------------------)))))))........ ( -16.71)
>DroEre_CAF1 79315 111 + 1
GAUCU--CUUCUACACAGCAGUUUGCCAUUUUCCCGGAAAACGCAUUUUGCCGCAAAUCGUUUUCCACCCCAUCUCCAUCUCCA---CC-UACCAUCGCCACGAAAUGCUCUAA-AAU
.....--.........((((...............((((((((.((((......))))))))))))..................---..-.....(((...)))..))))....-... ( -14.40)
>DroYak_CAF1 80311 116 + 1
GAUCUCUCUCCUUCGCAGCCGUUUGCCAUUUUCCCGGGAAACGCAUUUUGCCGCAAAUCGUUUUUAACCCCACCUCCUCCACCACACCC-UUCCCUCGCCACGAAAUGCUCUAA-AAU
....................((((.((........)).))))((((((((..((...................................-.......))..)))))))).....-... ( -14.35)
>consensus
GAUCU__CCCCCGCACAGCAGUUUGCCAUUUUCCCGGGAAACGCAUUUCGCCGCAAAUCGUUUUCCAACCCACCUCCC__ACC________ACC_UCGCCACGAAAUGCUCUAA_AAU
................((((((((.((........)).))))((........))....................................................))))........ ( -9.19 =  -8.88 +  -0.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:51 2006