Locus 1336

Sequence ID	3R_DroMel_CAF1
Location	3,938,454 – 3,938,562
Length	108
Max. P	0.906413

overview

Window 4

Location	3,938,454 – 3,938,562
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	91.38
Mean single sequence MFE	-25.40
Consensus MFE	-23.02
Energy contribution	-21.86
Covariance contribution	-1.16
Combinations/Pair	1.25
Mean z-score	-1.45
Structure conservation index	0.91
SVM decision value	1.05
SVM RNA-class probability	0.906413
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3938454 108 + 27905053
AAGUCAAAGUAAUUUCCAACGUGGAAUACAUGUACAUAUCUAUCCAACUCCCUCGCUCCCAUGGAGGCAAUUGGGGUGCGUUGAUAAGGAGCAAUGCUCCUUCCACCU
..(((((.(((.......(((((.....))))).........(((((...((((.(......)))))...))))).))).)))))(((((((...)))))))...... ( -27.90)
>DroSec_CAF1 6545 104 + 1
GAAUCAAAGUAAUUUUCAACAUGGAAUGCAUGU----AUCUAUCCAACUCCCUCGCUCCCACGAAGACAAUUGGGGUGUGUUGAUAAGGAGCAAUGCUCCUUCCACCU
..(((((...........(((((.....)))))----................(((.(((.(((......)))))).))))))))(((((((...)))))))...... ( -23.60)
>DroSim_CAF1 6998 104 + 1
AAAUCAAAGUAAUUUCCAACGUGGAAUGCAUGU----AUCUAUCCAACUCCCUCGCUCCCACGAAGACAAUUGGGGUGUGUUGAUAAGGAGCAAUGCUCCUUCCACCU
....................((((((.((((((----.(((...((((.....(((.((((..........))))))).))))...))).)).))))...)))))).. ( -24.30)
>DroEre_CAF1 6694 104 + 1
AAAUCAAAGUAAUUUCCACCGUGGAAUGCAUGU----AUCUAUCCCACUCCCUCGCUCCCAUUAAGACAAUUAGGGUGUGUUGAUAAGGAGCAAUGCUCCUUCCACCU
....................((((((.......----...((((.(((.((((...................)))).)))..)))).(((((...))))))))))).. ( -23.61)
>DroYak_CAF1 6775 104 + 1
AAAUCAAAGUAACUUCCACCGUGGAAUGCAUGU----AUCUAUCUUACUCCCUCGCUCCCAUGGACACAAUUAGGGUGUGUUGAUAAGGAGCAAUGCUCCUUCCACCU
....................((((((.((((((----(.......)))......(((((.((.((((((.......)))))).))..))))).))))...)))))).. ( -27.60)
>consensus
AAAUCAAAGUAAUUUCCAACGUGGAAUGCAUGU____AUCUAUCCAACUCCCUCGCUCCCAUGAAGACAAUUGGGGUGUGUUGAUAAGGAGCAAUGCUCCUUCCACCU
..(((((.(((..((((.....)))))))........................(((.(((.(((......)))))).))))))))(((((((...)))))))...... (-23.02 = -21.86 +  -1.16)

alignment

secondary structure

dotplot

Window 5

Location	3,938,454 – 3,938,562
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	91.38
Mean single sequence MFE	-30.10
Consensus MFE	-25.76
Energy contribution	-25.04
Covariance contribution	-0.72
Combinations/Pair	1.15
Mean z-score	-1.25
Structure conservation index	0.86
SVM decision value	0.06
SVM RNA-class probability	0.565195
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3938454 108 - 27905053
AGGUGGAAGGAGCAUUGCUCCUUAUCAACGCACCCCAAUUGCCUCCAUGGGAGCGAGGGAGUUGGAUAGAUAUGUACAUGUAUUCCACGUUGGAAAUUACUUUGACUU
..(((((((((((...))))).............((((((.(((((......).)))).)))))).................))))))((..((......))..)).. ( -32.60)
>DroSec_CAF1 6545 104 - 1
AGGUGGAAGGAGCAUUGCUCCUUAUCAACACACCCCAAUUGUCUUCGUGGGAGCGAGGGAGUUGGAUAGAU----ACAUGCAUUCCAUGUUGAAAAUUACUUUGAUUC
.((((.(((((((...))))))).......))))((((((.(((((((....)))))))))))))......----(((((.....))))).................. ( -29.60)
>DroSim_CAF1 6998 104 - 1
AGGUGGAAGGAGCAUUGCUCCUUAUCAACACACCCCAAUUGUCUUCGUGGGAGCGAGGGAGUUGGAUAGAU----ACAUGCAUUCCACGUUGGAAAUUACUUUGAUUU
.((((.(((((((...))))))).......))))((((((.(((((((....)))))))))))))......----.......((((.....))))............. ( -30.60)
>DroEre_CAF1 6694 104 - 1
AGGUGGAAGGAGCAUUGCUCCUUAUCAACACACCCUAAUUGUCUUAAUGGGAGCGAGGGAGUGGGAUAGAU----ACAUGCAUUCCACGGUGGAAAUUACUUUGAUUU
..(((((((((((...)))))(((((..(((.((((..((.((.....)).))..)))).))).)))))..----.......)))))).................... ( -29.60)
>DroYak_CAF1 6775 104 - 1
AGGUGGAAGGAGCAUUGCUCCUUAUCAACACACCCUAAUUGUGUCCAUGGGAGCGAGGGAGUAAGAUAGAU----ACAUGCAUUCCACGGUGGAAGUUACUUUGAUUU
..((((((...(((((((((((.....(((((.......)))))....))))))))....(((.......)----)).))).))))))(((.((((...)))).))). ( -28.10)
>consensus
AGGUGGAAGGAGCAUUGCUCCUUAUCAACACACCCCAAUUGUCUUCAUGGGAGCGAGGGAGUUGGAUAGAU____ACAUGCAUUCCACGUUGGAAAUUACUUUGAUUU
..(((((((((((...)))))(((((...((.(((...((((..(....)..))))))).))..))))).............)))))).................... (-25.76 = -25.04 +  -0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:04 2006