Locus 4047

Sequence ID	3R_DroMel_CAF1
Location	11,040,659 – 11,040,819
Length	160
Max. P	0.938209

overview

Window 0

Location	11,040,659 – 11,040,779
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.56
Mean single sequence MFE	-44.13
Consensus MFE	-42.59
Energy contribution	-42.60
Covariance contribution	0.01
Combinations/Pair	1.08
Mean z-score	-1.63
Structure conservation index	0.97
SVM decision value	0.33
SVM RNA-class probability	0.691314
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11040659 120 + 27905053
AGGGAUGCACCUUGGAGUGGCCAUCGGUUUUACUUUUGCCACCGGCAGUAUACUUGGAUAAUCGAAUGCUGGGCAUUGGUAGAAAGCCGGUGCUCAGCGGCAUUACAUCCAGCGAUAUGG
..((((((((......)))(((.((((((...(..(((((...))))).......)...))))))..(((((((((((((.....))))))))))))))))....))))).......... ( -44.30)
>DroSec_CAF1 3411 120 + 1
AGGGAUGCACCUUGGAGUGGCCAUCGGUCUUACUUUUGCCACCGGCAGUGUAUUUGGACAAUCGAAUGCUGGGCAUUGGCAGAAAGCCGGUACUCAGCGGCAUUACAUCCAGCGAUAUGG
..((((((((......)))(((.((((((((((..(((((...))))).)))...))))...)))..((((((.((((((.....)))))).)))))))))....))))).......... ( -41.70)
>DroSim_CAF1 3418 120 + 1
AGGGAUGCACCUUGGAGUGGCCAUCGGUCUUACUUUUGCCACCGGCUGUGUAUUUGGACAAUCGAAUGCUGGGCAUUGGCAGAAAGCCGGUGCUCAGCGGCAUCACAUCCAGCGAUAUGG
(((......)))((((((((((.((((((((((....(((...)))...)))...))))...)))..(((((((((((((.....))))))))))))))))..))).))))......... ( -46.40)
>consensus
AGGGAUGCACCUUGGAGUGGCCAUCGGUCUUACUUUUGCCACCGGCAGUGUAUUUGGACAAUCGAAUGCUGGGCAUUGGCAGAAAGCCGGUGCUCAGCGGCAUUACAUCCAGCGAUAUGG
..((((((((......)))(((.(((((((.....(((((...))))).......))))...)))..(((((((((((((.....))))))))))))))))....))))).......... (-42.59 = -42.60 +   0.01)

alignment

secondary structure

dotplot

Window 1

Location	11,040,699 – 11,040,819
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.11
Mean single sequence MFE	-42.00
Consensus MFE	-39.60
Energy contribution	-39.49
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-2.40
Structure conservation index	0.94
SVM decision value	1.29
SVM RNA-class probability	0.938209
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11040699 120 + 27905053
ACCGGCAGUAUACUUGGAUAAUCGAAUGCUGGGCAUUGGUAGAAAGCCGGUGCUCAGCGGCAUUACAUCCAGCGAUAUGGAAUGACUGUCGACGUCCUUCAUGGAUACGACACCUAAAAG
..(((((((.................((((((((((((((.....))))))))))))))......((((((......))).))))))))))..((((.....)))).............. ( -41.40)
>DroSec_CAF1 3451 120 + 1
ACCGGCAGUGUAUUUGGACAAUCGAAUGCUGGGCAUUGGCAGAAAGCCGGUACUCAGCGGCAUUACAUCCAGCGAUAUGGAAUGACUGUCGACGUCCUUCAUGGAUACGACACCUAAAAG
..((((((((((((((......)))))((((((.((((((.....)))))).)))))).))....((((((......))).))))))))))..((((.....)))).............. ( -37.50)
>DroSim_CAF1 3458 120 + 1
ACCGGCUGUGUAUUUGGACAAUCGAAUGCUGGGCAUUGGCAGAAAGCCGGUGCUCAGCGGCAUCACAUCCAGCGAUAUGGAAUGACUGUCGACGUCCUUCAUGGAUACGACACCUAAAAG
...((.(((((((((((((........(((((((((((((.....)))))))))))))(((((((..((((......)))).))).))))...)))).....)))))).)))))...... ( -47.10)
>consensus
ACCGGCAGUGUAUUUGGACAAUCGAAUGCUGGGCAUUGGCAGAAAGCCGGUGCUCAGCGGCAUUACAUCCAGCGAUAUGGAAUGACUGUCGACGUCCUUCAUGGAUACGACACCUAAAAG
...(((..(((..(((((........((((((((((((((.....))))))))))))))........)))))..)))..)......(((((..((((.....)))).)))))))...... (-39.60 = -39.49 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:41 2006