Locus 5439

Sequence ID	3L_DroMel_CAF1
Location	14,902,030 – 14,902,129
Length	99
Max. P	0.759141

overview

Window 6

Location	14,902,030 – 14,902,129
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	90.00
Mean single sequence MFE	-24.48
Consensus MFE	-20.48
Energy contribution	-20.24
Covariance contribution	-0.24
Combinations/Pair	1.12
Mean z-score	-1.41
Structure conservation index	0.84
SVM decision value	0.26
SVM RNA-class probability	0.659612
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14902030 99 + 23771897
CAUAUGCAGCCAGAAAUUUAAUAUCAAAUGGGGCAAUAAUUUUCCUAAUGGAUAUUGGCUUUAUCGCUUUGGGAACUCGGAGCUGCUUUUAAGUUGACC
.....(((((((........(((((...(((((.((....)))))))...)))))))))......(((((((....))))))))))............. ( -20.30)
>DroSec_CAF1 84147 99 + 1
CAUAUGCAGCUAGAAAUUUAAUGUCAAAUGGGCCAAUAAUUUGCCUAAUGGAUAUUGGCUUUAUCGCUUUGGGAACUCGGAGCUGCUUUUAAGUUGACC
......(((((.((((.((((((((...(((((.((....)))))))...)))))))).......(((((((....)))))))...)))).)))))... ( -24.20)
>DroSim_CAF1 80938 99 + 1
CAUAUGCAGCUAGAAAUUUAAUGUCAAAUGGGCCAAUAAUUUGCCUAAUGGAUAUUGGCUUUAUCGCUUUGGGAACUCGGAGCUGCUUUUAAGUUGACC
......(((((.((((.((((((((...(((((.((....)))))))...)))))))).......(((((((....)))))))...)))).)))))... ( -24.20)
>DroEre_CAF1 81766 99 + 1
CAUAUGCAGCCAGAAAUUUAAUGUCAAAUGGGGCAAUAAUUUGCCUAAUGGAUAUUGGCUUUAUCGCUUUGGGAGCUCGGAGCUGCUUUUGAGUUGAAA
......(((((((((..((((((((.....((((((....))))))....)))))))).......(((((((....)))))))...))))).))))... ( -28.30)
>DroYak_CAF1 76948 87 + 1
CAUAUGCAGCCAGGAAUUUAAUACCAAAUGGGGCAAUAAUUUGCCUAAUGGAUAUUGGCUUUAUCGCUUUGGAAACUCGAAGCUGCU------------
.....((((((((..(((((...((....))(((((....)))))...))))).)))))......(((((((....)))))))))).------------ ( -25.40)
>consensus
CAUAUGCAGCCAGAAAUUUAAUGUCAAAUGGGGCAAUAAUUUGCCUAAUGGAUAUUGGCUUUAUCGCUUUGGGAACUCGGAGCUGCUUUUAAGUUGACC
.....(((((((........(((((...((((.(((....)))))))...)))))))))......(((((((....))))))))))............. (-20.48 = -20.24 +  -0.24)

alignment

secondary structure

dotplot

Window 7

Location	14,902,030 – 14,902,129
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	90.00
Mean single sequence MFE	-20.79
Consensus MFE	-16.36
Energy contribution	-16.76
Covariance contribution	0.40
Combinations/Pair	1.07
Mean z-score	-1.68
Structure conservation index	0.79
SVM decision value	0.50
SVM RNA-class probability	0.759141
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14902030 99 - 23771897
GGUCAACUUAAAAGCAGCUCCGAGUUCCCAAAGCGAUAAAGCCAAUAUCCAUUAGGAAAAUUAUUGCCCCAUUUGAUAUUAAAUUUCUGGCUGCAUAUG
.............((((((..(((((..(((((((((((..(((((....))).))....)))))))....))))......)))))..))))))..... ( -16.60)
>DroSec_CAF1 84147 99 - 1
GGUCAACUUAAAAGCAGCUCCGAGUUCCCAAAGCGAUAAAGCCAAUAUCCAUUAGGCAAAUUAUUGGCCCAUUUGACAUUAAAUUUCUAGCUGCAUAUG
.............((((((..(((((.......(((....(((((((.((....)).....)))))))....)))......)))))..))))))..... ( -21.52)
>DroSim_CAF1 80938 99 - 1
GGUCAACUUAAAAGCAGCUCCGAGUUCCCAAAGCGAUAAAGCCAAUAUCCAUUAGGCAAAUUAUUGGCCCAUUUGACAUUAAAUUUCUAGCUGCAUAUG
.............((((((..(((((.......(((....(((((((.((....)).....)))))))....)))......)))))..))))))..... ( -21.52)
>DroEre_CAF1 81766 99 - 1
UUUCAACUCAAAAGCAGCUCCGAGCUCCCAAAGCGAUAAAGCCAAUAUCCAUUAGGCAAAUUAUUGCCCCAUUUGACAUUAAAUUUCUGGCUGCAUAUG
.............((((((..(((........(((((((.((((((....))).)))...)))))))...(((((....)))))))).))))))..... ( -17.80)
>DroYak_CAF1 76948 87 - 1
------------AGCAGCUUCGAGUUUCCAAAGCGAUAAAGCCAAUAUCCAUUAGGCAAAUUAUUGCCCCAUUUGGUAUUAAAUUCCUGGCUGCAUAUG
------------.((((((..((((((((((((((((((.((((((....))).)))...)))))))....)))))....))))))..))))))..... ( -26.50)
>consensus
GGUCAACUUAAAAGCAGCUCCGAGUUCCCAAAGCGAUAAAGCCAAUAUCCAUUAGGCAAAUUAUUGCCCCAUUUGACAUUAAAUUUCUGGCUGCAUAUG
.............((((((..(((((..(((((((((((.((((((....))).)))...)))))))....))))......)))))..))))))..... (-16.36 = -16.76 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:23 2006