Locus 3416

Sequence ID	2L_DroMel_CAF1
Location	9,885,016 – 9,885,152
Length	136
Max. P	0.995813

overview

Window 6

Location	9,885,016 – 9,885,112
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	88.27
Mean single sequence MFE	-26.19
Consensus MFE	-21.45
Energy contribution	-22.01
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.72
Structure conservation index	0.82
SVM decision value	2.62
SVM RNA-class probability	0.995813
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9885016 96 - 22407834
CCCAGGCUGGCGGAGGGAAAUCCCAGGCGAUUUCCUUCCAUUCCCUUAGUUCCACUCGCUUGCACAUUUUUUCCUUGGCUUGGCUUCUUAUCCUUC
.((((((..(.(((((((((((......)))))))))))..................(....)...........)..))))))............. ( -26.90)
>DroSec_CAF1 92934 96 - 1
CCCAGGCUGGCGGAGGGAAAUCCCAGGCGAUUUCCUUCCAUUCCCUUAGUUCCACUUGCUUGCGCAUUUUUUCCUUGGCUUGGCUUUUUAUCCUUC
.((((((..(.(((((((((((......))))))))))).................(((....)))........)..))))))............. ( -29.70)
>DroSim_CAF1 99788 96 - 1
CCCAGGCUGGCGGAGGGAAAUCCCAGGCGAUUUCCUUCCAUUCCCUUAGUUCCACUCGCUUGCGCAUUUUUUCCUUGGCUUGGCUUUUUAUCCUUC
.((((((..(.(((((((((((......)))))))))))..................((....)).........)..))))))............. ( -29.30)
>DroEre_CAF1 97841 91 - 1
CCCAGGCUGGCAGAGGGAAAUCCCAGGCGAUUUCCUUCUUUUCCUUCAGUUCCACUCGCUUGCCCAUUUUU-----GGCUUGGCUUUUUAUUCUGC
.(((((((((((((((((((((......)))))))))).........(((.......))))))).......-----)))))))............. ( -25.61)
>DroYak_CAF1 98940 91 - 1
CCCAGGCUGGCUGCGGGAAAUCCCAGGCGAUUUCCUCCUCUUCCUUUAGUUCCACUCGCUUGCACAUUUUU-----UGCUUGUCUUUCCAUUCUGC
....((..(((.(((((((((..(((((((.........((......))......)))))))...))))))-----)))..)))...))....... ( -19.46)
>consensus
CCCAGGCUGGCGGAGGGAAAUCCCAGGCGAUUUCCUUCCAUUCCCUUAGUUCCACUCGCUUGCACAUUUUUUCCUUGGCUUGGCUUUUUAUCCUUC
.(((((((((((((((((((((......)))))))))))........((.....)).)))................)))))))............. (-21.45 = -22.01 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	9,885,056 – 9,885,152
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	95.62
Mean single sequence MFE	-24.90
Consensus MFE	-23.58
Energy contribution	-23.94
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-1.06
Structure conservation index	0.95
SVM decision value	0.01
SVM RNA-class probability	0.539187
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9885056 96 - 22407834
GUUGCUUCUAACAGUUAUCUCCACGAAUCGGAGCAAUUUUCCCAGGCUGGCGGAGGGAAAUCCCAGGCGAUUUCCUUCCAUUCCCUUAGUUCCACU
((((....)))).................(((((.......((.....)).(((((((((((......))))))))))).........)))))... ( -25.60)
>DroSec_CAF1 92974 96 - 1
GUUGCUUCUGACAGUUAUCUCCACGAAUCGGAGCAAUUUUCCCAGGCUGGCGGAGGGAAAUCCCAGGCGAUUUCCUUCCAUUCCCUUAGUUCCACU
(((((((..((.((((..((((.......)))).)))).))..)))).)))(((((((((((......)))))))))))................. ( -27.20)
>DroSim_CAF1 99828 96 - 1
GUUGCUUCUGACAGUUAUCUCCACGAAUCGGAGCAAUUUUCCCAGGCUGGCGGAGGGAAAUCCCAGGCGAUUUCCUUCCAUUCCCUUAGUUCCACU
(((((((..((.((((..((((.......)))).)))).))..)))).)))(((((((((((......)))))))))))................. ( -27.20)
>DroEre_CAF1 97876 96 - 1
GUUGCUUCUGACAGUUAUCUCCACGAAUCGGAGCAAUUUUCCCAGGCUGGCAGAGGGAAAUCCCAGGCGAUUUCCUUCUUUUCCUUCAGUUCCACU
((((((.((((..((.......))...)))))))))).......((((((.(((((((((((......)))))))))))......))))))..... ( -24.70)
>DroYak_CAF1 98975 96 - 1
GUUGCUUCUGACAGUUAUCUCCACGAAUCGGAGCAAUUUUCCCAGGCUGGCUGCGGGAAAUCCCAGGCGAUUUCCUCCUCUUCCUUUAGUUCCACU
((((((.((((..((.......))...))))))))))......(((..((..(.((((((((......)))))))).).)).)))........... ( -19.80)
>consensus
GUUGCUUCUGACAGUUAUCUCCACGAAUCGGAGCAAUUUUCCCAGGCUGGCGGAGGGAAAUCCCAGGCGAUUUCCUUCCAUUCCCUUAGUUCCACU
(((((((..((.((((..((((.......)))).)))).))..)))).)))(((((((((((......)))))))))))................. (-23.58 = -23.94 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:57 2006