Locus 2877

Sequence ID	3L_DroMel_CAF1
Location	8,218,616 – 8,218,708
Length	92
Max. P	0.997916

overview

Window 2

Location	8,218,616 – 8,218,708
Length	92
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	76.99
Mean single sequence MFE	-38.30
Consensus MFE	-23.74
Energy contribution	-25.02
Covariance contribution	1.28
Combinations/Pair	1.08
Mean z-score	-2.79
Structure conservation index	0.62
SVM decision value	2.96
SVM RNA-class probability	0.997916
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8218616 92 + 23771897
UUGGGCCCAGCUGGAAAAGCCUGGGAAAUGCCAGGGAAAUCUGGCGGGA-----------CGGGAGGAAAGCCUGGGAAAGAGCCUUUUUCUUUCCUCCUCCU
..((.(((.((..((....(((((......)))))....))..))))).-----------.((((((((((...(((......)))....)))))))))))). ( -39.60)
>DroSec_CAF1 40856 86 + 1
UUGGGCCCAGCUGGAAAAGCCUGGGAAAUGCCAGGCAAAUCUGGCGGGA-----------CGGGGGGAAAACCCGGGAAAGAGCCUUUUUCUUUCCU------
.....(((.((..((...((((((......))))))...))..))))).-----------((((.......))))((((((((.....)))))))).------ ( -39.70)
>DroSim_CAF1 39138 80 + 1
UUGGGCCCAGCUGGAAAAGCCUGGGAAAUGCCAGGGAAAUCUGGCGG-----------------GGGAAAGCCUGGGAAAGAGCCUUUUUCUUUCCU------
..((((((.((..((....(((((......)))))....))..))..-----------------.))...))))(((((((((.....)))))))))------ ( -31.60)
>DroEre_CAF1 44328 90 + 1
UUGGGCCCGGCUGGGAAAGCCUGGGAAAUGCCAGGGAAAUCUGUG-------CAGGGGGGUG------GGGGAUGGGAAAGAGCCUUUUUCUUCCCUCCUCCU
.....(((((((.....)))).)))...(((((((....)))).)-------)).(((((.(------(((((.(..((((...))))..).))))))))))) ( -39.30)
>DroYak_CAF1 42673 103 + 1
UUGGGCCCAGCUGGGAAAGCCUGGGAAAUGCCAGGGAAAUCUGGGGGAAAUCUAGGGGCGAGGGGCGAGGGCCUGGGAAAGAGCCUUUUUCUUCCCUCCUCCU
....((((.(((.....)))(((((...(.(((((....))))).)....))))))))).(((((.(((((...(..((((...))))..)..)))))))))) ( -41.30)
>consensus
UUGGGCCCAGCUGGAAAAGCCUGGGAAAUGCCAGGGAAAUCUGGCGG_A___________CGGGGGGAAAGCCUGGGAAAGAGCCUUUUUCUUUCCUCCUCCU
..((((((((((.....)).)))))...(((((((....))))))).........................)))(((((((((.....)))))))))...... (-23.74 = -25.02 +   1.28)

alignment

secondary structure

dotplot

Window 3

Location	8,218,616 – 8,218,708
Length	92
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	76.99
Mean single sequence MFE	-30.48
Consensus MFE	-21.84
Energy contribution	-21.80
Covariance contribution	-0.04
Combinations/Pair	1.24
Mean z-score	-2.45
Structure conservation index	0.72
SVM decision value	2.49
SVM RNA-class probability	0.994539
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8218616 92 - 23771897
AGGAGGAGGAAAGAAAAAGGCUCUUUCCCAGGCUUUCCUCCCG-----------UCCCGCCAGAUUUCCCUGGCAUUUCCCAGGCUUUUCCAGCUGGGCCCAA
.((((((((((((.....((......))....)))))))))..-----------))).(((((......)))))....(((((.((.....)))))))..... ( -33.90)
>DroSec_CAF1 40856 86 - 1
------AGGAAAGAAAAAGGCUCUUUCCCGGGUUUUCCCCCCG-----------UCCCGCCAGAUUUGCCUGGCAUUUCCCAGGCUUUUCCAGCUGGGCCCAA
------.(((((((.......))))))).(((.......)))(-----------(((.((..((...((((((......))))))...))..)).)))).... ( -32.20)
>DroSim_CAF1 39138 80 - 1
------AGGAAAGAAAAAGGCUCUUUCCCAGGCUUUCCC-----------------CCGCCAGAUUUCCCUGGCAUUUCCCAGGCUUUUCCAGCUGGGCCCAA
------.(((((((.......)))))))..(((......-----------------..(((((......))))).....((((.((.....)))))))))... ( -26.20)
>DroEre_CAF1 44328 90 - 1
AGGAGGAGGGAAGAAAAAGGCUCUUUCCCAUCCCC------CACCCCCCUG-------CACAGAUUUCCCUGGCAUUUCCCAGGCUUUCCCAGCCGGGCCCAA
.((.((((((((((.......)).))))).))).)------)....(((((-------(.(((......)))))).......((((.....)))))))..... ( -29.00)
>DroYak_CAF1 42673 103 - 1
AGGAGGAGGGAAGAAAAAGGCUCUUUCCCAGGCCCUCGCCCCUCGCCCCUAGAUUUCCCCCAGAUUUCCCUGGCAUUUCCCAGGCUUUCCCAGCUGGGCCCAA
..((((.(((((((.......)))))))..(((....)))))))((((...((..((.....))..))(((((......)))))...........)))).... ( -31.10)
>consensus
AGGAGGAGGAAAGAAAAAGGCUCUUUCCCAGGCUUUCCCCCCG___________U_CCGCCAGAUUUCCCUGGCAUUUCCCAGGCUUUUCCAGCUGGGCCCAA
.......(((((((.......)))))))..(((((.......................(((((......)))))........((((.....)))))))))... (-21.84 = -21.80 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:58 2006