Locus 4942

Sequence ID	3L_DroMel_CAF1
Location	13,699,323 – 13,699,465
Length	142
Max. P	0.757949

overview

Window 3

Location	13,699,323 – 13,699,432
Length	109
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	88.25
Mean single sequence MFE	-27.78
Consensus MFE	-20.23
Energy contribution	-20.04
Covariance contribution	-0.19
Combinations/Pair	1.07
Mean z-score	-1.63
Structure conservation index	0.73
SVM decision value	0.18
SVM RNA-class probability	0.620410
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13699323 109 - 23771897
CCAACCAGGAUGUAGCCAAUACAUCUCUUUGUCUUGGCCUUAUCACCAGCAAUAUUCUGUUAAUACCUGUCCAUUGU---------UCGGUACACUCCUGCAGGGCACAAGUUAUUGG
((...((((((((.(((((.(((......))).)))))......(((((((((...(.((....))..)...)))))---------).)))))).)))))...))..(((....))). ( -25.00)
>DroSec_CAF1 106685 109 - 1
CCGCCCAGGAUGUAGCCAAUACAUCUCUUUGUCUUGGCCUUAUCACCAGCAAUAUUCUGUUAAUACCUGUCCAUUGU---------UCGGUACACUCCUGCAGGGCACAAGUUAUUGA
..((((..((((..(((((.(((......))).)))))..))))(((((((((...(.((....))..)...)))))---------).)))...........)))).(((....))). ( -28.40)
>DroEre_CAF1 112747 109 - 1
CCUCCCAGGAUGUAGCCAAUACAUCUCUUUGUCUUGGCCCUAUCACCAGCAAUAUUCUGUUAGUACCUGUCCAUUGU---------UCGGUAUAUUCCUGCAGGACACCAGUUAUUGA
........((((..(((((.(((......))).)))))..)))).....(((((..(((...((.(((((....(((---------.....))).....)))))))..))).))))). ( -24.00)
>DroYak_CAF1 115892 118 - 1
UCGCCCAGGAUGUAGCCAAUACAUCUCUUUGUCUUGGCCCUAUCACCAGCAAUAUGCUGUUGGCACCUGCCCUUUGUACAGUUGUUUCGGUAUAUUCCUGCAGGACACAAGUUAUUGG
..(((...((((..(((((.(((......))).)))))..))))..((((.....))))..))).(((((....(((((.(......).))))).....)))))...(((....))). ( -33.70)
>consensus
CCGCCCAGGAUGUAGCCAAUACAUCUCUUUGUCUUGGCCCUAUCACCAGCAAUAUUCUGUUAAUACCUGUCCAUUGU_________UCGGUACACUCCUGCAGGACACAAGUUAUUGA
........((((..(((((.(((......))).)))))..)))).....(((((...(((.....(((((....(((..............))).....)))))..)))...))))). (-20.23 = -20.04 +  -0.19)

alignment

secondary structure

dotplot

Window 4

Location	13,699,355 – 13,699,465
Length	110
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	88.01
Mean single sequence MFE	-32.28
Consensus MFE	-23.67
Energy contribution	-23.68
Covariance contribution	0.00
Combinations/Pair	1.10
Mean z-score	-1.89
Structure conservation index	0.73
SVM decision value	0.49
SVM RNA-class probability	0.757949
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13699355 110 - 23771897
GAAAGGGAACUCUAUAGAUG-----GGGAUAAAGCCAUCCAACCAGGAUGUAGCCAAUACAUCUCUUUGUCUUGGCCUUAUCACCAGCAAUAUUCUGUUAAUACCUGUCCAUUGU---
((.(((.(((...(((..((-----(.(((((.((((..(((...(((((((.....)))))))..)))...)))).))))).)))....)))...)))....))).))......--- ( -29.20)
>DroSec_CAF1 106717 110 - 1
GAACGGGAACUCUAUAGAUG-----GGGGUAAAGCCAUCCGCCCAGGAUGUAGCCAAUACAUCUCUUUGUCUUGGCCUUAUCACCAGCAAUAUUCUGUUAAUACCUGUCCAUUGU---
(.(((((......(((((.(-----((((.....)).)))((....((((..(((((.(((......))).)))))..))))....)).....))))).....))))).).....--- ( -29.70)
>DroEre_CAF1 112779 115 - 1
GAAUGGGAACUCUAUAGCCGGGCGGGGGGUAAAUCCAUCCUCCCAGGAUGUAGCCAAUACAUCUCUUUGUCUUGGCCCUAUCACCAGCAAUAUUCUGUUAGUACCUGUCCAUUGU---
(.(((((.(((..((((....((((((((.........))))))..((((..(((((.(((......))).)))))..))))....))......)))).))).))))).).....--- ( -33.50)
>DroYak_CAF1 115930 113 - 1
GAAUGGGCACUCCAUAGAUG-----GGGGUAAAUCCAUUCGCCCAGGAUGUAGCCAAUACAUCUCUUUGUCUUGGCCCUAUCACCAGCAAUAUGCUGUUGGCACCUGCCCUUUGUACA
....(((((..(((..((((-----((........(((((.....)))))..(((((.(((......))).)))))))))))..((((.....)))).)))....)))))........ ( -36.70)
>consensus
GAAUGGGAACUCUAUAGAUG_____GGGGUAAAGCCAUCCGCCCAGGAUGUAGCCAAUACAUCUCUUUGUCUUGGCCCUAUCACCAGCAAUAUUCUGUUAAUACCUGUCCAUUGU___
(.(((((..................((((((....(((((.....)))))..(((((.(((......))).)))))..)))).))((((......))))....))))).)........ (-23.67 = -23.68 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:35 2006