Locus 3065

Sequence ID	3L_DroMel_CAF1
Location	8,852,864 – 8,853,005
Length	141
Max. P	0.695154

overview

Window 1

Location	8,852,864 – 8,852,967
Length	103
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	80.44
Mean single sequence MFE	-30.83
Consensus MFE	-21.10
Energy contribution	-21.97
Covariance contribution	0.87
Combinations/Pair	1.19
Mean z-score	-1.73
Structure conservation index	0.68
SVM decision value	0.34
SVM RNA-class probability	0.695154
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8852864 103 + 23771897
CCGUAACUGAUAGUUAAAGGGUAACUUGACUGUCGCUGAUAACGCGUUU-------CUUGUUUGGGCCAAAAACUUGUGUCCCAAAUGGUGUACUCUUGUGCUUAUCGGC
........(((((((((.(.....))))))))))((((((((.......-------.(..((((((((((....))).).))))))..).((((....)))))))))))) ( -31.00)
>DroSec_CAF1 112899 102 + 1
CCGUAACUGAUAGUUAAAGGGUAACUUGUCUGUCGCUGAUAACGCGUUU-------CUUGUUUGGGCCAAAAAAUUCU-UCCCAAAUGGUGUACUCUUAUGCUUAUCGGC
........(((((...(((.....)))..)))))((((((((.((((..-------((..((((((............-.))))))..).).......)))))))))))) ( -25.42)
>DroEre_CAF1 116697 110 + 1
CUGCAACUGAUAGUUAGCGGGUAAAUAGUCUGUGGCUGAUAACGGGUAACGGGUUCCUUGUUUGGGCCAAAAACUUCGGGCCCAAAUGGCGCACUCUUGUGCUUAUCGGC
(((((((.....))).))))..............((((((((.(((........)))(..((((((((..........))))))))..).((((....)))))))))))) ( -35.50)
>DroYak_CAF1 115920 97 + 1
------CUGAUAGUUAAUGGCUAUCUUGUCUGCUACUGAUAACAAGGAA-------CUUGUUUGGGCCAAAAACUUCUGGCCCAAAUGGCAUACUCUUGUGCUUAUCGGC
------..((((((.....))))))..........((((((((((((..-------.(..(((((((((........)))))))))..).....))))))...)))))). ( -31.40)
>consensus
CCGUAACUGAUAGUUAAAGGGUAACUUGUCUGUCGCUGAUAACGCGUAA_______CUUGUUUGGGCCAAAAACUUCUGGCCCAAAUGGCGUACUCUUGUGCUUAUCGGC
........(((((.(((........))).)))))(((((((..................((((((((((........))))))))))((((((....))))))))))))) (-21.10 = -21.97 +   0.87)

alignment

secondary structure

dotplot

Window 2

Location	8,852,894 – 8,853,005
Length	111
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	85.15
Mean single sequence MFE	-33.77
Consensus MFE	-25.27
Energy contribution	-26.40
Covariance contribution	1.13
Combinations/Pair	1.03
Mean z-score	-1.46
Structure conservation index	0.75
SVM decision value	0.04
SVM RNA-class probability	0.551727
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8852894 111 - 23771897
GGUGCAAGUAAAGGAAACGCGUGCCAUAGCAACGUCGCGCCGAUAAGCACAAGAGUACACCAUUUGGGACACAAGUUUUUGGCCCAAACAAG-------AAACGCGUUAUCAGCGACA
(((((.......(....)((((((....)).)))).)))))(((((((((....))......((((((...(((....))).))))))....-------....)).)))))....... ( -28.40)
>DroSec_CAF1 112929 110 - 1
GGUGCAAGUAAAGGAAACGCGUGCCAUCGCAACGUCGCGCCGAUAAGCAUAAGAGUACACCAUUUGGGA-AGAAUUUUUUGGCCCAAACAAG-------AAACGCGUUAUCAGCGACA
(((((.......(....)((((((....)).)))).)))))(((((((....(.(....)).((((((.-.((.....))..))))))....-------....)).)))))....... ( -27.00)
>DroEre_CAF1 116727 118 - 1
GGUGCAAGUAAAGGAAACGCGUGCCAUCGCAACGACGCGCCGAUAAGCACAAGAGUGCGCCAUUUGGGCCCGAAGUUUUUGGCCCAAACAAGGAACCCGUUACCCGUUAUCAGCCACA
(((((.......(....)(((......)))......)))))(((((((((....)))).((.((((((((.((....)).))))))))...)).............)))))....... ( -37.70)
>DroYak_CAF1 115944 111 - 1
GCUGCAAGUGGAGGAAACGCGUGGCAUCUCAACGACGCGCCGAUAAGCACAAGAGUAUGCCAUUUGGGCCAGAAGUUUUUGGCCCAAACAAG-------UUCCUUGUUAUCAGUAGCA
(((((..(((((((((....((((((((((......((........))....))).)))))))((((((((((....)))))))))).....-------))))))..)))..))))). ( -42.00)
>consensus
GGUGCAAGUAAAGGAAACGCGUGCCAUCGCAACGACGCGCCGAUAAGCACAAGAGUACACCAUUUGGGACAGAAGUUUUUGGCCCAAACAAG_______AAACGCGUUAUCAGCGACA
(((((.......(....)((((((....)).))).))))))(((((((......))......(((((((((((....)))))))))))..................)))))....... (-25.27 = -26.40 +   1.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:41 2006