Locus 3060

Sequence ID	3L_DroMel_CAF1
Location	8,844,972 – 8,845,103
Length	131
Max. P	0.936041

overview

Window 3

Location	8,844,972 – 8,845,082
Length	110
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	81.25
Mean single sequence MFE	-32.82
Consensus MFE	-21.95
Energy contribution	-22.48
Covariance contribution	0.53
Combinations/Pair	1.24
Mean z-score	-1.47
Structure conservation index	0.67
SVM decision value	0.09
SVM RNA-class probability	0.578755
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8844972 110 + 23771897
GCCAUGGGGAAUACGCCUCGCUACUGCCGUUUUCGAUGGCUUUCAUUUGCUGGGCGCCCAGUUGUAUAAUUUGCAAUUGUUUGUUGUUGGCUUGCCCUGCGAAUGG-GAAU
(((((.(..(((..((.........)).)))..).)))))(..(((((((.(((((((((((((((.....)))))))).........)))..)))).))))))).-.).. ( -41.60)
>DroSec_CAF1 105198 100 + 1
GCCAUGGGGAAUAUGCCUCGAUACAGCCGUUUUCGAUGGCUUUCAUUUGCUGGGCGCCCAGUUGUAUAAUUUGCAAUUGUUUCUUGUU-GCUGGCCCUGCG----------
(((((((((......)))))(((((((((((...))))))........(((((....)))))))))).....(((((........)))-))))))......---------- ( -30.10)
>DroSim_CAF1 105971 100 + 1
GCCAUGGGGAAUAUGCCUCGAUACAGCCGUUUUCGAUGGCUUUCAUUUGCUGGGCGCCCAGUUGUAUAAUUUGCAAUUGUUUGUUGUU-GCUGGCCCUGCG----------
(((((.(..(((..((.........)).)))..).)))))........((.((((...((((...(((((..((....))..))))).-)))))))).)).---------- ( -30.70)
>DroEre_CAF1 109217 103 + 1
GCCAUGGGGAAU--GCCUCGAUACUGCGUAUUUCGAUGGCUUUCAUUUGCUGGGCGCCCAGUUGUAUAAUUUGCAAUGGCUUGUUGUU-GCUGGCCCUGUG-----UGAAU
(((((.(..(((--((.........)))).)..).))))).(((((..((.((((...((((...(((((..((....))..))))).-)))))))).)))-----)))). ( -33.10)
>DroWil_CAF1 137860 104 + 1
GCAAUUGCACAAAUGGAUUGAACUUUCCCAGUUUACUGGCUCUCAUUUGCUGGGCGCCGAGUUGUAUAAUUUGCAAUUGUUUGUUGUU-GUUGCCCCUGCUGGU------U
(((((.((((((((((((((........))))))..((((.((((.....)))).))))(((((((.....)))))))))))).))).-))))).((....)).------. ( -26.90)
>DroYak_CAF1 108193 108 + 1
GCCAUGGGGAAU--GCCUCGAUACUACGCUCUUCGAUGGCUUUCAUUUGCUGGGCGCCCAGUUGUAUAAUUUGCAAUUGCUUGUUGUU-GCUGGCCCUGUGAAUGGUGAAU
((((((((((..--((...........))))))).)))))..(((((..(.((((...((((...(((((..((....))..))))).-)))))))).)..)))))..... ( -34.50)
>consensus
GCCAUGGGGAAUAUGCCUCGAUACUGCCGUUUUCGAUGGCUUUCAUUUGCUGGGCGCCCAGUUGUAUAAUUUGCAAUUGUUUGUUGUU_GCUGGCCCUGCG_________U
(((((.(((((...((.........))..))))).)))))........((.((((...((((...(((((..((....))..)))))..)))))))).))........... (-21.95 = -22.48 +   0.53)

alignment

secondary structure

dotplot

Window 4

Location	8,845,007 – 8,845,103
Length	96
Sequences	4
Columns	97
Reading direction	forward
Mean pairwise identity	74.69
Mean single sequence MFE	-29.30
Consensus MFE	-16.34
Energy contribution	-17.22
Covariance contribution	0.88
Combinations/Pair	1.25
Mean z-score	-2.16
Structure conservation index	0.56
SVM decision value	1.25
SVM RNA-class probability	0.936041
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8845007 96 + 23771897
AUGGCUUUCAUUUGCUGGGCGCCCAGUUGUAUAAUUUGCAAUUGUUUGUUGUUGGCUUGCCCUGCGAAUGG-GAAUGCGAAUGUGUUGCUGCCCGGC
..((((..(((((((.(((((((((((((((.....)))))))).........)))..)))).))))))).-.)..((((.....)))).))).... ( -35.00)
>DroGri_CAF1 108619 83 + 1
CUGUCGUUCGUUUGCUGUGCGCCCAGUUGUAUAAUUUGCAAUUGUUUGUUGUU-AUUGCCGAGGCA--------A-----UGUUGUUGCUCAUCAGC
.............((((((.((.((((((((.....))))))))........(-(((((....)))--------)-----)).....)).)).)))) ( -20.80)
>DroEre_CAF1 109250 80 + 1
AUGGCUUUCAUUUGCUGGGCGCCCAGUUGUAUAAUUUGCAAUGGCUUGUUGUU-GCUGGCCCUGUG-----UGAAU-----------GGUGCCCAGC
.............((((((((((..((((((.....))))))((((.((....-)).)))).....-----.....-----------)))))))))) ( -31.10)
>DroYak_CAF1 108226 96 + 1
AUGGCUUUCAUUUGCUGGGCGCCCAGUUGUAUAAUUUGCAAUUGCUUGUUGUU-GCUGGCCCUGUGAAUGGUGAAUGCGAAUGUGUUGCUGCCCAGC
..(((..(((((..(.((((...((((...(((((..((....))..))))).-)))))))).)..))))).....((((.....)))).))).... ( -30.30)
>consensus
AUGGCUUUCAUUUGCUGGGCGCCCAGUUGUAUAAUUUGCAAUUGCUUGUUGUU_GCUGGCCCUGCG______GAAU____AUGUGUUGCUGCCCAGC
.............((((((((.(((((...(((((..((....))..)))))..)))))....((((..................)))))))))))) (-16.34 = -17.22 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:34 2006