Locus 2109

Sequence ID	3L_DroMel_CAF1
Location	5,781,308 – 5,781,406
Length	98
Max. P	0.844983

overview

Window 3

Location	5,781,308 – 5,781,406
Length	98
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	79.97
Mean single sequence MFE	-27.64
Consensus MFE	-16.99
Energy contribution	-18.55
Covariance contribution	1.56
Combinations/Pair	1.06
Mean z-score	-2.09
Structure conservation index	0.61
SVM decision value	0.76
SVM RNA-class probability	0.843127
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5781308 98 + 23771897
UGGGAAAGGAGCAGCCCACGUGCUAUAAAUAAAUCCCAU-GGCGUGCACGCGCCAAUUGUCACCUCCAUUCCGGUCCGUGCA--GCUCCUCCCUCCCCC------------AU
.((((.(((((((((......)))..............(-(((((....))))))..((.(((..((.....))...)))))--))))))...))))..------------.. ( -31.30)
>DroPse_CAF1 12932 86 + 1
UGGGAAAGGAGCAGCCCACGUGCUAUAAAUAAAUCCCAUCGGGCUGCACGCGCCAAUCGUCACCUCCACUUA--------------UCCCCCCUCC-CU------------AA
.((((..((.(((((((..(((..((......))..))).)))))))..(((.....)))............--------------...))..)))-).------------.. ( -22.80)
>DroSec_CAF1 6921 97 + 1
UGGGAAAGGAGCAGACCACGUGCUAUAAAUAAAUCCCAU-GGCGUGCACGCGCCAAUCGUCACCUCCAUUCAGGUCCGUGCA--GCUCCUCCCUCC-CC------------AU
.((((.((((((....((((..................(-(((((....))))))......((((......)))).))))..--))))))...)))-).------------.. ( -31.10)
>DroSim_CAF1 7381 97 + 1
UGGGAAAGGAGCAGCCCACGUGCUAUAAAUAAAUCCCAU-GGCGUGCACGCGCCAAUCGUCACCUCCAUUCCGGUCCGUGCA--GCUCCUCCCUCC-CC------------AU
.((((.((((((.........(((((...........))-))).((((((.(((..................))).))))))--))))))...)))-).------------.. ( -31.07)
>DroEre_CAF1 13485 109 + 1
UGGGAAAGGAGCAGCCCACGUGCUAUAAAUAAAUCCCAU-GGCGUGCACGCGCCAAUCAUCACCUCCAUUCUGGUCCGAGCA--GCUCCUCCCUCC-CCCUCCGCGUCCCCUU
.((((.((((((.((.(.....................(-(((((....))))))......(((........)))..).)).--))))))...)))-)............... ( -30.10)
>DroAna_CAF1 12649 106 + 1
UGGGAAAGGAGCAGCCCACAUGCUAUAAAUAAAUGCCAU-GGCCUGCACGCGCCAAUCGUCACCUCUCCUACCACUAGUCCACCAUUCCACCAUCC-CACC---AGUCU--AC
(((((.(((.((((.(((...((...........))..)-)).))))..(((.....)))..))).))))).........................-....---.....--.. ( -19.50)
>consensus
UGGGAAAGGAGCAGCCCACGUGCUAUAAAUAAAUCCCAU_GGCGUGCACGCGCCAAUCGUCACCUCCAUUCCGGUCCGUGCA__GCUCCUCCCUCC_CC____________AU
.((((..((((((((......)))................(((((....)))))..............................))))))))).................... (-16.99 = -18.55 +   1.56)

alignment

secondary structure

dotplot

Window 4

Location	5,781,308 – 5,781,406
Length	98
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	79.97
Mean single sequence MFE	-39.00
Consensus MFE	-23.25
Energy contribution	-24.12
Covariance contribution	0.86
Combinations/Pair	1.19
Mean z-score	-2.18
Structure conservation index	0.60
SVM decision value	0.77
SVM RNA-class probability	0.844983
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5781308 98 - 23771897
AU------------GGGGGAGGGAGGAGC--UGCACGGACCGGAAUGGAGGUGACAAUUGGCGCGUGCACGCC-AUGGGAUUUAUUUAUAGCACGUGGGCUGCUCCUUUCCCA
..------------.((((((((((.(((--(.((((..(..((((((((....)...(((((......))))-).....)))))))...)..)))))))).)))))))))). ( -44.50)
>DroPse_CAF1 12932 86 - 1
UU------------AG-GGAGGGGGGA--------------UAAGUGGAGGUGACGAUUGGCGCGUGCAGCCCGAUGGGAUUUAUUUAUAGCACGUGGGCUGCUCCUUUCCCA
..------------.(-(((((((((.--------------..(((...(....)......(((((((..(((...)))((......)).))))))).))).)))))))))). ( -34.20)
>DroSec_CAF1 6921 97 - 1
AU------------GG-GGAGGGAGGAGC--UGCACGGACCUGAAUGGAGGUGACGAUUGGCGCGUGCACGCC-AUGGGAUUUAUUUAUAGCACGUGGUCUGCUCCUUUCCCA
.(------------((-((((((((.((.--..(((((...(((((((((....)...(((((......))))-).....))))))))...).))))..)).))))))))))) ( -39.20)
>DroSim_CAF1 7381 97 - 1
AU------------GG-GGAGGGAGGAGC--UGCACGGACCGGAAUGGAGGUGACGAUUGGCGCGUGCACGCC-AUGGGAUUUAUUUAUAGCACGUGGGCUGCUCCUUUCCCA
.(------------((-((((((((.(((--(.((((..(..((((((((....)...(((((......))))-).....)))))))...)..)))))))).))))))))))) ( -44.70)
>DroEre_CAF1 13485 109 - 1
AAGGGGACGCGGAGGG-GGAGGGAGGAGC--UGCUCGGACCAGAAUGGAGGUGAUGAUUGGCGCGUGCACGCC-AUGGGAUUUAUUUAUAGCACGUGGGCUGCUCCUUUCCCA
..(....)......((-((((((((.(((--(..(((.(((........)))..)))....(((((((.....-................))))))))))).)))))))))). ( -40.70)
>DroAna_CAF1 12649 106 - 1
GU--AGACU---GGUG-GGAUGGUGGAAUGGUGGACUAGUGGUAGGAGAGGUGACGAUUGGCGCGUGCAGGCC-AUGGCAUUUAUUUAUAGCAUGUGGGCUGCUCCUUUCCCA
..--.....---..((-(((....(((...........(((.(((....(....)..))).)))..((((.((-(((((...........)).))))).)))))))..))))) ( -30.70)
>consensus
AU____________GG_GGAGGGAGGAGC__UGCACGGACCGGAAUGGAGGUGACGAUUGGCGCGUGCACGCC_AUGGGAUUUAUUUAUAGCACGUGGGCUGCUCCUUUCCCA
..............((.((((((((.(((....................(....)......(((((((......................))))))).))).)))))))))). (-23.25 = -24.12 +   0.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:36 2006