Locus 1024

Sequence ID	3R_DroMel_CAF1
Location	3,212,194 – 3,212,323
Length	129
Max. P	0.925973

overview

Window 8

Location	3,212,194 – 3,212,305
Length	111
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	91.25
Mean single sequence MFE	-31.42
Consensus MFE	-24.20
Energy contribution	-24.24
Covariance contribution	0.04
Combinations/Pair	1.15
Mean z-score	-2.23
Structure conservation index	0.77
SVM decision value	1.17
SVM RNA-class probability	0.925973
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3212194 111 - 27905053
AGCCUUCCACAUAAAAUACUGGAAAUUUUUAUGUGUAGCCAGCAAGGUGAAUGGUAUUGAAGGAGUGUUACUUUUAUUACAAAGGAUAAUACUCCUCAGGAUGUCUGGUAG-
.(((((((((((((((..........)))))))))..(((.....)))))).))).((((.((((((((((((((.....))))).)))))))))))))............- ( -29.50)
>DroSec_CAF1 36873 112 - 1
AGCCUUCCGCAUAAAAUACUGGAAAUUUUUAUGUGCAGCCAGCAAGGUGAAUGGUAUUAAAGGAGUGUUACUUUCAUUACAAAGGAUAAUACUCCUCAGGAUGUCCGGAGGU
.(((((((((((((((..........)))))))))..(((.....)))....((((((..((((((((((((((.......)))).))))))))))...)))).)))))))) ( -32.70)
>DroSim_CAF1 38338 112 - 1
AGCCUUCCACAUAAAAUACUGGAAAUUUUUAUGUGCAGCCAGCAAGGUGAAUGGUAUUGAAGGAGUGUUACUUUCAUUACAAAGGAUAAUACUCCUCAGGAUGUCUGGAGGU
.(((((((((((((((..........)))))))))..((((..........)))).((((.(((((((((((((.......)))).))))))))))))).......)))))) ( -31.00)
>DroEre_CAF1 31399 111 - 1
UGCCUUCCACAUAAAAUACUUGAAAUUUUUAUGUGCAGCCAGCAAGGUGAAUGGUAUUGAAGGAGUGUUGGUUUCCUUACAAAGAAAAAUGUU-CUGAGGAUGUCUGGAGGU
.(((((((((((((((..........))))))))).((((((((...(.(((...))).).....))))))))(((((....((((.....))-))))))).....)))))) ( -25.20)
>DroYak_CAF1 21699 112 - 1
UGGCUUCCACAUAAAAUACUUGAAAUUUUUAUGUGCAGCCAGCCAGGUGAAUGGUAUUGAAGGAGUGUUGCUUUCAUUUCGAAGGAUAAUACUCCUCAGGAUGUCUGGAGGU
(((((..(((((((((..........))))))))).))))).((((..(.......((((.((((((((((((((.....))))).)))))))))))))..)..)))).... ( -38.70)
>consensus
AGCCUUCCACAUAAAAUACUGGAAAUUUUUAUGUGCAGCCAGCAAGGUGAAUGGUAUUGAAGGAGUGUUACUUUCAUUACAAAGGAUAAUACUCCUCAGGAUGUCUGGAGGU
...(((((((((((((..........))))))))...(((.....)))....(..(((..((((((((((((((.......)))).))))))))))...)))..).))))). (-24.20 = -24.24 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	3,212,233 – 3,212,323
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	94.89
Mean single sequence MFE	-22.30
Consensus MFE	-17.88
Energy contribution	-17.76
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-1.62
Structure conservation index	0.80
SVM decision value	0.25
SVM RNA-class probability	0.655235
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3212233 90 - 27905053
AGCUAUGCUCGAAUUUAUAGCCUUCCACAUAAAAUACUGGAAAUUUUUAUGUGUAGCCAGCAAGGUGAAUGGUAUUGAAGGAGUGUUACU
((..((((((...((((..(((((((((((((((..........)))))))))..(((.....)))))).)))..)))).))))))..)) ( -19.70)
>DroSec_CAF1 36913 90 - 1
AGCUAUGCUCCAAUUUAUAGCCUUCCGCAUAAAAUACUGGAAAUUUUUAUGUGCAGCCAGCAAGGUGAAUGGUAUUAAAGGAGUGUUACU
((..(((((((..((((..(((((((((((((((..........)))))))))..(((.....)))))).)))..)))))))))))..)) ( -21.30)
>DroSim_CAF1 38378 90 - 1
AGCUAUGCUCGAAUUUAUAGCCUUCCACAUAAAAUACUGGAAAUUUUUAUGUGCAGCCAGCAAGGUGAAUGGUAUUGAAGGAGUGUUACU
((..((((((...((((..(((((((((((((((..........)))))))))..(((.....)))))).)))..)))).))))))..)) ( -19.50)
>DroEre_CAF1 31438 90 - 1
AGCUAUGCUCGAAUUUAUUGCCUUCCACAUAAAAUACUUGAAAUUUUUAUGUGCAGCCAGCAAGGUGAAUGGUAUUGAAGGAGUGUUGGU
.(((((((((...((((.((((((((((((((((..........)))))))))..(((.....)))))).)))).)))).))))).)))) ( -23.00)
>DroYak_CAF1 21739 90 - 1
AGCUAUGCUCGAAUUUAUUGGCUUCCACAUAAAAUACUUGAAAUUUUUAUGUGCAGCCAGCCAGGUGAAUGGUAUUGAAGGAGUGUUGCU
(((.((((((........(((((..(((((((((..........))))))))).)))))((((......)))).......)))))).))) ( -28.00)
>consensus
AGCUAUGCUCGAAUUUAUAGCCUUCCACAUAAAAUACUGGAAAUUUUUAUGUGCAGCCAGCAAGGUGAAUGGUAUUGAAGGAGUGUUACU
....((((((...((((..(((((((((((((((..........)))))))))..(((.....)))))).)))..)))).)))))).... (-17.88 = -17.76 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:39 2006