Locus 4116

Sequence ID	3L_DroMel_CAF1
Location	12,010,682 – 12,010,809
Length	127
Max. P	0.918979

overview

Window 1

Location	12,010,682 – 12,010,784
Length	102
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	84.25
Mean single sequence MFE	-21.45
Consensus MFE	-16.62
Energy contribution	-17.57
Covariance contribution	0.95
Combinations/Pair	1.12
Mean z-score	-2.19
Structure conservation index	0.77
SVM decision value	0.45
SVM RNA-class probability	0.742554
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12010682 102 + 23771897
CUUGGAGCAUUAGUCUUAUGCAUAAUCGGUGGGUCUAAAAUGCAUAAUUAUGCAGAUGAAAUAUCAUCUGCCCAAAAAUCUCUUCUUAUAUCUGACUAACUA
.........((((((((((((((....((.....))...))))))))....((((((((....))))))))......................))))))... ( -23.00)
>DroSec_CAF1 28768 102 + 1
CUUGGAGCAUUAGUCUUAUGCAUAAUCGGUGGGUCUAAAAUGCAUAAUUAUGCAGAUGAAAUAUCAUCUGCCCAAAAAUCUCUUCUUAUAUCUGACUAACUA
.........((((((((((((((....((.....))...))))))))....((((((((....))))))))......................))))))... ( -23.00)
>DroSim_CAF1 28005 102 + 1
CUUGGAGCAUUAGUCUUAUGCAUAAUCGGUGGGUCUAAAAUGCAUAAUUAUGCAGAUGAAAUAUCAUCUGCCCAAAAAUCUCUUCGUAUAUCUGCCUAACUA
.((((.(((((((.(((((.........))))).)))..))))........((((((((....))))))))))))........................... ( -22.30)
>DroEre_CAF1 29453 102 + 1
CUUGGAGCAUUAGUCUUAUACAUAAUCGGUGGGUCUAAAAUGCAUAAUUAUGCAGAUGAAAUAUCAUCUGCCCAAAAAUCUCUUCUUAUAUCUGCCUAACUA
.((((.(((((((.(((((.........))))).)))..))))........((((((((....))))))))))))........................... ( -22.60)
>DroYak_CAF1 28703 102 + 1
CUUGGAGCAUUAGUCUUAUGCAUAAUCGGUGGGCCUCAAAUGCAUAAUUAUGCAGAUGAAAUAUCAUCUGCCCAAAAAUCUCUUCUUUUAUCUGCCUAACUA
.((((.(((......((((((((....((....))....))))))))....((((((((....)))))))).....................)))))))... ( -24.90)
>DroAna_CAF1 27020 81 + 1
CUUGGAUCAUUAGUUUUAAACUUAAUCAGUUG-ACUAAAAUGCAUAAUUAUGCAUUUGAAUUCCUAUAUGCCUUUAAGCUUU--------------------
...((((((((((((...((((.....)))))-)))))(((((((....))))))))))..))).....((......))...-------------------- ( -12.90)
>consensus
CUUGGAGCAUUAGUCUUAUGCAUAAUCGGUGGGUCUAAAAUGCAUAAUUAUGCAGAUGAAAUAUCAUCUGCCCAAAAAUCUCUUCUUAUAUCUGCCUAACUA
.((((.(((((((.(((((.........))))).)))..))))........((((((((....))))))))))))........................... (-16.62 = -17.57 +   0.95)

alignment

secondary structure

dotplot

Window 2

Location	12,010,682 – 12,010,784
Length	102
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	84.25
Mean single sequence MFE	-24.85
Consensus MFE	-19.68
Energy contribution	-20.10
Covariance contribution	0.42
Combinations/Pair	1.21
Mean z-score	-2.61
Structure conservation index	0.79
SVM decision value	0.86
SVM RNA-class probability	0.868045
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12010682 102 - 23771897
UAGUUAGUCAGAUAUAAGAAGAGAUUUUUGGGCAGAUGAUAUUUCAUCUGCAUAAUUAUGCAUUUUAGACCCACCGAUUAUGCAUAAGACUAAUGCUCCAAG
..(((((((.....((((((....)))))).((((((((....))))))))....((((((((....(......)....)))))))))))))))........ ( -28.80)
>DroSec_CAF1 28768 102 - 1
UAGUUAGUCAGAUAUAAGAAGAGAUUUUUGGGCAGAUGAUAUUUCAUCUGCAUAAUUAUGCAUUUUAGACCCACCGAUUAUGCAUAAGACUAAUGCUCCAAG
..(((((((.....((((((....)))))).((((((((....))))))))....((((((((....(......)....)))))))))))))))........ ( -28.80)
>DroSim_CAF1 28005 102 - 1
UAGUUAGGCAGAUAUACGAAGAGAUUUUUGGGCAGAUGAUAUUUCAUCUGCAUAAUUAUGCAUUUUAGACCCACCGAUUAUGCAUAAGACUAAUGCUCCAAG
....................(((....((((((((((((....))))))))....((((((((....(......)....))))))))..))))..))).... ( -25.10)
>DroEre_CAF1 29453 102 - 1
UAGUUAGGCAGAUAUAAGAAGAGAUUUUUGGGCAGAUGAUAUUUCAUCUGCAUAAUUAUGCAUUUUAGACCCACCGAUUAUGUAUAAGACUAAUGCUCCAAG
....................(((....((((((((((((....))))))))....((((((((....(......)....))))))))..))))..))).... ( -23.10)
>DroYak_CAF1 28703 102 - 1
UAGUUAGGCAGAUAAAAGAAGAGAUUUUUGGGCAGAUGAUAUUUCAUCUGCAUAAUUAUGCAUUUGAGGCCCACCGAUUAUGCAUAAGACUAAUGCUCCAAG
....................(((....((((((((((((....))))))))....((((((((....((....))....))))))))..))))..))).... ( -27.80)
>DroAna_CAF1 27020 81 - 1
--------------------AAAGCUUAAAGGCAUAUAGGAAUUCAAAUGCAUAAUUAUGCAUUUUAGU-CAACUGAUUAAGUUUAAAACUAAUGAUCCAAG
--------------------...(((....))).....(((..((((((((((....)))))))(((((-(....))))))............))))))... ( -15.50)
>consensus
UAGUUAGGCAGAUAUAAGAAGAGAUUUUUGGGCAGAUGAUAUUUCAUCUGCAUAAUUAUGCAUUUUAGACCCACCGAUUAUGCAUAAGACUAAUGCUCCAAG
....................(((....((((((((((((....))))))))....((((((((....(......)....))))))))..))))..))).... (-19.68 = -20.10 +   0.42)

alignment

secondary structure

dotplot

Window 3

Location	12,010,712 – 12,010,809
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	94.12
Mean single sequence MFE	-23.66
Consensus MFE	-19.04
Energy contribution	-18.88
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.99
Structure conservation index	0.80
SVM decision value	1.12
SVM RNA-class probability	0.918979
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12010712 97 + 23771897
GGGUCUAAAAUGCAUAAUUAUGCAGAUGAAAUAUCAUCUGCCCAAAAAUCUCUUCUUAUAUCUGACUAACUAGUCGCUCGGCUUUGGAUUUGUAUUG
........((((((.......((((((((....))))))))(((((.................((((....))))((...)))))))...)))))). ( -21.80)
>DroSec_CAF1 28798 97 + 1
GGGUCUAAAAUGCAUAAUUAUGCAGAUGAAAUAUCAUCUGCCCAAAAAUCUCUUCUUAUAUCUGACUAACUAGUCGGUCGGCUUUGGACUUGUAUUG
(((((((((..((........((((((((....))))))))....................((((((....))))))...)))))))))))...... ( -26.40)
>DroSim_CAF1 28035 97 + 1
GGGUCUAAAAUGCAUAAUUAUGCAGAUGAAAUAUCAUCUGCCCAAAAAUCUCUUCGUAUAUCUGCCUAACUAGUCGGUCGGCUUUGGACUUGUAUUG
(((((((((............((((((((....))))))))......................(((..(((....))).))))))))))))...... ( -22.80)
>DroEre_CAF1 29483 96 + 1
GGGUCUAAAAUGCAUAAUUAUGCAGAUGAAAUAUCAUCUGCCCAAAAAUCUCUUCUUAUAUCUGCCUAACUAGUCGGUCGGCUUUGGACUUGU-AUU
(((((((((............((((((((....))))))))......................(((..(((....))).))))))))))))..-... ( -22.80)
>DroYak_CAF1 28733 97 + 1
GGGCCUCAAAUGCAUAAUUAUGCAGAUGAAAUAUCAUCUGCCCAAAAAUCUCUUCUUUUAUCUGCCUAACUAGUCGGUUGGCUUUGGAGUUGUUAUC
((((.......((((....))))((((((....))))))))))...(((..((((........(((.((((....)))))))...))))..)))... ( -24.50)
>consensus
GGGUCUAAAAUGCAUAAUUAUGCAGAUGAAAUAUCAUCUGCCCAAAAAUCUCUUCUUAUAUCUGCCUAACUAGUCGGUCGGCUUUGGACUUGUAUUG
((((.......((((....))))((((((....))))))))))......................((((..((((....)))))))).......... (-19.04 = -18.88 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:52 2006