Locus 238

Sequence ID	2L_DroMel_CAF1
Location	696,420 – 696,510
Length	90
Max. P	0.978418

overview

Window 0

Location	696,420 – 696,510
Length	90
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	79.89
Mean single sequence MFE	-25.39
Consensus MFE	-17.30
Energy contribution	-17.78
Covariance contribution	0.48
Combinations/Pair	1.05
Mean z-score	-2.43
Structure conservation index	0.68
SVM decision value	1.81
SVM RNA-class probability	0.978418
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 696420 90 + 22407834
AGAGCCCCACUGGGGCCAAACGUCAUAAAUCCACUAAUAAACAGUAACCACAGUAACCCGGCCAGUAU---------GGCCAGUAUGGCGAGUAUGGCA
.(.(((((...))))))....((((((...(((..........((.((....)).))..((((.....---------))))....)))....)))))). ( -25.60)
>DroSec_CAF1 75457 90 + 1
AGAGUCCCACUGGGGGCAAACGUCAUAAAUCCACUAAUAAACAGUAACCACAGUAACCCGGCCAGUAU---------GGCCAGUGUGGCCAGUAUGGCA
...(((((....)))))....((((((...((((.........((.((....)).))..((((.....---------))))...))))....)))))). ( -28.00)
>DroSim_CAF1 80356 99 + 1
AGAGCCCCACUGGGGGCAAACGUCAUAAAUCCACUAAUAAACAGUAACCACAGUAACCCGGCCAGUAUGGCCAGUAUGGCCAGUGUGGCCAGUAUGGCA
...(((((....)))))....((((((.....(((.......)))..............(((((...(((((.....)))))...)))))..)))))). ( -36.70)
>DroEre_CAF1 84599 69 + 1
AGAGCCCCACUGGGGGCAAACGUCAUAAAUCCACUAAUAAACAGUAACCACAG---CCC---------------------------GGCCAGUAUGGCA
...(((..(((((((((...................................)---)))---------------------------..)))))..))). ( -17.05)
>DroYak_CAF1 80604 69 + 1
AGAGCCCCACUGGGGGCAAACGUCAUAAAUCCACUAAUAAACAGUAACCACGG---CGC---------------------------GGCCAGUAUGGCA
...(((((....)))))....((((((.....(((.......)))......((---(..---------------------------.)))..)))))). ( -19.60)
>consensus
AGAGCCCCACUGGGGGCAAACGUCAUAAAUCCACUAAUAAACAGUAACCACAGUAACCCGGCCAGUAU_________GGCCAGU_UGGCCAGUAUGGCA
...(((((....)))))....((((((...(((((.......)))..............((((..............)))).....))....)))))). (-17.30 = -17.78 +   0.48)

alignment

secondary structure

dotplot

Window 1

Location	696,420 – 696,510
Length	90
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	79.89
Mean single sequence MFE	-28.24
Consensus MFE	-16.14
Energy contribution	-17.58
Covariance contribution	1.44
Combinations/Pair	1.04
Mean z-score	-1.81
Structure conservation index	0.57
SVM decision value	0.08
SVM RNA-class probability	0.572230
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 696420 90 - 22407834
UGCCAUACUCGCCAUACUGGCC---------AUACUGGCCGGGUUACUGUGGUUACUGUUUAUUAGUGGAUUUAUGACGUUUGGCCCCAGUGGGGCUCU
.(((.((((.((((..((((((---------.....))))))((((.((...((((((.....))))))...))))))...))))...)))).)))... ( -29.90)
>DroSec_CAF1 75457 90 - 1
UGCCAUACUGGCCACACUGGCC---------AUACUGGCCGGGUUACUGUGGUUACUGUUUAUUAGUGGAUUUAUGACGUUUGCCCCCAGUGGGACUCU
..((.(((((((((((((((((---------.....)))))).....)))))((((((.....)))))).................))))))))..... ( -28.20)
>DroSim_CAF1 80356 99 - 1
UGCCAUACUGGCCACACUGGCCAUACUGGCCAUACUGGCCGGGUUACUGUGGUUACUGUUUAUUAGUGGAUUUAUGACGUUUGCCCCCAGUGGGGCUCU
.(((((((((((((...(((((.....)))))...))))))).....))))))(((((.....)))))..............(((((....)))))... ( -38.10)
>DroEre_CAF1 84599 69 - 1
UGCCAUACUGGCC---------------------------GGG---CUGUGGUUACUGUUUAUUAGUGGAUUUAUGACGUUUGCCCCCAGUGGGGCUCU
.(((.((((((..---------------------------(((---(....((((..(((((....)))))...))))....)))))))))).)))... ( -23.80)
>DroYak_CAF1 80604 69 - 1
UGCCAUACUGGCC---------------------------GCG---CCGUGGUUACUGUUUAUUAGUGGAUUUAUGACGUUUGCCCCCAGUGGGGCUCU
.(((.((((((..---------------------------(((---.(((.(((((((.....))))).....)).)))..)))..)))))).)))... ( -21.20)
>consensus
UGCCAUACUGGCCA_ACUGGCC_________AUACUGGCCGGGUUACUGUGGUUACUGUUUAUUAGUGGAUUUAUGACGUUUGCCCCCAGUGGGGCUCU
.(((.((((((.......((((..............))))((((...(((.(((((((.....))))).....)).)))...)))))))))).)))... (-16.14 = -17.58 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:53 2006