Locus 1009

Sequence ID	3R_DroMel_CAF1
Location	3,202,615 – 3,202,773
Length	158
Max. P	0.950441

overview

Window 3

Location	3,202,615 – 3,202,733
Length	118
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	91.20
Mean single sequence MFE	-31.75
Consensus MFE	-26.24
Energy contribution	-26.80
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.06
Structure conservation index	0.83
SVM decision value	0.97
SVM RNA-class probability	0.891446
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3202615 118 + 27905053
GUUGUAAACGUAAGUGGUAUGUUACUCAUGCAGACAAUCAACACUUGUCAUGAAAUGGCACCAUUUCCGCAACCGAAGUACCCUGUGUGUUCAUACACAUGUCGGGUGGUUUGUUUUU
(((((....((((((((((((.....))))).(.....)..)))))).)..((((((....)))))).)))))((((.(((((.((((((....))))))...))))).))))..... ( -35.30)
>DroSec_CAF1 22049 113 + 1
AUUGUAAACGUAAGUGGCAUGA-----GUAAAGACCAUCAACACUUGUCAUGAAAUGGCACCAUUUCCGCAACCUAAGUACCCUGUGUGUUCAUACACAUGUCGGGUGCUUUGUUUUU
.((((....(((((((..(((.-----((....)))))...)))))).)..((((((....)))))).))))...((((((((.((((((....))))))...))))))))....... ( -31.10)
>DroSim_CAF1 28890 113 + 1
AUUGCUAACGUAAGUGGCAUGA-----GUAAAGACAAUCAACACUUGUCAUGAAAUGGCACCAUUUCCGCAACCUAAGUACCCUGUGUGUUCAUACACAUGUCGGGUGCUUUGUUUUU
..(((((.(....))))))...-----((...(((((.......)))))..((((((....)))))).))(((..((((((((.((((((....))))))...)))))))).)))... ( -33.60)
>DroEre_CAF1 21656 113 + 1
AUUGUUAACGUAUGUGGCAUGA-----GUAAAGGCAAUCAACACUUGUCAUGAAAUGGCACCAUUUCCGCAACCUAAGUACCCUGUGUGUUCAUACACAUUUCGGGCGCUUUGUUUUU
............((((((((((-----...(((..........))).)))))(((((....))))))))))((..(((..(((.((((((....))))))...)))..))).)).... ( -27.00)
>consensus
AUUGUAAACGUAAGUGGCAUGA_____GUAAAGACAAUCAACACUUGUCAUGAAAUGGCACCAUUUCCGCAACCUAAGUACCCUGUGUGUUCAUACACAUGUCGGGUGCUUUGUUUUU
.............(((................(((((.......)))))..((((((....)))))))))(((..((((((((.((((((....))))))...)))))))).)))... (-26.24 = -26.80 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	3,202,655 – 3,202,773
Length	118
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	97.46
Mean single sequence MFE	-30.98
Consensus MFE	-29.38
Energy contribution	-29.88
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.48
Structure conservation index	0.95
SVM decision value	1.40
SVM RNA-class probability	0.950441
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3202655 118 + 27905053
ACACUUGUCAUGAAAUGGCACCAUUUCCGCAACCGAAGUACCCUGUGUGUUCAUACACAUGUCGGGUGGUUUGUUUUUGCUGAACAUCUUUAUCCGAAACGAUAAUUUUAUUGGACAU
.....((((..((((((....)))))).((((.((((.(((((.((((((....))))))...))))).))))...))))...................(((((....))))))))). ( -30.90)
>DroSec_CAF1 22084 118 + 1
ACACUUGUCAUGAAAUGGCACCAUUUCCGCAACCUAAGUACCCUGUGUGUUCAUACACAUGUCGGGUGCUUUGUUUUUGCUGAACAUCUUUAUCCGAAACGAUAAUUUUAUUGGACAU
.....((((..((((((....)))))).((((...((((((((.((((((....))))))...)))))))).....))))...................(((((....))))))))). ( -31.80)
>DroSim_CAF1 28925 118 + 1
ACACUUGUCAUGAAAUGGCACCAUUUCCGCAACCUAAGUACCCUGUGUGUUCAUACACAUGUCGGGUGCUUUGUUUUUGCUGAACAUCUUUAUCCGAAACGAUAAUUUUAUUGGACAU
.....((((..((((((....)))))).((((...((((((((.((((((....))))))...)))))))).....))))...................(((((....))))))))). ( -31.80)
>DroEre_CAF1 21691 118 + 1
ACACUUGUCAUGAAAUGGCACCAUUUCCGCAACCUAAGUACCCUGUGUGUUCAUACACAUUUCGGGCGCUUUGUUUUUGCUGAACAGCUUUAUCUGAAACGAUAAUUUUAUUGGACAU
.....((((..((((((....)))))).((.....(((..(((.((((((....))))))...)))..)))(((((.....))))))).(((((......)))))........)))). ( -29.40)
>consensus
ACACUUGUCAUGAAAUGGCACCAUUUCCGCAACCUAAGUACCCUGUGUGUUCAUACACAUGUCGGGUGCUUUGUUUUUGCUGAACAUCUUUAUCCGAAACGAUAAUUUUAUUGGACAU
.....((((..((((((....)))))).((((...((((((((.((((((....))))))...)))))))).....)))).........(((((......)))))........)))). (-29.38 = -29.88 +   0.50)

alignment

secondary structure

dotplot

Window 5

Location	3,202,655 – 3,202,773
Length	118
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	97.46
Mean single sequence MFE	-30.28
Consensus MFE	-29.11
Energy contribution	-29.42
Covariance contribution	0.31
Combinations/Pair	1.03
Mean z-score	-1.89
Structure conservation index	0.96
SVM decision value	0.69
SVM RNA-class probability	0.822337
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3202655 118 - 27905053
AUGUCCAAUAAAAUUAUCGUUUCGGAUAAAGAUGUUCAGCAAAAACAAACCACCCGACAUGUGUAUGAACACACAGGGUACUUCGGUUGCGGAAAUGGUGCCAUUUCAUGACAAGUGU
.((((.........((((((((((((((....))))).((((.........((((....(((((....)))))..)))).(....))))).))))))))).........))))..... ( -28.07)
>DroSec_CAF1 22084 118 - 1
AUGUCCAAUAAAAUUAUCGUUUCGGAUAAAGAUGUUCAGCAAAAACAAAGCACCCGACAUGUGUAUGAACACACAGGGUACUUAGGUUGCGGAAAUGGUGCCAUUUCAUGACAAGUGU
.((((.........((((((((((((((....))))).((((...(.(((.((((....(((((....)))))..)))).))).).)))).))))))))).........))))..... ( -30.97)
>DroSim_CAF1 28925 118 - 1
AUGUCCAAUAAAAUUAUCGUUUCGGAUAAAGAUGUUCAGCAAAAACAAAGCACCCGACAUGUGUAUGAACACACAGGGUACUUAGGUUGCGGAAAUGGUGCCAUUUCAUGACAAGUGU
.((((.........((((((((((((((....))))).((((...(.(((.((((....(((((....)))))..)))).))).).)))).))))))))).........))))..... ( -30.97)
>DroEre_CAF1 21691 118 - 1
AUGUCCAAUAAAAUUAUCGUUUCAGAUAAAGCUGUUCAGCAAAAACAAAGCGCCCGAAAUGUGUAUGAACACACAGGGUACUUAGGUUGCGGAAAUGGUGCCAUUUCAUGACAAGUGU
.............(((((......))))).(((..(((((((...(.(((..(((....(((((....)))))..)))..))).).)))).((((((....)))))).)))..))).. ( -31.10)
>consensus
AUGUCCAAUAAAAUUAUCGUUUCGGAUAAAGAUGUUCAGCAAAAACAAAGCACCCGACAUGUGUAUGAACACACAGGGUACUUAGGUUGCGGAAAUGGUGCCAUUUCAUGACAAGUGU
.((((.........((((((((((((((....))))).((((...(.(((.((((....(((((....)))))..)))).))).).)))).))))))))).........))))..... (-29.11 = -29.42 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:16 2006