Locus 1964

Sequence ID	3L_DroMel_CAF1
Location	5,443,119 – 5,443,239
Length	120
Max. P	0.878836

overview

Window 3

Location	5,443,119 – 5,443,239
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.86
Mean single sequence MFE	-30.32
Consensus MFE	-26.75
Energy contribution	-27.00
Covariance contribution	0.25
Combinations/Pair	1.03
Mean z-score	-2.02
Structure conservation index	0.88
SVM decision value	0.91
SVM RNA-class probability	0.878836
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5443119 120 + 23771897
AAUUUAACCACAACCUUUGCACACAAGAAUACAUAAACAGAGAGACAAUGAAAAUGUUUCAUAAAAUUAGAUGUUAGCCUUUGAAGGUCCUGUUUUUGUGUUGUGGUGUGGCAUUUCGCC
......((((((((.((((....))))...(((.((((((.((((((.(....)))))))................((((....)))).)))))).)))))))))))..(((.....))) ( -29.60)
>DroSec_CAF1 4660 120 + 1
AAUUUAACCACAACCUUUGCACGCAAGAAUACAUAAACAGAGAGACAAUGAAAAUGUUUCAUAAAAUUAGAUGUGAGCCUUUGAAGGUCCUGUUUUUGUGUUGUGGUGUGGUAUUUCGCC
......((((((.((......(....)((((((.((((((.((((((.(....)))))))................((((....)))).)))))).))))))..))))))))........ ( -31.20)
>DroSim_CAF1 4711 120 + 1
AAUUUAACCACAACCUUUGCACACAAGAAUACAUAAACAGGGAGACAAUGAAAAUGUUUCAUAAAAUUAGAUGUGAGCCUUUGAAGGUCCUGUUUUUGUGUUGUGGUGCGGUAUUUCGCC
......((((((((.((((....))))...(((.(((((((((((((.(....)))))))................((((....))))))))))).)))))))))))((((....)))). ( -33.70)
>DroEre_CAF1 4570 120 + 1
AAUUUAACCACAACCUUUGCACACACGAAUACAUAAACAGAGAGACAAUGAAAAUGUUUCAUAACAUUACUGGUGAGCCUUUGAAGGUCCUGUUUUUGUGUUGUGCUAUGGCAUUUCGCC
..................(((((((((((.(((........((((((.(....)))))))...........((...((((....))))))))).)))))).)))))...(((.....))) ( -26.80)
>consensus
AAUUUAACCACAACCUUUGCACACAAGAAUACAUAAACAGAGAGACAAUGAAAAUGUUUCAUAAAAUUAGAUGUGAGCCUUUGAAGGUCCUGUUUUUGUGUUGUGGUGUGGCAUUUCGCC
......((((((((.((((....))))...(((.((((((.((((((.......))))))................((((....)))).)))))).)))))))))))..(((.....))) (-26.75 = -27.00 +   0.25)

alignment

secondary structure

dotplot

Window 4

Location	5,443,119 – 5,443,239
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.86
Mean single sequence MFE	-26.80
Consensus MFE	-23.51
Energy contribution	-24.07
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.62
Structure conservation index	0.88
SVM decision value	0.21
SVM RNA-class probability	0.634822
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5443119 120 - 23771897
GGCGAAAUGCCACACCACAACACAAAAACAGGACCUUCAAAGGCUAACAUCUAAUUUUAUGAAACAUUUUCAUUGUCUCUCUGUUUAUGUAUUCUUGUGUGCAAAGGUUGUGGUUAAAUU
(((.....)))..((((((((....(((((((.(((....))).................((.(((.......))).))))))))).(((((......)))))...))))))))...... ( -27.30)
>DroSec_CAF1 4660 120 - 1
GGCGAAAUACCACACCACAACACAAAAACAGGACCUUCAAAGGCUCACAUCUAAUUUUAUGAAACAUUUUCAUUGUCUCUCUGUUUAUGUAUUCUUGCGUGCAAAGGUUGUGGUUAAAUU
((.......))..(((((((((((.(((((((((((....))).))..............((.(((.......))).)).)))))).)))....(((....)))..))))))))...... ( -24.50)
>DroSim_CAF1 4711 120 - 1
GGCGAAAUACCGCACCACAACACAAAAACAGGACCUUCAAAGGCUCACAUCUAAUUUUAUGAAACAUUUUCAUUGUCUCCCUGUUUAUGUAUUCUUGUGUGCAAAGGUUGUGGUUAAAUU
.(((......)))((((((((....(((((((.(((....)))...............(((((.....)))))......))))))).(((((......)))))...))))))))...... ( -29.40)
>DroEre_CAF1 4570 120 - 1
GGCGAAAUGCCAUAGCACAACACAAAAACAGGACCUUCAAAGGCUCACCAGUAAUGUUAUGAAACAUUUUCAUUGUCUCUCUGUUUAUGUAUUCGUGUGUGCAAAGGUUGUGGUUAAAUU
(((.....)))....((((((....(((((((((((....))).))..((((((((((....))))))...)))).....)))))).(((((......)))))...))))))........ ( -26.00)
>consensus
GGCGAAAUACCACACCACAACACAAAAACAGGACCUUCAAAGGCUCACAUCUAAUUUUAUGAAACAUUUUCAUUGUCUCUCUGUUUAUGUAUUCUUGUGUGCAAAGGUUGUGGUUAAAUU
(((.....)))..((((((((....(((((((.(((....))).................((.(((.......))).))))))))).(((((......)))))...))))))))...... (-23.51 = -24.07 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:14 2006