Locus 8223

Sequence ID	3L_DroMel_CAF1
Location	21,624,819 – 21,624,932
Length	113
Max. P	0.922145

overview

Window 9

Location	21,624,819 – 21,624,932
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.39
Mean single sequence MFE	-38.44
Consensus MFE	-35.72
Energy contribution	-36.40
Covariance contribution	0.68
Combinations/Pair	1.07
Mean z-score	-1.27
Structure conservation index	0.93
SVM decision value	0.74
SVM RNA-class probability	0.838944
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21624819 113 + 23771897
GACGAGAAAGGGCGCUGGUUGAGCCAUGAUGAAAUUGUUGGCUUCGAUUUUGGCUAAUUGCCAGAGUCCAUUUGA-------AAUGCCCACUUAGGGCUAAUUGGUCCCCUCGGAAGCGC
..((((...(((.((..(((((((((............)))))).(((((((((.....))))))))).......-------...((((.....)))).)))..)))))))))....... ( -39.60)
>DroSec_CAF1 1173 113 + 1
GACGAGGAAGGGCGCUGGUUGAGCCAUGAUGAAAUUGUUGGCUUCGAUUUUGGCUAAUUGCCGGAGUCCAUUUGA-------AAUGCCCACUUAGGGCUAAUUGGUCCCCUCGGAAGCGC
..(((((..(((((......((((((............)))))).(((((((((.....))))))))).......-------..))))).....(((((....))))))))))....... ( -41.30)
>DroSim_CAF1 1161 113 + 1
GACGAGGAAGGGCGCUGGUUGAGCCAUGAUGAAAUUGUUGGCUUCAAUUUUGGCUAAUUGCCGGAGUCCAUUUGA-------AAUGCCCACUUAGAGCUAAUUGGUCCCCUCGGAAGCGC
..(((((..((((.(((((..(((((.....((((((.......)))))))))))....))))).))))......-------.....(((.(((....))).)))...)))))....... ( -34.60)
>DroEre_CAF1 143 113 + 1
GACGAGGAAGGGCGAUGGCUGAGCCAUGAUGAAAUUGUUGGCUUCGAUUUUGGCUAAUUGCCGGAGUCCAUUUGA-------AAUGCCCACUUAGGGCUAAUUGGUCCCCUCGGAAGCGC
..(((((..(((((......((((((............)))))).(((((((((.....))))))))).......-------..))))).....(((((....))))))))))....... ( -41.60)
>DroYak_CAF1 10586 120 + 1
GAUGUGUAAGGGCGAUGGUUGAGCCAUGAUGAAAUUGUUGGCUUCGAUUUUGGCUAAUUGCCGGAGUCCAUUUGAAAUGUGAAAUGCCCACUUAGGGCUAAUUGGUCCCCUCGGAAGCGC
...((((..(((((......((((((............)))))).(((((((((.....)))))))))................))))).....(((((....)))))........)))) ( -35.10)
>consensus
GACGAGGAAGGGCGCUGGUUGAGCCAUGAUGAAAUUGUUGGCUUCGAUUUUGGCUAAUUGCCGGAGUCCAUUUGA_______AAUGCCCACUUAGGGCUAAUUGGUCCCCUCGGAAGCGC
..(((((..(((((......((((((............)))))).(((((((((.....)))))))))................))))).....(((((....))))))))))....... (-35.72 = -36.40 +   0.68)

alignment

secondary structure

dotplot

Window 0

Location	21,624,819 – 21,624,932
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.39
Mean single sequence MFE	-30.74
Consensus MFE	-28.46
Energy contribution	-28.38
Covariance contribution	-0.08
Combinations/Pair	1.09
Mean z-score	-1.39
Structure conservation index	0.93
SVM decision value	1.15
SVM RNA-class probability	0.922145
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21624819 113 - 23771897
GCGCUUCCGAGGGGACCAAUUAGCCCUAAGUGGGCAUU-------UCAAAUGGACUCUGGCAAUUAGCCAAAAUCGAAGCCAACAAUUUCAUCAUGGCUCAACCAGCGCCCUUUCUCGUC
(((((..(((((((.(((....((((.....))))...-------.....))).))))(((.....)))....))).(((((............))))).....)))))........... ( -30.10)
>DroSec_CAF1 1173 113 - 1
GCGCUUCCGAGGGGACCAAUUAGCCCUAAGUGGGCAUU-------UCAAAUGGACUCCGGCAAUUAGCCAAAAUCGAAGCCAACAAUUUCAUCAUGGCUCAACCAGCGCCCUUCCUCGUC
(((((..(((((((.(((....((((.....))))...-------.....))).))))(((.....)))....))).(((((............))))).....)))))........... ( -33.00)
>DroSim_CAF1 1161 113 - 1
GCGCUUCCGAGGGGACCAAUUAGCUCUAAGUGGGCAUU-------UCAAAUGGACUCCGGCAAUUAGCCAAAAUUGAAGCCAACAAUUUCAUCAUGGCUCAACCAGCGCCCUUCCUCGUC
(((((.....((((.(((....((((.....))))...-------.....))).))))(((.....)))....((((.((((............))))))))..)))))........... ( -29.40)
>DroEre_CAF1 143 113 - 1
GCGCUUCCGAGGGGACCAAUUAGCCCUAAGUGGGCAUU-------UCAAAUGGACUCCGGCAAUUAGCCAAAAUCGAAGCCAACAAUUUCAUCAUGGCUCAGCCAUCGCCCUUCCUCGUC
(((((((.((((((.(((....((((.....))))...-------.....))).))))(((.....)))....))))))).............(((((...))))).))........... ( -31.60)
>DroYak_CAF1 10586 120 - 1
GCGCUUCCGAGGGGACCAAUUAGCCCUAAGUGGGCAUUUCACAUUUCAAAUGGACUCCGGCAAUUAGCCAAAAUCGAAGCCAACAAUUUCAUCAUGGCUCAACCAUCGCCCUUACACAUC
(((((((.((((((.((.....((((.....))))((((........)))))).))))(((.....)))....))))))).............((((.....)))).))........... ( -29.60)
>consensus
GCGCUUCCGAGGGGACCAAUUAGCCCUAAGUGGGCAUU_______UCAAAUGGACUCCGGCAAUUAGCCAAAAUCGAAGCCAACAAUUUCAUCAUGGCUCAACCAGCGCCCUUCCUCGUC
........((((((........((((.....))))...............(((.....(((.....)))......((.((((............))))))..)))...))))))...... (-28.46 = -28.38 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:47 2006