Locus 202

Sequence ID	3R_DroMel_CAF1
Location	866,645 – 866,804
Length	159
Max. P	0.538641

overview

Window 3

Location	866,645 – 866,764
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.42
Mean single sequence MFE	-27.94
Consensus MFE	-22.58
Energy contribution	-23.32
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.81
SVM decision value	-0.03
SVM RNA-class probability	0.517525
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 866645 119 + 27905053
GCGCAAGUCGAGCCUCAUUUAGUUCUGGCUUGCCAUUUGUAUCUCAAAGUCUGGCCAAAACAAAACAUAAUUUUGUUUGUUUAUGGCAGGC-UUUUCGCCGAAGUCAUUUUUUCUGUUUU
(((((((((((((........)))).)))))))............((((((((.((((((((((.((......))))))))).))))))))-)))..)).((((......))))...... ( -34.00)
>DroSec_CAF1 41651 120 + 1
CCGCAAGUCGAGCCUCAUUUAGUUCUGGCUUGCCAUUUGUAUCUCAAAGUCUGGCCAACACAAUACAUAAAUUUGUUUGUUUAUGGCAGGCCUUUUCGCCGAAGUCAUUUUUUCUGUUUU
..(((((((((((........)))).)))))))..((((.....))))(((((.(((..((((.(((......)))))))...))))))))......((.((((......)))).))... ( -27.90)
>DroSim_CAF1 40863 120 + 1
CCGCAAGUCGAGCCUCAUUUAGUUCUGGCUUGCCAUUUGUAUCUCAAAGUCUGGCCAACACAAUACAUAAAUUUGUUUUUUUAUGGCAGGCCUUUUCGCCGAAGUCAUUUUUUCUGUUUU
..(((((((((((........)))).)))))))..((((.....))))(((((.(((.......(((......))).......))))))))......((.((((......)))).))... ( -25.74)
>DroEre_CAF1 41153 119 + 1
CCGCAAGUCGAGCCUCAUUUAGUUCUGGCUUGCCAUUUGUAUCUCAAACUCUGCCCAACACAAUACAUAAAUUUGUUUGUUUAUGUCGGGCCUUUUCGCCGAAGUCAUUUUUU-UGUUUU
..(((((((((((........)))).)))))))..((((.....))))....((((.((((((.(((......)))))))....)).))))........(((((......)))-)).... ( -24.10)
>consensus
CCGCAAGUCGAGCCUCAUUUAGUUCUGGCUUGCCAUUUGUAUCUCAAAGUCUGGCCAACACAAUACAUAAAUUUGUUUGUUUAUGGCAGGCCUUUUCGCCGAAGUCAUUUUUUCUGUUUU
..(((((((((((........)))).)))))))....((.(..((........((((..((((.(((......)))))))...)))).(((......)))))..)))............. (-22.58 = -23.32 +   0.75)

alignment

secondary structure

dotplot

Window 4

Location	866,685 – 866,804
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.17
Mean single sequence MFE	-25.95
Consensus MFE	-19.52
Energy contribution	-20.78
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-2.26
Structure conservation index	0.75
SVM decision value	0.01
SVM RNA-class probability	0.538641
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 866685 119 - 27905053
CAAUUAACAAACACGGUACAUACGUGUUCCCUGAAUUUCAAAAACAGAAAAAAUGACUUCGGCGAAAA-GCCUGCCAUAAACAAACAAAAUUAUGUUUUGUUUUGGCCAGACUUUGAGAU
.........((((((.......))))))......((((((((..................(((.....-))).((((.(((((((((......)).))))))))))).....)))))))) ( -25.90)
>DroSec_CAF1 41691 120 - 1
CAAUUAACAAACACGGCACAUACGUGUUUCCUGAAUUUCAAAAACAGAAAAAAUGACUUCGGCGAAAAGGCCUGCCAUAAACAAACAAAUUUAUGUAUUGUGUUGGCCAGACUUUGAGAU
...(((..(((((((.......)))))))..)))((((((((..................(((......))).((((...(((((((......))).))))..)))).....)))))))) ( -26.00)
>DroSim_CAF1 40903 120 - 1
CAAUUAACAAACACGGCACAUACGUGUUUCCUGAAUUUCAAAAACAGAAAAAAUGACUUCGGCGAAAAGGCCUGCCAUAAAAAAACAAAUUUAUGUAUUGUGUUGGCCAGACUUUGAGAU
...(((..(((((((.......)))))))..)))((((((((...........((.(....)))....((((...(((((....(((......))).)))))..))))....)))))))) ( -23.40)
>DroEre_CAF1 41193 119 - 1
CAAUUAACAAACACAGCUCAUACGUGUUUCCUGAAUUUCAAAAACA-AAAAAAUGACUUCGGCGAAAAGGCCCGACAUAAACAAACAAAUUUAUGUAUUGUGUUGGGCAGAGUUUGAGAU
................((((.((...(((((((((..(((......-......))).))))).))))..((((((((((((((..........))).)))))))))))...)).)))).. ( -28.50)
>consensus
CAAUUAACAAACACGGCACAUACGUGUUUCCUGAAUUUCAAAAACAGAAAAAAUGACUUCGGCGAAAAGGCCUGCCAUAAACAAACAAAUUUAUGUAUUGUGUUGGCCAGACUUUGAGAU
...(((..(((((((.......)))))))..)))((((((((..................(((......))).((((...(((((((......))).))))..)))).....)))))))) (-19.52 = -20.78 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:18 2006