Locus 4796

Sequence ID	2R_DroMel_CAF1
Location	15,762,248 – 15,762,363
Length	115
Max. P	0.962374

overview

Window 7

Location	15,762,248 – 15,762,363
Length	115
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	85.80
Mean single sequence MFE	-34.95
Consensus MFE	-24.39
Energy contribution	-26.32
Covariance contribution	1.94
Combinations/Pair	1.17
Mean z-score	-2.41
Structure conservation index	0.70
SVM decision value	1.08
SVM RNA-class probability	0.911989
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15762248 115 + 20766785
UACUCCCAGAAAGUGGCCAAUAUGGCUGUCCUAAUCAAACUUGGAUCCUUUCCACGCUUUCUGCUCCCAUCGCCUUUGGAGUUCUUUUUUCCUGGCGUUGGCCACUUUCCCGAUU
........(((((((((((((((((................((((.....)))).((.....))..)))).(((...((((.......)))).))))))))))))))))...... ( -38.00)
>DroSim_CAF1 11601 115 + 1
UACUCCCAGAAAGUGGCCAGUAUGGCUGUCCUAAUCGAACUUGGAUCCUUUCCACGCUUUCUGCUCCCAUCGCCUUUGGAGGUUCUUUUGCCAGGUGUUGGCCACUUUCCGGAUU
.....((.((((((((((((..((((.(.......)(((((((((.....)))..((.....))..(((.......)))))))))....))))....)))))))))))).))... ( -38.50)
>DroEre_CAF1 11305 115 + 1
UACUCCCAGAAUGUGGCCAGUACGGCCGUCCUGAGCGAACUCGGCUCCUUCCUACGCUUCCUGCUCUCACCGCCUUUGGAGGUCCUUUUGCCUGGAGACGGCCACUUUCCCGACU
........(((.((((((.....(((......((((.......))))........((((((.((.......))....))))))......))).(....))))))).)))...... ( -32.30)
>DroYak_CAF1 11436 115 + 1
UACUCCCAAAAUGUGGCCAGUAUGGCCGUCCUGAGCAUACUCCGUUCCUUUCUACGCUUCCUGCUCUCACCGCCUUUGGAGGUCCUUUUGCCAGGUGAUGGCCACUUUCCCGACU
............(((((((...((((......(((((.....(((........))).....)))))..(((.((...)).)))......)))).....))))))).......... ( -31.00)
>consensus
UACUCCCAGAAAGUGGCCAGUAUGGCCGUCCUAAGCAAACUCGGAUCCUUUCCACGCUUCCUGCUCCCACCGCCUUUGGAGGUCCUUUUGCCAGGUGAUGGCCACUUUCCCGACU
........((((((((((((((((((......((((.......))))........((((((.((.......))....))))))......)))..)))))))))))))))...... (-24.39 = -26.32 +   1.94)

alignment

secondary structure

dotplot

Window 8

Location	15,762,248 – 15,762,363
Length	115
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	85.80
Mean single sequence MFE	-40.83
Consensus MFE	-28.83
Energy contribution	-28.95
Covariance contribution	0.12
Combinations/Pair	1.12
Mean z-score	-2.81
Structure conservation index	0.71
SVM decision value	1.54
SVM RNA-class probability	0.962374
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15762248 115 - 20766785
AAUCGGGAAAGUGGCCAACGCCAGGAAAAAAGAACUCCAAAGGCGAUGGGAGCAGAAAGCGUGGAAAGGAUCCAAGUUUGAUUAGGACAGCCAUAUUGGCCACUUUCUGGGAGUA
..((.(((((((((((((((((.(((.........)))...))))((((..((.....)).((((.....)))).((((.....))))..)))).))))))))))))).)).... ( -41.20)
>DroSim_CAF1 11601 115 - 1
AAUCCGGAAAGUGGCCAACACCUGGCAAAAGAACCUCCAAAGGCGAUGGGAGCAGAAAGCGUGGAAAGGAUCCAAGUUCGAUUAGGACAGCCAUACUGGCCACUUUCUGGGAGUA
..(((((((((((((((.....((((....((.((((((...((..((....))....)).))))..)).))...((((.....)))).))))...))))))))))))))).... ( -45.60)
>DroEre_CAF1 11305 115 - 1
AGUCGGGAAAGUGGCCGUCUCCAGGCAAAAGGACCUCCAAAGGCGGUGAGAGCAGGAAGCGUAGGAAGGAGCCGAGUUCGCUCAGGACGGCCGUACUGGCCACAUUCUGGGAGUA
..((.((((.(((((((((....)))....((.(((((...(((.((....)).(....)..........)))(((....))).))).)))).....)))))).)))).)).... ( -40.30)
>DroYak_CAF1 11436 115 - 1
AGUCGGGAAAGUGGCCAUCACCUGGCAAAAGGACCUCCAAAGGCGGUGAGAGCAGGAAGCGUAGAAAGGAACGGAGUAUGCUCAGGACGGCCAUACUGGCCACAUUUUGGGAGUA
..((.((((.(((((((...(((......))).........(((.((..(((((.....(((........))).....)))))...)).)))....))))))).)))).)).... ( -36.20)
>consensus
AAUCGGGAAAGUGGCCAACACCAGGCAAAAGGACCUCCAAAGGCGAUGAGAGCAGAAAGCGUAGAAAGGAUCCAAGUUCGAUCAGGACAGCCAUACUGGCCACAUUCUGGGAGUA
..((.((((((((((((......((...........))...(((.......((.....))...............((((.....)))).)))....)))))))))))).)).... (-28.83 = -28.95 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:29 2006