Locus 6169

Sequence ID	2R_DroMel_CAF1
Location	19,402,969 – 19,403,089
Length	120
Max. P	0.704048

overview

Window 2

Location	19,402,969 – 19,403,089
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.36
Mean single sequence MFE	-38.80
Consensus MFE	-27.79
Energy contribution	-28.73
Covariance contribution	0.94
Combinations/Pair	1.24
Mean z-score	-1.79
Structure conservation index	0.72
SVM decision value	0.36
SVM RNA-class probability	0.704048
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19402969 120 + 20766785
AUCGGACAAGGUGGAAAAGAACCUUGCUCACCUGCAAACGCUUCUGGAGAAAGCACAUGUGAAGCCCAGCGUGAUAUGCAGAGGCUGCAAUAUGCAGCGAUACUGCAGCCUGUCCCAUCU
...(((((((((........)))))......(((((.(((((...((.....((....))....)).)))))....)))))((((((((.(((......))).))))))))))))..... ( -40.40)
>DroSec_CAF1 6279 120 + 1
AUCGGACGAGGUGGAAAAGAACCUUGCCCACCUGCAAAAGCUUCUGGAGAGAUCACAUGUGAAGCCCAACGUGAUUUGCAGAGGCUGCAAUAUGCAGCGAUACUGCAGCCUGUCCCAUCU
...(((((((((((..(((...)))..))))))((...((((((((.(..((((((...((.....))..))))))).))))))))......(((((.....))))))).)))))..... ( -41.30)
>DroSim_CAF1 6296 120 + 1
AUCGGACGAGGUGGAAAAGAACCUUGCCCACCUGCAACAUCUUCUGGAGAAAGCACAUGUGAAGCCCAACGUGAUUUGCAGAGGCUGCAAUAUGCAGCGAUACUGCAGCCUGUCCCAUCU
...((((.((((((..(((...)))..))))))((((.(((...(((.(...((....))....))))....)))))))..((((((((.(((......))).))))))))))))..... ( -39.30)
>DroYak_CAF1 6288 120 + 1
CUCGGAUGACUUGGAAAGGAACCUAAUCUUCCUUCAGACGCUUCUGGAGAAAGCACACGUAAGGCCCAAAGUGAUUUGCAGAGGAUGCAAAAUCCAGCGAUACUGCAGCGUGUCGCAUCU
(((((((.((((((.............(((.(((((((....))))))).)))....(....)..)).)))).))))).)).((((.....)))).(((((((......))))))).... ( -34.20)
>consensus
AUCGGACGAGGUGGAAAAGAACCUUGCCCACCUGCAAAAGCUUCUGGAGAAAGCACAUGUGAAGCCCAACGUGAUUUGCAGAGGCUGCAAUAUGCAGCGAUACUGCAGCCUGUCCCAUCU
...((.((((((........)))))).))..(((((((...(((....)))....(((((........))))).)))))))((((((((.(((......))).))))))))......... (-27.79 = -28.73 +   0.94)

alignment

secondary structure

dotplot

Window 3

Location	19,402,969 – 19,403,089
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.36
Mean single sequence MFE	-40.48
Consensus MFE	-27.46
Energy contribution	-28.40
Covariance contribution	0.94
Combinations/Pair	1.16
Mean z-score	-1.62
Structure conservation index	0.68
SVM decision value	0.05
SVM RNA-class probability	0.559214
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19402969 120 - 20766785
AGAUGGGACAGGCUGCAGUAUCGCUGCAUAUUGCAGCCUCUGCAUAUCACGCUGGGCUUCACAUGUGCUUUCUCCAGAAGCGUUUGCAGGUGAGCAAGGUUCUUUUCCACCUUGUCCGAU
..((.((((((((((((((((......))))))))))))(((((....(((((((((.........))))((....))))))).)))))......(((((........))))))))).)) ( -41.10)
>DroSec_CAF1 6279 120 - 1
AGAUGGGACAGGCUGCAGUAUCGCUGCAUAUUGCAGCCUCUGCAAAUCACGUUGGGCUUCACAUGUGAUCUCUCCAGAAGCUUUUGCAGGUGGGCAAGGUUCUUUUCCACCUCGUCCGAU
..((.((((((((((((((((......)))))))))))).((((((.....(((((..(((....)))....))))).....))))))((((((.(((...))).))))))..)))).)) ( -45.70)
>DroSim_CAF1 6296 120 - 1
AGAUGGGACAGGCUGCAGUAUCGCUGCAUAUUGCAGCCUCUGCAAAUCACGUUGGGCUUCACAUGUGCUUUCUCCAGAAGAUGUUGCAGGUGGGCAAGGUUCUUUUCCACCUCGUCCGAU
..((.((((((((((((((((......)))))))))))).((((((((...(((((...((....)).....)))))..))).)))))((((((.(((...))).))))))..)))).)) ( -42.90)
>DroYak_CAF1 6288 120 - 1
AGAUGCGACACGCUGCAGUAUCGCUGGAUUUUGCAUCCUCUGCAAAUCACUUUGGGCCUUACGUGUGCUUUCUCCAGAAGCGUCUGAAGGAAGAUUAGGUUCCUUUCCAAGUCAUCCGAG
(((((((.(((((....(((..(((.((.((((((.....)))))).....)).)))..))))))))).(((....)))))))))...(((.((((.((.......)).)))).)))... ( -32.20)
>consensus
AGAUGGGACAGGCUGCAGUAUCGCUGCAUAUUGCAGCCUCUGCAAAUCACGUUGGGCUUCACAUGUGCUUUCUCCAGAAGCGUUUGCAGGUGGGCAAGGUUCUUUUCCACCUCGUCCGAU
.(((..(..((((((((((((......))))))))))))...)..)))..(((((((........((((((((.((((....)))).))).))))).((.......)).....))))))) (-27.46 = -28.40 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:34 2006