Locus 1625

Sequence ID	2R_DroMel_CAF1
Location	6,092,213 – 6,092,312
Length	99
Max. P	0.971255

overview

Window 9

Location	6,092,213 – 6,092,312
Length	99
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	93.24
Mean single sequence MFE	-25.74
Consensus MFE	-22.48
Energy contribution	-22.72
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.51
Structure conservation index	0.87
SVM decision value	1.67
SVM RNA-class probability	0.971255
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6092213 99 + 20766785
AAAGCCAACAAAUGAAAUGUAAGUUUCACUCAUCGAUGGCCAGCAGCAG---UGGAUACGACUAAAAUUGAAUCCAAUAUGAGCCGCCAAGCUGCUGAGCCA
............((((((....))))))........(((((((((((..---(((((.(((......))).)))))...((......)).))))))).)))) ( -28.30)
>DroSec_CAF1 109950 93 + 1
AAAGCCAACAAAUGAACUGUAAGUUUCACUCAUCGAUGGCCAGCAGC------GGAUACGACUAAAAUUGAAUCCAAUAUGAGC---CAAGCUGCUGAGCCA
.((((..(((.......)))..))))..........(((((((((((------((((.(((......))).))))....((...---)).))))))).)))) ( -23.60)
>DroEre_CAF1 113446 99 + 1
AAAGCCAACAAAUGAACUGUAAGUUUCACUCAGCGAUGGCCAGCAGCAGCGGCGGAUACGACUAAAAUUGAAUCCAAUAUGAGC---CAAGCUGCUGAGCCA
...((........((((.....))))......))..(((((((((((...(((((((.(((......))).)))).......))---)..))))))).)))) ( -27.45)
>DroYak_CAF1 111710 93 + 1
AAAGCCAACAAAUGAACUGUAAGUUUCACUCAUCGAUGGCCAGCAG------CGGAUACGACUAAAAUUGAAUCCAAUAUGAGC---CAAGCUGCUGAGCCA
.((((..(((.......)))..))))..........((((((((((------(((((.(((......))).))))....((...---)).))))))).)))) ( -23.60)
>consensus
AAAGCCAACAAAUGAACUGUAAGUUUCACUCAUCGAUGGCCAGCAGC_____CGGAUACGACUAAAAUUGAAUCCAAUAUGAGC___CAAGCUGCUGAGCCA
.((((..(((.......)))..))))..........(((((((((((......((((.(((......))).))))....((......)).))))))).)))) (-22.48 = -22.72 +   0.25)

alignment

secondary structure

dotplot

Window 0

Location	6,092,213 – 6,092,312
Length	99
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	93.24
Mean single sequence MFE	-34.58
Consensus MFE	-26.51
Energy contribution	-27.01
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-3.93
Structure conservation index	0.77
SVM decision value	0.54
SVM RNA-class probability	0.776405
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6092213 99 - 20766785
UGGCUCAGCAGCUUGGCGGCUCAUAUUGGAUUCAAUUUUAGUCGUAUCCA---CUGCUGCUGGCCAUCGAUGAGUGAAACUUACAUUUCAUUUGUUGGCUUU
((((.(((((((.((((((((...((((....))))...)))))...)))---..)))))))))))((((..(((((((......)))))))..)))).... ( -39.20)
>DroSec_CAF1 109950 93 - 1
UGGCUCAGCAGCUUG---GCUCAUAUUGGAUUCAAUUUUAGUCGUAUCC------GCUGCUGGCCAUCGAUGAGUGAAACUUACAGUUCAUUUGUUGGCUUU
((((.(((((((.((---(((...((((....))))...))))).....------)))))))))))((((..((((((........))))))..)))).... ( -33.20)
>DroEre_CAF1 113446 99 - 1
UGGCUCAGCAGCUUG---GCUCAUAUUGGAUUCAAUUUUAGUCGUAUCCGCCGCUGCUGCUGGCCAUCGCUGAGUGAAACUUACAGUUCAUUUGUUGGCUUU
((((.(((((((.((---((..((((..((((.......))))))))..))))..)))))))))))..((((((((((........)))))))...)))... ( -32.70)
>DroYak_CAF1 111710 93 - 1
UGGCUCAGCAGCUUG---GCUCAUAUUGGAUUCAAUUUUAGUCGUAUCCG------CUGCUGGCCAUCGAUGAGUGAAACUUACAGUUCAUUUGUUGGCUUU
((((.(((((((.((---(((...((((....))))...))))).....)------))))))))))((((..((((((........))))))..)))).... ( -33.20)
>consensus
UGGCUCAGCAGCUUG___GCUCAUAUUGGAUUCAAUUUUAGUCGUAUCCG_____GCUGCUGGCCAUCGAUGAGUGAAACUUACAGUUCAUUUGUUGGCUUU
((((.(((((((............((((((......)))))).............)))))))))))((((((((((((........)))))))))))).... (-26.51 = -27.01 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:09 2006