Locus 1578

Sequence ID 2R_DroMel_CAF1
Location 5,939,913 – 5,940,006
Length 93
Max. P 0.998221
window2643 window2644

overview

Window 3

Location 5,939,913 – 5,940,006
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 87.25
Mean single sequence MFE -36.33
Consensus MFE -32.67
Energy contribution -33.55
Covariance contribution 0.88
Combinations/Pair 1.22
Mean z-score -3.56
Structure conservation index 0.90
SVM decision value 3.04
SVM RNA-class probability 0.998221
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5939913 93 + 20766785
GGGAAAGAUGAGGCCUCGUACGGGGUCUCCAUAUUUGUGUGAACCUCAAGAGGGGCCUUAAAAAAACCUGUUUGGGGCGUCACACAAAAAUGG
.........((((((((....))))))))(((.(((((((((.(((((((.(((............))).)))))))..))))))))).))). ( -38.10)
>DroSec_CAF1 81961 92 + 1
GGGAAUGAUGAGGCCUCGUGCGGGGUCUCCAUAUUUGUGUGAAUCUGAACAGGGGCCUUAAA-AAACCUGCUUGGGGCUACACACAAAUAUGG
.........((((((((....))))))))((((((((((((..(((....)))((((((((.-........)))))))).)))))))))))). ( -37.10)
>DroSim_CAF1 79775 93 + 1
GGGAAUGAUGAGGCCUCGUGCGGGGUCUCCAUAUUUGUCUGAAUCUGAACAGGGGCCUUAAAAAAACCUGCUUGGGGCCUCACACAAAUAUGG
.........((((((((....))))))))(((((((((.(((.(((....)))((((((((..........))))))))))).))))))))). ( -34.00)
>DroEre_CAF1 67310 91 + 1
GGGAAUGAAGAGGCUUCGUGCGAGGUCUCCAUAUUUGUGUGGAACUCGACAGGGGCCUCUAA-AAACCUGA-UGGGGCCUCACCCAAGUAUGG
(((.....(((((((((...((((...((((((....)))))).))))...)))))))))..-...)))..-((((......))))....... ( -36.10)
>consensus
GGGAAUGAUGAGGCCUCGUGCGGGGUCUCCAUAUUUGUGUGAAUCUCAACAGGGGCCUUAAA_AAACCUGCUUGGGGCCUCACACAAAUAUGG
.........((((((((....))))))))(((((((((((((.(((....)))((((((((..........))))))))))))))))))))). (-32.67 = -33.55 +   0.88)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 4

Location 5,939,913 – 5,940,006
Length 93
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 87.25
Mean single sequence MFE -26.61
Consensus MFE -18.51
Energy contribution -20.82
Covariance contribution 2.31
Combinations/Pair 1.12
Mean z-score -2.17
Structure conservation index 0.70
SVM decision value 0.65
SVM RNA-class probability 0.810758
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5939913 93 - 20766785
CCAUUUUUGUGUGACGCCCCAAACAGGUUUUUUUAAGGCCCCUCUUGAGGUUCACACAAAUAUGGAGACCCCGUACGAGGCCUCAUCUUUCCC
((((.(((((((((.(((.(((...(((((.....)))))....))).)))))))))))).)))).((..((......))..))......... ( -27.30)
>DroSec_CAF1 81961 92 - 1
CCAUAUUUGUGUGUAGCCCCAAGCAGGUUU-UUUAAGGCCCCUGUUCAGAUUCACACAAAUAUGGAGACCCCGCACGAGGCCUCAUCAUUCCC
(((((((((((((........((((((..(-(....))..))))))......))))))))))))).((..((......))..))......... ( -26.94)
>DroSim_CAF1 79775 93 - 1
CCAUAUUUGUGUGAGGCCCCAAGCAGGUUUUUUUAAGGCCCCUGUUCAGAUUCAGACAAAUAUGGAGACCCCGCACGAGGCCUCAUCAUUCCC
((((((((((.((((...(..((((((..((.....))..))))))..).)))).)))))))))).((..((......))..))......... ( -26.10)
>DroEre_CAF1 67310 91 - 1
CCAUACUUGGGUGAGGCCCCA-UCAGGUUU-UUAGAGGCCCCUGUCGAGUUCCACACAAAUAUGGAGACCUCGCACGAAGCCUCUUCAUUCCC
.......((((......))))-...((...-..((((((...((((((((((((........)))))..)))).)))..)))))).....)). ( -26.10)
>consensus
CCAUAUUUGUGUGAGGCCCCAAGCAGGUUU_UUUAAGGCCCCUGUUCAGAUUCACACAAAUAUGGAGACCCCGCACGAGGCCUCAUCAUUCCC
(((((((((((((((......((((((.............))))))....))))))))))))))).((..((......))..))......... (-18.51 = -20.82 +   2.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:57 2006