Locus 8504

Sequence ID 3L_DroMel_CAF1
Location 22,296,278 – 22,296,398
Length 120
Max. P 0.971887
window13919 window13920

overview

Window 9

Location 22,296,278 – 22,296,398
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -31.95
Consensus MFE -27.70
Energy contribution -27.95
Covariance contribution 0.25
Combinations/Pair 1.09
Mean z-score -3.21
Structure conservation index 0.87
SVM decision value 1.57
SVM RNA-class probability 0.964328
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22296278 120 + 23771897
UUAAAACAAAAGUUCCCUUCAUACGUGAUAAAGUCAAAAUGUCGAAUGCAACUGUGAAAACAAUCGGAGCCCCCAACCCGGUACUCAAGCUGUUAAAACAGCAUUUGAUGGGGAACUUUU
.......(((((((((((.......((((...))))....(((((((((...(((...((((....(((..((......))..)))....))))...))))))))))))))))))))))) ( -33.50)
>DroSec_CAF1 54848 120 + 1
UUAAAACAAAAGUUCCCCUCAUACGUGAUAAAGUCAAAAUGUCGAAUGCAACUGUGAAAACAAUCGGAGCGCCCAGCUCGGUACUCAAGCUGUUAAAACAACAUUUGAUGGGGAACUUUU
.......(((((((((((.......((((...))))....((((((((....(((...((((....(((..((......))..)))....))))...))).))))))))))))))))))) ( -34.30)
>DroEre_CAF1 53559 120 + 1
UUAAAACAAAAGUUCCCUUCAUACGUGAUAAAGUCAAAAUGUCGAAUGCAACUGUGAAAACAAUCGGAGCCCUCAGCUCGGUACUCAAGCUGUUAAAACAACAUUUGAUGGGGAACUUUU
.......(((((((((((.......((((...))))....((((((((....(((....)))..(.((((.....)))).)....................))))))))))))))))))) ( -28.90)
>DroYak_CAF1 19730 120 + 1
UUAAAACAAAAGUUCCCUUCAUACGUGAUAAAGUCAAAAUGUCGAAUGCAACUGUAAAAACAAUCGGAGCCCGCAGCCCGGUACUCAAGUUGUAAAAGCAACAUUUAAUGGGGAACUUUU
.......(((((((((((.......((((...))))((((((.(..(((((((((....)).(((((.((.....))))))).....)))))))....).))))))...))))))))))) ( -31.10)
>consensus
UUAAAACAAAAGUUCCCUUCAUACGUGAUAAAGUCAAAAUGUCGAAUGCAACUGUGAAAACAAUCGGAGCCCCCAGCCCGGUACUCAAGCUGUUAAAACAACAUUUGAUGGGGAACUUUU
.......(((((((((((.......((((...))))....((((((((....(((...((((....(((..((......))..)))....))))...))).))))))))))))))))))) (-27.70 = -27.95 +   0.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,296,278 – 22,296,398
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -33.80
Consensus MFE -30.70
Energy contribution -29.70
Covariance contribution -1.00
Combinations/Pair 1.13
Mean z-score -2.49
Structure conservation index 0.91
SVM decision value 1.68
SVM RNA-class probability 0.971887
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22296278 120 - 23771897
AAAAGUUCCCCAUCAAAUGCUGUUUUAACAGCUUGAGUACCGGGUUGGGGGCUCCGAUUGUUUUCACAGUUGCAUUCGACAUUUUGACUUUAUCACGUAUGAAGGGAACUUUUGUUUUAA
((((((((((..(((...(((((....)))))..((((.....((((((.((...((((((....)))))))).))))))......)))).........))).))))))))))....... ( -31.80)
>DroSec_CAF1 54848 120 - 1
AAAAGUUCCCCAUCAAAUGUUGUUUUAACAGCUUGAGUACCGAGCUGGGCGCUCCGAUUGUUUUCACAGUUGCAUUCGACAUUUUGACUUUAUCACGUAUGAGGGGAACUUUUGUUUUAA
(((((((((((.((((((((((......(((((((.....))))))).......(((((((....)))))))....))))).))))).....(((....))))))))))))))....... ( -38.60)
>DroEre_CAF1 53559 120 - 1
AAAAGUUCCCCAUCAAAUGUUGUUUUAACAGCUUGAGUACCGAGCUGAGGGCUCCGAUUGUUUUCACAGUUGCAUUCGACAUUUUGACUUUAUCACGUAUGAAGGGAACUUUUGUUUUAA
((((((((((..((((((((((......(((((((.....))))))).......(((((((....)))))))....))))).))))).....(((....))).))))))))))....... ( -34.20)
>DroYak_CAF1 19730 120 - 1
AAAAGUUCCCCAUUAAAUGUUGCUUUUACAACUUGAGUACCGGGCUGCGGGCUCCGAUUGUUUUUACAGUUGCAUUCGACAUUUUGACUUUAUCACGUAUGAAGGGAACUUUUGUUUUAA
((((((((((....((((((((............((((.(((.....)))))))(((((((....)))))))....))))))))........(((....))).))))))))))....... ( -30.60)
>consensus
AAAAGUUCCCCAUCAAAUGUUGUUUUAACAGCUUGAGUACCGAGCUGGGGGCUCCGAUUGUUUUCACAGUUGCAUUCGACAUUUUGACUUUAUCACGUAUGAAGGGAACUUUUGUUUUAA
((((((((((..(((((.((((......))))((((((...((((.....))))(((((((....))))))).))))))...))))).....(((....))).))))))))))....... (-30.70 = -29.70 +  -1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:19 2006