Locus 439

Sequence ID 3L_DroMel_CAF1
Location 1,279,305 – 1,279,403
Length 98
Max. P 0.898295
window640 window641

overview

Window 0

Location 1,279,305 – 1,279,403
Length 98
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 80.53
Mean single sequence MFE -27.84
Consensus MFE -18.10
Energy contribution -18.62
Covariance contribution 0.52
Combinations/Pair 1.10
Mean z-score -1.76
Structure conservation index 0.65
SVM decision value 0.29
SVM RNA-class probability 0.668556
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1279305 98 + 23771897
---AAAUUAUA--------------U-UCAAAAGAGGGAAAUCCCCCUUGUACGAAGCGAACUAGUUCCAUUCGAUGGGCGGCUACUUAAAGCCGGCGAACCAGCUCAUCUCUAAC
---........--------------.-......(((((......)))))....(((..(((....)))..)))(((((((((((......))))((....)).)))))))...... ( -27.20)
>DroSec_CAF1 34061 98 + 1
---AAAUUUUA--------------U-UCAAAAGAGGGAAAUCCCCUUUGUACGAUGCGAACUAGUUCCAUUCGAUGGGCGGCUACUCAAAGCCGGCGAACCAACUCAUCUCUAAC
---........--------------.-.....((((((.....))))))....((((.(((....))))))).((((((.((((......))))((....))..))))))...... ( -23.80)
>DroSim_CAF1 34496 98 + 1
---AAAUUGUA--------------U-UCAAAAGAGGGAAAUCCCCUUUGUACGAUGCGAACUAGUUCCAUUCGAUGGGCGGCUACUCAAAGCCGGCGAACCAGCUCAUCUCUAAC
---...(((((--------------(-(....((((((.....))))))....))))))).............(((((((((((......))))((....)).)))))))...... ( -31.20)
>DroEre_CAF1 33950 112 + 1
---CAAUUUUAUAAUAAAUUCCCCUUAUCAAACAAGGGAAAUCCCCAUUGUACGAAGUGAACUGGUUCCAUUCGAUGGGCGGGUGCU-AAGGCCGGCGAACUAGCUCAUCCCUAAC
---.................(((((((((..(((((((.....))).))))..(((..(((....)))..))))))))).)))....-.(((..(((......)))....)))... ( -25.00)
>DroYak_CAF1 34903 115 + 1
AAGCGAUUUUAUAAUAAAUUCCCCUU-UCAAAAAAGGGAAAUCCCCAGUGUAGAAAGCGAACUGGUUCCAGUCGAUGGGCGGGUACUCAAUGCCGGCGAACCAGCUCAUCCCACAC
..((..(((((((....(((.(((((-(....)))))).)))......))))))).))((.(((((((((.....)).((.((((.....)))).))))))))).))......... ( -32.00)
>consensus
___AAAUUUUA______________U_UCAAAAGAGGGAAAUCCCCAUUGUACGAAGCGAACUAGUUCCAUUCGAUGGGCGGCUACUCAAAGCCGGCGAACCAGCUCAUCUCUAAC
...................................(((....)))...........(.(((....))))....(((((((((((......))))((....)).)))))))...... (-18.10 = -18.62 +   0.52) 

alignment

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secondary structure

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dotplot

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Window 1

Location 1,279,305 – 1,279,403
Length 98
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 80.53
Mean single sequence MFE -33.28
Consensus MFE -24.62
Energy contribution -24.98
Covariance contribution 0.36
Combinations/Pair 1.19
Mean z-score -1.96
Structure conservation index 0.74
SVM decision value 1.00
SVM RNA-class probability 0.898295
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1279305 98 - 23771897
GUUAGAGAUGAGCUGGUUCGCCGGCUUUAAGUAGCCGCCCAUCGAAUGGAACUAGUUCGCUUCGUACAAGGGGGAUUUCCCUCUUUUGA-A--------------UAUAAUUU---
....(((.(((((((((((..(((((......)))))..(((...)))))))))))))).)))....(((((((....)))))))....-.--------------........--- ( -33.40)
>DroSec_CAF1 34061 98 - 1
GUUAGAGAUGAGUUGGUUCGCCGGCUUUGAGUAGCCGCCCAUCGAAUGGAACUAGUUCGCAUCGUACAAAGGGGAUUUCCCUCUUUUGA-A--------------UAAAAUUU---
....((..(((..((((((..(((((......)))))..(((...)))))))))..)))..))...((((((((......)))))))).-.--------------........--- ( -26.40)
>DroSim_CAF1 34496 98 - 1
GUUAGAGAUGAGCUGGUUCGCCGGCUUUGAGUAGCCGCCCAUCGAAUGGAACUAGUUCGCAUCGUACAAAGGGGAUUUCCCUCUUUUGA-A--------------UACAAUUU---
....((..(((((((((((..(((((......)))))..(((...))))))))))))))..))(((((((((((......)))))))).-.--------------))).....--- ( -32.10)
>DroEre_CAF1 33950 112 - 1
GUUAGGGAUGAGCUAGUUCGCCGGCCUU-AGCACCCGCCCAUCGAAUGGAACCAGUUCACUUCGUACAAUGGGGAUUUCCCUUGUUUGAUAAGGGGAAUUUAUUAUAAAAUUG---
(((((((.((.((......)))).))))-))).((((.....((((..(((....)))..)))).....))))((((((((((((...)))))))))))).............--- ( -33.70)
>DroYak_CAF1 34903 115 - 1
GUGUGGGAUGAGCUGGUUCGCCGGCAUUGAGUACCCGCCCAUCGACUGGAACCAGUUCGCUUUCUACACUGGGGAUUUCCCUUUUUUGA-AAGGGGAAUUUAUUAUAAAAUCGCUU
(((((((((((((((((...(((((..((.((....)).))..).)))).)))))))))..))))))))...((((((((((((....)-)))))))))))............... ( -40.80)
>consensus
GUUAGAGAUGAGCUGGUUCGCCGGCUUUGAGUAGCCGCCCAUCGAAUGGAACUAGUUCGCUUCGUACAAAGGGGAUUUCCCUCUUUUGA_A______________UAAAAUUU___
....((..(((((((((((..(((((......)))))..((.....)))))))))))))..))...(((.((((....))))...)))............................ (-24.62 = -24.98 +   0.36) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:51 2006