Locus 5529

Sequence ID 2R_DroMel_CAF1
Location 17,666,516 – 17,666,622
Length 106
Max. P 0.974886
window8871 window8872

overview

Window 1

Location 17,666,516 – 17,666,622
Length 106
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.89
Mean single sequence MFE -33.88
Consensus MFE -26.73
Energy contribution -26.85
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -2.93
Structure conservation index 0.79
SVM decision value 1.74
SVM RNA-class probability 0.974886
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17666516 106 + 20766785
------GCUACUGUUGAAAAAUGUUGUUUACAGGCAAUUAAAAAAAUUACAUGUACGUGCUGCAGCGACGACAAAGUUGCUGCCAGUGCGCAGCAAGGC--------AGCAACAGCAUCA
------(((..(((((.....((((((.((((.(.((((.....)))).).)))).(..((((((((((......))))))).)))..)))))))...)--------))))..))).... ( -35.50)
>DroSec_CAF1 19928 108 + 1
----CAGCUACUGUUGAAAAAUGUUGUUUACCAGCAAUUAAAAAAAUUACAUGUACGUGCUGCAGCGACGACAAAGUUGCUGCCAGUCCGCAGCAAGGC--------AGCAUCGGCAUCA
----..(((..(((((.....(((((.....))))).............(.(((.((..((((((((((......))))))).)))..))..))).).)--------))))..))).... ( -32.00)
>DroEre_CAF1 20325 108 + 1
----CUGCUACUGUUGAGAAAUGUUGUUUACCAGCAAUUAAAAAAAUUACAUGUACGUGCAGCAGCAACGACAAAGUUGCUGCCAGUCCGCAGCAAGGC--------AGCAACAUCAUCG
----(((((..(((((.....(((((.....)))))...................((..(.((((((((......))))))))..)..))))))).)))--------))........... ( -29.80)
>DroYak_CAF1 32002 120 + 1
UUUGCUGCUACUGUUGAAAAAUGUUGUUUACCAGCAAUUAAAAAAAUUACAUGUACGUGCUGCAGCGACGACAAAGUUGCUGCCAGUCCGCAGCAAGGCAGCCAGGCAGCAUCAUCAUCA
..(((((((.(((((......(((((.....)))))...............(((.((..((((((((((......))))))).)))..))..))).)))))...)))))))......... ( -38.20)
>consensus
____CUGCUACUGUUGAAAAAUGUUGUUUACCAGCAAUUAAAAAAAUUACAUGUACGUGCUGCAGCGACGACAAAGUUGCUGCCAGUCCGCAGCAAGGC________AGCAACAGCAUCA
......(((..(((((.....(((((.....)))))...................((..((((((((((......))))))).)))..))))))).)))..................... (-26.73 = -26.85 +   0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,666,516 – 17,666,622
Length 106
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.89
Mean single sequence MFE -34.45
Consensus MFE -22.55
Energy contribution -22.68
Covariance contribution 0.13
Combinations/Pair 1.07
Mean z-score -2.46
Structure conservation index 0.65
SVM decision value 0.25
SVM RNA-class probability 0.651562
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17666516 106 - 20766785
UGAUGCUGUUGCU--------GCCUUGCUGCGCACUGGCAGCAACUUUGUCGUCGCUGCAGCACGUACAUGUAAUUUUUUUAAUUGCCUGUAAACAACAUUUUUCAACAGUAGC------
...((((((((..--------....((((((((..((((((.....))))))..)).))))))..((((.((((((.....)))))).))))............))))))))..------ ( -31.90)
>DroSec_CAF1 19928 108 - 1
UGAUGCCGAUGCU--------GCCUUGCUGCGGACUGGCAGCAACUUUGUCGUCGCUGCAGCACGUACAUGUAAUUUUUUUAAUUGCUGGUAAACAACAUUUUUCAACAGUAGCUG----
..........(((--------((..((((((((..((((((.....))))))...))))))))..(((..((((((.....))))))..))).................)))))..---- ( -28.50)
>DroEre_CAF1 20325 108 - 1
CGAUGAUGUUGCU--------GCCUUGCUGCGGACUGGCAGCAACUUUGUCGUUGCUGCUGCACGUACAUGUAAUUUUUUUAAUUGCUGGUAAACAACAUUUCUCAACAGUAGCAG----
(((..(.((((((--------(((...(....)...))))))))).)..))).((((((((......((.((((((.....))))))))((.....)).........)))))))).---- ( -37.00)
>DroYak_CAF1 32002 120 - 1
UGAUGAUGAUGCUGCCUGGCUGCCUUGCUGCGGACUGGCAGCAACUUUGUCGUCGCUGCAGCACGUACAUGUAAUUUUUUUAAUUGCUGGUAAACAACAUUUUUCAACAGUAGCAGCAAA
.(((((..((((((((...((((......))))...)))))))...)..)))))(((((.((.....((.((((((.....))))))))((.....))...........)).)))))... ( -40.40)
>consensus
UGAUGAUGAUGCU________GCCUUGCUGCGGACUGGCAGCAACUUUGUCGUCGCUGCAGCACGUACAUGUAAUUUUUUUAAUUGCUGGUAAACAACAUUUUUCAACAGUAGCAG____
.((((((...((.........)).(((((((......)))))))....))))))(((((...........((((((.....))))))..((.....))...........)))))...... (-22.55 = -22.68 +   0.13)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:00 2006