Locus 9258

Sequence ID 3R_DroMel_CAF1
Location 24,675,754 – 24,675,934
Length 180
Max. P 0.957108
window14804 window14805

overview

Window 4

Location 24,675,754 – 24,675,874
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.73
Mean single sequence MFE -37.18
Consensus MFE -31.70
Energy contribution -32.38
Covariance contribution 0.68
Combinations/Pair 1.07
Mean z-score -1.77
Structure conservation index 0.85
SVM decision value 1.47
SVM RNA-class probability 0.957108
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24675754 120 + 27905053
UAGGAGCCAAUUUUAGUGGUUUAGUCCAGCCACUUGACCCACAUUCCGGUGGUUUCCCUUUCCGCUGCCGGCGAGCGAGUUCCACUUUGUCGGCGACCUCAUAUUGUUGGCUAUAACACA
....(((((((..((((((...((...(((((((.((.......)).)))))))...))..))))((((((((((.(.....).).)))))))))......))..)))))))........ ( -37.30)
>DroSec_CAF1 16772 120 + 1
UAGGAGCUAAUUUUAGUGGUUUAGGCCAGCCACUUGACCCACAUUCCGGUGGUUUCCCCUUCCGCAGCCGGCGAGCGAGUUCCACUUUGUCGGCGACCUCAUAUUGCUGGCUAUAACACA
..((((((.......((((...(((..(((((((.((.......)).)))))))...))).)))).((......)).)))))).....((((((((.......))))))))......... ( -36.60)
>DroSim_CAF1 16822 120 + 1
UAGGAGCUAAUUUUAGUGGUUUAGGCCAGCCACUUGACCCACAUUCCGGUGGUUUCCCUUUCCGCAGUCGGCGAGCGAGUUCCACUUUGUCGGCGACCUCAUAUUGCUGGCUAUAACACA
..(((((........((((...(((..(((((((.((.......)).)))))))..)))..))))..(((.....)))))))).....((((((((.......))))))))......... ( -37.00)
>DroEre_CAF1 18195 114 + 1
--GUAGCUAAUUUUAGUGGUUUAGGCCAGCCACUUGACCCACAUUCCCGUGGUUUCCCUUUCCGCAGCCGGC----GAGUUCCACUUUGUCGGCGACCUCAUAUUGCUGGCUAUAACACA
--(((((((......((((...(((..((((((..((.......))..))))))..)))..)))).((((((----(((......))))))))).............)))))))...... ( -37.50)
>DroYak_CAF1 17242 116 + 1
UCGUAGCUAAUUUUAGUGGUUUUGGCCAGCCACUUGACCCACAUUCCCGUGGUUUCCCUUUCCGCAGCCGGC----GAGUUCCACUUUGUCGGCGACCUCAUAUUGCUGGCUAUAACACA
...............(((....((((((((....(((.((((......))))..............((((((----(((......)))))))))....)))....))))))))...))). ( -37.50)
>consensus
UAGGAGCUAAUUUUAGUGGUUUAGGCCAGCCACUUGACCCACAUUCCGGUGGUUUCCCUUUCCGCAGCCGGCGAGCGAGUUCCACUUUGUCGGCGACCUCAUAUUGCUGGCUAUAACACA
....(((((......((((...(((..(((((((.((.......)).)))))))..)))..)))).((((((....(((.....))).)))))).............)))))........ (-31.70 = -32.38 +   0.68)

alignment

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secondary structure

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dotplot

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Window 5

Location 24,675,834 – 24,675,934
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.20
Mean single sequence MFE -33.99
Consensus MFE -28.65
Energy contribution -28.53
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.56
Structure conservation index 0.84
SVM decision value 0.63
SVM RNA-class probability 0.803883
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24675834 100 + 27905053
UCCACUUUGUCGGCGACCUCAUAUUGUUGGCUAUAACACAAUUAAUUAAUUAAAUUCUUAAGCCUCCCCAGUGGCACUCGAGUGCAGGGGCGUCGCAGGG--------------------
....(((((.(((((.((((.(((((..((((............................))))....)))))((((....)))).))))))))))))))-------------------- ( -28.59)
>DroSec_CAF1 16852 105 + 1
UCCACUUUGUCGGCGACCUCAUAUUGCUGGCUAUAACACAAUUAAUUAAUUAAAUUCUUAAGCCUCCCCAGUGGCACACGAGUGCAGAGGCGUUGCAGGG-GG--------------GAG
(((.(((((.(((((.((((.(((((..((((............................))))....)))))((((....)))).))))))))))))))-.)--------------)). ( -32.39)
>DroSim_CAF1 16902 106 + 1
UCCACUUUGUCGGCGACCUCAUAUUGCUGGCUAUAACACAAUUAAUUAAUUAAAUUCUUAAGCCUCCCCAGUGGCACACGAGUGCAGGGGCGUCGCAGGGGGG--------------GAG
(((.(((((.(((((.((((.(((((..((((............................))))....)))))((((....)))).))))))))))))))..)--------------)). ( -33.49)
>DroEre_CAF1 18269 102 + 1
UCCACUUUGUCGGCGACCUCAUAUUGCUGGCUAUAACACAAUUAAUUAAUUAAAUUCUUAAGCCUCCCCAGUGGCACUUGAGUGCAGGGGCGUCGCUGGGGG------------------
........((((((((.......))))))))..................................((((((((((.((((....))))...)))))))))).------------------ ( -31.30)
>DroYak_CAF1 17318 120 + 1
UCCACUUUGUCGGCGACCUCAUAUUGCUGGCUAUAACACAAUUAAUUAAUUAAAUUCUUAAGCCUCCCCAGUGGCACUUGAGUGCAGGGGCGUCGCAGGGGGGGCAGAGGCGUCGUAGAA
.....((((.(((((.((((..((((.((.......))))))...................((((((((.(((((.((((....))))...))))).)))))))).))))))))))))). ( -44.20)
>consensus
UCCACUUUGUCGGCGACCUCAUAUUGCUGGCUAUAACACAAUUAAUUAAUUAAAUUCUUAAGCCUCCCCAGUGGCACUCGAGUGCAGGGGCGUCGCAGGGGGG______________GA_
....(((((.(((((.((((.(((((..((((............................))))....)))))((((....)))).)))))))))))))).................... (-28.65 = -28.53 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:30:07 2006