Locus 539

Sequence ID 2L_DroMel_CAF1
Location 1,676,223 – 1,676,331
Length 108
Max. P 0.980823
window860 window861

overview

Window 0

Location 1,676,223 – 1,676,331
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.78
Mean single sequence MFE -28.66
Consensus MFE -23.83
Energy contribution -23.89
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.75
Structure conservation index 0.83
SVM decision value 1.87
SVM RNA-class probability 0.980823
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1676223 108 + 22407834
-----UUUUGCCCGCUUUUUCUU-------ACACUGCCCAUUUUCAUUUAGGAAAUGCAUGCUGGAGUGAUAAUUCCAAAUCGGCAGUUUGAGUACGGACAGCCGCCUUCAUGAGUCCAC
-----...............(((-------(.(((((((((((((.....))))))).....((((((....))))))....)))))).))))...((((..............)))).. ( -27.94)
>DroSec_CAF1 2685 105 + 1
-----UUUUGCCCGCUUUUCCUU-------ACACUGCCCAUUUUCAUUUAGAAAAUGCAUGCUGGAGUGAUAAUUCCAAAUCGGCAGUUUGAGUACGGACAA---CCUUCAUUACUCCAC
-----..(((.(((......(((-------(.(((((((((((((.....))))))).....((((((....))))))....)))))).))))..))).)))---............... ( -27.40)
>DroSim_CAF1 3571 105 + 1
-----UUUUGCCCGCUUUUCCUU-------ACACUGCCCAUUUUCAUUUAGAAAAUGCAUGCUGGAGUGAUAAUUCCAAAUCGGCAGUUUGAGUACGGACAA---CCUUCAUUAGUCCAC
-----...............(((-------(.(((((((((((((.....))))))).....((((((....))))))....)))))).))))...((((..---.........)))).. ( -28.90)
>DroYak_CAF1 3684 117 + 1
UCUUUUUUUUGCCGCUUUUCCUUUCCUUGCACACUGCCCAUUUUCAUUUAGAAAAUGCAUGCUGGAGUGAUAAUUCCAAAUCGGCAGUUUGAGGACGGACAA---CCUUCAUUAGUCCAC
.......................((((..((.(((((((((((((.....))))))).....((((((....))))))....)))))).)))))).((((..---.........)))).. ( -30.40)
>consensus
_____UUUUGCCCGCUUUUCCUU_______ACACUGCCCAUUUUCAUUUAGAAAAUGCAUGCUGGAGUGAUAAUUCCAAAUCGGCAGUUUGAGUACGGACAA___CCUUCAUUAGUCCAC
................................(((((((((((((.....))))))).....((((((....))))))....))))))........((((..............)))).. (-23.83 = -23.89 +   0.06)

alignment

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secondary structure

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dotplot

Postscript

Window 1

Location 1,676,223 – 1,676,331
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.78
Mean single sequence MFE -30.73
Consensus MFE -24.92
Energy contribution -25.92
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.27
Structure conservation index 0.81
SVM decision value 1.23
SVM RNA-class probability 0.933892
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1676223 108 - 22407834
GUGGACUCAUGAAGGCGGCUGUCCGUACUCAAACUGCCGAUUUGGAAUUAUCACUCCAGCAUGCAUUUCCUAAAUGAAAAUGGGCAGUGU-------AAGAAAAAGCGGGCAAAA-----
((.(.((......))).))(((((((..((..((((((...(((((........)))))(((.((((.....))))...)))))))))..-------..))....)))))))...----- ( -27.30)
>DroSec_CAF1 2685 105 - 1
GUGGAGUAAUGAAGG---UUGUCCGUACUCAAACUGCCGAUUUGGAAUUAUCACUCCAGCAUGCAUUUUCUAAAUGAAAAUGGGCAGUGU-------AAGGAAAAGCGGGCAAAA-----
...............---((((((((..((..((((((...(((((........)))))....(((((((.....)))))))))))))..-------...))...))))))))..----- ( -32.10)
>DroSim_CAF1 3571 105 - 1
GUGGACUAAUGAAGG---UUGUCCGUACUCAAACUGCCGAUUUGGAAUUAUCACUCCAGCAUGCAUUUUCUAAAUGAAAAUGGGCAGUGU-------AAGGAAAAGCGGGCAAAA-----
...............---((((((((..((..((((((...(((((........)))))....(((((((.....)))))))))))))..-------...))...))))))))..----- ( -32.10)
>DroYak_CAF1 3684 117 - 1
GUGGACUAAUGAAGG---UUGUCCGUCCUCAAACUGCCGAUUUGGAAUUAUCACUCCAGCAUGCAUUUUCUAAAUGAAAAUGGGCAGUGUGCAAGGAAAGGAAAAGCGGCAAAAAAAAGA
.........((..(.---((.(((.((((((.((((((...(((((........)))))....(((((((.....))))))))))))).))..))))..))).)).)..))......... ( -31.40)
>consensus
GUGGACUAAUGAAGG___UUGUCCGUACUCAAACUGCCGAUUUGGAAUUAUCACUCCAGCAUGCAUUUUCUAAAUGAAAAUGGGCAGUGU_______AAGGAAAAGCGGGCAAAA_____
..................((((((((......((((((...(((((........)))))....(((((((.....))))))))))))).................))))))))....... (-24.92 = -25.92 +   1.00)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:40 2006