Locus 3876

Sequence ID X_DroMel_CAF1
Location 10,330,138 – 10,330,231
Length 93
Max. P 0.807642
window6372 window6373

overview

Window 2

Location 10,330,138 – 10,330,231
Length 93
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 81.49
Mean single sequence MFE -26.23
Consensus MFE -18.05
Energy contribution -19.43
Covariance contribution 1.38
Combinations/Pair 1.09
Mean z-score -1.90
Structure conservation index 0.69
SVM decision value 0.64
SVM RNA-class probability 0.807642
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10330138 93 + 22224390
-----------------GAUUGGGAUCCACUACACUUGCAGAAAAGGAAUGGCAGAGGGUAA-AACCCAAUCAACUCCCAAAUAAAUCAAGCAA-AGAGACGCCUCUGCGUC
-----------------..((((((((..(((..(((......)))...)))..))(((...-..))).......)))))).............-...(((((....))))) ( -21.00)
>DroSec_CAF1 2061 93 + 1
-----------------GAUUGGGAUCCACUGUACUUGCAGAAAAGGAAUGGCAGAGGACAA-AACCCAAUCAACUCCCAAAUAAAUCAAGCAA-AGAGACGCCUCUGCGUC
-----------------(((((((.(((.((((.(((......))).....)))).)))...-..)))))))......................-...(((((....))))) ( -24.40)
>DroEre_CAF1 2096 107 + 1
---UAUGGGAGAUGGGAGAUGGGGAGCCACUACACUUGCAGAAAGGGAAUGGCAGAGGGUAA-AACCCAAUCAACUCCCAAAUAAAUCAAGUAA-AGAGACGCCUCUGCGUC
---..(((.(..((((((.(((...((((...(.(((.....))))...))))...(((...-..)))..))).))))))..)...))).....-...(((((....))))) ( -30.50)
>DroYak_CAF1 2081 112 + 1
GGGAGAGCGGGAUUGGUGAUGGGGAGCCAAUACACUUGCAGAAAUGGAAUGGCAGAGGGUAAAAACCCAAUCAAUUCCCUAAUAAAUCAAGUAAAAGAGAAGCCUCUGCGUC
......((....(((((..((((((((((......((.((....)).))))))...((((....)))).......))))))....))))).....((((....))))))... ( -29.00)
>consensus
_________________GAUGGGGAGCCACUACACUUGCAGAAAAGGAAUGGCAGAGGGUAA_AACCCAAUCAACUCCCAAAUAAAUCAAGCAA_AGAGACGCCUCUGCGUC
...................((((((((((.....(((......)))...))))...((((....)))).......)))))).................(((((....))))) (-18.05 = -19.43 +   1.38)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 3

Location 10,330,138 – 10,330,231
Length 93
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 81.49
Mean single sequence MFE -26.73
Consensus MFE -22.72
Energy contribution -22.09
Covariance contribution -0.63
Combinations/Pair 1.27
Mean z-score -1.63
Structure conservation index 0.85
SVM decision value 0.53
SVM RNA-class probability 0.770608
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10330138 93 - 22224390
GACGCAGAGGCGUCUCU-UUGCUUGAUUUAUUUGGGAGUUGAUUGGGUU-UUACCCUCUGCCAUUCCUUUUCUGCAAGUGUAGUGGAUCCCAAUC-----------------
(((((....)))))...-.............((((((((.((..(((..-...))))).))...(((....((((....)))).)))))))))..----------------- ( -26.00)
>DroSec_CAF1 2061 93 - 1
GACGCAGAGGCGUCUCU-UUGCUUGAUUUAUUUGGGAGUUGAUUGGGUU-UUGUCCUCUGCCAUUCCUUUUCUGCAAGUACAGUGGAUCCCAAUC-----------------
(((((....)))))...-...((..(.....)..))....(((((((..-..((((.(((...((.(......).))...))).)))))))))))----------------- ( -24.60)
>DroEre_CAF1 2096 107 - 1
GACGCAGAGGCGUCUCU-UUACUUGAUUUAUUUGGGAGUUGAUUGGGUU-UUACCCUCUGCCAUUCCCUUUCUGCAAGUGUAGUGGCUCCCCAUCUCCCAUCUCCCAUA---
(((((....)))))...-..............((((((.((...(((..-...)))...((((((.((((.....))).).))))))....)).)))))).........--- ( -30.80)
>DroYak_CAF1 2081 112 - 1
GACGCAGAGGCUUCUCUUUUACUUGAUUUAUUAGGGAAUUGAUUGGGUUUUUACCCUCUGCCAUUCCAUUUCUGCAAGUGUAUUGGCUCCCCAUCACCAAUCCCGCUCUCCC
((.((((((....))))................((((.(((...((((....))))...((((...(((((....)))))...))))..........))))))))))).... ( -25.50)
>consensus
GACGCAGAGGCGUCUCU_UUACUUGAUUUAUUUGGGAGUUGAUUGGGUU_UUACCCUCUGCCAUUCCUUUUCUGCAAGUGUAGUGGAUCCCAAUC_________________
(((((....))))).....((((((........((((((.(...((((....))))....).))))))......))))))................................ (-22.72 = -22.09 +  -0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:50 2006