Locus 7976

Sequence ID X_DroMel_CAF1
Location 19,871,953 – 19,872,095
Length 142
Max. P 0.975274
window13084 window13085

overview

Window 4

Location 19,871,953 – 19,872,066
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.77
Mean single sequence MFE -35.34
Consensus MFE -31.04
Energy contribution -31.24
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.88
SVM decision value 1.75
SVM RNA-class probability 0.975274
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19871953 113 + 22224390
UUCAAGCAAAACAAUUUUGCAUUACAAAAGGGCAUAGAGCUCACGGGCCGCUGACCACCGACCAGAAAGCGCAACAAAGUGCUGGACACUGGUCGCCCCACGGGAUUUUGAGG-------
((((((((((.....))))).........((((.(((.(((....)))..)))......((((((..(((((......))))).....)))))))))).........))))).------- ( -34.50)
>DroSec_CAF1 26174 113 + 1
UUCAAGCAAAACAAUUUUGCAUUACAAAAGGGCAUAGAGCUCACGGGCCGCUGACCACCGACCAGAAAGCGCAACAAAGUGCUGGACACUGGUCGCCCCACGGGACUUUGCCG-------
.....(((((.....)))))..........((((..((((((..((((....(.....)((((((..(((((......))))).....))))))))))...))).))))))).------- ( -35.30)
>DroSim_CAF1 17314 119 + 1
UUCAAGCAAAACAAUUUUGCAUUACAAAAGGGCAUAGAGCUCACGGGCCGCUGAUCA-UGACCAGAAAGCGCAACAAAGUGCUGGACACUGGUCGCCCCACGGGACUUUGCCGGGAAAUG
(((..(((((.....))))).........((((.(((.(((....)))..)))....-.((((((..(((((......))))).....))))))))))..(((.......))).)))... ( -35.30)
>DroEre_CAF1 3722 112 + 1
UUCAAGCAAAACAAUUUUGCAUUACAAAAGGGCAUAGAGCUCACGGGCCGCUGACCACCGACCAGAAAGCGCAACAAAGUGCUGGACACUGGUCGCCCCGCGGGAUUUUCCC--------
.....(((((.....))))).........((((.(((.(((....)))..)))......((((((..(((((......))))).....))))))))))...(((.....)))-------- ( -35.70)
>DroYak_CAF1 1254 115 + 1
UUCAAGCAAAACAAUUUUGCAUUACAAAAGGGCAUAGAGCUCACGGGCCGCUGACCAGCGACCAGAAAGCGCAACAAAGUGCUGGACACUGGUCACCCACAGGGAUUUUUCC-----ACG
.....(((((.....))))).........((((.....))))..(((..(((....)))((((((..(((((......))))).....)))))).)))....(((....)))-----... ( -35.90)
>consensus
UUCAAGCAAAACAAUUUUGCAUUACAAAAGGGCAUAGAGCUCACGGGCCGCUGACCACCGACCAGAAAGCGCAACAAAGUGCUGGACACUGGUCGCCCCACGGGAUUUUGCCG_______
.....(((((.....))))).........((((.(((.(((....)))..)))......((((((..(((((......))))).....))))))))))...................... (-31.04 = -31.24 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,871,993 – 19,872,095
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.79
Mean single sequence MFE -37.58
Consensus MFE -28.61
Energy contribution -28.61
Covariance contribution -0.00
Combinations/Pair 1.22
Mean z-score -1.60
Structure conservation index 0.76
SVM decision value 0.24
SVM RNA-class probability 0.648373
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19871993 102 - 22224390
UUUU----------CCUGUGCUUUUCCCCGCAUUUCCCC--------CCUCAAAAUCCCGUGGGGCGACCAGUGUCCAGCACUUUGUUGCGCUUUCUGGUCGGUGGUCAGCGGCCCGUGA
...(----------(.((.(((.((..((((......((--------((.(........).))))(((((((.((.((((.....)))).))...)))))))))))..)).))).)).)) ( -34.00)
>DroSec_CAF1 26214 111 - 1
UUUUCCCCUCAUUUCCCGCGUUUUUCCCCGCAUUUCCC---------CGGCAAAGUCCCGUGGGGCGACCAGUGUCCAGCACUUUGUUGCGCUUUCUGGUCGGUGGUCAGCGGCCCGUGA
........((((...((((........((((...((((---------(((.......))).))))(((((((.((.((((.....)))).))...)))))))))))...))))...)))) ( -38.00)
>DroSim_CAF1 17354 119 - 1
UUUUCCCCUCAUUUCCCGCGCUUUUCCCCGCAUUUCCCCGCAUUUCCCGGCAAAGUCCCGUGGGGCGACCAGUGUCCAGCACUUUGUUGCGCUUUCUGGUCA-UGAUCAGCGGCCCGUGA
........((((...((((......((((((((((..(((.......)))..))))...)))))).((((((.((.((((.....)))).))...)))))).-......))))...)))) ( -37.40)
>DroEre_CAF1 3762 102 - 1
---------CAUUUUCUGCGCUUUUCCCCGCGUUUCCCC---------GGGAAAAUCCCGCGGGGCGACCAGUGUCCAGCACUUUGUUGCGCUUUCUGGUCGGUGGUCAGCGGCCCGUGA
---------.........((((.....((((...(((((---------(((.....)))).))))(((((((.((.((((.....)))).))...)))))))))))..))))........ ( -40.10)
>DroYak_CAF1 1294 108 - 1
-------CGCAUUUCCCGCGCUUUUCCUCGCAUUUCCCCCCGU-----GGAAAAAUCCCUGUGGGUGACCAGUGUCCAGCACUUUGUUGCGCUUUCUGGUCGCUGGUCAGCGGCCCGUGA
-------(((....(((((((........)).(((((......-----))))).......)))))(((((((((.(((((.(......).))....))).))))))))))))........ ( -38.40)
>consensus
UUUU___C_CAUUUCCCGCGCUUUUCCCCGCAUUUCCCC________CGGCAAAAUCCCGUGGGGCGACCAGUGUCCAGCACUUUGUUGCGCUUUCUGGUCGGUGGUCAGCGGCCCGUGA
...............((((......((((((............................))))))(((((((.((.((((.....)))).))...))))))).......))))....... (-28.61 = -28.61 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:52:10 2006