Locus 2990

Sequence ID 2R_DroMel_CAF1
Location 10,307,396 – 10,307,486
Length 90
Max. P 0.896431
window4938 window4939

overview

Window 8

Location 10,307,396 – 10,307,486
Length 90
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 78.42
Mean single sequence MFE -24.15
Consensus MFE -14.57
Energy contribution -14.94
Covariance contribution 0.36
Combinations/Pair 1.08
Mean z-score -1.57
Structure conservation index 0.60
SVM decision value 0.23
SVM RNA-class probability 0.643958
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10307396 90 + 20766785
UGCGCUCUCGUUUUCUGAU-----GCGAACGGGCUAAAUGGGCAAGGAACGCCCACAAAAACGAAGAGAAAU--------CGAGAAAGUAGUGCCACCGAUUG
.(((((((((.(((((...-----((......))....(((((.......)))))...........))))).--------))))).....))))......... ( -23.00)
>DroSec_CAF1 21861 93 + 1
UGCGCGCUCGUUUUCUGAU-----GCGAACGGGCUAAAUGGGCAGGGAACGCCCACAAAAACAGAGAGAAAUCGAGAAAUCGAGAAAGUCCGGCAAUC-----
(((.((((((.....))).-----)))..((((((...(((((.(....))))))................((((....))))...)))))))))...----- ( -30.90)
>DroSim_CAF1 21834 85 + 1
UGCGCGCUCGUUUUCUGAU-----GCGAACGGGCUAAAUGGGCAGGGAACGCCCACAAAAACGGAGAGAAAU--------CGAGAAAGUCGGGCAAUC-----
(((.(((((((((.(....-----).))))))))....(((((.(....))))))..........((....)--------).........).)))...----- ( -26.20)
>DroEre_CAF1 21971 82 + 1
UGCGCGCUCGUU-UCUGAU-----GCGAACGGGCUAAAUGGGCAAGAAACGCCCACAAAAGCGGAGGGAAAU--------CGAGAAAAGCGGGAAA-------
..(((.((((((-(((..(-----(((......)....(((((.......))))).....)))...))))).--------))))....))).....------- ( -22.70)
>DroYak_CAF1 22330 87 + 1
UGCGCGCUCGUU-UCUGAUGCGAUGCGAACGGGCUAAAUGGGCAAGAAACGCCCACAAAAGCGGAGAGAAAC--------UGAGAAAAGCUGGAAA-------
.((...((((((-(((..(((...((......))....(((((.......))))).....)))...))))))--------.)))....))......------- ( -24.00)
>DroAna_CAF1 25335 73 + 1
UGCGAGCUCGUUUUCUGAU-----CCGAAUGGGCUAAAUGGGCAAGAAACGCCCACAAA-ACGGAGAAAAAU--------UGAGAGG----------------
..(((((((((((......-----..)))))))))...(((((.......)))))....-.)).........--------.......---------------- ( -18.10)
>consensus
UGCGCGCUCGUUUUCUGAU_____GCGAACGGGCUAAAUGGGCAAGAAACGCCCACAAAAACGGAGAGAAAU________CGAGAAAGUCGGGCAA_______
.....((((((((.............))))))))....(((((.......)))))................................................ (-14.57 = -14.94 +   0.36)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,307,396 – 10,307,486
Length 90
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 78.42
Mean single sequence MFE -22.40
Consensus MFE -17.18
Energy contribution -17.68
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.77
SVM decision value 0.99
SVM RNA-class probability 0.896431
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10307396 90 - 20766785
CAAUCGGUGGCACUACUUUCUCG--------AUUUCUCUUCGUUUUUGUGGGCGUUCCUUGCCCAUUUAGCCCGUUCGC-----AUCAGAAAACGAGAGCGCA
.((((((.((........)))))--------))).((((.((((((((((((((.....)))))))...((......))-----....))))))))))).... ( -23.80)
>DroSec_CAF1 21861 93 - 1
-----GAUUGCCGGACUUUCUCGAUUUCUCGAUUUCUCUCUGUUUUUGUGGGCGUUCCCUGCCCAUUUAGCCCGUUCGC-----AUCAGAAAACGAGCGCGCA
-----......((((.....((((....))))......)))).....(((((((.....)))))))...((.((((((.-----.........)))))).)). ( -23.30)
>DroSim_CAF1 21834 85 - 1
-----GAUUGCCCGACUUUCUCG--------AUUUCUCUCCGUUUUUGUGGGCGUUCCCUGCCCAUUUAGCCCGUUCGC-----AUCAGAAAACGAGCGCGCA
-----...(((.((.....((((--------.(((((..........(((((((.....)))))))...((......))-----...))))).)))))).))) ( -20.70)
>DroEre_CAF1 21971 82 - 1
-------UUUCCCGCUUUUCUCG--------AUUUCCCUCCGCUUUUGUGGGCGUUUCUUGCCCAUUUAGCCCGUUCGC-----AUCAGA-AACGAGCGCGCA
-------.....(((((((((.(--------((........(((...(((((((.....)))))))..)))........-----))))))-)..))))).... ( -23.19)
>DroYak_CAF1 22330 87 - 1
-------UUUCCAGCUUUUCUCA--------GUUUCUCUCCGCUUUUGUGGGCGUUUCUUGCCCAUUUAGCCCGUUCGCAUCGCAUCAGA-AACGAGCGCGCA
-------......((........--------..........(((...(((((((.....)))))))..))).((((((..((......))-..)))))).)). ( -25.20)
>DroAna_CAF1 25335 73 - 1
----------------CCUCUCA--------AUUUUUCUCCGU-UUUGUGGGCGUUUCUUGCCCAUUUAGCCCAUUCGG-----AUCAGAAAACGAGCUCGCA
----------------...(((.--------..((((((..((-(..(((((((.....)))))))..)))((....))-----...)))))).)))...... ( -18.20)
>consensus
_______UUGCCCGACUUUCUCG________AUUUCUCUCCGUUUUUGUGGGCGUUCCUUGCCCAUUUAGCCCGUUCGC_____AUCAGAAAACGAGCGCGCA
...............................................(((((((.....)))))))...((.((((((...............)))))).)). (-17.18 = -17.68 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:42 2006