Locus 724

Sequence ID X_DroMel_CAF1
Location 1,986,408 – 1,986,528
Length 120
Max. P 0.967192
window1164 window1165

overview

Window 4

Location 1,986,408 – 1,986,528
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.22
Mean single sequence MFE -48.03
Consensus MFE -40.53
Energy contribution -40.77
Covariance contribution 0.25
Combinations/Pair 1.09
Mean z-score -1.82
Structure conservation index 0.84
SVM decision value 0.66
SVM RNA-class probability 0.814506
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1986408 120 + 22224390
UUGCUGAACCUGCUGCACCUGCUGGGUCUGUGUUGACCCAGUAGAUCCAGGACCCGUCGCCGCCUGGACCGCGCUACUGGUGGUAGUCACUUUCUGAACCACUUUCUGGGCCAGCUUGCC
..((((..((.((.((..((((((((((......)))))))))).((((((.(........)))))))..))))....((((((..(((.....)))))))))....))..))))..... ( -47.90)
>DroSec_CAF1 19946 120 + 1
UUGCUGAACCUGCUGCACCUGCUGGGUCUGUGUGGACCCAGCGGAUCCAGGACCCGUCGCCGCCUGGACCGCGCUACUGGUGGUAGUCACCUUCUGAACCACUUUCUGGGCCAGCUUGCC
..((((..((.((.((....(((((((((....)))))))))((.((((((.(........)))))))))))))....((((((..(((.....)))))))))....))..))))..... ( -50.00)
>DroEre_CAF1 9538 120 + 1
UUGCUGAACCUGCUGCACCUGCUGGGUCUGUGUAGACCCAGUGGAUCCAGGACCCGUCGCCGCCUGGACUGCGCUACUGGUGGUGGUCACCUUCUGAACCACUUUCUGGGCCAGCUUGCC
..((((..((.((.(((.(..((((((((....))))))))..).((((((.(........))))))).)))))....((.((((((((.....)).)))))).)).))..))))..... ( -48.20)
>DroYak_CAF1 20269 111 + 1
UUGCUGAACCU---------GCUGGGUCUGUGUCGACCCAGUGGAUCCAGGACCCGUCGCCGCCUGUACUGCGCUACUGGUGGUGGUCACCUUCUGAACCACUUUCUGGGUCAGCUUGCC
..(((((..(.---------.(((((((......)))))))..).(((((((......((((((.(((......))).))))))(((((.....)).)))...))))))))))))..... ( -46.00)
>consensus
UUGCUGAACCUGCUGCACCUGCUGGGUCUGUGUAGACCCAGUGGAUCCAGGACCCGUCGCCGCCUGGACCGCGCUACUGGUGGUAGUCACCUUCUGAACCACUUUCUGGGCCAGCUUGCC
..((((............((((((((((......)))))))))).((((((.(........)))))))..((.(....((((((..(((.....)))))))))....).))))))..... (-40.53 = -40.77 +   0.25) 

alignment

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secondary structure

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dotplot

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Window 5

Location 1,986,408 – 1,986,528
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.22
Mean single sequence MFE -51.40
Consensus MFE -42.96
Energy contribution -45.02
Covariance contribution 2.06
Combinations/Pair 1.03
Mean z-score -2.73
Structure conservation index 0.84
SVM decision value 1.61
SVM RNA-class probability 0.967192
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1986408 120 - 22224390
GGCAAGCUGGCCCAGAAAGUGGUUCAGAAAGUGACUACCACCAGUAGCGCGGUCCAGGCGGCGACGGGUCCUGGAUCUACUGGGUCAACACAGACCCAGCAGGUGCAGCAGGUUCAGCAA
.....((((..((.....((((((((.....)))..)))))..((.((((((((((((((....))...))))))))..(((((((......)))))))...)))).)).))..)))).. ( -52.90)
>DroSec_CAF1 19946 120 - 1
GGCAAGCUGGCCCAGAAAGUGGUUCAGAAGGUGACUACCACCAGUAGCGCGGUCCAGGCGGCGACGGGUCCUGGAUCCGCUGGGUCCACACAGACCCAGCAGGUGCAGCAGGUUCAGCAA
.....((((..((.....(((((.....((....)))))))..((.((((((((((((((....))...)))))))).((((((((......))))))))..)))).)).))..)))).. ( -58.10)
>DroEre_CAF1 9538 120 - 1
GGCAAGCUGGCCCAGAAAGUGGUUCAGAAGGUGACCACCACCAGUAGCGCAGUCCAGGCGGCGACGGGUCCUGGAUCCACUGGGUCUACACAGACCCAGCAGGUGCAGCAGGUUCAGCAA
.....((((..((.....((((((........)))))).....((.((((.(((((((((....))...)))))))...((((((((....))))))))...)))).)).))..)))).. ( -50.90)
>DroYak_CAF1 20269 111 - 1
GGCAAGCUGACCCAGAAAGUGGUUCAGAAGGUGACCACCACCAGUAGCGCAGUACAGGCGGCGACGGGUCCUGGAUCCACUGGGUCGACACAGACCCAGC---------AGGUUCAGCAA
.....(((((.((....((((((((((..(((....)))(((.....(((.((....)).)))...))).))))).)))))(((((......)))))...---------.)).))))).. ( -43.70)
>consensus
GGCAAGCUGGCCCAGAAAGUGGUUCAGAAGGUGACCACCACCAGUAGCGCAGUCCAGGCGGCGACGGGUCCUGGAUCCACUGGGUCAACACAGACCCAGCAGGUGCAGCAGGUUCAGCAA
.....(((((.((.....((((((((.....)))..)))))..((.((((((((((((((....))...))))))))..(((((((......)))))))...)))).)).)).))))).. (-42.96 = -45.02 +   2.06) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:07 2006