Locus 5508

Sequence ID X_DroMel_CAF1
Location 14,273,936 – 14,274,139
Length 203
Max. P 0.943685
window8937 window8938

overview

Window 7

Location 14,273,936 – 14,274,044
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.87
Mean single sequence MFE -43.25
Consensus MFE -37.60
Energy contribution -38.47
Covariance contribution 0.88
Combinations/Pair 1.03
Mean z-score -1.52
Structure conservation index 0.87
SVM decision value 0.29
SVM RNA-class probability 0.669495
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14273936 108 - 22224390
--------UCAGCCAGCGGGCGGAAGGUCGACCUGUGCCACCCCCUGUGC----CGCAGUUGGGGGGUGUUUUGGCACUGAUUGGCACUUCAUUUCGACUGCAGUCGGACUCCCAGCUCA
--------......((((((.((((((((((.(.(((((((((((((...----......)))))))).....))))).).))))).))))..((((((....))))))).))).))).. ( -44.10)
>DroSec_CAF1 14584 114 - 1
ACCCCCUUCCAGCCAGCGGGCGGAAGGUCGACCUGUGCCACCCCCUGUGC----CGCAGUUGGGGGG--UUUUGGCACUGAUUGGCACUUCAUUUCGACUGCAGUCGGACUCCCAGCUCA
..............((((((.((((((((((.(.(((((((((((((...----......)))))))--)...))))).).))))).))))..((((((....))))))).))).))).. ( -44.90)
>DroEre_CAF1 17006 105 - 1
-----------UCCAACGGGC-GAAGGUCGACCUGUGCCACCCCCUGUGCACCCCGCAGUUGGG-GG--UUUUGGCACUGAUUGGCACUUCAUUUCGACUGCAGUCGGACUCGCAGCUCG
-----------.....(((((-(((((((((.(.(((((((((((..(((.....)))...)))-))--)...))))).).))))).))))..((((((....))))))......))))) ( -47.20)
>DroYak_CAF1 17788 95 - 1
------------------UGG-GAAGGUCGACCUGUGCCACCUCCUGUGC----CGCAGUUGGGGGG--UUUUGGCACUGAUUGGCACUUCAUUUCGACUGCAGUCGGACUCCCAGCUCA
------------------(((-(((((((((.(.(((((((((((((...----......)))))))--)...))))).).))))).))))..((((((....))))))...)))..... ( -36.80)
>consensus
___________GCCAGCGGGC_GAAGGUCGACCUGUGCCACCCCCUGUGC____CGCAGUUGGGGGG__UUUUGGCACUGAUUGGCACUUCAUUUCGACUGCAGUCGGACUCCCAGCUCA
.................((((.(((((((((.(.((((((((((((((((.....)))..))))))).....)))))).).))))).))))..((((((....))))))......)))). (-37.60 = -38.47 +   0.88)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 8

Location 14,274,044 – 14,274,139
Length 95
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 79.23
Mean single sequence MFE -24.88
Consensus MFE -12.96
Energy contribution -13.27
Covariance contribution 0.31
Combinations/Pair 1.08
Mean z-score -2.80
Structure conservation index 0.52
SVM decision value 1.34
SVM RNA-class probability 0.943685
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14274044 95 + 22224390
-----------------------CACCCA-CACAUACAAAACAGACAAAACUCACAAGUCAUUUCGGCAAUCUCCUUCACGGAAACGGAAGAA-AAAAGUCUCUUAAGAUUUCCCGGGAC
-----------------------..(((.-.............(((...........))).....((.......((((.((....))))))..-..((((((....)))))).))))).. ( -18.80)
>DroSec_CAF1 14698 114 + 1
GGGUGGUGACUAUCCCACC----CACCCA-CACAUACAAAACAGACAAAACUCACAAGUCAUUUCGGCAAUCUCCUUCACGGAAACGGGAGAA-AAAAGUGUCUUAAGAUUUCCCGGGAC
((((((.(.....))))))----).(((.-............(((((..........(((.....)))..(((((....((....))))))).-.....)))))...(......)))).. ( -31.30)
>DroEre_CAF1 17111 110 + 1
---------UUUUCCCACCCCCACACACAAAGCACACAAAACACACAAAACUCACAAGUCAUUUCGGCCAUCUCCUUCCCGGAAACGGGGGAA-AAAGGUGUCUCAAAAGUUCCCGGGAC
---------...((((.(((((...........................(((....)))..((((((...........))))))..)))))..-...((...((....))...)))))). ( -22.30)
>DroYak_CAF1 17883 106 + 1
-------------CCCACACUCACACCCA-CACAUACAAAACAGACACAACUCACAAGUCAUUUCGGCAAUCUCCUGCACGGAAACGGGAGAAAAAAAGUGUCUAAGGAUUUCCCGGGAC
-------------............(((.-............((((((.........(((.....)))..(((((((........)))))))......))))))..((.....))))).. ( -27.10)
>consensus
_____________CCCACC____CACCCA_CACAUACAAAACAGACAAAACUCACAAGUCAUUUCGGCAAUCUCCUUCACGGAAACGGGAGAA_AAAAGUGUCUUAAGAUUUCCCGGGAC
.........................(((.............................(((.....)))..(((((....((....))))))).......................))).. (-12.96 = -13.27 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:39 2006