Locus 6688

Sequence ID 3L_DroMel_CAF1
Location 17,808,783 – 17,808,910
Length 127
Max. P 0.939828
window10883 window10884

overview

Window 3

Location 17,808,783 – 17,808,875
Length 92
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 76.45
Mean single sequence MFE -23.07
Consensus MFE -12.95
Energy contribution -13.71
Covariance contribution 0.75
Combinations/Pair 1.14
Mean z-score -1.72
Structure conservation index 0.56
SVM decision value 0.44
SVM RNA-class probability 0.736518
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17808783 92 - 23771897
AAUUUGGCGCCAAACACUUGUUAGCACUCUGUUGACUUUAACAUGGCGCAUUAACAGCUACGCUGAAAU----------------------CUGACAGA-UAGUAACAUAGCCUU
.(((((((((((.......((((((.....)))))).......)))))).....((((...))))....----------------------....))))-).............. ( -23.54)
>DroSec_CAF1 1710 92 - 1
AAUUUGGCGCCAAACACUUGUUAGCACUCUGUUGACUUUAACAGGGCGCACUAACAGCUCCCCUGAAAU----------------------CUGACAGA-UAGUAACAUAGCCUU
.....(((((..(((....))).))..(((((((..(((..(((((.((.......))..)))))))).----------------------.)))))))-..........))).. ( -21.10)
>DroSim_CAF1 1714 92 - 1
AAUUUGGCGCCAAACACUUGUUAGCACUCUGUUGACUUUAACAGGGCGCACUAACAGCUCCGCUGAAAU----------------------CUGACAGA-UAGUAACAUAGCCUU
.....(((.......((((((((((.((((((((....)))))))).)).....((((...))))....----------------------.)))))..-.)))......))).. ( -23.32)
>DroEre_CAF1 1630 92 - 1
AAUCUGCCGCCAAACACUUGUUAGCACUCUGUUGACUUUAACAUGGCGUCCUAACAGCAACGCUGAAAU----------------------CUGACAGC-UACUAGCAUAGCCUU
....((((((((.......((((((.....)))))).......))))).............((((....----------------------....))))-.....)))....... ( -19.74)
>DroYak_CAF1 1643 92 - 1
AAUCUGGCGCCAAACACUUGUUAGCACUCUGUUGACCUUAACAGGGCGCCCUAACAGCUACGCUGAAAU----------------------CUGACAGA-UACUAACAUAGCCAU
.((((((((((........((((((.....))))))........))))).....((((...))))....----------------------....))))-).............. ( -24.09)
>DroAna_CAF1 1401 112 - 1
AAGUUUGCGCCAAACACCUGUUAUCCAACACCAGUGCUUAACAGAGUGC--UAACAU-AACAGUGAAGUAGUUAACAGAAUGGCUCAGUUUUUGACGUACUGCUAACAGUGCGCU
....(((.((((.....((((((....((...((..(((....)))..)--)..(((-....)))..))...))))))..)))).))).......(((((((....))))))).. ( -26.60)
>consensus
AAUUUGGCGCCAAACACUUGUUAGCACUCUGUUGACUUUAACAGGGCGCACUAACAGCUACGCUGAAAU______________________CUGACAGA_UACUAACAUAGCCUU
......(((((........((((((.....))))))........))))).....(((.....))).................................................. (-12.95 = -13.71 +   0.75)

alignment

Postscript

secondary structure

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dotplot

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Window 4

Location 17,808,806 – 17,808,910
Length 104
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 90.87
Mean single sequence MFE -26.13
Consensus MFE -21.53
Energy contribution -21.65
Covariance contribution 0.12
Combinations/Pair 1.13
Mean z-score -1.87
Structure conservation index 0.82
SVM decision value 1.30
SVM RNA-class probability 0.939828
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17808806 104 - 23771897
ACAGAAGUUCUGCUUCCAAGGAGCCCUUAAAUUCAAAUUUGGCGCCAAACACUUGUUAGCACUCUGUUGACUUUAACAUGGCGCAUUAACAGCUACGCUGAAAU
...(((.....((((.....)))).......))).......((((((.......((((((.....)))))).......)))))).....((((...)))).... ( -25.54)
>DroSec_CAF1 1733 104 - 1
ACAGAAGUUCUGCUUCCAAGGAGCCCUUAAAUUCAAAUUUGGCGCCAAACACUUGUUAGCACUCUGUUGACUUUAACAGGGCGCACUAACAGCUCCCCUGAAAU
...((((.....))))...(((((...(((((....)))))(((((........((((((.....))))))........))))).......)))))........ ( -27.49)
>DroSim_CAF1 1737 104 - 1
ACAGAAGUUCUGCUCCCAAGGAGCCCUUAAAUUCAAAUUUGGCGCCAAACACUUGUUAGCACUCUGUUGACUUUAACAGGGCGCACUAACAGCUCCGCUGAAAU
...(((.....(((((...))))).......))).......(((((........((((((.....))))))........))))).....((((...)))).... ( -27.69)
>DroEre_CAF1 1653 104 - 1
AACGAACUUCUGCGUUCAAGAAGCCUUUAAAUUCAAAUCUGCCGCCAAACACUUGUUAGCACUCUGUUGACUUUAACAUGGCGUCCUAACAGCAACGCUGAAAU
.......(((.((((((..(((.........)))........(((((.......((((((.....)))))).......)))))........).))))).))).. ( -21.04)
>DroYak_CAF1 1666 104 - 1
AAUGAAGUUCUGCUUCCGAGGAGCCUUUGAAUUCAAAUCUGGCGCCAAACACUUGUUAGCACUCUGUUGACCUUAACAGGGCGCCCUAACAGCUACGCUGAAAU
..((((.(((.((((.....))))....))))))).....((((((........((((((.....))))))........))))))....((((...)))).... ( -28.89)
>consensus
ACAGAAGUUCUGCUUCCAAGGAGCCCUUAAAUUCAAAUUUGGCGCCAAACACUUGUUAGCACUCUGUUGACUUUAACAGGGCGCACUAACAGCUACGCUGAAAU
...(((.....(((((...))))).......))).......(((((........((((((.....))))))........))))).....((((...)))).... (-21.53 = -21.65 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:37 2006