Locus 5163

Sequence ID 3R_DroMel_CAF1
Location 13,552,233 – 13,552,380
Length 147
Max. P 0.940176
window8436 window8437

overview

Window 6

Location 13,552,233 – 13,552,340
Length 107
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 77.80
Mean single sequence MFE -26.98
Consensus MFE -14.52
Energy contribution -15.32
Covariance contribution 0.80
Combinations/Pair 1.24
Mean z-score -2.24
Structure conservation index 0.54
SVM decision value 1.31
SVM RNA-class probability 0.940176
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13552233 107 - 27905053
CAAAAACUCG--UGUGUGUGUGUCUCCAAGCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGUAUUUUGUGCGUUUAGAAAGCGCAUGGCCGU--UUCUAUCUAUCCAG
...(((((((--(((((.....(((....((..((((((((((((((((......)))))).))))))))))))....)))..))))))))..))--))............ ( -24.80)
>DroSec_CAF1 5127 111 - 1
CAAAAACUCGAGUGUGUGUGUGUCUCCAAGCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGCACUUUGUGCGUUUAGAAAGCGCAUUGCUGUGCGUCUAUCUAUCCGG
((...((......))...)).....((..((..((((((((((((((((......)))))).))))))))))))(..((((.(((((((....))))).)).))))..))) ( -31.50)
>DroSim_CAF1 5304 109 - 1
CAAAAACUCG--UGUGUGUGUGUCUCCAAGCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGCAUUUUGUGCGUUUAGAAAGCGCAUUGCUGUGCGUCUAUCUAUCCGG
((...((...--...))...))...((..((..((((((((((((((((......)))))).))))))))))))(..((((.(((((((....))))).)).))))..))) ( -29.20)
>DroEre_CAF1 18692 86 - 1
CAAAAACUCU--UGUG------UUGCUAA---------GUGCAUUUUAAUUUGUUUUA-AAUUGUAUUUUGUGUGUUUAGACAGCGCAGUGCC-------UGUGCAUACAG
..........--((((------(((((((---------(..(((..(((((((...))-)))))......)))..))))).)))))))((((.-------...)))).... ( -21.10)
>DroYak_CAF1 5308 96 - 1
CAAACACUCG--UGUG------UUUCUAAGCCAACAGAGUGCAUUUUAAUUGGUUUUA-AAUUGUAUUUUGUGCGCUUAGAAAGCUCAUUGUCU------UGUUUAUUGAG
..(((((...--.)))------))(((((((((.(((((((((.(((((......)))-)).))))))))))).)))))))...((((.((...------....)).)))) ( -28.30)
>consensus
CAAAAACUCG__UGUGUGUGUGUCUCCAAGCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGUAUUUUGUGCGUUUAGAAAGCGCAUUGCCGU___UCUAUCUAUCCAG
.................................((((((((((((((((......)))))).))))))))))(((((.....)))))........................ (-14.52 = -15.32 +   0.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,552,265 – 13,552,380
Length 115
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 81.19
Mean single sequence MFE -26.94
Consensus MFE -17.48
Energy contribution -17.96
Covariance contribution 0.48
Combinations/Pair 1.19
Mean z-score -2.12
Structure conservation index 0.65
SVM decision value 0.89
SVM RNA-class probability 0.875991
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13552265 115 - 27905053
GUUUUAUAAAUCAAAUUAGCUUUUGCCAGUUGGCUGACCGCAAAAACUCG--UGUGUGUGUGUCUCCAAGCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGUAUUUUGUGCGUU
..................((........((((((((((((((...((...--.)).)))).)))....)))))))((((((((((((((......)))))).))))))))..))... ( -28.30)
>DroSec_CAF1 5161 117 - 1
GUUUCAUAAAUCAAAUUAGCUUUUGCCAGUUGGCUGACCGCAAAAACUCGAGUGUGUGUGUGUCUCCAAGCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGCACUUUGUGCGUU
..................((........((((((((((((((...((....))...)))).)))....)))))))((((((((((((((......)))))).))))))))..))... ( -33.00)
>DroSim_CAF1 5338 115 - 1
GUUUCAUAAAUCAAAUUAGCUUUUGCCAGUUGGCUGACCGCAAAAACUCG--UGUGUGUGUGUCUCCAAGCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGCAUUUUGUGCGUU
..................((........((((((((((((((...((...--.)).)))).)))....)))))))((((((((((((((......)))))).))))))))..))... ( -30.30)
>DroEre_CAF1 18719 91 - 1
AUUUUAUAAAUCGAAUUAGCUU--------UGGCUGGCCGCAAAAACUCU--UGUG------UUGCUAA---------GUGCAUUUUAAUUUGUUUUA-AAUUGUAUUUUGUGUGUU
...............(((((..--------..))))).(((((......)--))))------..((.((---------(((((.(((((......)))-)).))))))).))..... ( -15.20)
>DroYak_CAF1 5336 100 - 1
GUUUUCUAAAUUAAGUUAGCUU--------UGGCUGGCCGCAAACACUCG--UGUG------UUUCUAAGCCAACAGAGUGCAUUUUAAUUGGUUUUA-AAUUGUAUUUUGUGCGCU
..............((((((..--------..)))))).((((((((...--.)))------)))....((..((((((((((.(((((......)))-)).)))))))))))))). ( -27.90)
>consensus
GUUUUAUAAAUCAAAUUAGCUUUUGCCAGUUGGCUGACCGCAAAAACUCG__UGUGUGUGUGUCUCCAAGCCAACAAAGUGCAUUUUAAUUUGUUUUAAAAUUGUAUUUUGUGCGUU
...............((((((..........)))))).(((....((......))..................((((((((((((((((......)))))).))))))))))))).. (-17.48 = -17.96 +   0.48)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:06 2006