Locus 5531

Sequence ID 3R_DroMel_CAF1
Location 14,589,653 – 14,589,793
Length 140
Max. P 0.998006
window9020 window9021 window9022

overview

Window 0

Location 14,589,653 – 14,589,758
Length 105
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 76.94
Mean single sequence MFE -17.69
Consensus MFE -8.95
Energy contribution -9.75
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.51
SVM decision value 0.22
SVM RNA-class probability 0.639154
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14589653 105 - 27905053
UUUCUUUAUCAAUUUCCACAACAAGCUC------AAGCUC---AGAGCUUAGUCCUGGGAAAAGCAAGAAGAGCAAGAAAAUCUAGAAAAAACCAAAGAACACGAAUUAGAUGA
((((((......((((((..((((((((------......---.)))))).))..))))))..((.......))))))))((((((....................)))))).. ( -18.95)
>DroSec_CAF1 4386 94 - 1
UUUCUUUAUCAAUUUCCACAACAAGCUCAAGCUCAAGCUC---AGAGCUUAGUCCUGGGAAAAGCAAGC-----------------AAAAAACCAAAGAACACGCAUUAGAUGA
.....(((((..((((((..((((((((.(((....))).---.)))))).))..))))))......((-----------------.................))....))))) ( -20.33)
>DroSim_CAF1 4316 93 - 1
UUUCUUUAUCAAUUUCCACAACAAGCUCAAGCUCAAGCUC---AGAGCUUAGUCCUGGUAAAAGCAAG------------------AAAAAACCAAAGAACACGCAUUAGAUGA
((((((.........(((..((((((((.(((....))).---.)))))).))..))).......)))------------------)))......................... ( -16.99)
>DroEre_CAF1 4276 106 - 1
UUUCUUUAUCAAUUUCCACA-CAAGCUC------AGGCUCAGAGGAGCUUAGUGCUGGGAAAAGCAGCAAAAACAAGAAAAACACG-AAAAACCCAAGAACACCAAAUAGAUGA
.....(((((..((((((((-(((((((------..........)))))).))).)))))).........................-..........(.....).....))))) ( -17.10)
>DroYak_CAF1 5226 94 - 1
UUUCUUUAUCAAUUUCCACA-CAAGCUC------AAGCUC---GGAGCUUAGUGCUGAGAAAAGAAGCAAAAACAAGAA----------AAACCAAAGAACACAAAAUAGAUGA
.((((((.....((((((((-(((((((------......---.)))))).))).)).))))..............(..----------....))))))).............. ( -15.10)
>consensus
UUUCUUUAUCAAUUUCCACAACAAGCUC______AAGCUC___AGAGCUUAGUCCUGGGAAAAGCAAGAA_A_CAAGAA_______AAAAAACCAAAGAACACGAAUUAGAUGA
.....(((((..((((((..((((((((................)))))).))..))))))....................................(....)......))))) ( -8.95 =  -9.75 +   0.80)

alignment

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secondary structure

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Window 1

Location 14,589,687 – 14,589,793
Length 106
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 82.29
Mean single sequence MFE -27.52
Consensus MFE -19.00
Energy contribution -18.82
Covariance contribution -0.19
Combinations/Pair 1.11
Mean z-score -2.26
Structure conservation index 0.69
SVM decision value 1.26
SVM RNA-class probability 0.937273
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14589687 106 + 27905053
UUUCUUGCUCUUCUUGCUUUUCCCAGGACUAAGCUCU---GAGCUU------GAGCUUGUUGUGGAAAUUGAUAAAGAAAUAUUAUUGUAGGAUAAAAUAUCCCACAAGCAGAGA
(((((.((..(((((.(..((.(((.(((.((((((.---......------))))))))).))).))..)...)))))......((((.(((((...))))).))))))))))) ( -30.80)
>DroSec_CAF1 4414 99 + 1
-----------GCUUGCUUUUCCCAGGACUAAGCUCU---GAGCUUGAGCUUGAGCUUGUUGUGGAAAUUGAUAAAGAAAUAUUAUUGUAGGAUACAAUAUCCCACAAGGAGA--
-----------.(((.(..((.(((.(((.((((((.---((((....))))))))))))).))).))..)...)))........((((.(((((...))))).)))).....-- ( -28.40)
>DroEre_CAF1 4309 106 + 1
UUUCUUGUUUUUGCUGCUUUUCCCAGCACUAAGCUCCUCUGAGCCU------GAGCUUG-UGUGGAAAUUGAUAAAGAAAUAUUAUUGUAGGAUACAAUAUCCCAGAAGCAGA--
....(((((((((.(((.(((((..((((.((((((..........------)))))))-)))))))).(((((......)))))..)))(((((...)))))))))))))).-- ( -25.30)
>DroYak_CAF1 5251 102 + 1
-UUCUUGUUUUUGCUUCUUUUCUCAGCACUAAGCUCC---GAGCUU------GAGCUUG-UGUGGAAAUUGAUAAAGAAAUAUUAUUGUAGGAUAGAAUAUCCCACAAGAAGA--
-(((.(((((((...((.(((((..((((.((((((.---......------)))))))-))))))))..))...)))))))...((((.(((((...))))).)))))))..-- ( -25.60)
>consensus
_UUCUUGUUUUUCCUGCUUUUCCCAGCACUAAGCUCC___GAGCUU______GAGCUUG_UGUGGAAAUUGAUAAAGAAAUAUUAUUGUAGGAUACAAUAUCCCACAAGCAGA__
.............((((.(((((((....(((((((................))))))).)).))))).................((((.(((((...))))).))))))))... (-19.00 = -18.82 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,589,687 – 14,589,793
Length 106
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 82.29
Mean single sequence MFE -29.05
Consensus MFE -19.14
Energy contribution -20.64
Covariance contribution 1.50
Combinations/Pair 1.04
Mean z-score -3.92
Structure conservation index 0.66
SVM decision value 2.98
SVM RNA-class probability 0.998006
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14589687 106 - 27905053
UCUCUGCUUGUGGGAUAUUUUAUCCUACAAUAAUAUUUCUUUAUCAAUUUCCACAACAAGCUC------AAGCUC---AGAGCUUAGUCCUGGGAAAAGCAAGAAGAGCAAGAAA
(((.(((((((((((((...))))))))........(((((......((((((..((((((((------......---.)))))).))..))))))....))))))))))))).. ( -31.60)
>DroSec_CAF1 4414 99 - 1
--UCUCCUUGUGGGAUAUUGUAUCCUACAAUAAUAUUUCUUUAUCAAUUUCCACAACAAGCUCAAGCUCAAGCUC---AGAGCUUAGUCCUGGGAAAAGCAAGC-----------
--....((((((..(((((((........)))))))..)........((((((..((((((((.(((....))).---.)))))).))..))))))..))))).----------- ( -28.40)
>DroEre_CAF1 4309 106 - 1
--UCUGCUUCUGGGAUAUUGUAUCCUACAAUAAUAUUUCUUUAUCAAUUUCCACA-CAAGCUC------AGGCUCAGAGGAGCUUAGUGCUGGGAAAAGCAGCAAAAACAAGAAA
--.((((((..(..(((((((........)))))))..)........((((((((-(((((((------..........)))))).))).))))))))))))............. ( -29.30)
>DroYak_CAF1 5251 102 - 1
--UCUUCUUGUGGGAUAUUCUAUCCUACAAUAAUAUUUCUUUAUCAAUUUCCACA-CAAGCUC------AAGCUC---GGAGCUUAGUGCUGAGAAAAGAAGCAAAAACAAGAA-
--.((((((((((((((...)))))))))..................((((((((-(((((((------......---.)))))).))).)).)))))))))............- ( -26.90)
>consensus
__UCUGCUUGUGGGAUAUUGUAUCCUACAAUAAUAUUUCUUUAUCAAUUUCCACA_CAAGCUC______AAGCUC___AGAGCUUAGUCCUGGGAAAAGCAACAAAAACAAGAA_
...((((((((((((((...))))))))...................((((((..((((((((................)))))).))..))))))))))))............. (-19.14 = -20.64 +   1.50)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:26 2006