Locus 2402

Sequence ID 3R_DroMel_CAF1
Location 6,752,412 – 6,752,557
Length 145
Max. P 0.985872
window3893 window3894 window3895

overview

Window 3

Location 6,752,412 – 6,752,523
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.24
Mean single sequence MFE -37.08
Consensus MFE -30.70
Energy contribution -30.58
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -2.25
Structure conservation index 0.83
SVM decision value 2.02
SVM RNA-class probability 0.985872
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6752412 111 + 27905053
UGUGCCAUGUAAGCAAUUUUGACGACUGCUUUUUGCUCGUUGACAUUGGAU-------UUUGGCUUAGCUUCGAUUUUCUCUUAGCUGAGCUUAAAGGCGUGGUCGGUGGGCGGGGC--U
...(((....(((((.((.....)).))))).(((((((..(((..((..(-------((.(((((((((..((.....))..))))))))).)))..))..)))..))))))))))--. ( -37.00)
>DroSec_CAF1 16606 111 + 1
UGUGCCAUGUAAGCAAUUUUGAUGACUGCUUUUUGCUCGUUGACAUUGGAU-------UUUGGCUUAGCUUCGAUUUUCUCUUUGCUGAGCUUAAAGGCGUGGUCGGUGGGCGAGGC--U
...(((....(((((.((.....)).))))).(((((((..(((..((..(-------((.((((((((...((.....))...)))))))).)))..))..)))..))))))))))--. ( -36.50)
>DroSim_CAF1 20978 111 + 1
UGUGCCAUGUAAGCAAUUUUGAUGACUGCUUUUUGCUCGUUGACAUUGGAU-------UUUGGCUUAGCUUCGAUUUUCUCUUAGCUGAGCUUAAAGGCGUGGUCGGUGGGCGGGGC--U
...(((....(((((.((.....)).))))).(((((((..(((..((..(-------((.(((((((((..((.....))..))))))))).)))..))..)))..))))))))))--. ( -37.70)
>DroEre_CAF1 896 113 + 1
UGUGCCAUGUAAGCAAUUUUGAUGACUGCUUUUUGCUCGUUGACAUUGGAU-------UUUGGCUUAGCUUCGAUUUUCUCUUAGCUGAGCUUAAAGGCGUGGCCGGUGGGCGGGCUACC
...(((.......((((.(..((((..((.....))))))..).))))..(-------((.(((((((((..((.....))..))))))))).))))))((((((.(....).)))))). ( -39.40)
>DroYak_CAF1 12898 118 + 1
UGUGCCAUGUAAGCAAUUUUGAUGACUGCUUUUUGCUCGUUGACAUUGGAUUUUGGAUUUUGGCUUAGCUUCGAUUUUCUCUUAGCUGAGCUUAAAGGCGUGGUCGGUGGGCGGGCC--U
...(((.......((((.(..((((..((.....))))))..).)))).........(((.(((((((((..((.....))..))))))))).))))))..((((.(....).))))--. ( -34.80)
>consensus
UGUGCCAUGUAAGCAAUUUUGAUGACUGCUUUUUGCUCGUUGACAUUGGAU_______UUUGGCUUAGCUUCGAUUUUCUCUUAGCUGAGCUUAAAGGCGUGGUCGGUGGGCGGGGC__U
...(((((((...((((.(..((((..((.....))))))..).)))).............(((((((((..((.....))..))))))))).....)))))))................ (-30.70 = -30.58 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,752,412 – 6,752,523
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.24
Mean single sequence MFE -22.89
Consensus MFE -19.70
Energy contribution -19.90
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.86
SVM decision value 1.08
SVM RNA-class probability 0.912427
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6752412 111 - 27905053
A--GCCCCGCCCACCGACCACGCCUUUAAGCUCAGCUAAGAGAAAAUCGAAGCUAAGCCAAA-------AUCCAAUGUCAACGAGCAAAAAGCAGUCGUCAAAAUUGCUUACAUGGCACA
.--(((..((.(...(((...........(((.((((..((.....))..)))).)))....-------.......)))...).))...(((((((.......)))))))....)))... ( -22.75)
>DroSec_CAF1 16606 111 - 1
A--GCCUCGCCCACCGACCACGCCUUUAAGCUCAGCAAAGAGAAAAUCGAAGCUAAGCCAAA-------AUCCAAUGUCAACGAGCAAAAAGCAGUCAUCAAAAUUGCUUACAUGGCACA
.--(((..((.(...(((...........(((.(((...((.....))...))).)))....-------.......)))...).))...(((((((.......)))))))....)))... ( -21.15)
>DroSim_CAF1 20978 111 - 1
A--GCCCCGCCCACCGACCACGCCUUUAAGCUCAGCUAAGAGAAAAUCGAAGCUAAGCCAAA-------AUCCAAUGUCAACGAGCAAAAAGCAGUCAUCAAAAUUGCUUACAUGGCACA
.--(((..((.(...(((...........(((.((((..((.....))..)))).)))....-------.......)))...).))...(((((((.......)))))))....)))... ( -22.75)
>DroEre_CAF1 896 113 - 1
GGUAGCCCGCCCACCGGCCACGCCUUUAAGCUCAGCUAAGAGAAAAUCGAAGCUAAGCCAAA-------AUCCAAUGUCAACGAGCAAAAAGCAGUCAUCAAAAUUGCUUACAUGGCACA
.((.(((........))).))(((.....((((((((..((.....))..))))..(.((..-------......)).)...))))...(((((((.......)))))))....)))... ( -25.90)
>DroYak_CAF1 12898 118 - 1
A--GGCCCGCCCACCGACCACGCCUUUAAGCUCAGCUAAGAGAAAAUCGAAGCUAAGCCAAAAUCCAAAAUCCAAUGUCAACGAGCAAAAAGCAGUCAUCAAAAUUGCUUACAUGGCACA
.--((....))..........(((.....((((((((..((.....))..))))......................(....)))))...(((((((.......)))))))....)))... ( -21.90)
>consensus
A__GCCCCGCCCACCGACCACGCCUUUAAGCUCAGCUAAGAGAAAAUCGAAGCUAAGCCAAA_______AUCCAAUGUCAACGAGCAAAAAGCAGUCAUCAAAAUUGCUUACAUGGCACA
.....................(((.....((((((((..((.....))..))))......................(....)))))...(((((((.......)))))))....)))... (-19.70 = -19.90 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,752,452 – 6,752,557
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.63
Mean single sequence MFE -38.54
Consensus MFE -28.56
Energy contribution -29.36
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.74
SVM decision value 0.50
SVM RNA-class probability 0.758504
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6752452 105 + 27905053
UGACAUUGGAU-------UUUGGCUUAGCUUCGAUUUUCUCUUAGCUGAGCUUAAAGGCGUGGUCGGUGGGCGGGGC--UGGU------ACACUCAGUGGGCCCACGGAAAAGUGAUGAU
...((((...(-------((.(((((((((..((.....))..))))))))).))).((....((.((((((...((--(((.------....)))))..)))))).))...)))))).. ( -35.90)
>DroSec_CAF1 16646 105 + 1
UGACAUUGGAU-------UUUGGCUUAGCUUCGAUUUUCUCUUUGCUGAGCUUAAAGGCGUGGUCGGUGGGCGAGGC--UGGU------ACACUCAGUCGGCCCACGGAAAAGUGAUGAU
...((((...(-------((.((((((((...((.....))...)))))))).))).((....((.((((((..(((--(((.------....)))))).)))))).))...)))))).. ( -37.40)
>DroSim_CAF1 21018 105 + 1
UGACAUUGGAU-------UUUGGCUUAGCUUCGAUUUUCUCUUAGCUGAGCUUAAAGGCGUGGUCGGUGGGCGGGGC--UGGU------ACACUCAGUCGGCCCACGGAAAAGUGAUGAU
...((((...(-------((.(((((((((..((.....))..))))))))).))).((....((.((((((..(((--(((.------....)))))).)))))).))...)))))).. ( -38.20)
>DroEre_CAF1 936 113 + 1
UGACAUUGGAU-------UUUGGCUUAGCUUCGAUUUUCUCUUAGCUGAGCUUAAAGGCGUGGCCGGUGGGCGGGCUACCAGUGUACCAACAUUCAGUCGGCCCACGGAAAAGUGAUGAU
...((((...(-------((.(((((((((..((.....))..))))))))).))).((....(((.(((((.((((...(((((....))))).)))).))))))))....)))))).. ( -39.80)
>DroYak_CAF1 12938 112 + 1
UGACAUUGGAUUUUGGAUUUUGGCUUAGCUUCGAUUUUCUCUUAGCUGAGCUUAAAGGCGUGGUCGGUGGGCGGGCC--UGGU------ACAUUCGGUCGGCCCACGGAAAAGUGAUGAU
...((((.(((..((..(((.(((((((((..((.....))..))))))))).)))..))..))).((((((.((((--.((.------....)))))).))))))........)))).. ( -41.40)
>consensus
UGACAUUGGAU_______UUUGGCUUAGCUUCGAUUUUCUCUUAGCUGAGCUUAAAGGCGUGGUCGGUGGGCGGGGC__UGGU______ACACUCAGUCGGCCCACGGAAAAGUGAUGAU
...((((..............(((((((((..((.....))..))))))))).....((....((.((((((.((......((......))......)).)))))).))...)))))).. (-28.56 = -29.36 +   0.80)

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 10:34:45 2006