Locus 6264

Sequence ID 2R_DroMel_CAF1
Location 19,662,529 – 19,662,661
Length 132
Max. P 0.849981
window10021 window10022 window10023

overview

Window 1

Location 19,662,529 – 19,662,634
Length 105
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 88.59
Mean single sequence MFE -31.47
Consensus MFE -24.33
Energy contribution -25.33
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.77
SVM decision value 0.45
SVM RNA-class probability 0.742466
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19662529 105 - 20766785
GGGAGUCCAACAUCAUGCUGGAUAUCAGCGACUGGUCCGGCAGCUUCUGCACUUCCAUGUU---------GCCUUUCUGGUUUUGUUUAUUGCAAAACGCUUUCUUUUGUUCUA
(..(((.((((((..((((((((..(((...)))))))))))((....))......)))))---------)........(((((((.....))))))))))..).......... ( -29.00)
>DroSim_CAF1 702 105 - 1
GGGAGUCCAGCAUCAUGCUGGAUAUCAGCGACUGGUCCGGCAGCUUCUGCACUUCCAUGUU---------GCCUUUCUGGUUUUGUUUAUUGCAAAACGCUUUCUUUUGUUCUU
(..((((((((.....)))))).....((((((((....((((...))))....))).)))---------))))..)..(((((((.....)))))))................ ( -33.70)
>DroYak_CAF1 772 114 - 1
UGGAGUCCAGCAUCAUGCUGGAGAGCAGCGACUGAUCCGGCAGCUUCUGCACUUCCAUGUUUGGUUUUUUUUCUUGCUGCUUUUGUUUAUUGCAAAACGCUUUCUUUUGUUCUA
(((((((((((.....))))))(((.((((........((((((..........(((....)))...........))))))(((((.....))))).))))))).....))))) ( -31.70)
>consensus
GGGAGUCCAGCAUCAUGCUGGAUAUCAGCGACUGGUCCGGCAGCUUCUGCACUUCCAUGUU_________GCCUUUCUGGUUUUGUUUAUUGCAAAACGCUUUCUUUUGUUCUA
((((((.(((.....(((((((...(((...))).)))))))....))).)))))).......................(((((((.....)))))))................ (-24.33 = -25.33 +   1.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,662,569 – 19,662,661
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.03
Mean single sequence MFE -33.27
Consensus MFE -20.67
Energy contribution -21.12
Covariance contribution 0.45
Combinations/Pair 1.17
Mean z-score -1.25
Structure conservation index 0.62
SVM decision value 0.22
SVM RNA-class probability 0.639399
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19662569 92 + 20766785
AGGC---------AACAUGGAAGUGCAGAAGCUGCCGGACCAGUCGCUGAUAUCCAGCAU------GAUGUUGGACUCCCGAUGUGGGGUAAGUGUGGCUCCAGCC-----------A--
.(((---------.((((((.(((.(((..((((......))))..)))....(((((..------...)))))))).)).))))(((((.......))))).)))-----------.-- ( -31.50)
>DroVir_CAF1 1 91 + 1
----------------AUGGAGGUACAAAAUAUGCGCGAGCAGCCGCUGCUGCAGAGCAAACGCCACAUCCUUGACUCCAGAUGUGCGGUAAGUGUGGCACA-------------CCAUA
----------------((((..((........(((....)))(((((((((....))))..(((.(((((..((....))))))))))......))))))).-------------)))). ( -29.50)
>DroSec_CAF1 1 85 + 1
----------------AUGGAAGUGCAGAACCUGCCGGACCAGUCGCUGAUAUCCAGCAU------GAUGCUGGACUCCCGAUGCGGGGUAAGUGUGGCUCCAGCC-----------A--
----------------.(((..(.((((...)))))((((((..((((....((((((..------...)))))).(((((...)))))..))))))).)))..))-----------)-- ( -30.10)
>DroSim_CAF1 742 92 + 1
AGGC---------AACAUGGAAGUGCAGAAGCUGCCGGACCAGUCGCUGAUAUCCAGCAU------GAUGCUGGACUCCCGAUGCGGGGUAAGUGUGGCUCCAGCC-----------A--
.(((---------.....((.(((......))).))((((((..((((....((((((..------...)))))).(((((...)))))..))))))).))).)))-----------.-- ( -34.70)
>DroEre_CAF1 1 96 + 1
----------------AUGGAAGUGCAGAAGCUGCCGGAUCAGUCGCUGAUAUCCAGCAU------GAUGCUGGACUCCAGAUGUGGGGUAAGUGUGGCUCCAGCCCAGCGGACAGCA--
----------------..............((((((..((((...((((.....)))).)------)))((((.((((((....))))))......(((....))))))))).)))).-- ( -33.50)
>DroYak_CAF1 812 114 + 1
AGAAAAAAAACCAAACAUGGAAGUGCAGAAGCUGCCGGAUCAGUCGCUGCUCUCCAGCAU------GAUGCUGGACUCCAGAUGUGGGGUAAGUGUGGCUCCCGCCCAGCGGACACCACC
.........(((..(((((((.(.((((..((((......))))..)))).)((((((..------...)))))).))))..)))..)))....((((...((((...))))...)))). ( -40.30)
>consensus
________________AUGGAAGUGCAGAAGCUGCCGGACCAGUCGCUGAUAUCCAGCAU______GAUGCUGGACUCCAGAUGUGGGGUAAGUGUGGCUCCAGCC___________A__
.................(((....((((...))))....)))(((((......(((((((.......)))))))(((((......)))))....)))))..................... (-20.67 = -21.12 +   0.45)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,662,569 – 19,662,661
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.03
Mean single sequence MFE -33.47
Consensus MFE -18.12
Energy contribution -19.27
Covariance contribution 1.14
Combinations/Pair 1.21
Mean z-score -1.75
Structure conservation index 0.54
SVM decision value 0.78
SVM RNA-class probability 0.849981
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19662569 92 - 20766785
--U-----------GGCUGGAGCCACACUUACCCCACAUCGGGAGUCCAACAUC------AUGCUGGAUAUCAGCGACUGGUCCGGCAGCUUCUGCACUUCCAUGUU---------GCCU
--(-----------(((....)))).......(((.....))).(((((.(...------..).)))))....((((((((....((((...))))....))).)))---------)).. ( -28.00)
>DroVir_CAF1 1 91 - 1
UAUGG-------------UGUGCCACACUUACCGCACAUCUGGAGUCAAGGAUGUGGCGUUUGCUCUGCAGCAGCGGCUGCUCGCGCAUAUUUUGUACCUCCAU----------------
...((-------------(((((..........)))))))(((((...(((((((((((...((.((((....))))..)).))).))))))))....))))).---------------- ( -32.80)
>DroSec_CAF1 1 85 - 1
--U-----------GGCUGGAGCCACACUUACCCCGCAUCGGGAGUCCAGCAUC------AUGCUGGAUAUCAGCGACUGGUCCGGCAGGUUCUGCACUUCCAU----------------
--(-----------(((....))))...............((((((.(((.(((------.((((((((..(((...)))))))))))))).))).))))))..---------------- ( -31.80)
>DroSim_CAF1 742 92 - 1
--U-----------GGCUGGAGCCACACUUACCCCGCAUCGGGAGUCCAGCAUC------AUGCUGGAUAUCAGCGACUGGUCCGGCAGCUUCUGCACUUCCAUGUU---------GCCU
--(-----------(((....)))).......((((...)))).(((((((...------..)))))))....((((((((....((((...))))....))).)))---------)).. ( -35.40)
>DroEre_CAF1 1 96 - 1
--UGCUGUCCGCUGGGCUGGAGCCACACUUACCCCACAUCUGGAGUCCAGCAUC------AUGCUGGAUAUCAGCGACUGAUCCGGCAGCUUCUGCACUUCCAU----------------
--.((((((((((((((....))).........(((....))).(((((((...------..)))))))..)))))........))))))..............---------------- ( -31.80)
>DroYak_CAF1 812 114 - 1
GGUGGUGUCCGCUGGGCGGGAGCCACACUUACCCCACAUCUGGAGUCCAGCAUC------AUGCUGGAGAGCAGCGACUGAUCCGGCAGCUUCUGCACUUCCAUGUUUGGUUUUUUUUCU
.(((((..((((...))))..))))).......(((.((.(((((((((((...------..))))))..((((...(((......)))...))))..))))).)).))).......... ( -41.00)
>consensus
__U___________GGCUGGAGCCACACUUACCCCACAUCGGGAGUCCAGCAUC______AUGCUGGAUAUCAGCGACUGGUCCGGCAGCUUCUGCACUUCCAU________________
..............(((....))).................((((((((((((.......)))))))))(((((...)))))...((((...))))...))).................. (-18.12 = -19.27 +   1.14)

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 12:06:56 2006