Locus 2069

Sequence ID 2L_DroMel_CAF1
Location 5,576,098 – 5,576,206
Length 108
Max. P 0.730194
window3342 window3343

overview

Window 2

Location 5,576,098 – 5,576,206
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.26
Mean single sequence MFE -41.64
Consensus MFE -22.14
Energy contribution -22.26
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -1.91
Structure conservation index 0.53
SVM decision value 0.19
SVM RNA-class probability 0.628538
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5576098 108 + 22407834
-------CUGGAGGAUUUCCUGCAGUUCCCAGCCACUUCAGCGUCGACCACAUAAAGUGUCAUUAGCUCGAGUGGCGAAGCGACUGGCUUGGUGGACCAGGAGCAGGAUUCGGCU-----
-------(((.(((....))).))).(((..(((((((.(((...(((.((.....)))))....))).)))))))...((..((((((....)).))))..)).))).......----- ( -41.00)
>DroSec_CAF1 20125 111 + 1
-------CUGGAGGACUUCCCGCAAUUCCCAGCCACUUCAGCCUCGACCACAUAAAGUGUCAUUAGCUCGAGUGGCGAGGCGACUGCCUUGGUGGACCAGGAGCAGGAUUUGGCUGGC--
-------.((..((....))..))....(((((((..((.((((((.((((.(..(((.......)))..)))))))))))..(((((((((....))))).))))))..))))))).-- ( -49.00)
>DroSim_CAF1 21793 112 + 1
-------CUGGAGGACUUCCCGCAGUUCCCAGCCACUUCUGCCUCGACCACAUAAAGUGUCAUUAGCUCGAGUGGCGAGGCGACUGCCUUGGUGGAC-AGGAGCAGGAUUCGGCUGGAGC
-------(((..((....))..)))...((((((.....(((((((.((((.(..(((.......)))..)))))))))))).((((((((.....)-))).)))).....))))))... ( -46.30)
>DroEre_CAF1 20046 90 + 1
-----------------UCCCGCAGUUCCCAGCCACUUCAGCCUCGACCACAUAAAGUGUCAUUAGCUCGAGUGGCGAGCAGACCA--------GGCCAGGAGCGGGAUUCGGCU-----
-----------------((((((.((((...(((((((.(((...(((.((.....)))))....))).)))))))))))...((.--------.....)).)))))).......----- ( -33.90)
>DroYak_CAF1 19948 102 + 1
AGCAGUGCUGAAGGACCUCCCGCAGUUCCCAGCCACUUCAGCCUCGGCCACAUAAAGUGUCAUUAGCUCGAGUGGCGAGGAGACC-------------AGGAGCAGCAUUCGGCU-----
......((((((((.....))((.(((((..(((((((.(((....(.(((.....))).)....))).)))))))(.(....))-------------.))))).)).)))))).----- ( -38.00)
>consensus
_______CUGGAGGACUUCCCGCAGUUCCCAGCCACUUCAGCCUCGACCACAUAAAGUGUCAUUAGCUCGAGUGGCGAGGCGACUG_CUUGGUGGACCAGGAGCAGGAUUCGGCU_____
...................(((..(((((..(((((((.(((...(((.((.....)))))....))).)))))))..(....)...............)))))......)))....... (-22.14 = -22.26 +   0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,576,098 – 5,576,206
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.26
Mean single sequence MFE -40.80
Consensus MFE -27.74
Energy contribution -29.30
Covariance contribution 1.56
Combinations/Pair 1.10
Mean z-score -1.70
Structure conservation index 0.68
SVM decision value 0.42
SVM RNA-class probability 0.730194
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5576098 108 - 22407834
-----AGCCGAAUCCUGCUCCUGGUCCACCAAGCCAGUCGCUUCGCCACUCGAGCUAAUGACACUUUAUGUGGUCGACGCUGAAGUGGCUGGGAACUGCAGGAAAUCCUCCAG-------
-----.......((((((...(((....)))..(((((((((((((...((((.(..((((....))))..).)))).)).))))))))))).....))))))..........------- ( -37.80)
>DroSec_CAF1 20125 111 - 1
--GCCAGCCAAAUCCUGCUCCUGGUCCACCAAGGCAGUCGCCUCGCCACUCGAGCUAAUGACACUUUAUGUGGUCGAGGCUGAAGUGGCUGGGAAUUGCGGGAAGUCCUCCAG-------
--.(((((((..(((((((..(((....))).)))))..((((((((((..(((.........)))...)))).)))))).))..)))))))....((.(((....))).)).------- ( -45.50)
>DroSim_CAF1 21793 112 - 1
GCUCCAGCCGAAUCCUGCUCCU-GUCCACCAAGGCAGUCGCCUCGCCACUCGAGCUAAUGACACUUUAUGUGGUCGAGGCAGAAGUGGCUGGGAACUGCGGGAAGUCCUCCAG-------
..((((((((..(((((((..(-(.....)).)))))..((((((((((..(((.........)))...)))).)))))).))..))))))))..(((.(((....))).)))------- ( -43.80)
>DroEre_CAF1 20046 90 - 1
-----AGCCGAAUCCCGCUCCUGGCC--------UGGUCUGCUCGCCACUCGAGCUAAUGACACUUUAUGUGGUCGAGGCUGAAGUGGCUGGGAACUGCGGGA-----------------
-----.......(((((((((..(((--------...((.(((((((((..(((.........)))...)))).))).)).))...)))..)))...))))))----------------- ( -38.10)
>DroYak_CAF1 19948 102 - 1
-----AGCCGAAUGCUGCUCCU-------------GGUCUCCUCGCCACUCGAGCUAAUGACACUUUAUGUGGCCGAGGCUGAAGUGGCUGGGAACUGCGGGAGGUCCUUCAGCACUGCU
-----(((.(..((((((((((-------------(...((((.((((((..((((.....(((.....))).....))))..)))))).))))....))))))......)))))).))) ( -38.80)
>consensus
_____AGCCGAAUCCUGCUCCUGGUCCACCAAG_CAGUCGCCUCGCCACUCGAGCUAAUGACACUUUAUGUGGUCGAGGCUGAAGUGGCUGGGAACUGCGGGAAGUCCUCCAG_______
............((((((((((((((...........((((((((((((..(((.........)))...)))).)))))).))...))))))))...))))))................. (-27.74 = -29.30 +   1.56)

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 10:18:45 2006