Locus 3122

Sequence ID 2L_DroMel_CAF1
Location 8,881,172 – 8,881,265
Length 93
Max. P 0.976004
window4962 window4963

overview

Window 2

Location 8,881,172 – 8,881,265
Length 93
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 84.87
Mean single sequence MFE -29.00
Consensus MFE -23.70
Energy contribution -24.53
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -3.08
Structure conservation index 0.82
SVM decision value 1.32
SVM RNA-class probability 0.942179
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8881172 93 + 22407834
GGGGCCGCCAUUAACGCAAAUGACUCUGCAAAAUGGCGGCCAUAUUAGGCAAGAAGACCAGGCCAAAACCCAAGAGCCA-------GUACCAGUAACACU
((((((((((((...(((........)))..))))))))))......(((..(.....)..)))...............-------...))......... ( -28.70)
>DroSec_CAF1 91238 93 + 1
GGGGCCGCCAUUAACGCAAAUGACUCUGCAAAAUGGCGGCCAUAUUAGGCAAGAAGCCCAAGCCAAAACCCAAGAGCCA-------GUACCAGUAACACU
((((((((((((...(((........)))..))))))))))......(((.....))).....................-------...))......... ( -28.10)
>DroSim_CAF1 89721 93 + 1
GGGGCCGCCAUUAACGCAAAUGACUCUGCAAAAUGGCGGCCAUAUUAGGCAAGAAGCCCAAGCCAAAACCCAAGAGCCA-------GUACCAGUAACACU
((((((((((((...(((........)))..))))))))))......(((.....))).....................-------...))......... ( -28.10)
>DroEre_CAF1 95717 99 + 1
GGGGCCGCCAUUAACGCAAAUGACUCUGCAAAAUGGCGGCCGUAUUAGGCAAGAAGCCCAGGCCAAAACCCAAGAGCCAGCA-CCAGUACCAGUAAAACU
((((((((((((...(((........)))..))))))))))((....(((.....)))..((((.........).))).)).-))............... ( -31.70)
>DroYak_CAF1 94247 100 + 1
GGGGCCGCCAUUAACGCAAAUGACUCUGCAAAAUGGCGGCCAUAUUAGGCAAGAAGCCCAGGCCAAAGCCCAAGAGCCAGUAUCCAGUACCAGUAACACU
((((((((((((...(((........)))..))))))))))(((((.(((..(.....).(((....))).....))))))))......))......... ( -32.00)
>DroPer_CAF1 123579 77 + 1
GGAGCCGCCAUUAACAGAGAUGACUCUGCAAAAUGGCGGCCAUAUUAGGCAAGAGAAGCAAG--AGGAGCCAAGAGUCA---------------------
((..((((((((..(((((....)))))...)))))).(((......)))............--.))..))........--------------------- ( -25.40)
>consensus
GGGGCCGCCAUUAACGCAAAUGACUCUGCAAAAUGGCGGCCAUAUUAGGCAAGAAGCCCAAGCCAAAACCCAAGAGCCA_______GUACCAGUAACACU
((((((((((((...(((........)))..))))))))))......(((..(.....)..))).....))............................. (-23.70 = -24.53 +   0.83)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,881,172 – 8,881,265
Length 93
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 84.87
Mean single sequence MFE -37.95
Consensus MFE -30.50
Energy contribution -30.95
Covariance contribution 0.45
Combinations/Pair 1.16
Mean z-score -4.18
Structure conservation index 0.80
SVM decision value 1.76
SVM RNA-class probability 0.976004
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8881172 93 - 22407834
AGUGUUACUGGUAC-------UGGCUCUUGGGUUUUGGCCUGGUCUUCUUGCCUAAUAUGGCCGCCAUUUUGCAGAGUCAUUUGCGUUAAUGGCGGCCCC
.((((((..((((.-------.((((...((((....))))))))....))))))))))((((((((((.((((((....))))))..)))))))))).. ( -37.40)
>DroSec_CAF1 91238 93 - 1
AGUGUUACUGGUAC-------UGGCUCUUGGGUUUUGGCUUGGGCUUCUUGCCUAAUAUGGCCGCCAUUUUGCAGAGUCAUUUGCGUUAAUGGCGGCCCC
.((((((..((((.-------.(((((...(((....))).)))))...))))))))))((((((((((.((((((....))))))..)))))))))).. ( -38.60)
>DroSim_CAF1 89721 93 - 1
AGUGUUACUGGUAC-------UGGCUCUUGGGUUUUGGCUUGGGCUUCUUGCCUAAUAUGGCCGCCAUUUUGCAGAGUCAUUUGCGUUAAUGGCGGCCCC
.((((((..((((.-------.(((((...(((....))).)))))...))))))))))((((((((((.((((((....))))))..)))))))))).. ( -38.60)
>DroEre_CAF1 95717 99 - 1
AGUUUUACUGGUACUGG-UGCUGGCUCUUGGGUUUUGGCCUGGGCUUCUUGCCUAAUACGGCCGCCAUUUUGCAGAGUCAUUUGCGUUAAUGGCGGCCCC
..........(((.(((-.((.(((((..((((....)))))))))....))))).)))((((((((((.((((((....))))))..)))))))))).. ( -41.50)
>DroYak_CAF1 94247 100 - 1
AGUGUUACUGGUACUGGAUACUGGCUCUUGGGCUUUGGCCUGGGCUUCUUGCCUAAUAUGGCCGCCAUUUUGCAGAGUCAUUUGCGUUAAUGGCGGCCCC
.((((((..((((..(((....(((((..((((....))))))))))))))))))))))((((((((((.((((((....))))))..)))))))))).. ( -42.50)
>DroPer_CAF1 123579 77 - 1
---------------------UGACUCUUGGCUCCU--CUUGCUUCUCUUGCCUAAUAUGGCCGCCAUUUUGCAGAGUCAUCUCUGUUAAUGGCGGCUCC
---------------------........(((....--............)))......((((((((((..((((((....)))))).)))))))))).. ( -29.09)
>consensus
AGUGUUACUGGUAC_______UGGCUCUUGGGUUUUGGCCUGGGCUUCUUGCCUAAUAUGGCCGCCAUUUUGCAGAGUCAUUUGCGUUAAUGGCGGCCCC
...........................((((((...(((....)))....))))))...((((((((((.((((((....))))))..)))))))))).. (-30.50 = -30.95 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:50 2006