Locus 8280

Sequence ID 3L_DroMel_CAF1
Location 21,732,123 – 21,732,237
Length 114
Max. P 0.682974
window13543 window13544

overview

Window 3

Location 21,732,123 – 21,732,237
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 96.15
Mean single sequence MFE -30.83
Consensus MFE -28.99
Energy contribution -28.77
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -0.94
Structure conservation index 0.94
SVM decision value 0.31
SVM RNA-class probability 0.682974
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21732123 114 + 23771897
------UGGGGCCAAGCCAAUCCGGUAGCCGGUCUGUCAGUAAGUUGAAAAUUGUUUUAAAAUUGCUGUUACAUGUCUGAAUGCAAGCAGAUUGAAUUACAAGCUGGCCGAGCAAAUGCU
------...(((((.((((..((((...))))..)).((((((.((((((....))))))..))))))...((.(((((........)))))))........))))))).(((....))) ( -28.40)
>DroPse_CAF1 42047 114 + 1
------UGAGGCCAGGCCAAUCCGGUAGCCAGUCUGUCAGUAAGUUGAAAAUUGUUUUAAAAUUGCUGUUACAUGUCUGAAUGCAAGCAGAUUGAAUUACAAGCUGGCCGAGCAAAUGCU
------...(((((((((.....)))...((((((((((((((.((((((....))))))..))))))...(((......)))...)))))))).........)))))).(((....))) ( -32.70)
>DroSim_CAF1 18889 114 + 1
------UGGGGCCAAGCCAAUCCGGUAGCCGGUCUGUCAGUAAGUUGAAAAUUGUUUUAAAAUUGCUGUUACAUGUCUGAAUGCAAGCAGAUUGAAUUACAAGCUGGCCGAGCAAAUGCU
------...(((((.((((..((((...))))..)).((((((.((((((....))))))..))))))...((.(((((........)))))))........))))))).(((....))) ( -28.40)
>DroPer_CAF1 40735 114 + 1
------UGAGGCCAGGCCAAUCCGGUAGCCAGUCUGUCAGUAAGUUGAAAAUUGUUUUAAAAUUGCUGUUACAUGUCUGAAUGCAAGCAGAUUGAAUUACAAGCUGGCCGAGCAAAUGCU
------...(((((((((.....)))...((((((((((((((.((((((....))))))..))))))...(((......)))...)))))))).........)))))).(((....))) ( -32.70)
>DroEre_CAF1 119 111 + 1
---------GGCCAAGCCAAUCCGGUAGCCGGUCUGUCAGUAAGUUGAAAAUUGUUUUAAAAUUGCUGUUACAUGUCUGAAUGCAAGCAGAUUGAAUUACAAGCUGGCCGAGCAAAUGCU
---------(((((.((((..((((...))))..)).((((((.((((((....))))))..))))))...((.(((((........)))))))........))))))).(((....))) ( -28.40)
>DroYak_CAF1 64980 120 + 1
GGGGCUUGGGGCCAAGCCAAUCCGGUAGCCGGUCUGUCAGUAAGUUGAAAAUUGUUUUAAAAUUGCUGUUACAUGUCUGAAUGCAAGCAGAUUGAAUUACAAGCUGGCCGAGCAAAUGCU
((((((((....))))))...))....(((((..(((((((((.((((((....))))))..))))))...((.(((((........)))))))....)))..)))))..(((....))) ( -34.40)
>consensus
______UGGGGCCAAGCCAAUCCGGUAGCCGGUCUGUCAGUAAGUUGAAAAUUGUUUUAAAAUUGCUGUUACAUGUCUGAAUGCAAGCAGAUUGAAUUACAAGCUGGCCGAGCAAAUGCU
.........(((((.(((.....)))...((((((((((((((.((((((....))))))..))))))...(((......)))...))))))))..........))))).(((....))) (-28.99 = -28.77 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,732,123 – 21,732,237
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.15
Mean single sequence MFE -25.00
Consensus MFE -24.79
Energy contribution -24.57
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -0.67
Structure conservation index 0.99
SVM decision value 0.22
SVM RNA-class probability 0.640188
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21732123 114 - 23771897
AGCAUUUGCUCGGCCAGCUUGUAAUUCAAUCUGCUUGCAUUCAGACAUGUAACAGCAAUUUUAAAACAAUUUUCAACUUACUGACAGACCGGCUACCGGAUUGGCUUGGCCCCA------
(((....))).(((((((((((.....(((.(((((((((......)))))..))))))).....))))...............(((.((((...)))).))))).)))))...------ ( -25.30)
>DroPse_CAF1 42047 114 - 1
AGCAUUUGCUCGGCCAGCUUGUAAUUCAAUCUGCUUGCAUUCAGACAUGUAACAGCAAUUUUAAAACAAUUUUCAACUUACUGACAGACUGGCUACCGGAUUGGCCUGGCCUCA------
.......(((.((((((((.(((..(((.((((.((((((......))))))....................(((......))))))).))).))).)).)))))).)))....------ ( -24.40)
>DroSim_CAF1 18889 114 - 1
AGCAUUUGCUCGGCCAGCUUGUAAUUCAAUCUGCUUGCAUUCAGACAUGUAACAGCAAUUUUAAAACAAUUUUCAACUUACUGACAGACCGGCUACCGGAUUGGCUUGGCCCCA------
(((....))).(((((((((((.....(((.(((((((((......)))))..))))))).....))))...............(((.((((...)))).))))).)))))...------ ( -25.30)
>DroPer_CAF1 40735 114 - 1
AGCAUUUGCUCGGCCAGCUUGUAAUUCAAUCUGCUUGCAUUCAGACAUGUAACAGCAAUUUUAAAACAAUUUUCAACUUACUGACAGACUGGCUACCGGAUUGGCCUGGCCUCA------
.......(((.((((((((.(((..(((.((((.((((((......))))))....................(((......))))))).))).))).)).)))))).)))....------ ( -24.40)
>DroEre_CAF1 119 111 - 1
AGCAUUUGCUCGGCCAGCUUGUAAUUCAAUCUGCUUGCAUUCAGACAUGUAACAGCAAUUUUAAAACAAUUUUCAACUUACUGACAGACCGGCUACCGGAUUGGCUUGGCC---------
(((....))).(((((((((((.....(((.(((((((((......)))))..))))))).....))))...............(((.((((...)))).))))).)))))--------- ( -24.50)
>DroYak_CAF1 64980 120 - 1
AGCAUUUGCUCGGCCAGCUUGUAAUUCAAUCUGCUUGCAUUCAGACAUGUAACAGCAAUUUUAAAACAAUUUUCAACUUACUGACAGACCGGCUACCGGAUUGGCUUGGCCCCAAGCCCC
.((....))((((..((((.((.........(((((((((......)))))..))))...............(((......)))...)).)))).))))...((((((....)))))).. ( -26.10)
>consensus
AGCAUUUGCUCGGCCAGCUUGUAAUUCAAUCUGCUUGCAUUCAGACAUGUAACAGCAAUUUUAAAACAAUUUUCAACUUACUGACAGACCGGCUACCGGAUUGGCUUGGCCCCA______
(((....))).(((((((((((.....(((.(((((((((......)))))..))))))).....))))...............(((.((((...)))).))))).)))))......... (-24.79 = -24.57 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:11:19 2006