Locus 1722

Sequence ID 3L_DroMel_CAF1
Location 4,998,777 – 4,998,919
Length 142
Max. P 0.993562
window2653 window2654

overview

Window 3

Location 4,998,777 – 4,998,897
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 93.38
Mean single sequence MFE -39.75
Consensus MFE -35.91
Energy contribution -36.80
Covariance contribution 0.89
Combinations/Pair 1.05
Mean z-score -2.19
Structure conservation index 0.90
SVM decision value 2.41
SVM RNA-class probability 0.993562
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4998777 120 + 23771897
UUGGCAACUUGCAUCCAUUGUUCGAGUGGCUGCUGGUGGCUGCGCCGGCGAAGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGU
..(....)..(((.(((((.....))))).))).((((((((.((((((..((((((((...))))))))..))).......((((((((((....)))))).))))))))))))))).. ( -42.20)
>DroSec_CAF1 219377 117 + 1
---GCAACUUGCAUUCAUUGUUCGAGUGGCUGCUGGUGGCUGCGCCGGCGAAGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGU
---((.....))............((((((((((((((....))))))).(((((....)))))((((..((((((......))))))((((....)))).......))))))))))).. ( -40.50)
>DroSim_CAF1 239144 117 + 1
---GCAACUUGCAUCCAUUGUUCGAGUGGCUGCUGGUGGCUGCGCCGGCGAAGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGU
---.......(((.(((((.....))))).))).((((((((.((((((..((((((((...))))))))..))).......((((((((((....)))))).))))))))))))))).. ( -41.70)
>DroEre_CAF1 222647 120 + 1
CUGGCAACUUGCAUCUAUUGUUCGAGUGGCUGCUGGUGGCUGCGCCGGCGAAGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGU
...((.....))............((((((((((((((....))))))).(((((....)))))((((..((((((......))))))((((....)))).......))))))))))).. ( -40.50)
>DroYak_CAF1 227502 120 + 1
UUGGCAACUUGCAUCUAUUGUUCGAGUGGCUGCUGGUGGCUGCGCCGGCGAAGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGU
...((.....))............((((((((((((((....))))))).(((((....)))))((((..((((((......))))))((((....)))).......))))))))))).. ( -40.50)
>DroAna_CAF1 229733 108 + 1
UUAACAACUUGCAUCUUUUGUUCGAGUGACUGCUGGUGG------------AGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGU
.......(..(((.....)))..)(((((((((((((.(------------((((....))))).)))..((((((......))))))((((....)))).......)).)))))))).. ( -33.10)
>consensus
UUGGCAACUUGCAUCCAUUGUUCGAGUGGCUGCUGGUGGCUGCGCCGGCGAAGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGU
...((((...(((.....)))..((.((((((((((((....)))))))..((((((((...))))))))((((((......))))))((((....)))).......))))).)).)))) (-35.91 = -36.80 +   0.89)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,998,817 – 4,998,919
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.03
Mean single sequence MFE -30.17
Consensus MFE -26.84
Energy contribution -28.32
Covariance contribution 1.48
Combinations/Pair 1.03
Mean z-score -1.99
Structure conservation index 0.89
SVM decision value 1.30
SVM RNA-class probability 0.939276
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4998817 102 + 23771897
UGCGCCGGCGAAGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGUUCGCACUCGUACACGC------------------ACACAU
((((...(((((.(((.(((...(((((..((((((......))))))((((....)))).......))))))))))).)))))...)))).....------------------...... ( -30.80)
>DroSec_CAF1 219414 110 + 1
UGCGCCGGCGAAGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGUUCGCACUCGCACACACACUCGC----AC------ACACAC
((((...(((((.(((.(((...(((((..((((((......))))))((((....)))).......))))))))))).)))))...))))...........----..------...... ( -32.80)
>DroEre_CAF1 222687 96 + 1
UGCGCCGGCGAAGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGUUCGCACUCGCACAC------------------------AC
((((...(((((.(((.(((...(((((..((((((......))))))((((....)))).......))))))))))).)))))...))))...------------------------.. ( -32.80)
>DroYak_CAF1 227542 100 + 1
UGCGCCGGCGAAGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGUUCGCACUCGCACACA--------------------CGCAC
((((...(((((.(((.(((...(((((..((((((......))))))((((....)))).......))))))))))).)))))...))))....--------------------..... ( -32.80)
>DroAna_CAF1 229772 109 + 1
-----------AGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGUUCGCACUCACACAUCCGCUUACGUUUAAACACACACGCAC
-----------((((((((...))))))))((((.......(((((.(((((....(((((.....))).)).....)).))).))))).......)))).................... ( -21.64)
>consensus
UGCGCCGGCGAAGGGUCGACCCUUGACCCUGAGCUCUAAUUUGAGUUUGACAUUUAUGUCAAUAUUUGGUCAGUCAUUGUUCGCACUCGCACACAC__________________ACACAC
((((...(((((.(((.(((...(((((..((((((......))))))((((....)))).......))))))))))).)))))...))))............................. (-26.84 = -28.32 +   1.48)

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 10:14:30 2006