Locus 2023

Sequence ID 3L_DroMel_CAF1
Location 5,573,251 – 5,573,351
Length 100
Max. P 0.717595
window3162 window3163

overview

Window 2

Location 5,573,251 – 5,573,351
Length 100
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 79.80
Mean single sequence MFE -36.67
Consensus MFE -22.41
Energy contribution -22.50
Covariance contribution 0.09
Combinations/Pair 1.28
Mean z-score -1.78
Structure conservation index 0.61
SVM decision value 0.39
SVM RNA-class probability 0.717595
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5573251 100 + 23771897
AAGGUGGAGGAGCUGGGCAUGGGAAACAAUAUCCAGGAGGACCAGGCGGUCCUGGUAAGCCUCUAGGCCCCUGGAUGAAAGGCAGAUUUGGGGGGUAAGG
....((((((..((((..((.(....).))..)))).((((((....))))))......))))))..((((..(((.........)))..))))...... ( -38.90)
>DroSim_CAF1 6544 100 + 1
AAGGUGGAGCAGCCGGGCAUGGGAAACAAUAUCCAGGAGGACCAGGCGGUCCUGGUAAUCCUCUCGGUCCCUGGAUGAAAGGCAGAUUUGGGGGGUAAGG
..(((......)))((..((.(....).))..))((((..((((((....))))))..))))((.(.((((..(((.........)))..)))).).)). ( -34.40)
>DroEre_CAF1 6189 100 + 1
AUGGUGGAGCAGCCGGGCAUGGGAAACAAUAUCCAGGAGGACCCGGCGGUCCUGGUAGGCCUCUAGGUCCCUGAAGGAAAGGCAGAUUUGGGGGGUAAGG
.....(((.(.((((((....(....)....(((....)))))))))).))).......(((((((((((((.......)))..))))))))))...... ( -36.40)
>DroWil_CAF1 7824 100 + 1
AUGGUGGUGCUGCCGGGCAGGGGAAACAGUAUCCUGGUGGACCCGGUGGUCCUGGCAUGCCUCGCGGUCCGGGUAUUAUUUGUACAUUCUGAUUGAAUGG
..(((((((((((((((....(....).....))))))((((((((.(((........)))))).))))).)))))))))....(((((.....))))). ( -36.70)
>DroYak_CAF1 6536 100 + 1
AUGGCGGACCAGCCGGGCAGGGGAAACAAUAUCCAGGAGGACCCGGUGGUCCUGGUAAGCCUCUGGGUCCCUGAAUGAAUGGCAGAUUUGGGGGAUAAGG
..(((((((((.(((((....(....)....(((....))))))))))))))......))).((...((((..(((.........)))..))))...)). ( -37.40)
>DroAna_CAF1 6478 100 + 1
CUGGCGGAAUGGCUGGGCAGGGGAAGCAAUAUCCAGGAGGUCCCGGUGGACCAGGUAGACCUCUAGGCCCCGGGAUAAUCGGAACAUUCGGUGGAAAAGG
.(.((.(((((.((((..(..(....)..)..))))((.(((((((.((.(((((....)))...)))))))))))..))....))))).)).)...... ( -36.20)
>consensus
AUGGUGGAGCAGCCGGGCAGGGGAAACAAUAUCCAGGAGGACCCGGCGGUCCUGGUAAGCCUCUAGGUCCCUGGAUGAAAGGCAGAUUUGGGGGGUAAGG
..((.((....(((((..(..(....)..)..))....(((((....))))).)))...)).))...(((((((((.........)))))))))...... (-22.41 = -22.50 +   0.09)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,573,251 – 5,573,351
Length 100
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 79.80
Mean single sequence MFE -27.56
Consensus MFE -16.58
Energy contribution -16.97
Covariance contribution 0.39
Combinations/Pair 1.14
Mean z-score -1.74
Structure conservation index 0.60
SVM decision value 0.27
SVM RNA-class probability 0.661543
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5573251 100 - 23771897
CCUUACCCCCCAAAUCUGCCUUUCAUCCAGGGGCCUAGAGGCUUACCAGGACCGCCUGGUCCUCCUGGAUAUUGUUUCCCAUGCCCAGCUCCUCCACCUU
........................(((((((((((....))))....((((((....))))))))))))).............................. ( -25.20)
>DroSim_CAF1 6544 100 - 1
CCUUACCCCCCAAAUCUGCCUUUCAUCCAGGGACCGAGAGGAUUACCAGGACCGCCUGGUCCUCCUGGAUAUUGUUUCCCAUGCCCGGCUGCUCCACCUU
.................(((....((((((((.((....))...((((((....))))))..))))))))...((.......))..)))........... ( -27.10)
>DroEre_CAF1 6189 100 - 1
CCUUACCCCCCAAAUCUGCCUUUCCUUCAGGGACCUAGAGGCCUACCAGGACCGCCGGGUCCUCCUGGAUAUUGUUUCCCAUGCCCGGCUGCUCCACCAU
.................((((((((.....)))....)))))......((((.(((((((......(((.......)))...))))))).).)))..... ( -28.30)
>DroWil_CAF1 7824 100 - 1
CCAUUCAAUCAGAAUGUACAAAUAAUACCCGGACCGCGAGGCAUGCCAGGACCACCGGGUCCACCAGGAUACUGUUUCCCCUGCCCGGCAGCACCACCAU
.(((((.....)))))..............((..(....)((.((((.(((((....)))))..((((...........))))...)))))).))..... ( -27.90)
>DroYak_CAF1 6536 100 - 1
CCUUAUCCCCCAAAUCUGCCAUUCAUUCAGGGACCCAGAGGCUUACCAGGACCACCGGGUCCUCCUGGAUAUUGUUUCCCCUGCCCGGCUGGUCCGCCAU
.....((((....................))))......(((......((((((((((((......(((.......)))...)))))).))))))))).. ( -30.05)
>DroAna_CAF1 6478 100 - 1
CCUUUUCCACCGAAUGUUCCGAUUAUCCCGGGGCCUAGAGGUCUACCUGGUCCACCGGGACCUCCUGGAUAUUGCUUCCCCUGCCCAGCCAUUCCGCCAG
...........(((((...((.......))((((...(((((...(((((....))))))))))..(((.......)))...))))...)))))...... ( -26.80)
>consensus
CCUUACCCCCCAAAUCUGCCUUUCAUCCAGGGACCUAGAGGCUUACCAGGACCACCGGGUCCUCCUGGAUAUUGUUUCCCAUGCCCGGCUGCUCCACCAU
........................(((((((..((....)).......(((((....))))).))))))).............................. (-16.58 = -16.97 +   0.39)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:40 2006