Locus 2936

Sequence ID 3R_DroMel_CAF1
Location 7,864,696 – 7,864,825
Length 129
Max. P 0.860145
window4725 window4726

overview

Window 5

Location 7,864,696 – 7,864,803
Length 107
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 77.90
Mean single sequence MFE -21.42
Consensus MFE -13.35
Energy contribution -13.94
Covariance contribution 0.59
Combinations/Pair 1.19
Mean z-score -1.80
Structure conservation index 0.62
SVM decision value 0.82
SVM RNA-class probability 0.860145
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7864696 107 + 27905053
-AACCGACCGACCGACAGCCAACCACCCACUUUUCCCACCACCCAAGGCCG-----------CGGAAAACCGUCGAUGGGAAUAAAAUAAACCAAUUUCCUAUCGUCGCAUUGCCGAAG
-.......((.(((.(.(((..........................))).)-----------))).....((.(((((((((..............))))))))).))......))... ( -21.41)
>DroPse_CAF1 27254 111 + 1
AAAC-AACCCAUC---GACCAACCAUCCAA----CCAACCAUCGAAAACCCCUCUGUACAGCCAACAAACUGUCGAUGGGAAUAAAAUAAACCAAUUUCCCAUCGUCGCAUUGCCGAAG
....-.......(---(((...........----.....................(.((((........)))))((((((((..............))))))))))))........... ( -17.94)
>DroSec_CAF1 25535 107 + 1
-AACGGACCGACCUACAGCUAACCACCAAAUUUUCCCACCACCCAAGGCCG-----------CGGAAAACCUUCGAUGGGAAUAAAAUAAACCAAUUUCCUAUCGUCGCAUUGCCGAAG
-..(((..((((..................(((((((.((......))..)-----------.)))))).....((((((((..............)))))))))))).....)))... ( -23.54)
>DroSim_CAF1 25844 107 + 1
-AACGGACCGACCUACAGCCAAACACCCACUUUUCCCACCAUCCAAGGCCG-----------CGGAAAACCGUCGAUGGGAAUAAAAUAAACCAAUUUCCUAUCGUCGCAUUGCCGAAG
-..(((..((((..................(((((((.((......))..)-----------.)))))).....((((((((..............)))))))))))).....)))... ( -23.34)
>DroEre_CAF1 25720 99 + 1
-AACGGAC--------ACCCACCCACCCACUUUUCGCACCACCCGAGGCCG-----------CAGAAAACCGUCGGUGGGAAUAAAAUAAACCAAUUUCCUAUCGUCGCAUUGCCGAAG
-..(((.(--------(.............(((((((.((......))..)-----------).))))).((.(((((((((..............))))))))).))...)))))... ( -22.54)
>DroYak_CAF1 26082 86 + 1
-AACGGAC--------ACCCACCCC-------------CCACGCAAGGCCG-----------CAGAAAACCGUCGAUGGGAAUAAAAUAAACCAAUUUCCUAUCGUCGCAUUGCCGAAG
-..(((.(--------(........-------------....((......)-----------).......((.(((((((((..............))))))))).))...)))))... ( -19.74)
>consensus
_AACGGACCGACC___AGCCAACCACCCACUUUUCCCACCACCCAAGGCCG___________CAGAAAACCGUCGAUGGGAAUAAAAUAAACCAAUUUCCUAUCGUCGCAUUGCCGAAG
...(((................................((......))......................((.(((((((((..............))))))))).)).....)))... (-13.35 = -13.94 +   0.59)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,864,735 – 7,864,825
Length 90
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 82.30
Mean single sequence MFE -29.22
Consensus MFE -20.48
Energy contribution -21.87
Covariance contribution 1.39
Combinations/Pair 1.15
Mean z-score -1.76
Structure conservation index 0.70
SVM decision value 0.27
SVM RNA-class probability 0.663624
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7864735 90 + 27905053
ACCCAAGGCCG-----------CGGAAAACCGUCGAUGGGAAUAAAAUAAACCAAUUUCCUAUCGUCGCAUUGCCGAAGGCUUCCGGUUGGGCGGGCGGAU
..((.(((((.-----------(((.....((.(((((((((..............))))))))).)).....)))..)))))(((......)))..)).. ( -30.04)
>DroPse_CAF1 27286 98 + 1
AUCGAAAACCCCUCUGUACAGCCAACAAACUGUCGAUGGGAAUAAAAUAAACCAAUUUCCCAUCGUCGCAUUGCCGAAGGCUUCCGGUGGAGA---GCGAC
...............(.((((........)))))((((((((..............))))))))(((((.(..(((........)))..)...---))))) ( -26.74)
>DroSim_CAF1 25883 90 + 1
AUCCAAGGCCG-----------CGGAAAACCGUCGAUGGGAAUAAAAUAAACCAAUUUCCUAUCGUCGCAUUGCCGAAGGCUUCCGGUUGGGCGGGCGGAU
((((.(((((.-----------(((.....((.(((((((((..............))))))))).)).....)))..)))))(((......)))..)))) ( -31.64)
>DroEre_CAF1 25751 90 + 1
ACCCGAGGCCG-----------CAGAAAACCGUCGGUGGGAAUAAAAUAAACCAAUUUCCUAUCGUCGCAUUGCCGAAGGCUUCCGGUUGGGCGGACGGAU
..(((...(((-----------(....(((((.(((((((((..............))))))))).).....(((...)))....))))..)))).))).. ( -31.04)
>DroYak_CAF1 26100 90 + 1
ACGCAAGGCCG-----------CAGAAAACCGUCGAUGGGAAUAAAAUAAACCAAUUUCCUAUCGUCGCAUUGCCGAAGGCUUCCGGUUGGGCGGGCGGAU
.(....).(((-----------(..........(((((((((..............)))))))))((((...((((........))))...)))))))).. ( -30.44)
>DroPer_CAF1 27249 98 + 1
AUCGAAAACCCCUCUGUACAGCCAACAAACUGUCGAUGGGAAUAAAAUAAACCAAUUUCCCAUCGUCGCAUUGCCGAAGGCUUCCGGUGGAGA---CCGAC
.(((....(.((.(((...((((..........(((((((((..............)))))))))(((......))).))))..))).)).).---.))). ( -25.44)
>consensus
ACCCAAGGCCG___________CAGAAAACCGUCGAUGGGAAUAAAAUAAACCAAUUUCCUAUCGUCGCAUUGCCGAAGGCUUCCGGUUGGGCGGGCGGAU
.............................(((((((((((((..............))))))))..(((...((((........))))...)))))))).. (-20.48 = -21.87 +   1.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:11 2006