Locus 6899

Sequence ID X_DroMel_CAF1
Location 17,271,129 – 17,271,235
Length 106
Max. P 0.991263
window11285 window11286

overview

Window 5

Location 17,271,129 – 17,271,235
Length 106
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 78.49
Mean single sequence MFE -25.48
Consensus MFE -11.86
Energy contribution -12.22
Covariance contribution 0.36
Combinations/Pair 1.21
Mean z-score -2.79
Structure conservation index 0.47
SVM decision value 2.26
SVM RNA-class probability 0.991263
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17271129 106 + 22224390
AAAAUAUGGGCGGCCAACAGACUUCAAUUUCAAUGGAUUGAAUUUGCCAUUUUUCCACU-CUGCAAAUACAAUCCCUAAAUUGGGAUUUAUUUU----UGAAGA-GGGCACA
............(((..((((.(((((((......)))))))))))...........((-((.((((...((((((......))))))....))----)).)))-))))... ( -27.00)
>DroSec_CAF1 116296 100 + 1
AAAAUAUGGGCGGCCAACAGACUUCAAUUUCAAUGGAUUGAAUUUCCCAUUUUAACCCUCCUUCAAAUACAAUCCCUAAAAUGGGAUUUCCUUU----UGAAAU--------
..((.(((((.(.....)....(((((((......)))))))...))))).))........((((((...((((((......))))))....))----))))..-------- ( -20.30)
>DroSim_CAF1 120032 100 + 1
AAAAUAUGGGCGGCCAACAGACUUCAAUUCCAAUGGAUUGAAUUUCCCAUUUUAACCCUCCUUCAAAUACAAUCCCUAAAAUGGGAUUUCCUUU----UGAAAU--------
..((.(((((.(.....)....((((((((....))))))))...))))).))........((((((...((((((......))))))....))----))))..-------- ( -21.80)
>DroEre_CAF1 120899 106 + 1
GAAAUGUGUGCGGUAAGCUGAAUUCAAUUUCACUGGAUUGAAUUAGCCAUUCUUGCCCU-UUGCAAAUACAAUCCCUAAAAUGGGAUUUAUUUU----UA-AAUGGGGCACA
......(((((.....(((((.(((((((......))))))))))))........((((-(((.(((((.((((((......))))))))))).----))-)).)))))))) ( -33.00)
>DroYak_CAF1 126169 106 + 1
UAAAUGCGUGCGGCAAGCUGACUUCAAUUUCACUGGAUUGGUUUUGCCAUUUUUCCCCUUUUGCAAAUGCCAUCCUUAAAAUGGGAUUUUCUUUUUUGUG-AAUGGG-----
...........(((((((..(.((((.......)))))..).)))))).......(((.((..((((....(((((......))))).......))))..-)).)))----- ( -25.30)
>consensus
AAAAUAUGGGCGGCCAACAGACUUCAAUUUCAAUGGAUUGAAUUUGCCAUUUUUACCCU_CUGCAAAUACAAUCCCUAAAAUGGGAUUUACUUU____UGAAAU_GG_____
...........(((....(((.(((((((......)))))))))))))......................((((((......))))))........................ (-11.86 = -12.22 +   0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,271,129 – 17,271,235
Length 106
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 78.49
Mean single sequence MFE -25.24
Consensus MFE -8.50
Energy contribution -9.74
Covariance contribution 1.24
Combinations/Pair 1.06
Mean z-score -2.16
Structure conservation index 0.34
SVM decision value 0.66
SVM RNA-class probability 0.815979
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17271129 106 - 22224390
UGUGCCC-UCUUCA----AAAAUAAAUCCCAAUUUAGGGAUUGUAUUUGCAG-AGUGGAAAAAUGGCAAAUUCAAUCCAUUGAAAUUGAAGUCUGUUGGCCGCCCAUAUUUU
(((((((-(((.((----((....((((((......))))))...)))).))-)).))......(((...((((((........))))))(((....))).))))))).... ( -27.20)
>DroSec_CAF1 116296 100 - 1
--------AUUUCA----AAAGGAAAUCCCAUUUUAGGGAUUGUAUUUGAAGGAGGGUUAAAAUGGGAAAUUCAAUCCAUUGAAAUUGAAGUCUGUUGGCCGCCCAUAUUUU
--------.(((((----((....((((((......))))))...)))))))..((((...((((((...((((((........)))))).))))))....))))....... ( -26.20)
>DroSim_CAF1 120032 100 - 1
--------AUUUCA----AAAGGAAAUCCCAUUUUAGGGAUUGUAUUUGAAGGAGGGUUAAAAUGGGAAAUUCAAUCCAUUGGAAUUGAAGUCUGUUGGCCGCCCAUAUUUU
--------.(((((----((....((((((......))))))...)))))))..((((...((((((...((((((((...)).)))))).))))))....))))....... ( -27.80)
>DroEre_CAF1 120899 106 - 1
UGUGCCCCAUU-UA----AAAAUAAAUCCCAUUUUAGGGAUUGUAUUUGCAA-AGGGCAAGAAUGGCUAAUUCAAUCCAGUGAAAUUGAAUUCAGCUUACCGCACACAUUUC
((((((((.((-(.----.(((((((((((......)))))).)))))..))-))))...(...((((((((((((........)))))))).))))...))))))...... ( -29.40)
>DroYak_CAF1 126169 106 - 1
-----CCCAUU-CACAAAAAAGAAAAUCCCAUUUUAAGGAUGGCAUUUGCAAAAGGGGAAAAAUGGCAAAACCAAUCCAGUGAAAUUGAAGUCAGCUUGCCGCACGCAUUUA
-----....((-(((......(.((((.(((((.....))))).)))).)......(((....(((.....))).))).)))))..........((.....))......... ( -15.60)
>consensus
_____CC_AUUUCA____AAAGGAAAUCCCAUUUUAGGGAUUGUAUUUGCAG_AGGGGAAAAAUGGCAAAUUCAAUCCAUUGAAAUUGAAGUCUGUUGGCCGCCCAUAUUUU
.............................((.(((..((((((.((((((...............)))))).))))))....))).))........................ ( -8.50 =  -9.74 +   1.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:30 2006