Locus 5895

Sequence ID X_DroMel_CAF1
Location 15,187,206 – 15,187,377
Length 171
Max. P 0.938912
window9572 window9573

overview

Window 2

Location 15,187,206 – 15,187,326
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 95.11
Mean single sequence MFE -39.34
Consensus MFE -34.91
Energy contribution -35.33
Covariance contribution 0.42
Combinations/Pair 1.16
Mean z-score -1.77
Structure conservation index 0.89
SVM decision value 1.30
SVM RNA-class probability 0.938912
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15187206 120 - 22224390
GAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGUUCUCUGGAAGCCUACUUCGCCGUCCAGCCGAGGCCAUCCGGUGAGAAAAUCGCAGCGAUUGCCGAAAAGCUGGAUUUGAAGAAAA
.....(((.((((((....((.((((....)).)).)).))))))))).(((((..(((((((...(((.((((.((((.....)))).).))).))).....))))))).))))).... ( -40.90)
>DroVir_CAF1 10918 120 - 1
GAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGUUCCCUGGAAGCCUAUUUCGCCGUCCAGCCGAGGCCGUCCGGUGAGAAAAUCGCUGCCAUUGCCGAAAAGCUGGACUUGAAGAAAA
((((.(((.((((((..(.((.((((....)).)).)))))))))))).))))...(((((((...(((....((((((.....)))))).....))).....))))))).......... ( -43.40)
>DroPse_CAF1 10338 120 - 1
GAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGUUCCCUGGAAGCCUACUUUGCCGUCCAGCCGAGGCCAUCCGGUGAGAAAAUCGCGGCCAUCGCAGAAAAGCUGGACUUGAAGAAAA
.....(((.((((((..(.((.((((....)).)).)))))))))))).((((...((((((((((((((...((((......)))).)))).))).......)))))))..)))).... ( -41.31)
>DroGri_CAF1 11634 120 - 1
GAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGUUCCCUGGAAGCCUACUUCGCCGUCCAGCCGAGGCCGUCGGGUGAGAAAAUCGCUGCCAUUGCCGAAAAGCUGGAUUUGAAGAAAA
.....(((.((((((..(.((.((((....)).)).)))))))))))).(((((..(((((((...(((.((.((((((.....))))..)))).))).....))))))).))))).... ( -40.60)
>DroWil_CAF1 13335 120 - 1
GAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGCUCCCUGGAAGCCUACUUUGCCGUCCAGCCGAGACCAUCUGGGGAGAAAAUCGCCGCCAUUGCCGAAAAGCUGGAUUUGAAGAAAA
.....(((.((((((..(.(((..((....)).))).).))))))))).((((...(((((((..........(((((.(.....).)).)))..........)))))))..)))).... ( -32.65)
>DroAna_CAF1 11634 120 - 1
GAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGUUCCCUGGAAGCCUACUUCGCCGUCCAGCCGAGACCAUCCGGUGAGAAAAUCGCUGCCAUUGCCGAAAAGCUGGAUUUGAAGAAAA
.....(((.((((((..(.((.((((....)).)).)))))))))))).(((((..(((((((((.(......((((((.....))))))......)))....))))))).))))).... ( -37.20)
>consensus
GAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGUUCCCUGGAAGCCUACUUCGCCGUCCAGCCGAGGCCAUCCGGUGAGAAAAUCGCUGCCAUUGCCGAAAAGCUGGAUUUGAAGAAAA
.....(((.((((((..(.((.((((....)).)).)))))))))))).(((((..(((((((...(((....((((((.....)))))).....))).....))))))).))))).... (-34.91 = -35.33 +   0.42)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,187,286 – 15,187,377
Length 91
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.58
Mean single sequence MFE -22.85
Consensus MFE -18.82
Energy contribution -18.93
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.83
Structure conservation index 0.82
SVM decision value 0.61
SVM RNA-class probability 0.799814
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15187286 91 - 22224390
---------------------------CGCAG--CUUAGGGCCCCGCUUCUAAAGUAAUCUAUAUCGAGUCUUUUUUCAAGAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGUUCUCU
---------------------------(((..--.(((((...((((......((....)).....(((((((((((....))))))))))).....))))..)))))...)))...... ( -24.20)
>DroVir_CAF1 10998 91 - 1
---------------------------CGAAU--GUUAGGGCCCCAUUUCUAAAGUAAUCUAUAUCGAGUCUUUUUUCAAGAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGUUCCCU
---------------------------.((((--(((((((((.((.......((....)).....(((((((((((....)))))))))))....)).))).))))....))))))... ( -23.30)
>DroPse_CAF1 10418 118 - 1
CAUUGCAUCCUCCCCCCAUAGACCAUUCCCAC--UCUAGGGCCCCAUUUCUAAAGUAAUCUAUAUCGAGUCUUUUUUCAAGAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGUUCCCU
....(((.......(((.((((..........--))))))).........................(((((((((((....)))))))))))....)))((.((((....)).)).)).. ( -22.20)
>DroGri_CAF1 11714 93 - 1
---------------------------GCAAUUAAUUAGGGCCCCAUUUCUAAAGUAAUCUAUAUCGAGUCUUUUUUCAAGAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGUUCCCU
---------------------------(((((...((((((......)))))).............(((((((((((....)))))))))))..)))))((.((((....)).)).)).. ( -20.40)
>DroWil_CAF1 13415 100 - 1
-----------------CUAAACCGUUCGCUG---UUAGGGCCCCAUUUCUAAAGUAAUCUAUAUCGAGUCUUUUUUCAAGAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGCUCCCU
-----------------.......(..((((.---((((((((.((.......((....)).....(((((((((((....)))))))))))....)).))).)))))..))))..)... ( -25.00)
>DroAna_CAF1 11714 89 - 1
-----------------------------CAG--GCUAGGGCCCCGCUUCUAAAGUAAUCUAUAUCGAGUCUUUUUUCAAGAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGUUCCCU
-----------------------------...--(((.(((..((((......((....)).....(((((((((((....))))))))))).....))))..)))....)))....... ( -22.00)
>consensus
___________________________CGCAG__GUUAGGGCCCCAUUUCUAAAGUAAUCUAUAUCGAGUCUUUUUUCAAGAAAAAGGACUUCCAUUGCGGCACCUGAAAAGCGUUCCCU
...................................((((((((.((.......((....)).....(((((((((((....)))))))))))....)).))).)))))............ (-18.82 = -18.93 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:05 2006