Locus 8124

Sequence ID X_DroMel_CAF1
Location 20,200,350 – 20,200,505
Length 155
Max. P 0.950101
window13347 window13348

overview

Window 7

Location 20,200,350 – 20,200,470
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.75
Mean single sequence MFE -41.48
Consensus MFE -30.02
Energy contribution -32.30
Covariance contribution 2.28
Combinations/Pair 1.24
Mean z-score -2.50
Structure conservation index 0.72
SVM decision value 1.40
SVM RNA-class probability 0.950101
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20200350 120 - 22224390
CCUGCGUGGCAUAGCAGCUAGCUUUUAGGCCUGUGCUCGCCAAUCGUUAUCGAAAGAUGGCAAUCGAGUAAGCGGGUAAAUUGAAGUUUAGCCGCAGGCGGGUAUUAGGUUUUCAGAUUA
...((.((((......))))))....(((((((((((((((....((((((....))))))..........((((.(((((....))))).)))).)))))))).)))))))........ ( -47.00)
>DroSec_CAF1 27129 120 - 1
CCUGCGUGGCAUAGCAGCUAGCUUUGAGGCCUGCGCUCGCCAAUCGUUAUCGAAAGAUGGCAAUCGAGUAAGCGGGUAAAUUGAAAUUUAGCCGCAGGCGGAUAUUAGGCUUUCAGAUUA
...((.((((......))))))(((((((((((...(((((....((((((....))))))..........((((.(((((....))))).)))).)))))....))))).))))))... ( -44.60)
>DroSim_CAF1 27050 120 - 1
CCUGCGUGGCAUAGCAGCUAGCUUUGAGGCCUGCGCUCGCCAAUCGUUAUCGAAAGAUGGCAAUCGAGUAAGCGGGUAAAUUGAAAUUUAGCCGCAGGCGGACAUUAGGCUUUCAGAUUA
...((.((((......))))))(((((((((((.(..((((....((((((....))))))..........((((.(((((....))))).)))).))))..)..))))).))))))... ( -45.70)
>DroEre_CAF1 17095 120 - 1
ACUGCGUGGUGUAGCAGCUAGCUUUGAGGUAUGUGCUCGCCAAUCGGUAUCGAAAGAUGGUAAUCGAGUAUGCGGCUAAAUUAAAAUGUAACAGCGGGCGGGCAUAAGAUGUUCGGGUUA
.((((........)))).(((((..((.((.((((((((((..((((((((....)))....)))))...(((.((...........))....)))))))))))))..)).))..))))) ( -36.50)
>DroYak_CAF1 18061 111 - 1
CCUGCGUGGCAUAGCAGCUAGCUUUCUGGCAAGUGCUCGCCAAUCGUUAUCGAAAGAUGCCAAUCGAGUAUGCGGGUAGAUUGAAAUUUAU---------GGUUUGGGGUUUCCAGAUUA
((((((((((..((((.((.(((....))).)))))).)))..(((.((((....)))).....)))..)))))))..............(---------(((((((.....)))))))) ( -33.60)
>consensus
CCUGCGUGGCAUAGCAGCUAGCUUUGAGGCCUGUGCUCGCCAAUCGUUAUCGAAAGAUGGCAAUCGAGUAAGCGGGUAAAUUGAAAUUUAGCCGCAGGCGGGUAUUAGGUUUUCAGAUUA
...((.((((......))))))((((((((((..(((((((....((((((....))))))..........((((.(((((....))))).)))).)))))))...)))).))))))... (-30.02 = -32.30 +   2.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,200,390 – 20,200,505
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.26
Mean single sequence MFE -34.02
Consensus MFE -26.26
Energy contribution -26.14
Covariance contribution -0.12
Combinations/Pair 1.17
Mean z-score -1.64
Structure conservation index 0.77
SVM decision value 0.39
SVM RNA-class probability 0.715130
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20200390 115 - 22224390
AGUGAAUUUAAUGUCAAAAAGGAAACCAUG-----AGUGUCCUGCGUGGCAUAGCAGCUAGCUUUUAGGCCUGUGCUCGCCAAUCGUUAUCGAAAGAUGGCAAUCGAGUAAGCGGGUAAA
..........((((((...((((.((....-----.)).))))...))))))(((.....))).....(((((((((((...((.((((((....)))))).)))))))..))))))... ( -34.90)
>DroSec_CAF1 27169 115 - 1
AGUGAAUGAAAUGUCAAAAAUGAAACCAUG-----CGUGUCCUGCGUGGCAUAGCAGCUAGCUUUGAGGCCUGCGCUCGCCAAUCGUUAUCGAAAGAUGGCAAUCGAGUAAGCGGGUAAA
.........................(((((-----((.....)))))))((.(((.....))).))..(((((((((((...((.((((((....)))))).)))))))..))))))... ( -34.70)
>DroSim_CAF1 27090 108 - 1
-------AAAAUGUCAAAAAUGAAACCAUG-----CGUGUCCUGCGUGGCAUAGCAGCUAGCUUUGAGGCCUGCGCUCGCCAAUCGUUAUCGAAAGAUGGCAAUCGAGUAAGCGGGUAAA
-------..................(((((-----((.....)))))))((.(((.....))).))..(((((((((((...((.((((((....)))))).)))))))..))))))... ( -34.70)
>DroEre_CAF1 17135 111 - 1
-------AAGGUGUUAAG--GAAAACCGUGGCUGUACUGUACUGCGUGGUGUAGCAGCUAGCUUUGAGGUAUGUGCUCGCCAAUCGGUAUCGAAAGAUGGUAAUCGAGUAUGCGGCUAAA
-------..(((......--....))).(((((((...(((((.(((((((.((((..((.(.....).))..)))))))))...(.((((....)))).)...)))))))))))))).. ( -32.20)
>DroYak_CAF1 18092 105 - 1
-------AUAGUGUUAAA--GUA-GCCAUG-----AGCGUCCUGCGUGGCAUAGCAGCUAGCUUUCUGGCAAGUGCUCGCCAAUCGUUAUCGAAAGAUGCCAAUCGAGUAUGCGGGUAGA
-------...........--...-((((.(-----(((...((((........))))...))))..))))...(((((((...(((.((((....)))).....)))....))))))).. ( -33.60)
>consensus
_______AAAAUGUCAAAAAGGAAACCAUG_____AGUGUCCUGCGUGGCAUAGCAGCUAGCUUUGAGGCCUGUGCUCGCCAAUCGUUAUCGAAAGAUGGCAAUCGAGUAAGCGGGUAAA
........................................(((((.((((..(((.((..(((....)))..))))).))))...((((((....))))))..........))))).... (-26.26 = -26.14 +  -0.12)

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 12:56:14 2006