Locus 1849

Sequence ID 2L_DroMel_CAF1
Location 5,087,908 – 5,088,106
Length 198
Max. P 0.779455
window2976 window2977 window2978

overview

Window 6

Location 5,087,908 – 5,088,026
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.70
Mean single sequence MFE -27.85
Consensus MFE -17.27
Energy contribution -18.90
Covariance contribution 1.63
Combinations/Pair 1.06
Mean z-score -2.72
Structure conservation index 0.62
SVM decision value 0.53
SVM RNA-class probability 0.769574
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5087908 118 + 22407834
AACUUAUUUGUGGUGGUGUGUCGAACCAGAGA--GAGAUGGAAACGCAAAAGUUGCUAAACAAAUGUGCGCAAAUAACAAAGUUAUUUGGCAACUAUUAACCCAAUAAUAUAAUUGGGUG
....(((((((((..((((((....(((....--....)))..)))))....)..))..)))))))(((.((((((((...))))))))))).......(((((((......))))))). ( -29.20)
>DroSec_CAF1 17317 113 + 1
AACUUAUUUGUGGUG-------GAACAAGAGAGCGAGAUGGAAACGCAAAAGUUUCUAAACAAAUGUGCGCAAAUAAUAAAGUUAUUUGGCAACUAUUUAGCCAAUAAUAUAAUUGGGUG
.(((((.(((((.((-------(......((.......(((((((......)))))))........(((.((((((((...))))))))))).))......)))....))))).))))). ( -25.00)
>DroSim_CAF1 19928 113 + 1
AACUUAUUUGUGGUG-------GAACAAGAGAGCGAGAUGGAAACGCAAAAGUUUCUAAACAAAUGUGCGCAAAUAAUAAAGUUAUUUGGCACCUAUUUAGCCAAUAAUAUAAUUGGGUG
.(((((.(((((.((-------(......((.......(((((((......))))))).......((((.((((((((...))))))))))))))......)))....))))).))))). ( -27.30)
>DroYak_CAF1 18838 111 + 1
AACUUAUUUGUGGUG---UGGGGAACAUGAGAGCA------AAACACAAAAGUUUCUCCACAAGUGUGCGCAAAUAAUAAAGUUAUUUGGCAACUAUUUACCCAAUAAUAUAAAUGAGUG
.(((((((((((...---((((.....((.(((..------((((......)))))))))..(((.(((.((((((((...)))))))))))))).....))))....))))))))))). ( -29.90)
>consensus
AACUUAUUUGUGGUG_______GAACAAGAGAGCGAGAUGGAAACGCAAAAGUUUCUAAACAAAUGUGCGCAAAUAAUAAAGUUAUUUGGCAACUAUUUACCCAAUAAUAUAAUUGGGUG
....(((((((.((..........))............(((((((......))))))).)))))))(((.((((((((...))))))))))).......(((((((......))))))). (-17.27 = -18.90 +   1.63)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,087,946 – 5,088,066
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.03
Mean single sequence MFE -25.18
Consensus MFE -17.99
Energy contribution -18.43
Covariance contribution 0.44
Combinations/Pair 1.10
Mean z-score -2.17
Structure conservation index 0.71
SVM decision value 0.55
SVM RNA-class probability 0.779455
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5087946 120 - 22407834
CUUCUUUUGGGGCAUACAAUUUGUCUGUUUUUCGCCGACCCACCCAAUUAUAUUAUUGGGUUAAUAGUUGCCAAAUAACUUUGUUAUUUGCGCACAUUUGUUUAGCAACUUUUGCGUUUC
.........(((((.......)))))......(((......(((((((......)))))))....((((((((((((((...)))))))).(((....)))...))))))...))).... ( -25.30)
>DroSec_CAF1 17350 120 - 1
CCUCUUUUGGGGCAUUCAAUUUGUCUGUUUUUCGCCGCUCCACCCAAUUAUAUUAUUGGCUAAAUAGUUGCCAAAUAACUUUAUUAUUUGCGCACAUUUGUUUAGAAACUUUUGCGUUUC
.........(((((.......))))).........(((.....(((((......)))))((((((((.((((((((((.....))))))).)))...))))))))........))).... ( -23.60)
>DroSim_CAF1 19961 120 - 1
CCUCUUUUGAGGCAUUCAAUUUGUCUGUUUUUCGCCGCCCCACCCAAUUAUAUUAUUGGCUAAAUAGGUGCCAAAUAACUUUAUUAUUUGCGCACAUUUGUUUAGAAACUUUUGCGUUUC
((((....)))).......................(((.....(((((......)))))(((((((.(((((((((((.....))))))).))))...)))))))........))).... ( -26.50)
>DroYak_CAF1 18870 119 - 1
CCACUUUAAGGGCAUUGAAUUUGUCUGUUUCUUCCCUCCUCACUCAUUUAUAUUAUUGGGUAAAUAGUUGCCAAAUAACUUUAUUAUUUGCGCACACUUGUGGAGAAACUUUUGUGUUU-
.(((.....(((((.......)))))((((((((.......(((((..........)))))....(((((((((((((.....))))))).))).)))...))))))))....)))...- ( -25.30)
>consensus
CCUCUUUUGGGGCAUUCAAUUUGUCUGUUUUUCGCCGCCCCACCCAAUUAUAUUAUUGGCUAAAUAGUUGCCAAAUAACUUUAUUAUUUGCGCACAUUUGUUUAGAAACUUUUGCGUUUC
.........(((((.......)))))((((((.........(((((((......))))))).....(.((((((((((.....))))))).))))........))))))........... (-17.99 = -18.43 +   0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,087,986 – 5,088,106
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.50
Mean single sequence MFE -22.84
Consensus MFE -16.02
Energy contribution -17.15
Covariance contribution 1.13
Combinations/Pair 1.22
Mean z-score -1.43
Structure conservation index 0.70
SVM decision value -0.05
SVM RNA-class probability 0.506588
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5087986 120 - 22407834
UACUUUAAAAUUAUUUUAAACAAAGAGCAGCGCUUAUAAGCUUCUUUUGGGGCAUACAAUUUGUCUGUUUUUCGCCGACCCACCCAAUUAUAUUAUUGGGUUAAUAGUUGCCAAAUAACU
..........((((((....(.(((((.(((........))).))))).)((((.((.....(((.((.....)).)))..(((((((......))))))).....)))))))))))).. ( -24.60)
>DroSec_CAF1 17390 120 - 1
UACUUUAAAAUUAUUUUAAACAAAGAGCAGCGCUUUUAAGCCUCUUUUGGGGCAUUCAAUUUGUCUGUUUUUCGCCGCUCCACCCAAUUAUAUUAUUGGCUAAAUAGUUGCCAAAUAACU
..........((((((..(((...((((.(((.......(((((....)))))....(((......)))...))).))))...(((((......))))).......)))...)))))).. ( -23.10)
>DroSim_CAF1 20001 120 - 1
UGCUUUAAAAUUAUUUUAAACAAAGAGCAGCGCUUUUAAGCCUCUUUUGAGGCAUUCAAUUUGUCUGUUUUUCGCCGCCCCACCCAAUUAUAUUAUUGGCUAAAUAGGUGCCAAAUAACU
..........((((((......((((((((((..((.(((((((....))))).)).))..)).))))))))((((.......(((((......))))).......))))..)))))).. ( -25.04)
>DroYak_CAF1 18909 120 - 1
UUCCUUUAAAUUAUUGUAAGCAAAGAGCUACAUUUUUAAGCCACUUUAAGGGCAUUGAAUUUGUCUGUUUCUUCCCUCCUCACUCAUUUAUAUUAUUGGGUAAAUAGUUGCCAAAUAACU
......(((((.(.((..((..((((((.(((..((((((((........))).)))))..)))..).)))))..))...)).).)))))..(((((.(((((....))))).))))).. ( -18.60)
>consensus
UACUUUAAAAUUAUUUUAAACAAAGAGCAGCGCUUUUAAGCCUCUUUUGGGGCAUUCAAUUUGUCUGUUUUUCGCCGCCCCACCCAAUUAUAUUAUUGGCUAAAUAGUUGCCAAAUAACU
........................(.(((((........(((((....)))))............................(((((((......))))))).....))))))........ (-16.02 = -17.15 +   1.13)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:53 2006