Locus 3982

Sequence ID 3R_DroMel_CAF1
Location 10,803,752 – 10,803,867
Length 115
Max. P 0.998870
window6384 window6385

overview

Window 4

Location 10,803,752 – 10,803,867
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 90.67
Mean single sequence MFE -34.86
Consensus MFE -30.51
Energy contribution -30.71
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.88
SVM decision value 0.80
SVM RNA-class probability 0.853696
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10803752 115 + 27905053
CAAUGCUAAUGCCUUUUGCAAGGCACUUAAAUACUUCGAUGGAGCGGCGAUUAGAGGUCCUGGCCCAUUUGCCAUUUUCCAUUCGCCAUAGCAAAUGGCCGAGAAGCGCCGCAGA
...(((...((((((....))))))........(((((((((((.(((((...(.(((....))))..)))))...))))))).(((((.....)))))...))))....))).. ( -34.90)
>DroSec_CAF1 73438 115 + 1
CAAUGCUAAUGCCUUUUGCAAGGCACUUAAAUACUUCGAUGGAGCGGCGAUUAGAGGUCCUGGCACAUUUGCCGUUUUCCAUUUGCCAUAGCAAAUGGCCGAGAAGCGCCGCAGA
.........((((((....))))))..................((((((......((....((((....)))).....((((((((....))))))))))......))))))... ( -37.20)
>DroSim_CAF1 77688 115 + 1
CAAUGCUAAUGCCUUUUGCAAGGCACUUAAAUACUUCGAUGGAGCGGCGAUUAGAGGUCCUGGAACAUUUGCCGUUUUCCAUUUGCCAUAGCAAAUGGCCGAGAAGCGCCGCAGA
...(((...((((((....))))))........((((..(((((((((((((((.....)))).....))))))))..((((((((....))))))))))).))))....))).. ( -34.60)
>DroEre_CAF1 75582 101 + 1
CAAUGCUAAUGCCUUUUGCAAGGCACUUAAAUACUUCGAUGGAGCGGCGAUUAGAGGUCCUGGCACAUUUGC--------------CAUUGCAAAUGGCCGAGAGGCGCCGCAGA
...(((...((((((....))))))...............(((.(..(.....).).))).(((.(((((((--------------....)))))))(((....))))))))).. ( -33.60)
>DroYak_CAF1 77538 101 + 1
CAAUGCUAAUGCCUUUUGCAAGGCACUUAAAUACUUCGAUGGAGCGGCGAUUAGAGGUCCUGGCACAUUUGC--------------CAUUGCAAAUGGCCGAGAAGCGCCGCAGA
.........((((((....))))))..................((((((........((.((((.(((((((--------------....))))))))))).))..))))))... ( -34.00)
>consensus
CAAUGCUAAUGCCUUUUGCAAGGCACUUAAAUACUUCGAUGGAGCGGCGAUUAGAGGUCCUGGCACAUUUGCC_UUUUCCAUU_GCCAUAGCAAAUGGCCGAGAAGCGCCGCAGA
.........((((((....))))))..................((((((........((.((((.(((((((..................))))))))))).))..))))))... (-30.51 = -30.71 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,803,752 – 10,803,867
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 90.67
Mean single sequence MFE -37.58
Consensus MFE -32.97
Energy contribution -33.17
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.45
Structure conservation index 0.88
SVM decision value 3.26
SVM RNA-class probability 0.998870
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10803752 115 - 27905053
UCUGCGGCGCUUCUCGGCCAUUUGCUAUGGCGAAUGGAAAAUGGCAAAUGGGCCAGGACCUCUAAUCGCCGCUCCAUCGAAGUAUUUAAGUGCCUUGCAAAAGGCAUUAGCAUUG
...((((((..((..(((((((((((((..(.....)...))))))))).))))..))........))))))................((((((((....))))))))....... ( -39.60)
>DroSec_CAF1 73438 115 - 1
UCUGCGGCGCUUCUCGGCCAUUUGCUAUGGCAAAUGGAAAACGGCAAAUGUGCCAGGACCUCUAAUCGCCGCUCCAUCGAAGUAUUUAAGUGCCUUGCAAAAGGCAUUAGCAUUG
...((((((......((((((((((....)))))))).....((((....))))....))......))))))................((((((((....))))))))....... ( -39.90)
>DroSim_CAF1 77688 115 - 1
UCUGCGGCGCUUCUCGGCCAUUUGCUAUGGCAAAUGGAAAACGGCAAAUGUUCCAGGACCUCUAAUCGCCGCUCCAUCGAAGUAUUUAAGUGCCUUGCAAAAGGCAUUAGCAUUG
...((((((((......((((((((....)))))))).....)))....(((....)))........)))))................((((((((....))))))))....... ( -36.40)
>DroEre_CAF1 75582 101 - 1
UCUGCGGCGCCUCUCGGCCAUUUGCAAUG--------------GCAAAUGUGCCAGGACCUCUAAUCGCCGCUCCAUCGAAGUAUUUAAGUGCCUUGCAAAAGGCAUUAGCAUUG
...((((((..((..((((((((((....--------------))))))).)))..))........))))))................((((((((....))))))))....... ( -36.00)
>DroYak_CAF1 77538 101 - 1
UCUGCGGCGCUUCUCGGCCAUUUGCAAUG--------------GCAAAUGUGCCAGGACCUCUAAUCGCCGCUCCAUCGAAGUAUUUAAGUGCCUUGCAAAAGGCAUUAGCAUUG
...((((((..((..((((((((((....--------------))))))).)))..))........))))))................((((((((....))))))))....... ( -36.00)
>consensus
UCUGCGGCGCUUCUCGGCCAUUUGCUAUGGC_AAUGGAAAA_GGCAAAUGUGCCAGGACCUCUAAUCGCCGCUCCAUCGAAGUAUUUAAGUGCCUUGCAAAAGGCAUUAGCAUUG
...((((((..((..((((((((((..................))))))).)))..))........))))))................((((((((....))))))))....... (-32.97 = -33.17 +   0.20)

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 11:15:08 2006