Locus 1353

Sequence ID 3R_DroMel_CAF1
Location 3,996,103 – 3,996,223
Length 120
Max. P 0.930393
window2221 window2222

overview

Window 1

Location 3,996,103 – 3,996,223
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.39
Mean single sequence MFE -26.91
Consensus MFE -25.92
Energy contribution -25.73
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -1.73
Structure conservation index 0.96
SVM decision value 1.21
SVM RNA-class probability 0.930393
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3996103 120 + 27905053
CUCUCUUUUGGCCCGUUCUCCUAUCUCUCUCUCUCUCUCUUGGACAUUUCUAUGGCGUUUUAAAAGCGUUUGACAGCGCUCAACGCUCUCAGCGCCUGUCCAUCUAAGCCAGAUCCAAAA
......((((((..(....)....................((((((.......((((((.....((((((.((......))))))))...)))))))))))).....))))))....... ( -25.71)
>DroSec_CAF1 1858 120 + 1
CUCUCUUUUGGCCCGUUCUCCUCUCUCACUCCCUCUCUCUUGGACAUUUCUAUGGCGUUUUAAAAGCGUUUGACAGCGCUCAACGCUCUCAGCGCCUGUCCAUCUAAGCCAGAUCCGAAA
.((...((((((..((...........))...........((((((.......((((((.....((((((.((......))))))))...)))))))))))).....))))))...)).. ( -26.41)
>DroSim_CAF1 1866 120 + 1
CUCUCUUUUGGCCCGUUCUCCUCUCGCACUCCCUCUCUCUUGGACAUUUCUAUGGCGUUUUAAAAGCGUUUGACAGCGCUCAACGCUCUCAGCGCCUGUCCAUCUAAGCCAGAUCCGAAA
.((...((((((.((.........))..............((((((.......((((((.....((((((.((......))))))))...)))))))))))).....))))))...)).. ( -27.41)
>DroYak_CAF1 1332 108 + 1
CUCUCUUUUGGCCCGCUCGCC------------UCUCUCUUGGACAUUUCUGUGGCGUUUUAAAAGCGUUUGACAGCGCUCAACGCUCUCAGCGCCUGUCCAUCUAAGCCAGGUUCGAAA
......((((..((....((.------------.......((((((...(((.((((((.....(((((......))))).))))))..)))....)))))).....))..))..)))). ( -28.12)
>consensus
CUCUCUUUUGGCCCGUUCUCCUCUCUCACUCCCUCUCUCUUGGACAUUUCUAUGGCGUUUUAAAAGCGUUUGACAGCGCUCAACGCUCUCAGCGCCUGUCCAUCUAAGCCAGAUCCGAAA
......((((((..(....)....................((((((.......((((((.....((((((.((......))))))))...)))))))))))).....))))))....... (-25.92 = -25.73 +  -0.19)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 3,996,103 – 3,996,223
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.39
Mean single sequence MFE -32.85
Consensus MFE -31.15
Energy contribution -30.96
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -1.30
Structure conservation index 0.95
SVM decision value 0.14
SVM RNA-class probability 0.602850
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3996103 120 - 27905053
UUUUGGAUCUGGCUUAGAUGGACAGGCGCUGAGAGCGUUGAGCGCUGUCAAACGCUUUUAAAACGCCAUAGAAAUGUCCAAGAGAGAGAGAGAGAGAUAGGAGAACGGGCCAAAAGAGAG
((((((.(((..(((...((((((((((.((((((((((((......)).))))))))))...)))).......))))))...)))..)))........(.....)...))))))..... ( -32.21)
>DroSec_CAF1 1858 120 - 1
UUUCGGAUCUGGCUUAGAUGGACAGGCGCUGAGAGCGUUGAGCGCUGUCAAACGCUUUUAAAACGCCAUAGAAAUGUCCAAGAGAGAGGGAGUGAGAGAGGAGAACGGGCCAAAAGAGAG
(((((..(((..(((...((((((((((.((((((((((((......)).))))))))))...)))).......))))))...)))..))).)))))..((........))......... ( -32.41)
>DroSim_CAF1 1866 120 - 1
UUUCGGAUCUGGCUUAGAUGGACAGGCGCUGAGAGCGUUGAGCGCUGUCAAACGCUUUUAAAACGCCAUAGAAAUGUCCAAGAGAGAGGGAGUGCGAGAGGAGAACGGGCCAAAAGAGAG
(((((.((((..(((...((((((((((.((((((((((((......)).))))))))))...)))).......))))))...)))..))).).)))))((........))......... ( -34.01)
>DroYak_CAF1 1332 108 - 1
UUUCGAACCUGGCUUAGAUGGACAGGCGCUGAGAGCGUUGAGCGCUGUCAAACGCUUUUAAAACGCCACAGAAAUGUCCAAGAGAGA------------GGCGAGCGGGCCAAAAGAGAG
((((.....((((((.....(((((.((((.((....)).)))))))))...(((((((........(((....))).......)))------------))))...))))))...)))). ( -32.76)
>consensus
UUUCGGAUCUGGCUUAGAUGGACAGGCGCUGAGAGCGUUGAGCGCUGUCAAACGCUUUUAAAACGCCAUAGAAAUGUCCAAGAGAGAGGGAGUGAGAGAGGAGAACGGGCCAAAAGAGAG
((((.....((((((...((((((((((.((((((((((((......)).))))))))))...)))).......))))))...................(.....)))))))...)))). (-31.15 = -30.96 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:43 2006