Locus 6453

Sequence ID 3R_DroMel_CAF1
Location 16,903,048 – 16,903,142
Length 94
Max. P 0.968970
window10512 window10513

overview

Window 2

Location 16,903,048 – 16,903,142
Length 94
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 78.29
Mean single sequence MFE -28.18
Consensus MFE -18.36
Energy contribution -19.03
Covariance contribution 0.67
Combinations/Pair 1.10
Mean z-score -1.54
Structure conservation index 0.65
SVM decision value 0.53
SVM RNA-class probability 0.772956
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16903048 94 + 27905053
UGUAGAAGCUGGCCGCCGGAUAGGCAUUGCAGUAGAGGGCGGCUGCAGCGGAGGCAGGAUUGGGGAAUCCUAUGGAUUAAAAAGGAAGA--CAGUU
......(((((((((((.....))).(((((((........)))))))....)))((((((....))))))..................--))))) ( -28.80)
>DroSec_CAF1 3739 94 + 1
UGUAGAAGCUGGCCGCCGGAUAGGCAUUGCAGUAGAGGGCGGCUGCAGCGGAGGCAGGAUUGGGGAAUCCUACGGGUUAUAAAUGAGGA--CAGGU
.....((.(((((((((.....))).(((((((........)))))))....)))((((((....)))))).))).))...........--..... ( -27.70)
>DroSim_CAF1 3744 94 + 1
UGUAGAAGCUGGCCGCCGGAUAGGCAUUGCAGUAGAGGGCGGCUGCAGCGGAGGCAGGAUUGGGGAAUCCUACGGGUAAUAAAUGAGGA--CAGGU
........(((((((((.....))).(((((((........)))))))....)))((((((....))))))..................--))).. ( -27.40)
>DroEre_CAF1 3982 94 + 1
UGUAGAAGCUGGCCGCCGGAUAGGCGUUGCAGUAGAGAGCGGCUGCAGCGGAGGCCGGGUUGGGGAAUCCUACGGGGCAUAAAGGACGA--CACAU
(((.....(((((((((.....)))((((((((........))))))))...))))))((((.....(((....))).........)))--)))). ( -35.84)
>DroWil_CAF1 1243 90 + 1
UGUAGAAACUAGCUGCCGGAUAGGCAUUGCAAUAGAGGGCAGCGGCUGCAGUGGCAGGAUUGGUGAAUCCUGAAAAAGA------ACAAACCACAA
(((((......((((((......((...)).......))))))..)))))(((((((((((....))))))).......------.....)))).. ( -27.12)
>DroAna_CAF1 6051 81 + 1
UGUAGAAGCUGGCCGCCGGAUAGGCGUUGCAAUAGAGAGCCGCGGCAGCAGUAGCAGGAUUGGGAAAGCCUGAAGAGAA-------AG--------
.......((((.(((((.....)))((.((........)).)))))))).....((((.((....)).)))).......-------..-------- ( -22.20)
>consensus
UGUAGAAGCUGGCCGCCGGAUAGGCAUUGCAGUAGAGGGCGGCUGCAGCGGAGGCAGGAUUGGGGAAUCCUACGGAUAAUAAA_GAAGA__CAGAU
.((....((((((((((.....)))...((........)))))..))))....))((((((....))))))......................... (-18.36 = -19.03 +   0.67)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,903,048 – 16,903,142
Length 94
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 78.29
Mean single sequence MFE -22.78
Consensus MFE -17.83
Energy contribution -17.72
Covariance contribution -0.11
Combinations/Pair 1.26
Mean z-score -2.31
Structure conservation index 0.78
SVM decision value 1.63
SVM RNA-class probability 0.968970
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16903048 94 - 27905053
AACUG--UCUUCCUUUUUAAUCCAUAGGAUUCCCCAAUCCUGCCUCCGCUGCAGCCGCCCUCUACUGCAAUGCCUAUCCGGCGGCCAGCUUCUACA
.....--.................(((((((....))))))).....((((..((((((.......((...))......))))))))))....... ( -22.12)
>DroSec_CAF1 3739 94 - 1
ACCUG--UCCUCAUUUAUAACCCGUAGGAUUCCCCAAUCCUGCCUCCGCUGCAGCCGCCCUCUACUGCAAUGCCUAUCCGGCGGCCAGCUUCUACA
.....--................((((((((....))))))))....((((..((((((.......((...))......))))))))))....... ( -25.42)
>DroSim_CAF1 3744 94 - 1
ACCUG--UCCUCAUUUAUUACCCGUAGGAUUCCCCAAUCCUGCCUCCGCUGCAGCCGCCCUCUACUGCAAUGCCUAUCCGGCGGCCAGCUUCUACA
.....--................((((((((....))))))))....((((..((((((.......((...))......))))))))))....... ( -25.42)
>DroEre_CAF1 3982 94 - 1
AUGUG--UCGUCCUUUAUGCCCCGUAGGAUUCCCCAACCCGGCCUCCGCUGCAGCCGCUCUCUACUGCAACGCCUAUCCGGCGGCCAGCUUCUACA
.((((--...........(((..((.((.....)).))..)))....((((..(((((........))...(((.....))))))))))...)))) ( -23.50)
>DroWil_CAF1 1243 90 - 1
UUGUGGUUUGU------UCUUUUUCAGGAUUCACCAAUCCUGCCACUGCAGCCGCUGCCCUCUAUUGCAAUGCCUAUCCGGCAGCUAGUUUCUACA
....((((.((------.......(((((((....))))))).....))))))((((((.......((...))......))))))........... ( -21.82)
>DroAna_CAF1 6051 81 - 1
--------CU-------UUCUCUUCAGGCUUUCCCAAUCCUGCUACUGCUGCCGCGGCUCUCUAUUGCAACGCCUAUCCGGCGGCCAGCUUCUACA
--------..-------.......((((.((....)).)))).....(((((((..((........))..)(((.....))))).))))....... ( -18.40)
>consensus
ACCUG__UCCUC_UUUAUAACCCGUAGGAUUCCCCAAUCCUGCCUCCGCUGCAGCCGCCCUCUACUGCAAUGCCUAUCCGGCGGCCAGCUUCUACA
........................(((((((....))))))).....((((..((((((.......((...))......))))))))))....... (-17.83 = -17.72 +  -0.11)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:52 2006