Locus 4027

Sequence ID 3R_DroMel_CAF1
Location 11,001,859 – 11,002,029
Length 170
Max. P 0.945673
window6448 window6449

overview

Window 8

Location 11,001,859 – 11,001,956
Length 97
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 78.49
Mean single sequence MFE -20.75
Consensus MFE -16.16
Energy contribution -16.00
Covariance contribution -0.17
Combinations/Pair 1.20
Mean z-score -1.95
Structure conservation index 0.78
SVM decision value 1.36
SVM RNA-class probability 0.945673
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11001859 97 - 27905053
UGCCCCUGGAGUACGAGCCAGAGGACAAGCUGCUGGCUGAGCUCAACAAGGGUAAGGAUAUCAAAGACAUUUUCUAAAUCCAA-------UGCCAGAC---A---CAAAA
(((((.((((((.(.((((((((......)).))))))).))))..)).))))).((((.....(((.....)))..))))..-------........---.---..... ( -25.20)
>DroPse_CAF1 78851 106 - 1
UGCCUUUGGAGUAUGAGCCAGAGGACAAGCUGCUGGCGGAGCUCAACAAGGGUAAGGACAAAAAAGACAUUUACUAAAAUCAAAAAACAAAUCCAAAC-CAA---AAAAA
((((((((((((....(((((((......)).)))))...))))..)))))))).(((..........((((....))))...........)))....-...---..... ( -22.50)
>DroGri_CAF1 77421 91 - 1
UGCCUUUGGAAUACGAGCCAGAGGAUAAGCUGUUGACAGAACUCAACAAGGGUAAGGAUAUUAAAGACAUUUUCUAAAUACG----------UCCAAAAAA---------
..(((((((........)))))))......((((((......)))))).......((((.....(((.....)))......)----------)))......--------- ( -18.20)
>DroWil_CAF1 72406 104 - 1
UGCCUUUGGAAUACGAGCCAGAGGACAAGUUGCUGGCACAACUCAACAAGGGUAAGGAUAUCAAAGACAUUUUCUAAACUCAAAAA--A-AACCAAAA---AAAAAAAAA
(((((((((........))))))).))(((((......)))))......((((..(((..............)))..)))).....--.-........---......... ( -16.94)
>DroMoj_CAF1 86362 97 - 1
UGCCUUUGGAAUACGAGCCAGAGGAUAAGCUGUUGGCUGAACUCAACAAGGGUAAGGAUAUCAAAGACAUUUUCUAAAUACG----------UCAAAAAAAA---AAAAA
((((((((.......((((((.((.....)).))))))........))))))))...........(((.............)----------))........---..... ( -18.58)
>DroPer_CAF1 76648 105 - 1
UGCCUUUGGAGUAUGAGCCAGAGGACAAGCUGCUGGCGGAGCUCAACAAGGGUAAGGACAAAAAAGACAUUUACUAAAAUCAAA-AACAAAUCCAAAC-CAA---AAAAA
((((((((((((....(((((((......)).)))))...))))..)))))))).(((..........((((....))))....-......)))....-...---..... ( -23.05)
>consensus
UGCCUUUGGAAUACGAGCCAGAGGACAAGCUGCUGGCAGAACUCAACAAGGGUAAGGAUAUCAAAGACAUUUUCUAAAUUCAA_______A_CCAAAA__AA___AAAAA
((((((((........(((((.((.....)).))))).........))))))))........................................................ (-16.16 = -16.00 +  -0.17)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,001,916 – 11,002,029
Length 113
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 81.73
Mean single sequence MFE -32.73
Consensus MFE -23.58
Energy contribution -24.33
Covariance contribution 0.75
Combinations/Pair 1.17
Mean z-score -1.39
Structure conservation index 0.72
SVM decision value 0.11
SVM RNA-class probability 0.587120
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11001916 113 - 27905053
UAUUAUC-----CACUUAGGUACCCAUCUCGCUAUGGUCUCUACUUGAGGGACAAGCCACUCACGCCCAACUCGCUGGUGCCCCUGGAGUACGAGCCAGAGGACAAGCUGCUGGCUGA
.....((-----(.((((((((.((((......))))....)))))))))))..(((((..((.((....((((((.(((((....).)))).)))..))).....)))).))))).. ( -34.30)
>DroVir_CAF1 97953 118 - 1
UAUUGUUUGUGCCUUUCAGAUAUCCAUCUCGCUAUGGUCUCUACUUGAGAGACAAGCCACUCACACCAAACUCUUUGGUGCCUUUGGAAUACGAGCCAGAGGAUAAGCUGUUGACUGA
................(((.(((((.(((.(((.((((((((.....))))))...(((....((((((.....))))))....)))....))))).))))))))..)))........ ( -30.80)
>DroGri_CAF1 77472 118 - 1
UAUUAUUUAUGCGUUGCAGAUAUCCAUCUCGCUAUGGUCUCUACUUGAGAGACAAGCCACUCACACCAAACUCUUUGGUGCCUUUGGAAUACGAGCCAGAGGAUAAGCUGUUGACAGA
............(((((((.(((((.(((.(((.((((((((.....))))))...(((....((((((.....))))))....)))....))))).))))))))..))).))))... ( -34.00)
>DroWil_CAF1 72470 105 - 1
-------------UUAUAGAUACCCAUCUCGCUAUGGUCUCUACUUGAGAGACAAGCCACUCACACCAAACUCCUUGGUGCCUUUGGAAUACGAGCCAGAGGACAAGUUGCUGGCACA
-------------....((((....)))).(((...((((((.....)))))).(((.(((..((((((.....))))))(((((((........)))))))...))).))))))... ( -31.90)
>DroMoj_CAF1 86419 107 - 1
-----------AUUUUCAGAUACCCAUCUCGCUAUGGUCUCUAUUUGAGAGACAAGCCACUCACACCAAACUCUUUGGUGCCUUUGGAAUACGAGCCAGAGGAUAAGCUGUUGGCUGA
-----------.((((((((((.((((......))))....))))))))))...(((((....((((((.....))))))(((((((........))))))).........))))).. ( -31.90)
>DroAna_CAF1 87345 107 - 1
------C-----UGGUUAGGUACCCAUCUCGCUAUGGUCUGUACUUGAAGGACAAGCCACUCACCCCCAACGCUCUGGUGCCCCUGGAGUACGAGCCAGAGGACAAGCUUCUGGCGGA
------.-----((((.((((....)))).))))(((..(((.((....)))))..))).......((...((((..(.....)..))))....((((((((.....)))))))))). ( -33.50)
>consensus
____________CUUUCAGAUACCCAUCUCGCUAUGGUCUCUACUUGAGAGACAAGCCACUCACACCAAACUCUUUGGUGCCUUUGGAAUACGAGCCAGAGGACAAGCUGCUGGCUGA
.................((((....)))).((((..((((((.....)))))).(((......((((((.....))))))(((((((........)))))))....)))..))))... (-23.58 = -24.33 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:09 2006