Locus 4414

Sequence ID 3L_DroMel_CAF1
Location 12,906,856 – 12,906,978
Length 122
Max. P 0.950664
window6840 window6841 window6842

overview

Window 0

Location 12,906,856 – 12,906,947
Length 91
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 85.42
Mean single sequence MFE -33.33
Consensus MFE -28.17
Energy contribution -27.98
Covariance contribution -0.19
Combinations/Pair 1.15
Mean z-score -2.78
Structure conservation index 0.85
SVM decision value 1.40
SVM RNA-class probability 0.950664
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12906856 91 + 23771897
-----CGACCU-----------UUCAACCCUCUGACUUG-AAGCCCAACGAUGUU--GAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCCAUUGUUGGGCGAA
-----......-----------(((((.........)))-))(((((((((((((--((((((((((((.((...)).))))))))))...)))).)))))))))))... ( -32.60)
>DroSec_CAF1 27648 91 + 1
-----CGACCU-----------UUCAACCCUCUGACUUG-AAGCCCAACGAUGUU--GAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCCAUUGUUGGGCAAA
-----......-----------(((((.........)))-))(((((((((((((--((((((((((((.((...)).))))))))))...)))).)))))))))))... ( -32.60)
>DroSim_CAF1 25437 91 + 1
-----CGACCU-----------UUCGACCCUCUGACUCG-AAGCCCAACGAUGUU--GAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCCAUUGUUGGGCGAA
-----......-----------(((((.........)))-))(((((((((((((--((((((((((((.((...)).))))))))))...)))).)))))))))))... ( -34.40)
>DroEre_CAF1 32859 94 + 1
---GACGACCU-----------UUCAACCCUCUGACUGCCAAGCCCAACGAUGUU--GAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCCAUUGUUGGGCGAA
---........-----------....................(((((((((((((--((((((((((((.((...)).))))))))))...)))).)))))))))))... ( -32.00)
>DroYak_CAF1 30232 91 + 1
-----CGACCU-----------UUCAACCCUCUGACUGG-AAGCCCAACGAUGUU--GAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCCAUUGUUGGGCGAA
-----...((.-----------.(((......)))..))-..(((((((((((((--((((((((((((.((...)).))))))))))...)))).)))))))))))... ( -35.60)
>DroAna_CAF1 54550 107 + 1
UCAGGCGACCCCGUCCUACGCCAUCGACC--CUGACAUA-GAGCUCAGCCCGGCUAGGAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCUUUUGUUGGCCCAA
..(((((....)).)))..((((.(((..--(((((...-.((((......))))...(((((((((((.((...)).))))))))))).)))))...))).)))).... ( -32.80)
>consensus
_____CGACCU___________UUCAACCCUCUGACUUG_AAGCCCAACGAUGUU__GAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCCAUUGUUGGGCGAA
..........................................(((((((((((((...(((((((((((.((...)).)))))))))))....))).))))))))))... (-28.17 = -27.98 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,906,879 – 12,906,978
Length 99
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 83.66
Mean single sequence MFE -41.17
Consensus MFE -31.27
Energy contribution -31.42
Covariance contribution 0.14
Combinations/Pair 1.13
Mean z-score -3.20
Structure conservation index 0.76
SVM decision value 1.07
SVM RNA-class probability 0.909561
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12906879 99 + 23771897
-AAGCCCAACGAUGUU--GAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCCAUUGUUGGGCGAAUCGCUGGAAAGGAGCAGCCGGA---------GGAGUUGGA
-..(((((((((((((--((((((((((((.((...)).))))))))))...)))).))))))))))).....((((........))))....---------......... ( -36.50)
>DroSec_CAF1 27671 108 + 1
-AAGCCCAACGAUGUU--GAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCCAUUGUUGGGCAAAAUGCUGGAAAGGAGCAGCCGGAGCAGCCGGUGGAGUUGGA
-..(((((((((((((--((((((((((((.((...)).))))))))))...)))).)))))))))))....((((.......))))(((((.....)))))......... ( -42.70)
>DroSim_CAF1 25460 108 + 1
-AAGCCCAACGAUGUU--GAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCCAUUGUUGGGCGAAAUGCUGGAAAGGAGCAGCCGGAGCAGCCGGUGGAGUUGGA
-..(((((((((((((--((((((((((((.((...)).))))))))))...)))).)))))))))))....((((.......))))(((((.....)))))......... ( -42.70)
>DroEre_CAF1 32884 109 + 1
CAAGCCCAACGAUGUU--GAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCCAUUGUUGGGCGAAAUGCUGGAAAGGAGCAGCCGGAGCAGUUGGAGCAGUUGGA
...(((((((((((((--((((((((((((.((...)).))))))))))...)))).)))))))))))....((((.......)))).((((.((.......))..)))). ( -38.10)
>DroYak_CAF1 30255 105 + 1
-AAGCCCAACGAUGUU--GAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCCAUUGUUGGGCGAACUGCUGGAAAGGAGCAGCCCGAGCAGUUGGAGCAG---GA
-..(((((((((((((--((((((((((((.((...)).))))))))))...)))).))))))))))).(((((((.(...((.....))).))))))).......---.. ( -42.20)
>DroAna_CAF1 54587 96 + 1
-GAGCUCAGCCCGGCUAGGAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCUUUUGUUGGCCCAAACGCCGGCGAGAAGGAGCUG-AGCUGC-------------
-.((((((((((((((...(((((((((((.((...)).)))))))))))))))...((((((((((......)))))))))).)).))))-))))..------------- ( -44.80)
>consensus
_AAGCCCAACGAUGUU__GAGUCGACAGUUUUCUAUGACAAUUGUUGGCUGGUCAGCCAUUGUUGGGCGAAAUGCUGGAAAGGAGCAGCCGGAGCAGC_GG_GGAGUUGGA
...(((((((((((((...(((((((((((.((...)).)))))))))))....))).)))))))))).....((((........))))...................... (-31.27 = -31.42 +   0.14)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,906,879 – 12,906,978
Length 99
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 83.66
Mean single sequence MFE -31.80
Consensus MFE -24.99
Energy contribution -25.85
Covariance contribution 0.86
Combinations/Pair 1.04
Mean z-score -3.13
Structure conservation index 0.79
SVM decision value 1.18
SVM RNA-class probability 0.927141
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12906879 99 - 23771897
UCCAACUCC---------UCCGGCUGCUCCUUUCCAGCGAUUCGCCCAACAAUGGCUGACCAGCCAACAAUUGUCAUAGAAAACUGUCGACUC--AACAUCGUUGGGCUU-
.........---------....((((........)))).....(((((((..(((((....)))))......(((((((....)))).)))..--......)))))))..- ( -29.70)
>DroSec_CAF1 27671 108 - 1
UCCAACUCCACCGGCUGCUCCGGCUGCUCCUUUCCAGCAUUUUGCCCAACAAUGGCUGACCAGCCAACAAUUGUCAUAGAAAACUGUCGACUC--AACAUCGUUGGGCUU-
..........((((.....)))).((((.......))))....(((((((..(((((....)))))......(((((((....)))).)))..--......)))))))..- ( -31.80)
>DroSim_CAF1 25460 108 - 1
UCCAACUCCACCGGCUGCUCCGGCUGCUCCUUUCCAGCAUUUCGCCCAACAAUGGCUGACCAGCCAACAAUUGUCAUAGAAAACUGUCGACUC--AACAUCGUUGGGCUU-
..........((((.....)))).((((.......))))....(((((((..(((((....)))))......(((((((....)))).)))..--......)))))))..- ( -32.10)
>DroEre_CAF1 32884 109 - 1
UCCAACUGCUCCAACUGCUCCGGCUGCUCCUUUCCAGCAUUUCGCCCAACAAUGGCUGACCAGCCAACAAUUGUCAUAGAAAACUGUCGACUC--AACAUCGUUGGGCUUG
.......((.......))....((((........)))).....(((((((..(((((....)))))......(((((((....)))).)))..--......)))))))... ( -30.40)
>DroYak_CAF1 30255 105 - 1
UC---CUGCUCCAACUGCUCGGGCUGCUCCUUUCCAGCAGUUCGCCCAACAAUGGCUGACCAGCCAACAAUUGUCAUAGAAAACUGUCGACUC--AACAUCGUUGGGCUU-
..---..((.......))..((((((((.......))))))))(((((((..(((((....)))))......(((((((....)))).)))..--......)))))))..- ( -36.40)
>DroAna_CAF1 54587 96 - 1
-------------GCAGCU-CAGCUCCUUCUCGCCGGCGUUUGGGCCAACAAAAGCUGACCAGCCAACAAUUGUCAUAGAAAACUGUCGACUCCUAGCCGGGCUGAGCUC-
-------------..((((-((((.........(((((....(((.........(((....)))........(((((((....)))).))))))..))))))))))))).- ( -30.40)
>consensus
UCCAACUCC_CC_GCUGCUCCGGCUGCUCCUUUCCAGCAUUUCGCCCAACAAUGGCUGACCAGCCAACAAUUGUCAUAGAAAACUGUCGACUC__AACAUCGUUGGGCUU_
......................((((........)))).....(((((((..(((((....)))))......(((((((....)))).)))..........)))))))... (-24.99 = -25.85 +   0.86)

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 11:22:01 2006