Locus 1825

Sequence ID X_DroMel_CAF1
Location 5,045,374 – 5,045,511
Length 137
Max. P 0.976913
window2969 window2970 window2971 window2972

overview

Window 9

Location 5,045,374 – 5,045,482
Length 108
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 80.80
Mean single sequence MFE -14.37
Consensus MFE -12.40
Energy contribution -12.73
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.86
SVM decision value 1.08
SVM RNA-class probability 0.911829
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5045374 108 + 22224390
CAAAAAAAAAGAAGA------GCCAAAAGCGCAGAAGAAAAUUUCGGUCUUAUUGCCAGUGUAAAAUUGUAAUUUUUACACCUUCACACCGCCCAAUAAACAACAAAAAAAAAG
..........((((.------((.....))((((((((.........)))).))))..((((((((.......))))))))))))............................. ( -15.10)
>DroEre_CAF1 9388 94 + 1
CAA-----AAGAAGA------ACCAAAAACGUAGAAGGAAAUUUCGGUCUUAUUGCCAGUGUAA-AUUGUAAUUUUUACACCUUCACACCGCCCUAUAAACAAAAA--------
...-----.......------.........((.(((((.......(((......)))..(((((-(........)))))))))))))...................-------- ( -13.70)
>DroYak_CAF1 9645 101 + 1
AAA-----AAAAAAAAAAAAGAUCAAAAACGUAGAAGGAAAUUUCGGUCUUAUUGCCAGUGUAAAAUUGUAAUUUUUACACCUUCACACCGCCCAAUAAACAAAAC--------
...-----......................((.(((((.......(((......)))..(((((((.......))))))))))))))...................-------- ( -14.30)
>consensus
CAA_____AAGAAGA______ACCAAAAACGUAGAAGGAAAUUUCGGUCUUAUUGCCAGUGUAAAAUUGUAAUUUUUACACCUUCACACCGCCCAAUAAACAAAAA________
.................................((((........(((......))).((((((((.......))))))))))))............................. (-12.40 = -12.73 +   0.33)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,045,374 – 5,045,482
Length 108
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 80.80
Mean single sequence MFE -20.84
Consensus MFE -16.85
Energy contribution -17.85
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 0.81
SVM decision value 0.39
SVM RNA-class probability 0.717526
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5045374 108 - 22224390
CUUUUUUUUUGUUGUUUAUUGGGCGGUGUGAAGGUGUAAAAAUUACAAUUUUACACUGGCAAUAAGACCGAAAUUUUCUUCUGCGCUUUUGGC------UCUUCUUUUUUUUUG
......(((((...((((((.(.((((((((((.((((.....)))).)))))))))).)))))))..)))))...........((.....))------............... ( -21.60)
>DroEre_CAF1 9388 94 - 1
--------UUUUUGUUUAUAGGGCGGUGUGAAGGUGUAAAAAUUACAAU-UUACACUGGCAAUAAGACCGAAAUUUCCUUCUACGUUUUUGGU------UCUUCUU-----UUG
--------.............(.(((((((((..((((.....)))).)-)))))))).)...((((((((((.............)))))).------))))...-----... ( -21.12)
>DroYak_CAF1 9645 101 - 1
--------GUUUUGUUUAUUGGGCGGUGUGAAGGUGUAAAAAUUACAAUUUUACACUGGCAAUAAGACCGAAAUUUCCUUCUACGUUUUUGAUCUUUUUUUUUUUU-----UUU
--------((((((((((((.(.((((((((((.((((.....)))).)))))))))).)))))))..))))))................................-----... ( -19.80)
>consensus
________UUUUUGUUUAUUGGGCGGUGUGAAGGUGUAAAAAUUACAAUUUUACACUGGCAAUAAGACCGAAAUUUCCUUCUACGUUUUUGGU______UCUUCUU_____UUG
..............((((((.(.((((((((((.((((.....)))).)))))))))).))))))).((((((.............))))))...................... (-16.85 = -17.85 +   1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,045,408 – 5,045,511
Length 103
Sequences 3
Columns 103
Reading direction forward
Mean pairwise identity 87.67
Mean single sequence MFE -18.21
Consensus MFE -11.64
Energy contribution -12.30
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.69
Structure conservation index 0.64
SVM decision value 0.06
SVM RNA-class probability 0.565129
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5045408 103 + 22224390
AUUUCGGUCUUAUUGCCAGUGUAAAAUUGUAAUUUUUACACCUUCACACCGCCCAAUAAACAACAAAAAAAAAGGAAGAAAAAAAAGUGGCAUUUCCACUUUU
.(((((((......))).((((((((.......))))))))....................................)))).((((((((.....)))))))) ( -18.30)
>DroEre_CAF1 9417 91 + 1
AUUUCGGUCUUAUUGCCAGUGUAA-AUUGUAAUUUUUACACCUUCACACCGCCCUAUAAACAAAAA----------GGAA-AAAAAAUGGCAUUUCCACUUUU
.....((......(((((((((((-(........)))))))...........(((..........)----------))..-......)))))...))...... ( -15.90)
>DroYak_CAF1 9680 94 + 1
AUUUCGGUCUUAUUGCCAGUGUAAAAUUGUAAUUUUUACACCUUCACACCGCCCAAUAAACAAAAC--------GCGGAA-CAAAAAUGGCAUUUCCACUUUU
.....((......(((((((((((((.......)))))))).......((((..............--------))))..-......)))))...))...... ( -20.44)
>consensus
AUUUCGGUCUUAUUGCCAGUGUAAAAUUGUAAUUUUUACACCUUCACACCGCCCAAUAAACAAAAA________G_GGAA_AAAAAAUGGCAUUUCCACUUUU
.....((......(((((((((((((.......)))))))).......((..........................)).........)))))...))...... (-11.64 = -12.30 +   0.67)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,045,408 – 5,045,511
Length 103
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 87.67
Mean single sequence MFE -26.43
Consensus MFE -23.25
Energy contribution -23.37
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -3.07
Structure conservation index 0.88
SVM decision value 1.78
SVM RNA-class probability 0.976913
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5045408 103 - 22224390
AAAAGUGGAAAUGCCACUUUUUUUUCUUCCUUUUUUUUUGUUGUUUAUUGGGCGGUGUGAAGGUGUAAAAAUUACAAUUUUACACUGGCAAUAAGACCGAAAU
((((((((.....))))))))..............(((((...((((((.(.((((((((((.((((.....)))).)))))))))).)))))))..))))). ( -28.20)
>DroEre_CAF1 9417 91 - 1
AAAAGUGGAAAUGCCAUUUUUU-UUCC----------UUUUUGUUUAUAGGGCGGUGUGAAGGUGUAAAAAUUACAAU-UUACACUGGCAAUAAGACCGAAAU
((((((((.....)))))))).-....----------((((.((((....(.(((((((((..((((.....)))).)-)))))))).)....)))).)))). ( -23.50)
>DroYak_CAF1 9680 94 - 1
AAAAGUGGAAAUGCCAUUUUUG-UUCCGC--------GUUUUGUUUAUUGGGCGGUGUGAAGGUGUAAAAAUUACAAUUUUACACUGGCAAUAAGACCGAAAU
((((((((.....)))))))).-...((.--------((((((((.....(.((((((((((.((((.....)))).)))))))))).))))))))))).... ( -27.60)
>consensus
AAAAGUGGAAAUGCCAUUUUUU_UUCC_C________UUUUUGUUUAUUGGGCGGUGUGAAGGUGUAAAAAUUACAAUUUUACACUGGCAAUAAGACCGAAAU
((((((((.....)))))))).....................((((....(.((((((((((.((((.....)))).)))))))))).)....))))...... (-23.25 = -23.37 +   0.11)

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 10:19:40 2006