Locus 2299

Sequence ID X_DroMel_CAF1
Location 6,228,519 – 6,228,694
Length 175
Max. P 0.988436
window3722 window3723 window3724 window3725 window3726

overview

Window 2

Location 6,228,519 – 6,228,616
Length 97
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 95.88
Mean single sequence MFE -28.53
Consensus MFE -26.17
Energy contribution -26.40
Covariance contribution 0.23
Combinations/Pair 1.10
Mean z-score -1.88
Structure conservation index 0.92
SVM decision value 0.35
SVM RNA-class probability 0.698262
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6228519 97 + 22224390
CGCGCAUAGUAAAUUGAAUUUUGUUGCCUUCUGCGGCGGCCAACAUCUCCUCCACUUUUGCCACCCACUUGUUUUGGUUUCUGUGGAGGCGACUCCA
......................((((((......)))))).....((.(((((((....((((...........))))....))))))).))..... ( -25.90)
>DroSec_CAF1 2911 97 + 1
CGCGCAUAGUAAAUUGAAUUUUUUUGCCUUCUGCGGCGGCCAACAUCUCCUCUGCUUUUGCCACCAACUUGUUUUGGUUUCUGUGGAGGAGACUCCA
((((((..(((((.........)))))....))).))).......(((((((..(....((((...........))))....)..)))))))..... ( -26.80)
>DroSim_CAF1 4975 97 + 1
CGCGCAUAGUAAAUUGAAUUUUGUUGCCUUCUGCGGCGGCCAACAUCUCCUCCGCUUUUGCCACCCACUUGGUUUGGUUUCUGUGGAGGAGACUCCA
......................((((((......)))))).....((((((((((....((((.((....))..))))....))))))))))..... ( -32.90)
>consensus
CGCGCAUAGUAAAUUGAAUUUUGUUGCCUUCUGCGGCGGCCAACAUCUCCUCCGCUUUUGCCACCCACUUGUUUUGGUUUCUGUGGAGGAGACUCCA
......................((((((......)))))).....((((((((((....((((...........))))....))))))))))..... (-26.17 = -26.40 +   0.23)

alignment

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secondary structure

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Window 3

Location 6,228,559 – 6,228,656
Length 97
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 95.88
Mean single sequence MFE -25.07
Consensus MFE -24.39
Energy contribution -24.07
Covariance contribution -0.33
Combinations/Pair 1.12
Mean z-score -4.28
Structure conservation index 0.97
SVM decision value 2.12
SVM RNA-class probability 0.988436
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6228559 97 + 22224390
CAACAUCUCCUCCACUUUUGCCACCCACUUGUUUUGGUUUCUGUGGAGGCGACUCCACUUUAUCACAUUUGUAUAAAUAUAUUACCCAAGUGUACUU
.....((.(((((((....((((...........))))....))))))).))............(((((((..(((.....)))..))))))).... ( -24.10)
>DroSec_CAF1 2951 97 + 1
CAACAUCUCCUCUGCUUUUGCCACCAACUUGUUUUGGUUUCUGUGGAGGAGACUCCACUUUAUCACAUUUGUAUAAAUAUAUUACCUAAGUGUACUU
.....(((((((..(....((((...........))))....)..)))))))............(((((((..(((.....)))..))))))).... ( -22.70)
>DroSim_CAF1 5015 97 + 1
CAACAUCUCCUCCGCUUUUGCCACCCACUUGGUUUGGUUUCUGUGGAGGAGACUCCACUUUAUCACAUUUGUAUAAAUAUAUUACCUAAGUGUACUU
.....((((((((((....((((.((....))..))))....))))))))))............(((((((..(((.....)))..))))))).... ( -28.40)
>consensus
CAACAUCUCCUCCGCUUUUGCCACCCACUUGUUUUGGUUUCUGUGGAGGAGACUCCACUUUAUCACAUUUGUAUAAAUAUAUUACCUAAGUGUACUU
.....((((((((((....((((...........))))....))))))))))............(((((((..(((.....)))..))))))).... (-24.39 = -24.07 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,228,559 – 6,228,656
Length 97
Sequences 3
Columns 97
Reading direction reverse
Mean pairwise identity 95.88
Mean single sequence MFE -24.37
Consensus MFE -20.19
Energy contribution -20.63
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -2.57
Structure conservation index 0.83
SVM decision value 0.44
SVM RNA-class probability 0.739156
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6228559 97 - 22224390
AAGUACACUUGGGUAAUAUAUUUAUACAAAUGUGAUAAAGUGGAGUCGCCUCCACAGAAACCAAAACAAGUGGGUGGCAAAAGUGGAGGAGAUGUUG
.....(((((......(((((((....)))))))...)))))..(((.(((((((.....(((...(....)..))).....))))))).))).... ( -24.00)
>DroSec_CAF1 2951 97 - 1
AAGUACACUUAGGUAAUAUAUUUAUACAAAUGUGAUAAAGUGGAGUCUCCUCCACAGAAACCAAAACAAGUUGGUGGCAAAAGCAGAGGAGAUGUUG
.....(((((...((.(((((((....))))))).)))))))..((((((((.......(((((......))))).((....)).)))))))).... ( -23.40)
>DroSim_CAF1 5015 97 - 1
AAGUACACUUAGGUAAUAUAUUUAUACAAAUGUGAUAAAGUGGAGUCUCCUCCACAGAAACCAAACCAAGUGGGUGGCAAAAGCGGAGGAGAUGUUG
.....(((((...((.(((((((....))))))).)))))))..(((((((((.(.....(((..((....)).))).....).))))))))).... ( -25.70)
>consensus
AAGUACACUUAGGUAAUAUAUUUAUACAAAUGUGAUAAAGUGGAGUCUCCUCCACAGAAACCAAAACAAGUGGGUGGCAAAAGCGGAGGAGAUGUUG
.....(((((...((.(((((((....))))))).)))))))..(((((((((......(((..........))).((....))))))))))).... (-20.19 = -20.63 +   0.45)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,228,576 – 6,228,694
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.08
Mean single sequence MFE -29.10
Consensus MFE -21.97
Energy contribution -22.59
Covariance contribution 0.62
Combinations/Pair 1.10
Mean z-score -2.28
Structure conservation index 0.75
SVM decision value 0.92
SVM RNA-class probability 0.882673
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6228576 118 + 22224390
UUGCCACCCACUUGUUUUGGUUUCUGUGGAGGCGACUCCACUUUAUCACAUUUGUAUAAAUAUAUUACCCAAGUGUACUUGAAGAAAAACCAGUGGUUUACGGAAAAUAGCUUUAU--UA
.......(((((.(((((..((((.((((((....))))))......(((((((..(((.....)))..)))))))....)))).))))).)))))....................--.. ( -30.70)
>DroSec_CAF1 2968 118 + 1
UUGCCACCAACUUGUUUUGGUUUCUGUGGAGGAGACUCCACUUUAUCACAUUUGUAUAAAUAUAUUACCUAAGUGUACUUGAAGAAAAACCAGUGCUUUACGGAAAAUGGUUUUAU--UA
..((((((.....((.(((((((((((((((....))))))......(((((((..(((.....)))..)))))))......)))..)))))).)).....))....)))).....--.. ( -28.10)
>DroSim_CAF1 5032 118 + 1
UUGCCACCCACUUGGUUUGGUUUCUGUGGAGGAGACUCCACUUUAUCACAUUUGUAUAAAUAUAUUACCUAAGUGUACUUGAAGAAAAACCAGUGCUUUACGGAAAAUGGUUUUAU--UA
..((((((((((.(((((..((((.((((((....))))))......(((((((..(((.....)))..)))))))....))))..)))))))))......))....)))).....--.. ( -31.00)
>DroYak_CAF1 10576 117 + 1
UUGCCACCCACUUGUUUUGGUUUGCGUGGAGGAGACUCCACUUUAUCACAUUUGUAUAAAUAUAUUACCCAAGUGCACUGAAAGAAAAAUAAGU---UCAAAAAGAUUGGUUUUUUCAUA
..((((...(((((((((..(((..((((((....)))))).......((((((..(((.....)))..)))))).....)))..)))))))))---((.....)).))))......... ( -26.60)
>consensus
UUGCCACCCACUUGUUUUGGUUUCUGUGGAGGAGACUCCACUUUAUCACAUUUGUAUAAAUAUAUUACCCAAGUGUACUUGAAGAAAAACCAGUGCUUUACGGAAAAUGGUUUUAU__UA
..((((((........(((((((..((((((....))))))......(((((((..(((.....)))..)))))))..........)))))))........))....))))......... (-21.97 = -22.59 +   0.62)

alignment

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secondary structure

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Window 6

Location 6,228,576 – 6,228,694
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.08
Mean single sequence MFE -24.90
Consensus MFE -19.40
Energy contribution -19.40
Covariance contribution 0.00
Combinations/Pair 1.10
Mean z-score -1.51
Structure conservation index 0.78
SVM decision value 0.12
SVM RNA-class probability 0.593401
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6228576 118 - 22224390
UA--AUAAAGCUAUUUUCCGUAAACCACUGGUUUUUCUUCAAGUACACUUGGGUAAUAUAUUUAUACAAAUGUGAUAAAGUGGAGUCGCCUCCACAGAAACCAAAACAAGUGGGUGGCAA
..--.....(((((..........(((((.(((((....((((....))))(((..(((((((....))))))).....((((((....))))))....)))))))).)))))))))).. ( -30.10)
>DroSec_CAF1 2968 118 - 1
UA--AUAAAACCAUUUUCCGUAAAGCACUGGUUUUUCUUCAAGUACACUUAGGUAAUAUAUUUAUACAAAUGUGAUAAAGUGGAGUCUCCUCCACAGAAACCAAAACAAGUUGGUGGCAA
..--......(((((..(.(.....)..((((((((.........(((....(((.((....)))))....))).....((((((....))))))))))))))......)..)))))... ( -22.30)
>DroSim_CAF1 5032 118 - 1
UA--AUAAAACCAUUUUCCGUAAAGCACUGGUUUUUCUUCAAGUACACUUAGGUAAUAUAUUUAUACAAAUGUGAUAAAGUGGAGUCUCCUCCACAGAAACCAAACCAAGUGGGUGGCAA
..--......(((((....(.(((((....))))).)........(((((.(((..(((((((....))))))).....((((((....)))))).........)))))))))))))... ( -24.50)
>DroYak_CAF1 10576 117 - 1
UAUGAAAAAACCAAUCUUUUUGA---ACUUAUUUUUCUUUCAGUGCACUUGGGUAAUAUAUUUAUACAAAUGUGAUAAAGUGGAGUCUCCUCCACGCAAACCAAAACAAGUGGGUGGCAA
.........(((.......((((---(...........)))))..(((((((((..(((((((....))))))).....((((((....))))))....)))....)))))))))..... ( -22.70)
>consensus
UA__AUAAAACCAUUUUCCGUAAAGCACUGGUUUUUCUUCAAGUACACUUAGGUAAUAUAUUUAUACAAAUGUGAUAAAGUGGAGUCUCCUCCACAGAAACCAAAACAAGUGGGUGGCAA
.........(((..............(((.(........).))).(((((((((..(((((((....))))))).....((((((....))))))....)))....)))))))))..... (-19.40 = -19.40 +   0.00)

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 10:30:58 2006