Locus 4391

Sequence ID 3L_DroMel_CAF1
Location 12,864,611 – 12,864,808
Length 197
Max. P 0.829413
window6804 window6805 window6806

overview

Window 4

Location 12,864,611 – 12,864,728
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.29
Mean single sequence MFE -34.35
Consensus MFE -21.32
Energy contribution -22.07
Covariance contribution 0.75
Combinations/Pair 1.20
Mean z-score -1.92
Structure conservation index 0.62
SVM decision value 0.34
SVM RNA-class probability 0.695456
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12864611 117 + 23771897
CUGAGCGAUUUCAGUAACUCCGA-UACAUUUGCCACCCAUGCAGGCCAACGGCAGGCUAAUG--UUUUGGUUAUUGUUCAAGAUGGUUCCCAGCAACCUCAACAGCCAAAUCCUUGGCUA
.((((((((..........((((-.(((((.(((...(.....)(((...))).))).))))--).))))..)))))))).((.((((......))))))...((((((....)))))). ( -31.60)
>DroSec_CAF1 103051 120 + 1
CUUAACCAUUUCACUAACCCCCUUUCCUUUUGCCACCCCAGUCUGGCUUCGCCCCGCCAUGGGUUUUGGGUUUUUGUUCAAGAUGGUUCCCAGCAAUCUCAGCAGCCAAAUCCUUGGCUG
...((((((((((..(((((...........((((........))))...((((......))))...)))))..))....))))))))..............(((((((....))))))) ( -31.60)
>DroEre_CAF1 108421 117 + 1
CUGACCGGUUUCGCUAACACCGA-UAUAUUGGCCACGCAUGCAGGGCAACGGCAGGCCAAUG--UUCUGGUUAUUGUACAAGAUGGUUCCCAACAAUCUCAACAGCCAAAUCCCUGGCUG
..(((((.....((....((((.-.(((((((((.....(((..(....).)))))))))))--)..))))....))......)))))..............((((((......)))))) ( -34.50)
>DroYak_CAF1 114416 117 + 1
CUGACCGAUUUCAGUAACUCCGA-UGCAUUGGCCACGCAUGCAGGGCAACGGCAGGCCAAUG--UUCUGGUUAUUGUUCAAGAUGGUUCCCAACAACCUCAACAGCCAAAUCCCUGGCUG
......((...((((((((..((-.(((((((((.....(((..(....).)))))))))))--))).)))))))).))..((.((((......))))))..((((((......)))))) ( -39.70)
>consensus
CUGACCGAUUUCACUAACUCCGA_UACAUUGGCCACCCAUGCAGGGCAACGGCAGGCCAAUG__UUCUGGUUAUUGUUCAAGAUGGUUCCCAACAACCUCAACAGCCAAAUCCCUGGCUG
...........((((((((.......((((((((.....((.....))......))))))))......)))))))).....((.((((......))))))..((((((......)))))) (-21.32 = -22.07 +   0.75)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,864,650 – 12,864,768
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.25
Mean single sequence MFE -36.70
Consensus MFE -25.92
Energy contribution -26.68
Covariance contribution 0.75
Combinations/Pair 1.17
Mean z-score -1.70
Structure conservation index 0.71
SVM decision value 0.24
SVM RNA-class probability 0.647079
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12864650 118 + 23771897
GCAGGCCAACGGCAGGCUAAUG--UUUUGGUUAUUGUUCAAGAUGGUUCCCAGCAACCUCAACAGCCAAAUCCUUGGCUAAAUCGAGGACAAAGUCCUCCCUGUACCAUCAGUCCGCUCU
((.((((((.((((......))--)))))))).........((((((...(((..........((((((....)))))).....((((((...)))))).))).)))))).....))... ( -35.00)
>DroSec_CAF1 103091 120 + 1
GUCUGGCUUCGCCCCGCCAUGGGUUUUGGGUUUUUGUUCAAGAUGGUUCCCAGCAAUCUCAGCAGCCAAAUCCUUGGCUGAAUCGAGGGCAAAGUCCCCCCUGUACCGUCAGUCCCCUCU
(.(((((...((((......))))...(((.((((((((.((((.((.....)).))))...(((((((....)))))))......)))))))).))).........))))).)...... ( -35.60)
>DroEre_CAF1 108460 118 + 1
GCAGGGCAACGGCAGGCCAAUG--UUCUGGUUAUUGUACAAGAUGGUUCCCAACAAUCUCAACAGCCAAAUCCCUGGCUGAAUCGAGGACAAAGUCCUCCCUGUACCGUCAGUCCCCUCU
...((((.((((((((....((--(..(((..((..(.....)..))..)))))).......((((((......))))))....((((((...))))))))))..))))..))))..... ( -36.60)
>DroYak_CAF1 114455 118 + 1
GCAGGGCAACGGCAGGCCAAUG--UUCUGGUUAUUGUUCAAGAUGGUUCCCAACAACCUCAACAGCCAAAUCCCUGGCUGAAUCGAGGACAAAGUUCUCCCUGUACCGUCAGUGCCCUCU
..(((((((((((((((((...--...)))...((((((..(((((((......))))....((((((......)))))).)))..)))))).......))))..))))...)))))).. ( -39.60)
>consensus
GCAGGGCAACGGCAGGCCAAUG__UUCUGGUUAUUGUUCAAGAUGGUUCCCAACAACCUCAACAGCCAAAUCCCUGGCUGAAUCGAGGACAAAGUCCUCCCUGUACCGUCAGUCCCCUCU
...((((.......(((((........))))).........((((((.....(((.......((((((......))))))....((((((...))))))..))))))))).))))..... (-25.92 = -26.68 +   0.75)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,864,688 – 12,864,808
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.39
Mean single sequence MFE -28.85
Consensus MFE -24.14
Energy contribution -24.70
Covariance contribution 0.56
Combinations/Pair 1.16
Mean z-score -1.84
Structure conservation index 0.84
SVM decision value 0.71
SVM RNA-class probability 0.829413
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12864688 120 + 23771897
AGAUGGUUCCCAGCAACCUCAACAGCCAAAUCCUUGGCUAAAUCGAGGACAAAGUCCUCCCUGUACCAUCAGUCCGCUCUACCCAUAUUCCUGUACUUAUCCCCGUUAUCCGAAUUCGGG
.((((((...(((..........((((((....)))))).....((((((...)))))).))).))))))...........(((..((((....((........)).....))))..))) ( -30.70)
>DroSec_CAF1 103131 120 + 1
AGAUGGUUCCCAGCAAUCUCAGCAGCCAAAUCCUUGGCUGAAUCGAGGGCAAAGUCCCCCCUGUACCGUCAGUCCCCUCUACCCAUAUUCCUGCACUUAUCCUGGUUAUCCGAAUUCGGG
.((((((...(((...((....(((((((....)))))))....))(((......)))..))).))))))...........(((..((((....(((......))).....))))..))) ( -29.60)
>DroEre_CAF1 108498 120 + 1
AGAUGGUUCCCAACAAUCUCAACAGCCAAAUCCCUGGCUGAAUCGAGGACAAAGUCCUCCCUGUACCGUCAGUCCCCUCUACCCAUAUUCCUGCACCUAUCCUGGUUUCCCGAAUUCUGG
.((((((...((..........((((((......))))))....((((((...))))))..)).))))))............(((.((((....(((......))).....))))..))) ( -30.70)
>DroYak_CAF1 114493 120 + 1
AGAUGGUUCCCAACAACCUCAACAGCCAAAUCCCUGGCUGAAUCGAGGACAAAGUUCUCCCUGUACCGUCAGUGCCCUCUACCCAUAUUCCUGCAAUUAUCCUGGUUAUCCGAAUUCCGG
.((((((...((..........((((((......))))))....((((((...))))))..)).))))))...............................((((...........)))) ( -24.40)
>consensus
AGAUGGUUCCCAACAACCUCAACAGCCAAAUCCCUGGCUGAAUCGAGGACAAAGUCCUCCCUGUACCGUCAGUCCCCUCUACCCAUAUUCCUGCACUUAUCCUGGUUAUCCGAAUUCGGG
.((((((.....(((.......((((((......))))))....((((((...))))))..)))))))))...........(((..((((....(((......))).....))))..))) (-24.14 = -24.70 +   0.56)

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 11:21:27 2006