Locus 2062

Sequence ID 2L_DroMel_CAF1
Location 5,572,697 – 5,572,849
Length 152
Max. P 0.994293
window3320 window3321 window3322

overview

Window 0

Location 5,572,697 – 5,572,809
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.03
Mean single sequence MFE -33.31
Consensus MFE -26.04
Energy contribution -26.72
Covariance contribution 0.68
Combinations/Pair 1.04
Mean z-score -1.62
Structure conservation index 0.78
SVM decision value 0.34
SVM RNA-class probability 0.694405
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5572697 112 - 22407834
GUACUUUACUGAGUACCUUGGUGGCCAGACAG--------AGUACCUUUACCAACACUGCCUAUAAGUUGGUAAACGAAUCAAAUUCUGGCAGGGCGACAAACCUUUGUGGCCAUAAUAA
((((((....)))))).......((((((..(--------(...(.(((((((((...........))))))))).)..))....))))))..(((.((((....)))).)))....... ( -33.80)
>DroSec_CAF1 16728 112 - 1
GUACUUUACUGAGUACCUUGGUGGCCGGGCAG--------AGUACCUUUACCAACACUGCCUAUAAGUUGGUAAACGAAUCAAAUUCUGGCAGGACGACAAAGCUUUGUGGCCAUAAUAA
((((((....))))))....((((((..((((--------((...((((.......(((((......(((((......))))).....)))))......))))))))))))))))..... ( -32.22)
>DroSim_CAF1 18103 112 - 1
GUACUUUACUGAGUACCUUGGUGGCCGGGCAG--------AGUACCUUUACCAACACUGCCUAUAAGUUGGUAAACGAAUCAAAUUCUGGCAGGACGACAAAGCUUUGUGGCCAUAAUAA
((((((....))))))....((((((..((((--------((...((((.......(((((......(((((......))))).....)))))......))))))))))))))))..... ( -32.22)
>DroEre_CAF1 16731 120 - 1
GUACCUUGCUCAGUACCUUGGUGGCCAGGCAGCGGCAAAUAGUACCUCUACCAUCACUGCCCAUAAGUUGGGAAACGAAUCAAAUUCUGGCAGGACGACAAAGCUUUGUGGCCAUAAUAA
((((........))))....(((((((.(.(((((....(((.....))))).((.(((((.....(((.(....).)))........))))))).......))).).)))))))..... ( -31.32)
>DroYak_CAF1 16566 120 - 1
GUACUUUACUCGGUACCUGGGUGGCCGAGCAGAGGCGAAUAGUACCUCAAACAGCACUGCCUAUAAGUUGGUAAGCGAAUCAAAUUCUGGCAGGGCGACAAAGCUUUGUGGCCAUAAUAA
(((((......)))))....((((((((((.((((.........)))).....((.(((((......(((((......))))).....))))).))......))))...))))))..... ( -37.00)
>consensus
GUACUUUACUGAGUACCUUGGUGGCCGGGCAG________AGUACCUUUACCAACACUGCCUAUAAGUUGGUAAACGAAUCAAAUUCUGGCAGGACGACAAAGCUUUGUGGCCAUAAUAA
((((((....))))))....((((((..............................(((((......(((((......))))).....)))))....((((....))))))))))..... (-26.04 = -26.72 +   0.68)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,572,737 – 5,572,849
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.88
Mean single sequence MFE -29.38
Consensus MFE -17.78
Energy contribution -18.90
Covariance contribution 1.12
Combinations/Pair 1.14
Mean z-score -2.08
Structure conservation index 0.61
SVM decision value 0.96
SVM RNA-class probability 0.891108
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5572737 112 + 22407834
AUUCGUUUACCAACUUAUAGGCAGUGUUGGUAAAGGUACU--------CUGUCUGGCCACCAAGGUACUCAGUAAAGUACCCAAAAAUAGUAGUAGGUAAAUGCAUAAUACACGAUUAAG
...((((((((.(((..(((((((.((..........)).--------)))))))........((((((......))))))..........))).))))))))................. ( -25.90)
>DroSec_CAF1 16768 101 + 1
AUUCGUUUACCAACUUAUAGGCAGUGUUGGUAAAGGUACU--------CUGCCCGGCCACCAAGGUACUCAGUAAAGUACCCAAAAAUAGUGGUGGGUAAAUGAAUUAU-----------
(((((((((((........(((((.((..........)).--------)))))....(((((.((((((......)))))).........))))))))))))))))...----------- ( -33.30)
>DroSim_CAF1 18143 101 + 1
AUUCGUUUACCAACUUAUAGGCAGUGUUGGUAAAGGUACU--------CUGCCCGGCCACCAAGGUACUCAGUAAAGUACCCAAAAAUAGUAAAUAGUAAAUGAAUAAU-----------
((((((((((.........(((((.((..........)).--------)))))..........((((((......))))))...............))))))))))...----------- ( -24.70)
>DroEre_CAF1 16771 119 + 1
AUUCGUUUCCCAACUUAUGGGCAGUGAUGGUAGAGGUACUAUUUGCCGCUGCCUGGCCACCAAGGUACUGAGCAAGGUACCCAAA-AAAGUGGUGAAUAAAUGAAUAGCACAUGAUUAAG
((((((((..........(((((((...((((((.......))))))))))))).(((((...((((((......))))))....-...)))))....)))))))).............. ( -33.20)
>DroYak_CAF1 16606 120 + 1
AUUCGCUUACCAACUUAUAGGCAGUGCUGUUUGAGGUACUAUUCGCCUCUGCUCGGCCACCCAGGUACCGAGUAAAGUACCCAAAAAAAGUAGUGAGUAAAUGAAUAAUACAUGAAUAAG
(((..(((((..((((...((..(((((....(((((.......)))))(((((((..((....)).))))))).))))))).....)))).)))))..))).................. ( -29.80)
>consensus
AUUCGUUUACCAACUUAUAGGCAGUGUUGGUAAAGGUACU________CUGCCCGGCCACCAAGGUACUCAGUAAAGUACCCAAAAAUAGUAGUGAGUAAAUGAAUAAUACA_GA_UAAG
((((((((((..(((....(((((....((((....))))........)))))..........((((((......))))))..........)))..)))))))))).............. (-17.78 = -18.90 +   1.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,572,737 – 5,572,849
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.88
Mean single sequence MFE -30.72
Consensus MFE -20.96
Energy contribution -21.32
Covariance contribution 0.36
Combinations/Pair 1.27
Mean z-score -2.67
Structure conservation index 0.68
SVM decision value 2.47
SVM RNA-class probability 0.994293
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5572737 112 - 22407834
CUUAAUCGUGUAUUAUGCAUUUACCUACUACUAUUUUUGGGUACUUUACUGAGUACCUUGGUGGCCAGACAG--------AGUACCUUUACCAACACUGCCUAUAAGUUGGUAAACGAAU
.....(((((((((.((..(((..((((((........((((((((....))))))))))))))..))))).--------)))))..((((((((...........)))))))))))).. ( -27.60)
>DroSec_CAF1 16768 101 - 1
-----------AUAAUUCAUUUACCCACCACUAUUUUUGGGUACUUUACUGAGUACCUUGGUGGCCGGGCAG--------AGUACCUUUACCAACACUGCCUAUAAGUUGGUAAACGAAU
-----------...((((.((((((..((((((.....((((((((....))))))))))))))..((((((--------.((..........)).)))))).......)))))).)))) ( -33.50)
>DroSim_CAF1 18143 101 - 1
-----------AUUAUUCAUUUACUAUUUACUAUUUUUGGGUACUUUACUGAGUACCUUGGUGGCCGGGCAG--------AGUACCUUUACCAACACUGCCUAUAAGUUGGUAAACGAAU
-----------...((((.((((((((((((((((...((((((((....)))))))).)))))..((((((--------.((..........)).)))))).)))).))))))).)))) ( -29.70)
>DroEre_CAF1 16771 119 - 1
CUUAAUCAUGUGCUAUUCAUUUAUUCACCACUUU-UUUGGGUACCUUGCUCAGUACCUUGGUGGCCAGGCAGCGGCAAAUAGUACCUCUACCAUCACUGCCCAUAAGUUGGGAAACGAAU
.........((((((((........(((((....-...((((((........)))))))))))(((.......))).))))))))........((....((((.....))))....)).. ( -29.21)
>DroYak_CAF1 16606 120 - 1
CUUAUUCAUGUAUUAUUCAUUUACUCACUACUUUUUUUGGGUACUUUACUCGGUACCUGGGUGGCCGAGCAGAGGCGAAUAGUACCUCAAACAGCACUGCCUAUAAGUUGGUAAGCGAAU
...((((..(((((((((...((((((..........))))))((((.((((((((....)).)))))).))))..)))))))))........((..((((........)))).)))))) ( -33.60)
>consensus
CUUA_UC_UGUAUUAUUCAUUUACUCACUACUAUUUUUGGGUACUUUACUGAGUACCUUGGUGGCCGGGCAG________AGUACCUUUACCAACACUGCCUAUAAGUUGGUAAACGAAU
..............((((.((((((..((((((.....((((((((....))))))))))))))..((((((........................)))))).......)))))).)))) (-20.96 = -21.32 +   0.36)

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 10:18:25 2006