Locus 6298

Sequence ID X_DroMel_CAF1
Location 15,963,284 – 15,963,423
Length 139
Max. P 0.997798
window10264 window10265 window10266

overview

Window 4

Location 15,963,284 – 15,963,394
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.14
Mean single sequence MFE -20.58
Consensus MFE -13.62
Energy contribution -14.50
Covariance contribution 0.88
Combinations/Pair 1.10
Mean z-score -1.83
Structure conservation index 0.66
SVM decision value 1.39
SVM RNA-class probability 0.949022
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15963284 110 + 22224390
CUAAAAAGGUACGAAAAAUGUGCCAACUGAUUGUGCACACAAAAGUUGUCCCAAUAAUCCGAAAGUCGACUAAUGUAGUCACUUUUCAUA---------CAUUUA-AAUUAAAUGCAUUU
.......((.((((....((((((((....))).)))))......)))).))........((((((.(((((...)))))))))))....---------((((((-...))))))..... ( -20.40)
>DroSec_CAF1 31433 94 + 1
CUAAAAAGGUACAAAAAAUGUGCCAACUGAUUGUGCACACAAAAGUUGUCCCAAUAAUCCUAAAGUCGACUAAUGUAGUCACU--------------------------UAAAUGCAUUU
.......((.((((....((((((((....))).)))))......)))).))..........((((.(((((...))))))))--------------------------).......... ( -18.10)
>DroSim_CAF1 22528 94 + 1
CUAAAAAGGUACGAAAAAUGUGCCAACUGAUUGUGCACACAAAAGUUGUCCCAAUAAUCCUAAAGUCGACUUAUGUAGUCACU--------------------------UAAAUGCAUUU
.......((.((((....((((((((....))).)))))......)))).))..........((((.((((.....)))))))--------------------------).......... ( -17.90)
>DroEre_CAF1 30064 108 + 1
CUAAAAAGGUACGAAAAAUGUGCCAAGUGAUUGAGCACACAAAAGUUGU------------AAAGUCGACUAAUGUACUCACUUCUCGGUUUUUUUGUGUGUUCAUAAUUAAAUGCAUUU
.......((((((.....)))))).(((...(((((((((((((((((.------------.((((..((....))....))))..)))..))))))))))))))..))).......... ( -26.60)
>DroYak_CAF1 13664 90 + 1
CUAAAAAGGUACGAAGAAUGUGUCAAGUGAUUGAGCACACAAAAGUUGUCCCAAUGAUCAUAUAGUCGACUAAUGUAGUCACUUUUUGGA------------------------------
(((((((((.((((....((((((((....)))).))))......)))).))..((((.((((((....)).)))).)))).))))))).------------------------------ ( -19.90)
>consensus
CUAAAAAGGUACGAAAAAUGUGCCAACUGAUUGUGCACACAAAAGUUGUCCCAAUAAUCCUAAAGUCGACUAAUGUAGUCACUU_U_______________________UAAAUGCAUUU
.......((.((((....((((((((....))).)))))......)))).))...........(((.((((.....)))))))..................................... (-13.62 = -14.50 +   0.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,963,324 – 15,963,423
Length 99
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 78.34
Mean single sequence MFE -16.80
Consensus MFE -13.40
Energy contribution -13.40
Covariance contribution 0.01
Combinations/Pair 1.13
Mean z-score -1.58
Structure conservation index 0.80
SVM decision value 0.89
SVM RNA-class probability 0.875429
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15963324 99 + 22224390
AAAAGUUGUCCCAAUAAUCCGAAAGUCGACUAAUGUAGUCACUUUUCAUACAUUUAAAUUAAAUGCAUUUUCAAUUGAAUUAUUGAAGCAGUUUAUUUU-----------
..((..(((..(((((((.(((((((.(((((...)))))))))))....((((((...))))))...........).)))))))..)))..)).....----------- ( -16.50)
>DroSec_CAF1 31473 94 + 1
AAAAGUUGUCCCAAUAAUCCUAAAGUCGACUAAUGUAGUCACU----------------UAAAUGCAUUUUCGAUUGAAUCAUUGAAACAGUUGACUUUAAAAUGCCAAA
....................(((((((((((((((((......----------------....))))))((((((......))))))..))))))))))).......... ( -17.40)
>DroSim_CAF1 22568 94 + 1
AAAAGUUGUCCCAAUAAUCCUAAAGUCGACUUAUGUAGUCACU----------------UAAAUGCAUUUUCGAUUGAAUCAUUGAAACAGUUGACUUUAAAAUGCCAAA
....................(((((((((((.(((((......----------------....)))))(((((((......))))))).))))))))))).......... ( -16.50)
>consensus
AAAAGUUGUCCCAAUAAUCCUAAAGUCGACUAAUGUAGUCACU________________UAAAUGCAUUUUCGAUUGAAUCAUUGAAACAGUUGACUUUAAAAUGCCAAA
....................(((((((((((.(((((..........................)))))(((((((......))))))).))))))))))).......... (-13.40 = -13.40 +   0.01)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,963,324 – 15,963,423
Length 99
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 78.34
Mean single sequence MFE -22.57
Consensus MFE -16.02
Energy contribution -16.13
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -2.74
Structure conservation index 0.71
SVM decision value 2.93
SVM RNA-class probability 0.997798
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15963324 99 - 22224390
-----------AAAAUAAACUGCUUCAAUAAUUCAAUUGAAAAUGCAUUUAAUUUAAAUGUAUGAAAAGUGACUACAUUAGUCGACUUUCGGAUUAUUGGGACAACUUUU
-----------.........((..((((((((((........(((((((((...)))))))))((((..((((((...))))))..))))))))))))))..))...... ( -24.10)
>DroSec_CAF1 31473 94 - 1
UUUGGCAUUUUAAAGUCAACUGUUUCAAUGAUUCAAUCGAAAAUGCAUUUA----------------AGUGACUACAUUAGUCGACUUUAGGAUUAUUGGGACAACUUUU
.(((((........))))).(((..(((((((((....(......)....(----------------((((((((...))))).))))..)))))))))..)))...... ( -21.90)
>DroSim_CAF1 22568 94 - 1
UUUGGCAUUUUAAAGUCAACUGUUUCAAUGAUUCAAUCGAAAAUGCAUUUA----------------AGUGACUACAUAAGUCGACUUUAGGAUUAUUGGGACAACUUUU
.(((((........))))).(((..(((((((((....(......)....(----------------(((((((.....)))).))))..)))))))))..)))...... ( -21.70)
>consensus
UUUGGCAUUUUAAAGUCAACUGUUUCAAUGAUUCAAUCGAAAAUGCAUUUA________________AGUGACUACAUUAGUCGACUUUAGGAUUAUUGGGACAACUUUU
....................((((((((((((((....(......).....................(((((((.....)))).)))...))))))))))))))...... (-16.02 = -16.13 +   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 12:09:59 2006