Locus 1479

Sequence ID X_DroMel_CAF1
Location 4,414,391 – 4,414,544
Length 153
Max. P 0.998764
window2368 window2369

overview

Window 8

Location 4,414,391 – 4,414,504
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.26
Mean single sequence MFE -23.66
Consensus MFE -23.52
Energy contribution -23.36
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.80
Structure conservation index 0.99
SVM decision value 3.22
SVM RNA-class probability 0.998764
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4414391 113 - 22224390
ACUAAAAA--A-----AAAAGAUGUACAUAAGGUGAAAAACAAAACAAAGGCGGCUACAAAAAACGGCGAAAACCGUUACGCCUUGGCACAAUGCCCAAGGGUCCUGCCAGCUUGUCCUU
........--.-----...........(((((((.....))........(((((..((....(((((......)))))...(((((((.....).)))))))).)))))..))))).... ( -24.30)
>DroSec_CAF1 16818 115 - 1
ACUUAAAAAAA-----AAAAGAUGUACAUAAAGUGAAAAACAAAACAAAGGCGGCUACAAAAAACGGCGAAAACCGUUACGCCUUGGCACAAUGCCCAAGGGUCCUGCCAGCUUGUCCUU
...........-----....((((..(.....((.....))........(((((..((....(((((......)))))...(((((((.....).)))))))).))))).)..))))... ( -23.30)
>DroSim_CAF1 18289 120 - 1
ACUUAAAAAAAAAUAAAAAAGAUGUACAUAAAGUGAAAAACAAAACAAAGGCGGCUACAAAAAACGGCGAAAACCGUUACGCCUUGGCACAAUGCCCAAGGGUCCUGCCAGCUUGUCCUU
....................((((..(.....((.....))........(((((..((....(((((......)))))...(((((((.....).)))))))).))))).)..))))... ( -23.30)
>DroEre_CAF1 17830 114 - 1
ACUAAAAAA-A-----AGAAGAUGUACAUAAAGUGAAAAACAAAACAAAGGCAGCUACAAAAAACGGCGAAAACCGUUACGCCUUGGCACAAUGCCCAAGGGUCCUGCCAGCUUGUCCUU
.........-.-----....((((..(.....((.....))........(((((..((....(((((......)))))...(((((((.....).)))))))).))))).)..))))... ( -24.00)
>DroYak_CAF1 17519 111 - 1
ACUAAAUAA-A-----A---GAUGUACAAAAAGUGAAAAACAAAACAAAGGCGGCUACAAAAAACGGCGAAAACCGUUACGCCUUGGCACAAUGCCCAAGGGUCCUGCCAGCUUGUCCUU
.........-.-----.---...(.((((...((.....))........(((((..((....(((((......)))))...(((((((.....).)))))))).)))))...)))).).. ( -23.40)
>consensus
ACUAAAAAA_A_____AAAAGAUGUACAUAAAGUGAAAAACAAAACAAAGGCGGCUACAAAAAACGGCGAAAACCGUUACGCCUUGGCACAAUGCCCAAGGGUCCUGCCAGCUUGUCCUU
....................((((..(.....((.....))........(((((..((....(((((......)))))...(((((((.....).)))))))).))))).)..))))... (-23.52 = -23.36 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,414,431 – 4,414,544
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.29
Mean single sequence MFE -22.63
Consensus MFE -19.00
Energy contribution -19.04
Covariance contribution 0.04
Combinations/Pair 1.06
Mean z-score -2.45
Structure conservation index 0.84
SVM decision value 2.71
SVM RNA-class probability 0.996498
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4414431 113 - 22224390
AAUUUGGCCUGCCAUUCAUCGGACACGUCCUGGACUUUCAACUAAAAA--A-----AAAAGAUGUACAUAAGGUGAAAAACAAAACAAAGGCGGCUACAAAAAACGGCGAAAACCGUUAC
....(((((.(((...(((((((....)))(((........)))....--.-----....))))........((.....))........)))))))).....(((((......))))).. ( -23.00)
>DroSec_CAF1 16858 115 - 1
AAUUUGGCCUGCCAUUCAACGGACACGUCCUGGACUUUCAACUUAAAAAAA-----AAAAGAUGUACAUAAAGUGAAAAACAAAACAAAGGCGGCUACAAAAAACGGCGAAAACCGUUAC
....(((((.(((.((((..(((....))))))).(((((.(((.......-----..............))))))))...........)))))))).....(((((......))))).. ( -22.40)
>DroSim_CAF1 18329 120 - 1
AAUUUGGCCUGCCAUUCAACGGACACGUUCUGGACUUUCAACUUAAAAAAAAAUAAAAAAGAUGUACAUAAAGUGAAAAACAAAACAAAGGCGGCUACAAAAAACGGCGAAAACCGUUAC
....(((((.(((.(((((((....)))..)))).(((((.(((..........................))))))))...........)))))))).....(((((......))))).. ( -21.47)
>DroEre_CAF1 17870 113 - 1
AAUUUGGCCUGCCAUUCAUCGGACACGUCCAGGAC-UUCAACUAAAAAA-A-----AGAAGAUGUACAUAAAGUGAAAAACAAAACAAAGGCAGCUACAAAAAACGGCGAAAACCGUUAC
..((((..(((((...(((((((....)))((...-.....))......-.-----....))))........((.....))........)))))...)))).(((((......))))).. ( -23.00)
>DroYak_CAF1 17559 111 - 1
AAUUUGGCCUGCCAUUCAUCGGACACGUCCAGGACAUUCAACUAAAUAA-A-----A---GAUGUACAAAAAGUGAAAAACAAAACAAAGGCGGCUACAAAAAACGGCGAAAACCGUUAC
....(((((.(((...(((((((....)))((.........))......-.-----.---))))........((.....))........)))))))).....(((((......))))).. ( -23.30)
>consensus
AAUUUGGCCUGCCAUUCAUCGGACACGUCCUGGACUUUCAACUAAAAAA_A_____AAAAGAUGUACAUAAAGUGAAAAACAAAACAAAGGCGGCUACAAAAAACGGCGAAAACCGUUAC
....(((((.(((.......(((....)))..........................................((.....))........)))))))).....(((((......))))).. (-19.00 = -19.04 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:33 2006