Locus 3917

Sequence ID X_DroMel_CAF1
Location 10,476,663 – 10,476,774
Length 111
Max. P 0.994006
window6428 window6429

overview

Window 8

Location 10,476,663 – 10,476,774
Length 111
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 94.24
Mean single sequence MFE -23.87
Consensus MFE -21.40
Energy contribution -21.64
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.91
Structure conservation index 0.90
SVM decision value 2.44
SVM RNA-class probability 0.994006
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10476663 111 + 22224390
AAAUUUUGUUGUACUCGAAUUCCCAACUGGCCAACUAAACCAGAGUUGGAAUUCGCAAUUGGCA-GCCAGAAGCCAAAACUGAACAGAAAACCAAACAGCAGCUACCAG------AAA
.....(((((((...((((((((...((((.........))))....))))))))...(((((.-.......)))))..................))))))).......------... ( -25.80)
>DroSec_CAF1 7512 118 + 1
AAAUUUUGUUGUACUCGAAUUCCCAACUGGCCAACUAAACCAUAGUUGGAAUACGCAAUUGGCAAGCCAGAAGCCAAAACUGAACAGAAAACAAAACAGCAGCUGCCAGACAAAGAAA
...((((((.......(......)..(((((((((((.....))))))......((..(((((.........)))))..((....))...........))....)))))))))))... ( -21.80)
>DroSim_CAF1 7698 118 + 1
AAAUUUUGUUGUACUCGAAUUCCCAACUGGCCAACUAAACCAUAGUUGGAAUUCGCAAUUGGCAAGCCAGAAGCCAAAACUGAACAGAAAACAAAACAGCAGCUGCCAGACAAAGAAA
...(((((((.....((((((((.(((((.............)))))))))))))....(((((.(((((.........)))....(....).........))))))))))))))... ( -24.22)
>DroEre_CAF1 8752 118 + 1
AAAUUUUGUUGUACUCGAAUUCCCAACUGGCCAACUAAACCAGAGUUGGAAUUUGCAAUUGGAAGGCCAGAAGCCAAAACUGAACAGAAAACAAAACAGCAGCUACCAGACAAAGAAA
...(((((((.....((((((((...((((.........))))....))))))))....(((..(((.....)))....(((..............)))......))))))))))... ( -22.04)
>DroYak_CAF1 9273 118 + 1
UAAUUUUGUUGUACUCGAAUUCCCAACUGGCCAACUAAACCAGAGUUGGAAUUCGCAAUUGGCAGGCCAGACGCCAAAACUGAACAGAAAACAAAACAGCAGCUACCAGACAAAGAAA
.....(((((((...((((((((...((((.........))))....))))))))...(((((.(......))))))..................)))))))................ ( -25.50)
>consensus
AAAUUUUGUUGUACUCGAAUUCCCAACUGGCCAACUAAACCAGAGUUGGAAUUCGCAAUUGGCAAGCCAGAAGCCAAAACUGAACAGAAAACAAAACAGCAGCUACCAGACAAAGAAA
.....(((((((...((((((((.((((((.........))..))))))))))))...(((((.........)))))..................)))))))................ (-21.40 = -21.64 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,476,663 – 10,476,774
Length 111
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 94.24
Mean single sequence MFE -29.90
Consensus MFE -25.14
Energy contribution -26.10
Covariance contribution 0.96
Combinations/Pair 1.03
Mean z-score -1.46
Structure conservation index 0.84
SVM decision value 0.48
SVM RNA-class probability 0.751277
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10476663 111 - 22224390
UUU------CUGGUAGCUGCUGUUUGGUUUUCUGUUCAGUUUUGGCUUCUGGC-UGCCAAUUGCGAAUUCCAACUCUGGUUUAGUUGGCCAGUUGGGAAUUCGAGUACAACAAAAUUU
...------.((((((((((((..(((....)))..))))..........)))-)))))....((((((((....((((((.....))))))...))))))))............... ( -34.90)
>DroSec_CAF1 7512 118 - 1
UUUCUUUGUCUGGCAGCUGCUGUUUUGUUUUCUGUUCAGUUUUGGCUUCUGGCUUGCCAAUUGCGUAUUCCAACUAUGGUUUAGUUGGCCAGUUGGGAAUUCGAGUACAACAAAAUUU
....((((((((((((..((......))...))).)))).(((((.(((..(((.((((((((......(((....)))..)))))))).)))..)))..)))))....))))).... ( -27.60)
>DroSim_CAF1 7698 118 - 1
UUUCUUUGUCUGGCAGCUGCUGUUUUGUUUUCUGUUCAGUUUUGGCUUCUGGCUUGCCAAUUGCGAAUUCCAACUAUGGUUUAGUUGGCCAGUUGGGAAUUCGAGUACAACAAAAUUU
....(((((.((((((((((((..(((.........)))...))))....))).)))))....((((((((.....(((((.....)))))....))))))))......))))).... ( -30.40)
>DroEre_CAF1 8752 118 - 1
UUUCUUUGUCUGGUAGCUGCUGUUUUGUUUUCUGUUCAGUUUUGGCUUCUGGCCUUCCAAUUGCAAAUUCCAACUCUGGUUUAGUUGGCCAGUUGGGAAUUCGAGUACAACAAAAUUU
....(((((...(((((.((((..(........)..))))...(((.....)))........)).((((((....((((((.....))))))...))))))....))).))))).... ( -24.60)
>DroYak_CAF1 9273 118 - 1
UUUCUUUGUCUGGUAGCUGCUGUUUUGUUUUCUGUUCAGUUUUGGCGUCUGGCCUGCCAAUUGCGAAUUCCAACUCUGGUUUAGUUGGCCAGUUGGGAAUUCGAGUACAACAAAAUUA
....(((((.(((((...((((..(........)..))))...(((.....))))))))....((((((((....((((((.....))))))...))))))))......))))).... ( -32.00)
>consensus
UUUCUUUGUCUGGUAGCUGCUGUUUUGUUUUCUGUUCAGUUUUGGCUUCUGGCCUGCCAAUUGCGAAUUCCAACUCUGGUUUAGUUGGCCAGUUGGGAAUUCGAGUACAACAAAAUUU
...........(((....)))((((((((..((........(((((.........)))))...((((((((....((((((.....))))))...))))))))))...)))))))).. (-25.14 = -26.10 +   0.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:41 2006