Locus 4567

Sequence ID 3R_DroMel_CAF1
Location 12,069,753 – 12,069,913
Length 160
Max. P 0.999907
window7475 window7476 window7477

overview

Window 5

Location 12,069,753 – 12,069,873
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.24
Mean single sequence MFE -38.22
Consensus MFE -34.49
Energy contribution -34.13
Covariance contribution -0.36
Combinations/Pair 1.22
Mean z-score -1.59
Structure conservation index 0.90
SVM decision value 1.60
SVM RNA-class probability 0.966752
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12069753 120 - 27905053
AUUGCUGAAUGGCAGCAGCCACCUAGAGUGGGCAUUGUUGCUGUUCUUGGGUUCGCUGCCAUGUCCCUUUGUUGUUGAGAACCUUCAUUACUCCUUACCCCAUGGUUUUGACUGGUAUUA
..((((..((((((((((((....((((..(.((....)))..))))..)))).))))))))...........(((.((((((....................))))))))).))))... ( -32.85)
>DroSec_CAF1 6365 120 - 1
AUUGCUGAAUGGCAGCAGCCACCGAGAGCGGGCAUUGUUGCUGUUCUUGGGUUCGCUGCCAUGUCCCUUUGUUGCUGAGAACCUUCAUUACUCCUUACCCCAUGGUUUUGGCUGGCAUUA
..((((..((((((((((((..(((((((((.((....))))))))))))))).))))))))...........(((.((((((....................))))))))).))))... ( -41.55)
>DroSim_CAF1 6813 120 - 1
AUUGCUGAAUGGCAGCAGCCACCGAGAGCGGGCAUUGUUGCUGUUCUUGGGUUCGCUGCCAUGUCCCUUUGUUGCUGAGAACCUUCAUUACUCCUUACCCCAUGGCUUUGGCUGGUAUUA
.(((((....)))))((((((((((((((((.((....)))))))))))).......((((((.......((...((((....))))..)).........))))))..))))))...... ( -38.89)
>DroEre_CAF1 8287 117 - 1
AUUGCUGAAUGGCAGCAGCCACCGAGAGCGAGCAUUGUUGCUGUUCUUG-GUUCGCUGCCAUGUCCCUUUGUUGUUGGGAACCUUCAUUACUCCUUAUCCCUUGCUUUUGGCUGGUAA--
...((..((.(((((((((.(((((((((.((((....)))))))))))-))..)))))....((((.........))))......................))))))..))......-- ( -40.90)
>DroYak_CAF1 8414 118 - 1
AUUGCUGAAUGGCAGCAGCCACCGAGAGCGGGCAUUGUUGCUGUUCUUGGGUUCGCUGUCAUGUCCCUUUGUUGCCGAGAACCUUCAUUACUCCUUAUCCCUUGGAUUUGGCUGGUAU--
........((((((((((((..(((((((((.((....))))))))))))))).))))))))..........(((((((....)))......((..((((...))))..))..)))).-- ( -36.90)
>consensus
AUUGCUGAAUGGCAGCAGCCACCGAGAGCGGGCAUUGUUGCUGUUCUUGGGUUCGCUGCCAUGUCCCUUUGUUGCUGAGAACCUUCAUUACUCCUUACCCCAUGGUUUUGGCUGGUAUUA
..((((..((((((((((((..(((((((.((((....))))))))))))))).))))))))...........(((.((((((....................))))))))).))))... (-34.49 = -34.13 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,069,793 – 12,069,913
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.17
Mean single sequence MFE -41.20
Consensus MFE -37.48
Energy contribution -38.28
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.60
Structure conservation index 0.91
SVM decision value 3.55
SVM RNA-class probability 0.999372
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12069793 120 + 27905053
UCUCAACAACAAAGGGACAUGGCAGCGAACCCAAGAACAGCAACAAUGCCCACUCUAGGUGGCUGCUGCCAUUCAGCAAUGUAAACAAUGCACAAGUUGCACGUGCAGCCAGCAGGCUGG
......((((.....((.(((((((((..(((.(((...(((....)))....))).)).)..))))))))))).(((.((....)).)))....))))......(((((....))))). ( -38.90)
>DroSec_CAF1 6405 120 + 1
UCUCAGCAACAAAGGGACAUGGCAGCGAACCCAAGAACAGCAACAAUGCCCGCUCUCGGUGGCUGCUGCCAUUCAGCAAUGUAAACAAUGCACAAGUUGCACGUGCAGCCAGCAGGCUGG
.....(((((.....((.(((((((((..(((.(((.(.(((....)))..).))).)).)..))))))))))).(((.((....)).)))....))))).....(((((....))))). ( -43.90)
>DroSim_CAF1 6853 120 + 1
UCUCAGCAACAAAGGGACAUGGCAGCGAACCCAAGAACAGCAACAAUGCCCGCUCUCGGUGGCUGCUGCCAUUCAGCAAUGUAAACAAUGCACAAGUUGCACGUGCAGCCAGCAGGCUGG
.....(((((.....((.(((((((((..(((.(((.(.(((....)))..).))).)).)..))))))))))).(((.((....)).)))....))))).....(((((....))))). ( -43.90)
>DroEre_CAF1 8325 119 + 1
UCCCAACAACAAAGGGACAUGGCAGCGAAC-CAAGAACAGCAACAAUGCUCGCUCUCGGUGGCUGCUGCCAUUCAGCAAUGUAAACAAUGCACAAGUUGCACGUGCAGCCAGCAGGCUGG
((((.........))))(((((((((((((-(.(((.(((((....)))).).))).)))(((....)))..)).(((.((....)).)))....))))).))))(((((....))))). ( -41.70)
>DroYak_CAF1 8452 120 + 1
UCUCGGCAACAAAGGGACAUGACAGCGAACCCAAGAACAGCAACAAUGCCCGCUCUCGGUGGCUGCUGCCAUUCAGCAAUGUAAACAAUGCACAAGUUGCACGUGCAGCCAGCAGGCUGG
.(.(((((((.....((.(((.(((((..(((.(((.(.(((....)))..).))).)).)..))))).))))).(((.((....)).)))....))))).)).)(((((....))))). ( -37.60)
>consensus
UCUCAGCAACAAAGGGACAUGGCAGCGAACCCAAGAACAGCAACAAUGCCCGCUCUCGGUGGCUGCUGCCAUUCAGCAAUGUAAACAAUGCACAAGUUGCACGUGCAGCCAGCAGGCUGG
.....(((((.....((.(((((((((..(((.(((...(((....)))....))).)).)..))))))))))).(((.((....)).)))....))))).....(((((....))))). (-37.48 = -38.28 +   0.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,069,793 – 12,069,913
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.17
Mean single sequence MFE -47.84
Consensus MFE -46.46
Energy contribution -45.98
Covariance contribution -0.48
Combinations/Pair 1.12
Mean z-score -2.65
Structure conservation index 0.97
SVM decision value 4.48
SVM RNA-class probability 0.999907
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12069793 120 - 27905053
CCAGCCUGCUGGCUGCACGUGCAACUUGUGCAUUGUUUACAUUGCUGAAUGGCAGCAGCCACCUAGAGUGGGCAUUGUUGCUGUUCUUGGGUUCGCUGCCAUGUCCCUUUGUUGUUGAGA
.(((((....)))))..(..(((((....(((.((....)).)))...((((((((((((....((((..(.((....)))..))))..)))).))))))))........)))))...). ( -42.80)
>DroSec_CAF1 6405 120 - 1
CCAGCCUGCUGGCUGCACGUGCAACUUGUGCAUUGUUUACAUUGCUGAAUGGCAGCAGCCACCGAGAGCGGGCAUUGUUGCUGUUCUUGGGUUCGCUGCCAUGUCCCUUUGUUGCUGAGA
.(((((....)))))..((.(((((....(((.((....)).)))...((((((((((((..(((((((((.((....))))))))))))))).))))))))........)))))))... ( -49.30)
>DroSim_CAF1 6853 120 - 1
CCAGCCUGCUGGCUGCACGUGCAACUUGUGCAUUGUUUACAUUGCUGAAUGGCAGCAGCCACCGAGAGCGGGCAUUGUUGCUGUUCUUGGGUUCGCUGCCAUGUCCCUUUGUUGCUGAGA
.(((((....)))))..((.(((((....(((.((....)).)))...((((((((((((..(((((((((.((....))))))))))))))).))))))))........)))))))... ( -49.30)
>DroEre_CAF1 8325 119 - 1
CCAGCCUGCUGGCUGCACGUGCAACUUGUGCAUUGUUUACAUUGCUGAAUGGCAGCAGCCACCGAGAGCGAGCAUUGUUGCUGUUCUUG-GUUCGCUGCCAUGUCCCUUUGUUGUUGGGA
.((((.((..(((((((((.......))))))..)))..))..)))).((((((((....(((((((((.((((....)))))))))))-))..)))))))).((((.........)))) ( -49.00)
>DroYak_CAF1 8452 120 - 1
CCAGCCUGCUGGCUGCACGUGCAACUUGUGCAUUGUUUACAUUGCUGAAUGGCAGCAGCCACCGAGAGCGGGCAUUGUUGCUGUUCUUGGGUUCGCUGUCAUGUCCCUUUGUUGCCGAGA
.(((((....)))))..((.(((((....(((.((....)).)))...((((((((((((..(((((((((.((....))))))))))))))).))))))))........)))))))... ( -48.80)
>consensus
CCAGCCUGCUGGCUGCACGUGCAACUUGUGCAUUGUUUACAUUGCUGAAUGGCAGCAGCCACCGAGAGCGGGCAUUGUUGCUGUUCUUGGGUUCGCUGCCAUGUCCCUUUGUUGCUGAGA
.(((((....)))))..((.(((((....(((.((....)).)))...((((((((((((..(((((((.((((....))))))))))))))).))))))))........)))))))... (-46.46 = -45.98 +  -0.48)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:51 2006