Locus 3503

Sequence ID 2L_DroMel_CAF1
Location 10,240,095 – 10,240,242
Length 147
Max. P 0.568086
window5531 window5532 window5533

overview

Window 1

Location 10,240,095 – 10,240,215
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.17
Mean single sequence MFE -29.90
Consensus MFE -25.22
Energy contribution -25.02
Covariance contribution -0.20
Combinations/Pair 1.12
Mean z-score -1.28
Structure conservation index 0.84
SVM decision value 0.07
SVM RNA-class probability 0.568086
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10240095 120 + 22407834
UUGCAUUUCAGCGCCAUGAACAGUUAUUCGUGGGCUGCCAUUUUAAAAUUUGGAGUAGCGUUUCUUUUUCUCUCCUCCAUAAAUGUGCGAAAGAGAAAAAAUGUUGAGUUCAAUCGCUUU
..((....((((.(((((((......)))))))))))............(((((.((((((((...(((((((..(((((....))).)).)))))))))))))))..)))))..))... ( -32.00)
>DroSec_CAF1 4423 120 + 1
UUCCAUUUCAGCGCCGUGAACAGUUAUUCGUGGGCUGCCAUUUUAAAAUUUGGAGUAGCGUUUCUUUUUCUCUCCUUCAUAAAAGUGCGAAAGAGAAAAAAUGUUGAGUUCAAUCGCAUU
..........(((...(((((.(((((((((((....))))...........))))))).((((((((((.(..(((.....))).).)))))))))).........)))))..)))... ( -27.30)
>DroSim_CAF1 4857 120 + 1
UUGCAUUUCAGCGCCGUGAACAGUUAUUCGUGGGCUGCCAUUUUAAAAUUUGGAGUAGCGUUUCUUUUUCUCUCCUUCAUAAAAGUGCGAAAGAGAAAAAAUGUUGAGUUCAAUCGCAUU
.(((....((((.(((((((......)))))))))))............(((((.((((((((...(((((((....(((....)))....)))))))))))))))..)))))..))).. ( -28.10)
>DroEre_CAF1 4356 120 + 1
UUGCACUUCAGCAGCGUGAACAGUUAUUCGUGGGCUGCCAUUUUAAAAUUUGGAGUAGCGUUUCUUUUUCUCUGCUCCAUAAAAGUGCGAAAGAGAAAAGAUGUUACGUCCAACCGCUUU
..((......(((((.((((......))))...)))))...........(((((((((((((...((((((((..(((((....))).)).)))))))))))))))).)))))..))... ( -33.60)
>DroYak_CAF1 4232 120 + 1
UUGCAUUUCAGCAGCGUGAACAGUUAUUCGUGGGCUGCCAUUUUAAAAUUUGGAGUAGCGUUUCUUUUUCUCUGCUCCACUAAAGUGCGAAAGAGAAAAGAUCUUAAGUUUAGUAGCUUU
.........(((.((.(((((.(((((((((((....))))...........))))))).....(((((((((..(((((....))).)).))))))))).......))))))).))).. ( -28.50)
>consensus
UUGCAUUUCAGCGCCGUGAACAGUUAUUCGUGGGCUGCCAUUUUAAAAUUUGGAGUAGCGUUUCUUUUUCUCUCCUCCAUAAAAGUGCGAAAGAGAAAAAAUGUUGAGUUCAAUCGCUUU
..........(((...(((((.(((((((((((....))))...........))))))).....(((((((((..(((((....))).)).))))))))).......)))))..)))... (-25.22 = -25.02 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,240,095 – 10,240,215
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.17
Mean single sequence MFE -28.34
Consensus MFE -20.40
Energy contribution -21.08
Covariance contribution 0.68
Combinations/Pair 1.11
Mean z-score -2.04
Structure conservation index 0.72
SVM decision value 0.05
SVM RNA-class probability 0.556796
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10240095 120 - 22407834
AAAGCGAUUGAACUCAACAUUUUUUCUCUUUCGCACAUUUAUGGAGGAGAGAAAAAGAAACGCUACUCCAAAUUUUAAAAUGGCAGCCCACGAAUAACUGUUCAUGGCGCUGAAAUGCAA
..((((.(((....)))..((((((((((((((........)))))))))))))).....))))...............((..(((((((.((((....)))).))).))))..)).... ( -31.60)
>DroSec_CAF1 4423 120 - 1
AAUGCGAUUGAACUCAACAUUUUUUCUCUUUCGCACUUUUAUGAAGGAGAGAAAAAGAAACGCUACUCCAAAUUUUAAAAUGGCAGCCCACGAAUAACUGUUCACGGCGCUGAAAUGGAA
...(((.(((....)))..((((((((((((((........)))))))))))))).....)))...((((.(((....)))..((((((..((((....))))..)).))))...)))). ( -28.50)
>DroSim_CAF1 4857 120 - 1
AAUGCGAUUGAACUCAACAUUUUUUCUCUUUCGCACUUUUAUGAAGGAGAGAAAAAGAAACGCUACUCCAAAUUUUAAAAUGGCAGCCCACGAAUAACUGUUCACGGCGCUGAAAUGCAA
...(((.(((....)))..((((((((((((((........)))))))))))))).....)))................((..((((((..((((....))))..)).))))..)).... ( -27.70)
>DroEre_CAF1 4356 120 - 1
AAAGCGGUUGGACGUAACAUCUUUUCUCUUUCGCACUUUUAUGGAGCAGAGAAAAAGAAACGCUACUCCAAAUUUUAAAAUGGCAGCCCACGAAUAACUGUUCACGCUGCUGAAGUGCAA
((((.((..(((.......)))..)).)))).(((((((..(((((.((.(.........).)).)))))...........((((((....((((....))))..))))))))))))).. ( -28.50)
>DroYak_CAF1 4232 120 - 1
AAAGCUACUAAACUUAAGAUCUUUUCUCUUUCGCACUUUAGUGGAGCAGAGAAAAAGAAACGCUACUCCAAAUUUUAAAAUGGCAGCCCACGAAUAACUGUUCACGCUGCUGAAAUGCAA
...((..............(((((((((((((.(((....)))))).)))).)))))).......................((((((....((((....))))..)))))).....)).. ( -25.40)
>consensus
AAAGCGAUUGAACUCAACAUUUUUUCUCUUUCGCACUUUUAUGGAGGAGAGAAAAAGAAACGCUACUCCAAAUUUUAAAAUGGCAGCCCACGAAUAACUGUUCACGGCGCUGAAAUGCAA
...(((..(((((......((((((((((((((........))))))))))))))......(((...(((..........))).)))............)))))...))).......... (-20.40 = -21.08 +   0.68)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,240,135 – 10,240,242
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.92
Mean single sequence MFE -21.61
Consensus MFE -13.12
Energy contribution -13.96
Covariance contribution 0.84
Combinations/Pair 1.19
Mean z-score -1.94
Structure conservation index 0.61
SVM decision value 0.02
SVM RNA-class probability 0.543707
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10240135 107 - 22407834
UUGAAUAU-------------UUAAGAACUGAACAAUCUAAAAGCGAUUGAACUCAACAUUUUUUCUCUUUCGCACAUUUAUGGAGGAGAGAAAAAGAAACGCUACUCCAAAUUUUAAAA
.......(-------------((((((..((..(((((.......))))).........((((((((((((((........)))))))))))))).............))..))))))). ( -19.90)
>DroSec_CAF1 4463 120 - 1
CUAAGUAUUAAACAAUUGAGUUUAAGAACUGAACAAUCUAAAUGCGAUUGAACUCAACAUUUUUUCUCUUUCGCACUUUUAUGAAGGAGAGAAAAAGAAACGCUACUCCAAAUUUUAAAA
...((((........((((((((((......................))))))))))..((((((((((((((........))))))))))))))........))))............. ( -22.95)
>DroSim_CAF1 4897 120 - 1
CUAAAUAUUAAACAAUUGAGUUUUAGAACUGAACAAUCUAAAUGCGAUUGAACUCAACAUUUUUUCUCUUUCGCACUUUUAUGAAGGAGAGAAAAAGAAACGCUACUCCAAAUUUUAAAA
.......(((((.....((((((((((.........)))))).(((.(((....)))..((((((((((((((........)))))))))))))).....))).)))).....))))).. ( -22.90)
>DroEre_CAF1 4396 120 - 1
UUAAAUAUAUAAAAAUACCGUUUAAAAACGGAGCAAUUUAAAAGCGGUUGGACGUAACAUCUUUUCUCUUUCGCACUUUUAUGGAGCAGAGAAAAAGAAACGCUACUCCAAAUUUUAAAA
.................(((((....))))).....(((((((....(((((.(((.(.((((((.(((((.((.((.....)).)))))))))))))...).)))))))).))))))). ( -24.30)
>DroYak_CAF1 4272 120 - 1
UUAAAUAUACAAUAAUCGAGUUUAAUAACUGGGCAAUAUAAAAGCUACUAAACUUAAGAUCUUUUCUCUUUCGCACUUUAGUGGAGCAGAGAAAAAGAAACGCUACUCCAAAUUUUAAAA
.................(((((((.......(((.........)))..)))))))....(((((((((((((.(((....)))))).)))).))))))...................... ( -18.00)
>consensus
UUAAAUAUAAAACAAUUGAGUUUAAGAACUGAACAAUCUAAAAGCGAUUGAACUCAACAUUUUUUCUCUUUCGCACUUUUAUGGAGGAGAGAAAAAGAAACGCUACUCCAAAUUUUAAAA
....................(((((((......(((((.......))))).........((((((((((((((........)))))))))))))).................))))))). (-13.12 = -13.96 +   0.84)

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 10:54:02 2006