Locus 170

Sequence ID 3R_DroMel_CAF1
Location 826,168 – 826,281
Length 113
Max. P 0.908248
window283 window284

overview

Window 3

Location 826,168 – 826,281
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.36
Mean single sequence MFE -36.14
Consensus MFE -24.92
Energy contribution -24.52
Covariance contribution -0.40
Combinations/Pair 1.18
Mean z-score -2.22
Structure conservation index 0.69
SVM decision value 1.06
SVM RNA-class probability 0.908248
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 826168 113 + 27905053
CGGCGAUUGCGACUGC-------AGCCAAAACUACCAGCUAAUGGCCAUCGAAACACGGCGGAUGUGCGAGCACGAAACGUGCUUUCCGAAUGGCCAAAUGGCGAAAUGGUCAAAACCAA
.(((...(((....))-------))))..........((((.(((((((((...((((.....)))).(((((((...)))))))..)).)))))))..))))....((((....)))). ( -36.00)
>DroSec_CAF1 8443 120 + 1
CGGCGACUGCAACUGCAGCCUGCAGCCAAAACUACCAGCAAUGGGCCAUCCAAACGCGGCGGAUGUGCGAGCACGAAACGUGCUUUCCGAAUGGCCAAAUGGCGAAAUGGCCAAAACCAA
.((((.((((....)))).)....((((.......((....))((((((((......))((((.....(((((((...))))))))))).))))))...))))......)))........ ( -40.40)
>DroSim_CAF1 5638 120 + 1
CGGCGACUGCAACUGCAGCCUGCAGCCAAAACUACCAGCAAUGGGCCAUCCAAACGCGGCGGAUGUGCGAGCACGAAACGUGCUUUCCGAAUGGCCAAAUGGCGAAAUGGCCAAAACCAA
.((((.((((....)))).)....((((.......((....))((((((((......))((((.....(((((((...))))))))))).))))))...))))......)))........ ( -40.40)
>DroEre_CAF1 10141 95 + 1
CGGC-------------------------AACUACCAACAAAUGGUCAUUCAAACGCGGCGGAUGUGCGAGCACGAAACGUGCUUUCCGAAUGGCCAAAUGGCGAAAUUGCCAAAACCAU
.(((-------------------------((.......((..(((((((((...((((.......))))((((((...))))))....)))))))))..))......)))))........ ( -31.12)
>DroYak_CAF1 8901 112 + 1
CAACGACUGCAACCGC-------AUCCAAAACUACCAACAAAUGGCCAUCUGAGCGCGGCGGAUGUGCGAGCACUAAACGUGCUUUCCGAAUGGCCAAAUGGCGAAAUUGCCAAAACC-C
....((.(((....))-------)))................((((((((.(((((((.....)))))((((((.....)))))))).).)))))))..(((((....))))).....-. ( -32.80)
>consensus
CGGCGACUGCAACUGC_______AGCCAAAACUACCAGCAAAUGGCCAUCCAAACGCGGCGGAUGUGCGAGCACGAAACGUGCUUUCCGAAUGGCCAAAUGGCGAAAUGGCCAAAACCAA
...........................................((((((((......))((((.....((((((.....)))))))))).))))))...((((......))))....... (-24.92 = -24.52 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 826,168 – 826,281
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.36
Mean single sequence MFE -40.56
Consensus MFE -27.12
Energy contribution -27.86
Covariance contribution 0.74
Combinations/Pair 1.17
Mean z-score -1.69
Structure conservation index 0.67
SVM decision value 0.09
SVM RNA-class probability 0.576689
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 826168 113 - 27905053
UUGGUUUUGACCAUUUCGCCAUUUGGCCAUUCGGAAAGCACGUUUCGUGCUCGCACAUCCGCCGUGUUUCGAUGGCCAUUAGCUGGUAGUUUUGGCU-------GCAGUCGCAAUCGCCG
.((((....))))....((....(((((((.((((.((((((...)))))).((((.......)))))))))))))))...)).((..(((.((((.-------...)))).)))..)). ( -37.30)
>DroSec_CAF1 8443 120 - 1
UUGGUUUUGGCCAUUUCGCCAUUUGGCCAUUCGGAAAGCACGUUUCGUGCUCGCACAUCCGCCGCGUUUGGAUGGCCCAUUGCUGGUAGUUUUGGCUGCAGGCUGCAGUUGCAGUCGCCG
..(((...(((((..(..(((...(((((((((((.((((((...))))))(((.........))))))))))))))......)))..)...)))))...((((((....))))))))). ( -46.90)
>DroSim_CAF1 5638 120 - 1
UUGGUUUUGGCCAUUUCGCCAUUUGGCCAUUCGGAAAGCACGUUUCGUGCUCGCACAUCCGCCGCGUUUGGAUGGCCCAUUGCUGGUAGUUUUGGCUGCAGGCUGCAGUUGCAGUCGCCG
..(((...(((((..(..(((...(((((((((((.((((((...))))))(((.........))))))))))))))......)))..)...)))))...((((((....))))))))). ( -46.90)
>DroEre_CAF1 10141 95 - 1
AUGGUUUUGGCAAUUUCGCCAUUUGGCCAUUCGGAAAGCACGUUUCGUGCUCGCACAUCCGCCGCGUUUGAAUGACCAUUUGUUGGUAGUU-------------------------GCCG
........((((((((((.((..(((.((((((((.((((((...))))))(((.........))))))))))).)))..)).))).))))-------------------------))). ( -32.80)
>DroYak_CAF1 8901 112 - 1
G-GGUUUUGGCAAUUUCGCCAUUUGGCCAUUCGGAAAGCACGUUUAGUGCUCGCACAUCCGCCGCGCUCAGAUGGCCAUUUGUUGGUAGUUUUGGAU-------GCGGUUGCAGUCGUUG
.-((((.((((......))))...))))...(((..(((((.....))))).(((.....((((((..((((..((((.....))))...))))..)-------))))))))..)))... ( -38.90)
>consensus
UUGGUUUUGGCCAUUUCGCCAUUUGGCCAUUCGGAAAGCACGUUUCGUGCUCGCACAUCCGCCGCGUUUGGAUGGCCAUUUGCUGGUAGUUUUGGCU_______GCAGUUGCAGUCGCCG
........(((......((((..((((((((((((.(((((.....)))))(((.........))))))))))))))).....)))).................((....))....))). (-27.12 = -27.86 +   0.74)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:44 2006