Locus 3512

Sequence ID 3R_DroMel_CAF1
Location 9,500,250 – 9,500,405
Length 155
Max. P 0.985229
window5641 window5642

overview

Window 1

Location 9,500,250 – 9,500,366
Length 116
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 97.16
Mean single sequence MFE -38.42
Consensus MFE -34.78
Energy contribution -34.82
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.87
Structure conservation index 0.91
SVM decision value 2.00
SVM RNA-class probability 0.985229
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9500250 116 + 27905053
GGCAAUCGGAUGCUGCGGCGCGGGUGAAAAAAGUUUUAAACUUUUACGCUGCGUGUUGCUUAAAUAGAUUUUCGGGCGAAAGCUCGUCCUGCCAAAUUCGCUCUCUUCGCGGAAAA
((((...((((...((((((((((((..((((((.....)))))).)))).))))))))..............((((....))))))))))))...(((((.......)))))... ( -40.60)
>DroSec_CAF1 130014 116 + 1
GGCAAUCGGAUGCUGCGGCGCGGGUGAUAAAAGUUUUAAACUUUUACGCUGCGUGUUGCUUAAAUAGAUUUUCGGGCGAAAGCUCGUCCUGCCAAAUUCUCUCUCUUCGCGGAAAA
((((...((((...((((((((((((.(((((((.....))))))))))).))))))))..............((((....))))))))))))....................... ( -38.80)
>DroSim_CAF1 120187 116 + 1
GGCAAUCGGAUGCUGCGGCGCGGGUGAAAAAAGUUUUAAACUUUUACGCUGCGUGUUGCUUAAAUAGAUUUUCGGGCGAAAGCUCGUCCUGCCAAAUUCUCUCUCUUCGCGGAAAA
((((...((((...((((((((((((..((((((.....)))))).)))).))))))))..............((((....))))))))))))....................... ( -35.90)
>DroEre_CAF1 137656 116 + 1
GGCAAUCGGAUGCUGCGGCGCGGGUGAAAAAAGUUUGAAACUUUUACGCUGCGUGUUGCUUAAAUAGAUUUUCUGGCGAAAGCUCGUCCUGCCAAAUUCGCUCUCUUCGCGGAAAA
((((...(((((..((((((((((((..((((((.....)))))).)))).))))))))...............(((....))))))))))))...(((((.......)))))... ( -38.30)
>DroYak_CAF1 131437 115 + 1
GGCAAUCGGAUGCUGCGGCGCGGGUGAAAAAAGUUUAAAACUUUUGCGCUGCGUGUUGCUUAAAUAGAUUUUCGGGCGAAAGCUCGUCCUGCCAAAU-CUCUCUCCUCGCGGAAAA
((((...((((...((((((((((((..((((((.....)))))).)))).))))))))..............((((....))))))))))))....-.....(((....)))... ( -38.50)
>consensus
GGCAAUCGGAUGCUGCGGCGCGGGUGAAAAAAGUUUUAAACUUUUACGCUGCGUGUUGCUUAAAUAGAUUUUCGGGCGAAAGCUCGUCCUGCCAAAUUCUCUCUCUUCGCGGAAAA
((((...((((...((((((((((((..((((((.....)))))).)))).))))))))..............((((....))))))))))))..........(((....)))... (-34.78 = -34.82 +   0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,500,290 – 9,500,405
Length 115
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 94.89
Mean single sequence MFE -29.64
Consensus MFE -25.85
Energy contribution -25.73
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -1.28
Structure conservation index 0.87
SVM decision value 0.23
SVM RNA-class probability 0.646475
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9500290 115 + 27905053
CUUUUACGCUGCGUGUUGCUUAAAUAGAUUUUCGGGCGAAAGCUCGUCCUGCCAAAUUCGCUCUCUUCGCGGAAAAU-CUCUCUCACUGUUAAGCUAACAUGUGUCCUAACCGGUU
..........(((((((((((((..((((((((((((....)))).............(((.......)))))))))-)).........)))))).)))))))............. ( -31.00)
>DroSec_CAF1 130054 115 + 1
CUUUUACGCUGCGUGUUGCUUAAAUAGAUUUUCGGGCGAAAGCUCGUCCUGCCAAAUUCUCUCUCUUCGCGGAAAAU-CUCUCUCGCUGUUAAGCUAACAUGUGUCCUAACCGGUU
..........(((((((((((((..((((((((((((....)))))..((((................)))))))))-)).........)))))).)))))))............. ( -27.49)
>DroSim_CAF1 120227 116 + 1
CUUUUACGCUGCGUGUUGCUUAAAUAGAUUUUCGGGCGAAAGCUCGUCCUGCCAAAUUCUCUCUCUUCGCGGAAAAUCCUCUCUCGCUGUUAAGCUAACAUGUGUCCUAACCGGUU
..........(((((((((((((.........(((((....)))))......................(((((........)).)))..)))))).)))))))............. ( -27.50)
>DroEre_CAF1 137696 115 + 1
CUUUUACGCUGCGUGUUGCUUAAAUAGAUUUUCUGGCGAAAGCUCGUCCUGCCAAAUUCGCUCUCUUCGCGGAAAAU-CACUCUCGCUGUUAAGAUAACAUGCGUCGUAACCGGUU
...(((((.(((((((((((((....(((((((((.(((((((................)))...))))))))))))-)((.......)))))).))))))))).)))))...... ( -31.79)
>DroYak_CAF1 131477 114 + 1
CUUUUGCGCUGCGUGUUGCUUAAAUAGAUUUUCGGGCGAAAGCUCGUCCUGCCAAAU-CUCUCUCCUCGCGGAAAAU-CUCUCUCGCUGUUAAGUUAACAUGCGCUCUAACCGGUU
.......((.(((((((((((((..((((((.(((((....))))).......))))-))........(((((....-...)).)))..))))).))))))))))........... ( -30.40)
>consensus
CUUUUACGCUGCGUGUUGCUUAAAUAGAUUUUCGGGCGAAAGCUCGUCCUGCCAAAUUCUCUCUCUUCGCGGAAAAU_CUCUCUCGCUGUUAAGCUAACAUGUGUCCUAACCGGUU
.......((.(((((((((((((.(((.....(((((....)))))..((((................))))..............))))))))).)))))))))........... (-25.85 = -25.73 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:57 2006