Locus 1062

Sequence ID 3R_DroMel_CAF1
Location 3,285,798 – 3,285,934
Length 136
Max. P 0.567814
window1717 window1718

overview

Window 7

Location 3,285,798 – 3,285,896
Length 98
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 97.03
Mean single sequence MFE -18.98
Consensus MFE -18.90
Energy contribution -18.74
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.03
Structure conservation index 1.00
SVM decision value -0.03
SVM RNA-class probability 0.516503
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3285798 98 - 27905053
UUUAAUUUUAUUUUCUGUCAUUGUUGCCGGCGUUGCUGCACAGACAGAUACUAAUUUAGUUGAAAGCAAAAGCAAAAUUUCAUUAGCAGUGAAAACGU
(((((((..(((.((((((..(((.((.(((...))))))))))))))....)))..))))))).((....))....((((((.....)))))).... ( -19.80)
>DroSec_CAF1 38879 92 - 1
UUUAAUUUUAUUUUCUGUCAUUGUUGCCGGCGUUGCUGCACAGACAGAUACUAAUUUAGUUGAAAG------CAAAAUUUCAUUAGCAGUGAAAACGU
(((((((..(((.((((((..(((.((.(((...))))))))))))))....)))..)))))))..------.....((((((.....)))))).... ( -18.60)
>DroSim_CAF1 40072 92 - 1
UUUAAUUUUAUUUUCUGUCAUUGUUGCCGGCGUUGCUGCACAGACAGAUACUAAUUUAGUUGAAAG------CAAAAUUUCAUUAGCAGUGAAAACGU
(((((((..(((.((((((..(((.((.(((...))))))))))))))....)))..)))))))..------.....((((((.....)))))).... ( -18.60)
>DroEre_CAF1 40451 92 - 1
UUUAAUUUUAUUUUCUGUCAUUGUUGCCGGCGUUGCUGCACAGACAGAUACUAAUUUAGUUGAAAG------CAAAAUUUCAUUAGCAGUGAAAACGU
(((((((..(((.((((((..(((.((.(((...))))))))))))))....)))..)))))))..------.....((((((.....)))))).... ( -18.60)
>DroYak_CAF1 58259 92 - 1
UUUAAUUUUAUUUUCUGUCAUUGUUGCCAGCGUUGCUGCACAGACAGAUACUAAUUUAGUUGAAAG------CAAAAUUUCAUUAGCAGUGAAAACGU
(((((((..(((.((((((..(((.((.(((...))))))))))))))....)))..)))))))..------.....((((((.....)))))).... ( -19.30)
>consensus
UUUAAUUUUAUUUUCUGUCAUUGUUGCCGGCGUUGCUGCACAGACAGAUACUAAUUUAGUUGAAAG______CAAAAUUUCAUUAGCAGUGAAAACGU
(((((((..(((.((((((..(((.((.(((...))))))))))))))....)))..))))))).............((((((.....)))))).... (-18.90 = -18.74 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,285,838 – 3,285,934
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 99.17
Mean single sequence MFE -16.94
Consensus MFE -16.22
Energy contribution -16.06
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -1.25
Structure conservation index 0.96
SVM decision value 0.07
SVM RNA-class probability 0.567814
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3285838 96 + 27905053
UAAAUUAGUAUCUGUCUGUGCAGCAACGCCGGCAACAAUGACAGAAAAUAAAAUUAAAUAAUGCAAGCACUUUUAGGUUAAUUAAACUUGAAUAGC
..........((((((..(((.((...))..))).....)))))).....................((...((((((((.....))))))))..)) ( -16.00)
>DroSec_CAF1 38913 96 + 1
UAAAUUAGUAUCUGUCUGUGCAGCAACGCCGGCAACAAUGACAGAAAAUAAAAUUAAAUAAUGCAAGCACUUUUAGGUUAAUUAAACUUGAAUAGC
..........((((((..(((.((...))..))).....)))))).....................((...((((((((.....))))))))..)) ( -16.00)
>DroSim_CAF1 40106 96 + 1
UAAAUUAGUAUCUGUCUGUGCAGCAACGCCGGCAACAAUGACAGAAAAUAAAAUUAAAUAAUGCAAGCACUUUUAGGUUAAUUAAACUUGAAUAGC
..........((((((..(((.((...))..))).....)))))).....................((...((((((((.....))))))))..)) ( -16.00)
>DroEre_CAF1 40485 96 + 1
UAAAUUAGUAUCUGUCUGUGCAGCAACGCCGGCAACAAUGACAGAAAAUAAAAUUAAAUAAUGCAAGCACUUUUAGGUUAAUUAAACCUGAAUAGC
..........((((((..(((.((...))..))).....)))))).....................((...((((((((.....))))))))..)) ( -18.70)
>DroYak_CAF1 58293 96 + 1
UAAAUUAGUAUCUGUCUGUGCAGCAACGCUGGCAACAAUGACAGAAAAUAAAAUUAAAUAAUGCAAGCACUUUUAGGUUAAUUAAACUUGAAUAGC
..........((((((..((((((...))).))).....)))))).....................((...((((((((.....))))))))..)) ( -18.00)
>consensus
UAAAUUAGUAUCUGUCUGUGCAGCAACGCCGGCAACAAUGACAGAAAAUAAAAUUAAAUAAUGCAAGCACUUUUAGGUUAAUUAAACUUGAAUAGC
..........((((((..(((.((...))..))).....)))))).....................((...((((((((.....))))))))..)) (-16.22 = -16.06 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:35 2006