Locus 5012

Sequence ID 3R_DroMel_CAF1
Location 13,211,538 – 13,211,661
Length 123
Max. P 0.755405
window8193 window8194

overview

Window 3

Location 13,211,538 – 13,211,643
Length 105
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 84.04
Mean single sequence MFE -33.20
Consensus MFE -22.80
Energy contribution -23.43
Covariance contribution 0.63
Combinations/Pair 1.17
Mean z-score -1.87
Structure conservation index 0.69
SVM decision value 0.49
SVM RNA-class probability 0.755405
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13211538 105 - 27905053
UUCCAAGCAGUGUUGUAUUCGAAUCAGCUGAGUAUAACGAAUGGGAAAUGUGUUGAAAAGGU-UUAAGUCGUGGCCUUUCGCCAGCUGGUCACACCAAUUUGCUGC
......(((((((((((((((.......))))))))))((((.((...((((..((((.(((-(........))))))))(((....))))))))).))))))))) ( -27.40)
>DroSec_CAF1 239433 105 - 1
UUCCAAGCAGUGUUGUAUUCGGAUCAGCUGAGUAUAACGGUUGGGUAAGGUGCUGAAAAGGU-UUAAUUCGUGGCCUUUUGCCAGCUGGUCACACCAAUUUGCUGC
......((((((((((((((((.....)))))))))))((((((((.....(((((((((((-(........))))))))..)))).....)).)))))).))))) ( -36.10)
>DroSim_CAF1 225826 105 - 1
UUCCAAGCAGUGUUGUAUUCGGAUCAGCUGAGUAUAACGGUUGGGUAAUGUGCUGAGAAGGU-UUGAUUCGUGGGCUUUUGCCAGCUGGUCACACCAAUUUGCUGC
......((((((((((((((((.....)))))))))))((((((((.((..((((.((((((-..(.....)..))))))..))))..)).)).)))))).))))) ( -36.10)
>DroYak_CAF1 240454 94 - 1
UUGCAACCAGUGUUGUAUUCGGAUCAGCUGUGUGUAAUGGCUGG------------AAAGGUGGUAAUUCAUGGCCUUUUGCCAGCUGGUCACACGAAUCUGCUGG
.((((((....)))))).......((((((((((...(((((((------------.(((((.((.....)).)))))...)))))))..)))))).....)))). ( -33.20)
>consensus
UUCCAAGCAGUGUUGUAUUCGGAUCAGCUGAGUAUAACGGUUGGGUAAUGUGCUGAAAAGGU_UUAAUUCGUGGCCUUUUGCCAGCUGGUCACACCAAUUUGCUGC
......((((((((((((((((.....)))))))))))((((((...............((.......))((((((...........)))))).)))))).))))) (-22.80 = -23.43 +   0.63)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,211,565 – 13,211,661
Length 96
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 82.56
Mean single sequence MFE -27.30
Consensus MFE -17.36
Energy contribution -17.93
Covariance contribution 0.56
Combinations/Pair 1.15
Mean z-score -1.67
Structure conservation index 0.64
SVM decision value -0.00
SVM RNA-class probability 0.533200
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13211565 96 - 27905053
UCGAGGGCUGGAAAGCGAUUCCAAGCAGUGUUGUAUUCGAAUCAGCUGAGUAUAACGAAUGGGAAAUGUGUUGAAAAGGU-UUAAGUCGUGGCCUUU
((((.((((....)))..((((......(((((((((((.......)))))))))))....))))...).))))((((((-(........))))))) ( -25.20)
>DroSec_CAF1 239460 96 - 1
UCGAGGGCUGGAAAGCGAUUCCAAGCAGUGUUGUAUUCGGAUCAGCUGAGUAUAACGGUUGGGUAAGGUGCUGAAAAGGU-UUAAUUCGUGGCCUUU
..(((((((.....((((.(((((.(...(((((((((((.....)))))))))))).))))).......((....))..-.....))))))))))) ( -27.80)
>DroSim_CAF1 225853 96 - 1
UCGAGGGCUGGAAAGCUGUUCCAAGCAGUGUUGUAUUCGGAUCAGCUGAGUAUAACGGUUGGGUAAUGUGCUGAGAAGGU-UUGAUUCGUGGGCUUU
..((.((((....)))).))((((.(...(((((((((((.....)))))))))))).)))).......(((.((((...-....))).).)))... ( -26.30)
>DroYak_CAF1 240481 85 - 1
GCGAGGGCUGGAAAGCUUUUGCAACCAGUGUUGUAUUCGGAUCAGCUGUGUGUAAUGGCUGG------------AAAGGUGGUAAUUCAUGGCCUUU
(((((((((....)))))))))..((((((((((((.(((.....))).))))))).)))))------------((((((.((.....)).)))))) ( -29.90)
>consensus
UCGAGGGCUGGAAAGCGAUUCCAAGCAGUGUUGUAUUCGGAUCAGCUGAGUAUAACGGUUGGGUAAUGUGCUGAAAAGGU_UUAAUUCGUGGCCUUU
..(((((((((((.....))))...(((((((((((((((.....))))))))))).)))).............................))))))) (-17.36 = -17.93 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:16 2006