Locus 4678

Sequence ID 3L_DroMel_CAF1
Location 13,220,323 – 13,220,423
Length 100
Max. P 0.946797
window7368 window7369

overview

Window 8

Location 13,220,323 – 13,220,423
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.67
Mean single sequence MFE -22.54
Consensus MFE -14.11
Energy contribution -15.27
Covariance contribution 1.17
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.63
SVM decision value 0.84
SVM RNA-class probability 0.863581
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13220323 100 + 23771897
GUUUUUG------------UCUCUUUCUGCCUGCGCCAUGCAAUUAAAUGCAUUUGCAUACAUAAUAAAUAAAUAAUGCAGACGCAAAAUUGCAGCAUUAACUUUGCCGCUG--------
.......------------.............(((...(((((((...(((.(((((((................))))))).))).)))))))(((.......))))))..-------- ( -20.29)
>DroSim_CAF1 18824 99 + 1
GUUUUUG------------UCUCUCUCUGCCUGCGCCAUGCAAUUAAAUGCAUUUGCAUACAUAAUAAAUAAAUAAUGCAGACGCAA-AUUGCAGCAUUAACUUUGCCGCUG--------
.......------------.............(((...(((((((...(((.(((((((................))))))).))))-))))))(((.......))))))..-------- ( -20.19)
>DroEre_CAF1 3473 100 + 1
GUUUUUG------------UCUCUUUCUGCCUGCGCCAUGCAAUUAAAUGCAUUUGCAUACAUAAUAAAUAAAUAAUGCAGACGCAAAACUGCAGCAUUAACUUUGCCGCUG--------
.......------------.............(((....((((...(((((.(((((((................))))))).(((....))).)))))....)))))))..-------- ( -17.99)
>DroWil_CAF1 178090 100 + 1
GCUCUCA------------UAUUUUGCAACAUUCGCAUUGCAAUUAAAUGCAUUUGCAUACAUAAUAAAUAAAUAAUGCAGA--------UGCAGCAGUAACUCGGCUGCCACUGCCUCU
((.....------------....((((((........)))))).....(((((((((((................)))))))--------))))(((((......)))))....)).... ( -24.29)
>DroYak_CAF1 13565 100 + 1
GCUGCUG------------UCUCUUUCUGCCUGCGCCAUGCAAUUAAAUGCAUUUGCAUACAUAAUAAAUAAAUAAUGCAGACGCAAAAUUGCAGCAUUAACUUUGCCGCUG--------
((.((..------------.........))..))((..(((((((...(((.(((((((................))))))).))).)))))))(((.......))).))..-------- ( -21.19)
>DroAna_CAF1 101421 111 + 1
AUCCAGGGCAUCCCAGCAAAGUCCUCCCGCC-AUGCCAUGCAAUUAAAUGCAUUUGCAUACAUAAUAAAUAAAUAAUGCAGAUGCAACAUUGCAGCAUUAACUUUGCUGCUG--------
.....(((...)))((((((((.........-((((..((((((....(((((((((((................)))))))))))..))))))))))..))))))))....-------- ( -31.29)
>consensus
GUUUUUG____________UCUCUUUCUGCCUGCGCCAUGCAAUUAAAUGCAUUUGCAUACAUAAUAAAUAAAUAAUGCAGACGCAAAAUUGCAGCAUUAACUUUGCCGCUG________
..................................((..((((((....(((.(((((((................))))))).)))..))))))(((.......))).)).......... (-14.11 = -15.27 +   1.17)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,220,323 – 13,220,423
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.67
Mean single sequence MFE -28.67
Consensus MFE -19.95
Energy contribution -21.45
Covariance contribution 1.50
Combinations/Pair 1.08
Mean z-score -2.43
Structure conservation index 0.70
SVM decision value 1.37
SVM RNA-class probability 0.946797
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13220323 100 - 23771897
--------CAGCGGCAAAGUUAAUGCUGCAAUUUUGCGUCUGCAUUAUUUAUUUAUUAUGUAUGCAAAUGCAUUUAAUUGCAUGGCGCAGGCAGAAAGAGA------------CAAAAAC
--------..((((((.......))))))...(((((((((((((....((.....))...))))).(((((......)))))))))))))..........------------....... ( -26.60)
>DroSim_CAF1 18824 99 - 1
--------CAGCGGCAAAGUUAAUGCUGCAAU-UUGCGUCUGCAUUAUUUAUUUAUUAUGUAUGCAAAUGCAUUUAAUUGCAUGGCGCAGGCAGAGAGAGA------------CAAAAAC
--------..((((((.......))))))..(-((((((((((((....((.....))...))))).(((((......)))))))))))))..........------------....... ( -26.70)
>DroEre_CAF1 3473 100 - 1
--------CAGCGGCAAAGUUAAUGCUGCAGUUUUGCGUCUGCAUUAUUUAUUUAUUAUGUAUGCAAAUGCAUUUAAUUGCAUGGCGCAGGCAGAAAGAGA------------CAAAAAC
--------..((((((.......)))))).(((((...(((((..(((.((.....)).)))(((..(((((......)))))...))).)))))..))))------------)...... ( -28.30)
>DroWil_CAF1 178090 100 - 1
AGAGGCAGUGGCAGCCGAGUUACUGCUGCA--------UCUGCAUUAUUUAUUUAUUAUGUAUGCAAAUGCAUUUAAUUGCAAUGCGAAUGUUGCAAAAUA------------UGAGAGC
...(((((((((......)))))))))(((--------(.(((((....((.....))...))))).))))......(((((((......)))))))....------------....... ( -28.60)
>DroYak_CAF1 13565 100 - 1
--------CAGCGGCAAAGUUAAUGCUGCAAUUUUGCGUCUGCAUUAUUUAUUUAUUAUGUAUGCAAAUGCAUUUAAUUGCAUGGCGCAGGCAGAAAGAGA------------CAGCAGC
--------..((((((.......))))))...(((((((((((((....((.....))...))))).(((((......)))))))))))))..........------------....... ( -26.60)
>DroAna_CAF1 101421 111 - 1
--------CAGCAGCAAAGUUAAUGCUGCAAUGUUGCAUCUGCAUUAUUUAUUUAUUAUGUAUGCAAAUGCAUUUAAUUGCAUGGCAU-GGCGGGAGGACUUUGCUGGGAUGCCCUGGAU
--------...((((((((((.((((((((((..(((((.(((((....((.....))...))))).)))))....)))))..)))))-..(....)))))))))))((....))..... ( -35.20)
>consensus
________CAGCGGCAAAGUUAAUGCUGCAAUUUUGCGUCUGCAUUAUUUAUUUAUUAUGUAUGCAAAUGCAUUUAAUUGCAUGGCGCAGGCAGAAAGAGA____________CAAAAAC
..........((((((.......))))))....((((((((((((....((.....))...))))).(((((......)))))))))))).............................. (-19.95 = -21.45 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:32 2006