Locus 5975

Sequence ID 3L_DroMel_CAF1
Location 15,984,329 – 15,984,505
Length 176
Max. P 0.914087
window9549 window9550

overview

Window 9

Location 15,984,329 – 15,984,425
Length 96
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 85.94
Mean single sequence MFE -18.87
Consensus MFE -18.02
Energy contribution -17.80
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -1.49
Structure conservation index 0.96
SVM decision value 1.09
SVM RNA-class probability 0.914087
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15984329 96 - 23771897
GUCCAGUUCCUGGACCUCCUCGUCUCCUCCCUGCCUUUCCUU-----UUU-----UUCCAGCAUCCCCUCUGUUCUUAAUCAAGAAACGCAUCGGCGGCGUAUCAC
((((((...)))))).....((((.((....(((.((((.((-----..(-----(...((((.......))))...))..)))))).)))..)).))))...... ( -17.80)
>DroEre_CAF1 14308 101 - 1
GUCCAGUUCCUGGACCUCCUCGCCUCCUCCCCCCGUCACCUUCUCCGUUU-----UUCCAGCAUCCCCUCUGUUCUUAAUCAAGAAACGCAGCGGCGGCGUAUCAC
((((((...)))))).....((((......................(((.-----....)))....((.((((((((....))))...)))).)).))))...... ( -20.10)
>DroYak_CAF1 13813 106 - 1
GUCCAGUUCCUGGACCUCCUCGCCUCCUUUCCCCGUCACCUUCUUCACCUUCACCUUCCAGCAUCCCCUCUGUUCUUAAUCAAGAAACGCAGCGGCGGCGUAUCAC
((((((...)))))).....((((.((...............................(((........)))(((((....))))).......)).))))...... ( -18.70)
>consensus
GUCCAGUUCCUGGACCUCCUCGCCUCCUCCCCCCGUCACCUUCU_C_UUU_____UUCCAGCAUCCCCUCUGUUCUUAAUCAAGAAACGCAGCGGCGGCGUAUCAC
((((((...)))))).....((((.((...............................(((........)))(((((....))))).......)).))))...... (-18.02 = -17.80 +  -0.22)

alignment

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secondary structure

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dotplot

Postscript

Window 0

Location 15,984,399 – 15,984,505
Length 106
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 81.17
Mean single sequence MFE -32.52
Consensus MFE -23.81
Energy contribution -25.38
Covariance contribution 1.56
Combinations/Pair 1.06
Mean z-score -1.57
Structure conservation index 0.73
SVM decision value 0.12
SVM RNA-class probability 0.594769
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15984399 106 + 23771897
GAGA----------CGAGGAGGUCCAGGAACUGGACUUGCAUUUAUUUGGCGGCAAGAAAUGCGCAUACCCGUUACCUGACCAGCAAUAGGGUAUGUUGCACUCCACAUGGAGCAA
..((----------((.((((((((((...))))))))((((((.((((....)))))))))).....)))))).........((((((.....)))))).((((....))))... ( -34.00)
>DroSec_CAF1 13549 103 + 1
GAGAGAGGAGAGAG-------------GAACUGGACUUGCAUUUAUUUGGCGGCAAGAAAUGCGCAUACCCGUUACCUCGCCAGCAAUAGGGUAUGUUGCACUCCACAUAAAGAAG
......((((.(((-------------((((.((...(((((((.((((....)))))))))))....)).))).))))....((((((.....)))))).))))........... ( -30.50)
>DroEre_CAF1 14383 104 + 1
GAGG----------CGAGGAGGUCCAGGAACUGGACUUGCAUUUAUUUGGCGGCAAGAAAUGUGCAUACCCGUUAGCUGUCCAGAAAUAGGGUAUGUUGUACUCCACGUGGA--AU
...(----------((.((((((((((...))))))..((((((.((((....))))))))))((((((((.....((....)).....))))))))....)))).)))...--.. ( -35.10)
>DroYak_CAF1 13893 104 + 1
GAGG----------CGAGGAGGUCCAGGAACUGGACUUGCAUUUAUUUGGCGGCAAGAAAUGUACAUACCCGUUACCUGUCCAGAAAUAGGGUAUGUUGUACUCCACAGGGA--AU
....----------...((((((((((...))))))..((((((.((((....))))))))))((((((((.....((....)).....))))))))....)))).......--.. ( -30.50)
>consensus
GAGA__________CGAGGAGGUCCAGGAACUGGACUUGCAUUUAUUUGGCGGCAAGAAAUGCGCAUACCCGUUACCUGUCCAGAAAUAGGGUAUGUUGCACUCCACAUGGA__AU
(((................((((((((...))))))))((((((.((((....))))))))))((((((((.....((....)).....))))))))....)))............ (-23.81 = -25.38 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:41 2006