Locus 4315

Sequence ID 3L_DroMel_CAF1
Location 12,687,251 – 12,687,359
Length 108
Max. P 0.913445
window6674 window6675

overview

Window 4

Location 12,687,251 – 12,687,359
Length 108
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 85.20
Mean single sequence MFE -26.03
Consensus MFE -17.96
Energy contribution -18.65
Covariance contribution 0.69
Combinations/Pair 1.12
Mean z-score -1.44
Structure conservation index 0.69
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12687251 108 + 23771897
--------UGAAAAAUCAUUCGACUAAGGGGUGAUCAGUAGGUUGGAUACACCCCAAAAAUAUGAAAGGCACAUGCAGAAUAAUUGGUCUCUAGAAUUUUAGCUAGAGAAGUAAUG
--------.........((((......(((((((((.........))).)))))).............((....)).)))).((((.(((((((........)))))))..)))). ( -26.00)
>DroSec_CAF1 50998 116 + 1
UUGGGGCAUGAAAAAUCAUUCGACUAAGGGGUGGCCAGUAGAUUGGAUCCACCCCAAAAAUAUGAAAGGCACAUGCAGAAUAAUUGGUCUCUAGAAUUUUAGCUAUAUAAUUAAUG
....(((((((....))))..(((((((((((((((((....))))..))))))).............((....)).......))))))............)))............ ( -28.30)
>DroSim_CAF1 49788 116 + 1
UUGGGGCAUGAAAAAUCAUUCGACUAAGGGGUGAUCAGUAGGUUGGAUACACCCCAAAAAUAUGAAAGGCACAUGCAGAAUAAUUGGUCUCUAGAAUUUUUGCUAUAUAAAUAAUG
....((((..((((.((....(((((((((((((((.........))).)))))).............((....)).......))))))....)).))))))))............ ( -24.60)
>DroEre_CAF1 51633 114 + 1
UUGGGGCAGGAAAAAUCUUUCGAAUG-GGGGUGACCAGCAGGUAGGACACACCCCAAAAAU-GGAAUUGCACAUGCAGAGUAAUUGGACUAUAGAAUUUUACCUAUAGAAGAAAUG
...............((((((((.((-((((((.((........)).))).))))).....-....((((....)))).....)))).((((((........)))))))))).... ( -25.20)
>consensus
UUGGGGCAUGAAAAAUCAUUCGACUAAGGGGUGACCAGUAGGUUGGAUACACCCCAAAAAUAUGAAAGGCACAUGCAGAAUAAUUGGUCUCUAGAAUUUUAGCUAUAGAAGUAAUG
.........((..(((.((((......((((((.((((....))))...)))))).............((....)).)))).)))..))(((((........)))))......... (-17.96 = -18.65 +   0.69)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,687,251 – 12,687,359
Length 108
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 85.20
Mean single sequence MFE -25.63
Consensus MFE -16.25
Energy contribution -18.12
Covariance contribution 1.88
Combinations/Pair 1.04
Mean z-score -2.81
Structure conservation index 0.63
SVM decision value 1.09
SVM RNA-class probability 0.913445
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12687251 108 - 23771897
CAUUACUUCUCUAGCUAAAAUUCUAGAGACCAAUUAUUCUGCAUGUGCCUUUCAUAUUUUUGGGGUGUAUCCAACCUACUGAUCACCCCUUAGUCGAAUGAUUUUUCA--------
.......(((((((........)))))))..((((((((.(((((((.....)))))....((((((.(((.........)))))))))...)).)))))))).....-------- ( -27.10)
>DroSec_CAF1 50998 116 - 1
CAUUAAUUAUAUAGCUAAAAUUCUAGAGACCAAUUAUUCUGCAUGUGCCUUUCAUAUUUUUGGGGUGGAUCCAAUCUACUGGCCACCCCUUAGUCGAAUGAUUUUUCAUGCCCCAA
.........................((((..((((((((.(((((((.....)))))....(((((((..(((......))))))))))...)).))))))))))))......... ( -26.60)
>DroSim_CAF1 49788 116 - 1
CAUUAUUUAUAUAGCAAAAAUUCUAGAGACCAAUUAUUCUGCAUGUGCCUUUCAUAUUUUUGGGGUGUAUCCAACCUACUGAUCACCCCUUAGUCGAAUGAUUUUUCAUGCCCCAA
.........................((((..((((((((.(((((((.....)))))....((((((.(((.........)))))))))...)).))))))))))))......... ( -22.10)
>DroEre_CAF1 51633 114 - 1
CAUUUCUUCUAUAGGUAAAAUUCUAUAGUCCAAUUACUCUGCAUGUGCAAUUCC-AUUUUUGGGGUGUGUCCUACCUGCUGGUCACCCC-CAUUCGAAAGAUUUUUCCUGCCCCAA
........(((((((......)))))))...........(((....))).....-.....(((((.(((.((........)).))))))-)).((....))............... ( -26.70)
>consensus
CAUUACUUAUAUAGCUAAAAUUCUAGAGACCAAUUAUUCUGCAUGUGCCUUUCAUAUUUUUGGGGUGUAUCCAACCUACUGAUCACCCCUUAGUCGAAUGAUUUUUCAUGCCCCAA
.........(((((........)))))((..((((((((.((....)).............((((((...(((......))).))))))......))))))))..))......... (-16.25 = -18.12 +   1.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:20 2006