Locus 3856

Sequence ID 3L_DroMel_CAF1
Location 11,165,698 – 11,165,795
Length 97
Max. P 0.999942
window6003 window6004

overview

Window 3

Location 11,165,698 – 11,165,795
Length 97
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 94.64
Mean single sequence MFE -31.50
Consensus MFE -29.48
Energy contribution -30.08
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.53
Structure conservation index 0.94
SVM decision value 4.41
SVM RNA-class probability 0.999891
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11165698 97 + 23771897
GGGGAAAAAUGGAUGGAAAAUGGGGGAAAUCACAUGAGUUGGCUGAAAACGAA-AAAGUAGCCGCAGAGGCGCCGGCACUUGGCGCCGGAUUUCCUCG
......................(((((((((......((.(((((........-....)))))))...(((((((.....))))))).))))))))). ( -32.30)
>DroSec_CAF1 26106 97 + 1
GGGGGAAAAUGGAUGGAAAAUGGGGGAAAACACAUGAGUUGGCUGAAAACGAA-AAAGUAGCCGCAGAGGCGCCGGCACUUGGCGCCGGAUUUCCUCG
.....................(((((((..(......((.(((((........-....)))))))...(((((((.....))))))))..))))))). ( -28.50)
>DroSim_CAF1 26850 95 + 1
-GGGGAAAAUGGAUGGA-AAUGGGGGAAAACACAUGAGUUGGCUGAAAACGAA-AAAGUAGCCGCAGAGGCGCCGGCACUUGGCGCCGGAUUUCCUCG
-................-...(((((((..(......((.(((((........-....)))))))...(((((((.....))))))))..))))))). ( -28.50)
>DroEre_CAF1 27469 97 + 1
-GGGGAAAGCGGAUGGAAAAUGUGGGAAAUCACAUGAGUUGGCUGAAAAGGAAAAAAGUAGCCGCAGAGGCGCCGGCACUUGGCGCCGGAUUUCCUCA
-(((((((((((.......((((((....)))))).......((....))...........))))...(((((((.....)))))))...))))))). ( -35.70)
>DroYak_CAF1 27844 96 + 1
-GGGGAAAAUGGUUGGAAAAUGGGGGAAAUCACAUGAGUUGGCUGAAAAGGAA-AAAGUAGCCGCAGAGGCGCCGGCACUUGGCGCCGGAUUUCCUCA
-..........(((....))).(((((((((......((.(((((........-....)))))))...(((((((.....))))))).))))))))). ( -32.50)
>consensus
_GGGGAAAAUGGAUGGAAAAUGGGGGAAAUCACAUGAGUUGGCUGAAAACGAA_AAAGUAGCCGCAGAGGCGCCGGCACUUGGCGCCGGAUUUCCUCG
......................(((((((((......((.(((((.............)))))))...(((((((.....))))))).))))))))). (-29.48 = -30.08 +   0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,165,698 – 11,165,795
Length 97
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 94.64
Mean single sequence MFE -24.90
Consensus MFE -23.86
Energy contribution -24.26
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.96
SVM decision value 4.71
SVM RNA-class probability 0.999942
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11165698 97 - 23771897
CGAGGAAAUCCGGCGCCAAGUGCCGGCGCCUCUGCGGCUACUUU-UUCGUUUUCAGCCAACUCAUGUGAUUUCCCCCAUUUUCCAUCCAUUUUUCCCC
...((((((((((((((.......)))))).....((((((...-...))....)))).......).)))))))........................ ( -25.90)
>DroSec_CAF1 26106 97 - 1
CGAGGAAAUCCGGCGCCAAGUGCCGGCGCCUCUGCGGCUACUUU-UUCGUUUUCAGCCAACUCAUGUGUUUUCCCCCAUUUUCCAUCCAUUUUCCCCC
.((((....(((((((...)))))))..))))...((((((...-...))....))))........................................ ( -22.40)
>DroSim_CAF1 26850 95 - 1
CGAGGAAAUCCGGCGCCAAGUGCCGGCGCCUCUGCGGCUACUUU-UUCGUUUUCAGCCAACUCAUGUGUUUUCCCCCAUU-UCCAUCCAUUUUCCCC-
...((((((..((((((.......)))))).....((((((...-...))....))))...................)))-))).............- ( -23.10)
>DroEre_CAF1 27469 97 - 1
UGAGGAAAUCCGGCGCCAAGUGCCGGCGCCUCUGCGGCUACUUUUUUCCUUUUCAGCCAACUCAUGUGAUUUCCCACAUUUUCCAUCCGCUUUCCCC-
.((((....(((((((...)))))))..)))).((((((...............)))).....(((((......))))).........)).......- ( -27.36)
>DroYak_CAF1 27844 96 - 1
UGAGGAAAUCCGGCGCCAAGUGCCGGCGCCUCUGCGGCUACUUU-UUCCUUUUCAGCCAACUCAUGUGAUUUCCCCCAUUUUCCAACCAUUUUCCCC-
...((((((((((((((.......)))))).....((((.....-.........)))).......).))))))).......................- ( -25.74)
>consensus
CGAGGAAAUCCGGCGCCAAGUGCCGGCGCCUCUGCGGCUACUUU_UUCGUUUUCAGCCAACUCAUGUGAUUUCCCCCAUUUUCCAUCCAUUUUCCCC_
...((((((((((((((.......)))))).....((((...............)))).......).)))))))........................ (-23.86 = -24.26 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:27 2006