Locus 1837

Sequence ID 2R_DroMel_CAF1
Location 6,892,569 – 6,892,683
Length 114
Max. P 0.994850
window3052 window3053

overview

Window 2

Location 6,892,569 – 6,892,683
Length 114
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 93.27
Mean single sequence MFE -58.33
Consensus MFE -53.71
Energy contribution -53.90
Covariance contribution 0.19
Combinations/Pair 1.09
Mean z-score -3.15
Structure conservation index 0.92
SVM decision value 2.52
SVM RNA-class probability 0.994850
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6892569 114 + 20766785
AAGCAGCGGGAGCAGGAGGAGGCCCGAGUUCUCGAGGAGGCGGAGGCCGCCGAAGCGGCUGCUGCAGCCGCAAUCCUUGAGAGCGGCGAAAAGGAUGGUCGCAAGCCUCCAGUC
.....((....))....((((((....((((((((((((((((...)))))...(((((((...)))))))..))))))))))).((((.........))))..)))))).... ( -59.90)
>DroSec_CAF1 8336 114 + 1
AAGCAGCGGGAGCAGGAGGAGGCCCGGAUCCUCGAGGAGGCGGAGGCCGCCGAAGCGGCUGCUGCAGCCGCAAUCCUCGAGAGCGGCGAAAAGGAGGGUCGCAAGCCUCCAGUC
.....((....))....((((((.......(((((((((((((...)))))...(((((((...)))))))..)))))))).(((((..........)))))..)))))).... ( -59.00)
>DroSim_CAF1 12482 114 + 1
AAGCAGCGGGAGCAGGAGGAGGCCCGGGUACUCGAGGAGGCGGAGGCUGCCGAAGCGGCUGCUGCAGCCGCAAUCCUCGAGAGCGGCGAAAAGGAGGGUCGCAAGCCACCAUUC
.....((....))....((.(((.......(((((((((((((...)))))...(((((((...)))))))..)))))))).(((((..........)))))..))).)).... ( -52.10)
>DroEre_CAF1 12944 114 + 1
AAGCAGCGCGAGCAGGAGGAGGCCCGGGUUCUCGAGGAGGCGGAGGCCGCUGAGGCGGCCGCUGCAGCCGCCAUCCUCGAGAGCGGCGAGAAGGAGGGUCGCAAGCCCCCAGUC
.....((....))........(((...((((((((((((((((.((((((....)))))).......))))).)))))))))))))).....((.(((.(....)))))).... ( -62.30)
>consensus
AAGCAGCGGGAGCAGGAGGAGGCCCGGGUUCUCGAGGAGGCGGAGGCCGCCGAAGCGGCUGCUGCAGCCGCAAUCCUCGAGAGCGGCGAAAAGGAGGGUCGCAAGCCUCCAGUC
.....((....))....((((((.......(((((((((((((...)))))...(((((((...)))))))..)))))))).(((((..........)))))..)))))).... (-53.71 = -53.90 +   0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,892,569 – 6,892,683
Length 114
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 93.27
Mean single sequence MFE -49.80
Consensus MFE -46.16
Energy contribution -46.98
Covariance contribution 0.81
Combinations/Pair 1.09
Mean z-score -2.06
Structure conservation index 0.93
SVM decision value 1.51
SVM RNA-class probability 0.960387
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6892569 114 - 20766785
GACUGGAGGCUUGCGACCAUCCUUUUCGCCGCUCUCAAGGAUUGCGGCUGCAGCAGCCGCUUCGGCGGCCUCCGCCUCCUCGAGAACUCGGGCCUCCUCCUGCUCCCGCUGCUU
....((((((((((((.........))))...((((.((((..(((((((...)))))))...(((((...))))))))).))))....))))))))....((.......)).. ( -47.70)
>DroSec_CAF1 8336 114 - 1
GACUGGAGGCUUGCGACCCUCCUUUUCGCCGCUCUCGAGGAUUGCGGCUGCAGCAGCCGCUUCGGCGGCCUCCGCCUCCUCGAGGAUCCGGGCCUCCUCCUGCUCCCGCUGCUU
....((((((((((((.........))))...(((((((((..(((((((...)))))))...(((((...))))))))))))))....))))))))....((.......)).. ( -52.70)
>DroSim_CAF1 12482 114 - 1
GAAUGGUGGCUUGCGACCCUCCUUUUCGCCGCUCUCGAGGAUUGCGGCUGCAGCAGCCGCUUCGGCAGCCUCCGCCUCCUCGAGUACCCGGGCCUCCUCCUGCUCCCGCUGCUU
....((.(((((((((.........)))).(..((((((((..(((((((...)))))))...(((.......)))))))))))..)..))))).))....((.......)).. ( -43.10)
>DroEre_CAF1 12944 114 - 1
GACUGGGGGCUUGCGACCCUCCUUCUCGCCGCUCUCGAGGAUGGCGGCUGCAGCGGCCGCCUCAGCGGCCUCCGCCUCCUCGAGAACCCGGGCCUCCUCCUGCUCGCGCUGCUU
((..((((((....).)))))..))..((.(((((((((((.((((((....))((((((....))))))..)))))))))))))...(((((........))))).)).)).. ( -55.70)
>consensus
GACUGGAGGCUUGCGACCCUCCUUUUCGCCGCUCUCGAGGAUUGCGGCUGCAGCAGCCGCUUCGGCGGCCUCCGCCUCCUCGAGAACCCGGGCCUCCUCCUGCUCCCGCUGCUU
....((((((((((((.........))))...(((((((((..(((((((...)))))))...(((((...))))))))))))))....))))))))....((.......)).. (-46.16 = -46.98 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:26 2006