Locus 5494

Sequence ID 3R_DroMel_CAF1
Location 14,465,193 – 14,465,351
Length 158
Max. P 0.991300
window8966 window8967 window8968

overview

Window 6

Location 14,465,193 – 14,465,311
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.74
Mean single sequence MFE -40.23
Consensus MFE -38.24
Energy contribution -38.13
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.36
Structure conservation index 0.95
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14465193 118 - 27905053
AGUUUUGGCCACUUGGCGCAUGCGUAACUUUUUUGCUGGC--GCUGGGAAGAGCCAGCCAGUUGCAAAAUGCGCAGUCCGACACGACACCAUGCGAAAUAUUCGAGUGUUUUAUUGGCCA
.....((((((....((((((..((((((.....((((((--.((....)).)))))).))))))...))))))..........(((((....(((.....))).)))))....)))))) ( -43.00)
>DroSim_CAF1 23079 120 - 1
AGUUUGGGCCACUUGGCGCAUGCGUAACUUUUUUGCUGGCGCGCUGGGAAGAGUCAGCCAGUUGCAAAAUGCGCAGUCCGACACGACACCAUGCGAAAUAUUCGAAUGUUUUAUUGGCCA
......(((((....((((((..((((((.....((((((...((....)).)))))).))))))...)))))).(((......)))..(((.(((.....))).)))......))))). ( -38.70)
>DroYak_CAF1 24871 116 - 1
AGAUUUGGCCACUUGGCGCAUGCGUAACUU-CUUGCUGGC--GCUGGGAAGAGCCA-CAAGUUGCACAAUGCGCAGUCCGACACGACACCAUGCGAAGUAUUCGAGUGUUUUAUUGGCCG
......(((((....(((((((.((((((.-..((.((((--.((....)).))))-)))))))).).))))))..........(((((....(((.....))).)))))....))))). ( -39.00)
>consensus
AGUUUUGGCCACUUGGCGCAUGCGUAACUUUUUUGCUGGC__GCUGGGAAGAGCCAGCCAGUUGCAAAAUGCGCAGUCCGACACGACACCAUGCGAAAUAUUCGAGUGUUUUAUUGGCCA
......(((((....((((((..((((((.....((((((...((....)).)))))).))))))...)))))).(((......)))..(((.(((.....))).)))......))))). (-38.24 = -38.13 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,465,233 – 14,465,351
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.52
Mean single sequence MFE -44.77
Consensus MFE -32.73
Energy contribution -33.40
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.73
Structure conservation index 0.73
SVM decision value 2.18
SVM RNA-class probability 0.989808
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14465233 118 + 27905053
CGGACUGCGCAUUUUGCAACUGGCUGGCUCUUCCCAGC--GCCAGCAAAAAAGUUACGCAUGCGCCAAGUGGCCAAAACUAUGGCCACCCGAUGGAAAGCCAGCCAGCAGACCGACCGAC
(((.((((((.....))...(((((((((.((((..((--((..((...........))..))))...(((((((......))))))).....))))))))))))))))).)))...... ( -53.50)
>DroSim_CAF1 23119 120 + 1
CGGACUGCGCAUUUUGCAACUGGCUGACUCUUCCCAGCGCGCCAGCAAAAAAGUUACGCAUGCGCCAAGUGGCCCAAACUAUGGCCACCCGAUGGAAAGCCAGACAGCAGACCCACCAAC
.((.((((((.....))..((((((.....((((..((((((.(((......)))..))..))))...((((((........)))))).....))))))))))...)))).))....... ( -40.00)
>DroYak_CAF1 24911 99 + 1
CGGACUGCGCAUUGUGCAACUUG-UGGCUCUUCCCAGC--GCCAGCAAG-AAGUUACGCAUGCGCCAAGUGGCCAAAUCUAUGGCCACCCGAUGGAAAUCCAG-----------------
(((...(((((((((((..((((-((((.((....)).--)))).))))-..).)))).))))))...(((((((......)))))))))).(((....))).----------------- ( -40.80)
>consensus
CGGACUGCGCAUUUUGCAACUGGCUGGCUCUUCCCAGC__GCCAGCAAAAAAGUUACGCAUGCGCCAAGUGGCCAAAACUAUGGCCACCCGAUGGAAAGCCAG_CAGCAGACC_ACC_AC
(((...(((((...(((((((.((((((............)))))).....))))..))))))))...((((((........))))))))).(((....))).................. (-32.73 = -33.40 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,465,233 – 14,465,351
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.52
Mean single sequence MFE -52.57
Consensus MFE -41.66
Energy contribution -44.67
Covariance contribution 3.00
Combinations/Pair 1.05
Mean z-score -3.61
Structure conservation index 0.79
SVM decision value 2.26
SVM RNA-class probability 0.991300
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14465233 118 - 27905053
GUCGGUCGGUCUGCUGGCUGGCUUUCCAUCGGGUGGCCAUAGUUUUGGCCACUUGGCGCAUGCGUAACUUUUUUGCUGGC--GCUGGGAAGAGCCAGCCAGUUGCAAAAUGCGCAGUCCG
......(((.(((((((((((((((((..((((((((((......))))))))))((((..(((.........)))..))--))..)).)))))))))))...((.....)))))).))) ( -61.50)
>DroSim_CAF1 23119 120 - 1
GUUGGUGGGUCUGCUGUCUGGCUUUCCAUCGGGUGGCCAUAGUUUGGGCCACUUGGCGCAUGCGUAACUUUUUUGCUGGCGCGCUGGGAAGAGUCAGCCAGUUGCAAAAUGCGCAGUCCG
.......((.((((((.((((((((((..(((((((((........)))))))))((((..(((.........)))..))))....)).)))))))).))...((.....)))))).)). ( -49.40)
>DroYak_CAF1 24911 99 - 1
-----------------CUGGAUUUCCAUCGGGUGGCCAUAGAUUUGGCCACUUGGCGCAUGCGUAACUU-CUUGCUGGC--GCUGGGAAGAGCCA-CAAGUUGCACAAUGCGCAGUCCG
-----------------..(((((.....((((((((((......))))))))))(((((((.((((((.-..((.((((--.((....)).))))-)))))))).).))))))))))). ( -46.80)
>consensus
GU_GGU_GGUCUGCUG_CUGGCUUUCCAUCGGGUGGCCAUAGUUUUGGCCACUUGGCGCAUGCGUAACUUUUUUGCUGGC__GCUGGGAAGAGCCAGCCAGUUGCAAAAUGCGCAGUCCG
(((((((((....))))))))).......((((((((((......))))))))))((((((..((((((.....((((((...((....)).)))))).))))))...))))))...... (-41.66 = -44.67 +   3.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:34 2006