Locus 78

Sequence ID 2R_DroMel_CAF1
Location 1,331,240 – 1,331,428
Length 188
Max. P 0.871958
window157 window158 window159 window160

overview

Window 7

Location 1,331,240 – 1,331,360
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.06
Mean single sequence MFE -22.60
Consensus MFE -22.44
Energy contribution -22.25
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -1.66
Structure conservation index 0.99
SVM decision value 0.23
SVM RNA-class probability 0.643393
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1331240 120 + 20766785
CCUUUCCUGCAGCAGCACAUGAAAAUGUUUAAAUAUUUAUGAAAUUAUGCUAAAGUUUCAACAAGUCAUAAAUCUCUGUUGAUGUUUGACUUUUUAUGCAAAAUGUAUUUCAUUUGCAUA
......((..((((...((((((.((......)).))))))......))))..)).......((((((...(((......)))...))))))..((((((((.((.....)))))))))) ( -22.10)
>DroSec_CAF1 49767 120 + 1
CCUUUCCUGCAGCAGCACAUGAAAAUGUUUAAAUAUUUAUGAAAUUAUGCUAAAGUUUCAACAAGUCAUAAAUCUCUGUUGAUGUUUGACUUUUUAUGCAAAAUGUAUUUCAUUUGCAUA
......((..((((...((((((.((......)).))))))......))))..)).......((((((...(((......)))...))))))..((((((((.((.....)))))))))) ( -22.10)
>DroEre_CAF1 31423 120 + 1
CCUUUUCUGUAGCAGCACAUGAAAAUGUUUAAAUAUUUAUGAAAUUAUGCUAAAGUUUCAACAAGUCAUAAAUCUCUGUUGAUGUUUGACUUUUUAUGCAAAAUGUAUUUCAUUUGCAUA
......((.(((((...((((((.((......)).))))))......))))).)).......((((((...(((......)))...))))))..((((((((.((.....)))))))))) ( -23.20)
>DroYak_CAF1 16741 120 + 1
CCUUUUUUGUAGCAGCACAUGAAAAUAUUUAAAUAUUUAUGAAAUUAUGCUAAAGUUUCAACAAGUCAUAAAUCUCUGUUGAUGUUUGACUUUUUAUGCAAAAUGUAUUUCAUUUGCAUA
..............(((.((((((((((((.........(((((((.......)))))))..((((((...(((......)))...))))))........)))))).)))))).)))... ( -23.00)
>consensus
CCUUUCCUGCAGCAGCACAUGAAAAUGUUUAAAUAUUUAUGAAAUUAUGCUAAAGUUUCAACAAGUCAUAAAUCUCUGUUGAUGUUUGACUUUUUAUGCAAAAUGUAUUUCAUUUGCAUA
..............(((.((((((((((((.........(((((((.......)))))))..((((((...(((......)))...))))))........)))))).)))))).)))... (-22.44 = -22.25 +  -0.19)

alignment

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secondary structure

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Window 8

Location 1,331,280 – 1,331,400
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.75
Mean single sequence MFE -25.37
Consensus MFE -25.19
Energy contribution -25.19
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.99
SVM decision value 0.44
SVM RNA-class probability 0.737994
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1331280 120 + 20766785
GAAAUUAUGCUAAAGUUUCAACAAGUCAUAAAUCUCUGUUGAUGUUUGACUUUUUAUGCAAAAUGUAUUUCAUUUGCAUAAAAAUGGCUGACAAAAUAUUUUCCAAGCCGAUAUUCAUGG
((((((.......))))))...((((((...(((......)))...))))))((((((((((.((.....))))))))))))..(((((................))))).......... ( -25.19)
>DroSec_CAF1 49807 120 + 1
GAAAUUAUGCUAAAGUUUCAACAAGUCAUAAAUCUCUGUUGAUGUUUGACUUUUUAUGCAAAAUGUAUUUCAUUUGCAUAAAAAUGGCUGACAAAAUAUUUUCCAAGCCGAUAUUCAUGG
((((((.......))))))...((((((...(((......)))...))))))((((((((((.((.....))))))))))))..(((((................))))).......... ( -25.19)
>DroEre_CAF1 31463 120 + 1
GAAAUUAUGCUAAAGUUUCAACAAGUCAUAAAUCUCUGUUGAUGUUUGACUUUUUAUGCAAAAUGUAUUUCAUUUGCAUAAAAAUGGCUGACAAAAUAUUAUCCAAGCCGAUGUUCAGGG
((((((.......))))))((((.((((...(((......)))...))))((((((((((((.((.....))))))))))))))(((((................))))).))))..... ( -25.89)
>DroYak_CAF1 16781 120 + 1
GAAAUUAUGCUAAAGUUUCAACAAGUCAUAAAUCUCUGUUGAUGUUUGACUUUUUAUGCAAAAUGUAUUUCAUUUGCAUAAAAAUGGCUGACAAAAUAUUUUCCAAGCCGAUAUUCAUGG
((((((.......))))))...((((((...(((......)))...))))))((((((((((.((.....))))))))))))..(((((................))))).......... ( -25.19)
>consensus
GAAAUUAUGCUAAAGUUUCAACAAGUCAUAAAUCUCUGUUGAUGUUUGACUUUUUAUGCAAAAUGUAUUUCAUUUGCAUAAAAAUGGCUGACAAAAUAUUUUCCAAGCCGAUAUUCAUGG
((((((.......))))))...((((((...(((......)))...))))))((((((((((.((.....))))))))))))..(((((................))))).......... (-25.19 = -25.19 +  -0.00)

alignment

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secondary structure

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Window 9

Location 1,331,280 – 1,331,400
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.75
Mean single sequence MFE -26.32
Consensus MFE -24.02
Energy contribution -24.77
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.70
Structure conservation index 0.91
SVM decision value 0.84
SVM RNA-class probability 0.864879
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1331280 120 - 20766785
CCAUGAAUAUCGGCUUGGAAAAUAUUUUGUCAGCCAUUUUUAUGCAAAUGAAAUACAUUUUGCAUAAAAAGUCAAACAUCAACAGAGAUUUAUGACUUGUUGAAACUUUAGCAUAAUUUC
.(((((((.((((((.(.(((....))).).)))).((((((((((((((.....)).))))))))))))..............)).)))))))...((((((....))))))....... ( -26.30)
>DroSec_CAF1 49807 120 - 1
CCAUGAAUAUCGGCUUGGAAAAUAUUUUGUCAGCCAUUUUUAUGCAAAUGAAAUACAUUUUGCAUAAAAAGUCAAACAUCAACAGAGAUUUAUGACUUGUUGAAACUUUAGCAUAAUUUC
.(((((((.((((((.(.(((....))).).)))).((((((((((((((.....)).))))))))))))..............)).)))))))...((((((....))))))....... ( -26.30)
>DroEre_CAF1 31463 120 - 1
CCCUGAACAUCGGCUUGGAUAAUAUUUUGUCAGCCAUUUUUAUGCAAAUGAAAUACAUUUUGCAUAAAAAGUCAAACAUCAACAGAGAUUUAUGACUUGUUGAAACUUUAGCAUAAUUUC
...........((((..(((((....))))))))).((((((((((((((.....)).))))))))))))((((.(.(((......))).).)))).((((((....))))))....... ( -26.40)
>DroYak_CAF1 16781 120 - 1
CCAUGAAUAUCGGCUUGGAAAAUAUUUUGUCAGCCAUUUUUAUGCAAAUGAAAUACAUUUUGCAUAAAAAGUCAAACAUCAACAGAGAUUUAUGACUUGUUGAAACUUUAGCAUAAUUUC
.(((((((.((((((.(.(((....))).).)))).((((((((((((((.....)).))))))))))))..............)).)))))))...((((((....))))))....... ( -26.30)
>consensus
CCAUGAAUAUCGGCUUGGAAAAUAUUUUGUCAGCCAUUUUUAUGCAAAUGAAAUACAUUUUGCAUAAAAAGUCAAACAUCAACAGAGAUUUAUGACUUGUUGAAACUUUAGCAUAAUUUC
.(((((((.((((((.(.(((....))).).)))).((((((((((((((.....)).))))))))))))..............)).)))))))...((((((....))))))....... (-24.02 = -24.77 +   0.75)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,331,320 – 1,331,428
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.54
Mean single sequence MFE -22.45
Consensus MFE -17.45
Energy contribution -17.70
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.78
SVM decision value 0.87
SVM RNA-class probability 0.871958
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1331320 108 - 20766785
C------CC------CCGCCAGCCGCUGCGCGCCCCACUCCCAUGAAUAUCGGCUUGGAAAAUAUUUUGUCAGCCAUUUUUAUGCAAAUGAAAUACAUUUUGCAUAAAAAGUCAAACAUC
.------..------.((((((...))).)))...........(((.....((((.(.(((....))).).)))).((((((((((((((.....)).)))))))))))).)))...... ( -22.40)
>DroSec_CAF1 49847 114 - 1
C------CCCCGCCCCCGCCAGCCGCUGGGCGCCCCACUCCCAUGAAUAUCGGCUUGGAAAAUAUUUUGUCAGCCAUUUUUAUGCAAAUGAAAUACAUUUUGCAUAAAAAGUCAAACAUC
.------...(((((..((.....)).)))))...........(((.....((((.(.(((....))).).)))).((((((((((((((.....)).)))))))))))).)))...... ( -27.50)
>DroEre_CAF1 31503 120 - 1
CCCACGCCCCCUCCCCCACCAGCCGCCGCACGCCCCACUACCCUGAACAUCGGCUUGGAUAAUAUUUUGUCAGCCAUUUUUAUGCAAAUGAAAUACAUUUUGCAUAAAAAGUCAAACAUC
.....................((....))..............(((.....((((..(((((....))))))))).((((((((((((((.....)).)))))))))))).)))...... ( -21.00)
>DroYak_CAF1 16821 108 - 1
C------------CCCCACCAUCCGCCGCACGCCCCAUUCCCAUGAAUAUCGGCUUGGAAAAUAUUUUGUCAGCCAUUUUUAUGCAAAUGAAAUACAUUUUGCAUAAAAAGUCAAACAUC
.------------.....(((...((((.......(((....))).....)))).))).........(((......((((((((((((((.....)).)))))))))))).....))).. ( -18.90)
>consensus
C______CC____CCCCACCAGCCGCCGCACGCCCCACUCCCAUGAAUAUCGGCUUGGAAAAUAUUUUGUCAGCCAUUUUUAUGCAAAUGAAAUACAUUUUGCAUAAAAAGUCAAACAUC
..................((((((((.....))..((......))......))).))).........(((......((((((((((((((.....)).)))))))))))).....))).. (-17.45 = -17.70 +   0.25)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:26:05 2006