Locus 1024

Sequence ID X_DroMel_CAF1
Location 2,992,902 – 2,993,001
Length 99
Max. P 0.693819
window1650 window1651

overview

Window 0

Location 2,992,902 – 2,993,001
Length 99
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 78.63
Mean single sequence MFE -19.38
Consensus MFE -14.30
Energy contribution -14.68
Covariance contribution 0.37
Combinations/Pair 1.06
Mean z-score -1.56
Structure conservation index 0.74
SVM decision value 0.23
SVM RNA-class probability 0.643087
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2992902 99 + 22224390
CUCUAGGCACUCUUUCCUUUGUGUUUUCUCACUGCGCUAUUUGCUCGCUAGUAGUGAGUGGCCAACUUCCUU--------UCCAGCUUUGGAAGCGAACUCUCCUCC
.....(((((((........(((......)))...((((((.(....).)))))))))).)))...(((.((--------(((......))))).)))......... ( -21.80)
>DroSec_CAF1 370085 86 + 1
-----AGCACUCUUUCCUUUGUGUUUUCUCACUGCGCUAUUUGCUCGCCA---GUGAGUGGCUAACUUCCUU--------UCCAGCUUUGGAAGCGAACU-----CC
-----(((((..........)))))..(((((((.((.........))))---)))))........(((.((--------(((......))))).)))..-----.. ( -20.00)
>DroSim_CAF1 335300 86 + 1
-----AGCACUCUUUCCUUUGUGUUUUCUCACUGCGCUAUUUGCUCGCCA---GUGAGUGGCCAACUUCCUU--------UCCAGCUUUGGAAGCGAACU-----CC
-----.((..........(((.(((..(((((((.((.........))))---))))).))))))......(--------(((......)))))).....-----.. ( -20.70)
>DroYak_CAF1 382517 89 + 1
CUU----UACUUUUU-UUUUUUAUUUUUUUACUGCGCUAUUUGCUCUG-------GAGUGGCCAACUUCCU-UCCAACUUUCCAGCUUUGGAAGCGAACU-----CC
...----........-................((.(((((((......-------)))))))))..(((((-(((((..........))))))).)))..-----.. ( -15.00)
>consensus
_____AGCACUCUUUCCUUUGUGUUUUCUCACUGCGCUAUUUGCUCGCCA___GUGAGUGGCCAACUUCCUU________UCCAGCUUUGGAAGCGAACU_____CC
....................(((......)))..((((..(..(((((.....)))))..)...................(((......)))))))........... (-14.30 = -14.68 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 2,992,902 – 2,993,001
Length 99
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 78.63
Mean single sequence MFE -22.05
Consensus MFE -14.15
Energy contribution -14.33
Covariance contribution 0.19
Combinations/Pair 1.10
Mean z-score -1.78
Structure conservation index 0.64
SVM decision value 0.34
SVM RNA-class probability 0.693819
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2992902 99 - 22224390
GGAGGAGAGUUCGCUUCCAAAGCUGGA--------AAGGAAGUUGGCCACUCACUACUAGCGAGCAAAUAGCGCAGUGAGAAAACACAAAGGAAAGAGUGCCUAGAG
(((((.(....).)))))..((((...--------.....))))(((.((((.......(((.........))).(((......)))........)))))))..... ( -22.90)
>DroSec_CAF1 370085 86 - 1
GG-----AGUUCGCUUCCAAAGCUGGA--------AAGGAAGUUAGCCACUCAC---UGGCGAGCAAAUAGCGCAGUGAGAAAACACAAAGGAAAGAGUGCU-----
((-----..(((..((((...(((((.--------.......)))))..(((((---((((.........)).)))))))..........)))).)))..))----- ( -23.00)
>DroSim_CAF1 335300 86 - 1
GG-----AGUUCGCUUCCAAAGCUGGA--------AAGGAAGUUGGCCACUCAC---UGGCGAGCAAAUAGCGCAGUGAGAAAACACAAAGGAAAGAGUGCU-----
((-----..(((..((((...((..(.--------.......)..))..(((((---((((.........)).)))))))..........)))).)))..))----- ( -22.90)
>DroYak_CAF1 382517 89 - 1
GG-----AGUUCGCUUCCAAAGCUGGAAAGUUGGA-AGGAAGUUGGCCACUC-------CAGAGCAAAUAGCGCAGUAAAAAAAUAAAAAA-AAAAAGUA----AAG
((-----(((((((((((..((((....))))...-.))))).)))..))))-------).(.((.....)).).................-........----... ( -19.40)
>consensus
GG_____AGUUCGCUUCCAAAGCUGGA________AAGGAAGUUGGCCACUCAC___UGGCGAGCAAAUAGCGCAGUGAGAAAACACAAAGGAAAGAGUGCU_____
........(((.((((((...................)))))).)))(((((.........(.((.....)).).(((......)))........)))))....... (-14.15 = -14.33 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:32 2006