Locus 1121

Sequence ID 3R_DroMel_CAF1
Location 3,381,239 – 3,381,382
Length 143
Max. P 0.953824
window1836 window1837

overview

Window 6

Location 3,381,239 – 3,381,344
Length 105
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 92.37
Mean single sequence MFE -25.12
Consensus MFE -21.62
Energy contribution -22.38
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.86
SVM decision value 1.44
SVM RNA-class probability 0.953824
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3381239 105 - 27905053
CACAUUU-----AAGUUGGCAAAACAAGCAUGGCAUGCCGCAACAUUUGCAUACCCAAAUGGGCUCACAGCCGCCCAUUCUUUCAUGCCAAAAA-U-AAAACGGCCCUUGUA
......(-----(((..(((..........(((((((..(((.....))).......(((((((........)))))))....)))))))....-.-......))))))).. ( -26.80)
>DroSec_CAF1 9573 107 - 1
CACAUUU-----AAGUUGGCAAAACAUGCAUGGCAAGCCGCAACAUUUGCAUACCCAAAUGGGCUCACAGCGGCCCAUUCUUCCAUGCCAAAAAAUAAAAACGGCCCUUGUA
.(((...-----..(((((((.....))).(((((....(((.....))).......((((((((......))))))))......)))))...........))))...))). ( -25.50)
>DroSim_CAF1 10410 107 - 1
CACAUUU-----AAGUUGGCAAAACAAGCAUCGUAAGCCGCAACAUUUGCAUACCCAAAUGGGCUCACAGCGGCCCAUUCUUCCAUGCCAAAAAAUAAAAACGGCCCUUGUA
......(-----(((..(((.......((..(....)..)).......((((.....((((((((......)))))))).....))))...............))))))).. ( -22.10)
>DroEre_CAF1 9925 110 - 1
CACAUUUAACAUAAGUUGGCAAAACAAGCAUGGCAAGCCGCAACAUUUGCAUACCCAAAUGGGCUCACAGCGGCCCAUUCUUCCAUGCCAAAAA-U-AAAAAGCCCGUUGUA
......((((....(((.....)))..((((((.(((..(((.....))).......((((((((......)))))))))))))))))......-.-.........)))).. ( -26.10)
>consensus
CACAUUU_____AAGUUGGCAAAACAAGCAUGGCAAGCCGCAACAUUUGCAUACCCAAAUGGGCUCACAGCGGCCCAUUCUUCCAUGCCAAAAA_U_AAAACGGCCCUUGUA
...............((((((....(((.((((...(((((..((((((......))))))(.....).))))))))).)))...))))))..................... (-21.62 = -22.38 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 3,381,269 – 3,381,382
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.50
Mean single sequence MFE -30.58
Consensus MFE -24.71
Energy contribution -25.02
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -1.75
Structure conservation index 0.81
SVM decision value 0.57
SVM RNA-class probability 0.786108
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3381269 113 - 27905053
AUAACCUCCCCAUGGCUUCGCUCGAAAGUGGGCUUC--GCCACAUUU-----AAGUUGGCAAAACAAGCAUGGCAUGCCGCAACAUUUGCAUACCCAAAUGGGCUCACAGCCGCCCAUUC
.........(((((.(((.(((((....)))))...--(((((....-----..).)))).....))))))))......(((.....))).......(((((((........))))))). ( -29.10)
>DroSec_CAF1 9605 110 - 1
AUAAUCUUCCCAUGGCUUCGCUCGAAAGUGGGUC-----CCACAUUU-----AAGUUGGCAAAACAUGCAUGGCAAGCCGCAACAUUUGCAUACCCAAAUGGGCUCACAGCGGCCCAUUC
.............(((((.(((.....((((...-----))))....-----......(((.....)))..))))))))(((.....))).......((((((((......)))))))). ( -29.10)
>DroSim_CAF1 10442 110 - 1
AUAAUCUCCCCAUGGCUUCGCUCGAAAGUGGGUC-----CCACAUUU-----AAGUUGGCAAAACAAGCAUCGUAAGCCGCAACAUUUGCAUACCCAAAUGGGCUCACAGCGGCCCAUUC
.............(((((((((..((.((((...-----)))).)).-----.)))..((.......))...).)))))(((.....))).......((((((((......)))))))). ( -27.80)
>DroEre_CAF1 9955 117 - 1
AUAAG---CCCUUGGGUUUGCUCAAAAGUGGCUCCCAUCCCACAUUUAACAUAAGUUGGCAAAACAAGCAUGGCAAGCCGCAACAUUUGCAUACCCAAAUGGGCUCACAGCGGCCCAUUC
.....---....(((((.(((......((((((.((((........((((....))))((.......))))))..)))))).......))).)))))((((((((......)))))))). ( -36.32)
>consensus
AUAAUCUCCCCAUGGCUUCGCUCGAAAGUGGGUC_____CCACAUUU_____AAGUUGGCAAAACAAGCAUGGCAAGCCGCAACAUUUGCAUACCCAAAUGGGCUCACAGCGGCCCAUUC
.............(((((.((......((((........))))...........(((.....))).......)))))))(((.....))).......(((((((........))))))). (-24.71 = -25.02 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:28 2006