Locus 3683

Sequence ID X_DroMel_CAF1
Location 9,832,453 – 9,832,564
Length 111
Max. P 0.599113
window6033 window6034

overview

Window 3

Location 9,832,453 – 9,832,564
Length 111
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 86.01
Mean single sequence MFE -30.37
Consensus MFE -23.67
Energy contribution -24.23
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -1.87
Structure conservation index 0.78
SVM decision value 0.13
SVM RNA-class probability 0.599113
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9832453 111 + 22224390
CUGAUUUCGAACGCAUGCAACUUUUAGUGAGUUAGUUUAGUGAGUCUCACUAGUCGACCGACCGACUGACUGAUUUUGGCUCGCCUGCCUUCGCAUUUGCUAUUGCUUUGC-------
........(((.(((.((.((.....))(((((((.(((((.((((......(((....))).)))).)))))..))))))))).))).)))(((...((....))..)))------- ( -30.30)
>DroSec_CAF1 11278 111 + 1
CUGAUUUCGAACGCAUGCAACUUUUAGUGAGUUAGUUUAGUGAGUCUCACUAGUC-------UGACUGACUGAUUUUGGCUGGCCUGCCUUCGCAUUUGCUAUUGCUUUGCUUUUGCU
........(((.(((.((..((.(((((.((((((.((((((.....)))))).)-------))))).)))))....))...)).))).)))(((...((....))..)))....... ( -34.20)
>DroEre_CAF1 9317 103 + 1
CUGAUUUCGAACGCAUGCAACUUUUAGUCAGUUUGCUUAGUGAGUCUCACCAGUCGAC----CGACUGACUGAUUUUGGCUCGCCUGCCUUCGCAUUUGCUAUUGCU-----------
........(((.(((.((..((...(((((((.......(((.....)))(((((...----.))))))))))))..))...)).))).)))(((........))).----------- ( -26.60)
>consensus
CUGAUUUCGAACGCAUGCAACUUUUAGUGAGUUAGUUUAGUGAGUCUCACUAGUCGAC____CGACUGACUGAUUUUGGCUCGCCUGCCUUCGCAUUUGCUAUUGCUUUGC_______
........(((.(((.(((((((.....))))).))...((((((((((.((((((......))))))..)))....))))))).))).)))(((........)))............ (-23.67 = -24.23 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 9,832,453 – 9,832,564
Length 111
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 86.01
Mean single sequence MFE -27.13
Consensus MFE -22.19
Energy contribution -22.64
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -1.62
Structure conservation index 0.82
SVM decision value -0.04
SVM RNA-class probability 0.515308
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9832453 111 - 22224390
-------GCAAAGCAAUAGCAAAUGCGAAGGCAGGCGAGCCAAAAUCAGUCAGUCGGUCGGUCGACUAGUGAGACUCACUAAACUAACUCACUAAAAGUUGCAUGCGUUCGAAAUCAG
-------(((..(((((.((...(((....))).))(((.............(((((....)))))(((((.....)))))......))).......))))).)))............ ( -27.90)
>DroSec_CAF1 11278 111 - 1
AGCAAAAGCAAAGCAAUAGCAAAUGCGAAGGCAGGCCAGCCAAAAUCAGUCAGUCA-------GACUAGUGAGACUCACUAAACUAACUCACUAAAAGUUGCAUGCGUUCGAAAUCAG
.......(((..(((((.((...(((....))).))...........(((.(((.(-------(..(((((.....)))))..)).))).)))....))))).)))............ ( -25.10)
>DroEre_CAF1 9317 103 - 1
-----------AGCAAUAGCAAAUGCGAAGGCAGGCGAGCCAAAAUCAGUCAGUCG----GUCGACUGGUGAGACUCACUAAGCAAACUGACUAAAAGUUGCAUGCGUUCGAAAUCAG
-----------.(((((.((...(((....))).))...........(((((((..----((....(((((.....))))).))..)))))))....)))))................ ( -28.40)
>consensus
_______GCAAAGCAAUAGCAAAUGCGAAGGCAGGCGAGCCAAAAUCAGUCAGUCG____GUCGACUAGUGAGACUCACUAAACUAACUCACUAAAAGUUGCAUGCGUUCGAAAUCAG
............((....)).....((((.(((.((.(((............((((......))))(((((((..............)))))))...))))).))).))))....... (-22.19 = -22.64 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:35 2006