Locus 5046

Sequence ID	X_DroMel_CAF1
Location	13,207,141 – 13,207,248
Length	107
Max. P	0.998297

overview

Window 1

Location	13,207,141 – 13,207,248
Length	107
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	74.71
Mean single sequence MFE	-31.80
Consensus MFE	-16.68
Energy contribution	-18.12
Covariance contribution	1.44
Combinations/Pair	1.04
Mean z-score	-1.74
Structure conservation index	0.52
SVM decision value	0.22
SVM RNA-class probability	0.639283
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13207141 107 + 22224390
----------AGUUGCUUGUGCAAAGCCCCAAAACUCUGAUAAGAAAUGCUCGAUUGCAGUUUUGAAAUGCGCGCCUUGCGGCGAGUGCAAUUGGGUUUGAGUCUAGGAUAAAUGCA--
----------.(((.((((.((.(((((((((((((((....)))..(((......)))))))))...((((((((....)))..)))))...))))))..)).))))...)))...-- ( -29.40)
>DroSec_CAF1 35443 84 + 1
-----------------------------------UUUGAUAAGAAAUGCUCGAAUGCAGUUUUGAAAUGCGCGCCUUGCGGCGAGUGCAUUUGGGUUUGAGUCUAGGCUAAAUGCACC
-----------------------------------.......(((...(((((((((((((........)).((((....))))..))))))))))).....)))..((.....))... ( -23.70)
>DroSim_CAF1 36217 108 + 1
----------AGUUGUUUGUGCAAAGCCC-GAAACUCUGAUAAGAAAUGCUCGAAUGCAGUUUUGAAAUGCGCGCCUUGCGGCGAUUGCAUUUGGGUUUGAGCCUAGGCUAAAUGCACC
----------........(((((((((((-((((((((....)))..(((......)))))))).((((((.((((....))))...)))))))))))).(((....)))...))))). ( -36.50)
>DroEre_CAF1 44992 117 + 1
UCGUAAACUUUGUUGUUUUUGGAAAACCG-AAAACUCAGAUACGAAAUGCUUGAUUGCACUUUUAAAGUGCGCGCCUUGCGGCGAGUGCAUUU-GGUUUGAGUCUAGGCUAAAUGCACA
(((((...((((..((((((((....)))-))))).)))))))))...........(((((.....))))).((((....)))).((((((((-((((((....)))))))))))))). ( -43.20)
>DroYak_CAF1 44088 103 + 1
---------------AUUUUGCAGUAUCG-GAAACUCAGAUAAGAAAUGCAUAGUUGCAGUUUUGAAAUGCGCGCCUUGCGACGAGUGCAUCGGGGUUUGAGUCCAGGCUAAAUGCACA
---------------....((((.(((((-....)...)))).....))))..(((((((................)))))))..((((((...((((((....))))))..)))))). ( -26.19)
>consensus
___________GUUGUUUGUGCAAAACCC_AAAACUCUGAUAAGAAAUGCUCGAUUGCAGUUUUGAAAUGCGCGCCUUGCGGCGAGUGCAUUUGGGUUUGAGUCUAGGCUAAAUGCACA
..........................................((((.(((......))).))))........((((....)))).((((((((.((((((....)))))))))))))). (-16.68 = -18.12 +   1.44)

alignment

secondary structure

dotplot

Window 2

Location	13,207,141 – 13,207,248
Length	107
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	74.71
Mean single sequence MFE	-28.75
Consensus MFE	-17.65
Energy contribution	-19.49
Covariance contribution	1.84
Combinations/Pair	1.17
Mean z-score	-2.65
Structure conservation index	0.61
SVM decision value	3.06
SVM RNA-class probability	0.998297
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13207141 107 - 22224390
--UGCAUUUAUCCUAGACUCAAACCCAAUUGCACUCGCCGCAAGGCGCGCAUUUCAAAACUGCAAUCGAGCAUUUCUUAUCAGAGUUUUGGGGCUUUGCACAAGCAACU----------
--((((....(((.((((((.........(((...((((....)))).))).........(((......)))..........)))))).)))....)))).........---------- ( -28.90)
>DroSec_CAF1 35443 84 - 1
GGUGCAUUUAGCCUAGACUCAAACCCAAAUGCACUCGCCGCAAGGCGCGCAUUUCAAAACUGCAUUCGAGCAUUUCUUAUCAAA-----------------------------------
(((((((((.................)))))))))((((....)))).............(((......)))............----------------------------------- ( -18.63)
>DroSim_CAF1 36217 108 - 1
GGUGCAUUUAGCCUAGGCUCAAACCCAAAUGCAAUCGCCGCAAGGCGCGCAUUUCAAAACUGCAUUCGAGCAUUUCUUAUCAGAGUUUC-GGGCUUUGCACAAACAACU----------
.(((((...(((((((((((......((((((...((((....)))).))))))......(((......)))..........)))))).-))))).)))))........---------- ( -38.40)
>DroEre_CAF1 44992 117 - 1
UGUGCAUUUAGCCUAGACUCAAACC-AAAUGCACUCGCCGCAAGGCGCGCACUUUAAAAGUGCAAUCAAGCAUUUCGUAUCUGAGUUUU-CGGUUUUCCAAAAACAACAAAGUUUACGA
(((......((((.(((((((.((.-((((((...((((....)))).(((((.....)))))......)))))).))...))))))).-.))))........)))............. ( -34.14)
>DroYak_CAF1 44088 103 - 1
UGUGCAUUUAGCCUGGACUCAAACCCCGAUGCACUCGUCGCAAGGCGCGCAUUUCAAAACUGCAACUAUGCAUUUCUUAUCUGAGUUUC-CGAUACUGCAAAAU---------------
..((((.....(..(((((((......(((((...((((....)))).))))).......((((....)))).........))))))).-.)....))))....--------------- ( -23.70)
>consensus
GGUGCAUUUAGCCUAGACUCAAACCCAAAUGCACUCGCCGCAAGGCGCGCAUUUCAAAACUGCAAUCGAGCAUUUCUUAUCAGAGUUUC_CGGCUUUGCAAAAACAAC___________
..((((........((((((......((((((...((((....)))).(((.........)))......)))))).......))))))........))))................... (-17.65 = -19.49 +   1.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:53 2006