Locus 118

Sequence ID	2L_DroMel_CAF1
Location	378,967 – 379,127
Length	160
Max. P	0.985437

overview

Window 9

Location	378,967 – 379,087
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-27.66
Consensus MFE	-24.76
Energy contribution	-25.76
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.90
SVM decision value	1.16
SVM RNA-class probability	0.924241
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 378967 120 + 22407834
AAUUUUAUUAACUCAAUUUUGAGGGUCGAAAGAUUUCGCCUUUGCCUUAGCUGAUAGUUCGAUAAGUUUAUCGCUGAUUGGUUUUAAUUAAACACCAUUAAAGAGUACAAAUUGUCAGCA
....................(((((.((((....)))))))))......(((((((((((((((....)))))((...((((.((.....)).))))....))......)))))))))). ( -25.40)
>DroSec_CAF1 46605 120 + 1
AAAUUUAUUAACUCAAUUUUGAGGGGCGAAAGAUUUCGCCUUUGCCUUAGCUGAUAGUUCGAUAAGUUUAUCGCUGAUUGGUUUUAAUUAAACACCAUUAAAGAGUACAAAUUGUCAGCG
...........((((....))))(((((((....)))))))........(((((((((((((((....)))))((...((((.((.....)).))))....))......)))))))))). ( -30.00)
>DroSim_CAF1 47267 120 + 1
AAUUUUAUUAACUCAAUUUUGAGGGGCGAAAGAUUUCGCCUUUGCCUUAGCUGAUAGUACGAUAAGUUUAUCGCUGAUUGGUUUUAAUUAAACACCAUUAAAGAGUACAAAUUGUCAGCG
...........((((....))))(((((((....)))))))........(((((((((.(((((....)))))((...((((.((.....)).))))....)).......))))))))). ( -30.10)
>DroEre_CAF1 53581 120 + 1
AACUUUAUUAACUCAAUUUUGAGGAGCACAAGAUUUCGCCUUUGCCUUUGCUGAUAGUUCGAUAAGUAUAUCGCUGAUUGGUUUUAAUUAAACACCAUUAAAGAGUACAAAUUGUCAGCG
...........((((....))))..(((.(((.......))))))....(((((((((((((((....)))))((...((((.((.....)).))))....))......)))))))))). ( -22.80)
>DroYak_CAF1 47819 120 + 1
AACUUUAUUAACUCAACUCCGAGGGGCGAAAGAUUUCGCCUUCGCCUGAGCUGAUAGUUCGAUAAGUUUAUCGCUGAUUGGUUUUAAUUAAACACCAUUAAAGAGUACAAAUUGUCAGCG
...........(((......)))(((((((.(......).)))))))..(((((((((((((((....)))))((...((((.((.....)).))))....))......)))))))))). ( -30.00)
>consensus
AACUUUAUUAACUCAAUUUUGAGGGGCGAAAGAUUUCGCCUUUGCCUUAGCUGAUAGUUCGAUAAGUUUAUCGCUGAUUGGUUUUAAUUAAACACCAUUAAAGAGUACAAAUUGUCAGCG
...........(((......)))(((((((....)))))))........(((((((((((((((....)))))((...((((.((.....)).))))....))......)))))))))). (-24.76 = -25.76 +   1.00)

alignment

secondary structure

dotplot

Window 0

Location	378,967 – 379,087
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-24.28
Consensus MFE	-21.02
Energy contribution	-20.94
Covariance contribution	-0.08
Combinations/Pair	1.12
Mean z-score	-1.38
Structure conservation index	0.87
SVM decision value	0.46
SVM RNA-class probability	0.744804
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 378967 120 - 22407834
UGCUGACAAUUUGUACUCUUUAAUGGUGUUUAAUUAAAACCAAUCAGCGAUAAACUUAUCGAACUAUCAGCUAAGGCAAAGGCGAAAUCUUUCGACCCUCAAAAUUGAGUUAAUAAAAUU
.(((((.................((((...........)))).....(((((....))))).....))))).........((((((....)))).))((((....))))........... ( -19.60)
>DroSec_CAF1 46605 120 - 1
CGCUGACAAUUUGUACUCUUUAAUGGUGUUUAAUUAAAACCAAUCAGCGAUAAACUUAUCGAACUAUCAGCUAAGGCAAAGGCGAAAUCUUUCGCCCCUCAAAAUUGAGUUAAUAAAUUU
.(((((.................((((...........)))).....(((((....))))).....))))).........((((((....)))))).((((....))))........... ( -23.70)
>DroSim_CAF1 47267 120 - 1
CGCUGACAAUUUGUACUCUUUAAUGGUGUUUAAUUAAAACCAAUCAGCGAUAAACUUAUCGUACUAUCAGCUAAGGCAAAGGCGAAAUCUUUCGCCCCUCAAAAUUGAGUUAAUAAAAUU
.(((((.................((((...........))))....((((((....))))))....))))).........((((((....)))))).((((....))))........... ( -25.40)
>DroEre_CAF1 53581 120 - 1
CGCUGACAAUUUGUACUCUUUAAUGGUGUUUAAUUAAAACCAAUCAGCGAUAUACUUAUCGAACUAUCAGCAAAGGCAAAGGCGAAAUCUUGUGCUCCUCAAAAUUGAGUUAAUAAAGUU
.(((((.................((((...........)))).....(((((....))))).....)))))...((((((((.....)))).)))).((((....))))........... ( -20.50)
>DroYak_CAF1 47819 120 - 1
CGCUGACAAUUUGUACUCUUUAAUGGUGUUUAAUUAAAACCAAUCAGCGAUAAACUUAUCGAACUAUCAGCUCAGGCGAAGGCGAAAUCUUUCGCCCCUCGGAGUUGAGUUAAUAAAGUU
(((((((.....)).........((((...........))))..)))))...(((((....(((..(((((((.((((((((......)))))))).....))))))))))....))))) ( -32.20)
>consensus
CGCUGACAAUUUGUACUCUUUAAUGGUGUUUAAUUAAAACCAAUCAGCGAUAAACUUAUCGAACUAUCAGCUAAGGCAAAGGCGAAAUCUUUCGCCCCUCAAAAUUGAGUUAAUAAAAUU
.(((((.................((((...........)))).....(((((....))))).....))))).........((((((....)))))).((((....))))........... (-21.02 = -20.94 +  -0.08)

alignment

secondary structure

dotplot

Window 1

Location	379,007 – 379,127
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.67
Mean single sequence MFE	-30.58
Consensus MFE	-28.00
Energy contribution	-28.44
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.87
Structure conservation index	0.92
SVM decision value	2.01
SVM RNA-class probability	0.985437
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 379007 120 + 22407834
UUUGCCUUAGCUGAUAGUUCGAUAAGUUUAUCGCUGAUUGGUUUUAAUUAAACACCAUUAAAGAGUACAAAUUGUCAGCAGUGCAGUCAGCGCCAAUAAAUCACGUUUUGUCUAGCUGAU
......(((((((((((..((....(((((((((((((((((((.....)))).................((((....)))).)))))))))...))))))..))..))))).)))))). ( -29.90)
>DroSec_CAF1 46645 120 + 1
UUUGCCUUAGCUGAUAGUUCGAUAAGUUUAUCGCUGAUUGGUUUUAAUUAAACACCAUUAAAGAGUACAAAUUGUCAGCGGUGCAGUCAGCGCCAAUAAAUCACGUUUUGUCUAGCUGAU
......(((((((((((..((....((((((.((((((((.(((((((........)))))))....))....))))))(((((.....))))).))))))..))..))))).)))))). ( -31.20)
>DroSim_CAF1 47307 120 + 1
UUUGCCUUAGCUGAUAGUACGAUAAGUUUAUCGCUGAUUGGUUUUAAUUAAACACCAUUAAAGAGUACAAAUUGUCAGCGGUGCAGUCAGCACCAAUAAAUCACGUUUUGUCUAGCUGAU
......(((((((((((.(((....((((((.((((((((.(((((((........)))))))....))....))))))(((((.....))))).))))))..))).))))).)))))). ( -32.10)
>DroEre_CAF1 53621 120 + 1
UUUGCCUUUGCUGAUAGUUCGAUAAGUAUAUCGCUGAUUGGUUUUAAUUAAACACCAUUAAAGAGUACAAAUUGUCAGCGGUGCAGUCAGCGCCAAUAAAUCACGUUUUGUCUAGCUGAU
..(((..(((((((((((((((((....)))))((...((((.((.....)).))))....))......)))))))))))).)))((((((....(((((......)))))...)))))) ( -30.40)
>DroYak_CAF1 47859 120 + 1
UUCGCCUGAGCUGAUAGUUCGAUAAGUUUAUCGCUGAUUGGUUUUAAUUAAACACCAUUAAAGAGUACAAAUUGUCAGCGGUGCAGUCAGCGCCAAUAAAUCACGUUUUGUCUAGCUGAU
........(((((((((..((....((((((.((((((((.(((((((........)))))))....))....))))))(((((.....))))).))))))..))..))))).))))... ( -29.30)
>consensus
UUUGCCUUAGCUGAUAGUUCGAUAAGUUUAUCGCUGAUUGGUUUUAAUUAAACACCAUUAAAGAGUACAAAUUGUCAGCGGUGCAGUCAGCGCCAAUAAAUCACGUUUUGUCUAGCUGAU
......(((((((((((..((...........((((((((.(((((((........)))))))....))....))))))(((((.....))))).........))..))))).)))))). (-28.00 = -28.44 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:26:25 2006