Locus 248

Sequence ID	X_DroMel_CAF1
Location	838,173 – 838,273
Length	100
Max. P	0.983539

overview

Window 4

Location	838,173 – 838,273
Length	100
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	90.94
Mean single sequence MFE	-26.05
Consensus MFE	-23.41
Energy contribution	-23.93
Covariance contribution	0.53
Combinations/Pair	1.04
Mean z-score	-1.28
Structure conservation index	0.90
SVM decision value	0.21
SVM RNA-class probability	0.637441
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 838173 100 + 22224390
--------------------GCAGUGGCAAUUUGCUAAUUUCGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCAUGCCGCGGGCGAU
--------------------((.((((((....((..((((((((.....))))))))....))......((((((..((((((........)))..))).))))))))))))..))... ( -26.50)
>DroSec_CAF1 39029 100 + 1
--------------------GCAGUGGCAAUUUGCUAAUUUCGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCAUGCCGCGGGCGAU
--------------------((.((((((....((..((((((((.....))))))))....))......((((((..((((((........)))..))).))))))))))))..))... ( -26.50)
>DroSim_CAF1 35276 100 + 1
--------------------GCAGUGGCAAUUUGCUAAUUUCGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCAUGCCGCGGGCGAU
--------------------((.((((((....((..((((((((.....))))))))....))......((((((..((((((........)))..))).))))))))))))..))... ( -26.50)
>DroEre_CAF1 38541 100 + 1
--------------------GCAGUGGCAAUUUGCUAAUUUCGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCAUGCCGCGGGCGAU
--------------------((.((((((....((..((((((((.....))))))))....))......((((((..((((((........)))..))).))))))))))))..))... ( -26.50)
>DroYak_CAF1 35883 100 + 1
--------------------GCAGUGGCAAUUUGCUAAUUUGGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCAUGCCGCGGGCGAU
--------------------((.((((((..(((.(((...(..(((...((..(((((((.(((.(((...)))))).)))))))..)).)))..)))).)))...))))))..))... ( -24.70)
>DroAna_CAF1 38000 120 + 1
CCACCUAAAACUACAAAAACCCAACAGCAAUUUGCUAAUUUCGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCACGCCGUGGGCGUG
.(((...((((..............(((.....))).((((((((.....))))))))))))(((((...((((((..((((((........)))..))).)))))).....)))))))) ( -25.60)
>consensus
____________________GCAGUGGCAAUUUGCUAAUUUCGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCAUGCCGCGGGCGAU
........................((((.....))))((((((((.....))))))))..((((((...((((....))))..........(((((........)))))....)))))). (-23.41 = -23.93 +   0.53)

alignment

secondary structure

dotplot

Window 5

Location	838,173 – 838,273
Length	100
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	90.94
Mean single sequence MFE	-27.25
Consensus MFE	-26.13
Energy contribution	-26.02
Covariance contribution	-0.11
Combinations/Pair	1.07
Mean z-score	-1.59
Structure conservation index	0.96
SVM decision value	1.95
SVM RNA-class probability	0.983539
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 838173 100 - 22224390
AUCGCCCGCGGCAUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCGAAAUUAGCAAAUUGCCACUGC--------------------
...((((..(((((((((....)))))))))........((((....))))...))))....((((((((.....))))))))..((.....))......-------------------- ( -26.80)
>DroSec_CAF1 39029 100 - 1
AUCGCCCGCGGCAUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCGAAAUUAGCAAAUUGCCACUGC--------------------
...((((..(((((((((....)))))))))........((((....))))...))))....((((((((.....))))))))..((.....))......-------------------- ( -26.80)
>DroSim_CAF1 35276 100 - 1
AUCGCCCGCGGCAUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCGAAAUUAGCAAAUUGCCACUGC--------------------
...((((..(((((((((....)))))))))........((((....))))...))))....((((((((.....))))))))..((.....))......-------------------- ( -26.80)
>DroEre_CAF1 38541 100 - 1
AUCGCCCGCGGCAUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCGAAAUUAGCAAAUUGCCACUGC--------------------
...((((..(((((((((....)))))))))........((((....))))...))))....((((((((.....))))))))..((.....))......-------------------- ( -26.80)
>DroYak_CAF1 35883 100 - 1
AUCGCCCGCGGCAUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCCAAAUUAGCAAAUUGCCACUGC--------------------
.......(((((((((((....))))))))((..((((((((.((((.....)))).).)))))))..)).)))...........((.....))......-------------------- ( -22.50)
>DroAna_CAF1 38000 120 - 1
CACGCCCACGGCGUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCGAAAUUAGCAAAUUGCUGUUGGGUUUUUGUAGUUUUAGGUGG
((((((((.(((((((((....)))))))))........((((....))))..)))))((((((((((((.....))))))))..(((((..(((....))).))))).))))...))). ( -33.80)
>consensus
AUCGCCCGCGGCAUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCGAAAUUAGCAAAUUGCCACUGC____________________
...(((((.(((((((((....)))))))))........((((....))))..)))))....((((((((.....))))))))..((.....)).......................... (-26.13 = -26.02 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:55 2006