Locus 208

Sequence ID	3L_DroMel_CAF1
Location	572,811 – 572,921
Length	110
Max. P	0.885906

overview

Window 6

Location	572,811 – 572,921
Length	110
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	86.75
Mean single sequence MFE	-35.53
Consensus MFE	-24.69
Energy contribution	-27.00
Covariance contribution	2.31
Combinations/Pair	1.10
Mean z-score	-2.42
Structure conservation index	0.69
SVM decision value	0.94
SVM RNA-class probability	0.885906
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 572811 110 + 23771897
GCCAGACCACUUACAGUUUUUACAUCUUGCGACCGCU---GCCGCCGCGGCGAUUCU---UCUGCCUCCGGC---GGCGUCCACCUCGCGGUCUCGGUCUCCCAUCCUCUCCUACAUUU
...(((((.......((....)).....(.(((((((---(((((((.(((((....---)).)))..))))---))))........)))))).))))))................... ( -37.70)
>DroSec_CAF1 4232 110 + 1
GCCAGACCACUUACAGUUUUUACAUCUUGCGGCCGCU---GCUGCCGAGGCGAUUCU---UCUGCCUCCGGC---GGCGUCCACCUCGCGGUCUCGGUCUCCCAUCCCCUCGUACAUUU
...(((((.......((....)).....(.(((((((---(((((((((((((....---)).)))).))))---))))........)))))).))))))................... ( -37.50)
>DroSim_CAF1 4657 110 + 1
GCCAGACCACUUACAGUUUUUACAUCUUGCGGCCGCU---GCUGCCGAGGCGAUUCU---UCUGCCUCCGGC---GGCGUUCACCUCGCGGUCUCGUUCUCCCAUCCUCUCCUACGUUU
((.(((((.......((....)).....((((....(---(((((((((((((....---)).)))).))))---))))......))))))))).))...................... ( -33.10)
>DroEre_CAF1 4176 112 + 1
GCCACACCACUUACAGUUUUUACAUCUUGCGGCCGCCGACGCUGCCGCGGCGAUUCUUCUUCUGCCUCCGGCGGCGGCGUCCACCUCGCG-------CCUCCCACCCUCUCCUACGUGC
..(((..........((....)).......(((((..((((((((((((((((.......)).)))....))))))))))).....)).)-------))................))). ( -33.80)
>consensus
GCCAGACCACUUACAGUUUUUACAUCUUGCGGCCGCU___GCUGCCGAGGCGAUUCU___UCUGCCUCCGGC___GGCGUCCACCUCGCGGUCUCGGUCUCCCAUCCUCUCCUACAUUU
((((((((.......((....)).....((((.(((((((((((..((((((..........)))))))))))))))))......))))))))).)))..................... (-24.69 = -27.00 +   2.31)

alignment

secondary structure

dotplot

Window 7

Location	572,811 – 572,921
Length	110
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	86.75
Mean single sequence MFE	-39.53
Consensus MFE	-26.63
Energy contribution	-27.44
Covariance contribution	0.81
Combinations/Pair	1.04
Mean z-score	-1.48
Structure conservation index	0.67
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 572811 110 - 23771897
AAAUGUAGGAGAGGAUGGGAGACCGAGACCGCGAGGUGGACGCC---GCCGGAGGCAGA---AGAAUCGCCGCGGCGGC---AGCGGUCGCAAGAUGUAAAAACUGUAAGUGGUCUGGC
...............(((....)))(((((((..(((..(((((---((((..(((.((---....))))).)))))))---....(((....)))))....)))....)))))))... ( -45.30)
>DroSec_CAF1 4232 110 - 1
AAAUGUACGAGGGGAUGGGAGACCGAGACCGCGAGGUGGACGCC---GCCGGAGGCAGA---AGAAUCGCCUCGGCAGC---AGCGGCCGCAAGAUGUAAAAACUGUAAGUGGUCUGGC
...............(((....)))(((((((..(((.(..((.---((((.((((.((---....)))))))))).))---..).)))((.....))...........)))))))... ( -39.50)
>DroSim_CAF1 4657 110 - 1
AAACGUAGGAGAGGAUGGGAGAACGAGACCGCGAGGUGAACGCC---GCCGGAGGCAGA---AGAAUCGCCUCGGCAGC---AGCGGCCGCAAGAUGUAAAAACUGUAAGUGGUCUGGC
.......................(.(((((((..(((....((.---((((.((((.((---....)))))))))).))---.(((..(....).)))....)))....))))))).). ( -34.30)
>DroEre_CAF1 4176 112 - 1
GCACGUAGGAGAGGGUGGGAGG-------CGCGAGGUGGACGCCGCCGCCGGAGGCAGAAGAAGAAUCGCCGCGGCAGCGUCGGCGGCCGCAAGAUGUAAAAACUGUAAGUGGUGUGGC
((((.........(((((..((-------(((......).)))).)))))....((((.......(((...(((((.((....)).)))))..))).......)))).....))))... ( -39.04)
>consensus
AAACGUAGGAGAGGAUGGGAGACCGAGACCGCGAGGUGGACGCC___GCCGGAGGCAGA___AGAAUCGCCGCGGCAGC___AGCGGCCGCAAGAUGUAAAAACUGUAAGUGGUCUGGC
...........................(((....)))....(((...((((...((((.......(((...(((((.((....)).)))))..))).......))))...))))..))) (-26.63 = -27.44 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:09 2006