Locus 9992

Sequence ID	3R_DroMel_CAF1
Location	26,764,734 – 26,764,835
Length	101
Max. P	0.952888

overview

Window 5

Location	26,764,734 – 26,764,835
Length	101
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	85.31
Mean single sequence MFE	-33.18
Consensus MFE	-24.60
Energy contribution	-26.56
Covariance contribution	1.96
Combinations/Pair	1.11
Mean z-score	-2.47
Structure conservation index	0.74
SVM decision value	1.43
SVM RNA-class probability	0.952888
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26764734 101 + 27905053
UCUUCGCAGGAAGAUAUAUCCAGA--UCCGGAUCCGGAGCCG------------GAGUCAGAGCCUCCUGACGGGGGCUCUAGUUAAAUAUGGAAACAAUAUCGAAAUGCCAACU
.....(((....(((((.(((.(.--((((....)))).).)------------))...(((((((((....))))))))).........((....)))))))....)))..... ( -36.40)
>DroSec_CAF1 68525 101 + 1
UCUUCGCAGGAAGAUAUAUCCAGA--UCCGGAUCCGGAGCCG------------GAGCCAGAGCCUCCUGACUGGGGCUCUAGUUAAAUAUGGAAACAAUAUCGAAAUGCCAACU
.....(((....(((((.(((.(.--((((....)))).).)------------))((.((((((.((.....)))))))).))......((....)))))))....)))..... ( -33.70)
>DroSim_CAF1 72200 100 + 1
UCUUCGCAGGAAGAUAUAUCCAGA--UCCGGAUCCGGAGCCG-------------AGCCAGAGCCUCCUGACGGGGGCUCUAGUUAAAUAUGGAAACAAUAUCGAAAUGCCAACU
.....(((....(((((.((((..--((((....))))....-------------(((.(((((((((....))))))))).))).....))))....)))))....)))..... ( -35.40)
>DroEre_CAF1 69821 99 + 1
UCUUCGCAGAAAGAUACAUCCAGA--UCCGGAUCCGGAUCCU-----------GC--CUCCUGCCCACUGACGG-GGCUCUAGUUAAAUAUGGAAACAAUAUCGAAAUGCCAGCU
.....(((....((((..((((((--((((....))))))..-----------..--.....((((.......)-)))............)))).....))))....)))..... ( -25.90)
>DroYak_CAF1 71184 115 + 1
UCUUCGCAGGAAGAUACAUUCAGAUAUCCAGAUCCGGAUGCAGAAAUGGAGCUGCAGCUGAAGCCUCCUGACGGGGGCUCUAGUUAAAUAUGGAAACAAUAUCGAAAUGCCAACU
(((((....)))))..((((..(((((.....((((...((((........))))(((((.(((((((....))))))).))))).....))))....)))))..))))...... ( -34.50)
>consensus
UCUUCGCAGGAAGAUAUAUCCAGA__UCCGGAUCCGGAGCCG____________CAGCCAGAGCCUCCUGACGGGGGCUCUAGUUAAAUAUGGAAACAAUAUCGAAAUGCCAACU
.....(((....(((((.((((....((((....)))).................(((.(((((((((....))))))))).))).....))))....)))))....)))..... (-24.60 = -26.56 +   1.96)

alignment

secondary structure

dotplot

Window 6

Location	26,764,734 – 26,764,835
Length	101
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	85.31
Mean single sequence MFE	-33.80
Consensus MFE	-24.94
Energy contribution	-25.98
Covariance contribution	1.04
Combinations/Pair	1.14
Mean z-score	-2.12
Structure conservation index	0.74
SVM decision value	0.87
SVM RNA-class probability	0.870430
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26764734 101 - 27905053
AGUUGGCAUUUCGAUAUUGUUUCCAUAUUUAACUAGAGCCCCCGUCAGGAGGCUCUGACUC------------CGGCUCCGGAUCCGGA--UCUGGAUAUAUCUUCCUGCGAAGA
..((.(((....(((((................(((((((.((....)).)))))))..((------------(((.((((....))))--.))))).)))))....))).)).. ( -34.00)
>DroSec_CAF1 68525 101 - 1
AGUUGGCAUUUCGAUAUUGUUUCCAUAUUUAACUAGAGCCCCAGUCAGGAGGCUCUGGCUC------------CGGCUCCGGAUCCGGA--UCUGGAUAUAUCUUCCUGCGAAGA
..((.(((....(((((...............((((((((((.....)).)))))))).((------------(((.((((....))))--.))))).)))))....))).)).. ( -35.70)
>DroSim_CAF1 72200 100 - 1
AGUUGGCAUUUCGAUAUUGUUUCCAUAUUUAACUAGAGCCCCCGUCAGGAGGCUCUGGCU-------------CGGCUCCGGAUCCGGA--UCUGGAUAUAUCUUCCUGCGAAGA
..((.(((....(((((....(((........((((((((.((....)).))))))))..-------------.((.((((....))))--.))))).)))))....))).)).. ( -34.10)
>DroEre_CAF1 69821 99 - 1
AGCUGGCAUUUCGAUAUUGUUUCCAUAUUUAACUAGAGCC-CCGUCAGUGGGCAGGAG--GC-----------AGGAUCCGGAUCCGGA--UCUGGAUGUAUCUUUCUGCGAAGA
..((.(((....((((((((((((...(((....)))(((-((....).)))).))))--))-----------)(((((((....))))--)))....)))))....)))..)). ( -31.80)
>DroYak_CAF1 71184 115 - 1
AGUUGGCAUUUCGAUAUUGUUUCCAUAUUUAACUAGAGCCCCCGUCAGGAGGCUUCAGCUGCAGCUCCAUUUCUGCAUCCGGAUCUGGAUAUCUGAAUGUAUCUUCCUGCGAAGA
.....((((((.((((((...(((........((..((((.((....)).))))..)).(((((........)))))...)))....)))))).)))))).(((((....))))) ( -33.40)
>consensus
AGUUGGCAUUUCGAUAUUGUUUCCAUAUUUAACUAGAGCCCCCGUCAGGAGGCUCUGGCUC____________CGGCUCCGGAUCCGGA__UCUGGAUAUAUCUUCCUGCGAAGA
..((.(((....(((((....((((.......((((((((.((....)).))))))))...................((((....))))....)))).)))))....))).)).. (-24.94 = -25.98 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:46:32 2006