Locus 7444

Sequence ID	3R_DroMel_CAF1
Location	19,830,838 – 19,830,954
Length	116
Max. P	0.776094

overview

Window 5

Location	19,830,838 – 19,830,954
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.09
Mean single sequence MFE	-28.56
Consensus MFE	-17.71
Energy contribution	-18.03
Covariance contribution	0.32
Combinations/Pair	1.07
Mean z-score	-2.71
Structure conservation index	0.62
SVM decision value	0.54
SVM RNA-class probability	0.776094
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19830838 116 + 27905053
UGGAAAUGCCUUAU----AGAUUAGCUUAUGCUAAUUUCUGGGAAAUUCCUGAAUAGGCAUGGGAAGAAGAAAUUAGAACAAGUUAAUCCUAAGAGAUAUCUGACAGAAUCUAUGCAAAU
......(((((((.----.(((((((((...(((((((((......(((((..........)))))..)))))))))...))))))))).))))((((.((.....))))))..)))... ( -27.80)
>DroSec_CAF1 9067 116 + 1
UGGAAAUGCCUUAU----AGAUUAGCUUAUGCUAAUUUCUGGGAAAUUCCUAAAAAGGCAUGGCUAGAAGGAACUAGAACAAGGUAAUCCUAAGAGAUAUCUGACUGAAUCUAGUUAAAU
(((..(((((((..----((((((((....)))))))).((((.....))))..)))))))..))).....(((((((...(((....))).(((....))).......))))))).... ( -32.60)
>DroSim_CAF1 13790 116 + 1
UGGAAAUGCCUUAU----AGAUUAGCUUAUGCUAAUUUCUGGGAAAUUCCUAAAAAGGCAUGGCUAGAAGGAACUAGAACAAGGUAAUCCUAAGAUAUAUCUCACUGAAUCUAGUUAAAU
(((..(((((((..----((((((((....)))))))).((((.....))))..)))))))..))).....(((((((...(((....)))........((.....)).))))))).... ( -31.50)
>DroEre_CAF1 9132 105 + 1
UGGAAAUGCCUUAU----AGAUUAGCUUAUGCUAAUUUCUGCGAAAUUCCUUAAAAG-----GGUAGAAGGAACUAGAACAAGGUAUUCCUAAGAGAUAUCUGACUGAAUCUAG------
.((((.((((((.(----((.(((((....)))))(((((((......(((....))-----))))))))...)))....))))))))))....((((.((.....))))))..------ ( -24.10)
>DroYak_CAF1 9081 116 + 1
UGGAAAUGCCUUAUACAUAGAUUAGCUUAUGCUAAUUUUUGGGAAAUUCCGGAAAAGGCAUGGAUGGAAGGCACUAGAACAAGGUAAUCCUGAAAGAUAUCAGACUGAAUCUAA----AU
.....(((((((...((.((((((((....)))))))).))((.....))....)))))))((((...((((.((......))))....((((......)))).))..))))..----.. ( -26.80)
>consensus
UGGAAAUGCCUUAU____AGAUUAGCUUAUGCUAAUUUCUGGGAAAUUCCUAAAAAGGCAUGGCUAGAAGGAACUAGAACAAGGUAAUCCUAAGAGAUAUCUGACUGAAUCUAG__AAAU
.(((..((((((.......(((((((....)))))))(((((....(((.................)))....)))))..)))))).)))....((((.((.....))))))........ (-17.71 = -18.03 +   0.32)

alignment

secondary structure

dotplot

Window 6

Location	19,830,838 – 19,830,954
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.09
Mean single sequence MFE	-22.39
Consensus MFE	-14.15
Energy contribution	-14.43
Covariance contribution	0.28
Combinations/Pair	1.09
Mean z-score	-2.00
Structure conservation index	0.63
SVM decision value	-0.04
SVM RNA-class probability	0.512054
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19830838 116 - 27905053
AUUUGCAUAGAUUCUGUCAGAUAUCUCUUAGGAUUAACUUGUUCUAAUUUCUUCUUCCCAUGCCUAUUCAGGAAUUUCCCAGAAAUUAGCAUAAGCUAAUCU----AUAAGGCAUUUCCA
...(((..((((((.....)).))))((((((((((.(((((.(((((((((..........(((....)))........))))))))).))))).))))))----.)))))))...... ( -25.47)
>DroSec_CAF1 9067 116 - 1
AUUUAACUAGAUUCAGUCAGAUAUCUCUUAGGAUUACCUUGUUCUAGUUCCUUCUAGCCAUGCCUUUUUAGGAAUUUCCCAGAAAUUAGCAUAAGCUAAUCU----AUAAGGCAUUUCCA
....(((((((..(((......((((....))))....))).)))))))..........(((((((....((......))(((..(((((....))))))))----..)))))))..... ( -21.60)
>DroSim_CAF1 13790 116 - 1
AUUUAACUAGAUUCAGUGAGAUAUAUCUUAGGAUUACCUUGUUCUAGUUCCUUCUAGCCAUGCCUUUUUAGGAAUUUCCCAGAAAUUAGCAUAAGCUAAUCU----AUAAGGCAUUUCCA
....(((((((..((((((((....)))))((....))))).)))))))..........(((((((....((......))(((..(((((....))))))))----..)))))))..... ( -23.40)
>DroEre_CAF1 9132 105 - 1
------CUAGAUUCAGUCAGAUAUCUCUUAGGAAUACCUUGUUCUAGUUCCUUCUACC-----CUUUUAAGGAAUUUCGCAGAAAUUAGCAUAAGCUAAUCU----AUAAGGCAUUUCCA
------..((((((.....)).))))....((((..(((((((((((((((((.....-----.....))))))))....))))((((((....))))))..----.)))))...)))). ( -21.10)
>DroYak_CAF1 9081 116 - 1
AU----UUAGAUUCAGUCUGAUAUCUUUCAGGAUUACCUUGUUCUAGUGCCUUCCAUCCAUGCCUUUUCCGGAAUUUCCCAAAAAUUAGCAUAAGCUAAUCUAUGUAUAAGGCAUUUCCA
..----.((((..((((((((......)))))......))).))))(((((((..((.((((........((......))....((((((....)))))).)))).)))))))))..... ( -20.40)
>consensus
AUUU__CUAGAUUCAGUCAGAUAUCUCUUAGGAUUACCUUGUUCUAGUUCCUUCUACCCAUGCCUUUUCAGGAAUUUCCCAGAAAUUAGCAUAAGCUAAUCU____AUAAGGCAUUUCCA
..............................(((...((((((...(((((((.................)))))))........((((((....))))))......))))))....))). (-14.15 = -14.43 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:11 2006