Locus 6083

Sequence ID	3L_DroMel_CAF1
Location	16,163,294 – 16,163,483
Length	189
Max. P	0.698747

overview

Window 4

Location	16,163,294 – 16,163,406
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.22
Mean single sequence MFE	-19.72
Consensus MFE	-15.83
Energy contribution	-16.52
Covariance contribution	0.69
Combinations/Pair	1.08
Mean z-score	-1.63
Structure conservation index	0.80
SVM decision value	0.35
SVM RNA-class probability	0.698747
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16163294 112 - 23771897
--------UUUCAUAAAAUUUACCGCACUUACCAUUAUAUUAUUGAUGGGAAGUAUAUACAACUUCAAAUUAAUAUCUAUAUAUUUAUGUGUCCGAUUUACCGCCUUGAUGCGGCACAUU
--------.......(((((....((((.......((((.(((((((..(((((.......)))))..)))))))..)))).......))))..))))).((((......))))...... ( -19.74)
>DroSec_CAF1 20485 112 - 1
--------UUUUAUACAAUUUACCGCACUUACCAUUAUAUUAUUGAUGGGAAGUAUAUCCAACUUCAAAUCAAUAUGUAUAUAUUUAUGUGUUCGAUUUACCGCCUUGAUGCGGCACAUU
--------..............(((((....((((((......))))))(((((.......)))))(((((((((((((......)))))))).)))))..........)))))...... ( -24.50)
>DroSim_CAF1 23164 112 - 1
--------UUUUAUAAAAUUUAGCGCACUUACCAUUAUAUUAUUGAUGGGAAGUAUAUCCAACUUUAAAUCAAUAUCUAUAUAUUUAUGUGUUCGAUUUACCGCCUUGAUGCGGCACAUU
--------.......(((((.((((((........((((.(((((((..(((((.......)))))..)))))))..))))......)))))).))))).((((......))))...... ( -22.74)
>DroEre_CAF1 20243 120 - 1
CUUAAUUUUUUCAUUAAAAUUGCCGCACUUACCAUUAUAUUAUUAAUAGGAAGCAUAUUCAACUUCAAAUCCAUAUCUAUAUAUUUAUGUGUUCGAUUUACCGCCUUGAUGCGACACAUU
..(((((((......))))))).(((((((.((((((......)))).))))).....((((....(((((.((((.((......)).))))..)))))......))))))))....... ( -11.90)
>consensus
________UUUCAUAAAAUUUACCGCACUUACCAUUAUAUUAUUGAUGGGAAGUAUAUCCAACUUCAAAUCAAUAUCUAUAUAUUUAUGUGUUCGAUUUACCGCCUUGAUGCGGCACAUU
........................((((.......((((.(((((((..(((((.......)))))..)))))))..)))).......))))........((((......))))...... (-15.83 = -16.52 +   0.69)

alignment

secondary structure

dotplot

Window 5

Location	16,163,374 – 16,163,483
Length	109
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.97
Mean single sequence MFE	-17.50
Consensus MFE	-11.44
Energy contribution	-12.25
Covariance contribution	0.81
Combinations/Pair	1.06
Mean z-score	-1.76
Structure conservation index	0.65
SVM decision value	0.21
SVM RNA-class probability	0.635367
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16163374 109 - 23771897
AAAAAAUGGGCGGUAUCCAUUGGUAUAUCGCUUCGAAUCUAAUUUAAUCUAGAAAUUUUAAAACUGAAAGUUAAAAC-----------UUUCAUAAAAUUUACCGCACUUACCAUUAUAU
....((((((((((((((...)).))))))).....................((((((((....(((((((....))-----------)))))))))))))..........))))).... ( -21.80)
>DroSec_CAF1 20565 109 - 1
AAAAAAUGGUCGGUAUCCAUUGUUAUACCGCUUCGAUUCUAAUUUAAUCUAGAAAUUUUAAAACUAAUUGUUACAAC-----------UUUUAUACAAUUUACCGCACUUACCAUUAUAU
....(((((((((((...(((((.(((.........(((((........))))).......(((.....))).....-----------...)))))))).))))).....)))))).... ( -15.40)
>DroSim_CAF1 23244 109 - 1
AAAAAACGGGCGGUAUCCAUUGUUAUACCGCUUCGAUUCUAAUUUAAUCUAGAAAUUUUAAAACUAAUAGUUACAAC-----------UUUUAUAAAAUUUAGCGCACUUACCAUUAUAU
......((((((((((........))))))).))).................((((((((....(((.(((....))-----------).)))))))))))................... ( -14.50)
>DroEre_CAF1 20323 120 - 1
AAAAAACGGGCGGUAUCCAUUGUCAUACCGCCUUGUUUCUAUUUUAAGCUAGAAAUCAAAAAACUUAUAUUUAUUACAUUCUUAAUUUUUUCAUUAAAAUUGCCGCACUUACCAUUAUAU
.......(((((((((........))))))))).(((((((........)))))))..........................(((((((......))))))).................. ( -18.30)
>consensus
AAAAAACGGGCGGUAUCCAUUGUUAUACCGCUUCGAUUCUAAUUUAAUCUAGAAAUUUUAAAACUAAUAGUUACAAC___________UUUCAUAAAAUUUACCGCACUUACCAUUAUAU
....((((((((((((........))))))).....(((((........))))).........................................................))))).... (-11.44 = -12.25 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:38 2006