Locus 6980

Sequence ID	2L_DroMel_CAF1
Location	19,399,746 – 19,399,836
Length	90
Max. P	0.955988

overview

Window 4

Location	19,399,746 – 19,399,836
Length	90
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	74.34
Mean single sequence MFE	-18.02
Consensus MFE	-8.34
Energy contribution	-8.38
Covariance contribution	0.04
Combinations/Pair	1.07
Mean z-score	-2.06
Structure conservation index	0.46
SVM decision value	1.15
SVM RNA-class probability	0.922864
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19399746 90 + 22407834
ACAUUUAGAUUCCGAAUGCUAAAUGAAUGCUAGAUGUCUAGUC-----AAGAUGUGUAAAAUUCAUAUAGAGGAAUCAAAUGUGUCAGUGGCAAA
((((((.((((((.....(((.((((((..((.((((((....-----.)))))).))..)))))).))).))))))))))))((.....))... ( -25.60)
>DroSec_CAF1 2743 83 + 1
ACAUUUCGAUUCCGAAUGGUAAAUGAAG-------GUCUAGUC-----UAGAUGUGUGAAAUGCAUAUAGAGGAAUCAAAUGUGUCAGUGGCAAA
((((((.((((((((.(((.........-------..))).))-----...((((((.....))))))...))))))))))))((.....))... ( -17.40)
>DroSim_CAF1 2742 83 + 1
ACAUUUCGAUUCCGAAUGGUAAAUGAAG-------GUGUAGUC-----UAGAGGUGUGAAAUACAUAUAGAGGAAUCAAAUGUGUCAGUGGCAAA
((((((.((((((..((.....))....-------......((-----((...(((((...))))).))))))))))))))))((.....))... ( -15.70)
>DroEre_CAF1 2685 73 + 1
GCAUUUAGAUUCCCAAUGGUAA-UAGAG-------GUAUAAAU---------UA-AUUAAAUCCAUUUAAAGGAAUCAAAUGUGCCAGUAG----
((((((.((((((.((((((((-(.((.-------.......)---------).-))))...)))))....))))))))))))........---- ( -14.20)
>DroYak_CAF1 2698 87 + 1
ACAUUUAGAUUCCCAAUGGUAUGUGUAA-------GUAUAGAUAGGCUUAGAUA-UAGAAACCCAUAUAAAAGAAUCAAAUGUGUCAGUGGCAAA
((((((.(((((...(((((((((.(((-------((........))))).)))-)).....))))......)))))))))))((.....))... ( -17.20)
>consensus
ACAUUUAGAUUCCGAAUGGUAAAUGAAG_______GUAUAGUC_____UAGAUGUGUGAAAUCCAUAUAGAGGAAUCAAAUGUGUCAGUGGCAAA
((((((.((((((..(((.............................................))).....))))))))))))............ ( -8.34 =  -8.38 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	19,399,746 – 19,399,836
Length	90
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	74.34
Mean single sequence MFE	-13.80
Consensus MFE	-7.54
Energy contribution	-7.58
Covariance contribution	0.04
Combinations/Pair	1.08
Mean z-score	-2.09
Structure conservation index	0.55
SVM decision value	1.46
SVM RNA-class probability	0.955988
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19399746 90 - 22407834
UUUGCCACUGACACAUUUGAUUCCUCUAUAUGAAUUUUACACAUCUU-----GACUAGACAUCUAGCAUUCAUUUAGCAUUCGGAAUCUAAAUGU
............((((((((((((.(((.((((((....((.....)-----).((((....)))).)))))).))).....)))))).)))))) ( -17.40)
>DroSec_CAF1 2743 83 - 1
UUUGCCACUGACACAUUUGAUUCCUCUAUAUGCAUUUCACACAUCUA-----GACUAGAC-------CUUCAUUUACCAUUCGGAAUCGAAAUGU
............((((((((((((((((.(((.........))).))-----))...(..-------...)...........)))))).)))))) ( -12.80)
>DroSim_CAF1 2742 83 - 1
UUUGCCACUGACACAUUUGAUUCCUCUAUAUGUAUUUCACACCUCUA-----GACUACAC-------CUUCAUUUACCAUUCGGAAUCGAAAUGU
............((((((((((((......(((.....)))......-----((......-------..))...........)))))).)))))) ( -10.50)
>DroEre_CAF1 2685 73 - 1
----CUACUGGCACAUUUGAUUCCUUUAAAUGGAUUUAAU-UA---------AUUUAUAC-------CUCUA-UUACCAUUGGGAAUCUAAAUGC
----.........((((((((((((...((((((..(((.-..---------..)))...-------.))))-))......))))))).))))). ( -13.30)
>DroYak_CAF1 2698 87 - 1
UUUGCCACUGACACAUUUGAUUCUUUUAUAUGGGUUUCUA-UAUCUAAGCCUAUCUAUAC-------UUACACAUACCAUUGGGAAUCUAAAUGU
............((((((((((((..((.((((((((...-.....)))))))).))...-------.....((......)))))))).)))))) ( -15.00)
>consensus
UUUGCCACUGACACAUUUGAUUCCUCUAUAUGGAUUUCACACAUCUA_____GACUAGAC_______CUUCAUUUACCAUUCGGAAUCUAAAUGU
............((((((((((((..........................................................)))))).)))))) ( -7.54 =  -7.58 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:29 2006