Locus 3342

Sequence ID	2L_DroMel_CAF1
Location	9,674,786 – 9,674,882
Length	96
Max. P	0.999483

overview

Window 1

Location	9,674,786 – 9,674,882
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	76.80
Mean single sequence MFE	-23.24
Consensus MFE	-18.42
Energy contribution	-18.10
Covariance contribution	-0.32
Combinations/Pair	1.25
Mean z-score	-3.49
Structure conservation index	0.79
SVM decision value	3.64
SVM RNA-class probability	0.999483
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9674786 96 + 22407834
AACCACCCAUUCAGACCACUCAGCCCACUCAGCCCGUUCAGCCAUUACGUUAUGGAGGCUUUUCAAGCCUGAAUAGUAAUCGAGUGGGCCACCCUU
......................((((((((.((..((((..((((......))))(((((.....))))))))).))....))))))))....... ( -27.00)
>DroSec_CAF1 32931 77 + 1
AACCACCC------------------ACUCAGCCCACUCAACCAUUCCGUUCUGGAGGCUUUUCAAGCCUGAAUAGUAAUCGAGUGGGCCACCCU-
........------------------.....((((((((..(((........)))(((((.....)))))...........))))))))......- ( -25.10)
>DroSim_CAF1 37741 77 + 1
AACCACCC------------------ACUCAACCCAUUCAGCCAUUCCGUUCUGGAGGCUUUUCAAGCCUGAAUAGUAAUCGAGUGGGCCACCCU-
.....(((------------------((((...........(((........)))(((((.....)))))...........))))))).......- ( -21.30)
>DroEre_CAF1 38624 72 + 1
AACC------------------ACCCACUCAGCCCACUCAGCCACUCCGUUCUAGAGGCUUUUCAAGCCUGAAUAGUAAUCGAGUGGGCC------
....------------------.........((((((((....(((..((((...(((((.....))))))))))))....)))))))).------ ( -23.90)
>DroYak_CAF1 33336 92 + 1
AACC---CACUCAACCCACUCAAUCCACUCAAUCCACUCAGCCAUUCCGUUCCAGAGGCUUUUCAAGCCUGAAUAGUAAUCGAGUGGGCCACCCA-
....---.......(((((((...............((((((......)))...)))(((.((((....)))).)))....))))))).......- ( -18.90)
>consensus
AACCACCC________________CCACUCAGCCCACUCAGCCAUUCCGUUCUGGAGGCUUUUCAAGCCUGAAUAGUAAUCGAGUGGGCCACCCU_
...............................(((((((((((......)))....(((((.....)))))...........))))))))....... (-18.42 = -18.10 +  -0.32)

alignment

secondary structure

dotplot

Window 2

Location	9,674,786 – 9,674,882
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	76.80
Mean single sequence MFE	-31.48
Consensus MFE	-21.08
Energy contribution	-21.68
Covariance contribution	0.60
Combinations/Pair	1.10
Mean z-score	-3.10
Structure conservation index	0.67
SVM decision value	3.54
SVM RNA-class probability	0.999357
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9674786 96 - 22407834
AAGGGUGGCCCACUCGAUUACUAUUCAGGCUUGAAAAGCCUCCAUAACGUAAUGGCUGAACGGGCUGAGUGGGCUGAGUGGUCUGAAUGGGUGGUU
.....(.(((((.(((...(((((((((.((.....(((((((((......))))......)))))....)).))))))))).))).))))).).. ( -33.10)
>DroSec_CAF1 32931 77 - 1
-AGGGUGGCCCACUCGAUUACUAUUCAGGCUUGAAAAGCCUCCAGAACGGAAUGGUUGAGUGGGCUGAGU------------------GGGUGGUU
-....(.(((((((((....(((((((((((.....))))(((.....))).....)))))))..)))))------------------)))).).. ( -29.80)
>DroSim_CAF1 37741 77 - 1
-AGGGUGGCCCACUCGAUUACUAUUCAGGCUUGAAAAGCCUCCAGAACGGAAUGGCUGAAUGGGUUGAGU------------------GGGUGGUU
-....(.(((((((((((..(((((((((((.....))))(((.....))).....))))))))))))))------------------)))).).. ( -31.70)
>DroEre_CAF1 38624 72 - 1
------GGCCCACUCGAUUACUAUUCAGGCUUGAAAAGCCUCUAGAACGGAGUGGCUGAGUGGGCUGAGUGGGU------------------GGUU
------.(((((((((....(((((((((((.....)))((((.....))))...))))))))..)))))))))------------------.... ( -29.10)
>DroYak_CAF1 33336 92 - 1
-UGGGUGGCCCACUCGAUUACUAUUCAGGCUUGAAAAGCCUCUGGAACGGAAUGGCUGAGUGGAUUGAGUGGAUUGAGUGGGUUGAGUG---GGUU
-.....((((((((((((..((((((((.((.....((((((((...))))..))))....)).)))))))))))))))))))).....---.... ( -33.70)
>consensus
_AGGGUGGCCCACUCGAUUACUAUUCAGGCUUGAAAAGCCUCCAGAACGGAAUGGCUGAGUGGGCUGAGUGG________________GGGUGGUU
......((((((((((....(((((((((((.....)))))........)))))).)))))))))).............................. (-21.08 = -21.68 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:14 2006