Locus 4876

Sequence ID	3R_DroMel_CAF1
Location	12,830,397 – 12,830,517
Length	120
Max. P	0.810911

overview

Window 5

Location	12,830,397 – 12,830,517
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.00
Mean single sequence MFE	-41.70
Consensus MFE	-32.76
Energy contribution	-32.56
Covariance contribution	-0.20
Combinations/Pair	1.19
Mean z-score	-1.57
Structure conservation index	0.79
SVM decision value	0.29
SVM RNA-class probability	0.670152
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12830397 120 + 27905053
AAACCACUUCCGGAGGGCAGUAGCUUGCGAACUGAGUGUGAGAACUCACUCAAGGGAAAUCGAGAGGGUCACUAUGCUUUCAGAAGGCUACUUGGGAGCAGCCACUACAGGAACGGUUUC
(((((..((((..((((((((..(((.(((.(((((((........))))).)).....)))...)))..))).((((..(((........)))..))))))).))...)))).))))). ( -38.10)
>DroSec_CAF1 7643 120 + 1
AAACCACUUCCGGUGGGCAGUAGUUUGCGAACCGAGUGUGAAAAUUCGCUCAAGGGAAACCAGGAGGGUCACCAUGCCUUCAGGAGGCUACUCGGGAGUAGCCACUAUAGGAACGGUUUC
(((((.((((((((..((((....))))..)))(((((........)))))..((....)).))))).........(((..((..(((((((....))))))).))..)))...))))). ( -47.20)
>DroSim_CAF1 6589 120 + 1
AAACCACUUCCGGUGGGCAGUAGUUUGCGAACCGAGUGUGAAAAUUCGCUCAAAGGAAACCGGGAGGGUCACCAUGCCUUCAGGAGGCUACUCGGGAGCAGCCACUACAGGAACGGUUUC
(((((..((((.(((((.((((((((.(...(((((((........)))))...(....).))((((((......)))))).).)))))))))((......)).)))).)))).))))). ( -40.60)
>DroEre_CAF1 7765 120 + 1
AAACCACUUCCCGAGGGCAGUAGUUUGCGCACCGAGUGUGAAAACUCGCUCACGGGAAACGGGGAGGGUCACCAUGCCUUCAGGAGGCUACUUGGGAGCAGCCACUACAGGGACGGUUUC
(((((.(((((((.(.((((....)))).).(((.(.((((....)))).).)))....))))))).(((.((...((....)).((((.((....)).))))......)))))))))). ( -44.50)
>DroYak_CAF1 7822 120 + 1
AAACCACUUCCAGAGGGCAGUAGUUUACGAACGGAGUGUGAAAACUCGCUCAAGGGAAACCGAGAGGGUCACCAUGCUUUUAGGAGGCUACUUGGUAGCAGCCACUACAGGAAUGGAUUC
...(((.((((..(((((((((((((.(....((((((((...((((.(((..((....))))).))))...))))))))..).))))))))((....))))).))...))))))).... ( -38.10)
>consensus
AAACCACUUCCGGAGGGCAGUAGUUUGCGAACCGAGUGUGAAAACUCGCUCAAGGGAAACCGGGAGGGUCACCAUGCCUUCAGGAGGCUACUUGGGAGCAGCCACUACAGGAACGGUUUC
(((((..((((..(((((((((((((.(.....(((((........)))))..((....))..((((((......)))))).).)))))))).(....).))).))...)))).))))). (-32.76 = -32.56 +  -0.20)

alignment

secondary structure

dotplot

Window 6

Location	12,830,397 – 12,830,517
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.00
Mean single sequence MFE	-38.76
Consensus MFE	-33.64
Energy contribution	-33.60
Covariance contribution	-0.04
Combinations/Pair	1.23
Mean z-score	-1.48
Structure conservation index	0.87
SVM decision value	0.65
SVM RNA-class probability	0.810911
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12830397 120 - 27905053
GAAACCGUUCCUGUAGUGGCUGCUCCCAAGUAGCCUUCUGAAAGCAUAGUGACCCUCUCGAUUUCCCUUGAGUGAGUUCUCACACUCAGUUCGCAAGCUACUGCCCUCCGGAAGUGGUUU
.((((((((((.((((((((((((....))))))).......(((...((((....(((((......)))))(((((......)))))..))))..)))))))).....)))).)))))) ( -35.00)
>DroSec_CAF1 7643 120 - 1
GAAACCGUUCCUAUAGUGGCUACUCCCGAGUAGCCUCCUGAAGGCAUGGUGACCCUCCUGGUUUCCCUUGAGCGAAUUUUCACACUCGGUUCGCAAACUACUGCCCACCGGAAGUGGUUU
...(((((.(((.(((.(((((((....)))))))..))).))).)))))((((.....))))........(((((((.........)))))))((((((((.((....)).)))))))) ( -39.90)
>DroSim_CAF1 6589 120 - 1
GAAACCGUUCCUGUAGUGGCUGCUCCCGAGUAGCCUCCUGAAGGCAUGGUGACCCUCCCGGUUUCCUUUGAGCGAAUUUUCACACUCGGUUCGCAAACUACUGCCCACCGGAAGUGGUUU
...(((((.(((.(((.(((((((....)))))))..))).))).)))))((((((.(((((.......(((.(........).)))((...(((......)))))))))).)).)))). ( -41.20)
>DroEre_CAF1 7765 120 - 1
GAAACCGUCCCUGUAGUGGCUGCUCCCAAGUAGCCUCCUGAAGGCAUGGUGACCCUCCCCGUUUCCCGUGAGCGAGUUUUCACACUCGGUGCGCAAACUACUGCCCUCGGGAAGUGGUUU
...(((((.(((.(((.(((((((....)))))))..))).))).)))))........((((((((((.(.((.(((((.(.(((...))).).)))))...)).).))))))))))... ( -44.10)
>DroYak_CAF1 7822 120 - 1
GAAUCCAUUCCUGUAGUGGCUGCUACCAAGUAGCCUCCUAAAAGCAUGGUGACCCUCUCGGUUUCCCUUGAGCGAGUUUUCACACUCCGUUCGUAAACUACUGCCCUCUGGAAGUGGUUU
((((.(((.(...(((.(((((((....)))))))..)))...).)))((((....((((.((......)).))))...)))).....))))..((((((((.((....)).)))))))) ( -33.60)
>consensus
GAAACCGUUCCUGUAGUGGCUGCUCCCAAGUAGCCUCCUGAAGGCAUGGUGACCCUCCCGGUUUCCCUUGAGCGAGUUUUCACACUCGGUUCGCAAACUACUGCCCUCCGGAAGUGGUUU
...(((((.(((.(((.(((((((....)))))))..))).))).)))))((((((.((((........((((((((......)))).))))(((......)))...)))).)).)))). (-33.64 = -33.60 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:01 2006