Locus 3964

Sequence ID	3R_DroMel_CAF1
Location	10,722,771 – 10,722,931
Length	160
Max. P	0.969583

overview

Window 9

Location	10,722,771 – 10,722,891
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.33
Mean single sequence MFE	-27.46
Consensus MFE	-24.60
Energy contribution	-24.80
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.57
Structure conservation index	0.90
SVM decision value	1.21
SVM RNA-class probability	0.930529
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10722771 120 - 27905053
UGCAGAUCGCAAUGCCGGCGAAACCAAUUCCAAAAUAGAAAACCAACUGCGACUGCAGUACGCCAACAAAAUACGCAACUCCACCGAUGCCUAUAAGAAGGCCGUUUACUGCAUCCUUUU
(((((...((...(((((((.......(((.......))).....(((((....))))).))))......(((.(((.(......).))).))).....))).))...)))))....... ( -26.00)
>DroSec_CAF1 10505 120 - 1
UGCAGAUCGCAAUGCGGGCGAAACCAAUUCCAAAAUAGAAAACCAACUGCGAUUGCAGUACGCCAACAAAAUACGCAACUCCACCGAUGCCUAUAAGAAGGCUGUUUACUGCAUCCUUUU
(((((...(((.((((((((.......(((.......))).....(((((....))))).)))).........))))...........((((......)))))))...)))))....... ( -27.20)
>DroSim_CAF1 10495 120 - 1
UGCAGAUCGCAAUGCGGGCGAAACCAAUUCCAAAAUAGAAAACCAACUGCGACUGCAGUACGCCAACAAAAUACGUAACUCCACCGAUGCCUAUAAGAAGGCUGUUUACUGCAUCCUUUU
(((((((((...((..((((.......(((.......))).....(((((....))))).))))..))......((......))))))((((......))))......)))))....... ( -27.00)
>DroEre_CAF1 11887 120 - 1
UGCAGAUCGAAAUGCGGGCGAAACCAAUUCGAGAAUAGAAAACCAACUGCGACUGCAGUACGCCAACAAAAUACGCAACUCCACCGAUGCCUAUAAGAAGGCUGUUUACUGCAUCCUUUU
(((((((((...((((((((.......(((.......))).....(((((....))))).)))).........)))).......))))((((......))))......)))))....... ( -28.40)
>DroYak_CAF1 10423 120 - 1
UGCAGAUAGAAAUGCGGGCGAAACCAAUUCCAGAAUUGAAAACCAACUGCGACUGCAGUACGCCAACAAAAUACGCAACUCCACCGAUGCCUAUAAGAAAGCUGUUUACUGCAUCCUUUU
(((((.((((...((.((((....(((((....))))).......(((((....))))).))))......(((.(((.(......).))).)))......))..)))))))))....... ( -28.70)
>consensus
UGCAGAUCGCAAUGCGGGCGAAACCAAUUCCAAAAUAGAAAACCAACUGCGACUGCAGUACGCCAACAAAAUACGCAACUCCACCGAUGCCUAUAAGAAGGCUGUUUACUGCAUCCUUUU
(((((.......((..((((.......(((.......))).....(((((....))))).))))..))....................((((......))))......)))))....... (-24.60 = -24.80 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	10,722,811 – 10,722,931
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.67
Mean single sequence MFE	-33.92
Consensus MFE	-31.10
Energy contribution	-30.62
Covariance contribution	-0.48
Combinations/Pair	1.10
Mean z-score	-1.59
Structure conservation index	0.92
SVM decision value	1.64
SVM RNA-class probability	0.969583
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10722811 120 - 27905053
GCGAAGCGGGCAGUAGCCACGAUGAGUUUGCCCAGCUCGUUGCAGAUCGCAAUGCCGGCGAAACCAAUUCCAAAAUAGAAAACCAACUGCGACUGCAGUACGCCAACAAAAUACGCAACU
(((..((((((....))).(((((((((.....))))))))).....)))......((((.......(((.......))).....(((((....))))).)))).........))).... ( -34.70)
>DroSec_CAF1 10545 120 - 1
GCGAAGCCGGCAGUAGCCACGAUGAGUUUGCCCAGCUCGUUGCAGAUCGCAAUGCGGGCGAAACCAAUUCCAAAAUAGAAAACCAACUGCGAUUGCAGUACGCCAACAAAAUACGCAACU
(((..((.(((....))).(((((((((.....)))))))))......))..((..((((.......(((.......))).....(((((....))))).))))..)).....))).... ( -33.70)
>DroSim_CAF1 10535 120 - 1
GCGAAGCCGGCAGUAGCCACGAUGAGUUUGCCCAGCUCGUUGCAGAUCGCAAUGCGGGCGAAACCAAUUCCAAAAUAGAAAACCAACUGCGACUGCAGUACGCCAACAAAAUACGUAACU
((((....(((....))).(((((((((.....)))))))))....))))..((..((((.......(((.......))).....(((((....))))).))))..))............ ( -33.30)
>DroEre_CAF1 11927 120 - 1
GCGAAGCGGGCAGUAGCCACGAUGAGUUUGCCCAGCUUGUUGCAGAUCGAAAUGCGGGCGAAACCAAUUCGAGAAUAGAAAACCAACUGCGACUGCAGUACGCCAACAAAAUACGCAACU
(((((((((((((...(......)...)))))).))))((((((........))).((((.......(((.......))).....(((((....))))).)))))))......))).... ( -34.50)
>DroYak_CAF1 10463 120 - 1
GUGAAGCUGGCAGUAGCCACGAUGAGUUUGCCCAGCUCGUUGCAGAUAGAAAUGCGGGCGAAACCAAUUCCAGAAUUGAAAACCAACUGCGACUGCAGUACGCCAACAAAAUACGCAACU
(((..((((((....))))(((((((((.....)))))))))...........)).((((....(((((....))))).......(((((....))))).)))).........))).... ( -33.40)
>consensus
GCGAAGCCGGCAGUAGCCACGAUGAGUUUGCCCAGCUCGUUGCAGAUCGCAAUGCGGGCGAAACCAAUUCCAAAAUAGAAAACCAACUGCGACUGCAGUACGCCAACAAAAUACGCAACU
(((..((.(((....))).(((((((((.....)))))))))...........)).((((.......(((.......))).....(((((....))))).)))).........))).... (-31.10 = -30.62 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:43 2006