Locus 258

Sequence ID	3R_DroMel_CAF1
Location	996,752 – 996,846
Length	94
Max. P	0.818503

overview

Window 8

Location	996,752 – 996,846
Length	94
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	82.08
Mean single sequence MFE	-36.22
Consensus MFE	-25.61
Energy contribution	-28.12
Covariance contribution	2.50
Combinations/Pair	1.12
Mean z-score	-1.47
Structure conservation index	0.71
SVM decision value	0.08
SVM RNA-class probability	0.575916
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 996752 94 + 27905053
GUGGCUGUCCCGCAUUUUUCCUGCAGUUUUCCCUGUUGCUUCU------GCGGUGUCGCCACCGCCAGCUGGGGGAUAUUGACAGCGGCGGAUCGGGAGU
.......(((((.(((..(((((((((.((((((...(((...------((((((....)))))).))).)))))).)))).))).))..)))))))).. ( -39.30)
>DroPse_CAF1 52275 83 + 1
GCGGCUUGUCCGCAGUUUUCGCGCAGUUUUCCCUGUUGCUUUCCCACCAGCAGCAGCUGGAGCACCAGCUGGAGGAUAUUGAC-----------------
((((.....))))............(((((((..((((((........))))))((((((....)))))))))))))......----------------- ( -27.80)
>DroSec_CAF1 41590 94 + 1
GUGGUUGUCCCGCAUUUUUCCUGCAGUUUUCCCUGUUGCUUCU------GCGGUGUGGCCACCGCCAGCUGGGGGAUAUUGACAGCGGCGGAUCGGGAGU
.......(((((.(((..(((((((((.((((((...(((...------((((((....)))))).))).)))))).)))).))).))..)))))))).. ( -39.30)
>DroSim_CAF1 43980 94 + 1
GUGGCUGUCCCGCAUUUUUCCUGCAGUUUUCCCUGUUGCUUCU------GCGGUGUGGCCACCGCCAGCUGGGGGAUAUUGACAGCGGCGGAUCGGGAGU
.......(((((.(((..(((((((((.((((((...(((...------((((((....)))))).))).)))))).)))).))).))..)))))))).. ( -39.30)
>DroEre_CAF1 43856 93 + 1
GUG-CUGUCCCGCAUUUUUCCUGCAGCUUUCCCUGUUGCUUCU------GCGGUGUGGCCACUGCCAGCUGGGGGAUAUUGACAGCGGCGGAUCGGGAGU
...-...(((((.(((..((((((((..((((((...(((...------((((((....)))))).))).))))))..))).))).))..)))))))).. ( -35.80)
>DroYak_CAF1 46177 94 + 1
GUGGCUGUUCCGCAUUUUUCCUGCAGUUUUCCCCGUUGCUUCU------GCGGUGUGGCCACUGUCAGCUGGGGGAUAUUGACAGCGGCGGAUCGGAAGU
....(((.(((((.......(((((((.(((((((..(((...------((((((....)))))).)))))))))).)))).)))..))))).))).... ( -35.80)
>consensus
GUGGCUGUCCCGCAUUUUUCCUGCAGUUUUCCCUGUUGCUUCU______GCGGUGUGGCCACCGCCAGCUGGGGGAUAUUGACAGCGGCGGAUCGGGAGU
.......(((((.(((..(((((((((.((((((((((...........((((((....)))))))))).)))))).)))).))).))..)))))))).. (-25.61 = -28.12 +   2.50)

alignment

secondary structure

dotplot

Window 9

Location	996,752 – 996,846
Length	94
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	82.08
Mean single sequence MFE	-33.00
Consensus MFE	-21.69
Energy contribution	-23.38
Covariance contribution	1.70
Combinations/Pair	1.21
Mean z-score	-2.47
Structure conservation index	0.66
SVM decision value	0.67
SVM RNA-class probability	0.818503
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 996752 94 - 27905053
ACUCCCGAUCCGCCGCUGUCAAUAUCCCCCAGCUGGCGGUGGCGACACCGC------AGAAGCAACAGGGAAAACUGCAGGAAAAAUGCGGGACAGCCAC
..............((((((....((((...(((.((((((....))))))------...)))....))))...(((((.......)))))))))))... ( -39.30)
>DroPse_CAF1 52275 83 - 1
-----------------GUCAAUAUCCUCCAGCUGGUGCUCCAGCUGCUGCUGGUGGGAAAGCAACAGGGAAAACUGCGCGAAAACUGCGGACAAGCCGC
-----------------(((....((((.(((((((....))))))).((((........))))...))))......((((.....)))))))....... ( -26.20)
>DroSec_CAF1 41590 94 - 1
ACUCCCGAUCCGCCGCUGUCAAUAUCCCCCAGCUGGCGGUGGCCACACCGC------AGAAGCAACAGGGAAAACUGCAGGAAAAAUGCGGGACAACCAC
..(((((........((((.....((((...(((.((((((....))))))------...)))....)))).....))))........)))))....... ( -33.19)
>DroSim_CAF1 43980 94 - 1
ACUCCCGAUCCGCCGCUGUCAAUAUCCCCCAGCUGGCGGUGGCCACACCGC------AGAAGCAACAGGGAAAACUGCAGGAAAAAUGCGGGACAGCCAC
..............((((((....((((...(((.((((((....))))))------...)))....))))...(((((.......)))))))))))... ( -37.80)
>DroEre_CAF1 43856 93 - 1
ACUCCCGAUCCGCCGCUGUCAAUAUCCCCCAGCUGGCAGUGGCCACACCGC------AGAAGCAACAGGGAAAGCUGCAGGAAAAAUGCGGGACAG-CAC
..............((((((....((((...(((.((.(((....))).))------...)))....))))...(((((.......))))))))))-).. ( -32.30)
>DroYak_CAF1 46177 94 - 1
ACUUCCGAUCCGCCGCUGUCAAUAUCCCCCAGCUGACAGUGGCCACACCGC------AGAAGCAACGGGGAAAACUGCAGGAAAAAUGCGGAACAGCCAC
....(((....((((((((((............))))))))))......((------....))..)))((....(((((.......))))).....)).. ( -29.20)
>consensus
ACUCCCGAUCCGCCGCUGUCAAUAUCCCCCAGCUGGCGGUGGCCACACCGC______AGAAGCAACAGGGAAAACUGCAGGAAAAAUGCGGGACAGCCAC
..............((((((....((((...(((.((((((....)))))).........)))....))))...(((((.......)))))))))))... (-21.69 = -23.38 +   1.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:50 2006