Locus 5913

Sequence ID	3R_DroMel_CAF1
Location	15,565,004 – 15,565,193
Length	189
Max. P	0.637303

overview

Window 7

Location	15,565,004 – 15,565,100
Length	96
Sequences	4
Columns	96
Reading direction	reverse
Mean pairwise identity	80.84
Mean single sequence MFE	-29.00
Consensus MFE	-18.08
Energy contribution	-19.58
Covariance contribution	1.50
Combinations/Pair	1.04
Mean z-score	-1.74
Structure conservation index	0.62
SVM decision value	0.04
SVM RNA-class probability	0.555604
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15565004 96 - 27905053
AGGCGUUCGCCACAUGCCUGUGUGUGUGUAGCGUGUGAUUUUGUGGCGCUUGCGUGUGUGUGUAAUAAACGCCGCAGAUAGACGGACGUACUAUAU
..(((((((.(((((((.............)))))))..(((((((((.(((((......)))))....)))))))))....)))))))....... ( -31.52)
>DroSec_CAF1 90213 94 - 1
AGGCGUUCGCCACAUGCAUGUGUGUGUGUAGCGUGUGAUUUUGUGGCGCGU--GUGUGUGUGUAAUAAACGCCGCAGAUAGACGGACGUACUAUAU
..((((((((((((..((..(((.......)))..))....))))))..((--.((((.((((.....)))))))).))....))))))....... ( -32.90)
>DroSim_CAF1 84198 94 - 1
AGGCGUUCGCCACAUGCAUGUGUGUGUGUAGCGUGUGAUUUUGUGGCGCGU--GUGUGUGUGUAAUAAACGCCGCAGAUAGACGGACGUACUAUAU
..((((((((((((..((..(((.......)))..))....))))))..((--.((((.((((.....)))))))).))....))))))....... ( -32.90)
>DroYak_CAF1 88847 75 - 1
AGGCCUG-----------UGUAUGUGUACAGUGUGAU--UU-------UGUGG-GGUGUGUGUAAUAAACGCCGCAGAUAGACAGACGUACUAUAU
.......-----------.(((((.((((.((.((..--((-------(((((-.((...........)).)))))))....)).))))))))))) ( -18.70)
>consensus
AGGCGUUCGCCACAUGCAUGUGUGUGUGUAGCGUGUGAUUUUGUGGCGCGU__GUGUGUGUGUAAUAAACGCCGCAGAUAGACGGACGUACUAUAU
..((((((((((((..(((..((.......))..)))....))))))........(((.((((.....)))))))........))))))....... (-18.08 = -19.58 +   1.50)

alignment

secondary structure

dotplot

Window 8

Location	15,565,100 – 15,565,193
Length	93
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	81.13
Mean single sequence MFE	-27.79
Consensus MFE	-21.75
Energy contribution	-21.53
Covariance contribution	-0.22
Combinations/Pair	1.19
Mean z-score	-1.32
Structure conservation index	0.78
SVM decision value	0.21
SVM RNA-class probability	0.637303
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15565100 93 - 27905053
AGGGGCAAGGCCAACUAAUUGCGGCGACAUAACUUGUUGCGCCCCUCGGAGCCACGCCCCCUCCCACCUAACCGUGCACCCCGCAU-CCAAAAG
.(((((..((((........(((.(((((.....))))))))......).)))..))))).............((((.....))))-....... ( -26.74)
>DroSec_CAF1 90307 93 - 1
AGGGGCAAGGCCAACUAAUUGCGGCGACAUAACUUGUUGCGCCCCUCGGAGCCACGCC-CCUCCCACUUAGCCGAGCACCCCGCGCCCCAAAAG
.(((((..(((.........(((.(((((.....)))))))).....((((.......-.))))......)))..((.....)))))))..... ( -31.50)
>DroSim_CAF1 84292 94 - 1
AGGGGCAAGGCCAACUAAUUGCGGCGACAUAACUUGUUGCGCCCCUCGGAGCCACGCCCCCUCCCACCUAGCCGAGCACCACGCGCCCCAAAAG
.(((((..(((.........(((.(((((.....)))))))).....((((.........))))......)))..((.....)))))))..... ( -30.70)
>DroEre_CAF1 79806 78 - 1
AGGGGCAAGGCCAACUAAUUGCGGCGACAUAACUUGUUGCGCCCCUCGCUGCCACGCCCCCUCC--------------UCCCG--CCCCCAAAG
.(((((..(((.........(((.(((((.....))))))))........)))..)))))....--------------.....--......... ( -23.73)
>DroYak_CAF1 88922 92 - 1
AGGGGCAAGGCCAACUAAUUGCGGCGACAUAACUUGUUGCGCCCCUCGGAGCCACGCCCUCUUCCUACUAGCCGUGCACCCCG--CCCCCAAAG
.(((((..((((((....)))..((((((.....)))))))))....((.((.(((.(............).))))).))..)--))))..... ( -25.90)
>DroAna_CAF1 90990 72 - 1
AGGGGCAAGGCCAACUAAUUGCGGCGGCAUAACUUGUUGCGCCCCUUGGAGCCACGCCUC-UGCCCCU------------------CCCCA---
(((((((((((............((((((.....))))))((((...)).))...)))).-)))))))------------------.....--- ( -28.20)
>consensus
AGGGGCAAGGCCAACUAAUUGCGGCGACAUAACUUGUUGCGCCCCUCGGAGCCACGCCCCCUCCCACCUAGCCG_GCACCCCG__CCCCAAAAG
.(((((..(((.........(((.(((((.....))))))))........)))..))))).................................. (-21.75 = -21.53 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:38 2006