Locus 7554

Sequence ID	3R_DroMel_CAF1
Location	20,236,268 – 20,236,358
Length	90
Max. P	0.914098

overview

Window 1

Location	20,236,268 – 20,236,358
Length	90
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	70.33
Mean single sequence MFE	-31.00
Consensus MFE	-9.04
Energy contribution	-8.58
Covariance contribution	-0.45
Combinations/Pair	1.46
Mean z-score	-2.07
Structure conservation index	0.29
SVM decision value	0.26
SVM RNA-class probability	0.656486
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20236268 90 + 27905053
-CUGAAUGUGCCGCGUUUUUGCAAGGAUAUGAAUGUAUGAGUGUGAGUG----U-------GUGGCACAAAUGCCGCACGCAACGCACGCAGGUAUUUUUUU------
-..(((.((((((((....)))...............((.(((((.(((----(-------((((((....))))))))))..))))).))))))).)))..------ ( -32.00)
>DroVir_CAF1 62478 90 + 1
UGCGCGUGUGU-ACGCGUC--------UGCAAACGUGUGUCCGUGUGUGUAAGC-------GUGGU-UAAGUGUGGCACAC-ACGCUGGCAGGUAUUUGUACCCGUAG
.((((((....-)))))).--------((((((..(.(((((((((((((..((-------.....-...))...))))))-)))..)))).)..))))))....... ( -33.80)
>DroSec_CAF1 47304 94 + 1
-CUGAAUGUGCCGCGUUUUUGCAAGGAUAUGAAUGUAUGCGUGUGAGUG----UGUUGUGUGUGCCACAAAUGCCGCACGCAACGCACGCAGGUAUUUU---------
-......(((((((....(..((.(.((((....)))).).))..)(((----(((((((((((.((....)).)))))))))))))))).)))))...--------- ( -36.30)
>DroSim_CAF1 51302 94 + 1
-CUGAAUGUGCCGCGUUUUUGCAAGGAUAUGAAUGUAUGAGUGUGAGUG----UGUUGUGUGUGCCACAAAUGCCGCACGCAACGCACGCAGGUAUUUU---------
-......(((((((....(..((...((((....))))...))..)(((----(((((((((((.((....)).)))))))))))))))).)))))...--------- ( -34.10)
>DroEre_CAF1 48461 86 + 1
-CUGAAUGUGCCGCGCUUUUGCAAGGAUAUGAAUGUACGAGUG----------U-------GUGGUGCAAAUGCCGCACGCAACGCACGCAGGUAUUUUUUUG----G
-(..((.(((((((((....))............((.((.(((----------(-------(((((......)))))))))..)).)))).)))))...))..----) ( -27.00)
>DroYak_CAF1 49575 86 + 1
-CUGAAUGUGCGGCGUUUCUGCAAGGAUAUGAAUGUAUGGGUA----------U-------GUGCCACAAAUGCCGCACGCAACGCACGCAGGUAUUUUUUUG----U
-....((.(((((((((.((((....((((....)))).((((----------(-------.........)))))))).).))))).)))).)).........----. ( -22.80)
>consensus
_CUGAAUGUGCCGCGUUUUUGCAAGGAUAUGAAUGUAUGAGUGUGAGUG____U_______GUGCCACAAAUGCCGCACGCAACGCACGCAGGUAUUUUUUU______
......(((((.((((((.((............................................)).)))))).)))))............................ ( -9.04 =  -8.58 +  -0.45)

alignment

secondary structure

dotplot

Window 2

Location	20,236,268 – 20,236,358
Length	90
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	70.33
Mean single sequence MFE	-22.43
Consensus MFE	-12.14
Energy contribution	-12.58
Covariance contribution	0.43
Combinations/Pair	1.31
Mean z-score	-1.76
Structure conservation index	0.54
SVM decision value	1.09
SVM RNA-class probability	0.914098
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20236268 90 - 27905053
------AAAAAAAUACCUGCGUGCGUUGCGUGCGGCAUUUGUGCCAC-------A----CACUCACACUCAUACAUUCAUAUCCUUGCAAAAACGCGGCACAUUCAG-
------..........((((((...(((((((.((((....)))).)-------)----)..........(((......)))....))))..)))))).........- ( -21.70)
>DroVir_CAF1 62478 90 - 1
CUACGGGUACAAAUACCUGCCAGCGU-GUGUGCCACACUUA-ACCAC-------GCUUACACACACGGACACACGUUUGCA--------GACGCGU-ACACACGCGCA
...((((((....))))))...((((-(((((.........-...((-------((.....((.(((......))).))..--------...))))-.))))))))). ( -26.92)
>DroSec_CAF1 47304 94 - 1
---------AAAAUACCUGCGUGCGUUGCGUGCGGCAUUUGUGGCACACACAACA----CACUCACACGCAUACAUUCAUAUCCUUGCAAAAACGCGGCACAUUCAG-
---------.......(((.(((.(((((((((.((....)).))))........----.........(((..............)))......))))).))).)))- ( -23.64)
>DroSim_CAF1 51302 94 - 1
---------AAAAUACCUGCGUGCGUUGCGUGCGGCAUUUGUGGCACACACAACA----CACUCACACUCAUACAUUCAUAUCCUUGCAAAAACGCGGCACAUUCAG-
---------.......(((.(((.(((((((...(((.(((((.....)))))..----...........(((......)))...)))....))))))).))).)))- ( -21.00)
>DroEre_CAF1 48461 86 - 1
C----CAAAAAAAUACCUGCGUGCGUUGCGUGCGGCAUUUGCACCAC-------A----------CACUCGUACAUUCAUAUCCUUGCAAAAGCGCGGCACAUUCAG-
.----...........(((((((((.((.(((..((....))..)))-------.----------))..)))))............((....)))))).........- ( -21.00)
>DroYak_CAF1 49575 86 - 1
A----CAAAAAAAUACCUGCGUGCGUUGCGUGCGGCAUUUGUGGCAC-------A----------UACCCAUACAUUCAUAUCCUUGCAGAAACGCCGCACAUUCAG-
.----............((((.(((((.(((((.((....)).))))-------.----------............((......))..).))))))))).......- ( -20.30)
>consensus
______AAAAAAAUACCUGCGUGCGUUGCGUGCGGCAUUUGUGCCAC_______A____CACUCACACUCAUACAUUCAUAUCCUUGCAAAAACGCGGCACAUUCAG_
................(((.(((.(((((((...(((................................................)))....))))))).))).))). (-12.14 = -12.58 +   0.43)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:44 2006