Locus 1696

Sequence ID	X_DroMel_CAF1
Location	4,728,456 – 4,728,552
Length	96
Max. P	0.802859

overview

Window 5

Location	4,728,456 – 4,728,552
Length	96
Sequences	3
Columns	110
Reading direction	forward
Mean pairwise identity	79.81
Mean single sequence MFE	-9.09
Consensus MFE	-7.20
Energy contribution	-7.20
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.79
SVM decision value	0.62
SVM RNA-class probability	0.802859
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4728456 96 + 22224390
CUUUCUCCACAUUUUGCAGCUUUACAGCUCGCCACAAUGAAACUUUUUAGUUGAUUUUAUUAUUUUUUCCCCACUUC-----------CAUUCAAUUU---UUGUUUUUU
.........((((..((((((....)))).))...))))((((.....((((((.......................-----------...)))))).---..))))... (  -8.87)
>DroSec_CAF1 21484 89 + 1
CUUUCUCGACAUUUUGCAGCUUUGCAGCUCGCCACAAUGAAACUUUUUAGUUUAUUUUAUUAUUUUUUCCCCACUUC-----------CAUUCA----------UUUUUU
.........((((..((((((....)))).))...))))(((((....)))))........................-----------......----------...... (  -8.40)
>DroEre_CAF1 24815 105 + 1
CUUUUUCGACAUUUUGCAGCUUUACAGCUCGCCACAAUGAAACUUUUUAGUUGAUUUUAUUAUUUUUUCCCCACUUUCCCUUACAUUCGGUUUG----GUAUUUUUUUU-
((...((((((((..((((((....)))).))...)))).((((....))))..................................))))...)----)..........- ( -10.00)
>consensus
CUUUCUCGACAUUUUGCAGCUUUACAGCUCGCCACAAUGAAACUUUUUAGUUGAUUUUAUUAUUUUUUCCCCACUUC___________CAUUCA_______UU_UUUUUU
.........((((..((((((....)))).))...)))).((((....)))).......................................................... ( -7.20 =  -7.20 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	4,728,456 – 4,728,552
Length	96
Sequences	3
Columns	110
Reading direction	reverse
Mean pairwise identity	79.81
Mean single sequence MFE	-12.09
Consensus MFE	-9.10
Energy contribution	-9.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	0.75
SVM decision value	0.14
SVM RNA-class probability	0.601492
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4728456 96 - 22224390
AAAAAACAA---AAAUUGAAUG-----------GAAGUGGGGAAAAAAUAAUAAAAUCAACUAAAAAGUUUCAUUGUGGCGAGCUGUAAAGCUGCAAAAUGUGGAGAAAG
.....(((.---......((((-----------(((.(.((...................))....).)))))))...((.((((....))))))....)))........ ( -11.21)
>DroSec_CAF1 21484 89 - 1
AAAAAA----------UGAAUG-----------GAAGUGGGGAAAAAAUAAUAAAAUAAACUAAAAAGUUUCAUUGUGGCGAGCUGCAAAGCUGCAAAAUGUCGAGAAAG
....((----------((((..-----------....(((....................)))......))))))...((.((((....))))))............... ( -10.65)
>DroEre_CAF1 24815 105 - 1
-AAAAAAAAUAC----CAAACCGAAUGUAAGGGAAAGUGGGGAAAAAAUAAUAAAAUCAACUAAAAAGUUUCAUUGUGGCGAGCUGUAAAGCUGCAAAAUGUCGAAAAAG
-..........(----((..((........)).....)))................((((((....)))).((((...((.((((....))))))..))))..))..... ( -14.40)
>consensus
AAAAAA_AA_______UGAAUG___________GAAGUGGGGAAAAAAUAAUAAAAUCAACUAAAAAGUUUCAUUGUGGCGAGCUGUAAAGCUGCAAAAUGUCGAGAAAG
.......................................................................((((...((.((((....))))))..))))......... ( -9.10 =  -9.10 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:51 2006