Locus 6565

Sequence ID	3L_DroMel_CAF1
Location	17,379,197 – 17,379,418
Length	221
Max. P	0.999398

overview

Window 9

Location	17,379,197 – 17,379,301
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	96.06
Mean single sequence MFE	-25.28
Consensus MFE	-23.58
Energy contribution	-24.18
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.24
Structure conservation index	0.93
SVM decision value	3.57
SVM RNA-class probability	0.999398
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17379197 104 - 23771897
GGAUGCCGAGAUACUCGUACUCGUACUCGUGCUCGUGCAGAUACUUUUACUUGUGUCGCCUGAGUUUCAAUUCAAUUUGCACAUAAUUUUACAUAAUCUUCCCC
(((.((((((.(((........))))))).))..((((((((((........)))))...(((((....)))))...))))).................))).. ( -25.50)
>DroSec_CAF1 6080 104 - 1
GGAUGCCGAGAUACUCGUACUCGUACUCGUGCUCGUGCAGAUACUUUUACUUGUGUCGCCUGAGUUUCAAUUCAAUUUGCACAUAAUUUUACAUAAUCUUCCCC
(((.((((((.(((........))))))).))..((((((((((........)))))...(((((....)))))...))))).................))).. ( -25.50)
>DroSim_CAF1 5772 104 - 1
GGAUGCCGAGAUACUCGUACUGGUACUCGUGCUCGUGCAGAUACUUUUACUUGUGUCGCCUGAGUUUCAAUUCAAUUUGCACAUAAUUUUACAUAAUCUUCCCC
(((.((((((.((((......)))))))).))..((((((((((........)))))...(((((....)))))...))))).................))).. ( -26.40)
>DroEre_CAF1 6230 98 - 1
GGAUGCCGAGA------UACUCGUACUCGUGCUCGUGCAGAUACUUUUACUUGUGUCGCCUGAGUUUCAAUUCAAUUUGCACAUAAUUUUACAUAAUCUUCCCG
(((.((((((.------((....)))))).))..((((((((((........)))))...(((((....)))))...))))).................))).. ( -23.40)
>DroYak_CAF1 7133 104 - 1
GGAUGCCGAGAUACAGAUACUCGUACUCGUGCUCGUGCAGAUACUUUUACUUGUGUCGCCUGAGUUUCAAUUCAAUUUGCACAUAAUUUUACAUAAUCUUCCCC
(((.((((((.(((........))))))).))..((((((((((........)))))...(((((....)))))...))))).................))).. ( -25.60)
>consensus
GGAUGCCGAGAUACUCGUACUCGUACUCGUGCUCGUGCAGAUACUUUUACUUGUGUCGCCUGAGUUUCAAUUCAAUUUGCACAUAAUUUUACAUAAUCUUCCCC
(((.((((((.(((........))))))).))..((((((((((........)))))...(((((....)))))...))))).................))).. (-23.58 = -24.18 +   0.60)

alignment

secondary structure

dotplot

Window 0

Location	17,379,301 – 17,379,418
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.86
Mean single sequence MFE	-31.08
Consensus MFE	-21.88
Energy contribution	-22.18
Covariance contribution	0.31
Combinations/Pair	1.08
Mean z-score	-1.15
Structure conservation index	0.70
SVM decision value	0.03
SVM RNA-class probability	0.548455
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17379301 117 + 23771897
G--CGCGUGUCUGUAUCGCAUUGAUUGCCCCCUAUUGAUUGUCCAAUUCCAAUCGAGUCUAAUUAAUGCUGUCCGCUCUGGGGACACGGACCGCGGACCACUGCAAA-AUCUCGCCUAGC
(--((.((((((((...((((((((((..(....(((((((........))))))))..)))))))))).(((((...((....))))))).))))).))))))...-............ ( -35.30)
>DroPse_CAF1 5055 101 + 1
AUAUGUGUAUCUGUAUCGCUUUGAUUGCUCUUUAUUGAUUGUU------CAAUCGAAUGUAAUUAAUGCUGUCCGCUGUGGGGACACGGACUA-------CUGCAAAUAUCUCU------
...(((((((((((...((.((((((((..((.(((((....)------)))).))..)))))))).)).((((.(...).))))))))).))-------).))).........------ ( -26.30)
>DroSec_CAF1 6184 117 + 1
G--CGCGUGUCUGUAUCGCAUUGAUUGCCCCCUAUUGAUUGUCCAAUUCCAAUCGAGUCUAAUUAAUGCUGUCCGCUCUGGGGACACGGACCACGGACCAGUGCAAA-AUCUUGCCGGGC
(--(((..((((((...((((((((((..(....(((((((........))))))))..)))))))))).(((((...((....))))))).))))))..))))...-............ ( -37.40)
>DroEre_CAF1 6328 110 + 1
G--CGCGUGUCGGUAUCGCAUUGAUUGCCUCUUAUUGAAUGUCCAAUUUCAAUCGAGUCUAAUUAAUGCUGUCCGCUCUGGGGAUACGGACCA-------CAGCAAA-AUCUCGCCGAGC
(--(..(((((.(((((((((((((((.(((..((((((........)))))).)))..))))))))))...((......))))))).)).))-------).))...-............ ( -32.00)
>DroYak_CAF1 7237 110 + 1
G--CGCGUGUCGGUAUCGCAUUGAUUGCCUCUUAUUGAAUGUCCAAUUCCAAUCGAGUCUAAUUAAUGCUGUCCGCUCUGGGGACACGGACCA-------CUGCAAA-AUCUCGCCGGGC
.--......(((((...((((((((((.(((.....((((.....)))).....)))..)))))))))).(((((...((....)))))))..-------.......-.....))))).. ( -29.20)
>DroPer_CAF1 5070 100 + 1
AUAUGUGUAUCUGUAUCGCUUUGAUUGCUCUUUAUUGAUUGUU------CAAUCGAAUGUAAUUAAUGCUGUCCGCUGUGGGGACACGGACUA-------CUGCAAAUAUCUC-------
...(((((((((((...((.((((((((..((.(((((....)------)))).))..)))))))).)).((((.(...).))))))))).))-------).)))........------- ( -26.30)
>consensus
G__CGCGUGUCUGUAUCGCAUUGAUUGCCCCUUAUUGAUUGUCCAAUUCCAAUCGAGUCUAAUUAAUGCUGUCCGCUCUGGGGACACGGACCA_______CUGCAAA_AUCUCGCCG_GC
....((...........((((((((((.......(((((((........)))))))...)))))))))).(((((...((....)))))))...........))................ (-21.88 = -22.18 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:31 2006