Locus 4183

Sequence ID	2L_DroMel_CAF1
Location	11,980,307 – 11,980,437
Length	130
Max. P	0.999019

overview

Window 2

Location	11,980,307 – 11,980,411
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	69.94
Mean single sequence MFE	-20.87
Consensus MFE	-11.34
Energy contribution	-13.54
Covariance contribution	2.20
Combinations/Pair	1.22
Mean z-score	-2.67
Structure conservation index	0.54
SVM decision value	3.33
SVM RNA-class probability	0.999019
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11980307 104 - 22407834
UCUACCCCUAGAUGCAUAUGUGUACGGAUACAUCUCUAUUCGUACACUGAAAACAAUUACCA----------------AUUCCUAUUAUAAUAGAUCUGUCUAAAUUACAUGUGUAUCUU
.........(((((((((((((((((((((......))))))))).................----------------.............((((....))))....)))))))))))). ( -25.80)
>DroSec_CAF1 199715 104 - 1
UCUACCCCUAGGUGCAUAUGUGUACGGAUACAUCUCUAUUCGUACACUGAAAACAAUUACCA----------------AUUACUAAUAUAAAAUAUCUGUCCAAAUUACAUGUGUAUCUU
.........(((((((((((((((((((((......))))))))).................----------------...((..((((...))))..)).......)))))))))))). ( -22.40)
>DroSim_CAF1 166171 104 - 1
UCUACCCCUAGGUGCAUAUGUGUACGGAUACAUCUCUAUUCGUACACUGGAAACAAUUACCA----------------AUUACUAAUAUAAAAUAUCUGUCCAAAUUACAUGUGUAUCUU
.........(((((((((((((((((((((......)))))))))..((....)).......----------------.............................)))))))))))). ( -26.10)
>DroEre_CAF1 174306 119 - 1
UCUACCCCUAGGUGCAUACGUGUACAGAUAUGUCUUCAUUCGCACACUGGAAAUAAUUACGUUGCGCCUCGUAUUUCAAAAACUUUUCUAUAAGAUCUUUUCUAUUUGAUCAACUAU-UU
.........(((((((.(((((..(((...(((........)))..)))........))))))))))))........................((((..........))))......-.. ( -18.70)
>DroYak_CAF1 171338 114 - 1
UCUACCCCUAGUUGCAUAUGUGUACAGAUAUAUCUUCAUUUGCACACUGAAAAUAAUUACUAUAUGUCAUGUAUUUAAAAG-----UUAGUAAAGUACUUAACAAUUGAUCAAUCAU-UU
........((((((.....((((.(((((........))))).)))).........((((((...................-----.)))))).........)))))).........-.. ( -11.35)
>consensus
UCUACCCCUAGGUGCAUAUGUGUACGGAUACAUCUCUAUUCGUACACUGAAAACAAUUACCA________________AUUACUAAUAUAAAAGAUCUGUCCAAAUUACAUGUGUAUCUU
.........(((((((((((((((((((((......)))))))))))((....))......................................................)))))))))). (-11.34 = -13.54 +   2.20)

alignment

secondary structure

dotplot

Window 3

Location	11,980,347 – 11,980,437
Length	90
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	82.21
Mean single sequence MFE	-22.86
Consensus MFE	-18.56
Energy contribution	-19.40
Covariance contribution	0.84
Combinations/Pair	1.08
Mean z-score	-1.53
Structure conservation index	0.81
SVM decision value	0.15
SVM RNA-class probability	0.605974
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11980347 90 - 22407834
UCGUGACUGGAACCCCAUGUGAUGGCUCUACCCCUAGAUGCAUAUGUGUACGGAUACAUCUCUAUUCGUACACUGAAAACAAUUACCA----------------AU
.(((.(((((....))).)).)))((((((....)))).))....(((((((((((......)))))))))))...............----------------.. ( -23.80)
>DroSec_CAF1 199755 90 - 1
UCGUGACUGGAACCCCAUGUGAUGGCUCUACCCCUAGGUGCAUAUGUGUACGGAUACAUCUCUAUUCGUACACUGAAAACAAUUACCA----------------AU
.(((.(((((....))).)).)))((((((....)))).))....(((((((((((......)))))))))))...............----------------.. ( -22.90)
>DroSim_CAF1 166211 90 - 1
UCGUGACUGGAACCCCAUGUGAUGGCUCUACCCCUAGGUGCAUAUGUGUACGGAUACAUCUCUAUUCGUACACUGGAAACAAUUACCA----------------AU
((((.(((((....))).)).))))...........((((.....(((((((((((......)))))))))))((....))..)))).----------------.. ( -26.40)
>DroEre_CAF1 174345 106 - 1
UCGUGACUGGAACCCCAUGUGAUGGCUCUACCCCUAGGUGCAUACGUGUACAGAUAUGUCUUCAUUCGCACACUGGAAAUAAUUACGUUGCGCCUCGUAUUUCAAA
((((.(((((....))).)).))))..........(((((((.(((((..(((...(((........)))..)))........))))))))))))........... ( -21.90)
>DroYak_CAF1 171372 106 - 1
UCGUGACUGGAACCCCAUGUGAUGGCUCUACCCCUAGUUGCAUAUGUGUACAGAUAUAUCUUCAUUUGCACACUGAAAAUAAUUACUAUAUGUCAUGUAUUUAAAA
.(((((((((....))).(((((.((.(((....)))..))....((((.(((((........))))).))))........))))).....))))))......... ( -19.30)
>consensus
UCGUGACUGGAACCCCAUGUGAUGGCUCUACCCCUAGGUGCAUAUGUGUACGGAUACAUCUCUAUUCGUACACUGAAAACAAUUACCA________________AU
.(((.(((((....))).)).)))((((((....)))).))....(((((((((((......)))))))))))................................. (-18.56 = -19.40 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:50 2006