Locus 4141

Sequence ID	2L_DroMel_CAF1
Location	11,922,649 – 11,922,743
Length	94
Max. P	0.999952

overview

Window 2

Location	11,922,649 – 11,922,743
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	97.44
Mean single sequence MFE	-17.29
Consensus MFE	-16.71
Energy contribution	-16.91
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-3.18
Structure conservation index	0.97
SVM decision value	4.81
SVM RNA-class probability	0.999952
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11922649 94 + 22407834
CCUCCUUUUCUAGCCAGCCAGCGCUGACUCUUUCUAUUUUUUUGCUCCAUCUCUCUCUAUUACUUUGCCGCUGGCAUUUACAUGGACAAUCUAC
..(((.......((((((..(((..(....................................)..))).))))))........)))........ ( -12.28)
>DroSec_CAF1 142078 93 + 1
CCUCCUUUUCUAGCCAGCCAGCGCUGGCUCUUUCUAUUU-UUUGCUCCAUCUCUCUCUAUUACUUUGCCGCUGGCAUUUACAUGGACAAUCUAC
...........(((((((....)))))))..........-.(((.(((((...............((((...)))).....))))))))..... ( -18.25)
>DroSim_CAF1 108627 93 + 1
CCUCCUUUUCUAGCCAGCCAGCGCUGGCUCUUUCUAUUU-UUUGCUCCAUCUCUCUCUAUUACUUUGCCGCUGGCAUUUACAUGGACAAUCUAC
...........(((((((....)))))))..........-.(((.(((((...............((((...)))).....))))))))..... ( -18.25)
>DroEre_CAF1 113263 93 + 1
CCUCCUUUUCUAGCCAGCCAGCGCUGGCUCUUUCUAUUU-UUUGCUCCAUCUCUCUCUAUUACUUUGCCACUGGCAUUUACAUGGACAAUCUAC
...........(((((((....)))))))..........-.(((.(((((...............((((...)))).....))))))))..... ( -18.25)
>DroYak_CAF1 111253 94 + 1
CCUCCUUUUCUAGCCAGCCAGCGCUGGCUCUUUCUAUUUUUUUGCUCCAUCUCUCUCUGUUACAUUGCCACUGGCAUUUACAUGGACAAUCUAC
...........(((((((....)))))))............(((.((((........(((.....((((...))))...))))))))))..... ( -19.40)
>consensus
CCUCCUUUUCUAGCCAGCCAGCGCUGGCUCUUUCUAUUU_UUUGCUCCAUCUCUCUCUAUUACUUUGCCGCUGGCAUUUACAUGGACAAUCUAC
...........(((((((....)))))))............(((.(((((...............((((...)))).....))))))))..... (-16.71 = -16.91 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	11,922,649 – 11,922,743
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	97.44
Mean single sequence MFE	-21.16
Consensus MFE	-20.71
Energy contribution	-20.55
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-2.39
Structure conservation index	0.98
SVM decision value	4.03
SVM RNA-class probability	0.999763
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11922649 94 - 22407834
GUAGAUUGUCCAUGUAAAUGCCAGCGGCAAAGUAAUAGAGAGAGAUGGAGCAAAAAAAUAGAAAGAGUCAGCGCUGGCUGGCUAGAAAAGGAGG
.....((((((((.(...((((...)))).(....)......).))))).)))............(((((((....)))))))........... ( -18.80)
>DroSec_CAF1 142078 93 - 1
GUAGAUUGUCCAUGUAAAUGCCAGCGGCAAAGUAAUAGAGAGAGAUGGAGCAAA-AAAUAGAAAGAGCCAGCGCUGGCUGGCUAGAAAAGGAGG
.....((((((((.(...((((...)))).(....)......).))))).))).-..........(((((((....)))))))........... ( -21.50)
>DroSim_CAF1 108627 93 - 1
GUAGAUUGUCCAUGUAAAUGCCAGCGGCAAAGUAAUAGAGAGAGAUGGAGCAAA-AAAUAGAAAGAGCCAGCGCUGGCUGGCUAGAAAAGGAGG
.....((((((((.(...((((...)))).(....)......).))))).))).-..........(((((((....)))))))........... ( -21.50)
>DroEre_CAF1 113263 93 - 1
GUAGAUUGUCCAUGUAAAUGCCAGUGGCAAAGUAAUAGAGAGAGAUGGAGCAAA-AAAUAGAAAGAGCCAGCGCUGGCUGGCUAGAAAAGGAGG
.....((((((((.(...((((...)))).(....)......).))))).))).-..........(((((((....)))))))........... ( -21.50)
>DroYak_CAF1 111253 94 - 1
GUAGAUUGUCCAUGUAAAUGCCAGUGGCAAUGUAACAGAGAGAGAUGGAGCAAAAAAAUAGAAAGAGCCAGCGCUGGCUGGCUAGAAAAGGAGG
........(((.......((((...)))).(((..((........))..))).............(((((((....)))))))......))).. ( -22.50)
>consensus
GUAGAUUGUCCAUGUAAAUGCCAGCGGCAAAGUAAUAGAGAGAGAUGGAGCAAA_AAAUAGAAAGAGCCAGCGCUGGCUGGCUAGAAAAGGAGG
.....((((((((.(...((((...)))).............).))))).)))............(((((((....)))))))........... (-20.71 = -20.55 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:35 2006