Locus 6533

Sequence ID	3R_DroMel_CAF1
Location	17,240,847 – 17,240,939
Length	92
Max. P	0.870251

overview

Window 1

Location	17,240,847 – 17,240,939
Length	92
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	81.36
Mean single sequence MFE	-26.53
Consensus MFE	-22.06
Energy contribution	-22.54
Covariance contribution	0.48
Combinations/Pair	1.15
Mean z-score	-1.60
Structure conservation index	0.83
SVM decision value	0.41
SVM RNA-class probability	0.725916
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17240847 92 + 27905053
---------CCCGA------AUAUGAAAAUAAGAGUAACCCACUUUGGGUUCUGGAAUCUCGGGAUCUGGUAUAUGGUAUAUGGUAUCUGGAAUCCGAGAUCCCAGC
---------(((..------.(((....)))(((((.....))))))))..((((.((((((((.((..(.((((.(....).)))))..)).)))))))).)))). ( -30.50)
>DroSec_CAF1 37382 84 + 1
---------CCCGA------AUAUGAAAAUAAGAGUA-CCCACUUUGGGUUUUGGAAUCUCGGGAUCUGGUAUA-------UGGUAUCUGGAAUCCGAGAUCCCAGC
---------(((..------.(((....)))(((((.-...))))))))..((((.((((((((.((..(....-------......)..)).)))))))).)))). ( -26.20)
>DroSim_CAF1 37895 84 + 1
---------CCCGA------AUAUGAAAAUAAGAGUA-CCCACUUUGGGUUUUGGAAUCUCGGGAUCUGGUAUA-------UGGUAUCUGGAAUCCGAGAUCCCAGC
---------(((..------.(((....)))(((((.-...))))))))..((((.((((((((.((..(....-------......)..)).)))))))).)))). ( -26.20)
>DroEre_CAF1 38074 93 + 1
AUUCCCGCUCCCGA------AUAUGAAUAUAGGAGUA-CCCACUUUGGGUUCUGAAAUCUCGGGAUCUGGCACAU-------GGUAUCUGGAAUUUGAGAUUCCAGC
......(((((...------...........)))))(-((....(..((((((((....))))))))..).....-------)))..((((((((...)))))))). ( -24.74)
>DroYak_CAF1 57431 106 + 1
AUUCCCGCUCCCGAAAAUGAAUAUGAAUAUAAGAGUG-CCCAAUUUGGGUUCUGAAAUCUCGGGAUCUGGUAUAUGGUGUAUGGUAUCUGGAAUCCGAGAUCCCCGC
......((.........................((.(-(((.....)))).))...((((((((.((..(.((((.(....).)))))..)).))))))))....)) ( -25.00)
>consensus
_________CCCGA______AUAUGAAAAUAAGAGUA_CCCACUUUGGGUUCUGGAAUCUCGGGAUCUGGUAUAU______UGGUAUCUGGAAUCCGAGAUCCCAGC
.........(((((.......(((..........))).......)))))..((((.((((((((.((..(.((((........)))))..)).)))))))).)))). (-22.06 = -22.54 +   0.48)

alignment

secondary structure

dotplot

Window 2

Location	17,240,847 – 17,240,939
Length	92
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	81.36
Mean single sequence MFE	-24.90
Consensus MFE	-18.32
Energy contribution	-18.76
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-1.95
Structure conservation index	0.74
SVM decision value	0.87
SVM RNA-class probability	0.870251
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17240847 92 - 27905053
GCUGGGAUCUCGGAUUCCAGAUACCAUAUACCAUAUACCAGAUCCCGAGAUUCCAGAACCCAAAGUGGGUUACUCUUAUUUUCAUAU------UCGGG---------
.((((((((((((..((...(((..........)))....))..))))))))))))(((((.....)))))................------.....--------- ( -27.20)
>DroSec_CAF1 37382 84 - 1
GCUGGGAUCUCGGAUUCCAGAUACCA-------UAUACCAGAUCCCGAGAUUCCAAAACCCAAAGUGGG-UACUCUUAUUUUCAUAU------UCGGG---------
..(((((((((((..((.........-------.......))..)))))))))))..((((.....)))-)................------.....--------- ( -23.49)
>DroSim_CAF1 37895 84 - 1
GCUGGGAUCUCGGAUUCCAGAUACCA-------UAUACCAGAUCCCGAGAUUCCAAAACCCAAAGUGGG-UACUCUUAUUUUCAUAU------UCGGG---------
..(((((((((((..((.........-------.......))..)))))))))))..((((.....)))-)................------.....--------- ( -23.49)
>DroEre_CAF1 38074 93 - 1
GCUGGAAUCUCAAAUUCCAGAUACC-------AUGUGCCAGAUCCCGAGAUUUCAGAACCCAAAGUGGG-UACUCCUAUAUUCAUAU------UCGGGAGCGGGAAU
.(((((((.....))))))).....-------..........(((((..........((((.....)))-).(((((..((....))------..)))))))))).. ( -27.20)
>DroYak_CAF1 57431 106 - 1
GCGGGGAUCUCGGAUUCCAGAUACCAUACACCAUAUACCAGAUCCCGAGAUUUCAGAACCCAAAUUGGG-CACUCUUAUAUUCAUAUUCAUUUUCGGGAGCGGGAAU
...(..(((((((..((...(((..........)))....))..)))))))..)(((.(((.....)))-...))).............(((..((....))..))) ( -23.10)
>consensus
GCUGGGAUCUCGGAUUCCAGAUACCA______AUAUACCAGAUCCCGAGAUUCCAGAACCCAAAGUGGG_UACUCUUAUUUUCAUAU______UCGGG_________
.((((((((((((..((..((((..........))).)..))..))))))))))))..(((.....)))...................................... (-18.32 = -18.76 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:45 2006