Locus 3574

Sequence ID	2R_DroMel_CAF1
Location	11,894,710 – 11,894,820
Length	110
Max. P	0.998897

overview

Window 3

Location	11,894,710 – 11,894,820
Length	110
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	93.77
Mean single sequence MFE	-34.75
Consensus MFE	-31.50
Energy contribution	-30.58
Covariance contribution	-0.92
Combinations/Pair	1.14
Mean z-score	-1.62
Structure conservation index	0.91
SVM decision value	1.75
SVM RNA-class probability	0.975322
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11894710 110 + 20766785
GAUGAAGCUGCUCCUGCUUUUGCUUUCCCAUCGCUGCUGGCUGUUUCCGCAGCAGGAGUGGCGCAAAAAUAUCAGGCACAACAACAUCGCCUCGG------AUGGCAGCAACAACU
((((..((..(((((((....)).........(((((.((......))))))))))))..))((...........)).......))))(((....------..))).......... ( -36.30)
>DroSec_CAF1 35218 110 + 1
GAUGAAGCUGCUCCUGCUUUUGCUUUCCCAUCGCCGCUGGCUGUUUCCGCAGCAGGAGUGGCGCAAAAAUAUCAGGCACAACAACAUCGCCUCGG------AUGGCAGCAACAACU
..((..(((((.((((.((((((.........((((((.(((((....)))))...))))))))))))....))))........((((......)------))))))))..))... ( -35.80)
>DroSim_CAF1 35559 110 + 1
GAUGAAGCUGCUCCUGCUUUUGCUUUCCCAUCGCCGCUGGCUGUUUCCGCAGCAGGAGUGGCGCAAAAAUAUCAGGCACAACAACAUCGCCUCGG------AUGGCAGCAACAACU
..((..(((((.((((.((((((.........((((((.(((((....)))))...))))))))))))....))))........((((......)------))))))))..))... ( -35.80)
>DroEre_CAF1 37139 110 + 1
GAUGAAGCCGCUCCUGCUUUUGCUUUCCUAUCGCCGCUGGCUGUUUCCGCAGCAAGAGUGGCGCAAAAAUAUCAAGCACAACAACAUCGCUUUGG------AUAGCAGCAACAACU
..((..((.((....))...((((.(((...(((((((.(((((....)))))...)))))))..........((((...........)))).))------).))))))..))... ( -31.30)
>DroYak_CAF1 35725 116 + 1
GAUGAAGCUGCUCCUGCUUUUGCUUUCCUAUCGCCGCUGGCUGUUUCCGCAGCAAGAGUGGCGCAAAAAUAUCAAGCUCAACAACAUCGCUUCGGCUUCAAAUAGCAGCAACAACU
..((..((((((...((((............(((((((.(((((....)))))...)))))))..........))))...........((....)).......))))))..))... ( -34.55)
>consensus
GAUGAAGCUGCUCCUGCUUUUGCUUUCCCAUCGCCGCUGGCUGUUUCCGCAGCAGGAGUGGCGCAAAAAUAUCAGGCACAACAACAUCGCCUCGG______AUGGCAGCAACAACU
..((..((((((...((....))....((..(((((((.(((((....)))))...)))))))..........((((...........)))).))........))))))..))... (-31.50 = -30.58 +  -0.92)

alignment

secondary structure

dotplot

Window 4

Location	11,894,710 – 11,894,820
Length	110
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	93.77
Mean single sequence MFE	-40.48
Consensus MFE	-38.80
Energy contribution	-37.96
Covariance contribution	-0.84
Combinations/Pair	1.12
Mean z-score	-1.92
Structure conservation index	0.96
SVM decision value	3.27
SVM RNA-class probability	0.998897
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11894710 110 - 20766785
AGUUGUUGCUGCCAU------CCGAGGCGAUGUUGUUGUGCCUGAUAUUUUUGCGCCACUCCUGCUGCGGAAACAGCCAGCAGCGAUGGGAAAGCAAAAGCAGGAGCAGCUUCAUC
..........(((..------....)))((((..(((((.((((....((((((.((..((((((((((....).).)))))).))..))...)))))).)))).)))))..)))) ( -42.00)
>DroSec_CAF1 35218 110 - 1
AGUUGUUGCUGCCAU------CCGAGGCGAUGUUGUUGUGCCUGAUAUUUUUGCGCCACUCCUGCUGCGGAAACAGCCAGCGGCGAUGGGAAAGCAAAAGCAGGAGCAGCUUCAUC
..........(((..------....)))((((..(((((.((((....((((((.((..((((((((((....).).)))))).))..))...)))))).)))).)))))..)))) ( -41.30)
>DroSim_CAF1 35559 110 - 1
AGUUGUUGCUGCCAU------CCGAGGCGAUGUUGUUGUGCCUGAUAUUUUUGCGCCACUCCUGCUGCGGAAACAGCCAGCGGCGAUGGGAAAGCAAAAGCAGGAGCAGCUUCAUC
..........(((..------....)))((((..(((((.((((....((((((.((..((((((((((....).).)))))).))..))...)))))).)))).)))))..)))) ( -41.30)
>DroEre_CAF1 37139 110 - 1
AGUUGUUGCUGCUAU------CCAAAGCGAUGUUGUUGUGCUUGAUAUUUUUGCGCCACUCUUGCUGCGGAAACAGCCAGCGGCGAUAGGAAAGCAAAAGCAGGAGCGGCUUCAUC
(((((((.(((((((------(....(((((...)))))....)))).((((((....((.(((((((((......)).))))))).))....)))))))))).)))))))..... ( -37.90)
>DroYak_CAF1 35725 116 - 1
AGUUGUUGCUGCUAUUUGAAGCCGAAGCGAUGUUGUUGAGCUUGAUAUUUUUGCGCCACUCUUGCUGCGGAAACAGCCAGCGGCGAUAGGAAAGCAAAAGCAGGAGCAGCUUCAUC
(((((((.(((((...(.((((...((((....))))..)))).)....(((((....((.(((((((((......)).))))))).))....)))))))))).)))))))..... ( -39.90)
>consensus
AGUUGUUGCUGCCAU______CCGAGGCGAUGUUGUUGUGCCUGAUAUUUUUGCGCCACUCCUGCUGCGGAAACAGCCAGCGGCGAUGGGAAAGCAAAAGCAGGAGCAGCUUCAUC
(((((((.((((............(((((.........))))).....((((((.((..((((((((((....).).)))))).))..))...)))))))))).)))))))..... (-38.80 = -37.96 +  -0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:57 2006