Locus 6950

Sequence ID	2L_DroMel_CAF1
Location	19,318,749 – 19,318,869
Length	120
Max. P	0.896451

overview

Window 3

Location	19,318,749 – 19,318,869
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.18
Mean single sequence MFE	-39.88
Consensus MFE	-28.26
Energy contribution	-29.10
Covariance contribution	0.84
Combinations/Pair	1.16
Mean z-score	-2.40
Structure conservation index	0.71
SVM decision value	0.99
SVM RNA-class probability	0.896451
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19318749 120 + 22407834
AUCAGGAGAUGUGACAAAUGAACUGUCACAAUAAUGCCAGCGACGAAAGGGAAUGACGACACAUGUGUUGGCACCGUUUCGGUUCUGGAGGAGUUUUCGGAUCUCCGGAUACGACUUCCC
....(((..(((((((.......)))))))......((((...(((((.((..((.(((((....))))).)))).)))))...))))((..((.(((((....))))).))..))))). ( -40.10)
>DroSec_CAF1 11333 119 + 1
AUCAGGAGAUGUGACAAAUGAACUGUCACAAUAAUGCCAGCGACGAAAGGGAAUGACGACACAUGUGUUGGCACUGUUUCGGCUCUGGAGGAGUCUCCGGAUCUCUGGUUACGAG-UCCC
....((((((((((((.......)))))).......((((.(.(((((.((..((.(((((....))))).)))).))))).).))))....))))))(((.(((.......)))-))). ( -40.70)
>DroSim_CAF1 13170 119 + 1
AUCAGGAGAUGUGACAAAUGAACUGUCACAAUAAUGCCAGCGACGAAAGGGAAUGACGACACAUGUGUUGGCACCGUUUCGGCUCUGGAGGAGUCUCCGGAUCUCUGGUUACGAG-UCCC
....((((((((((((.......)))))).......((((.(.(((((.((..((.(((((....))))).)))).))))).).))))....))))))(((.(((.......)))-))). ( -42.50)
>DroEre_CAF1 10523 100 + 1
AUCAGAGGAUGUGACAAAUGAACUGUCACAAUAAUGCCAGCGACGAAAGGGAAUGACGACACACAUGCUGGC-------------------AGUCUCCGGAUUUCUGGAGACGCG-ACCC
......((.(((((((.......)))))))....(((((((..(....)...(((........)))))))))-------------------)((((((((....))))))))...-.)). ( -38.20)
>DroYak_CAF1 11613 119 + 1
AUCAGUGGAUGUGACAAAUGAACUGUCACAAUAAUGCCAGCGACGAAAGGGAAUGACGACACAUAUGUUGGCACCGUUUCGCAACUGGAGGAGUCUCCGGAUCUCUGGAUACGAG-ACCG
......((.(((((((.......)))))))....((((((((.(....)...(((......))).))))))))))((((((...((((((....))))))(((....))).))))-)).. ( -37.90)
>consensus
AUCAGGAGAUGUGACAAAUGAACUGUCACAAUAAUGCCAGCGACGAAAGGGAAUGACGACACAUGUGUUGGCACCGUUUCGGCUCUGGAGGAGUCUCCGGAUCUCUGGAUACGAG_UCCC
....((((((((((((.......)))))).....((((((((.(....)...(((......))).))))))))...................))))))(((.(((.(....)))).))). (-28.26 = -29.10 +   0.84)

alignment

secondary structure

dotplot

Window 4

Location	19,318,749 – 19,318,869
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.18
Mean single sequence MFE	-35.38
Consensus MFE	-23.48
Energy contribution	-25.88
Covariance contribution	2.40
Combinations/Pair	1.06
Mean z-score	-1.83
Structure conservation index	0.66
SVM decision value	-0.00
SVM RNA-class probability	0.532153
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19318749 120 - 22407834
GGGAAGUCGUAUCCGGAGAUCCGAAAACUCCUCCAGAACCGAAACGGUGCCAACACAUGUGUCGUCAUUCCCUUUCGUCGCUGGCAUUAUUGUGACAGUUCAUUUGUCACAUCUCCUGAU
.(((.......)))(((((.............((((...(((((.((((.(.(((....))).).))..)).)))))...))))......((((((((.....))))))))))))).... ( -32.20)
>DroSec_CAF1 11333 119 - 1
GGGA-CUCGUAACCAGAGAUCCGGAGACUCCUCCAGAGCCGAAACAGUGCCAACACAUGUGUCGUCAUUCCCUUUCGUCGCUGGCAUUAUUGUGACAGUUCAUUUGUCACAUCUCCUGAU
.(((-(((.......))).)))(((((.....((((.(.(((((.((((.(.(((....))).).))))...))))).).))))......((((((((.....))))))))))))).... ( -36.50)
>DroSim_CAF1 13170 119 - 1
GGGA-CUCGUAACCAGAGAUCCGGAGACUCCUCCAGAGCCGAAACGGUGCCAACACAUGUGUCGUCAUUCCCUUUCGUCGCUGGCAUUAUUGUGACAGUUCAUUUGUCACAUCUCCUGAU
.(((-(((.......))).)))(((((.....((((.(.(((((.((((.(.(((....))).).))..)).))))).).))))......((((((((.....))))))))))))).... ( -37.50)
>DroEre_CAF1 10523 100 - 1
GGGU-CGCGUCUCCAGAAAUCCGGAGACU-------------------GCCAGCAUGUGUGUCGUCAUUCCCUUUCGUCGCUGGCAUUAUUGUGACAGUUCAUUUGUCACAUCCUCUGAU
((((-...((((((.(....).))))))(-------------------(((((((((.(((....))).......))).))))))).....(((((((.....)))))))))))...... ( -33.60)
>DroYak_CAF1 11613 119 - 1
CGGU-CUCGUAUCCAGAGAUCCGGAGACUCCUCCAGUUGCGAAACGGUGCCAACAUAUGUGUCGUCAUUCCCUUUCGUCGCUGGCAUUAUUGUGACAGUUCAUUUGUCACAUCCACUGAU
.(((-(((.......)))))).(((.......(((((.((((((.((((.(.(((....))).).))..)).)))))).)))))......((((((((.....)))))))))))...... ( -37.10)
>consensus
GGGA_CUCGUAUCCAGAGAUCCGGAGACUCCUCCAGAGCCGAAACGGUGCCAACACAUGUGUCGUCAUUCCCUUUCGUCGCUGGCAUUAUUGUGACAGUUCAUUUGUCACAUCUCCUGAU
.(((.(((.......))).)))(((((..................(((((((......(((.((...........)).))))))))))..((((((((.....))))))))))))).... (-23.48 = -25.88 +   2.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:43 2006