Locus 2420

Sequence ID	2L_DroMel_CAF1
Location	6,608,513 – 6,608,633
Length	120
Max. P	0.846221

overview

Window 2

Location	6,608,513 – 6,608,633
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.33
Mean single sequence MFE	-26.49
Consensus MFE	-22.23
Energy contribution	-21.87
Covariance contribution	-0.36
Combinations/Pair	1.14
Mean z-score	-1.48
Structure conservation index	0.84
SVM decision value	0.38
SVM RNA-class probability	0.713883
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6608513 120 + 22407834
GUCAGGAGUUUUAACGCAUUCUGCUUGUACAAAAAGCGAUAAUAAAUGACCUGCAGUCAUCGGUUUUUGCCGGAGAAAGUUUAAUUAAAUUGGUAAAAUCAAUAAGUAAAUUGAUUACUU
(((((((((........)))))((((.......)))).........))))..((..((..((((....))))..))..))...........((((..((((((......)))))))))). ( -20.70)
>DroSec_CAF1 35727 120 + 1
GUCAGCAGUUUAAACGCAUUCUGCUUGUGCAAAAAGCGAUAAUAAAUGACCUGCAGUCAUCGGUUUUUGCCGGAGAAAGUUUAAUUAAAUUGGUAAAAUCAAUAAGUAAAUUGAUUACUU
.....((((((((..((.((((.((.(.(((((((.(((.......((((.....))))))).)))))))))))))).))....))))))))....(((((((......))))))).... ( -25.31)
>DroSim_CAF1 36920 120 + 1
GUCAGCAGUUUAAACGCAUUCUGCUUGUGCAAAAAGCGAUAAUAAAUGACCUGCAGUCAUCGGUUUUUGCCGGAGAAAGUUUAAUUAAAUUGGUAAAAUCAAUAAGUAAAUUGAUUACUU
.....((((((((..((.((((.((.(.(((((((.(((.......((((.....))))))).)))))))))))))).))....))))))))....(((((((......))))))).... ( -25.31)
>DroEre_CAF1 36862 120 + 1
GUCAGGAGUUUAAGCGCAUUCUGCUUGUGCAAAAAGCGAUAAUAAAUGACCUGCAGUCAUCGCUUUUUGCCAGAGAAAGUUUAAUUAAAUUGGCAAAAUCAAUAAGUAAAUUGAUUACUU
(((((....((((((...((((.((.(.(((((((((((.......((((.....)))))))))))))))))))))).)))))).....)))))..(((((((......))))))).... ( -33.71)
>DroYak_CAF1 37527 120 + 1
GUCAGGAGCUUAAACGCAUUUUGCUUGUGCAAGAAGCGAUAAUAAAUGACCUGCAGUCAUCACUUUUUGCCAGAGAAAGUUUAAUUAAAUUGGCAAAAUCAAUAGGUAAAUUGAUUACUU
(((((..(((((..(((.((((((....)))))).))).......(((((.....)))))....(((((((((...((......))...)))))))))....)))))...)))))..... ( -27.40)
>consensus
GUCAGGAGUUUAAACGCAUUCUGCUUGUGCAAAAAGCGAUAAUAAAUGACCUGCAGUCAUCGGUUUUUGCCGGAGAAAGUUUAAUUAAAUUGGUAAAAUCAAUAAGUAAAUUGAUUACUU
(((((....((((((...(((((.....(((((((.(((.......((((.....))))))).))))))))))))...)))))).....)))))..(((((((......))))))).... (-22.23 = -21.87 +  -0.36)

alignment

secondary structure

dotplot

Window 3

Location	6,608,513 – 6,608,633
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.33
Mean single sequence MFE	-24.55
Consensus MFE	-19.54
Energy contribution	-19.66
Covariance contribution	0.12
Combinations/Pair	1.10
Mean z-score	-1.99
Structure conservation index	0.80
SVM decision value	0.77
SVM RNA-class probability	0.846221
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6608513 120 - 22407834
AAGUAAUCAAUUUACUUAUUGAUUUUACCAAUUUAAUUAAACUUUCUCCGGCAAAAACCGAUGACUGCAGGUCAUUUAUUAUCGCUUUUUGUACAAGCAGAAUGCGUUAAAACUCCUGAC
....(((((((......)))))))....................((..(((......)))..))...((((...((((....(((.((((((....)))))).))).))))...)))).. ( -21.70)
>DroSec_CAF1 35727 120 - 1
AAGUAAUCAAUUUACUUAUUGAUUUUACCAAUUUAAUUAAACUUUCUCCGGCAAAAACCGAUGACUGCAGGUCAUUUAUUAUCGCUUUUUGCACAAGCAGAAUGCGUUUAAACUGCUGAC
....(((((((......)))))))........................(((((......((((((.....))))))..(((.(((.((((((....)))))).)))..)))..))))).. ( -24.80)
>DroSim_CAF1 36920 120 - 1
AAGUAAUCAAUUUACUUAUUGAUUUUACCAAUUUAAUUAAACUUUCUCCGGCAAAAACCGAUGACUGCAGGUCAUUUAUUAUCGCUUUUUGCACAAGCAGAAUGCGUUUAAACUGCUGAC
....(((((((......)))))))........................(((((......((((((.....))))))..(((.(((.((((((....)))))).)))..)))..))))).. ( -24.80)
>DroEre_CAF1 36862 120 - 1
AAGUAAUCAAUUUACUUAUUGAUUUUGCCAAUUUAAUUAAACUUUCUCUGGCAAAAAGCGAUGACUGCAGGUCAUUUAUUAUCGCUUUUUGCACAAGCAGAAUGCGCUUAAACUCCUGAC
((((((.....))))))......(((((((..................)))))))((((((((((.....)))))).......((.((((((....)))))).))))))........... ( -27.67)
>DroYak_CAF1 37527 120 - 1
AAGUAAUCAAUUUACCUAUUGAUUUUGCCAAUUUAAUUAAACUUUCUCUGGCAAAAAGUGAUGACUGCAGGUCAUUUAUUAUCGCUUCUUGCACAAGCAAAAUGCGUUUAAGCUCCUGAC
.(((..(((((......)))))((((((((..................)))))))).......))).((((...((((....(((...((((....))))...)))..))))..)))).. ( -23.77)
>consensus
AAGUAAUCAAUUUACUUAUUGAUUUUACCAAUUUAAUUAAACUUUCUCCGGCAAAAACCGAUGACUGCAGGUCAUUUAUUAUCGCUUUUUGCACAAGCAGAAUGCGUUUAAACUCCUGAC
.((((((((((......)))))))............((((((.................((((((.....)))))).......((.((((((....)))))).)))))))))))...... (-19.54 = -19.66 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:36 2006