Locus 9504

Sequence ID	3R_DroMel_CAF1
Location	25,118,747 – 25,118,843
Length	96
Max. P	0.933895

overview

Window 4

Location	25,118,747 – 25,118,843
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	83.28
Mean single sequence MFE	-19.02
Consensus MFE	-10.76
Energy contribution	-11.12
Covariance contribution	0.36
Combinations/Pair	1.06
Mean z-score	-2.35
Structure conservation index	0.57
SVM decision value	0.44
SVM RNA-class probability	0.738113
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25118747 96 + 27905053
AGGAUACUUGAAUUCUGAACACUUCAGUUCAUAUUUCUAUGGAGUACUGCUGUUCUUCCUAAGAGCAGUCCUUACAAUUUCUUCAUAUAUCUACUA
.(((((..((((..((((.....))))((((((....))))))(((..((((((((.....))))))))...)))......))))..))))).... ( -21.80)
>DroSec_CAF1 47311 96 + 1
AAGAUACUUGAAUUCUGAACACUUGAGCUCAUAUUUCUAAGGAGUACUGCUGUUUUUACUAAAAGCAGUCCUUACAAUUUGUUCAUAUAUCCACUG
..((((..(((((..(((.(......).)))......((((((...(((((............)))))))))))......)))))..))))..... ( -16.90)
>DroSim_CAF1 49862 96 + 1
AGGAUACUUGAAUUCUGAACACUUCAGCUCAUAUUUCUAAGGAGUACUGCUGUUUUUCCUAAGAGCAGUCCUUACAAUUUGUUCAUAUAUCCACUA
.(((((..(((((.((((.....))))..........((((((...(((((.((......)).)))))))))))......)))))..))))).... ( -25.20)
>DroEre_CAF1 50152 78 + 1
AGAAUACUCGAAUUCUAAACACUUCAGCUCAUAUUUCCAAGGAGCACUGCUGUUUU-CCUAAGAGCAGUCCUU---------------A--UACUA
(((((......)))))..........((((...........))))((((((.((..-...)).))))))....---------------.--..... ( -14.70)
>DroYak_CAF1 49326 93 + 1
AGAAUACUUGAAUUCAAAACACUUCAGCUCAUAUUUCUAAGGAGUACUGCUGUUUU-UCCAAGAGCAGUCCUUACAGUUUGUUCAAAUA--UACUA
((.(((.((((((...((((......((((...........))))((((((.((..-...)).)))))).......)))))))))).))--).)). ( -16.50)
>consensus
AGGAUACUUGAAUUCUGAACACUUCAGCUCAUAUUUCUAAGGAGUACUGCUGUUUUUCCUAAGAGCAGUCCUUACAAUUUGUUCAUAUAUCUACUA
.((((......))))......................((((((...(((((.((......)).)))))))))))...................... (-10.76 = -11.12 +   0.36)

alignment

secondary structure

dotplot

Window 5

Location	25,118,747 – 25,118,843
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	83.28
Mean single sequence MFE	-22.34
Consensus MFE	-15.68
Energy contribution	-15.88
Covariance contribution	0.20
Combinations/Pair	1.10
Mean z-score	-2.36
Structure conservation index	0.70
SVM decision value	1.23
SVM RNA-class probability	0.933895
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25118747 96 - 27905053
UAGUAGAUAUAUGAAGAAAUUGUAAGGACUGCUCUUAGGAAGAACAGCAGUACUCCAUAGAAAUAUGAACUGAAGUGUUCAGAAUUCAAGUAUCCU
.....(((((.((((....((.(((((.....))))).)).(((((.((((....((((....)))).))))...)))))....)))).))))).. ( -21.50)
>DroSec_CAF1 47311 96 - 1
CAGUGGAUAUAUGAACAAAUUGUAAGGACUGCUUUUAGUAAAAACAGCAGUACUCCUUAGAAAUAUGAGCUCAAGUGUUCAGAAUUCAAGUAUCUU
....((((((.((((....((.(((((((((((.((......)).)))))...)))))).))...(((((......)))))...)))).)))))). ( -24.50)
>DroSim_CAF1 49862 96 - 1
UAGUGGAUAUAUGAACAAAUUGUAAGGACUGCUCUUAGGAAAAACAGCAGUACUCCUUAGAAAUAUGAGCUGAAGUGUUCAGAAUUCAAGUAUCCU
....((((((.((((....((.(((((((((((.((......)).)))))...)))))).))...(((((......)))))...)))).)))))). ( -27.10)
>DroEre_CAF1 50152 78 - 1
UAGUA--U---------------AAGGACUGCUCUUAGG-AAAACAGCAGUGCUCCUUGGAAAUAUGAGCUGAAGUGUUUAGAAUUCGAGUAUUCU
.....--.---------------.((.((((((.((...-..)).)))))).)).((((((....(((((......)))))...))))))...... ( -16.50)
>DroYak_CAF1 49326 93 - 1
UAGUA--UAUUUGAACAAACUGUAAGGACUGCUCUUGGA-AAAACAGCAGUACUCCUUAGAAAUAUGAGCUGAAGUGUUUUGAAUUCAAGUAUUCU
.((.(--((((((((.......((((((.((((.(((..-....))).)))).))))))(((((((........)))))))...))))))))).)) ( -22.10)
>consensus
UAGUAGAUAUAUGAACAAAUUGUAAGGACUGCUCUUAGGAAAAACAGCAGUACUCCUUAGAAAUAUGAGCUGAAGUGUUCAGAAUUCAAGUAUCCU
......................(((((((((((.((......)).)))))...))))))(((...(((((......)))))...)))......... (-15.68 = -15.88 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:36:05 2006