Locus 9523

Sequence ID	3R_DroMel_CAF1
Location	25,166,435 – 25,166,529
Length	94
Max. P	0.987118

overview

Window 7

Location	25,166,435 – 25,166,529
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	93.40
Mean single sequence MFE	-23.60
Consensus MFE	-18.34
Energy contribution	-18.30
Covariance contribution	-0.04
Combinations/Pair	1.05
Mean z-score	-2.02
Structure conservation index	0.78
SVM decision value	0.78
SVM RNA-class probability	0.849152
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25166435 94 + 27905053
AAAACAAGCAGCGUCAGCAUCAACGUUUUAUAUUAAAAACAACAACCGCAAUGGUGCACUGAGAAAAAAGGGGGGUUUUUUAGCUGCUGUUAUU
..((((.(((((............(((((......)))))(((..(((((....))).((........))))..))).....)))))))))... ( -21.20)
>DroSec_CAF1 25179 93 + 1
AAAACAAGCAGCGUCAGCAUCAACGUUUUAUAUUAAAAACAACAACCGCAAUGGUGCACUGACAAAAA-GGGGGGUUUUUUAGCUGCUGCUGUU
......(((((((.((((......(((((......)))))(((..(((((....))).((.......)-)))..))).....)))).))))))) ( -24.30)
>DroSim_CAF1 25145 94 + 1
AAAACAAGCAGCGUCAGCAUCAACGUUUUAUAUUAAAAACAACAACCGCAAUGGUGCACUGACAAAAACGGGGGGUUUUUUAGCUGCUGCUGUU
..(((((((((((((((.......(((((......))))).......(((....))).)))))((((((.....))))))..))))))..)))) ( -24.60)
>DroEre_CAF1 25936 94 + 1
AAAAUAAGCAGCGUCAGCAUCAACGUUUUAUAUUAAAAACAACAACCGCAGUGGAGCACUGACAAAAAAGGGGGCUGCUUUAGCUGCUGUUUUU
((((((.(((((...((((((..((((((......))))).......((((((...))))).)......)..)).))))...))))))))))). ( -24.40)
>DroYak_CAF1 25626 94 + 1
AAAAUAAGCAGCGUCAGCAUCAACGUUUUAUAUUAAAAACAACAACCGCAAUGGAGCACUGACAAAAAGGGGGGUUGCUUUAGCUGCUGUUUUU
((((((.(((((...(((......(((((......)))))(((..((((......)).((.......))))..))))))...))))))))))). ( -23.50)
>consensus
AAAACAAGCAGCGUCAGCAUCAACGUUUUAUAUUAAAAACAACAACCGCAAUGGUGCACUGACAAAAAAGGGGGGUUUUUUAGCUGCUGUUGUU
......(((((((((((.......(((((......))))).......((......)).)))))......((((....)))).))))))...... (-18.34 = -18.30 +  -0.04)

alignment

secondary structure

dotplot

Window 8

Location	25,166,435 – 25,166,529
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	93.40
Mean single sequence MFE	-23.08
Consensus MFE	-20.06
Energy contribution	-20.42
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-1.91
Structure conservation index	0.87
SVM decision value	2.07
SVM RNA-class probability	0.987118
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25166435 94 - 27905053
AAUAACAGCAGCUAAAAAACCCCCCUUUUUUCUCAGUGCACCAUUGCGGUUGUUGUUUUUAAUAUAAAACGUUGAUGCUGACGCUGCUUGUUUU
...(((((((((.((((((......)))))).((((((((....))).(((..((((((......))))))..)))))))).))))).)))).. ( -20.20)
>DroSec_CAF1 25179 93 - 1
AACAGCAGCAGCUAAAAAACCCCCC-UUUUUGUCAGUGCACCAUUGCGGUUGUUGUUUUUAAUAUAAAACGUUGAUGCUGACGCUGCUUGUUUU
(((((((((.....(((((......-)))))(((((((((....))).(((..((((((......))))))..)))))))))))))).)))).. ( -24.10)
>DroSim_CAF1 25145 94 - 1
AACAGCAGCAGCUAAAAAACCCCCCGUUUUUGUCAGUGCACCAUUGCGGUUGUUGUUUUUAAUAUAAAACGUUGAUGCUGACGCUGCUUGUUUU
(((((((((.....((((((.....))))))(((((((((....))).(((..((((((......))))))..)))))))))))))).)))).. ( -26.80)
>DroEre_CAF1 25936 94 - 1
AAAAACAGCAGCUAAAGCAGCCCCCUUUUUUGUCAGUGCUCCACUGCGGUUGUUGUUUUUAAUAUAAAACGUUGAUGCUGACGCUGCUUAUUUU
......((((((.((((.......))))...((((((((......)).(((..((((((......))))))..)))))))))))))))...... ( -22.00)
>DroYak_CAF1 25626 94 - 1
AAAAACAGCAGCUAAAGCAACCCCCCUUUUUGUCAGUGCUCCAUUGCGGUUGUUGUUUUUAAUAUAAAACGUUGAUGCUGACGCUGCUUAUUUU
......((((((.((((........))))..((((((((......)).(((..((((((......))))))..)))))))))))))))...... ( -22.30)
>consensus
AAAAACAGCAGCUAAAAAACCCCCCUUUUUUGUCAGUGCACCAUUGCGGUUGUUGUUUUUAAUAUAAAACGUUGAUGCUGACGCUGCUUGUUUU
......((((((.(((((........)))))((((((((......)).(((..((((((......))))))..)))))))))))))))...... (-20.06 = -20.42 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:36:26 2006