Locus 411

Sequence ID	2R_DroMel_CAF1
Location	2,432,828 – 2,432,922
Length	94
Max. P	0.944693

overview

Window 1

Location	2,432,828 – 2,432,922
Length	94
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	78.90
Mean single sequence MFE	-29.66
Consensus MFE	-16.92
Energy contribution	-18.52
Covariance contribution	1.60
Combinations/Pair	1.00
Mean z-score	-2.30
Structure conservation index	0.57
SVM decision value	1.35
SVM RNA-class probability	0.944693
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2432828 94 + 20766785
GAUGUCUCCCACGGGAGAAGGCAUUUUGAAGACUCGUAGU----GCCGUUCUCCUCGAAAGGAGUUCCUUUUGAUGGCAAAAUAAUGGCUCAA-CGCGA
..((((.......((((((((((((.(((....))).)))----))).))))))((((((((....)))))))).))))........((....-.)).. ( -31.60)
>DroSec_CAF1 88726 93 + 1
GAUUUCUCCCACGGGAGAAGGCAUU-UGAAGACUCGUAGU----GCCGUUCUCCUCGAAAGGAGUUCCUUUUGAUGGCAAAAUAAUAGCUCAA-CGCGA
...((((((....))))))((((((-(((....))).)))----))).....((((((((((....)))))))).))..........((....-.)).. ( -29.80)
>DroSim_CAF1 46203 94 + 1
GAUUUCUCCCACGGGAGAAGGCAUUUUGAAGACUCGUAGU----GCCGUUCUCCUCGAAAGGAGUUCCUUUUGAUGGCAAAAUAAUGGCUAAA-CGCGA
.........(.((((((((((((((.(((....))).)))----))).))))))((((((((....))))))))((((.........))))..-)).). ( -30.50)
>DroEre_CAF1 44554 77 + 1
GAUUUCUCCCAUGGGAGAAGGCGUUUUG--------------GAGCCGUU-------CAAGGAGCUC-UUCUGAUGGCAAAAUGAUGGCUCAGUCGCGU
..(((((((....)))))))(((.....--------------(((((((.-------((....(((.-.......)))....)))))))))...))).. ( -27.20)
>DroYak_CAF1 45059 92 + 1
GAUUUCUCCCAUGGGAGAAGGGAGUUUAAAGACUCGUAGAAGGACGCGAU-------AAAGGAGUUCCUUUUGAUGGCAAAAUAAUAGCUCAGUCGCGU
..(((((((....))))))).(((((....)))))........(((((((-------....(((((..(((((....)))))....))))).))))))) ( -29.20)
>consensus
GAUUUCUCCCACGGGAGAAGGCAUUUUGAAGACUCGUAGU____GCCGUUCUCCUCGAAAGGAGUUCCUUUUGAUGGCAAAAUAAUGGCUCAA_CGCGA
..(((((((....)))))))........................((((((......((((((....)))))))))))).........((......)).. (-16.92 = -18.52 +   1.60)

alignment

secondary structure

dotplot

Window 2

Location	2,432,828 – 2,432,922
Length	94
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	78.90
Mean single sequence MFE	-24.84
Consensus MFE	-11.75
Energy contribution	-12.23
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-2.00
Structure conservation index	0.47
SVM decision value	0.27
SVM RNA-class probability	0.660775
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2432828 94 - 20766785
UCGCG-UUGAGCCAUUAUUUUGCCAUCAAAAGGAACUCCUUUCGAGGAGAACGGC----ACUACGAGUCUUCAAAAUGCCUUCUCCCGUGGGAGACAUC
((...-((((..((......))...))))...)).(((((..((.((((((.(((----(....(......)....)))))))))))).)))))..... ( -25.70)
>DroSec_CAF1 88726 93 - 1
UCGCG-UUGAGCUAUUAUUUUGCCAUCAAAAGGAACUCCUUUCGAGGAGAACGGC----ACUACGAGUCUUCA-AAUGCCUUCUCCCGUGGGAGAAAUC
..(((-(((((...(..(..((((.((.....)).(((((....)))))...)))----)..)..)...))).-))))).((((((....))))))... ( -26.10)
>DroSim_CAF1 46203 94 - 1
UCGCG-UUUAGCCAUUAUUUUGCCAUCAAAAGGAACUCCUUUCGAGGAGAACGGC----ACUACGAGUCUUCAAAAUGCCUUCUCCCGUGGGAGAAAUC
..(((-(((................((.(((((....))))).))(((((.((..----....))..))))).)))))).((((((....))))))... ( -25.60)
>DroEre_CAF1 44554 77 - 1
ACGCGACUGAGCCAUCAUUUUGCCAUCAGAA-GAGCUCCUUG-------AACGGCUC--------------CAAAACGCCUUCUCCCAUGGGAGAAAUC
..(((.((((..((......))...))))..-(((((.....-------...)))))--------------.....))).((((((....))))))... ( -22.30)
>DroYak_CAF1 45059 92 - 1
ACGCGACUGAGCUAUUAUUUUGCCAUCAAAAGGAACUCCUUU-------AUCGCGUCCUUCUACGAGUCUUUAAACUCCCUUCUCCCAUGGGAGAAAUC
((((((.((.((.........))))...(((((....)))))-------.))))))........((((......))))..((((((....))))))... ( -24.50)
>consensus
UCGCG_UUGAGCCAUUAUUUUGCCAUCAAAAGGAACUCCUUUCGAGGAGAACGGC____ACUACGAGUCUUCAAAAUGCCUUCUCCCGUGGGAGAAAUC
..((......))................(((((....)))))..........(((......................)))((((((....))))))... (-11.75 = -12.23 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:54 2006