Locus 4754

Sequence ID	2L_DroMel_CAF1
Location	13,573,230 – 13,573,390
Length	160
Max. P	0.870948

overview

Window 1

Location	13,573,230 – 13,573,350
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.47
Mean single sequence MFE	-35.73
Consensus MFE	-32.14
Energy contribution	-31.82
Covariance contribution	-0.31
Combinations/Pair	1.12
Mean z-score	-1.78
Structure conservation index	0.90
SVM decision value	0.81
SVM RNA-class probability	0.856134
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13573230 120 - 22407834
ACAAUGGGCGCUAGGGGGUGUGGCAGCUGCCAAAAAGGGAGUGGCUAAAUCCACCAUGGCAGCAGAUUAGCAUAACAAAAGUAAAUGACGACUGCUAAAUGUGUCAAUUUUGCGACACGA
.........((((((((((.((((.(((.((.....)).))).)))).)))).)).))))(((((.((..(((.((....))..)))..)))))))...((((((........)))))). ( -37.70)
>DroSec_CAF1 6471 120 - 1
ACAAUGGGCGCUAGGGGGCGUGGCAGCUGCCAAAAAGGGAGUGGCUAAAUCCACCAUGGCAGCAGAUUAGCAUAACAAAAGUAAAUGACGACUGCUAAAUGUGUCAAUUCUGCGACACGA
.........(((((((((..((((.(((.((.....)).))).))))..))).)).))))(((((.((..(((.((....))..)))..)))))))...((((((........)))))). ( -36.70)
>DroSim_CAF1 6048 120 - 1
ACAAUGGGCGCCAGGGGGCGUGGCAGCUGCCAAAAAGGGAGUGGCUAAAUCCACCAUGGCAGCAGAUUAGCAUAACAAAAGUAAAUGACGACUGCUAAAUGUGUCAAUUCUGCGACACGA
.........(((((((((..((((.(((.((.....)).))).))))..))).)).))))(((((.((..(((.((....))..)))..)))))))...((((((........)))))). ( -39.00)
>DroYak_CAF1 3580 119 - 1
GCAAUGGGCGACAAGGGGCGUGGCAGUUGCCAGAA-GGGAGUGGCUGGAUCCACCAUGGCAGCAGAUUAGCAUAACAAAAGUAAAUGACGACUGCUAAAUGUGUCAGUUUUACGAAGCGA
((.(((.((.((.......)).)).(((((((...-..(.((((......))))).))))))).......))).......(((((((((.((........))))))..)))))...)).. ( -29.50)
>consensus
ACAAUGGGCGCCAGGGGGCGUGGCAGCUGCCAAAAAGGGAGUGGCUAAAUCCACCAUGGCAGCAGAUUAGCAUAACAAAAGUAAAUGACGACUGCUAAAUGUGUCAAUUCUGCGACACGA
.........((((.((((..((((..((.((.....)).))..))))...)).)).))))(((((.((..(((.((....))..)))..)))))))...((((((........)))))). (-32.14 = -31.82 +  -0.31)

alignment

secondary structure

dotplot

Window 2

Location	13,573,270 – 13,573,390
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.86
Mean single sequence MFE	-38.34
Consensus MFE	-34.33
Energy contribution	-34.95
Covariance contribution	0.62
Combinations/Pair	1.07
Mean z-score	-1.93
Structure conservation index	0.90
SVM decision value	0.87
SVM RNA-class probability	0.870948
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13573270 120 - 22407834
CAGCAAAGCGUUAUAAUAGGGCUUAUUAGGGUUACUCCCGACAAUGGGCGCUAGGGGGUGUGGCAGCUGCCAAAAAGGGAGUGGCUAAAUCCACCAUGGCAGCAGAUUAGCAUAACAAAA
.........(((((......(((((((.(((.....)))...)))))))((((((((((.((((.(((.((.....)).))).)))).)))).)).)))).((......))))))).... ( -39.60)
>DroSec_CAF1 6511 120 - 1
CAGCAAAGCGUUAUAAUAGGGCUUAUUAGGGUUACCCCCGACAAUGGGCGCUAGGGGGCGUGGCAGCUGCCAAAAAGGGAGUGGCUAAAUCCACCAUGGCAGCAGAUUAGCAUAACAAAA
..((...(((((....(((.(((((((.(((.....)))...))))))).)))...))))).)).(((((((.....(((.........)))....)))))))................. ( -40.10)
>DroSim_CAF1 6088 120 - 1
CAGCAAAGCGUUAUAAUAGGGCUUAUUAGGGUUACCCCCGACAAUGGGCGCCAGGGGGCGUGGCAGCUGCCAAAAAGGGAGUGGCUAAAUCCACCAUGGCAGCAGAUUAGCAUAACAAAA
.........(((((......(((((((.(((.....)))...)))))))(((((((((..((((.(((.((.....)).))).))))..))).)).)))).((......))))))).... ( -40.40)
>DroYak_CAF1 3620 118 - 1
CAGCAAAGCGUUAUAAUAGGGCUUAUUAGGGUUACC-CCGGCAAUGGGCGACAAGGGGCGUGGCAGUUGCCAGAA-GGGAGUGGCUGGAUCCACCAUGGCAGCAGAUUAGCAUAACAAAA
..((...(((((........(((((((.(((....)-))...))))))).......))))).)).(((((((...-..(.((((......))))).)))))))................. ( -33.26)
>consensus
CAGCAAAGCGUUAUAAUAGGGCUUAUUAGGGUUACCCCCGACAAUGGGCGCCAGGGGGCGUGGCAGCUGCCAAAAAGGGAGUGGCUAAAUCCACCAUGGCAGCAGAUUAGCAUAACAAAA
..((...(((((....(((.(((((((.(((.....)))...))))))).)))...))))).)).(((((((.....(((.........)))....)))))))................. (-34.33 = -34.95 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:25 2006