Locus 1863

Sequence ID	3R_DroMel_CAF1
Location	5,349,266 – 5,349,358
Length	92
Max. P	0.993894

overview

Window 4

Location	5,349,266 – 5,349,358
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	98.48
Mean single sequence MFE	-31.58
Consensus MFE	-30.08
Energy contribution	-30.48
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.95
SVM decision value	2.43
SVM RNA-class probability	0.993894
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5349266 92 + 27905053
AACAGCAACCGGCAGAGGCCUUAACUCCAACCGCAAGUGCCACUGCAAUUGCAGCGGCGAGUGCGCCUGGGAAGAAGCAAUUGAACGCAACG
....((....(((....))).....((((..((((..((((.((((....)))).))))..))))..))))...............)).... ( -32.20)
>DroSec_CAF1 8713 92 + 1
AACAGCAACCGGCAGAGGCCUUAACUCCAACCGCAAGUGCCACUGCAAUCGCAGCGGCGAGUGCGCCUGGGAAGAAGCAAUUGAACGCAACG
....((....(((....))).....((((..((((..((((.((((....)))).))))..))))..))))...............)).... ( -31.90)
>DroSim_CAF1 8106 92 + 1
AACAGCAACCGGCAGAGGCCUUAACUCCAACCGCAAGUGCCACUGCAAUCGCAGCGGCGAGUGCGCCUGGGAAGAAGCAAUUGAACGCAACG
....((....(((....))).....((((..((((..((((.((((....)))).))))..))))..))))...............)).... ( -31.90)
>DroEre_CAF1 8703 92 + 1
AACAGCAACCGGCAGAGGCCUUAACUCCAACCGCAAGUGCCACUGCAAUUGCAGCGGCGAGUGCGCCGGGGAAGAAGCAAUUGAACGCAACG
........(((((.(((.......))).....(((..((((.((((....)))).))))..)))))))).......((........)).... ( -34.30)
>DroYak_CAF1 9751 92 + 1
AACAGCAACCGGCAGAGGCCUUAACUCCAACCGCAAGUGCCACUGCAAUUGCUGCGGCGAGUGCGCCUGGGAAGAAGCAAUUGAACGCAACG
....((....(((....))).....((((..((((..((((.(.((....)).).))))..))))..))))...............)).... ( -27.60)
>consensus
AACAGCAACCGGCAGAGGCCUUAACUCCAACCGCAAGUGCCACUGCAAUUGCAGCGGCGAGUGCGCCUGGGAAGAAGCAAUUGAACGCAACG
....((....(((....))).....((((..((((..((((.((((....)))).))))..))))..))))...............)).... (-30.08 = -30.48 +   0.40)

alignment

secondary structure

dotplot

Window 5

Location	5,349,266 – 5,349,358
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	98.48
Mean single sequence MFE	-34.34
Consensus MFE	-33.14
Energy contribution	-33.54
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.97
SVM decision value	1.24
SVM RNA-class probability	0.934925
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5349266 92 - 27905053
CGUUGCGUUCAAUUGCUUCUUCCCAGGCGCACUCGCCGCUGCAAUUGCAGUGGCACUUGCGGUUGGAGUUAAGGCCUCUGCCGGUUGCUGUU
....(((......)))......((((.((((...((((((((....))))))))...)))).))))(((...(((....)))....)))... ( -35.20)
>DroSec_CAF1 8713 92 - 1
CGUUGCGUUCAAUUGCUUCUUCCCAGGCGCACUCGCCGCUGCGAUUGCAGUGGCACUUGCGGUUGGAGUUAAGGCCUCUGCCGGUUGCUGUU
....(((......)))......((((.((((...((((((((....))))))))...)))).))))(((...(((....)))....)))... ( -34.50)
>DroSim_CAF1 8106 92 - 1
CGUUGCGUUCAAUUGCUUCUUCCCAGGCGCACUCGCCGCUGCGAUUGCAGUGGCACUUGCGGUUGGAGUUAAGGCCUCUGCCGGUUGCUGUU
....(((......)))......((((.((((...((((((((....))))))))...)))).))))(((...(((....)))....)))... ( -34.50)
>DroEre_CAF1 8703 92 - 1
CGUUGCGUUCAAUUGCUUCUUCCCCGGCGCACUCGCCGCUGCAAUUGCAGUGGCACUUGCGGUUGGAGUUAAGGCCUCUGCCGGUUGCUGUU
....(((......))).......((((((((...((((((((....))))))))...)))((((........))))...)))))........ ( -34.30)
>DroYak_CAF1 9751 92 - 1
CGUUGCGUUCAAUUGCUUCUUCCCAGGCGCACUCGCCGCAGCAAUUGCAGUGGCACUUGCGGUUGGAGUUAAGGCCUCUGCCGGUUGCUGUU
....(((......))).........((((....))))(((((((((((((.(((.(((((.......).))))))).))).)))))))))). ( -33.20)
>consensus
CGUUGCGUUCAAUUGCUUCUUCCCAGGCGCACUCGCCGCUGCAAUUGCAGUGGCACUUGCGGUUGGAGUUAAGGCCUCUGCCGGUUGCUGUU
....(((......)))......((((.((((...((((((((....))))))))...)))).))))(((...(((....)))....)))... (-33.14 = -33.54 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:24 2006