Locus 7187

Sequence ID	3R_DroMel_CAF1
Location	18,957,325 – 18,957,472
Length	147
Max. P	0.999213

overview

Window 5

Location	18,957,325 – 18,957,432
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	98.88
Mean single sequence MFE	-31.23
Consensus MFE	-29.45
Energy contribution	-29.29
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.65
Structure conservation index	0.94
SVM decision value	3.44
SVM RNA-class probability	0.999213
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18957325 107 + 27905053
UGGCGGCUCCUUUCAUAAGCAAUUAGAAUCAAUGAGCAAGGACACUCGGCUCCGUUUCCUUUCCAUCGCCCUUUUGUCCUGCCGCAAUCUUUAUGGGCCGCCACCAA
(((((((((..(((.(((....)))))).......((.((((((...(((.................)))....))))))...)).........))))))))).... ( -31.53)
>DroSec_CAF1 68755 107 + 1
UGGCGGCUCCUUUCAUAAGCAAUUAGAAUCAAUGAGCAAGGACACUCGGCUCCGUUUCCUUUCCCUCGCCCUUUUGUCCUGCCGCAAUCUUUAUGGGCCGCCACCAA
(((((((((..(((.(((....)))))).......((.((((((...(((.................)))....))))))...)).........))))))))).... ( -31.53)
>DroSim_CAF1 69901 107 + 1
UGGCGGCUCCUUUCAUAAGCAAUUAGAAUCAAUGAGCAAGGACACUCGGCUCCGUUUCCUUUCCCUCGCCCUUUUGUCCUGCCGCAAUCUUUAUGGGCCGCCACCAA
(((((((((..(((.(((....)))))).......((.((((((...(((.................)))....))))))...)).........))))))))).... ( -31.53)
>DroEre_CAF1 68912 107 + 1
AGGCGGCUCCUUUCAUAAGCAAUUAGAAUCAAUGAGCAAGGACACUCGGCUCCGUUUCCUUUCCCUCGCCCUUUUGUCCUGCCGCAAUCUUUAUGGGCCGCCACCAA
.((((((((..(((.(((....)))))).......((.((((((...(((.................)))....))))))...)).........))))))))..... ( -31.33)
>DroYak_CAF1 70995 107 + 1
UGGCGGCUCCUUUUAUAAGCAAUUAGAAUCAAUGAGCAAGGACACUCGGCUCCGUUUCCUUUCCCUCGCCCUUUUGUCCUGCCGCAAUCUUUAUGGGCCGCCACCAA
(((((((((......(((....)))..........((.((((((...(((.................)))....))))))...)).........))))))))).... ( -30.23)
>consensus
UGGCGGCUCCUUUCAUAAGCAAUUAGAAUCAAUGAGCAAGGACACUCGGCUCCGUUUCCUUUCCCUCGCCCUUUUGUCCUGCCGCAAUCUUUAUGGGCCGCCACCAA
.((((((((...((((...............))))((.((((((...(((.................)))....))))))...)).........))))))))..... (-29.45 = -29.29 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	18,957,325 – 18,957,432
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	98.88
Mean single sequence MFE	-35.70
Consensus MFE	-34.55
Energy contribution	-34.75
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.97
SVM decision value	2.26
SVM RNA-class probability	0.991313
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18957325 107 - 27905053
UUGGUGGCGGCCCAUAAAGAUUGCGGCAGGACAAAAGGGCGAUGGAAAGGAAACGGAGCCGAGUGUCCUUGCUCAUUGAUUCUAAUUGCUUAUGAAAGGAGCCGCCA
....(((((((((........((.(((((((((....(((..((.........))..)))...))))).))))))....(((...........))).)).))))))) ( -35.00)
>DroSec_CAF1 68755 107 - 1
UUGGUGGCGGCCCAUAAAGAUUGCGGCAGGACAAAAGGGCGAGGGAAAGGAAACGGAGCCGAGUGUCCUUGCUCAUUGAUUCUAAUUGCUUAUGAAAGGAGCCGCCA
....(((((((((.........((((.((((..((.(((((((((...((........)).....))))))))).))..))))..))))........)).))))))) ( -36.03)
>DroSim_CAF1 69901 107 - 1
UUGGUGGCGGCCCAUAAAGAUUGCGGCAGGACAAAAGGGCGAGGGAAAGGAAACGGAGCCGAGUGUCCUUGCUCAUUGAUUCUAAUUGCUUAUGAAAGGAGCCGCCA
....(((((((((.........((((.((((..((.(((((((((...((........)).....))))))))).))..))))..))))........)).))))))) ( -36.03)
>DroEre_CAF1 68912 107 - 1
UUGGUGGCGGCCCAUAAAGAUUGCGGCAGGACAAAAGGGCGAGGGAAAGGAAACGGAGCCGAGUGUCCUUGCUCAUUGAUUCUAAUUGCUUAUGAAAGGAGCCGCCU
.....((((((((.........((((.((((..((.(((((((((...((........)).....))))))))).))..))))..))))........)).)))))). ( -35.43)
>DroYak_CAF1 70995 107 - 1
UUGGUGGCGGCCCAUAAAGAUUGCGGCAGGACAAAAGGGCGAGGGAAAGGAAACGGAGCCGAGUGUCCUUGCUCAUUGAUUCUAAUUGCUUAUAAAAGGAGCCGCCA
....(((((((((.........((((.((((..((.(((((((((...((........)).....))))))))).))..))))..))))........)).))))))) ( -36.03)
>consensus
UUGGUGGCGGCCCAUAAAGAUUGCGGCAGGACAAAAGGGCGAGGGAAAGGAAACGGAGCCGAGUGUCCUUGCUCAUUGAUUCUAAUUGCUUAUGAAAGGAGCCGCCA
.....((((((((.........((((.((((..((.(((((((((...((........)).....))))))))).))..))))..))))........)).)))))). (-34.55 = -34.75 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	18,957,365 – 18,957,472
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	99.63
Mean single sequence MFE	-35.40
Consensus MFE	-34.80
Energy contribution	-35.00
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	0.98
SVM decision value	0.69
SVM RNA-class probability	0.822788
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18957365 107 - 27905053
UCUUUCCCACACACGCAGUCGAGUCACAAUAUUGUGACUUUUGGUGGCGGCCCAUAAAGAUUGCGGCAGGACAAAAGGGCGAUGGAAAGGAAACGGAGCCGAGUGUC
........((((.(((((((((((((((....))))))))...((((....))))...)))))))............(((..((.........))..)))..)))). ( -32.60)
>DroSec_CAF1 68795 107 - 1
UCUUUCCCACACACGCAGUCGAGUCACAAUAUUGUGACUUUUGGUGGCGGCCCAUAAAGAUUGCGGCAGGACAAAAGGGCGAGGGAAAGGAAACGGAGCCGAGUGUC
((((((((.....(((((((((((((((....))))))))...((((....))))...)))))))((...........))..))))))))...((....))...... ( -36.10)
>DroSim_CAF1 69941 107 - 1
UCUUUCCCACACACGCAGUCGAGUCACAAUAUUGUGACUUUUGGUGGCGGCCCAUAAAGAUUGCGGCAGGACAAAAGGGCGAGGGAAAGGAAACGGAGCCGAGUGUC
((((((((.....(((((((((((((((....))))))))...((((....))))...)))))))((...........))..))))))))...((....))...... ( -36.10)
>DroEre_CAF1 68952 107 - 1
UCUUUCCCACACACGCAGUCGAGUCACAAUAUUGUGACUUUUGGUGGCGGCCCAUAAAGAUUGCGGCAGGACAAAAGGGCGAGGGAAAGGAAACGGAGCCGAGUGUC
((((((((.....(((((((((((((((....))))))))...((((....))))...)))))))((...........))..))))))))...((....))...... ( -36.10)
>DroYak_CAF1 71035 107 - 1
UCUUUCCCACACACGCAGUCGAGUCACAAUAUUGUGACUUUUGGUGGCGGCCCAUAAAGAUUGCGGCAGGACAAAAGGGCGAGGGAAAGGAAACGGAGCCGAGUGUC
((((((((.....(((((((((((((((....))))))))...((((....))))...)))))))((...........))..))))))))...((....))...... ( -36.10)
>consensus
UCUUUCCCACACACGCAGUCGAGUCACAAUAUUGUGACUUUUGGUGGCGGCCCAUAAAGAUUGCGGCAGGACAAAAGGGCGAGGGAAAGGAAACGGAGCCGAGUGUC
((((((((.(...(((((((((((((((....))))))))...((((....))))...)))))))((...........))).))))))))...((....))...... (-34.80 = -35.00 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:36 2006