Locus 1858

Sequence ID	3R_DroMel_CAF1
Location	5,331,097 – 5,331,199
Length	102
Max. P	0.971317

overview

Window 5

Location	5,331,097 – 5,331,199
Length	102
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	74.58
Mean single sequence MFE	-36.06
Consensus MFE	-19.58
Energy contribution	-18.56
Covariance contribution	-1.02
Combinations/Pair	1.43
Mean z-score	-2.22
Structure conservation index	0.54
SVM decision value	1.67
SVM RNA-class probability	0.971317
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5331097 102 + 27905053
------CCCGCUG--UGGCCAACACUGCAACCGCAGUGGCAGUGGCCAUCAAUAAAUCCUCUAGUGCCUCCAUUACGGCCAACAAAGGUAACAAGGAAACCGAGGAGCAG
------...((.(--((((((.((((((....))))))....))))))).......(((((..(.(((........))))......(((.........)))))))))).. ( -36.70)
>DroSec_CAF1 7639 102 + 1
------CCAGCUG--UGGCCAAAACUGCAAACGCAGUGGCAGUGGCAAUCAAUAAAUCCUCUAGUGCCUCCAUUACGGCCAACAAGGGUAACAAGGAGACCGAGGAGCAG
------....(((--(.((((..(((((....))))).....))))..........(((((..((..((((......(((......))).....)))))).))))))))) ( -30.20)
>DroEre_CAF1 7829 108 + 1
GCCGCACCCGCUG--UGGCCACCACUGCAACCGCAGUUGCUGCAGCCAUCAAUAAAUCCUCUAGUGCCUCCAUUACGGCCAACAAGGGCAAUAAGGAGACGGAGGAGCAG
...((....((((--..((....(((((....))))).))..))))..........((((((.((..((((.(((..(((......)))..))))))))))))))))).. ( -40.50)
>DroYak_CAF1 573 108 + 1
GCUGCUCCCGCUG--UGGCCACCACUGCAACCGCAGUUGCUGCGGCCAUCAGUAAAUCCUCUAGUGCCUCGAUUACAGCCAACAAAGGCAACAAGGAGACGGAGGAGCAG
(((.((((.((((--(((((.(.(((((....)))))....).))))).))))...((((....(((((................)))))...))))...)))).))).. ( -41.79)
>DroMoj_CAF1 9144 105 + 1
GCGAAAGCCGCUG--CUGCUUCAGCUGC---AACUGCUUCAUCAGCGGUCAACAAGUCUUCGUCGGCUUCAAUAAAGGCCAACAAGGGCAACAAGGAAACGGAGGAACAG
((....)).((.(--(((...)))).))---.((((((.....)))))).......(((((((.(((((......))))).))...(....)..(....).))))).... ( -31.00)
>DroAna_CAF1 8661 99 + 1
------CCCGCAGCAUCGCCA--GCUGC---GGCUGGUGCAGCUGCUGUAAACAAAUCGUCUAGCGCCUCCAUUACCGACAACAAGGGCAACAAGGAGACGGACGAACAG
------...(((((..(((((--((...---.)))))))..)))))..........((((((..(.(((......((........))......))).)..)))))).... ( -36.20)
>consensus
______CCCGCUG__UGGCCACCACUGCAACCGCAGUUGCAGCGGCCAUCAAUAAAUCCUCUAGUGCCUCCAUUACGGCCAACAAGGGCAACAAGGAGACGGAGGAGCAG
.........((((....((....(((((....))))).))..))))..........(((((....((((................)))).....(....).))))).... (-19.58 = -18.56 +  -1.02)

alignment

secondary structure

dotplot

Window 6

Location	5,331,097 – 5,331,199
Length	102
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	74.58
Mean single sequence MFE	-39.50
Consensus MFE	-24.63
Energy contribution	-25.05
Covariance contribution	0.42
Combinations/Pair	1.33
Mean z-score	-1.66
Structure conservation index	0.62
SVM decision value	1.02
SVM RNA-class probability	0.901190
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5331097 102 - 27905053
CUGCUCCUCGGUUUCCUUGUUACCUUUGUUGGCCGUAAUGGAGGCACUAGAGGAUUUAUUGAUGGCCACUGCCACUGCGGUUGCAGUGUUGGCCA--CAGCGGG------
(((((((((.(((((((((...((......))...))).))))))....))))).....((.((((((....((((((....)))))).))))))--)))))).------ ( -39.60)
>DroSec_CAF1 7639 102 - 1
CUGCUCCUCGGUCUCCUUGUUACCCUUGUUGGCCGUAAUGGAGGCACUAGAGGAUUUAUUGAUUGCCACUGCCACUGCGUUUGCAGUUUUGGCCA--CAGCUGG------
..(((((((.((((((..(((((((.....))..)))))))))))....)))))..........((((.....(((((....)))))..))))..--..))...------ ( -31.70)
>DroEre_CAF1 7829 108 - 1
CUGCUCCUCCGUCUCCUUAUUGCCCUUGUUGGCCGUAAUGGAGGCACUAGAGGAUUUAUUGAUGGCUGCAGCAACUGCGGUUGCAGUGGUGGCCA--CAGCGGGUGCGGC
....(((((.((((((((((.(((......))).)))).))))))....)))))..........((((((.(..(((.(((..(....)..))).--)))..).)))))) ( -46.00)
>DroYak_CAF1 573 108 - 1
CUGCUCCUCCGUCUCCUUGUUGCCUUUGUUGGCUGUAAUCGAGGCACUAGAGGAUUUACUGAUGGCCGCAGCAACUGCGGUUGCAGUGGUGGCCA--CAGCGGGAGCAGC
((((((((.....(((((..((((((.((((....)))).))))))...)))))....(((.(((((((....(((((....))))).)))))))--))).)))))))). ( -51.40)
>DroMoj_CAF1 9144 105 - 1
CUGUUCCUCCGUUUCCUUGUUGCCCUUGUUGGCCUUUAUUGAAGCCGACGAAGACUUGUUGACCGCUGAUGAAGCAGUU---GCAGCUGAAGCAG--CAGCGGCUUUCGC
..........(((..(..(((....((((((((.((....)).)))))))).)))..)..)))(((((.((...((((.---...))))...)).--)))))........ ( -29.10)
>DroAna_CAF1 8661 99 - 1
CUGUUCGUCCGUCUCCUUGUUGCCCUUGUUGUCGGUAAUGGAGGCGCUAGACGAUUUGUUUACAGCAGCUGCACCAGCC---GCAGC--UGGCGAUGCUGCGGG------
....((((((((((((..((((((.........)))))))))))))...)))))..........(((((..(.(((((.---...))--))).)..)))))...------ ( -39.20)
>consensus
CUGCUCCUCCGUCUCCUUGUUGCCCUUGUUGGCCGUAAUGGAGGCACUAGAGGAUUUAUUGAUGGCCGCUGCAACUGCGGUUGCAGUGGUGGCCA__CAGCGGG______
(((((((((.(((((((((..(((......)))..))).))))))....)))))..........((((.....(((((....)))))..))))......))))....... (-24.63 = -25.05 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:15 2006