Locus 9562

Sequence ID	3R_DroMel_CAF1
Location	25,260,652 – 25,260,759
Length	107
Max. P	0.957121

overview

Window 1

Location	25,260,652 – 25,260,759
Length	107
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	79.59
Mean single sequence MFE	-25.97
Consensus MFE	-17.81
Energy contribution	-18.45
Covariance contribution	0.64
Combinations/Pair	1.13
Mean z-score	-1.43
Structure conservation index	0.69
SVM decision value	0.37
SVM RNA-class probability	0.709953
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25260652 107 + 27905053
GCCC----CCCCCCCCCCCCCAUCCGCCUGGCAAAACAACGCCCACCUCUAAAAGAUGGUUCAGCGCAUCCGCUGGCUGCUUUUAAAGCGCCAGCCGCAGAAAAUGGACCA
....----...........((((....(((.(.......(((..(((((.....)).)))...))).....((((((.(((.....))))))))).))))...)))).... ( -25.90)
>DroSec_CAF1 117807 97 + 1
GCCC--------------CCCAUCCGCCUGGAAAAACAACGCCCACCUCUAAAAGAUGGUUCAGCGCAUCCGCUGGCUGCUUUUAAAGCGCCAGCCGCAGAAAACGGACCA
....--------------....((((.(((.........(((..(((((.....)).)))...))).....((((((.(((.....)))))))))..)))....))))... ( -26.40)
>DroSim_CAF1 120025 96 + 1
GCCC---------------CCAUCCGCCUGGAAAAACAACGCCCACCUCUAAAAGAUGGUUCAGCGCAUCCGCUGGCUGCUUUUAAAGCGCCAGCCGCAGAAAACGGACCA
....---------------...((((.(((.........(((..(((((.....)).)))...))).....((((((.(((.....)))))))))..)))....))))... ( -26.40)
>DroEre_CAF1 134914 90 + 1
GCC---------------------CCUUUGGAAAAACACCGCCCACCUCUAAAAGAUGGUUCGGCGCAUCCGCUGGCUGCUUUUAAAGCGCCAGCCACAGAAAACGGACCA
...---------------------....(((........((((.(((((.....)).)))..))))..(((((((((.(((.....)))))))))....(....))))))) ( -26.50)
>DroYak_CAF1 122390 93 + 1
GCCC--------------CC----CCUCUGGAAAAACACCGCCCACCUCUAAAAGAUGGUUCGGCGCAUCCGCUGGCUGCUUUUAAAGCGCCAGCCGCAGAAAACGGACCA
..((--------------..----..((((.........((((.(((((.....)).)))..)))).....((((((.(((.....)))))))))..))))....)).... ( -28.80)
>DroAna_CAF1 114464 106 + 1
CCACCCCACAGCUUCCACCCCAU---CACGGAAAAUGGAAAACCACCUCGAAAAGAUGGUUCAGUGCAUCCGUUGACUGCUUUUAAAGCGCAAGCCGCAACAAAUGGAA--
......(((...(((((..((..---...))....)))))(((((.((.....)).)))))..)))..((((((...(((.......((....)).)))...)))))).-- ( -21.80)
>consensus
GCCC______________CCCAU_CGCCUGGAAAAACAACGCCCACCUCUAAAAGAUGGUUCAGCGCAUCCGCUGGCUGCUUUUAAAGCGCCAGCCGCAGAAAACGGACCA
.........................................................((((((........((((((.(((.....))))))))).........)))))). (-17.81 = -18.45 +   0.64)

alignment

secondary structure

dotplot

Window 2

Location	25,260,652 – 25,260,759
Length	107
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	79.59
Mean single sequence MFE	-41.55
Consensus MFE	-25.39
Energy contribution	-26.17
Covariance contribution	0.78
Combinations/Pair	1.14
Mean z-score	-2.73
Structure conservation index	0.61
SVM decision value	1.47
SVM RNA-class probability	0.957121
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25260652 107 - 27905053
UGGUCCAUUUUCUGCGGCUGGCGCUUUAAAAGCAGCCAGCGGAUGCGCUGAACCAUCUUUUAGAGGUGGGCGUUGUUUUGCCAGGCGGAUGGGGGGGGGGGGG----GGGC
..((((.((..((.(.(((((((((.....))).))))))..((.((((....((((((...))))))((((......)))).)))).))....).))..)).----)))) ( -41.00)
>DroSec_CAF1 117807 97 - 1
UGGUCCGUUUUCUGCGGCUGGCGCUUUAAAAGCAGCCAGCGGAUGCGCUGAACCAUCUUUUAGAGGUGGGCGUUGUUUUUCCAGGCGGAUGGG--------------GGGC
..((((.(..(((((.(((((((((.....))).))))))(((.(((((..(((.((.....))))).)))))......)))..)))))..).--------------)))) ( -42.20)
>DroSim_CAF1 120025 96 - 1
UGGUCCGUUUUCUGCGGCUGGCGCUUUAAAAGCAGCCAGCGGAUGCGCUGAACCAUCUUUUAGAGGUGGGCGUUGUUUUUCCAGGCGGAUGG---------------GGGC
..((((.(..(((((.(((((((((.....))).))))))(((.(((((..(((.((.....))))).)))))......)))..))))).).---------------)))) ( -40.20)
>DroEre_CAF1 134914 90 - 1
UGGUCCGUUUUCUGUGGCUGGCGCUUUAAAAGCAGCCAGCGGAUGCGCCGAACCAUCUUUUAGAGGUGGGCGGUGUUUUUCCAAAGG---------------------GGC
..((((.(((......(((((((((.....))).))))))(((.((((((..(((((((...))))))).))))))...)))))).)---------------------))) ( -41.10)
>DroYak_CAF1 122390 93 - 1
UGGUCCGUUUUCUGCGGCUGGCGCUUUAAAAGCAGCCAGCGGAUGCGCCGAACCAUCUUUUAGAGGUGGGCGGUGUUUUUCCAGAGG----GG--------------GGGC
..((((.((((((...(((((((((.....))).))))))(((.((((((..(((((((...))))))).))))))...))))))))----).--------------)))) ( -46.00)
>DroAna_CAF1 114464 106 - 1
--UUCCAUUUGUUGCGGCUUGCGCUUUAAAAGCAGUCAACGGAUGCACUGAACCAUCUUUUCGAGGUGGUUUUCCAUUUUCCGUG---AUGGGGUGGAAGCUGUGGGGUGG
--..(((((..(..((((((.((((((.......((((.((((......((((((((((...)))))))))).......))))))---)))))))).))))))..)))))) ( -38.83)
>consensus
UGGUCCGUUUUCUGCGGCUGGCGCUUUAAAAGCAGCCAGCGGAUGCGCUGAACCAUCUUUUAGAGGUGGGCGUUGUUUUUCCAGGCG_AUGGG______________GGGC
..((((..........(((((((((.....))).))))))(((.(((.((..(((((((...))))))).)).)))...))).........................)))) (-25.39 = -26.17 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:37:13 2006