Locus 3824

Sequence ID	3R_DroMel_CAF1
Location	10,425,572 – 10,425,671
Length	99
Max. P	0.998778

overview

Window 4

Location	10,425,572 – 10,425,671
Length	99
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	77.72
Mean single sequence MFE	-38.10
Consensus MFE	-22.90
Energy contribution	-25.08
Covariance contribution	2.18
Combinations/Pair	1.09
Mean z-score	-3.05
Structure conservation index	0.60
SVM decision value	3.22
SVM RNA-class probability	0.998778
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10425572 99 + 27905053
AUAUGUGCCCUUUUUUUGAGGUGGGGGGAUGGGAAAUGCCUGUGCUUCAUUUUC-------CAUGACGCGGCACGCAGCGUGAAAAUGCUGCACCCCAUCCGCGGA
.......((((((....)))).))(.(((((((...((((.(((..((((....-------.))))))))))).(((((((....)))))))..))))))).)... ( -40.70)
>DroSec_CAF1 89064 87 + 1
----------UUUUUUUGGGAUGGG--GAGUGGAAAUGCCUGUGCUUCAUUUUC-------CAUGACGCGGCACGCAGCGUGAAAAUGCUGCACCCCAUCCGCGGA
----------....(((((((((((--(........((((.(((..((((....-------.))))))))))).(((((((....))))))).)))))))).)))) ( -39.70)
>DroSim_CAF1 76706 85 + 1
----------UUUUUU-GGGGU-GG--GAGUGGAAAUGCCUAUGCUUCAUUUUC-------CAUGACGCGGCACGCAGCGUGAAAAUGCUGCACCCCAUCCGCGGA
----------...(((-(((((-((--(.((.....((((...((.((((....-------.)))).)))))).(((((((....)))))))))))))))).)))) ( -36.30)
>DroEre_CAF1 86117 91 + 1
-----GGCCCUUU--U-GGGGC-------AGGGGCAUGCCCGUGCCUCGUUUUCCAUUUGCCAUGACGCGGCACGCAGCGUGAAAAUGCUGCACCCCAUCCGCGGA
-----.((((...--.-.))))-------.((((.......(((((.((((.............)))).)))))(((((((....))))))).))))......... ( -42.02)
>DroYak_CAF1 87456 84 + 1
AUACUGGCCCUUU--U-GGG------------GGAAUGCUUGUGCUUCAUUUUC-------CAUGACGCGGCACGCAGCGUGAAAAUGCUGCACCCCAUCCGCGGA
.......(((...--(-(((------------(........(((((((((....-------.))))...)))))(((((((....))))))).)))))...).)). ( -31.80)
>consensus
______GCCCUUUUUU_GGGGU_GG__GAGGGGAAAUGCCUGUGCUUCAUUUUC_______CAUGACGCGGCACGCAGCGUGAAAAUGCUGCACCCCAUCCGCGGA
.................(((((..............((((...((.((((............)))).)))))).(((((((....))))))))))))......... (-22.90 = -25.08 +   2.18)

alignment

secondary structure

dotplot

Window 5

Location	10,425,572 – 10,425,671
Length	99
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	77.72
Mean single sequence MFE	-33.40
Consensus MFE	-23.04
Energy contribution	-23.44
Covariance contribution	0.40
Combinations/Pair	1.14
Mean z-score	-2.43
Structure conservation index	0.69
SVM decision value	2.25
SVM RNA-class probability	0.991105
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10425572 99 - 27905053
UCCGCGGAUGGGGUGCAGCAUUUUCACGCUGCGUGCCGCGUCAUG-------GAAAAUGAAGCACAGGCAUUUCCCAUCCCCCCACCUCAAAAAAAGGGCACAUAU
...((((((((((.(((((........)))))(((((((.((((.-------....)))).))...))))).)))))))).....(((.......)))))...... ( -37.00)
>DroSec_CAF1 89064 87 - 1
UCCGCGGAUGGGGUGCAGCAUUUUCACGCUGCGUGCCGCGUCAUG-------GAAAAUGAAGCACAGGCAUUUCCACUC--CCCAUCCCAAAAAAA----------
...(.((((((((.(((((........)))))(((((((.((((.-------....)))).))...))))).......)--)))))))).......---------- ( -35.60)
>DroSim_CAF1 76706 85 - 1
UCCGCGGAUGGGGUGCAGCAUUUUCACGCUGCGUGCCGCGUCAUG-------GAAAAUGAAGCAUAGGCAUUUCCACUC--CC-ACCCC-AAAAAA----------
........(((((((((((........)))))(((((((.((((.-------....)))).))...)))))........--..-)))))-).....---------- ( -29.90)
>DroEre_CAF1 86117 91 - 1
UCCGCGGAUGGGGUGCAGCAUUUUCACGCUGCGUGCCGCGUCAUGGCAAAUGGAAAACGAGGCACGGGCAUGCCCCU-------GCCCC-A--AAAGGGCC-----
(((.....(((((((((((........)))))(((((.((((((.....)))....))).)))))(((....)))..-------)))))-)--...)))..----- ( -37.50)
>DroYak_CAF1 87456 84 - 1
UCCGCGGAUGGGGUGCAGCAUUUUCACGCUGCGUGCCGCGUCAUG-------GAAAAUGAAGCACAAGCAUUCC------------CCC-A--AAAGGGCCAGUAU
(((.....(((((.(((((........)))))((((....((((.-------....)))).))))........)------------)))-)--...)))....... ( -27.00)
>consensus
UCCGCGGAUGGGGUGCAGCAUUUUCACGCUGCGUGCCGCGUCAUG_______GAAAAUGAAGCACAGGCAUUUCCACUC__CC_ACCCC_AAAAAAGGGC______
.........((((((((((........)))))(((((((.((((............)))).))...))))).............)))))................. (-23.04 = -23.44 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:56 2006