Locus 6750

Sequence ID	X_DroMel_CAF1
Location	16,766,556 – 16,766,652
Length	96
Max. P	0.929031

overview

Window 2

Location	16,766,556 – 16,766,652
Length	96
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	76.28
Mean single sequence MFE	-34.23
Consensus MFE	-17.35
Energy contribution	-18.17
Covariance contribution	0.82
Combinations/Pair	1.05
Mean z-score	-2.24
Structure conservation index	0.51
SVM decision value	1.19
SVM RNA-class probability	0.929031
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16766556 96 + 22224390
UUUCGAUGGCCAUUUUGGAGGCGAAAAGCGGGCAGAGGGCGCGCCACGCAUGCGCAAUGCGAAAAACGCGC-----------GCGAAACGCGAGCAAAACGCGUGCG
(((((....((.....))...))))).(((.((.....)).)))..(((((.....))))).....(((((-----------(((...(....).....)))))))) ( -34.20)
>DroPse_CAF1 47954 77 + 1
UUUUUAUGGCCAUUU------------------AAAGGCCGCAUCACGCAUGCGCCAUGC-AAAAGCGCCC-----------GCGAAACGCGAGCAAAACGCGUGCG
.......((((....------------------...))))......((((((((....((-....))((.(-----------(((...)))).))....)))))))) ( -29.20)
>DroSec_CAF1 4038 96 + 1
CUUCGAUGGCCAUUUCGGAGGCGACAAGCGGGCAGAGGGCACGCCACGCAUGCGCAAUGCGAAAAACGCGC-----------GCGAAACGCGAGCAAAACGCGUGCG
((((((........))))))(((.((.((((((.........))).))).)))))...........(((((-----------(((...(....).....)))))))) ( -35.90)
>DroEre_CAF1 6946 94 + 1
UUUCGAUGGCCAUUUUGGAGGCGAAAAACGGGCA--GGGCGCGCCACGCAUGCGCAAUGCGAAAAACGCGC-----------GCGAAACGCGCGCAAAACGCGUGCG
(((((....((.....))...)))))........--..((((((..(((((.....)))))......((((-----------(((...))))))).....)))))). ( -37.30)
>DroAna_CAF1 48812 99 + 1
UUUUGAUGGCCAAUUUAAGCGCCAAAA--------AGGCCGCGGCACGCAUGCGCAAUGCGAAAAACGCGCGCGAAACGCGCGCGAAACGCGAGCAAAACGCGUGCG
........(((.......(((((....--------.)).)))))).((((((((...(((......((((((((...))))))))........)))...)))))))) ( -39.55)
>DroPer_CAF1 48518 77 + 1
UUUUUAUGGCCAUUU------------------AAAGGCCGCAUCACGCAUGCGCCAUGC-AAAAGCGCCC-----------GCGAAACGCGAGCAAAACGCGUGCG
.......((((....------------------...))))......((((((((....((-....))((.(-----------(((...)))).))....)))))))) ( -29.20)
>consensus
UUUCGAUGGCCAUUUUGGAGGCGAAAA______A_AGGCCGCGCCACGCAUGCGCAAUGCGAAAAACGCGC___________GCGAAACGCGAGCAAAACGCGUGCG
......((.((.........................)).)).....((((((((...(((........((((((.....))))))........)))...)))))))) (-17.35 = -18.17 +   0.82)

alignment

secondary structure

dotplot

Window 3

Location	16,766,556 – 16,766,652
Length	96
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	76.28
Mean single sequence MFE	-34.45
Consensus MFE	-17.89
Energy contribution	-18.82
Covariance contribution	0.93
Combinations/Pair	1.14
Mean z-score	-1.96
Structure conservation index	0.52
SVM decision value	0.67
SVM RNA-class probability	0.818239
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16766556 96 - 22224390
CGCACGCGUUUUGCUCGCGUUUCGC-----------GCGCGUUUUUCGCAUUGCGCAUGCGUGGCGCGCCCUCUGCCCGCUUUUCGCCUCCAAAAUGGCCAUCGAAA
.(((.((((..(((.(((((.....-----------)))))......)))..)))).)))((((.(((.....))))))).....(((........)))........ ( -32.40)
>DroPse_CAF1 47954 77 - 1
CGCACGCGUUUUGCUCGCGUUUCGC-----------GGGCGCUUUU-GCAUGGCGCAUGCGUGAUGCGGCCUUU------------------AAAUGGCCAUAAAAA
((((.(((((..(((((((...)))-----------))))((....-))..))))).))))......((((...------------------....))))....... ( -32.50)
>DroSec_CAF1 4038 96 - 1
CGCACGCGUUUUGCUCGCGUUUCGC-----------GCGCGUUUUUCGCAUUGCGCAUGCGUGGCGUGCCCUCUGCCCGCUUGUCGCCUCCGAAAUGGCCAUCGAAG
((((.((((..(((.(((((.....-----------)))))......)))..)))).)))).((((.((.....)).))))....(((........)))........ ( -31.60)
>DroEre_CAF1 6946 94 - 1
CGCACGCGUUUUGCGCGCGUUUCGC-----------GCGCGUUUUUCGCAUUGCGCAUGCGUGGCGCGCCC--UGCCCGUUUUUCGCCUCCAAAAUGGCCAUCGAAA
((((.(((....(((((((.....)-----------))))))....)))..))))...(((.((((.....--))))))).....(((........)))........ ( -33.70)
>DroAna_CAF1 48812 99 - 1
CGCACGCGUUUUGCUCGCGUUUCGCGCGCGUUUCGCGCGCGUUUUUCGCAUUGCGCAUGCGUGCCGCGGCCU--------UUUUGGCGCUUAAAUUGGCCAUCAAAA
.((((((((..(((..(((...((((((((...)))))))).....)))...))).))))))))...((((.--------.((((.....))))..))))....... ( -44.00)
>DroPer_CAF1 48518 77 - 1
CGCACGCGUUUUGCUCGCGUUUCGC-----------GGGCGCUUUU-GCAUGGCGCAUGCGUGAUGCGGCCUUU------------------AAAUGGCCAUAAAAA
((((.(((((..(((((((...)))-----------))))((....-))..))))).))))......((((...------------------....))))....... ( -32.50)
>consensus
CGCACGCGUUUUGCUCGCGUUUCGC___________GCGCGUUUUUCGCAUUGCGCAUGCGUGGCGCGCCCU_U______UUUUCGCCUCCAAAAUGGCCAUCAAAA
....((((((.(((..((((...(((((.....)))))(((.....)))...))))..))).))))))....................................... (-17.89 = -18.82 +   0.93)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:54 2006