Locus 6272

Sequence ID	3L_DroMel_CAF1
Location	16,716,658 – 16,716,752
Length	94
Max. P	0.991962

overview

Window 1

Location	16,716,658 – 16,716,752
Length	94
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	87.57
Mean single sequence MFE	-22.24
Consensus MFE	-17.22
Energy contribution	-16.98
Covariance contribution	-0.24
Combinations/Pair	1.08
Mean z-score	-2.94
Structure conservation index	0.77
SVM decision value	2.30
SVM RNA-class probability	0.991962
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16716658 94 + 23771897
----GCUAGCGCUGAUUAUUUCAGCACUUAUUAAAUUUUAGCACAGCCACAUCCAGCACAAGUGGCAACAACAACCAUGGGGCA--ACAGCACCCAUAAC
----(((((.(((((.....))))).))...........)))...(((((...........)))))..........(((((((.--...)).)))))... ( -26.10)
>DroSec_CAF1 24078 84 + 1
----GCCAGCGCUGAUUAUUUCAGCACUUAUUAAAUUUUAGCACAGCCACAUGCAGCACAAGUGGCAACAACAACC------------AGCAGCCAUAAC
----((..(((((((.....)))))....................(((((.((.....)).)))))..........------------.)).))...... ( -19.70)
>DroSim_CAF1 28509 84 + 1
----GCCAGCGCUGAUUAUUUCAGCACUUAUUAAAUUUUAGCACAGCCACAUGCAGCACAAGUGGCAACAACAACC------------AGCAGCCAUAAC
----((..(((((((.....)))))....................(((((.((.....)).)))))..........------------.)).))...... ( -19.70)
>DroEre_CAF1 25000 93 + 1
----GCCAGCGCUGAUUAUUUCAGCACUUAUUAAAUUUUAGCACAGCUACAUCCAGCACAAGUGGCAACAACAACCACGGG-CA--ACAGCGCCCAUAAC
----((((..(((((.....)))))....................(((......))).....))))............(((-(.--.....))))..... ( -24.30)
>DroYak_CAF1 26856 99 + 1
CAAAGCCAGCGCUGAUUAUUUCAGCACUUAUUAAAUUUUAGCACAGCUACAUCCAGCACAAGUGGCAACAACAACCACGGG-CAAAACAGCAGCCAUUGC
....(((.(((((((.....))))).............((((...))))......))....((((.........)))).))-)......((((...)))) ( -21.40)
>consensus
____GCCAGCGCUGAUUAUUUCAGCACUUAUUAAAUUUUAGCACAGCCACAUCCAGCACAAGUGGCAACAACAACCA_GGG_CA__ACAGCAGCCAUAAC
........(((((((.....)))))....................(((((...........))))).......................))......... (-17.22 = -16.98 +  -0.24)

alignment

secondary structure

dotplot

Window 2

Location	16,716,658 – 16,716,752
Length	94
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	87.57
Mean single sequence MFE	-29.10
Consensus MFE	-19.23
Energy contribution	-19.95
Covariance contribution	0.72
Combinations/Pair	1.09
Mean z-score	-2.12
Structure conservation index	0.66
SVM decision value	0.08
SVM RNA-class probability	0.572464
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16716658 94 - 23771897
GUUAUGGGUGCUGU--UGCCCCAUGGUUGUUGUUGCCACUUGUGCUGGAUGUGGCUGUGCUAAAAUUUAAUAAGUGCUGAAAUAAUCAGCGCUAGC----
.(((((((.((...--.))))))))).....((.(((((...........)))))...))............((((((((.....))))))))...---- ( -30.20)
>DroSec_CAF1 24078 84 - 1
GUUAUGGCUGCU------------GGUUGUUGUUGCCACUUGUGCUGCAUGUGGCUGUGCUAAAAUUUAAUAAGUGCUGAAAUAAUCAGCGCUGGC----
.....(((.(((------------(((((((...(((((.((.....)).))))).(..((...........))..)...)))))))))))))...---- ( -27.00)
>DroSim_CAF1 28509 84 - 1
GUUAUGGCUGCU------------GGUUGUUGUUGCCACUUGUGCUGCAUGUGGCUGUGCUAAAAUUUAAUAAGUGCUGAAAUAAUCAGCGCUGGC----
.....(((.(((------------(((((((...(((((.((.....)).))))).(..((...........))..)...)))))))))))))...---- ( -27.00)
>DroEre_CAF1 25000 93 - 1
GUUAUGGGCGCUGU--UG-CCCGUGGUUGUUGUUGCCACUUGUGCUGGAUGUAGCUGUGCUAAAAUUUAAUAAGUGCUGAAAUAAUCAGCGCUGGC----
.(((((((((....--))-)))))))........((((...(((((((.(((..(.(..((...........))..).)..))).)))))))))))---- ( -29.20)
>DroYak_CAF1 26856 99 - 1
GCAAUGGCUGCUGUUUUG-CCCGUGGUUGUUGUUGCCACUUGUGCUGGAUGUAGCUGUGCUAAAAUUUAAUAAGUGCUGAAAUAAUCAGCGCUGGCUUUG
(((.(((((((.(((..(-((.(((((.......)))))..).))..)))))))))))))............((((((((.....))))))))....... ( -32.10)
>consensus
GUUAUGGCUGCUGU__UG_CCC_UGGUUGUUGUUGCCACUUGUGCUGGAUGUGGCUGUGCUAAAAUUUAAUAAGUGCUGAAAUAAUCAGCGCUGGC____
((.((((((((............((((.......))))............))))))))))............((((((((.....))))))))....... (-19.23 = -19.95 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:23 2006