Locus 4339

Sequence ID	3L_DroMel_CAF1
Location	12,755,049 – 12,755,154
Length	105
Max. P	0.960075

overview

Window 3

Location	12,755,049 – 12,755,154
Length	105
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	86.88
Mean single sequence MFE	-22.78
Consensus MFE	-16.36
Energy contribution	-17.44
Covariance contribution	1.08
Combinations/Pair	1.15
Mean z-score	-1.71
Structure conservation index	0.72
SVM decision value	0.11
SVM RNA-class probability	0.587445
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12755049 105 + 23771897
AUUUUGUAAUGUCAUUUUUUUGACCAAAACUAAAAAGAGAGUUUUGGUCGACAUAAAUAGUAAGUUAAAUAAACCAAGGAAGUCUUUUUGUUUACAAGGUUUCUC----
(((((((((((..((((..((((((((((((........))))))))))))...))))..))............((((((....)))))).))))))))).....---- ( -22.30)
>DroSec_CAF1 12018 109 + 1
AUUUUGUAAUGUCAUUUUUUUGACCAAAACUAAAAAGAGAGUUUUGGUCGACAUAAAUAGUAAGUUAAAUGAACCAAGGAAGUCUUUCUGUUUAAAAGGUUUCUUUAUU
.........((..((((..((((((((((((........))))))))))))...))))..)).............((((((..((((.......))))..))))))... ( -23.60)
>DroSim_CAF1 14301 109 + 1
AUUUUGUAAUGUCAUUUUUUUGACCAAAACUAAAAAGAGAGUUUUGGUCGACAUAAAUAGUAAGUUAAAUGAACCAAGGAAGUCUUUCUGUUUAAAAGGUUUCUUUAUU
.........((..((((..((((((((((((........))))))))))))...))))..)).............((((((..((((.......))))..))))))... ( -23.60)
>DroEre_CAF1 12218 106 + 1
AUUUUGUAAUGCCAUUUUUUUGACCAAAACUUAAAAGAGCGUUUUGGUCGACAGCAAUUAUAAGUUAAACAAACCGG-GAAAUCUUUUUGUCUACAAGGAUA--UUAUU
.....((((((((......(((((((((((..........)))))))))))............((...(((((..((-(....))))))))..))..)).))--)))). ( -20.00)
>DroYak_CAF1 12363 109 + 1
AUUUUGUAAUGUCAUUUUUUUGACCAAAACUAAAAAGAGCGUUUUGGUCGACAGCACUUAUAAGCUUAACAAACCGGGGAAGUCUUCCUGUUUACAAGGAUGCUUUAUU
.(((((((((((.......(((((((((((..........))))))))))).(((........)))..)))...((((((....)))))).)))))))).......... ( -24.40)
>consensus
AUUUUGUAAUGUCAUUUUUUUGACCAAAACUAAAAAGAGAGUUUUGGUCGACAUAAAUAGUAAGUUAAAUAAACCAAGGAAGUCUUUCUGUUUACAAGGUUUCUUUAUU
.((((((((..........((((((((((((........)))))))))))).......................((((((....)))))).)))))))).......... (-16.36 = -17.44 +   1.08)

alignment

secondary structure

dotplot

Window 4

Location	12,755,049 – 12,755,154
Length	105
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	86.88
Mean single sequence MFE	-20.60
Consensus MFE	-15.99
Energy contribution	-15.91
Covariance contribution	-0.08
Combinations/Pair	1.14
Mean z-score	-2.36
Structure conservation index	0.78
SVM decision value	1.51
SVM RNA-class probability	0.960075
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12755049 105 - 23771897
----GAGAAACCUUGUAAACAAAAAGACUUCCUUGGUUUAUUUAACUUACUAUUUAUGUCGACCAAAACUCUCUUUUUAGUUUUGGUCAAAAAAAUGACAUUACAAAAU
----........((((((.......(((.....((((...........)))).....)))((((((((((........))))))))))............))))))... ( -21.40)
>DroSec_CAF1 12018 109 - 1
AAUAAAGAAACCUUUUAAACAGAAAGACUUCCUUGGUUCAUUUAACUUACUAUUUAUGUCGACCAAAACUCUCUUUUUAGUUUUGGUCAAAAAAAUGACAUUACAAAAU
..(((.(((..(((((.....)))))..))).)))..((((((.....((.......)).((((((((((........))))))))))....))))))........... ( -18.10)
>DroSim_CAF1 14301 109 - 1
AAUAAAGAAACCUUUUAAACAGAAAGACUUCCUUGGUUCAUUUAACUUACUAUUUAUGUCGACCAAAACUCUCUUUUUAGUUUUGGUCAAAAAAAUGACAUUACAAAAU
..(((.(((..(((((.....)))))..))).)))..((((((.....((.......)).((((((((((........))))))))))....))))))........... ( -18.10)
>DroEre_CAF1 12218 106 - 1
AAUAA--UAUCCUUGUAGACAAAAAGAUUUC-CCGGUUUGUUUAACUUAUAAUUGCUGUCGACCAAAACGCUCUUUUAAGUUUUGGUCAAAAAAAUGGCAUUACAAAAU
.....--.....(((((((((....((((..-..((((.....))))...))))..))))(((((((((..........))))))))).............)))))... ( -21.00)
>DroYak_CAF1 12363 109 - 1
AAUAAAGCAUCCUUGUAAACAGGAAGACUUCCCCGGUUUGUUAAGCUUAUAAGUGCUGUCGACCAAAACGCUCUUUUUAGUUUUGGUCAAAAAAAUGACAUUACAAAAU
....((((.((((.(....)))))(((((.....))))).....))))....(((.(((((((((((((..........)))))))))........)))).)))..... ( -24.40)
>consensus
AAUAAAGAAACCUUGUAAACAGAAAGACUUCCUUGGUUUAUUUAACUUACUAUUUAUGUCGACCAAAACUCUCUUUUUAGUUUUGGUCAAAAAAAUGACAUUACAAAAU
............((((((.......(((......((((.....))))..........)))(((((((((..........)))))))))............))))))... (-15.99 = -15.91 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:58 2006