Locus 4056

Sequence ID	2L_DroMel_CAF1
Location	11,737,825 – 11,737,940
Length	115
Max. P	0.854458

overview

Window 2

Location	11,737,825 – 11,737,940
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.79
Mean single sequence MFE	-33.20
Consensus MFE	-24.58
Energy contribution	-25.82
Covariance contribution	1.25
Combinations/Pair	1.10
Mean z-score	-2.22
Structure conservation index	0.74
SVM decision value	0.80
SVM RNA-class probability	0.854458
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11737825 115 + 22407834
AUGUAUCAUGUGCUCCGUUAAUCAAACGUUGCCAUACCAACAGGAGCACGUGACUCACGAUAAGACCGGCGUACUUAGGACGGUUUCCAUAGAACGCG-----CCUGAUAAACAAAGCAC
.((..((((((((((((((.....)))((((......)))).)))))))))))..))..........(((((.((..(((.....)))..))...)))-----))............... ( -34.00)
>DroSim_CAF1 197448 114 + 1
AUGAAUCAUGUGCUCCGUUAAUCAAACGUUGCCAUACCAACAGGAGCACGUGACUCACGAUAAGACCGGCGUACUUAGGACGGUUUCCAUAGAACGCG-----C-UGAUAAACAAAGCAC
.(((.((((((((((((((.....)))((((......)))).))))))))))).)))...........((((.((..(((.....)))..)).))))(-----(-(.........))).. ( -37.00)
>DroYak_CAF1 191148 115 + 1
AUGAAUCAUGUGCUCCGUUAAUCAAACGUUGCCAUACCAACCGGAGCACGUGACUCACGAUAAGACCGGCGUACUUAGGACGGUUUCCAUAGAACGCG-----CCUGAUAAACAAAGCAC
.(((.((((((((((((((.....)))((((......)))).))))))))))).)))..........(((((.((..(((.....)))..))...)))-----))............... ( -34.80)
>DroAna_CAF1 194979 119 + 1
AUGAAUCAUGUGCUCCAGCAAUCAUUCGUUGCCAUAUCAACUAGGGCACGUGACUCUCGAUAAGACCUUCGUACUUAAGAUGGU-ACCAUAGAGCCCGUACUGCUUGAUAAACAAAGCAC
.....((((((((((..(((((.....)))))...........))))))))))..(((......(((.((........)).)))-......))).......(((((........))))). ( -27.02)
>consensus
AUGAAUCAUGUGCUCCGUUAAUCAAACGUUGCCAUACCAACAGGAGCACGUGACUCACGAUAAGACCGGCGUACUUAGGACGGUUUCCAUAGAACGCG_____CCUGAUAAACAAAGCAC
..((.((((((((((((((.....)))((((......)))).))))))))))).))............((((.((..(((.....)))..)).))))....................... (-24.58 = -25.82 +   1.25)

alignment

secondary structure

dotplot

Window 3

Location	11,737,825 – 11,737,940
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.79
Mean single sequence MFE	-39.05
Consensus MFE	-27.94
Energy contribution	-28.25
Covariance contribution	0.31
Combinations/Pair	1.14
Mean z-score	-2.26
Structure conservation index	0.72
SVM decision value	0.66
SVM RNA-class probability	0.815963
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11737825 115 - 22407834
GUGCUUUGUUUAUCAGG-----CGCGUUCUAUGGAAACCGUCCUAAGUACGCCGGUCUUAUCGUGAGUCACGUGCUCCUGUUGGUAUGGCAACGUUUGAUUAACGGAGCACAUGAUACAU
((((((((((.((((((-----(((((.((..(((.....)))..)).))))..(((.(((((.((((.....))))....))))).)))...))))))).))))))))))......... ( -39.20)
>DroSim_CAF1 197448 114 - 1
GUGCUUUGUUUAUCA-G-----CGCGUUCUAUGGAAACCGUCCUAAGUACGCCGGUCUUAUCGUGAGUCACGUGCUCCUGUUGGUAUGGCAACGUUUGAUUAACGGAGCACAUGAUUCAU
..(((.........)-)-----)((((.((..(((.....)))..)).))))..........((((((((.(((((((.(((((((((....)))...))))))))))))).)))))))) ( -38.30)
>DroYak_CAF1 191148 115 - 1
GUGCUUUGUUUAUCAGG-----CGCGUUCUAUGGAAACCGUCCUAAGUACGCCGGUCUUAUCGUGAGUCACGUGCUCCGGUUGGUAUGGCAACGUUUGAUUAACGGAGCACAUGAUUCAU
((((((((((.((((((-----((.((.((..(((.....)))..)).))((((..((.((((.((((.....)))))))).))..))))..)))))))).))))))))))......... ( -42.30)
>DroAna_CAF1 194979 119 - 1
GUGCUUUGUUUAUCAAGCAGUACGGGCUCUAUGGU-ACCAUCUUAAGUACGAAGGUCUUAUCGAGAGUCACGUGCCCUAGUUGAUAUGGCAACGAAUGAUUGCUGGAGCACAUGAUUCAU
(((((((((..((((..(.(((((((((((.((((-(..(((((.......)))))..))))))))))).)))))....((((......)))))..)))).)).)))))))......... ( -36.40)
>consensus
GUGCUUUGUUUAUCAGG_____CGCGUUCUAUGGAAACCGUCCUAAGUACGCCGGUCUUAUCGUGAGUCACGUGCUCCUGUUGGUAUGGCAACGUUUGAUUAACGGAGCACAUGAUUCAU
((((((((.....))...............((((...))))...))))))............((((((((.(((((((.(((((((((....)))...))))))))))))).)))))))) (-27.94 = -28.25 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:14 2006