Locus 7009

Sequence ID	3R_DroMel_CAF1
Location	18,474,970 – 18,475,090
Length	120
Max. P	0.999892

overview

Window 1

Location	18,474,970 – 18,475,090
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.25
Mean single sequence MFE	-41.32
Consensus MFE	-38.40
Energy contribution	-38.60
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-3.27
Structure conservation index	0.93
SVM decision value	4.41
SVM RNA-class probability	0.999892
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18474970 120 + 27905053
GCAGACAACUGGGCCAGGAAAUGUAGCCGGACAACGGUUCUUUUAAUUACUUUCUGCAUAAAUUUGCACUCAUUUCCGGCCCUCGUUCUCUGGAGAUGUCUGAUCCAGCUGGACACUAAA
.((((((...(((((.(((((((.(((((.....)))))...............((((......))))..))))))))))))....(((....))))))))).(((....)))....... ( -39.50)
>DroSec_CAF1 30128 120 + 1
GCAGACAACUGGGCCAGGAAAUGUAGCCGGACAACGGUUCUUUUAAUUACUUUCUGCAUAAAUUUGCACUCAUUUCCGGCCCUCGUUCUCUGGAGUUGUCUGAUCCAGCUGGACACUAAA
.((((((((((((((.(((((((.(((((.....)))))...............((((......))))..))))))))))))(((.....)))))))))))).(((....)))....... ( -42.30)
>DroSim_CAF1 29814 120 + 1
GCAGACAACUGGGCCAGGAAAUGUAGCCGGACAACGGUUCUUUUAAUUACUUUCUGCAUAAAUUUGCACUCAUUUCCGGCCCUCGUUCUCUGGAGAUGUCUGAUCCAGCUGGACACUAAA
.((((((...(((((.(((((((.(((((.....)))))...............((((......))))..))))))))))))....(((....))))))))).(((....)))....... ( -39.50)
>DroEre_CAF1 30275 120 + 1
GCAGACAACUGGGCCGGGAAAUGUAGCCGGACAACGGUUCUUUUAAUUACUUUCUGCAUAAAUUUGCACUCAUUUCCGGCCCUCGUUCUCCGUAGAUGUCUGGGCCAGCUGGACACUAAA
...((.(((.((((((((((....(((((.....)))))...............((((......))))....))))))))))..))).))..(((.((((..(.....)..))))))).. ( -39.60)
>DroYak_CAF1 31221 120 + 1
GCAGAGAACUGGGCCGGGAAAUGUAGCCGGACAACGGUUCUUUUAAUUACUUUCUGCAUAAAUUUGCACUCAUUUCCGGCCCUCGUUCUCUGGAGAUGUCUGAACCAGCUGGACACUAAA
.((((((((.((((((((((....(((((.....)))))...............((((......))))....))))))))))..)))))))).((.(((((.........)))))))... ( -45.70)
>consensus
GCAGACAACUGGGCCAGGAAAUGUAGCCGGACAACGGUUCUUUUAAUUACUUUCUGCAUAAAUUUGCACUCAUUUCCGGCCCUCGUUCUCUGGAGAUGUCUGAUCCAGCUGGACACUAAA
.((((.(((.(((((.(((((((.(((((.....)))))...............((((......))))..))))))))))))..))).)))).((.((((((.......))))))))... (-38.40 = -38.60 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	18,474,970 – 18,475,090
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.25
Mean single sequence MFE	-38.62
Consensus MFE	-35.88
Energy contribution	-35.92
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.13
Structure conservation index	0.93
SVM decision value	2.95
SVM RNA-class probability	0.997884
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18474970 120 - 27905053
UUUAGUGUCCAGCUGGAUCAGACAUCUCCAGAGAACGAGGGCCGGAAAUGAGUGCAAAUUUAUGCAGAAAGUAAUUAAAAGAACCGUUGUCCGGCUACAUUUCCUGGCCCAGUUGUCUGC
....((((((....))))...)).....((((.(((..((((((((((((..((((......)))).................(((.....)))...))))))).))))).))).)))). ( -37.60)
>DroSec_CAF1 30128 120 - 1
UUUAGUGUCCAGCUGGAUCAGACAACUCCAGAGAACGAGGGCCGGAAAUGAGUGCAAAUUUAUGCAGAAAGUAAUUAAAAGAACCGUUGUCCGGCUACAUUUCCUGGCCCAGUUGUCUGC
......((((....))))(((((((((((((.(((....(((((((((((..((((......))))..((....))........)))).)))))))....)))))))...))))))))). ( -39.60)
>DroSim_CAF1 29814 120 - 1
UUUAGUGUCCAGCUGGAUCAGACAUCUCCAGAGAACGAGGGCCGGAAAUGAGUGCAAAUUUAUGCAGAAAGUAAUUAAAAGAACCGUUGUCCGGCUACAUUUCCUGGCCCAGUUGUCUGC
....((((((....))))...)).....((((.(((..((((((((((((..((((......)))).................(((.....)))...))))))).))))).))).)))). ( -37.60)
>DroEre_CAF1 30275 120 - 1
UUUAGUGUCCAGCUGGCCCAGACAUCUACGGAGAACGAGGGCCGGAAAUGAGUGCAAAUUUAUGCAGAAAGUAAUUAAAAGAACCGUUGUCCGGCUACAUUUCCCGGCCCAGUUGUCUGC
.(((((.....)))))..((((((.((.((.....)).((((((((((((..((((......)))).................(((.....)))...))))).))))))))).)))))). ( -37.40)
>DroYak_CAF1 31221 120 - 1
UUUAGUGUCCAGCUGGUUCAGACAUCUCCAGAGAACGAGGGCCGGAAAUGAGUGCAAAUUUAUGCAGAAAGUAAUUAAAAGAACCGUUGUCCGGCUACAUUUCCCGGCCCAGUUCUCUGC
....(((((...........)))))...((((((((..((((((((((((..((((......)))).................(((.....)))...))))).))))))).)))))))). ( -40.90)
>consensus
UUUAGUGUCCAGCUGGAUCAGACAUCUCCAGAGAACGAGGGCCGGAAAUGAGUGCAAAUUUAUGCAGAAAGUAAUUAAAAGAACCGUUGUCCGGCUACAUUUCCUGGCCCAGUUGUCUGC
....(((((...........)))))...((((.(((..((((((((((((..((((......)))).................(((.....)))...))))))).))))).))).)))). (-35.88 = -35.92 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:26 2006