Locus 3783

Sequence ID	3R_DroMel_CAF1
Location	10,252,958 – 10,253,109
Length	151
Max. P	0.574943

overview

Window 6

Location	10,252,958 – 10,253,069
Length	111
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	82.32
Mean single sequence MFE	-31.73
Consensus MFE	-25.95
Energy contribution	-26.95
Covariance contribution	1.00
Combinations/Pair	1.04
Mean z-score	-1.42
Structure conservation index	0.82
SVM decision value	-0.01
SVM RNA-class probability	0.527953
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10252958 111 - 27905053
GCCAAUACGGAAGCAAUGUUGCCGCUGCACUUGCAACAGGAGCAACAUUGGCAACAUCGGCAACAUCGGCCACAUC------AUCGGCAACGGGAGCAACAUCGCCAGGCAGCCACA
(((....(....)..(((((((((.(((.((((...)))).)))....((....)).))))))))).(((......------.(((....)))((......))))).)))....... ( -34.20)
>DroSim_CAF1 109225 99 - 1
GCCAAUACGGAAGCAAUGUUGCCGCUGCACUUGCAACAGGAGCAACAUUGGCAACAGGAGCAACAU------------------CGGCAACGGGAGCAACAUCGCCAGGCAGCCACA
(((....(....)..(((((((((((((.((((...)))).))....(((....))).)))....(------------------((....)))).))))))).....)))....... ( -28.20)
>DroEre_CAF1 111321 90 - 1
GCCAAUACGGAAGCAAUGUUGCCGCUGCACUUGCAACAGGAGCAACAUCGGCCACA---------------------------UCGGCAACGGGUGCAACAUCGCCAGGCAGCCACA
(((....((...((.((((.((((.(((.((((...)))).)))....)))).)))---------------------------)..))..))((((......)))).)))....... ( -27.30)
>DroYak_CAF1 117267 117 - 1
GCCAAUACGGAAGCAAUGUUGCCGCUGCACUUGCAACAGGAGCAACAUCGGCAACAUCAGCAACAUUGGCAACAUCGACCACAGCGGCAACGGGUGCAACAACGCCAGGCAGCCACA
(((....(....)...(((((((((((...((((.....((......))(....)....))))...((....)).......)))))))))))((((......)))).)))....... ( -37.20)
>consensus
GCCAAUACGGAAGCAAUGUUGCCGCUGCACUUGCAACAGGAGCAACAUCGGCAACAUCAGCAACAU_________________UCGGCAACGGGAGCAACAUCGCCAGGCAGCCACA
(((.........((..((((((((.(((.((((...)))).)))....))))))))...)).......................((....))((((......)))).)))....... (-25.95 = -26.95 +   1.00)

alignment

secondary structure

dotplot

Window 7

Location	10,252,993 – 10,253,109
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.40
Mean single sequence MFE	-39.17
Consensus MFE	-27.46
Energy contribution	-28.35
Covariance contribution	0.89
Combinations/Pair	1.06
Mean z-score	-1.55
Structure conservation index	0.70
SVM decision value	0.08
SVM RNA-class probability	0.574943
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10252993 116 + 27905053
----GAUGUGGCCGAUGUUGCCGAUGUUGCCAAUGUUGCUCCUGUUGCAAGUGCAGCGGCAACAUUGCUUCCGUAUUGGCGGGUUCGCGGCAUGGUUGCACAACCGGUGCUAAAAACGCU
----..((..(((.(((((((((((((((((...(((((..((......)).)))))))))))))))..(((((....)))))...))))))))))..)).....((((.......)))) ( -44.20)
>DroSec_CAF1 110748 106 + 1
--------------AUGUUGCUCCUGUUGCCAAUGUUGCUCCUGUUGCAAGUGCAGCGGCAACAUUGCUUCCGUAUUGGCGGGUUCGCGGCAUGGUUGCACAACCGGUGCUAAAAACGCU
--------------.....((.((((((((((((((((((...(((((....)))))))))))))))..(((((....)))))...)))))).((((....)))))).)).......... ( -39.10)
>DroSim_CAF1 109258 106 + 1
--------------AUGUUGCUCCUGUUGCCAAUGUUGCUCCUGUUGCAAGUGCAGCGGCAACAUUGCUUCCGUAUUGGCGGGUUCGCGGCAUGGUUGCACAACCGGUGCUAAAAACGCU
--------------.....((.((((((((((((((((((...(((((....)))))))))))))))..(((((....)))))...)))))).((((....)))))).)).......... ( -39.10)
>DroEre_CAF1 111355 96 + 1
------------------------UGUGGCCGAUGUUGCUCCUGUUGCAAGUGCAGCGGCAACAUUGCUUCCGUAUUGGCGAGUUCGCGGCAUGGUUGCACAACCGGUGCUAAAAACGCU
------------------------.(((((((((((((((...(((((....))))))))))))))............(((....))))))......((((.....))))......))). ( -33.60)
>DroWil_CAF1 123812 96 + 1
---------------UGUUGCAGCCAUUGCCGAGGCAGCUACU---ACUAGUGCA------GCAUUGCUUCCGUAUUGGCGUGUGCGAGGCAUGGUUGCACAACCGGUGCUAAAAACGCU
---------------(((.((((((((.((((((((((((.(.---......).)------))..))))))(((((......))))).))))))))))))))...((((.......)))) ( -34.30)
>DroYak_CAF1 117304 120 + 1
GGUCGAUGUUGCCAAUGUUGCUGAUGUUGCCGAUGUUGCUCCUGUUGCAAGUGCAGCGGCAACAUUGCUUCCGUAUUGGCGAGUUCGCGGCAUGGUUGCACAACCGGUGCUAAAAACGCU
.(.(((..(((((((((..((.((((((((((.((((((.......)))...))).)))))))))))).....)))))))))..))))(((((((((....)))).)))))......... ( -44.70)
>consensus
______________AUGUUGCUGCUGUUGCCAAUGUUGCUCCUGUUGCAAGUGCAGCGGCAACAUUGCUUCCGUAUUGGCGGGUUCGCGGCAUGGUUGCACAACCGGUGCUAAAAACGCU
............................((.(((((((((...(((((....))))))))))))))))...(((....(((....)))(((((((((....)))).)))))....))).. (-27.46 = -28.35 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:01 2006