Locus 8859

Sequence ID	3R_DroMel_CAF1
Location	23,776,349 – 23,776,456
Length	107
Max. P	0.939397

overview

Window 2

Location	23,776,349 – 23,776,456
Length	107
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	73.81
Mean single sequence MFE	-23.44
Consensus MFE	-9.52
Energy contribution	-10.36
Covariance contribution	0.84
Combinations/Pair	1.11
Mean z-score	-1.72
Structure conservation index	0.41
SVM decision value	-0.03
SVM RNA-class probability	0.518377
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23776349 107 + 27905053
CUUUGCCUGUUCAAAUAAUUAGUUAUUUAU----------GAUAAGCAUUUCCGCAGAAUCCAUUAUAAUAUGGAGAAUAGAAUGACGUGUAUUAUUUUUU--GCCAACAAAUUAAUAU
.((((...((..(((((((..(((((((..----------.....((......))....(((((......))))).....)))))))....)))))))...--))...))))....... ( -15.90)
>DroSec_CAF1 10844 101 + 1
--------------AUGAUUAGUUAUUUAUGGAUACUGCUGAUAAGCAUAUCCGCAGAAUCCAUUAUAAUAUUGAGAAUAG--UGACGUGUAUUAUUAUUU--GCCAGCUAUGCAAUAU
--------------.......(((((..((((((.((((.((((....)))).)))).)))))).)))))((((...((((--(...(.(((........)--))).))))).)))).. ( -24.60)
>DroSim_CAF1 8048 101 + 1
--------------AUGAUUAGUUAUUUAUGGAUACUGCUGAUAAGCAUUUCCGCAGAAUCCAUUAUAAUAUUGAGAAUAG--UGACGUGUAUUAUUAUUU--GCCAGCUAUGCAAUAU
--------------.......(((((..((((((.((((.((........)).)))).)))))).)))))((((...((((--(...(.(((........)--))).))))).)))).. ( -23.00)
>DroEre_CAF1 8070 114 + 1
UUUU-CAUACUUAAACUGGGAGUUAUUUAUGGAUCCUGCUGAUAAGAAUUUCCGCAGAAUCCAUUUUAAUAUUGACCACGG--UGACGUGUAUUCUUUUUU--GCCAGCCUUUUAUUAU
....-..........((((.(((((...((((((.((((.((........)).)))).))))))..))))......((((.--...))))..........)--.))))........... ( -28.50)
>DroYak_CAF1 10915 118 + 1
AUUU-CAUGCUAAACCGGGGAAUUAUUUAUGGAUCAUGCUGAUAAGAAGUUCCGCAGAAUCCAUUUUAAUAUUGACCAUAGUGUGACGUGUAUUCUUUUUUGUGCCAGCCUUUUAUUUU
...(-(((((((.....((..(.((((.((((((..(((.((........)).)))..))))))...)))).)..)).)))))))).(.((((........)))))............. ( -25.20)
>consensus
_UUU_C_U__U_AAAUGAUUAGUUAUUUAUGGAUACUGCUGAUAAGCAUUUCCGCAGAAUCCAUUAUAAUAUUGAGAAUAG__UGACGUGUAUUAUUUUUU__GCCAGCCAUUUAAUAU
..................((...((((.((((((.((((.((........)).)))).))))))...))))....)).......................................... ( -9.52 = -10.36 +   0.84)

alignment

secondary structure

dotplot

Window 3

Location	23,776,349 – 23,776,456
Length	107
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	73.81
Mean single sequence MFE	-21.02
Consensus MFE	-7.80
Energy contribution	-9.60
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-2.10
Structure conservation index	0.37
SVM decision value	1.30
SVM RNA-class probability	0.939397
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23776349 107 - 27905053
AUAUUAAUUUGUUGGC--AAAAAAUAAUACACGUCAUUCUAUUCUCCAUAUUAUAAUGGAUUCUGCGGAAAUGCUUAUC----------AUAAAUAACUAAUUAUUUGAACAGGCAAAG
.......((((((...--...(((((((................(((((......)))))....(((....))).....----------...........))))))).....)))))). ( -12.80)
>DroSec_CAF1 10844 101 - 1
AUAUUGCAUAGCUGGC--AAAUAAUAAUACACGUCA--CUAUUCUCAAUAUUAUAAUGGAUUCUGCGGAUAUGCUUAUCAGCAGUAUCCAUAAAUAACUAAUCAU--------------
((((((.((((.((((--..............))))--))))...))))))....((((((.((((.((((....)))).)))).))))))..............-------------- ( -23.24)
>DroSim_CAF1 8048 101 - 1
AUAUUGCAUAGCUGGC--AAAUAAUAAUACACGUCA--CUAUUCUCAAUAUUAUAAUGGAUUCUGCGGAAAUGCUUAUCAGCAGUAUCCAUAAAUAACUAAUCAU--------------
((((((.((((.((((--..............))))--))))...))))))....((((((.((((.((........)).)))).))))))..............-------------- ( -20.04)
>DroEre_CAF1 8070 114 - 1
AUAAUAAAAGGCUGGC--AAAAAAGAAUACACGUCA--CCGUGGUCAAUAUUAAAAUGGAUUCUGCGGAAAUUCUUAUCAGCAGGAUCCAUAAAUAACUCCCAGUUUAAGUAUG-AAAA
........(((((((.--......((...((((...--.)))).)).........(((((((((((.((........)).))))))))))).........))))))).......-.... ( -30.50)
>DroYak_CAF1 10915 118 - 1
AAAAUAAAAGGCUGGCACAAAAAAGAAUACACGUCACACUAUGGUCAAUAUUAAAAUGGAUUCUGCGGAACUUCUUAUCAGCAUGAUCCAUAAAUAAUUCCCCGGUUUAGCAUG-AAAU
........(((((((................(((......)))............(((((((.(((.((........)).))).)))))))..........)))))))......-.... ( -18.50)
>consensus
AUAUUAAAUAGCUGGC__AAAAAAUAAUACACGUCA__CUAUUCUCAAUAUUAUAAUGGAUUCUGCGGAAAUGCUUAUCAGCAGGAUCCAUAAAUAACUAAUCAUUU_A__A_G_AAA_
.......................................................((((((.((((.((........)).)))).))))))............................ ( -7.80 =  -9.60 +   1.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:21:27 2006