Locus 34

Sequence ID	2L_DroMel_CAF1
Location	148,313 – 148,445
Length	132
Max. P	0.778121

overview

Window 0

Location	148,313 – 148,405
Length	92
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	66.56
Mean single sequence MFE	-25.52
Consensus MFE	-17.72
Energy contribution	-17.28
Covariance contribution	-0.44
Combinations/Pair	1.45
Mean z-score	-1.02
Structure conservation index	0.69
SVM decision value	0.55
SVM RNA-class probability	0.778121
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 148313 92 - 22407834
GCUGCAAGCAGCCAGC---GCAAUGUACUUGGGGGAGCGGAAGCAAAAAACAAGAAUGAUCCAUUCCCCAGGUACGAAACAAGGUUUACU------UAGAG--------------
((((....))))....---....(((((((((((((((....))......((....)).....)))))))))))))....(((.....))------)....-------------- ( -30.00)
>DroSec_CAF1 30757 92 - 1
GCUGCAAGCAGCCAGC---GCAAUGUACUUGGGGGAGCAGAAGCAAAAAACAAGAAUGAUCCAUUCCCUAGGUACGAAACAAGGUUUACC------UAAAG--------------
((((....))))....---....(((((((((((((((....))......((....)).....))))))))))))).....(((....))------)....-------------- ( -25.90)
>DroSim_CAF1 32399 92 - 1
GCUGCAAGCAGCCAGC---GCAAUGUUCUUGGGGGAGCAGAAGCAAAAAACAAGAAUGAUCCAUUCCCUAGGUACGAAACAAGGUUUACC------UAAAG--------------
((((....))))....---....(((.(((((((((((....))......((....)).....))))))))).))).....(((....))------)....-------------- ( -21.30)
>DroEre_CAF1 42371 112 - 1
GCGGCAACCAGCCAGC---GCGAUGUACUUGGGGGCGCGGAGGCUAAACGCAAGAAUGAUCCAUUCCCUAGGUACGAAUAUAGGUUUACCAUUUCCCAAAGGUUCCCAUUUUAAG
(((((.....))).))---....((((((((((((...(((..(....(....)...).)))..))))))))))))......((...(((..........)))..))........ ( -30.40)
>DroYak_CAF1 30954 91 - 1
GCUGCCAGCAGUCAGC---GCGAUGUACUUGGGGGCGCGGAAGCCAAGCACAAGAAUGAUCCAUUCCCUAGGUACGAA---AGGU------------------UCCCACUUUAAG
((((.(....).))))---....(((((((((((((......)))........(((((...)))))))))))))))((---((..------------------.....))))... ( -26.60)
>DroAna_CAF1 31014 78 - 1
GCCGCGAGUCGUCAACAGGGAAACUUUCAGGAGGGCGCAGAUGUCAAAGACUUCAAGGACACGUUUCGUAGGUGGG--------UU-----------------------------
((((((((((.((...(((....)))....)).))).....((((...(....)...))))....)))).)))...--------..----------------------------- ( -18.90)
>consensus
GCUGCAAGCAGCCAGC___GCAAUGUACUUGGGGGAGCAGAAGCAAAAAACAAGAAUGAUCCAUUCCCUAGGUACGAAACAAGGUUUACC______UAAAG______________
((((....))))...........((((((((((((.((....))......((....))......))))))))))))....................................... (-17.72 = -17.28 +  -0.44)

alignment

secondary structure

dotplot

Window 1

Location	148,333 – 148,445
Length	112
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	83.72
Mean single sequence MFE	-38.78
Consensus MFE	-29.95
Energy contribution	-30.15
Covariance contribution	0.20
Combinations/Pair	1.27
Mean z-score	-1.74
Structure conservation index	0.77
SVM decision value	0.18
SVM RNA-class probability	0.623445
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 148333 112 - 22407834
CUCUGCCUCUCCCAAUACAAUUAAGAGGCGACGCAUGCGGGCUGCAAGCAGCCAGC---GCAAUGUACUUGGGGGAGCGGAAGCAAAAAACAAGAAUGAUCCAUUCCCCAGGUAC
...(((((((.............))))))).....(((((((((....)))))..)---)))..((((((((((((((....))......((....)).....)))))))))))) ( -44.42)
>DroSec_CAF1 30777 112 - 1
CUCUGCCUCUCCCAAUACAAUUAAGAGGCGACGCAUGCGGGCUGCAAGCAGCCAGC---GCAAUGUACUUGGGGGAGCAGAAGCAAAAAACAAGAAUGAUCCAUUCCCUAGGUAC
.(((((.((((((((((((.....(.(....).).(((((((((....)))))..)---))).)))).)))))))))))))............(((((...)))))......... ( -38.70)
>DroSim_CAF1 32419 112 - 1
CUCUGCCUCUCCCAAUACAAUUAAGAGGCGACGCAUGCGGGCUGCAAGCAGCCAGC---GCAAUGUUCUUGGGGGAGCAGAAGCAAAAAACAAGAAUGAUCCAUUCCCUAGGUAC
.(((((.((((((((.(((.....(.(....).).(((((((((....)))))..)---))).)))..)))))))))))))............(((((...)))))......... ( -36.90)
>DroEre_CAF1 42411 112 - 1
CUCUGCCUCUCCCAAUACAAUUAAGAGGCGACGCAUGCGGGCGGCAACCAGCCAGC---GCGAUGUACUUGGGGGCGCGGAGGCUAAACGCAAGAAUGAUCCAUUCCCUAGGUAC
...(((((((.............))))))).(((..((.(((........))).))---)))..(((((((((((...(((..(....(....)...).)))..))))))))))) ( -38.12)
>DroYak_CAF1 30973 112 - 1
CUCCGCCUCUCCCAACACAAUUAAGAGGCGUCGCAUGCGGGCUGCCAGCAGUCAGC---GCGAUGUACUUGGGGGCGCGGAAGCCAAGCACAAGAAUGAUCCAUUCCCUAGGUAC
....((((((.............))))))(((((..((.(((((....))))).))---)))))((((((((((((......)))........(((((...)))))))))))))) ( -42.82)
>DroAna_CAF1 31017 115 - 1
CUCAGCCUCGCCGAACACCAUCAAGAGGCGUCGCAUGCGGGCCGCGAGUCGUCAACAGGGAAACUUUCAGGAGGGCGCAGAUGUCAAAGACUUCAAGGACACGUUUCGUAGGUGG
....(((((...((......))..)))))..(((.(((((..((.(.(((.((...(((....)))....)).)))...((.(((...))).)).....).))..))))).))). ( -31.70)
>consensus
CUCUGCCUCUCCCAAUACAAUUAAGAGGCGACGCAUGCGGGCUGCAAGCAGCCAGC___GCAAUGUACUUGGGGGAGCAGAAGCAAAAAACAAGAAUGAUCCAUUCCCUAGGUAC
....((((((.............))))))...((..((.(((((....))))).))...))...(((((((((((.((....))......((....))......))))))))))) (-29.95 = -30.15 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:23:48 2006