Locus 5220

Sequence ID	2R_DroMel_CAF1
Location	16,982,472 – 16,982,599
Length	127
Max. P	0.895124

overview

Window 7

Location	16,982,472 – 16,982,567
Length	95
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	81.43
Mean single sequence MFE	-19.21
Consensus MFE	-8.64
Energy contribution	-9.28
Covariance contribution	0.64
Combinations/Pair	1.06
Mean z-score	-2.69
Structure conservation index	0.45
SVM decision value	0.99
SVM RNA-class probability	0.895124
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16982472 95 - 20766785
UGUACAUACAUAUGUAUGU----------------GCGUACGGUGGAAUCUGCUUCUUGCCAUCUACUCCCACUCUUAGCUCAACUCUUCCUCUGUGUCUUCUUCUCCGCC
.((((((((....))))))----------------))....((((((....((.....))..........(((.....................)))........)))))) ( -19.80)
>DroSec_CAF1 79022 95 - 1
UGUACAUACAUAUGUAUGU----------------GCGUGCGGUGGAAUCUGCUUCUUGCCAUCUACUCCCACUCUUAGCUCAACUCUUCCUCUGUAACUUCCUCUCCACC
.((((((((....))))))----------------)).(((((.((((...(((.......................))).......)))).))))).............. ( -19.10)
>DroSim_CAF1 84866 95 - 1
UGUACAUACAUAUGUAUGU----------------GCGUGCGGUGGAAUCUGCUUCUUGCCAUCUACUCCCACUCUUAGCUCAACUCUUCCUCUGUAUCUUCCUCUCCACC
.((((((((....))))))----------------))((((((.((((...(((.......................))).......)))).))))))............. ( -19.90)
>DroEre_CAF1 80584 100 - 1
UGAACAUACAUACAUAUGUACAUGCAUAUGC-----------GUGUAUUCUGCUUCUUGCCAUCUACUCCCACUCUUAGCUCAACUCUUCCUCUGUGUCUUCUCCUCCACC
.(((.(((((.......((((((((....))-----------))))))...((.....)).................................))))).)))......... ( -14.90)
>DroYak_CAF1 87443 108 - 1
UGUACAUACAUACAUAUGUACAUAUGGAUGUAUGUUUGUACGGUGGAUUCUGC---UUGCCAUCUACUCCCACUCUUAGCUCAACUCUUCCUCUGUGUCUUCUCCUCCACC
.(((((.((((((((.(((....))).)))))))).)))))((((((....((---(....................)))...((.(.......).)).......)))))) ( -22.35)
>consensus
UGUACAUACAUAUGUAUGU________________GCGUACGGUGGAAUCUGCUUCUUGCCAUCUACUCCCACUCUUAGCUCAACUCUUCCUCUGUGUCUUCUUCUCCACC
...((((((....))))))......................((((((....((.....)).......................((.........)).........)))))) ( -8.64 =  -9.28 +   0.64)

alignment

secondary structure

dotplot

Window 8

Location	16,982,509 – 16,982,599
Length	90
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	81.90
Mean single sequence MFE	-22.31
Consensus MFE	-16.38
Energy contribution	-16.22
Covariance contribution	-0.16
Combinations/Pair	1.14
Mean z-score	-1.53
Structure conservation index	0.73
SVM decision value	0.04
SVM RNA-class probability	0.555770
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16982509 90 + 20766785
AGUGGGAGUAGAUGGCAAGAAGCAGAUUCCACCGUACGC----------------ACAUACAUAUGUAUGUACACGUUGUUCGUCAGUAAACCGCAAAACGAGACA
.((((.....(((((((((((.....)))....(((((.----------------((((....)))).)))))...))).)))))......))))........... ( -18.90)
>DroSec_CAF1 79059 90 + 1
AGUGGGAGUAGAUGGCAAGAAGCAGAUUCCACCGCACGC----------------ACAUACAUAUGUAUGUACAAGUUGUCCGUCAGUAAACCGCAAAACGAAACA
.((((.....((((((((...((.(......).))..(.----------------((((((....)))))).)...))).)))))......))))........... ( -20.70)
>DroSim_CAF1 84903 90 + 1
AGUGGGAGUAGAUGGCAAGAAGCAGAUUCCACCGCACGC----------------ACAUACAUAUGUAUGUACAAGUUGUCCGUCAGUAAACCGCAAAACGAAACA
.((((.....((((((((...((.(......).))..(.----------------((((((....)))))).)...))).)))))......))))........... ( -20.70)
>DroEre_CAF1 80621 95 + 1
AGUGGGAGUAGAUGGCAAGAAGCAGAAUACAC-----------GCAUAUGCAUGUACAUAUGUAUGUAUGUUCAAGUUGUCCGUCAGUAAACCGCAAAACGAAACA
.((((.....((((((((........(((((.-----------.((((((......))))))..))))).......))).)))))......))))........... ( -25.86)
>DroYak_CAF1 87480 103 + 1
AGUGGGAGUAGAUGGCAA---GCAGAAUCCACCGUACAAACAUACAUCCAUAUGUACAUAUGUAUGUAUGUACAAGUUGUCCGUCAGUAAACCGCAAAACGAAACA
.((((.....((((((((---...(....)...(((((.((((((((............)))))))).)))))...))).)))))......))))........... ( -25.40)
>consensus
AGUGGGAGUAGAUGGCAAGAAGCAGAUUCCACCGCACGC________________ACAUACAUAUGUAUGUACAAGUUGUCCGUCAGUAAACCGCAAAACGAAACA
.((((.....((((((((...((.(......).))....................((((((....)))))).....))).)))))......))))........... (-16.38 = -16.22 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:25 2006