Locus 1232

Sequence ID	2R_DroMel_CAF1
Location	4,848,659 – 4,848,789
Length	130
Max. P	0.965181

overview

Window 2

Location	4,848,659 – 4,848,763
Length	104
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	79.34
Mean single sequence MFE	-23.98
Consensus MFE	-15.21
Energy contribution	-14.78
Covariance contribution	-0.44
Combinations/Pair	1.11
Mean z-score	-2.36
Structure conservation index	0.63
SVM decision value	1.58
SVM RNA-class probability	0.965181
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4848659 104 - 20766785
CCCACUUGGGUAGCCACUUUCGCCACACUUGAUCCUUUUGUUUAUGCAAAUCAAAAACUGUUGCCCAUGGCCCACAUUUCUGUG-----GUAUCCUUUUCCUACCUCAG
....((.(((((((((.....((.(((.((......(((((....))))).....)).))).))...))))(((((....))))-----)...........))))).)) ( -21.40)
>DroGri_CAF1 20024 81 - 1
CCCACUUGGGUGGCCACUUUCGGUACACUUGAACC-UUUGUUUAUGCAAAUCAA-AACGGUUGCCCAUGGCCCACUUUG----------UC---GC-------------
.(((..((((..(((......(((.(....).)))-(((((....)))))....-...)))..))))))).........----------..---..------------- ( -22.00)
>DroEre_CAF1 5280 109 - 1
CCCACUUGGGCAGCUACUUUCGCCACACUUGAUCCCUUUGUUUAUGCAAAUCAAAAACUGUUGCCCAUGGCCCACAUUUCAGUGGGUAGGAAUCCUUUUCCUACCUCAG
.(((..((((((((.....(((.......)))....(((((....))))).........)))))))))))..(((......)))((((((((.....)))))))).... ( -30.60)
>DroYak_CAF1 9516 104 - 1
CCCACUUGGGCAGCCACUUUCGCCACACUUGAUCCUUUUGUUUAUGCAAAUCAAAAACUGUUGCCCAUGGCCCACAUUUCUGUG-----GAAUCAUUUUCCUACCUCAG
.(((..((((((((.....(((.......)))....(((((....))))).........))))))))))).(((((....))))-----)................... ( -21.90)
>consensus
CCCACUUGGGCAGCCACUUUCGCCACACUUGAUCCUUUUGUUUAUGCAAAUCAAAAACUGUUGCCCAUGGCCCACAUUUCUGUG_____GAAUCCUUUUCCUACCUCAG
.(((..((((((((.....(((.......)))....(((((....))))).........)))))))))))....................................... (-15.21 = -14.78 +  -0.44)

alignment

secondary structure

dotplot

Window 3

Location	4,848,691 – 4,848,789
Length	98
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	79.87
Mean single sequence MFE	-24.35
Consensus MFE	-11.04
Energy contribution	-11.82
Covariance contribution	0.78
Combinations/Pair	1.09
Mean z-score	-2.34
Structure conservation index	0.45
SVM decision value	0.81
SVM RNA-class probability	0.856702
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4848691 98 - 20766785
--GCAGCCGCAUCAUCUUCAAUCAGCU------------GCCCACUUGGGUAGCCACUUUCGCCACACUUGAUCCUUUUGUUUAUGCAAAUCAAAAACUGUUGCCCAUGGCC
--...((((...............(((------------((((....))))))).......((.(((.((......(((((....))))).....)).))).))...)))). ( -23.40)
>DroGri_CAF1 20035 109 - 1
UUGUGGCAACAUCAUCUUCAAUCAGUU-AGCCCUAUCAUGCCCACUUGGGUGGCCACUUUCGGUACACUUGAACC-UUUGUUUAUGCAAAUCAA-AACGGUUGCCCAUGGCC
....((((((..............)))-.))).......(((....((((..(((......(((.(....).)))-(((((....)))))....-...)))..)))).))). ( -27.44)
>DroEre_CAF1 5317 98 - 1
--ACAGCCGCAUCAUCUUCAAUCAGCU------------GCCCACUUGGGCAGCUACUUUCGCCACACUUGAUCCCUUUGUUUAUGCAAAUCAAAAACUGUUGCCCAUGGCC
--...((((..............((((------------((((....))))))))......((.(((.(((((....((((....)))))))))....))).))...)))). ( -26.80)
>DroYak_CAF1 9548 98 - 1
--ACAGCCGCAUCAUCUUCAAUCAGCU------------GCCCACUUGGGCAGCCACUUUCGCCACACUUGAUCCUUUUGUUUAUGCAAAUCAAAAACUGUUGCCCAUGGCC
--...((((...............(((------------((((....))))))).......((.(((.((......(((((....))))).....)).))).))...)))). ( -25.40)
>DroMoj_CAF1 27328 100 - 1
CUGUGGCAACAUCAUCUUCAAUCAGUUUGGCCCUAUACU----------GUGCCCACUUUCGCUACACUUGAACC-UUUGUUUAUGCAAAUCAA-AACUGUUGCCCAUGGCC
(((((((((((............(((..(((.(......----------).))).)))..........((((...-(((((....)))))))))-...))))).)))))).. ( -18.70)
>consensus
__GCAGCCGCAUCAUCUUCAAUCAGCU____________GCCCACUUGGGUAGCCACUUUCGCCACACUUGAUCC_UUUGUUUAUGCAAAUCAAAAACUGUUGCCCAUGGCC
.......................................((((....)))).((((.....((.(((.((((....(((((....)))))))))....))).))...)))). (-11.04 = -11.82 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:39 2006