Locus 5370

Sequence ID	3R_DroMel_CAF1
Location	14,104,829 – 14,104,968
Length	139
Max. P	0.819374

overview

Window 1

Location	14,104,829 – 14,104,931
Length	102
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	89.19
Mean single sequence MFE	-45.00
Consensus MFE	-40.74
Energy contribution	-41.10
Covariance contribution	0.36
Combinations/Pair	1.15
Mean z-score	-1.52
Structure conservation index	0.91
SVM decision value	0.68
SVM RNA-class probability	0.819374
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14104829 102 - 27905053
CAUCCUCCGGCUCCAUACAGCUGCCCACUGUGCGCAAGUGCG---GCGGUGGCAGAUCUGCGGGAGCAGCCCACACAAUGGCCAUGAAUUUGGCGGCCUACGGGC
.....(((((((((...((((((((.(((((.(((....)))---))))))))))..)))..))))).(((((.....))((((......)))))))...)))). ( -43.30)
>DroSec_CAF1 3992 102 - 1
CAUCCUCCGGCUCCAUCCAGCUGCCCACCGUGCGCAAAUGCG---GCGGUGGCAGCUCUGCGGGAGCAGCCCACACCAUGGCCAUGAAUUUGGCGGCCUACGGGC
.....(((((((((....(((((((.(((((.(((....)))---)))))))))))).....))))).(((((.....))((((......)))))))...)))). ( -48.30)
>DroSim_CAF1 4148 102 - 1
CAUCCUCCGGCUCCAUCCAGCUGCCCACCGUGCGCAAAUGCG---GCGGUGGCAGCUCUGCGGGAGCAGCCCACACCAUGGCCAUGAAUUUGGCGGCCUACGGGC
.....(((((((((....(((((((.(((((.(((....)))---)))))))))))).....))))).(((((.....))((((......)))))))...)))). ( -48.30)
>DroEre_CAF1 4422 102 - 1
CAUCCUCCGGCUCCAUGCAGCUGCCCACCGUGCGCAAGUGCG---GCGGUGGCGGCUCCGCGGGAGCAGCCCACACCAUGGCCAUGAAUUUGGCGGCCUACGGGC
.....(((((((((.((((((((((.(((((.(((....)))---))))))))))))..)))))))).(((((.....))((((......)))))))...)))). ( -49.90)
>DroYak_CAF1 7735 102 - 1
CAUCCUCCGGCUCCAUGCAGCUGCCCACCGUGCGCAAGUGCG---GCGGUGGCGGCACCACGGGAGCAGCCCACACUAUGGCCAUGAAUUUGGCGGCCUACGGAC
.....(((((((((.(((.((..((..(((..(....)..))---).))..)).))).....))))).(((((.....))((((......)))))))...)))). ( -47.50)
>DroAna_CAF1 3812 102 - 1
CACAUUCCGGCUCCAUGCAGCUCCCCACCGUUCGCAAGUGUGCCAGCGUUGGCGGC---GGUGGAUCAGCUCACACCAUGGCCAUGAAUCUAGCGGCAUACGGGC
.........((.((.((((((........))).))).(((((((.((..((((.(.---((((((.....)).)))).).))))........))))))))))))) ( -32.70)
>consensus
CAUCCUCCGGCUCCAUGCAGCUGCCCACCGUGCGCAAGUGCG___GCGGUGGCAGCUCUGCGGGAGCAGCCCACACCAUGGCCAUGAAUUUGGCGGCCUACGGGC
.....(((((((((....(((((((.(((((.(((....)))...)))))))))))).....))))).(((((.....))((((......)))))))...)))). (-40.74 = -41.10 +   0.36)

alignment

secondary structure

dotplot

Window 2

Location	14,104,868 – 14,104,968
Length	100
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	87.45
Mean single sequence MFE	-42.28
Consensus MFE	-34.91
Energy contribution	-35.88
Covariance contribution	0.97
Combinations/Pair	1.10
Mean z-score	-1.96
Structure conservation index	0.83
SVM decision value	0.32
SVM RNA-class probability	0.688020
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14104868 100 - 27905053
UCCACCAUAGCCAGUAUUAUGGUGGUACUAA---GCUCUGCAUCCUCCGGCUCCAUACAGCUGCCCACUGUGCGCAAGUGCG---GCGGUGGCAGAUCUGCGGGAG
.(((((((((......)))))))))..((.(---(.(((((......(((((......)))))(((.(((..(....)..))---).)).)))))).))..))... ( -38.40)
>DroSec_CAF1 4031 100 - 1
UCCACCAUAGCCAGUAUUAUGGUGGUACUAA---GCUCUGCAUCCUCCGGCUCCAUCCAGCUGCCCACCGUGCGCAAAUGCG---GCGGUGGCAGCUCUGCGGGAG
.(((((((((......)))))))))......---..........((((.((.......(((((((.(((((.(((....)))---))))))))))))..)).)))) ( -44.20)
>DroSim_CAF1 4187 100 - 1
UCCACCAUAGCCAGUAUUAUGGUGGUACUAA---GCUCUGCAUCCUCCGGCUCCAUCCAGCUGCCCACCGUGCGCAAAUGCG---GCGGUGGCAGCUCUGCGGGAG
.(((((((((......)))))))))......---..........((((.((.......(((((((.(((((.(((....)))---))))))))))))..)).)))) ( -44.20)
>DroEre_CAF1 4461 100 - 1
UCCACCAUAGCCAGCAUUAUGGUGGUUCUCA---GCUCUGCAUCCUCCGGCUCCAUGCAGCUGCCCACCGUGCGCAAGUGCG---GCGGUGGCGGCUCCGCGGGAG
.(((((((((......)))))))))......---..........((((.((.....((.((..((..(((..(....)..))---).))..)).))...)).)))) ( -43.80)
>DroYak_CAF1 7774 100 - 1
UCCACCAUAGCCAGCAUUAUGGUGGUGCUCA---GCUCUGCAUCCUCCGGCUCCAUGCAGCUGCCCACCGUGCGCAAGUGCG---GCGGUGGCGGCACCACGGGAG
.(((((((((......)))))))))(((...---.....)))..((((.((.....)).((((((.(((((.(((....)))---)))))))))))......)))) ( -44.20)
>DroAna_CAF1 3851 103 - 1
ACCACCAUAGCCAGCAUUAUGGUCGUGCUCAGUGGCUCAGCACAUUCCGGCUCCAUGCAGCUCCCCACCGUUCGCAAGUGUGCCAGCGUUGGCGGC---GGUGGAU
.(((((...((((((.....((..(((((.((...)).)))))...))(((.((.((((((........))).))).).).)))...))))))...---))))).. ( -38.90)
>consensus
UCCACCAUAGCCAGCAUUAUGGUGGUACUAA___GCUCUGCAUCCUCCGGCUCCAUGCAGCUGCCCACCGUGCGCAAGUGCG___GCGGUGGCAGCUCUGCGGGAG
.(((((((((......)))))))))...................((((.((.......(((((((.(((((.(((....)))...))))))))))))..)).)))) (-34.91 = -35.88 +   0.97)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:07 2006