Locus 6181

Sequence ID	3L_DroMel_CAF1
Location	16,368,607 – 16,368,737
Length	130
Max. P	0.991791

overview

Window 2

Location	16,368,607 – 16,368,714
Length	107
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	94.71
Mean single sequence MFE	-23.30
Consensus MFE	-19.49
Energy contribution	-19.80
Covariance contribution	0.31
Combinations/Pair	1.05
Mean z-score	-1.88
Structure conservation index	0.84
SVM decision value	0.37
SVM RNA-class probability	0.706713
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16368607 107 - 23771897
GCGGGGAGGUCACUACCCCCCUCGCGUUCUCCUACUCCAACACUUUCUCCCUUUACAUCCAGUUGGCCUUCCGUUUAUUCACGGAUUCCUCGGUGUUUAUUGUUUUC
((((((.(((....))).))).))).............((((((.....((...((.....)).))...(((((......)))))......)))))).......... ( -23.30)
>DroSec_CAF1 8727 101 - 1
GCGGGGAGGUCACU---CCCCUCGCGUUCUCCUACUCCAACACUUUCUCCCUU---AUCCAGUCGGCCUUCCGUUUAUUCACGGAUUCCUCGGAGUUUAUUGUUUUC
((((((((....))---))))..))........(((((...(((.........---....))).((...(((((......)))))..))..)))))........... ( -25.72)
>DroSim_CAF1 8857 101 - 1
GCGGGGAGGUCACU---CCCCUCGCGUUCUCCUACUCCAACACUUUCUCCCUU---AUCCAGUCGGCCUUCCGUUUAUUCACGGAUUCCUCGGUGUUUAUUGUUUUC
((((((((....))---))))..)).............((((((......((.---....))..((...(((((......)))))..))..)))))).......... ( -23.20)
>DroEre_CAF1 8619 100 - 1
GCGGGGAGGUCACU---CCCCUCGCGUUCUCCUACUCCAAUACUUUCUCC-UU---AUCCAGUCGGCCUCCCGUUUAUUCACGGAUUCCUCGGUGUUUAUUGUUUUC
((((((((....))---))))..))............(((((....(.((-..---..((....))....((((......)))).......)).)..)))))..... ( -21.00)
>consensus
GCGGGGAGGUCACU___CCCCUCGCGUUCUCCUACUCCAACACUUUCUCCCUU___AUCCAGUCGGCCUUCCGUUUAUUCACGGAUUCCUCGGUGUUUAUUGUUUUC
((((((.((........)))))))).............((((((..............((....))...(((((......)))))......)))))).......... (-19.49 = -19.80 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	16,368,640 – 16,368,737
Length	97
Sequences	4
Columns	97
Reading direction	forward
Mean pairwise identity	94.68
Mean single sequence MFE	-33.60
Consensus MFE	-27.27
Energy contribution	-26.90
Covariance contribution	-0.37
Combinations/Pair	1.08
Mean z-score	-2.04
Structure conservation index	0.81
SVM decision value	0.34
SVM RNA-class probability	0.697069
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16368640 97 + 23771897
ACGGAAGGCCAACUGGAUGUAAAGGGAGAAAGUGUUGGAGUAGGAGAACGCGAGGGGGGUAGUGACCUCCCCGCGGAGAAUUCUUCCAGUUCUUCCG
.(....).((....)).......(((((((....(((((..((((...((((.(((((((....))))))))))).....)))))))))))))))). ( -37.10)
>DroSec_CAF1 8760 91 + 1
ACGGAAGGCCGACUGGAU---AAGGGAGAAAGUGUUGGAGUAGGAGAACGCGAGGGG---AGUGACCUCCCCGCGGAGAAUUCUUCCAGUUCUUCCG
.(((((((((....))..---..(((((((.(((((..........)))))(.((((---((....)))))).)......)))))))...))))))) ( -33.20)
>DroSim_CAF1 8890 91 + 1
ACGGAAGGCCGACUGGAU---AAGGGAGAAAGUGUUGGAGUAGGAGAACGCGAGGGG---AGUGACCUCCCCGCGGAGAAUUCUUCCAGUUCUUCCG
.(((((((((....))..---..(((((((.(((((..........)))))(.((((---((....)))))).)......)))))))...))))))) ( -33.20)
>DroEre_CAF1 8652 90 + 1
ACGGGAGGCCGACUGGAU---AA-GGAGAAAGUAUUGGAGUAGGAGAACGCGAGGGG---AGUGACCUCCCCGCGGAGAAUUCUUCCAGUUCUUCCG
.(((((((.(..((....---.)-)..).....((((((..((((...(((..((((---((....))))))))).....))))))))))))))))) ( -30.90)
>consensus
ACGGAAGGCCGACUGGAU___AAGGGAGAAAGUGUUGGAGUAGGAGAACGCGAGGGG___AGUGACCUCCCCGCGGAGAAUUCUUCCAGUUCUUCCG
.((((((...(((((((........................((((...((((.((((..........)))))))).....))))))))))))))))) (-27.27 = -26.90 +  -0.37)

alignment

secondary structure

dotplot

Window 4

Location	16,368,640 – 16,368,737
Length	97
Sequences	4
Columns	97
Reading direction	reverse
Mean pairwise identity	94.68
Mean single sequence MFE	-28.67
Consensus MFE	-27.20
Energy contribution	-27.45
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.71
Structure conservation index	0.95
SVM decision value	2.29
SVM RNA-class probability	0.991791
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16368640 97 - 23771897
CGGAAGAACUGGAAGAAUUCUCCGCGGGGAGGUCACUACCCCCCUCGCGUUCUCCUACUCCAACACUUUCUCCCUUUACAUCCAGUUGGCCUUCCGU
(((((((((((((((....)).(((((((.(((....))).))).))))...............................)))))))...)))))). ( -30.30)
>DroSec_CAF1 8760 91 - 1
CGGAAGAACUGGAAGAAUUCUCCGCGGGGAGGUCACU---CCCCUCGCGUUCUCCUACUCCAACACUUUCUCCCUU---AUCCAGUCGGCCUUCCGU
((((((.((((((((....)).(((((((((....))---))))..)))...........................---.))))))....)))))). ( -29.40)
>DroSim_CAF1 8890 91 - 1
CGGAAGAACUGGAAGAAUUCUCCGCGGGGAGGUCACU---CCCCUCGCGUUCUCCUACUCCAACACUUUCUCCCUU---AUCCAGUCGGCCUUCCGU
((((((.((((((((....)).(((((((((....))---))))..)))...........................---.))))))....)))))). ( -29.40)
>DroEre_CAF1 8652 90 - 1
CGGAAGAACUGGAAGAAUUCUCCGCGGGGAGGUCACU---CCCCUCGCGUUCUCCUACUCCAAUACUUUCUCC-UU---AUCCAGUCGGCCUCCCGU
.((..((.((((((((((....((.((((((....))---)))).)).)))))....................-..---.)))))))..))...... ( -25.60)
>consensus
CGGAAGAACUGGAAGAAUUCUCCGCGGGGAGGUCACU___CCCCUCGCGUUCUCCUACUCCAACACUUUCUCCCUU___AUCCAGUCGGCCUUCCGU
((((((.((((((((....)).(((((((.((........)))))))))...............................))))))....)))))). (-27.20 = -27.45 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:07 2006