Locus 1121

Sequence ID 2R_DroMel_CAF1
Location 4,496,489 – 4,496,579
Length 90
Max. P 0.997718
window1977 window1978

overview

Window 7

Location 4,496,489 – 4,496,579
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 87.96
Mean single sequence MFE -24.70
Consensus MFE -18.26
Energy contribution -19.30
Covariance contribution 1.04
Combinations/Pair 1.05
Mean z-score -1.85
Structure conservation index 0.74
SVM decision value 0.40
SVM RNA-class probability 0.721699
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4496489 90 + 20766785
GAGUGAAAGCCCCCGUUGGUGGGGAUGGGAUGCGAUGGCUAAGUGAGCCAAAGUGAACCAAAGUGAGGCAGCAAAAGCCACUGACACGAU
..(((..((.(((((....))))).(((..(((..(((((.....)))))..)))..)))......(((.......))).))..)))... ( -27.80)
>DroSec_CAF1 29647 79 + 1
GAGUGAAAGCCCCCGUUGGAG-GGAUGGGUUGGGAUGGCUAAGUGAGCCAA----------AGUGAGGCAGCAGAAGCCACUGACACGAU
..(((..(((((((......)-)...))))).((.(((((..((..(((..----------.....))).))...)))))))..)))... ( -22.30)
>DroSim_CAF1 29929 80 + 1
GAGUGAAAGCCCCCGUUGGAGGGGAUGAGUUGGGAUGGCUAAGUGAGCCAA----------AGUGAGGCAGCAAAAGCCACUGACACGAU
..((....))((((......))))....((..(..(((((.....))))).----------.....(((.......))).)..))..... ( -24.30)
>DroEre_CAF1 29980 75 + 1
GAGUGAAAGCCCCCGAUAGAG-----GGGAUGGGAUGGCUAAGUGAGCCAA----------AGUGAGGCAGCAAAAGCCGCUGACACGAU
..(((..(((((((......)-----))).......((((..((..(((..----------.....))).))...)))))))..)))... ( -25.70)
>DroYak_CAF1 32945 80 + 1
GAGUGAAAGCCCCCGAUGGAGGGGAGGGGAUGGGAUGGCUAAGUGAGCCAA----------AGUGAGGCAGCAAAAGCCACUGACACGAU
..(((.....((((......))))......(.((.(((((..((..(((..----------.....))).))...))))))).))))... ( -23.40)
>consensus
GAGUGAAAGCCCCCGUUGGAGGGGAUGGGAUGGGAUGGCUAAGUGAGCCAA__________AGUGAGGCAGCAAAAGCCACUGACACGAU
.((((...(((((((((......))))))......(((((.....)))))................))).((....))))))........ (-18.26 = -19.30 +   1.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 4,496,489 – 4,496,579
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 87.96
Mean single sequence MFE -23.95
Consensus MFE -18.89
Energy contribution -19.53
Covariance contribution 0.64
Combinations/Pair 1.06
Mean z-score -3.35
Structure conservation index 0.79
SVM decision value 2.92
SVM RNA-class probability 0.997718
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4496489 90 - 20766785
AUCGUGUCAGUGGCUUUUGCUGCCUCACUUUGGUUCACUUUGGCUCACUUAGCCAUCGCAUCCCAUCCCCACCAACGGGGGCUUUCACUC
...(((..((((((.......)))......(((.......(((((.....))))).......))).((((......)))))))..))).. ( -24.44)
>DroSec_CAF1 29647 79 - 1
AUCGUGUCAGUGGCUUCUGCUGCCUCACU----------UUGGCUCACUUAGCCAUCCCAACCCAUCC-CUCCAACGGGGGCUUUCACUC
...(((..(((((((......(((.....----------..)))......))))...........(((-(......)))))))..))).. ( -21.30)
>DroSim_CAF1 29929 80 - 1
AUCGUGUCAGUGGCUUUUGCUGCCUCACU----------UUGGCUCACUUAGCCAUCCCAACUCAUCCCCUCCAACGGGGGCUUUCACUC
...(((..(((((((......(((.....----------..)))......))))............((((......)))))))..))).. ( -23.90)
>DroEre_CAF1 29980 75 - 1
AUCGUGUCAGCGGCUUUUGCUGCCUCACU----------UUGGCUCACUUAGCCAUCCCAUCCC-----CUCUAUCGGGGGCUUUCACUC
...(((..(((((((......(((.....----------..)))......)))).......(((-----(......)))))))..))).. ( -26.20)
>DroYak_CAF1 32945 80 - 1
AUCGUGUCAGUGGCUUUUGCUGCCUCACU----------UUGGCUCACUUAGCCAUCCCAUCCCCUCCCCUCCAUCGGGGGCUUUCACUC
...(((..(((((((......(((.....----------..)))......))))............((((......)))))))..))).. ( -23.90)
>consensus
AUCGUGUCAGUGGCUUUUGCUGCCUCACU__________UUGGCUCACUUAGCCAUCCCAUCCCAUCCCCUCCAACGGGGGCUUUCACUC
...(((..(((((((......(((.................)))......))))............((((......)))))))..))).. (-18.89 = -19.53 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:02 2006