Locus 2704

Sequence ID 3L_DroMel_CAF1
Location 7,542,429 – 7,542,537
Length 108
Max. P 0.870510
window4235 window4236

overview

Window 5

Location 7,542,429 – 7,542,537
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.78
Mean single sequence MFE -19.03
Consensus MFE -15.25
Energy contribution -15.03
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -2.56
Structure conservation index 0.80
SVM decision value 0.83
SVM RNA-class probability 0.861392
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7542429 108 + 23771897
UUCAUUCUCAUUUCCUGCAUUCAAAGCCCUGGAUGCAACUCCAAAACCAGUUUCCUUUACCAAAUUCCAAGUUUUCCCAGAUUCUGAGUCAUCAGAGCACUCGAAACU------------
...............((((((((......))))))))...........((((((.......((((.....)))).....(.((((((....)))))))....))))))------------ ( -17.70)
>DroSec_CAF1 11636 120 + 1
UUCAUACUCAUUUCCUGCAUUCAAAGCCCUGGAUGCAACUCCAAAACCAGUUUCCUUUACCAAUUUCCACGUUUCCACAGAUUCUGAGUCAUUACCCUACUCGAAACUAGAGUCUCUUUC
.....((((......((((((((......))))))))...........((((((................(..((....))..).((((.........)))))))))).))))....... ( -19.70)
>DroSim_CAF1 11545 120 + 1
UUCAUACUCAUUUCCUGCAUUCAAAGCCCUGGAUGCAACUCCAAAACCAGUUUCCUUUACCAAUUUCCACGUUUCCACAGAUUCUGAGUCAUUACCCUACUCGAAACUAGAGUCUCUUUC
.....((((......((((((((......))))))))...........((((((................(..((....))..).((((.........)))))))))).))))....... ( -19.70)
>consensus
UUCAUACUCAUUUCCUGCAUUCAAAGCCCUGGAUGCAACUCCAAAACCAGUUUCCUUUACCAAUUUCCACGUUUCCACAGAUUCUGAGUCAUUACCCUACUCGAAACUAGAGUCUCUUUC
...............((((((((......))))))))...........((((((................(..((....))..).((((.........))))))))))............ (-15.25 = -15.03 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 7,542,429 – 7,542,537
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.78
Mean single sequence MFE -29.83
Consensus MFE -25.51
Energy contribution -25.07
Covariance contribution -0.44
Combinations/Pair 1.04
Mean z-score -2.29
Structure conservation index 0.86
SVM decision value 0.87
SVM RNA-class probability 0.870510
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7542429 108 - 23771897
------------AGUUUCGAGUGCUCUGAUGACUCAGAAUCUGGGAAAACUUGGAAUUUGGUAAAGGAAACUGGUUUUGGAGUUGCAUCCAGGGCUUUGAAUGCAGGAAAUGAGAAUGAA
------------.((((((((.(((((((((.(((((...)))))..(((((.(((.(..((.......))..).))).))))).))).)))))))))))).))................ ( -27.70)
>DroSec_CAF1 11636 120 - 1
GAAAGAGACUCUAGUUUCGAGUAGGGUAAUGACUCAGAAUCUGUGGAAACGUGGAAAUUGGUAAAGGAAACUGGUUUUGGAGUUGCAUCCAGGGCUUUGAAUGCAGGAAAUGAGUAUGAA
.......((((((.(....).))))))....(((((...((..((....))..)).....(((.((....))(((((((((......))))))))).....)))......)))))..... ( -30.90)
>DroSim_CAF1 11545 120 - 1
GAAAGAGACUCUAGUUUCGAGUAGGGUAAUGACUCAGAAUCUGUGGAAACGUGGAAAUUGGUAAAGGAAACUGGUUUUGGAGUUGCAUCCAGGGCUUUGAAUGCAGGAAAUGAGUAUGAA
.......((((((.(....).))))))....(((((...((..((....))..)).....(((.((....))(((((((((......))))))))).....)))......)))))..... ( -30.90)
>consensus
GAAAGAGACUCUAGUUUCGAGUAGGGUAAUGACUCAGAAUCUGUGGAAACGUGGAAAUUGGUAAAGGAAACUGGUUUUGGAGUUGCAUCCAGGGCUUUGAAUGCAGGAAAUGAGUAUGAA
.............(((((((((.........))))....((..((....))..)).....(((.((....))(((((((((......))))))))).....)))..)))))......... (-25.51 = -25.07 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:48 2006