Locus 8128

Sequence ID X_DroMel_CAF1
Location 20,212,927 – 20,213,159
Length 232
Max. P 0.869032
window13357 window13358

overview

Window 7

Location 20,212,927 – 20,213,047
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 81.38
Mean single sequence MFE -21.23
Consensus MFE -18.22
Energy contribution -18.33
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -1.19
Structure conservation index 0.86
SVM decision value 0.21
SVM RNA-class probability 0.634346
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20212927 120 - 22224390
CCAGAACUUACCCGUCCUCGCCCACCUCACUAAUGAUGCGACCCUCGCCGGGUGGAUUGCCAUCCUGGUCACCCCAUUUCCAGUCCGCUCCCCGCACAAUUCUGGUGCCGAUCUUCAUAA
((((((...........((((.....(((....))).)))).....((.((((((((((......(((.....)))....))))))))))...))....))))))............... ( -26.30)
>DroSim_CAF1 1 93 - 1
CCACAACUUACCCGUCCUCGCCCACCUCACUAAUGAUGCGACCCUCGCCGGGCGGAUUGCCAUCCUGGUCACCCCACUUCCAGUCCGCUCCCC---------------------------
...................((((...(((....))).(((.....))).))))((((((......(((.....)))....)))))).......--------------------------- ( -20.10)
>DroYak_CAF1 1 93 - 1
CCACAACUUACCCGUCCUCGCCCACCUCACUAAUGAUGCGACCCUCGCCCGGCGGAUUGCCAUCCUGGUCACCCCACUUCCAGUCCGCUCCCC---------------------------
.....................................(((.....)))..(((((((((......(((.....)))....)))))))))....--------------------------- ( -17.30)
>consensus
CCACAACUUACCCGUCCUCGCCCACCUCACUAAUGAUGCGACCCUCGCCGGGCGGAUUGCCAUCCUGGUCACCCCACUUCCAGUCCGCUCCCC___________________________
.....................................(((.....))).((((((((((......(((.....)))....)))))))))).............................. (-18.22 = -18.33 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 20,213,047 – 20,213,159
Length 112
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 75.85
Mean single sequence MFE -37.49
Consensus MFE -27.35
Energy contribution -27.48
Covariance contribution 0.12
Combinations/Pair 1.27
Mean z-score -1.69
Structure conservation index 0.73
SVM decision value 0.86
SVM RNA-class probability 0.869032
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20213047 112 + 22224390
CGCUGAUUCUAUUUCCAGAUAUCACAACUAACUGAUCUUCUUUU-CCAGGUGGGUGCGUGUGGAAUGGUACACCGGAGCCACCAACUCGUAUCGCAUGGGCAAGGAGGGUCAG
.(.(((((((......))).)))))......((((((((((((.-((..(((((((((.((((..(((....)))...)))).....)))))).))).)).)))))))))))) ( -38.10)
>DroVir_CAF1 1 95 + 1
---------------CUAAUAACGCUACU--CUCAUCCUGC-CAAUUAGCUGGGUGCGCGUCGAGUGGUAUACGGGCGCCACCAAUUCGUAUCGCAUGGGCAAGGAGGGCCAA
---------------........(((.((--((..((((((-..........((((.(((((..(((...))).)))))))))..........))).)))...)))))))... ( -26.75)
>DroSim_CAF1 94 112 + 1
CGAAGAUUCUAUUUCCUGAUAUCACAACUAAAUGACCUUCUUGU-CCAGGUGGGUGCGUGUGGAAUGGUACACCGGAGCCACCAACUCGUACCGUAUGGGCAAGGAGGGUCAG
...............(((((.(((........)))(((((((((-(((....((((((.((((..(((....)))...)))).....))))))...))))))))))))))))) ( -41.70)
>DroYak_CAF1 94 112 + 1
CACUGAUUUUAUUUAGUGAUAUCGCAACUAAUUGACCUUCUUGA-CCAGGUGGGUGCGCGUGGAGUGGUACACCGGAGCCACCAACUCGUAUCGCAUGGGUAAGGAGGGUCAG
((((((......))))))..............((((((((((.(-((..(((((((((.((.(.(((((........)))))).)).)))))).))).))).)))))))))). ( -43.40)
>consensus
CGCUGAUUCUAUUUCCUGAUAUCACAACUAACUGACCUUCUUGA_CCAGGUGGGUGCGCGUGGAAUGGUACACCGGAGCCACCAACUCGUAUCGCAUGGGCAAGGAGGGUCAG
................................((((((((((...(((....((((((.((...(((((........)))))..)).))))))...)))...)))))))))). (-27.35 = -27.48 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:56:23 2006