Locus 2612

Sequence ID 3R_DroMel_CAF1
Location 7,059,725 – 7,059,885
Length 160
Max. P 0.758558
window4253 window4254

overview

Window 3

Location 7,059,725 – 7,059,845
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.50
Mean single sequence MFE -39.05
Consensus MFE -26.22
Energy contribution -24.50
Covariance contribution -1.72
Combinations/Pair 1.50
Mean z-score -1.72
Structure conservation index 0.67
SVM decision value 0.50
SVM RNA-class probability 0.758558
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7059725 120 + 27905053
AGUUGAGCGCAUUAAGCAGCAGCUCGCCGUUCUUGGUGAGAUUGCGCUGCGUCUCCGAAUUGCACGUGAACUCUUUCUGCAGCUCGGGGUUCUUCUGGGCCAGAUCGGCGAAGGAGUCGG
......(((((....((.(((((((((((....))))))).)))))))))))((((((.(((((...(((....)))))))).))))))..(((((..(((.....)))..))))).... ( -44.30)
>DroVir_CAF1 3401 120 + 1
AGUUUAACGCAUUCAAGAGUAAUUCGCCAUUUUUGGUCAAGUUUCGUUGCGUCUCCGAAUUGCAGAUGAACUCCUUCUGCAGUUCGGGAUUUUUUUGUGCCAAAUCGGCGAAGGCGUCUG
......(((((((....)))..((((((...(((((((((((......))(((.((((((((((((.(.....).)))))))))))))))....))).))))))..)))))).))))... ( -41.00)
>DroGri_CAF1 3094 120 + 1
AGUUCAGUGCGUUCAAGAGCAGUUCGCCGUUCUUGGUCAAGUUGCGUUGCGUCUCCGAAUUGCAGAUGAAUUCCUUCUGCAGUUCGGGAUUCUUUUGCGCCAGAUCAGCAAAGGCAUCUG
....(((((((..(((((((.(....).)))))))..).....((((.(.(((.((((((((((((.(.....).))))))))))))))).)....)))).............))).))) ( -41.20)
>DroWil_CAF1 2612 120 + 1
AGUUAAGUGCAUUUAGCAACAAUUCACCAUUCUUGGUUAAAUUUCGUUGUGUCUCCGAAUUGCAGGUGAAUUCUUUUUGGAGUUCAGGGUUCUUUUGAGCUAAAUCCGCAAAUGAAUCAG
......(((.(((((((.........(((....)))(((((...(.(((...(((((((....(((.....))).)))))))..))).)....)))))))))))).)))........... ( -25.60)
>DroMoj_CAF1 2920 120 + 1
AGUUUAAUGCAUUUAACAGCAGUUCACCAUUUUUGGUCAAAUUUCGUUGCGUUUCCGAGUUGCAGAUGAACUCCUUCUGCAGCUCGGGAUUCUUCUGCGCCAGAUCAGCGAACGCAUCGG
.......(((........)))....((((....)))).......((.(((((((((((((((((((.(.....).))))))))))))))........(((.......))).))))).)). ( -38.70)
>DroAna_CAF1 3077 120 + 1
AAUUAAGCGCAUUGAGGAGCAGCUCGCCGUUCUUGGUCAGGUUUCGCUGCGUCUCCGAGUUGCAGGUGAACUCCUUUUGCAGCUCUGGAUUCUUUUGUGCCAGAUCCGCAAAAGAAUCUG
.....((((((..((((((....(((((((.(((((..(.((......)).)..)))))..)).))))).)))))).))).)))..(((((((((((((.......))))))))))))). ( -43.50)
>consensus
AGUUAAGCGCAUUCAACAGCAGUUCGCCAUUCUUGGUCAAAUUUCGUUGCGUCUCCGAAUUGCAGAUGAACUCCUUCUGCAGCUCGGGAUUCUUUUGCGCCAGAUCAGCAAAGGAAUCUG
..................((((((.((((....)))).))......))))....((((((((((((.........))))))))))))(((.(((((((.........))))))).))).. (-26.22 = -24.50 +  -1.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 7,059,765 – 7,059,885
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.56
Mean single sequence MFE -44.18
Consensus MFE -24.88
Energy contribution -25.22
Covariance contribution 0.34
Combinations/Pair 1.37
Mean z-score -1.91
Structure conservation index 0.56
SVM decision value 0.09
SVM RNA-class probability 0.579313
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7059765 120 + 27905053
AUUGCGCUGCGUCUCCGAAUUGCACGUGAACUCUUUCUGCAGCUCGGGGUUCUUCUGGGCCAGAUCGGCGAAGGAGUCGGCCAGGGCGUGCUGUGUGACGACCACGUGCUGGAAGUGCGA
.(((((((.....((((....(((((((..(((...(.(((((((..(((.(((((..(((.....)))..)))))...))).)))).))).)...)).)..)))))))))))))))))) ( -45.20)
>DroVir_CAF1 3441 120 + 1
GUUUCGUUGCGUCUCCGAAUUGCAGAUGAACUCCUUCUGCAGUUCGGGAUUUUUUUGUGCCAAAUCGGCGAAGGCGUCUGCCAGUGAUUGCUGCGACACCACAACGUGUUGGAAAUGUGA
(((((((.((((((((((((((((((.(.....).))))))))))))..........((((.....)))).))))))..))((((....))))((((((......))))))))))).... ( -42.10)
>DroGri_CAF1 3134 120 + 1
GUUGCGUUGCGUCUCCGAAUUGCAGAUGAAUUCCUUCUGCAGUUCGGGAUUCUUUUGCGCCAGAUCAGCAAAGGCAUCUGCUAGCGCCUGCUGCGACACAACAACAUGCUGGAAAUGUGA
((((.((((((((.((((((((((((.(.....).)))))))))))))))......(((((((((..((....)))))))...)))).....))))).)))).((((.......)))).. ( -45.60)
>DroWil_CAF1 2652 120 + 1
AUUUCGUUGUGUCUCCGAAUUGCAGGUGAAUUCUUUUUGGAGUUCAGGGUUCUUUUGAGCUAAAUCCGCAAAUGAAUCAGCCAGAGCAUGCUGAGUAACAACCACAUGCUGGAAAUGUGA
.....(((((..(((.(...(((.(((..(((((((.((((......(((((....)))))...)))).))).))))..)))...)))..).)))..)))))(((((.......))))). ( -32.00)
>DroMoj_CAF1 2960 120 + 1
AUUUCGUUGCGUUUCCGAGUUGCAGAUGAACUCCUUCUGCAGCUCGGGAUUCUUCUGCGCCAGAUCAGCGAACGCAUCGGCCAGCGAUUGCUGCGAGGCGACAACGUGUUGAAAGUGUGA
.(((((..((((((((((((((((((.(.....).))))))))))))))......((((((....((((((.(((........))).))))))...)))).))))))..)))))...... ( -49.40)
>DroAna_CAF1 3117 120 + 1
GUUUCGCUGCGUCUCCGAGUUGCAGGUGAACUCCUUUUGCAGCUCUGGAUUCUUUUGUGCCAGAUCCGCAAAAGAAUCUGCCAGCGCGUGCUGGGUGACGACCACGUGUUGAAAGUGGGA
.(..((((((......((((((((((.(.....).)))))))))).(((((((((((((.......)))))))))))))))(((((((((.(.(....).).)))))))))..))))..) ( -50.80)
>consensus
AUUUCGUUGCGUCUCCGAAUUGCAGAUGAACUCCUUCUGCAGCUCGGGAUUCUUUUGCGCCAGAUCAGCAAAGGAAUCUGCCAGCGCGUGCUGCGAGACGACAACGUGCUGGAAAUGUGA
.(((((..((((..((((((((((((.........))))))))))))(((.(((((((.........))))))).)))...((((....))))..........))))..)))))...... (-24.88 = -25.22 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:32 2006