Locus 6246

Sequence ID 3R_DroMel_CAF1
Location 16,296,764 – 16,296,922
Length 158
Max. P 0.979187
window10188 window10189 window10190 window10191

overview

Window 8

Location 16,296,764 – 16,296,882
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -35.08
Consensus MFE -34.27
Energy contribution -33.50
Covariance contribution -0.77
Combinations/Pair 1.11
Mean z-score -1.39
Structure conservation index 0.98
SVM decision value 0.02
SVM RNA-class probability 0.542296
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16296764 118 + 27905053
UCUAACAAACAUGAAUGGUUGCGUG--CUGUUCUAGGGUCAGAGUGUAAUUAACUUUGAAGCCCGCCCUCAUUUGCAGCCCAUCAAGGAGAUGAAGAGCAAAUUAGAGGUGCGGAAUAAG
.........(..(((((((.....)--))))))...).(((((((.......)))))))...((((((((((((((....((((.....))))....))))))..)))).))))...... ( -34.30)
>DroSec_CAF1 17428 120 + 1
UCCGGCAAACAUGAAUGGUUGCGUGCGCUGCUCUAGGGUCAAAGUGUAAUUAACUUUGAAGCCCGCCCUCAUUUGCAGCCCAUAAAGAAGAUGAAGAGCAAAUUAGAGGUGCGGAAUAAG
(((.((((.((....)).))))..((((..(((((((((((((((.......))))))..))))(((.((((((..............)))))).).))....))))))))))))..... ( -34.44)
>DroSim_CAF1 9587 120 + 1
UCCGGCAAACAUGAAUGGUUGCGUGCGCUGCUCUAGGGUCAAAGUGUAAUUAACUUUGAAGCCCGCCCUCAUUUGCAGCCCAUCAAGGAGAUGAAGAGCAAAUUAGAGGUGCGGAAUAAG
(((((((..((((........))))...))))...((((((((((.......))))))..))))((((((((((((....((((.....))))....))))))..)))).)))))..... ( -36.50)
>consensus
UCCGGCAAACAUGAAUGGUUGCGUGCGCUGCUCUAGGGUCAAAGUGUAAUUAACUUUGAAGCCCGCCCUCAUUUGCAGCCCAUCAAGGAGAUGAAGAGCAAAUUAGAGGUGCGGAAUAAG
(((((((..((((........))))...))))...((((((((((.......))))))..))))((((((((((((....((((.....))))....))))))..)))).)))))..... (-34.27 = -33.50 +  -0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 16,296,764 – 16,296,882
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -33.85
Consensus MFE -31.29
Energy contribution -31.73
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.22
Structure conservation index 0.92
SVM decision value 0.94
SVM RNA-class probability 0.885979
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16296764 118 - 27905053
CUUAUUCCGCACCUCUAAUUUGCUCUUCAUCUCCUUGAUGGGCUGCAAAUGAGGGCGGGCUUCAAAGUUAAUUACACUCUGACCCUAGAACAG--CACGCAACCAUUCAUGUUUGUUAGA
.....(((((.((((..((((((..((((((.....))))))..)))))))))))))))..................((((((....(((((.--..............))))))))))) ( -31.46)
>DroSec_CAF1 17428 120 - 1
CUUAUUCCGCACCUCUAAUUUGCUCUUCAUCUUCUUUAUGGGCUGCAAAUGAGGGCGGGCUUCAAAGUUAAUUACACUUUGACCCUAGAGCAGCGCACGCAACCAUUCAUGUUUGCCGGA
.....(((((.((((..((((((..(((((.......)))))..))))))))))))(((..(((((((.......)))))))))).......(.(((.(((........))).))))))) ( -32.70)
>DroSim_CAF1 9587 120 - 1
CUUAUUCCGCACCUCUAAUUUGCUCUUCAUCUCCUUGAUGGGCUGCAAAUGAGGGCGGGCUUCAAAGUUAAUUACACUUUGACCCUAGAGCAGCGCACGCAACCAUUCAUGUUUGCCGGA
.....(((((.((((..((((((..((((((.....))))))..))))))))))))(((..(((((((.......)))))))))).......(.(((.(((........))).))))))) ( -37.40)
>consensus
CUUAUUCCGCACCUCUAAUUUGCUCUUCAUCUCCUUGAUGGGCUGCAAAUGAGGGCGGGCUUCAAAGUUAAUUACACUUUGACCCUAGAGCAGCGCACGCAACCAUUCAUGUUUGCCGGA
.....(((((.((((..((((((..((((((.....))))))..)))))))))))))))..(((((((.......)))))))................((((.((....)).)))).... (-31.29 = -31.73 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 16,296,802 – 16,296,922
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -30.90
Consensus MFE -30.47
Energy contribution -30.80
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.51
Structure conservation index 0.99
SVM decision value 1.83
SVM RNA-class probability 0.979187
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16296802 120 + 27905053
AGAGUGUAAUUAACUUUGAAGCCCGCCCUCAUUUGCAGCCCAUCAAGGAGAUGAAGAGCAAAUUAGAGGUGCGGAAUAAGAAAUCCCAACGAAAGAAUGGAAAAGAAACAAAGACGCGUC
...((((......(((((....((((((((((((((....((((.....))))....))))))..)))).)))).........(((...(....)...))).......)))))))))... ( -32.10)
>DroSec_CAF1 17468 120 + 1
AAAGUGUAAUUAACUUUGAAGCCCGCCCUCAUUUGCAGCCCAUAAAGAAGAUGAAGAGCAAAUUAGAGGUGCGGAAUAAGGAAUCCCGACGAAAGAAUGGAAAAGAAACAAAGACGCGUA
...((((......(((((....((((((((((((((....(((.......)))....))))))..)))).)))).........(((...(....)...))).......)))))))))... ( -28.50)
>DroSim_CAF1 9627 120 + 1
AAAGUGUAAUUAACUUUGAAGCCCGCCCUCAUUUGCAGCCCAUCAAGGAGAUGAAGAGCAAAUUAGAGGUGCGGAAUAAGGAAUCCCGCCGAAAGAAUGGAAAAGAAACAAAGACGCGUC
...((((......(((((....((((((((((((((....((((.....))))....))))))..)))).)))).........(((...(....)...))).......)))))))))... ( -32.10)
>consensus
AAAGUGUAAUUAACUUUGAAGCCCGCCCUCAUUUGCAGCCCAUCAAGGAGAUGAAGAGCAAAUUAGAGGUGCGGAAUAAGGAAUCCCGACGAAAGAAUGGAAAAGAAACAAAGACGCGUC
...((((......(((((....((((((((((((((....((((.....))))....))))))..)))).)))).........(((...(....)...))).......)))))))))... (-30.47 = -30.80 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 16,296,802 – 16,296,922
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -30.50
Consensus MFE -28.70
Energy contribution -29.03
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.45
Structure conservation index 0.94
SVM decision value 1.34
SVM RNA-class probability 0.943515
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16296802 120 - 27905053
GACGCGUCUUUGUUUCUUUUCCAUUCUUUCGUUGGGAUUUCUUAUUCCGCACCUCUAAUUUGCUCUUCAUCUCCUUGAUGGGCUGCAAAUGAGGGCGGGCUUCAAAGUUAAUUACACUCU
((.((.............(((((.........))))).........((((.((((..((((((..((((((.....))))))..)))))))))))))))).))................. ( -32.70)
>DroSec_CAF1 17468 120 - 1
UACGCGUCUUUGUUUCUUUUCCAUUCUUUCGUCGGGAUUCCUUAUUCCGCACCUCUAAUUUGCUCUUCAUCUUCUUUAUGGGCUGCAAAUGAGGGCGGGCUUCAAAGUUAAUUACACUUU
.......(((((.......(((...(....)...)))........(((((.((((..((((((..(((((.......)))))..)))))))))))))))...)))))............. ( -26.00)
>DroSim_CAF1 9627 120 - 1
GACGCGUCUUUGUUUCUUUUCCAUUCUUUCGGCGGGAUUCCUUAUUCCGCACCUCUAAUUUGCUCUUCAUCUCCUUGAUGGGCUGCAAAUGAGGGCGGGCUUCAAAGUUAAUUACACUUU
..(((..........................(((((((.....))))))).((((..((((((..((((((.....))))))..)))))))))))))((((....))))........... ( -32.80)
>consensus
GACGCGUCUUUGUUUCUUUUCCAUUCUUUCGUCGGGAUUCCUUAUUCCGCACCUCUAAUUUGCUCUUCAUCUCCUUGAUGGGCUGCAAAUGAGGGCGGGCUUCAAAGUUAAUUACACUUU
.......(((((......((((...........))))........(((((.((((..((((((..((((((.....))))))..)))))))))))))))...)))))............. (-28.70 = -29.03 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:39 2006