Locus 5927

Sequence ID 3L_DroMel_CAF1
Location 15,910,102 – 15,910,218
Length 116
Max. P 0.961706
window9465 window9466

overview

Window 5

Location 15,910,102 – 15,910,218
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.85
Mean single sequence MFE -25.12
Consensus MFE -17.94
Energy contribution -19.04
Covariance contribution 1.10
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.71
SVM decision value 1.04
SVM RNA-class probability 0.905185
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15910102 116 + 23771897
GCCAUUUAUAAUCCGGCAACCCAACC----CAUUCCCAUUUCAUCUGGGAUACCAUGCACACGCAUGGCAUGAUAUCCGGUCUGGUUUAUUUACUUCUUACGGAUUUCUCUCGAAAAUCG
(((...........)))((((..(((----...(((((.......)))))..((((((....))))))..........)))..)))).............(((.((((....)))).))) ( -27.30)
>DroSec_CAF1 11820 97 + 1
GCCAUUUAUAAUCGAGCAACCCAACCCAACCAUUCCCAUUUCAUCUGGGA-----------------------UAUCCGGUCUGGUUUAUUUACUUCUUACGGAUUUCUCUCGAAAAUCG
...........(((((.................(((((.......)))))-----------------------.(((((....(((......))).....)))))....)))))...... ( -18.50)
>DroSim_CAF1 12085 120 + 1
GCCAUUUAUAAUCGAGCAACCCAACCCAACCAUUCCCAUUUCAUCUGGGAUACCAUGCACACGCAUGGCAUGAUAUCCGGUCUGGUUUAUUUACUUCUUACGGAUUUCUCUCGAAAAUCG
...........(((((.................(((((.......)))))..((((((....))))))...((.(((((....(((......))).....))))).)).)))))...... ( -29.20)
>DroEre_CAF1 9588 111 + 1
GCCAUUUAUAAUCCCGCAACC---------CAUUCCCAUUCCAUCUGGGAUACCAUGCACACGCAUGGCAUGAUUUCCGCUCUGGUUUAUUUACUUCUUACGGAUUUCUCUCGAAAAUCG
.....................---------...(((((.......)))))..((((((....))))))...((..((((....(((......))).....))))..))............ ( -22.50)
>DroYak_CAF1 9625 111 + 1
GCCAUUUAUAAUCCAGCAGCC---------CAUUCCCAUUUCAUUUGGGAUACCAUGCACACGCAUGGCAUGACUUCCGCUGUGGUUUAUUUACUUCUUACGGAUUUCUCUCGAAAAUCG
.......((((.(((.((((.---------...(((((.......)))))..((((((....))))))..........))))))).))))..........(((.((((....)))).))) ( -28.10)
>consensus
GCCAUUUAUAAUCCAGCAACCCAACC____CAUUCCCAUUUCAUCUGGGAUACCAUGCACACGCAUGGCAUGAUAUCCGGUCUGGUUUAUUUACUUCUUACGGAUUUCUCUCGAAAAUCG
.................................(((((.......)))))..((((((....))))))...((.(((((....(((......))).....))))).))............ (-17.94 = -19.04 +   1.10)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,910,102 – 15,910,218
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.85
Mean single sequence MFE -33.44
Consensus MFE -23.66
Energy contribution -25.86
Covariance contribution 2.20
Combinations/Pair 1.00
Mean z-score -2.59
Structure conservation index 0.71
SVM decision value 1.53
SVM RNA-class probability 0.961706
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15910102 116 - 23771897
CGAUUUUCGAGAGAAAUCCGUAAGAAGUAAAUAAACCAGACCGGAUAUCAUGCCAUGCGUGUGCAUGGUAUCCCAGAUGAAAUGGGAAUG----GGUUGGGUUGCCGGAUUAUAAAUGGC
((..((((....))))..)).............((((.((((........((((((((....))))))))(((((.......)))))...----)))).))))((((.........)))) ( -35.70)
>DroSec_CAF1 11820 97 - 1
CGAUUUUCGAGAGAAAUCCGUAAGAAGUAAAUAAACCAGACCGGAUA-----------------------UCCCAGAUGAAAUGGGAAUGGUUGGGUUGGGUUGCUCGAUUAUAAAUGGC
((..((((....))))..))...((.((((...((((.(((((....-----------------------(((((.......))))).))))).))))...))))))............. ( -27.10)
>DroSim_CAF1 12085 120 - 1
CGAUUUUCGAGAGAAAUCCGUAAGAAGUAAAUAAACCAGACCGGAUAUCAUGCCAUGCGUGUGCAUGGUAUCCCAGAUGAAAUGGGAAUGGUUGGGUUGGGUUGCUCGAUUAUAAAUGGC
((..((((....))))..))...((.((((...((((.(((((.......((((((((....))))))))(((((.......))))).))))).))))...))))))............. ( -38.70)
>DroEre_CAF1 9588 111 - 1
CGAUUUUCGAGAGAAAUCCGUAAGAAGUAAAUAAACCAGAGCGGAAAUCAUGCCAUGCGUGUGCAUGGUAUCCCAGAUGGAAUGGGAAUG---------GGUUGCGGGAUUAUAAAUGGC
((..((((....))))..))..........((((.((...((((...(((((((((((....))))))).(((((.......))))))))---------).)))).)).))))....... ( -31.90)
>DroYak_CAF1 9625 111 - 1
CGAUUUUCGAGAGAAAUCCGUAAGAAGUAAAUAAACCACAGCGGAAGUCAUGCCAUGCGUGUGCAUGGUAUCCCAAAUGAAAUGGGAAUG---------GGCUGCUGGAUUAUAAAUGGC
((..((((....))))..))..........((((.(((((((........((((((((....))))))))(((((.......)))))...---------.)))).))).))))....... ( -33.80)
>consensus
CGAUUUUCGAGAGAAAUCCGUAAGAAGUAAAUAAACCAGACCGGAUAUCAUGCCAUGCGUGUGCAUGGUAUCCCAGAUGAAAUGGGAAUG____GGUUGGGUUGCUGGAUUAUAAAUGGC
....((((....)))).((((....(((.....((((.((((........((((((((....))))))))(((((.......))))).......)))).)))).....)))....)))). (-23.66 = -25.86 +   2.20)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:18 2006