Locus 4747

Sequence ID 3R_DroMel_CAF1
Location 12,456,021 – 12,456,160
Length 139
Max. P 0.949049
window7791 window7792

overview

Window 1

Location 12,456,021 – 12,456,121
Length 100
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 81.36
Mean single sequence MFE -34.25
Consensus MFE -23.54
Energy contribution -24.35
Covariance contribution 0.81
Combinations/Pair 1.05
Mean z-score -2.10
Structure conservation index 0.69
SVM decision value 1.04
SVM RNA-class probability 0.905315
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12456021 100 - 27905053
CUGGCCA-AGAGAGUGCCCUGCUGUUAAGUGGGGUCCUGGGGAAUGGCUGUGGCAUAUGUCACAGUGUCACAGGUUGAUAUGGGAUA----------CGUUCAGGUAUAAU
...(((.-....((..(((..((....))..)))..))...(((((((((((((....))))))))(((.((........)).))).----------))))).)))..... ( -35.40)
>DroAna_CAF1 3724 103 - 1
CUGGCAGGAUACAGUGCCCUGCUGCUAAGUGGGGUAUUAGGGACUGGAAGUGGCAUAUGUCA--------AUGGAUGAUGUAGGAUAGGACAUUCGGCAUUCAGGUACAAA
(((.(((..(..(((((((..((....))..)))))))..)..)))..((((.(.(((((((--------.....)))))))((((.....))))).)))))))....... ( -29.40)
>DroSim_CAF1 4258 100 - 1
CUGGCCA-GGAGAGUGCCCUGCUGUUAAGUGGGGUCCUAGGGACUGGCUGUGGCAUAUGUCACAGUGUCACAGGUUGAUAUGGGAUA----------CGUUCAGGUAUAAU
(((((((-(...((..(((..((....))..)))..)).....)))))((((((....))))))(((((.((........)).))))----------)...)))....... ( -38.20)
>DroEre_CAF1 4200 100 - 1
CUGGCCA-AGAGAGUGCCCUGCUGUUAAGUGGGGUCCUAGGGACUGGCUGUGGCAUAUGUCACAGUGUCACAGGUUGAUAUAGGAUA----------CGUUCAGGUAUAAU
..((((.-....((..(((..((....))..)))..))...(((..((((((((....)))))))))))...)))).((((..((..----------...))..))))... ( -34.00)
>consensus
CUGGCCA_AGAGAGUGCCCUGCUGUUAAGUGGGGUCCUAGGGACUGGCUGUGGCAUAUGUCACAGUGUCACAGGUUGAUAUAGGAUA__________CGUUCAGGUAUAAU
((((........((.((((..((....))..)))).))........((((((((....))))))))..................................))))....... (-23.54 = -24.35 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 12,456,051 – 12,456,160
Length 109
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 87.27
Mean single sequence MFE -39.50
Consensus MFE -34.92
Energy contribution -36.30
Covariance contribution 1.38
Combinations/Pair 1.06
Mean z-score -2.06
Structure conservation index 0.88
SVM decision value 1.39
SVM RNA-class probability 0.949049
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12456051 109 - 27905053
U-GCUGGUGUCUAUAUCGCUCUCGAAAUGUUUUCGCUUAUCUGGCCA-AGAGAGUGCCCUGCUGUUAAGUGGGGUCCUGGGGAAUGGCUGUGGCAUAUGUCACAGUGUCAC
.-.(..(..........(((((((((.....)))(((.....)))..-.))))))((((..((....))..)))).)..).((...((((((((....)))))))).)).. ( -36.60)
>DroAna_CAF1 3764 103 - 1
UGGCCGGCUUCUAUUACGCUCUCGAAAUGUUUUCGCUUAUCUGGCAGGAUACAGUGCCCUGCUGCUAAGUGGGGUAUUAGGGACUGGAAGUGGCAUAUGUCA--------A
..((((.((((((....(.((((.....((.((((((.....))).))).))(((((((..((....))..))))))).)))))))))))))))........--------. ( -34.00)
>DroSim_CAF1 4288 109 - 1
U-GCCGGUGUCUAUAUCGCUCUCGAAAUGUUUUCGCUUAUCUGGCCA-GGAGAGUGCCCUGCUGUUAAGUGGGGUCCUAGGGACUGGCUGUGGCAUAUGUCACAGUGUCAC
.-((((((.((((....(((((((((.....)))(((.....)))..-.))))))((((..((....))..))))..)))).))))))((((((....))))))....... ( -43.60)
>DroEre_CAF1 4230 109 - 1
U-GCCGGUGUCUAUAUCGCUCUCGAAAUGUUUUCGCUUAUCUGGCCA-AGAGAGUGCCCUGCUGUUAAGUGGGGUCCUAGGGACUGGCUGUGGCAUAUGUCACAGUGUCAC
.-((((((.((((....(((((((((.....)))(((.....)))..-.))))))((((..((....))..))))..)))).))))))((((((....))))))....... ( -43.80)
>consensus
U_GCCGGUGUCUAUAUCGCUCUCGAAAUGUUUUCGCUUAUCUGGCCA_AGAGAGUGCCCUGCUGUUAAGUGGGGUCCUAGGGACUGGCUGUGGCAUAUGUCACAGUGUCAC
..((((((.((((....(((((((((.....)))(((.....)))....))))))((((..((....))..))))..)))).))))))((((((....))))))....... (-34.92 = -36.30 +   1.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:57 2006