Locus 859

Sequence ID 2R_DroMel_CAF1
Location 4,016,534 – 4,016,694
Length 160
Max. P 0.777776
window1484 window1485 window1486

overview

Window 4

Location 4,016,534 – 4,016,654
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.44
Mean single sequence MFE -32.47
Consensus MFE -30.41
Energy contribution -30.20
Covariance contribution -0.21
Combinations/Pair 1.10
Mean z-score -1.87
Structure conservation index 0.94
SVM decision value 0.55
SVM RNA-class probability 0.777776
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4016534 120 + 20766785
UCAGCCAUUUUCCAGCUUGUUUUUAAAGUGUCGUAAAUCACGUAGUAGUUUGUAGUUUGCACAGUUUCUGCCUUUUUGGCCAUGGCUUGUGGCAGAUUAUGAUUUAUUGCUUUGGGAGAU
......(((((((((............(((........)))(((((((.(..((((((((((((((...(((.....)))...))).))).))))))))..).))))))).))))))))) ( -34.70)
>DroSim_CAF1 1439 120 + 1
UCGGCCAUUUUCCAGCUUGUUUUUAAAGUGUCGUAAAUCAUGUAGUAGUUUGUAGUUUGCACAGUUUCUGCCUUUUUGGCCAUGGCCUGUGGCAGAUUAUGAUUUAUUGCUUUGGGAGAU
......((((((((((((.......))))((.((((((((((..((((........))))......((((((.....(((....)))...)))))).)))))))))).))..)))))))) ( -35.50)
>DroYak_CAF1 1204 120 + 1
CCGGCCAUUUUCCAGCAUGUUUUUUAAGUGUCGUAAAUCACGUAGUAGUUUGCAGUUUGUACAGUUCCUACCUUUUUGGCCAUGGCCUGUGGCAGAUUAUGAUUUAUUGCUUUGGGAGAU
......(((((((((............(((........)))(((((((.((..(((((((((((..((..((.....))....)).)))).)))))))..)).))))))).))))))))) ( -27.20)
>consensus
UCGGCCAUUUUCCAGCUUGUUUUUAAAGUGUCGUAAAUCACGUAGUAGUUUGUAGUUUGCACAGUUUCUGCCUUUUUGGCCAUGGCCUGUGGCAGAUUAUGAUUUAUUGCUUUGGGAGAU
......(((((((((............(((........)))(((((((.(((((((((((((((..((.(((.....)))...)).)))).))))))))))).))))))).))))))))) (-30.41 = -30.20 +  -0.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 4,016,534 – 4,016,654
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -22.51
Consensus MFE -21.17
Energy contribution -20.40
Covariance contribution -0.77
Combinations/Pair 1.20
Mean z-score -1.63
Structure conservation index 0.94
SVM decision value 0.19
SVM RNA-class probability 0.627363
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4016534 120 - 20766785
AUCUCCCAAAGCAAUAAAUCAUAAUCUGCCACAAGCCAUGGCCAAAAAGGCAGAAACUGUGCAAACUACAAACUACUACGUGAUUUACGACACUUUAAAAACAAGCUGGAAAAUGGCUGA
.......((((...((((((((..((((((....((....))......))))))...((((.....)))).........)))))))).....)))).......(((((.....))))).. ( -20.90)
>DroSim_CAF1 1439 120 - 1
AUCUCCCAAAGCAAUAAAUCAUAAUCUGCCACAGGCCAUGGCCAAAAAGGCAGAAACUGUGCAAACUACAAACUACUACAUGAUUUACGACACUUUAAAAACAAGCUGGAAAAUGGCCGA
.((..(((......((((((((..((((((...(((....))).....))))))...((((.....)))).........))))))))...(((((.......))).)).....)))..)) ( -22.80)
>DroYak_CAF1 1204 120 - 1
AUCUCCCAAAGCAAUAAAUCAUAAUCUGCCACAGGCCAUGGCCAAAAAGGUAGGAACUGUACAAACUGCAAACUACUACGUGAUUUACGACACUUAAAAAACAUGCUGGAAAAUGGCCGG
.....((...(((.............)))....((((((..(((....(((((....((((.....))))..)))))..(((........))).............)))...)))))))) ( -23.82)
>consensus
AUCUCCCAAAGCAAUAAAUCAUAAUCUGCCACAGGCCAUGGCCAAAAAGGCAGAAACUGUGCAAACUACAAACUACUACGUGAUUUACGACACUUUAAAAACAAGCUGGAAAAUGGCCGA
..............((((((((..((((((...(((....))).....))))))...((((.....)))).........)))))))).................((((.....))))... (-21.17 = -20.40 +  -0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,016,574 – 4,016,694
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.67
Mean single sequence MFE -35.37
Consensus MFE -31.47
Energy contribution -31.37
Covariance contribution -0.10
Combinations/Pair 1.12
Mean z-score -1.90
Structure conservation index 0.89
SVM decision value 0.36
SVM RNA-class probability 0.702502
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4016574 120 + 20766785
CGUAGUAGUUUGUAGUUUGCACAGUUUCUGCCUUUUUGGCCAUGGCUUGUGGCAGAUUAUGAUUUAUUGCUUUGGGAGAUUGCAGAUCCAACUUGCAGGAUGCAGUUAAUUCCUUCGGUA
.(((((((.(..((((((((((((((...(((.....)))...))).))).))))))))..).)))))))...(((((((((((..(((........))))))))))..))))....... ( -37.60)
>DroSim_CAF1 1479 120 + 1
UGUAGUAGUUUGUAGUUUGCACAGUUUCUGCCUUUUUGGCCAUGGCCUGUGGCAGAUUAUGAUUUAUUGCUUUGGGAGAUUGCAGCUCCAACUUGCAGGAUGCAGUUAAUUCCUUCGGUA
.(((((((.(..((((((((((((((...(((.....)))...)).)))).))))))))..).)))))))...(((((((((((..(((........))))))))))..))))....... ( -37.30)
>DroYak_CAF1 1244 120 + 1
CGUAGUAGUUUGCAGUUUGUACAGUUCCUACCUUUUUGGCCAUGGCCUGUGGCAGAUUAUGAUUUAUUGCUUUGGGAGAUUGCAGCUUCAACUUGCCGGUUGCAGUAAAUUUCUUUCGAA
.(((((((.((..(((((((((((..((..((.....))....)).)))).)))))))..)).))))))).(((..(((.....(((.(((((....))))).))).....)))..))). ( -31.20)
>consensus
CGUAGUAGUUUGUAGUUUGCACAGUUUCUGCCUUUUUGGCCAUGGCCUGUGGCAGAUUAUGAUUUAUUGCUUUGGGAGAUUGCAGCUCCAACUUGCAGGAUGCAGUUAAUUCCUUCGGUA
.(((((((.(((((((((((((((..((.(((.....)))...)).)))).))))))))))).)))))))...((((.((((((..(((........)))))))))...))))....... (-31.47 = -31.37 +  -0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:05 2006