Locus 7007

Sequence ID 3R_DroMel_CAF1
Location 18,473,852 – 18,474,031
Length 179
Max. P 0.865085
window11358 window11359

overview

Window 8

Location 18,473,852 – 18,473,961
Length 109
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 77.50
Mean single sequence MFE -34.95
Consensus MFE -16.97
Energy contribution -18.18
Covariance contribution 1.21
Combinations/Pair 1.11
Mean z-score -2.11
Structure conservation index 0.49
SVM decision value 0.84
SVM RNA-class probability 0.865085
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18473852 109 + 27905053
GGGCAGUCUGCA-AAAAAAACAAUGGGCUUCUUGGGU--------CAUUUUUUGGCUUGCCAGGUAUCGACAGUGUUUGUCUUGGAUUUCGGUAAAGUUCGAUGGAAAAAGGCAGACA
.....((((((.-.......((.((((((((((((((--------((.....))))...)))))((((((.(((.(.......).)))))))))))))))).)).......)))))). ( -28.56)
>DroSec_CAF1 29008 108 + 1
GAGCAGUCUGCA-AAA-AAACAAUGGGCUUCUUGGGC--------CAUUUUUUGGCUGGCCAGGUAUCGACAGUGUUUGUCUUGGAUUUCGGUGAAGUUCGAAGGAAGAAGGCAGACA
.....((((((.-...-...(..((((((((...(((--------((.....))))).(((.((.((((((((...)))))...))).)))))))))))))..).......)))))). ( -32.54)
>DroSim_CAF1 28669 108 + 1
GAGCAGUCUGCA-AAA-AAACAAUGGGCUUCUUGGGC--------CAUUUUUUGGCUGGCCAGGUAUCGACAGUGUUUGGCUUGGAUUUCGGUGAAGUUCGAUGGAAGAAGGCAGACA
.....((((((.-...-...((.((((((((((((((--------((.....)))))(((((..(((.....)))..))))).......))).)))))))).)).......)))))). ( -37.94)
>DroEre_CAF1 29277 82 + 1
GGGCAGUCUGCC-AAA-AAACAAUGGGCUUCUUGGGC--------CAUUUUUUGGCUGA--------------UACC------------UGGAGAAGUUCGGUGGAGGAGGGCAGACA
.....(((((((-...-...((.((((((((((((((--------((.....))))...--------------..))------------..)))))))))).))......))))))). ( -32.30)
>DroYak_CAF1 30043 117 + 1
GGGCAGUCUGCCGAAA-AAACAAUGGGCUUCUUGGGCUGGCUGGCUCUUUUUUGGCUGGCCAGGUAUCGAGAAUACUGGGCUUAGAUUUCGGUGCAGUUUGGUGGAGGAAGGCAGACA
.....(((((((....-..((.......(((((((.(((((..(((.......)))..)))))...))))))).((((.(((........))).))))...)).......))))))). ( -43.42)
>consensus
GGGCAGUCUGCA_AAA_AAACAAUGGGCUUCUUGGGC________CAUUUUUUGGCUGGCCAGGUAUCGACAGUGUUUGGCUUGGAUUUCGGUGAAGUUCGAUGGAAGAAGGCAGACA
.....((((((.........((.((((((((..............((.....))((((.(((((................)))))....)))))))))))).)).......)))))). (-16.97 = -18.18 +   1.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 18,473,921 – 18,474,031
Length 110
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 90.00
Mean single sequence MFE -32.55
Consensus MFE -23.56
Energy contribution -24.00
Covariance contribution 0.44
Combinations/Pair 1.14
Mean z-score -1.66
Structure conservation index 0.72
SVM decision value 0.04
SVM RNA-class probability 0.552111
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18473921 110 - 27905053
CUUGUGGCAAGGCUUUAGUCCUGUUCUCGUAGACAACGGAGAAACAUGAGAGGCUUCAAUGGCAGGACUUUGUCUGCCUUUUUCCAUCGAACUUUACCGAAAUCCAAGAC
((((.((((.(((...((((((((((((((.....)).))))..((((((....))).)))))))))))..)))))))........(((........)))....)))).. ( -30.90)
>DroSec_CAF1 29076 110 - 1
CUUGUGGCAAGGCUUUAGUCCUGUUCCCGUAGACAACGUGGAAACAUGAGAGGUUUCAAUGGCAGGACUUUGUCUGCCUUCUUCCUUCGAACUUCACCGAAAUCCAAGAC
((((.((((.(((...(((((((...((((((((..((((....))))....))))..)))))))))))..))))))).......((((........))))...)))).. ( -35.40)
>DroSim_CAF1 28737 110 - 1
CUUGUGGCAAGGCUUUAGUCCUGUUCUCGUAGACAACGUGGAAACAUGAGAGGCUUCAAUGGCAGGACUUUGUCUGCCUUCUUCCAUCGAACUUCACCGAAAUCCAAGCC
((((.((((.(((...(((((((((.....((....((((....)))).....)).....)))))))))..)))))))........(((........)))....)))).. ( -32.80)
>DroYak_CAF1 30120 110 - 1
CAUGUGGCAAGGCUUAAGUUUUGUUCCCAUAGACAACUGGGAAACAUGAGAGGCUACAACGGCAGGACUUUGUCUGCCUUCCUCCACCAAACUGCACCGAAAUCUAAGCC
..........((((((..(((((((((((........))))))...((.((((....((.((((((......))))))))))))))...........)))))..)))))) ( -31.10)
>consensus
CUUGUGGCAAGGCUUUAGUCCUGUUCCCGUAGACAACGGGGAAACAUGAGAGGCUUCAAUGGCAGGACUUUGUCUGCCUUCUUCCAUCGAACUUCACCGAAAUCCAAGAC
.....((((.(((...(((((((((.....((....((((....)))).....)).....)))))))))..)))))))................................ (-23.56 = -24.00 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:23 2006