Locus 2047

Sequence ID 3R_DroMel_CAF1
Location 5,806,596 – 5,806,716
Length 120
Max. P 0.615280
window3352 window3353

overview

Window 2

Location 5,806,596 – 5,806,716
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.83
Mean single sequence MFE -24.80
Consensus MFE -17.21
Energy contribution -18.03
Covariance contribution 0.81
Combinations/Pair 1.06
Mean z-score -2.12
Structure conservation index 0.69
SVM decision value 0.06
SVM RNA-class probability 0.561432
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5806596 120 + 27905053
AAGCUGCUAGCACCGCACCGAAAAUAAAUGGGAUUAAAGAUGAUAAAAGGUUAUUACAUUUUAUUAACAUAUCCCACAUAAUUUUCACUUUAGAACAUCAUGCUAAUCCGGUUUAUUAGA
((((((.(((((.......((((((...((((((....(.((((((((.((....)).)))))))).)..))))))....))))))......(.....).)))))...))))))...... ( -23.20)
>DroSec_CAF1 98110 120 + 1
AAGCUGUUAGCACGGCACCGGAAAUAAAUGGGAUUAAAGAUGAUAAAAGGUUAUUACAUUUUAUUAACAUAUCCCACAUAAUUUUCACUUUAGAACAUCAUGCUAAUCCGGUUUAUUAGA
..(((((....)))))((((((......((((((....(.((((((((.((....)).)))))))).)..))))))(((.((.(((......))).)).)))....))))))........ ( -28.30)
>DroSim_CAF1 98833 120 + 1
AAGCUGUUAGCACGGCACCGGAAAUAAAUGGGAUUAAAGAUGAUAAAAGAUUAUUACAUUUUAUUAACACAUCCCACAUAAUUUUCACUUUAGAACAUCAUGCUAAUCCGGUUUAUUAGA
..(((((....)))))((((((......((((((....(.((((((((..........)))))))).)..))))))(((.((.(((......))).)).)))....))))))........ ( -25.90)
>DroYak_CAF1 84070 118 + 1
AAGCUGUUGGGA--ACACCGAAAAUAAAUGGGAUUAAGGAUGAUAAAAUGAUAUUACCUUUUAUUAACAUAUCCCACAUAAGUUUCACUUUGGAAUACCAUGCUUAACCGAUUUAUUAUA
......((((..--...)))).(((((((.((.(((((.(((......(((((........)))))...(((.(((...(((.....)))))).))).))).))))))).)))))))... ( -21.80)
>consensus
AAGCUGUUAGCACGGCACCGAAAAUAAAUGGGAUUAAAGAUGAUAAAAGGUUAUUACAUUUUAUUAACAUAUCCCACAUAAUUUUCACUUUAGAACAUCAUGCUAAUCCGGUUUAUUAGA
((((((((((((.......((((((...((((((....(.((((((((..........)))))))).)..))))))....))))))......(.....).))))))..))))))...... (-17.21 = -18.03 +   0.81)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,806,596 – 5,806,716
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.83
Mean single sequence MFE -24.88
Consensus MFE -22.11
Energy contribution -21.68
Covariance contribution -0.44
Combinations/Pair 1.18
Mean z-score -1.40
Structure conservation index 0.89
SVM decision value 0.17
SVM RNA-class probability 0.615280
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5806596 120 - 27905053
UCUAAUAAACCGGAUUAGCAUGAUGUUCUAAAGUGAAAAUUAUGUGGGAUAUGUUAAUAAAAUGUAAUAACCUUUUAUCAUCUUUAAUCCCAUUUAUUUUCGGUGCGGUGCUAGCAGCUU
........((((((...(((((((.(((......))).)))))))(((((..(...((((((.((....)).))))))...)....))))).......))))))((.((....)).)).. ( -24.50)
>DroSec_CAF1 98110 120 - 1
UCUAAUAAACCGGAUUAGCAUGAUGUUCUAAAGUGAAAAUUAUGUGGGAUAUGUUAAUAAAAUGUAAUAACCUUUUAUCAUCUUUAAUCCCAUUUAUUUCCGGUGCCGUGCUAACAGCUU
........((((((...(((((((.(((......))).)))))))(((((..(...((((((.((....)).))))))...)....))))).......))))))((.((....)).)).. ( -27.70)
>DroSim_CAF1 98833 120 - 1
UCUAAUAAACCGGAUUAGCAUGAUGUUCUAAAGUGAAAAUUAUGUGGGAUGUGUUAAUAAAAUGUAAUAAUCUUUUAUCAUCUUUAAUCCCAUUUAUUUCCGGUGCCGUGCUAACAGCUU
........((((((...(((((((.(((......))).)))))))(((((..(...((((((.((....)).))))))...)....))))).......))))))((.((....)).)).. ( -27.40)
>DroYak_CAF1 84070 118 - 1
UAUAAUAAAUCGGUUAAGCAUGGUAUUCCAAAGUGAAACUUAUGUGGGAUAUGUUAAUAAAAGGUAAUAUCAUUUUAUCAUCCUUAAUCCCAUUUAUUUUCGGUGU--UCCCAACAGCUU
...(((((((.(((((((.((((((((((((((.....)))...))))))))....(((((((((...))).))))))))).))))).)).)))))))...(.(((--.....))).).. ( -19.90)
>consensus
UCUAAUAAACCGGAUUAGCAUGAUGUUCUAAAGUGAAAAUUAUGUGGGAUAUGUUAAUAAAAUGUAAUAACCUUUUAUCAUCUUUAAUCCCAUUUAUUUCCGGUGCCGUGCUAACAGCUU
........((((((...(((((((.(((......))).)))))))(((((..(...((((((.(......).))))))...)....))))).......))))))((.((....)).)).. (-22.11 = -21.68 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:06 2006