Locus 842

Sequence ID 2R_DroMel_CAF1
Location 3,954,381 – 3,954,565
Length 184
Max. P 0.599638
window1463 window1464

overview

Window 3

Location 3,954,381 – 3,954,501
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.73
Mean single sequence MFE -32.12
Consensus MFE -20.07
Energy contribution -19.72
Covariance contribution -0.36
Combinations/Pair 1.30
Mean z-score -1.44
Structure conservation index 0.62
SVM decision value 0.13
SVM RNA-class probability 0.599638
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3954381 120 - 20766785
UCAACUACAUAGACCACAUGGCUGGCAUCAUGGAGAUGAUCCCAGGACCCACGCCAUACCCCUUCGUGGGUAAUCUGUUCCAGUUCGGUCUCAAGCCAGCCGGUGAGUACUGACCAAAUA
.........((((((((.((((((((......(((((((...(((((((((((...........)))))))..)))).......)).)))))..))))))))))).)).)))........ ( -37.50)
>DroVir_CAF1 1609 112 - 1
UCAAUUAUAUUGAUCACAUGGCUGGCAUUAUGGAAAUGAUACCGGGCCCAACGCCAUACCCAUUUGUGGGUAAUAUCUUUCAGUUCGGUCUGAAGCCAGCCGGUAAGCACAA--------
(((((...)))))..((.(((((((((((((....)))))(((((((.....))).((((((....)))))).............)))).....))))))))))........-------- ( -36.00)
>DroGri_CAF1 1425 118 - 1
UCAAUUACCUAGAUCACAUGGCUGGUAUUAUGGAAAUGAUACCGGGUCCAACGCCCUAUCCCUUUGUGGGUAACCUAUUUCAGUUUGGACUUAAGCCAGCCGGUAAGCACAA--UAAAUC
....(((((..(....).(((((((((((((....))))))))((((((((.((((...........))))...((.....)).)))))))).)))))...)))))......--...... ( -32.60)
>DroWil_CAF1 1277 110 - 1
UCAACUAUUUGGAUCAUAUGGCUGGUAUAAUGGAAAUGAUACCAGGACCCACACCAUAUCCAUUUGUUGGUAAUCUCUUUCAGUUCGGUCUCAAGCCAGACGGUGAGUG----------A
(((((....((((...((((((((((((.((....)).)))))))........)))))))))...)))))...((.(((...((..(((.....)))..))...))).)----------) ( -28.30)
>DroMoj_CAF1 1804 118 - 1
UCAACUACAUAGAUCACAUGGCUGGCAUUAUGGAAAUGAUACCGGGACCCACGCCCUAUCCGUUCGUGGGCAAUAUCUUUCAGUUCGGCCUGAAGCCAGCCGGUAAGCCCAA--UAGAUA
............(((....((((((((((((....))))).....(.((((((..(.....)..))))))).......(((((......))))))))))))((....))...--..))). ( -34.90)
>DroAna_CAF1 1164 113 - 1
UCAAUUAUAUUGAUCAUAUGGCGAGCAUUAUGGAAAUGAUACCAGGACCGACGCCAUAUCCAUUCGUUGGCAAUCUAUUUCAAUUUGGCCUUAAGCCCGCCGGUAAGUACUGG-------
........(((((..((((((((.......(((........))).......))))))))(((.....))).........)))))..(((.....)))..(((((....)))))------- ( -23.44)
>consensus
UCAACUACAUAGAUCACAUGGCUGGCAUUAUGGAAAUGAUACCAGGACCCACGCCAUAUCCAUUCGUGGGUAAUCUCUUUCAGUUCGGUCUCAAGCCAGCCGGUAAGCACAA_______A
..................(((((((((((((....))))).((.(......)((((...........))))...............))......)))))))).................. (-20.07 = -19.72 +  -0.36) 

alignment

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secondary structure

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dotplot

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Window 4

Location 3,954,461 – 3,954,565
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.51
Mean single sequence MFE -28.48
Consensus MFE -16.62
Energy contribution -16.90
Covariance contribution 0.28
Combinations/Pair 1.41
Mean z-score -1.69
Structure conservation index 0.58
SVM decision value 0.11
SVM RNA-class probability 0.588161
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3954461 104 - 20766785
----------------AUGUUUCUAAUAGCCAUUGCCAUUAUUUUGGCCACCAUUUUGGUGUUCAAGGGAGUGAGGAUAUUCAACUACAUAGACCACAUGGCUGGCAUCAUGGAGAUGAU
----------------..(((((((...((((..(((((..(((((..((((.....))))..)))))..(((.(..(((........)))..)))))))))))))....)))))))... ( -30.20)
>DroVir_CAF1 1681 120 - 1
GAAAAAAGAAAACAGCAUGUUUCUGCUAGCAGCGGCAAUCGUUUUGGCCACAAUUUUGGUGUUCAAGGGUGUCAAGAUAUUCAAUUAUAUUGAUCACAUGGCUGGCAUUAUGGAAAUGAU
......(((((........)))))((((((...........(((((..(((.......)))..)))))(((((((.(((......))).)))).)))...))))))(((((....))))) ( -26.00)
>DroGri_CAF1 1503 104 - 1
----------------AUGUUUCUGUUAGCGGCGGCAAUAAUCUUGGCCACCAUUUUGGUGUUCAAGGGUGUCAGGAUAUUCAAUUACCUAGAUCACAUGGCUGGUAUUAUGGAAAUGAU
----------------..((((((((((.((((((((....(((((..((((.....))))..))))).))))(((.((......)))))..........)))).))..))))))))... ( -30.50)
>DroWil_CAF1 1347 104 - 1
----------------AUGUUUUUAUUAGCUGCUGCCAUUUUAUUGGCCACCAUUUUGGUGUUCAAGGGCGUGAAAAUCUUCAACUAUUUGGAUCAUAUGGCUGGUAUAAUGGAAAUGAU
----------------...................(((((.(((..((((((.....)))(((((((....((((....))))....))))))).....)))..))).)))))....... ( -25.80)
>DroMoj_CAF1 1882 104 - 1
----------------AUGUUUCUGCUAGUCUUUGGCAUUAUUUUGGCCACCAUUCUGGUGGUCAAGGGCGUGAGGAUAUUCAACUACAUAGAUCACAUGGCUGGCAUUAUGGAAAUGAU
----------------..(((((((((((((....((....(((((((((((.....)))))))))))))((((...(((........)))..))))..))))))).....))))))... ( -33.10)
>DroAna_CAF1 1237 104 - 1
----------------AUGUUUCUGAUAGCCAUAGCCAUUAUUUUGGCCACCAUUCUGGUGUUCAAGGGAGUGAAAAUAUUCAAUUAUAUUGAUCAUAUGGCGAGCAUUAUGGAAAUGAU
----------------..(((((((((.((....(((((..(((((..((((.....))))..)))))..((((.(((((......)))))..)))))))))..)))))..))))))... ( -25.30)
>consensus
________________AUGUUUCUGAUAGCCGCUGCCAUUAUUUUGGCCACCAUUUUGGUGUUCAAGGGAGUGAAGAUAUUCAACUACAUAGAUCACAUGGCUGGCAUUAUGGAAAUGAU
..................((((((((((((((.........(((((..((((.....))))..)))))...((((....))))...............)))))))).....))))))... (-16.62 = -16.90 +   0.28) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:44 2006