Locus 3206

Sequence ID 2R_DroMel_CAF1
Location 10,958,492 – 10,958,585
Length 93
Max. P 0.874553
window5272 window5273

overview

Window 2

Location 10,958,492 – 10,958,585
Length 93
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 71.09
Mean single sequence MFE -27.73
Consensus MFE -15.34
Energy contribution -15.84
Covariance contribution 0.50
Combinations/Pair 1.13
Mean z-score -1.58
Structure conservation index 0.55
SVM decision value 0.62
SVM RNA-class probability 0.801746
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10958492 93 + 20766785
AAAUUUCCGAGUAGGCCACGAAAUUGGCAGGGGGCACGGGAUCUGGCUCCGGCUC------------AGGCUGAGGCUCAGCCAGAUACCAGAGACCAGAAACCA--------------
...(..((......((((......)))).))..)...((..((((((((.((.((------------.(((((.....))))).))..)).))).)))))..)).-------------- ( -35.70)
>DroPse_CAF1 66654 71 + 1
AAAUUUCCGAGUAGGCCACGAAAUUGGCAAGGCACUC------CCGCUCC-----------------------AGGUCCUGCCGCUU-----CGACUAGUCUUCC--------------
........((.(((((((......))))..((((...------((.....-----------------------.))...))))....-----...))).))....-------------- ( -18.30)
>DroSec_CAF1 70887 81 + 1
AAAUUUCCGAGUAGGCCACGAAAUUGGCAGAGGACACGGGAUCUGGCUC------------------------AGGCUCAGCCAGAUACCAGAGACCAAAAACCA--------------
.....(((......((((......))))...)))...((..(((((.((------------------------.(((...))).))..)))))..))........-------------- ( -23.10)
>DroSim_CAF1 73180 81 + 1
AAAUUUCCGAGUAGGCCACGAAAUUGGCAGAGGGCACGGGAUCUGGCUC------------------------AGGCUCAGCCAGAUACCAGAGACCAAAAACCA--------------
...((((((.((..((((......)))).....)).))((((((((((.------------------------......)))))))).)).))))..........-------------- ( -22.80)
>DroEre_CAF1 73210 105 + 1
AAAUUUCCGAGUAGGCCACGAAAUUGGCAGAGGGCACGGGAUCUGGCUCAGGCUCCGGCUCCGGCUCCGGCUGAGGCUCAGCCAGAUACCAGUAACCAAAAACCA--------------
..............((((......))))...((..((.((((((((((..(((..((((..((....))))))..))).)))))))).)).))..))........-------------- ( -37.80)
>DroYak_CAF1 74161 107 + 1
AAAUUUCCGAGUAGGCCACGAAAUUGGCAGAGGCCACGGGAUCUGGCUCACGCUC------------AGGCUGAGGCUCAGCCAGAUACCAGAUACCAGAAACCAGCAACCAAAAAACC
...((((.(.(((((((.(..........).))))..((.((((((((....(((------------.....)))....)))))))).))...)))).))))................. ( -28.70)
>consensus
AAAUUUCCGAGUAGGCCACGAAAUUGGCAGAGGGCACGGGAUCUGGCUC________________________AGGCUCAGCCAGAUACCAGAGACCAAAAACCA______________
..............((((......))))...((.....(((((((((.................................))))))).)).....))...................... (-15.34 = -15.84 +   0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,958,492 – 10,958,585
Length 93
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 71.09
Mean single sequence MFE -31.67
Consensus MFE -17.55
Energy contribution -18.46
Covariance contribution 0.92
Combinations/Pair 1.13
Mean z-score -1.67
Structure conservation index 0.55
SVM decision value 0.89
SVM RNA-class probability 0.874553
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10958492 93 - 20766785
--------------UGGUUUCUGGUCUCUGGUAUCUGGCUGAGCCUCAGCCU------------GAGCCGGAGCCAGAUCCCGUGCCCCCUGCCAAUUUCGUGGCCUACUCGGAAAUUU
--------------.((..(((((.(((((((.((.(((((.....))))).------------))))))))))))))..))...((....((((......))))......))...... ( -39.50)
>DroPse_CAF1 66654 71 - 1
--------------GGAAGACUAGUCG-----AAGCGGCAGGACCU-----------------------GGAGCGG------GAGUGCCUUGCCAAUUUCGUGGCCUACUCGGAAAUUU
--------------....((.(((.((-----(((.((((((.(((-----------------------(...)))------)....)).))))..)))))....))).))........ ( -15.90)
>DroSec_CAF1 70887 81 - 1
--------------UGGUUUUUGGUCUCUGGUAUCUGGCUGAGCCU------------------------GAGCCAGAUCCCGUGUCCUCUGCCAAUUUCGUGGCCUACUCGGAAAUUU
--------------((((....((.(.(.((.((((((((......------------------------.)))))))))).).).))...)))).(((((.(.....).))))).... ( -27.10)
>DroSim_CAF1 73180 81 - 1
--------------UGGUUUUUGGUCUCUGGUAUCUGGCUGAGCCU------------------------GAGCCAGAUCCCGUGCCCUCUGCCAAUUUCGUGGCCUACUCGGAAAUUU
--------------((((....(((...(((.((((((((......------------------------.)))))))).))).)))....)))).(((((.(.....).))))).... ( -26.30)
>DroEre_CAF1 73210 105 - 1
--------------UGGUUUUUGGUUACUGGUAUCUGGCUGAGCCUCAGCCGGAGCCGGAGCCGGAGCCUGAGCCAGAUCCCGUGCCCUCUGCCAAUUUCGUGGCCUACUCGGAAAUUU
--------------((((....((.(((.((.((((((((.((.(((..(((....))).....))).)).)))))))))).))).))...)))).(((((.(.....).))))).... ( -41.50)
>DroYak_CAF1 74161 107 - 1
GGUUUUUUGGUUGCUGGUUUCUGGUAUCUGGUAUCUGGCUGAGCCUCAGCCU------------GAGCGUGAGCCAGAUCCCGUGGCCUCUGCCAAUUUCGUGGCCUACUCGGAAAUUU
(((.....(((..(.((..((((((.((.....((.(((((.....))))).------------))....))))))))..)))..)))...)))..(((((.(.....).))))).... ( -39.70)
>consensus
______________UGGUUUCUGGUCUCUGGUAUCUGGCUGAGCCU________________________GAGCCAGAUCCCGUGCCCUCUGCCAAUUUCGUGGCCUACUCGGAAAUUU
...............(((((((((.....((.((((((((...............................)))))))).)).........((((......))))....))))))))). (-17.55 = -18.46 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:01 2006