Locus 6150

Sequence ID 2L_DroMel_CAF1
Location 17,149,528 – 17,149,687
Length 159
Max. P 0.901067
window9827 window9828 window9829

overview

Window 7

Location 17,149,528 – 17,149,647
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.16
Mean single sequence MFE -43.86
Consensus MFE -32.29
Energy contribution -33.26
Covariance contribution 0.97
Combinations/Pair 1.05
Mean z-score -2.09
Structure conservation index 0.74
SVM decision value 0.49
SVM RNA-class probability 0.754856
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17149528 119 + 22407834
UCUUGCGGUUGCUUUUCCGCCCCGGAAAAUCUCCCACGGGAAAG-GGGCCGGGGCACCCUGACCCCAAGCCAAGCGCGGAAAUUGUGCGCCGCAAUCUCUUAAGACCGGCGACAAAUAUA
..(((((((.((.(((((((((((............))))...(-(((.((((....)))).)))).........)))))))....)))))))))............(....)....... ( -44.90)
>DroSec_CAF1 110356 118 + 1
UCUUGCGGUUGCUUUUCCGCCUCGGACAAUCUCUC--GGGAAAGGGGGCAGGGGCCACCUAACCCCAAGCCAAGCGCGGAAAUUGUGCGCCGCAAUCUCUUAAGACCGGCGACAAAUAUA
..(((((((.((.(((((((((.((.(..(((...--.)))..((((..(((.....)))..))))..))).)).)))))))....)))))))))............(....)....... ( -42.60)
>DroSim_CAF1 122556 118 + 1
UCUUGCGGUUGCUUUUCCGCCCCGGAAAAUCUCCC--GGGAAAGGGGGCAGGGGCCACCUGACCCCAAGCCAAGCGCGGAAAUUGUGCGCCGCAAUCUCUUAAGACCGGCGACAAAUAUA
..(((((((.((.((((((((((((........))--)))...((((.((((.....)))).)))).........)))))))....)))))))))............(....)....... ( -48.60)
>DroEre_CAF1 107828 106 + 1
UCUUGCGGUUGCUUUUCCGC--CGGAAAAUCUCGC--GGGAAAGCGGGC---------CUGACCCCA-ACCAAGCGCGGAAAUUGUGCGCCGCAAUCUCUUAAGACCGGCGACAAAUAUA
(((.(((.((((((((((((--.((.....)).))--))))))))(((.---------.....))).-...)).))))))..((((.(((((...(((....))).)))))))))..... ( -39.90)
>DroYak_CAF1 110318 118 + 1
UCUUGCGGUUGCUUUUCCGCCCCGGAAAAUCUCCC--GGGAAGGCGGGCAGGGGCCACAUGACCCCAAACCAAGCGCGGAAAUUGUGCGCCGCAAUCUCUUAAGACCGGCGACAAAUAUA
..(((((((.((.((((((((((((........))--)))...((((...((((.(....).))))...))..)))))))))....)))))))))............(....)....... ( -43.30)
>consensus
UCUUGCGGUUGCUUUUCCGCCCCGGAAAAUCUCCC__GGGAAAGCGGGCAGGGGCCACCUGACCCCAAGCCAAGCGCGGAAAUUGUGCGCCGCAAUCUCUUAAGACCGGCGACAAAUAUA
(((.(((.((((((((((.....(((.....)))...))))))).(((((((.....)))).))).....))).))))))..((((.(((((...(((....))).)))))))))..... (-32.29 = -33.26 +   0.97)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,149,528 – 17,149,647
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.16
Mean single sequence MFE -47.98
Consensus MFE -37.07
Energy contribution -38.64
Covariance contribution 1.57
Combinations/Pair 1.05
Mean z-score -2.09
Structure conservation index 0.77
SVM decision value 1.02
SVM RNA-class probability 0.901067
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17149528 119 - 22407834
UAUAUUUGUCGCCGGUCUUAAGAGAUUGCGGCGCACAAUUUCCGCGCUUGGCUUGGGGUCAGGGUGCCCCGGCCC-CUUUCCCGUGGGAGAUUUUCCGGGGCGGAAAAGCAACCGCAAGA
.....(((((((((((((....))))..))))).))))(((((((.(((((...((((((.((....)).)))))-)(((((....)))))....)))))))))))).((....)).... ( -51.30)
>DroSec_CAF1 110356 118 - 1
UAUAUUUGUCGCCGGUCUUAAGAGAUUGCGGCGCACAAUUUCCGCGCUUGGCUUGGGGUUAGGUGGCCCCUGCCCCCUUUCCC--GAGAGAUUGUCCGAGGCGGAAAAGCAACCGCAAGA
.....(((((((((((((....))))..))))).))))(((((((.((((((((((((..(((.(((....))).))).))))--))).......)))))))))))).((....)).... ( -48.21)
>DroSim_CAF1 122556 118 - 1
UAUAUUUGUCGCCGGUCUUAAGAGAUUGCGGCGCACAAUUUCCGCGCUUGGCUUGGGGUCAGGUGGCCCCUGCCCCCUUUCCC--GGGAGAUUUUCCGGGGCGGAAAAGCAACCGCAAGA
.....(((((((((((((....))))..))))).))))(((((((....(((..((((((....)))))).)))......(((--((((....)))))))))))))).((....)).... ( -52.40)
>DroEre_CAF1 107828 106 - 1
UAUAUUUGUCGCCGGUCUUAAGAGAUUGCGGCGCACAAUUUCCGCGCUUGGU-UGGGGUCAG---------GCCCGCUUUCCC--GCGAGAUUUUCCG--GCGGAAAAGCAACCGCAAGA
.....(((((((((((((....))))..))))).)))).......((..(((-(.(((....---------.)))(((((.((--((..(.....)..--)))).))))))))))).... ( -35.80)
>DroYak_CAF1 110318 118 - 1
UAUAUUUGUCGCCGGUCUUAAGAGAUUGCGGCGCACAAUUUCCGCGCUUGGUUUGGGGUCAUGUGGCCCCUGCCCGCCUUCCC--GGGAGAUUUUCCGGGGCGGAAAAGCAACCGCAAGA
.....(((((((((((((....))))..))))).))))(((((((((..(((..((((((....)))))).))).))...(((--((((....)))))))))))))).((....)).... ( -52.20)
>consensus
UAUAUUUGUCGCCGGUCUUAAGAGAUUGCGGCGCACAAUUUCCGCGCUUGGCUUGGGGUCAGGUGGCCCCUGCCCCCUUUCCC__GGGAGAUUUUCCGGGGCGGAAAAGCAACCGCAAGA
.....(((((((((((((....))))..))))).))))(((((((.(((((....(((.((((.....)))))))..(((((....)))))....)))))))))))).((....)).... (-37.07 = -38.64 +   1.57)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,149,568 – 17,149,687
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.22
Mean single sequence MFE -41.66
Consensus MFE -34.54
Energy contribution -35.34
Covariance contribution 0.80
Combinations/Pair 1.06
Mean z-score -1.62
Structure conservation index 0.83
SVM decision value 0.67
SVM RNA-class probability 0.816335
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17149568 119 - 22407834
CCGCCCCAAAAUCCCAAACCUCCUCCGAUGCCAGGCCAGGUAUAUUUGUCGCCGGUCUUAAGAGAUUGCGGCGCACAAUUUCCGCGCUUGGCUUGGGGUCAGGGUGCCCCGGCCC-CUUU
..(((((((.(((.............)))(((((((..((.....(((((((((((((....))))..))))).))))...))..)))))))))))))).((((.((....))))-)).. ( -46.12)
>DroSec_CAF1 110394 120 - 1
CCGCCCCAAAAUCCCAGACCUCCUCCAAUGCCAGGCCAGGUAUAUUUGUCGCCGGUCUUAAGAGAUUGCGGCGCACAAUUUCCGCGCUUGGCUUGGGGUUAGGUGGCCCCUGCCCCCUUU
..(((((((.......((.....))....(((((((..((.....(((((((((((((....))))..))))).))))...))..)))))))))))))).(((.(((....))).))).. ( -43.80)
>DroSim_CAF1 122594 120 - 1
CCGCCCCAAAAUCCCAGACCUCCUCCAAUGCCAGGCCAGGUAUAUUUGUCGCCGGUCUUAAGAGAUUGCGGCGCACAAUUUCCGCGCUUGGCUUGGGGUCAGGUGGCCCCUGCCCCCUUU
................((((....((((.(((((((..((.....(((((((((((((....))))..))))).))))...))..)))))))))))))))(((.(((....))).))).. ( -44.40)
>DroEre_CAF1 107864 107 - 1
CCCGCUGCAAAUCCCAAACCA---CCAAUGCCAGGCCAGGUAUAUUUGUCGCCGGUCUUAAGAGAUUGCGGCGCACAAUUUCCGCGCUUGGU-UGGGGUCAG---------GCCCGCUUU
...((.((..((((((.....---.....(((((((..((.....(((((((((((((....))))..))))).))))...))..)))))))-))))))...---------))..))... ( -35.90)
>DroYak_CAF1 110356 117 - 1
CCGCCCCCAAAUCCCAAACCU---CCAAUGCCAGGCCAGGUAUAUUUGUCGCCGGUCUUAAGAGAUUGCGGCGCACAAUUUCCGCGCUUGGUUUGGGGUCAUGUGGCCCCUGCCCGCCUU
..((.................---.....(((((((..((.....(((((((((((((....))))..))))).))))...))..)))))))..((((((....)))))).....))... ( -38.10)
>consensus
CCGCCCCAAAAUCCCAAACCUCCUCCAAUGCCAGGCCAGGUAUAUUUGUCGCCGGUCUUAAGAGAUUGCGGCGCACAAUUUCCGCGCUUGGCUUGGGGUCAGGUGGCCCCUGCCCCCUUU
..(((.(...(((((((............(((((((..((.....(((((((((((((....))))..))))).))))...))..))))))))))))))...).)))............. (-34.54 = -35.34 +   0.80)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:45 2006