Locus 5093

Sequence ID 3R_DroMel_CAF1
Location 13,426,451 – 13,426,596
Length 145
Max. P 0.640963
window8301 window8302

overview

Window 1

Location 13,426,451 – 13,426,566
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.34
Mean single sequence MFE -28.37
Consensus MFE -16.65
Energy contribution -18.52
Covariance contribution 1.87
Combinations/Pair 1.19
Mean z-score -1.80
Structure conservation index 0.59
SVM decision value 0.16
SVM RNA-class probability 0.612506
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13426451 115 - 27905053
A-GGCGACAAGUAAUUUUACUUGGCAAAAUAAAUUGCACAAAGUCUUUU-UUUUUUGCGAUUUGUCGUGUUUAUCUCUUUUGCUGUCUGUGCC---GACUUUGUGGUGUUCGUCAUGUGU
.-(((((((.((((........((((..((((((((((.((((......-)))).))))))))))..))))........)))))))).(..((---(......)))..)..)))...... ( -27.99)
>DroPse_CAF1 52911 100 - 1
A-AGCGACAAGUAAUUUUACUUGGAAAAAUAAAUUUCACA--GUCUUCU------CUGGCUUUGUGCUGCUCAUGAGAUUUUCUCUGUGUGCCUGUGUGUGUGUGAUGG-----------
.-.....((((((....))))))............(((((--(((....------..)))...(..(.((.((((((.....))).))).))..)..)...)))))...----------- ( -20.50)
>DroSec_CAF1 52327 113 - 1
A-GGCGACAAGUAAUUUUACUUGGCAAAAUAAAUUGCACAAAGUCCUUU-UU--UUUCGAUUUGUCGUGUUUAUUUCUUUUGCUGUCUGCGCC---GACUUUGUGGUGUUCGUCAUGUGU
.-(((((((((((....))))))((((((.((((.((((.(((((....-..--....)))))...))))..)))).)))))).....(((((---(......)))))))))))...... ( -28.90)
>DroSim_CAF1 55032 114 - 1
AUCGCGACAAGUAAUUUUACUUGGCAAAAUAAAUUGCACAAAGUCCUUU-UU--UUGCGAUUUGUCGUGUUUAUUUCUUUUGCUGUCUGCGCC---GACUUUGUGGUGUUCCUCUUGUGU
..(((((((.((((........((((..((((((((((.((((....))-))--.))))))))))..))))........)))))))).(((((---(......)))))).......))). ( -29.09)
>DroEre_CAF1 52618 112 - 1
A-GGCGACAAGUAAUUUUACUUGGCAAAAUGAAUUGCACAAAGUCCUUU-UU--UUGCGAUUUGUCGUGC-CAUCUCUUUAGCUGUCUGCUCC---GGCUUUGUGGUGUUCGUCAUGUGU
.-(((((((((((....))))))(((..(..(((((((.((((....))-))--.)))))))..)..)))-((((.(...(((((.......)---))))..).)))).)))))...... ( -33.80)
>DroYak_CAF1 57346 113 - 1
A-GGCGACAAGUAAUUUUACUUGGCAAAAUGAAUUGCACAAAGUCCUUUUUU--UUGCGCUUUCUCGUGC-CAUCUCCUUUGCUUUCUGCUCC---GGCUUUAUGGUGUUCGCCAUGUGU
.-(((((.((((((.......(((((....(((..((.(((((.......))--))).)).)))...)))-))......))))))...((.((---(......))).)))))))...... ( -29.92)
>consensus
A_GGCGACAAGUAAUUUUACUUGGCAAAAUAAAUUGCACAAAGUCCUUU_UU__UUGCGAUUUGUCGUGCUCAUCUCUUUUGCUGUCUGCGCC___GACUUUGUGGUGUUCGUCAUGUGU
..(((((((((((....)))))).............(((((((((..........((((......))))............((.....))......)))))))))....)))))...... (-16.65 = -18.52 +   1.87)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,426,488 – 13,426,596
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.54
Mean single sequence MFE -21.78
Consensus MFE -12.20
Energy contribution -12.56
Covariance contribution 0.36
Combinations/Pair 1.17
Mean z-score -1.77
Structure conservation index 0.56
SVM decision value 0.22
SVM RNA-class probability 0.640963
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13426488 108 - 27905053
----AUAGCCAUGCCACAAC------AUAUCCAUCCCUCCA-GGCGACAAGUAAUUUUACUUGGCAAAAUAAAUUGCACAAAGUCUUUU-UUUUUUGCGAUUUGUCGUGUUUAUCUCUUU
----.......((((.....------...............-)))).((((((....))))))(((..((((((((((.((((......-)))).))))))))))..))).......... ( -21.45)
>DroSec_CAF1 52364 106 - 1
----AUACCCAUGCCACAAC------AUAUCCAUCCCUCCA-GGCGACAAGUAAUUUUACUUGGCAAAAUAAAUUGCACAAAGUCCUUU-UU--UUUCGAUUUGUCGUGUUUAUUUCUUU
----..........(((.((------(.(((..........-(((..((((((....))))))((((......)))).....)))....-..--....))).))).)))........... ( -16.55)
>DroSim_CAF1 55069 107 - 1
----AUACCCAUGCCACAAC------AUAUCCAUCCCUCCAUCGCGACAAGUAAUUUUACUUGGCAAAAUAAAUUGCACAAAGUCCUUU-UU--UUGCGAUUUGUCGUGUUUAUUUCUUU
----................------................(((((((((((....))))))......(((((((((.((((....))-))--.))))))))))))))........... ( -18.80)
>DroEre_CAF1 52655 105 - 1
----AUACCCAUGCCAUGUU------ACAUCAUUCCCUCCA-GGCGACAAGUAAUUUUACUUGGCAAAAUGAAUUGCACAAAGUCCUUU-UU--UUGCGAUUUGUCGUGC-CAUCUCUUU
----.......((((.((..------.............))-))))..(((((....)))))((((..(..(((((((.((((....))-))--.)))))))..)..)))-)........ ( -23.16)
>DroYak_CAF1 57383 112 - 1
----AUACCCAUGCCACGUUGCGAGUAUAUCAUUCCCUCCA-GGCGACAAGUAAUUUUACUUGGCAAAAUGAAUUGCACAAAGUCCUUUUUU--UUGCGCUUUCUCGUGC-CAUCUCCUU
----......(((.((((((((...........((((....-)).))((((((....))))))))))...(((..((.(((((.......))--))).)).))).)))).-)))...... ( -22.10)
>DroPer_CAF1 53750 105 - 1
CCCCAUGCCCAUGCUCGGCA------GGCUCUUUGGCCGGA-AGCGACAAGUAAUUUUACUUGGAAAAAUAAAUUUCACA--GUCUUCU------CUGGCUUUGUGCUGCUCAUGAGAUU
.........((((..(((((------((((....)))).((-(((..((((((....))))))((((......)))).((--(......------)))))))).)))))..))))..... ( -28.60)
>consensus
____AUACCCAUGCCACAAC______AUAUCCAUCCCUCCA_GGCGACAAGUAAUUUUACUUGGCAAAAUAAAUUGCACAAAGUCCUUU_UU__UUGCGAUUUGUCGUGCUCAUCUCUUU
...........((((...........................)))).((((((....))))))(((..((((((((((.................))))))))))..))).......... (-12.20 = -12.56 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:00 2006