Locus 7358

Sequence ID 2L_DroMel_CAF1
Location 20,504,175 – 20,504,280
Length 105
Max. P 0.616744
window11811 window11812

overview

Window 1

Location 20,504,175 – 20,504,268
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.03
Mean single sequence MFE -31.15
Consensus MFE -21.35
Energy contribution -21.02
Covariance contribution -0.33
Combinations/Pair 1.15
Mean z-score -1.13
Structure conservation index 0.69
SVM decision value 0.00
SVM RNA-class probability 0.534092
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20504175 93 + 22407834
--------AGA-------------------AAGCAGCAUGCAAUGCGGCAUUGUGCUUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGGUGGCG
--------...-------------------..((.((((((((((.(((.....))).).)))))((((((((........))))))))...)))).....((.((....))))...)). ( -23.60)
>DroPse_CAF1 60383 119 + 1
GGAGGGGGAGCUGGCGCCGG-CUCUCUGGCUCUGUGGAUGCGAUGCGGCAUUGCGCCUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGCUGGCG
....(((((((((....)))-)))))).(((..((((...(.(((((..(((((((......((..(((((((........)))))))..)))))))))..))))).)...)))).))). ( -45.70)
>DroSec_CAF1 21292 93 + 1
--------AGA-------------------AAGCAGCAUGCGCUUCGGCAUUGUGCCUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGGUGGCG
--------...-------------------..((.....))((....)).....((((((((((..(((((((........)))))))..).((((......))))...)))))).))). ( -26.50)
>DroYak_CAF1 20139 90 + 1
------------------------------AAGCAGCAUGCGAUGCGGCGUUGUGCCUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGGUGGCG
------------------------------..(((((.(((...)))..)))))((((((((((..(((((((........)))))))..).((((......))))...)))))).))). ( -26.30)
>DroAna_CAF1 12648 90 + 1
------------------------------UCUCUGGAUGCGAUGCGGCAUUGCGCCUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGCUGGCG
------------------------------...(..(...(.(((((..(((((((......((..(((((((........)))))))..)))))))))..))))).)......)..).. ( -24.80)
>DroPer_CAF1 66162 120 + 1
GGGGGGGGAGGGGGCGCGGGACGCUCUGGCUCUGUGGAUGCGAUGCGGCAUUGCGCCUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGCUGGCG
....((((..((((((.....))))))..))))((((...(.(((((..(((((((......((..(((((((........)))))))..)))))))))..))))).)...))))..... ( -40.00)
>consensus
________AG____________________AAGCAGCAUGCGAUGCGGCAUUGCGCCUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGCUGGCG
.......................................((((((...))))))(((.((((((..(((((((........)))))))..).((((......))))...)))))..))). (-21.35 = -21.02 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,504,188 – 20,504,280
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.35
Mean single sequence MFE -30.35
Consensus MFE -20.05
Energy contribution -20.13
Covariance contribution 0.08
Combinations/Pair 1.05
Mean z-score -1.36
Structure conservation index 0.66
SVM decision value 0.17
SVM RNA-class probability 0.616744
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20504188 92 + 22407834
CAAUGCGGCAUUGUGCUUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGGUGGCGUUCUCU----------------------------UUCCAC
..((((((((((((((.......))((((((((........))))))))))))))).....)))))(((((..((......))..)----------------------------)))).. ( -24.10)
>DroPse_CAF1 60422 120 + 1
CGAUGCGGCAUUGCGCCUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGCUGGCGUUCCCGCAGGGUCUGGUGCGGGGGGCCUACCCCCUGGCAG
...(((((....(((((.((((((..(((((((........)))))))..).((((......))))...)))))..)))))..)))))........(((((((((....)))))).))). ( -45.50)
>DroSec_CAF1 21305 92 + 1
CGCUUCGGCAUUGUGCCUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGGUGGCGUUCUCU----------------------------GUCCAC
.((....)).....((((((((((..(((((((........)))))))..).((((......))))...)))))).))).......----------------------------...... ( -25.00)
>DroEre_CAF1 20215 91 + 1
CGAUGCGGCAUUGUGCCUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGGUGGCGU-CUCU----------------------------GUGCAC
...((((.((..((((((((((((..(((((((........)))))))..).((((......))))...)))))).)))).-)..)----------------------------))))). ( -25.90)
>DroAna_CAF1 12658 86 + 1
CGAUGCGGCAUUGCGCCUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGCUGGCGUUCAC----------------------------------C
......((....(((((.((((((..(((((((........)))))))..).((((......))))...)))))..)))))...)----------------------------------) ( -23.20)
>DroPer_CAF1 66202 108 + 1
CGAUGCGGCAUUGCGCCUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGCUGGCGUUCCCGCAGGGUCUGGUGCGGGGGGC-UA-----------
(.(((((..(((((((......((..(((((((........)))))))..)))))))))..))))).).......((((.((((((((........))))))))))-))----------- ( -38.40)
>consensus
CGAUGCGGCAUUGCGCCUCGAUUGCGAUUGACACAAUAAAUUGUCAAUUACAGUGCAAUUACGUAUGGAAAUCGCUGGCGUUCUCU_____________________________U_CAC
(.(((((..(((((((......((..(((((((........)))))))..)))))))))..))))).).................................................... (-20.05 = -20.13 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:40 2006