Locus 4000

Sequence ID 3R_DroMel_CAF1
Location 10,896,757 – 10,896,853
Length 96
Max. P 0.500000
window6412

overview

Window 2

Location 10,896,757 – 10,896,853
Length 96
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 79.91
Mean single sequence MFE -17.78
Consensus MFE -12.21
Energy contribution -11.43
Covariance contribution -0.77
Combinations/Pair 1.33
Mean z-score -1.13
Structure conservation index 0.69
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10896757 96 + 27905053
AAAAAAAAAAAGAAAA--CC---AAUUGGAAUGGGAAAUGAGCUUGGGCUGUGUGGAUAAGGCCAAAAC-UGUAGCCGGAAUUAAGGCAAAGGCAAUGCCAU
................--((---....)).((((...((..((((.((((..........)))).....-....(((........)))..)))).)).)))) ( -16.40)
>DroSec_CAF1 161941 85 + 1
AAA-----------AA--CC---AAUUGGAAUGGGAAAUGAGCUUGGGCUGUGUGGAUAAGGCCAAAAC-UGUAGCCGGAAUUAAGGCAAAGGCAAUGCCAU
...-----------..--((---....)).((((...((..((((.((((..........)))).....-....(((........)))..)))).)).)))) ( -16.40)
>DroSim_CAF1 170031 85 + 1
AAA-----------AA--CC---AAUUUGAAUGGGAAAUGAGCUUGGGCUGUGUGGAUAAGGCCAAAAC-UGUAGCCGGAAUUAAGGCAAAGGCAAUGCCAU
...-----------..--((---(.......)))....(((..((.(((((..(((......)))....-..))))).)).))).((((.......)))).. ( -16.30)
>DroEre_CAF1 165095 81 + 1
AAA---------------GC---AAUUGGAAUGGGAAAUGAGCUUGGCCUG--UGGAUAAAGCCAAAAC-UGUAGCCGGAAUUAAGGCAGAGGAAAAGCCAU
...---------------..---..............(((.((((..(((.--(((......)))....-....(((........)))..)))..))))))) ( -17.60)
>DroYak_CAF1 174193 85 + 1
AAA-----------AAAUGC---AAUUGGAAUGGGAAAUGAGCUUGGCCUG--UGGAUAAAGCCAAAAC-UGUAGCCGGAAUUAAGGCGGAGGCAGAGCCAU
...-----------......---..............(((.((((.((((.--(((......)))....-....(((........)))..)))).))))))) ( -20.00)
>DroAna_CAF1 165342 82 + 1
AAA-----------AG--CCAGUGAUUGGAAUGGAAAAUGAGCUUGGCUUG--UGGCUGGGGCCAGAAUUUGUUGCUGG-AUUAUGGCUA----AAAACUAU
...-----------((--(((.((((((.((..((...((..((..((...--..))..))..))...))..)).)..)-))))))))).----........ ( -20.00)
>consensus
AAA___________AA__CC___AAUUGGAAUGGGAAAUGAGCUUGGCCUG__UGGAUAAGGCCAAAAC_UGUAGCCGGAAUUAAGGCAAAGGCAAAGCCAU
..............................((((....((.((((...((....))...)))))).........(((........)))..........)))) (-12.21 = -11.43 +  -0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:33 2006