Locus 5485

Sequence ID	X_DroMel_CAF1
Location	14,248,813 – 14,248,944
Length	131
Max. P	0.628675

overview

Window 6

Location	14,248,813 – 14,248,910
Length	97
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	91.32
Mean single sequence MFE	-28.04
Consensus MFE	-24.38
Energy contribution	-24.70
Covariance contribution	0.32
Combinations/Pair	1.08
Mean z-score	-1.23
Structure conservation index	0.87
SVM decision value	0.06
SVM RNA-class probability	0.561646
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14248813 97 + 22224390
CGCUUUCGUUGCGCUGCCAACUCAAUUAAAGUGUCCCCACGGACACGGAGUAGUAGCAGUUU--------UUGGCAGUUUGGCAUAUAUGCGCACACACAGGCAC
.((((..((((((((((((((((.((((..((((((....))))))....)))).).)))..--------.)))))))...(((....)))))).))..)))).. ( -32.10)
>DroSec_CAF1 157000 97 + 1
CGCUUUCGUUUCGCUGCCAACUCAAUUAAAGUGUCCCCACGGACACGGAGUAGUAGCAGUUU--------UUGGCAGUUUGGCAUUUAUACGCACACACAGGCAC
.((((.......(((((((((((.((((..((((((....))))))....)))).).)))..--------.))))))).((((........)).))...)))).. ( -26.80)
>DroSim_CAF1 138338 97 + 1
CGCUUUCGUUUCGCUGCCAACUCAAUUAAAGUGUCCCCACGGACACGGAGUAGUAGCAGUUU--------UUGGCAGUUUGGCAUAUAUACGCACACACAGGCAC
.((((.......(((((((((((.((((..((((((....))))))....)))).).)))..--------.))))))).((((........)).))...)))).. ( -26.80)
>DroEre_CAF1 144127 105 + 1
CGCUUUCGUUUCGCUGCCAACUCAAUUAAAGUGUCCCCACGGACACGGAGUAGCAGCAGUUUUCCUUUUUUCGCCAGUUUGGCAUAUGUACGCACACACCAGCAC
.(((........(((((..((((.......((((((....)))))).)))).)))))...............(((.....))).................))).. ( -28.90)
>DroYak_CAF1 149159 96 + 1
UGCUUUCGUUGCGCUGCCAACUCAAUUAAAGUGUCCCCACGGACAGGGAGUAGUAGCAGUUU--------UUGGCAGUUUGGCAUAUAUGCGCACACACAUGCA-
.((....((((((((((((((((.((((...(((((....))))).....)))).).)))..--------.)))))))...(((....)))))).))....)).- ( -25.60)
>consensus
CGCUUUCGUUUCGCUGCCAACUCAAUUAAAGUGUCCCCACGGACACGGAGUAGUAGCAGUUU________UUGGCAGUUUGGCAUAUAUACGCACACACAGGCAC
.((((.......(((((..((((.......((((((....)))))).)))).)))))...................((.((((........)).)).)))))).. (-24.38 = -24.70 +   0.32)

alignment

secondary structure

dotplot

Window 7

Location	14,248,849 – 14,248,944
Length	95
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	73.56
Mean single sequence MFE	-32.14
Consensus MFE	-10.94
Energy contribution	-14.38
Covariance contribution	3.44
Combinations/Pair	1.20
Mean z-score	-1.76
Structure conservation index	0.34
SVM decision value	0.20
SVM RNA-class probability	0.628675
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14248849 95 - 22224390
GCAUGUGGCGUAUGGCGUAUGGCGUAUGGCA------UAUGUGCCUGUGUGUGCGCAUAUAUGCCAAACUGCCAA--------AAACUGCUACUACUCCGUGUCCGUGG
(.(..(((.(((((((((.((((((.(((((------((((((((.......).)))))))))))).)).)))).--------..)).)))).))).)))..).).... ( -37.20)
>DroSec_CAF1 157036 90 - 1
-----------GUGGCGUAUGGCGUAUGGCAUAUAUGUAUGUGCCUGUGUGUGCGUAUAAAUGCCAAACUGCCAA--------AAACUGCUACUACUCCGUGUCCGUGG
-----------(((((((.((((((.(((((((((((((..((....))..))))))))..))))).)).)))).--------..)).)))))................ ( -29.30)
>DroSim_CAF1 138374 101 - 1
GCAUGUGGCAUGUGGCGUAUGGCGUAUGGCAUAUAUGUAUGUGCCUGUGUGUGCGUAUAUAUGCCAAACUGCCAA--------AAACUGCUACUACUCCGUGUCCGUGG
.((((.((((((((((((.((((((.((((((((..(((((..(......)..))))))))))))).)).)))).--------..)).)))))......))))))))). ( -38.20)
>DroEre_CAF1 144163 102 - 1
GCAUGCGGCAUGUGGCUCGUGGCGUAU-------GUGUUGGUGCUGGUGUGUGCGUACAUAUGCCAAACUGGCGAAAAAAGGAAAACUGCUGCUACUCCGUGUCCGUGG
.((((.((((((..(...(..((....-------.(((..((..(((((((((....))))))))).))..))).....((.....))))..)..)..)))))))))). ( -35.40)
>DroYak_CAF1 149195 74 - 1
GCAUGCGGC--------------GUAU-------G------UGCAUGUGUGUGCGCAUAUAUGCCAAACUGCCAA--------AAACUGCUACUACUCCCUGUCCGUGG
......(((--------------((.(-------(------.(((((((((....))))))))))).)).)))..--------......((((.((.....))..)))) ( -20.60)
>consensus
GCAUGCGGC_UGUGGCGUAUGGCGUAUGGCA___AUGUAUGUGCCUGUGUGUGCGUAUAUAUGCCAAACUGCCAA________AAACUGCUACUACUCCGUGUCCGUGG
......((((..(((((((((((((((.......................)))))).)))))))))...))))................((((.((.....))..)))) (-10.94 = -14.38 +   3.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:03 2006