Locus 6678

Sequence ID	X_DroMel_CAF1
Location	16,682,599 – 16,682,736
Length	137
Max. P	0.938828

overview

Window 4

Location	16,682,599 – 16,682,717
Length	118
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	92.37
Mean single sequence MFE	-47.97
Consensus MFE	-41.96
Energy contribution	-43.15
Covariance contribution	1.19
Combinations/Pair	1.06
Mean z-score	-2.09
Structure conservation index	0.87
SVM decision value	1.27
SVM RNA-class probability	0.938828
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16682599 118 + 22224390
GAGUUGUGGAUCUCGAGAUGCUCGGCGGAUUACUAAAUCUCGUCGUGGCUACCGUGCUGGUUAAUCUCGGCCUAAUCGAUGGCUUGGCCAGUCGGUAGCUGCUGCUCGCUUUGCUACG
.....((((....((((......((((((((....)))).))))(..(((((((.((((((((.....((((........)))))))))))))))))))..)..)))).....)))). ( -48.50)
>DroSec_CAF1 7581 118 + 1
GAGUUGUGGAUCUCGAGAUGCUCGGCGGAUUACUAAAUCUCGUCGUGGCUACCGUGCUUGUUAAUCUCGGCCUAAUCGAGGGCUUGGCCAGACGGUAGCUGCUGCUCGCUUUGCUCUU
((((.(((((((....)))((..((((((((....)))).))))(..((((((((.((.(((((((((((.....))))))..))))).))))))))))..).))))))...)))).. ( -43.90)
>DroEre_CAF1 7732 118 + 1
GAGUUGUGGAUCUCGAGAUGCUCGGCGGAUUACUAAAUCUCGUAGUGGCUACCGUGCUGCUUAGUCUCGGCCGUAUCGAGGGCUUGGCCAGUCGGUAGCUGCUGCUCGCCUUGCUCCU
((((.(.(.(((....))).).)((((((((....))))..((((..(((((((.((((((.((((((((.....)))).)))).)).)))))))))))..)))).))))..)))).. ( -49.30)
>DroYak_CAF1 16146 118 + 1
GUGUUGUGGAUCUCGAGAUGCUCGGCGGAUUGCUAAAUCGCGUGGUGGCUACCGUGCUGGUUAAUCUCGGCCUGCUCGAUGGCUUGGCCAGUCGGUAGCUGCUGCUCGCCUUGCUCCU
.......(((((....)).((..((((((((....))))..(..(..(((((((.((((((((.....((((........)))))))))))))))))))..)..).))))..))))). ( -50.20)
>consensus
GAGUUGUGGAUCUCGAGAUGCUCGGCGGAUUACUAAAUCUCGUCGUGGCUACCGUGCUGGUUAAUCUCGGCCUAAUCGAGGGCUUGGCCAGUCGGUAGCUGCUGCUCGCCUUGCUCCU
(((........))).....((..((((((((....))))..((((..(((((((.((((((((.....((((........)))))))))))))))))))..)))).))))..)).... (-41.96 = -43.15 +   1.19)

alignment

secondary structure

dotplot

Window 5

Location	16,682,639 – 16,682,736
Length	97
Sequences	3
Columns	107
Reading direction	forward
Mean pairwise identity	85.13
Mean single sequence MFE	-42.13
Consensus MFE	-34.34
Energy contribution	-35.57
Covariance contribution	1.23
Combinations/Pair	1.06
Mean z-score	-2.27
Structure conservation index	0.82
SVM decision value	0.88
SVM RNA-class probability	0.873347
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16682639 97 + 22224390
CGUCGUGGCUACCGUGCUGGUUAAUCUCGGCCUAAUCGAUGGCUUGGCCAGUCGGUAGCUGCUGCUCGCUUUGCUACGCAAAGGAGUUUGCUUCGUC----------
....(..(((((((.((((((((.....((((........)))))))))))))))))))..).((((.((((((...))))))))))..........---------- ( -42.50)
>DroSec_CAF1 7621 102 + 1
CGUCGUGGCUACCGUGCUUGUUAAUCUCGGCCUAAUCGAGGGCUUGGCCAGACGGUAGCUGCUGCUCGCUUUGCUCUUCAAAGGAGUUGGCUUCGUCGUUGU-----
.((.(..((((((((.((.(((((((((((.....))))))..))))).))))))))))..).))..(((..(((((.....))))).)))...........----- ( -37.70)
>DroEre_CAF1 7772 107 + 1
CGUAGUGGCUACCGUGCUGCUUAGUCUCGGCCGUAUCGAGGGCUUGGCCAGUCGGUAGCUGCUGCUCGCCUUGCUCCUCAAAGGAGUUUGCUUCGUCGUCGUGGUGG
.((((..(((((((.((((((.((((((((.....)))).)))).)).)))))))))))..)))).((((..(((((.....)))))......((....)).)))). ( -46.20)
>consensus
CGUCGUGGCUACCGUGCUGGUUAAUCUCGGCCUAAUCGAGGGCUUGGCCAGUCGGUAGCUGCUGCUCGCUUUGCUCCUCAAAGGAGUUUGCUUCGUCGU_GU_____
.((.(..(((((((.(((((((((((((((.....))))))..))))))))))))))))..).))..((...(((((.....)))))..))................ (-34.34 = -35.57 +   1.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:49 2006