Locus 6054

Sequence ID	2L_DroMel_CAF1
Location	17,044,731 – 17,044,848
Length	117
Max. P	0.992292

overview

Window 0

Location	17,044,731 – 17,044,848
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.02
Mean single sequence MFE	-28.08
Consensus MFE	-24.30
Energy contribution	-24.78
Covariance contribution	0.48
Combinations/Pair	1.03
Mean z-score	-2.18
Structure conservation index	0.87
SVM decision value	2.32
SVM RNA-class probability	0.992292
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17044731 117 + 22407834
GAAUACCGCAAAUUGACAAAUAUUUUCGUUUGGCCAACAAGAAGAAGACCAAAAGCA---CCCAGCACUCUAAUUCAAUCUGGCUGGUGUAUUUUAAUUGAUUUGCGCUAAAAUUUAUUG
...((.(((((((..(......(((((.((((.....))))..)))))......(((---((.(((.(.............))))))))).......)..))))))).)).......... ( -22.72)
>DroSec_CAF1 8865 117 + 1
GAAUACCGCAAAUUGACAAAUAUUUUCGUUUGGCCAACAAGAAGAAGGCCAAAAGCA---CCCAGCACUCUAAUUCAAUCUGGCUGGUGUAUUUUAAUUGAUUUGCGCUAAAAUUUAUUG
...((.(((((((..(............(((((((..(.....)..))))))).(((---((.(((.(.............))))))))).......)..))))))).)).......... ( -29.12)
>DroSim_CAF1 2512 120 + 1
GAAUACCGCAAAUUGACAAAUAUUUUCGUUUGGCCAACAAGAAGAAGGCCAAAAGCACCACCCAGCACUCUAAUUCAAUCUGGCUGGUGUAUUUUAAUUGAUUUGCGCUAAAAUUUAUUG
...((.(((((((..(............(((((((..(.....)..))))))).((((((.((((..............)))).)))))).......)..))))))).)).......... ( -32.74)
>DroEre_CAF1 8669 116 + 1
GCAUACCGCAAAUGGACAAAUAUUUUCGUUUGGCCAACAAGAAGAAGGCCAAAAGCA---CCCAGCACUCUAAUUCAAUCUGGCUGGUGUAUUUUAAUUGAUUUGCGCUAA-AUUUAUUG
...((.(((((((.((............(((((((..(.....)..))))))).(((---((.(((.(.............))))))))).......)).))))))).)).-........ ( -27.92)
>DroYak_CAF1 6415 116 + 1
GAAUACCGCAAAUCGACAAAUAUUUUUGUUUGGCCAACAAAAAGAAGACCAAAAGCA---CCCAGCACUCUAAUUCAAUCUGGCUGGGGUAUUUUAAUUGAUUUGCGCUAA-AUUUAUUG
...((.((((((((((......((((((((.....)))))))).......((((...---((((((.(.............)))))))...))))..)))))))))).)).-........ ( -27.92)
>consensus
GAAUACCGCAAAUUGACAAAUAUUUUCGUUUGGCCAACAAGAAGAAGGCCAAAAGCA___CCCAGCACUCUAAUUCAAUCUGGCUGGUGUAUUUUAAUUGAUUUGCGCUAAAAUUUAUUG
...((.((((((((((.((((((.....(((((((..(.....)..)))))))........(((((.(.............)))))).))))))...)))))))))).)).......... (-24.30 = -24.78 +   0.48)

alignment

secondary structure

dotplot

Window 1

Location	17,044,731 – 17,044,848
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.02
Mean single sequence MFE	-28.30
Consensus MFE	-25.44
Energy contribution	-25.20
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-1.59
Structure conservation index	0.90
SVM decision value	1.36
SVM RNA-class probability	0.946297
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17044731 117 - 22407834
CAAUAAAUUUUAGCGCAAAUCAAUUAAAAUACACCAGCCAGAUUGAAUUAGAGUGCUGGG---UGCUUUUGGUCUUCUUCUUGUUGGCCAAACGAAAAUAUUUGUCAAUUUGCGGUAUUC
..........((.((((((((((.((...(((.((((((.............).))))))---))..(((((((..(.....)..)))))))......)).)))...))))))).))... ( -24.12)
>DroSec_CAF1 8865 117 - 1
CAAUAAAUUUUAGCGCAAAUCAAUUAAAAUACACCAGCCAGAUUGAAUUAGAGUGCUGGG---UGCUUUUGGCCUUCUUCUUGUUGGCCAAACGAAAAUAUUUGUCAAUUUGCGGUAUUC
..........((.((((((((((.((...(((.((((((.............).))))))---))..(((((((..(.....)..)))))))......)).)))...))))))).))... ( -26.82)
>DroSim_CAF1 2512 120 - 1
CAAUAAAUUUUAGCGCAAAUCAAUUAAAAUACACCAGCCAGAUUGAAUUAGAGUGCUGGGUGGUGCUUUUGGCCUUCUUCUUGUUGGCCAAACGAAAAUAUUUGUCAAUUUGCGGUAUUC
..........((.(((((((......((((((((((.((((.((......))...)))).)))))..(((((((..(.....)..)))))))......)))))....))))))).))... ( -34.00)
>DroEre_CAF1 8669 116 - 1
CAAUAAAU-UUAGCGCAAAUCAAUUAAAAUACACCAGCCAGAUUGAAUUAGAGUGCUGGG---UGCUUUUGGCCUUCUUCUUGUUGGCCAAACGAAAAUAUUUGUCCAUUUGCGGUAUGC
........-.((.((((((((((.((...(((.((((((.............).))))))---))..(((((((..(.....)..)))))))......)).)))...))))))).))... ( -26.82)
>DroYak_CAF1 6415 116 - 1
CAAUAAAU-UUAGCGCAAAUCAAUUAAAAUACCCCAGCCAGAUUGAAUUAGAGUGCUGGG---UGCUUUUGGUCUUCUUUUUGUUGGCCAAACAAAAAUAUUUGUCGAUUUGCGGUAUUC
........-.((.((((((((...........(((((((.............).))))))---....(((((((..(.....)..)))))))..............)))))))).))... ( -29.72)
>consensus
CAAUAAAUUUUAGCGCAAAUCAAUUAAAAUACACCAGCCAGAUUGAAUUAGAGUGCUGGG___UGCUUUUGGCCUUCUUCUUGUUGGCCAAACGAAAAUAUUUGUCAAUUUGCGGUAUUC
..........((.(((((((......(((((..((((((.............).)))))........(((((((..(.....)..)))))))......)))))....))))))).))... (-25.44 = -25.20 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:50 2006