Locus 3903

Sequence ID	2L_DroMel_CAF1
Location	11,410,026 – 11,410,209
Length	183
Max. P	0.677768

overview

Window 1

Location	11,410,026 – 11,410,116
Length	90
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	83.89
Mean single sequence MFE	-22.53
Consensus MFE	-17.54
Energy contribution	-17.90
Covariance contribution	0.36
Combinations/Pair	1.09
Mean z-score	-1.89
Structure conservation index	0.78
SVM decision value	0.30
SVM RNA-class probability	0.677768
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11410026 90 - 22407834
AAUAUUGCUGGUCGCCAUAAAAGCCGCAUUGUGAAAAUGAAAUUUUCAUUUAUGCGUCCACUU-----CGUC-CACUUAAUCAAAGGCCAGUUGCA--
......(((((((((.......))(((((.((((((((...))))))))..))))).......-----....-............)))))))....-- ( -21.40)
>DroPse_CAF1 156484 88 - 1
AAUAUUGCUGGCCACAAUAAAAACCGCAUUGUGAAAAUGAAAUUUUCAUUUAUGCGCUCGUUCUGCAGCGCAGCUGUUGAUCAAUGCC----------
.........(((............(((((.((((((((...))))))))..)))))...(.((.(((((...))))).)).)...)))---------- ( -20.10)
>DroSec_CAF1 127414 90 - 1
AAUAUUGCUGGUCGCCAUAAAAGCCGCAUUGUGAAAAUGAAAUUUUCAUUUAUGCGUUCACUU-----CGUC-CACUUAAUCAAAGGCCAGUUGCA--
......(((((((((.......))(((((.((((((((...))))))))..))))).......-----....-............)))))))....-- ( -21.40)
>DroSim_CAF1 134191 90 - 1
AAUAUUGCUGGUCGCCAUAAAGGCCGCAUUGUGAAAAUGAAAUUUUCAUUUAUGCGUUCACUU-----CGUC-CACUUAAUCAAAGGCCAGUUGCA--
......((((((((((.....)))(((((.((((((((...))))))))..))))).......-----....-............)))))))....-- ( -25.50)
>DroEre_CAF1 134924 90 - 1
AAUAUUGCUGGUCGCCAUGAAAGCCGCAUUGUGAAAAUGAAAUUUUCAUUUAUGCGU-CGCUC-----CGCAGUUGUUAAUCAAAGGCCAGUUGCA--
......(((((((((...((..(.(((((.((((((((...))))))))..))))).-)..))-----.))..(((.....))).)))))))....-- ( -24.10)
>DroYak_CAF1 131886 93 - 1
AAUAUUGCUGGUCGCCAUGAAAGCUGCAUUGUGAAAAUGAAAUUUUCAUUUAUGCCUCCGCUC-----CGCAGUUGUUAAUCAAAGGCCAGUUGCACU
......(((((((....(((.((((((...((((((((...))))))))....((....))..-----.)))))).....)))..)))))))...... ( -22.70)
>consensus
AAUAUUGCUGGUCGCCAUAAAAGCCGCAUUGUGAAAAUGAAAUUUUCAUUUAUGCGUUCACUC_____CGCA_CACUUAAUCAAAGGCCAGUUGCA__
......(((((((...........(((((.((((((((...))))))))..)))))...((........))..............)))))))...... (-17.54 = -17.90 +   0.36)

alignment

secondary structure

dotplot

Window 2

Location	11,410,116 – 11,410,209
Length	93
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	93.38
Mean single sequence MFE	-33.35
Consensus MFE	-27.75
Energy contribution	-28.00
Covariance contribution	0.25
Combinations/Pair	1.11
Mean z-score	-1.76
Structure conservation index	0.83
SVM decision value	0.05
SVM RNA-class probability	0.559221
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11410116 93 - 22407834
UGGCAGAUGUGGGACUCA--CGGCUCAUAAAUAUGCAUUUCAGAUGCGGCAAACUGGCUCCAUUGUGCCGCCGUGUUGGCCGCAUAUUAGUGGCA
..((.((((((((...((--((((..........(((((...)))))((((...((....))...))))))))))....)).))))))....)). ( -32.60)
>DroSec_CAF1 127504 93 - 1
UGGCAGAUGUGGGACUCA--CGGCUCAUAAAUAUGCAUUUCAGAUGCGGCAAACUGGCUCCAUUGUGCCGCCGUGUUGGCCGCAUAUUAGUGGCA
..((.((((((((...((--((((..........(((((...)))))((((...((....))...))))))))))....)).))))))....)). ( -32.60)
>DroSim_CAF1 134281 93 - 1
UGGCAGAUGUGGGACUCA--CGGCUCAUAAAUAUGCAUUUCAGAUGCGGCAAACUGGCUCCAUUGUGCCGCCGUGUUGGCCGCAUAUUAGUGGCA
..((.((((((((...((--((((..........(((((...)))))((((...((....))...))))))))))....)).))))))....)). ( -32.60)
>DroEre_CAF1 135014 93 - 1
UGCCAGAUGUGGGACCCA--CGGCUCAUAAAUAUGCAUUUCAGAUGCGGCAGGCCGGCUCCAUUGUGCCGCCGUGUUGGCCGCAUAUUAGUGGCA
.((((((((((((.((((--((((..........(((((...)))))((....))(((........)))))))))..)))).))))))..)))). ( -37.00)
>DroYak_CAF1 131979 93 - 1
UGGCAGAUGUGGGACUCA--CGGCUCAUAAAUAUGCAUUUCAGAUGCGGCAAACUGGCUCCAUUGUGCCGCCGUGUUGGCCGCAUAUUAGUGGCA
..((.((((((((...((--((((..........(((((...)))))((((...((....))...))))))))))....)).))))))....)). ( -32.60)
>DroAna_CAF1 114549 95 - 1
UGGCACUGAUGCCACUCAACGGGCUCAUAAAUAUGCAUUUCAGAUGCGGCUCUUUGGCUCCAUUGUGCCGUCGUGUUGGCCGCAUAUUAGUGGCA
(((((....)))))..((((((((..........(((((...)))))(((.(..((....))..).)))))).)))))(((((......))))). ( -32.70)
>consensus
UGGCAGAUGUGGGACUCA__CGGCUCAUAAAUAUGCAUUUCAGAUGCGGCAAACUGGCUCCAUUGUGCCGCCGUGUUGGCCGCAUAUUAGUGGCA
..(((..((((((.((.....))))))))....)))......((((((((.....(((........))))))))))).(((((......))))). (-27.75 = -28.00 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:20 2006