Locus 923

Sequence ID	3L_DroMel_CAF1
Location	2,783,588 – 2,783,692
Length	104
Max. P	0.988639

overview

Window 0

Location	2,783,588 – 2,783,692
Length	104
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	87.46
Mean single sequence MFE	-23.79
Consensus MFE	-19.26
Energy contribution	-19.30
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-2.51
Structure conservation index	0.81
SVM decision value	2.13
SVM RNA-class probability	0.988639
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2783588 104 + 23771897
CCAUUUGCUCUAACGGCAAAUGCAAUUUCUAUGAUUGCAUCCAGGCAUCUCGCCUGCUCGCCUGCAUUUUCCAUU-------UUCCAUU-------UUCCUGGCCCUGGUUUUUCGGU
((...(((......(((..((((((((.....)))))))).(((((.....)))))...))).)))....(((..-------..(((..-------....)))...)))......)). ( -24.80)
>DroSec_CAF1 28956 109 + 1
CCAUUUGCUCUAACGGCAAAUGCAAUUUCUAUUAUUGCAUCCAGGCAUCUCG--UGCUCGCCUGCAUUUUCCAUUUUCCAUUUUCCAUU-------UUCCUGGCCCUGGUUUUUCGGU
((((((((.(....)))))))(((((.......)))))..(((((......(--(((......)))).................(((..-------....))).)))))......)). ( -23.00)
>DroSim_CAF1 18404 102 + 1
CCAUUUGCUCUAACGGCAAAUGCAAUUUCUAUGAUUGCAUCCAGGCAUCUCG--UGCUCGCCUGCAUUUUCCAUU-------UUCCAUU-------UUCCUGGCCCUGGUUUUUCGGU
((((((((.(....)))))))((((((.....))))))..(((((......(--(((......))))........-------..(((..-------....))).)))))......)). ( -24.60)
>DroEre_CAF1 30549 116 + 1
CCAUUUGCUCUAACGGCAAAUGCAAUUUCUAUGAUUGCAUCCAGGCAUCUCG--UGCUCGCCUGCAUUUCCCAUUUUCCAUUUUCCAUUUUCCCUUUGCCUGGCCCUGGUUUUUCGUU
..((((((.(....)))))))((((((.....))))))..((((((((...)--)))..(((.(((..............................)))..))).))))......... ( -24.41)
>DroYak_CAF1 29682 109 + 1
CCAUUUGCUCUAACGGCAAAUGCAAUUUCUAUGAUUGCAUCCAGGCAUCUCG--UGCCCGCCUGCAUU-------UUCCAUUUUCCAUUUUCCCUUUUCCUGGCUCUGGUUUUUCGGU
((((((((.(....)))))))((((((.....))))))..((((((((...)--)))).(((......-------..........................)))..)))......)). ( -22.15)
>consensus
CCAUUUGCUCUAACGGCAAAUGCAAUUUCUAUGAUUGCAUCCAGGCAUCUCG__UGCUCGCCUGCAUUUUCCAUUUUCCAUUUUCCAUU_______UUCCUGGCCCUGGUUUUUCGGU
..(((((((.....)))))))((((((.....))))))..(((((.........(((......)))..................(((.............))).)))))......... (-19.26 = -19.30 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	2,783,588 – 2,783,692
Length	104
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	87.46
Mean single sequence MFE	-26.46
Consensus MFE	-20.07
Energy contribution	-20.07
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.06
Structure conservation index	0.76
SVM decision value	0.88
SVM RNA-class probability	0.873152
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2783588 104 - 23771897
ACCGAAAAACCAGGGCCAGGAA-------AAUGGAA-------AAUGGAAAAUGCAGGCGAGCAGGCGAGAUGCCUGGAUGCAAUCAUAGAAAUUGCAUUUGCCGUUAGAGCAAAUGG
.(((.....(((...(((....-------..)))..-------..)))....(((.(((((.(((((.....))))).(((((((.......))))))))))))......)))..))) ( -28.80)
>DroSec_CAF1 28956 109 - 1
ACCGAAAAACCAGGGCCAGGAA-------AAUGGAAAAUGGAAAAUGGAAAAUGCAGGCGAGCA--CGAGAUGCCUGGAUGCAAUAAUAGAAAUUGCAUUUGCCGUUAGAGCAAAUGG
.(((.....(((...(((....-------..)))....)))..(((((......((((((..(.--...).))))))((((((((.......))))))))..)))))........))) ( -26.20)
>DroSim_CAF1 18404 102 - 1
ACCGAAAAACCAGGGCCAGGAA-------AAUGGAA-------AAUGGAAAAUGCAGGCGAGCA--CGAGAUGCCUGGAUGCAAUCAUAGAAAUUGCAUUUGCCGUUAGAGCAAAUGG
.((......(((...(((....-------..)))..-------..)))...((.((((((..(.--...).)))))).))(((((.......)))))(((((((....).)))))))) ( -23.90)
>DroEre_CAF1 30549 116 - 1
AACGAAAAACCAGGGCCAGGCAAAGGGAAAAUGGAAAAUGGAAAAUGGGAAAUGCAGGCGAGCA--CGAGAUGCCUGGAUGCAAUCAUAGAAAUUGCAUUUGCCGUUAGAGCAAAUGG
.........(((...(((.............)))....)))...((((...((.((((((..(.--...).)))))).))....))))........((((((((....).))))))). ( -24.82)
>DroYak_CAF1 29682 109 - 1
ACCGAAAAACCAGAGCCAGGAAAAGGGAAAAUGGAAAAUGGAA-------AAUGCAGGCGGGCA--CGAGAUGCCUGGAUGCAAUCAUAGAAAUUGCAUUUGCCGUUAGAGCAAAUGG
.(((.....(((...((........))....)))....)))..-------..((((..((((((--.....))))))..)))).............((((((((....).))))))). ( -28.60)
>consensus
ACCGAAAAACCAGGGCCAGGAA_______AAUGGAAAAUGGAAAAUGGAAAAUGCAGGCGAGCA__CGAGAUGCCUGGAUGCAAUCAUAGAAAUUGCAUUUGCCGUUAGAGCAAAUGG
.........(((..((.............(((((....................((((((..(....)...))))))((((((((.......))))))))..)))))...))...))) (-20.07 = -20.07 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:32 2006