Locus 5542

Sequence ID	3L_DroMel_CAF1
Location	15,218,733 – 15,218,867
Length	134
Max. P	0.934859

overview

Window 8

Location	15,218,733 – 15,218,847
Length	114
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	95.16
Mean single sequence MFE	-30.03
Consensus MFE	-25.26
Energy contribution	-26.98
Covariance contribution	1.72
Combinations/Pair	1.07
Mean z-score	-2.35
Structure conservation index	0.84
SVM decision value	1.15
SVM RNA-class probability	0.923291
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15218733 114 + 23771897
AACUAGGACAAAACUGUUUUUGGUCACAUGACUCAAAUUAGAAAUGCGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGA---GGGAAAUGAGAGGCCGG--
..((((((((....))))(((((((....))).))))))))...((.((((..((((((((....(((((....)))))....(((.......))).---))))))))..)))))).-- ( -30.70)
>DroSec_CAF1 108259 114 + 1
AACUAGGACAAAACUGUUUUUGGUCACAUGACUCAAAUUAGAAAUGCGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGA---GGGAAAUGAGAGGCUGG--
..((((((((....))))(((((((....))).))))))))......((((..((((((((....(((((....)))))....(((.......))).---))))))))..))))...-- ( -30.70)
>DroSim_CAF1 115584 114 + 1
AAAUAGGACAAAACUGUUUUUGGUCACAUGACUCAAAUUAGAAAUGCGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGA---GGGAAAUGAGAGGCUGG--
.(((((.......)))))(((((((....))).))))..........((((..((((((((....(((((....)))))....(((.......))).---))))))))..))))...-- ( -30.40)
>DroEre_CAF1 108493 114 + 1
AACUAGGACAAAACUGUUUUUGGUCACAUGACUCAAAUUAGAAAUGCGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGA---GGGAAAUGAGAGGCUGG--
..((((((((....))))(((((((....))).))))))))......((((..((((((((....(((((....)))))....(((.......))).---))))))))..))))...-- ( -30.70)
>DroYak_CAF1 112931 114 + 1
AACUAGGACAAAACUGUUUUUGGUCACAUGACUCAAAUUAGAAAUGCGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGA---GGGAAAUGAGAGGCUGG--
..((((((((....))))(((((((....))).))))))))......((((..((((((((....(((((....)))))....(((.......))).---))))))))..))))...-- ( -30.70)
>DroAna_CAF1 103305 119 + 1
AACUAGGACAAAACUGUUUUUGGUCACAUGACUCAAAUUAGAAAUGUGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGCACCGAGAGAUCCGAGUUAGAAA
((((.(((......((((...((.(((((..((......))..))))))).))))(((((.....(((((....)))))..(((((.......)))))..))))).))).))))..... ( -27.00)
>consensus
AACUAGGACAAAACUGUUUUUGGUCACAUGACUCAAAUUAGAAAUGCGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGA___GGGAAAUGAGAGGCUGG__
.............(((..(((((((....))).)))).)))......((((..((((((((....(((((....)))))....(((.......)))....))))))))..))))..... (-25.26 = -26.98 +   1.72)

alignment

secondary structure

dotplot

Window 9

Location	15,218,773 – 15,218,867
Length	94
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	80.85
Mean single sequence MFE	-26.83
Consensus MFE	-19.06
Energy contribution	-20.78
Covariance contribution	1.72
Combinations/Pair	1.10
Mean z-score	-2.66
Structure conservation index	0.71
SVM decision value	1.24
SVM RNA-class probability	0.934859
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15218773 94 + 23771897
GAAAUGCGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGA---GGGAAAUGAGAGGCCGG--------------CGAAA-------GAGCGUGAAGGAGGC-
...((((((((..((((((((....(((((....)))))....(((.......))).---))))))))..))))...--------------(....-------).)))).........- ( -28.60)
>DroSec_CAF1 108299 94 + 1
GAAAUGCGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGA---GGGAAAUGAGAGGCUGG--------------CGAAA-------GAGCGUGAAGGAGGC-
...((((((((..((((((((....(((((....)))))....(((.......))).---))))))))..))))...--------------(....-------).)))).........- ( -29.00)
>DroSim_CAF1 115624 94 + 1
GAAAUGCGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGA---GGGAAAUGAGAGGCUGG--------------CGAAA-------GAGCGUGAAGGAGGC-
...((((((((..((((((((....(((((....)))))....(((.......))).---))))))))..))))...--------------(....-------).)))).........- ( -29.00)
>DroEre_CAF1 108533 80 + 1
GAAAUGCGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGA---GGGAAAUGAGAGGCUGG--------------CCAAA-----------------G-----
.......((((..((((((((....(((((....)))))....(((.......))).---))))))))..))))...--------------.....-----------------.----- ( -24.10)
>DroYak_CAF1 112971 101 + 1
GAAAUGCGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGA---GGGAAAUGAGAGGCUGG--------------CUGCAAAUGCGAGAGCGUGAAGGAGGC-
.......((((..((((((((....(((((....)))))....(((.......))).---))))))))..)))).(.--------------((.(..((((....))))...).)).)- ( -32.20)
>DroAna_CAF1 103345 112 + 1
GAAAUGUGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGCACCGAGAGAUCCGAGUUAGAAAAAAAAAUAAACACAGAA-------GACACUAAAGGAGGUG
.......(((.....(((((.....(((((....)))))..(((((.......)))))..))))).(((...((((....................-------....)))).)))))). ( -18.06)
>consensus
GAAAUGCGCCUGGCAUUUUCCAUAAUAAAUGAAAAUUUAAAUGCGCGCACACAGCGA___GGGAAAUGAGAGGCUGG______________CGAAA_______GAGCGUGAAGGAGGC_
.......((((..((((((((....(((((....)))))....(((.......)))....))))))))..))))............................................. (-19.06 = -20.78 +   1.72)

alignment

secondary structure

dotplot

Window 0

Location	15,218,773 – 15,218,867
Length	94
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	80.85
Mean single sequence MFE	-19.76
Consensus MFE	-13.14
Energy contribution	-13.70
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-1.32
Structure conservation index	0.67
SVM decision value	-0.03
SVM RNA-class probability	0.517278
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15218773 94 - 23771897
-GCCUCCUUCACGCUC-------UUUCG--------------CCGGCCUCUCAUUUCCC---UCGCUGUGUGCGCGCAUUUAAAUUUUCAUUUAUUAUGGAAAAUGCCAGGCGCAUUUC
-((((.......((..-------....)--------------).(((...........(---.(((.....))).)........(((((((.....)))))))..)))))))....... ( -17.70)
>DroSec_CAF1 108299 94 - 1
-GCCUCCUUCACGCUC-------UUUCG--------------CCAGCCUCUCAUUUCCC---UCGCUGUGUGCGCGCAUUUAAAUUUUCAUUUAUUAUGGAAAAUGCCAGGCGCAUUUC
-((((.......((..-------...((--------------(((((............---..)))).))).))((((((.....(((((.....))))))))))).))))....... ( -17.94)
>DroSim_CAF1 115624 94 - 1
-GCCUCCUUCACGCUC-------UUUCG--------------CCAGCCUCUCAUUUCCC---UCGCUGUGUGCGCGCAUUUAAAUUUUCAUUUAUUAUGGAAAAUGCCAGGCGCAUUUC
-((((.......((..-------...((--------------(((((............---..)))).))).))((((((.....(((((.....))))))))))).))))....... ( -17.94)
>DroEre_CAF1 108533 80 - 1
-----C-----------------UUUGG--------------CCAGCCUCUCAUUUCCC---UCGCUGUGUGCGCGCAUUUAAAUUUUCAUUUAUUAUGGAAAAUGCCAGGCGCAUUUC
-----.-----------------....(--------------(((((............---..)))).))((((((((((.....(((((.....)))))))))))...))))..... ( -16.54)
>DroYak_CAF1 112971 101 - 1
-GCCUCCUUCACGCUCUCGCAUUUGCAG--------------CCAGCCUCUCAUUUCCC---UCGCUGUGUGCGCGCAUUUAAAUUUUCAUUUAUUAUGGAAAAUGCCAGGCGCAUUUC
-((((.......((...(((((..((((--------------(.((............)---).)))))))))).)).......(((((((.....))))))).....))))....... ( -22.70)
>DroAna_CAF1 103345 112 - 1
CACCUCCUUUAGUGUC-------UUCUGUGUUUAUUUUUUUUUCUAACUCGGAUCUCUCGGUGCGCUGUGUGCGCGCAUUUAAAUUUUCAUUUAUUAUGGAAAAUGCCAGGCACAUUUC
...........(((((-------(((((.(((.............))).))))......(((((((.....)))).........(((((((.....)))))))..)))))))))..... ( -25.72)
>consensus
_GCCUCCUUCACGCUC_______UUUCG______________CCAGCCUCUCAUUUCCC___UCGCUGUGUGCGCGCAUUUAAAUUUUCAUUUAUUAUGGAAAAUGCCAGGCGCAUUUC
...........................................((((.................)))).((((((((((((.....(((((.....)))))))))))...))))))... (-13.14 = -13.70 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:52 2006