Locus 3145

Sequence ID	X_DroMel_CAF1
Location	8,365,684 – 8,365,833
Length	149
Max. P	0.999802

overview

Window 5

Location	8,365,684 – 8,365,795
Length	111
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	88.38
Mean single sequence MFE	-28.56
Consensus MFE	-23.88
Energy contribution	-24.08
Covariance contribution	0.20
Combinations/Pair	1.08
Mean z-score	-2.88
Structure conservation index	0.84
SVM decision value	3.10
SVM RNA-class probability	0.998425
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8365684 111 + 22224390
UUGUUAUAAUUAAAAUGGAACGCCCCAAAAAGUUGGGGGAGCUGGUAGGAAUCAGCAGGCAUAUAUACUCGUACACAAAUUUGUGCGUUCCAAGUGGAUAAAUACAUACAU-
.(((....(((....((((((.((((((....))))))..((((((....))))))..............(((((......)))))))))))....)))....))).....- ( -30.30)
>DroSec_CAF1 30900 108 + 1
UUGUUAUAAUUAAAAUGGAACGCCCCAAAAAGUUGGGGGAGCUGGUAGGAAUCAGCAG---UAUAUACUCGUAUACAAAUUUGUGCGUUCCAAGUGGAUAAAUACAUACAU-
.(((....(((....(((((((((((((....)))))...((((((....)))))).(---(((((....))))))........))))))))....)))....))).....- ( -31.00)
>DroSim_CAF1 34079 108 + 1
UUGUUAUAAUUAAAAUGGAACGCCCCAAAAAGUUGGGGGAGCUGUUAGGAAUCAGCAG---CAUAUACUCGUAUACAAAUUUGUGCGUUCCAAGUGGAUA-AUACAUACAUA
.((((((.....(..((((((.((((((....))))))..((((((.......)))))---)........(((((......)))))))))))..)..)))-)))........ ( -28.20)
>DroEre_CAF1 28021 101 + 1
UUGUUAUAAUUAAAAUGGAACGCCCCAAAAAGUUGGGGGAACUGGUAGGAAUCAGCAG---CAUAUAC------AAAAAUGUGUGCUUUCCAAGUGGAUAAAUACAUACA--
.(((....(((....(((((..((((((....))))))...(((((....))))).((---((((((.------.....)))))))))))))....)))....)))....-- ( -24.30)
>DroYak_CAF1 29719 103 + 1
UUGUUAUAAUUAAAAUGGAACGCCCCAGAAAGUUGGGCAAACUGGUAGGAAUCAGUGG---CAUAUAC------AAAAAUGUGUGCGUUCCAAGUGGAUAACUACAUAUACA
...............(((((((((((((....)))))...((((((....)))))).(---(((((..------....)))))))))))))).((((....))))....... ( -29.00)
>consensus
UUGUUAUAAUUAAAAUGGAACGCCCCAAAAAGUUGGGGGAGCUGGUAGGAAUCAGCAG___CAUAUACUCGUA_ACAAAUUUGUGCGUUCCAAGUGGAUAAAUACAUACAU_
.(((....(((....(((((((((((((....)))))...((((((....))))))............................))))))))....)))....)))...... (-23.88 = -24.08 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	8,365,684 – 8,365,795
Length	111
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	88.38
Mean single sequence MFE	-26.38
Consensus MFE	-23.18
Energy contribution	-23.58
Covariance contribution	0.40
Combinations/Pair	1.07
Mean z-score	-3.23
Structure conservation index	0.88
SVM decision value	4.11
SVM RNA-class probability	0.999802
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8365684 111 - 22224390
-AUGUAUGUAUUUAUCCACUUGGAACGCACAAAUUUGUGUACGAGUAUAUAUGCCUGCUGAUUCCUACCAGCUCCCCCAACUUUUUGGGGCGUUCCAUUUUAAUUAUAACAA
-.(((.((((.(((......((((((((.......((((((....)))))).....((((........))))...(((((....)))))))))))))...))).))))))). ( -29.00)
>DroSec_CAF1 30900 108 - 1
-AUGUAUGUAUUUAUCCACUUGGAACGCACAAAUUUGUAUACGAGUAUAUA---CUGCUGAUUCCUACCAGCUCCCCCAACUUUUUGGGGCGUUCCAUUUUAAUUAUAACAA
-.(((.((((.(((......((((((((.......((((((....))))))---..((((........))))...(((((....)))))))))))))...))).))))))). ( -28.90)
>DroSim_CAF1 34079 108 - 1
UAUGUAUGUAU-UAUCCACUUGGAACGCACAAAUUUGUAUACGAGUAUAUG---CUGCUGAUUCCUAACAGCUCCCCCAACUUUUUGGGGCGUUCCAUUUUAAUUAUAACAA
..(((.((((.-........((((((((........(((((......))))---).((((........))))...(((((....))))))))))))).......))))))). ( -26.99)
>DroEre_CAF1 28021 101 - 1
--UGUAUGUAUUUAUCCACUUGGAAAGCACACAUUUUU------GUAUAUG---CUGCUGAUUCCUACCAGUUCCCCCAACUUUUUGGGGCGUUCCAUUUUAAUUAUAACAA
--(((.((((.(((......(((((((((.(((....)------))...))---))((((........))))..((((((....))))))..)))))...))).))))))). ( -21.10)
>DroYak_CAF1 29719 103 - 1
UGUAUAUGUAGUUAUCCACUUGGAACGCACACAUUUUU------GUAUAUG---CCACUGAUUCCUACCAGUUUGCCCAACUUUCUGGGGCGUUCCAUUUUAAUUAUAACAA
......((((((((......((((((((..........------.......---..((((........))))...((((......))))))))))))...)))))))).... ( -25.90)
>consensus
_AUGUAUGUAUUUAUCCACUUGGAACGCACAAAUUUGU_UACGAGUAUAUG___CUGCUGAUUCCUACCAGCUCCCCCAACUUUUUGGGGCGUUCCAUUUUAAUUAUAACAA
..(((.((((.(((......((((((((............................((((........))))...(((((....)))))))))))))...))).))))))). (-23.18 = -23.58 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	8,365,716 – 8,365,833
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.55
Mean single sequence MFE	-22.73
Consensus MFE	-14.56
Energy contribution	-14.50
Covariance contribution	-0.06
Combinations/Pair	1.14
Mean z-score	-2.22
Structure conservation index	0.64
SVM decision value	0.89
SVM RNA-class probability	0.875299
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8365716 117 - 22224390
GCACAAAAACGCAUAAAUUUAUAGGUACAU-AUAUACAU--AUGUAUGUAUUUAUCCACUUGGAACGCACAAAUUUGUGUACGAGUAUAUAUGCCUGCUGAUUCCUACCAGCUCCCCCAA
..........(((((.....((((((((((-((((....--))))))))))))))..(((((..(((((......))))).)))))...)))))..((((........))))........ ( -29.50)
>DroSec_CAF1 30932 113 - 1
NNNN-NAAACGCAUAAAUUUAUAGGUACAU-AUAUGCAU--AUGUAUGUAUUUAUCCACUUGGAACGCACAAAUUUGUAUACGAGUAUAUA---CUGCUGAUUCCUACCAGCUCCCCCAA
....-.....((.........(((((((((-((((....--)))))))))))))(((....)))..)).......((((((....))))))---..((((........))))........ ( -22.50)
>DroSim_CAF1 34111 114 - 1
GCAC-AAAACGCAUAAAUUUAUAGGUACAU-AUAUGCAUAUAUGUAUGUAU-UAUCCACUUGGAACGCACAAAUUUGUAUACGAGUAUAUG---CUGCUGAUUCCUAACAGCUCCCCCAA
....-.....(((((........(((((((-(((((....)))))))))))-)....(((((....(((......)))...))))).))))---).((((........))))........ ( -23.70)
>DroEre_CAF1 28053 96 - 1
---------CGCAUAAAUUUAUAGGUAUAUAAUGCA------UGUAUGUAUUUAUCCACUUGGAAAGCACACAUUUUU------GUAUAUG---CUGCUGAUUCCUACCAGUUCCCCCAA
---------..............((((((((....(------(((.(((.....(((....)))..))).))))....------.))))))---))((((........))))........ ( -15.20)
>consensus
______AAACGCAUAAAUUUAUAGGUACAU_AUAUACAU__AUGUAUGUAUUUAUCCACUUGGAACGCACAAAUUUGUAUACGAGUAUAUA___CUGCUGAUUCCUACCAGCUCCCCCAA
..........((.........(((((((((.((((......)))))))))))))(((....)))..))............................((((........))))........ (-14.56 = -14.50 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:05 2006