Locus 3234

Sequence ID	X_DroMel_CAF1
Location	8,552,544 – 8,552,658
Length	114
Max. P	0.900436

overview

Window 1

Location	8,552,544 – 8,552,658
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.23
Mean single sequence MFE	-27.93
Consensus MFE	-20.14
Energy contribution	-22.07
Covariance contribution	1.94
Combinations/Pair	1.05
Mean z-score	-2.02
Structure conservation index	0.72
SVM decision value	1.01
SVM RNA-class probability	0.900436
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8552544 114 + 22224390
CAGUAAUUCUUUUGACCUUAUUUUUCCCAGUGCAGACGCAUCUGUGCAUCUGCAUUGUCCUGGAGCGACAGGAACAGCUGCAGCUCCUCAUCAUCAUAGAGUCUACCGCC------UUCC
..((((((((..(((............(((((((((.(((....))).)))))))))....(((((..(((......)))..)))))......))).))))).)))....------.... ( -35.10)
>DroSec_CAF1 13256 99 + 1
--------------ACCGUUUUUUUCCCAGUGCAGACGCAUCUGUGCAUUUGCAUUGUCCUGGAGCGACAGGAACAGCUGCAGCUCCUCAUCAUCAU-GACUCUACUGCC------UUCG
--------------.............(((((((((.(((....))).)))))))))....(((((..(((......)))..)))))((((....))-))..........------.... ( -27.10)
>DroEre_CAF1 14021 102 + 1
-----------UUGACCGUAUUUUUCCCAGUGCCUCCACAUCUGUGCAUCUGCAUUGUCCUGGAGCGACAGGACCAGCUACAGCUGCUCCUCAUCAU-GACUCUACCGCC------UUCC
-----------.................((.(((((((...(.((((....)))).)...))))).((.((((.((((....)))).))))..))..-.........)))------)... ( -23.10)
>DroYak_CAF1 15144 107 + 1
-----------UUCA-CUAAUUUAUCCCAGUGCAUCCGCAUCUGUGCAUCUGCAUUGUCCUGGAGCGACAGGACCAGCUGCAGCUGCUCCUCAUCAU-GACUCUACCGCCCACAUCCUCC
-----------....-...........(((((((...(((....)))...)))))))...(((.(((...(((.((((....)))).)))((.....-))......))))))........ ( -26.40)
>consensus
___________UUGACCGUAUUUUUCCCAGUGCAGACGCAUCUGUGCAUCUGCAUUGUCCUGGAGCGACAGGAACAGCUGCAGCUCCUCAUCAUCAU_GACUCUACCGCC______UUCC
...........................(((((((((.(((....))).)))))))))(((((......))))).((((....)))).................................. (-20.14 = -22.07 +   1.94)

alignment

secondary structure

dotplot

Window 2

Location	8,552,544 – 8,552,658
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.23
Mean single sequence MFE	-33.85
Consensus MFE	-20.58
Energy contribution	-20.95
Covariance contribution	0.37
Combinations/Pair	1.10
Mean z-score	-1.74
Structure conservation index	0.61
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8552544 114 - 22224390
GGAA------GGCGGUAGACUCUAUGAUGAUGAGGAGCUGCAGCUGUUCCUGUCGCUCCAGGACAAUGCAGAUGCACAGAUGCGUCUGCACUGGGAAAAAUAAGGUCAAAAGAAUUACUG
....------..((((((..(((.((((.....(((((.((((......)))).)))))....((.((((((((((....)))))))))).))...........))))..))).)))))) ( -37.70)
>DroSec_CAF1 13256 99 - 1
CGAA------GGCAGUAGAGUC-AUGAUGAUGAGGAGCUGCAGCUGUUCCUGUCGCUCCAGGACAAUGCAAAUGCACAGAUGCGUCUGCACUGGGAAAAAAACGGU--------------
....------.(((((....((-((....))))...))))).((((((((((......)))))((.((((.(((((....))))).)))).))........)))))-------------- ( -28.30)
>DroEre_CAF1 14021 102 - 1
GGAA------GGCGGUAGAGUC-AUGAUGAGGAGCAGCUGUAGCUGGUCCUGUCGCUCCAGGACAAUGCAGAUGCACAGAUGUGGAGGCACUGGGAAAAAUACGGUCAA-----------
....------(((.(((...((-..(((.((((.((((....)))).)))))))((((((.(.(..(((....)))..).).)))).)).....))....))).)))..----------- ( -34.30)
>DroYak_CAF1 15144 107 - 1
GGAGGAUGUGGGCGGUAGAGUC-AUGAUGAGGAGCAGCUGCAGCUGGUCCUGUCGCUCCAGGACAAUGCAGAUGCACAGAUGCGGAUGCACUGGGAUAAAUUAG-UGAA-----------
(((((((...(((......)))-......((((.((((....)))).))))))).))))....((.((((..((((....))))..)))).))...........-....----------- ( -35.10)
>consensus
GGAA______GGCGGUAGAGUC_AUGAUGAGGAGCAGCUGCAGCUGGUCCUGUCGCUCCAGGACAAUGCAGAUGCACAGAUGCGGAUGCACUGGGAAAAAUAAGGUCAA___________
.................................(((.(((((..((.(((((......))))))).))))).))).(((.(((....))))))........................... (-20.58 = -20.95 +   0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:32 2006