Locus 4804

Sequence ID	3L_DroMel_CAF1
Location	13,431,435 – 13,431,655
Length	220
Max. P	0.896508

overview

Window 0

Location	13,431,435 – 13,431,535
Length	100
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.44
Mean single sequence MFE	-37.44
Consensus MFE	-28.67
Energy contribution	-29.05
Covariance contribution	0.38
Combinations/Pair	1.07
Mean z-score	-2.08
Structure conservation index	0.77
SVM decision value	0.99
SVM RNA-class probability	0.896508
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13431435 100 + 23771897
UGUCAAAUUAAUCAGCGGCAGCGUAGCUGCACAGCAAGUGUCGGCACUCCCCU--------------------GGCCACCACUUCAUCCGCUUCGGCUGCAGCUGCAUUUGCAUGGCAGA
(((((.........((....))(((((((((..(.(((((..(((.(......--------------------))))..))))))....((....))))))))))).......))))).. ( -36.80)
>DroSim_CAF1 30482 100 + 1
UGUCAAAUUAAUCAGCGGCAGCGGAGCUGCACAGCAAGUGUCGGCACUCCCCU--------------------GGCCACCACUUCAUCCGCUUUGGCUGCAGCUGCAUUUGCAUGGCAGA
(((((.........((((((((((((((....)))(((((..(((.(......--------------------))))..)))))..))))))...)))))...(((....)))))))).. ( -37.00)
>DroEre_CAF1 29642 120 + 1
UGUCAAAUUAAUCAGCGGCAGCGGAGCUGCACAGCAAGUGUCGGCCCUCCCCUGCCAUACCCUGCCAUCUCCUGCCCACCACUUCAUCCACAUCGGUUGCAGCUGCAUUUGCAUGGCAGA
................(((((.((((((((((.....))).))))..))).))))).....(((((((...((((..(((..............))).))))..((....))))))))). ( -39.04)
>DroYak_CAF1 28848 110 + 1
UGUCAAAUUAAUCAGCGGCAGCGGAGCUGCACAGCAAGUGUCGGCACUCCCCUGCACUGCCC----------UGCCCUCCACUUCAUCCGCUUCGGUUGCAGCUGCAUUUGCAUGGCAGA
(((((....(((((((.(((((((((..(((..(((.((((.((......)).)))))))..----------))).))))........((...))))))).)))).)))....))))).. ( -36.90)
>consensus
UGUCAAAUUAAUCAGCGGCAGCGGAGCUGCACAGCAAGUGUCGGCACUCCCCU____________________GCCCACCACUUCAUCCGCUUCGGCUGCAGCUGCAUUUGCAUGGCAGA
(((((....(((((((.(((((.(((((....)))(((((..(((.............................)))..)))))........)).))))).)))).)))....))))).. (-28.67 = -29.05 +   0.38)

alignment

secondary structure

dotplot

Window 1

Location	13,431,535 – 13,431,655
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.69
Mean single sequence MFE	-40.83
Consensus MFE	-38.47
Energy contribution	-38.60
Covariance contribution	0.13
Combinations/Pair	1.06
Mean z-score	-1.41
Structure conservation index	0.94
SVM decision value	-0.00
SVM RNA-class probability	0.532515
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13431535 120 + 23771897
CAAAUUGCAUUUAAUUGCCUGACAGCCUCAAGAGGCGAGGGCCACCGGCACUCGGAGUGGGCUGUGGCUCGGAAAAUGUGUAGCAAACUUCACGCCAAUCCCCAAUCCGUCAGCUCCUCC
......(((......)))(((((.((((....))))(((.(((...))).)))(((.((((...((((...(((..((.....))...)))..))))...)))).))))))))....... ( -40.90)
>DroSim_CAF1 30582 120 + 1
CAAAUUGCAUUUAAUUGCCUGACAGCCUCAAGAGGCGAGGGCCACCGGCACUCGGAGUGGGCUGUGGCUCGGAAAAUGUGUAGCAAACUUCACGCCAAUCCCCAAUCCGUCAGCUUCCCA
......(((......)))(((((.((((....))))(((.(((...))).)))(((.((((...((((...(((..((.....))...)))..))))...)))).))))))))....... ( -40.90)
>DroEre_CAF1 29762 120 + 1
CAAAUUGCAUUUAAUUGCCUGACAGCCUCAAGAGGCGAGGGCUGCUGGCACUCGGAGUGGGCCGCGGCUCGGAAAAUGUGUAGCAAACUUCACGCCAAUCCCCAAUCCGUCGGCUCCUCC
...............((((.(.(((((((.......)).)))))).))))...((((.(((((((((...(((...((((.((....)).))))....))).....))).)))))))))) ( -41.50)
>DroYak_CAF1 28958 120 + 1
CCAAUUGCAUUUAAUUGCCUGACAGCCUCAAGAGGCGAGGGCCACCGGCACUCGGAGUGGGCUGCGGCUCGGAAAAUGUGUAGCAAACUUCACGCCAAUCCCCAAUCCGUCAGCUCCUCC
......(((......)))......((((....))))(((.(((...))).)))((((.(((((((((...(((...((((.((....)).))))....))).....))).)))))))))) ( -40.00)
>consensus
CAAAUUGCAUUUAAUUGCCUGACAGCCUCAAGAGGCGAGGGCCACCGGCACUCGGAGUGGGCUGCGGCUCGGAAAAUGUGUAGCAAACUUCACGCCAAUCCCCAAUCCGUCAGCUCCUCC
......(((......)))(((((.((((....))))(((.(((...))).)))(((.((((...((((...(((..((.....))...)))..))))...)))).))))))))....... (-38.47 = -38.60 +   0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:50 2006