Locus 2020

Sequence ID	X_DroMel_CAF1
Location	5,536,729 – 5,536,837
Length	108
Max. P	0.994160

overview

Window 4

Location	5,536,729 – 5,536,837
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	94.07
Mean single sequence MFE	-27.91
Consensus MFE	-23.87
Energy contribution	-24.51
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-2.20
Structure conservation index	0.86
SVM decision value	2.46
SVM RNA-class probability	0.994160
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5536729 108 + 22224390
GUGGGCCAAAAAAAGUUUAUUGAUGCUGUAAAUAAGUAAAUAAAUAAUAGCCUGUAAUCAUUCCGAUGGGGUUUUCGGGAAAUGCAAUUUACGUUUGGCCCACAUGAU
((((((((((....((..((((..(((((.................))))).........((((((........))))))....))))..)).))))))))))..... ( -32.43)
>DroSec_CAF1 26404 103 + 1
GUGGUCCAAGAAAAGUUUAUUGACGCUGUAAAUAAGUAAAUAAAUAAUAGCCUGUAAUCAUUCCGAUGGGGUUUUCGGGAA-----AUUUACGUUUGGCCCACAUGAU
((((.(((((....(((((((...(((.......))).)))))))........((((...((((((........)))))).-----..)))).))))).))))..... ( -25.60)
>DroSim_CAF1 28942 108 + 1
GUGGUCCAAGAAAAGUUUAUUGACGCUGUAAAUAAGUAAAUAAAUAAUAGCCUGUAAUCAUUCCGAUGGGGUUUUCGGGAAAUGCAAUUUACGUUUGGCCCACAUGAU
((((.(((((....((..((((.((((((.................))))).........((((((........))))))...)))))..)).))))).))))..... ( -25.33)
>DroEre_CAF1 26924 108 + 1
GUGGGCCAAGAAAAGUUUAUUGAUGGUGUAAAUAAGUAAAUAAAUAAUAGCCUGUAAUCAUUCCAAUGGGGAUUUCGGGAAAUGCAAUUUACGUUUGGCCCACAUGAU
((((((((((....((((((.......))))))..((((((.....((..((((.((((...((...)).)))).))))..))...)))))).))))))))))..... ( -31.30)
>DroYak_CAF1 27029 108 + 1
GUGCGCCAAGAACAGUUUAUUGAUGGUGUAUAUAAGUAAAUAAAUAAUAGCCUGUAAUCAUUCCGAUGGGGAUUUCGGGAAAUGCAAUUUACGUUUGGCCCACAUGAU
(((.((((((....((..((((..(((.(((.((......)).)))...)))........((((((........))))))....))))..)).)))))).)))..... ( -24.90)
>consensus
GUGGGCCAAGAAAAGUUUAUUGAUGCUGUAAAUAAGUAAAUAAAUAAUAGCCUGUAAUCAUUCCGAUGGGGUUUUCGGGAAAUGCAAUUUACGUUUGGCCCACAUGAU
((((((((((....((((((.......))))))..((((((.........((((.......(((....)))....)))).......)))))).))))))))))..... (-23.87 = -24.51 +   0.64)

alignment

secondary structure

dotplot

Window 5

Location	5,536,729 – 5,536,837
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	94.07
Mean single sequence MFE	-19.79
Consensus MFE	-17.34
Energy contribution	-17.98
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.51
Structure conservation index	0.88
SVM decision value	1.03
SVM RNA-class probability	0.903665
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5536729 108 - 22224390
AUCAUGUGGGCCAAACGUAAAUUGCAUUUCCCGAAAACCCCAUCGGAAUGAUUACAGGCUAUUAUUUAUUUACUUAUUUACAGCAUCAAUAAACUUUUUUUGGCCCAC
.....((((((((((.((((....((((..((((........)))))))).))))..(((..((..((......))..)).)))..............)))))))))) ( -25.40)
>DroSec_CAF1 26404 103 - 1
AUCAUGUGGGCCAAACGUAAAU-----UUCCCGAAAACCCCAUCGGAAUGAUUACAGGCUAUUAUUUAUUUACUUAUUUACAGCGUCAAUAAACUUUUCUUGGACCAC
.....((((.((((..((((((-----...((((........))))((((((........)))))).))))))(((((.((...)).))))).......)))).)))) ( -16.60)
>DroSim_CAF1 28942 108 - 1
AUCAUGUGGGCCAAACGUAAAUUGCAUUUCCCGAAAACCCCAUCGGAAUGAUUACAGGCUAUUAUUUAUUUACUUAUUUACAGCGUCAAUAAACUUUUCUUGGACCAC
.....((((.((((..((((....((((..((((........)))))))).))))..(((..((..((......))..)).)))...............)))).)))) ( -17.60)
>DroEre_CAF1 26924 108 - 1
AUCAUGUGGGCCAAACGUAAAUUGCAUUUCCCGAAAUCCCCAUUGGAAUGAUUACAGGCUAUUAUUUAUUUACUUAUUUACACCAUCAAUAAACUUUUCUUGGCCCAC
.....(((((((((..((((....((((..((((........)))))))).)))).((....((..((......))..))..))...............))))))))) ( -20.60)
>DroYak_CAF1 27029 108 - 1
AUCAUGUGGGCCAAACGUAAAUUGCAUUUCCCGAAAUCCCCAUCGGAAUGAUUACAGGCUAUUAUUUAUUUACUUAUAUACACCAUCAAUAAACUGUUCUUGGCGCAC
.....(((.(((((..........((((..((((........))))))))...((((..((((........................))))..))))..))))).))) ( -18.76)
>consensus
AUCAUGUGGGCCAAACGUAAAUUGCAUUUCCCGAAAACCCCAUCGGAAUGAUUACAGGCUAUUAUUUAUUUACUUAUUUACAGCAUCAAUAAACUUUUCUUGGCCCAC
.....(((((((((..((((((........((((........))))((((((........)))))).))))))(((((.........))))).......))))))))) (-17.34 = -17.98 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:17 2006