Locus 2059

Sequence ID	X_DroMel_CAF1
Location	5,656,730 – 5,656,825
Length	95
Max. P	0.930547

overview

Window 8

Location	5,656,730 – 5,656,825
Length	95
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.88
Mean single sequence MFE	-35.90
Consensus MFE	-23.48
Energy contribution	-23.16
Covariance contribution	-0.32
Combinations/Pair	1.10
Mean z-score	-1.94
Structure conservation index	0.65
SVM decision value	0.18
SVM RNA-class probability	0.623943
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5656730 95 + 22224390
UAUUUACGGGCACUUGGCCAACAGAUGGCCAGGAAGCGCUGUUCCGGAGUGCUCC-------------------------AUCUGGCCAUCCGCCGACCUAGGCGCACUAAUUGAAUCAC
........(((.....)))....((((((((((.((((((.......))))))..-------------------------.))))))))))((((......))))............... ( -35.30)
>DroSec_CAF1 2613 92 + 1
UAUUUACGGGCACUUGGCCACCAGAUGGCCAGGAAGCGCUGUUCCGGAGUGCUCC-------------------------AUCUGGCCAUCC---GACCUAGGCGCACUAAUUGAAUCAC
.......((((.(((((....(.((((((((((.((((((.......))))))..-------------------------.)))))))))).---)..))))).)).))........... ( -31.80)
>DroSim_CAF1 2323 92 + 1
UAUUUACGGGCACUUGGCCACCAGAUGGCCAGGAAGCGCUGUUCCGGAGUGCUCC-------------------------AUCUGGCCAUCC---GACCUAGGCACACUAAUUGAAUCAC
......(((((.....)))....((((((((((.((((((.......))))))..-------------------------.)))))))))))---)...(((.....))).......... ( -30.30)
>DroEre_CAF1 2253 92 + 1
UAUUUACGGGCACUUGGCCACCAGAUGGCCAGGAAGCGCUGCUCCGGAGCGCUCC-------------------------AGCUGGCCACCC---GAGCUAGGCGCACUAAUUGAAUCAC
......((((((((((((((.....))))))))......))).)))..(((((..-------------------------((((((....))---.)))).))))).............. ( -33.30)
>DroYak_CAF1 2447 117 + 1
UAUUUACGGCCACUUGGCCACCAGAUGGCCAGGAAGCGUUGUUCCGGAGUGCACCGGAGUGGCCAUCUGGCCAUCUGGCCAUCUGACCAUCC---GACCUAGGCGCACUAAUUGAAUCAC
.......((((....))))..((((((((((((........((((((......))))))(((((....)))))))))))))))))......(---((..(((.....))).)))...... ( -48.80)
>consensus
UAUUUACGGGCACUUGGCCACCAGAUGGCCAGGAAGCGCUGUUCCGGAGUGCUCC_________________________AUCUGGCCAUCC___GACCUAGGCGCACUAAUUGAAUCAC
.......((.((((((((((.....))))))))..(((((.......)))))...............................)).))...........(((.....))).......... (-23.48 = -23.16 +  -0.32)

alignment

secondary structure

dotplot

Window 9

Location	5,656,730 – 5,656,825
Length	95
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.88
Mean single sequence MFE	-40.58
Consensus MFE	-29.24
Energy contribution	-29.20
Covariance contribution	-0.04
Combinations/Pair	1.16
Mean z-score	-2.39
Structure conservation index	0.72
SVM decision value	1.21
SVM RNA-class probability	0.930547
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5656730 95 - 22224390
GUGAUUCAAUUAGUGCGCCUAGGUCGGCGGAUGGCCAGAU-------------------------GGAGCACUCCGGAACAGCGCUUCCUGGCCAUCUGUUGGCCAAGUGCCCGUAAAUA
............(.((((...(((((((((((((((((..-------------------------(((((.((.......)).))))))))))))))))))))))..)))).)....... ( -43.60)
>DroSec_CAF1 2613 92 - 1
GUGAUUCAAUUAGUGCGCCUAGGUC---GGAUGGCCAGAU-------------------------GGAGCACUCCGGAACAGCGCUUCCUGGCCAUCUGGUGGCCAAGUGCCCGUAAAUA
............(.((((...((((---((((((((((..-------------------------(((((.((.......)).)))))))))))))))...))))..)))).)....... ( -34.10)
>DroSim_CAF1 2323 92 - 1
GUGAUUCAAUUAGUGUGCCUAGGUC---GGAUGGCCAGAU-------------------------GGAGCACUCCGGAACAGCGCUUCCUGGCCAUCUGGUGGCCAAGUGCCCGUAAAUA
........(((..((.((((.((((---((((((((((..-------------------------(((((.((.......)).)))))))))))))))...)))).)).)).))..))). ( -33.70)
>DroEre_CAF1 2253 92 - 1
GUGAUUCAAUUAGUGCGCCUAGCUC---GGGUGGCCAGCU-------------------------GGAGCGCUCCGGAGCAGCGCUUCCUGGCCAUCUGGUGGCCAAGUGCCCGUAAAUA
............(.((((...((((---((((((((((..-------------------------((((((((.......)))))))))))))))))))..)))...)))).)....... ( -39.20)
>DroYak_CAF1 2447 117 - 1
GUGAUUCAAUUAGUGCGCCUAGGUC---GGAUGGUCAGAUGGCCAGAUGGCCAGAUGGCCACUCCGGUGCACUCCGGAACAACGCUUCCUGGCCAUCUGGUGGCCAAGUGGCCGUAAAUA
((..(((....((((((((......---(((((((((..(((((....)))))..)))))).)))))))))))...)))..))(((.(.(((((((...))))))).).)))........ ( -52.30)
>consensus
GUGAUUCAAUUAGUGCGCCUAGGUC___GGAUGGCCAGAU_________________________GGAGCACUCCGGAACAGCGCUUCCUGGCCAUCUGGUGGCCAAGUGCCCGUAAAUA
............(.((((...((((...(((((((((............................(((....)))((((......)))))))))))))...))))..)))).)....... (-29.24 = -29.20 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:15 2006