Locus 5335

Sequence ID	X_DroMel_CAF1
Location	13,924,084 – 13,924,223
Length	139
Max. P	0.807354

overview

Window 1

Location	13,924,084 – 13,924,199
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.73
Mean single sequence MFE	-37.63
Consensus MFE	-32.80
Energy contribution	-33.20
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.24
Structure conservation index	0.87
SVM decision value	0.01
SVM RNA-class probability	0.537279
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13924084 115 - 22224390
GAAUUCUGGCUAAUUGCCAAGGCAAACAGAGCGGUUGGUAGCACUGUGAUUAU----GGCCAGCCGCUUAUGAUUGAACAAUCAAACACGCCUCCCCGAAAACGCCCACGGCCCA-GGGG
......((((.....))))((((.....(((((((((((..............----.))))))))))).(((((....))))).....))))((((......(((...)))...-)))) ( -40.26)
>DroSec_CAF1 4253 114 - 1
GAAUUCCGGCUAAUUGCCAAGGCAAACAGAGCGGUUGGGAGCACUGUGAUUAU----GGCCAGCCGCUUAUGAUUGAACAAUCAAACACGCCUCCCCGAAAACGCCCACGGCCCA-G-GG
.......(((.....))).((((.....((((((((((...............----..)))))))))).(((((....))))).....)))).(((......(((...)))...-)-)) ( -34.83)
>DroSim_CAF1 6208 115 - 1
GAAUUCCGGCUAAUUGCCAAGGCAAACAGAGCGGUUGGGAGCACUGUGAUUAU----GGCCAGCCGCUUAUGAUUGAACAAUCAAACACGCCUCCCCGAAAACGCCCACGGCCCA-GGGG
.......(((.....))).((((.....((((((((((...............----..)))))))))).(((((....))))).....))))((((......(((...)))...-)))) ( -37.93)
>DroEre_CAF1 6169 115 - 1
GAAUUCUGGCUAAUUGCCAAGGCAAACAGAGCGGUUGGGAGCACUGUGAUUAU----GGCCAGCCGCUUAUGAUUGAACAAUCAAACACGCCUCCCCGAAAACGCCCACGGCCCA-GGGG
......((((.....))))((((.....((((((((((...............----..)))))))))).(((((....))))).....))))((((......(((...)))...-)))) ( -38.43)
>DroYak_CAF1 5742 120 - 1
GAAUUCCGGCUAAUUGCCAAGGCAAACAGUGCGGUUGGGAGCACUGUGAUUAUGGAUGGCCAGCCGCUUAUGAUUGAACAAUCAAACACGCCUACCCGAAAACGCCCACGGCCCUCAGGG
.......(((.....))).((((..(((((((........)))))))(((((((..(((....)))..)))))))..............)))).(((......(((...))).....))) ( -36.70)
>consensus
GAAUUCCGGCUAAUUGCCAAGGCAAACAGAGCGGUUGGGAGCACUGUGAUUAU____GGCCAGCCGCUUAUGAUUGAACAAUCAAACACGCCUCCCCGAAAACGCCCACGGCCCA_GGGG
.......(((.....))).((((.....((((((((((.....................)))))))))).(((((....))))).....)))).(((......(((...))).....))) (-32.80 = -33.20 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	13,924,123 – 13,924,223
Length	100
Sequences	4
Columns	100
Reading direction	forward
Mean pairwise identity	96.31
Mean single sequence MFE	-26.44
Consensus MFE	-25.44
Energy contribution	-25.00
Covariance contribution	-0.44
Combinations/Pair	1.08
Mean z-score	-1.72
Structure conservation index	0.96
SVM decision value	0.64
SVM RNA-class probability	0.807354
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13924123 100 + 22224390
UGUUCAAUCAUAAGCGGCUGGCCAUAAUCACAGUGCUACCAACCGCUCUGUUUGCCUUGGCAAUUAGCCAGAAUUCCCCGCACUUUGGCAAACGUAGAUA
......(((...(((((.(((.(((.......)))...))).)))))..((((((((((((.....)))))...............)))))))...))). ( -26.06)
>DroSec_CAF1 4291 99 + 1
UGUUCAAUCAUAAGCGGCUGGCCAUAAUCACAGUGCUCCCAACCGCUCUGUUUGCCUUGGCAAUUAGCCGGAAUUCCCCGCACUUU-GCAACCGCAGAUA
.............(((((((((.......((((.((........)).))))((((....))))...)))))........((.....-))..))))..... ( -26.60)
>DroSim_CAF1 6247 99 + 1
UGUUCAAUCAUAAGCGGCUGGCCAUAAUCACAGUGCUCCCAACCGCUCUGUUUGCCUUGGCAAUUAGCCGGAAUUCCCCGCACUUU-GCAACCGCAGAUA
.............(((((((((.......((((.((........)).))))((((....))))...)))))........((.....-))..))))..... ( -26.60)
>DroEre_CAF1 6208 99 + 1
UGUUCAAUCAUAAGCGGCUGGCCAUAAUCACAGUGCUCCCAACCGCUCUGUUUGCCUUGGCAAUUAGCCAGAAUUCCCCGCACAUU-GCCACCGCAGAUA
............(((((.(((.(((.......)))...))).))))).(((((((..(((((((..((..(.....)..))..)))-))))..))))))) ( -26.50)
>consensus
UGUUCAAUCAUAAGCGGCUGGCCAUAAUCACAGUGCUCCCAACCGCUCUGUUUGCCUUGGCAAUUAGCCAGAAUUCCCCGCACUUU_GCAACCGCAGAUA
......(((....(((((((((.......((((.((........)).))))((((....))))...)))))......))))......((....)).))). (-25.44 = -25.00 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:16 2006