Locus 4302

Sequence ID	2L_DroMel_CAF1
Location	12,301,933 – 12,302,026
Length	93
Max. P	0.845785

overview

Window 3

Location	12,301,933 – 12,302,026
Length	93
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	83.30
Mean single sequence MFE	-30.78
Consensus MFE	-20.91
Energy contribution	-22.59
Covariance contribution	1.68
Combinations/Pair	1.08
Mean z-score	-2.14
Structure conservation index	0.68
SVM decision value	0.77
SVM RNA-class probability	0.845785
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12301933 93 + 22407834
AAAAAUUCUUUGCCCCGGGAGCGAGCGGAUGGAGUCCGACGAU-----UCGGACUCGAAGGAGAUGUCCUCCGUCUGUUACAUCCUUUCACUUCGAAU
.................((((.(((.(((((((((((((....-----))))))))((.((((.....)))).)).....))))).))).)))).... ( -35.00)
>DroSec_CAF1 124655 93 + 1
AAAAAUUCUUUGCCCCGGCA----GCGGAUGGAGUCCGACGAUUCAU-UCGGACUCGAAGGAGAUGUCCUCCGUCUGUUACAUCCUUCCCCUGCGAAU
....((((.((((....)))----).(((((((((((((........-))))))))((.((((.....)))).)).....))))).........)))) ( -32.30)
>DroSim_CAF1 128312 93 + 1
AAAAAUUCUUUGCCCCGGCA----GCGGAUGGAGUCCGACGAUUCAU-UCGGACUCGAAGGAGAUGUCCUCCGUCUGUUACAUCCUUCCCCUGCGAAU
....((((.((((....)))----).(((((((((((((........-))))))))((.((((.....)))).)).....))))).........)))) ( -32.30)
>DroEre_CAF1 122691 75 + 1
AAAAAUUCUCUGCC-CGGGA----GCGGAU------------------UCGGACUCGAAGGAGAUGUCCUCCGUCUGUUACAUCCUGCGCCUUGGAGU
.......((((((.-(((((----((((((------------------..((((((......)).))))...))))))....))))).))...)))). ( -23.30)
>DroYak_CAF1 129090 94 + 1
AAAAAUUCUUUGCCCCAGGA----GCGGAUGGAGUCCGACGAUUCGGACCGGACUCGAAGGAGAUGUCCUCCGUCUGUUACAUCCUUUCCCUUCGAAC
................((((----(((((((((((((((....)))))).((((((......)).)))))))))))))....))))............ ( -31.00)
>consensus
AAAAAUUCUUUGCCCCGGGA____GCGGAUGGAGUCCGACGAUUC___UCGGACUCGAAGGAGAUGUCCUCCGUCUGUUACAUCCUUCCCCUUCGAAU
....((((........((((....((((((.(((((((...........)))))))...((((.....))))))))))....))))........)))) (-20.91 = -22.59 +   1.68)

alignment

secondary structure

dotplot

Window 4

Location	12,301,933 – 12,302,026
Length	93
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	83.30
Mean single sequence MFE	-32.21
Consensus MFE	-19.96
Energy contribution	-21.64
Covariance contribution	1.68
Combinations/Pair	1.05
Mean z-score	-2.25
Structure conservation index	0.62
SVM decision value	0.61
SVM RNA-class probability	0.799857
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12301933 93 - 22407834
AUUCGAAGUGAAAGGAUGUAACAGACGGAGGACAUCUCCUUCGAGUCCGA-----AUCGUCGGACUCCAUCCGCUCGCUCCCGGGGCAAAGAAUUUUU
.((((.(((((..(((((........((((((....))))))((((((((-----....)))))))))))))..)))))..))))............. ( -35.40)
>DroSec_CAF1 124655 93 - 1
AUUCGCAGGGGAAGGAUGUAACAGACGGAGGACAUCUCCUUCGAGUCCGA-AUGAAUCGUCGGACUCCAUCCGC----UGCCGGGGCAAAGAAUUUUU
.(((((((.(((.(((.........(((((((....))))))).((((((-........))))))))).))).)----)).))))............. ( -34.40)
>DroSim_CAF1 128312 93 - 1
AUUCGCAGGGGAAGGAUGUAACAGACGGAGGACAUCUCCUUCGAGUCCGA-AUGAAUCGUCGGACUCCAUCCGC----UGCCGGGGCAAAGAAUUUUU
.(((((((.(((.(((.........(((((((....))))))).((((((-........))))))))).))).)----)).))))............. ( -34.40)
>DroEre_CAF1 122691 75 - 1
ACUCCAAGGCGCAGGAUGUAACAGACGGAGGACAUCUCCUUCGAGUCCGA------------------AUCCGC----UCCCG-GGCAGAGAAUUUUU
.((((..((.((.((((........(((((((....))))))).......------------------))))))----.))..-)).))......... ( -22.06)
>DroYak_CAF1 129090 94 - 1
GUUCGAAGGGAAAGGAUGUAACAGACGGAGGACAUCUCCUUCGAGUCCGGUCCGAAUCGUCGGACUCCAUCCGC----UCCUGGGGCAAAGAAUUUUU
((((...((((..(((((........((((((....))))))((((((((.(......))))))))))))))..----)))).))))........... ( -34.80)
>consensus
AUUCGAAGGGGAAGGAUGUAACAGACGGAGGACAUCUCCUUCGAGUCCGA___GAAUCGUCGGACUCCAUCCGC____UCCCGGGGCAAAGAAUUUUU
.............(((((........((((((....))))))((((((((.........))))))))))))).......................... (-19.96 = -21.64 +   1.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:35 2006