Locus 1580

Sequence ID	X_DroMel_CAF1
Location	4,529,559 – 4,529,660
Length	101
Max. P	0.989137

overview

Window 1

Location	4,529,559 – 4,529,660
Length	101
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	94.48
Mean single sequence MFE	-22.34
Consensus MFE	-17.50
Energy contribution	-17.70
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.78
SVM decision value	0.73
SVM RNA-class probability	0.834963
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4529559 101 + 22224390
UAUAUCGAA-ACGACGGAUAUUGAUAUUUCCCACACAGAUACACACCUACAAACGUGUAUCUGCGUUUCUGGCAUCCCUUGAAUUUCUGUGUACAUUGUUUU
(((((.(((-((((.((((...((....))..((.(((((((((..........))))))))).)).......)))).)))..)))).)))))......... ( -20.90)
>DroSec_CAF1 2825 101 + 1
AAUAUCGAA-ACGACGGGUAUUGAUAUUUCCCACACAGAUACACACCUACAAACGUGUAUCUGCGUUUCUGGCAUCCCUUGAAUUUCUGUGUACUUUGUUUU
......(((-(((..(((...........)))...(((((((((..........)))))))))))))))................................. ( -21.90)
>DroSim_CAF1 2450 99 + 1
AAUAUCGAA-ACGA--GGUAUUGAUAUUUCCCACACAGAUACACACCUACAAACGUGUAUCUGCGUUUCUGGCAUCCCUUGAAUUUCUGUGUACUUUGUUUU
......(((-((((--(((((.((...(((..((.(((((((((..........))))))))).))....((....))..)))..))...)))))))))))) ( -25.60)
>DroEre_CAF1 3762 102 + 1
AAUAUCGAAAACGACGAAUAUUGAUAUUUCCCACACAGAUACACACCAACAAACGUGUAUCUGCGUUUCUGGCAUCCCUUGAAUUUCUGUGUACGUUGUGUU
..........((((((.((((.((...(((..((.(((((((((..........))))))))).))....((....))..)))..)).)))).))))))... ( -23.80)
>DroYak_CAF1 3714 101 + 1
AAUAUCGAA-AUGACGAAUAUUGAUAUUUUCCACACAGAUACACACAUACAAACGUGUAUCUGCGUUUCUGGCAUCCCUUGAAUUUCUGUGUACAUUGUUUU
((((((((.-((.....)).))))))))...(((((((((((((..........))))))))).((((..((....))..))))...))))........... ( -19.50)
>consensus
AAUAUCGAA_ACGACGGAUAUUGAUAUUUCCCACACAGAUACACACCUACAAACGUGUAUCUGCGUUUCUGGCAUCCCUUGAAUUUCUGUGUACAUUGUUUU
((((((((............))))))))...(((((((((((((..........))))))))).((((..((....))..))))...))))........... (-17.50 = -17.70 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	4,529,559 – 4,529,660
Length	101
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	94.48
Mean single sequence MFE	-25.32
Consensus MFE	-21.94
Energy contribution	-22.34
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.87
SVM decision value	2.15
SVM RNA-class probability	0.989137
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4529559 101 - 22224390
AAAACAAUGUACACAGAAAUUCAAGGGAUGCCAGAAACGCAGAUACACGUUUGUAGGUGUGUAUCUGUGUGGGAAAUAUCAAUAUCCGUCGU-UUCGAUAUA
...............(((((...(.(((((((....(((((((((((((........))))))))))))).)).........))))).).))-)))...... ( -26.20)
>DroSec_CAF1 2825 101 - 1
AAAACAAAGUACACAGAAAUUCAAGGGAUGCCAGAAACGCAGAUACACGUUUGUAGGUGUGUAUCUGUGUGGGAAAUAUCAAUACCCGUCGU-UUCGAUAUU
...............(((((....(((((.((....(((((((((((((........))))))))))))).))........)).)))...))-)))...... ( -26.90)
>DroSim_CAF1 2450 99 - 1
AAAACAAAGUACACAGAAAUUCAAGGGAUGCCAGAAACGCAGAUACACGUUUGUAGGUGUGUAUCUGUGUGGGAAAUAUCAAUACC--UCGU-UUCGAUAUU
...............(((((...(((((((((....(((((((((((((........))))))))))))).))...))))....))--).))-)))...... ( -25.30)
>DroEre_CAF1 3762 102 - 1
AACACAACGUACACAGAAAUUCAAGGGAUGCCAGAAACGCAGAUACACGUUUGUUGGUGUGUAUCUGUGUGGGAAAUAUCAAUAUUCGUCGUUUUCGAUAUU
..........................((((((....(((((((((((((........))))))))))))).))...)))).......((((....))))... ( -24.40)
>DroYak_CAF1 3714 101 - 1
AAAACAAUGUACACAGAAAUUCAAGGGAUGCCAGAAACGCAGAUACACGUUUGUAUGUGUGUAUCUGUGUGGAAAAUAUCAAUAUUCGUCAU-UUCGAUAUU
........................(..(((...((((((((((((((((........))))))))))))).((.....))....)))..)))-..)...... ( -23.80)
>consensus
AAAACAAAGUACACAGAAAUUCAAGGGAUGCCAGAAACGCAGAUACACGUUUGUAGGUGUGUAUCUGUGUGGGAAAUAUCAAUAUCCGUCGU_UUCGAUAUU
..........................((((......(((((((((((((........)))))))))))))......)))).......((((....))))... (-21.94 = -22.34 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:56 2006