Locus 1748

Sequence ID	3L_DroMel_CAF1
Location	5,042,870 – 5,042,970
Length	100
Max. P	0.629295

overview

Window 9

Location	5,042,870 – 5,042,970
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	96.30
Mean single sequence MFE	-22.58
Consensus MFE	-18.58
Energy contribution	-19.46
Covariance contribution	0.88
Combinations/Pair	1.04
Mean z-score	-1.57
Structure conservation index	0.82
SVM decision value	0.20
SVM RNA-class probability	0.629295
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5042870 100 + 23771897
AGAAAAUUCAUUAAUUAAACAAAUUAAGCUAAUGGCUGCGGCUUGACUGCUCCCAACAAAAAAGCCUUCUCGUUCGCCAGGGAAAAACUCUUCAGGCCGC
.......((((((.((((.....))))..))))))..(((((((((..(((...........))).(((((........))))).......))))))))) ( -21.90)
>DroSec_CAF1 249344 100 + 1
AGCAAAUUCAUUAAUUAAACAAAUUAAGCUAAUGGCUGCGGCUUGACUGCUCCCAACAAAAAAGCCUUCUCGUUCGCCAGGGAAAAACUCUUCAGGCCGC
(((.......((((((.....)))))).......)))(((((((((..(((...........))).(((((........))))).......))))))))) ( -23.44)
>DroSim_CAF1 270213 97 + 1
AGCAAAUUCAUUAAUUAAACAAAUUAAGCUAAUGGCUGCGGCUUGACUGCUCCCAACAAAAAAGCCUUCUCGUUCGCCAGGGAAAAACUCUUCAGG---C
.(((...((((((.((((.....))))..)))))).)))(((((...((.......))...))))).........(((((((.....))))...))---) ( -16.60)
>DroEre_CAF1 252790 99 + 1
AGCAAAUUCAUUAAUUAAACAAAUUAAGCUAAUGGCUGCGGCUUGACUGCUCCCAACAAGAAAGCCUUCUCGUUUGCCAGGGA-AAACUCUUCAGGCCGC
(((.......((((((.....)))))).......)))(((((((((....(((((((.((((....)))).))).....))))-.......))))))))) ( -25.34)
>DroYak_CAF1 259193 100 + 1
AGCAAAUUCAUUAAUUAAACAAAUUAAGCUAAUGGCUGCGGCUUGACUGCUUCCAACAAAAAAGCCUUCUCGUUUGCCAGGGAGAAACUCUUCAGGCCGC
(((.......((((((.....)))))).......)))(((((((((...(((((..((((..((....))..))))...))))).......))))))))) ( -25.64)
>consensus
AGCAAAUUCAUUAAUUAAACAAAUUAAGCUAAUGGCUGCGGCUUGACUGCUCCCAACAAAAAAGCCUUCUCGUUCGCCAGGGAAAAACUCUUCAGGCCGC
(((.......((((((.....)))))).......)))(((((((((..(((...........))).(((((........))))).......))))))))) (-18.58 = -19.46 +   0.88)

alignment

secondary structure

dotplot

Window 0

Location	5,042,870 – 5,042,970
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	96.30
Mean single sequence MFE	-27.48
Consensus MFE	-24.52
Energy contribution	-25.28
Covariance contribution	0.76
Combinations/Pair	1.03
Mean z-score	-1.21
Structure conservation index	0.89
SVM decision value	0.04
SVM RNA-class probability	0.556190
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5042870 100 - 23771897
GCGGCCUGAAGAGUUUUUCCCUGGCGAACGAGAAGGCUUUUUUGUUGGGAGCAGUCAAGCCGCAGCCAUUAGCUUAAUUUGUUUAAUUAAUGAAUUUUCU
(((((.(((...(((....((..(((((.(((....))).)))))..)))))..))).)))))...((((((.((((.....))))))))))........ ( -28.60)
>DroSec_CAF1 249344 100 - 1
GCGGCCUGAAGAGUUUUUCCCUGGCGAACGAGAAGGCUUUUUUGUUGGGAGCAGUCAAGCCGCAGCCAUUAGCUUAAUUUGUUUAAUUAAUGAAUUUGCU
(((((.(((...(((....((..(((((.(((....))).)))))..)))))..))).))))).......(((..((((..((.....))..)))).))) ( -29.70)
>DroSim_CAF1 270213 97 - 1
G---CCUGAAGAGUUUUUCCCUGGCGAACGAGAAGGCUUUUUUGUUGGGAGCAGUCAAGCCGCAGCCAUUAGCUUAAUUUGUUUAAUUAAUGAAUUUGCU
(---((.((((....))))...))).........(((((..((((.....))))..)))))((((.((((((.((((.....))))))))))...)))). ( -21.50)
>DroEre_CAF1 252790 99 - 1
GCGGCCUGAAGAGUUU-UCCCUGGCAAACGAGAAGGCUUUCUUGUUGGGAGCAGUCAAGCCGCAGCCAUUAGCUUAAUUUGUUUAAUUAAUGAAUUUGCU
(((((.(((...((..-((((.....((((((((....))))))))))))))..))).))))).......(((..((((..((.....))..)))).))) ( -29.00)
>DroYak_CAF1 259193 100 - 1
GCGGCCUGAAGAGUUUCUCCCUGGCAAACGAGAAGGCUUUUUUGUUGGAAGCAGUCAAGCCGCAGCCAUUAGCUUAAUUUGUUUAAUUAAUGAAUUUGCU
(((((.(((...((((((....((((((.(((....))).))))))))))))..))).))))).......(((..((((..((.....))..)))).))) ( -28.60)
>consensus
GCGGCCUGAAGAGUUUUUCCCUGGCGAACGAGAAGGCUUUUUUGUUGGGAGCAGUCAAGCCGCAGCCAUUAGCUUAAUUUGUUUAAUUAAUGAAUUUGCU
(((((.(((...(((....((..(((((.(((....))).)))))..)))))..))).)))))...((((((.((((.....))))))))))........ (-24.52 = -25.28 +   0.76)

alignment

secondary structure

dotplot

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