Locus 3039

Sequence ID	X_DroMel_CAF1
Location	8,114,841 – 8,114,936
Length	95
Max. P	0.988280

overview

Window 2

Location	8,114,841 – 8,114,936
Length	95
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	77.13
Mean single sequence MFE	-33.13
Consensus MFE	-19.59
Energy contribution	-22.03
Covariance contribution	2.45
Combinations/Pair	1.17
Mean z-score	-2.75
Structure conservation index	0.59
SVM decision value	2.11
SVM RNA-class probability	0.988280
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8114841 95 + 22224390
CCUCCUCCUCCACGGUCACAUCGUCCUCCACCGCCGCCCGCAUAGCCACCAAGGCUCCCAUUUUGGCGGCUGUUC---------------CGGCUGCCCAGGAGCAAAUC
....(((((....((.(.....).))......((.(((.(.((((((.((((((......)))))).)))))).)---------------.))).))..)))))...... ( -30.30)
>DroPse_CAF1 15924 101 + 1
CUUCCUCCUCCGCCG---CCUACUCCUCCUCCACCACCCGCUCAGCCACAAAGCCAACUG------CAGCUGGAGCCCAGCCCGUCCAGUCAGCAGCGCAGGAGCAGAUC
....(((((.(((.(---(..(((...............((...((......)).....)------).(((((...)))))......)))..)).))).)))))...... ( -24.30)
>DroSec_CAF1 17850 95 + 1
CCUCCUCCACCACGGUCACAUCCUCCUCCACCGCCGCCCGCACAGCCACCAAGGCUCCCGUUUUGGCGGCUGUUC---------------CGGCUGCCCAGGAGCAGAUC
.((.((((.....((......)).........((.(((.(.((((((.(((((((....))))))).)))))).)---------------.))).))...)))).))... ( -36.90)
>DroSim_CAF1 5771 93 + 1
--UCCUCUUUAAUUUUAACAUCCUCCUCCACCGCCGCCCGCACAGCCACCAAGGCUCCCGUUUUGGCGGCUGUUC---------------CGGCUGCCCAGGAGCAGAUC
--....................((.((((...((.(((.(.((((((.(((((((....))))))).)))))).)---------------.))).))...)))).))... ( -35.60)
>DroEre_CAF1 4698 95 + 1
CCUCCUCCUCCGCGGUCACAUCCUCCGCCACCGCCGCCCGCACGGCCACCAAGGCACCCGUUUUGGCCGCUGGAC---------------CGGCUGCCCAGGAGCAGAUC
.((.(((((..((((.........))))....((.(((.(..((((..(((((((....)))))))..))))..)---------------.))).))..))))).))... ( -35.50)
>DroYak_CAF1 5272 95 + 1
CCUCCUCCUCCGCGGUCACUUCCUCCUCCACCGCCGCCCGCACAGCCACCAAGGCACCCGUUCUGGCGGCUGGAA---------------AGGCUGCUCAGGAGCAGAUC
.((.(((((..((((((...............((.....)).(((((.(((..((....))..))).)))))...---------------.))))))..))))).))... ( -36.20)
>consensus
CCUCCUCCUCCACGGUCACAUCCUCCUCCACCGCCGCCCGCACAGCCACCAAGGCACCCGUUUUGGCGGCUGGAC_______________CGGCUGCCCAGGAGCAGAUC
....(((((...(((((...............((.....)).(((((.(((((((....))))))).)))))...................)))))...)))))...... (-19.59 = -22.03 +   2.45)

alignment

secondary structure

dotplot

Window 3

Location	8,114,841 – 8,114,936
Length	95
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	77.13
Mean single sequence MFE	-42.85
Consensus MFE	-24.48
Energy contribution	-25.54
Covariance contribution	1.06
Combinations/Pair	1.33
Mean z-score	-2.18
Structure conservation index	0.57
SVM decision value	1.29
SVM RNA-class probability	0.938469
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8114841 95 - 22224390
GAUUUGCUCCUGGGCAGCCG---------------GAACAGCCGCCAAAAUGGGAGCCUUGGUGGCUAUGCGGGCGGCGGUGGAGGACGAUGUGACCGUGGAGGAGGAGG
..(((.((((((((((.((.---------------..((.((((((...((((..((....))..))))...)))))).))...))....)))..))).)))).)))... ( -36.20)
>DroPse_CAF1 15924 101 - 1
GAUCUGCUCCUGCGCUGCUGACUGGACGGGCUGGGCUCCAGCUG------CAGUUGGCUUUGUGGCUGAGCGGGUGGUGGAGGAGGAGUAGG---CGGCGGAGGAGGAAG
......(((((.(((((((.(((.(((.((((((...)))))).------..)))..(((..(.(((.....))).)..)))....))).))---))))).))))).... ( -42.00)
>DroSec_CAF1 17850 95 - 1
GAUCUGCUCCUGGGCAGCCG---------------GAACAGCCGCCAAAACGGGAGCCUUGGUGGCUGUGCGGGCGGCGGUGGAGGAGGAUGUGACCGUGGUGGAGGAGG
......(((((..((.(((.---------------(.(((((((((((..(....)..))))))))))).).))).(((((.(.........).))))).))..))))). ( -43.40)
>DroSim_CAF1 5771 93 - 1
GAUCUGCUCCUGGGCAGCCG---------------GAACAGCCGCCAAAACGGGAGCCUUGGUGGCUGUGCGGGCGGCGGUGGAGGAGGAUGUUAAAAUUAAAGAGGA--
..(((.((((...((.(((.---------------(.(((((((((((..(....)..))))))))))).).))).))...)))).)))...................-- ( -41.40)
>DroEre_CAF1 4698 95 - 1
GAUCUGCUCCUGGGCAGCCG---------------GUCCAGCGGCCAAAACGGGUGCCUUGGUGGCCGUGCGGGCGGCGGUGGCGGAGGAUGUGACCGCGGAGGAGGAGG
...((.(((((..((.((((---------------.(((.(((((((...((((...)))).)))))))..)))))))(((.(((.....))).)))))..))))).)). ( -48.40)
>DroYak_CAF1 5272 95 - 1
GAUCUGCUCCUGAGCAGCCU---------------UUCCAGCCGCCAGAACGGGUGCCUUGGUGGCUGUGCGGGCGGCGGUGGAGGAGGAAGUGACCGCGGAGGAGGAGG
...((.(((((..((..(((---------------(..(.((((((...((((.(((....))).))))...)))))).)..)))).((......))))..))))).)). ( -45.70)
>consensus
GAUCUGCUCCUGGGCAGCCG_______________GAACAGCCGCCAAAACGGGAGCCUUGGUGGCUGUGCGGGCGGCGGUGGAGGAGGAUGUGACCGCGGAGGAGGAGG
...((.(((((..((.........................((((((...((((..((....))..))))...))))))(((.............)))))..))))).)). (-24.48 = -25.54 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:31 2006