Locus 1706

Sequence ID	2R_DroMel_CAF1
Location	6,452,594 – 6,452,739
Length	145
Max. P	0.942237

overview

Window 9

Location	6,452,594 – 6,452,706
Length	112
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	83.19
Mean single sequence MFE	-21.05
Consensus MFE	-15.44
Energy contribution	-15.50
Covariance contribution	0.06
Combinations/Pair	1.06
Mean z-score	-1.55
Structure conservation index	0.73
SVM decision value	0.11
SVM RNA-class probability	0.589221
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6452594 112 - 20766785
GCCGUCAUCCAGGCAAAACUCUUGAUGAGCAGCAACUGCGGCCAAACUAAAGCGACACCGAAAAAAAAACAACACAAGAAUA--UACAUCACUCUAUCUUUAAGAAACAAUAAU
(((.(((((.(((......))).)))))((((...)))))))........................................--.............................. ( -14.50)
>DroSec_CAF1 28319 110 - 1
GCCGUCAUCCAGGCAAAACUCCUGAUGAGCAGCAACUGCGGCCAAACUAAAGCGGCACCGAAAA--AAACAGCACAAGGAUA--UACAACACUCCAUCUUUAAGAAUCAAUAAU
(((.(((((.(((.......))))))))((((...))))))).....(((((((....))....--...........(((..--........)))..)))))............ ( -19.40)
>DroEre_CAF1 26864 114 - 1
GCCGUCAUCCAGGCAAAACUCCUGAUGAGCGGCAACUGCGGCCAAACUAAAGCGGCACCGCAAAAAAUGCCUCACAAGAAUACAUAUGUACCUUCAUCCGUACCUAUCAAUUAU
(((((((((.(((.......)))))))).))))...(((((..........(((....)))................((((((....)))..)))..)))))............ ( -26.80)
>DroYak_CAF1 30047 112 - 1
GCCGUCAUCCAGGCAAAACUCCUGAUGAGCUGCAACUGCGGCCAAACUAAAGCGGCACCGAAAAAAAAAACUCUCAAUAAUA--UAUGCACCUUAAUAUGUAACGAUCAAUAAG
(((((((((.(((.......))))))))(((((....)))))..........)))).......................(((--(((........))))))............. ( -23.50)
>consensus
GCCGUCAUCCAGGCAAAACUCCUGAUGAGCAGCAACUGCGGCCAAACUAAAGCGGCACCGAAAAAAAAACAUCACAAGAAUA__UACAUAACUCCAUCUGUAACAAUCAAUAAU
(((((((((.(((.......))))))))((.((....)).))..........)))).......................................................... (-15.44 = -15.50 +   0.06)

alignment

secondary structure

dotplot

Window 0

Location	6,452,632 – 6,452,739
Length	107
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	85.93
Mean single sequence MFE	-32.60
Consensus MFE	-25.96
Energy contribution	-26.68
Covariance contribution	0.72
Combinations/Pair	1.12
Mean z-score	-2.17
Structure conservation index	0.80
SVM decision value	1.32
SVM RNA-class probability	0.942237
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6452632 107 - 20766785
GGCCGUGCAAAGUGCUGCCGUUGCUGAUAAUAAGC--CGUCAUCCAGGCAAAACUCUUGAUGAGCAGCAACUGCGGCC-AAACUAAAGCGACACCGAAAAAAAAACAACA
((...(((..((((((((.(((((((.......((--(........)))....(((.....)))))))))).))))).-..)))...)))...))............... ( -32.20)
>DroSec_CAF1 28357 105 - 1
GGCCGUGCAAAGUGCUGCCGUUGCUGAUAAUAAGC--CGUCAUCCAGGCAAAACUCCUGAUGAGCAGCAACUGCGGCC-AAACUAAAGCGGCACCGAAAA--AAACAGCA
.(((((....((((((((.(((((((.......((--(........)))....(((.....)))))))))).))))).-..)))...)))))........--........ ( -36.10)
>DroEre_CAF1 26904 107 - 1
GGCCGUGCAAAGUGCUGCCGUUGCUGAUAAUAAGC--CGUCAUCCAGGCAAAACUCCUGAUGAGCGGCAACUGCGGCC-AAACUAAAGCGGCACCGCAAAAAAUGCCUCA
.(((((....((((((((.(((((((.......((--(........)))....(((.....)))))))))).))))).-..)))...)))))...(((.....))).... ( -36.70)
>DroYak_CAF1 30085 107 - 1
GGCCGUGCAAAGUGCUGCCGUUGCUGAUAAUAAGC--CGUCAUCCAGGCAAAACUCCUGAUGAGCUGCAACUGCGGCC-AAACUAAAGCGGCACCGAAAAAAAAAACUCU
.(((((....((((((((.(((((........(((--..(((((.(((.......)))))))))))))))).))))).-..)))...))))).................. ( -32.70)
>DroAna_CAF1 24989 99 - 1
UGGCGUGCAAAGUGCUGCCGUUGCUGAUAAUAAGCCCCGUCAUCCCGGCAAAACUCCUGAUGAGCUGCAACAGAGGCUGAAACUGAGUUGCAACCGAAG-----------
.((((.((.....))))))(((((.........(((..........)))..(((((....(.((((........)))).)....)))))))))).....----------- ( -25.30)
>consensus
GGCCGUGCAAAGUGCUGCCGUUGCUGAUAAUAAGC__CGUCAUCCAGGCAAAACUCCUGAUGAGCAGCAACUGCGGCC_AAACUAAAGCGGCACCGAAAAAAAAACAUCA
.(((((....((((((((.(((((((............(((.....)))....(((.....)))))))))).)))))....)))...))))).................. (-25.96 = -26.68 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:15 2006