Locus 6461

Sequence ID	X_DroMel_CAF1
Location	16,210,738 – 16,210,828
Length	90
Max. P	0.720644

overview

Window 9

Location	16,210,738 – 16,210,828
Length	90
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	78.00
Mean single sequence MFE	-14.88
Consensus MFE	-12.01
Energy contribution	-12.18
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.05
Structure conservation index	0.81
SVM decision value	0.40
SVM RNA-class probability	0.720644
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16210738 90 + 22224390
AAAAAAAAAUCAAUGA----------UCAAUUGUUAAAAAUACUAUUUAAAC----GCAGGAUCCCGAGGCCUCUUUCGAUAUAAAUGGCAACGAUUCGGAUCC
..........((((..----------...))))...................----...((((((((..(((...............)))..))....)))))) ( -13.86)
>DroSec_CAF1 865 89 + 1
AAAAA-AAUCCAAUGA----------UCAAUUGUUCAAAAUACUAUUUAAAC----GCAGGAUCCCGAGGCCUCUUUUGAUAUUAAUGGCAACGAUUCGGAUCC
.....-.((((...((----------((...((((.(((......))).)))----)...)))).((..(((...............)))..))....)))).. ( -14.26)
>DroSim_CAF1 852 89 + 1
AAAAA-AAUCCUAUGA----------UCAAUUGUUAAAAAUACGAUUUAAAC----GCAGGAUCCCGAGGCCUCUUUCGAUAUUAAUGGCAACGAUUCGGAUCC
.....-..........----------..((((((.......)))))).....----...((((((((..(((...............)))..))....)))))) ( -14.96)
>DroEre_CAF1 837 88 + 1
AAAAA-UAUCAAAACA----------CCAAAUGUA-AAAACACUAUUUAAAC----ACAGGAUCCCGAAGCCUCUUUCGACAUAAAUGGCAACGAUUCGGAUCC
.....-..........----------.........-................----...(((((((((((....))))).......((....))....)))))) ( -12.80)
>DroYak_CAF1 877 84 + 1
AAAAA-AGUCAA--------------UUAAUUGUU-AAAAAACUAUUUAAAC----ACAGGACCCCGAAGCCUCUUUCGACAUAAAUGGCAACGAUUCGGAUCC
.....-......--------------.....((((-.(((.....))).)))----)..(((..((((((((...............))).....))))).))) (  -9.86)
>DroPer_CAF1 1772 99 + 1
--AAA-AGUGCUAUGUAAAAUAUGCUCUAA-CGG-AAACAUACUCUUUCCGCAUUUUCAGGAUCCCGAUGCCUCAUUCGAUAUCAAUGGCAACGAUUCGGAUCC
--.((-(((((...(((.....))).....-.((-(((.......))))))))))))..((((((((.((((...............)))).))....)))))) ( -23.56)
>consensus
AAAAA_AAUCCAAUGA__________UCAAUUGUUAAAAAUACUAUUUAAAC____GCAGGAUCCCGAGGCCUCUUUCGAUAUAAAUGGCAACGAUUCGGAUCC
...........................................................((((((((..(((...............)))..))....)))))) (-12.01 = -12.18 +   0.17)

alignment

secondary structure

dotplot

Window 0

Location	16,210,738 – 16,210,828
Length	90
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	78.00
Mean single sequence MFE	-20.03
Consensus MFE	-14.22
Energy contribution	-14.08
Covariance contribution	-0.14
Combinations/Pair	1.08
Mean z-score	-1.06
Structure conservation index	0.71
SVM decision value	0.11
SVM RNA-class probability	0.590133
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16210738 90 - 22224390
GGAUCCGAAUCGUUGCCAUUUAUAUCGAAAGAGGCCUCGGGAUCCUGC----GUUUAAAUAGUAUUUUUAACAAUUGA----------UCAUUGAUUUUUUUUU
((((((....((..(((.......((....)))))..))))))))...----(((.(((......))).)))......----------................ ( -16.71)
>DroSec_CAF1 865 89 - 1
GGAUCCGAAUCGUUGCCAUUAAUAUCAAAAGAGGCCUCGGGAUCCUGC----GUUUAAAUAGUAUUUUGAACAAUUGA----------UCAUUGGAUU-UUUUU
((((((((.(((..(((...............)))..)))((((....----(((((((......)))))))....))----------)).)))))))-).... ( -20.66)
>DroSim_CAF1 852 89 - 1
GGAUCCGAAUCGUUGCCAUUAAUAUCGAAAGAGGCCUCGGGAUCCUGC----GUUUAAAUCGUAUUUUUAACAAUUGA----------UCAUAGGAUU-UUUUU
((((((....((..(((.......((....)))))..))))))))...----....(((((.(((..(((.....)))----------..))).))))-).... ( -19.71)
>DroEre_CAF1 837 88 - 1
GGAUCCGAAUCGUUGCCAUUUAUGUCGAAAGAGGCUUCGGGAUCCUGU----GUUUAAAUAGUGUUUU-UACAUUUGG----------UGUUUUGAUA-UUUUU
((((((....((..(((.......((....)))))..)))))))).((----(((.(((((((((...-.))))....----------))))).))))-).... ( -19.21)
>DroYak_CAF1 877 84 - 1
GGAUCCGAAUCGUUGCCAUUUAUGUCGAAAGAGGCUUCGGGGUCCUGU----GUUUAAAUAGUUUUUU-AACAAUUAA--------------UUGACU-UUUUU
((((((....((..(((.......((....)))))..))))))))...----....(((.((((..((-(.....)))--------------..))))-.))). ( -16.71)
>DroPer_CAF1 1772 99 - 1
GGAUCCGAAUCGUUGCCAUUGAUAUCGAAUGAGGCAUCGGGAUCCUGAAAAUGCGGAAAGAGUAUGUUU-CCG-UUAGAGCAUAUUUUACAUAGCACU-UUU--
((((((....((.((((.(((....)))....)))).)))))))).((((.(((....(((((((((((-...-...))))))))))).....))).)-)))-- ( -27.20)
>consensus
GGAUCCGAAUCGUUGCCAUUUAUAUCGAAAGAGGCCUCGGGAUCCUGC____GUUUAAAUAGUAUUUUUAACAAUUGA__________UCAUUGGAUU_UUUUU
((((((....((..(((.......((....)))))..))))))))........................................................... (-14.22 = -14.08 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:21 2006