Locus 2933

Sequence ID	2R_DroMel_CAF1
Location	10,161,886 – 10,162,003
Length	117
Max. P	0.708293

overview

Window 0

Location	10,161,886 – 10,162,003
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.94
Mean single sequence MFE	-29.45
Consensus MFE	-19.58
Energy contribution	-21.34
Covariance contribution	1.76
Combinations/Pair	1.08
Mean z-score	-1.85
Structure conservation index	0.66
SVM decision value	0.13
SVM RNA-class probability	0.598270
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10161886 117 + 20766785
AAGUAAGUAAUGGCAAUGGCAAUGGCUAUGGAAAUGACAGCAUGCCAAUGGAAAUCUGCUUACAAUUUUUAUGCCAGGCCAUUCCAAAUUUGAUUGCCAGCCAACC---AAAGGCCCGGU
..........(((.((((((..((((.((((((((...((((..((...)).....))))....)))))))))))).))))))))).........(((.(((....---...)))..))) ( -31.80)
>DroSec_CAF1 1689 113 + 1
AAGUAAGUAAUGGCAAUGGCAAUGUC------AAUGGCAGCAUGCCAAUGGAAAUCUGCUUACAAUUUUUAUGCCAGACCAUUCCAAAUUUGAUUGCCAGCCAACC-CCAUUGGCUCGGU
..........(((((((((((.(((.------....)))...))))..(((((.(((((.............).))))...)))))......)))))))(((((..-...)))))..... ( -29.92)
>DroSim_CAF1 1616 113 + 1
AAGUAAGUAAUGGCAAUGGCAAUGUC------AAUGGCAGCAUGCCAAUGGAAAUCUGCUUACAAUUUUUAUGCCAGACCAUUCCAAAUUUGAUUGCCAGCCAACC-CCAUUGGCUCGGU
..........(((((((((((.(((.------....)))...))))..(((((.(((((.............).))))...)))))......)))))))(((((..-...)))))..... ( -29.92)
>DroEre_CAF1 1684 98 + 1
UAGUAAGUAAUGGCACUG------------------GCAGCAUGCCAGUGGAAAUCUGCUUACAAUU-UUAUGCCAGACCGUUCCAAAUUUGAUUGCCAGCCA---ACCAUUGGCUCGGU
..(((((((((..(((((------------------((.....)))))))...)).)))))))....-...........................((((((((---.....))))).))) ( -29.00)
>DroYak_CAF1 1654 102 + 1
UAGUAAGUAAUGGCAAUG------------------GCAGCAUGCCAAUGGAAAUCUGCUUACAAUUUUUAUGCCAAACCAUUCCAAAUUUGAUUGCCAGCCAGCCACCAUUGGCUCGGU
..........((((((((------------------((.....)))..(((((....((.............)).......)))))......)))))))((((((((....))))).))) ( -26.62)
>consensus
AAGUAAGUAAUGGCAAUGGCAAUG_C______AAUGGCAGCAUGCCAAUGGAAAUCUGCUUACAAUUUUUAUGCCAGACCAUUCCAAAUUUGAUUGCCAGCCAACC_CCAUUGGCUCGGU
..........(((((((.................((((.....)))).(((((.(((((.............).))))...)))))......)))))))(((((......)))))..... (-19.58 = -21.34 +   1.76)

alignment

secondary structure

dotplot

Window 1

Location	10,161,886 – 10,162,003
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.94
Mean single sequence MFE	-31.56
Consensus MFE	-22.46
Energy contribution	-23.38
Covariance contribution	0.92
Combinations/Pair	1.11
Mean z-score	-1.86
Structure conservation index	0.71
SVM decision value	0.37
SVM RNA-class probability	0.708293
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10161886 117 - 20766785
ACCGGGCCUUU---GGUUGGCUGGCAAUCAAAUUUGGAAUGGCCUGGCAUAAAAAUUGUAAGCAGAUUUCCAUUGGCAUGCUGUCAUUUCCAUAGCCAUUGCCAUUGCCAUUACUUACUU
.((((((((((---(((((.....))))))))........)))))))..........(((((..(((...((.(((((.(((((.......)))))...))))).))..))).))))).. ( -33.50)
>DroSec_CAF1 1689 113 - 1
ACCGAGCCAAUGG-GGUUGGCUGGCAAUCAAAUUUGGAAUGGUCUGGCAUAAAAAUUGUAAGCAGAUUUCCAUUGGCAUGCUGCCAUU------GACAUUGCCAUUGCCAUUACUUACUU
..........(((-(..((((((((((((((...(((((..((((((((.......)))...)))))))))).((((.....))))))------))..))))))..))))...))))... ( -32.20)
>DroSim_CAF1 1616 113 - 1
ACCGAGCCAAUGG-GGUUGGCUGGCAAUCAAAUUUGGAAUGGUCUGGCAUAAAAAUUGUAAGCAGAUUUCCAUUGGCAUGCUGCCAUU------GACAUUGCCAUUGCCAUUACUUACUU
..........(((-(..((((((((((((((...(((((..((((((((.......)))...)))))))))).((((.....))))))------))..))))))..))))...))))... ( -32.20)
>DroEre_CAF1 1684 98 - 1
ACCGAGCCAAUGGU---UGGCUGGCAAUCAAAUUUGGAACGGUCUGGCAUAA-AAUUGUAAGCAGAUUUCCACUGGCAUGCUGC------------------CAGUGCCAUUACUUACUA
....(((((.....---)))))(((..........((((..((((((((...-...)))...)))))))))((((((.....))------------------)))))))........... ( -30.60)
>DroYak_CAF1 1654 102 - 1
ACCGAGCCAAUGGUGGCUGGCUGGCAAUCAAAUUUGGAAUGGUUUGGCAUAAAAAUUGUAAGCAGAUUUCCAUUGGCAUGCUGC------------------CAUUGCCAUUACUUACUA
.((.(((((....))))))).((((((.......(((((..(((((.((.......)))))))....))))).((((.....))------------------)))))))).......... ( -29.30)
>consensus
ACCGAGCCAAUGG_GGUUGGCUGGCAAUCAAAUUUGGAAUGGUCUGGCAUAAAAAUUGUAAGCAGAUUUCCAUUGGCAUGCUGCCAUU______G_CAUUGCCAUUGCCAUUACUUACUU
....(((((........)))))((((((......(((((..((((((((.......)))...)))))))))).((((.....)))).................))))))........... (-22.46 = -23.38 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:10 2006