Locus 3413

Sequence ID	X_DroMel_CAF1
Location	9,128,034 – 9,128,193
Length	159
Max. P	0.928469

overview

Window 1

Location	9,128,034 – 9,128,129
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	94.53
Mean single sequence MFE	-38.54
Consensus MFE	-35.90
Energy contribution	-36.70
Covariance contribution	0.80
Combinations/Pair	1.10
Mean z-score	-1.39
Structure conservation index	0.93
SVM decision value	1.19
SVM RNA-class probability	0.928469
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9128034 95 + 22224390
CAUUGGGCGCCGCUGUGGCGGUAGAUGCAUCGGCAUUUCCAGUGGCGGCGCUAUUUCCAGCAGCUGAUUUGUUGUUGGCGGAUCCUCCCCCUGUG
(((.(((((((((..(...((.((((((....)))))))).)..))))))).....((((((((......)))))))).((.....)).)).))) ( -40.50)
>DroSec_CAF1 3859 95 + 1
CAACGGGCGCCGCUGCGGCGGUAGAUGCAUCGGCAUUUCCAGUGGCGGCGCUAUUUACAACAGCUGAUUUAUUGUUGGUGGAUCCUCCCCCUGUG
..(((((((((((..(...((.((((((....)))))))).)..))))))).(((((((((((........))))).)))))).......)))). ( -36.20)
>DroSim_CAF1 2486 95 + 1
CAACGGGCGCCGCUACGGCGGUAGAUGCAUCGGCAUUUCCAGUGGCGGCGCUAUUUCCAGCAGCUGAUUUGUUGUUGGUGGAUCCUCCCCCUGUG
..((((((((((((((...((.((((((....)))))))).)))))))))).....((((((((......)))))))).((.....))..)))). ( -43.80)
>DroEre_CAF1 3842 95 + 1
CAACGGGCGCCGCUGAGGCGGCAGCUGCAUCGGCAUUUCCAGUGGCGGCGCUAUUUCCAGCAGCUGAUUUGUUGUUGGUGGAUCCUCCCCCUGCG
.....((((((((....))))).)))(((..((....(((((((((...)))))..((((((((......)))))))))))).....))..))). ( -35.90)
>DroYak_CAF1 3933 95 + 1
CAACGGGCGCCGCUGAGGCGGCAGCUGCAUCGGCAUUUCCAGUGGCGGCGCUAUUUCCAGCAGCUGAUUUGUUGUUGGUGGAUCCUCCCCCUGUG
..(((((.(((((((.(((....)))((....)).....)))))))((..(((...((((((((......)))))))))))..))....))))). ( -36.30)
>consensus
CAACGGGCGCCGCUGAGGCGGUAGAUGCAUCGGCAUUUCCAGUGGCGGCGCUAUUUCCAGCAGCUGAUUUGUUGUUGGUGGAUCCUCCCCCUGUG
.....(((((((((((...((.((((((....)))))))).)))))))))))....((((((((......)))))))).((.....))....... (-35.90 = -36.70 +   0.80)

alignment

secondary structure

dotplot

Window 2

Location	9,128,103 – 9,128,193
Length	90
Sequences	4
Columns	96
Reading direction	forward
Mean pairwise identity	90.50
Mean single sequence MFE	-30.58
Consensus MFE	-28.01
Energy contribution	-27.95
Covariance contribution	-0.06
Combinations/Pair	1.12
Mean z-score	-1.59
Structure conservation index	0.92
SVM decision value	0.67
SVM RNA-class probability	0.818908
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9128103 90 + 22224390
UGUUGUUGGCGGAUCCUCCCCCUGUGGCAGCACCACUACC------ACCGCCGCCAACCCCUCGGCCGUCCAUCUUCUUGGUGGAAUUGCGCGUUC
....((((((((...........((((.....))))....------....))))))))....((((..((((((.....))))))...)).))... ( -29.81)
>DroSec_CAF1 3928 90 + 1
UAUUGUUGGUGGAUCCUCCCCCUGUGGCAGCACCACCACC------GCCGCCGCCAACCCCUCGCCCAUCCAUCUUCUUGGUGGAAUUGCGCGUUC
....((((((((...........((((.....))))....------....))))))))....(((.((((((((.....))))))..)).)))... ( -27.41)
>DroSim_CAF1 2555 90 + 1
UGUUGUUGGUGGAUCCUCCCCCUGUGGCAGCACCACCACC------GCCGCCGCCAACCCCUCGCCCGUCCAUCUUCUUGGUGGAAUUGCGCGUUC
....((((((((...........((((.....))))....------....))))))))..(.(((...((((((.....))))))...))).)... ( -28.21)
>DroYak_CAF1 4002 96 + 1
UGUUGUUGGUGGAUCCUCCCCCUGUGGCAGCGCCACCCCCGCCGCCACCGCCAGCAGCCCCUCGCCCAUCCAUCUUCUUGGUGGAAUUGCGCGUUC
.(((((((((((.....))....(((((.(((.......))).))))).)))))))))....(((.((((((((.....))))))..)).)))... ( -36.90)
>consensus
UGUUGUUGGUGGAUCCUCCCCCUGUGGCAGCACCACCACC______ACCGCCGCCAACCCCUCGCCCAUCCAUCUUCUUGGUGGAAUUGCGCGUUC
.((((.((((((...........((((.....))))...........)))))).))))..(.(((...((((((.....))))))...))).)... (-28.01 = -27.95 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:44 2006