Locus 7042

Sequence ID	X_DroMel_CAF1
Location	17,611,616 – 17,611,709
Length	93
Max. P	0.995075

overview

Window 7

Location	17,611,616 – 17,611,709
Length	93
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	85.77
Mean single sequence MFE	-39.44
Consensus MFE	-32.72
Energy contribution	-33.16
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-2.11
Structure conservation index	0.83
SVM decision value	1.42
SVM RNA-class probability	0.952639
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17611616 93 + 22224390
----GCACGGGCACCAGCACAACCACC------------AUCAGCACCACCUUCAUCAUGGCAGUGCAUCCGCCUCGGCGGC---GGCAGCAGUGGCCAAUCUGGUGCACCA
----....(((((((((.....((((.------------....((((..((........))..))))..(((((.....)))---)).....)))).....))))))).)). ( -38.50)
>DroSec_CAF1 9004 93 + 1
----GCACGGGCACCAGCACAACCACC------------AUCAGCACCACCUUCACCAUGGCAGUGCAUCCGCCUCGGCGGC---GGCGGCAGUGGCCAAUCUGGUGCACCA
----....(((((((((.....((((.------------.((.((((..((........))..))))..(((((.....)))---)).))..)))).....))))))).)). ( -39.30)
>DroSim_CAF1 1274 93 + 1
----GCACGGGCACCAGCACAACCACC------------AUCAGCACCACCUUCACCAUGGCAGUGCAUCCGCCUCGGCGGC---GGCGGCAGUGGCCAAUCUGGUGCACCA
----....(((((((((.....((((.------------.((.((((..((........))..))))..(((((.....)))---)).))..)))).....))))))).)). ( -39.30)
>DroEre_CAF1 10781 109 + 1
ACGGGCAUGGGCAGCAGCACAACCACCACCAGCAUCAGCAUCAGCACCACCUUCAUCAUGGCAGUGCAUCCGCCUCGGCGGC---GGCGGCAGUGGCCAAUCUGGUGCACCA
.......((((((.(((.....((((..((.((....))....((((..((........))..))))..(((((.....)))---)).))..)))).....))).))).))) ( -38.00)
>DroYak_CAF1 8203 112 + 1
AUGGGCAUGGGCACCAGCACAACCAGCACCAGCAUCCGCAUCAGCACCAUCUACACCAUGGCAGUGCAUCCGCCUCGGCGGCGGCGGCGGCAGUUGCGAAUCUGGUGCACCA
.(((((.(((...))))).......(((((((.((.((((.(.((((..((........))..))))..((((((((....))).)))))..).)))).))))))))).))) ( -42.10)
>consensus
____GCACGGGCACCAGCACAACCACC____________AUCAGCACCACCUUCACCAUGGCAGUGCAUCCGCCUCGGCGGC___GGCGGCAGUGGCCAAUCUGGUGCACCA
........(((((((((.....((((.................((((..((........))..))))..((((....))))...........)))).....))))))).)). (-32.72 = -33.16 +   0.44)

alignment

secondary structure

dotplot

Window 8

Location	17,611,616 – 17,611,709
Length	93
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	85.77
Mean single sequence MFE	-50.68
Consensus MFE	-42.50
Energy contribution	-42.90
Covariance contribution	0.40
Combinations/Pair	1.06
Mean z-score	-2.66
Structure conservation index	0.84
SVM decision value	2.54
SVM RNA-class probability	0.995075
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17611616 93 - 22224390
UGGUGCACCAGAUUGGCCACUGCUGCC---GCCGCCGAGGCGGAUGCACUGCCAUGAUGAAGGUGGUGCUGAU------------GGUGGUUGUGCUGGUGCCCGUGC----
.((.(((((((...(((((((....((---(((.....)))))..((((..((........))..))))....------------)))))))...)))))))))....---- ( -49.40)
>DroSec_CAF1 9004 93 - 1
UGGUGCACCAGAUUGGCCACUGCCGCC---GCCGCCGAGGCGGAUGCACUGCCAUGGUGAAGGUGGUGCUGAU------------GGUGGUUGUGCUGGUGCCCGUGC----
.((.(((((((...(((((((((((((---..(((((.(((((.....))))).)))))..))))))......------------)))))))...)))))))))....---- ( -50.90)
>DroSim_CAF1 1274 93 - 1
UGGUGCACCAGAUUGGCCACUGCCGCC---GCCGCCGAGGCGGAUGCACUGCCAUGGUGAAGGUGGUGCUGAU------------GGUGGUUGUGCUGGUGCCCGUGC----
.((.(((((((...(((((((((((((---..(((((.(((((.....))))).)))))..))))))......------------)))))))...)))))))))....---- ( -50.90)
>DroEre_CAF1 10781 109 - 1
UGGUGCACCAGAUUGGCCACUGCCGCC---GCCGCCGAGGCGGAUGCACUGCCAUGAUGAAGGUGGUGCUGAUGCUGAUGCUGGUGGUGGUUGUGCUGCUGCCCAUGCCCGU
(((.(((.(((...((((((..((.((---(((.....)))))..((((..((........))..))))....((....)).))..))))))...))).))))))....... ( -50.80)
>DroYak_CAF1 8203 112 - 1
UGGUGCACCAGAUUCGCAACUGCCGCCGCCGCCGCCGAGGCGGAUGCACUGCCAUGGUGUAGAUGGUGCUGAUGCGGAUGCUGGUGCUGGUUGUGCUGGUGCCCAUGCCCAU
(((.(((((((...(((((((..((((.(((((.....)))))..(((((((...((..(.....)..))...)))).))).))))..)))))))))))))))))....... ( -51.40)
>consensus
UGGUGCACCAGAUUGGCCACUGCCGCC___GCCGCCGAGGCGGAUGCACUGCCAUGGUGAAGGUGGUGCUGAU____________GGUGGUUGUGCUGGUGCCCGUGC____
(((.(((((((......(((.((((((....((((....))))..((((((((........))))))))................)))))).)))))))))))))....... (-42.50 = -42.90 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:50 2006