Locus 6613

Sequence ID	X_DroMel_CAF1
Location	16,487,787 – 16,487,947
Length	160
Max. P	0.974351

overview

Window 1

Location	16,487,787 – 16,487,907
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.42
Mean single sequence MFE	-46.37
Consensus MFE	-38.00
Energy contribution	-39.04
Covariance contribution	1.04
Combinations/Pair	1.12
Mean z-score	-1.95
Structure conservation index	0.82
SVM decision value	1.24
SVM RNA-class probability	0.934829
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16487787 120 - 22224390
CUGGCACACCAGCGCCGUGAUCUUCAUCAUGGUGCUGGUCUUUGUGGCCCACUACUUCCCCAUUUCGUGGACGAACCAGAUCAAGUUCAUGUAUCGCCGCCGUUUUCCGCUAAAGAGGCG
..(((..((((((((((((((....))))))))))))))......(((((((..............))))..((((........)))).......))))))......((((.....)))) ( -43.34)
>DroSec_CAF1 25962 120 - 1
CUGGUACACGAGCGCCGUCGCCUUGAUCAUGGUGCUGGUCUUUGCGGCCCACUACUUCCCCAGUUCGUGGGCGAACCAGAUCAAGACCAUGUACCGCCGCCGCUUUCCGCCAAAUAGGCG
..((((((.(.(((....)))(((((((.((((((........)).((((((.(((.....)))..))))))..)))))))))))..).))))))((....))....((((.....)))) ( -43.70)
>DroSim_CAF1 23071 120 - 1
CUGGUACACCAGCGCCGUGGCCUUCAUCAUGGUGCUGGUCUUUGCGGCCCACUACUUCCCCAGUUCGUGGGCGAACCAGAUCAAGACCAUGUACCGCCGCCGCUUUCCGCCAAAGAGGCG
..((((((..((((((((((......))))))))))((((((....((((((.(((.....)))..))))))((......)))))))).))))))..((((.((((.....)))).)))) ( -50.20)
>DroEre_CAF1 16965 120 - 1
CUGGCACACCAGCGCCCUGGUCUUUAUCAUGGUUCUGCUCUUUGUGGCCUACUACUUUCCCAGGUCGUGGGCCCGCCAGGUCAAGAUCAUGUACCGUCGCCGCUUUCCGCCAAAGAGGCG
..((((((((((....)))))......((((((..((..(((.(((((((((.(((......))).))))).)))).))).))..))))))....)).)))......((((.....)))) ( -41.60)
>DroYak_CAF1 18017 120 - 1
CUGGCACACCAGCGCCCUGGUCUUCAUCACGGUGCUGGUCUUUGUGGCCCACUACUUUCCCAGGUCGUGGGCGCGCCAGGCGAAGAUCAUGUACCGCCGCCGCUUUCCGCCAAAGAGGCG
.((((.((((((((((.((((....)))).))))))))).......((((((.(((......))).))))))).))))((((............))))(((.((((.....)))).))). ( -53.00)
>consensus
CUGGCACACCAGCGCCGUGGUCUUCAUCAUGGUGCUGGUCUUUGUGGCCCACUACUUCCCCAGUUCGUGGGCGAACCAGAUCAAGAUCAUGUACCGCCGCCGCUUUCCGCCAAAGAGGCG
(((((..(((((((((((((......))))))))))))).......((((((..............))))))..)))))..................((((.((((.....)))).)))) (-38.00 = -39.04 +   1.04)

alignment

secondary structure

dotplot

Window 2

Location	16,487,827 – 16,487,947
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.33
Mean single sequence MFE	-44.52
Consensus MFE	-34.06
Energy contribution	-34.62
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.46
Structure conservation index	0.77
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16487827 120 + 22224390
UCUGGUUCGUCCACGAAAUGGGGAAGUAGUGGGCCACAAAGACCAGCACCAUGAUGAAGAUCACGGCGCUGGUGUGCCAGCUGCUGAAGUAAGCCAUAACGGCGCCAAUGGCCUGCAGCA
(((..((((....))))..)))...((.(..(((((.....((((((.((.((((....)))).)).))))))(((((....(((......)))......)))))...)))))..).)). ( -46.00)
>DroSec_CAF1 26002 120 + 1
UCUGGUUCGCCCACGAACUGGGGAAGUAGUGGGCCGCAAAGACCAGCACCAUGAUCAAGGCGACGGCGCUCGUGUACCAGCUGCUUAAGUAAACCAUGAAGCCGCCUAUGGCCUGCAGCA
((..(((((....)))))..))...((.(..((((((........))..........((((...(((..(((((.....(((.....)))....))))).)))))))..))))..).)). ( -41.00)
>DroSim_CAF1 23111 120 + 1
UCUGGUUCGCCCACGAACUGGGGAAGUAGUGGGCCGCAAAGACCAGCACCAUGAUGAAGGCCACGGCGCUGGUGUACCAGCUGCUUAAGUAAACCAUGAAGCCGCCUAUGGCCUGCAGCA
.((((((.((((((..(((.....))).))))))......)))))).....((.((.(((((((((((((((....)))))(((....))).........))))....)))))).)).)) ( -45.70)
>DroEre_CAF1 17005 120 + 1
CCUGGCGGGCCCACGACCUGGGAAAGUAGUAGGCCACAAAGAGCAGAACCAUGAUAAAGACCAGGGCGCUGGUGUGCCAGCUGCUGAAGUAAACCAGGACACCGCCAAUGGCUUGCAGCA
..((((((........(((((...((((((.((((((....(((....((.((........))))..))).))).))).))))))........)))))...))))))...((.....)). ( -39.20)
>DroYak_CAF1 18057 120 + 1
CCUGGCGCGCCCACGACCUGGGAAAGUAGUGGGCCACAAAGACCAGCACCGUGAUGAAGACCAGGGCGCUGGUGUGCCAGCUGCUGAAGUAAACCAGGACAACGCCCAUGGCCUGCAGCA
.(((((((((((((...((.....))..)))))).......((((((.((.((........)).)).)))))))))))))..((((.((....(((((.......)).))).)).)))). ( -50.70)
>consensus
UCUGGUUCGCCCACGAACUGGGGAAGUAGUGGGCCACAAAGACCAGCACCAUGAUGAAGACCACGGCGCUGGUGUGCCAGCUGCUGAAGUAAACCAUGACGCCGCCAAUGGCCUGCAGCA
..((((..((((((...((.....))..)))))).....(.((((((.((.((........)).)).)))))).)))))(((((....(....).........(((...)))..))))). (-34.06 = -34.62 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	16,487,827 – 16,487,947
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.33
Mean single sequence MFE	-48.85
Consensus MFE	-40.28
Energy contribution	-41.56
Covariance contribution	1.28
Combinations/Pair	1.16
Mean z-score	-2.21
Structure conservation index	0.82
SVM decision value	1.73
SVM RNA-class probability	0.974351
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16487827 120 - 22224390
UGCUGCAGGCCAUUGGCGCCGUUAUGGCUUACUUCAGCAGCUGGCACACCAGCGCCGUGAUCUUCAUCAUGGUGCUGGUCUUUGUGGCCCACUACUUCCCCAUUUCGUGGACGAACCAGA
(((((.(((((...)))(((.....)))...)).))))).(((((((((((((((((((((....))))))))))))))....)))..((((..............)))).....)))). ( -48.14)
>DroSec_CAF1 26002 120 - 1
UGCUGCAGGCCAUAGGCGGCUUCAUGGUUUACUUAAGCAGCUGGUACACGAGCGCCGUCGCCUUGAUCAUGGUGCUGGUCUUUGCGGCCCACUACUUCCCCAGUUCGUGGGCGAACCAGA
.((((((((((......)))))...((....))...)))))((((.(.((((.((((.((((........)))).)))).)))).)((((((.(((.....)))..))))))..)))).. ( -42.80)
>DroSim_CAF1 23111 120 - 1
UGCUGCAGGCCAUAGGCGGCUUCAUGGUUUACUUAAGCAGCUGGUACACCAGCGCCGUGGCCUUCAUCAUGGUGCUGGUCUUUGCGGCCCACUACUUCCCCAGUUCGUGGGCGAACCAGA
.((((((((((......)))))...((....))...)))))((((.((((((((((((((......))))))))))))).......((((((.(((.....)))..))))))).)))).. ( -51.00)
>DroEre_CAF1 17005 120 - 1
UGCUGCAAGCCAUUGGCGGUGUCCUGGUUUACUUCAGCAGCUGGCACACCAGCGCCCUGGUCUUUAUCAUGGUUCUGCUCUUUGUGGCCUACUACUUUCCCAGGUCGUGGGCCCGCCAGG
.(((((.........)))))..((((((.......(((((((((....)))))(((.((((....)))).)))..))))....(.(((((((.(((......))).)))))))))))))) ( -44.00)
>DroYak_CAF1 18057 120 - 1
UGCUGCAGGCCAUGGGCGUUGUCCUGGUUUACUUCAGCAGCUGGCACACCAGCGCCCUGGUCUUCAUCACGGUGCUGGUCUUUGUGGCCCACUACUUUCCCAGGUCGUGGGCGCGCCAGG
(((((.((((((.((((...))))))))...)).))))).(((((.((((((((((.((((....)))).))))))))).......((((((.(((......))).))))))).))))). ( -58.30)
>consensus
UGCUGCAGGCCAUAGGCGGCGUCAUGGUUUACUUCAGCAGCUGGCACACCAGCGCCGUGGUCUUCAUCAUGGUGCUGGUCUUUGUGGCCCACUACUUCCCCAGUUCGUGGGCGAACCAGA
(((((.(((((((.((.....)))))))))....))))).(((((..(((((((((((((......))))))))))))).......((((((..............))))))..))))). (-40.28 = -41.56 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:18 2006