Locus 7736

Sequence ID	3R_DroMel_CAF1
Location	20,777,512 – 20,777,606
Length	94
Max. P	0.902851

overview

Window 2

Location	20,777,512 – 20,777,606
Length	94
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	74.31
Mean single sequence MFE	-27.93
Consensus MFE	-16.81
Energy contribution	-17.59
Covariance contribution	0.78
Combinations/Pair	1.33
Mean z-score	-1.72
Structure conservation index	0.60
SVM decision value	1.03
SVM RNA-class probability	0.902851
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20777512 94 + 27905053
-UGGCGUUCGAUCUAUC------------GAUCGGACGAUCGAACUGUAACGUCUUUCAAAUGGCCAUUUAUGGUGGUUACU------UCUACUGGCCACCGCCAGUUGCUUU
-.(((((((((((....------------))))))))).)).....((((((((........)))......(((((((..((------......))..))))))))))))... ( -31.00)
>DroSim_CAF1 20667 94 + 1
-UGGCGUUCGAUCUAUC------------GAUCGGACGAUCGAACUGUAACGUCUUUCAAAUGGCCAUUUAUGGUGGUUACU------UCUGCUGGCCACCGCCAGUCGCUUU
-((((((((((((....------------))))))))..............(((........))).......(((((((((.------...).))))))))))))........ ( -30.10)
>DroEre_CAF1 21397 103 + 1
-UGGCGUUCGAUCGAUCGGACUAUUGGACGAUUGGACGAUCGAACUGUAACGUCUUUCAAAUGGCCAUUUAUGGUGGUUACU------UCUGGUGGCC---GCCGGUUGCUUU
-....(((((((((((((..(....)..))))....))))))))).((((((((........)))......((((((((((.------....))))))---)))))))))... ( -39.80)
>DroYak_CAF1 19491 87 + 1
-UGGUGUUCGAUCGAUCGG----------------ACGAUCGAACUGUAACGUCUUUCAAAUGGCCAUUUAUGGUGGUUACU------UCUGCUGGCC---GCCGGUUGCUUU
-....(((((((((.....----------------.))))))))).((((((((........)))......((((((((((.------...).)))))---)))))))))... ( -30.80)
>DroAna_CAF1 19366 74 + 1
UUGGCGUUCCAUC------------------------GAUCGAACUGUAACGUCUUUCAAAUGGCCAUUUAUGGUGGCUGCU------CGUUUU---------UGGCUGCUUU
..((((((.((((------------------------....))..)).))))))........(((((...(((((....)).------)))...---------)))))..... ( -15.90)
>DroPer_CAF1 19793 87 + 1
-UGGCGCUCGCUCGAUC--------------------GAUCGAACUGUAACGUCUUUCAAAUAGCCAUUUAUGGCCGCUUCUGACUGCUCUGCUCGUU---GCUGG--GCUUU
-....((((..((((..--------------------..))))...((((((...........((((....)))).((........))......))))---)).))--))... ( -20.00)
>consensus
_UGGCGUUCGAUCGAUC__________________ACGAUCGAACUGUAACGUCUUUCAAAUGGCCAUUUAUGGUGGUUACU______UCUGCUGGCC___GCCGGUUGCUUU
..(((((((((((........................))))))))................(((((((.....)))))))...........((((((....)))))).))).. (-16.81 = -17.59 +   0.78)

alignment

secondary structure

dotplot

Window 3

Location	20,777,512 – 20,777,606
Length	94
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	74.31
Mean single sequence MFE	-24.65
Consensus MFE	-12.30
Energy contribution	-13.44
Covariance contribution	1.14
Combinations/Pair	1.10
Mean z-score	-1.93
Structure conservation index	0.50
SVM decision value	0.78
SVM RNA-class probability	0.848727
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20777512 94 - 27905053
AAAGCAACUGGCGGUGGCCAGUAGA------AGUAACCACCAUAAAUGGCCAUUUGAAAGACGUUACAGUUCGAUCGUCCGAUC------------GAUAGAUCGAACGCCA-
.........(((((((((((.....------.((....))......))))))))..............(((((((((((.....------------))).))))))))))).- ( -28.80)
>DroSim_CAF1 20667 94 - 1
AAAGCGACUGGCGGUGGCCAGCAGA------AGUAACCACCAUAAAUGGCCAUUUGAAAGACGUUACAGUUCGAUCGUCCGAUC------------GAUAGAUCGAACGCCA-
.........(((((((((((.....------.((....))......))))))))..............(((((((((((.....------------))).))))))))))).- ( -28.80)
>DroEre_CAF1 21397 103 - 1
AAAGCAACCGGC---GGCCACCAGA------AGUAACCACCAUAAAUGGCCAUUUGAAAGACGUUACAGUUCGAUCGUCCAAUCGUCCAAUAGUCCGAUCGAUCGAACGCCA-
.........(((---(((((.....------.((....))......))))).................(((((((((....((((..(....)..)))))))))))))))).- ( -30.50)
>DroYak_CAF1 19491 87 - 1
AAAGCAACCGGC---GGCCAGCAGA------AGUAACCACCAUAAAUGGCCAUUUGAAAGACGUUACAGUUCGAUCGU----------------CCGAUCGAUCGAACACCA-
.........((.---(((((.....------.((....))......))))).................(((((((((.----------------.....))))))))).)).- ( -24.50)
>DroAna_CAF1 19366 74 - 1
AAAGCAGCCA---------AAAACG------AGCAGCCACCAUAAAUGGCCAUUUGAAAGACGUUACAGUUCGAUC------------------------GAUGGAACGCCAA
...((..(((---------....((------(((.((((.......))))...((....)).......)))))...------------------------..)))...))... ( -12.90)
>DroPer_CAF1 19793 87 - 1
AAAGC--CCAGC---AACGAGCAGAGCAGUCAGAAGCGGCCAUAAAUGGCUAUUUGAAAGACGUUACAGUUCGAUC--------------------GAUCGAGCGAGCGCCA-
...((--.(.((---.....)).).))..(((((...(((((....))))).)))))..(.((((...((((((..--------------------..)))))).)))).).- ( -22.40)
>consensus
AAAGCAACCGGC___GGCCAGCAGA______AGUAACCACCAUAAAUGGCCAUUUGAAAGACGUUACAGUUCGAUCGU__________________GAUCGAUCGAACGCCA_
.........(((....................(((((..(((....)))....((....)).))))).((((((((........................))))))))))).. (-12.30 = -13.44 +   1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:15 2006