Locus 1162

Sequence ID	X_DroMel_CAF1
Location	3,466,847 – 3,466,996
Length	149
Max. P	0.934713

overview

Window 7

Location	3,466,847 – 3,466,963
Length	116
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	92.12
Mean single sequence MFE	-19.18
Consensus MFE	-15.14
Energy contribution	-15.50
Covariance contribution	0.36
Combinations/Pair	1.05
Mean z-score	-1.49
Structure conservation index	0.79
SVM decision value	0.13
SVM RNA-class probability	0.597657
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3466847 116 + 22224390
CGCAUUUCCCCCAAACGAACUUAUCCCGAGUCCCAAAUUUGUGAAAAGUAAUAACAAAAGGCGGCCAAAAGAAGCCGCCAAAAUACGUUUGAAUUGCUCACAAAUAAUAAAGAAAU
.(((.(((....(((((.((((.((.(((((.....))))).)).))))..........((((((........))))))......)))))))).)))................... ( -26.70)
>DroSec_CAF1 27095 113 + 1
CGCAUUUCCCCCA-CCAAACUUAUC-CGAGUCCCAAAA-UGUGAAAAGUAGUAACAAAAGGCGGGCAAAAGAAGCCGCCAAAAUACGAUUGAAUUUCCCACAAAUAAUAAAGAAAU
...(((((.....-....((((...-.)))).......-((((....((....))....(((((.(.......))))))...................)))).........))))) ( -14.00)
>DroSim_CAF1 26875 113 + 1
CGCAUUUCCCCCA-CCACACUUAUC-CGAGUCCCAAAA-UGUGAAAAGUAGUAACAAAAGGCGGCCAAAAGAAGCCGCCAAAAUACGAUUGAAUUGCCCACAAAUAAUAAAGAAAU
.(((.(((.....-..((((((.((-...((......)-)..)).)))).)).......((((((........))))))...........))).)))................... ( -19.20)
>DroEre_CAF1 30463 113 + 1
CGCAUUUCCUCCA-CCGAACUUAUC-CAACUCCCAAAU-UGUGAAAAGUAGUAACAAAAGACGGCCAAAAGAAGCCGCCAAACUACGCUUGAAUUGCACACAAAUAAUAAAGAAAU
.(((.(((.....-....((((.((-(((........)-)).)).))))..........(.((((........)))).)...........))).)))................... ( -15.20)
>DroYak_CAF1 28575 111 + 1
CGCAUUUCC-CCA-CCGAACUUAUC-CAAGUCCCAAAA-UGUGAAAAGUAGUAACAAAAGGCGGCCAA-AGAAGCCGCCAAACUACGCUUGAAUUGCCCACAAAUAAUAAAGAAAU
...(((((.-...-..(.((((...-.)))).).....-((((....(((((.......((((((...-....))))))..)))))((.......)).)))).........))))) ( -20.80)
>consensus
CGCAUUUCCCCCA_CCGAACUUAUC_CGAGUCCCAAAA_UGUGAAAAGUAGUAACAAAAGGCGGCCAAAAGAAGCCGCCAAAAUACGAUUGAAUUGCCCACAAAUAAUAAAGAAAU
.(((.(((..........((((.((.((...........)).)).))))..........((((((........))))))...........))).)))................... (-15.14 = -15.50 +   0.36)

alignment

secondary structure

dotplot

Window 8

Location	3,466,883 – 3,466,996
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.40
Mean single sequence MFE	-24.90
Consensus MFE	-10.64
Energy contribution	-11.67
Covariance contribution	1.03
Combinations/Pair	1.36
Mean z-score	-2.31
Structure conservation index	0.43
SVM decision value	1.24
SVM RNA-class probability	0.934713
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3466883 113 - 22224390
-------ACAAAGUGAAAUAGGCAAUGCUCAAAUUGAAUUAUUUCUUUAUUAUUUGUGAGCAAUUCAAACGUAUUUUGGCGGCUUCUUUUGGCCGCCUUUUGUUAUUACUUUUCACAAAU
-------.....((((((.((....((((((.....(((.........))).....)))))).....((((......(((((((......)))))))...))))....)))))))).... ( -29.30)
>DroSec_CAF1 27129 101 - 1
-------ACAAAGGG-----------GCUCAAAUUGAAUUAUUUCUUUAUUAUUUGUGGGAAAUUCAAUCGUAUUUUGGCGGCUUCUUUUGCCCGCCUUUUGUUACUACUUUUCACA-UU
-------((((((((-----------(((.(((((((...(((((((..........)))))))....))).)))).)))(((.......)))..))))))))..............-.. ( -21.00)
>DroSim_CAF1 26909 101 - 1
-------ACAAAGUG-----------GCUCAAAUUGAAUUAUUUCUUUAUUAUUUGUGGGCAAUUCAAUCGUAUUUUGGCGGCUUCUUUUGGCCGCCUUUUGUUACUACUUUUCACA-UU
-------..((((((-----------(..(((((((((((...(((.((.....)).))).))))))).........(((((((......))))))).))))...))))))).....-.. ( -24.60)
>DroEre_CAF1 30497 117 - 1
AAACAAAAAAAGGG--AAUAGGCAAUGUUGAAAUUGAAUUAUUUCUUUAUUAUUUGUGUGCAAUUCAAGCGUAGUUUGGCGGCUUCUUUUGGCCGUCUUUUGUUACUACUUUUCACA-AU
.........(((((--(((((.((((......))))..)))))))))).....(((((.((.......))(((((..(((((((......))))))).......)))))....))))-). ( -28.50)
>DroYak_CAF1 28608 109 - 1
-------AAAAAGG--AAUAGGCAAUGUUCAAAUUGAAUUAUUUCUUUAUUAUUUGUGGGCAAUUCAAGCGUAGUUUGGCGGCUUCU-UUGGCCGCCUUUUGUUACUACUUUUCACA-UU
-------..(((((--(((((.((((......))))..))))))))))......(((((((.......))(((((..(((((((...-..))))))).......)))))...)))))-.. ( -31.70)
>DroAna_CAF1 50995 94 - 1
-------AUUAAGCA-AAAAGGCGGAAUGGAAAUUAAAUUACAUCCUUAAUGAUUUUUUUUGUUUCA--CGUAGUUUGGCGGUUUCUU---------------UACCACUUUUCGGA-UU
-------......(.-.(((((.((...((((((((((((((......((..(......)..))...--.))))))))...)))))).---------------..)).)))))..).-.. ( -14.30)
>consensus
_______ACAAAGGG_AAUAGGCAAUGCUCAAAUUGAAUUAUUUCUUUAUUAUUUGUGGGCAAUUCAAGCGUAGUUUGGCGGCUUCUUUUGGCCGCCUUUUGUUACUACUUUUCACA_UU
.........((((.............(((((.....(((.........))).....))))).........(((....(((((((......)))))))......)))..))))........ (-10.64 = -11.67 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:50 2006