Locus 1065

Sequence ID	2L_DroMel_CAF1
Location	2,947,015 – 2,947,132
Length	117
Max. P	0.921003

overview

Window 2

Location	2,947,015 – 2,947,132
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.98
Mean single sequence MFE	-46.80
Consensus MFE	-36.61
Energy contribution	-36.67
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-2.01
Structure conservation index	0.78
SVM decision value	0.51
SVM RNA-class probability	0.763680
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2947015 117 + 22407834
GCCGCGUCCGCGACCACUUCGCUGCCCGGCCAGCAACAGC---ACUACCAGCAACAGCAGCGACCGCCUACGUAUGUGAAGCAGGCGGACAAUAAGCCGCCGUACAAUGGUCGCGGCGGC
(((((...(((((((((((((((((..(((..((....))---.......((....)).......)))...))).))))))..(((((........)))))......))))))))))))) ( -48.50)
>DroSim_CAF1 63210 117 + 1
GCCGCGUCCGCGACCACUUCGCUGCCCGGCCAGCAACAGC---ACUACCAGCAACAGCAGCGACCGCCAACGUAUGUGAAGCAGGCGGACAAUAAGCCGCCGUACAAUGGUCGCGGCGGC
(((((...(((((((((((((((((..(((..((....))---.......((....)).......)))...))).))))))..(((((........)))))......))))))))))))) ( -48.50)
>DroEre_CAF1 64280 120 + 1
UCCGCAUCCGCCACCACUGCGCUGCCCGGCCAGCAACAACAGCACUACCAGCAGCAGCAGCGACCGCCGACGUAUGUGAAACAGGCGGACAAUAAGCCGCCGUACAACGGCCGUGGCGGC
.......((((((((.(((((((((..((...((.......))....)).))))).)))).)...((((..(((((.....).(((((........)))))))))..)))).))))))). ( -49.00)
>DroYak_CAF1 64373 117 + 1
UCCGCAUCCGCAACGACUGCGCUGCCCGGCCAGCAACAAC---ACUACCAGCAACAGCAGCGACCGCCAACGUAUGUGAAGCAGGCGGAUAAUAAGCCGCCGUACAACGGUCGCGGCGGC
.....((((((.....((((((((......)))).....(---(((((..((....)).((....))....))).)))..)))))))))).....((((((((((....)).)))))))) ( -41.20)
>consensus
GCCGCAUCCGCGACCACUGCGCUGCCCGGCCAGCAACAAC___ACUACCAGCAACAGCAGCGACCGCCAACGUAUGUGAAGCAGGCGGACAAUAAGCCGCCGUACAACGGUCGCGGCGGC
...((....)).........(((((((((((.((.(((............((....)).(((........))).)))...)).(((((........))))).......))))).)))))) (-36.61 = -36.67 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	2,947,015 – 2,947,132
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.98
Mean single sequence MFE	-59.10
Consensus MFE	-48.01
Energy contribution	-48.33
Covariance contribution	0.31
Combinations/Pair	1.13
Mean z-score	-2.39
Structure conservation index	0.81
SVM decision value	1.14
SVM RNA-class probability	0.921003
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2947015 117 - 22407834
GCCGCCGCGACCAUUGUACGGCGGCUUAUUGUCCGCCUGCUUCACAUACGUAGGCGGUCGCUGCUGUUGCUGGUAGU---GCUGUUGCUGGCCGGGCAGCGAAGUGGUCGCGGACGCGGC
(((((((((((((((....((((((.....(.((((((((.........)))))))).)))))))(((((((((...---((....))..))).))))))..))))))))))...))))) ( -62.40)
>DroSim_CAF1 63210 117 - 1
GCCGCCGCGACCAUUGUACGGCGGCUUAUUGUCCGCCUGCUUCACAUACGUUGGCGGUCGCUGCUGUUGCUGGUAGU---GCUGUUGCUGGCCGGGCAGCGAAGUGGUCGCGGACGCGGC
((((((((((((((((((.((((((.....).))))))))........((....)).((((((((...((..((((.---....))))..))..))))))))))))))))))...))))) ( -59.10)
>DroEre_CAF1 64280 120 - 1
GCCGCCACGGCCGUUGUACGGCGGCUUAUUGUCCGCCUGUUUCACAUACGUCGGCGGUCGCUGCUGCUGCUGGUAGUGCUGUUGUUGCUGGCCGGGCAGCGCAGUGGUGGCGGAUGCGGA
.(((((((((((((((.((((((((.....).))))).((.......))))))))))))(((((.(((((((((...((.......))..))).))))))))))).)))))))....... ( -62.10)
>DroYak_CAF1 64373 117 - 1
GCCGCCGCGACCGUUGUACGGCGGCUUAUUAUCCGCCUGCUUCACAUACGUUGGCGGUCGCUGCUGUUGCUGGUAGU---GUUGUUGCUGGCCGGGCAGCGCAGUCGUUGCGGAUGCGGA
....(((((.((((...(((((.((.......(((((.((.........)).)))))..((((((...((..((((.---....))))..))..)))))))).))))).)))).))))). ( -52.80)
>consensus
GCCGCCGCGACCAUUGUACGGCGGCUUAUUGUCCGCCUGCUUCACAUACGUUGGCGGUCGCUGCUGUUGCUGGUAGU___GCUGUUGCUGGCCGGGCAGCGAAGUGGUCGCGGACGCGGA
((..(((((((((((((..(((((........(((((.((.........)).))))))))))((((((((..((((........))))..))..)))))))))))))))))))..))... (-48.01 = -48.33 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:35 2006