Locus 8277

Sequence ID	3R_DroMel_CAF1
Location	22,141,852 – 22,142,012
Length	160
Max. P	0.997566

overview

Window 7

Location	22,141,852 – 22,141,972
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.17
Mean single sequence MFE	-35.48
Consensus MFE	-32.58
Energy contribution	-33.34
Covariance contribution	0.76
Combinations/Pair	1.02
Mean z-score	-2.16
Structure conservation index	0.92
SVM decision value	2.88
SVM RNA-class probability	0.997566
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22141852 120 - 27905053
GAGAUUGUAAUUAGUUUUUGUUGCUCCUGGGUUUAACUGGAGGGAAACUUUCAAAUUGAACCAAAGACGGCGGCAAAGGGAUGGAAUAUUUUGCGGUUCCAACUUUUACUCACUGGUCUU
((((((((((..(((((((((((((....(((((((.((((((....))))))..)))))))......)))))))))(((((.(((....)).).))))))))).)))).....)))))) ( -34.70)
>DroSec_CAF1 72247 120 - 1
GAGAUUGUAAUUAGUUUUUGUUGCUCCUGGGUUUAACUGGAGGGAAACUUUCAAAUUGAACCAAAGACGGCGGCAAAGGGAUGGAAUAUUUUGCGGUUCCAACUUUUACACACUGCUCUU
(((..(((((..(((((((((((((....(((((((.((((((....))))))..)))))))......)))))))))(((((.(((....)).).))))))))).))))).....))).. ( -36.50)
>DroSim_CAF1 65254 120 - 1
GAGAUUGUAAUUAGUUUUUGUUGCUCCUGGGUUUAACUGGAGGGAAACUUUCAAAUUGAACCAAAGACGGCGGCAAAGGGAUGGAAUAUUUUGCGGUUCCAACUUUUACACACUGGUCUU
((((((((((..(((((((((((((....(((((((.((((((....))))))..)))))))......)))))))))(((((.(((....)).).))))))))).))))).....))))) ( -35.80)
>DroEre_CAF1 67515 120 - 1
GAGAUUGUAAUUAGUUUUUGUUGCUUCUGGGUUUAACUGGAGGGAAACUUUGAAAUUGAACCAAAGACGCCGGCAAAGGGAUGGAAUAUUUUGCGGUCCCAACUUUUACACAUUGGUCUU
((((((((((..((((((((((((.(((.(((((((.(.((((....)))).)..)))))))..))).).)))))))(((((.(((....)).).))))))))).))))).....))))) ( -33.60)
>DroYak_CAF1 64827 120 - 1
GAGAUUGUAAUUAGUUUUUGUUGCUUCUGGGUUUAACUGGAGGGAAACUUUCAAAUUGAACCAAAGACGCCGGCAAAGGGAUGGAAUAUUUUGCGGUCCCAACUUUUACACACUGGUCUU
((((((((((..((((((((((((.(((.(((((((.((((((....))))))..)))))))..))).).)))))))(((((.(((....)).).))))))))).))))).....))))) ( -36.80)
>consensus
GAGAUUGUAAUUAGUUUUUGUUGCUCCUGGGUUUAACUGGAGGGAAACUUUCAAAUUGAACCAAAGACGGCGGCAAAGGGAUGGAAUAUUUUGCGGUUCCAACUUUUACACACUGGUCUU
((((((((((..(((((((((((((....(((((((.((((((....))))))..)))))))......)))))))))(((((.(((....)).).))))))))).))))).....))))) (-32.58 = -33.34 +   0.76)

alignment

secondary structure

dotplot

Window 8

Location	22,141,892 – 22,142,012
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.16
Mean single sequence MFE	-32.33
Consensus MFE	-27.90
Energy contribution	-28.50
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.82
Structure conservation index	0.86
SVM decision value	1.46
SVM RNA-class probability	0.956217
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22141892 120 - 27905053
CAUUUAGCUUUAAGUUGGCCGAGUGUUGAAAAAACAACUUGAGAUUGUAAUUAGUUUUUGUUGCUCCUGGGUUUAACUGGAGGGAAACUUUCAAAUUGAACCAAAGACGGCGGCAAAGGG
......(((.......)))((((((((.....))).))))).............(((((((((((....(((((((.((((((....))))))..)))))))......))))))))))). ( -32.50)
>DroSec_CAF1 72287 120 - 1
CAUUUAGAUUUAAGUUGGCCGAGUGUUGAAAAAACAACUUGAGAUUGUAAUUAGUUUUUGUUGCUCCUGGGUUUAACUGGAGGGAAACUUUCAAAUUGAACCAAAGACGGCGGCAAAGGG
........(((((((((.................)))))))))...........(((((((((((....(((((((.((((((....))))))..)))))))......))))))))))). ( -32.53)
>DroSim_CAF1 65294 120 - 1
CAUUUAGCUUUAAGUUGGCCGAGUGUUGAAAAAACAACUUGAGAUUGUAAUUAGUUUUUGUUGCUCCUGGGUUUAACUGGAGGGAAACUUUCAAAUUGAACCAAAGACGGCGGCAAAGGG
......(((.......)))((((((((.....))).))))).............(((((((((((....(((((((.((((((....))))))..)))))))......))))))))))). ( -32.50)
>DroEre_CAF1 67555 117 - 1
CAUUUAGCUUUAAG---GCCGAGUGCUGAAAAAACCACUUGAGAUUGUAAUUAGUUUUUGUUGCUUCUGGGUUUAACUGGAGGGAAACUUUGAAAUUGAACCAAAGACGCCGGCAAAGGG
.......((((...---((((.(((((..............(((..(((((........))))).))).(((((((.(.((((....)))).)..)))))))..)).))))))).)))). ( -28.70)
>DroYak_CAF1 64867 117 - 1
CAUUUAGCUUUAAG---GCCGAGUGUUGAAAAAACAACUUGAGAUUGUAAUUAGUUUUUGUUGCUUCUGGGUUUAACUGGAGGGAAACUUUCAAAUUGAACCAAAGACGCCGGCAAAGGG
.......((((...---((((.(((((.......((((..(((((((....))))))).))))......(((((((.((((((....))))))..)))))))...))))))))).)))). ( -35.40)
>consensus
CAUUUAGCUUUAAGUUGGCCGAGUGUUGAAAAAACAACUUGAGAUUGUAAUUAGUUUUUGUUGCUCCUGGGUUUAACUGGAGGGAAACUUUCAAAUUGAACCAAAGACGGCGGCAAAGGG
.................((((.((.((.......((((..(((((((....))))))).))))......(((((((.((((((....))))))..))))))).)).))..))))...... (-27.90 = -28.50 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:07:37 2006