Locus 70

Sequence ID	X_DroMel_CAF1
Location	316,416 – 316,571
Length	155
Max. P	0.844556

overview

Window 6

Location	316,416 – 316,516
Length	100
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	92.05
Mean single sequence MFE	-32.45
Consensus MFE	-28.50
Energy contribution	-29.10
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.38
Structure conservation index	0.88
SVM decision value	0.64
SVM RNA-class probability	0.807055
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 316416 100 + 22224390
GAA--------------UGAGGACGUGGCAUCCUGGAUCAAAAACCGGUAGUCGGUCGUCGCAAGUUUCUUCUCCCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACC
(((--------------.((((((.((((.....((((....((((((..(..((..(.(....)...)..))..)..))))))))))...)).)).)))))))))........ ( -28.80)
>DroSec_CAF1 59388 100 + 1
GAA--------------UGAGGACUUGGCAUCCUGGAUCGAAAACCGGUAGACGGUCGUCGCAAGUUUCUUCUCCCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACC
(((--------------.(((((((((((.....((((....((((((((((.((....(....)..)).)))....)))))))))))...)).))))))))))))........ ( -32.00)
>DroSim_CAF1 80023 100 + 1
GAA--------------UGAGGACUUGGCAUCCUGGAUCGAAAACCGGUAGACGGUCGUCGCAAGUUUCUUCUCCCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACC
(((--------------.(((((((((((.....((((....((((((((((.((....(....)..)).)))....)))))))))))...)).))))))))))))........ ( -32.00)
>DroEre_CAF1 60064 100 + 1
GAA--------------UGAGGACUUGGCAUCCUGGAUCGAAAACCGGUAGUCGUUCGUCGCAAGUUUCUUCUCCCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACC
(((--------------.(((((((((((.....((((....((((((..(........(....)..........)..))))))))))...)).))))))))))))........ ( -29.97)
>DroYak_CAF1 80781 114 + 1
GAAUGAGGAAUAAGGAAUGAGGACUUGGCAUCCUGGAUCGCAAACCGGUAGUCGUUCGUCGCAAGUUUCUGCUCCCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACC
......((..(((((((.(((((((((((.....((((....(((((((.(..((....(....).....))..)..)))))))))))...)).))))))))))))))))..)) ( -39.50)
>consensus
GAA______________UGAGGACUUGGCAUCCUGGAUCGAAAACCGGUAGUCGGUCGUCGCAAGUUUCUUCUCCCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACC
..................(((((((((((.....((((....((((((..(..((....(....)......))..)..))))))))))...)).)))))))))........... (-28.50 = -29.10 +   0.60)

alignment

secondary structure

dotplot

Window 7

Location	316,442 – 316,556
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	97.89
Mean single sequence MFE	-27.89
Consensus MFE	-26.60
Energy contribution	-27.00
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.27
Structure conservation index	0.95
SVM decision value	0.46
SVM RNA-class probability	0.744066
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 316442 114 + 22224390
AAAACCGGUAGUCGGUCGUCGCAAGUUUCUUCUCCCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACCUUUUAAGUGAACUCAAGUUUAUAAAUUGUGCAGCAAGUAC
..((((((..(..((..(.(....)...)..))..)..))))))...(((((((((((........))))).........((((((....)))))).....))))))....... ( -29.10)
>DroSec_CAF1 59414 114 + 1
AAAACCGGUAGACGGUCGUCGCAAGUUUCUUCUCCCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACCUUUCAAGUGAACUCAAGUUUAUAAAUUGUGCAGCAAGUAC
..((((((((((.((....(....)..)).)))....)))))))...(((((((((((........))))).........((((((....)))))).....))))))....... ( -28.20)
>DroSim_CAF1 80049 114 + 1
AAAACCGGUAGACGGUCGUCGCAAGUUUCUUCUCCCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACCUUUCAAGUGAACUCAAGUUUAUAAAUUGUGCAGCAAGUAC
..((((((((((.((....(....)..)).)))....)))))))...(((((((((((........))))).........((((((....)))))).....))))))....... ( -28.20)
>DroEre_CAF1 60090 114 + 1
AAAACCGGUAGUCGUUCGUCGCAAGUUUCUUCUCCCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACCUUUCAAGUGAACUCAAGUUUAUAAAUUGUGCAGCAAGUAC
..((((((..(........(....)..........)..))))))...(((((((((((........))))).........((((((....)))))).....))))))....... ( -26.17)
>DroYak_CAF1 80821 114 + 1
CAAACCGGUAGUCGUUCGUCGCAAGUUUCUGCUCCCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACCUUUCAAGUGAACUCAAGUUUAUAAAUUGUGCAGCAAGUAC
..(((((((.(..((....(....).....))..)..)))))))...(((((((((((........))))).........((((((....)))))).....))))))....... ( -27.80)
>consensus
AAAACCGGUAGUCGGUCGUCGCAAGUUUCUUCUCCCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACCUUUCAAGUGAACUCAAGUUUAUAAAUUGUGCAGCAAGUAC
..((((((..(..((....(....)......))..)..))))))...(((((((((((........))))).........((((((....)))))).....))))))....... (-26.60 = -27.00 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	316,476 – 316,571
Length	95
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	93.18
Mean single sequence MFE	-18.32
Consensus MFE	-16.90
Energy contribution	-16.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.29
Structure conservation index	0.92
SVM decision value	0.76
SVM RNA-class probability	0.844556
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 316476 95 + 22224390
CCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACCUUUUAAGUGAACUCAAGUUUAUAAAUUGUGCAGCAAGUACAACACAC--ACACA--------UAU
..(((.((....)).))).(((((........))))).........((((((....))))))...((((((.....)))))).....--.....--------... ( -16.90)
>DroSec_CAF1 59448 97 + 1
CCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACCUUUCAAGUGAACUCAAGUUUAUAAAUUGUGCAGCAAGUACAACACACACACACA--------UAU
..(((.((....)).))).(((((........))))).........((((((....))))))...((((((.....))))))............--------... ( -16.90)
>DroSim_CAF1 80083 97 + 1
CCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACCUUUCAAGUGAACUCAAGUUUAUAAAUUGUGCAGCAAGUACAACACACACACACA--------UAU
..(((.((....)).))).(((((........))))).........((((((....))))))...((((((.....))))))............--------... ( -16.90)
>DroEre_CAF1 60124 105 + 1
CCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACCUUUCAAGUGAACUCAAGUUUAUAAAUUGUGCAGCAAGUACAACACACACGCACACAUACGUGUAU
..(((.((....)).))).(((((........))))).........((((((....))))))...((((((.....))))))...(((((........))))).. ( -21.80)
>DroYak_CAF1 80855 105 + 1
CCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACCUUUCAAGUGAACUCAAGUUUAUAAAUUGUGCAGCAAGUACAACACACACAUACAUAUACUUGUAU
..(((.((....)).))).(((((........))))).........((((((....))))))...((((((.....)))))).......(((((......))))) ( -19.10)
>consensus
CCCGCCGGUUAUCCUGCGCUCAAGUCCUUUUCCUUGAACCUUUCAAGUGAACUCAAGUUUAUAAAUUGUGCAGCAAGUACAACACACACACACA________UAU
..(((.((....)).))).(((((........))))).........((((((....))))))...((((((.....))))))....................... (-16.90 = -16.90 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:03 2006