Locus 1170

Sequence ID	2R_DroMel_CAF1
Location	4,640,536 – 4,640,660
Length	124
Max. P	0.973345

overview

Window 8

Location	4,640,536 – 4,640,628
Length	92
Sequences	3
Columns	92
Reading direction	forward
Mean pairwise identity	88.41
Mean single sequence MFE	-31.43
Consensus MFE	-27.65
Energy contribution	-27.67
Covariance contribution	0.01
Combinations/Pair	1.20
Mean z-score	-3.04
Structure conservation index	0.88
SVM decision value	1.71
SVM RNA-class probability	0.973345
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4640536 92 + 20766785
UUUUAUUUGCCCCGGCUACUCAUUGCCUGGCCUUGCUCAUCGCGCGUUGCCCAAUGUUACGCAUGAUGAGUUGUUGAUACUUGGCUGUACAG
........((((((((........))).))....((((((((.((((.((.....)).)))).))))))))...........)))....... ( -26.50)
>DroEre_CAF1 12113 92 + 1
UUGUAUUUGCUUUGACUACUCAUUGCCUGGCCUUGCUCAUCAUGCGUUGCCCAACGUUAUGCAUGAUGAGUUGUUAAUACUUGGCAGUGCAG
..................(((((((((((((...(((((((((((((.((.....)).))))))))))))).))))......))))))).)) ( -30.70)
>DroYak_CAF1 11732 92 + 1
UUGUAUUUGCUCCGGCUACUCAUUGCCUGGCCUUGCUCAUCAUGCGUUGCCCAAUGCUUCGCAUGAUGAGUGGUUAAUACCUGGCUGUGCAG
.(((((.......(((........))).((((..((((((((((((..((.....))..))))))))))))(((....))).))))))))). ( -37.10)
>consensus
UUGUAUUUGCUCCGGCUACUCAUUGCCUGGCCUUGCUCAUCAUGCGUUGCCCAAUGUUACGCAUGAUGAGUUGUUAAUACUUGGCUGUGCAG
.(((((..(((..(((........)))((((...(((((((((((((.((.....)).))))))))))))).))))......))).))))). (-27.65 = -27.67 +   0.01)

alignment

secondary structure

dotplot

Window 9

Location	4,640,536 – 4,640,628
Length	92
Sequences	3
Columns	92
Reading direction	reverse
Mean pairwise identity	88.41
Mean single sequence MFE	-27.97
Consensus MFE	-23.85
Energy contribution	-23.85
Covariance contribution	0.01
Combinations/Pair	1.14
Mean z-score	-2.77
Structure conservation index	0.85
SVM decision value	1.29
SVM RNA-class probability	0.938765
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4640536 92 - 20766785
CUGUACAGCCAAGUAUCAACAACUCAUCAUGCGUAACAUUGGGCAACGCGCGAUGAGCAAGGCCAGGCAAUGAGUAGCCGGGGCAAAUAAAA
.......(((............((((((.(((((...........))))).)))))).....((.(((........))))))))........ ( -24.90)
>DroEre_CAF1 12113 92 - 1
CUGCACUGCCAAGUAUUAACAACUCAUCAUGCAUAACGUUGGGCAACGCAUGAUGAGCAAGGCCAGGCAAUGAGUAGUCAAAGCAAAUACAA
.(((.(((((..((....))..((((((((((.....(((....)))))))))))))...)).))))))....................... ( -23.20)
>DroYak_CAF1 11732 92 - 1
CUGCACAGCCAGGUAUUAACCACUCAUCAUGCGAAGCAUUGGGCAACGCAUGAUGAGCAAGGCCAGGCAAUGAGUAGCCGGAGCAAAUACAA
.(((...(((.(((....))).(((((((((((..((.....))..)))))))))))...)))..(((........)))...)))....... ( -35.80)
>consensus
CUGCACAGCCAAGUAUUAACAACUCAUCAUGCGUAACAUUGGGCAACGCAUGAUGAGCAAGGCCAGGCAAUGAGUAGCCGGAGCAAAUACAA
.(((...(((..((....))..(((((((((((.............)))))))))))...)))..(((........)))...)))....... (-23.85 = -23.85 +   0.01)

alignment

secondary structure

dotplot

Window 0

Location	4,640,552 – 4,640,660
Length	108
Sequences	3
Columns	115
Reading direction	forward
Mean pairwise identity	85.42
Mean single sequence MFE	-35.07
Consensus MFE	-31.88
Energy contribution	-32.33
Covariance contribution	0.45
Combinations/Pair	1.13
Mean z-score	-2.32
Structure conservation index	0.91
SVM decision value	1.62
SVM RNA-class probability	0.968096
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4640552 108 + 20766785
UACUCAUUGCCUGGCCUUGCUCAUCGCGCGUUGCCCAAUGUUACGCAUGAUGAGUUGUUGAUACUUGGCUGUACAGUGGAUAAAAACGAGUUCAA--UUGAUGUGAUAUG-----
..(.(((((..((..(((((((((((.((((.((.....)).)))).)))))))(..(((.(((......))))))..).......))))..)).--.))))).).....----- ( -27.90)
>DroEre_CAF1 12129 115 + 1
UACUCAUUGCCUGGCCUUGCUCAUCAUGCGUUGCCCAACGUUAUGCAUGAUGAGUUGUUAAUACUUGGCAGUGCAGUGGAUGAAAACGAGUUCAGUAUAUAUAUGAUUUGGAAAA
(((((((((((((((...(((((((((((((.((.....)).))))))))))))).))))......))))))).))))........(((((.((.........)))))))..... ( -35.60)
>DroYak_CAF1 11748 113 + 1
UACUCAUUGCCUGGCCUUGCUCAUCAUGCGUUGCCCAAUGCUUCGCAUGAUGAGUGGUUAAUACCUGGCUGUGCAGUGGAUAGAAACGAGUUCAA--UAGAUAUGAUUUGGAAAA
((..((((((.(((((..((((((((((((..((.....))..))))))))))))(((....))).))))).))))))..))....(((((.((.--......)))))))..... ( -41.70)
>consensus
UACUCAUUGCCUGGCCUUGCUCAUCAUGCGUUGCCCAAUGUUACGCAUGAUGAGUUGUUAAUACUUGGCUGUGCAGUGGAUAAAAACGAGUUCAA__UAGAUAUGAUUUGGAAAA
((..((((((.(((((..(((((((((((((.((.....)).))))))))))))).((....))..))))).))))))..))................................. (-31.88 = -32.33 +   0.45)

alignment

secondary structure

dotplot

Window 1

Location	4,640,552 – 4,640,660
Length	108
Sequences	3
Columns	115
Reading direction	reverse
Mean pairwise identity	85.42
Mean single sequence MFE	-28.77
Consensus MFE	-24.79
Energy contribution	-25.02
Covariance contribution	0.23
Combinations/Pair	1.08
Mean z-score	-2.15
Structure conservation index	0.86
SVM decision value	0.98
SVM RNA-class probability	0.894021
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4640552 108 - 20766785
-----CAUAUCACAUCAA--UUGAACUCGUUUUUAUCCACUGUACAGCCAAGUAUCAACAACUCAUCAUGCGUAACAUUGGGCAACGCGCGAUGAGCAAGGCCAGGCAAUGAGUA
-----.............--....((((((..........(((...(((..((....))..((((((.(((((...........))))).))))))...)))...))))))))). ( -23.30)
>DroEre_CAF1 12129 115 - 1
UUUUCCAAAUCAUAUAUAUACUGAACUCGUUUUCAUCCACUGCACUGCCAAGUAUUAACAACUCAUCAUGCAUAACGUUGGGCAACGCAUGAUGAGCAAGGCCAGGCAAUGAGUA
........................((((((..........(((.(((((..((....))..((((((((((.....(((....)))))))))))))...)).)))))))))))). ( -26.90)
>DroYak_CAF1 11748 113 - 1
UUUUCCAAAUCAUAUCUA--UUGAACUCGUUUCUAUCCACUGCACAGCCAGGUAUUAACCACUCAUCAUGCGAAGCAUUGGGCAACGCAUGAUGAGCAAGGCCAGGCAAUGAGUA
.........(((......--.)))((((((..........(((...(((.(((....))).(((((((((((..((.....))..)))))))))))...)))...))))))))). ( -36.10)
>consensus
UUUUCCAAAUCAUAUCUA__UUGAACUCGUUUUUAUCCACUGCACAGCCAAGUAUUAACAACUCAUCAUGCGUAACAUUGGGCAACGCAUGAUGAGCAAGGCCAGGCAAUGAGUA
........................((((((..........(((...(((..((....))..(((((((((((.............)))))))))))...)))...))))))))). (-24.79 = -25.02 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:11 2006