Locus 4580

Sequence ID	X_DroMel_CAF1
Location	12,014,413 – 12,014,542
Length	129
Max. P	0.999921

overview

Window 2

Location	12,014,413 – 12,014,504
Length	91
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	94.53
Mean single sequence MFE	-24.06
Consensus MFE	-22.24
Energy contribution	-22.08
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.09
Structure conservation index	0.92
SVM decision value	3.31
SVM RNA-class probability	0.998973
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12014413 91 + 22224390
GACAAUUUGCCAAACAAUCUGUCAAGCCGGAAACAAUUCGCACAACUUUCUCUAGAGUAAUCAGAGCACUCGCGAAAGUGCGAA----------CGGAACG
((((..(((.....)))..))))...(((....)..(((((((...(((((((.((....)))))((....)))))))))))))----------.)).... ( -24.10)
>DroSec_CAF1 47859 91 + 1
GACAAUUUGCCAAACAAUCUGUCAAGCCGGAAACAAUUCGCACAACUUUCUCUAGAGUAAUCAGAGCACUCGCGAAAGUGCGAA----------CGGAACG
((((..(((.....)))..))))...(((....)..(((((((...(((((((.((....)))))((....)))))))))))))----------.)).... ( -24.10)
>DroSim_CAF1 47061 91 + 1
GACAAUUUGCCAAACAAUCUGUCAAGCCGGAAACAAUUCGCACAACUUUCUCUAGAGUAAUCAGAGCACUCGCGAAAGUGCGAA----------CGGAACG
((((..(((.....)))..))))...(((....)..(((((((...(((((((.((....)))))((....)))))))))))))----------.)).... ( -24.10)
>DroEre_CAF1 44950 91 + 1
GACAAUUUGCCAAACAAUCUGUCAAGCCGGAAACAAUUCGCACAACUUUCUCCAGAGUAAUCAGAGCACUCGCGAAAGUGCGAA----------CGGAACG
((((..(((.....)))..))))...(((....)..(((((((...((((....((....))...((....)))))))))))))----------.)).... ( -22.80)
>DroYak_CAF1 46035 101 + 1
GACAAUUUGCCAAACAAUCUGUCAAGCCGGAAACAAUUCGCACAACUUUCUCUAGAGUAAUCAGAGUGCUCGCGAAAGUGCGAAUGGAACAGUACGGAACG
((((..(((.....)))..))))...(((....).((((((((...((((....(((((.......)))))..))))))))))))..........)).... ( -25.20)
>consensus
GACAAUUUGCCAAACAAUCUGUCAAGCCGGAAACAAUUCGCACAACUUUCUCUAGAGUAAUCAGAGCACUCGCGAAAGUGCGAA__________CGGAACG
((((..(((.....)))..))))...(((....)..(((((((.((((......)))).......((....))....)))))))...........)).... (-22.24 = -22.08 +  -0.16)

alignment

secondary structure

dotplot

Window 3

Location	12,014,448 – 12,014,542
Length	94
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	93.93
Mean single sequence MFE	-30.76
Consensus MFE	-27.92
Energy contribution	-29.10
Covariance contribution	1.18
Combinations/Pair	1.07
Mean z-score	-2.90
Structure conservation index	0.91
SVM decision value	4.56
SVM RNA-class probability	0.999921
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12014448 94 + 22224390
AUUCGCACAACUUUCUCUAGAGUAAUCAGAGCACUCGCGAAAGUGCGAA----------CGGAACGGAGAGUUUGCGAAAUAAUCAAGGGGGUACUUGAUGAGU--
.((((((.((((((((((.((....)))))(((((......)))))...----------.......)))))))))))))...((((((......))))))....-- ( -30.20)
>DroSec_CAF1 47894 94 + 1
AUUCGCACAACUUUCUCUAGAGUAAUCAGAGCACUCGCGAAAGUGCGAA----------CGGAACGGAGAGUUUGCGAAAUAAUCAAGGGGGUACUUGAUGAGU--
.((((((.((((((((((.((....)))))(((((......)))))...----------.......)))))))))))))...((((((......))))))....-- ( -30.20)
>DroSim_CAF1 47096 94 + 1
AUUCGCACAACUUUCUCUAGAGUAAUCAGAGCACUCGCGAAAGUGCGAA----------CGGAACGGAGAGUUUGCGAAAUAAUCAAGGGGGUACUUGAUGAGU--
.((((((.((((((((((.((....)))))(((((......)))))...----------.......)))))))))))))...((((((......))))))....-- ( -30.20)
>DroEre_CAF1 44985 94 + 1
AUUCGCACAACUUUCUCCAGAGUAAUCAGAGCACUCGCGAAAGUGCGAA----------CGGAACGGAGAGUUUGCGAAAUAAUCAAGGGGGUACUUGAUGAGU--
.((((((.((((((((((.((....))...(((((......)))))...----------.)))...)))))))))))))...((((((......))))))....-- ( -31.70)
>DroYak_CAF1 46070 106 + 1
AUUCGCACAACUUUCUCUAGAGUAAUCAGAGUGCUCGCGAAAGUGCGAAUGGAACAGUACGGAACGGAGAGUUUGCGAAAUAAUCAAGGGGGUACUUGAUGAGUAG
.((((((.((((((((((.((....)))))((((((((....)))..........)))))......)))))))))))))...((((((......))))))...... ( -31.50)
>consensus
AUUCGCACAACUUUCUCUAGAGUAAUCAGAGCACUCGCGAAAGUGCGAA__________CGGAACGGAGAGUUUGCGAAAUAAUCAAGGGGGUACUUGAUGAGU__
.((((((.((((((((...((....))...(((((......)))))...................))))))))))))))...((((((......))))))...... (-27.92 = -29.10 +   1.18)

alignment

secondary structure

dotplot

Window 4

Location	12,014,448 – 12,014,542
Length	94
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	93.93
Mean single sequence MFE	-23.16
Consensus MFE	-21.70
Energy contribution	-21.54
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.96
Structure conservation index	0.94
SVM decision value	3.14
SVM RNA-class probability	0.998549
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12014448 94 - 22224390
--ACUCAUCAAGUACCCCCUUGAUUAUUUCGCAAACUCUCCGUUCCG----------UUCGCACUUUCGCGAGUGCUCUGAUUACUCUAGAGAAAGUUGUGCGAAU
--....((((((......))))))...((((((((((.((.......----------...((((((....))))))((((.......)))))).)))).)))))). ( -22.60)
>DroSec_CAF1 47894 94 - 1
--ACUCAUCAAGUACCCCCUUGAUUAUUUCGCAAACUCUCCGUUCCG----------UUCGCACUUUCGCGAGUGCUCUGAUUACUCUAGAGAAAGUUGUGCGAAU
--....((((((......))))))...((((((((((.((.......----------...((((((....))))))((((.......)))))).)))).)))))). ( -22.60)
>DroSim_CAF1 47096 94 - 1
--ACUCAUCAAGUACCCCCUUGAUUAUUUCGCAAACUCUCCGUUCCG----------UUCGCACUUUCGCGAGUGCUCUGAUUACUCUAGAGAAAGUUGUGCGAAU
--....((((((......))))))...((((((((((.((.......----------...((((((....))))))((((.......)))))).)))).)))))). ( -22.60)
>DroEre_CAF1 44985 94 - 1
--ACUCAUCAAGUACCCCCUUGAUUAUUUCGCAAACUCUCCGUUCCG----------UUCGCACUUUCGCGAGUGCUCUGAUUACUCUGGAGAAAGUUGUGCGAAU
--....((((((......))))))...(((((((((((((((.....----------.((((((((....))))))...))......))))))..))).)))))). ( -25.50)
>DroYak_CAF1 46070 106 - 1
CUACUCAUCAAGUACCCCCUUGAUUAUUUCGCAAACUCUCCGUUCCGUACUGUUCCAUUCGCACUUUCGCGAGCACUCUGAUUACUCUAGAGAAAGUUGUGCGAAU
......((((((......))))))...((((((((((....((((((...(((.......)))....)).)))).(((((.......)))))..)))).)))))). ( -22.50)
>consensus
__ACUCAUCAAGUACCCCCUUGAUUAUUUCGCAAACUCUCCGUUCCG__________UUCGCACUUUCGCGAGUGCUCUGAUUACUCUAGAGAAAGUUGUGCGAAU
......((((((......))))))...((((((((((....................(((((......)))))..(((((.......)))))..)))).)))))). (-21.70 = -21.54 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:41 2006