Locus 6049

Sequence ID	3R_DroMel_CAF1
Location	15,918,225 – 15,918,416
Length	191
Max. P	0.999982

overview

Window 7

Location	15,918,225 – 15,918,339
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	96.49
Mean single sequence MFE	-36.70
Consensus MFE	-33.88
Energy contribution	-34.32
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.59
Structure conservation index	0.92
SVM decision value	3.96
SVM RNA-class probability	0.999731
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15918225 114 + 27905053
GAGUUGGCCAAAGUAACAUAAUUUGCAAAUAACGGCAACGCGAACCUAAAACGCCAUGGCGGCCGCCAUUGUGCAAUUGCAAAGUGGCAAAAGGGCGGAAUGGCGAAAUGGCGG
......((((..((((......))))......((....))...........((((((..((.((((((((.(((....))).))))))....)).))..))))))...)))).. ( -38.00)
>DroSec_CAF1 35923 113 + 1
GAGUUGGCCAAAGUAACAUAAUUUGCAAAUAACGGCAACGCGAACCUAAAACGCCAUGGCGGCCGCCAUUGUGCAAUUGCAAAGUGGCAAAAGGGCGGAAUGGCGA-AUGGCGG
......((((..((((......))))......((....))...........((((((..((.((((((((.(((....))).))))))....)).))..)))))).-.)))).. ( -38.00)
>DroSim_CAF1 25722 114 + 1
GAGUUGGCCAAAGUAACAUAAUUUGCAAAUAACGGCAACGCGAACCUAAAACGCCAUGGCGGCCGCCAUUGUGCAAUUGCAAAGUGGCAAAAGGGCGGAAUGGCGAAAUGGCGG
......((((..((((......))))......((....))...........((((((..((.((((((((.(((....))).))))))....)).))..))))))...)))).. ( -38.00)
>DroEre_CAF1 25211 114 + 1
GAGUUGGCCAAAGUAACAUAAUUUGCAAAUAACGGCAACGCGAACCCAAAACGCCACGGCGGCCGCCAUUGUGCAAUUGCAAAGUGGCAAAAGGGCGAAAUGGCGAAAUGGCGG
......((((..((((......))))......((....))...........(((((...((.((((((((.(((....))).))))))....)).))...)))))...)))).. ( -36.00)
>DroYak_CAF1 28564 114 + 1
GAGUUGGACAAAGUAACAUAAUUUGCAAAUAACGGCAGCGCGAACGCAAAACGCCAUGGCGGCCGCCAUUGUGCAAUUGCAAAGUGGCAAAAGGGCGAAAUGGUAAAAUGGCGG
............((((......))))......((.(((((....))).....(((((..((.((((((((.(((....))).))))))....)).))..)))))....)).)). ( -33.50)
>consensus
GAGUUGGCCAAAGUAACAUAAUUUGCAAAUAACGGCAACGCGAACCUAAAACGCCAUGGCGGCCGCCAUUGUGCAAUUGCAAAGUGGCAAAAGGGCGGAAUGGCGAAAUGGCGG
......((((..((((......))))......((....))...........((((((..((.((((((((.(((....))).))))))....)).))..))))))...)))).. (-33.88 = -34.32 +   0.44)

alignment

secondary structure

dotplot

Window 8

Location	15,918,225 – 15,918,339
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	96.49
Mean single sequence MFE	-29.84
Consensus MFE	-26.64
Energy contribution	-26.68
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.25
Structure conservation index	0.89
SVM decision value	0.16
SVM RNA-class probability	0.611863
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15918225 114 - 27905053
CCGCCAUUUCGCCAUUCCGCCCUUUUGCCACUUUGCAAUUGCACAAUGGCGGCCGCCAUGGCGUUUUAGGUUCGCGUUGCCGUUAUUUGCAAAUUAUGUUACUUUGGCCAACUC
..(((....((((((..((.((....((((.(.(((....))).).)))))).))..)))))).....)))....(((((((......(((.....))).....))).)))).. ( -29.90)
>DroSec_CAF1 35923 113 - 1
CCGCCAU-UCGCCAUUCCGCCCUUUUGCCACUUUGCAAUUGCACAAUGGCGGCCGCCAUGGCGUUUUAGGUUCGCGUUGCCGUUAUUUGCAAAUUAUGUUACUUUGGCCAACUC
.((((((-((((((((..((....((((......))))..))..)))))))).....))))))............(((((((......(((.....))).....))).)))).. ( -29.90)
>DroSim_CAF1 25722 114 - 1
CCGCCAUUUCGCCAUUCCGCCCUUUUGCCACUUUGCAAUUGCACAAUGGCGGCCGCCAUGGCGUUUUAGGUUCGCGUUGCCGUUAUUUGCAAAUUAUGUUACUUUGGCCAACUC
..(((....((((((..((.((....((((.(.(((....))).).)))))).))..)))))).....)))....(((((((......(((.....))).....))).)))).. ( -29.90)
>DroEre_CAF1 25211 114 - 1
CCGCCAUUUCGCCAUUUCGCCCUUUUGCCACUUUGCAAUUGCACAAUGGCGGCCGCCGUGGCGUUUUGGGUUCGCGUUGCCGUUAUUUGCAAAUUAUGUUACUUUGGCCAACUC
..((((...(((......((((...((((((..(((....)))....(((....)))))))))....))))..)))((((........))))............))))...... ( -32.30)
>DroYak_CAF1 28564 114 - 1
CCGCCAUUUUACCAUUUCGCCCUUUUGCCACUUUGCAAUUGCACAAUGGCGGCCGCCAUGGCGUUUUGCGUUCGCGCUGCCGUUAUUUGCAAAUUAUGUUACUUUGUCCAACUC
........................((((......))))(((((.((((((((((((....)))....(((....))).))))))))))))))...................... ( -27.20)
>consensus
CCGCCAUUUCGCCAUUCCGCCCUUUUGCCACUUUGCAAUUGCACAAUGGCGGCCGCCAUGGCGUUUUAGGUUCGCGUUGCCGUUAUUUGCAAAUUAUGUUACUUUGGCCAACUC
..((((......(((.........((((......))))(((((.(((((((((.((....(((.........))))).))))))))))))))...)))......))))...... (-26.64 = -26.68 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	15,918,263 – 15,918,377
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	92.98
Mean single sequence MFE	-39.14
Consensus MFE	-35.28
Energy contribution	-36.32
Covariance contribution	1.04
Combinations/Pair	1.09
Mean z-score	-3.43
Structure conservation index	0.90
SVM decision value	4.90
SVM RNA-class probability	0.999961
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15918263 114 + 27905053
CGCGAACCUAAAACGCCAUGGCGGCCGCCAUUGUGCAAUUGCAAAGUGGCAAAAGGGCGGAAUGGCGAAAUGGCGGCCAAGUUAGGCUCGAAAAAAGUUGCAAAUGCAAAAGAG
..(((.(((((...((....))((((((((((.(((..((((....(....)....))))....))).))))))))))...))))).))).......((((....))))..... ( -40.30)
>DroSec_CAF1 35961 113 + 1
CGCGAACCUAAAACGCCAUGGCGGCCGCCAUUGUGCAAUUGCAAAGUGGCAAAAGGGCGGAAUGGCGA-AUGGCGGCCAAGUUAGGCUCGAAAAAAGUUGCAAAUGCAAAAGAG
..(((.(((((..((((((..((.((((((((.(((....))).))))))....)).))..)))))).-.(((...)))..))))).))).......((((....))))..... ( -40.10)
>DroSim_CAF1 25760 114 + 1
CGCGAACCUAAAACGCCAUGGCGGCCGCCAUUGUGCAAUUGCAAAGUGGCAAAAGGGCGGAAUGGCGAAAUGGCGGCCAAGUUAGGCUCGAAAAAAGUUGCAAAUGCAAAAGAG
..(((.(((((...((....))((((((((((.(((..((((....(....)....))))....))).))))))))))...))))).))).......((((....))))..... ( -40.30)
>DroEre_CAF1 25249 102 + 1
CGCGAACCCAAAACGCCACGGCGGCCGCCAUUGUGCAAUUGCAAAGUGGCAAAAGGGCGAAAUGGCGAAAUGGCGGCCAAGUUAGGCUCGA------------AUGCAAAAGAG
.(((...(((...(((((...((.((((((((.(((....))).))))))....)).))...)))))...)))(((((......))).)).------------.)))....... ( -36.80)
>DroYak_CAF1 28602 114 + 1
CGCGAACGCAAAACGCCAUGGCGGCCGCCAUUGUGCAAUUGCAAAGUGGCAAAAGGGCGAAAUGGUAAAAUGGCGGCCAAGUUAGGCUCGAAAAAAGUUGCAAAUGCAAAAGAG
..(((.(((.....(((((..((.((((((((.(((....))).))))))....)).))..)))))......)))(((......)))))).......((((....))))..... ( -38.20)
>consensus
CGCGAACCUAAAACGCCAUGGCGGCCGCCAUUGUGCAAUUGCAAAGUGGCAAAAGGGCGGAAUGGCGAAAUGGCGGCCAAGUUAGGCUCGAAAAAAGUUGCAAAUGCAAAAGAG
..(((.(((((...((....))((((((((((.(((..((((....(....)....))))....))).))))))))))...))))).))).......((((....))))..... (-35.28 = -36.32 +   1.04)

alignment

secondary structure

dotplot

Window 0

Location	15,918,263 – 15,918,377
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	92.98
Mean single sequence MFE	-37.82
Consensus MFE	-34.90
Energy contribution	-35.86
Covariance contribution	0.96
Combinations/Pair	1.03
Mean z-score	-3.78
Structure conservation index	0.92
SVM decision value	5.28
SVM RNA-class probability	0.999982
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15918263 114 - 27905053
CUCUUUUGCAUUUGCAACUUUUUUCGAGCCUAACUUGGCCGCCAUUUCGCCAUUCCGCCCUUUUGCCACUUUGCAAUUGCACAAUGGCGGCCGCCAUGGCGUUUUAGGUUCGCG
.....((((....)))).......(((((((((...((((((((((..((......)).(..((((......))))..)...))))))))))((....))...))))))))).. ( -39.70)
>DroSec_CAF1 35961 113 - 1
CUCUUUUGCAUUUGCAACUUUUUUCGAGCCUAACUUGGCCGCCAU-UCGCCAUUCCGCCCUUUUGCCACUUUGCAAUUGCACAAUGGCGGCCGCCAUGGCGUUUUAGGUUCGCG
.....((((....)))).......(((((((((...(((((((((-(.((......)).(..((((......))))..)...))))))))))((....))...))))))))).. ( -39.70)
>DroSim_CAF1 25760 114 - 1
CUCUUUUGCAUUUGCAACUUUUUUCGAGCCUAACUUGGCCGCCAUUUCGCCAUUCCGCCCUUUUGCCACUUUGCAAUUGCACAAUGGCGGCCGCCAUGGCGUUUUAGGUUCGCG
.....((((....)))).......(((((((((...((((((((((..((......)).(..((((......))))..)...))))))))))((....))...))))))))).. ( -39.70)
>DroEre_CAF1 25249 102 - 1
CUCUUUUGCAU------------UCGAGCCUAACUUGGCCGCCAUUUCGCCAUUUCGCCCUUUUGCCACUUUGCAAUUGCACAAUGGCGGCCGCCGUGGCGUUUUGGGUUCGCG
...........------------.(((((((((...((((((((((..((......)).(..((((......))))..)...))))))))))((....))...))))))))).. ( -36.60)
>DroYak_CAF1 28602 114 - 1
CUCUUUUGCAUUUGCAACUUUUUUCGAGCCUAACUUGGCCGCCAUUUUACCAUUUCGCCCUUUUGCCACUUUGCAAUUGCACAAUGGCGGCCGCCAUGGCGUUUUGCGUUCGCG
.....((((....)))).......((((((.(((..((((((((((..........((......)).....(((....))).))))))))))((....)))))..).))))).. ( -33.40)
>consensus
CUCUUUUGCAUUUGCAACUUUUUUCGAGCCUAACUUGGCCGCCAUUUCGCCAUUCCGCCCUUUUGCCACUUUGCAAUUGCACAAUGGCGGCCGCCAUGGCGUUUUAGGUUCGCG
.....((((....)))).......(((((((((...((((((((((..........((......)).....(((....))).))))))))))((....))...))))))))).. (-34.90 = -35.86 +   0.96)

alignment

secondary structure

dotplot

Window 1

Location	15,918,299 – 15,918,416
Length	117
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	93.16
Mean single sequence MFE	-27.69
Consensus MFE	-24.62
Energy contribution	-24.86
Covariance contribution	0.24
Combinations/Pair	1.13
Mean z-score	-2.56
Structure conservation index	0.89
SVM decision value	3.78
SVM RNA-class probability	0.999611
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15918299 117 + 27905053
AAUUGCAAAGUGGCAAAAGGGCGGAAUGGCGAAAUGGCGGCCAAGUUAGGCUCGAAAAAAGUUGCAAAUGCAAAAGAGAAAUGAUUUAAAAACUUGGCUAGCUAGGUAGGAGUUCGA
..((((......)))).......((((..(....(((((((((((((....(((.......((((....))))........)))......))))))))).))))....)..)))).. ( -26.76)
>DroSec_CAF1 35997 116 + 1
AAUUGCAAAGUGGCAAAAGGGCGGAAUGGCGA-AUGGCGGCCAAGUUAGGCUCGAAAAAAGUUGCAAAUGCAAAAGAGAAAUGAUUUAAAAACUUGGCCAGCUAGGUGGGAGUUCGA
..((((......)))).....((((....((.-.(((((((((((((....(((.......((((....))))........)))......))))))))).))))..))....)))). ( -29.76)
>DroSim_CAF1 25796 117 + 1
AAUUGCAAAGUGGCAAAAGGGCGGAAUGGCGAAAUGGCGGCCAAGUUAGGCUCGAAAAAAGUUGCAAAUGCAAAAGAGAAAUGAUUUAAAAACUUGGCCAGCUAGGUGGGAGUUCGA
..((((......)))).......((((..(.(..(((((((((((((....(((.......((((....))))........)))......))))))))).))))..).)..)))).. ( -30.46)
>DroEre_CAF1 25285 105 + 1
AAUUGCAAAGUGGCAAAAGGGCGAAAUGGCGAAAUGGCGGCCAAGUUAGGCUCGA------------AUGCAAAAGAGAAAUGAUUUAAAAACUUGGCUAGCUAGGUGGGAGUUCGA
..((((......)))).....((((....(.(..(((((((((((((..((....------------..)).....(....)........))))))))).))))..).)...)))). ( -25.20)
>DroYak_CAF1 28638 117 + 1
AAUUGCAAAGUGGCAAAAGGGCGAAAUGGUAAAAUGGCGGCCAAGUUAGGCUCGAAAAAAGUUGCAAAUGCAAAAGAGAAAUGAUUUAAAAACUUGGCUAGCUAGGUGGAAGUUCGA
..((((......)))).....((((......(..(((((((((((((....(((.......((((....))))........)))......))))))))).))))..).....)))). ( -26.26)
>consensus
AAUUGCAAAGUGGCAAAAGGGCGGAAUGGCGAAAUGGCGGCCAAGUUAGGCUCGAAAAAAGUUGCAAAUGCAAAAGAGAAAUGAUUUAAAAACUUGGCUAGCUAGGUGGGAGUUCGA
..((((......)))).....((((....((...(((((((((((((....(((.......((((....))))........)))......))))))))).))))..))....)))). (-24.62 = -24.86 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:24 2006