Locus 6770

Sequence ID	3R_DroMel_CAF1
Location	17,857,608 – 17,857,742
Length	134
Max. P	0.993626

overview

Window 1

Location	17,857,608 – 17,857,706
Length	98
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	94.31
Mean single sequence MFE	-38.24
Consensus MFE	-32.92
Energy contribution	-32.80
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-2.14
Structure conservation index	0.86
SVM decision value	2.41
SVM RNA-class probability	0.993626
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17857608 98 + 27905053
GUGGAAAAUAUCGAUUUUGGCCAGCACUACUCGCAUAUGUUUUGACUUGCCAGUGGGGGUGGCUGGGCCA-UUGGGUGGUGGGCCGACCAUCCGUCGAG
..........(((((..((((((((.(((((.(((...((....)).))).))))).....))).)))))-..(((((((......)))))))))))). ( -36.60)
>DroSec_CAF1 2154 98 + 1
GUGGAAAAUAUCGAUUUUGGCCAGCACUACUCGCAUAUGUUUUGGCUUGCAAGUGGGGGUGGCUGGGCCA-UAGGGUGGUGGGCGGACCAUCCGUCGAG
..........(((((..((((((((.(.((((.(((.(((........))).))).)))))))).)))))-..(((((((......)))))))))))). ( -38.60)
>DroSim_CAF1 2160 98 + 1
GUGGAAAAUAUCGAUUUUGGCCAGCACUACUCGCAUAUGUUUUGGCUUGCAAGUGGGGGUGGAUGGGCCA-UAGGGUGGUGGGCGGACCAUCCGUCGAG
..........(((((..(((((....((((((.(((.(((........))).))).))))))...)))))-..(((((((......)))))))))))). ( -38.50)
>DroEre_CAF1 2198 98 + 1
GUGGAAAAUAUCGAUUUUGGCCAGCACUACUCGCAUAUGUUUUGGCUUUACUGCGGGGGUGGCUGGGCCA-UUGGGUGGUGGGCGGACCAUCCGUCGAG
..........(((((..(((((((((((.((((((...((....)).....))))))))).))).)))))-..(((((((......)))))))))))). ( -37.50)
>DroYak_CAF1 2206 99 + 1
GUGGAAAAUAUCGAUUUUGGCCAGCACUACUCGCAUAUGUUUUGGCUUGACUGUGGGGGUGGCUGGGCCAAAUGGGUGGUGGGCGGACCAUCCGUCGAU
.........((((((((((((((((.(.((((.((((.(((.......))))))).)))))))).))))))).(((((((......))))))))))))) ( -40.00)
>consensus
GUGGAAAAUAUCGAUUUUGGCCAGCACUACUCGCAUAUGUUUUGGCUUGCCAGUGGGGGUGGCUGGGCCA_UUGGGUGGUGGGCGGACCAUCCGUCGAG
..........(((((..(((((((((((.(((((....((....))......)))))))).))).)))))...(((((((......)))))))))))). (-32.92 = -32.80 +  -0.12)

alignment

secondary structure

dotplot

Window 2

Location	17,857,608 – 17,857,706
Length	98
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	94.31
Mean single sequence MFE	-26.98
Consensus MFE	-19.96
Energy contribution	-21.00
Covariance contribution	1.04
Combinations/Pair	1.04
Mean z-score	-2.20
Structure conservation index	0.74
SVM decision value	0.18
SVM RNA-class probability	0.623927
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17857608 98 - 27905053
CUCGACGGAUGGUCGGCCCACCACCCAA-UGGCCCAGCCACCCCCACUGGCAAGUCAAAACAUAUGCGAGUAGUGCUGGCCAAAAUCGAUAUUUUCCAC
.((((.((.((((......)))).))..-(((((.(((.((....(((.(((.((......)).))).))).))))))))))...)))).......... ( -27.80)
>DroSec_CAF1 2154 98 - 1
CUCGACGGAUGGUCCGCCCACCACCCUA-UGGCCCAGCCACCCCCACUUGCAAGCCAAAACAUAUGCGAGUAGUGCUGGCCAAAAUCGAUAUUUUCCAC
.((((.((.((((......)))).))..-(((((.(((.((....(((((((............))))))).))))))))))...)))).......... ( -28.20)
>DroSim_CAF1 2160 98 - 1
CUCGACGGAUGGUCCGCCCACCACCCUA-UGGCCCAUCCACCCCCACUUGCAAGCCAAAACAUAUGCGAGUAGUGCUGGCCAAAAUCGAUAUUUUCCAC
.((((.((.((((......)))).))..-(((((....(((....(((((((............))))))).)))..)))))...)))).......... ( -25.20)
>DroEre_CAF1 2198 98 - 1
CUCGACGGAUGGUCCGCCCACCACCCAA-UGGCCCAGCCACCCCCGCAGUAAAGCCAAAACAUAUGCGAGUAGUGCUGGCCAAAAUCGAUAUUUUCCAC
.((((.((.((((......)))).))..-(((((.(((.((..(((((................)))).)..))))))))))...)))).......... ( -28.09)
>DroYak_CAF1 2206 99 - 1
AUCGACGGAUGGUCCGCCCACCACCCAUUUGGCCCAGCCACCCCCACAGUCAAGCCAAAACAUAUGCGAGUAGUGCUGGCCAAAAUCGAUAUUUUCCAC
(((((.((.((((......)))).)).(((((((.(((.((..((.((................)).).)..)))))))))))).)))))......... ( -25.59)
>consensus
CUCGACGGAUGGUCCGCCCACCACCCAA_UGGCCCAGCCACCCCCACUGGCAAGCCAAAACAUAUGCGAGUAGUGCUGGCCAAAAUCGAUAUUUUCCAC
.((((.((.((((......)))).))...(((((.(((.((....(((.(((............))).))).))))))))))...)))).......... (-19.96 = -21.00 +   1.04)

alignment

secondary structure

dotplot

Window 3

Location	17,857,644 – 17,857,742
Length	98
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	93.50
Mean single sequence MFE	-26.04
Consensus MFE	-24.30
Energy contribution	-24.34
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-1.21
Structure conservation index	0.93
SVM decision value	0.54
SVM RNA-class probability	0.776464
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17857644 98 - 27905053
AGUACGCAUGCGCAGUGCAUGUGAAAUGGCAAACAACUCGACGGAUGGUCGGCCCACCACCCAA-UGGCCCAGCCACCCCCACUGGCAAGUCAAAACAU
....(((((((.....)))))))...((((.........(((.....)))((((..........-.))))..((((.......))))..))))...... ( -26.20)
>DroSec_CAF1 2190 98 - 1
AGUCCGCAUGCGCAGUGCAUGUGAAAUGGCAAACAACUCGACGGAUGGUCCGCCCACCACCCUA-UGGCCCAGCCACCCCCACUUGCAAGCCAAAACAU
....(((((((.....)))))))...((((............((.((((......)))).))..-((((...)))).............))))...... ( -25.60)
>DroSim_CAF1 2196 98 - 1
AGUCCGCAUGCGCAGUGCAUGUGAAAUGGCAAACAACUCGACGGAUGGUCCGCCCACCACCCUA-UGGCCCAUCCACCCCCACUUGCAAGCCAAAACAU
....(((((((.....)))))))...((((...(.....)..((((((.(((............-))).))))))..............))))...... ( -25.60)
>DroEre_CAF1 2234 98 - 1
AGUCCGCAUGCGCAGUGCAUGUGAAAUGGCAAACAACUCGACGGAUGGUCCGCCCACCACCCAA-UGGCCCAGCCACCCCCGCAGUAAAGCCAAAACAU
....(((((((.....)))))))...((((.....(((((..((.((((......)))).))..-((((...))))....)).)))...))))...... ( -26.90)
>DroYak_CAF1 2242 99 - 1
AGUCCGCAUGCGCAGUGCAUGUGAAGUGGCAAACAAAUCGACGGAUGGUCCGCCCACCACCCAUUUGGCCCAGCCACCCCCACAGUCAAGCCAAAACAU
....(((((((.....)))))))...((((............((.((((......)))).))...((((...)))).............))))...... ( -25.90)
>consensus
AGUCCGCAUGCGCAGUGCAUGUGAAAUGGCAAACAACUCGACGGAUGGUCCGCCCACCACCCAA_UGGCCCAGCCACCCCCACUGGCAAGCCAAAACAU
....(((((((.....)))))))...((((............((.((((......)))).))...((((...)))).............))))...... (-24.30 = -24.34 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:29:31 2006