Locus 7610

Sequence ID	3R_DroMel_CAF1
Location	20,407,860 – 20,407,984
Length	124
Max. P	0.999995

overview

Window 8

Location	20,407,860 – 20,407,957
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	95.03
Mean single sequence MFE	-37.04
Consensus MFE	-36.94
Energy contribution	-36.94
Covariance contribution	0.00
Combinations/Pair	1.06
Mean z-score	-3.56
Structure conservation index	1.00
SVM decision value	5.92
SVM RNA-class probability	0.999995
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20407860 97 + 27905053
AAGCUGCAGCGAGCGACAGGCGCGUGCAUGCGCCAAAUGCCUGAUUGGAAUGGUACGUACACAUUUCAACAUUUCCACACGUUUCUGCAGCUGAAAA
.((((((((.(((((.(((((((((....)))).....))))).((((((((((....)).))))))))..........)))))))))))))..... ( -38.00)
>DroSec_CAF1 30245 97 + 1
AAGCUGCAGCGAGCGACAGGCGCGUGCAUGCGCCAAAUGCCUGAUUGGAAUGGUACGUACACAUUUCAACAUUUCCACACGUUUCUGCAGCUGGAAA
.((((((((.(((((.(((((((((....)))).....))))).((((((((((....)).))))))))..........)))))))))))))..... ( -38.00)
>DroSim_CAF1 33535 97 + 1
AAGCUGCAGCGAGCGACAGGCGCGUGCAUGCGCCAAAUGCCUGAUUGGAAUGGUACGUACACAUUUCAACAUUUCCACACGUUUCUGCAGCUGGAAA
.((((((((.(((((.(((((((((....)))).....))))).((((((((((....)).))))))))..........)))))))))))))..... ( -38.00)
>DroEre_CAF1 29823 93 + 1
AAGCUGCAGCGAACGACAGGCGCGUGCAUGCGCCAAAUGCCUGAUUGGAUUGGU----ACACAUUUCAACAUUUCCCCACGUUUCUGCAGCUGGAAA
.((((((((.(((((.(((((((((....)))).....))))).(((((.((..----...)).)))))..........)))))))))))))..... ( -35.00)
>DroYak_CAF1 34162 93 + 1
AAGCUGCAGCGAACGACAGGCGCGUGCAUGCGCCAAAUGCCUGAUUGGAUUGGU----ACACAUUUCAGCAUUUCCACACGUUUCUGCAGCUGGAAA
.((((((((.(((((...((((((....))))))((((((.(((.((.......----...))..))))))))).....)))))))))))))..... ( -36.20)
>consensus
AAGCUGCAGCGAGCGACAGGCGCGUGCAUGCGCCAAAUGCCUGAUUGGAAUGGUACGUACACAUUUCAACAUUUCCACACGUUUCUGCAGCUGGAAA
.((((((((.(((((.(((((((((....)))).....))))).((((((((((....)).))))))))..........)))))))))))))..... (-36.94 = -36.94 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	20,407,860 – 20,407,957
Length	97
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	95.03
Mean single sequence MFE	-32.44
Consensus MFE	-30.48
Energy contribution	-30.68
Covariance contribution	0.20
Combinations/Pair	1.06
Mean z-score	-1.89
Structure conservation index	0.94
SVM decision value	2.91
SVM RNA-class probability	0.997668
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20407860 97 - 27905053
UUUUCAGCUGCAGAAACGUGUGGAAAUGUUGAAAUGUGUACGUACCAUUCCAAUCAGGCAUUUGGCGCAUGCACGCGCCUGUCGCUCGCUGCAGCUU
.....((((((((...((.(((((((((((((((((.((....))))))....))).))))))(((((......)))))..)))).)))))))))). ( -33.30)
>DroSec_CAF1 30245 97 - 1
UUUCCAGCUGCAGAAACGUGUGGAAAUGUUGAAAUGUGUACGUACCAUUCCAAUCAGGCAUUUGGCGCAUGCACGCGCCUGUCGCUCGCUGCAGCUU
.....((((((((...((.(((((((((((((((((.((....))))))....))).))))))(((((......)))))..)))).)))))))))). ( -33.30)
>DroSim_CAF1 33535 97 - 1
UUUCCAGCUGCAGAAACGUGUGGAAAUGUUGAAAUGUGUACGUACCAUUCCAAUCAGGCAUUUGGCGCAUGCACGCGCCUGUCGCUCGCUGCAGCUU
.....((((((((...((.(((((((((((((((((.((....))))))....))).))))))(((((......)))))..)))).)))))))))). ( -33.30)
>DroEre_CAF1 29823 93 - 1
UUUCCAGCUGCAGAAACGUGGGGAAAUGUUGAAAUGUGU----ACCAAUCCAAUCAGGCAUUUGGCGCAUGCACGCGCCUGUCGUUCGCUGCAGCUU
.....((((((((.(((.(((....((((....))))..----.))).........((((...(((((......))))))))))))..)))))))). ( -30.10)
>DroYak_CAF1 34162 93 - 1
UUUCCAGCUGCAGAAACGUGUGGAAAUGCUGAAAUGUGU----ACCAAUCCAAUCAGGCAUUUGGCGCAUGCACGCGCCUGUCGUUCGCUGCAGCUU
.....((((((((.((((.....(((((((....((..(----....)..))....)))))))(((((......)))))...))))..)))))))). ( -32.20)
>consensus
UUUCCAGCUGCAGAAACGUGUGGAAAUGUUGAAAUGUGUACGUACCAUUCCAAUCAGGCAUUUGGCGCAUGCACGCGCCUGUCGCUCGCUGCAGCUU
.....((((((((...((.(((((((((((((((((.((....))))))....))).))))))(((((......)))))..)))).)))))))))). (-30.48 = -30.68 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	20,407,880 – 20,407,984
Length	104
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	94.40
Mean single sequence MFE	-32.04
Consensus MFE	-30.84
Energy contribution	-31.32
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-1.93
Structure conservation index	0.96
SVM decision value	3.32
SVM RNA-class probability	0.998998
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20407880 104 + 27905053
CGCGUGCAUGCGCCAAAUGCCUGAUUGGAAUGGUACGUACACAUUUCAACAUUUCCACACGUUUCUGCAGCUGAAAAGCUUUUGGCGCCAAUUUUGCGCCAAGC
.(.(((((.((((((((....((.((((((((((....)).)))))))))).................((((....))))))))))))......)))))).... ( -30.30)
>DroSec_CAF1 30265 104 + 1
CGCGUGCAUGCGCCAAAUGCCUGAUUGGAAUGGUACGUACACAUUUCAACAUUUCCACACGUUUCUGCAGCUGGAAAGCUUUUGGCGCCAAUUUCGCGCCAACC
.(((((...((((((((.((.((.((((((((((....)).))))))))))((((((...((....))...)))))))).))))))))......)))))..... ( -34.40)
>DroSim_CAF1 33555 104 + 1
CGCGUGCAUGCGCCAAAUGCCUGAUUGGAAUGGUACGUACACAUUUCAACAUUUCCACACGUUUCUGCAGCUGGAAAGCUUUUGGCGCCAAUUUCGCGCCAACC
.(((((...((((((((.((.((.((((((((((....)).))))))))))((((((...((....))...)))))))).))))))))......)))))..... ( -34.40)
>DroEre_CAF1 29843 100 + 1
CGCGUGCAUGCGCCAAAUGCCUGAUUGGAUUGGU----ACACAUUUCAACAUUUCCCCACGUUUCUGCAGCUGGAAAGCUUUUGGCGCCAAUUUCGCGCCACGC
.(((((...((((((((.((.((.(((((.((..----...)).)))))))(((((....((....))....))))))).))))))))......)))))..... ( -29.70)
>DroYak_CAF1 34182 100 + 1
CGCGUGCAUGCGCCAAAUGCCUGAUUGGAUUGGU----ACACAUUUCAGCAUUUCCACACGUUUCUGCAGCUGGAAAGCUUUUGGCGCCAAUUUCGCGCCACGC
.(((((...((((((((.((.((.(((((.((..----...)).)))))))((((((...((....))...)))))))).))))))))......)))))..... ( -31.40)
>consensus
CGCGUGCAUGCGCCAAAUGCCUGAUUGGAAUGGUACGUACACAUUUCAACAUUUCCACACGUUUCUGCAGCUGGAAAGCUUUUGGCGCCAAUUUCGCGCCAAGC
.(((((...((((((((.((.((.((((((((((....)).))))))))))((((((...((....))...)))))))).))))))))......)))))..... (-30.84 = -31.32 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:07 2006