Locus 2942

Sequence ID	2R_DroMel_CAF1
Location	10,168,237 – 10,168,375
Length	138
Max. P	0.999435

overview

Window 3

Location	10,168,237 – 10,168,357
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.33
Mean single sequence MFE	-32.82
Consensus MFE	-32.06
Energy contribution	-32.26
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.49
Structure conservation index	0.98
SVM decision value	0.94
SVM RNA-class probability	0.885788
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10168237 120 + 20766785
AAUAAUUUAGCAACCGGAGCGGACAAUAAAAUUUCGAGCCCAAAUGUCAUACGCAUGCAUUUGCAUAUGAUUUAGCCGGCGCUGGGUGAACAGUAUCCGUAUCCGAAUCGGAUUCGGAAU
.............((((((((((..............(((.....((((((.(((......))).))))))......)))((((......)))).))))).((((...)))))))))... ( -33.80)
>DroSec_CAF1 8103 120 + 1
AAUAAUUUAGCAACCGGAGCGGACAAUAAAAUUUCGAGCCCAAAUGUCAUACGCAUGCAUUUGCAUAUGAUUUAGCCGGCGCUGGGUGAACAGUAUCCGUAUCCGAAUCGGAUUCGGAAU
.............((((((((((..............(((.....((((((.(((......))).))))))......)))((((......)))).))))).((((...)))))))))... ( -33.80)
>DroSim_CAF1 7943 120 + 1
AAUAAUUUAGCAACCGGAGCGGACAAUAAAAUUUCGAGCCCAAAUGUCAUACGCAUGCAUUUGCAUAUGAUUUAGCCGGCGCUGGGUGAACAGUAUCCGUAUCCGAAUCGGAUUCGGAAU
.............((((((((((..............(((.....((((((.(((......))).))))))......)))((((......)))).))))).((((...)))))))))... ( -33.80)
>DroEre_CAF1 8101 120 + 1
AAUAAUUUAGCAACCGGAGCGGACAAUAAAAUUUCGAGCCCAAAUGUCAUACGCAUGCAUUUGCAUAUGAUUUAGCCGGCGCUGGGUGAACAGUAUCCGUAUCCGAAUCGGAUUCGGAAU
.............((((((((((..............(((.....((((((.(((......))).))))))......)))((((......)))).))))).((((...)))))))))... ( -33.80)
>DroYak_CAF1 7885 120 + 1
AAUAAUUUAGCAACCGGAGCGGACAAUAAAAUUUCGAGCCCAAAUGUCAUACGCAUGCAUUUGCAUAUGAUUUAGCCGGCGCUGGGUGAACAGUAUCCGUAUCCAAAUCGGAUUCAGAAU
...............((((((((..............(((.....((((((.(((......))).))))))......)))((((......)))).))))).)))................ ( -28.90)
>consensus
AAUAAUUUAGCAACCGGAGCGGACAAUAAAAUUUCGAGCCCAAAUGUCAUACGCAUGCAUUUGCAUAUGAUUUAGCCGGCGCUGGGUGAACAGUAUCCGUAUCCGAAUCGGAUUCGGAAU
.............((((((((((..............(((.....((((((.(((......))).))))))......)))((((......)))).))))).(((.....))))))))... (-32.06 = -32.26 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	10,168,237 – 10,168,357
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.33
Mean single sequence MFE	-35.74
Consensus MFE	-36.00
Energy contribution	-35.68
Covariance contribution	-0.32
Combinations/Pair	1.07
Mean z-score	-2.50
Structure conservation index	1.01
SVM decision value	3.60
SVM RNA-class probability	0.999435
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10168237 120 - 20766785
AUUCCGAAUCCGAUUCGGAUACGGAUACUGUUCACCCAGCGCCGGCUAAAUCAUAUGCAAAUGCAUGCGUAUGACAUUUGGGCUCGAAAUUUUAUUGUCCGCUCCGGUUGCUAAAUUAUU
..((((.(((((...))))).))))............((((((((.....(((((((((......))))))))).....((((.............))))...)))).))))........ ( -36.42)
>DroSec_CAF1 8103 120 - 1
AUUCCGAAUCCGAUUCGGAUACGGAUACUGUUCACCCAGCGCCGGCUAAAUCAUAUGCAAAUGCAUGCGUAUGACAUUUGGGCUCGAAAUUUUAUUGUCCGCUCCGGUUGCUAAAUUAUU
..((((.(((((...))))).))))............((((((((.....(((((((((......))))))))).....((((.............))))...)))).))))........ ( -36.42)
>DroSim_CAF1 7943 120 - 1
AUUCCGAAUCCGAUUCGGAUACGGAUACUGUUCACCCAGCGCCGGCUAAAUCAUAUGCAAAUGCAUGCGUAUGACAUUUGGGCUCGAAAUUUUAUUGUCCGCUCCGGUUGCUAAAUUAUU
..((((.(((((...))))).))))............((((((((.....(((((((((......))))))))).....((((.............))))...)))).))))........ ( -36.42)
>DroEre_CAF1 8101 120 - 1
AUUCCGAAUCCGAUUCGGAUACGGAUACUGUUCACCCAGCGCCGGCUAAAUCAUAUGCAAAUGCAUGCGUAUGACAUUUGGGCUCGAAAUUUUAUUGUCCGCUCCGGUUGCUAAAUUAUU
..((((.(((((...))))).))))............((((((((.....(((((((((......))))))))).....((((.............))))...)))).))))........ ( -36.42)
>DroYak_CAF1 7885 120 - 1
AUUCUGAAUCCGAUUUGGAUACGGAUACUGUUCACCCAGCGCCGGCUAAAUCAUAUGCAAAUGCAUGCGUAUGACAUUUGGGCUCGAAAUUUUAUUGUCCGCUCCGGUUGCUAAAUUAUU
..((((.((((.....)))).))))............((((((((.....(((((((((......))))))))).....((((.............))))...)))).))))........ ( -33.02)
>consensus
AUUCCGAAUCCGAUUCGGAUACGGAUACUGUUCACCCAGCGCCGGCUAAAUCAUAUGCAAAUGCAUGCGUAUGACAUUUGGGCUCGAAAUUUUAUUGUCCGCUCCGGUUGCUAAAUUAUU
..((((.(((((...))))).))))............((((((((.....(((((((((......))))))))).....((((.............))))...)))).))))........ (-36.00 = -35.68 +  -0.32)

alignment

secondary structure

dotplot

Window 5

Location	10,168,277 – 10,168,375
Length	98
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.89
Mean single sequence MFE	-27.08
Consensus MFE	-23.08
Energy contribution	-22.60
Covariance contribution	-0.48
Combinations/Pair	1.12
Mean z-score	-1.41
Structure conservation index	0.85
SVM decision value	0.24
SVM RNA-class probability	0.650495
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10168277 98 - 20766785
CCUGAUUCUG----UGA------------------UUCUGAUUCCGAAUCCGAUUCGGAUACGGAUACUGUUCACCCAGCGCCGGCUAAAUCAUAUGCAAAUGCAUGCGUAUGACAUUUG
.........(----(((------------------.......((((.(((((...))))).))))......))))..(((....)))...(((((((((......)))))))))...... ( -27.12)
>DroSec_CAF1 8143 98 - 1
CCUGAUUUUG----UGA------------------UUCUGAUUCCGAAUCCGAUUCGGAUACGGAUACUGUUCACCCAGCGCCGGCUAAAUCAUAUGCAAAUGCAUGCGUAUGACAUUUG
.........(----(((------------------.......((((.(((((...))))).))))......))))..(((....)))...(((((((((......)))))))))...... ( -27.12)
>DroSim_CAF1 7983 98 - 1
CCUGAUUCUG----UGA------------------UUCUGAUUCCGAAUCCGAUUCGGAUACGGAUACUGUUCACCCAGCGCCGGCUAAAUCAUAUGCAAAUGCAUGCGUAUGACAUUUG
.........(----(((------------------.......((((.(((((...))))).))))......))))..(((....)))...(((((((((......)))))))))...... ( -27.12)
>DroEre_CAF1 8141 102 - 1
CCCGAUCCUGCUCCUGA------------------UUCUGAUUCCGAAUCCGAUUCGGAUACGGAUACUGUUCACCCAGCGCCGGCUAAAUCAUAUGCAAAUGCAUGCGUAUGACAUUUG
.(((....((((..(((------------------.......((((.(((((...))))).))))......)))...)))).))).....(((((((((......)))))))))...... ( -27.72)
>DroYak_CAF1 7925 120 - 1
CCUGACUCUGCUCCUGAUUCUGCUUCUCAUUCUGAUUCUGAUUCUGAAUCCGAUUUGGAUACGGAUACUGUUCACCCAGCGCCGGCUAAAUCAUAUGCAAAUGCAUGCGUAUGACAUUUG
.(((.(.(((....(((.((((..(((...((.(((((.......))))).))...)))..))))......)))..))).).))).....(((((((((......)))))))))...... ( -26.30)
>consensus
CCUGAUUCUG____UGA__________________UUCUGAUUCCGAAUCCGAUUCGGAUACGGAUACUGUUCACCCAGCGCCGGCUAAAUCAUAUGCAAAUGCAUGCGUAUGACAUUUG
.(((......................................((((.(((((...))))).))))..(((......)))...))).....(((((((((......)))))))))...... (-23.08 = -22.60 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:24 2006