Locus 6970

Sequence ID	3L_DroMel_CAF1
Location	18,816,430 – 18,816,589
Length	159
Max. P	0.984144

overview

Window 2

Location	18,816,430 – 18,816,549
Length	119
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	94.44
Mean single sequence MFE	-31.93
Consensus MFE	-30.43
Energy contribution	-31.10
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.85
Structure conservation index	0.95
SVM decision value	1.97
SVM RNA-class probability	0.984144
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18816430 119 + 23771897
UACAA-AAGGGUUAGUUCCUAAGCUGUUCGAAUGCAACACAUACUGCAUUAAUUCGACUUGGCAUGAUGAGUGUAUACGAAGUCAUCUGCGAGUCAAAUGUAUAACUAAGCACCUUAAUC
.....-(((((((((((.............((((((........)))))).....((((((.((.(((((.(........).)))))))))))))........)))).))).)))).... ( -28.00)
>DroSec_CAF1 23904 120 + 1
AACAAAAAGGGUUAGUUCCAAAGCUGUUCGAAUGCAACACAUACUGCAUUUAUUUGACUUGGCAUGAUGAGUGCAUUCACAGUCAUCUGCGAGUCAAAUGUAUAACUAAGCACCUUAAUC
......(((((((((((............(((((((........)))))))((((((((((.((.(((((.((......)).)))))))))))))))))....)))).))).)))).... ( -34.60)
>DroSim_CAF1 24183 119 + 1
AACAAAAAGGGUUAGUUCCUAAGCUGUUCGAAUGCAACACA-ACUGCAUUAAUUUGACUUGGCAUGAUGAGUGCAUUCACAGUCAUCUGCGAGUCAAAUGUAUAACUAAGCACCUUAAUC
......(((((((((((.............((((((.....-..)))))).((((((((((.((.(((((.((......)).)))))))))))))))))....)))).))).)))).... ( -33.20)
>consensus
AACAAAAAGGGUUAGUUCCUAAGCUGUUCGAAUGCAACACAUACUGCAUUAAUUUGACUUGGCAUGAUGAGUGCAUUCACAGUCAUCUGCGAGUCAAAUGUAUAACUAAGCACCUUAAUC
......(((((((((((.............((((((........)))))).((((((((((.((.(((((.((......)).)))))))))))))))))....)))).))).)))).... (-30.43 = -31.10 +   0.67)

alignment

secondary structure

dotplot

Window 3

Location	18,816,430 – 18,816,549
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	94.44
Mean single sequence MFE	-29.43
Consensus MFE	-28.72
Energy contribution	-29.17
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-1.48
Structure conservation index	0.98
SVM decision value	0.21
SVM RNA-class probability	0.635794
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18816430 119 - 23771897
GAUUAAGGUGCUUAGUUAUACAUUUGACUCGCAGAUGACUUCGUAUACACUCAUCAUGCCAAGUCGAAUUAAUGCAGUAUGUGUUGCAUUCGAACAGCUUAGGAACUAACCCUU-UUGUA
....((((.(.((((((...(((((((((.((((((((............))))).)))..)))))))).(((((((......)))))))...........).)))))))))))-..... ( -26.10)
>DroSec_CAF1 23904 120 - 1
GAUUAAGGUGCUUAGUUAUACAUUUGACUCGCAGAUGACUGUGAAUGCACUCAUCAUGCCAAGUCAAAUAAAUGCAGUAUGUGUUGCAUUCGAACAGCUUUGGAACUAACCCUUUUUGUU
....((((.(.((((((....((((((((.((((((((.(((....))).))))).)))..)))))))).(((((((......))))))).............)))))))))))...... ( -31.50)
>DroSim_CAF1 24183 119 - 1
GAUUAAGGUGCUUAGUUAUACAUUUGACUCGCAGAUGACUGUGAAUGCACUCAUCAUGCCAAGUCAAAUUAAUGCAGU-UGUGUUGCAUUCGAACAGCUUAGGAACUAACCCUUUUUGUU
....((((.(.((((((...(((((((((.((((((((.(((....))).))))).)))..)))))))).(((((((.-....)))))))...........).)))))))))))...... ( -30.70)
>consensus
GAUUAAGGUGCUUAGUUAUACAUUUGACUCGCAGAUGACUGUGAAUGCACUCAUCAUGCCAAGUCAAAUUAAUGCAGUAUGUGUUGCAUUCGAACAGCUUAGGAACUAACCCUUUUUGUU
....((((.(.((((((...(((((((((.((((((((.(((....))).))))).)))..)))))))).(((((((......)))))))...........).)))))))))))...... (-28.72 = -29.17 +   0.45)

alignment

secondary structure

dotplot

Window 4

Location	18,816,469 – 18,816,589
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	91.67
Mean single sequence MFE	-27.27
Consensus MFE	-23.92
Energy contribution	-24.70
Covariance contribution	0.78
Combinations/Pair	1.03
Mean z-score	-1.73
Structure conservation index	0.88
SVM decision value	0.03
SVM RNA-class probability	0.549841
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18816469 120 + 23771897
AUACUGCAUUAAUUCGACUUGGCAUGAUGAGUGUAUACGAAGUCAUCUGCGAGUCAAAUGUAUAACUAAGCACCUUAAUCCAUUAUCCUUAUGGUAAUCAUUUUCAUGGCAGGACGUCUA
...((((........((((((.((.(((((.(........).)))))))))))))........................((((.......))))..............))))........ ( -24.20)
>DroSec_CAF1 23944 120 + 1
AUACUGCAUUUAUUUGACUUGGCAUGAUGAGUGCAUUCACAGUCAUCUGCGAGUCAAAUGUAUAACUAAGCACCUUAAUCCAUUAUCCUUAUGGUAAUAAUUUUUAUGGUAGGAAUUCUU
..........(((((((((((.((.(((((.((......)).)))))))))))))))))).........................((((.((.((((......)))).))))))...... ( -28.90)
>DroSim_CAF1 24223 119 + 1
A-ACUGCAUUAAUUUGACUUGGCAUGAUGAGUGCAUUCACAGUCAUCUGCGAGUCAAAUGUAUAACUAAGCACCUUAAUCCAUUAUCCUUAAGGUAAUCAUUUUUAUGGUCGGAAUUCUU
.-.(((.((((((((((((((.((.(((((.((......)).)))))))))))))))))............(((((((..........)))))))...........)))))))....... ( -28.70)
>consensus
AUACUGCAUUAAUUUGACUUGGCAUGAUGAGUGCAUUCACAGUCAUCUGCGAGUCAAAUGUAUAACUAAGCACCUUAAUCCAUUAUCCUUAUGGUAAUCAUUUUUAUGGUAGGAAUUCUU
...((((....((((((((((.((.(((((.((......)).)))))))))))))))))......................((((((.....))))))..........))))........ (-23.92 = -24.70 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:25 2006