Locus 6565

Sequence ID	2L_DroMel_CAF1
Location	18,467,336 – 18,467,456
Length	120
Max. P	0.999991

overview

Window 2

Location	18,467,336 – 18,467,456
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	97.72
Mean single sequence MFE	-34.37
Consensus MFE	-34.37
Energy contribution	-34.37
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.96
Structure conservation index	1.00
SVM decision value	5.62
SVM RNA-class probability	0.999991
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18467336 120 + 22407834
UGAAAUGGUGCAUACUUACAUAUGGACCAUUAACAGAAACCCGUAAAUCCGAACUUGUGCUGUUUUAUAUCUGUUACAAGACCGGCAUUAUGGGAGUCUGUCAAUGCAAACAACUGGUUU
...((((((.((((......)))).)))))).(((((..(((((((..(((..(((((((.(........).).))))))..)))..)))))))..)))))................... ( -34.20)
>DroGri_CAF1 26320 120 + 1
AGAAAUGGUGCAUACUUACAUAUGGACCAUUAACAGAAACCCGUAAAUCCGAACUUGUGCUGUUUUUUAUCUGUUACAAGACCGGCAUUAUGGGAGUCUGUCAAUGCAAACAACUGGUUU
...((((((.((((......)))).)))))).(((((..(((((((..(((..(((((((.(........).).))))))..)))..)))))))..)))))................... ( -34.20)
>DroSec_CAF1 21701 120 + 1
CGAAAUGGUGCAUACUUACAUAUGGACCAUUAACAGAAACCCGUAAAUCCGAACUUGUGCUGUUUUAUAUCUGUUACAAGACCGGCAUUAUGGGAGUCUGUCAAUGCAAACAACUGGUUU
...((((((.((((......)))).)))))).(((((..(((((((..(((..(((((((.(........).).))))))..)))..)))))))..)))))................... ( -34.20)
>DroWil_CAF1 28377 120 + 1
AAAAAUGGUGCAUAGUCACAUAUGGACCAUUAACAGAAACCCGUAAAUCCGAACUUGUGCUGUUUUAUAUCUGUUACAAGACCGGCAUUAUGGGAGUCUGUCAAUGCAAACAACUGGUUU
...((((((.((((......)))).)))))).(((((..(((((((..(((..(((((((.(........).).))))))..)))..)))))))..)))))................... ( -35.20)
>DroYak_CAF1 21558 120 + 1
UGAAAUGGUGCAUACUUACAUAUGGACCAUUAACAGAAACCCGUAAAUCCGAACUUGUGCUGUUUUAUAUCUGUUACAAGACCGGCAUUAUGGGAGUCUGUCAAUGCAAACAACUGGUUU
...((((((.((((......)))).)))))).(((((..(((((((..(((..(((((((.(........).).))))))..)))..)))))))..)))))................... ( -34.20)
>DroAna_CAF1 17810 120 + 1
UCAAAUGGUGCAUACUCACAUAUGGACCAUUAACAGAAACCCGUAAAUCCGAACUUGUGCUGUUUUUUAUCUGUUACAAGACCGGCAUUAUGGGAGUCUGUCAAUGCAAACAACUGGUUU
...((((((.((((......)))).)))))).(((((..(((((((..(((..(((((((.(........).).))))))..)))..)))))))..)))))................... ( -34.20)
>consensus
UGAAAUGGUGCAUACUUACAUAUGGACCAUUAACAGAAACCCGUAAAUCCGAACUUGUGCUGUUUUAUAUCUGUUACAAGACCGGCAUUAUGGGAGUCUGUCAAUGCAAACAACUGGUUU
...((((((.((((......)))).)))))).(((((..(((((((..(((..(((((((.(........).).))))))..)))..)))))))..)))))................... (-34.37 = -34.37 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	18,467,336 – 18,467,456
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	97.72
Mean single sequence MFE	-32.76
Consensus MFE	-32.40
Energy contribution	-32.56
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.48
Structure conservation index	0.99
SVM decision value	4.85
SVM RNA-class probability	0.999956
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18467336 120 - 22407834
AAACCAGUUGUUUGCAUUGACAGACUCCCAUAAUGCCGGUCUUGUAACAGAUAUAAAACAGCACAAGUUCGGAUUUACGGGUUUCUGUUAAUGGUCCAUAUGUAAGUAUGCACCAUUUCA
...............(((((((((..(((.(((..(((..(((((.................)))))..)))..))).)))..)))))))))(((.(((((....))))).)))...... ( -32.93)
>DroGri_CAF1 26320 120 - 1
AAACCAGUUGUUUGCAUUGACAGACUCCCAUAAUGCCGGUCUUGUAACAGAUAAAAAACAGCACAAGUUCGGAUUUACGGGUUUCUGUUAAUGGUCCAUAUGUAAGUAUGCACCAUUUCU
...............(((((((((..(((.(((..(((..(((((.................)))))..)))..))).)))..)))))))))(((.(((((....))))).)))...... ( -32.93)
>DroSec_CAF1 21701 120 - 1
AAACCAGUUGUUUGCAUUGACAGACUCCCAUAAUGCCGGUCUUGUAACAGAUAUAAAACAGCACAAGUUCGGAUUUACGGGUUUCUGUUAAUGGUCCAUAUGUAAGUAUGCACCAUUUCG
...............(((((((((..(((.(((..(((..(((((.................)))))..)))..))).)))..)))))))))(((.(((((....))))).)))...... ( -32.93)
>DroWil_CAF1 28377 120 - 1
AAACCAGUUGUUUGCAUUGACAGACUCCCAUAAUGCCGGUCUUGUAACAGAUAUAAAACAGCACAAGUUCGGAUUUACGGGUUUCUGUUAAUGGUCCAUAUGUGACUAUGCACCAUUUUU
............((((((((((((..(((.(((..(((..(((((.................)))))..)))..))).)))..))))))))((((((....).)))))))))........ ( -31.93)
>DroYak_CAF1 21558 120 - 1
AAACCAGUUGUUUGCAUUGACAGACUCCCAUAAUGCCGGUCUUGUAACAGAUAUAAAACAGCACAAGUUCGGAUUUACGGGUUUCUGUUAAUGGUCCAUAUGUAAGUAUGCACCAUUUCA
...............(((((((((..(((.(((..(((..(((((.................)))))..)))..))).)))..)))))))))(((.(((((....))))).)))...... ( -32.93)
>DroAna_CAF1 17810 120 - 1
AAACCAGUUGUUUGCAUUGACAGACUCCCAUAAUGCCGGUCUUGUAACAGAUAAAAAACAGCACAAGUUCGGAUUUACGGGUUUCUGUUAAUGGUCCAUAUGUGAGUAUGCACCAUUUGA
...............(((((((((..(((.(((..(((..(((((.................)))))..)))..))).)))..)))))))))(((.(((((....))))).)))...... ( -32.93)
>consensus
AAACCAGUUGUUUGCAUUGACAGACUCCCAUAAUGCCGGUCUUGUAACAGAUAUAAAACAGCACAAGUUCGGAUUUACGGGUUUCUGUUAAUGGUCCAUAUGUAAGUAUGCACCAUUUCA
...............(((((((((..(((.(((..(((..(((((.................)))))..)))..))).)))..)))))))))(((.(((((....))))).)))...... (-32.40 = -32.56 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:18 2006