Locus 1078

Sequence ID	2L_DroMel_CAF1
Location	2,976,254 – 2,976,445
Length	191
Max. P	0.605837

overview

Window 6

Location	2,976,254 – 2,976,374
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.75
Mean single sequence MFE	-45.72
Consensus MFE	-35.70
Energy contribution	-37.06
Covariance contribution	1.36
Combinations/Pair	1.09
Mean z-score	-1.52
Structure conservation index	0.78
SVM decision value	0.02
SVM RNA-class probability	0.544409
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2976254 120 - 22407834
GGACUGCCGGAACACAUUCGCAAGGAGCUAUCGCUCCUUGGCCCCGCCAAGCGCAAGUGGUUCUUUCGCUAUCUGGACACGGGCAUCAGCAAUGAAAAGGCCCUUAUGAAGGCCUCGGAA
......(((.....(((((.((((((((....))))))))((((..(((((((.(((.....))).))))...)))....))))....).))))...(((((........)))))))).. ( -43.10)
>DroSec_CAF1 6236 120 - 1
GGCCUGCCGGACCAUAUUCGCAGGGAGCUAACGCUCCUUGGCGCCACCAAGCGCAGGAGUUUCUUUCGCUAUCUGGACACGGGCAUCAGCAUUGAAAGGGCCCUCAUUAAGGCCUCGGAA
(((((.(((((((.......((((((((....))))))))((((......)))).))(((.......))).)))))....((((.((......))....))))......)))))...... ( -46.20)
>DroSim_CAF1 6231 120 - 1
GGCCUGCCGGACCAUAUUCGCAGGGAGCUAACGCUCCUUGGCGCCACCAAGCGCAGGAGUUUCUUUCGCUAUCUGGACACGGGCAUCAGCAUUGAAAGGGCCCUCAUUAAGGCCUCGGAA
(((((.(((((((.......((((((((....))))))))((((......)))).))(((.......))).)))))....((((.((......))....))))......)))))...... ( -46.20)
>DroEre_CAF1 6376 120 - 1
GGCCUGCCGGACCACAUUCUCAAGGAGCUUUCGCACCUUAGCGCCGCCAAGCGCAAGUGGUUCUUUCACUAUGUGGACAUGGGCUUCAGCAAUGAGAAGGCCCUCGCCAGGGCCUCGGAA
(((((...(((((((......((((.((....)).)))).((((......))))..)))))))..........(((....((((((((....)))...)))))...))))))))...... ( -47.30)
>DroYak_CAF1 6369 120 - 1
GGCCUGCCGGAACACAUACGCAAGGAGCUUUCGCACCUUAGCGCCGCCAAGCGCAAGUGGUUCUAUCGCUUCCUGGACGGGGGCUGCAGCAAUGAGAAGGCCCUCACCAAGGCCUUGGAA
(((((((.(((((.(((....((((.((....)).)))).((((......))))..))))))))...))....(((..(((((((.((....))....))))))).))))))))...... ( -45.80)
>consensus
GGCCUGCCGGACCACAUUCGCAAGGAGCUAUCGCUCCUUGGCGCCGCCAAGCGCAAGUGGUUCUUUCGCUAUCUGGACACGGGCAUCAGCAAUGAAAAGGCCCUCAUCAAGGCCUCGGAA
(((((.(((((.......((((((((((....))))))).)))......((((.(((.....))).)))).)))))....((((.(((....)))....))))......)))))...... (-35.70 = -37.06 +   1.36)

alignment

secondary structure

dotplot

Window 7

Location	2,976,334 – 2,976,445
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.48
Mean single sequence MFE	-46.39
Consensus MFE	-32.83
Energy contribution	-34.47
Covariance contribution	1.64
Combinations/Pair	1.17
Mean z-score	-1.57
Structure conservation index	0.71
SVM decision value	0.15
SVM RNA-class probability	0.605837
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2976334 111 - 22407834
ACGGCGGCCCUUCCGACGGGAGCCAUUGGCCCACUCCGAACUCA---------UCCAUGCAGGUGACAUCGGGUGAAAGGGGACUGCCGGAACACAUUCGCAAGGAGCUAUCGCUCCUUG
.(((((((((((((....)))(((...))).(((.((((..(((---------((......)))))..)))))))...)))).))))))...........((((((((....)))))))) ( -47.30)
>DroSec_CAF1 6316 111 - 1
ACGGCGGCCCUUCCAACGGGAGCCAUUGGCCCACUUCGAACUCA---------UCCAUGCAGGUGCCAGCGGGUGAAAGGGGCCUGCCGGACCAUAUUCGCAGGGAGCUAACGCUCCUUG
.((((((((((......))).)))...(((((.(((.....(((---------(((..((.(....).)))))))))))))))).))))...........((((((((....)))))))) ( -49.80)
>DroSim_CAF1 6311 111 - 1
ACGGCGGCCCUUCCAACGGGAGCCAUUGGCCCACUUCGAACUCA---------UCCAUGCAGGUGCCAGCGGGUAAAGGGGGCCUGCCGGACCAUAUUCGCAGGGAGCUAACGCUCCUUG
.(((((((((((((....)))(((.(((((((............---------........)).)))))..)))....)))))).))))...........((((((((....)))))))) ( -46.65)
>DroEre_CAF1 6456 120 - 1
ACGGCGGCCCUGCCAAUGCCAGCCAGUGGUCUAAUCCGAACCCAAAAAAGCAGUCCAUGCCGUUGCCACCGGAGGAUAGGGGCCUGCCGGACCACAUUCUCAAGGAGCUUUCGCACCUUA
.((((((((((.((...((((.....))))....((((....(((....(((.....)))..)))....))))))...)))))).))))............((((.((....)).)))). ( -40.00)
>DroYak_CAF1 6449 120 - 1
ACGGCGGCCCUUCCAACGGCAGCCAGUGGUCCACUGCAAGCCCAAACGUGCAGUCCGUGCAGGUGCCGGCGGAGGAGAGGGGCCUGCCGGAACACAUACGCAAGGAGCUUUCGCACCUUA
.(((((((((((((..(((((.((.((((...((((((.(......).))))))))..)).)))))))..))).....)))))).))))............((((.((....)).)))). ( -48.20)
>consensus
ACGGCGGCCCUUCCAACGGGAGCCAUUGGCCCACUCCGAACUCA_________UCCAUGCAGGUGCCAGCGGGUGAAAGGGGCCUGCCGGACCACAUUCGCAAGGAGCUAUCGCUCCUUG
.(((((((((((((....))).((.(((((((.............................)).))))).))......)))))).))))...........((((((((....)))))))) (-32.83 = -34.47 +   1.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:58 2006