Locus 1330

Sequence ID	2L_DroMel_CAF1
Location	3,519,747 – 3,519,847
Length	100
Max. P	0.783959

overview

Window 2

Location	3,519,747 – 3,519,847
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	82.70
Mean single sequence MFE	-38.46
Consensus MFE	-27.68
Energy contribution	-30.16
Covariance contribution	2.48
Combinations/Pair	1.07
Mean z-score	-1.80
Structure conservation index	0.72
SVM decision value	0.42
SVM RNA-class probability	0.727750
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3519747 100 + 22407834
UCCCGGAGAACUGGAUUGGGAUCGAGGACUUGCUUUGUCGAGGUGGAUUACCGGAGUCCUCCCUCCCAGGAUGGUCAGGAAUGUGUCCUUCGGGAGGAGU
(((((((((.(((..((((((..(((((((((((((...)))))((....)).))))))))..))))))..))))).(((.....))))))))))..... ( -39.10)
>DroSec_CAF1 28745 100 + 1
UCCCGGAAAACUGGAUUGGGAUCGAGGACUUGCUUCGUCGAGGUGGAUUGGCGGAGUCCUCGCUCACAGGAUGAUAAGGAAAGUGUCCUUCGGGAGGAAU
(((((((...(((...((((..(((((((((....((((((......))))))))))))))))))))))........(((.....))))))))))..... ( -36.20)
>DroSim_CAF1 28692 100 + 1
UCCCGGAGAACUGGAUUGGGAUCGAGGACUUGCUUAGUCGAGGUGGAUUGGCGGAGUCCUCGCUCCCAGGAUGAUAAGAAAAGUGUCCUGCGGGAGGAAU
(((((.((.......((((((.((((((((((((.((((......))))))).))))))))).))))))...((((.......)))))).)))))..... ( -41.90)
>DroEre_CAF1 26623 100 + 1
UCCCGGAGCACUGGAUUGGGCACCAGGAGCUGCUUCAUCGACUUUGAGUGGCGGAGUCCUCGCUCCCAGGAUGGGCAAGGGAGUGUCCUUAGGGAGGAAU
((((((((((((((........))))....))))))...(((((((.....)))))))..(((((((..(.....)..)))))))......))))..... ( -35.30)
>DroYak_CAF1 28100 100 + 1
UCCCGGAGCACUAUGUUGGGCACGAGGAGCUGCUUCGUCAACGUGGAGUGGCGACAUCCUAGCUCCCAGGAUGGUCAAGAGAGUGUCCUUAGGGAGGAGU
(((((((((.((((((((...((((((.....)))))))))))))).(((....)))....))))).((((((.((....)).))))))..))))..... ( -39.80)
>consensus
UCCCGGAGAACUGGAUUGGGAUCGAGGACUUGCUUCGUCGAGGUGGAUUGGCGGAGUCCUCGCUCCCAGGAUGGUCAGGAAAGUGUCCUUCGGGAGGAAU
(((((((.........(((((.((((((((((((...((......))..))).))))))))).)))))((((............)))))))))))..... (-27.68 = -30.16 +   2.48)

alignment

secondary structure

dotplot

Window 3

Location	3,519,747 – 3,519,847
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	82.70
Mean single sequence MFE	-30.12
Consensus MFE	-19.76
Energy contribution	-22.68
Covariance contribution	2.92
Combinations/Pair	1.07
Mean z-score	-2.03
Structure conservation index	0.66
SVM decision value	0.57
SVM RNA-class probability	0.783959
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3519747 100 - 22407834
ACUCCUCCCGAAGGACACAUUCCUGACCAUCCUGGGAGGGAGGACUCCGGUAAUCCACCUCGACAAAGCAAGUCCUCGAUCCCAAUCCAGUUCUCCGGGA
.....(((((.(((((.((....)).......(((((..(((((((..(((.....)))..(......).)))))))..))))).....))))).))))) ( -33.10)
>DroSec_CAF1 28745 100 - 1
AUUCCUCCCGAAGGACACUUUCCUUAUCAUCCUGUGAGCGAGGACUCCGCCAAUCCACCUCGACGAAGCAAGUCCUCGAUCCCAAUCCAGUUUUCCGGGA
.....((((((((((.....))))).......((.((.((((((((..((...((......))....)).)))))))).)).))...........))))) ( -27.30)
>DroSim_CAF1 28692 100 - 1
AUUCCUCCCGCAGGACACUUUUCUUAUCAUCCUGGGAGCGAGGACUCCGCCAAUCCACCUCGACUAAGCAAGUCCUCGAUCCCAAUCCAGUUCUCCGGGA
.....(((((.(((((..(......)......(((((.((((((((..((...((......))....)).)))))))).))))).....))))).))))) ( -32.60)
>DroEre_CAF1 26623 100 - 1
AUUCCUCCCUAAGGACACUCCCUUGCCCAUCCUGGGAGCGAGGACUCCGCCACUCAAAGUCGAUGAAGCAGCUCCUGGUGCCCAAUCCAGUGCUCCGGGA
.....((((...(((((((.((((((((......)).))))))..................(((...(((.(....).)))...))).)))).))))))) ( -28.80)
>DroYak_CAF1 28100 100 - 1
ACUCCUCCCUAAGGACACUCUCUUGACCAUCCUGGGAGCUAGGAUGUCGCCACUCCACGUUGACGAAGCAGCUCCUCGUGCCCAACAUAGUGCUCCGGGA
.....((((...(((((((.(.(((..(((...(((((((.(((.((....)))))..(((.....)))))))))).)))..))).).)))).))))))) ( -28.80)
>consensus
AUUCCUCCCGAAGGACACUUUCCUGACCAUCCUGGGAGCGAGGACUCCGCCAAUCCACCUCGACGAAGCAAGUCCUCGAUCCCAAUCCAGUUCUCCGGGA
.....(((((.(((((.(......).......(((((.((((((((..((...((......))....)).)))))))).))))).....))))).))))) (-19.76 = -22.68 +   2.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:48 2006