Locus 6972

Sequence ID	2L_DroMel_CAF1
Location	19,365,088 – 19,365,217
Length	129
Max. P	0.876786

overview

Window 9

Location	19,365,088 – 19,365,181
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	90.96
Mean single sequence MFE	-29.29
Consensus MFE	-21.42
Energy contribution	-22.94
Covariance contribution	1.52
Combinations/Pair	1.12
Mean z-score	-2.02
Structure conservation index	0.73
SVM decision value	0.35
SVM RNA-class probability	0.700639
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19365088 93 - 22407834
AAAUCAGCCGGAUCAUAAUUUAUUGGAGCCAAAAUGGAUGGUACUGCCCACCGGCGAGCUAUGGGCCACAAAAUGGACAAAAGGCCGUGGCUU
......(((((......(((((((........)))))))((.....))..)))))(((((((((.((...............))))))))))) ( -27.46)
>DroSec_CAF1 28571 87 - 1
AAAUCAGCCGGAUCAUAAUUUAUUGGAGCCAAAAUGGGUGGAACUGCCCACCGGCGAGCUGUGGGCCACAAAAUGGACAAAAGG------CUU
......(((((...........(((....)))..(((((......))))))))))(((((.((..(((.....))).))...))------))) ( -27.40)
>DroSim_CAF1 28961 93 - 1
AAAUCAGCCGGAUCAUAAUUUAUUGGAGCCAAAAUGGGUGGAACUGCCCACCGGCGAGCUGUGGGCCACAAAAUGGACAAAAGGCCGUGGCUU
......(((((...........(((....)))..(((((......))))))))))((((..(((.((...............)))))..)))) ( -30.86)
>DroEre_CAF1 27762 90 - 1
AAAUCAGCCGGAUCAUAAUUUAUUGGAGCCGAAAUGGG-GGAAUUUCCCACCGGCG-GCUGUGGACCACAAAAUGGACAAA-GGCCGUGGCUU
.....((((((.((((..........(((((...((((-((.....))).))).))-))))))).)).....((((.....-..)))))))). ( -28.40)
>DroYak_CAF1 32658 92 - 1
AAAUCAGCCGGAUCAUAAUUUAUUGGAGCCCAAAUGGGGGGAGUUUCCCACCGGCGAGCUGUGGGCCACAAAAUGAACAAA-GGCCGUGGCUU
......(((((.................(((....)))(((.....))).)))))((((..(((.((..............-)))))..)))) ( -32.34)
>consensus
AAAUCAGCCGGAUCAUAAUUUAUUGGAGCCAAAAUGGGUGGAACUGCCCACCGGCGAGCUGUGGGCCACAAAAUGGACAAAAGGCCGUGGCUU
......(((((...........(((....)))..(((((......))))))))))(((((((((.((...............))))))))))) (-21.42 = -22.94 +   1.52)

alignment

secondary structure

dotplot

Window 0

Location	19,365,107 – 19,365,217
Length	110
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	81.54
Mean single sequence MFE	-36.10
Consensus MFE	-25.94
Energy contribution	-28.67
Covariance contribution	2.72
Combinations/Pair	1.23
Mean z-score	-2.32
Structure conservation index	0.72
SVM decision value	0.90
SVM RNA-class probability	0.876786
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19365107 110 - 22407834
----CACUGGAAGCUCCAGCUUUCACAAUGGCCACAGCGCAAAUCAGCCGGAUCAUAAUUUAUUGGAGCCAAAAUGGAUGGU--ACUGCCCACCGGCGAGCUAUGGGCCACAAAAU
----...(((((((....)))))))...(((((.((..((...((.(((((......(((((((........)))))))((.--....))..)))))))))..)))))))...... ( -32.70)
>DroSec_CAF1 28584 110 - 1
----CACUGGAAGCUGCAGCUUUCACAAUGGCCACAGCGCAAAUCAGCCGGAUCAUAAUUUAUUGGAGCCAAAAUGGGUGGA--ACUGCCCACCGGCGAGCUGUGGGCCACAAAAU
----...(((((((....)))))))...((((((((((........(((((...........(((....)))..(((((...--...))))))))))..))))).)))))...... ( -41.80)
>DroSim_CAF1 28980 110 - 1
----CACUGGAAGCUGCAGCUUUCACAAUGGCCACAGCGCAAAUCAGCCGGAUCAUAAUUUAUUGGAGCCAAAAUGGGUGGA--ACUGCCCACCGGCGAGCUGUGGGCCACAAAAU
----...(((((((....)))))))...((((((((((........(((((...........(((....)))..(((((...--...))))))))))..))))).)))))...... ( -41.80)
>DroEre_CAF1 27780 102 - 1
----------AAGCUAGAGCUUUCACAAUGGCCACGGCGCAAAUCAGCCGGAUCAUAAUUUAUUGGAGCCGAAAUGGG-GGA--AUUUCCCACCGGCG-GCUGUGGACCACAAAAU
----------((((....))))......((((((((((........))).................(((((...((((-((.--....))).))).))-))))))).)))...... ( -35.30)
>DroYak_CAF1 32676 114 - 1
CUCGCAGUGGAAGCUAGAGCUUUUACAAUGGCCACAGCGCAAAUCAGCCGGAUCAUAAUUUAUUGGAGCCCAAAUGGGGGGA--GUUUCCCACCGGCGAGCUGUGGGCCACAAAAU
......((((((((....))))))))..((((((((((........(((((.................(((....)))(((.--....))).)))))..))))).)))))...... ( -45.10)
>DroPer_CAF1 47684 99 - 1
----CACAGGGGCUCCGAGCGCUUACAAUGGCCACAGCGCAAAUCAGCCAGAUCAUAAUUUAUUGGU-CCGAAAUGGAAGGCCUAUAGAACACCAGCU------------CAAAAU
----....(((.(((((.(((((............)))))..........(((((........))))-).....))).)).)))..............------------...... ( -19.90)
>consensus
____CACUGGAAGCUACAGCUUUCACAAUGGCCACAGCGCAAAUCAGCCGGAUCAUAAUUUAUUGGAGCCAAAAUGGGUGGA__ACUGCCCACCGGCGAGCUGUGGGCCACAAAAU
........((((((....))))))....((((((((((........(((((...........(((....)))..(((((((....))))))))))))..))))))).)))...... (-25.94 = -28.67 +   2.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:16 2006