Locus 3932

Sequence ID	X_DroMel_CAF1
Location	10,491,325 – 10,491,433
Length	108
Max. P	0.866952

overview

Window 8

Location	10,491,325 – 10,491,433
Length	108
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	83.39
Mean single sequence MFE	-34.90
Consensus MFE	-31.46
Energy contribution	-32.26
Covariance contribution	0.80
Combinations/Pair	1.18
Mean z-score	-1.77
Structure conservation index	0.90
SVM decision value	0.85
SVM RNA-class probability	0.866952
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10491325 108 + 22224390
CGCUACCCCUCCCCC-----CAGCC-CCCGACACUGCACACGCUGUAAUUGUGGCCAGCUUUGAGCUGAGAAUUUUCCCUCAGCUUGUGUGCGUGUUGGCGAGAUUGCUGUCAA
...............-----(((((-((((((((.((((((((((..........))))...((((((((........))))))))))))))))))))).).)...)))).... ( -39.90)
>DroSec_CAF1 22582 114 + 1
CGCUACCCCUCCACCACCCCCUCCGCCCAAGCACUGCACACGCUGUAAUUGUGGCCAGCUUUGAGCUGAGAAUUUUCCCUGAGCUUGUGUGCGUGCUUGCGAGAUUGCUGUCAA
.......................(((..((((((.((((((((((..........))))...(((((.((........)).)))))))))))))))))))).(((....))).. ( -34.50)
>DroSim_CAF1 22768 114 + 1
CGCUACCCCUCCGCCACCCCCUCCGCCCAAGCACUGCACACGCUGUAAUUGUGGCCAGCUUUGAGCUGAGAAUUUUCCCUGAGCUUGUGUGCGUGCUUGCGAGAUUGCUGUCAA
.((.....(((.((..........)).(((((((.((((((((((..........))))...(((((.((........)).)))))))))))))))))).)))...))...... ( -34.70)
>DroEre_CAF1 24185 94 + 1
CGCUCCCCCU--------------------GCACUGCACACGCUGUAAUUGUGGCCAGCUUUGAGCUGAGAAUUUCCCCUCAGCUUGUGUGCGUGUUUGCGAGAUUGCUGUCAA
(((.......--------------------((((.((((((((((..........))))...((((((((........))))))))))))))))))..))).(((....))).. ( -33.50)
>DroYak_CAF1 24224 94 + 1
CGCUCCACCU--------------------GCACUGCACACGCUGUAAUUGUGGCCAGCUUUGAGCUGAGACUUACCCUUCAGCUUGUGUGCGUGUUAGCGAGAUUGCUGUCAA
((((......--------------------((((.((((((((((..........))))...((((((((........)))))))))))))))))).)))).(((....))).. ( -31.90)
>consensus
CGCUACCCCUCC_CC_____C__C__CC__GCACUGCACACGCUGUAAUUGUGGCCAGCUUUGAGCUGAGAAUUUUCCCUCAGCUUGUGUGCGUGUUUGCGAGAUUGCUGUCAA
...........................(((((((.((((((((((..........))))...((((((((........)))))))))))))))))))))...(((....))).. (-31.46 = -32.26 +   0.80)

alignment

secondary structure

dotplot

Window 9

Location	10,491,325 – 10,491,433
Length	108
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	83.39
Mean single sequence MFE	-38.10
Consensus MFE	-29.33
Energy contribution	-30.77
Covariance contribution	1.44
Combinations/Pair	1.03
Mean z-score	-1.86
Structure conservation index	0.77
SVM decision value	0.64
SVM RNA-class probability	0.808393
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10491325 108 - 22224390
UUGACAGCAAUCUCGCCAACACGCACACAAGCUGAGGGAAAAUUCUCAGCUCAAAGCUGGCCACAAUUACAGCGUGUGCAGUGUCGGG-GGCUG-----GGGGGAGGGGUAGCG
......((.(((((.((.((((((((((.(((((((((....)))))))))....((((..........)))))))))).))))(((.-..)))-----...)).))))).)). ( -40.50)
>DroSec_CAF1 22582 114 - 1
UUGACAGCAAUCUCGCAAGCACGCACACAAGCUCAGGGAAAAUUCUCAGCUCAAAGCUGGCCACAAUUACAGCGUGUGCAGUGCUUGGGCGGAGGGGGUGGUGGAGGGGUAGCG
((.((.((..((((((.(((((((((((.((((..((((....))))))))....((((..........)))))))))).)))))...)).))))..)).)).))......... ( -39.60)
>DroSim_CAF1 22768 114 - 1
UUGACAGCAAUCUCGCAAGCACGCACACAAGCUCAGGGAAAAUUCUCAGCUCAAAGCUGGCCACAAUUACAGCGUGUGCAGUGCUUGGGCGGAGGGGGUGGCGGAGGGGUAGCG
......((.(((((.(((((((((((((.((((..((((....))))))))....((((..........)))))))))).))))))).((.(......).))...))))).)). ( -41.60)
>DroEre_CAF1 24185 94 - 1
UUGACAGCAAUCUCGCAAACACGCACACAAGCUGAGGGGAAAUUCUCAGCUCAAAGCUGGCCACAAUUACAGCGUGUGCAGUGC--------------------AGGGGGAGCG
......((..(((((((.....((((((.(((((((((....)))))))))....((((..........))))))))))..)))--------------------.))))..)). ( -36.60)
>DroYak_CAF1 24224 94 - 1
UUGACAGCAAUCUCGCUAACACGCACACAAGCUGAAGGGUAAGUCUCAGCUCAAAGCUGGCCACAAUUACAGCGUGUGCAGUGC--------------------AGGUGGAGCG
......((..((.((((..(((((((((.((((((.((.....))))))))....((((..........)))))))))).))).--------------------.)))))))). ( -32.20)
>consensus
UUGACAGCAAUCUCGCAAACACGCACACAAGCUGAGGGAAAAUUCUCAGCUCAAAGCUGGCCACAAUUACAGCGUGUGCAGUGC__GG__G__G_____GG_GGAGGGGUAGCG
......((.(((((....((((((((((.((((((((......))))))))....((((..........)))))))))).)))).....................))))).)). (-29.33 = -30.77 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:08 2006