Locus 6183

Sequence ID	3R_DroMel_CAF1
Location	16,180,817 – 16,180,962
Length	145
Max. P	0.983614

overview

Window 6

Location	16,180,817 – 16,180,922
Length	105
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	75.99
Mean single sequence MFE	-27.27
Consensus MFE	-19.27
Energy contribution	-20.15
Covariance contribution	0.88
Combinations/Pair	1.10
Mean z-score	-2.11
Structure conservation index	0.71
SVM decision value	1.95
SVM RNA-class probability	0.983614
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16180817 105 + 27905053
-------AUUCUUAGGA--UACAAAUUAUUUUCAAUUUUGGAAAUAUUAACUUGGUAUUUUUUCUAGUGACCUUUGCCACCGUUGGCUUCCCUUUGGUGGCUGAGCUUUAAAUG
-------......((((--(((....((((((((....))))))))........)))))))..........(((.(((((((..((....))..))))))).)))......... ( -24.00)
>DroSec_CAF1 9990 114 + 1
CAUUAAGAUUCUUAAGAAAUGAAAAUUUGUUUUAAUUUUUGUAUGACUCACUUGAUAUUUUUUCGAGUGACCUUUGCCACCGUUGGCUUCCCUUUGGUGGCUGAGCUUUAAAUG
(((.((((((...((.((((....)))).))..))))))...)))..((((((((.......)))))))).(((.(((((((..((....))..))))))).)))......... ( -31.10)
>DroSim_CAF1 3504 114 + 1
CAUUAAGAUUCUUAAGAAAUGAAAAUUUGUGUUAAUUUUUGUACGACUCACUUGAUAUUUUUUCGAGUGACCUUUGCCACCGUUGGCUUCCCUUUGGUGGCUGAGCUUUAAAUG
..(((((...)))))...(..((((((......))))))..).....((((((((.......)))))))).(((.(((((((..((....))..))))))).)))......... ( -29.40)
>DroEre_CAF1 8860 99 + 1
-GUAAAGGUUCUUGAAUAAGG--------------AAUUUGUACGACACACUUGAUAUUUUUUUGAGUGAACUUCGCCACCGCUGGUUUCCGUUUGGGGGCUGAGCCUUAAAUG
-(((.((((((((.....)))--------------))))).)))....((((..(.......)..))))............((((((..((....))..))).)))........ ( -24.60)
>consensus
_AUUAAGAUUCUUAAGAAAUGAAAAUUUGUUUUAAUUUUUGUACGACUCACUUGAUAUUUUUUCGAGUGACCUUUGCCACCGUUGGCUUCCCUUUGGUGGCUGAGCUUUAAAUG
...............................................((((((((.......)))))))).(((.(((((((..((....))..))))))).)))......... (-19.27 = -20.15 +   0.88)

alignment

secondary structure

dotplot

Window 7

Location	16,180,842 – 16,180,962
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.49
Mean single sequence MFE	-30.42
Consensus MFE	-20.11
Energy contribution	-20.95
Covariance contribution	0.84
Combinations/Pair	1.21
Mean z-score	-1.60
Structure conservation index	0.66
SVM decision value	0.15
SVM RNA-class probability	0.607321
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16180842 120 - 27905053
ACGUCGUCAAUAGAGCGUCAAGUGUACGCUUGUCCACGCCCAUUUAAAGCUCAGCCACCAAAGGGAAGCCAACGGUGGCAAAGGUCACUAGAAAAAAUACCAAGUUAAUAUUUCCAAAAU
..((..((....((((...(((((..((........))..)))))...)))).((((((...((....))...))))))...))..))................................ ( -27.10)
>DroPse_CAF1 9898 94 - 1
GCGUCGUCAAUACGGCGUCAAGUGUGCGCUUGUCCACGCCCAUUUAGGGCUCAUCCGCA-AAAGGAAACCAAAG---GCAAGGAACAUCAGAAGGAAG----------------------
.((((((....))))))((..((((.(.((((((...((((.....))))...(((...-...))).......)---)))))).))))..))......---------------------- ( -27.60)
>DroSec_CAF1 10024 120 - 1
ACGUCGUCAAUAGAGCGUCAAGUGUGCGCUUGUCCACGCCCAUUUAAAGCUCAGCCACCAAAGGGAAGCCAACGGUGGCAAAGGUCACUCGAAAAAAUAUCAAGUGAGUCAUACAAAAAU
............((((...(((((.(((........))).)))))...)))).((((((...((....))...))))))...(((((((.((.......)).))))).)).......... ( -34.30)
>DroSim_CAF1 3538 120 - 1
ACGUCGUCAAUAGAGCGUCAAGUGUGCGCUUGUCCACGCCCAUUUAAAGCUCAGCCACCAAAGGGAAGCCAACGGUGGCAAAGGUCACUCGAAAAAAUAUCAAGUGAGUCGUACAAAAAU
..((((.(....((((...(((((.(((........))).)))))...)))).((((((...((....))...)))))).....(((((.((.......)).)))))).)).))...... ( -36.60)
>DroEre_CAF1 8880 119 - 1
ACGUCGUCAAUAGAGCGUCAAAUGUGCGCUUGUCCACGCCCAUUUAAGGCUCAGCCCCCAAACGGAAACCAGCGGUGGCGAAGUUCACUCAAAAAAAUAUCAAGUGUGUCGUACAAAUU-
..((((.((...((((.(.(((((.(((........))).))))).).)))).(((.((....(....)....)).)))......((((.............)))))).)).)).....- ( -27.82)
>DroYak_CAF1 11124 120 - 1
ACGUCGUCAAUAGAGCGUCAAGUGUGCGCUUGUCCACGCCCAUUUAAAGCUCAGCCACCAAACGGAAACCAACGGUGGCAAAGGUCACUCGAAAAAAUAUCAAGUCUAUCAUACAAAAAU
...(((......((((...(((((.(((........))).)))))...)))).((((((....(....)....))))))..........)))............................ ( -29.10)
>consensus
ACGUCGUCAAUAGAGCGUCAAGUGUGCGCUUGUCCACGCCCAUUUAAAGCUCAGCCACCAAAGGGAAACCAACGGUGGCAAAGGUCACUCGAAAAAAUAUCAAGUGAGUCAUACAAAAAU
..((..((....((((.(.(((((.(((........))).))))).).)))).((((((....(....)....))))))...))..))................................ (-20.11 = -20.95 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:47 2006