Locus 8003

Sequence ID	3R_DroMel_CAF1
Location	21,467,964 – 21,468,075
Length	111
Max. P	0.995486

overview

Window 1

Location	21,467,964 – 21,468,075
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	75.00
Mean single sequence MFE	-21.54
Consensus MFE	-5.00
Energy contribution	-6.72
Covariance contribution	1.72
Combinations/Pair	1.30
Mean z-score	-1.74
Structure conservation index	0.23
SVM decision value	0.42
SVM RNA-class probability	0.731114
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21467964 111 + 27905053
AUUUAUGUAU---------AAUAGUUGAAUGCGGAAUUGCAAGUACGCCUUCAACUUUUAACUGCCAUGUUUCGGUUAAAUCCCAAUUCUCUAAGGACAGUUCCCUAGAGGAAAUUGCAU
....(((((.---------...(((((((.(((............))).)))))))((((((((........))))))))......(((((((.(((....))).)))))))...))))) ( -27.90)
>DroSec_CAF1 74727 108 + 1
---AAUGUAU---------AUUAGUUGAAUGCGGAAUUGCAAGUUCCCAUUCAACUUUUAAUUGCCAUCUUCGAAUUAAUUCCCAAUUCCCUUAGGACAAUUCCCCAGAGAAAACUUUAU
---......(---------(..(((((((((.(((((.....))))))))))))))..))..........................(((.((..(((....)))..)).)))........ ( -21.50)
>DroSim_CAF1 59631 108 + 1
---AAUGUAU---------AUUAGUUGAAUGCGGAAUUCCAAGUUCCCAUUCAACUUUUAAUUGCCAUCUUCCGAUUAAUUCCCAAUUCCCUUAGGACAAUUCCCCAGAGAAAACUGUAU
---.......---------...(((((((((.(((((.....)))))))))))))).(((((((........))))))).......(((.((..(((....)))..)).)))........ ( -22.50)
>DroEre_CAF1 75899 99 + 1
---AAUGUAUGUAUAUACUAAAAGUUGAAUACGGAAUUGCAAAUU------------------GCCAUGUUCCGGUCAAUUCCCAAUUCGCAAAGGACAAUUCCCCAGUGGAAAUUGUAU
---...........((((....((((((...((((((.((.....------------------))...)))))).)))))).....(((((...(((....)))...)))))....)))) ( -19.90)
>DroYak_CAF1 66542 106 + 1
---AAUGUAU---------ACAAGUUGAAUGCGAAAUUGCCAAUUCACAUGCAACUUUUUAAUGCCAUG-UCCGGUUAAUUCCCAAUUCUCCAAAGACAAUUCCCCAGUGGAA-CUGUAU
---...((((---------..((((((.(((.(((........))).))).))))))....))))....-...((..(((.....)))..))....(((.((((.....))))-.))).. ( -15.90)
>consensus
___AAUGUAU_________AAUAGUUGAAUGCGGAAUUGCAAGUUCCCAUUCAACUUUUAAUUGCCAUGUUCCGGUUAAUUCCCAAUUCCCUAAGGACAAUUCCCCAGAGGAAACUGUAU
......................((((...((.(((((((..................(((((((........)))))))........(((....)))))))))).)).....)))).... ( -5.00 =  -6.72 +   1.72)

alignment

secondary structure

dotplot

Window 2

Location	21,467,964 – 21,468,075
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	75.00
Mean single sequence MFE	-28.24
Consensus MFE	-11.10
Energy contribution	-11.69
Covariance contribution	0.59
Combinations/Pair	1.22
Mean z-score	-2.58
Structure conservation index	0.39
SVM decision value	2.58
SVM RNA-class probability	0.995486
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21467964 111 - 27905053
AUGCAAUUUCCUCUAGGGAACUGUCCUUAGAGAAUUGGGAUUUAACCGAAACAUGGCAGUUAAAAGUUGAAGGCGUACUUGCAAUUCCGCAUUCAACUAUU---------AUACAUAAAU
.(((......(((((((((....)))))))))..((((.......))))......)))(((((.(((((((.(((............))).))))))).))---------).))...... ( -30.00)
>DroSec_CAF1 74727 108 - 1
AUAAAGUUUUCUCUGGGGAAUUGUCCUAAGGGAAUUGGGAAUUAAUUCGAAGAUGGCAAUUAAAAGUUGAAUGGGAACUUGCAAUUCCGCAUUCAACUAAU---------AUACAUU---
.....((..(((.((((......((((((.....)))))).....)))).)))..)).......(((((((((((((.......)))).)))))))))...---------.......--- ( -27.40)
>DroSim_CAF1 59631 108 - 1
AUACAGUUUUCUCUGGGGAAUUGUCCUAAGGGAAUUGGGAAUUAAUCGGAAGAUGGCAAUUAAAAGUUGAAUGGGAACUUGGAAUUCCGCAUUCAACUAAU---------AUACAUU---
...(((((..((.(((((.....)))))))..))))).......(((....)))..........(((((((((((((.......)))).)))))))))...---------.......--- ( -30.30)
>DroEre_CAF1 75899 99 - 1
AUACAAUUUCCACUGGGGAAUUGUCCUUUGCGAAUUGGGAAUUGACCGGAACAUGGC------------------AAUUUGCAAUUCCGUAUUCAACUUUUAGUAUAUACAUACAUU---
..(((((((((....)))))))))....(((((((((.((((((.(((.....))))------------------))))).))))).))))...........((((....))))...--- ( -26.80)
>DroYak_CAF1 66542 106 - 1
AUACAG-UUCCACUGGGGAAUUGUCUUUGGAGAAUUGGGAAUUAACCGGA-CAUGGCAUUAAAAAGUUGCAUGUGAAUUGGCAAUUUCGCAUUCAACUUGU---------AUACAUU---
((((((-(.(((((((..((((.((..(.....)..)).))))..)))).-..))).)))...((((((.(((((((........))))))).))))))))---------)).....--- ( -26.70)
>consensus
AUACAGUUUCCUCUGGGGAAUUGUCCUUAGAGAAUUGGGAAUUAACCGGAACAUGGCAAUUAAAAGUUGAAUGGGAACUUGCAAUUCCGCAUUCAACUAAU_________AUACAUU___
..(((((((((....))))))))).......((((..((((((.............((((.....)))).............))))))..)))).......................... (-11.10 = -11.69 +   0.59)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:01 2006