Locus 8551

Sequence ID	3R_DroMel_CAF1
Location	22,820,732 – 22,820,837
Length	105
Max. P	0.834433

overview

Window 2

Location	22,820,732 – 22,820,837
Length	105
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	79.87
Mean single sequence MFE	-30.12
Consensus MFE	-20.54
Energy contribution	-20.43
Covariance contribution	-0.11
Combinations/Pair	1.11
Mean z-score	-1.78
Structure conservation index	0.68
SVM decision value	0.73
SVM RNA-class probability	0.834433
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22820732 105 + 27905053
CCCGUA---CUCCUACCACGGAUUGCCUCAGCAGCAGAGCCAGCGGGCUUUGCCACUCAAUGGUAAGUG-------GGCGGAGGAUGA---AAUAGAAACAUUAUAGGAAAUUAAAGC
.((...---((((..((((...(((((..((..((((((((....))))))))..))....))))))))-------)..))))((((.---........))))...)).......... ( -32.70)
>DroSec_CAF1 78 91 + 1
CCCGUA---CUCCUACCACGGAUUACCUCAGCAGCAGAGCCAGCGGGCUUUGCCACUCAAUGGUAAGUG-------GGCGGAGGAUGA---AAUUGAAAAAUU----------C----
..(((.---((((..((((...(((((..((..((((((((....))))))))..))....))))))))-------)..)))).))).---((((....))))----------.---- ( -32.30)
>DroSim_CAF1 78 91 + 1
CCCGUA---CUCCUACCACGGAUUACCUCAGCAGCAGAGCCAGCGGGCUUUGCCACUCAAUGGUAAGUG-------GGCGGAGGAUGA---AACCAAAAAAUU----------C----
..(((.---((((..((((...(((((..((..((((((((....))))))))..))....))))))))-------)..)))).))).---............----------.---- ( -32.20)
>DroEre_CAF1 78 90 + 1
CCCGUA---CUCCUACCACGGAUUACCUCAGCAGCAGAGCCAGCGGGCUUUGCCACUCAAUGGUAAGUG-------GCGAGAGGAUGA---AU-CUAAAAAUC----------C----
.((((.---........))))....((((.((.((((((((....))))))))((((........))))-------))..))))....---..-.........----------.---- ( -27.70)
>DroYak_CAF1 78 91 + 1
CCCGUA---CGCCUACCACGGAUUACCUCAGCAGCAGAGCCAGCGGGCUUUGCCACUCAAUGGUAAGUG-------GCGAGAGGAUGA---AUUCAAAAAAUU----------C----
.((((.---........))))....((((.((.((((((((....))))))))((((........))))-------))..))))....---............----------.---- ( -27.70)
>DroAna_CAF1 9542 104 + 1
CCCCUAUGCCGCCUACCAUGGAUUACCACAGCAGCAGAGCCAGCGGGCUUUGCCACUAAACGGUGAGUUUGAAUUGAGCUCAGAAGGAUAUGUUUCAAAAUAU----------C----
..(((..((((((......))........((..((((((((....))))))))..))...))))((((((.....))))))...)))................----------.---- ( -28.10)
>consensus
CCCGUA___CUCCUACCACGGAUUACCUCAGCAGCAGAGCCAGCGGGCUUUGCCACUCAAUGGUAAGUG_______GGCGGAGGAUGA___AAUCAAAAAAUU__________C____
.((((............)))).(((((..((..((((((((....))))))))..))....))))).................................................... (-20.54 = -20.43 +  -0.11)

alignment

secondary structure

dotplot

Window 3

Location	22,820,732 – 22,820,837
Length	105
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	79.87
Mean single sequence MFE	-31.45
Consensus MFE	-25.11
Energy contribution	-25.00
Covariance contribution	-0.11
Combinations/Pair	1.11
Mean z-score	-1.45
Structure conservation index	0.80
SVM decision value	0.60
SVM RNA-class probability	0.797084
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22820732 105 - 27905053
GCUUUAAUUUCCUAUAAUGUUUCUAUU---UCAUCCUCCGCC-------CACUUACCAUUGAGUGGCAAAGCCCGCUGGCUCUGCUGCUGAGGCAAUCCGUGGUAGGAG---UACGGG
...........................---.......(((..-------(.(((((((((.((..(((.((((....)))).)))..)).)((....)))))))))).)---..))). ( -30.30)
>DroSec_CAF1 78 91 - 1
----G----------AAUUUUUCAAUU---UCAUCCUCCGCC-------CACUUACCAUUGAGUGGCAAAGCCCGCUGGCUCUGCUGCUGAGGUAAUCCGUGGUAGGAG---UACGGG
----.----------............---.....((((..(-------((((((((..(.((..(((.((((....)))).)))..)).))))))...))))..))))---...... ( -31.50)
>DroSim_CAF1 78 91 - 1
----G----------AAUUUUUUGGUU---UCAUCCUCCGCC-------CACUUACCAUUGAGUGGCAAAGCCCGCUGGCUCUGCUGCUGAGGUAAUCCGUGGUAGGAG---UACGGG
----.----------........((..---....)).(((..-------(.(((((((((.((..(((.((((....)))).)))..)).)((....)))))))))).)---..))). ( -31.90)
>DroEre_CAF1 78 90 - 1
----G----------GAUUUUUAG-AU---UCAUCCUCUCGC-------CACUUACCAUUGAGUGGCAAAGCCCGCUGGCUCUGCUGCUGAGGUAAUCCGUGGUAGGAG---UACGGG
----(----------((((....)-))---))...((((..(-------((((((((..(.((..(((.((((....)))).)))..)).))))))...))))..))))---...... ( -33.90)
>DroYak_CAF1 78 91 - 1
----G----------AAUUUUUUGAAU---UCAUCCUCUCGC-------CACUUACCAUUGAGUGGCAAAGCCCGCUGGCUCUGCUGCUGAGGUAAUCCGUGGUAGGCG---UACGGG
----(----------(((((...))))---))..((...(((-------(...(((((((.((..(((.((((....)))).)))..)).)((....))))))))))))---...)). ( -32.80)
>DroAna_CAF1 9542 104 - 1
----G----------AUAUUUUGAAACAUAUCCUUCUGAGCUCAAUUCAAACUCACCGUUUAGUGGCAAAGCCCGCUGGCUCUGCUGCUGUGGUAAUCCAUGGUAGGCGGCAUAGGGG
----(----------((((........)))))((((((((...........))).((((((((..(((.((((....)))).)))..).((((....))))..)))))))...))))) ( -28.30)
>consensus
____G__________AAUUUUUCGAAU___UCAUCCUCCGCC_______CACUUACCAUUGAGUGGCAAAGCCCGCUGGCUCUGCUGCUGAGGUAAUCCGUGGUAGGAG___UACGGG
...................................................((((((((..((..(((.((((....)))).)))..))..((....))))))))))........... (-25.11 = -25.00 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:13:55 2006