Locus 7380

Sequence ID	3R_DroMel_CAF1
Location	19,573,074 – 19,573,174
Length	100
Max. P	0.730738

overview

Window 2

Location	19,573,074 – 19,573,174
Length	100
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	79.05
Mean single sequence MFE	-40.45
Consensus MFE	-22.40
Energy contribution	-23.85
Covariance contribution	1.45
Combinations/Pair	1.17
Mean z-score	-1.88
Structure conservation index	0.55
SVM decision value	0.28
SVM RNA-class probability	0.664341
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19573074 100 + 27905053
A---AUACCACCAUCGUCUAUGGGU---GGCUCGGCCACCUCCAGCCGGCACAGGCCCUGUCACGGUUGGAGCCAAUCCUGUGAUGGCCUAGAGGCCGAAUACAAU
.---...(((((..........)))---)).((((((...((((((((..((((...))))..))))))))((((.((....)))))).....))))))....... ( -40.50)
>DroVir_CAF1 222 96 + 1
----GCGCCACCCCCGAUCAUUGCCAGCGCA------ACAUCGAGCCGCCACCGGCCCUGCCACGGCUGGAGUCAAUCCUGCGAUGGCCUCGAGGCCGAGUACAAU
----(((.....(.((((..((((....)))------).)))).).))).((((((((.((((..((.(((.....))).))..))))...).))))).))..... ( -29.10)
>DroSec_CAF1 256 100 + 1
A---AUACCACCACCGUCUAUGGGU---GGCUCGGCCACUUCCAGCCGGCACAGGCCCUGUCACGGAUGGAGCCAAUCCUGUGAUGGUCUGGAGGCCGAAUACAAU
.---......(((((.......)))---)).((((((...((((((((((....)))..((((((((((....).)))).))))))).)))))))))))....... ( -42.00)
>DroEre_CAF1 246 100 + 1
C---AUACCACCAUCAUCAAUAGGC---GGCUCGGCCACCUCCAGCCGGCACAGGCCCUGUCACGGAUGGAGCCAAUCCUGUGAUGGCCUGGAGGCCGAGUACAAU
.---...((.((..........)).---))(((((((...((((((((((....)))..((((((((((....).)))).))))))).))))))))))))...... ( -39.90)
>DroYak_CAF1 258 100 + 1
C---AUACCGCCGCCAACGAUGGGC---GGUUCGGCCACCUCCAGUCGGCACAGGCCGUGUCACGGAUGGAGCCAAUCGUGUGAUGGCCUGGAGGCCGAGUACAAU
.---.(((.((((((.......)))---)))((((((....((....))..((((((((..(((((.((....)).)))))..))))))))..))))))))).... ( -46.00)
>DroAna_CAF1 249 106 + 1
CAGCAUUCCGCCCCCGGUUGUGGGCGGUGGAUCAGCCACAUCCAGCCGGCACAGGCCCUGCCACGGCUGGAGCCAAUCCUGCGAUGGUCUGGAAGCGGAAUACAAU
..(.(((((((..((((.....(((.((((.....)))).((((((((.....(((...))).)))))))))))...((......)).))))..))))))).)... ( -45.20)
>consensus
C___AUACCACCACCGUCUAUGGGC___GGCUCGGCCACCUCCAGCCGGCACAGGCCCUGUCACGGAUGGAGCCAAUCCUGUGAUGGCCUGGAGGCCGAAUACAAU
...............................((((((...((((((((.((((((....((..(....)..))....)))))).))).)))))))))))....... (-22.40 = -23.85 +   1.45)

alignment

secondary structure

dotplot

Window 3

Location	19,573,074 – 19,573,174
Length	100
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	79.05
Mean single sequence MFE	-44.60
Consensus MFE	-25.37
Energy contribution	-26.23
Covariance contribution	0.86
Combinations/Pair	1.28
Mean z-score	-1.90
Structure conservation index	0.57
SVM decision value	0.42
SVM RNA-class probability	0.730738
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19573074 100 - 27905053
AUUGUAUUCGGCCUCUAGGCCAUCACAGGAUUGGCUCCAACCGUGACAGGGCCUGUGCCGGCUGGAGGUGGCCGAGCC---ACCCAUAGACGAUGGUGGUAU---U
.......(((((((((.((((..((((((.(((....)))((......)).))))))..))))..))).))))))(((---(((.((.....))))))))..---. ( -41.90)
>DroVir_CAF1 222 96 - 1
AUUGUACUCGGCCUCGAGGCCAUCGCAGGAUUGACUCCAGCCGUGGCAGGGCCGGUGGCGGCUCGAUGU------UGCGCUGGCAAUGAUCGGGGGUGGCGC----
......((((....))))((((((.(..(((((...(((((.(..(((((((((....))))))..)))------..))))))...))))).).))))))..---- ( -43.60)
>DroSec_CAF1 256 100 - 1
AUUGUAUUCGGCCUCCAGACCAUCACAGGAUUGGCUCCAUCCGUGACAGGGCCUGUGCCGGCUGGAAGUGGCCGAGCC---ACCCAUAGACGGUGGUGGUAU---U
.......(((((((((((.((.((((.((((.(....)))))))))...(((....))))))))))...))))))(((---(((.......)))))).....---. ( -42.30)
>DroEre_CAF1 246 100 - 1
AUUGUACUCGGCCUCCAGGCCAUCACAGGAUUGGCUCCAUCCGUGACAGGGCCUGUGCCGGCUGGAGGUGGCCGAGCC---GCCUAUUGAUGAUGGUGGUAU---G
......(((((((..((((((.((((.((((.(....)))))))))...)))))).(((.......))))))))))((---(((..........)))))...---. ( -44.20)
>DroYak_CAF1 258 100 - 1
AUUGUACUCGGCCUCCAGGCCAUCACACGAUUGGCUCCAUCCGUGACACGGCCUGUGCCGACUGGAGGUGGCCGAACC---GCCCAUCGUUGGCGGCGGUAU---G
...(((((..(((..((((((....((((..((....))..))))....)))))).((((((..(.(((((.....))---))))...))))))))))))))---. ( -43.50)
>DroAna_CAF1 249 106 - 1
AUUGUAUUCCGCUUCCAGACCAUCGCAGGAUUGGCUCCAGCCGUGGCAGGGCCUGUGCCGGCUGGAUGUGGCUGAUCCACCGCCCACAACCGGGGGCGGAAUGCUG
...(((((((((((((.(.....)...((((..((((((((((..((((...))))..))))))))....))..)))).............))))))))))))).. ( -52.10)
>consensus
AUUGUACUCGGCCUCCAGGCCAUCACAGGAUUGGCUCCAUCCGUGACAGGGCCUGUGCCGGCUGGAGGUGGCCGAGCC___GCCCAUAGACGGUGGUGGUAU___G
.......(((((((((((.((..((((((..((....)).((......)).))))))..)))))))...))))))(((...(((..........))))))...... (-25.37 = -26.23 +   0.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:44:32 2006