Locus 4891

Sequence ID	3R_DroMel_CAF1
Location	12,857,865 – 12,858,048
Length	183
Max. P	0.914696

overview

Window 7

Location	12,857,865 – 12,857,975
Length	110
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	77.16
Mean single sequence MFE	-32.94
Consensus MFE	-14.88
Energy contribution	-17.19
Covariance contribution	2.31
Combinations/Pair	1.30
Mean z-score	-2.31
Structure conservation index	0.45
SVM decision value	0.76
SVM RNA-class probability	0.842610
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12857865 110 - 27905053
GUCCAGGUAGUCC-UGGUGGACCAAUUGGUCCCGGAAAUCCAGUUUUACCCGGCCUACCCCUUUGACCACUUUCUCCACGGUCACCACGAUCCCCCUUUUCUCCUGGCGCU
((((((((((.((-.((((((((....))))).((....))......))).)).)))))....(((((...........)))))....................))).)). ( -31.40)
>DroPse_CAF1 29140 92 - 1
GACCAGU----------UGGUCCAAUUGGUCCUGCUUUUCCUCUAUUUCCUUUCCUGCCACGUAGACCACUGUCUCC---------GCGUUCACCCUUUUCACCAGAAACG
(((((((----------((...)))))))))............................((((((((....))))..---------)))).......((((....)))).. ( -15.50)
>DroSec_CAF1 27651 110 - 1
GGCCAGGUAGUCC-UGGUGGCCCAAUGGGUCCCGAAAAUCCAGUAUAACCCGGCCUACCCCUUUUGCCACUUUCUCCACGGUCACCACGAUCCCCCUUUUCACCUGGCGCU
.(((((((.(((.-((((((((....((((.................))))(((...........)))...........)))))))).)))..........)))))))... ( -33.83)
>DroSim_CAF1 28213 111 - 1
AGCCAGGUAGUCGAUGGUGGACCAAUGGGUCCCGGAAAUCCGGUAUAACCCGGCCUACCCCUUGGGCCACUUUCUCCACGGUCACCACGAUCCCCCUUUUCACCUGGCGCU
.(((((((.((((.(((((.(((...((((.((((....))))....))))((((((.....))))))...........))))))))))))..........)))))))... ( -48.80)
>DroEre_CAF1 27381 110 - 1
GGCCAGGUAGUCC-UGGUGGGCCAAUGGGCCCCGGAAACCCAGAAUAACCCGGCCUUCCUCUUUUUCCGCUUUCUCCGCGGUCACCAUGAUCUCCUUUUUCACCUGGCGCU
.(((((((((((.-(((((((((....))))).((((..((.(......).))..)))).......((((.......))))..)))).)).))........)))))))... ( -37.90)
>DroYak_CAF1 27620 110 - 1
GCCCAGGUUGUCC-AGGUGGCCCAAUGGGCCCCGGAAAUCCAGUAUAACCCGGCCUUCCUCUUUUUCCACUUUCUCCACGGUCACCACGAUCCCCCUUUUCCCCUGGCGCU
(((((((......-.((.(((((...)))))))((((..((.(......).))..))))....................((((.....))))..........))))).)). ( -30.20)
>consensus
GGCCAGGUAGUCC_UGGUGGACCAAUGGGUCCCGGAAAUCCAGUAUAACCCGGCCUACCCCUUUGACCACUUUCUCCACGGUCACCACGAUCCCCCUUUUCACCUGGCGCU
..(((((........((((((.....((((.((((..............))))...)))).....))))))........((((.....))))..........))))).... (-14.88 = -17.19 +   2.31)

alignment

secondary structure

dotplot

Window 8

Location	12,857,905 – 12,858,015
Length	110
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	74.32
Mean single sequence MFE	-39.02
Consensus MFE	-20.20
Energy contribution	-21.70
Covariance contribution	1.50
Combinations/Pair	1.36
Mean z-score	-2.01
Structure conservation index	0.52
SVM decision value	1.10
SVM RNA-class probability	0.914696
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12857905 110 + 27905053
AGUGGUCAAAGGGGUAGGCCGGGUAAAACUGGAUUUCCGGGACCAAUUGGUCCACCA-GGACUACCUGGACCACCAGGCCGCCCUGGCAAAUCUUCAUCGCAUGAACAGAA
.(((((....(((((..((((((.....((((.......(((((....))))).(((-((....)))))....)))).....))))))..))))).))))).......... ( -42.10)
>DroPse_CAF1 29171 100 + 1
AGUGGUCUACGUGGCAGGAAAGGAAAUAGAGGAAAAGCAGGACCAAUUGGACCA----------ACUGGUCCGCAAGGACUUACUAGAAAAUAUUCAACGCAUCU-AAGAA
(((((((((..((((..(...................)..).)))..)))))).----------)))(((((....)))))........................-..... ( -20.81)
>DroSec_CAF1 27691 110 + 1
AGUGGCAAAAGGGGUAGGCCGGGUUAUACUGGAUUUUCGGGACCCAUUGGGCCACCA-GGACUACCUGGCCCACCGGGCCGCCCUGGAAAAUCUCCAUCUCAUGGACAGAA
.(((((......(((.((((((((....((((.......((.(((...))))).)))-)....)))))))).)))..))))).((((.....)(((((...)))))))).. ( -41.00)
>DroSim_CAF1 28253 111 + 1
AGUGGCCCAAGGGGUAGGCCGGGUUAUACCGGAUUUCCGGGACCCAUUGGUCCACCAUCGACUACCUGGCUCACCGGGCCGCCCUGGAAAAUCUCCAUCGCAUGGACAGAA
.(((((((....(((..(((((((.....(((....)))(((((....)))))..........)))))))..)))))))))).((((.....)(((((...)))))))).. ( -46.90)
>DroEre_CAF1 27421 101 + 1
AGCGGAAAAAGAGGAAGGCCGGGUUAUUCUGGGUUUCCGGGGCCCAUUGGCCCACCA-GGACUACCUGGCCCACCGGGCCGCCCUGGAACAUCU---------UAUCAGAA
.((((.......((..((((((((..((((((.......(((((....))))).)))-)))..))))))))..))...)))).((((.......---------..)))).. ( -43.30)
>DroYak_CAF1 27660 110 + 1
AGUGGAAAAAGAGGAAGGCCGGGUUAUACUGGAUUUCCGGGGCCCAUUGGGCCACCU-GGACAACCUGGGCCAAAGGGACGCCCUGGAAAAUCUCCAUCGCAUCAACAGAA
.((.((....(((((...((((......)))).((((((((((((....((((....-((....))..))))....))..))))))))))...))).))...)).)).... ( -40.00)
>consensus
AGUGGAAAAAGGGGUAGGCCGGGUUAUACUGGAUUUCCGGGACCCAUUGGGCCACCA_GGACUACCUGGCCCACCGGGCCGCCCUGGAAAAUCUCCAUCGCAUGAACAGAA
...........(((..((((((((....((((....)))).))))..(((((((............)))))))...))))..))).......................... (-20.20 = -21.70 +   1.50)

alignment

secondary structure

dotplot

Window 9

Location	12,857,936 – 12,858,048
Length	112
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	75.56
Mean single sequence MFE	-30.58
Consensus MFE	-13.80
Energy contribution	-14.83
Covariance contribution	1.03
Combinations/Pair	1.25
Mean z-score	-2.08
Structure conservation index	0.45
SVM decision value	0.57
SVM RNA-class probability	0.783811
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12857936 112 + 27905053
GAUUUCCGGGACCAAUUGGUCCACCA-GGACUACCUGGACCACCAGGCCGCCCUGGCAAAUCUUCAUCGCAUGAACAGAAACAAGGUACAACC-AUUAUUUACUUGCCAGCAAU
....(((.(((((....)))))....-)))...(((((....))))).....(((((((.(((((((...))))..))).....((.....))-.........))))))).... ( -32.00)
>DroSec_CAF1 27722 112 + 1
GAUUUUCGGGACCCAUUGGGCCACCA-GGACUACCUGGCCCACCGGGCCGCCCUGGAAAAUCUCCAUCUCAUGGACAGAAACAAGGUUCAACC-AUUAUUUACUUGCCAGCAAU
((((((((((.(((..(((((((...-((....)))))))))..)))...)))..)))))))(((((...))))).........((.....))-.................... ( -33.40)
>DroSim_CAF1 28284 113 + 1
GAUUUCCGGGACCCAUUGGUCCACCAUCGACUACCUGGCUCACCGGGCCGCCCUGGAAAAUCUCCAUCGCAUGGACAGAAACAAGGUCCAACC-AUUAUUUACUUGCCAUCAAU
(((...(((((.(((.(((((.......)))))..))).)).)))(((.((..((((.....))))..)).(((((.........)))))...-...........))))))... ( -29.40)
>DroEre_CAF1 27452 103 + 1
GGUUUCCGGGGCCCAUUGGCCCACCA-GGACUACCUGGCCCACCGGGCCGCCCUGGAACAUCU---------UAUCAGAAACCAGGUCCAACA-AUUAUUUACUUGCCAGCAAU
((((((.((((((....))))).(((-((.(..(((((....)))))..).))))).......---------...).)))))).(((......-...........)))...... ( -35.03)
>DroYak_CAF1 27691 112 + 1
GAUUUCCGGGGCCCAUUGGGCCACCU-GGACAACCUGGGCCAAAGGGACGCCCUGGAAAAUCUCCAUCGCAUCAACAGAAACAAGGCCCAACC-AUUAUUUACUUGCCAGCAAU
((((((((((((((....((((....-((....))..))))....))..))))))).)))))......((.((....)).....(((......-...........))).))... ( -33.83)
>DroAna_CAF1 28485 94 + 1
GUUUCCCCGGACCCAUAGGGCCUCCU-G------------------GGCCCCCUGGAAAAUCCGUAAUUCAUC-ACAAAAGCGAACCCCCACAAAUAAUUUAUUUGCCUGCACA
.......((((.(((..(((((....-.------------------)))))..)))....)))).........-......(((......).((((((...))))))...))... ( -19.80)
>consensus
GAUUUCCGGGACCCAUUGGGCCACCA_GGACUACCUGGCCCACCGGGCCGCCCUGGAAAAUCUCCAUCGCAUGAACAGAAACAAGGUCCAACC_AUUAUUUACUUGCCAGCAAU
((((((((((.((...(((....))).))....(((((....)))))....))))).)))))...................((((.................))))........ (-13.80 = -14.83 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:23 2006