Locus 2831

Sequence ID	3R_DroMel_CAF1
Location	7,586,209 – 7,586,414
Length	205
Max. P	0.999123

overview

Window 7

Location	7,586,209 – 7,586,313
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	83.88
Mean single sequence MFE	-20.80
Consensus MFE	-14.14
Energy contribution	-14.90
Covariance contribution	0.76
Combinations/Pair	1.13
Mean z-score	-2.08
Structure conservation index	0.68
SVM decision value	0.61
SVM RNA-class probability	0.800220
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7586209 104 - 27905053
UCGAAAGACAAGAACUCGAUCGGCAAACACAUAGCUAAUGUUUUCUCUUUGCCAUCGAGAUCUCAGCAAAUAUGAGUUUGUAUCGACCAACUAACUUGACUCGA
((....))((((..((((((.((((((.....(((....))).....))))))))))))......((((((....)))))).............))))...... ( -26.10)
>DroSec_CAF1 7651 100 - 1
UCGAAAGACAAGAACUCGAUCGGCAAACACAAAGCUAAUAUUUUCUCUUUGCCAUGGAGUUCUCAAUAAAUAUGAAUUUAUAUCGACCGA----CUUGACUCGA
((((......(((((((.((.((((((.(.((((......)))).).)))))))).)))))))..((((((....)))))).)))).(((----......))). ( -21.60)
>DroSim_CAF1 7713 100 - 1
UCGAAAGACAAGAACUCGAUCGGCAAACACAAAGCUAAUAUUUUCUCUUUGCCAUGGAGUUCUCAAUAAAUAUGAAUUUAUAUCGACCGA----CUUGACUCGA
((((......(((((((.((.((((((.(.((((......)))).).)))))))).)))))))..((((((....)))))).)))).(((----......))). ( -21.60)
>DroEre_CAF1 8388 90 - 1
UCGA-----AAGAUUUCGAUCGGCAAACACCAAGCUAAUGUUUUCUUUUUGCCAUCGAGUUCUGAACAAAUAUGAAUUUAUAUCGACCA---------GCUCGA
((((-----.(((.((((((.((((((....((((....))))....)))))))))))).)))......(((......))).))))...---------...... ( -19.60)
>DroYak_CAF1 7786 95 - 1
UCAAAGACCAAGAUCUCCAUCGGCAAACACAAAGCCAAUGUUUUCUUUUUGCCAUCGAGUUCUCAACAAAUAUGAAUUUAUAUCGACUA---------ACUCGA
..........(((.(((.((.((((((.(.(((((....))))).).)))))))).))).)))...................((((...---------..)))) ( -15.10)
>consensus
UCGAAAGACAAGAACUCGAUCGGCAAACACAAAGCUAAUGUUUUCUCUUUGCCAUCGAGUUCUCAACAAAUAUGAAUUUAUAUCGACCAA____CUUGACUCGA
((((......(((.(((.((.((((((.(.(((((....))))).).)))))))).))).)))..((((((....)))))).)))).................. (-14.14 = -14.90 +   0.76)

alignment

secondary structure

dotplot

Window 8

Location	7,586,313 – 7,586,414
Length	101
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	83.35
Mean single sequence MFE	-33.80
Consensus MFE	-28.04
Energy contribution	-28.28
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-3.48
Structure conservation index	0.83
SVM decision value	3.38
SVM RNA-class probability	0.999123
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7586313 101 - 27905053
GGCCAGGUUGUGUGAUAACACAGGUAUCGGUGGAGGUACAGGUAUCAGUAUCGGUUACCUC-----CUUAAUCUGGCCUAAACUAGUGUGUCAAUAUUUACACCCC
(((((((((((((....))))..........(((((((..((((....))))...))))))-----)..))))))))).......(((((........)))))... ( -36.10)
>DroSec_CAF1 7751 83 - 1
GGCCAGGUUGUGUGAUAACACAGGUAUCG------------------GCAUCGGUUACCUC-----CUUAAUCUGGCCUAAACUAGUGUGUCAAUACUUACACCCC
(((((((((((((....))))((((((((------------------....))).))))).-----...))))))))).......(((((........)))))... ( -28.90)
>DroSim_CAF1 7813 83 - 1
GGCCAGGUUGUGUGAUAACACAGGUAUCG------------------GUAUCGGUUACCUC-----CUUAAUCUGGCCUAAACUAGUGUGUCAAUACUUACACCCC
(((((((((((((....))))((((((((------------------....))).))))).-----...))))))))).......(((((........)))))... ( -28.90)
>DroEre_CAF1 8478 106 - 1
GGCCAGGUUGUGUGAUAACACAGGUAUCGGUUGAGGUAUAGGUAUCGGUAUCGGUUACCUCCAAUCCUUAAUCUGGCCUAAACUAGUGUGUCAAUAUUUACACCCC
(((((((((((((....)))).......((((((((((..((((....))))...))))).)))))...))))))))).......(((((........)))))... ( -35.50)
>DroYak_CAF1 7881 106 - 1
GGCCAGGUUGUGUGAUAACACAGGUAUCGUUGGAGGUAUUGGUAUCGGUAUCGGUUACCUCCAUUCCAUAAUCUGGCCUAAACUAGUGUGUCAAUAUUUGCACCUC
((((((((((((.((((.......))))..((((((((((((((....)))))).))))))))...)))))))))))).......(((((........)))))... ( -39.60)
>consensus
GGCCAGGUUGUGUGAUAACACAGGUAUCG_U_GAGGUA__GGUAUC_GUAUCGGUUACCUC_____CUUAAUCUGGCCUAAACUAGUGUGUCAAUAUUUACACCCC
(((((((((((((....))))((((((((.....((((....)))).....))).))))).........))))))))).......(((((........)))))... (-28.04 = -28.28 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:45 2006