Locus 3208

Sequence ID	2R_DroMel_CAF1
Location	10,961,145 – 10,961,323
Length	178
Max. P	0.796244

overview

Window 5

Location	10,961,145 – 10,961,259
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	92.37
Mean single sequence MFE	-18.10
Consensus MFE	-16.52
Energy contribution	-16.96
Covariance contribution	0.44
Combinations/Pair	1.05
Mean z-score	-1.18
Structure conservation index	0.91
SVM decision value	0.23
SVM RNA-class probability	0.645512
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10961145 114 - 20766785
GCGGUUUUUCAUCACAACGAAAAACCCUGUCAUUUUCCCACUCCAAGCGCAGUAGAAAUUCAAUAACUGAAACCACUAUCUGCAAACGCAAUCGCCUAUGAACCUAUUCUAAAU
((((((((((........))))))))......................(((((((...((((.....))))....))).))))....))......................... ( -19.30)
>DroSec_CAF1 73500 114 - 1
GCGGUUUUUCAUCACAACGAAAAACCCUGUCAUUUUCCCACUCCAAGCGCAGUAGGAAUUCAAUAACUGAAACAACUAUCUGCAAACGCAAUGGCCUAUGAACAUAUUCUAAAU
..((((((((........)))))))).((((((....(((........(((((((...((((.....))))....))).))))........)))...))).))).......... ( -21.19)
>DroSim_CAF1 75777 114 - 1
GCGGUUUUUCAUCACAACGAAAAACCCUGUCAUUUUCCCACUCCAAGCGCAGUAGGAAUUCAAUAACUGAAACCACUAUCUGCAAACGCAAUCGCCUAUGAACAUAUUCUAAAC
((((((((((........))))))))......................((((((((..((((.....))))..).))).))))....))......................... ( -20.40)
>DroEre_CAF1 75810 113 - 1
GCGGUU-UUCAUCACAGCGAAAAACCCUGUCAGUUUCCCACACCAAGCGCAGUGGAAAUUCAAUAACUGAAACGACUAUCUGCUAACACAAUCGCCUAUGAACAUGUUUUAAAU
(((...-(((((....((((............((((........))))(((((((...((((.....))))....))).))))........))))..)))))..)))....... ( -15.80)
>DroYak_CAF1 76925 114 - 1
GCGGUUUUUCAUCACAACGAAAAACCCUGUCAUAUUCCCACACCGAGCGCAGUAGAAAUUCCAUAACUGAAACAAAUAUCUGCCAACACAAUCGCCUAUGAACAUAUUUUAAAU
((((((((((........))))))))....................(.((((((....(((.......))).....)).))))).........))................... ( -13.80)
>consensus
GCGGUUUUUCAUCACAACGAAAAACCCUGUCAUUUUCCCACUCCAAGCGCAGUAGAAAUUCAAUAACUGAAACAACUAUCUGCAAACGCAAUCGCCUAUGAACAUAUUCUAAAU
((((((((((........))))))))......................(((((((...((((.....))))....))).))))..........))................... (-16.52 = -16.96 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	10,961,224 – 10,961,323
Length	99
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	77.42
Mean single sequence MFE	-20.28
Consensus MFE	-7.85
Energy contribution	-8.35
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.52
Structure conservation index	0.39
SVM decision value	0.60
SVM RNA-class probability	0.796244
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10961224 99 - 20766785
ACCAGAAAGGAAAUCAAAAUAUUUCCGCAACUCAAAUUGAAAAUUGUCAAUU-------UUU--UAUUUCGUU-----GCGGUUUUU-CAUCA--CAACGAAAAACCCUGUCAUUU
..(((...((((((......))))))(((((..((((.((((((.....)))-------)))--.)))).)))-----))(((((((-(....--....)))))))))))...... ( -24.00)
>DroPse_CAF1 68427 112 - 1
ACCA-AAAGGAAAUCAAAAUAUUUCCGCAGCUCAAAUUGAAAAUUGUCAAUUUUCAAUUUUU--UAUUUCUUUCUGUAGCGGUUACC-CAUCGACCCACAUCCGACCCCGCCAGGU
(((.-...((((((......))))))((((...((((.((((((((........))))))))--.))))....)))).((((.....-..(((.........)))..))))..))) ( -20.40)
>DroSec_CAF1 73579 97 - 1
CCCAGAAAGGAAAUCAAAAUAUUUCCGCAACUCAAAUUGAAAAUUGUCAAUU---------U--UAUCUCGUU-----GCGGUUUUU-CAUCA--CAACGAAAAACCCUGUCAUUU
..(((...((((((......))))))(((((..(((((((......))))))---------)--......)))-----))(((((((-(....--....)))))))))))...... ( -23.90)
>DroEre_CAF1 75889 98 - 1
ACCAGAAAGGAAAUCAAAAUAUUUCCGCAACUCAAAUUGAAAAUUGUCCAUU-------UUU--UAUCUCGUU-----GCGGUU-UU-CAUCA--CAGCGAAAAACCCUGUCAGUU
....((.(((..............(((((((......((((((........)-------)))--))....)))-----))))((-((-(....--....)))))..))).)).... ( -18.30)
>DroAna_CAF1 73858 96 - 1
ACCAGAAAGGAAAUCAAAAUAUUUCCGCAACUCAAAUUGAAAAUUGACAAUU-------UUUUGUAUCUCCUU-----GUGGUUUUCGCAUC-------CAA-UCUUCUGCCUCUU
..(((((.((((((......))))))((.((..((((((........)))))-------)...))....((..-----..)).....))...-------...-..)))))...... ( -14.10)
>DroPer_CAF1 69093 112 - 1
ACCA-AAAGGAAAUCAAAAUAUUUCCGCAGCUCAAAUUGAAAAUUGUCAAUUUUCAAUUUUU--UAUUUCUUUCUGUAGCGGUUGCC-CAUCGACCCACAUCCGACCCCGUCAGGU
(((.-...((((((......))))))((((...((((.((((((((........))))))))--.))))....)))).(.(((((..-...))))))......(((...))).))) ( -21.00)
>consensus
ACCAGAAAGGAAAUCAAAAUAUUUCCGCAACUCAAAUUGAAAAUUGUCAAUU_______UUU__UAUCUCGUU_____GCGGUUUUC_CAUCA__CAACGAAAAACCCUGUCAGUU
(((.....((((((......))))))........((((((......))))))............................)))................................. ( -7.85 =  -8.35 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:04 2006