Locus 6334

Sequence ID	3L_DroMel_CAF1
Location	16,955,595 – 16,955,702
Length	107
Max. P	0.999591

overview

Window 4

Location	16,955,595 – 16,955,702
Length	107
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	72.84
Mean single sequence MFE	-25.60
Consensus MFE	-15.67
Energy contribution	-16.39
Covariance contribution	0.72
Combinations/Pair	1.12
Mean z-score	-2.83
Structure conservation index	0.61
SVM decision value	3.62
SVM RNA-class probability	0.999453
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16955595 107 + 23771897
UAAUCAGACGAUUUCCCCGAAGUAU----UUGUAAGGUUGUUACAAAAUAAUGAUGAUAUAUAAGAUAGAAAUUUUCGUUCGGUGGAAAUCGUCUGAAGUCGUAG-AAAAUC
...((((((((((((((((((.(((----((.....((..(((........)))..)).....)))))((.....)).))))).)))))))))))))........-...... ( -32.40)
>DroSec_CAF1 31000 107 + 1
UAAUCAGACGAUUUCCCCAAUGAAU----UUACAAAGUUGUCAUUAAAUAAUGGUUAUAUUAAAAUUAGAAUUUUUUUUUUGGUGGAAAUCAUUUGAAGUCGCAG-AAAAUC
...(((((.(((((((((((.((((----(((((....)))((((....))))...............)))))).....)))).))))))).)))))........-...... ( -19.30)
>DroSim_CAF1 34113 107 + 1
GAAUCAGACGAUUUCCCCCAUGAAU----UUAUAAAGUUGUCAUUAAAUAAUGGUUAUAUAAAAUGUAGAAAUUUUCUUUUGGUGGAAAUCGUUUGAAGUCGCAG-AAAAUC
((.(((((((((((((.(((.....----.(((((.(((((......)))))..))))).(((((......)))))....))).)))))))))))))..))....-...... ( -25.70)
>DroEre_CAF1 30773 100 + 1
AAAUGAGACUAUUUCCUCCAUAAACUUGUGCUUAAG------------UAAUACGUAUACAACAUUUCGAAAGUUUCUUUUGGAGGAAAUGGUCUGAAGUCGCAGUAAAAUC
...(.(((((((((((((((...(((((....))))------------)..................(....).......))))))))))))))).)............... ( -27.50)
>DroYak_CAF1 32051 101 + 1
AAGUCAGACGAUUUCCUCCAUGAAU----AAAUAAGGCCAU-------UAAUAAGUAUAUAAAAUUCCGAAAUUUUCUUUUGGUGGAAAUGGUCUGAAGUCGCAAUCAAAUC
...((((((.((((((.(((.(((.----......((....-------..(((....)))......))......)))...))).)))))).))))))............... ( -23.12)
>consensus
AAAUCAGACGAUUUCCCCCAUGAAU____UUAUAAGGUUGU_A__AAAUAAUGAUUAUAUAAAAUUUAGAAAUUUUCUUUUGGUGGAAAUCGUCUGAAGUCGCAG_AAAAUC
...(((((((((((((.(((............................................................))).)))))))))))))............... (-15.67 = -16.39 +   0.72)

alignment

secondary structure

dotplot

Window 5

Location	16,955,595 – 16,955,702
Length	107
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	72.84
Mean single sequence MFE	-22.78
Consensus MFE	-13.53
Energy contribution	-14.61
Covariance contribution	1.08
Combinations/Pair	1.12
Mean z-score	-2.91
Structure conservation index	0.59
SVM decision value	3.76
SVM RNA-class probability	0.999591
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16955595 107 - 23771897
GAUUUU-CUACGACUUCAGACGAUUUCCACCGAACGAAAAUUUCUAUCUUAUAUAUCAUCAUUAUUUUGUAACAACCUUACAA----AUACUUCGGGGAAAUCGUCUGAUUA
......-........(((((((((((((.(((((.((.....)).....................(((((((.....))))))----)...))))))))))))))))))... ( -30.70)
>DroSec_CAF1 31000 107 - 1
GAUUUU-CUGCGACUUCAAAUGAUUUCCACCAAAAAAAAAAUUCUAAUUUUAAUAUAACCAUUAUUUAAUGACAACUUUGUAA----AUUCAUUGGGGAAAUCGUCUGAUUA
......-........(((.(((((((((.((((..........................((((....))))(((....)))..----.....))))))))))))).)))... ( -18.70)
>DroSim_CAF1 34113 107 - 1
GAUUUU-CUGCGACUUCAAACGAUUUCCACCAAAAGAAAAUUUCUACAUUUUAUAUAACCAUUAUUUAAUGACAACUUUAUAA----AUUCAUGGGGGAAAUCGUCUGAUUC
......-........(((.(((((((((.(((..(((.....))).((((..(((.......)))..))))............----.....))).))))))))).)))... ( -21.60)
>DroEre_CAF1 30773 100 - 1
GAUUUUACUGCGACUUCAGACCAUUUCCUCCAAAAGAAACUUUCGAAAUGUUGUAUACGUAUUA------------CUUAAGCACAAGUUUAUGGAGGAAAUAGUCUCAUUU
.................((((.((((((((((...............((((.....))))....------------..(((((....))))))))))))))).))))..... ( -22.20)
>DroYak_CAF1 32051 101 - 1
GAUUUGAUUGCGACUUCAGACCAUUUCCACCAAAAGAAAAUUUCGGAAUUUUAUAUACUUAUUA-------AUGGCCUUAUUU----AUUCAUGGAGGAAAUCGUCUGACUU
...............((((((.((((((.(((..((.((((...((......(((....)))..-------....))..))))----.))..))).)))))).))))))... ( -20.70)
>consensus
GAUUUU_CUGCGACUUCAGACGAUUUCCACCAAAAGAAAAUUUCUAAAUUUUAUAUAACCAUUAUUU__U_ACAACCUUAUAA____AUUCAUGGGGGAAAUCGUCUGAUUA
...............(((((((((((((.(((............................................................))).)))))))))))))... (-13.53 = -14.61 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:54 2006