Locus 5170

Sequence ID	2L_DroMel_CAF1
Location	14,638,412 – 14,638,547
Length	135
Max. P	0.986160

overview

Window 2

Location	14,638,412 – 14,638,509
Length	97
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	76.95
Mean single sequence MFE	-19.34
Consensus MFE	-11.89
Energy contribution	-12.61
Covariance contribution	0.72
Combinations/Pair	1.12
Mean z-score	-2.60
Structure conservation index	0.61
SVM decision value	2.03
SVM RNA-class probability	0.986160
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14638412 97 + 22407834
UCGCUGUUUUGCUUGUUUGGG-G----GA-AAAAAAAAUA---A--AAAACUUUUACGAAAACUACAGGCGAAAAAAAUUGGCAAAAUUCGUGACUAAAUGAGUCACA
..(((.((((((((((((.(.-.----((-(.........---.--.....)))..).))....))))))))))......))).......((((((.....)))))). ( -19.36)
>DroSec_CAF1 2330 103 + 1
UCGCUGUUUUGCUUGUUUGGA-AAAUAGA-AAAAAAUAAA---AAAAAAACUUUUACGAAAACUACAGGCGAAAAAAAUUGGCAAAAUUCGCGACUAAAUGAGUCACA
..(((.((((((((((.....-...((((-(.........---........)))))........))))))))))......))).......(.((((.....)))).). ( -15.32)
>DroSim_CAF1 3629 101 + 1
UUGCUGUUUUGCUUGUUUGGA-AAAUAGA-AAAAAAUAAA---A--AAAACUUUUACGAAAACUACAGGCGAAAAAAAUUGGCAAAAUUCGUGACUAAAUGAGUCACA
(((((.((((((((((.....-...((((-(.........---.--.....)))))........))))))))))......))))).....((((((.....)))))). ( -20.65)
>DroEre_CAF1 1918 90 + 1
UCGCUGUUUUGCUUGUUUGGA-AAAUAGA-----------------AAAAAUUUUACAAAAACUACAGGCGAAAAAAAUUGGCAAAAUUCGUGACUAAAUGAGUCACA
..(((.(((((((((((((.(-((((...-----------------....))))).))).....))))))))))......))).......((((((.....)))))). ( -20.70)
>DroYak_CAF1 2358 91 + 1
UUGCUGUUUUGCUUGUUUGAA-AAAUAAA---------U-------AAAAAAUUUACGAAAACUACAGGCGAAAAAAAUGGACAAAAUUCGUGACUAAAUGAGUCACA
(((((.((((((((((.....-...((((---------(-------.....)))))........)))))))))).....)).))).....((((((.....)))))). ( -18.99)
>DroPer_CAF1 6543 96 + 1
UCGUCUGGUU-GUUGUUUGCACAAAUAC-CAAAAAAAACACCGA--AAAAUUGUUUAAAAAAAAGUCGGUGAAAA--------AAAAAUCGUGACUAAAUGAGUCACA
.....((((.-.((((....))))..))-)).......((((((--....((.......))....))))))....--------.......((((((.....)))))). ( -21.00)
>consensus
UCGCUGUUUUGCUUGUUUGGA_AAAUAGA_AAAAAA_AAA___A__AAAACUUUUACGAAAACUACAGGCGAAAAAAAUUGGCAAAAUUCGUGACUAAAUGAGUCACA
......((((((((((................................................))))))))))................((((((.....)))))). (-11.89 = -12.61 +   0.72)

alignment

secondary structure

dotplot

Window 3

Location	14,638,436 – 14,638,547
Length	111
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	83.22
Mean single sequence MFE	-18.86
Consensus MFE	-14.57
Energy contribution	-15.03
Covariance contribution	0.46
Combinations/Pair	1.08
Mean z-score	-1.62
Structure conservation index	0.77
SVM decision value	0.16
SVM RNA-class probability	0.614281
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14638436 111 + 22407834
AAAAAAAAUAA--AAAACUUUUACGAAAACUACAGGCGAAAAAAAUUGGCAAAAUUCGUGACUAAAUGAGUCACAAUUGUCUUCUAAAUUGUGCGAACUGUUUUCCAUUUUCG
...........--..........((((((..((((((.((.....)).))....(((((((((.....))))((((((........)))))))))))))))......)))))) ( -19.50)
>DroSec_CAF1 2358 113 + 1
AAAAAAUAAAAAAAAAACUUUUACGAAAACUACAGGCGAAAAAAAUUGGCAAAAUUCGCGACUAAAUGAGUCACAAUUGUCUUCUAAAUUGUGCGAACUGUUUUCCAUUUUCG
.......................((((((..((((((.((.....)).))....(((((((((.....))))((((((........)))))))))))))))......)))))) ( -22.00)
>DroSim_CAF1 3657 111 + 1
AAAAAAUAAAA--AAAACUUUUACGAAAACUACAGGCGAAAAAAAUUGGCAAAAUUCGUGACUAAAUGAGUCACAAUUGUCUUCUAAAUUGUGCGAACUGUUUUCCAUUUUCG
...........--..........((((((..((((((.((.....)).))....(((((((((.....))))((((((........)))))))))))))))......)))))) ( -19.50)
>DroEre_CAF1 1946 100 + 1
-------------AAAAAUUUUACAAAAACUACAGGCGAAAAAAAUUGGCAAAAUUCGUGACUAAAUGAGUCACAAUUGUCUUCUAAAUUGUGCGAACUGUUUUCCAUUUUCG
-------------.......................((((((....(((.(((.(((((((((.....))))((((((........)))))))))))...))).))))))))) ( -17.10)
>DroYak_CAF1 2386 101 + 1
--------U----AAAAAAUUUACGAAAACUACAGGCGAAAAAAAUGGACAAAAUUCGUGACUAAAUGAGUCACAAUUGUCUUCUAAAUUGUGCGAACUGUUUUCCAUUUUCG
--------.----...........((((((.....(((........((((((.....((((((.....))))))..)))))).........))).....))))))........ ( -19.53)
>DroAna_CAF1 2222 85 + 1
-------AUAA--AAAAUUUAUACAAAAAGUACUCGGGAAAA-------------UCGUGACUAAAUGAGUCACAAUUGUCUUCCAAAUUGUGCGAACUGA------UUUUCG
-------....--................((((...((((((-------------(.((((((.....)))))).)))...)))).....))))(((....------..))). ( -15.50)
>consensus
_______AUAA__AAAACUUUUACGAAAACUACAGGCGAAAAAAAUUGGCAAAAUUCGUGACUAAAUGAGUCACAAUUGUCUUCUAAAUUGUGCGAACUGUUUUCCAUUUUCG
.....................................(((((.....((((...(((((((((.....))))((((((........))))))))))).)))).....))))). (-14.57 = -15.03 +   0.46)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:46 2006