Locus 1060

Sequence ID	3L_DroMel_CAF1
Location	3,108,861 – 3,109,027
Length	166
Max. P	0.991111

overview

Window 0

Location	3,108,861 – 3,108,962
Length	101
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	91.08
Mean single sequence MFE	-40.68
Consensus MFE	-35.76
Energy contribution	-35.96
Covariance contribution	0.20
Combinations/Pair	1.07
Mean z-score	-1.93
Structure conservation index	0.88
SVM decision value	2.13
SVM RNA-class probability	0.988693
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3108861 101 + 23771897
AUCCACAUCUUUUCAUUUCGGACCGCCUCCGCCAAGUGACAUCCACAUCGAAUUUGGAACAGCCGGCUG------GG------AGGUGGAGUCCAUGGACGGCGGUUCGAGGC
...............((((((((((((((((((........((((.........)))).(((....)))------..------.))))))(((....))))))))))))))). ( -39.90)
>DroSec_CAF1 41826 101 + 1
AUCUACAUCUUUUCAUUUCGGACCGCCUCCGCCAAGUGACAUCCACAUCGAAUUUGGAACAGCCGGCGG------GG------AGGCGGAGUCCAUGGACGGCGGUUCGAGGC
...............((((((((((((((((((..(((.....))).(((....(((.....))).)))------..------.))))))(((....))))))))))))))). ( -40.90)
>DroSim_CAF1 46194 101 + 1
AUCUACAUCUUUUCAUUUCGGACCGCCUCCGCCAAGUGACAUCCACAUCGAAUUUGGAACAGCCGGCGG------UG------AGGCGGAGUCCAUGGACGGCGGUUCGAGGC
...............((((((((((((((((((..(((.....)))((((....(((.....))).)))------).------.))))))(((....))))))))))))))). ( -42.20)
>DroEre_CAF1 46168 107 + 1
AUCUACAUCUUUUCAUUUCAGACCGCCUCCGCCAAGUGACAUCCACAUCGAAUUUGGAACAGCCGGCGG------GGAGGUGGAGGUGGACUCCAUGGACGGCGGUUCGAGGC
...............((((..((((((((((((..(((.....))).........((.....)))))))------)...((((((.....))))))....))))))..)))). ( -38.90)
>DroYak_CAF1 45813 113 + 1
AUCUACAUCUUUUCAAUUCAAACCGCCUCCGCCAAGUGACAUCCACAUCGAAUUUGGAACAGCCGGCGGAGAAGUGGAGGUGGAGGUGGAGUCCAUGGACGGCGGUUCGAGGC
................(((.(((((((((((((...(.((.(((((.((....((((.....))))....)).))))).)).).))))))(((....)))))))))).))).. ( -41.50)
>consensus
AUCUACAUCUUUUCAUUUCGGACCGCCUCCGCCAAGUGACAUCCACAUCGAAUUUGGAACAGCCGGCGG______GG______AGGUGGAGUCCAUGGACGGCGGUUCGAGGC
................(((((((((((((((((..(((.....))).......((((.....))))..................))))))(((....)))))))))))))).. (-35.76 = -35.96 +   0.20)

alignment

secondary structure

dotplot

Window 1

Location	3,108,931 – 3,109,027
Length	96
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	93.01
Mean single sequence MFE	-28.08
Consensus MFE	-25.62
Energy contribution	-25.86
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.77
Structure conservation index	0.91
SVM decision value	2.25
SVM RNA-class probability	0.991111
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3108931 96 - 23771897
GAGUUUUUGCUUUGGCACGACUUCACUCCAUCGGCAGGGCAACCUGUUCUCUUGCGAUGUCUUUCGCCUCGAACCGCCGUCCAUGGACUCCACCU------C
(((((..(((....))).)))))...((((((((((((....)))((((....((((......))))...)))).))))...)))))........------. ( -29.00)
>DroSec_CAF1 41896 96 - 1
GAGUUUUUGCUUUGGCACGACUUCACUCCAUCGGCAGGGCAACCUGUUCUCUUGCGAUGUCUUUCGCCUCGAACCGCCGUCCAUGGACUCCGCCU------C
(((((..(((....))).)))))...((((((((((((....)))((((....((((......))))...)))).))))...)))))........------. ( -29.00)
>DroSim_CAF1 46264 96 - 1
GAGUUUUUGCUUUGGCACGACUUCACUACAUCGGCAGGGCAACCUGUUCUCUUGCGAUGUCUUUCGCCUCGAACCGCCGUCCAUGGACUCCGCCU------C
((((....)))).(((................((((((....)))((((....((((......))))...)))).)))(((....)))...))).------. ( -28.20)
>DroEre_CAF1 46238 102 - 1
GAGUUUUUGCUUUGGCACGACUUCACUCCAUUGGCAGGGCAACCUGUUCUCUUGCAAUAUCUUUCGCCUCGAACCGCCGUCCAUGGAGUCCACCUCCACCUC
(((((..(((....))).))))).((((((((((((((....)))((((....((..........))...)))).))))...)))))))............. ( -26.10)
>DroYak_CAF1 45889 102 - 1
GAGUUUUUGCUUUGGCACGACUUCACUACAUCGGCAGGGCAACCUGUUCUUUUGCGAUAUCUUUCGCCUCGAACCGCCGUCCAUGGACUCCACCUCCACCUC
(((((..((...((((..(....)......((((((((....)))))......((((......))))..)))...))))..))..)))))............ ( -28.10)
>consensus
GAGUUUUUGCUUUGGCACGACUUCACUCCAUCGGCAGGGCAACCUGUUCUCUUGCGAUGUCUUUCGCCUCGAACCGCCGUCCAUGGACUCCACCU______C
(((((..((...((((..(....)......((((((((....)))))......((((......))))..)))...))))..))..)))))............ (-25.62 = -25.86 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:02 2006