Locus 2811

Sequence ID	3L_DroMel_CAF1
Location	8,033,507 – 8,033,605
Length	98
Max. P	0.940800

overview

Window 0

Location	8,033,507 – 8,033,605
Length	98
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	92.15
Mean single sequence MFE	-22.74
Consensus MFE	-18.29
Energy contribution	-18.37
Covariance contribution	0.08
Combinations/Pair	1.09
Mean z-score	-1.43
Structure conservation index	0.80
SVM decision value	0.15
SVM RNA-class probability	0.605827
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8033507 98 + 23771897
----GCUUGCAGCUUCUUGCUGUCACAUGCCAAUUGACCCAUUCGCCUGUUAUGGCCAGGCCAGCCUCAAUU---------UCUCAAGUGCUAAAGCAAAUAAAACUUUAA
----(((((((((.....)))))(((.((..((((((.......(((((.......))))).....))))))---------...)).)))...)))).............. ( -22.10)
>DroSec_CAF1 4914 98 + 1
----GCUUGCAGCUUCUUGCUGUCACAUGCCAAUUGACCCAUUCGCCUGUUAUGGCCAGGCCAGCCUCAAUU---------UCUCAAGUGCUAAAGCAAAUAAAACUUUAA
----(((((((((.....)))))(((.((..((((((.......(((((.......))))).....))))))---------...)).)))...)))).............. ( -22.10)
>DroSim_CAF1 4838 98 + 1
----GCUUGCAGCUUCUUGCUGUCACAUGCCAAUUGACCCAUUCGCCUGUUAUGGCCAGGCCAGCCUCAAUU---------UCUCAAGUGCUAAAGCAAAUAAAACUUUAA
----(((((((((.....)))))(((.((..((((((.......(((((.......))))).....))))))---------...)).)))...)))).............. ( -22.10)
>DroEre_CAF1 4878 97 + 1
----ACUUGCAGCUUCUUGCUGUCACAUGCCAAUUGACCCAUUCGCCUGUUAUGGCCGGGCCAGCCUCAAUU---------UCUCAAGUGCUAAGGCAAAUAAAAUUUU-A
----....(((((.....)))))....((((....(.(((....(((......))).))).)(((((.....---------.....)).)))..))))...........-. ( -22.20)
>DroYak_CAF1 4958 111 + 1
UGCAUCUUGCAGCUUCUUGCUGUCACAUGGCAAUUGACCCAUUCGCCUGUUAUGGCCAGGCCAGCCUCAAUUUCUAGUGUUUCUCAAGUGCUAAAGCAAAUAAAAUUUUAA
.(((.((((((((.....)))).(((.(((.((((((.......(((((.......))))).....)))))).)))))).....))))))).................... ( -25.20)
>consensus
____GCUUGCAGCUUCUUGCUGUCACAUGCCAAUUGACCCAUUCGCCUGUUAUGGCCAGGCCAGCCUCAAUU_________UCUCAAGUGCUAAAGCAAAUAAAACUUUAA
....((((..(((..((((............((((((.......(((((.......))))).....))))))............)))).))).)))).............. (-18.29 = -18.37 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	8,033,507 – 8,033,605
Length	98
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	92.15
Mean single sequence MFE	-29.74
Consensus MFE	-24.14
Energy contribution	-24.02
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-1.95
Structure conservation index	0.81
SVM decision value	1.31
SVM RNA-class probability	0.940800
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8033507 98 - 23771897
UUAAAGUUUUAUUUGCUUUAGCACUUGAGA---------AAUUGAGGCUGGCCUGGCCAUAACAGGCGAAUGGGUCAAUUGGCAUGUGACAGCAAGAAGCUGCAAGC----
..............((((((((.((..(..---------..)..))(((((((((.......)))))......(((....)))......)))).....)))).))))---- ( -29.50)
>DroSec_CAF1 4914 98 - 1
UUAAAGUUUUAUUUGCUUUAGCACUUGAGA---------AAUUGAGGCUGGCCUGGCCAUAACAGGCGAAUGGGUCAAUUGGCAUGUGACAGCAAGAAGCUGCAAGC----
..............((((((((.((..(..---------..)..))(((((((((.......)))))......(((....)))......)))).....)))).))))---- ( -29.50)
>DroSim_CAF1 4838 98 - 1
UUAAAGUUUUAUUUGCUUUAGCACUUGAGA---------AAUUGAGGCUGGCCUGGCCAUAACAGGCGAAUGGGUCAAUUGGCAUGUGACAGCAAGAAGCUGCAAGC----
..............((((((((.((..(..---------..)..))(((((((((.......)))))......(((....)))......)))).....)))).))))---- ( -29.50)
>DroEre_CAF1 4878 97 - 1
U-AAAAUUUUAUUUGCCUUAGCACUUGAGA---------AAUUGAGGCUGGCCCGGCCAUAACAGGCGAAUGGGUCAAUUGGCAUGUGACAGCAAGAAGCUGCAAGU----
.-......((((.((((..(((.((..(..---------..)..)))))(((((((((......)))...))))))....)))).))))((((.....)))).....---- ( -32.70)
>DroYak_CAF1 4958 111 - 1
UUAAAAUUUUAUUUGCUUUAGCACUUGAGAAACACUAGAAAUUGAGGCUGGCCUGGCCAUAACAGGCGAAUGGGUCAAUUGCCAUGUGACAGCAAGAAGCUGCAAGAUGCA
....................(((((((.....(((....((((((..((.(((((.......))))).)..)..)))))).....))).((((.....)))))))).))). ( -27.50)
>consensus
UUAAAGUUUUAUUUGCUUUAGCACUUGAGA_________AAUUGAGGCUGGCCUGGCCAUAACAGGCGAAUGGGUCAAUUGGCAUGUGACAGCAAGAAGCUGCAAGC____
........((((.((((..(((.((..(.............)..)))))(((((((((......)))...))))))....)))).))))((((.....))))......... (-24.14 = -24.02 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:18 2006