Locus 3748

Sequence ID	2L_DroMel_CAF1
Location	10,894,058 – 10,894,208
Length	150
Max. P	0.727169

overview

Window 1

Location	10,894,058 – 10,894,149
Length	91
Sequences	4
Columns	91
Reading direction	forward
Mean pairwise identity	89.07
Mean single sequence MFE	-22.25
Consensus MFE	-18.91
Energy contribution	-19.35
Covariance contribution	0.44
Combinations/Pair	1.09
Mean z-score	-1.33
Structure conservation index	0.85
SVM decision value	-0.05
SVM RNA-class probability	0.505785
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10894058 91 + 22407834
CUGGAGCUGUAGAUGGAACUGAAAGGGAAGGCAAAGAAAAGCUUUGCAUACAUGUGUGAUUGUGUCCCGGCUUUGACACUUGAAGUGAAGA
..((((((.(((......)))...((((..((((((.....)))))).((((........))))))))))))))..(((.....))).... ( -21.80)
>DroSec_CAF1 33622 85 + 1
AUGGA------GCUAUAGCUGGAAAGGAAGGCAAAGAAAAGCUUUGCAUACAUGUGUGAUUGUGUCCCGGCUUUGACACUUGAAGUGAAGA
.....------..((.((((((........((((((.....))))))(((((........))))).)))))).)).(((.....))).... ( -19.90)
>DroSim_CAF1 34505 91 + 1
AUGGAGCUGAAGCUGAAGCUGGAAAGGAAGGCAAAGAAAAGCUUUGCAUACAUGUGUGAUUGUGUCCCGGCUUUGACACUUGAAGUGAAGA
....(((....)))((((((((........((((((.....))))))(((((........))))).))))))))..(((.....))).... ( -24.80)
>DroEre_CAF1 33827 85 + 1
CCGGA------GAUGGAGCUGGAGAGGAAGGCAAAGAAAAGCUUUGCAUACAUGUGUGAUUGUGUCCCGGCUUUGACACUUGAAGUGGAGA
.....------...((((((((.((.....((((((.....)))))).((((........))))))))))))))..(((.....))).... ( -22.50)
>consensus
AUGGA______GAUGGAGCUGGAAAGGAAGGCAAAGAAAAGCUUUGCAUACAUGUGUGAUUGUGUCCCGGCUUUGACACUUGAAGUGAAGA
.............(((((((((........((((((.....))))))(((((........))))).))))))))).(((.....))).... (-18.91 = -19.35 +   0.44)

alignment

secondary structure

dotplot

Window 2

Location	10,894,110 – 10,894,208
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	89.80
Mean single sequence MFE	-25.32
Consensus MFE	-20.44
Energy contribution	-20.48
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.56
Structure conservation index	0.81
SVM decision value	0.41
SVM RNA-class probability	0.727169
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10894110 98 - 22407834
AACACUCGAGCAGCAGGAGUGCUAGACUAACUAGACGCAUGAAUCCUACUCGGCAAAGUUCUUCACUUCAAGUGUCAAAGCCGGGACACAAUCACACA
....((((.((((.(((((((((((.....)))).))).....)))).)).((((((((.....))))....))))...))))))............. ( -19.70)
>DroSec_CAF1 33668 98 - 1
CACACUCGAGCAGCAGGAGUGCUAGACUAACUAGACGCAUGAAUCCUGCUCGGCAAAGUUCUUCACUUCAAGUGUCAAAGCCGGGACACAAUCACACA
....((((.((((((((((((((((.....)))).))).....))))))).((((((((.....))))....))))...))))))............. ( -26.30)
>DroSim_CAF1 34557 98 - 1
CACACUCGAGCAGCAGGAGUGCUAGGCUAACUAGACGCAUGAAUCCUGCUCGGCAAAGUUCUUCACUUCAAGUGUCAAAGCCGGGACACAAUCACACA
....((((.((((((((((((((((.....)))).))).....))))))).((((((((.....))))....))))...))))))............. ( -27.60)
>DroEre_CAF1 33873 98 - 1
CACACUCGAGCAGCAGGAGUGCUAGACUAACUAGACGCAUGAAUCCUGCUCGGCAGAGUUCUCCACUUCAAGUGUCAAAGCCGGGACACAAUCACACA
...((((..((((((((((((((((.....)))).))).....)))))))..)).))))............(((((........)))))......... ( -27.70)
>DroYak_CAF1 34660 81 - 1
CACACUCGAGCAGCAGGAGUGCUAGACUAACUAGACGCAUGAAUCCUGCUCGGCCGAGUUCUCCACUUUAAGUGUC-----------------ACACA
...(((((.((((((((((((((((.....)))).))).....)))))))..)))))))....(((.....)))..-----------------..... ( -25.30)
>consensus
CACACUCGAGCAGCAGGAGUGCUAGACUAACUAGACGCAUGAAUCCUGCUCGGCAAAGUUCUUCACUUCAAGUGUCAAAGCCGGGACACAAUCACACA
.(((((.((((((((((((((((((.....)))).))).....)))))))..))..(((.....))))).)))))....................... (-20.44 = -20.48 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:04 2006