Locus 3983

Sequence ID	2L_DroMel_CAF1
Location	11,600,775 – 11,600,865
Length	90
Max. P	0.999872

overview

Window 1

Location	11,600,775 – 11,600,865
Length	90
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	89.45
Mean single sequence MFE	-22.42
Consensus MFE	-18.42
Energy contribution	-19.08
Covariance contribution	0.66
Combinations/Pair	1.10
Mean z-score	-1.34
Structure conservation index	0.82
SVM decision value	-0.01
SVM RNA-class probability	0.526056
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11600775 90 + 22407834
CA----UAUAUA------UGUGUGUAUAUUUAUGCCGGCAAUCCGGCUGAAAUUUACAAGUAUUUUGGGUGCUUAUAAAUUGGGUGGUUGAAAGGUUGCG--
((----((.(((------((....))))).))))...((((((((((((.((((((.((((((.....)))))).))))))...))))))...)))))).-- ( -21.10)
>DroSec_CAF1 55033 98 + 1
CA----UAUAUAUUUAUGUGUGUGUAUAUUUAUGCCGGCAAUCCGGCUGAAAUUUACAAGUAUUUUGGGUGCUUAUAAAUUGGGUGGAUGAAAGGUUGCGGU
((----((((((....)))))))).........(((....(((((.((..((((((.((((((.....)))))).)))))))).)))))....)))...... ( -23.20)
>DroSim_CAF1 57684 102 + 1
CACAUAUAUAUAUAUAUGUGUGUGUAUAUUUAUGCCGGCAAUCCGGCUGAAAUUUACAAGUAUUUUGGGUGCUUAUAAAUUGGGUGGAUGAAAGGUUGCGGU
((((((((((....)))))))))).........(((....(((((.((..((((((.((((((.....)))))).)))))))).)))))....)))...... ( -27.50)
>DroEre_CAF1 85885 88 + 1
CA----UAU--A--------UAUGUACAUUUAUGCCGGCAAUCCGGCUGAAAUUUACAAGUAUUUUGGGUGCUUAUAAAUUGGGUGGAUGAAAGGUUGCGGU
..----...--.--------......((((((((((((....)))))...((((((.((((((.....)))))).))))))..)))))))............ ( -20.30)
>DroYak_CAF1 56680 90 + 1
CA----UAUAUA--------UAUGUAUAUUUACGCCGGCAAUCCGGCUGAAAUUUACAAGUAUUUUGGGCGCUUAUAAAUUGGGUGGAUGAAAGGUUGCGGU
((----...(((--------(.((((.((((..(((((....)))))..)))).)))).))))..))..((((((.....))))))................ ( -20.00)
>consensus
CA____UAUAUA______UGUGUGUAUAUUUAUGCCGGCAAUCCGGCUGAAAUUUACAAGUAUUUUGGGUGCUUAUAAAUUGGGUGGAUGAAAGGUUGCGGU
......(((((((......)))))))((((((((((((....)))))...((((((.((((((.....)))))).))))))..)))))))............ (-18.42 = -19.08 +   0.66)

alignment

secondary structure

dotplot

Window 2

Location	11,600,775 – 11,600,865
Length	90
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	89.45
Mean single sequence MFE	-16.48
Consensus MFE	-14.90
Energy contribution	-14.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.97
Structure conservation index	0.90
SVM decision value	4.33
SVM RNA-class probability	0.999872
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11600775 90 - 22407834
--CGCAACCUUUCAACCACCCAAUUUAUAAGCACCCAAAAUACUUGUAAAUUUCAGCCGGAUUGCCGGCAUAAAUAUACACACA------UAUAUA----UG
--...................((((((((((...........))))))))))...(((((....)))))...............------......----.. ( -14.90)
>DroSec_CAF1 55033 98 - 1
ACCGCAACCUUUCAUCCACCCAAUUUAUAAGCACCCAAAAUACUUGUAAAUUUCAGCCGGAUUGCCGGCAUAAAUAUACACACACAUAAAUAUAUA----UG
.....................((((((((((...........))))))))))...(((((....)))))...........................----.. ( -14.90)
>DroSim_CAF1 57684 102 - 1
ACCGCAACCUUUCAUCCACCCAAUUUAUAAGCACCCAAAAUACUUGUAAAUUUCAGCCGGAUUGCCGGCAUAAAUAUACACACACAUAUAUAUAUAUAUGUG
.....................((((((((((...........))))))))))...(((((....))))).............((((((((....)))))))) ( -21.30)
>DroEre_CAF1 85885 88 - 1
ACCGCAACCUUUCAUCCACCCAAUUUAUAAGCACCCAAAAUACUUGUAAAUUUCAGCCGGAUUGCCGGCAUAAAUGUACAUA--------U--AUA----UG
...(((...............((((((((((...........))))))))))...(((((....))))).....))).....--------.--...----.. ( -16.00)
>DroYak_CAF1 56680 90 - 1
ACCGCAACCUUUCAUCCACCCAAUUUAUAAGCGCCCAAAAUACUUGUAAAUUUCAGCCGGAUUGCCGGCGUAAAUAUACAUA--------UAUAUA----UG
...((................((((((((((...........))))))))))...(((((....)))))))...........--------......----.. ( -15.30)
>consensus
ACCGCAACCUUUCAUCCACCCAAUUUAUAAGCACCCAAAAUACUUGUAAAUUUCAGCCGGAUUGCCGGCAUAAAUAUACACACA______UAUAUA____UG
.....................((((((((((...........))))))))))...(((((....)))))................................. (-14.90 = -14.90 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:26 2006