Locus 9704

Sequence ID	3R_DroMel_CAF1
Location	25,663,881 – 25,663,984
Length	103
Max. P	0.999655

overview

Window 1

Location	25,663,881 – 25,663,984
Length	103
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	77.89
Mean single sequence MFE	-34.79
Consensus MFE	-22.88
Energy contribution	-26.16
Covariance contribution	3.28
Combinations/Pair	1.06
Mean z-score	-2.27
Structure conservation index	0.66
SVM decision value	1.79
SVM RNA-class probability	0.977346
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25663881 103 + 27905053
--------------CUGGCUGUUUUGUGCACUGGUGCAUUG-GUGCAAUUGUGGCGAGGCUGUCACUAGGACAUGCCACAAUUGUUGGCCUUUAAUACCAAUGGUCCAAUGCUGCACA
--------------..........((((((.....((((((-(.((((((((((((....((((.....))))))))))))))))..(((............)))))))))))))))) ( -36.90)
>DroSec_CAF1 10361 103 + 1
--------------CUGGCUCUUUUGUGCACUGGUGCAUUG-GUGCAAUUGUGGCGAGGCUGUCACUAGGACAUGCCACAAUUGUUGGCCUUUAAUACCAAUGGUCCAAUGCUGCACA
--------------..........((((((.....((((((-(.((((((((((((....((((.....))))))))))))))))..(((............)))))))))))))))) ( -36.90)
>DroSim_CAF1 11291 103 + 1
--------------CUGGCUGUUUUGUGCACUGGUGCAUUG-GUGCAAUUGUGGCGAGGCUGUCACUAGGACAUGCCACAAUUGUUGGCCUUUAAUACCAAUGGUCCAAUGCUGCACA
--------------..........((((((.....((((((-(.((((((((((((....((((.....))))))))))))))))..(((............)))))))))))))))) ( -36.90)
>DroYak_CAF1 11153 114 + 1
GCAGCUAUUCCACAUUGGUACAUUGCUGCAUUGGUGCAUUG-GUGCAAUUGUGGCGAGGCUGUCACUAGGACAUGCCACAAUUGUUGGCCUUUAAUACCAAUGGUCCAAUGCUGC---
(((((.......((((((((......((((....))))..(-((((((((((((((....((((.....))))))))))))))))..))).....)))))))).......)))))--- ( -44.54)
>DroAna_CAF1 10460 82 + 1
--------------------GUUUUGUGUUAU--UGUAUUUACUCGGAGUUUGGCGAGGCUGUCACUAGGACAUGCCACAAUUGUUGGCCUUUAAUGCC--------------GCAAA
--------------------...(((((....--........((((........))))((((((.....)))).)))))))((((.(((.......)))--------------)))). ( -18.70)
>consensus
______________CUGGCUGUUUUGUGCACUGGUGCAUUG_GUGCAAUUGUGGCGAGGCUGUCACUAGGACAUGCCACAAUUGUUGGCCUUUAAUACCAAUGGUCCAAUGCUGCACA
.........................(((((.....((((((...((((((((((((....((((.....)))))))))))))))).((((............))))))))))))))). (-22.88 = -26.16 +   3.28)

alignment

secondary structure

dotplot

Window 2

Location	25,663,881 – 25,663,984
Length	103
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	77.89
Mean single sequence MFE	-34.82
Consensus MFE	-24.84
Energy contribution	-26.86
Covariance contribution	2.02
Combinations/Pair	1.08
Mean z-score	-3.66
Structure conservation index	0.71
SVM decision value	3.84
SVM RNA-class probability	0.999655
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25663881 103 - 27905053
UGUGCAGCAUUGGACCAUUGGUAUUAAAGGCCAACAAUUGUGGCAUGUCCUAGUGACAGCCUCGCCACAAUUGCAC-CAAUGCACCAGUGCACAAAACAGCCAG--------------
(((((((((((((....(((((.......)))))((((((((((.((((.....)))).....))))))))))..)-)))))).....))))))..........-------------- ( -38.70)
>DroSec_CAF1 10361 103 - 1
UGUGCAGCAUUGGACCAUUGGUAUUAAAGGCCAACAAUUGUGGCAUGUCCUAGUGACAGCCUCGCCACAAUUGCAC-CAAUGCACCAGUGCACAAAAGAGCCAG--------------
(((((((((((((....(((((.......)))))((((((((((.((((.....)))).....))))))))))..)-)))))).....))))))..........-------------- ( -38.70)
>DroSim_CAF1 11291 103 - 1
UGUGCAGCAUUGGACCAUUGGUAUUAAAGGCCAACAAUUGUGGCAUGUCCUAGUGACAGCCUCGCCACAAUUGCAC-CAAUGCACCAGUGCACAAAACAGCCAG--------------
(((((((((((((....(((((.......)))))((((((((((.((((.....)))).....))))))))))..)-)))))).....))))))..........-------------- ( -38.70)
>DroYak_CAF1 11153 114 - 1
---GCAGCAUUGGACCAUUGGUAUUAAAGGCCAACAAUUGUGGCAUGUCCUAGUGACAGCCUCGCCACAAUUGCAC-CAAUGCACCAAUGCAGCAAUGUACCAAUGUGGAAUAGCUGC
---...(((((((....(((((.......)))))((((((((((.((((.....)))).....))))))))))..)-))))))......(((((..(((.((.....)).)))))))) ( -41.40)
>DroAna_CAF1 10460 82 - 1
UUUGC--------------GGCAUUAAAGGCCAACAAUUGUGGCAUGUCCUAGUGACAGCCUCGCCAAACUCCGAGUAAAUACA--AUAACACAAAAC--------------------
.....--------------(((.......))).....(((((((.((((.....))))))((((........))))........--....)))))...-------------------- ( -16.60)
>consensus
UGUGCAGCAUUGGACCAUUGGUAUUAAAGGCCAACAAUUGUGGCAUGUCCUAGUGACAGCCUCGCCACAAUUGCAC_CAAUGCACCAGUGCACAAAACAGCCAG______________
......(((((((....(((((.......)))))((((((((((.((((.....)))).....))))))))))...........)))))))........................... (-24.84 = -26.86 +   2.02)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:40:15 2006