Locus 1162

Sequence ID	3R_DroMel_CAF1
Location	3,514,101 – 3,514,204
Length	103
Max. P	0.999330

overview

Window 8

Location	3,514,101 – 3,514,204
Length	103
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	92.88
Mean single sequence MFE	-28.39
Consensus MFE	-25.16
Energy contribution	-25.49
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.23
Structure conservation index	0.89
SVM decision value	3.37
SVM RNA-class probability	0.999094
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3514101 103 + 27905053
UUUCUAAUUUCCCAAGCUGAGCAAUAAACUCAGCGAGCCGAAAACUUUGGCAAAACAAGUUCCAAUUUAUUUAGGCAUAAUCGAGGGAAAGCAGAUGAAAACG---
..(((..((((((..((((((.......))))))..(((.......((((.((......))))))........)))........))))))..)))........--- ( -27.56)
>DroSec_CAF1 112212 103 + 1
UUUCUAAUUUCCCAAGCUGAGCAAUAAACUCAGCGAGCCGAAAACUUUGGCAAAACAAGUUCCAAUUUAUUUAGGCAUAAUCGAGGGAAAGCAGAUGGAAACG---
..(((..((((((..((((((.......))))))..(((.......((((.((......))))))........)))........))))))..))).(....).--- ( -29.06)
>DroSim_CAF1 137054 103 + 1
UUUCUAAUUUCCCAAGCUGAGCAAUAAACUCAGCGAGCCGAAAACUUUGGCAAAACAAGUUCCAAUUUAUUUAGGCAUAAUCGAGGGAAAGCAGAUGGAAACG---
..(((..((((((..((((((.......))))))..(((.......((((.((......))))))........)))........))))))..))).(....).--- ( -29.06)
>DroEre_CAF1 122268 103 + 1
UUUCUAAUUUCCCAAGCUGAGCAAUAAACUCAGCGAGCCGAAAACUUUGGCAAAACAAGUUCCAAUUUAUUUAGGCAUAAUAGAGGGAAACGAGAUGAGAACG---
..(((..((((((..((((((.......))))))..(((.......((((.((......))))))........)))........))))))..)))........--- ( -27.56)
>DroYak_CAF1 178066 103 + 1
UUUCUAAUUUCACAAGCUGAGCAAUAAACUCAGCGAGCCGAAAACUUUGGCAAAACAAGUUCCAAUUUAUUUAGGCAUAAUAGAGGGAAACGAGAUGAAAACG---
((((..(((((....((((((.......))))))..(((((.....)))))........((((..((((((.......)))))).))))..)))))))))...--- ( -23.50)
>DroAna_CAF1 105896 106 + 1
CGUCUAAUUUCCCGGGCUGAGCAAUAAACGCAGCCAGCCAGAAACUUUGGCAAAACAAGUUCCAAUUUAUUUGGGCACAAUCGAGGGAAAAGAGAUGAAAACGACA
(((((..((((((.(((((.(.......).))))).((((((...)))))).......(((((((.....))))).))......))))))..)))))......... ( -33.60)
>consensus
UUUCUAAUUUCCCAAGCUGAGCAAUAAACUCAGCGAGCCGAAAACUUUGGCAAAACAAGUUCCAAUUUAUUUAGGCAUAAUCGAGGGAAAGCAGAUGAAAACG___
..(((..((((((..((((((.......))))))..(((.......((((.((......))))))........)))........))))))..)))........... (-25.16 = -25.49 +   0.33)

alignment

secondary structure

dotplot

Window 9

Location	3,514,101 – 3,514,204
Length	103
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	92.88
Mean single sequence MFE	-28.00
Consensus MFE	-25.87
Energy contribution	-26.37
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.59
Structure conservation index	0.92
SVM decision value	3.52
SVM RNA-class probability	0.999330
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3514101 103 - 27905053
---CGUUUUCAUCUGCUUUCCCUCGAUUAUGCCUAAAUAAAUUGGAACUUGUUUUGCCAAAGUUUUCGGCUCGCUGAGUUUAUUGCUCAGCUUGGGAAAUUAGAAA
---........((((.((((((........(((.(((....((((...........))))...))).)))..(((((((.....)))))))..)))))).)))).. ( -29.30)
>DroSec_CAF1 112212 103 - 1
---CGUUUCCAUCUGCUUUCCCUCGAUUAUGCCUAAAUAAAUUGGAACUUGUUUUGCCAAAGUUUUCGGCUCGCUGAGUUUAUUGCUCAGCUUGGGAAAUUAGAAA
---........((((.((((((........(((.(((....((((...........))))...))).)))..(((((((.....)))))))..)))))).)))).. ( -29.30)
>DroSim_CAF1 137054 103 - 1
---CGUUUCCAUCUGCUUUCCCUCGAUUAUGCCUAAAUAAAUUGGAACUUGUUUUGCCAAAGUUUUCGGCUCGCUGAGUUUAUUGCUCAGCUUGGGAAAUUAGAAA
---........((((.((((((........(((.(((....((((...........))))...))).)))..(((((((.....)))))))..)))))).)))).. ( -29.30)
>DroEre_CAF1 122268 103 - 1
---CGUUCUCAUCUCGUUUCCCUCUAUUAUGCCUAAAUAAAUUGGAACUUGUUUUGCCAAAGUUUUCGGCUCGCUGAGUUUAUUGCUCAGCUUGGGAAAUUAGAAA
---........(((.(((((((........(((.(((....((((...........))))...))).)))..(((((((.....)))))))..))))))).))).. ( -29.70)
>DroYak_CAF1 178066 103 - 1
---CGUUUUCAUCUCGUUUCCCUCUAUUAUGCCUAAAUAAAUUGGAACUUGUUUUGCCAAAGUUUUCGGCUCGCUGAGUUUAUUGCUCAGCUUGUGAAAUUAGAAA
---........(((.(((((..........(((.(((....((((...........))))...))).)))..(((((((.....)))))))....))))).))).. ( -22.70)
>DroAna_CAF1 105896 106 - 1
UGUCGUUUUCAUCUCUUUUCCCUCGAUUGUGCCCAAAUAAAUUGGAACUUGUUUUGCCAAAGUUUCUGGCUGGCUGCGUUUAUUGCUCAGCCCGGGAAAUUAGACG
...........(((..((((((......((..((((.....)))).)).......((((.......)))).(((((.((.....)).))))).))))))..))).. ( -27.70)
>consensus
___CGUUUUCAUCUCCUUUCCCUCGAUUAUGCCUAAAUAAAUUGGAACUUGUUUUGCCAAAGUUUUCGGCUCGCUGAGUUUAUUGCUCAGCUUGGGAAAUUAGAAA
...........(((..((((((........(((.(((....((((...........))))...))).)))..(((((((.....)))))))..))))))..))).. (-25.87 = -26.37 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:35 2006