Locus 4955

Sequence ID	X_DroMel_CAF1
Location	12,948,121 – 12,948,259
Length	138
Max. P	0.999969

overview

Window 4

Location	12,948,121 – 12,948,231
Length	110
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	94.98
Mean single sequence MFE	-32.56
Consensus MFE	-31.42
Energy contribution	-31.62
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.68
Structure conservation index	0.96
SVM decision value	5.02
SVM RNA-class probability	0.999969
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12948121 110 - 22224390
--AUCGGACCAUCAAUUGUGGUCGCUGGCAAAGUGAAAACAAUGGCAAACAACUUUUACAAUGUCAGCGGCUGCGGA-------GUCGAAGAAAAGUGACAGUGGAGCAAGCAAUUAAA
--......((((...(((..((((((((((..((((((....((.....))..))))))..))))))))))..))).-------((((........)))).)))).............. ( -32.10)
>DroSec_CAF1 6486 110 - 1
--AUCGGACCAUCAAUUGUGGUCGCUGGCAAAGUGAAAACAAUGGCAAACAACUUUUACAAUGUCAGCGGCUGCGGA-------GUCGAAGAAAAGUGACAGUGGAGCAAGCAAUUAAA
--......((((...(((..((((((((((..((((((....((.....))..))))))..))))))))))..))).-------((((........)))).)))).............. ( -32.10)
>DroSim_CAF1 7265 110 - 1
--AUCGGACCAUCAAUUGUGGUCGCUGGCAAAGUGAAAACAAUGGCAAACAACUUUUACAAUGUCAGCGGCUGCGGA-------GUCGAAGAAAAGUGACAGUGGAGCAAGCAAUUAAA
--......((((...(((..((((((((((..((((((....((.....))..))))))..))))))))))..))).-------((((........)))).)))).............. ( -32.10)
>DroEre_CAF1 6018 117 - 1
--UACGGACCAUCAAUUGUGGUCGCUGGCAAAGUGAAAACAAUGGCAAACAACUUUUACAAUGUCAGCGGCUGCGGAGUGCAGAGUCGAAGAAAAGUGACAGUGGAGCAAGCAAUUAAA
--......((((...(((..((((((((((..((((((....((.....))..))))))..))))))))))..)))........((((........)))).)))).............. ( -32.10)
>DroYak_CAF1 5982 112 - 1
UGGACGGACCAUCAAUUGUGGUCGCUGGCAAAGUGAAAACAAUGGCAAACAACUUUUACAAUGUCAGCGGCUGCGCG-------GUCGAAGAAAAGUGACAGUGGAGCAAGCAAUUAAA
......((((((.....))))))(((((((..((((((....((.....))..))))))..))))))).(((.(((.-------((((........)))).))).)))........... ( -34.40)
>consensus
__AUCGGACCAUCAAUUGUGGUCGCUGGCAAAGUGAAAACAAUGGCAAACAACUUUUACAAUGUCAGCGGCUGCGGA_______GUCGAAGAAAAGUGACAGUGGAGCAAGCAAUUAAA
........((((...(((..((((((((((..((((((....((.....))..))))))..))))))))))..)))........((((........)))).)))).............. (-31.42 = -31.62 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	12,948,156 – 12,948,259
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.67
Mean single sequence MFE	-40.62
Consensus MFE	-33.88
Energy contribution	-33.76
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-3.07
Structure conservation index	0.83
SVM decision value	3.26
SVM RNA-class probability	0.998864
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12948156 103 - 22224390
----------UUGGAGCUGUUUCGGGCCUCCGAACCCG----AUCGGACCAUCAAUUGUGGUCGCUGGCAAAGUGAAAACAAUGGCAAACAACUUUUACAAUGUCAGCGGCUGCGGA---
----------.(((..(((..(((((........))))----).))).)))....(((..((((((((((..((((((....((.....))..))))))..))))))))))..))).--- ( -38.30)
>DroSec_CAF1 6521 102 - 1
----------UUGGAGCUGUUU-GGGCCUCCGAGCCCG----AUCGGACCAUCAAUUGUGGUCGCUGGCAAAGUGAAAACAAUGGCAAACAACUUUUACAAUGUCAGCGGCUGCGGA---
----------.(((..(((.((-((((......)))))----).))).)))....(((..((((((((((..((((((....((.....))..))))))..))))))))))..))).--- ( -40.70)
>DroSim_CAF1 7300 102 - 1
----------UUGGAGCUGUUU-GGGCCACCGGGCCCG----AUCGGACCAUCAAUUGUGGUCGCUGGCAAAGUGAAAACAAUGGCAAACAACUUUUACAAUGUCAGCGGCUGCGGA---
----------.(((..(((.((-(((((....))))))----).))).)))....(((..((((((((((..((((((....((.....))..))))))..))))))))))..))).--- ( -44.20)
>DroEre_CAF1 6057 103 - 1
---------UUUGGAGCUGUUU-GGGCC---AAGUCCG----UACGGACCAUCAAUUGUGGUCGCUGGCAAAGUGAAAACAAUGGCAAACAACUUUUACAAUGUCAGCGGCUGCGGAGUG
---------..(((..((((.(-((((.---..)))))----.)))).)))....(((..((((((((((..((((((....((.....))..))))))..))))))))))..))).... ( -36.90)
>DroYak_CAF1 6017 116 - 1
UUGGAGCUGUUUGGAGUUGUUU-GGGCCUUCAAGCCCGACUGGACGGACCAUCAAUUGUGGUCGCUGGCAAAGUGAAAACAAUGGCAAACAACUUUUACAAUGUCAGCGGCUGCGCG---
.(((..(((((..(......((-((((......)))))))..))))).)))......(..((((((((((..((((((....((.....))..))))))..))))))))))..)...--- ( -43.00)
>consensus
__________UUGGAGCUGUUU_GGGCCUCCGAGCCCG____AUCGGACCAUCAAUUGUGGUCGCUGGCAAAGUGAAAACAAUGGCAAACAACUUUUACAAUGUCAGCGGCUGCGGA___
...........((.((((.....((((......)))).........((((((.....))))))(((((((..((((((....((.....))..))))))..))))))))))).))..... (-33.88 = -33.76 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:50 2006