Locus 4004

Sequence ID	2R_DroMel_CAF1
Location	13,240,101 – 13,240,257
Length	156
Max. P	0.884354

overview

Window 3

Location	13,240,101 – 13,240,220
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	79.37
Mean single sequence MFE	-32.39
Consensus MFE	-27.76
Energy contribution	-26.33
Covariance contribution	-1.43
Combinations/Pair	1.25
Mean z-score	-1.45
Structure conservation index	0.86
SVM decision value	0.93
SVM RNA-class probability	0.884354
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13240101 119 - 20766785
CCAAAAUCCAGUUGGACGUGCGUGUGCGUACAACAUUAUGCUGAGCAUAACUCUACGCAACUGCGCCGCUUG-GAUGCAAAUCCAAUACAAUAAUACAAACCAAGUGCAUAUCGAGGGGU
((......((.((((.((.((((.((((((.....((((((...))))))...))))))...)))))).(((-(((....))))))..............)))).)).........)).. ( -30.76)
>DroPse_CAF1 20794 109 - 1
----AGGCCAGUUCAACGUGCGCGUGGGUUCAAUAUUAUGCUGAGCAUAACCCUGCCCACCCGCACCGCUCGUGGAACACAUCCA------UAUCCAAAACCAAGUGCAUAUCGAGGCG-
----..(((.((((.(((((((.((((((......((((((...))))))....)))))).))))).....)).))))...((.(------(((.((........)).)))).))))).- ( -33.20)
>DroPer_CAF1 20836 109 - 1
----AGGCCAGUUCAACGUGCGCGUGGGUUCAAUAUUAUGCUGAGCAUAACCCUGCCCACCCGCACCGCUCGUGGAACACAUCCA------UAUCCAAAACCAAGUGCAUAUCGAGGCG-
----..(((.((((.(((((((.((((((......((((((...))))))....)))))).))))).....)).))))...((.(------(((.((........)).)))).))))).- ( -33.20)
>consensus
____AGGCCAGUUCAACGUGCGCGUGGGUUCAAUAUUAUGCUGAGCAUAACCCUGCCCACCCGCACCGCUCGUGGAACACAUCCA______UAUCCAAAACCAAGUGCAUAUCGAGGCG_
......(((........(((((.((((((......((((((...))))))....)))))).)))))((((..((((.................))))......))))........))).. (-27.76 = -26.33 +  -1.43)

alignment

secondary structure

dotplot

Window 4

Location	13,240,141 – 13,240,257
Length	116
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	72.86
Mean single sequence MFE	-37.33
Consensus MFE	-27.86
Energy contribution	-28.87
Covariance contribution	1.01
Combinations/Pair	1.16
Mean z-score	-1.24
Structure conservation index	0.75
SVM decision value	0.74
SVM RNA-class probability	0.838334
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13240141 116 - 20766785
GGGAAUAAAGUAGACCUUCG---CCAAUCGGAGGUGAUAACCAAAAUCCAGUUGGACGUGCGUGUGCGUACAACAUUAUGCUGAGCAUAACUCUACGCAACUGCGCCGCUUG-GAUGCAA
.........(((.(((((((---.....))))))).....((((..(((....)))((.((((.((((((.....((((((...))))))...))))))...)))))).)))-).))).. ( -33.50)
>DroPse_CAF1 20827 110 - 1
GGGCUUGAAAUAAGCCAGCAAAUUCUAUGGGGGG----------AGGCCAGUUCAACGUGCGCGUGGGUUCAAUAUUAUGCUGAGCAUAACCCUGCCCACCCGCACCGCUCGUGGAACAC
.((((((...))))))......(((((((((.((----------((.....)))...(((((.((((((......((((((...))))))....)))))).)))))).)))))))))... ( -40.40)
>DroPer_CAF1 20869 110 - 1
GGGCUUGAAAUAAGCCAGCAAUAGCUAUGGGGGG----------AGGCCAGUUCAACGUGCGCGUGGGUUCAAUAUUAUGCUGAGCAUAACCCUGCCCACCCGCACCGCUCGUGGAACAC
.((((((...))))))........(((((((.((----------((.....)))...(((((.((((((......((((((...))))))....)))))).)))))).)))))))..... ( -38.10)
>consensus
GGGCUUGAAAUAAGCCAGCAA__CCUAUGGGGGG__________AGGCCAGUUCAACGUGCGCGUGGGUUCAAUAUUAUGCUGAGCAUAACCCUGCCCACCCGCACCGCUCGUGGAACAC
.((((((...))))))........(((((((.(.................(.....)(((((.((((((......((((((...))))))....)))))).)))))).)))))))..... (-27.86 = -28.87 +   1.01)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:28 2006