SIX13 (FOXG_17131 - 5′ extended) is part of a duplicated region on chromosome 6 (sc 42), which is different from the interchromosomal duplication shared with chromosome 3.
Through the neighborhood graph and the resulting hierarchical clustering (see Additional file 4) made on GSS before paralog identification and synteny anchor collapsing (bpisac), we determined the bounds of each duplicated part (duplicates are on a thick line on GSSs bpisac in Figure 1 and Figure 4).
A domain corresponding to the unknown upstream region of the smallest human pART (pART15) is observed also in a pART from the malaria mosquito Anopheles gambiae, and a duplicated truncated pART catalytic domain as in pARTs 16 and 17 is observed also in a pART from the microfungus Gibberella zeae.
Since parallelism implies the duplication of only one part of the architecture (the ratio of the duplicated part in a nonparallelized chip area is denoted ), area overhead can be rewritten (4).
In A. waldeni, CRI ends directly at the duplicated part of Cytb, whereas CRII continues after a spacer of 15 bp with another tandem repeat region.
In P. panini, CRII passes directly into this second repeat region, whereas a spacer of 12 bp is situated between CRI and the duplicated part of Cytb.
In order to integrate the duplicated synteny anchors in the dataset, we first looked for the bounds of the duplicated part, then we reintroduced all deleted synteny anchors yielding two juxtaposed identical parts, and finally collapsed the synteny anchors involved in the two parts by re-numbering them to obtain the part before tandem duplication.
Similarly, almost 60% of the duplicated part of the genome of mouse (approximately 2%) is believed to be misassembled or collapsed in the draft working sequence [ 7].
This region contains the duplicated part of Cytb, tRNA T, tRNA P, NADH6, and tRNA E, and the first part of domain I of the control regions (CR, Figure 1).
This homogenization encompasses the whole duplicated part of Cytb, tRNA T/tRNA P/ NADH6/tRNA E, the first and last nucleotides of domain I and the sequenced part of domain II of the CR (altogether at least 1,771 bp in A. waldeni and 1,871 bp in P. panini).
All that will be left will be the duplicated part of the image.
