Figure 1

The results of AB-PCR, Inverse PCR, internal-SINE PCR. Part A: the aligned nucleotide sequences of the cloned AB-PCR products in silver carp and bighead carp. Hmo: Hypophthalmichthys molitrix, common name: silver carp; Amo: Aristichthys mobilis, common name: bighead carp; The corresponding consensus sequences are given below and above the sequences, respectively. The dots indicate nucleotides identical to the consensus sequences and the region of A box and B box are shown by thick bar. A pair of inverse primer (primer IvR and IvF) was designed to perform Inverse PCR. Part B: Inverse PCR sequences in silver carp that were obtained using primer IvR and IvF and recovered according to the procedure schemed and described in Additional file 1. The region of LINE2-related region followed by short tandem repeats are marked and underlined, respectively. Hmo141_Iv shows a completed SINE copies in amplified flanking region from a clone. A pair of internal primer (primer ItF and ItR) was designed to amplify many different SINE copies in silver carp. Part C: Alignment of internal region of many individual SINEs obtained using primer ItF and ItR (GenBank accession numbers: FJ171654-FJ171662). Nucleotides matched between three parts are denoted by asterisks. The different nucleotides are shaded.