Additional file 1:

Alignment of DNA sequences from all copies of ISPsy8 in Pseudomonas syringae DC3000 and their flanking regions. In the case named IS8-5 the broken REP element is in the plus strand and 32 bases of the REP element are upstream of the IS element while the remaining 20 bases are downstream. Symmetrically, in the four cases (IS8-1, IS8-2, IS8-3 and IS8-4) in which the REP element is placed in the minus strand, the 20 last bases of the REP sequence are in the minus strand upstream ISPsy8 and the first 31 bases of REP sequence are downstream.

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Additional File 2:

Alignment of DNA sequences from all copies of ISPa11 in Pseudomonas aeruginosa and their flanking regions.

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Additional File 3:

Alignment of DNA sequences from all copies of ISPpu9 in Pseudomonas putida KT2440 and their flanking regions.

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Additional File 4:

Alignment of DNA sequences from all copies of ISPpu10 in Pseudomonas putida KT2440 and their flanking regions.

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Additional File 5:

Alignment of DNA sequences from all copies of ISRm22 in Sinorhizobium meliloti and their flanking regions.

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Additional File 6:

Alignment of DNA sequences from all copies of ISRm19 in Sinorhizobium meliloti and their flanking regions.

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Additional File 7:

Positions of all ISPsy8 copies with adjacent genes and REP sequences.

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Additional File 8:

Alignment of each reconstructed REP sequence with REP sequences with its same orientation and cluster.

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Additional File 9:

Alignment of DNA sequences from all copies of ISPsy7 in Pseudomonas syringae DC3000 and their flanking regions.

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Additional File 10:

Alignment of DNA sequences from all copies of ISRm5 in Sinorhizobium meliloti and their flanking regions.

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Additional File 11:

Alignment of DNA sequences from all copies of ISNm1106 in Neisseria meningitidis MC58 with type 2 association with REP sequences and their flanking regions.

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Additional File 12:

Copies of IS1106 in Neisseria meningitidis Z2491with type 2 association with REP sequences and their flanking regions.

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Additional File 13:

IS1397 inserted into an E. coli REP element in E. coli CFT073 genome

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Additional File 14:

Analyzed genomes

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Additional File 15:

Canonical REP sequences corresponding to each analyzed species

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