Additional data file 1:

Details about the algorithms used to evaluate fingerprint similarity and fragment specificity, to select enzymes, to score fingerprint alignments, to determine alignment edges and to design PCR primers.

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Additional data file 2:

Regions containing clone alignments are composited horizontally. Alternating vertical white/grey bands indicate disparate regions. Distant alignments of a given clone are joined by horizontal lines. FPP alignments are either black, if validated by BES alignments, or red if no BES alignment is nearby. BES alignments are indicated by small white circles. Blunt termination of FPP alignments is indicative of a breakpoint and these boundaries are denoted by vertical red lines. The boundaries are coded by N(L, R), where N uniquely indexes the breakpoint and L, R indicates whether the breakpoint is on the left or right of the FPP alignment. The breakpoint map generated by FPP alignments is more accurate and complete. FPP alignments captured nearly all breakpoints detected by FPP to a higher degree of spatial accuracy (for example, 3R, 18L). In numerous cases, internal breakpoints were detected by FPP (for example, 7L, 8R). Regions of this figure are presented in greater detail in Figure 7.

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Additional data file 3:

Detailed view of selected regions of chromosomes 1, 3, 17 and 20 from Additional data file 2.

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Additional data file 4:

Restriction maps for each of the five enzymes (EcoRI (e) HindIII (h) BglII (g) NcoI (n) and PvuII (p)) in the neighborhood of regions of M0003F05 detected by FPP. Restriction map fragments matched by experimental fragments in the corresponding fingerprint are shown in green. The FPP alignment is delineated by black vertical lines and the extent of the BLAT alignment is delineated by blue vertical lines.

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Additional data file 5:

Images of individual fingerprints of M0003F05 are accompanied by the image of the nearest marker lane. Fragment sizes are shown to the left of the fragment's band. Correspondence to FPP alignments A, C, D or E (Figure 6) for each fragment is shown. Fragments marked by an asterisk are derived from the digest of the vector.

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Additional data file 6:

The figure depicts the restriction map for each of the five digests used to fingerprint the MCF7 clones. Each clone is shown as a set of five rows, with each row corresponding to the local restriction map of EcoRI, HindIII, NcoI, BglII and PvuII (top to bottom). Fragments within each map are colored green if they were experimentally detected, or red if they were not found in the clone's fingerprint. Adjacent fragments with the same match status are shown with alternating brightness to aid in distinguishing the fragments' extent.

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