Patterned sequence in the transcriptome of vascular plants

Additional File 1:

Observed and expected per-megabase frequencies by motif length in a subset of 12 genera. This Excel table lists total per-megabase frequencies of repeated motifs, grouped by motif length, in 12 of the 88 total genera. For comparison, it also lists the frequencies expected by chance under Equations 1 and 2 for random sequences matched in length to the observed sequences.

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Additional File 2:

Per-megabase frequency of canonical motifs in perfect microsatellites in 88 genera of vascular plants. This Excel table lists numerical values of the eight quantities defined in the Abbreviations for all canonical motifs from one to six bases long observed in perfect microsatellites in the 88 genera examined. Canonical motifs are motifs in their lexicographically least form, considering all possible rotations and reverse complementation. For example, AC is the canonical form of AC, CA, GT, and TG.

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Additional File 3:

Per-megabase frequency of canonical motifs in microsatellites in 88 genera, allowing one mismatched repeat position. This Excel table parallels Additional file 2. Here the values of the eight quantities defined in the Abbreviations are tabulated for canonical motifs in microsatellites with up to one mismatch allowed among repeats.

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Additional File 4:

Per-megabase frequency of canonical motifs in microsatellites in 88 genera, allowing two mismatched repeat positions. This Excel table is also parallels Additional file 2, with up to two mismatches allowed among repeats.

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Additional File 5:

Collective per-megabase frequency, repeat count, and polymorphism by canonical microsatellite motif in perfect loci. This Excel table lists values, sorted from greatest to least, for the eight quantities defined in the Abbreviations, collected over all 88 genera. It thus provides the overall ranking of motifs for these quantities.

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Additional File 6:

Collective per-megabase frequency, repeat count, and polymorphism by canonical microsatellite motif with one allowed mismatched repeat position. This Excel table parallels Additional File 5, allowing up to one mismatched nucleotide among motifs in the microsatellite locus.

Format: XLS Size: 135KB Download file

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Additional File 7:

Collective per-megabase frequency, repeat count, and polymorphism by canonical microsatellite motif with two allowed mismatched repeat positions. This Excel table also parallels Additional File 5, allowing up to two mismatches among motifs in the microsatellite locus.

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Additional File 8:

Motif rankings by number of genera in which motif held first place for frequency, repeat count, and polymorphism in perfect microsatellites. For the eight quantities defined in the Abbreviations, this Excel table lists the number of genera in which each motif ranked first.

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Additional File 9:

Motif rankings by number of genera in which the motif held first place for frequency, repeat count, and polymorphism in microsatellites with one allowed mismatched repeat position. This Excel table parallels Additional File 8, allowing up to one mismatched nucleotide among motifs in the microsatellite locus.

Format: XLS Size: 51KB Download file

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Additional File 10:

Motif rankings by number of genera in which motif held first place for frequency, repeat count, and polymorphism in microsatellites with two allowed mismatched repeat positions. This Excel table parallels Additional File 9, allowing up to two mismatched nucleotides among motifs in the microsatellite locus.

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Additional File 11:

Regression coefficients of microsatellite characteristics versus GC content. For the eight properties defined in the Abbreviations, this Excel table provides regression coefficients to a quadratic model of property versus motif GC content. Significance is also indicated.

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Additional File 12:

Mean within-group ranking difference of genera for total motif frequency in perfect microsatellite loci. For groups of genera defined by the maximum-likelihood tree of perfect-microsatellite similarity in Fig. 3, this Excel table lists the motifs that were the most consistently ranked and therefore that most likely defined the groups. The highest frequency has the highest ranking.

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Additional File 13:

Mean within-group ranking difference of genera for total motif frequency in microsatellite loci with one allowed mismatch. This Excel table parallels Additional File 12, but the groups were drawn from Fig. 4, where one nucleotide mismatch was allowed.

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Additional File 14:

Mean within-group ranking difference of genera for total motif frequency in microsatellite loci with two allowed mismatches. This Excel table parallels Additional File 12, but the groups were drawn from Fig. 5, where two mismatched nucleotides were allowed.

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Additional File 15:

Observed and published microsatellite motif frequency rankings in 16 genera. This Excel table lists observed and previously published rankings of di- and tri-nucleotide motif frequencies in these genera, and provides the size of the minimum microsatellite locus recognized in each case.

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