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Table 2 Analysis of Stagonospora nodorum repeat families for evidence of RIP ranked by CpA↔TpA dominance.

From: RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences

Repeat Family T p A A p T MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaqcfa4aaSaaaeaacqWGubavcqWGWbaCcqWGbbqqaeaacqWGbbqqcqWGWbaCcqWGubavaaaaaa@33BD@ C p A + T p G A p C + G p T MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaqcfa4aaSaaaeaacqWGdbWqcqWGWbaCcqWGbbqqcqGHRaWkcqWGubavcqWGWbaCcqWGhbWraeaacqWGbbqqcqWGWbaCcqWGdbWqcqGHRaWkcqWGhbWrcqWGWbaCcqWGubavaaaaaa@3C9F@ CpA↔TpA Dominance Alignment Length Description/Homology
R8 1.70 ± 0.03 0.74 ± 0.02 2.96 9548 Ubiquitin conjugating enzyme
X0 1.75 ± 0.02 0.49 ± 0.02 2.13 4103 Non LTR transposon
R10 1.76 ± 0.06 0.56 ± 0.05 1.91 1360 Unknown
R9 1.99 ± 0.03 0.48 ± 0.02 1.88 4483 Non LTR transposon
X48 1.35 ± 0.11 1.26 ± 0.13 1.82 275 Sub-telomeric repeat
rDNA Non-tandem 2.68 ± 0.18 0.69 ± 0.04 1.50 9938 Non-array rDNA repeats ≥ 1 kb
X35 1.76 ± 0.07 0.58 ± 0.07 1.50 1185 Sub-telomeric repeat
MOLLY 1.90 ± 0.06 0.40 ± 0.04 1.21 1946 Mariner-like transposon
R22 1.73 ± 0.08 0.27 ± 0.04 1.20 710 Sub-telomeric repeat
X26 1.70 ± 0.03 0.52 ± 0.02 1.16 5034 Sub-telomeric repeat/Transposon remnant
R31 1.65 ± 0.04 0.44 ± 0.04 0.99 3119 Unknown
X36 1.97 ± 0.18 0.44 ± 0.10 0.89 516 Unknown
X96 1.87 ± 0.19 0.56 ± 0.18 0.87 319 Unknown
ELSA 1.67 ± 0.04 0.46 ± 0.05 0.86 5273 Copia-like transposon
X11 2.04 ± 0.03 0.38 ± 0.02 0.83 7570 Gypsy-like transposon
X28 2.22 ± 0.13 0.39 ± 0.03 0.83 1975 Unknown
PIXIE 1.84 ± 0.07 0.36 ± 0.03 0.77 1918 Mariner-like transposon
X12 2.06 ± 0.07 0.33 ± 0.04 0.67 2059 Gypsy-like transposon
X3 1.91 ± 0.03 0.74 ± 0.01 0.63 10673 Helicase
X15 1.87 ± 0.04 0.33 ± 0.02 0.61 6437 Sub-telomeric repeat/Gypsy-like transposon
R39 1.92 ± 0.08 0.30 ± 0.03 0.59 2102 Unknown
rDNA Tandem 2.08 ± 0.09 0.94 ± 0.02 0.53 9938 rDNA repeats in tandem array
R37 1.85 ± 0.03 0.28 ± 0.02 0.49 2264 Mariner-like transposon
R51 1.93 ± 0.07 0.27 ± 0.03 0.47 870 Unknown
X23 1.85 ± 0.09 0.31 ± 0.03 0.45 613 Unknown
rDNA Short 3.55 ± 0.39 0.25 ± 0.03 0.26 280* Non-array rDNA repeats < 1 kb
R25 2.16 ± 0.15 0.31 ± 0.03 0.25 3407 Transposon remnant
R38 2.10 ± 0.18 0.24 ± 0.05 0.20 391 Unknown
Non-Repetitive Control 0.83 ± 0.01 1.25 ± 0.00 N/A N/A Genomic regions not corresponding to repeat matches
  1. Two RIP index scores are given within a 95% confidence interval. The alignment-based comparison of CpA↔TpA RIP-mutation is used to give dominance score. CpA↔TpA dominance is a numerical indicator of frequency of that mutation over other CpN↔TpN mutations as described in the methods. Values for the rDNA repeat are sub-classified according to physical location and length. The length of the alignment is also given. (*rDNA short alignments are a subset of the full-length rDNA alignment.)