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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.)
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BMC Bioinformatics

ISSN: 1471-2105

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