Table 2

Analysis of Stagonospora nodorum repeat families for evidence of RIP ranked by CpA↔TpA dominance.
Repeat Family
 Math
 Math
 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

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.)

Hane and Oliver BMC Bioinformatics 2008 9:478   doi:10.1186/1471-2105-9-478