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Analysis of Stagonospora nodorum repeat families for evidence of RIP ranked by CpA↔TpA dominance. |
Repeat Family
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CpA↔TpA Dominance
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Alignment Length
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Description/Homology
|
|
R8
|
1.70 ± 0.03
|
0.74 ± 0.02
|
2.96
|
9548
|
Ubiquitin conjugating enzyme
|
X0
|
1.75 ± 0.02
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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
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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
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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
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Sub-telomeric repeat/Transposon remnant
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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
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ELSA
|
1.67 ± 0.04
|
0.46 ± 0.05
|
0.86
|
5273
|
Copia-like transposon
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X11
|
2.04 ± 0.03
|
0.38 ± 0.02
|
0.83
|
7570
|
Gypsy-like transposon
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X28
|
2.22 ± 0.13
|
0.39 ± 0.03
|
0.83
|
1975
|
Unknown
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PIXIE
|
1.84 ± 0.07
|
0.36 ± 0.03
|
0.77
|
1918
|
Mariner-like transposon
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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
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X15
|
1.87 ± 0.04
|
0.33 ± 0.02
|
0.61
|
6437
|
Sub-telomeric repeat/Gypsy-like transposon
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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
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R51
|
1.93 ± 0.07
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0.27 ± 0.03
|
0.47
|
870
|
Unknown
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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*
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Non-array rDNA repeats < 1 kb
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R25
|
2.16 ± 0.15
|
0.31 ± 0.03
|
0.25
|
3407
|
Transposon remnant
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R38
|
2.10 ± 0.18
|
0.24 ± 0.05
|
0.20
|
391
|
Unknown
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Non-Repetitive Control
|
0.83 ± 0.01
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1.25 ± 0.00
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N/A
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N/A
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Genomic regions not corresponding to repeat matches
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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
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