Table 2 |
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|
Analysis of Stagonospora nodorum repeat families for evidence of RIP ranked by CpA↔TpA dominance. |
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|
Repeat Family |
|
|
CpA↔TpA Dominance |
Alignment Length |
Description/Homology |
|
|
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|
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 |
|
|
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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.) |
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|
Hane and Oliver BMC Bioinformatics 2008 9:478 doi:10.1186/1471-2105-9-478 |
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