Spreadsheet: 32d634a9-7572-46c4-98b0-2e7ed809bf58
Sheet: Sheet1

Unnamed: 0 | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12 | Unnamed: 13 | Unnamed: 14 | Unnamed: 15 | Unnamed: 16 | Unnamed: 17 | Unnamed: 18
Table S2.  [NAME]
Locus1 | Scaffold2 | Start | Stop | Comments | Length | Asymmetry3 | Number of distinct small RNAs4 | Repeat Normalized Abundance | Uniquely matched small RNAs?5 | [NAME] abundance from a single inverted repeat | Percent of locus in stems of inverted repeats | Median percent identity of overlapping inverted repeats | Fraction of abundance from small RNA "dyads"6 | Percent of locus in tandem repeats (Tandem Repeat Finder) | Percent of locus overlapping LTR-retrotranspons (CENSOR) | Percent of locus overlapping Helitrons (CENSOR) | Percent of locus overlaping intact, non-nested LTR-retrotransposons (LTR_FINDER) | Percent of locus overlaping intact, nested LTR-retrotransposons (LTR_FINDER)
Pp21SR1 | scaffold_342 | 334454 | 334815 | Inverted Repeat, Diffuse Processing | 362 | 1 | 176 | 910.5 | y | 910.5 | 93.646408839779 | 93 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR2 | scaffold_81 | 496712 | 496832 | Inverted Repeat, Diffuse Processing | 121 | 0.5008237232561359 | 73 | 607 | y | 605.333333333334 | 64.46280991735537 | 100 | 0.9983525847919261 | 0 | 0 | 0 | 0 | 0
Pp21SR3 | scaffold_99 | 649088 | 649189 | Inverted Repeat, Diffuse Processing | 102 | 0.5 | 58 | 350 | y* | 350 | 76.47058823529412 | 100 | 1 | 0 | 0 | 0 | 0 | 0
Pp21SR4 | scaffold_170 | 61538 | 61648 | NOT Inverted Repeat, Discrete Processing | 111 | 1 | 16 | 320 | y | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR5 | scaffold_81 | 691600 | 691638 | NOT Inverted Repeat, Diffuse Processing | 39 | 0.6061606033613262 | 36 | 303 | n | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR6 | scaffold_1 | 812885 | 813279 | NOT Inverted Repeat, Diffuse Processing | 395 | 0.5423728813559322 | 148 | 234 | y | 233 | 100 | 26 | 0 | 0.9974683544303797 | 0 | 0 | 0 | 0
Pp21SR7 | scaffold_4 | 4023915 | 4025075 | Inverted Repeat, Diffuse Processing | 1161 | 0.6229508196721312 | 190 | 182 | y | 182 | 60.20671834625323 | 98 | 0.7377049180327869 | 0 | 0 | 0 | 0 | 0
Pp21SR8 | scaffold_220 | 755727 | 756670 | NOT Inverted Repeat, Diffuse Processing | 944 | 0.7511973671519795 | 130 | 173.676262626263 | y | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR9 | scaffold_86 | 1002709 | 1002816 | NOT Inverted Repeat, Discrete Processing | 108 | 1 | 13 | 144.033333333333 | y | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR10 | scaffold_163 | 928769 | 929018 | NOT Inverted Repeat, Discrete Processing | 250 | 0.9999880950322408 | 9 | 137.00163132137 | y | 0 | 0 | 0 | 0 | 0.188 | 0 | 0 | 0 | 0
Pp21SR11 | scaffold_419 | 83309 | 89381 | Inverted Repeat, Diffuse Processing | 6073 | 0.509009009009009 | 165 | 110 | y | 100 | 78.511444096822 | 99 | 0.954954954954955 | 0 | 0 | 0 | 0 | 0
Pp21SR12 | scaffold_17 | 49032 | 49838 | Inverted Repeat, Diffuse Processing | 807 | 0.8657407407407407 | 76 | 107 | y | 107 | 28.62453531598513 | 95 | 0.2685185185185185 | 0.06567534076827757 | 0 | 0 | 0 | 0
Pp21SR13 | scaffold_180 | 833572 | 833669 | NOT Inverted Repeat, Discrete Processing | 98 | 0.9982919444459047 | 22 | 97.5770363408521 | y | 79.6577380952381 | 90.81632653061224 | 67 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR14 | scaffold_74 | 1407634 | 1407691 | NOT Inverted Repeat, Discrete Processing | 58 | 0.694300518134715 | 19 | 96.5 | y | 0 | 29.3103448275862 | 91 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR15 | scaffold_82 | 424637 | 425134 | Inverted Repeat, Diffuse Processing | 498 | 1 | 24 | 94 | y | 93 | 15.66265060240964 | 81 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR16 | scaffold_243 | 414050 | 416288 | NOT Inverted Repeat, Diffuse Processing | 2239 | 0.6423356702390158 | 109 | 93.1676047529706 | y | 0 | 0 | 0 | 0 | 0.01161232693166592 | 0 | 0 | 0 | 0
Pp21SR17 | scaffold_73 | 203029 | 204200 | NOT Inverted Repeat, Diffuse Processing | 1172 | 1 | 24 | 92.6666666666667 | y | 38 | 5.631399317406143 | 89 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR18 | scaffold_132 | 926363 | 927687 | NOT Inverted Repeat, Diffuse Processing | 1325 | 0.9719095319213432 | 80 | 88.5412291915212 | y | 2 | 27.62264150943397 | 87 | 0.05613855566274282 | 0.03094339622641509 | 0.8083018867924529 | 0 | 0 | 0
Pp21SR19 | scaffold_376 | 374909 | 375799 | NOT Inverted Repeat, Discrete Processing | 891 | 0.8632449319727892 | 64 | 86.45 | y | 0 | 0 | 0 | 0 | 0.08417508417508418 | 0 | 0 | 0 | 0
Pp21SR20 | scaffold_15 | 809815 | 809912 | NOT Inverted Repeat, Discrete Processing | 98 | 1 | 16 | 84.9417748917749 | y | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR21 | scaffold_651 | 69 | 3281 | Inverted Repeat, Diffuse Processing | 3213 | 0.5488936878864443 | 195 | 81.8101393743731 | y | 56.810139374373 | 65.29723000311236 | 99 | 0.6944144011289188 | 0.01618425147836913 | 0 | 0 | 0 | 0
Pp21SR22 | scaffold_30 | 2039626 | 2039703 | Inverted Repeat, Diffuse Processing | 78 | 0.7564102470414198 | 46 | 78 | y | 78 | 100 | 91 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR23 | scaffold_118 | 622602 | 622739 | Inverted Repeat, Diffuse Processing | 138 | 0.7253521126760564 | 33 | 71 | y | 71 | 60.86956521739131 | 97 | 0.5211267605633803 | 0 | 0 | 0 | 0 | 0
Pp21SR24 | scaffold_196 | 372854 | 373854 | NOT Inverted Repeat, Diffuse Processing | 1001 | 0.5961265904216022 | 35 | 70.5666666666667 | y | 0 | 0.999000999000999 | 94 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR25 | scaffold_7 | 2886292 | 2886350 | NOT Inverted Repeat, Diffuse Processing | 59 | 0.6046511566612582 | 39 | 64.5 | n | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR26 | scaffold_82 | 423884 | 423954 | Inverted Repeat, Diffuse Processing | 71 | 1 | 14 | 64 | y | 64 | 100 | 81 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR27 | scaffold_60 | 880013 | 881738 | NOT Inverted Repeat, Diffuse Processing | 1726 | 0.5317460317460317 | 60 | 63 | y | 9 | 11.41367323290846 | 96 | 0.1428571428571428 | 0 | 0 | 0 | 0 | 0
Pp21SR28 | scaffold_398 | 319554 | 320566 | NOT Inverted Repeat, Diffuse Processing | 1013 | 0.592067979423637 | 51 | 58.8333333333333 | y | 0 | 0 | 0 | 0 | 0.08489634748272458 | 0 | 0 | 0 | 0
Pp21SR29 | scaffold_446 | 176348 | 186867 | NOT Inverted Repeat, Diffuse Processing | 10520 | 0.5061326435030977 | 731 | 58.6568843956133 | y | 1.44281880155714 | 10.22813688212928 | 88 | 0.0003376109464996057 | 0.04230038022813688 | 0.4874524714828897 | 0 | 0 | 0
Pp21SR30 | scaffold_90 | 869613 | 869704 | Inverted Repeat, Diffuse Processing | 92 | 0.5263157894736842 | 16 | 57 | y | 55 | 91.30434782608695 | 96 | 0.9473684210526315 | 0 | 0 | 0 | 0 | 0
Pp21SR31 | scaffold_115 | 679232 | 684639 | Inverted Repeat, Diffuse Processing | 5408 | 0.5272727272727272 | 94 | 55 | y | 53 | 70.46967455621301 | 99 | 0.9454545454545454 | 0 | 0 | 0 | 0 | 0
Pp21SR32 | scaffold_30 | 2040960 | 2041030 | Inverted Repeat, Diffuse Processing | 71 | 0.7570093457943925 | 39 | 53.5 | y | 53.5 | 100 | 91 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR33 | scaffold_276 | 489712 | 489848 | NOT Inverted Repeat, Diffuse Processing | 137 | 1 | 9 | 50.3119047619048 | y | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR34 | scaffold_99 | 916525 | 917318 | Inverted Repeat, Diffuse Processing | 794 | 0.5 | 146 | 48.5947796613432 | y* | 48.5947796613432 | 62.72040302267003 | 100 | 0.9999999930310047 | 0 | 0 | 0 | 0 | 0
Pp21SR35 | scaffold_111 | 54969 | 54995 | NOT Inverted Repeat, Discrete Processing | 27 | 0.979381443298969 | 7 | 48.5 | y | 48 | 100 | 90 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR36 | scaffold_7 | 2440792 | 2441038 | Inverted Repeat, Diffuse Processing | 247 | 0.5208333333333333 | 27 | 48 | y | 46 | 32.38866396761134 | 100 | 0.9583333333333334 | 0 | 0 | 0 | 0 | 0
Pp21SR37 | scaffold_1821 | 109 | 1271 | NOT Inverted Repeat, Diffuse Processing | 1163 | 0.773481301991421 | 41 | 44.1464646464647 | y | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR38 | scaffold_26 | 761291 | 761373 | Inverted Repeat, Diffuse Processing | 83 | 0.7441860465116279 | 18 | 43 | n | 43 | 86.74698795180723 | 97 | 1 | 0 | 0 | 0 | 0 | 0
Pp21SR39 | scaffold_61 | 111893 | 112505 | NOT Inverted Repeat, Diffuse Processing | 613 | 0.5 | 21 | 43 | y | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR40 | scaffold_281 | 200183 | 201053 | Inverted Repeat, Diffuse Processing | 871 | 0.5127118648376903 | 53 | 39.3333333333333 | y | 39.3333333333333 | 100 | 30 | 0.9745762794455609 | 0 | 0 | 0 | 0 | 0
Pp21SR41 | scaffold_124 | 417634 | 418490 | NOT Inverted Repeat, Diffuse Processing | 857 | 0.974025974025974 | 21 | 38.5 | y | 3.5 | 42.82380396732789 | 84 | 0 | 0.1505250875145858 | 0 | 0 | 0 | 0
Pp21SR42 | [NAME] | 336639 | 337238 | NOT Inverted Repeat, Diffuse Processing | 600 | 0.5364607420979467 | 36 | 37.2813852813853 | y | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
Pp21SR43 | scaffold_28 | 2081709 | 2085266 | Inverted Repeat, Diffuse Processing | 3558 | 0.5 | 58 | 36.6666666666667 | n | 36.6666666666667 | 84.03597526700393 | 100 | 0.9999999909090918 | 0 | 0 | 0 | 0 | 0
1 Does not include 21nt loci which were annotated as miRNAs -- see Table S1
2 Coordinates relative to the draft genome assembly version 1.1
3 Fraction of repeat normalized abundance emanating from the most abundant genomic strand.  1 = all small RNAs came from a single strand, 0.5 = exactly equal distribution of small RNAs between the two genomic strands
4 From NCBI GEO GSE5103
5 From NCBI GEO GSE5103, except cases marked with an asterisk -- these had one or more uniquely mapping small RNAs from [NAME] but not GSE5103
6 Small RNA "dyads" were when a single small RNA sequence mapped exactly twice to a locus, once in one polarity, and once in the other polarity.  This is diagnostic of perfect inverted repeats.