Spreadsheet: 36a50916-f1d9-43c4-b863-8bf809e8d93a
Sheet: Sheet1

Table S3.  Pp23SR loci | 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
Locus | Scaffold1 | Start | Stop | Length | Asymmetry2 | Number of distinct small RNAs3 | Repeat Normalized Abundance | Uniquely matched small RNAs?4 | [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"5 | 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)
Pp23SR1 | scaffold_83 | 372155 | 397479 | 25325 | 0.52307162527116 | 6960 | 6200.854522000001 | y | 3816.16393113587 | 0.2082527147087858 | 0.72 | 3.343137368677572e-05 | 0.2082527147087858 | 0.2895557749259625 | 0 | 0 | 0.9569200394866733
Pp23SR2 | scaffold_287 | 353140 | 366703 | 13564 | 0.5501655547648288 | 4178 | 2613.507653 | y | 9.50021671816651 | 0.02108522559716898 | 0.72 | 0 | 0.02108522559716898 | 0.5145974638749632 | 0 | 1 | 0
Pp23SR3 | scaffold_356 | 364664 | 380267 | 15604 | 0.5348592433944024 | 1513 | 1360.459471 | y | 20.1627796056689 | 0.05351192002050756 | 0.81 | 9.962163143239128e-05 | 0.05351192002050756 | 0.3806075365290951 | 0 | 0 | 0
[NAME] | scaffold_120 | 1010265 | 1022401 | 12137 | 0.5038405345662692 | 3511 | 1355.922389 | y | 0.358344955834495 | 0.01573700255417319 | 0.81 | 0 | 0.01573700255417319 | 0.3868336491719535 | 0 | 0 | 0
Pp23SR5 | scaffold_18 | 1578170 | 1593382 | 15213 | 0.5601280041761741 | 4002 | 1210.570274 | y | 0 | 0 | 0 | 0 | 0 | 0.4981923355025307 | 0 | 0.4049825806875698 | 0
Pp23SR6 | scaffold_250 | 402634 | 452560 | 49927 | 0.5353964712284724 | 7094 | 1031.143545 | y | 6.35605851355562 | 0.0256574598914415 | 0.81 | 0.02090360442139547 | 0.0256574598914415 | 0.2428345384261021 | 0.07186492278726941 | 0.1976685961503795 | 0
Pp23SR7 | scaffold_182 | 636712 | 656273 | 19562 | 0.5445892548351232 | 3742 | 927.4035140000001 | y | 0 | 0.005111951743175545 | 0.95 | 0 | 0.005111951743175545 | 0.4657499233207238 | 0 | 0 | 0.8332992536550455
Pp23SR8 | scaffold_83 | 355703 | 371439 | 15737 | 0.5189793457301195 | 2617 | 800.89149 | y | 0.0507279305557419 | 0.008769142784520557 | 1 | 0 | 0.008769142784520557 | 0.4267014043337358 | 0 | 0 | 1
Pp23SR9 | scaffold_32 | 1004253 | 1020128 | 15876 | 0.5177820048216396 | 2705 | 683.377478 | y | 24.9162603260735 | 0.05561854371378181 | 0.77 | 0 | 0.05561854371378181 | 0.4025573192239859 | 0 | 0.3835978835978836 | 0
Pp23SR10 | scaffold_265 | 295613 | 322766 | 27154 | 0.5288761827229412 | 2969 | 345.2045879999999 | y | 0.0345589991068851 | 0.01005376740075127 | 0.91 | 0.0001032409375293025 | 0.01005376740075127 | 0.3928702953524343 | 0 | 0 | 0
Pp23SR11 | scaffold_33 | 2000643 | 2006602 | 5960 | 0.6016136970907584 | 1157 | 341.203334 | y | 0.382787648473494 | 0.04580536912751678 | 0.77 | 0 | 0.04580536912751678 | 0.1731543624161074 | 0 | 0 | 0
Pp23SR12 | scaffold_167 | 807705 | 818757 | 11053 | 0.5660036289929392 | 3068 | 287.424652 | y | 4 | 0.04279381163485026 | 0.75 | 0 | 0.04279381163485026 | 0.5245634669320547 | 0 | 0 | 0
Pp23SR13 | scaffold_468 | 167607 | 182114 | 14508 | 0.5008579576667538 | 1370 | 167.969819 | y | 0 | 0.00206782464846981 | 0.89 | 0 | 0.00206782464846981 | 0.4813895781637717 | 0 | 0 | 0
Pp23SR14 | scaffold_273 | 310536 | 328398 | 17863 | 0.5962439145672699 | 1210 | 149.576257 | y | 1.32783733722486 | 0.07417567038011533 | 0.86 | 0.0004318626149776598 | 0.07417567038011533 | 0.3313553154565302 | 0 | 1 | 0
Pp23SR15 | scaffold_293 | 295573 | 306175 | 10603 | 0.5337098099898926 | 2199 | 129.826184 | y | 18.0394166713202 | 0.3398094878807885 | 0.81 | 3.327259798104972e-05 | 0.3398094878807885 | 0.5591813637649722 | 0 | 0.917664811845704 | 0
Pp23SR16 | scaffold_223 | 388694 | 396419 | 7726 | 0.5437402085913495 | 523 | 114.82643 | y | 0 | 0.006471654154801968 | 0.96 | 0 | 0.006471654154801968 | 0.769867978255242 | 0 | 0 | 0
Pp23SR17 | scaffold_35 | 943105 | 949583 | 6479 | 0.5665893729173155 | 505 | 103.855752 | y | 1.31333360898854 | 0.02361475536348202 | 0.87 | 0 | 0.02361475536348202 | 0.5622781293409477 | 0 | 0 | 0
Pp23SR18 | scaffold_188 | 145329 | 159330 | 14002 | 0.5136863353809615 | 258 | 93.85557299999999 | y | 0 | 0.007070418511641194 | 0.85 | 0 | 0.007070418511641194 | 0.4865733466647622 | 0 | 0 | 0
Pp23SR19 | [NAME] | 240147 | 263777 | 23631 | 0.5335985724159497 | 1354 | 90.563076 | y | 0 | 0.002454403114552918 | 0.7 | 0 | 0.002454403114552918 | 0.342219965299818 | 0 | 0.3910541238204054 | 0
Pp23SR20 | scaffold_83 | 401768 | 405981 | 4214 | 0.5292532480274633 | 234 | 90.353461 | y | 0 | 0.01495016611295681 | 0.87 | 0 | 0.01495016611295681 | 0.7033697199810157 | 0 | 0 | 0
Pp23SR21 | scaffold_293 | 324536 | 336607 | 12072 | 0.5194472875310754 | 889 | 73.046591 | y | 0.236174824100136 | 0.02004638833664679 | 0.75 | 0 | 0.02004638833664679 | 0.538104705102717 | 0 | 0 | 0
Pp23SR22 | scaffold_33 | 2033548 | 2045803 | 12256 | 0.5899253334935589 | 699 | 59.21651499999999 | y | 0.382787648473494 | 0.01093342036553525 | 0.76 | 0 | 0.01093342036553525 | 0.3639849869451697 | 0 | 0 | 0
Pp23SR23 | scaffold_179 | 227062 | 268370 | 41309 | 0.5225116553226529 | 4563 | 56.30796599999999 | y* | 5.36796536956841 | 0.398436176135951 | 0.91 | 0.1035748228567095 | 0.398436176135951 | 0.7293325909608076 | 0 | 0.3761407925633639 | 0
Pp23SR24 | [NAME] | 229051 | 239417 | 10367 | 0.6688622118269999 | 2289 | 55.209979 | y | 0 | 0 | 0 | 0 | 0 | 0.5301437252821453 | 0 | 0 | 0
Pp23SR25 | scaffold_5 | 1043250 | 1050480 | 7231 | 0.585593164436779 | 385 | 53.968338 | y | 0.493076538765234 | 0.01659521504632831 | 0.76 | 0 | 0.01659521504632831 | 0.6017148388881206 | 0 | 0 | 0
Pp23SR26 | scaffold_269 | 470130 | 478031 | 7902 | 0.5290476425111336 | 604 | 52.80741500000001 | n | 0 | 0 | 0 | 0 | 0 | 0.08314350797266515 | 0.2630979498861048 | 0 | 0
Pp23SR27 | scaffold_226 | 3826 | 4729 | 904 | 0.528721043930682 | 98 | 52.516669 | n | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
Pp23SR28 | scaffold_154 | 1021258 | 1033991 | 12734 | 0.6008491738427533 | 1196 | 52.14715099999999 | y | 0.26351384405894 | 0.02112454845296058 | 0.75 | 0 | 0.02112454845296058 | 0.6510130359667033 | 0 | 0 | 0
Pp23SR29 | scaffold_43 | 2097016 | 2140012 | 42997 | 0.5473654570383675 | 3989 | 48.227628 | y | 2.31780652317495 | 0.195711328697351 | 0.27 | 0.1172552914184838 | 0.195711328697351 | 0.7697513780031165 | 0 | 0 | 1
Pp23SR30 | scaffold_324 | 10962 | 29119 | 18158 | 0.6137590966824612 | 1708 | 47.030196 | y | 4.06964285714286 | 0.06388368763079634 | 0.88 | 0.2970859565796792 | 0.06388368763079634 | 0.6715497301464919 | 0 | 0 | 0
Pp23SR31 | scaffold_117 | 1192632 | 1193665 | 1034 | 0.7335243691554261 | 74 | 46.533333 | y* | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0
Pp23SR32 | scaffold_446 | 168228 | 172960 | 4733 | 0.7247510336789449 | 50 | 45.79033 | y | 10.25 | 0.1504331290935981 | 0.94 | 0 | 0.1504331290935981 | 0.51151489541517 | 0 | 0 | 0
Pp23SR33 | scaffold_182 | 694018 | 699603 | 5586 | 0.5539060496894548 | 1599 | 45.76097499999999 | y | 0.413275497854769 | 0.0309702828499821 | 0.86 | 0 | 0.0309702828499821 | 0.6845685642678124 | 0 | 0.9863945578231292 | 0
Pp23SR34 | scaffold_273 | 331219 | 338855 | 7637 | 0.5895542932980726 | 284 | 43.406889 | y | 0 | 0 | 0 | 0 | 0 | 0.5774518790100825 | 0 | 1 | 0
Pp23SR35 | scaffold_65 | 445133 | 451036 | 5904 | 0.5518206397083629 | 430 | 41.07625 | y* | 0 | 0.007113821138211382 | 0.95 | 0 | 0.007113821138211382 | 0 | 0.6603997289972899 | 0 | 0
Pp23SR36 | scaffold_349 | 353509 | 378307 | 24799 | 0.5795939979216553 | 3126 | 41.041314 | y | 9.13479967589429 | 0.6824468728577764 | 0.26 | 0.2621069835298377 | 0.6824468728577764 | 0.7767248679382233 | 0 | 0 | 1
Pp23SR37 | scaffold_5 | 159283 | 166086 | 6804 | 0.5513313194999327 | 475 | 40.663079 | y | 0 | 0.01058201058201058 | 1 | 0 | 0.01058201058201058 | 0.07730746619635509 | 0.5711346266901822 | 0 | 0
Pp23SR38 | scaffold_2 | 3298470 | 3304190 | 5721 | 0.5898210713980805 | 443 | 40.59753600000001 | n | 0 | 0 | 0 | 0 | 0 | 0 | 0.665443104352386 | 0 | 0
Pp23SR39 | scaffold_151 | 720147 | 750081 | 29935 | 0.529391134109491 | 2814 | 40.30564 | y | 9.56957573603677 | 0.4471020544513112 | 0.27 | 0.130113970300422 | 0.4471020544513112 | 0.6054785368297979 | 0 | 0 | 1
Pp23SR40 | scaffold_201 | 88048 | 94200 | 6153 | 0.5568758952145065 | 402 | 40.135634 | n | 0 | 0.006825938566552902 | 1 | 0 | 0.006825938566552902 | 0.07996099463676255 | 0.6367625548512921 | 0 | 0
Pp23SR41 | scaffold_42 | 1958581 | 1964492 | 5912 | 0.5560726709885668 | 452 | 40.110751 | y | 0 | 0.01200947225981055 | 0.95 | 0 | 0.01200947225981055 | 0 | 0.6640730717185386 | 0 | 0
Pp23SR42 | scaffold_183 | 632877 | 638669 | 5793 | 0.522227567495716 | 427 | 40.097731 | y | 0 | 0.007250129466597618 | 1 | 0 | 0.007250129466597618 | 0 | 0.677369238736406 | 0 | 0
Pp23SR43 | scaffold_277 | 512722 | 518535 | 5814 | 0.5459544138998156 | 415 | 38.867684 | y* | 0 | 0.007223942208462331 | 1 | 0 | 0.007223942208462331 | 0 | 0.6754385964912281 | 0 | 0
Pp23SR44 | scaffold_140 | 442978 | 454711 | 11734 | 0.5361748900199981 | 2616 | 38.353105 | y | 0.788073579058107 | 0.06851883415715017 | 0.88 | 0.01188357987252748 | 0.06851883415715017 | 0.6028634736662689 | 0 | 0 | 0
Pp23SR45 | scaffold_32 | 1021481 | 1044002 | 22522 | 0.5903344654849905 | 825 | 38.187169 | y | 0.524937956133748 | 0.03569842820353432 | 0.76 | 0.005091528533134075 | 0.03569842820353432 | 0.5440902228931711 | 0 | 0 | 0
Pp23SR46 | scaffold_295 | 219127 | 225070 | 5944 | 0.5632517380229674 | 426 | 37.56711 | y | 0 | 0.01127187079407806 | 1 | 0 | 0.01127187079407806 | 0 | 0.6606662180349933 | 0 | 0
Pp23SR47 | scaffold_18 | 2034233 | 2040705 | 6473 | 0.5899112680056982 | 420 | 37.177122 | y* | 0 | 0.01838405685153715 | 1 | 0 | 0.01838405685153715 | 0 | 0.6065193882280241 | 0 | 0
Pp23SR48 | scaffold_255 | 69726 | 96484 | 26759 | 0.508844694522768 | 3015 | 36.208034 | y | 9.93576406505023 | 0.4078254045367913 | 0.25 | 0.0706644780688623 | 0.4078254045367913 | 0.6638887850816547 | 0 | 0 | 0.918494712059494
1 Coordinates relative to the draft genome assembly version 1.1
2 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
3 From NCBI GEO GSE5103
4 From NCBI GEO GSE5103, except cases marked with an asterisk -- these had one or more uniquely mapping small RNAs from [NAME] but not GSE5103
5 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.