# Annotated CM search results, using SmY seed (68 sequences) as query # for Infernal 1.0rc3. # # For each genome, tabfile output from Infernal is excerpted to show # only the hit table (eliding the other Infernal output information), # sorted on E-value, and truncated after the top scoring hit we believe # to be nonhomologous. (Including the top "false" hit helps show # where E-values cease to be significant, and helps illustrate how # well separated "signal" is from "noise" in these searches; keeping # in mind that there's selection bias, because we don't know how many # true SmY homologs might be going undetected below the noise.) # # Two additional annotation columns are then added manually. "Assign" # is a manual # assignment of "gene", "pseudo", "dup", or "NO", # corresponding to our best (but subjective) effort to guess whether a # locus is a true SmY gene, a pseudogene, a duplicate sequence # resulting from underassembly of draft genome data, or not an SmY # homolog. "Name" is the assigned name of the locus in C.elegans or # C.briggsae; in all other species, we identify putative SmY genes # solely by coordinates, and no names have been assigned. # ############################################################################# # # target coord query coord # ---------------------- ------------ # target name start stop start stop bit sc E-value GC% Assign Name # ---------------- ---------- ---------- ----- ----- -------- -------- --- ------ -------- #=========== Caenorhabditis elegans (WS150): 12 genes CHROMOSOME_IV 14863947 14864028 1 80 76.12 9.87e-16 43 gene SmY-11 CHROMOSOME_V 14099058 14098977 1 80 75.47 1.48e-15 44 gene SmY-5 CHROMOSOME_IV 6460748 6460667 1 80 73.36 5.37e-15 45 gene SmY-7 CHROMOSOME_V 14095157 14095239 1 80 72.43 9.45e-15 47 gene SmY-3 CHROMOSOME_IV 9511817 9511740 1 80 71.34 1.85e-14 47 gene SmY-1 CHROMOSOME_V 14100105 14100024 1 80 70.98 2.30e-14 44 gene SmY-6 CHROMOSOME_IV 9511446 9511370 1 80 70.67 2.78e-14 45 gene SmY-2 CHROMOSOME_IV 13602165 13602245 1 80 68.33 1.16e-13 41 gene SmY-9 CHROMOSOME_IV 13600814 13600894 1 80 67.47 1.98e-13 43 gene SmY-8 CHROMOSOME_IV 14864705 14864786 1 80 64.93 9.33e-13 39 gene SmY-12 CHROMOSOME_V 14097290 14097209 1 80 61.65 6.96e-12 45 gene SmY-4 CHROMOSOME_IV 13601614 13601694 1 80 55.63 2.77e-10 35 gene SmY-10 CHROMOSOME_IV 2421255 2421181 1 80 22.13 2.24e-01 40 NO - #=========== Caenorhabditis briggsae: 11 genes, 1 pseudo, 7 assembly dups chrIV 9065593 9065671 1 80 75.05 2.36e-15 46 gene CbSmY-1 cb25.fpc0090 976914 976833 1 80 74.77 2.81e-15 46 dup - chrV 12863241 12863160 1 80 74.77 2.81e-15 46 gene CbSmY-2 cb25.fpc0090 688489 688404 1 80 73.37 6.62e-15 45 dup - chrV 12574816 12574731 1 80 73.37 6.62e-15 45 gene CbSmY-6 chrIV 9066035 9065959 1 80 65.45 8.44e-13 47 gene CbSmY-3 cb25.fpc0090 704986 705070 1 80 59.21 3.86e-11 38 dup - chrV 12591313 12591397 1 80 59.21 3.86e-11 38 gene CbSmY-8 cb25.fpc0090 705691 705775 1 80 58.85 4.79e-11 35 dup - chrV 12592018 12592102 1 80 58.85 4.79e-11 35 gene CbSmY-12 cb25.fpc0090 677031 677114 1 80 58.29 6.75e-11 40 dup - chrV 12563358 12563441 1 80 58.29 6.75e-11 40 gene CbSmY-5 cb25.fpc0090 650889 650806 1 80 57.73 9.51e-11 44 dup - chrV 12537216 12537133 1 80 57.73 9.51e-11 44 gene CbSmY-7 chrIV 9100165 9100245 1 80 57.35 1.20e-10 56 gene CbSmY-9 cb25.fpc0090 702204 702287 1 80 55.71 3.27e-10 43 dup - chrV 12588531 12588614 1 80 55.71 3.27e-10 43 gene CbSmY-4 chrIV 9104340 9104422 1 80 51.08 5.59e-09 53 gene CbSmY-11 chrIV 9102086 9102167 1 80 35.45 8.00e-05 52 pseudo - chrX 18729418 18729338 1 80 28.66 5.09e-03 40 NO - #=========== Caenorhabditis remanei: 22 genes, 7 pseudos Contig2 1581908 1581989 1 80 77.74 5.33e-16 41 gene - Contig2 1578744 1578825 1 80 74.19 4.66e-15 46 gene - Contig2 1595709 1595790 1 80 70.71 3.94e-14 43 gene - Contig10 511550 511467 1 80 68.86 1.22e-13 40 gene - Contig10 1052647 1052564 1 80 68.27 1.75e-13 38 gene - Contig200 88734 88656 1 80 68.15 1.89e-13 41 gene - Contig1528 211 289 1 80 67.17 3.45e-13 42 pseudo - Contig137 142319 142239 1 80 64.06 2.31e-12 38 gene - Contig10 1101933 1102014 1 80 63.82 2.67e-12 46 pseudo - Contig200 88250 88173 1 80 63.47 3.30e-12 49 gene - Contig2 1874842 1874925 1 80 62.27 6.93e-12 45 gene - Contig2 1589250 1589173 1 80 62.16 7.38e-12 41 gene - Contig11 252915 252996 1 80 61.82 9.12e-12 43 gene - Contig0 3332058 3331977 1 80 61.47 1.13e-11 45 gene - Contig2 1578235 1578154 1 80 61.46 1.13e-11 38 gene - Contig0 3326826 3326745 1 80 58.77 5.88e-11 44 gene - Contig0 3334186 3334105 1 80 58.77 5.88e-11 44 gene - Contig10 510122 510205 1 80 57.94 9.77e-11 42 gene - Contig10 1107030 1107113 1 80 55.29 4.95e-10 42 pseudo - Contig10 648631 648548 1 80 55.22 5.18e-10 36 pseudo - Contig254 17552 17474 1 80 53.07 1.92e-09 43 gene - Contig2338 4726 4804 1 80 52.26 3.17e-09 44 gene - Contig254 12038 12116 1 80 52.26 3.17e-09 44 gene - Contig1766 5417 5495 1 80 52.09 3.52e-09 44 gene - Contig1528 682 759 1 80 50.26 1.08e-08 49 pseudo - Contig200 106744 106823 1 80 44.24 4.31e-07 50 gene - Contig5588 566 487 1 80 44.24 4.31e-07 50 gene - Contig10 506497 506590 1 80 36.78 4.13e-05 36 pseudo - Contig254 13665 13739 1 80 32.39 6.06e-04 40 pseudo - Contig46 590997 591073 1 80 27.74 1.05e-02 43 NO - #=========== Caenorhabditis japonica: 10 genes, 6 pseudos Contig258 103352 103272 1 80 70.17 5.73e-14 40 gene - Contig1440 26106 26025 1 80 65.68 8.92e-13 37 gene - Contig258 105775 105856 1 80 64.44 1.91e-12 37 gene - Contig1484 2758 2837 1 80 64.23 2.17e-12 45 gene - Contig1544 18365 18284 1 80 63.21 4.05e-12 34 gene - Contig1544 18566 18647 1 80 63.16 4.19e-12 39 gene - Contig1440 25238 25158 1 80 62.50 6.26e-12 36 gene - Contig1440 27718 27794 1 80 61.91 8.98e-12 38 gene - Contig1440 27517 27436 1 80 61.79 9.65e-12 35 gene - Contig258 104872 104953 1 80 59.63 3.64e-11 41 pseudo - Contig370 26489 26409 1 80 56.24 2.88e-10 48 gene - Contig1440 26933 27014 1 80 50.65 8.84e-09 39 pseudo - Contig1396 8013 7934 1 80 47.58 5.78e-08 43 pseudo - Contig1440 25407 25493 1 80 37.12 3.50e-05 37 pseudo - Contig497 7707 7633 1 80 33.38 3.47e-04 55 pseudo - Contig802 56680 56762 1 80 30.22 2.39e-03 53 pseudo - Contig606 72424 72338 1 80 25.98 3.21e-02 39 NO - #=========== Caenorhabditis brenneri: 26 genes, 10 pseudos Contig3 215017 214938 1 80 84.16 1.41e-17 45 gene - Contig3 58313 58392 1 80 81.64 6.60e-17 40 gene - Contig799 28050 28129 1 80 81.57 6.93e-17 43 gene - Contig3 56758 56837 1 80 81.54 7.04e-17 40 gene - Contig3 54041 54120 1 80 78.68 4.06e-16 49 gene - Contig799 3042 3122 1 80 78.34 5.00e-16 43 gene - Contig3 280402 280481 1 80 77.79 6.98e-16 41 gene - Contig3 58108 58029 1 80 77.38 8.98e-16 40 gene - Contig3 301521 301442 1 80 77.31 9.35e-16 44 gene - Contig3 54543 54464 1 80 76.98 1.15e-15 43 gene - Contig3 300557 300636 1 80 76.68 1.38e-15 40 gene - Contig105 48485 48405 1 80 76.67 1.39e-15 41 gene - Contig3 299394 299315 1 80 73.88 7.65e-15 36 gene - Contig185 160297 160218 1 80 73.46 9.88e-15 44 gene - Contig183 7569 7648 1 80 73.18 1.17e-14 38 gene - Contig3 294485 294564 1 80 73.13 1.21e-14 46 gene - Contig291 910 826 1 80 71.78 2.77e-14 46 gene - Contig72 83388 83465 1 80 70.19 7.35e-14 38 gene - Contig105 48807 48887 1 80 69.03 1.49e-13 38 pseudo - Contig585 6512 6592 1 80 68.32 2.30e-13 42 gene - Contig585 1597 1518 1 80 68.22 2.45e-13 43 pseudo - Contig105 113605 113684 1 80 67.90 2.98e-13 40 gene - Contig2073 14589 14512 1 80 65.91 1.01e-12 44 gene - Contig884 26436 26513 1 80 65.91 1.01e-12 44 gene - Contig183 6890 6811 1 80 65.43 1.35e-12 36 pseudo - Contig105 169005 168925 1 80 64.84 1.94e-12 41 gene - Contig2073 15091 15013 1 80 62.77 6.91e-12 44 gene - Contig884 25927 26005 1 80 62.77 6.91e-12 44 gene - Contig3 54759 54838 1 80 62.64 7.44e-12 44 gene - Contig799 27550 27476 1 80 59.66 4.62e-11 43 pseudo - Contig105 167633 167712 1 80 54.48 1.10e-09 41 pseudo - Contig3 58902 58981 1 80 50.69 1.12e-08 40 pseudo - Contig9599 380 301 1 80 46.41 1.54e-07 43 pseudo - Contig105 49369 49449 1 80 45.47 2.74e-07 41 pseudo - Contig799 2475 2545 1 80 40.43 5.99e-06 51 pseudo - Contig799 4197 4117 1 80 35.56 1.18e-04 46 pseudo - Contig2820 2556 2628 1 80 24.49 1.04e-01 37 NO - #=========== Pristionchus pacificus: 26 genes, 2 pseudos Contig48 288048 287970 1 80 62.14 8.54e-12 48 gene - Contig120 11483 11560 1 80 61.51 1.25e-11 50 gene - Contig120 15917 15840 1 80 61.51 1.25e-11 50 gene - Contig2 389921 389842 1 80 57.09 1.88e-10 54 gene - Contig122 156544 156622 1 80 56.68 2.41e-10 53 gene - Contig122 154912 154834 1 80 55.64 4.55e-10 54 gene - Contig2 720515 720437 1 80 54.70 8.10e-10 46 gene - Contig2 721346 721268 1 80 54.70 8.10e-10 46 gene - Contig2 718786 718708 1 80 54.48 9.29e-10 43 gene - Contig2 722078 722000 1 80 52.58 2.96e-09 41 gene - Contig2 723071 722993 1 80 52.58 2.96e-09 41 gene - Contig2 718291 718213 1 80 52.50 3.11e-09 42 gene - Contig2 718539 718461 1 80 52.50 3.11e-09 42 gene - Contig2 719033 718955 1 80 52.50 3.11e-09 42 gene - Contig2 719533 719455 1 80 52.50 3.11e-09 42 gene - Contig2 720024 719946 1 80 52.50 3.11e-09 42 gene - Contig2 720271 720193 1 80 52.50 3.11e-09 42 gene - Contig2 721590 721512 1 80 52.50 3.11e-09 42 gene - Contig2 718045 717967 1 80 52.33 3.46e-09 42 gene - Contig2 721834 721756 1 80 52.33 3.46e-09 42 gene - Contig2 907373 907451 1 80 51.21 6.89e-09 46 gene - Contig2 720759 720681 1 80 48.20 4.34e-08 43 gene - Contig2 721102 721024 1 80 48.20 4.34e-08 43 gene - Contig2 719777 719699 1 80 48.16 4.43e-08 42 gene - Contig28 401901 401979 1 80 47.73 5.79e-08 47 pseudo - Contig2 722824 722746 1 80 47.67 5.99e-08 46 gene - Contig2 723315 723237 1 80 47.67 5.99e-08 46 gene - Contig2 906465 906543 1 80 44.06 5.46e-07 52 pseudo - Contig88 241143 241052 1 80 23.74 1.38e-01 50 NO - #=========== Haemonchus contortus: 4 genes contig043130 475 399 1 80 55.63 2.58e-10 43 gene - contig025547 1209 1285 1 80 55.39 3.00e-10 44 gene - contig033048 781 859 1 80 35.84 4.73e-05 46 gene - contig071712 344 420 1 80 33.71 1.73e-04 55 gene - contig059341 2619 2691 1 80 25.89 2.08e-02 47 NO - #=========== Heterodera glycines: 2 genes gi|170548577|gb|ABLA01022309.1| 286 366 1 80 32.01 4.26e-04 51 gene - gi|170550871|gb|ABLA01020015.1| 643 564 1 80 31.84 4.74e-04 44 gene - gi|170563973|gb|ABLA01006937.1| 2244 2326 1 80 22.75 1.24e-01 45 NO - #=========== Meloidogyne hapla: 1 gene Mh10g200708_Contig1500 18638 18562 1 80 34.63 5.62e-05 51 gene - Mh10g200708_Contig601 23850 23932 1 80 23.13 6.41e-02 40 NO - #=========== Meloidogyne incognita: 1 gene CABB01001438; 774 851 1 80 31.86 4.74e-04 45 gene - CABB01000427; 1847 1919 1 80 25.21 2.78e-02 40 NO - #=========== Ascaris suum: 5 genes Contig5095.1 369 291 1 80 62.52 1.16e-11 51 gene - AUAC-aaf40h12.b1 295 221 1 80 49.86 2.70e-08 57 gene - AUAC-aae50e10.b1 615 541 1 80 48.29 7.08e-08 60 gene - AUAC-aac93a10.b1 191 114 1 80 43.57 1.27e-06 56 gene - Contig6576.2 644 572 1 80 43.13 1.66e-06 51 gene - AUAC-aaa36h01.b1 471 553 1 80 24.18 1.82e-01 58 NO - #=========== Brugia malayi: 1 gene gi|154231291|gb|AAQA01004525.1| 623 545 1 80 53.91 7.10e-10 57 gene - gi|154235617|gb|AAQA01000199.1| 44099 44020 1 80 46.98 4.94e-08 57 dup - gi|154235690|gb|AAQA01000126.1| 31399 31319 1 80 20.31 6.08e-01 40 NO -