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Table 31 Top classification hits in S. elongatus

From: Secondary structural entropy in RNA switch (Riboswitch) identification

R Start End Strand Upstream operon Dist. to upstream Uracil Dist. to downstream Downstream operon Probability
1 2239899 2240048 forward psbV -2288 0.34666 1277 coaD 0.9169
2 1788275 1788424 reverse syc1657_c -1875 0.19333 5099 syc1649_c 0.9156
3 1673354 1673503 forward accB -811 0.22666 3377 desC 0.9078
4 734659 734808 forward syc0660_d -635 0.24666 8177 syc0665_d 0.9004
5 1108388 1108537 reverse lacF -1124 0.41333 1124 devB 0.8967
6 838999 839148 forward gst1 -2009 0.20666 2552 hisG 0.8906
7 734734 734883 forward syc0660_d -710 0.28 8102 syc0665_d 0.886
8 1674179 1674328 forward accB -1636 0.28 2552 desC 0.8857
9 936254 936403 forward syc0839_d -190 0.26 77 syc0840_d 0.8855
10 1706450 1706599 forward syc1578_d -2580 0.28 5252 gpsA 0.8834
11 2686971 2687120 reverse syc2516_c -462 0.24666 674 ycf49 0.8809
12 464795 464944 forward syc0415_d -1330 0.46 377 syc0416_d 0.8784
13 546798 546947 reverse syc0485_c -190 0.26666 74 syc0484_c 0.8778
14 1527281 1527430 reverse holB -916 0.34 6674 syc1405_c 0.8749
15 2251075 2251224 reverse masA -985 0.25333 674 syc2098_c 0.8741
16 590779 590928 reverse syc0539_c -11831 0.2 2624 syc0528_c 0.8733
17 1870479 1870628 forward syc1725_d -722 0.21333 5102 syc1732_d 0.873
18 2098418 2098567 forward sui1 -7782 0.27333 2252 dapB 0.8715
19 793922 794071 reverse asnS -1542 0.46666 224 syc0707_c 0.8703
20 1218955 1219104 reverse trpF -430 0.34 1799 sycRNA024_c 0.8703
21 1751997 1752146 reverse syc1625_c -3772 0.32666 3899 syc1619_c 0.8691
22 1526981 1527130 reverse holB -1216 0.32 6374 syc1405_c 0.8686
23 1120163 1120312 reverse syc1011_c -4710 0.22 3749 syc1002_c 0.8684
24 69102 69251 reverse syc0062_c -2424 0.18666 974 syc0058_c 0.8668
25 132050 132199 reverse argC -633 0.21333 7724 syc0114_c 0.8668
26 1348202 1348351 reverse syc1238_c -2618 0.22 1049 syc1235_c 0.8666
27 1674104 1674253 forward accB -1561 0.26666 2627 desC 0.8663
28 479806 479955 forward syc0423_d -3318 0.34666 302 syc0428_d 0.8656
29 2009813 2009962 forward syc1856_d 36 0.29333 1352 syc1859_d 0.8647
30 1674554 1674703 forward accB -2011 0.27333 2177 desC 0.8646
31 1372776 1372925 reverse syc1262_c -154 0.28666 824 gyrA 0.863
32 702997 703146 forward syc0629_d -3402 0.27333 3452 acnB 0.8622
33 1673054 1673203 forward accB -511 0.29333 3677 desC 0.8622
34 971765 971914 reverse priA -1871 0.3 1199 psbDI 0.861
35 2574891 2575040 forward syc2417_d -956 0.21333 6227 syc2423_d 0.8585
36 2033882 2034031 forward prfA 38 0.26 527 alr 0.8579
37 2633236 2633385 forward syc2468_d -1767 0.22666 902 rps4 0.8555
38 2031022 2031171 reverse mrcA -2764 0.22 14249 syc1864_c 0.8549
39 1706375 1706524 forward syc1578_d -2505 0.29333 5327 gpsA 0.8543
40 69327 69476 reverse syc0062_c -2199 0.21333 1199 syc0058_c 0.8532
41 2383320 2383469 forward syc2228_d -2586 0.26 1052 natB 0.8531
42 2162031 2162180 forward syc2015_d -852 0.33333 5402 pilB 0.8527
43 1848963 1849112 forward syc1711_d -916 0.23333 6527 syc1716_d 0.8521
44 437513 437662 forward syc0392_d -5939 0.35333 677 syc0396_d 0.8509
45 1108838 1108987 reverse lacF -674 0.30666 1574 devB 0.8508
46 1763242 1763391 forward syc1627_d -4972 0.26 5027 aroE 0.8504
47 298041 298190 reverse syc0257_c -92 0.40666 224 syc0256_c 0.8502
48 1357802 1357951 reverse uppS -635 0.22 749 gidB 0.8501
49 1674704 1674853 forward accB -2161 0.34666 2027 desC 0.8495
50 2225318 2225467 reverse syc2077_c -5809 0.26666 1724 rfaG 0.8493
51 1967731 1967880 reverse amt1 -197 0.26 974 syc1819_c 0.8483
52 1108913 1109062 reverse lacF -599 0.34666 1649 devB 0.848
53 2664277 2664426 forward syc2500_d -688 0.24666 1502 pcrA 0.8477
54 838924 839073 forward gst1 -1934 0.18 2627 hisG 0.8469
55 1996234 1996383 reverse sycRNA048_c -2339 0.26 4799 syc1843_c 0.8453
56 1674479 1674628 forward accB -1936 0.29333 2252 desC 0.8435
57 1320549 1320698 reverse ssb -269 0.26 1349 syc1209_c 0.8421
58 542490 542639 forward syc0480_d -2611 0.28 19127 syc0503_d 0.8419
59 1089898 1090047 reverse nhaS4 -886 0.2 974 syc0972_c 0.8417
60 2383395 2383544 forward syc2228_d -2661 0.27333 977 natB 0.8416
61 2201969 2202118 reverse syc2052_c -3184 0.32666 3074 gcvH 0.8408
62 2475474 2475623 forward syc2315_d -359 0.28666 4427 syc2322_d 0.8399
63 1910646 1910795 forward psaL -4022 0.21333 752 syc1766_d 0.8391
64 2244572 2244721 forward syc2089_d -2066 0.26 902 syc2094_d 0.8378
65 2202119 2202268 reverse syc2052_c -3034 0.33333 3224 gcvH 0.8378
66 979835 979984 reverse hemL -205 0.31333 149 syc0880_c 0.8371
67 2201519 2201668 reverse syc2052_c -3634 0.32 2624 gcvH 0.8366
68 2436792 2436941 forward htpG -4101 0.35333 3227 syc2285_d 0.8358
69 2379191 2379340 forward syc2225_d -348 0.22666 977 syc2228_d 0.8347
70 751797 751946 forward syc0670_d -2744 0.20666 3527 syc0679_d 0.8335
71 2488156 2488305 forward syc2327_d -3334 0.24666 2402 syc2333_d 0.8333
72 1099747 1099896 forward syc0978_d -5042 0.31333 1727 psaC 0.8327
73 316592 316741 forward moaA -195 0.38 302 syc0272_d 0.8319
74 979910 980059 reverse hemL -130 0.29333 224 syc0880_c 0.8319
75 636787 636936 forward prk -916 0.22 1802 syc0569_d 0.8318
76 1709000 1709149 forward syc1578_d -5130 0.26666 2702 gpsA 0.8317
77 888391 888540 forward syc0774_d -22228 0.19333 14402 syc0808_d 0.8304
78 542940 543089 forward syc0480_d -3061 0.29333 18677 syc0503_d 0.8303
79 1736496 1736645 reverse gyrB -7265 0.24666 1724 aroF 0.83
80 542265 542414 forward syc0480_d -2386 0.28 19352 syc0503_d 0.8299
81 482179 482328 reverse syc0432_c -3508 0.2 2249 rpl33 0.8299
82 882016 882165 forward syc0774_d -15853 0.2 20777 syc0808_d 0.8297
83 2239824 2239973 forward psbV -2213 0.32666 1352 coaD 0.8293
84 55214 55363 forward syc0043_d -1501 0.24666 4802 syc0049_d 0.8292
85 707052 707201 reverse syc0639_c -3061 0.22 824 syc0636_c 0.8292
86 992221 992370 reverse syc0895_c -5003 0.34 2099 eno 0.8289
87 234289 234438 reverse syc0202_c -357 0.38666 149 syc0201_c 0.828
88 1674629 1674778 forward accB -2086 0.29333 2102 desC 0.8278
89 1788200 1788349 reverse syc1657_c -1950 0.16 5024 syc1649_c 0.8273
90 1084661 1084810 reverse nfrC -959 0.21333 449 syc0967_c 0.8273
91 131975 132124 reverse argC -708 0.22 7649 syc0114_c 0.8271
92 632779 632928 reverse petH -327 0.32666 3599 syc0562_c 0.8269
93 2612915 2613064 reverse syc2455_c -5717 0.28666 2624 syc2447_c 0.8266
94 539354 539503 reverse pdhC -603 0.22666 3074 syc0476_c 0.8263
95 2360335 2360484 reverse syc2221_c -10564 0.19333 899 recJ 0.8245
96 503343 503492 reverse syc0452_c -2439 0.26 1274 syc0448_c 0.8242
97 621230 621379 reverse syc0558_c -3271 0.20666 299 syc0552_c 0.8195
98 2077186 2077335 reverse syc1942_c -5748 0.18666 1349 apcF 0.8187
99 971165 971314 reverse priA -2471 0.28 599 psbDI 0.8163
100 1555584 1555733 reverse syc1449_c -12609 0.35333 8549 pepP 0.815
  1. Top 50 hits of the forward and reverse strands of the S. elongatus intergenic regions using 75 nt-overlap 150 nt window and under the LMFEGCRND model. The ranking of each hit is denoted in column R. Distance from upstream and downstream operons are the distance from the center of the hit to the stop and start codons of upstream and downstream operons, respectively. Probability denotes the multinomial regression likelihood of being a riboswitch under the LMFEGCRND model.