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Table 22 Top classification hits in B. subtilis

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

R Start End Strand Upstream operon Upstream gene Dist. to upstream Uracil Dist. to downstream Downstream gene Downstream operon Probability
1 3717569 3717725 reverse BSU36100 ywrD -1486 0.4076 550 cotH BSU36060 0.943
2 3717412 3717568 reverse BSU36100 ywrD -1643 0.4076 393 cotH BSU36060 0.935
3 4134175 4134331 reverse BSU40230 yydA -182 0.3439 79 yydB BSU40220 0.931
4 3714883 3715039 forward BSU36030 ywrK -859 0.3949 2277 cotG BSU36070 0.922
5 748990 749146 forward BSU06780 yeeC -2912 0.414 707 yeeG BSU06820 0.919
6 3666640 3666796 reverse BSU35680 ggaB -490 0.4968 1335 mnaA BSU35660 0.908
7 3866327 3866483 reverse BSU37690 ywfG -1881 0.3503 79 eutD BSU37660 0.903
8 681153 681309 forward BSU06260 ydjN -201 0.3885 5731 yeaB BSU06320 0.899
9 2987548 2987704 reverse BSU29200 accA -104 0.4268 79 pfkA BSU29190 0.898
10 1680274 1680430 forward BSU16080 ylqH 63 0.3822 79 sucC BSU16090 0.897
11 2730227 2730383 reverse BSU26730 yrdF -254 0.4204 79 azlB BSU26720 0.896
12 2316268 2316424 reverse BSU22040 ypbQ -99 0.363 236 ypbR BSU22030 0.896
13 2219985 2220141 forward BSU20929 yoyI -6828 0.4204 2277 yonP BSU21030 0.896
14 688027 688183 forward BSU06320 yeaB -114 0.3885 79 yeaC BSU06330 0.893
15 243578 243734 forward BSU02170 ybfB -5370 0.363 236 purT BSU02230 0.89
16 984466 984622 reverse BSU09120 yhcK -1189 0.3885 79 cspB BSU09100 0.889
17 2376780 2376936 forward BSU22510 ypjC -15199 0.4395 16564 ypzI BSU22869 0.888
18 748205 748361 forward BSU06780 yeeC -2127 0.4395 1492 yeeG BSU06820 0.886
19 3421066 3421222 reverse BSU33340 sspJ -320 0.3312 79 lysP BSU33330 0.885
20 2093235 2093391 forward BSU19200 desR -852 0.4331 4789 yoyB BSU19259 0.88
21 3941212 3941368 reverse BSU38430 gspA -3269 0.4777 1649 ywbA BSU38390 0.879
22 1493630 1493786 forward BSU14230 ykuV -230 0.3503 79 rok BSU14240 0.879
23 2531945 2532101 forward BSU24210 yqiG -14308 0.3439 9028 yqhQ BSU24490 0.879
24 746478 746634 forward BSU06780 yeeC -400 0.5095 3219 yeeG BSU06820 0.878
25 2096100 2096256 reverse BSU19230 yocJ -171 0.4268 393 yocI BSU19220 0.877
26 300673 300829 forward BSU02770 yccK -1196 0.3822 79 ycdB BSU02790 0.875
27 3373963 3374119 reverse BSU32890 yusQ -2575 0.4076 393 fadM BSU32850 0.874
28 3686143 3686299 forward BSU35770 tagC -1298 0.4586 2591 gerBA BSU35800 0.87
29 1335487 1335643 reverse BSU12820 spoIISB -12876 0.5032 13895 xre BSU12510 0.868
30 4139318 4139474 forward BSU40240 yycS -3475 0.3567 864 rapG BSU40300 0.865
31 1268672 1268828 forward BSU11970 yjcS -1 0.4458 79 yjdA BSU11980 0.865
32 3685829 3685985 forward BSU35770 tagC -984 0.414 2905 gerBA BSU35800 0.865
33 3681213 3681369 forward BSU35670 gtaB -14627 0.363 79 tagA BSU35750 0.864
34 1122705 1122861 forward BSU10490 sipV 55 0.4013 79 yhjG BSU10500 0.86
35 3671690 3671846 reverse BSU35700 tagH -1795 0.3694 393 ggaA BSU35690 0.859
36 2160701 2160857 forward BSU20000 yosU -1938 0.4395 9028 yosA BSU20190 0.859
37 1097850 1098006 reverse BSU10230 yhfH -191 0.465 79 gltT BSU10220 0.858
38 1467020 1467176 forward BSU13960 ykwC -342 0.414 707 pbpH BSU13980 0.857
39 191850 192006 forward BSU01590 ybaS -12186 0.3057 2277 trnSL-Glu2 BSU_tRNA_75 0.856
40 20723 20879 forward BSU00120 yaaE -86 0.3185 79 serS BSU00130 0.856
41 2691445 2691601 reverse BSU26240 yqaO -1121 0.3439 79 yqaQ BSU26220 0.852
42 3158851 3159007 reverse BSU30890 ytxO -328 0.363 3376 ytdA BSU30850 0.852
43 1958206 1958362 forward BSU18190 yngC -9863 0.3949 44353 iseA BSU18380 0.852
44 557716 557872 forward BSU05100 yddT -188 0.3503 79 ydzN BSU05109 0.851
45 3907629 3907785 reverse BSU38100 ywcH -2594 0.3567 393 ywcI BSU38080 0.851
46 1926523 1926679 forward BSU17950 yneJ -1482 0.3949 79 citB BSU18000 0.851
47 1017271 1017427 forward BSU09400 spoVR -139 0.363 1649 lytE BSU09420 0.85
48 1493595 1493751 reverse BSU14250 yknT -729 0.4522 1649 ykuT BSU14210 0.85
49 2477743 2477899 forward BSU23830 yqjL 66 0.4076 1335 zwf BSU23850 0.849
50 2769617 2769773 reverse BSU27160 cypB -4194 0.3185 1021 yrhP BSU27100 0.849
51 2739991 2740147 reverse BSU26830 yrpE -1287 0.3694 3533 aadK BSU26790 0.849
52 644384 644540 forward BSU05940 gcp -7 0.3694 2120 moaC BSU05960 0.848
53 4039599 4039755 forward BSU39100 yxiO -23552 0.4713 1806 hutP BSU39340 0.847
54 2203622 2203778 forward BSU20580 yoqM -7279 0.363 79 yopS BSU20780 0.847
55 3014345 3014501 reverse BSU29460 moaB -90 0.3694 79 argG BSU29450 0.847
56 749147 749303 forward BSU06780 yeeC -3069 0.363 550 yeeG BSU06820 0.846
57 665425 665581 forward BSU06130 ydjC -677 0.3439 1963 gutB BSU06150 0.846
58 2106272 2106428 reverse BSU19360 odhB -1154 0.3949 79 yocR BSU19340 0.846
59 226409 226565 forward BSU02050 ybdO -82 0.3885 79 ybxG BSU02060 0.844
60 2106333 2106489 forward BSU19330 sodF -1353 0.3885 79 yocS BSU19350 0.844
61 308175 308331 forward BSU02840 ycdG 48 0.3503 79 adcA BSU02850 0.843
62 2678925 2679081 forward BSU26050 yqdB -427 0.363 12639 yqaP BSU26230 0.843
63 3875571 3875727 reverse BSU37760 rocC -130 0.3121 79 ywfA BSU37750 0.843
64 2433680 2433836 reverse BSU23340 ypuB -384 0.3885 236 ypzJ BSU23328 0.843
65 2879134 2879290 reverse BSU28190 engB -669 0.4013 79 hemA BSU28170 0.842
66 1533806 1533962 forward BSU14610 pdhD -445 0.3503 236 ykzW BSU14629 0.841
67 368137 368293 forward BSU03360 yciC -802 0.3312 1021 yckC BSU03390 0.841
68 447000 447156 forward BSU03930 gdh -792 0.3121 2120 ycnL BSU03970 0.84
69 3726630 3726786 forward BSU36160 ywqM -2216 0.4331 7144 ywqB BSU36270 0.84
70 543132 543288 reverse BSU05000 yddK -2955 0.4904 11697 immR BSU04820 0.84
71 3268320 3268476 forward BSU31810 yuzE -4017 0.4522 8557 yukF BSU31920 0.84
72 2065804 2065960 forward BSU18960 yozM -348 0.3758 8557 yobN BSU19020 0.839
73 45296 45452 reverse BSU01550 gerD -113140 0.3822 236 abrB BSU00370 0.837
74 2048779 2048935 reverse BSU18810 yobA -1092 0.363 550 yoaZ BSU18790 0.836
75 3153718 3153874 reverse BSU30850 ytdA -938 0.3439 79 menF BSU30830 0.836
76 3388260 3388416 reverse BSU33040 fumC -685 0.3312 393 yuzO BSU33029 0.834
77 205252 205408 forward BSU01820 adaB -283 0.3248 79 ndhF BSU01830 0.834
78 469269 469425 forward BSU04160 mtlR 24 0.3121 79 ydaB BSU04170 0.834
79 1868460 1868616 forward BSU17360 ymzA -7 0.3885 79 nrdI BSU17370 0.834
80 3746069 3746225 forward BSU36380 rapD -577 0.3822 2905 ywoH BSU36440 0.833
81 3467327 3467483 reverse BSU33800 opuCD -140 0.3376 79 sdpR BSU33790 0.832
82 1264932 1265088 reverse BSU11990 yjdB -4722 0.5223 79 yjcM BSU11910 0.832
83 1903262 1903418 reverse BSU17690 yncM -170 0.3822 1963 cotU BSU17670 0.831
84 4204441 4204597 reverse BSU40960 parB -1036 0.414 79 yyaD BSU40940 0.831
85 1017114 1017270 forward BSU09400 spoVR 18 0.3376 1806 lytE BSU09420 0.831
86 2709577 2709733 reverse BSU26490 yrkJ -346 0.3503 236 yrkK BSU26480 0.829
87 955738 955894 forward BSU08780 ygaJ -74 0.3822 79 thiC BSU08790 0.828
88 554386 554542 reverse BSU05130 ydeB -5686 0.4395 1963 lrpB BSU05060 0.828
89 3988764 3988920 reverse BSU38860 galE -1105 0.293 79 yxkD BSU38840 0.825
90 2186812 2186968 reverse BSU20420 yorD -94 0.2611 79 yorE BSU20410 0.825
91 2926840 2926996 reverse BSU28630 pheT -89 0.3185 1021 yshA BSU28610 0.823
92 2054401 2054557 reverse BSU18840 xynA -119 0.3822 550 pps BSU18830 0.822
93 610963 611119 reverse BSU05660 ydgI -1149 0.3121 2277 dinB BSU05630 0.822
94 3457144 3457300 reverse BSU33700 opuBD -2583 0.3185 707 yvzC BSU33650 0.821
95 736435 736591 reverse BSU06740 yefB -2481 0.3376 3690 yerO BSU06700 0.82
96 2061478 2061634 reverse BSU18930 yobH -1953 0.3439 864 yozJ BSU18900 0.82
97 2262616 2262772 reverse BSU21440 bdbB -2530 0.3885 15151 youB BSU21329 0.819
98 4118717 4118873 reverse BSU40110 bglA -2370 0.3758 5574 glxK BSU40040 0.818
99 4204755 4204911 reverse BSU40960 parB -722 0.3949 393 yyaD BSU40940 0.818
100 3648264 3648420 reverse BSU35530 tagO -311 0.363 1806 degS BSU35500 0.818
  1. Top 50 hits of the forward and reverse strands of the B. subtilis intergenic regions using no-overlap 157 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.
  2. Interesting hits are shown in bold.