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Table 26 Top entropy hits in B. subtilis reverse strand

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

B. subtilis Start End Strand Upstream operon Upstream gene Dist. to upstream MFE MFE p. Val. GC RND RND p. Val. Uracil Dist. to downstream Downstream gene Downstream operon Probability
200 nt 3717398 3717597 reverse BSU36100 ywrD -1637 -51.30 - 0.3650 130.8540039 - 0.3950 399 cotH BSU36060 0.9702541828
200 nt 3717498 3717697 reverse BSU36100 ywrD -1537 -50.60 - 0.3500 129.2720032 - 0.4000 499 cotH BSU36060 0.9603169560
200 nt 4066209 4066408 reverse BSU39600 yxeC -299 -67.50 - 0.4900 125.4860001 - 0.3650 799 yxeF BSU39570 0.9434255362
200 nt 786306 786505 reverse BSU07220 yetL -3247 -72.30 - 0.5600 125.9049988 - 0.3050 499 yetH BSU07160 0.9432973266
200 nt 2249144 2249343 reverse BSU21440 bdbB -15982 -49.00 - 0.3700 127.3170013 - 0.3850 1699 youB BSU21329 0.9216341376
200 nt 2596201 2596400 reverse BSU25170 yqfO -1202 -42.96 - 0.3650 129.5290070 - 0.4950 799 cshB BSU25140 0.9206426144
200 nt 3717298 3717497 reverse BSU36100 ywrD -1737 -45.43 - 0.3750 128.8240051 - 0.4200 299 cotH BSU36060 0.9199228883
200 nt 3671576 3671775 reverse BSU35700 tagH -1889 -33.00 - 0.2350 128.6049957 - 0.4550 299 ggaA BSU35690 0.9113640189
200 nt 3717598 3717797 reverse BSU36100 ywrD -1437 -50.50 - 0.3850 126.3860016 - 0.4350 599 cotH BSU36060 0.9073441625
200 nt 3373949 3374148 reverse BSU32890 yusQ -2569 -67.60 - 0.4800 122.0930023 - 0.3600 399 fadM BSU32850 0.8957566023
200 nt 3666584 3666783 reverse BSU35680 ggaB -526 -44.06 - 0.3300 126.5329971 - 0.4650 1299 mnaA BSU35660 0.8957416415
200 nt 3941142 3941341 reverse BSU38430 gspA -3319 -43.33 - 0.3950 128.7100067 - 0.4800 1599 ywbA BSU38390 0.8889677525
200 nt 2879134 2879333 reverse BSU28190 engB -649 -38.80 - 0.2800 126.4779968 - 0.4100 99 hemA BSU28170 0.8852627277
200 nt 3907615 3907814 reverse BSU38100 ywcH -2588 -46.12 - 0.2950 123.9560013 - 0.3600 399 ywcI BSU38080 0.8837128878
200 nt 1248822 1249021 reverse BSU11740 cotZ -521 -54.90 - 0.5300 128.1889954 - 0.4000 8799 yjbP BSU11630 0.8796436787
200 nt 2004047 2004246 reverse BSU18400 yoeD -116 -40.10 - 0.3150 126.8629990 - 0.3900 199 yoeC BSU18390 0.8789740205
200 nt 3671676 3671875 reverse BSU35700 tagH -1789 -35.80 - 0.2600 126.5380020 - 0.3900 399 ggaA BSU35690 0.8741892576
200 nt 2257744 2257943 reverse BSU21440 bdbB -7382 -38.35 - 0.3350 128.0359955 - 0.4600 10299 youB BSU21329 0.8739098310
200 nt 2294238 2294437 reverse BSU21800 ypkP -1645 -57.60 - 0.3900 122.0520020 - 0.3950 299 ilvA BSU21770 0.8724481463
200 nt 791156 791355 reverse BSU07240 yetN -207 -70.84 - 0.5850 123.2480011 - 0.2900 1099 yetL BSU07220 0.8711011410
200 nt 494742 494941 reverse BSU04430 ydbD -899 -52.90 - 0.4250 125.0230026 - 0.4350 1399 ydaT BSU04380 0.8695754409
200 nt 1355092 1355291 reverse BSU12900 htrA -2745 -71.91 - 0.5400 121.2139969 - 0.3050 2499 ykbA BSU12860 0.8692007065
200 nt 737924 738123 reverse BSU06740 yefB -972 -70.30 - 0.5400 121.8629990 - 0.3150 5199 yerO BSU06700 0.8691427112
200 nt 937998 938197 reverse BSU08700 ygaE -3071 -54.20 - 0.4350 124.7170029 - 0.4200 1099 yfhS BSU08640 0.8665797114
200 nt 3421066 3421265 reverse BSU33340 sspJ -300 -64.50 - 0.4850 122.1780014 - 0.3150 99 lysP BSU33330 0.8648849726
200 nt 2739937 2740136 reverse BSU26830 yrpE -1321 -49.69 - 0.4200 125.9660034 - 0.3800 3499 aadK BSU26790 0.8648592830
200 nt 1097850 1098049 reverse BSU10230 yhfH -171 -36.90 - 0.2550 125.4639969 - 0.4450 99 gltT BSU10220 0.8626419306
200 nt 3851617 3851816 reverse BSU37520 ywhD -470 -68.42 - 0.5500 122.7009964 - 0.3000 2099 speE BSU37500 0.8624630570
200 nt 2724828 2725027 reverse BSU26660 yrdN -187 -37.44 - 0.2200 124.0479965 - 0.3800 99 czcD BSU26650 0.8623370528
200 nt 1204503 1204702 reverse BSU11270 yjzD -129 -59.84 - 0.5050 124.6380005 - 0.3600 13299 yitU BSU11140 0.8622197509
200 nt 2692345 2692544 reverse BSU26240 yqaO -201 -47.40 - 0.3350 123.8980026 - 0.4100 999 yqaQ BSU26220 0.8618891239
200 nt 3108926 3109125 reverse BSU30370 bceB -372 -32.52 - 0.3250 129.4949951 - 0.5250 599 yttB BSU30350 0.8596788645
200 nt 1493525 1493724 reverse BSU14250 yknT -779 -39.60 - 0.2150 122.8750000 - 0.4750 1599 ykuT BSU14210 0.8589127660
200 nt 2111609 2111808 reverse BSU19380 yojO -129 -37.20 - 0.2700 125.5370026 - 0.4050 99 sucA BSU19370 0.8542534709
200 nt 1678852 1679051 reverse BSU17060 ymzD -101667 -62.81 - 0.4750 122.0299988 - 0.3300 7299 ylqB BSU15960 0.8517054319
200 nt 4109617 4109816 reverse BSU40030 yxaB -1233 -52.14 - 0.3400 121.7229996 - 0.3900 99 yxaD BSU40010 0.8503260016
200 nt 3373849 3374048 reverse BSU32890 yusQ -2669 -56.90 - 0.5000 125.1539993 - 0.3500 299 fadM BSU32850 0.8485122919
200 nt 1886780 1886979 reverse BSU17590 xylR -3633 -42.30 - 0.3150 124.7409973 - 0.3500 13299 cwlC BSU17410 0.8470579386
200 nt 3153718 3153917 reverse BSU30850 ytdA -918 -51.80 - 0.3600 122.3779984 - 0.3500 99 menF BSU30830 0.8457853198
200 nt 984466 984665 reverse BSU09120 yhcK -1169 -40.11 - 0.2800 124.3939972 - 0.3750 99 cspB BSU09100 0.8457109332
200 nt 3464551 3464750 reverse BSU33780 sdpI -1784 -40.60 - 0.3100 125.1740036 - 0.4450 1399 opuBA BSU33730 0.8446103930
200 nt 3684271 3684470 reverse BSU35780 lytD -456 -43.90 - 0.3450 125.0149994 - 0.3500 3399 tagD BSU35740 0.8443253636
200 nt 2770775 2770974 reverse BSU27160 cypB -3016 -41.20 - 0.3550 126.4410019 - 0.4050 2199 yrhP BSU27100 0.8441781402
200 nt 1666288 1666487 reverse BSU15960 ylqB -4779 -56.60 - 0.4500 123.3949966 - 0.3650 10599 rpmB BSU15820 0.8431691527
200 nt 2343862 2344061 reverse BSU22330 ypoC -303 -43.50 - 0.3800 126.2779999 - 0.4850 3199 yppC BSU22300 0.8418609500
200 nt 3158854 3159053 reverse BSU30890 ytxO -305 -56.71 - 0.4200 122.1419983 - 0.3650 3399 ytdA BSU30850 0.8375009298
200 nt 4129648 4129847 reverse BSU40200 yydD -831 -66.70 - 0.5050 120.9280014 - 0.3350 2099 yydF BSU40180 0.8359215260
200 nt 4134175 4134374 reverse BSU40230 yydA -162 -30.70 - 0.2450 126.6350021 - 0.3400 99 yydB BSU40220 0.8344783783
200 nt 245362 245561 reverse BSU02340 gltP -8057 -57.10 - 0.4500 122.8600006 - 0.3500 1799 ybfI BSU02220 0.8332447410
200 nt 3996389 3996588 reverse BSU38970 yxjF -4051 -40.50 - 0.3750 126.9710007 - 0.4250 4899 yxkA BSU38870 0.8313001394
200 nt 2739837 2740036 reverse BSU26830 yrpE -1421 -64.40 - 0.4950 121.3069992 - 0.3300 3399 aadK BSU26790 0.8294041157
200 nt 1903178 1903377 reverse BSU17690 yncM -234 -35.20 - 0.2700 125.4830017 - 0.4250 1899 cotU BSU17670 0.8289884329
200 nt 933665 933864 reverse BSU08620 yfhP -693 -62.04 - 0.4700 121.3809967 - 0.3750 5499 sspK BSU08550 0.8283531070
200 nt 2054430 2054629 reverse BSU18840 xynA -70 -52.10 - 0.3850 122.5159988 - 0.3450 599 pps BSU18830 0.8281581998
200 nt 737824 738023 reverse BSU06740 yefB -1072 -69.00 - 0.5350 120.7480011 - 0.3100 5099 yerO BSU06700 0.8277365565
200 nt 198226 198425 reverse BSU01800 alkA -4222 -30.81 - 0.3750 130.7449951 - 0.5150 4299 ybbK BSU01720 0.8267450333
200 nt 3604668 3604867 reverse BSU35100 yvlD -1995 -39.30 - 0.2750 123.9219971 - 0.3550 199 yvmC BSU35070 0.8267388940
200 nt 3098465 3098664 reverse BSU30310 ytwF -3637 -48.30 - 0.3850 123.9609985 - 0.4100 1999 ytaP BSU30250 0.8252500296
200 nt 419514 419713 reverse BSU03690 yczF -150 -54.00 - 0.4400 123.4860001 - 0.3300 1899 dtpT BSU03670 0.8242135644
200 nt 2221888 2222087 reverse BSU21080 yonI -6769 -36.60 - 0.3550 127.6279984 - 0.3150 599 yonR BSU21020 0.8236665726
200 nt 2434023 2434222 reverse BSU23340 ypuB -21 -56.65 - 0.4750 123.5520020 - 0.3050 599 ypzJ BSU23328 0.8226841688
200 nt 3241980 3242179 reverse BSU31590 yufS -4073 -57.60 - 0.4600 122.6460037 - 0.3500 5099 yufK BSU31510 0.8222519755
200 nt 1700752 1700951 reverse BSU17060 ymzD -79767 -52.70 - 0.4300 123.5100021 - 0.3150 29199 ylqB BSU15960 0.8189544678
200 nt 2709820 2710019 reverse BSU26490 yrkJ -83 -48.40 - 0.3600 122.8440018 - 0.3550 499 yrkK BSU26480 0.8178487420
200 nt 153939 154138 reverse BSU01550 gerD -4477 -50.70 - 0.4100 123.6019974 - 0.3700 108899 abrB BSU00370 0.8176639676
200 nt 3239080 3239279 reverse BSU31590 yufS -6973 -58.30 - 0.4150 120.6800003 - 0.3750 2199 yufK BSU31510 0.8171101809
200 nt 3467327 3467526 reverse BSU33800 opuCD -120 -32.10 - 0.2350 125.1719971 - 0.3550 99 sdpR BSU33790 0.8168275952
200 nt 543114 543313 reverse BSU05000 yddK -2953 -43.99 - 0.3600 124.5599976 - 0.4700 11699 immR BSU04820 0.8156080246
200 nt 3108826 3109025 reverse BSU30370 bceB -472 -37.52 - 0.3400 126.4919968 - 0.4900 499 yttB BSU30350 0.8153505921
200 nt 3334388 3334587 reverse BSU32470 pucE -1264 -54.50 - 0.4850 124.4670029 - 0.3050 5899 pucH BSU32410 0.8130649924
200 nt 3684371 3684570 reverse BSU35780 lytD -356 -42.00 - 0.3250 124.1009979 - 0.3650 3499 tagD BSU35740 0.8130072355
200 nt 881307 881506 reverse BSU08120 yfjF -4438 -52.36 - 0.4850 125.3059998 - 0.3900 9099 yfjQ BSU08000 0.8121696115
200 nt 2926798 2926997 reverse BSU28630 pheT -111 -60.46 - 0.4950 122.2929993 - 0.3200 999 yshA BSU28610 0.8096395731
200 nt 4066309 4066508 reverse BSU39600 yxeC -199 -55.60 - 0.4600 123.0559998 - 0.3600 899 yxeF BSU39570 0.8090547919
200 nt 3688648 3688847 reverse BSU35830 ywtG -3786 -49.93 - 0.3300 120.9260025 - 0.3550 199 yvyI BSU35790 0.8084035516
200 nt 1668788 1668987 reverse BSU15960 ylqB -2279 -51.60 - 0.4050 122.7809982 - 0.4150 13099 rpmB BSU15820 0.8080439568
200 nt 3334288 3334487 reverse BSU32470 pucE -1364 -62.06 - 0.4700 120.7320023 - 0.2950 5799 pucH BSU32410 0.8073683381
200 nt 3723732 3723931 reverse BSU36170 ywqL -589 -55.50 - 0.4550 122.8669968 - 0.3300 499 ywqN BSU36150 0.8070057034
200 nt 899787 899986 reverse BSU08340 padR -9312 -54.60 - 0.3900 121.0039978 - 0.3550 10199 yfjA BSU08170 0.8061554432
200 nt 2813434 2813633 reverse BSU27540 yrvM -110 -48.20 - 0.3850 123.3710022 - 0.4200 1399 cymR BSU27520 0.8043378592
200 nt 3458216 3458415 reverse BSU33700 opuBD -1491 -44.09 - 0.3500 123.8420029 - 0.4200 1799 yvzC BSU33650 0.8041363358
200 nt 3918262 3918461 reverse BSU38190 galT -732 -37.50 - 0.2900 124.4739990 - 0.3100 99 qoxA BSU38170 0.8040998578
200 nt 2576788 2576987 reverse BSU24950 pstBB -323 -53.30 - 0.3700 120.7910004 - 0.4100 699 yqgL BSU24920 0.8040402532
200 nt 2316211 2316410 reverse BSU22040 ypbQ -136 -50.40 - 0.3350 120.7730026 - 0.3850 199 ypbR BSU22030 0.8038558364
200 nt 2249344 2249543 reverse BSU21440 bdbB -15782 -43.38 - 0.3500 124.1179962 - 0.4650 1899 youB BSU21329 0.8037469983
200 nt 2333112 2333311 reverse BSU22210 yprB -113 -43.21 - 0.3300 123.4840012 - 0.4200 199 cotD BSU22200 0.8028732538
200 nt 2116670 2116869 reverse BSU19420 yojK -282 -43.45 - 0.3300 123.3679962 - 0.3150 99 cwlS BSU19410 0.8022140265
200 nt 3941242 3941441 reverse BSU38430 gspA -3219 -42.84 - 0.4300 126.9950027 - 0.4600 1699 ywbA BSU38390 0.8019362092
200 nt 1248722 1248921 reverse BSU11740 cotZ -621 -64.39 - 0.5300 121.6650009 - 0.3550 8699 yjbP BSU11630 0.8019282818
200 nt 3014345 3014544 reverse BSU29460 moaB -70 -39.90 - 0.2550 122.2269974 - 0.3300 99 argG BSU29450 0.8009542227
200 nt 2542225 2542424 reverse BSU24510 yqhO -115 -57.14 - 0.4800 122.8730011 - 0.4100 1499 yqhR BSU24480 0.8008475304
200 nt 2096086 2096285 reverse BSU19230 yocJ -165 -39.50 - 0.2800 123.2190018 - 0.4150 399 yocI BSU19220 0.8003621101
200 nt 4107928 4108127 reverse BSU40010 yxaD -1158 -51.01 - 0.4150 123.1330032 - 0.3800 99 yxaF BSU39990 0.8002312183
200 nt 2659771 2659970 reverse BSU25880 yqxJ -3681 -49.60 - 0.3800 122.5149994 - 0.3600 1099 yqcI BSU25820 0.8001416922
  1. Significant hits of the forward and reverse strands (only showing reverse strand here) of the B. subtilis intergenic regions having significantly high RND entropy (p-Val. <0.0500) and LMFEGCRND probability higher than 0.8. 100 nt overlap used for 200 nt scan (44847 segments). 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. Negative values indicate distance to upstream operon. Columns Upsream/Downstream Operon show gene ID within the operon.
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