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Table 25 Top entropy hits in B. subtilis forward 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 3714838 3715037 forward BSU36030 ywrK -794 -49.70 - 0.3300 126.0619965 - 0.3850 2302 cotG BSU36070 0.9275143743
200 nt 3359769 3359968 forward BSU32650 yurS -5183 -66.40 - 0.4600 123.4530029 - 0.3450 12702 yuzL BSU32849 0.9236087203
200 nt 243592 243791 forward BSU02170 ybfB -5364 -57.00 - 0.4450 126.5479965 - 0.3700 202 purT BSU02230 0.9204539061
200 nt 2093202 2093401 forward BSU19200 desR -799 -55.20 - 0.4350 126.5859985 - 0.4400 4802 yoyB BSU19259 0.9146069884
200 nt 749075 749274 forward BSU06780 yeeC -2977 -58.19 - 0.4450 125.6159973 - 0.3900 602 yeeG BSU06820 0.9128865004
200 nt 1467005 1467204 forward BSU13960 ykwC -307 -60.40 - 0.4100 123.2139969 - 0.4150 702 pbpH BSU13980 0.9070840478
200 nt 2281367 2281566 forward BSU21620 yokE 95 -44.60 - 0.2600 124.4599991 - 0.4300 202 yokD BSU21630 0.9058990479
200 nt 850067 850266 forward BSU07750 yflA -3783 -57.20 - 0.4000 124.1029968 - 0.3800 202 treP BSU07800 0.9058393836
200 nt 1466905 1467104 forward BSU13960 ykwC -207 -56.93 - 0.3900 123.7220001 - 0.4200 802 pbpH BSU13980 0.9029595852
200 nt 3759694 3759893 forward BSU36530 bcrC -467 -62.40 - 0.3850 121.3089981 - 0.4500 902 ywnH BSU36560 0.9023656249
200 nt 3268355 3268554 forward BSU31810 yuzE -4032 -44.66 - 0.3750 127.7630005 - 0.4450 8502 yukF BSU31920 0.8946693540
200 nt 2073039 2073238 forward BSU18960 yozM -7563 -52.00 - 0.3250 123.0869980 - 0.4450 1302 yobN BSU19020 0.8944090009
200 nt 748975 749174 forward BSU06780 yeeC -2877 -58.80 - 0.4750 125.1039963 - 0.3750 702 yeeG BSU06820 0.8876969814
200 nt 432172 432371 forward BSU03780 phrC -1988 -51.70 - 0.3050 122.0960007 - 0.3450 102 yclN BSU03800 0.8850299716
200 nt 4039583 4039782 forward BSU39100 yxiO -23516 -53.00 - 0.4350 125.9430008 - 0.4350 1802 hutP BSU39340 0.8843178153
200 nt 531587 531786 forward BSU_tRNA_51 trnS-Leu2 -2066 -46.60 - 0.2650 122.5979996 - 0.3850 102 sacV BSU04830 0.8803396225
200 nt 665366 665565 forward BSU06130 ydjC -598 -64.50 - 0.4900 122.9229965 - 0.3300 2002 gutB BSU06150 0.8790112138
200 nt 3714938 3715137 forward BSU36030 ywrK -894 -41.70 - 0.3350 126.8040009 - 0.3550 2202 cotG BSU36070 0.8768669963
200 nt 3685812 3686011 forward BSU35770 tagC -947 -51.80 - 0.3900 124.4950027 - 0.4150 2902 gerBA BSU35800 0.8747953176
200 nt 2093302 2093501 forward BSU19200 desR -899 -61.40 - 0.4400 122.2649994 - 0.3700 4702 yoyB BSU19259 0.8738172650
200 nt 1012447 1012646 forward BSU09360 yhdC -598 -51.20 - 0.3650 123.8079987 - 0.4100 3102 spoVR BSU09400 0.8727893829
200 nt 955595 955794 forward BSU08780 ygaJ 89 -59.79 - 0.4050 121.6190033 - 0.3600 202 thiC BSU08790 0.8710888028
200 nt 3685912 3686111 forward BSU35770 tagC -1047 -53.60 - 0.3950 123.7610016 - 0.3950 2802 gerBA BSU35800 0.8705116510
200 nt 4134651 4134850 forward BSU40190 fbp -4508 -58.20 - 0.4900 125.0049973 - 0.3900 602 yycS BSU40240 0.8676616549
200 nt 45433 45632 forward BSU00360 yabC -535 -42.70 - 0.3000 124.7969971 - 0.4200 102 metS BSU00380 0.8666248322
200 nt 2531951 2532150 forward BSU24210 yqiG -14294 -62.90 - 0.5050 123.5699997 - 0.3450 9002 yqhQ BSU24490 0.8666005135
200 nt 2531951 2532150 forward BSU24210 yqiG -14294 -62.90 - 0.5050 123.5699997 - 0.3450 9002 yqhQ BSU24490 0.8666005135
200 nt 1540786 1540985 forward BSU14680 ykzC -1995 -57.52 - 0.4350 123.3629990 - 0.3750 1002 ylaA BSU14710 0.8663020134
200 nt 1406312 1406511 forward BSU13390 ykoT -1721 -71.55 - 0.5450 121.3809967 - 0.3250 3502 ykoX BSU13430 0.8654530644
200 nt 4029283 4029482 forward BSU39100 yxiO -13216 -50.90 - 0.3850 124.3079987 - 0.4000 12102 hutP BSU39340 0.8653051257
200 nt 1526531 1526730 forward BSU14550 ykrA -273 -63.20 - 0.4800 122.5350037 - 0.3350 602 ykyA BSU14570 0.8648978472
200 nt 2220040 2220239 forward BSU20929 yoyI -6863 -38.72 - 0.3800 129.0460052 - 0.3700 2202 yonP BSU21030 0.8647925854
200 nt 192105 192304 forward BSU01590 ybaS -12421 -51.20 - 0.4350 125.8399963 - 0.4100 2002 trnSL-Glu2 BSU_tRNA_75 0.8642573953
200 nt 1780406 1780605 forward BSU17050 mutL -87 -52.60 - 0.3550 122.5059967 - 0.3650 1402 pksA BSU17080 0.8627771139
200 nt 4037783 4037982 forward BSU39100 yxiO -21716 -57.74 - 0.4400 123.2249985 - 0.3950 3602 hutP BSU39340 0.8606380820
200 nt 1264357 1264556 forward BSU_tRNA_83 trnSL-Val2 -1397 -33.05 - 0.2700 127.4010010 - 0.4200 602 yjcN BSU11920 0.8592507839
200 nt 847767 847966 forward BSU07750 yflA -1483 -59.62 - 0.4500 122.6080017 - 0.3550 2502 treP BSU07800 0.8554052114
200 nt 226266 226465 forward BSU02050 ybdO 81 -37.20 - 0.2300 124.2030029 - 0.3550 202 ybxG BSU02060 0.8548350334
200 nt 3052246 3052445 forward BSU29710 acuC -9592 -61.90 - 0.4900 123.0039978 - 0.3400 2402 ytoQ BSU29850 0.8543979526
200 nt 530887 531086 forward BSU_tRNA_51 trnS-Leu2 -1366 -42.20 - 0.3250 125.3190002 - 0.4000 802 sacV BSU04830 0.8526363969
200 nt 2617117 2617316 forward BSU25220 antE -13743 -59.90 - 0.4500 122.3389969 - 0.4200 3502 yqeW BSU25420 0.8511158824
200 nt 2221540 2221739 forward BSU20929 yoyI -8363 -46.30 - 0.2850 122.2210007 - 0.3450 702 yonP BSU21030 0.8502966762
200 nt 2054178 2054377 forward BSU18820 yobB -3127 -48.70 - 0.3450 123.2819977 - 0.4000 2002 yobD BSU18850 0.8502687216
200 nt 3042946 3043145 forward BSU29710 acuC -292 -49.94 - 0.4350 125.8190002 - 0.4150 11702 ytoQ BSU29850 0.8499680161
200 nt 2780909 2781108 forward BSU27150 yrhK -7164 -47.80 - 0.3250 122.8980026 - 0.3750 202 yrhE BSU27220 0.8482846022
200 nt 2723337 2723536 forward BSU26630 yrdQ -594 -44.00 - 0.2950 123.3580017 - 0.4300 2402 gltR BSU26670 0.8465546370
200 nt 683762 683961 forward BSU06260 ydjN -2790 -59.40 - 0.4800 123.3310013 - 0.3600 3102 yeaB BSU06320 0.8446838856
200 nt 3052346 3052545 forward BSU29710 acuC -9692 -56.62 - 0.4400 123.0849991 - 0.3800 2302 ytoQ BSU29850 0.8442399502
200 nt 2405829 2406028 forward BSU22869 ypzI -12171 -60.30 - 0.4650 122.4049988 - 0.4150 3802 fer BSU23040 0.8431282043
200 nt 579341 579540 forward BSU05329 ydzO -10 -47.40 - 0.3850 124.9130020 - 0.3050 102 aseR BSU05330 0.8431255221
200 nt 748875 749074 forward BSU06780 yeeC -2777 -60.60 - 0.4600 122.0989990 - 0.3950 802 yeeG BSU06820 0.8426845670
200 nt 339225 339424 forward BSU03130 nadE -20 -63.60 - 0.4700 121.1809998 - 0.3250 702 aroK BSU03150 0.8414211273
200 nt 1251377 1251576 forward BSU11730 cotO -1930 -35.49 - 0.3200 127.4260025 - 0.4800 702 yjcA BSU11790 0.8401102424
200 nt 3640353 3640552 forward BSU35210 yvkA -19956 -52.60 - 0.3600 121.8539963 - 0.4250 6302 yvyE BSU35510 0.8399478197
200 nt 3686112 3686311 forward BSU35770 tagC -1247 -51.99 - 0.3750 122.5879974 - 0.4300 2602 gerBA BSU35800 0.8393257856
200 nt 3686112 3686311 forward BSU35770 tagC -1247 -51.99 - 0.3750 122.5879974 - 0.4300 2602 gerBA BSU35800 0.8393257856
200 nt 1494405 1494604 forward BSU14240 rok 56 -52.70 - 0.4100 123.4729996 - 0.4150 1002 mobA BSU14260 0.8389207721
200 nt 373532 373731 forward BSU03410 bglC -1741 -56.90 - 0.4500 123.1060028 - 0.3800 2402 hxlR BSU03470 0.8382304311
200 nt 3686212 3686411 forward BSU35770 tagC -1347 -45.70 - 0.4000 125.9280014 - 0.4250 2502 gerBA BSU35800 0.8377878666
200 nt 374532 374731 forward BSU03410 bglC -2741 -56.99 - 0.3750 120.5049973 - 0.3400 1402 hxlR BSU03470 0.8375294805
200 nt 1540186 1540385 forward BSU14680 ykzC -1395 -61.11 - 0.4650 121.7969971 - 0.3500 1602 ylaA BSU14710 0.8347978592
200 nt 360837 361036 forward BSU03270 ycgT -6870 -59.70 - 0.5000 123.5510025 - 0.3300 2002 nasA BSU03330 0.8347288966
200 nt 213641 213840 forward BSU01900 ybcM -73 -36.30 - 0.2750 125.3079987 - 0.3950 202 skfA BSU01910 0.8321032524
200 nt 739678 739877 forward BSU06730 yefA -597 -51.16 - 0.3900 123.1309967 - 0.4150 102 yefC BSU06750 0.8301935792
200 nt 1495005 1495204 forward BSU14240 rok -544 -50.26 - 0.4150 124.2959976 - 0.3800 402 mobA BSU14260 0.8287579417
200 nt 1541686 1541885 forward BSU14680 ykzC -2895 -43.10 - 0.3250 124.1309967 - 0.3650 102 ylaA BSU14710 0.8283772469
200 nt 1268629 1268828 forward BSU11970 yjcS 62 -40.70 - 0.2700 123.2060013 - 0.4250 102 yjdA BSU11980 0.8273611665
200 nt 652232 652431 forward BSU06030 groEL -265 -37.70 - 0.2950 125.2659988 - 0.4500 1102 ydiM BSU06040 0.8273396492
200 nt 2108093 2108292 forward BSU19350 yocS -539 -59.80 - 0.4700 122.2429962 - 0.3700 11202 yojI BSU19440 0.8269666433
200 nt 728532 728731 forward BSU06640 yerI -2436 -46.30 - 0.3100 122.2779999 - 0.3600 102 gatC BSU06670 0.8268005848
200 nt 1540686 1540885 forward BSU14680 ykzC -1895 -60.72 - 0.4350 120.6729965 - 0.3350 1102 ylaA BSU14710 0.8265900016
200 nt 3746052 3746251 forward BSU36380 rapD -540 -57.10 - 0.4350 122.1200027 - 0.3850 2902 ywoH BSU36440 0.8260388970
200 nt 1495105 1495304 forward BSU14240 rok -644 -55.30 - 0.3950 121.4899979 - 0.4000 302 mobA BSU14260 0.8259468675
200 nt 1923034 1923233 forward BSU17910 yneF -168 -40.60 - 0.2500 122.5039978 - 0.3500 102 ccdA BSU17930 0.8253148198
200 nt 746475 746674 forward BSU06780 yeeC -377 -31.51 - 0.2650 126.6760025 - 0.5000 3202 yeeG BSU06820 0.8248795867
200 nt 2625315 2625514 forward BSU25420 yqeW -3576 -54.30 - 0.4850 124.8850021 - 0.3550 10402 rpsT BSU25550 0.8240758777
200 nt 4007404 4007603 forward BSU39020 yxjA -360 -48.97 - 0.4150 124.6660004 - 0.3950 2902 citH BSU39060 0.8239642382
200 nt 2376722 2376921 forward BSU22510 ypjC -15121 -44.40 - 0.3450 124.1429977 - 0.4000 16602 ypzI BSU22869 0.8239628077
200 nt 3640453 3640652 forward BSU35210 yvkA -20056 -45.52 - 0.3450 123.6029968 - 0.4400 6202 yvyE BSU35510 0.8211722970
200 nt 530787 530986 forward BSU_tRNA_51 trnS-Leu2 -1266 -47.10 - 0.3350 122.6100006 - 0.3850 902 sacV BSU04830 0.8206871748
200 nt 4139260 4139459 forward BSU40240 yycS -3397 -60.10 - 0.5050 123.1039963 - 0.3450 902 rapG BSU40300 0.8204663396
200 nt 184305 184504 forward BSU01590 ybaS -4621 -44.20 - 0.4000 125.9649963 - 0.4400 9802 trnSL-Glu2 BSU_tRNA_75 0.8200225234
200 nt 792182 792381 forward BSU07230 yetM -656 -69.00 - 0.5400 120.5859985 - 0.3000 402 yetO BSU07250 0.8170907497
200 nt 4007304 4007503 forward BSU39020 yxjA -260 -49.30 - 0.4200 124.4300003 - 0.3950 3002 citH BSU39060 0.8151187301
200 nt 3726352 3726551 forward BSU36160 ywqM -1918 -63.90 - 0.5250 122.0380020 - 0.3200 7402 ywqB BSU36270 0.8136813045
200 nt 3201391 3201590 forward BSU31170 yulF -3400 -50.17 - 0.4150 123.8629990 - 0.3950 11102 tgl BSU31270 0.8136008978
200 nt 3714738 3714937 forward BSU36030 ywrK -694 -38.82 - 0.3050 124.7269974 - 0.4300 2402 cotG BSU36070 0.8135811090
200 nt 2160707 2160906 forward BSU20000 yosU -1924 -34.70 - 0.3050 126.3850021 - 0.4300 9002 yosA BSU20190 0.8132891059
200 nt 192805 193004 forward BSU01590 ybaS -13121 -48.80 - 0.4150 124.4029999 - 0.3650 1302 trnSL-Glu2 BSU_tRNA_75 0.8131257892
200 nt 2217640 2217839 forward BSU20929 yoyI -4463 -44.10 - 0.2800 121.7109985 - 0.4100 4602 yonP BSU21030 0.8124790788
200 nt 182405 182604 forward BSU01590 ybaS -2721 -53.80 - 0.4150 122.3399963 - 0.3550 11702 trnSL-Glu2 BSU_tRNA_75 0.8117757440
200 nt 2276877 2277076 forward BSU21520 yolC -4287 -38.90 - 0.3250 125.3180008 - 0.4500 3002 yokF BSU21610 0.8117634654
200 nt 1997137 1997336 forward BSU18190 yngC -48774 -50.97 - 0.4000 122.9609985 - 0.3250 5402 iseA BSU18380 0.8112495542
200 nt 2276977 2277176 forward BSU21520 yolC -4387 -39.30 - 0.3200 124.9540024 - 0.4200 2902 yokF BSU21610 0.8106592894
200 nt 749175 749374 forward BSU06780 yeeC -3077 -58.49 - 0.4600 121.9140015 - 0.3700 502 yeeG BSU06820 0.8099753261
200 nt 3726652 3726851 forward BSU36160 ywqM -2218 -52.11 - 0.4550 124.3000031 - 0.3950 7102 ywqB BSU36270 0.8091073036
200 nt 1251277 1251476 forward BSU11730 cotO -1830 -37.50 - 0.3650 127.1539993 - 0.5150 802 yjcA BSU11790 0.8088676929
200 nt 1405212 1405411 forward BSU13390 ykoT -621 -56.26 - 0.4050 120.9140015 - 0.3500 4602 ykoX BSU13430 0.8086636066
200 nt 3268455 3268654 forward BSU31810 yuzE -4132 -52.90 - 0.3900 121.7509995 - 0.4200 8402 yukF BSU31920 0.8081850410
200 nt 1467105 1467304 forward BSU13960 ykwC -407 -41.17 - 0.3700 125.7789993 - 0.4650 602 pbpH BSU13980 0.8068280816
200 nt 1406412 1406611 forward BSU13390 ykoT -1821 -67.24 - 0.5600 121.6240005 - 0.3150 3402 ykoX BSU13430 0.8052443266
200 nt 2897488 2897687 forward BSU28180 ysxD -17529 -28.00 - 0.2150 125.7649994 - 0.4100 202 ysnD BSU28320 0.8036175966
200 nt 1474672 1474871 forward BSU14010 cheV -57 -50.60 - 0.3800 122.1959991 - 0.3650 3302 ykuF BSU14060 0.8031342626
200 nt 746375 746574 forward BSU06780 yeeC -277 -31.50 - 0.2800 126.4580002 - 0.5000 3302 yeeG BSU06820 0.8004485369
  1. Significant hits of the forward and reverse strands (only showing forward 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 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.