# TF - HisR: CLONEX_00021
>CLONEX_00021(hisR) Score=5 Pos=-54 [Clostridium nexile DSM 1787]
GAGTTTACTGTGCTAAAATA
>CLONEX_03079(hisX) Score=4.8 Pos=-54 [Clostridium nexile DSM 1787]
TAATTTAGTGTGGTAGAGTA
>CLONEX_02879(hisZ) Score=4.4 Pos=-40 [Clostridium nexile DSM 1787]
TATTTTAATATGGTAGCGTA
>CLONEX_02879(hisZ) Score=4.6 Pos=-32 [Clostridium nexile DSM 1787]
TATGGTAGCGTAATAAAGTA
# TF - NiaR: CLONEX_03261
>CLONEX_03264(nadA) Score=6 Pos=-3 [Clostridium nexile DSM 1787]
AGCATGTGTCTTGTCACCTGTA
>CLONEX_03876(niaY) Score=5.8 Pos=-47 [Clostridium nexile DSM 1787]
TGCTAGTGACAAGACACATGTA
# RNA - Cobalamin
>CLONEX_02595 Score=110.5 Pos=-393 [Clostridium nexile DSM 1787]
AGAGTGAAAATGTATGCGGTTGCTTTTGAATGATACAAAAGCATGAAAAGGGAATCCGGTGAAAAACCGGAGCAGTCACCTCTACTGTAACGCGGACGATGAGACAATAGGCCATTGACAGAATAATGTTGAGAAGGTGTTTTCAAAGAAAGATGCGAAGCCAGGAGACCTGCCGTATATAGGAAAGAATGTTT
# RNA - FMN
>CLONEX_02849(ribU) Score=113.4 Pos=-239 [Clostridium nexile DSM 1787]
GGATTCTTCGGGGCAGGGTGTAATTCCCTACCGGCGGTTACAGTCCGCGACCCATGAAAATGGCTGAACTGGTGGAATTCCAGTACCGACAGTAAAGTCTGGATGTGAGAAGAAGGTGTG
# RNA - GEMM_RNA_motif
>CLONEX_03566 Score=25.1 Pos=-402 [Clostridium nexile DSM 1787]
ATAATCGCAAAGACAAACTTATAGAAATATGAGGATACAAAGGTAGAGGTCGAAGACCAATATGTATAGGCAGTTCGACTGTGATG
# RNA - Glycine
>CLONEX_04109(alsT) Score=51.2 Pos=-187 [Clostridium nexile DSM 1787]
TTAAAAAAACTCTGGAGAGTCTCAAATATTAGAGCGCCGAAGGTGTACGGCAGACAGAAATGTCTGTTAATCTCTCAGGCAAAAGGACAGGGCAAATGTA
# RNA - L10_leader
>CLONEX_01917(rplJ) Score=81.1 Pos=-183 [Clostridium nexile DSM 1787]
AACTTATATTAGAAAACTGCCGAAGACAGTAGGTGCCGTAAGGCATAAGTAGTGAACGCCTACCGAGGAGATTTGAATTCGATGAATTATGTGAATTTACTGTCCTCTTGTCGTGTGGCGAGAGGATTTTTTATCTTTATT
# RNA - L19_leader
>CLONEX_03041(rplS) Score=27.5 Pos=-64 [Clostridium nexile DSM 1787]
AGAGATGGTCCTCTGATACAGAATATGTATTAAGAACGTCCA
# RNA - L20_leader
>CLONEX_02671(infC) Score=31.1 Pos=-210 [Clostridium nexile DSM 1787]
AAAAAGAAAGCAGAGTTCCACTCTCACCTTAGCACAAGTGGGTGACTAATGGTTGATATTGAAGCATAAAAATAGAATTTCTATTTTGTGTGCAGAAATGGAGTGGATAGCTGTGAGCTATTCATTTTTTTTACGCATC
# RNA - L21_leader
>CLONEX_01673(rplU) Score=26.4 Pos=-73 [Clostridium nexile DSM 1787]
CCGCACAATGAGGTTTGCAAGTTCTGCAATGCAGACACCGTAATTGGCGAGT
# RNA - Lysine
>CLONEX_03655(lysW) Score=108.1 Pos=-368 [Clostridium nexile DSM 1787]
CTAAAAGGATAGAGGTGCGGATTTCATCAGTATTGTGTGGCAAAGTTGGACAGCCGCCACATACGAAAGGGAAAGTCGCCGAAGAGATGTTTTTTTGTCCAGAAAGATATCTCTGGGATATTGCAGAATATGCAATATACTGTCACTTATGTGGAGAGCTATCGTTGGT
# RNA - PreQ1
>CLONEX_03575(queT) Score=20.9 Pos=-55 [Clostridium nexile DSM 1787]
AAAGAGTGTTCGCGACCTTCCACTCGTAAAACAAAACTAAAGGAGAAA
>CLONEX_00551(iunH) Score=49.7 Pos=-87 [Clostridium nexile DSM 1787]
CTGGACTGGTTCGAAAACTTCCCAGAATAAAAAACTAAGGATTGAA
# RNA - SAM
>CLONEX_00524(metK) Score=63.7 Pos=-212 [Clostridium nexile DSM 1787]
TCTTATTCAGAGTGGTGGAGGTAAAAGGATCTATGAAGCCACGGCAACCCCGGGAACGGAAGGTGCCAACCTGAGCGAGTAATCGAACAATAAGAGGA
# RNA - T-box(Cys)
>CLONEX_00247(cysE) Score=110.1 Pos=-311 [Clostridium nexile DSM 1787]
GAGAAAGACTTAGAACGAAAAGAGTAGTATATTTGGAACTGACAGAGAGAGATTGCCATCGGCTGAAAGCAATTTTGAGGAAAGAATATATGAAGTGCATTCGGGAGTTGGTTTGGCGAACAGACAGTAGCCGAATTCGGGCAGCATACGTTACATGCATCAAGTGAAGGAAGGAGATTCCTTTATTAGAGTGGAACCGCGGATTGAACTTCGTCTCTAGA
# RNA - T-box(Ile)
>CLONEX_02311(ileS) Score=80.3 Pos=-170 [Clostridium nexile DSM 1787]
TGAAAAAACGTTGACGAAGACAGTAGGATATATTTTAAAGTCAAAGAGAGTCAGGGATGGTGAGAGCCTGATACGAGTAGAATATATTTGAAGATCACTTCTGAGTTGCAGTGACCGAACGAAGTTGTCCAATAGGTACTGCCGGGATTCCACCGTTAGCAGGAACGCATATGTCAGTATGGTGTAATAGGTGGTATAACGAAGGTTTTACAGCTCTCGTCCTGATT
# RNA - T-box(Leu)
>CLONEX_03143(leuS) Score=97 Pos=-419 [Clostridium nexile DSM 1787]
TCAAAAAACATAGATGAGGAGTATTAAGAGCCTATCGTTTTCAGAGAGCTGTCGGATGGTGCAAGACAGCAGCGTAATCTCCCAACTCGCCTCGGAGTTCTTTTGCTGAAATGACTGATGAAAAAAATTTCGTCAAGTAACAGAAATAGAAACAACTACATCGCTAGGTTCGAAAGAACCTCACCAAGCCGATGAGTTGTACCTTGTTACTAGACTCGAAAAGACCTCGTCAAGTAACATAGGCAGAAGCGGGACTTCCCGTTACAGAAGCAATGAGTGCATTTCGCAGGATGCGGAATGAATGAGAGTGGTACCACGGAAATTCAAGCCTTTTCGTCTCTTTT
# RNA - T-box(Met)
>CLONEX_03592(metS) Score=75.5 Pos=-267 [Clostridium nexile DSM 1787]
AGGAAACGCAATGATGGAAAGAGTAGATATTTCAGACATTTACAGAGAAGTCTCATGAAGCTGAGAAGAGACGATGAAAGAGATATCGAAGATGGCTCCTGAGCGGTGTGCCAAGCTGAAAGATTTTAGTGAAGCACAAAGGGATCGCCCTTTACAGCGACAGAGTATGGTGTATGAGCATACTTGATAAGGTTTATACTGTGAAGTATAAGCGAAGAGAAGTGGTAACACGGTATCAGACCCGTCTTCTTA
# RNA - T-box(Phe)
>CLONEX_03195(pheS) Score=110.8 Pos=-283 [Clostridium nexile DSM 1787]
CAAAAAGGCATGGAACGTGTTTAGTAGAGCACTATTTTCTAACAGAGAGAGGAAATCATCGGCTGGAAGTTTCCTTTAGTTCAAATGGGAATCGAATTTCGCACGGGAGCTGTATCTTTGAACGATATAAAGAAAAGTAGAAGATAACGTATCTGCACGTTACGCAGTCCGAGTGCTCATGGAGATTTCTGTGAGAAGTAGGGTGGTACCGCGATATAGCCTCGTCCCTTTT
# RNA - T-box(Pro)
>CLONEX_03542(proS2) Score=107.3 Pos=-297 [Clostridium nexile DSM 1787]
AATATTGGCTGTGAAGAGGAATAGTATATACAGGACGAGCCACAGAGAGAGAATTGATTGGTGAAAGATTCTTGCAAGAAGTGTATGGAACCTACCTTGGAGCCACTGTGTGAAAATGCAGCGTGACATCAGCGTTAATGATGACTAAAGAGAATTGTAGAGGAATCTATGATTAATTAGGGTGGTACCGCCGAGTCTTTCGGTCCCTTTT
# RNA - T-box(Thr)
>CLONEX_02841(thrS) Score=98.7 Pos=-327 [Clostridium nexile DSM 1787]
AGAAAACACGTTGATGAGACGAGTAAGATGTGAAAGGATACAGAGAGAGAGGTCGCAGGCTGGAAGCCTCTTATTGCGGAAACATCTGAAAACTACCTCGGAGTGGCTGCAAAACAGTCCGGTGATTCCGTTATAATCAGTTGAGTGGTTCTGGTATTTGCCAGTACAATTTGGGTGGAACCGCGAGTAAAGAGAACTCGTCCCTTGT
# RNA - T-box(Trp)
>CLONEX_03129(trpE) Score=84.3 Pos=-394 [Clostridium nexile DSM 1787]
CGTCAAACCGTTGAAGCGGAGATAACGGCAATGATGCCTTTACAGAGAGTTTGGGATGCTGAGAACCAGATGAGAAACAAGTTGTCAAATGGACCGCGGAGGGTGCAGTCAAATGTAAAGTTTATATTTACAGAGTATTCTGCAACGTGTAGGCATACGTCAGTTGCCGAGGGTATGTTTGTATCCTGCTAAGAGCACGGAGATTCCGTGAATTCAAGGTGGCACCGCGGATTGTGTCGTACCTGTTATACATGTACACTATTCGTCCTTGAC
>CLONEX_00452(trpB2) Score=84.6 Pos=-345 [Clostridium nexile DSM 1787]
AAATAAACCGATGAGGAAGAGTAAGTATCTTCAGTGTTTGCTTCACAGAGAACTGCAGATGGTGGGAGTGCAGTAAGATGTAGCTGTAGAGAATGGGCTTCCGAGGGCGAGCTGAACGGCAAAGATTTACAGTAGGTGAGCCGGAGACAGTACTCCGTTAACAAAGTTCGCATATGTCAGTATGCATAAGTGGGTATATAGTGAAAGATATACCAAGCCGGGTGGCACCGCAGGAGTTGAATTATGTACTCTTGTCCCTGCA
# RNA - T-box(Tyr)
>CLONEX_01102(tyrS) Score=107.5 Pos=-352 [Clostridium nexile DSM 1787]
AAACGGCGAAGAAAAGAAAAAGTAATAATTGAGACGCCATACAGAAAGCTGCCGGTTGATGAGAGGCGCATGGAAAGTCGATTATGAATACATCTTGGAGCTTTGCACCGAACAGTGACATAATTCTAAGTAGGCTGCAACGGGATGGCACACGTTATCGTGCCTGAGTATTGATAGATACTTGCAGAGGCGTTTGCTGTGAAGTGAATGCGAATGAAGGTGGTACCGCGGGATTACACTCGCCCTTTATGT
# RNA - T-box(Val)
>CLONEX_03903(valS) Score=94.8 Pos=-195 [Clostridium nexile DSM 1787]
GCAAAAGGTAATGAGAAAGAGGAGTACACATAAGTCGCTTGAAAGAGAGAACCGCTCTTAGGCTGAAAGGTGGTTTCAAGATAGAAATGTAGAAGGTAGCTTTCGAACCGGATTTCTGAACTGTGTATAATTATATAATAAGGTCAAAGTAGGAAGTCACGGGGTGGTTCACGTTAAAGAACCGACGAGATATATATGAAAGATTTCGTATATAACAAAGGTGGTACCGCGATTATTCGCCCTTTAC
# RNA - TPP
>CLONEX_00344(COG0011) Score=67.1 Pos=-226 [Clostridium nexile DSM 1787]
GAAAAGAAATCAGGGGTGCCGGGAGAACCTGGCTGAGAGTAAACTACGAGAATGTTTAGACCCTTAACCTGATCTGGGTAATGCCAGCGTAGGGAGAATATTGAAACACAAA
>CLONEX_00625(tenA) Score=49.7 Pos=-163 [Clostridium nexile DSM 1787]
TGTGTTTGCGAGGGAACTGAACAAGTTGAAAAAGGTAAGACCTGACCTCTGGACCTGTCGGCTAATACCGGCGTAGGGAAGCAATTTCTTACGCTCGTA
>CLONEX_00625(tenA) Score=70.9 Pos=-323 [Clostridium nexile DSM 1787]
TACTCAAGCAGGGGGACTACCTTGTAGTTGAGAAGGTTAAAACCTGACCCTTTGAACCTGTTGGCTAATACCAACGCAGGGAGCTGAAGAATACAGATTCG
>CLONEX_00550(thiT) Score=60 Pos=-38 [Clostridium nexile DSM 1787]
CAATTTGCTAGGGGAGCCATGAGCTGAGAATCACACAGATGTGTGTTGACCCTCATTACTTGAACCGGTTAGTACCGGCGGAAGGAAGCAGTACCAAAGTGGTTC
>CLONEX_00816(thiW) Score=66.3 Pos=-166 [Clostridium nexile DSM 1787]
CAAAAACATAGGGGAGCTTGTATTGGCAGGCTGAGAGGAAGTAATCAACTTCGACCCTTTAACCTGATGCGGATAATGCCGCCGTAGGAAATCATAATTGCTGATTTTT
# RNA - ykoK
>CLONEX_03217(mgtE) Score=76.8 Pos=-354 [Clostridium nexile DSM 1787]
ATAAGATTCGGTAGGTGAGGCTACCACAGGGATTTGGATTTTCCTAAGATTGCTGCCGCAACAACGTGGAGACACGATTCGCTGGTTAGCAGGATATGTCGCAGATAAGGCATATCTTAATGCAATTTATATGCCCTGTGATGCTAAAGCTTGAACGATGTTGTCACGGAAT
# RNA - yybP-ykoY
>CLONEX_03625(atcL) Score=55.6 Pos=-203 [Clostridium nexile DSM 1787]
TTTTATAGATAAAAGGGAGTAACTAGCGTTACTAAACGTTTACGATGTCGTCAATACGATGAATTTCATCCGTATCGTAATGAAATAGTGAGACTTTTATTGCATAA
>CLONEX_00436(COG1971) Score=52.3 Pos=-140 [Clostridium nexile DSM 1787]
TTCAGAGACGATAAGGGAGTAGTTAGCGTAATTACGTAGTATTGTCAACATACTGGCAGTTTGACTGTCTGGCATTACTTTAAATAATGAGACTTATCCGTAGATA
# RNA - THF
>CLONEX_03228(folT) Score=100.5 Pos=-106 [Clostridium nexile DSM 1787]
AAGCAGAGTAAGAGTATGTGCGTTAAGTGCCAGTTGGACGGGGAGTTGCCAGTCGGACGAAAAGCAAAATTGCTTGCGGTACATACTCTGCATCCCGCTGCT
# TF - HrcA: CLONEX_00289
>CLONEX_00414(groEL) Score=7 Pos=-375 [Clostridium nexile DSM 1787]
TTAGCACTCGGACAAAGTGAGTGCTAA
>CLONEX_00415(groES) Score=7 Pos=-63 [Clostridium nexile DSM 1787]
TTAGCACTCGGACAAAGTGAGTGCTAA
>CLONEX_03837(htpG) Score=7.5 Pos=-92 [Clostridium nexile DSM 1787]
TTAGCACTCACTTTAAAAGAGTGCTAA
>CLONEX_00290(hrcA) Score=7.3 Pos=-54 [Clostridium nexile DSM 1787]
TTAGCACTCGAAAGAATAGAGTGCTAA
>CLONEX_03691(hsp20) Score=7.2 Pos=-136 [Clostridium nexile DSM 1787]
TTAGCACTCACCTCTTGACAGTGCTAA
>CLONEX_03685(clpB) Score=7.1 Pos=-89 [Clostridium nexile DSM 1787]
TTAGCACTCACCCCTTGACAGTGCTAA
# TF - ArgR: CLONEX_02981
>CLONEX_00308(argC) Score=5.1 Pos=-129 [Clostridium nexile DSM 1787]
ATGTATACTTATGCAA
# TF - Rex: CLONEX_01590
>CLONEX_04092(adhE) Score=5 Pos=-73 [Clostridium nexile DSM 1787]
TTGACAAATATTTAACGA
>CLONEX_04091(stpK) Score=4.8 Pos=-102 [Clostridium nexile DSM 1787]
TTGTTAAAAAATACTCAA
>CLONEX_01601(bdh) Score=4.6 Pos=-71 [Clostridium nexile DSM 1787]
GCGTTAAATAATTAACAG
>CLONEX_01601(bdh) Score=4.5 Pos=-43 [Clostridium nexile DSM 1787]
CTGTTAAAAGGTTAACAA
>CLONEX_00392(aroE) Score=5.5 Pos=-63 [Clostridium nexile DSM 1787]
TTGTTTAAAATTTAACAA
# TF - LexA: CLONEX_01664
>CLONEX_03018(recA) Score=5.2 Pos=-19 [Clostridium nexile DSM 1787]
ACGAACATAAGTTCGC
>CLONEX_01664(lexA) Score=4.9 Pos=-163 [Clostridium nexile DSM 1787]
CCGAACAACTGTTCTT
>CLONEX_01664(lexA) Score=5.2 Pos=-130 [Clostridium nexile DSM 1787]
AAGAACAAATGTTTGT
>CLONEX_01664(lexA) Score=5 Pos=-94 [Clostridium nexile DSM 1787]
ACGAACATATTTTCTA
>CLONEX_00280(COG4277) Score=4.6 Pos=-67 [Clostridium nexile DSM 1787]
GCAAACATCTGTTCTG
>CLONEX_01663(PF01476) Score=5 Pos=-126 [Clostridium nexile DSM 1787]
TAGAAAATATGTTCGT
>CLONEX_01663(PF01476) Score=5.2 Pos=-90 [Clostridium nexile DSM 1787]
ACAAACATTTGTTCTT
>CLONEX_01663(PF01476) Score=4.9 Pos=-57 [Clostridium nexile DSM 1787]
AAGAACAGTTGTTCGG
# RNA - TPP
>CLONEX_00816(thiW) Score=66.3 Pos=-166 [Clostridium nexile DSM 1787]
CAAAAACATAGGGGAGCTTGTATTGGCAGGCTGAGAGGAAGTAATCAACTTCGACCCTTTAACCTGATGCGGATAATGCCGCCGTAGGAAATCATAATTGCTGATTTTT
>CLONEX_00625(tenA) Score=49.7 Pos=-163 [Clostridium nexile DSM 1787]
TGTGTTTGCGAGGGAACTGAACAAGTTGAAAAAGGTAAGACCTGACCTCTGGACCTGTCGGCTAATACCGGCGTAGGGAAGCAATTTCTTACGCTCGTA
>CLONEX_00625(tenA) Score=70.9 Pos=-323 [Clostridium nexile DSM 1787]
TACTCAAGCAGGGGGACTACCTTGTAGTTGAGAAGGTTAAAACCTGACCCTTTGAACCTGTTGGCTAATACCAACGCAGGGAGCTGAAGAATACAGATTCG
>CLONEX_00550(thiT) Score=60 Pos=-38 [Clostridium nexile DSM 1787]
CAATTTGCTAGGGGAGCCATGAGCTGAGAATCACACAGATGTGTGTTGACCCTCATTACTTGAACCGGTTAGTACCGGCGGAAGGAAGCAGTACCAAAGTGGTTC
# RNA - FMN
>CLONEX_02849(ribU) Score=113.4 Pos=-239 [Clostridium nexile DSM 1787]
GGATTCTTCGGGGCAGGGTGTAATTCCCTACCGGCGGTTACAGTCCGCGACCCATGAAAATGGCTGAACTGGTGGAATTCCAGTACCGACAGTAAAGTCTGGATGTGAGAAGAAGGTGTG
# TF - YhcF: CLONEX_00374
>CLONEX_00374(yhcF) Score=6.5 Pos=-40 [Clostridium nexile DSM 1787]
ATTGTATTATATATTTAATACAAA
>CLONEX_00079(BLAHAN_01094) Score=6.1 Pos=-44 [Clostridium nexile DSM 1787]
ATTGTATTAACTCAATAATACATT
# TF - IscR: CLONEX_03012
>CLONEX_03012(iscR) Score=5.9 Pos=-51 [Clostridium nexile DSM 1787]
ATAAACCCTAGTAATTCACTAGGAATTAA
# TF - BirA: CLONEX_00545
>CLONEX_00515(bioY) Score=9 Pos=-85 [Clostridium nexile DSM 1787]
TTGTTAAC---------------GTTGACAA
# TF - PdxR: CLONEX_00239
>CLONEX_02290(pdxU) Score=9.4 Pos=-97 [Clostridium nexile DSM 1787]
AACTGGACT-(15)-AACTGGTAT-(8)-ATACCAGAA
# TF - DtxR: CLONEX_03800, CLONEX_00478
>CLONEX_03805(COG1132) Score=6.2 Pos=-37 [Clostridium nexile DSM 1787]
GGTTAGTTTTTTCTAACT
>CLONEX_00483(PF09605) Score=6.5 Pos=-50 [Clostridium nexile DSM 1787]
GGTTAGTTTTAGCTAACC
# TF - CzrA: CLONEX_04063
>CLONEX_04065(cadA) Score=5.1 Pos=-51 [Clostridium nexile DSM 1787]
AATATGGTTATATGAACATATG
>CLONEX_04065(cadA) Score=5.7 Pos=-35 [Clostridium nexile DSM 1787]
CATATGAACAATCACTCATATG
# TF - Fur: CLONEX_01963
>CLONEX_01942(PF12672) Score=4.7 Pos=-275 [Clostridium nexile DSM 1787]
TTGGAGAAAAATTTTCATT
>CLONEX_01967(BACPEC_02635) Score=5.4 Pos=-39 [Clostridium nexile DSM 1787]
AATGAAATTGTTTATCATT
>CLONEX_01962(BACPEC_03058) Score=5.7 Pos=-92 [Clostridium nexile DSM 1787]
AATGATAAAATTTATCGAT
# TF - IdeR: CLONEX_01968
>CLONEX_01968(ideR) Score=6 Pos=-139 [Clostridium nexile DSM 1787]
ATGGTTAGTATACTCTAACGTT
>CLONEX_01967 Score=6.5 Pos=-65 [Clostridium nexile DSM 1787]
AACGTTAGAGTATACTAACCAT
>CLONEX_01965(feoB) Score=4.9 Pos=-58 [Clostridium nexile DSM 1787]
ATGGTTAGTTAAAACTAATAAA
>CLONEX_01942 Score=4.9 Pos=-32 [Clostridium nexile DSM 1787]
TAAGTTAGAAATAACTAACTCA
>CLONEX_02589(PF05031) Score=5.1 Pos=-63 [Clostridium nexile DSM 1787]
CTGGTTAGTTTAATCTAACAAA
# TF - NrdR: CLONEX_03933
>CLONEX_03145(nrdE) Score=5.1 Pos=-60 [Clostridium nexile DSM 1787]
CAACTATATATTGTGG
>CLONEX_03145(nrdE) Score=5 Pos=-28 [Clostridium nexile DSM 1787]
ATACTATAAATAGTAA
>CLONEX_02838(nrdD2) Score=4.3 Pos=-122 [Clostridium nexile DSM 1787]
TAACAATATATAGGAA
>CLONEX_02838(nrdD2) Score=4.9 Pos=-91 [Clostridium nexile DSM 1787]
ACACAATATATGGTTT