TransTermHP v2.07 (built on Jan 21 2009) 25 bins; sample size is 20000000 --pval-conf=/fs/szasmg2/carlk/TTupdate2/expterm.dat --gc=-2.3 --au=-0.9 --gu=1.3 --mm=3.5 --gap=6 --max-len=59 --min-stem=4 --max-loop=13 --min-loop=3 --uwin-length=6 --uwin-require=3 --max-hp-score=-2 --max-tail-score=-2.5 --loop-penalty=1,2,3,4,5,6,7,8,9,10,11 --start-cut=0 --end-cut=25 Genes: 0.368337 %AT, 58908 nt, 412 terms. Intergenic: 0.404174 %AT, H2T: 9615 nt, 96 terms; T2T: 4216 nt, 85 terms; H2H: 5552 nt, 96 terms. Each terminator entry starts in column 3 and is of the form: term # start - end +/- regionconf hp tail | notes Followed by the sequence of the 5' tail, 5' stem, loop, 3' stem, and 3' tail. Genes are interspersed, and start the first column. SEQUENCE gi|217980115|ref|NC_011667.1| Thauera sp. MZ1T plasmid pTha01, complete sequence (length 78374) Tmz1t_2335 23 - 301 + | hypothetical protein Tmz1t_2336 298 - 627 + | addiction module toxin, RelE/StbE family Tmz1t_2337 1022 - 597 - | hypothetical protein TERM 1 1199 - 1170 - H 73 -10.7 -3.61527 | ACTTAAAAACATCAA GCCGGGAGACTCT GGAA AATGTCTCCCGAC CACCCTACTCCACAA TERM 2 1307 - 1292 - g 80 -4.6 -4.77567 | overlap 1293 ATGGTCACAAGAAAA GCTCGC CTTC GAGAGC GGACTGGATCGCAGC Tmz1t_2338 1188 - 1436 + | helix-turn-helix domain protein TERM 3 1672 - 1634 - f 95 -19.9 -2.52543 | gap 1, opp_overlap 1645, overlap 1645 AGGGGTGGCAATCCA GACGCATACAACATGCAG CATG CTGCATGTTGTATGCG-C ATACTGAATGCTGCA TERM 4 1645 - 1662 + F 70 -9.9 -3.49653 | opp_overlap 1634 1645 TCCAGACGCATACAA CATGCAG CATG CTGCATG TTGTATGCGCATACT TERM 5 1662 - 1645 - f 70 -9.9 -3.53722 | opp_overlap 1645, overlap 1634 TCCAGACGCATACAA CATGCAG CATG CTGCATG TTGTATGCGCATACT TERM 6 1781 - 1834 + F 76 -13.8 -3.01712 | gap 1, opp_overlap 1754 1780 GGGCGGGGAACCGAC GCGCCAGGGGACGCCCATCTGCG AGGCGCAGC CG-AGTCGGGCGGCCTCTGGCGC TGTTCGGGGGCGCAG TERM 7 3388 - 3377 - g 75 -3.6 -4.79949 | CTGGCAAAAAAAGAA CACC CTTT GGCG ATGGCAGGTTGAAGA Tmz1t_2339 2478 - 3515 + | hypothetical protein TERM 8 3598 - 3651 + F 88 -19.5 -2.86164 | gap 1 AGCGCTACACCGCCC G-CAGGGGCTCGGGGGCAGGTCCCGC GAT GCGAAACCTGCCCCCGAGCTCGAGGC TATGCTGGTTCAGAC Tmz1t_2340 3912 - 4400 + | nuclease (SNase domain protein) Tmz1t_2341 4659 - 4405 - | hypothetical protein Tmz1t_2342 5296 - 4691 - | Exonuclease RNase T and DNA polymerase III TERM 9 5179 - 5211 + g 71 -9.8 -3.70902 | gap 1, overlap 5182 CGATCACGGCGAGCT CGAC-GACCTCGGCG TCGT CGCCGAGGCCCGTGG TTTCGGTGTCGAGGA TERM 10 5306 - 5320 + r 73 -10 -3.64703 | overlap 5311 AGCCATTACCGCCGA CCTTGC CGC GCAAGG TTTCCATCAGCGCGG Tmz1t_2343 6245 - 5289 - | hypothetical protein TERM 11 5529 - 5576 + g 71 -9.1 -3.75153 | gap 3 GTCTACCTTCGCCTT CGCCGCGGCGAGCTCGTTGCGCAG GCC CTCGGCATCG-GC-CGCCGCG-CG TTTGAGTTCGCCGCG TERM 12 6301 - 6273 - R 79 -12.1 -3.54653 | opp_overlap 6273 6270 6276 6276, overlap 6270 6276 ATCGGGACTAGATAA TAATCATAATAAT ATG ATTATTATGATTA TGCAAGTGATTATTT TERM 13 6298 - 6276 - R 73 -9.4 -3.9093 | opp_overlap 6273 6270 6276 6276, overlap 6270 6273 GGGACTAGATAATAA TCATAATAAT ATG ATTATTATGA TTATGCAAGTGATTA TERM 14 6316 - 6339 + r 71 -8 -4.07568 | overlap 6317 ATGCAAGTGATTATT TGCCCGCTGC TCAC GCAGGGGGCC TTTTCCACGGAGGGC Tmz1t_2344 7106 - 6426 - | protein of unknown function DUF159 TERM 15 7075 - 7058 - G 76 -9.1 -4.07568 | overlap 7059 GCTCCGCCTCGAAAA CCTCGCG CAGG CGCGAGA CCGGACCGTAGAGCG Tmz1t_2345 10212 - 7246 - | transposase Tn3 family protein Tmz1t_2347 10508 - 11122 + | Resolvase domain protein TERM 16 11995 - 12005 + G 93 -4.6 -5.45802 | TATCGTTGACAGCGC GGGC AAA GCTC TTTTTGTTTTACACC Tmz1t_2348 11522 - 12298 + | hypothetical protein TERM 17 12316 - 12361 + T 85 -18.5 -2.57781 | opp_overlap 12328, overlap 12312 12328 CTGTCGGTTTAACTG GAGGTTACAGCAGCATTCCAA AGCT TTGGGATGCTGCTGTAACCAA TGAATTAGCTATTTC TERM 18 13270 - 13227 - T 86 -13.8 -3.53012 | gap 1 TCCTTTTCCGCGAAA CCACAGCCCG-CAACGGGTCG AGA CGACTCGTCGGCGAGCGGCGG CTTACGGGAAGCGAA Tmz1t_2349 14186 - 13377 - | hypothetical protein Tmz1t_2350 15252 - 14299 - | Sel1 domain protein repeat-containing protein Tmz1t_2351 15417 - 15686 + | hypothetical protein TERM 19 15876 - 15906 + G 75 -7.5 -4.20918 | gap 1, overlap 15877 ATCAGTTGATCCATG ACCGGGTG-CGCCG CAGT TGGCGACACCTGGA TTTCTTCCAGTTCGA Tmz1t_2352 15704 - 17026 + | transposase ISL3 family protein TERM 20 17630 - 17616 - T 79 -7.8 -4.51994 | opp_overlap 17616 17615 CGAAGCAAGAACAAA GGCACG CAG CATGCC GTTCTCAACTCCGTT Tmz1t_2353 18498 - 18148 - | DNA polymerase beta domain protein region Tmz1t_2354 19900 - 18863 - | helix-turn-helix, type 11 domain-containing protein TERM 21 20595 - 20578 - H 76 -14.1 -3.08679 | CCTCCCCATTGAACA GGCCCCC CCAG GGGGGCC ATAAACCAGCCCCCC TERM 22 21161 - 21139 - g 73 -14.8 -2.52464 | GCCTGTCCGAACTGA GGCGACCGGC AGA GGCGGTCGCC CCGCTGCAGCGGGCG Tmz1t_2356 20799 - 21878 + | Tetratricopeptide TPR_2 repeat protein Tmz1t_2357 21898 - 22428 + | hypothetical protein Tmz1t_2358 23115 - 22504 - | hypothetical protein Tmz1t_2359 23625 - 23287 - | hypothetical protein TERM 23 23986 - 24018 + G 75 -10.5 -3.87815 | gap 1 GTTCCGGGCGGCGTT CCG-CCGCCGGCGC TGCATC GTGCCGGCGAACGG TTTCTACGAGTGGCA Tmz1t_2360 23714 - 24382 + | protein of unknown function DUF159 TERM 24 24569 - 24597 + F 79 -12.1 -3.54475 | opp_overlap 24572 24575 24578 24581, overlap 24572 24575 GCATAGCTGCTTGCA TAATCATAATAAT CAT ATTATTATGATTA TTATCTAGTCACGCC TERM 25 24572 - 24594 + F 73 -9.4 -3.9093 | opp_overlap 24572 24575 24578 24581, overlap 24569 24575 TAGCTGCTTGCATAA TCATAATAAT CAT ATTATTATGA TTATTATCTAGTCAC TERM 26 25523 - 25509 - g 71 -10 -3.64822 | AGGCGCTGATGGAAA CCTTGC GCG GCAAGG TCGGCGGCAATGGTT Tmz1t_2361 24626 - 25540 + | hypothetical protein TERM 27 25650 - 25618 - g 90 -15.6 -3.70902 | gap 1 TCCTCGACACCGAAA CGACGGGCCTCGGCG ACGA CGCCGAGGTC-GTCG AGATCGCGGTGATCG Tmz1t_2362 25533 - 26138 + | Exonuclease RNase T and DNA polymerase III Tmz1t_2363 26169 - 26429 + | hypothetical protein Tmz1t_2364 26952 - 26437 - | nuclease (SNase domain protein) TERM 28 26667 - 26687 + g 85 -12.5 -4.08767 | CCTTGATCTTGCACA CCGCCCGCT TGT AGCGGTCGG TTTTCCGGCAGTCGG Tmz1t_2365 27818 - 27294 - | membrane-bound metal-dependent hydrolase Tmz1t_2366 28552 - 27815 - | hypothetical protein Tmz1t_2367 29238 - 28549 - | hypothetical protein TERM 29 28635 - 28607 - G 75 -15.2 -2.78463 | opp_overlap 28626, overlap 28587 AGGCCCCCGACCACA GCCGCCACCGGC CAGGC GCCGGCGGCGGT CGCCAGCACGGCGAT TERM 30 30697 - 30671 - H 83 -17.2 -2.64274 | overlap 30668 30667 ACGGTCGGAAAGTCA GAGGCGCCGCGC TGC GCGCAGCGCCGC AAGGGTGGCCCGGCC TERM 31 31463 - 31519 + H 100 -8.6 -5.40072 | gap 1, opp_overlap 31492, overlap 31466 31467 CACACCCGCCCCTAT CGCGGGGGGCTCGGGGGCTGGGGGT AAAAGGCC ACCCCCAGCCCTCGAGCAAG-CGTA TTTTTTTGCGCGGCG TERM 32 31466 - 31517 + H 100 -13.6 -4.34482 | opp_overlap 31492, overlap 31463 31467 ACCCGCCCCTATCGC GGGGGGCTCGGGGGCTGGGGGT AAAAGGCC ACCCCCAGCCCTCGAGCAAGCG TATTTTTTTGCGCGG TERM 33 31467 - 31516 + H 89 -17.1 -3.19966 | opp_overlap 31492, overlap 31466 31463 CCCGCCCCTATCGCG GGGGGCTCGGGGGCTGGGGGT AAAAGGCC ACCCCCAGCCCTCGAGCAAGC GTATTTTTTTGCGCG TERM 34 31949 - 31931 - H 95 -11.7 -4.62069 | opp_overlap 31917 CGGCGACCCGAAAAA CGGGACG CATAT CGTCCCG TTAAAACGCTATAGT Tmz1t_2368 32004 - 32675 + | Resolvase domain protein TERM 35 32749 - 32710 - f 100 -14.8 -4.35116 | gap 1, opp_overlap 32711 32713 32715 32719, overlap 32711 32713 32732 GATTCGACATCAAAA GCATATCAATATGATATCA AAG TGATATCATATTGATAT-C GTTCTAGCGGCAGAA TERM 36 32711 - 32750 + F 86 -14.8 -3.28712 | gap 1, opp_overlap 32710 32711 32713 32732, overlap 32713 32715 32719 ATTCGACATCAAAAG C-ATATCAATATGATATCA AAG TGATATCATATTGATATCG TTCTAGCGGCAGAAG TERM 37 32749 - 32711 - f 82 -15 -3.20588 | opp_overlap 32711 32713 32715 32719, overlap 32710 32713 32732 ATTCGACATCAAAAG CATATCAATATGATATCA AAG TGATATCATATTGATATC GTTCTAGCGGCAGAA TERM 38 32747 - 32713 - f 89 -17.6 -3.16202 | opp_overlap 32711 32713 32715 32719, overlap 32710 32711 32732 TCGACATCAAAAGCA TATCAATATGATATCA AAG TGATATCATATTGATA TCGTTCTAGCGGCAG TERM 39 32713 - 32747 + F 84 -17.6 -2.82623 | opp_overlap 32713 32710 32711 32732, overlap 32711 32715 32719 TCGACATCAAAAGCA TATCAATATGATATCA AAG TGATATCATATTGATA TCGTTCTAGCGGCAG TERM 40 32715 - 32745 + F 81 -15.8 -2.96274 | opp_overlap 32713 32710 32711 32732, overlap 32713 32711 32719 GACATCAAAAGCATA TCAATATGATATCA AAG TGATATCATATTGA TATCGTTCTAGCGGC Tmz1t_2369 32822 - 33052 + | hypothetical protein Tmz1t_2370 33049 - 33639 + | hypothetical protein TERM 41 33615 - 33627 + F 74 -3.4 -4.73613 | CATGGATCGCGAACG CCAT CCGGA ATGG TTTTCTTCCTGATGC Tmz1t_2371 33755 - 35014 + | DNA-cytosine methyltransferase Tmz1t_2372 35047 - 35460 + | DNA mismatch endonuclease Vsr Tmz1t_2373 35503 - 36504 + | restriction endonuclease-like protein Tmz1t_2374 36652 - 37293 + | Cobyrinic acid ac-diamide synthase Tmz1t_2375 37356 - 37643 + | CopG domain protein DNA-binding domain protein Tmz1t_2376 37667 - 38719 + | plasmid encoded RepA protein Tmz1t_2378 40250 - 39162 - | cointegrate resolution protein T Tmz1t_2379 41075 - 40518 - | Ankyrin Tmz1t_2380 41537 - 41160 - | hypothetical protein Tmz1t_2381 41989 - 41603 - | hypothetical protein Tmz1t_2382 45150 - 42031 - | heavy metal efflux pump, CzcA family TERM 42 42263 - 42226 - G 77 -11.9 -3.59979 | overlap 42210 42207 CGGTGCCAGCGCAAA GGCCGTCACCAGCGCCG TCAT CAGCACCGGCGATAGCC GTTCCAGCGAGCCGC TERM 43 44529 - 44515 - G 72 -7 -4.25104 | opp_overlap 44518 GGTGTTCGACGAAAA GCCGCG GAT CGCCGC TTCCATCTGTTCCAG Tmz1t_2383 46278 - 45166 - | hypothetical protein TERM 44 45476 - 45455 - G 77 -12.3 -3.64703 | gap 1, overlap 45437 45459 CCCGCGGCACCGAAA GCGAGC-GGC AGC GCCTGCTCGC GCAGACTGCGCGCCG Tmz1t_2384 46838 - 46275 - | hypothetical protein Tmz1t_2385 48121 - 46856 - | outer membrane efflux protein TERM 45 47033 - 47019 - G 72 -8.5 -4.15044 | opp_overlap 47023, overlap 47020 GCCTTCTGGAAGAAA CCGCG CGACT CGCGG GCCAACTGCGCGCGC Tmz1t_2386 48602 - 48255 - | hypothetical protein TERM 46 48650 - 48640 - R 77 -3.2 -5.01042 | AACGGAAATGAAAAA TAGC GTT GCCA ACATCTTGTTGCCCG Tmz1t_2387 49069 - 48731 - | hypothetical protein Tmz1t_2388 49238 - 49924 + | heavy metal response regulator Tmz1t_2389 49927 - 51264 + | heavy metal sensor kinase Tmz1t_2390 53685 - 51283 - | heavy metal translocating P-type ATPase TERM 47 51883 - 51903 + g 100 -12.6 -4.70659 | GGCCGTCTTGCCTTG GCGCTCGA GCGTG TCGAGCGC TTTTTCGATGTCGGG TERM 48 53835 - 53803 - g 70 -5.3 -4.33105 | overlap 53794 53804 CAAGCACGATGAAAA TCGGTGAGCTGGCCA GAG TGACCGGCACCCCGG TAGAGACCATCCGCT Tmz1t_2391 53796 - 54251 + | Cd(II)/Pb(II)-responsive transcriptional regulator TERM 49 55009 - 55023 + G 76 -5.6 -4.56597 | overlap 55010 TCAACAGCGTCACGC CGCTGC TGC GCAGCA TTTTTGAGCGCGCGG Tmz1t_2392 54306 - 55247 + | integrase family protein Tmz1t_2393 55591 - 55235 - | Tn4652, TnpA repressor protein TnpC, putative Tmz1t_2394 58617 - 55594 - | transposase Tn3 family protein TERM 50 56682 - 56696 + g 71 -12.8 -3.02511 | opp_overlap 56676 CGAAGGACAGCATGT GCGGCG TGA CGCCGC TGTTGCCCAGATGGC Tmz1t_2395 58857 - 58708 - | hypothetical protein TERM 51 59311 - 59281 - g 70 -11.1 -3.31144 | gap 1 CTTCCAGGTCGATAA CGCGAACTG-GCCG AGCT CGGCCCAGCACGCG CAGGAATGGTGGGCT Tmz1t_2396 59042 - 59356 + | hypothetical protein Tmz1t_2397 59920 - 59390 - | hypothetical protein TERM 52 59828 - 59867 + g 88 -15.8 -3.35679 | gap 1, opp_overlap 59822, overlap 59829 GCCGACGAAGGCCAT CG-GCGCGAGCTCCTCG CCCTGCT CGAGGAGCTCGCGCGCC TTGTCGATCAGCGGC TERM 53 59829 - 59866 + g 89 -19.3 -2.61264 | gap 1, opp_overlap 59822, overlap 59828 CCGACGAAGGCCATC G-GCGCGAGCTCCTCG CCCTGCT CGAGGAGCTCGCGCGC CTTGTCGATCAGCGG TERM 54 61211 - 61228 + r 78 -14.1 -3.12803 | overlap 61208 GGGGGGCTAGTTCAT GGCCCCC TTGG GGGGGCC TGTTCAATGTGGATG Tmz1t_2399 62686 - 61742 - | hypothetical protein Tmz1t_2400 63007 - 62726 - | CopG domain protein DNA-binding domain protein TERM 55 63096 - 63079 - R 74 -5.5 -4.57533 | overlap 63088 AAGAATATCAGAAAA GCGCACT AACC AGCGCAC TGATCTCCTCGCAAG Tmz1t_2401 63712 - 63071 - | Cobyrinic acid ac-diamide synthase TERM 56 63729 - 63763 + r 77 -11.6 -3.57561 | opp_overlap 63729 63731, overlap 63731 TATATATCTTATCAA TATCGGATAGATATCT TTT AGATATCTATCCGCAA TTTAGCACATTACCC TERM 57 63761 - 63731 - R 78 -14.2 -3.15078 | opp_overlap 63731 63729, overlap 63729 TATATCTTATCAATA TCGGATAGATATCT TTT AGATATCTATCCGC AATTTAGCACATTAC Tmz1t_2402 65776 - 63812 - | protein of unknown function DUF524 Tmz1t_2403 67793 - 65778 - | site-specific DNA-methyltransferase, cytosine-specific TERM 58 66594 - 66555 - G 75 -12 -3.44146 | opp_overlap 66558 GTTTTTTACAAGCAA CGCGGCCGACTCAGCCTC TGCT GAAGCCGGGTCCTCCGCG TTCAGCAGCTCCGAT Tmz1t_2404 68751 - 67834 - | DNA methylase N-4/N-6 domain protein Tmz1t_2405 69107 - 68886 - | hypothetical protein Tmz1t_2406 69461 - 69829 + | hypothetical protein TERM 59 69870 - 69910 + T 90 -18.5 -3.21593 | opp_overlap 69876, overlap 69871 69876 ACAGATTGGTGGTCA GGAAAAGGGCGTTGCCT CCTCGCC AGGCAACGCCCTTTTCA TATTCTCGGGGCGTC TERM 60 69871 - 69909 + T 100 -22 -2.52742 | opp_overlap 69876, overlap 69870 69876 CAGATTGGTGGTCAG GAAAAGGGCGTTGCCT CCTCGCC AGGCAACGCCCTTTTC ATATTCTCGGGGCGT TERM 61 69876 - 69904 + T 100 -16.1 -4.46656 | opp_overlap 69876, overlap 69871 69870 TGGTGGTCAGGAAAA GGGCGTTGCCT CCTCGCC AGGCAACGCCC TTTTCATATTCTCGG TERM 62 69904 - 69876 - T 100 -16.1 -4.25104 | opp_overlap 69876 69871 69870 TGGTGGTCAGGAAAA GGGCGTTGCCT CCTCGCC AGGCAACGCCC TTTTCATATTCTCGG TERM 63 70270 - 70258 - T 73 -10.5 -3.5944 | ATTTAGACGTCTAAA CCGGC GGT GCCGG TGTGGGACGCCACCG TERM 64 70741 - 70713 - T 74 -11.5 -3.48395 | opp_overlap 70713, overlap 70722 70723 AGTGTGCGCAGAGAA GCCCGCAAAGGGC GTA GCCCGAAGCGGGC TTCTCTGCGCGGGCG TERM 65 70713 - 70741 + T 74 -11.5 -3.48276 | opp_overlap 70713 70722 70723 AGTGTGCGCAGAGAA GCCCGCAAAGGGC GTA GCCCGAAGCGGGC TTCTCTGCGCGGGCG Tmz1t_2407 71559 - 70762 - | IstB domain protein ATP-binding protein TERM 66 71223 - 71173 - G 77 -9 -4.25848 | gap 3 AACGGTCGAGTAAAA GCGCAC-CCGCTTGCCGTG-CCGGG TGAT CCCGGACACGCCCAGCGCCGTG-GC CAGGTGCGACTTGCC Tmz1t_2408 73042 - 71552 - | Integrase catalytic region TERM 67 72596 - 72566 - G 70 -7.4 -3.96148 | overlap 72583 CGCCTGCACGACAAA GGCACGGCTGTAGC ACA GCTTCAGGTGCGCC ACGAGCACCTTGCGC TERM 68 73429 - 73449 + r 71 -6.7 -4.16921 | overlap 73430 73432 ACCTTGATGCCTGGA GCGTGGGGC GCA GCCCCGTGA TTTTCGACGTTGTTG Tmz1t_2409 74252 - 73527 - | hypothetical protein Tmz1t_2410 74989 - 74321 - | hypothetical protein TERM 69 75202 - 75244 + r 73 -10.6 -3.60792 | gap 2, opp_overlap 75202 75203 75206, overlap 75203 75208 TCGTTCAACGCAGAA GTCAC-CGG-CGCTGCGCGG CTTTA TCGCGCAGCGTCCGCGTGGA TTTCCGGGTTAGACG TERM 70 75203 - 75243 + r 73 -14.1 -2.76261 | gap 2, opp_overlap 75203 75202 75206, overlap 75202 75208 CGTTCAACGCAGAAG TCAC-CGG-CGCTGCGCGG CTTTA TCGCGCAGCGTCCGCGTGG ATTTCCGGGTTAGAC Tmz1t_2411 76200 - 75253 - | HNH endonuclease TERM 71 75849 - 75869 + g 76 -5.5 -4.49939 | CCAGTTGCCGCTCCG TTTGTTCTA GGG TGGAACGAA TTTTATCAATTATGT Tmz1t_2412 77427 - 76600 - | hypothetical protein TERM 72 77287 - 77301 + g 93 -2.8 -5.252 | GGCGCGGAACTCCGA CTTAAG TTG CTCAAG TTTTTTATCGAACTC TERM 73 77746 - 77762 + H 100 -10.8 -5.40072 | opp_overlap 77743, overlap 77743 CACCCCCAGCAACGG CGCGGC TTTGC GCCGCG TTTTTTTCCCGAACA Tmz1t_2413 77790 - 78338 + | integrase family protein