TransTermHP v2.08 (built on Jan 14 2011) 25 bins; sample size is 20000000 --pval-conf=/data/pg-molgen/software/bagel4/tools/transterm_hp_v2.09/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: 0.501114 %AT, 17948 nt, 98 terms. Intergenic: 0.529083 %AT, H2T: 4977 nt, 18 terms; T2T: 666 nt, 16 terms; H2H: 3110 nt, 3 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 NZ_QEKY010000041.28.AOI_01 (length 21101) sORF_1 1645 - 1740 + | sORF_24 1831 - 1733 - | orf00004 1851 - 3080 + | orf00005 3085 - 4017 + | orf00006 4076 - 5707 + | orf00008 5746 - 6573 + | sORF_2 6633 - 6827 + | sORF_3 6720 - 6827 + | sORF_23 6943 - 6830 - | sORF_4 6824 - 6940 + | orf00011 6937 - 7752 + | orf00012 7774 - 8892 + | sORF_5 8864 - 8965 + | orf00015 8967 - 9956 + | orf00016 9975 - 11135 + | sORF_6 11141 - 11248 + | sORF_22 11396 - 11277 - | orf00021 11404 - 12078 + | sORF_21 12181 - 12056 - | TERM 1 12114 - 12149 + gF 100 -17.8 -4.31166 | opp_overlap 12114 TTCTCTGAGATAGAA GAGGGCATGTCGAAAT AAAA ATTTTGGCATGCCCTC TTTCTCTGTTTGTAA orf00024 12171 - 12299 + | sORF_7 12318 - 12410 + | orf00026 12410 - 13756 + | sORF_8 13761 - 13901 + | sORF_9 13891 - 13995 + | TERM 2 14006 - 14039 + TF 79 -9.7 -3.86524 | opp_overlap 14008, overlap 14008 14014 GCTAATACCATAAAG AACAGAAGTGTCCTT CACT GAGGACATTTCTGTC TTTCTCGAAGGATGT TERM 3 14037 - 14008 - Tf 80 -9.4 -4.14977 | opp_overlap 14006 14008 14014 TAATACCATAAAGAA CAGAAGTGTCCT TCACTG AGGACATTTCTG TCTTTCTCGAAGGAT TERM 4 14008 - 14037 + TF 86 -12.3 -3.52113 | opp_overlap 14008, overlap 14006 14014 TAATACCATAAAGAA CAGAAGTGTCCTT CACT GAGGACATTTCTG TCTTTCTCGAAGGAT sORF_20 14151 - 14020 - | sORF_19 14258 - 14169 - | sORF_10 14013 - 14255 + | sORF_11 14100 - 14255 + | sORF_18 14367 - 14206 - | sORF_12 14200 - 14298 + | sORF_17 14482 - 14264 - | sORF_13 14280 - 14462 + | orf00035 14463 - 15182 + | orf00036 15289 - 16206 + | orf00037 16331 - 16660 + | TERM 5 16705 - 16732 + TF 100 -9.8 -5.59879 | opp_overlap 16708, overlap 16708 TAATGCTTATTGCGA TAAGGGCTGCCG ATTG TGGCGGCCCTTC TTTTTTCTCTTTGTC TERM 6 16708 - 16729 + TF 100 -11.5 -4.8277 | opp_overlap 16708, overlap 16705 TGCTTATTGCGATAA GGGCTGCCG ATTG TGGCGGCCC TTCTTTTTTCTCTTT sORF_16 16806 - 16696 - | sORF_14 16718 - 16852 + | orf00040 16865 - 17122 + | sORF_15 17222 - 17103 - | orf00044 17192 - 19297 + | TERM 7 19332 - 19390 + Tr 100 -37.3 -3.14132 | gap 1, opp_overlap 19317 19333 19338, overlap 19333 19338 GCTGAGAGACGAATC -AGCAAACACCCGTGTAGAGAGGAGCAG TTCG CTGCTCCTCTCTACACGGGTGTTTGCTG TTAATGAAAAGACAA TERM 8 19388 - 19333 - TR 100 -42.4 -2.83345 | opp_overlap 19332 19333 19338, overlap 19317 19338 CTGAGAGACGAATCA GCAAACACCCGTGTAGAGAGGAGCAG TTCG CTGCTCCTCTCTACACGGGTGTTTGC TGTTAATGAAAAGAC TERM 9 19333 - 19388 + Tr 100 -42.4 -3.13403 | opp_overlap 19317 19333 19338, overlap 19332 19338 CTGAGAGACGAATCA GCAAACACCCGTGTAGAGAGGAGCAG TTCG CTGCTCCTCTCTACACGGGTGTTTGC TGTTAATGAAAAGAC TERM 10 19383 - 19338 - TR 100 -35.1 -3.86106 | opp_overlap 19333 19332 19338, overlap 19333 AGACGAATCAGCAAA CACCCGTGTAGAGAGGAGCAG TTCG CTGCTCCTCTCTACACGGGTG TTTGCTGTTAATGAA TERM 11 19338 - 19383 + Tr 100 -35.1 -3.95022 | opp_overlap 19338 19333, overlap 19333 19332 AGACGAATCAGCAAA CACCCGTGTAGAGAGGAGCAG TTCG CTGCTCCTCTCTACACGGGTG TTTGCTGTTAATGAA orf00045 20991 - 19468 - |