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: 0.540758 %AT, 11323 nt, 79 terms. Intergenic: 0.545473 %AT, H2T: 4190 nt, 20 terms; T2T: 1768 nt, 16 terms; H2H: 2308 nt, 5 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_JACCCY0100000031.4.AOI_01 (length 21113) orf00026 8552 - 7656 - | orf00032 9733 - 8585 - | orf00033 9743 - 9904 + | TERM 1 9959 - 9928 - T 100 -11 -5.99154 | gap 1, opp_overlap 9927 TATTAAATAAAAAAA CCTCCT-TGTTCCAT AGA AAGGAACAGAGGAGG CTCTATATATCATAG orf00036 11141 - 9984 - | orf00039 12142 - 11153 - | orf00044 13240 - 12146 - | sORF_59 13382 - 13242 - | sORF_58 13475 - 13242 - | sORF_57 13559 - 13242 - | sORF_56 13652 - 13242 - | sORF_55 13769 - 13242 - | sORF_54 13862 - 13242 - | sORF_3 13610 - 13705 + | sORF_1 13392 - 13760 + | sORF_2 13527 - 13760 + | sORF_53 13956 - 13843 - | TERM 2 14021 - 13979 - R 100 -18.2 -4.85599 | opp_overlap 13983 13987, overlap 13983 13987 GCTATGGTATAAAAA CAAAGAAAGTAAAGGCTTTT TAT AAAAACCTTTACTTTCTTTA ATAGGAATAAACGTA TERM 3 14017 - 13983 - R 100 -16.8 -4.96501 | opp_overlap 13983 13987, overlap 13979 13987 TGGTATAAAAACAAA GAAAGTAAAGGCTTTT TAT AAAAACCTTTACTTTC TTTAATAGGAATAAA TERM 4 14013 - 13987 - R 100 -11.8 -4.96845 | opp_overlap 13987 13983, overlap 13983 13979 ATAAAAACAAAGAAA GTAAAGGCTTTT TAT AAAAACCTTTAC TTTCTTTAATAGGAA sORF_52 14140 - 14051 - | orf00049 14156 - 14281 + | TERM 5 14382 - 14357 - Tf 100 -12.7 -6.02919 | opp_overlap 14357 GTATAAACAAAAAAA GGAGTCAGTTC AATT GAACTAACTCC TTCTCTAAAAACGGC TERM 6 14357 - 14382 + TF 79 -10.5 -3.48276 | opp_overlap 14357 GTATAAACAAAAAAA GGAGTCAGTTC AATT GAACTAACTCC TTCTCTAAAAACGGC sORF_51 14497 - 14387 - | orf00051 14474 - 14686 + | sORF_50 14908 - 14753 - | sORF_49 14983 - 14753 - | sORF_48 15132 - 15016 - | sORF_7 14998 - 15096 + | sORF_4 14721 - 15179 + | sORF_6 14913 - 15179 + | sORF_5 14823 - 15179 + | sORF_47 15243 - 15154 - | sORF_8 15118 - 15270 + | sORF_46 15358 - 15233 - | sORF_9 15209 - 15337 + | sORF_10 15468 - 15602 + | orf00058 15634 - 15777 + | sORF_11 15762 - 15851 + | sORF_45 15963 - 15859 - | sORF_12 15855 - 16037 + | sORF_13 15947 - 16042 + | sORF_14 16044 - 16142 + | sORF_15 16544 - 16654 + | sORF_16 16618 - 16725 + | sORF_44 16873 - 16778 - | sORF_17 16763 - 16867 + | sORF_18 16905 - 17021 + | sORF_43 17212 - 17120 - | sORF_42 17502 - 17371 - | sORF_21 17323 - 17514 + | sORF_19 17163 - 17525 + | sORF_20 17247 - 17525 + | orf00065 17501 - 17638 + | sORF_22 17788 - 17886 + | sORF_41 18133 - 18032 - | sORF_40 18249 - 18058 - | sORF_38 18465 - 18058 - | sORF_24 18075 - 18227 + | sORF_23 17958 - 18227 + | sORF_39 18350 - 18192 - | sORF_25 18293 - 18409 + | sORF_37 18619 - 18488 - | sORF_36 18701 - 18600 - | sORF_28 18587 - 18694 + | sORF_27 18491 - 18694 + | sORF_26 18413 - 18694 + | sORF_35 18824 - 18729 - | orf00072 18819 - 18950 + | sORF_34 19141 - 19010 - | sORF_33 19233 - 19126 - | sORF_29 19199 - 19348 + | sORF_32 19426 - 19304 - | orf00075 19408 - 19569 + | orf00076 19636 - 19956 + | sORF_31 20097 - 19999 - | sORF_30 19938 - 20123 + | orf00081 21109 - 20105 - |