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: 0.535007 %AT, 10955 nt, 65 terms.
Intergenic: 0.586732 %AT, H2T: 390 nt, 1 terms; T2T: 373 nt, 9 terms; H2H: 1476 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_ACNN010000311.6.AOI_01  (length 14256)

orf00003          993 - 2072     + | 
sORF_5           2143 - 2051     - | 
orf00005         2115 - 3107     + | 
orf00006         3104 - 4276     + | 
orf00008         4338 - 5294     + | 
  TERM 1         5390 - 5419     + T   100  -8.7 -5.38047 | gap 1, opp_overlap 5389
  TCGGATTCATTATAG       GGGAGC-ACACT CATACGT AGTGTAGCTCCC       TTTTTTGTCTCCATA
orf00009         5577 - 5365     - | 
orf00010         5603 - 6199     + | 
orf00011         6196 - 7221     + | 
  TERM 2         7344 - 7317     - T    91  -8.4 -4.69549 | gap 1, opp_overlap 7317, overlap 7312
  AATCCAAAACCAAAA        GAGCTTGCCCACA ATA CG-GGGCAGGCTC        TTTTTCTATTTTCTC
  TERM 3         7317 - 7344     + T   100 -10.6 -5.32599 | opp_overlap 7317 7312
  AATCCAAAACCAAAA        GAGCTTGCCC ACAATACG GGGCAGGCTC         TTTTTCTATTTTCTC
orf00012         7588 - 7298     - | 
orf00013         7800 - 9881     + | 
sORF_4           9968 - 9873     - | 
sORF_2          10274 - 10041    - | 
sORF_3          10139 - 10041    - | 
sORF_1          10101 - 10214    + | 
orf00016        10288 - 12021    + | 
orf00017        12794 - 12030    - |