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: 0.49985 %AT, 9983 nt, 76 terms.
Intergenic: 0.525155 %AT, H2T: 1974 nt, 12 terms; T2T: 1775 nt, 26 terms; H2H: 747 nt, 1 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_JRNN010000691.88.AOI_01  (length 14249)

sORF_1           2080 - 2199     + | 
sORF_15          2466 - 2233     - | 
sORF_2           2246 - 2401     + | 
orf00007         3779 - 3642     - | 
orf00008         4332 - 3793     - | 
  TERM 1         4379 - 4343     - gRH  76   -11 -3.16676 | gap 1, overlap 4341
  TTCATTAAGTCAACA   GCACTCTCATC-CGTCG ATCC CGACCCGATGAGAATGC    CCAAAAGCTCGGCGT
sORF_14          4499 - 4332     - | 
sORF_4           4376 - 4519     + | 
sORF_3           4304 - 4519     + | 
orf00010         5605 - 4553     - | 
sORF_5           5622 - 5801     + | 
orf00012         6423 - 5857     - | 
sORF_13          6579 - 6487     - | 
sORF_12          6685 - 6545     - | 
sORF_11          6775 - 6545     - | 
sORF_6           6616 - 6771     + | 
sORF_10          6873 - 6739     - | 
sORF_7           6785 - 6898     + | 
orf00017         7054 - 6923     - | 
orf00019         7084 - 7893     + | 
orf00022         7900 - 8967     + | 
orf00023         8987 - 9988     + | 
orf00025         9998 - 11146    + | 
orf00026        11140 - 11793    + | 
sORF_8          11783 - 11977    + | 
sORF_9          11886 - 11984    + | 
orf00031        14018 - 12051    - |