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: 0.495265 %AT, 18479 nt, 116 terms.
Intergenic: 0.544901 %AT, H2T: 1182 nt, 6 terms; T2T: 255 nt, 8 terms; H2H: 782 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_RQYF010000031.72.AOI_01  (length 21140)

orf00006         1369 - 3168     + | 
orf00007         3248 - 3802     + | 
orf00010         3863 - 5530     + | 
orf00012         5547 - 6791     + | 
sORF_8           6888 - 6763     - | 
sORF_6           7100 - 6813     - | 
sORF_7           7013 - 6813     - | 
sORF_1           6901 - 7005     + | 
sORF_2           6998 - 7141     + | 
orf00018         7223 - 7879     + | 
orf00020         7907 - 9004     + | 
orf00022         9001 - 9975     + | 
orf00023        10000 - 11154    + | 
orf00024        11159 - 11842    + | 
orf00025        11850 - 12236    + | 
sORF_5          12437 - 12339    - | 
orf00027        13453 - 12518    - | 
orf00029        14715 - 13495    - | 
orf00031        15865 - 14765    - | 
orf00032        16094 - 15855    - | 
sORF_4          16179 - 16078    - | 
orf00034        17008 - 16169    - | 
  TERM 1        17087 - 17060    - RH  100  -9.2 -5.60689 | opp_overlap 17063, overlap 17063
  GGATATAATAAAAAA        TAAGCGCGAATA AAAC TATCCGCGCTTG         CATATCAAAAAAAAG
  TERM 2        17084 - 17063    - RH  100 -10.9 -4.84921 | opp_overlap 17063, overlap 17060
  TATAATAAAAAATAA           GCGCGAATA AAAC TATCCGCGC            TTGCATATCAAAAAA
orf00037        17595 - 17119    - | 
sORF_3          17570 - 17698    + | 
orf00039        18196 - 17681    - | 
orf00041        20879 - 18240    - | 
orf00043        21107 - 20907    - |