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: 0.621001 %AT, 9971 nt, 67 terms.
Intergenic: 0.706734 %AT, H2T: 623 nt, 8 terms; T2T: 228 nt, 5 terms; H2H: 672 nt, 2 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_FQTV010000191.22.AOI_01  (length 12587)

orf00005         1442 - 768      - | 
orf00006         2590 - 1433     - | 
orf00008         3569 - 2595     - | 
orf00009         4669 - 3566     - | 
orf00010         5265 - 4660     - | 
orf00011         5291 - 5416     + | 
orf00013         5448 - 5678     + | 
sORF_2           5812 - 5717     - | 
orf00014         5790 - 6356     + | 
  TERM 1         6382 - 6400     + FH  100 -10.3 -4.84311 | 
  AATAATATTTTTTAA             TCCCCTC TTTTT GAGGGGA             TTTTGTTATATACAA
orf00015         6403 - 7413     + | 
  TERM 2         7437 - 7476     + F   100  -8.6 -5.77988 | opp_overlap 7437, overlap 7429
  ACCTATTTTAAAGAA  GCACGAATTCAGGTAGGA AGTT TCCTTGTTGAATCCGTGC   TTTTTTTATCTCTAT
orf00016         7500 - 8189     + | 
orf00018         8241 - 8552     + | 
orf00019         8559 - 9329     + | 
  TERM 3         9367 - 9397     + T    95  -7.7 -5.63517 | gap 1, opp_overlap 9367 9369, overlap 9369
  GAATGATAAAAAAAA      GA-GAGGAATCTGC AAAA GCAAATTCCTCTTC       TTTTTTATTTCGAAA
  TERM 4         9396 - 9367     - T   100 -10.1 -6.02345 | opp_overlap 9367 9369, overlap 9369
  GAATGATAAAAAAAA       GAGAGGAATCTGC AAAA GCAAATTCCTCTT        CTTTTTTATTTCGAA
  TERM 5         9369 - 9394     + T   100 -10.5 -4.88687 | opp_overlap 9367 9369, overlap 9367
  ATGATAAAAAAAAGA         GAGGAATCTGC AAAA GCAAATTCCTC          TTCTTTTTTATTTCG
  TERM 6         9394 - 9369     - T   100 -12.7  -4.6341 | opp_overlap 9369 9367, overlap 9367
  ATGATAAAAAAAAGA         GAGGAATCTGC AAAA GCAAATTCCTC          TTCTTTTTTATTTCG
orf00021         9782 - 9420     - | 
sORF_1           9840 - 9932     + | 
orf00023         9936 - 10724    + | 
orf00024        10734 - 11585    + |