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: 0.549234 %AT, 10511 nt, 47 terms.
Intergenic: 0.614301 %AT, H2T: 1846 nt, 3 terms; T2T: 201 nt, 6 terms; H2H: 917 nt, 0 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_QSPP010000601.936.AOI_01  (length 12448)

orf00004         2449 - 1292     - | 
orf00006         3452 - 2478     - | 
orf00007         4528 - 3449     - | 
orf00009         5182 - 4541     - | 
sORF_2           5355 - 5239     - | 
sORF_1           5169 - 5309     + | 
orf00012         5332 - 6678     + | 
  TERM 1         6766 - 6708     - TR  100 -19.6 -4.28994 | gap 2, opp_overlap 6709 6710 6727, overlap 6709 6727
  CAGTATTCATTAAAA CTTGATAGACAAAGAAAAAGGATTTTCC TGCAT GGAAAATCCTTTTTCTTTGTCTATCA-- AGTTTACTCTATTAA
  TERM 2         6709 - 6767     + Tr  100 -32.5 -2.95877 | opp_overlap 6708 6709 6727, overlap 6710 6727
  AGTATTCATTAAAAC TTGATAGACAAAGAAAAAGGATTTTCC TGCAT GGAAAATCCTTTTTCTTTGTCTATCAA GTTTACTCTATTAAT
  TERM 3         6767 - 6709     - TR  100 -32.5 -3.16914 | opp_overlap 6709 6710 6727, overlap 6708 6727
  AGTATTCATTAAAAC TTGATAGACAAAGAAAAAGGATTTTCC TGCAT GGAAAATCCTTTTTCTTTGTCTATCAA GTTTACTCTATTAAT
  TERM 4         6710 - 6768     + Tr  100 -19.6 -3.94936 | gap 2, opp_overlap 6708 6709 6727, overlap 6709 6727
  GTATTCATTAAAACT --TGATAGACAAAGAAAAAGGATTTTCC TGCAT GGAAAATCCTTTTTCTTTGTCTATCAAG TTTACTCTATTAATT
  TERM 5         6727 - 6749     + Tr  100 -10.7  -5.4433 | opp_overlap 6727 6708 6709, overlap 6709 6710
  ATAGACAAAGAAAAA           GGATTTTCC TGCAT GGAAAATCC           TTTTTCTTTGTCTAT
  TERM 6         6749 - 6727     - TR  100 -10.7  -5.4433 | opp_overlap 6709 6710 6727, overlap 6708 6709
  ATAGACAAAGAAAAA           GGATTTTCC TGCAT GGAAAATCC           TTTTTCTTTGTCTAT
orf00015         7023 - 6778     - | 
orf00016         7152 - 7286     + | 
orf00017        11221 - 7289     - | 
orf00018        12427 - 11357    - |