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: 0.535627 %AT, 11073 nt, 75 terms.
Intergenic: 0.618234 %AT, H2T: 1519 nt, 1 terms; T2T: 414 nt, 0 terms; H2H: 600 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_BBRU010005551.34.AOI_01  (length 12675)

orf00005         1021 - 2595     + | 
sORF_26          2769 - 2674     - | 
  TERM 1         2797 - 2778     - gRH  87 -12.2  -3.1739 | 
  ACAGCACTTTATTAA            CCGTAGAC TTCA GTCTACGG             GAGTGACGGAGCCAC
sORF_25          3023 - 2787     - | 
sORF_3           2800 - 2907     + | 
sORF_1           2611 - 2907     + | 
sORF_2           2704 - 2907     + | 
  TERM 2         2919 - 2938     + gF   87 -12.2  -3.1739 | 
  CTGAGCATTTTTATA            CCGTAGAC TGAA GTCTACGG             TTAATAAAGTGCTGT
orf00010         3058 - 4161     + | 
orf00011         4181 - 5254     + | 
orf00013         5277 - 6293     + | 
sORF_24          6385 - 6290     - | 
  TERM 3         6413 - 6394     - R    87 -12.2  -3.1739 | 
  ACAGCACTTTATTAA            CCGTAGAC TTTA GTCTACGG             TATAAAAGATGCTAA
sORF_23          6534 - 6436     - | 
sORF_22          6663 - 6436     - | 
  TERM 4         6587 - 6565     - GR   79  -8.4 -4.16842 | 
  TCTACGGTTAATAAA           GTGCTGTCCC TGC GGGACAAAAC           GAGCCGCACAATTCT
orf00015         7876 - 6656     - | 
orf00017         8705 - 7881     - | 
orf00019         8734 - 10020    + | 
sORF_21         10356 - 10189    - | 
sORF_20         10437 - 10189    - | 
sORF_18         10597 - 10334    - | 
sORF_19         10516 - 10334    - | 
sORF_17         10671 - 10513    - | 
sORF_16         10825 - 10682    - | 
sORF_15         10938 - 10831    - | 
sORF_14         11117 - 10866    - | 
  TERM 5        11066 - 11031    - GgR 100 -14.2 -5.29846 | overlap 11057 11058
  AAGCGGAAATAAAAA    TCTTCGACAGCTACCT CGAA AAGCAACTGTCGAAGA     TTGACATCCCCAACA
sORF_4           9998 - 11167    + | 
sORF_5          10073 - 11167    + | 
sORF_6          10160 - 11167    + | 
sORF_7          10247 - 11167    + | 
sORF_8          10322 - 11167    + | 
sORF_9          10400 - 11167    + | 
sORF_10         10481 - 11167    + | 
sORF_11         10604 - 11167    + | 
sORF_12         10778 - 11167    + | 
sORF_13         10913 - 11167    + | 
orf00023        12477 - 11140    - |