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: 0.51589 %AT, 16205 nt, 104 terms.
Intergenic: 0.609307 %AT, H2T: 1143 nt, 5 terms; T2T: 533 nt, 6 terms; H2H: 317 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_BAKR010000071.8.AOI_01  (length 19407)

orf00004         1903 - 2691     + | 
sORF_11          2815 - 2705     - | 
sORF_1           2667 - 2828     + | 
sORF_10          2963 - 2871     - | 
sORF_2           2800 - 2991     + | 
sORF_9           3077 - 2988     - | 
orf00007         3107 - 5209     + | 
orf00009         5206 - 5400     + | 
orf00012         5443 - 6765     + | 
orf00016         6762 - 8114     + | 
  TERM 1         8115 - 8160     + GT  100 -26.5 -4.67608 | opp_overlap 8115 8122
  GATGGATATACTTAA TGGCAAAGGCCGTGTCATAAA TTTC TCTATGACACGGCCTTTGCCA TTTTGTCTTCCGATG
  TERM 2         8160 - 8115     - gT  100 -28.7 -3.16475 | opp_overlap 8115, overlap 8122
  GATGGATATACTTAA TGGCAAAGGCCGTGTCATAAA TTTC TCTATGACACGGCCTTTGCCA TTTTGTCTTCCGATG
sORF_8           8184 - 8092     - | 
sORF_3           8101 - 8193     + | 
orf00018         8951 - 8277     - | 
orf00020         9397 - 8969     - | 
orf00021         9992 - 9414     - | 
orf00022        11164 - 9989     - | 
orf00024        12195 - 11182    - | 
orf00025        12374 - 12216    - | 
orf00027        13497 - 12415    - | 
orf00029        13612 - 13818    + | 
orf00031        13828 - 14787    + | 
orf00032        14811 - 15767    + | 
sORF_7          15878 - 15753    - | 
sORF_6          16037 - 15948    - | 
orf00035        16448 - 16071    - | 
orf00036        18081 - 16471    - | 
orf00038        18256 - 19050    + | 
sORF_4          19057 - 19191    + | 
sORF_5          19133 - 19231    + | 
orf00039        19407 - 19279    - |