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: 0.44328 %AT, 13355 nt, 89 terms.
Intergenic: 0.524894 %AT, H2T: 1147 nt, 4 terms; T2T: 217 nt, 1 terms; H2H: 1217 nt, 13 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_KI5353091.61.AOI_01  (length 16097)

sORF_11           561 - 460      - | 
sORF_10           749 - 600      - | 
sORF_9            841 - 680      - | 
orf00005         1636 - 3579     + | 
orf00007         3604 - 4359     + | 
sORF_1           4369 - 4494     + | 
orf00010         4531 - 4902     + | 
orf00011         6124 - 4952     - | 
orf00012         7110 - 6121     - | 
orf00014         8119 - 7139     - | 
orf00015         8864 - 8247     - | 
orf00016        10476 - 8974     - | 
sORF_2          10506 - 10619    + | 
orf00017        11510 - 10608    - | 
sORF_8          11731 - 11636    - | 
sORF_7          11927 - 11811    - | 
orf00018        13177 - 11981    - | 
sORF_5          13462 - 13199    - | 
sORF_6          13363 - 13199    - | 
sORF_3          13353 - 13490    + | 
sORF_4          13491 - 13595    + | 
orf00023        14966 - 13626    - | 
orf00024        15335 - 14988    - | 
orf00027        15946 - 15362    - |