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: 0.622339 %AT, 14889 nt, 83 terms.
Intergenic: 0.642989 %AT, H2T: 2505 nt, 12 terms; T2T: 439 nt, 9 terms; H2H: 430 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_BAKK010000541.76.AOI_01  (length 20574)

orf00007         3516 - 4202     + | 
sORF_1           4202 - 4291     + | 
orf00008         4347 - 4901     + | 
orf00009         4996 - 5187     + | 
orf00010         5189 - 5566     + | 
orf00011         5639 - 6112     + | 
  TERM 1         6203 - 6180     - T    88  -5.2  -5.5454 | opp_overlap 6180
  CGAAACAAATAAAAA          GTCCGAGCTT TTTC AGGTTCGGAC           TTTAAAATAAATAAT
  TERM 2         6180 - 6203     + T    78  -9.6 -3.61356 | opp_overlap 6180
  CGAAACAAATAAAAA          GTCCGAGCTT TTTC AGGTTCGGAC           TTTAAAATAAATAAT
orf00013         6857 - 6264     - | 
orf00014         7471 - 6878     - | 
sORF_5           7550 - 7443     - | 
sORF_2           7472 - 7561     + | 
orf00016         7674 - 8570     + | 
  TERM 3         8589 - 8639     + F   100 -13.1 -3.60798 | gap 1, opp_overlap 8592, overlap 8592
  AATATCAATTTAGTA GAATATCCTTTTTTCTATTCCTTA TTAA TGAGAAATAGAAAAA-GGATATTC TTAATTTATAGAACT
  TERM 4         8592 - 8636     + F    80    -9 -3.93401 | gap 1, opp_overlap 8592, overlap 8589
  ATCAATTTAGTAGAA TATCCTTTTTTCTATTCCTTA TTAA TGAGAAATAGAAAAA-GGATA TTCTTAATTTATAGA
sORF_3           8616 - 8714     + | 
orf00019         8976 - 9854     + | 
orf00021         9954 - 11093    + | 
orf00022        12374 - 11166    - | 
orf00024        13442 - 12390    - | 
orf00026        16025 - 13530    - | 
orf00028        16344 - 16033    - | 
orf00029        16333 - 16713    + | 
  TERM 5        16803 - 16773    - TR   80  -6.3 -5.00412 | gap 1, opp_overlap 16773
  AAATATAACCAAAAA      GTACTGCT-TACCA ATAA TGGTATAGTAGTAC       TTTTTGTTTTTTTGA
  TERM 6        16773 - 16803    + Tr  100  -8.5 -5.86609 | gap 1, opp_overlap 16773
  AAATATAACCAAAAA      GTACTGCT-TACCA ATAA TGGTATAGTAGTAC       TTTTTGTTTTTTTGA
sORF_4          16884 - 16780    - | 
orf00030        17505 - 16915    - | 
orf00032        18972 - 17530    - | 
orf00033        19986 - 19111    - | 
orf00035        20309 - 19983    - |