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: 0.490191 %AT, 15394 nt, 92 terms.
Intergenic: 0.562588 %AT, H2T: 1628 nt, 11 terms; T2T: 925 nt, 14 terms; H2H: 1598 nt, 11 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_KB8941301.9.AOI_01  (length 21128)

orf00005         5139 - 3895     - | 
orf00009         6394 - 5144     - | 
orf00011         8002 - 6401     - | 
sORF_14          8250 - 8140     - | 
orf00013         8327 - 9112     + | 
sORF_1           9087 - 9212     + | 
  TERM 1         9228 - 9242     + T    77    -7   -4.564 | 
  TCCGTTTCTTACCCG               CCGCAC AAG GAGCGG               TTTTCGTTTCACCTT
orf00016         9957 - 9274     - | 
orf00019        11134 - 9995     - | 
orf00021        12202 - 11228    - | 
orf00023        13269 - 12199    - | 
orf00025        14042 - 13326    - | 
  TERM 2        14174 - 14143    - RH  100 -13.8 -5.18371 | opp_overlap 14139 14143
  TTTCACAAAAGAAAA      GCCGCAAAACACTG TCAC CAGTCCTTTGCGGC       TTCCTTATTTCTATC
orf00028        14363 - 14202    - | 
sORF_2          14346 - 14444    + | 
orf00030        14549 - 15115    + | 
  TERM 3        15183 - 15147    - T   100 -17.3 -3.57239 | opp_overlap 15150, overlap 15139 15150
  AGTGAAATATGAGAA    TTATCCCGCCCGGTTCG TTT CGAACCGGACGGGATTT    TTTATGCGGACTTTG
  TERM 4        15150 - 15180    + T   100 -21.2 -5.24531 | opp_overlap 15147 15139 15150
  GAAATATGAGAATTA       TCCCGCCCGGTTCG TTT CGAACCGGACGGGA       TTTTTTATGCGGACT
  TERM 5        15180 - 15150    - T   100 -23.4 -2.90598 | opp_overlap 15150, overlap 15147 15139
  GAAATATGAGAATTA       TCCCGCCCGGTTCG TTT CGAACCGGACGGGA       TTTTTTATGCGGACT
orf00032        15272 - 15147    - | 
  TERM 6        15377 - 15359    - gR   76 -10.4 -3.28472 | overlap 15357 15356
  CCGGATTAAAAAGCA             GATTGGTT CCC AACCAATC             CAATACCGAGCCTGA
sORF_13         15459 - 15349    - | 
sORF_3          15298 - 15444    + | 
orf00036        15508 - 16236    + | 
sORF_12         16404 - 16294    - | 
sORF_4          16338 - 16430    + | 
sORF_11         16492 - 16382    - | 
sORF_10         16601 - 16443    - | 
sORF_9          16677 - 16534    - | 
sORF_5          16482 - 16631    + | 
sORF_8          16780 - 16667    - | 
orf00041        16875 - 16750    - | 
orf00043        16905 - 17981    + | 
orf00046        17978 - 18706    + | 
sORF_6          18687 - 18785    + | 
orf00048        18782 - 19093    + | 
orf00049        19124 - 19888    + | 
sORF_7          19930 - 20025    + | 
orf00054        20013 - 20222    + | 
  TERM 7        20393 - 20447    + T    89 -14.7 -2.71268 | gap 1, opp_overlap 20393, overlap 20392 20395
  ATTAGCACGAATTAA TACGGATTGGTACGGATATT-TTCTT TATC GAGAATAAAATCCATACCAATCCGTA TAATCTGTGGTGAAA
  TERM 8        20447 - 20393    - T   100 -16.2 -3.41961 | gap 1, opp_overlap 20393 20392 20395
  ATTAGCACGAATTAA TACGGATTGGTACGGATATT-TTCT TTATCG AGAATAAAATCCATACCAATCCGTA TAATCTGTGGTGAAA
  TERM 9        20395 - 20445    + T    86 -12.9 -2.89971 | gap 1, opp_overlap 20393, overlap 20393 20392
  TAGCACGAATTAATA CGGATTGGTACGGATATT-TTCTT TATC GAGAATAAAATCCATACCAATCCG TATAATCTGTGGTGA
orf00059        21098 - 20469    - |