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: 0.541314 %AT, 18529 nt, 110 terms.
Intergenic: 0.661815 %AT, H2T: 1918 nt, 2 terms; T2T: 333 nt, 7 terms; H2H: 837 nt, 1 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_EQ9736361.7.AOI_01  (length 21140)

orf00005         2028 - 1117     - | 
sORF_9           2236 - 2144     - | 
orf00008         2654 - 2211     - | 
sORF_8           2841 - 2749     - | 
orf00010         5980 - 2870     - | 
orf00011         6980 - 6012     - | 
orf00012         7464 - 6994     - | 
orf00015         7691 - 7461     - | 
sORF_7           7771 - 7664     - | 
orf00017         7872 - 8834     + | 
  TERM 1         8892 - 8841     - T    93  -9.7 -4.27117 | opp_overlap 8842, overlap 8842
  GCTTTATAATAGAAA GCGGGGATTTACTTTTTCTTC AGACCTTTTG GATAAAAAAGTAAATCCCCGT TCTTGAAACAGCTTA
  TERM 2         8842 - 8891     + T   100 -14.7 -3.61894 | gap 1, opp_overlap 8842 8841
  CTTTATAATAGAAAG CGGGGATTTACTTT-TTCTTCAGA CCT TTTGGATAAAAAAGTAAATCCCCG TTCTTGAAACAGCTT
  TERM 3         8891 - 8842     - T    91 -13.2 -3.15788 | opp_overlap 8842, overlap 8841
  CTTTATAATAGAAAG CGGGGATTTACTTTTTCTTC AGACCTTTTG GATAAAAAAGTAAATCCCCG TTCTTGAAACAGCTT
orf00018         9310 - 8912     - | 
orf00019         9991 - 9335     - | 
orf00020        11142 - 9988     - | 
orf00022        11284 - 11144    - | 
orf00023        12290 - 11310    - | 
orf00024        13357 - 12293    - | 
orf00026        14030 - 13383    - | 
sORF_6          14168 - 14061    - | 
orf00027        14339 - 14178    - | 
sORF_1          14322 - 14432    + | 
sORF_5          14508 - 14389    - | 
orf00030        14530 - 15096    + | 
sORF_2          15097 - 15204    + | 
orf00032        16062 - 15178    - | 
orf00033        16543 - 16088    - | 
orf00034        17012 - 16551    - | 
orf00035        17515 - 17009    - | 
sORF_4          17663 - 17544    - | 
sORF_3          17494 - 17601    + | 
orf00038        17666 - 18655    + | 
orf00040        18655 - 19347    + | 
orf00041        19410 - 19730    + | 
orf00043        19742 - 20554    + | 
  TERM 4        20632 - 20599    - T   100 -21.1 -4.85599 | gap 1, opp_overlap 20600 20601, overlap 20601
  CTGACGGGATAAAAA     GAGCCCGGCCTCGCTG TCG CAGCGAAGCCGGGC-C     TTTCTACTTATTAAA
  TERM 5        20600 - 20632    + T   100 -19.1 -4.14257 | opp_overlap 20599 20601, overlap 20601
  TGACGGGATAAAAAG      AGCCCGGCCTCGCTG TCG CAGCGAAGCCGGGCC      TTTCTACTTATTAAA
  TERM 6        20631 - 20601    - T   100 -24.8 -4.05067 | opp_overlap 20600 20601, overlap 20599
  GACGGGATAAAAAGA       GCCCGGCCTCGCTG TCG CAGCGAAGCCGGGC       CTTTCTACTTATTAA
  TERM 7        20601 - 20631    + T   100 -22.6 -3.07831 | opp_overlap 20601 20599, overlap 20600
  GACGGGATAAAAAGA       GCCCGGCCTCGCTG TCG CAGCGAAGCCGGGC       CTTTCTACTTATTAA
orf00046        21140 - 20682    - |