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: 0.586804 %AT, 17142 nt, 119 terms.
Intergenic: 0.612389 %AT, H2T: 762 nt, 8 terms; T2T: 499 nt, 15 terms; H2H: 229 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_FXDJ010000031.6.AOI_01  (length 21125)

orf00004         3541 - 2441     - | 
orf00005         5542 - 3548     - | 
orf00006         5649 - 5783     + | 
orf00008         6013 - 6180     + | 
  TERM 1         6292 - 6263     - T   100 -18.7 -4.10188 | opp_overlap 6256 6266, overlap 6266
  TACATTTATAAAGAA       CAATGGCCCTCCC AAAC GGGAGAGCCATTG        CTATAGATTATAAAC
  TERM 2         6289 - 6266     - T   100 -14.6 -4.16305 | opp_overlap 6256 6266, overlap 6263
  ATTTATAAAGAACAA          TGGCCCTCCC AAAC GGGAGAGCCA           TTGCTATAGATTATA
  TERM 3         6266 - 6289     + T    89 -12.4 -3.30453 | opp_overlap 6266 6263, overlap 6256
  ATTTATAAAGAACAA          TGGCCCTCCC AAAC GGGAGAGCCA           TTGCTATAGATTATA
orf00009         9697 - 6320     - | 
sORF_7           9815 - 9714     - | 
sORF_1           9891 - 9989     + | 
orf00011        11155 - 9992     - | 
orf00013        12156 - 11170    - | 
orf00014        13231 - 12158    - | 
orf00015        13859 - 13233    - | 
orf00017        14065 - 13928    - | 
sORF_2          14095 - 14220    + | 
sORF_3          14221 - 14316    + | 
sORF_4          14297 - 14404    + | 
  TERM 4        14540 - 14486    - T    79  -6.9 -4.67755 | opp_overlap 14486 14488, overlap 14488
  ATACCTACCCAAAAA CATAAAGGTTATTTTTGGAAAAATA AAGGA TATATTTTAAAAAATAACCTTTATA TTTTTTTTCATATAG
  TERM 5        14486 - 14540    + T   100  -6.9 -5.90981 | opp_overlap 14486 14488, overlap 14488
  ATACCTACCCAAAAA CATAAAGGTTATTTTTGGAAAAATA AAGGA TATATTTTAAAAAATAACCTTTATA TTTTTTTTCATATAG
  TERM 6        14488 - 14538    + T    88  -9.5 -4.59226 | opp_overlap 14488 14486, overlap 14486
  ACCTACCCAAAAACA TAAAGGTTATTTTTGGAAAAATA AAGGA TATATTTTAAAAAATAACCTTTA TATTTTTTTTCATAT
sORF_6          14638 - 14522    - | 
  TERM 7        14700 - 14680    - R    91  -6.9 -5.45652 | opp_overlap 14669 14680
  ATGGGCAATAAAAAA            GGTATCC TTTTGGG GGATACC            TTTTTTATTCATTAA
sORF_5          14821 - 14732    - | 
orf00021        14841 - 14981    + | 
orf00023        15973 - 15023    - | 
orf00026        18347 - 16032    - | 
orf00027        21097 - 18344    - |