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: 0.537134 %AT, 9506 nt, 61 terms.
Intergenic: 0.616419 %AT, H2T: 504 nt, 1 terms; T2T: 123 nt, 5 terms; H2H: 580 nt, 2 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_RAYS010000321.965.AOI_01  (length 12463)

orf00003         2473 - 1325     - | 
orf00005         3455 - 2481     - | 
orf00007         4525 - 3452     - | 
orf00009         5208 - 4552     - | 
sORF_3           5354 - 5214     - | 
sORF_2           5476 - 5366     - | 
  TERM 1         5424 - 5403     - GR  100  -8.7 -5.76237 | opp_overlap 5403
  TACAGAAACAAAAAA           GGCGAAGAA TATA CTCTCCGCC            TTTTTTGTTTCCCTG
orf00013         5612 - 5451     - | 
orf00015         5805 - 6371     + | 
  TERM 2         6392 - 6419     + T    90  -8.4 -4.99035 | opp_overlap 6392 6394, overlap 6394
  AAGAACATATAAAAA        CAGCCGATAGTC CAAT GACTACCGGCTA         TTTTTATATACATAC
  TERM 3         6419 - 6392     - T   100 -12.8  -5.1383 | opp_overlap 6392 6394, overlap 6394
  AAGAACATATAAAAA        CAGCCGATAGTC CAAT GACTACCGGCTA         TTTTTATATACATAC
  TERM 4         6417 - 6394     - T   100 -13.2 -4.16832 | opp_overlap 6392 6394, overlap 6392
  GAACATATAAAAACA          GCCGATAGTC CAAT GACTACCGGC           TATTTTTATATACAT
  TERM 5         6394 - 6417     + T    86   -11 -4.11744 | opp_overlap 6394 6392, overlap 6392
  GAACATATAAAAACA          GCCGATAGTC CAAT GACTACCGGC           TATTTTTATATACAT
orf00018         7845 - 6445     - | 
orf00019         9515 - 7920     - | 
sORF_1           9619 - 9527     - | 
orf00020         9879 - 9709     - | 
orf00023         9872 - 11614    + |