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: 0.475641 %AT, 16298 nt, 76 terms.
Intergenic: 0.503102 %AT, H2T: 5475 nt, 36 terms; T2T: 2065 nt, 39 terms; H2H: 3043 nt, 29 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 NC_0155011.50.AOI_01  (length 21140)

sORF_19          2013 - 1906     - | 
sORF_18          2126 - 1962     - | 
sORF_17          2201 - 1962     - | 
sORF_1           1919 - 2044     + | 
  TERM 1         2153 - 2122     - GTfRH  79 -12.4 -3.09518 | overlap 2114 2141
  GGAAAATCGCGAATA      TCCACGTGGAAAAT AAAA ATTCTCCACGTGGG       GAAGAAATAAAACTT
  TERM 2         2159 - 2141     - GgTR  86  -3.8 -5.45802 | overlap 2122
  CGTGGAAAATAAAAA             TTCTCCAC GTG GGGAAGAA             ATAAAACTTCGGAGG
sORF_16          2296 - 2198     - | 
sORF_2           2127 - 2255     + | 
  TERM 3         2590 - 2612     + TFrH  76 -11.4 -3.32765 | opp_overlap 2589 2588
  TTATAGAGAGCAATC           GTTTGAGAGA GGA TCTCTCGAAC           TTGATCTATGGGCTT
orf00007         3766 - 3386     - | 
  TERM 4         3861 - 3826     - gR  100 -17.8 -5.86976 | opp_overlap 3826
  GGACAAAATAAAAAA    TAGCCACGTGGAAATT TGGA ATTTTCCACGTGGCTA     TTGTGTATGACTCGG
sORF_3           3758 - 3871     + | 
orf00010         4118 - 3912     - | 
orf00011         8147 - 4287     - | 
sORF_15          8353 - 8201     - | 
sORF_4           8249 - 8431     + | 
orf00015         9853 - 8411     - | 
orf00017        11165 - 9987     - | 
orf00018        12151 - 11162    - | 
orf00020        13168 - 12182    - | 
sORF_5          13148 - 13252    + | 
orf00021        13907 - 13290    - | 
sORF_6          13987 - 14085    + | 
orf00023        14157 - 14549    + | 
orf00025        14581 - 15639    + | 
orf00026        17646 - 15766    - | 
sORF_7          17637 - 17861    + | 
sORF_8          17724 - 17861    + | 
sORF_14         17975 - 17814    - | 
orf00030        18174 - 17950    - | 
sORF_9          18225 - 18329    + | 
sORF_10         18311 - 18430    + | 
sORF_13         18587 - 18405    - | 
sORF_11         18384 - 18518    + | 
orf00034        18754 - 19350    + | 
orf00035        19347 - 20252    + | 
  TERM 5        20295 - 20324    + T   100 -13.7 -4.89477 | opp_overlap 20297, overlap 20297
  TGTTGTATGTAGAAT       AAGGGAGAACCTT TATA AAGGTTCTCCCTA        TTTTGTTCTTCGCGA
  TERM 6        20322 - 20297    - T   100 -16.3  -3.8211 | opp_overlap 20295 20297
  TTGTATGTAGAATAA         GGGAGAACCTT TATA AAGGTTCTCCC          TATTTTGTTCTTCGC
  TERM 7        20297 - 20322    + T   100 -16.3 -4.06582 | opp_overlap 20297, overlap 20295
  TTGTATGTAGAATAA         GGGAGAACCTT TATA AAGGTTCTCCC          TATTTTGTTCTTCGC
orf00036        20505 - 20341    - | 
sORF_12         20782 - 20693    - | 
  TERM 8        20829 - 20791    - R    91 -16.9   -2.836 | opp_overlap 20792 20796, overlap 20796
  CTAACATCTAATAAC   TTAAAGAGAGGCACCCC GCATT GGGATGCCTCTCTTTAT   TTGTCTTTGAGCCAA
  TERM 9        20824 - 20796    - R   100 -16.8  -3.8579 | opp_overlap 20792 20796, overlap 20791
  ATCTAATAACTTAAA        GAGAGGCACCCC GCATT GGGATGCCTCTC        TTTATTTGTCTTTGA
orf00038        21133 - 20849    - |