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: 0.504322 %AT, 15734 nt, 92 terms.
Intergenic: 0.511878 %AT, H2T: 5254 nt, 56 terms; T2T: 3672 nt, 59 terms; H2H: 5342 nt, 58 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_LT6357831.0.AOI_01  (length 21140)

sORF_1            841 - 930      + | 
sORF_11          1096 - 950      - | 
sORF_2            960 - 1085     + | 
  TERM 1         1195 - 1170     - TfRH 100   -14 -5.96521 | 
  ATGAAGCAAAAAAAA         CGCCCCGACC GGGAAG GGTCGGAGCG          TTACAGTCATAAACT
orf00007         5274 - 4369     - | 
sORF_3           5246 - 5356     + | 
sORF_4           5479 - 5595     + | 
orf00009         6095 - 5628     - | 
orf00011         6322 - 6092     - | 
sORF_5           6408 - 6503     + | 
orf00013         6511 - 7770     + | 
orf00015         7843 - 8805     + | 
  TERM 2         8822 - 8871     + T   100 -17.3 -4.77867 | gap 1, opp_overlap 8810 8825, overlap 8825
  AATCAGCACTAAAAT AAATGCCGTGACGGGCG-GAGGGA TAT TCCCTCTTGTCGGTCACGGCATTC TTTTATCTTATCTGT
  TERM 3         8868 - 8825     - T   100 -14.6 -4.73614 | gap 1, opp_overlap 8822 8825, overlap 8810
  CAGCACTAAAATAAA TGCCGTGACGGGC-GGAGGGA TAT TCCCTCTTGTCGGTCACGGCA TTCTTTTATCTTATC
  TERM 4         8825 - 8868     + T   100   -19 -4.46621 | gap 1, opp_overlap 8810 8825, overlap 8822
  CAGCACTAAAATAAA TGCCGTGACGGGCG-GAGGGA TAT TCCCTCTTGTCGGTCACGGCA TTCTTTTATCTTATC
orf00017         9279 - 8917     - | 
orf00018         9905 - 9327     - | 
orf00020        11143 - 9989     - | 
orf00022        12157 - 11180    - | 
orf00024        13230 - 12160    - | 
orf00026        13896 - 13246    - | 
sORF_10         13997 - 13893    - | 
sORF_6          13869 - 13958    + | 
sORF_7          13984 - 14085    + | 
sORF_9          14177 - 14269    + | 
sORF_8          14075 - 14269    + | 
orf00029        15221 - 14247    - | 
orf00031        17711 - 15270    - | 
orf00032        18808 - 17735    - | 
orf00034        20611 - 18839    - | 
orf00036        21122 - 20634    - |