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: 0.463609 %AT, 14674 nt, 126 terms.
Intergenic: 0.510314 %AT, H2T: 1135 nt, 10 terms; T2T: 1852 nt, 25 terms; H2H: 1825 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_KB2910321.7.AOI_01  (length 21137)

sORF_1           3585 - 3683     + | 
orf00007         5624 - 5172     - | 
orf00008         6064 - 5645     - | 
orf00010         6867 - 6223     - | 
orf00012         7721 - 6918     - | 
orf00013         8285 - 7740     - | 
orf00014         8610 - 8317     - | 
sORF_2           8600 - 8692     + | 
sORF_12          8820 - 8662     - | 
sORF_11          8932 - 8834     - | 
orf00017         8926 - 9972     + | 
orf00018         9987 - 11150    + | 
orf00019        11239 - 12720    + | 
  TERM 1        12752 - 12797    + T   100  -6.1 -5.74122 | overlap 12756
  CTCCCTTTATTCTCC CTTCCCCCGAGGTTTAGCTTG CATG TAGGCTAAGTCTCGGGGTTAC TTTTTTTCTCTGCTG
  TERM 2        12756 - 12793    + T   100 -15.7 -4.10161 | overlap 12752
  CTTTATTCTCCCTTC   CCCCGAGGTTTAGCTTG CATG TAGGCTAAGTCTCGGGG    TTACTTTTTTTCTCT
sORF_10         12888 - 12781    - | 
orf00020        13068 - 14165    + | 
orf00022        14176 - 15048    + | 
orf00024        15053 - 16603    + | 
  TERM 3        16620 - 16662    + F   100 -15.6 -3.29263 | opp_overlap 16627, overlap 16622
  TTATCGTACCTTTGT GAGCGAACCCTACGACAGCT AAT GGCTGGAGTAGGGTTCGCTA TTGTAGCGAAAATAT
  TERM 4        16622 - 16660    + F   100 -18.2 -3.21395 | opp_overlap 16627, overlap 16620
  ATCGTACCTTTGTGA   GCGAACCCTACGACAGCT AAT GGCTGGAGTAGGGTTCGC   TATTGTAGCGAAAAT
orf00025        16641 - 17216    + | 
orf00026        17244 - 17636    + | 
orf00028        17645 - 18955    + | 
sORF_9          19154 - 18960    - | 
  TERM 5        19037 - 19008    - GgTf  78 -12.3 -2.53903 | opp_overlap 19007, overlap 19007 19005
  CGGTGCAAAAATTAG       GTATATACGGTGC AAGT GCACCCTATATAC        GGTGCTAATGCATGG
sORF_7          19333 - 19091    - | 
sORF_8          19252 - 19091    - | 
  TERM 6        19126 - 19184    + GgF 100 -19.9 -3.12895 | gap 1, opp_overlap 19121 19125 19147 19165, overlap 19125 19143
  TTGCGACCAATATAC -CTCGCATTTGCGACGTATATACCTCGC ACTC GCGACCAATATACGTCGCAAATGCGAGG TATATTGGTCGCAAA
sORF_4          19045 - 19233    + | 
sORF_3          18973 - 19233    + | 
sORF_5          19133 - 19342    + | 
sORF_6          19220 - 19342    + | 
orf00035        19361 - 21001    + |