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: 0.492275 %AT, 16375 nt, 114 terms.
Intergenic: 0.556684 %AT, H2T: 1887 nt, 15 terms; T2T: 656 nt, 19 terms; H2H: 2561 nt, 10 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_NHRU010000011.958.AOI_01  (length 21125)

orf00009         4258 - 3041     - | 
orf00010         5010 - 4321     - | 
sORF_17          5225 - 5121     - | 
sORF_1           5084 - 5239     + | 
orf00014         5242 - 5850     + | 
sORF_16          5982 - 5857     - | 
sORF_15          6057 - 5857     - | 
  TERM 1         6080 - 6065     - R    83  -6.2 -5.05606 | opp_overlap 6065, overlap 6061
  GCTAACAAAAATAAA              TTTTCC GGCC GGAAAA               TCTCTATCCAAAGCC
  TERM 2         6145 - 6106     - R   100   -16 -2.87463 | opp_overlap 6093 6106 6110, overlap 6081 6093 6110
  AAGCCTTCGGATATA  TAAACGAAGCCTTTGGAT ACAT ATCCGAAAGCTTCGTTTA   TATATCCGAAACCTT
orf00017         6236 - 6084     - | 
sORF_14          6409 - 6242     - | 
sORF_2           6335 - 6442     + | 
sORF_13          6521 - 6429     - | 
orf00022         6514 - 8568     + | 
  TERM 3         8594 - 8625     + FH   93 -11.5 -4.34402 | opp_overlap 8592 8587 8595, overlap 8595
  GTCACAAACGAAAGG      AGGCGGGCAGACA CGATAT TGTCAGCCCGCCC       TTTTCATCTCAACCA
  TERM 4         8595 - 8624     + FH   95   -15  -3.2032 | opp_overlap 8595 8592 8587, overlap 8594
  TCACAAACGAAAGGA       GGCGGGCAGACA CGATAT TGTCAGCCCGCC        CTTTTCATCTCAACC
orf00024         8653 - 9279     + | 
  TERM 5         9319 - 9284     - T    79  -7.7 -4.42514 | gap 2, opp_overlap 9283 9284, overlap 9281
  AACAGAAATAAAGAA   GGGCTGTAC--CGCGAA TCGT TTCGCTCCGTACAGCCC    CCTTTTCGTATCGAA
orf00027         9765 - 9346     - | 
sORF_12          9937 - 9746     - | 
orf00030        11149 - 9983     - | 
orf00031        12163 - 11168    - | 
orf00033        13348 - 12227    - | 
orf00035        14375 - 13362    - | 
sORF_11         14552 - 14394    - | 
sORF_3          14438 - 14572    + | 
orf00039        14554 - 15156    + | 
orf00040        15153 - 15704    + | 
orf00041        15763 - 16977    + | 
orf00043        16988 - 17593    + | 
orf00044        17619 - 17846    + | 
orf00045        17843 - 18295    + | 
orf00047        18328 - 19242    + | 
orf00049        19265 - 19786    + | 
  TERM 6        20084 - 20029    - Tf   77  -9.6 -3.63092 | opp_overlap 20031, overlap 20002 20003 20027 20031
  ACACTGACAGAAAGA CAGGTCGACCTAGCCGAGCGTTTAGG TCGA CCTTACGGAGCGGTTAGGTCGACCTA AAACGGACGGAAGGT
  TERM 7        20060 - 20031    - Tf   80 -10.7 -3.38696 | opp_overlap 20031, overlap 20002 20003 20027 20029
  ACTGACAGAAAGACA       GGTCGACCTAGCC GAGC GTTTAGGTCGACC        TTACGGAGCGGTTAG
sORF_10         20225 - 20082    - | 
sORF_4          20127 - 20240    + | 
sORF_5          20303 - 20401    + | 
sORF_9          20483 - 20364    - | 
sORF_6          20401 - 20538    + | 
sORF_8          20601 - 20509    - | 
sORF_7          20483 - 20608    + | 
orf00055        21103 - 20630    - |