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: 0.608398 %AT, 17362 nt, 121 terms.
Intergenic: 0.647239 %AT, H2T: 1974 nt, 10 terms; T2T: 587 nt, 15 terms; H2H: 2349 nt, 7 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_AUKF010000081.93.AOI_01  (length 21128)

orf00006         2123 - 3265     + | 
orf00007         3267 - 4052     + | 
  TERM 1         4068 - 4112     + F   100 -15.4 -4.64676 | gap 1, opp_overlap 4075
  ACTTTAAAGAGTTTT TCTAAAATGCTGCACA-TGAT AAAT ACCAATGTGCAGCATTTTAGA TTTTATTACAAATAC
orf00009         4210 - 4764     + | 
orf00010         4775 - 6460     + | 
  TERM 2         6468 - 6492     + F    79 -10.8 -2.96711 | opp_overlap 6466 6465 6470 6487, overlap 6470
  AAAAATAAACCACTA          GAGGTATGCT ACAAA GGCATACCTC          TCTATAAATTATAAG
orf00012         6517 - 7587     + | 
orf00014         7622 - 8869     + | 
orf00015         8904 - 9899     + | 
sORF_1           9886 - 9978     + | 
orf00016        11131 - 9983     - | 
orf00017        12136 - 11141    - | 
orf00019        13211 - 12153    - | 
orf00021        13921 - 13214    - | 
  TERM 3        13995 - 13960    - gRH 100   -15 -6.04378 | opp_overlap 13960 13966
  AAAGTACAAAAAAAA    CAGAAAGAAGCAAAGA TATA CCTTTACTTCTTTCTG     TTTTAATCAGTTTTC
sORF_2          13912 - 14001    + | 
sORF_7          14182 - 14027    - | 
orf00025        14159 - 14380    + | 
orf00027        14440 - 15006    + | 
  TERM 4        15027 - 15055    + F   100 -12.4 -4.75174 | opp_overlap 15025 15020, overlap 15031
  TAATTCAAGCATATT        GATGGGGGCGGA CTTTA TCCGCCCCTAAC        TTTTTACATTAACTA
  TERM 5        15031 - 15051    + F   100   -14 -2.86432 | opp_overlap 15025 15020, overlap 15027
  TCAAGCATATTGATG            GGGGCGGA CTTTA TCCGCCCC            TAACTTTTTACATTA
orf00028        15079 - 16116    + | 
orf00030        16138 - 16830    + | 
sORF_6          16912 - 16823    - | 
orf00031        16904 - 17224    + | 
orf00033        17217 - 18005    + | 
  TERM 6        18032 - 18052    + GF   93 -11.2 -4.32951 | opp_overlap 18032
  TAATCCATTTAAAAA            GCCTTGTC ATCAC GACAAGGC            TTTCTTGCTTAAAGT
sORF_4          18057 - 18176    + | 
sORF_3          17980 - 18186    + | 
  TERM 7        18228 - 18197    - T   100 -10.2 -6.01725 | 
  AATAAAAATAAAAAA      GGACTGACTTTGCT TCCC AGCTAAATCAGCCC       ACGTACTAGTACTTT
  TERM 8        18490 - 18468    - T   100 -12.1 -4.84246 | opp_overlap 18468
  AAAACAACAAATAAA           GGCAACAGT TATTT ACTGTTGCC           TTATATAAATTATCT
  TERM 9        18468 - 18490    + T    90 -12.1 -3.56959 | opp_overlap 18468
  AAAACAACAAATAAA           GGCAACAGT TATTT ACTGTTGCC           TTATATAAATTATCT
orf00036        19564 - 18518    - | 
sORF_5          19653 - 19769    + | 
orf00037        20947 - 19745    - |