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: 0.606989 %AT, 17857 nt, 115 terms.
Intergenic: 0.634759 %AT, H2T: 2248 nt, 18 terms; T2T: 675 nt, 13 terms; H2H: 985 nt, 9 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_0149331.0.AOI_01  (length 20912)

orf00005          971 - 1189     + | 
orf00007         1302 - 1826     + | 
orf00008         1831 - 2463     + | 
orf00010         2570 - 6199     + | 
orf00011         6196 - 8019     + | 
orf00013         8186 - 8058     - | 
sORF_18          8293 - 8183     - | 
sORF_1           8159 - 8332     + | 
sORF_2           8262 - 8375     + | 
orf00014         8356 - 8643     + | 
orf00015         8669 - 8794     + | 
sORF_17          8881 - 8786     - | 
sORF_3           8788 - 8883     + | 
orf00017         8916 - 9950     + | 
orf00019         9976 - 11514    + | 
  TERM 1        11736 - 11759    + F   100 -13.2 -3.90328 | opp_overlap 11736 11735 11734
  AGAAGAATGAAAATT          TGGGAGCCTC TTTA GAGGTTCCCA           TTTATCAACCTTATC
orf00021        11800 - 12222    + | 
  TERM 2        12325 - 12349    + TF  100 -11.5 -5.00267 | 
  GACTTATAATTTTGG          GGTGGAACTCT AAA AAAGTTCCACC          TTTCTTTTTGTCATT
sORF_16         12415 - 12305    - | 
sORF_15         12521 - 12420    - | 
sORF_4          12364 - 12480    + | 
orf00024        12499 - 12903    + | 
orf00027        13124 - 13789    + | 
orf00029        14011 - 13868    - | 
orf00032        14126 - 14260    + | 
sORF_14         14343 - 14236    - | 
sORF_13         14492 - 14367    - | 
orf00037        14884 - 14477    - | 
sORF_12         14995 - 14891    - | 
sORF_5          14898 - 14999    + | 
sORF_11         15083 - 14964    - | 
sORF_6          14978 - 15067    + | 
sORF_10         15159 - 15040    - | 
orf00040        16349 - 15183    - | 
sORF_7          16352 - 16459    + | 
sORF_9          16554 - 16417    - | 
  TERM 3        16483 - 16529    + gF   90 -13.3 -2.78891 | gap 1, opp_overlap 16483 16486 16491, overlap 16486 16491
  TGATATACAGCTAAA CAACGAAA-GGCAAGCAGTC TTTTTATC GACTACTTGCCTTTTCGTTG TGATTCCGTTGCGAT
  TERM 4        16486 - 16526    + gF   78  -9.2 -3.54109 | gap 1, opp_overlap 16483 16486 16491, overlap 16483 16491
  TATACAGCTAAACAA CGAAA-GGCAAGCAGTC TTTTTATC GACTACTTGCCTTTTCG  TTGTGATTCCGTTGC
  TERM 5        16491 - 16520    + gF   82  -7.9 -4.52781 | opp_overlap 16486 16483 16491, overlap 16486 16483
  AGCTAAACAACGAAA       GGCAAGCAGTC TTTTTATC GACTACTTGCC        TTTTCGTTGTGATTC
sORF_8          16516 - 16611    + | 
orf00050        18234 - 16780    - | 
orf00052        18976 - 18248    - | 
orf00054        20803 - 19028    - |