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: 0.576664 %AT, 16755 nt, 112 terms.
Intergenic: 0.632757 %AT, H2T: 1340 nt, 10 terms; T2T: 714 nt, 11 terms; H2H: 1150 nt, 3 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_VVYE010000011.942.AOI_01  (length 21128)

orf00003         2604 - 3119     + | 
  TERM 1         3145 - 3183     + F   100   -12 -5.58454 | gap 1, opp_overlap 3145 3158
  TAAGAAATTCTAAAA  GGGAAAGGGAAAAGAAG CACAGA CTTCTTT-CTCTTTCCC   TTTTTTTCATGTACA
orf00005         3192 - 4067     + | 
orf00006         4144 - 4377     + | 
orf00007         4544 - 4374     - | 
orf00009         4625 - 5740     + | 
orf00010         5763 - 7016     + | 
orf00012         7044 - 8054     + | 
orf00013         8059 - 8763     + | 
orf00014         9275 - 8880     - | 
orf00016         9942 - 9286     - | 
orf00017        11138 - 9990     - | 
orf00018        12121 - 11147    - | 
orf00021        13227 - 12118    - | 
orf00022        13868 - 13218    - | 
orf00023        13932 - 14096    + | 
  TERM 2        14231 - 14179    - Tf  100 -31.2 -5.01811 | opp_overlap 14185 14195, overlap 14195
  TTAGCAAATTAAAAA TCAGAAGAAACAAAAAGGCGAAGA GTTAT TCTTCGCCTTTTTGTTTCTTCTGA TGACTAGTGATTACC
  TERM 3        14185 - 14225    + TF  100 -23.7 -3.42996 | opp_overlap 14179 14195, overlap 14195
  AATTAAAAATCAGAA  GAAACAAAAAGGCGAAGAG TTA TTCTTCGCCTTTTTGTTTC  TTCTGATGACTAGTG
  TERM 4        14215 - 14195    - Tf  100 -11.2 -5.50774 | opp_overlap 14185 14195, overlap 14179
  CAGAAGAAACAAAAA            GGCGAAGA GTTAT TCTTCGCC            TTTTTGTTTCTTCTG
  TERM 5        14195 - 14215    + TF  100 -11.9 -5.50774 | opp_overlap 14195 14179, overlap 14185
  CAGAAGAAACAAAAA            GGCGAAGAG TTA TTCTTCGCC            TTTTTGTTTCTTCTG
orf00024        14403 - 14242    - | 
  TERM 6        14346 - 14358    + gF  100  -9.1 -5.19003 | 
  CCGATGCCATTCTCT                CACGG AAA CCGTG                TTTGTTTTTTCTCTT
sORF_1          14391 - 14486    + | 
orf00025        14597 - 15163    + | 
  TERM 7        15181 - 15223    + F    78 -10.1 -3.32997 | gap 1, opp_overlap 15181 15189, overlap 15189
  GTTATATAAATGACA TAAAGAAACGGTGGATTTGC TACG GCATCTCCACCGTTT-TTTA TTAACTTTGTGCCAC
  TERM 8        15189 - 15216    + F   100  -9.8 -5.52096 | opp_overlap 15181 15189, overlap 15181
  AATGACATAAAGAAA        CGGTGGATTTGC TACG GCATCTCCACCG         TTTTTTATTAACTTT
orf00026        15191 - 16666    + | 
orf00027        17509 - 16745    - | 
orf00029        17817 - 17506    - | 
  TERM 9        17879 - 17857    - R    88  -4.9  -5.4492 | 
  GATAGAGATAAAAAA           TTAGACACG GAATG CGTACCTAA           CTAAAAAACATACCG
sORF_5          17955 - 17857    - | 
orf00031        18628 - 17933    - | 
sORF_2          18614 - 18730    + | 
  TERM 10       18750 - 18777    + GFH  86 -10.1 -3.93695 | 
  TTCAAGCCTTGGGAA        CTTTAGTTTCA AGCGTC TGAAACTAAAG         TTTCTCCATGATGAA
sORF_3          18706 - 18813    + | 
  TERM 11       18828 - 18876    + GT  100 -14.8  -3.6363 | opp_overlap 18821 18816 18838 18844, overlap 18824 18838
  AAACTATAGTTTCTC TACGGCGAAACCAAAGGTTCCA ATGCA TGAAACTATTGGTTTTGCCGTA TTAATTTATAGTCAT
sORF_4          18785 - 18880    + | 
orf00033        19932 - 18943    - | 
  TERM 12       20047 - 20025    - R    90  -6.9  -5.1675 | opp_overlap 20025
  CTATTCATTAAAAAA           GGCGACACT TGTAT AGAGCCGCC           TTATCATATATACAA
orf00036        21090 - 20074    - |