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: 0.542433 %AT, 17392 nt, 100 terms.
Intergenic: 0.619329 %AT, H2T: 2371 nt, 17 terms; T2T: 620 nt, 11 terms; H2H: 2268 nt, 6 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_QRZF010000011.961.AOI_01  (length 21119)

orf00006         4102 - 1721     - | 
orf00007         4095 - 4223     + | 
sORF_8           4411 - 4220     - | 
sORF_1           4356 - 4454     + | 
sORF_7           4739 - 4638     - | 
orf00010         4714 - 5961     + | 
orf00012         6028 - 6981     + | 
  TERM 1         7015 - 7061     + F   100 -16.2 -4.72272 | opp_overlap 7021
  GACATTGAACTATTA TATAAATTTCGCCTTAGTTTGT CTT ACACTCTAAGGCGAAATTTGTA TTTTTGCTCAAAAAG
orf00014         7172 - 7813     + | 
orf00016         7873 - 8946     + | 
orf00017         8943 - 9917     + | 
orf00018         9991 - 11148    + | 
orf00019        11157 - 11843    + | 
orf00021        11848 - 12237    + | 
  TERM 2        12301 - 12271    - Tf  100 -14.1 -4.78848 | opp_overlap 12271
  GGCTCAAATAGAAAA       GCCGCAAAGCACT TTATC AGTCCTTTGCGGC       TTTCTTATTCTTTAT
  TERM 3        12271 - 12301    + TF  100 -14.1 -4.64159 | opp_overlap 12271
  GGCTCAAATAGAAAA       GCCGCAAAGCACT TTATC AGTCCTTTGCGGC       TTTCTTATTCTTTAT
orf00025        12494 - 12333    - | 
  TERM 4        12437 - 12449    + gF  100  -9.1 -5.19003 | 
  CGGAAGCCATTCTCT                CACGG AAA CCGTG                TTTGTTTTTTCTCTT
sORF_2          12477 - 12575    + | 
orf00027        12597 - 13250    + | 
  TERM 5        13322 - 13284    - Tf   83   -11 -3.56541 | opp_overlap 13285, overlap 13285
  AGTACGATTATACAA   GCTGCCTGTCAGAAGAAT TAA ACACTTCTGGCAGGCAGT   TTTTTTTCTATAGGG
  TERM 6        13321 - 13285    - Tf   95 -14.5 -2.73443 | opp_overlap 13285, overlap 13284
  GTACGATTATACAAG    CTGCCTGTCAGAAGAAT TAA ACACTTCTGGCAGGCAG    TTTTTTTTCTATAGG
  TERM 7        13285 - 13321    + TF  100 -14.6 -6.02914 | opp_overlap 13285 13284
  GTACGATTATACAAG    CTGCCTGTCAGAAG AATTAAACA CTTCTGGCAGGCAG    TTTTTTTTCTATAGG
sORF_6          13443 - 13330    - | 
orf00029        13418 - 13741    + | 
orf00031        13767 - 14756    + | 
orf00032        14776 - 15462    + | 
sORF_3          15525 - 15620    + | 
sORF_4          15634 - 15726    + | 
orf00033        15825 - 16136    + | 
orf00035        16182 - 16946    + | 
orf00037        16993 - 18852    + | 
orf00039        18967 - 19176    + | 
sORF_5          19188 - 19283    + | 
orf00041        20701 - 19301    - | 
orf00042        20844 - 20698    - | 
orf00043        21117 - 20884    - |