#---------------------------------------------------------------------------------
# qrna 1.2b (Tue Dec 18 15:04:38 CST 2001) using squid 1.5m (Sept 1997)
#---------------------------------------------------------------------------------
# PAM model = BLOSUM62 scaled by 1.000
#---------------------------------------------------------------------------------
# RNA model = /mix_tied_linux.cfg
#---------------------------------------------------------------------------------
# seq file = tst.out
# #seqs: 2 (max_len = 290)
#---------------------------------------------------------------------------------
# window version: window = 150 slide = 50 -- length range = [0,9999999]
#---------------------------------------------------------------------------------
# 1 [+ strand]
>Contig1/24732-25017 (290)
>chr5.pseudo/527251-527533 (290)
length of whole alignment after removing common gaps: 290
length alignment: 150 (id=62.67)
posX: 0-149 [0-149](150) -- (0.19 0.25 0.31 0.25)
posY: 0-149 [0-145](146) -- (0.14 0.31 0.25 0.31)
34.327235 39.943369 26.661628
28.676235 4.323732 17.984592
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = COD
OTH ends = 0 149
COD ends = 0 149
RNA ends = 76 91
OTH = 33.356 COD = 38.943 RNA = 25.665
logoddspostOTH = 0.000 logoddspostCOD = 5.588 logoddspostRNA = -7.691
length alignment: 150 (id=64.00)
posX: 50-199 [50-198](149) -- (0.19 0.26 0.29 0.26)
posY: 50-199 [47-195](149) -- (0.17 0.29 0.24 0.30)
39.662831 22.857014 31.781677
35.882277 13.531348 24.975088
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 50 199
COD ends = 51 197
RNA ends = 76 91
OTH = 38.764 COD = 21.859 RNA = 30.795
logoddspostOTH = 0.000 logoddspostCOD = -16.905 logoddspostRNA = -7.970
length alignment: 150 (id=61.33)
posX: 100-249 [100-246](147) -- (0.24 0.24 0.28 0.23)
posY: 100-249 [97-243](147) -- (0.22 0.26 0.28 0.24)
29.980841 -9.710794 19.504746
29.998914 -25.369993 19.522819
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 249 100
COD ends = 100 240
RNA ends = 250 250
OTH = 29.990 COD = -10.711 RNA = 19.514
logoddspostOTH = 0.000 logoddspostCOD = -40.701 logoddspostRNA = -10.476
length alignment: 140 (id=62.86)
posX: 150-289 [150-285](136) -- (0.22 0.25 0.27 0.26)
posY: 150-289 [146-282](137) -- (0.27 0.23 0.26 0.24)
27.136986 -17.070736 17.286579
28.477528 -24.525347 18.465446
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH
OTH ends = 289 150
COD ends = 154 288
RNA ends = 190 290
OTH = 27.958 COD = -18.063 RNA = 17.993
logoddspostOTH = 0.000 logoddspostCOD = -46.020 logoddspostRNA = -9.964