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#---------------------------------------------------------------------------------
#      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  =  ecoli-trna.blast.q
#                   #seqs: 94 (max_len = 78)
#---------------------------------------------------------------------------------
#      full length version:  -- length range = [0,1000]
#---------------------------------------------------------------------------------
# 1  [+ strand] 
>DA0780-1- (76)
>ECOLI-225501- (76)

length alignment: 76 (id=77.63)
posX: 0-75 [0-72](73) -- (0.18 0.30 0.36 0.16) 
posY: 0-75 [0-71](72) -- (0.17 0.29 0.33 0.21) 
 21.414226 -10.515196 16.075247
 19.988807 -3.972533 12.698167
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 75
COD  ends = 74 0
RNA  ends = 0 12
              OTH =       20.871             COD =       -4.957             RNA =       15.208 
   logoddspostOTH =        0.000  logoddspostCOD =      -25.828  logoddspostRNA =       -5.663 

# 2  [+ strand] 
>DA0780-1- (76)
>ECOLI-4034592- (76)

length alignment: 76 (id=77.63)
posX: 0-75 [0-72](73) -- (0.18 0.30 0.36 0.16) 
posY: 0-75 [0-71](72) -- (0.17 0.29 0.33 0.21) 
 21.414226 -10.515196 16.075247
 19.988807 -3.972533 12.698167
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 75
COD  ends = 74 0
RNA  ends = 0 12
              OTH =       20.871             COD =       -4.957             RNA =       15.208 
   logoddspostOTH =        0.000  logoddspostCOD =      -25.828  logoddspostRNA =       -5.663 

# 3  [+ strand] 
>DA0780-1- (70)
>ECOLI-3979754- (70)

length alignment: 70 (id=72.86)
posX: 0-69 [0-68](69) -- (0.17 0.29 0.38 0.16) 
posY: 0-69 [0-69](70) -- (0.16 0.30 0.36 0.19) 
 21.384909 12.463364 22.249356
 21.249381 17.921616 22.037246
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 69
COD  ends = 68 1
RNA  ends = 3 69
              OTH =       21.319             COD =       16.954             RNA =       22.147 
   logoddspostOTH =        0.000  logoddspostCOD =       -4.365  logoddspostRNA =        0.828 

# 4  [+ strand] 
>DA0780-8- (56)
>ECOLI-779995- (56)

length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18) 
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18) 
 14.761275 -0.369781 17.076846
 14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 55 0
COD  ends = 54 0
RNA  ends = 35 19
              OTH =       14.801             COD =        9.226             RNA =       20.928 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.574  logoddspostRNA =        6.127 

# 5  [+ strand] 
>DA0780-8- (56)
>ECOLI-780298- (56)

length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18) 
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18) 
 14.761275 -0.369781 17.076846
 14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 55 0
COD  ends = 54 0
RNA  ends = 35 19
              OTH =       14.801             COD =        9.226             RNA =       20.928 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.574  logoddspostRNA =        6.127 

# 6  [+ strand] 
>DA0780-8- (56)
>ECOLI-2518730- (56)

length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18) 
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18) 
 14.761275 -0.369781 17.076846
 14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 55 0
COD  ends = 54 0
RNA  ends = 35 19
              OTH =       14.801             COD =        9.226             RNA =       20.928 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.574  logoddspostRNA =        6.127 

# 7  [+ strand] 
>DA0780-8- (56)
>ECOLI-2518850- (56)

length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18) 
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18) 
 14.761275 -0.369781 17.076846
 14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 55 0
COD  ends = 54 0
RNA  ends = 35 19
              OTH =       14.801             COD =        9.226             RNA =       20.928 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.574  logoddspostRNA =        6.127 

# 8  [+ strand] 
>DA0780-8- (56)
>ECOLI-2518972- (56)

length alignment: 56 (id=71.43)
posX: 0-55 [0-55](56) -- (0.20 0.29 0.34 0.18) 
posY: 0-55 [0-54](55) -- (0.18 0.29 0.35 0.18) 
 14.761275 -0.369781 17.076846
 14.838704 10.225100 21.877122
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 55 0
COD  ends = 54 0
RNA  ends = 35 19
              OTH =       14.801             COD =        9.226             RNA =       20.928 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.574  logoddspostRNA =        6.127 

# 9  [+ strand] 
>DA0780-2- (73)
>ECOLI-2284230- (73)

length alignment: 73 (id=64.38)
posX: 0-72 [0-71](72) -- (0.18 0.31 0.35 0.17) 
posY: 0-72 [0-72](73) -- (0.15 0.27 0.38 0.19) 
 13.918545 -8.608490 24.007519
 15.073192 7.016852 12.344431
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 72 0
COD  ends = 72 0
RNA  ends = 0 70
              OTH =       14.608             COD =        6.017             RNA =       23.008 
   logoddspostOTH =        0.000  logoddspostCOD =       -8.592  logoddspostRNA =        8.400 

# 10  [+ strand] 
>DA0780-7- (59)
>ECOLI-2945191- (59)

length alignment: 59 (id=67.80)
posX: 0-58 [0-55](56) -- (0.20 0.27 0.36 0.18) 
posY: 0-58 [0-56](57) -- (0.19 0.28 0.32 0.21) 
 7.994668 -17.443195 7.730549
 8.785962 -9.672509 13.155362
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 58 0
COD  ends = 58 1
RNA  ends = 39 21
              OTH =        8.444             COD =      -10.666             RNA =       12.189 
   logoddspostOTH =        0.000  logoddspostCOD =      -19.110  logoddspostRNA =        3.745 

# 11  [+ strand] 
>DA0780-7- (59)
>ECOLI-2945301- (59)

length alignment: 59 (id=67.80)
posX: 0-58 [0-55](56) -- (0.20 0.27 0.36 0.18) 
posY: 0-58 [0-56](57) -- (0.19 0.28 0.32 0.21) 
 7.994668 -17.443195 7.730549
 8.785962 -9.672509 13.155362
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 58 0
COD  ends = 58 1
RNA  ends = 39 21
              OTH =        8.444             COD =      -10.666             RNA =       12.189 
   logoddspostOTH =        0.000  logoddspostCOD =      -19.110  logoddspostRNA =        3.745 

# 12  [+ strand] 
>DA0780-7- (59)
>ECOLI-2945411- (59)

length alignment: 59 (id=67.80)
posX: 0-58 [0-55](56) -- (0.20 0.27 0.36 0.18) 
posY: 0-58 [0-56](57) -- (0.19 0.28 0.32 0.21) 
 7.994668 -17.443195 7.730549
 8.785962 -9.672509 13.155362
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 58 0
COD  ends = 58 1
RNA  ends = 39 21
              OTH =        8.444             COD =      -10.666             RNA =       12.189 
   logoddspostOTH =        0.000  logoddspostCOD =      -19.110  logoddspostRNA =        3.745 

# 13  [+ strand] 
>DA0780-1- (76)
>ECOLI-3424373- (76)

length alignment: 76 (id=77.63)
posX: 0-75 [0-72](73) -- (0.16 0.36 0.30 0.18) 
posY: 0-75 [0-71](72) -- (0.21 0.33 0.29 0.17) 
 20.682006 -9.755632 13.248665
 21.241284 -22.237923 16.258281
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 75 0
COD  ends = 1 68
RNA  ends = 75 63
              OTH =       20.989             COD =      -10.755             RNA =       15.427 
   logoddspostOTH =        0.000  logoddspostCOD =      -31.744  logoddspostRNA =       -5.561 

# 14  [+ strand] 
>DA0780-6- (71)
>ECOLI-2815582- (71)

length alignment: 71 (id=71.83)
posX: 0-70 [0-67](68) -- (0.16 0.34 0.31 0.19) 
posY: 0-70 [0-68](69) -- (0.19 0.32 0.28 0.22) 
 16.431838 -14.269383 12.463979
 16.326307 -7.331733 13.720289
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 70
COD  ends = 70 1
RNA  ends = 24 8
              OTH =       16.380             COD =       -8.320             RNA =       13.225 
   logoddspostOTH =        0.000  logoddspostCOD =      -24.700  logoddspostRNA =       -3.155 

# 15  [+ strand] 
>DA0780-6- (71)
>ECOLI-2815857- (71)

length alignment: 71 (id=71.83)
posX: 0-70 [0-67](68) -- (0.16 0.34 0.31 0.19) 
posY: 0-70 [0-68](69) -- (0.19 0.32 0.28 0.22) 
 16.431838 -14.269383 12.463979
 16.326307 -7.331733 13.720289
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 70
COD  ends = 70 1
RNA  ends = 24 8
              OTH =       16.380             COD =       -8.320             RNA =       13.225 
   logoddspostOTH =        0.000  logoddspostCOD =      -24.700  logoddspostRNA =       -3.155 

# 16  [+ strand] 
>DA0780-6- (71)
>ECOLI-2815996- (71)

length alignment: 71 (id=71.83)
posX: 0-70 [0-67](68) -- (0.16 0.34 0.31 0.19) 
posY: 0-70 [0-68](69) -- (0.19 0.32 0.28 0.22) 
 16.431838 -14.269383 12.463979
 16.326307 -7.331733 13.720289
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 70
COD  ends = 70 1
RNA  ends = 24 8
              OTH =       16.380             COD =       -8.320             RNA =       13.225 
   logoddspostOTH =        0.000  logoddspostCOD =      -24.700  logoddspostRNA =       -3.155 

# 17  [+ strand] 
>DA0780-6- (71)
>ECOLI-2816271- (71)

length alignment: 71 (id=71.83)
posX: 0-70 [0-67](68) -- (0.16 0.34 0.31 0.19) 
posY: 0-70 [0-68](69) -- (0.19 0.32 0.28 0.22) 
 16.431838 -14.269383 12.463979
 16.326307 -7.331733 13.720289
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 70
COD  ends = 70 1
RNA  ends = 24 8
              OTH =       16.380             COD =       -8.320             RNA =       13.225 
   logoddspostOTH =        0.000  logoddspostCOD =      -24.700  logoddspostRNA =       -3.155 

# 18  [+ strand] 
>DA0780-1- (76)
>ECOLI-2515836- (76)

length alignment: 76 (id=71.05)
posX: 0-75 [0-72](73) -- (0.16 0.36 0.30 0.18) 
posY: 0-75 [0-71](72) -- (0.21 0.33 0.26 0.19) 
 14.736984 -14.375325 8.884532
 14.851236 -24.156886 9.868232
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 75 0
COD  ends = 1 75
RNA  ends = 75 63
              OTH =       14.795             COD =      -15.374             RNA =        9.459 
   logoddspostOTH =        0.000  logoddspostCOD =      -30.169  logoddspostRNA =       -5.337 

# 19  [+ strand] 
>DA0780-1- (76)
>ECOLI-2515951- (76)

length alignment: 76 (id=71.05)
posX: 0-75 [0-72](73) -- (0.16 0.36 0.30 0.18) 
posY: 0-75 [0-71](72) -- (0.21 0.33 0.26 0.19) 
 14.736984 -14.375325 8.884532
 14.851236 -24.156886 9.868232
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 75 0
COD  ends = 1 75
RNA  ends = 75 63
              OTH =       14.795             COD =      -15.374             RNA =        9.459 
   logoddspostOTH =        0.000  logoddspostCOD =      -30.169  logoddspostRNA =       -5.337 

# 20  [+ strand] 
>DA0780-6- (52)
>ECOLI-2155594- (52)

length alignment: 52 (id=71.15)
posX: 0-51 [0-48](49) -- (0.16 0.41 0.27 0.16) 
posY: 0-51 [0-48](49) -- (0.18 0.41 0.29 0.12) 
 5.862400 -19.930995 -1.194701
 7.783836 -15.355771 0.726735
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 51 0
COD  ends = 50 0
RNA  ends = 52 52
              OTH =        7.122             COD =      -16.296             RNA =        0.065 
   logoddspostOTH =        0.000  logoddspostCOD =      -23.418  logoddspostRNA =       -7.057 

# 21  [+ strand] 
>DA0780-7- (59)
>ECOLI-3315645- (59)

length alignment: 59 (id=66.10)
posX: 0-58 [0-55](56) -- (0.18 0.36 0.27 0.20) 
posY: 0-58 [0-56](57) -- (0.21 0.30 0.28 0.21) 
 7.886726 -12.920042 12.597060
 6.999592 -16.997763 6.986972
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 58
COD  ends = 0 58
RNA  ends = 20 36
              OTH =        7.510             COD =      -13.837             RNA =       11.626 
   logoddspostOTH =        0.000  logoddspostCOD =      -21.347  logoddspostRNA =        4.116 

# 22  [+ strand] 
>DA0940-1- (77)
>ECOLI-225500- (77)

length alignment: 77 (id=75.32)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.16 0.31 0.33 0.20) 
 24.181055 -0.353323 26.401988
 23.109013 11.590026 23.929123
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 76
COD  ends = 76 0
RNA  ends = 0 73
              OTH =       23.742             COD =       10.590             RNA =       25.641 
   logoddspostOTH =        0.000  logoddspostCOD =      -13.152  logoddspostRNA =        1.899 

# 23  [+ strand] 
>DA0940-1- (77)
>ECOLI-4034591- (77)

length alignment: 77 (id=75.32)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.16 0.31 0.33 0.20) 
 24.181055 -0.353323 26.401988
 23.109013 11.590026 23.929123
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 76
COD  ends = 76 0
RNA  ends = 0 73
              OTH =       23.742             COD =       10.590             RNA =       25.641 
   logoddspostOTH =        0.000  logoddspostCOD =      -13.152  logoddspostRNA =        1.899 

# 24  [+ strand] 
>DA0940-1- (77)
>ECOLI-779777- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28) 
 19.326669 -6.735706 19.727199
 19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 76 0
COD  ends = 74 1
RNA  ends = 0 73
              OTH =       19.344             COD =       -2.948             RNA =       18.779 
   logoddspostOTH =        0.000  logoddspostCOD =      -22.291  logoddspostRNA =       -0.564 

# 25  [+ strand] 
>DA0940-1- (77)
>ECOLI-780066- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28) 
 19.326669 -6.735706 19.727199
 19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 76 0
COD  ends = 74 1
RNA  ends = 0 73
              OTH =       19.344             COD =       -2.948             RNA =       18.779 
   logoddspostOTH =        0.000  logoddspostCOD =      -22.291  logoddspostRNA =       -0.564 

# 26  [+ strand] 
>DA0940-1- (77)
>ECOLI-780370- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28) 
 19.326669 -6.735706 19.727199
 19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 76 0
COD  ends = 74 1
RNA  ends = 0 73
              OTH =       19.344             COD =       -2.948             RNA =       18.779 
   logoddspostOTH =        0.000  logoddspostCOD =      -22.291  logoddspostRNA =       -0.564 

# 27  [+ strand] 
>DA0940-1- (77)
>ECOLI-780592- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28) 
 19.326669 -6.735706 19.727199
 19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 76 0
COD  ends = 74 1
RNA  ends = 0 73
              OTH =       19.344             COD =       -2.948             RNA =       18.779 
   logoddspostOTH =        0.000  logoddspostCOD =      -22.291  logoddspostRNA =       -0.564 

# 28  [+ strand] 
>DA0940-1- (77)
>ECOLI-780800- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28) 
 19.326669 -6.735706 19.727199
 19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 76 0
COD  ends = 74 1
RNA  ends = 0 73
              OTH =       19.344             COD =       -2.948             RNA =       18.779 
   logoddspostOTH =        0.000  logoddspostCOD =      -22.291  logoddspostRNA =       -0.564 

# 29  [+ strand] 
>DA0940-1- (77)
>ECOLI-2519045- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-76 [0-74](75) -- (0.21 0.24 0.27 0.28) 
 19.326669 -6.735706 19.727199
 19.360233 -2.001147 14.966454
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 76 0
COD  ends = 74 1
RNA  ends = 0 73
              OTH =       19.344             COD =       -2.948             RNA =       18.779 
   logoddspostOTH =        0.000  logoddspostCOD =      -22.291  logoddspostRNA =       -0.564 

# 30  [+ strand] 
>DA0940-1- (78)
>ECOLI-563946- (78)

length alignment: 78 (id=69.23)
posX: 0-77 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-77 [0-75](76) -- (0.18 0.30 0.32 0.20) 
 17.963663 -9.269558 17.104482
 18.280556 -6.326426 22.143566
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 77 0
COD  ends = 72 1
RNA  ends = 44 28
              OTH =       18.131             COD =       -7.150             RNA =       21.187 
   logoddspostOTH =        0.000  logoddspostCOD =      -25.281  logoddspostRNA =        3.056 

# 31  [+ strand] 
>DA0940-1- (78)
>ECOLI-3979754- (78)

length alignment: 78 (id=69.23)
posX: 0-77 [0-75](76) -- (0.14 0.34 0.37 0.14) 
posY: 0-77 [0-75](76) -- (0.14 0.33 0.36 0.17) 
 18.718315 -12.877073 20.514241
 18.551819 -5.649083 11.109117
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 77
COD  ends = 76 1
RNA  ends = 0 74
              OTH =       18.637             COD =       -6.639             RNA =       19.516 
   logoddspostOTH =        0.000  logoddspostCOD =      -25.277  logoddspostRNA =        0.879 

# 32  [+ strand] 
>DA0940-2- (75)
>ECOLI-3980115- (75)

length alignment: 75 (id=64.00)
posX: 0-74 [0-74](75) -- (0.15 0.35 0.36 0.15) 
posY: 0-74 [0-74](75) -- (0.16 0.27 0.36 0.21) 
 16.673417 5.650160 34.947176
 16.791520 4.389619 18.597200
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 74 0
COD  ends = 2 73
RNA  ends = 0 70
              OTH =       16.734             COD =        5.153             RNA =       33.947 
   logoddspostOTH =        0.000  logoddspostCOD =      -11.580  logoddspostRNA =       17.214 

# 33  [+ strand] 
>DA0940-8- (58)
>ECOLI-3979896- (58)

length alignment: 58 (id=68.97)
posX: 0-57 [0-56](57) -- (0.18 0.32 0.33 0.18) 
posY: 0-57 [0-55](56) -- (0.16 0.21 0.30 0.32) 
 11.514323 -1.612738 9.963681
 11.181613 -0.641287 8.426787
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 57
COD  ends = 57 0
RNA  ends = 20 37
              OTH =       11.358             COD =       -1.047             RNA =        9.391 
   logoddspostOTH =        0.000  logoddspostCOD =      -12.404  logoddspostRNA =       -1.967 

# 34  [+ strand] 
>DA0940-1- (77)
>ECOLI-3424371- (77)

length alignment: 77 (id=75.32)
posX: 0-76 [0-75](76) -- (0.14 0.37 0.34 0.14) 
posY: 0-76 [0-74](75) -- (0.20 0.33 0.31 0.16) 
 23.109013 5.520843 24.913393
 24.181055 9.917873 33.181724
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 76 0
COD  ends = 76 2
RNA  ends = 76 3
              OTH =       23.742             COD =        8.985             RNA =       32.186 
   logoddspostOTH =        0.000  logoddspostCOD =      -14.758  logoddspostRNA =        8.444 

# 35  [+ strand] 
>DA0940-1- (77)
>ECOLI-2515834- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.37 0.34 0.14) 
posY: 0-76 [0-74](75) -- (0.20 0.33 0.28 0.19) 
 18.645991 3.152473 25.533618
 18.627918 3.690656 29.967242
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 76
COD  ends = 76 2
RNA  ends = 76 3
              OTH =       18.637             COD =        3.447             RNA =       29.033 
   logoddspostOTH =        0.000  logoddspostCOD =      -15.190  logoddspostRNA =       10.396 

# 36  [+ strand] 
>DA0940-1- (77)
>ECOLI-2515949- (77)

length alignment: 77 (id=70.13)
posX: 0-76 [0-75](76) -- (0.14 0.37 0.34 0.14) 
posY: 0-76 [0-74](75) -- (0.20 0.33 0.28 0.19) 
 18.645991 3.152473 25.533618
 18.627918 3.690656 29.967242
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 76
COD  ends = 76 2
RNA  ends = 76 3
              OTH =       18.637             COD =        3.447             RNA =       29.033 
   logoddspostOTH =        0.000  logoddspostCOD =      -15.190  logoddspostRNA =       10.396 

# 37  [+ strand] 
>DA0940-5- (76)
>ECOLI-2815580- (76)

length alignment: 76 (id=71.05)
posX: 0-75 [0-71](72) -- (0.15 0.35 0.35 0.15) 
posY: 0-75 [0-71](72) -- (0.18 0.31 0.31 0.21) 
 13.333636 -36.156781 13.057277
 13.159042 -36.377514 9.144681
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 75
COD  ends = 0 73
RNA  ends = 32 52
              OTH =       13.249             COD =      -36.263             RNA =       12.150 
   logoddspostOTH =        0.000  logoddspostCOD =      -49.512  logoddspostRNA =       -1.099 

# 38  [+ strand] 
>DA0940-5- (76)
>ECOLI-2815855- (76)

length alignment: 76 (id=71.05)
posX: 0-75 [0-71](72) -- (0.15 0.35 0.35 0.15) 
posY: 0-75 [0-71](72) -- (0.18 0.31 0.31 0.21) 
 13.333636 -36.156781 13.057277
 13.159042 -36.377514 9.144681
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 75
COD  ends = 0 73
RNA  ends = 32 52
              OTH =       13.249             COD =      -36.263             RNA =       12.150 
   logoddspostOTH =        0.000  logoddspostCOD =      -49.512  logoddspostRNA =       -1.099 

# 39  [+ strand] 
>DA0940-5- (76)
>ECOLI-2815994- (76)

length alignment: 76 (id=71.05)
posX: 0-75 [0-71](72) -- (0.15 0.35 0.35 0.15) 
posY: 0-75 [0-71](72) -- (0.18 0.31 0.31 0.21) 
 13.333636 -36.156781 13.057277
 13.159042 -36.377514 9.144681
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 75
COD  ends = 0 73
RNA  ends = 32 52
              OTH =       13.249             COD =      -36.263             RNA =       12.150 
   logoddspostOTH =        0.000  logoddspostCOD =      -49.512  logoddspostRNA =       -1.099 

# 40  [+ strand] 
>DA0940-5- (76)
>ECOLI-2816269- (76)

length alignment: 76 (id=71.05)
posX: 0-75 [0-71](72) -- (0.15 0.35 0.35 0.15) 
posY: 0-75 [0-71](72) -- (0.18 0.31 0.31 0.21) 
 13.333636 -36.156781 13.057277
 13.159042 -36.377514 9.144681
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 75
COD  ends = 0 73
RNA  ends = 32 52
              OTH =       13.249             COD =      -36.263             RNA =       12.150 
   logoddspostOTH =        0.000  logoddspostCOD =      -49.512  logoddspostRNA =       -1.099 

# 41  [+ strand] 
>DA0940-9- (69)
>ECOLI-1804478- (69)

length alignment: 69 (id=66.67)
posX: 0-68 [0-67](68) -- (0.15 0.34 0.35 0.16) 
posY: 0-68 [0-66](67) -- (0.13 0.39 0.31 0.16) 
 10.953909 -9.639667 10.662024
 12.823044 -5.075973 10.777964
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 68 0
COD  ends = 66 1
RNA  ends = 51 31
              OTH =       12.172             COD =       -6.016             RNA =       10.721 
   logoddspostOTH =        0.000  logoddspostCOD =      -18.188  logoddspostRNA =       -1.451 

# 42  [+ strand] 
>DA0940-8- (58)
>ECOLI-3706024- (58)

length alignment: 58 (id=68.97)
posX: 0-57 [0-55](56) -- (0.18 0.34 0.30 0.18) 
posY: 0-57 [0-55](56) -- (0.20 0.39 0.25 0.16) 
 9.771742 -15.688073 2.357499
 9.187335 -13.325765 1.773092
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 57
COD  ends = 55 1
RNA  ends = -1 -1
              OTH =        9.509             COD =      -14.069             RNA =        2.095 
   logoddspostOTH =        0.000  logoddspostCOD =      -23.578  logoddspostRNA =       -7.414 

# 43  [+ strand] 
>DA0940-7- (73)
>ECOLI-695888- (73)

length alignment: 73 (id=64.38)
posX: 0-72 [0-69](70) -- (0.16 0.34 0.34 0.16) 
posY: 0-72 [0-69](70) -- (0.24 0.26 0.26 0.24) 
 10.281468 -22.207847 3.873799
 9.636380 -19.716135 1.831177
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 72
COD  ends = 72 1
RNA  ends = 10 26
              OTH =        9.995             COD =      -20.480             RNA =        3.187 
   logoddspostOTH =        0.000  logoddspostCOD =      -30.475  logoddspostRNA =       -6.807 

# 44  [+ strand] 
>DA0940-7- (73)
>ECOLI-696281- (73)

length alignment: 73 (id=64.38)
posX: 0-72 [0-69](70) -- (0.16 0.34 0.34 0.16) 
posY: 0-72 [0-69](70) -- (0.24 0.26 0.26 0.24) 
 10.281468 -22.207847 3.873799
 9.636380 -19.716135 1.831177
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 72
COD  ends = 72 1
RNA  ends = 10 26
              OTH =        9.995             COD =      -20.480             RNA =        3.187 
   logoddspostOTH =        0.000  logoddspostCOD =      -30.475  logoddspostRNA =       -6.807 

# 45  [+ strand] 
>DA0940-6- (62)
>ECOLI-695990- (62)

length alignment: 62 (id=62.90)
posX: 0-61 [0-60](61) -- (0.16 0.38 0.30 0.16) 
posY: 0-61 [0-60](61) -- (0.25 0.30 0.26 0.20) 
 10.452429 5.015902 10.936383
 9.772183 2.186248 11.450894
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 61
COD  ends = 0 61
RNA  ends = 38 22
              OTH =       10.152             COD =        4.206             RNA =       11.216 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.946  logoddspostRNA =        1.064 

# 46  [+ strand] 
>DA0940-6- (62)
>ECOLI-696099- (62)

length alignment: 62 (id=62.90)
posX: 0-61 [0-60](61) -- (0.16 0.38 0.30 0.16) 
posY: 0-61 [0-60](61) -- (0.25 0.30 0.26 0.20) 
 10.452429 5.015902 10.936383
 9.772183 2.186248 11.450894
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = RNA 
OTH  ends = 0 61
COD  ends = 0 61
RNA  ends = 38 22
              OTH =       10.152             COD =        4.206             RNA =       11.216 
   logoddspostOTH =        0.000  logoddspostCOD =       -5.946  logoddspostRNA =        1.064 

# 47  [+ strand] 
>DA0940-10- (69)
>ECOLI-2816349- (69)

length alignment: 69 (id=63.77)
posX: 0-68 [0-66](67) -- (0.15 0.34 0.36 0.15) 
posY: 0-68 [0-65](66) -- (0.18 0.27 0.36 0.18) 
 9.155278 -17.238488 5.252253
 9.115589 -17.289968 6.575597
LOCAL_DIAG_VITERBI -- [Inside SCFG]
winner = OTH 
OTH  ends = 0 68
COD  ends = 0 56
RNA  ends = 26 10
              OTH =        9.136             COD =      -17.264             RNA =        6.061 
   logoddspostOTH =        0.000  logoddspostCOD =      -26.400  logoddspostRNA =       -3.075