# LAST version 1584
#
# a=29 b=1 A=28 B=1 e=185 d=116 x=184 y=52 z=184 H=100 E=3.87001
# R=01 u=2 s=2 S=1 M=0 T=0 m=10 l=1 n=10 C=2 k=1 w=1000 t=5.22312 j=3 Q=0
# /home/mcfrith/data/genome/mammal/homSap/last/homSap-cMAM4
# Reference sequences=195 normal letters=2934876451
# lambda=0.207774 K=0.191089
#
#     A   C   G   T   M   S   K   W   R   Y   B   D   H   V
# A   4  -6  -2  -6   2  -4  -4   1   2  -6  -5   1   0   1
# C  -6   6  -6  -2   2   3  -3  -4  -6   2   1  -4   1   0
# G  -2  -6   6  -6  -3   3   2  -4   2  -6   0   1  -4   1
# T  -6  -2  -6   4  -4  -4   2   1  -6   2   1   0   1  -5
# M   2   2  -3  -4   2   0  -4   0   1  -1  -2  -1   0   1
# S  -4   3   3  -4   0   3   0  -4   0   0   1  -1  -1   1
# K  -4  -3   2   2  -4   0   2   0  -1   1   1   0  -1  -2
# W   1  -4  -4   1   0  -4   0   1   0   0  -1   0   0  -1
# R   2  -6   2  -6   1   0  -1   0   2  -6  -2   1  -1   1
# Y  -6   2  -6   2  -1   0   1   0  -6   2   1  -1   1  -2
# B  -5   1   0   1  -2   1   1  -1  -2   1   1  -1   0  -1
# D   1  -4   1   0  -1  -1   0   0   1  -1  -1   0   0   0
# H   0   1  -4   1   0  -1  -1   0  -1   1   0   0   0  -1
# V   1   0   1  -5   1   1  -2  -1   1  -2  -1   0  -1   1
#
# Coordinates are 0-based.  For - strand matches, coordinates
# in the reverse complement of the 2nd sequence are used.
#
# name start alnSize strand seqSize alignment
#
# m=1 s=185
#
# m=1 s=185
#
# Query sequences=13 normal letters=3554259256
a score=355 mismap=0.63
s chr1            47567 300 + 248956422 TtttttccTTACTTTCCATCACCAAGTAACTCTTCTGATATTTTTTCTCTTGAGAAAATTAATATGACTCATAGATCTGGTTCCCAAGAGAAATCAATGGAGGCCTGGTTACAAGGATCTAAGAAGCATCAATGGGTCACTAACATCTAGTGGTACTAATTAACTCTGTTAATCATTGGGAAGAAAATGTATATATACTTTTGTCTTGGAGCTGATTCTACTAGAAAGCAGAAATCAAAATGATCAGTTTCCCAGTGT----CACTACTGCACACCCTGGAACAGAACAGGTAGGTCAGAAAAA
s NC_077227.1 171526596 292 + 760810273 TTCtctctctctgttttATCACTAAGCAACCTTTCTAATGTTTTTCCTCTTGGGAAAACTAGTGTGACTTCAAGAAACAATTACCAAGGGAATTAATCATAAGCTAGGTATTAGAAGTCTAAGAAGCATCATTGGGTCACTGACAGTCAGAGCAACTAAGTATGTTGCTTTCTCTTAGGGAAGAACTTAGTTTAACTTTTTTTCTTTAGAGGTTATTAAATTACATTTCTGAATT------------TTTCTCATTCTTAAATACAATTTCATATTCTGTGATAGAACAGGTAGGTGAGAGGAA

a score=2697 mismap=0.01
s chr1            62902 978 + 248956422  
s NC_077227.1 171564230 981 + 760810273  

a score=601 mismap=0.64
s chr1            69075 254 + 248956422 GAAACGAATAACTCTATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTCATAACAGTGGTATCTGACTCCCACCTTCACT---CTCCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTCACAGCCCCCAAGATGATTACTGACTTTTTCAG
s NC_077227.1 171835366 257 + 760810273 GAGATGAATAACTCTATGGTGAATGAATTCATTTTGTTGGGACTCACCAATTCTTGGGAACTTGAGATTTTCTTTTTtgtggttttctttCTGGCCTATACATTAATCTTGACTGGGAACTTTCTCATTATACTCATGGTGACTCTTGACTCCCATCTGCATTCAACCCCCATGTACTTCCTCCTGGCCAACCTCTCTCTTTTTGACATGTCTCTTTCCACTGTTACTGTCCCCAAAATGATCATAGACTTCTTCAG

# LAST version 1584
#
# a=29 b=1 A=28 B=1 e=185 d=116 x=184 y=52 z=184 H=100 E=3.87001
# R=01 u=2 s=2 S=1 M=0 T=0 m=10 l=1 n=10 C=2 k=1 w=1000 t=5.22312 j=3 Q=0
# /home/mcfrith/data/genome/mammal/homSap/last/homSap-cMAM4
# Reference sequences=195 normal letters=2934876451
# lambda=0.207774 K=0.191089
#
#     A   C   G   T   M   S   K   W   R   Y   B   D   H   V
# A   4  -6  -2  -6   2  -4  -4   1   2  -6  -5   1   0   1
# C  -6   6  -6  -2   2   3  -3  -4  -6   2   1  -4   1   0
# G  -2  -6   6  -6  -3   3   2  -4   2  -6   0   1  -4   1
# T  -6  -2  -6   4  -4  -4   2   1  -6   2   1   0   1  -5
# M   2   2  -3  -4   2   0  -4   0   1  -1  -2  -1   0   1
# S  -4   3   3  -4   0   3   0  -4   0   0   1  -1  -1   1
# K  -4  -3   2   2  -4   0   2   0  -1   1   1   0  -1  -2
# W   1  -4  -4   1   0  -4   0   1   0   0  -1   0   0  -1
# R   2  -6   2  -6   1   0  -1   0   2  -6  -2   1  -1   1
# Y  -6   2  -6   2  -1   0   1   0  -6   2   1  -1   1  -2
# B  -5   1   0   1  -2   1   1  -1  -2   1   1  -1   0  -1
# D   1  -4   1   0  -1  -1   0   0   1  -1  -1   0   0   0
# H   0   1  -4   1   0  -1  -1   0  -1   1   0   0   0  -1
# V   1   0   1  -5   1   1  -2  -1   1  -2  -1   0  -1   1
#
# Coordinates are 0-based.  For - strand matches, coordinates
# in the reverse complement of the 2nd sequence are used.
#
# name start alnSize strand seqSize alignment
#
# m=1 s=185
#
# m=1 s=185
#
# Query sequences=13 normal letters=3554259256
a score=355 mismap=0.63
s chr1            47567 300 + 248956422 TtttttccTTACTTTCCATCACCAAGTAACTCTTCTGATATTTTTTCTCTTGAGAAAATTAATATGACTCATAGATCTGGTTCCCAAGAGAAATCAATGGAGGCCTGGTTACAAGGATCTAAGAAGCATCAATGGGTCACTAACATCTAGTGGTACTAATTAACTCTGTTAATCATTGGGAAGAAAATGTATATATACTTTTGTCTTGGAGCTGATTCTACTAGAAAGCAGAAATCAAAATGATCAGTTTCCCAGTGT----CACTACTGCACACCCTGGAACAGAACAGGTAGGTCAGAAAAA
s NC_077227.1 171526596 292 + 760810273 TTCtctctctctgttttATCACTAAGCAACCTTTCTAATGTTTTTCCTCTTGGGAAAACTAGTGTGACTTCAAGAAACAATTACCAAGGGAATTAATCATAAGCTAGGTATTAGAAGTCTAAGAAGCATCATTGGGTCACTGACAGTCAGAGCAACTAAGTATGTTGCTTTCTCTTAGGGAAGAACTTAGTTTAACTTTTTTTCTTTAGAGGTTATTAAATTACATTTCTGAATT------------TTTCTCATTCTTAAATACAATTTCATATTCTGTGATAGAACAGGTAGGTGAGAGGAA

a score=2697 mismap=0.01
s chr1            62902 978 + 248956422  
s NC_077227.1 171564230 981 + 760810273  

a score=9115 mismap=8.94e-10 sense=6.5 acc=AG
s chr7  121348853 1697 + 159345973  
s 90089        47 1655 -      2478  
p                                  ',28=DJIHHJNNNNQQRRRLJLRJHHJRRNNRIGGG520/.''%&*=BIOLJLQC@=%"%"36%""7KMNNRRRRJHHJRNNRRRNNQJHHJNNLJLRRRRNNNNG9%""69KRQA><;%""ANPRJHHJRQQPQQRRRRRNNRQQRRLJLRRRQQPQNNRRRNNIGGGIRLJLJHHJROML@=&$""9@MNRLJLLJLRQQPQNNNNRRRRLJLRNNRRRO?<$#<?LMQRRNNRRRLJLRNNNNNNQLJLRRRRRRRNNLJLRNNRRRRNNQQLJLNNRLJLNNRRNNRNNRRRRNNNNNNRNNNNLJLRRRRRRLJLRNNRRRRRRRRRRJHHJPB;I=~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~1414KMQRRRNNRJGEA!!#$'BIQRRRNNNNLJLRQQLJLRRRRLJLJHHJRRLJLPPPNMLIC!!"$%(?ADRRNNRRRRRRNNRLJLRRRNNRNNRNNRJHHJRRLJLQQRRNNRRRQQRRRNNRLJLRNNRNNNJI9"$&"$&?CLRNNRRRRLJLPPQQNNRNNNNLJLQNNNNLJLRRLJLRRJHHJNNRNNQQRRQQNNLJLRRRRRNNQNNNNNNLJLNNRRNNNNRRNNRRRRRRRNNRNNNNNNQIGGGIRPD=#7?#7FLONNRRQQRLJLPPQQRRRRRNNRRRRRRNNRRNNRRRNNRNNNNRMLF?"%"$+""$':PNNNNNNRNNNNQQNNRRK@="%"%?DQRRRNNRNNRNNRRNNRQRQQQRLJLRRRRNNQQQRJHHJRQ?<:HKOMMLJLRQPK>AMMPPPLJLRNNRRRNNRRRQQNNRNNRLJLRRNNRRRRRRRLJKOOOOOKJKO;!!"$%(DPPQPQQRRRNNNNRNNJHHJRNNQQRRJHHJQQQQQQQNNRRRRRRRRJHHJRRQQNNLJLRRNNNNRRRRLJLQNNLJLNNNNJGF;!!#$';HRRRRRJHHJQQNNRRRRRRRNNPPPQRRNNRRRRRLJLRRNNRQG;!"!"#$%&)8IRRRNNLJLQPPPIGGGINNLJLJHHJRQRNNRRRRRRQQQNNRRRNNRQQPQQRLJLQIB""#&:DEFIRLJLRRRRLG@""%7HGHJRLJLRRNNRNNNNRRRQQQJHHJRRRRRRNNRRRRPONMMMNOPRNMPOOPIGGGIQQQLJLNNRNNRRRNNQQPQQNNQPQQRPN9""$'BNMNLJLJHHJQQQRRRNNRNNRRRRQOF.**>ADQRNNRRRRJHHI9""%468521#0$2EKMRRRNNNNRRRRRRLJLRRRRRNNQQQRRRRNNRLJLRRNNRRRRRRRQRLJLRRRNNRRRNNRLJLRNNRNNRRQQPNB""#&:DFIRNNRRRRRRRRQOOOOOMNNNRRRNNRRRRQH?###++""$'AFHJLQQPQQRRRRQQRRNNRLJLQQRRQPPPKJLRNNMFB?+3("#&:MNNL8""%8CGONNJ=:83##25IKMLJLNNRNNRRRRNNRRNMNB!!#$';OQRRRNNNNNNRLJI@;"%4"%>CPRNNNNRRNNNNRRQQLJLRLJLRRRRNNNNRNNRNNQLJKKF@:5
p                                  zz{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{o{{{{{{{{{{{{{{ii{{{{U{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{p{{{{{{{{{{{p{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{p{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{ii{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{ii{{{{{{{{{{{{{{{m{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{m{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{aaa{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{ZZZ{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{zzziizzzhzzzzzzzzzzzzzzzzzzzzzzzzziizzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzozzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzozzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzNNzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzvvvvvvvvvvvvvvvvvnttttoooooooolkkkkkkUbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb`_\\\[[[YXXXXXXXXXXXXXXXXXXXXXXXXXXXXWWWWWWVVVVVVVUUUUUTTTTTTTTTTTTTTTTTTTTTTTTSSSSSSSSSSSSSSSRRRRRRRRRRRRRRRRRRRKLKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKJJJJJJJJJJJEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEEEE??>>>>>>>>>>>=<;;;;;:::::9999999999999999999998888888888877777777777777777777777777777777766666666664444444444444444444444444333333333333333333

a score=493 mismap=0.014 sense=6.5 acc=GC don=GT
s chr7  121351142 114 + 159345973 CTGTTCAAAAGGGCTTTTTGTCTTAATGCCCTTCCCACCACAGAAGACCCAGTTGTCTCTAAAACCAAGATTAGTAATAGATGTGCTCCCCAAATCAGCAATGAGCCGCCGTGC
s 90089      1702 101 -      2478 CTGTTCAAA-GGGCTTTTTA--TTAATGCCCTTCCCACCACAGAAGACCCAGTTGTCTCTAAA-CC-AGATTAGTAATAGATGTGCT-CCCAAATCAGCAATGAGCC-------
p                                 &,1578&$""57:J9643*'*'~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~1..#$7ENNRRRNNRRRRRQQQG8""$'>?BRRRRRNNOIC,)$''()%+$
p                                 3333333310000,,,,,,,,,,,,,,,,,))))))))((('''''''&&&&&&&&%%%%%%%%%$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

