<<<<< Input Tree (Top_node = 29) >>>>>

( seq0020{28}:0.1529, ( seq0018{26}:0.1741, ( ( seq0015{23}:0.1492, ( seq0013{20}:0.1827, seq0014{21}:0.1659 ){22}:0.0049 ){24}:0.0297, ( ( seq0008{16}:0.0865, seq0009{17}:0.1286 ){18}:0.0335, ( ( seq0005{10}:0.0368, ( seq0006{11}:0.0286, seq0007{12}:0.0362 ){13}:0.0065 ){14}:0.0368, ( ( seq0000{1}:0.0054, seq0001{2}:0.0081 ){3}:0.0232, ( seq0002{4}:0.0189, ( seq0003{5}:0.0124, seq0004{6}:0.0108 ){7}:0.0070 ){8}:0.0270 ){9}:0.0205 ){15}:0.0703 ){19}:0.0383 ){25}:0.0314 ){27}:0.0130 ){29};


<<<<< Input MSA >>>>>

#{Sequences} = 15 .
#{Sites in the segment}_ref = 237 ,
#{Sites in the segment}_rec = 175 .


<< Correspondence between sequence IDs and sequence indices >>

Indx:	Seq_ID

0:	seq0000
1:	seq0001
2:	seq0002
3:	seq0003
4:	seq0004
5:	seq0005
6:	seq0006
7:	seq0007
8:	seq0008
9:	seq0009
10:	seq0013
11:	seq0014
12:	seq0015
13:	seq0018
14:	seq0020


<< Original Segment of the Reference Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GTTGACCGT-ACTGGTGTACGAA----------TCCGA----------------------
seq0001        GTTGACCGT-ACTGGTGTACGAA----------TCCGA----------------------
seq0002        GTTGACCGT-AGCGGTGTACGAA----------TCCAA----------------------
seq0003        GTTGACCGT-AGCGGTGTACGAA----------TCCAA----------------------
seq0004        GTTGACCGT-AGCGGTGTACGAA----------TCCAA----------------------
seq0005        GTTGACCGT-ACTGGTGTACTACTTCACGGGGATCCAA----------------------
seq0006        GTTGGCCGT-ACTGGTGTACGACTTCACGG-GATCCAAAATGCCCAATCAAGATACAAGA
seq0007        GTTGACCGT-ACTGGTGTACGACTTCACGG-GATCCAA----------------------
seq0008        GGTGACCGT-TCTGGTGTACGAA----------TCCGA----------------------
seq0009        GTTCA-------------------------------------------------------
seq0013        TTTCACAG--TC---CGTAC-AA----------TCTGA----------------------
seq0014        TTCCCCCGCCTCTGGCGTAC-AA----------TCCGA----------------------
seq0015        GTTTACCGT-CCTGGCGTAC-A------------C-------------------------
seq0018        GTTGACCGT-TCTGACGCAC-AG----------TCCGA----------------------
seq0020        GTTGACCGT-TCTTGGGTCC-AG----------TCCGA----------------------

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ---CGTGTGGCA------------------------------------------------
seq0001        ---CGTGTGGCA------------------------------------------------
seq0002        ---CGTTTGGCA------------------------------------------------
seq0003        ---CGTGTGGCA------------------------------------------------
seq0004        ---CGTGTGGCA------------------------------------------------
seq0005        ---CGCGTGGCA------------------------------------------------
seq0006        ATTCGTGTGGCA------------------------------------------------
seq0007        ---CGTGTGGCA------------------------------------------------
seq0008        ---CGTGTGGCG------------------------------------------------
seq0009        ------------------------------------------------------------
seq0013        ---CGTGCGGCT------------------------------------------------
seq0014        ---CGTGTTGAAAGATCTAAACAGCGATTTTGGGGAGACAAATGTAGAGACTTCGCCCGC
seq0015        ---AGTGTGGCA------------------------------------------------
seq0018        ---CGTGTGGCA------------------------------------------------
seq0020        ---CGTGTGGCA------------------------------------------------

(position)     111111111111111111111111111111111111111111111111111111111111
               222222222233333333334444444444555555555566666666667777777777
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ----------------------------------CGGATAGTCCTCGACACGGTGGGCGA
seq0001        ----------------------------------CGGATAGTCCGCGACACGGTGGGCGA
seq0002        ----------------------------------CGGATAGTCCGCGACACGGTGGGAGA
seq0003        ----------------------------------CGGATAGTCCGCGACACGGTTGGAGA
seq0004        ----------------------------------CGGATAGTCCGCGACACGGTTGGAGA
seq0005        ----------------------------------CCGATAGTCCACGACACTATGGGCGA
seq0006        ----------------------------------CCGATAGTCCACGACACCGTGGGCGA
seq0007        ----------------------------------CCGATAGGCCACGACATCGTGGGCGA
seq0008        ----------------------------------CGGAAAGTCCACGAAACGTTGGGCAA
seq0009        ------------------------------------------------------------
seq0013        ----------------------------------CGGTGAGTC-ACGACAGGTTGAGCCA
seq0014        GGTGGCTCTAAGACGCCTAAGACTTTCAAGGCTATGGTTAATC-----------------
seq0015        ----------------------------------CGGATAATCCACGACCCGTTGGGCCA
seq0018        ----------------------------------CGGCTCGTCC-CGACAAGTTGGGCGA
seq0020        ----------------------------------CGGATAGTCC-CCACACGTTGGGCGA

(position)     111111111111111111112222222222222222222222222222222222222
               888888888899999999990000000000111111111122222222223333333
               012345678901234567890123456789012345678901234567890123456
                                                                        
seq0000        ACCTGATTTACTTGAC-----------------------------------------
seq0001        ACCTGATTTACTTGAC-----------------------------------------
seq0002        ACCTGATATACTTCAC-----------------------------------------
seq0003        ACCTGATATGCTTCAC-----------------------------------------
seq0004        ACCTGATATACTTCAC-----------------------------------------
seq0005        ACCTGATATACTACAC-----------------------------------------
seq0006        ACCTCATATACTACAC-----------------------------------------
seq0007        ACCTGATATACGACAC-----------------------------------------
seq0008        ACCTGATATAGTTCAC-----------------------------------------
seq0009        ---------------C-----------------------------------------
seq0013        ACCAGATATAGTTCAC-----------------------------------------
seq0014        ----GAAA-ATTTCAC-----------------------------------------
seq0015        ACCTGGTATAGTTCAA-----------------------------------------
seq0018        A---GAAATAGTTGACCCGTCGACAATTAGTTACAACTGTTCCTGCGACATATTCAC
seq0020        T---GATTTAGTTGAA-----------------------------------------


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GTTGACCG-TACTGGTGTACGA----------ATCCGA----------------------
seq0001        GTTGACCG-TACTGGTGTACGA----------ATCCGA----------------------
seq0002        GTTGACCG-TAGCGGTGTACGA----------ATCCAA----------------------
seq0003        GTTGACCG-TAGCGGTGTACGA----------ATCCAA----------------------
seq0004        GTTGACCG-TAGCGGTGTACGA----------ATCCAA----------------------
seq0005        GTTGACCG-TACTGGTGTACTACTTCACGGGGATCCAA----------------------
seq0006        GTTGGCCG-TACTGGTGTACGACTTCAC-GGGATCCAAAATGCCCAATCAAGATACAAGA
seq0007        GTTGACCG-TACTGGTGTACGACTTCAC-GGGATCCAA----------------------
seq0008        GGTGACCG-TTCTGGTGTACGA----------ATCCGA----------------------
seq0009        ------------------------------------------------------------
seq0013        TTTCACAG-TCC----GTACAA-----------TCTGA----------------------
seq0014        TTCCCCCGCCTCTGGCGTACAA-----------TCCGA----------------------
seq0015        GTTTACCG-TCCTGGCGTACAC--------------------------------------
seq0018        GTTGACCG-TTCTGACGCACAG-----------TCCGA----------------------
seq0020        GTTGACCG-TTCTTGGGTCCAG-----------TCCGA----------------------

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ---CGTGTGGCACGGATAGTCCTCGACACGGTGGGCGAACCT------------------
seq0001        ---CGTGTGGCACGGATAGTCCGCGACACGGTGGGCGAACCT------------------
seq0002        ---CGTTTGGCACGGATAGTCCGCGACACGGTGGGAGAACCT------------------
seq0003        ---CGTGTGGCACGGATAGTCCGCGACACGGTTGGAGAACCT------------------
seq0004        ---CGTGTGGCACGGATAGTCCGCGACACGGTTGGAGAACCT------------------
seq0005        ---CGCGTGGCACCGATAGTCCACGACACTATGGGCGAACCT------------------
seq0006        ATTCGTGTGGCACCGATAGTCCACGACACCGTGGGCGAACCT------------------
seq0007        ---CGTGTGGCACCGATAGGCCACGACATCGTGGGCGAACCT------------------
seq0008        ---CGTGTGGCGCGGAAAGTCCACGAAACGTTGGGCAAACCT------------------
seq0009        ------------------------------------------------------------
seq0013        ---CGTGCGGCTCGGTGAGTCA-CGACAGGTTGAGCCAACCA------------------
seq0014        ---CGTGTTGAAAGATCTAAAC-AGCGATTTTGGGGAGACAAATGTAGAGACTTCGCCCG
seq0015        ---AGTGTGGCACGGATAATCCACGACCCGTTGGGCCAACCT------------------
seq0018        ---CGTGTGGCACGGCTCGTCC-CGACAAGTTGGGCGAAGAAAT------AGTTGACCC-
seq0020        ---CGTGTGGCACGGATAGTCC-CCACACGTTGGGCGAT---------------------

(position)     1111111111111111111111111111111111111111111111111111111
               2222222222333333333344444444445555555555666666666677777
               0123456789012345678901234567890123456789012345678901234
                                                                      
seq0000        -------------------------------------------GATTTACTTGAC
seq0001        -------------------------------------------GATTTACTTGAC
seq0002        -------------------------------------------GATATACTTCAC
seq0003        -------------------------------------------GATATGCTTCAC
seq0004        -------------------------------------------GATATACTTCAC
seq0005        -------------------------------------------GATATACTACAC
seq0006        -------------------------------------------CATATACTACAC
seq0007        -------------------------------------------GATATACGACAC
seq0008        -------------------------------------------GATATAGTTCAC
seq0009        -------------------------------------------------GTTCAC
seq0013        -------------------------------------------GATATAGTTCAC
seq0014        CGGTGGCTCTAAGACGCCTAAGACTTTCAAGGCTATGGTTAATCGAAAATTTCAC
seq0015        -------------------------------------------GGTATAGTTCAA
seq0018        ------------GTCGACAATTAGTTACAA----CTGTTCCTGCGACATATTCAC
seq0020        -------------------------------------------GATTTAGTTGAA


<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<< Output of 'map_shifts_respos_bw_2msas' >>

($shift_lf, $shift_rf) = (0, -62) .

[ Shifts in the Reconstructed MSA ]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   49

seq0000   	    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -   10    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -   10    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -   10    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -   10    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -   10    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -   10    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    0    0    0    0    0    0    0    0    -   -1   -1   -4    -    -    -    -    0    0    0    0   -1   -1    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0    0    0    0    0   -1  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0    -    1    0    0    0    0    0    0    0    0    0    0   -1   -1    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82
seq0006   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -83    -  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82    -  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -85
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82    -  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82    -



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114  115  116  117  118  119  120  121  122  123  124  125  126  127  128  129  130  131  132  133  134  135  136  137  138  139  140  141  142  143  144  145  146  147  148  149

seq0000   	  -82  -82    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	  -82  -82    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	  -82  -82    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	  -82  -82    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	  -82  -82    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	  -82  -82    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	  -82  -82    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	  -82  -82    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	  -82  -82    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	  -82  -82    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0015   	  -82  -82    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	  -85  -85  -85  -85    -    -    -    -    -    -  -79  -79  -79  -79  -79  -79  -79  -79  -79    -    -    -    -    -    -    -    -    -    -    -    -    -  -66  -66  -66  -66  -66  -66  -66  -66  -66  -66  -66  -66  -66  -66  -66  -66  -66  -66
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	  150  151  152  153  154  155  156  157  158  159  160  161  162  163  164  165  166  167  168  169  170  171  172  173  174

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seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21
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seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21
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seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  169  169  169  169  169  -21
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seq0018   	    -    -    -    -  -62  -62  -62  -62  -62  -62  -62  -62  -62  -62  -62  -62  -62  -62  -62  -62  -62  -62  -62  -62  -62
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21  -21



<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<< Output of 'br_list_classes_shift_respos' >>

$commoner_shift_flank = 0 .


<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

... NO CHANGES were made ...


<<<<< Preliminary (4): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

SKIPPED the Calculation, because either reference or reconstructed MSA contains (a) gap(s) or (a) gapped segment(s) that is (are) too long ...


