<<<<< 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 = 134 ,
#{Sites in the segment}_rec = 137 .


<< 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        TCTTCAGCACTGTTAACGAACTTCCTACTAGAGCCGTGGTGCC-CAGTAATAGGGTAGAG
seq0001        TCTTCAGCACTGTTAACGAACTTCCTACTAGAGCCGTGCTGCC-CAGTAATAGGGTAGAG
seq0002        TCTT--------------------------------------------------------
seq0003        TCTT--------------------------------------------------------
seq0004        TCTT--------------------------------------------------------
seq0005        TCTACAGCACTGGGAACGAACTTCCTCATAGAGCCATGATGCC-CAGTAATAAGGTAGAT
seq0006        TCTACAGCACTGTGAACGAACTTCCTCATAGAGCCATGATGCC-CAGTAATAAGGTAGAT
seq0007        TGTACAGCACTGTGAACGAACTTCCTCATAGAGCCATGATGCC-CAGTAATAAGGTAGAT
seq0008        TT-----------------------TCCTAGTGCCATGA-GCTCCAGTAAAAAGGTAGAG
seq0009        GC----------------------CTCCTAGTGCCATGATGCCCGAATAATAAGGTAGTG
seq0013        TCTTCTGCACC---ATCGCACTTC--TCTAGAGCGGCGACGCCCCAGTA--AAGAGAGAG
seq0014        TCATCTGCTCT---ACCGAACTACCTCCTAGAGCCATGATGCCCCGTTA--ACGAGCGAA
seq0015        TGCTCTGCACT---GTCGAACTATCT--TAGGGCCATGATCCTCCGGTA--AAGTTAGAG
seq0018        TCTTCAGCACT---TTCGATCCACTGCCTGGAGCCA---------AGTG--AATAGAGAG
seq0020        CCTCCAGCACA---ATTGAACTACTTCCTAGGGCCTTAATGCCCG-G-A--AAGACGGAG

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        CGTTCGCACCCAG--TGC--------A-----------CCACG-----------------
seq0001        CGTTCGCACCCAG--TGC--------A-----------CCACG-----------------
seq0002        ------------------------------------------------------------
seq0003        ------------------------------------------------------------
seq0004        ------------------------------------------------------------
seq0005        CTTTCGCGCCCAG--TGC--------A-----------ACACG-----------------
seq0006        CTTTCGCGCCCAG--TGC--------A-----------AAACG-----------------
seq0007        CTTTCGCGCCCAG--TGC--------A-----------ACACG-----------------
seq0008        CTTTAGCAGCCTG--AGC--------A-----------AAACC-----------------
seq0009        CTTTCTCACCCTG--AGC--------A-----------GCGCC-----------------
seq0013        CCTTCACACCCAG--AGC--------ATACGATACGCCT---------------------
seq0014        ATTTCGCGCCCAG--TGG--------CTTAGATAGGTCTCACA-----------------
seq0015        CTTTCGCACCAAGGTTGC--GGGCATATACGATAGACCTCACA-----------------
seq0018        CTTGCGCTCCCAG--TGC--------ATAAGATAGGGGTCACACGGTTAATAATATGGCG
seq0020        CTTGCGCACCTAG--TGCTA------ATAAGATTGGCGTCACA-----------------

(position)     11111111111111
               22222222223333
               01234567890123
                             
seq0000        -------CTGCAAA
seq0001        -------CTGCAAA
seq0002        --------------
seq0003        --------------
seq0004        --------------
seq0005        -------CTGTAAA
seq0006        -------CTGTAAA
seq0007        -------CTGTAAA
seq0008        -------CTGCAAA
seq0009        -------CTGC--A
seq0013        ---------GCA--
seq0014        -------CTGCG--
seq0015        -------CTCCA--
seq0018        TGTACGGCTGGAAA
seq0020        -------CCGCAAA


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        -TCTTCAGCACTGTTAACGAACTTC--CTACTAGAGCCGTGGTGC-CCAGTAATAGGGTA
seq0001        -TCTTCAGCACTGTTAACGAACTTC--CTACTAGAGCCGTGCTGC-CCAGTAATAGGGTA
seq0002        -TCTT-------------------------------------------------------
seq0003        -TCTT-------------------------------------------------------
seq0004        -TCTT-------------------------------------------------------
seq0005        -TCTACAGCACTGGGAACGAACTTC--CTCATAGAGCCATGATGC-CCAGTAATAAGGTA
seq0006        -TCTACAGCACTGTGAACGAACTTC--CTCATAGAGCCATGATGC-CCAGTAATAAGGTA
seq0007        -TGTACAGCACTGTGAACGAACTTC--CTCATAGAGCCATGATGC-CCAGTAATAAGGTA
seq0008        -TTT-------------------------CCTAGTGCCATGA-GCTCCAGTAAAAAGGTA
seq0009        GCCT-------------------------CCTAGTGCCATGATGCCCGAATAATAAGGTA
seq0013        -TCTTCTGCACCAT---CGCACTTC----TCTAGAGCGGCGACGCCCCAGTA--AAGAGA
seq0014        -TCATCTGCTCTAC---CGAACTACCT--CCTAGAGCCATGATGCCCCGTTA--ACGAGC
seq0015        -TGCTCTGCACTGT---CGAACTAT----CTTAGGGCCATGATCCTCCGGTA--AAGTTA
seq0018        -TCTTCAGCACTTT---CGATCCAC--TGCCTGGAGCCA---------AGTG--AATAGA
seq0020        -CCTCCAGCACAAT---TGAACTAC--TTCCTAGGGCCTTAATGCCC--GGA--AAGACG

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GAGCGTTCGCACCCAG--TGC--------A-----------CCACGC-------------
seq0001        GAGCGTTCGCACCCAG--TGC--------A-----------CCACGC-------------
seq0002        ------------------------------------------------------------
seq0003        ------------------------------------------------------------
seq0004        ------------------------------------------------------------
seq0005        GATCTTTCGCGCCCAG--TGC--------A-----------ACACGC-------------
seq0006        GATCTTTCGCGCCCAG--TGC--------A-----------AAACGC-------------
seq0007        GATCTTTCGCGCCCAG--TGC--------A-----------ACACGC-------------
seq0008        GAGCTTTAGCAGCCTG--AGC--------A-----------AAACCC-------------
seq0009        GTGCTTTCTCACCCTG--AGC--------A-----------GCGCCC-------------
seq0013        GAGCCTTCACACCCAG--AGC--------ATACGATACGC------C-------------
seq0014        GAAATTTCGCGCCCAG--TGG--------CTTAGATAGGTCTCACAC-------------
seq0015        GAGCTTTCGCACCAAGGTTGC--GGGCATATACGATAGACCTCACAC-------------
seq0018        GAGCTTGCGCTCCCAG--TGC--------ATAAGATAGGGGTCACACGGTTAATAATATG
seq0020        GAGCTTGCGCACCTAG--TGCTA------ATAAGATTGGCGTCACAC-------------

(position)     11111111111111111
               22222222223333333
               01234567890123456
                                
seq0000        -----------TGCAAA
seq0001        -----------TGCAAA
seq0002        -----------------
seq0003        -----------------
seq0004        -----------------
seq0005        -----------TGTAAA
seq0006        -----------TGTAAA
seq0007        -----------TGTAAA
seq0008        -----------TGCAAA
seq0009        -----------TGCA--
seq0013        -----------TGCA--
seq0014        -----------TGCG--
seq0015        -----------TCCA--
seq0018        GCGTGTACGGCTGGAAA
seq0020        -----------CGCAAA


<<<<< 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, 3) .

[ 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   	    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    4    3    3    3
seq0001   	    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    4    3    3    3
seq0002   	    -    1    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    1    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    1    1    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    4    3    3    3
seq0006   	    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    4    3    3    3
seq0007   	    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    4    3    3    3
seq0008   	    -    1    1  -22    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    -    3    3    3    3    3    3    3
seq0009   	    0    0  -22  -22    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3
seq0013   	    -    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -    -    -    1    1    1    1    1    1    1    1    -    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3
seq0014   	    -    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -    -    -    1    1    1    1    1    1    1    1    1    1    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3
seq0015   	    -    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -    -    -    1    1    1    1    1    1    1    1    -    -    -    -    5    5    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3
seq0018   	    -    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -    -    -    1    1    1    1    1    1    1    1    -    -    3    3    3    3    3    3    3    3    3    3    3    3    -    -    -    -    -    -    -    -    -    3    3
seq0020   	    -    1    1    1    1    1    1    1    1    1    1    1   -2   -2    -    -    -    1    1    1    1    1    1    1    1    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    5



(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   	    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    3    3    3    -    -    -    -    -    -    -    -    3    -    -    -    -    -    -    -    -    -    -
seq0001   	    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    3    3    3    -    -    -    -    -    -    -    -    3    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    3    3    3    -    -    -    -    -    -    -    -    3    -    -    -    -    -    -    -    -    -    -
seq0006   	    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    3    3    3    -    -    -    -    -    -    -    -    3    -    -    -    -    -    -    -    -    -    -
seq0007   	    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    3    3    3    -    -    -    -    -    -    -    -    3    -    -    -    -    -    -    -    -    -    -
seq0008   	    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    3    3    3    -    -    -    -    -    -    -    -    3    -    -    -    -    -    -    -    -    -    -
seq0009   	    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    3    3    3    -    -    -    -    -    -    -    -    3    -    -    -    -    -    -    -    -    -    -
seq0013   	    3    3    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    3    3    3    -    -    -    -    -    -    -    -    3    3    3    3    3    3    3    3    3    3    3
seq0014   	    3    3    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    3    3    3    -    -    -    -    -    -    -    -    3    3    3    3    3    3    3    3    3    3    3
seq0015   	    3    3    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3
seq0018   	    3    3    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    3    3    3    -    -    -    -    -    -    -    -    3    3    3    3    3    3    3    3    3    3    3
seq0020   	    4    3    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    -    3    3    3    3    3    -    -    -    -    -    -    3    3    3    3    3    3    3    3    3    3    3



(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

seq0000   	    -    3    3    3    3    3  -21    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    3    3    3
seq0001   	    -    3    3    3    3    3  -21    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    3    3    3
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    3    3    3    3    3  -21    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    3    3    3
seq0006   	    -    3    3    3    3    3  -21    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    3    3    3
seq0007   	    -    3    3    3    3    3  -21    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    3    3    3
seq0008   	    -    3    3    3    3    3  -21    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    3    3    3
seq0009   	    -    3    3    3    3    3  -21    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    1    -    -
seq0013   	    -    -    -    -    -    -    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   33    3    3    3    -    -
seq0014   	    3    3    3    3    3    3  -21    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    3    -    -
seq0015   	    3    3    3    3    3    3  -21    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    3    -    -
seq0018   	    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3
seq0020   	    3    3    3    3    3    3  -21    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    3    3    3




[INFORMATION] The original $commoner_shift_flank = 3. Thus, we will shift the entire reference MSA ...

<< REVISED Output of 'map_shifts_respos_bw_2msas' >>

New ($shift_lf, $shift_rf) = (0, 0) .

[ New 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   	    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0    0
seq0001   	    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0    0
seq0002   	    -   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -   -2   -2   -2   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0    0
seq0006   	    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0    0
seq0007   	    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    0    0    0
seq0008   	    -   -2   -2  -25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0
seq0009   	   -3   -3  -25  -25    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0013   	    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -    -    -   -2   -2   -2   -2   -2   -2   -2   -2    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0014   	    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -    -    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -    -    -   -2   -2   -2   -2   -2   -2   -2   -2    -    -    -    -    2    2    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -    -    -   -2   -2   -2   -2   -2   -2   -2   -2    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    -    -    -    -    -    -    0    0
seq0020   	    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5   -5    -    -    -   -2   -2   -2   -2   -2   -2   -2   -2    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    2



(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    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    0    0    0    -    -    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -
seq0001   	    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    0    -    -    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    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    0    -    -    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -
seq0006   	    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    0    -    -    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -
seq0007   	    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    0    -    -    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -
seq0008   	    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    0    -    -    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -
seq0009   	    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    0    -    -    -    -    -    -    -    -    0    -    -    -    -    -    -    -    -    -    -
seq0013   	    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    0    0    0    0    0    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    0    0    0    0    -    -    0    0    0    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    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    0    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    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    0    0    0    0    0    0    0    0    0    0
seq0020   	    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    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0



(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

seq0000   	    -    0    0    0    0    0  -24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0001   	    -    0    0    0    0    0  -24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    0    0    0    0    0  -24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0006   	    -    0    0    0    0    0  -24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0007   	    -    0    0    0    0    0  -24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0008   	    -    0    0    0    0    0  -24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0
seq0009   	    -    0    0    0    0    0  -24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0   -2    -    -
seq0013   	    -    -    -    -    -    -    6    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   30    0    0    0    -    -
seq0014   	    0    0    0    0    0    0  -24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    -    -
seq0015   	    0    0    0    0    0    0  -24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    -    -
seq0018   	    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    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0  -24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0



<<<<< 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... >>>>>

... The MINI-classes increased by 1 compared to the old set!! ...


<<<<< 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 ...


