<<<<< 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 = 179 ,
#{Sites in the segment}_rec = 166 .


<< 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        GGTACGAT-C--CACGGTATG-ACAC-TCTGCTCGACGACT-----AAAAAGAGCAATAG
seq0001        GGTACGAT-C--CACGGTATG-ACAC-TCTGCTCGACGACT-----AAAAAGAGCAATAG
seq0002        GGTACGAT-C--CACGATATG-ACAC-TCTTCTCGACGTCT-----AAAAAGAGCAATAG
seq0003        GGTACGAC-C--CACGGTATG-ACAC-TCTTCTAGACGTCT-----AAAAAG--------
seq0004        GGTACGAC-C--CAGGGTATG-ACAC-TCTTCTCGACGTCT-----AACAAG--------
seq0005        GGTACGAT-C--CACCGTATG-ACAC-TCTTCTCGACGACT-----CAAAAGAGCAATAG
seq0006        GGTACGAT-C--CACCGTATG-ACACTTCTTCTCGACGACT-----AAAAAGAGCAATAC
seq0007        GGTACGAT-C--CACCGGATG-ACAC-TCTTCTCGACGACTCCGGCAAAAAGAGCAATAC
seq0008        GGTACG------------------------------------------GAAGAGCTATAG
seq0009        TGTCTGTA-C--CACCGTAAGCACAC-ACCTCTCTACTTCT-----AAGA----------
seq0013        -GTATCGTAC--C--CGTATG-AAAC-GATTTTCACTTACA-----AAAGCAAGGTATAG
seq0014        GTTACCAT-CATCACTCTATG-ACAG-GCTTGTGCACTACA-----AAAAAGAGGTAT--
seq0015        GGTATGAT-C--CACCGTATG-ACAC-GCTGTTCCACTAGG-----AAGAAGAGGTATAG
seq0018        GGTACAAT-C--CACCCCACG-ACAT-ACTTCTCGACTGCT-----AAAAAGCTGAAGAG
seq0020        GGTACGAT-C--TACCGTCCG-ACAC-ACTTCTCGACTACA-----CACAAGAGGTAGAA

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        CGA--CTCAGGCGCCG-CATAACTCAA-----CTACCCA-----GC--------------
seq0001        CGA--CTCAGGCGCCG-CATAACTCAA-----CTACCCA-----GC--------------
seq0002        CGA--CTCAGGCGCCG-CATAACTCAA-----CTACCCA-----GC--------------
seq0003        ------------------------------------------------------------
seq0004        ------------------------------------------------------------
seq0005        CGA--CTCAGGCGCGG-CATAACTCAA-----CTACCCA-----GG--------------
seq0006        CGA--CTCAGGCGTCG-CATAACTCAA-----CAACCCA-----GC--------------
seq0007        CGA--CTCAGGCGCCG-CATAAATCAA-----CTACCCA-----GCTCCAATGTTCGTTT
seq0008        CCA--CTGATGCTTCT-TACAACCCAACCAGCCAACACT-----CC--------------
seq0009        -------------------CAACCCAAGCAGTCAACGCA-----CC--------------
seq0013        CCA--GCACTGCTTCG-TCCTTCACATCCAGTCTAAATA-----CC--------------
seq0014        CGA--GTGATGCTTCG-TACACCACAGCCTGTCTCCCAA-----TC--------------
seq0015        CGA--CAAATTCTTCG-TACAACACGACCAGTGGACTAACCAGTCC--------------
seq0018        TGA--ATAATG--TCGG--CAACCCAACGAGACTA---A-----CC--------------
seq0020        TGACCCTAATGCTTCT-TACAACCCAACCGGTATCCTCA-----CC--------------

(position)     11111111111111111111111111111111111111111111111111111111111
               22222222223333333333444444444455555555556666666666777777777
               01234567890123456789012345678901234567890123456789012345678
                                                                          
seq0000        -------------------------------------------------------AAAT
seq0001        -------------------------------------------------------AAAT
seq0002        -------------------------------------------------------AAAT
seq0003        ------------------------------------------------------T----
seq0004        ------------------------------------------------------T----
seq0005        -------------------------------------------------------AAAT
seq0006        -------------------------------------------------------AAAT
seq0007        GTGAAAGAGCGTTACAAACAGAGCGGAACAGTTCTACGGTGTCGACCAGACCAG-AAAT
seq0008        -------------------------------------------------------AAAT
seq0009        -------------------------------------------------------ATAT
seq0013        -------------------------------------------------------AGAT
seq0014        -------------------------------------------------------CGCT
seq0015        -------------------------------------------------------AGAT
seq0018        -------------------------------------------------------AGAT
seq0020        -------------------------------------------------------GGAA


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GGTACGATC--CACGGTATG-ACAC-TCTGCTCGACGACT-----AAAAAGAGCAATAGC
seq0001        GGTACGATC--CACGGTATG-ACAC-TCTGCTCGACGACT-----AAAAAGAGCAATAGC
seq0002        GGTACGATC--CACGATATG-ACAC-TCTTCTCGACGTCT-----AAAAAGAGCAATAGC
seq0003        GGTACGACC--CACGGTATG-ACAC-TCTTCTAGACGTCT-----AAAAAG---------
seq0004        GGTACGACC--CAGGGTATG-ACAC-TCTTCTCGACGTCT-----AACAAG---------
seq0005        GGTACGATC--CACCGTATG-ACAC-TCTTCTCGACGACT-----CAAAAGAGCAATAGC
seq0006        GGTACGATC--CACCGTATG-ACACTTCTTCTCGACGACT-----AAAAAGAGCAATACC
seq0007        GGTACGATC--CACCGGATG-ACAC-TCTTCTCGACGACTCCGGCAAAAAGAGCAATACC
seq0008        GGTACGGAA-----------------------------------------GAGCTATAGC
seq0009        TGTCTGTAC--CACCGTAAGCACAC-ACCTCTCTACTTCT--------------------
seq0013        GTATCGTAC----CCGTATG-AAAC-GATTTTCACTTACA-----AAAGCAAGGTATAGC
seq0014        GTTACCATCATCACTCTATG-ACAG-GCTTGTGCACTACA-----AAAAAGAGGTAT--C
seq0015        GGTATGATC--CACCGTATG-ACAC-GCTGTTCCACTAGG-----AAGAAGAGGTATAGC
seq0018        GGTACAATC--CACCCCACG-ACAT-ACTTCTCGACTGCT-----AAAAAGCTGAAGAGT
seq0020        GGTACGATC--TACCGTCCG-ACAC-ACTTCTCGACTACA-----CACAAGAGGTAGAAT

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GA--CTCAGGCGCCGCATAACTCAACTACCCAGC--------------------------
seq0001        GA--CTCAGGCGCCGCATAACTCAACTACCCAGC--------------------------
seq0002        GA--CTCAGGCGCCGCATAACTCAACTACCCAGC--------------------------
seq0003        ------------------------------------------------------------
seq0004        ------------------------------------------------------------
seq0005        GA--CTCAGGCGCGGCATAACTCAACTACCCAGG--------------------------
seq0006        GA--CTCAGGCGTCGCATAACTCAACAACCCAGC--------------------------
seq0007        GA--CTCAGGCGCCGCATAAATCAACTACCCAGCTCCAATGTTCGTTTGTGAAAGAGCGT
seq0008        CA--CTGATGCTTCTTACAACCCAACCAGCCAACACT-----------------------
seq0009        -------------AAGACAACCCAAGCAGTCAACGCA-----------------------
seq0013        CA--GCACTGCTTCGTCCTTCACATCCAGTCTAAATA-----------------------
seq0014        GA--GTGATGCTTCGTACACCACAGCCTGTCTCCCAA-----------------------
seq0015        GA--CAAATTCTTCGTACAACACGACCAGTGGACTAAC----------------------
seq0018        GA--ATAATG---TCGGCAACCCAACGAGACTAA--------------------------
seq0020        GACCCTAATGCTTCTTACAACCCAACCGGTATCCTCA-----------------------

(position)     1111111111111111111111111111111111111111111111
               2222222222333333333344444444445555555555666666
               0123456789012345678901234567890123456789012345
                                                             
seq0000        ------------------------------------------AAAT
seq0001        ------------------------------------------AAAT
seq0002        ------------------------------------------AAAT
seq0003        ---------------------------------------------T
seq0004        ---------------------------------------------T
seq0005        ------------------------------------------AAAT
seq0006        ------------------------------------------AAAT
seq0007        TACAAACAGAGCGGAACAGTTCTACGGTGTCGACCAGACCAGAAAT
seq0008        ----------------------------------------CCAAAT
seq0009        ----------------------------------------CCATAT
seq0013        ----------------------------------------CCAGAT
seq0014        ----------------------------------------TCCGCT
seq0015        ------CAG------------------------------TCCAGAT
seq0018        ----------------------------------------CCAGAT
seq0020        ----------------------------------------CCGGAA


<<<<< 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, -13) .

[ 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    -    -   -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
seq0001   	    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   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -   -1   -1   -1   -1   -1
seq0002   	    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   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -   -1   -1   -1   -1   -1
seq0003   	    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   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -   -1   -1   -1   -1   -1
seq0004   	    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   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -   -1   -1   -1   -1   -1
seq0005   	    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   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -   -1   -1   -1   -1   -1
seq0006   	    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   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -   -1   -1   -1   -1   -1
seq0007   	    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   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0008   	    0    0    0    0    0    0  -42  -42  -42    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    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   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    -    -
seq0013   	   -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
seq0014   	    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   -1   -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   -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
seq0018   	    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   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -   -1   -1   -1   -1   -1
seq0020   	    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   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -   -1   -1   -1   -1   -1



(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   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -7   -7   -7   -7   -7   -7   -7  -12  -12    -    -    -    -    -    -
seq0001   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -7   -7   -7   -7   -7   -7   -7  -12  -12    -    -    -    -    -    -
seq0002   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -7   -7   -7   -7   -7   -7   -7  -12  -12    -    -    -    -    -    -
seq0003   	   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	   -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   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -7   -7   -7   -7   -7   -7   -7  -12  -12    -    -    -    -    -    -
seq0006   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -7   -7   -7   -7   -7   -7   -7  -12  -12    -    -    -    -    -    -
seq0007   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -7   -7   -7   -7   -7   -7   -7  -12  -12  -12  -12  -12  -12  -12  -12
seq0008   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   27   27   27   27   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    -
seq0013   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    -
seq0014   	   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    -
seq0015   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -
seq0018   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -1   -1   -1   -1   -1   -1    -    -    -    0    0    0    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -5    -    -    -    -    -    -
seq0020   	   -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   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    -



(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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   26   26   26    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(position)	  150  151  152  153  154  155  156  157  158  159  160  161  162  163  164  165

seq0000   	    -    -    -    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -9
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -9
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13
seq0007   	  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -12  -13  -13  -13  -13
seq0008   	    -    -    -    -    -    -    -    -    -    -   56   56  -13  -13  -13  -13
seq0009   	    -    -    -    -    -    -    -    -    -    -   56   56  -13  -13  -13  -13
seq0013   	    -    -    -    -    -    -    -    -    -    -   56   56  -13  -13  -13  -13
seq0014   	    -    -    -    -    -    -    -    -    -    -   56   56  -13  -13  -13  -13
seq0015   	    -    -    -    -    -    -    -    -    -   56   56   56  -13  -13  -13  -13
seq0018   	    -    -    -    -    -    -    -    -    -    -   56   56  -13  -13  -13  -13
seq0020   	    -    -    -    -    -    -    -    -    -    -   56   56  -13  -13  -13  -13



<<<<< 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 ...


