<<<<< 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 = 121 ,
#{Sites in the segment}_rec = 116 .


<< 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        GCATT-----------------------GATACGGG--GTATGCTTACA-CAG-------
seq0001        GCATT-----------------------GATACGGGCTGTATGCTTACA-CAG-------
seq0002        GCATT-----------------------GATAAGGG--GTGTGCATACA-CAG-------
seq0003        GCATT-----------------------GATAAGGG--GTATGCATACA-CAG-------
seq0004        GCATT-----------------------GATAAGGG--GTATGCATACA-CAG-------
seq0005        ----T-----------------------GATAAAGG--GTATGCTTACA-CAG-------
seq0006        ----A-----------------------GATAAAGG--GTATGCTTACA-CAG-------
seq0007        ----T-----------------------GATAAAGG--GTACGCTTACA-CAG-------
seq0008        ----TTTGTTATG----GTGACA--TCAGATAAAGG--GTATGCATATA-CAG-------
seq0009        ----TTTGTTATG----GTGATA--GCAGATAAAGG--GAAGGCATATACTAG-------
seq0013        ----TTTGATATTATAGTAGATA--TCAGACAACG----TGTGCATACA-CAGGCTTGAG
seq0014        ----TTTGTTATTATAAGTTCCA----------AGT--GAATTCATACA-CAGGCACGCA
seq0015        ----ATTGTTATTATAGGTGATACATCATTTAAAGC--GTATTGAGACA-CAG-------
seq0018        ----TTTGTTACTATAGGTGAGA--TCATATCAAGG--ATAATAATTC------------
seq0020        ----TCTGTTACTATAGGTAGTA--TCATATCAAGG--GTAATGATACT-CAA-------

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        -------------TAAAC--------TTCACCGCGCAACCCCCCACGATTCCAGCATAA-
seq0001        -------------TAAAC--------TTCACCGCGGAACCCCCCACGATTCCAGCATAA-
seq0002        -------------TAAAC--------TTCACCG---------CAAGGATTCCAGCCTAA-
seq0003        -------------TAAAC--------TTCACCG---------CCAGGGTTCCAGCCTAA-
seq0004        -------------TAAAC--------TTCACCG---------CCAGGATTCCAGCCTAA-
seq0005        -------------TAAAC--------TTCACCACCCAACCCCCCAGGCTCCCAGCATAA-
seq0006        -------------TAAAC--------TTCACCGCCCAACCCCCCAGGATGTCAGCATAA-
seq0007        -------------TAAAC--------TTCACCGCCCAACCCCCCAAGATCTCAGCATAA-
seq0008        -------------TTAAC--------TTCATCGCGCATCCCCCAAGGGTTCCAGCATAA-
seq0009        -------------TCAAC--------AGTACCGCGCAACCTCCCAGGGTTCCAGCATAA-
seq0013        CTGCTAATGAACGGAAAC--------ATCACCGCGCAGCCCCCAAGTGTTCCAGCATAAG
seq0014        CTGCTAA----------T--------TTGACCGGGCAACCCCCAAGGGTTCCTGCATAA-
seq0015        -------------TAAACTAGACTTCTTCACCGCGGAACCCCCAAGGGTTACGTCAAAA-
seq0018        -------------------------------------------------------ATCA-
seq0020        -------------AAAAC--------TTTACCGGGCAACTCCCAAGCG-TCCAGTATCA-

(position)     1
               2
               0
                
seq0000        -
seq0001        -
seq0002        -
seq0003        -
seq0004        -
seq0005        -
seq0006        -
seq0007        -
seq0008        -
seq0009        -
seq0013        G
seq0014        -
seq0015        -
seq0018        -
seq0020        -


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GCATT-------------------GATACGGG--GTATGCTTACAC--------------
seq0001        GCATT-------------------GATACGGGCTGTATGCTTACAC--------------
seq0002        GCATT-------------------GATAAGGG--GTGTGCATACAC--------------
seq0003        GCATT-------------------GATAAGGG--GTATGCATACAC--------------
seq0004        GCATT-------------------GATAAGGG--GTATGCATACAC--------------
seq0005        T-----------------------GATAAAGG--GTATGCTTACAC--------------
seq0006        A-----------------------GATAAAGG--GTATGCTTACAC--------------
seq0007        T-----------------------GATAAAGG--GTACGCTTACAC--------------
seq0008        TTTGTTAT----GGTGA--CATCAGATAAAGG--GTATGCATATAC--------------
seq0009        TTTGTTAT----GGTGA--TAGCAGATAAAGG--GAAGGCATATACT-------------
seq0013        TTTGATATTATAGTAGA--TATCAGACAA----CGTGTGCATACACAGGCTTGAGCTGCT
seq0014        TTTGTTATTATAAGTTCCAAGTGAATTCATAC--ACAGGCACGCAC--------------
seq0015        ATTGTTATTATAGGTGATACATCATTTAAAGC--GTATTGAGACAC--------------
seq0018        TTTGTTACTATAGGTGA--GATCATATCAAGG--ATAATAATTCATC-------------
seq0020        TCTGTTACTATAGGTAG--TATCATATCAAGG--GTAATGATACTC--------------

(position)     00000000000000000000000000000000000000001111111111111111
               66666666667777777777888888888899999999990000000000111111
               01234567890123456789012345678901234567890123456789012345
                                                                       
seq0000        ------AGTAAA--------CTTCACCGCGCAACCCCCCACGATTCCAGCATAA--
seq0001        ------AGTAAA--------CTTCACCGCGGAACCCCCCACGATTCCAGCATAA--
seq0002        ------AGTAAA--------CTTCACCG---------CAAGGATTCCAGCCTAA--
seq0003        ------AGTAAA--------CTTCACCG---------CCAGGGTTCCAGCCTAA--
seq0004        ------AGTAAA--------CTTCACCG---------CCAGGATTCCAGCCTAA--
seq0005        ------AGTAAA--------CTTCACCACCCAACCCCCCAGGCTCCCAGCATAA--
seq0006        ------AGTAAA--------CTTCACCGCCCAACCCCCCAGGATGTCAGCATAA--
seq0007        ------AGTAAA--------CTTCACCGCCCAACCCCCCAAGATCTCAGCATAA--
seq0008        ------AGTTAA--------CTTCATCGCGCATCCCCCAAGGGTTCCAGCATAA--
seq0009        ------AGTCAA--------CAGTACCGCGCAACCTCCCAGGGTTCCAGCATAA--
seq0013        AATGAACGGAAA--------CATCACCGCGCAGCCCCCAAGTGTTCCAGCATAAGG
seq0014        ------TGCTAA--------TTTGACCGGGCAACCCCCAAGGGTTCCTGCATAA--
seq0015        ------AGTAAACTAGACTTCTTCACCGCGGAACCCCCAAGGGTTACGTCAAAA--
seq0018        -----A--------------------------------------------------
seq0020        ------AAAAAA--------CTTTACCGGGCAACTCCCAAGCG-TCCAGTATCA--


<<<<< 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, -5) .

[ 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    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5    -    -    -    -
seq0001   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5    -    -    -    -
seq0002   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5    -    -    -    -
seq0003   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5    -    -    -    -
seq0004   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5    -    -    -    -
seq0005   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5    -    -    -    -
seq0006   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5    -    -    -    -
seq0007   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5    -    -    -    -
seq0008   	   -4   -4   -4   -4   -4   -4   -4   -4    -    -    -    -    0   -4   -4   -4   -4    -    -   -2   -2   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5    -    -    -    -
seq0009   	   -4   -4   -4   -4   -4   -4   -4   -4    -    -    -    -    0   -4   -4   -4   -4    -    -   -2   -2   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4    -    -    -
seq0013   	   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -2   -2   -4   -4   -4   -4   -4   -4   -4   -4    -    -    -    -    0    0   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5   -5   -5   -5   -5
seq0014   	   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4  -14  -14  -14  -16  -16  -16  -16  -16  -16  -16  -16  -16  -16    -    -  -14  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15  -15    -    -    -    -
seq0015   	   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5    -    -    -    -
seq0018   	   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -2   -2   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4  -71  -71  -71    -    -    -
seq0020   	   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -2   -2   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   15   15   -5   -5   -5   -5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   15   15   -5   -5   -5   -5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   15   15   -5   -5   -5   -5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5    -    -    -    -    -    -    -    -    -   -5   -5   -5
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   15   15   -5   -5   -5   -5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5    -    -    -    -    -    -    -    -    -   -5   -5   -5
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   15   15   -5   -5   -5   -5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5    -    -    -    -    -    -    -    -    -   -5   -5   -5
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   15   15   -5   -5   -5   -5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   15   15   -5   -5   -5   -5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   15   15   -5   -5   -5   -5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   15   15   -5   -5   -5   -5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   15   15   -5   -5   -5   -5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0013   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    5    5    5    5    5    5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   15   15   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -53    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   15   15   -5   -5   -5   -5    -    -    -    -    -    -    -    -    3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5



(position)	  100  101  102  103  104  105  106  107  108  109  110  111  112  113  114  115

seq0000   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -
seq0001   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -
seq0002   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -
seq0003   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -
seq0004   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -
seq0005   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -
seq0006   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -
seq0007   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -
seq0008   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -
seq0009   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -
seq0013   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0014   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -
seq0015   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	   -5   -5   -5    -   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5    -    -




[INFORMATION] The original $commoner_shift_flank = -5. Thus, we will shift the entire reconstructed 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   	    -    -    -    -    -    5    5    5    5    5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1
seq0001   	    -    -    -    -    -    5    5    5    5    5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
seq0002   	    -    -    -    -    -    5    5    5    5    5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1
seq0003   	    -    -    -    -    -    5    5    5    5    5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1
seq0004   	    -    -    -    -    -    5    5    5    5    5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    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
seq0006   	    -    -    -    -    -    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1
seq0007   	    -    -    -    -    -    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1
seq0008   	    -    -    -    -    -    1    1    1    1    1    1    1    1    -    -    -    -    5    1    1    1    1    -    -    3    3    1    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1    1
seq0009   	    -    -    -    -    -    1    1    1    1    1    1    1    1    -    -    -    -    5    1    1    1    1    -    -    3    3    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    -    -    3    3    1    1    1    1    1    1    1    1    -    -    -    -    5    5    1    1    1    1    1    1    1    1    1    1
seq0014   	    -    -    -    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1   -9   -9   -9  -11  -11  -11  -11  -11  -11  -11  -11  -11  -11    -    -   -9  -10  -10  -10  -10  -10  -10  -10  -10  -10  -10
seq0015   	    -    -    -    -    -    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
seq0018   	    -    -    -    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    3    3    1    1    1    1    1    1    1    1    1    1    1    -    -    1    1    1    1    1    1    1    1    1    1  -66
seq0020   	    -    -    -    -    -    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    3    3    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   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   20   20    0    0    0    0    -    -    -    -    -    -    -    -    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   20   20    0    0    0    0    -    -    -    -    -    -    -    -    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   20   20    0    0    0    0    -    -    -    -    -    -    -    -    8    0    0    0    0    0    0    0    -    -    -    -    -    -    -
seq0003   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   20   20    0    0    0    0    -    -    -    -    -    -    -    -    8    0    0    0    0    0    0    0    -    -    -    -    -    -    -
seq0004   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   20   20    0    0    0    0    -    -    -    -    -    -    -    -    8    0    0    0    0    0    0    0    -    -    -    -    -    -    -
seq0005   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   20   20    0    0    0    0    -    -    -    -    -    -    -    -    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   20   20    0    0    0    0    -    -    -    -    -    -    -    -    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   20   20    0    0    0    0    -    -    -    -    -    -    -    -    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   20   20    0    0    0    0    -    -    -    -    -    -    -    -    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    1    1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   20   20    0    0    0    0    -    -    -    -    -    -    -    -    8    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    -    -    -    -    -    -    -    -    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0014   	  -10    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   10   10   10   10   10   10    -    -    -    -    -    -    -    -    8    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   20   20    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   	  -66  -66    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -48    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   20   20    0    0    0    0    -    -    -    -    -    -    -    -    8    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

seq0000   	    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    -    -
seq0002   	    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -
seq0003   	    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -
seq0004   	    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -
seq0005   	    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    -    -
seq0007   	    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    -    -
seq0009   	    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
seq0014   	    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    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0    -    0    0    0    0    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). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<< Output of 'lump_together_similar_blocks': Content of @{$composite_miniblocks} (#{composite_miniblocks} = 21) >>

Indx_cmp_miniblock	beg_cmb	end_cmb	mrca	indices,constituent,miniblocks	list,position,shifts	merger,types	indices,involved,seqs

0	5	9	9	23	5	n/a	0,1,2,3,4
1	5	21	29	9	1	n/a	10,13,14
2	5	23	21	15	1	n/a	11
3	5	49	25	11	1	n/a	5,6,7,12
4	5	21	18	13,22,14	1,5,1	0,0	8,9
5	24	36	21	4,2	-9,-11	0	11
6	24	25	29	21	3	n/a	8,9,10,13,14
7	26	33	20	18	1	n/a	10
8	26	48	26	12	1	n/a	13
9	26	49	28	10	1	n/a	14
10	26	49	16	20	1	n/a	8
11	26	51	17	17	1	n/a	9
12	29	49	9	16	1	n/a	0,1,2,3,4
13	38	39	20	24	5	n/a	10
14	39	50	21	5,3	-9,-10	0	11
15	40	49	20	19	1	n/a	10
16	49	70	26	0,1	-66,-48	0	13
17	50	50	29	6	0	n/a	0,1,2,3,4,5,6,7,8,12,14
18	71	72	29	27	20	n/a	0,1,2,3,4,5,6,7,8,9,12,14
19	71	76	21	26	10	n/a	11
20	85	85	29	25	8	n/a	0,1,2,3,4,5,6,7,8,9,10,11,14



<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<< (1) For Reference MSA >>>

<<< (2) For Reconstructed MSA >>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 21) >>>>>


[[ Results of the Main Process (1st Round) ]]

[ Contents of @cblk_wise_cts_invlvd_indels ]

Indx_cmp_blk	#{rlv_indels}_ref	#{rlv_indels}_rec	#{rltd_indels}_ref	#{rltd_indels}_rec	#{other_involved}_ref	#{other_involved}_rec

0	1	0	1	2	0	0
1
2	1	0	0	1	0	0
3
4	0	0	0	0	0	0
5	1	1	0	2	0	0
6
7	0	1	1	0	0	0
8	1	0	0	0	0	0
9	0	0	0	0	0	0
10	0	0	1	0	0	0
11	1	0	0	1	0	0
12	0	0	1	1	0	0
13	1	1	1	1	0	0
14	0	2	0	0	0	0
15	1	0	0	0	0	0
16	1	1	0	1	0	0
17	0	0	0	2	0	0
18	1	0	0	2	0	0
19	0	1	2	0	0	0
20	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 5): 1, 3, 4, 6, 9 . ]


[ Contents of @cblk_wise_msa_errors ]

Indx_cmp_blk	Indx_error	len_cblk_ref	len_cblk_rec	Type	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(ref)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(rec)

0	0	5	5	Partial-Neighboring-Branch-Merge(2ins)(+shift)(?)	9:0:3:-/15:5:27:X	15:10:28:X/14:6:9:X
1	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
2	0	19	19	Complex(???)	21:25:32:X	20:22:23:X
3	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
4	Skipped!!(NO_ASSOCIATED_EVENT(???))
5	0	15	13	Complex	21:25:32:X	21:38:38:X/20:22:23:X/20:34:36:X
6	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
7	0	8	8	Complex(???)	21:25:32:X	20:34:36:X
8	0	23	23	Complex(???)	26:48:114:X	None
9	Skipped!!(NO_ASSOCIATED_EVENT(???))
10	0	24	24	NO_ASSOCIATED_EVENT(???)	17:49:49:-	None
11	0	26	26	Complex(???)	17:49:49:-	16:51:51:X
12	0	21	21	Complex(???)	15:5:27:X	15:10:28:X
13	0	2	2	Complex(???)	20:35:38:X/21:25:32:X	20:34:36:X/21:38:38:X
14	0	13	12	Complex(???)	None	21:38:38:X/21:51:70:X
15	0	10	10	Complex(???)	20:35:38:X	None
16	0	4	22	Complex(???)	26:48:114:X	26:71:118:X/27:51:70:-
17	0	1	1	Complex	None	23:51:70:X/21:51:70:X
18	0	2	2	Complex	22:53:66:-	23:51:70:X/21:51:70:X
19	0	6	6	Complex	20:67:72:-/22:53:66:-	21:51:70:X
20	0	1	1	Shift	23:78:85:-	23:77:84:-


[ Contents of %indel_ref2assoc_cblks ]

Br:beg:end(ref)	indices,of,associated,composite-blocks

9:0:3	0
15:5:27	0,12
19:13:16	None
23:23:24	None
21:25:32	2,5,7,13
20:35:38	13,15
2:36:37	None
26:48:114	8,16
17:49:49	10,11
22:53:66	18,19
20:67:72	19
21:73:76	None
23:78:85	20
8:93:101	{Equivalent to '8:93:101'(rec)}
25:108:108	{Equivalent to '25:108:108'(rec)}
20:119:120	{Equivalent to '20:119:120'(rec)}


[ Contents of %indel_rec2assoc_cblks ]

Br:beg:end(rec)	indices,of,associated,composite-blocks

14:6:9	0
15:10:28	0,12
19:13:16	None
24:22:23	None
20:22:23	2,5
20:34:36	5,7,13
2:37:37	None
25:38:38	None
23:38:38	None
21:38:38	5,13,14
18:38:38	None
14:38:38	None
8:38:38	None
1:38:38	None
27:51:70	16
23:51:70	17,18
21:51:70	14,17,18,19
16:51:51	11
15:51:51	None
20:52:69	None
19:70:70	None
26:71:118	16
23:77:84	20
8:93:101	{Equivalent to '8:93:101'(ref)}
25:108:108	{Equivalent to '25:108:108'(ref)}
20:119:120	{Equivalent to '20:119:120'(ref)}


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>

[[ Interim Results ]]

[ Contents of %cb2hard_linked (#{keys} = 2) ]

Indx_cmp_blk	=> [indices,cblks,hard,linked,by,the,key]

1	=> [2],
10	=> [11],


[ Contents of %cb2hard_linking (#{keys} = 2) ]

Indx_cmp_blk	=> [indices,cblks,hard,linking,the,key]

2	=> [1],
11	=> [10],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 2) ]

Indx_cblk_A	indx_cblk_B

0	12
8	16


[[ Results of the Main Process (2nd Round) ]]

[ For the 1 th pair: (0, 12) ]


{ The representative path is: 0  -> 12 }


( Rough frameworks of the 1st- & 2nd-moved c-blocks )

Subject_c-block	beg_cb	end_cb	shift_le	shift_re	rlv_branch	indices,invlvd,seqs,le	indices,invlvd,seqs,re

1st(intermediate)	5	9	5	5	9	0,1,2,3,4	0,1,2,3,4
2nd(reconstructed)	29	49	1	1	9	0,1,2,3,4	0,1,2,3,4


( Errors associated with the c-blocks )

Subject_c-block	Type	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	9:0:3:-/15:5:27:X	15:10:27:X
2nd(reconstructed)	Complex(???)	9:49:49:X/15:10:27:X	15:10:28:X


[ For the 2 th pair: (8, 16) ]

