<<<<< 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 = 205 ,
#{Sites in the segment}_rec = 163 .


<< 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        GGTACTCAT-GTC--------AGGAACGTTTCAACTTCAACAGACGAA-CTTATT-GTTC
seq0001        GGTACTCAT-GTC--------AGGAACGTTTCAACTTCCACAGACGAG-CTTATT-GTTC
seq0002        GGTACTCAT-GTC--------AGGAACGTTTCAACTTCAACAGACGTA-CTTCTT-GTTC
seq0003        GGTACTCAT-GTC--------AGGAACGTTTCAACTTCAACAGACGTA-CTTCTT-GTTC
seq0004        GGTACCCAT-GTC--------AGGAACGTTTCAACTTCAACAGACGTA-CTTCTT-GTTC
seq0005        GGTACTCAT-ATC--------AAGAACGTTTCAATTTCAACAGACGTA-CTTCAT-GTTC
seq0006        GGTACTCAT-GTC--------AAGAACGTTTCAACGTCAACAGACGTA-CTTCTT-GTTC
seq0007        GGTACTCAT-GTC--------AAAAACGTTTCAACTTCAACAGACGTA-CTTCTT-GTTC
seq0008        GGTACTCATCATC--------AGGTACGTTTCAAATTCAACAGACGTA-CTTCTT-GTTC
seq0009        GGTACTCAG-ATC--------AGGAACGTTTCAATTTCTATAGACGTA-CTTCTT-GTTC
seq0013        GGGACTCAT-TACTGATTTTGTGGAACGTTACCATGTCAACCGACTTA-ATGCATCGTTC
seq0014        ------------------------------------------------------------
seq0015        GGTACTCAA-AGA--------AGGACCGTTTCCAGTTCACCAAAAGTA-CGGCTT-GTTC
seq0018        GGGGCTTAT-ATC--------GGGAAAAGTTCAATTGCA---------------------
seq0020        GGTGCGGAT-ATC--------ATGAACATTTTAATTGCAACAGAAGTACCATATT-TTTC

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GCT--CCAAGCAACTTATGGCCCCGAATCTGTCA-----CGTCTTT--------------
seq0001        GCT--CCAAGCAACTTATGGCCCCGAATCTGTCA-----CGTCTTT--------------
seq0002        ACG--CCAAGCAACTTATGGCTCCGAAACTTTCA-----CGTCTGT--------------
seq0003        ACG--CCAAGCAACTTATGGCCCCGAAACTTTCA-----CGTCTGT--------------
seq0004        ACG--CCATGCAACTTATGGCCCCGAAACTTTCA-----CGTCTTT--------------
seq0005        GCG--CCAAGCAACTTTCGGCCCCGAATATGTCA-----CGTCTTT--------------
seq0006        GCG--CCAAGCAACTTTCGGCCCCGAATCTGTAC-----CGTCTTT--------------
seq0007        GCG--CCACGCAACTTTAGGCCCCGAATCTGTAA-----CGTCTCT--------------
seq0008        GTG--CCAAACAAATTTCGGCGCCGAATCCGTCA-----CATGTCT--------------
seq0009        GCGGCCGAA--AAATTTCCGCACCGAATTTGTCA-----CATATCT--------------
seq0013        GCT--CC-------------------AGCTGTCA-----CAGGTTT--------------
seq0014        -----------------------------TGTC------TATGTTT--------------
seq0015        GCA--CCAAGCAAGTTTCGGCCCCAAAGCTGTCACGACTCATGCTT--------------
seq0018        -------------------GCCCACAATCTGTAA-----CATGTTT--------------
seq0020        GCG--CCAAGCAAATTTTGGGCACCAATAGGTCA-----CATGTTTTTGGGATAGTTAGA

(position)     111111111111111111111111111111111111111111111111111111111111
               222222222233333333334444444444555555555566666666667777777777
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        -------GTG-----------C--GC----------------------------------
seq0001        -------GTG-----------C--GC----------------------------------
seq0002        -------GTC-----------C--GC----------------------------------
seq0003        -------GTG-----------C--GC----------------------------------
seq0004        -------GTG-----------C--TC----------------------------------
seq0005        -------GTG-----------C--GC----------------------------------
seq0006        -------GTG-----------C--GC----------------------------------
seq0007        -------GTG-----------C--GC----------------------------------
seq0008        -------ATG-----------C--GC----------------------------------
seq0009        -------GTC-----------C--GC----------------------------------
seq0013        -------GGC-----------C--GC----------------------------------
seq0014        -------GTG-----------C--GCCTAATGTCAACTATAGTGCCTCTAGTGGCCCTAA
seq0015        ------CGTGACGGGTAGAAAAACCC----------------------------------
seq0018        -------GCG-----------C--AC----------------------------------
seq0020        GTAAGA-GTG-----------C--GC----------------------------------

(position)     1111111111111111111122222
               8888888888999999999900000
               0123456789012345678901234
                                        
seq0000        ------------AGTCAAC-----A
seq0001        ------------AGTCAAC-----A
seq0002        ------------AGTCAAC-----A
seq0003        ------------AGTCAAC-----A
seq0004        ------------AGTCAAC-----A
seq0005        ------------AGTCATT-----C
seq0006        ------------AGTCAAT-----C
seq0007        ------------AGTCCAT-----C
seq0008        ------------CGTCCAC-----A
seq0009        ------------CGGCAAC-----A
seq0013        ----------ACAGAAAAG-----A
seq0014        AGTATCATAA-GAGATAACTCGGCA
seq0015        -----------GAGACAAC-----A
seq0018        -----------TAGACAAC-----A
seq0020        -----------CAGACTCC-----A


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GGTACTCA-----T-GTC---AGGAACGTTTCAACTTCAACA---GACGAACT-TATTGT
seq0001        GGTACTCA-----T-GTC---AGGAACGTTTCAACTTCCACA---GACGAGCT-TATTGT
seq0002        GGTACTCA-----T-GTC---AGGAACGTTTCAACTTCAACA---GACGTACT-TCTTGT
seq0003        GGTACTCA-----T-GTC---AGGAACGTTTCAACTTCAACA---GACGTACT-TCTTGT
seq0004        GGTACCCA-----T-GTC---AGGAACGTTTCAACTTCAACA---GACGTACT-TCTTGT
seq0005        GGTACTCA-----T-ATC---AAGAACGTTTCAATTTCAACA---GACGTACT-TCATGT
seq0006        GGTACTCA-----T-GTC---AAGAACGTTTCAACGTCAACA---GACGTACT-TCTTGT
seq0007        GGTACTCA-----T-GTC---AAAAACGTTTCAACTTCAACA---GACGTACT-TCTTGT
seq0008        GGTACTCA-----TCATC---AGGTACGTTTCAAATTCAACA---GACGTACT-TCTTGT
seq0009        GGTACTCA-----G-ATC---AGGAACGTTTCAATTTCTATA---GACGTACT-TCTTGT
seq0013        GGGACTCATTACTG-ATTTTGTGGAACGTTACCATGTCAACCGACTTAAT--G-CATCGT
seq0014        --------TGTCTA-TGTTTGTGCGCC--TA--ATGTCAACT---ATAGT--G-CCTCTA
seq0015        GGTACTCA-----A-AGA---AGGACCGTTTCCAGTTCACCA---AAAGTACG-GCTTGT
seq0018        GGGGCTTA-----T-ATC---GGGAAAAGTTCAATTGCA---------------------
seq0020        GGTGCGGA-----T-ATC---ATGAACATTTTAATTGCAACA---GAAGTACCATATTTT

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        TCGCTCCAAGCAACTTATGGCCCCGAATCTGTCACGTCTTT-------------------
seq0001        TCGCTCCAAGCAACTTATGGCCCCGAATCTGTCACGTCTTT-------------------
seq0002        TCACGCCAAGCAACTTATGGCTCCGAAACTTTCACGTCTGT-------------------
seq0003        TCACGCCAAGCAACTTATGGCCCCGAAACTTTCACGTCTGT-------------------
seq0004        TCACGCCATGCAACTTATGGCCCCGAAACTTTCACGTCTTT-------------------
seq0005        TCGCGCCAAGCAACTTTCGGCCCCGAATATGTCACGTCTTT-------------------
seq0006        TCGCGCCAAGCAACTTTCGGCCCCGAATCTGTACCGTCTTT-------------------
seq0007        TCGCGCCACGCAACTTTAGGCCCCGAATCTGTAACGTCTCT-------------------
seq0008        TCGTGCCAAACAAATTTCGGCGCCGAATCCGTCACATGTCT-------------------
seq0009        TCGCGGCCGAAAAATTTCCGCACCGAATTTGTCACATATCT-------------------
seq0013        TCGCTCCAG--CTGTCAC--------AGGTTTGGCCGCA---------------------
seq0014        GTGGCCCTA--AAGTATC--------ATAAGAGATAACT---------------------
seq0015        TCGCACCAAGCAAGTTTCGGCCCCAAAGCTGTCACGACT---------------------
seq0018        -------------------GCCCACAATCTGTAACATGTTT-------------------
seq0020        TCGCGCCAAGCAAATTTTGGGCACCAATAGGTCACATGTTTTTGGGATAGTTAGAGTAAG

(position)     1111111111111111111111111111111111111111111
               2222222222333333333344444444445555555555666
               0123456789012345678901234567890123456789012
                                                          
seq0000        -GTGCGC-A---------------------------GTCAACA
seq0001        -GTGCGC-A---------------------------GTCAACA
seq0002        -GTCCGC-A---------------------------GTCAACA
seq0003        -GTGCGC-A---------------------------GTCAACA
seq0004        -GTGCTC-A---------------------------GTCAACA
seq0005        -GTGCGC-A---------------------------GTCATTC
seq0006        -GTGCGC-A---------------------------GTCAATC
seq0007        -GTGCGC-A---------------------------GTCCATC
seq0008        -ATGCGC-C---------------------------GTCCACA
seq0009        -GTCCGC-C---------------------------GGCAACA
seq0013        ------C-A---------------------------GAAAAGA
seq0014        ------C-G---------------------------GCA----
seq0015        ------C-ATGCTTCGTGACGGGTAGAAAAACCCGAGACAACA
seq0018        -GCGCACTA---------------------------GACAACA
seq0020        AGTGCGCCA---------------------------GACTCCA


<<<<< 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, -42) .

[ 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    -    -    -    -    -    5    -    5    5    5    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3
seq0001   	    0    0    0    0    0    0    0    0    -    -    -    -    -    5    -    5    5    5    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3
seq0002   	    0    0    0    0    0    0    0    0    -    -    -    -    -    5    -    5    5    5    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3
seq0003   	    0    0    0    0    0    0    0    0    -    -    -    -    -    5    -    5    5    5    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3
seq0004   	    0    0    0    0    0    0    0    0    -    -    -    -    -    5    -    5    5    5    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3
seq0005   	    0    0    0    0    0    0    0    0    -    -    -    -    -    5    -    5    5    5    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3
seq0006   	    0    0    0    0    0    0    0    0    -    -    -    -    -    5    -    5    5    5    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3
seq0007   	    0    0    0    0    0    0    0    0    -    -    -    -    -    5    -    5    5    5    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3
seq0008   	    0    0    0    0    0    0    0    0    -    -    -    -    -    5    5    5    5    5    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3
seq0009   	    0    0    0    0    0    0    0    0    -    -    -    -    -    5    -    5    5    5    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3
seq0013   	    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -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   -1   -1
seq0014   	    -    -    -    -    -    -    -    -  -81  -81  -81  -81  -87  -87    -  -86  -86  -86  -86  -86 -107 -107 -107 -118 -120 -120 -120    -    - -118 -118    -    - -116 -116 -116 -116 -116 -116 -116 -116 -116    -    -    - -113 -113 -113 -113 -113
seq0015   	    0    0    0    0    0    0    0    0    -    -    -    -    -    5    -    5    5    5    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3
seq0018   	    0    0    0    0    0    0    0    0    -    -    -    -    -    5    -    5    5    5    -    -    -    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    0    0    -    -    -    -    -    5    -    5    5    5    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3    3    3    3    3



(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    2    2    -    3    3    3    3    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    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5
seq0001   	    3    2    2    -    3    3    3    3    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    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5
seq0002   	    3    2    2    -    3    3    3    3    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    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5
seq0003   	    3    2    2    -    3    3    3    3    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    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5
seq0004   	    3    2    2    -    3    3    3    3    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    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5
seq0005   	    3    2    2    -    3    3    3    3    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    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5
seq0006   	    3    2    2    -    3    3    3    3    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    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5
seq0007   	    3    2    2    -    3    3    3    3    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    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5
seq0008   	    3    2    2    -    3    3    3    3    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    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5
seq0009   	    3    2    2    -    3    3    3    3    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    0    0    0    0    0   -5   -5   -5   -5   -5   -5
seq0013   	    -    -    1    -    2    2    2    2    2    2    2    2    2    2    2    0    0  -19  -19    -    -  -17  -17  -17  -17  -17  -17  -22    -    -    -    -    -    -    -    -  -14  -14  -14  -14  -14  -14  -35  -35  -35  -46  -48  -48  -92    -
seq0014   	    -    - -111    - -110 -110 -110 -110 -110 -110 -110 -110 -110 -110 -110 -110 -110 -110 -110    -    - -108 -108 -108 -108 -108 -108 -108    -    -    -    -    -    -    -    - -100 -100 -100 -100 -101 -101 -101 -101 -101 -101 -101 -101 -101    -
seq0015   	    3    2    2    -    3    3    3    3    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    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   -5   -5   -5   -5   -5   -5
seq0020   	    3    3    3    3    3    3    3    3    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    0    0    0    0    0    0    0    0   -5   -5   -5   -5   -5   -5



(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   	   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6  -17  -19  -19    -  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6  -17  -19  -19    -  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6  -17  -19  -19    -  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6  -17  -19  -19    -  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6  -17  -19  -19    -  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6  -17  -19  -19    -  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6  -17  -19  -19    -  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6  -17  -19  -19    -  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6  -17  -19  -19    -  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6  -17  -19  -19    -  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -65    -  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -74    -  -73    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   27    -   28   28   28   28   28   28    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8
seq0018   	   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6   -6  -17  -19  -19  -64  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -6   -6   -6  -17  -19  -19  -64  -64    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



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

seq0000   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42
seq0001   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42
seq0002   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42
seq0003   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42
seq0004   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42
seq0005   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42
seq0006   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42
seq0007   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42
seq0008   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42
seq0009   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42
seq0013   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42
seq0014   	    -    -    -    -    -    -  -46  -46  -46    -    -    -    -
seq0015   	    8    8    8    8  -37  -37  -37  -37  -37  -37  -37  -37  -42
seq0018   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42
seq0020   	    -    -    -    -    -    -  -37  -37  -37  -37  -37  -37  -42



<<<<< 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). >>>>>

<<<<< 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} = 31) >>

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

0	8	11	21	14	-81	n/a	11
1	9	66	20	36,43,37,45,49,44	-1,0,-1,1,2,0	0,0,0,0,0	10
2	12	19	21	12,13	-87,-86	0	11
3	13	17	29	53	5	n/a	0,1,2,3,4,5,6,7,8,9,12,13,14
4	20	26	21	8,1,0	-107,-118,-120	0,0	11
5	21	41	29	39	0	n/a	0,1,2,3,4,5,6,7,8,9,12,14
6	21	93	26	40	0	n/a	13
7	29	30	21	2	-118	n/a	11
8	33	77	21	3,4,5,6,7	-116,-113,-111,-110,-108	0,0,0,0	11
9	45	57	25	51,47,52	3,2,3	0,0	0,1,2,3,4,5,6,7,8,9,12
10	45	57	28	50	3	n/a	14
11	58	64	29	46	2	n/a	0,1,2,3,4,5,6,7,8,12,14
12	58	70	17	48	2	n/a	9
13	65	93	29	38	0	n/a	0,1,2,3,4,5,6,7,8,14
14	65	98	23	41	0	n/a	12
15	67	77	20	29,31,27	-19,-17,-22	0,0	10
16	71	93	17	42	0	n/a	9
17	86	91	20	32	-14	n/a	10
18	86	98	21	10,9	-100,-101	0	11
19	92	98	20	26,22,20,11	-35,-46,-48,-92	0,0,0	10
20	94	100	27	34	-5	n/a	0,1,2,3,4,5,6,7,8,9,13
21	94	120	28	35	-5	n/a	14
22	121	126	29	33,30,28	-6,-17,-19	0,0	0,1,2,3,4,5,6,7,8,9,13,14
23	126	126	20	17	-65	n/a	10
24	126	158	21	15,16,21	-74,-73,-46	0,0	11
25	126	153	23	55,56,54	27,28,8	0,0	12
26	127	128	29	18	-64	n/a	13,14
27	128	128	25	19	-64	n/a	0,1,2,3,4,5,6,7,8,9,10
28	154	161	23	25	-37	n/a	12
29	156	161	29	24	-37	n/a	0,1,2,3,4,5,6,7,8,9,10,13,14
30	162	162	29	23	-42	n/a	0,1,2,3,4,5,6,7,8,9,10,12,13,14



<<<<< 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} = 31) >>>>>


[[ 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	2	1	0	1	0	0
1	2	1	1	0	0	0
2	1	0	0	0	0	0
3	0	2	1	0	0	0
4	1	1	0	0	0	0
5	0	1	1	1	0	0
6	1	1	0	0	0	0
7	0	2	0	0	0	0
8	0	1	0	1	0	0
9
10	1	1	0	0	0	0
11	0	0	1	0	0	0
12	2	0	0	0	0	0
13	0	0	1	0	0	0
14	1	0	0	1	0	0
15	0	0	1	1	0	0
16	1	0	0	0	0	0
17	0	0	0	1	0	0
18	2	0	0	1	0	0
19	1	0	0	0	0	0
20	0	1	1	0	0	0
21	0	0	0	0	0	0
22	0	1	2	1	0	0
23	1	0	0	0	0	0
24	1	1	0	0	0	0
25	4	1	0	1	0	0
26	0	1	1	0	0	0
27
28	0	1	0	0	0	0
29
30	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 4): 9, 21, 27, 29 . ]


[ 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	4	4	Complex	21:0:88:X/21:93:93:X	21:0:7:X/22:8:12:-
1	0	57	58	Complex	20:13:20:-/20:55:55:-/22:67:85:X	20:42:44:-
2	0	7	8	Complex(???)	21:93:93:X	None
3	0	5	5	Complex	20:13:20:-	22:8:12:-/22:18:20:-
4	0	20	7	Complex(???)	21:146:189:-	21:27:28:X
5	0	21	21	Complex(???)	20:13:20:-	22:18:20:-/20:42:44:-
6	0	73	73	Shift(???)	26:39:78:X	26:39:78:X
7	0	2	2	Complex(???)	None	21:27:28:X/21:31:32:X
8	0	37	45	Complex(???)	None	21:31:32:X/22:78:85:X
9	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
10	0	13	13	Shift(???)	28:48:48:-	28:53:53:-
11	0	7	7	NO_ASSOCIATED_EVENT(???)	20:55:55:-	None
12	0	13	13	Purge(?)	17:69:70:X/17:63:64:-	None
13	0	29	29	NO_ASSOCIATED_EVENT(???)	23:94:98:-	None
14	0	34	34	Complex(???)	23:94:98:-	24:99:125:X
15	0	14	11	Complex(???)	22:67:85:X	22:78:85:X
16	0	23	23	Complex(???)	17:69:70:X	None
17	0	6	6	NO_ASSOCIATED_EVENT(???)	None	22:78:85:X
18	0	14	13	Complex	21:199:203:-/21:146:189:-	22:78:85:X
19	0	64	7	Complex(???)	20:190:190:-	None
20	0	7	7	Complex(???)	23:94:98:-	24:99:125:X
21	Skipped!!(NO_ASSOCIATED_EVENT(???))
22	0	19	6	Complex(???)	23:126:126:-/19:191:191:X	24:99:125:X/25:127:127:X
23	0	1	1	Complex(???)	20:190:190:-	None
24	0	5	33	Complex(???)	21:199:203:-	21:159:162:X
25	0	47	28	Complex	23:94:98:-/23:126:126:-/23:130:140:-/23:142:143:-	23:129:155:-/24:99:125:X
26	0	2	2	Complex(???)	19:191:191:X	25:127:127:X
27	Skipped!!(NO_RELEVANT_BRANCH)
28	0	8	8	Complex(???)	None	23:129:155:-
29	Skipped!!(NO_RELEVANT_BRANCH)
30	0	1	1	Complex(???)	21:199:203:-	21:159:162:X


[ Contents of %indel_ref2assoc_cblks ]

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

21:0:88	0
16:9:9	{Equivalent to '16:14:14'(rec)}
20:13:20	1,3,5
26:39:78	6
28:48:48	10
20:55:55	1,11
17:63:64	12
22:67:85	1,15
17:69:70	12,16
21:93:93	0,2
23:94:98	13,14,20,25
28:106:125	{Equivalent to '28:101:120'(rec)}
23:126:126	22,25
23:130:140	25
23:142:143	25
21:146:189	4,18
20:190:190	19,23
19:191:191	22,26
21:199:203	18,24,30


[ Contents of %indel_rec2assoc_cblks ]

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

21:0:7	0
22:8:12	0,3
16:14:14	{Equivalent to '16:9:9'(ref)}
22:18:20	3,5
21:27:28	4,7
21:31:32	7,8
26:39:78	6
20:42:44	1,5
22:50:51	None
28:53:53	10
22:69:70	None
22:78:85	8,15,17,18
24:99:125	14,20,22,25
28:101:120	{Equivalent to '28:106:125'(ref)}
25:127:127	22,26
23:129:155	25,28
21:159:162	24,30


<<<< (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} = 4) ]

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

11	=> [1],
13	=> [14],
27	=> [26],
29	=> [28],


[ Contents of %cb2hard_linking (#{keys} = 4) ]

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

1	=> [11],
14	=> [13],
26	=> [27],
28	=> [29],


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

Indx_cblk_A	indx_cblk_B

12	16
19	23


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

[ For the 1 th pair: (12, 16) ]

[ For the 2 th pair: (19, 23) ]

