<<<<< 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 = 192 ,
#{Sites in the segment}_rec = 158 .


<< 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        AAC-TTACTAGCTCGGCAAGACTAGGAATA------------------------------
seq0001        AAC-TTACTAGCTCGGCAAGACTAGGAATA------------------------------
seq0002        AAC-TTACTAGCTCGGCAAGACTAGGAATA------------------------------
seq0003        AAC-TTACTAGCTCGGCAAGACTAGGAATA------------------------------
seq0004        AAC-TTACTAGCTCGGCAAGACTAGGAATA------------------------------
seq0005        AAC-TTAGTAGCTCCGCAAGACTAGGAATA------------------------------
seq0006        AGC-TTAGTAGCTCGGCAAGACTAGGTATA------------------------------
seq0007        AGC-TTAGTAGCTCCGCAAGACTAGGTATA------------------------------
seq0008        AAT-TTAGTAGATCCGCTAGATAAGGTAAATACCTCACGCTTAAGAAAGACGTGTATCGC
seq0009        AAC-CTAGTAGATCCGCAATATAAGGAATA------------------------------
seq0013        T-CTTTGGTATATCGGCGACAACAGCTATA------------------------------
seq0014        A-A-TTCGTATATACGCAGGATCAAGAATA------------------------------
seq0015        C-C-TGA-----------------------------------------------------
seq0018        A-C-TTAATATATCCATAAAAGCAGGAATA------------------------------
seq0020        A-C-TTCGTATATCCGCAAGAGCAGGAATA------------------------------

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ---------GAC--CTCGTCATGCGG-AATATTCG-TAGAATTGCAA----AGGC-CTGG
seq0001        ---------GAC--CTCGTCATGCGG-AATATTCG-TAGAATTGCAA----AGGC-CTGG
seq0002        ---------GAC--CTCCTCATGAGG-AATATTCG-TAGAATTGCAA----AGGC-CTGG
seq0003        ---------GAC--CTCCTCATGAGG-AATATTCG-TAGAATTGTAA----AGGC-CTGG
seq0004        ---------GAC--CTCCTCATGAGG-AATATTCG-TAGAATTGTAA----AGGC-CTGG
seq0005        ---------GAC--CTCCTCATGAGG-AATATTCG-TAGAATTGCAA----AGGC-CTGG
seq0006        ---------GAC--CTCCTCATGAGG-CATATTCG-TAGAATTGCGA----ACGC-CTGG
seq0007        ---------GAC--CTCCTCATGAGG-AATATTCG-TAGAATTGCGA----AGGC-CTGG
seq0008        AAAAAAATGGAC--CTCCTCATGAGGTCATATTCG-TAGAATTGCAA----AGGC-CTAC
seq0009        ---------GAA--CTCCTGATGAGC-GATAATCG-TAAAATTGCAA----AGGC-CTCC
seq0013        ---------GACT-CTACTCATTAGA-CATCCTCG-TAGAATTGCTA----AGGA-GTAC
seq0014        ---------GACATCACCTCGTAGAG-CATATTCG-TAGCATTGTTATAATAGGCCGTAC
seq0015        ---------------TCCTCATAAGG-CATAGTTTTCAGAATTGCTA----AGGC-GTAC
seq0018        ---------GGGA-CTCCACATGAGT-CATATTCG-TAGAATTAATA----AGGC-CTAC
seq0020        ---------TACA-CTCCT-ATGAGG-CATACTCC-TAGGATTGCAA----AGGC-TTCC

(position)     111111111111111111111111111111111111111111111111111111111111
               222222222233333333334444444444555555555566666666667777777777
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        CTGGTTCCAGA-------------------------------------------------
seq0001        CTGGTTCCATA-------------------------------------------------
seq0002        CTGGTTCCAGA-------------------------------------------------
seq0003        CTGGTTCCAGA-------------------------------------------------
seq0004        CTGGTTCCAGA-------------------------------------------------
seq0005        CTGGTTCCAGG-------------------------------------------------
seq0006        CTGGTT--AGA-------------------------------------------------
seq0007        CTGGTTCCAGA-------------------------------------------------
seq0008        ATGTTTCCAGT-------------------------------------------------
seq0009        CTGGATCCCGT-------------------------------------------------
seq0013        CTGGTTCCAAT-------------------------------------------------
seq0014        CTGGTTCCCGT-------------------------------------------------
seq0015        CTAGTGCCAGTCGTACAGCGTTTGAGAAGGAGAGAGACAATATTACTCACCCGACCAGTC
seq0018        CTGGCTCGAGT-------------------------------------------------
seq0020        CCTGCTCCAGT-------------------------------------------------

(position)     111111111111
               888888888899
               012345678901
                           
seq0000        ------------
seq0001        ------------
seq0002        ------------
seq0003        ------------
seq0004        ------------
seq0005        ------------
seq0006        ------------
seq0007        ------------
seq0008        ------------
seq0009        ------------
seq0013        ------------
seq0014        ------------
seq0015        CGGATATATAAT
seq0018        ------------
seq0020        ------------


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        --AACTTACTAGCTCGGCA--------AGACTAGG-------------------------
seq0001        --AACTTACTAGCTCGGCA--------AGACTAGG-------------------------
seq0002        --AACTTACTAGCTCGGCA--------AGACTAGG-------------------------
seq0003        --AACTTACTAGCTCGGCA--------AGACTAGG-------------------------
seq0004        --AACTTACTAGCTCGGCA--------AGACTAGG-------------------------
seq0005        --AACTTAGTAGCTCCGCA--------AGACTAGG-------------------------
seq0006        --AGCTTAGTAGCTCGGCA--------AGACTAGG-------------------------
seq0007        --AGCTTAGTAGCTCCGCA--------AGACTAGG-------------------------
seq0008        --AATTTAGTAGATCCGCT--------AGATAAGGTAAATACCTCACGCTTAAGAAAGAC
seq0009        --AACCTAGTAGATCCGCA--------ATATAAGG-------------------------
seq0013        --TCTTTGGTATATCGGCG--------ACAACAGC-------------------------
seq0014        ---AATTCGTATATACGCA--------GGATCAAG-------------------------
seq0015        CCTGATCCTCATA-AGGCATAGTTTTCAGAATTGC-------------------------
seq0018        ---ACTTAATATATCCATA--------AAAGCAGG-------------------------
seq0020        ---ACTTCGTATATCCGCA--------AGAGCAGG-------------------------

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        --------------AATAG---A-CCT----C--GTCATGC-GGAATATTCGTAGAATTG
seq0001        --------------AATAG---A-CCT----C--GTCATGC-GGAATATTCGTAGAATTG
seq0002        --------------AATAG---A-CCT----C--CTCATGA-GGAATATTCGTAGAATTG
seq0003        --------------AATAG---A-CCT----C--CTCATGA-GGAATATTCGTAGAATTG
seq0004        --------------AATAG---A-CCT----C--CTCATGA-GGAATATTCGTAGAATTG
seq0005        --------------AATAG---A-CCT----C--CTCATGA-GGAATATTCGTAGAATTG
seq0006        --------------TATAG---A-CCT----C--CTCATGA-GGCATATTCGTAGAATTG
seq0007        --------------TATAG---A-CCT----C--CTCATGA-GGAATATTCGTAGAATTG
seq0008        GTGTATCGCAAAAAAATGG---A-CCT----C--CTCATGAGGTCATATTCGTAGAATTG
seq0009        --------------AATAG---A-ACT----C--CTGATGA-GCGATAATCGTAAAATTG
seq0013        --------------TATAG---A-C-T----CTACTCATTA-GACATCCTCGTAGAATTG
seq0014        --------------AATAG---A-CAT----CACCTCGTAG-AGCATATTCGTAGCATTG
seq0015        --------------TAAGGCGTA-CCTAGTGCCAGTCGTAC-AGCGTTTGAGAAGGAGAG
seq0018        --------------AATAG---GGACT----C--CACATGA-GTCATATTCGTAGAATTA
seq0020        --------------AATAT---ACACT----C--CT-ATGA-GGCATACTCCTAGGATTG

(position)     11111111111111111111111111111111111111
               22222222223333333333444444444455555555
               01234567890123456789012345678901234567
                                                     
seq0000        CAA----AGGCC-TGGCTG----GTTCC-------AGA
seq0001        CAA----AGGCC-TGGCTG----GTTCC-------ATA
seq0002        CAA----AGGCC-TGGCTG----GTTCC-------AGA
seq0003        TAA----AGGCC-TGGCTG----GTTCC-------AGA
seq0004        TAA----AGGCC-TGGCTG----GTTCC-------AGA
seq0005        CAA----AGGCC-TGGCTG----GTTCC-------AGG
seq0006        CGA----ACGCC-TGGCTG----GTT---------AGA
seq0007        CGA----AGGCC-TGGCTG----GTTCC-------AGA
seq0008        CAA----AGGCC-TACATG----TTTCC-------AGT
seq0009        CAA----AGGCC-TCCCTG----GATCC-------CGT
seq0013        CTA----AGG-AGTACCTG----GTTCC-------AAT
seq0014        TTATAATAGGCCGTACCTG----GTTCC-------CGT
seq0015        AGACAATATTACTCACCCGACCAGTCCGGATATATAAT
seq0018        ATA----AGGCC-TACCTG----GCTCG-------AGT
seq0020        CAA----AGGCT-TCCCCT----GCTCC-------AGT


<<<<< 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, -34) .

[ 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    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    2    2    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    2    2    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    2    2    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    2    2    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    2    2    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    2    2    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    2    2    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    2    2    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9
seq0009   	    -    -    2    2    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    3    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    0   -1   -2   -2   -2  -70  -70  -70  -70  -70  -70  -70  -70    -  -69  -69  -69  -70  -70  -70  -70  -70  -70  -70  -70  -70  -70  -70  -70  -70  -70  -70  -70  -70  -70    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    3    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    3    2    1    1    1    1    1    1    1    1    1    1    1    1    1    1    -    -    -    -    -    -    -    -    9    9    9    9    9    9    9    9    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12    -   13   11   11    -    -    -    -   15    -    -   17   17   17   17   17   17
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12    -   13   11   11    -    -    -    -   15    -    -   17   17   17   17   17   17
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12    -   13   11   11    -    -    -    -   15    -    -   17   17   17   17   17   17
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12    -   13   11   11    -    -    -    -   15    -    -   17   17   17   17   17   17
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12    -   13   11   11    -    -    -    -   15    -    -   17   17   17   17   17   17
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12    -   13   11   11    -    -    -    -   15    -    -   17   17   17   17   17   17
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12    -   13   11   11    -    -    -    -   15    -    -   17   17   17   17   17   17
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12    -   13   11   11    -    -    -    -   15    -    -   17   17   17   17   17   17
seq0008   	    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    -    -    -   12    -   13   11   11    -    -    -    -   15    -    -   17   17   17   17   17   17
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12    -   13   11   11    -    -    -    -   15    -    -   17   17   17   17   17   17
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12    -   13    -   14    -    -    -    -   17   17   17   17   17   17   17   17   17
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12    -   13   13   13    -    -    -    -   17   17   17   17   17   17   17   17   17
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -31  -31  -35  -35  -35  -35  -36  -36  -36    -  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35  -35
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12   12   12   11   11    -    -    -    -   15    -    -   17   17   17   17   17   17
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   48   48   48   48    9    -    -    -   12   12   12   11   11    -    -    -    -   15    -    -   17   17    -   17   17   17



(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   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16   16   15    -   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -
seq0001   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16   16   15    -   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -
seq0002   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16   16   15    -   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -
seq0003   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16   16   15    -   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -
seq0004   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16   16   15    -   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -
seq0005   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16   16   15    -   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -
seq0006   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16   16   15    -   16   16   16   16   16   16    -    -    -    -   20   20   20    -    -    -    -
seq0007   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16   16   15    -   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -
seq0008   	   17   17   17   17   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16   16   15    -   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -
seq0009   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16   16   15    -   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -
seq0013   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16    -   17   16   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -
seq0014   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -
seq0015   	  -35    -  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34  -34
seq0018   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16   16   15    -   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -
seq0020   	   17    -   18   18   17   17   17   17   17   17   17   17   16   16   16   16   16   16   16   16   16   16   16    -    -    -    -   16   16   16   16   15    -   16   16   16   16   16   16    -    -    -    -   20   20   20   20   20    -    -



(position)	  150  151  152  153  154  155  156  157

seq0000   	    -    -    -    -    -   27   27   27
seq0001   	    -    -    -    -    -   27   27   27
seq0002   	    -    -    -    -    -   27   27   27
seq0003   	    -    -    -    -    -   27   27   27
seq0004   	    -    -    -    -    -   27   27   27
seq0005   	    -    -    -    -    -   27   27   27
seq0006   	    -    -    -    -    -   27   27   27
seq0007   	    -    -    -    -    -   27   27   27
seq0008   	    -    -    -    -    -   27   27   27
seq0009   	    -    -    -    -    -   27   27   27
seq0013   	    -    -    -    -    -   27   27   27
seq0014   	    -    -    -    -    -   27   27   27
seq0015   	  -34  -34  -34  -34  -34  -34  -34  -34
seq0018   	    -    -    -    -    -   27   27   27
seq0020   	    -    -    -    -    -   27   27   27




[INFORMATION] The original $commoner_shift_flank = -34. 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36   35   35   35   35   35   35   35   35   35   35   35
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36   35   35   35   35   35   35   35   35   35   35   35
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36   35   35   35   35   35   35   35   35   35   35   35
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36   35   35   35   35   35   35   35   35   35   35   35
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36   35   35   35   35   35   35   35   35   35   35   35
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36   35   35   35   35   35   35   35   35   35   35   35
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36   35   35   35   35   35   35   35   35   35   35   35
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36   35   35   35   35   35   35   35   35   35   35   35
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36   35   35   35   35   35   35   35   35   35   35   35
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36   35   35   35   35   35   35   35   35   35   35   35
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   35   35   35   35   35   35   35   35   35   35   35   35   35
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   37   36   35   35   35   35   35   35   35   35   35   35   35
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   33   32   32   32  -36  -36  -36  -36  -36  -36  -36  -36    -  -35  -35
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   37   36   35   35   35   35   35   35   35   35   35   35   35
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   37   36   35   35   35   35   35   35   35   35   35   35   35



(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   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43   43
seq0009   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	  -35  -36  -36  -36  -36  -36  -36  -36  -36  -36  -36  -36  -36  -36  -36  -36  -36  -36  -36    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	   35   35   35    -    -    -    -    -    -    -    -   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



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

seq0000   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46    -   47   45   45    -    -    -    -   49    -    -   51   51   51   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50
seq0001   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46    -   47   45   45    -    -    -    -   49    -    -   51   51   51   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50
seq0002   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46    -   47   45   45    -    -    -    -   49    -    -   51   51   51   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50
seq0003   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46    -   47   45   45    -    -    -    -   49    -    -   51   51   51   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50
seq0004   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46    -   47   45   45    -    -    -    -   49    -    -   51   51   51   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50
seq0005   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46    -   47   45   45    -    -    -    -   49    -    -   51   51   51   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50
seq0006   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46    -   47   45   45    -    -    -    -   49    -    -   51   51   51   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50
seq0007   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46    -   47   45   45    -    -    -    -   49    -    -   51   51   51   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50
seq0008   	   43   43   43   43   43   43   43   43   43   43   43   43   43    -    -    -   46    -   47   45   45    -    -    -    -   49    -    -   51   51   51   51   51   51   51   51   51   51   51   51   51   51   51   51   51   51   50   50   50   50
seq0009   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46    -   47   45   45    -    -    -    -   49    -    -   51   51   51   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50
seq0013   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46    -   47    -   48    -    -    -    -   51   51   51   51   51   51   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50
seq0014   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46    -   47   47   47    -    -    -    -   51   51   51   51   51   51   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50
seq0015   	    -    -    -    -    -    -    -    -    3    3   -1   -1   -1   -1   -2   -2   -2    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46   46   46   45   45    -    -    -    -   49    -    -   51   51   51   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50
seq0020   	    -    -    -    -    -    -    -    -   82   82   82   82   43    -    -    -   46   46   46   45   45    -    -    -    -   49    -    -   51   51    -   51   51   51   51    -   52   52   51   51   51   51   51   51   51   51   50   50   50   50



(position)	  150  151  152  153  154  155  156  157  158  159  160  161  162  163  164  165  166  167  168  169  170  171  172  173  174  175  176  177  178  179  180  181  182  183  184  185  186  187  188  189  190  191

seq0000   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50   50   49    -   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61
seq0001   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50   50   49    -   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61
seq0002   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50   50   49    -   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61
seq0003   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50   50   49    -   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61
seq0004   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50   50   49    -   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61
seq0005   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50   50   49    -   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61
seq0006   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50   50   49    -   50   50   50   50   50   50    -    -    -    -   54   54   54    -    -    -    -    -    -    -    -    -   61   61   61
seq0007   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50   50   49    -   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61
seq0008   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50   50   49    -   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61
seq0009   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50   50   49    -   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61
seq0013   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50    -   51   50   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61
seq0014   	   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61
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
seq0018   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50   50   49    -   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61
seq0020   	   50   50   50   50   50   50   50    -    -    -    -   50   50   50   50   49    -   50   50   50   50   50   50    -    -    -    -   54   54   54   54   54    -    -    -    -    -    -    -   61   61   61



<<<<< 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} = 28) >>

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

0	34	38	23	9,8,7	34,33,32	0,0	12
1	36	38	19	13	36	n/a	0,1,2,3,4,5,6,7,8,9
2	36	52	20	14,11	36,35	0	10
3	37	37	29	15	37	n/a	11,13,14
4	38	38	29	12	36	n/a	11,13,14
5	39	52	29	10	35	n/a	0,1,2,3,4,5,6,7,8,9,11,13,14
6	39	46	23	0	-36	n/a	12
7	48	134	23	2,1,6,4,3,5	-35,-36,3,-1,-2,-1	0,0,0,0,0	12
8	61	112	29	16	43	n/a	0,1,2,3,4,5,6,7,8,9,10,11,13,14
9	108	111	29	37	82	n/a	0,1,2,3,4,5,6,7,9,10,11,13,14
10	116	116	25	19	46	n/a	0,1,2,3,4,5,6,7,8,9,10,11
11	116	118	29	18	46	n/a	13,14
12	118	118	25	20	47	n/a	0,1,2,3,4,5,6,7,8,9,10
13	118	120	21	21	47	n/a	11
14	119	125	29	17,23	45,49	0	0,1,2,3,4,5,6,7,8,9,13,14
15	120	120	20	22	48	n/a	10
16	125	134	22	30	51	n/a	10,11
17	128	134	29	29	51	n/a	0,1,2,3,4,5,6,7,9,13,14
18	128	145	16	31	51	n/a	8
19	136	137	29	33	52	n/a	0,1,2,3,4,5,6,7,9,10,11,13,14
20	138	145	29	28	51	n/a	0,1,2,3,4,5,6,7,9,10,11,13,14
21	146	165	29	25,24	50,49	0	0,1,2,3,4,5,6,7,8,9,13,14
22	146	172	22	27	50	n/a	10,11
23	165	165	20	32	51	n/a	10
24	167	172	29	26	50	n/a	0,1,2,3,4,5,6,7,8,9,13,14
25	177	181	29	34	54	n/a	0,1,2,3,4,5,7,8,9,10,11,13,14
26	177	179	11	35	54	n/a	6
27	189	191	29	36	61	n/a	0,1,2,3,4,5,6,7,8,9,10,11,13,14



<<<<< 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} = 28) >>>>>


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


[ Skipped Composite-Blocks (#{cblocks} = 9): 3, 4, 5, 10, 12, 19, 20, 25, 26 . ]


[ 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	7	5	Complex(???)	23:7:74:X	23:34:35:-
1	0	3	3	Collapse-of-Independent-Insertions(+overshoot(??))(+0)(?)	20:3:3:-/19:1:1:-	25:36:36:-/21:36:36:X
2	0	18	17	Complex(???)	20:3:3:-	21:36:36:X
3	Skipped!!(NO_RELEVANT_BRANCH)
4	Skipped!!(NO_RELEVANT_BRANCH)
5	Skipped!!(NO_RELEVANT_BRANCH)
6	0	8	8	Complex(???)	23:7:74:X	23:47:47:X
7	0	53	87	Complex	23:95:95:-/23:131:191:-	23:47:47:X/23:53:60:-/23:113:115:-/23:121:124:-
8	0	52	52	Complex(???)	None	23:53:60:-/23:113:115:-
9	0	4	4	Shift	16:30:68:-	16:69:107:-
10	Skipped!!(NO_RELEVANT_BRANCH)
11	0	3	3	Complex(???)	19:72:72:X	25:117:117:X
12	Skipped!!(NO_RELEVANT_BRANCH)
13	0	3	3	Complex(???)	21:73:73:-	None
14	0	3	7	Complex(???)	19:72:72:X	24:126:127:-
15	0	1	1	Complex(???)	21:73:73:-	20:119:119:X
16	0	10	10	Complex(???)	21:73:73:-	23:121:124:-
17	0	7	7	Complex(???)	None	24:126:127:-
18	0	18	18	Shift(???)	16:86:86:-	16:135:135:-
19	Skipped!!(NO_RELEVANT_BRANCH)
20	Skipped!!(NO_RELEVANT_BRANCH)
21	0	21	20	Complex	23:95:95:-	24:166:166:-/24:157:160:-
22	0	27	27	Complex(???)	23:95:95:-	23:173:176:-
23	0	1	1	Complex(???)	21:115:115:-	20:164:164:X
24	0	6	6	Complex(???)	None	24:166:166:-/23:173:176:-
25	Skipped!!(NO_RELEVANT_BRANCH)
26	Skipped!!(NO_ASSOCIATED_EVENT(???))
27	0	3	3	Complex(???)	23:131:191:-	23:182:188:-


[ Contents of %indel_ref2assoc_cblks ]

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

19:1:1	1
20:3:3	1,2
23:7:74	0,6
16:30:68	9
19:72:72	11,14
21:73:73	13,15,16
27:79:79	None
16:86:86	18
23:95:95	7,21,22
21:107:110	None
21:115:115	23
11:126:127	{Equivalent to '11:180:181'(rec)}
23:131:191	7,27


[ Contents of %indel_rec2assoc_cblks ]

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

23:34:35	0
25:36:36	1
21:36:36	1,2
23:47:47	6,7
23:53:60	7,8
16:69:107	9
23:113:115	7,8
25:117:117	11
20:119:119	15
23:121:124	7,16
24:126:127	14,17
27:130:130	None
16:135:135	18
24:157:160	21
20:157:160	None
20:164:164	23
24:166:166	21,24
23:173:176	22,24
11:180:181	{Equivalent to '11:126:127'(ref)}
23:182:188	27


<<<< (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} = 5) ]

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

4	=> [1],
5	=> [2],
10	=> [11],
12	=> [13],
20	=> [18],


[ Contents of %cb2hard_linking (#{keys} = 5) ]

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

1	=> [4],
2	=> [5],
11	=> [10],
13	=> [12],
18	=> [20],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 1) ]

Indx_cblk_A	indx_cblk_B

1	2


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

[ For the 1 th pair: (1, 2) ]

