<<<<< 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 = 170 ,
#{Sites in the segment}_rec = 166 .


<< Correspondence between sequence IDs and sequence indices >>

Indx:	Seq_ID

0:	seq0000
1:	seq0001
2:	seq0002
3:	seq0003
4:	seq0004
5:	seq0005
6:	seq0006
7:	seq0007
8:	seq0008
9:	seq0009
10:	seq0013
11:	seq0014
12:	seq0015
13:	seq0018
14:	seq0020


<< Original Segment of the Reference Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ----ACG-------------TAGTCATCGGTCTTGCCAGCCGAGTTTGAAAC-GTC----
seq0001        ----ACG-------------TAGACATCGGTCTTGCCAGCCGAGTTTGAAAC-GTC----
seq0002        ----ACG-------------TAGTCATCGGTCTTGCCAGCCCAGTCTGACAC-GTC----
seq0003        ----ACG-------------TAATCATCGGTCTTGCCAGCC-AGTCTGACAC-GTC----
seq0004        ----ACG-------------TAGTCATCGGTCTTGCCAGCCCAGTCTGACAG-GTC----
seq0005        ----ACG-------------TATTCAGCGGTCTTGCCAGCCCAGTCTGAAAC-TTC----
seq0006        ----ACG-------------TAATCATCGGTCTTGCCAGCCCAGTCTGAAAC-TTC----
seq0007        ----ACG-------------TATTCATCGGTCTTGCCAGCCCAGTCTGAAAC-T------
seq0008        ----ATG-------------TTGTCATCGCTCTTGCCAGCCCAGCCTGAAACGGTC----
seq0009        ----ATG-----------------------------------------------------
seq0013        ----ATG-------------TTATTATCG-TCATGCC-CCCCATCCAGCGAC-TAC----
seq0014        ----ATT-------------TTGTTATCGGTCTTGCCAGCCAGGACTG---C-GTC----
seq0015        ----ACC-------------TTGTT-TGGGTCTAGCCAGCCCAGCCCGAAAC-ATC----
seq0018        ----ACGCGCGAGACCATTTGTGTCATCGGTCTTGACCGCCCAACCTTAAAC-GTCTCTG
seq0020        GTACATGCGCGTAACCCTTTTTAGGATCGGTCATGACCACCCAT--ATAAAC-GTC----

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ------------------------------------------------------------
seq0001        ------------------------------------------------------------
seq0002        ------------------------------------------------------------
seq0003        ------------------------------------------------------------
seq0004        ------------------------------------------------------------
seq0005        ------------------------------------------------------------
seq0006        ------------------------------------------------------------
seq0007        ------------------------------------------------------------
seq0008        ------------------------------------------------------------
seq0009        ------------------------------------------------------------
seq0013        ------------------------------------------------------------
seq0014        ------------------------------------------------------------
seq0015        ------------------------------------------------------------
seq0018        TTACGGTGGGGTGATGGGTCAGGATTTGCTACCCCGTAGAGACGATGAAGCGCTAATTTC
seq0020        ------------------------------------------------------------

(position)     11111111111111111111111111111111111111111111111111
               22222222223333333333444444444455555555556666666666
               01234567890123456789012345678901234567890123456789
                                                                 
seq0000        ----------------------CGGCGC-ATTAACTAGGCCACC-TGC--
seq0001        ----------------------CGGCGC-ATTAACTAGGCCACC-TGC--
seq0002        ----------------------CGGCGC-ATTAACTAGGCCACC-TGC--
seq0003        ----------------------CGGCAC-ATTAACTAGGCCACC-TGC--
seq0004        ----------------------CGGCGC-ATTAACTAGGCCACC-TGC--
seq0005        ----------------------GGGCGC-ATTAACTAGGCCACC-TGC--
seq0006        ----------------------GAGCGC-ATTAACTAGGCCACC-TGC--
seq0007        -------------------------CGC-ATTGACTAGGCCACC-TGC--
seq0008        ----------------------GTGCGC-ATCAACGTG-GCACG-GGTCC
seq0009        -----------------------------------------------TCC
seq0013        ----------------------CGGCGC-ATGAACTAGGCCACC-GCC--
seq0014        ----------------------GTGCGC-ATGAACTAGGCCACC-GCC--
seq0015        ----------------------GGGCGC-ATGAACTAGGCCACCCGCC--
seq0018        CCAATGGCACTTGATTGTAAAGGGGCGC-ATGAACTAGGCCACC-TAC--
seq0020        ----------------------CGGCGCCATGAACTAGGCCACC-GGG--


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        A-----------------CGTAGTCATCGGTCTTGCCAGCCGAGTTTGAAACGTC-----
seq0001        A-----------------CGTAGACATCGGTCTTGCCAGCCGAGTTTGAAACGTC-----
seq0002        A-----------------CGTAGTCATCGGTCTTGCCAGCCCAGTCTGACACGTC-----
seq0003        A-----------------CGTAATCATCGGTCTTGCCAG-CCAGTCTGACACGTC-----
seq0004        A-----------------CGTAGTCATCGGTCTTGCCAGCCCAGTCTGACAGGTC-----
seq0005        A-----------------CGTATTCAGCGGTCTTGCCAGCCCAGTCTGAAACTTC-----
seq0006        A-----------------CGTAATCATCGGTCTTGCCAGCCCAGTCTGAAACTTC-----
seq0007        A-----------------CGTATTCATCGGTCTTGCCAGCCCAGTCTGAAACT-------
seq0008        A-----------------TGTTGTCATCGCTCTTGCCAGCCCAGCCTGAAACGGT-----
seq0009        A-----------------TGT---------------------------------------
seq0013        A-----------------TGTTATTATCGTCATGCCC--CCCATCCAGCGACTAC-----
seq0014        A-----------------TTTTGTTATCGGTCTTGCCAGCCAGGACTG---CGTC-----
seq0015        A-----------------CCTTGTT-TGGGTCTAGCCAGCCCAGCCCGAAACATC-----
seq0018        A----CGCGCGAGACCATTTGTGTCATCGGTCTTGACCGCCCAACCTTAAACGTCTCTGT
seq0020        GTACATGCGCGTAACCCTTTTTAGGATCGGTCATGACCACCCA--TATAAACGTC-----

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ------------------------------------------------------------
seq0001        ------------------------------------------------------------
seq0002        ------------------------------------------------------------
seq0003        ------------------------------------------------------------
seq0004        ------------------------------------------------------------
seq0005        ------------------------------------------------------------
seq0006        ------------------------------------------------------------
seq0007        ------------------------------------------------------------
seq0008        ------------------------------------------------------------
seq0009        ------------------------------------------------------------
seq0013        ------------------------------------------------------------
seq0014        ------------------------------------------------------------
seq0015        ------------------------------------------------------------
seq0018        TACGGTGGGGTGATGGGTCAGGATTTGCTACCCCGTAGAGACGATGAAGCGCTAATTTCC
seq0020        ------------------------------------------------------------

(position)     1111111111111111111111111111111111111111111111
               2222222222333333333344444444445555555555666666
               0123456789012345678901234567890123456789012345
                                                             
seq0000        ---------------------CGGCGCATTAACTAGGCCA-CCTGC
seq0001        ---------------------CGGCGCATTAACTAGGCCA-CCTGC
seq0002        ---------------------CGGCGCATTAACTAGGCCA-CCTGC
seq0003        ---------------------CGGCACATTAACTAGGCCA-CCTGC
seq0004        ---------------------CGGCGCATTAACTAGGCCA-CCTGC
seq0005        ---------------------GGGCGCATTAACTAGGCCA-CCTGC
seq0006        ---------------------GAGCGCATTAACTAGGCCA-CCTGC
seq0007        ------------------------CGCATTGACTAGGCCA-CCTGC
seq0008        --------------------CGTGCGCATCAACGTGGCACGGGTCC
seq0009        --------------------------------------------CC
seq0013        ---------------------CGGCGCATGAACTAGGCCA-CCGCC
seq0014        ---------------------GTGCGCATGAACTAGGCCA-CCGCC
seq0015        ---------------------GGGCGCATGAACTAGGCCACCCGCC
seq0018        CAATGGCACTTGATTGTAAAGGGGCGCATGAACTAGGCCA-CCTAC
seq0020        --------------------CGGCGCCATGAACTAGGCCA-CCGGG


<<<<< 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, -4) .

[ 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   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0001   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0002   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13    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
seq0003   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    1    1    0    0    0    0    0    0    0    0
seq0004   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13    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
seq0005   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0006   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0007   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0008   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13 -147    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1   -1   -1   -1   -2    -    -    0    0    0    0    0    0    0    0    0    0    0
seq0014   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -
seq0015   	   -4    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   13   13    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   	   -4    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    2    0    0    0    0



(position)	   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   97   98   99

seq0000   	    0    0   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    0    0   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    0    0   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    0    0   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    0    0   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    0    0   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    0    0   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    0    0   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    0    0    0    0    0    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    0    0   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    0   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    0    0   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    0    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0020   	    0    0   -1   -1   -1    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -2   -2   -2
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   85   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -2   -2   -2
seq0018   	   -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   -1   -1   -1   -1   -2   -2   -2
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2



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

seq0000   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -2   -2   -2
seq0001   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -2   -2   -2
seq0002   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -2   -2   -2
seq0003   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -2   -2   -2
seq0004   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -2   -2   -2
seq0005   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -2   -2   -2
seq0006   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -2   -2   -2
seq0007   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -2   -2   -2
seq0008   	   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -4   -4   -4   -4   -4
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -4   -4
seq0013   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -2   -2   -2
seq0014   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -2   -2   -2
seq0015   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0018   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -2   -2   -2
seq0020   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -   -1   -1   -2   -2   -2



<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<< Output of 'br_list_classes_shift_respos' >>

$commoner_shift_flank = 0 .


<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

... NO CHANGES were made ...


<<<<< Preliminary (4): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

SKIPPED the Calculation, because either reference or reconstructed MSA contains (a) gap(s) or (a) gapped segment(s) that is (are) too long ...


