<<<<< 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 = 134 ,
#{Sites in the segment}_rec = 108 .


<< 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        ---GACCC--GCGATTTACATCGTGGATGC-----TG------------------TCCCT
seq0001        ---GACCC--GCGATTTACATCGTGGATGC-----TG------------------TCCCT
seq0002        ---GACCC--GCGCTTTACGTCGTGGATGC-----TG------------------TCCCT
seq0003        ---GACCC--GCGCTTTACGTCGTGGATGC-----TG------------------TCCCT
seq0004        ---GACCC--GCGCTTTACGTCGTGGATGC-----TG------------------TCCCT
seq0005        ---GACCC--GCGATTTACATCGTGGATGC-----TG------------------TCCCT
seq0006        ---GACCC--GCGATTTACATCGTGGATGC-----TG------------------TCCCT
seq0007        ---GACCC--GCGATTTACATCGTGGATGC-----TG------------------TCCGT
seq0008        ---GACCCGGGCGATTTACATAGTGGATGA-----TT------------------TCACT
seq0009        ---GTTCCGGGCGATTTGCATCGTGGATGC-----TT------------------TCCCC
seq0013        ACTGACCCCGGGGCGTTACATAGGCGGTGCGTGCGAT------------------TCGCT
seq0014        ---GACCCGTGTGAATTAC-TCGAGGATGC-----TA------------------TCCTT
seq0015        ---GACCGGGGGGATTTACATCGTGGATGC-----TGATGGATAAACCATGTACTTCGCT
seq0018        ---GTCCCGGACAATTTACATCGTGGAAGC-----TG------------------TCCCT
seq0020        ---GGCACGGACGCATTACGTCGTGGATGT-----GG------------------TCCCT

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GCATTGTCATTTTTC---------------------------------------------
seq0001        GCATTGTCATTTTTC---------------------------------------------
seq0002        GCAATGTCATTTTTC---------------------------------------------
seq0003        GCATTGTCATTTTTC---------------------------------------------
seq0004        GCATTGTCATTTTTC---------------------------------------------
seq0005        GCATTGTCATTTTTC---------------------------------------------
seq0006        GCATTGTCATTTTTC---------------------------------------------
seq0007        GCATTGTCATTTTTC---------------------------------------------
seq0008        GCATTGTCTTTTTTC---------------------------------------------
seq0009        GCATTGTCTTTTTTC---------------------------------------------
seq0013        ACCCTGTCGTTTTTA---------------------------------------------
seq0014        ATATTGTCATTTTTTAAGGCTAAGTTTTCTATGCTATTCCAATCTAAAGCTTCCCAAACA
seq0015        GCATTGTTATTTATC---------------------------------------------
seq0018        GGAAAGTCATTTTTC---------------------------------------------
seq0020        GCC-AATAATTTTTC---------------------------------------------

(position)     11111111111111
               22222222223333
               01234567890123
                             
seq0000        -----------CCG
seq0001        -----------CCG
seq0002        -----------CCG
seq0003        -----------CCG
seq0004        -----------CCG
seq0005        -----------CCG
seq0006        -----------CCG
seq0007        -----------CCG
seq0008        -----------CGG
seq0009        -----------CCG
seq0013        -----------CGA
seq0014        TCCCTGATAAGAGG
seq0015        -----------CGG
seq0018        -----------TGG
seq0020        -----------C-G


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GACCCG--CGATTTACATCGTGGATG------CT--------------------------
seq0001        GACCCG--CGATTTACATCGTGGATG------CT--------------------------
seq0002        GACCCG--CGCTTTACGTCGTGGATG------CT--------------------------
seq0003        GACCCG--CGCTTTACGTCGTGGATG------CT--------------------------
seq0004        GACCCG--CGCTTTACGTCGTGGATG------CT--------------------------
seq0005        GACCCG--CGATTTACATCGTGGATG------CT--------------------------
seq0006        GACCCG--CGATTTACATCGTGGATG------CT--------------------------
seq0007        GACCCG--CGATTTACATCGTGGATG------CT--------------------------
seq0008        GACCCGGGCGATTTACATAGTGGATG------AT--------------------------
seq0009        GTTCCGGGCGATTTGCATCGTGGATG------CT--------------------------
seq0013        ----------ACTGAC-CCCGGGGCG------TTACATAGGCGGT-------GCG-----
seq0014        GACCCGTGTGAATTAC-TCGAGGATGCTATCCTTATATTGTCATTTTTTAAGGCTAAGTT
seq0015        GACCGGGGGGATTTACATCGTGGATG------CT-GATGGATAAA-------CCA-----
seq0018        GTCCCGGACAATTTACATCGTGGAAG------CT--------------------------
seq0020        GGCACGGACGCATTACGTCGTGGATG------TG--------------------------

(position)     000000000000000000000000000000000000000011111111
               666666666677777777778888888888999999999900000000
               012345678901234567890123456789012345678901234567
                                                               
seq0000        ----------GTC---------CCTGCATTG---TCATTTTTCCCG--
seq0001        ----------GTC---------CCTGCATTG---TCATTTTTCCCG--
seq0002        ----------GTC---------CCTGCAATG---TCATTTTTCCCG--
seq0003        ----------GTC---------CCTGCATTG---TCATTTTTCCCG--
seq0004        ----------GTC---------CCTGCATTG---TCATTTTTCCCG--
seq0005        ----------GTC---------CCTGCATTG---TCATTTTTCCCG--
seq0006        ----------GTC---------CCTGCATTG---TCATTTTTCCCG--
seq0007        ----------GTC---------CGTGCATTG---TCATTTTTCCCG--
seq0008        ----------TTC---------ACTGCATTG---TCTTTTTTCCGG--
seq0009        ----------TTC---------CCCGCATTG---TCTTTTTTCCCG--
seq0013        -----TGCGATTC---------GCTACCCTG---TCGTTTTTACGA--
seq0014        TTCTATGCTATTCCAATCTAAAGCTTCCCAAACATCCCTGATAAGAGG
seq0015        -----TGTACTTC---------GCTGCATTG---TTATTTATCCGG--
seq0018        ----------GTC---------CCTGGAAAG---TCATTTTTCTGG--
seq0020        ----------GTC---------CCTGCCAA----TAATTTTTCC-G--


<<<<< 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, -26) .

[ 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   	   -3   -3   -3   -3   -3   -5    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	   -3   -3   -3   -3   -3   -5    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	   -3   -3   -3   -3   -3   -5    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	   -3   -3   -3   -3   -3   -5    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	   -3   -3   -3   -3   -3   -5    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	   -3   -3   -3   -3   -3   -5    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	   -3   -3   -3   -3   -3   -5    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	   -3   -3   -3   -3   -3   -5    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -   10   10   10   10   10   10    -   11   11   11   11   11   11   11   11   11    -    -    -    -    -    -   17   17   17   17   17   17   17   17   17   17   17   17   17    -    -    -    -    -
seq0014   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -8   -8  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26
seq0015   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -
seq0018   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    3   -2    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0013   	    -    -   24   24   24    -    -    -    -    -    -    -    -    -    -   34   34   34   34   34   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0014   	  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26  -26
seq0015   	    -    -    6    6    6    -    -    -    -    -    -    -    -    -    -   16   16   16   16   16   16   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   25   25   25    -    -    -   28   28   28   28   28   28
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   34   16   16    -    -    -    -    -    -    -    -    -   25   25   25   25   25   25   24   24    -    -    -    -   28   28   28   28   28   28



(position)	  100  101  102  103  104  105  106  107

seq0000   	   28   28   28  -28  -28  -28    -    -
seq0001   	   28   28   28  -28  -28  -28    -    -
seq0002   	   28   28   28  -28  -28  -28    -    -
seq0003   	   28   28   28  -28  -28  -28    -    -
seq0004   	   28   28   28  -28  -28  -28    -    -
seq0005   	   28   28   28  -28  -28  -28    -    -
seq0006   	   28   28   28  -28  -28  -28    -    -
seq0007   	   28   28   28  -28  -28  -28    -    -
seq0008   	   28   28   28  -28  -28  -28    -    -
seq0009   	   28   28   28  -28  -28  -28    -    -
seq0013   	   28   28   28  -28  -28  -28    -    -
seq0014   	  -26  -26  -26  -26  -26  -26  -26  -26
seq0015   	   28   28   28  -28  -28  -28    -    -
seq0018   	   28   28   28  -28  -28  -28    -    -
seq0020   	   28   28   28  -28    -  -28    -    -




[INFORMATION] The original $commoner_shift_flank = -26. 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   21    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   21    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   21    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   21    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   21    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   21    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   21    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   21    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   36   36   36   36   36   36    -   37   37   37   37   37   37   37
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23    -   23   23   23   23   23   23   23
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23   23



(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   	   23   23    -    -    -    -    -    -   29   24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   60   42   42    -
seq0001   	   23   23    -    -    -    -    -    -   29   24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   60   42   42    -
seq0002   	   23   23    -    -    -    -    -    -   29   24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   60   42   42    -
seq0003   	   23   23    -    -    -    -    -    -   29   24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   60   42   42    -
seq0004   	   23   23    -    -    -    -    -    -   29   24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   60   42   42    -
seq0005   	   23   23    -    -    -    -    -    -   29   24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   60   42   42    -
seq0006   	   23   23    -    -    -    -    -    -   29   24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   60   42   42    -
seq0007   	   23   23    -    -    -    -    -    -   29   24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   60   42   42    -
seq0008   	   23   23    -    -    -    -    -    -   29   24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   60   42   42    -
seq0009   	   23   23    -    -    -    -    -    -   29   24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   60   42   42    -
seq0013   	   37   37    -    -    -    -    -    -   43   43   43   43   43   43   43   43   43   43   43   43   43    -    -    -    -    -    -    -   50   50   50    -    -    -    -    -    -    -    -    -    -   60   60   60   60   60   60   42   42    -
seq0014   	   23   23   23   18   18    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
seq0015   	   23   23    -    -    -    -    -    -   29   24    -   25   25   25   25   25   25   25   25   25   25    -    -    -    -    -    -    -   32   32   32    -    -    -    -    -    -    -    -    -    -   42   42   42   42   42   42   42   42    -
seq0018   	   23   23    -    -    -    -    -    -   29   24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   60   42   42    -
seq0020   	   23   23    -    -    -    -    -    -   29   24    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   60   42   42    -



(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

seq0000   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0001   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0002   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0003   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0004   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0005   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0006   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0007   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0008   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0009   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0013   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0014   	    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
seq0015   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0018   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   51   51   51    -    -    -   54   54   54   54   54   54   54   54   54   -2   -2   -2    -    -
seq0020   	    -    -    -    -    -    -    -    -   51   51   51   51   51   51   50   50    -    -    -    -   54   54   54   54   54   54   54   54   54   -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). >>>>>

<<<<< 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} = 12) >>

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

0	26	59	29	3,7,5	23,29,24	0,0	0,1,2,3,4,5,6,7,8,9,12,13,14
1	26	54	21	4,1	23,18	0	11
2	31	31	15	2	21	n/a	0,1,2,3,4,5,6,7
3	36	96	20	9,10,13,15,20	36,37,43,50,60	0,0,0,0	10
4	61	98	23	6,8,12	25,32,42	0,0	12
5	96	96	29	19	60	n/a	0,1,2,3,4,5,6,7,8,9,13,14
6	97	98	29	11	42	n/a	0,1,2,3,4,5,6,7,8,9,10,13,14
7	108	116	27	16	51	n/a	0,1,2,3,4,5,6,7,8,9,10,12,13
8	108	113	28	17	51	n/a	14
9	114	115	28	14	50	n/a	14
10	120	128	29	18	54	n/a	0,1,2,3,4,5,6,7,8,9,10,12,13,14
11	129	131	29	0	-2	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} = 12) >>>>>


[[ 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	0	2	1	1	0	0
1	1	1	1	1	0	0
2	1	1	0	0	0	0
3	2	1	0	0	0	0
4	1	0	0	2	0	0
5	0	1	1	0	0	0
6	0	1	0	0	0	0
7	0	2	0	0	0	0
8	1	0	0	0	0	0
9	1	1	0	0	0	0
10	1	1	0	0	0	0
11	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 0):  . ]


[ 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	33	34	Complex	20:0:2:-	22:60:60:-/22:42:42:X/20:26:35:X
1	0	34	29	Complex(???)	21:19:19:X/20:0:2:-	21:52:57:-/20:26:35:X
2	0	1	1	Shift	15:8:9:X	15:32:33:X
3	0	37	61	Complex(???)	20:0:2:-/20:30:34:-	20:26:35:X
4	0	21	38	Complex	23:37:54:-	22:60:60:-/24:61:95:-
5	0	1	1	Complex(???)	23:37:54:-	24:61:95:-
6	0	2	2	Complex(???)	None	21:99:107:-
7	0	9	9	Complex(???)	None	21:99:107:-/21:117:119:-
8	0	6	6	Complex(???)	27:63:63:-	None
9	0	2	2	Shift	27:63:63:-	27:116:116:-
10	0	9	9	Complex(???)	21:75:130:-	21:117:119:-
11	0	3	3	Complex(???)	21:75:130:-	21:132:133:-


[ Contents of %indel_ref2assoc_cblks ]

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

20:0:2	0,1,3
15:8:9	2
21:19:19	1
20:30:34	3
23:37:54	4,5
27:63:63	8,9
21:75:130	10,11
27:132:132	None


[ Contents of %indel_rec2assoc_cblks ]

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

20:26:35	0,1,3
15:32:33	2
22:42:42	0
21:52:57	1
22:60:60	0,4
24:61:95	4,5
21:71:77	None
21:81:90	None
21:99:107	6,7
27:116:116	9
21:117:119	7,10
27:130:130	None
21:132:133	11


<<<< (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} = 0) ]

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



[ Contents of %cb2hard_linking (#{keys} = 0) ]

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



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

Indx_cblk_A	indx_cblk_B

9	8


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

[ For the 1 th pair: (9, 8) ]

