<<<<< 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 = 96 ,
#{Sites in the segment}_rec = 83 .


<< 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)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        --------------TAGAGGCTCAGAATGG-TCGTGGCTCCG--CAATT-TATC------
seq0001        --------------TAGAGGCTCAGAATGGTTCGTGGCTCCG--CACTT-TATC------
seq0002        --------------TAGAGGCTCAGAATGG-TCGAGGCTCCG--CAATT-TATC------
seq0003        --------------TAGAGGCTCAGAATGG-TCGAGGCTCCG--CAATT-TATC------
seq0004        --------------TAGAGGCTCAGAATGG-TCGAGGCTCCG--CAATT-TATC------
seq0005        --------------TAGAGGCTCAGAATGG-ACGAGGCTCCG--CAATT-TGTC------
seq0006        --------------TAGAGGCTCAGAATGG-TCGAGGCTCCG--CAAGT-TGTC------
seq0007        --------------TAGAGGCTCAGAATGG-TCTAGGCTCCG--CAATT-TGTC------
seq0008        --------------TAGAGACTCAGAAGGG-TCGAGGCTCCGTCCAATTTGTTC------
seq0009        --------------TAGAGGGTCAGAATGG-TCGAGACTCGG--CTATT-GATC------
seq0013        --------------TAGAGGACCCGAATG----TAAGCTCCG--GTATT-GATC------
seq0014        --------------TAGAGGCCCTGTA-GG-TCAAGGCTAAG--GAATT-GATC------
seq0015        --------------TGGAGGCC-AGAATCG-TCAACGCTCCG--GGATT-CGTCGCTAAC
seq0018        --------------TAGAGGCTCAGAATGG-TCACGACCCCG--CAATT-GATC------
seq0020        AGTGTTAGCAGCCATAAAGGCTCAGCCTAA-TCAAGGCTTGG--CTATT-ACTC------

(position)     666666666677777777778888888888999999
               012345678901234567890123456789012345
                                                   
seq0000        -----------CTGATGGTGGTTTGCCCAAT-CCA-
seq0001        -----------CTTATGGTGGTTTGCCCAAT-CCA-
seq0002        -----------TTGATGGTGGTTCGACCA-T-CCA-
seq0003        -----------TTGATGGTGGTTCGACCA-T-CCA-
seq0004        -----------TTGATGGTGGTTC---CA-T-CCA-
seq0005        -----------CTGATGGTGGTTCGACCAAT-CCA-
seq0006        -----------CTGATGGTGGTTCGACAAAC-CCA-
seq0007        -----------CTGATGGTGGTTCGACCAAT-CCA-
seq0008        -----------CTAATGGTAGTTCGACCAAT-CCA-
seq0009        -----------CTAATGGGAGTTCGACCAATCCCA-
seq0013        -----------ATAATGGTTGCTCGACCAAT-CCA-
seq0014        -----------GAAAGGG-----CGACCAAT-CCA-
seq0015        CATGACCGCGTAGAATGGCAGTTCGCCCAAT-TCA-
seq0018        -----------CTAATGGCGG-TCAACCAAT-ACAA
seq0020        -----------CT-----------------------


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        TAGAGGCTCAGAAT-GG-TCGTGGCTCCG-CAA--TTTATCC-----------------T
seq0001        TAGAGGCTCAGAAT-GGTTCGTGGCTCCG-CAC--TTTATCC-----------------T
seq0002        TAGAGGCTCAGAAT-GG-TCGAGGCTCCG-CAA--TTTATCT-----------------T
seq0003        TAGAGGCTCAGAAT-GG-TCGAGGCTCCG-CAA--TTTATCT-----------------T
seq0004        TAGAGGCTCAGAAT-GG-TCGAGGCTCCG-CAA--TTTATCT-----------------T
seq0005        TAGAGGCTCAGAAT-GG-ACGAGGCTCCG-CAA--TTTGTCC-----------------T
seq0006        TAGAGGCTCAGAAT-GG-TCGAGGCTCCG-CAA--GTTGTCC-----------------T
seq0007        TAGAGGCTCAGAAT-GG-TCTAGGCTCCG-CAA--TTTGTCC-----------------T
seq0008        TAGAGACTCAGAAG-GG-TCGAGGCTCCGTCCAATTTGTTCC-----------------T
seq0009        TAGAGGGTCAGAAT-GG-TCGAGACTCGG-CTA--TTGATCC-----------------T
seq0013        TAGAGGACCCGAA--TG-TAA--GCTCCG-GTA--TTGATCA-----------------T
seq0014        TAGAGGCCCTGTA--GG-TCAAGGCTAAG-GAA--TTGATCG-----------------A
seq0015        TGGAGGCCAGAAT--CG-TCAACGCTCCG-GGA--TTCGTCGCTAACCATGACCGCGTAG
seq0018        TAGAGGCTCAGAAT-GG-TCACGACCCCG-CAA--TTGATCC-----------------T
seq0020        ---AGTGTTAGCAGCCA-TAAAGGCTCAG-CC----TAATC-------------------

(position)     66666666667777777777888
               01234567890123456789012
                                      
seq0000        GATGGTGGTTTGCCCAATCC-A-
seq0001        TATGGTGGTTTGCCCAATCC-A-
seq0002        GATGGTGGTTCGACCA-TCC-A-
seq0003        GATGGTGGTTCGACCA-TCC-A-
seq0004        GATGGTGGTTC---CA-TCC-A-
seq0005        GATGGTGGTTCGACCAATCC-A-
seq0006        GATGGTGGTTCGACAAACCC-A-
seq0007        GATGGTGGTTCGACCAATCC-A-
seq0008        AATGGTAGTTCGACCAATCC-A-
seq0009        AATGGGAGTTCGACCAATCCCA-
seq0013        AATGGTTGCTCGACCAATCC-A-
seq0014        AAGGG-----CGACCAATCC-A-
seq0015        AATGGCAGTTCGCCCAATTC-A-
seq0018        AATGGCGG-TCAACCAATAC-AA
seq0020        AAGGCTTG-GCTATTACTCC-T-


<<<<< 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, -13) .

[ 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   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0001   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0002   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0003   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0004   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0005   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0006   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0007   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0008   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0009   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0013   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -    -  -12  -12    -  -15  -15  -15    -    -  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0014   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -    -  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0015   	  -14  -14  -14  -14  -14  -14  -14  -14  -15  -15  -15  -15  -15    -    -  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13
seq0018   	  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14  -14    -  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -14  -14  -14    -    -  -12  -12  -13  -13  -13  -13  -30    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    3    3    3    3    3    3    3    3    3    3    3    3    3    3    -    4    4    4    4    4    4    4    4    4    4    4    -    5    5    -    -    -    -    9    9    9    8    8    -    -    -    -    -    -    -    -    -



(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

seq0000   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -14  -14    -  -13    -
seq0001   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -14  -14    -  -13    -
seq0002   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -13  -14  -14    -  -13    -
seq0003   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -13  -14  -14    -  -13    -
seq0004   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -    -    -  -13  -13    -  -13  -14  -14    -  -13    -
seq0005   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -14  -14    -  -13    -
seq0006   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -14  -14    -  -13    -
seq0007   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -14  -14    -  -13    -
seq0008   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -14  -14    -  -13    -
seq0009   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13    -
seq0013   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -14  -14    -  -13    -
seq0014   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -14  -14    -  -13    -
seq0015   	  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -13  -14  -14    -  -13    -
seq0018   	    -    -    -    -    -    -    -    -    -  -13  -13  -13  -13  -13  -13  -13  -13  -13    -  -13  -13  -13  -13  -13  -13  -13  -13  -13  -14  -14    -  -13  -13
seq0020   	    -    -    -    -    -    -    -    -    -    -   27   27   27   27   27   27   27   27    -   28   26   26   26   26   26   25   25   25   25    8    -    9    -




[INFORMATION] The original $commoner_shift_flank = -13. 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    -   -1   -1   -1    -    -    1    1
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    -   -1   -1   -1    -    -    1    1
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    -   -1   -1   -1    -    -    1    1
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    -   -1   -1   -1    -    -    1    1
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    -   -1   -1   -1    -    -    1    1
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    -   -1   -1   -1    -    -    1    1
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    -   -1   -1   -1    -    -    1    1
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    -   -1   -1   -1    -    -    1    1
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    0    0    0    0    0    0    0
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    -   -1   -1   -1    -    -    1    1
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    1    1    -   -2   -2   -2    -    -    0    0    0    0    0    0    -   -1   -1   -1    -    -    1    1
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    -   -1   -1   -1    -    -    1    1
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2    -    -    0    0    -    0    0    0    0    0    0    0    0    0    0    0    -   -1   -1   -1    -    -    1    1
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -   -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    -   -1   -1   -1    -    -    1    1
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   16   16   16   16   16   16   16   16   16   16   16   16   16   16    -   17   17   17   17   17   17   17   17   17   17   17    -   18   18    -    -    -    -   22



(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

seq0000   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    -
seq0001   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    -
seq0002   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0   -1   -1    -    0    -
seq0003   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    0   -1   -1    -    0    -
seq0004   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    0    0    -    0   -1   -1    -    0    -
seq0005   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    -
seq0006   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    -
seq0007   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    -
seq0008   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    -
seq0009   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -
seq0013   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1    -    0    -
seq0014   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0   -1   -1    -    0    -
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   -1   -1    -    0    -
seq0018   	    0    0    0    0  -17    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    0    0    0    0    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0   -1   -1    -    0    0
seq0020   	   22   22   21   21    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   40   40   40   40   40   40   40   40    -   41   39   39   39   39   39   38   38   38   38   21    -   22    -



<<<<< 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} = 17) >>

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

0	13	26	27	4	-1	n/a	0,1,2,3,4,5,6,7,8,9,13
1	13	25	22	6	-1	n/a	10,11
2	13	20	23	7	-1	n/a	12
3	16	44	28	16,17,18	16,17,18	0,0	14
4	21	25	23	1	-2	n/a	12
5	28	41	27	10	0	n/a	0,1,2,3,4,5,6,7,9,11,12,13
6	28	29	20	15	1	n/a	10
7	28	53	16	12	0	n/a	8
8	31	33	20	2	-2	n/a	10
9	36	41	20	13	0	n/a	10
10	43	45	27	5	-1	n/a	0,1,2,3,4,5,6,7,9,10,11,12,13
11	48	49	27	14	1	n/a	0,1,2,3,4,5,6,7,9,10,11,12,13
12	49	53	28	21,19	22,21	0	14
13	50	53	27	9	0	n/a	0,1,2,3,4,5,6,7,9,10,11,13
14	54	54	27	0	-17	n/a	0,1,2,3,4,5,6,7,8,9,10,11,13
15	73	94	28	25,26,24,23,20,22	40,41,39,38,21,22	0,0,0,0,0	14
16	91	92	27	3	-1	n/a	0,1,2,3,4,5,6,7,8,10,11,12,13



<<<<< 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} = 17) >>>>>


[[ 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	1	0	0	0	0
1	0	0	1	1	0	0
2	1	0	0	0	0	0
3	1	3	0	0	0	0
4	1	0	0	1	0	0
5
6	1	0	1	0	0	0
7	2	2	0	0	0	0
8	1	1	0	0	0	0
9	0	1	0	0	0	0
10
11
12	0	2	0	0	0	0
13	1	0	0	0	0	0
14	1	1	0	0	0	0
15	1	1	0	0	0	0
16	1	1	0	0	0	0


[ Skipped Composite-Blocks (#{cblocks} = 3): 5, 10, 11 . ]


[ 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	14	14	Complex(???)	None	24:26:26:X
1	0	13	13	Complex(???)	21:27:27:X	24:26:26:X
2	0	8	8	Complex(???)	23:22:22:X	None
3	0	27	29	Complex	28:0:13:-	27:13:15:-/27:45:48:-/28:27:27:-
4	0	5	5	Complex(???)	23:22:22:X	24:26:26:X
5	Skipped!!(NO_RELEVANT_BRANCH)
6	0	2	2	Complex(???)	20:29:32:X/21:27:27:X	None
7	0	26	26	Complex(???)	16:42:43:-/16:49:49:-	16:42:42:-/16:46:47:-
8	0	3	3	Complex(???)	20:29:32:X	20:34:35:X
9	0	6	6	Complex(???)	None	20:34:35:X
10	Skipped!!(NO_RELEVANT_BRANCH)
11	Skipped!!(NO_RELEVANT_BRANCH)
12	0	6	5	Complex(???)	None	27:45:48:-/27:54:72:-
13	0	4	4	Complex(???)	23:54:70:-	None
14	0	1	1	Shift	23:54:70:-	23:55:71:-
15	0	40	22	Complex(???)	27:73:94:-	27:54:72:-
16	0	2	2	Shift	17:91:91:-	17:93:93:-


[ Contents of %indel_ref2assoc_cblks ]

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

28:0:13	3
23:22:22	2,4
21:27:27	1,6
20:29:32	6,8
2:30:30	{Equivalent to '2:30:30'(rec)}
16:42:43	7
16:49:49	7
23:54:70	13,14
27:73:94	15
21:78:82	{Equivalent to '21:78:82'(rec)}
25:81:81	{Equivalent to '25:81:81'(rec)}
6:84:86	{Equivalent to '6:84:86'(rec)}
8:89:89	{Equivalent to '8:89:89'(rec)}
17:91:91	16
26:95:95	{Equivalent to '26:95:95'(rec)}


[ Contents of %indel_rec2assoc_cblks ]

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

27:13:15	3
24:26:26	0,1,4
28:27:27	3
2:30:30	{Equivalent to '2:30:30'(ref)}
20:34:35	8,9
16:42:42	7
27:45:48	3,12
16:46:47	7
27:54:72	12,15
23:55:71	14
21:78:82	{Equivalent to '21:78:82'(ref)}
25:81:81	{Equivalent to '25:81:81'(ref)}
6:84:86	{Equivalent to '6:84:86'(ref)}
8:89:89	{Equivalent to '8:89:89'(ref)}
17:93:93	16
26:95:95	{Equivalent to '26:95:95'(ref)}


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

[[ Interim Results ]]

[ Contents of %cb2hard_linked (#{keys} = 1) ]

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

5	=> [7],


[ Contents of %cb2hard_linking (#{keys} = 1) ]

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

7	=> [5],


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

Indx_cblk_A	indx_cblk_B

14	13


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

[ For the 1 th pair: (14, 13) ]

