<<<<< 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 = 213 ,
#{Sites in the segment}_rec = 143 .


<< 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        -AAATGCACGGTACTCAT-GTC--------AGGAACGTTTCAACTTCAACAGACGAA-CT
seq0001        -AAATGCACGGTACTCAT-GTC--------AGGAACGTTTCAACTTCCACAGACGAG-CT
seq0002        -AAATGCTCGGTACTCAT-GTC--------AGGAACGTTTCAACTTCAACAGACGTA-CT
seq0003        -ACATGCTCGGTACTCAT-GTC--------AGGAACGTTTCAACTTCAACAGACGTA-CT
seq0004        -ACATGCTCGGTACCCAT-GTC--------AGGAACGTTTCAACTTCAACAGACGTA-CT
seq0005        -AACTTCTTGGTACTCAT-ATC--------AAGAACGTTTCAATTTCAACAGACGTA-CT
seq0006        -AAATTATCGGTACTCAT-GTC--------AAGAACGTTTCAACGTCAACAGACGTA-CT
seq0007        -AAATTCTCGGTACTCAT-GTC--------AAAAACGTTTCAACTTCAACAGACGTA-CT
seq0008        -AAATGCTCGGTACTCATCATC--------AGGTACGTTTCAAATTCAACAGACGTA-CT
seq0009        -AAA-GCTCGGTACTCAG-ATC--------AGGAACGTTTCAATTTCTATAGACGTA-CT
seq0013        -AGATCCTCGGGACTCAT-TACTGATTTTGTGGAACGTTACCATGTCAACCGACTTA-AT
seq0014        GAAATCTTC---------------------------------------------------
seq0015        -GGATCCTCGGTACTCAA-AGA--------AGGACCGTTTCCAGTTCACCAAAAGTA-CG
seq0018        -CGGTCCTCGGGGCTTAT-ATC--------GGGAAAAGTTCAATTGCA------------
seq0020        -CGATCCTCGGTGCGGAT-ATC--------ATGAACATTTTAATTGCAACAGAAGTACCA

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        TATT-GTTCGCT--CCAAGCAACTTATGGCCCCGAATCTGTCA-----CGTCTTT-----
seq0001        TATT-GTTCGCT--CCAAGCAACTTATGGCCCCGAATCTGTCA-----CGTCTTT-----
seq0002        TCTT-GTTCACG--CCAAGCAACTTATGGCTCCGAAACTTTCA-----CGTCTGT-----
seq0003        TCTT-GTTCACG--CCAAGCAACTTATGGCCCCGAAACTTTCA-----CGTCTGT-----
seq0004        TCTT-GTTCACG--CCATGCAACTTATGGCCCCGAAACTTTCA-----CGTCTTT-----
seq0005        TCAT-GTTCGCG--CCAAGCAACTTTCGGCCCCGAATATGTCA-----CGTCTTT-----
seq0006        TCTT-GTTCGCG--CCAAGCAACTTTCGGCCCCGAATCTGTAC-----CGTCTTT-----
seq0007        TCTT-GTTCGCG--CCACGCAACTTTAGGCCCCGAATCTGTAA-----CGTCTCT-----
seq0008        TCTT-GTTCGTG--CCAAACAAATTTCGGCGCCGAATCCGTCA-----CATGTCT-----
seq0009        TCTT-GTTCGCGGCCGAA--AAATTTCCGCACCGAATTTGTCA-----CATATCT-----
seq0013        GCATCGTTCGCT--CC-------------------AGCTGTCA-----CAGGTTT-----
seq0014        --------------------------------------TGTC------TATGTTT-----
seq0015        GCTT-GTTCGCA--CCAAGCAAGTTTCGGCCCCAAAGCTGTCACGACTCATGCTT-----
seq0018        ----------------------------GCCCACAATCTGTAA-----CATGTTT-----
seq0020        TATT-TTTCGCG--CCAAGCAAATTTTGGGCACCAATAGGTCA-----CATGTTTTTGGG

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

(position)     111111111111111111112222222222222
               888888888899999999990000000000111
               012345678901234567890123456789012
                                                
seq0000        ---------------------AGTCAAC-----
seq0001        ---------------------AGTCAAC-----
seq0002        ---------------------AGTCAAC-----
seq0003        ---------------------AGTCAAC-----
seq0004        ---------------------AGTCAAC-----
seq0005        ---------------------AGTCATT-----
seq0006        ---------------------AGTCAAT-----
seq0007        ---------------------AGTCCAT-----
seq0008        ---------------------CGTCCAC-----
seq0009        ---------------------CGGCAAC-----
seq0013        -------------------ACAGAAAAG-----
seq0014        TGGCCCTAAAGTATCATAA-GAGATAACTCGGC
seq0015        --------------------GAGACAAC-----
seq0018        --------------------TAGACAAC-----
seq0020        --------------------CAGACTCC-----


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        AAATGCACGGTACTCAT--------GTCAGGAACGTTTCAACTTCAACAGACGAA-CTTA
seq0001        AAATGCACGGTACTCAT--------GTCAGGAACGTTTCAACTTCCACAGACGAG-CTTA
seq0002        AAATGCTCGGTACTCAT--------GTCAGGAACGTTTCAACTTCAACAGACGTA-CTTC
seq0003        ACATGCTCGGTACTCAT--------GTCAGGAACGTTTCAACTTCAACAGACGTA-CTTC
seq0004        ACATGCTCGGTACCCAT--------GTCAGGAACGTTTCAACTTCAACAGACGTA-CTTC
seq0005        AACTTCTTGGTACTCAT--------ATCAAGAACGTTTCAATTTCAACAGACGTA-CTTC
seq0006        AAATTATCGGTACTCAT--------GTCAAGAACGTTTCAACGTCAACAGACGTA-CTTC
seq0007        AAATTCTCGGTACTCAT--------GTCAAAAACGTTTCAACTTCAACAGACGTA-CTTC
seq0008        AAATGCTCGGTACTCAT-------CATCAGGTACGTTTCAAATTCAACAGACGTA-CTTC
seq0009        AAA-GCTCGGTACTCAG--------ATCAGGAACGTTTCAATTTCTATAGACGTA-CTTC
seq0013        AGATCCTCGGGACTCATTACTGATTTTGTGGAACGTTACCATGTCAACCGACTTAATGCA
seq0014        GAAATCTTCTGTCT-----------ATGTTTGTGCGCCTAATGTCAACTATAGTG-CCTC
seq0015        GGATCCTCGGTACTCAA--------AGAAGGACCGTTTCCAGTTCACCAAAAGTA-CGGC
seq0018        CGGTCCTCGGGGCTTAT--------ATCGGGAAAAGTTCAATTGCA--------------
seq0020        CGATCCTCGGTGCGGAT--------ATCATGAACATTTTAATTGCAACAGAAGTACCATA

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        TTGTTCGCTCCAAGCAACTTATGGCCCCGAATCTGTCACGTCTTTG--------------
seq0001        TTGTTCGCTCCAAGCAACTTATGGCCCCGAATCTGTCACGTCTTTG--------------
seq0002        TTGTTCACGCCAAGCAACTTATGGCTCCGAAACTTTCACGTCTGTG--------------
seq0003        TTGTTCACGCCAAGCAACTTATGGCCCCGAAACTTTCACGTCTGTG--------------
seq0004        TTGTTCACGCCATGCAACTTATGGCCCCGAAACTTTCACGTCTTTG--------------
seq0005        ATGTTCGCGCCAAGCAACTTTCGGCCCCGAATATGTCACGTCTTTG--------------
seq0006        TTGTTCGCGCCAAGCAACTTTCGGCCCCGAATCTGTACCGTCTTTG--------------
seq0007        TTGTTCGCGCCACGCAACTTTAGGCCCCGAATCTGTAACGTCTCTG--------------
seq0008        TTGTTCGTGCCAAACAAATTTCGGCGCCGAATCCGTCACATGTCTA--------------
seq0009        TTGTTCGCGGCCGAAAAATTTCCGCACCGAATTTGTCACATATCTG--------------
seq0013        TCGTTCGCTCC-------------------AGCTGTCACAGGTTTG--------------
seq0014        TAGT-------------------GGCCCTAAAGTATCATAAG------------------
seq0015        TTGTTCGCACCAAGCAAGTTTCGGCCCCAAAGCTGTCACGACTCATGCTTCGTGACGGGT
seq0018        -----------------------GCCCACAATCTGTAACATGTTTG--------------
seq0020        TTTTTCGCGCCAAGCAAATTTTGGGCACCAATAGGTCACATGTTTT----TGGGATAGTT

(position)     11111111111111111111111
               22222222223333333333444
               01234567890123456789012
                                      
seq0000        -----------TGCGCAGTCAAC
seq0001        -----------TGCGCAGTCAAC
seq0002        -----------TCCGCAGTCAAC
seq0003        -----------TGCGCAGTCAAC
seq0004        -----------TGCTCAGTCAAC
seq0005        -----------TGCGCAGTCATT
seq0006        -----------TGCGCAGTCAAT
seq0007        -----------TGCGCAGTCCAT
seq0008        -----------TGCGCCGTCCAC
seq0009        -----------TCCGCCGGCAAC
seq0013        ---------GCCGCACAGAAAAG
seq0014        -----------AGATAACTCGGC
seq0015        AGAAA-----AACCCGAGACAAC
seq0018        ----------CGCACTAGACAAC
seq0020        AGAGTAAGAGTGCGCCAGACTCC


<<<<< 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, -70) .

[ 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   -1   -1   -1    -    -    -    -    -    -    -    -    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0001   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0002   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0003   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0004   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0005   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0006   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0007   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0008   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    6    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0009   	   -1   -1   -1    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0013   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0014   	    0    0    0    0    0    0    0    0    0  -89  -89  -89  -89  -95    -    -    -    -    -    -    -    -    -    -    -  -84  -84  -84  -84  -84  -84 -105 -105 -105 -116 -118 -118 -118 -118 -118 -118 -118 -118 -118 -118 -118 -118 -118 -118 -118
seq0015   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2
seq0018   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2    -    -    -    -
seq0020   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    -    -    -    -    -    -    6    6    6   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -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   	   -2   -2   -2   -2   -2    -   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10
seq0001   	   -2   -2   -2   -2   -2    -   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10
seq0002   	   -2   -2   -2   -2   -2    -   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10
seq0003   	   -2   -2   -2   -2   -2    -   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10
seq0004   	   -2   -2   -2   -2   -2    -   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10
seq0005   	   -2   -2   -2   -2   -2    -   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10
seq0006   	   -2   -2   -2   -2   -2    -   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10
seq0007   	   -2   -2   -2   -2   -2    -   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10
seq0008   	   -2   -2   -2   -2   -2    -   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10
seq0009   	   -2   -2   -2   -2   -2    -   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10
seq0013   	   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -5   -5    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10
seq0014   	 -118 -118 -118 -118 -118    - -117 -117 -117 -117 -117 -117 -117 -117    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -98  -98  -98  -98  -98  -98  -98  -98  -98  -98  -98  -98  -98  -98  -98  -98  -98
seq0015   	   -2   -2   -2   -2   -2    -   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10
seq0020   	   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3   -3   -3   -3   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -10  -10



(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

seq0000   	  -10  -10  -10  -10  -10  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6  -17  -19  -19  -65  -65  -65  -65  -65  -65  -65
seq0001   	  -10  -10  -10  -10  -10  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6  -17  -19  -19  -65  -65  -65  -65  -65  -65  -65
seq0002   	  -10  -10  -10  -10  -10  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6  -17  -19  -19  -65  -65  -65  -65  -65  -65  -65
seq0003   	  -10  -10  -10  -10  -10  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6  -17  -19  -19  -65  -65  -65  -65  -65  -65  -65
seq0004   	  -10  -10  -10  -10  -10  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6  -17  -19  -19  -65  -65  -65  -65  -65  -65  -65
seq0005   	  -10  -10  -10  -10  -10  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6  -17  -19  -19  -65  -65  -65  -65  -65  -65  -65
seq0006   	  -10  -10  -10  -10  -10  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6  -17  -19  -19  -65  -65  -65  -65  -65  -65  -65
seq0007   	  -10  -10  -10  -10  -10  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6  -17  -19  -19  -65  -65  -65  -65  -65  -65  -65
seq0008   	  -10  -10  -10  -10  -10  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6  -17  -19  -19  -65  -65  -65  -65  -65  -65  -65
seq0009   	  -10  -10  -10  -10  -10  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -6   -6  -17  -19  -19  -65  -65  -65  -65  -65  -65  -65
seq0013   	  -10  -10  -10  -10  -10  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -8   -8  -19  -21  -21  -65  -65  -65  -65  -65  -65  -65  -65  -65
seq0014   	  -98  -99    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -70  -70  -70  -70  -70  -70  -70  -70  -70  -70  -70  -70
seq0015   	   -5   -5   -5   -5   -5   -5   -5   -5   -5   -5  -25  -25  -25  -25  -25  -25  -25  -25  -25  -25  -25  -25  -25  -25  -25    -    -    -    -    -  -20  -20  -20  -20  -20  -65  -65  -65  -65  -65  -65  -65  -65
seq0018   	  -10  -10  -10  -10  -10  -31    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -7   -7  -18  -20  -20  -65  -65  -65  -65  -65  -65  -65  -65
seq0020   	  -10  -10  -10  -10  -10  -10    -    -    -    -   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -6   -7   -7   -7  -18  -20  -20  -65  -65  -65  -65  -65  -65  -65  -65




[INFORMATION] The original $commoner_shift_flank = -70. 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -    -   76   76   76   68   68
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -    -   76   76   76   68   68
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -    -   76   76   76   68   68
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -    -   76   76   76   68   68
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -    -   76   76   76   68   68
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -    -   76   76   76   68   68
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -    -   76   76   76   68   68
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -    -   76   76   76   68   68
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -   76   76   76   76   68   68
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69    -   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -    -   76   76   76   68   68
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   68   68   68   68   68   68   68   68   68   68   68   68   68
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   70   70   70   70   70   70   70   70   70  -19  -19  -19  -19  -25    -    -    -    -    -    -    -    -    -    -    -  -14  -14  -14  -14  -14
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -    -   76   76   76   68   68
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -    -   76   76   76   68   68
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69   69    -    -    -    -    -    -    -    -   76   76   76   68   68



(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   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68    -   68   68   68   68   68   68   67   67   67   67   67   67   67   65   65   65   65   65   65   65   65   65   65   65
seq0001   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68    -   68   68   68   68   68   68   67   67   67   67   67   67   67   65   65   65   65   65   65   65   65   65   65   65
seq0002   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68    -   68   68   68   68   68   68   67   67   67   67   67   67   67   65   65   65   65   65   65   65   65   65   65   65
seq0003   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68    -   68   68   68   68   68   68   67   67   67   67   67   67   67   65   65   65   65   65   65   65   65   65   65   65
seq0004   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68    -   68   68   68   68   68   68   67   67   67   67   67   67   67   65   65   65   65   65   65   65   65   65   65   65
seq0005   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68    -   68   68   68   68   68   68   67   67   67   67   67   67   67   65   65   65   65   65   65   65   65   65   65   65
seq0006   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68    -   68   68   68   68   68   68   67   67   67   67   67   67   67   65   65   65   65   65   65   65   65   65   65   65
seq0007   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68    -   68   68   68   68   68   68   67   67   67   67   67   67   67   65   65   65   65   65   65   65   65   65   65   65
seq0008   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68    -   68   68   68   68   68   68   67   67   67   67   67   67   67   65   65   65   65   65   65   65   65   65   65   65
seq0009   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68    -   68   68   68   68   68   68   67   67   67   67   67   67   67   67   67   67   67   67   67   65   65   65   65   65
seq0013   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   67   67   67   67   67   67   67   67   67   67   67   67   67   67   65   65    -    -    -    -    -    -    -    -    -
seq0014   	  -14  -35  -35  -35  -46  -48  -48  -48  -48  -48  -48  -48  -48  -48  -48  -48  -48  -48  -48  -48  -48  -48  -48  -48  -48    -  -47  -47  -47  -47  -47  -47  -47  -47    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68    -   68   68   68   68   68   68   67   67   67   67   67   67   67   65   65   65   65   65   65   65   65   65   65   65
seq0018   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   68   67   67   67   67   67   67   67   65   65   65   65   65   65   65   65   65   65   65



(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  192  193  194  195  196  197  198  199

seq0000   	   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   62
seq0014   	    -    -    -  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -29    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   45   45   45   45   45   45   45   45   45   45   45   45   45   45   45    -    -    -    -    -
seq0018   	    -    -    -   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   39    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   65   60   60   60   60   60   60   60   60    -    -    -    -   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   63



(position)	  200  201  202  203  204  205  206  207  208  209  210  211  212

seq0000   	    -   64   64   53   51   51    5    5    5    5    5    5    5
seq0001   	    -   64   64   53   51   51    5    5    5    5    5    5    5
seq0002   	    -   64   64   53   51   51    5    5    5    5    5    5    5
seq0003   	    -   64   64   53   51   51    5    5    5    5    5    5    5
seq0004   	    -   64   64   53   51   51    5    5    5    5    5    5    5
seq0005   	    -   64   64   53   51   51    5    5    5    5    5    5    5
seq0006   	    -   64   64   53   51   51    5    5    5    5    5    5    5
seq0007   	    -   64   64   53   51   51    5    5    5    5    5    5    5
seq0008   	    -   64   64   53   51   51    5    5    5    5    5    5    5
seq0009   	    -   64   64   53   51   51    5    5    5    5    5    5    5
seq0013   	   62   51   49   49    5    5    5    5    5    5    5    5    5
seq0014   	    -    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	   50   50   50   50   50    5    5    5    5    5    5    5    5
seq0018   	   63   63   52   50   50    5    5    5    5    5    5    5    5
seq0020   	   63   63   52   50   50    5    5    5    5    5    5    5    5



<<<<< 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} = 29) >>

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

0	70	86	29	38	69	n/a	0,1,2,3,4,5,6,7,8,9,10,12,13,14
1	70	78	21	39	70	n/a	11
2	79	82	21	7	-19	n/a	11
3	83	83	21	6	-25	n/a	11
4	87	138	20	37,34	68,67	0	10
5	94	97	16	41	76	n/a	8
6	95	97	29	40	76	n/a	0,1,2,3,4,5,6,7,9,12,13,14
7	95	100	21	8	-14	n/a	11
8	98	131	29	35	68	n/a	0,1,2,3,4,5,6,7,8,9,12,14
9	98	115	26	36	68	n/a	13
10	101	124	21	3,2,0	-35,-46,-48	0,0	11
11	126	133	21	1	-47	n/a	11
12	132	138	29	32	67	n/a	0,1,2,3,4,5,6,7,8,12,14
13	132	144	17	33	67	n/a	9
14	139	167	29	28	65	n/a	0,1,2,3,4,5,6,7,8,10,14
15	139	194	23	30,13	65,45	0	12
16	145	167	17	31	65	n/a	9
17	153	171	21	5,4	-28,-29	0	11
18	153	167	26	29	65	n/a	13
19	168	174	27	21	60	n/a	0,1,2,3,4,5,6,7,8,9,10,13
20	168	201	28	22,26,24	60,64,63	0,0	14
21	175	175	27	12	39	n/a	0,1,2,3,4,5,6,7,8,9,10,13
22	199	212	20	23,18,14,11	62,51,49,5	0,0,0	10
23	200	204	23	16	50	n/a	12
24	200	201	26	25	63	n/a	13
25	201	205	19	27,20,17	64,53,51	0,0	0,1,2,3,4,5,6,7,8,9
26	202	204	29	19,15	52,50	0	13,14
27	205	212	29	9	5	n/a	12,13,14
28	206	212	19	10	5	n/a	0,1,2,3,4,5,6,7,8,9



<<<<< 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} = 29) >>>>>


[[ Results of the Main Process (1st Round) ]]

[ Contents of @cblk_wise_cts_invlvd_indels ]

Indx_cmp_blk	#{rlv_indels}_ref	#{rlv_indels}_rec	#{rltd_indels}_ref	#{rltd_indels}_rec	#{other_involved}_ref	#{other_involved}_rec

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


[ Skipped Composite-Blocks (#{cblocks} = 4): 12, 14, 19, 21 . ]


[ 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	17	17	Complex	21:0:0:-/21:9:97:X	21:84:94:X/20:87:93:-
1	0	9	9	Complex(???)	21:9:97:X/21:0:0:-	None
2	0	4	4	Complex(???)	21:9:97:X/21:102:102:X	None
3	0	1	1	Complex(???)	21:102:102:X	21:84:94:X
4	0	53	52	Complex(???)	20:22:29:-/20:64:64:-	20:87:93:-
5	0	4	4	Incomplete-Collapse-of-Independent-Insertions(+overshoot(??))(+3)(?)	20:22:29:-/16:18:18:-	25:94:94:-/23:94:94:X/15:94:94:X/17:94:94:X
6	0	3	3	Complex	20:22:29:-	23:94:94:X/21:84:94:X
7	0	6	6	Complex(???)	None	21:84:94:X
8	0	34	34	Complex	20:22:29:-/20:64:64:-	None
9	0	18	18	Complex(???)	26:48:87:X	26:116:152:X
10	0	37	24	Complex(???)	21:155:198:-	21:125:125:X
11	0	8	8	Complex(???)	None	21:125:125:X/21:134:140:X
12	Skipped!!(MULTIPLE_RELEVANT_BRANCHES(#{branches}=2))
13	0	13	13	Purge(?)	17:78:79:X/17:72:73:-	None
14	Skipped!!(NO_RELEVANT_BRANCH)
15	0	76	56	Complex	23:139:149:-/23:103:107:-/23:135:135:-	23:199:199:X/23:176:179:-/22:180:194:X
16	0	23	23	Complex(???)	17:78:79:X	None
17	0	20	19	Complex	21:155:198:-	21:172:200:X/22:141:152:X/20:153:159:X
18	0	15	15	Complex(???)	26:48:87:X	26:116:152:X
19	Skipped!!(NO_RELEVANT_BRANCH)
20	0	31	34	Complex(???)	28:115:134:-	28:195:198:-
21	Skipped!!(NO_RELEVANT_BRANCH)
22	0	71	14	Complex(???)	20:199:199:-/21:208:212:-	22:180:194:X
23	0	5	5	Complex(???)	23:139:149:-/23:151:152:-	23:199:199:X
24	0	2	2	Complex(???)	None	26:180:199:X
25	0	18	5	Complex(???)	19:200:200:X	19:180:200:X
26	0	5	3	NO_ASSOCIATED_EVENT(???)	19:200:200:X	None
27	0	8	8	Complex	20:199:199:-/21:208:212:-	None
28	0	7	7	Complex(???)	19:200:200:X	None


[ Contents of %indel_ref2assoc_cblks ]

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

21:0:0	0,1
17:4:4	{Equivalent to '17:73:73'(rec)}
21:9:97	0,1,2
16:18:18	5
20:22:29	4,5,6,8
26:48:87	9,18
28:57:57	None
20:64:64	4,8
17:72:73	13
22:76:94	None
17:78:79	13,16
21:102:102	2,3
23:103:107	15
28:115:134	20
23:135:135	15
23:139:149	15,23
23:151:152	23
21:155:198	10,17
20:199:199	22,27
19:200:200	25,26,28
21:208:212	22,27


[ Contents of %indel_rec2assoc_cblks ]

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

17:73:73	{Equivalent to '17:4:4'(ref)}
21:84:94	0,3,6,7
20:87:93	0,4
25:94:94	5
23:94:94	5,6
17:94:94	5
15:94:94	5
26:116:152	9,18
23:125:125	None
21:125:125	10,11
19:125:125	None
21:134:140	11
22:141:152	17
20:153:159	17
21:172:200	17
23:176:179	15
26:180:199	24
22:180:194	15,22
19:180:200	25
28:195:198	20
23:199:199	15,23


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

[[ Interim Results ]]

[ Contents of %cb2hard_linked (#{keys} = 4) ]

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

12	=> [4,13],
14	=> [15],
19	=> [20],
27	=> [22],


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

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

4	=> [12],
13	=> [12],
15	=> [14],
20	=> [19],
22	=> [27],


[ 'Soft-linked' pairs of composite-blocks (#{pairs} = 3) ]

Indx_cblk_A	indx_cblk_B

9	18
13	16
25	28


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

[ For the 1 th pair: (9, 18) ]

[ For the 2 th pair: (13, 16) ]

[ For the 3 th pair: (25, 28) ]

