<<<<< 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 = 278 ,
#{Sites in the segment}_rec = 173 .


<< 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        ----------CAA---CC---ATGTGC---TTAGACCGA--CTCAGACGGGTAGGAGGGG
seq0001        ----------CAA---CC---ATGTGC---TTAGACCGA--CTCAGACGGGTAGGAGGGG
seq0002        ----------CAA---CC---ATGTGC---TTTGACCGA--CTCAGACGGCTAGGAGGGG
seq0003        ----------CAA---CC---ATGTGC---TTTGACCGA--CTCAGACGGCTAGGGGGGG
seq0004        ----------CAA---CC---ATGTGC---TTTGACCGA--CTCAGACGGCTAGGAGGGG
seq0005        ----------CAA---CG---ATGTGC---TTTGACCGA--CTCAGAAGGGTAGGAGGGG
seq0006        ----------CAA---CC---ATGTGC---TTTGACCGAACCTCAGACGGGTAGGAGGTG
seq0007        ----------CAA---CC---ATGTGC---GTTGACCGA--CTCAGACGGGTAGGAGGGG
seq0008        ----------CAA---CC---GTGTGC---TAT---------------------------
seq0009        ----------CAAGGACC---TGGCGC---TTC---------------------------
seq0013        ----------TAA---AC---GTGCGCCTATTT---------------------------
seq0014        ----------TAA---CC---GTTGGC---TTT---------------------------
seq0015        ----------TAA---CC----TGGGC---CTT---------------------------
seq0018        ----------CAA---CC---GAGTG----AGT---------------------------
seq0020        CACACTTAGTCAA---CGTCGGTGTGC---ATT---------------------------

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        GTCGGG------------------------------------ATACTTCGGGCTCCTTG-
seq0001        GTCGGG------------------------------------ATACTTCGGGCTCCTTG-
seq0002        GTCGGG------------------------------------ATTCTTCGGGCTCCTGG-
seq0003        GTCGGG------------------------------------ATTCTTCGGGCTCCTTG-
seq0004        GTCGGG------------------------------------ATTCTTCGGGCTCCTTG-
seq0005        GTCGGG------------------------------------ATCCTGCGGGCTTCCAG-
seq0006        GTCGGG------------------------------------ATCCTTCGGGCTCCCAG-
seq0007        GTCGGG------------------------------------GTCCTTCGGGCCCCCAG-
seq0008        -TCGGGAAGGCGCCCCCCGGACGCTGACCATGACCCCGGTAAATTC---GGGCTCCTTG-
seq0009        ---GGA------------------------------------ATTC---GGCCTCCTTG-
seq0013        -TCCTG------------------------------------AGCC---GGGCTACGTG-
seq0014        -TCCAG------------------------------------ATCC---GGGATCCTTG-
seq0015        -TCCGC------------------------------------ATCA---GGGAT-CTTGC
seq0018        -TCGGG------------------------------------ATC----GGGCTCCATG-
seq0020        -TCG--------------------------------------ATCC---GGGCTCCTTG-

(position)     111111111111111111111111111111111111111111111111111111111111
               222222222233333333334444444444555555555566666666667777777777
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ------------------------------------------------------------
seq0001        ------------------------------------------------------------
seq0002        ------------------------------------------------------------
seq0003        ------------------------------------------------------------
seq0004        ------------------------------------------------------------
seq0005        ------------------------------------------------------------
seq0006        ------------------------------------------------------------
seq0007        ------------------------------------------------------------
seq0008        ------------------------------------------------------------
seq0009        ------------------------------------------------------------
seq0013        ------------------------------------------------------------
seq0014        ------------------------------------------------------------
seq0015        GGCACTACGTGTGTCAATATCGTCCCAAGTGCCCGTCGAGTCCGCGGATTACTTCAGTGG
seq0018        ------------------------------------------------------------
seq0020        ------------------------------------------------------------

(position)     111111111111111111112222222222222222222222222222222222222222
               888888888899999999990000000000111111111122222222223333333333
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        ------GCTT-GAGCTA----CGTCCGCACTG---------------------------T
seq0001        ------GCTT-GAGCTA----CGTCCGCACTG---------------------------T
seq0002        ------GCTT-GAGCCA----CGTCCGCACTG----------------------------
seq0003        ------GCTT-GAGCCA----CGTCCGCACTG----------------------------
seq0004        ------GCTT-GAGCCA----CGTCCGCACTG----------------------------
seq0005        ------GCGTCGAGCTA----CGTCCGCACTC----------------------------
seq0006        ------GCTTCGAGCTA----CGTCCGCACTC----------------------------
seq0007        ------GCTTCGAGCTA----CGTCCGCACTC----------------------------
seq0008        ------GCTTCGAG-TA----CGTCCGTACTG----------------------------
seq0009        ------GCCTCGAG-CCGGGCCGCCCGGACTG----------------------------
seq0013        ------GA--------------GTCCTCCCGG----------------------------
seq0014        ------GTTTCAAG-TA----CGTCCGCCCTGACGAGAAGCCCTCGAACATTCACGACA-
seq0015        CAACTC------------------------------------------------------
seq0018        ------GATGCGAG-CA----CGTCCGCCATG----------------------------
seq0020        ------GCTTGGAG-TA----CATCCGCCAGC----------------------------

(position)     22222222222222222222222222222222222222
               44444444445555555555666666666677777777
               01234567890123456789012345678901234567
                                                     
seq0000        G--C-GC-CCGTTTCTTATTACT--CTGGATACAT---
seq0001        G--C-GC-CCGTTTCTTTTTACT--CTGGATACAT---
seq0002        C--C-GCACTGTTTCTTATTTCT--CT-GATTAAGTCT
seq0003        G--C-GCACCGTTTCTTATTTCT--CTGGATTAAGTCT
seq0004        G--C-GCACCGTTTCTTATTTCT--CTGGATTAAGTCT
seq0005        GTTC-GC-ACGTTTCTTATTTCT--CTGGATTAAT---
seq0006        GTTC-GC-ACGTTTATTATTTCT--TTGGATTAAT---
seq0007        GTTC-GC-ACGTTTCTTATTTCT--CTGGATTAAT---
seq0008        GGTC-CC-GCGATTCTTCTTGCT--CTCGGGTAAT---
seq0009        GGTC-CC-GCGGTAATTCTTGGT--CTCGAGTATT---
seq0013        TGTC-CC-GCGTTCCTC----CA--CGAGAGTACT---
seq0014        GGTC-TC-GCTTTCCTTCTTGCA--CTCAAGTAAT---
seq0015        --------------------------------------
seq0018        GGTC-GC-GCTCGCTTTATACCA--CTCGAGTGAT---
seq0020        TGTCGCT-CCGTTCCTTATTGCTAGATCGAGTAAT---


<< Original Segment of the Reconstructed Alignment: >>

(position)     000000000000000000000000000000000000000000000000000000000000
               000000000011111111112222222222333333333344444444445555555555
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        CAACC-------------ATGTGC---TTAGACCGA----------CTCAGACGGGTAGG
seq0001        CAACC-------------ATGTGC---TTAGACCGA----------CTCAGACGGGTAGG
seq0002        CAACC-------------ATGTGC---TTTGACCGA----------CTCAGACGGCTAGG
seq0003        CAACC-------------ATGTGC---TTTGACCGA----------CTCAGACGGCTAGG
seq0004        CAACC-------------ATGTGC---TTTGACCGA----------CTCAGACGGCTAGG
seq0005        CAACG-------------ATGTGC---TTTGACCGA----------CTCAGAAGGGTAGG
seq0006        CAACC-------------ATGTGC---TTTGACCGA--------ACCTCAGACGGGTAGG
seq0007        CAACC-------------ATGTGC---GTTGACCGA----------CTCAGACGGGTAGG
seq0008        CAACC-------------GTGTGC---TATTCGGGAAGGCGCCC--CCCGGACGCTGACC
seq0009        CAAGG-------------ACCTGG---CGCTTCGGA------------------------
seq0013        TAAAC-------------GTGCGCCTATTTTCCTGA------------------------
seq0014        TAACC-------------GTTGGC---TTTTCCAGA------------------------
seq0015        TAACC--------------TGGGC---CTTTCCGCA------------------------
seq0018        CAACC-------------GAGTGA---GTT------------------------------
seq0020        CACACTTAGTCAACGTCGGTGTGC---ATT------------------------------

(position)     000000000000000000000000000000000000000011111111111111111111
               666666666677777777778888888888999999999900000000001111111111
               012345678901234567890123456789012345678901234567890123456789
                                                                           
seq0000        AGGGGGTCGGGATACTTCG---------GG--CTCCTTGGCT-----T-GA----GCTAC
seq0001        AGGGGGTCGGGATACTTCG---------GG--CTCCTTGGCT-----T-GA----GCTAC
seq0002        AGGGGGTCGGGATTCTTCG---------GG--CTCCTGGGCT-----T-GA----GCCAC
seq0003        GGGGGGTCGGGATTCTTCG---------GG--CTCCTTGGCT-----T-GA----GCCAC
seq0004        AGGGGGTCGGGATTCTTCG---------GG--CTCCTTGGCT-----T-GA----GCCAC
seq0005        AGGGGGTCGGGATCCTGCG---------GG--CTTCCAGGCG-----TCGA----GCTAC
seq0006        AGGTGGTCGGGATCCTTCG---------GG--CTCCCAGGCT-----TCGA----GCTAC
seq0007        AGGGGGTCGGGGTCCTTCG---------GG--CCCCCAGGCT-----TCGA----GCTAC
seq0008        ATGACCCCGGTAAA-TTCG---------GG--CTCCTTGGCT-----TCGA----G-TAC
seq0009        -------------A-TTCG---------GC--CTCCTTGGCC-----TCGAGCCGG-GCC
seq0013        -----GCCGGGCTACGTGG---------AGTCCTCCCGGT--------------------
seq0014        -----TCCGGGATCCTTGGTTTCAAGTACGTCCGCCCTGACGAGAAGCCCT----CGAAC
seq0015        -----TCAGGGAT-CTTGC---------GGCACTACGTGTGTCAATATCGT----CCCAA
seq0018        -------CGGGA----TCG---------GG--CTCCATGGAT-----GCGA----GC-AC
seq0020        -------TCGAT----CCG---------GG--CTCCTTGGCT-----TGGA----GT-AC

(position)     11111111111111111111111111111111111111111111111111111
               22222222223333333333444444444455555555556666666666777
               01234567890123456789012345678901234567890123456789012
                                                                    
seq0000        GTCCGCACT-GTGCG-C--CCGTTTCTT----ATTACT--CTGGATACA---T
seq0001        GTCCGCACT-GTGCG-C--CCGTTTCTT----TTTACT--CTGGATACA---T
seq0002        GTCCGCACT-G-CCG-C-ACTGTTTCTT----ATTTCT--CT-GATTAAGTCT
seq0003        GTCCGCACT-G-GCG-C-ACCGTTTCTT----ATTTCT--CTGGATTAAGTCT
seq0004        GTCCGCACT-G-GCG-C-ACCGTTTCTT----ATTTCT--CTGGATTAAGTCT
seq0005        GTCCGCACTCGTTCG-C--ACGTTTCTT----ATTTCT--CTGGATTAA---T
seq0006        GTCCGCACTCGTTCG-C--ACGTTTATT----ATTTCT--TTGGATTAA---T
seq0007        GTCCGCACTCGTTCG-C--ACGTTTCTT----ATTTCT--CTGGATTAA---T
seq0008        GTCCGTACTGGGTCC-C--GCGATTCTT----CTTGCT--CTCGGGTAA---T
seq0009        GCCCGGACTGGGTCC-C--GCGGTAATT----CTTGGT--CTCGAGTAT---T
seq0013        -----------GTCC-C--GCGTTCCTC--------CA--CGAGAGTAC---T
seq0014        ATTCACGACAGGTCT-C--GCTTTCCTTCTTG----CA--CTCAAGTAA---T
seq0015        GTGCCCGTCGAGTCCGC--GGATTACTT--------CA--GTGGCAACT---C
seq0018        GTCCGCCATGGGTCG-C--GCTCGCTTT----ATACCA--CTCGAGTGA---T
seq0020        ATCCGCCAGCTGTCG-CT-CCGTTCCTT----ATTGCTAGATCGAGTAA---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, -105) .

[ 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   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3    -    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    -    -    -    -    5    5    5    5
seq0001   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3    -    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    -    -    -    -    5    5    5    5
seq0002   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3    -    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    -    -    -    -    5    5    5    5
seq0003   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3    -    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    -    -    -    -    5    5    5    5
seq0004   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3    -    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    -    -    -    -    5    5    5    5
seq0005   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3    -    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    -    -    -    -    5    5    5    5
seq0006   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3    -    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    -    -    5    5    5    5    5    5
seq0007   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3    -    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -    -    -    -    -    -    -    -    5    5    5    5
seq0008   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3    -    -    -   -3   -3   -3  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31  -31    -    -  -29  -29  -29  -29
seq0009   	  -10  -10  -10  -10  -10    -    -    -    -    -    -    -    -    -    -    -    -    -    3    3    3    0    0    0    -    -    -    3    3    3    0    0    0  -30  -30  -30    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3  -31  -31  -31  -31  -31  -67    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -3    -    -    -   -3   -3   -3  -31  -31  -31  -31  -31  -67    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3    -    -    -   -3   -3   -3  -31  -31  -31  -31  -31  -67    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	  -10  -10  -10  -13  -13    -    -    -    -    -    -    -    -    -    -    -    -    -   -3   -3   -3   -3   -3   -7    -    -    -   -4   -4  -32    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3   -3    -    -    -   -3   -3   -3    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(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   	    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5  -31  -31  -31  -31  -31  -31  -31  -31    -    -    -    -    -    -    -    -    -  -22  -22    -    -  -20  -20  -20  -20  -20  -20  -20  -87
seq0001   	    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5  -31  -31  -31  -31  -31  -31  -31  -31    -    -    -    -    -    -    -    -    -  -22  -22    -    -  -20  -20  -20  -20  -20  -20  -20  -87
seq0002   	    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5  -31  -31  -31  -31  -31  -31  -31  -31    -    -    -    -    -    -    -    -    -  -22  -22    -    -  -20  -20  -20  -20  -20  -20  -20  -87
seq0003   	    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5  -31  -31  -31  -31  -31  -31  -31  -31    -    -    -    -    -    -    -    -    -  -22  -22    -    -  -20  -20  -20  -20  -20  -20  -20  -87
seq0004   	    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5  -31  -31  -31  -31  -31  -31  -31  -31    -    -    -    -    -    -    -    -    -  -22  -22    -    -  -20  -20  -20  -20  -20  -20  -20  -87
seq0005   	    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5  -31  -31  -31  -31  -31  -31  -31  -31    -    -    -    -    -    -    -    -    -  -22  -22    -    -  -20  -20  -20  -20  -20  -20  -20  -87
seq0006   	    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5  -31  -31  -31  -31  -31  -31  -31  -31    -    -    -    -    -    -    -    -    -  -22  -22    -    -  -20  -20  -20  -20  -20  -20  -20  -87
seq0007   	    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5  -31  -31  -31  -31  -31  -31  -31  -31    -    -    -    -    -    -    -    -    -  -22  -22    -    -  -20  -20  -20  -20  -20  -20  -20  -87
seq0008   	  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29  -29    -  -28  -28  -28  -31    -    -    -    -    -    -    -    -    -  -22  -22    -    -  -20  -20  -20  -20  -20  -20  -20  -87
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -29    -  -28  -28  -28  -31    -    -    -    -    -    -    -    -    -  -22  -22    -    -  -20  -20  -20  -20  -20  -20  -20  -87
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41 -108    -    -    -    -    -    -    -    -    -  -99 -113 -113 -113 -113 -113 -113 -113 -113 -113 -113 -141
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38  -41  -41  -41  -41  -41  -41  -41  -41  -41  -41 -108 -108 -108 -108 -108 -108 -108 -108 -109 -109 -113 -113 -113 -113 -113 -113 -113 -113 -113 -113 -113 -113
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  -38  -38  -38  -41  -41  -41  -41  -41    -  -41  -41  -41  -41  -41    -    -    -    -    -    -    -    -    -  -32  -32  -32  -32  -32  -32  -32  -32  -32  -32  -32  -32
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    5    5    5    5  -31    -    -    -    -  -27  -27  -31    -    -    -    -    -    -    -    -    -  -22  -22    -    -  -20  -20  -20  -20  -20  -20  -20  -87
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    6    6    6  -32  -32    -    -    -    -  -28  -28  -31    -    -    -    -    -    -    -    -    -  -22  -22    -    -  -20  -20  -20  -20  -20  -20  -20  -87



(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   	  -87  -87    -    -    -    -    -  -82    -  -82  -82    -    -    -    -  -78  -78  -78  -78  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82    -  -81 -108 -108 -110 -111    - -110    -    - -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -
seq0001   	  -87  -87    -    -    -    -    -  -82    -  -82  -82    -    -    -    -  -78  -78  -78  -78  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82    -  -81 -108 -108 -110 -111    - -110    -    - -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -
seq0002   	  -87  -87    -    -    -    -    -  -82    -  -82  -82    -    -    -    -  -78  -78  -78  -78  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82    -  -81    - -108 -110 -111    - -110    - -109 -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -
seq0003   	  -87  -87    -    -    -    -    -  -82    -  -82  -82    -    -    -    -  -78  -78  -78  -78  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82    -  -81    - -108 -110 -111    - -110    - -109 -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -
seq0004   	  -87  -87    -    -    -    -    -  -82    -  -82  -82    -    -    -    -  -78  -78  -78  -78  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82    -  -81    - -108 -110 -111    - -110    - -109 -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -
seq0005   	  -87  -87    -    -    -    -    -  -82  -82  -82  -82    -    -    -    -  -78  -78  -78  -78  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82 -110 -110 -110 -110 -111    - -110    -    - -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -
seq0006   	  -87  -87    -    -    -    -    -  -82  -82  -82  -82    -    -    -    -  -78  -78  -78  -78  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82 -110 -110 -110 -110 -111    - -110    -    - -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -
seq0007   	  -87  -87    -    -    -    -    -  -82  -82  -82  -82    -    -    -    -  -78  -78  -78  -78  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82 -110 -110 -110 -110 -111    - -110    -    - -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -
seq0008   	  -87  -87    -    -    -    -    -  -82  -82  -82  -82    -    -    -    -  -78    -  -78  -78  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82 -110 -110 -110 -110 -111    - -110    -    - -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -
seq0009   	  -87  -87    -    -    -    -    -  -82  -82  -82  -82  -82  -83  -83  -83  -83    -  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82 -110 -110 -110 -110 -111    - -110    -    - -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    - -110 -110 -110 -111    - -110    -    - -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -
seq0014   	 -113 -113 -113 -113 -113 -113 -113 -113 -113 -113 -113    -    -    -    - -109 -109 -109 -109 -109 -109 -109 -109 -109 -109 -109 -109 -109 -109 -109 -110 -110 -110 -110 -111    - -110    -    - -109 -109 -109 -109 -109 -109 -109 -109 -109 -109 -109
seq0015   	  -32  -32  -32  -32  -32  -32  -32  -32  -32  -32  -32    -    -    -    -  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28  -28    -    -  -26  -26  -26  -26  -26  -26  -26  -26  -26    -    -
seq0018   	  -87  -87    -    -    -    -    -  -82  -82  -82  -82    -    -    -    -  -78  -79    -  -78  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82 -110 -110 -110 -110 -111    - -110    -    - -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -
seq0020   	  -87  -87    -    -    -    -    -  -82  -82  -82  -82    -    -    -    -  -78  -79    -  -78  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82  -82 -110 -110 -110 -110 -110    - -109 -109    - -109 -109 -109 -109 -109 -109 -109 -109 -109    -    -



(position)	  150  151  152  153  154  155  156  157  158  159  160  161  162  163  164  165  166  167  168  169  170  171  172

seq0000   	    -    - -105 -105 -105 -105 -105 -105    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105    -    -    - -102
seq0001   	    -    - -105 -105 -105 -105 -105 -105    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105    -    -    - -102
seq0002   	    -    - -105 -105 -105 -105 -105 -105    -    - -105 -105    - -105 -105 -105 -105 -105 -105 -105 -105 -105 -105
seq0003   	    -    - -105 -105 -105 -105 -105 -105    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105
seq0004   	    -    - -105 -105 -105 -105 -105 -105    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105
seq0005   	    -    - -105 -105 -105 -105 -105 -105    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105    -    -    - -102
seq0006   	    -    - -105 -105 -105 -105 -105 -105    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105    -    -    - -102
seq0007   	    -    - -105 -105 -105 -105 -105 -105    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105    -    -    - -102
seq0008   	    -    - -105 -105 -105 -105 -105 -105    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105    -    -    - -102
seq0009   	    -    - -105 -105 -105 -105 -105 -105    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105    -    -    - -102
seq0013   	    -    -    -    -    -    - -105 -105    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105    -    -    - -102
seq0014   	 -109 -109    -    -    -    - -105 -105    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105    -    -    - -102
seq0015   	    -    -    -    -    -    -  -18  -18    -    -  -16  -16  -16  -16  -16  -16  -16  -16  -16    -    -    -  -13
seq0018   	    -    - -105 -105 -105 -105 -105 -105    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105    -    -    - -102
seq0020   	    -    - -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105 -105    -    -    - -102




[INFORMATION] The original $commoner_shift_flank = -105. 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   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0007   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(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   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102  102    -    -    -  102  102  102  102  102  102  102  102  102    -    -    -    -    -    -    -    -    -
seq0001   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102  102    -    -    -  102  102  102  102  102  102  102  102  102    -    -    -    -    -    -    -    -    -
seq0002   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102  102    -    -    -  102  102  102  102  102  102  102  102  102    -    -    -    -    -    -    -    -    -
seq0003   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102  102    -    -    -  102  102  102  102  102  102  102  102  102    -    -    -    -    -    -    -    -    -
seq0004   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102  102    -    -    -  102  102  102  102  102  102  102  102  102    -    -    -    -    -    -    -    -    -
seq0005   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102  102    -    -    -  102  102  102  102  102  102  102  102  102    -    -    -    -    -    -    -    -    -
seq0006   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102  102    -    -    -  102  102  102  102  102  102  102  102  102    -    -    -    -    -    -    -    -  110
seq0007   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102  102    -    -    -  102  102  102  102  102  102  102  102  102    -    -    -    -    -    -    -    -    -
seq0008   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102  102    -    -    -  102  102  102   74   74   74   74   74   74   74   74   74   74   74   74   74   74    -
seq0009   	    -    -    -    -    -   95   95   95   95   95    -    -    -    -    -    -    -    -    -    -    -    -    -  108  108  108  105  105  105    -    -    -  108  108  108  105  105  105   75   75   75    -    -    -    -    -    -    -    -    -
seq0013   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102  102  102  102  102  102  102  102   74   74   74   74   74   38    -    -    -    -    -    -    -    -    -
seq0014   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102  102    -    -    -  102  102  102   74   74   74   74   74   38    -    -    -    -    -    -    -    -    -
seq0015   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102    -    -    -  102  102  102   74   74   74   74   74   38    -    -    -    -    -    -    -    -    -
seq0018   	    -    -    -    -    -   95   95   95   92   92    -    -    -    -    -    -    -    -    -    -    -    -    -  102  102  102  102  102   98    -    -    -  101  101   73    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -
seq0020   	    -    -    -    -    -  105  105  105  105  105  105  105  105  105  105  105  105  105  102  102  102  102  102  102  102  102  102  102  102    -    -    -  102  102  102    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -



(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   	    -  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110   74   74   74   74   74   74   74   74    -    -    -    -    -    -    -    -    -   83   83    -    -   85   85   85
seq0001   	    -  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110   74   74   74   74   74   74   74   74    -    -    -    -    -    -    -    -    -   83   83    -    -   85   85   85
seq0002   	    -  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110   74   74   74   74   74   74   74   74    -    -    -    -    -    -    -    -    -   83   83    -    -   85   85   85
seq0003   	    -  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110   74   74   74   74   74   74   74   74    -    -    -    -    -    -    -    -    -   83   83    -    -   85   85   85
seq0004   	    -  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110   74   74   74   74   74   74   74   74    -    -    -    -    -    -    -    -    -   83   83    -    -   85   85   85
seq0005   	    -  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110   74   74   74   74   74   74   74   74    -    -    -    -    -    -    -    -    -   83   83    -    -   85   85   85
seq0006   	  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110   74   74   74   74   74   74   74   74    -    -    -    -    -    -    -    -    -   83   83    -    -   85   85   85
seq0007   	    -  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110  110   74   74   74   74   74   74   74   74    -    -    -    -    -    -    -    -    -   83   83    -    -   85   85   85
seq0008   	    -   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76   76    -   77   77   77   74    -    -    -    -    -    -    -    -    -   83   83    -    -   85   85   85
seq0009   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   76    -   77   77   77   74    -    -    -    -    -    -    -    -    -   83   83    -    -   85   85   85
seq0013   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   67   67   67   64   64   64   64   64   64   64   64   64   64   -3    -    -    -    -    -    -    -    -    -    6   -8   -8   -8   -8   -8   -8
seq0014   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   67   67   67   64   64   64   64   64   64   64   64   64   64   -3   -3   -3   -3   -3   -3   -3   -3   -4   -4   -8   -8   -8   -8   -8   -8   -8
seq0015   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   67   67   67   64   64   64   64   64    -   64   64   64   64   64    -    -    -    -    -    -    -    -    -   73   73   73   73   73   73   73
seq0018   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  110  110  110  110   74    -    -    -    -   78   78   74    -    -    -    -    -    -    -    -    -   83   83    -    -   85   85   85
seq0020   	    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -  111  111  111   73   73    -    -    -    -   77   77   74    -    -    -    -    -    -    -    -    -   83   83    -    -   85   85   85



(position)	  200  201  202  203  204  205  206  207  208  209  210  211  212  213  214  215  216  217  218  219  220  221  222  223  224  225  226  227  228  229  230  231  232  233  234  235  236  237  238  239  240  241  242  243  244  245  246  247  248  249

seq0000   	   85   85   85   85   18   18   18    -    -    -    -    -   23    -   23   23    -    -    -    -   27   27   27   27   23   23   23   23   23   23   23   23   23   23    -   24   -3   -3   -5   -6    -   -5    -    -   -4   -4   -4   -4   -4   -4
seq0001   	   85   85   85   85   18   18   18    -    -    -    -    -   23    -   23   23    -    -    -    -   27   27   27   27   23   23   23   23   23   23   23   23   23   23    -   24   -3   -3   -5   -6    -   -5    -    -   -4   -4   -4   -4   -4   -4
seq0002   	   85   85   85   85   18   18   18    -    -    -    -    -   23    -   23   23    -    -    -    -   27   27   27   27   23   23   23   23   23   23   23   23   23   23    -   24    -   -3   -5   -6    -   -5    -   -4   -4   -4   -4   -4   -4   -4
seq0003   	   85   85   85   85   18   18   18    -    -    -    -    -   23    -   23   23    -    -    -    -   27   27   27   27   23   23   23   23   23   23   23   23   23   23    -   24    -   -3   -5   -6    -   -5    -   -4   -4   -4   -4   -4   -4   -4
seq0004   	   85   85   85   85   18   18   18    -    -    -    -    -   23    -   23   23    -    -    -    -   27   27   27   27   23   23   23   23   23   23   23   23   23   23    -   24    -   -3   -5   -6    -   -5    -   -4   -4   -4   -4   -4   -4   -4
seq0005   	   85   85   85   85   18   18   18    -    -    -    -    -   23   23   23   23    -    -    -    -   27   27   27   27   23   23   23   23   23   23   23   23   23   23   23   -5   -5   -5   -5   -6    -   -5    -    -   -4   -4   -4   -4   -4   -4
seq0006   	   85   85   85   85   18   18   18    -    -    -    -    -   23   23   23   23    -    -    -    -   27   27   27   27   23   23   23   23   23   23   23   23   23   23   23   -5   -5   -5   -5   -6    -   -5    -    -   -4   -4   -4   -4   -4   -4
seq0007   	   85   85   85   85   18   18   18    -    -    -    -    -   23   23   23   23    -    -    -    -   27   27   27   27   23   23   23   23   23   23   23   23   23   23   23   -5   -5   -5   -5   -6    -   -5    -    -   -4   -4   -4   -4   -4   -4
seq0008   	   85   85   85   85   18   18   18    -    -    -    -    -   23   23   23   23    -    -    -    -   27    -   27   27   23   23   23   23   23   23   23   23   23   23   23   -5   -5   -5   -5   -6    -   -5    -    -   -4   -4   -4   -4   -4   -4
seq0009   	   85   85   85   85   18   18   18    -    -    -    -    -   23   23   23   23   23   22   22   22   22    -   23   23   23   23   23   23   23   23   23   23   23   23   23   -5   -5   -5   -5   -6    -   -5    -    -   -4   -4   -4   -4   -4   -4
seq0013   	   -8   -8   -8   -8  -36    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -    -   -5   -5   -5   -6    -   -5    -    -   -4   -4   -4   -4   -4   -4
seq0014   	   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8   -8    -    -    -    -   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -4   -5   -5   -5   -5   -6    -   -5    -    -   -4   -4   -4   -4   -4   -4
seq0015   	   73   73   73   73   73   73   73   73   73   73   73   73   73   73   73   73    -    -    -    -   77   77   77   77   77   77   77   77   77   77   77   77   77   77   77   77   77   77   77   77   77   77    -    -   79   79   79   79   79   79
seq0018   	   85   85   85   85   18   18   18    -    -    -    -    -   23   23   23   23    -    -    -    -   27   26    -   27   23   23   23   23   23   23   23   23   23   23   23   -5   -5   -5   -5   -6    -   -5    -    -   -4   -4   -4   -4   -4   -4
seq0020   	   85   85   85   85   18   18   18    -    -    -    -    -   23   23   23   23    -    -    -    -   27   26    -   27   23   23   23   23   23   23   23   23   23   23   23   -5   -5   -5   -5   -5    -   -4   -4    -   -4   -4   -4   -4   -4   -4



(position)	  250  251  252  253  254  255  256  257  258  259  260  261  262  263  264  265  266  267  268  269  270  271  272  273  274  275  276  277

seq0000   	   -4   -4   -4    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    -    -    -    3
seq0001   	   -4   -4   -4    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    -    -    -    3
seq0002   	   -4   -4   -4    -    -    -    -    0    0    0    0    0    0    -    -    0    0    -    0    0    0    0    0    0    0    0    0    0
seq0003   	   -4   -4   -4    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0004   	   -4   -4   -4    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0005   	   -4   -4   -4    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    -    -    -    3
seq0006   	   -4   -4   -4    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    -    -    -    3
seq0007   	   -4   -4   -4    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    -    -    -    3
seq0008   	   -4   -4   -4    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    -    -    -    3
seq0009   	   -4   -4   -4    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    -    -    -    3
seq0013   	   -4   -4   -4    -    -    -    -    -    -    -    -    0    0    -    -    0    0    0    0    0    0    0    0    0    -    -    -    3
seq0014   	   -4   -4   -4   -4   -4   -4   -4    -    -    -    -    0    0    -    -    0    0    0    0    0    0    0    0    0    -    -    -    3
seq0015   	   79   79   79    -    -    -    -    -    -    -    -   87   87    -    -   89   89   89   89   89   89   89   89   89    -    -    -   92
seq0018   	   -4   -4   -4    -    -    -    -    0    0    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    -    -    -    3
seq0020   	   -4   -4   -4    -    -    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    -    -    -    3



<<<<< 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... >>>>>

... The MINI-classes increased by 1 compared to the old set!! ...


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

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

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

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


