|   | megamerger | 
The sequences can be very long. The program does a match of all sequence words of size 20 (by default). It then reduces this to the minimum set of overlapping matches by sorting the matches in order of size (largest size first) and then for each such match it removes any smaller matches that overlap. The result is a set of the longest ungapped alignments between the two sequences that do not overlap with each other. If the two sequences are identical in their region of overlap then there will be one region of match and no mismatches.
It should be possible to merge sequences that are Mega bytes long. Compare this with the program merger which does a more accurate alignment of more divergent sequences using the Needle and Wunsch algorithm but which uses much more memory.
The sequences should ideally be identical in their region of overlap. If there are any mismatches between the two sequences then megamerger will still attempt to create a merged sequence, but you should check that this is what you required.
A report of the actions of megamerger is written out. Any actions that require a choice between using regions of the two sequences where they have a mismatch is marked with the word WARNING!. The sequence in these regions is written out in uppercase. All other regions of the output sequence are written in lowercase.
Where there is a mismatch then the sequence that is chosen to supply the region of the mismatch in the final merged sequence is that sequence whose mismatch region is furthest from the start of end of the sequence.
| % megamerger tembl:v00295 tembl:v00296 Merge two large overlapping nucleic acid sequences Word size [20]: output sequence [v00295.merged]: Output file [v00295.megamerger]: report | 
Go to the input files for this example
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
  [-bsequence]         sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
   -wordsize           integer    [20] Word size (Integer 2 or more)
  [-outseq]            seqout     [ | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-asequence] (Parameter 1) | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required | 
| [-bsequence] (Parameter 2) | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required | 
| -wordsize | Word size | Integer 2 or more | 20 | 
| [-outseq] (Parameter 3) | Sequence filename and optional format (output USA) | Writeable sequence | <*>.format | 
| [-outfile] (Parameter 4) | Output file name | Output file | <*>.megamerger | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| -prefer | When a mismatch between the two sequence is discovered, one or other of the two sequences must be used to create the merged sequence over this mismatch region. The default action is to create the merged sequence using the sequence where the mismatch is closest to that sequence's centre. If this option is used, then the first sequence (seqa) will always be used in preference to the other sequence when there is a mismatch. | Boolean value Yes/No | No | 
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
| 
ID   V00295; SV 1; linear; genomic DNA; STD; PRO; 1500 BP.
XX
AC   V00295;
XX
DT   09-JUN-1982 (Rel. 01, Created)
DT   07-JUL-1995 (Rel. 44, Last updated, Version 4)
XX
DE   E. coli lacY gene (codes for lactose permease).
XX
KW   membrane protein.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC   Enterobacteriaceae; Escherichia.
XX
RN   [1]
RP   1-1500
RX   DOI; 10.1038/283541a0.
RX   PUBMED; 6444453.
RA   Buechel D.E., Gronenborn B., Mueller-Hill B.;
RT   "Sequence of the lactose permease gene";
RL   Nature 283(5747):541-545(1980).
XX
CC   lacZ is a beta-galactosidase and lacA is transacetylase.
CC   KST ECO.LACY
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1500
FT                   /organism="Escherichia coli"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:562"
FT   CDS             <1..54
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /note="reading frame (lacZ)"
FT                   /db_xref="GOA:P00722"
FT                   /db_xref="PDB:1BGL"
FT                   /db_xref="PDB:1BGM"
FT                   /db_xref="PDB:1DP0"
FT                   /db_xref="PDB:1F49"
FT                   /db_xref="PDB:1F4A"
FT                   /db_xref="PDB:1F4H"
FT                   /db_xref="PDB:1GHO"
FT                   /db_xref="PDB:1HN1"
FT                   /db_xref="PDB:1JYN"
FT                   /db_xref="PDB:1JYV"
FT                   /db_xref="PDB:1JYW"
FT                   /db_xref="PDB:1JYX"
FT                   /db_xref="PDB:1JYY"
  [Part of this file has been deleted for brevity]
FT                   /db_xref="PDB:2CFP"
FT                   /db_xref="PDB:2CFQ"
FT                   /db_xref="UniProtKB/Swiss-Prot:P02920"
FT                   /protein_id="CAA23571.1"
FT                   /translation="MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDT
FT                   GIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNIL
FT                   VGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFT
FT                   INNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKL
FT                   WFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPL
FT                   IINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQ
FT                   FEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFT
FT                   LSGPGPLSLLRRQVNEVA"
FT   CDS             1423..>1500
FT                   /transl_table=11
FT                   /note="reading frame (lacA)"
FT                   /db_xref="GOA:P07464"
FT                   /db_xref="PDB:1KQA"
FT                   /db_xref="PDB:1KRR"
FT                   /db_xref="PDB:1KRU"
FT                   /db_xref="PDB:1KRV"
FT                   /db_xref="UniProtKB/Swiss-Prot:P07464"
FT                   /protein_id="CAA23572.1"
FT                   /translation="MNMPMTERIRAGKLFTDMCEGLPEKR"
XX
SQ   Sequence 1500 BP; 315 A; 342 C; 357 G; 486 T; 0 other;
     ttccagctga gcgccggtcg ctaccattac cagttggtct ggtgtcaaaa ataataataa        60
     ccgggcaggc catgtctgcc cgtatttcgc gtaaggaaat ccattatgta ctatttaaaa       120
     aacacaaact tttggatgtt cggtttattc tttttctttt acttttttat catgggagcc       180
     tacttcccgt ttttcccgat ttggctacat gacatcaacc atatcagcaa aagtgatacg       240
     ggtattattt ttgccgctat ttctctgttc tcgctattat tccaaccgct gtttggtctg       300
     ctttctgaca aactcgggct gcgcaaatac ctgctgtgga ttattaccgg catgttagtg       360
     atgtttgcgc cgttctttat ttttatcttc gggccactgt tacaatacaa cattttagta       420
     ggatcgattg ttggtggtat ttatctaggc ttttgtttta acgccggtgc gccagcagta       480
     gaggcattta ttgagaaagt cagccgtcgc agtaatttcg aatttggtcg cgcgcggatg       540
     tttggctgtg ttggctgggc gctgtgtgcc tcgattgtcg gcatcatgtt caccatcaat       600
     aatcagtttg ttttctggct gggctctggc tgtgcactca tcctcgccgt tttactcttt       660
     ttcgccaaaa cggatgcgcc ctcttctgcc acggttgcca atgcggtagg tgccaaccat       720
     tcggcattta gccttaagct ggcactggaa ctgttcagac agccaaaact gtggtttttg       780
     tcactgtatg ttattggcgt ttcctgcacc tacgatgttt ttgaccaaca gtttgctaat       840
     ttctttactt cgttctttgc taccggtgaa cagggtacgc gggtatttgg ctacgtaacg       900
     acaatgggcg aattacttaa cgcctcgatt atgttctttg cgccactgat cattaatcgc       960
     atcggtggga aaaacgccct gctgctggct ggcactatta tgtctgtacg tattattggc      1020
     tcatcgttcg ccacctcagc gctggaagtg gttattctga aaacgctgca tatgtttgaa      1080
     gtaccgttcc tgctggtggg ctgctttaaa tatattacca gccagtttga agtgcgtttt      1140
     tcagcgacga tttatctggt ctgtttctgc ttctttaagc aactggcgat gatttttatg      1200
     tctgtactgg cgggcaatat gtatgaaagc atcggtttcc agggcgctta tctggtgctg      1260
     ggtctggtgg cgctgggctt caccttaatt tccgtgttca cgcttagcgg ccccggcccg      1320
     ctttccctgc tgcgtcgtca ggtgaatgaa gtcgcttaag caatcaatgt cggatgcggc      1380
     gcgacgctta tccgaccaac atatcataac ggagtgatcg cattgaacat gccaatgacc      1440
     gaaagaataa gagcaggcaa gctatttacc gatatgtgcg aaggcttacc ggaaaaaaga      1500
//
 | 
| 
ID   V00296; SV 1; linear; genomic DNA; STD; PRO; 3078 BP.
XX
AC   V00296;
XX
DT   13-JUL-1983 (Rel. 03, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 5)
XX
DE   E. coli gene lacZ coding for beta-galactosidase (EC 3.2.1.23).
XX
KW   galactosidase.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC   Enterobacteriaceae; Escherichia.
XX
RN   [1]
RP   1-3078
RX   PUBMED; 6313347.
RA   Kalnins A., Otto K., Ruether U., Mueller-Hill B.;
RT   "Sequence of the lacZ gene of Escherichia coli";
RL   EMBO J. 2(4):593-597(1983).
XX
RN   [2]
RX   PUBMED; 3038536.
RA   Zell R., Fritz H.J.;
RT   "DNA mismatch-repair in Escherichia coli counteracting the hydrolytic
RT   deamination of 5-methyl-cytosine residues";
RL   EMBO J. 6(6):1809-1815(1987).
XX
CC   Data kindly reviewed (18-MAY-1983) by U. Ruether
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..3078
FT                   /organism="Escherichia coli"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:562"
FT   CDS             <1..3072
FT                   /transl_table=11
FT                   /note="galactosidase"
FT                   /db_xref="GOA:P00722"
FT                   /db_xref="PDB:1BGL"
FT                   /db_xref="PDB:1BGM"
FT                   /db_xref="PDB:1DP0"
FT                   /db_xref="PDB:1F49"
FT                   /db_xref="PDB:1F4A"
FT                   /db_xref="PDB:1F4H"
FT                   /db_xref="PDB:1GHO"
FT                   /db_xref="PDB:1HN1"
FT                   /db_xref="PDB:1JYN"
  [Part of this file has been deleted for brevity]
     gaggcccgca ccgatcgccc ttcccaacag ttgcgcagcc tgaatggcga atggcgcttt       180
     gcctggtttc cggcaccaga agcggtgccg gaaagctggc tggagtgcga tcttcctgag       240
     gccgatactg tcgtcgtccc ctcaaactgg cagatgcacg gttacgatgc gcccatctac       300
     accaacgtaa cctatcccat tacggtcaat ccgccgtttg ttcccacgga gaatccgacg       360
     ggttgttact cgctcacatt taatgttgat gaaagctggc tacaggaagg ccagacgcga       420
     attatttttg atggcgttaa ctcggcgttt catctgtggt gcaacgggcg ctgggtcggt       480
     tacggccagg acagtcgttt gccgtctgaa tttgacctga gcgcattttt acgcgccgga       540
     gaaaaccgcc tcgcggtgat ggtgctgcgt tggagtgacg gcagttatct ggaagatcag       600
     gatatgtggc ggatgagcgg cattttccgt gacgtctcgt tgctgcataa accgactaca       660
     caaatcagcg atttccatgt tgccactcgc tttaatgatg atttcagccg cgctgtactg       720
     gaggctgaag ttcagatgtg cggcgagttg cgtgactacc tacgggtaac agtttcttta       780
     tggcagggtg aaacgcaggt cgccagcggc accgcgcctt tcggcggtga aattatcgat       840
     gagcgtggtg gttatgccga tcgcgtcaca ctacgtctga acgtcgaaaa cccgaaactg       900
     tggagcgccg aaatcccgaa tctctatcgt gcggtggttg aactgcacac cgccgacggc       960
     acgctgattg aagcagaagc ctgcgatgtc ggtttccgcg aggtgcggat tgaaaatggt      1020
     ctgctgctgc tgaacggcaa gccgttgctg attcgaggcg ttaaccgtca cgagcatcat      1080
     cctctgcatg gtcaggtcat ggatgagcag acgatggtgc aggatatcct gctgatgaag      1140
     cagaacaact ttaacgccgt gcgctgttcg cattatccga accatccgct gtggtacacg      1200
     ctgtgcgacc gctacggcct gtatgtggtg gatgaagcca atattgaaac ccacggcatg      1260
     gtgccaatga atcgtctgac cgatgatccg cgctggctac cggcgatgag cgaacgcgta      1320
     acgcgaatgg tgcagcgcga tcgtaatcac ccgagtgtga tcatctggtc gctggggaat      1380
     gaatcaggcc acggcgctaa tcacgacgcg ctgtatcgct ggatcaaatc tgtcgatcct      1440
     tcccgcccgg tgcagtatga aggcggcgga gccgacacca cggccaccga tattatttgc      1500
     ccgatgtacg cgcgcgtgga tgaagaccag cccttcccgg ctgtgccgaa atggtccatc      1560
     aaaaaatggc tttcgctacc tggagagacg cgcccgctga tcctttgcga atacgcccac      1620
     gcgatgggta acagtcttgg cggtttcgct aaatactggc aggcgtttcg tcagtatccc      1680
     cgtttacagg gcggcttcgt ctgggactgg gtggatcagt cgctgattaa atatgatgaa      1740
     aacggcaacc cgtggtcggc ttacggcggt gattttggcg atacgccgaa cgatcgccag      1800
     ttctgtatga acggtctggt ctttgccgac cgcacgccgc atccagcgct gacggaagca      1860
     aaacaccagc agcagttttt ccagttccgt ttatccgggc aaaccatcga agtgaccagc      1920
     gaatacctgt tccgtcatag cgataacgag ctcctgcact ggatggtggc gctggatggt      1980
     aagccgctgg caagcggtga agtgcctctg gatgtcgctc cacaaggtaa acagttgatt      2040
     gaactgcctg aactaccgca gccggagagc gccgggcaac tctggctcac agtacgcgta      2100
     gtgcaaccga acgcgaccgc atggtcagaa gccgggcaca tcagcgcctg gcagcagtgg      2160
     cgtctggcgg aaaacctcag tgtgacgctc cccgccgcgt cccacgccat cccgcatctg      2220
     accaccagcg aaatggattt ttgcatcgag ctgggtaata agcgttggca atttaaccgc      2280
     cagtcaggct ttctttcaca gatgtggatt ggcgataaaa aacaactgct gacgccgctg      2340
     cgcgatcagt tcacccgtgc accgctggat aacgacattg gcgtaagtga agcgacccgc      2400
     attgacccta acgcctgggt cgaacgctgg aaggcggcgg gccattacca ggccgaagca      2460
     gcgttgttgc agtgcacggc agatacactt gctgatgcgg tgctgattac gaccgctcac      2520
     gcgtggcagc atcaggggaa aaccttattt atcagccgga aaacctaccg gattgatggt      2580
     agtggtcaaa tggcgattac cgttgatgtt gaagtggcga gcgatacacc gcatccggcg      2640
     cggattggcc tgaactgcca gctggcgcag gtagcagagc gggtaaactg gctcggatta      2700
     gggccgcaag aaaactatcc cgaccgcctt actgccgcct gttttgaccg ctgggatctg      2760
     ccattgtcag acatgtatac cccgtacgtc ttcccgagcg aaaacggtct gcgctgcggg      2820
     acgcgcgaat tgaattatgg cccacaccag tggcgcggcg acttccagtt caacatcagc      2880
     cgctacagtc aacagcaact gatggaaacc agccatcgcc atctgctgca cgcggaagaa      2940
     ggcacatggc tgaatatcga cggtttccat atggggattg gtggcgacga ctcctggagc      3000
     ccgtcagtat cggcggaatt ccagctgagc gccggtcgct accattacca gttggtctgg      3060
     tgtcaaaaat aataataa                                                    3078
//
 | 
| # Report of megamerger of: V00295 and V00296 V00295 overlap starts at 1 V00296 overlap starts at 3019 Using V00296 1-3018 as the initial sequence Matching region V00295 1-60 : V00296 3019-3078 Length of match: 60 V00295 overlap ends at 60 V00296 overlap ends at 3078 Using V00295 61-1500 as the final sequence | 
| >V00295 V00295.1 E. coli lacY gene (codes for lactose permease). accatgattacggattcactggccgtcgttttacaacgtcgtgactgggaaaaccctggc gttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaa gaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcttt gcctggtttccggcaccagaagcggtgccggaaagctggctggagtgcgatcttcctgag gccgatactgtcgtcgtcccctcaaactggcagatgcacggttacgatgcgcccatctac accaacgtaacctatcccattacggtcaatccgccgtttgttcccacggagaatccgacg ggttgttactcgctcacatttaatgttgatgaaagctggctacaggaaggccagacgcga attatttttgatggcgttaactcggcgtttcatctgtggtgcaacgggcgctgggtcggt tacggccaggacagtcgtttgccgtctgaatttgacctgagcgcatttttacgcgccgga gaaaaccgcctcgcggtgatggtgctgcgttggagtgacggcagttatctggaagatcag gatatgtggcggatgagcggcattttccgtgacgtctcgttgctgcataaaccgactaca caaatcagcgatttccatgttgccactcgctttaatgatgatttcagccgcgctgtactg gaggctgaagttcagatgtgcggcgagttgcgtgactacctacgggtaacagtttcttta tggcagggtgaaacgcaggtcgccagcggcaccgcgcctttcggcggtgaaattatcgat gagcgtggtggttatgccgatcgcgtcacactacgtctgaacgtcgaaaacccgaaactg tggagcgccgaaatcccgaatctctatcgtgcggtggttgaactgcacaccgccgacggc acgctgattgaagcagaagcctgcgatgtcggtttccgcgaggtgcggattgaaaatggt ctgctgctgctgaacggcaagccgttgctgattcgaggcgttaaccgtcacgagcatcat cctctgcatggtcaggtcatggatgagcagacgatggtgcaggatatcctgctgatgaag cagaacaactttaacgccgtgcgctgttcgcattatccgaaccatccgctgtggtacacg ctgtgcgaccgctacggcctgtatgtggtggatgaagccaatattgaaacccacggcatg gtgccaatgaatcgtctgaccgatgatccgcgctggctaccggcgatgagcgaacgcgta acgcgaatggtgcagcgcgatcgtaatcacccgagtgtgatcatctggtcgctggggaat gaatcaggccacggcgctaatcacgacgcgctgtatcgctggatcaaatctgtcgatcct tcccgcccggtgcagtatgaaggcggcggagccgacaccacggccaccgatattatttgc ccgatgtacgcgcgcgtggatgaagaccagcccttcccggctgtgccgaaatggtccatc aaaaaatggctttcgctacctggagagacgcgcccgctgatcctttgcgaatacgcccac gcgatgggtaacagtcttggcggtttcgctaaatactggcaggcgtttcgtcagtatccc cgtttacagggcggcttcgtctgggactgggtggatcagtcgctgattaaatatgatgaa aacggcaacccgtggtcggcttacggcggtgattttggcgatacgccgaacgatcgccag ttctgtatgaacggtctggtctttgccgaccgcacgccgcatccagcgctgacggaagca aaacaccagcagcagtttttccagttccgtttatccgggcaaaccatcgaagtgaccagc gaatacctgttccgtcatagcgataacgagctcctgcactggatggtggcgctggatggt aagccgctggcaagcggtgaagtgcctctggatgtcgctccacaaggtaaacagttgatt gaactgcctgaactaccgcagccggagagcgccgggcaactctggctcacagtacgcgta gtgcaaccgaacgcgaccgcatggtcagaagccgggcacatcagcgcctggcagcagtgg cgtctggcggaaaacctcagtgtgacgctccccgccgcgtcccacgccatcccgcatctg accaccagcgaaatggatttttgcatcgagctgggtaataagcgttggcaatttaaccgc cagtcaggctttctttcacagatgtggattggcgataaaaaacaactgctgacgccgctg cgcgatcagttcacccgtgcaccgctggataacgacattggcgtaagtgaagcgacccgc attgaccctaacgcctgggtcgaacgctggaaggcggcgggccattaccaggccgaagca gcgttgttgcagtgcacggcagatacacttgctgatgcggtgctgattacgaccgctcac gcgtggcagcatcaggggaaaaccttatttatcagccggaaaacctaccggattgatggt agtggtcaaatggcgattaccgttgatgttgaagtggcgagcgatacaccgcatccggcg cggattggcctgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccgctgggatctg ccattgtcagacatgtataccccgtacgtcttcccgagcgaaaacggtctgcgctgcggg acgcgcgaattgaattatggcccacaccagtggcgcggcgacttccagttcaacatcagc cgctacagtcaacagcaactgatggaaaccagccatcgccatctgctgcacgcggaagaa ggcacatggctgaatatcgacggtttccatatggggattggtggcgacgactcctggagc ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattaccagttggtctgg tgtcaaaaataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaatcc attatgtactatttaaaaaacacaaacttttggatgttcggtttattctttttcttttac ttttttatcatgggagcctacttcccgtttttcccgatttggctacatgacatcaaccat atcagcaaaagtgatacgggtattatttttgccgctatttctctgttctcgctattattc caaccgctgtttggtctgctttctgacaaactcgggctgcgcaaatacctgctgtggatt attaccggcatgttagtgatgtttgcgccgttctttatttttatcttcgggccactgtta caatacaacattttagtaggatcgattgttggtggtatttatctaggcttttgttttaac gccggtgcgccagcagtagaggcatttattgagaaagtcagccgtcgcagtaatttcgaa tttggtcgcgcgcggatgtttggctgtgttggctgggcgctgtgtgcctcgattgtcggc atcatgttcaccatcaataatcagtttgttttctggctgggctctggctgtgcactcatc ctcgccgttttactctttttcgccaaaacggatgcgccctcttctgccacggttgccaat gcggtaggtgccaaccattcggcatttagccttaagctggcactggaactgttcagacag ccaaaactgtggtttttgtcactgtatgttattggcgtttcctgcacctacgatgttttt gaccaacagtttgctaatttctttacttcgttctttgctaccggtgaacagggtacgcgg gtatttggctacgtaacgacaatgggcgaattacttaacgcctcgattatgttctttgcg ccactgatcattaatcgcatcggtgggaaaaacgccctgctgctggctggcactattatg tctgtacgtattattggctcatcgttcgccacctcagcgctggaagtggttattctgaaa acgctgcatatgtttgaagtaccgttcctgctggtgggctgctttaaatatattaccagc cagtttgaagtgcgtttttcagcgacgatttatctggtctgtttctgcttctttaagcaa ctggcgatgatttttatgtctgtactggcgggcaatatgtatgaaagcatcggtttccag ggcgcttatctggtgctgggtctggtggcgctgggcttcaccttaatttccgtgttcacg cttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaagtcgcttaagca atcaatgtcggatgcggcgcgacgcttatccgaccaacatatcataacggagtgatcgca ttgaacatgccaatgaccgaaagaataagagcaggcaagctatttaccgatatgtgcgaa ggcttaccggaaaaaaga | 
A merged sequence is written out.
Where there has been a mismatch between the two sequences, the merged sequence is written out in uppercase and the sequence whose mismatch region is furthest from the edges of the sequence is used in the merged sequence.
The name and description of the first input sequence is used for the name and description of the output sequence.
A report of the merger is written out.
| Program name | Description | 
|---|---|
| cons | Creates a consensus from multiple alignments | 
| merger | Merge two overlapping sequences | 
Compare this with the program merger which does a more accurate alignment of more divergent sequences using the Needle and Wunsch algorithm but which uses much more memory.
A graphical dotplot of the matches used in this merge can be displayed using the program dotpath.