Reading in original template sequences... (for comparison)
Reading sequence from ./data/XMT1-coding.txt
Sequence read complete!
Reading sequence from ./data/DXMT1-coding.txt
Sequence read complete!
Correct AA seq1: MELQEVLRMNGGEGDTSYAKNSAYNQLVLAKVKPVLEQCVRELLRANLPNINKCIKVADLGCASGPNTLLTVRDIVQSIDKVGQEKKNELERPTIQIFLNDLFPNDFNSVFKLLPSFYRKLEKENGRKIGSCLIGAMPGSFYSRLFPEESMHFLHSCYCLQWLSQVPSGLVTELGIGTNKGSIYSSKASRLPVQKAYLDQFTKDFTTFLRIHSEELFSHGRMLLTCICKGVELDARNAIDLLEMAINDLVVEGHLEEEKLDSFNLPVYIPSAEEVKCIVEEEGSFEILYLETFKVLYDAGFSIDDEHIKAEYVASSVRAVYEPILASHFGEAIIPDIFHRFAKHAAKVLPLGKGFYNNLIISLAKKPEKSDM*
Correct AA seq2: MELQEVLHMNGGEGDTSYAKNSSYNLFLIRVKPVLEQCIQELLRANLPNINKCFKVGDLGCASGPNTFSTVRDIVQSIDKVGQEKKNELERPTIQIFLNDLFQNDFNSVFKLLPSFYRNLEKENGRKIGSCLIGAMPGSFYSRLFPEESMHFLHSCYCLHWLSQVPSGLVTELGISVNKGCIYSSKASRPPIQKAYLDQFTKDFTTFLRIHSEELISRGRMLLTFICKEDEFDHPNSMDLLEMSINDLVIEGHLEEEKLDSFNVPIYAPSTEEVKRIVEEEGSFEILYLETFNAPYDAGFSIDDDYQGRSHSPVSCDEHARAAHVASVVRSIYEPILASHFGEAILPDLSHRIAKNAAKVLRSGKGFYDSVIISLAKKPEKADM*


Reading in sequences for optimizing...
Reading sequence from ./data/XMT1_Optimized_NoCutSites_DoubleStopCodon.txt
Sequence read complete!
Reading sequence from ./data/DXMT1_opt_coding1_Misha.txt
Sequence read complete!
seq1: ATGGAATTGCAAGAAGTTTTGAGAATGAACGGTGGTGAAGGTGACACTTCTTACGCTAAGAACTCTGCTTACAACCAATTGGTTTTGGCTAAGGTTAAGCCAGTTTTGGAACAATGTGTTAGAGAATTGTTGAGAGCTAACTTGCCAAACATCAACAAGTGTATCAAGGTTGCTGACTTGGGTTGTGCTTCTGGTCCAAACACTTTGTTGACTGTTAGAGACATCGTTCAATCTATCGACAAGGTTGGTCAAGAAAAGAAGAACGAATTGGAAAGACCAACTATCCAAATCTTCTTGAACGACTTGTTCCCAAACGACTTCAACTCTGTTTTCAAGTTGTTGCCATCTTTCTACAGAAAGTTGGAAAAGGAAAACGGTAGAAAGATCGGTTCTTGTTTGATCGGTGCTATGCCAGGTTCTTTCTACTCTCGTTTGTTCCCAGAAGAATCTATGCACTTCTTGCACTCTTGTTACTGTTTGCAATGGTTGTCTCAAGTTCCATCTGGTTTGGTTACTGAATTGGGTATCGGTACTAACAAGGGTTCTATCTACTCTTCTAAGGCTTCTCGTTTGCCAGTTCAAAAGGCTTACTTGGACCAATTCACTAAGGACTTCACTACTTTCTTGAGAATCCACTCTGAAGAATTGTTCTCTCACGGTAGAATGTTGTTGACTTGTATCTGTAAGGGTGTTGAATTGGACGCTAGAAACGCTATCGACTTGTTGGAAATGGCTATCAACGACTTGGTTGTTGAAGGTCACTTGGAAGAAGAAAAGTTGGACTCTTTCAACTTGCCAGTTTACATCCCATCTGCTGAAGAAGTTAAGTGTATCGTTGAAGAAGAAGGTTCTTTCGAAATCTTGTACTTGGAAACTTTCAAGGTTTTGTACGACGCTGGTTTCTCTATCGACGACGAACACATCAAGGCTGAATACGTTGCTTCTTCTGTTAGAGCTGTTTACGAACCAATCTTGGCTTCTCACTTCGGTGAAGCTATCATCCCAGACATCTTCCACAGATTCGCTAAGCACGCTGCTAAGGTTTTGCCATTGGGTAAGGGTTTCTACAACAACTTGATCATCTCTTTGGCTAAGAAGCCAGAAAAGTCTGACATGTAATAA
seq2: ATGGAATTGCAAGAAGTTTTGCACATGAACGGTGGTGAAGGTGACACTTCTTACGCTAAGAACTCTTCTTACAACTTGTTCTTGATCAGAGTTAAGCCAGTTTTGGAACAATGTATCCAAGAATTGTTGAGAGCTAACTTGCCAAACATCAACAAGTGTTTCAAGGTTGGTGACTTGGGTTGTGCTTCTGGTCCAAACACTTTCTCTACTGTTAGAGACATCGTTCAATCTATCGACAAGGTTGGTCAAGAAAAGAAGAACGAATTGGAAAGACCAACTATCCAAATCTTCTTGAACGACTTGTTCCAAAACGACTTCAACTCTGTTTTCAAGTTGTTGCCATCTTTCTACAGAAACTTGGAAAAGGAAAACGGTAGAAAGATCGGTTCTTGTTTGATCGGTGCTATGCCAGGTTCTTTCTACTCTCGTTTGTTCCCAGAAGAATCTATGCACTTCTTGCACTCTTGTTACTGTTTGCACTGGTTGTCTCAAGTTCCATCTGGTTTGGTTACTGAATTGGGTATCTCTGTTAACAAGGGTTGTATCTACTCTTCTAAGGCTTCTCGTCCACCAATCCAAAAGGCTTACTTGGACCAATTCACTAAGGACTTCACTACTTTCTTGAGAATCCACTCTGAAGAATTGATCTCTCGTGGTAGAATGTTGTTGACTTTCATCTGTAAGGAAGACGAATTTGACCACCCAAACTCTATGGACTTGTTGGAAATGTCTATCAACGACTTGGTTATCGAAGGTCACTTGGAAGAAGAAAAGTTGGACTCTTTCAACGTTCCAATCTACGCTCCATCTACTGAAGAAGTTAAGAGAATCGTTGAAGAAGAAGGTTCTTTCGAAATCTTGTACTTGGAAACTTTCAACGCTCCATACGACGCTGGTTTCTCTATCGACGACGACTACCAAGGTAGATCGCACTCTCCAGTTTCTTGTGACGAACACGCTAGAGCTGCTCACGTTGCTTCTGTTGTTAGATCGATCTACGAACCAATCTTGGCTTCTCACTTCGGTGAAGCTATCTTGCCAGACTTGTCTCACAGAATCGCTAAGAACGCTGCTAAGGTTTTGAGATCGGGTAAGGGTTTCTACGACTCTGTTATCATCTCTTTGGCTAAGAAGCCAGAAAAGGCTGACATGTAATAA


Comparing accuracy of input sequences with correct sequences...
The Amino acid sequences are: 
MELQEVLRMNGGEGDTSYAKNSAYNQLVLAKVKPVLEQCVRELLRANLPNINKCIKVADLGCASGPNTLLTVRDIVQSIDKVGQEKKNELERPTIQIFLNDLFPNDFNSVFKLLPSFYRKLEKENGRKIGSCLIGAMPGSFYSRLFPEESMHFLHSCYCLQWLSQVPSGLVTELGIGTNKGSIYSSKASRLPVQKAYLDQFTKDFTTFLRIHSEELFSHGRMLLTCICKGVELDARNAIDLLEMAINDLVVEGHLEEEKLDSFNLPVYIPSAEEVKCIVEEEGSFEILYLETFKVLYDAGFSIDDEHIKAEYVASSVRAVYEPILASHFGEAIIPDIFHRFAKHAAKVLPLGKGFYNNLIISLAKKPEKSDM**
MELQEVLHMNGGEGDTSYAKNSSYNLFLIRVKPVLEQCIQELLRANLPNINKCFKVGDLGCASGPNTFSTVRDIVQSIDKVGQEKKNELERPTIQIFLNDLFQNDFNSVFKLLPSFYRNLEKENGRKIGSCLIGAMPGSFYSRLFPEESMHFLHSCYCLHWLSQVPSGLVTELGISVNKGCIYSSKASRPPIQKAYLDQFTKDFTTFLRIHSEELISRGRMLLTFICKEDEFDHPNSMDLLEMSINDLVIEGHLEEEKLDSFNVPIYAPSTEEVKRIVEEEGSFEILYLETFNAPYDAGFSIDDDYQGRSHSPVSCDEHARAAHVASVVRSIYEPILASHFGEAILPDLSHRIAKNAAKVLRSGKGFYDSVIISLAKKPEKADM**
The number of character differences for seq1 is: 0
The number of character differences for seq2 is: 0


Aligning input sequences...
Aligned sequences:
ATGGAATTGCAAGAAGTTTTGAGAATGAACGGTGGTGAAGGTGACACTTCTTACGCTAAGAACTCTGCTTACAACCAATTGGTTTTGGCTAAGGTTAAGCCAGTTTTGGAACAATGTGTTAGAGAATTGTTGAGAGCTAACTTGCCAAACATCAACAAGTGTATCAAGGTTGCTGACTTGGGTTGTGCTTCTGGTCCAAACACTTTGTTGACTGTTAGAGACATCGTTCAATCTATCGACAAGGTTGGTCAAGAAAAGAAGAACGAATTGGAAAGACCAACTATCCAAATCTTCTTGAACGACTTGTTCCCAAACGACTTCAACTCTGTTTTCAAGTTGTTGCCATCTTTCTACAGAAAGTTGGAAAAGGAAAACGGTAGAAAGATCGGTTCTTGTTTGATCGGTGCTATGCCAGGTTCTTTCTACTCTCGTTTGTTCCCAGAAGAATCTATGCACTTCTTGCACTCTTGTTACTGTTTGCAATGGTTGTCTCAAGTTCCATCTGGTTTGGTTACTGAATTGGGTATCGGTACTAACAAGGGTTCTATCTACTCTTCTAAGGCTTCTCGTTTGCCAGTTCAAAAGGCTTACTTGGACCAATTCACTAAGGACTTCACTACTTTCTTGAGAATCCACTCTGAAGAATTGTTCTCTCACGGTAGAATGTTGTTGACTTGTATCTGTAAGGGTGTTGAATTGGACGCTAGAAACGCTATCGACTTGTTGGAAATGGCTATCAACGACTTGGTTGTTGAAGGTCACTTGGAAGAAGAAAAGTTGGACTCTTTCAACTTGCCAGTTTACATCCCATCTGCTGAAGAAGTTAAGTGTATCGTTGAAGAAGAAGGTTCTTTCGAAATCTTGTACTTGGAAACTTTCAAGGTTTTGTACGACGCTGGTTTCTCTATCGACGACGA  AC A        C  A TCA  AGG  CT G  A  AT ACG T     TGCT    T  CTTCTGTTAG AGCT GTT TACGAACCAATCTTGGCTTCTCACTTCGGTGAAGCTATCATCCCAGACATCTTCCACAGATTCGCTAAGCACGCTGCTAAGGTTTTGCCATTGGGTAAGGGTTTCTACAACAACTTGATCATCTCTTTGGCTAAGAAGCCAGAAAAGTCTGACATGTAATAA
ATGGAATTGCAAGAAGTTTTGCACATGAACGGTGGTGAAGGTGACACTTCTTACGCTAAGAACTCTTCTTACAACTTGTT  CTTGATCAGAG TTAAGCCAGTTTTGGAACAATGTATCCAAGAATTGTTGAGAGCTAACTTGCCAAACATCAACAAGTGTTTCAAGGTTGGTGACTTGGGTTGTGCTTCTGGTCCAAACACTTTCTCTACTGTTAGAGACATCGTTCAATCTATCGACAAGGTTGGTCAAGAAAAGAAGAACGAATTGGAAAGACCAACTATCCAAATCTTCTTGAACGACTTGTTCCAAAACGACTTCAACTCTGTTTTCAAGTTGTTGCCATCTTTCTACAGAAACTTGGAAAAGGAAAACGGTAGAAAGATCGGTTCTTGTTTGATCGGTGCTATGCCAGGTTCTTTCTACTCTCGTTTGTTCCCAGAAGAATCTATGCACTTCTTGCACTCTTGTTACTGTTTGCACTGGTTGTCTCAAGTTCCATCTGGTTTGGTTACTGAATTGGGTATCTCTGTTAACAAGGGTTGTATCTACTCTTCTAAGGCTTCTCGTCCACCAATCCAAAAGGCTTACTTGGACCAATTCACTAAGGACTTCACTACTTTCTTGAGAATCCACTCTGAAGAATTGATCTCTCGTGGTAGAATGTTGTTGACTTTCATCTGTAAGGAAGACGAATTTGACCACCCAAACTCTATGGACTTGTTGGAAATGTCTATCAACGACTTGGTTATCGAAGGTCACTTGGAAGAAGAAAAGTTGGACTCTTTCAACGTTCCAATCTACGCTCCATCTACTGAAGAAGTTAAGAGAATCGTTGAAGAAGAAGGTTCTTTCGAAATCTTGTACTTGGAAACTTTCAACGCTCCATACGACGCTGGTTTCTCTATCGACGACGACTACCAAGGTAGATCGCACTCTCCAGTTTCTTGTGACGAACACGCTAGAGCTGCTCACGTTGCTTCTGTTGTTAGATCGATCTACGAACCAATCTTGGCTTCTCACTTCGGTGAAGCTATCTTGCCAGACTTGTCTCACAGAATCGCTAAGAACGCTGCTAAGGTTTTGAGATCGGGTAAGGGTTTCTACGACTCTGTTATCATCTCTTTGGCTAAGAAGCCAGAAAAGGCTGACATGTAATAA
Testing similarity of sequences:
The percentage similarity is: 0.8778966131907309
The number of long equivalent stretches (>=20bp): 16


Illegal Restriction Sites in Seq1:
EcoRI - 0
XbaI - 0
SpeI - 0
PstI - 0
BglII - 0
BamHI - 0
NdeI - 0
NcoI - 0
XhoI - 0
NotI - 0
AvrII - 0
Illegal sites? null
Illegal Restriction Sites in Seq2:
EcoRI - 0
XbaI - 0
SpeI - 0
PstI - 0
BglII - 0
BamHI - 0
NdeI - 0
NcoI - 0
XhoI - 0
NotI - 0
AvrII - 0
Illegal sites? null


Results:
New sequence 1: ATGGAATTGCAGGAAGTTTTGAGAATGAACGGTGGTGAAGGTGATACTTCTTACGCTAAGAACTCTGCTTACAACCAATTGGTTTTGGCTAAGGTTAAGCCAGTCTTGGAACAATGTGTTAGAGAATTGTTGAGAGCTAACTTACCAAACATCAACAAGTGTATCAAGGTTGCTGACTTGGGATGTGCTTCTGGTCCAAACACTTTGTTGACTGTTAGAGATATCGTTCAATCTATCGATAAGGTTGGTCAAGAAAAGAAAAACGAATTGGAAAGACCAACAATCCAAATCTTCTTGAATGACTTGTTCCCAAACGACTTCAACTCTGTTTTTAAGTTGTTGCCATCTTTCTACAGAAAGTTGGAAAAGGAGAACGGTAGAAAGATCGGATCTTGTTTGATCGGTGCTATGCCTGGTTCTTTCTACTCTAGGTTGTTCCCAGAAGAATCAATGCACTTCTTGCACTCTTGCTACTGTTTGCAATGGTTGTCTCAAGTTCCATCAGGTTTGGTTACTGAATTGGGTATCGGTACTAACAAGGGTTCTATCTACTCATCTAAGGCTTCTCGTTTGCCAGTTCAAAAGGCTTACTTGGACCAGTTCACTAAGGACTTCACTACATTCTTGAGAATCCACTCTGAAGAATTGTTCTCTCACGGTAGAATGTTGTTGACTTGTATCTGTAAGGGTGTTGAATTGGACGCTAGAAACGCTATCGACTTGTTGGAAATGGCTATCAACGACTTGGTTGTTGAAGGTCACTTAGAAGAAGAAAAGTTGGACTCTTTCAACTTGCCAGTTTACATCCCATCTGCTGAAGAAGTTAAGTGTATCGTTGAAGAGGAAGGTTCTTTCGAAATTTTGTACTTGGAAACTTTCAAGGTTTTGTACGACGCTGGATTCTCTATCGACGACGAACACATCAAGGCTGAATACGTTGCTTCTTCTGTTAGAGCTGTTTACGAACCAATCTTGGCTTCACACTTCGGTGAAGCTATCATCCCAGACATCTTCCACAGATTCGCTAAGCACGCTGCTAAGGTTTTGCCATTGGGTAAGGGTTTCTACAACAACTTGATCATCTCTTTGGCTAAGAAACCAGAAAAGTCTGACATGTAATAA
New sequence 2: ATGGAATTGCAAGAAGTTTTGCACATGAACGGTGGAGAAGGTGACACTTCTTATGCTAAGAACTCTTCTTACAACTTGTTCTTGATCAGAGTTAAGCCAGTTTTGGAACAATGTATCCAAGAATTGTTAAGAGCTAACTTGCCAAACATTAACAAGTGTTTCAAGGTTGGTGACTTGGGTTGTGCTTCTGGACCAAACACTTTCTCTACTGTTAGAGACATCGTTCAGTCTATCGACAAGGTTGGTCAGGAAAAGAAGAACGAATTAGAAAGACCAACTATCCAAATTTTCTTGAACGACTTGTTCCAAAACGACTTTAACTCTGTTTTCAAGTTGTTACCATCTTTCTACAGAAACTTGGAAAAGGAAAACGGTAGGAAGATCGGTTCTTGTTTGATTGGTGCTATGCCAGGTTCATTCTACTCTCGTTTGTTCCCTGAAGAATCTATGCACTTCTTACACTCTTGTTACTGTTTGCACTGGTTGTCTCAGGTTCCATCTGGTTTGGTCACTGAATTGGGTATCTCTGTTAACAAGGGTTGTATCTACTCTTCTAAGGCTTCTCGTCCACCAATCCAAAAGGCTTATTTGGACCAATTCACTAAAGACTTCACTACTTTCTTGCGTATCCACTCTGAAGAATTGATCTCTCGTGGTAGAATGTTGTTGACTTTCATCTGTAAGGAAGACGAATTTGACCACCCAAACTCTATGGACTTGTTGGAAATGTCTATCAACGACTTGGTTATCGAAGGTCACTTGGAAGAAGAGAAGTTGGACTCTTTCAACGTTCCAATCTACGCTCCATCTACTGAAGAAGTTAAGAGAATCGTTGAAGAAGAAGGTTCATTCGAAATCTTGTACTTGGAGACTTTCAACGCTCCATACGACGCTGGTTTCTCTATCGACGACGACTACCAAGGTAGATCGCACTCTCCAGTTTCTTGTGACGAACACGCTAGAGCTGCTCACGTTGCTTCTGTTGTTAGATCGATCTACGAACCAATTTTGGCTTCTCACTTCGGTGAAGCTATCTTGCCAGACTTGTCTCACAGAATCGCTAAGAACGCTGCTAAGGTTTTGAGATCGGGTAAGGGTTTCTACGACTCTGTTATCATCTCTTTAGCTAAGAAGCCAGAAAAGGCTGACATGTAATAA


Testing variation from correct template...
The differences in codons b/w the correct and the co-optimized sequences is: 
For seq1: 0
For seq2: 0


Illegal Restriction Sites in New Seq1:
EcoRI - 0
XbaI - 0
SpeI - 0
PstI - 0
BglII - 0
BamHI - 0
NdeI - 0
NcoI - 0
XhoI - 0
NotI - 0
AvrII - 0
Illegal sites? null
Illegal Restriction Sites in New Seq2:
EcoRI - 0
XbaI - 0
SpeI - 0
PstI - 0
BglII - 0
BamHI - 0
NdeI - 0
NcoI - 0
XhoI - 0
NotI - 0
AvrII - 0
Illegal sites? null


Testing similarity of sequences:
The percentage difference is: 0.8288770053475936
The number of long equivalent stretches (>=20bp): 0


Outputting concurrently optimized sequences to file...
Program executed successfully!