File: example1.txt

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>At1g02580 mRNA (2291 bp) UTR's and CDS
aggcgagtggttaatggagaaggaaaaccatgaggacgatggtgagggtttgccacccgaactaaatcagataaaa
gagcaaatcgaaaaggagagatttctgcatatcaagagaaaattcgagctgagatacattccaagtgtggctactc
atgcttcacaccatcaatcgtttgacttaaaccagcccgctgcagaggatgataatggaggagacaacaaatcact
tttgtcgagaatgcaaaacccacttcgtcatttcagtgcctcatctgattataattcttacgaagatcaaggttat
gttcttgatgaggatcaagattatgctcttgaagaagatgtaccattatttcttgatgaagatgtaccattattac
caagtgtcaagcttccaattgttgagaagctaccacgatccattacatgggtcttcaccaaaagtagccagctgat
ggctgaaagtgattctgtgattggtaagagacaaatctattatttgaatggtgaggcactagaattgagcagtgaa
gaagatgaggaagatgaagaagaagatgaggaagaaatcaagaaagaaaaatgcgaattttctgaagatgtagacc
gatttatatggacggttgggcaggactatggtttggatgatctggtcgtgcggcgtgctctcgccaagtacctcga
agtggatgtttcggacatattggaaagatacaatgaactcaagcttaagaatgatggaactgctggtgaggcttct
gatttgacatccaagacaataactactgctttccaggattttgctgatagacgtcattgccgtcgttgcatgatat
tcgattgtcatatgcatgagaagtatgagcccgagtctagatccagcgaagacaaatctagtttgtttgaggatga
agatagacaaccatgcagtgagcattgttacctcaaggtgaggagtgtgacagaagctgatcatgtgatggataat
gataactctatatcaaacaagattgtggtctcagatccaaacaacactatgtggacgcctgtagagaaggatcttt
acttgaaaggaattgagatatttgggagaaacagttgtgatgttgcattaaacatacttcgggggcttaagacgtg
cctagagatttacaattacatgcgcgaacaagatcaatgtactatgtcattagaccttaacaaaactacacaaaga
cacaatcaggttaccaaaaaagtatctcgaaaaagtagtaggtcggtccgcaaaaaatcgagactccgaaaatatg
ctcgttatccgcctgctttaaagaaaacaactagtggagaagctaagttttataagcactacacaccatgcacttg
caagtcaaaatgtggacagcaatgcccttgtttaactcacgaaaattgctgcgagaaatattgcgggtgctcaaag
gattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctg
ctaatcgtgaatgcgatcca  gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacacc
agtgcaaatccaatgcaagaacatgcaattcctccttcaaaccaataaaaagattctcattggaaagtctgatgtt
catggatggggtgcatttacatgggactctct  taaaaagaatgagtatctcggagaatatactggagaactgatca
ctcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatca
gctcgaaatcgatgctcgccgtaaaggaaacgagttcaaatttctcaatcactcagcaagacctaactgctacgcc
aagttgatgattgtgagaggagatcagaggattggtctatttgcggagagagcaatcgaagaaggtgaggagcttt
tcttcgactactgctatggaccagaacatgcggattggtcgcgtggtcgagaacctagaaagactggtgcttctaa
aaggtctaaggaagcccgtccagctcgttagtttttgatctgaggagaagcagcaattcaagcagtccttttttta
tgttatggtatatcaattaataatgtaatgctattttgtgttactaaaccaaaacttaagtttctgttttatttgt
tttagggtgttttgtttgtatcatatgtgtcttaactttcaaagttttctttttgtatttcaatttaaaaacaatg
tttatgttgtt

>At1g65300: mRNA 837bp
atgaagagaaagatgaagttatcgttaatagaaaacagtgtatcgaggaaaacaacattcaccaaaaggaagaaag
ggatgacgaagaaactaaccgagctagtcactctatgtggtgttgaagcatgtgcggtcgtctatagtccgttcaa
ctcgatcccggaggcttggccgtcaagggaaggcgttgaagacgtggtgtcgaaatttatggagttgtcggtgttg
gaccggaccaagaagatggtggatcaagagacttttataagtcaaaggatcgccaaagaaaaagagcagctgcaga
agctacgtgatgagaaccataattctcagattcgggagttaatgtttggttgtctcaaaggggagacgaatgtgta
taatcttgatggaagggatcttcaagatttgagtttatatattgataagtatcttaatggtcttactcgcaggatt
ga  gatcctTAttgagaacggtgagtcttcttcatctttacctcttcctattgttgcgaatgcagctgcaccagtcg
gatttgatggtcctatgtttcaatatcataatcaaaatcagcaaaagccggttcaattccaatatcaggctcttta
tgatttttatgatcagattccaaagaaaattcatggttt  taatatgaatatgaataaggattcgaatcaaagtatg
gttttggatttgaatcaaaatcttaatgatggagaggacgagggcattccttgcatggacaacaacaactaccacc
ccgaaatcgattgtctcgctaccgtcaccactgcccccactgatgtttgtgctcctaacatcaccaatgatctcta
g

>At1g65300: mRNA 837bp (shortened at end)
atgaagagaaagatgaagttatcgttaatagaaaacagtgtatcgaggaaaacaacattcaccaaaaggaagaaag
ggatgacgaagaaactaaccgagctagtcactctatgtggtgttgaagcatgtgcggtcgtctatagtccgttcaa
ctcgatcccggaggcttggccgtcaagggaaggcgttgaagacgtggtgtcgaaatttatggagttgtcggtgttg
gaccggaccaagaagatggtggatcaagagacttttataagtcaaaggatcgccaaagaaaaagagcagctgcaga
agctacgtgatgagaaccataattctcagattcgggagttaatgtttggttgtctcaaaggggagacgaatgtgta
taatcttgatggaagggatcttcaagatttgagtttatatattgataagtatcttaatggtcttactcgcaggatt
gagatcctTAttgagaacggtgagtcttcttcatctttacctcttcctattgttgcgaatgcagctgcaccagtcg
gatttgatggtcctatgtttcaatatcataatcaaaatcagcaaaagccggttcaattccaatatcaggctcttta
tgatttttatgatcag


>At1g65300: mRNA 837bp (shortened from start)
ttcatctttacctcttcctattgttgcgaatgcagctgcaccagtcg
gatttgatggtcctatgtttcaatatcataatcaaaatcagcaaaagccggttcaattccaatatcaggctcttta
tgatttttatgatcagattccaaagaaaattcatggttttaatatgaatatgaataaggattcgaatcaaagtatg
gttttggatttgaatcaaaatcttaatgatggagaggacgagggcattccttgcatggacaacaacaactaccacc
ccgaaatcgattgtctcgctaccgtcaccactgcccccactgatgtttgtgctcctaacatcaccaatgatctcta
g


>At1g02580 - shortened for test - inserted cutpoint
gattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctg
ctaatcgtgaatgcgatcca  gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacacc
agtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggt
tttaattggggtgcatttacatgggactctct  taaaaagaatgagtatctcggagaatatactggagaactgatca
ctcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatca