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COI DNA barcode primer locations
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Reference COI is NC_003128 Buteo buteo COI | |
TZBRD035-15.COI-5P [648bp] ctgatctttggtgnatgagcaggcatagccggcacagcacttagcctactaatccgcgcagaactaggacagccaggaacactattgggagacgaccaaatctacaatgtaatcgtaacagcccacgctttcgtcataatcttcttcatagtcatacctattatgatcggaggcttcggaaactgactggttccactcataattggcgccccagacatagcattcccccgcataaataatatgagcttctgactcctcccaccttcttttctcctcctactagcctcctctacagtagaagccggggctggcactggatgaactgtttatccacccctagccggtaatcttgcccacgcgggcgcatcagtagacctggctattttttcccttcacttggcaggcgtgtcgtccatcttaggagctattaactttatcaccacaattattaacataaagccccctgcactatcacaatatcaaacacccctcttcgtatgatccgtcctcattactgctatcctcttactactatccctgccagtcctagccgccgggattacaatactcctcaccgatcgcaacctcaacactacattctttgaccctgcaggaggaggagacccaatcctgtatcaacacctattc | |
TZBRD019-15.COI-5P tcttcggcgcctgagctggtatagtcggcaccgccctcagcttactcatccgtgcagaactcggccaacccggcacactcctaggtgacgaccaaatttataacgtaatcgttaccgcacatgccttcgtaataatcttcttcatagttataccaatcatgatcggaggattcggaaactgacttgttccactcataattggcgctcccgacatagcctttccacgcataaacaacataagcttctgactactccccccatccttcctcctcctactagcttcctcaacagtagaagcaggagccggtactggatgaactgtctatcctcccttagctggcaacatagcccatgccggagcttcagtagacctagccatcttctctctacacttagccggagtttcatccattctaggggcgatcaacttcatcacaaccgccattaatataaaacccccagcactctcccagtaccaaacacccctgtttgtatgatctgtactcatcactgccgtccttctactactctcactcccagtcctagccgctggcatcactatactacttacagaccgaaacctaaacacaacattctttgaccctgccggcggaggcgatcccatcctctaccaacatctcttc | |
SYROC231-15.COI gacactttatttcatttttggagcttgagcaggaatagtgggaacatctttaagaattttaattcgaacagaattaggtcatccaggagctttaattggtgatgatcaaatttataatgtaattgtaacagctcatgcttttgtaataattttttttatagtaatacctattataattggaggtttcggaaactgattagttcctttaatattaggagctcctgatatagcttttcctcgaataaataatataagtttttgaatacttcccccatctcttactcttcttcttataagaagtatagtagaaaatggagctggaactggctgaaccgtttaccctcccctttcttctactattgctcatagaggagcttcagttgatttagctattttttctcttcatcttgctggaatttcttcaattttaggagcagtaaattttattactacagtaattaatatacgaagctctggaattttatttgatcgaatacctttatttgtctgatcagtattaattactgctattcttttattattatctcttccagttttagcaggagcaattactatattattaactgatcgaaatttaaatacatccttttttgatcctgcaggtggaggtgatcctattttatatcaacacttattt | |
FARAN267-14.COI-5P (fish) cctttatctagtatttggtgcctgagccggaatagtaggcacagctctaagcctcctcattcgagcggagctaagccaacccggcgccctcctgggagacgaccaaatttataatgtccttgttacagcgcatgcgttcgtaataatcttctttatagtaataccaattatgatcgggggttttggaaactgacttgtacccttgataatcggggccccggacatagcattcccccggataaacaacatgagcttttgactccttcccccatcttttctcctcctccttgcctcttcgggggtggaggcgggcgctggaacggggtgaacagtttacccccctctctcaggtaacttagcccacgcaggggcctccgttgatttaacaatcttttccctccacctagcaggaatttcttcgatcctcggagcaattaatttcattacaaccatcatcaacatgaaaccccctgcgatctctcagtaccagacacccctcttcgtctggtccgtacttgtcacggcggtcctgctcctcctctctcttcccgtcctcgcagccggtatcactatgctcctgacagatcgtaacctaaacaccaccttcttcgaccccgccgggggaggagacccaatcctttaccaacacctg | |
gtgacatttatcaatcgatgattattctcaaccaatcacaaagacatcggcaccctatacctaatcttcggtgcctgagccggtatagtcggcaccgccctcagcctacttattcgtgcagaactcggccaaccaggcacactcctaggtgacgaccagatctacaacgtaatcgttaccgcacatgccttcgtaataattttctttatagttataccaattatgatcggaggcttcggaaactgacttgttccactcataatcggcgcccccgatatagccttcccacgcataaacaacataagcttctgactacttcctccatcctttctcctcctcctagcctcctcaacagtagaagcaggagccggcactggatgaactgtctatcccccactagctggcaacatagcccatgccggagcttcagtagacctagccatcttctccctccacttagccggagtctcgtccattctaggagcaatcaactttatcacaaccgccatcaacataaagcccccagccctctcccagtaccaaacacccctattcgtatgatctgtcctcattaccgctgtccttctactactctcactcccagtcctagccgccggcattaccatactacttacagaccgaaacctaaacacaacattctttgaccccgccggcggaggtgatcctatcctataccaacatctcttttgattcttcggacacccagaagtttacatcctaatcctacccggcttcggaattatctcccacgtagtaacatactatgcaggcaaaaaagaaccattcggttacataggaatagtatgagccatactatcaatcggattcctagggttcatcgtatgagctcatcacatatttacagtagggatagacgtggacacccgagcatacttcacatctgctactataatcattgctatcccaactggtattaaagtcttcagctgactagcaacgctccacggaggaactatcaaatgagaccctccaatattatgagcccttggcttcatcttcctctttaccatcggaggcctaacaggaatcgtcctagctaactcctcactagacatcgctctacacgacgcatactatgtagttgcccacttccactacgtcctctcaataggagctgtctttgccattctagcaggattcacccactgattccctctattaactggattcaccctccaccccacatgagctaaagcccacttcggggttatattcacaggagtaaatctaactttcttcccacaacacttcctaggcctcgccggaatacctcgacgatattccgactacccagacgcctataccctatgaaacaccctatcctctatcggctcactaatctcaataacagccgtaatcatactaatattcatcatctgagaagcctttgcctcaaaacgaaaaatcctacaaccagaactaaccacaaccaatgtcgaatgaatccacggctgcccacctccataccacacctttgaagaaccagcctttgttcaagtacaagaaagg | |
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minbarF1 tccactaatcacaargatattggtac gctcatgccttcattatgattttc minibarR1 reverse complement caggatttggaattatctcccacgt BirdR1 | |
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1 54 61 180 708 748 | |
BirdF1 ttctccaaccacaaagacattggcac | |
minbarF1 tccactaatcacaargatattggtac | |
minbarR1 gaaaatcataatgaaggcatgagc | |
A universal DNA mini-barcode for biodiversity analysis | |
http://dx.doi.org/10.1186/1471-2164-9-214 | |
Applicability of DNA barcoding to museum specimens of birds from the Democratic Republic of the Congo | |
http://biostor.org/reference/137082 | |
Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S., & Francis, C. M. (2004, September 28). Identification of Birds through DNA Barcodes. (Charles Godfray, Ed.)PLoS Biology. Public Library of Science (PLoS). http://doi.org/10.1371/journal.pbio.0020312 |
Author
rdmpage
commented
May 10, 2016
NGS barcodes used in Rudolf Meier's lab, e.g. Meier, R., Wong, W., Srivathsan, A., & Foo, M. (2015). $1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples. Cladistics, 32(1), 100–110. doi:10.1111/cla.12115
Below is traditional COI barcode from LC096192 and NGS barcode KP461672 for same species, with the m1CO1intF primer (forward). Bird COI sequence and mini barcode primer from above is shown for comparison (insect sequences are aligned with bird sequence to make coordinates compatible).
Tanytarsus oscillans $1 barcode NGS
LC096192.1 aacattatattttatttttggagcctgatctggaatagtagggacttctttaagtatactaatccgtgcagaattaggacaccccggaacatttatcggtgatgaccaaatttataatgtaattgttacagcccacgcttttattataattttttttatagttatgcctattttaattggaggatttggaaattgacttcttcctttaatattaggggccccagatatagccttccctcgaataaataatataagtttttgacttttaccaccctctcttacacttcttctttctagttcaattgtagaaaatggagccggaacaggatgaacagtttatcctcccctatctgctagaattgctcacagaggggcttctgttgatttagctattttttctcttcatcttgcagggatttcttctattttaggatctgtaaattttattactactgctattaatatacgagcaaatggaattacccttgatcgcatacccttatttgtttgatcagttgtaattacaactgttcttcttcttctttcccttccggttcttgctggtgcaattactatacttttaacagatcgaaatttaaatacttcattttttgatccagcaggaggaggagatcctattctttatcaacacttattt
KP461672 cctatctgctagaattgctcatagtggagcctctgttgatttagctattttttctcttcaccttgcaggaatttcttccattttaggttcagtaaattttattactacagctatcaatatacgagcaaatggaattacacttgaccgaatacctttatttgtttgatccgttgtaattacaactgttctccttcttctttcccttccagttctagctggtgcaattactatacttttaacagaccgaaatttaaacacatcattttttgacccggcaggaggaggggaccctatcctctatcaacatttattt
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m1CO1intF GGWACWGGWTGAACWGTWTAYCCYCC
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371
gtgacatttatcaatcgatgattattctcaaccaatcacaaagacatcggcaccctatacctaatcttcggtgcctgagccggtatagtcggcaccgccctcagcctacttattcgtgcagaactcggccaaccaggcacactcctaggtgacgaccagatctacaacgtaatcgttaccgcacatgccttcgtaataattttctttatagttataccaattatgatcggaggcttcggaaactgacttgttccactcataatcggcgcccccgatatagccttcccacgcataaacaacataagcttctgactacttcctccatcctttctcctcctcctagcctcctcaacagtagaagcaggagccggcactggatgaactgtctatcccccactagctggcaacatagcccatgccggagcttcagtagacctagccatcttctccctccacttagccggagtctcgtccattctaggagcaatcaactttatcacaaccgccatcaacataaagcccccagccctctcccagtaccaaacacccctattcgtatgatctgtcctcattaccgctgtccttctactactctcactcccagtcctagccgccggcattaccatactacttacagaccgaaacctaaacacaacattctttgaccccgccggcggaggtgatcctatcctataccaacatctcttttgattcttcggacacccagaagtttacatcctaatcctacccggcttcggaattatctcccacgtagtaacatactatgcaggcaaaaaagaaccattcggttacataggaatagtatgagccatactatcaatcggattcctagggttcatcgtatgagctcatcacatatttacagtagggatagacgtggacacccgagcatacttcacatctgctactataatcattgctatcccaactggtattaaagtcttcagctgactagcaacgctccacggaggaactatcaaatgagaccctccaatattatgagcccttggcttcatcttcctctttaccatcggaggcctaacaggaatcgtcctagctaactcctcactagacatcgctctacacgacgcatactatgtagttgcccacttccactacgtcctctcaataggagctgtctttgccattctagcaggattcacccactgattccctctattaactggattcaccctccaccccacatgagctaaagcccacttcggggttatattcacaggagtaaatctaactttcttcccacaacacttcctaggcctcgccggaatacctcgacgatattccgactacccagacgcctataccctatgaaacaccctatcctctatcggctcactaatctcaataacagccgtaatcatactaatattcatcatctgagaagcctttgcctcaaaacgaaaaatcctacaaccagaactaaccacaaccaatgtcgaatgaatccacggctgcccacctccataccacacctttgaagaaccagcctttgttcaagtacaagaaagg
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minbarF1 tccactaatcacaargatattggtac gctcatgccttcattatgattttc minibarR1 reverse complement caggatttggaattatctcccacgt BirdR1
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