Multiple sequence alignment - TraesCS5A01G088200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G088200 chr5A 100.000 2192 0 0 1 2192 118667955 118670146 0.000000e+00 4048
1 TraesCS5A01G088200 chr5B 95.010 1503 45 5 3 1479 123757449 123758947 0.000000e+00 2333
2 TraesCS5A01G088200 chr5B 90.890 472 28 5 1727 2192 123759649 123760111 8.600000e-174 619
3 TraesCS5A01G088200 chr5B 95.753 259 11 0 1478 1736 123758980 123759238 3.370000e-113 418
4 TraesCS5A01G088200 chr5D 93.373 1509 61 10 1 1479 113388681 113390180 0.000000e+00 2196
5 TraesCS5A01G088200 chr5D 94.965 715 30 4 1478 2192 113390213 113390921 0.000000e+00 1116
6 TraesCS5A01G088200 chr7B 84.151 265 33 7 1083 1345 293067335 293067078 4.670000e-62 248


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G088200 chr5A 118667955 118670146 2191 False 4048.000000 4048 100.000000 1 2192 1 chr5A.!!$F1 2191
1 TraesCS5A01G088200 chr5B 123757449 123760111 2662 False 1123.333333 2333 93.884333 3 2192 3 chr5B.!!$F1 2189
2 TraesCS5A01G088200 chr5D 113388681 113390921 2240 False 1656.000000 2196 94.169000 1 2192 2 chr5D.!!$F1 2191

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
237 259 0.108186 TGGCTGAGTGCTTCGTATGG 60.108 55.0 0.0 0.0 42.39 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2513 0.396435 TAGCCCACACCAAGTCTGTG 59.604 55.0 0.0 0.0 39.05 3.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 6.642540 GTGATTTCTTGAATTTGAGTGAACCC 59.357 38.462 0.00 0.00 0.00 4.11
179 180 9.661563 AATATGCATTGTGTTGAAGAAAATGAT 57.338 25.926 3.54 3.38 31.34 2.45
222 244 5.774690 TGTTATTGTCCATCTTCTTTTGGCT 59.225 36.000 0.00 0.00 32.80 4.75
237 259 0.108186 TGGCTGAGTGCTTCGTATGG 60.108 55.000 0.00 0.00 42.39 2.74
268 290 5.577945 GCATAATTTGAGTGGTGATTGTTGG 59.422 40.000 0.00 0.00 0.00 3.77
360 382 4.247258 TGCTTTGCCTCATTTATGCTTTG 58.753 39.130 0.00 0.00 0.00 2.77
373 395 0.856641 TGCTTTGTTGACTACGACGC 59.143 50.000 0.00 0.00 36.26 5.19
374 396 0.163146 GCTTTGTTGACTACGACGCC 59.837 55.000 0.00 0.00 30.97 5.68
615 642 6.495181 TGTTCTCTAGAGAGGTTTTGATGAGT 59.505 38.462 21.34 0.00 42.30 3.41
620 647 8.423906 TCTAGAGAGGTTTTGATGAGTAGTTT 57.576 34.615 0.00 0.00 0.00 2.66
623 650 7.158021 AGAGAGGTTTTGATGAGTAGTTTGAG 58.842 38.462 0.00 0.00 0.00 3.02
636 663 5.799213 AGTAGTTTGAGGAATCAGAACCTG 58.201 41.667 4.49 0.00 36.57 4.00
640 667 3.703001 TGAGGAATCAGAACCTGTTCC 57.297 47.619 6.41 14.66 39.54 3.62
644 671 3.008485 AGGAATCAGAACCTGTTCCTCAC 59.992 47.826 17.25 0.00 42.45 3.51
759 786 4.087182 TCTTCCAGTCTCAACTCGGTTAT 58.913 43.478 0.00 0.00 31.71 1.89
777 804 8.155821 TCGGTTATGTCTTGAAAATTTGTACA 57.844 30.769 0.00 0.00 0.00 2.90
790 817 8.439286 TGAAAATTTGTACAGACTTGTTTTTGC 58.561 29.630 0.00 0.00 38.76 3.68
819 846 1.308998 CCAAGTGACCTTTGAACGCT 58.691 50.000 0.00 0.00 0.00 5.07
827 854 4.803613 GTGACCTTTGAACGCTTGAAAAAT 59.196 37.500 0.00 0.00 0.00 1.82
933 963 0.250901 GCTGTCACCATGTTCCCACT 60.251 55.000 0.00 0.00 0.00 4.00
1134 1165 0.456995 GGAACGAGCAGAGGAAGACG 60.457 60.000 0.00 0.00 0.00 4.18
1155 1186 2.799917 GCGATCCTTCTACGACATGCTT 60.800 50.000 0.00 0.00 0.00 3.91
1494 1559 5.017490 AGTGAGCTAACAAGCTACTCCTTA 58.983 41.667 3.43 0.00 46.36 2.69
1538 1603 4.202050 GGAACAAGCACCATCATTATGACC 60.202 45.833 0.00 0.00 34.84 4.02
1639 1704 1.062258 TCGTTTTCGTATGCGGTCAC 58.938 50.000 2.62 0.00 44.46 3.67
1682 1747 1.698165 TCTCGTTCTGCTTGCTTACG 58.302 50.000 0.00 0.00 0.00 3.18
1687 1752 2.066262 GTTCTGCTTGCTTACGCTACA 58.934 47.619 0.00 0.00 36.97 2.74
1695 1760 4.026475 GCTTGCTTACGCTACAGTCATTAG 60.026 45.833 0.00 0.00 36.97 1.73
1736 2221 6.051717 ACTGATCAAAGGTGCTGATGTATAC 58.948 40.000 0.00 0.00 33.63 1.47
1755 2246 1.308998 CGCTGTTTCTTCCCTGTTGT 58.691 50.000 0.00 0.00 0.00 3.32
1776 2267 6.435430 TGTAACACATATCTTGATGGTTGC 57.565 37.500 0.00 0.00 0.00 4.17
1784 2275 1.003003 TCTTGATGGTTGCGACATGGA 59.997 47.619 6.39 0.00 0.00 3.41
1832 2323 2.356665 TGTCACCTTGCTTTTGCCTA 57.643 45.000 0.00 0.00 46.87 3.93
1835 2326 2.819608 GTCACCTTGCTTTTGCCTATGA 59.180 45.455 0.00 0.00 46.87 2.15
1855 2346 7.232127 CCTATGAAAAGGTTGGAATAGATGCAT 59.768 37.037 0.00 0.00 31.46 3.96
1857 2348 4.660789 AAAGGTTGGAATAGATGCATGC 57.339 40.909 11.82 11.82 0.00 4.06
1860 2351 3.635373 AGGTTGGAATAGATGCATGCAAG 59.365 43.478 26.68 0.00 0.00 4.01
1861 2352 3.633525 GGTTGGAATAGATGCATGCAAGA 59.366 43.478 26.68 13.24 0.00 3.02
1862 2353 4.098349 GGTTGGAATAGATGCATGCAAGAA 59.902 41.667 26.68 13.02 0.00 2.52
1863 2354 5.394443 GGTTGGAATAGATGCATGCAAGAAA 60.394 40.000 26.68 11.09 0.00 2.52
1864 2355 5.918426 TGGAATAGATGCATGCAAGAAAA 57.082 34.783 26.68 9.20 0.00 2.29
1865 2356 6.474140 TGGAATAGATGCATGCAAGAAAAT 57.526 33.333 26.68 6.72 0.00 1.82
1866 2357 7.585579 TGGAATAGATGCATGCAAGAAAATA 57.414 32.000 26.68 11.33 0.00 1.40
1950 2441 2.224606 TCTCTGCTTTTGAGCACTTGG 58.775 47.619 0.00 0.00 40.23 3.61
1969 2460 1.265365 GGTGTTTCTCTGCACTCAAGC 59.735 52.381 0.00 0.00 36.03 4.01
2004 2495 5.048713 CCTTCCACCTTACTTGTGATTTGAC 60.049 44.000 0.00 0.00 35.74 3.18
2022 2513 3.609853 TGACATGAGCCCACAGATTTAC 58.390 45.455 0.00 0.00 0.00 2.01
2025 2516 3.244875 ACATGAGCCCACAGATTTACACA 60.245 43.478 0.00 0.00 0.00 3.72
2041 2532 0.396435 CACAGACTTGGTGTGGGCTA 59.604 55.000 0.32 0.00 41.43 3.93
2120 2611 0.472471 ACCAACATCCGGTGACTGTT 59.528 50.000 0.00 5.03 34.69 3.16
2161 2652 8.691661 ACACTTGAATTATTACTTGGAACACT 57.308 30.769 0.00 0.00 39.29 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 6.645415 ACAAACTACAAGATAAGTCAAGACCG 59.355 38.462 0.00 0.00 0.00 4.79
179 180 5.981088 AACATCATAATTGCCACAACAGA 57.019 34.783 0.00 0.00 0.00 3.41
222 244 3.394674 TTGTTCCATACGAAGCACTCA 57.605 42.857 0.00 0.00 0.00 3.41
237 259 6.389091 TCACCACTCAAATTATGCATTGTTC 58.611 36.000 3.54 0.00 0.00 3.18
360 382 0.318445 ACACAGGCGTCGTAGTCAAC 60.318 55.000 0.00 0.00 0.00 3.18
373 395 0.322648 TCATGCACAGAGGACACAGG 59.677 55.000 0.00 0.00 0.00 4.00
374 396 1.001746 ACTCATGCACAGAGGACACAG 59.998 52.381 18.96 0.00 37.43 3.66
507 534 2.546368 CCGCCCAAGTTTTTAAAAAGGC 59.454 45.455 22.55 22.55 34.19 4.35
615 642 5.825593 ACAGGTTCTGATTCCTCAAACTA 57.174 39.130 1.59 0.00 35.18 2.24
620 647 3.251484 AGGAACAGGTTCTGATTCCTCA 58.749 45.455 17.68 0.00 42.45 3.86
623 650 3.244561 TGTGAGGAACAGGTTCTGATTCC 60.245 47.826 11.56 15.13 39.54 3.01
636 663 4.508124 CACAAACAGTAGAGTGTGAGGAAC 59.492 45.833 0.00 0.00 43.23 3.62
644 671 5.410746 AGCATGATTCACAAACAGTAGAGTG 59.589 40.000 0.00 0.00 0.00 3.51
716 743 9.171877 GGAAGAACTAGAATGTGAATCAAGAAT 57.828 33.333 0.00 0.00 0.00 2.40
728 755 6.696411 AGTTGAGACTGGAAGAACTAGAATG 58.304 40.000 0.00 0.00 37.43 2.67
759 786 8.050778 ACAAGTCTGTACAAATTTTCAAGACA 57.949 30.769 16.44 5.54 32.54 3.41
777 804 4.506288 GGTTAATTGCGCAAAAACAAGTCT 59.494 37.500 33.85 15.17 0.00 3.24
790 817 2.159382 AGGTCACTTGGGTTAATTGCG 58.841 47.619 0.00 0.00 0.00 4.85
933 963 6.939622 TGAGAAGATTCTGTGAGCTGATTTA 58.060 36.000 0.00 0.00 37.73 1.40
1134 1165 1.132588 GCATGTCGTAGAAGGATCGC 58.867 55.000 0.00 0.00 39.69 4.58
1155 1186 1.910722 GCTGATCTGCCCCTTCTCA 59.089 57.895 13.26 0.00 0.00 3.27
1403 1434 1.747355 AGCCTTCCAATCGCTGAATTG 59.253 47.619 0.00 0.00 36.57 2.32
1538 1603 6.266558 ACCAGATAGAAGAGCACCAGTTATAG 59.733 42.308 0.00 0.00 0.00 1.31
1639 1704 4.921515 TCCGTCATCAGAAAACTAAACTCG 59.078 41.667 0.00 0.00 0.00 4.18
1682 1747 5.615544 CGCAATAATGGCTAATGACTGTAGC 60.616 44.000 0.00 0.00 42.73 3.58
1687 1752 4.450976 TCACGCAATAATGGCTAATGACT 58.549 39.130 0.00 0.00 0.00 3.41
1695 1760 4.811555 TCAGTAATCACGCAATAATGGC 57.188 40.909 0.00 0.00 0.00 4.40
1736 2221 1.308998 ACAACAGGGAAGAAACAGCG 58.691 50.000 0.00 0.00 0.00 5.18
1755 2246 5.293324 GTCGCAACCATCAAGATATGTGTTA 59.707 40.000 0.00 0.00 0.00 2.41
1776 2267 3.190079 CACTAGGTCACAATCCATGTCG 58.810 50.000 0.00 0.00 41.46 4.35
1832 2323 6.684613 GCATGCATCTATTCCAACCTTTTCAT 60.685 38.462 14.21 0.00 0.00 2.57
1835 2326 4.467082 TGCATGCATCTATTCCAACCTTTT 59.533 37.500 18.46 0.00 0.00 2.27
1855 2346 9.809096 TGTTCTATGTTGTTTTATTTTCTTGCA 57.191 25.926 0.00 0.00 0.00 4.08
1861 2352 9.899226 GCTCTCTGTTCTATGTTGTTTTATTTT 57.101 29.630 0.00 0.00 0.00 1.82
1862 2353 9.289782 AGCTCTCTGTTCTATGTTGTTTTATTT 57.710 29.630 0.00 0.00 0.00 1.40
1863 2354 8.725148 CAGCTCTCTGTTCTATGTTGTTTTATT 58.275 33.333 0.00 0.00 35.61 1.40
1864 2355 8.261492 CAGCTCTCTGTTCTATGTTGTTTTAT 57.739 34.615 0.00 0.00 35.61 1.40
1865 2356 7.658179 CAGCTCTCTGTTCTATGTTGTTTTA 57.342 36.000 0.00 0.00 35.61 1.52
1866 2357 6.551385 CAGCTCTCTGTTCTATGTTGTTTT 57.449 37.500 0.00 0.00 35.61 2.43
1950 2441 2.032204 CAGCTTGAGTGCAGAGAAACAC 60.032 50.000 0.00 0.00 37.05 3.32
1969 2460 1.134280 AGGTGGAAGGCATCGAATCAG 60.134 52.381 0.00 0.00 0.00 2.90
2004 2495 3.346315 TGTGTAAATCTGTGGGCTCATG 58.654 45.455 0.00 0.00 0.00 3.07
2022 2513 0.396435 TAGCCCACACCAAGTCTGTG 59.604 55.000 0.00 0.00 39.05 3.66
2025 2516 3.306472 TTTTTAGCCCACACCAAGTCT 57.694 42.857 0.00 0.00 0.00 3.24
2062 2553 3.130340 TGAAGAACAGTTTGGCCAGTTTC 59.870 43.478 5.11 5.69 0.00 2.78
2161 2652 4.275689 CCAGTGTTCAGTGTAAATTCTGCA 59.724 41.667 6.84 0.00 0.00 4.41


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.