Multiple sequence alignment - TraesCS2A01G460300

Loading Multiple Alignment...

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 TraesCS2A01G460300 chr2A 100.000 2288 0 0 1 2288 706884751 706887038 0.000000e+00 4226
1 TraesCS2A01G460300 chr7D 93.248 1718 71 7 1 1684 621162331 621164037 0.000000e+00 2488
2 TraesCS2A01G460300 chr3B 94.584 1588 78 5 1 1582 97752877 97751292 0.000000e+00 2449
3 TraesCS2A01G460300 chr3B 93.514 1588 94 4 1 1579 200855007 200856594 0.000000e+00 2353
4 TraesCS2A01G460300 chr7A 94.266 1587 84 7 1 1582 86218349 86216765 0.000000e+00 2420
5 TraesCS2A01G460300 chr7A 90.939 1501 75 14 213 1678 638576300 638574826 0.000000e+00 1962
6 TraesCS2A01G460300 chr7B 92.370 1717 95 13 1 1682 457414300 457416015 0.000000e+00 2412
7 TraesCS2A01G460300 chr7B 93.699 1587 91 6 2 1582 480272332 480270749 0.000000e+00 2368
8 TraesCS2A01G460300 chr7B 90.798 1717 113 17 1 1681 537082178 537080471 0.000000e+00 2254
9 TraesCS2A01G460300 chr1D 92.195 1704 107 12 1 1684 467434237 467435934 0.000000e+00 2386
10 TraesCS2A01G460300 chr3D 92.167 1698 114 9 1 1680 55369174 55370870 0.000000e+00 2381
11 TraesCS2A01G460300 chr3D 88.371 1737 115 33 1 1679 562585149 562583442 0.000000e+00 2008
12 TraesCS2A01G460300 chr6B 91.895 1715 98 13 1 1681 618934448 618936155 0.000000e+00 2359
13 TraesCS2A01G460300 chr5D 93.518 1589 70 8 1 1582 424049048 424047486 0.000000e+00 2333
14 TraesCS2A01G460300 chr4D 93.073 1588 69 14 1 1577 466289378 466290935 0.000000e+00 2285
15 TraesCS2A01G460300 chr4D 88.745 462 20 3 1254 1683 398285778 398286239 9.300000e-149 536
16 TraesCS2A01G460300 chr1B 91.079 1715 107 14 1 1680 61492735 61491032 0.000000e+00 2278
17 TraesCS2A01G460300 chr5B 90.540 1723 107 23 2 1689 54116519 54114818 0.000000e+00 2228
18 TraesCS2A01G460300 chr2D 91.572 617 41 5 1679 2288 567017022 567017634 0.000000e+00 841
19 TraesCS2A01G460300 chr2D 92.647 544 32 6 1744 2285 567038758 567039295 0.000000e+00 776
20 TraesCS2A01G460300 chr1A 85.000 320 30 4 1381 1683 88345313 88345631 2.210000e-80 309
21 TraesCS2A01G460300 chr2B 79.186 442 50 20 1818 2240 680039992 680040410 3.750000e-68 268


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 TraesCS2A01G460300 chr2A 706884751 706887038 2287 False 4226 4226 100.000 1 2288 1 chr2A.!!$F1 2287
1 TraesCS2A01G460300 chr7D 621162331 621164037 1706 False 2488 2488 93.248 1 1684 1 chr7D.!!$F1 1683
2 TraesCS2A01G460300 chr3B 97751292 97752877 1585 True 2449 2449 94.584 1 1582 1 chr3B.!!$R1 1581
3 TraesCS2A01G460300 chr3B 200855007 200856594 1587 False 2353 2353 93.514 1 1579 1 chr3B.!!$F1 1578
4 TraesCS2A01G460300 chr7A 86216765 86218349 1584 True 2420 2420 94.266 1 1582 1 chr7A.!!$R1 1581
5 TraesCS2A01G460300 chr7A 638574826 638576300 1474 True 1962 1962 90.939 213 1678 1 chr7A.!!$R2 1465
6 TraesCS2A01G460300 chr7B 457414300 457416015 1715 False 2412 2412 92.370 1 1682 1 chr7B.!!$F1 1681
7 TraesCS2A01G460300 chr7B 480270749 480272332 1583 True 2368 2368 93.699 2 1582 1 chr7B.!!$R1 1580
8 TraesCS2A01G460300 chr7B 537080471 537082178 1707 True 2254 2254 90.798 1 1681 1 chr7B.!!$R2 1680
9 TraesCS2A01G460300 chr1D 467434237 467435934 1697 False 2386 2386 92.195 1 1684 1 chr1D.!!$F1 1683
10 TraesCS2A01G460300 chr3D 55369174 55370870 1696 False 2381 2381 92.167 1 1680 1 chr3D.!!$F1 1679
11 TraesCS2A01G460300 chr3D 562583442 562585149 1707 True 2008 2008 88.371 1 1679 1 chr3D.!!$R1 1678
12 TraesCS2A01G460300 chr6B 618934448 618936155 1707 False 2359 2359 91.895 1 1681 1 chr6B.!!$F1 1680
13 TraesCS2A01G460300 chr5D 424047486 424049048 1562 True 2333 2333 93.518 1 1582 1 chr5D.!!$R1 1581
14 TraesCS2A01G460300 chr4D 466289378 466290935 1557 False 2285 2285 93.073 1 1577 1 chr4D.!!$F2 1576
15 TraesCS2A01G460300 chr1B 61491032 61492735 1703 True 2278 2278 91.079 1 1680 1 chr1B.!!$R1 1679
16 TraesCS2A01G460300 chr5B 54114818 54116519 1701 True 2228 2228 90.540 2 1689 1 chr5B.!!$R1 1687
17 TraesCS2A01G460300 chr2D 567017022 567017634 612 False 841 841 91.572 1679 2288 1 chr2D.!!$F1 609
18 TraesCS2A01G460300 chr2D 567038758 567039295 537 False 776 776 92.647 1744 2285 1 chr2D.!!$F2 541

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
496 499 1.166129 CGTCCACTCGAGGAAGAAGA 58.834 55.0 18.41 0.91 39.92 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1894 0.094558 CGAACATGCGCGCTAGAAAA 59.905 50.0 33.29 11.41 0.0 2.29 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
140 141 3.252627 TAGCTGGCATGTGCACCGT 62.253 57.895 15.69 0.00 44.36 4.83
377 380 4.321304 CGTCTTCAGCTCTTCTTTAGTGGA 60.321 45.833 0.00 0.00 0.00 4.02
467 470 1.509703 GTGTTCTCGAACTTGGTCCC 58.490 55.000 10.75 0.00 41.67 4.46
484 487 2.561956 CCGTCACCAGTCGTCCACT 61.562 63.158 0.00 0.00 34.67 4.00
496 499 1.166129 CGTCCACTCGAGGAAGAAGA 58.834 55.000 18.41 0.91 39.92 2.87
646 654 5.137255 TGAGTAAATATAGGGGGTGGAGAGA 59.863 44.000 0.00 0.00 0.00 3.10
648 656 6.458784 AGTAAATATAGGGGGTGGAGAGAAA 58.541 40.000 0.00 0.00 0.00 2.52
683 693 7.542534 ACAGTCATGTCGTTTTAACTACAAA 57.457 32.000 4.40 0.00 37.98 2.83
759 769 6.209391 TGCAGATCGAGGATAACAATGAGATA 59.791 38.462 0.00 0.00 0.00 1.98
834 844 2.182030 CCCGACGAGGTTGAGCTC 59.818 66.667 6.82 6.82 38.74 4.09
1065 1077 4.265073 AGTTCAAGCTCAGAAACAACACT 58.735 39.130 3.40 0.00 0.00 3.55
1077 1089 1.228063 CAACACTGGCTGCTCCTGT 60.228 57.895 0.00 3.09 46.46 4.00
1106 1118 2.695359 GGTCAAGCTGATGAACGGTAA 58.305 47.619 0.00 0.00 0.00 2.85
1161 1175 3.875727 CAGCCGTTCATCAGATCAAGATT 59.124 43.478 0.00 0.00 0.00 2.40
1225 1239 2.092323 AGGTCATCATCTTCGACGACA 58.908 47.619 0.00 0.00 0.00 4.35
1229 1243 3.859961 GTCATCATCTTCGACGACAATGT 59.140 43.478 14.83 0.00 0.00 2.71
1341 1365 6.871492 TCGAGTCTGCTTTGAACATGTTTATA 59.129 34.615 13.36 2.86 0.00 0.98
1458 1500 0.250166 GCCGAAGTGTGGTGGTAACT 60.250 55.000 0.00 0.00 37.61 2.24
1479 1521 2.334977 TCACCAACTAGCCAAAGAGGA 58.665 47.619 0.00 0.00 41.22 3.71
1486 1528 2.431057 ACTAGCCAAAGAGGATACCACG 59.569 50.000 0.00 0.00 41.22 4.94
1523 1565 1.411977 CAACCAAACACCATGCCTTGA 59.588 47.619 0.00 0.00 0.00 3.02
1525 1567 0.037975 CCAAACACCATGCCTTGAGC 60.038 55.000 0.00 0.00 44.14 4.26
1625 1705 6.847956 GCATTTGCATAGCCAAATTGAATA 57.152 33.333 0.00 0.00 41.97 1.75
1691 1774 2.950309 CACGTCCCTAGTGTAGCATAGT 59.050 50.000 0.00 0.00 35.08 2.12
1731 1814 3.660111 GCACAGCACCCGAACCAC 61.660 66.667 0.00 0.00 0.00 4.16
1756 1839 1.728971 CACATCTTCACTTCTGTCGGC 59.271 52.381 0.00 0.00 0.00 5.54
1806 1889 0.318955 GTGTGCACATCCAGGTTTGC 60.319 55.000 24.69 1.49 35.45 3.68
1807 1890 1.290009 GTGCACATCCAGGTTTGCC 59.710 57.895 13.17 0.00 33.86 4.52
1808 1891 2.267351 TGCACATCCAGGTTTGCCG 61.267 57.895 7.09 0.00 40.50 5.69
1811 1894 0.673437 CACATCCAGGTTTGCCGTTT 59.327 50.000 0.00 0.00 40.50 3.60
1846 1929 3.366396 TGTTCGCTTCCTAGGAGATCTT 58.634 45.455 12.26 0.00 0.00 2.40
1923 2010 6.099159 ACTAGTCAGGGTCAGTCTAAAAAC 57.901 41.667 0.00 0.00 0.00 2.43
1927 2014 1.162698 GGGTCAGTCTAAAAACGGGC 58.837 55.000 0.00 0.00 0.00 6.13
1946 2034 0.449388 CGGAGCTTTGAACATGGAGC 59.551 55.000 0.00 0.00 35.42 4.70
2114 2205 6.358118 AGTATACATGTTAACCACGCAATG 57.642 37.500 2.30 1.63 0.00 2.82
2143 2234 2.821378 CAGCCCACATGATTCAAACTCA 59.179 45.455 0.00 0.00 0.00 3.41
2181 2272 1.371183 CCCTGTTCTCGGCACTTGA 59.629 57.895 0.00 0.00 0.00 3.02
2270 2361 8.908903 TGGTGTGAAATACTGTCTTTTAAACAT 58.091 29.630 6.23 0.00 0.00 2.71
2271 2362 9.180678 GGTGTGAAATACTGTCTTTTAAACATG 57.819 33.333 6.23 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
289 290 1.076485 GCTGGGCCATGAATCAGGT 60.076 57.895 6.72 0.00 0.00 4.00
377 380 2.093500 TCTAATGCCGTGCTCATGAAGT 60.093 45.455 0.00 0.00 0.00 3.01
467 470 1.081376 GAGTGGACGACTGGTGACG 60.081 63.158 0.00 0.00 33.83 4.35
476 479 1.166129 CTTCTTCCTCGAGTGGACGA 58.834 55.000 12.31 3.69 40.00 4.20
496 499 0.345502 TGGGGTATTGGCTAGAGGGT 59.654 55.000 0.00 0.00 0.00 4.34
560 564 1.612442 TCAACCTTCCTCCTCCCCG 60.612 63.158 0.00 0.00 0.00 5.73
646 654 5.543507 ACATGACTGTCACTCTTCTCTTT 57.456 39.130 13.50 0.00 0.00 2.52
683 693 6.059787 AGAGTTCATGGCTAATTCAAGAGT 57.940 37.500 0.00 0.00 0.00 3.24
846 856 1.511768 CGTCTTCGGGTCTTCCTCC 59.488 63.158 0.00 0.00 0.00 4.30
878 888 2.281345 CCTCCATGCCCTCATCGC 60.281 66.667 0.00 0.00 0.00 4.58
1056 1068 0.106519 AGGAGCAGCCAGTGTTGTTT 60.107 50.000 0.00 0.00 40.02 2.83
1065 1077 1.679311 CACCTTACAGGAGCAGCCA 59.321 57.895 0.00 0.00 37.67 4.75
1077 1089 1.003839 CAGCTTGACCGCCACCTTA 60.004 57.895 0.00 0.00 0.00 2.69
1161 1175 0.682292 TGAACGTCACCATGTAGCCA 59.318 50.000 0.00 0.00 0.00 4.75
1225 1239 3.738982 TGTTGACGACCTCAATGACATT 58.261 40.909 0.00 0.00 41.10 2.71
1229 1243 3.130633 CACTTGTTGACGACCTCAATGA 58.869 45.455 0.00 0.00 41.10 2.57
1341 1365 8.604035 CAGATATAACAGTTCAACGCATAAACT 58.396 33.333 0.00 0.00 33.63 2.66
1458 1500 2.708861 TCCTCTTTGGCTAGTTGGTGAA 59.291 45.455 0.00 0.00 35.26 3.18
1479 1521 0.464373 CAAGGCCTGATGCGTGGTAT 60.464 55.000 5.69 0.00 42.61 2.73
1486 1528 1.105457 TTGTATGCAAGGCCTGATGC 58.895 50.000 20.57 20.57 42.86 3.91
1523 1565 3.619979 GCCTACATGTTAGTCCACAAGCT 60.620 47.826 2.30 0.00 0.00 3.74
1525 1567 3.937814 TGCCTACATGTTAGTCCACAAG 58.062 45.455 2.30 0.00 0.00 3.16
1617 1694 9.090692 GCATTGCATACACTTCTTTATTCAATT 57.909 29.630 3.15 0.00 0.00 2.32
1618 1695 7.433131 CGCATTGCATACACTTCTTTATTCAAT 59.567 33.333 9.69 0.00 0.00 2.57
1623 1700 4.036734 CCCGCATTGCATACACTTCTTTAT 59.963 41.667 9.69 0.00 0.00 1.40
1625 1705 2.164219 CCCGCATTGCATACACTTCTTT 59.836 45.455 9.69 0.00 0.00 2.52
1685 1768 0.464452 ACACCGGCTTCCTACTATGC 59.536 55.000 0.00 0.00 0.00 3.14
1689 1772 1.328430 GCCTACACCGGCTTCCTACT 61.328 60.000 0.00 0.00 46.63 2.57
1691 1774 3.625099 GCCTACACCGGCTTCCTA 58.375 61.111 0.00 0.00 46.63 2.94
1756 1839 4.838486 GCTCTCAGGTCGCCGACG 62.838 72.222 11.60 0.00 42.01 5.12
1780 1863 0.319813 TGGATGTGCACACGAGACAG 60.320 55.000 24.37 0.00 0.00 3.51
1811 1894 0.094558 CGAACATGCGCGCTAGAAAA 59.905 50.000 33.29 11.41 0.00 2.29
1822 1905 1.137086 TCTCCTAGGAAGCGAACATGC 59.863 52.381 13.77 0.00 0.00 4.06
1835 1918 2.768527 TGCTGGGAACAAGATCTCCTAG 59.231 50.000 7.51 7.51 41.88 3.02
1838 1921 1.280421 AGTGCTGGGAACAAGATCTCC 59.720 52.381 0.00 0.00 42.06 3.71
1846 1929 1.005037 CTGCGTAGTGCTGGGAACA 60.005 57.895 0.00 0.00 46.63 3.18
1894 1981 3.764434 GACTGACCCTGACTAGTCATGAA 59.236 47.826 25.35 10.91 41.90 2.57
1895 1982 3.010696 AGACTGACCCTGACTAGTCATGA 59.989 47.826 25.35 5.03 41.90 3.07
1896 1983 3.360867 AGACTGACCCTGACTAGTCATG 58.639 50.000 25.35 21.52 41.90 3.07
1923 2010 2.040544 ATGTTCAAAGCTCCGCCCG 61.041 57.895 0.00 0.00 0.00 6.13
1927 2014 0.449388 GCTCCATGTTCAAAGCTCCG 59.551 55.000 0.00 0.00 0.00 4.63
1942 2030 5.238868 TGAACGTAGAGATGTATACTGCTCC 59.761 44.000 16.73 6.76 0.00 4.70
1946 2034 6.360947 GCACATGAACGTAGAGATGTATACTG 59.639 42.308 0.00 0.00 0.00 2.74
2083 2174 6.420008 GTGGTTAACATGTATACTCCGATCAC 59.580 42.308 8.10 0.00 0.00 3.06
2114 2205 4.883585 TGAATCATGTGGGCTGAAATAGTC 59.116 41.667 0.00 0.00 0.00 2.59
2165 2256 2.600731 CTAGTCAAGTGCCGAGAACAG 58.399 52.381 0.00 0.00 0.00 3.16
2181 2272 2.868964 TAAGTGGATGGGCTCCTAGT 57.131 50.000 0.00 0.00 45.21 2.57


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

AutoCloner maintained by Alex Coulton.