Multiple sequence alignment - TraesCS6A01G170500

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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 TraesCS6A01G170500 chr6A 100.000 2476 0 0 1 2476 180929562 180927087 0.000000e+00 4573.0
1 TraesCS6A01G170500 chr6A 88.125 320 33 3 2150 2465 606307026 606307344 2.320000e-100 375.0
2 TraesCS6A01G170500 chr2D 96.146 1505 56 2 1 1503 531631183 531629679 0.000000e+00 2457.0
3 TraesCS6A01G170500 chr5A 94.719 1515 76 4 1 1513 122126472 122127984 0.000000e+00 2351.0
4 TraesCS6A01G170500 chr6B 94.682 1354 67 4 1 1350 546087719 546086367 0.000000e+00 2097.0
5 TraesCS6A01G170500 chr6B 88.341 669 48 15 1502 2141 237704825 237704158 0.000000e+00 776.0
6 TraesCS6A01G170500 chr6B 86.970 330 36 6 2150 2474 681233451 681233124 5.030000e-97 364.0
7 TraesCS6A01G170500 chr4A 91.711 1508 122 3 1 1505 486299632 486298125 0.000000e+00 2089.0
8 TraesCS6A01G170500 chr4B 91.018 1503 133 2 1 1501 591235040 591233538 0.000000e+00 2026.0
9 TraesCS6A01G170500 chr4B 86.970 330 34 5 2150 2471 15923651 15923323 1.810000e-96 363.0
10 TraesCS6A01G170500 chr4B 82.171 129 14 6 1735 1860 63934855 63934977 4.360000e-18 102.0
11 TraesCS6A01G170500 chr4B 80.620 129 15 9 1735 1860 63798620 63798741 9.430000e-15 91.6
12 TraesCS6A01G170500 chr6D 90.915 1508 126 9 1 1504 128082525 128084025 0.000000e+00 2015.0
13 TraesCS6A01G170500 chr6D 91.332 473 30 6 1520 1992 138367367 138366906 9.660000e-179 636.0
14 TraesCS6A01G170500 chr6D 90.680 397 30 6 2082 2474 138366632 138366239 2.820000e-144 521.0
15 TraesCS6A01G170500 chr5D 92.718 1126 71 11 1 1122 511890221 511889103 0.000000e+00 1615.0
16 TraesCS6A01G170500 chr5D 87.616 323 35 4 2150 2470 423970821 423970502 1.080000e-98 370.0
17 TraesCS6A01G170500 chr5D 86.095 338 33 10 2148 2474 537690079 537689745 3.920000e-93 351.0
18 TraesCS6A01G170500 chr5D 86.239 327 40 4 2151 2474 555423238 555422914 1.410000e-92 350.0
19 TraesCS6A01G170500 chr1D 92.371 1101 81 3 346 1444 74292546 74293645 0.000000e+00 1565.0
20 TraesCS6A01G170500 chr7D 83.521 1511 229 18 1 1502 244949397 244950896 0.000000e+00 1393.0
21 TraesCS6A01G170500 chr7A 83.850 1418 213 13 90 1501 223791337 223792744 0.000000e+00 1336.0
22 TraesCS6A01G170500 chr7A 84.507 142 20 2 1721 1861 93123612 93123752 3.320000e-29 139.0
23 TraesCS6A01G170500 chr2B 87.195 328 33 7 2150 2471 43229135 43228811 5.030000e-97 364.0
24 TraesCS6A01G170500 chr2A 88.026 309 33 2 2150 2454 619858025 619858333 1.810000e-96 363.0
25 TraesCS6A01G170500 chr2A 91.304 46 3 1 1762 1806 775035814 775035859 7.390000e-06 62.1
26 TraesCS6A01G170500 chr3A 87.179 117 14 1 1746 1861 624718736 624718620 5.560000e-27 132.0
27 TraesCS6A01G170500 chr3D 85.600 125 17 1 1746 1869 481580271 481580147 2.000000e-26 130.0
28 TraesCS6A01G170500 chr3B 88.136 59 5 2 1761 1818 245968763 245968706 4.420000e-08 69.4


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 TraesCS6A01G170500 chr6A 180927087 180929562 2475 True 4573.0 4573 100.000 1 2476 1 chr6A.!!$R1 2475
1 TraesCS6A01G170500 chr2D 531629679 531631183 1504 True 2457.0 2457 96.146 1 1503 1 chr2D.!!$R1 1502
2 TraesCS6A01G170500 chr5A 122126472 122127984 1512 False 2351.0 2351 94.719 1 1513 1 chr5A.!!$F1 1512
3 TraesCS6A01G170500 chr6B 546086367 546087719 1352 True 2097.0 2097 94.682 1 1350 1 chr6B.!!$R2 1349
4 TraesCS6A01G170500 chr6B 237704158 237704825 667 True 776.0 776 88.341 1502 2141 1 chr6B.!!$R1 639
5 TraesCS6A01G170500 chr4A 486298125 486299632 1507 True 2089.0 2089 91.711 1 1505 1 chr4A.!!$R1 1504
6 TraesCS6A01G170500 chr4B 591233538 591235040 1502 True 2026.0 2026 91.018 1 1501 1 chr4B.!!$R2 1500
7 TraesCS6A01G170500 chr6D 128082525 128084025 1500 False 2015.0 2015 90.915 1 1504 1 chr6D.!!$F1 1503
8 TraesCS6A01G170500 chr6D 138366239 138367367 1128 True 578.5 636 91.006 1520 2474 2 chr6D.!!$R1 954
9 TraesCS6A01G170500 chr5D 511889103 511890221 1118 True 1615.0 1615 92.718 1 1122 1 chr5D.!!$R2 1121
10 TraesCS6A01G170500 chr1D 74292546 74293645 1099 False 1565.0 1565 92.371 346 1444 1 chr1D.!!$F1 1098
11 TraesCS6A01G170500 chr7D 244949397 244950896 1499 False 1393.0 1393 83.521 1 1502 1 chr7D.!!$F1 1501
12 TraesCS6A01G170500 chr7A 223791337 223792744 1407 False 1336.0 1336 83.850 90 1501 1 chr7A.!!$F2 1411

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
564 569 1.097547 ATCTGGCGTACCTTGCATGC 61.098 55.0 11.82 11.82 36.63 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 2517 1.129811 GACGGTATTTCCTTTGCCACG 59.87 52.381 0.0 0.0 0.0 4.94 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
125 127 5.121298 GCGGGAGTAAACTCGTTAAGAAATT 59.879 40.000 4.13 0.00 43.76 1.82
157 159 2.749776 CGGGTTGGAAATGGACAAAAC 58.250 47.619 0.00 0.00 0.00 2.43
299 301 4.397417 GGGATGAAGATTTGGTGAGACAAG 59.603 45.833 0.00 0.00 0.00 3.16
301 303 3.819368 TGAAGATTTGGTGAGACAAGCA 58.181 40.909 0.00 0.00 0.00 3.91
474 479 2.300433 GCAACATGCTGATGGTATGGA 58.700 47.619 0.00 0.00 41.36 3.41
564 569 1.097547 ATCTGGCGTACCTTGCATGC 61.098 55.000 11.82 11.82 36.63 4.06
613 618 7.977789 TGCTAATAGACACATGAAAGTTTCA 57.022 32.000 20.14 20.14 45.01 2.69
686 692 4.998671 TTCATGTGTCAAAAGGCAAAGA 57.001 36.364 0.00 0.00 0.00 2.52
1059 1067 2.878406 CCATGATTTACTTAGGGGCACG 59.122 50.000 0.00 0.00 0.00 5.34
1144 1153 3.932822 TGGTGTGCTGACGTATTAACAT 58.067 40.909 0.00 0.00 0.00 2.71
1284 1293 3.524606 GGAGCGGCGGCAGTAGTA 61.525 66.667 19.21 0.00 43.41 1.82
1376 1386 1.188863 AGGTGGCTCATGAAATTGCC 58.811 50.000 15.09 15.09 41.94 4.52
1528 1539 2.507471 CTCCTTAAAGAGGGCCATCACT 59.493 50.000 21.34 8.37 46.31 3.41
1531 1542 3.308402 CCTTAAAGAGGGCCATCACTTCA 60.308 47.826 21.34 3.21 42.26 3.02
1555 1566 3.118884 GCCTAATGACGTTCCAGAAGGTA 60.119 47.826 5.77 0.00 39.23 3.08
1571 1582 4.597507 AGAAGGTATGGAAGAACTTGACCA 59.402 41.667 0.00 0.00 36.83 4.02
1586 1597 3.775654 CCAGGAGGTCGTCAGGGC 61.776 72.222 0.00 0.00 0.00 5.19
1620 1632 1.751733 CGGATTCATGCCCTTGATGGT 60.752 52.381 0.00 0.00 0.00 3.55
1649 1661 1.671901 CTCCTCCTCAGAGAACGGGC 61.672 65.000 0.00 0.00 43.39 6.13
1694 1706 0.106015 AGCCCACCTTTATCCCATGC 60.106 55.000 0.00 0.00 0.00 4.06
1732 1744 1.675483 CGCCATGCCATGCTAGTTTTA 59.325 47.619 0.00 0.00 0.00 1.52
1733 1745 2.541588 CGCCATGCCATGCTAGTTTTAC 60.542 50.000 0.00 0.00 0.00 2.01
1734 1746 2.689983 GCCATGCCATGCTAGTTTTACT 59.310 45.455 0.00 0.00 0.00 2.24
1735 1747 3.243201 GCCATGCCATGCTAGTTTTACTC 60.243 47.826 0.00 0.00 0.00 2.59
1736 1748 4.202441 CCATGCCATGCTAGTTTTACTCT 58.798 43.478 0.00 0.00 0.00 3.24
1743 1756 6.094048 GCCATGCTAGTTTTACTCTTTCATGA 59.906 38.462 0.00 0.00 32.83 3.07
1818 1831 8.746922 AGTCTAATTTATGTTTTGTGTGCATG 57.253 30.769 0.00 0.00 0.00 4.06
1819 1832 7.329226 AGTCTAATTTATGTTTTGTGTGCATGC 59.671 33.333 11.82 11.82 0.00 4.06
1835 1849 2.923605 GCATGCTTGTGTTTCTTGCGAT 60.924 45.455 11.37 0.00 0.00 4.58
1838 1852 2.031769 TGCTTGTGTTTCTTGCGATGAG 60.032 45.455 0.00 0.00 0.00 2.90
1969 1983 7.812648 TGTAGTAAGGAACACAAATATGCAAC 58.187 34.615 0.00 0.00 0.00 4.17
1972 1986 5.743636 AAGGAACACAAATATGCAACCAT 57.256 34.783 0.00 0.00 35.44 3.55
1992 2006 9.703892 CAACCATAACATAAATTGGACTTTCAA 57.296 29.630 0.00 0.00 33.36 2.69
2059 2267 2.284754 TGGGTGAAACATGCAAGCTA 57.715 45.000 0.00 0.00 39.98 3.32
2063 2271 3.181493 GGGTGAAACATGCAAGCTATGAG 60.181 47.826 1.94 0.00 39.98 2.90
2166 2374 7.817962 TGTACTAGAAAAATACACAAGAGCTCC 59.182 37.037 10.93 0.00 0.00 4.70
2168 2376 8.135382 ACTAGAAAAATACACAAGAGCTCCTA 57.865 34.615 10.93 0.00 0.00 2.94
2169 2377 8.254508 ACTAGAAAAATACACAAGAGCTCCTAG 58.745 37.037 10.93 11.03 0.00 3.02
2200 2408 7.070946 TCCACACCCCTATACGAATATTAAACA 59.929 37.037 0.00 0.00 0.00 2.83
2270 2478 3.246167 ACCTGGGTTCTCAATCTACTCCT 60.246 47.826 0.00 0.00 0.00 3.69
2273 2481 2.501723 GGGTTCTCAATCTACTCCTGCA 59.498 50.000 0.00 0.00 0.00 4.41
2349 2559 4.342378 TCCGAACAAAAATCCATCCAAACA 59.658 37.500 0.00 0.00 0.00 2.83
2440 2650 8.383619 CACTAAATTTCACAAGGAAGTAGATCG 58.616 37.037 0.00 0.00 36.72 3.69
2445 2655 4.030913 TCACAAGGAAGTAGATCGGGAAT 58.969 43.478 0.00 0.00 0.00 3.01
2460 2670 3.973973 TCGGGAATCCAGGTTTGATATCT 59.026 43.478 0.09 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 127 2.120312 TCCAACCCGCCAGATATAACA 58.880 47.619 0.00 0.00 0.00 2.41
157 159 5.337250 CCATGCATCTCCCCAAATATCAATG 60.337 44.000 0.00 0.00 0.00 2.82
299 301 1.011333 GCATCAATTGGCCACAATGC 58.989 50.000 19.24 19.24 46.25 3.56
301 303 2.181125 TGAGCATCAATTGGCCACAAT 58.819 42.857 3.88 0.00 45.97 2.71
393 397 4.569943 AGCTGATCGTACAGTGAAAACAT 58.430 39.130 0.00 0.00 39.73 2.71
474 479 7.668886 CCCAGATAGGATTAGCATTGATTCTTT 59.331 37.037 0.00 0.00 41.22 2.52
613 618 2.391678 GAGCATGATGGGAAATTGGGT 58.608 47.619 0.00 0.00 0.00 4.51
686 692 2.241430 GTCCTAACTTGCCCCATACCTT 59.759 50.000 0.00 0.00 0.00 3.50
1009 1017 3.793559 AGGCGTCGACATTAAGCTTAAT 58.206 40.909 23.22 23.22 33.82 1.40
1059 1067 2.045536 CTGAGAACAGCCCCAGCC 60.046 66.667 0.00 0.00 41.25 4.85
1306 1315 9.033481 CAAATCTAACAAGCAAAAATCACAAGA 57.967 29.630 0.00 0.00 0.00 3.02
1339 1349 4.714308 CCACCTTATTTGCTTCCCCATTAA 59.286 41.667 0.00 0.00 0.00 1.40
1376 1386 3.256558 GGCTGAAAATTTTGCTAGCCTG 58.743 45.455 27.20 12.34 45.44 4.85
1512 1523 3.889815 CATGAAGTGATGGCCCTCTTTA 58.110 45.455 9.61 0.73 0.00 1.85
1528 1539 3.055458 TCTGGAACGTCATTAGGCATGAA 60.055 43.478 0.00 0.00 43.93 2.57
1531 1542 3.535561 CTTCTGGAACGTCATTAGGCAT 58.464 45.455 0.00 0.00 0.00 4.40
1555 1566 2.307098 CCTCCTGGTCAAGTTCTTCCAT 59.693 50.000 0.00 0.00 0.00 3.41
1595 1607 2.026641 CAAGGGCATGAATCCGATGTT 58.973 47.619 0.00 0.00 0.00 2.71
1620 1632 1.566703 CTGAGGAGGAGGTCTGGACTA 59.433 57.143 0.67 0.00 0.00 2.59
1694 1706 1.514087 GCAATGGGTGGAGCACATG 59.486 57.895 0.00 0.00 41.09 3.21
1732 1744 8.230472 AGTCAAATGAAAAGTCATGAAAGAGT 57.770 30.769 0.00 0.00 44.02 3.24
1733 1745 9.525409 AAAGTCAAATGAAAAGTCATGAAAGAG 57.475 29.630 0.00 0.00 44.02 2.85
1734 1746 9.520204 GAAAGTCAAATGAAAAGTCATGAAAGA 57.480 29.630 0.00 0.00 44.02 2.52
1735 1747 9.304731 TGAAAGTCAAATGAAAAGTCATGAAAG 57.695 29.630 0.00 0.00 44.02 2.62
1736 1748 9.650539 TTGAAAGTCAAATGAAAAGTCATGAAA 57.349 25.926 0.00 0.00 44.02 2.69
1835 1849 3.945285 GTGGTCTTGTTTCAAAGTCCTCA 59.055 43.478 0.00 0.00 36.62 3.86
1838 1852 4.200092 AGAGTGGTCTTGTTTCAAAGTCC 58.800 43.478 0.00 0.00 36.33 3.85
1931 1945 7.497909 TGTTCCTTACTACAAGGACTTTCAAAG 59.502 37.037 5.24 0.00 45.47 2.77
2006 2020 2.548057 TGACTTTCAATGTCGAACCTGC 59.452 45.455 0.00 0.00 37.26 4.85
2038 2052 2.806434 AGCTTGCATGTTTCACCCATA 58.194 42.857 1.14 0.00 0.00 2.74
2046 2087 5.166398 GCTTTTCTCATAGCTTGCATGTTT 58.834 37.500 0.00 0.00 34.57 2.83
2049 2090 4.365899 TGCTTTTCTCATAGCTTGCATG 57.634 40.909 0.00 0.00 38.22 4.06
2078 2286 4.144297 CCCATCAATCACGTTTATCCCAT 58.856 43.478 0.00 0.00 0.00 4.00
2112 2320 4.130118 GGTCATTACCAGGTATTGCTCTG 58.870 47.826 14.48 1.59 45.98 3.35
2233 2441 3.078305 ACCCAGGTTTGATATCCCCAAAA 59.922 43.478 0.00 0.00 35.57 2.44
2240 2448 6.360618 AGATTGAGAACCCAGGTTTGATATC 58.639 40.000 3.05 0.00 38.60 1.63
2304 2514 2.164338 GGTATTTCCTTTGCCACGGAA 58.836 47.619 0.00 0.00 37.52 4.30
2307 2517 1.129811 GACGGTATTTCCTTTGCCACG 59.870 52.381 0.00 0.00 0.00 4.94
2417 2627 6.821665 CCCGATCTACTTCCTTGTGAAATTTA 59.178 38.462 0.00 0.00 31.06 1.40
2428 2638 3.235200 CTGGATTCCCGATCTACTTCCT 58.765 50.000 0.00 0.00 35.02 3.36
2429 2639 2.300437 CCTGGATTCCCGATCTACTTCC 59.700 54.545 0.00 0.00 35.02 3.46
2430 2640 2.966516 ACCTGGATTCCCGATCTACTTC 59.033 50.000 0.00 0.00 35.02 3.01
2431 2641 3.047695 ACCTGGATTCCCGATCTACTT 57.952 47.619 0.00 0.00 35.02 2.24
2440 2650 5.310409 TGAGATATCAAACCTGGATTCCC 57.690 43.478 5.32 0.00 0.00 3.97
2445 2655 7.632861 TGAGATTTTGAGATATCAAACCTGGA 58.367 34.615 14.84 1.00 39.06 3.86


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

AutoCloner maintained by Alex Coulton.