Multiple sequence alignment - TraesCS6A01G327100

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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 TraesCS6A01G327100 chr6A 100.000 3440 0 0 1 3440 560443255 560446694 0.000000e+00 6353
1 TraesCS6A01G327100 chr6A 98.010 1256 11 6 2188 3440 560489285 560490529 0.000000e+00 2169
2 TraesCS6A01G327100 chr6A 97.697 1259 27 1 1 1257 560488032 560489290 0.000000e+00 2163
3 TraesCS6A01G327100 chr6A 88.663 1473 125 11 986 2428 560192894 560191434 0.000000e+00 1757
4 TraesCS6A01G327100 chr6D 91.237 2191 141 15 282 2426 417775101 417777286 0.000000e+00 2935
5 TraesCS6A01G327100 chr6D 88.963 1504 119 13 986 2459 417752093 417750607 0.000000e+00 1814
6 TraesCS6A01G327100 chr6D 90.099 303 28 2 1 302 417774784 417775085 3.220000e-105 392
7 TraesCS6A01G327100 chr6B 88.589 1481 118 13 986 2428 626643900 626645367 0.000000e+00 1751
8 TraesCS6A01G327100 chr6B 89.578 1113 84 11 1346 2428 626489330 626488220 0.000000e+00 1384
9 TraesCS6A01G327100 chr6B 87.634 372 41 3 986 1353 626525230 626524860 8.820000e-116 427
10 TraesCS6A01G327100 chr6B 79.174 557 86 16 3 555 54902686 54902156 3.260000e-95 359
11 TraesCS6A01G327100 chr6B 94.737 76 3 1 826 901 626525433 626525359 2.170000e-22 117
12 TraesCS6A01G327100 chr3D 85.655 1450 174 11 1009 2426 17343128 17341681 0.000000e+00 1495
13 TraesCS6A01G327100 chr3D 82.197 1438 210 18 1009 2417 17698284 17699704 0.000000e+00 1195
14 TraesCS6A01G327100 chr3D 89.286 560 55 5 1 556 497379190 497378632 0.000000e+00 697
15 TraesCS6A01G327100 chr3D 83.539 729 97 18 18 727 419656896 419656172 0.000000e+00 660
16 TraesCS6A01G327100 chr7A 95.414 676 27 4 2767 3440 77164851 77165524 0.000000e+00 1074
17 TraesCS6A01G327100 chr7A 94.502 673 32 5 2769 3440 257151034 257150366 0.000000e+00 1033
18 TraesCS6A01G327100 chr7A 94.074 675 36 4 2767 3440 645073894 645074565 0.000000e+00 1022
19 TraesCS6A01G327100 chr7A 93.648 677 39 4 2765 3440 648423734 648424407 0.000000e+00 1009
20 TraesCS6A01G327100 chr3A 94.527 676 32 4 2767 3440 30524581 30525253 0.000000e+00 1038
21 TraesCS6A01G327100 chr3A 81.108 1101 161 20 1009 2078 18818919 18820003 0.000000e+00 837
22 TraesCS6A01G327100 chr3A 81.108 1101 161 20 1009 2078 19266061 19264977 0.000000e+00 837
23 TraesCS6A01G327100 chr3A 83.598 567 71 10 10 556 729688321 729687757 2.370000e-141 512
24 TraesCS6A01G327100 chr3A 83.363 565 72 10 3 547 728020943 728021505 1.430000e-138 503
25 TraesCS6A01G327100 chr3A 83.363 565 72 10 3 547 728035734 728036296 1.430000e-138 503
26 TraesCS6A01G327100 chr5A 93.787 676 38 4 2767 3440 546514435 546515108 0.000000e+00 1013
27 TraesCS6A01G327100 chr5A 93.778 675 39 3 2767 3440 588408853 588409525 0.000000e+00 1011
28 TraesCS6A01G327100 chr5A 93.778 675 38 3 2767 3440 664307733 664307062 0.000000e+00 1011
29 TraesCS6A01G327100 chr2A 93.658 678 36 7 2766 3440 744076628 744077301 0.000000e+00 1007
30 TraesCS6A01G327100 chr1B 78.761 1469 248 36 1005 2433 590091035 590092479 0.000000e+00 926
31 TraesCS6A01G327100 chr3B 86.470 813 89 8 1626 2417 24902082 24901270 0.000000e+00 872
32 TraesCS6A01G327100 chr3B 81.782 763 89 19 3 727 68436713 68437463 8.220000e-166 593
33 TraesCS6A01G327100 chr1D 77.815 1190 196 38 1276 2433 436120202 436121355 0.000000e+00 673
34 TraesCS6A01G327100 chr2B 88.222 450 47 6 285 729 385538698 385538250 1.820000e-147 532
35 TraesCS6A01G327100 chr2B 84.232 482 57 10 91 556 503068783 503068305 5.240000e-123 451
36 TraesCS6A01G327100 chr2B 80.899 445 67 17 1 433 385539019 385538581 5.500000e-88 335
37 TraesCS6A01G327100 chr7D 82.821 553 59 18 8 556 34140638 34140118 2.420000e-126 462
38 TraesCS6A01G327100 chr5B 84.116 447 55 7 1 433 263945871 263945427 5.310000e-113 418
39 TraesCS6A01G327100 chr1A 77.734 768 96 41 3 730 559230945 559231677 5.350000e-108 401


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 TraesCS6A01G327100 chr6A 560443255 560446694 3439 False 6353.0 6353 100.0000 1 3440 1 chr6A.!!$F1 3439
1 TraesCS6A01G327100 chr6A 560488032 560490529 2497 False 2166.0 2169 97.8535 1 3440 2 chr6A.!!$F2 3439
2 TraesCS6A01G327100 chr6A 560191434 560192894 1460 True 1757.0 1757 88.6630 986 2428 1 chr6A.!!$R1 1442
3 TraesCS6A01G327100 chr6D 417750607 417752093 1486 True 1814.0 1814 88.9630 986 2459 1 chr6D.!!$R1 1473
4 TraesCS6A01G327100 chr6D 417774784 417777286 2502 False 1663.5 2935 90.6680 1 2426 2 chr6D.!!$F1 2425
5 TraesCS6A01G327100 chr6B 626643900 626645367 1467 False 1751.0 1751 88.5890 986 2428 1 chr6B.!!$F1 1442
6 TraesCS6A01G327100 chr6B 626488220 626489330 1110 True 1384.0 1384 89.5780 1346 2428 1 chr6B.!!$R2 1082
7 TraesCS6A01G327100 chr6B 54902156 54902686 530 True 359.0 359 79.1740 3 555 1 chr6B.!!$R1 552
8 TraesCS6A01G327100 chr6B 626524860 626525433 573 True 272.0 427 91.1855 826 1353 2 chr6B.!!$R3 527
9 TraesCS6A01G327100 chr3D 17341681 17343128 1447 True 1495.0 1495 85.6550 1009 2426 1 chr3D.!!$R1 1417
10 TraesCS6A01G327100 chr3D 17698284 17699704 1420 False 1195.0 1195 82.1970 1009 2417 1 chr3D.!!$F1 1408
11 TraesCS6A01G327100 chr3D 497378632 497379190 558 True 697.0 697 89.2860 1 556 1 chr3D.!!$R3 555
12 TraesCS6A01G327100 chr3D 419656172 419656896 724 True 660.0 660 83.5390 18 727 1 chr3D.!!$R2 709
13 TraesCS6A01G327100 chr7A 77164851 77165524 673 False 1074.0 1074 95.4140 2767 3440 1 chr7A.!!$F1 673
14 TraesCS6A01G327100 chr7A 257150366 257151034 668 True 1033.0 1033 94.5020 2769 3440 1 chr7A.!!$R1 671
15 TraesCS6A01G327100 chr7A 645073894 645074565 671 False 1022.0 1022 94.0740 2767 3440 1 chr7A.!!$F2 673
16 TraesCS6A01G327100 chr7A 648423734 648424407 673 False 1009.0 1009 93.6480 2765 3440 1 chr7A.!!$F3 675
17 TraesCS6A01G327100 chr3A 30524581 30525253 672 False 1038.0 1038 94.5270 2767 3440 1 chr3A.!!$F2 673
18 TraesCS6A01G327100 chr3A 18818919 18820003 1084 False 837.0 837 81.1080 1009 2078 1 chr3A.!!$F1 1069
19 TraesCS6A01G327100 chr3A 19264977 19266061 1084 True 837.0 837 81.1080 1009 2078 1 chr3A.!!$R1 1069
20 TraesCS6A01G327100 chr3A 729687757 729688321 564 True 512.0 512 83.5980 10 556 1 chr3A.!!$R2 546
21 TraesCS6A01G327100 chr3A 728020943 728021505 562 False 503.0 503 83.3630 3 547 1 chr3A.!!$F3 544
22 TraesCS6A01G327100 chr3A 728035734 728036296 562 False 503.0 503 83.3630 3 547 1 chr3A.!!$F4 544
23 TraesCS6A01G327100 chr5A 546514435 546515108 673 False 1013.0 1013 93.7870 2767 3440 1 chr5A.!!$F1 673
24 TraesCS6A01G327100 chr5A 588408853 588409525 672 False 1011.0 1011 93.7780 2767 3440 1 chr5A.!!$F2 673
25 TraesCS6A01G327100 chr5A 664307062 664307733 671 True 1011.0 1011 93.7780 2767 3440 1 chr5A.!!$R1 673
26 TraesCS6A01G327100 chr2A 744076628 744077301 673 False 1007.0 1007 93.6580 2766 3440 1 chr2A.!!$F1 674
27 TraesCS6A01G327100 chr1B 590091035 590092479 1444 False 926.0 926 78.7610 1005 2433 1 chr1B.!!$F1 1428
28 TraesCS6A01G327100 chr3B 24901270 24902082 812 True 872.0 872 86.4700 1626 2417 1 chr3B.!!$R1 791
29 TraesCS6A01G327100 chr3B 68436713 68437463 750 False 593.0 593 81.7820 3 727 1 chr3B.!!$F1 724
30 TraesCS6A01G327100 chr1D 436120202 436121355 1153 False 673.0 673 77.8150 1276 2433 1 chr1D.!!$F1 1157
31 TraesCS6A01G327100 chr2B 385538250 385539019 769 True 433.5 532 84.5605 1 729 2 chr2B.!!$R2 728
32 TraesCS6A01G327100 chr7D 34140118 34140638 520 True 462.0 462 82.8210 8 556 1 chr7D.!!$R1 548
33 TraesCS6A01G327100 chr1A 559230945 559231677 732 False 401.0 401 77.7340 3 730 1 chr1A.!!$F1 727

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
144 149 1.068055 GTTAAACTCGACCTGCTCCGA 60.068 52.381 0.0 0.0 0.00 4.55 F
1316 1468 0.540923 GACTTCCTCTGCTCCATGCT 59.459 55.000 0.0 0.0 43.37 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 1876 0.412244 TACACTGGAGGCAGTACCCT 59.588 55.000 0.00 0.0 40.58 4.34 R
3190 3412 1.816835 CGTCTTATATAGGCCGAGGCA 59.183 52.381 16.65 0.0 44.11 4.75 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
60 64 3.849951 ATCGCCGACGCCAAGGAT 61.850 61.111 0.00 0.00 39.84 3.24
144 149 1.068055 GTTAAACTCGACCTGCTCCGA 60.068 52.381 0.00 0.00 0.00 4.55
196 201 1.503542 CTGGCGTTCTTGATGTGGC 59.496 57.895 0.00 0.00 0.00 5.01
526 580 6.919188 CGAACTATCGTTTATGTTTGATCGT 58.081 36.000 0.00 0.00 44.06 3.73
651 742 2.787249 CGAACTGCATTGCCTCCG 59.213 61.111 6.12 1.09 0.00 4.63
1057 1203 2.325583 TTTCGTGAGCCACTTTGTCT 57.674 45.000 4.21 0.00 31.34 3.41
1316 1468 0.540923 GACTTCCTCTGCTCCATGCT 59.459 55.000 0.00 0.00 43.37 3.79
1317 1469 0.990374 ACTTCCTCTGCTCCATGCTT 59.010 50.000 0.00 0.00 43.37 3.91
1447 1614 3.949885 TTCGCCCAGCTCCCTACGA 62.950 63.158 0.00 0.00 0.00 3.43
1521 1698 1.452108 CTTCGGCCTTCCACCCATC 60.452 63.158 0.00 0.00 0.00 3.51
1563 1740 2.574399 GTGCTCGAGGACCTGGAC 59.426 66.667 25.07 0.52 0.00 4.02
1607 1784 3.197790 CTTGCTGTGCCGGATCCG 61.198 66.667 27.65 27.65 39.44 4.18
1681 1858 2.297129 GCTGCTCTCAGGGACCCTT 61.297 63.158 11.56 0.00 40.65 3.95
1682 1859 1.846712 GCTGCTCTCAGGGACCCTTT 61.847 60.000 11.56 0.00 40.65 3.11
1696 1876 2.203280 CTTTGTGTGTCCCCGGCA 60.203 61.111 0.00 0.00 0.00 5.69
1726 1912 1.733041 CCAGTGTACTGCGTCGGTG 60.733 63.158 6.50 0.00 42.47 4.94
1870 2062 0.683828 CTCTGAGGAGCAGCTCAGGA 60.684 60.000 24.09 13.58 45.07 3.86
2106 2322 1.305930 GGTGGAATTCGGTGCTGGAC 61.306 60.000 0.00 0.00 0.00 4.02
2170 2386 2.300152 TCGGAGCAGAAGATGAACAAGT 59.700 45.455 0.00 0.00 0.00 3.16
2459 2679 3.576550 TGAGCTTGGCATATCCGTACATA 59.423 43.478 0.00 0.00 37.80 2.29
3217 3439 0.175073 CCTATATAAGACGCGCCCCC 59.825 60.000 5.73 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 4.865761 GGCGTCGGCGATGCACTA 62.866 66.667 43.14 7.30 45.37 2.74
196 201 0.371301 CCATTGTCGACATGTCTGCG 59.629 55.000 20.80 11.44 0.00 5.18
526 580 2.554142 GATCATCATGCCACAGTTCGA 58.446 47.619 0.00 0.00 0.00 3.71
759 854 1.823610 ACCCACTTAAGGCTACTCGAC 59.176 52.381 7.53 0.00 0.00 4.20
1316 1468 4.973055 CGTGGACGTTCCGGGCAA 62.973 66.667 0.00 0.00 40.17 4.52
1334 1486 1.970114 ACCGAGTCGACGACCACAT 60.970 57.895 23.76 5.74 32.18 3.21
1372 1530 3.470888 CCCGGGCCTCTTCACGAT 61.471 66.667 8.08 0.00 0.00 3.73
1559 1736 1.337728 CCTTGTATGTGTCGCTGTCCA 60.338 52.381 0.00 0.00 0.00 4.02
1563 1740 0.735978 TCGCCTTGTATGTGTCGCTG 60.736 55.000 0.00 0.00 0.00 5.18
1660 1837 2.373707 GGTCCCTGAGAGCAGCCAT 61.374 63.158 0.00 0.00 42.81 4.40
1681 1858 4.263572 CCTGCCGGGGACACACAA 62.264 66.667 2.18 0.00 0.00 3.33
1696 1876 0.412244 TACACTGGAGGCAGTACCCT 59.588 55.000 0.00 0.00 40.58 4.34
1702 1882 1.446792 CGCAGTACACTGGAGGCAG 60.447 63.158 11.18 0.00 43.94 4.85
1726 1912 1.584483 CGATGCTGCCGACAAATGC 60.584 57.895 0.00 0.00 0.00 3.56
1754 1946 1.359459 CTCGTGCCGCTCTTTTACCC 61.359 60.000 0.00 0.00 0.00 3.69
1757 1949 2.822306 CACTCGTGCCGCTCTTTTA 58.178 52.632 0.00 0.00 0.00 1.52
1949 2163 3.367743 CGTTGAGGTCCGGGTCGA 61.368 66.667 0.00 0.00 0.00 4.20
1983 2197 1.086696 CGTTGGTTCGCTCCATGAAT 58.913 50.000 0.00 0.00 37.33 2.57
2170 2386 2.091640 ATGTCCCCCACCATGTGCAA 62.092 55.000 0.00 0.00 31.34 4.08
3088 3310 3.602104 CCCTTGAGGCATCAATGGT 57.398 52.632 22.55 0.00 44.32 3.55
3190 3412 1.816835 CGTCTTATATAGGCCGAGGCA 59.183 52.381 16.65 0.00 44.11 4.75


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

AutoCloner maintained by Alex Coulton.