Multiple sequence alignment - TraesCS6B01G220500

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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 TraesCS6B01G220500 chr6B 100.000 2549 0 0 1 2549 314294231 314291683 0.000000e+00 4708.0
1 TraesCS6B01G220500 chr5B 94.978 1334 66 1 564 1897 682396001 682394669 0.000000e+00 2091.0
2 TraesCS6B01G220500 chr5B 94.299 1333 75 1 565 1897 81902662 81903993 0.000000e+00 2039.0
3 TraesCS6B01G220500 chr2D 94.686 1336 67 3 565 1897 64508693 64510027 0.000000e+00 2071.0
4 TraesCS6B01G220500 chr2D 97.859 654 14 0 1896 2549 610936408 610937061 0.000000e+00 1131.0
5 TraesCS6B01G220500 chr2D 97.699 652 15 0 1898 2549 64514498 64515149 0.000000e+00 1122.0
6 TraesCS6B01G220500 chrUn 94.658 1329 70 1 569 1897 60558711 60560038 0.000000e+00 2060.0
7 TraesCS6B01G220500 chr4B 94.511 1330 69 3 568 1897 372353118 372351793 0.000000e+00 2049.0
8 TraesCS6B01G220500 chr4B 97.706 654 15 0 1896 2549 80647797 80647144 0.000000e+00 1125.0
9 TraesCS6B01G220500 chr4B 97.706 654 15 0 1896 2549 657227816 657227163 0.000000e+00 1125.0
10 TraesCS6B01G220500 chr2B 94.074 1350 77 2 548 1897 458657403 458658749 0.000000e+00 2047.0
11 TraesCS6B01G220500 chr2B 98.012 654 13 0 1896 2549 667884776 667884123 0.000000e+00 1136.0
12 TraesCS6B01G220500 chr7B 94.440 1331 71 2 569 1897 677862790 677861461 0.000000e+00 2045.0
13 TraesCS6B01G220500 chr1B 94.299 1333 74 2 565 1897 307939702 307941032 0.000000e+00 2039.0
14 TraesCS6B01G220500 chr1B 94.299 1333 74 1 567 1897 581717563 581716231 0.000000e+00 2039.0
15 TraesCS6B01G220500 chr5D 98.012 654 13 0 1896 2549 473092884 473093537 0.000000e+00 1136.0
16 TraesCS6B01G220500 chr5D 86.420 567 64 10 1 562 193534630 193534072 2.170000e-170 608.0
17 TraesCS6B01G220500 chr3D 98.012 654 13 0 1896 2549 132613438 132612785 0.000000e+00 1136.0
18 TraesCS6B01G220500 chr3D 97.554 654 16 0 1896 2549 475112720 475113373 0.000000e+00 1120.0
19 TraesCS6B01G220500 chr3D 87.965 565 63 4 1 563 424244287 424244848 0.000000e+00 662.0
20 TraesCS6B01G220500 chr7D 97.706 654 15 0 1896 2549 604951837 604952490 0.000000e+00 1125.0
21 TraesCS6B01G220500 chr7D 91.594 571 43 4 1 568 253323631 253323063 0.000000e+00 784.0
22 TraesCS6B01G220500 chr7D 89.130 552 57 3 1 550 245992146 245991596 0.000000e+00 684.0
23 TraesCS6B01G220500 chr7D 87.762 572 62 6 1 568 314854150 314854717 0.000000e+00 662.0
24 TraesCS6B01G220500 chr6D 92.995 571 37 3 1 568 229047950 229047380 0.000000e+00 830.0
25 TraesCS6B01G220500 chr6D 88.246 570 61 4 1 568 145469496 145470061 0.000000e+00 676.0
26 TraesCS6B01G220500 chr6D 86.014 572 69 8 2 568 211213024 211213589 1.010000e-168 603.0
27 TraesCS6B01G220500 chr6D 88.820 483 52 2 83 563 344590659 344591141 2.180000e-165 592.0
28 TraesCS6B01G220500 chr6D 85.563 568 65 12 2 562 212437060 212436503 1.700000e-161 579.0
29 TraesCS6B01G220500 chr6D 87.730 489 55 5 78 563 413245501 413245987 1.320000e-157 566.0
30 TraesCS6B01G220500 chr6D 88.692 451 49 2 78 527 211481768 211481319 1.330000e-152 549.0
31 TraesCS6B01G220500 chr6D 88.641 449 48 3 78 524 140246710 140247157 6.200000e-151 544.0
32 TraesCS6B01G220500 chr6D 82.686 566 72 14 1 562 211708236 211707693 1.770000e-131 479.0
33 TraesCS6B01G220500 chr6D 90.196 51 3 2 1 50 413245454 413245503 5.890000e-07 65.8
34 TraesCS6B01G220500 chr6D 88.000 50 6 0 1 50 206713393 206713442 2.740000e-05 60.2
35 TraesCS6B01G220500 chr1D 92.456 570 41 2 1 568 159847935 159847366 0.000000e+00 813.0
36 TraesCS6B01G220500 chr1D 88.434 562 62 3 3 561 171042103 171041542 0.000000e+00 675.0
37 TraesCS6B01G220500 chr1D 85.714 560 74 5 9 566 264920155 264919600 1.020000e-163 586.0
38 TraesCS6B01G220500 chr1D 84.843 574 75 10 1 568 29650702 29651269 3.680000e-158 568.0
39 TraesCS6B01G220500 chr1D 88.000 50 6 0 1 50 172913026 172912977 2.740000e-05 60.2
40 TraesCS6B01G220500 chr1A 90.877 570 46 5 3 568 237250328 237250895 0.000000e+00 760.0
41 TraesCS6B01G220500 chr1A 91.119 563 45 5 9 568 164796699 164796139 0.000000e+00 758.0
42 TraesCS6B01G220500 chr1A 90.418 574 52 3 1 572 234654025 234653453 0.000000e+00 752.0
43 TraesCS6B01G220500 chr1A 90.510 569 49 5 3 568 164815497 164814931 0.000000e+00 747.0
44 TraesCS6B01G220500 chr3B 90.000 570 55 2 1 568 345644769 345644200 0.000000e+00 736.0
45 TraesCS6B01G220500 chr4D 89.261 568 59 2 1 566 384521957 384521390 0.000000e+00 710.0
46 TraesCS6B01G220500 chr4D 88.908 568 59 4 2 566 256808414 256808980 0.000000e+00 697.0
47 TraesCS6B01G220500 chr4D 89.474 494 50 2 70 561 441889938 441889445 7.740000e-175 623.0


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 TraesCS6B01G220500 chr6B 314291683 314294231 2548 True 4708.0 4708 100.000 1 2549 1 chr6B.!!$R1 2548
1 TraesCS6B01G220500 chr5B 682394669 682396001 1332 True 2091.0 2091 94.978 564 1897 1 chr5B.!!$R1 1333
2 TraesCS6B01G220500 chr5B 81902662 81903993 1331 False 2039.0 2039 94.299 565 1897 1 chr5B.!!$F1 1332
3 TraesCS6B01G220500 chr2D 64508693 64510027 1334 False 2071.0 2071 94.686 565 1897 1 chr2D.!!$F1 1332
4 TraesCS6B01G220500 chr2D 610936408 610937061 653 False 1131.0 1131 97.859 1896 2549 1 chr2D.!!$F3 653
5 TraesCS6B01G220500 chr2D 64514498 64515149 651 False 1122.0 1122 97.699 1898 2549 1 chr2D.!!$F2 651
6 TraesCS6B01G220500 chrUn 60558711 60560038 1327 False 2060.0 2060 94.658 569 1897 1 chrUn.!!$F1 1328
7 TraesCS6B01G220500 chr4B 372351793 372353118 1325 True 2049.0 2049 94.511 568 1897 1 chr4B.!!$R2 1329
8 TraesCS6B01G220500 chr4B 80647144 80647797 653 True 1125.0 1125 97.706 1896 2549 1 chr4B.!!$R1 653
9 TraesCS6B01G220500 chr4B 657227163 657227816 653 True 1125.0 1125 97.706 1896 2549 1 chr4B.!!$R3 653
10 TraesCS6B01G220500 chr2B 458657403 458658749 1346 False 2047.0 2047 94.074 548 1897 1 chr2B.!!$F1 1349
11 TraesCS6B01G220500 chr2B 667884123 667884776 653 True 1136.0 1136 98.012 1896 2549 1 chr2B.!!$R1 653
12 TraesCS6B01G220500 chr7B 677861461 677862790 1329 True 2045.0 2045 94.440 569 1897 1 chr7B.!!$R1 1328
13 TraesCS6B01G220500 chr1B 307939702 307941032 1330 False 2039.0 2039 94.299 565 1897 1 chr1B.!!$F1 1332
14 TraesCS6B01G220500 chr1B 581716231 581717563 1332 True 2039.0 2039 94.299 567 1897 1 chr1B.!!$R1 1330
15 TraesCS6B01G220500 chr5D 473092884 473093537 653 False 1136.0 1136 98.012 1896 2549 1 chr5D.!!$F1 653
16 TraesCS6B01G220500 chr5D 193534072 193534630 558 True 608.0 608 86.420 1 562 1 chr5D.!!$R1 561
17 TraesCS6B01G220500 chr3D 132612785 132613438 653 True 1136.0 1136 98.012 1896 2549 1 chr3D.!!$R1 653
18 TraesCS6B01G220500 chr3D 475112720 475113373 653 False 1120.0 1120 97.554 1896 2549 1 chr3D.!!$F2 653
19 TraesCS6B01G220500 chr3D 424244287 424244848 561 False 662.0 662 87.965 1 563 1 chr3D.!!$F1 562
20 TraesCS6B01G220500 chr7D 604951837 604952490 653 False 1125.0 1125 97.706 1896 2549 1 chr7D.!!$F2 653
21 TraesCS6B01G220500 chr7D 253323063 253323631 568 True 784.0 784 91.594 1 568 1 chr7D.!!$R2 567
22 TraesCS6B01G220500 chr7D 245991596 245992146 550 True 684.0 684 89.130 1 550 1 chr7D.!!$R1 549
23 TraesCS6B01G220500 chr7D 314854150 314854717 567 False 662.0 662 87.762 1 568 1 chr7D.!!$F1 567
24 TraesCS6B01G220500 chr6D 229047380 229047950 570 True 830.0 830 92.995 1 568 1 chr6D.!!$R4 567
25 TraesCS6B01G220500 chr6D 145469496 145470061 565 False 676.0 676 88.246 1 568 1 chr6D.!!$F2 567
26 TraesCS6B01G220500 chr6D 211213024 211213589 565 False 603.0 603 86.014 2 568 1 chr6D.!!$F4 566
27 TraesCS6B01G220500 chr6D 212436503 212437060 557 True 579.0 579 85.563 2 562 1 chr6D.!!$R3 560
28 TraesCS6B01G220500 chr6D 211707693 211708236 543 True 479.0 479 82.686 1 562 1 chr6D.!!$R2 561
29 TraesCS6B01G220500 chr6D 413245454 413245987 533 False 315.9 566 88.963 1 563 2 chr6D.!!$F6 562
30 TraesCS6B01G220500 chr1D 159847366 159847935 569 True 813.0 813 92.456 1 568 1 chr1D.!!$R1 567
31 TraesCS6B01G220500 chr1D 171041542 171042103 561 True 675.0 675 88.434 3 561 1 chr1D.!!$R2 558
32 TraesCS6B01G220500 chr1D 264919600 264920155 555 True 586.0 586 85.714 9 566 1 chr1D.!!$R4 557
33 TraesCS6B01G220500 chr1D 29650702 29651269 567 False 568.0 568 84.843 1 568 1 chr1D.!!$F1 567
34 TraesCS6B01G220500 chr1A 237250328 237250895 567 False 760.0 760 90.877 3 568 1 chr1A.!!$F1 565
35 TraesCS6B01G220500 chr1A 164796139 164796699 560 True 758.0 758 91.119 9 568 1 chr1A.!!$R1 559
36 TraesCS6B01G220500 chr1A 234653453 234654025 572 True 752.0 752 90.418 1 572 1 chr1A.!!$R3 571
37 TraesCS6B01G220500 chr1A 164814931 164815497 566 True 747.0 747 90.510 3 568 1 chr1A.!!$R2 565
38 TraesCS6B01G220500 chr3B 345644200 345644769 569 True 736.0 736 90.000 1 568 1 chr3B.!!$R1 567
39 TraesCS6B01G220500 chr4D 384521390 384521957 567 True 710.0 710 89.261 1 566 1 chr4D.!!$R1 565
40 TraesCS6B01G220500 chr4D 256808414 256808980 566 False 697.0 697 88.908 2 566 1 chr4D.!!$F1 564

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
907 922 0.100325 CGAGAGAGCAAGAGCACGAT 59.9 55.0 0.0 0.0 45.49 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2165 0.897621 GGGTCCAAAGGAATTGCAGG 59.102 55.0 0.0 0.0 37.73 4.85 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
142 146 5.978814 ACATAGGTGATGGTACTTCAGTTC 58.021 41.667 0.00 0.00 40.18 3.01
244 248 6.364701 TCTACATGCTTATATTTGCCACCTT 58.635 36.000 0.00 0.00 0.00 3.50
359 368 7.072177 TCATGTTTGACGATCCATTAAACTC 57.928 36.000 11.16 0.00 33.61 3.01
420 429 9.098355 TCATTGCAAACTCATCATAGTAACTAC 57.902 33.333 1.71 0.00 0.00 2.73
438 448 8.545420 AGTAACTACGCATACCAATTAAAATCG 58.455 33.333 0.00 0.00 0.00 3.34
530 540 4.862902 TGCTATGCTACCTTTGCAAAAA 57.137 36.364 13.84 1.01 44.01 1.94
684 695 3.113322 CGACTCGTTCTGTGAACTTTGA 58.887 45.455 8.51 0.00 0.00 2.69
692 703 2.135933 CTGTGAACTTTGACGTCTCCC 58.864 52.381 17.92 0.00 0.00 4.30
702 713 1.187087 GACGTCTCCCTCAGGTCAAT 58.813 55.000 8.70 0.00 0.00 2.57
763 774 4.347607 AGGCAGCCAATTTTATTCAGACT 58.652 39.130 15.80 0.00 0.00 3.24
845 860 2.295253 GCTATATAAGCGGGCGACAT 57.705 50.000 0.00 0.00 42.53 3.06
897 912 1.953231 CTGACCATGGCGAGAGAGCA 61.953 60.000 13.04 0.00 39.27 4.26
907 922 0.100325 CGAGAGAGCAAGAGCACGAT 59.900 55.000 0.00 0.00 45.49 3.73
916 931 1.830587 AAGAGCACGATGGCAGTGGA 61.831 55.000 8.70 0.00 39.80 4.02
936 951 3.775654 GCTAGCTGTGGAGGGCGT 61.776 66.667 7.70 0.00 0.00 5.68
983 998 4.467084 GGCGGCGTTGAGATCCCA 62.467 66.667 9.37 0.00 0.00 4.37
1046 1061 2.676471 GTGGATGCAAAGCCGGGT 60.676 61.111 0.00 0.00 0.00 5.28
1076 1093 2.636893 AGATGCCTGTCTTTGTCTGTCT 59.363 45.455 0.00 0.00 0.00 3.41
1117 1134 0.679505 TCGGAGGGTTTCTCACACAG 59.320 55.000 0.00 0.00 44.19 3.66
1128 1145 1.202687 TCTCACACAGCAAGGAACCAG 60.203 52.381 0.00 0.00 0.00 4.00
1136 1153 1.625818 AGCAAGGAACCAGAATCGTCT 59.374 47.619 0.00 0.00 32.85 4.18
1230 1247 3.605634 CAATGGGTTGATCTGTTCCGTA 58.394 45.455 0.00 0.00 37.53 4.02
1258 1275 4.997395 TGTAGGTGACATGCTTCTTTCTTC 59.003 41.667 0.00 0.00 31.20 2.87
1282 1299 0.392193 CGATGCTCTGGCCAAGACTT 60.392 55.000 7.01 0.00 37.74 3.01
1322 1339 2.799017 AGAGCATGAAGAATGGTTGCA 58.201 42.857 0.00 0.00 46.95 4.08
1372 1389 0.609681 ACGAGCTCCGGAAGAAGAGT 60.610 55.000 5.23 0.00 43.93 3.24
1511 1528 5.302360 GGCATTTGTAGGTATGGTAATCGA 58.698 41.667 0.00 0.00 0.00 3.59
1515 1532 7.654520 GCATTTGTAGGTATGGTAATCGAACTA 59.345 37.037 0.00 0.00 0.00 2.24
1628 1645 8.245701 TGTTGGTCAAAGTTGTTTAAATGTTC 57.754 30.769 0.00 0.00 0.00 3.18
1631 1648 8.472683 TGGTCAAAGTTGTTTAAATGTTCAAG 57.527 30.769 0.00 0.00 0.00 3.02
1696 1714 8.482852 AAAAGGAGAAGAAATGAGGAATTCAA 57.517 30.769 7.93 0.00 39.77 2.69
1935 1953 4.404185 AACCCTCCTAAAGCATTCCTTT 57.596 40.909 0.00 0.00 45.44 3.11
2358 2376 0.391597 GACAACCCTCAGTCGGACAA 59.608 55.000 11.27 0.00 0.00 3.18
2435 2453 4.270245 TGATGCAGTATGTCACAAGTGA 57.730 40.909 0.00 0.00 39.31 3.41
2438 2456 6.405538 TGATGCAGTATGTCACAAGTGAATA 58.594 36.000 4.20 3.38 41.85 1.75
2498 2516 4.376223 TCCATATGAGGGTTCAAAGGGTA 58.624 43.478 3.65 0.00 36.78 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
359 368 6.193514 AGATCTCACTCATAGCATATGACG 57.806 41.667 6.97 0.00 0.00 4.35
420 429 5.049060 TGGGATCGATTTTAATTGGTATGCG 60.049 40.000 0.00 0.00 0.00 4.73
438 448 2.694628 TGCCATAAGTGCAAATGGGATC 59.305 45.455 20.00 8.68 42.51 3.36
530 540 8.564574 GCATGGCATATGAAATGAATTGATTTT 58.435 29.630 17.60 0.00 0.00 1.82
532 542 6.653320 GGCATGGCATATGAAATGAATTGATT 59.347 34.615 15.47 0.00 0.00 2.57
684 695 0.898320 CATTGACCTGAGGGAGACGT 59.102 55.000 2.38 0.00 36.25 4.34
702 713 1.141254 TGTAAGGGCCGAGTCAAAACA 59.859 47.619 0.00 0.00 0.00 2.83
745 756 7.260603 GTGCAATAGTCTGAATAAAATTGGCT 58.739 34.615 0.00 0.00 0.00 4.75
763 774 2.866750 CAAGCCACGCGTGCAATA 59.133 55.556 33.17 0.00 30.89 1.90
861 876 2.340078 GCACCGTGCTCTCTGTCA 59.660 61.111 16.51 0.00 40.96 3.58
897 912 1.376424 CCACTGCCATCGTGCTCTT 60.376 57.895 0.00 0.00 0.00 2.85
907 922 0.321919 CAGCTAGCTTTCCACTGCCA 60.322 55.000 16.46 0.00 0.00 4.92
916 931 1.301293 GCCCTCCACAGCTAGCTTT 59.699 57.895 16.46 5.89 0.00 3.51
936 951 1.920325 AGCTAGCTTCCCACTGCCA 60.920 57.895 12.68 0.00 0.00 4.92
1030 1045 2.676121 CACCCGGCTTTGCATCCA 60.676 61.111 0.00 0.00 0.00 3.41
1046 1061 2.230994 GACAGGCATCTCCTCACGCA 62.231 60.000 0.00 0.00 45.52 5.24
1068 1085 4.662961 CGGCACCGCAGACAGACA 62.663 66.667 0.00 0.00 0.00 3.41
1117 1134 1.734465 CAGACGATTCTGGTTCCTTGC 59.266 52.381 0.00 0.00 45.06 4.01
1128 1145 2.341760 GCACACGTAGAACAGACGATTC 59.658 50.000 1.71 0.00 42.98 2.52
1136 1153 0.663269 CTCGCTGCACACGTAGAACA 60.663 55.000 0.00 0.00 0.00 3.18
1258 1275 4.899239 GGCCAGAGCATCGACCCG 62.899 72.222 0.00 0.00 42.67 5.28
1282 1299 6.207221 TGCTCTTCTTGCAGTTCATTTATCAA 59.793 34.615 0.00 0.00 35.31 2.57
1322 1339 2.990967 CGGTTTGGGGCAGCATGT 60.991 61.111 0.00 0.00 39.31 3.21
1372 1389 2.281484 GTGTGCTTCGCCCTCCAA 60.281 61.111 0.00 0.00 0.00 3.53
1388 1405 2.366916 ACAGCTAGCTCTTTGTCAGTGT 59.633 45.455 16.15 3.48 0.00 3.55
1462 1479 8.997323 CCAAAAGTATTTGCAAATGGTTATTGA 58.003 29.630 30.43 8.73 43.73 2.57
1468 1485 4.071423 GCCCAAAAGTATTTGCAAATGGT 58.929 39.130 30.43 16.65 43.73 3.55
1628 1645 6.683974 TGGTCACTTCTTCTCTTTTTCTTG 57.316 37.500 0.00 0.00 0.00 3.02
1631 1648 6.436843 TGTTGGTCACTTCTTCTCTTTTTC 57.563 37.500 0.00 0.00 0.00 2.29
1696 1714 7.227910 AGCTGCATTTCATTGATCAAAAGTTTT 59.772 29.630 13.09 0.00 0.00 2.43
1835 1853 6.949715 AGGCATATTTTCCATGACATTTTGT 58.050 32.000 0.00 0.00 33.54 2.83
1854 1872 1.412079 CTCTACCAGAGCTGAGGCAT 58.588 55.000 0.00 0.00 41.70 4.40
1935 1953 1.801242 TCAGGGGAGTGACAAAGACA 58.199 50.000 0.00 0.00 0.00 3.41
2147 2165 0.897621 GGGTCCAAAGGAATTGCAGG 59.102 55.000 0.00 0.00 37.73 4.85
2177 2195 6.768381 AGAAGTAAAGAAGTGGGTGAAAGAAG 59.232 38.462 0.00 0.00 0.00 2.85
2358 2376 4.514781 TCAAGTACGTTACAGAGTGCAT 57.485 40.909 0.00 0.00 0.00 3.96
2435 2453 7.455891 TGCATCCATGAATGAGTGTAGATATT 58.544 34.615 0.00 0.00 0.00 1.28
2438 2456 5.300411 TGCATCCATGAATGAGTGTAGAT 57.700 39.130 0.00 0.00 0.00 1.98
2498 2516 3.019564 GACCTTGCAGCTATTGAATGGT 58.980 45.455 0.00 0.00 43.82 3.55


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

AutoCloner maintained by Alex Coulton.