Multiple sequence alignment - TraesCS2A01G036000

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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 TraesCS2A01G036000 chr2A 100.000 2513 0 0 1 2513 15543251 15540739 0.000000e+00 4641
1 TraesCS2A01G036000 chr2A 97.119 243 7 0 2271 2513 52814752 52814510 6.470000e-111 411
2 TraesCS2A01G036000 chr2A 97.119 243 7 0 2271 2513 596740632 596740390 6.470000e-111 411
3 TraesCS2A01G036000 chr7D 96.791 1527 40 7 1 1522 421675284 421676806 0.000000e+00 2540
4 TraesCS2A01G036000 chr3A 96.491 1539 40 11 1 1531 679383986 679382454 0.000000e+00 2531
5 TraesCS2A01G036000 chr3A 87.822 583 58 13 1655 2229 674906667 674906090 0.000000e+00 671
6 TraesCS2A01G036000 chr3A 97.531 243 6 0 2271 2513 480298175 480298417 1.390000e-112 416
7 TraesCS2A01G036000 chr3A 97.794 136 2 1 1517 1651 480297647 480297782 1.500000e-57 233
8 TraesCS2A01G036000 chr3A 97.794 136 2 1 1517 1651 654168555 654168690 1.500000e-57 233
9 TraesCS2A01G036000 chr6A 96.422 1537 46 7 1 1531 468224297 468225830 0.000000e+00 2525
10 TraesCS2A01G036000 chr6A 97.531 243 6 0 2271 2513 468226407 468226649 1.390000e-112 416
11 TraesCS2A01G036000 chr6A 98.529 136 1 1 1517 1651 461949341 461949476 3.230000e-59 239
12 TraesCS2A01G036000 chr6A 97.794 136 2 1 1517 1651 468225879 468226014 1.500000e-57 233
13 TraesCS2A01G036000 chr6D 96.408 1531 42 10 1 1523 451143987 451145512 0.000000e+00 2510
14 TraesCS2A01G036000 chr6D 96.289 1536 45 10 1 1531 451600147 451598619 0.000000e+00 2510
15 TraesCS2A01G036000 chr6D 96.166 1539 45 9 1 1531 397854470 397852938 0.000000e+00 2503
16 TraesCS2A01G036000 chr1A 96.231 1539 46 10 1 1531 257591383 257589849 0.000000e+00 2510
17 TraesCS2A01G036000 chr1A 88.067 595 66 5 1656 2246 551333012 551332419 0.000000e+00 701
18 TraesCS2A01G036000 chr1A 97.942 243 5 0 2271 2513 257589267 257589025 2.990000e-114 422
19 TraesCS2A01G036000 chr1A 97.794 136 2 1 1517 1651 257589800 257589665 1.500000e-57 233
20 TraesCS2A01G036000 chr1A 97.794 136 2 1 1517 1651 582807578 582807713 1.500000e-57 233
21 TraesCS2A01G036000 chr2B 96.229 1538 46 9 1 1531 143026815 143025283 0.000000e+00 2508
22 TraesCS2A01G036000 chr1D 96.106 1541 45 13 1 1531 361004141 361005676 0.000000e+00 2499
23 TraesCS2A01G036000 chr6B 94.850 602 28 3 1655 2254 711338291 711338891 0.000000e+00 937
24 TraesCS2A01G036000 chr4A 88.758 596 62 5 1655 2246 479188483 479189077 0.000000e+00 725
25 TraesCS2A01G036000 chr4A 86.297 613 70 13 1655 2260 510876729 510877334 0.000000e+00 654
26 TraesCS2A01G036000 chr4A 86.700 594 65 14 1661 2246 547905729 547906316 0.000000e+00 647
27 TraesCS2A01G036000 chr4A 97.119 243 7 0 2271 2513 9468999 9469241 6.470000e-111 411
28 TraesCS2A01G036000 chr4A 97.059 136 3 1 1517 1651 638450246 638450111 6.990000e-56 228
29 TraesCS2A01G036000 chr5A 88.739 595 60 7 1657 2246 207962837 207962245 0.000000e+00 721
30 TraesCS2A01G036000 chr5A 87.919 596 64 8 1655 2246 207953153 207952562 0.000000e+00 695
31 TraesCS2A01G036000 chr5A 97.531 243 6 0 2271 2513 673330312 673330070 1.390000e-112 416
32 TraesCS2A01G036000 chr5A 97.119 243 7 0 2271 2513 483353490 483353248 6.470000e-111 411
33 TraesCS2A01G036000 chr5A 97.794 136 2 1 1517 1651 608321287 608321422 1.500000e-57 233
34 TraesCS2A01G036000 chr7A 87.500 584 64 9 1655 2233 604673324 604672745 0.000000e+00 665
35 TraesCS2A01G036000 chr7A 97.119 243 7 0 2271 2513 709082656 709082414 6.470000e-111 411
36 TraesCS2A01G036000 chr7A 97.744 133 3 0 1519 1651 452021314 452021446 1.940000e-56 230


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 TraesCS2A01G036000 chr2A 15540739 15543251 2512 True 4641.0 4641 100.000000 1 2513 1 chr2A.!!$R1 2512
1 TraesCS2A01G036000 chr7D 421675284 421676806 1522 False 2540.0 2540 96.791000 1 1522 1 chr7D.!!$F1 1521
2 TraesCS2A01G036000 chr3A 679382454 679383986 1532 True 2531.0 2531 96.491000 1 1531 1 chr3A.!!$R2 1530
3 TraesCS2A01G036000 chr3A 674906090 674906667 577 True 671.0 671 87.822000 1655 2229 1 chr3A.!!$R1 574
4 TraesCS2A01G036000 chr3A 480297647 480298417 770 False 324.5 416 97.662500 1517 2513 2 chr3A.!!$F2 996
5 TraesCS2A01G036000 chr6A 468224297 468226649 2352 False 1058.0 2525 97.249000 1 2513 3 chr6A.!!$F2 2512
6 TraesCS2A01G036000 chr6D 451143987 451145512 1525 False 2510.0 2510 96.408000 1 1523 1 chr6D.!!$F1 1522
7 TraesCS2A01G036000 chr6D 451598619 451600147 1528 True 2510.0 2510 96.289000 1 1531 1 chr6D.!!$R2 1530
8 TraesCS2A01G036000 chr6D 397852938 397854470 1532 True 2503.0 2503 96.166000 1 1531 1 chr6D.!!$R1 1530
9 TraesCS2A01G036000 chr1A 257589025 257591383 2358 True 1055.0 2510 97.322333 1 2513 3 chr1A.!!$R2 2512
10 TraesCS2A01G036000 chr1A 551332419 551333012 593 True 701.0 701 88.067000 1656 2246 1 chr1A.!!$R1 590
11 TraesCS2A01G036000 chr2B 143025283 143026815 1532 True 2508.0 2508 96.229000 1 1531 1 chr2B.!!$R1 1530
12 TraesCS2A01G036000 chr1D 361004141 361005676 1535 False 2499.0 2499 96.106000 1 1531 1 chr1D.!!$F1 1530
13 TraesCS2A01G036000 chr6B 711338291 711338891 600 False 937.0 937 94.850000 1655 2254 1 chr6B.!!$F1 599
14 TraesCS2A01G036000 chr4A 479188483 479189077 594 False 725.0 725 88.758000 1655 2246 1 chr4A.!!$F2 591
15 TraesCS2A01G036000 chr4A 510876729 510877334 605 False 654.0 654 86.297000 1655 2260 1 chr4A.!!$F3 605
16 TraesCS2A01G036000 chr4A 547905729 547906316 587 False 647.0 647 86.700000 1661 2246 1 chr4A.!!$F4 585
17 TraesCS2A01G036000 chr5A 207962245 207962837 592 True 721.0 721 88.739000 1657 2246 1 chr5A.!!$R2 589
18 TraesCS2A01G036000 chr5A 207952562 207953153 591 True 695.0 695 87.919000 1655 2246 1 chr5A.!!$R1 591
19 TraesCS2A01G036000 chr7A 604672745 604673324 579 True 665.0 665 87.500000 1655 2233 1 chr7A.!!$R1 578

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
550 566 1.06643 GTTGACTCGCTCATAACCCCA 60.066 52.381 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1736 0.036105 TGTCCAGTGCGCTTGATGAT 60.036 50.0 9.73 0.0 0.0 2.45 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
550 566 1.066430 GTTGACTCGCTCATAACCCCA 60.066 52.381 0.00 0.00 0.00 4.96
673 689 1.839354 TGCATCCTGATTGGCTACTGA 59.161 47.619 0.00 0.00 35.26 3.41
674 690 2.216898 GCATCCTGATTGGCTACTGAC 58.783 52.381 0.00 0.00 35.26 3.51
711 736 1.349688 ACGATCTGCCCCACTTTACAA 59.650 47.619 0.00 0.00 0.00 2.41
841 866 4.053009 TCTCCTCTTCTCCATCTGACAA 57.947 45.455 0.00 0.00 0.00 3.18
1158 1183 6.030548 TCCTCGCATCCTTTATCTCTAATG 57.969 41.667 0.00 0.00 0.00 1.90
1392 1417 5.297547 GTGGTAGATGTTGAACTGAAGACA 58.702 41.667 0.00 0.00 0.00 3.41
1395 1420 6.014242 TGGTAGATGTTGAACTGAAGACAGAT 60.014 38.462 0.00 0.00 46.03 2.90
1425 1450 6.489361 AGAAGATGAACAAGAACTTCAAGCAT 59.511 34.615 0.00 0.00 39.22 3.79
1645 1735 8.332996 TGTTAGCTAATAACCTCGAGTATAGG 57.667 38.462 9.88 0.00 42.74 2.57
1646 1736 8.159447 TGTTAGCTAATAACCTCGAGTATAGGA 58.841 37.037 9.88 0.00 42.74 2.94
1647 1737 9.176460 GTTAGCTAATAACCTCGAGTATAGGAT 57.824 37.037 9.88 2.32 38.27 3.24
1648 1738 7.868906 AGCTAATAACCTCGAGTATAGGATC 57.131 40.000 12.31 0.00 37.57 3.36
1649 1739 7.403671 AGCTAATAACCTCGAGTATAGGATCA 58.596 38.462 12.31 0.00 37.57 2.92
1650 1740 8.056400 AGCTAATAACCTCGAGTATAGGATCAT 58.944 37.037 12.31 0.00 37.57 2.45
1651 1741 8.347035 GCTAATAACCTCGAGTATAGGATCATC 58.653 40.741 12.31 0.00 37.57 2.92
1652 1742 9.397280 CTAATAACCTCGAGTATAGGATCATCA 57.603 37.037 12.31 0.00 37.57 3.07
1653 1743 8.651589 AATAACCTCGAGTATAGGATCATCAA 57.348 34.615 12.31 0.00 37.57 2.57
1664 1754 0.654683 GATCATCAAGCGCACTGGAC 59.345 55.000 11.47 0.00 0.00 4.02
1749 1839 1.338973 AGAAAACGACACTGCCGACTA 59.661 47.619 0.00 0.00 0.00 2.59
1750 1840 1.454653 GAAAACGACACTGCCGACTAC 59.545 52.381 0.00 0.00 0.00 2.73
1844 1939 7.765695 TGTGGAAAATTTTTCTAGAGCTGAT 57.234 32.000 18.63 0.00 0.00 2.90
1845 1940 7.820648 TGTGGAAAATTTTTCTAGAGCTGATC 58.179 34.615 18.63 2.67 0.00 2.92
1846 1941 7.667219 TGTGGAAAATTTTTCTAGAGCTGATCT 59.333 33.333 18.63 0.00 42.47 2.75
1862 1957 2.711009 TGATCTTTGGTGAGGTGGTCTT 59.289 45.455 0.00 0.00 0.00 3.01
1873 1968 2.424956 GAGGTGGTCTTTTGATGCATCC 59.575 50.000 23.67 7.79 0.00 3.51
1875 1970 2.562298 GGTGGTCTTTTGATGCATCCAA 59.438 45.455 23.67 16.38 0.00 3.53
1976 2071 3.515071 GCAGCAAGCACATTTTGAAAG 57.485 42.857 0.00 0.00 44.79 2.62
2079 2200 5.128499 TCAAAACTCAAAGGAAATCTGGCAA 59.872 36.000 0.00 0.00 0.00 4.52
2182 2313 5.111293 CAGTTGAAACTTGCTGGAAATTGT 58.889 37.500 0.00 0.00 37.08 2.71
2489 2767 9.907229 TTAGTTTGTTTGGTTAATTTTTCCCAT 57.093 25.926 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 78 6.881065 TCATTTTGGAGTGAGTAAGAAGGATG 59.119 38.462 0.00 0.00 0.00 3.51
149 154 2.026169 GGAGAGAGGGTTTAGGGTTTGG 60.026 54.545 0.00 0.00 0.00 3.28
336 348 9.658799 TGTCCAAATCAAGTTCAAATGTTTTTA 57.341 25.926 0.00 0.00 0.00 1.52
550 566 2.683211 AGGGTTTGGAGCATTTCTGT 57.317 45.000 0.00 0.00 0.00 3.41
711 736 8.434661 GTCATGTGCGAAAAATACAATTTCATT 58.565 29.630 0.00 0.00 36.75 2.57
841 866 2.012673 GATCTGCTCGATGCCTTTGTT 58.987 47.619 4.73 0.00 42.00 2.83
1121 1146 5.510520 GGATGCGAGGAAAACTCAGATCTAT 60.511 44.000 0.00 0.00 46.98 1.98
1347 1372 2.185867 GGGTATTCTGGACGCGCA 59.814 61.111 5.73 0.00 0.00 6.09
1392 1417 8.688747 AGTTCTTGTTCATCTTCTTCAAATCT 57.311 30.769 0.00 0.00 0.00 2.40
1395 1420 8.279970 TGAAGTTCTTGTTCATCTTCTTCAAA 57.720 30.769 4.17 0.00 37.61 2.69
1425 1450 5.413833 GGATTGCTTCTTCAACTCAATCAGA 59.586 40.000 13.15 0.00 42.67 3.27
1643 1733 0.463295 CCAGTGCGCTTGATGATCCT 60.463 55.000 9.73 0.00 0.00 3.24
1644 1734 0.462581 TCCAGTGCGCTTGATGATCC 60.463 55.000 9.73 0.00 0.00 3.36
1645 1735 0.654683 GTCCAGTGCGCTTGATGATC 59.345 55.000 9.73 0.00 0.00 2.92
1646 1736 0.036105 TGTCCAGTGCGCTTGATGAT 60.036 50.000 9.73 0.00 0.00 2.45
1647 1737 0.250252 TTGTCCAGTGCGCTTGATGA 60.250 50.000 9.73 0.00 0.00 2.92
1648 1738 0.167470 CTTGTCCAGTGCGCTTGATG 59.833 55.000 9.73 1.60 0.00 3.07
1649 1739 0.957395 CCTTGTCCAGTGCGCTTGAT 60.957 55.000 9.73 0.00 0.00 2.57
1650 1740 1.597854 CCTTGTCCAGTGCGCTTGA 60.598 57.895 9.73 0.00 0.00 3.02
1651 1741 1.572085 CTCCTTGTCCAGTGCGCTTG 61.572 60.000 9.73 7.27 0.00 4.01
1652 1742 1.302033 CTCCTTGTCCAGTGCGCTT 60.302 57.895 9.73 0.00 0.00 4.68
1653 1743 2.345244 CTCCTTGTCCAGTGCGCT 59.655 61.111 9.73 0.00 0.00 5.92
1664 1754 1.541368 TCCCTGTTCCCCCTCCTTG 60.541 63.158 0.00 0.00 0.00 3.61
1749 1839 4.471904 TCAGAGTTCAGTGTTCAGTTGT 57.528 40.909 0.00 0.00 0.00 3.32
1750 1840 5.352569 AGTTTCAGAGTTCAGTGTTCAGTTG 59.647 40.000 0.00 0.00 0.00 3.16
1844 1939 3.053991 TCAAAAGACCACCTCACCAAAGA 60.054 43.478 0.00 0.00 0.00 2.52
1845 1940 3.287222 TCAAAAGACCACCTCACCAAAG 58.713 45.455 0.00 0.00 0.00 2.77
1846 1941 3.374042 TCAAAAGACCACCTCACCAAA 57.626 42.857 0.00 0.00 0.00 3.28
1873 1968 3.006110 TGAGAAAAATCAGGCAGCCTTTG 59.994 43.478 12.86 1.99 0.00 2.77
1875 1970 2.824341 CTGAGAAAAATCAGGCAGCCTT 59.176 45.455 12.86 0.00 42.52 4.35
1915 2010 6.968250 TGCCATTTTTGGTGAAATTCATTTC 58.032 32.000 0.00 5.46 44.83 2.17
1976 2071 3.826157 TCCACTGGTCCACAATTCAAATC 59.174 43.478 0.00 0.00 0.00 2.17
2079 2200 5.074515 TGGACCTTAGAGTTTCCAAAGGAAT 59.925 40.000 6.95 0.00 41.71 3.01
2182 2313 0.752054 CTTTGGGTCAAGCCAAGCAA 59.248 50.000 12.94 0.00 39.65 3.91
2394 2672 3.423996 TTTGTACACGGCTTTGGTTTC 57.576 42.857 0.00 0.00 0.00 2.78
2431 2709 8.044060 TGTGTTTATAGATGCCTTCTCAAAAG 57.956 34.615 0.00 0.00 35.79 2.27
2436 2714 7.976135 ATGATGTGTTTATAGATGCCTTCTC 57.024 36.000 0.00 0.00 35.79 2.87
2489 2767 2.745281 GTTTAGACACGGCTAATTGGCA 59.255 45.455 16.20 0.00 41.89 4.92


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

AutoCloner maintained by Alex Coulton.