Multiple sequence alignment - TraesCS3D01G098300

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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 TraesCS3D01G098300 chr3D 100.000 2432 0 0 1 2432 49966467 49964036 0.000000e+00 4492.0
1 TraesCS3D01G098300 chr3D 88.067 595 44 17 1021 1592 134640366 134640956 0.000000e+00 680.0
2 TraesCS3D01G098300 chr3D 86.214 457 33 3 596 1022 134639833 134640289 3.660000e-128 468.0
3 TraesCS3D01G098300 chr2D 98.431 1593 16 6 1 1592 103241649 103240065 0.000000e+00 2795.0
4 TraesCS3D01G098300 chr2D 95.906 855 17 5 1593 2432 621363934 621363083 0.000000e+00 1369.0
5 TraesCS3D01G098300 chr1A 95.611 1595 57 8 1 1592 571865858 571864274 0.000000e+00 2545.0
6 TraesCS3D01G098300 chr1A 96.429 56 2 0 1537 1592 517327245 517327300 2.570000e-15 93.5
7 TraesCS3D01G098300 chr5B 92.987 1597 88 11 1 1592 178915760 178914183 0.000000e+00 2307.0
8 TraesCS3D01G098300 chr5B 89.555 517 50 4 1024 1536 5103419 5102903 0.000000e+00 652.0
9 TraesCS3D01G098300 chr5B 86.871 457 30 5 596 1022 607482454 607482910 3.640000e-133 484.0
10 TraesCS3D01G098300 chr2B 95.602 773 28 4 1660 2432 600082340 600081574 0.000000e+00 1234.0
11 TraesCS3D01G098300 chr2B 86.263 859 82 24 1591 2432 776823603 776822764 0.000000e+00 900.0
12 TraesCS3D01G098300 chr2B 92.017 476 35 1 1024 1499 138737314 138736842 0.000000e+00 665.0
13 TraesCS3D01G098300 chr2B 92.581 310 21 2 315 623 227898103 227897795 6.170000e-121 444.0
14 TraesCS3D01G098300 chr2B 83.202 381 40 17 1235 1592 25467917 25467538 6.480000e-86 327.0
15 TraesCS3D01G098300 chr2B 93.194 191 13 0 1 191 227898313 227898123 5.120000e-72 281.0
16 TraesCS3D01G098300 chr2B 84.030 263 17 10 1593 1836 600082476 600082220 1.880000e-56 230.0
17 TraesCS3D01G098300 chr1B 94.286 805 35 7 1630 2432 7319133 7319928 0.000000e+00 1221.0
18 TraesCS3D01G098300 chr1B 83.333 606 72 10 1 597 414554855 414555440 1.280000e-147 532.0
19 TraesCS3D01G098300 chr1B 87.361 451 27 7 602 1022 494554990 494554540 7.810000e-135 490.0
20 TraesCS3D01G098300 chr1B 86.652 457 31 7 596 1022 414556747 414557203 1.690000e-131 479.0
21 TraesCS3D01G098300 chr1B 83.333 258 15 14 1590 1828 7318972 7319220 1.890000e-51 213.0
22 TraesCS3D01G098300 chr6B 94.037 805 37 7 1630 2432 127847556 127848351 0.000000e+00 1210.0
23 TraesCS3D01G098300 chr6B 89.353 695 55 9 138 818 203463253 203462564 0.000000e+00 856.0
24 TraesCS3D01G098300 chr6B 87.527 457 27 7 596 1022 132658482 132658026 3.610000e-138 501.0
25 TraesCS3D01G098300 chr6B 83.083 266 17 12 1590 1836 127847395 127847651 1.460000e-52 217.0
26 TraesCS3D01G098300 chr6B 91.946 149 12 0 4 152 203463419 203463271 2.450000e-50 209.0
27 TraesCS3D01G098300 chr3B 86.578 1058 87 14 1 1021 775177369 775176330 0.000000e+00 1116.0
28 TraesCS3D01G098300 chr3B 90.772 661 46 9 1 659 769386618 769385971 0.000000e+00 869.0
29 TraesCS3D01G098300 chr4B 92.317 794 37 16 1660 2432 411178245 411179035 0.000000e+00 1107.0
30 TraesCS3D01G098300 chr4A 90.216 695 50 7 138 818 709876034 709875344 0.000000e+00 891.0
31 TraesCS3D01G098300 chr4A 91.881 505 36 4 1929 2432 645767598 645768098 0.000000e+00 701.0
32 TraesCS3D01G098300 chr4A 84.683 457 51 10 1139 1594 428743243 428742805 2.870000e-119 438.0
33 TraesCS3D01G098300 chr4A 91.946 149 12 0 4 152 709876198 709876050 2.450000e-50 209.0
34 TraesCS3D01G098300 chr5A 93.491 507 29 4 1021 1523 697889952 697890458 0.000000e+00 750.0
35 TraesCS3D01G098300 chr5A 87.309 457 28 9 596 1022 697889419 697889875 1.680000e-136 496.0
36 TraesCS3D01G098300 chr5A 87.361 451 27 5 602 1022 651581528 651581078 7.810000e-135 490.0
37 TraesCS3D01G098300 chr7A 90.637 534 47 2 1899 2432 683627567 683627037 0.000000e+00 706.0
38 TraesCS3D01G098300 chr7A 90.200 500 33 10 105 597 729165266 729164776 2.640000e-179 638.0
39 TraesCS3D01G098300 chr7A 87.634 558 46 9 45 597 729166619 729167158 5.710000e-176 627.0
40 TraesCS3D01G098300 chr7A 96.610 59 2 0 1537 1595 706402698 706402640 5.530000e-17 99.0
41 TraesCS3D01G098300 chr7A 98.214 56 1 0 1537 1592 712074614 712074669 5.530000e-17 99.0
42 TraesCS3D01G098300 chr1D 90.637 534 47 2 1899 2432 108679517 108680047 0.000000e+00 706.0
43 TraesCS3D01G098300 chr1D 91.331 496 39 4 1021 1515 481612242 481612734 0.000000e+00 675.0
44 TraesCS3D01G098300 chr4D 91.429 490 41 1 1021 1509 398867666 398868155 0.000000e+00 671.0
45 TraesCS3D01G098300 chr4D 86.681 458 30 4 596 1022 398867132 398867589 1.690000e-131 479.0
46 TraesCS3D01G098300 chr5D 90.392 510 47 2 1024 1532 292726617 292726109 0.000000e+00 669.0
47 TraesCS3D01G098300 chr5D 86.522 460 31 4 596 1025 292727152 292726694 6.080000e-131 477.0


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 TraesCS3D01G098300 chr3D 49964036 49966467 2431 True 4492.0 4492 100.0000 1 2432 1 chr3D.!!$R1 2431
1 TraesCS3D01G098300 chr3D 134639833 134640956 1123 False 574.0 680 87.1405 596 1592 2 chr3D.!!$F1 996
2 TraesCS3D01G098300 chr2D 103240065 103241649 1584 True 2795.0 2795 98.4310 1 1592 1 chr2D.!!$R1 1591
3 TraesCS3D01G098300 chr2D 621363083 621363934 851 True 1369.0 1369 95.9060 1593 2432 1 chr2D.!!$R2 839
4 TraesCS3D01G098300 chr1A 571864274 571865858 1584 True 2545.0 2545 95.6110 1 1592 1 chr1A.!!$R1 1591
5 TraesCS3D01G098300 chr5B 178914183 178915760 1577 True 2307.0 2307 92.9870 1 1592 1 chr5B.!!$R2 1591
6 TraesCS3D01G098300 chr5B 5102903 5103419 516 True 652.0 652 89.5550 1024 1536 1 chr5B.!!$R1 512
7 TraesCS3D01G098300 chr2B 776822764 776823603 839 True 900.0 900 86.2630 1591 2432 1 chr2B.!!$R3 841
8 TraesCS3D01G098300 chr2B 600081574 600082476 902 True 732.0 1234 89.8160 1593 2432 2 chr2B.!!$R5 839
9 TraesCS3D01G098300 chr2B 227897795 227898313 518 True 362.5 444 92.8875 1 623 2 chr2B.!!$R4 622
10 TraesCS3D01G098300 chr1B 7318972 7319928 956 False 717.0 1221 88.8095 1590 2432 2 chr1B.!!$F1 842
11 TraesCS3D01G098300 chr1B 414554855 414557203 2348 False 505.5 532 84.9925 1 1022 2 chr1B.!!$F2 1021
12 TraesCS3D01G098300 chr6B 127847395 127848351 956 False 713.5 1210 88.5600 1590 2432 2 chr6B.!!$F1 842
13 TraesCS3D01G098300 chr6B 203462564 203463419 855 True 532.5 856 90.6495 4 818 2 chr6B.!!$R2 814
14 TraesCS3D01G098300 chr3B 775176330 775177369 1039 True 1116.0 1116 86.5780 1 1021 1 chr3B.!!$R2 1020
15 TraesCS3D01G098300 chr3B 769385971 769386618 647 True 869.0 869 90.7720 1 659 1 chr3B.!!$R1 658
16 TraesCS3D01G098300 chr4B 411178245 411179035 790 False 1107.0 1107 92.3170 1660 2432 1 chr4B.!!$F1 772
17 TraesCS3D01G098300 chr4A 645767598 645768098 500 False 701.0 701 91.8810 1929 2432 1 chr4A.!!$F1 503
18 TraesCS3D01G098300 chr4A 709875344 709876198 854 True 550.0 891 91.0810 4 818 2 chr4A.!!$R2 814
19 TraesCS3D01G098300 chr5A 697889419 697890458 1039 False 623.0 750 90.4000 596 1523 2 chr5A.!!$F1 927
20 TraesCS3D01G098300 chr7A 683627037 683627567 530 True 706.0 706 90.6370 1899 2432 1 chr7A.!!$R1 533
21 TraesCS3D01G098300 chr7A 729166619 729167158 539 False 627.0 627 87.6340 45 597 1 chr7A.!!$F2 552
22 TraesCS3D01G098300 chr1D 108679517 108680047 530 False 706.0 706 90.6370 1899 2432 1 chr1D.!!$F1 533
23 TraesCS3D01G098300 chr4D 398867132 398868155 1023 False 575.0 671 89.0550 596 1509 2 chr4D.!!$F1 913
24 TraesCS3D01G098300 chr5D 292726109 292727152 1043 True 573.0 669 88.4570 596 1532 2 chr5D.!!$R1 936

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
348 394 3.811083 TCAGGTAGCGACAAAAGGAAAA 58.189 40.909 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1658 3177 0.445436 GTGCTGCTGTGTATGTGCTC 59.555 55.0 0.0 0.0 0.0 4.26 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
158 191 4.857588 CGTCTGCAGACTTTAGAAACGTAT 59.142 41.667 36.78 0.00 42.66 3.06
348 394 3.811083 TCAGGTAGCGACAAAAGGAAAA 58.189 40.909 0.00 0.00 0.00 2.29
349 395 4.200874 TCAGGTAGCGACAAAAGGAAAAA 58.799 39.130 0.00 0.00 0.00 1.94
1048 2535 4.671377 TGAACTTGAAGAATGTTGCACAC 58.329 39.130 0.00 0.00 0.00 3.82
1280 2767 6.073602 GCCGAAAGAAGCTTTTCAAATTTGAT 60.074 34.615 21.10 5.58 36.99 2.57
1583 3094 1.709994 GGCCCCCGAAATCTCAGGAT 61.710 60.000 0.00 0.00 0.00 3.24
1658 3177 0.955428 AACACATACACGGCAGCTGG 60.955 55.000 17.12 1.57 0.00 4.85
1803 3482 7.737972 ACAGCATATACAGTAACAACAACAA 57.262 32.000 0.00 0.00 0.00 2.83
1804 3483 7.581476 ACAGCATATACAGTAACAACAACAAC 58.419 34.615 0.00 0.00 0.00 3.32
1805 3484 7.227711 ACAGCATATACAGTAACAACAACAACA 59.772 33.333 0.00 0.00 0.00 3.33
1812 3491 7.328277 ACAGTAACAACAACAACACATACAT 57.672 32.000 0.00 0.00 0.00 2.29
1831 3510 2.620251 TCAACAGCAGCACTTGTACT 57.380 45.000 0.00 0.00 0.00 2.73
2091 3777 7.735917 TCACTAAGGATGAGTTTACCATATGG 58.264 38.462 20.68 20.68 42.17 2.74
2112 3798 1.000717 TCGCAACATGTCAGAACGAGA 60.001 47.619 0.00 0.00 0.00 4.04
2205 3891 6.349611 GGCTCAAGTGATTTCAAAGCATCTTA 60.350 38.462 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 191 5.250982 TGATGGTCGAACTTCTGTAGTCTA 58.749 41.667 16.38 0.00 35.54 2.59
1048 2535 9.688592 ATTAAGAGAGAAAGTTTCTGCAAATTG 57.311 29.630 22.68 0.00 40.87 2.32
1583 3094 1.558167 TTAAGTGCATCCAGGGCCGA 61.558 55.000 0.00 0.00 0.00 5.54
1658 3177 0.445436 GTGCTGCTGTGTATGTGCTC 59.555 55.000 0.00 0.00 0.00 4.26
1803 3482 2.485426 GTGCTGCTGTTGATGTATGTGT 59.515 45.455 0.00 0.00 0.00 3.72
1804 3483 2.745821 AGTGCTGCTGTTGATGTATGTG 59.254 45.455 0.00 0.00 0.00 3.21
1805 3484 3.063510 AGTGCTGCTGTTGATGTATGT 57.936 42.857 0.00 0.00 0.00 2.29
1812 3491 2.212652 CAGTACAAGTGCTGCTGTTGA 58.787 47.619 17.59 3.35 36.56 3.18
1831 3510 4.640201 GGCTGATTTATAAGTGTTCCTGCA 59.360 41.667 0.00 0.00 0.00 4.41
2091 3777 1.125021 CTCGTTCTGACATGTTGCGAC 59.875 52.381 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.