Multiple sequence alignment - TraesCS3D01G515000

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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 TraesCS3D01G515000 chr3D 100.000 3386 0 0 1 3386 598727081 598723696 0.000000e+00 6253.0
1 TraesCS3D01G515000 chr3B 96.634 2020 65 2 733 2749 806058735 806056716 0.000000e+00 3350.0
2 TraesCS3D01G515000 chr3B 93.431 1918 104 11 211 2124 805812641 805810742 0.000000e+00 2824.0
3 TraesCS3D01G515000 chr3B 95.521 826 37 0 1211 2036 805968584 805967759 0.000000e+00 1321.0
4 TraesCS3D01G515000 chr3B 92.442 860 36 9 359 1215 805977987 805977154 0.000000e+00 1201.0
5 TraesCS3D01G515000 chr3B 93.279 610 36 5 2750 3358 612308205 612308810 0.000000e+00 894.0
6 TraesCS3D01G515000 chr3B 92.742 620 39 6 2741 3358 309400505 309401120 0.000000e+00 891.0
7 TraesCS3D01G515000 chr3B 95.265 528 25 0 763 1290 806003669 806003142 0.000000e+00 837.0
8 TraesCS3D01G515000 chr3B 96.970 396 12 0 1 396 806016759 806016364 0.000000e+00 665.0
9 TraesCS3D01G515000 chr3B 95.263 380 18 0 2123 2502 805810687 805810308 1.340000e-168 603.0
10 TraesCS3D01G515000 chr3B 95.628 366 12 2 10 371 805979953 805979588 4.870000e-163 584.0
11 TraesCS3D01G515000 chr3B 95.796 333 14 0 2417 2749 805931914 805931582 3.840000e-149 538.0
12 TraesCS3D01G515000 chr3B 81.481 432 71 7 2110 2539 810193031 810192607 2.500000e-91 346.0
13 TraesCS3D01G515000 chr3B 96.552 174 6 0 667 840 806058876 806058703 4.270000e-74 289.0
14 TraesCS3D01G515000 chr3B 93.567 171 2 1 1 171 805812799 805812638 2.610000e-61 246.0
15 TraesCS3D01G515000 chr3B 95.238 105 4 1 667 771 806004220 806004117 7.520000e-37 165.0
16 TraesCS3D01G515000 chr3A 95.816 1649 67 1 1103 2749 728915280 728913632 0.000000e+00 2662.0
17 TraesCS3D01G515000 chr3A 83.578 1705 182 52 478 2124 732405048 732403384 0.000000e+00 1507.0
18 TraesCS3D01G515000 chr3A 92.677 437 24 1 669 1105 728925374 728924946 1.030000e-174 623.0
19 TraesCS3D01G515000 chr3A 94.660 206 8 1 1 203 728930942 728930737 1.960000e-82 316.0
20 TraesCS3D01G515000 chr7A 86.027 2147 205 37 41 2124 566988714 566990828 0.000000e+00 2215.0
21 TraesCS3D01G515000 chr7A 82.606 1788 178 75 412 2124 566909837 566911566 0.000000e+00 1456.0
22 TraesCS3D01G515000 chr7A 83.607 1159 143 28 991 2124 566790499 566791635 0.000000e+00 1044.0
23 TraesCS3D01G515000 chr7A 84.607 877 98 21 1267 2124 619305129 619305987 0.000000e+00 837.0
24 TraesCS3D01G515000 chr7A 92.710 535 36 3 2791 3324 173070048 173069516 0.000000e+00 769.0
25 TraesCS3D01G515000 chr7A 82.942 639 79 18 2110 2743 566990858 566991471 1.780000e-152 549.0
26 TraesCS3D01G515000 chr7A 81.804 621 93 11 2123 2734 566791679 566792288 1.400000e-138 503.0
27 TraesCS3D01G515000 chr7A 86.344 227 22 4 155 380 566789676 566789894 4.370000e-59 239.0
28 TraesCS3D01G515000 chr7A 80.233 258 19 14 412 656 566789988 566790226 7.520000e-37 165.0
29 TraesCS3D01G515000 chrUn 85.322 1383 130 33 788 2125 86611945 86613299 0.000000e+00 1362.0
30 TraesCS3D01G515000 chrUn 83.762 622 73 16 2123 2743 86613341 86613935 6.340000e-157 564.0
31 TraesCS3D01G515000 chrUn 86.498 237 23 4 422 655 86611620 86611850 5.610000e-63 252.0
32 TraesCS3D01G515000 chr7D 84.855 1380 152 36 788 2125 500776011 500777375 0.000000e+00 1338.0
33 TraesCS3D01G515000 chr7D 86.904 1153 111 22 991 2124 113583065 113584196 0.000000e+00 1256.0
34 TraesCS3D01G515000 chr7D 93.432 609 38 2 2750 3358 163602540 163603146 0.000000e+00 902.0
35 TraesCS3D01G515000 chr7D 84.000 625 72 15 2123 2743 500777417 500778017 2.930000e-160 575.0
36 TraesCS3D01G515000 chr7D 77.816 293 17 24 412 682 500775644 500775910 1.640000e-28 137.0
37 TraesCS3D01G515000 chr7B 83.358 1370 174 40 788 2124 528873675 528875023 0.000000e+00 1218.0
38 TraesCS3D01G515000 chr7B 88.909 559 59 3 2749 3307 630498984 630499539 0.000000e+00 686.0
39 TraesCS3D01G515000 chr7B 82.126 621 87 12 2123 2734 528875068 528875673 8.380000e-141 510.0
40 TraesCS3D01G515000 chr7B 82.175 561 80 13 2123 2678 73139933 73140478 6.620000e-127 464.0
41 TraesCS3D01G515000 chr7B 84.589 292 25 12 421 700 664399436 664399153 4.310000e-69 272.0
42 TraesCS3D01G515000 chr7B 74.956 563 60 42 412 931 73175916 73176440 2.080000e-42 183.0
43 TraesCS3D01G515000 chr7B 85.955 178 18 3 763 933 664399068 664398891 2.080000e-42 183.0
44 TraesCS3D01G515000 chr5A 82.682 1126 164 17 998 2117 605245730 605244630 0.000000e+00 970.0
45 TraesCS3D01G515000 chr5A 92.962 611 39 4 2750 3358 567493251 567492643 0.000000e+00 887.0
46 TraesCS3D01G515000 chr4D 93.721 637 37 3 2750 3384 64631476 64630841 0.000000e+00 952.0
47 TraesCS3D01G515000 chr4D 91.028 613 46 8 2749 3358 24179544 24178938 0.000000e+00 819.0
48 TraesCS3D01G515000 chr4D 89.491 609 51 13 2745 3348 109918959 109918359 0.000000e+00 758.0
49 TraesCS3D01G515000 chr4D 89.185 601 60 5 2739 3338 83101277 83100681 0.000000e+00 745.0
50 TraesCS3D01G515000 chr4D 100.000 28 0 0 3359 3386 46051725 46051698 6.000000e-03 52.8
51 TraesCS3D01G515000 chr4D 100.000 28 0 0 3359 3386 60139514 60139487 6.000000e-03 52.8
52 TraesCS3D01G515000 chr4D 100.000 28 0 0 3359 3386 81322096 81322069 6.000000e-03 52.8
53 TraesCS3D01G515000 chr2B 93.617 611 32 6 2750 3358 625160178 625160783 0.000000e+00 905.0
54 TraesCS3D01G515000 chr4B 93.042 618 36 7 2743 3358 419587856 419588468 0.000000e+00 896.0
55 TraesCS3D01G515000 chr1B 93.301 612 34 7 2749 3358 283376749 283376143 0.000000e+00 896.0
56 TraesCS3D01G515000 chr5D 93.268 609 38 3 2750 3358 188816171 188816776 0.000000e+00 894.0
57 TraesCS3D01G515000 chr5B 84.307 599 78 10 2135 2728 595009066 595008479 3.790000e-159 571.0


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 TraesCS3D01G515000 chr3D 598723696 598727081 3385 True 6253.000000 6253 100.000000 1 3386 1 chr3D.!!$R1 3385
1 TraesCS3D01G515000 chr3B 806056716 806058876 2160 True 1819.500000 3350 96.593000 667 2749 2 chr3B.!!$R8 2082
2 TraesCS3D01G515000 chr3B 805967759 805968584 825 True 1321.000000 1321 95.521000 1211 2036 1 chr3B.!!$R2 825
3 TraesCS3D01G515000 chr3B 805810308 805812799 2491 True 1224.333333 2824 94.087000 1 2502 3 chr3B.!!$R5 2501
4 TraesCS3D01G515000 chr3B 612308205 612308810 605 False 894.000000 894 93.279000 2750 3358 1 chr3B.!!$F2 608
5 TraesCS3D01G515000 chr3B 805977154 805979953 2799 True 892.500000 1201 94.035000 10 1215 2 chr3B.!!$R6 1205
6 TraesCS3D01G515000 chr3B 309400505 309401120 615 False 891.000000 891 92.742000 2741 3358 1 chr3B.!!$F1 617
7 TraesCS3D01G515000 chr3B 806003142 806004220 1078 True 501.000000 837 95.251500 667 1290 2 chr3B.!!$R7 623
8 TraesCS3D01G515000 chr3A 728913632 728915280 1648 True 2662.000000 2662 95.816000 1103 2749 1 chr3A.!!$R1 1646
9 TraesCS3D01G515000 chr3A 732403384 732405048 1664 True 1507.000000 1507 83.578000 478 2124 1 chr3A.!!$R4 1646
10 TraesCS3D01G515000 chr7A 566909837 566911566 1729 False 1456.000000 1456 82.606000 412 2124 1 chr7A.!!$F1 1712
11 TraesCS3D01G515000 chr7A 566988714 566991471 2757 False 1382.000000 2215 84.484500 41 2743 2 chr7A.!!$F4 2702
12 TraesCS3D01G515000 chr7A 619305129 619305987 858 False 837.000000 837 84.607000 1267 2124 1 chr7A.!!$F2 857
13 TraesCS3D01G515000 chr7A 173069516 173070048 532 True 769.000000 769 92.710000 2791 3324 1 chr7A.!!$R1 533
14 TraesCS3D01G515000 chr7A 566789676 566792288 2612 False 487.750000 1044 82.997000 155 2734 4 chr7A.!!$F3 2579
15 TraesCS3D01G515000 chrUn 86611620 86613935 2315 False 726.000000 1362 85.194000 422 2743 3 chrUn.!!$F1 2321
16 TraesCS3D01G515000 chr7D 113583065 113584196 1131 False 1256.000000 1256 86.904000 991 2124 1 chr7D.!!$F1 1133
17 TraesCS3D01G515000 chr7D 163602540 163603146 606 False 902.000000 902 93.432000 2750 3358 1 chr7D.!!$F2 608
18 TraesCS3D01G515000 chr7D 500775644 500778017 2373 False 683.333333 1338 82.223667 412 2743 3 chr7D.!!$F3 2331
19 TraesCS3D01G515000 chr7B 528873675 528875673 1998 False 864.000000 1218 82.742000 788 2734 2 chr7B.!!$F4 1946
20 TraesCS3D01G515000 chr7B 630498984 630499539 555 False 686.000000 686 88.909000 2749 3307 1 chr7B.!!$F3 558
21 TraesCS3D01G515000 chr7B 73139933 73140478 545 False 464.000000 464 82.175000 2123 2678 1 chr7B.!!$F1 555
22 TraesCS3D01G515000 chr7B 664398891 664399436 545 True 227.500000 272 85.272000 421 933 2 chr7B.!!$R1 512
23 TraesCS3D01G515000 chr5A 605244630 605245730 1100 True 970.000000 970 82.682000 998 2117 1 chr5A.!!$R2 1119
24 TraesCS3D01G515000 chr5A 567492643 567493251 608 True 887.000000 887 92.962000 2750 3358 1 chr5A.!!$R1 608
25 TraesCS3D01G515000 chr4D 64630841 64631476 635 True 952.000000 952 93.721000 2750 3384 1 chr4D.!!$R4 634
26 TraesCS3D01G515000 chr4D 24178938 24179544 606 True 819.000000 819 91.028000 2749 3358 1 chr4D.!!$R1 609
27 TraesCS3D01G515000 chr4D 109918359 109918959 600 True 758.000000 758 89.491000 2745 3348 1 chr4D.!!$R7 603
28 TraesCS3D01G515000 chr4D 83100681 83101277 596 True 745.000000 745 89.185000 2739 3338 1 chr4D.!!$R6 599
29 TraesCS3D01G515000 chr2B 625160178 625160783 605 False 905.000000 905 93.617000 2750 3358 1 chr2B.!!$F1 608
30 TraesCS3D01G515000 chr4B 419587856 419588468 612 False 896.000000 896 93.042000 2743 3358 1 chr4B.!!$F1 615
31 TraesCS3D01G515000 chr1B 283376143 283376749 606 True 896.000000 896 93.301000 2749 3358 1 chr1B.!!$R1 609
32 TraesCS3D01G515000 chr5D 188816171 188816776 605 False 894.000000 894 93.268000 2750 3358 1 chr5D.!!$F1 608
33 TraesCS3D01G515000 chr5B 595008479 595009066 587 True 571.000000 571 84.307000 2135 2728 1 chr5B.!!$R1 593

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
703 2489 0.831307 ATGCAGAGATGAGCAGCTGA 59.169 50.000 20.43 0.0 44.94 4.26 F
2240 4784 2.281070 CTGTGGACAGCAAGGCGT 60.281 61.111 0.00 0.0 37.15 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 4843 1.233950 TGCGTTGGATGCATGTCGTT 61.234 50.0 2.46 0.0 34.76 3.85 R
3228 5802 2.485814 GGAGTCACATGGAGTCTTTTGC 59.514 50.0 14.74 0.0 44.09 3.68 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
102 103 7.445402 TCTTTTCTTCATGTCTTAGTTTGGAGG 59.555 37.037 0.00 0.0 0.00 4.30
313 330 6.930667 TTTAACTTTGGTAGTCACTTGGTC 57.069 37.500 0.00 0.0 35.54 4.02
322 339 3.127425 AGTCACTTGGTCCTACTTTGC 57.873 47.619 0.00 0.0 0.00 3.68
458 2154 4.261197 CCCTTTGCAACTGTTACTGAGAAC 60.261 45.833 0.00 0.0 0.00 3.01
464 2160 4.360563 CAACTGTTACTGAGAACGTGACT 58.639 43.478 0.00 0.0 31.59 3.41
703 2489 0.831307 ATGCAGAGATGAGCAGCTGA 59.169 50.000 20.43 0.0 44.94 4.26
1045 3448 4.144727 TCGCCCTCCTCCTCCTCC 62.145 72.222 0.00 0.0 0.00 4.30
1594 4032 5.246981 TCAAGAAGATGGTCAAAGATGGT 57.753 39.130 0.00 0.0 0.00 3.55
2028 4504 3.526931 AGAATGTCCACATCGTCGATT 57.473 42.857 4.63 0.0 35.10 3.34
2240 4784 2.281070 CTGTGGACAGCAAGGCGT 60.281 61.111 0.00 0.0 37.15 5.68
2263 4807 3.026630 TGTCCACAGAGCTTCTTTACG 57.973 47.619 0.00 0.0 0.00 3.18
2781 5351 1.611977 TCCGAAGCCATATCGTCGATT 59.388 47.619 13.91 0.0 39.65 3.34
2796 5366 2.621998 GTCGATTATCCGAGGACCAAGA 59.378 50.000 0.00 0.0 39.43 3.02
2832 5404 3.426191 CGACACCGAGATTTGTTAACGAA 59.574 43.478 10.70 10.7 38.22 3.85
2900 5473 1.533625 CCCATGACACCGTCACAATT 58.466 50.000 0.00 0.0 45.65 2.32
2955 5529 2.987125 GGCTTCCCCTGCGTTCTA 59.013 61.111 0.00 0.0 0.00 2.10
3104 5678 4.879197 ACTGTAACCTACCTTGTACACC 57.121 45.455 0.00 0.0 0.00 4.16
3214 5788 7.616935 ACATTGAACTTGAGTTTATCCCATGAT 59.383 33.333 0.00 0.0 38.56 2.45
3228 5802 1.215244 CATGATCACCGCTGCTACTG 58.785 55.000 0.00 0.0 0.00 2.74
3330 5906 9.895138 TTAAGTTCCTTGTTACTCTAGTTTGTT 57.105 29.630 0.00 0.0 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
313 330 6.681368 GCATAATTTTCCTCAGGCAAAGTAGG 60.681 42.308 3.94 3.94 0.00 3.18
322 339 8.912988 TGGTAAATAAGCATAATTTTCCTCAGG 58.087 33.333 12.17 0.00 35.76 3.86
458 2154 0.101399 CCTCGATCTTGGGAGTCACG 59.899 60.000 0.00 0.00 0.00 4.35
464 2160 1.602237 GTTGGCCTCGATCTTGGGA 59.398 57.895 3.32 0.00 0.00 4.37
539 2249 0.608308 GCTGTTAACCTCCACCCCAC 60.608 60.000 2.48 0.00 0.00 4.61
633 2361 4.539083 TCCACGCCGTTGCACACT 62.539 61.111 0.00 0.00 37.32 3.55
641 2369 4.680537 AGACCTCCTCCACGCCGT 62.681 66.667 0.00 0.00 0.00 5.68
703 2489 2.354305 GCGTCGTCGTTCACTGGT 60.354 61.111 3.66 0.00 39.49 4.00
1045 3448 0.107017 ACGCCATTGGGATTCAGGAG 60.107 55.000 4.53 0.00 35.59 3.69
1594 4032 4.693566 GTCAATTGTTTCTCCGTGATGGTA 59.306 41.667 5.13 0.00 39.52 3.25
1646 4084 2.476821 GGTGCTTGCATAATCATTGCC 58.523 47.619 0.00 0.00 39.39 4.52
1689 4153 7.992008 TGTTGATATAGTACTCACATCGTTGA 58.008 34.615 0.00 0.00 0.00 3.18
2127 4671 8.830580 CCTTTACCTACATCAATGTACATCAAG 58.169 37.037 9.23 2.79 41.97 3.02
2140 4684 3.386402 AGCTCTGAGCCTTTACCTACATC 59.614 47.826 25.09 0.00 43.77 3.06
2240 4784 3.281727 AAAGAAGCTCTGTGGACAACA 57.718 42.857 0.00 0.00 37.22 3.33
2263 4807 3.712881 GGACTTGTCGCACACGGC 61.713 66.667 0.00 0.00 46.48 5.68
2299 4843 1.233950 TGCGTTGGATGCATGTCGTT 61.234 50.000 2.46 0.00 34.76 3.85
2766 5336 3.014623 TCGGATAATCGACGATATGGCT 58.985 45.455 11.42 0.00 33.92 4.75
2768 5338 3.626217 TCCTCGGATAATCGACGATATGG 59.374 47.826 11.42 6.13 35.93 2.74
2781 5351 3.772572 TGTGATTTCTTGGTCCTCGGATA 59.227 43.478 0.00 0.00 0.00 2.59
2796 5366 1.595794 GGTGTCGTGTTCGTGTGATTT 59.404 47.619 0.00 0.00 38.33 2.17
2832 5404 5.657302 GGGGATATAGTCATATCGGTGAACT 59.343 44.000 0.00 0.00 42.75 3.01
2846 5418 0.192566 TCAAGCCCCGGGGATATAGT 59.807 55.000 44.86 20.62 37.50 2.12
2955 5529 5.310409 ACCTATGCCAACATAATAGCACT 57.690 39.130 0.00 0.00 38.29 4.40
3104 5678 5.605564 TTGTTGGAGTTGTGTCGAATATG 57.394 39.130 0.00 0.00 0.00 1.78
3228 5802 2.485814 GGAGTCACATGGAGTCTTTTGC 59.514 50.000 14.74 0.00 44.09 3.68
3230 5804 3.496870 GGTGGAGTCACATGGAGTCTTTT 60.497 47.826 14.74 0.00 45.32 2.27
3330 5906 3.375699 GGATACTCTGGAAGTTGGGAGA 58.624 50.000 0.00 0.00 39.55 3.71


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

AutoCloner maintained by Alex Coulton.