Multiple sequence alignment - TraesCS5B01G001100

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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 TraesCS5B01G001100 chr5B 100.000 4243 0 0 2461 6703 864135 859893 0.000000e+00 7836.0
1 TraesCS5B01G001100 chr5B 100.000 2151 0 0 1 2151 866595 864445 0.000000e+00 3973.0
2 TraesCS5B01G001100 chr5B 83.903 1609 248 9 3893 5494 44140287 44141891 0.000000e+00 1526.0
3 TraesCS5B01G001100 chr5B 95.708 932 23 7 5775 6703 400664014 400664931 0.000000e+00 1483.0
4 TraesCS5B01G001100 chr5B 98.758 322 4 0 1830 2151 411933655 411933334 2.100000e-159 573.0
5 TraesCS5B01G001100 chr5B 93.889 360 15 6 6345 6701 407242802 407242447 2.750000e-148 536.0
6 TraesCS5B01G001100 chr5B 98.286 175 3 0 2461 2635 137415231 137415057 2.350000e-79 307.0
7 TraesCS5B01G001100 chr5B 94.845 97 2 3 3688 3782 13350146 13350051 1.510000e-31 148.0
8 TraesCS5B01G001100 chr5B 93.814 97 2 3 3684 3780 13364611 13364703 7.010000e-30 143.0
9 TraesCS5B01G001100 chr5B 92.157 102 6 2 3691 3792 687331438 687331339 7.010000e-30 143.0
10 TraesCS5B01G001100 chr5B 100.000 56 0 0 3563 3618 862982 862927 3.310000e-18 104.0
11 TraesCS5B01G001100 chr5B 100.000 56 0 0 3614 3669 863033 862978 3.310000e-18 104.0
12 TraesCS5B01G001100 chr5D 92.653 2137 133 14 3640 5766 6822804 6820682 0.000000e+00 3055.0
13 TraesCS5B01G001100 chr5D 84.217 1603 246 5 3896 5493 44571487 44569887 0.000000e+00 1552.0
14 TraesCS5B01G001100 chr5D 84.484 1057 63 36 696 1670 6824192 6823155 0.000000e+00 950.0
15 TraesCS5B01G001100 chr5D 87.053 587 35 20 5775 6346 72364071 72364631 5.710000e-175 625.0
16 TraesCS5B01G001100 chr5D 92.222 360 21 6 6345 6701 536867438 536867083 2.790000e-138 503.0
17 TraesCS5B01G001100 chr5D 80.414 531 77 17 3683 4190 3810217 3809691 4.910000e-101 379.0
18 TraesCS5B01G001100 chr5D 86.879 282 14 11 3043 3319 6823114 6822851 1.830000e-75 294.0
19 TraesCS5B01G001100 chr5D 96.667 90 2 1 3699 3788 544801961 544801873 1.510000e-31 148.0
20 TraesCS5B01G001100 chr5D 92.157 102 6 2 3682 3782 13909890 13909790 7.010000e-30 143.0
21 TraesCS5B01G001100 chr5D 92.941 85 6 0 4 88 6824767 6824683 2.540000e-24 124.0
22 TraesCS5B01G001100 chr5A 94.794 1921 90 5 3842 5760 3086832 3088744 0.000000e+00 2985.0
23 TraesCS5B01G001100 chr5A 83.770 1602 255 3 3896 5493 34982768 34981168 0.000000e+00 1513.0
24 TraesCS5B01G001100 chr5A 85.600 1250 172 7 3880 5124 3132588 3133834 0.000000e+00 1304.0
25 TraesCS5B01G001100 chr5A 81.036 1313 91 71 471 1670 3085028 3086295 0.000000e+00 900.0
26 TraesCS5B01G001100 chr5A 95.495 111 4 1 3689 3798 3086722 3086832 6.910000e-40 176.0
27 TraesCS5B01G001100 chr5A 96.078 51 2 0 1213 1263 34986385 34986335 4.310000e-12 84.2
28 TraesCS5B01G001100 chr5A 90.476 63 5 1 3026 3087 3086561 3086623 1.550000e-11 82.4
29 TraesCS5B01G001100 chr6A 96.026 931 20 7 5775 6703 107169508 107170423 0.000000e+00 1498.0
30 TraesCS5B01G001100 chr7A 95.334 943 26 8 5764 6703 482328886 482329813 0.000000e+00 1482.0
31 TraesCS5B01G001100 chr7A 85.566 1157 160 6 4345 5498 47511682 47512834 0.000000e+00 1205.0
32 TraesCS5B01G001100 chr7A 88.756 587 43 13 5775 6346 219167424 219168002 0.000000e+00 697.0
33 TraesCS5B01G001100 chr7A 98.039 51 1 0 1213 1263 47511529 47511579 9.260000e-14 89.8
34 TraesCS5B01G001100 chr2D 82.884 1595 260 10 3911 5503 15991423 15989840 0.000000e+00 1421.0
35 TraesCS5B01G001100 chr2D 82.127 1589 273 9 3911 5498 15935339 15933761 0.000000e+00 1351.0
36 TraesCS5B01G001100 chr2D 85.802 324 29 12 5770 6087 56312282 56312594 1.800000e-85 327.0
37 TraesCS5B01G001100 chr4A 82.078 1607 256 18 3901 5492 657071326 657072915 0.000000e+00 1343.0
38 TraesCS5B01G001100 chr4B 94.347 513 7 3 2463 2975 672314765 672314275 0.000000e+00 767.0
39 TraesCS5B01G001100 chr4B 97.455 393 10 0 2634 3026 28265887 28265495 0.000000e+00 671.0
40 TraesCS5B01G001100 chr4B 97.853 326 7 0 1826 2151 479219509 479219184 1.260000e-156 564.0
41 TraesCS5B01G001100 chr4B 97.826 322 7 0 1830 2151 28266972 28266651 2.110000e-154 556.0
42 TraesCS5B01G001100 chr4B 98.286 175 3 0 2461 2635 479219139 479218965 2.350000e-79 307.0
43 TraesCS5B01G001100 chr4B 85.874 269 22 10 5767 6027 66189475 66189215 8.570000e-69 272.0
44 TraesCS5B01G001100 chr4B 94.898 98 2 2 3681 3778 14343227 14343321 4.190000e-32 150.0
45 TraesCS5B01G001100 chr2B 98.219 393 7 0 2634 3026 752930639 752930247 0.000000e+00 688.0
46 TraesCS5B01G001100 chr2B 97.710 393 9 0 2634 3026 617149735 617150127 0.000000e+00 676.0
47 TraesCS5B01G001100 chr2B 89.041 438 29 8 5781 6206 547098842 547098412 5.950000e-145 525.0
48 TraesCS5B01G001100 chr2B 97.714 175 4 0 2461 2635 617147648 617147822 1.090000e-77 302.0
49 TraesCS5B01G001100 chr1B 97.975 395 8 0 2634 3028 61991509 61991903 0.000000e+00 686.0
50 TraesCS5B01G001100 chr1B 98.148 324 6 0 1828 2151 61990714 61991037 3.510000e-157 566.0
51 TraesCS5B01G001100 chr1B 97.714 175 4 0 2461 2635 61991093 61991267 1.090000e-77 302.0
52 TraesCS5B01G001100 chr6B 97.022 403 11 1 2634 3035 704691248 704691650 0.000000e+00 676.0
53 TraesCS5B01G001100 chr6B 98.137 322 4 1 1830 2151 451676786 451676467 1.630000e-155 560.0
54 TraesCS5B01G001100 chr6B 96.657 329 10 1 1824 2151 693802863 693803191 4.570000e-151 545.0
55 TraesCS5B01G001100 chr6B 91.922 359 23 5 6345 6701 708393038 708392684 1.300000e-136 497.0
56 TraesCS5B01G001100 chr6B 97.714 175 4 0 2461 2635 670897839 670897665 1.090000e-77 302.0
57 TraesCS5B01G001100 chr6B 97.714 175 4 0 2461 2635 704689161 704689335 1.090000e-77 302.0
58 TraesCS5B01G001100 chr3B 97.710 393 9 0 2634 3026 671136584 671136192 0.000000e+00 676.0
59 TraesCS5B01G001100 chr3B 96.970 396 12 0 2634 3029 726355859 726356254 0.000000e+00 665.0
60 TraesCS5B01G001100 chr3B 97.840 324 7 0 1828 2151 49153443 49153766 1.630000e-155 560.0
61 TraesCS5B01G001100 chr3B 97.714 175 4 0 2461 2635 516428580 516428754 1.090000e-77 302.0
62 TraesCS5B01G001100 chr7B 97.250 400 8 2 2630 3028 698922857 698922460 0.000000e+00 675.0
63 TraesCS5B01G001100 chr7B 97.215 395 9 1 2634 3028 693386471 693386079 0.000000e+00 667.0
64 TraesCS5B01G001100 chr7B 97.516 322 8 0 1828 2149 693387279 693386958 9.820000e-153 551.0
65 TraesCS5B01G001100 chr7B 97.508 321 8 0 1831 2151 6895944 6895624 3.530000e-152 549.0
66 TraesCS5B01G001100 chr7B 97.714 175 4 0 2461 2635 246382919 246383093 1.090000e-77 302.0
67 TraesCS5B01G001100 chrUn 87.415 588 49 12 5775 6349 49961906 49961331 0.000000e+00 652.0
68 TraesCS5B01G001100 chr7D 85.110 591 41 20 5775 6349 4171625 4171066 1.630000e-155 560.0
69 TraesCS5B01G001100 chr7D 92.244 361 19 8 6345 6701 586687459 586687814 2.790000e-138 503.0
70 TraesCS5B01G001100 chr7D 89.091 385 25 6 5777 6150 552324313 552323935 4.740000e-126 462.0
71 TraesCS5B01G001100 chr7D 91.513 271 17 5 6082 6349 431154176 431153909 1.060000e-97 368.0
72 TraesCS5B01G001100 chr7D 87.307 323 26 10 5770 6087 33694291 33694603 8.270000e-94 355.0
73 TraesCS5B01G001100 chr7D 88.119 303 26 5 5771 6069 431164695 431164399 1.070000e-92 351.0
74 TraesCS5B01G001100 chr7D 91.633 251 15 5 6098 6346 586687159 586687405 6.440000e-90 342.0
75 TraesCS5B01G001100 chr3A 92.244 361 19 8 6345 6701 357059041 357059396 2.790000e-138 503.0
76 TraesCS5B01G001100 chr2A 91.413 361 23 7 6345 6701 733098018 733098374 7.810000e-134 488.0
77 TraesCS5B01G001100 chr4D 87.133 443 23 12 5775 6206 400894868 400894449 7.870000e-129 472.0
78 TraesCS5B01G001100 chr4D 87.133 443 22 16 5775 6206 472925584 472925166 2.830000e-128 470.0
79 TraesCS5B01G001100 chr4D 80.526 190 37 0 3906 4095 11867190 11867001 5.420000e-31 147.0
80 TraesCS5B01G001100 chr4D 96.512 86 3 0 3687 3772 7904979 7905064 7.010000e-30 143.0


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 TraesCS5B01G001100 chr5B 859893 866595 6702 True 3004.25 7836 100.000000 1 6703 4 chr5B.!!$R6 6702
1 TraesCS5B01G001100 chr5B 44140287 44141891 1604 False 1526.00 1526 83.903000 3893 5494 1 chr5B.!!$F2 1601
2 TraesCS5B01G001100 chr5B 400664014 400664931 917 False 1483.00 1483 95.708000 5775 6703 1 chr5B.!!$F3 928
3 TraesCS5B01G001100 chr5D 44569887 44571487 1600 True 1552.00 1552 84.217000 3896 5493 1 chr5D.!!$R3 1597
4 TraesCS5B01G001100 chr5D 6820682 6824767 4085 True 1105.75 3055 89.239250 4 5766 4 chr5D.!!$R6 5762
5 TraesCS5B01G001100 chr5D 72364071 72364631 560 False 625.00 625 87.053000 5775 6346 1 chr5D.!!$F1 571
6 TraesCS5B01G001100 chr5D 3809691 3810217 526 True 379.00 379 80.414000 3683 4190 1 chr5D.!!$R1 507
7 TraesCS5B01G001100 chr5A 3132588 3133834 1246 False 1304.00 1304 85.600000 3880 5124 1 chr5A.!!$F1 1244
8 TraesCS5B01G001100 chr5A 3085028 3088744 3716 False 1035.85 2985 90.450250 471 5760 4 chr5A.!!$F2 5289
9 TraesCS5B01G001100 chr5A 34981168 34986385 5217 True 798.60 1513 89.924000 1213 5493 2 chr5A.!!$R1 4280
10 TraesCS5B01G001100 chr6A 107169508 107170423 915 False 1498.00 1498 96.026000 5775 6703 1 chr6A.!!$F1 928
11 TraesCS5B01G001100 chr7A 482328886 482329813 927 False 1482.00 1482 95.334000 5764 6703 1 chr7A.!!$F2 939
12 TraesCS5B01G001100 chr7A 219167424 219168002 578 False 697.00 697 88.756000 5775 6346 1 chr7A.!!$F1 571
13 TraesCS5B01G001100 chr7A 47511529 47512834 1305 False 647.40 1205 91.802500 1213 5498 2 chr7A.!!$F3 4285
14 TraesCS5B01G001100 chr2D 15989840 15991423 1583 True 1421.00 1421 82.884000 3911 5503 1 chr2D.!!$R2 1592
15 TraesCS5B01G001100 chr2D 15933761 15935339 1578 True 1351.00 1351 82.127000 3911 5498 1 chr2D.!!$R1 1587
16 TraesCS5B01G001100 chr4A 657071326 657072915 1589 False 1343.00 1343 82.078000 3901 5492 1 chr4A.!!$F1 1591
17 TraesCS5B01G001100 chr4B 28265495 28266972 1477 True 613.50 671 97.640500 1830 3026 2 chr4B.!!$R3 1196
18 TraesCS5B01G001100 chr4B 479218965 479219509 544 True 435.50 564 98.069500 1826 2635 2 chr4B.!!$R4 809
19 TraesCS5B01G001100 chr2B 617147648 617150127 2479 False 489.00 676 97.712000 2461 3026 2 chr2B.!!$F1 565
20 TraesCS5B01G001100 chr1B 61990714 61991903 1189 False 518.00 686 97.945667 1828 3028 3 chr1B.!!$F1 1200
21 TraesCS5B01G001100 chr6B 704689161 704691650 2489 False 489.00 676 97.368000 2461 3035 2 chr6B.!!$F2 574
22 TraesCS5B01G001100 chr7B 693386079 693387279 1200 True 609.00 667 97.365500 1828 3028 2 chr7B.!!$R3 1200
23 TraesCS5B01G001100 chrUn 49961331 49961906 575 True 652.00 652 87.415000 5775 6349 1 chrUn.!!$R1 574
24 TraesCS5B01G001100 chr7D 4171066 4171625 559 True 560.00 560 85.110000 5775 6349 1 chr7D.!!$R1 574
25 TraesCS5B01G001100 chr7D 586687159 586687814 655 False 422.50 503 91.938500 6098 6701 2 chr7D.!!$F2 603


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
227 323 0.039798 GCAATATGGTGCATCCGCTG 60.040 55.000 0.00 0.0 44.29 5.18 F
1039 1228 0.039437 CTACCTACCTATGTGCGCCG 60.039 60.000 4.18 0.0 0.00 6.46 F
1294 1533 0.179207 GCATGCACATGTCACACTCG 60.179 55.000 14.21 0.0 40.80 4.18 F
1628 1890 0.409092 TGAGTGCCCACAATCCCATT 59.591 50.000 0.82 0.0 40.16 3.16 F
1799 2226 0.443869 GAGCGAAATCATGTGCGTGT 59.556 50.000 0.00 0.0 0.00 4.49 F
3426 5833 0.856982 TTTCCTCTTCCTTTGGGGCA 59.143 50.000 0.00 0.0 34.39 5.36 F
3492 5899 0.396435 ACTGTCGCTGAAATGGGTGA 59.604 50.000 0.00 0.0 0.00 4.02 F
3493 5900 1.202758 ACTGTCGCTGAAATGGGTGAA 60.203 47.619 0.00 0.0 0.00 3.18 F
4130 8672 1.490490 GCCACCATGTCCTCCTTCATA 59.510 52.381 0.00 0.0 0.00 2.15 F
5549 10107 0.905337 ACAGCCCGAAGAAGCCTAGT 60.905 55.000 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 1868 0.034186 GGGATTGTGGGCACTCATCA 60.034 55.000 0.00 0.00 0.00 3.07 R
2997 5373 0.811219 CCAACAGCTGCGCTATAGCA 60.811 55.000 23.99 6.02 45.96 3.49 R
3039 5415 1.552792 AGCTACACAGGAAAGAGAGGC 59.447 52.381 0.00 0.00 0.00 4.70 R
3473 5880 0.396435 TCACCCATTTCAGCGACAGT 59.604 50.000 0.00 0.00 0.00 3.55 R
3474 5881 1.522668 TTCACCCATTTCAGCGACAG 58.477 50.000 0.00 0.00 0.00 3.51 R
5015 9570 1.207593 CTTTGTGAAGCGGCGAAGG 59.792 57.895 12.98 0.00 0.00 3.46 R
5436 9994 1.613836 AAGTAGACGAGGTTCACGGT 58.386 50.000 0.00 0.00 34.93 4.83 R
5504 10062 1.219124 GAGCTCAACATCTCCGGCA 59.781 57.895 9.40 0.00 0.00 5.69 R
5651 10215 0.172127 CGGGATCGATCGATGAGCAT 59.828 55.000 33.86 11.11 39.00 3.79 R
6384 11038 2.543777 AGTTGCAACCGCTAAGAGAA 57.456 45.000 25.62 0.00 39.64 2.87 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)



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

AutoCloner maintained by Alex Coulton.