Multiple sequence alignment - TraesCS7A01G111300

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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 TraesCS7A01G111300 chr7A 100.000 8661 0 0 1 8661 68095141 68086481 0.000000e+00 15994.0
1 TraesCS7A01G111300 chr7A 92.680 724 44 8 7463 8180 68040066 68039346 0.000000e+00 1035.0
2 TraesCS7A01G111300 chr7A 83.942 685 64 23 7548 8187 67990529 67989846 1.600000e-171 614.0
3 TraesCS7A01G111300 chr7A 85.575 409 41 6 4926 5332 67837348 67836956 6.260000e-111 412.0
4 TraesCS7A01G111300 chr7A 81.657 338 36 12 4160 4495 67597619 67597932 3.100000e-64 257.0
5 TraesCS7A01G111300 chr7A 81.194 335 37 13 4163 4495 67980377 67980067 6.720000e-61 246.0
6 TraesCS7A01G111300 chr7A 84.475 219 13 4 7964 8180 67590632 67590831 6.860000e-46 196.0
7 TraesCS7A01G111300 chr7A 90.972 144 13 0 8198 8341 68039257 68039114 2.470000e-45 195.0
8 TraesCS7A01G111300 chr7A 86.335 161 19 2 8490 8650 68038615 68038458 1.160000e-38 172.0
9 TraesCS7A01G111300 chr7A 96.078 102 2 1 8379 8478 68039744 68039643 1.930000e-36 165.0
10 TraesCS7A01G111300 chr7A 94.059 101 5 1 7786 7886 68086763 68086664 1.510000e-32 152.0
11 TraesCS7A01G111300 chr7A 94.059 101 5 1 8379 8478 68087356 68087256 1.510000e-32 152.0
12 TraesCS7A01G111300 chr7A 91.429 105 9 0 8198 8302 67590920 67591024 2.520000e-30 145.0
13 TraesCS7A01G111300 chr7A 96.721 61 1 1 4372 4431 68090595 68090535 5.530000e-17 100.0
14 TraesCS7A01G111300 chr7A 96.721 61 1 1 4547 4607 68090770 68090711 5.530000e-17 100.0
15 TraesCS7A01G111300 chr7D 89.669 4104 235 100 279 4273 64278241 64274218 0.000000e+00 5055.0
16 TraesCS7A01G111300 chr7D 95.026 2352 77 14 5768 8093 64272879 64270542 0.000000e+00 3659.0
17 TraesCS7A01G111300 chr7D 91.080 796 35 20 4918 5677 64273670 64272875 0.000000e+00 1044.0
18 TraesCS7A01G111300 chr7D 84.329 887 71 38 5770 6639 64179339 64178504 0.000000e+00 806.0
19 TraesCS7A01G111300 chr7D 95.876 485 11 3 4272 4747 64274136 64273652 0.000000e+00 776.0
20 TraesCS7A01G111300 chr7D 81.096 730 95 28 4968 5672 64180061 64179350 2.130000e-150 544.0
21 TraesCS7A01G111300 chr7D 92.973 185 11 1 8198 8382 64270329 64270147 1.430000e-67 268.0
22 TraesCS7A01G111300 chr7D 92.432 185 14 0 8198 8382 64249982 64249798 1.850000e-66 265.0
23 TraesCS7A01G111300 chr7D 90.426 188 16 2 8475 8661 64270070 64269884 6.720000e-61 246.0
24 TraesCS7A01G111300 chr7D 86.782 174 17 3 8006 8173 64250265 64250092 1.150000e-43 189.0
25 TraesCS7A01G111300 chr7D 97.030 101 2 1 8379 8478 64270851 64270751 1.500000e-37 169.0
26 TraesCS7A01G111300 chr7D 96.610 59 1 1 4372 4429 64273853 64273795 7.160000e-16 97.1
27 TraesCS7A01G111300 chr7B 84.803 2132 144 70 234 2261 5521709 5519654 0.000000e+00 1977.0
28 TraesCS7A01G111300 chr7B 87.254 1271 122 24 2261 3519 5519623 5518381 0.000000e+00 1413.0
29 TraesCS7A01G111300 chr7B 94.866 857 37 5 7255 8109 5514763 5513912 0.000000e+00 1332.0
30 TraesCS7A01G111300 chr7B 89.526 1012 89 10 3521 4527 5518098 5517099 0.000000e+00 1266.0
31 TraesCS7A01G111300 chr7B 90.378 873 59 13 5782 6639 5516177 5515315 0.000000e+00 1123.0
32 TraesCS7A01G111300 chr7B 95.341 558 17 4 6670 7223 5515313 5514761 0.000000e+00 878.0
33 TraesCS7A01G111300 chr7B 94.628 484 17 5 7346 7823 5342398 5341918 0.000000e+00 741.0
34 TraesCS7A01G111300 chr7B 83.588 786 91 27 4923 5677 5516962 5516184 0.000000e+00 702.0
35 TraesCS7A01G111300 chr7B 85.782 422 45 9 5852 6263 5264648 5264232 4.800000e-117 433.0
36 TraesCS7A01G111300 chr7B 90.506 316 30 0 4936 5251 5189317 5189002 1.340000e-112 418.0
37 TraesCS7A01G111300 chr7B 81.651 545 49 29 3991 4527 5189986 5189485 1.050000e-108 405.0
38 TraesCS7A01G111300 chr7B 94.706 170 9 0 4745 4914 244640663 244640494 1.850000e-66 265.0
39 TraesCS7A01G111300 chr7B 86.127 173 23 1 3774 3945 5265693 5265521 1.480000e-42 185.0
40 TraesCS7A01G111300 chr7B 91.667 108 8 1 5669 5775 610379492 610379385 1.950000e-31 148.0
41 TraesCS7A01G111300 chr7B 86.458 96 7 2 5334 5423 5188858 5188763 5.530000e-17 100.0
42 TraesCS7A01G111300 chr7B 93.443 61 4 0 4550 4610 5517116 5517056 3.330000e-14 91.6
43 TraesCS7A01G111300 chr7B 97.368 38 1 0 8379 8416 5341955 5341918 2.020000e-06 65.8
44 TraesCS7A01G111300 chr3A 94.915 177 9 0 4744 4920 609950957 609951133 2.380000e-70 278.0
45 TraesCS7A01G111300 chr4A 94.857 175 9 0 4744 4918 584667603 584667429 3.080000e-69 274.0
46 TraesCS7A01G111300 chr4A 92.857 182 12 1 4747 4928 109430423 109430603 6.670000e-66 263.0
47 TraesCS7A01G111300 chr4A 86.765 136 18 0 1323 1458 120606896 120606761 1.510000e-32 152.0
48 TraesCS7A01G111300 chr3D 94.857 175 9 0 4744 4918 467283488 467283662 3.080000e-69 274.0
49 TraesCS7A01G111300 chr3D 95.960 99 4 0 5675 5773 445343050 445342952 2.500000e-35 161.0
50 TraesCS7A01G111300 chr3D 93.204 103 6 1 5675 5776 613073452 613073350 5.420000e-32 150.0
51 TraesCS7A01G111300 chr5B 94.828 174 9 0 4745 4918 573003546 573003719 1.110000e-68 272.0
52 TraesCS7A01G111300 chr4B 95.783 166 7 0 4745 4910 206802591 206802756 1.430000e-67 268.0
53 TraesCS7A01G111300 chr4B 94.059 101 6 0 5674 5774 193527581 193527681 4.190000e-33 154.0
54 TraesCS7A01G111300 chr4B 94.059 101 6 0 5675 5775 597480596 597480496 4.190000e-33 154.0
55 TraesCS7A01G111300 chr5A 93.820 178 10 1 4739 4916 271053816 271053640 5.150000e-67 267.0
56 TraesCS7A01G111300 chr2B 94.737 171 9 0 4743 4913 316008200 316008030 5.150000e-67 267.0
57 TraesCS7A01G111300 chr6B 94.118 102 5 1 5670 5771 633054118 633054018 4.190000e-33 154.0
58 TraesCS7A01G111300 chr6B 91.743 109 7 2 5667 5775 315650202 315650308 5.420000e-32 150.0
59 TraesCS7A01G111300 chr5D 96.739 92 3 0 1 92 224722343 224722252 4.190000e-33 154.0
60 TraesCS7A01G111300 chr5D 91.818 110 6 3 5662 5771 266749346 266749452 5.420000e-32 150.0
61 TraesCS7A01G111300 chr6D 95.652 92 4 0 1 92 30854252 30854161 1.950000e-31 148.0
62 TraesCS7A01G111300 chr6D 95.652 92 4 0 1 92 348318938 348318847 1.950000e-31 148.0
63 TraesCS7A01G111300 chr4D 95.652 92 4 0 1 92 81191471 81191562 1.950000e-31 148.0
64 TraesCS7A01G111300 chr4D 95.652 92 4 0 1 92 100002514 100002605 1.950000e-31 148.0
65 TraesCS7A01G111300 chr4D 95.652 92 4 0 1 92 116869280 116869371 1.950000e-31 148.0
66 TraesCS7A01G111300 chr4D 95.652 92 4 0 1 92 118206229 118206138 1.950000e-31 148.0
67 TraesCS7A01G111300 chr4D 95.652 92 4 0 1 92 328487647 328487738 1.950000e-31 148.0
68 TraesCS7A01G111300 chr4D 95.652 92 4 0 1 92 381918156 381918065 1.950000e-31 148.0
69 TraesCS7A01G111300 chr6A 90.826 109 8 2 5670 5777 617653913 617653806 2.520000e-30 145.0


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 TraesCS7A01G111300 chr7A 68086481 68095141 8660 True 15994.000000 15994 100.000000 1 8661 1 chr7A.!!$R4 8660
1 TraesCS7A01G111300 chr7A 67989846 67990529 683 True 614.000000 614 83.942000 7548 8187 1 chr7A.!!$R3 639
2 TraesCS7A01G111300 chr7A 68038458 68040066 1608 True 391.750000 1035 91.516250 7463 8650 4 chr7A.!!$R5 1187
3 TraesCS7A01G111300 chr7D 64269884 64278241 8357 True 1414.262500 5055 93.586250 279 8661 8 chr7D.!!$R3 8382
4 TraesCS7A01G111300 chr7D 64178504 64180061 1557 True 675.000000 806 82.712500 4968 6639 2 chr7D.!!$R1 1671
5 TraesCS7A01G111300 chr7B 5513912 5521709 7797 True 1097.825000 1977 89.899875 234 8109 8 chr7B.!!$R6 7875
6 TraesCS7A01G111300 chr7B 5264232 5265693 1461 True 309.000000 433 85.954500 3774 6263 2 chr7B.!!$R4 2489
7 TraesCS7A01G111300 chr7B 5188763 5189986 1223 True 307.666667 418 86.205000 3991 5423 3 chr7B.!!$R3 1432


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
167 168 0.109272 CTTCGCGAGGTGCTTGTAGA 60.109 55.000 9.59 0.0 43.27 2.59 F
1594 1731 0.107606 TTAGATTTTAGCCGCCGCCA 60.108 50.000 0.00 0.0 34.57 5.69 F
1885 2050 0.110486 GGGTGTGTGGTGGAAGTGAT 59.890 55.000 0.00 0.0 0.00 3.06 F
2897 3115 0.036388 CAGGACCACTTACGCCACAT 60.036 55.000 0.00 0.0 0.00 3.21 F
4354 5676 1.197721 GTGTTCATCAGCTTTCCACGG 59.802 52.381 0.00 0.0 0.00 4.94 F
4767 6118 0.034089 GGGAGCCTTGGTGCAGTAAT 60.034 55.000 0.00 0.0 0.00 1.89 F
4805 6156 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.0 0.00 2.69 F
4814 6165 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.0 35.79 3.53 F
6050 7535 0.327924 TGTCAGTGCATACTTGGGGG 59.672 55.000 0.00 0.0 34.07 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 1884 0.034896 GGTGTGCCGAGGAAGAAGAA 59.965 55.000 0.00 0.00 0.00 2.52 R
2828 3046 0.108585 TTCTCCTGTGCTGTGGTTCC 59.891 55.000 0.00 0.00 0.00 3.62 R
3353 3576 1.630369 TCTAGCTGCACATGTTCCCTT 59.370 47.619 1.02 0.00 0.00 3.95 R
4748 6099 0.034089 ATTACTGCACCAAGGCTCCC 60.034 55.000 0.00 0.00 34.04 4.30 R
5756 7236 0.398318 GCATGTACTCCCTCCATCCC 59.602 60.000 0.00 0.00 0.00 3.85 R
5774 7254 0.649475 CTGATGTGTCAGCGCTAAGC 59.351 55.000 10.99 3.54 44.86 3.09 R
6758 8273 1.337703 GTGTTCCAATGAGCTGCAACA 59.662 47.619 1.02 1.89 0.00 3.33 R
6954 8469 6.403636 GGTTAAATCACTAGAACACATGCCAG 60.404 42.308 0.00 0.00 0.00 4.85 R
7661 9182 1.087501 GCCGATCAAAGGAACTCCAC 58.912 55.000 0.00 0.00 38.49 4.02 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)



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AutoCloner maintained by Alex Coulton.