Multiple sequence alignment - TraesCS7A01G111300
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 pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
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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 primersListed 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. |
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Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.