Multiple sequence alignment - TraesCS3D01G520200

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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 TraesCS3D01G520200 chr3D 100.000 5380 0 0 1 5380 602754019 602748640 0.000000e+00 9936.0
1 TraesCS3D01G520200 chr3D 97.596 4659 81 17 1 4646 603864817 603869457 0.000000e+00 7954.0
2 TraesCS3D01G520200 chr3D 94.541 1319 37 12 1516 2824 602427654 602428947 0.000000e+00 2004.0
3 TraesCS3D01G520200 chr3D 89.493 1618 91 30 2822 4384 602430577 602432170 0.000000e+00 1973.0
4 TraesCS3D01G520200 chr3D 92.301 1208 64 18 2822 4008 602656104 602657303 0.000000e+00 1688.0
5 TraesCS3D01G520200 chr3D 90.723 1121 72 12 1516 2611 602653464 602654577 0.000000e+00 1465.0
6 TraesCS3D01G520200 chr3D 96.674 872 29 0 2822 3693 602428984 602429855 0.000000e+00 1450.0
7 TraesCS3D01G520200 chr3D 82.761 1688 200 35 1166 2804 568493603 568495248 0.000000e+00 1421.0
8 TraesCS3D01G520200 chr3D 85.688 1097 114 24 2829 3912 568495319 568496385 0.000000e+00 1116.0
9 TraesCS3D01G520200 chr3D 93.054 691 30 5 2146 2824 602429856 602430540 0.000000e+00 994.0
10 TraesCS3D01G520200 chr3D 85.387 568 75 6 4778 5341 512253408 512253971 2.790000e-162 582.0
11 TraesCS3D01G520200 chr3D 84.848 396 32 12 3909 4300 568496482 568496853 1.830000e-99 374.0
12 TraesCS3D01G520200 chr3D 84.524 336 28 12 4065 4384 602666738 602667065 1.460000e-80 311.0
13 TraesCS3D01G520200 chr3D 91.080 213 15 2 1300 1512 602653299 602653507 8.820000e-73 285.0
14 TraesCS3D01G520200 chr3D 87.451 255 20 9 1264 1507 602458188 602457935 3.170000e-72 283.0
15 TraesCS3D01G520200 chr3D 89.671 213 20 2 1300 1512 602427487 602427697 2.470000e-68 270.0
16 TraesCS3D01G520200 chr3D 90.909 154 11 2 2673 2823 602655913 602656066 2.540000e-48 204.0
17 TraesCS3D01G520200 chr3D 87.013 77 5 1 1135 1211 602427381 602427452 1.240000e-11 82.4
18 TraesCS3D01G520200 chr3D 87.671 73 4 1 1139 1211 602653196 602653263 4.470000e-11 80.5
19 TraesCS3D01G520200 chr3D 90.698 43 4 0 5338 5380 404006099 404006057 2.090000e-04 58.4
20 TraesCS3D01G520200 chrUn 97.596 4659 81 17 1 4646 276045929 276041289 0.000000e+00 7954.0
21 TraesCS3D01G520200 chr5A 95.885 2479 79 9 362 2824 31570433 31572904 0.000000e+00 3991.0
22 TraesCS3D01G520200 chr5A 92.312 1847 95 23 2822 4625 31572941 31574783 0.000000e+00 2580.0
23 TraesCS3D01G520200 chr5A 95.935 246 10 0 1 246 31550596 31550841 3.020000e-107 399.0
24 TraesCS3D01G520200 chr5A 96.825 126 4 0 241 366 31562047 31562172 1.520000e-50 211.0
25 TraesCS3D01G520200 chr3B 97.264 2120 50 5 1516 3628 809625908 809628026 0.000000e+00 3587.0
26 TraesCS3D01G520200 chr3B 95.556 765 24 6 4625 5380 809631423 809632186 0.000000e+00 1216.0
27 TraesCS3D01G520200 chr3B 98.444 514 7 1 3401 3914 809629975 809630487 0.000000e+00 904.0
28 TraesCS3D01G520200 chr3B 95.298 553 15 8 3909 4452 809630611 809631161 0.000000e+00 867.0
29 TraesCS3D01G520200 chr3B 81.818 528 91 3 4818 5342 674418416 674418941 6.400000e-119 438.0
30 TraesCS3D01G520200 chr3B 78.049 615 104 14 4751 5342 488314613 488314007 5.120000e-95 359.0
31 TraesCS3D01G520200 chr3B 95.506 178 3 2 4498 4670 809631157 809631334 4.100000e-71 279.0
32 TraesCS3D01G520200 chr3B 89.671 213 20 2 1300 1512 809625741 809625951 2.470000e-68 270.0
33 TraesCS3D01G520200 chr3B 85.000 220 19 8 1261 1466 809831942 809832161 1.520000e-50 211.0
34 TraesCS3D01G520200 chr3B 86.316 95 7 2 1135 1228 809625641 809625730 1.230000e-16 99.0
35 TraesCS3D01G520200 chr3B 93.617 47 1 2 4625 4670 809631356 809631401 9.670000e-08 69.4
36 TraesCS3D01G520200 chr3A 93.357 1701 77 14 2713 4384 732076588 732078281 0.000000e+00 2483.0
37 TraesCS3D01G520200 chr3A 91.750 1297 73 19 3031 4300 731991683 731990394 0.000000e+00 1772.0
38 TraesCS3D01G520200 chr3A 92.667 1050 70 5 1567 2611 731995351 731994304 0.000000e+00 1506.0
39 TraesCS3D01G520200 chr3A 91.190 1101 69 10 1516 2608 732099229 732100309 0.000000e+00 1471.0
40 TraesCS3D01G520200 chr3A 82.725 1343 168 38 2834 4134 732421161 732422481 0.000000e+00 1136.0
41 TraesCS3D01G520200 chr3A 78.972 1479 203 62 2507 3912 732081793 732083236 0.000000e+00 909.0
42 TraesCS3D01G520200 chr3A 85.038 528 67 10 2834 3356 732428180 732428700 1.330000e-145 527.0
43 TraesCS3D01G520200 chr3A 79.668 723 99 30 3508 4199 732428752 732429457 1.360000e-130 477.0
44 TraesCS3D01G520200 chr3A 98.095 210 4 0 2829 3038 731992750 731992541 3.060000e-97 366.0
45 TraesCS3D01G520200 chr3A 80.240 501 66 25 1261 1759 732299735 732300204 3.990000e-91 346.0
46 TraesCS3D01G520200 chr3A 97.030 202 4 1 2521 2720 732073363 732073564 6.670000e-89 339.0
47 TraesCS3D01G520200 chr3A 77.928 444 87 7 1530 1966 732426995 732427434 3.190000e-67 267.0
48 TraesCS3D01G520200 chr3A 88.496 226 14 2 2609 2823 731993021 731992797 4.130000e-66 263.0
49 TraesCS3D01G520200 chr3A 90.230 174 17 0 1334 1507 732099095 732099268 1.510000e-55 228.0
50 TraesCS3D01G520200 chr3A 88.770 187 18 3 1304 1489 731995529 731995345 5.420000e-55 226.0
51 TraesCS3D01G520200 chr3A 80.909 220 31 7 1300 1512 732069237 732069022 4.310000e-36 163.0
52 TraesCS3D01G520200 chr3A 74.434 309 66 11 2045 2350 552543373 552543075 2.630000e-23 121.0
53 TraesCS3D01G520200 chr3A 91.176 68 1 1 1135 1202 732099000 732099062 2.670000e-13 87.9
54 TraesCS3D01G520200 chr3A 81.148 122 8 5 1135 1254 731995625 731995517 3.450000e-12 84.2
55 TraesCS3D01G520200 chr7A 83.333 696 85 14 4669 5342 166480571 166481257 9.900000e-172 614.0
56 TraesCS3D01G520200 chr6D 83.161 677 98 13 4669 5341 356803850 356803186 5.960000e-169 604.0
57 TraesCS3D01G520200 chr6D 82.640 697 93 15 4669 5342 115644942 115644251 4.640000e-165 592.0
58 TraesCS3D01G520200 chr6D 85.714 420 51 5 4928 5340 53850626 53851043 8.280000e-118 435.0
59 TraesCS3D01G520200 chr6B 80.730 794 96 24 4588 5332 563292577 563291792 2.810000e-157 566.0
60 TraesCS3D01G520200 chr6B 84.337 83 9 4 4587 4667 515154807 515154887 1.610000e-10 78.7
61 TraesCS3D01G520200 chr6A 86.193 507 58 5 4669 5169 541244072 541244572 6.130000e-149 538.0
62 TraesCS3D01G520200 chr6A 79.416 685 105 16 4675 5339 136229164 136229832 8.220000e-123 451.0
63 TraesCS3D01G520200 chr5D 82.594 609 64 20 4756 5342 417381136 417381724 2.890000e-137 499.0
64 TraesCS3D01G520200 chr5D 82.414 580 83 13 4759 5329 317677978 317678547 6.260000e-134 488.0
65 TraesCS3D01G520200 chr4D 80.650 677 97 20 4675 5329 459302205 459302869 1.350000e-135 494.0
66 TraesCS3D01G520200 chr1A 79.351 678 104 17 4669 5342 463457060 463457705 1.380000e-120 444.0
67 TraesCS3D01G520200 chr4B 78.398 699 109 26 4669 5342 484781666 484780985 3.000000e-112 416.0
68 TraesCS3D01G520200 chr7D 83.484 442 59 10 4669 5100 101248699 101248262 3.020000e-107 399.0
69 TraesCS3D01G520200 chr7D 89.143 175 14 4 742 913 23359650 23359478 4.220000e-51 213.0
70 TraesCS3D01G520200 chr1B 90.698 86 7 1 4586 4670 606582972 606582887 4.400000e-21 113.0
71 TraesCS3D01G520200 chr1D 90.476 42 4 0 4620 4661 218973214 218973255 7.530000e-04 56.5


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 TraesCS3D01G520200 chr3D 602748640 602754019 5379 True 9936.000000 9936 100.000000 1 5380 1 chr3D.!!$R3 5379
1 TraesCS3D01G520200 chr3D 603864817 603869457 4640 False 7954.000000 7954 97.596000 1 4646 1 chr3D.!!$F3 4645
2 TraesCS3D01G520200 chr3D 602427381 602432170 4789 False 1128.900000 2004 91.741000 1135 4384 6 chr3D.!!$F5 3249
3 TraesCS3D01G520200 chr3D 568493603 568496853 3250 False 970.333333 1421 84.432333 1166 4300 3 chr3D.!!$F4 3134
4 TraesCS3D01G520200 chr3D 602653196 602657303 4107 False 744.500000 1688 90.536800 1139 4008 5 chr3D.!!$F6 2869
5 TraesCS3D01G520200 chr3D 512253408 512253971 563 False 582.000000 582 85.387000 4778 5341 1 chr3D.!!$F1 563
6 TraesCS3D01G520200 chrUn 276041289 276045929 4640 True 7954.000000 7954 97.596000 1 4646 1 chrUn.!!$R1 4645
7 TraesCS3D01G520200 chr5A 31570433 31574783 4350 False 3285.500000 3991 94.098500 362 4625 2 chr5A.!!$F3 4263
8 TraesCS3D01G520200 chr3B 809625641 809632186 6545 False 911.425000 3587 93.959000 1135 5380 8 chr3B.!!$F3 4245
9 TraesCS3D01G520200 chr3B 674418416 674418941 525 False 438.000000 438 81.818000 4818 5342 1 chr3B.!!$F1 524
10 TraesCS3D01G520200 chr3B 488314007 488314613 606 True 359.000000 359 78.049000 4751 5342 1 chr3B.!!$R1 591
11 TraesCS3D01G520200 chr3A 732073363 732083236 9873 False 1243.666667 2483 89.786333 2507 4384 3 chr3A.!!$F3 1877
12 TraesCS3D01G520200 chr3A 732421161 732422481 1320 False 1136.000000 1136 82.725000 2834 4134 1 chr3A.!!$F2 1300
13 TraesCS3D01G520200 chr3A 731990394 731995625 5231 True 702.866667 1772 90.154333 1135 4300 6 chr3A.!!$R3 3165
14 TraesCS3D01G520200 chr3A 732099000 732100309 1309 False 595.633333 1471 90.865333 1135 2608 3 chr3A.!!$F4 1473
15 TraesCS3D01G520200 chr3A 732426995 732429457 2462 False 423.666667 527 80.878000 1530 4199 3 chr3A.!!$F5 2669
16 TraesCS3D01G520200 chr7A 166480571 166481257 686 False 614.000000 614 83.333000 4669 5342 1 chr7A.!!$F1 673
17 TraesCS3D01G520200 chr6D 356803186 356803850 664 True 604.000000 604 83.161000 4669 5341 1 chr6D.!!$R2 672
18 TraesCS3D01G520200 chr6D 115644251 115644942 691 True 592.000000 592 82.640000 4669 5342 1 chr6D.!!$R1 673
19 TraesCS3D01G520200 chr6B 563291792 563292577 785 True 566.000000 566 80.730000 4588 5332 1 chr6B.!!$R1 744
20 TraesCS3D01G520200 chr6A 541244072 541244572 500 False 538.000000 538 86.193000 4669 5169 1 chr6A.!!$F2 500
21 TraesCS3D01G520200 chr6A 136229164 136229832 668 False 451.000000 451 79.416000 4675 5339 1 chr6A.!!$F1 664
22 TraesCS3D01G520200 chr5D 417381136 417381724 588 False 499.000000 499 82.594000 4756 5342 1 chr5D.!!$F2 586
23 TraesCS3D01G520200 chr5D 317677978 317678547 569 False 488.000000 488 82.414000 4759 5329 1 chr5D.!!$F1 570
24 TraesCS3D01G520200 chr4D 459302205 459302869 664 False 494.000000 494 80.650000 4675 5329 1 chr4D.!!$F1 654
25 TraesCS3D01G520200 chr1A 463457060 463457705 645 False 444.000000 444 79.351000 4669 5342 1 chr1A.!!$F1 673
26 TraesCS3D01G520200 chr4B 484780985 484781666 681 True 416.000000 416 78.398000 4669 5342 1 chr4B.!!$R1 673

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
4128 13712 1.153449 TATGCACAGTACGCCAGGC 60.153 57.895 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
5196 17925 1.148048 GCAGAGGGCAAGGGAGATC 59.852 63.158 0.0 0.0 43.97 2.75 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
4128 13712 1.153449 TATGCACAGTACGCCAGGC 60.153 57.895 0.0 0.0 0.00 4.85
4148 13732 0.324285 AGAAGCTCCAGGTTGCAGAG 59.676 55.000 9.3 0.0 35.69 3.35
4466 14107 1.032114 CAAGATTTGTCTCCCGGCCC 61.032 60.000 0.0 0.0 0.00 5.80
4488 14130 1.377725 CTCATTTGCCACCGCTCCT 60.378 57.895 0.0 0.0 35.36 3.69
4555 14211 3.134804 GCTCAATACCCTAGAAAGAGCCA 59.865 47.826 0.0 0.0 40.68 4.75
4736 15579 9.938280 AAACATCATCAAAAGATCATCAAACAT 57.062 25.926 0.0 0.0 0.00 2.71
5249 17984 2.680352 ATGTGCCTCCGACTCCGT 60.680 61.111 0.0 0.0 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2932 7567 2.717639 ATCAGCATCAGGGGTGTTAC 57.282 50.000 0.00 0.00 37.53 2.50
3918 13358 3.181467 CCAAGGAGAGACATCAGACCATC 60.181 52.174 0.00 0.00 0.00 3.51
4128 13712 0.035881 TCTGCAACCTGGAGCTTCTG 59.964 55.000 14.77 0.00 35.65 3.02
4466 14107 0.813184 AGCGGTGGCAAATGAGAATG 59.187 50.000 0.00 0.00 43.41 2.67
4488 14130 5.875224 TGATCATTGGTCTTGGAAAGTACA 58.125 37.500 0.00 0.00 46.34 2.90
4555 14211 3.438087 CACAGATCGGATTTGCAAAGTCT 59.562 43.478 18.19 11.81 32.53 3.24
4736 15579 7.255695 GGATCATTGAACTCCATGAATTATGCA 60.256 37.037 0.00 0.00 35.37 3.96
4747 15590 2.301583 TGTGTCGGATCATTGAACTCCA 59.698 45.455 7.02 0.00 0.00 3.86
5196 17925 1.148048 GCAGAGGGCAAGGGAGATC 59.852 63.158 0.00 0.00 43.97 2.75


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

AutoCloner maintained by Alex Coulton.