Multiple sequence alignment - TraesCS3D01G520300

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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 TraesCS3D01G520300 chr3D 100.000 3498 0 0 1 3498 602782389 602778892 0.000000e+00 6460
1 TraesCS3D01G520300 chr3D 91.439 1939 117 21 639 2562 603943418 603945322 0.000000e+00 2615
2 TraesCS3D01G520300 chr3D 87.822 1864 185 22 722 2573 602803981 602802148 0.000000e+00 2146
3 TraesCS3D01G520300 chr3D 84.463 605 52 24 2586 3188 603945468 603946032 3.050000e-155 558
4 TraesCS3D01G520300 chr3B 95.395 2606 70 15 1 2573 810969547 810972135 0.000000e+00 4102
5 TraesCS3D01G520300 chr3B 89.817 1964 163 17 639 2573 810977750 810979705 0.000000e+00 2484
6 TraesCS3D01G520300 chr3B 91.789 1632 101 13 932 2562 811040914 811042513 0.000000e+00 2241
7 TraesCS3D01G520300 chr3B 86.351 1861 205 30 722 2570 810948009 810949832 0.000000e+00 1984
8 TraesCS3D01G520300 chr3B 83.434 1829 259 27 682 2493 811141436 811139635 0.000000e+00 1659
9 TraesCS3D01G520300 chr3B 82.160 1861 275 30 682 2516 811079283 811081112 0.000000e+00 1544
10 TraesCS3D01G520300 chr3B 95.591 930 35 2 2569 3498 810972268 810973191 0.000000e+00 1485
11 TraesCS3D01G520300 chr3B 83.855 607 55 26 2586 3188 811042659 811043226 3.970000e-149 538
12 TraesCS3D01G520300 chr3B 84.501 471 35 8 3032 3498 810980388 810980824 6.940000e-117 431
13 TraesCS3D01G520300 chr3B 86.926 283 20 9 639 906 811040638 811040918 5.670000e-78 302
14 TraesCS3D01G520300 chr3B 74.583 539 86 25 136 638 473185509 473184986 4.610000e-44 189
15 TraesCS3D01G520300 chr3A 94.131 2573 100 17 1 2545 733435461 733438010 0.000000e+00 3868
16 TraesCS3D01G520300 chr3A 93.818 2572 108 18 1 2545 733410666 733413213 0.000000e+00 3821
17 TraesCS3D01G520300 chr3A 90.557 1938 162 10 641 2562 733332997 733334929 0.000000e+00 2545
18 TraesCS3D01G520300 chr3A 90.675 1941 131 25 639 2562 733465233 733467140 0.000000e+00 2536
19 TraesCS3D01G520300 chr3A 86.273 1865 204 32 722 2570 733039218 733041046 0.000000e+00 1978
20 TraesCS3D01G520300 chr3A 85.965 798 82 16 2723 3498 733438292 733439081 0.000000e+00 826
21 TraesCS3D01G520300 chr3A 87.416 445 37 7 2759 3188 733467454 733467894 8.720000e-136 494
22 TraesCS3D01G520300 chr3A 84.582 467 39 11 3032 3498 733188290 733188723 1.930000e-117 433
23 TraesCS3D01G520300 chr3A 82.738 336 35 5 2772 3088 733335254 733335585 9.560000e-71 278
24 TraesCS3D01G520300 chr3A 78.961 385 58 13 136 510 484106671 484106300 1.250000e-59 241
25 TraesCS3D01G520300 chr3A 84.483 174 16 4 2569 2731 733467282 733467455 1.000000e-35 161
26 TraesCS3D01G520300 chr3A 83.060 183 20 4 2569 2740 733335070 733335252 4.670000e-34 156
27 TraesCS3D01G520300 chr4D 82.274 299 42 8 28 322 75049153 75049444 7.500000e-62 248
28 TraesCS3D01G520300 chr7D 89.595 173 16 2 152 322 628689790 628689618 5.880000e-53 219
29 TraesCS3D01G520300 chr5D 94.521 73 4 0 567 639 424347852 424347780 2.850000e-21 113
30 TraesCS3D01G520300 chr7B 80.233 172 10 10 490 637 426540394 426540565 1.330000e-19 108
31 TraesCS3D01G520300 chr5B 93.151 73 5 0 567 639 513598344 513598272 1.330000e-19 108


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 TraesCS3D01G520300 chr3D 602778892 602782389 3497 True 6460.000000 6460 100.000000 1 3498 1 chr3D.!!$R1 3497
1 TraesCS3D01G520300 chr3D 602802148 602803981 1833 True 2146.000000 2146 87.822000 722 2573 1 chr3D.!!$R2 1851
2 TraesCS3D01G520300 chr3D 603943418 603946032 2614 False 1586.500000 2615 87.951000 639 3188 2 chr3D.!!$F1 2549
3 TraesCS3D01G520300 chr3B 810969547 810973191 3644 False 2793.500000 4102 95.493000 1 3498 2 chr3B.!!$F3 3497
4 TraesCS3D01G520300 chr3B 810948009 810949832 1823 False 1984.000000 1984 86.351000 722 2570 1 chr3B.!!$F1 1848
5 TraesCS3D01G520300 chr3B 811139635 811141436 1801 True 1659.000000 1659 83.434000 682 2493 1 chr3B.!!$R2 1811
6 TraesCS3D01G520300 chr3B 811079283 811081112 1829 False 1544.000000 1544 82.160000 682 2516 1 chr3B.!!$F2 1834
7 TraesCS3D01G520300 chr3B 810977750 810980824 3074 False 1457.500000 2484 87.159000 639 3498 2 chr3B.!!$F4 2859
8 TraesCS3D01G520300 chr3B 811040638 811043226 2588 False 1027.000000 2241 87.523333 639 3188 3 chr3B.!!$F5 2549
9 TraesCS3D01G520300 chr3A 733410666 733413213 2547 False 3821.000000 3821 93.818000 1 2545 1 chr3A.!!$F3 2544
10 TraesCS3D01G520300 chr3A 733435461 733439081 3620 False 2347.000000 3868 90.048000 1 3498 2 chr3A.!!$F5 3497
11 TraesCS3D01G520300 chr3A 733039218 733041046 1828 False 1978.000000 1978 86.273000 722 2570 1 chr3A.!!$F1 1848
12 TraesCS3D01G520300 chr3A 733465233 733467894 2661 False 1063.666667 2536 87.524667 639 3188 3 chr3A.!!$F6 2549
13 TraesCS3D01G520300 chr3A 733332997 733335585 2588 False 993.000000 2545 85.451667 641 3088 3 chr3A.!!$F4 2447

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
609 643 0.387929 GTATCAGCACGGGGATTCGA 59.612 55.0 0.0 0.0 0.00 3.71 F
1535 1608 0.321122 ACTCGCCTCAGCCTGAAAAG 60.321 55.0 0.0 0.0 34.57 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 2361 0.105593 TCTGGAATGCTCGCCTGATC 59.894 55.000 0.0 0.0 0.0 2.92 R
3221 3684 1.079490 TCAGGAGAATGTGGAGGAGGT 59.921 52.381 0.0 0.0 0.0 3.85 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
132 133 4.402155 AGAACAACATGAGGAAGCAACAAA 59.598 37.500 0.00 0.00 0.00 2.83
300 302 2.581354 CGTTGGGAGGAGAGGCTG 59.419 66.667 0.00 0.00 0.00 4.85
330 332 1.776034 GAGACGGCGGCAAATCCATC 61.776 60.000 18.30 0.00 34.01 3.51
331 333 2.828549 ACGGCGGCAAATCCATCC 60.829 61.111 13.24 0.00 34.01 3.51
607 641 2.900528 CGTATCAGCACGGGGATTC 58.099 57.895 0.00 0.00 38.26 2.52
609 643 0.387929 GTATCAGCACGGGGATTCGA 59.612 55.000 0.00 0.00 0.00 3.71
665 699 2.227865 TGACAAAACTGCTAAATCCGCC 59.772 45.455 0.00 0.00 0.00 6.13
689 731 2.352001 GCTTGCAGCATGATCGCG 60.352 61.111 12.42 0.00 41.89 5.87
770 814 7.607991 TCTTCAAGATCACAAATTAGGGTCTTC 59.392 37.037 0.00 0.00 0.00 2.87
783 827 6.620877 TTAGGGTCTTCTAACACATGTCAT 57.379 37.500 0.00 0.00 0.00 3.06
833 883 2.731976 CGCAGTAGTCAAGTTCAGTTCC 59.268 50.000 0.00 0.00 0.00 3.62
882 937 1.202580 CCTAAACTGCCATCTCTCGGG 60.203 57.143 0.00 0.00 0.00 5.14
1077 1150 4.161565 AGGGCGAAATCTACATCTGTTGTA 59.838 41.667 0.00 0.00 39.87 2.41
1535 1608 0.321122 ACTCGCCTCAGCCTGAAAAG 60.321 55.000 0.00 0.00 34.57 2.27
1907 1991 2.431454 CCTTCTTTTGGCTCCTGACTC 58.569 52.381 0.00 0.00 0.00 3.36
1919 2003 4.040217 GGCTCCTGACTCATCTGTATTGAT 59.960 45.833 0.00 0.00 0.00 2.57
2251 2360 2.617658 TGGGATCAGGATCAGGATCAG 58.382 52.381 20.75 3.64 41.30 2.90
2252 2361 1.907936 GGGATCAGGATCAGGATCAGG 59.092 57.143 20.75 2.97 41.30 3.86
2253 2362 2.494250 GGGATCAGGATCAGGATCAGGA 60.494 54.545 20.75 7.82 41.30 3.86
2254 2363 3.452878 GGATCAGGATCAGGATCAGGAT 58.547 50.000 20.75 11.66 41.30 3.24
2255 2364 3.451902 GGATCAGGATCAGGATCAGGATC 59.548 52.174 21.74 21.74 42.19 3.36
2256 2365 3.625252 TCAGGATCAGGATCAGGATCA 57.375 47.619 20.75 4.90 41.30 2.92
2622 2973 0.390124 TCCCGTTGTTCTGCGTAACT 59.610 50.000 3.07 0.00 0.00 2.24
2637 2988 6.876789 TCTGCGTAACTTAAATTCCTGATTCA 59.123 34.615 0.00 0.00 0.00 2.57
2699 3061 9.932699 CATCATCTTGTATGAAGAAGAATGAAC 57.067 33.333 0.00 0.00 38.39 3.18
2781 3173 8.641498 AATCAGTGTACTTTCTGGAAATCAAT 57.359 30.769 11.24 0.00 33.13 2.57
2890 3291 8.764524 AATATTTCTATATCACTGTCGCCTTC 57.235 34.615 0.00 0.00 0.00 3.46
2897 3298 8.367911 TCTATATCACTGTCGCCTTCAATATTT 58.632 33.333 0.00 0.00 0.00 1.40
3090 3542 1.379176 CACTCGAGGCTCCAGAGGA 60.379 63.158 16.33 2.53 36.40 3.71
3096 3548 3.104512 TCGAGGCTCCAGAGGAAAAATA 58.895 45.455 9.32 0.00 0.00 1.40
3159 3616 4.810345 TCCAAACAAACAAACCCTAGGAT 58.190 39.130 11.48 0.00 0.00 3.24
3221 3684 2.840038 AGCACCATGTCACTATCCTTGA 59.160 45.455 0.00 0.00 0.00 3.02
3326 3789 1.125021 CTTCGTCATCGCTTCACACAC 59.875 52.381 0.00 0.00 36.96 3.82
3368 3831 2.092158 TCCTCATCCTCGTCATCACTCT 60.092 50.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 1.242076 GTTCCTGTGATGCTGCTTGT 58.758 50.000 0.00 0.00 0.00 3.16
300 302 2.743928 CCGTCTCCCAAGTGCAGC 60.744 66.667 0.00 0.00 0.00 5.25
609 643 2.665185 GGACGCGGCAGAAGTTGT 60.665 61.111 17.00 0.00 0.00 3.32
689 731 4.443063 GGGTTTCTTTTGTTGAATACGTGC 59.557 41.667 0.00 0.00 0.00 5.34
802 846 1.341852 TGACTACTGCGTTGGTAAGCA 59.658 47.619 0.00 0.00 41.55 3.91
833 883 4.679662 AGTCCGGTATGTTTCTATGAACG 58.320 43.478 0.00 0.00 32.18 3.95
1403 1476 3.252351 GAGGGAATCCTATAACCTGGCT 58.748 50.000 0.00 0.00 45.05 4.75
1919 2003 9.801873 CATGAACAGAAAAAGAAAAAGGAAGTA 57.198 29.630 0.00 0.00 0.00 2.24
2251 2360 0.883814 CTGGAATGCTCGCCTGATCC 60.884 60.000 0.00 0.00 0.00 3.36
2252 2361 0.105593 TCTGGAATGCTCGCCTGATC 59.894 55.000 0.00 0.00 0.00 2.92
2253 2362 0.106335 CTCTGGAATGCTCGCCTGAT 59.894 55.000 0.00 0.00 32.68 2.90
2254 2363 1.519246 CTCTGGAATGCTCGCCTGA 59.481 57.895 0.00 0.00 0.00 3.86
2255 2364 2.178890 GCTCTGGAATGCTCGCCTG 61.179 63.158 0.00 0.00 0.00 4.85
2256 2365 1.908340 AAGCTCTGGAATGCTCGCCT 61.908 55.000 0.00 0.00 38.75 5.52
2472 2581 2.969821 TGTAACAATGACCTTGGCCT 57.030 45.000 3.32 0.00 39.30 5.19
2674 3036 9.676861 TGTTCATTCTTCTTCATACAAGATGAT 57.323 29.630 1.94 0.00 32.70 2.45
2689 3051 6.309737 GCCTTTGATTCACATGTTCATTCTTC 59.690 38.462 0.00 0.00 0.00 2.87
2699 3061 5.803461 CAGTTACATGCCTTTGATTCACATG 59.197 40.000 11.42 11.42 42.92 3.21
2781 3173 5.559770 TCTGAAACCAGTCTGATAAATGCA 58.440 37.500 0.00 0.00 33.49 3.96
2890 3291 8.400947 ACTGAAGCACACAATAGCTAAATATTG 58.599 33.333 0.00 0.97 44.96 1.90
2897 3298 9.261180 GAATAATACTGAAGCACACAATAGCTA 57.739 33.333 0.00 0.00 40.90 3.32
3090 3542 6.910433 CACAAGACAGCAACTTACGTATTTTT 59.090 34.615 0.00 0.00 0.00 1.94
3096 3548 2.901249 ACACAAGACAGCAACTTACGT 58.099 42.857 0.00 0.00 0.00 3.57
3212 3669 2.752030 TGTGGAGGAGGTCAAGGATAG 58.248 52.381 0.00 0.00 0.00 2.08
3221 3684 1.079490 TCAGGAGAATGTGGAGGAGGT 59.921 52.381 0.00 0.00 0.00 3.85
3326 3789 1.792949 GGTAGCTAATGACGATTGCGG 59.207 52.381 0.00 0.00 43.17 5.69
3368 3831 2.863740 GCGATGACGATTCCATTGTGTA 59.136 45.455 0.00 0.00 42.66 2.90


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

AutoCloner maintained by Alex Coulton.