Multiple sequence alignment - TraesCS1B01G312400

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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 TraesCS1B01G312400 chr1B 100.000 3410 0 0 1 3410 535941187 535937778 0.000000e+00 6298.0
1 TraesCS1B01G312400 chr1B 98.167 2018 19 1 1 2000 535916076 535914059 0.000000e+00 3506.0
2 TraesCS1B01G312400 chr1B 94.109 1952 91 5 986 2914 536122917 536120967 0.000000e+00 2946.0
3 TraesCS1B01G312400 chr1B 92.157 1530 96 9 960 2468 535799451 535797925 0.000000e+00 2139.0
4 TraesCS1B01G312400 chr1B 91.373 823 47 8 1 799 535917565 535916743 0.000000e+00 1105.0
5 TraesCS1B01G312400 chr1B 96.667 510 14 2 1998 2504 535908613 535908104 0.000000e+00 845.0
6 TraesCS1B01G312400 chr1B 94.231 416 21 3 2501 2914 535908024 535907610 1.730000e-177 632.0
7 TraesCS1B01G312400 chr1B 86.007 536 52 13 1 513 47711276 47711811 1.380000e-153 553.0
8 TraesCS1B01G312400 chr1B 92.958 213 8 3 767 972 535799678 535799466 1.540000e-78 303.0
9 TraesCS1B01G312400 chr1B 94.828 58 3 0 653 710 535799743 535799686 1.300000e-14 91.6
10 TraesCS1B01G312400 chr1D 89.848 2108 145 31 860 2914 399415368 399413277 0.000000e+00 2643.0
11 TraesCS1B01G312400 chr1D 90.255 1683 116 20 823 2468 399394959 399393288 0.000000e+00 2156.0
12 TraesCS1B01G312400 chr1D 82.984 382 36 14 653 1033 399411321 399410968 5.490000e-83 318.0
13 TraesCS1B01G312400 chr1D 94.231 52 2 1 2863 2914 399547332 399547282 1.010000e-10 78.7
14 TraesCS1B01G312400 chr1D 90.000 60 4 2 637 695 399395615 399395557 3.650000e-10 76.8
15 TraesCS1B01G312400 chr1A 90.152 1584 118 18 917 2469 496143467 496141891 0.000000e+00 2026.0
16 TraesCS1B01G312400 chr7A 84.280 1444 188 24 1000 2413 156549129 156550563 0.000000e+00 1373.0
17 TraesCS1B01G312400 chr7B 83.390 1475 206 26 967 2413 116753282 116754745 0.000000e+00 1330.0
18 TraesCS1B01G312400 chr7B 86.676 713 90 4 1046 1757 45052424 45051716 0.000000e+00 785.0
19 TraesCS1B01G312400 chr7B 85.434 611 84 3 1802 2411 45051632 45051026 6.210000e-177 630.0
20 TraesCS1B01G312400 chr7B 88.209 441 50 2 2912 3351 459600264 459599825 3.010000e-145 525.0
21 TraesCS1B01G312400 chr7D 83.322 1463 204 26 990 2423 154935832 154934381 0.000000e+00 1314.0
22 TraesCS1B01G312400 chr7D 72.297 1267 293 44 1056 2302 178475050 178476278 3.260000e-90 342.0
23 TraesCS1B01G312400 chr3B 89.137 672 48 4 1 647 503771406 503772077 0.000000e+00 813.0
24 TraesCS1B01G312400 chr3B 87.838 518 45 2 2909 3408 513989286 513988769 2.930000e-165 592.0
25 TraesCS1B01G312400 chr3B 90.930 430 39 0 2916 3345 316571123 316571552 2.280000e-161 579.0
26 TraesCS1B01G312400 chr5B 88.988 672 47 7 1 647 345852556 345853225 0.000000e+00 806.0
27 TraesCS1B01G312400 chr5B 88.410 673 51 8 1 647 478551490 478550819 0.000000e+00 785.0
28 TraesCS1B01G312400 chr5B 88.110 656 57 6 9 647 530260078 530260729 0.000000e+00 760.0
29 TraesCS1B01G312400 chr5B 87.370 673 47 15 1 647 514923930 514924590 0.000000e+00 737.0
30 TraesCS1B01G312400 chr5B 86.996 669 60 14 1 643 653225326 653225993 0.000000e+00 728.0
31 TraesCS1B01G312400 chr5B 86.036 666 72 11 1 647 486089644 486088981 0.000000e+00 695.0
32 TraesCS1B01G312400 chr5B 88.086 512 43 2 2916 3410 477090660 477090150 2.930000e-165 592.0
33 TraesCS1B01G312400 chr5D 88.031 635 55 13 1 617 373957572 373956941 0.000000e+00 732.0
34 TraesCS1B01G312400 chr6D 86.316 665 53 12 1 647 36286218 36286862 0.000000e+00 689.0
35 TraesCS1B01G312400 chr3D 85.481 675 54 15 1 648 6449324 6448667 0.000000e+00 664.0
36 TraesCS1B01G312400 chr3D 93.424 441 28 1 2909 3348 357434652 357434212 0.000000e+00 652.0
37 TraesCS1B01G312400 chrUn 85.628 661 57 19 1 639 42149475 42150119 0.000000e+00 660.0
38 TraesCS1B01G312400 chr3A 90.411 511 32 5 2916 3409 87774536 87774026 0.000000e+00 656.0
39 TraesCS1B01G312400 chr2D 84.858 667 62 13 1 647 538072198 538072845 1.330000e-178 636.0
40 TraesCS1B01G312400 chr2B 90.497 463 36 3 190 644 569075755 569076217 3.760000e-169 604.0
41 TraesCS1B01G312400 chr6B 91.514 436 37 0 2913 3348 256347763 256347328 4.870000e-168 601.0
42 TraesCS1B01G312400 chr6B 91.237 388 34 0 2911 3298 473067022 473066635 2.330000e-146 529.0
43 TraesCS1B01G312400 chr4A 85.126 437 62 3 2916 3351 191001222 191000788 8.680000e-121 444.0


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 TraesCS1B01G312400 chr1B 535937778 535941187 3409 True 6298.000000 6298 100.000000 1 3410 1 chr1B.!!$R1 3409
1 TraesCS1B01G312400 chr1B 536120967 536122917 1950 True 2946.000000 2946 94.109000 986 2914 1 chr1B.!!$R2 1928
2 TraesCS1B01G312400 chr1B 535914059 535917565 3506 True 2305.500000 3506 94.770000 1 2000 2 chr1B.!!$R5 1999
3 TraesCS1B01G312400 chr1B 535797925 535799743 1818 True 844.533333 2139 93.314333 653 2468 3 chr1B.!!$R3 1815
4 TraesCS1B01G312400 chr1B 535907610 535908613 1003 True 738.500000 845 95.449000 1998 2914 2 chr1B.!!$R4 916
5 TraesCS1B01G312400 chr1B 47711276 47711811 535 False 553.000000 553 86.007000 1 513 1 chr1B.!!$F1 512
6 TraesCS1B01G312400 chr1D 399410968 399415368 4400 True 1480.500000 2643 86.416000 653 2914 2 chr1D.!!$R3 2261
7 TraesCS1B01G312400 chr1D 399393288 399395615 2327 True 1116.400000 2156 90.127500 637 2468 2 chr1D.!!$R2 1831
8 TraesCS1B01G312400 chr1A 496141891 496143467 1576 True 2026.000000 2026 90.152000 917 2469 1 chr1A.!!$R1 1552
9 TraesCS1B01G312400 chr7A 156549129 156550563 1434 False 1373.000000 1373 84.280000 1000 2413 1 chr7A.!!$F1 1413
10 TraesCS1B01G312400 chr7B 116753282 116754745 1463 False 1330.000000 1330 83.390000 967 2413 1 chr7B.!!$F1 1446
11 TraesCS1B01G312400 chr7B 45051026 45052424 1398 True 707.500000 785 86.055000 1046 2411 2 chr7B.!!$R2 1365
12 TraesCS1B01G312400 chr7D 154934381 154935832 1451 True 1314.000000 1314 83.322000 990 2423 1 chr7D.!!$R1 1433
13 TraesCS1B01G312400 chr7D 178475050 178476278 1228 False 342.000000 342 72.297000 1056 2302 1 chr7D.!!$F1 1246
14 TraesCS1B01G312400 chr3B 503771406 503772077 671 False 813.000000 813 89.137000 1 647 1 chr3B.!!$F2 646
15 TraesCS1B01G312400 chr3B 513988769 513989286 517 True 592.000000 592 87.838000 2909 3408 1 chr3B.!!$R1 499
16 TraesCS1B01G312400 chr5B 345852556 345853225 669 False 806.000000 806 88.988000 1 647 1 chr5B.!!$F1 646
17 TraesCS1B01G312400 chr5B 478550819 478551490 671 True 785.000000 785 88.410000 1 647 1 chr5B.!!$R2 646
18 TraesCS1B01G312400 chr5B 530260078 530260729 651 False 760.000000 760 88.110000 9 647 1 chr5B.!!$F3 638
19 TraesCS1B01G312400 chr5B 514923930 514924590 660 False 737.000000 737 87.370000 1 647 1 chr5B.!!$F2 646
20 TraesCS1B01G312400 chr5B 653225326 653225993 667 False 728.000000 728 86.996000 1 643 1 chr5B.!!$F4 642
21 TraesCS1B01G312400 chr5B 486088981 486089644 663 True 695.000000 695 86.036000 1 647 1 chr5B.!!$R3 646
22 TraesCS1B01G312400 chr5B 477090150 477090660 510 True 592.000000 592 88.086000 2916 3410 1 chr5B.!!$R1 494
23 TraesCS1B01G312400 chr5D 373956941 373957572 631 True 732.000000 732 88.031000 1 617 1 chr5D.!!$R1 616
24 TraesCS1B01G312400 chr6D 36286218 36286862 644 False 689.000000 689 86.316000 1 647 1 chr6D.!!$F1 646
25 TraesCS1B01G312400 chr3D 6448667 6449324 657 True 664.000000 664 85.481000 1 648 1 chr3D.!!$R1 647
26 TraesCS1B01G312400 chrUn 42149475 42150119 644 False 660.000000 660 85.628000 1 639 1 chrUn.!!$F1 638
27 TraesCS1B01G312400 chr3A 87774026 87774536 510 True 656.000000 656 90.411000 2916 3409 1 chr3A.!!$R1 493
28 TraesCS1B01G312400 chr2D 538072198 538072845 647 False 636.000000 636 84.858000 1 647 1 chr2D.!!$F1 646

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
319 344 0.250553 ATCGTCGGTTTGGGCTGAAA 60.251 50.000 0.0 0.0 0.0 2.69 F
377 410 0.833949 TGTGGTGTTGGTGTGCTAGA 59.166 50.000 0.0 0.0 0.0 2.43 F
1495 3574 2.686106 TCGCCTACTTCCCCACCC 60.686 66.667 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1385 3464 0.107459 GATGACCTGGGAAGCCAGAC 60.107 60.000 0.0 0.00 39.96 3.51 R
1758 3838 1.878088 TCTGTGCTCGTCGACTTAAGT 59.122 47.619 14.7 8.13 0.00 2.24 R
3186 6344 1.482182 CCTCCCTTGTGATCATCGTCA 59.518 52.381 0.0 0.00 0.00 4.35 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
219 241 2.303022 AGGCAGCAGAACAAGCTTACTA 59.697 45.455 0.00 0.00 41.14 1.82
319 344 0.250553 ATCGTCGGTTTGGGCTGAAA 60.251 50.000 0.00 0.00 0.00 2.69
377 410 0.833949 TGTGGTGTTGGTGTGCTAGA 59.166 50.000 0.00 0.00 0.00 2.43
402 436 3.264193 TGATCATTGTGGGTAAGCTCACT 59.736 43.478 5.05 0.00 46.03 3.41
1495 3574 2.686106 TCGCCTACTTCCCCACCC 60.686 66.667 0.00 0.00 0.00 4.61
1758 3838 4.980805 GTGTTCGCAGTCGGCCCA 62.981 66.667 0.00 0.00 40.31 5.36
2571 4798 6.767902 CCTGAAAATAAAGAGCCAGCTATGTA 59.232 38.462 0.00 0.00 0.00 2.29
2610 4838 4.797693 TTTGTTGTAAGTCAATTCGCGA 57.202 36.364 3.71 3.71 38.38 5.87
2619 4851 1.014044 TCAATTCGCGAGTGAGGCAC 61.014 55.000 17.62 0.00 34.10 5.01
2666 4898 2.227388 ACGCTTTCTTCTTTCTGCCATG 59.773 45.455 0.00 0.00 0.00 3.66
2956 5901 9.578439 CATAGAGCGTATCATTTCATTGATAGA 57.422 33.333 0.00 0.00 38.83 1.98
3008 5953 0.614979 ACACTCGTGGCCAGACCTAT 60.615 55.000 5.11 0.00 40.22 2.57
3097 6042 2.993264 GTGGCCCACATTGCTGCT 60.993 61.111 9.55 0.00 34.08 4.24
3107 6052 1.303561 ATTGCTGCTTCGGCCAGAA 60.304 52.632 2.24 6.71 40.91 3.02
3136 6081 3.681835 GCCTCGGTCACTGACGGT 61.682 66.667 14.48 0.00 35.03 4.83
3143 6088 1.592400 GGTCACTGACGGTCGGATGA 61.592 60.000 23.15 17.90 32.65 2.92
3186 6344 1.920835 GCTTCCAGAGGGTCCAGGT 60.921 63.158 0.00 0.00 34.93 4.00
3252 6711 1.676678 GCAGAGGACGTGGATGCCTA 61.677 60.000 0.00 0.00 30.70 3.93
3300 6820 0.917533 AGAGGAATGCTGCTGGTGAT 59.082 50.000 0.00 0.00 0.00 3.06
3319 6839 3.958147 TGATTCGTAGCCTGGAGAATACA 59.042 43.478 0.00 1.55 33.95 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.039004 AGCACACAAATAACAATGGAGCAA 59.961 37.500 0.00 0.00 0.00 3.91
243 268 3.610040 TGTCACTGTCAACACTTCTGT 57.390 42.857 0.00 0.00 0.00 3.41
247 272 3.350219 ACCTTGTCACTGTCAACACTT 57.650 42.857 0.00 0.00 0.00 3.16
319 344 4.629200 GCGAAGATGATGAAGTTCTTCAGT 59.371 41.667 21.74 12.02 43.50 3.41
377 410 4.202441 GAGCTTACCCACAATGATCACAT 58.798 43.478 0.00 0.00 38.50 3.21
402 436 5.085920 TGTGCTTACCTTGTACCCTAGTTA 58.914 41.667 0.00 0.00 0.00 2.24
1385 3464 0.107459 GATGACCTGGGAAGCCAGAC 60.107 60.000 0.00 0.00 39.96 3.51
1495 3574 3.554692 GTTGGCGCCGTCGAGATG 61.555 66.667 23.90 0.00 38.10 2.90
1758 3838 1.878088 TCTGTGCTCGTCGACTTAAGT 59.122 47.619 14.70 8.13 0.00 2.24
2610 4838 3.438087 CGATTTCAATTCAGTGCCTCACT 59.562 43.478 0.00 0.00 46.51 3.41
2619 4851 4.641989 AGGGATGGTTCGATTTCAATTCAG 59.358 41.667 0.00 0.00 0.00 3.02
2890 5145 5.482686 AAATTCAAAAACCACATGCACAC 57.517 34.783 0.00 0.00 0.00 3.82
2956 5901 1.827969 AGCGCATGTAAACTCCTCTCT 59.172 47.619 11.47 0.00 0.00 3.10
2986 5931 1.956170 GTCTGGCCACGAGTGTGTG 60.956 63.158 0.00 0.00 44.92 3.82
3008 5953 3.543665 ACCTTGTAACCGTAACTTTGCA 58.456 40.909 0.00 0.00 0.00 4.08
3079 6024 2.993264 GCAGCAATGTGGGCCACT 60.993 61.111 34.69 19.01 35.11 4.00
3136 6081 1.504900 CACCTTCGACGTCATCCGA 59.495 57.895 17.16 4.48 40.70 4.55
3143 6088 2.731691 AATGCCTGCACCTTCGACGT 62.732 55.000 0.00 0.00 0.00 4.34
3186 6344 1.482182 CCTCCCTTGTGATCATCGTCA 59.518 52.381 0.00 0.00 0.00 4.35
3252 6711 2.058675 CCCTTCTTCGACTGGTGGT 58.941 57.895 0.00 0.00 0.00 4.16
3300 6820 3.004419 CGATGTATTCTCCAGGCTACGAA 59.996 47.826 0.00 0.00 0.00 3.85
3319 6839 3.126879 CGCATGGTGTGGCACGAT 61.127 61.111 13.77 1.87 33.29 3.73


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

AutoCloner maintained by Alex Coulton.