Multiple sequence alignment - TraesCS2A01G145600

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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 TraesCS2A01G145600 chr2A 100.000 3419 0 0 1 3419 90578570 90575152 0.000000e+00 6314
1 TraesCS2A01G145600 chr2B 96.312 2576 67 11 507 3055 143824485 143821911 0.000000e+00 4205
2 TraesCS2A01G145600 chr2D 97.899 2189 43 2 507 2692 90818457 90816269 0.000000e+00 3784
3 TraesCS2A01G145600 chr5D 97.342 1919 51 0 507 2425 370452653 370450735 0.000000e+00 3262
4 TraesCS2A01G145600 chr5D 92.039 515 38 3 1 513 484051633 484052146 0.000000e+00 721
5 TraesCS2A01G145600 chr5A 97.134 1919 55 0 507 2425 472920504 472918586 0.000000e+00 3240
6 TraesCS2A01G145600 chr5A 98.352 364 5 1 3053 3416 675453755 675454117 3.720000e-179 638
7 TraesCS2A01G145600 chr4D 93.436 518 31 3 1 516 460922269 460921753 0.000000e+00 765
8 TraesCS2A01G145600 chr4D 93.243 518 32 3 1 516 460872926 460872410 0.000000e+00 760
9 TraesCS2A01G145600 chr4D 92.664 518 35 3 1 516 460862059 460861543 0.000000e+00 743
10 TraesCS2A01G145600 chr3A 92.115 520 36 4 1 516 698719908 698719390 0.000000e+00 728
11 TraesCS2A01G145600 chr3A 92.353 510 35 3 1 506 38011600 38012109 0.000000e+00 723
12 TraesCS2A01G145600 chr3A 91.876 517 36 5 1 513 37996406 37996920 0.000000e+00 717
13 TraesCS2A01G145600 chr1A 92.263 517 35 4 1 513 24798396 24798911 0.000000e+00 728
14 TraesCS2A01G145600 chr1A 98.352 364 5 1 3056 3419 471299651 471299289 3.720000e-179 638
15 TraesCS2A01G145600 chr5B 90.074 544 46 8 1 539 434924967 434924427 0.000000e+00 699
16 TraesCS2A01G145600 chr7A 98.626 364 4 1 3056 3419 110072188 110071826 0.000000e+00 643
17 TraesCS2A01G145600 chrUn 98.615 361 4 1 3056 3416 64723616 64723975 3.720000e-179 638
18 TraesCS2A01G145600 chrUn 98.615 361 4 1 3056 3416 64726046 64726405 3.720000e-179 638
19 TraesCS2A01G145600 chrUn 98.352 364 5 1 3056 3419 439938537 439938175 3.720000e-179 638
20 TraesCS2A01G145600 chr7B 98.352 364 5 1 3056 3419 558309521 558309159 3.720000e-179 638
21 TraesCS2A01G145600 chr4B 98.615 361 4 1 3056 3416 12028755 12029114 3.720000e-179 638
22 TraesCS2A01G145600 chr1B 97.090 378 7 4 3043 3419 39864644 39864270 4.810000e-178 634


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 TraesCS2A01G145600 chr2A 90575152 90578570 3418 True 6314 6314 100.000 1 3419 1 chr2A.!!$R1 3418
1 TraesCS2A01G145600 chr2B 143821911 143824485 2574 True 4205 4205 96.312 507 3055 1 chr2B.!!$R1 2548
2 TraesCS2A01G145600 chr2D 90816269 90818457 2188 True 3784 3784 97.899 507 2692 1 chr2D.!!$R1 2185
3 TraesCS2A01G145600 chr5D 370450735 370452653 1918 True 3262 3262 97.342 507 2425 1 chr5D.!!$R1 1918
4 TraesCS2A01G145600 chr5D 484051633 484052146 513 False 721 721 92.039 1 513 1 chr5D.!!$F1 512
5 TraesCS2A01G145600 chr5A 472918586 472920504 1918 True 3240 3240 97.134 507 2425 1 chr5A.!!$R1 1918
6 TraesCS2A01G145600 chr4D 460921753 460922269 516 True 765 765 93.436 1 516 1 chr4D.!!$R3 515
7 TraesCS2A01G145600 chr4D 460872410 460872926 516 True 760 760 93.243 1 516 1 chr4D.!!$R2 515
8 TraesCS2A01G145600 chr4D 460861543 460862059 516 True 743 743 92.664 1 516 1 chr4D.!!$R1 515
9 TraesCS2A01G145600 chr3A 698719390 698719908 518 True 728 728 92.115 1 516 1 chr3A.!!$R1 515
10 TraesCS2A01G145600 chr3A 38011600 38012109 509 False 723 723 92.353 1 506 1 chr3A.!!$F2 505
11 TraesCS2A01G145600 chr3A 37996406 37996920 514 False 717 717 91.876 1 513 1 chr3A.!!$F1 512
12 TraesCS2A01G145600 chr1A 24798396 24798911 515 False 728 728 92.263 1 513 1 chr1A.!!$F1 512
13 TraesCS2A01G145600 chr5B 434924427 434924967 540 True 699 699 90.074 1 539 1 chr5B.!!$R1 538
14 TraesCS2A01G145600 chrUn 64723616 64726405 2789 False 638 638 98.615 3056 3416 2 chrUn.!!$F1 360

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
283 287 3.104512 TCCTTCCAATCATCGGTGTACT 58.895 45.455 0.0 0.0 0.0 2.73 F
386 392 3.880490 ACGTTCCAGCAAGTAACAATTCA 59.120 39.130 0.0 0.0 0.0 2.57 F
1438 1445 0.471617 GATGGTGGATGCTGGCTACT 59.528 55.000 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1445 1.804151 GTATGTTTTGAGGTCAGCGCA 59.196 47.619 11.47 0.0 0.0 6.09 R
2044 2051 6.409704 TCTCTACATTTCCAAGACAATCTGG 58.590 40.000 0.00 0.0 0.0 3.86 R
2551 2558 0.034574 CCCCCAACGAATGATCACCA 60.035 55.000 0.00 0.0 0.0 4.17 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
17 19 4.226249 AGGCTAGGGGTAGGGACT 57.774 61.111 0.00 0.00 46.37 3.85
50 52 4.202315 TGTCTTTTCGAAGAATCCACCTCA 60.202 41.667 0.00 0.00 45.90 3.86
54 56 6.763135 TCTTTTCGAAGAATCCACCTCATATG 59.237 38.462 0.00 0.00 45.90 1.78
104 108 5.069251 CACTAGTTTCCGGAATAGAGTCCAT 59.931 44.000 24.98 5.11 37.56 3.41
114 118 9.046846 TCCGGAATAGAGTCCATATCAAATTAT 57.953 33.333 0.00 0.00 37.56 1.28
163 167 3.729862 GGATTCTATCCGTTTCGTCCT 57.270 47.619 0.00 0.00 40.13 3.85
276 280 4.533919 ATCTAGCTCCTTCCAATCATCG 57.466 45.455 0.00 0.00 0.00 3.84
283 287 3.104512 TCCTTCCAATCATCGGTGTACT 58.895 45.455 0.00 0.00 0.00 2.73
299 303 4.202030 GGTGTACTCGGATAGTCTTTCCAG 60.202 50.000 9.68 8.15 39.80 3.86
386 392 3.880490 ACGTTCCAGCAAGTAACAATTCA 59.120 39.130 0.00 0.00 0.00 2.57
410 416 9.979578 TCAATGCTAAACATGTAAAACAATTCT 57.020 25.926 0.00 0.00 39.60 2.40
509 516 5.126061 GCAGGACACATAATTCCAACATCTT 59.874 40.000 0.00 0.00 33.92 2.40
1438 1445 0.471617 GATGGTGGATGCTGGCTACT 59.528 55.000 0.00 0.00 0.00 2.57
1654 1661 4.737177 AGCTGAGCTTGCCTGCCC 62.737 66.667 0.00 0.00 33.89 5.36
1866 1873 0.528033 CAGATGACTGCGAGCCAGAG 60.528 60.000 0.00 0.00 44.64 3.35
2044 2051 3.904136 ATGCAGCTGTTTCACTTGTAC 57.096 42.857 16.64 0.00 0.00 2.90
2239 2246 3.459145 TGCAAGTACGCAACTTCAACTA 58.541 40.909 0.98 0.00 45.64 2.24
2313 2320 7.982224 AGGCTAATTTTATTGTTTACGAGGAC 58.018 34.615 0.00 0.00 0.00 3.85
2386 2393 6.183360 TGGATTGAAGTTCTTCAACCTTGAAC 60.183 38.462 24.09 12.85 42.91 3.18
2506 2513 4.987832 TCGATCTCTTTGCTGAACTAGTC 58.012 43.478 0.00 0.00 0.00 2.59
2509 2516 5.669477 GATCTCTTTGCTGAACTAGTCCAT 58.331 41.667 0.00 0.00 0.00 3.41
2543 2550 5.368523 TGAATGGGGAAAAGATATAGGACGT 59.631 40.000 0.00 0.00 0.00 4.34
2551 2558 8.148999 GGGAAAAGATATAGGACGTGTTTATCT 58.851 37.037 0.00 0.00 32.42 1.98
2554 2561 7.598759 AAGATATAGGACGTGTTTATCTGGT 57.401 36.000 0.00 0.00 31.69 4.00
2559 2566 3.513912 AGGACGTGTTTATCTGGTGATCA 59.486 43.478 0.00 0.00 34.32 2.92
2606 2613 1.064505 CACCTCAATTGCCATGCTACG 59.935 52.381 0.00 0.00 0.00 3.51
2610 2617 3.376859 CCTCAATTGCCATGCTACGTTTA 59.623 43.478 0.00 0.00 0.00 2.01
2611 2618 4.142491 CCTCAATTGCCATGCTACGTTTAA 60.142 41.667 0.00 0.00 0.00 1.52
2612 2619 5.378292 TCAATTGCCATGCTACGTTTAAA 57.622 34.783 0.00 0.00 0.00 1.52
2616 2623 7.386299 TCAATTGCCATGCTACGTTTAAATTTT 59.614 29.630 0.00 0.00 0.00 1.82
2847 2858 5.683859 GCATAAGCTAGTGATCGGAAATTG 58.316 41.667 2.66 0.00 37.91 2.32
2868 2879 4.415596 TGAGGGTACTAAAGGGTTTCGTA 58.584 43.478 0.00 0.00 0.00 3.43
2870 2881 5.484998 TGAGGGTACTAAAGGGTTTCGTATT 59.515 40.000 0.00 0.00 0.00 1.89
2871 2882 6.013466 TGAGGGTACTAAAGGGTTTCGTATTT 60.013 38.462 0.00 0.00 0.00 1.40
2873 2884 5.939883 GGGTACTAAAGGGTTTCGTATTTGT 59.060 40.000 0.00 0.00 0.00 2.83
2874 2885 6.430925 GGGTACTAAAGGGTTTCGTATTTGTT 59.569 38.462 0.00 0.00 0.00 2.83
2875 2886 7.300320 GGTACTAAAGGGTTTCGTATTTGTTG 58.700 38.462 0.00 0.00 0.00 3.33
2876 2887 6.947644 ACTAAAGGGTTTCGTATTTGTTGT 57.052 33.333 0.00 0.00 0.00 3.32
2877 2888 6.731164 ACTAAAGGGTTTCGTATTTGTTGTG 58.269 36.000 0.00 0.00 0.00 3.33
2879 2890 5.838531 AAGGGTTTCGTATTTGTTGTGAA 57.161 34.783 0.00 0.00 0.00 3.18
2880 2891 6.399639 AAGGGTTTCGTATTTGTTGTGAAT 57.600 33.333 0.00 0.00 0.00 2.57
2881 2892 7.513371 AAGGGTTTCGTATTTGTTGTGAATA 57.487 32.000 0.00 0.00 0.00 1.75
2882 2893 7.141100 AGGGTTTCGTATTTGTTGTGAATAG 57.859 36.000 0.00 0.00 0.00 1.73
2883 2894 5.798434 GGGTTTCGTATTTGTTGTGAATAGC 59.202 40.000 0.00 0.00 0.00 2.97
2885 2896 7.081976 GGTTTCGTATTTGTTGTGAATAGCTT 58.918 34.615 0.00 0.00 0.00 3.74
2886 2897 8.231837 GGTTTCGTATTTGTTGTGAATAGCTTA 58.768 33.333 0.00 0.00 0.00 3.09
2887 2898 9.601971 GTTTCGTATTTGTTGTGAATAGCTTAA 57.398 29.630 0.00 0.00 0.00 1.85
2888 2899 9.601971 TTTCGTATTTGTTGTGAATAGCTTAAC 57.398 29.630 0.00 0.00 0.00 2.01
2889 2900 7.745015 TCGTATTTGTTGTGAATAGCTTAACC 58.255 34.615 0.00 0.00 0.00 2.85
2891 2902 8.234546 CGTATTTGTTGTGAATAGCTTAACCTT 58.765 33.333 0.00 0.00 0.00 3.50
2958 2993 6.649141 ACAAACTTAATCATTCGCACAGTCTA 59.351 34.615 0.00 0.00 0.00 2.59
3175 5640 3.979948 TGCACGTACTAAGCAAACAGTA 58.020 40.909 0.00 0.00 34.97 2.74
3199 5664 9.021863 GTAAGACAAATCTACACATACTGCTAC 57.978 37.037 0.00 0.00 33.57 3.58
3416 5881 1.139734 GATCGGAAGCGAGCAGTCA 59.860 57.895 0.00 0.00 0.00 3.41
3417 5882 1.142778 GATCGGAAGCGAGCAGTCAC 61.143 60.000 0.00 0.00 0.00 3.67
3418 5883 2.874010 ATCGGAAGCGAGCAGTCACG 62.874 60.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 38 4.965814 TCTGCATATGAGGTGGATTCTTC 58.034 43.478 6.97 0.00 0.00 2.87
41 43 7.984859 TCTTATATCTGCATATGAGGTGGAT 57.015 36.000 6.97 4.57 32.00 3.41
114 118 5.487433 ACAGACAAATATGATCGTGGTTGA 58.513 37.500 15.53 0.00 0.00 3.18
254 258 4.262808 CCGATGATTGGAAGGAGCTAGATT 60.263 45.833 0.00 0.00 0.00 2.40
276 280 3.698040 TGGAAAGACTATCCGAGTACACC 59.302 47.826 0.00 0.00 39.06 4.16
283 287 9.584008 ACTATTTATACTGGAAAGACTATCCGA 57.416 33.333 0.00 0.00 39.98 4.55
468 475 9.407380 TGTGTCCTGCAACTATATTCAAATTAT 57.593 29.630 0.00 0.00 0.00 1.28
1438 1445 1.804151 GTATGTTTTGAGGTCAGCGCA 59.196 47.619 11.47 0.00 0.00 6.09
1654 1661 7.201565 CCTCAAGAAGTCCGCTAAAAATTCTAG 60.202 40.741 0.00 0.00 0.00 2.43
2044 2051 6.409704 TCTCTACATTTCCAAGACAATCTGG 58.590 40.000 0.00 0.00 0.00 3.86
2386 2393 5.786311 TCTGCTTCTCCATTTCAATTTTGG 58.214 37.500 0.00 0.00 0.00 3.28
2494 2501 6.129874 ACTGTATAGATGGACTAGTTCAGCA 58.870 40.000 21.20 7.95 34.14 4.41
2506 2513 5.567037 TCCCCATTCAACTGTATAGATGG 57.433 43.478 0.00 0.00 0.00 3.51
2509 2516 7.265599 TCTTTTCCCCATTCAACTGTATAGA 57.734 36.000 0.00 0.00 0.00 1.98
2543 2550 5.353956 CCAACGAATGATCACCAGATAAACA 59.646 40.000 0.00 0.00 33.72 2.83
2551 2558 0.034574 CCCCCAACGAATGATCACCA 60.035 55.000 0.00 0.00 0.00 4.17
2554 2561 1.578897 TCTCCCCCAACGAATGATCA 58.421 50.000 0.00 0.00 0.00 2.92
2559 2566 3.112263 TGATAGTTCTCCCCCAACGAAT 58.888 45.455 0.00 0.00 0.00 3.34
2616 2623 1.883275 CCCTCAAACATACACGGCAAA 59.117 47.619 0.00 0.00 0.00 3.68
2630 2638 1.425066 AGTGCATGGAAAGTCCCTCAA 59.575 47.619 0.00 0.00 35.03 3.02
2724 2734 7.703621 CGAATTTAAAGCAGTTGGATCATGATT 59.296 33.333 10.14 0.00 0.00 2.57
2790 2800 9.490379 GATGTGAAGTTATACCTTCGGAAATAT 57.510 33.333 5.65 0.00 43.06 1.28
2838 2849 4.080751 CCCTTTAGTACCCTCAATTTCCGA 60.081 45.833 0.00 0.00 0.00 4.55
2847 2858 3.969287 ACGAAACCCTTTAGTACCCTC 57.031 47.619 0.00 0.00 0.00 4.30
2870 2881 7.175816 TGCATAAGGTTAAGCTATTCACAACAA 59.824 33.333 7.76 0.00 0.00 2.83
2871 2882 6.657117 TGCATAAGGTTAAGCTATTCACAACA 59.343 34.615 7.76 0.00 0.00 3.33
2873 2884 7.880160 ATGCATAAGGTTAAGCTATTCACAA 57.120 32.000 7.76 0.00 0.00 3.33
2874 2885 7.880160 AATGCATAAGGTTAAGCTATTCACA 57.120 32.000 7.76 3.95 0.00 3.58
2875 2886 9.057089 ACTAATGCATAAGGTTAAGCTATTCAC 57.943 33.333 7.76 0.00 0.00 3.18
2948 2983 1.135972 GCACCACATTTAGACTGTGCG 60.136 52.381 0.00 0.00 42.10 5.34
2958 2993 1.964373 GTCCGTCCGCACCACATTT 60.964 57.895 0.00 0.00 0.00 2.32
3175 5640 7.841956 AGTAGCAGTATGTGTAGATTTGTCTT 58.158 34.615 0.00 0.00 39.31 3.01
3346 5811 1.559219 TCATCACCATGTCCACCGATT 59.441 47.619 0.00 0.00 0.00 3.34
3347 5812 1.203237 TCATCACCATGTCCACCGAT 58.797 50.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.