Multiple sequence alignment - TraesCS3B01G406600

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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 TraesCS3B01G406600 chr3B 100.000 4253 0 0 1 4253 642216546 642212294 0.000000e+00 7854.0
1 TraesCS3B01G406600 chr3B 80.946 2813 433 53 939 3709 690430427 690433178 0.000000e+00 2130.0
2 TraesCS3B01G406600 chr3B 81.557 2364 403 22 932 3280 690446835 690449180 0.000000e+00 1919.0
3 TraesCS3B01G406600 chr3B 81.567 2284 382 32 993 3257 689352092 689349829 0.000000e+00 1849.0
4 TraesCS3B01G406600 chr3B 80.316 2403 390 54 1248 3612 689007195 689004838 0.000000e+00 1740.0
5 TraesCS3B01G406600 chr3B 79.613 2271 439 17 995 3257 690459883 690462137 0.000000e+00 1607.0
6 TraesCS3B01G406600 chr3B 85.536 560 61 17 3707 4253 685399621 685399069 6.170000e-158 568.0
7 TraesCS3B01G406600 chr3B 85.455 550 62 14 3707 4248 96829668 96830207 1.340000e-154 556.0
8 TraesCS3B01G406600 chr3B 97.297 37 1 0 783 819 690446665 690446701 3.550000e-06 63.9
9 TraesCS3B01G406600 chr3D 96.611 3718 82 18 1 3686 523333575 523337280 0.000000e+00 6128.0
10 TraesCS3B01G406600 chr3D 81.546 2639 415 40 907 3507 523407773 523410377 0.000000e+00 2109.0
11 TraesCS3B01G406600 chr3D 80.508 2714 433 63 936 3602 523555261 523557925 0.000000e+00 1993.0
12 TraesCS3B01G406600 chr3D 79.740 2157 407 28 1092 3232 523569675 523571817 0.000000e+00 1535.0
13 TraesCS3B01G406600 chr3D 80.144 1662 294 27 907 2551 523560073 523561715 0.000000e+00 1208.0
14 TraesCS3B01G406600 chr3D 87.245 196 18 3 3490 3679 523416204 523416398 2.580000e-52 217.0
15 TraesCS3B01G406600 chr3D 80.625 160 31 0 2254 2413 523598149 523598308 1.610000e-24 124.0
16 TraesCS3B01G406600 chr3D 94.231 52 1 2 773 822 523555060 523555111 1.270000e-10 78.7
17 TraesCS3B01G406600 chr3D 97.222 36 1 0 2311 2346 523569149 523569184 1.280000e-05 62.1
18 TraesCS3B01G406600 chr3A 82.340 2752 408 46 991 3697 658303556 658306274 0.000000e+00 2318.0
19 TraesCS3B01G406600 chr3A 80.373 2736 446 56 993 3679 658289047 658291740 0.000000e+00 1993.0
20 TraesCS3B01G406600 chr3A 79.075 2227 415 43 1084 3281 36071238 36069034 0.000000e+00 1483.0
21 TraesCS3B01G406600 chr3A 96.875 96 2 1 3614 3709 658247957 658248051 4.400000e-35 159.0
22 TraesCS3B01G406600 chrUn 80.552 2391 396 49 907 3258 330560985 330563345 0.000000e+00 1775.0
23 TraesCS3B01G406600 chrUn 81.499 2162 314 44 1486 3604 342677770 342679888 0.000000e+00 1698.0
24 TraesCS3B01G406600 chrUn 82.797 1180 141 27 2453 3604 405666925 405668070 0.000000e+00 998.0
25 TraesCS3B01G406600 chrUn 79.737 533 84 16 930 1448 454390270 454389748 8.690000e-97 364.0
26 TraesCS3B01G406600 chrUn 86.585 328 18 8 3268 3579 353196073 353196390 5.270000e-89 339.0
27 TraesCS3B01G406600 chrUn 93.191 235 8 3 3346 3579 471389946 471389719 5.270000e-89 339.0
28 TraesCS3B01G406600 chrUn 96.875 96 2 1 3614 3709 353196887 353196981 4.400000e-35 159.0
29 TraesCS3B01G406600 chrUn 96.104 77 2 1 1 77 425345912 425345837 1.610000e-24 124.0
30 TraesCS3B01G406600 chr7D 86.182 550 57 15 3715 4253 265266679 265266138 1.030000e-160 577.0
31 TraesCS3B01G406600 chr7D 96.104 77 2 1 1 77 231576386 231576311 1.610000e-24 124.0
32 TraesCS3B01G406600 chr1D 86.000 550 59 13 3714 4252 127840438 127839896 1.330000e-159 573.0
33 TraesCS3B01G406600 chr1D 96.104 77 2 1 1 77 254439270 254439345 1.610000e-24 124.0
34 TraesCS3B01G406600 chr1D 96.104 77 2 1 1 77 491424697 491424622 1.610000e-24 124.0
35 TraesCS3B01G406600 chr5B 85.870 552 58 14 3707 4248 398439971 398440512 1.720000e-158 569.0
36 TraesCS3B01G406600 chr2D 85.688 552 57 19 3714 4253 21013351 21013892 2.870000e-156 562.0
37 TraesCS3B01G406600 chr7A 85.952 541 54 17 3718 4248 100549325 100549853 3.710000e-155 558.0
38 TraesCS3B01G406600 chr7A 85.455 550 62 15 3707 4248 724362360 724362899 1.340000e-154 556.0
39 TraesCS3B01G406600 chr6B 85.635 543 64 11 3714 4248 276669948 276669412 3.710000e-155 558.0
40 TraesCS3B01G406600 chr5D 96.104 77 2 1 1 77 6172697 6172622 1.610000e-24 124.0
41 TraesCS3B01G406600 chr5D 96.104 77 2 1 1 77 6271766 6271691 1.610000e-24 124.0
42 TraesCS3B01G406600 chr5D 96.104 77 2 1 1 77 512413482 512413557 1.610000e-24 124.0
43 TraesCS3B01G406600 chr4D 96.104 77 2 1 1 77 19872745 19872820 1.610000e-24 124.0


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 TraesCS3B01G406600 chr3B 642212294 642216546 4252 True 7854.000000 7854 100.000 1 4253 1 chr3B.!!$R1 4252
1 TraesCS3B01G406600 chr3B 690430427 690433178 2751 False 2130.000000 2130 80.946 939 3709 1 chr3B.!!$F2 2770
2 TraesCS3B01G406600 chr3B 689349829 689352092 2263 True 1849.000000 1849 81.567 993 3257 1 chr3B.!!$R4 2264
3 TraesCS3B01G406600 chr3B 689004838 689007195 2357 True 1740.000000 1740 80.316 1248 3612 1 chr3B.!!$R3 2364
4 TraesCS3B01G406600 chr3B 690459883 690462137 2254 False 1607.000000 1607 79.613 995 3257 1 chr3B.!!$F3 2262
5 TraesCS3B01G406600 chr3B 690446665 690449180 2515 False 991.450000 1919 89.427 783 3280 2 chr3B.!!$F4 2497
6 TraesCS3B01G406600 chr3B 685399069 685399621 552 True 568.000000 568 85.536 3707 4253 1 chr3B.!!$R2 546
7 TraesCS3B01G406600 chr3B 96829668 96830207 539 False 556.000000 556 85.455 3707 4248 1 chr3B.!!$F1 541
8 TraesCS3B01G406600 chr3D 523333575 523337280 3705 False 6128.000000 6128 96.611 1 3686 1 chr3D.!!$F1 3685
9 TraesCS3B01G406600 chr3D 523407773 523410377 2604 False 2109.000000 2109 81.546 907 3507 1 chr3D.!!$F2 2600
10 TraesCS3B01G406600 chr3D 523555060 523561715 6655 False 1093.233333 1993 84.961 773 3602 3 chr3D.!!$F5 2829
11 TraesCS3B01G406600 chr3D 523569149 523571817 2668 False 798.550000 1535 88.481 1092 3232 2 chr3D.!!$F6 2140
12 TraesCS3B01G406600 chr3A 658303556 658306274 2718 False 2318.000000 2318 82.340 991 3697 1 chr3A.!!$F3 2706
13 TraesCS3B01G406600 chr3A 658289047 658291740 2693 False 1993.000000 1993 80.373 993 3679 1 chr3A.!!$F2 2686
14 TraesCS3B01G406600 chr3A 36069034 36071238 2204 True 1483.000000 1483 79.075 1084 3281 1 chr3A.!!$R1 2197
15 TraesCS3B01G406600 chrUn 330560985 330563345 2360 False 1775.000000 1775 80.552 907 3258 1 chrUn.!!$F1 2351
16 TraesCS3B01G406600 chrUn 342677770 342679888 2118 False 1698.000000 1698 81.499 1486 3604 1 chrUn.!!$F2 2118
17 TraesCS3B01G406600 chrUn 405666925 405668070 1145 False 998.000000 998 82.797 2453 3604 1 chrUn.!!$F3 1151
18 TraesCS3B01G406600 chrUn 454389748 454390270 522 True 364.000000 364 79.737 930 1448 1 chrUn.!!$R2 518
19 TraesCS3B01G406600 chrUn 353196073 353196981 908 False 249.000000 339 91.730 3268 3709 2 chrUn.!!$F4 441
20 TraesCS3B01G406600 chr7D 265266138 265266679 541 True 577.000000 577 86.182 3715 4253 1 chr7D.!!$R2 538
21 TraesCS3B01G406600 chr1D 127839896 127840438 542 True 573.000000 573 86.000 3714 4252 1 chr1D.!!$R1 538
22 TraesCS3B01G406600 chr5B 398439971 398440512 541 False 569.000000 569 85.870 3707 4248 1 chr5B.!!$F1 541
23 TraesCS3B01G406600 chr2D 21013351 21013892 541 False 562.000000 562 85.688 3714 4253 1 chr2D.!!$F1 539
24 TraesCS3B01G406600 chr7A 100549325 100549853 528 False 558.000000 558 85.952 3718 4248 1 chr7A.!!$F1 530
25 TraesCS3B01G406600 chr7A 724362360 724362899 539 False 556.000000 556 85.455 3707 4248 1 chr7A.!!$F2 541
26 TraesCS3B01G406600 chr6B 276669412 276669948 536 True 558.000000 558 85.635 3714 4248 1 chr6B.!!$R1 534

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
979 1043 0.533755 ACATATCCTCCGCAGCAAGC 60.534 55.0 0.00 0.00 40.87 4.01 F
1536 1620 1.015109 TGGACGAGCTCGATCTGTAC 58.985 55.0 40.58 20.36 43.02 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 2508 3.807622 TGTTGGATGACAGACGAAGAAAC 59.192 43.478 0.00 0.00 0.00 2.78 R
3368 3522 0.874175 GGTTTCAGCGCCACAAAACC 60.874 55.000 20.59 20.59 42.61 3.27 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
149 150 2.026262 TGCTTTCTTCCGGGCTTAGATT 60.026 45.455 0.00 0.00 0.00 2.40
545 546 4.466370 TCACTATTAGAGTTGACACCCTGG 59.534 45.833 0.00 0.00 35.64 4.45
553 554 8.612486 TTAGAGTTGACACCCTGGTAATTATA 57.388 34.615 0.00 0.00 0.00 0.98
558 559 7.559897 AGTTGACACCCTGGTAATTATATTTGG 59.440 37.037 0.00 0.00 0.00 3.28
683 686 2.359900 GCAGGACCAAGGTTCTATGTG 58.640 52.381 0.00 0.00 30.97 3.21
707 710 3.118775 TCAGCATTGGTAGCGTATTGTCT 60.119 43.478 0.00 0.00 37.01 3.41
708 711 4.098807 TCAGCATTGGTAGCGTATTGTCTA 59.901 41.667 0.00 0.00 37.01 2.59
716 719 6.636705 TGGTAGCGTATTGTCTATTTGTCTT 58.363 36.000 0.00 0.00 0.00 3.01
726 729 7.977789 TTGTCTATTTGTCTTCAGCATGTTA 57.022 32.000 0.00 0.00 37.40 2.41
757 760 6.867519 ACAATATATCGGGTGATATGGTCA 57.132 37.500 7.80 0.00 45.32 4.02
762 765 4.602340 ATCGGGTGATATGGTCAAGTAC 57.398 45.455 0.00 0.00 38.90 2.73
763 766 3.638860 TCGGGTGATATGGTCAAGTACT 58.361 45.455 0.00 0.00 38.90 2.73
764 767 3.383505 TCGGGTGATATGGTCAAGTACTG 59.616 47.826 0.00 0.00 38.90 2.74
824 827 6.018994 GTGTCACCCTGATAACGACATATTTC 60.019 42.308 0.00 0.00 38.72 2.17
853 856 6.029431 TCTTATTATGGGCAGCCCTCTATAA 58.971 40.000 31.51 24.58 45.70 0.98
855 858 4.574674 TTATGGGCAGCCCTCTATAATG 57.425 45.455 31.51 0.00 45.70 1.90
856 859 1.067295 TGGGCAGCCCTCTATAATGG 58.933 55.000 31.51 0.00 45.70 3.16
878 891 6.660800 TGGACTACTAAGACTAGCATGTAGT 58.339 40.000 11.67 11.67 41.87 2.73
896 909 4.941263 TGTAGTGCTTGCCCTTAATGTAAG 59.059 41.667 0.00 0.49 35.56 2.34
979 1043 0.533755 ACATATCCTCCGCAGCAAGC 60.534 55.000 0.00 0.00 40.87 4.01
1227 1308 2.036098 TTGGCTGGGCACATCAGG 59.964 61.111 0.00 0.00 33.16 3.86
1535 1619 1.671328 CTTGGACGAGCTCGATCTGTA 59.329 52.381 40.58 18.94 43.02 2.74
1536 1620 1.015109 TGGACGAGCTCGATCTGTAC 58.985 55.000 40.58 20.36 43.02 2.90
1537 1621 1.301423 GGACGAGCTCGATCTGTACT 58.699 55.000 40.58 17.32 43.02 2.73
2249 2351 3.131223 CCATTCTCGAGGACATGTAGTGT 59.869 47.826 13.56 0.00 45.83 3.55
2304 2406 1.580059 TCATAGGAGCCTTCCCGTTT 58.420 50.000 0.00 0.00 45.24 3.60
2390 2492 5.991606 CGATACCATCTTGGATAAGCAAGAA 59.008 40.000 0.00 0.00 40.96 2.52
2406 2508 3.748568 GCAAGAACTTACCTGGACTCAAG 59.251 47.826 0.00 0.80 0.00 3.02
2424 2527 4.307432 TCAAGTTTCTTCGTCTGTCATCC 58.693 43.478 0.00 0.00 0.00 3.51
2685 2794 1.067776 GCCGGTATCGACTTATCTGGG 60.068 57.143 1.90 0.00 39.00 4.45
3138 3253 1.549203 ACTGGGGCATGTTCATGTTC 58.451 50.000 13.24 7.05 0.00 3.18
3171 3286 7.331026 AGACATGGAGATTTTCGTTCTATCAA 58.669 34.615 0.00 0.00 0.00 2.57
3364 3518 8.473796 GGACGTTTTGTTGTAATTTGATGTTAC 58.526 33.333 0.00 0.00 33.67 2.50
4038 4693 3.927854 TGGAAAATGTTGACCATGCATG 58.072 40.909 20.19 20.19 32.82 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
478 479 9.499479 CTGGTTGATATCTAATATGCTCTTTGT 57.501 33.333 3.98 0.00 0.00 2.83
535 536 5.830991 GCCAAATATAATTACCAGGGTGTCA 59.169 40.000 0.06 0.00 0.00 3.58
571 572 8.237267 AGAAGAGAAACATAGGCAAATAAAACG 58.763 33.333 0.00 0.00 0.00 3.60
634 637 1.311859 CAGCAGTTCAGGCTTCAACA 58.688 50.000 8.44 0.00 40.23 3.33
635 638 0.039708 GCAGCAGTTCAGGCTTCAAC 60.040 55.000 0.00 0.00 40.23 3.18
683 686 3.374058 ACAATACGCTACCAATGCTGAAC 59.626 43.478 0.00 0.00 0.00 3.18
708 711 8.969260 TGATATCTAACATGCTGAAGACAAAT 57.031 30.769 3.98 0.00 0.00 2.32
743 746 3.492656 CCAGTACTTGACCATATCACCCG 60.493 52.174 0.00 0.00 36.92 5.28
746 749 5.599999 ACTCCAGTACTTGACCATATCAC 57.400 43.478 0.00 0.00 36.92 3.06
757 760 9.113838 CAATATGCTTAATCAACTCCAGTACTT 57.886 33.333 0.00 0.00 0.00 2.24
824 827 5.904362 GGGCTGCCCATAATAAGAATAAG 57.096 43.478 32.46 0.00 44.65 1.73
853 856 7.229707 CACTACATGCTAGTCTTAGTAGTCCAT 59.770 40.741 0.00 0.00 39.87 3.41
855 858 6.961576 CACTACATGCTAGTCTTAGTAGTCC 58.038 44.000 0.00 0.00 39.87 3.85
878 891 3.085952 AGCTTACATTAAGGGCAAGCA 57.914 42.857 22.45 0.00 43.15 3.91
896 909 2.500098 TGGTCTGGTGGAGTATTGTAGC 59.500 50.000 0.00 0.00 0.00 3.58
979 1043 1.936547 GATGGCTTGGTAGAAGCTTCG 59.063 52.381 20.43 6.61 42.62 3.79
986 1057 2.239402 TGCTTCATGATGGCTTGGTAGA 59.761 45.455 17.89 0.00 0.00 2.59
1535 1619 3.709653 TGACCCTGTCAAAGTAACTGAGT 59.290 43.478 0.00 0.00 39.78 3.41
1536 1620 4.336889 TGACCCTGTCAAAGTAACTGAG 57.663 45.455 0.00 0.00 39.78 3.35
2249 2351 6.265649 GGCTAGGTGTAGATAGTTCAGATCAA 59.734 42.308 0.00 0.00 0.00 2.57
2304 2406 8.754991 TCAGGTTTTTACATTTCTTAAGACCA 57.245 30.769 4.18 0.00 0.00 4.02
2390 2492 5.612351 GAAGAAACTTGAGTCCAGGTAAGT 58.388 41.667 0.00 0.00 35.06 2.24
2406 2508 3.807622 TGTTGGATGACAGACGAAGAAAC 59.192 43.478 0.00 0.00 0.00 2.78
2424 2527 4.142902 GGTATGACACCTTCGAATGTGTTG 60.143 45.833 31.06 12.67 45.24 3.33
2685 2794 5.765182 TGGGATCTCTTGTGAAAGAAAGTTC 59.235 40.000 0.00 0.00 0.00 3.01
3138 3253 2.360949 ATCTCCATGTCTCGCTGCGG 62.361 60.000 23.03 12.92 0.00 5.69
3171 3286 2.428171 GGCTTGCATGTTGTCCACATAT 59.572 45.455 1.14 0.00 45.06 1.78
3364 3518 1.165907 TCAGCGCCACAAAACCTGAG 61.166 55.000 2.29 0.00 0.00 3.35
3368 3522 0.874175 GGTTTCAGCGCCACAAAACC 60.874 55.000 20.59 20.59 42.61 3.27
3587 4203 4.806640 CCATGTGTTGGGAGCTAAAAAT 57.193 40.909 0.00 0.00 42.33 1.82
3867 4515 0.107214 GGCCGACTGGATCCAATCAA 60.107 55.000 22.29 0.00 37.49 2.57
3906 4554 2.281761 CAGCAGTGGGCCGACTTT 60.282 61.111 19.00 6.77 46.50 2.66
3907 4555 4.335647 CCAGCAGTGGGCCGACTT 62.336 66.667 19.00 1.30 46.50 3.01
3928 4576 1.610886 GGAAGTAGACTGGGTGCCAAC 60.611 57.143 0.00 0.00 30.80 3.77
4012 4660 5.931146 TGCATGGTCAACATTTTCCAAATAC 59.069 36.000 0.00 0.00 37.84 1.89
4013 4661 6.106648 TGCATGGTCAACATTTTCCAAATA 57.893 33.333 0.00 0.00 37.84 1.40
4014 4662 4.970711 TGCATGGTCAACATTTTCCAAAT 58.029 34.783 0.00 0.00 37.84 2.32
4016 4664 4.202336 ACATGCATGGTCAACATTTTCCAA 60.202 37.500 29.41 0.00 37.84 3.53
4018 4666 3.929094 ACATGCATGGTCAACATTTTCC 58.071 40.909 29.41 0.00 37.84 3.13
4019 4667 7.418840 TTTTACATGCATGGTCAACATTTTC 57.581 32.000 29.41 0.00 37.84 2.29


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

AutoCloner maintained by Alex Coulton.