Multiple sequence alignment - TraesCS3D01G545800

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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 TraesCS3D01G545800 chr3D 100.000 3360 0 0 1 3360 615476438 615473079 0.000000e+00 6205.0
1 TraesCS3D01G545800 chr3D 85.415 1577 173 21 620 2175 614477672 614476132 0.000000e+00 1585.0
2 TraesCS3D01G545800 chr3D 77.682 466 95 9 2899 3358 48792954 48793416 3.300000e-70 276.0
3 TraesCS3D01G545800 chr3B 95.349 1849 62 7 620 2460 825869968 825868136 0.000000e+00 2916.0
4 TraesCS3D01G545800 chr3B 91.798 1719 131 4 804 2519 788514541 788516252 0.000000e+00 2385.0
5 TraesCS3D01G545800 chr3B 90.161 1555 111 5 778 2321 825887608 825886085 0.000000e+00 1986.0
6 TraesCS3D01G545800 chr3B 86.413 1759 198 26 620 2347 779689457 779687709 0.000000e+00 1886.0
7 TraesCS3D01G545800 chr3B 85.544 1757 215 26 617 2347 825538570 825540313 0.000000e+00 1801.0
8 TraesCS3D01G545800 chr3B 87.509 1369 149 10 965 2321 825859827 825858469 0.000000e+00 1561.0
9 TraesCS3D01G545800 chr3B 91.156 848 75 0 2513 3360 788551385 788552232 0.000000e+00 1151.0
10 TraesCS3D01G545800 chr3B 89.983 599 56 3 2265 2863 825866376 825865782 0.000000e+00 771.0
11 TraesCS3D01G545800 chr3B 86.550 513 60 4 2857 3360 825865746 825865234 1.050000e-154 556.0
12 TraesCS3D01G545800 chr3B 93.373 166 11 0 620 785 825887967 825887802 2.590000e-61 246.0
13 TraesCS3D01G545800 chr3B 82.407 108 15 4 2505 2609 534164813 534164919 1.280000e-14 91.6
14 TraesCS3D01G545800 chrUn 92.979 1467 102 1 1895 3360 37097985 37099451 0.000000e+00 2137.0
15 TraesCS3D01G545800 chrUn 85.821 1742 212 22 631 2347 209288803 209287072 0.000000e+00 1816.0
16 TraesCS3D01G545800 chrUn 87.004 1362 155 11 971 2321 37102673 37104023 0.000000e+00 1515.0
17 TraesCS3D01G545800 chrUn 85.366 82 10 2 2539 2619 226924953 226924873 2.150000e-12 84.2
18 TraesCS3D01G545800 chr7B 85.821 1742 212 22 631 2347 642248936 642247205 0.000000e+00 1816.0
19 TraesCS3D01G545800 chr3A 95.558 1013 38 2 1760 2766 749866816 749867827 0.000000e+00 1615.0
20 TraesCS3D01G545800 chr3A 87.362 633 42 23 7 631 685395464 685396066 0.000000e+00 691.0
21 TraesCS3D01G545800 chr3A 89.161 286 17 6 617 895 749866539 749866817 8.930000e-91 344.0
22 TraesCS3D01G545800 chr2A 94.222 623 28 8 1 618 587020804 587021423 0.000000e+00 944.0
23 TraesCS3D01G545800 chr2A 79.323 266 40 10 2528 2790 114824423 114824676 4.460000e-39 172.0
24 TraesCS3D01G545800 chr2A 81.295 139 23 2 2658 2795 11045864 11046000 3.540000e-20 110.0
25 TraesCS3D01G545800 chr5A 87.742 620 42 21 7 620 65978851 65978260 0.000000e+00 693.0
26 TraesCS3D01G545800 chr1D 85.991 464 56 8 171 630 442153423 442153881 3.900000e-134 488.0
27 TraesCS3D01G545800 chr1D 84.615 455 58 12 173 620 226471429 226470980 3.080000e-120 442.0
28 TraesCS3D01G545800 chr2D 82.055 613 67 27 52 627 30739882 30739276 1.810000e-132 483.0
29 TraesCS3D01G545800 chr2B 81.695 590 81 23 52 620 786239327 786239910 1.830000e-127 466.0
30 TraesCS3D01G545800 chr2B 82.414 580 57 29 67 609 775835243 775835814 6.570000e-127 464.0
31 TraesCS3D01G545800 chr2B 79.009 424 80 8 2939 3356 96047780 96048200 7.100000e-72 281.0
32 TraesCS3D01G545800 chr2B 76.953 512 100 16 2861 3358 95939973 95940480 3.300000e-70 276.0
33 TraesCS3D01G545800 chr7D 84.816 461 56 13 173 623 41696891 41696435 5.110000e-123 451.0
34 TraesCS3D01G545800 chr7D 77.725 211 36 6 2660 2860 158962226 158962017 5.890000e-23 119.0
35 TraesCS3D01G545800 chr7D 77.778 144 28 4 2485 2626 57701600 57701459 5.970000e-13 86.1
36 TraesCS3D01G545800 chr5B 75.785 669 138 16 2711 3358 462560828 462561493 1.950000e-82 316.0
37 TraesCS3D01G545800 chr5D 79.587 436 83 6 2927 3358 462596506 462596073 1.170000e-79 307.0
38 TraesCS3D01G545800 chr6D 77.826 460 87 12 2905 3358 394835536 394835086 1.540000e-68 270.0
39 TraesCS3D01G545800 chr4A 77.872 235 40 11 2494 2725 681793047 681793272 5.850000e-28 135.0
40 TraesCS3D01G545800 chr4A 75.627 279 56 6 2463 2739 686533731 686533463 9.790000e-26 128.0
41 TraesCS3D01G545800 chr6B 74.717 265 52 10 2506 2767 200512287 200512539 1.650000e-18 104.0
42 TraesCS3D01G545800 chr7A 84.706 85 11 2 2526 2609 41808972 41809055 2.150000e-12 84.2


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 TraesCS3D01G545800 chr3D 615473079 615476438 3359 True 6205.000000 6205 100.000000 1 3360 1 chr3D.!!$R2 3359
1 TraesCS3D01G545800 chr3D 614476132 614477672 1540 True 1585.000000 1585 85.415000 620 2175 1 chr3D.!!$R1 1555
2 TraesCS3D01G545800 chr3B 788514541 788516252 1711 False 2385.000000 2385 91.798000 804 2519 1 chr3B.!!$F2 1715
3 TraesCS3D01G545800 chr3B 779687709 779689457 1748 True 1886.000000 1886 86.413000 620 2347 1 chr3B.!!$R1 1727
4 TraesCS3D01G545800 chr3B 825538570 825540313 1743 False 1801.000000 1801 85.544000 617 2347 1 chr3B.!!$F4 1730
5 TraesCS3D01G545800 chr3B 825858469 825859827 1358 True 1561.000000 1561 87.509000 965 2321 1 chr3B.!!$R2 1356
6 TraesCS3D01G545800 chr3B 825865234 825869968 4734 True 1414.333333 2916 90.627333 620 3360 3 chr3B.!!$R3 2740
7 TraesCS3D01G545800 chr3B 788551385 788552232 847 False 1151.000000 1151 91.156000 2513 3360 1 chr3B.!!$F3 847
8 TraesCS3D01G545800 chr3B 825886085 825887967 1882 True 1116.000000 1986 91.767000 620 2321 2 chr3B.!!$R4 1701
9 TraesCS3D01G545800 chrUn 37097985 37104023 6038 False 1826.000000 2137 89.991500 971 3360 2 chrUn.!!$F1 2389
10 TraesCS3D01G545800 chrUn 209287072 209288803 1731 True 1816.000000 1816 85.821000 631 2347 1 chrUn.!!$R1 1716
11 TraesCS3D01G545800 chr7B 642247205 642248936 1731 True 1816.000000 1816 85.821000 631 2347 1 chr7B.!!$R1 1716
12 TraesCS3D01G545800 chr3A 749866539 749867827 1288 False 979.500000 1615 92.359500 617 2766 2 chr3A.!!$F2 2149
13 TraesCS3D01G545800 chr3A 685395464 685396066 602 False 691.000000 691 87.362000 7 631 1 chr3A.!!$F1 624
14 TraesCS3D01G545800 chr2A 587020804 587021423 619 False 944.000000 944 94.222000 1 618 1 chr2A.!!$F3 617
15 TraesCS3D01G545800 chr5A 65978260 65978851 591 True 693.000000 693 87.742000 7 620 1 chr5A.!!$R1 613
16 TraesCS3D01G545800 chr2D 30739276 30739882 606 True 483.000000 483 82.055000 52 627 1 chr2D.!!$R1 575
17 TraesCS3D01G545800 chr2B 786239327 786239910 583 False 466.000000 466 81.695000 52 620 1 chr2B.!!$F4 568
18 TraesCS3D01G545800 chr2B 775835243 775835814 571 False 464.000000 464 82.414000 67 609 1 chr2B.!!$F3 542
19 TraesCS3D01G545800 chr2B 95939973 95940480 507 False 276.000000 276 76.953000 2861 3358 1 chr2B.!!$F1 497
20 TraesCS3D01G545800 chr5B 462560828 462561493 665 False 316.000000 316 75.785000 2711 3358 1 chr5B.!!$F1 647

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
663 735 4.109766 CGTCGAATAATGGACTAGCAACA 58.89 43.478 0.0 0.0 32.61 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2472 8169 0.178964 CCCACCCACACATTTGAGGT 60.179 55.0 0.0 0.0 34.46 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
279 332 6.750039 TGTTCGTGAACTTCAAAAGAAATTCC 59.250 34.615 13.40 0.00 41.67 3.01
663 735 4.109766 CGTCGAATAATGGACTAGCAACA 58.890 43.478 0.00 0.00 32.61 3.33
1080 4801 0.175760 GCCTGGTGCTGATCGTTCTA 59.824 55.000 0.00 0.00 36.87 2.10
1641 5383 3.209812 CTCGATGAGGCGTCCGGA 61.210 66.667 0.00 0.00 0.00 5.14
2298 6047 3.002791 TGAGCTATCTTTCCAAACAGCG 58.997 45.455 0.00 0.00 34.26 5.18
2710 8409 2.357517 CGCTCCTCGTGCCAAACT 60.358 61.111 0.00 0.00 0.00 2.66
2725 8424 3.744660 CCAAACTCTAGCCACTTCACTT 58.255 45.455 0.00 0.00 0.00 3.16
2756 8455 2.033602 CACCCAAACTCCCGTCCC 59.966 66.667 0.00 0.00 0.00 4.46
2943 8693 2.796557 CTAGATCATCGTGGCCCTCTA 58.203 52.381 0.00 0.00 0.00 2.43
2972 8722 5.600069 GCCTTCCAATCTATCTTTTCCCATT 59.400 40.000 0.00 0.00 0.00 3.16
2977 8727 6.062095 CCAATCTATCTTTTCCCATTACCGT 58.938 40.000 0.00 0.00 0.00 4.83
2999 8749 1.825474 CCGCCGGAGTATGAATCCTAT 59.175 52.381 5.05 0.00 34.45 2.57
3144 8897 1.349688 TCCGCCCACATTGTAAGAAGT 59.650 47.619 0.00 0.00 0.00 3.01
3145 8898 2.159382 CCGCCCACATTGTAAGAAGTT 58.841 47.619 0.00 0.00 0.00 2.66
3184 8937 1.894756 CCCTCGCCCGAGAGTAGAG 60.895 68.421 18.41 1.39 44.53 2.43
3245 8999 1.292242 AGAAGGAGGGCTATGACAGGA 59.708 52.381 0.00 0.00 0.00 3.86
3263 9017 2.185350 CGGACAGCTCTGGCGATT 59.815 61.111 1.66 0.00 40.25 3.34
3328 9082 0.250338 GCAAGAAGGACGTCAAGGGT 60.250 55.000 18.91 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
663 735 7.033185 GTGTGTTTTTACCATTGTTCTCAACT 58.967 34.615 0.00 0.00 36.33 3.16
1080 4801 1.947678 GCAGCACTGGAGCATAACACT 60.948 52.381 0.00 0.00 36.85 3.55
1308 5040 3.068064 TCGATGAGTGCCTCCGCA 61.068 61.111 0.50 0.00 44.78 5.69
1495 5236 0.814010 CCGTAGAAGGCCCCGAAATG 60.814 60.000 0.00 0.00 0.00 2.32
2298 6047 1.736681 GATCAGAGTTTGCTGCAGTCC 59.263 52.381 16.64 0.00 35.86 3.85
2472 8169 0.178964 CCCACCCACACATTTGAGGT 60.179 55.000 0.00 0.00 34.46 3.85
2506 8204 1.515081 GTCGGATGTTTTTGACCGGA 58.485 50.000 9.46 0.00 44.57 5.14
2548 8246 1.662446 GTCGACTCGGGCGTTTGAA 60.662 57.895 8.70 0.00 0.00 2.69
2710 8409 2.563179 GGAGTGAAGTGAAGTGGCTAGA 59.437 50.000 0.00 0.00 0.00 2.43
2725 8424 1.841556 GGGTGGTGGAGTGGAGTGA 60.842 63.158 0.00 0.00 0.00 3.41
2756 8455 1.384525 AGAGAAGGTCGGAGATCACG 58.615 55.000 0.00 0.00 42.44 4.35
2863 8604 2.512705 GGATAGATCCTACCGTCGGTT 58.487 52.381 24.36 3.64 43.73 4.44
2943 8693 3.359110 AGATAGATTGGAAGGCTCCCT 57.641 47.619 0.00 0.00 41.64 4.20
2977 8727 0.391597 GGATTCATACTCCGGCGGAA 59.608 55.000 30.59 17.11 0.00 4.30
3031 8781 2.835431 CCTCAGCGACCCCGATCT 60.835 66.667 0.00 0.00 38.22 2.75
3144 8897 1.165907 CGCTTGTTCCTCCACTGCAA 61.166 55.000 0.00 0.00 0.00 4.08
3145 8898 1.597854 CGCTTGTTCCTCCACTGCA 60.598 57.895 0.00 0.00 0.00 4.41
3184 8937 4.760047 ATGCCACGGACCGCAGAC 62.760 66.667 15.39 0.00 38.64 3.51
3245 8999 1.320344 TAATCGCCAGAGCTGTCCGT 61.320 55.000 0.00 0.00 36.60 4.69
3274 9028 5.229921 TGAAAACATAGTGCGGATTAAGC 57.770 39.130 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.