Multiple sequence alignment - TraesCS2D01G009600

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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 TraesCS2D01G009600 chr2D 100.000 7084 0 0 1 7084 5157690 5164773 0.000000e+00 13082.0
1 TraesCS2D01G009600 chr2D 94.800 750 32 4 1 750 47657272 47656530 0.000000e+00 1162.0
2 TraesCS2D01G009600 chr2D 81.022 274 44 8 6582 6854 610356612 610356878 2.000000e-50 211.0
3 TraesCS2D01G009600 chr2B 95.602 3479 108 20 1690 5133 6315550 6312082 0.000000e+00 5535.0
4 TraesCS2D01G009600 chr2B 90.579 1210 61 23 5313 6499 6311824 6310645 0.000000e+00 1554.0
5 TraesCS2D01G009600 chr2B 91.592 559 32 6 868 1415 6316390 6315836 0.000000e+00 758.0
6 TraesCS2D01G009600 chr2B 92.149 242 17 2 1413 1653 6315791 6315551 2.450000e-89 340.0
7 TraesCS2D01G009600 chr2B 92.593 189 14 0 5129 5317 6312044 6311856 9.050000e-69 272.0
8 TraesCS2D01G009600 chr2B 88.991 109 12 0 3569 3677 703596917 703596809 1.240000e-27 135.0
9 TraesCS2D01G009600 chr2A 93.414 3538 139 46 1834 5317 3443148 3446645 0.000000e+00 5156.0
10 TraesCS2D01G009600 chr2A 92.327 1199 70 14 5313 6499 3446677 3447865 0.000000e+00 1685.0
11 TraesCS2D01G009600 chr2A 85.213 940 85 34 822 1723 3442225 3443148 0.000000e+00 917.0
12 TraesCS2D01G009600 chr2A 87.909 397 45 1 4152 4545 726019870 726020266 1.390000e-126 464.0
13 TraesCS2D01G009600 chr2A 87.817 394 45 1 4155 4545 695304486 695304093 6.480000e-125 459.0
14 TraesCS2D01G009600 chr2A 85.788 387 47 5 4193 4576 214686199 214686580 3.080000e-108 403.0
15 TraesCS2D01G009600 chr2A 93.991 233 9 4 6854 7084 3448240 3448469 1.460000e-91 348.0
16 TraesCS2D01G009600 chr2A 90.377 239 14 4 6565 6795 3447978 3448215 8.930000e-79 305.0
17 TraesCS2D01G009600 chr2A 91.743 109 9 0 3569 3677 214686085 214686193 1.230000e-32 152.0
18 TraesCS2D01G009600 chr5A 95.067 750 30 6 1 750 612874907 612874165 0.000000e+00 1173.0
19 TraesCS2D01G009600 chr5A 94.667 750 29 7 1 750 470149086 470148348 0.000000e+00 1153.0
20 TraesCS2D01G009600 chr5A 83.594 128 15 5 6788 6909 245502281 245502154 1.610000e-21 115.0
21 TraesCS2D01G009600 chr6A 91.892 518 29 9 1 512 364214359 364213849 0.000000e+00 712.0
22 TraesCS2D01G009600 chr1A 87.597 387 42 3 4193 4576 523145217 523144834 1.810000e-120 444.0
23 TraesCS2D01G009600 chr1A 86.528 386 46 3 4194 4576 524983514 524983896 3.060000e-113 420.0
24 TraesCS2D01G009600 chr1A 88.983 118 13 0 3569 3686 523145332 523145215 5.730000e-31 147.0
25 TraesCS2D01G009600 chr1A 90.826 109 10 0 3569 3677 524983399 524983507 5.730000e-31 147.0
26 TraesCS2D01G009600 chr3A 85.316 395 45 4 4155 4546 655522964 655522580 5.150000e-106 396.0
27 TraesCS2D01G009600 chr3A 85.795 176 23 2 1 176 463820655 463820828 1.210000e-42 185.0
28 TraesCS2D01G009600 chr3A 91.743 109 9 0 3569 3677 588140314 588140206 1.230000e-32 152.0
29 TraesCS2D01G009600 chr1B 95.798 238 10 0 514 751 142832367 142832130 1.110000e-102 385.0
30 TraesCS2D01G009600 chr1B 83.051 177 27 3 1 176 595494120 595493946 2.650000e-34 158.0
31 TraesCS2D01G009600 chr1D 94.958 238 12 0 514 751 375796208 375796445 2.410000e-99 374.0
32 TraesCS2D01G009600 chr1D 83.979 387 45 3 4193 4576 480316695 480316323 8.740000e-94 355.0
33 TraesCS2D01G009600 chr1D 80.808 99 11 7 6991 7084 62146182 62146087 3.550000e-08 71.3
34 TraesCS2D01G009600 chr5D 94.239 243 14 0 514 756 2601513 2601271 8.680000e-99 372.0
35 TraesCS2D01G009600 chr7D 94.515 237 13 0 514 750 511622597 511622361 4.040000e-97 366.0
36 TraesCS2D01G009600 chr5B 94.515 237 13 0 514 750 702399173 702399409 4.040000e-97 366.0
37 TraesCS2D01G009600 chr5B 92.095 253 18 1 514 764 491300792 491300540 8.740000e-94 355.0
38 TraesCS2D01G009600 chr5B 83.862 347 35 18 167 512 290582781 290583107 1.920000e-80 311.0
39 TraesCS2D01G009600 chr5B 82.609 184 28 4 4 186 352314510 352314330 7.360000e-35 159.0
40 TraesCS2D01G009600 chr7B 85.014 347 30 19 167 512 40957365 40957690 4.100000e-87 333.0
41 TraesCS2D01G009600 chr7B 83.430 344 36 18 167 509 558923179 558923502 4.150000e-77 300.0
42 TraesCS2D01G009600 chr7B 82.486 177 28 3 1 176 699541087 699540913 1.230000e-32 152.0
43 TraesCS2D01G009600 chr7B 74.550 389 53 27 6564 6921 19536723 19537096 2.070000e-25 128.0
44 TraesCS2D01G009600 chr3B 84.104 346 33 19 167 511 644001728 644001404 1.480000e-81 315.0
45 TraesCS2D01G009600 chr3B 82.486 177 28 3 1 176 147678303 147678477 1.230000e-32 152.0
46 TraesCS2D01G009600 chr3B 74.486 243 37 13 6690 6910 658426740 658426979 1.640000e-11 82.4
47 TraesCS2D01G009600 chr4A 91.262 206 11 5 186 385 359183586 359183790 2.520000e-69 274.0
48 TraesCS2D01G009600 chr3D 78.049 328 51 17 6598 6908 134828881 134829204 3.370000e-43 187.0
49 TraesCS2D01G009600 chr3D 94.595 37 2 0 7048 7084 74330996 74330960 2.760000e-04 58.4
50 TraesCS2D01G009600 chr4D 91.743 109 9 0 3569 3677 158362573 158362465 1.230000e-32 152.0
51 TraesCS2D01G009600 chr6D 82.828 99 12 4 6788 6884 276128394 276128299 4.550000e-12 84.2
52 TraesCS2D01G009600 chrUn 86.765 68 8 1 6788 6854 354652576 354652643 2.740000e-09 75.0


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 TraesCS2D01G009600 chr2D 5157690 5164773 7083 False 13082.0 13082 100.0000 1 7084 1 chr2D.!!$F1 7083
1 TraesCS2D01G009600 chr2D 47656530 47657272 742 True 1162.0 1162 94.8000 1 750 1 chr2D.!!$R1 749
2 TraesCS2D01G009600 chr2B 6310645 6316390 5745 True 1691.8 5535 92.5030 868 6499 5 chr2B.!!$R2 5631
3 TraesCS2D01G009600 chr2A 3442225 3448469 6244 False 1682.2 5156 91.0644 822 7084 5 chr2A.!!$F2 6262
4 TraesCS2D01G009600 chr5A 612874165 612874907 742 True 1173.0 1173 95.0670 1 750 1 chr5A.!!$R3 749
5 TraesCS2D01G009600 chr5A 470148348 470149086 738 True 1153.0 1153 94.6670 1 750 1 chr5A.!!$R2 749
6 TraesCS2D01G009600 chr6A 364213849 364214359 510 True 712.0 712 91.8920 1 512 1 chr6A.!!$R1 511


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
864 871 0.178938 TTTCCAGCATTGGCCCTTCA 60.179 50.0 0.0 0.0 44.63 3.02 F
1355 1372 0.179145 CCTGCGTGTAGTTACTCCGG 60.179 60.0 0.0 0.0 0.00 5.14 F
1390 1407 0.368907 CGGTCGTGCTTTATCGGTTG 59.631 55.0 0.0 0.0 0.00 3.77 F
1623 1692 0.600057 GAAAGAAGCAAGCCTGTGGG 59.400 55.0 0.0 0.0 0.00 4.61 F
2043 2124 0.827368 CAGCCTCTGAACTACCCCTC 59.173 60.0 0.0 0.0 32.44 4.30 F
3390 3509 0.684479 GGGGAGAACCTTTGGATGGC 60.684 60.0 0.0 0.0 40.03 4.40 F
4970 5107 1.241165 TTGCATGTCTTCTGCTGTGG 58.759 50.0 0.0 0.0 40.34 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2127 0.178998 GATGGGAGATGCAGGCATGT 60.179 55.000 12.12 7.66 36.70 3.21 R
2703 2820 0.392706 TCGTGCACTCTGTGTCCATT 59.607 50.000 16.19 0.00 35.75 3.16 R
3086 3204 2.224606 CGCCCTATGTTGCATCAGAAT 58.775 47.619 3.50 0.00 0.00 2.40 R
3390 3509 1.597854 TGCCCTTGCAACAGAGTCG 60.598 57.895 0.00 0.00 46.66 4.18 R
3703 3825 1.073284 GGTCAAGGGAGCAAGGTACAA 59.927 52.381 0.00 0.00 41.19 2.41 R
5097 5240 1.131126 CCATTTGGCAGCTACGAACAG 59.869 52.381 0.00 0.00 0.00 3.16 R
6876 7181 0.244450 CATGGTTCCATGTGCACCAC 59.756 55.000 20.05 3.13 43.44 4.16 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)



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AutoCloner maintained by Alex Coulton.