Multiple sequence alignment - TraesCS3D01G226900

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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 TraesCS3D01G226900 chr3D 100.000 3395 0 0 1 3395 308567409 308564015 0 6270
1 TraesCS3D01G226900 chr3D 96.578 906 31 0 1 906 308575809 308574904 0 1502
2 TraesCS3D01G226900 chr3D 92.936 906 61 3 3 907 36326528 36327431 0 1315
3 TraesCS3D01G226900 chr3D 92.944 907 58 5 1 906 311100398 311101299 0 1315
4 TraesCS3D01G226900 chrUn 97.359 1742 46 0 907 2648 86478499 86480240 0 2963
5 TraesCS3D01G226900 chrUn 97.131 1743 49 1 907 2648 186190970 186189228 0 2940
6 TraesCS3D01G226900 chrUn 97.754 757 17 0 2639 3395 86483966 86484722 0 1304
7 TraesCS3D01G226900 chrUn 97.754 757 17 0 2639 3395 405903080 405902324 0 1304
8 TraesCS3D01G226900 chrUn 97.503 761 15 1 2639 3395 186185501 186184741 0 1297
9 TraesCS3D01G226900 chrUn 97.490 757 19 0 2639 3395 221557999 221558755 0 1293
10 TraesCS3D01G226900 chrUn 97.358 757 20 0 2639 3395 270846081 270845325 0 1288
11 TraesCS3D01G226900 chr1A 97.303 1743 46 1 907 2648 112004462 112002720 0 2957
12 TraesCS3D01G226900 chr1A 97.754 757 17 0 2639 3395 111998994 111998238 0 1304
13 TraesCS3D01G226900 chr7D 97.246 1743 47 1 907 2648 579030178 579031920 0 2952
14 TraesCS3D01G226900 chr7D 93.839 909 51 5 1 907 438841303 438842208 0 1363
15 TraesCS3D01G226900 chr7D 93.370 905 57 3 3 906 511109226 511110128 0 1336
16 TraesCS3D01G226900 chr7D 97.754 757 17 0 2639 3395 579035647 579036403 0 1304
17 TraesCS3D01G226900 chr7B 97.245 1742 48 0 907 2648 743006509 743008250 0 2952
18 TraesCS3D01G226900 chr7A 97.187 1742 49 0 907 2648 60242589 60240848 0 2946
19 TraesCS3D01G226900 chr7A 97.074 1743 50 1 907 2648 60154890 60156632 0 2935
20 TraesCS3D01G226900 chr4B 96.900 1742 52 2 907 2648 209270863 209269124 0 2916
21 TraesCS3D01G226900 chr6D 96.670 1742 56 2 907 2648 283153675 283151936 0 2894
22 TraesCS3D01G226900 chr6D 94.260 906 51 1 1 906 232443339 232444243 0 1384
23 TraesCS3D01G226900 chr2D 93.275 907 59 2 1 906 81581684 81582589 0 1336
24 TraesCS3D01G226900 chr2D 92.731 908 64 2 1 907 81589943 81590849 0 1310
25 TraesCS3D01G226900 chr4D 93.069 909 58 4 1 907 282216675 282217580 0 1325
26 TraesCS3D01G226900 chr2A 97.490 757 19 0 2639 3395 605920428 605921184 0 1293
27 TraesCS3D01G226900 chr5B 97.226 757 21 0 2639 3395 130636079 130635323 0 1282


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 TraesCS3D01G226900 chr3D 308564015 308567409 3394 True 6270.0 6270 100.0000 1 3395 1 chr3D.!!$R1 3394
1 TraesCS3D01G226900 chr3D 308574904 308575809 905 True 1502.0 1502 96.5780 1 906 1 chr3D.!!$R2 905
2 TraesCS3D01G226900 chr3D 36326528 36327431 903 False 1315.0 1315 92.9360 3 907 1 chr3D.!!$F1 904
3 TraesCS3D01G226900 chr3D 311100398 311101299 901 False 1315.0 1315 92.9440 1 906 1 chr3D.!!$F2 905
4 TraesCS3D01G226900 chrUn 86478499 86484722 6223 False 2133.5 2963 97.5565 907 3395 2 chrUn.!!$F2 2488
5 TraesCS3D01G226900 chrUn 186184741 186190970 6229 True 2118.5 2940 97.3170 907 3395 2 chrUn.!!$R3 2488
6 TraesCS3D01G226900 chrUn 405902324 405903080 756 True 1304.0 1304 97.7540 2639 3395 1 chrUn.!!$R2 756
7 TraesCS3D01G226900 chrUn 221557999 221558755 756 False 1293.0 1293 97.4900 2639 3395 1 chrUn.!!$F1 756
8 TraesCS3D01G226900 chrUn 270845325 270846081 756 True 1288.0 1288 97.3580 2639 3395 1 chrUn.!!$R1 756
9 TraesCS3D01G226900 chr1A 111998238 112004462 6224 True 2130.5 2957 97.5285 907 3395 2 chr1A.!!$R1 2488
10 TraesCS3D01G226900 chr7D 579030178 579036403 6225 False 2128.0 2952 97.5000 907 3395 2 chr7D.!!$F3 2488
11 TraesCS3D01G226900 chr7D 438841303 438842208 905 False 1363.0 1363 93.8390 1 907 1 chr7D.!!$F1 906
12 TraesCS3D01G226900 chr7D 511109226 511110128 902 False 1336.0 1336 93.3700 3 906 1 chr7D.!!$F2 903
13 TraesCS3D01G226900 chr7B 743006509 743008250 1741 False 2952.0 2952 97.2450 907 2648 1 chr7B.!!$F1 1741
14 TraesCS3D01G226900 chr7A 60240848 60242589 1741 True 2946.0 2946 97.1870 907 2648 1 chr7A.!!$R1 1741
15 TraesCS3D01G226900 chr7A 60154890 60156632 1742 False 2935.0 2935 97.0740 907 2648 1 chr7A.!!$F1 1741
16 TraesCS3D01G226900 chr4B 209269124 209270863 1739 True 2916.0 2916 96.9000 907 2648 1 chr4B.!!$R1 1741
17 TraesCS3D01G226900 chr6D 283151936 283153675 1739 True 2894.0 2894 96.6700 907 2648 1 chr6D.!!$R1 1741
18 TraesCS3D01G226900 chr6D 232443339 232444243 904 False 1384.0 1384 94.2600 1 906 1 chr6D.!!$F1 905
19 TraesCS3D01G226900 chr2D 81581684 81582589 905 False 1336.0 1336 93.2750 1 906 1 chr2D.!!$F1 905
20 TraesCS3D01G226900 chr2D 81589943 81590849 906 False 1310.0 1310 92.7310 1 907 1 chr2D.!!$F2 906
21 TraesCS3D01G226900 chr4D 282216675 282217580 905 False 1325.0 1325 93.0690 1 907 1 chr4D.!!$F1 906
22 TraesCS3D01G226900 chr2A 605920428 605921184 756 False 1293.0 1293 97.4900 2639 3395 1 chr2A.!!$F1 756
23 TraesCS3D01G226900 chr5B 130635323 130636079 756 True 1282.0 1282 97.2260 2639 3395 1 chr5B.!!$R1 756

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
189 191 0.396811 AGTGCCAGATATAACCCGGC 59.603 55.0 0.00 4.57 43.28 6.13 F
586 592 1.100510 CTACTACTACGTGCAGGCCA 58.899 55.0 5.01 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 1810 2.193127 TGTATCGAACCTCCCCACATT 58.807 47.619 0.0 0.0 0.0 2.71 R
2486 2494 0.462759 GCCAACCTAATCTGCGAGCT 60.463 55.000 0.0 0.0 0.0 4.09 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
189 191 0.396811 AGTGCCAGATATAACCCGGC 59.603 55.000 0.00 4.57 43.28 6.13
294 297 3.260380 ACTCTCTTCTACATGCTGCAAGT 59.740 43.478 15.25 15.25 35.30 3.16
303 306 1.342174 CATGCTGCAAGTTGGAGGTTT 59.658 47.619 23.79 0.00 36.25 3.27
420 424 4.081420 CCCTGCATATGTAGTGTAGATCCC 60.081 50.000 18.08 0.00 31.92 3.85
422 426 5.247110 CCTGCATATGTAGTGTAGATCCCTT 59.753 44.000 18.08 0.00 31.92 3.95
427 431 7.472100 GCATATGTAGTGTAGATCCCTTCTTGT 60.472 40.741 4.29 0.00 35.79 3.16
455 459 3.587797 TTGGATGAGTACTCACGGTTC 57.412 47.619 27.41 19.62 43.11 3.62
511 517 1.438651 GTTGTCGCAACCAGATGCTA 58.561 50.000 10.43 0.00 44.21 3.49
524 530 2.433231 GATGCTAGAGCCCAGGAGCG 62.433 65.000 0.00 0.00 41.18 5.03
586 592 1.100510 CTACTACTACGTGCAGGCCA 58.899 55.000 5.01 0.00 0.00 5.36
650 656 1.869754 GCATGCGCCTCTTTCGATCTA 60.870 52.381 4.18 0.00 0.00 1.98
658 664 4.882427 CGCCTCTTTCGATCTATATCCCTA 59.118 45.833 0.00 0.00 0.00 3.53
835 842 6.365970 AGAGTTGTGTTGTGATATCTTCCT 57.634 37.500 3.98 0.00 0.00 3.36
844 851 3.381590 TGTGATATCTTCCTGTGAGTCCG 59.618 47.826 3.98 0.00 0.00 4.79
900 907 2.291801 TACGGTCAAATCGGGGGCA 61.292 57.895 0.00 0.00 0.00 5.36
956 963 1.507140 ATGGAATTAGCCTGACCCGA 58.493 50.000 0.00 0.00 0.00 5.14
975 982 2.742053 CGACGATCAAATTCTTGGTGGT 59.258 45.455 0.00 0.00 37.32 4.16
1017 1024 3.763097 TTAATGACGGCTCATGCTTTG 57.237 42.857 0.00 0.00 37.20 2.77
1264 1271 2.562738 TCTCGAGGAGCAGTTGATTCAA 59.437 45.455 13.56 0.00 0.00 2.69
1482 1489 7.424227 AACCGATCGAAACTTTAATACAACA 57.576 32.000 18.66 0.00 0.00 3.33
1509 1516 2.040043 CCTGCAGGAGGGGGAGAT 60.040 66.667 29.88 0.00 38.36 2.75
1687 1694 9.099454 GTATAGGTGTTCTTGGATTTCTAGTTG 57.901 37.037 0.00 0.00 0.00 3.16
1702 1709 2.965671 AGTTGGGGCTCATCATATGG 57.034 50.000 2.13 0.00 0.00 2.74
1803 1810 6.876789 TCAAAATCTTTAGTTGGATCGCTACA 59.123 34.615 0.00 0.00 0.00 2.74
1903 1910 4.116238 GCTCACTGGAATAGTTCTAGCAC 58.884 47.826 3.38 0.00 41.47 4.40
1964 1971 3.618150 GTGGTTGCACATTTCCATTATGC 59.382 43.478 0.00 0.00 36.81 3.14
2025 2032 9.423964 GGATTTTACTATTGGGTGGGTAAAATA 57.576 33.333 17.01 0.00 46.02 1.40
2129 2136 2.092323 GCATTTCTTAGGGCTTTCGGT 58.908 47.619 0.00 0.00 0.00 4.69
2269 2276 3.378112 CACTTCAAGCAGTGGAAAGAACA 59.622 43.478 0.00 0.00 40.60 3.18
2317 2324 5.651387 TGTTGAACAGAATCCAAACACAA 57.349 34.783 0.00 0.00 0.00 3.33
2395 2402 5.851703 GCGGTAAAAGAGACAAAAAGCTAAG 59.148 40.000 0.00 0.00 0.00 2.18
2486 2494 0.326927 GTTAGTTGGCTGGCCTACCA 59.673 55.000 19.19 12.73 46.51 3.25
2616 2624 2.542896 GGTCGTTCGTTCGTGTGC 59.457 61.111 2.67 0.00 0.00 4.57
2636 2644 4.644685 GTGCAGAATCTCTCTCCTTACTCT 59.355 45.833 0.00 0.00 29.07 3.24
2637 2645 5.825679 GTGCAGAATCTCTCTCCTTACTCTA 59.174 44.000 0.00 0.00 29.07 2.43
2730 6474 4.363991 TGGTATTGCCAAAGCCAAAAAT 57.636 36.364 1.51 0.00 45.94 1.82
2731 6475 4.070716 TGGTATTGCCAAAGCCAAAAATG 58.929 39.130 1.51 0.00 45.94 2.32
2732 6476 3.439825 GGTATTGCCAAAGCCAAAAATGG 59.560 43.478 0.00 0.00 38.69 3.16
2742 6486 1.881324 GCCAAAAATGGTGCTGCATTT 59.119 42.857 5.27 0.00 32.98 2.32
2917 6661 3.135994 GCAACAAGTTCTCCGTTTCCTA 58.864 45.455 0.00 0.00 0.00 2.94
2987 6735 3.300009 GCATAAGTTGTATGCATTCGGC 58.700 45.455 3.54 0.00 46.89 5.54
3008 6756 1.134560 GCCCTCAAGTAGGTACGACTG 59.865 57.143 0.00 0.00 45.31 3.51
3090 6838 5.866092 GGATGAAGGAAACAAAGAATGAAGC 59.134 40.000 0.00 0.00 0.00 3.86
3191 6939 2.766263 CAGGTGACAGTCTATAGCCCAA 59.234 50.000 1.31 0.00 0.00 4.12
3216 6964 6.269538 AGAGAGTACCATTGCTGACATGATAT 59.730 38.462 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 191 0.318275 GCCCTGTTAGAGAGCGATCG 60.318 60.000 11.69 11.69 0.00 3.69
303 306 1.817357 TCGAAGACTACGCTTCTGGA 58.183 50.000 0.00 0.00 41.60 3.86
420 424 6.226787 ACTCATCCAAAGTACTCACAAGAAG 58.773 40.000 0.00 0.00 0.00 2.85
422 426 5.808366 ACTCATCCAAAGTACTCACAAGA 57.192 39.130 0.00 0.00 0.00 3.02
455 459 1.006043 GGGGAAAGGAGGGAGAAAAGG 59.994 57.143 0.00 0.00 0.00 3.11
511 517 2.757917 GTCTCGCTCCTGGGCTCT 60.758 66.667 0.00 0.00 0.00 4.09
524 530 2.579787 CGTCGATGGTGGCGTCTC 60.580 66.667 0.00 0.00 0.00 3.36
586 592 0.035881 TACTCCTGGTCGTCGTCAGT 59.964 55.000 13.93 2.78 0.00 3.41
650 656 6.275461 AGATGGCTAGGACAAATAGGGATAT 58.725 40.000 0.00 0.00 0.00 1.63
835 842 2.159379 CGATCAAGATCACGGACTCACA 60.159 50.000 10.39 0.00 37.69 3.58
844 851 5.258622 GCAAATGTGTACGATCAAGATCAC 58.741 41.667 10.39 2.88 37.69 3.06
900 907 0.257905 AGCATGTGCCCATCTGTGAT 59.742 50.000 0.57 0.00 43.38 3.06
949 956 3.000041 CAAGAATTTGATCGTCGGGTCA 59.000 45.455 0.00 0.00 36.36 4.02
956 963 5.943416 TGATTACCACCAAGAATTTGATCGT 59.057 36.000 0.00 0.00 36.36 3.73
994 1001 4.782019 AAGCATGAGCCGTCATTAAAAA 57.218 36.364 0.00 0.00 40.84 1.94
1002 1009 3.126858 TCATTAACAAAGCATGAGCCGTC 59.873 43.478 0.00 0.00 43.56 4.79
1246 1253 2.416747 TGTTGAATCAACTGCTCCTCG 58.583 47.619 24.30 0.00 43.85 4.63
1320 1327 6.684131 CACGCATGTTGAAGATAGTTGTTATG 59.316 38.462 0.00 0.00 0.00 1.90
1390 1397 6.552445 AAGTAGGAATGCTGTCACTAGAAT 57.448 37.500 0.00 0.00 0.00 2.40
1509 1516 9.288576 CAAAAGAGATGCTGGTATAATATTGGA 57.711 33.333 0.00 0.00 0.00 3.53
1687 1694 3.073062 ACAGTAACCATATGATGAGCCCC 59.927 47.826 3.65 0.00 0.00 5.80
1702 1709 2.735134 CAACGTCTAAGCCCACAGTAAC 59.265 50.000 0.00 0.00 0.00 2.50
1803 1810 2.193127 TGTATCGAACCTCCCCACATT 58.807 47.619 0.00 0.00 0.00 2.71
1849 1856 6.074648 TGGTGAACAAAAAGATGAACCCTAT 58.925 36.000 0.00 0.00 0.00 2.57
1964 1971 2.403252 AACGGCTCCCATAGAAAGTG 57.597 50.000 0.00 0.00 0.00 3.16
2076 2083 4.332828 AGGTCAGATTAACCCCGAAAAAG 58.667 43.478 0.00 0.00 37.52 2.27
2193 2200 9.615660 ATCCCAACTACAGATATATAAGAACCA 57.384 33.333 0.00 0.00 0.00 3.67
2312 2319 6.294508 GCTTTGTACCAACCATTCTATTGTGT 60.295 38.462 0.00 0.00 0.00 3.72
2317 2324 5.570320 AGTGCTTTGTACCAACCATTCTAT 58.430 37.500 0.00 0.00 0.00 1.98
2338 2345 3.081804 CAAAAGTATGAAAGGCCGGAGT 58.918 45.455 5.05 0.00 0.00 3.85
2395 2402 7.621796 TCCTTCATAGTTAGGAGAGGTTTTTC 58.378 38.462 0.00 0.00 35.66 2.29
2486 2494 0.462759 GCCAACCTAATCTGCGAGCT 60.463 55.000 0.00 0.00 0.00 4.09
2616 2624 8.924511 AATCTAGAGTAAGGAGAGAGATTCTG 57.075 38.462 0.00 0.00 35.87 3.02
2730 6474 1.540797 GCCTTTTCAAATGCAGCACCA 60.541 47.619 0.00 0.00 31.09 4.17
2731 6475 1.150827 GCCTTTTCAAATGCAGCACC 58.849 50.000 0.00 0.00 31.09 5.01
2732 6476 0.785979 CGCCTTTTCAAATGCAGCAC 59.214 50.000 0.00 0.00 31.09 4.40
2968 6716 2.032030 GCGCCGAATGCATACAACTTAT 60.032 45.455 0.00 0.00 41.33 1.73
2973 6721 2.477176 GGGCGCCGAATGCATACAA 61.477 57.895 22.54 0.00 41.33 2.41
3008 6756 7.888250 AAAGGAAAGGAATAGAATGATCCAC 57.112 36.000 0.00 0.00 35.62 4.02
3090 6838 2.839486 TCAGTAGTCAAAGGTGCAGG 57.161 50.000 0.00 0.00 0.00 4.85
3191 6939 3.771479 TCATGTCAGCAATGGTACTCTCT 59.229 43.478 0.00 0.00 0.00 3.10
3216 6964 5.456921 AATCTGAAGAGGAAGGCCAATTA 57.543 39.130 5.01 0.00 36.29 1.40


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

AutoCloner maintained by Alex Coulton.