Multiple sequence alignment - TraesCS2A01G083900

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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 TraesCS2A01G083900 chr2A 100.000 3275 0 0 1 3275 38517557 38514283 0.000000e+00 6048.0
1 TraesCS2A01G083900 chr2A 94.587 2217 72 20 275 2462 38569104 38571301 0.000000e+00 3386.0
2 TraesCS2A01G083900 chr2A 82.862 636 81 17 5 627 38529796 38529176 2.220000e-151 545.0
3 TraesCS2A01G083900 chr2A 86.517 356 30 13 2034 2381 38398170 38397825 3.090000e-100 375.0
4 TraesCS2A01G083900 chr2A 79.264 299 41 11 3 280 38545116 38545414 4.310000e-44 189.0
5 TraesCS2A01G083900 chr2B 86.466 2453 169 51 74 2462 58312811 58310458 0.000000e+00 2540.0
6 TraesCS2A01G083900 chr2B 88.348 1931 138 45 585 2462 58344007 58345903 0.000000e+00 2239.0
7 TraesCS2A01G083900 chr2B 86.209 1994 159 45 474 2421 58092554 58090631 0.000000e+00 2052.0
8 TraesCS2A01G083900 chr2B 88.274 1518 106 26 840 2338 58536337 58537801 0.000000e+00 1751.0
9 TraesCS2A01G083900 chr2B 93.581 997 51 4 1379 2367 58237226 58236235 0.000000e+00 1474.0
10 TraesCS2A01G083900 chr2B 88.064 687 56 14 4 669 58239633 58238952 0.000000e+00 791.0
11 TraesCS2A01G083900 chr2B 90.167 539 42 6 1 533 58534319 58534852 0.000000e+00 691.0
12 TraesCS2A01G083900 chr2B 89.770 479 43 3 4 476 58094736 58094258 2.790000e-170 608.0
13 TraesCS2A01G083900 chr2B 83.472 599 81 11 4 591 58096963 58096372 2.870000e-150 542.0
14 TraesCS2A01G083900 chr2B 90.663 407 32 5 1 402 58334128 58334533 1.340000e-148 536.0
15 TraesCS2A01G083900 chr2B 82.160 639 86 13 5 627 58326546 58327172 1.040000e-144 523.0
16 TraesCS2A01G083900 chr2B 82.558 602 83 12 5 591 58532033 58532627 8.110000e-141 510.0
17 TraesCS2A01G083900 chr2B 81.720 558 57 23 838 1362 58238840 58238295 1.090000e-114 424.0
18 TraesCS2A01G083900 chr2B 85.496 262 19 9 1341 1597 57787767 57788014 4.190000e-64 255.0
19 TraesCS2A01G083900 chr2B 87.204 211 20 5 197 403 58546602 58546809 1.960000e-57 233.0
20 TraesCS2A01G083900 chr2B 82.775 209 30 3 426 631 58354540 58354745 7.220000e-42 182.0
21 TraesCS2A01G083900 chr2B 87.234 141 7 5 452 585 58334538 58334674 2.040000e-32 150.0
22 TraesCS2A01G083900 chr2B 93.333 45 2 1 713 756 58238918 58238874 7.590000e-07 65.8
23 TraesCS2A01G083900 chr2D 92.234 1455 84 11 1023 2462 35314967 35316407 0.000000e+00 2034.0
24 TraesCS2A01G083900 chr2D 89.806 1442 80 29 1023 2437 35242297 35240896 0.000000e+00 1786.0
25 TraesCS2A01G083900 chr2D 87.268 377 34 7 602 978 35314444 35314806 5.050000e-113 418.0
26 TraesCS2A01G083900 chr2D 83.585 463 52 10 575 1015 35242791 35242331 2.350000e-111 412.0
27 TraesCS2A01G083900 chr2D 81.186 388 40 17 3 367 35243490 35243113 6.920000e-72 281.0
28 TraesCS2A01G083900 chr7B 91.283 826 55 13 2461 3275 7444001 7443182 0.000000e+00 1110.0
29 TraesCS2A01G083900 chr7B 89.563 824 55 17 2461 3275 463534550 463535351 0.000000e+00 1016.0
30 TraesCS2A01G083900 chr3D 90.931 827 57 14 2461 3275 582522367 582523187 0.000000e+00 1096.0
31 TraesCS2A01G083900 chr5B 90.953 829 52 17 2461 3275 540353846 540353027 0.000000e+00 1094.0
32 TraesCS2A01G083900 chr7A 96.840 633 13 6 2647 3275 78436060 78436689 0.000000e+00 1051.0
33 TraesCS2A01G083900 chr7D 91.080 639 38 11 2647 3275 435413868 435414497 0.000000e+00 846.0
34 TraesCS2A01G083900 chr1D 90.312 640 42 11 2647 3275 143363578 143364208 0.000000e+00 821.0
35 TraesCS2A01G083900 chr5D 89.860 641 47 9 2647 3275 524934766 524934132 0.000000e+00 808.0
36 TraesCS2A01G083900 chr4D 92.439 529 27 9 2757 3275 108907735 108908260 0.000000e+00 743.0
37 TraesCS2A01G083900 chr4A 95.601 341 9 5 2471 2808 83760959 83761296 2.870000e-150 542.0
38 TraesCS2A01G083900 chr6D 87.611 226 17 4 2461 2684 315173021 315172805 5.420000e-63 252.0
39 TraesCS2A01G083900 chr1B 100.000 29 0 0 2461 2489 174605099 174605127 2.000000e-03 54.7


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 TraesCS2A01G083900 chr2A 38514283 38517557 3274 True 6048.000000 6048 100.000000 1 3275 1 chr2A.!!$R2 3274
1 TraesCS2A01G083900 chr2A 38569104 38571301 2197 False 3386.000000 3386 94.587000 275 2462 1 chr2A.!!$F2 2187
2 TraesCS2A01G083900 chr2A 38529176 38529796 620 True 545.000000 545 82.862000 5 627 1 chr2A.!!$R3 622
3 TraesCS2A01G083900 chr2B 58310458 58312811 2353 True 2540.000000 2540 86.466000 74 2462 1 chr2B.!!$R1 2388
4 TraesCS2A01G083900 chr2B 58344007 58345903 1896 False 2239.000000 2239 88.348000 585 2462 1 chr2B.!!$F3 1877
5 TraesCS2A01G083900 chr2B 58090631 58096963 6332 True 1067.333333 2052 86.483667 4 2421 3 chr2B.!!$R2 2417
6 TraesCS2A01G083900 chr2B 58532033 58537801 5768 False 984.000000 1751 86.999667 1 2338 3 chr2B.!!$F7 2337
7 TraesCS2A01G083900 chr2B 58236235 58239633 3398 True 688.700000 1474 89.174500 4 2367 4 chr2B.!!$R3 2363
8 TraesCS2A01G083900 chr2B 58326546 58327172 626 False 523.000000 523 82.160000 5 627 1 chr2B.!!$F2 622
9 TraesCS2A01G083900 chr2B 58334128 58334674 546 False 343.000000 536 88.948500 1 585 2 chr2B.!!$F6 584
10 TraesCS2A01G083900 chr2D 35314444 35316407 1963 False 1226.000000 2034 89.751000 602 2462 2 chr2D.!!$F1 1860
11 TraesCS2A01G083900 chr2D 35240896 35243490 2594 True 826.333333 1786 84.859000 3 2437 3 chr2D.!!$R1 2434
12 TraesCS2A01G083900 chr7B 7443182 7444001 819 True 1110.000000 1110 91.283000 2461 3275 1 chr7B.!!$R1 814
13 TraesCS2A01G083900 chr7B 463534550 463535351 801 False 1016.000000 1016 89.563000 2461 3275 1 chr7B.!!$F1 814
14 TraesCS2A01G083900 chr3D 582522367 582523187 820 False 1096.000000 1096 90.931000 2461 3275 1 chr3D.!!$F1 814
15 TraesCS2A01G083900 chr5B 540353027 540353846 819 True 1094.000000 1094 90.953000 2461 3275 1 chr5B.!!$R1 814
16 TraesCS2A01G083900 chr7A 78436060 78436689 629 False 1051.000000 1051 96.840000 2647 3275 1 chr7A.!!$F1 628
17 TraesCS2A01G083900 chr7D 435413868 435414497 629 False 846.000000 846 91.080000 2647 3275 1 chr7D.!!$F1 628
18 TraesCS2A01G083900 chr1D 143363578 143364208 630 False 821.000000 821 90.312000 2647 3275 1 chr1D.!!$F1 628
19 TraesCS2A01G083900 chr5D 524934132 524934766 634 True 808.000000 808 89.860000 2647 3275 1 chr5D.!!$R1 628
20 TraesCS2A01G083900 chr4D 108907735 108908260 525 False 743.000000 743 92.439000 2757 3275 1 chr4D.!!$F1 518

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
552 4891 0.322456 CCATCTTGCTTGTTCCGGGA 60.322 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2517 9421 4.037208 AGTTGTCAATGAAAGAGCCACAAG 59.963 41.667 0.0 0.0 0.0 3.16 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 2582 1.087771 CGGTGTAAATCGAGGCCCAC 61.088 60.000 0.00 0.00 0.00 4.61
139 2661 6.704050 GTGTAAAGTGGTGGTGCAAATAAAAT 59.296 34.615 0.00 0.00 0.00 1.82
141 2663 8.589338 TGTAAAGTGGTGGTGCAAATAAAATAT 58.411 29.630 0.00 0.00 0.00 1.28
174 2699 3.719268 TGATCCGCATTATTAGGCCAT 57.281 42.857 5.01 0.00 0.00 4.40
220 2761 5.773176 TCGCAATAACTGAGATATAGGGTCA 59.227 40.000 0.00 0.00 0.00 4.02
228 2769 4.152647 TGAGATATAGGGTCAACGATGCT 58.847 43.478 0.00 0.00 0.00 3.79
326 2894 4.893795 AGAGTTTGTCGTATTATTTGCGC 58.106 39.130 0.00 0.00 32.98 6.09
447 3025 2.783135 TCAAGCCTGATTGAGACCAAC 58.217 47.619 0.00 0.00 34.31 3.77
448 3026 2.106338 TCAAGCCTGATTGAGACCAACA 59.894 45.455 0.00 0.00 34.31 3.33
499 4783 3.022287 CCACGCAACGCTGAAACT 58.978 55.556 0.00 0.00 0.00 2.66
552 4891 0.322456 CCATCTTGCTTGTTCCGGGA 60.322 55.000 0.00 0.00 0.00 5.14
595 4939 0.390340 TGTGGATCTCTGCTGCGAAC 60.390 55.000 0.00 0.00 0.00 3.95
674 6243 0.999406 CAAGTCAGGTAACCGATGCG 59.001 55.000 0.00 0.00 37.17 4.73
691 6261 0.454957 GCGTGCATTCATTTCAGCGT 60.455 50.000 0.00 0.00 0.00 5.07
780 6364 1.656818 ATTCAGGAAATGCACGCCCG 61.657 55.000 0.00 0.00 0.00 6.13
815 6399 2.520980 TGGTAGGGAGGGCATAGAACTA 59.479 50.000 0.00 0.00 0.00 2.24
1122 6901 4.853924 ATTTGTAAAGGCCAGTGAACTG 57.146 40.909 5.01 3.35 43.40 3.16
1123 6902 3.569194 TTGTAAAGGCCAGTGAACTGA 57.431 42.857 12.05 0.00 46.59 3.41
1124 6903 3.569194 TGTAAAGGCCAGTGAACTGAA 57.431 42.857 12.05 0.00 46.59 3.02
1307 7117 0.742505 TGCTTAATCTGCTGCCATGC 59.257 50.000 0.00 0.00 0.00 4.06
1308 7118 0.031721 GCTTAATCTGCTGCCATGCC 59.968 55.000 0.00 0.00 0.00 4.40
1309 7119 1.395635 CTTAATCTGCTGCCATGCCA 58.604 50.000 0.00 0.00 0.00 4.92
1310 7120 1.961394 CTTAATCTGCTGCCATGCCAT 59.039 47.619 0.00 0.00 0.00 4.40
1311 7121 2.076207 TAATCTGCTGCCATGCCATT 57.924 45.000 0.00 0.00 0.00 3.16
2472 9375 6.073765 GCGTTATCCGAATTCTATGTCACATT 60.074 38.462 0.00 0.00 39.56 2.71
2552 9458 5.610398 TCATTGACAACTTTCTACAGCTGA 58.390 37.500 23.35 2.95 0.00 4.26
2561 9467 7.225931 ACAACTTTCTACAGCTGATTCGTTTAA 59.774 33.333 23.35 2.60 0.00 1.52
2631 9538 2.505118 GAGTGCGTCTCGACTGGC 60.505 66.667 0.00 0.00 33.25 4.85
2632 9539 4.406173 AGTGCGTCTCGACTGGCG 62.406 66.667 0.00 0.00 42.69 5.69
2680 9588 2.171659 TCTTGGTTTGTAGCACACAGGA 59.828 45.455 0.00 0.00 38.72 3.86
2681 9589 2.719531 TGGTTTGTAGCACACAGGAA 57.280 45.000 0.00 0.00 38.72 3.36
2829 9742 8.131100 CACTAGAATAAATGGATGTTTGCGATT 58.869 33.333 0.00 0.00 0.00 3.34
3096 10016 2.164827 ACTTTCCCAAAAACACGGACAC 59.835 45.455 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 2541 3.968724 GTGTCGCTTCAAAATGTTCACTC 59.031 43.478 0.00 0.00 0.00 3.51
99 2621 7.496591 ACCACTTTACACTATTTCACTCGAAAA 59.503 33.333 0.00 0.00 44.12 2.29
103 2625 5.120208 CCACCACTTTACACTATTTCACTCG 59.880 44.000 0.00 0.00 0.00 4.18
120 2642 8.128322 TGTAATATTTTATTTGCACCACCACT 57.872 30.769 0.00 0.00 0.00 4.00
141 2663 9.868277 AATAATGCGGATCATTTCTTTTTGTAA 57.132 25.926 0.00 0.00 42.48 2.41
174 2699 2.884012 CCGTTCTTATTATGCATGGCCA 59.116 45.455 8.56 8.56 0.00 5.36
228 2769 4.343231 ACAAAGTGGAATCATGGCATGTA 58.657 39.130 25.62 13.70 0.00 2.29
299 2858 9.779237 CGCAAATAATACGACAAACTCTATAAG 57.221 33.333 0.00 0.00 0.00 1.73
413 2989 1.271656 GGCTTGATGCTGCAAGTTTCT 59.728 47.619 6.36 0.00 45.41 2.52
447 3025 1.872952 TGAAACTCGGACAGCAATGTG 59.127 47.619 0.00 0.00 0.00 3.21
448 3026 2.146342 CTGAAACTCGGACAGCAATGT 58.854 47.619 0.00 0.00 0.00 2.71
536 4875 0.889186 GCTTCCCGGAACAAGCAAGA 60.889 55.000 21.30 0.00 43.87 3.02
552 4891 3.584733 AAAACCTCTGAGAACTGGCTT 57.415 42.857 6.17 0.00 0.00 4.35
595 4939 7.259290 ACCGAATATGGCACTAAACATAAAG 57.741 36.000 0.00 0.00 33.69 1.85
674 6243 3.735240 TGAAAACGCTGAAATGAATGCAC 59.265 39.130 0.00 0.00 0.00 4.57
691 6261 7.028962 GCAGTGTATATGCAGTTGAATGAAAA 58.971 34.615 0.00 0.00 43.31 2.29
803 6387 0.601311 CAGCGGCTAGTTCTATGCCC 60.601 60.000 0.26 0.00 43.42 5.36
815 6399 0.947244 CTGAAACAAGAACAGCGGCT 59.053 50.000 0.00 0.00 0.00 5.52
1122 6901 2.499289 TGAGCTCAGACCCATCTTCTTC 59.501 50.000 13.74 0.00 30.42 2.87
1123 6902 2.544721 TGAGCTCAGACCCATCTTCTT 58.455 47.619 13.74 0.00 30.42 2.52
1124 6903 2.244486 TGAGCTCAGACCCATCTTCT 57.756 50.000 13.74 0.00 30.42 2.85
2517 9421 4.037208 AGTTGTCAATGAAAGAGCCACAAG 59.963 41.667 0.00 0.00 0.00 3.16
2552 9458 9.928236 CAACCATCAAACAAAAATTAAACGAAT 57.072 25.926 0.00 0.00 0.00 3.34
2561 9467 6.676237 GTTGGACAACCATCAAACAAAAAT 57.324 33.333 3.85 0.00 46.34 1.82
2583 9490 0.249741 CACCAACGGAGAAACTCGGT 60.250 55.000 6.23 6.23 43.97 4.69
2586 9493 2.450609 TAGCACCAACGGAGAAACTC 57.549 50.000 0.00 0.00 0.00 3.01
2631 9538 1.037493 TGCCTAGCTGTGTATACCCG 58.963 55.000 0.00 0.00 0.00 5.28
2632 9539 1.070289 GGTGCCTAGCTGTGTATACCC 59.930 57.143 0.00 0.00 0.00 3.69
2720 9631 7.489574 TTTTGTCTTGCAACTTTTTCTTGTT 57.510 28.000 0.00 0.00 36.72 2.83
2721 9632 6.347644 GCTTTTGTCTTGCAACTTTTTCTTGT 60.348 34.615 0.00 0.00 36.72 3.16
3174 10097 3.188048 GGCACACTCATCTGCTATTATGC 59.812 47.826 0.00 0.00 33.63 3.14
3177 10102 3.181462 CCAGGCACACTCATCTGCTATTA 60.181 47.826 0.00 0.00 33.63 0.98


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

AutoCloner maintained by Alex Coulton.