Multiple sequence alignment - TraesCS2B01G548200

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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 TraesCS2B01G548200 chr2B 100.000 1643 0 0 1584 3226 744318422 744316780 0.000000e+00 3035.0
1 TraesCS2B01G548200 chr2B 100.000 1363 0 0 1 1363 744320005 744318643 0.000000e+00 2518.0
2 TraesCS2B01G548200 chr2B 96.816 848 26 1 2380 3226 51803807 51804654 0.000000e+00 1415.0
3 TraesCS2B01G548200 chr2B 94.257 888 32 8 28 902 774837989 774838870 0.000000e+00 1339.0
4 TraesCS2B01G548200 chr2B 96.535 808 22 3 1586 2387 774839370 774840177 0.000000e+00 1332.0
5 TraesCS2B01G548200 chr2B 97.737 486 7 3 881 1363 774838877 774839361 0.000000e+00 833.0
6 TraesCS2B01G548200 chr2B 79.525 547 65 25 1662 2187 627836825 627837345 2.380000e-91 346.0
7 TraesCS2B01G548200 chr2B 80.041 491 64 24 1693 2158 627545184 627544703 1.850000e-87 333.0
8 TraesCS2B01G548200 chr2B 90.698 86 8 0 1811 1896 790307032 790306947 7.310000e-22 115.0
9 TraesCS2B01G548200 chr2B 84.314 102 16 0 2287 2388 748202251 748202352 2.050000e-17 100.0
10 TraesCS2B01G548200 chr2B 100.000 38 0 0 1 38 774811815 774811852 1.610000e-08 71.3
11 TraesCS2B01G548200 chr2B 100.000 38 0 0 1 38 774820093 774820130 1.610000e-08 71.3
12 TraesCS2B01G548200 chr7D 96.934 848 25 1 2380 3226 10428949 10429796 0.000000e+00 1421.0
13 TraesCS2B01G548200 chr7D 96.812 847 27 0 2380 3226 442801205 442802051 0.000000e+00 1415.0
14 TraesCS2B01G548200 chr7D 97.173 672 19 0 2381 3052 45202150 45202821 0.000000e+00 1136.0
15 TraesCS2B01G548200 chr7D 95.101 694 30 4 55 748 185909061 185908372 0.000000e+00 1090.0
16 TraesCS2B01G548200 chr7D 93.247 696 38 6 55 748 575531626 575530938 0.000000e+00 1016.0
17 TraesCS2B01G548200 chr7D 89.971 698 57 11 55 745 578351822 578351131 0.000000e+00 889.0
18 TraesCS2B01G548200 chr7D 93.750 112 7 0 750 861 575530854 575530743 5.530000e-38 169.0
19 TraesCS2B01G548200 chr7D 87.500 112 5 4 750 861 185908287 185908185 1.570000e-23 121.0
20 TraesCS2B01G548200 chr7D 94.203 69 4 0 793 861 575529921 575529853 4.400000e-19 106.0
21 TraesCS2B01G548200 chr1A 95.967 843 34 0 2383 3225 472211597 472210755 0.000000e+00 1369.0
22 TraesCS2B01G548200 chr2D 97.497 799 20 0 1586 2384 631307255 631308053 0.000000e+00 1365.0
23 TraesCS2B01G548200 chr2D 95.695 511 11 5 861 1363 631306749 631307256 0.000000e+00 811.0
24 TraesCS2B01G548200 chr2D 82.772 505 67 16 1694 2194 645203934 645203446 1.780000e-117 433.0
25 TraesCS2B01G548200 chr2D 100.000 50 0 0 1 50 631306707 631306756 3.430000e-15 93.5
26 TraesCS2B01G548200 chr1B 96.512 774 27 0 2453 3226 350406485 350407258 0.000000e+00 1280.0
27 TraesCS2B01G548200 chr1B 92.941 85 6 0 2381 2465 350399706 350399790 1.220000e-24 124.0
28 TraesCS2B01G548200 chr5D 95.116 778 38 0 2449 3226 198396374 198395597 0.000000e+00 1227.0
29 TraesCS2B01G548200 chr5D 91.944 782 43 2 2421 3202 198465204 198464443 0.000000e+00 1077.0
30 TraesCS2B01G548200 chr5D 94.643 112 6 0 2276 2387 388860944 388861055 1.190000e-39 174.0
31 TraesCS2B01G548200 chr1D 96.043 657 25 1 1587 2242 432550598 432549942 0.000000e+00 1068.0
32 TraesCS2B01G548200 chr1D 96.813 251 7 1 890 1139 432551121 432550871 4.980000e-113 418.0
33 TraesCS2B01G548200 chr1D 94.239 243 11 2 1124 1363 432550851 432550609 5.080000e-98 368.0
34 TraesCS2B01G548200 chr1D 96.552 58 2 0 2229 2286 432548398 432548341 2.650000e-16 97.1
35 TraesCS2B01G548200 chr1D 100.000 44 0 0 1 44 432551152 432551109 7.420000e-12 82.4
36 TraesCS2B01G548200 chr3B 93.050 705 36 7 52 748 764490445 764491144 0.000000e+00 1018.0
37 TraesCS2B01G548200 chr3B 96.591 88 2 1 750 837 764491228 764491314 9.330000e-31 145.0
38 TraesCS2B01G548200 chr3B 93.478 92 6 0 2287 2378 81302670 81302761 1.560000e-28 137.0
39 TraesCS2B01G548200 chr7A 90.388 541 44 8 110 646 670492913 670492377 0.000000e+00 704.0
40 TraesCS2B01G548200 chr7A 94.118 68 2 2 750 816 670492290 670492224 5.690000e-18 102.0
41 TraesCS2B01G548200 chr7A 97.436 39 0 1 698 736 707852702 707852739 7.470000e-07 65.8
42 TraesCS2B01G548200 chr4A 85.206 703 75 21 55 748 627621496 627620814 0.000000e+00 695.0
43 TraesCS2B01G548200 chr4A 84.844 706 80 25 52 748 627741011 627741698 0.000000e+00 686.0
44 TraesCS2B01G548200 chr6A 84.203 709 84 16 52 748 76922155 76922847 0.000000e+00 664.0
45 TraesCS2B01G548200 chr6A 86.792 583 62 5 1613 2194 31587623 31587055 1.260000e-178 636.0
46 TraesCS2B01G548200 chr6A 86.449 583 65 4 1613 2194 31635936 31636505 7.600000e-176 627.0
47 TraesCS2B01G548200 chr6A 95.210 167 8 0 2380 2546 541243136 541242970 6.860000e-67 265.0
48 TraesCS2B01G548200 chrUn 87.241 580 56 5 1613 2191 31352923 31353485 0.000000e+00 645.0
49 TraesCS2B01G548200 chrUn 86.964 583 62 4 1613 2194 104052807 104052238 0.000000e+00 643.0
50 TraesCS2B01G548200 chrUn 86.106 583 67 4 1613 2194 76957294 76957863 1.640000e-172 616.0
51 TraesCS2B01G548200 chrUn 87.324 142 17 1 2380 2520 24963385 24963526 9.260000e-36 161.0
52 TraesCS2B01G548200 chr7B 95.098 102 5 0 2287 2388 687432048 687432149 9.260000e-36 161.0
53 TraesCS2B01G548200 chr2A 86.429 140 19 0 2381 2520 35901790 35901929 1.550000e-33 154.0
54 TraesCS2B01G548200 chr4B 90.090 111 11 0 2276 2386 104815555 104815665 9.330000e-31 145.0
55 TraesCS2B01G548200 chr6B 95.062 81 4 0 2307 2387 174570240 174570320 9.390000e-26 128.0
56 TraesCS2B01G548200 chr6D 91.667 84 7 0 2300 2383 292399928 292399845 2.030000e-22 117.0
57 TraesCS2B01G548200 chr5A 91.667 48 3 1 701 748 504144859 504144905 7.470000e-07 65.8


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 TraesCS2B01G548200 chr2B 744316780 744320005 3225 True 2776.500000 3035 100.000000 1 3226 2 chr2B.!!$R3 3225
1 TraesCS2B01G548200 chr2B 51803807 51804654 847 False 1415.000000 1415 96.816000 2380 3226 1 chr2B.!!$F1 846
2 TraesCS2B01G548200 chr2B 774837989 774840177 2188 False 1168.000000 1339 96.176333 28 2387 3 chr2B.!!$F6 2359
3 TraesCS2B01G548200 chr2B 627836825 627837345 520 False 346.000000 346 79.525000 1662 2187 1 chr2B.!!$F2 525
4 TraesCS2B01G548200 chr7D 10428949 10429796 847 False 1421.000000 1421 96.934000 2380 3226 1 chr7D.!!$F1 846
5 TraesCS2B01G548200 chr7D 442801205 442802051 846 False 1415.000000 1415 96.812000 2380 3226 1 chr7D.!!$F3 846
6 TraesCS2B01G548200 chr7D 45202150 45202821 671 False 1136.000000 1136 97.173000 2381 3052 1 chr7D.!!$F2 671
7 TraesCS2B01G548200 chr7D 578351131 578351822 691 True 889.000000 889 89.971000 55 745 1 chr7D.!!$R1 690
8 TraesCS2B01G548200 chr7D 185908185 185909061 876 True 605.500000 1090 91.300500 55 861 2 chr7D.!!$R2 806
9 TraesCS2B01G548200 chr7D 575529853 575531626 1773 True 430.333333 1016 93.733333 55 861 3 chr7D.!!$R3 806
10 TraesCS2B01G548200 chr1A 472210755 472211597 842 True 1369.000000 1369 95.967000 2383 3225 1 chr1A.!!$R1 842
11 TraesCS2B01G548200 chr2D 631306707 631308053 1346 False 756.500000 1365 97.730667 1 2384 3 chr2D.!!$F1 2383
12 TraesCS2B01G548200 chr1B 350406485 350407258 773 False 1280.000000 1280 96.512000 2453 3226 1 chr1B.!!$F2 773
13 TraesCS2B01G548200 chr5D 198395597 198396374 777 True 1227.000000 1227 95.116000 2449 3226 1 chr5D.!!$R1 777
14 TraesCS2B01G548200 chr5D 198464443 198465204 761 True 1077.000000 1077 91.944000 2421 3202 1 chr5D.!!$R2 781
15 TraesCS2B01G548200 chr1D 432548341 432551152 2811 True 406.700000 1068 96.729400 1 2286 5 chr1D.!!$R1 2285
16 TraesCS2B01G548200 chr3B 764490445 764491314 869 False 581.500000 1018 94.820500 52 837 2 chr3B.!!$F2 785
17 TraesCS2B01G548200 chr7A 670492224 670492913 689 True 403.000000 704 92.253000 110 816 2 chr7A.!!$R1 706
18 TraesCS2B01G548200 chr4A 627620814 627621496 682 True 695.000000 695 85.206000 55 748 1 chr4A.!!$R1 693
19 TraesCS2B01G548200 chr4A 627741011 627741698 687 False 686.000000 686 84.844000 52 748 1 chr4A.!!$F1 696
20 TraesCS2B01G548200 chr6A 76922155 76922847 692 False 664.000000 664 84.203000 52 748 1 chr6A.!!$F2 696
21 TraesCS2B01G548200 chr6A 31587055 31587623 568 True 636.000000 636 86.792000 1613 2194 1 chr6A.!!$R1 581
22 TraesCS2B01G548200 chr6A 31635936 31636505 569 False 627.000000 627 86.449000 1613 2194 1 chr6A.!!$F1 581
23 TraesCS2B01G548200 chrUn 31352923 31353485 562 False 645.000000 645 87.241000 1613 2191 1 chrUn.!!$F2 578
24 TraesCS2B01G548200 chrUn 104052238 104052807 569 True 643.000000 643 86.964000 1613 2194 1 chrUn.!!$R1 581
25 TraesCS2B01G548200 chrUn 76957294 76957863 569 False 616.000000 616 86.106000 1613 2194 1 chrUn.!!$F3 581

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
179 181 0.249398 GCCTCCTTCGCTGTTTCCTA 59.751 55.000 0.00 0.00 0.00 2.94 F
824 945 0.465287 TTCAGATAGCGCATCCTGCA 59.535 50.000 11.47 0.20 45.36 4.41 F
854 975 1.080025 GGGTTTGACGCTAGCGAGT 60.080 57.895 41.33 22.32 42.83 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1184 1382 0.409092 ATGGTTGGGGCAATCAGACA 59.591 50.000 0.0 0.0 37.91 3.41 R
2003 2248 0.594796 GGCACAACGGCTTTTCTGTG 60.595 55.000 0.0 0.0 41.68 3.66 R
2673 4549 6.486657 CCGGGTGATATTTATGACAGATTGTT 59.513 38.462 0.0 0.0 0.00 2.83 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
87 88 2.658224 CGTTCGTTAGCGTCAAAAGGTG 60.658 50.000 0.00 0.00 39.49 4.00
179 181 0.249398 GCCTCCTTCGCTGTTTCCTA 59.751 55.000 0.00 0.00 0.00 2.94
254 260 4.522722 TTGTTCGGTTTTCCAGTTGTTT 57.477 36.364 0.00 0.00 40.70 2.83
824 945 0.465287 TTCAGATAGCGCATCCTGCA 59.535 50.000 11.47 0.20 45.36 4.41
854 975 1.080025 GGGTTTGACGCTAGCGAGT 60.080 57.895 41.33 22.32 42.83 4.18
856 977 1.416434 GTTTGACGCTAGCGAGTGC 59.584 57.895 41.33 25.63 42.83 4.40
1281 1483 3.384014 GACAGAGAGGACGTCGCCG 62.384 68.421 9.92 0.00 40.83 6.46
1657 1877 8.093118 ACATATGATTGGGAATTTGAAATGGT 57.907 30.769 10.38 0.00 0.00 3.55
1683 1903 2.360350 ATGCAGGGTGCCGAGTTG 60.360 61.111 0.00 0.00 44.23 3.16
1806 2027 2.265739 GATGCCACCGCTGAGACA 59.734 61.111 0.00 0.00 35.36 3.41
2443 4319 2.949826 GGTTAAATCACCGGCCACA 58.050 52.632 0.00 0.00 0.00 4.17
2444 4320 1.470051 GGTTAAATCACCGGCCACAT 58.530 50.000 0.00 0.00 0.00 3.21
2451 4327 1.302431 CACCGGCCACATCACTGAA 60.302 57.895 0.00 0.00 0.00 3.02
2673 4549 4.917385 TCTATGGCTTGCTTCAAAGGTAA 58.083 39.130 0.00 0.00 0.00 2.85
2949 4840 2.038329 CGGGGGTCTGGTAGGTGA 59.962 66.667 0.00 0.00 0.00 4.02
3013 4904 0.033228 TTGCAAATTCCGGTGGCAAG 59.967 50.000 0.00 0.00 39.33 4.01
3081 4972 2.027192 GCCACAGGAGACAAATCACCTA 60.027 50.000 0.00 0.00 43.48 3.08
3133 5024 4.680237 TCCAGCACCTCCAACGCG 62.680 66.667 3.53 3.53 0.00 6.01
3198 5089 0.033228 GCTCGCCACATAGCTCTGAT 59.967 55.000 6.05 0.00 35.80 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.134560 GAACGTCAAGTAGGATCCGCT 59.865 52.381 5.98 6.06 0.00 5.52
53 54 2.935481 ACGAACGTCAAGTAGGATCC 57.065 50.000 2.48 2.48 0.00 3.36
228 234 4.104696 ACTGGAAAACCGAACAAAACAG 57.895 40.909 0.00 0.00 0.00 3.16
254 260 7.390162 AGAAATCAAAGCAAAACACAAGGAAAA 59.610 29.630 0.00 0.00 0.00 2.29
264 270 8.450180 TGAAGGAAAAAGAAATCAAAGCAAAAC 58.550 29.630 0.00 0.00 0.00 2.43
413 433 6.593382 TGGTGAACTTTTTCAGAAAACAATGG 59.407 34.615 7.89 0.31 42.60 3.16
824 945 1.597027 CAAACCCACGAGCTTCCGT 60.597 57.895 0.00 0.00 44.43 4.69
1184 1382 0.409092 ATGGTTGGGGCAATCAGACA 59.591 50.000 0.00 0.00 37.91 3.41
1248 1450 5.316987 CTCTCTGTCCCCAAATAAACAAGT 58.683 41.667 0.00 0.00 0.00 3.16
1281 1483 2.027688 CGACAAGCGTAGAAATTCGGAC 59.972 50.000 0.00 0.00 34.64 4.79
1583 1790 5.240623 GTGTGTGTATATGAGAGAGAGAGGG 59.759 48.000 0.00 0.00 0.00 4.30
1584 1791 5.240623 GGTGTGTGTATATGAGAGAGAGAGG 59.759 48.000 0.00 0.00 0.00 3.69
1585 1792 5.825151 TGGTGTGTGTATATGAGAGAGAGAG 59.175 44.000 0.00 0.00 0.00 3.20
1586 1793 5.590663 GTGGTGTGTGTATATGAGAGAGAGA 59.409 44.000 0.00 0.00 0.00 3.10
1587 1794 5.504830 CGTGGTGTGTGTATATGAGAGAGAG 60.505 48.000 0.00 0.00 0.00 3.20
1588 1795 4.335594 CGTGGTGTGTGTATATGAGAGAGA 59.664 45.833 0.00 0.00 0.00 3.10
1652 1872 2.945510 TGCATCGCAGTGAACCATT 58.054 47.368 0.00 0.00 33.32 3.16
1806 2027 2.017049 AGCTCAGCGAAAAAGTGTTGT 58.983 42.857 0.00 0.00 0.00 3.32
2003 2248 0.594796 GGCACAACGGCTTTTCTGTG 60.595 55.000 0.00 0.00 41.68 3.66
2281 4153 8.812513 AGATGTGAATTGGTCATTCTGATAAA 57.187 30.769 0.00 0.00 41.91 1.40
2451 4327 6.939163 GCTCAATGATTTACCTCCTGATGTAT 59.061 38.462 0.00 0.00 0.00 2.29
2534 4410 7.552458 AGAAATCACGTGAATGTAATATGCA 57.448 32.000 24.13 0.00 0.00 3.96
2577 4453 8.478877 CCAAGTATCAACTACAGATAGGTTTCT 58.521 37.037 0.00 0.00 33.75 2.52
2673 4549 6.486657 CCGGGTGATATTTATGACAGATTGTT 59.513 38.462 0.00 0.00 0.00 2.83
3007 4898 2.288025 GGAGGGTACGACCTTGCCA 61.288 63.158 0.00 0.00 42.10 4.92
3013 4904 1.683418 GACATGGGGAGGGTACGACC 61.683 65.000 0.00 0.00 37.60 4.79
3081 4972 6.393171 GCATTTCCTGAGCAAAAGAAACTAT 58.607 36.000 0.00 0.00 31.51 2.12
3133 5024 2.887151 ATATTATGCAGGCTCCCACC 57.113 50.000 0.00 0.00 0.00 4.61
3198 5089 1.478510 TCTTTTTCCGTTGCAAGGCAA 59.521 42.857 13.63 2.10 46.80 4.52


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

AutoCloner maintained by Alex Coulton.