Multiple sequence alignment - TraesCS5A01G537700

Loading Multiple Alignment...

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 TraesCS5A01G537700 chr5A 100.000 4719 0 0 1 4719 694530263 694534981 0.000000e+00 8715.0
1 TraesCS5A01G537700 chr5A 99.608 3317 13 0 2 3318 694550695 694554011 0.000000e+00 6054.0
2 TraesCS5A01G537700 chr5A 100.000 2710 0 0 5606 8315 694535868 694538577 0.000000e+00 5005.0
3 TraesCS5A01G537700 chr5A 99.889 2701 2 1 1 2701 694571065 694573764 0.000000e+00 4970.0
4 TraesCS5A01G537700 chr5A 99.336 2711 17 1 5606 8315 694556273 694558983 0.000000e+00 4905.0
5 TraesCS5A01G537700 chr5A 99.152 2711 22 1 5606 8315 694577804 694580514 0.000000e+00 4878.0
6 TraesCS5A01G537700 chr5A 96.490 1966 54 4 2764 4718 694573742 694575703 0.000000e+00 3234.0
7 TraesCS5A01G537700 chr5A 92.595 1904 113 10 2670 4570 69515641 69517519 0.000000e+00 2710.0
8 TraesCS5A01G537700 chr5A 85.501 1876 241 18 5606 7465 704370060 704371920 0.000000e+00 1929.0
9 TraesCS5A01G537700 chr5A 89.633 1254 121 3 1065 2309 704368586 704369839 0.000000e+00 1587.0
10 TraesCS5A01G537700 chr5A 84.608 1072 143 13 5617 6674 704452042 704453105 0.000000e+00 1046.0
11 TraesCS5A01G537700 chr5A 90.280 607 27 5 2670 3276 119569421 119569995 0.000000e+00 765.0
12 TraesCS5A01G537700 chr5A 92.063 252 17 2 634 883 704367642 704367892 1.330000e-92 351.0
13 TraesCS5A01G537700 chr5A 92.778 180 12 1 2356 2534 229211656 229211835 8.280000e-65 259.0
14 TraesCS5A01G537700 chr5A 88.535 157 8 1 4569 4715 626130301 626130457 1.840000e-41 182.0
15 TraesCS5A01G537700 chr5A 85.897 156 12 4 4569 4714 573358976 573358821 3.110000e-34 158.0
16 TraesCS5A01G537700 chr5A 97.143 35 1 0 906 940 704368549 704368583 9.010000e-05 60.2
17 TraesCS5A01G537700 chr7A 94.839 1899 97 1 2672 4570 95235809 95233912 0.000000e+00 2963.0
18 TraesCS5A01G537700 chr7A 94.787 1899 99 0 2672 4570 95228634 95226736 0.000000e+00 2959.0
19 TraesCS5A01G537700 chr7A 93.635 1901 119 2 2670 4570 571812478 571814376 0.000000e+00 2839.0
20 TraesCS5A01G537700 chr7A 91.237 194 15 1 2343 2534 315530404 315530597 6.400000e-66 263.0
21 TraesCS5A01G537700 chr7A 93.750 144 9 0 2530 2673 640634769 640634626 5.050000e-52 217.0
22 TraesCS5A01G537700 chr7A 87.821 156 9 4 4569 4714 454125778 454125933 3.090000e-39 174.0
23 TraesCS5A01G537700 chr7A 94.495 109 6 0 4571 4679 537370552 537370660 1.440000e-37 169.0
24 TraesCS5A01G537700 chrUn 94.778 1896 98 1 2672 4567 82678567 82680461 0.000000e+00 2952.0
25 TraesCS5A01G537700 chrUn 89.041 1314 126 10 5606 6906 264519436 264520744 0.000000e+00 1613.0
26 TraesCS5A01G537700 chrUn 88.939 895 99 0 1411 2305 264518339 264519233 0.000000e+00 1105.0
27 TraesCS5A01G537700 chrUn 85.022 454 54 7 7007 7450 264520826 264521275 4.580000e-122 449.0
28 TraesCS5A01G537700 chrUn 84.211 152 24 0 7911 8062 264521418 264521569 1.870000e-31 148.0
29 TraesCS5A01G537700 chr6A 94.415 1898 102 4 2672 4567 602741366 602743261 0.000000e+00 2915.0
30 TraesCS5A01G537700 chr6A 94.207 1899 106 4 2672 4570 104451594 104449700 0.000000e+00 2894.0
31 TraesCS5A01G537700 chr6A 92.614 176 11 1 1 174 189198496 189198321 1.390000e-62 252.0
32 TraesCS5A01G537700 chr6A 92.655 177 10 1 1 174 194459151 194459327 1.390000e-62 252.0
33 TraesCS5A01G537700 chr6A 77.654 179 31 7 6387 6561 609154390 609154563 5.310000e-17 100.0
34 TraesCS5A01G537700 chr3A 93.727 1897 112 3 2672 4567 171126943 171125053 0.000000e+00 2837.0
35 TraesCS5A01G537700 chr3A 95.455 242 10 1 8075 8315 465692551 465692792 1.310000e-102 385.0
36 TraesCS5A01G537700 chr3A 85.256 156 13 3 4567 4712 57872229 57872074 1.450000e-32 152.0
37 TraesCS5A01G537700 chr3A 84.472 161 14 4 4569 4718 267080937 267081097 1.870000e-31 148.0
38 TraesCS5A01G537700 chr2A 93.550 1907 111 9 2666 4567 76515906 76514007 0.000000e+00 2830.0
39 TraesCS5A01G537700 chr2A 95.102 245 11 1 8072 8315 563713609 563713853 1.310000e-102 385.0
40 TraesCS5A01G537700 chr2A 93.143 175 10 1 2 174 713226280 713226454 1.070000e-63 255.0
41 TraesCS5A01G537700 chr2A 95.105 143 6 1 2529 2670 654337741 654337883 3.020000e-54 224.0
42 TraesCS5A01G537700 chr2A 93.750 144 9 0 2527 2670 689530129 689530272 5.050000e-52 217.0
43 TraesCS5A01G537700 chr4D 90.422 1681 146 11 634 2313 508339232 508340898 0.000000e+00 2198.0
44 TraesCS5A01G537700 chr4D 86.546 1873 221 16 5608 7465 508341121 508342977 0.000000e+00 2034.0
45 TraesCS5A01G537700 chr4D 91.844 1361 109 1 987 2345 504518201 504519561 0.000000e+00 1897.0
46 TraesCS5A01G537700 chr4D 91.076 1143 96 3 5608 6746 504520444 504521584 0.000000e+00 1541.0
47 TraesCS5A01G537700 chr4D 89.247 744 79 1 6801 7543 504521584 504522327 0.000000e+00 929.0
48 TraesCS5A01G537700 chr4D 90.503 179 17 0 2356 2534 104153251 104153073 3.880000e-58 237.0
49 TraesCS5A01G537700 chr4D 90.556 180 16 1 2356 2534 214923944 214924123 3.880000e-58 237.0
50 TraesCS5A01G537700 chr4D 88.312 154 8 1 4569 4712 85684107 85683954 8.580000e-40 176.0
51 TraesCS5A01G537700 chr4B 85.791 1872 202 36 5606 7450 659499364 659497530 0.000000e+00 1925.0
52 TraesCS5A01G537700 chr4B 88.737 1314 129 10 5606 6905 659483830 659482522 0.000000e+00 1589.0
53 TraesCS5A01G537700 chr4B 86.315 1308 163 8 1012 2305 659485338 659484033 0.000000e+00 1410.0
54 TraesCS5A01G537700 chr4B 86.236 1315 157 13 1012 2305 659513648 659512337 0.000000e+00 1404.0
55 TraesCS5A01G537700 chr4B 85.920 1321 156 17 1012 2305 659500884 659499567 0.000000e+00 1382.0
56 TraesCS5A01G537700 chr4B 83.619 525 57 16 6941 7450 659482522 659482012 4.550000e-127 466.0
57 TraesCS5A01G537700 chr4B 95.851 241 9 1 8075 8314 327147260 327147020 1.010000e-103 388.0
58 TraesCS5A01G537700 chr4B 90.556 180 16 1 2356 2534 29934478 29934299 3.880000e-58 237.0
59 TraesCS5A01G537700 chr4B 86.842 152 20 0 7911 8062 659481869 659481718 3.990000e-38 171.0
60 TraesCS5A01G537700 chr4B 84.211 152 23 1 7911 8062 659497390 659497240 6.730000e-31 147.0
61 TraesCS5A01G537700 chr7D 92.963 270 18 1 7533 7801 41057251 41057520 7.820000e-105 392.0
62 TraesCS5A01G537700 chr7D 90.426 188 16 2 2349 2534 119016619 119016432 6.450000e-61 246.0
63 TraesCS5A01G537700 chr7D 95.139 144 7 0 2530 2673 207910944 207910801 2.330000e-55 228.0
64 TraesCS5A01G537700 chr2D 93.156 263 18 0 7538 7800 37526875 37526613 3.640000e-103 387.0
65 TraesCS5A01G537700 chr2D 92.653 245 16 1 1 243 290742842 290743086 1.330000e-92 351.0
66 TraesCS5A01G537700 chr2D 76.494 251 55 4 6359 6607 12626168 12625920 5.240000e-27 134.0
67 TraesCS5A01G537700 chr5D 96.170 235 9 0 8081 8315 328932420 328932186 1.310000e-102 385.0
68 TraesCS5A01G537700 chr5D 95.816 239 9 1 8078 8315 406247777 406247539 1.310000e-102 385.0
69 TraesCS5A01G537700 chr5D 90.036 281 26 2 7525 7804 85566761 85567040 6.130000e-96 363.0
70 TraesCS5A01G537700 chr5D 94.326 141 8 0 2533 2673 284116797 284116657 5.050000e-52 217.0
71 TraesCS5A01G537700 chr1D 95.798 238 10 0 8078 8315 201703861 201703624 1.310000e-102 385.0
72 TraesCS5A01G537700 chr1D 94.964 139 7 0 2532 2670 377577483 377577621 1.410000e-52 219.0
73 TraesCS5A01G537700 chr1D 88.961 154 7 1 4569 4712 483105310 483105463 1.840000e-41 182.0
74 TraesCS5A01G537700 chr1D 90.000 110 11 0 440 549 439068362 439068253 8.700000e-30 143.0
75 TraesCS5A01G537700 chr6D 94.355 248 13 1 8068 8315 439669670 439669916 6.090000e-101 379.0
76 TraesCS5A01G537700 chr6D 92.692 260 19 0 7540 7799 270874224 270873965 7.880000e-100 375.0
77 TraesCS5A01G537700 chr6D 88.235 153 8 1 4569 4711 123976564 123976716 3.090000e-39 174.0
78 TraesCS5A01G537700 chr6D 93.694 111 7 0 4569 4679 465128829 465128939 5.160000e-37 167.0
79 TraesCS5A01G537700 chr6D 74.444 180 42 3 6425 6602 462394300 462394477 3.220000e-09 75.0
80 TraesCS5A01G537700 chr6B 88.779 303 27 7 7539 7837 4953243 4952944 1.710000e-96 364.0
81 TraesCS5A01G537700 chr6B 88.779 303 27 7 7539 7837 4975625 4975326 1.710000e-96 364.0
82 TraesCS5A01G537700 chr6B 93.061 245 15 1 1 243 270780280 270780524 2.850000e-94 357.0
83 TraesCS5A01G537700 chr6B 88.119 303 29 7 7539 7837 5033020 5032721 3.690000e-93 353.0
84 TraesCS5A01G537700 chr6B 91.429 245 19 1 1 243 270817490 270817734 1.340000e-87 335.0
85 TraesCS5A01G537700 chr2B 91.200 250 18 2 1 246 361646088 361646337 3.720000e-88 337.0
86 TraesCS5A01G537700 chr2B 86.538 156 11 4 4569 4714 341324483 341324328 6.680000e-36 163.0
87 TraesCS5A01G537700 chr1A 93.103 174 10 1 1 172 557995118 557995291 3.850000e-63 254.0
88 TraesCS5A01G537700 chr1A 92.045 176 12 1 1 174 513906989 513907164 6.450000e-61 246.0
89 TraesCS5A01G537700 chr1A 90.556 180 16 1 2356 2534 126539680 126539859 3.880000e-58 237.0
90 TraesCS5A01G537700 chr1A 88.535 157 8 5 4569 4715 306130739 306130583 1.840000e-41 182.0
91 TraesCS5A01G537700 chr1A 92.727 110 8 0 440 549 535324237 535324128 8.640000e-35 159.0
92 TraesCS5A01G537700 chr4A 92.045 176 12 1 1 174 419977123 419977298 6.450000e-61 246.0
93 TraesCS5A01G537700 chr4A 92.045 176 12 1 1 174 484237442 484237267 6.450000e-61 246.0
94 TraesCS5A01G537700 chr3D 93.750 144 9 0 2530 2673 24203406 24203263 5.050000e-52 217.0
95 TraesCS5A01G537700 chr3D 88.750 160 8 6 4567 4716 111763004 111763163 3.960000e-43 187.0
96 TraesCS5A01G537700 chr5B 88.742 151 14 2 4569 4718 528709087 528708939 1.840000e-41 182.0
97 TraesCS5A01G537700 chr1B 87.261 157 10 4 4569 4715 631824052 631824208 3.990000e-38 171.0
98 TraesCS5A01G537700 chr1B 91.818 110 9 0 440 549 595331554 595331445 4.020000e-33 154.0


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 TraesCS5A01G537700 chr5A 694530263 694538577 8314 False 6860.000000 8715 100.000000 1 8315 2 chr5A.!!$F6 8314
1 TraesCS5A01G537700 chr5A 694550695 694558983 8288 False 5479.500000 6054 99.472000 2 8315 2 chr5A.!!$F7 8313
2 TraesCS5A01G537700 chr5A 694571065 694580514 9449 False 4360.666667 4970 98.510333 1 8315 3 chr5A.!!$F8 8314
3 TraesCS5A01G537700 chr5A 69515641 69517519 1878 False 2710.000000 2710 92.595000 2670 4570 1 chr5A.!!$F1 1900
4 TraesCS5A01G537700 chr5A 704452042 704453105 1063 False 1046.000000 1046 84.608000 5617 6674 1 chr5A.!!$F5 1057
5 TraesCS5A01G537700 chr5A 704367642 704371920 4278 False 981.800000 1929 91.085000 634 7465 4 chr5A.!!$F9 6831
6 TraesCS5A01G537700 chr5A 119569421 119569995 574 False 765.000000 765 90.280000 2670 3276 1 chr5A.!!$F2 606
7 TraesCS5A01G537700 chr7A 95233912 95235809 1897 True 2963.000000 2963 94.839000 2672 4570 1 chr7A.!!$R2 1898
8 TraesCS5A01G537700 chr7A 95226736 95228634 1898 True 2959.000000 2959 94.787000 2672 4570 1 chr7A.!!$R1 1898
9 TraesCS5A01G537700 chr7A 571812478 571814376 1898 False 2839.000000 2839 93.635000 2670 4570 1 chr7A.!!$F4 1900
10 TraesCS5A01G537700 chrUn 82678567 82680461 1894 False 2952.000000 2952 94.778000 2672 4567 1 chrUn.!!$F1 1895
11 TraesCS5A01G537700 chrUn 264518339 264521569 3230 False 828.750000 1613 86.803250 1411 8062 4 chrUn.!!$F2 6651
12 TraesCS5A01G537700 chr6A 602741366 602743261 1895 False 2915.000000 2915 94.415000 2672 4567 1 chr6A.!!$F2 1895
13 TraesCS5A01G537700 chr6A 104449700 104451594 1894 True 2894.000000 2894 94.207000 2672 4570 1 chr6A.!!$R1 1898
14 TraesCS5A01G537700 chr3A 171125053 171126943 1890 True 2837.000000 2837 93.727000 2672 4567 1 chr3A.!!$R2 1895
15 TraesCS5A01G537700 chr2A 76514007 76515906 1899 True 2830.000000 2830 93.550000 2666 4567 1 chr2A.!!$R1 1901
16 TraesCS5A01G537700 chr4D 508339232 508342977 3745 False 2116.000000 2198 88.484000 634 7465 2 chr4D.!!$F3 6831
17 TraesCS5A01G537700 chr4D 504518201 504522327 4126 False 1455.666667 1897 90.722333 987 7543 3 chr4D.!!$F2 6556
18 TraesCS5A01G537700 chr4B 659512337 659513648 1311 True 1404.000000 1404 86.236000 1012 2305 1 chr4B.!!$R3 1293
19 TraesCS5A01G537700 chr4B 659497240 659500884 3644 True 1151.333333 1925 85.307333 1012 8062 3 chr4B.!!$R5 7050
20 TraesCS5A01G537700 chr4B 659481718 659485338 3620 True 909.000000 1589 86.378250 1012 8062 4 chr4B.!!$R4 7050

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
2894 3579 3.175929 CCAAACACGATAAATTTCGGCC 58.824 45.455 4.68 0.0 43.33 6.13 F
3833 4564 0.327591 ACGACCTAGACTTCCTCGGT 59.672 55.000 0.00 0.0 42.98 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4467 5199 0.611896 CCACCAGGAGCCCGATTTTT 60.612 55.000 0.0 0.0 36.89 1.94 R
7472 9986 8.220755 TGTTTAGATGCACTGTAAAAGAACTT 57.779 30.769 0.0 0.0 0.00 2.66 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
2894 3579 3.175929 CCAAACACGATAAATTTCGGCC 58.824 45.455 4.68 0.00 43.33 6.13
3320 4049 4.016706 CCCCGGCTCCGTCTTTGT 62.017 66.667 7.59 0.00 37.81 2.83
3675 4406 4.379243 CGCCCCTCGCTGTTCTGT 62.379 66.667 0.00 0.00 34.21 3.41
3833 4564 0.327591 ACGACCTAGACTTCCTCGGT 59.672 55.000 0.00 0.00 42.98 4.69
7147 9600 2.029844 GGACTCTTGTCGGTGCAGC 61.030 63.158 5.64 5.64 43.79 5.25
7535 10049 7.337689 TCATTTCCAGTCATTCAATGGACTAAG 59.662 37.037 0.00 0.00 42.72 2.18
7768 10283 8.667463 ACAAAATTTGACTTTGACCAAATCTTG 58.333 29.630 13.19 10.51 42.16 3.02
7804 10319 6.897706 AAAGAAACGGAGAGAGTACTACTT 57.102 37.500 0.00 0.00 0.00 2.24
8118 10634 3.056891 GGGATCGCAACAATTTTCAAGGA 60.057 43.478 4.64 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2729 3412 2.653702 CCCAATTTTTGCGCCGGA 59.346 55.556 5.05 0.00 0.00 5.14
2894 3579 2.703409 CGAGCTTCGCCGAAATGG 59.297 61.111 0.00 0.00 42.50 3.16
2908 3593 4.211164 TGCTATGTAATGAAAATCCGCGAG 59.789 41.667 8.23 0.00 0.00 5.03
2944 3629 8.472007 TTCAGCCAGTTTTTCCTTTAGATTAA 57.528 30.769 0.00 0.00 0.00 1.40
2993 3678 2.282958 AGGAGAAGGCCGACGACA 60.283 61.111 0.00 0.00 0.00 4.35
3320 4049 1.176619 TCCTCCGCACTTCGTCAAGA 61.177 55.000 0.00 0.00 36.19 3.02
4467 5199 0.611896 CCACCAGGAGCCCGATTTTT 60.612 55.000 0.00 0.00 36.89 1.94
7472 9986 8.220755 TGTTTAGATGCACTGTAAAAGAACTT 57.779 30.769 0.00 0.00 0.00 2.66
7733 10248 9.753669 GTCAAAGTCAAATTTTGTAAAGTTTGG 57.246 29.630 18.81 8.05 42.40 3.28
7768 10283 7.748847 TCTCCGTTTCTTTTTAATCTGCATAC 58.251 34.615 0.00 0.00 0.00 2.39
7804 10319 9.851686 AATGGCTTCATACTACTGATATTTTCA 57.148 29.630 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.