Multiple sequence alignment - TraesCS5A01G469900

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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 TraesCS5A01G469900 chr5A 100.000 9349 0 0 1 9349 646954236 646963584 0.000000e+00 17265.0
1 TraesCS5A01G469900 chr5A 95.329 578 23 3 1 576 408298673 408298098 0.000000e+00 915.0
2 TraesCS5A01G469900 chr5A 95.312 576 27 0 1 576 490055813 490056388 0.000000e+00 915.0
3 TraesCS5A01G469900 chr5A 95.017 582 23 1 1 576 621550513 621551094 0.000000e+00 909.0
4 TraesCS5A01G469900 chr5A 96.104 77 3 0 9273 9349 11959967 11960043 9.860000e-25 126.0
5 TraesCS5A01G469900 chr5A 97.297 74 2 0 9276 9349 117564859 117564786 9.860000e-25 126.0
6 TraesCS5A01G469900 chr5A 96.104 77 3 0 9273 9349 271944419 271944495 9.860000e-25 126.0
7 TraesCS5A01G469900 chr5A 96.104 77 3 0 9273 9349 700937846 700937922 9.860000e-25 126.0
8 TraesCS5A01G469900 chr7A 98.997 3491 15 3 3014 6501 703888737 703885264 0.000000e+00 6235.0
9 TraesCS5A01G469900 chr7A 97.959 931 17 2 6498 7427 703885198 703884269 0.000000e+00 1613.0
10 TraesCS5A01G469900 chr7A 89.886 791 63 8 3500 4284 509150575 509149796 0.000000e+00 1002.0
11 TraesCS5A01G469900 chr7A 87.821 624 43 7 6826 7419 731340402 731341022 0.000000e+00 701.0
12 TraesCS5A01G469900 chr7A 89.876 484 39 7 3012 3493 509151429 509150954 1.730000e-171 614.0
13 TraesCS5A01G469900 chr7A 90.625 384 31 4 4286 4667 509148571 509148191 1.080000e-138 505.0
14 TraesCS5A01G469900 chr7A 92.652 313 21 2 6172 6482 47776858 47777170 5.150000e-122 449.0
15 TraesCS5A01G469900 chr7A 84.013 319 23 15 4800 5114 509148118 509147824 1.990000e-71 281.0
16 TraesCS5A01G469900 chr7A 87.611 113 12 2 7329 7440 77595374 77595263 7.620000e-26 130.0
17 TraesCS5A01G469900 chr7A 97.297 74 2 0 9276 9349 233708408 233708335 9.860000e-25 126.0
18 TraesCS5A01G469900 chr7A 96.104 77 3 0 9273 9349 414544511 414544587 9.860000e-25 126.0
19 TraesCS5A01G469900 chr7A 81.690 142 20 4 7286 7427 577488538 577488403 7.670000e-21 113.0
20 TraesCS5A01G469900 chr7A 82.090 134 7 5 5632 5765 47776440 47776556 2.150000e-16 99.0
21 TraesCS5A01G469900 chrUn 98.940 3492 17 3 3013 6501 65677194 65680668 0.000000e+00 6226.0
22 TraesCS5A01G469900 chrUn 96.923 1690 51 1 7429 9117 155231587 155233276 0.000000e+00 2832.0
23 TraesCS5A01G469900 chrUn 95.465 1742 66 7 577 2307 155229181 155230920 0.000000e+00 2767.0
24 TraesCS5A01G469900 chrUn 95.520 1451 64 1 7721 9171 335149658 335151107 0.000000e+00 2318.0
25 TraesCS5A01G469900 chrUn 98.980 882 7 2 6498 7378 65680734 65681614 0.000000e+00 1578.0
26 TraesCS5A01G469900 chrUn 95.082 305 15 0 7427 7731 335149402 335149706 1.830000e-131 481.0
27 TraesCS5A01G469900 chrUn 86.047 86 7 3 6091 6175 154624851 154624770 4.650000e-13 87.9
28 TraesCS5A01G469900 chr6A 98.597 3493 23 6 3012 6501 149025236 149028705 0.000000e+00 6156.0
29 TraesCS5A01G469900 chr6A 98.648 2441 29 3 576 3014 557669502 557671940 0.000000e+00 4322.0
30 TraesCS5A01G469900 chr6A 98.756 1849 23 0 7427 9275 557671940 557673788 0.000000e+00 3288.0
31 TraesCS5A01G469900 chr6A 98.178 933 15 2 6498 7429 149028771 149029702 0.000000e+00 1628.0
32 TraesCS5A01G469900 chr6A 90.416 793 58 11 3500 4284 447900787 447900005 0.000000e+00 1027.0
33 TraesCS5A01G469900 chr6A 90.683 483 35 7 3013 3493 447901640 447901166 1.320000e-177 634.0
34 TraesCS5A01G469900 chr6A 90.365 384 32 4 4286 4667 447898781 447898401 5.040000e-137 499.0
35 TraesCS5A01G469900 chr6A 93.313 329 20 2 6175 6501 474452624 474452952 1.410000e-132 484.0
36 TraesCS5A01G469900 chr6A 92.988 328 21 2 6176 6501 474882467 474882794 2.360000e-130 477.0
37 TraesCS5A01G469900 chr6A 89.862 217 19 3 4901 5114 447898251 447898035 9.250000e-70 276.0
38 TraesCS5A01G469900 chr6A 85.652 230 31 1 6595 6824 474453148 474453375 3.370000e-59 241.0
39 TraesCS5A01G469900 chr6A 98.990 99 1 0 6502 6600 474882865 474882963 2.680000e-40 178.0
40 TraesCS5A01G469900 chr6A 97.297 74 2 0 9276 9349 447329214 447329141 9.860000e-25 126.0
41 TraesCS5A01G469900 chr6A 97.297 74 2 0 9276 9349 450073799 450073726 9.860000e-25 126.0
42 TraesCS5A01G469900 chr6A 91.228 57 3 1 4843 4897 447898227 447898171 1.010000e-09 76.8
43 TraesCS5A01G469900 chr6A 85.135 74 3 2 4800 4872 447898328 447898262 1.680000e-07 69.4
44 TraesCS5A01G469900 chr2B 96.299 2999 74 13 3130 6122 37439757 37442724 0.000000e+00 4889.0
45 TraesCS5A01G469900 chr2B 94.298 684 37 2 6498 7180 37443103 37443785 0.000000e+00 1046.0
46 TraesCS5A01G469900 chr2B 97.313 335 6 3 6168 6501 37442705 37443037 4.900000e-157 566.0
47 TraesCS5A01G469900 chr2B 93.365 211 11 3 7219 7428 37443914 37444122 9.120000e-80 309.0
48 TraesCS5A01G469900 chr7B 96.367 2450 63 14 577 3014 144868557 144866122 0.000000e+00 4008.0
49 TraesCS5A01G469900 chr7B 95.393 2453 96 7 574 3014 398611053 398613500 0.000000e+00 3888.0
50 TraesCS5A01G469900 chr7B 95.626 1852 74 7 7427 9277 398613500 398615345 0.000000e+00 2964.0
51 TraesCS5A01G469900 chr7B 96.214 1796 63 5 7427 9219 144866122 144864329 0.000000e+00 2935.0
52 TraesCS5A01G469900 chr7B 95.353 1571 62 6 7602 9171 670701056 670699496 0.000000e+00 2486.0
53 TraesCS5A01G469900 chr7B 88.047 594 55 10 1 587 311418206 311417622 0.000000e+00 689.0
54 TraesCS5A01G469900 chr7B 96.377 276 10 0 9000 9275 39446433 39446158 1.110000e-123 455.0
55 TraesCS5A01G469900 chr6B 94.430 2388 116 11 579 2953 363476811 363479194 0.000000e+00 3657.0
56 TraesCS5A01G469900 chr6B 95.735 422 10 2 4801 5221 247035105 247034691 0.000000e+00 673.0
57 TraesCS5A01G469900 chr1D 94.391 2068 78 17 968 3013 38867046 38869097 0.000000e+00 3142.0
58 TraesCS5A01G469900 chr1D 91.309 1703 98 18 577 2277 425079406 425081060 0.000000e+00 2279.0
59 TraesCS5A01G469900 chr1D 93.417 319 17 4 5805 6122 356417434 356417119 3.950000e-128 470.0
60 TraesCS5A01G469900 chr1D 80.077 261 21 11 7080 7309 136497638 136497378 2.090000e-36 165.0
61 TraesCS5A01G469900 chr1D 94.737 76 4 0 5690 5765 356417512 356417437 1.650000e-22 119.0
62 TraesCS5A01G469900 chr1D 100.000 57 0 0 6119 6175 154202754 154202810 1.280000e-18 106.0
63 TraesCS5A01G469900 chr1B 96.680 1747 55 3 7427 9171 36188564 36190309 0.000000e+00 2902.0
64 TraesCS5A01G469900 chr1B 95.069 1744 71 4 577 2307 36186158 36187899 0.000000e+00 2730.0
65 TraesCS5A01G469900 chr1B 95.373 1556 49 8 1424 2961 235395192 235396742 0.000000e+00 2453.0
66 TraesCS5A01G469900 chr1B 94.501 1564 71 6 576 2129 595831218 595832776 0.000000e+00 2398.0
67 TraesCS5A01G469900 chr1B 94.501 1564 71 6 576 2129 595882632 595884190 0.000000e+00 2398.0
68 TraesCS5A01G469900 chr1B 95.520 1451 64 1 7721 9171 595833875 595835324 0.000000e+00 2318.0
69 TraesCS5A01G469900 chr1B 95.520 1451 64 1 7721 9171 595885288 595886737 0.000000e+00 2318.0
70 TraesCS5A01G469900 chr1B 96.375 1407 36 6 896 2291 284048246 284046844 0.000000e+00 2302.0
71 TraesCS5A01G469900 chr1B 96.544 839 25 4 2177 3014 595832784 595833619 0.000000e+00 1386.0
72 TraesCS5A01G469900 chr1B 96.544 839 24 5 2177 3014 595884198 595885032 0.000000e+00 1384.0
73 TraesCS5A01G469900 chr1B 97.823 735 14 2 2282 3014 284046249 284045515 0.000000e+00 1267.0
74 TraesCS5A01G469900 chr1B 93.865 326 17 2 577 900 284057459 284057135 1.090000e-133 488.0
75 TraesCS5A01G469900 chr1B 95.082 305 15 0 7427 7731 595833619 595833923 1.830000e-131 481.0
76 TraesCS5A01G469900 chr5D 92.225 1492 88 12 575 2063 254079392 254080858 0.000000e+00 2087.0
77 TraesCS5A01G469900 chr5D 100.000 58 0 0 6119 6176 400325797 400325854 3.570000e-19 108.0
78 TraesCS5A01G469900 chr3A 97.838 925 16 2 6498 7421 37569700 37570621 0.000000e+00 1594.0
79 TraesCS5A01G469900 chr3A 95.172 580 24 1 1 576 63706988 63707567 0.000000e+00 913.0
80 TraesCS5A01G469900 chr3A 92.449 437 23 3 3854 4284 575768119 575767687 4.800000e-172 616.0
81 TraesCS5A01G469900 chr3A 93.865 326 15 5 3014 3336 575768824 575768501 3.920000e-133 486.0
82 TraesCS5A01G469900 chr3A 92.169 332 24 2 6172 6501 511212623 511212954 1.420000e-127 468.0
83 TraesCS5A01G469900 chr3A 86.087 230 30 1 6595 6824 511213150 511213377 7.250000e-61 246.0
84 TraesCS5A01G469900 chr3A 98.990 99 1 0 6502 6600 511213025 511213123 2.680000e-40 178.0
85 TraesCS5A01G469900 chr3A 97.297 74 2 0 9276 9349 76451765 76451692 9.860000e-25 126.0
86 TraesCS5A01G469900 chr3A 94.872 78 4 0 5690 5767 511212246 511212323 1.270000e-23 122.0
87 TraesCS5A01G469900 chr4A 90.314 795 58 12 3500 4284 477786236 477785451 0.000000e+00 1024.0
88 TraesCS5A01G469900 chr4A 95.502 578 22 3 1 576 120511942 120512517 0.000000e+00 920.0
89 TraesCS5A01G469900 chr4A 87.825 616 56 10 6826 7428 209505395 209506004 0.000000e+00 704.0
90 TraesCS5A01G469900 chr4A 90.625 384 31 4 4286 4667 477784227 477783847 1.080000e-138 505.0
91 TraesCS5A01G469900 chr4A 85.799 507 37 17 3014 3493 477787113 477786615 1.080000e-138 505.0
92 TraesCS5A01G469900 chr4A 90.055 181 17 1 4901 5080 477783696 477783516 5.640000e-57 233.0
93 TraesCS5A01G469900 chr4A 82.353 187 17 7 7080 7251 146496703 146496888 2.100000e-31 148.0
94 TraesCS5A01G469900 chr1A 89.560 795 66 10 3500 4284 332967664 332966877 0.000000e+00 992.0
95 TraesCS5A01G469900 chr1A 95.660 576 21 1 1 576 527701098 527701669 0.000000e+00 922.0
96 TraesCS5A01G469900 chr1A 95.147 577 24 4 1 576 102279728 102280301 0.000000e+00 907.0
97 TraesCS5A01G469900 chr1A 91.982 449 32 3 5676 6122 107936095 107935649 2.220000e-175 627.0
98 TraesCS5A01G469900 chr1A 90.456 482 36 7 3014 3493 332968516 332968043 2.220000e-175 627.0
99 TraesCS5A01G469900 chr1A 90.078 383 35 3 4286 4667 332965654 332965274 2.350000e-135 494.0
100 TraesCS5A01G469900 chr1A 89.401 217 20 3 4901 5114 332965123 332964907 4.300000e-68 270.0
101 TraesCS5A01G469900 chr1A 91.228 57 3 1 4843 4897 332965099 332965043 1.010000e-09 76.8
102 TraesCS5A01G469900 chr2A 95.841 577 23 1 1 576 562611439 562610863 0.000000e+00 931.0
103 TraesCS5A01G469900 chr2A 93.750 448 25 3 5676 6122 598465777 598466222 0.000000e+00 669.0
104 TraesCS5A01G469900 chr2A 93.512 447 27 2 5676 6122 603916530 603916974 0.000000e+00 664.0
105 TraesCS5A01G469900 chr2A 93.182 396 23 3 3434 3829 409146185 409145794 6.290000e-161 579.0
106 TraesCS5A01G469900 chr2A 93.884 327 19 1 6176 6501 603916962 603917288 8.440000e-135 492.0
107 TraesCS5A01G469900 chr2A 93.865 326 15 5 3014 3336 409146503 409146180 3.920000e-133 486.0
108 TraesCS5A01G469900 chr2A 92.857 280 19 1 6498 6776 598466685 598466964 1.130000e-108 405.0
109 TraesCS5A01G469900 chr2A 93.066 274 19 0 6503 6776 603917360 603917633 1.460000e-107 401.0
110 TraesCS5A01G469900 chr2A 100.000 44 0 0 5632 5675 603916503 603916546 2.160000e-11 82.4
111 TraesCS5A01G469900 chr2A 97.674 43 1 0 5631 5673 598465749 598465791 3.620000e-09 75.0
112 TraesCS5A01G469900 chr4D 91.667 576 45 2 1 573 382727941 382728516 0.000000e+00 795.0
113 TraesCS5A01G469900 chr3D 83.968 867 98 23 1486 2344 609104511 609105344 0.000000e+00 793.0
114 TraesCS5A01G469900 chr2D 93.103 319 18 3 5805 6122 21436616 21436931 1.840000e-126 464.0
115 TraesCS5A01G469900 chr3B 90.323 341 29 4 8940 9278 721884849 721884511 2.400000e-120 444.0
116 TraesCS5A01G469900 chr5B 92.708 96 4 3 5671 5765 203498012 203498105 1.640000e-27 135.0
117 TraesCS5A01G469900 chr7D 100.000 57 0 0 6119 6175 19677166 19677110 1.280000e-18 106.0
118 TraesCS5A01G469900 chr6D 100.000 57 0 0 6119 6175 52092978 52092922 1.280000e-18 106.0
119 TraesCS5A01G469900 chr6D 100.000 57 0 0 6119 6175 298713066 298713122 1.280000e-18 106.0
120 TraesCS5A01G469900 chr6D 95.385 65 3 0 5726 5790 440665311 440665247 4.620000e-18 104.0


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 TraesCS5A01G469900 chr5A 646954236 646963584 9348 False 17265.000000 17265 100.000000 1 9349 1 chr5A.!!$F5 9348
1 TraesCS5A01G469900 chr5A 408298098 408298673 575 True 915.000000 915 95.329000 1 576 1 chr5A.!!$R2 575
2 TraesCS5A01G469900 chr5A 490055813 490056388 575 False 915.000000 915 95.312000 1 576 1 chr5A.!!$F3 575
3 TraesCS5A01G469900 chr5A 621550513 621551094 581 False 909.000000 909 95.017000 1 576 1 chr5A.!!$F4 575
4 TraesCS5A01G469900 chr7A 703884269 703888737 4468 True 3924.000000 6235 98.478000 3014 7427 2 chr7A.!!$R5 4413
5 TraesCS5A01G469900 chr7A 731340402 731341022 620 False 701.000000 701 87.821000 6826 7419 1 chr7A.!!$F2 593
6 TraesCS5A01G469900 chr7A 509147824 509151429 3605 True 600.500000 1002 88.600000 3012 5114 4 chr7A.!!$R4 2102
7 TraesCS5A01G469900 chr7A 47776440 47777170 730 False 274.000000 449 87.371000 5632 6482 2 chr7A.!!$F3 850
8 TraesCS5A01G469900 chrUn 65677194 65681614 4420 False 3902.000000 6226 98.960000 3013 7378 2 chrUn.!!$F1 4365
9 TraesCS5A01G469900 chrUn 155229181 155233276 4095 False 2799.500000 2832 96.194000 577 9117 2 chrUn.!!$F2 8540
10 TraesCS5A01G469900 chrUn 335149402 335151107 1705 False 1399.500000 2318 95.301000 7427 9171 2 chrUn.!!$F3 1744
11 TraesCS5A01G469900 chr6A 149025236 149029702 4466 False 3892.000000 6156 98.387500 3012 7429 2 chr6A.!!$F1 4417
12 TraesCS5A01G469900 chr6A 557669502 557673788 4286 False 3805.000000 4322 98.702000 576 9275 2 chr6A.!!$F4 8699
13 TraesCS5A01G469900 chr6A 447898035 447901640 3605 True 430.366667 1027 89.614833 3013 5114 6 chr6A.!!$R3 2101
14 TraesCS5A01G469900 chr6A 474452624 474453375 751 False 362.500000 484 89.482500 6175 6824 2 chr6A.!!$F2 649
15 TraesCS5A01G469900 chr2B 37439757 37444122 4365 False 1702.500000 4889 95.318750 3130 7428 4 chr2B.!!$F1 4298
16 TraesCS5A01G469900 chr7B 144864329 144868557 4228 True 3471.500000 4008 96.290500 577 9219 2 chr7B.!!$R4 8642
17 TraesCS5A01G469900 chr7B 398611053 398615345 4292 False 3426.000000 3888 95.509500 574 9277 2 chr7B.!!$F1 8703
18 TraesCS5A01G469900 chr7B 670699496 670701056 1560 True 2486.000000 2486 95.353000 7602 9171 1 chr7B.!!$R3 1569
19 TraesCS5A01G469900 chr7B 311417622 311418206 584 True 689.000000 689 88.047000 1 587 1 chr7B.!!$R2 586
20 TraesCS5A01G469900 chr6B 363476811 363479194 2383 False 3657.000000 3657 94.430000 579 2953 1 chr6B.!!$F1 2374
21 TraesCS5A01G469900 chr1D 38867046 38869097 2051 False 3142.000000 3142 94.391000 968 3013 1 chr1D.!!$F1 2045
22 TraesCS5A01G469900 chr1D 425079406 425081060 1654 False 2279.000000 2279 91.309000 577 2277 1 chr1D.!!$F3 1700
23 TraesCS5A01G469900 chr1B 36186158 36190309 4151 False 2816.000000 2902 95.874500 577 9171 2 chr1B.!!$F2 8594
24 TraesCS5A01G469900 chr1B 235395192 235396742 1550 False 2453.000000 2453 95.373000 1424 2961 1 chr1B.!!$F1 1537
25 TraesCS5A01G469900 chr1B 595882632 595886737 4105 False 2033.333333 2398 95.521667 576 9171 3 chr1B.!!$F4 8595
26 TraesCS5A01G469900 chr1B 284045515 284048246 2731 True 1784.500000 2302 97.099000 896 3014 2 chr1B.!!$R2 2118
27 TraesCS5A01G469900 chr1B 595831218 595835324 4106 False 1645.750000 2398 95.411750 576 9171 4 chr1B.!!$F3 8595
28 TraesCS5A01G469900 chr5D 254079392 254080858 1466 False 2087.000000 2087 92.225000 575 2063 1 chr5D.!!$F1 1488
29 TraesCS5A01G469900 chr3A 37569700 37570621 921 False 1594.000000 1594 97.838000 6498 7421 1 chr3A.!!$F1 923
30 TraesCS5A01G469900 chr3A 63706988 63707567 579 False 913.000000 913 95.172000 1 576 1 chr3A.!!$F2 575
31 TraesCS5A01G469900 chr3A 575767687 575768824 1137 True 551.000000 616 93.157000 3014 4284 2 chr3A.!!$R2 1270
32 TraesCS5A01G469900 chr3A 511212246 511213377 1131 False 253.500000 468 93.029500 5690 6824 4 chr3A.!!$F3 1134
33 TraesCS5A01G469900 chr4A 120511942 120512517 575 False 920.000000 920 95.502000 1 576 1 chr4A.!!$F1 575
34 TraesCS5A01G469900 chr4A 209505395 209506004 609 False 704.000000 704 87.825000 6826 7428 1 chr4A.!!$F3 602
35 TraesCS5A01G469900 chr4A 477783516 477787113 3597 True 566.750000 1024 89.198250 3014 5080 4 chr4A.!!$R1 2066
36 TraesCS5A01G469900 chr1A 527701098 527701669 571 False 922.000000 922 95.660000 1 576 1 chr1A.!!$F2 575
37 TraesCS5A01G469900 chr1A 102279728 102280301 573 False 907.000000 907 95.147000 1 576 1 chr1A.!!$F1 575
38 TraesCS5A01G469900 chr1A 332964907 332968516 3609 True 491.960000 992 90.144600 3014 5114 5 chr1A.!!$R2 2100
39 TraesCS5A01G469900 chr2A 562610863 562611439 576 True 931.000000 931 95.841000 1 576 1 chr2A.!!$R1 575
40 TraesCS5A01G469900 chr2A 409145794 409146503 709 True 532.500000 579 93.523500 3014 3829 2 chr2A.!!$R2 815
41 TraesCS5A01G469900 chr2A 603916503 603917633 1130 False 409.850000 664 95.115500 5632 6776 4 chr2A.!!$F2 1144
42 TraesCS5A01G469900 chr2A 598465749 598466964 1215 False 383.000000 669 94.760333 5631 6776 3 chr2A.!!$F1 1145
43 TraesCS5A01G469900 chr4D 382727941 382728516 575 False 795.000000 795 91.667000 1 573 1 chr4D.!!$F1 572
44 TraesCS5A01G469900 chr3D 609104511 609105344 833 False 793.000000 793 83.968000 1486 2344 1 chr3D.!!$F1 858

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
111 115 0.804989 GGAACCCGCAAGTTGATCAG 59.195 55.000 7.16 0.0 0.00 2.90 F
433 465 1.607801 CCTCGTCATGGAGAGCACCA 61.608 60.000 11.32 0.0 44.41 4.17 F
1175 1213 3.465403 CCTCTCCCCGCTCACCAG 61.465 72.222 0.00 0.0 0.00 4.00 F
2369 3043 3.706086 AGTTGACTGCTTCAAACCCAATT 59.294 39.130 3.26 0.0 46.09 2.32 F
4388 6711 1.295792 GCCTTGTGCGAATATCCGAA 58.704 50.000 0.00 0.0 0.00 4.30 F
6501 8930 0.321298 ACAAATTGAGGACCGTCCCG 60.321 55.000 14.32 0.0 37.19 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1175 1213 0.670854 GAGAAACCGGTCAGTGGAGC 60.671 60.000 8.04 0.00 38.17 4.70 R
2369 3043 2.232756 TCACTAAACAGCAAGCACGA 57.767 45.000 0.00 0.00 0.00 4.35 R
4388 6711 9.911138 AAAACAAAATTGCTCATTCTTGTTTTT 57.089 22.222 21.90 15.13 43.18 1.94 R
5676 8019 3.818787 CAACGCTGCAGCCCCATC 61.819 66.667 32.07 4.82 37.91 3.51 R
6847 9378 0.978146 ACTGGGAGGAGCGCAACTAT 60.978 55.000 11.47 0.00 39.13 2.12 R
9299 11947 0.037605 CCAGAGGTCCACCAACGTAC 60.038 60.000 0.00 0.00 38.89 3.67 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
33 34 1.202927 CCTCAAAGAGTGCCCCAAAGA 60.203 52.381 0.00 0.00 0.00 2.52
41 42 1.992557 AGTGCCCCAAAGATTCTACCA 59.007 47.619 0.00 0.00 0.00 3.25
65 66 4.442706 AGAGTCAAGACGAAAATGTGTGT 58.557 39.130 0.00 0.00 36.20 3.72
111 115 0.804989 GGAACCCGCAAGTTGATCAG 59.195 55.000 7.16 0.00 0.00 2.90
129 133 7.920160 TGATCAGCAAAACATACATCAAGTA 57.080 32.000 0.00 0.00 37.06 2.24
215 219 7.826252 TCTCAAATCCTTAAAGACTCAATCTGG 59.174 37.037 0.00 0.00 37.88 3.86
411 443 3.590643 CCCGAGGGAGAACTACTCA 57.409 57.895 0.84 0.00 46.54 3.41
433 465 1.607801 CCTCGTCATGGAGAGCACCA 61.608 60.000 11.32 0.00 44.41 4.17
829 866 9.537192 ACGATCTAACGGATATTATTTTTGTCA 57.463 29.630 0.00 0.00 34.33 3.58
1175 1213 3.465403 CCTCTCCCCGCTCACCAG 61.465 72.222 0.00 0.00 0.00 4.00
2239 2309 5.105023 TCAATAAATTGGCAAATGGCTGCTA 60.105 36.000 3.01 0.00 44.01 3.49
2369 3043 3.706086 AGTTGACTGCTTCAAACCCAATT 59.294 39.130 3.26 0.00 46.09 2.32
2990 3676 5.509840 GGTGCATGTCTTCGAATATACTCCT 60.510 44.000 0.00 0.00 0.00 3.69
4122 5212 9.303116 CCATCTACACTTGATACTTATAGGAGT 57.697 37.037 0.00 0.00 0.00 3.85
4388 6711 1.295792 GCCTTGTGCGAATATCCGAA 58.704 50.000 0.00 0.00 0.00 4.30
5675 8018 3.083349 AGATGGGGCTGCAGCGTA 61.083 61.111 31.19 20.05 43.26 4.42
5676 8019 2.590007 GATGGGGCTGCAGCGTAG 60.590 66.667 31.19 0.00 43.26 3.51
5677 8020 3.083349 ATGGGGCTGCAGCGTAGA 61.083 61.111 31.19 15.85 43.26 2.59
5678 8021 2.388890 GATGGGGCTGCAGCGTAGAT 62.389 60.000 31.19 19.68 43.26 1.98
5686 8029 2.590007 CAGCGTAGATGGGGCTGC 60.590 66.667 0.00 0.00 46.39 5.25
5687 8030 3.083349 AGCGTAGATGGGGCTGCA 61.083 61.111 0.50 0.00 35.31 4.41
6501 8930 0.321298 ACAAATTGAGGACCGTCCCG 60.321 55.000 14.32 0.00 37.19 5.14
6847 9378 4.156622 CGCGAGCGACGGACTACA 62.157 66.667 12.58 0.00 42.83 2.74
6924 9455 2.614969 AATCCCCAGCTCCAGCCA 60.615 61.111 0.00 0.00 43.38 4.75
7421 10065 6.001460 CCCAATCCGTGCTTTATTATTAGGA 58.999 40.000 0.00 0.00 0.00 2.94
7819 10464 5.653507 TGAATTTGGTTGCTGCTATTCATC 58.346 37.500 0.00 0.00 29.76 2.92
8157 10802 4.497291 TGTTGTACCACAGTTCCTTCTT 57.503 40.909 0.00 0.00 0.00 2.52
8252 10897 5.022122 TCAAACCCATCCATGCAAAATCTA 58.978 37.500 0.00 0.00 0.00 1.98
8367 11012 1.290324 GAGGACGAGCAGCAACAGA 59.710 57.895 0.00 0.00 0.00 3.41
8619 11265 3.843619 TCTGGATTGTAGTGTCCATCCAA 59.156 43.478 1.57 0.00 43.20 3.53
9277 11925 7.093289 ACAAAGTAGCTGATTCCTGTAGTGTAT 60.093 37.037 0.00 0.00 0.00 2.29
9278 11926 6.398234 AGTAGCTGATTCCTGTAGTGTATG 57.602 41.667 0.00 0.00 0.00 2.39
9279 11927 4.679373 AGCTGATTCCTGTAGTGTATGG 57.321 45.455 0.00 0.00 0.00 2.74
9280 11928 3.389329 AGCTGATTCCTGTAGTGTATGGG 59.611 47.826 0.00 0.00 0.00 4.00
9281 11929 3.134804 GCTGATTCCTGTAGTGTATGGGT 59.865 47.826 0.00 0.00 0.00 4.51
9282 11930 4.344102 GCTGATTCCTGTAGTGTATGGGTA 59.656 45.833 0.00 0.00 0.00 3.69
9283 11931 5.012148 GCTGATTCCTGTAGTGTATGGGTAT 59.988 44.000 0.00 0.00 0.00 2.73
9284 11932 6.210784 GCTGATTCCTGTAGTGTATGGGTATA 59.789 42.308 0.00 0.00 0.00 1.47
9285 11933 7.093289 GCTGATTCCTGTAGTGTATGGGTATAT 60.093 40.741 0.00 0.00 0.00 0.86
9286 11934 9.475620 CTGATTCCTGTAGTGTATGGGTATATA 57.524 37.037 0.00 0.00 0.00 0.86
9289 11937 8.603898 TTCCTGTAGTGTATGGGTATATATGG 57.396 38.462 0.00 0.00 0.00 2.74
9290 11938 7.130099 TCCTGTAGTGTATGGGTATATATGGG 58.870 42.308 0.00 0.00 0.00 4.00
9291 11939 7.035690 TCCTGTAGTGTATGGGTATATATGGGA 60.036 40.741 0.00 0.00 0.00 4.37
9292 11940 7.287927 CCTGTAGTGTATGGGTATATATGGGAG 59.712 44.444 0.00 0.00 0.00 4.30
9293 11941 7.130099 TGTAGTGTATGGGTATATATGGGAGG 58.870 42.308 0.00 0.00 0.00 4.30
9294 11942 6.432190 AGTGTATGGGTATATATGGGAGGA 57.568 41.667 0.00 0.00 0.00 3.71
9295 11943 6.822374 AGTGTATGGGTATATATGGGAGGAA 58.178 40.000 0.00 0.00 0.00 3.36
9296 11944 6.903534 AGTGTATGGGTATATATGGGAGGAAG 59.096 42.308 0.00 0.00 0.00 3.46
9297 11945 6.901300 GTGTATGGGTATATATGGGAGGAAGA 59.099 42.308 0.00 0.00 0.00 2.87
9298 11946 7.402071 GTGTATGGGTATATATGGGAGGAAGAA 59.598 40.741 0.00 0.00 0.00 2.52
9299 11947 7.623677 TGTATGGGTATATATGGGAGGAAGAAG 59.376 40.741 0.00 0.00 0.00 2.85
9300 11948 5.989717 TGGGTATATATGGGAGGAAGAAGT 58.010 41.667 0.00 0.00 0.00 3.01
9301 11949 7.123560 TGGGTATATATGGGAGGAAGAAGTA 57.876 40.000 0.00 0.00 0.00 2.24
9302 11950 6.958192 TGGGTATATATGGGAGGAAGAAGTAC 59.042 42.308 0.00 0.00 0.00 2.73
9303 11951 6.096564 GGGTATATATGGGAGGAAGAAGTACG 59.903 46.154 0.00 0.00 0.00 3.67
9304 11952 6.662663 GGTATATATGGGAGGAAGAAGTACGT 59.337 42.308 0.00 0.00 0.00 3.57
9305 11953 7.178097 GGTATATATGGGAGGAAGAAGTACGTT 59.822 40.741 0.00 0.00 0.00 3.99
9306 11954 3.611766 ATGGGAGGAAGAAGTACGTTG 57.388 47.619 0.00 0.00 0.00 4.10
9307 11955 1.621814 TGGGAGGAAGAAGTACGTTGG 59.378 52.381 0.00 0.00 0.00 3.77
9308 11956 1.622312 GGGAGGAAGAAGTACGTTGGT 59.378 52.381 0.00 0.00 0.00 3.67
9309 11957 2.612221 GGGAGGAAGAAGTACGTTGGTG 60.612 54.545 0.00 0.00 0.00 4.17
9310 11958 2.612221 GGAGGAAGAAGTACGTTGGTGG 60.612 54.545 0.00 0.00 0.00 4.61
9311 11959 2.298163 GAGGAAGAAGTACGTTGGTGGA 59.702 50.000 0.00 0.00 0.00 4.02
9312 11960 2.036862 AGGAAGAAGTACGTTGGTGGAC 59.963 50.000 0.00 0.00 0.00 4.02
9313 11961 2.410939 GAAGAAGTACGTTGGTGGACC 58.589 52.381 0.00 0.00 0.00 4.46
9314 11962 1.713297 AGAAGTACGTTGGTGGACCT 58.287 50.000 0.00 0.00 36.82 3.85
9315 11963 1.617357 AGAAGTACGTTGGTGGACCTC 59.383 52.381 0.00 0.00 36.82 3.85
9316 11964 1.617357 GAAGTACGTTGGTGGACCTCT 59.383 52.381 0.00 0.00 36.82 3.69
9317 11965 0.966920 AGTACGTTGGTGGACCTCTG 59.033 55.000 0.00 0.00 36.82 3.35
9318 11966 0.037605 GTACGTTGGTGGACCTCTGG 60.038 60.000 0.00 0.00 36.82 3.86
9319 11967 1.189524 TACGTTGGTGGACCTCTGGG 61.190 60.000 0.00 0.00 36.82 4.45
9320 11968 2.034221 GTTGGTGGACCTCTGGGC 59.966 66.667 0.00 0.00 36.82 5.36
9321 11969 2.121963 TTGGTGGACCTCTGGGCT 60.122 61.111 0.00 0.00 36.82 5.19
9322 11970 2.528818 TTGGTGGACCTCTGGGCTG 61.529 63.158 0.00 0.00 36.82 4.85
9323 11971 2.930562 GGTGGACCTCTGGGCTGT 60.931 66.667 0.00 0.00 35.63 4.40
9324 11972 2.665603 GTGGACCTCTGGGCTGTC 59.334 66.667 0.00 0.00 35.63 3.51
9326 11974 2.607750 GGACCTCTGGGCTGTCCA 60.608 66.667 0.00 0.00 46.29 4.02
9327 11975 2.665603 GACCTCTGGGCTGTCCAC 59.334 66.667 0.00 0.00 41.46 4.02
9328 11976 3.302347 GACCTCTGGGCTGTCCACG 62.302 68.421 0.00 0.00 41.46 4.94
9329 11977 2.997315 CCTCTGGGCTGTCCACGA 60.997 66.667 0.00 0.00 41.46 4.35
9330 11978 2.575993 CTCTGGGCTGTCCACGAG 59.424 66.667 0.00 5.15 41.46 4.18
9331 11979 2.997315 TCTGGGCTGTCCACGAGG 60.997 66.667 0.00 0.00 41.46 4.63
9332 11980 4.767255 CTGGGCTGTCCACGAGGC 62.767 72.222 0.00 0.00 41.46 4.70
9334 11982 4.767255 GGGCTGTCCACGAGGCAG 62.767 72.222 15.33 15.33 40.10 4.85
9335 11983 4.767255 GGCTGTCCACGAGGCAGG 62.767 72.222 19.08 3.82 38.61 4.85
9336 11984 4.767255 GCTGTCCACGAGGCAGGG 62.767 72.222 19.08 3.15 38.61 4.45
9337 11985 4.087892 CTGTCCACGAGGCAGGGG 62.088 72.222 12.94 0.00 36.21 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.590918 TCGTCTTGACTCTCTGGTAGAAT 58.409 43.478 0.00 0.00 32.46 2.40
41 42 4.747108 CACACATTTTCGTCTTGACTCTCT 59.253 41.667 0.00 0.00 0.00 3.10
129 133 7.227156 GTGACAATGGGGTATTCTATTGATCT 58.773 38.462 7.70 0.00 35.21 2.75
215 219 9.063615 TGAGTTTTCCCTTTGAAGTTATCTTAC 57.936 33.333 0.00 0.00 33.63 2.34
433 465 1.144503 GGTGGCCATCTTCATCATCCT 59.855 52.381 9.72 0.00 0.00 3.24
544 578 6.594159 CCTAAAAACTTCGAGGAGCAGAATAA 59.406 38.462 0.00 0.00 0.00 1.40
1001 1039 1.100463 GTGTGGGTGTGTGTGCATCA 61.100 55.000 0.00 0.00 0.00 3.07
1175 1213 0.670854 GAGAAACCGGTCAGTGGAGC 60.671 60.000 8.04 0.00 38.17 4.70
2239 2309 6.209192 TGAACAAAGCCAGTCAATCATACATT 59.791 34.615 0.00 0.00 0.00 2.71
2369 3043 2.232756 TCACTAAACAGCAAGCACGA 57.767 45.000 0.00 0.00 0.00 4.35
4388 6711 9.911138 AAAACAAAATTGCTCATTCTTGTTTTT 57.089 22.222 21.90 15.13 43.18 1.94
5675 8018 4.039092 AACGCTGCAGCCCCATCT 62.039 61.111 32.07 7.99 37.91 2.90
5676 8019 3.818787 CAACGCTGCAGCCCCATC 61.819 66.667 32.07 4.82 37.91 3.51
5686 8029 6.582295 AGAAAATTTATGTGTAAGCAACGCTG 59.418 34.615 0.00 0.00 39.62 5.18
5687 8030 6.677913 AGAAAATTTATGTGTAAGCAACGCT 58.322 32.000 0.00 0.00 42.56 5.07
5801 8144 2.873133 AAATGCGGGTTCGTTTTTCA 57.127 40.000 0.00 0.00 38.89 2.69
6501 8930 4.800471 GCTGTTTGCAGGCTATAATTGTTC 59.200 41.667 0.00 0.00 42.78 3.18
6847 9378 0.978146 ACTGGGAGGAGCGCAACTAT 60.978 55.000 11.47 0.00 39.13 2.12
6924 9455 4.595538 TTGCAGAACGACGGCGGT 62.596 61.111 18.49 9.30 42.31 5.68
7245 9875 4.920112 CCCACACACGAACCGCCA 62.920 66.667 0.00 0.00 0.00 5.69
7311 9954 2.741228 GCAGTCCTGATGGCTAAGTGAG 60.741 54.545 0.00 0.00 0.00 3.51
8157 10802 7.221450 ACCTGCAGTACAAATACAACTCTAAA 58.779 34.615 13.81 0.00 33.30 1.85
8367 11012 5.138276 CCCCATCATCATCAGACTGATTTT 58.862 41.667 15.50 3.30 34.28 1.82
8619 11265 2.941415 GCAGCAACAGCACCTAACCTAT 60.941 50.000 0.00 0.00 0.00 2.57
9251 11899 5.012148 ACACTACAGGAATCAGCTACTTTGT 59.988 40.000 0.00 0.00 0.00 2.83
9277 11925 5.989717 ACTTCTTCCTCCCATATATACCCA 58.010 41.667 0.00 0.00 0.00 4.51
9278 11926 6.096564 CGTACTTCTTCCTCCCATATATACCC 59.903 46.154 0.00 0.00 0.00 3.69
9279 11927 6.662663 ACGTACTTCTTCCTCCCATATATACC 59.337 42.308 0.00 0.00 0.00 2.73
9280 11928 7.700022 ACGTACTTCTTCCTCCCATATATAC 57.300 40.000 0.00 0.00 0.00 1.47
9281 11929 7.177921 CCAACGTACTTCTTCCTCCCATATATA 59.822 40.741 0.00 0.00 0.00 0.86
9282 11930 6.014499 CCAACGTACTTCTTCCTCCCATATAT 60.014 42.308 0.00 0.00 0.00 0.86
9283 11931 5.303589 CCAACGTACTTCTTCCTCCCATATA 59.696 44.000 0.00 0.00 0.00 0.86
9284 11932 4.101119 CCAACGTACTTCTTCCTCCCATAT 59.899 45.833 0.00 0.00 0.00 1.78
9285 11933 3.449737 CCAACGTACTTCTTCCTCCCATA 59.550 47.826 0.00 0.00 0.00 2.74
9286 11934 2.236395 CCAACGTACTTCTTCCTCCCAT 59.764 50.000 0.00 0.00 0.00 4.00
9287 11935 1.621814 CCAACGTACTTCTTCCTCCCA 59.378 52.381 0.00 0.00 0.00 4.37
9288 11936 1.622312 ACCAACGTACTTCTTCCTCCC 59.378 52.381 0.00 0.00 0.00 4.30
9289 11937 2.612221 CCACCAACGTACTTCTTCCTCC 60.612 54.545 0.00 0.00 0.00 4.30
9290 11938 2.298163 TCCACCAACGTACTTCTTCCTC 59.702 50.000 0.00 0.00 0.00 3.71
9291 11939 2.036862 GTCCACCAACGTACTTCTTCCT 59.963 50.000 0.00 0.00 0.00 3.36
9292 11940 2.410939 GTCCACCAACGTACTTCTTCC 58.589 52.381 0.00 0.00 0.00 3.46
9293 11941 2.036862 AGGTCCACCAACGTACTTCTTC 59.963 50.000 0.00 0.00 38.89 2.87
9294 11942 2.036862 GAGGTCCACCAACGTACTTCTT 59.963 50.000 0.00 0.00 38.89 2.52
9295 11943 1.617357 GAGGTCCACCAACGTACTTCT 59.383 52.381 0.00 0.00 38.89 2.85
9296 11944 1.617357 AGAGGTCCACCAACGTACTTC 59.383 52.381 0.00 0.00 38.89 3.01
9297 11945 1.343465 CAGAGGTCCACCAACGTACTT 59.657 52.381 0.00 0.00 38.89 2.24
9298 11946 0.966920 CAGAGGTCCACCAACGTACT 59.033 55.000 0.00 0.00 38.89 2.73
9299 11947 0.037605 CCAGAGGTCCACCAACGTAC 60.038 60.000 0.00 0.00 38.89 3.67
9300 11948 1.189524 CCCAGAGGTCCACCAACGTA 61.190 60.000 0.00 0.00 38.89 3.57
9301 11949 2.516888 CCCAGAGGTCCACCAACGT 61.517 63.158 0.00 0.00 38.89 3.99
9302 11950 2.347490 CCCAGAGGTCCACCAACG 59.653 66.667 0.00 0.00 38.89 4.10
9303 11951 2.034221 GCCCAGAGGTCCACCAAC 59.966 66.667 0.00 0.00 38.89 3.77
9304 11952 2.121963 AGCCCAGAGGTCCACCAA 60.122 61.111 0.00 0.00 38.89 3.67
9305 11953 2.930019 CAGCCCAGAGGTCCACCA 60.930 66.667 0.00 0.00 38.89 4.17
9306 11954 2.930562 ACAGCCCAGAGGTCCACC 60.931 66.667 0.00 0.00 34.57 4.61
9307 11955 2.665603 GACAGCCCAGAGGTCCAC 59.334 66.667 0.00 0.00 34.57 4.02
9317 11965 4.767255 CTGCCTCGTGGACAGCCC 62.767 72.222 7.92 0.00 33.30 5.19
9318 11966 4.767255 CCTGCCTCGTGGACAGCC 62.767 72.222 7.92 0.00 36.69 4.85
9319 11967 4.767255 CCCTGCCTCGTGGACAGC 62.767 72.222 7.92 0.00 36.69 4.40
9320 11968 4.087892 CCCCTGCCTCGTGGACAG 62.088 72.222 7.92 13.27 37.29 3.51


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

AutoCloner maintained by Alex Coulton.