Multiple sequence alignment - TraesCS1B01G341800

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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 TraesCS1B01G341800 chr1B 100.000 2348 0 0 1 2348 570018083 570015736 0.000000e+00 4337.0
1 TraesCS1B01G341800 chr1B 89.019 856 54 17 1532 2348 272402688 272403542 0.000000e+00 1024.0
2 TraesCS1B01G341800 chr1B 86.502 526 56 10 1831 2348 40439851 40440369 4.380000e-157 564.0
3 TraesCS1B01G341800 chr3B 90.635 1858 125 22 531 2348 708915183 708913335 0.000000e+00 2422.0
4 TraesCS1B01G341800 chr3B 89.501 1762 144 7 531 2251 8005382 8003621 0.000000e+00 2191.0
5 TraesCS1B01G341800 chr3B 91.892 1295 103 2 531 1825 415920803 415922095 0.000000e+00 1808.0
6 TraesCS1B01G341800 chr3B 91.240 1290 108 5 543 1830 499767046 499768332 0.000000e+00 1751.0
7 TraesCS1B01G341800 chr3B 90.979 521 38 6 1 521 198471828 198471317 0.000000e+00 693.0
8 TraesCS1B01G341800 chr2B 90.371 1859 126 21 533 2348 424514683 424512835 0.000000e+00 2392.0
9 TraesCS1B01G341800 chr2B 90.211 521 42 5 1 520 105228826 105229338 0.000000e+00 671.0
10 TraesCS1B01G341800 chr4B 90.363 1847 129 7 542 2348 652822924 652824761 0.000000e+00 2379.0
11 TraesCS1B01G341800 chr4B 89.715 1857 130 14 534 2348 489011575 489009738 0.000000e+00 2314.0
12 TraesCS1B01G341800 chr4B 91.506 518 35 6 1 518 221688209 221688717 0.000000e+00 704.0
13 TraesCS1B01G341800 chr4B 90.595 521 41 5 1 521 341750550 341750038 0.000000e+00 684.0
14 TraesCS1B01G341800 chr4B 90.385 520 38 7 3 521 302650802 302651310 0.000000e+00 673.0
15 TraesCS1B01G341800 chr4B 90.196 510 36 7 1852 2348 673247249 673246741 0.000000e+00 652.0
16 TraesCS1B01G341800 chr4B 82.787 244 30 8 2110 2348 176653002 176652766 8.500000e-50 207.0
17 TraesCS1B01G341800 chr5B 89.699 1825 146 5 565 2348 523441633 523439810 0.000000e+00 2290.0
18 TraesCS1B01G341800 chr5B 89.562 1600 120 17 791 2348 94967017 94965423 0.000000e+00 1986.0
19 TraesCS1B01G341800 chr5B 91.821 1296 104 2 531 1825 580099558 580098264 0.000000e+00 1805.0
20 TraesCS1B01G341800 chr5B 89.130 782 43 3 1608 2348 653396866 653396086 0.000000e+00 935.0
21 TraesCS1B01G341800 chr5B 86.211 921 45 16 1472 2348 595076397 595077279 0.000000e+00 922.0
22 TraesCS1B01G341800 chr5B 91.683 517 30 5 1845 2348 580089433 580088917 0.000000e+00 704.0
23 TraesCS1B01G341800 chr6B 90.428 1776 111 10 619 2348 484540856 484539094 0.000000e+00 2283.0
24 TraesCS1B01G341800 chr6B 88.546 1877 156 24 531 2348 217465805 217467681 0.000000e+00 2220.0
25 TraesCS1B01G341800 chr6B 91.620 537 32 2 1824 2348 19544005 19544540 0.000000e+00 730.0
26 TraesCS1B01G341800 chr6B 90.769 520 38 6 1 520 331572601 331572092 0.000000e+00 686.0
27 TraesCS1B01G341800 chr7B 89.437 1846 137 31 542 2348 554784600 554786426 0.000000e+00 2276.0
28 TraesCS1B01G341800 chr7B 91.512 1296 107 3 536 1830 654021704 654020411 0.000000e+00 1781.0
29 TraesCS1B01G341800 chr7B 91.806 537 32 4 1824 2348 6063924 6063388 0.000000e+00 737.0
30 TraesCS1B01G341800 chr7B 91.555 521 37 2 1 521 550754250 550753737 0.000000e+00 712.0
31 TraesCS1B01G341800 chr7B 90.385 520 41 6 2 521 5631813 5631303 0.000000e+00 675.0
32 TraesCS1B01G341800 chr3D 88.806 1867 154 16 531 2348 422944560 422942700 0.000000e+00 2239.0
33 TraesCS1B01G341800 chr3D 87.527 1836 174 23 531 2314 299682568 299684400 0.000000e+00 2071.0
34 TraesCS1B01G341800 chr3D 89.041 1679 129 16 719 2348 47209773 47208101 0.000000e+00 2030.0
35 TraesCS1B01G341800 chr3D 86.905 1848 188 21 544 2348 13188816 13186980 0.000000e+00 2023.0
36 TraesCS1B01G341800 chr3D 86.263 1849 171 33 544 2348 406174918 406176727 0.000000e+00 1930.0
37 TraesCS1B01G341800 chr3D 87.410 834 58 9 1560 2348 467276587 467275756 0.000000e+00 915.0
38 TraesCS1B01G341800 chr3D 89.815 540 40 8 1824 2348 126394269 126394808 0.000000e+00 678.0
39 TraesCS1B01G341800 chr4D 88.804 1840 161 20 542 2348 11877147 11875320 0.000000e+00 2215.0
40 TraesCS1B01G341800 chr4D 88.267 1858 164 23 538 2348 75774624 75772774 0.000000e+00 2174.0
41 TraesCS1B01G341800 chr4D 87.963 540 46 13 1824 2348 336531279 336531814 9.220000e-174 619.0
42 TraesCS1B01G341800 chr1A 88.006 1851 168 26 544 2348 561699852 561698010 0.000000e+00 2139.0
43 TraesCS1B01G341800 chr1A 85.653 1868 207 29 533 2348 249131751 249129893 0.000000e+00 1908.0
44 TraesCS1B01G341800 chr1A 87.903 496 42 6 1824 2304 290368573 290369065 3.390000e-158 568.0
45 TraesCS1B01G341800 chr1A 88.630 387 29 7 1975 2348 412453153 412452769 7.650000e-125 457.0
46 TraesCS1B01G341800 chr5D 87.741 1868 170 22 531 2348 35280221 35278363 0.000000e+00 2126.0
47 TraesCS1B01G341800 chr5D 87.431 1623 148 32 775 2348 217059791 217061406 0.000000e+00 1816.0
48 TraesCS1B01G341800 chr5D 90.000 540 36 5 1824 2348 462345275 462345811 0.000000e+00 682.0
49 TraesCS1B01G341800 chr5D 89.373 367 23 8 1998 2348 344690636 344690270 4.600000e-122 448.0
50 TraesCS1B01G341800 chr5D 88.034 351 25 10 2013 2348 519953374 519953026 1.310000e-107 399.0
51 TraesCS1B01G341800 chr7D 87.433 1870 175 24 531 2348 558451296 558453157 0.000000e+00 2097.0
52 TraesCS1B01G341800 chr7D 90.020 511 35 7 1854 2348 393581484 393580974 0.000000e+00 647.0
53 TraesCS1B01G341800 chr7D 88.086 512 47 6 1851 2348 66965144 66965655 1.550000e-166 595.0
54 TraesCS1B01G341800 chr6D 87.440 1871 170 18 531 2348 463788519 463786661 0.000000e+00 2093.0
55 TraesCS1B01G341800 chr6D 85.046 1839 206 34 569 2348 396931591 396929763 0.000000e+00 1808.0
56 TraesCS1B01G341800 chr6D 86.341 1618 163 28 783 2348 177795512 177797123 0.000000e+00 1711.0
57 TraesCS1B01G341800 chr6D 86.532 1188 109 16 1206 2348 302582445 302581264 0.000000e+00 1260.0
58 TraesCS1B01G341800 chr6D 85.290 707 70 13 1525 2199 427341368 427342072 0.000000e+00 699.0
59 TraesCS1B01G341800 chr6D 87.199 539 47 11 1826 2348 199606562 199606030 5.590000e-166 593.0
60 TraesCS1B01G341800 chr6D 86.972 545 40 18 1826 2348 130198395 130197860 3.360000e-163 584.0
61 TraesCS1B01G341800 chr6D 86.025 551 46 15 1824 2348 20358905 20358360 1.580000e-156 562.0
62 TraesCS1B01G341800 chr6D 84.555 382 33 12 1985 2348 321119890 321119517 2.870000e-94 355.0
63 TraesCS1B01G341800 chr2D 88.974 1705 146 19 531 2199 366494653 366496351 0.000000e+00 2069.0
64 TraesCS1B01G341800 chr1D 86.389 1800 186 17 600 2348 174777612 174775821 0.000000e+00 1912.0
65 TraesCS1B01G341800 chr1D 86.107 1382 133 26 1017 2348 236078895 236080267 0.000000e+00 1434.0
66 TraesCS1B01G341800 chr1D 88.158 1216 97 17 1177 2348 232155173 232156385 0.000000e+00 1404.0
67 TraesCS1B01G341800 chr1D 82.860 951 99 30 1449 2348 469096733 469095796 0.000000e+00 795.0
68 TraesCS1B01G341800 chr1D 90.097 515 37 4 1824 2324 217010200 217009686 0.000000e+00 656.0
69 TraesCS1B01G341800 chr1D 84.242 679 60 8 1713 2348 434618819 434619493 3.320000e-173 617.0
70 TraesCS1B01G341800 chr1D 90.000 370 35 2 1831 2199 196083278 196083646 5.870000e-131 477.0
71 TraesCS1B01G341800 chr1D 89.812 373 36 2 1828 2199 439065652 439066023 5.870000e-131 477.0
72 TraesCS1B01G341800 chr1D 83.333 312 26 13 2055 2348 253350239 253349936 4.980000e-67 265.0
73 TraesCS1B01G341800 chr4A 91.389 1289 108 3 543 1830 653629098 653630384 0.000000e+00 1762.0
74 TraesCS1B01G341800 chr4A 83.201 1506 177 46 884 2348 366670010 366671480 0.000000e+00 1310.0
75 TraesCS1B01G341800 chrUn 80.682 1817 252 56 535 2284 35058161 35056377 0.000000e+00 1319.0
76 TraesCS1B01G341800 chrUn 89.091 495 41 9 1867 2348 108278877 108278383 9.280000e-169 603.0
77 TraesCS1B01G341800 chrUn 86.923 520 46 13 1845 2348 270108035 270107522 4.380000e-157 564.0
78 TraesCS1B01G341800 chrUn 86.923 520 46 13 1845 2348 293811760 293811247 4.380000e-157 564.0
79 TraesCS1B01G341800 chrUn 83.442 616 55 22 1684 2257 400214631 400214021 1.600000e-146 529.0
80 TraesCS1B01G341800 chrUn 85.288 503 57 12 1824 2320 218122164 218121673 9.690000e-139 503.0
81 TraesCS1B01G341800 chrUn 83.889 540 60 16 1828 2348 295919600 295920131 7.540000e-135 490.0
82 TraesCS1B01G341800 chrUn 83.985 537 59 16 1831 2348 326793715 326793187 7.540000e-135 490.0
83 TraesCS1B01G341800 chrUn 80.769 702 69 22 1695 2348 462208055 462207372 2.710000e-134 488.0
84 TraesCS1B01G341800 chrUn 89.326 356 36 2 1845 2199 292180391 292180037 1.660000e-121 446.0
85 TraesCS1B01G341800 chrUn 89.453 256 27 0 1831 2086 82727102 82726847 8.090000e-85 324.0
86 TraesCS1B01G341800 chrUn 85.185 243 21 5 2033 2261 296444556 296444797 3.900000e-58 235.0
87 TraesCS1B01G341800 chrUn 92.188 64 5 0 2285 2348 87030057 87030120 8.940000e-15 91.6
88 TraesCS1B01G341800 chrUn 94.231 52 3 0 2297 2348 61034517 61034466 1.930000e-11 80.5
89 TraesCS1B01G341800 chr5A 89.474 551 41 6 1814 2348 487249211 487249760 0.000000e+00 680.0
90 TraesCS1B01G341800 chr6A 90.230 522 38 9 1 521 5662854 5662345 0.000000e+00 669.0
91 TraesCS1B01G341800 chr6A 85.009 527 58 11 1824 2348 250212627 250213134 1.240000e-142 516.0


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 TraesCS1B01G341800 chr1B 570015736 570018083 2347 True 4337 4337 100.000 1 2348 1 chr1B.!!$R1 2347
1 TraesCS1B01G341800 chr1B 272402688 272403542 854 False 1024 1024 89.019 1532 2348 1 chr1B.!!$F2 816
2 TraesCS1B01G341800 chr1B 40439851 40440369 518 False 564 564 86.502 1831 2348 1 chr1B.!!$F1 517
3 TraesCS1B01G341800 chr3B 708913335 708915183 1848 True 2422 2422 90.635 531 2348 1 chr3B.!!$R3 1817
4 TraesCS1B01G341800 chr3B 8003621 8005382 1761 True 2191 2191 89.501 531 2251 1 chr3B.!!$R1 1720
5 TraesCS1B01G341800 chr3B 415920803 415922095 1292 False 1808 1808 91.892 531 1825 1 chr3B.!!$F1 1294
6 TraesCS1B01G341800 chr3B 499767046 499768332 1286 False 1751 1751 91.240 543 1830 1 chr3B.!!$F2 1287
7 TraesCS1B01G341800 chr3B 198471317 198471828 511 True 693 693 90.979 1 521 1 chr3B.!!$R2 520
8 TraesCS1B01G341800 chr2B 424512835 424514683 1848 True 2392 2392 90.371 533 2348 1 chr2B.!!$R1 1815
9 TraesCS1B01G341800 chr2B 105228826 105229338 512 False 671 671 90.211 1 520 1 chr2B.!!$F1 519
10 TraesCS1B01G341800 chr4B 652822924 652824761 1837 False 2379 2379 90.363 542 2348 1 chr4B.!!$F3 1806
11 TraesCS1B01G341800 chr4B 489009738 489011575 1837 True 2314 2314 89.715 534 2348 1 chr4B.!!$R3 1814
12 TraesCS1B01G341800 chr4B 221688209 221688717 508 False 704 704 91.506 1 518 1 chr4B.!!$F1 517
13 TraesCS1B01G341800 chr4B 341750038 341750550 512 True 684 684 90.595 1 521 1 chr4B.!!$R2 520
14 TraesCS1B01G341800 chr4B 302650802 302651310 508 False 673 673 90.385 3 521 1 chr4B.!!$F2 518
15 TraesCS1B01G341800 chr4B 673246741 673247249 508 True 652 652 90.196 1852 2348 1 chr4B.!!$R4 496
16 TraesCS1B01G341800 chr5B 523439810 523441633 1823 True 2290 2290 89.699 565 2348 1 chr5B.!!$R2 1783
17 TraesCS1B01G341800 chr5B 94965423 94967017 1594 True 1986 1986 89.562 791 2348 1 chr5B.!!$R1 1557
18 TraesCS1B01G341800 chr5B 580098264 580099558 1294 True 1805 1805 91.821 531 1825 1 chr5B.!!$R4 1294
19 TraesCS1B01G341800 chr5B 653396086 653396866 780 True 935 935 89.130 1608 2348 1 chr5B.!!$R5 740
20 TraesCS1B01G341800 chr5B 595076397 595077279 882 False 922 922 86.211 1472 2348 1 chr5B.!!$F1 876
21 TraesCS1B01G341800 chr5B 580088917 580089433 516 True 704 704 91.683 1845 2348 1 chr5B.!!$R3 503
22 TraesCS1B01G341800 chr6B 484539094 484540856 1762 True 2283 2283 90.428 619 2348 1 chr6B.!!$R2 1729
23 TraesCS1B01G341800 chr6B 217465805 217467681 1876 False 2220 2220 88.546 531 2348 1 chr6B.!!$F2 1817
24 TraesCS1B01G341800 chr6B 19544005 19544540 535 False 730 730 91.620 1824 2348 1 chr6B.!!$F1 524
25 TraesCS1B01G341800 chr6B 331572092 331572601 509 True 686 686 90.769 1 520 1 chr6B.!!$R1 519
26 TraesCS1B01G341800 chr7B 554784600 554786426 1826 False 2276 2276 89.437 542 2348 1 chr7B.!!$F1 1806
27 TraesCS1B01G341800 chr7B 654020411 654021704 1293 True 1781 1781 91.512 536 1830 1 chr7B.!!$R4 1294
28 TraesCS1B01G341800 chr7B 6063388 6063924 536 True 737 737 91.806 1824 2348 1 chr7B.!!$R2 524
29 TraesCS1B01G341800 chr7B 550753737 550754250 513 True 712 712 91.555 1 521 1 chr7B.!!$R3 520
30 TraesCS1B01G341800 chr7B 5631303 5631813 510 True 675 675 90.385 2 521 1 chr7B.!!$R1 519
31 TraesCS1B01G341800 chr3D 422942700 422944560 1860 True 2239 2239 88.806 531 2348 1 chr3D.!!$R3 1817
32 TraesCS1B01G341800 chr3D 299682568 299684400 1832 False 2071 2071 87.527 531 2314 1 chr3D.!!$F2 1783
33 TraesCS1B01G341800 chr3D 47208101 47209773 1672 True 2030 2030 89.041 719 2348 1 chr3D.!!$R2 1629
34 TraesCS1B01G341800 chr3D 13186980 13188816 1836 True 2023 2023 86.905 544 2348 1 chr3D.!!$R1 1804
35 TraesCS1B01G341800 chr3D 406174918 406176727 1809 False 1930 1930 86.263 544 2348 1 chr3D.!!$F3 1804
36 TraesCS1B01G341800 chr3D 467275756 467276587 831 True 915 915 87.410 1560 2348 1 chr3D.!!$R4 788
37 TraesCS1B01G341800 chr3D 126394269 126394808 539 False 678 678 89.815 1824 2348 1 chr3D.!!$F1 524
38 TraesCS1B01G341800 chr4D 11875320 11877147 1827 True 2215 2215 88.804 542 2348 1 chr4D.!!$R1 1806
39 TraesCS1B01G341800 chr4D 75772774 75774624 1850 True 2174 2174 88.267 538 2348 1 chr4D.!!$R2 1810
40 TraesCS1B01G341800 chr4D 336531279 336531814 535 False 619 619 87.963 1824 2348 1 chr4D.!!$F1 524
41 TraesCS1B01G341800 chr1A 561698010 561699852 1842 True 2139 2139 88.006 544 2348 1 chr1A.!!$R3 1804
42 TraesCS1B01G341800 chr1A 249129893 249131751 1858 True 1908 1908 85.653 533 2348 1 chr1A.!!$R1 1815
43 TraesCS1B01G341800 chr5D 35278363 35280221 1858 True 2126 2126 87.741 531 2348 1 chr5D.!!$R1 1817
44 TraesCS1B01G341800 chr5D 217059791 217061406 1615 False 1816 1816 87.431 775 2348 1 chr5D.!!$F1 1573
45 TraesCS1B01G341800 chr5D 462345275 462345811 536 False 682 682 90.000 1824 2348 1 chr5D.!!$F2 524
46 TraesCS1B01G341800 chr7D 558451296 558453157 1861 False 2097 2097 87.433 531 2348 1 chr7D.!!$F2 1817
47 TraesCS1B01G341800 chr7D 393580974 393581484 510 True 647 647 90.020 1854 2348 1 chr7D.!!$R1 494
48 TraesCS1B01G341800 chr7D 66965144 66965655 511 False 595 595 88.086 1851 2348 1 chr7D.!!$F1 497
49 TraesCS1B01G341800 chr6D 463786661 463788519 1858 True 2093 2093 87.440 531 2348 1 chr6D.!!$R7 1817
50 TraesCS1B01G341800 chr6D 396929763 396931591 1828 True 1808 1808 85.046 569 2348 1 chr6D.!!$R6 1779
51 TraesCS1B01G341800 chr6D 177795512 177797123 1611 False 1711 1711 86.341 783 2348 1 chr6D.!!$F1 1565
52 TraesCS1B01G341800 chr6D 302581264 302582445 1181 True 1260 1260 86.532 1206 2348 1 chr6D.!!$R4 1142
53 TraesCS1B01G341800 chr6D 427341368 427342072 704 False 699 699 85.290 1525 2199 1 chr6D.!!$F2 674
54 TraesCS1B01G341800 chr6D 199606030 199606562 532 True 593 593 87.199 1826 2348 1 chr6D.!!$R3 522
55 TraesCS1B01G341800 chr6D 130197860 130198395 535 True 584 584 86.972 1826 2348 1 chr6D.!!$R2 522
56 TraesCS1B01G341800 chr6D 20358360 20358905 545 True 562 562 86.025 1824 2348 1 chr6D.!!$R1 524
57 TraesCS1B01G341800 chr2D 366494653 366496351 1698 False 2069 2069 88.974 531 2199 1 chr2D.!!$F1 1668
58 TraesCS1B01G341800 chr1D 174775821 174777612 1791 True 1912 1912 86.389 600 2348 1 chr1D.!!$R1 1748
59 TraesCS1B01G341800 chr1D 236078895 236080267 1372 False 1434 1434 86.107 1017 2348 1 chr1D.!!$F3 1331
60 TraesCS1B01G341800 chr1D 232155173 232156385 1212 False 1404 1404 88.158 1177 2348 1 chr1D.!!$F2 1171
61 TraesCS1B01G341800 chr1D 469095796 469096733 937 True 795 795 82.860 1449 2348 1 chr1D.!!$R4 899
62 TraesCS1B01G341800 chr1D 217009686 217010200 514 True 656 656 90.097 1824 2324 1 chr1D.!!$R2 500
63 TraesCS1B01G341800 chr1D 434618819 434619493 674 False 617 617 84.242 1713 2348 1 chr1D.!!$F4 635
64 TraesCS1B01G341800 chr4A 653629098 653630384 1286 False 1762 1762 91.389 543 1830 1 chr4A.!!$F2 1287
65 TraesCS1B01G341800 chr4A 366670010 366671480 1470 False 1310 1310 83.201 884 2348 1 chr4A.!!$F1 1464
66 TraesCS1B01G341800 chrUn 35056377 35058161 1784 True 1319 1319 80.682 535 2284 1 chrUn.!!$R1 1749
67 TraesCS1B01G341800 chrUn 270107522 270108035 513 True 564 564 86.923 1845 2348 1 chrUn.!!$R6 503
68 TraesCS1B01G341800 chrUn 293811247 293811760 513 True 564 564 86.923 1845 2348 1 chrUn.!!$R8 503
69 TraesCS1B01G341800 chrUn 400214021 400214631 610 True 529 529 83.442 1684 2257 1 chrUn.!!$R10 573
70 TraesCS1B01G341800 chrUn 295919600 295920131 531 False 490 490 83.889 1828 2348 1 chrUn.!!$F2 520
71 TraesCS1B01G341800 chrUn 326793187 326793715 528 True 490 490 83.985 1831 2348 1 chrUn.!!$R9 517
72 TraesCS1B01G341800 chrUn 462207372 462208055 683 True 488 488 80.769 1695 2348 1 chrUn.!!$R11 653
73 TraesCS1B01G341800 chr5A 487249211 487249760 549 False 680 680 89.474 1814 2348 1 chr5A.!!$F1 534
74 TraesCS1B01G341800 chr6A 5662345 5662854 509 True 669 669 90.230 1 521 1 chr6A.!!$R1 520
75 TraesCS1B01G341800 chr6A 250212627 250213134 507 False 516 516 85.009 1824 2348 1 chr6A.!!$F1 524

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
521 527 0.03889 TGAATCGGGGGCATCACAAA 59.961 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 1942 1.587547 GATCTCCATGAAGGCGTTCC 58.412 55.0 16.06 0.0 37.29 3.62 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
47 48 2.939103 GCTTGCGAGTACTTTGGATGAT 59.061 45.455 2.14 0.00 0.00 2.45
52 53 5.348986 TGCGAGTACTTTGGATGATTACTC 58.651 41.667 0.00 0.00 36.73 2.59
53 54 5.105513 TGCGAGTACTTTGGATGATTACTCA 60.106 40.000 0.00 0.00 38.98 3.41
54 55 5.232414 GCGAGTACTTTGGATGATTACTCAC 59.768 44.000 0.00 0.00 38.98 3.51
55 56 5.455849 CGAGTACTTTGGATGATTACTCACG 59.544 44.000 0.00 0.00 38.98 4.35
56 57 5.661458 AGTACTTTGGATGATTACTCACGG 58.339 41.667 0.00 0.00 33.22 4.94
57 58 4.819105 ACTTTGGATGATTACTCACGGA 57.181 40.909 0.00 0.00 33.22 4.69
58 59 4.504858 ACTTTGGATGATTACTCACGGAC 58.495 43.478 0.00 0.00 33.22 4.79
100 102 2.992847 TTCCCCCTCTTTCCTTTTCC 57.007 50.000 0.00 0.00 0.00 3.13
193 198 2.291153 TGGAGGTGCCTACTACTACGTT 60.291 50.000 0.00 0.00 37.63 3.99
196 201 2.751806 AGGTGCCTACTACTACGTTCAC 59.248 50.000 0.00 0.00 0.00 3.18
246 251 1.385206 GGATCCCAGGAAGGAGGCT 60.385 63.158 0.00 0.00 39.95 4.58
478 484 8.637196 AGTCCTTGATCTTGATCGTACATATA 57.363 34.615 6.19 0.00 0.00 0.86
482 488 7.978414 CCTTGATCTTGATCGTACATATATGCT 59.022 37.037 12.79 3.21 0.00 3.79
497 503 8.037382 ACATATATGCTTGCATGATTAGTGTC 57.963 34.615 17.26 0.00 0.00 3.67
521 527 0.038890 TGAATCGGGGGCATCACAAA 59.961 50.000 0.00 0.00 0.00 2.83
522 528 1.181786 GAATCGGGGGCATCACAAAA 58.818 50.000 0.00 0.00 0.00 2.44
523 529 0.894835 AATCGGGGGCATCACAAAAC 59.105 50.000 0.00 0.00 0.00 2.43
524 530 0.039618 ATCGGGGGCATCACAAAACT 59.960 50.000 0.00 0.00 0.00 2.66
525 531 0.608035 TCGGGGGCATCACAAAACTC 60.608 55.000 0.00 0.00 0.00 3.01
526 532 0.609131 CGGGGGCATCACAAAACTCT 60.609 55.000 0.00 0.00 0.00 3.24
527 533 1.339631 CGGGGGCATCACAAAACTCTA 60.340 52.381 0.00 0.00 0.00 2.43
528 534 2.369394 GGGGGCATCACAAAACTCTAG 58.631 52.381 0.00 0.00 0.00 2.43
529 535 1.745653 GGGGCATCACAAAACTCTAGC 59.254 52.381 0.00 0.00 0.00 3.42
763 787 3.461773 CCGGTGGCTCGTCATCCT 61.462 66.667 0.00 0.00 0.00 3.24
811 837 2.767445 CCGACCGACATGCTACCGA 61.767 63.158 0.00 0.00 0.00 4.69
876 902 4.290093 AGGACTACATGCAGAACCTCATA 58.710 43.478 0.00 0.00 0.00 2.15
1086 1142 3.244215 ACGAGTGTGACATCAAAGTGGAT 60.244 43.478 0.00 0.00 0.00 3.41
1251 1310 2.468831 GCCGAACAAAAGCATTCAACA 58.531 42.857 0.00 0.00 0.00 3.33
1435 1500 0.940126 GAGCGGAATCGACATGCAAT 59.060 50.000 0.00 0.00 39.00 3.56
1457 1531 2.288666 CATGGTATGTTAGCAAGCCGT 58.711 47.619 0.00 0.00 39.89 5.68
1515 1596 0.609151 TTGCATCCCATTTGTGCCAG 59.391 50.000 0.00 0.00 38.06 4.85
1822 1942 3.831911 ACAAGAAGGACTCAAGAGAGGAG 59.168 47.826 3.73 0.00 46.44 3.69
2023 2164 1.274167 GGTGGATCTCAACACCGTGTA 59.726 52.381 4.17 0.00 46.61 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 0.032403 CAACCGTGGTCCGTGAGTAA 59.968 55.000 0.00 0.00 33.66 2.24
52 53 2.184167 AAAGCAACCGTGGTCCGTG 61.184 57.895 0.00 0.00 33.24 4.94
53 54 2.184167 CAAAGCAACCGTGGTCCGT 61.184 57.895 0.00 0.00 33.24 4.69
54 55 2.637025 CAAAGCAACCGTGGTCCG 59.363 61.111 0.00 0.00 33.24 4.79
55 56 2.130073 GAGCAAAGCAACCGTGGTCC 62.130 60.000 0.00 0.00 34.47 4.46
56 57 1.282875 GAGCAAAGCAACCGTGGTC 59.717 57.895 0.00 0.00 33.24 4.02
57 58 2.193536 GGAGCAAAGCAACCGTGGT 61.194 57.895 0.00 0.00 36.94 4.16
58 59 2.644992 GGAGCAAAGCAACCGTGG 59.355 61.111 0.00 0.00 0.00 4.94
130 132 2.359169 GGTGGCGTCTGGATCCTGA 61.359 63.158 16.80 16.80 0.00 3.86
211 216 4.387664 GGGATCCTCCTAAACTACTCCTGA 60.388 50.000 12.58 0.00 36.57 3.86
246 251 7.644503 GGGATACAGATCGAAAGAGGCACAA 62.645 48.000 0.00 0.00 41.83 3.33
478 484 2.615447 CGGACACTAATCATGCAAGCAT 59.385 45.455 0.86 0.86 37.08 3.79
482 488 4.512484 TCAATCGGACACTAATCATGCAA 58.488 39.130 0.00 0.00 0.00 4.08
521 527 4.796231 CGGCGGCGTGCTAGAGTT 62.796 66.667 24.74 0.00 45.43 3.01
763 787 1.805539 CGCATTTCCTCGCGTCTCA 60.806 57.895 5.77 0.00 46.23 3.27
811 837 3.284449 GAACAGGTTGCGGGCGTT 61.284 61.111 0.00 0.00 0.00 4.84
1086 1142 1.416401 AGCTCGTCCTCAAACAAAGGA 59.584 47.619 0.00 0.00 40.67 3.36
1435 1500 3.118555 ACGGCTTGCTAACATACCATGTA 60.119 43.478 0.00 0.00 44.07 2.29
1457 1531 5.436175 TGAACTTGATGACACAAAAGAGGA 58.564 37.500 0.00 0.00 0.00 3.71
1822 1942 1.587547 GATCTCCATGAAGGCGTTCC 58.412 55.000 16.06 0.00 37.29 3.62


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

AutoCloner maintained by Alex Coulton.