Multiple sequence alignment - TraesCS3D01G489900

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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 TraesCS3D01G489900 chr3D 100.000 3211 0 0 1 3211 584274527 584271317 0.000000e+00 5930.0
1 TraesCS3D01G489900 chr3D 92.541 1153 65 10 1656 2791 208124964 208126112 0.000000e+00 1633.0
2 TraesCS3D01G489900 chr3D 90.520 538 28 10 290 804 530609258 530608721 0.000000e+00 689.0
3 TraesCS3D01G489900 chr3D 96.403 417 15 0 2792 3208 253890126 253890542 0.000000e+00 688.0
4 TraesCS3D01G489900 chr3D 92.289 402 22 6 295 695 596563483 596563090 2.160000e-156 562.0
5 TraesCS3D01G489900 chr3D 95.973 298 10 2 1 298 439784961 439784666 1.730000e-132 483.0
6 TraesCS3D01G489900 chr2D 95.462 1719 67 4 843 2554 621299235 621300949 0.000000e+00 2732.0
7 TraesCS3D01G489900 chr2D 94.630 1434 62 6 808 2230 95307537 95308966 0.000000e+00 2207.0
8 TraesCS3D01G489900 chr2D 93.180 1129 61 6 1679 2791 77284208 77285336 0.000000e+00 1644.0
9 TraesCS3D01G489900 chr2D 96.172 418 16 0 2792 3209 305479672 305480089 0.000000e+00 684.0
10 TraesCS3D01G489900 chr2D 94.444 324 15 2 373 696 503931408 503931088 2.220000e-136 496.0
11 TraesCS3D01G489900 chr2D 95.370 216 10 0 589 804 95307215 95307430 8.530000e-91 344.0
12 TraesCS3D01G489900 chr1B 92.344 1907 111 18 918 2791 600249409 600251313 0.000000e+00 2680.0
13 TraesCS3D01G489900 chr1B 88.235 408 33 10 290 695 577602178 577601784 1.040000e-129 473.0
14 TraesCS3D01G489900 chr5D 95.524 1430 55 3 806 2228 277324061 277325488 0.000000e+00 2278.0
15 TraesCS3D01G489900 chr5D 94.479 1431 67 3 806 2229 506927169 506925744 0.000000e+00 2194.0
16 TraesCS3D01G489900 chr5D 92.883 1124 69 2 1679 2791 438884305 438883182 0.000000e+00 1622.0
17 TraesCS3D01G489900 chr5D 92.366 524 31 5 287 804 550354619 550355139 0.000000e+00 737.0
18 TraesCS3D01G489900 chr5D 96.411 418 15 0 2792 3209 261373193 261372776 0.000000e+00 689.0
19 TraesCS3D01G489900 chr5D 89.493 533 22 14 295 793 506927916 506927384 0.000000e+00 643.0
20 TraesCS3D01G489900 chr5D 90.496 484 23 12 339 804 328740114 328739636 4.550000e-173 617.0
21 TraesCS3D01G489900 chr5D 88.376 542 24 16 290 804 475487668 475487139 1.640000e-172 616.0
22 TraesCS3D01G489900 chr5D 88.235 544 21 8 290 804 277313314 277313843 7.620000e-171 610.0
23 TraesCS3D01G489900 chr5D 96.897 290 8 1 1 290 87923887 87923599 4.820000e-133 484.0
24 TraesCS3D01G489900 chr5D 95.638 298 12 1 1 298 320917877 320917581 8.060000e-131 477.0
25 TraesCS3D01G489900 chr5D 96.194 289 11 0 1 289 252308688 252308976 1.040000e-129 473.0
26 TraesCS3D01G489900 chr5D 86.557 424 28 14 290 695 392067388 392066976 1.060000e-119 440.0
27 TraesCS3D01G489900 chr7D 93.711 1431 81 3 806 2228 344498612 344497183 0.000000e+00 2135.0
28 TraesCS3D01G489900 chr7D 92.876 1151 67 6 1656 2791 132580255 132579105 0.000000e+00 1657.0
29 TraesCS3D01G489900 chr7D 95.418 982 30 6 844 1818 70084990 70085963 0.000000e+00 1550.0
30 TraesCS3D01G489900 chr7D 96.172 418 16 0 2792 3209 163849801 163850218 0.000000e+00 684.0
31 TraesCS3D01G489900 chr7D 89.981 529 24 5 290 804 344499221 344498708 0.000000e+00 656.0
32 TraesCS3D01G489900 chr7D 89.168 517 23 13 313 804 563472652 563472144 5.890000e-172 614.0
33 TraesCS3D01G489900 chr4B 91.833 1506 99 9 844 2342 134397819 134396331 0.000000e+00 2078.0
34 TraesCS3D01G489900 chr7B 93.508 1371 78 2 1437 2796 645574607 645573237 0.000000e+00 2028.0
35 TraesCS3D01G489900 chr5B 93.567 1368 74 5 1437 2792 108851457 108850092 0.000000e+00 2026.0
36 TraesCS3D01G489900 chr5B 93.563 1367 75 4 1437 2791 10028216 10026851 0.000000e+00 2025.0
37 TraesCS3D01G489900 chr5B 89.203 389 27 10 311 695 560838563 560838186 3.750000e-129 472.0
38 TraesCS3D01G489900 chr4A 93.285 1370 74 8 1437 2791 677157968 677156602 0.000000e+00 2004.0
39 TraesCS3D01G489900 chr7A 94.489 1234 54 6 899 2126 8981525 8980300 0.000000e+00 1890.0
40 TraesCS3D01G489900 chr7A 93.732 351 17 2 295 643 702399053 702398706 3.670000e-144 521.0
41 TraesCS3D01G489900 chr6D 94.324 1057 48 4 806 1855 166340691 166339640 0.000000e+00 1609.0
42 TraesCS3D01G489900 chr6D 91.650 515 36 7 295 804 166341456 166340944 0.000000e+00 706.0
43 TraesCS3D01G489900 chr6D 90.421 522 24 13 292 804 333952775 333952271 0.000000e+00 664.0
44 TraesCS3D01G489900 chr6D 92.457 464 22 10 346 804 324889097 324888642 0.000000e+00 651.0
45 TraesCS3D01G489900 chr6D 97.232 289 7 1 1 289 152872594 152872881 3.720000e-134 488.0
46 TraesCS3D01G489900 chr6D 96.907 291 7 2 1 290 131714049 131714338 1.340000e-133 486.0
47 TraesCS3D01G489900 chr6D 95.318 299 14 0 290 588 5518669 5518967 2.900000e-130 475.0
48 TraesCS3D01G489900 chr6D 96.194 289 11 0 1 289 249548860 249548572 1.040000e-129 473.0
49 TraesCS3D01G489900 chr6D 95.593 295 11 2 1 295 89588221 89587929 3.750000e-129 472.0
50 TraesCS3D01G489900 chr6D 94.231 312 13 4 1 312 99260529 99260835 3.750000e-129 472.0
51 TraesCS3D01G489900 chr6D 95.593 295 12 1 4 298 289234422 289234129 3.750000e-129 472.0
52 TraesCS3D01G489900 chr6D 95.302 298 13 1 1 298 450760443 450760147 3.750000e-129 472.0
53 TraesCS3D01G489900 chr6D 96.167 287 10 1 373 658 458397692 458397978 4.850000e-128 468.0
54 TraesCS3D01G489900 chr6D 95.614 228 9 1 578 804 5530750 5530977 6.550000e-97 364.0
55 TraesCS3D01G489900 chr6D 94.393 107 5 1 699 804 452533846 452533952 2.560000e-36 163.0
56 TraesCS3D01G489900 chr6B 95.132 986 39 3 840 1818 645808491 645807508 0.000000e+00 1546.0
57 TraesCS3D01G489900 chr6B 97.297 37 1 0 806 842 591567526 591567562 2.670000e-06 63.9
58 TraesCS3D01G489900 chr4D 93.729 590 27 3 1656 2237 152900999 152901586 0.000000e+00 876.0
59 TraesCS3D01G489900 chr4D 91.182 533 16 7 290 804 92666271 92666790 0.000000e+00 695.0
60 TraesCS3D01G489900 chr4D 95.962 421 16 1 2792 3211 93818076 93817656 0.000000e+00 682.0
61 TraesCS3D01G489900 chr4D 95.952 420 17 0 2792 3211 324763131 324763550 0.000000e+00 682.0
62 TraesCS3D01G489900 chr4D 88.504 548 57 6 2665 3209 496128067 496127523 0.000000e+00 658.0
63 TraesCS3D01G489900 chr4D 91.220 410 17 4 290 681 494799252 494799660 1.010000e-149 540.0
64 TraesCS3D01G489900 chr4D 91.935 372 18 6 295 655 61177186 61176816 7.950000e-141 510.0
65 TraesCS3D01G489900 chr4D 95.638 298 12 1 1 298 294997866 294997570 8.060000e-131 477.0
66 TraesCS3D01G489900 chr4D 96.194 289 10 1 1 289 110098927 110099214 3.750000e-129 472.0
67 TraesCS3D01G489900 chr4D 94.212 311 12 6 1 310 57642285 57641980 1.350000e-128 470.0
68 TraesCS3D01G489900 chr4D 95.848 289 11 1 1 289 392216426 392216713 1.740000e-127 466.0
69 TraesCS3D01G489900 chr4D 95.533 291 12 1 1 291 380062344 380062055 6.270000e-127 464.0
70 TraesCS3D01G489900 chr4D 95.533 291 12 1 1 291 441591822 441592111 6.270000e-127 464.0
71 TraesCS3D01G489900 chr4D 94.949 297 12 3 2 298 392200323 392200616 2.260000e-126 462.0
72 TraesCS3D01G489900 chr4D 95.517 290 12 1 1 290 445151959 445152247 2.260000e-126 462.0
73 TraesCS3D01G489900 chr4D 94.631 298 15 1 1 298 72978115 72977819 8.120000e-126 460.0
74 TraesCS3D01G489900 chr4D 95.502 289 12 1 1 289 81264703 81264990 8.120000e-126 460.0
75 TraesCS3D01G489900 chr4D 94.631 298 14 2 1 298 287362706 287362411 8.120000e-126 460.0
76 TraesCS3D01G489900 chr4D 94.915 295 13 2 4 298 420679462 420679170 8.120000e-126 460.0
77 TraesCS3D01G489900 chr4D 87.990 408 24 10 295 695 166791104 166791493 2.920000e-125 459.0
78 TraesCS3D01G489900 chr4D 88.770 374 19 5 290 648 509564108 509564473 1.370000e-118 436.0
79 TraesCS3D01G489900 chr4D 93.238 281 13 5 373 647 113890776 113890496 2.980000e-110 409.0
80 TraesCS3D01G489900 chr4D 91.468 293 18 6 373 658 66653891 66654183 2.320000e-106 396.0
81 TraesCS3D01G489900 chr4D 84.750 400 26 15 296 695 342257003 342257367 5.060000e-98 368.0
82 TraesCS3D01G489900 chr4D 93.452 168 7 3 570 734 509564531 509564697 2.470000e-61 246.0
83 TraesCS3D01G489900 chr4D 82.791 215 21 13 598 804 195374201 195374407 9.150000e-41 178.0
84 TraesCS3D01G489900 chr4D 94.340 106 6 0 699 804 465615149 465615254 2.560000e-36 163.0
85 TraesCS3D01G489900 chr4D 97.101 69 1 1 736 804 55004629 55004562 7.280000e-22 115.0
86 TraesCS3D01G489900 chr4D 97.101 69 1 1 736 804 65557811 65557878 7.280000e-22 115.0
87 TraesCS3D01G489900 chr4D 95.652 69 1 2 736 804 113890445 113890379 3.390000e-20 110.0
88 TraesCS3D01G489900 chr4D 83.929 112 11 7 1654 1762 3263187 3263080 2.040000e-17 100.0
89 TraesCS3D01G489900 chr1D 96.651 418 14 0 2792 3209 153788063 153787646 0.000000e+00 695.0
90 TraesCS3D01G489900 chr1D 95.630 389 13 4 295 681 198932907 198933293 3.520000e-174 621.0
91 TraesCS3D01G489900 chr1D 90.887 406 17 10 290 695 283585022 283584637 7.890000e-146 527.0
92 TraesCS3D01G489900 chr1D 91.854 356 21 7 295 643 418185187 418184833 1.040000e-134 490.0
93 TraesCS3D01G489900 chr1D 96.540 289 9 1 1 289 308416446 308416733 8.060000e-131 477.0
94 TraesCS3D01G489900 chr1D 95.302 298 12 2 1 298 104247518 104247223 3.750000e-129 472.0
95 TraesCS3D01G489900 chr1D 96.194 289 10 1 1 289 308409841 308410128 3.750000e-129 472.0
96 TraesCS3D01G489900 chr1D 80.616 552 66 31 290 804 10975974 10976521 3.880000e-104 388.0
97 TraesCS3D01G489900 chr1D 95.625 160 7 0 645 804 418184883 418184724 1.140000e-64 257.0
98 TraesCS3D01G489900 chr1D 75.992 479 58 35 352 804 493118594 493118147 9.090000e-46 195.0
99 TraesCS3D01G489900 chr6A 85.070 643 77 15 2576 3211 270721715 270722345 3.490000e-179 638.0
100 TraesCS3D01G489900 chr3A 90.984 488 19 9 333 804 125067921 125068399 4.520000e-178 634.0
101 TraesCS3D01G489900 chr3B 91.762 437 21 11 299 734 2414222 2413800 7.670000e-166 593.0
102 TraesCS3D01G489900 chr1A 88.161 473 41 11 340 804 493339223 493339688 1.680000e-152 549.0
103 TraesCS3D01G489900 chr1A 95.638 298 12 1 1 298 533658785 533658489 8.060000e-131 477.0
104 TraesCS3D01G489900 chr1A 91.729 133 10 1 671 803 383163535 383163404 1.970000e-42 183.0
105 TraesCS3D01G489900 chrUn 91.714 350 12 7 318 658 19935916 19936257 1.350000e-128 470.0
106 TraesCS3D01G489900 chrUn 87.586 435 17 8 290 695 341515484 341515910 1.350000e-128 470.0
107 TraesCS3D01G489900 chrUn 87.952 415 26 11 295 695 68600714 68600310 4.850000e-128 468.0
108 TraesCS3D01G489900 chrUn 95.862 290 11 1 1 290 73849115 73848827 4.850000e-128 468.0
109 TraesCS3D01G489900 chrUn 87.356 435 18 8 290 695 338376778 338376352 6.270000e-127 464.0
110 TraesCS3D01G489900 chrUn 95.423 284 11 2 6 289 73865011 73864730 4.880000e-123 451.0
111 TraesCS3D01G489900 chrUn 94.502 291 15 1 1 291 110815463 110815174 6.320000e-122 448.0
112 TraesCS3D01G489900 chrUn 93.898 295 16 2 3 297 26116328 26116036 8.170000e-121 444.0
113 TraesCS3D01G489900 chrUn 94.464 289 15 1 1 289 91411122 91411409 8.170000e-121 444.0
114 TraesCS3D01G489900 chrUn 88.325 394 15 10 325 695 131959482 131959097 8.170000e-121 444.0
115 TraesCS3D01G489900 chrUn 94.158 291 15 2 1 291 137717003 137717291 2.940000e-120 442.0
116 TraesCS3D01G489900 chrUn 89.373 367 16 10 295 646 97186109 97186467 1.060000e-119 440.0
117 TraesCS3D01G489900 chrUn 94.118 289 17 0 1 289 354145585 354145297 1.060000e-119 440.0
118 TraesCS3D01G489900 chrUn 94.118 289 17 0 1 289 354147787 354147499 1.060000e-119 440.0
119 TraesCS3D01G489900 chrUn 94.118 289 17 0 1 289 461728211 461727923 1.060000e-119 440.0
120 TraesCS3D01G489900 chrUn 93.311 299 17 3 1 298 365790995 365790699 3.800000e-119 438.0
121 TraesCS3D01G489900 chrUn 93.266 297 18 2 1 297 144233638 144233344 1.370000e-118 436.0
122 TraesCS3D01G489900 chrUn 85.577 416 40 11 293 695 34643452 34643860 4.950000e-113 418.0
123 TraesCS3D01G489900 chrUn 88.451 355 29 9 300 648 41853602 41853950 4.950000e-113 418.0
124 TraesCS3D01G489900 chrUn 88.352 352 18 8 295 631 97266448 97266791 4.990000e-108 401.0
125 TraesCS3D01G489900 chrUn 84.597 422 42 17 399 804 293979502 293979916 6.450000e-107 398.0
126 TraesCS3D01G489900 chrUn 83.623 403 22 7 293 695 343934206 343933848 3.970000e-89 339.0
127 TraesCS3D01G489900 chrUn 85.274 292 10 8 379 667 96873141 96872880 1.470000e-68 270.0
128 TraesCS3D01G489900 chrUn 92.593 162 10 1 531 692 23488767 23488926 6.930000e-57 231.0
129 TraesCS3D01G489900 chrUn 90.230 174 6 4 531 695 295271266 295271095 1.940000e-52 217.0
130 TraesCS3D01G489900 chrUn 89.714 175 7 5 531 696 142562671 142562843 2.510000e-51 213.0
131 TraesCS3D01G489900 chrUn 89.655 174 7 4 531 695 23488617 23488788 9.020000e-51 211.0
132 TraesCS3D01G489900 chrUn 92.568 148 9 1 545 692 23488831 23488976 9.020000e-51 211.0
133 TraesCS3D01G489900 chrUn 89.655 174 7 5 531 695 130266781 130266952 9.020000e-51 211.0
134 TraesCS3D01G489900 chrUn 92.053 151 10 1 545 695 130266854 130267002 9.020000e-51 211.0
135 TraesCS3D01G489900 chrUn 89.697 165 14 2 531 695 187221368 187221207 1.170000e-49 207.0
136 TraesCS3D01G489900 chrUn 82.870 216 18 12 595 804 19936135 19936337 3.290000e-40 176.0
137 TraesCS3D01G489900 chrUn 79.538 303 16 25 517 804 30250249 30250520 1.180000e-39 174.0
138 TraesCS3D01G489900 chrUn 80.315 254 23 17 572 804 111666270 111666023 1.980000e-37 167.0


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 TraesCS3D01G489900 chr3D 584271317 584274527 3210 True 5930.0 5930 100.000 1 3211 1 chr3D.!!$R3 3210
1 TraesCS3D01G489900 chr3D 208124964 208126112 1148 False 1633.0 1633 92.541 1656 2791 1 chr3D.!!$F1 1135
2 TraesCS3D01G489900 chr3D 530608721 530609258 537 True 689.0 689 90.520 290 804 1 chr3D.!!$R2 514
3 TraesCS3D01G489900 chr2D 621299235 621300949 1714 False 2732.0 2732 95.462 843 2554 1 chr2D.!!$F3 1711
4 TraesCS3D01G489900 chr2D 77284208 77285336 1128 False 1644.0 1644 93.180 1679 2791 1 chr2D.!!$F1 1112
5 TraesCS3D01G489900 chr2D 95307215 95308966 1751 False 1275.5 2207 95.000 589 2230 2 chr2D.!!$F4 1641
6 TraesCS3D01G489900 chr1B 600249409 600251313 1904 False 2680.0 2680 92.344 918 2791 1 chr1B.!!$F1 1873
7 TraesCS3D01G489900 chr5D 277324061 277325488 1427 False 2278.0 2278 95.524 806 2228 1 chr5D.!!$F3 1422
8 TraesCS3D01G489900 chr5D 438883182 438884305 1123 True 1622.0 1622 92.883 1679 2791 1 chr5D.!!$R6 1112
9 TraesCS3D01G489900 chr5D 506925744 506927916 2172 True 1418.5 2194 91.986 295 2229 2 chr5D.!!$R8 1934
10 TraesCS3D01G489900 chr5D 550354619 550355139 520 False 737.0 737 92.366 287 804 1 chr5D.!!$F4 517
11 TraesCS3D01G489900 chr5D 475487139 475487668 529 True 616.0 616 88.376 290 804 1 chr5D.!!$R7 514
12 TraesCS3D01G489900 chr5D 277313314 277313843 529 False 610.0 610 88.235 290 804 1 chr5D.!!$F2 514
13 TraesCS3D01G489900 chr7D 132579105 132580255 1150 True 1657.0 1657 92.876 1656 2791 1 chr7D.!!$R1 1135
14 TraesCS3D01G489900 chr7D 70084990 70085963 973 False 1550.0 1550 95.418 844 1818 1 chr7D.!!$F1 974
15 TraesCS3D01G489900 chr7D 344497183 344499221 2038 True 1395.5 2135 91.846 290 2228 2 chr7D.!!$R3 1938
16 TraesCS3D01G489900 chr7D 563472144 563472652 508 True 614.0 614 89.168 313 804 1 chr7D.!!$R2 491
17 TraesCS3D01G489900 chr4B 134396331 134397819 1488 True 2078.0 2078 91.833 844 2342 1 chr4B.!!$R1 1498
18 TraesCS3D01G489900 chr7B 645573237 645574607 1370 True 2028.0 2028 93.508 1437 2796 1 chr7B.!!$R1 1359
19 TraesCS3D01G489900 chr5B 108850092 108851457 1365 True 2026.0 2026 93.567 1437 2792 1 chr5B.!!$R2 1355
20 TraesCS3D01G489900 chr5B 10026851 10028216 1365 True 2025.0 2025 93.563 1437 2791 1 chr5B.!!$R1 1354
21 TraesCS3D01G489900 chr4A 677156602 677157968 1366 True 2004.0 2004 93.285 1437 2791 1 chr4A.!!$R1 1354
22 TraesCS3D01G489900 chr7A 8980300 8981525 1225 True 1890.0 1890 94.489 899 2126 1 chr7A.!!$R1 1227
23 TraesCS3D01G489900 chr6D 166339640 166341456 1816 True 1157.5 1609 92.987 295 1855 2 chr6D.!!$R7 1560
24 TraesCS3D01G489900 chr6D 333952271 333952775 504 True 664.0 664 90.421 292 804 1 chr6D.!!$R5 512
25 TraesCS3D01G489900 chr6B 645807508 645808491 983 True 1546.0 1546 95.132 840 1818 1 chr6B.!!$R1 978
26 TraesCS3D01G489900 chr4D 152900999 152901586 587 False 876.0 876 93.729 1656 2237 1 chr4D.!!$F6 581
27 TraesCS3D01G489900 chr4D 92666271 92666790 519 False 695.0 695 91.182 290 804 1 chr4D.!!$F4 514
28 TraesCS3D01G489900 chr4D 496127523 496128067 544 True 658.0 658 88.504 2665 3209 1 chr4D.!!$R11 544
29 TraesCS3D01G489900 chr4D 509564108 509564697 589 False 341.0 436 91.111 290 734 2 chr4D.!!$F17 444
30 TraesCS3D01G489900 chr1D 10975974 10976521 547 False 388.0 388 80.616 290 804 1 chr1D.!!$F1 514
31 TraesCS3D01G489900 chr6A 270721715 270722345 630 False 638.0 638 85.070 2576 3211 1 chr6A.!!$F1 635
32 TraesCS3D01G489900 chrUn 354145297 354147787 2490 True 440.0 440 94.118 1 289 2 chrUn.!!$R16 288

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
37 38 0.252881 ACTCTTCTGGCCCATCTCCA 60.253 55.000 0.00 0.0 0.00 3.86 F
40 41 1.213678 TCTTCTGGCCCATCTCCAATG 59.786 52.381 0.00 0.0 32.41 2.82 F
90 91 1.808411 TCTCCGTGAAATTGCAGGTC 58.192 50.000 5.43 0.0 0.00 3.85 F
2128 3957 1.740025 CCTCGTTGGCAAGAATCTTCC 59.260 52.381 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1191 2590 0.739813 GCATGGGACGGTCTGTGTAC 60.740 60.000 8.23 0.0 0.0 2.90 R
2037 3780 1.001181 GCGGTAAGTACAGGTGGTGAA 59.999 52.381 0.00 0.0 0.0 3.18 R
2172 4002 2.036862 CGATCATCATCCTCAAGCCTGA 59.963 50.000 0.00 0.0 0.0 3.86 R
3050 4886 0.313043 CAAAGTGTGCAAGCTCCAGG 59.687 55.000 0.00 0.0 0.0 4.45 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
37 38 0.252881 ACTCTTCTGGCCCATCTCCA 60.253 55.000 0.00 0.00 0.00 3.86
40 41 1.213678 TCTTCTGGCCCATCTCCAATG 59.786 52.381 0.00 0.00 32.41 2.82
76 77 5.880332 TCTTCTGGTCCAAAAATAATCTCCG 59.120 40.000 0.00 0.00 0.00 4.63
81 82 5.770663 TGGTCCAAAAATAATCTCCGTGAAA 59.229 36.000 0.00 0.00 0.00 2.69
84 85 7.275560 GGTCCAAAAATAATCTCCGTGAAATTG 59.724 37.037 0.00 0.00 0.00 2.32
90 91 1.808411 TCTCCGTGAAATTGCAGGTC 58.192 50.000 5.43 0.00 0.00 3.85
385 479 3.674050 TACCACCCTCCTCCTCCGC 62.674 68.421 0.00 0.00 0.00 5.54
970 2295 2.831526 TCATTCCTGTGAAGTGGATCGA 59.168 45.455 0.00 0.00 33.05 3.59
1250 2652 2.598565 ACAAGCTGACAGGAGACACTA 58.401 47.619 4.26 0.00 0.00 2.74
1324 2756 2.175878 ATATGTCGCAGATTGGAGGC 57.824 50.000 0.00 0.00 40.67 4.70
1329 2761 4.863707 GCAGATTGGAGGCGATGA 57.136 55.556 0.00 0.00 0.00 2.92
1459 3149 6.990939 TGGAAGATGATGAAGATGATGAAGAC 59.009 38.462 0.00 0.00 0.00 3.01
1556 3282 3.071206 TGAGCGAGGAGGAGGTGC 61.071 66.667 0.00 0.00 0.00 5.01
1659 3385 6.033937 GTCGATCGACATGATATGGTATGTTG 59.966 42.308 36.61 0.00 44.02 3.33
1860 3603 7.866393 AGTACAAATGTGTAGTACTGTGTCTTC 59.134 37.037 5.39 0.00 44.77 2.87
1865 3608 6.013842 TGTGTAGTACTGTGTCTTCTGATG 57.986 41.667 5.39 0.00 0.00 3.07
2128 3957 1.740025 CCTCGTTGGCAAGAATCTTCC 59.260 52.381 0.00 0.00 0.00 3.46
2166 3996 7.016661 CCATCCTAATTACTATCAGGAACACCT 59.983 40.741 0.00 0.00 40.48 4.00
2199 4029 4.793028 GCTTGAGGATGATGATCGTCGTTA 60.793 45.833 10.97 4.74 43.57 3.18
2230 4060 6.330278 TCTAGAACTACATATGTGTGTGTGC 58.670 40.000 18.81 10.06 39.39 4.57
2266 4096 7.668525 AGAACTACATATGATGATCGTCGTA 57.331 36.000 17.23 17.23 0.00 3.43
2409 4241 3.947612 ATCTAGTACTCCCTCCGTTCA 57.052 47.619 0.00 0.00 0.00 3.18
2620 4456 3.492829 GCTAGGAAACCGCTACAGCTAAT 60.493 47.826 0.00 0.00 39.32 1.73
2768 4604 2.396157 CCTCAAAACCCGCGCTACC 61.396 63.158 5.56 0.00 0.00 3.18
2830 4666 5.534654 TCACCGAGGTCTTTCATTGAAAAAT 59.465 36.000 12.62 0.14 30.84 1.82
2884 4720 9.971922 CCAGAAATTCTGTATTATTTCCAATCC 57.028 33.333 20.18 0.00 42.80 3.01
3077 4913 2.479389 GCTTGCACACTTTGTTAGCACA 60.479 45.455 0.00 0.00 35.21 4.57
3086 4922 7.370383 CACACTTTGTTAGCACATTTAGGATT 58.630 34.615 0.00 0.00 31.06 3.01
3119 4955 4.037222 TCTGGTGGGATCATAAGCAACTA 58.963 43.478 0.00 0.00 0.00 2.24
3122 4958 5.765510 TGGTGGGATCATAAGCAACTATTT 58.234 37.500 0.00 0.00 0.00 1.40
3190 5026 8.550376 GCCAAATTTCATAATCATAAAATGCGT 58.450 29.630 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.043940 AGATGGGCCAGAAGAGTCCT 59.956 55.000 13.78 0.00 0.00 3.85
37 38 0.678048 GAAGAAGCCCACGGAGCATT 60.678 55.000 0.00 0.00 0.00 3.56
40 41 1.743252 CAGAAGAAGCCCACGGAGC 60.743 63.158 0.00 0.00 0.00 4.70
81 82 5.707169 ACGGAGTCCAATTGACCTGCAAT 62.707 47.826 10.49 0.00 44.01 3.56
84 85 0.321653 ACGGAGTCCAATTGACCTGC 60.322 55.000 10.49 6.40 45.68 4.85
90 91 3.726291 AAACCAAACGGAGTCCAATTG 57.274 42.857 10.49 12.80 45.00 2.32
157 158 5.839606 ACTAACCTATTAACCTAGAGCCCAG 59.160 44.000 0.00 0.00 0.00 4.45
278 279 1.688627 GGGGGAGGACTGATACGTCTT 60.689 57.143 0.00 0.00 34.38 3.01
281 282 1.455217 CGGGGGAGGACTGATACGT 60.455 63.158 0.00 0.00 0.00 3.57
282 283 2.857744 GCGGGGGAGGACTGATACG 61.858 68.421 0.00 0.00 0.00 3.06
337 413 0.612174 CAAGGAGGAGGAGGTGACGA 60.612 60.000 0.00 0.00 0.00 4.20
385 479 2.041405 GGAGGAGTGGAGGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
622 1224 9.530633 AACTAAATCAACTAGCCTACTAAATCG 57.469 33.333 0.00 0.00 0.00 3.34
697 1307 2.151202 GGTCGTGCCAAATCTTCAGAA 58.849 47.619 0.00 0.00 37.17 3.02
951 2276 5.614324 TTATCGATCCACTTCACAGGAAT 57.386 39.130 0.00 0.00 37.48 3.01
970 2295 6.699575 AAAGCAATACGAGCAAAGGATTAT 57.300 33.333 0.00 0.00 0.00 1.28
1191 2590 0.739813 GCATGGGACGGTCTGTGTAC 60.740 60.000 8.23 0.00 0.00 2.90
1250 2652 1.064166 CCCAGGAGCCTCAAATGTCAT 60.064 52.381 0.00 0.00 0.00 3.06
1324 2756 1.724582 GGAAACGGGCCCATTCATCG 61.725 60.000 29.09 14.97 0.00 3.84
1329 2761 2.045340 CGAGGAAACGGGCCCATT 60.045 61.111 24.92 16.71 0.00 3.16
1459 3149 4.039730 AGTGGGTCCTCATTATCTTCATCG 59.960 45.833 0.00 0.00 0.00 3.84
1556 3282 3.502211 GGAATTATGTCCCATAGGTTGCG 59.498 47.826 0.00 0.00 0.00 4.85
1659 3385 9.169468 CATCGGATAATTTGCATTTGTAAGTAC 57.831 33.333 0.00 0.00 0.00 2.73
1725 3462 6.584184 CGGACTCTACACTAAAGCATATCATG 59.416 42.308 0.00 0.00 0.00 3.07
1826 3565 6.985188 ACTACACATTTGTACTAAGCATGG 57.015 37.500 0.00 0.00 37.15 3.66
1894 3637 3.486375 CCTCGCACATACTCTTGCAAATG 60.486 47.826 0.00 3.82 38.76 2.32
2037 3780 1.001181 GCGGTAAGTACAGGTGGTGAA 59.999 52.381 0.00 0.00 0.00 3.18
2172 4002 2.036862 CGATCATCATCCTCAAGCCTGA 59.963 50.000 0.00 0.00 0.00 3.86
2288 4118 5.597235 GATGATATTGACGACGATCATCG 57.403 43.478 10.03 10.03 42.70 3.84
2409 4241 6.849588 ACTAAAACCACGACGAGTAATTTT 57.150 33.333 0.00 3.46 34.99 1.82
2559 4392 3.773560 TCTTTCATCATTCCCCCGTTTT 58.226 40.909 0.00 0.00 0.00 2.43
2568 4404 7.463913 GCGCTACTGCTATATCTTTCATCATTC 60.464 40.741 0.00 0.00 36.97 2.67
2716 4552 2.412065 CGGGTAGTCGCGCTACTAATAC 60.412 54.545 27.56 13.15 46.99 1.89
2873 4709 8.003629 TGGATGACATATTGTGGATTGGAAATA 58.996 33.333 0.00 0.00 0.00 1.40
3050 4886 0.313043 CAAAGTGTGCAAGCTCCAGG 59.687 55.000 0.00 0.00 0.00 4.45
3077 4913 7.232118 CCAGAAGGTTTTGTCAATCCTAAAT 57.768 36.000 9.35 0.00 31.69 1.40
3130 4966 7.395772 TGTCAAAACTGCATTCCTTAATGGATA 59.604 33.333 0.00 0.00 45.68 2.59


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

AutoCloner maintained by Alex Coulton.