Multiple sequence alignment - TraesCS6A01G222500

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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 TraesCS6A01G222500 chr6A 100.000 3096 0 0 1 3096 416439734 416442829 0.000000e+00 5718.0
1 TraesCS6A01G222500 chr6A 97.999 3098 59 2 1 3096 416472674 416475770 0.000000e+00 5374.0
2 TraesCS6A01G222500 chr6A 93.414 1412 93 0 1 1412 416513966 416515377 0.000000e+00 2093.0
3 TraesCS6A01G222500 chr6A 97.183 923 25 1 1407 2328 416535572 416536494 0.000000e+00 1559.0
4 TraesCS6A01G222500 chr6A 86.036 1067 130 16 2040 3096 214471448 214470391 0.000000e+00 1127.0
5 TraesCS6A01G222500 chr6A 85.688 1069 135 14 2040 3096 347454608 347455670 0.000000e+00 1110.0
6 TraesCS6A01G222500 chr6A 83.671 692 77 27 2 683 400192082 400191417 1.220000e-173 619.0
7 TraesCS6A01G222500 chr6A 81.481 675 92 26 14 672 310227976 310228633 9.840000e-145 523.0
8 TraesCS6A01G222500 chr6A 81.305 567 77 23 20 565 375680896 375681454 1.710000e-117 433.0
9 TraesCS6A01G222500 chr6A 91.613 310 19 7 1215 1520 258910721 258910415 3.690000e-114 422.0
10 TraesCS6A01G222500 chr6A 90.159 315 29 2 362 676 159011617 159011305 2.870000e-110 409.0
11 TraesCS6A01G222500 chr6A 86.436 376 47 4 562 933 336814914 336815289 2.870000e-110 409.0
12 TraesCS6A01G222500 chr6A 90.032 311 23 6 1215 1520 31087205 31086898 2.240000e-106 396.0
13 TraesCS6A01G222500 chr6A 91.096 292 19 7 1215 1502 294491716 294492004 3.740000e-104 388.0
14 TraesCS6A01G222500 chr6A 85.450 378 40 14 3 374 89345700 89346068 2.250000e-101 379.0
15 TraesCS6A01G222500 chr6A 85.185 378 41 14 3 374 89354281 89354649 1.050000e-99 374.0
16 TraesCS6A01G222500 chr6A 79.928 558 69 24 2 527 155186460 155187006 1.360000e-98 370.0
17 TraesCS6A01G222500 chr6A 83.092 414 53 12 1 410 108455329 108455729 8.160000e-96 361.0
18 TraesCS6A01G222500 chr6A 83.005 406 56 12 1 402 548518967 548518571 3.800000e-94 355.0
19 TraesCS6A01G222500 chr6A 88.889 162 14 4 1223 1382 612403969 612404128 2.440000e-46 196.0
20 TraesCS6A01G222500 chr6A 90.000 130 10 3 1254 1382 612412246 612412373 6.870000e-37 165.0
21 TraesCS6A01G222500 chr6A 96.053 76 2 1 1067 1141 31087263 31087188 4.190000e-24 122.0
22 TraesCS6A01G222500 chr6A 97.183 71 2 0 1066 1136 294491657 294491727 1.510000e-23 121.0
23 TraesCS6A01G222500 chr6A 98.529 68 1 0 1069 1136 608766324 608766391 1.510000e-23 121.0
24 TraesCS6A01G222500 chr6A 96.923 65 2 0 1508 1572 280472004 280471940 3.260000e-20 110.0
25 TraesCS6A01G222500 chr6A 94.828 58 1 2 1528 1583 142413236 142413293 4.250000e-14 89.8
26 TraesCS6A01G222500 chr6A 90.000 70 5 2 1528 1595 238165423 238165354 4.250000e-14 89.8
27 TraesCS6A01G222500 chr6A 95.556 45 0 2 1569 1612 528223339 528223382 1.540000e-08 71.3
28 TraesCS6A01G222500 chr1A 92.013 1515 107 13 14 1520 341916719 341918227 0.000000e+00 2115.0
29 TraesCS6A01G222500 chr1A 91.281 1514 118 13 14 1520 341924715 341926221 0.000000e+00 2052.0
30 TraesCS6A01G222500 chr1A 86.926 1155 127 20 2 1139 432406735 432405588 0.000000e+00 1275.0
31 TraesCS6A01G222500 chr1A 86.056 502 61 9 436 933 423609138 423608642 5.880000e-147 531.0
32 TraesCS6A01G222500 chr1A 82.933 416 53 14 1 407 69756906 69757312 2.940000e-95 359.0
33 TraesCS6A01G222500 chr1A 83.204 387 50 14 2 380 177717469 177717848 1.060000e-89 340.0
34 TraesCS6A01G222500 chr1A 84.821 336 43 7 1 333 111816446 111816776 6.400000e-87 331.0
35 TraesCS6A01G222500 chr1A 81.687 415 60 12 3 410 473468758 473469163 6.400000e-87 331.0
36 TraesCS6A01G222500 chr1A 90.438 251 23 1 426 676 175075391 175075640 2.300000e-86 329.0
37 TraesCS6A01G222500 chr1A 84.639 332 44 7 2 330 369286251 369286578 1.070000e-84 324.0
38 TraesCS6A01G222500 chr1A 83.824 340 38 14 1 335 412245127 412245454 1.080000e-79 307.0
39 TraesCS6A01G222500 chr1A 80.241 415 66 12 3 410 473477240 473477645 6.490000e-77 298.0
40 TraesCS6A01G222500 chr1A 87.347 245 29 2 417 660 305522748 305522505 2.350000e-71 279.0
41 TraesCS6A01G222500 chr1A 90.964 166 15 0 362 527 64556351 64556516 1.120000e-54 224.0
42 TraesCS6A01G222500 chr1A 88.000 150 17 1 418 567 279689333 279689185 3.170000e-40 176.0
43 TraesCS6A01G222500 chr1A 89.051 137 15 0 543 679 556150857 556150721 1.480000e-38 171.0
44 TraesCS6A01G222500 chr1A 88.321 137 16 0 543 679 190169648 190169512 6.870000e-37 165.0
45 TraesCS6A01G222500 chr1A 84.663 163 23 1 543 705 227295203 227295363 8.880000e-36 161.0
46 TraesCS6A01G222500 chr1A 97.368 38 1 0 1387 1424 402127811 402127848 7.170000e-07 65.8
47 TraesCS6A01G222500 chr1A 97.368 38 1 0 1387 1424 402135494 402135531 7.170000e-07 65.8
48 TraesCS6A01G222500 chr1A 97.143 35 1 0 1388 1422 368459708 368459742 3.330000e-05 60.2
49 TraesCS6A01G222500 chr2A 90.585 1094 72 20 1475 2567 680598484 680599547 0.000000e+00 1421.0
50 TraesCS6A01G222500 chr2A 81.883 977 117 41 2 933 199949365 199950326 0.000000e+00 769.0
51 TraesCS6A01G222500 chr2A 83.953 511 59 20 1829 2332 549091482 549091976 4.670000e-128 468.0
52 TraesCS6A01G222500 chr2A 81.818 550 58 29 1 522 422856309 422855774 1.030000e-114 424.0
53 TraesCS6A01G222500 chr2A 80.603 531 72 25 13 522 258898040 258898560 6.260000e-102 381.0
54 TraesCS6A01G222500 chr2A 83.413 416 52 13 1 407 457328387 457327980 1.360000e-98 370.0
55 TraesCS6A01G222500 chr2A 86.036 222 22 8 1574 1792 587532950 587533165 2.400000e-56 230.0
56 TraesCS6A01G222500 chr2A 89.076 119 13 0 1125 1243 350270195 350270077 6.920000e-32 148.0
57 TraesCS6A01G222500 chr2A 88.136 118 9 3 1574 1688 587541043 587541158 5.390000e-28 135.0
58 TraesCS6A01G222500 chr2A 95.062 81 2 2 1508 1586 236923225 236923305 3.240000e-25 126.0
59 TraesCS6A01G222500 chr2A 94.805 77 3 1 1508 1583 236850003 236850079 5.420000e-23 119.0
60 TraesCS6A01G222500 chr3A 86.534 1255 139 21 1844 3086 355079973 355078737 0.000000e+00 1354.0
61 TraesCS6A01G222500 chr3A 88.010 1151 106 20 14 1139 369661486 369662629 0.000000e+00 1332.0
62 TraesCS6A01G222500 chr3A 86.471 1057 122 18 2040 3084 141874467 141873420 0.000000e+00 1140.0
63 TraesCS6A01G222500 chr3A 86.249 1069 121 21 2040 3096 47202047 47200993 0.000000e+00 1136.0
64 TraesCS6A01G222500 chr3A 85.500 1069 133 20 2040 3096 352851231 352850173 0.000000e+00 1096.0
65 TraesCS6A01G222500 chr3A 90.461 629 44 14 1613 2237 189086656 189087272 0.000000e+00 815.0
66 TraesCS6A01G222500 chr3A 86.676 713 58 26 1623 2329 451689866 451689185 0.000000e+00 756.0
67 TraesCS6A01G222500 chr3A 85.856 403 45 9 13 411 353634314 353634708 4.780000e-113 418.0
68 TraesCS6A01G222500 chr3A 91.262 309 21 6 1215 1520 329357565 329357870 1.720000e-112 416.0
69 TraesCS6A01G222500 chr3A 90.291 309 22 7 1215 1520 213764097 213764400 6.220000e-107 398.0
70 TraesCS6A01G222500 chr3A 84.746 413 45 17 3 408 222021213 222020812 6.220000e-107 398.0
71 TraesCS6A01G222500 chr4A 86.171 1063 129 17 2040 3094 266990938 266991990 0.000000e+00 1133.0
72 TraesCS6A01G222500 chr4A 82.135 862 120 23 97 933 297775534 297776386 0.000000e+00 708.0
73 TraesCS6A01G222500 chr4A 83.229 638 70 29 1 611 25155369 25154742 4.510000e-153 551.0
74 TraesCS6A01G222500 chr4A 91.563 403 22 5 1125 1520 485501905 485502302 2.100000e-151 545.0
75 TraesCS6A01G222500 chr4A 82.889 637 75 24 1 610 213040861 213040232 2.720000e-150 542.0
76 TraesCS6A01G222500 chr4A 83.016 630 74 22 2 606 213061817 213061196 9.770000e-150 540.0
77 TraesCS6A01G222500 chr4A 87.469 399 47 3 537 933 422962716 422963113 1.010000e-124 457.0
78 TraesCS6A01G222500 chr4A 87.437 398 49 1 537 933 422988202 422988599 1.010000e-124 457.0
79 TraesCS6A01G222500 chr4A 89.614 337 25 10 2 334 293466679 293466349 1.330000e-113 420.0
80 TraesCS6A01G222500 chr4A 89.968 309 25 6 1215 1520 283089861 283090166 8.050000e-106 394.0
81 TraesCS6A01G222500 chr4A 90.404 198 17 2 939 1135 222137229 222137033 3.060000e-65 259.0
82 TraesCS6A01G222500 chr4A 89.231 195 19 2 942 1135 222116856 222116663 3.080000e-60 243.0
83 TraesCS6A01G222500 chr5A 85.169 1126 142 17 1880 2993 132225609 132224497 0.000000e+00 1131.0
84 TraesCS6A01G222500 chr5A 88.604 781 73 10 1550 2328 97773688 97772922 0.000000e+00 935.0
85 TraesCS6A01G222500 chr5A 89.009 555 59 2 537 1089 454542607 454543161 0.000000e+00 686.0
86 TraesCS6A01G222500 chr7A 86.528 527 69 2 408 933 311959166 311959691 2.070000e-161 579.0
87 TraesCS6A01G222500 chr7A 90.584 308 22 6 1215 1520 312190147 312189845 4.810000e-108 401.0
88 TraesCS6A01G222500 chr7A 90.032 311 23 8 1215 1520 301046049 301046356 2.240000e-106 396.0
89 TraesCS6A01G222500 chr7A 89.899 198 18 2 939 1135 333945487 333945291 1.420000e-63 254.0
90 TraesCS6A01G222500 chr4D 80.440 409 55 17 14 402 205398867 205399270 3.910000e-74 289.0
91 TraesCS6A01G222500 chr4D 82.371 329 36 14 2 322 55524021 55524335 1.830000e-67 267.0
92 TraesCS6A01G222500 chr4D 78.641 412 58 20 12 414 276005517 276005127 2.380000e-61 246.0
93 TraesCS6A01G222500 chr4D 79.943 349 46 18 2 335 232249362 232249023 5.160000e-58 235.0
94 TraesCS6A01G222500 chr4D 75.379 528 72 35 13 521 225512611 225512123 5.240000e-48 202.0
95 TraesCS6A01G222500 chr4D 90.426 94 9 0 560 653 145377677 145377770 1.170000e-24 124.0
96 TraesCS6A01G222500 chr4D 88.660 97 6 3 1429 1520 191600021 191599925 2.520000e-21 113.0
97 TraesCS6A01G222500 chr4D 86.598 97 8 3 1429 1520 135951896 135951800 5.460000e-18 102.0
98 TraesCS6A01G222500 chr4D 86.598 97 8 2 1429 1520 159247938 159247842 5.460000e-18 102.0
99 TraesCS6A01G222500 chr4D 86.598 97 8 3 1429 1520 191607772 191607676 5.460000e-18 102.0
100 TraesCS6A01G222500 chr4D 85.714 98 13 1 536 633 475934822 475934918 5.460000e-18 102.0
101 TraesCS6A01G222500 chr4D 90.278 72 7 0 562 633 89652903 89652974 9.140000e-16 95.3
102 TraesCS6A01G222500 chr4D 83.673 98 15 1 536 633 475942798 475942894 1.180000e-14 91.6
103 TraesCS6A01G222500 chr4D 88.000 75 7 1 559 633 331625045 331625117 1.530000e-13 87.9
104 TraesCS6A01G222500 chrUn 79.259 405 66 14 3 401 46699604 46699996 1.830000e-67 267.0
105 TraesCS6A01G222500 chrUn 76.652 454 69 29 1 433 262191700 262192137 1.870000e-52 217.0
106 TraesCS6A01G222500 chrUn 76.652 454 69 29 1 433 321643576 321644013 1.870000e-52 217.0
107 TraesCS6A01G222500 chrUn 76.652 454 69 29 1 433 353181570 353182007 1.870000e-52 217.0
108 TraesCS6A01G222500 chrUn 77.427 412 56 17 15 405 20581911 20581516 8.700000e-51 211.0
109 TraesCS6A01G222500 chrUn 82.716 243 27 12 1 235 58793798 58794033 5.240000e-48 202.0
110 TraesCS6A01G222500 chrUn 74.860 537 78 39 2 521 212065625 212066121 1.130000e-44 191.0
111 TraesCS6A01G222500 chrUn 74.860 537 78 39 2 521 229118807 229119303 1.130000e-44 191.0
112 TraesCS6A01G222500 chrUn 87.273 165 15 4 15 177 335339298 335339138 1.900000e-42 183.0
113 TraesCS6A01G222500 chrUn 83.495 206 22 10 13 212 25852497 25852696 6.820000e-42 182.0
114 TraesCS6A01G222500 chrUn 77.337 353 49 25 2 333 242016731 242016389 2.450000e-41 180.0
115 TraesCS6A01G222500 chr1D 81.459 329 39 15 12 331 159397313 159396998 1.840000e-62 250.0
116 TraesCS6A01G222500 chr1D 81.250 320 38 14 1 311 56747034 56747340 3.990000e-59 239.0
117 TraesCS6A01G222500 chr1D 79.603 353 48 15 14 347 342052176 342052523 6.680000e-57 231.0
118 TraesCS6A01G222500 chr1D 79.272 357 47 17 12 347 196842180 196841830 1.120000e-54 224.0
119 TraesCS6A01G222500 chr1D 79.819 332 46 16 13 329 408896003 408896328 4.020000e-54 222.0
120 TraesCS6A01G222500 chr1D 83.402 241 28 10 2 235 429292328 429292093 2.420000e-51 213.0
121 TraesCS6A01G222500 chr1D 87.629 97 7 3 1429 1520 483861032 483860936 1.170000e-19 108.0
122 TraesCS6A01G222500 chr1D 87.838 74 9 0 560 633 77372461 77372388 1.530000e-13 87.9
123 TraesCS6A01G222500 chr1D 92.308 39 3 0 367 405 292649213 292649175 4.310000e-04 56.5
124 TraesCS6A01G222500 chr6D 78.641 412 57 19 12 414 176595803 176595414 8.580000e-61 244.0
125 TraesCS6A01G222500 chr6D 85.246 244 21 12 1 235 243809782 243809545 1.440000e-58 237.0
126 TraesCS6A01G222500 chr6D 79.714 350 41 22 2 333 212367736 212367399 3.110000e-55 226.0
127 TraesCS6A01G222500 chr6D 79.487 351 42 22 2 334 231597293 231596955 4.020000e-54 222.0
128 TraesCS6A01G222500 chr6D 76.091 527 67 35 14 521 364475703 364476189 1.450000e-53 220.0
129 TraesCS6A01G222500 chr6D 85.577 104 13 2 419 521 204299304 204299202 1.170000e-19 108.0
130 TraesCS6A01G222500 chr6D 85.567 97 9 3 1429 1520 275048852 275048948 2.540000e-16 97.1
131 TraesCS6A01G222500 chr6D 89.189 74 8 0 560 633 197638866 197638793 3.290000e-15 93.5
132 TraesCS6A01G222500 chr6D 85.882 85 9 2 549 633 273692799 273692718 1.530000e-13 87.9
133 TraesCS6A01G222500 chr6D 84.706 85 10 2 549 633 273700970 273700889 7.120000e-12 82.4
134 TraesCS6A01G222500 chr5D 89.691 97 5 3 1429 1520 214950031 214950127 5.420000e-23 119.0
135 TraesCS6A01G222500 chr5D 86.538 104 12 2 419 521 39847571 39847673 2.520000e-21 113.0
136 TraesCS6A01G222500 chr5D 91.892 74 6 0 560 633 224009360 224009287 1.520000e-18 104.0
137 TraesCS6A01G222500 chr1B 93.590 78 5 0 1038 1115 67647691 67647614 1.950000e-22 117.0
138 TraesCS6A01G222500 chr4B 91.358 81 7 0 1035 1115 439534364 439534444 9.080000e-21 111.0


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 TraesCS6A01G222500 chr6A 416439734 416442829 3095 False 5718 5718 100.000 1 3096 1 chr6A.!!$F10 3095
1 TraesCS6A01G222500 chr6A 416472674 416475770 3096 False 5374 5374 97.999 1 3096 1 chr6A.!!$F11 3095
2 TraesCS6A01G222500 chr6A 416513966 416515377 1411 False 2093 2093 93.414 1 1412 1 chr6A.!!$F12 1411
3 TraesCS6A01G222500 chr6A 416535572 416536494 922 False 1559 1559 97.183 1407 2328 1 chr6A.!!$F13 921
4 TraesCS6A01G222500 chr6A 214470391 214471448 1057 True 1127 1127 86.036 2040 3096 1 chr6A.!!$R2 1056
5 TraesCS6A01G222500 chr6A 347454608 347455670 1062 False 1110 1110 85.688 2040 3096 1 chr6A.!!$F8 1056
6 TraesCS6A01G222500 chr6A 400191417 400192082 665 True 619 619 83.671 2 683 1 chr6A.!!$R6 681
7 TraesCS6A01G222500 chr6A 310227976 310228633 657 False 523 523 81.481 14 672 1 chr6A.!!$F6 658
8 TraesCS6A01G222500 chr6A 375680896 375681454 558 False 433 433 81.305 20 565 1 chr6A.!!$F9 545
9 TraesCS6A01G222500 chr6A 155186460 155187006 546 False 370 370 79.928 2 527 1 chr6A.!!$F5 525
10 TraesCS6A01G222500 chr1A 341916719 341918227 1508 False 2115 2115 92.013 14 1520 1 chr1A.!!$F7 1506
11 TraesCS6A01G222500 chr1A 341924715 341926221 1506 False 2052 2052 91.281 14 1520 1 chr1A.!!$F8 1506
12 TraesCS6A01G222500 chr1A 432405588 432406735 1147 True 1275 1275 86.926 2 1139 1 chr1A.!!$R5 1137
13 TraesCS6A01G222500 chr2A 680598484 680599547 1063 False 1421 1421 90.585 1475 2567 1 chr2A.!!$F8 1092
14 TraesCS6A01G222500 chr2A 199949365 199950326 961 False 769 769 81.883 2 933 1 chr2A.!!$F1 931
15 TraesCS6A01G222500 chr2A 422855774 422856309 535 True 424 424 81.818 1 522 1 chr2A.!!$R2 521
16 TraesCS6A01G222500 chr2A 258898040 258898560 520 False 381 381 80.603 13 522 1 chr2A.!!$F4 509
17 TraesCS6A01G222500 chr3A 355078737 355079973 1236 True 1354 1354 86.534 1844 3086 1 chr3A.!!$R5 1242
18 TraesCS6A01G222500 chr3A 369661486 369662629 1143 False 1332 1332 88.010 14 1139 1 chr3A.!!$F5 1125
19 TraesCS6A01G222500 chr3A 141873420 141874467 1047 True 1140 1140 86.471 2040 3084 1 chr3A.!!$R2 1044
20 TraesCS6A01G222500 chr3A 47200993 47202047 1054 True 1136 1136 86.249 2040 3096 1 chr3A.!!$R1 1056
21 TraesCS6A01G222500 chr3A 352850173 352851231 1058 True 1096 1096 85.500 2040 3096 1 chr3A.!!$R4 1056
22 TraesCS6A01G222500 chr3A 189086656 189087272 616 False 815 815 90.461 1613 2237 1 chr3A.!!$F1 624
23 TraesCS6A01G222500 chr3A 451689185 451689866 681 True 756 756 86.676 1623 2329 1 chr3A.!!$R6 706
24 TraesCS6A01G222500 chr4A 266990938 266991990 1052 False 1133 1133 86.171 2040 3094 1 chr4A.!!$F1 1054
25 TraesCS6A01G222500 chr4A 297775534 297776386 852 False 708 708 82.135 97 933 1 chr4A.!!$F3 836
26 TraesCS6A01G222500 chr4A 25154742 25155369 627 True 551 551 83.229 1 611 1 chr4A.!!$R1 610
27 TraesCS6A01G222500 chr4A 213040232 213040861 629 True 542 542 82.889 1 610 1 chr4A.!!$R2 609
28 TraesCS6A01G222500 chr4A 213061196 213061817 621 True 540 540 83.016 2 606 1 chr4A.!!$R3 604
29 TraesCS6A01G222500 chr5A 132224497 132225609 1112 True 1131 1131 85.169 1880 2993 1 chr5A.!!$R2 1113
30 TraesCS6A01G222500 chr5A 97772922 97773688 766 True 935 935 88.604 1550 2328 1 chr5A.!!$R1 778
31 TraesCS6A01G222500 chr5A 454542607 454543161 554 False 686 686 89.009 537 1089 1 chr5A.!!$F1 552
32 TraesCS6A01G222500 chr7A 311959166 311959691 525 False 579 579 86.528 408 933 1 chr7A.!!$F2 525

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
291 329 5.449451 GCATCTCATACAACACATGCAATCA 60.449 40.000 0.00 0.0 37.24 2.57 F
1246 1345 4.124943 AGGAGGCGGCTCGGTCTA 62.125 66.667 29.95 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1282 1382 1.380515 CCAGGCTCCTCTTCCTCGA 60.381 63.158 0.00 0.0 0.0 4.04 R
2576 2752 5.735922 GCTTGTACTTCTTGTCCATTGCAAA 60.736 40.000 1.71 0.0 0.0 3.68 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
291 329 5.449451 GCATCTCATACAACACATGCAATCA 60.449 40.000 0.00 0.00 37.24 2.57
1246 1345 4.124943 AGGAGGCGGCTCGGTCTA 62.125 66.667 29.95 0.00 0.00 2.59
1773 1880 7.015292 GGACTTTGGTAGGGAGAAAAATCTTTT 59.985 37.037 0.00 0.00 0.00 2.27
1774 1881 8.319057 ACTTTGGTAGGGAGAAAAATCTTTTT 57.681 30.769 0.43 0.43 42.60 1.94
1800 1907 6.239008 GGACTCACAAAAATGTGAAGGATGAA 60.239 38.462 12.23 0.00 46.60 2.57
1937 2044 6.236409 ACTAGATGTGATTTATGGGCAGATG 58.764 40.000 0.00 0.00 0.00 2.90
2576 2752 9.403583 TGTAGGTTGAAAGACATAAGAAAAAGT 57.596 29.630 0.00 0.00 0.00 2.66
2677 2855 3.146066 CACTTCGGTTGGAAATGGAAGA 58.854 45.455 6.13 0.00 39.09 2.87
2776 2957 5.047802 TCCGGTTAAAACAAGATAGAGACGT 60.048 40.000 0.00 0.00 0.00 4.34
3022 3210 2.951642 CCGGTTGAATGGATAAGCATGT 59.048 45.455 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
291 329 0.455633 CGAGACGACCGTCCGAAAAT 60.456 55.000 17.62 0.00 45.59 1.82
1246 1345 2.835705 CGAGCATCCGAGTAGCCGT 61.836 63.158 0.00 0.00 0.00 5.68
1282 1382 1.380515 CCAGGCTCCTCTTCCTCGA 60.381 63.158 0.00 0.00 0.00 4.04
1800 1907 6.747280 CGAAGAATGCTCGAACCATTTTATTT 59.253 34.615 11.05 5.74 33.34 1.40
2576 2752 5.735922 GCTTGTACTTCTTGTCCATTGCAAA 60.736 40.000 1.71 0.00 0.00 3.68
2677 2855 8.133024 TCATTTTGCCAAGTCCTTATTATTGT 57.867 30.769 0.00 0.00 0.00 2.71
2800 2982 6.228258 TCCTTACATTTATAATCGGAGTGCC 58.772 40.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.