Multiple sequence alignment - TraesCS2B01G237400

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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 TraesCS2B01G237400 chr2B 100.000 4845 0 0 1 4845 238087698 238082854 0.000000e+00 8948
1 TraesCS2B01G237400 chr2B 92.562 1842 120 8 3017 4845 473738427 473740264 0.000000e+00 2627
2 TraesCS2B01G237400 chr2B 92.204 1847 127 7 3015 4845 435818904 435820749 0.000000e+00 2597
3 TraesCS2B01G237400 chr2B 90.647 1390 122 5 1 1387 279796579 279795195 0.000000e+00 1840
4 TraesCS2B01G237400 chr2B 91.040 1183 81 5 1856 3015 389549061 389550241 0.000000e+00 1574
5 TraesCS2B01G237400 chr2B 90.776 477 37 6 1388 1860 210893139 210893612 8.850000e-177 630
6 TraesCS2B01G237400 chr2B 89.419 482 48 3 1382 1860 400210177 400209696 5.360000e-169 604
7 TraesCS2B01G237400 chr2B 91.844 282 23 0 1856 2137 137843095 137843376 1.260000e-105 394
8 TraesCS2B01G237400 chr3B 92.621 1843 120 7 3015 4845 391666805 391664967 0.000000e+00 2636
9 TraesCS2B01G237400 chr3B 92.137 1844 125 11 3015 4845 462524413 462522577 0.000000e+00 2584
10 TraesCS2B01G237400 chr3B 91.430 1832 145 11 3019 4845 418800168 418801992 0.000000e+00 2503
11 TraesCS2B01G237400 chr3B 90.504 1390 124 4 1 1387 242386962 242388346 0.000000e+00 1829
12 TraesCS2B01G237400 chr3B 89.132 1187 102 6 1856 3016 467992811 467993996 0.000000e+00 1452
13 TraesCS2B01G237400 chr4D 92.566 1843 119 8 3015 4845 331713102 331714938 0.000000e+00 2628
14 TraesCS2B01G237400 chrUn 92.316 1848 123 7 3015 4845 17561809 17559964 0.000000e+00 2608
15 TraesCS2B01G237400 chrUn 89.882 1186 92 12 1856 3015 56173578 56172395 0.000000e+00 1500
16 TraesCS2B01G237400 chrUn 88.043 1196 105 14 1856 3015 328536475 328535282 0.000000e+00 1382
17 TraesCS2B01G237400 chrUn 87.225 1182 125 13 1856 3014 58329234 58328056 0.000000e+00 1323
18 TraesCS2B01G237400 chrUn 87.225 1182 125 13 1856 3014 320250340 320249162 0.000000e+00 1323
19 TraesCS2B01G237400 chrUn 86.993 1184 128 12 1856 3015 52679720 52678539 0.000000e+00 1310
20 TraesCS2B01G237400 chrUn 83.666 1402 201 15 1 1387 296742461 296741073 0.000000e+00 1295
21 TraesCS2B01G237400 chrUn 83.666 1402 201 15 1 1387 296747481 296746093 0.000000e+00 1295
22 TraesCS2B01G237400 chrUn 85.176 1194 138 17 1856 3014 119185826 119187015 0.000000e+00 1188
23 TraesCS2B01G237400 chrUn 87.789 909 104 5 3 907 293904305 293905210 0.000000e+00 1057
24 TraesCS2B01G237400 chrUn 87.582 910 105 5 3 907 293882984 293883890 0.000000e+00 1048
25 TraesCS2B01G237400 chrUn 87.666 527 62 3 381 907 377589894 377590417 1.150000e-170 610
26 TraesCS2B01G237400 chrUn 88.174 482 52 4 1382 1860 293884398 293884877 1.960000e-158 569
27 TraesCS2B01G237400 chrUn 88.174 482 52 4 1382 1860 293905718 293906197 1.960000e-158 569
28 TraesCS2B01G237400 chrUn 88.174 482 52 4 1382 1860 377590925 377591404 1.960000e-158 569
29 TraesCS2B01G237400 chrUn 83.577 548 67 12 1856 2380 472961281 472961828 4.360000e-135 492
30 TraesCS2B01G237400 chrUn 82.158 482 80 5 1382 1860 119185313 119185791 4.510000e-110 409
31 TraesCS2B01G237400 chrUn 84.404 436 45 2 1856 2268 430125810 430125375 1.620000e-109 407
32 TraesCS2B01G237400 chrUn 88.000 300 35 1 1557 1855 319527640 319527341 2.150000e-93 353
33 TraesCS2B01G237400 chrUn 88.000 300 35 1 1557 1855 319531043 319530744 2.150000e-93 353
34 TraesCS2B01G237400 chrUn 88.215 297 34 1 1557 1852 394568296 394568592 2.150000e-93 353
35 TraesCS2B01G237400 chrUn 87.919 298 33 2 1563 1859 462598309 462598014 9.980000e-92 348
36 TraesCS2B01G237400 chrUn 86.218 312 39 3 1551 1860 124302046 124301737 7.770000e-88 335
37 TraesCS2B01G237400 chrUn 79.744 469 83 10 1398 1860 84911309 84910847 3.620000e-86 329
38 TraesCS2B01G237400 chrUn 83.710 221 34 2 1023 1242 58528610 58528391 1.770000e-49 207
39 TraesCS2B01G237400 chrUn 83.710 221 34 2 1023 1242 344832436 344832217 1.770000e-49 207
40 TraesCS2B01G237400 chrUn 87.429 175 21 1 1388 1561 37906902 37906728 2.960000e-47 200
41 TraesCS2B01G237400 chrUn 86.592 179 21 1 3 178 319172674 319172496 1.380000e-45 195
42 TraesCS2B01G237400 chrUn 86.441 177 23 1 1385 1560 36564279 36564103 4.950000e-45 193
43 TraesCS2B01G237400 chrUn 86.441 177 23 1 1385 1560 269505465 269505289 4.950000e-45 193
44 TraesCS2B01G237400 chrUn 85.714 182 22 4 1385 1564 2108767 2108588 6.400000e-44 189
45 TraesCS2B01G237400 chrUn 82.439 205 31 5 1041 1242 57723736 57723938 1.790000e-39 174
46 TraesCS2B01G237400 chrUn 81.095 201 38 0 1042 1242 55259148 55258948 1.400000e-35 161
47 TraesCS2B01G237400 chrUn 81.095 201 38 0 1042 1242 249914870 249914670 1.400000e-35 161
48 TraesCS2B01G237400 chrUn 81.095 201 38 0 1042 1242 249926406 249926206 1.400000e-35 161
49 TraesCS2B01G237400 chrUn 80.667 150 27 2 1044 1192 73412412 73412560 1.100000e-21 115
50 TraesCS2B01G237400 chr6B 92.312 1847 123 7 3015 4845 570067078 570065235 0.000000e+00 2606
51 TraesCS2B01G237400 chr6B 92.287 1841 125 7 3017 4845 376736909 376738744 0.000000e+00 2597
52 TraesCS2B01G237400 chr6B 92.878 1390 91 4 1 1387 663633607 663634991 0.000000e+00 2012
53 TraesCS2B01G237400 chr6B 91.855 1326 93 5 3015 4328 388820918 388822240 0.000000e+00 1836
54 TraesCS2B01G237400 chr6B 89.296 1392 139 6 1 1387 334536304 334534918 0.000000e+00 1736
55 TraesCS2B01G237400 chr6B 89.627 482 44 5 1382 1860 237442488 237442010 4.150000e-170 608
56 TraesCS2B01G237400 chr6B 89.605 481 46 4 1382 1860 423229972 423230450 4.150000e-170 608
57 TraesCS2B01G237400 chr6B 93.455 275 18 0 1856 2130 663635623 663635897 4.510000e-110 409
58 TraesCS2B01G237400 chr4B 91.983 1846 123 8 3015 4845 186617283 186615448 0.000000e+00 2566
59 TraesCS2B01G237400 chr4B 91.427 1843 141 8 3015 4845 371513537 371511700 0.000000e+00 2512
60 TraesCS2B01G237400 chr4B 91.264 1843 144 7 3015 4845 315256078 315257915 0.000000e+00 2495
61 TraesCS2B01G237400 chr4B 90.569 1389 121 6 3 1387 422924897 422923515 0.000000e+00 1831
62 TraesCS2B01G237400 chr4B 89.360 1391 131 9 1 1387 290919022 290917645 0.000000e+00 1733
63 TraesCS2B01G237400 chr4B 88.489 1390 145 8 1 1387 150845521 150844144 0.000000e+00 1666
64 TraesCS2B01G237400 chr4B 88.345 1390 148 6 1 1387 374539090 374537712 0.000000e+00 1657
65 TraesCS2B01G237400 chr4B 88.003 1392 145 8 1 1387 189999616 189998242 0.000000e+00 1626
66 TraesCS2B01G237400 chr4B 87.554 1390 165 4 1 1387 355680829 355679445 0.000000e+00 1602
67 TraesCS2B01G237400 chr4B 90.871 1183 83 10 1856 3014 118134811 118135992 0.000000e+00 1563
68 TraesCS2B01G237400 chr4B 90.312 1187 91 3 1856 3018 624054205 624053019 0.000000e+00 1533
69 TraesCS2B01G237400 chr4B 89.873 1185 96 4 1856 3017 305989667 305990850 0.000000e+00 1502
70 TraesCS2B01G237400 chr4B 89.823 1189 90 19 1856 3016 510671180 510669995 0.000000e+00 1496
71 TraesCS2B01G237400 chr4B 89.679 1182 99 11 1856 3014 125559875 125558694 0.000000e+00 1485
72 TraesCS2B01G237400 chr4B 89.679 1182 95 9 1856 3014 143172136 143173313 0.000000e+00 1482
73 TraesCS2B01G237400 chr4B 85.926 1414 167 6 1 1387 291750993 291752401 0.000000e+00 1480
74 TraesCS2B01G237400 chr4B 89.434 1183 100 10 1856 3015 150843508 150842328 0.000000e+00 1469
75 TraesCS2B01G237400 chr4B 89.322 1180 102 3 1856 3012 308876195 308875017 0.000000e+00 1459
76 TraesCS2B01G237400 chr4B 89.003 1164 121 4 1856 3014 202226129 202227290 0.000000e+00 1434
77 TraesCS2B01G237400 chr4B 89.127 1122 95 12 1856 2954 510500471 510501588 0.000000e+00 1371
78 TraesCS2B01G237400 chr4B 88.899 1090 118 3 299 1387 236645523 236644436 0.000000e+00 1339
79 TraesCS2B01G237400 chr4B 90.041 482 43 4 1382 1860 118134297 118134776 1.920000e-173 619
80 TraesCS2B01G237400 chr4B 89.895 475 41 4 1388 1860 532565529 532565060 5.360000e-169 604
81 TraesCS2B01G237400 chr4B 89.224 464 44 5 1400 1860 369541017 369540557 4.210000e-160 575
82 TraesCS2B01G237400 chr4B 88.174 482 52 4 1382 1860 364313720 364313241 1.960000e-158 569
83 TraesCS2B01G237400 chr7B 91.274 1845 142 9 3015 4845 326354830 326356669 0.000000e+00 2497
84 TraesCS2B01G237400 chr7B 91.073 1389 115 5 3 1387 205517879 205519262 0.000000e+00 1869
85 TraesCS2B01G237400 chr7B 90.473 1375 123 4 12 1383 560410725 560412094 0.000000e+00 1807
86 TraesCS2B01G237400 chr7B 88.849 1390 146 5 1 1387 634074556 634073173 0.000000e+00 1700
87 TraesCS2B01G237400 chr7B 89.882 1186 94 9 1856 3015 517052182 517053367 0.000000e+00 1502
88 TraesCS2B01G237400 chr7B 88.908 1163 119 6 1856 3014 343469286 343470442 0.000000e+00 1424
89 TraesCS2B01G237400 chr7B 93.341 886 59 0 2127 3012 230858654 230859539 0.000000e+00 1310
90 TraesCS2B01G237400 chr7B 91.183 465 34 6 1401 1860 735475988 735475526 4.120000e-175 625
91 TraesCS2B01G237400 chr7B 87.336 458 34 5 1856 2290 409205451 409205907 2.010000e-138 503
92 TraesCS2B01G237400 chr1B 89.884 1384 132 4 7 1387 134548652 134547274 0.000000e+00 1773
93 TraesCS2B01G237400 chr1B 87.581 1393 161 8 1 1387 216913003 216914389 0.000000e+00 1604
94 TraesCS2B01G237400 chr1B 87.482 1390 166 4 1 1387 156820147 156818763 0.000000e+00 1596
95 TraesCS2B01G237400 chr1B 90.717 1185 81 7 1856 3014 57321675 57322856 0.000000e+00 1552
96 TraesCS2B01G237400 chr1B 90.686 1181 87 6 1856 3014 382196672 382197851 0.000000e+00 1550
97 TraesCS2B01G237400 chr1B 89.198 1185 94 8 1856 3017 389427602 389426429 0.000000e+00 1448
98 TraesCS2B01G237400 chr1B 90.871 482 38 5 1382 1860 542970075 542970553 4.090000e-180 641
99 TraesCS2B01G237400 chr1B 90.664 482 40 5 1382 1860 275237733 275238212 1.900000e-178 636
100 TraesCS2B01G237400 chr1B 90.249 482 42 4 1382 1860 188034752 188034273 4.120000e-175 625
101 TraesCS2B01G237400 chr1B 89.167 480 48 3 1384 1861 189040744 189041221 3.230000e-166 595
102 TraesCS2B01G237400 chr1B 89.004 482 48 4 1382 1860 212613716 212613237 4.180000e-165 592
103 TraesCS2B01G237400 chr5B 88.777 1390 143 7 1 1387 316846741 316848120 0.000000e+00 1690
104 TraesCS2B01G237400 chr5B 87.275 1391 158 11 1 1387 342585355 342583980 0.000000e+00 1570
105 TraesCS2B01G237400 chr5B 90.794 1184 81 8 1856 3014 682964966 682963786 0.000000e+00 1557
106 TraesCS2B01G237400 chr5B 90.694 1182 90 8 1856 3017 113631408 113632589 0.000000e+00 1555
107 TraesCS2B01G237400 chr5B 90.763 1180 86 5 1857 3013 555497417 555498596 0.000000e+00 1554
108 TraesCS2B01G237400 chr5B 90.355 1182 90 2 1856 3014 316848788 316849968 0.000000e+00 1530
109 TraesCS2B01G237400 chr5B 91.323 945 69 4 3015 3947 478021988 478021045 0.000000e+00 1279
110 TraesCS2B01G237400 chr5B 90.000 470 42 5 1392 1860 167860047 167860512 1.930000e-168 603
111 TraesCS2B01G237400 chr5B 88.912 478 49 3 1385 1860 243064604 243064129 1.940000e-163 586
112 TraesCS2B01G237400 chr5B 88.750 480 49 4 1382 1858 292623800 292623323 2.510000e-162 582
113 TraesCS2B01G237400 chr5B 88.430 484 50 5 1382 1860 194119157 194118675 3.250000e-161 579
114 TraesCS2B01G237400 chr4A 91.363 1181 79 2 1856 3013 686611690 686612870 0.000000e+00 1594
115 TraesCS2B01G237400 chr2D 90.372 1184 89 9 1856 3014 163289662 163288479 0.000000e+00 1531
116 TraesCS2B01G237400 chr2D 89.283 1185 102 3 1856 3015 628533040 628534224 0.000000e+00 1461
117 TraesCS2B01G237400 chr2D 91.621 919 69 3 1 916 163291594 163290681 0.000000e+00 1264
118 TraesCS2B01G237400 chr2D 86.285 926 106 8 1 922 610579957 610579049 0.000000e+00 987
119 TraesCS2B01G237400 chr2D 90.329 486 40 5 1382 1860 163290182 163289697 8.850000e-177 630
120 TraesCS2B01G237400 chr2D 88.589 482 49 6 1382 1860 610578607 610578129 9.040000e-162 580
121 TraesCS2B01G237400 chr2D 91.315 403 35 0 985 1387 163290676 163290274 7.090000e-153 551
122 TraesCS2B01G237400 chr2D 87.164 483 57 5 1382 1860 520113347 520112866 1.190000e-150 544
123 TraesCS2B01G237400 chr2D 88.986 345 38 0 1040 1384 610579046 610578702 1.250000e-115 427
124 TraesCS2B01G237400 chr2D 85.755 351 50 0 1037 1387 628532058 628532408 5.920000e-99 372
125 TraesCS2B01G237400 chr1D 88.898 1180 101 17 1856 3014 206816462 206817632 0.000000e+00 1426
126 TraesCS2B01G237400 chr1D 85.149 1414 171 18 1 1387 206814413 206815814 0.000000e+00 1411
127 TraesCS2B01G237400 chr1D 84.441 1414 174 12 1 1387 209241262 209242656 0.000000e+00 1351
128 TraesCS2B01G237400 chr1D 88.769 926 78 7 1856 2758 493283597 493284519 0.000000e+00 1110
129 TraesCS2B01G237400 chr1D 88.462 182 19 2 1382 1561 206815906 206816087 8.160000e-53 219
130 TraesCS2B01G237400 chr7D 85.791 929 112 9 1 922 157214472 157213557 0.000000e+00 966
131 TraesCS2B01G237400 chr7D 88.150 481 53 3 1382 1860 157213115 157212637 1.960000e-158 569
132 TraesCS2B01G237400 chr7D 89.103 312 30 3 1551 1860 429177491 429177800 7.610000e-103 385
133 TraesCS2B01G237400 chr6D 85.084 476 61 7 1388 1860 465612432 465611964 1.220000e-130 477
134 TraesCS2B01G237400 chr6D 82.983 476 71 9 1388 1859 408340653 408340184 5.800000e-114 422
135 TraesCS2B01G237400 chr3D 88.462 312 34 2 1551 1860 32042489 32042178 4.580000e-100 375
136 TraesCS2B01G237400 chr5D 84.456 193 28 2 1043 1234 395399478 395399669 6.400000e-44 189


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 TraesCS2B01G237400 chr2B 238082854 238087698 4844 True 8948.000000 8948 100.000000 1 4845 1 chr2B.!!$R1 4844
1 TraesCS2B01G237400 chr2B 473738427 473740264 1837 False 2627.000000 2627 92.562000 3017 4845 1 chr2B.!!$F5 1828
2 TraesCS2B01G237400 chr2B 435818904 435820749 1845 False 2597.000000 2597 92.204000 3015 4845 1 chr2B.!!$F4 1830
3 TraesCS2B01G237400 chr2B 279795195 279796579 1384 True 1840.000000 1840 90.647000 1 1387 1 chr2B.!!$R2 1386
4 TraesCS2B01G237400 chr2B 389549061 389550241 1180 False 1574.000000 1574 91.040000 1856 3015 1 chr2B.!!$F3 1159
5 TraesCS2B01G237400 chr3B 391664967 391666805 1838 True 2636.000000 2636 92.621000 3015 4845 1 chr3B.!!$R1 1830
6 TraesCS2B01G237400 chr3B 462522577 462524413 1836 True 2584.000000 2584 92.137000 3015 4845 1 chr3B.!!$R2 1830
7 TraesCS2B01G237400 chr3B 418800168 418801992 1824 False 2503.000000 2503 91.430000 3019 4845 1 chr3B.!!$F2 1826
8 TraesCS2B01G237400 chr3B 242386962 242388346 1384 False 1829.000000 1829 90.504000 1 1387 1 chr3B.!!$F1 1386
9 TraesCS2B01G237400 chr3B 467992811 467993996 1185 False 1452.000000 1452 89.132000 1856 3016 1 chr3B.!!$F3 1160
10 TraesCS2B01G237400 chr4D 331713102 331714938 1836 False 2628.000000 2628 92.566000 3015 4845 1 chr4D.!!$F1 1830
11 TraesCS2B01G237400 chrUn 17559964 17561809 1845 True 2608.000000 2608 92.316000 3015 4845 1 chrUn.!!$R2 1830
12 TraesCS2B01G237400 chrUn 56172395 56173578 1183 True 1500.000000 1500 89.882000 1856 3015 1 chrUn.!!$R7 1159
13 TraesCS2B01G237400 chrUn 328535282 328536475 1193 True 1382.000000 1382 88.043000 1856 3015 1 chrUn.!!$R17 1159
14 TraesCS2B01G237400 chrUn 58328056 58329234 1178 True 1323.000000 1323 87.225000 1856 3014 1 chrUn.!!$R8 1158
15 TraesCS2B01G237400 chrUn 320249162 320250340 1178 True 1323.000000 1323 87.225000 1856 3014 1 chrUn.!!$R16 1158
16 TraesCS2B01G237400 chrUn 52678539 52679720 1181 True 1310.000000 1310 86.993000 1856 3015 1 chrUn.!!$R5 1159
17 TraesCS2B01G237400 chrUn 296741073 296747481 6408 True 1295.000000 1295 83.666000 1 1387 2 chrUn.!!$R21 1386
18 TraesCS2B01G237400 chrUn 293904305 293906197 1892 False 813.000000 1057 87.981500 3 1860 2 chrUn.!!$F7 1857
19 TraesCS2B01G237400 chrUn 293882984 293884877 1893 False 808.500000 1048 87.878000 3 1860 2 chrUn.!!$F6 1857
20 TraesCS2B01G237400 chrUn 119185313 119187015 1702 False 798.500000 1188 83.667000 1382 3014 2 chrUn.!!$F5 1632
21 TraesCS2B01G237400 chrUn 377589894 377591404 1510 False 589.500000 610 87.920000 381 1860 2 chrUn.!!$F8 1479
22 TraesCS2B01G237400 chrUn 472961281 472961828 547 False 492.000000 492 83.577000 1856 2380 1 chrUn.!!$F4 524
23 TraesCS2B01G237400 chrUn 319527341 319531043 3702 True 353.000000 353 88.000000 1557 1855 2 chrUn.!!$R22 298
24 TraesCS2B01G237400 chr6B 570065235 570067078 1843 True 2606.000000 2606 92.312000 3015 4845 1 chr6B.!!$R3 1830
25 TraesCS2B01G237400 chr6B 376736909 376738744 1835 False 2597.000000 2597 92.287000 3017 4845 1 chr6B.!!$F1 1828
26 TraesCS2B01G237400 chr6B 388820918 388822240 1322 False 1836.000000 1836 91.855000 3015 4328 1 chr6B.!!$F2 1313
27 TraesCS2B01G237400 chr6B 334534918 334536304 1386 True 1736.000000 1736 89.296000 1 1387 1 chr6B.!!$R2 1386
28 TraesCS2B01G237400 chr6B 663633607 663635897 2290 False 1210.500000 2012 93.166500 1 2130 2 chr6B.!!$F4 2129
29 TraesCS2B01G237400 chr4B 186615448 186617283 1835 True 2566.000000 2566 91.983000 3015 4845 1 chr4B.!!$R2 1830
30 TraesCS2B01G237400 chr4B 371511700 371513537 1837 True 2512.000000 2512 91.427000 3015 4845 1 chr4B.!!$R10 1830
31 TraesCS2B01G237400 chr4B 315256078 315257915 1837 False 2495.000000 2495 91.264000 3015 4845 1 chr4B.!!$F5 1830
32 TraesCS2B01G237400 chr4B 422923515 422924897 1382 True 1831.000000 1831 90.569000 3 1387 1 chr4B.!!$R12 1384
33 TraesCS2B01G237400 chr4B 290917645 290919022 1377 True 1733.000000 1733 89.360000 1 1387 1 chr4B.!!$R5 1386
34 TraesCS2B01G237400 chr4B 374537712 374539090 1378 True 1657.000000 1657 88.345000 1 1387 1 chr4B.!!$R11 1386
35 TraesCS2B01G237400 chr4B 189998242 189999616 1374 True 1626.000000 1626 88.003000 1 1387 1 chr4B.!!$R3 1386
36 TraesCS2B01G237400 chr4B 355679445 355680829 1384 True 1602.000000 1602 87.554000 1 1387 1 chr4B.!!$R7 1386
37 TraesCS2B01G237400 chr4B 150842328 150845521 3193 True 1567.500000 1666 88.961500 1 3015 2 chr4B.!!$R16 3014
38 TraesCS2B01G237400 chr4B 624053019 624054205 1186 True 1533.000000 1533 90.312000 1856 3018 1 chr4B.!!$R15 1162
39 TraesCS2B01G237400 chr4B 305989667 305990850 1183 False 1502.000000 1502 89.873000 1856 3017 1 chr4B.!!$F4 1161
40 TraesCS2B01G237400 chr4B 510669995 510671180 1185 True 1496.000000 1496 89.823000 1856 3016 1 chr4B.!!$R13 1160
41 TraesCS2B01G237400 chr4B 125558694 125559875 1181 True 1485.000000 1485 89.679000 1856 3014 1 chr4B.!!$R1 1158
42 TraesCS2B01G237400 chr4B 143172136 143173313 1177 False 1482.000000 1482 89.679000 1856 3014 1 chr4B.!!$F1 1158
43 TraesCS2B01G237400 chr4B 291750993 291752401 1408 False 1480.000000 1480 85.926000 1 1387 1 chr4B.!!$F3 1386
44 TraesCS2B01G237400 chr4B 308875017 308876195 1178 True 1459.000000 1459 89.322000 1856 3012 1 chr4B.!!$R6 1156
45 TraesCS2B01G237400 chr4B 202226129 202227290 1161 False 1434.000000 1434 89.003000 1856 3014 1 chr4B.!!$F2 1158
46 TraesCS2B01G237400 chr4B 510500471 510501588 1117 False 1371.000000 1371 89.127000 1856 2954 1 chr4B.!!$F6 1098
47 TraesCS2B01G237400 chr4B 236644436 236645523 1087 True 1339.000000 1339 88.899000 299 1387 1 chr4B.!!$R4 1088
48 TraesCS2B01G237400 chr4B 118134297 118135992 1695 False 1091.000000 1563 90.456000 1382 3014 2 chr4B.!!$F7 1632
49 TraesCS2B01G237400 chr7B 326354830 326356669 1839 False 2497.000000 2497 91.274000 3015 4845 1 chr7B.!!$F3 1830
50 TraesCS2B01G237400 chr7B 205517879 205519262 1383 False 1869.000000 1869 91.073000 3 1387 1 chr7B.!!$F1 1384
51 TraesCS2B01G237400 chr7B 560410725 560412094 1369 False 1807.000000 1807 90.473000 12 1383 1 chr7B.!!$F7 1371
52 TraesCS2B01G237400 chr7B 634073173 634074556 1383 True 1700.000000 1700 88.849000 1 1387 1 chr7B.!!$R1 1386
53 TraesCS2B01G237400 chr7B 517052182 517053367 1185 False 1502.000000 1502 89.882000 1856 3015 1 chr7B.!!$F6 1159
54 TraesCS2B01G237400 chr7B 343469286 343470442 1156 False 1424.000000 1424 88.908000 1856 3014 1 chr7B.!!$F4 1158
55 TraesCS2B01G237400 chr7B 230858654 230859539 885 False 1310.000000 1310 93.341000 2127 3012 1 chr7B.!!$F2 885
56 TraesCS2B01G237400 chr1B 134547274 134548652 1378 True 1773.000000 1773 89.884000 7 1387 1 chr1B.!!$R1 1380
57 TraesCS2B01G237400 chr1B 216913003 216914389 1386 False 1604.000000 1604 87.581000 1 1387 1 chr1B.!!$F3 1386
58 TraesCS2B01G237400 chr1B 156818763 156820147 1384 True 1596.000000 1596 87.482000 1 1387 1 chr1B.!!$R2 1386
59 TraesCS2B01G237400 chr1B 57321675 57322856 1181 False 1552.000000 1552 90.717000 1856 3014 1 chr1B.!!$F1 1158
60 TraesCS2B01G237400 chr1B 382196672 382197851 1179 False 1550.000000 1550 90.686000 1856 3014 1 chr1B.!!$F5 1158
61 TraesCS2B01G237400 chr1B 389426429 389427602 1173 True 1448.000000 1448 89.198000 1856 3017 1 chr1B.!!$R5 1161
62 TraesCS2B01G237400 chr5B 316846741 316849968 3227 False 1610.000000 1690 89.566000 1 3014 2 chr5B.!!$F4 3013
63 TraesCS2B01G237400 chr5B 342583980 342585355 1375 True 1570.000000 1570 87.275000 1 1387 1 chr5B.!!$R4 1386
64 TraesCS2B01G237400 chr5B 682963786 682964966 1180 True 1557.000000 1557 90.794000 1856 3014 1 chr5B.!!$R6 1158
65 TraesCS2B01G237400 chr5B 113631408 113632589 1181 False 1555.000000 1555 90.694000 1856 3017 1 chr5B.!!$F1 1161
66 TraesCS2B01G237400 chr5B 555497417 555498596 1179 False 1554.000000 1554 90.763000 1857 3013 1 chr5B.!!$F3 1156
67 TraesCS2B01G237400 chr5B 478021045 478021988 943 True 1279.000000 1279 91.323000 3015 3947 1 chr5B.!!$R5 932
68 TraesCS2B01G237400 chr4A 686611690 686612870 1180 False 1594.000000 1594 91.363000 1856 3013 1 chr4A.!!$F1 1157
69 TraesCS2B01G237400 chr2D 163288479 163291594 3115 True 994.000000 1531 90.909250 1 3014 4 chr2D.!!$R2 3013
70 TraesCS2B01G237400 chr2D 628532058 628534224 2166 False 916.500000 1461 87.519000 1037 3015 2 chr2D.!!$F1 1978
71 TraesCS2B01G237400 chr2D 610578129 610579957 1828 True 664.666667 987 87.953333 1 1860 3 chr2D.!!$R3 1859
72 TraesCS2B01G237400 chr1D 209241262 209242656 1394 False 1351.000000 1351 84.441000 1 1387 1 chr1D.!!$F1 1386
73 TraesCS2B01G237400 chr1D 493283597 493284519 922 False 1110.000000 1110 88.769000 1856 2758 1 chr1D.!!$F2 902
74 TraesCS2B01G237400 chr1D 206814413 206817632 3219 False 1018.666667 1426 87.503000 1 3014 3 chr1D.!!$F3 3013
75 TraesCS2B01G237400 chr7D 157212637 157214472 1835 True 767.500000 966 86.970500 1 1860 2 chr7D.!!$R1 1859

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
517 555 0.179001 GTTTGGCCTGGTGTGGTACT 60.179 55.0 3.32 0.0 0.0 2.73 F
1839 3764 0.387929 ACATCGTCGTCCACACAGTT 59.612 50.0 0.00 0.0 0.0 3.16 F
3422 6393 0.250124 ACCGCAATCGACTCCAACAA 60.250 50.0 0.00 0.0 38.1 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 4061 0.179020 CCAAGGAAGCCTGTGTCACA 60.179 55.000 5.36 5.36 32.13 3.58 R
3572 6544 0.250209 CGATAGCCATGGCAGAGCTT 60.250 55.000 37.18 18.83 44.88 3.74 R
4373 8518 1.000896 CTCCAAGTTGGGGCCGATT 60.001 57.895 21.85 0.00 38.32 3.34 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
139 142 1.026718 CGGATTGGAGGAGGTTGTGC 61.027 60.000 0.00 0.00 0.00 4.57
172 178 0.545309 TCCAGACTGTCTCCTTGGGG 60.545 60.000 7.49 5.33 0.00 4.96
173 179 1.557269 CCAGACTGTCTCCTTGGGGG 61.557 65.000 7.49 0.36 0.00 5.40
240 251 0.518636 CGCCATTCCTGTTCTGTGTG 59.481 55.000 0.00 0.00 0.00 3.82
517 555 0.179001 GTTTGGCCTGGTGTGGTACT 60.179 55.000 3.32 0.00 0.00 2.73
579 618 8.896722 ATATGGTAGTTACTGTATAAGGGGAG 57.103 38.462 0.00 0.00 0.00 4.30
655 694 1.002134 CAGGGTGGTTGGCCTGTAG 60.002 63.158 3.32 0.00 35.27 2.74
673 712 1.007387 GAACTTGGCCTTTGCACCG 60.007 57.895 3.32 0.00 40.13 4.94
815 856 2.154462 GTGTGAGATGGAACCCACAAG 58.846 52.381 0.00 0.00 40.63 3.16
1008 1049 1.974265 TTGACCTCGCCATGTTTGAA 58.026 45.000 0.00 0.00 0.00 2.69
1202 1253 2.951642 TGTTCTTTTTCTGCTGACCAGG 59.048 45.455 0.00 0.00 42.05 4.45
1269 1322 6.581919 TGTCATCATTATTTTTGTGACGCTTG 59.418 34.615 0.00 0.00 38.94 4.01
1286 1339 2.407090 CTTGTGTCTGTTGCATCGAGA 58.593 47.619 0.00 0.00 0.00 4.04
1597 3475 0.759346 AGGCTGGTCGGGATTGTATC 59.241 55.000 0.00 0.00 0.00 2.24
1620 3498 4.353737 CGTCTTCGTTAACATCCGGATTA 58.646 43.478 16.19 3.41 0.00 1.75
1645 3523 2.227089 GACTCCTGTGCCGGTACTGG 62.227 65.000 33.43 33.43 40.03 4.00
1647 3525 1.827399 CTCCTGTGCCGGTACTGGTT 61.827 60.000 35.69 0.00 39.75 3.67
1836 3761 0.524414 CCTACATCGTCGTCCACACA 59.476 55.000 0.00 0.00 0.00 3.72
1839 3764 0.387929 ACATCGTCGTCCACACAGTT 59.612 50.000 0.00 0.00 0.00 3.16
1893 3857 2.614481 GGTAGTGAATTCCCTTGTCGCA 60.614 50.000 2.27 0.00 0.00 5.10
2095 4061 1.152312 ACACGAGTCTGGGGGTCTT 60.152 57.895 0.00 0.00 0.00 3.01
2130 4119 0.856982 TTGGGGGTGGAATCTGTGTT 59.143 50.000 0.00 0.00 0.00 3.32
2132 4121 0.404040 GGGGGTGGAATCTGTGTTCA 59.596 55.000 0.00 0.00 0.00 3.18
2310 4299 5.759506 GAGTCCATCGAAGATCAAGTCTA 57.240 43.478 0.00 0.00 45.12 2.59
2329 4318 3.943381 TCTACACAGATATCGGTCGTGTT 59.057 43.478 20.56 10.58 37.22 3.32
2353 4342 1.266989 CAAGTTTCCGAACCTGGCTTC 59.733 52.381 0.00 0.00 36.39 3.86
2476 4465 2.631428 CTGGACCGCGTTGTTGTG 59.369 61.111 4.92 0.00 0.00 3.33
2484 4473 1.735018 CCGCGTTGTTGTGGATGATTA 59.265 47.619 4.92 0.00 42.25 1.75
2497 4486 4.276926 GTGGATGATTAAAGGAGCCATCAC 59.723 45.833 0.00 0.00 36.32 3.06
2498 4487 4.079844 TGGATGATTAAAGGAGCCATCACA 60.080 41.667 0.00 0.00 36.32 3.58
2576 4567 2.521224 GCGGATCTCGGGTAGGGT 60.521 66.667 5.87 0.00 39.69 4.34
2947 5606 4.040217 AGTCTTGAGTCTTGCATCTTCACT 59.960 41.667 0.00 0.00 0.00 3.41
3164 5825 9.284594 TGACTTTGTTCGAAGTAAATTTTCTTG 57.715 29.630 14.00 7.46 39.84 3.02
3419 6390 0.320374 AGAACCGCAATCGACTCCAA 59.680 50.000 0.00 0.00 38.10 3.53
3422 6393 0.250124 ACCGCAATCGACTCCAACAA 60.250 50.000 0.00 0.00 38.10 2.83
3464 6435 3.393800 CTCCCCGATGATATGTTGACAC 58.606 50.000 0.00 0.00 0.00 3.67
3544 6516 1.218844 GGCACCCCCTATGGAACTTA 58.781 55.000 0.00 0.00 35.39 2.24
3545 6517 1.133884 GGCACCCCCTATGGAACTTAC 60.134 57.143 0.00 0.00 35.39 2.34
3547 6519 2.488836 CACCCCCTATGGAACTTACCT 58.511 52.381 0.00 0.00 35.39 3.08
3549 6521 2.321296 ACCCCCTATGGAACTTACCTCT 59.679 50.000 0.00 0.00 35.39 3.69
3572 6544 1.972198 GACCTCATCGACACCCACA 59.028 57.895 0.00 0.00 0.00 4.17
3623 6595 1.561643 TGCGTTCTCCAAGATCCTCT 58.438 50.000 0.00 0.00 0.00 3.69
3681 6653 1.339610 CAAGTTCCATTCCAACGGCAA 59.660 47.619 0.00 0.00 0.00 4.52
3695 6667 4.500265 GCAAGGACCAAGCCAAGA 57.500 55.556 0.00 0.00 0.00 3.02
3725 6697 1.386772 TTTGGATCCCCCGCCCTAT 60.387 57.895 9.90 0.00 37.93 2.57
3899 6885 0.952497 ACCTCGAGCTCGTTGTCGTA 60.952 55.000 33.33 13.31 40.80 3.43
4115 7102 8.465999 ACATCTGACTTGAGAGATTACTTGTAG 58.534 37.037 0.00 0.00 0.00 2.74
4172 7159 0.031857 TGCGCCAAAATTGACAGTGG 59.968 50.000 4.18 0.00 0.00 4.00
4335 8480 1.626321 TGATTCCGACAAGCCTAACCA 59.374 47.619 0.00 0.00 0.00 3.67
4373 8518 3.582647 TGAAGGTCTTGGCACTAGAATCA 59.417 43.478 0.00 0.00 0.00 2.57
4411 8556 3.817647 GAGCAAGTTGTCACTTTCCTGAT 59.182 43.478 4.48 0.00 40.66 2.90
4529 8675 7.809546 TCCAAGTTTACAATGACAATGTACA 57.190 32.000 2.76 0.00 33.22 2.90
4776 9043 7.443575 TGGCATGTTAGTGCATTTTACAATTTT 59.556 29.630 0.00 0.00 46.81 1.82
4792 9059 8.964476 TTACAATTTTTGCAAACCAAATAGGA 57.036 26.923 12.39 0.00 42.63 2.94
4795 9062 8.207545 ACAATTTTTGCAAACCAAATAGGACTA 58.792 29.630 12.39 0.00 42.63 2.59
4822 9089 4.973168 AGTGTTCAAAACTGCATCTAGGA 58.027 39.130 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 179 1.917568 TGGGAACACATAAGTACCCCC 59.082 52.381 0.00 0.00 35.07 5.40
517 555 1.211969 GTCGGCTAGACTCAACGCA 59.788 57.895 0.00 0.00 46.13 5.24
655 694 1.007387 CGGTGCAAAGGCCAAGTTC 60.007 57.895 5.01 0.00 40.13 3.01
673 712 4.007659 TCTTCTAAAAAGATGCGGTTCCC 58.992 43.478 0.00 0.00 0.00 3.97
706 747 1.258445 ACCGCTCGAGGATCAAACCT 61.258 55.000 15.58 0.00 43.64 3.50
815 856 1.692519 ACCTACCATCGACCCAATAGC 59.307 52.381 0.00 0.00 0.00 2.97
949 990 2.287547 CCAACAAGGGAACGAATGTGTG 60.288 50.000 0.00 0.00 0.00 3.82
1008 1049 2.120718 AACGAGGAGCCCAGACCT 59.879 61.111 0.00 0.00 39.41 3.85
1147 1198 3.849951 CCCGGGCAGCATACTCGT 61.850 66.667 8.08 0.00 0.00 4.18
1202 1253 1.453928 GAATACCACAGCCCCCAGC 60.454 63.158 0.00 0.00 44.25 4.85
1269 1322 5.496387 CATAAATCTCGATGCAACAGACAC 58.504 41.667 0.00 0.00 0.00 3.67
1286 1339 1.242076 GCGAGGCAGCATCCATAAAT 58.758 50.000 0.43 0.00 37.05 1.40
1518 1671 1.074775 GGAGGACAACCACATGCCA 59.925 57.895 0.00 0.00 38.94 4.92
1597 3475 1.135315 TCCGGATGTTAACGAAGACGG 60.135 52.381 0.00 16.07 44.46 4.79
1609 3487 5.590259 CAGGAGTCAAAAATAATCCGGATGT 59.410 40.000 19.95 10.85 35.13 3.06
1620 3498 1.247567 CCGGCACAGGAGTCAAAAAT 58.752 50.000 0.00 0.00 0.00 1.82
1645 3523 2.935740 GCTCCAAGCCCTGCCAAAC 61.936 63.158 0.00 0.00 34.48 2.93
1765 3675 2.301296 CTGGACAGCCACCTCCTATATG 59.699 54.545 0.00 0.00 39.92 1.78
1766 3676 2.614259 CTGGACAGCCACCTCCTATAT 58.386 52.381 0.00 0.00 39.92 0.86
1797 3722 1.070289 GAGAAGAACAGGAACCACCGT 59.930 52.381 0.00 0.00 44.74 4.83
1836 3761 4.279671 ACTTCGACTCTGAAGACATCAACT 59.720 41.667 10.22 0.00 46.64 3.16
1839 3764 3.057245 CCACTTCGACTCTGAAGACATCA 60.057 47.826 10.22 0.00 46.64 3.07
1893 3857 2.586792 GGCTCGAGTGGGAAGCAT 59.413 61.111 15.13 0.00 0.00 3.79
1924 3888 3.078097 CTCTTTGTCAGGAGACTCTCGA 58.922 50.000 1.74 0.00 45.20 4.04
2095 4061 0.179020 CCAAGGAAGCCTGTGTCACA 60.179 55.000 5.36 5.36 32.13 3.58
2290 4279 5.038033 GTGTAGACTTGATCTTCGATGGAC 58.962 45.833 0.00 0.00 39.04 4.02
2310 4299 2.230508 ACAACACGACCGATATCTGTGT 59.769 45.455 4.33 8.85 45.01 3.72
2329 4318 2.294074 CCAGGTTCGGAAACTTGAACA 58.706 47.619 5.35 0.00 43.25 3.18
2476 4465 4.276926 GTGTGATGGCTCCTTTAATCATCC 59.723 45.833 0.00 0.00 34.87 3.51
2484 4473 1.915141 CAAGGTGTGATGGCTCCTTT 58.085 50.000 0.00 0.00 39.49 3.11
2497 4486 0.809636 TGTGTCGTCACTGCAAGGTG 60.810 55.000 13.77 0.00 44.14 4.00
2498 4487 0.530650 CTGTGTCGTCACTGCAAGGT 60.531 55.000 13.77 0.00 44.14 3.50
2576 4567 0.678684 TAGACGCACAGATCGGGACA 60.679 55.000 0.00 0.00 0.00 4.02
3410 6381 2.826128 AGTCTATGCTTGTTGGAGTCGA 59.174 45.455 0.00 0.00 0.00 4.20
3419 6390 4.190001 CTGCTGATGAAGTCTATGCTTGT 58.810 43.478 0.00 0.00 0.00 3.16
3422 6393 2.485124 GGCTGCTGATGAAGTCTATGCT 60.485 50.000 0.00 0.00 0.00 3.79
3464 6435 1.132913 TGGGAGGAGGGAGATGATGAG 60.133 57.143 0.00 0.00 0.00 2.90
3572 6544 0.250209 CGATAGCCATGGCAGAGCTT 60.250 55.000 37.18 18.83 44.88 3.74
3623 6595 1.845664 TTGGGCTAGGGTGACTGCA 60.846 57.895 0.00 0.00 0.00 4.41
3681 6653 2.309755 TCATCAATCTTGGCTTGGTCCT 59.690 45.455 0.00 0.00 0.00 3.85
3695 6667 3.628257 GGGGATCCAAACCAGTCATCAAT 60.628 47.826 15.23 0.00 0.00 2.57
3831 6806 3.004090 GTCATTAAGGGCGGGGGT 58.996 61.111 0.00 0.00 0.00 4.95
3837 6823 3.583086 GGGCGCGTCATTAAGGGC 61.583 66.667 14.93 0.00 44.19 5.19
3899 6885 2.885135 TGTCACCATTTGAGAGGCAT 57.115 45.000 0.00 0.00 33.71 4.40
4115 7102 5.305585 TCTTGTTGGACCTACTTGATCAAC 58.694 41.667 3.38 0.00 36.15 3.18
4172 7159 0.601558 TTGTCAGACGAGTAGCCCAC 59.398 55.000 0.00 0.00 0.00 4.61
4331 8476 2.047151 CTGTGCGCAGTTTCGTGGTT 62.047 55.000 19.30 0.00 37.92 3.67
4373 8518 1.000896 CTCCAAGTTGGGGCCGATT 60.001 57.895 21.85 0.00 38.32 3.34
4529 8675 6.490040 TCCAAAAGAATCCTTCAGAAATCGTT 59.510 34.615 0.00 0.00 0.00 3.85
4776 9043 8.545472 ACTACTATAGTCCTATTTGGTTTGCAA 58.455 33.333 9.12 0.00 32.47 4.08
4792 9059 8.314751 AGATGCAGTTTTGAACACTACTATAGT 58.685 33.333 10.87 10.87 40.28 2.12
4795 9062 7.766278 CCTAGATGCAGTTTTGAACACTACTAT 59.234 37.037 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.