Multiple sequence alignment - TraesCS3B01G609400

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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 TraesCS3B01G609400 chr3B 100.000 4063 0 0 1 4063 828423063 828419001 0.000000e+00 7504
1 TraesCS3B01G609400 chr3B 98.352 3580 45 4 490 4063 828762777 828766348 0.000000e+00 6272
2 TraesCS3B01G609400 chr3B 91.781 365 25 4 1 364 828757509 828757869 1.690000e-138 503
3 TraesCS3B01G609400 chr3B 78.322 286 55 6 3287 3569 720221073 720221354 1.160000e-40 178
4 TraesCS3B01G609400 chr3D 89.716 2499 158 44 792 3231 610806275 610803817 0.000000e+00 3099
5 TraesCS3B01G609400 chr3D 85.714 749 45 30 1 737 610807778 610807080 0.000000e+00 734
6 TraesCS3B01G609400 chr3D 86.383 235 25 5 3631 3859 610802751 610802518 2.420000e-62 250
7 TraesCS3B01G609400 chr3D 81.224 245 26 12 3826 4063 610802497 610802266 3.230000e-41 180
8 TraesCS3B01G609400 chr3A 91.437 1308 95 9 1955 3247 745513616 745512311 0.000000e+00 1779
9 TraesCS3B01G609400 chr3A 90.690 956 49 14 1005 1960 745517985 745517070 0.000000e+00 1236
10 TraesCS3B01G609400 chr3A 78.947 399 72 9 22 413 745521394 745521001 1.120000e-65 261
11 TraesCS3B01G609400 chr1B 84.141 908 132 7 2038 2941 592172843 592171944 0.000000e+00 869
12 TraesCS3B01G609400 chr1B 82.195 483 78 5 1072 1547 592173986 592173505 3.780000e-110 409
13 TraesCS3B01G609400 chr1B 84.475 219 28 5 1691 1905 592173383 592173167 1.140000e-50 211
14 TraesCS3B01G609400 chr1A 84.071 904 134 9 2038 2938 534051258 534050362 0.000000e+00 863
15 TraesCS3B01G609400 chr1A 82.759 174 28 2 3323 3495 583435343 583435171 1.960000e-33 154
16 TraesCS3B01G609400 chr1D 83.811 908 136 8 2038 2941 437000496 436999596 0.000000e+00 852
17 TraesCS3B01G609400 chr1D 78.519 810 147 16 1108 1905 437001615 437000821 1.300000e-139 507
18 TraesCS3B01G609400 chr1D 82.353 153 27 0 3343 3495 13059785 13059937 2.550000e-27 134
19 TraesCS3B01G609400 chr2A 75.812 831 175 18 2041 2853 174245678 174246500 8.180000e-107 398
20 TraesCS3B01G609400 chr2A 75.056 898 196 22 2041 2920 174027294 174028181 3.810000e-105 392
21 TraesCS3B01G609400 chr2A 83.117 154 24 2 3343 3495 3098745 3098593 5.480000e-29 139
22 TraesCS3B01G609400 chr2D 74.916 897 198 21 2041 2920 174324532 174325418 6.370000e-103 385
23 TraesCS3B01G609400 chr6A 80.913 482 80 7 1076 1551 599831994 599831519 1.780000e-98 370
24 TraesCS3B01G609400 chr6A 79.422 277 43 10 1623 1894 599831388 599831121 2.490000e-42 183
25 TraesCS3B01G609400 chr5D 83.521 267 40 4 3287 3551 541703313 541703577 3.140000e-61 246
26 TraesCS3B01G609400 chr7D 80.894 246 47 0 3323 3568 3181136 3181381 1.150000e-45 195
27 TraesCS3B01G609400 chr7D 81.690 213 35 4 3285 3495 94094415 94094205 1.500000e-39 174
28 TraesCS3B01G609400 chr6B 86.127 173 24 0 3323 3495 526964461 526964633 1.930000e-43 187


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 TraesCS3B01G609400 chr3B 828419001 828423063 4062 True 7504.000000 7504 100.000000 1 4063 1 chr3B.!!$R1 4062
1 TraesCS3B01G609400 chr3B 828762777 828766348 3571 False 6272.000000 6272 98.352000 490 4063 1 chr3B.!!$F3 3573
2 TraesCS3B01G609400 chr3D 610802266 610807778 5512 True 1065.750000 3099 85.759250 1 4063 4 chr3D.!!$R1 4062
3 TraesCS3B01G609400 chr3A 745512311 745521394 9083 True 1092.000000 1779 87.024667 22 3247 3 chr3A.!!$R1 3225
4 TraesCS3B01G609400 chr1B 592171944 592173986 2042 True 496.333333 869 83.603667 1072 2941 3 chr1B.!!$R1 1869
5 TraesCS3B01G609400 chr1A 534050362 534051258 896 True 863.000000 863 84.071000 2038 2938 1 chr1A.!!$R1 900
6 TraesCS3B01G609400 chr1D 436999596 437001615 2019 True 679.500000 852 81.165000 1108 2941 2 chr1D.!!$R1 1833
7 TraesCS3B01G609400 chr2A 174245678 174246500 822 False 398.000000 398 75.812000 2041 2853 1 chr2A.!!$F2 812
8 TraesCS3B01G609400 chr2A 174027294 174028181 887 False 392.000000 392 75.056000 2041 2920 1 chr2A.!!$F1 879
9 TraesCS3B01G609400 chr2D 174324532 174325418 886 False 385.000000 385 74.916000 2041 2920 1 chr2D.!!$F1 879
10 TraesCS3B01G609400 chr6A 599831121 599831994 873 True 276.500000 370 80.167500 1076 1894 2 chr6A.!!$R1 818

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
228 229 0.386476 CATGCCAGCGCCATAACAAT 59.614 50.0 2.29 0.0 0.00 2.71 F
890 3637 0.895100 ATGTCCACATGCCACACCAC 60.895 55.0 0.00 0.0 34.83 4.16 F
1444 4258 1.192146 AGGTCAAGTTCCCTGCGCTA 61.192 55.0 9.73 0.0 0.00 4.26 F
2321 8770 0.524414 TACTCACGTGGACGATGGTG 59.476 55.0 17.00 0.0 43.02 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 8466 0.589729 GTGCACTTGCGTTGTCAGTG 60.590 55.000 10.32 0.00 45.83 3.66 R
2321 8770 1.209504 TCTGGGTGCATGCTAAGTACC 59.790 52.381 20.33 16.92 40.52 3.34 R
2456 8908 2.238646 ACCTCCGATCCTATGTTTGCAA 59.761 45.455 0.00 0.00 0.00 4.08 R
3628 11121 5.457799 CGGTAGGTTGATGTTTATCTACACG 59.542 44.000 0.00 0.00 39.72 4.49 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
19 20 2.603075 AATCCACCTTAGCCTGCAAA 57.397 45.000 0.00 0.00 0.00 3.68
20 21 2.834638 ATCCACCTTAGCCTGCAAAT 57.165 45.000 0.00 0.00 0.00 2.32
191 192 1.255767 AATAAAAATCACGCGTGCGC 58.744 45.000 33.63 8.17 44.19 6.09
228 229 0.386476 CATGCCAGCGCCATAACAAT 59.614 50.000 2.29 0.00 0.00 2.71
234 235 2.176369 CAGCGCCATAACAATTCGTTG 58.824 47.619 2.29 0.00 38.63 4.10
236 237 2.682856 AGCGCCATAACAATTCGTTGAT 59.317 40.909 2.29 0.00 38.63 2.57
239 240 3.115554 GCCATAACAATTCGTTGATGGC 58.884 45.455 21.00 21.00 46.04 4.40
242 243 5.350633 CCATAACAATTCGTTGATGGCATT 58.649 37.500 0.00 0.00 38.63 3.56
255 282 3.202818 TGATGGCATTAGAGGAACCACAT 59.797 43.478 0.00 0.00 32.13 3.21
267 294 6.074648 AGAGGAACCACATCCAACAATTTAA 58.925 36.000 0.00 0.00 42.27 1.52
293 320 8.437575 ACCTCCTCTTCTTGTTTGTATTCTAAA 58.562 33.333 0.00 0.00 0.00 1.85
294 321 9.454859 CCTCCTCTTCTTGTTTGTATTCTAAAT 57.545 33.333 0.00 0.00 0.00 1.40
346 377 2.599597 CCCTTGCCATCTGAGGGG 59.400 66.667 10.73 2.08 45.27 4.79
376 407 7.038302 TCAGGTGGTTACTTGATTCTAACTCAT 60.038 37.037 0.00 0.00 37.91 2.90
406 437 4.393239 TGGTACTGTAGGAGTGTAGGTT 57.607 45.455 0.00 0.00 35.96 3.50
408 439 4.768968 TGGTACTGTAGGAGTGTAGGTTTC 59.231 45.833 0.00 0.00 35.96 2.78
413 444 5.160607 TGTAGGAGTGTAGGTTTCATTGG 57.839 43.478 0.00 0.00 0.00 3.16
457 488 8.603898 TTAAGATTCTCATTGGTACTGTAGGA 57.396 34.615 0.00 0.00 0.00 2.94
459 490 7.682787 AGATTCTCATTGGTACTGTAGGAAT 57.317 36.000 0.00 0.00 0.00 3.01
460 491 7.504403 AGATTCTCATTGGTACTGTAGGAATG 58.496 38.462 10.46 10.46 0.00 2.67
461 492 6.620877 TTCTCATTGGTACTGTAGGAATGT 57.379 37.500 14.05 0.00 0.00 2.71
462 493 7.727578 TTCTCATTGGTACTGTAGGAATGTA 57.272 36.000 14.05 5.96 0.00 2.29
463 494 7.348080 TCTCATTGGTACTGTAGGAATGTAG 57.652 40.000 14.05 11.40 0.00 2.74
464 495 6.323996 TCTCATTGGTACTGTAGGAATGTAGG 59.676 42.308 14.05 8.90 0.00 3.18
465 496 5.962031 TCATTGGTACTGTAGGAATGTAGGT 59.038 40.000 14.05 0.00 0.00 3.08
466 497 6.442564 TCATTGGTACTGTAGGAATGTAGGTT 59.557 38.462 14.05 0.00 0.00 3.50
467 498 6.691255 TTGGTACTGTAGGAATGTAGGTTT 57.309 37.500 0.00 0.00 0.00 3.27
468 499 6.691255 TGGTACTGTAGGAATGTAGGTTTT 57.309 37.500 0.00 0.00 0.00 2.43
470 501 7.614494 TGGTACTGTAGGAATGTAGGTTTTAC 58.386 38.462 0.00 0.00 0.00 2.01
471 502 7.455638 TGGTACTGTAGGAATGTAGGTTTTACT 59.544 37.037 0.00 0.00 0.00 2.24
472 503 8.316946 GGTACTGTAGGAATGTAGGTTTTACTT 58.683 37.037 0.00 0.00 0.00 2.24
473 504 9.148104 GTACTGTAGGAATGTAGGTTTTACTTG 57.852 37.037 0.00 0.00 0.00 3.16
474 505 7.970102 ACTGTAGGAATGTAGGTTTTACTTGA 58.030 34.615 0.00 0.00 0.00 3.02
476 507 8.611654 TGTAGGAATGTAGGTTTTACTTGAAC 57.388 34.615 0.00 0.00 0.00 3.18
477 508 7.662669 TGTAGGAATGTAGGTTTTACTTGAACC 59.337 37.037 0.00 0.00 45.49 3.62
478 509 6.008331 AGGAATGTAGGTTTTACTTGAACCC 58.992 40.000 2.59 0.00 46.14 4.11
480 511 6.436218 GGAATGTAGGTTTTACTTGAACCCAT 59.564 38.462 2.59 0.00 46.14 4.00
481 512 6.834168 ATGTAGGTTTTACTTGAACCCATG 57.166 37.500 2.59 0.00 46.14 3.66
482 513 4.521256 TGTAGGTTTTACTTGAACCCATGC 59.479 41.667 2.59 0.00 46.14 4.06
483 514 3.844640 AGGTTTTACTTGAACCCATGCT 58.155 40.909 2.59 0.00 46.14 3.79
484 515 4.993028 AGGTTTTACTTGAACCCATGCTA 58.007 39.130 2.59 0.00 46.14 3.49
485 516 5.580022 AGGTTTTACTTGAACCCATGCTAT 58.420 37.500 2.59 0.00 46.14 2.97
486 517 5.652452 AGGTTTTACTTGAACCCATGCTATC 59.348 40.000 2.59 0.00 46.14 2.08
487 518 5.652452 GGTTTTACTTGAACCCATGCTATCT 59.348 40.000 0.00 0.00 40.52 1.98
488 519 6.826741 GGTTTTACTTGAACCCATGCTATCTA 59.173 38.462 0.00 0.00 40.52 1.98
890 3637 0.895100 ATGTCCACATGCCACACCAC 60.895 55.000 0.00 0.00 34.83 4.16
1332 4143 2.047274 GGAGCACGGCAAGCAGTA 60.047 61.111 0.00 0.00 0.00 2.74
1438 4252 2.118403 TCCAGAAGGTCAAGTTCCCT 57.882 50.000 0.00 0.00 35.89 4.20
1444 4258 1.192146 AGGTCAAGTTCCCTGCGCTA 61.192 55.000 9.73 0.00 0.00 4.26
1876 4749 4.556898 GCAGCCATTCACAAGATCATGATC 60.557 45.833 25.42 25.42 38.09 2.92
2017 8466 6.013689 GTGCTTTGTGCTTATTTACTCGTAC 58.986 40.000 0.00 0.00 43.37 3.67
2309 8758 6.756542 TGGAGACAACATCAATATTACTCACG 59.243 38.462 0.00 0.00 37.44 4.35
2321 8770 0.524414 TACTCACGTGGACGATGGTG 59.476 55.000 17.00 0.00 43.02 4.17
2733 9214 0.250727 TCCAAGGCTTCCAAGGAACG 60.251 55.000 0.00 0.00 0.00 3.95
2735 9216 0.250727 CAAGGCTTCCAAGGAACGGA 60.251 55.000 0.00 0.00 0.00 4.69
3167 9675 7.226523 GCATTCATATGATGTAACACTGGTACA 59.773 37.037 9.40 9.40 33.37 2.90
3377 10870 0.884704 TTTGCCGAGAGTTGCACTCC 60.885 55.000 11.24 4.57 46.18 3.85
3628 11121 4.443394 CGTATACGGAAATTCCAGTAGTGC 59.557 45.833 17.61 8.31 35.91 4.40
3699 11192 9.606631 ATCCTGACTGTCATTAAAGAAATAGAC 57.393 33.333 11.45 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.578928 CGGTTAATATTTGCAGGCTAAGGT 59.421 41.667 0.00 0.00 0.00 3.50
10 11 6.952773 TTAATCGGTTAATATTTGCAGGCT 57.047 33.333 0.00 0.00 0.00 4.58
38 39 6.037720 AGACTAATGTGAGATGACTAGACGTG 59.962 42.308 0.00 0.00 0.00 4.49
228 229 3.904800 TCCTCTAATGCCATCAACGAA 57.095 42.857 0.00 0.00 0.00 3.85
234 235 3.281727 TGTGGTTCCTCTAATGCCATC 57.718 47.619 0.00 0.00 0.00 3.51
236 237 2.092429 GGATGTGGTTCCTCTAATGCCA 60.092 50.000 0.00 0.00 32.68 4.92
239 240 4.588899 TGTTGGATGTGGTTCCTCTAATG 58.411 43.478 0.00 0.00 36.68 1.90
242 243 4.927267 ATTGTTGGATGTGGTTCCTCTA 57.073 40.909 0.00 0.00 36.68 2.43
255 282 6.200878 AGAAGAGGAGGTTAAATTGTTGGA 57.799 37.500 0.00 0.00 0.00 3.53
267 294 6.441088 AGAATACAAACAAGAAGAGGAGGT 57.559 37.500 0.00 0.00 0.00 3.85
303 330 4.963318 ATAGGCTCAGAATTCGGATTCA 57.037 40.909 18.62 0.00 43.35 2.57
346 377 5.491982 AGAATCAAGTAACCACCTGACATC 58.508 41.667 0.00 0.00 27.94 3.06
383 414 4.944177 ACCTACACTCCTACAGTACCAAT 58.056 43.478 0.00 0.00 32.21 3.16
390 421 5.046591 TCCAATGAAACCTACACTCCTACAG 60.047 44.000 0.00 0.00 0.00 2.74
439 470 6.323996 CCTACATTCCTACAGTACCAATGAGA 59.676 42.308 11.48 2.29 0.00 3.27
440 471 6.098409 ACCTACATTCCTACAGTACCAATGAG 59.902 42.308 11.48 6.53 0.00 2.90
441 472 5.962031 ACCTACATTCCTACAGTACCAATGA 59.038 40.000 11.48 0.00 0.00 2.57
442 473 6.235231 ACCTACATTCCTACAGTACCAATG 57.765 41.667 0.00 5.62 0.00 2.82
443 474 6.886178 AACCTACATTCCTACAGTACCAAT 57.114 37.500 0.00 0.00 0.00 3.16
447 478 9.148104 CAAGTAAAACCTACATTCCTACAGTAC 57.852 37.037 0.00 0.00 0.00 2.73
449 480 7.970102 TCAAGTAAAACCTACATTCCTACAGT 58.030 34.615 0.00 0.00 0.00 3.55
450 481 8.718734 GTTCAAGTAAAACCTACATTCCTACAG 58.281 37.037 0.00 0.00 0.00 2.74
451 482 7.662669 GGTTCAAGTAAAACCTACATTCCTACA 59.337 37.037 0.00 0.00 42.42 2.74
452 483 7.120285 GGGTTCAAGTAAAACCTACATTCCTAC 59.880 40.741 5.13 0.00 44.62 3.18
453 484 7.170277 GGGTTCAAGTAAAACCTACATTCCTA 58.830 38.462 5.13 0.00 44.62 2.94
455 486 5.771165 TGGGTTCAAGTAAAACCTACATTCC 59.229 40.000 5.13 0.00 44.62 3.01
456 487 6.887626 TGGGTTCAAGTAAAACCTACATTC 57.112 37.500 5.13 0.00 44.62 2.67
457 488 6.295067 GCATGGGTTCAAGTAAAACCTACATT 60.295 38.462 5.13 0.00 44.62 2.71
459 490 4.521256 GCATGGGTTCAAGTAAAACCTACA 59.479 41.667 5.13 0.00 44.62 2.74
460 491 4.765339 AGCATGGGTTCAAGTAAAACCTAC 59.235 41.667 5.13 0.00 44.62 3.18
461 492 4.993028 AGCATGGGTTCAAGTAAAACCTA 58.007 39.130 5.13 0.00 44.62 3.08
462 493 3.844640 AGCATGGGTTCAAGTAAAACCT 58.155 40.909 5.13 0.00 44.62 3.50
463 494 5.652452 AGATAGCATGGGTTCAAGTAAAACC 59.348 40.000 0.00 0.00 44.52 3.27
464 495 6.759497 AGATAGCATGGGTTCAAGTAAAAC 57.241 37.500 0.00 0.00 0.00 2.43
465 496 9.474313 AAATAGATAGCATGGGTTCAAGTAAAA 57.526 29.630 0.00 0.00 0.00 1.52
466 497 9.474313 AAAATAGATAGCATGGGTTCAAGTAAA 57.526 29.630 0.00 0.00 0.00 2.01
467 498 9.474313 AAAAATAGATAGCATGGGTTCAAGTAA 57.526 29.630 0.00 0.00 0.00 2.24
468 499 8.902806 CAAAAATAGATAGCATGGGTTCAAGTA 58.097 33.333 0.00 0.00 0.00 2.24
470 501 7.999679 TCAAAAATAGATAGCATGGGTTCAAG 58.000 34.615 0.00 0.00 0.00 3.02
471 502 7.953005 TCAAAAATAGATAGCATGGGTTCAA 57.047 32.000 0.00 0.00 0.00 2.69
472 503 7.833682 TCTTCAAAAATAGATAGCATGGGTTCA 59.166 33.333 0.00 0.00 0.00 3.18
473 504 8.225603 TCTTCAAAAATAGATAGCATGGGTTC 57.774 34.615 0.00 0.00 0.00 3.62
474 505 8.593945 TTCTTCAAAAATAGATAGCATGGGTT 57.406 30.769 0.00 0.00 0.00 4.11
481 512 9.952188 GGGTGTATTTCTTCAAAAATAGATAGC 57.048 33.333 0.00 0.00 33.05 2.97
483 514 9.893634 TCGGGTGTATTTCTTCAAAAATAGATA 57.106 29.630 0.00 0.00 33.05 1.98
484 515 8.801882 TCGGGTGTATTTCTTCAAAAATAGAT 57.198 30.769 0.00 0.00 33.05 1.98
485 516 8.624367 TTCGGGTGTATTTCTTCAAAAATAGA 57.376 30.769 0.00 0.00 33.05 1.98
486 517 7.968405 CCTTCGGGTGTATTTCTTCAAAAATAG 59.032 37.037 0.00 0.00 33.05 1.73
487 518 7.094118 CCCTTCGGGTGTATTTCTTCAAAAATA 60.094 37.037 0.00 0.00 38.25 1.40
488 519 6.295067 CCCTTCGGGTGTATTTCTTCAAAAAT 60.295 38.462 0.00 0.00 38.25 1.82
1332 4143 1.605058 CGGACCGAACCAGGAGATGT 61.605 60.000 8.64 0.00 34.73 3.06
1876 4749 2.081462 GAAACTCACATGTAACCGGGG 58.919 52.381 6.32 0.00 0.00 5.73
2017 8466 0.589729 GTGCACTTGCGTTGTCAGTG 60.590 55.000 10.32 0.00 45.83 3.66
2309 8758 2.737679 GCTAAGTACCACCATCGTCCAC 60.738 54.545 0.00 0.00 0.00 4.02
2321 8770 1.209504 TCTGGGTGCATGCTAAGTACC 59.790 52.381 20.33 16.92 40.52 3.34
2440 8892 7.897575 TGTTTGCAACAACTCAAGTAATTTT 57.102 28.000 0.00 0.00 38.72 1.82
2456 8908 2.238646 ACCTCCGATCCTATGTTTGCAA 59.761 45.455 0.00 0.00 0.00 4.08
2472 8924 9.477484 CATATATTAATAAGATGCCGTACCTCC 57.523 37.037 0.00 0.00 0.00 4.30
2733 9214 2.352715 CCAAACGGGAAAAATGCTCTCC 60.353 50.000 0.00 0.00 40.01 3.71
2735 9216 2.593026 TCCAAACGGGAAAAATGCTCT 58.407 42.857 0.00 0.00 44.80 4.09
3628 11121 5.457799 CGGTAGGTTGATGTTTATCTACACG 59.542 44.000 0.00 0.00 39.72 4.49


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

AutoCloner maintained by Alex Coulton.