Multiple sequence alignment - TraesCS3A01G529500

Loading Multiple Alignment...

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 TraesCS3A01G529500 chr3A 100.000 2384 0 0 1 2384 742929008 742931391 0.000000e+00 4403.0
1 TraesCS3A01G529500 chr3A 84.772 834 93 17 1 833 742955174 742955974 0.000000e+00 806.0
2 TraesCS3A01G529500 chr3A 88.288 222 26 0 1198 1419 742962573 742962794 1.400000e-67 267.0
3 TraesCS3A01G529500 chr3D 94.244 2380 101 20 1 2371 609363884 609366236 0.000000e+00 3603.0
4 TraesCS3A01G529500 chr3D 78.182 440 58 14 1852 2277 609352036 609352451 1.830000e-61 246.0
5 TraesCS3A01G529500 chr3B 91.518 1957 97 17 458 2371 820114801 820116731 0.000000e+00 2630.0
6 TraesCS3A01G529500 chr3B 87.213 2307 245 21 1 2294 820178904 820176635 0.000000e+00 2580.0
7 TraesCS3A01G529500 chr3B 92.003 1388 108 3 1 1386 820185810 820184424 0.000000e+00 1945.0
8 TraesCS3A01G529500 chr3B 89.367 1486 150 6 1 1481 819991890 819990408 0.000000e+00 1862.0
9 TraesCS3A01G529500 chr3B 86.752 1487 188 7 1 1481 820122986 820124469 0.000000e+00 1646.0
10 TraesCS3A01G529500 chr3B 83.486 654 78 14 1696 2323 820217106 820216457 1.230000e-162 582.0
11 TraesCS3A01G529500 chr3B 97.583 331 8 0 1 331 820114473 820114803 3.440000e-158 568.0
12 TraesCS3A01G529500 chr3B 87.736 318 35 2 2053 2370 820109389 820109702 3.740000e-98 368.0
13 TraesCS3A01G529500 chr3B 88.235 102 7 3 1629 1729 820090784 820090881 1.500000e-22 117.0
14 TraesCS3A01G529500 chr1A 85.305 1395 191 8 1 1391 578941074 578939690 0.000000e+00 1428.0
15 TraesCS3A01G529500 chr1D 85.908 887 116 5 1 887 482243397 482242520 0.000000e+00 937.0
16 TraesCS3A01G529500 chr2A 75.543 184 38 7 957 1136 763333057 763332877 1.520000e-12 84.2
17 TraesCS3A01G529500 chr2D 87.500 64 8 0 1030 1093 568410234 568410297 9.140000e-10 75.0
18 TraesCS3A01G529500 chr2D 88.525 61 7 0 1033 1093 568727372 568727432 9.140000e-10 75.0


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 TraesCS3A01G529500 chr3A 742929008 742931391 2383 False 4403 4403 100.0000 1 2384 1 chr3A.!!$F1 2383
1 TraesCS3A01G529500 chr3A 742955174 742955974 800 False 806 806 84.7720 1 833 1 chr3A.!!$F2 832
2 TraesCS3A01G529500 chr3D 609363884 609366236 2352 False 3603 3603 94.2440 1 2371 1 chr3D.!!$F2 2370
3 TraesCS3A01G529500 chr3B 820176635 820178904 2269 True 2580 2580 87.2130 1 2294 1 chr3B.!!$R2 2293
4 TraesCS3A01G529500 chr3B 820184424 820185810 1386 True 1945 1945 92.0030 1 1386 1 chr3B.!!$R3 1385
5 TraesCS3A01G529500 chr3B 819990408 819991890 1482 True 1862 1862 89.3670 1 1481 1 chr3B.!!$R1 1480
6 TraesCS3A01G529500 chr3B 820122986 820124469 1483 False 1646 1646 86.7520 1 1481 1 chr3B.!!$F3 1480
7 TraesCS3A01G529500 chr3B 820114473 820116731 2258 False 1599 2630 94.5505 1 2371 2 chr3B.!!$F4 2370
8 TraesCS3A01G529500 chr3B 820216457 820217106 649 True 582 582 83.4860 1696 2323 1 chr3B.!!$R4 627
9 TraesCS3A01G529500 chr1A 578939690 578941074 1384 True 1428 1428 85.3050 1 1391 1 chr1A.!!$R1 1390
10 TraesCS3A01G529500 chr1D 482242520 482243397 877 True 937 937 85.9080 1 887 1 chr1D.!!$R1 886

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
271 274 1.071699 ACCGGAAAAGCTTGCACTCTA 59.928 47.619 9.46 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2024 0.250338 GTGAACCTGTGGACCACTCC 60.25 60.0 24.81 10.01 35.11 3.85 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
271 274 1.071699 ACCGGAAAAGCTTGCACTCTA 59.928 47.619 9.46 0.00 0.00 2.43
327 330 1.135689 GTTTGCATGAATCTCGGCGTT 60.136 47.619 6.85 0.00 0.00 4.84
454 457 2.387445 CCGCTCAATTTCGTCGGCA 61.387 57.895 0.00 0.00 33.36 5.69
675 678 2.669229 TACTGCGTCGGTCCGTCA 60.669 61.111 11.88 7.25 0.00 4.35
780 786 2.745152 CGTGTTCTTCTGTTTGGGGAGT 60.745 50.000 0.00 0.00 0.00 3.85
794 800 1.153549 GGAGTAAGGGCACGCTCTG 60.154 63.158 0.00 0.00 0.00 3.35
937 943 1.214589 GGAACTTGACGCGCTCCTA 59.785 57.895 5.73 0.00 0.00 2.94
986 993 3.229697 GCAGGGGCCTATTATCAAGTT 57.770 47.619 0.84 0.00 0.00 2.66
1063 1070 0.174845 CTGCGGATGGAACTCGGTAA 59.825 55.000 0.00 0.00 0.00 2.85
1317 1324 2.935481 CTGGAGGAAGGTGGCCCA 60.935 66.667 0.00 0.00 0.00 5.36
1353 1360 3.476552 TGTCCAGTTTCTGTTGGATGTC 58.523 45.455 0.00 0.00 44.74 3.06
1356 1363 3.138304 CCAGTTTCTGTTGGATGTCGAA 58.862 45.455 0.00 0.00 36.55 3.71
1432 1442 1.825090 CATGTTGCTAGTCCAAGCCA 58.175 50.000 0.00 0.00 42.05 4.75
1449 1459 3.313791 AGCCACCCCTGTTTACATTTTT 58.686 40.909 0.00 0.00 0.00 1.94
1459 1469 6.102663 CCTGTTTACATTTTTGTTGTGTGGA 58.897 36.000 0.00 0.00 0.00 4.02
1460 1470 6.760770 CCTGTTTACATTTTTGTTGTGTGGAT 59.239 34.615 0.00 0.00 0.00 3.41
1489 1499 2.021355 AGTCACTACTACCTCCGTCG 57.979 55.000 0.00 0.00 32.84 5.12
1556 1566 8.439971 ACTAGGCACATTATTCATAGATTTGGA 58.560 33.333 0.00 0.00 0.00 3.53
1605 1615 5.779771 AGTCCATCCTTTATTGCCAGAAAAA 59.220 36.000 0.00 0.00 0.00 1.94
1607 1617 5.187576 TCCATCCTTTATTGCCAGAAAAAGG 59.812 40.000 6.39 6.39 46.14 3.11
1785 1800 1.691196 TTTCCCAACAGTCAGCCAAG 58.309 50.000 0.00 0.00 0.00 3.61
1788 1803 0.109342 CCCAACAGTCAGCCAAGAGT 59.891 55.000 0.00 0.00 0.00 3.24
1808 1823 1.189752 CTGCTGGTCAGGAAGCTAGA 58.810 55.000 0.00 0.00 40.21 2.43
1833 1860 3.569194 TTGTCCAACCAGCTTTCAGTA 57.431 42.857 0.00 0.00 0.00 2.74
1857 1884 2.621998 AGAATGCTTGGCACAGATATGC 59.378 45.455 0.00 0.00 43.04 3.14
1995 2052 0.105964 TCCACAGGTTCACCAACTCG 59.894 55.000 0.00 0.00 38.89 4.18
2255 2326 2.630098 GGCATCACTAGAGCATGAGGTA 59.370 50.000 0.00 0.00 0.00 3.08
2348 2419 4.272018 CCTCCTGCGTCAATCTATTTCTTG 59.728 45.833 0.00 0.00 0.00 3.02
2361 2432 5.083122 TCTATTTCTTGGGTGCCAAATTGA 58.917 37.500 0.00 0.00 43.44 2.57
2371 2442 3.446873 GGTGCCAAATTGACCACATGATA 59.553 43.478 14.97 0.00 0.00 2.15
2372 2443 4.081752 GGTGCCAAATTGACCACATGATAA 60.082 41.667 14.97 0.00 0.00 1.75
2373 2444 5.477510 GTGCCAAATTGACCACATGATAAA 58.522 37.500 0.00 0.00 0.00 1.40
2374 2445 5.577945 GTGCCAAATTGACCACATGATAAAG 59.422 40.000 0.00 0.00 0.00 1.85
2375 2446 5.479724 TGCCAAATTGACCACATGATAAAGA 59.520 36.000 0.00 0.00 0.00 2.52
2376 2447 5.807011 GCCAAATTGACCACATGATAAAGAC 59.193 40.000 0.00 0.00 0.00 3.01
2377 2448 6.572119 GCCAAATTGACCACATGATAAAGACA 60.572 38.462 0.00 0.00 0.00 3.41
2378 2449 6.808212 CCAAATTGACCACATGATAAAGACAC 59.192 38.462 0.00 0.00 0.00 3.67
2379 2450 5.801350 ATTGACCACATGATAAAGACACG 57.199 39.130 0.00 0.00 0.00 4.49
2380 2451 4.529109 TGACCACATGATAAAGACACGA 57.471 40.909 0.00 0.00 0.00 4.35
2381 2452 5.084818 TGACCACATGATAAAGACACGAT 57.915 39.130 0.00 0.00 0.00 3.73
2382 2453 4.869861 TGACCACATGATAAAGACACGATG 59.130 41.667 0.00 0.00 0.00 3.84
2383 2454 5.084818 ACCACATGATAAAGACACGATGA 57.915 39.130 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
271 274 2.289631 TGCAGAACATGTCGAGGACAAT 60.290 45.455 0.00 0.00 45.96 2.71
327 330 0.040157 CGAAGAACGTGTACACCGGA 60.040 55.000 20.11 0.00 37.22 5.14
333 336 0.038892 TCCCTGCGAAGAACGTGTAC 60.039 55.000 0.00 0.00 44.60 2.90
727 733 2.356313 CTGCACGTCGAGCCACTT 60.356 61.111 12.18 0.00 0.00 3.16
780 786 1.888436 CTGTCCAGAGCGTGCCCTTA 61.888 60.000 0.00 0.00 0.00 2.69
794 800 0.108233 CTCCTTCAGCTGCTCTGTCC 60.108 60.000 9.47 0.00 43.32 4.02
976 982 1.102978 GGCGCCCACAACTTGATAAT 58.897 50.000 18.11 0.00 0.00 1.28
979 985 3.055719 CGGCGCCCACAACTTGAT 61.056 61.111 23.46 0.00 0.00 2.57
1334 1341 2.367241 TCGACATCCAACAGAAACTGGA 59.633 45.455 0.00 0.00 45.65 3.86
1353 1360 3.908382 CGAGTTGCTTTCCAAGATTTTCG 59.092 43.478 0.00 0.00 33.21 3.46
1356 1363 2.029918 GCCGAGTTGCTTTCCAAGATTT 60.030 45.455 0.00 0.00 33.21 2.17
1432 1442 5.046231 ACACAACAAAAATGTAAACAGGGGT 60.046 36.000 0.00 0.00 0.00 4.95
1449 1459 8.995220 GTGACTTAAGTTATTATCCACACAACA 58.005 33.333 10.02 0.00 0.00 3.33
1460 1470 9.113838 CGGAGGTAGTAGTGACTTAAGTTATTA 57.886 37.037 10.02 4.01 37.10 0.98
1489 1499 7.009179 TCCATATGGGTCATATTCTTGAGAC 57.991 40.000 21.78 0.00 35.18 3.36
1590 1600 7.504403 TGATGTTTCCTTTTTCTGGCAATAAA 58.496 30.769 0.00 0.00 0.00 1.40
1768 1783 0.397941 CTCTTGGCTGACTGTTGGGA 59.602 55.000 0.00 0.00 0.00 4.37
1808 1823 3.513515 TGAAAGCTGGTTGGACAAAACTT 59.486 39.130 0.00 0.00 0.00 2.66
1833 1860 3.641434 ATCTGTGCCAAGCATTCTAGT 57.359 42.857 0.00 0.00 41.91 2.57
1857 1884 6.801539 TTAAGATCAATTAATAGCCTGGCG 57.198 37.500 13.96 0.00 0.00 5.69
1969 2024 0.250338 GTGAACCTGTGGACCACTCC 60.250 60.000 24.81 10.01 35.11 3.85
1980 2035 0.393077 ACCTCGAGTTGGTGAACCTG 59.607 55.000 12.31 0.00 36.30 4.00
2255 2326 3.096852 TCACACTCGTGGATATTCCTGT 58.903 45.455 1.77 0.00 43.79 4.00
2348 2419 0.975887 ATGTGGTCAATTTGGCACCC 59.024 50.000 3.03 0.00 0.00 4.61
2361 2432 5.084818 TCATCGTGTCTTTATCATGTGGT 57.915 39.130 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.