Multiple sequence alignment - TraesCS3A01G418400

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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 TraesCS3A01G418400 chr3A 100.000 2847 0 0 1 2847 660235949 660238795 0.000000e+00 5258.0
1 TraesCS3A01G418400 chr3B 94.376 2845 117 18 18 2847 694323657 694326473 0.000000e+00 4327.0
2 TraesCS3A01G418400 chr3B 80.214 374 52 14 2223 2589 140589901 140590259 7.820000e-66 261.0
3 TraesCS3A01G418400 chr3B 100.000 29 0 0 1 29 694323604 694323632 1.000000e-03 54.7
4 TraesCS3A01G418400 chr3D 93.836 2839 142 14 17 2843 526047809 526050626 0.000000e+00 4242.0
5 TraesCS3A01G418400 chr7D 81.333 375 44 18 2223 2592 162017692 162017339 6.010000e-72 281.0


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 TraesCS3A01G418400 chr3A 660235949 660238795 2846 False 5258.00 5258 100.000 1 2847 1 chr3A.!!$F1 2846
1 TraesCS3A01G418400 chr3B 694323604 694326473 2869 False 2190.85 4327 97.188 1 2847 2 chr3B.!!$F2 2846
2 TraesCS3A01G418400 chr3D 526047809 526050626 2817 False 4242.00 4242 93.836 17 2843 1 chr3D.!!$F1 2826

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
316 353 0.036010 AGCCAGTGGTTTCATCTCGG 60.036 55.0 11.74 0.0 0.0 4.63 F
408 445 0.442310 TTACGCTGCATCACGAAAGC 59.558 50.0 10.43 0.0 0.0 3.51 F
923 963 0.461693 GCTCACCCACTCATCTGCTC 60.462 60.0 0.00 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1154 1204 1.374758 GACTTCACCGGAGCCACTG 60.375 63.158 9.46 0.0 0.00 3.66 R
1254 1304 1.374758 GGTGTCCTTGCAGACCTCG 60.375 63.158 3.85 0.0 35.83 4.63 R
2277 2333 1.751351 TCGGATTGCGATCTCTCAACT 59.249 47.619 13.72 0.0 32.66 3.16 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
64 101 4.151157 GCGATGGTTACGTGTTTTTCTACT 59.849 41.667 0.00 0.00 0.00 2.57
66 103 6.294363 CGATGGTTACGTGTTTTTCTACTTC 58.706 40.000 0.00 0.00 0.00 3.01
131 168 2.536761 CGGTAAAATATCTCCGGCCA 57.463 50.000 2.24 0.00 39.41 5.36
197 234 4.400567 ACTTTGCCATCCAAGCTAGATTTC 59.599 41.667 0.00 0.00 34.34 2.17
209 246 2.475187 GCTAGATTTCGTGCAAGCTGTG 60.475 50.000 0.00 0.00 0.00 3.66
237 274 3.254629 TGGCAAGACAGGCAGAATC 57.745 52.632 0.00 0.00 39.34 2.52
250 287 1.671054 AGAATCCGCACAACGTGGG 60.671 57.895 0.00 4.34 46.14 4.61
295 332 6.370442 GCGATCTATACTTCTGCTAGAGAGAA 59.630 42.308 0.00 0.00 30.18 2.87
316 353 0.036010 AGCCAGTGGTTTCATCTCGG 60.036 55.000 11.74 0.00 0.00 4.63
319 356 1.363744 CAGTGGTTTCATCTCGGCTC 58.636 55.000 0.00 0.00 0.00 4.70
320 357 1.066573 CAGTGGTTTCATCTCGGCTCT 60.067 52.381 0.00 0.00 0.00 4.09
361 398 3.674997 TGGAGATGCTGGTTACTTTGTC 58.325 45.455 0.00 0.00 0.00 3.18
371 408 3.456644 TGGTTACTTTGTCCACTGGAGAA 59.543 43.478 3.48 3.48 33.04 2.87
374 411 3.864789 ACTTTGTCCACTGGAGAATGT 57.135 42.857 16.65 16.65 38.10 2.71
402 439 1.331756 CCCTGAATTACGCTGCATCAC 59.668 52.381 0.00 0.00 0.00 3.06
408 445 0.442310 TTACGCTGCATCACGAAAGC 59.558 50.000 10.43 0.00 0.00 3.51
411 448 1.510623 GCTGCATCACGAAAGCACG 60.511 57.895 0.00 0.00 35.69 5.34
458 495 7.509141 TCATGAAAGTAATTGAAGCAGAACA 57.491 32.000 0.00 0.00 0.00 3.18
467 507 8.887717 AGTAATTGAAGCAGAACATAGATGAAC 58.112 33.333 0.00 0.00 0.00 3.18
474 514 6.000219 AGCAGAACATAGATGAACACAAAGT 59.000 36.000 0.00 0.00 0.00 2.66
480 520 3.678056 AGATGAACACAAAGTAGGCGA 57.322 42.857 0.00 0.00 0.00 5.54
481 521 3.589988 AGATGAACACAAAGTAGGCGAG 58.410 45.455 0.00 0.00 0.00 5.03
553 593 6.759272 TGCTGATTCCATGTACTCCTAATAC 58.241 40.000 0.00 0.00 0.00 1.89
590 630 3.440522 CAGGAGTCATCAACTAGTCACGA 59.559 47.826 0.00 0.00 38.74 4.35
670 710 4.012895 CGCCGGTGCAAGTGTCAC 62.013 66.667 0.00 0.00 37.32 3.67
768 808 1.477195 CGGTTACCCAAAACACCCTCA 60.477 52.381 0.00 0.00 0.00 3.86
770 810 1.611977 GTTACCCAAAACACCCTCAGC 59.388 52.381 0.00 0.00 0.00 4.26
772 812 2.268076 CCCAAAACACCCTCAGCGG 61.268 63.158 0.00 0.00 0.00 5.52
860 900 2.909006 TCAGAAGAAACCATCTCTGCCT 59.091 45.455 0.00 0.00 37.42 4.75
870 910 0.965439 ATCTCTGCCTGATAGCCGAC 59.035 55.000 0.00 0.00 0.00 4.79
923 963 0.461693 GCTCACCCACTCATCTGCTC 60.462 60.000 0.00 0.00 0.00 4.26
928 978 1.525923 CCACTCATCTGCTCCAGGG 59.474 63.158 0.00 0.00 31.51 4.45
944 994 2.289694 CCAGGGAAACACCACTCTGTAG 60.290 54.545 0.00 0.00 41.20 2.74
969 1019 0.462937 CAACTCACACCACCCGTTGA 60.463 55.000 0.00 0.00 37.69 3.18
1141 1191 1.742880 CTGATGGTGGTGTCTGGCG 60.743 63.158 0.00 0.00 0.00 5.69
1399 1449 5.635417 TCACTGATGAACTACTGTCTCAG 57.365 43.478 0.00 0.00 35.29 3.35
1404 1454 4.702612 TGATGAACTACTGTCTCAGTCTCC 59.297 45.833 5.66 0.00 41.21 3.71
1506 1556 2.746362 CAGCAGAGTGATGAAACTTCCC 59.254 50.000 0.00 0.00 35.45 3.97
1654 1704 1.400846 CCATCTTGCTGTCTCATGTGC 59.599 52.381 0.00 0.00 0.00 4.57
1655 1705 1.062148 CATCTTGCTGTCTCATGTGCG 59.938 52.381 0.00 0.00 0.00 5.34
1657 1707 0.870393 CTTGCTGTCTCATGTGCGTT 59.130 50.000 0.00 0.00 0.00 4.84
1669 1719 5.912396 TCTCATGTGCGTTTTGTATTTTGTC 59.088 36.000 0.00 0.00 0.00 3.18
1714 1769 1.885887 GGTGCTTGTCAATTGTAGCCA 59.114 47.619 19.59 10.35 32.73 4.75
1822 1877 0.376852 TTGATGAATTAGCGCGTGCC 59.623 50.000 19.02 1.77 44.31 5.01
1873 1928 1.619827 CCCTGGAAAGAAATGCAGCAA 59.380 47.619 0.00 0.00 37.43 3.91
2258 2314 8.609176 TGTCAATAACTTCAAATATTAGCCGTC 58.391 33.333 0.00 0.00 0.00 4.79
2277 2333 4.546570 CGTCGGATATGCTCTATCAAACA 58.453 43.478 8.50 0.00 0.00 2.83
2345 2401 8.196771 AGTTTTCAACTCATAAGATTTTGCACA 58.803 29.630 0.00 0.00 37.02 4.57
2372 2428 4.319177 CTTCTAACTGAACCCCAACTCTG 58.681 47.826 0.00 0.00 0.00 3.35
2589 2645 4.532276 TGCAAAGCACGTACAATTTACTG 58.468 39.130 0.00 0.00 31.71 2.74
2689 2747 9.628500 ATTATGGAAAAGTAACTCTGAATACCC 57.372 33.333 0.00 0.00 0.00 3.69
2734 2792 6.180472 ACCATGGTGAGTTCCAAGTATAAAG 58.820 40.000 18.99 0.00 41.09 1.85
2748 2806 6.312426 CCAAGTATAAAGTGAGCTGTGAAGAG 59.688 42.308 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 68 1.727511 TAACCATCGCGGACGGTAGG 61.728 60.000 6.13 0.39 40.63 3.18
48 85 4.805192 ACGCAGAAGTAGAAAAACACGTAA 59.195 37.500 0.00 0.00 0.00 3.18
64 101 1.297378 CTACGATCGCGACGCAGAA 60.297 57.895 24.04 4.74 41.64 3.02
66 103 3.379625 GCTACGATCGCGACGCAG 61.380 66.667 24.04 21.90 41.64 5.18
131 168 4.978099 TCAGAGAAGCAATGGAAAGTTCT 58.022 39.130 0.00 0.00 0.00 3.01
159 196 0.685097 AAAGTCTGTGGCTCCGCTAA 59.315 50.000 0.86 0.00 0.00 3.09
176 213 3.378112 CGAAATCTAGCTTGGATGGCAAA 59.622 43.478 0.00 0.00 0.00 3.68
197 234 1.447317 AAACCTCCACAGCTTGCACG 61.447 55.000 0.00 0.00 0.00 5.34
209 246 1.882623 CTGTCTTGCCAGAAAACCTCC 59.117 52.381 0.00 0.00 34.23 4.30
295 332 2.154462 CGAGATGAAACCACTGGCTTT 58.846 47.619 0.00 0.00 0.00 3.51
316 353 0.179062 AATCAGCATCACCCGAGAGC 60.179 55.000 0.00 0.00 0.00 4.09
319 356 0.179100 ACGAATCAGCATCACCCGAG 60.179 55.000 0.00 0.00 0.00 4.63
320 357 0.249120 AACGAATCAGCATCACCCGA 59.751 50.000 0.00 0.00 0.00 5.14
361 398 2.741228 GCAGCTCTACATTCTCCAGTGG 60.741 54.545 1.40 1.40 0.00 4.00
371 408 3.493350 CGTAATTCAGGGCAGCTCTACAT 60.493 47.826 0.00 0.00 0.00 2.29
374 411 1.202533 GCGTAATTCAGGGCAGCTCTA 60.203 52.381 0.00 0.00 0.00 2.43
433 470 8.114331 TGTTCTGCTTCAATTACTTTCATGAT 57.886 30.769 0.00 0.00 0.00 2.45
434 471 7.509141 TGTTCTGCTTCAATTACTTTCATGA 57.491 32.000 0.00 0.00 0.00 3.07
435 472 9.499585 CTATGTTCTGCTTCAATTACTTTCATG 57.500 33.333 0.00 0.00 0.00 3.07
458 495 5.339008 TCGCCTACTTTGTGTTCATCTAT 57.661 39.130 0.00 0.00 0.00 1.98
467 507 3.314541 AGTTACCTCGCCTACTTTGTG 57.685 47.619 0.00 0.00 0.00 3.33
474 514 3.347216 ACGAGTAAAGTTACCTCGCCTA 58.653 45.455 18.73 0.00 37.58 3.93
480 520 6.040166 TCTGACTGAAACGAGTAAAGTTACCT 59.960 38.462 0.00 0.00 34.19 3.08
481 521 6.211515 TCTGACTGAAACGAGTAAAGTTACC 58.788 40.000 0.00 0.00 34.19 2.85
553 593 1.615883 CTCCTGAGGTATCACGATGGG 59.384 57.143 0.00 0.00 0.00 4.00
590 630 0.245266 TCGTCGCCACATGTGTGTAT 59.755 50.000 23.79 0.00 44.21 2.29
670 710 2.346545 CAGCGTGTGTGACATCTGTATG 59.653 50.000 0.00 0.00 39.17 2.39
768 808 1.204941 GATCCTGTACTTGTCACCGCT 59.795 52.381 0.00 0.00 0.00 5.52
770 810 1.548719 TGGATCCTGTACTTGTCACCG 59.451 52.381 14.23 0.00 0.00 4.94
772 812 2.622436 GCTGGATCCTGTACTTGTCAC 58.378 52.381 18.82 0.00 0.00 3.67
774 814 1.204941 ACGCTGGATCCTGTACTTGTC 59.795 52.381 18.82 1.01 0.00 3.18
860 900 3.502356 TGGTGGTATATGTCGGCTATCA 58.498 45.455 0.00 0.00 0.00 2.15
870 910 1.946768 CCGGTTGCTTGGTGGTATATG 59.053 52.381 0.00 0.00 0.00 1.78
923 963 0.474184 ACAGAGTGGTGTTTCCCTGG 59.526 55.000 0.00 0.00 34.77 4.45
928 978 3.391049 GTGGTCTACAGAGTGGTGTTTC 58.609 50.000 0.00 0.00 31.46 2.78
944 994 0.818040 GGTGGTGTGAGTTGGTGGTC 60.818 60.000 0.00 0.00 0.00 4.02
969 1019 1.144298 AGTTTTGGAAGGTAACGCCCT 59.856 47.619 0.00 0.00 46.39 5.19
1044 1094 4.593864 GAGGAGATGGCCGGCGAC 62.594 72.222 22.54 14.10 0.00 5.19
1154 1204 1.374758 GACTTCACCGGAGCCACTG 60.375 63.158 9.46 0.00 0.00 3.66
1203 1253 4.373116 GGCGCTTCCACCTCGTCA 62.373 66.667 7.64 0.00 34.01 4.35
1254 1304 1.374758 GGTGTCCTTGCAGACCTCG 60.375 63.158 3.85 0.00 35.83 4.63
1399 1449 5.808366 TGTATGTCAGGAATATGGGAGAC 57.192 43.478 0.00 0.00 0.00 3.36
1404 1454 6.169094 CCTAGCTTGTATGTCAGGAATATGG 58.831 44.000 0.00 0.00 0.00 2.74
1484 1534 3.406764 GGAAGTTTCATCACTCTGCTGT 58.593 45.455 0.00 0.00 0.00 4.40
1669 1719 8.944029 CCAAGAAGCTTACCATGATATATTCAG 58.056 37.037 0.00 0.00 37.89 3.02
1714 1769 2.656947 TACCAAGCTCCTTTGCAAGT 57.343 45.000 0.00 0.00 34.99 3.16
1822 1877 4.070716 AGCTTGACTTCACTTCCTCAATG 58.929 43.478 0.00 0.00 0.00 2.82
1873 1928 7.014711 AGTGTACACTAGTGATAGCATGCTAAT 59.985 37.037 30.06 18.37 40.43 1.73
2056 2111 3.798202 AGATCAGGAAGCAACCGTATTC 58.202 45.455 0.00 0.00 34.73 1.75
2145 2201 2.915349 AGCTTAGTGTCATGATGCCTG 58.085 47.619 0.00 0.00 0.00 4.85
2233 2289 7.792508 CGACGGCTAATATTTGAAGTTATTGAC 59.207 37.037 0.77 0.00 0.00 3.18
2258 2314 5.985530 TCAACTGTTTGATAGAGCATATCCG 59.014 40.000 6.52 0.00 36.79 4.18
2277 2333 1.751351 TCGGATTGCGATCTCTCAACT 59.249 47.619 13.72 0.00 32.66 3.16
2288 2344 2.794910 AGATGATAACGTTCGGATTGCG 59.205 45.455 2.82 0.00 0.00 4.85
2345 2401 2.378547 TGGGGTTCAGTTAGAAGGCAAT 59.621 45.455 0.00 0.00 36.78 3.56
2372 2428 7.763528 AGATGTTTCTAGAACACATCAGATGAC 59.236 37.037 33.29 20.57 46.30 3.06
2439 2495 5.221621 CCCCTCTAGAATCCAGATTGTTCTC 60.222 48.000 0.00 0.00 34.33 2.87
2617 2675 4.326826 TGCTATTGCAGTTTAAGCTCTGT 58.673 39.130 0.00 0.00 45.31 3.41
2734 2792 3.260740 CCTTCATCTCTTCACAGCTCAC 58.739 50.000 0.00 0.00 0.00 3.51
2748 2806 3.543680 TGCTAGCAAGGTACCTTCATC 57.456 47.619 24.73 15.64 33.42 2.92


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

AutoCloner maintained by Alex Coulton.