Multiple sequence alignment - TraesCS3B01G218400

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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 TraesCS3B01G218400 chr3B 100.000 3119 0 0 1 3119 261785476 261788594 0 5760
1 TraesCS3B01G218400 chr3D 93.675 3162 83 37 1 3119 182593428 182596515 0 4623
2 TraesCS3B01G218400 chr3A 93.402 3183 90 44 1 3119 231668922 231672048 0 4604


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 TraesCS3B01G218400 chr3B 261785476 261788594 3118 False 5760 5760 100.000 1 3119 1 chr3B.!!$F1 3118
1 TraesCS3B01G218400 chr3D 182593428 182596515 3087 False 4623 4623 93.675 1 3119 1 chr3D.!!$F1 3118
2 TraesCS3B01G218400 chr3A 231668922 231672048 3126 False 4604 4604 93.402 1 3119 1 chr3A.!!$F1 3118

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
765 791 2.280389 CGATGTGCATCCCTCCCG 60.28 66.667 6.6 0.0 34.4 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2204 0.107831 GTAGGTATGGCAATGGCGGA 59.892 55.0 1.51 0.0 42.47 5.54 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
684 710 5.752036 TGTGAATTGATTCTGTCTCTCCT 57.248 39.130 5.42 0.00 37.67 3.69
713 739 5.957798 TGCATTTGGTTCTTGATGAGATTC 58.042 37.500 0.00 0.00 33.49 2.52
765 791 2.280389 CGATGTGCATCCCTCCCG 60.280 66.667 6.60 0.00 34.40 5.14
906 951 2.577563 TCAGATTCTTGGCCATTCCTGA 59.422 45.455 6.09 12.56 35.26 3.86
937 982 5.744594 GCTCTAATCTTCCCCTTCCTGATTC 60.745 48.000 0.00 0.00 0.00 2.52
1749 1800 1.669115 CAGGCACAGGTTCCACTCG 60.669 63.158 0.00 0.00 0.00 4.18
1858 1909 4.082523 GCAGCGGCAGTGGGAGTA 62.083 66.667 3.18 0.00 40.72 2.59
1859 1910 2.185350 CAGCGGCAGTGGGAGTAG 59.815 66.667 1.45 0.00 0.00 2.57
1860 1911 3.775654 AGCGGCAGTGGGAGTAGC 61.776 66.667 1.45 0.00 0.00 3.58
1932 1983 1.477553 ATGTGGATGGTCATGGCAAC 58.522 50.000 0.00 0.00 0.00 4.17
1992 2043 1.226974 CGAAGACGGCGATGTGGAT 60.227 57.895 16.62 0.00 35.72 3.41
2006 2057 1.142060 TGTGGATGGTGAAGGAAACGT 59.858 47.619 0.00 0.00 0.00 3.99
2073 2124 1.217585 CGCAGGCTACATCACCATCG 61.218 60.000 0.00 0.00 0.00 3.84
2141 2203 0.036732 TGCTCTGCTCCGTTTGGATT 59.963 50.000 0.00 0.00 45.33 3.01
2142 2204 1.168714 GCTCTGCTCCGTTTGGATTT 58.831 50.000 0.00 0.00 45.33 2.17
2143 2205 1.131315 GCTCTGCTCCGTTTGGATTTC 59.869 52.381 0.00 0.00 45.33 2.17
2144 2206 1.740025 CTCTGCTCCGTTTGGATTTCC 59.260 52.381 0.00 0.00 45.33 3.13
2344 2406 1.774639 TTCAAACTCTACACGACGGC 58.225 50.000 0.00 0.00 0.00 5.68
2351 2413 2.094182 ACTCTACACGACGGCAATCAAT 60.094 45.455 0.00 0.00 0.00 2.57
2354 2416 0.321210 ACACGACGGCAATCAATCCA 60.321 50.000 0.00 0.00 0.00 3.41
2355 2417 1.016627 CACGACGGCAATCAATCCAT 58.983 50.000 0.00 0.00 0.00 3.41
2356 2418 1.003545 CACGACGGCAATCAATCCATC 60.004 52.381 0.00 0.00 0.00 3.51
2357 2419 0.588252 CGACGGCAATCAATCCATCC 59.412 55.000 0.00 0.00 0.00 3.51
2358 2420 1.811558 CGACGGCAATCAATCCATCCT 60.812 52.381 0.00 0.00 0.00 3.24
2359 2421 1.605710 GACGGCAATCAATCCATCCTG 59.394 52.381 0.00 0.00 0.00 3.86
2360 2422 1.064463 ACGGCAATCAATCCATCCTGT 60.064 47.619 0.00 0.00 0.00 4.00
2362 2424 2.381911 GGCAATCAATCCATCCTGTGT 58.618 47.619 0.00 0.00 0.00 3.72
2365 2427 3.181493 GCAATCAATCCATCCTGTGTCAC 60.181 47.826 0.00 0.00 0.00 3.67
2368 2430 3.678289 TCAATCCATCCTGTGTCACAAG 58.322 45.455 7.18 0.61 0.00 3.16
2370 2432 2.839486 TCCATCCTGTGTCACAAGTC 57.161 50.000 7.18 0.00 0.00 3.01
2372 2434 2.146342 CCATCCTGTGTCACAAGTCAC 58.854 52.381 7.18 0.00 34.90 3.67
2383 2445 0.179018 ACAAGTCACAAGTCTGGGCC 60.179 55.000 0.00 0.00 0.00 5.80
2384 2446 0.890996 CAAGTCACAAGTCTGGGCCC 60.891 60.000 17.59 17.59 0.00 5.80
2388 2450 0.038166 TCACAAGTCTGGGCCCAATC 59.962 55.000 28.29 20.96 0.00 2.67
2390 2452 2.044946 AAGTCTGGGCCCAATCGC 60.045 61.111 28.29 15.65 0.00 4.58
2392 2454 2.044946 GTCTGGGCCCAATCGCTT 60.045 61.111 28.29 0.00 0.00 4.68
2394 2456 0.179018 GTCTGGGCCCAATCGCTTAT 60.179 55.000 28.29 0.00 0.00 1.73
2395 2457 0.179020 TCTGGGCCCAATCGCTTATG 60.179 55.000 28.29 11.02 0.00 1.90
2396 2458 0.466189 CTGGGCCCAATCGCTTATGT 60.466 55.000 28.29 0.00 0.00 2.29
2397 2459 0.033601 TGGGCCCAATCGCTTATGTT 60.034 50.000 26.33 0.00 0.00 2.71
2398 2460 1.213182 TGGGCCCAATCGCTTATGTTA 59.787 47.619 26.33 0.00 0.00 2.41
2399 2461 1.880027 GGGCCCAATCGCTTATGTTAG 59.120 52.381 19.95 0.00 0.00 2.34
2400 2462 2.486548 GGGCCCAATCGCTTATGTTAGA 60.487 50.000 19.95 0.00 0.00 2.10
2401 2463 3.211045 GGCCCAATCGCTTATGTTAGAA 58.789 45.455 0.00 0.00 0.00 2.10
2402 2464 3.630312 GGCCCAATCGCTTATGTTAGAAA 59.370 43.478 0.00 0.00 0.00 2.52
2403 2465 4.278419 GGCCCAATCGCTTATGTTAGAAAT 59.722 41.667 0.00 0.00 0.00 2.17
2404 2466 5.472137 GGCCCAATCGCTTATGTTAGAAATA 59.528 40.000 0.00 0.00 0.00 1.40
2405 2467 6.016610 GGCCCAATCGCTTATGTTAGAAATAA 60.017 38.462 0.00 0.00 0.00 1.40
2406 2468 7.422399 GCCCAATCGCTTATGTTAGAAATAAA 58.578 34.615 0.00 0.00 0.00 1.40
2407 2469 7.378728 GCCCAATCGCTTATGTTAGAAATAAAC 59.621 37.037 0.00 0.00 0.00 2.01
2409 2471 9.781834 CCAATCGCTTATGTTAGAAATAAACAA 57.218 29.630 0.00 0.00 40.05 2.83
2412 2474 8.868744 TCGCTTATGTTAGAAATAAACAAACG 57.131 30.769 0.00 0.00 40.05 3.60
2413 2475 7.479291 TCGCTTATGTTAGAAATAAACAAACGC 59.521 33.333 0.00 0.00 40.05 4.84
2414 2476 7.253190 CGCTTATGTTAGAAATAAACAAACGCC 60.253 37.037 0.00 0.00 40.05 5.68
2415 2477 7.753580 GCTTATGTTAGAAATAAACAAACGCCT 59.246 33.333 0.00 0.00 40.05 5.52
2416 2478 9.620660 CTTATGTTAGAAATAAACAAACGCCTT 57.379 29.630 0.00 0.00 40.05 4.35
2417 2479 9.968870 TTATGTTAGAAATAAACAAACGCCTTT 57.031 25.926 0.00 0.00 40.05 3.11
2418 2480 7.687005 TGTTAGAAATAAACAAACGCCTTTG 57.313 32.000 6.63 6.63 42.33 2.77
2431 2493 3.733337 ACGCCTTTGTATCATCATCCTC 58.267 45.455 0.00 0.00 0.00 3.71
2432 2494 2.733552 CGCCTTTGTATCATCATCCTCG 59.266 50.000 0.00 0.00 0.00 4.63
2446 2508 4.445453 TCATCCTCGACCATTTTGAGATG 58.555 43.478 0.00 0.00 37.93 2.90
2455 2524 5.122239 CGACCATTTTGAGATGAACTAGCAA 59.878 40.000 0.00 0.00 0.00 3.91
2458 2527 7.168219 ACCATTTTGAGATGAACTAGCAAGTA 58.832 34.615 0.00 0.00 33.75 2.24
2459 2528 7.335422 ACCATTTTGAGATGAACTAGCAAGTAG 59.665 37.037 0.00 0.00 33.75 2.57
2460 2529 6.727824 TTTTGAGATGAACTAGCAAGTAGC 57.272 37.500 0.00 0.00 46.19 3.58
2543 2612 8.418662 AGGTAGTTCAATCGTTGCATATAAGTA 58.581 33.333 0.00 0.00 0.00 2.24
2546 2615 8.718102 AGTTCAATCGTTGCATATAAGTAAGT 57.282 30.769 0.00 0.00 0.00 2.24
2598 2675 5.648526 TGCGATAATAGTTTTGGTGGCTAAA 59.351 36.000 0.00 0.00 0.00 1.85
2713 2792 2.961522 CGTAGCCTCGCAAAAAGAAA 57.038 45.000 0.00 0.00 0.00 2.52
2714 2793 2.839474 CGTAGCCTCGCAAAAAGAAAG 58.161 47.619 0.00 0.00 0.00 2.62
2715 2794 2.478894 CGTAGCCTCGCAAAAAGAAAGA 59.521 45.455 0.00 0.00 0.00 2.52
2716 2795 3.059188 CGTAGCCTCGCAAAAAGAAAGAA 60.059 43.478 0.00 0.00 0.00 2.52
2717 2796 3.632855 AGCCTCGCAAAAAGAAAGAAG 57.367 42.857 0.00 0.00 0.00 2.85
2755 2834 0.961019 ATGGTGTTGCATTGTCGCTT 59.039 45.000 0.00 0.00 0.00 4.68
2756 2835 0.310543 TGGTGTTGCATTGTCGCTTC 59.689 50.000 0.00 0.00 0.00 3.86
2757 2836 0.725784 GGTGTTGCATTGTCGCTTCG 60.726 55.000 0.00 0.00 0.00 3.79
2758 2837 1.082169 TGTTGCATTGTCGCTTCGC 60.082 52.632 0.00 0.00 0.00 4.70
2759 2838 1.207593 GTTGCATTGTCGCTTCGCT 59.792 52.632 0.00 0.00 0.00 4.93
2829 2908 0.967380 GGTGAAGGGCCACAATGGAG 60.967 60.000 6.18 0.00 40.96 3.86
2847 2926 1.008538 GTCACCAGCGTTGCAAAGG 60.009 57.895 14.31 10.21 34.21 3.11
2958 3037 1.592669 GATCACGCCCCTCACGATG 60.593 63.158 0.00 0.00 0.00 3.84
3030 3109 0.687354 TCTTGAGCTCAGGAACCACC 59.313 55.000 24.81 0.00 39.35 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 75 4.696877 CCATCTCAGCAAACATCTGTTACA 59.303 41.667 0.00 0.00 37.25 2.41
193 209 9.489084 AGGCTCAAGGAAAACATTTTATTTTAC 57.511 29.630 0.00 0.00 31.08 2.01
621 643 3.131223 TCGGAGGAGAATGATGAACAGAC 59.869 47.826 0.00 0.00 0.00 3.51
684 710 4.478206 TCAAGAACCAAATGCAAAACCA 57.522 36.364 0.00 0.00 0.00 3.67
713 739 5.772521 CTCCAAAAACAACATCTACCCAAG 58.227 41.667 0.00 0.00 0.00 3.61
765 791 6.077197 TGTTTTTGTCATCGAATCGAATGAC 58.923 36.000 26.07 26.07 39.99 3.06
795 826 3.019564 GCTAACCACATGAGATTGCCTT 58.980 45.455 0.00 0.00 0.00 4.35
796 827 2.240667 AGCTAACCACATGAGATTGCCT 59.759 45.455 0.00 0.00 0.00 4.75
906 951 2.630580 GGGGAAGATTAGAGCTCGACAT 59.369 50.000 8.37 1.27 0.00 3.06
937 982 4.158949 TCTTGGATTTGGCACTGATGAATG 59.841 41.667 0.00 0.00 0.00 2.67
1632 1683 3.966543 CCACCCACCACCTCCACC 61.967 72.222 0.00 0.00 0.00 4.61
1815 1866 1.737008 GCTCTTTGGGTCGTCGTCC 60.737 63.158 0.00 0.00 0.00 4.79
1858 1909 4.962836 GGTGGTGGTGCTGCTGCT 62.963 66.667 17.00 0.00 40.48 4.24
1860 1911 3.289834 GTGGTGGTGGTGCTGCTG 61.290 66.667 0.00 0.00 0.00 4.41
1932 1983 0.108898 CTGCCTCAACTCCACTCTCG 60.109 60.000 0.00 0.00 0.00 4.04
1941 1992 3.574074 ATTGCCCGCTGCCTCAACT 62.574 57.895 0.00 0.00 40.16 3.16
1943 1994 3.063704 CATTGCCCGCTGCCTCAA 61.064 61.111 0.00 0.00 40.16 3.02
1975 2026 1.154205 CCATCCACATCGCCGTCTTC 61.154 60.000 0.00 0.00 0.00 2.87
1992 2043 0.534203 GGCTCACGTTTCCTTCACCA 60.534 55.000 0.00 0.00 0.00 4.17
2040 2091 1.758514 CTGCGGGGAGAAGAGGCTA 60.759 63.158 0.00 0.00 0.00 3.93
2061 2112 2.167693 GGAAGTGGACGATGGTGATGTA 59.832 50.000 0.00 0.00 0.00 2.29
2073 2124 1.671379 GCCGGAAGTGGAAGTGGAC 60.671 63.158 5.05 0.00 0.00 4.02
2141 2203 0.840617 TAGGTATGGCAATGGCGGAA 59.159 50.000 1.51 0.00 42.47 4.30
2142 2204 0.107831 GTAGGTATGGCAATGGCGGA 59.892 55.000 1.51 0.00 42.47 5.54
2143 2205 0.889186 GGTAGGTATGGCAATGGCGG 60.889 60.000 1.51 0.00 42.47 6.13
2144 2206 0.179032 TGGTAGGTATGGCAATGGCG 60.179 55.000 1.51 0.00 42.47 5.69
2344 2406 4.011698 TGTGACACAGGATGGATTGATTG 58.988 43.478 3.56 0.00 43.62 2.67
2351 2413 2.046292 TGACTTGTGACACAGGATGGA 58.954 47.619 23.09 0.00 43.62 3.41
2354 2416 3.118261 ACTTGTGACTTGTGACACAGGAT 60.118 43.478 23.09 8.36 45.90 3.24
2355 2417 2.236146 ACTTGTGACTTGTGACACAGGA 59.764 45.455 23.09 2.19 45.90 3.86
2356 2418 2.609459 GACTTGTGACTTGTGACACAGG 59.391 50.000 15.57 15.57 45.90 4.00
2357 2419 3.308053 CAGACTTGTGACTTGTGACACAG 59.692 47.826 8.55 6.00 45.90 3.66
2358 2420 3.261580 CAGACTTGTGACTTGTGACACA 58.738 45.455 3.56 3.56 44.36 3.72
2359 2421 2.609459 CCAGACTTGTGACTTGTGACAC 59.391 50.000 0.00 0.00 38.85 3.67
2360 2422 2.419990 CCCAGACTTGTGACTTGTGACA 60.420 50.000 0.00 0.00 0.00 3.58
2362 2424 1.475034 GCCCAGACTTGTGACTTGTGA 60.475 52.381 0.00 0.00 0.00 3.58
2365 2427 0.890996 GGGCCCAGACTTGTGACTTG 60.891 60.000 19.95 0.00 0.00 3.16
2368 2430 0.251341 ATTGGGCCCAGACTTGTGAC 60.251 55.000 26.87 0.00 0.00 3.67
2370 2432 1.308069 CGATTGGGCCCAGACTTGTG 61.308 60.000 26.87 8.18 0.00 3.33
2372 2434 2.409870 GCGATTGGGCCCAGACTTG 61.410 63.158 26.87 17.95 0.00 3.16
2383 2445 9.781834 TTGTTTATTTCTAACATAAGCGATTGG 57.218 29.630 0.00 0.00 35.60 3.16
2388 2450 7.253190 GGCGTTTGTTTATTTCTAACATAAGCG 60.253 37.037 0.00 0.00 40.17 4.68
2390 2452 9.620660 AAGGCGTTTGTTTATTTCTAACATAAG 57.379 29.630 0.00 0.00 35.60 1.73
2392 2454 9.400638 CAAAGGCGTTTGTTTATTTCTAACATA 57.599 29.630 20.91 0.00 38.64 2.29
2394 2456 7.687005 CAAAGGCGTTTGTTTATTTCTAACA 57.313 32.000 20.91 0.00 38.64 2.41
2409 2471 4.130118 GAGGATGATGATACAAAGGCGTT 58.870 43.478 0.00 0.00 0.00 4.84
2411 2473 2.733552 CGAGGATGATGATACAAAGGCG 59.266 50.000 0.00 0.00 0.00 5.52
2412 2474 3.743396 GTCGAGGATGATGATACAAAGGC 59.257 47.826 0.00 0.00 0.00 4.35
2413 2475 4.202253 TGGTCGAGGATGATGATACAAAGG 60.202 45.833 0.00 0.00 0.00 3.11
2414 2476 4.948847 TGGTCGAGGATGATGATACAAAG 58.051 43.478 0.00 0.00 0.00 2.77
2415 2477 5.551305 ATGGTCGAGGATGATGATACAAA 57.449 39.130 0.00 0.00 0.00 2.83
2416 2478 5.551305 AATGGTCGAGGATGATGATACAA 57.449 39.130 0.00 0.00 0.00 2.41
2417 2479 5.551305 AAATGGTCGAGGATGATGATACA 57.449 39.130 0.00 0.00 0.00 2.29
2418 2480 5.991606 TCAAAATGGTCGAGGATGATGATAC 59.008 40.000 0.00 0.00 0.00 2.24
2419 2481 6.041979 TCTCAAAATGGTCGAGGATGATGATA 59.958 38.462 0.00 0.00 0.00 2.15
2431 2493 4.631377 TGCTAGTTCATCTCAAAATGGTCG 59.369 41.667 0.00 0.00 0.00 4.79
2432 2494 6.150140 ACTTGCTAGTTCATCTCAAAATGGTC 59.850 38.462 0.00 0.00 0.00 4.02
2446 2508 4.685169 TGCATTTGCTACTTGCTAGTTC 57.315 40.909 6.03 0.00 43.37 3.01
2455 2524 6.912591 GCGTTATATTTCTTGCATTTGCTACT 59.087 34.615 3.94 0.00 42.66 2.57
2458 2527 5.649557 TGCGTTATATTTCTTGCATTTGCT 58.350 33.333 3.94 0.00 42.66 3.91
2459 2528 5.947503 TGCGTTATATTTCTTGCATTTGC 57.052 34.783 0.00 0.00 42.50 3.68
2460 2529 7.727955 TGTTTGCGTTATATTTCTTGCATTTG 58.272 30.769 0.00 0.00 31.70 2.32
2461 2530 7.881643 TGTTTGCGTTATATTTCTTGCATTT 57.118 28.000 0.00 0.00 31.70 2.32
2462 2531 7.383572 TGTTGTTTGCGTTATATTTCTTGCATT 59.616 29.630 0.00 0.00 31.70 3.56
2463 2532 6.865726 TGTTGTTTGCGTTATATTTCTTGCAT 59.134 30.769 0.00 0.00 31.70 3.96
2464 2533 6.209361 TGTTGTTTGCGTTATATTTCTTGCA 58.791 32.000 0.00 0.00 0.00 4.08
2465 2534 6.183359 CCTGTTGTTTGCGTTATATTTCTTGC 60.183 38.462 0.00 0.00 0.00 4.01
2466 2535 6.183359 GCCTGTTGTTTGCGTTATATTTCTTG 60.183 38.462 0.00 0.00 0.00 3.02
2467 2536 5.861787 GCCTGTTGTTTGCGTTATATTTCTT 59.138 36.000 0.00 0.00 0.00 2.52
2545 2614 9.583765 AGCTTGTTTTGCTACTACTACTATAAC 57.416 33.333 0.00 0.00 39.21 1.89
2546 2615 9.582431 CAGCTTGTTTTGCTACTACTACTATAA 57.418 33.333 0.00 0.00 38.92 0.98
2755 2834 0.108804 GTGTAAGCTAGTGGCAGCGA 60.109 55.000 0.00 0.00 46.52 4.93
2756 2835 1.413767 CGTGTAAGCTAGTGGCAGCG 61.414 60.000 0.00 0.00 46.52 5.18
2757 2836 1.084370 CCGTGTAAGCTAGTGGCAGC 61.084 60.000 0.00 0.00 44.79 5.25
2758 2837 0.246635 ACCGTGTAAGCTAGTGGCAG 59.753 55.000 0.00 0.00 44.79 4.85
2759 2838 0.245539 GACCGTGTAAGCTAGTGGCA 59.754 55.000 0.00 0.00 44.79 4.92
2829 2908 1.008538 CCTTTGCAACGCTGGTGAC 60.009 57.895 0.00 0.00 0.00 3.67
2847 2926 2.044946 AACGCCAAGGAGATGGGC 60.045 61.111 0.00 0.00 44.27 5.36
2931 3010 1.004440 GGGCGTGATCCCTATGCTC 60.004 63.158 0.00 0.00 43.13 4.26
3030 3109 1.136891 TCCATGCCGATACTGTCTGTG 59.863 52.381 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.