Multiple sequence alignment - TraesCS4A01G051500

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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 TraesCS4A01G051500 chr4A 100.000 2405 0 0 1 2405 42260067 42262471 0.000000e+00 4442
1 TraesCS4A01G051500 chr4A 98.624 218 3 0 488 705 42254988 42254771 1.040000e-103 387
2 TraesCS4A01G051500 chr4D 92.401 1724 88 21 708 2405 421557629 421555923 0.000000e+00 2418
3 TraesCS4A01G051500 chr4B 93.200 1500 58 17 744 2225 518688203 518686730 0.000000e+00 2165
4 TraesCS4A01G051500 chr4B 94.444 144 8 0 2262 2405 518678143 518678000 3.110000e-54 222
5 TraesCS4A01G051500 chr2B 99.151 707 5 1 1 706 423900522 423899816 0.000000e+00 1271
6 TraesCS4A01G051500 chr2B 92.160 727 34 8 1 705 655905341 655906066 0.000000e+00 1005
7 TraesCS4A01G051500 chr3A 98.584 706 9 1 1 705 443993629 443994334 0.000000e+00 1247
8 TraesCS4A01G051500 chr3A 88.308 727 61 7 1 705 210224924 210224200 0.000000e+00 850
9 TraesCS4A01G051500 chr1B 98.584 706 9 1 1 705 391583099 391583804 0.000000e+00 1247
10 TraesCS4A01G051500 chr1B 98.159 706 12 1 1 705 346966583 346965878 0.000000e+00 1230
11 TraesCS4A01G051500 chr1B 99.083 218 2 0 488 705 391577711 391577494 2.240000e-105 392
12 TraesCS4A01G051500 chr1B 98.198 222 4 0 485 706 346968500 346968721 2.900000e-104 388
13 TraesCS4A01G051500 chr6B 98.023 708 13 1 1 707 551807695 551808402 0.000000e+00 1229
14 TraesCS4A01G051500 chr6B 98.630 219 3 0 488 706 551804902 551804684 2.900000e-104 388
15 TraesCS4A01G051500 chr5A 89.271 727 55 9 1 705 665966144 665966869 0.000000e+00 889
16 TraesCS4A01G051500 chr2A 80.320 813 81 36 1400 2157 727169136 727168348 2.100000e-150 542


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 TraesCS4A01G051500 chr4A 42260067 42262471 2404 False 4442 4442 100.000 1 2405 1 chr4A.!!$F1 2404
1 TraesCS4A01G051500 chr4D 421555923 421557629 1706 True 2418 2418 92.401 708 2405 1 chr4D.!!$R1 1697
2 TraesCS4A01G051500 chr4B 518686730 518688203 1473 True 2165 2165 93.200 744 2225 1 chr4B.!!$R2 1481
3 TraesCS4A01G051500 chr2B 423899816 423900522 706 True 1271 1271 99.151 1 706 1 chr2B.!!$R1 705
4 TraesCS4A01G051500 chr2B 655905341 655906066 725 False 1005 1005 92.160 1 705 1 chr2B.!!$F1 704
5 TraesCS4A01G051500 chr3A 443993629 443994334 705 False 1247 1247 98.584 1 705 1 chr3A.!!$F1 704
6 TraesCS4A01G051500 chr3A 210224200 210224924 724 True 850 850 88.308 1 705 1 chr3A.!!$R1 704
7 TraesCS4A01G051500 chr1B 391583099 391583804 705 False 1247 1247 98.584 1 705 1 chr1B.!!$F2 704
8 TraesCS4A01G051500 chr1B 346965878 346966583 705 True 1230 1230 98.159 1 705 1 chr1B.!!$R1 704
9 TraesCS4A01G051500 chr6B 551807695 551808402 707 False 1229 1229 98.023 1 707 1 chr6B.!!$F1 706
10 TraesCS4A01G051500 chr5A 665966144 665966869 725 False 889 889 89.271 1 705 1 chr5A.!!$F1 704
11 TraesCS4A01G051500 chr2A 727168348 727169136 788 True 542 542 80.320 1400 2157 1 chr2A.!!$R1 757

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
762 785 0.988063 AAGAGAACAGCCTCCTTCCC 59.012 55.0 0.0 0.0 33.76 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 1814 0.322546 AGAACGAAGGGTGGATTGCC 60.323 55.0 0.0 0.0 0.0 4.52 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
137 138 1.716826 CTCCTCGCCGTCTCCTACAC 61.717 65.000 0.00 0.00 0.00 2.90
719 742 6.573434 CAATTATCTCTTAAAAAGGCCACCC 58.427 40.000 5.01 0.00 0.00 4.61
742 765 4.899239 CGCCGCATCCTCCTCCAC 62.899 72.222 0.00 0.00 0.00 4.02
752 775 2.251818 TCCTCCTCCACAAGAGAACAG 58.748 52.381 0.00 0.00 46.50 3.16
753 776 1.338579 CCTCCTCCACAAGAGAACAGC 60.339 57.143 0.00 0.00 46.50 4.40
759 782 1.072965 CCACAAGAGAACAGCCTCCTT 59.927 52.381 0.00 0.00 33.76 3.36
762 785 0.988063 AAGAGAACAGCCTCCTTCCC 59.012 55.000 0.00 0.00 33.76 3.97
977 1007 2.115343 CCTGCCTAGGGTTTTGAGTC 57.885 55.000 11.72 0.00 40.63 3.36
1420 1455 4.144703 GAGCCCCGGACGAGAACC 62.145 72.222 0.73 0.00 0.00 3.62
1562 1604 1.938585 TCAGTAGCTGCTGGTTACCT 58.061 50.000 28.47 0.00 37.12 3.08
1641 1685 1.131126 CACCTTGTCGTGGCAATGATC 59.869 52.381 0.00 0.00 0.00 2.92
1650 1694 3.129113 TCGTGGCAATGATCCAAGATTTG 59.871 43.478 0.00 0.00 37.22 2.32
1749 1814 2.836981 TGGAACAAGGCCCAAATTATGG 59.163 45.455 0.00 1.03 42.79 2.74
1794 1859 2.767505 CAGTAGTGTGTTCTGAACCCC 58.232 52.381 17.26 8.85 0.00 4.95
1805 1870 1.281867 TCTGAACCCCGATCATGCTTT 59.718 47.619 0.00 0.00 0.00 3.51
1824 1889 8.500773 CATGCTTTTATTTGAATTTTCTGTGCT 58.499 29.630 0.00 0.00 0.00 4.40
1906 1977 7.815068 TCTCACTTTTAGTATGCTCTGTCTTTC 59.185 37.037 0.00 0.00 0.00 2.62
2003 2084 3.697045 ACCTACTGGTCGAATTCTGAGAG 59.303 47.826 3.52 4.79 44.78 3.20
2031 2112 4.023291 AGTCAAGCCCTTCTGTTTCAAAA 58.977 39.130 0.00 0.00 0.00 2.44
2032 2113 4.112634 GTCAAGCCCTTCTGTTTCAAAAC 58.887 43.478 0.00 0.00 39.33 2.43
2033 2114 3.132111 TCAAGCCCTTCTGTTTCAAAACC 59.868 43.478 3.33 0.00 38.11 3.27
2119 2210 3.885484 ATTGCTGAATATGCAGTACGC 57.115 42.857 12.50 0.00 41.71 4.42
2126 2217 3.809279 TGAATATGCAGTACGCCAATCAG 59.191 43.478 0.00 0.00 41.33 2.90
2140 2231 3.087031 CCAATCAGAACATTGTGCCTCT 58.913 45.455 0.00 0.00 32.61 3.69
2146 2237 2.079925 GAACATTGTGCCTCTCAGTCC 58.920 52.381 0.00 0.00 0.00 3.85
2149 2240 2.289945 ACATTGTGCCTCTCAGTCCTTC 60.290 50.000 0.00 0.00 0.00 3.46
2191 2284 2.916702 TTGTGTCTCAGTCACTGCAT 57.083 45.000 0.00 0.00 36.83 3.96
2214 2307 7.389607 GCATTGAAGGAGTTTTACTAGTTGGTA 59.610 37.037 0.00 0.00 0.00 3.25
2250 2343 5.330455 TGAGTCAGTATTTGCTACTCTGG 57.670 43.478 0.00 0.00 38.68 3.86
2252 2345 2.860735 GTCAGTATTTGCTACTCTGGCG 59.139 50.000 0.00 0.00 38.68 5.69
2261 2354 3.982475 TGCTACTCTGGCGATTATCTTG 58.018 45.455 0.00 0.00 0.00 3.02
2277 2370 6.605471 TTATCTTGTAGCAAGGAGTCTTCA 57.395 37.500 8.74 0.00 0.00 3.02
2286 2379 3.563390 GCAAGGAGTCTTCATATCTTGCC 59.437 47.826 13.80 0.00 46.38 4.52
2287 2380 3.742433 AGGAGTCTTCATATCTTGCCG 57.258 47.619 0.00 0.00 0.00 5.69
2309 2402 4.010349 GTTGCTAGTGAAGGCCAAGTATT 58.990 43.478 5.01 0.00 0.00 1.89
2350 2443 7.340122 TCAGTAAATCTCGAGTTCATCATCT 57.660 36.000 13.13 0.00 0.00 2.90
2400 2493 9.885743 GCAATATTTTGTAGCGAAAATAAACAG 57.114 29.630 12.42 6.85 39.84 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 1.949847 CTCGTCCTACTGGCCACTGG 61.950 65.000 0.00 4.21 0.00 4.00
329 330 3.812019 GGAGAGCGAAGACGGCGA 61.812 66.667 16.62 0.00 40.15 5.54
606 629 3.135167 ACGGTCCCGGTACATGAAAATAT 59.865 43.478 10.91 0.00 44.69 1.28
729 752 1.198713 TCTCTTGTGGAGGAGGATGC 58.801 55.000 0.00 0.00 42.10 3.91
742 765 1.339535 GGGAAGGAGGCTGTTCTCTTG 60.340 57.143 0.00 0.00 34.39 3.02
792 815 2.423479 AAAGGGGAGAGGAGGCCAGT 62.423 60.000 5.01 0.00 0.00 4.00
793 816 1.617839 AAAGGGGAGAGGAGGCCAG 60.618 63.158 5.01 0.00 0.00 4.85
794 817 1.616628 GAAAGGGGAGAGGAGGCCA 60.617 63.158 5.01 0.00 0.00 5.36
795 818 0.916845 AAGAAAGGGGAGAGGAGGCC 60.917 60.000 0.00 0.00 0.00 5.19
796 819 0.254462 CAAGAAAGGGGAGAGGAGGC 59.746 60.000 0.00 0.00 0.00 4.70
797 820 1.958288 TCAAGAAAGGGGAGAGGAGG 58.042 55.000 0.00 0.00 0.00 4.30
798 821 2.355615 GCTTCAAGAAAGGGGAGAGGAG 60.356 54.545 0.00 0.00 35.37 3.69
799 822 1.630878 GCTTCAAGAAAGGGGAGAGGA 59.369 52.381 0.00 0.00 35.37 3.71
887 910 1.309499 TTAAAAGCGGTGGCGATGGG 61.309 55.000 0.00 0.00 46.35 4.00
960 990 0.696501 GGGACTCAAAACCCTAGGCA 59.303 55.000 2.05 0.00 42.56 4.75
1373 1408 2.035155 TCTCCTCCTTGACGGCGA 59.965 61.111 16.62 0.00 0.00 5.54
1420 1455 3.001464 TCGAAGCATAATCGAAACGAACG 60.001 43.478 0.00 0.00 45.46 3.95
1421 1456 4.494597 TCGAAGCATAATCGAAACGAAC 57.505 40.909 0.00 0.00 45.46 3.95
1457 1492 0.917259 CGCACACGAACTCTAGATGC 59.083 55.000 0.00 0.00 43.93 3.91
1641 1685 5.126067 ACAGATATTCCGGTCAAATCTTGG 58.874 41.667 0.00 0.00 0.00 3.61
1650 1694 3.458189 CTTGGTGACAGATATTCCGGTC 58.542 50.000 0.00 0.00 44.54 4.79
1749 1814 0.322546 AGAACGAAGGGTGGATTGCC 60.323 55.000 0.00 0.00 0.00 4.52
1794 1859 9.895894 CAGAAAATTCAAATAAAAGCATGATCG 57.104 29.630 0.00 0.00 0.00 3.69
1805 1870 8.956426 CCCTACTAGCACAGAAAATTCAAATAA 58.044 33.333 0.00 0.00 0.00 1.40
1824 1889 9.559732 CATCATTAATCAAATGTGTCCCTACTA 57.440 33.333 0.00 0.00 44.58 1.82
1906 1977 5.007136 CCTTGCTTAAGAGATAGAAAAGGCG 59.993 44.000 6.67 0.00 0.00 5.52
2003 2084 0.892063 AGAAGGGCTTGACTCTCGAC 59.108 55.000 0.00 0.00 0.00 4.20
2031 2112 3.772387 TCACTGATCAGAGTTCAGAGGT 58.228 45.455 29.27 0.01 42.63 3.85
2032 2113 5.341872 AATCACTGATCAGAGTTCAGAGG 57.658 43.478 29.27 0.00 42.63 3.69
2033 2114 8.034215 ACTAAAATCACTGATCAGAGTTCAGAG 58.966 37.037 29.27 18.20 42.63 3.35
2119 2210 3.087031 AGAGGCACAATGTTCTGATTGG 58.913 45.455 0.00 0.00 37.60 3.16
2126 2217 2.079925 GGACTGAGAGGCACAATGTTC 58.920 52.381 0.00 0.00 0.00 3.18
2162 2253 4.816385 TGACTGAGACACAATGTTCCTTTC 59.184 41.667 0.00 0.00 0.00 2.62
2191 2284 9.856162 AAATACCAACTAGTAAAACTCCTTCAA 57.144 29.630 0.00 0.00 0.00 2.69
2228 2321 4.382040 GCCAGAGTAGCAAATACTGACTCA 60.382 45.833 0.00 0.00 45.06 3.41
2250 2343 4.372656 ACTCCTTGCTACAAGATAATCGC 58.627 43.478 8.87 0.00 0.00 4.58
2252 2345 7.268586 TGAAGACTCCTTGCTACAAGATAATC 58.731 38.462 8.87 1.90 31.62 1.75
2277 2370 3.819564 TCACTAGCAACGGCAAGATAT 57.180 42.857 0.00 0.00 44.61 1.63
2286 2379 0.798776 CTTGGCCTTCACTAGCAACG 59.201 55.000 3.32 0.00 0.00 4.10
2287 2380 1.897560 ACTTGGCCTTCACTAGCAAC 58.102 50.000 3.32 0.00 0.00 4.17
2309 2402 9.167311 GATTTACTGAAAGCAGAAAGGAGAATA 57.833 33.333 0.00 0.00 45.17 1.75


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

AutoCloner maintained by Alex Coulton.