Multiple sequence alignment - TraesCS4D01G273200

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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 TraesCS4D01G273200 chr4D 100.000 4795 0 0 626 5420 442908242 442903448 0.000000e+00 8855
1 TraesCS4D01G273200 chr4D 100.000 84 0 0 1 84 442908867 442908784 7.270000e-34 156
2 TraesCS4D01G273200 chr4A 95.394 4386 95 22 627 4950 24753452 24757792 0.000000e+00 6881
3 TraesCS4D01G273200 chr4A 88.832 394 28 9 4944 5322 24757957 24758349 2.290000e-128 470
4 TraesCS4D01G273200 chr4A 98.810 84 1 0 1 84 24752780 24752863 3.380000e-32 150
5 TraesCS4D01G273200 chr4B 94.002 4585 162 42 902 5420 552033363 552028826 0.000000e+00 6839
6 TraesCS4D01G273200 chr4B 97.490 239 6 0 626 864 552033603 552033365 5.050000e-110 409
7 TraesCS4D01G273200 chr4B 97.619 84 1 1 1 84 552033993 552033911 5.660000e-30 143
8 TraesCS4D01G273200 chr5A 93.669 616 37 2 3298 3912 268042021 268041407 0.000000e+00 920
9 TraesCS4D01G273200 chr3D 93.669 616 37 2 3298 3912 546264217 546263603 0.000000e+00 920
10 TraesCS4D01G273200 chr1A 93.344 616 39 2 3298 3912 536684244 536684858 0.000000e+00 909
11 TraesCS4D01G273200 chr6B 93.344 616 38 3 3298 3912 48058367 48058980 0.000000e+00 907
12 TraesCS4D01G273200 chr6B 93.182 616 39 3 3298 3912 48066619 48067232 0.000000e+00 902
13 TraesCS4D01G273200 chr6A 93.182 616 40 2 3298 3912 545336288 545335674 0.000000e+00 904
14 TraesCS4D01G273200 chr3A 93.019 616 41 2 3298 3912 716906566 716905952 0.000000e+00 898


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 TraesCS4D01G273200 chr4D 442903448 442908867 5419 True 4505.500000 8855 100.000000 1 5420 2 chr4D.!!$R1 5419
1 TraesCS4D01G273200 chr4A 24752780 24758349 5569 False 2500.333333 6881 94.345333 1 5322 3 chr4A.!!$F1 5321
2 TraesCS4D01G273200 chr4B 552028826 552033993 5167 True 2463.666667 6839 96.370333 1 5420 3 chr4B.!!$R1 5419
3 TraesCS4D01G273200 chr5A 268041407 268042021 614 True 920.000000 920 93.669000 3298 3912 1 chr5A.!!$R1 614
4 TraesCS4D01G273200 chr3D 546263603 546264217 614 True 920.000000 920 93.669000 3298 3912 1 chr3D.!!$R1 614
5 TraesCS4D01G273200 chr1A 536684244 536684858 614 False 909.000000 909 93.344000 3298 3912 1 chr1A.!!$F1 614
6 TraesCS4D01G273200 chr6B 48058367 48058980 613 False 907.000000 907 93.344000 3298 3912 1 chr6B.!!$F1 614
7 TraesCS4D01G273200 chr6B 48066619 48067232 613 False 902.000000 902 93.182000 3298 3912 1 chr6B.!!$F2 614
8 TraesCS4D01G273200 chr6A 545335674 545336288 614 True 904.000000 904 93.182000 3298 3912 1 chr6A.!!$R1 614
9 TraesCS4D01G273200 chr3A 716905952 716906566 614 True 898.000000 898 93.019000 3298 3912 1 chr3A.!!$R1 614

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
970 1019 6.258068 ACTCCTTAATTCGACGATTTTGATCC 59.742 38.462 9.97 0.00 0.00 3.36 F
1926 1998 0.955919 GGTATGCTCCTTATGGCGCC 60.956 60.000 22.73 22.73 43.04 6.53 F
1977 2049 3.504906 CAGTTGATGGTCAGATGTTTGCT 59.495 43.478 0.00 0.00 0.00 3.91 F
3468 3576 1.634702 GACGATCTCCACACTTGCTC 58.365 55.000 0.00 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2483 2558 2.291465 GCATGAGCAGAAAACAGTGACA 59.709 45.455 0.0 0.0 41.58 3.58 R
3453 3561 0.035630 GCAGGAGCAAGTGTGGAGAT 60.036 55.000 0.0 0.0 41.58 2.75 R
3657 3766 1.890876 TGTTGGGAACATCCTTGACG 58.109 50.000 0.0 0.0 42.32 4.35 R
4980 5290 0.177836 AAGCCACACCTTTGCCAAAC 59.822 50.000 0.0 0.0 0.00 2.93 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
940 989 6.557568 AGGTTTGGGATCTATTTTTACACCA 58.442 36.000 0.00 0.00 0.00 4.17
970 1019 6.258068 ACTCCTTAATTCGACGATTTTGATCC 59.742 38.462 9.97 0.00 0.00 3.36
1020 1069 3.774528 TCGCTGGAATCGCAGCCT 61.775 61.111 14.84 0.00 41.06 4.58
1021 1070 3.267860 CGCTGGAATCGCAGCCTC 61.268 66.667 14.84 0.00 41.06 4.70
1022 1071 2.124983 GCTGGAATCGCAGCCTCA 60.125 61.111 11.11 0.00 38.42 3.86
1023 1072 2.178890 GCTGGAATCGCAGCCTCAG 61.179 63.158 11.11 0.00 38.42 3.35
1024 1073 2.124983 TGGAATCGCAGCCTCAGC 60.125 61.111 0.00 0.00 40.32 4.26
1025 1074 2.899339 GGAATCGCAGCCTCAGCC 60.899 66.667 0.00 0.00 41.25 4.85
1160 1213 8.530311 AGGTGATATGTGATTCTGATATGTCTC 58.470 37.037 0.00 0.00 0.00 3.36
1174 1227 1.286501 TGTCTCGTGTTGCTGTTGAC 58.713 50.000 0.00 0.00 0.00 3.18
1364 1419 7.041712 GCTGCTTCTTTTCAGTCTACTTACTTT 60.042 37.037 0.00 0.00 33.09 2.66
1664 1730 7.378181 CAGCCATTCTTTTAGTATGGTTTGTT 58.622 34.615 12.15 0.00 42.89 2.83
1711 1777 8.213518 TCTTATTATGGTCTGTGCAGAATTTC 57.786 34.615 3.19 0.00 39.48 2.17
1810 1882 9.467258 CAACATCTTGTATCTCATTTTGTTGTT 57.533 29.630 0.00 0.00 36.15 2.83
1926 1998 0.955919 GGTATGCTCCTTATGGCGCC 60.956 60.000 22.73 22.73 43.04 6.53
1977 2049 3.504906 CAGTTGATGGTCAGATGTTTGCT 59.495 43.478 0.00 0.00 0.00 3.91
2058 2130 4.402851 GGTGACCAGCAGCATTCA 57.597 55.556 0.00 0.00 44.31 2.57
2441 2516 4.416620 CAGACGGTGAGTACAGAGAAATC 58.583 47.826 0.00 0.00 0.00 2.17
2483 2558 6.610075 ATTGTGGATCAAAGGCATTTAGTT 57.390 33.333 0.00 0.00 39.62 2.24
2490 2565 5.437289 TCAAAGGCATTTAGTTGTCACTG 57.563 39.130 0.00 0.00 34.06 3.66
2598 2676 7.109501 TCCTTGCAATGAAGTTATAAGCTACA 58.890 34.615 0.00 0.00 0.00 2.74
2873 2951 3.660865 CACCCAGTCTTACAACCAGTAC 58.339 50.000 0.00 0.00 30.91 2.73
3228 3336 5.050091 AGTGAAAACAAGAATGCTAGTGACG 60.050 40.000 0.00 0.00 0.00 4.35
3453 3561 3.731652 TGTTTTTCTCGGTAAGGACGA 57.268 42.857 0.00 0.00 38.79 4.20
3468 3576 1.634702 GACGATCTCCACACTTGCTC 58.365 55.000 0.00 0.00 0.00 4.26
3510 3619 6.768483 AGTTTGATTTCCTTGGGTTAATTGG 58.232 36.000 0.00 0.00 0.00 3.16
3537 3646 7.116736 TCTCCTTTCTTACAAACTTTCAGGTT 58.883 34.615 0.00 0.00 0.00 3.50
3657 3766 2.462456 TCTCTGTCAAGTGGCACATC 57.538 50.000 21.41 7.35 44.52 3.06
3944 4055 1.406887 GCCTTCTATGAGAACCGCCAA 60.407 52.381 0.00 0.00 29.89 4.52
4288 4399 2.359107 CAGAGAAAGCCGCTGCCA 60.359 61.111 0.00 0.00 35.96 4.92
4289 4400 2.359230 AGAGAAAGCCGCTGCCAC 60.359 61.111 0.00 0.00 38.69 5.01
4290 4401 3.435186 GAGAAAGCCGCTGCCACC 61.435 66.667 0.00 0.00 38.69 4.61
4358 4469 2.821810 GGCCGAGAAGAAGCCTGC 60.822 66.667 0.00 0.00 43.62 4.85
4383 4494 0.038159 CCGAGAAGAAGCCTGTCGTT 60.038 55.000 0.00 0.00 31.36 3.85
4595 4710 5.292834 TCTTCTTCTGTCGTCGTCGTATTAT 59.707 40.000 1.33 0.00 38.33 1.28
4596 4711 5.075670 TCTTCTGTCGTCGTCGTATTATC 57.924 43.478 1.33 0.00 38.33 1.75
4597 4712 3.494309 TCTGTCGTCGTCGTATTATCG 57.506 47.619 1.33 0.00 38.33 2.92
4718 4850 3.993584 GTGTCGTACCCGGTGGCA 61.994 66.667 0.00 0.00 33.59 4.92
4901 5039 2.279741 TGGTTTCGTATCTGCTGATGC 58.720 47.619 15.71 13.23 40.20 3.91
4980 5290 2.597217 TGACCGGGCAAAGGCAAG 60.597 61.111 8.12 0.00 43.71 4.01
4981 5291 2.597510 GACCGGGCAAAGGCAAGT 60.598 61.111 0.00 0.00 43.71 3.16
4982 5292 2.123468 ACCGGGCAAAGGCAAGTT 60.123 55.556 6.32 0.00 43.71 2.66
5057 5369 0.039527 CCGTTTGGGGAAGAAAAGCG 60.040 55.000 0.00 0.00 0.00 4.68
5239 5560 6.801862 AGCTTAAAAAGAATTTGGAACGATCG 59.198 34.615 14.88 14.88 39.02 3.69
5280 5618 3.196901 TGGTGTCACTACTTGTCAACACT 59.803 43.478 2.35 0.00 36.22 3.55
5295 5633 3.007940 TCAACACTACTCCATGGTTCAGG 59.992 47.826 12.58 2.52 0.00 3.86
5296 5634 1.279271 ACACTACTCCATGGTTCAGGC 59.721 52.381 12.58 0.00 0.00 4.85
5301 5639 2.242043 ACTCCATGGTTCAGGCTTTTG 58.758 47.619 12.58 0.00 0.00 2.44
5302 5640 1.547372 CTCCATGGTTCAGGCTTTTGG 59.453 52.381 12.58 0.00 0.00 3.28
5339 5679 6.745794 TTGGGATCTTTGTTTCAATTCCTT 57.254 33.333 0.00 0.00 0.00 3.36
5346 5686 9.399403 GATCTTTGTTTCAATTCCTTGACTAAC 57.601 33.333 0.00 0.00 41.05 2.34
5358 5698 3.569701 CCTTGACTAACATGCACCTTGTT 59.430 43.478 9.03 9.03 40.30 2.83
5360 5700 5.451798 CCTTGACTAACATGCACCTTGTTTT 60.452 40.000 9.31 0.00 38.26 2.43
5381 5721 8.399425 TGTTTTACATGGTTGTAACAAGTGTAG 58.601 33.333 0.00 0.00 45.60 2.74
5394 5734 7.845800 TGTAACAAGTGTAGGGGTATATACCTT 59.154 37.037 27.24 19.09 45.72 3.50
5398 5738 6.304831 AGTGTAGGGGTATATACCTTCCTT 57.695 41.667 25.94 13.30 45.72 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
665 713 2.890474 CCCGGCCGAATCGACAAG 60.890 66.667 30.73 5.91 0.00 3.16
864 912 6.453092 GGAGCAATCCTACGCTACTTAATTA 58.547 40.000 0.00 0.00 38.99 1.40
940 989 4.713824 TCGTCGAATTAAGGAGTCACAT 57.286 40.909 0.00 0.00 0.00 3.21
970 1019 1.129998 CAGATCTGTGGCTTCTTTGCG 59.870 52.381 14.95 0.00 0.00 4.85
1096 1145 5.796424 ACTTGCACAAATTGGAGAAGAAT 57.204 34.783 0.00 0.00 0.00 2.40
1364 1419 4.640771 AGACCCAATTCTGTTAGCTTGA 57.359 40.909 0.00 0.00 0.00 3.02
1641 1707 6.811665 GGAACAAACCATACTAAAAGAATGGC 59.188 38.462 0.54 0.00 43.33 4.40
1642 1708 8.122472 AGGAACAAACCATACTAAAAGAATGG 57.878 34.615 0.00 0.00 44.76 3.16
1643 1709 9.981114 AAAGGAACAAACCATACTAAAAGAATG 57.019 29.630 0.00 0.00 0.00 2.67
1644 1710 9.981114 CAAAGGAACAAACCATACTAAAAGAAT 57.019 29.630 0.00 0.00 0.00 2.40
1652 1718 4.772100 CCCATCAAAGGAACAAACCATACT 59.228 41.667 0.00 0.00 0.00 2.12
1664 1730 4.051661 AGCAGAAAATCCCATCAAAGGA 57.948 40.909 0.00 0.00 37.93 3.36
1711 1777 9.369904 CAATACTTTTGAATAACAATTGGGAGG 57.630 33.333 10.83 0.00 38.36 4.30
1740 1809 0.894141 AGTGGCAAACAAACAGCACA 59.106 45.000 0.00 0.00 0.00 4.57
1810 1882 7.827236 CCTTGGAAGTAACACAAATATGTAGGA 59.173 37.037 0.00 0.00 37.82 2.94
1926 1998 2.312390 GGGGAACTAGCTGGAGAGTAG 58.688 57.143 3.17 0.00 0.00 2.57
1977 2049 4.260985 CTGGATACTGGTAATGTTGTGCA 58.739 43.478 0.00 0.00 37.61 4.57
2221 2296 3.374318 CCAGTAGAAGGGACTCCACCTAT 60.374 52.174 0.00 0.00 38.49 2.57
2483 2558 2.291465 GCATGAGCAGAAAACAGTGACA 59.709 45.455 0.00 0.00 41.58 3.58
2598 2676 6.161855 TGAGATCGCATCCTAACAAATACT 57.838 37.500 0.00 0.00 0.00 2.12
2873 2951 2.292292 ACCAGTTTTGACCGAATTTCCG 59.708 45.455 0.00 0.00 0.00 4.30
2966 3074 2.509336 CTTCCGTAGCCACTGCCG 60.509 66.667 0.00 0.00 38.69 5.69
2967 3075 2.820037 GCTTCCGTAGCCACTGCC 60.820 66.667 0.00 0.00 44.48 4.85
3389 3497 3.626670 CCTTTGCCTGAGCTTCTTGATAG 59.373 47.826 0.00 0.00 40.80 2.08
3453 3561 0.035630 GCAGGAGCAAGTGTGGAGAT 60.036 55.000 0.00 0.00 41.58 2.75
3510 3619 7.445707 ACCTGAAAGTTTGTAAGAAAGGAGATC 59.554 37.037 0.00 0.00 0.00 2.75
3537 3646 6.038825 CACCAACAAACTGTCCACTTGTATTA 59.961 38.462 0.00 0.00 33.05 0.98
3657 3766 1.890876 TGTTGGGAACATCCTTGACG 58.109 50.000 0.00 0.00 42.32 4.35
3944 4055 4.630644 TCTCTTCTCCTGCATCAACTTT 57.369 40.909 0.00 0.00 0.00 2.66
4187 4298 2.354259 CATCCTGCTGTTTCTCTCCAC 58.646 52.381 0.00 0.00 0.00 4.02
4383 4494 2.124529 TTGACAGCACCGTTGGCA 60.125 55.556 0.00 0.00 0.00 4.92
4496 4608 3.347216 CTTTGGTGATCAGTACCTTGGG 58.653 50.000 0.00 0.00 39.01 4.12
4595 4710 3.938963 GCAAACTGAAATAGGGATGACGA 59.061 43.478 0.00 0.00 0.00 4.20
4596 4711 3.941483 AGCAAACTGAAATAGGGATGACG 59.059 43.478 0.00 0.00 0.00 4.35
4597 4712 5.904362 AAGCAAACTGAAATAGGGATGAC 57.096 39.130 0.00 0.00 0.00 3.06
4980 5290 0.177836 AAGCCACACCTTTGCCAAAC 59.822 50.000 0.00 0.00 0.00 2.93
4981 5291 0.463620 GAAGCCACACCTTTGCCAAA 59.536 50.000 0.00 0.00 0.00 3.28
4982 5292 0.396974 AGAAGCCACACCTTTGCCAA 60.397 50.000 0.00 0.00 0.00 4.52
5057 5369 0.751643 ACTCAACCAAGCACACCACC 60.752 55.000 0.00 0.00 0.00 4.61
5239 5560 0.392193 ACCATGACACAGCAGCTAGC 60.392 55.000 6.62 6.62 46.19 3.42
5280 5618 3.420893 CAAAAGCCTGAACCATGGAGTA 58.579 45.455 21.47 2.39 0.00 2.59
5295 5633 3.552132 TTTCCCTGGAAAACCAAAAGC 57.448 42.857 8.88 0.00 40.63 3.51
5296 5634 4.821260 CCAATTTCCCTGGAAAACCAAAAG 59.179 41.667 14.88 1.76 45.60 2.27
5301 5639 2.615391 TCCCAATTTCCCTGGAAAACC 58.385 47.619 14.88 0.00 45.60 3.27
5302 5640 4.096681 AGATCCCAATTTCCCTGGAAAAC 58.903 43.478 14.88 2.70 45.60 2.43
5339 5679 5.590663 TGTAAAACAAGGTGCATGTTAGTCA 59.409 36.000 4.67 2.68 39.98 3.41
5360 5700 5.513441 CCCCTACACTTGTTACAACCATGTA 60.513 44.000 0.00 3.29 41.05 2.29
5394 5734 2.783510 AGGTCAAAACAAGAGGGAAGGA 59.216 45.455 0.00 0.00 0.00 3.36
5398 5738 4.086706 GAAGAGGTCAAAACAAGAGGGA 57.913 45.455 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.