Multiple sequence alignment - TraesCS2D01G214600

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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 TraesCS2D01G214600 chr2D 100.000 3411 0 0 1 3411 176159851 176163261 0.000000e+00 6300.0
1 TraesCS2D01G214600 chr2A 93.512 2728 91 43 717 3411 187949885 187952559 0.000000e+00 3978.0
2 TraesCS2D01G214600 chr2A 87.654 162 6 3 332 493 187948204 187948351 3.500000e-40 176.0
3 TraesCS2D01G214600 chr2A 95.876 97 4 0 484 580 187949595 187949691 1.270000e-34 158.0
4 TraesCS2D01G214600 chr2B 95.736 2017 32 15 717 2685 233265464 233267474 0.000000e+00 3199.0
5 TraesCS2D01G214600 chr2B 94.527 676 23 8 2747 3411 233267472 233268144 0.000000e+00 1031.0
6 TraesCS2D01G214600 chr2B 91.803 610 23 15 1 601 233264816 233265407 0.000000e+00 824.0
7 TraesCS2D01G214600 chr2B 87.500 72 4 3 628 699 233265400 233265466 1.010000e-10 78.7
8 TraesCS2D01G214600 chr7D 86.989 538 47 12 2881 3411 581036187 581035666 4.900000e-163 584.0
9 TraesCS2D01G214600 chr3D 86.458 480 31 16 2881 3342 604597854 604598317 2.360000e-136 496.0


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 TraesCS2D01G214600 chr2D 176159851 176163261 3410 False 6300.000000 6300 100.000000 1 3411 1 chr2D.!!$F1 3410
1 TraesCS2D01G214600 chr2A 187948204 187952559 4355 False 1437.333333 3978 92.347333 332 3411 3 chr2A.!!$F1 3079
2 TraesCS2D01G214600 chr2B 233264816 233268144 3328 False 1283.175000 3199 92.391500 1 3411 4 chr2B.!!$F1 3410
3 TraesCS2D01G214600 chr7D 581035666 581036187 521 True 584.000000 584 86.989000 2881 3411 1 chr7D.!!$R1 530

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
932 2262 0.325671 AAATCTCGCCCTCCTCTCCA 60.326 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2749 4137 0.407139 AATGCCAGGAAAGGAGCAGT 59.593 50.0 0.0 0.0 38.89 4.4 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
21 22 0.743345 AAGCCCTACGCGAATTGGAC 60.743 55.000 15.93 1.01 44.76 4.02
33 34 2.748058 AATTGGACCGGCGTGCTCTT 62.748 55.000 6.01 0.00 0.00 2.85
167 174 6.458751 CCACATCGTTTCTGATTCCCAATAAG 60.459 42.308 0.00 0.00 0.00 1.73
297 304 3.418068 GCTGTCTGTGCTCGTGCC 61.418 66.667 7.05 0.00 38.71 5.01
335 342 2.159707 CGTGGCACGGTTCAGAATTTAG 60.160 50.000 31.19 0.00 38.08 1.85
466 478 1.690985 GTGAGGAAGGGAGGGGAGG 60.691 68.421 0.00 0.00 0.00 4.30
467 479 2.040359 GAGGAAGGGAGGGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
468 480 3.711782 AGGAAGGGAGGGGAGGGG 61.712 72.222 0.00 0.00 0.00 4.79
469 481 3.707189 GGAAGGGAGGGGAGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
470 482 2.040359 GAAGGGAGGGGAGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
471 483 2.543637 AAGGGAGGGGAGGGGAGA 60.544 66.667 0.00 0.00 0.00 3.71
472 484 2.613576 GAAGGGAGGGGAGGGGAGAG 62.614 70.000 0.00 0.00 0.00 3.20
473 485 3.036959 GGGAGGGGAGGGGAGAGA 61.037 72.222 0.00 0.00 0.00 3.10
474 486 2.612251 GGAGGGGAGGGGAGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
478 490 1.385206 GGGGAGGGGAGAGAGCAAT 60.385 63.158 0.00 0.00 0.00 3.56
565 1835 6.407299 CCTGGGATCAATAATTTTGTCCCTTG 60.407 42.308 22.62 18.62 44.47 3.61
604 1886 4.747108 CACTCTTGGATCATCCGATACAAC 59.253 45.833 0.00 0.00 45.75 3.32
605 1887 4.651503 ACTCTTGGATCATCCGATACAACT 59.348 41.667 0.00 0.00 45.75 3.16
608 1890 3.576861 TGGATCATCCGATACAACTCCT 58.423 45.455 0.00 0.00 39.67 3.69
610 1892 4.408921 TGGATCATCCGATACAACTCCTTT 59.591 41.667 0.00 0.00 39.67 3.11
639 1921 7.624360 TTTTTGAAGCATATCCGATACAACT 57.376 32.000 0.00 0.00 0.00 3.16
640 1922 6.844696 TTTGAAGCATATCCGATACAACTC 57.155 37.500 0.00 0.00 0.00 3.01
641 1923 4.883083 TGAAGCATATCCGATACAACTCC 58.117 43.478 0.00 0.00 0.00 3.85
642 1924 4.588951 TGAAGCATATCCGATACAACTCCT 59.411 41.667 0.00 0.00 0.00 3.69
643 1925 5.773176 TGAAGCATATCCGATACAACTCCTA 59.227 40.000 0.00 0.00 0.00 2.94
670 1952 2.025226 ACTGGTCTCCAACGATAGAGGA 60.025 50.000 0.00 0.00 40.43 3.71
688 1970 6.019656 AGAGGAGGAGTTTCTTTCCTTTTT 57.980 37.500 0.00 0.00 45.00 1.94
690 1972 6.019656 AGGAGGAGTTTCTTTCCTTTTTCT 57.980 37.500 0.00 0.00 45.00 2.52
693 1975 5.141182 AGGAGTTTCTTTCCTTTTTCTCCC 58.859 41.667 0.00 0.00 42.40 4.30
694 1976 4.023107 GGAGTTTCTTTCCTTTTTCTCCCG 60.023 45.833 0.00 0.00 35.56 5.14
695 1977 3.318275 AGTTTCTTTCCTTTTTCTCCCGC 59.682 43.478 0.00 0.00 0.00 6.13
696 1978 2.649531 TCTTTCCTTTTTCTCCCGCA 57.350 45.000 0.00 0.00 0.00 5.69
697 1979 2.938838 TCTTTCCTTTTTCTCCCGCAA 58.061 42.857 0.00 0.00 0.00 4.85
698 1980 3.292460 TCTTTCCTTTTTCTCCCGCAAA 58.708 40.909 0.00 0.00 0.00 3.68
699 1981 3.702045 TCTTTCCTTTTTCTCCCGCAAAA 59.298 39.130 0.00 0.00 0.00 2.44
700 1982 4.160626 TCTTTCCTTTTTCTCCCGCAAAAA 59.839 37.500 0.00 0.00 32.93 1.94
780 2109 3.392882 CAACTGGCAAAGAAATTCACCC 58.607 45.455 0.00 0.00 0.00 4.61
872 2202 1.009829 GGTTTGGATCACAGCTAGCG 58.990 55.000 9.55 7.05 0.00 4.26
932 2262 0.325671 AAATCTCGCCCTCCTCTCCA 60.326 55.000 0.00 0.00 0.00 3.86
939 2269 2.452114 CCTCCTCTCCACCCACCT 59.548 66.667 0.00 0.00 0.00 4.00
940 2270 1.687493 CCTCCTCTCCACCCACCTC 60.687 68.421 0.00 0.00 0.00 3.85
1080 2425 2.511373 GCGCCCATGACGTCATCA 60.511 61.111 27.79 2.44 43.13 3.07
1973 3336 3.188786 CTACCTCAACGCGGCTGC 61.189 66.667 12.47 7.70 37.91 5.25
2184 3547 0.528470 CGGAAGGTGAGTCTCACTCC 59.472 60.000 27.82 25.07 46.19 3.85
2233 3615 3.136123 CGCATGGGCTGTTCCTGG 61.136 66.667 0.00 0.00 38.10 4.45
2242 3624 1.239968 GCTGTTCCTGGAGCTGGTTG 61.240 60.000 16.80 2.81 32.12 3.77
2473 3857 5.456921 ACTGTAATGTGGGATTGGATTCT 57.543 39.130 0.00 0.00 0.00 2.40
2474 3858 5.440610 ACTGTAATGTGGGATTGGATTCTC 58.559 41.667 0.00 0.00 0.00 2.87
2475 3859 5.192522 ACTGTAATGTGGGATTGGATTCTCT 59.807 40.000 0.00 0.00 0.00 3.10
2476 3860 6.078456 TGTAATGTGGGATTGGATTCTCTT 57.922 37.500 0.00 0.00 0.00 2.85
2477 3861 6.122277 TGTAATGTGGGATTGGATTCTCTTC 58.878 40.000 0.00 0.00 0.00 2.87
2592 3979 9.343539 TCCATGAATGTCCTATATATCTACTCG 57.656 37.037 0.00 0.00 0.00 4.18
2711 4098 2.224161 TGCTTTTGGTAACCCACATTGC 60.224 45.455 0.00 0.00 41.67 3.56
2729 4116 8.991026 CCACATTGCTTCATTTCTTCATTTTTA 58.009 29.630 0.00 0.00 0.00 1.52
2730 4117 9.801714 CACATTGCTTCATTTCTTCATTTTTAC 57.198 29.630 0.00 0.00 0.00 2.01
2731 4118 8.702438 ACATTGCTTCATTTCTTCATTTTTACG 58.298 29.630 0.00 0.00 0.00 3.18
2732 4119 6.689178 TGCTTCATTTCTTCATTTTTACGC 57.311 33.333 0.00 0.00 0.00 4.42
2733 4120 6.446318 TGCTTCATTTCTTCATTTTTACGCT 58.554 32.000 0.00 0.00 0.00 5.07
2735 4122 7.096106 TGCTTCATTTCTTCATTTTTACGCTTG 60.096 33.333 0.00 0.00 0.00 4.01
2736 4123 7.114811 GCTTCATTTCTTCATTTTTACGCTTGA 59.885 33.333 0.00 0.00 0.00 3.02
2749 4137 7.441890 TTTTACGCTTGATGTTTATCCTGAA 57.558 32.000 0.00 0.00 32.09 3.02
2751 4139 4.579869 ACGCTTGATGTTTATCCTGAACT 58.420 39.130 0.00 0.00 32.09 3.01
2756 4144 4.517285 TGATGTTTATCCTGAACTGCTCC 58.483 43.478 0.00 0.00 32.09 4.70
2777 4165 4.019174 CCTTTCCTGGCATTAACATGTCT 58.981 43.478 0.00 0.00 35.84 3.41
2813 4201 7.538575 GGATGAATTTTAACATATCCGGATGG 58.461 38.462 27.55 20.16 0.00 3.51
2915 4303 5.934781 ACTTGATTCAAGAGGAAAGTGTCT 58.065 37.500 28.60 3.14 43.42 3.41
2985 4373 5.016831 TCTAGAGACAGTGGCTTGTATCAA 58.983 41.667 0.00 3.14 40.76 2.57
2988 4376 5.564550 AGAGACAGTGGCTTGTATCAATTT 58.435 37.500 0.00 0.00 40.76 1.82
3051 4448 4.161754 TGCAGATATGCCATCCTATCTCTG 59.838 45.833 10.32 0.00 33.45 3.35
3103 4501 7.178451 TGTCTAGATTCAGGAGATGTGTGTTTA 59.822 37.037 0.00 0.00 0.00 2.01
3267 4676 8.090831 TGCATTTATAGCAGGAGTAGTCTTATG 58.909 37.037 0.00 0.00 37.02 1.90
3268 4677 8.091449 GCATTTATAGCAGGAGTAGTCTTATGT 58.909 37.037 0.00 0.00 0.00 2.29
3310 4719 3.812053 GCAGGAGGCTTAACATATCACAG 59.188 47.826 0.00 0.00 40.25 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.522638 GCCGGTCCAATTCGCGTAG 61.523 63.158 5.77 0.00 0.00 3.51
39 40 3.195002 ATTGCGCATCCACGTCCG 61.195 61.111 12.75 0.00 34.88 4.79
112 119 2.899838 TCTTGGCACACACGCACC 60.900 61.111 0.00 0.00 39.29 5.01
297 304 2.561373 GGCGAAAAAGCTGGACGG 59.439 61.111 0.00 0.00 37.29 4.79
335 342 1.140407 CGTCGCTCGATCAAACCTCC 61.140 60.000 0.00 0.00 42.86 4.30
455 463 3.039526 CTCTCCCCTCCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
466 478 0.758123 CTCCTCCATTGCTCTCTCCC 59.242 60.000 0.00 0.00 0.00 4.30
467 479 1.412343 GACTCCTCCATTGCTCTCTCC 59.588 57.143 0.00 0.00 0.00 3.71
468 480 1.412343 GGACTCCTCCATTGCTCTCTC 59.588 57.143 0.00 0.00 36.42 3.20
469 481 1.008206 AGGACTCCTCCATTGCTCTCT 59.992 52.381 0.00 0.00 39.39 3.10
470 482 1.494960 AGGACTCCTCCATTGCTCTC 58.505 55.000 0.00 0.00 39.39 3.20
471 483 2.676748 CTAGGACTCCTCCATTGCTCT 58.323 52.381 0.00 0.00 39.39 4.09
472 484 1.691434 CCTAGGACTCCTCCATTGCTC 59.309 57.143 1.05 0.00 39.39 4.26
473 485 1.799933 CCTAGGACTCCTCCATTGCT 58.200 55.000 1.05 0.00 39.39 3.91
474 486 0.107643 GCCTAGGACTCCTCCATTGC 59.892 60.000 14.75 0.00 39.39 3.56
478 490 1.311403 CAGGCCTAGGACTCCTCCA 59.689 63.158 16.67 0.00 39.39 3.86
616 1898 6.260050 GGAGTTGTATCGGATATGCTTCAAAA 59.740 38.462 0.29 0.00 0.00 2.44
619 1901 4.588951 AGGAGTTGTATCGGATATGCTTCA 59.411 41.667 0.29 0.00 0.00 3.02
622 1904 5.326069 AGTAGGAGTTGTATCGGATATGCT 58.674 41.667 0.29 0.00 0.00 3.79
623 1905 5.646577 AGTAGGAGTTGTATCGGATATGC 57.353 43.478 0.29 0.00 0.00 3.14
624 1906 7.925043 AGTAGTAGGAGTTGTATCGGATATG 57.075 40.000 0.29 0.00 0.00 1.78
626 1908 8.093307 CAGTAGTAGTAGGAGTTGTATCGGATA 58.907 40.741 0.00 0.00 0.00 2.59
627 1909 6.935771 CAGTAGTAGTAGGAGTTGTATCGGAT 59.064 42.308 0.00 0.00 0.00 4.18
628 1910 6.286758 CAGTAGTAGTAGGAGTTGTATCGGA 58.713 44.000 0.00 0.00 0.00 4.55
629 1911 5.469421 CCAGTAGTAGTAGGAGTTGTATCGG 59.531 48.000 0.00 0.00 0.00 4.18
630 1912 6.054295 ACCAGTAGTAGTAGGAGTTGTATCG 58.946 44.000 0.00 0.00 0.00 2.92
631 1913 7.281841 AGACCAGTAGTAGTAGGAGTTGTATC 58.718 42.308 0.00 0.00 0.00 2.24
632 1914 7.210618 AGACCAGTAGTAGTAGGAGTTGTAT 57.789 40.000 0.00 0.00 0.00 2.29
633 1915 6.352565 GGAGACCAGTAGTAGTAGGAGTTGTA 60.353 46.154 0.00 0.00 0.00 2.41
634 1916 5.499313 GAGACCAGTAGTAGTAGGAGTTGT 58.501 45.833 0.00 0.00 0.00 3.32
635 1917 4.883006 GGAGACCAGTAGTAGTAGGAGTTG 59.117 50.000 0.00 0.00 0.00 3.16
636 1918 4.539293 TGGAGACCAGTAGTAGTAGGAGTT 59.461 45.833 0.00 0.00 0.00 3.01
638 1920 4.774660 TGGAGACCAGTAGTAGTAGGAG 57.225 50.000 0.00 0.00 0.00 3.69
639 1921 4.624843 CGTTGGAGACCAGTAGTAGTAGGA 60.625 50.000 0.00 0.00 33.81 2.94
640 1922 3.626670 CGTTGGAGACCAGTAGTAGTAGG 59.373 52.174 0.00 0.00 33.81 3.18
641 1923 4.511527 TCGTTGGAGACCAGTAGTAGTAG 58.488 47.826 0.00 0.00 33.81 2.57
642 1924 4.558226 TCGTTGGAGACCAGTAGTAGTA 57.442 45.455 0.00 0.00 33.81 1.82
643 1925 3.430042 TCGTTGGAGACCAGTAGTAGT 57.570 47.619 0.00 0.00 33.81 2.73
670 1952 5.141182 GGGAGAAAAAGGAAAGAAACTCCT 58.859 41.667 0.00 0.00 45.66 3.69
672 1954 4.556898 GCGGGAGAAAAAGGAAAGAAACTC 60.557 45.833 0.00 0.00 0.00 3.01
731 2058 7.674471 ATCTCTACTTACAACTTTCCTTTGC 57.326 36.000 0.00 0.00 0.00 3.68
872 2202 2.442830 GGGAAGCTGGGCCCATTC 60.443 66.667 28.82 26.24 44.07 2.67
932 2262 0.853586 AGAGAGAGAGGGAGGTGGGT 60.854 60.000 0.00 0.00 0.00 4.51
939 2269 1.275421 TGCGAGGAGAGAGAGAGGGA 61.275 60.000 0.00 0.00 0.00 4.20
940 2270 0.395036 TTGCGAGGAGAGAGAGAGGG 60.395 60.000 0.00 0.00 0.00 4.30
2233 3615 3.493877 CGATCATCAGAATCAACCAGCTC 59.506 47.826 0.00 0.00 0.00 4.09
2242 3624 7.167968 GCTCAGATATAAGCGATCATCAGAATC 59.832 40.741 0.00 0.00 0.00 2.52
2592 3979 2.343544 GCAAACATTCGCATCAAAGCTC 59.656 45.455 0.00 0.00 0.00 4.09
2711 4098 8.506140 TCAAGCGTAAAAATGAAGAAATGAAG 57.494 30.769 0.00 0.00 0.00 3.02
2729 4116 4.393062 CAGTTCAGGATAAACATCAAGCGT 59.607 41.667 0.00 0.00 0.00 5.07
2730 4117 4.728882 GCAGTTCAGGATAAACATCAAGCG 60.729 45.833 0.00 0.00 0.00 4.68
2731 4118 4.397417 AGCAGTTCAGGATAAACATCAAGC 59.603 41.667 0.00 0.00 0.00 4.01
2732 4119 5.065731 GGAGCAGTTCAGGATAAACATCAAG 59.934 44.000 0.00 0.00 0.00 3.02
2733 4120 4.943705 GGAGCAGTTCAGGATAAACATCAA 59.056 41.667 0.00 0.00 0.00 2.57
2735 4122 4.775236 AGGAGCAGTTCAGGATAAACATC 58.225 43.478 0.00 0.00 0.00 3.06
2736 4123 4.851639 AGGAGCAGTTCAGGATAAACAT 57.148 40.909 0.00 0.00 0.00 2.71
2749 4137 0.407139 AATGCCAGGAAAGGAGCAGT 59.593 50.000 0.00 0.00 38.89 4.40
2751 4139 2.224992 TGTTAATGCCAGGAAAGGAGCA 60.225 45.455 0.00 0.00 40.00 4.26
2756 4144 4.142315 CCAGACATGTTAATGCCAGGAAAG 60.142 45.833 0.00 0.00 37.29 2.62
2813 4201 8.894768 ACATGCCATTCTAATAAGTAGAGAAC 57.105 34.615 0.00 0.00 40.04 3.01
2856 4244 9.508642 AACTTTAATTCTTTCTCCCTAGTTCTG 57.491 33.333 0.00 0.00 0.00 3.02
2915 4303 4.692625 GCATAGCTTCTCTGTTCAGAAACA 59.307 41.667 0.00 0.00 43.06 2.83
3071 4468 6.897966 ACATCTCCTGAATCTAGACAACCTAA 59.102 38.462 0.00 0.00 0.00 2.69
3103 4501 7.856415 ACTCTTTCTATAGCTGATCAAACCTT 58.144 34.615 0.00 0.00 0.00 3.50
3267 4676 2.531206 CAGTCCTAAGAACGCTGCTAC 58.469 52.381 0.00 0.00 0.00 3.58
3268 4677 1.476891 CCAGTCCTAAGAACGCTGCTA 59.523 52.381 0.00 0.00 0.00 3.49
3310 4719 2.758089 CGGCAGCAATGCTCACTCC 61.758 63.158 4.03 3.55 36.40 3.85


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

AutoCloner maintained by Alex Coulton.