Multiple sequence alignment - TraesCS7A01G067400

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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 TraesCS7A01G067400 chr7A 100.000 5596 0 0 1 5596 33869467 33875062 0.000000e+00 10334
1 TraesCS7A01G067400 chr6A 95.144 5560 244 9 1 5546 532800529 532794982 0.000000e+00 8748
2 TraesCS7A01G067400 chr6A 96.422 4696 133 8 884 5546 81107489 81102796 0.000000e+00 7709
3 TraesCS7A01G067400 chr6A 96.166 3991 126 13 1578 5547 435544119 435548103 0.000000e+00 6497
4 TraesCS7A01G067400 chr6A 86.308 818 74 25 1 801 81108337 81107541 0.000000e+00 856
5 TraesCS7A01G067400 chr6A 85.595 840 74 21 1 801 435541345 435542176 0.000000e+00 837
6 TraesCS7A01G067400 chr6A 96.270 429 14 2 1 428 435547757 435548184 0.000000e+00 702
7 TraesCS7A01G067400 chr6A 95.853 434 17 1 1 433 81103141 81102708 0.000000e+00 701
8 TraesCS7A01G067400 chr6A 92.396 434 30 2 1 433 532795325 532794894 2.860000e-172 616
9 TraesCS7A01G067400 chr4A 97.118 4685 93 9 884 5547 29784858 29789521 0.000000e+00 7866
10 TraesCS7A01G067400 chr4A 86.190 840 69 22 1 801 29783975 29784806 0.000000e+00 865
11 TraesCS7A01G067400 chr4A 96.322 435 16 0 1 435 29789175 29789609 0.000000e+00 715
12 TraesCS7A01G067400 chr6B 92.567 4682 279 21 884 5514 271933992 271929329 0.000000e+00 6654
13 TraesCS7A01G067400 chr1D 92.206 4683 314 22 884 5547 464133042 464137692 0.000000e+00 6578
14 TraesCS7A01G067400 chr1D 96.627 2105 70 1 3061 5165 20725122 20723019 0.000000e+00 3493
15 TraesCS7A01G067400 chr1D 94.635 2162 98 6 884 3027 20727291 20725130 0.000000e+00 3334
16 TraesCS7A01G067400 chr1D 91.685 890 72 2 884 1773 464112204 464113091 0.000000e+00 1232
17 TraesCS7A01G067400 chr1D 91.489 893 74 2 884 1776 464116171 464117061 0.000000e+00 1227
18 TraesCS7A01G067400 chr1D 82.100 581 58 21 258 801 20727914 20727343 6.610000e-124 455
19 TraesCS7A01G067400 chr5D 96.069 3765 130 6 1798 5550 423013283 423009525 0.000000e+00 6117
20 TraesCS7A01G067400 chr5D 95.392 434 18 2 1 433 423009873 423009441 0.000000e+00 689
21 TraesCS7A01G067400 chr5A 93.404 4124 227 17 1367 5468 579320279 579316179 0.000000e+00 6067
22 TraesCS7A01G067400 chr1A 91.609 3730 273 20 884 4591 556280986 556284697 0.000000e+00 5118
23 TraesCS7A01G067400 chr1B 93.101 2667 171 5 2534 5200 640150191 640152844 0.000000e+00 3893
24 TraesCS7A01G067400 chr2D 93.929 1960 114 5 3541 5499 612871182 612869227 0.000000e+00 2955


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 TraesCS7A01G067400 chr7A 33869467 33875062 5595 False 10334.000000 10334 100.000000 1 5596 1 chr7A.!!$F1 5595
1 TraesCS7A01G067400 chr6A 532794894 532800529 5635 True 4682.000000 8748 93.770000 1 5546 2 chr6A.!!$R2 5545
2 TraesCS7A01G067400 chr6A 81102708 81108337 5629 True 3088.666667 7709 92.861000 1 5546 3 chr6A.!!$R1 5545
3 TraesCS7A01G067400 chr6A 435541345 435548184 6839 False 2678.666667 6497 92.677000 1 5547 3 chr6A.!!$F1 5546
4 TraesCS7A01G067400 chr4A 29783975 29789609 5634 False 3148.666667 7866 93.210000 1 5547 3 chr4A.!!$F1 5546
5 TraesCS7A01G067400 chr6B 271929329 271933992 4663 True 6654.000000 6654 92.567000 884 5514 1 chr6B.!!$R1 4630
6 TraesCS7A01G067400 chr1D 464133042 464137692 4650 False 6578.000000 6578 92.206000 884 5547 1 chr1D.!!$F1 4663
7 TraesCS7A01G067400 chr1D 20723019 20727914 4895 True 2427.333333 3493 91.120667 258 5165 3 chr1D.!!$R1 4907
8 TraesCS7A01G067400 chr1D 464112204 464117061 4857 False 1229.500000 1232 91.587000 884 1776 2 chr1D.!!$F2 892
9 TraesCS7A01G067400 chr5D 423009441 423013283 3842 True 3403.000000 6117 95.730500 1 5550 2 chr5D.!!$R1 5549
10 TraesCS7A01G067400 chr5A 579316179 579320279 4100 True 6067.000000 6067 93.404000 1367 5468 1 chr5A.!!$R1 4101
11 TraesCS7A01G067400 chr1A 556280986 556284697 3711 False 5118.000000 5118 91.609000 884 4591 1 chr1A.!!$F1 3707
12 TraesCS7A01G067400 chr1B 640150191 640152844 2653 False 3893.000000 3893 93.101000 2534 5200 1 chr1B.!!$F1 2666
13 TraesCS7A01G067400 chr2D 612869227 612871182 1955 True 2955.000000 2955 93.929000 3541 5499 1 chr2D.!!$R1 1958

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
331 332 0.234884 GCGGACTCTTTGGAAACGTG 59.765 55.000 0.00 0.00 0.0 4.49 F
368 369 0.784495 TCCCCTAGCCTCGGATATGT 59.216 55.000 0.00 0.00 0.0 2.29 F
512 515 0.796312 AACAAATCCGCTGCGTACTG 59.204 50.000 21.59 14.00 0.0 2.74 F
513 516 1.019278 ACAAATCCGCTGCGTACTGG 61.019 55.000 21.59 9.73 0.0 4.00 F
618 657 1.224722 GATCGATTCCCTTGCCTCGC 61.225 60.000 0.00 0.00 0.0 5.03 F
621 660 1.524482 GATTCCCTTGCCTCGCTCT 59.476 57.895 0.00 0.00 0.0 4.09 F
930 1056 1.620323 GCTTGGAAATTGTCTGGGCTT 59.380 47.619 0.00 0.00 0.0 4.35 F
3729 9095 0.593128 CACAAAGGGAAGGCGTTGAG 59.407 55.000 0.00 0.00 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 7306 3.334280 AGTGGAACCAGAGTCTACTACCT 59.666 47.826 0.00 0.00 37.80 3.08 R
2346 7686 4.556233 TCACTACCGAGTTCTGTTCATTG 58.444 43.478 0.00 0.00 31.73 2.82 R
2869 8219 3.552604 TTCAGCTACGCCATTTTGTTC 57.447 42.857 0.00 0.00 0.00 3.18 R
3334 8689 2.224992 TGCCATCAGCTTGGTTTTCCTA 60.225 45.455 6.32 0.00 44.23 2.94 R
3543 8902 1.667236 TTAGTTCCTCATGCATGGCG 58.333 50.000 25.97 16.69 0.00 5.69 R
3729 9095 4.481368 AGGGGAAAAAGTTTCCACAAAC 57.519 40.909 21.08 4.98 44.38 2.93 R
3884 9275 7.371126 TGATTTTCCTTTTCAACAAAACCAC 57.629 32.000 0.00 0.00 0.00 4.16 R
5570 11056 0.107831 TACCATGCCAAGCCGTATCC 59.892 55.000 0.00 0.00 0.00 2.59 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
242 243 8.471609 TCCACTAACAGACAAATTATATCGTGA 58.528 33.333 0.00 0.00 0.00 4.35
330 331 0.883370 GGCGGACTCTTTGGAAACGT 60.883 55.000 0.00 0.00 0.00 3.99
331 332 0.234884 GCGGACTCTTTGGAAACGTG 59.765 55.000 0.00 0.00 0.00 4.49
368 369 0.784495 TCCCCTAGCCTCGGATATGT 59.216 55.000 0.00 0.00 0.00 2.29
441 444 8.192774 CACAACATATTTCTAACATTGGCATCT 58.807 33.333 0.00 0.00 0.00 2.90
493 496 1.268386 CGACTCGATTCGATCCGGAAA 60.268 52.381 19.22 0.00 41.78 3.13
498 501 3.327626 TCGATTCGATCCGGAAAACAAA 58.672 40.909 9.01 0.00 0.00 2.83
512 515 0.796312 AACAAATCCGCTGCGTACTG 59.204 50.000 21.59 14.00 0.00 2.74
513 516 1.019278 ACAAATCCGCTGCGTACTGG 61.019 55.000 21.59 9.73 0.00 4.00
514 517 1.019278 CAAATCCGCTGCGTACTGGT 61.019 55.000 21.59 0.00 0.00 4.00
618 657 1.224722 GATCGATTCCCTTGCCTCGC 61.225 60.000 0.00 0.00 0.00 5.03
619 658 1.690219 ATCGATTCCCTTGCCTCGCT 61.690 55.000 0.00 0.00 0.00 4.93
621 660 1.524482 GATTCCCTTGCCTCGCTCT 59.476 57.895 0.00 0.00 0.00 4.09
801 927 4.785453 GCCCTCCACCGGAAGCTG 62.785 72.222 9.46 0.00 31.00 4.24
930 1056 1.620323 GCTTGGAAATTGTCTGGGCTT 59.380 47.619 0.00 0.00 0.00 4.35
975 1101 5.860941 TTCAACACTGCCAAAGGAATTTA 57.139 34.783 0.00 0.00 0.00 1.40
989 1115 8.244113 CCAAAGGAATTTATTCTGTACTGAACC 58.756 37.037 16.36 11.98 37.00 3.62
1970 7306 9.587772 GTTTACTACTTCAGCTTCAGATCATTA 57.412 33.333 0.00 0.00 0.00 1.90
2346 7686 4.079970 TCGATAGGATGGACTGTATGGTC 58.920 47.826 0.00 0.00 35.66 4.02
2869 8219 9.268282 ACCATTATACCTTACCATATACTCCTG 57.732 37.037 0.00 0.00 0.00 3.86
3334 8689 9.520204 CAAGTGTTGAAACTGATTCTAACAATT 57.480 29.630 15.38 15.38 41.84 2.32
3538 8897 7.502226 TGTCTTGTTCAGAATCAAAGTTATGGT 59.498 33.333 0.00 0.00 31.28 3.55
3543 8902 6.817765 TCAGAATCAAAGTTATGGTTGGAC 57.182 37.500 0.00 0.00 0.00 4.02
3729 9095 0.593128 CACAAAGGGAAGGCGTTGAG 59.407 55.000 0.00 0.00 0.00 3.02
3751 9117 5.601583 GTTTGTGGAAACTTTTTCCCCTA 57.398 39.130 13.85 0.00 38.78 3.53
3884 9275 8.428063 AGAAGAGATTTATATGTCTCAACCTGG 58.572 37.037 14.04 0.00 42.57 4.45
4779 10185 3.686016 GGTGTGGCTGAAGGAATTTCTA 58.314 45.455 0.00 0.00 36.71 2.10
4781 10187 4.096984 GGTGTGGCTGAAGGAATTTCTATG 59.903 45.833 0.00 0.00 36.71 2.23
4856 10262 5.488262 AATCAGGCTGCAATAAAGGTTTT 57.512 34.783 10.34 0.00 0.00 2.43
5249 10663 8.078959 CGGTCAATTATCGGTGAAATACAATA 57.921 34.615 0.00 0.00 0.00 1.90
5461 10877 4.394729 GTGGTTGGTAGTTTGATCTGGAA 58.605 43.478 0.00 0.00 0.00 3.53
5531 10947 1.491563 CGGACTCTTTGGAAACGCG 59.508 57.895 3.53 3.53 0.00 6.01
5565 11051 5.712917 GGTCCCCACAACATATTTCTAACAA 59.287 40.000 0.00 0.00 0.00 2.83
5567 11053 7.257722 GTCCCCACAACATATTTCTAACAATG 58.742 38.462 0.00 0.00 0.00 2.82
5568 11054 7.122055 GTCCCCACAACATATTTCTAACAATGA 59.878 37.037 0.00 0.00 0.00 2.57
5569 11055 7.671819 TCCCCACAACATATTTCTAACAATGAA 59.328 33.333 0.00 0.00 0.00 2.57
5570 11056 7.975616 CCCCACAACATATTTCTAACAATGAAG 59.024 37.037 0.00 0.00 0.00 3.02
5571 11057 7.975616 CCCACAACATATTTCTAACAATGAAGG 59.024 37.037 0.00 0.00 0.00 3.46
5572 11058 8.739039 CCACAACATATTTCTAACAATGAAGGA 58.261 33.333 0.00 0.00 0.00 3.36
5577 11063 9.273016 ACATATTTCTAACAATGAAGGATACGG 57.727 33.333 0.00 0.00 46.39 4.02
5578 11064 6.619801 ATTTCTAACAATGAAGGATACGGC 57.380 37.500 0.00 0.00 46.39 5.68
5579 11065 5.353394 TTCTAACAATGAAGGATACGGCT 57.647 39.130 0.00 0.00 46.39 5.52
5580 11066 5.353394 TCTAACAATGAAGGATACGGCTT 57.647 39.130 0.00 0.00 46.39 4.35
5581 11067 5.116180 TCTAACAATGAAGGATACGGCTTG 58.884 41.667 0.00 0.00 46.39 4.01
5582 11068 2.643551 ACAATGAAGGATACGGCTTGG 58.356 47.619 0.00 0.00 46.39 3.61
5583 11069 1.334869 CAATGAAGGATACGGCTTGGC 59.665 52.381 0.00 0.00 46.39 4.52
5584 11070 0.546122 ATGAAGGATACGGCTTGGCA 59.454 50.000 0.00 0.00 46.39 4.92
5585 11071 0.546122 TGAAGGATACGGCTTGGCAT 59.454 50.000 0.00 0.00 46.39 4.40
5586 11072 0.947244 GAAGGATACGGCTTGGCATG 59.053 55.000 0.00 0.00 46.39 4.06
5587 11073 0.466189 AAGGATACGGCTTGGCATGG 60.466 55.000 2.33 0.00 46.39 3.66
5588 11074 1.152963 GGATACGGCTTGGCATGGT 60.153 57.895 2.33 0.00 0.00 3.55
5589 11075 0.107831 GGATACGGCTTGGCATGGTA 59.892 55.000 2.33 0.00 0.00 3.25
5590 11076 1.512926 GATACGGCTTGGCATGGTAG 58.487 55.000 2.33 0.00 0.00 3.18
5591 11077 0.535102 ATACGGCTTGGCATGGTAGC 60.535 55.000 0.20 0.20 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 3.452990 TCTTCCAATTATCAGCGTACCCA 59.547 43.478 0.00 0.00 0.00 4.51
242 243 7.202047 GGATAGAGTCCAGATCAAACTACCAAT 60.202 40.741 0.00 0.00 46.96 3.16
330 331 4.451760 GGGGATAGGGACCTTCTTATACCA 60.452 50.000 0.00 0.00 0.00 3.25
331 332 4.102598 GGGGATAGGGACCTTCTTATACC 58.897 52.174 0.00 0.00 0.00 2.73
493 496 0.796312 CAGTACGCAGCGGATTTGTT 59.204 50.000 21.15 0.00 0.00 2.83
498 501 2.494918 GACCAGTACGCAGCGGAT 59.505 61.111 21.15 0.56 0.00 4.18
512 515 3.005155 ACTTGTACTAGTTGACCACGACC 59.995 47.826 0.00 0.00 0.00 4.79
513 516 4.225208 GACTTGTACTAGTTGACCACGAC 58.775 47.826 11.32 0.00 0.00 4.34
514 517 3.254166 GGACTTGTACTAGTTGACCACGA 59.746 47.826 11.32 0.00 0.00 4.35
878 1004 3.399330 GACTAGCTTGTGTACCTTGCAA 58.601 45.455 5.27 0.00 0.00 4.08
930 1056 0.036952 GAGCAGCAGTAGCAGGTGAA 60.037 55.000 0.00 0.00 45.49 3.18
975 1101 4.974645 TCCACAAGGTTCAGTACAGAAT 57.025 40.909 3.84 0.00 35.89 2.40
989 1115 1.272092 TGGAGGCCATCTTTCCACAAG 60.272 52.381 5.01 0.00 36.13 3.16
1064 1190 5.139727 ACATCATCTTCCTTTTCCACACAA 58.860 37.500 0.00 0.00 0.00 3.33
1857 7151 4.141846 CCCTGATGCTGCTTCTTAGACTTA 60.142 45.833 15.38 0.00 0.00 2.24
1970 7306 3.334280 AGTGGAACCAGAGTCTACTACCT 59.666 47.826 0.00 0.00 37.80 3.08
2337 7677 5.062683 CGAGTTCTGTTCATTGACCATACAG 59.937 44.000 9.11 9.11 38.00 2.74
2346 7686 4.556233 TCACTACCGAGTTCTGTTCATTG 58.444 43.478 0.00 0.00 31.73 2.82
2869 8219 3.552604 TTCAGCTACGCCATTTTGTTC 57.447 42.857 0.00 0.00 0.00 3.18
3334 8689 2.224992 TGCCATCAGCTTGGTTTTCCTA 60.225 45.455 6.32 0.00 44.23 2.94
3538 8897 1.750018 CCTCATGCATGGCGTCCAA 60.750 57.895 25.97 4.34 36.95 3.53
3543 8902 1.667236 TTAGTTCCTCATGCATGGCG 58.333 50.000 25.97 16.69 0.00 5.69
3729 9095 4.481368 AGGGGAAAAAGTTTCCACAAAC 57.519 40.909 21.08 4.98 44.38 2.93
3884 9275 7.371126 TGATTTTCCTTTTCAACAAAACCAC 57.629 32.000 0.00 0.00 0.00 4.16
4779 10185 6.206243 CACTCTCAACAATCTTCAAAGTCCAT 59.794 38.462 0.00 0.00 0.00 3.41
4781 10187 5.561725 GCACTCTCAACAATCTTCAAAGTCC 60.562 44.000 0.00 0.00 0.00 3.85
4856 10262 3.118261 GCTGTGGAACTTGGGATATCTGA 60.118 47.826 2.05 0.00 38.04 3.27
5461 10877 8.979534 AGTCTTTAAACTAGTTTCCGGATAGAT 58.020 33.333 23.76 2.93 34.23 1.98
5565 11051 0.546122 TGCCAAGCCGTATCCTTCAT 59.454 50.000 0.00 0.00 0.00 2.57
5567 11053 0.947244 CATGCCAAGCCGTATCCTTC 59.053 55.000 0.00 0.00 0.00 3.46
5568 11054 0.466189 CCATGCCAAGCCGTATCCTT 60.466 55.000 0.00 0.00 0.00 3.36
5569 11055 1.149174 CCATGCCAAGCCGTATCCT 59.851 57.895 0.00 0.00 0.00 3.24
5570 11056 0.107831 TACCATGCCAAGCCGTATCC 59.892 55.000 0.00 0.00 0.00 2.59
5571 11057 1.512926 CTACCATGCCAAGCCGTATC 58.487 55.000 0.00 0.00 0.00 2.24
5572 11058 0.535102 GCTACCATGCCAAGCCGTAT 60.535 55.000 1.81 0.00 0.00 3.06
5573 11059 1.153249 GCTACCATGCCAAGCCGTA 60.153 57.895 1.81 0.00 0.00 4.02
5574 11060 2.438434 GCTACCATGCCAAGCCGT 60.438 61.111 1.81 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.