Multiple sequence alignment - TraesCS6D01G203400

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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 TraesCS6D01G203400 chr6D 100.000 4760 0 0 1 4760 287238952 287243711 0.000000e+00 8791.0
1 TraesCS6D01G203400 chr6D 99.430 1578 9 0 2254 3831 79090994 79092571 0.000000e+00 2865.0
2 TraesCS6D01G203400 chr6D 98.847 1474 17 0 663 2136 79089520 79090993 0.000000e+00 2628.0
3 TraesCS6D01G203400 chr6D 96.131 336 11 2 3832 4167 224537863 224538196 9.010000e-152 547.0
4 TraesCS6D01G203400 chr6D 98.929 280 3 0 660 939 287242503 287242782 7.110000e-138 501.0
5 TraesCS6D01G203400 chr6D 98.571 280 4 0 660 939 79092292 79092571 3.310000e-136 496.0
6 TraesCS6D01G203400 chr2B 90.565 2586 212 14 665 3248 463350783 463353338 0.000000e+00 3395.0
7 TraesCS6D01G203400 chr2B 89.196 1120 119 2 2714 3831 757829417 757830536 0.000000e+00 1397.0
8 TraesCS6D01G203400 chr2B 88.025 1119 131 3 2714 3831 757690008 757691124 0.000000e+00 1321.0
9 TraesCS6D01G203400 chr2B 85.660 530 73 2 3304 3832 463353334 463353861 5.380000e-154 555.0
10 TraesCS6D01G203400 chr2B 86.667 300 36 3 660 956 757687431 757687729 3.550000e-86 329.0
11 TraesCS6D01G203400 chr1A 91.161 1120 87 10 2714 3832 544036023 544037131 0.000000e+00 1509.0
12 TraesCS6D01G203400 chr1A 83.460 919 136 13 3845 4758 208767401 208766494 0.000000e+00 841.0
13 TraesCS6D01G203400 chr1A 85.393 178 23 3 3129 3305 144783972 144783797 1.050000e-41 182.0
14 TraesCS6D01G203400 chr1B 88.287 1127 127 5 2714 3837 329207245 329208369 0.000000e+00 1345.0
15 TraesCS6D01G203400 chr1B 90.224 491 42 4 3299 3784 457027365 457026876 1.870000e-178 636.0
16 TraesCS6D01G203400 chr1B 87.713 293 36 0 665 957 329204679 329204971 4.560000e-90 342.0
17 TraesCS6D01G203400 chr4B 86.763 967 115 4 1355 2321 47046024 47046977 0.000000e+00 1064.0
18 TraesCS6D01G203400 chr4B 91.039 491 38 4 3299 3784 630465869 630466358 0.000000e+00 658.0
19 TraesCS6D01G203400 chr4B 86.278 583 79 1 2317 2899 47156374 47156955 2.420000e-177 632.0
20 TraesCS6D01G203400 chr4B 87.500 432 49 4 2676 3106 51751717 51751290 1.190000e-135 494.0
21 TraesCS6D01G203400 chr4B 87.634 186 23 0 3125 3310 630465666 630465851 2.880000e-52 217.0
22 TraesCS6D01G203400 chr4B 86.813 91 12 0 3029 3119 630465534 630465624 8.430000e-18 102.0
23 TraesCS6D01G203400 chrUn 98.328 598 10 0 4163 4760 20187533 20186936 0.000000e+00 1050.0
24 TraesCS6D01G203400 chrUn 97.990 597 12 0 4163 4759 111884340 111883744 0.000000e+00 1037.0
25 TraesCS6D01G203400 chr3D 98.328 598 10 0 4163 4760 352353475 352354072 0.000000e+00 1050.0
26 TraesCS6D01G203400 chr3D 97.997 599 11 1 4163 4760 64784713 64785311 0.000000e+00 1038.0
27 TraesCS6D01G203400 chr3D 94.895 666 31 2 1 663 565888717 565888052 0.000000e+00 1038.0
28 TraesCS6D01G203400 chr3D 94.895 666 31 2 1 663 570874097 570874762 0.000000e+00 1038.0
29 TraesCS6D01G203400 chr3D 97.993 598 12 0 4163 4760 583374146 583373549 0.000000e+00 1038.0
30 TraesCS6D01G203400 chr3D 94.745 666 32 2 1 663 432497255 432497920 0.000000e+00 1033.0
31 TraesCS6D01G203400 chr3D 86.156 809 106 6 748 1553 274424236 274423431 0.000000e+00 869.0
32 TraesCS6D01G203400 chr3D 86.032 809 107 6 748 1553 274636270 274635465 0.000000e+00 863.0
33 TraesCS6D01G203400 chr3D 96.131 336 12 1 3832 4167 405209855 405209521 9.010000e-152 547.0
34 TraesCS6D01G203400 chr2D 98.328 598 9 1 4163 4760 187478515 187479111 0.000000e+00 1048.0
35 TraesCS6D01G203400 chr2D 97.993 598 9 1 4163 4760 577274188 577273594 0.000000e+00 1035.0
36 TraesCS6D01G203400 chr2D 94.603 667 32 3 1 663 316182168 316181502 0.000000e+00 1029.0
37 TraesCS6D01G203400 chr2D 99.278 277 2 0 663 939 16366236 16365960 7.110000e-138 501.0
38 TraesCS6D01G203400 chr1D 94.895 666 31 2 1 663 458867012 458867677 0.000000e+00 1038.0
39 TraesCS6D01G203400 chr1D 97.993 598 10 2 4163 4760 228391659 228392254 0.000000e+00 1037.0
40 TraesCS6D01G203400 chr1D 96.726 336 10 1 3832 4167 479165808 479166142 4.160000e-155 558.0
41 TraesCS6D01G203400 chr1D 96.429 336 10 2 3832 4167 226279738 226279405 1.940000e-153 553.0
42 TraesCS6D01G203400 chr1D 96.418 335 11 1 3832 4165 458867672 458868006 6.960000e-153 551.0
43 TraesCS6D01G203400 chr1D 85.311 177 23 1 3129 3305 144448141 144448314 3.780000e-41 180.0
44 TraesCS6D01G203400 chr4D 94.745 666 32 2 1 663 327364272 327364937 0.000000e+00 1033.0
45 TraesCS6D01G203400 chr4D 94.745 666 32 2 1 663 379457179 379457844 0.000000e+00 1033.0
46 TraesCS6D01G203400 chr4D 96.716 335 11 0 3832 4166 54221965 54221631 4.160000e-155 558.0
47 TraesCS6D01G203400 chr4D 96.726 336 10 1 3832 4167 455067054 455067388 4.160000e-155 558.0
48 TraesCS6D01G203400 chr4D 79.521 835 125 20 748 1553 175183982 175184799 1.940000e-153 553.0
49 TraesCS6D01G203400 chr7D 94.603 667 32 3 1 663 254568452 254569118 0.000000e+00 1029.0
50 TraesCS6D01G203400 chr7D 88.705 664 48 9 3125 3784 510378164 510378804 0.000000e+00 785.0
51 TraesCS6D01G203400 chr7D 92.015 526 42 0 2678 3203 342398511 342397986 0.000000e+00 739.0
52 TraesCS6D01G203400 chr7D 96.439 337 9 3 3832 4167 525313902 525313568 1.940000e-153 553.0
53 TraesCS6D01G203400 chr7D 85.714 91 13 0 3029 3119 510378032 510378122 3.920000e-16 97.1
54 TraesCS6D01G203400 chr5D 94.603 667 32 3 1 663 355073113 355073779 0.000000e+00 1029.0
55 TraesCS6D01G203400 chr7A 91.400 500 43 0 2705 3204 353210494 353209995 0.000000e+00 686.0
56 TraesCS6D01G203400 chr7B 91.667 156 11 2 2715 2869 287962789 287962943 1.040000e-51 215.0


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 TraesCS6D01G203400 chr6D 287238952 287243711 4759 False 4646.000000 8791 99.464500 1 4760 2 chr6D.!!$F3 4759
1 TraesCS6D01G203400 chr6D 79089520 79092571 3051 False 1996.333333 2865 98.949333 660 3831 3 chr6D.!!$F2 3171
2 TraesCS6D01G203400 chr2B 463350783 463353861 3078 False 1975.000000 3395 88.112500 665 3832 2 chr2B.!!$F2 3167
3 TraesCS6D01G203400 chr2B 757829417 757830536 1119 False 1397.000000 1397 89.196000 2714 3831 1 chr2B.!!$F1 1117
4 TraesCS6D01G203400 chr2B 757687431 757691124 3693 False 825.000000 1321 87.346000 660 3831 2 chr2B.!!$F3 3171
5 TraesCS6D01G203400 chr1A 544036023 544037131 1108 False 1509.000000 1509 91.161000 2714 3832 1 chr1A.!!$F1 1118
6 TraesCS6D01G203400 chr1A 208766494 208767401 907 True 841.000000 841 83.460000 3845 4758 1 chr1A.!!$R2 913
7 TraesCS6D01G203400 chr1B 329204679 329208369 3690 False 843.500000 1345 88.000000 665 3837 2 chr1B.!!$F1 3172
8 TraesCS6D01G203400 chr4B 47046024 47046977 953 False 1064.000000 1064 86.763000 1355 2321 1 chr4B.!!$F1 966
9 TraesCS6D01G203400 chr4B 47156374 47156955 581 False 632.000000 632 86.278000 2317 2899 1 chr4B.!!$F2 582
10 TraesCS6D01G203400 chr4B 630465534 630466358 824 False 325.666667 658 88.495333 3029 3784 3 chr4B.!!$F3 755
11 TraesCS6D01G203400 chrUn 20186936 20187533 597 True 1050.000000 1050 98.328000 4163 4760 1 chrUn.!!$R1 597
12 TraesCS6D01G203400 chrUn 111883744 111884340 596 True 1037.000000 1037 97.990000 4163 4759 1 chrUn.!!$R2 596
13 TraesCS6D01G203400 chr3D 352353475 352354072 597 False 1050.000000 1050 98.328000 4163 4760 1 chr3D.!!$F2 597
14 TraesCS6D01G203400 chr3D 64784713 64785311 598 False 1038.000000 1038 97.997000 4163 4760 1 chr3D.!!$F1 597
15 TraesCS6D01G203400 chr3D 565888052 565888717 665 True 1038.000000 1038 94.895000 1 663 1 chr3D.!!$R4 662
16 TraesCS6D01G203400 chr3D 570874097 570874762 665 False 1038.000000 1038 94.895000 1 663 1 chr3D.!!$F4 662
17 TraesCS6D01G203400 chr3D 583373549 583374146 597 True 1038.000000 1038 97.993000 4163 4760 1 chr3D.!!$R5 597
18 TraesCS6D01G203400 chr3D 432497255 432497920 665 False 1033.000000 1033 94.745000 1 663 1 chr3D.!!$F3 662
19 TraesCS6D01G203400 chr3D 274423431 274424236 805 True 869.000000 869 86.156000 748 1553 1 chr3D.!!$R1 805
20 TraesCS6D01G203400 chr3D 274635465 274636270 805 True 863.000000 863 86.032000 748 1553 1 chr3D.!!$R2 805
21 TraesCS6D01G203400 chr2D 187478515 187479111 596 False 1048.000000 1048 98.328000 4163 4760 1 chr2D.!!$F1 597
22 TraesCS6D01G203400 chr2D 577273594 577274188 594 True 1035.000000 1035 97.993000 4163 4760 1 chr2D.!!$R3 597
23 TraesCS6D01G203400 chr2D 316181502 316182168 666 True 1029.000000 1029 94.603000 1 663 1 chr2D.!!$R2 662
24 TraesCS6D01G203400 chr1D 228391659 228392254 595 False 1037.000000 1037 97.993000 4163 4760 1 chr1D.!!$F2 597
25 TraesCS6D01G203400 chr1D 458867012 458868006 994 False 794.500000 1038 95.656500 1 4165 2 chr1D.!!$F4 4164
26 TraesCS6D01G203400 chr4D 327364272 327364937 665 False 1033.000000 1033 94.745000 1 663 1 chr4D.!!$F2 662
27 TraesCS6D01G203400 chr4D 379457179 379457844 665 False 1033.000000 1033 94.745000 1 663 1 chr4D.!!$F3 662
28 TraesCS6D01G203400 chr4D 175183982 175184799 817 False 553.000000 553 79.521000 748 1553 1 chr4D.!!$F1 805
29 TraesCS6D01G203400 chr7D 254568452 254569118 666 False 1029.000000 1029 94.603000 1 663 1 chr7D.!!$F1 662
30 TraesCS6D01G203400 chr7D 342397986 342398511 525 True 739.000000 739 92.015000 2678 3203 1 chr7D.!!$R1 525
31 TraesCS6D01G203400 chr7D 510378032 510378804 772 False 441.050000 785 87.209500 3029 3784 2 chr7D.!!$F2 755
32 TraesCS6D01G203400 chr5D 355073113 355073779 666 False 1029.000000 1029 94.603000 1 663 1 chr5D.!!$F1 662

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
967 980 0.038744 CAGAGCCAATTCCCACCACT 59.961 55.000 0.00 0.0 0.00 4.00 F
1457 1752 1.068250 GCTTCGGCCTCGAGCTAAT 59.932 57.895 6.99 0.0 46.75 1.73 F
2041 2520 1.202639 AGGACGACATCAACAGCAACA 60.203 47.619 0.00 0.0 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2618 0.249868 CCTGAAGCTGACGGTCAACA 60.250 55.000 12.54 8.99 0.00 3.33 R
3471 4707 2.028839 CCATGGTGCTTGATGCTTCAAA 60.029 45.455 15.12 1.88 41.22 2.69 R
3976 6248 0.463116 GTGTGTTATAGGGGGTGCGG 60.463 60.000 0.00 0.00 0.00 5.69 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
47 48 1.079750 GCTTCCGAGTGACTGACCC 60.080 63.158 0.00 0.00 0.00 4.46
121 126 1.862602 AAAAAGGCGGCGCGAGAATT 61.863 50.000 26.95 13.78 0.00 2.17
166 171 1.271840 AATTACTGCGGCCTCCTCCA 61.272 55.000 0.00 0.00 0.00 3.86
255 260 2.171448 AGATCTCCACCACATTAGCACC 59.829 50.000 0.00 0.00 0.00 5.01
270 275 2.284699 ACCCGGACCTCTTCCAGG 60.285 66.667 0.73 0.00 46.76 4.45
300 306 2.076863 CTCGACAAACCAGGAATGGAC 58.923 52.381 0.31 0.00 0.00 4.02
393 400 4.548346 CGCGAAAAATGAGTCGGAAGTATC 60.548 45.833 0.00 0.00 37.73 2.24
443 450 1.202927 CCATTCGGGGGCTAATGATGT 60.203 52.381 0.00 0.00 35.53 3.06
496 503 4.376223 TGATGTAAATACCCTCCCCAAGA 58.624 43.478 0.00 0.00 0.00 3.02
512 519 3.372206 CCCAAGAACATCACTCTAAAGCG 59.628 47.826 0.00 0.00 0.00 4.68
563 570 4.039973 ACTCGACCAGAAACATTTCCACTA 59.960 41.667 0.68 0.00 37.92 2.74
571 578 5.412904 CAGAAACATTTCCACTAGGAGGAAC 59.587 44.000 15.98 6.37 46.74 3.62
663 670 4.498345 GGTCGAGCATTAACTCCTAGACTG 60.498 50.000 10.30 0.00 32.79 3.51
967 980 0.038744 CAGAGCCAATTCCCACCACT 59.961 55.000 0.00 0.00 0.00 4.00
1375 1670 4.953868 CCGTGCCGGTGTCAACGA 62.954 66.667 12.97 0.00 42.73 3.85
1457 1752 1.068250 GCTTCGGCCTCGAGCTAAT 59.932 57.895 6.99 0.00 46.75 1.73
1907 2230 1.478510 ACCATCTCTTGCGTTCTCGAT 59.521 47.619 0.00 0.00 39.71 3.59
2041 2520 1.202639 AGGACGACATCAACAGCAACA 60.203 47.619 0.00 0.00 0.00 3.33
2139 2618 2.325484 GTCCACCCCCTGAAATTGTTT 58.675 47.619 0.00 0.00 0.00 2.83
2142 2621 2.437651 CCACCCCCTGAAATTGTTTGTT 59.562 45.455 0.00 0.00 0.00 2.83
2181 2660 3.059120 CACACAATCACTCTCAGTTGCAG 60.059 47.826 0.00 0.00 0.00 4.41
2240 2719 7.707624 TGGCAATTGATTCTATCTTGTCTTT 57.292 32.000 10.34 0.00 0.00 2.52
2241 2720 8.125978 TGGCAATTGATTCTATCTTGTCTTTT 57.874 30.769 10.34 0.00 0.00 2.27
3471 4707 1.239968 ACTACGACCTCGGCGAAGTT 61.240 55.000 13.01 0.09 44.95 2.66
3640 4876 0.106268 TGGGAAGCAACAGAAGGCAA 60.106 50.000 0.00 0.00 0.00 4.52
3834 5089 7.392393 TCTGTACTAGTGTGTTGCTAACATAGA 59.608 37.037 5.39 0.00 44.35 1.98
3835 5090 7.310664 TGTACTAGTGTGTTGCTAACATAGAC 58.689 38.462 5.39 7.38 44.35 2.59
3836 5091 6.591750 ACTAGTGTGTTGCTAACATAGACT 57.408 37.500 0.00 11.75 44.35 3.24
3976 6248 0.962356 CCTCCACATGCACAAGGGTC 60.962 60.000 0.00 0.00 0.00 4.46
4009 6324 5.839262 ATAACACACACGCATATAATCCG 57.161 39.130 0.00 0.00 0.00 4.18
4041 6356 2.124403 GGCTCCGAGACGTAGGGA 60.124 66.667 0.00 0.00 0.00 4.20
4080 6395 2.074576 GGGCCTGAACTCGTAAAACTC 58.925 52.381 0.84 0.00 0.00 3.01
4150 6465 3.369892 CCCCCATTCTACTGTCAGACTTG 60.370 52.174 6.91 0.00 0.00 3.16
4157 6472 4.160329 TCTACTGTCAGACTTGGAACCAT 58.840 43.478 6.91 0.00 0.00 3.55
4723 7039 1.952296 GCCCTTACGTTATCGAGGAGA 59.048 52.381 0.00 0.00 40.62 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.400599 AAGATTGCCCGGGCCTACG 62.401 63.158 41.75 5.78 41.09 3.51
116 121 1.811860 GCAATGCCGCCTCAATTCT 59.188 52.632 0.00 0.00 0.00 2.40
171 176 2.403586 GAATTTCGGGAAGCGCGG 59.596 61.111 8.83 0.00 40.17 6.46
270 275 4.495844 CCTGGTTTGTCGAGTGAACTTTTC 60.496 45.833 0.00 0.00 0.00 2.29
300 306 2.618709 ACTTCTTTTTCAGTCGCCTTGG 59.381 45.455 0.00 0.00 0.00 3.61
393 400 4.342862 TTGAGTGGAGAAGGAGTTGAAG 57.657 45.455 0.00 0.00 0.00 3.02
443 450 2.090943 CCCTACCCTAGGTACATGTCCA 60.091 54.545 8.29 0.00 44.73 4.02
465 472 4.079787 AGGGTATTTACATCAGGCATGTGT 60.080 41.667 10.51 10.51 45.98 3.72
477 484 3.917629 TGTTCTTGGGGAGGGTATTTACA 59.082 43.478 0.00 0.00 0.00 2.41
478 485 4.579647 TGTTCTTGGGGAGGGTATTTAC 57.420 45.455 0.00 0.00 0.00 2.01
496 503 3.929610 GCTTCTCGCTTTAGAGTGATGTT 59.070 43.478 0.00 0.00 41.31 2.71
512 519 1.202545 GGTACCCCTCGAATGCTTCTC 60.203 57.143 0.00 0.00 0.00 2.87
563 570 1.827969 CGAGTGATCTTGGTTCCTCCT 59.172 52.381 0.00 0.00 37.07 3.69
571 578 2.094906 TGTTACGGTCGAGTGATCTTGG 60.095 50.000 0.00 0.00 0.00 3.61
633 640 2.094390 AGTTAATGCTCGACCGTTGCTA 60.094 45.455 0.00 0.00 0.00 3.49
663 670 2.477754 GAGTGTACGGTTGGTTGCTAAC 59.522 50.000 0.00 0.00 0.00 2.34
967 980 4.516698 GCTGAGTGGTGAAATTGAAGAAGA 59.483 41.667 0.00 0.00 0.00 2.87
1457 1752 1.970114 GGAGTCGAGGTCGTGGTCA 60.970 63.158 0.00 0.00 40.80 4.02
1907 2230 5.804639 ACCTTGTTGCTGTGATATGAGTAA 58.195 37.500 0.00 0.00 0.00 2.24
1961 2284 1.676635 GCTTGCACCATGAGCTCCA 60.677 57.895 12.15 0.00 33.72 3.86
2139 2618 0.249868 CCTGAAGCTGACGGTCAACA 60.250 55.000 12.54 8.99 0.00 3.33
2142 2621 2.343758 GCCTGAAGCTGACGGTCA 59.656 61.111 10.88 10.88 38.99 4.02
2181 2660 4.255833 TGAAATTGATGTTGGTCCTTGC 57.744 40.909 0.00 0.00 0.00 4.01
2215 2694 7.893124 AAGACAAGATAGAATCAATTGCCAT 57.107 32.000 0.00 0.00 0.00 4.40
2216 2695 7.707624 AAAGACAAGATAGAATCAATTGCCA 57.292 32.000 0.00 0.00 0.00 4.92
2240 2719 4.168101 ACCATCAGGACTACAAGGAAGAA 58.832 43.478 0.00 0.00 38.69 2.52
2241 2720 3.791320 ACCATCAGGACTACAAGGAAGA 58.209 45.455 0.00 0.00 38.69 2.87
3471 4707 2.028839 CCATGGTGCTTGATGCTTCAAA 60.029 45.455 15.12 1.88 41.22 2.69
3640 4876 4.802039 CCGTTCGCTTGTATATGTAGTTGT 59.198 41.667 0.00 0.00 0.00 3.32
3976 6248 0.463116 GTGTGTTATAGGGGGTGCGG 60.463 60.000 0.00 0.00 0.00 5.69
4041 6356 2.766828 CCCTTCTCGGAGGAAGTAACAT 59.233 50.000 4.96 0.00 40.56 2.71
4080 6395 1.710013 ATGGAGAAGTTGTACGCACG 58.290 50.000 0.00 0.00 0.00 5.34
4150 6465 2.293399 GTGAACAACCTGTCATGGTTCC 59.707 50.000 0.00 0.00 46.37 3.62
4157 6472 5.883115 TGAATAAAGTGTGAACAACCTGTCA 59.117 36.000 0.00 0.00 0.00 3.58
4165 6480 4.826733 AGCACCATGAATAAAGTGTGAACA 59.173 37.500 0.00 0.00 32.75 3.18


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

AutoCloner maintained by Alex Coulton.