Multiple sequence alignment - TraesCS7D01G285100

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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 TraesCS7D01G285100 chr7D 100.000 2447 0 0 1 2447 306583071 306585517 0.000000e+00 4519
1 TraesCS7D01G285100 chr7D 93.750 944 58 1 1 943 307192602 307193545 0.000000e+00 1415
2 TraesCS7D01G285100 chr7B 94.185 1737 74 6 738 2447 52952051 52950315 0.000000e+00 2623
3 TraesCS7D01G285100 chr7B 95.062 1600 53 4 874 2447 742965114 742966713 0.000000e+00 2494
4 TraesCS7D01G285100 chr7B 93.592 515 31 2 409 921 247412914 247413428 0.000000e+00 767
5 TraesCS7D01G285100 chr7B 93.230 517 31 3 409 921 47133104 47133620 0.000000e+00 758
6 TraesCS7D01G285100 chr6D 95.288 1634 48 7 843 2447 430466785 430465152 0.000000e+00 2564
7 TraesCS7D01G285100 chr6D 94.018 1237 46 7 843 2052 370000899 369999664 0.000000e+00 1849
8 TraesCS7D01G285100 chr3D 95.226 1634 48 8 843 2447 202625481 202623849 0.000000e+00 2558
9 TraesCS7D01G285100 chr3D 94.507 983 29 5 1490 2447 478089711 478088729 0.000000e+00 1493
10 TraesCS7D01G285100 chr6B 93.433 1736 88 5 738 2447 625537518 625535783 0.000000e+00 2551
11 TraesCS7D01G285100 chr5A 94.689 1638 60 5 837 2447 162145422 162143785 0.000000e+00 2518
12 TraesCS7D01G285100 chr5A 96.746 338 11 0 1 338 19819793 19820130 4.570000e-157 564
13 TraesCS7D01G285100 chr5A 95.858 338 14 0 1 338 667827264 667826927 4.600000e-152 547
14 TraesCS7D01G285100 chr1D 94.611 1633 60 7 843 2447 350977669 350979301 0.000000e+00 2503
15 TraesCS7D01G285100 chr3B 95.000 1600 53 7 874 2447 92226594 92224996 0.000000e+00 2486
16 TraesCS7D01G285100 chr3B 94.875 1600 56 4 874 2447 92237823 92239422 0.000000e+00 2477
17 TraesCS7D01G285100 chr3B 94.812 1600 57 4 874 2447 201583729 201582130 0.000000e+00 2471
18 TraesCS7D01G285100 chr3B 93.524 525 33 1 409 932 669851611 669851087 0.000000e+00 780
19 TraesCS7D01G285100 chr3B 93.143 525 35 1 409 932 669826373 669825849 0.000000e+00 769
20 TraesCS7D01G285100 chr4D 94.363 1632 65 6 843 2447 97361818 97363449 0.000000e+00 2479
21 TraesCS7D01G285100 chr4D 96.486 683 24 0 1 683 123500679 123501361 0.000000e+00 1129
22 TraesCS7D01G285100 chr4D 96.667 60 2 0 31 90 67979440 67979381 1.550000e-17 100
23 TraesCS7D01G285100 chr1B 92.202 1744 106 8 732 2447 286076897 286078638 0.000000e+00 2440
24 TraesCS7D01G285100 chrUn 95.461 1454 40 4 1020 2447 45134210 45132757 0.000000e+00 2296
25 TraesCS7D01G285100 chr2D 93.946 925 50 4 1 919 306150656 306151580 0.000000e+00 1393
26 TraesCS7D01G285100 chr2A 92.888 928 59 5 1 922 444300689 444301615 0.000000e+00 1341
27 TraesCS7D01G285100 chr3A 91.129 620 40 8 314 921 51894581 51895197 0.000000e+00 826
28 TraesCS7D01G285100 chr3A 96.889 225 6 1 100 323 545365160 545365384 2.300000e-100 375
29 TraesCS7D01G285100 chr7A 97.633 338 8 0 1 338 4911487 4911824 4.540000e-162 580
30 TraesCS7D01G285100 chr4A 97.337 338 9 0 1 338 67505225 67504888 2.110000e-160 575


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 TraesCS7D01G285100 chr7D 306583071 306585517 2446 False 4519 4519 100.000 1 2447 1 chr7D.!!$F1 2446
1 TraesCS7D01G285100 chr7D 307192602 307193545 943 False 1415 1415 93.750 1 943 1 chr7D.!!$F2 942
2 TraesCS7D01G285100 chr7B 52950315 52952051 1736 True 2623 2623 94.185 738 2447 1 chr7B.!!$R1 1709
3 TraesCS7D01G285100 chr7B 742965114 742966713 1599 False 2494 2494 95.062 874 2447 1 chr7B.!!$F3 1573
4 TraesCS7D01G285100 chr7B 247412914 247413428 514 False 767 767 93.592 409 921 1 chr7B.!!$F2 512
5 TraesCS7D01G285100 chr7B 47133104 47133620 516 False 758 758 93.230 409 921 1 chr7B.!!$F1 512
6 TraesCS7D01G285100 chr6D 430465152 430466785 1633 True 2564 2564 95.288 843 2447 1 chr6D.!!$R2 1604
7 TraesCS7D01G285100 chr6D 369999664 370000899 1235 True 1849 1849 94.018 843 2052 1 chr6D.!!$R1 1209
8 TraesCS7D01G285100 chr3D 202623849 202625481 1632 True 2558 2558 95.226 843 2447 1 chr3D.!!$R1 1604
9 TraesCS7D01G285100 chr3D 478088729 478089711 982 True 1493 1493 94.507 1490 2447 1 chr3D.!!$R2 957
10 TraesCS7D01G285100 chr6B 625535783 625537518 1735 True 2551 2551 93.433 738 2447 1 chr6B.!!$R1 1709
11 TraesCS7D01G285100 chr5A 162143785 162145422 1637 True 2518 2518 94.689 837 2447 1 chr5A.!!$R1 1610
12 TraesCS7D01G285100 chr1D 350977669 350979301 1632 False 2503 2503 94.611 843 2447 1 chr1D.!!$F1 1604
13 TraesCS7D01G285100 chr3B 92224996 92226594 1598 True 2486 2486 95.000 874 2447 1 chr3B.!!$R1 1573
14 TraesCS7D01G285100 chr3B 92237823 92239422 1599 False 2477 2477 94.875 874 2447 1 chr3B.!!$F1 1573
15 TraesCS7D01G285100 chr3B 201582130 201583729 1599 True 2471 2471 94.812 874 2447 1 chr3B.!!$R2 1573
16 TraesCS7D01G285100 chr3B 669851087 669851611 524 True 780 780 93.524 409 932 1 chr3B.!!$R4 523
17 TraesCS7D01G285100 chr3B 669825849 669826373 524 True 769 769 93.143 409 932 1 chr3B.!!$R3 523
18 TraesCS7D01G285100 chr4D 97361818 97363449 1631 False 2479 2479 94.363 843 2447 1 chr4D.!!$F1 1604
19 TraesCS7D01G285100 chr4D 123500679 123501361 682 False 1129 1129 96.486 1 683 1 chr4D.!!$F2 682
20 TraesCS7D01G285100 chr1B 286076897 286078638 1741 False 2440 2440 92.202 732 2447 1 chr1B.!!$F1 1715
21 TraesCS7D01G285100 chrUn 45132757 45134210 1453 True 2296 2296 95.461 1020 2447 1 chrUn.!!$R1 1427
22 TraesCS7D01G285100 chr2D 306150656 306151580 924 False 1393 1393 93.946 1 919 1 chr2D.!!$F1 918
23 TraesCS7D01G285100 chr2A 444300689 444301615 926 False 1341 1341 92.888 1 922 1 chr2A.!!$F1 921
24 TraesCS7D01G285100 chr3A 51894581 51895197 616 False 826 826 91.129 314 921 1 chr3A.!!$F1 607

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
216 217 0.108963 TTCATTTCGGGGTGGACGTT 59.891 50.0 0.0 0.0 0.0 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2129 0.310854 CCAGTGAAAACCCACGCTTC 59.689 55.0 0.0 0.0 41.67 3.86 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
94 95 0.317479 ATCTCGGGTTAGGTATGCGC 59.683 55.000 0.00 0.00 0.00 6.09
149 150 3.641986 GGACGCGTGCGGAAACAA 61.642 61.111 20.70 0.00 44.69 2.83
181 182 1.381327 CGGCCTAGAACTGAGGGGA 60.381 63.158 0.00 0.00 34.35 4.81
200 201 3.306502 GGGACGACACAAGACCTATTTCA 60.307 47.826 0.00 0.00 0.00 2.69
216 217 0.108963 TTCATTTCGGGGTGGACGTT 59.891 50.000 0.00 0.00 0.00 3.99
218 219 0.519961 CATTTCGGGGTGGACGTTTC 59.480 55.000 0.00 0.00 0.00 2.78
290 291 3.810310 AAGGGTTTTGTTTGATGCGAA 57.190 38.095 0.00 0.00 0.00 4.70
425 426 2.581354 GGCGACTGACAGGATGCT 59.419 61.111 7.51 0.00 42.53 3.79
500 501 7.482743 CGCGATCTAGTTAACAACACTTTAGTA 59.517 37.037 0.00 0.00 0.00 1.82
573 579 9.778741 TTGAATACATCAAGTTGGATATAGGTC 57.221 33.333 2.34 0.00 43.08 3.85
677 683 3.069443 CAGCTGCTTTTAAAAAGTCCCCA 59.931 43.478 0.00 0.00 0.00 4.96
721 727 2.037772 TCTCAACACCAGCTTCTCTTCC 59.962 50.000 0.00 0.00 0.00 3.46
743 753 8.458951 TTCCCTTTTCTTAAGTATAAGAGGGT 57.541 34.615 21.32 0.00 46.15 4.34
850 862 9.881529 CAATCCAAAACTTATTCATTTTGTTGG 57.118 29.630 8.23 0.00 41.95 3.77
859 871 9.625747 ACTTATTCATTTTGTTGGAAAACCAAT 57.374 25.926 5.01 0.00 32.08 3.16
881 893 1.468914 CCGACGTCAAGATCAGTCTCA 59.531 52.381 17.16 0.00 32.15 3.27
975 990 1.078759 CGTCATCGAAAGCGGCTTCT 61.079 55.000 16.70 6.41 39.71 2.85
980 995 3.938963 TCATCGAAAGCGGCTTCTAATTT 59.061 39.130 16.70 0.00 38.28 1.82
1195 1210 2.030007 CCAATGTGCGAAGTGGTCAAAT 60.030 45.455 0.00 0.00 0.00 2.32
1205 1220 4.566987 GAAGTGGTCAAATTAGGAGTCGT 58.433 43.478 0.00 0.00 0.00 4.34
1404 1419 5.533112 AGAAGGGAGAATCTTCATGGACTA 58.467 41.667 6.60 0.00 42.09 2.59
1430 1445 1.289109 ACCAATCGGAGTTTCACGCG 61.289 55.000 3.53 3.53 35.59 6.01
1504 1519 9.869844 CAGTCATACTCAACAAAAGTAAGAAAG 57.130 33.333 0.00 0.00 31.09 2.62
1511 1526 8.244113 ACTCAACAAAAGTAAGAAAGGTTTGAG 58.756 33.333 0.00 0.00 34.16 3.02
1514 1529 5.420739 ACAAAAGTAAGAAAGGTTTGAGCCA 59.579 36.000 0.00 0.00 34.16 4.75
1558 1573 4.879197 AGAAAGAAAATTGGCCTTCCTG 57.121 40.909 3.32 0.00 0.00 3.86
1612 1652 3.058160 CAAGAGGCCTGCCCGTTG 61.058 66.667 12.00 1.64 39.21 4.10
1667 1707 4.540099 TCAGGTGGAATGAATAGGAAAGGT 59.460 41.667 0.00 0.00 0.00 3.50
1734 1774 5.427036 TTTCGCCTTATTTCGTTTGACTT 57.573 34.783 0.00 0.00 0.00 3.01
1761 1801 6.169800 GGAGCTGAGAAATCTACTTCAAAGT 58.830 40.000 0.00 0.46 42.91 2.66
1832 1872 2.760159 CGAAATCCGTTGCGCCCAT 61.760 57.895 4.18 0.00 0.00 4.00
1863 1903 7.775053 ATGTTTTCTTGCTGGGTAATTTCTA 57.225 32.000 0.00 0.00 0.00 2.10
2087 2129 1.217882 AACTGAACTTCGCCTTCACG 58.782 50.000 0.00 0.00 0.00 4.35
2113 2155 3.558033 GTGGGTTTTCACTGGTCCTAAA 58.442 45.455 0.00 0.00 34.98 1.85
2146 2188 1.701847 AGCGATCCCCTATTCTGCATT 59.298 47.619 0.00 0.00 0.00 3.56
2170 2212 0.397816 AGATTAGACGGCCCAGAGCT 60.398 55.000 0.00 0.00 43.05 4.09
2197 2239 4.331168 GCGATCATTCAAGCAAGTTACTCT 59.669 41.667 0.00 0.00 0.00 3.24
2317 2362 3.795688 TGGAAGCTTCAGAAACCATCT 57.204 42.857 27.02 0.00 39.68 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 2.091885 ACAAAGAGGGGAGTTTTGCTCA 60.092 45.455 0.00 0.00 45.88 4.26
94 95 4.021102 ACAACCCATTTCTGGTGTCTAG 57.979 45.455 0.00 0.00 41.37 2.43
149 150 0.966370 AGGCCGAAGTAGAGCGAACT 60.966 55.000 0.00 0.00 0.00 3.01
181 182 5.120208 CGAAATGAAATAGGTCTTGTGTCGT 59.880 40.000 0.00 0.00 0.00 4.34
200 201 0.952010 CGAAACGTCCACCCCGAAAT 60.952 55.000 0.00 0.00 0.00 2.17
216 217 2.092861 TCCCCTCAACTGTTTGAACGAA 60.093 45.455 0.00 0.00 41.34 3.85
218 219 1.961793 TCCCCTCAACTGTTTGAACG 58.038 50.000 0.00 0.00 41.34 3.95
425 426 1.123077 ATGGAATAGCACTCGCAGGA 58.877 50.000 0.00 0.00 42.27 3.86
555 561 5.072329 CCACCTGACCTATATCCAACTTGAT 59.928 44.000 0.00 0.00 0.00 2.57
573 579 2.025887 AGGCATTCTTAAGTCCCACCTG 60.026 50.000 1.63 0.00 0.00 4.00
677 683 3.637821 TGAGAAGTGGGCTATATCCCT 57.362 47.619 12.85 0.00 46.67 4.20
721 727 9.833917 CCTAACCCTCTTATACTTAAGAAAAGG 57.166 37.037 10.09 6.77 42.46 3.11
743 753 2.701951 CCGGCCAGGAATAAGTACCTAA 59.298 50.000 2.24 0.00 45.00 2.69
809 819 7.449395 AGTTTTGGATTGAGATTTCACATCAGA 59.551 33.333 9.18 0.00 31.71 3.27
850 862 0.589223 TGACGTCGGCATTGGTTTTC 59.411 50.000 11.62 0.00 0.00 2.29
859 871 0.109272 GACTGATCTTGACGTCGGCA 60.109 55.000 11.62 0.00 0.00 5.69
881 893 4.042934 TCCTCCCGAAAAGAGAAAGGAAAT 59.957 41.667 0.00 0.00 32.86 2.17
980 995 6.013898 CCCCATATAGCTGAGAATTTCTGAGA 60.014 42.308 15.92 0.00 28.58 3.27
1103 1118 0.319083 TCGAGCTAGGCGGTGAAAAA 59.681 50.000 0.00 0.00 0.00 1.94
1179 1194 3.071479 TCCTAATTTGACCACTTCGCAC 58.929 45.455 0.00 0.00 0.00 5.34
1205 1220 8.014263 TCCCAGGAACATCATAAATAGTACCTA 58.986 37.037 0.00 0.00 0.00 3.08
1404 1419 0.693049 AACTCCGATTGGTGGAAGCT 59.307 50.000 6.03 0.00 34.44 3.74
1430 1445 6.093633 GGTATCACTTTACCACCATCTGAAAC 59.906 42.308 0.00 0.00 41.18 2.78
1558 1573 5.782845 ACTCTATGAATGAAGGGGGAGTATC 59.217 44.000 0.00 0.00 32.12 2.24
1650 1690 5.694995 TGATCCACCTTTCCTATTCATTCC 58.305 41.667 0.00 0.00 0.00 3.01
1660 1700 5.920193 TGATTTGATTGATCCACCTTTCC 57.080 39.130 0.00 0.00 0.00 3.13
1667 1707 7.288158 TCATGGCTTATTGATTTGATTGATCCA 59.712 33.333 0.00 0.00 0.00 3.41
1734 1774 4.528206 TGAAGTAGATTTCTCAGCTCCACA 59.472 41.667 0.00 0.00 0.00 4.17
1761 1801 2.180276 GGACTAGCACTCTTTCCCTCA 58.820 52.381 0.00 0.00 0.00 3.86
1832 1872 2.415759 CCAGCAAGAAAACATATGCGCA 60.416 45.455 14.96 14.96 43.39 6.09
1863 1903 7.877612 AGGAATCAACAACACAAAAACTTTCTT 59.122 29.630 0.00 0.00 0.00 2.52
1985 2027 9.453572 TTCAATTGTAGATTTGAGTATTGAGCT 57.546 29.630 5.13 0.00 33.59 4.09
2087 2129 0.310854 CCAGTGAAAACCCACGCTTC 59.689 55.000 0.00 0.00 41.67 3.86
2113 2155 1.956477 GGATCGCTTGCCAACCATTAT 59.044 47.619 0.00 0.00 0.00 1.28
2146 2188 0.685131 TGGGCCGTCTAATCTTCGGA 60.685 55.000 7.01 0.00 46.05 4.55
2170 2212 2.011947 CTTGCTTGAATGATCGCTCCA 58.988 47.619 0.00 0.00 0.00 3.86
2197 2239 5.833406 TGATTGACTGAAAAACTCAAGCA 57.167 34.783 0.00 0.00 37.84 3.91
2317 2362 9.784531 AACATTTCTTGTTTCTAGAAGATCTCA 57.215 29.630 5.12 0.00 46.51 3.27


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

AutoCloner maintained by Alex Coulton.