Multiple sequence alignment - TraesCS4A01G128700

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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 TraesCS4A01G128700 chr4A 100.000 2504 0 0 1 2504 165711374 165713877 0.000000e+00 4625.0
1 TraesCS4A01G128700 chr4A 87.119 854 105 5 1652 2501 602857669 602858521 0.000000e+00 963.0
2 TraesCS4A01G128700 chr4D 94.277 1625 66 15 1 1608 309510193 309508579 0.000000e+00 2460.0
3 TraesCS4A01G128700 chr3A 90.738 799 71 3 1705 2502 716571190 716571986 0.000000e+00 1062.0
4 TraesCS4A01G128700 chr3A 92.958 71 4 1 330 399 440635038 440634968 4.410000e-18 102.0
5 TraesCS4A01G128700 chr3A 92.857 56 4 0 483 538 7457454 7457509 5.740000e-12 82.4
6 TraesCS4A01G128700 chr3A 92.857 56 4 0 483 538 7463999 7464054 5.740000e-12 82.4
7 TraesCS4A01G128700 chr4B 87.660 859 93 8 1652 2502 626519369 626520222 0.000000e+00 987.0
8 TraesCS4A01G128700 chr4B 89.920 754 29 18 200 944 386222989 386222274 0.000000e+00 928.0
9 TraesCS4A01G128700 chr4B 92.799 611 38 1 1009 1613 386213995 386213385 0.000000e+00 880.0
10 TraesCS4A01G128700 chr4B 92.799 611 38 1 1009 1613 386218774 386218164 0.000000e+00 880.0
11 TraesCS4A01G128700 chr4B 92.799 611 38 1 1009 1613 386220595 386219985 0.000000e+00 880.0
12 TraesCS4A01G128700 chr4B 92.635 611 39 1 1009 1613 386216953 386216343 0.000000e+00 874.0
13 TraesCS4A01G128700 chr4B 90.276 689 32 15 1 688 386223651 386222997 0.000000e+00 869.0
14 TraesCS4A01G128700 chr4B 84.923 849 119 9 1655 2498 581951118 581951962 0.000000e+00 850.0
15 TraesCS4A01G128700 chr4B 100.000 55 0 0 963 1017 386222277 386222223 4.410000e-18 102.0
16 TraesCS4A01G128700 chr3B 86.845 859 103 10 1652 2504 707575050 707575904 0.000000e+00 952.0
17 TraesCS4A01G128700 chr3B 91.549 71 5 1 330 399 422472529 422472599 2.050000e-16 97.1
18 TraesCS4A01G128700 chr3B 97.674 43 1 0 1614 1656 386062145 386062187 9.610000e-10 75.0
19 TraesCS4A01G128700 chr7B 85.631 856 110 13 1655 2503 678291106 678290257 0.000000e+00 887.0
20 TraesCS4A01G128700 chr7B 83.274 849 117 8 1656 2502 633679450 633678625 0.000000e+00 758.0
21 TraesCS4A01G128700 chr7B 91.667 48 2 2 1610 1657 113068064 113068019 5.780000e-07 65.8
22 TraesCS4A01G128700 chr2B 85.263 855 112 13 1656 2503 778804277 778803430 0.000000e+00 869.0
23 TraesCS4A01G128700 chr2B 89.362 47 4 1 310 356 493968981 493969026 9.670000e-05 58.4
24 TraesCS4A01G128700 chr7A 89.164 646 68 2 1860 2504 28408308 28408952 0.000000e+00 804.0
25 TraesCS4A01G128700 chr7A 89.320 206 18 4 1655 1860 28359010 28359211 3.200000e-64 255.0
26 TraesCS4A01G128700 chr7A 90.141 71 6 1 330 399 68881102 68881172 9.540000e-15 91.6
27 TraesCS4A01G128700 chr7A 97.917 48 1 0 483 530 693453467 693453420 1.600000e-12 84.2
28 TraesCS4A01G128700 chr5A 85.275 781 92 10 1655 2431 4227036 4226275 0.000000e+00 784.0
29 TraesCS4A01G128700 chr5A 95.455 44 0 1 1615 1656 82867948 82867905 4.470000e-08 69.4
30 TraesCS4A01G128700 chr5A 88.000 50 4 2 314 362 474916870 474916918 9.670000e-05 58.4
31 TraesCS4A01G128700 chr5A 84.211 57 5 3 302 355 629924936 629924991 5.000000e-03 52.8
32 TraesCS4A01G128700 chr1A 89.342 441 41 6 1656 2095 533287131 533286696 1.310000e-152 549.0
33 TraesCS4A01G128700 chr1A 75.926 540 118 9 1856 2389 9954883 9955416 1.480000e-67 267.0
34 TraesCS4A01G128700 chr6B 89.773 88 7 2 314 399 541936638 541936725 7.320000e-21 111.0
35 TraesCS4A01G128700 chr6B 88.235 51 4 2 1605 1655 212623484 212623436 2.690000e-05 60.2
36 TraesCS4A01G128700 chr6A 88.636 88 8 2 314 399 501479274 501479361 3.410000e-19 106.0
37 TraesCS4A01G128700 chr7D 91.781 73 4 2 330 401 46702663 46702734 1.580000e-17 100.0
38 TraesCS4A01G128700 chr7D 90.541 74 4 2 330 400 184573430 184573357 7.370000e-16 95.3
39 TraesCS4A01G128700 chr7D 91.379 58 3 2 483 539 168580908 168580852 7.430000e-11 78.7
40 TraesCS4A01G128700 chr7D 91.304 46 3 1 314 359 4643978 4644022 7.480000e-06 62.1
41 TraesCS4A01G128700 chrUn 96.491 57 2 0 1009 1065 414074371 414074315 7.370000e-16 95.3
42 TraesCS4A01G128700 chr1D 90.541 74 4 2 329 401 464799795 464799724 7.370000e-16 95.3
43 TraesCS4A01G128700 chr3D 94.444 54 1 2 486 537 272290707 272290760 5.740000e-12 82.4
44 TraesCS4A01G128700 chr2D 91.228 57 4 1 475 531 7229333 7229278 2.670000e-10 76.8
45 TraesCS4A01G128700 chr1B 95.745 47 2 0 1610 1656 196649297 196649251 2.670000e-10 76.8
46 TraesCS4A01G128700 chr1B 93.617 47 3 0 1610 1656 196628972 196628926 1.240000e-08 71.3


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 TraesCS4A01G128700 chr4A 165711374 165713877 2503 False 4625.000000 4625 100.000000 1 2504 1 chr4A.!!$F1 2503
1 TraesCS4A01G128700 chr4A 602857669 602858521 852 False 963.000000 963 87.119000 1652 2501 1 chr4A.!!$F2 849
2 TraesCS4A01G128700 chr4D 309508579 309510193 1614 True 2460.000000 2460 94.277000 1 1608 1 chr4D.!!$R1 1607
3 TraesCS4A01G128700 chr3A 716571190 716571986 796 False 1062.000000 1062 90.738000 1705 2502 1 chr3A.!!$F3 797
4 TraesCS4A01G128700 chr4B 626519369 626520222 853 False 987.000000 987 87.660000 1652 2502 1 chr4B.!!$F2 850
5 TraesCS4A01G128700 chr4B 581951118 581951962 844 False 850.000000 850 84.923000 1655 2498 1 chr4B.!!$F1 843
6 TraesCS4A01G128700 chr4B 386213385 386223651 10266 True 773.285714 928 93.032571 1 1613 7 chr4B.!!$R1 1612
7 TraesCS4A01G128700 chr3B 707575050 707575904 854 False 952.000000 952 86.845000 1652 2504 1 chr3B.!!$F3 852
8 TraesCS4A01G128700 chr7B 678290257 678291106 849 True 887.000000 887 85.631000 1655 2503 1 chr7B.!!$R3 848
9 TraesCS4A01G128700 chr7B 633678625 633679450 825 True 758.000000 758 83.274000 1656 2502 1 chr7B.!!$R2 846
10 TraesCS4A01G128700 chr2B 778803430 778804277 847 True 869.000000 869 85.263000 1656 2503 1 chr2B.!!$R1 847
11 TraesCS4A01G128700 chr7A 28408308 28408952 644 False 804.000000 804 89.164000 1860 2504 1 chr7A.!!$F2 644
12 TraesCS4A01G128700 chr5A 4226275 4227036 761 True 784.000000 784 85.275000 1655 2431 1 chr5A.!!$R1 776
13 TraesCS4A01G128700 chr1A 9954883 9955416 533 False 267.000000 267 75.926000 1856 2389 1 chr1A.!!$F1 533


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
238 239 0.326595 TTGCCGAAACCATCCTGCTA 59.673 50.0 0.0 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 7646 1.152839 GTCCCTCCTCTCCCTCTCG 60.153 68.421 0.0 0.0 0.0 4.04 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
238 239 0.326595 TTGCCGAAACCATCCTGCTA 59.673 50.000 0.00 0.00 0.00 3.49
270 271 4.096382 TGGACAAGAAACTTGAAGCTGAAC 59.904 41.667 16.65 0.00 0.00 3.18
274 275 3.134458 AGAAACTTGAAGCTGAACTCGG 58.866 45.455 0.00 0.00 0.00 4.63
285 286 2.625737 CTGAACTCGGCTCATTGATGT 58.374 47.619 0.00 0.00 0.00 3.06
291 292 2.076100 TCGGCTCATTGATGTGTGTTC 58.924 47.619 0.00 0.00 0.00 3.18
338 339 9.597170 CTATTTTACTTGTTTAGTACTCCCTCC 57.403 37.037 0.00 0.00 39.05 4.30
340 341 3.504375 ACTTGTTTAGTACTCCCTCCGT 58.496 45.455 0.00 0.00 34.56 4.69
363 470 7.309867 CCGTCCCATAATATAAGAGCTTAGTGT 60.310 40.741 0.00 0.00 0.00 3.55
364 471 7.755822 CGTCCCATAATATAAGAGCTTAGTGTC 59.244 40.741 0.00 0.00 0.00 3.67
365 472 8.585881 GTCCCATAATATAAGAGCTTAGTGTCA 58.414 37.037 0.00 0.00 0.00 3.58
418 861 2.967887 AGTTCTGGTTACCGGTGTTACT 59.032 45.455 19.93 7.85 0.00 2.24
425 868 7.491682 TCTGGTTACCGGTGTTACTTATATTC 58.508 38.462 19.93 0.00 0.00 1.75
485 931 4.084287 TCCTTGTTCGTGTCCATAGTACT 58.916 43.478 0.00 0.00 0.00 2.73
573 1021 2.484417 GGTGTGTGCCCTCTCATATCAG 60.484 54.545 0.00 0.00 0.00 2.90
606 1054 4.761739 CCTATGGTGTGAACATTTGACAGT 59.238 41.667 0.00 0.00 0.00 3.55
613 1061 5.682862 GTGTGAACATTTGACAGTGCTTTAG 59.317 40.000 0.00 0.00 0.00 1.85
624 1073 4.336280 ACAGTGCTTTAGGGATCCTTTTC 58.664 43.478 12.58 0.00 34.61 2.29
644 1093 1.135257 CGGCAGACGTCTCTTCAGATT 60.135 52.381 16.96 0.00 37.93 2.40
647 1096 4.495422 GGCAGACGTCTCTTCAGATTTTA 58.505 43.478 16.96 0.00 0.00 1.52
664 1114 7.182206 TCAGATTTTAAGTCTTAGCTAACCCCT 59.818 37.037 0.86 0.00 0.00 4.79
715 1165 2.041350 TGGGTCTCCGGGATCTAGATAC 59.959 54.545 6.38 6.38 35.24 2.24
716 1166 2.309458 GGGTCTCCGGGATCTAGATACT 59.691 54.545 14.76 0.00 0.00 2.12
717 1167 3.522750 GGGTCTCCGGGATCTAGATACTA 59.477 52.174 14.76 0.57 0.00 1.82
724 1174 7.347485 TCTCCGGGATCTAGATACTATGTGATA 59.653 40.741 14.76 0.00 0.00 2.15
739 1189 2.289631 TGTGATACTGTGCAGACCCTTG 60.290 50.000 6.17 0.00 0.00 3.61
946 1404 0.812549 AAACAGGAAACCGCGTTTGT 59.187 45.000 4.92 0.00 35.77 2.83
1048 4963 4.083324 ACAACAACTCGATAAGCACAATGG 60.083 41.667 0.00 0.00 0.00 3.16
1179 5094 2.679092 CAGGAATGCTGGGAGGCA 59.321 61.111 0.00 0.00 46.63 4.75
1404 7140 2.740055 CTCACGGTCACAGCTGCC 60.740 66.667 15.27 6.17 0.00 4.85
1600 7342 5.451242 CCCGTGGGATTTATTGTTGTAATGG 60.451 44.000 0.00 0.00 37.50 3.16
1641 7383 6.415798 TTTTTAACAAGGCAAAAGACTTGC 57.584 33.333 10.80 0.78 46.03 4.01
1653 7395 7.188468 GCAAAAGACTTGCCAATTTCATTAA 57.812 32.000 0.00 0.00 39.38 1.40
1753 7646 3.493699 GGGGGAAACAAGGTTTTTACAGC 60.494 47.826 0.00 0.00 0.00 4.40
1869 9284 0.038251 TAGCCAGAGTGCGTGAACAG 60.038 55.000 0.00 0.00 36.02 3.16
2107 9522 0.323360 GAGCCCCAACATTGTAGCCA 60.323 55.000 0.00 0.00 0.00 4.75
2244 10046 1.262950 CGCAGTGACGATGGTTTTTCA 59.737 47.619 0.00 0.00 34.06 2.69
2255 10057 1.157585 GGTTTTTCAGAGGAGGACGC 58.842 55.000 0.00 0.00 0.00 5.19
2259 10061 3.539593 TTCAGAGGAGGACGCCCCA 62.540 63.158 0.00 0.00 37.41 4.96
2347 10272 0.798776 AGATGAACTCGGCAAAAGCG 59.201 50.000 0.00 0.00 0.00 4.68
2365 10290 4.740822 GCCTGCACCCCACCGAAT 62.741 66.667 0.00 0.00 0.00 3.34
2371 10296 1.617947 GCACCCCACCGAATCTCTCT 61.618 60.000 0.00 0.00 0.00 3.10
2389 10314 1.021202 CTAGAGCGTAGACAGCTGCT 58.979 55.000 15.27 14.40 46.13 4.24
2432 10364 2.280797 GCACAACACCGAGCTCCA 60.281 61.111 8.47 0.00 0.00 3.86
2485 10417 1.305297 ATGAGCGTCAGGAGGGTGA 60.305 57.895 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.487668 TGCAAACATAGATATCAGGTGATTGG 59.512 38.462 17.93 6.97 36.05 3.16
10 11 6.236409 CCTGCAAACATAGATATCAGGTGAT 58.764 40.000 5.32 0.00 35.97 3.06
12 13 5.936686 CCTGCAAACATAGATATCAGGTG 57.063 43.478 5.32 3.23 35.97 4.00
187 188 0.877071 AGCAAATGTTCCTCGCACAG 59.123 50.000 0.00 0.00 0.00 3.66
238 239 8.408043 TTCAAGTTTCTTGTCCATACATTCAT 57.592 30.769 8.93 0.00 34.97 2.57
270 271 1.730501 ACACACATCAATGAGCCGAG 58.269 50.000 0.00 0.00 0.00 4.63
274 275 4.214971 AGAACAGAACACACATCAATGAGC 59.785 41.667 0.00 0.00 0.00 4.26
285 286 7.439356 CAGACTGAATAGAAAGAACAGAACACA 59.561 37.037 0.00 0.00 33.53 3.72
291 292 8.715191 AATAGCAGACTGAATAGAAAGAACAG 57.285 34.615 6.65 0.00 35.14 3.16
338 339 7.603651 ACACTAAGCTCTTATATTATGGGACG 58.396 38.462 0.00 0.00 0.00 4.79
340 341 8.721133 TGACACTAAGCTCTTATATTATGGGA 57.279 34.615 0.00 0.00 0.00 4.37
370 477 8.884323 ACTCCTTCAATCCATAATATAAGAGCA 58.116 33.333 0.00 0.00 0.00 4.26
388 831 3.508793 CGGTAACCAGAACTACTCCTTCA 59.491 47.826 0.00 0.00 0.00 3.02
446 892 3.851458 AGGATCAAGCATGCAGACATA 57.149 42.857 21.98 0.00 33.67 2.29
448 894 2.089201 CAAGGATCAAGCATGCAGACA 58.911 47.619 21.98 0.23 0.00 3.41
519 965 2.032620 CGGCTAGTGATGTACTCCCTT 58.967 52.381 0.00 0.00 40.89 3.95
573 1021 0.839946 ACACCATAGGCAGACCATCC 59.160 55.000 0.00 0.00 39.06 3.51
606 1054 2.944094 GCCGAAAAGGATCCCTAAAGCA 60.944 50.000 8.55 0.00 45.00 3.91
613 1061 1.090052 CGTCTGCCGAAAAGGATCCC 61.090 60.000 8.55 0.00 45.00 3.85
624 1073 0.453793 ATCTGAAGAGACGTCTGCCG 59.546 55.000 25.58 8.63 44.03 5.69
644 1093 5.548836 TCCAAGGGGTTAGCTAAGACTTAAA 59.451 40.000 6.38 1.38 34.93 1.52
647 1096 3.527937 TCCAAGGGGTTAGCTAAGACTT 58.472 45.455 6.38 8.70 34.93 3.01
715 1165 3.386078 AGGGTCTGCACAGTATCACATAG 59.614 47.826 0.00 0.00 0.00 2.23
716 1166 3.374764 AGGGTCTGCACAGTATCACATA 58.625 45.455 0.00 0.00 0.00 2.29
717 1167 2.191400 AGGGTCTGCACAGTATCACAT 58.809 47.619 0.00 0.00 0.00 3.21
946 1404 2.095213 GCAACGTCAAGAACAACTGTCA 59.905 45.455 0.00 0.00 0.00 3.58
1286 5201 4.767255 GGCACCTGAGCACCCTCG 62.767 72.222 0.00 0.00 41.13 4.63
1404 7140 4.697756 TCTTCCCCGGCGTGCTTG 62.698 66.667 6.01 0.00 0.00 4.01
1534 7276 2.046314 ATCGTTCAGGCCGTTGGG 60.046 61.111 0.00 0.00 0.00 4.12
1618 7360 6.415798 GCAAGTCTTTTGCCTTGTTAAAAA 57.584 33.333 0.54 0.00 40.13 1.94
1629 7371 5.678132 AATGAAATTGGCAAGTCTTTTGC 57.322 34.783 5.96 3.39 44.22 3.68
1689 7433 6.806668 AGGAAAAAGAAAATTCAGGTGGAA 57.193 33.333 0.00 0.00 40.46 3.53
1727 7474 1.951923 AAACCTTGTTTCCCCCGGGT 61.952 55.000 21.85 0.00 36.47 5.28
1753 7646 1.152839 GTCCCTCCTCTCCCTCTCG 60.153 68.421 0.00 0.00 0.00 4.04
1869 9284 3.357079 CCGACAGGTGGTTGCTGC 61.357 66.667 0.00 0.00 0.00 5.25
2107 9522 4.052229 CTCGAGGTGGCCGAACGT 62.052 66.667 3.91 0.00 35.48 3.99
2255 10057 4.579384 AAGGGTGCACACGTGGGG 62.579 66.667 21.41 12.57 0.00 4.96
2259 10061 4.235762 AGCGAAGGGTGCACACGT 62.236 61.111 20.43 14.48 33.85 4.49
2365 10290 2.432874 AGCTGTCTACGCTCTAGAGAGA 59.567 50.000 27.65 16.46 44.74 3.10
2371 10296 0.735471 CAGCAGCTGTCTACGCTCTA 59.265 55.000 16.64 0.00 35.07 2.43
2432 10364 0.036306 GACCCCAGGAAATGACGTGT 59.964 55.000 0.00 0.00 0.00 4.49



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

AutoCloner maintained by Alex Coulton.