Multiple sequence alignment - TraesCS3A01G447200

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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 TraesCS3A01G447200 chr3A 100.000 2615 0 0 1 2615 687102288 687104902 0.000000e+00 4830.0
1 TraesCS3A01G447200 chr3D 95.350 1441 48 9 760 2187 550269733 550271167 0.000000e+00 2272.0
2 TraesCS3A01G447200 chr3D 96.610 767 22 4 1 766 550268941 550269704 0.000000e+00 1269.0
3 TraesCS3A01G447200 chr3D 96.476 454 10 5 2163 2615 550271201 550271649 0.000000e+00 745.0
4 TraesCS3A01G447200 chr3D 83.478 690 83 17 87 766 362865929 362865261 4.780000e-172 614.0
5 TraesCS3A01G447200 chr3D 86.019 422 49 8 1767 2187 267221472 267221060 6.640000e-121 444.0
6 TraesCS3A01G447200 chr3D 86.190 420 47 10 2163 2575 446909082 446909497 6.640000e-121 444.0
7 TraesCS3A01G447200 chr3D 85.315 429 52 11 2163 2585 537593518 537593941 1.440000e-117 433.0
8 TraesCS3A01G447200 chr3B 89.033 1468 108 18 763 2187 729724144 729725601 0.000000e+00 1770.0
9 TraesCS3A01G447200 chr3B 84.348 690 87 20 87 766 472630043 472629365 0.000000e+00 656.0
10 TraesCS3A01G447200 chr3B 91.285 459 28 11 2163 2615 729725635 729726087 1.330000e-172 616.0
11 TraesCS3A01G447200 chr3B 82.701 422 67 6 1767 2187 201885742 201886158 1.140000e-98 370.0
12 TraesCS3A01G447200 chr4D 87.231 697 89 0 944 1640 136500411 136501107 0.000000e+00 795.0
13 TraesCS3A01G447200 chr4D 86.949 613 71 6 157 764 483204553 483203945 0.000000e+00 680.0
14 TraesCS3A01G447200 chr4D 90.281 391 34 3 1659 2047 136501157 136501545 2.320000e-140 508.0
15 TraesCS3A01G447200 chr4D 97.619 42 1 0 87 128 483204593 483204552 3.610000e-09 73.1
16 TraesCS3A01G447200 chr6A 84.448 688 92 11 87 765 454544397 454543716 0.000000e+00 664.0
17 TraesCS3A01G447200 chr7B 83.406 687 105 9 87 766 333355511 333354827 1.710000e-176 628.0
18 TraesCS3A01G447200 chr5A 83.699 638 95 8 83 714 693493381 693494015 6.230000e-166 593.0
19 TraesCS3A01G447200 chr5A 82.473 639 99 12 83 714 693409608 693410240 4.920000e-152 547.0
20 TraesCS3A01G447200 chr7A 82.242 687 110 11 83 763 195201562 195202242 1.350000e-162 582.0
21 TraesCS3A01G447200 chr7D 80.733 737 127 14 1888 2615 442208889 442208159 6.320000e-156 560.0
22 TraesCS3A01G447200 chr7D 84.282 439 64 5 2182 2615 47386588 47387026 8.650000e-115 424.0
23 TraesCS3A01G447200 chr4B 86.918 451 45 14 2163 2605 228418180 228418624 6.500000e-136 494.0
24 TraesCS3A01G447200 chr2D 86.755 453 42 16 2163 2605 398645663 398646107 3.020000e-134 488.0
25 TraesCS3A01G447200 chr2A 86.123 454 44 17 2163 2605 535834283 535834728 3.050000e-129 472.0
26 TraesCS3A01G447200 chr4A 87.000 400 47 4 1657 2053 397261434 397261037 1.850000e-121 446.0
27 TraesCS3A01G447200 chr4A 81.991 422 68 8 1767 2187 133846279 133845865 4.140000e-93 351.0
28 TraesCS3A01G447200 chr4A 92.157 102 8 0 944 1045 397291707 397291606 7.540000e-31 145.0
29 TraesCS3A01G447200 chr6B 83.765 425 58 9 1767 2187 471005280 471004863 2.440000e-105 392.0
30 TraesCS3A01G447200 chr2B 88.177 203 20 3 566 766 753919220 753919020 3.360000e-59 239.0


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 TraesCS3A01G447200 chr3A 687102288 687104902 2614 False 4830.000000 4830 100.000000 1 2615 1 chr3A.!!$F1 2614
1 TraesCS3A01G447200 chr3D 550268941 550271649 2708 False 1428.666667 2272 96.145333 1 2615 3 chr3D.!!$F3 2614
2 TraesCS3A01G447200 chr3D 362865261 362865929 668 True 614.000000 614 83.478000 87 766 1 chr3D.!!$R2 679
3 TraesCS3A01G447200 chr3B 729724144 729726087 1943 False 1193.000000 1770 90.159000 763 2615 2 chr3B.!!$F2 1852
4 TraesCS3A01G447200 chr3B 472629365 472630043 678 True 656.000000 656 84.348000 87 766 1 chr3B.!!$R1 679
5 TraesCS3A01G447200 chr4D 136500411 136501545 1134 False 651.500000 795 88.756000 944 2047 2 chr4D.!!$F1 1103
6 TraesCS3A01G447200 chr4D 483203945 483204593 648 True 376.550000 680 92.284000 87 764 2 chr4D.!!$R1 677
7 TraesCS3A01G447200 chr6A 454543716 454544397 681 True 664.000000 664 84.448000 87 765 1 chr6A.!!$R1 678
8 TraesCS3A01G447200 chr7B 333354827 333355511 684 True 628.000000 628 83.406000 87 766 1 chr7B.!!$R1 679
9 TraesCS3A01G447200 chr5A 693493381 693494015 634 False 593.000000 593 83.699000 83 714 1 chr5A.!!$F2 631
10 TraesCS3A01G447200 chr5A 693409608 693410240 632 False 547.000000 547 82.473000 83 714 1 chr5A.!!$F1 631
11 TraesCS3A01G447200 chr7A 195201562 195202242 680 False 582.000000 582 82.242000 83 763 1 chr7A.!!$F1 680
12 TraesCS3A01G447200 chr7D 442208159 442208889 730 True 560.000000 560 80.733000 1888 2615 1 chr7D.!!$R1 727

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
774 839 1.204704 GGGCTTTTATGTTGGACTGCC 59.795 52.381 0.0 0.0 38.49 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1831 1944 2.505819 AGGTGGGTCATACATTCTCACC 59.494 50.0 5.42 5.42 42.31 4.02 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 4.021456 ACCCCGAATTGTTTGGAGATTTTC 60.021 41.667 0.00 0.00 36.18 2.29
78 79 5.497464 TCTTCATGTATTTCCAGTGTCCA 57.503 39.130 0.00 0.00 0.00 4.02
187 193 8.385898 TGTATTGGATCCAATATTAACGTTCC 57.614 34.615 37.67 25.49 46.44 3.62
348 357 4.142359 TGGCAAGTACGTGTGTGAATTTTT 60.142 37.500 10.54 0.00 0.00 1.94
774 839 1.204704 GGGCTTTTATGTTGGACTGCC 59.795 52.381 0.00 0.00 38.49 4.85
791 856 5.465724 GGACTGCCGGTTGATTAGTATAAAG 59.534 44.000 1.90 0.00 0.00 1.85
797 862 6.037830 GCCGGTTGATTAGTATAAAGCTCAAA 59.962 38.462 1.90 0.00 0.00 2.69
851 920 2.159517 CCAACTTAAAGATGGACTGCGC 60.160 50.000 0.00 0.00 40.25 6.09
911 980 1.471287 ACGACGGACGATCAGAAATGA 59.529 47.619 6.90 0.00 45.77 2.57
973 1052 2.815478 GCGCCATGCTCCTCTATATAC 58.185 52.381 0.00 0.00 41.73 1.47
1014 1093 1.354337 CTTGCATCACCTCCACGACG 61.354 60.000 0.00 0.00 0.00 5.12
1158 1237 0.959553 AGTACTGTGTCACCGTCCTG 59.040 55.000 3.03 0.00 0.00 3.86
1192 1271 1.204941 AGAGTAAATCTGCGGACGCTT 59.795 47.619 18.04 6.23 42.51 4.68
1371 1450 3.760035 AACGTGAGGCTCGCCGAT 61.760 61.111 26.47 15.88 41.95 4.18
1512 1591 1.746239 CATGGGCGTCATGTCTGCA 60.746 57.895 11.13 0.00 46.11 4.41
1652 1762 9.511144 AATATAAATTTTTCGTCCGACCAATTC 57.489 29.630 0.00 0.00 0.00 2.17
1795 1908 3.075085 GCGCGGTTGCCTTACGTAC 62.075 63.158 8.83 0.00 38.08 3.67
1797 1910 1.374505 GCGGTTGCCTTACGTACCA 60.375 57.895 0.00 0.00 33.98 3.25
1831 1944 4.892433 ACCACTCACTTCTTCTGAGATTG 58.108 43.478 2.47 0.00 37.90 2.67
1911 2024 8.506168 TTTTCTTGTTAGTCAAATCAGTGTCT 57.494 30.769 0.00 0.00 35.48 3.41
1949 2063 4.374399 AGTACACGTTTTGTCAGGTAAGG 58.626 43.478 0.00 0.00 39.91 2.69
2106 2220 3.003480 GCGGTGTCAAGAGCTTTAGAAT 58.997 45.455 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.272792 TCGGGGTGGCCTATTCTTAATATTTA 59.727 38.462 3.32 0.00 0.00 1.40
20 21 1.291906 CAAACAATTCGGGGTGGCC 59.708 57.895 0.00 0.00 0.00 5.36
24 25 2.899303 ATCTCCAAACAATTCGGGGT 57.101 45.000 0.00 0.00 0.00 4.95
187 193 7.439157 TCCAAACAATTCTTGTGATAGTCAG 57.561 36.000 0.00 0.00 44.59 3.51
300 307 8.889717 CACCGGACTACACTATTCATTTTTATT 58.110 33.333 9.46 0.00 0.00 1.40
370 379 4.819105 ACATGTCCCATAGTCGAAGAAA 57.181 40.909 0.00 0.00 39.69 2.52
371 380 4.707934 TGTACATGTCCCATAGTCGAAGAA 59.292 41.667 0.00 0.00 39.69 2.52
526 537 1.403647 CGTCATTCCTTCGTACCAGCA 60.404 52.381 0.00 0.00 0.00 4.41
774 839 7.280205 ACCTTTGAGCTTTATACTAATCAACCG 59.720 37.037 0.00 0.00 0.00 4.44
911 980 7.667557 TCTCTACCTAATAATAAAGCACGCAT 58.332 34.615 0.00 0.00 0.00 4.73
973 1052 1.102154 TTGCATGGTGCTATTTCCCG 58.898 50.000 3.41 0.00 45.31 5.14
997 1076 1.604147 ATCGTCGTGGAGGTGATGCA 61.604 55.000 0.00 0.00 0.00 3.96
1037 1116 2.604686 AGAGGGAGAAGGCACGCA 60.605 61.111 0.00 0.00 0.00 5.24
1045 1124 2.180308 GGAATAGGAGGGAGAGGGAGAA 59.820 54.545 0.00 0.00 0.00 2.87
1158 1237 0.175760 TACTCTTCGGGCATGCTGAC 59.824 55.000 18.92 7.56 0.00 3.51
1192 1271 4.451150 AATCTCGGCCAGCGCGAA 62.451 61.111 12.10 0.00 35.02 4.70
1371 1450 2.679934 CGCAATGAAGCTCCGCACA 61.680 57.895 0.00 0.00 0.00 4.57
1411 1490 1.730501 CACTCATCGCAGTTCCACAT 58.269 50.000 0.00 0.00 0.00 3.21
1795 1908 3.092301 TGAGTGGTCTCAGATGTACTGG 58.908 50.000 0.00 0.00 44.58 4.00
1831 1944 2.505819 AGGTGGGTCATACATTCTCACC 59.494 50.000 5.42 5.42 42.31 4.02
1911 2024 3.574826 GTGTACTTTGGGCCCATTAAACA 59.425 43.478 29.23 23.83 0.00 2.83
1949 2063 4.378774 AGAGAAGAGACATGCATGCATAC 58.621 43.478 31.73 25.85 34.91 2.39
2106 2220 8.116651 TCGAAATGTTTCCAAAATCCATCTAA 57.883 30.769 0.25 0.00 33.68 2.10
2175 2289 8.938906 GTTAAATAGGTTTCGGTGAAATGAGTA 58.061 33.333 0.00 0.00 33.97 2.59
2376 2550 7.873719 TCACAAGTTGAGATTTTAGGTTCAA 57.126 32.000 10.54 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.