Multiple sequence alignment - TraesCS3A01G168000

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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 TraesCS3A01G168000 chr3A 100.000 2264 0 0 1 2264 174769294 174767031 0.000000e+00 4181.0
1 TraesCS3A01G168000 chr3A 95.502 667 28 2 1 666 174792214 174791549 0.000000e+00 1064.0
2 TraesCS3A01G168000 chr3A 90.406 813 55 15 6 807 595748620 595749420 0.000000e+00 1048.0
3 TraesCS3A01G168000 chr3A 97.122 417 10 2 1503 1919 174790464 174790050 0.000000e+00 702.0
4 TraesCS3A01G168000 chr3A 89.546 507 42 9 1761 2264 628088513 628089011 1.140000e-177 632.0
5 TraesCS3A01G168000 chr5A 94.566 1509 76 4 1 1504 334642428 334640921 0.000000e+00 2327.0
6 TraesCS3A01G168000 chr5A 94.451 793 44 0 712 1504 334649900 334649108 0.000000e+00 1221.0
7 TraesCS3A01G168000 chr5A 94.803 635 27 3 1 630 334650759 334650126 0.000000e+00 985.0
8 TraesCS3A01G168000 chr5A 97.619 420 10 0 1500 1919 334649072 334648653 0.000000e+00 721.0
9 TraesCS3A01G168000 chr5A 87.400 500 58 4 1761 2258 130153563 130153067 9.070000e-159 569.0
10 TraesCS3A01G168000 chr3B 91.519 1521 108 18 1 1504 116638707 116637191 0.000000e+00 2074.0
11 TraesCS3A01G168000 chr3B 95.636 825 33 3 682 1504 234961690 234960867 0.000000e+00 1321.0
12 TraesCS3A01G168000 chr3B 94.934 829 39 2 678 1504 116648290 116647463 0.000000e+00 1295.0
13 TraesCS3A01G168000 chr3B 94.737 779 37 3 729 1504 116649452 116648675 0.000000e+00 1208.0
14 TraesCS3A01G168000 chr3B 96.897 419 13 0 1501 1919 234952384 234951966 0.000000e+00 702.0
15 TraesCS3A01G168000 chr3B 96.659 419 14 0 1501 1919 234960829 234960411 0.000000e+00 697.0
16 TraesCS3A01G168000 chr2A 94.749 857 42 3 651 1504 485967318 485968174 0.000000e+00 1330.0
17 TraesCS3A01G168000 chr2A 98.571 420 6 0 1500 1919 485968210 485968629 0.000000e+00 743.0
18 TraesCS3A01G168000 chr2A 96.190 420 16 0 1500 1919 485976118 485976537 0.000000e+00 688.0
19 TraesCS3A01G168000 chrUn 95.478 774 32 2 733 1504 461942744 461941972 0.000000e+00 1232.0
20 TraesCS3A01G168000 chr7B 95.567 767 31 2 740 1504 388612786 388613551 0.000000e+00 1225.0
21 TraesCS3A01G168000 chr7B 87.844 617 70 3 1 612 120184435 120185051 0.000000e+00 719.0
22 TraesCS3A01G168000 chr7B 93.556 419 27 0 1501 1919 323255655 323255237 1.910000e-175 625.0
23 TraesCS3A01G168000 chr7B 95.755 212 9 0 1297 1508 323255900 323255689 2.150000e-90 342.0
24 TraesCS3A01G168000 chr7B 97.945 146 3 0 1359 1504 388604228 388604373 1.040000e-63 254.0
25 TraesCS3A01G168000 chr7A 94.703 623 30 3 1 621 485699067 485698446 0.000000e+00 965.0
26 TraesCS3A01G168000 chr7A 94.961 516 24 2 1 516 485690975 485690462 0.000000e+00 808.0
27 TraesCS3A01G168000 chr7A 97.619 420 10 0 1500 1919 485697354 485696935 0.000000e+00 721.0
28 TraesCS3A01G168000 chr7A 97.143 420 12 0 1500 1919 485689237 485688818 0.000000e+00 710.0
29 TraesCS3A01G168000 chr1B 83.883 819 94 15 1 807 217610778 217611570 0.000000e+00 747.0
30 TraesCS3A01G168000 chr1B 86.256 633 73 6 1 630 217617889 217618510 0.000000e+00 675.0
31 TraesCS3A01G168000 chr1B 97.945 146 3 0 1359 1504 190293686 190293541 1.040000e-63 254.0
32 TraesCS3A01G168000 chr5D 90.421 522 46 4 1744 2264 505591623 505592141 0.000000e+00 684.0
33 TraesCS3A01G168000 chr5D 98.567 349 5 0 1916 2264 17541139 17541487 3.190000e-173 617.0
34 TraesCS3A01G168000 chr5D 98.844 346 4 0 1919 2264 85207009 85206664 3.190000e-173 617.0
35 TraesCS3A01G168000 chr5D 95.082 61 3 0 1443 1503 336637992 336637932 1.850000e-16 97.1
36 TraesCS3A01G168000 chr5D 91.803 61 5 0 1443 1503 336662892 336662952 4.010000e-13 86.1
37 TraesCS3A01G168000 chr1D 98.854 349 4 0 1916 2264 365145238 365145586 6.870000e-175 623.0
38 TraesCS3A01G168000 chr4D 98.844 346 4 0 1919 2264 26583998 26583653 3.190000e-173 617.0
39 TraesCS3A01G168000 chr3D 98.844 346 4 0 1919 2264 293149189 293148844 3.190000e-173 617.0
40 TraesCS3A01G168000 chr7D 87.525 505 54 9 1761 2259 416519752 416519251 1.950000e-160 575.0
41 TraesCS3A01G168000 chr1A 87.554 233 20 4 575 807 39075836 39075613 6.200000e-66 261.0
42 TraesCS3A01G168000 chr4B 88.073 218 20 6 1293 1508 179584327 179584114 1.040000e-63 254.0


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 TraesCS3A01G168000 chr3A 174767031 174769294 2263 True 4181.000000 4181 100.000000 1 2264 1 chr3A.!!$R1 2263
1 TraesCS3A01G168000 chr3A 595748620 595749420 800 False 1048.000000 1048 90.406000 6 807 1 chr3A.!!$F1 801
2 TraesCS3A01G168000 chr3A 174790050 174792214 2164 True 883.000000 1064 96.312000 1 1919 2 chr3A.!!$R2 1918
3 TraesCS3A01G168000 chr5A 334640921 334642428 1507 True 2327.000000 2327 94.566000 1 1504 1 chr5A.!!$R2 1503
4 TraesCS3A01G168000 chr5A 334648653 334650759 2106 True 975.666667 1221 95.624333 1 1919 3 chr5A.!!$R3 1918
5 TraesCS3A01G168000 chr3B 116637191 116638707 1516 True 2074.000000 2074 91.519000 1 1504 1 chr3B.!!$R1 1503
6 TraesCS3A01G168000 chr3B 116647463 116649452 1989 True 1251.500000 1295 94.835500 678 1504 2 chr3B.!!$R3 826
7 TraesCS3A01G168000 chr3B 234960411 234961690 1279 True 1009.000000 1321 96.147500 682 1919 2 chr3B.!!$R4 1237
8 TraesCS3A01G168000 chr2A 485967318 485968629 1311 False 1036.500000 1330 96.660000 651 1919 2 chr2A.!!$F2 1268
9 TraesCS3A01G168000 chrUn 461941972 461942744 772 True 1232.000000 1232 95.478000 733 1504 1 chrUn.!!$R1 771
10 TraesCS3A01G168000 chr7B 388612786 388613551 765 False 1225.000000 1225 95.567000 740 1504 1 chr7B.!!$F3 764
11 TraesCS3A01G168000 chr7B 120184435 120185051 616 False 719.000000 719 87.844000 1 612 1 chr7B.!!$F1 611
12 TraesCS3A01G168000 chr7B 323255237 323255900 663 True 483.500000 625 94.655500 1297 1919 2 chr7B.!!$R1 622
13 TraesCS3A01G168000 chr7A 485696935 485699067 2132 True 843.000000 965 96.161000 1 1919 2 chr7A.!!$R2 1918
14 TraesCS3A01G168000 chr7A 485688818 485690975 2157 True 759.000000 808 96.052000 1 1919 2 chr7A.!!$R1 1918
15 TraesCS3A01G168000 chr1B 217610778 217611570 792 False 747.000000 747 83.883000 1 807 1 chr1B.!!$F1 806
16 TraesCS3A01G168000 chr1B 217617889 217618510 621 False 675.000000 675 86.256000 1 630 1 chr1B.!!$F2 629
17 TraesCS3A01G168000 chr5D 505591623 505592141 518 False 684.000000 684 90.421000 1744 2264 1 chr5D.!!$F3 520
18 TraesCS3A01G168000 chr7D 416519251 416519752 501 True 575.000000 575 87.525000 1761 2259 1 chr7D.!!$R1 498

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
431 452 1.322538 GGGACCCACATGTCATTGGC 61.323 60.0 5.33 0.0 36.97 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 1839 1.160989 TTATGTGCCACGTTTCGCAT 58.839 45.0 14.72 14.72 37.33 4.73 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
152 155 5.239306 TCTGAGCAACTTTCATGTACAAAGG 59.761 40.000 0.00 0.0 35.49 3.11
339 357 5.892160 ACATTGACCATTCAACAGATGAG 57.108 39.130 0.00 0.0 44.66 2.90
367 388 1.587066 GGGGGTCCCACATGTAAGTA 58.413 55.000 10.98 0.0 44.65 2.24
431 452 1.322538 GGGACCCACATGTCATTGGC 61.323 60.000 5.33 0.0 36.97 4.52
493 514 4.564616 AAGGGGCCCACTAGTTAGTATA 57.435 45.455 27.72 0.0 34.13 1.47
901 1145 4.074526 GCAGTCAGAGGCGAGGCA 62.075 66.667 0.00 0.0 0.00 4.75
931 1177 1.444895 GTACGCGACGGTGGTCAAT 60.445 57.895 15.93 0.0 43.61 2.57
961 1207 3.334691 CTCAACGAATTGGTGCCTAAGA 58.665 45.455 0.00 0.0 36.39 2.10
1047 1293 4.360405 GGGAAGCCGGGGAAGCAA 62.360 66.667 2.18 0.0 0.00 3.91
1152 1398 2.564947 CAGCTCCTTCTACTCAGGTGTT 59.435 50.000 0.00 0.0 32.59 3.32
1283 1529 1.433837 GAGGGAGAGAGACGAGCGAC 61.434 65.000 0.00 0.0 0.00 5.19
1525 1813 6.932356 TTTTTGCCTATGTTTGCATTTTCA 57.068 29.167 0.00 0.0 37.33 2.69
1949 2727 6.512415 GCCTTAAGCAAGATGACATGATGTAC 60.512 42.308 0.00 0.0 42.97 2.90
1959 2737 7.982252 AGATGACATGATGTACAGGGATAAAT 58.018 34.615 0.00 0.0 34.35 1.40
1964 2742 9.725019 GACATGATGTACAGGGATAAATTCATA 57.275 33.333 0.00 0.0 34.35 2.15
2086 2864 2.553028 CCCAAAGCTAAGCACTTCTCCA 60.553 50.000 0.00 0.0 0.00 3.86
2232 3010 6.118852 TGATCATAAACCCACAATTCATCGA 58.881 36.000 0.00 0.0 0.00 3.59
2254 3033 2.229062 TCTCAACAAACACACCGCAAAA 59.771 40.909 0.00 0.0 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
250 257 2.615493 GGCTAGCCAACAGTGTGTGTAT 60.615 50.000 29.33 0.00 39.03 2.29
326 344 5.129485 CCCCTGTACTACTCATCTGTTGAAT 59.871 44.000 0.00 0.00 32.78 2.57
431 452 6.149474 CCAAATCCCTCTGTTAAAGTGTACAG 59.851 42.308 0.00 0.00 42.41 2.74
493 514 5.790618 TGATTAGGCTACCCCTGCTAATTAT 59.209 40.000 0.00 0.00 45.91 1.28
533 563 0.034863 CCGGCCCCTGTTTAGCTTAA 60.035 55.000 0.00 0.00 0.00 1.85
652 682 3.644606 CCCACTGAGCTGGTGCCT 61.645 66.667 10.04 0.00 40.80 4.75
714 954 3.352222 GCTCACGTGCTGCTTGCT 61.352 61.111 20.67 0.00 43.37 3.91
931 1177 2.463589 AATTCGTTGAGCTCCGCCCA 62.464 55.000 12.15 0.00 0.00 5.36
943 1189 2.711542 CCTCTTAGGCACCAATTCGTT 58.288 47.619 0.00 0.00 0.00 3.85
961 1207 1.695597 CTTCCTCCTCCCCATGCCT 60.696 63.158 0.00 0.00 0.00 4.75
1004 1250 1.608025 CCACTACGAGCACCAATGTGT 60.608 52.381 0.00 0.00 44.65 3.72
1047 1293 1.810532 GTTGATCCGCTCGACCTCT 59.189 57.895 0.00 0.00 32.75 3.69
1117 1363 0.528470 GAGCTGTACTGCGGAGTTCT 59.472 55.000 16.89 7.69 38.13 3.01
1283 1529 1.743995 CTAGCCCACCGTTTTCCCG 60.744 63.158 0.00 0.00 0.00 5.14
1551 1839 1.160989 TTATGTGCCACGTTTCGCAT 58.839 45.000 14.72 14.72 37.33 4.73
1552 1840 1.160989 ATTATGTGCCACGTTTCGCA 58.839 45.000 0.00 2.99 0.00 5.10
1964 2742 8.608185 ACAAGATGGGGTTTTTATCATATTGT 57.392 30.769 8.68 8.68 43.04 2.71
2086 2864 9.118300 CCTACTAGATTGATCTTTCTTGCAATT 57.882 33.333 0.00 0.00 38.32 2.32
2232 3010 1.674359 TGCGGTGTGTTTGTTGAGAT 58.326 45.000 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.