Multiple sequence alignment - TraesCS2A01G433400

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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 TraesCS2A01G433400 chr2A 100.000 3139 0 0 1 3139 686615461 686612323 0.000000e+00 5797.0
1 TraesCS2A01G433400 chr2A 98.628 1895 22 2 506 2397 686524083 686522190 0.000000e+00 3352.0
2 TraesCS2A01G433400 chr2A 98.422 1901 21 1 506 2397 686323076 686321176 0.000000e+00 3336.0
3 TraesCS2A01G433400 chr2A 97.018 1811 40 3 598 2397 686297401 686295594 0.000000e+00 3033.0
4 TraesCS2A01G433400 chr2A 96.510 745 26 0 2395 3139 170074737 170073993 0.000000e+00 1232.0
5 TraesCS2A01G433400 chr2A 88.889 423 25 4 4 406 686624858 686624438 4.670000e-138 501.0
6 TraesCS2A01G433400 chr2A 87.613 444 32 8 4 426 686323992 686323551 7.820000e-136 494.0
7 TraesCS2A01G433400 chr2A 88.084 428 29 5 19 426 686300209 686299784 3.640000e-134 488.0
8 TraesCS2A01G433400 chr2A 87.387 444 33 4 4 426 686525002 686524561 3.640000e-134 488.0
9 TraesCS2A01G433400 chr2A 93.962 265 11 3 506 770 686623681 686623422 2.270000e-106 396.0
10 TraesCS2A01G433400 chr2A 85.294 306 19 12 421 700 686622828 686622523 3.060000e-75 292.0
11 TraesCS2A01G433400 chr2A 92.537 134 10 0 293 426 686623423 686623290 3.190000e-45 193.0
12 TraesCS2A01G433400 chr2A 93.069 101 7 0 506 606 686299070 686298970 7.010000e-32 148.0
13 TraesCS2A01G433400 chr2B 90.744 1545 94 22 790 2321 648931637 648930129 0.000000e+00 2015.0
14 TraesCS2A01G433400 chr2B 89.738 1335 105 28 834 2154 649370753 649369437 0.000000e+00 1677.0
15 TraesCS2A01G433400 chr2B 85.564 665 94 2 2476 3139 302914307 302913644 0.000000e+00 695.0
16 TraesCS2A01G433400 chr2B 91.033 513 26 4 1893 2397 649192246 649191746 0.000000e+00 675.0
17 TraesCS2A01G433400 chr2B 82.857 245 31 5 178 420 648936172 648935937 3.170000e-50 209.0
18 TraesCS2A01G433400 chr2B 98.113 53 1 0 547 599 649053783 649053731 3.330000e-15 93.5
19 TraesCS2A01G433400 chr2D 89.051 1507 115 33 836 2322 543532118 543530642 0.000000e+00 1823.0
20 TraesCS2A01G433400 chr2D 87.414 1605 133 40 784 2362 543762098 543760537 0.000000e+00 1781.0
21 TraesCS2A01G433400 chr2D 87.775 1546 131 38 834 2362 543813744 543812240 0.000000e+00 1755.0
22 TraesCS2A01G433400 chr2D 85.946 1416 128 40 886 2268 543589155 543587778 0.000000e+00 1447.0
23 TraesCS2A01G433400 chr2D 84.000 750 116 4 2392 3139 118322615 118323362 0.000000e+00 717.0
24 TraesCS2A01G433400 chr2D 83.445 749 121 3 2392 3139 214271618 214272364 0.000000e+00 693.0
25 TraesCS2A01G433400 chr2D 89.815 216 18 3 579 794 543589501 543589290 1.110000e-69 274.0
26 TraesCS2A01G433400 chr2D 89.450 218 17 3 513 730 543816142 543815931 1.430000e-68 270.0
27 TraesCS2A01G433400 chr2D 91.489 188 14 2 601 788 543532429 543532244 1.120000e-64 257.0
28 TraesCS2A01G433400 chr2D 85.526 228 23 5 174 398 543816871 543816651 2.440000e-56 230.0
29 TraesCS2A01G433400 chr2D 87.709 179 12 3 220 398 543533314 543533146 1.910000e-47 200.0
30 TraesCS2A01G433400 chr3D 85.963 748 102 3 2392 3139 289716802 289717546 0.000000e+00 797.0
31 TraesCS2A01G433400 chr3D 84.027 745 119 0 2395 3139 380842202 380841458 0.000000e+00 717.0
32 TraesCS2A01G433400 chr1B 85.778 668 93 2 2473 3139 444937775 444938441 0.000000e+00 706.0
33 TraesCS2A01G433400 chr5B 84.218 697 110 0 2443 3139 621794335 621795031 0.000000e+00 678.0
34 TraesCS2A01G433400 chr6D 82.967 728 121 3 2411 3137 405579111 405578386 0.000000e+00 654.0


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 TraesCS2A01G433400 chr2A 686612323 686615461 3138 True 5797.000000 5797 100.000000 1 3139 1 chr2A.!!$R2 3138
1 TraesCS2A01G433400 chr2A 686522190 686525002 2812 True 1920.000000 3352 93.007500 4 2397 2 chr2A.!!$R5 2393
2 TraesCS2A01G433400 chr2A 686321176 686323992 2816 True 1915.000000 3336 93.017500 4 2397 2 chr2A.!!$R4 2393
3 TraesCS2A01G433400 chr2A 170073993 170074737 744 True 1232.000000 1232 96.510000 2395 3139 1 chr2A.!!$R1 744
4 TraesCS2A01G433400 chr2A 686295594 686300209 4615 True 1223.000000 3033 92.723667 19 2397 3 chr2A.!!$R3 2378
5 TraesCS2A01G433400 chr2A 686622523 686624858 2335 True 345.500000 501 90.170500 4 770 4 chr2A.!!$R6 766
6 TraesCS2A01G433400 chr2B 648930129 648931637 1508 True 2015.000000 2015 90.744000 790 2321 1 chr2B.!!$R2 1531
7 TraesCS2A01G433400 chr2B 649369437 649370753 1316 True 1677.000000 1677 89.738000 834 2154 1 chr2B.!!$R6 1320
8 TraesCS2A01G433400 chr2B 302913644 302914307 663 True 695.000000 695 85.564000 2476 3139 1 chr2B.!!$R1 663
9 TraesCS2A01G433400 chr2B 649191746 649192246 500 True 675.000000 675 91.033000 1893 2397 1 chr2B.!!$R5 504
10 TraesCS2A01G433400 chr2D 543760537 543762098 1561 True 1781.000000 1781 87.414000 784 2362 1 chr2D.!!$R1 1578
11 TraesCS2A01G433400 chr2D 543587778 543589501 1723 True 860.500000 1447 87.880500 579 2268 2 chr2D.!!$R3 1689
12 TraesCS2A01G433400 chr2D 543530642 543533314 2672 True 760.000000 1823 89.416333 220 2322 3 chr2D.!!$R2 2102
13 TraesCS2A01G433400 chr2D 543812240 543816871 4631 True 751.666667 1755 87.583667 174 2362 3 chr2D.!!$R4 2188
14 TraesCS2A01G433400 chr2D 118322615 118323362 747 False 717.000000 717 84.000000 2392 3139 1 chr2D.!!$F1 747
15 TraesCS2A01G433400 chr2D 214271618 214272364 746 False 693.000000 693 83.445000 2392 3139 1 chr2D.!!$F2 747
16 TraesCS2A01G433400 chr3D 289716802 289717546 744 False 797.000000 797 85.963000 2392 3139 1 chr3D.!!$F1 747
17 TraesCS2A01G433400 chr3D 380841458 380842202 744 True 717.000000 717 84.027000 2395 3139 1 chr3D.!!$R1 744
18 TraesCS2A01G433400 chr1B 444937775 444938441 666 False 706.000000 706 85.778000 2473 3139 1 chr1B.!!$F1 666
19 TraesCS2A01G433400 chr5B 621794335 621795031 696 False 678.000000 678 84.218000 2443 3139 1 chr5B.!!$F1 696
20 TraesCS2A01G433400 chr6D 405578386 405579111 725 True 654.000000 654 82.967000 2411 3137 1 chr6D.!!$R1 726

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
77 78 0.597568 TGCGGTTCAGCATTGGAAAG 59.402 50.000 0.00 0.0 42.92 2.62 F
434 2214 1.063764 GTAGTCGTTCGGCTCTGGTAG 59.936 57.143 1.81 0.0 0.00 3.18 F
1282 7063 0.459237 CGGTGAGCACTCCATGTCTC 60.459 60.000 3.17 0.0 34.13 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1173 6944 0.404426 GGTTGGAGCAGTAGGGGTTT 59.596 55.0 0.0 0.0 0.00 3.27 R
1336 7119 1.026182 TGATGGAACGCATGAGCCAC 61.026 55.0 0.0 0.0 37.52 5.01 R
2797 8611 0.107993 CTCCTCCGCAAGATTGAGCA 60.108 55.0 0.0 0.0 43.02 4.26 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
17 18 4.827481 CGTATCCTTGTCCGTGGG 57.173 61.111 0.00 0.00 0.00 4.61
40 41 1.306141 TCCCCTTCTGTCTGCGGAT 60.306 57.895 0.00 0.00 0.00 4.18
63 64 2.662527 CGGTGTACGGTTTGCGGT 60.663 61.111 0.00 0.00 39.42 5.68
75 76 4.490696 TGCGGTTCAGCATTGGAA 57.509 50.000 0.00 0.00 42.92 3.53
77 78 0.597568 TGCGGTTCAGCATTGGAAAG 59.402 50.000 0.00 0.00 42.92 2.62
319 1468 4.474651 AGATCACCAATCACCATAGGACAA 59.525 41.667 0.00 0.00 36.79 3.18
360 1513 8.454106 AGACATAATAGAAGTGCAACAAATCAC 58.546 33.333 0.00 0.00 41.43 3.06
408 1567 6.801539 TTGGACGGAATGATTATGCTAATC 57.198 37.500 8.24 8.24 0.00 1.75
434 2214 1.063764 GTAGTCGTTCGGCTCTGGTAG 59.936 57.143 1.81 0.00 0.00 3.18
455 2236 2.367894 GGAGAGAGGCATGATGATGACA 59.632 50.000 0.00 0.00 40.57 3.58
469 2250 2.812011 TGATGACACTCTTTCGACTCGA 59.188 45.455 0.00 0.00 0.00 4.04
521 2326 6.870439 GCATAAACAAGCTTTTCCAGATTCTT 59.130 34.615 0.00 0.00 0.00 2.52
539 2344 6.486657 AGATTCTTGAAATTTGACTTCGTCCA 59.513 34.615 0.00 0.00 0.00 4.02
1173 6944 0.614979 GCAGTGAGAGTCCCAGGGTA 60.615 60.000 5.01 0.00 0.00 3.69
1282 7063 0.459237 CGGTGAGCACTCCATGTCTC 60.459 60.000 3.17 0.00 34.13 3.36
1351 7134 1.210155 GTTGTGGCTCATGCGTTCC 59.790 57.895 0.00 0.00 40.82 3.62
1352 7135 1.228094 TTGTGGCTCATGCGTTCCA 60.228 52.632 0.00 0.00 40.82 3.53
1353 7136 0.608856 TTGTGGCTCATGCGTTCCAT 60.609 50.000 0.00 0.00 40.82 3.41
2214 8026 1.468520 GCATGCACGGTTGACAAGTAT 59.531 47.619 14.21 0.00 0.00 2.12
2346 8160 8.552034 CCAACGAAGAATATCCTATCAAACTTC 58.448 37.037 0.00 0.00 0.00 3.01
2393 8207 4.693566 CACCTCGGAACTTTTGCACTATTA 59.306 41.667 0.00 0.00 0.00 0.98
2465 8279 5.117406 AGGGGAATTTATCTGACAAGGAC 57.883 43.478 0.00 0.00 0.00 3.85
2545 8359 1.373497 CGCTGCTCAAGGAGTTCGT 60.373 57.895 0.00 0.00 35.78 3.85
2693 8507 4.215109 TGGGATTCGACTGTGATGATCTA 58.785 43.478 0.00 0.00 0.00 1.98
2797 8611 3.305471 GCTATCTTCGGGAAAGCGATACT 60.305 47.826 0.00 0.00 34.76 2.12
3070 8884 2.555547 GCATGGGGCCGAACTATGC 61.556 63.158 11.88 11.88 37.56 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.520787 GCCCACGGACAAGGATACG 60.521 63.158 0.00 0.00 46.39 3.06
1 2 1.068741 CTAGCCCACGGACAAGGATAC 59.931 57.143 0.00 0.00 0.00 2.24
2 3 1.342674 ACTAGCCCACGGACAAGGATA 60.343 52.381 0.00 0.00 0.00 2.59
7 8 3.384348 GGACTAGCCCACGGACAA 58.616 61.111 0.00 0.00 0.00 3.18
17 18 0.176910 GCAGACAGAAGGGGACTAGC 59.823 60.000 0.00 0.00 42.68 3.42
40 41 0.951525 CAAACCGTACACCGCATCCA 60.952 55.000 0.00 0.00 34.38 3.41
63 64 0.968405 GGGCACTTTCCAATGCTGAA 59.032 50.000 0.00 0.00 41.74 3.02
360 1513 3.616956 TCAGAGGTAAATGCAGACCTG 57.383 47.619 19.50 9.44 46.36 4.00
434 2214 2.367894 TGTCATCATCATGCCTCTCTCC 59.632 50.000 0.00 0.00 0.00 3.71
469 2250 5.207110 AGCGATGACTATAAGCACTGAAT 57.793 39.130 0.00 0.00 0.00 2.57
539 2344 8.533657 TCCTATTCATTTTGTTGCATCATTCTT 58.466 29.630 0.00 0.00 0.00 2.52
1173 6944 0.404426 GGTTGGAGCAGTAGGGGTTT 59.596 55.000 0.00 0.00 0.00 3.27
1282 7063 5.967088 ACTATAGTTGTACCTGCAGAGTTG 58.033 41.667 17.39 0.00 0.00 3.16
1319 7102 4.093011 AGCCACAACCATTATTAGCCAAA 58.907 39.130 0.00 0.00 0.00 3.28
1336 7119 1.026182 TGATGGAACGCATGAGCCAC 61.026 55.000 0.00 0.00 37.52 5.01
1351 7134 1.855213 CGGGGTGTTGCACACTGATG 61.855 60.000 15.74 4.33 46.14 3.07
1352 7135 1.600636 CGGGGTGTTGCACACTGAT 60.601 57.895 15.74 0.00 46.14 2.90
1353 7136 2.203139 CGGGGTGTTGCACACTGA 60.203 61.111 15.74 0.00 46.14 3.41
2214 8026 6.108687 CCTCTGCTTATTCATGTGAAGTACA 58.891 40.000 0.00 0.00 44.87 2.90
2235 8047 4.440525 CCACACACATCAAATTATGCCCTC 60.441 45.833 0.00 0.00 0.00 4.30
2393 8207 1.165907 CCGATGCATTACCGCCATGT 61.166 55.000 0.00 0.00 0.00 3.21
2465 8279 1.358759 GTTTCCAAGTGCCACCACG 59.641 57.895 0.00 0.00 46.62 4.94
2545 8359 0.910566 TTTAACCCCTCGCAGCCCTA 60.911 55.000 0.00 0.00 0.00 3.53
2797 8611 0.107993 CTCCTCCGCAAGATTGAGCA 60.108 55.000 0.00 0.00 43.02 4.26
3070 8884 3.800506 CGCCGGTAAGTAGGTGAAATTAG 59.199 47.826 1.90 0.00 40.26 1.73


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

AutoCloner maintained by Alex Coulton.