Multiple sequence alignment - TraesCS3A01G477800

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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 TraesCS3A01G477800 chr3A 100.000 2739 0 0 1 2739 709970842 709968104 0.000000e+00 5059.0
1 TraesCS3A01G477800 chr3A 90.995 211 14 5 394 601 8148901 8149109 2.080000e-71 279.0
2 TraesCS3A01G477800 chr3A 87.568 185 23 0 800 984 8149102 8149286 5.940000e-52 215.0
3 TraesCS3A01G477800 chr4A 95.983 1917 37 7 860 2739 684070833 684068920 0.000000e+00 3077.0
4 TraesCS3A01G477800 chr4A 98.176 329 5 1 501 829 684071161 684070834 8.510000e-160 573.0
5 TraesCS3A01G477800 chr4A 94.526 274 13 2 1 272 684071433 684071160 3.260000e-114 422.0
6 TraesCS3A01G477800 chr4A 88.128 219 16 5 1100 1313 618099994 618100207 4.530000e-63 252.0
7 TraesCS3A01G477800 chr4A 80.055 366 34 8 48 409 618091484 618091814 4.560000e-58 235.0
8 TraesCS3A01G477800 chr3B 95.722 1917 42 12 860 2739 771791912 771789999 0.000000e+00 3049.0
9 TraesCS3A01G477800 chr3B 98.176 329 5 1 501 829 771792240 771791913 8.510000e-160 573.0
10 TraesCS3A01G477800 chr3B 94.891 274 12 2 1 272 771792512 771792239 7.010000e-116 427.0
11 TraesCS3A01G477800 chr3B 81.034 406 45 10 48 449 393317345 393317722 7.420000e-76 294.0
12 TraesCS3A01G477800 chr5B 96.894 1610 34 8 1143 2739 3906021 3904415 0.000000e+00 2682.0
13 TraesCS3A01G477800 chr5B 97.568 329 7 1 501 829 3916058 3915731 1.840000e-156 562.0
14 TraesCS3A01G477800 chr5B 93.796 274 15 2 1 272 3916330 3916057 7.060000e-111 411.0
15 TraesCS3A01G477800 chr5B 92.258 155 3 1 860 1014 3915730 3915585 7.680000e-51 211.0
16 TraesCS3A01G477800 chr6D 92.789 1054 29 9 766 1772 451077613 451078666 0.000000e+00 1482.0
17 TraesCS3A01G477800 chr6D 91.150 565 25 10 31 581 451077029 451077582 0.000000e+00 743.0
18 TraesCS3A01G477800 chr6D 93.186 499 15 3 2242 2735 451078667 451079151 0.000000e+00 715.0
19 TraesCS3A01G477800 chr6D 81.527 406 44 9 48 449 466529523 466529901 3.430000e-79 305.0
20 TraesCS3A01G477800 chr6D 82.769 325 31 10 800 1100 466529972 466530295 1.620000e-67 267.0
21 TraesCS3A01G477800 chr6D 91.111 135 12 0 2605 2739 435934041 435934175 1.680000e-42 183.0
22 TraesCS3A01G477800 chr6D 95.349 43 2 0 843 885 292958582 292958624 4.890000e-08 69.4
23 TraesCS3A01G477800 chr7B 97.587 829 17 2 1015 1842 701062633 701063459 0.000000e+00 1417.0
24 TraesCS3A01G477800 chr7B 80.662 393 46 8 60 449 706496793 706496428 7.470000e-71 278.0
25 TraesCS3A01G477800 chr7B 82.769 325 32 9 800 1100 706496357 706496033 4.500000e-68 268.0
26 TraesCS3A01G477800 chr7B 93.750 48 2 1 1316 1363 507354938 507354892 1.360000e-08 71.3
27 TraesCS3A01G477800 chr6B 92.044 905 37 7 653 1523 6639622 6640525 0.000000e+00 1240.0
28 TraesCS3A01G477800 chr6B 94.133 392 22 1 2348 2739 6642304 6642694 1.820000e-166 595.0
29 TraesCS3A01G477800 chr6B 86.234 385 41 11 2 384 6637968 6638342 9.130000e-110 407.0
30 TraesCS3A01G477800 chr6B 93.214 280 7 3 376 653 6639242 6639511 4.250000e-108 401.0
31 TraesCS3A01G477800 chr2A 93.976 747 40 5 2 745 765959995 765959251 0.000000e+00 1125.0
32 TraesCS3A01G477800 chr2A 96.000 300 12 0 1889 2188 765959245 765958946 3.170000e-134 488.0
33 TraesCS3A01G477800 chr4D 94.816 598 28 3 51 646 497909010 497909606 0.000000e+00 929.0
34 TraesCS3A01G477800 chr4D 90.458 524 13 5 2068 2591 497909605 497910091 0.000000e+00 656.0
35 TraesCS3A01G477800 chr4D 91.667 84 5 2 3 84 497908921 497909004 6.200000e-22 115.0
36 TraesCS3A01G477800 chr4D 100.000 34 0 0 2706 2739 497910102 497910135 2.280000e-06 63.9
37 TraesCS3A01G477800 chr1D 83.333 864 92 15 1308 2165 460736821 460736004 0.000000e+00 750.0
38 TraesCS3A01G477800 chr1D 81.886 403 42 9 51 449 460740202 460739827 7.370000e-81 311.0
39 TraesCS3A01G477800 chr1D 83.077 325 30 10 800 1100 460739756 460739433 3.480000e-69 272.0
40 TraesCS3A01G477800 chr1D 89.344 122 13 0 2618 2739 460735760 460735639 1.310000e-33 154.0
41 TraesCS3A01G477800 chr7D 83.032 831 91 15 1342 2165 632123430 632122643 0.000000e+00 708.0
42 TraesCS3A01G477800 chr7D 81.638 403 43 9 51 449 632126876 632126501 3.430000e-79 305.0
43 TraesCS3A01G477800 chr7D 87.222 180 22 1 1729 1908 36859473 36859651 1.290000e-48 204.0
44 TraesCS3A01G477800 chr2B 83.986 587 57 15 1589 2165 11368806 11369365 1.870000e-146 529.0
45 TraesCS3A01G477800 chr6A 84.308 325 27 7 800 1100 60541597 60541273 2.060000e-76 296.0
46 TraesCS3A01G477800 chr6A 90.058 171 15 2 433 601 60541760 60541590 1.280000e-53 220.0
47 TraesCS3A01G477800 chr5A 88.584 219 15 5 1100 1313 104241196 104241409 9.730000e-65 257.0
48 TraesCS3A01G477800 chr7A 88.128 219 16 5 1100 1313 721735180 721735393 4.530000e-63 252.0
49 TraesCS3A01G477800 chr3D 86.784 227 28 2 1732 1958 532108630 532108406 4.530000e-63 252.0
50 TraesCS3A01G477800 chr3D 81.538 325 36 4 800 1100 1136627 1136303 2.110000e-61 246.0


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 TraesCS3A01G477800 chr3A 709968104 709970842 2738 True 5059.000000 5059 100.000000 1 2739 1 chr3A.!!$R1 2738
1 TraesCS3A01G477800 chr4A 684068920 684071433 2513 True 1357.333333 3077 96.228333 1 2739 3 chr4A.!!$R1 2738
2 TraesCS3A01G477800 chr3B 771789999 771792512 2513 True 1349.666667 3049 96.263000 1 2739 3 chr3B.!!$R1 2738
3 TraesCS3A01G477800 chr5B 3904415 3906021 1606 True 2682.000000 2682 96.894000 1143 2739 1 chr5B.!!$R1 1596
4 TraesCS3A01G477800 chr5B 3915585 3916330 745 True 394.666667 562 94.540667 1 1014 3 chr5B.!!$R2 1013
5 TraesCS3A01G477800 chr6D 451077029 451079151 2122 False 980.000000 1482 92.375000 31 2735 3 chr6D.!!$F3 2704
6 TraesCS3A01G477800 chr6D 466529523 466530295 772 False 286.000000 305 82.148000 48 1100 2 chr6D.!!$F4 1052
7 TraesCS3A01G477800 chr7B 701062633 701063459 826 False 1417.000000 1417 97.587000 1015 1842 1 chr7B.!!$F1 827
8 TraesCS3A01G477800 chr7B 706496033 706496793 760 True 273.000000 278 81.715500 60 1100 2 chr7B.!!$R2 1040
9 TraesCS3A01G477800 chr6B 6637968 6642694 4726 False 660.750000 1240 91.406250 2 2739 4 chr6B.!!$F1 2737
10 TraesCS3A01G477800 chr2A 765958946 765959995 1049 True 806.500000 1125 94.988000 2 2188 2 chr2A.!!$R1 2186
11 TraesCS3A01G477800 chr4D 497908921 497910135 1214 False 440.975000 929 94.235250 3 2739 4 chr4D.!!$F1 2736
12 TraesCS3A01G477800 chr1D 460735639 460740202 4563 True 371.750000 750 84.410000 51 2739 4 chr1D.!!$R1 2688
13 TraesCS3A01G477800 chr7D 632122643 632126876 4233 True 506.500000 708 82.335000 51 2165 2 chr7D.!!$R1 2114
14 TraesCS3A01G477800 chr2B 11368806 11369365 559 False 529.000000 529 83.986000 1589 2165 1 chr2B.!!$F1 576

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
214 259 0.036671 GATCGGTTCCTTCGTGGGTT 60.037 55.0 0.0 0.0 36.2 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 5627 1.696884 TGGCTATGGACAGTTGTCACA 59.303 47.619 13.73 9.52 46.47 3.58 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
110 153 1.153647 CGCCGCAGTATCTTGGACA 60.154 57.895 0.00 0.00 0.00 4.02
115 158 0.811616 GCAGTATCTTGGACAGGGCG 60.812 60.000 0.00 0.00 0.00 6.13
209 254 1.807886 CGGAGATCGGTTCCTTCGT 59.192 57.895 0.00 0.00 34.75 3.85
214 259 0.036671 GATCGGTTCCTTCGTGGGTT 60.037 55.000 0.00 0.00 36.20 4.11
228 273 1.078426 GGGTTGTGGTGGAGATCCG 60.078 63.158 0.00 0.00 39.43 4.18
240 285 1.884579 GGAGATCCGTCGCATAGGTAA 59.115 52.381 0.00 0.00 0.00 2.85
293 347 2.580815 GGCATGAAAAGGGCTGCC 59.419 61.111 11.05 11.05 46.54 4.85
306 360 2.046988 CTGCCGGATCTGTGTGCA 60.047 61.111 5.05 2.36 0.00 4.57
499 1473 7.201617 GGGTTTGTACTGTGACTATAATGCTTC 60.202 40.741 0.00 0.00 0.00 3.86
790 1875 4.633126 TGCTATGTGAACAGAAGCAATCTC 59.367 41.667 16.59 0.00 42.26 2.75
809 1894 8.368126 GCAATCTCGAACAATAAACATGAAAAG 58.632 33.333 0.00 0.00 0.00 2.27
1237 4712 2.038387 ACCCTGTTTCGATACCATGC 57.962 50.000 3.47 0.00 0.00 4.06
1539 5126 3.424703 ACAGGTGAATGAACATCCTTGG 58.575 45.455 0.00 0.00 0.00 3.61
1956 5554 6.346896 TCTGACGCTAGAGAGTATAGTTTGA 58.653 40.000 0.00 0.00 0.00 2.69
2005 5609 0.467290 TCCTTCAAAAGCAAGGCCGT 60.467 50.000 0.00 0.00 40.43 5.68
2023 5627 3.206150 CCGTAGTAGCCAATGCATCTTT 58.794 45.455 0.00 0.00 41.13 2.52
2424 7767 7.361713 GGTCATTCATGAACGAATTTTACAGGA 60.362 37.037 11.07 0.00 38.75 3.86
2628 7999 6.938030 ACAAAATAAGGACCGAACACTTGATA 59.062 34.615 0.00 0.00 0.00 2.15
2654 8025 1.899814 CTGGGGAGTTAGTGCAGTACA 59.100 52.381 0.00 0.00 0.00 2.90
2677 8048 1.623686 AGAGGTTGGGGATGGCCAT 60.624 57.895 20.96 20.96 35.15 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 153 0.678048 GTTGAAGATCTTGGCGCCCT 60.678 55.000 26.77 10.63 0.00 5.19
115 158 1.425428 CGCCGTTGAAGATCTTGGC 59.575 57.895 19.74 19.74 39.10 4.52
209 254 1.836999 CGGATCTCCACCACAACCCA 61.837 60.000 0.00 0.00 35.14 4.51
214 259 3.001902 GCGACGGATCTCCACCACA 62.002 63.158 0.00 0.00 35.14 4.17
293 347 0.391528 TCCACATGCACACAGATCCG 60.392 55.000 0.00 0.00 0.00 4.18
306 360 2.050350 GCACAGCCAGCATCCACAT 61.050 57.895 0.00 0.00 0.00 3.21
499 1473 3.324117 CTCATAATCTGAGGTGATGGCG 58.676 50.000 0.00 0.00 46.52 5.69
574 1548 6.039717 TCAGGTTCTGAGAAATCTTGGTTTTG 59.960 38.462 0.00 0.00 35.39 2.44
790 1875 7.598493 ACCCATTCTTTTCATGTTTATTGTTCG 59.402 33.333 0.00 0.00 0.00 3.95
809 1894 4.953579 TGGGCAGAGTAATTTAACCCATTC 59.046 41.667 0.00 0.00 40.90 2.67
1422 5001 5.411831 AGAGACAACACTGATGCATCTTA 57.588 39.130 26.32 7.39 0.00 2.10
1539 5126 4.479786 AGGATTAGCACCAGAGAAACTC 57.520 45.455 0.00 0.00 0.00 3.01
1634 5227 4.573900 AGAGAAAGCGTCTGAACATTCAT 58.426 39.130 0.00 0.00 36.41 2.57
1956 5554 9.566432 GGACCAACAAATATCAGAATTAGAGAT 57.434 33.333 0.00 0.00 0.00 2.75
1979 5577 3.254411 CCTTGCTTTTGAAGGAGAAGGAC 59.746 47.826 0.00 0.00 42.44 3.85
2005 5609 4.635765 GTCACAAAGATGCATTGGCTACTA 59.364 41.667 0.00 0.00 41.91 1.82
2023 5627 1.696884 TGGCTATGGACAGTTGTCACA 59.303 47.619 13.73 9.52 46.47 3.58
2424 7767 3.056536 TCTCATGTAACGAAGAAGCAGCT 60.057 43.478 0.00 0.00 0.00 4.24
2628 7999 1.084842 ACTAACTCCCCAGGGGCAT 59.915 57.895 21.90 10.70 43.94 4.40
2654 8025 1.707427 GCCATCCCCAACCTCTCATAT 59.293 52.381 0.00 0.00 0.00 1.78
2677 8048 0.977627 ATGTCATGCCGACCTCCTCA 60.978 55.000 1.29 0.00 44.71 3.86


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

AutoCloner maintained by Alex Coulton.