Multiple sequence alignment - TraesCS2B01G543800

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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 TraesCS2B01G543800 chr2B 100.000 8480 0 0 1 8480 741249342 741240863 0.000000e+00 15586.0
1 TraesCS2B01G543800 chr2B 99.383 4865 27 2 1 4864 741219769 741214907 0.000000e+00 8815.0
2 TraesCS2B01G543800 chr2B 99.241 2636 18 2 5846 8480 741213764 741211130 0.000000e+00 4756.0
3 TraesCS2B01G543800 chr2B 99.792 961 2 0 4875 5835 741214860 741213900 0.000000e+00 1764.0
4 TraesCS2B01G543800 chr2B 97.453 746 19 0 7734 8479 615587889 615587144 0.000000e+00 1273.0
5 TraesCS2B01G543800 chr2B 97.196 749 21 0 7732 8480 318083052 318083800 0.000000e+00 1267.0
6 TraesCS2B01G543800 chr2B 97.189 747 20 1 7734 8480 564815993 564815248 0.000000e+00 1262.0
7 TraesCS2B01G543800 chr2B 96.085 281 11 0 2665 2945 511849661 511849941 7.760000e-125 459.0
8 TraesCS2B01G543800 chr2B 92.226 283 18 4 3219 3501 27626142 27625864 1.720000e-106 398.0
9 TraesCS2B01G543800 chr2B 91.958 286 19 1 3219 3504 242971041 242970760 1.720000e-106 398.0
10 TraesCS2B01G543800 chr2B 92.780 277 16 3 3221 3497 737765304 737765032 1.720000e-106 398.0
11 TraesCS2B01G543800 chr2B 83.616 177 28 1 5653 5829 481459273 481459098 1.890000e-36 165.0
12 TraesCS2B01G543800 chr2B 87.681 138 15 1 5650 5785 801156716 801156853 8.810000e-35 159.0
13 TraesCS2B01G543800 chr2A 91.545 1230 62 12 151 1357 739491861 739490651 0.000000e+00 1657.0
14 TraesCS2B01G543800 chr2A 87.167 1200 125 19 6025 7206 739482936 739481748 0.000000e+00 1336.0
15 TraesCS2B01G543800 chr2A 93.906 722 39 2 1372 2090 739490667 739489948 0.000000e+00 1085.0
16 TraesCS2B01G543800 chr2A 91.344 543 41 4 4081 4620 739485237 739484698 0.000000e+00 737.0
17 TraesCS2B01G543800 chr2A 94.181 464 25 2 7273 7735 739481464 739481002 0.000000e+00 706.0
18 TraesCS2B01G543800 chr2A 86.545 550 40 12 2130 2671 739489952 739489429 7.380000e-160 575.0
19 TraesCS2B01G543800 chr2A 87.458 295 30 3 3799 4087 739489298 739489005 4.910000e-87 333.0
20 TraesCS2B01G543800 chr2A 96.296 108 4 0 3691 3798 449280138 449280031 2.430000e-40 178.0
21 TraesCS2B01G543800 chr2A 96.330 109 3 1 3583 3691 739489407 739489300 2.430000e-40 178.0
22 TraesCS2B01G543800 chr2A 88.636 132 13 2 5655 5785 726576102 726576232 8.810000e-35 159.0
23 TraesCS2B01G543800 chr2A 88.800 125 14 0 1 125 739492362 739492238 4.100000e-33 154.0
24 TraesCS2B01G543800 chr2A 86.466 133 18 0 5515 5647 739484694 739484562 6.860000e-31 147.0
25 TraesCS2B01G543800 chr6B 98.527 747 10 1 7734 8480 131695262 131696007 0.000000e+00 1317.0
26 TraesCS2B01G543800 chr6B 97.992 747 15 0 7734 8480 712550669 712549923 0.000000e+00 1297.0
27 TraesCS2B01G543800 chr6B 96.296 108 4 0 3691 3798 506127983 506128090 2.430000e-40 178.0
28 TraesCS2B01G543800 chr6B 79.429 175 26 1 5655 5829 642913256 642913092 1.930000e-21 115.0
29 TraesCS2B01G543800 chr1B 98.128 748 12 2 7734 8480 20558422 20559168 0.000000e+00 1303.0
30 TraesCS2B01G543800 chr1B 98.128 748 13 1 7733 8480 321011905 321011159 0.000000e+00 1303.0
31 TraesCS2B01G543800 chr1B 95.423 284 13 0 2662 2945 391329976 391330259 3.610000e-123 453.0
32 TraesCS2B01G543800 chr1B 93.502 277 14 3 3221 3497 612400491 612400219 7.920000e-110 409.0
33 TraesCS2B01G543800 chr1B 86.420 162 22 0 5655 5816 49318968 49319129 2.430000e-40 178.0
34 TraesCS2B01G543800 chr5B 97.847 743 16 0 7738 8480 610024106 610024848 0.000000e+00 1284.0
35 TraesCS2B01G543800 chr5B 94.667 750 37 3 7732 8480 589823570 589824317 0.000000e+00 1160.0
36 TraesCS2B01G543800 chr5B 97.070 273 8 0 2673 2945 522895060 522895332 2.160000e-125 460.0
37 TraesCS2B01G543800 chr5B 93.141 277 14 4 3221 3497 578920093 578920364 1.330000e-107 401.0
38 TraesCS2B01G543800 chr2D 90.541 740 47 17 1372 2095 607996685 607995953 0.000000e+00 957.0
39 TraesCS2B01G543800 chr2D 88.105 723 45 20 1 684 607999393 607998673 0.000000e+00 821.0
40 TraesCS2B01G543800 chr2D 92.903 465 15 4 903 1357 607997125 607996669 0.000000e+00 660.0
41 TraesCS2B01G543800 chr2D 79.395 859 118 36 3797 4634 607993684 607992864 1.240000e-152 551.0
42 TraesCS2B01G543800 chr2D 80.797 703 73 30 5990 6670 607989927 607989265 2.130000e-135 494.0
43 TraesCS2B01G543800 chr2D 95.604 182 8 0 694 875 607997422 607997241 8.330000e-75 292.0
44 TraesCS2B01G543800 chrUn 97.091 275 8 0 2671 2945 36437383 36437109 1.670000e-126 464.0
45 TraesCS2B01G543800 chrUn 83.750 160 25 1 5670 5829 264105672 264105830 5.300000e-32 150.0
46 TraesCS2B01G543800 chr7B 97.091 275 8 0 2671 2945 589400747 589400473 1.670000e-126 464.0
47 TraesCS2B01G543800 chr7B 97.080 274 8 0 2672 2945 636357188 636356915 6.000000e-126 462.0
48 TraesCS2B01G543800 chr7B 93.662 284 14 1 3219 3502 83906604 83906883 1.020000e-113 422.0
49 TraesCS2B01G543800 chr7B 94.961 258 12 1 2965 3221 138014865 138014608 3.690000e-108 403.0
50 TraesCS2B01G543800 chr7B 84.868 152 23 0 5679 5830 570411326 570411175 4.100000e-33 154.0
51 TraesCS2B01G543800 chr7B 92.045 88 6 1 3499 3586 138014610 138014524 1.160000e-23 122.0
52 TraesCS2B01G543800 chr4B 97.080 274 8 0 2672 2945 418491294 418491021 6.000000e-126 462.0
53 TraesCS2B01G543800 chr4B 93.502 277 14 3 3221 3497 70104405 70104677 7.920000e-110 409.0
54 TraesCS2B01G543800 chr4B 95.238 42 2 0 159 200 172315854 172315895 5.490000e-07 67.6
55 TraesCS2B01G543800 chr3B 96.364 275 10 0 2671 2945 72793558 72793284 3.610000e-123 453.0
56 TraesCS2B01G543800 chr4A 92.419 277 17 3 3221 3497 689946772 689947044 7.980000e-105 392.0
57 TraesCS2B01G543800 chr4A 85.946 185 23 3 5647 5829 52619292 52619109 2.420000e-45 195.0
58 TraesCS2B01G543800 chr7D 85.393 178 26 0 5655 5832 17234594 17234417 1.450000e-42 185.0
59 TraesCS2B01G543800 chr7D 77.151 372 50 20 6923 7276 15237366 15237012 5.230000e-42 183.0
60 TraesCS2B01G543800 chr7D 95.370 108 4 1 3691 3798 60693373 60693479 4.070000e-38 171.0
61 TraesCS2B01G543800 chr7D 83.616 177 29 0 5655 5831 23526371 23526195 5.270000e-37 167.0
62 TraesCS2B01G543800 chr7D 75.328 381 54 23 6923 7276 15233359 15232992 6.860000e-31 147.0
63 TraesCS2B01G543800 chr6D 95.370 108 5 0 3691 3798 388543030 388542923 1.130000e-38 172.0
64 TraesCS2B01G543800 chr3D 94.595 111 6 0 3691 3801 104404937 104404827 1.130000e-38 172.0
65 TraesCS2B01G543800 chr3D 76.882 186 35 6 7092 7277 582104885 582104708 1.950000e-16 99.0
66 TraesCS2B01G543800 chr1D 95.370 108 5 0 3691 3798 465596804 465596911 1.130000e-38 172.0
67 TraesCS2B01G543800 chr1A 93.860 114 7 0 3691 3804 13308423 13308536 1.130000e-38 172.0
68 TraesCS2B01G543800 chr5A 94.444 108 6 0 3691 3798 658993803 658993696 5.270000e-37 167.0
69 TraesCS2B01G543800 chr4D 97.297 37 1 0 164 200 111134767 111134803 7.110000e-06 63.9
70 TraesCS2B01G543800 chr4D 82.857 70 12 0 7095 7164 230465032 230464963 7.110000e-06 63.9


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 TraesCS2B01G543800 chr2B 741240863 741249342 8479 True 15586.000000 15586 100.000000 1 8480 1 chr2B.!!$R7 8479
1 TraesCS2B01G543800 chr2B 741211130 741219769 8639 True 5111.666667 8815 99.472000 1 8480 3 chr2B.!!$R8 8479
2 TraesCS2B01G543800 chr2B 615587144 615587889 745 True 1273.000000 1273 97.453000 7734 8479 1 chr2B.!!$R5 745
3 TraesCS2B01G543800 chr2B 318083052 318083800 748 False 1267.000000 1267 97.196000 7732 8480 1 chr2B.!!$F1 748
4 TraesCS2B01G543800 chr2B 564815248 564815993 745 True 1262.000000 1262 97.189000 7734 8480 1 chr2B.!!$R4 746
5 TraesCS2B01G543800 chr2A 739481002 739492362 11360 True 690.800000 1657 90.374200 1 7735 10 chr2A.!!$R2 7734
6 TraesCS2B01G543800 chr6B 131695262 131696007 745 False 1317.000000 1317 98.527000 7734 8480 1 chr6B.!!$F1 746
7 TraesCS2B01G543800 chr6B 712549923 712550669 746 True 1297.000000 1297 97.992000 7734 8480 1 chr6B.!!$R2 746
8 TraesCS2B01G543800 chr1B 20558422 20559168 746 False 1303.000000 1303 98.128000 7734 8480 1 chr1B.!!$F1 746
9 TraesCS2B01G543800 chr1B 321011159 321011905 746 True 1303.000000 1303 98.128000 7733 8480 1 chr1B.!!$R1 747
10 TraesCS2B01G543800 chr5B 610024106 610024848 742 False 1284.000000 1284 97.847000 7738 8480 1 chr5B.!!$F4 742
11 TraesCS2B01G543800 chr5B 589823570 589824317 747 False 1160.000000 1160 94.667000 7732 8480 1 chr5B.!!$F3 748
12 TraesCS2B01G543800 chr2D 607989265 607999393 10128 True 629.166667 957 87.890833 1 6670 6 chr2D.!!$R1 6669

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
865 2471 7.779326 GGGTATCTTTCTCCAGTACTAGTAGTT 59.221 40.741 8.40 0.00 0.00 2.24 F
2283 5410 2.108976 ACAGACCACTGCCACGTG 59.891 61.111 9.08 9.08 46.95 4.49 F
2825 6130 7.119846 GTCCCAATGCAATATGAGTCTATAACC 59.880 40.741 0.00 0.00 0.00 2.85 F
3182 6487 0.603707 GCAGCAGTTACCACTCAGCA 60.604 55.000 0.00 0.00 0.00 4.41 F
3236 6541 2.326428 GGTAAGGCTAGCCATAGTGGA 58.674 52.381 34.70 5.32 40.96 4.02 F
5018 12186 2.817258 GTCATGAAAACGATGGGGTGAA 59.183 45.455 0.00 0.00 0.00 3.18 F
6521 16925 2.839202 GTCACGAAGCGAGACTTTTC 57.161 50.000 9.53 0.00 42.34 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2602 5907 0.250295 CAGAAACCTCTTGCGGTGGA 60.250 55.000 4.91 0.00 37.36 4.02 R
3182 6487 2.745152 GCAGCGTATCCACCAATACCTT 60.745 50.000 0.00 0.00 0.00 3.50 R
4119 11210 8.451908 TCTGAGTATTATTGAGAAGACATCGA 57.548 34.615 0.00 0.00 0.00 3.59 R
5018 12186 0.623723 AGGTTTGACACACACCACCT 59.376 50.000 9.26 0.00 36.73 4.00 R
6521 16925 2.468831 GCGATTTACAGAGCCTCTCAG 58.531 52.381 0.00 0.00 32.06 3.35 R
7147 17576 1.409064 TCCGGAGTACATGATGTCTGC 59.591 52.381 0.00 4.06 0.00 4.26 R
8341 18987 1.759445 CTTCTCGTCCTGTCATCCCAT 59.241 52.381 0.00 0.00 0.00 4.00 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
722 2328 8.316640 AGGTCTATTATAGTACCGAAACTACG 57.683 38.462 12.03 0.00 34.87 3.51
865 2471 7.779326 GGGTATCTTTCTCCAGTACTAGTAGTT 59.221 40.741 8.40 0.00 0.00 2.24
866 2472 9.187996 GGTATCTTTCTCCAGTACTAGTAGTTT 57.812 37.037 8.40 0.00 0.00 2.66
1555 3273 3.743396 AGAAAGAGAAACTTGCTAGTGCG 59.257 43.478 0.36 0.00 42.27 5.34
2283 5410 2.108976 ACAGACCACTGCCACGTG 59.891 61.111 9.08 9.08 46.95 4.49
2825 6130 7.119846 GTCCCAATGCAATATGAGTCTATAACC 59.880 40.741 0.00 0.00 0.00 2.85
3182 6487 0.603707 GCAGCAGTTACCACTCAGCA 60.604 55.000 0.00 0.00 0.00 4.41
3236 6541 2.326428 GGTAAGGCTAGCCATAGTGGA 58.674 52.381 34.70 5.32 40.96 4.02
3309 6614 5.131642 TGGCATGAAGTTAATGAGGAGAGAT 59.868 40.000 4.20 0.00 0.00 2.75
3497 6802 6.961360 AGTTACTATGCACTATGACTAGCA 57.039 37.500 0.00 0.00 41.73 3.49
4119 11210 6.533730 TCAACCATCTGTTATGTTCTGACTT 58.466 36.000 0.00 0.00 34.69 3.01
4194 11286 3.696051 CCGTCATTGGAATTGAGGTTCAT 59.304 43.478 0.00 0.00 0.00 2.57
5018 12186 2.817258 GTCATGAAAACGATGGGGTGAA 59.183 45.455 0.00 0.00 0.00 3.18
6521 16925 2.839202 GTCACGAAGCGAGACTTTTC 57.161 50.000 9.53 0.00 42.34 2.29
6570 16974 5.854010 ATTGTAGAGGTGATACGTGATGT 57.146 39.130 0.00 0.00 0.00 3.06
7147 17576 3.984018 CAAATGCTCTGAAATTTGGCG 57.016 42.857 13.68 0.00 39.19 5.69
7149 17578 0.889994 ATGCTCTGAAATTTGGCGCA 59.110 45.000 10.83 1.66 0.00 6.09
7907 18553 6.990939 ACCCTATTAGCCGTTCTTTTAATCTC 59.009 38.462 0.00 0.00 0.00 2.75
8206 18852 0.777446 AGCCCTTAAAGCCTCCACAA 59.223 50.000 0.00 0.00 0.00 3.33
8341 18987 5.993055 TGATGCTAATCTCCATCTTGACAA 58.007 37.500 0.00 0.00 38.84 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.189180 TGCAAACAAAGCAAAGGGTTTTAT 58.811 33.333 0.00 0.00 42.47 1.40
722 2328 9.445786 GCTTATATTTATAGAGCGAGAGATGAC 57.554 37.037 0.00 0.00 0.00 3.06
1199 2917 1.307517 TTCTTATGGGAGCCGGGGT 60.308 57.895 2.18 0.00 0.00 4.95
1555 3273 1.202891 AGTACCCCTGGTTTGCAGTTC 60.203 52.381 0.00 0.00 37.09 3.01
2283 5410 3.367992 TTTGACATGGACATTGTGTGC 57.632 42.857 0.00 0.00 39.30 4.57
2420 5722 4.404691 GCTAGCACCACAAAGCCT 57.595 55.556 10.63 0.00 0.00 4.58
2524 5826 3.839293 CGATTATTTCCTAGAGGCGGAG 58.161 50.000 0.00 0.00 34.44 4.63
2602 5907 0.250295 CAGAAACCTCTTGCGGTGGA 60.250 55.000 4.91 0.00 37.36 4.02
3182 6487 2.745152 GCAGCGTATCCACCAATACCTT 60.745 50.000 0.00 0.00 0.00 3.50
3236 6541 9.028284 TGTGCTATGTTACTACCTAAGTTACTT 57.972 33.333 2.32 2.32 38.33 2.24
4119 11210 8.451908 TCTGAGTATTATTGAGAAGACATCGA 57.548 34.615 0.00 0.00 0.00 3.59
4945 12113 3.149196 CTGCCATATAATGTCACCCCAC 58.851 50.000 0.00 0.00 0.00 4.61
5018 12186 0.623723 AGGTTTGACACACACCACCT 59.376 50.000 9.26 0.00 36.73 4.00
6521 16925 2.468831 GCGATTTACAGAGCCTCTCAG 58.531 52.381 0.00 0.00 32.06 3.35
6570 16974 8.347557 ACTATACCTCTAGAGAACCTAAAGGA 57.652 38.462 21.76 0.00 37.73 3.36
7043 17470 2.035066 GTGCACTGCTTGAACCTGATTT 59.965 45.455 10.32 0.00 0.00 2.17
7147 17576 1.409064 TCCGGAGTACATGATGTCTGC 59.591 52.381 0.00 4.06 0.00 4.26
7149 17578 4.219115 AGATTCCGGAGTACATGATGTCT 58.781 43.478 3.34 0.00 0.00 3.41
7159 17588 2.901192 TGTGGTGAAAGATTCCGGAGTA 59.099 45.455 3.34 0.00 0.00 2.59
7907 18553 6.558771 TGATGATAAATTGCAAGATACCCG 57.441 37.500 4.94 0.00 0.00 5.28
8341 18987 1.759445 CTTCTCGTCCTGTCATCCCAT 59.241 52.381 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.