Multiple sequence alignment - TraesCS2B01G487100

Loading Multiple Alignment...

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 TraesCS2B01G487100 chr2B 100.000 5676 0 0 1 5676 683488437 683482762 0.000000e+00 10482.0
1 TraesCS2B01G487100 chr2B 94.550 4771 180 37 955 5676 683689573 683684834 0.000000e+00 7297.0
2 TraesCS2B01G487100 chr2B 90.111 2427 139 40 1 2360 683275607 683273215 0.000000e+00 3059.0
3 TraesCS2B01G487100 chr2B 91.317 2119 114 40 837 2905 683386509 683384411 0.000000e+00 2830.0
4 TraesCS2B01G487100 chr2B 92.441 1852 98 20 844 2675 683592366 683590537 0.000000e+00 2606.0
5 TraesCS2B01G487100 chr2B 92.798 1458 70 5 849 2290 683310130 683308692 0.000000e+00 2078.0
6 TraesCS2B01G487100 chr2B 90.444 879 47 17 1 843 683311162 683310285 0.000000e+00 1123.0
7 TraesCS2B01G487100 chr2B 95.694 627 19 6 2286 2905 683308531 683307906 0.000000e+00 1002.0
8 TraesCS2B01G487100 chr2B 86.967 867 71 21 4232 5076 683272657 683271811 0.000000e+00 937.0
9 TraesCS2B01G487100 chr2B 85.228 941 90 27 1 919 683690487 683689574 0.000000e+00 922.0
10 TraesCS2B01G487100 chr2B 93.613 548 32 1 2358 2905 683273188 683272644 0.000000e+00 815.0
11 TraesCS2B01G487100 chr2B 87.483 719 46 16 4230 4940 683307921 683307239 0.000000e+00 789.0
12 TraesCS2B01G487100 chr2B 87.483 719 46 18 4230 4940 683590237 683589555 0.000000e+00 789.0
13 TraesCS2B01G487100 chr2B 87.928 613 66 4 1 606 683702783 683702172 0.000000e+00 715.0
14 TraesCS2B01G487100 chr2B 89.024 574 37 11 4406 4975 683384284 683383733 0.000000e+00 688.0
15 TraesCS2B01G487100 chr2B 95.745 235 8 1 2673 2905 683590456 683590222 1.490000e-100 377.0
16 TraesCS2B01G487100 chr2B 89.881 168 14 3 4983 5148 683383630 683383464 4.450000e-51 213.0
17 TraesCS2B01G487100 chr2B 83.673 245 16 8 602 823 683694156 683693913 5.760000e-50 209.0
18 TraesCS2B01G487100 chr2B 89.412 170 9 7 4 165 683322710 683322542 7.450000e-49 206.0
19 TraesCS2B01G487100 chr2B 84.483 174 17 6 4688 4858 683747785 683747619 4.550000e-36 163.0
20 TraesCS2B01G487100 chr2B 83.432 169 18 5 5466 5634 683302879 683302721 1.270000e-31 148.0
21 TraesCS2B01G487100 chr2B 82.143 168 17 5 5471 5634 683562185 683562027 1.280000e-26 132.0
22 TraesCS2B01G487100 chr2D 89.929 2959 195 38 4 2905 571663358 571660446 0.000000e+00 3718.0
23 TraesCS2B01G487100 chr2D 88.004 1784 124 26 455 2178 571550337 571548584 0.000000e+00 2026.0
24 TraesCS2B01G487100 chr2D 89.744 780 52 13 4383 5149 571660264 571659500 0.000000e+00 972.0
25 TraesCS2B01G487100 chr2D 94.581 609 30 3 2299 2905 571548585 571547978 0.000000e+00 939.0
26 TraesCS2B01G487100 chr2D 87.778 540 32 16 4392 4924 571546244 571545732 8.140000e-168 601.0
27 TraesCS2B01G487100 chr2D 86.651 427 28 9 4 422 571550742 571550337 4.030000e-121 446.0
28 TraesCS2B01G487100 chr2D 87.727 220 21 5 4932 5149 571545604 571545389 9.440000e-63 252.0
29 TraesCS2B01G487100 chr2D 85.143 175 15 7 4230 4404 571547993 571547830 9.780000e-38 169.0
30 TraesCS2B01G487100 chr2A 89.287 2035 149 25 4 1983 710276662 710274642 0.000000e+00 2486.0
31 TraesCS2B01G487100 chr2A 92.072 946 56 11 1968 2902 710274601 710273664 0.000000e+00 1314.0
32 TraesCS2B01G487100 chr2A 89.583 912 53 14 1939 2848 710345177 710344306 0.000000e+00 1120.0
33 TraesCS2B01G487100 chr2A 88.267 554 44 10 4606 5149 710273206 710272664 1.330000e-180 643.0
34 TraesCS2B01G487100 chr2A 92.260 323 18 5 4284 4599 710344256 710343934 8.670000e-123 451.0
35 TraesCS2B01G487100 chr2A 91.288 264 15 7 2152 2408 710345538 710345276 2.520000e-93 353.0
36 TraesCS2B01G487100 chr2A 86.322 329 26 4 4606 4922 710343174 710342853 1.960000e-89 340.0
37 TraesCS2B01G487100 chr2A 86.755 302 16 8 4230 4529 710273676 710273397 1.190000e-81 315.0
38 TraesCS2B01G487100 chr7D 95.012 1303 64 1 2920 4222 17845961 17844660 0.000000e+00 2045.0
39 TraesCS2B01G487100 chr7D 85.714 56 6 2 1764 1818 579065016 579064962 2.210000e-04 58.4
40 TraesCS2B01G487100 chr7B 94.882 1309 66 1 2914 4222 369858869 369860176 0.000000e+00 2045.0
41 TraesCS2B01G487100 chr4B 94.419 1308 70 2 2915 4222 654318154 654316850 0.000000e+00 2008.0
42 TraesCS2B01G487100 chr4B 93.832 1297 77 3 2928 4222 43764243 43762948 0.000000e+00 1949.0
43 TraesCS2B01G487100 chr4B 81.988 322 52 6 1027 1345 82277255 82276937 9.370000e-68 268.0
44 TraesCS2B01G487100 chr1D 94.127 1311 74 3 2913 4222 394748560 394747252 0.000000e+00 1991.0
45 TraesCS2B01G487100 chr1D 93.802 1323 73 5 2915 4232 62153456 62152138 0.000000e+00 1980.0
46 TraesCS2B01G487100 chr1D 93.822 1311 72 6 2915 4222 420001509 420002813 0.000000e+00 1964.0
47 TraesCS2B01G487100 chr3A 93.435 1310 79 5 2915 4222 10685626 10684322 0.000000e+00 1936.0
48 TraesCS2B01G487100 chr4D 82.120 632 92 8 165 791 465604962 465604347 6.520000e-144 521.0
49 TraesCS2B01G487100 chr4A 81.776 642 78 13 174 791 628876047 628876673 8.490000e-138 501.0


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 TraesCS2B01G487100 chr2B 683482762 683488437 5675 True 10482.000000 10482 100.000000 1 5676 1 chr2B.!!$R3 5675
1 TraesCS2B01G487100 chr2B 683684834 683694156 9322 True 2809.333333 7297 87.817000 1 5676 3 chr2B.!!$R11 5675
2 TraesCS2B01G487100 chr2B 683271811 683275607 3796 True 1603.666667 3059 90.230333 1 5076 3 chr2B.!!$R7 5075
3 TraesCS2B01G487100 chr2B 683589555 683592366 2811 True 1257.333333 2606 91.889667 844 4940 3 chr2B.!!$R10 4096
4 TraesCS2B01G487100 chr2B 683307239 683311162 3923 True 1248.000000 2078 91.604750 1 4940 4 chr2B.!!$R8 4939
5 TraesCS2B01G487100 chr2B 683383464 683386509 3045 True 1243.666667 2830 90.074000 837 5148 3 chr2B.!!$R9 4311
6 TraesCS2B01G487100 chr2B 683702172 683702783 611 True 715.000000 715 87.928000 1 606 1 chr2B.!!$R5 605
7 TraesCS2B01G487100 chr2D 571659500 571663358 3858 True 2345.000000 3718 89.836500 4 5149 2 chr2D.!!$R2 5145
8 TraesCS2B01G487100 chr2D 571545389 571550742 5353 True 738.833333 2026 88.314000 4 5149 6 chr2D.!!$R1 5145
9 TraesCS2B01G487100 chr2A 710272664 710276662 3998 True 1189.500000 2486 89.095250 4 5149 4 chr2A.!!$R1 5145
10 TraesCS2B01G487100 chr2A 710342853 710345538 2685 True 566.000000 1120 89.863250 1939 4922 4 chr2A.!!$R2 2983
11 TraesCS2B01G487100 chr7D 17844660 17845961 1301 True 2045.000000 2045 95.012000 2920 4222 1 chr7D.!!$R1 1302
12 TraesCS2B01G487100 chr7B 369858869 369860176 1307 False 2045.000000 2045 94.882000 2914 4222 1 chr7B.!!$F1 1308
13 TraesCS2B01G487100 chr4B 654316850 654318154 1304 True 2008.000000 2008 94.419000 2915 4222 1 chr4B.!!$R3 1307
14 TraesCS2B01G487100 chr4B 43762948 43764243 1295 True 1949.000000 1949 93.832000 2928 4222 1 chr4B.!!$R1 1294
15 TraesCS2B01G487100 chr1D 394747252 394748560 1308 True 1991.000000 1991 94.127000 2913 4222 1 chr1D.!!$R2 1309
16 TraesCS2B01G487100 chr1D 62152138 62153456 1318 True 1980.000000 1980 93.802000 2915 4232 1 chr1D.!!$R1 1317
17 TraesCS2B01G487100 chr1D 420001509 420002813 1304 False 1964.000000 1964 93.822000 2915 4222 1 chr1D.!!$F1 1307
18 TraesCS2B01G487100 chr3A 10684322 10685626 1304 True 1936.000000 1936 93.435000 2915 4222 1 chr3A.!!$R1 1307
19 TraesCS2B01G487100 chr4D 465604347 465604962 615 True 521.000000 521 82.120000 165 791 1 chr4D.!!$R1 626
20 TraesCS2B01G487100 chr4A 628876047 628876673 626 False 501.000000 501 81.776000 174 791 1 chr4A.!!$F1 617

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
897 4803 0.606944 TTATTTCCCCACTGCGCGTT 60.607 50.0 8.43 0.0 0.00 4.84 F
1431 5356 1.162800 GCGCCACCTTCATGGATCTC 61.163 60.0 0.00 0.0 43.02 2.75 F
2051 6068 0.894141 TGTTGTTTGTTGCTGCAGGT 59.106 45.0 17.12 0.0 0.00 4.00 F
3426 7732 1.043816 GATCTCCTTGGGATCGAGCA 58.956 55.0 1.84 0.0 31.79 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 5806 0.322636 TCTCCCGGAGTGTGTCTCTC 60.323 60.0 14.36 0.0 42.40 3.20 R
3360 7666 2.485479 GCTGTCAAGAACCAGACAAGGA 60.485 50.0 0.00 0.0 43.48 3.36 R
3654 7961 0.676736 CGGAAGACCCAGATCTAGGC 59.323 60.0 7.15 0.0 34.14 3.93 R
5114 12220 0.741221 GTCCATCTTGTCGGCTCCAC 60.741 60.0 0.00 0.0 0.00 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
207 3890 7.346961 GAAATATTCGAATTTCGTCCGAAAC 57.653 36.000 17.19 5.10 45.34 2.78
289 3973 4.272511 TTCGAGCCCGGCCCAAAA 62.273 61.111 5.55 0.00 36.24 2.44
440 4150 3.181454 CCTCCTCCAACACAGTAACAACT 60.181 47.826 0.00 0.00 0.00 3.16
475 4185 2.566724 CTCAAGCACTCCTTCTCCTTCT 59.433 50.000 0.00 0.00 0.00 2.85
745 4480 6.753107 TGTCCGGAATTCTCCTAAAAATTC 57.247 37.500 5.23 0.00 39.93 2.17
817 4560 2.490903 CCAAAATCTTGGTCAGGAGCAG 59.509 50.000 1.16 0.00 46.25 4.24
825 4578 3.313524 TCAGGAGCAGGCGAGCAA 61.314 61.111 7.67 0.00 36.85 3.91
897 4803 0.606944 TTATTTCCCCACTGCGCGTT 60.607 50.000 8.43 0.00 0.00 4.84
1006 4921 2.612493 CGGGGTCTTTCCATGGGGT 61.612 63.158 13.02 0.00 38.11 4.95
1251 5175 1.216977 CGGCGTGGACATCTACCAA 59.783 57.895 0.00 0.00 39.22 3.67
1431 5356 1.162800 GCGCCACCTTCATGGATCTC 61.163 60.000 0.00 0.00 43.02 2.75
1521 5446 2.705821 CCGCTCGCTGGAGAGACTT 61.706 63.158 5.57 0.00 42.04 3.01
1674 5599 1.447838 CGTAGTGGAGCACGGCAAT 60.448 57.895 0.00 0.00 39.64 3.56
1984 5931 7.177216 TGTCTCATATCCTGCTTGTTCAATTTT 59.823 33.333 0.00 0.00 0.00 1.82
2036 6053 4.261322 CCAGGATGTCTTGTCAAACTGTTG 60.261 45.833 0.00 0.00 35.95 3.33
2051 6068 0.894141 TGTTGTTTGTTGCTGCAGGT 59.106 45.000 17.12 0.00 0.00 4.00
2435 6651 4.528206 TGTCTCTGTGATGAGCCTAAGAAA 59.472 41.667 0.00 0.00 34.29 2.52
2444 6660 5.190528 TGATGAGCCTAAGAAATGGAGAACT 59.809 40.000 0.00 0.00 0.00 3.01
2510 6726 2.582436 GGCGGGGAAGATCACGAA 59.418 61.111 0.00 0.00 0.00 3.85
2527 6743 6.991485 TCACGAATTTGATTTCTTGAAAGC 57.009 33.333 0.00 4.61 32.78 3.51
3426 7732 1.043816 GATCTCCTTGGGATCGAGCA 58.956 55.000 1.84 0.00 31.79 4.26
3546 7852 1.737793 GGAACTGCCGATGAAAATCGT 59.262 47.619 7.28 0.00 42.07 3.73
3654 7961 2.193248 GGATGCTCCGGGGGAAAG 59.807 66.667 0.00 0.00 0.00 2.62
3984 8294 1.374125 CGTCTGACCGGATTGTGCA 60.374 57.895 9.46 0.00 0.00 4.57
4119 8429 2.800629 GCATATGTTGCCAAGATGGTGC 60.801 50.000 4.29 9.73 46.15 5.01
4176 8488 7.926555 GGTCCTCGAGAATAATCAATAAAGTGA 59.073 37.037 15.71 0.00 0.00 3.41
4293 8616 8.366671 TGCTAGTCTTTTTCTTAGTTTCAGTC 57.633 34.615 0.00 0.00 0.00 3.51
4307 8637 4.762251 AGTTTCAGTCTCCCTTTAATGCAC 59.238 41.667 0.00 0.00 0.00 4.57
4728 11614 1.095600 CAAGATCGTCCTCTCCGACA 58.904 55.000 0.00 0.00 37.12 4.35
5245 12353 6.446318 TGTGCTCCATATGTTGAAGAAAAAC 58.554 36.000 1.24 0.00 0.00 2.43
5415 12523 6.035542 GGTTTTCTTTCGAAGTTTTGCATTCA 59.964 34.615 0.00 0.00 0.00 2.57
5416 12524 7.412455 GGTTTTCTTTCGAAGTTTTGCATTCAA 60.412 33.333 0.00 0.00 0.00 2.69
5466 12574 5.248640 ACACTCCACTGGTCTGAATTAATG 58.751 41.667 0.00 0.00 0.00 1.90
5603 12711 7.880160 TTGTGTATAGATTTTCATCCAAGGG 57.120 36.000 0.00 0.00 0.00 3.95
5613 12721 1.854939 TCATCCAAGGGCCTGATTGAT 59.145 47.619 6.92 4.06 0.00 2.57
5647 12755 6.780457 AGGTCCCATGATCTTATGTTTTTG 57.220 37.500 0.00 0.00 0.00 2.44
5654 12762 8.960591 CCCATGATCTTATGTTTTTGTAGAACT 58.039 33.333 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 3871 4.579270 GAGTTTCGGACGAAATTCGAAT 57.421 40.909 22.92 4.39 43.74 3.34
207 3890 3.788766 CGTGGCGAAAAGGGCGAG 61.789 66.667 0.00 0.00 34.76 5.03
289 3973 0.328258 AAAAGAGGTGCGTGGGCTAT 59.672 50.000 0.00 0.00 40.82 2.97
416 4104 2.367567 TGTTACTGTGTTGGAGGAGGAC 59.632 50.000 0.00 0.00 0.00 3.85
440 4150 0.035881 CTTGAGCCTTGAGCAGGTGA 59.964 55.000 0.00 0.00 46.07 4.02
475 4185 0.175760 GCGCTCTACAACCTCCATGA 59.824 55.000 0.00 0.00 0.00 3.07
548 4259 0.038744 CCTTGACCTCATGTGGCCTT 59.961 55.000 13.75 0.00 0.00 4.35
701 4434 8.325282 CGGACAAAAAGAGTAAACCAAAATTTC 58.675 33.333 0.00 0.00 0.00 2.17
722 4457 5.650703 GGAATTTTTAGGAGAATTCCGGACA 59.349 40.000 1.83 0.00 46.52 4.02
745 4480 0.577269 GCGAAATTCGTCATCTCGGG 59.423 55.000 17.05 0.00 42.81 5.14
817 4560 1.328986 GCAGAGAATAAGTTGCTCGCC 59.671 52.381 0.00 0.00 33.98 5.54
1006 4921 0.606096 TCGGATCTTTTGCTCGACCA 59.394 50.000 0.00 0.00 0.00 4.02
1251 5175 2.809601 GCGACGCGGATGTTGAGT 60.810 61.111 12.47 0.00 0.00 3.41
1363 5287 0.397941 CAGGAGACTTGCAGGTTCCA 59.602 55.000 22.69 0.00 40.21 3.53
1421 5346 4.950062 GCGCGCGGAGATCCATGA 62.950 66.667 33.06 0.00 35.14 3.07
1674 5599 1.829533 GGTACGGCGGGTCCATCTA 60.830 63.158 13.24 0.00 34.01 1.98
1871 5806 0.322636 TCTCCCGGAGTGTGTCTCTC 60.323 60.000 14.36 0.00 42.40 3.20
2036 6053 2.195922 CTGAAACCTGCAGCAACAAAC 58.804 47.619 8.66 0.00 0.00 2.93
2042 6059 1.202806 AGCTAACTGAAACCTGCAGCA 60.203 47.619 8.66 0.00 36.86 4.41
2043 6060 1.528129 AGCTAACTGAAACCTGCAGC 58.472 50.000 8.66 0.00 36.86 5.25
2044 6061 3.057946 GGAAAGCTAACTGAAACCTGCAG 60.058 47.826 6.78 6.78 39.26 4.41
2051 6068 5.301551 TCTGCATTTGGAAAGCTAACTGAAA 59.698 36.000 0.00 0.00 0.00 2.69
2100 6120 7.806180 AGAAGCTGGTAACCATATGTTTATCT 58.194 34.615 5.06 0.00 38.42 1.98
2120 6140 0.898320 TAGGTGCAGACCAGAGAAGC 59.102 55.000 0.00 0.00 45.98 3.86
2134 6154 2.625737 CTTGGTGCTGAGATGTAGGTG 58.374 52.381 0.00 0.00 0.00 4.00
2435 6651 6.176183 CAAGGTGATAGTTTCAGTTCTCCAT 58.824 40.000 0.00 0.00 34.17 3.41
2444 6660 4.574674 ATCAGCCAAGGTGATAGTTTCA 57.425 40.909 7.47 0.00 46.83 2.69
2527 6743 4.032217 GCATCGGAGCACATCTAAATATCG 59.968 45.833 0.00 0.00 0.00 2.92
3255 7561 4.664677 GCATAGATCCGGCCGCGT 62.665 66.667 22.85 10.45 0.00 6.01
3360 7666 2.485479 GCTGTCAAGAACCAGACAAGGA 60.485 50.000 0.00 0.00 43.48 3.36
3484 7790 1.371558 GTCGCTGGTCCCTTCAACT 59.628 57.895 0.00 0.00 0.00 3.16
3654 7961 0.676736 CGGAAGACCCAGATCTAGGC 59.323 60.000 7.15 0.00 34.14 3.93
3678 7985 4.997905 CGATAAAACGCCATCATCATCT 57.002 40.909 0.00 0.00 0.00 2.90
3896 8206 2.672961 TTGAGGCATCTACCTTGTCG 57.327 50.000 0.00 0.00 41.32 4.35
3984 8294 2.666098 GCCACATACCGGGTCTGGT 61.666 63.158 15.92 6.71 46.26 4.00
4119 8429 8.761575 AAGTATTACAACAAAATGCCTGAATG 57.238 30.769 0.00 0.00 0.00 2.67
4176 8488 1.345741 CATCTGGGAGATGCATACGGT 59.654 52.381 0.00 0.00 44.69 4.83
4235 8553 2.680913 ATTGCTGAAGCGTGCGGAC 61.681 57.895 0.00 0.00 45.83 4.79
4286 8609 3.751175 CGTGCATTAAAGGGAGACTGAAA 59.249 43.478 0.00 0.00 0.00 2.69
4293 8616 1.133025 CTTGGCGTGCATTAAAGGGAG 59.867 52.381 0.00 0.00 0.00 4.30
4536 10512 5.163550 GGTAACAAAGTTATGGAAGATGGCC 60.164 44.000 0.00 0.00 0.00 5.36
4728 11614 2.233305 ACAGATAGGAGTTGGTCGGT 57.767 50.000 0.00 0.00 0.00 4.69
5114 12220 0.741221 GTCCATCTTGTCGGCTCCAC 60.741 60.000 0.00 0.00 0.00 4.02
5415 12523 3.551846 TCAACCCTCGCTCTTTCTTTTT 58.448 40.909 0.00 0.00 0.00 1.94
5416 12524 3.208747 TCAACCCTCGCTCTTTCTTTT 57.791 42.857 0.00 0.00 0.00 2.27
5466 12574 5.692814 GATGGGTTTACAAAACCTTCGTAC 58.307 41.667 18.35 4.48 46.14 3.67
5603 12711 3.465742 TGCTCAGACTATCAATCAGGC 57.534 47.619 0.00 0.00 0.00 4.85
5613 12721 1.833630 CATGGGACCTTGCTCAGACTA 59.166 52.381 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.