Multiple sequence alignment - TraesCS6B01G125400

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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 TraesCS6B01G125400 chr6B 100.000 3461 0 0 1 3461 120596115 120592655 0.000000e+00 6392.0
1 TraesCS6B01G125400 chr6B 89.642 2288 199 23 378 2650 120355402 120353138 0.000000e+00 2878.0
2 TraesCS6B01G125400 chr6B 90.227 2067 166 25 594 2641 120132997 120130948 0.000000e+00 2665.0
3 TraesCS6B01G125400 chr6B 92.358 615 31 5 2507 3110 120310752 120310143 0.000000e+00 861.0
4 TraesCS6B01G125400 chr6B 93.575 358 21 2 3105 3461 120217875 120217519 1.830000e-147 532.0
5 TraesCS6B01G125400 chr6B 87.234 282 26 5 310 586 120133428 120133152 2.590000e-81 313.0
6 TraesCS6B01G125400 chr6B 95.181 166 7 1 490 655 120317737 120317573 9.530000e-66 261.0
7 TraesCS6B01G125400 chr6B 82.060 301 23 9 4 303 120133897 120133627 9.660000e-56 228.0
8 TraesCS6B01G125400 chr6B 77.003 287 25 18 148 432 120318104 120317857 3.630000e-25 126.0
9 TraesCS6B01G125400 chr6D 91.702 3495 172 55 5 3461 51348171 51351585 0.000000e+00 4739.0
10 TraesCS6B01G125400 chr6D 93.990 2945 127 23 533 3461 50948978 50951888 0.000000e+00 4412.0
11 TraesCS6B01G125400 chr6D 90.729 3225 185 55 5 3191 51073388 51076536 0.000000e+00 4194.0
12 TraesCS6B01G125400 chr6D 93.296 2655 154 15 3 2650 51342245 51344882 0.000000e+00 3895.0
13 TraesCS6B01G125400 chr6D 88.392 2481 220 29 194 2650 53176500 53174064 0.000000e+00 2924.0
14 TraesCS6B01G125400 chr6D 89.522 2300 188 27 379 2650 51067884 51070158 0.000000e+00 2863.0
15 TraesCS6B01G125400 chr6D 87.619 2520 234 38 156 2646 50955828 50958298 0.000000e+00 2854.0
16 TraesCS6B01G125400 chr6D 82.402 358 30 10 2651 2980 53142821 53142469 7.310000e-72 281.0
17 TraesCS6B01G125400 chr6D 81.818 319 31 11 24 337 51067576 51067872 3.450000e-60 243.0
18 TraesCS6B01G125400 chr6D 95.798 119 5 0 3224 3342 51076533 51076651 3.530000e-45 193.0
19 TraesCS6B01G125400 chr6D 95.918 49 1 1 2987 3034 51070700 51070748 1.030000e-10 78.7
20 TraesCS6B01G125400 chr6D 95.918 49 1 1 2987 3034 51345424 51345472 1.030000e-10 78.7
21 TraesCS6B01G125400 chr6A 92.857 2562 142 14 918 3460 64174550 64172011 0.000000e+00 3679.0
22 TraesCS6B01G125400 chr6A 86.096 935 64 24 3 918 64175791 64174904 0.000000e+00 946.0
23 TraesCS6B01G125400 chr6A 83.193 357 30 9 2651 2980 64064199 64063846 2.020000e-77 300.0
24 TraesCS6B01G125400 chr6A 90.566 53 5 0 3267 3319 613496083 613496135 1.720000e-08 71.3
25 TraesCS6B01G125400 chr7A 86.806 2539 210 57 145 2619 631983853 631986330 0.000000e+00 2717.0
26 TraesCS6B01G125400 chr7B 86.239 2616 212 64 148 2683 591461048 591463595 0.000000e+00 2700.0
27 TraesCS6B01G125400 chr7D 85.860 2652 232 58 39 2619 548230409 548232988 0.000000e+00 2687.0
28 TraesCS6B01G125400 chr1B 87.643 2355 213 37 347 2650 4109825 4112152 0.000000e+00 2665.0
29 TraesCS6B01G125400 chr1B 81.905 315 35 12 2645 2942 4112196 4112505 2.670000e-61 246.0
30 TraesCS6B01G125400 chr1B 83.154 279 30 4 2656 2919 4798061 4797785 4.460000e-59 239.0
31 TraesCS6B01G125400 chr1B 83.004 253 30 4 2651 2894 4516992 4516744 2.090000e-52 217.0
32 TraesCS6B01G125400 chr1B 79.918 244 28 12 298 524 70232451 70232690 3.580000e-35 159.0
33 TraesCS6B01G125400 chr1B 89.394 66 7 0 2917 2982 4803065 4803000 2.210000e-12 84.2
34 TraesCS6B01G125400 chr1B 97.727 44 1 0 2987 3030 4516547 4516504 3.700000e-10 76.8
35 TraesCS6B01G125400 chr1B 91.071 56 5 0 3267 3322 46827863 46827808 3.700000e-10 76.8
36 TraesCS6B01G125400 chr5D 89.501 2086 162 25 586 2633 57819423 57821489 0.000000e+00 2586.0
37 TraesCS6B01G125400 chr5B 83.095 349 35 8 2652 2979 60823958 60823613 2.610000e-76 296.0
38 TraesCS6B01G125400 chr1D 81.763 329 43 8 2655 2969 387434 387759 3.430000e-65 259.0
39 TraesCS6B01G125400 chr1D 92.453 53 4 0 3267 3319 387874 387926 3.700000e-10 76.8
40 TraesCS6B01G125400 chr3D 81.424 323 28 10 2655 2948 560022861 560022542 5.770000e-58 235.0
41 TraesCS6B01G125400 chr4A 86.765 136 16 2 3034 3168 730394444 730394310 2.150000e-32 150.0
42 TraesCS6B01G125400 chr1A 100.000 42 0 0 2987 3028 3011164 3011205 1.030000e-10 78.7
43 TraesCS6B01G125400 chr1A 90.566 53 5 0 3267 3319 3015535 3015587 1.720000e-08 71.3


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 TraesCS6B01G125400 chr6B 120592655 120596115 3460 True 6392.000000 6392 100.000000 1 3461 1 chr6B.!!$R4 3460
1 TraesCS6B01G125400 chr6B 120353138 120355402 2264 True 2878.000000 2878 89.642000 378 2650 1 chr6B.!!$R3 2272
2 TraesCS6B01G125400 chr6B 120130948 120133897 2949 True 1068.666667 2665 86.507000 4 2641 3 chr6B.!!$R5 2637
3 TraesCS6B01G125400 chr6B 120310143 120310752 609 True 861.000000 861 92.358000 2507 3110 1 chr6B.!!$R2 603
4 TraesCS6B01G125400 chr6D 50948978 50958298 9320 False 3633.000000 4412 90.804500 156 3461 2 chr6D.!!$F1 3305
5 TraesCS6B01G125400 chr6D 53174064 53176500 2436 True 2924.000000 2924 88.392000 194 2650 1 chr6D.!!$R2 2456
6 TraesCS6B01G125400 chr6D 51342245 51351585 9340 False 2904.233333 4739 93.638667 3 3461 3 chr6D.!!$F3 3458
7 TraesCS6B01G125400 chr6D 51067576 51076651 9075 False 1514.340000 4194 90.757000 5 3342 5 chr6D.!!$F2 3337
8 TraesCS6B01G125400 chr6A 64172011 64175791 3780 True 2312.500000 3679 89.476500 3 3460 2 chr6A.!!$R2 3457
9 TraesCS6B01G125400 chr7A 631983853 631986330 2477 False 2717.000000 2717 86.806000 145 2619 1 chr7A.!!$F1 2474
10 TraesCS6B01G125400 chr7B 591461048 591463595 2547 False 2700.000000 2700 86.239000 148 2683 1 chr7B.!!$F1 2535
11 TraesCS6B01G125400 chr7D 548230409 548232988 2579 False 2687.000000 2687 85.860000 39 2619 1 chr7D.!!$F1 2580
12 TraesCS6B01G125400 chr1B 4109825 4112505 2680 False 1455.500000 2665 84.774000 347 2942 2 chr1B.!!$F2 2595
13 TraesCS6B01G125400 chr5D 57819423 57821489 2066 False 2586.000000 2586 89.501000 586 2633 1 chr5D.!!$F1 2047

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
19 20 0.636733 CAACGAAATGCGATGCAAGC 59.363 50.000 10.19 10.19 43.62 4.01 F
28 29 1.153449 CGATGCAAGCGGGGACTAA 60.153 57.895 0.00 0.00 45.34 2.24 F
47 48 2.715763 AGGGTTTACACTCCTCTCCA 57.284 50.000 0.00 0.00 0.00 3.86 F
1158 8691 0.792640 CTGGTCTTTGCACTGCTACG 59.207 55.000 1.98 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1116 8649 2.171448 ACCAACATGGATAGCACCTCTC 59.829 50.000 2.85 0.0 40.96 3.20 R
1119 8652 2.578021 AGAACCAACATGGATAGCACCT 59.422 45.455 2.85 0.0 40.96 4.00 R
1345 8878 3.482110 GTCTTGCAACAAGCTAAACAACG 59.518 43.478 0.00 0.0 45.94 4.10 R
2798 22133 1.272490 TCTTCAAGATCGCTTCCGTGT 59.728 47.619 0.00 0.0 35.54 4.49 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
19 20 0.636733 CAACGAAATGCGATGCAAGC 59.363 50.000 10.19 10.19 43.62 4.01
28 29 1.153449 CGATGCAAGCGGGGACTAA 60.153 57.895 0.00 0.00 45.34 2.24
47 48 2.715763 AGGGTTTACACTCCTCTCCA 57.284 50.000 0.00 0.00 0.00 3.86
110 121 3.942439 GCAGGGGCGGAGATACCC 61.942 72.222 0.00 0.00 46.24 3.69
122 133 3.154827 GAGATACCCTCCTCTCCTCTG 57.845 57.143 0.00 0.00 35.87 3.35
313 7205 4.811557 GGTAGTGTCATCCATGAAGTTAGC 59.188 45.833 0.00 0.00 38.75 3.09
382 7282 4.142600 GCATTTTGCAACTAGGTAGGAGTG 60.143 45.833 0.00 0.00 44.26 3.51
545 7495 6.375455 AGCTACAAGTAGTAATTTGCATGCTT 59.625 34.615 20.33 7.61 35.65 3.91
767 7916 5.067273 TCTAGAGACAGATAAGGTGCTAGC 58.933 45.833 8.10 8.10 0.00 3.42
768 7917 3.909732 AGAGACAGATAAGGTGCTAGCT 58.090 45.455 17.23 0.00 0.00 3.32
769 7918 5.055265 AGAGACAGATAAGGTGCTAGCTA 57.945 43.478 17.23 0.00 0.00 3.32
770 7919 5.070001 AGAGACAGATAAGGTGCTAGCTAG 58.930 45.833 16.84 16.84 0.00 3.42
830 7990 5.053811 CCAGTTTTGGATGGGTACAAAAAC 58.946 41.667 4.39 0.00 46.75 2.43
1116 8649 5.047377 GCTCTACAAGATAGAGGGGAATCAG 60.047 48.000 11.84 0.00 40.92 2.90
1119 8652 5.149584 ACAAGATAGAGGGGAATCAGAGA 57.850 43.478 0.00 0.00 0.00 3.10
1158 8691 0.792640 CTGGTCTTTGCACTGCTACG 59.207 55.000 1.98 0.00 0.00 3.51
1226 8759 7.839680 AAGTGGAAATTGATTACTCTGGTTT 57.160 32.000 0.00 0.00 0.00 3.27
1345 8878 1.863267 CATCGATGACTCTGGGCTTC 58.137 55.000 21.02 0.00 0.00 3.86
1392 8925 1.892474 GTGTCTCTCAGGCTGAACTCT 59.108 52.381 19.29 0.00 0.00 3.24
1477 14899 2.874701 CTCCACCTTATTGATTGCGAGG 59.125 50.000 0.00 0.00 0.00 4.63
2007 15433 5.426504 CTCAACTGTCCTATGCTTCAGATT 58.573 41.667 0.00 0.00 0.00 2.40
2553 15980 1.028330 CAAGGCTGTGCATCATCCGT 61.028 55.000 0.00 0.00 37.41 4.69
2562 15989 0.531532 GCATCATCCGTCCCAGACTG 60.532 60.000 0.00 0.00 0.00 3.51
2683 22003 9.959721 AATTCTGGTTGCTTAATTTCTACTCTA 57.040 29.630 0.00 0.00 0.00 2.43
2729 22049 4.432741 GGCCCCAAGAGTCCCTGC 62.433 72.222 0.00 0.00 0.00 4.85
2730 22050 4.432741 GCCCCAAGAGTCCCTGCC 62.433 72.222 0.00 0.00 0.00 4.85
3033 22386 8.251383 ACTACTGAAGGCATATAACATACTGT 57.749 34.615 0.00 0.00 0.00 3.55
3034 22387 9.363401 ACTACTGAAGGCATATAACATACTGTA 57.637 33.333 0.00 0.00 0.00 2.74
3035 22388 9.627395 CTACTGAAGGCATATAACATACTGTAC 57.373 37.037 0.00 0.00 0.00 2.90
3036 22389 8.251383 ACTGAAGGCATATAACATACTGTACT 57.749 34.615 0.00 0.00 0.00 2.73
3037 22390 8.361139 ACTGAAGGCATATAACATACTGTACTC 58.639 37.037 0.00 0.00 0.00 2.59
3038 22391 7.368059 TGAAGGCATATAACATACTGTACTCG 58.632 38.462 0.00 0.00 0.00 4.18
3039 22392 7.229907 TGAAGGCATATAACATACTGTACTCGA 59.770 37.037 0.00 0.00 0.00 4.04
3073 22430 9.453325 CTAAAACTAAGGCGTATTTTTGTTTCA 57.547 29.630 15.20 0.00 33.38 2.69
3150 22508 9.850628 CATGAAATTTGTGTCACTAGATTCATT 57.149 29.630 18.23 2.84 33.93 2.57
3226 22584 8.044060 TGATCAAATTCTTGTCTTAGCGAAAT 57.956 30.769 0.00 0.00 33.94 2.17
3235 22593 8.716646 TCTTGTCTTAGCGAAATGAAATATGA 57.283 30.769 0.00 0.00 0.00 2.15
3367 22726 7.038587 TGGCTACGTTCTTATATTATGGGATGT 60.039 37.037 0.00 0.00 0.00 3.06
3368 22727 8.472413 GGCTACGTTCTTATATTATGGGATGTA 58.528 37.037 0.00 0.00 0.00 2.29
3386 22745 9.496710 TGGGATGTAGGAAGTACTTTATTCTTA 57.503 33.333 10.02 0.00 32.19 2.10
3407 22766 2.086869 AGCTAACATGAAACATGCGCT 58.913 42.857 9.73 12.54 0.00 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.587088 CCCGCTTGCATCGCATTTC 60.587 57.895 8.90 0.00 38.76 2.17
6 7 3.520862 CCCCGCTTGCATCGCATT 61.521 61.111 8.90 0.00 38.76 3.56
7 8 4.488136 TCCCCGCTTGCATCGCAT 62.488 61.111 8.90 0.00 38.76 4.73
10 11 1.153449 TTAGTCCCCGCTTGCATCG 60.153 57.895 0.00 0.00 0.00 3.84
11 12 0.815615 CCTTAGTCCCCGCTTGCATC 60.816 60.000 0.00 0.00 0.00 3.91
12 13 1.224592 CCTTAGTCCCCGCTTGCAT 59.775 57.895 0.00 0.00 0.00 3.96
13 14 2.668632 CCTTAGTCCCCGCTTGCA 59.331 61.111 0.00 0.00 0.00 4.08
15 16 0.037734 AAACCCTTAGTCCCCGCTTG 59.962 55.000 0.00 0.00 0.00 4.01
16 17 1.280133 GTAAACCCTTAGTCCCCGCTT 59.720 52.381 0.00 0.00 0.00 4.68
17 18 0.907486 GTAAACCCTTAGTCCCCGCT 59.093 55.000 0.00 0.00 0.00 5.52
19 20 1.904537 AGTGTAAACCCTTAGTCCCCG 59.095 52.381 0.00 0.00 0.00 5.73
22 23 4.095211 AGAGGAGTGTAAACCCTTAGTCC 58.905 47.826 0.00 0.00 0.00 3.85
23 24 4.160065 GGAGAGGAGTGTAAACCCTTAGTC 59.840 50.000 0.00 0.00 0.00 2.59
25 26 4.094476 TGGAGAGGAGTGTAAACCCTTAG 58.906 47.826 0.00 0.00 0.00 2.18
28 29 2.715763 TGGAGAGGAGTGTAAACCCT 57.284 50.000 0.00 0.00 0.00 4.34
47 48 4.583871 AGAGTGCTTCTTTGATTCGGATT 58.416 39.130 0.00 0.00 29.61 3.01
110 121 0.468029 GGGAGAGCAGAGGAGAGGAG 60.468 65.000 0.00 0.00 0.00 3.69
112 123 1.042559 GTGGGAGAGCAGAGGAGAGG 61.043 65.000 0.00 0.00 0.00 3.69
113 124 1.383456 CGTGGGAGAGCAGAGGAGAG 61.383 65.000 0.00 0.00 0.00 3.20
122 133 1.617947 AATGGAGACCGTGGGAGAGC 61.618 60.000 0.00 0.00 0.00 4.09
258 7022 1.151668 CCTGTCAAGAAAGCGACCTG 58.848 55.000 0.00 0.00 0.00 4.00
313 7205 6.540189 CCAGGAGAATGGTTAGACAACATTAG 59.460 42.308 0.00 0.00 36.29 1.73
382 7282 0.813210 CTGCTGCAACCCTAGCTAGC 60.813 60.000 15.74 6.62 40.52 3.42
545 7495 9.646427 GCACCTAATTAATAACATGAAAACCAA 57.354 29.630 0.00 0.00 0.00 3.67
767 7916 9.717942 AGCATGGAGAATTATTAAAGTAGCTAG 57.282 33.333 0.00 0.00 0.00 3.42
769 7918 8.986929 AAGCATGGAGAATTATTAAAGTAGCT 57.013 30.769 0.00 0.00 0.00 3.32
826 7986 5.841957 ACTGATGAAGTTTGAGCAGTTTT 57.158 34.783 0.00 0.00 34.57 2.43
830 7990 4.993584 ACAGTACTGATGAAGTTTGAGCAG 59.006 41.667 29.30 0.00 40.56 4.24
1116 8649 2.171448 ACCAACATGGATAGCACCTCTC 59.829 50.000 2.85 0.00 40.96 3.20
1119 8652 2.578021 AGAACCAACATGGATAGCACCT 59.422 45.455 2.85 0.00 40.96 4.00
1226 8759 4.227300 ACTGCTTTCCATGTCCAGGTATAA 59.773 41.667 0.00 0.00 0.00 0.98
1345 8878 3.482110 GTCTTGCAACAAGCTAAACAACG 59.518 43.478 0.00 0.00 45.94 4.10
1392 8925 4.747108 CCAATTGACGTTATTTTTGGTGCA 59.253 37.500 7.12 0.00 31.19 4.57
1477 14899 4.153117 CAGCCACTCTACACTGTCAATTTC 59.847 45.833 0.00 0.00 0.00 2.17
2007 15433 5.417894 ACATCGTGTAAATCTGAGGTCTACA 59.582 40.000 0.00 0.00 0.00 2.74
2553 15980 2.894126 GTTCAGAGAAGACAGTCTGGGA 59.106 50.000 3.05 0.00 40.61 4.37
2562 15989 5.037385 GGCAACAAAAAGTTCAGAGAAGAC 58.963 41.667 0.00 0.00 38.74 3.01
2683 22003 1.538075 CCGGTTTTGAAACGGCTACAT 59.462 47.619 4.03 0.00 39.77 2.29
2729 22049 3.914426 ATAGTGCCTCCACAGTAAAGG 57.086 47.619 0.00 0.00 44.53 3.11
2730 22050 5.918608 ACATATAGTGCCTCCACAGTAAAG 58.081 41.667 0.00 0.00 44.53 1.85
2798 22133 1.272490 TCTTCAAGATCGCTTCCGTGT 59.728 47.619 0.00 0.00 35.54 4.49
2966 22319 3.555168 CCTGGTTGACTAGTGACTTCCAC 60.555 52.174 0.00 0.00 46.03 4.02
3033 22386 7.686127 GCCTTAGTTTTAGGAATGGATCGAGTA 60.686 40.741 0.00 0.00 34.56 2.59
3034 22387 6.583562 CCTTAGTTTTAGGAATGGATCGAGT 58.416 40.000 0.00 0.00 34.56 4.18
3035 22388 5.467063 GCCTTAGTTTTAGGAATGGATCGAG 59.533 44.000 0.00 0.00 34.56 4.04
3036 22389 5.365619 GCCTTAGTTTTAGGAATGGATCGA 58.634 41.667 0.00 0.00 34.56 3.59
3037 22390 4.211374 CGCCTTAGTTTTAGGAATGGATCG 59.789 45.833 0.00 0.00 34.56 3.69
3038 22391 5.123936 ACGCCTTAGTTTTAGGAATGGATC 58.876 41.667 0.00 0.00 34.56 3.36
3039 22392 5.112129 ACGCCTTAGTTTTAGGAATGGAT 57.888 39.130 0.00 0.00 34.56 3.41
3235 22593 3.386726 TCCATCCGTTCCGATGAATAAGT 59.613 43.478 0.17 0.00 41.92 2.24
3266 22624 5.187772 AGCAAAGACATGATGTGACTACCTA 59.812 40.000 1.23 0.00 32.50 3.08
3386 22745 2.489329 AGCGCATGTTTCATGTTAGCTT 59.511 40.909 11.47 7.62 0.00 3.74


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

AutoCloner maintained by Alex Coulton.