Multiple sequence alignment - TraesCS3D01G058900

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 TraesCS3D01G058900 chr3D 100.000 4184 0 0 1 4184 25527785 25523602 0.000000e+00 7727.0
1 TraesCS3D01G058900 chr3D 87.432 183 17 5 13 192 25528512 25528333 5.480000e-49 206.0
2 TraesCS3D01G058900 chr3D 87.821 156 17 2 354 508 25528314 25528160 9.240000e-42 182.0
3 TraesCS3D01G058900 chr3D 97.872 47 0 1 3631 3676 25524110 25524064 3.470000e-11 80.5
4 TraesCS3D01G058900 chr3D 97.872 47 0 1 3676 3722 25524155 25524110 3.470000e-11 80.5
5 TraesCS3D01G058900 chr7D 97.318 4213 41 13 1 4184 37658764 37662933 0.000000e+00 7088.0
6 TraesCS3D01G058900 chr7D 88.038 744 59 8 816 1547 37625515 37626240 0.000000e+00 854.0
7 TraesCS3D01G058900 chr7D 85.795 176 16 6 360 534 37615171 37615338 1.200000e-40 178.0
8 TraesCS3D01G058900 chr7D 82.796 186 18 8 362 546 37554108 37554280 2.010000e-33 154.0
9 TraesCS3D01G058900 chr7D 86.667 120 15 1 230 348 536146629 536146510 9.440000e-27 132.0
10 TraesCS3D01G058900 chr2A 96.105 1412 31 8 640 2044 720388466 720387072 0.000000e+00 2281.0
11 TraesCS3D01G058900 chr2A 91.702 940 68 4 2367 3304 720386469 720385538 0.000000e+00 1295.0
12 TraesCS3D01G058900 chr2A 90.236 635 53 7 916 1547 720354047 720353419 0.000000e+00 821.0
13 TraesCS3D01G058900 chr2A 95.950 321 10 2 2038 2358 720386900 720386583 6.200000e-143 518.0
14 TraesCS3D01G058900 chr2A 85.067 375 24 11 1 366 720388858 720388507 1.850000e-93 353.0
15 TraesCS3D01G058900 chr2A 87.826 230 13 7 3958 4183 720384901 720384683 5.370000e-64 255.0
16 TraesCS3D01G058900 chr2A 100.000 32 0 0 613 644 720388505 720388474 4.520000e-05 60.2
17 TraesCS3D01G058900 chr4A 94.521 1241 51 9 816 2044 687321186 687319951 0.000000e+00 1899.0
18 TraesCS3D01G058900 chr4A 90.342 497 33 9 2367 2848 687319316 687318820 4.560000e-179 638.0
19 TraesCS3D01G058900 chr4A 93.711 318 19 1 2041 2358 687319763 687319447 3.790000e-130 475.0
20 TraesCS3D01G058900 chr4A 86.124 418 42 9 2891 3304 687318823 687318418 1.790000e-118 436.0
21 TraesCS3D01G058900 chr4A 86.667 210 12 4 3980 4184 687317572 687317374 7.040000e-53 219.0
22 TraesCS3D01G058900 chr4A 83.908 87 8 4 1632 1712 647378594 647378680 1.250000e-10 78.7
23 TraesCS3D01G058900 chr5A 85.870 1472 122 42 674 2099 379094448 379093017 0.000000e+00 1487.0
24 TraesCS3D01G058900 chr5A 90.000 80 7 1 2078 2157 379093012 379092934 7.400000e-18 102.0
25 TraesCS3D01G058900 chr5A 93.220 59 3 1 2300 2358 379092845 379092788 7.450000e-13 86.1
26 TraesCS3D01G058900 chr5B 88.898 1171 93 22 674 1824 325965667 325964514 0.000000e+00 1408.0
27 TraesCS3D01G058900 chr5B 78.793 646 76 37 2469 3094 325962692 325962088 1.100000e-100 377.0
28 TraesCS3D01G058900 chr5B 94.915 59 2 1 2300 2358 325964081 325964024 1.600000e-14 91.6
29 TraesCS3D01G058900 chr5D 88.230 1198 97 23 674 1835 287017761 287016572 0.000000e+00 1391.0
30 TraesCS3D01G058900 chr5D 79.380 645 75 31 2469 3094 287015931 287015326 6.520000e-108 401.0
31 TraesCS3D01G058900 chr5D 81.250 128 10 8 1856 1976 287016512 287016392 1.600000e-14 91.6
32 TraesCS3D01G058900 chr1B 90.517 116 10 1 235 349 229263276 229263161 7.240000e-33 152.0
33 TraesCS3D01G058900 chr1B 87.786 131 13 2 241 370 57618134 57618262 2.610000e-32 150.0
34 TraesCS3D01G058900 chr1B 90.654 107 10 0 242 348 626498463 626498569 4.360000e-30 143.0
35 TraesCS3D01G058900 chr7B 90.991 111 10 0 240 350 15305659 15305769 2.610000e-32 150.0
36 TraesCS3D01G058900 chr7B 88.793 116 12 1 241 355 682034396 682034281 1.570000e-29 141.0
37 TraesCS3D01G058900 chr1D 88.696 115 13 0 242 356 452799 452913 1.570000e-29 141.0
38 TraesCS3D01G058900 chr1D 89.815 108 11 0 242 349 11419447 11419340 5.640000e-29 139.0
39 TraesCS3D01G058900 chr3A 75.275 182 43 2 2513 2693 456440834 456440654 7.450000e-13 86.1
40 TraesCS3D01G058900 chr4D 88.136 59 5 2 3601 3658 75407395 75407338 7.510000e-08 69.4


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 TraesCS3D01G058900 chr3D 25523602 25527785 4183 True 2629.333333 7727 98.581333 1 4184 3 chr3D.!!$R1 4183
1 TraesCS3D01G058900 chr7D 37658764 37662933 4169 False 7088.000000 7088 97.318000 1 4184 1 chr7D.!!$F4 4183
2 TraesCS3D01G058900 chr7D 37625515 37626240 725 False 854.000000 854 88.038000 816 1547 1 chr7D.!!$F3 731
3 TraesCS3D01G058900 chr2A 720353419 720354047 628 True 821.000000 821 90.236000 916 1547 1 chr2A.!!$R1 631
4 TraesCS3D01G058900 chr2A 720384683 720388858 4175 True 793.700000 2281 92.775000 1 4183 6 chr2A.!!$R2 4182
5 TraesCS3D01G058900 chr4A 687317374 687321186 3812 True 733.400000 1899 90.273000 816 4184 5 chr4A.!!$R1 3368
6 TraesCS3D01G058900 chr5A 379092788 379094448 1660 True 558.366667 1487 89.696667 674 2358 3 chr5A.!!$R1 1684
7 TraesCS3D01G058900 chr5B 325962088 325965667 3579 True 625.533333 1408 87.535333 674 3094 3 chr5B.!!$R1 2420
8 TraesCS3D01G058900 chr5D 287015326 287017761 2435 True 627.866667 1391 82.953333 674 3094 3 chr5D.!!$R1 2420

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
533 546 1.729284 TCGGAGGCGATTTTTGGTAC 58.271 50.000 0.0 0.0 0.0 3.34 F
569 582 1.758936 TCGCCCGTATTGAGAGAGAA 58.241 50.000 0.0 0.0 0.0 2.87 F
990 1040 3.323403 TGTCTTGCCCCCTTTGTTATTTG 59.677 43.478 0.0 0.0 0.0 2.32 F
2565 4257 4.998672 CGTGGTACTTAACTGGGAAAATCA 59.001 41.667 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 2404 1.352083 TCAGACTTCCCCTGGTTCAG 58.648 55.000 0.00 0.0 32.73 3.02 R
2284 2687 7.228507 TGTGGCATTGTCCATTATAAGATGTAC 59.771 37.037 0.00 0.0 38.57 2.90 R
2899 4615 3.756117 ACCATGGAAGACTCAAAACTCC 58.244 45.455 21.47 0.0 0.00 3.85 R
4019 6254 1.665735 CGTCAATTTTCGTTGCCCTGG 60.666 52.381 0.00 0.0 0.00 4.45 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
277 286 6.070538 TCCCAAAAAGTTTGTTCCTCAAATGA 60.071 34.615 0.00 0.00 45.88 2.57
366 375 7.069331 AGGGAGTATTCAACAAAAATGTGTGAA 59.931 33.333 8.13 8.13 0.00 3.18
367 376 7.169140 GGGAGTATTCAACAAAAATGTGTGAAC 59.831 37.037 7.96 0.00 0.00 3.18
368 377 7.704472 GGAGTATTCAACAAAAATGTGTGAACA 59.296 33.333 7.96 0.00 0.00 3.18
369 378 9.248291 GAGTATTCAACAAAAATGTGTGAACAT 57.752 29.630 7.96 0.00 0.00 2.71
370 379 9.033481 AGTATTCAACAAAAATGTGTGAACATG 57.967 29.630 0.00 0.00 0.00 3.21
462 475 1.811941 GCCCATGGAGTAGCAAGTAGC 60.812 57.143 15.22 0.00 46.19 3.58
533 546 1.729284 TCGGAGGCGATTTTTGGTAC 58.271 50.000 0.00 0.00 0.00 3.34
569 582 1.758936 TCGCCCGTATTGAGAGAGAA 58.241 50.000 0.00 0.00 0.00 2.87
990 1040 3.323403 TGTCTTGCCCCCTTTGTTATTTG 59.677 43.478 0.00 0.00 0.00 2.32
2565 4257 4.998672 CGTGGTACTTAACTGGGAAAATCA 59.001 41.667 0.00 0.00 0.00 2.57
2899 4615 5.485708 TCCCCCTTTTACCAATTTACCAATG 59.514 40.000 0.00 0.00 0.00 2.82
3695 5919 7.633018 TGTCTATTAGGCTCCCTCATATTTT 57.367 36.000 0.00 0.00 34.61 1.82
3800 6024 7.856145 AAAACCTTGTGAAATGTTATTTGCA 57.144 28.000 0.00 0.00 0.00 4.08
3806 6030 8.140677 CTTGTGAAATGTTATTTGCAAGGAAA 57.859 30.769 0.00 0.00 0.00 3.13
3817 6041 3.726557 TGCAAGGAAACCTCATGATCT 57.273 42.857 0.00 0.00 30.89 2.75
3857 6081 3.608316 TGTTGAGCCTTTGTTGCTTTT 57.392 38.095 0.00 0.00 39.69 2.27
3862 6086 4.870363 TGAGCCTTTGTTGCTTTTGATAC 58.130 39.130 0.00 0.00 39.69 2.24
3910 6143 4.281688 ACTGCCAAACATAAATCAGCACTT 59.718 37.500 0.00 0.00 0.00 3.16
3914 6147 6.867816 TGCCAAACATAAATCAGCACTTAAAG 59.132 34.615 0.00 0.00 0.00 1.85
3943 6176 8.314021 TCTTAAGATATGAAAGAAGCACTGTGA 58.686 33.333 12.86 0.00 0.00 3.58
3944 6177 8.846943 TTAAGATATGAAAGAAGCACTGTGAA 57.153 30.769 12.86 0.00 0.00 3.18
3954 6189 7.516198 AAGAAGCACTGTGAACTATGAAAAT 57.484 32.000 12.86 0.00 0.00 1.82
3969 6204 7.989826 ACTATGAAAATGCTACCAAATCTGAC 58.010 34.615 0.00 0.00 0.00 3.51
3972 6207 5.769662 TGAAAATGCTACCAAATCTGACAGT 59.230 36.000 1.59 0.00 0.00 3.55
3984 6219 6.352222 CCAAATCTGACAGTAGGTCCAATAGT 60.352 42.308 1.59 0.00 46.38 2.12
3987 6222 4.950475 TCTGACAGTAGGTCCAATAGTGAG 59.050 45.833 1.59 0.00 46.38 3.51
4019 6254 1.200716 CATCCATTCCAGCACACACAC 59.799 52.381 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.475135 GCCGTCCCTGAAGCTCCC 62.475 72.222 0.00 0.00 0.00 4.30
317 326 2.351350 CGTCCGGAAAAATTTGTCCCTG 60.351 50.000 19.86 12.29 0.00 4.45
366 375 0.621571 TCCTCCAAGCCTAGGCATGT 60.622 55.000 34.70 17.16 44.88 3.21
367 376 0.108207 CTCCTCCAAGCCTAGGCATG 59.892 60.000 34.70 31.33 44.88 4.06
368 377 1.704007 GCTCCTCCAAGCCTAGGCAT 61.704 60.000 34.70 22.07 44.88 4.40
369 378 2.370445 GCTCCTCCAAGCCTAGGCA 61.370 63.158 34.70 13.97 44.88 4.75
370 379 2.370445 TGCTCCTCCAAGCCTAGGC 61.370 63.158 27.19 27.19 41.77 3.93
462 475 1.576246 CGCAAACACGTACGTAGCTAG 59.424 52.381 22.34 10.93 0.00 3.42
463 476 1.605500 CGCAAACACGTACGTAGCTA 58.394 50.000 22.34 0.00 0.00 3.32
464 477 1.611592 GCGCAAACACGTACGTAGCT 61.612 55.000 22.34 5.38 34.88 3.32
465 478 1.225289 GCGCAAACACGTACGTAGC 60.225 57.895 22.34 19.89 34.88 3.58
533 546 3.125316 GGGCGAACAAACTTCACTAGATG 59.875 47.826 0.00 0.00 0.00 2.90
569 582 2.676342 GCCCTTGTGTATCGACGAAAAT 59.324 45.455 0.00 0.00 0.00 1.82
599 614 0.693049 TCAGCAGTTCCCTTTCTCCC 59.307 55.000 0.00 0.00 0.00 4.30
990 1040 4.443034 GGGATATCCGCCATTATGTCCTAC 60.443 50.000 15.69 0.00 34.68 3.18
2055 2404 1.352083 TCAGACTTCCCCTGGTTCAG 58.648 55.000 0.00 0.00 32.73 3.02
2284 2687 7.228507 TGTGGCATTGTCCATTATAAGATGTAC 59.771 37.037 0.00 0.00 38.57 2.90
2899 4615 3.756117 ACCATGGAAGACTCAAAACTCC 58.244 45.455 21.47 0.00 0.00 3.85
3695 5919 4.584638 ACCAGCATTATACTTTGACCCA 57.415 40.909 0.00 0.00 0.00 4.51
3800 6024 5.012893 GGAACAAGATCATGAGGTTTCCTT 58.987 41.667 4.68 0.00 31.76 3.36
3881 6109 4.220382 TGATTTATGTTTGGCAGTGGAAGG 59.780 41.667 0.00 0.00 0.00 3.46
3882 6110 5.389859 TGATTTATGTTTGGCAGTGGAAG 57.610 39.130 0.00 0.00 0.00 3.46
3920 6153 8.097038 AGTTCACAGTGCTTCTTTCATATCTTA 58.903 33.333 0.00 0.00 0.00 2.10
3935 6168 5.051891 AGCATTTTCATAGTTCACAGTGC 57.948 39.130 0.00 0.00 0.00 4.40
3937 6170 6.237901 TGGTAGCATTTTCATAGTTCACAGT 58.762 36.000 0.00 0.00 0.00 3.55
3943 6176 8.462016 GTCAGATTTGGTAGCATTTTCATAGTT 58.538 33.333 0.00 0.00 0.00 2.24
3944 6177 7.611467 TGTCAGATTTGGTAGCATTTTCATAGT 59.389 33.333 0.00 0.00 0.00 2.12
3954 6189 3.838317 ACCTACTGTCAGATTTGGTAGCA 59.162 43.478 6.91 0.00 31.47 3.49
3969 6204 2.766263 TGGCTCACTATTGGACCTACTG 59.234 50.000 0.00 0.00 0.00 2.74
3972 6207 3.384168 ACATGGCTCACTATTGGACCTA 58.616 45.455 0.00 0.00 0.00 3.08
3984 6219 5.769662 GGAATGGATGTTTATACATGGCTCA 59.230 40.000 3.33 0.00 44.90 4.26
3987 6222 5.565439 GCTGGAATGGATGTTTATACATGGC 60.565 44.000 3.33 0.00 44.90 4.40
4019 6254 1.665735 CGTCAATTTTCGTTGCCCTGG 60.666 52.381 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.