Multiple sequence alignment - TraesCS5A01G132000

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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 TraesCS5A01G132000 chr5A 100.000 2396 0 0 1 2396 297721117 297723512 0.000000e+00 4425
1 TraesCS5A01G132000 chr5A 76.094 891 162 31 1 854 42281400 42282276 3.680000e-113 418
2 TraesCS5A01G132000 chr5A 77.235 716 135 22 17 722 22057007 22057704 6.210000e-106 394
3 TraesCS5A01G132000 chr5A 93.210 162 8 2 1752 1910 605231304 605231143 3.980000e-58 235
4 TraesCS5A01G132000 chr5A 91.228 171 11 3 1743 1910 320214236 320214405 1.850000e-56 230
5 TraesCS5A01G132000 chr5B 96.440 2416 65 10 1 2396 248388445 248390859 0.000000e+00 3965
6 TraesCS5A01G132000 chr5B 76.089 895 168 30 1 867 57116074 57116950 2.200000e-115 425
7 TraesCS5A01G132000 chr5B 77.063 715 139 22 17 722 24772968 24773666 2.890000e-104 388
8 TraesCS5A01G132000 chr3D 78.723 658 120 10 1 649 442975295 442975941 2.850000e-114 422
9 TraesCS5A01G132000 chr3D 93.827 162 7 3 1752 1910 449740443 449740282 8.560000e-60 241
10 TraesCS5A01G132000 chr5D 77.841 704 128 25 17 710 37049463 37048778 6.160000e-111 411
11 TraesCS5A01G132000 chr5D 77.525 703 132 23 17 710 33046353 33047038 1.330000e-107 399
12 TraesCS5A01G132000 chr5D 76.611 714 143 21 17 722 33052741 33053438 2.910000e-99 372
13 TraesCS5A01G132000 chr5D 76.676 716 139 22 17 722 37043066 37042369 2.910000e-99 372
14 TraesCS5A01G132000 chr3A 76.083 577 125 13 59 630 699105825 699105257 3.010000e-74 289
15 TraesCS5A01G132000 chr3A 93.210 162 8 2 1752 1910 600921016 600920855 3.980000e-58 235
16 TraesCS5A01G132000 chr3A 83.085 201 30 4 59 256 699545742 699545941 1.890000e-41 180
17 TraesCS5A01G132000 chr3B 93.413 167 7 3 1752 1915 154663205 154663040 6.620000e-61 244
18 TraesCS5A01G132000 chr3B 80.321 249 40 8 16 256 752915845 752915598 1.890000e-41 180
19 TraesCS5A01G132000 chr7B 92.771 166 9 3 1748 1910 102234313 102234478 1.110000e-58 237
20 TraesCS5A01G132000 chr7A 93.252 163 8 2 1751 1910 494786991 494786829 1.110000e-58 237
21 TraesCS5A01G132000 chr1D 93.252 163 7 3 1752 1911 30100423 30100584 1.110000e-58 237


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 TraesCS5A01G132000 chr5A 297721117 297723512 2395 False 4425 4425 100.000 1 2396 1 chr5A.!!$F3 2395
1 TraesCS5A01G132000 chr5A 42281400 42282276 876 False 418 418 76.094 1 854 1 chr5A.!!$F2 853
2 TraesCS5A01G132000 chr5A 22057007 22057704 697 False 394 394 77.235 17 722 1 chr5A.!!$F1 705
3 TraesCS5A01G132000 chr5B 248388445 248390859 2414 False 3965 3965 96.440 1 2396 1 chr5B.!!$F3 2395
4 TraesCS5A01G132000 chr5B 57116074 57116950 876 False 425 425 76.089 1 867 1 chr5B.!!$F2 866
5 TraesCS5A01G132000 chr5B 24772968 24773666 698 False 388 388 77.063 17 722 1 chr5B.!!$F1 705
6 TraesCS5A01G132000 chr3D 442975295 442975941 646 False 422 422 78.723 1 649 1 chr3D.!!$F1 648
7 TraesCS5A01G132000 chr5D 37048778 37049463 685 True 411 411 77.841 17 710 1 chr5D.!!$R2 693
8 TraesCS5A01G132000 chr5D 33046353 33047038 685 False 399 399 77.525 17 710 1 chr5D.!!$F1 693
9 TraesCS5A01G132000 chr5D 33052741 33053438 697 False 372 372 76.611 17 722 1 chr5D.!!$F2 705
10 TraesCS5A01G132000 chr5D 37042369 37043066 697 True 372 372 76.676 17 722 1 chr5D.!!$R1 705
11 TraesCS5A01G132000 chr3A 699105257 699105825 568 True 289 289 76.083 59 630 1 chr3A.!!$R2 571

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
276 285 1.336887 GCAGTAGTGCCACGAAAGAGA 60.337 52.381 11.74 0.0 44.72 3.10 F
1075 1121 1.364328 AGGAGGGAGGTCTGTCTGATT 59.636 52.381 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 1432 0.338120 ACCCTCCTAGCAGCTCTCTT 59.662 55.0 0.0 0.0 0.0 2.85 R
1960 2012 0.890683 CAACTTTGCCCCCATCAGTC 59.109 55.0 0.0 0.0 0.0 3.51 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
46 47 8.927721 TCGAATTTGAAACACGATGACTTTATA 58.072 29.630 4.64 0.00 0.00 0.98
219 222 4.712476 ACTGCATCCAAGTATCCATCTTC 58.288 43.478 0.00 0.00 0.00 2.87
276 285 1.336887 GCAGTAGTGCCACGAAAGAGA 60.337 52.381 11.74 0.00 44.72 3.10
602 617 1.918262 AGGGCCAGTCATCTCAATGAA 59.082 47.619 6.18 0.00 43.42 2.57
724 769 8.640063 TCAAATACATGGCAGCATAGAATAAT 57.360 30.769 0.00 0.00 0.00 1.28
768 813 4.525912 AAATCTGGCTGAACATGAAACC 57.474 40.909 0.00 0.00 0.00 3.27
867 913 2.205074 CATCCTCGAAGGCACATGTAC 58.795 52.381 0.00 0.00 34.61 2.90
880 926 5.007626 AGGCACATGTACGCACATATAAAAG 59.992 40.000 10.05 0.00 43.73 2.27
895 941 8.960591 CACATATAAAAGTCCTCAAAGTGGAAT 58.039 33.333 0.00 0.00 35.10 3.01
932 978 5.402398 GCCGCAGATCTTTGTTCTTTATTT 58.598 37.500 0.00 0.00 0.00 1.40
1004 1050 3.748568 GGGAGTGACAAAACAGAGATGTC 59.251 47.826 0.00 0.00 42.90 3.06
1047 1093 4.637771 GGTCCAATGGAGGAACCG 57.362 61.111 0.27 0.00 39.57 4.44
1075 1121 1.364328 AGGAGGGAGGTCTGTCTGATT 59.636 52.381 0.00 0.00 0.00 2.57
1138 1184 3.540314 ATGATGCAGAGGAAGAGTGTC 57.460 47.619 0.00 0.00 0.00 3.67
1229 1279 6.488683 TCTTTACTTATTGTTGGTTCACAGGG 59.511 38.462 0.00 0.00 0.00 4.45
1254 1304 2.421424 GCTTGTCCAATCCACTGATGAC 59.579 50.000 0.00 0.00 0.00 3.06
1382 1432 5.186021 GTGAGACTATGAGAGGGTTGAAGAA 59.814 44.000 0.00 0.00 0.00 2.52
1503 1553 9.975218 TTAAAGCTTTAGAAATAGGGATTGACT 57.025 29.630 17.91 0.00 0.00 3.41
1534 1584 9.753674 TTTACTTCCTCTGGAAACATTTGATAT 57.246 29.630 0.53 0.00 41.54 1.63
1581 1631 9.330063 CTAGGTCAATAACTTGCATCATAAGAA 57.670 33.333 0.00 0.00 32.11 2.52
1582 1632 7.989826 AGGTCAATAACTTGCATCATAAGAAC 58.010 34.615 0.00 0.00 32.11 3.01
1667 1717 9.418839 TGGATGATATTGTTGATGATTTTACCA 57.581 29.630 0.00 0.00 0.00 3.25
1678 1728 6.591935 TGATGATTTTACCATGGTAGTCTCC 58.408 40.000 23.40 16.71 31.71 3.71
1910 1962 9.725206 ACTTATATTTAGGAACAGAGGGAGTAA 57.275 33.333 0.00 0.00 0.00 2.24
1946 1998 3.754965 ACTGTGCAAACCAGATGTATGT 58.245 40.909 9.59 0.00 34.04 2.29
1960 2012 9.388506 ACCAGATGTATGTTGAGAAATAAGAAG 57.611 33.333 0.00 0.00 0.00 2.85
1972 2024 3.584733 AATAAGAAGACTGATGGGGGC 57.415 47.619 0.00 0.00 0.00 5.80
1973 2025 1.965414 TAAGAAGACTGATGGGGGCA 58.035 50.000 0.00 0.00 0.00 5.36
2175 2227 3.691609 GGGCTACAGGAAACAATGAAGAG 59.308 47.826 0.00 0.00 0.00 2.85
2198 2250 9.071276 AGAGAAATTATTCTGCAAGTTTCTTCA 57.929 29.630 7.72 0.00 45.91 3.02
2216 2269 7.666063 TTCTTCAGGAAGATGATCATACTGA 57.334 36.000 19.60 19.60 45.78 3.41
2252 2305 4.508662 CACTAGATTCCCTCTGTTGGAAC 58.491 47.826 0.00 0.00 44.30 3.62
2267 2320 5.942961 TGTTGGAACCCTGTAGATTTAACA 58.057 37.500 0.00 0.00 0.00 2.41
2268 2321 6.548321 TGTTGGAACCCTGTAGATTTAACAT 58.452 36.000 0.00 0.00 0.00 2.71
2271 2324 8.456471 GTTGGAACCCTGTAGATTTAACATTAC 58.544 37.037 0.00 0.00 0.00 1.89
2272 2325 7.924541 TGGAACCCTGTAGATTTAACATTACT 58.075 34.615 0.00 0.00 0.00 2.24
2273 2326 7.827236 TGGAACCCTGTAGATTTAACATTACTG 59.173 37.037 0.00 0.00 0.00 2.74
2274 2327 8.044908 GGAACCCTGTAGATTTAACATTACTGA 58.955 37.037 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 3.515316 CTTGGTCGACCGTGCCAGT 62.515 63.158 28.70 0.00 39.43 4.00
219 222 1.736126 AGAAGATGCGTGATTGCTGTG 59.264 47.619 0.00 0.00 35.36 3.66
602 617 5.823861 AATAATGGTTTTGCAGGGTTCTT 57.176 34.783 0.00 0.00 0.00 2.52
768 813 4.514545 TGCGCGATTTATCAAGTGTTAG 57.485 40.909 12.10 0.00 0.00 2.34
867 913 6.250819 CACTTTGAGGACTTTTATATGTGCG 58.749 40.000 0.00 0.00 0.00 5.34
880 926 3.140325 TGGTGATTCCACTTTGAGGAC 57.860 47.619 0.00 0.00 41.93 3.85
895 941 2.358125 CGGCGTTGGTGATGGTGA 60.358 61.111 0.00 0.00 0.00 4.02
957 1003 7.845066 GGACTTAACCGACTCTTTCATAAAT 57.155 36.000 0.00 0.00 0.00 1.40
982 1028 3.744660 ACATCTCTGTTTTGTCACTCCC 58.255 45.455 0.00 0.00 28.70 4.30
1004 1050 4.811557 GGTGGTCCTGATATTCTTTCTTCG 59.188 45.833 0.00 0.00 0.00 3.79
1032 1078 0.618458 CTTCCGGTTCCTCCATTGGA 59.382 55.000 5.05 5.05 35.57 3.53
1047 1093 0.906066 GACCTCCCTCCTGTTCTTCC 59.094 60.000 0.00 0.00 0.00 3.46
1229 1279 1.267806 CAGTGGATTGGACAAGCACAC 59.732 52.381 11.37 11.37 32.22 3.82
1254 1304 3.741249 AGCAGCATCATCTCCAGTAATG 58.259 45.455 0.00 0.00 0.00 1.90
1326 1376 3.444742 CCATTTGAGCAATTCTGGCACTA 59.555 43.478 0.00 0.00 0.00 2.74
1382 1432 0.338120 ACCCTCCTAGCAGCTCTCTT 59.662 55.000 0.00 0.00 0.00 2.85
1444 1494 9.170734 TCATCATCAGATAAAACAGAAAAGGAG 57.829 33.333 0.00 0.00 31.88 3.69
1503 1553 5.935945 TGTTTCCAGAGGAAGTAAATCACA 58.064 37.500 0.00 0.00 43.06 3.58
1581 1631 5.762179 TTTCTCCACCTCATCATTACAGT 57.238 39.130 0.00 0.00 0.00 3.55
1582 1632 7.636150 ATTTTTCTCCACCTCATCATTACAG 57.364 36.000 0.00 0.00 0.00 2.74
1656 1706 6.386927 TCTGGAGACTACCATGGTAAAATCAT 59.613 38.462 24.59 12.10 39.34 2.45
1667 1717 6.523035 TTCTAGAGATCTGGAGACTACCAT 57.477 41.667 0.00 0.00 39.34 3.55
1678 1728 9.875675 CTTTTTCAAAGTGTTTCTAGAGATCTG 57.124 33.333 0.00 0.00 0.00 2.90
1807 1857 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
1840 1892 9.647918 ATGGACTACATACGGATGAATATAGAT 57.352 33.333 16.36 0.00 38.26 1.98
1900 1952 6.794534 ACCTTGATTCAAATTTACTCCCTCT 58.205 36.000 0.01 0.00 0.00 3.69
1910 1962 6.403866 TTGCACAGTACCTTGATTCAAATT 57.596 33.333 0.01 0.00 0.00 1.82
1946 1998 6.418101 CCCCATCAGTCTTCTTATTTCTCAA 58.582 40.000 0.00 0.00 0.00 3.02
1960 2012 0.890683 CAACTTTGCCCCCATCAGTC 59.109 55.000 0.00 0.00 0.00 3.51
1972 2024 3.094572 AGGATGGGATTCAGCAACTTTG 58.905 45.455 0.00 0.00 32.50 2.77
1973 2025 3.463048 AGGATGGGATTCAGCAACTTT 57.537 42.857 0.00 0.00 32.50 2.66
2175 2227 8.299570 TCCTGAAGAAACTTGCAGAATAATTTC 58.700 33.333 0.00 0.00 0.00 2.17
2216 2269 6.097412 GGGAATCTAGTGCCAAGAAAATTGAT 59.903 38.462 0.00 0.00 0.00 2.57
2282 2347 7.380536 TGAATTTTGATGTGAAATCTCCCTTG 58.619 34.615 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.