Multiple sequence alignment - TraesCS3A01G001300

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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 TraesCS3A01G001300 chr3A 100.000 2378 0 0 1 2378 913421 911044 0.000000e+00 4392
1 TraesCS3A01G001300 chr4A 97.040 2399 38 4 12 2378 616307158 616304761 0.000000e+00 4006
2 TraesCS3A01G001300 chr2A 96.956 2398 39 5 12 2378 597215999 597218393 0.000000e+00 3993
3 TraesCS3A01G001300 chr6A 96.460 2401 45 4 17 2378 18029828 18032227 0.000000e+00 3927
4 TraesCS3A01G001300 chr3D 92.896 2407 82 20 12 2378 598248526 598250883 0.000000e+00 3415
5 TraesCS3A01G001300 chr3D 90.468 2329 115 38 91 2378 181205586 181203324 0.000000e+00 2972
6 TraesCS3A01G001300 chr4B 91.680 2416 108 23 13 2378 633799123 633801495 0.000000e+00 3262
7 TraesCS3A01G001300 chr1B 91.153 2419 122 22 12 2378 517558070 517555692 0.000000e+00 3197
8 TraesCS3A01G001300 chr6B 92.854 2155 106 16 14 2142 633372918 633375050 0.000000e+00 3083
9 TraesCS3A01G001300 chr6B 90.751 1438 118 10 798 2230 143714156 143715583 0.000000e+00 1905
10 TraesCS3A01G001300 chr6B 86.716 271 6 1 2138 2378 633389167 633389437 8.370000e-70 274
11 TraesCS3A01G001300 chr6D 93.162 1872 116 6 363 2227 111523673 111525539 0.000000e+00 2737
12 TraesCS3A01G001300 chr6D 91.453 351 23 2 12 361 111512199 111512543 2.140000e-130 475
13 TraesCS3A01G001300 chr7A 91.439 1320 98 6 919 2230 680112050 680113362 0.000000e+00 1797
14 TraesCS3A01G001300 chr7A 83.357 715 54 26 16 717 680858128 680857466 3.380000e-168 601
15 TraesCS3A01G001300 chr3B 91.383 824 41 14 1585 2378 203552439 203551616 0.000000e+00 1101
16 TraesCS3A01G001300 chr3B 83.292 401 54 9 665 1064 750677708 750677320 8.080000e-95 357
17 TraesCS3A01G001300 chr3B 73.592 746 107 56 12 711 750678421 750677720 1.110000e-48 204
18 TraesCS3A01G001300 chr7B 86.294 912 72 24 105 988 637648005 637648891 0.000000e+00 942
19 TraesCS3A01G001300 chr2D 93.190 558 32 5 12 567 584979239 584978686 0.000000e+00 815


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 TraesCS3A01G001300 chr3A 911044 913421 2377 True 4392.0 4392 100.000 1 2378 1 chr3A.!!$R1 2377
1 TraesCS3A01G001300 chr4A 616304761 616307158 2397 True 4006.0 4006 97.040 12 2378 1 chr4A.!!$R1 2366
2 TraesCS3A01G001300 chr2A 597215999 597218393 2394 False 3993.0 3993 96.956 12 2378 1 chr2A.!!$F1 2366
3 TraesCS3A01G001300 chr6A 18029828 18032227 2399 False 3927.0 3927 96.460 17 2378 1 chr6A.!!$F1 2361
4 TraesCS3A01G001300 chr3D 598248526 598250883 2357 False 3415.0 3415 92.896 12 2378 1 chr3D.!!$F1 2366
5 TraesCS3A01G001300 chr3D 181203324 181205586 2262 True 2972.0 2972 90.468 91 2378 1 chr3D.!!$R1 2287
6 TraesCS3A01G001300 chr4B 633799123 633801495 2372 False 3262.0 3262 91.680 13 2378 1 chr4B.!!$F1 2365
7 TraesCS3A01G001300 chr1B 517555692 517558070 2378 True 3197.0 3197 91.153 12 2378 1 chr1B.!!$R1 2366
8 TraesCS3A01G001300 chr6B 633372918 633375050 2132 False 3083.0 3083 92.854 14 2142 1 chr6B.!!$F2 2128
9 TraesCS3A01G001300 chr6B 143714156 143715583 1427 False 1905.0 1905 90.751 798 2230 1 chr6B.!!$F1 1432
10 TraesCS3A01G001300 chr6D 111523673 111525539 1866 False 2737.0 2737 93.162 363 2227 1 chr6D.!!$F2 1864
11 TraesCS3A01G001300 chr7A 680112050 680113362 1312 False 1797.0 1797 91.439 919 2230 1 chr7A.!!$F1 1311
12 TraesCS3A01G001300 chr7A 680857466 680858128 662 True 601.0 601 83.357 16 717 1 chr7A.!!$R1 701
13 TraesCS3A01G001300 chr3B 203551616 203552439 823 True 1101.0 1101 91.383 1585 2378 1 chr3B.!!$R1 793
14 TraesCS3A01G001300 chr3B 750677320 750678421 1101 True 280.5 357 78.442 12 1064 2 chr3B.!!$R2 1052
15 TraesCS3A01G001300 chr7B 637648005 637648891 886 False 942.0 942 86.294 105 988 1 chr7B.!!$F1 883
16 TraesCS3A01G001300 chr2D 584978686 584979239 553 True 815.0 815 93.190 12 567 1 chr2D.!!$R1 555

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
181 186 0.253044 TGAGGCAGCCCATTGTCTAC 59.747 55.0 8.22 0.0 32.08 2.59 F
750 923 0.464373 ATATTGTCCACGCAGCAGGG 60.464 55.0 1.21 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1176 1366 0.451383 CTGTGTCAGGAGCTCTCTCG 59.549 60.0 14.64 4.86 40.26 4.04 R
2284 2510 2.026262 GGGTTAGTTGAAGCTGATGGGA 60.026 50.0 0.00 0.00 35.76 4.37 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
181 186 0.253044 TGAGGCAGCCCATTGTCTAC 59.747 55.000 8.22 0.00 32.08 2.59
199 204 1.924731 ACTTCTCCTCATCACCACGA 58.075 50.000 0.00 0.00 0.00 4.35
401 462 3.324930 CAGGGTCCAGAGCTGCCA 61.325 66.667 0.00 0.00 0.00 4.92
508 588 0.969149 CCTTGCCCCTTTTGGTTCTC 59.031 55.000 0.00 0.00 38.10 2.87
741 914 4.666237 GCTTTTGCTCTCATATTGTCCAC 58.334 43.478 0.00 0.00 43.35 4.02
750 923 0.464373 ATATTGTCCACGCAGCAGGG 60.464 55.000 1.21 0.00 0.00 4.45
1176 1366 2.159382 CACACAATACCACCTGAACCC 58.841 52.381 0.00 0.00 0.00 4.11
1189 1379 0.967887 TGAACCCGAGAGAGCTCCTG 60.968 60.000 10.93 0.00 37.91 3.86
1439 1630 2.278013 CGGAGGTAAGCGTCGCTC 60.278 66.667 21.98 8.92 38.25 5.03
1577 1770 7.947890 AGATAGTTTTGTTAATGGAGGGTTCAA 59.052 33.333 0.00 0.00 0.00 2.69
1939 2133 8.658499 TTGTCAGATGATAGATCACAAGATTG 57.342 34.615 0.00 0.00 40.03 2.67
2014 2210 3.882888 GGAACTTGGTGATGAGTGTTTCA 59.117 43.478 0.00 0.00 40.85 2.69
2284 2510 7.870509 TCTGCTTATTATGTTCATTGCTTCT 57.129 32.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 160 2.562298 CAATGGGCTGCCTCACTTTTTA 59.438 45.455 19.68 0.00 0.00 1.52
181 186 2.611518 GTTCGTGGTGATGAGGAGAAG 58.388 52.381 0.00 0.00 0.00 2.85
214 219 2.617274 GCGAGTGACTTGGGCCAAC 61.617 63.158 16.66 6.39 0.00 3.77
508 588 7.118390 CCACCTACAACAGAGATTAGAAAGTTG 59.882 40.741 0.00 0.00 41.37 3.16
621 728 5.064441 CCAATTTCTGGGTCAAGTGATTC 57.936 43.478 0.00 0.00 42.17 2.52
717 885 3.375299 GGACAATATGAGAGCAAAAGCGT 59.625 43.478 0.00 0.00 0.00 5.07
741 914 3.121030 GTACTGCACCCTGCTGCG 61.121 66.667 0.00 0.00 44.72 5.18
750 923 2.221981 GTCTTGCACTTCTGTACTGCAC 59.778 50.000 6.25 0.00 35.07 4.57
1176 1366 0.451383 CTGTGTCAGGAGCTCTCTCG 59.549 60.000 14.64 4.86 40.26 4.04
1189 1379 0.464554 GCTATTGGGGCCTCTGTGTC 60.465 60.000 3.07 0.00 0.00 3.67
1346 1536 3.778075 TGCAATGTAGGCCCTTCTAACTA 59.222 43.478 0.00 0.00 0.00 2.24
1583 1776 9.255304 GCTTACGAAATCTCTCTTTCATATTCT 57.745 33.333 0.00 0.00 35.32 2.40
1595 1788 3.201290 CCAGCATGCTTACGAAATCTCT 58.799 45.455 19.98 0.00 31.97 3.10
1939 2133 7.862873 AGCACAAGAACTAATAAGCTGTTTTTC 59.137 33.333 0.00 0.00 0.00 2.29
2284 2510 2.026262 GGGTTAGTTGAAGCTGATGGGA 60.026 50.000 0.00 0.00 35.76 4.37


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

AutoCloner maintained by Alex Coulton.