Multiple sequence alignment - TraesCS6A01G199400

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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 TraesCS6A01G199400 chr6A 100.000 2705 0 0 1 2705 315406056 315408760 0.000000e+00 4996
1 TraesCS6A01G199400 chr6A 87.511 1161 93 23 1243 2365 70063906 70065052 0.000000e+00 1293
2 TraesCS6A01G199400 chr6A 90.313 671 46 10 412 1070 70063245 70063908 0.000000e+00 861
3 TraesCS6A01G199400 chr7A 97.603 2712 45 8 1 2705 57964038 57961340 0.000000e+00 4630
4 TraesCS6A01G199400 chr4B 95.836 1633 60 5 1080 2705 633178312 633176681 0.000000e+00 2632
5 TraesCS6A01G199400 chr4B 96.753 1047 32 1 1 1047 633179353 633178309 0.000000e+00 1744
6 TraesCS6A01G199400 chr4B 86.822 1161 101 22 1243 2365 125739564 125740710 0.000000e+00 1249
7 TraesCS6A01G199400 chr3D 87.849 2222 179 44 412 2583 33867197 33865017 0.000000e+00 2523
8 TraesCS6A01G199400 chr2A 86.359 2104 203 42 518 2577 552865042 552862979 0.000000e+00 2218
9 TraesCS6A01G199400 chr2A 86.911 573 46 7 1848 2393 445929320 445928750 1.380000e-172 616
10 TraesCS6A01G199400 chr2A 96.000 125 5 0 2579 2703 552862572 552862448 1.270000e-48 204
11 TraesCS6A01G199400 chr7B 88.672 1483 111 19 412 1872 1757851 1759298 0.000000e+00 1755
12 TraesCS6A01G199400 chr7B 88.427 1011 78 16 1418 2393 693933330 693932324 0.000000e+00 1182
13 TraesCS6A01G199400 chr7B 95.868 121 5 0 2583 2703 693932034 693931914 2.120000e-46 196
14 TraesCS6A01G199400 chr5A 98.384 928 14 1 1 928 436605095 436606021 0.000000e+00 1629
15 TraesCS6A01G199400 chr5A 98.049 615 10 2 2092 2705 436608118 436608731 0.000000e+00 1068
16 TraesCS6A01G199400 chr4D 86.352 1165 90 32 1243 2365 487999872 488001009 0.000000e+00 1206
17 TraesCS6A01G199400 chr4D 90.105 667 49 11 412 1070 487999217 487999874 0.000000e+00 850
18 TraesCS6A01G199400 chr1A 86.866 1104 107 21 521 1612 517327301 517328378 0.000000e+00 1201
19 TraesCS6A01G199400 chr1A 87.195 1023 78 25 1593 2580 517328964 517329968 0.000000e+00 1114
20 TraesCS6A01G199400 chr1A 96.000 125 5 0 2579 2703 517330339 517330463 1.270000e-48 204
21 TraesCS6A01G199400 chr1A 90.833 120 8 1 412 528 517325761 517325880 1.000000e-34 158
22 TraesCS6A01G199400 chr3B 87.773 1006 77 16 1418 2387 8745307 8744312 0.000000e+00 1134
23 TraesCS6A01G199400 chr3B 96.694 121 4 0 2583 2703 8744017 8743897 4.570000e-48 202
24 TraesCS6A01G199400 chr3A 87.065 804 87 11 821 1613 36801821 36801024 0.000000e+00 893
25 TraesCS6A01G199400 chr3A 84.588 571 59 6 2031 2575 36800548 36799981 8.520000e-150 540
26 TraesCS6A01G199400 chr4A 88.408 578 47 15 1826 2393 293331393 293330826 0.000000e+00 678
27 TraesCS6A01G199400 chr2B 92.424 264 17 3 2318 2580 541601761 541602022 9.150000e-100 374
28 TraesCS6A01G199400 chr2B 93.798 129 7 1 2576 2703 541602335 541602463 2.750000e-45 193
29 TraesCS6A01G199400 chr1B 92.975 242 14 2 1147 1385 54951361 54951120 1.540000e-92 350
30 TraesCS6A01G199400 chr5D 97.521 121 3 0 2583 2703 548609867 548609987 9.820000e-50 207


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 TraesCS6A01G199400 chr6A 315406056 315408760 2704 False 4996.00 4996 100.0000 1 2705 1 chr6A.!!$F1 2704
1 TraesCS6A01G199400 chr6A 70063245 70065052 1807 False 1077.00 1293 88.9120 412 2365 2 chr6A.!!$F2 1953
2 TraesCS6A01G199400 chr7A 57961340 57964038 2698 True 4630.00 4630 97.6030 1 2705 1 chr7A.!!$R1 2704
3 TraesCS6A01G199400 chr4B 633176681 633179353 2672 True 2188.00 2632 96.2945 1 2705 2 chr4B.!!$R1 2704
4 TraesCS6A01G199400 chr4B 125739564 125740710 1146 False 1249.00 1249 86.8220 1243 2365 1 chr4B.!!$F1 1122
5 TraesCS6A01G199400 chr3D 33865017 33867197 2180 True 2523.00 2523 87.8490 412 2583 1 chr3D.!!$R1 2171
6 TraesCS6A01G199400 chr2A 552862448 552865042 2594 True 1211.00 2218 91.1795 518 2703 2 chr2A.!!$R2 2185
7 TraesCS6A01G199400 chr2A 445928750 445929320 570 True 616.00 616 86.9110 1848 2393 1 chr2A.!!$R1 545
8 TraesCS6A01G199400 chr7B 1757851 1759298 1447 False 1755.00 1755 88.6720 412 1872 1 chr7B.!!$F1 1460
9 TraesCS6A01G199400 chr7B 693931914 693933330 1416 True 689.00 1182 92.1475 1418 2703 2 chr7B.!!$R1 1285
10 TraesCS6A01G199400 chr5A 436605095 436608731 3636 False 1348.50 1629 98.2165 1 2705 2 chr5A.!!$F1 2704
11 TraesCS6A01G199400 chr4D 487999217 488001009 1792 False 1028.00 1206 88.2285 412 2365 2 chr4D.!!$F1 1953
12 TraesCS6A01G199400 chr1A 517325761 517330463 4702 False 669.25 1201 90.2235 412 2703 4 chr1A.!!$F1 2291
13 TraesCS6A01G199400 chr3B 8743897 8745307 1410 True 668.00 1134 92.2335 1418 2703 2 chr3B.!!$R1 1285
14 TraesCS6A01G199400 chr3A 36799981 36801821 1840 True 716.50 893 85.8265 821 2575 2 chr3A.!!$R1 1754
15 TraesCS6A01G199400 chr4A 293330826 293331393 567 True 678.00 678 88.4080 1826 2393 1 chr4A.!!$R1 567
16 TraesCS6A01G199400 chr2B 541601761 541602463 702 False 283.50 374 93.1110 2318 2703 2 chr2B.!!$F1 385

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
769 2213 2.158871 CCTTGGCGCCCTACTATTTACA 60.159 50.000 26.77 0.0 0.00 2.41 F
1179 2654 4.480480 CCTCTGGGGAAGTAGGCA 57.520 61.111 0.00 0.0 37.23 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1603 4277 1.102978 GTTGTTGGTGGTTCAGCTGT 58.897 50.000 14.67 0.0 32.61 4.40 R
2580 6393 5.479306 TCGAGTCCAAAGGTCTAAGAAATG 58.521 41.667 0.00 0.0 0.00 2.32 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
96 97 5.105997 GCTCTAAAACAGGACATGCATTTCT 60.106 40.000 12.39 0.47 0.00 2.52
224 225 6.458751 GCTTCAGTTTCAGAATTTCAGTCACA 60.459 38.462 0.00 0.00 0.00 3.58
406 407 4.249661 CAGTTCTAGAAGGAGCTCAAACC 58.750 47.826 17.19 0.00 0.00 3.27
736 2180 7.765695 TGGAAAATTGCATTTCTCTAGTCTT 57.234 32.000 11.51 0.00 38.92 3.01
769 2213 2.158871 CCTTGGCGCCCTACTATTTACA 60.159 50.000 26.77 0.00 0.00 2.41
1179 2654 4.480480 CCTCTGGGGAAGTAGGCA 57.520 61.111 0.00 0.00 37.23 4.75
1300 3347 4.639135 ACTCAAGCACCTCTTTTTGAAC 57.361 40.909 0.00 0.00 31.27 3.18
1311 3358 5.473504 ACCTCTTTTTGAACGTTATGCATCT 59.526 36.000 0.19 0.00 0.00 2.90
1603 4277 5.398603 TTTGCAGAAACAACCTGAAGAAA 57.601 34.783 0.00 0.00 33.65 2.52
1740 4504 5.697826 CATCAAGTTCTCTTTTCTCAAGGC 58.302 41.667 0.00 0.00 0.00 4.35
2313 6124 9.995003 AAAATACTTGACCATTATTTTTCTGCA 57.005 25.926 0.00 0.00 33.56 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 6.381801 CACTCAGGAAATAACATGTCCAAAC 58.618 40.000 0.00 0.0 33.57 2.93
96 97 3.133901 TGTCAGAGTTTGGAGCTGTTACA 59.866 43.478 0.00 0.0 0.00 2.41
406 407 6.771749 AGGAAATTCAGAGGCATGAGAAATAG 59.228 38.462 0.00 0.0 0.00 1.73
736 2180 1.877443 GCGCCAAGGAAGAACAAACTA 59.123 47.619 0.00 0.0 0.00 2.24
795 2239 7.566879 AGATAGGAGAAGTGGACATTCATTACT 59.433 37.037 0.00 0.0 0.00 2.24
873 2320 5.010213 GGTTAAAACTGCACTATCCACCAAA 59.990 40.000 0.00 0.0 0.00 3.28
1213 3260 4.085357 ACACTTAGCAATGACAACTCCA 57.915 40.909 0.00 0.0 0.00 3.86
1262 3309 5.125417 GCTTGAGTTTACCAATTCATGCCTA 59.875 40.000 6.93 0.0 40.83 3.93
1300 3347 5.991328 ACCAACTAATCAGATGCATAACG 57.009 39.130 0.00 0.0 0.00 3.18
1447 3504 9.495572 TGATGTGTATGTGTGACTAACAATTAA 57.504 29.630 0.00 0.0 41.57 1.40
1603 4277 1.102978 GTTGTTGGTGGTTCAGCTGT 58.897 50.000 14.67 0.0 32.61 4.40
1740 4504 5.707298 ACCTAGTGTTTCCACATTTCTGATG 59.293 40.000 0.00 0.0 44.39 3.07
1878 4834 6.716898 CAAAGATTGCCCAAAAGAAGAATC 57.283 37.500 0.00 0.0 0.00 2.52
2313 6124 7.394359 ACATGTGGACTGAACTAAATATGCTTT 59.606 33.333 0.00 0.0 0.00 3.51
2580 6393 5.479306 TCGAGTCCAAAGGTCTAAGAAATG 58.521 41.667 0.00 0.0 0.00 2.32


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

AutoCloner maintained by Alex Coulton.