Multiple sequence alignment - TraesCS6A01G048900

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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 TraesCS6A01G048900 chr6A 100.000 3197 0 0 1 3197 24920546 24923742 0.000000e+00 5904
1 TraesCS6A01G048900 chr6A 85.437 206 22 8 239 439 269531877 269531675 1.160000e-49 207
2 TraesCS6A01G048900 chr6B 91.913 2770 165 28 432 3197 43383697 43386411 0.000000e+00 3819
3 TraesCS6A01G048900 chr6B 89.894 1890 148 24 1318 3197 43436604 43438460 0.000000e+00 2392
4 TraesCS6A01G048900 chr6B 90.403 1688 124 9 1531 3197 43481166 43482836 0.000000e+00 2185
5 TraesCS6A01G048900 chr6B 92.313 1405 98 8 1797 3197 43476055 43477453 0.000000e+00 1988
6 TraesCS6A01G048900 chr6B 88.520 1655 151 22 1358 2997 43868604 43870234 0.000000e+00 1967
7 TraesCS6A01G048900 chr6B 87.294 1637 157 32 1359 2989 43922989 43924580 0.000000e+00 1823
8 TraesCS6A01G048900 chr6B 91.496 1317 65 13 432 1747 43474403 43475673 0.000000e+00 1768
9 TraesCS6A01G048900 chr6B 90.472 1102 73 10 432 1531 43867742 43868813 0.000000e+00 1424
10 TraesCS6A01G048900 chr6B 94.167 240 13 1 1 240 44060936 44061174 6.520000e-97 364
11 TraesCS6A01G048900 chr6B 92.917 240 17 0 1 240 43857161 43857400 1.820000e-92 350
12 TraesCS6A01G048900 chr6B 92.917 240 17 0 1 240 43867506 43867745 1.820000e-92 350
13 TraesCS6A01G048900 chr6B 88.945 199 21 1 3000 3197 44063785 44063983 8.860000e-61 244
14 TraesCS6A01G048900 chr6B 86.449 214 19 8 237 440 460164540 460164327 3.210000e-55 226
15 TraesCS6A01G048900 chr6B 86.139 202 23 2 3000 3197 44038841 44039041 2.500000e-51 213
16 TraesCS6A01G048900 chrUn 94.072 1923 78 21 1282 3197 229104389 229106282 0.000000e+00 2887
17 TraesCS6A01G048900 chrUn 98.637 1541 20 1 1 1541 197716486 197718025 0.000000e+00 2728
18 TraesCS6A01G048900 chrUn 99.003 1504 15 0 1 1504 229103147 229104650 0.000000e+00 2695
19 TraesCS6A01G048900 chrUn 90.880 1897 128 26 1304 3197 94214857 94216711 0.000000e+00 2503
20 TraesCS6A01G048900 chrUn 91.796 1548 67 16 1 1507 94213571 94215099 0.000000e+00 2100
21 TraesCS6A01G048900 chrUn 88.364 1650 151 27 1358 2997 181033292 181034910 0.000000e+00 1945
22 TraesCS6A01G048900 chrUn 88.203 1653 157 24 1358 2997 180994597 180996224 0.000000e+00 1938
23 TraesCS6A01G048900 chrUn 89.506 1458 123 17 1552 2997 387096605 387098044 0.000000e+00 1818
24 TraesCS6A01G048900 chrUn 87.908 1472 125 31 1081 2539 355223074 355224505 0.000000e+00 1683
25 TraesCS6A01G048900 chrUn 90.594 1095 69 11 432 1522 180993733 180994797 0.000000e+00 1421
26 TraesCS6A01G048900 chrUn 90.708 1087 69 10 432 1516 181032430 181033486 0.000000e+00 1419
27 TraesCS6A01G048900 chrUn 90.708 1087 64 12 432 1513 395593064 395592010 0.000000e+00 1413
28 TraesCS6A01G048900 chrUn 88.159 1157 103 21 1447 2593 433932781 433933913 0.000000e+00 1347
29 TraesCS6A01G048900 chrUn 86.476 1257 125 29 1304 2539 325490257 325489025 0.000000e+00 1338
30 TraesCS6A01G048900 chrUn 100.000 204 0 0 2994 3197 480526082 480525879 8.370000e-101 377
31 TraesCS6A01G048900 chrUn 93.750 240 15 0 1 240 94682007 94682246 8.430000e-96 361
32 TraesCS6A01G048900 chrUn 92.917 240 17 0 1 240 181005929 181006168 1.820000e-92 350
33 TraesCS6A01G048900 chrUn 92.500 240 18 0 1 240 181032194 181032433 8.490000e-91 344
34 TraesCS6A01G048900 chr7D 87.081 209 16 7 237 435 240351574 240351367 3.210000e-55 226
35 TraesCS6A01G048900 chr6D 86.124 209 23 6 237 439 432226059 432226267 1.490000e-53 220
36 TraesCS6A01G048900 chr5A 83.962 212 25 6 237 439 386648490 386648701 9.050000e-46 195
37 TraesCS6A01G048900 chr4A 84.239 184 22 5 246 428 196574520 196574343 4.240000e-39 172


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 TraesCS6A01G048900 chr6A 24920546 24923742 3196 False 5904.000000 5904 100.000000 1 3197 1 chr6A.!!$F1 3196
1 TraesCS6A01G048900 chr6B 43383697 43386411 2714 False 3819.000000 3819 91.913000 432 3197 1 chr6B.!!$F1 2765
2 TraesCS6A01G048900 chr6B 43436604 43438460 1856 False 2392.000000 2392 89.894000 1318 3197 1 chr6B.!!$F2 1879
3 TraesCS6A01G048900 chr6B 43474403 43482836 8433 False 1980.333333 2185 91.404000 432 3197 3 chr6B.!!$F6 2765
4 TraesCS6A01G048900 chr6B 43922989 43924580 1591 False 1823.000000 1823 87.294000 1359 2989 1 chr6B.!!$F4 1630
5 TraesCS6A01G048900 chr6B 43867506 43870234 2728 False 1247.000000 1967 90.636333 1 2997 3 chr6B.!!$F7 2996
6 TraesCS6A01G048900 chr6B 44060936 44063983 3047 False 304.000000 364 91.556000 1 3197 2 chr6B.!!$F8 3196
7 TraesCS6A01G048900 chrUn 229103147 229106282 3135 False 2791.000000 2887 96.537500 1 3197 2 chrUn.!!$F10 3196
8 TraesCS6A01G048900 chrUn 197716486 197718025 1539 False 2728.000000 2728 98.637000 1 1541 1 chrUn.!!$F3 1540
9 TraesCS6A01G048900 chrUn 94213571 94216711 3140 False 2301.500000 2503 91.338000 1 3197 2 chrUn.!!$F7 3196
10 TraesCS6A01G048900 chrUn 387096605 387098044 1439 False 1818.000000 1818 89.506000 1552 2997 1 chrUn.!!$F5 1445
11 TraesCS6A01G048900 chrUn 355223074 355224505 1431 False 1683.000000 1683 87.908000 1081 2539 1 chrUn.!!$F4 1458
12 TraesCS6A01G048900 chrUn 180993733 180996224 2491 False 1679.500000 1938 89.398500 432 2997 2 chrUn.!!$F8 2565
13 TraesCS6A01G048900 chrUn 395592010 395593064 1054 True 1413.000000 1413 90.708000 432 1513 1 chrUn.!!$R2 1081
14 TraesCS6A01G048900 chrUn 433932781 433933913 1132 False 1347.000000 1347 88.159000 1447 2593 1 chrUn.!!$F6 1146
15 TraesCS6A01G048900 chrUn 325489025 325490257 1232 True 1338.000000 1338 86.476000 1304 2539 1 chrUn.!!$R1 1235
16 TraesCS6A01G048900 chrUn 181032194 181034910 2716 False 1236.000000 1945 90.524000 1 2997 3 chrUn.!!$F9 2996

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
1437 1688 1.327303 ATCCACAACCGCAAACACAT 58.673 45.0 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2992 3914 1.33644 CACGACCAAACAATCCAGCAA 59.664 47.619 0.0 0.0 0.0 3.91 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
1437 1688 1.327303 ATCCACAACCGCAAACACAT 58.673 45.000 0.00 0.00 0.00 3.21
1475 1726 1.408702 ACCAATTTCGCAGCAACAAGT 59.591 42.857 0.00 0.00 0.00 3.16
1525 1779 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
1526 1780 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1527 1781 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
1529 1783 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1530 1784 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
1537 1791 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
1538 1792 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1539 1793 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
1541 1795 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
1547 1801 5.112686 ACAACAACAACAACAACAACAACT 58.887 33.333 0.00 0.00 0.00 3.16
1550 1804 6.079424 ACAACAACAACAACAACAACTACT 57.921 33.333 0.00 0.00 0.00 2.57
1553 1807 7.040961 ACAACAACAACAACAACAACTACTACT 60.041 33.333 0.00 0.00 0.00 2.57
1592 2146 5.233225 TCAACAAATTCTGCAACAACAACA 58.767 33.333 0.00 0.00 0.00 3.33
1593 2147 5.698089 TCAACAAATTCTGCAACAACAACAA 59.302 32.000 0.00 0.00 0.00 2.83
1594 2148 5.529014 ACAAATTCTGCAACAACAACAAC 57.471 34.783 0.00 0.00 0.00 3.32
1711 2265 3.176708 CAATTATGTTGTCAGCAGCTGC 58.823 45.455 31.53 31.53 42.49 5.25
1773 2327 8.764287 CACAATGTCGTTCATGCTATTATTCTA 58.236 33.333 0.00 0.00 36.81 2.10
1813 2711 5.649602 ACAACAACAACAACAACAACAAG 57.350 34.783 0.00 0.00 0.00 3.16
1814 2712 4.509600 ACAACAACAACAACAACAACAAGG 59.490 37.500 0.00 0.00 0.00 3.61
1947 2863 0.482446 AACCTCAACATCTGCCCCAA 59.518 50.000 0.00 0.00 0.00 4.12
1962 2878 2.355818 GCCCCAACTCGAGGAAATAAGT 60.356 50.000 18.41 0.00 0.00 2.24
2254 3171 9.527157 TGATTGTTTATTTGAGTTCCATTCCTA 57.473 29.630 0.00 0.00 0.00 2.94
2276 3193 0.881118 CCCATTCACAAGTTCACCCG 59.119 55.000 0.00 0.00 0.00 5.28
2436 3353 0.613012 ACATCCTTGGCTTGCCCTTC 60.613 55.000 9.35 0.00 0.00 3.46
2542 3462 1.108776 TACGGCTACTCCAAATCGCT 58.891 50.000 0.00 0.00 34.01 4.93
2845 3767 6.012771 ACTCTTAACTTGGCTTGTACCCTAAT 60.013 38.462 0.00 0.00 0.00 1.73
2886 3808 6.840780 ATTGTTCTTCCCCATTAGACAAAG 57.159 37.500 0.00 0.00 0.00 2.77
2992 3914 0.476771 ACCCACGACCAAATGTCCTT 59.523 50.000 0.00 0.00 41.18 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
886 933 2.936202 GTGGCACTATCATTCCACCAT 58.064 47.619 11.13 0.00 42.25 3.55
1437 1688 1.680735 GGTTGTTGTGGTTGCAGATGA 59.319 47.619 0.00 0.00 0.00 2.92
1475 1726 6.040247 TGTTGTTGTTGTTGTTGTTGTTGTA 58.960 32.000 0.00 0.00 0.00 2.41
1525 1779 5.649602 AGTTGTTGTTGTTGTTGTTGTTG 57.350 34.783 0.00 0.00 0.00 3.33
1526 1780 6.508777 AGTAGTTGTTGTTGTTGTTGTTGTT 58.491 32.000 0.00 0.00 0.00 2.83
1527 1781 6.079424 AGTAGTTGTTGTTGTTGTTGTTGT 57.921 33.333 0.00 0.00 0.00 3.32
1529 1783 7.443259 AGTAGTAGTTGTTGTTGTTGTTGTT 57.557 32.000 0.00 0.00 0.00 2.83
1530 1784 7.603404 TGTAGTAGTAGTTGTTGTTGTTGTTGT 59.397 33.333 0.00 0.00 0.00 3.32
1537 1791 7.966111 TGTTGTTGTAGTAGTAGTTGTTGTTG 58.034 34.615 0.00 0.00 0.00 3.33
1538 1792 8.550710 TTGTTGTTGTAGTAGTAGTTGTTGTT 57.449 30.769 0.00 0.00 0.00 2.83
1539 1793 8.550710 TTTGTTGTTGTAGTAGTAGTTGTTGT 57.449 30.769 0.00 0.00 0.00 3.32
1541 1795 8.833493 GGATTTGTTGTTGTAGTAGTAGTTGTT 58.167 33.333 0.00 0.00 0.00 2.83
1547 1801 9.048446 GTTGAAGGATTTGTTGTTGTAGTAGTA 57.952 33.333 0.00 0.00 0.00 1.82
1550 1804 7.867305 TGTTGAAGGATTTGTTGTTGTAGTA 57.133 32.000 0.00 0.00 0.00 1.82
1553 1807 9.092876 GAATTTGTTGAAGGATTTGTTGTTGTA 57.907 29.630 0.00 0.00 0.00 2.41
1592 2146 2.024655 ACATCCCTGCATGGAATCAGTT 60.025 45.455 15.14 0.00 38.10 3.16
1593 2147 1.567649 ACATCCCTGCATGGAATCAGT 59.432 47.619 15.14 8.55 38.10 3.41
1594 2148 2.228059 GACATCCCTGCATGGAATCAG 58.772 52.381 15.14 7.97 38.10 2.90
1711 2265 4.598894 CTGCTCGGGGATCAGCCG 62.599 72.222 0.00 0.00 37.63 5.52
1715 2269 3.838271 GCGACTGCTCGGGGATCA 61.838 66.667 0.00 0.00 40.53 2.92
1773 2327 5.292765 TGTTGTTGTTGTTGTTGTTGATGT 58.707 33.333 0.00 0.00 0.00 3.06
1813 2711 1.068474 CTCGACGGTTGATGTTGTCC 58.932 55.000 0.00 0.00 0.00 4.02
1814 2712 0.438830 GCTCGACGGTTGATGTTGTC 59.561 55.000 0.00 0.00 0.00 3.18
1947 2863 5.221009 CGCTAGGTTACTTATTTCCTCGAGT 60.221 44.000 12.31 0.00 0.00 4.18
1962 2878 1.138883 CGTCTGCAGCGCTAGGTTA 59.861 57.895 10.99 0.00 0.00 2.85
2254 3171 1.895131 GGTGAACTTGTGAATGGGCAT 59.105 47.619 0.00 0.00 0.00 4.40
2411 3328 2.378038 GCAAGCCAAGGATGTGGATAA 58.622 47.619 0.00 0.00 41.65 1.75
2436 3353 6.956202 AAGCTTCTCTGGGAATAATTGATG 57.044 37.500 0.00 0.00 33.01 3.07
2542 3462 5.176774 CGCTATTAATGCTTCGGTTATGTGA 59.823 40.000 0.00 0.00 0.00 3.58
2811 3733 7.722285 ACAAGCCAAGTTAAGAGTATTTTGGTA 59.278 33.333 2.34 0.00 37.85 3.25
2845 3767 7.206687 AGAACAATTGAAAAGGCAACGAAATA 58.793 30.769 13.59 0.00 46.39 1.40
2886 3808 3.130693 GGTGTGGTAGATGGACTGTCTAC 59.869 52.174 7.85 2.36 44.60 2.59
2992 3914 1.336440 CACGACCAAACAATCCAGCAA 59.664 47.619 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.