Multiple sequence alignment - TraesCS6D01G013500

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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 TraesCS6D01G013500 chr6D 100.000 3412 0 0 1 3412 5493220 5496631 0.000000e+00 6301.0
1 TraesCS6D01G013500 chr2A 99.043 1672 15 1 1742 3412 25038544 25036873 0.000000e+00 2998.0
2 TraesCS6D01G013500 chr2A 98.344 966 16 0 745 1710 25039494 25038529 0.000000e+00 1696.0
3 TraesCS6D01G013500 chr2A 96.987 697 19 1 1 697 25040192 25039498 0.000000e+00 1170.0
4 TraesCS6D01G013500 chr2A 81.630 675 124 0 2738 3412 751722128 751722802 8.270000e-156 560.0
5 TraesCS6D01G013500 chr6B 98.923 1672 16 2 1742 3412 25958931 25960601 0.000000e+00 2987.0
6 TraesCS6D01G013500 chr6B 98.240 966 17 0 745 1710 25957981 25958946 0.000000e+00 1690.0
7 TraesCS6D01G013500 chr6B 96.126 697 24 2 1 697 25957284 25957977 0.000000e+00 1134.0
8 TraesCS6D01G013500 chr1B 96.738 1410 40 5 1 1407 7413787 7415193 0.000000e+00 2344.0
9 TraesCS6D01G013500 chr1B 99.296 142 1 0 3271 3412 7415191 7415332 1.210000e-64 257.0
10 TraesCS6D01G013500 chr3B 96.605 1414 40 4 1 1407 22076585 22075173 0.000000e+00 2338.0
11 TraesCS6D01G013500 chr3B 99.296 142 1 0 3271 3412 22075175 22075034 1.210000e-64 257.0
12 TraesCS6D01G013500 chr3B 72.751 389 93 11 1305 1688 125866249 125866629 5.980000e-23 119.0
13 TraesCS6D01G013500 chr4D 98.913 460 5 0 2950 3409 430796499 430796958 0.000000e+00 822.0
14 TraesCS6D01G013500 chr1A 82.942 639 103 6 2738 3373 52566309 52566944 3.820000e-159 571.0
15 TraesCS6D01G013500 chr1A 82.390 636 107 5 2738 3371 52561325 52560693 1.790000e-152 549.0
16 TraesCS6D01G013500 chr5A 86.792 371 39 6 687 1051 546792502 546792136 4.100000e-109 405.0
17 TraesCS6D01G013500 chr5A 76.935 646 79 39 2 618 546793145 546792541 1.540000e-78 303.0
18 TraesCS6D01G013500 chr5A 73.158 380 89 11 1314 1688 694511823 694511452 1.290000e-24 124.0
19 TraesCS6D01G013500 chr7A 85.904 376 53 0 2996 3371 208088988 208089363 5.300000e-108 401.0
20 TraesCS6D01G013500 chr5B 83.249 394 40 14 1 376 415111896 415111511 4.220000e-89 339.0
21 TraesCS6D01G013500 chr5B 78.000 250 55 0 2143 2392 70441053 70441302 1.270000e-34 158.0
22 TraesCS6D01G013500 chr1D 73.158 380 89 11 1314 1688 172863844 172863473 1.290000e-24 124.0
23 TraesCS6D01G013500 chr2B 72.895 380 90 11 1314 1688 777556645 777556274 5.980000e-23 119.0
24 TraesCS6D01G013500 chrUn 81.651 109 16 4 1311 1417 74787545 74787651 1.690000e-13 87.9
25 TraesCS6D01G013500 chr7B 90.385 52 4 1 1698 1748 24122491 24122440 2.200000e-07 67.6
26 TraesCS6D01G013500 chr7D 97.059 34 1 0 1712 1745 601360223 601360256 1.320000e-04 58.4


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 TraesCS6D01G013500 chr6D 5493220 5496631 3411 False 6301.000000 6301 100.000000 1 3412 1 chr6D.!!$F1 3411
1 TraesCS6D01G013500 chr2A 25036873 25040192 3319 True 1954.666667 2998 98.124667 1 3412 3 chr2A.!!$R1 3411
2 TraesCS6D01G013500 chr2A 751722128 751722802 674 False 560.000000 560 81.630000 2738 3412 1 chr2A.!!$F1 674
3 TraesCS6D01G013500 chr6B 25957284 25960601 3317 False 1937.000000 2987 97.763000 1 3412 3 chr6B.!!$F1 3411
4 TraesCS6D01G013500 chr1B 7413787 7415332 1545 False 1300.500000 2344 98.017000 1 3412 2 chr1B.!!$F1 3411
5 TraesCS6D01G013500 chr3B 22075034 22076585 1551 True 1297.500000 2338 97.950500 1 3412 2 chr3B.!!$R1 3411
6 TraesCS6D01G013500 chr1A 52566309 52566944 635 False 571.000000 571 82.942000 2738 3373 1 chr1A.!!$F1 635
7 TraesCS6D01G013500 chr1A 52560693 52561325 632 True 549.000000 549 82.390000 2738 3371 1 chr1A.!!$R1 633
8 TraesCS6D01G013500 chr5A 546792136 546793145 1009 True 354.000000 405 81.863500 2 1051 2 chr5A.!!$R2 1049

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
747 804 0.608130 TGATCTGCGTGCTAGTTGGT 59.392 50.0 0.0 0.0 0.00 3.67 F
1642 1705 0.389817 TCCAATGGCGAGACAAGTCG 60.390 55.0 0.0 0.0 43.08 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2283 2347 0.456653 GATGCCAACAACACATCGCC 60.457 55.0 0.0 0.0 31.7 5.54 R
3111 3175 7.622893 ATCATCTAAAAGAACAAGGAGAAGC 57.377 36.0 0.0 0.0 0.0 3.86 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
79 80 2.429610 GCATTTGGATCACAGGATTGCT 59.570 45.455 0.00 0.0 32.67 3.91
608 648 1.675310 CGAGGGCTGTTGATGGCAA 60.675 57.895 0.00 0.0 0.00 4.52
747 804 0.608130 TGATCTGCGTGCTAGTTGGT 59.392 50.000 0.00 0.0 0.00 3.67
907 970 5.423015 TGAGAGATGGAAGTGCTGTATTTC 58.577 41.667 0.00 0.0 0.00 2.17
1032 1095 2.476854 GCTTAACTCATTTGAGCTGCCG 60.477 50.000 7.48 0.0 45.79 5.69
1075 1138 6.071728 ACAAGGATTTCTTCACATGGATGTTC 60.072 38.462 0.00 0.0 34.23 3.18
1124 1187 4.263462 ACAAGGACTTGGTGCTATTGATGA 60.263 41.667 15.72 0.0 44.45 2.92
1141 1204 1.801913 GACGATCGTGCTCGCAGTT 60.802 57.895 28.12 0.0 42.35 3.16
1146 1209 3.716006 CGTGCTCGCAGTTGTGGG 61.716 66.667 0.00 0.0 37.98 4.61
1177 1240 5.698741 AGGACTTGGTGATATTGATGACA 57.301 39.130 0.00 0.0 0.00 3.58
1642 1705 0.389817 TCCAATGGCGAGACAAGTCG 60.390 55.000 0.00 0.0 43.08 4.18
1702 1765 9.450807 GATGGTTAGTTTAACATTACATGATGC 57.549 33.333 0.00 0.0 40.39 3.91
1703 1766 8.574251 TGGTTAGTTTAACATTACATGATGCT 57.426 30.769 0.00 0.0 40.39 3.79
1704 1767 9.019656 TGGTTAGTTTAACATTACATGATGCTT 57.980 29.630 0.00 0.0 40.39 3.91
1705 1768 9.855021 GGTTAGTTTAACATTACATGATGCTTT 57.145 29.630 0.00 0.0 40.39 3.51
1729 1792 8.570068 TTTTTACGAGTCTATAAAAATGCCCT 57.430 30.769 13.71 0.0 36.06 5.19
1730 1793 8.570068 TTTTACGAGTCTATAAAAATGCCCTT 57.430 30.769 0.00 0.0 29.52 3.95
1731 1794 8.570068 TTTACGAGTCTATAAAAATGCCCTTT 57.430 30.769 0.00 0.0 0.00 3.11
1732 1795 9.669887 TTTACGAGTCTATAAAAATGCCCTTTA 57.330 29.630 0.00 0.0 0.00 1.85
1733 1796 9.841295 TTACGAGTCTATAAAAATGCCCTTTAT 57.159 29.630 0.00 0.0 34.25 1.40
1734 1797 8.379457 ACGAGTCTATAAAAATGCCCTTTATC 57.621 34.615 0.00 0.0 32.54 1.75
1735 1798 7.170998 ACGAGTCTATAAAAATGCCCTTTATCG 59.829 37.037 0.00 0.0 32.54 2.92
1736 1799 7.384115 CGAGTCTATAAAAATGCCCTTTATCGA 59.616 37.037 0.00 0.0 32.54 3.59
1737 1800 8.974060 AGTCTATAAAAATGCCCTTTATCGAA 57.026 30.769 0.00 0.0 32.54 3.71
1738 1801 9.403583 AGTCTATAAAAATGCCCTTTATCGAAA 57.596 29.630 0.00 0.0 32.54 3.46
2086 2150 2.203422 CCCAAAAGCACCCACCGA 60.203 61.111 0.00 0.0 0.00 4.69
2267 2331 4.100529 GCATCACAACGATTGAAGGATTG 58.899 43.478 0.00 0.0 29.21 2.67
2283 2347 4.796606 AGGATTGGATGGTCTACAATTGG 58.203 43.478 10.83 0.0 35.17 3.16
2289 2353 2.036958 TGGTCTACAATTGGGCGATG 57.963 50.000 10.83 0.0 0.00 3.84
2607 2671 5.097742 TGAGTTCTTTGTTTCAGACTCCA 57.902 39.130 0.00 0.0 0.00 3.86
2713 2777 8.743085 ACAACTTGCATATCATATCTTCACTT 57.257 30.769 0.00 0.0 0.00 3.16
2957 3021 0.455410 GCAGAACACAACAAGCCACA 59.545 50.000 0.00 0.0 0.00 4.17
3111 3175 2.507339 ATTTTGTGGCCTTTGACGTG 57.493 45.000 3.32 0.0 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 7.016296 ACCCAATCCTAAGGAATTTTGAGAAA 58.984 34.615 0.00 0.00 34.34 2.52
260 291 4.753516 TTATTTCCTTCCAGAGCGATCA 57.246 40.909 2.38 0.00 0.00 2.92
608 648 4.514577 CGACATCCGCTTCGCCCT 62.515 66.667 0.00 0.00 0.00 5.19
907 970 2.009774 GCAGTACACACCAAGGCATAG 58.990 52.381 0.00 0.00 0.00 2.23
1032 1095 4.120331 GATTGCACACGGCTGCCC 62.120 66.667 14.12 0.00 45.15 5.36
1063 1126 1.064505 GGCACGATGAACATCCATGTG 59.935 52.381 8.87 11.32 41.61 3.21
1124 1187 2.088763 CAACTGCGAGCACGATCGT 61.089 57.895 16.60 16.60 44.53 3.73
1141 1204 0.478072 AGTCCTTGTGATTGCCCACA 59.522 50.000 0.00 0.00 44.45 4.17
1146 1209 2.229792 TCACCAAGTCCTTGTGATTGC 58.770 47.619 6.31 0.00 38.85 3.56
1177 1240 0.981183 TACTCAACAGCCCCGTGATT 59.019 50.000 0.00 0.00 0.00 2.57
1642 1705 9.087424 GAAGCCAAATCATTAAAGTATGGAAAC 57.913 33.333 0.00 0.00 0.00 2.78
1704 1767 8.570068 AGGGCATTTTTATAGACTCGTAAAAA 57.430 30.769 15.28 15.28 41.36 1.94
1705 1768 8.570068 AAGGGCATTTTTATAGACTCGTAAAA 57.430 30.769 0.00 3.01 0.00 1.52
1706 1769 8.570068 AAAGGGCATTTTTATAGACTCGTAAA 57.430 30.769 0.00 0.00 0.00 2.01
1707 1770 9.841295 ATAAAGGGCATTTTTATAGACTCGTAA 57.159 29.630 1.20 0.00 30.94 3.18
1708 1771 9.485206 GATAAAGGGCATTTTTATAGACTCGTA 57.515 33.333 1.20 0.00 32.42 3.43
1709 1772 7.170998 CGATAAAGGGCATTTTTATAGACTCGT 59.829 37.037 1.20 0.00 32.42 4.18
1710 1773 7.384115 TCGATAAAGGGCATTTTTATAGACTCG 59.616 37.037 1.20 3.00 31.56 4.18
1711 1774 8.603242 TCGATAAAGGGCATTTTTATAGACTC 57.397 34.615 1.20 0.00 31.56 3.36
1712 1775 8.974060 TTCGATAAAGGGCATTTTTATAGACT 57.026 30.769 1.20 0.00 34.25 3.24
2086 2150 2.500392 ACGTCTACTCTCAGGCTTCT 57.500 50.000 0.00 0.00 0.00 2.85
2267 2331 1.134220 TCGCCCAATTGTAGACCATCC 60.134 52.381 4.43 0.00 0.00 3.51
2283 2347 0.456653 GATGCCAACAACACATCGCC 60.457 55.000 0.00 0.00 31.70 5.54
2289 2353 2.816087 AGATGTCTGATGCCAACAACAC 59.184 45.455 0.00 0.00 0.00 3.32
2430 2494 3.309296 TCATTGCTAGAGAAGGGTAGGG 58.691 50.000 0.00 0.00 0.00 3.53
3111 3175 7.622893 ATCATCTAAAAGAACAAGGAGAAGC 57.377 36.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.