Multiple sequence alignment - TraesCS2D01G344700

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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 TraesCS2D01G344700 chr2D 100.000 2780 0 0 1 2780 440767135 440769914 0.000000e+00 5134.0
1 TraesCS2D01G344700 chr2D 99.456 735 4 0 1 735 185368037 185368771 0.000000e+00 1336.0
2 TraesCS2D01G344700 chr2D 85.467 578 79 3 5 578 440634022 440634598 5.120000e-167 597.0
3 TraesCS2D01G344700 chr2A 95.738 2792 80 16 1 2780 584510872 584513636 0.000000e+00 4460.0
4 TraesCS2D01G344700 chr2A 85.665 579 77 4 5 578 584143481 584144058 3.060000e-169 604.0
5 TraesCS2D01G344700 chr2B 95.663 2421 82 11 1 2417 518739858 518742259 0.000000e+00 3868.0
6 TraesCS2D01G344700 chr2B 89.503 362 26 4 2419 2772 518742386 518742743 5.460000e-122 448.0
7 TraesCS2D01G344700 chr2B 91.667 48 1 3 2243 2287 572592428 572592381 2.310000e-06 63.9
8 TraesCS2D01G344700 chr6D 99.456 735 3 1 1 735 100570339 100569606 0.000000e+00 1334.0
9 TraesCS2D01G344700 chr6D 99.320 735 5 0 1 735 216836565 216837299 0.000000e+00 1330.0
10 TraesCS2D01G344700 chr3D 99.320 735 5 0 1 735 241044568 241043834 0.000000e+00 1330.0
11 TraesCS2D01G344700 chr3D 92.377 446 31 3 3 447 456355582 456355139 1.400000e-177 632.0
12 TraesCS2D01G344700 chr3D 95.000 40 2 0 2240 2279 595230733 595230772 2.310000e-06 63.9
13 TraesCS2D01G344700 chr7D 98.316 475 7 1 261 735 255422881 255423354 0.000000e+00 832.0
14 TraesCS2D01G344700 chr6A 100.000 36 0 0 2243 2278 441426956 441426991 1.790000e-07 67.6
15 TraesCS2D01G344700 chr6A 96.875 32 0 1 2338 2368 33306915 33306884 5.000000e-03 52.8
16 TraesCS2D01G344700 chr6B 100.000 35 0 0 2243 2277 470123452 470123486 6.430000e-07 65.8
17 TraesCS2D01G344700 chr5B 95.000 40 2 0 2240 2279 655296988 655296949 2.310000e-06 63.9
18 TraesCS2D01G344700 chr4D 97.297 37 1 0 2243 2279 85586296 85586332 2.310000e-06 63.9
19 TraesCS2D01G344700 chr1B 95.000 40 2 0 2240 2279 625095340 625095301 2.310000e-06 63.9


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 TraesCS2D01G344700 chr2D 440767135 440769914 2779 False 5134 5134 100.000 1 2780 1 chr2D.!!$F3 2779
1 TraesCS2D01G344700 chr2D 185368037 185368771 734 False 1336 1336 99.456 1 735 1 chr2D.!!$F1 734
2 TraesCS2D01G344700 chr2D 440634022 440634598 576 False 597 597 85.467 5 578 1 chr2D.!!$F2 573
3 TraesCS2D01G344700 chr2A 584510872 584513636 2764 False 4460 4460 95.738 1 2780 1 chr2A.!!$F2 2779
4 TraesCS2D01G344700 chr2A 584143481 584144058 577 False 604 604 85.665 5 578 1 chr2A.!!$F1 573
5 TraesCS2D01G344700 chr2B 518739858 518742743 2885 False 2158 3868 92.583 1 2772 2 chr2B.!!$F1 2771
6 TraesCS2D01G344700 chr6D 100569606 100570339 733 True 1334 1334 99.456 1 735 1 chr6D.!!$R1 734
7 TraesCS2D01G344700 chr6D 216836565 216837299 734 False 1330 1330 99.320 1 735 1 chr6D.!!$F1 734
8 TraesCS2D01G344700 chr3D 241043834 241044568 734 True 1330 1330 99.320 1 735 1 chr3D.!!$R1 734

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
375 379 0.962356 CCAACTGCCGCTTCCTCAAT 60.962 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1804 0.179004 ACCAAGCGGTTCACAATCCA 60.179 50.0 0.0 0.0 46.31 3.41 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
375 379 0.962356 CCAACTGCCGCTTCCTCAAT 60.962 55.000 0.00 0.00 0.00 2.57
1251 1256 1.000283 CACCAGAACTTGAGCTCGAGT 60.000 52.381 27.99 27.99 42.20 4.18
1278 1283 2.355132 GCTTCTCGACGAGGACTATGAA 59.645 50.000 23.92 8.87 0.00 2.57
1341 1346 1.003233 GCCAGGTGAAGGTGGAGAC 60.003 63.158 0.00 0.00 35.67 3.36
1541 1546 2.025321 GGACACTGGTGGATTGGGTATT 60.025 50.000 5.70 0.00 34.19 1.89
1575 1580 3.338676 GGACGAATCGCCGATGCC 61.339 66.667 0.00 0.00 0.00 4.40
1644 1649 4.072131 TGAAGGTGGCTTTTCAGTGTATC 58.928 43.478 0.00 0.00 0.00 2.24
1650 1655 1.201921 GCTTTTCAGTGTATCGTGGCG 60.202 52.381 0.00 0.00 0.00 5.69
1789 1794 3.950794 GACACCTGATGGCGGCGAA 62.951 63.158 12.98 0.00 36.63 4.70
1790 1795 3.499737 CACCTGATGGCGGCGAAC 61.500 66.667 12.98 2.36 36.63 3.95
1870 1875 3.055891 TCTGGCTGTTGAATTGATCGAGA 60.056 43.478 0.00 0.00 0.00 4.04
1874 1879 4.256140 CTGTTGAATTGATCGAGAGCAC 57.744 45.455 0.00 0.00 0.00 4.40
1937 1942 0.460284 AGTTCGATCATGGCACCGTC 60.460 55.000 0.00 0.00 0.00 4.79
2017 2022 4.553756 TGCTAGTGCTTGTAGTATCTCG 57.446 45.455 0.00 0.00 40.48 4.04
2188 2193 2.036475 TGTTTGCATGGCCGTTTTGTAT 59.964 40.909 0.00 0.00 0.00 2.29
2205 2210 5.614324 TTGTATCACCCTGTTATCTCCTG 57.386 43.478 0.00 0.00 0.00 3.86
2216 2221 6.047870 CCTGTTATCTCCTGCTCATATATGC 58.952 44.000 7.92 0.00 0.00 3.14
2218 2223 7.069208 CCTGTTATCTCCTGCTCATATATGCTA 59.931 40.741 7.92 0.00 0.00 3.49
2297 2305 6.974622 GGTTTTGTGAATTTGCTCGATGATAT 59.025 34.615 0.00 0.00 0.00 1.63
2436 2570 6.593770 TCTCATATATTTTGTGTGTTCTGCGT 59.406 34.615 0.00 0.00 0.00 5.24
2439 2573 8.387354 TCATATATTTTGTGTGTTCTGCGTTAG 58.613 33.333 0.00 0.00 0.00 2.34
2440 2574 6.795098 ATATTTTGTGTGTTCTGCGTTAGA 57.205 33.333 0.00 0.00 0.00 2.10
2577 2715 4.402155 CCTCTGCTCTGTATTCTGAAGACT 59.598 45.833 15.33 0.00 0.00 3.24
2578 2716 5.592282 CCTCTGCTCTGTATTCTGAAGACTA 59.408 44.000 15.33 4.19 0.00 2.59
2661 2804 1.564483 ATTTCCCCCTAAACCCGCGA 61.564 55.000 8.23 0.00 0.00 5.87
2664 2807 1.070275 CCCCCTAAACCCGCGATAC 59.930 63.158 8.23 0.00 0.00 2.24
2668 2811 1.038280 CCTAAACCCGCGATACCTCT 58.962 55.000 8.23 0.00 0.00 3.69
2689 2832 0.548031 TTCTTATCTGGCTGGCCCTG 59.452 55.000 9.28 2.54 34.56 4.45
2750 2893 9.499585 CAGCTCTTTGTGATTGATAACAATAAG 57.500 33.333 0.00 0.00 45.30 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1251 1256 3.610791 CTCGTCGAGAAGCACCGCA 62.611 63.158 17.52 0.00 0.00 5.69
1278 1283 1.134580 CCAACATCTGTGATCCGAGCT 60.135 52.381 0.00 0.00 0.00 4.09
1341 1346 1.180029 CATTGAGGAAGGGGCTTGTG 58.820 55.000 0.00 0.00 0.00 3.33
1491 1496 2.644299 TCCTTCACCCACATCACTTGAT 59.356 45.455 0.00 0.00 34.56 2.57
1525 1530 2.689983 GCTGAAATACCCAATCCACCAG 59.310 50.000 0.00 0.00 0.00 4.00
1541 1546 1.004560 CCGGTGCTCTTGAGCTGAA 60.005 57.895 21.17 0.00 35.49 3.02
1575 1580 2.614057 GCCCTTCAATGACTTATCCACG 59.386 50.000 0.00 0.00 0.00 4.94
1650 1655 1.524849 GATCCTCTCCTTTGGCCGC 60.525 63.158 0.00 0.00 0.00 6.53
1789 1794 1.153369 CACAATCCATCCGAGGCGT 60.153 57.895 0.00 0.00 0.00 5.68
1790 1795 0.461870 TTCACAATCCATCCGAGGCG 60.462 55.000 0.00 0.00 0.00 5.52
1791 1796 1.017387 GTTCACAATCCATCCGAGGC 58.983 55.000 0.00 0.00 0.00 4.70
1793 1798 1.290203 CGGTTCACAATCCATCCGAG 58.710 55.000 0.00 0.00 40.29 4.63
1794 1799 0.742990 GCGGTTCACAATCCATCCGA 60.743 55.000 5.60 0.00 40.29 4.55
1795 1800 0.744414 AGCGGTTCACAATCCATCCG 60.744 55.000 0.00 0.00 40.72 4.18
1796 1801 1.133025 CAAGCGGTTCACAATCCATCC 59.867 52.381 0.00 0.00 0.00 3.51
1797 1802 1.133025 CCAAGCGGTTCACAATCCATC 59.867 52.381 0.00 0.00 0.00 3.51
1798 1803 1.176527 CCAAGCGGTTCACAATCCAT 58.823 50.000 0.00 0.00 0.00 3.41
1799 1804 0.179004 ACCAAGCGGTTCACAATCCA 60.179 50.000 0.00 0.00 46.31 3.41
1870 1875 2.725312 ATGGATGTCTCGGCGTGCT 61.725 57.895 6.85 0.00 0.00 4.40
1874 1879 2.969238 GCCATGGATGTCTCGGCG 60.969 66.667 18.40 0.00 32.14 6.46
1937 1942 7.117956 CAGCTTACATGATTATCTCACCATGAG 59.882 40.741 0.00 0.00 45.59 2.90
2017 2022 5.067283 ACACAACAAGAATTACAGTTCCACC 59.933 40.000 0.00 0.00 0.00 4.61
2188 2193 2.111384 GAGCAGGAGATAACAGGGTGA 58.889 52.381 0.00 0.00 0.00 4.02
2216 2221 8.743085 ATGGGATTAGCATGCTACATAATTAG 57.257 34.615 26.87 0.00 0.00 1.73
2218 2223 8.426569 AAATGGGATTAGCATGCTACATAATT 57.573 30.769 26.87 18.15 0.00 1.40
2313 2321 8.088463 AGAGACAGATGACCAAAATAAGAGAT 57.912 34.615 0.00 0.00 0.00 2.75
2423 2557 2.159156 AGTGTCTAACGCAGAACACACA 60.159 45.455 12.39 0.00 37.57 3.72
2429 2563 2.543848 CAGCAAAGTGTCTAACGCAGAA 59.456 45.455 0.00 0.00 34.17 3.02
2436 2570 3.181491 GCCAACAACAGCAAAGTGTCTAA 60.181 43.478 0.00 0.00 0.00 2.10
2439 2573 1.135141 TGCCAACAACAGCAAAGTGTC 60.135 47.619 0.00 0.00 35.69 3.67
2440 2574 0.894141 TGCCAACAACAGCAAAGTGT 59.106 45.000 0.00 0.00 35.69 3.55
2577 2715 5.750547 TCGTTTGCACAATGCTTCAAAATTA 59.249 32.000 2.02 0.00 45.31 1.40
2578 2716 4.569966 TCGTTTGCACAATGCTTCAAAATT 59.430 33.333 2.02 0.00 45.31 1.82
2631 2774 5.530176 TTAGGGGGAAATGAAAAGCTACT 57.470 39.130 0.00 0.00 0.00 2.57
2632 2775 5.105473 GGTTTAGGGGGAAATGAAAAGCTAC 60.105 44.000 0.00 0.00 0.00 3.58
2633 2776 5.020795 GGTTTAGGGGGAAATGAAAAGCTA 58.979 41.667 0.00 0.00 0.00 3.32
2661 2804 4.346418 CCAGCCAGATAAGAACAGAGGTAT 59.654 45.833 0.00 0.00 0.00 2.73
2664 2807 2.744494 GCCAGCCAGATAAGAACAGAGG 60.744 54.545 0.00 0.00 0.00 3.69
2668 2811 0.255890 GGGCCAGCCAGATAAGAACA 59.744 55.000 11.50 0.00 37.98 3.18
2689 2832 8.909708 TCAAACAAAGCATACAATATAACAGC 57.090 30.769 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.