Multiple sequence alignment - TraesCS1A01G371000

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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 TraesCS1A01G371000 chr1A 100.000 2468 0 0 1 2468 548404131 548406598 0.000000e+00 4558.0
1 TraesCS1A01G371000 chr1A 91.084 572 44 2 1901 2466 573398626 573399196 0.000000e+00 767.0
2 TraesCS1A01G371000 chr1A 84.519 239 33 4 342 578 582747419 582747655 1.480000e-57 233.0
3 TraesCS1A01G371000 chr1D 92.641 1916 88 20 1 1898 453404377 453406257 0.000000e+00 2708.0
4 TraesCS1A01G371000 chr1D 92.069 1866 75 30 1 1855 453475659 453477462 0.000000e+00 2558.0
5 TraesCS1A01G371000 chr1D 88.889 378 33 4 991 1359 453347706 453348083 8.040000e-125 457.0
6 TraesCS1A01G371000 chr1B 89.576 1909 103 47 1 1894 623831970 623833797 0.000000e+00 2335.0
7 TraesCS1A01G371000 chr1B 90.958 1681 82 19 1 1673 623914030 623915648 0.000000e+00 2198.0
8 TraesCS1A01G371000 chr1B 90.566 371 33 1 991 1359 623822631 623823001 7.930000e-135 490.0
9 TraesCS1A01G371000 chr1B 91.579 190 15 1 1708 1897 623915644 623915832 6.770000e-66 261.0
10 TraesCS1A01G371000 chr6A 91.958 572 39 5 1901 2466 33587804 33587234 0.000000e+00 795.0
11 TraesCS1A01G371000 chr7A 91.783 572 40 5 1901 2466 605172230 605172800 0.000000e+00 789.0
12 TraesCS1A01G371000 chr2D 91.783 572 40 5 1901 2466 20082482 20081912 0.000000e+00 789.0
13 TraesCS1A01G371000 chr2D 87.391 230 26 2 351 579 491379756 491379983 6.770000e-66 261.0
14 TraesCS1A01G371000 chr6B 91.608 572 41 5 1901 2466 192049879 192050449 0.000000e+00 784.0
15 TraesCS1A01G371000 chr5B 91.434 572 42 2 1901 2466 278794292 278793722 0.000000e+00 778.0
16 TraesCS1A01G371000 chr5B 92.937 538 31 5 1935 2466 314239363 314238827 0.000000e+00 776.0
17 TraesCS1A01G371000 chr2B 91.050 581 45 5 1892 2466 24750025 24750604 0.000000e+00 778.0
18 TraesCS1A01G371000 chr5A 91.259 572 43 5 1901 2466 487672875 487672305 0.000000e+00 773.0
19 TraesCS1A01G371000 chr5A 84.874 238 33 3 350 586 631470030 631470265 1.140000e-58 237.0
20 TraesCS1A01G371000 chr7B 85.000 240 33 2 348 586 732473864 732474101 8.820000e-60 241.0
21 TraesCS1A01G371000 chr3B 84.322 236 34 2 351 585 829545704 829545937 6.870000e-56 228.0
22 TraesCS1A01G371000 chr3A 76.636 214 42 8 1 210 121233661 121233870 7.210000e-21 111.0
23 TraesCS1A01G371000 chr7D 92.500 40 2 1 597 636 587298392 587298430 3.430000e-04 56.5


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 TraesCS1A01G371000 chr1A 548404131 548406598 2467 False 4558.0 4558 100.0000 1 2468 1 chr1A.!!$F1 2467
1 TraesCS1A01G371000 chr1A 573398626 573399196 570 False 767.0 767 91.0840 1901 2466 1 chr1A.!!$F2 565
2 TraesCS1A01G371000 chr1D 453404377 453406257 1880 False 2708.0 2708 92.6410 1 1898 1 chr1D.!!$F2 1897
3 TraesCS1A01G371000 chr1D 453475659 453477462 1803 False 2558.0 2558 92.0690 1 1855 1 chr1D.!!$F3 1854
4 TraesCS1A01G371000 chr1B 623831970 623833797 1827 False 2335.0 2335 89.5760 1 1894 1 chr1B.!!$F2 1893
5 TraesCS1A01G371000 chr1B 623914030 623915832 1802 False 1229.5 2198 91.2685 1 1897 2 chr1B.!!$F3 1896
6 TraesCS1A01G371000 chr6A 33587234 33587804 570 True 795.0 795 91.9580 1901 2466 1 chr6A.!!$R1 565
7 TraesCS1A01G371000 chr7A 605172230 605172800 570 False 789.0 789 91.7830 1901 2466 1 chr7A.!!$F1 565
8 TraesCS1A01G371000 chr2D 20081912 20082482 570 True 789.0 789 91.7830 1901 2466 1 chr2D.!!$R1 565
9 TraesCS1A01G371000 chr6B 192049879 192050449 570 False 784.0 784 91.6080 1901 2466 1 chr6B.!!$F1 565
10 TraesCS1A01G371000 chr5B 278793722 278794292 570 True 778.0 778 91.4340 1901 2466 1 chr5B.!!$R1 565
11 TraesCS1A01G371000 chr5B 314238827 314239363 536 True 776.0 776 92.9370 1935 2466 1 chr5B.!!$R2 531
12 TraesCS1A01G371000 chr2B 24750025 24750604 579 False 778.0 778 91.0500 1892 2466 1 chr2B.!!$F1 574
13 TraesCS1A01G371000 chr5A 487672305 487672875 570 True 773.0 773 91.2590 1901 2466 1 chr5A.!!$R1 565

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
153 157 0.395311 ATTACTCCGTCGAGCTCCCA 60.395 55.0 8.47 0.0 40.03 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1894 1.098712 GGATGCACGGCGGGAAATAA 61.099 55.0 16.21 0.0 0.0 1.4 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
85 89 0.658897 GGAAACGTCGAAGTTTGGCA 59.341 50.000 29.70 0.00 43.54 4.92
153 157 0.395311 ATTACTCCGTCGAGCTCCCA 60.395 55.000 8.47 0.00 40.03 4.37
367 371 3.338126 CTACTTGCTCCGTCCGCGT 62.338 63.158 4.92 0.00 36.15 6.01
376 380 2.084681 CCGTCCGCGTGTAAGTGTC 61.085 63.158 4.92 0.00 36.15 3.67
390 394 6.422701 CGTGTAAGTGTCCATCTAGTTTTTGA 59.577 38.462 0.00 0.00 0.00 2.69
440 444 9.302345 TGATCAACTTTATAGAGAAAAGTAGCG 57.698 33.333 0.00 0.00 44.35 4.26
580 585 9.763465 TTTTAAGACTTGACTTAGAACAAAACG 57.237 29.630 0.00 0.00 34.51 3.60
581 586 6.980051 AAGACTTGACTTAGAACAAAACGT 57.020 33.333 0.00 0.00 0.00 3.99
582 587 9.585099 TTAAGACTTGACTTAGAACAAAACGTA 57.415 29.630 0.00 0.00 34.51 3.57
583 588 7.695869 AGACTTGACTTAGAACAAAACGTAG 57.304 36.000 0.00 0.00 0.00 3.51
584 589 7.486647 AGACTTGACTTAGAACAAAACGTAGA 58.513 34.615 0.00 0.00 0.00 2.59
585 590 7.977853 AGACTTGACTTAGAACAAAACGTAGAA 59.022 33.333 0.00 0.00 0.00 2.10
586 591 7.903062 ACTTGACTTAGAACAAAACGTAGAAC 58.097 34.615 0.00 0.00 0.00 3.01
587 592 6.833342 TGACTTAGAACAAAACGTAGAACC 57.167 37.500 0.00 0.00 0.00 3.62
588 593 6.339730 TGACTTAGAACAAAACGTAGAACCA 58.660 36.000 0.00 0.00 0.00 3.67
589 594 6.987992 TGACTTAGAACAAAACGTAGAACCAT 59.012 34.615 0.00 0.00 0.00 3.55
590 595 7.170320 TGACTTAGAACAAAACGTAGAACCATC 59.830 37.037 0.00 0.00 0.00 3.51
591 596 4.985044 AGAACAAAACGTAGAACCATCG 57.015 40.909 0.00 0.00 0.00 3.84
592 597 3.185797 AGAACAAAACGTAGAACCATCGC 59.814 43.478 0.00 0.00 0.00 4.58
596 601 4.201930 ACAAAACGTAGAACCATCGCAAAA 60.202 37.500 0.00 0.00 0.00 2.44
845 870 4.954118 ACGGTGACCTCCCTGGCA 62.954 66.667 0.00 0.00 40.22 4.92
851 876 1.377856 GACCTCCCTGGCAAAGAGC 60.378 63.158 7.71 0.00 44.65 4.09
852 877 1.846712 GACCTCCCTGGCAAAGAGCT 61.847 60.000 7.71 0.00 44.79 4.09
916 941 0.673644 GGGAGAGCAAGCGCAAGTAA 60.674 55.000 11.47 0.00 42.27 2.24
957 994 5.477291 CCATCCATCTATAGACTACACCGTT 59.523 44.000 4.10 0.00 0.00 4.44
997 1034 4.951963 GCTAGCTAGCCACCGCGG 62.952 72.222 31.67 26.86 43.39 6.46
1104 1141 3.615056 TGTGTGACTACGAGTTTGTTGTG 59.385 43.478 0.00 0.00 0.00 3.33
1305 1342 0.895530 TCCGCCTAGAGGTTCACAAG 59.104 55.000 0.00 0.00 37.57 3.16
1608 1651 1.102809 CGGCAGCTCCCATGCATAAA 61.103 55.000 0.00 0.00 45.68 1.40
1717 1764 0.379316 GGGCTCGTCGTTTGTGTTTT 59.621 50.000 0.00 0.00 0.00 2.43
1723 1770 4.190304 TCGTCGTTTGTGTTTTCATCAG 57.810 40.909 0.00 0.00 0.00 2.90
1792 1844 6.818142 CCCTGCCTTCCTGTTTAATTTATTTG 59.182 38.462 0.00 0.00 0.00 2.32
1837 1894 2.696989 TCCATGCATGATGACTCGTT 57.303 45.000 28.31 0.00 33.31 3.85
1876 1933 0.664224 TTCGCCATGCATGCACATAG 59.336 50.000 25.37 15.13 0.00 2.23
1885 1942 3.523547 TGCATGCACATAGCCAATTTTC 58.476 40.909 18.46 0.00 44.83 2.29
1898 1955 5.252547 AGCCAATTTTCTGTTTGGTGTTTT 58.747 33.333 3.85 0.00 43.54 2.43
1899 1956 5.123661 AGCCAATTTTCTGTTTGGTGTTTTG 59.876 36.000 3.85 0.00 43.54 2.44
1920 1977 1.948611 GCAAGCCACCTCCGTGAATTA 60.949 52.381 0.00 0.00 43.14 1.40
1968 2025 8.387813 AGAACTGTTAAAACAAGGGGTCATATA 58.612 33.333 0.00 0.00 38.66 0.86
2035 2092 3.157087 GGCTTCCAAGAATTTCAGGACA 58.843 45.455 9.37 3.03 0.00 4.02
2096 2153 5.418840 GTGGGTGTTGGAATTATTCATGAGT 59.581 40.000 7.29 0.00 0.00 3.41
2128 2191 8.316497 TGGGATGAAAATTTGATTAGGCATTA 57.684 30.769 0.00 0.00 0.00 1.90
2129 2192 8.423349 TGGGATGAAAATTTGATTAGGCATTAG 58.577 33.333 0.00 0.00 0.00 1.73
2199 2262 2.496470 GTGGGAGACGGTGATCTAGTTT 59.504 50.000 0.00 0.00 0.00 2.66
2211 2274 6.461092 CGGTGATCTAGTTTCTTGGCACTATA 60.461 42.308 0.00 0.00 0.00 1.31
2248 2311 3.990092 TCTCTGTGAAAAGTGCGTACAT 58.010 40.909 6.38 0.00 0.00 2.29
2274 2337 6.084326 TGGCTTTAAATCTCAAGAACAACC 57.916 37.500 0.00 0.00 0.00 3.77
2284 2347 1.064825 AAGAACAACCGGGGTGAGAT 58.935 50.000 21.14 4.12 0.00 2.75
2304 2367 5.336945 AGATAGGAATATCCAGTGCTGCTA 58.663 41.667 0.00 0.00 39.61 3.49
2328 2391 0.034896 TGAGGAAAGAAGACCGTGGC 59.965 55.000 0.00 0.00 0.00 5.01
2409 2472 1.879380 CCAACAGTTTGGCGATTCAGA 59.121 47.619 0.00 0.00 46.09 3.27
2420 2483 6.405278 TTGGCGATTCAGATGAATAGAGTA 57.595 37.500 16.75 2.73 44.14 2.59
2461 2524 5.182570 TCTCCGGTATGTGTACTATATGTGC 59.817 44.000 0.00 0.00 0.00 4.57
2466 2529 6.700081 CGGTATGTGTACTATATGTGCAGTTT 59.300 38.462 0.00 0.00 41.75 2.66
2467 2530 7.863877 CGGTATGTGTACTATATGTGCAGTTTA 59.136 37.037 0.00 0.00 41.75 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 89 1.087202 TTGACAGTGACGCGCAACTT 61.087 50.000 5.73 1.19 0.00 2.66
153 157 3.119708 GGCTTCGCTGAGTTCAATTCATT 60.120 43.478 0.00 0.00 0.00 2.57
177 181 3.752665 TCTCGGATATCGCCTAGTTCTT 58.247 45.455 0.00 0.00 39.05 2.52
367 371 6.708949 GGTCAAAAACTAGATGGACACTTACA 59.291 38.462 0.00 0.00 0.00 2.41
376 380 9.846248 CTTTGATTTAGGTCAAAAACTAGATGG 57.154 33.333 0.00 0.00 44.76 3.51
429 433 3.871594 GTCATACATGCCGCTACTTTTCT 59.128 43.478 0.00 0.00 0.00 2.52
440 444 5.924475 ACTAATTTAGCGTCATACATGCC 57.076 39.130 3.28 0.00 37.82 4.40
501 505 9.914131 GTAGTAGCATATATGACATCAAGTTGA 57.086 33.333 17.10 8.27 0.00 3.18
571 576 3.059461 TGCGATGGTTCTACGTTTTGTTC 60.059 43.478 0.00 0.00 0.00 3.18
572 577 2.873472 TGCGATGGTTCTACGTTTTGTT 59.127 40.909 0.00 0.00 0.00 2.83
573 578 2.485903 TGCGATGGTTCTACGTTTTGT 58.514 42.857 0.00 0.00 0.00 2.83
574 579 3.529634 TTGCGATGGTTCTACGTTTTG 57.470 42.857 0.00 0.00 0.00 2.44
575 580 4.555348 TTTTGCGATGGTTCTACGTTTT 57.445 36.364 0.00 0.00 0.00 2.43
576 581 4.555348 TTTTTGCGATGGTTCTACGTTT 57.445 36.364 0.00 0.00 0.00 3.60
596 601 7.130269 GTGAATAAGTGCACTTCTACGTTTTT 58.870 34.615 34.29 15.56 37.40 1.94
845 870 7.821846 GGTAGCTGCATTTATATAGAGCTCTTT 59.178 37.037 23.84 17.09 37.86 2.52
916 941 5.150715 TGGATGGATAGATGAGTTGCTAGT 58.849 41.667 0.00 0.00 0.00 2.57
957 994 7.907389 AGCTTACCTCCGATATGAATATGAAA 58.093 34.615 0.00 0.00 0.00 2.69
1104 1141 3.911964 CCCAATTTTCATTGAACGTCGAC 59.088 43.478 5.18 5.18 42.35 4.20
1305 1342 1.524482 GATCTCCAGCCACCAGGTC 59.476 63.158 0.00 0.00 37.19 3.85
1608 1651 3.197333 AGCTGCTGATGACAAGATACAGT 59.803 43.478 0.00 0.00 0.00 3.55
1717 1764 4.704540 AGGAAACAAACACAACACTGATGA 59.295 37.500 0.00 0.00 0.00 2.92
1723 1770 4.816392 AGGAAAGGAAACAAACACAACAC 58.184 39.130 0.00 0.00 0.00 3.32
1792 1844 1.451651 CGCAAACAATGAGCCGAAAAC 59.548 47.619 0.00 0.00 0.00 2.43
1837 1894 1.098712 GGATGCACGGCGGGAAATAA 61.099 55.000 16.21 0.00 0.00 1.40
1885 1942 1.665169 GCTTGCCAAAACACCAAACAG 59.335 47.619 0.00 0.00 0.00 3.16
1898 1955 4.641645 CACGGAGGTGGCTTGCCA 62.642 66.667 10.65 10.65 40.58 4.92
1899 1956 3.842925 TTCACGGAGGTGGCTTGCC 62.843 63.158 4.43 4.43 44.50 4.52
1909 1966 4.693283 TGATACCTTGCTAATTCACGGAG 58.307 43.478 0.00 0.00 0.00 4.63
1920 1977 6.077993 TCTAGACCATACATGATACCTTGCT 58.922 40.000 0.00 0.00 0.00 3.91
1968 2025 4.884668 TTTTTACCATCGACCACTCTCT 57.115 40.909 0.00 0.00 0.00 3.10
1991 2048 9.646522 AGCCAGTTATATCTCCAAATGTTAATT 57.353 29.630 0.00 0.00 0.00 1.40
1992 2049 9.646522 AAGCCAGTTATATCTCCAAATGTTAAT 57.353 29.630 0.00 0.00 0.00 1.40
2007 2064 6.603201 CCTGAAATTCTTGGAAGCCAGTTATA 59.397 38.462 0.00 0.00 33.81 0.98
2096 2153 4.945411 TCAAATTTTCATCCCATCTCCCA 58.055 39.130 0.00 0.00 0.00 4.37
2128 2191 3.877559 TCGGCATCATGATGAAAGAACT 58.122 40.909 34.65 0.00 41.20 3.01
2129 2192 4.333649 TCTTCGGCATCATGATGAAAGAAC 59.666 41.667 34.65 17.73 41.20 3.01
2186 2249 2.673368 GTGCCAAGAAACTAGATCACCG 59.327 50.000 0.00 0.00 0.00 4.94
2199 2262 5.876357 ACCACTTTTCTTATAGTGCCAAGA 58.124 37.500 0.00 0.00 40.28 3.02
2211 2274 6.591935 TCACAGAGAACATACCACTTTTCTT 58.408 36.000 0.00 0.00 0.00 2.52
2248 2311 7.040686 GGTTGTTCTTGAGATTTAAAGCCAGTA 60.041 37.037 0.00 0.00 0.00 2.74
2274 2337 3.441101 TGGATATTCCTATCTCACCCCG 58.559 50.000 0.00 0.00 37.46 5.73
2284 2347 7.553504 TTAATAGCAGCACTGGATATTCCTA 57.446 36.000 0.00 0.00 37.46 2.94
2304 2367 5.186198 CCACGGTCTTCTTTCCTCATTAAT 58.814 41.667 0.00 0.00 0.00 1.40
2328 2391 4.007659 ACCTTAGCCTTCCAAATAACGTG 58.992 43.478 0.00 0.00 0.00 4.49
2403 2466 8.311395 TGGTGAGTTACTCTATTCATCTGAAT 57.689 34.615 13.86 10.10 45.77 2.57
2409 2472 7.492669 CGTTTGATGGTGAGTTACTCTATTCAT 59.507 37.037 13.86 10.86 0.00 2.57
2420 2483 2.550208 GGAGACCGTTTGATGGTGAGTT 60.550 50.000 0.00 0.00 37.69 3.01


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

AutoCloner maintained by Alex Coulton.