Multiple sequence alignment - TraesCS1D01G230700

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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 TraesCS1D01G230700 chr1D 100.000 2633 0 0 1 2633 318737549 318740181 0.000000e+00 4863.0
1 TraesCS1D01G230700 chr1A 93.852 2586 93 24 87 2633 405009717 405007159 0.000000e+00 3834.0
2 TraesCS1D01G230700 chr1A 95.294 85 3 1 1 84 405010044 405009960 1.640000e-27 134.0
3 TraesCS1D01G230700 chr1B 91.245 2627 127 39 84 2633 431196849 431199449 0.000000e+00 3482.0
4 TraesCS1D01G230700 chr1B 92.941 85 5 1 1 84 431196527 431196611 3.560000e-24 122.0
5 TraesCS1D01G230700 chr3A 87.619 105 13 0 2343 2447 382152023 382152127 3.560000e-24 122.0
6 TraesCS1D01G230700 chr7A 81.481 108 17 3 2053 2159 701239912 701239807 4.670000e-13 86.1
7 TraesCS1D01G230700 chr5B 79.310 116 13 6 2022 2128 43818587 43818474 1.310000e-08 71.3


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 TraesCS1D01G230700 chr1D 318737549 318740181 2632 False 4863 4863 100.000 1 2633 1 chr1D.!!$F1 2632
1 TraesCS1D01G230700 chr1A 405007159 405010044 2885 True 1984 3834 94.573 1 2633 2 chr1A.!!$R1 2632
2 TraesCS1D01G230700 chr1B 431196527 431199449 2922 False 1802 3482 92.093 1 2633 2 chr1B.!!$F1 2632

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
85 87 0.453615 GCTAGAGATCGCGGATGTCG 60.454 60.0 6.13 0.0 37.41 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 1916 2.047655 TGAACGATGTCGGTGGGC 60.048 61.111 7.38 0.0 40.66 5.36 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
46 47 5.776173 AGACCAAGAGACTCAATATACGG 57.224 43.478 5.02 0.00 0.00 4.02
49 51 6.380274 AGACCAAGAGACTCAATATACGGAAA 59.620 38.462 5.02 0.00 0.00 3.13
84 86 0.593618 TGCTAGAGATCGCGGATGTC 59.406 55.000 6.13 6.92 33.31 3.06
85 87 0.453615 GCTAGAGATCGCGGATGTCG 60.454 60.000 6.13 0.00 37.41 4.35
97 339 1.125384 CGGATGTCGTTTACACAACGG 59.875 52.381 7.23 0.00 42.09 4.44
114 356 1.805943 ACGGTACAATTTACAACCCGC 59.194 47.619 0.00 0.00 37.51 6.13
310 552 7.686438 ACTATCAAAAATGCTCACATACACA 57.314 32.000 0.00 0.00 34.62 3.72
325 567 7.762382 TCACATACACACACAAAACAACATTA 58.238 30.769 0.00 0.00 0.00 1.90
516 758 9.965902 AGGAAAACATGATAAATCAGTAGAACT 57.034 29.630 0.00 0.00 40.64 3.01
702 947 0.606096 AAATAAAAGGCGTGGGTGGC 59.394 50.000 0.00 0.00 0.00 5.01
742 987 6.206634 CCTTTTGGCTCAAAACATACTCACTA 59.793 38.462 8.46 0.00 38.24 2.74
794 1039 2.097466 GGCCCACACGTCATTCTTTATG 59.903 50.000 0.00 0.00 35.45 1.90
925 1170 8.538409 AGCAACCATTCTAAAATTAGCAAAAG 57.462 30.769 0.00 0.00 0.00 2.27
1033 1278 0.745486 CATGATCACCTTCGCAGCCA 60.745 55.000 0.00 0.00 0.00 4.75
1257 1502 1.667830 CCTGCAACGGCTCTTCGAA 60.668 57.895 0.00 0.00 41.91 3.71
1275 1520 3.119459 TCGAATCCGAAGACCTCAAGAAG 60.119 47.826 0.00 0.00 42.51 2.85
1660 1916 2.602257 TCTGGGTTCTGCGATGTATG 57.398 50.000 0.00 0.00 0.00 2.39
1694 1950 3.120199 CGTTCAGCTGGTCAGTTATTTGG 60.120 47.826 15.13 0.00 0.00 3.28
1912 2168 7.067008 ACACACTTAAATGGTGGAATACTATGC 59.933 37.037 0.00 0.00 38.83 3.14
2175 2461 1.330655 ACATCTCTAGCCCACCCGTG 61.331 60.000 0.00 0.00 0.00 4.94
2201 2487 2.649034 GTCGGTTCTGGCAGACGA 59.351 61.111 21.77 21.77 0.00 4.20
2204 2491 2.343758 GGTTCTGGCAGACGAGCA 59.656 61.111 18.55 0.00 35.83 4.26
2283 2570 0.827925 TCACTCCCGCTCACTCTGTT 60.828 55.000 0.00 0.00 0.00 3.16
2298 2587 3.181412 ACTCTGTTTCCTCTCTCTCCCTT 60.181 47.826 0.00 0.00 0.00 3.95
2363 2676 4.394712 GAGGTGGCACGTGGGGAG 62.395 72.222 18.66 0.00 0.00 4.30
2392 2705 7.162082 GTGGAGATTATTCGGAAGTGGATAAT 58.838 38.462 0.00 0.00 0.00 1.28
2404 2717 2.203294 GATAATTGGCCGGGCGGT 60.203 61.111 24.45 11.60 37.65 5.68
2419 2732 3.286751 GGTGGCAGCTTCGCAACA 61.287 61.111 9.90 0.00 37.59 3.33
2463 2776 0.179124 CCGAGGCAGAAGCAGACTAC 60.179 60.000 0.00 0.00 44.61 2.73
2464 2777 0.528017 CGAGGCAGAAGCAGACTACA 59.472 55.000 0.00 0.00 44.61 2.74
2465 2778 1.734047 CGAGGCAGAAGCAGACTACAC 60.734 57.143 0.00 0.00 44.61 2.90
2466 2779 0.610687 AGGCAGAAGCAGACTACACC 59.389 55.000 0.00 0.00 44.61 4.16
2467 2780 0.321671 GGCAGAAGCAGACTACACCA 59.678 55.000 0.00 0.00 44.61 4.17
2468 2781 1.674221 GGCAGAAGCAGACTACACCAG 60.674 57.143 0.00 0.00 44.61 4.00
2469 2782 1.273606 GCAGAAGCAGACTACACCAGA 59.726 52.381 0.00 0.00 41.58 3.86
2470 2783 2.673610 GCAGAAGCAGACTACACCAGAG 60.674 54.545 0.00 0.00 41.58 3.35
2471 2784 2.094286 CAGAAGCAGACTACACCAGAGG 60.094 54.545 0.00 0.00 0.00 3.69
2472 2785 0.610687 AAGCAGACTACACCAGAGGC 59.389 55.000 0.00 0.00 0.00 4.70
2473 2786 0.542938 AGCAGACTACACCAGAGGCA 60.543 55.000 0.00 0.00 0.00 4.75
2474 2787 0.108424 GCAGACTACACCAGAGGCAG 60.108 60.000 0.00 0.00 0.00 4.85
2475 2788 1.550327 CAGACTACACCAGAGGCAGA 58.450 55.000 0.00 0.00 0.00 4.26
2476 2789 1.895798 CAGACTACACCAGAGGCAGAA 59.104 52.381 0.00 0.00 0.00 3.02
2477 2790 1.896465 AGACTACACCAGAGGCAGAAC 59.104 52.381 0.00 0.00 0.00 3.01
2478 2791 0.977395 ACTACACCAGAGGCAGAACC 59.023 55.000 0.00 0.00 39.61 3.62
2600 2922 2.273449 CGCTGGGCCTCTGGATTT 59.727 61.111 4.53 0.00 0.00 2.17
2601 2923 1.379044 CGCTGGGCCTCTGGATTTT 60.379 57.895 4.53 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 7.724506 TCCGTATATTGAGTCTCTTGGTCTAAT 59.275 37.037 0.65 0.00 0.00 1.73
46 47 9.171701 CTCTAGCATTAACGTAGTACATCTTTC 57.828 37.037 0.38 0.00 45.00 2.62
49 51 8.624367 ATCTCTAGCATTAACGTAGTACATCT 57.376 34.615 0.38 0.00 45.00 2.90
84 86 6.417327 TGTAAATTGTACCGTTGTGTAAACG 58.583 36.000 3.72 3.72 42.74 3.60
85 87 7.165647 GGTTGTAAATTGTACCGTTGTGTAAAC 59.834 37.037 0.00 0.00 0.00 2.01
97 339 5.868043 AGTAAGCGGGTTGTAAATTGTAC 57.132 39.130 2.08 0.00 0.00 2.90
200 442 7.472334 AGGTTTCATTACTGCTTCATTTCAT 57.528 32.000 0.00 0.00 0.00 2.57
245 487 8.876275 TGTTTAATAGACACACTTCTACGTTT 57.124 30.769 0.00 0.00 30.75 3.60
246 488 9.485206 AATGTTTAATAGACACACTTCTACGTT 57.515 29.630 0.00 0.00 30.75 3.99
516 758 9.504710 TTTGACTCGTTTCATTCGAAATTTTAA 57.495 25.926 0.00 0.00 42.90 1.52
522 764 6.720343 TCATTTTGACTCGTTTCATTCGAAA 58.280 32.000 0.00 0.00 38.83 3.46
629 874 6.357579 TGAACCAAATGCCTGATTTATGTT 57.642 33.333 0.00 0.00 33.81 2.71
742 987 1.627195 GGGGTCCCATGGTAAGTAGGT 60.627 57.143 11.73 0.00 35.81 3.08
794 1039 8.073768 TGGATTGAATCACGTTCTTCTTAAAAC 58.926 33.333 7.56 0.00 37.72 2.43
864 1109 0.887933 CAATTACAGGGTGTGGGTGC 59.112 55.000 0.00 0.00 0.00 5.01
925 1170 2.152016 GGGTATTTATCCTTGCGAGGC 58.848 52.381 16.01 0.00 43.21 4.70
1257 1502 4.026744 TCATCTTCTTGAGGTCTTCGGAT 58.973 43.478 0.00 0.00 0.00 4.18
1660 1916 2.047655 TGAACGATGTCGGTGGGC 60.048 61.111 7.38 0.00 40.66 5.36
1780 2036 9.116054 GCTAGCACGTAGTACTAATTTCTATTC 57.884 37.037 10.63 0.00 41.61 1.75
1782 2038 8.393671 AGCTAGCACGTAGTACTAATTTCTAT 57.606 34.615 18.83 0.00 41.61 1.98
1783 2039 7.798596 AGCTAGCACGTAGTACTAATTTCTA 57.201 36.000 18.83 4.06 41.61 2.10
1787 2043 7.063074 CACAAAAGCTAGCACGTAGTACTAATT 59.937 37.037 18.83 0.00 41.61 1.40
1789 2045 5.860182 CACAAAAGCTAGCACGTAGTACTAA 59.140 40.000 18.83 0.00 41.61 2.24
1790 2046 5.396484 CACAAAAGCTAGCACGTAGTACTA 58.604 41.667 18.83 0.00 41.61 1.82
1791 2047 4.235360 CACAAAAGCTAGCACGTAGTACT 58.765 43.478 18.83 0.00 41.61 2.73
1792 2048 3.367025 CCACAAAAGCTAGCACGTAGTAC 59.633 47.826 18.83 0.00 41.61 2.73
1795 2051 2.683968 TCCACAAAAGCTAGCACGTAG 58.316 47.619 18.83 5.10 0.00 3.51
2175 2461 1.080705 CAGAACCGACGTGGACCTC 60.081 63.158 10.46 4.88 42.00 3.85
2204 2491 1.134401 CCCTAATGGACGTCAGCACAT 60.134 52.381 18.91 8.54 35.39 3.21
2215 2502 2.124901 CGGTTGCGCCCTAATGGA 60.125 61.111 4.18 0.00 35.39 3.41
2283 2570 3.629539 CCAGATCAAGGGAGAGAGAGGAA 60.630 52.174 0.00 0.00 0.00 3.36
2298 2587 3.292492 TCGCTTAGGTCTACCAGATCA 57.708 47.619 1.26 0.00 38.89 2.92
2357 2670 1.023719 TAATCTCCACCCTCTCCCCA 58.976 55.000 0.00 0.00 0.00 4.96
2363 2676 3.388350 ACTTCCGAATAATCTCCACCCTC 59.612 47.826 0.00 0.00 0.00 4.30
2368 2681 6.740944 TTATCCACTTCCGAATAATCTCCA 57.259 37.500 0.00 0.00 0.00 3.86
2443 2756 1.949847 TAGTCTGCTTCTGCCTCGGC 61.950 60.000 0.00 0.00 42.35 5.54
2463 2776 1.302832 GTGGGTTCTGCCTCTGGTG 60.303 63.158 0.00 0.00 37.43 4.17
2464 2777 2.529744 GGTGGGTTCTGCCTCTGGT 61.530 63.158 0.00 0.00 37.43 4.00
2465 2778 2.352805 GGTGGGTTCTGCCTCTGG 59.647 66.667 0.00 0.00 37.43 3.86
2466 2779 1.002868 CTGGTGGGTTCTGCCTCTG 60.003 63.158 0.00 0.00 37.43 3.35
2467 2780 1.152030 TCTGGTGGGTTCTGCCTCT 60.152 57.895 0.00 0.00 37.43 3.69
2468 2781 1.298014 CTCTGGTGGGTTCTGCCTC 59.702 63.158 0.00 0.00 37.43 4.70
2469 2782 2.227036 CCTCTGGTGGGTTCTGCCT 61.227 63.158 0.00 0.00 37.43 4.75
2470 2783 2.352805 CCTCTGGTGGGTTCTGCC 59.647 66.667 0.00 0.00 0.00 4.85
2471 2784 2.360475 GCCTCTGGTGGGTTCTGC 60.360 66.667 0.00 0.00 0.00 4.26
2472 2785 1.302832 GTGCCTCTGGTGGGTTCTG 60.303 63.158 0.00 0.00 0.00 3.02
2473 2786 1.352622 TTGTGCCTCTGGTGGGTTCT 61.353 55.000 0.00 0.00 0.00 3.01
2474 2787 1.150536 TTGTGCCTCTGGTGGGTTC 59.849 57.895 0.00 0.00 0.00 3.62
2475 2788 1.152756 GTTGTGCCTCTGGTGGGTT 60.153 57.895 0.00 0.00 0.00 4.11
2476 2789 2.515901 GTTGTGCCTCTGGTGGGT 59.484 61.111 0.00 0.00 0.00 4.51
2477 2790 1.488705 TAGGTTGTGCCTCTGGTGGG 61.489 60.000 0.00 0.00 46.96 4.61
2478 2791 0.321653 GTAGGTTGTGCCTCTGGTGG 60.322 60.000 0.00 0.00 46.96 4.61
2600 2922 9.439500 AATATAACAAACTTACTCAACGCCTAA 57.561 29.630 0.00 0.00 0.00 2.69
2601 2923 9.090692 GAATATAACAAACTTACTCAACGCCTA 57.909 33.333 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.