Multiple sequence alignment - TraesCS5D01G133900

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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 TraesCS5D01G133900 chr5D 100.000 2339 0 0 1 2339 213946614 213944276 0.000000e+00 4320
1 TraesCS5D01G133900 chr5A 95.076 1767 45 14 1 1733 279102500 279100742 0.000000e+00 2743
2 TraesCS5D01G133900 chr5A 89.013 628 24 22 1750 2339 279100685 279100065 0.000000e+00 736
3 TraesCS5D01G133900 chr5B 91.934 1686 52 23 123 1747 228498351 228496689 0.000000e+00 2283
4 TraesCS5D01G133900 chr5B 89.493 533 20 21 1829 2339 228496116 228495598 1.960000e-180 641
5 TraesCS5D01G133900 chr5B 97.037 135 0 1 1 131 228498611 228498477 8.410000e-55 224
6 TraesCS5D01G133900 chr5B 87.234 94 3 4 1737 1829 228496469 228496384 5.320000e-17 99


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 TraesCS5D01G133900 chr5D 213944276 213946614 2338 True 4320.00 4320 100.0000 1 2339 1 chr5D.!!$R1 2338
1 TraesCS5D01G133900 chr5A 279100065 279102500 2435 True 1739.50 2743 92.0445 1 2339 2 chr5A.!!$R1 2338
2 TraesCS5D01G133900 chr5B 228495598 228498611 3013 True 811.75 2283 91.4245 1 2339 4 chr5B.!!$R1 2338

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
942 1103 1.004745 TGCCCACCTGAAGAGGAAATC 59.995 52.381 0.0 0.0 42.93 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2708 1.150827 TCGATGCTGCTGTGTTTCAG 58.849 50.0 0.0 0.0 46.12 3.02 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
200 339 2.295885 GGACTGCAGGATTCCATTGAG 58.704 52.381 19.93 0.00 0.00 3.02
201 340 2.356535 GGACTGCAGGATTCCATTGAGT 60.357 50.000 19.93 1.18 0.00 3.41
203 342 4.445448 GGACTGCAGGATTCCATTGAGTAT 60.445 45.833 19.93 0.00 0.00 2.12
204 343 5.221722 GGACTGCAGGATTCCATTGAGTATA 60.222 44.000 19.93 0.00 0.00 1.47
205 344 5.615289 ACTGCAGGATTCCATTGAGTATAC 58.385 41.667 19.93 0.00 0.00 1.47
256 411 4.435121 GCTCGGTTAAAGACACCATTTACG 60.435 45.833 0.00 0.00 33.36 3.18
503 658 2.371841 TGGCCTCACAAATGTGTCTAGT 59.628 45.455 12.87 0.00 45.76 2.57
506 661 4.278419 GGCCTCACAAATGTGTCTAGTTTT 59.722 41.667 12.87 0.00 45.76 2.43
542 697 4.778534 TCTCCTGTTTTCCTGTAGTACG 57.221 45.455 0.00 0.00 0.00 3.67
543 698 4.147321 TCTCCTGTTTTCCTGTAGTACGT 58.853 43.478 0.00 0.00 0.00 3.57
544 699 5.316167 TCTCCTGTTTTCCTGTAGTACGTA 58.684 41.667 0.00 0.00 0.00 3.57
545 700 5.182001 TCTCCTGTTTTCCTGTAGTACGTAC 59.818 44.000 18.10 18.10 0.00 3.67
546 701 5.072741 TCCTGTTTTCCTGTAGTACGTACT 58.927 41.667 29.62 29.62 40.24 2.73
547 702 5.048504 TCCTGTTTTCCTGTAGTACGTACTG 60.049 44.000 33.23 19.09 37.10 2.74
775 932 4.466726 CCCTCCTATATAAAGACCTTCGGG 59.533 50.000 0.00 0.00 41.87 5.14
888 1045 4.498177 GCTTTTCCTTGTGTTCTTCCTCAC 60.498 45.833 0.00 0.00 35.43 3.51
912 1069 3.801698 AGGAGTATGTTATGCAGCAGTG 58.198 45.455 0.00 0.00 0.00 3.66
925 1086 2.331132 GCAGTGCCTCTGTTCTGCC 61.331 63.158 2.85 0.00 44.84 4.85
942 1103 1.004745 TGCCCACCTGAAGAGGAAATC 59.995 52.381 0.00 0.00 42.93 2.17
1272 1458 3.655810 CTGCCTCGTGGACCTGCTC 62.656 68.421 7.92 0.00 34.57 4.26
1417 1603 2.732468 CTCGATCAGGCGATGCGG 60.732 66.667 0.00 0.00 39.85 5.69
1559 1755 5.065474 GGTCAGTTTAATTAGCGTTATGGCA 59.935 40.000 0.00 0.00 34.64 4.92
1579 1775 3.371168 CAAGTTTCCGATTGGTGTTGTG 58.629 45.455 0.00 0.00 36.30 3.33
1674 1870 2.280628 GCTAAGCTAGCGATGGTTGTT 58.719 47.619 9.55 0.00 42.62 2.83
1680 1876 2.423538 GCTAGCGATGGTTGTTTCCAAT 59.576 45.455 0.00 0.00 41.09 3.16
1681 1877 3.625764 GCTAGCGATGGTTGTTTCCAATA 59.374 43.478 0.00 0.00 41.09 1.90
1683 1879 5.221048 GCTAGCGATGGTTGTTTCCAATAAT 60.221 40.000 0.00 0.00 41.09 1.28
1686 1882 5.868801 AGCGATGGTTGTTTCCAATAATTTG 59.131 36.000 0.00 0.00 41.09 2.32
1699 1899 6.908825 TCCAATAATTTGTAGTCAACTGTGC 58.091 36.000 0.00 0.00 32.93 4.57
1702 1902 7.538678 CCAATAATTTGTAGTCAACTGTGCTTC 59.461 37.037 0.00 0.00 32.93 3.86
1704 1904 3.838244 TTGTAGTCAACTGTGCTTCCT 57.162 42.857 0.00 0.00 0.00 3.36
1724 1924 5.669477 TCCTCCATGTTTTTCTGGTTTTTG 58.331 37.500 0.00 0.00 34.03 2.44
1730 1930 7.609532 TCCATGTTTTTCTGGTTTTTGTTCAAT 59.390 29.630 0.00 0.00 34.03 2.57
1733 1933 8.558973 TGTTTTTCTGGTTTTTGTTCAATGAT 57.441 26.923 0.00 0.00 0.00 2.45
1734 1934 8.449397 TGTTTTTCTGGTTTTTGTTCAATGATG 58.551 29.630 0.00 0.00 0.00 3.07
1735 1935 8.663911 GTTTTTCTGGTTTTTGTTCAATGATGA 58.336 29.630 0.00 0.00 0.00 2.92
1740 2167 8.352201 TCTGGTTTTTGTTCAATGATGACTTAG 58.648 33.333 0.00 0.00 34.61 2.18
1831 2543 8.021955 AGTTAACACTAATTTTGTAGTACCGC 57.978 34.615 8.61 0.00 32.92 5.68
1842 2554 2.252127 TAGTACCGCGAAACCCGTCG 62.252 60.000 8.23 0.00 43.98 5.12
1893 2606 3.160679 ACCAAGTATTTGAGCCTTGCT 57.839 42.857 0.00 0.00 43.88 3.91
1926 2639 1.828832 CATAGCTCTGTTCGTCGTCC 58.171 55.000 0.00 0.00 0.00 4.79
1991 2704 1.377366 GGCTCAGATCGACTGTCGGA 61.377 60.000 27.69 16.53 45.86 4.55
1992 2705 0.248296 GCTCAGATCGACTGTCGGAC 60.248 60.000 27.69 20.79 45.86 4.79
1993 2706 1.374560 CTCAGATCGACTGTCGGACT 58.625 55.000 27.69 22.40 45.86 3.85
1994 2707 1.063321 CTCAGATCGACTGTCGGACTG 59.937 57.143 30.82 30.82 45.86 3.51
1995 2708 0.524392 CAGATCGACTGTCGGACTGC 60.524 60.000 28.31 16.73 40.88 4.40
1996 2709 0.678366 AGATCGACTGTCGGACTGCT 60.678 55.000 27.69 15.35 40.88 4.24
2075 2800 4.422073 TGACACACAGACTGGAAGAAAT 57.578 40.909 7.51 0.00 37.43 2.17
2079 2804 6.998074 TGACACACAGACTGGAAGAAATTAAT 59.002 34.615 7.51 0.00 37.43 1.40
2080 2805 7.502226 TGACACACAGACTGGAAGAAATTAATT 59.498 33.333 7.51 0.00 37.43 1.40
2264 2999 5.513094 CGGCCTGATCAAAAGGGAGATTATA 60.513 44.000 0.00 0.00 35.17 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 339 2.914695 TGGCCGTACCCATTGTATAC 57.085 50.000 0.00 0.00 37.83 1.47
201 340 2.485835 GCTTGGCCGTACCCATTGTATA 60.486 50.000 0.00 0.00 37.83 1.47
203 342 0.393267 GCTTGGCCGTACCCATTGTA 60.393 55.000 0.00 0.00 37.83 2.41
204 343 1.677633 GCTTGGCCGTACCCATTGT 60.678 57.895 0.00 0.00 37.83 2.71
205 344 2.414785 GGCTTGGCCGTACCCATTG 61.415 63.158 0.00 0.00 39.62 2.82
256 411 2.596904 TAGGAGATGCGCCACTTTAC 57.403 50.000 4.18 0.00 0.00 2.01
459 614 7.272731 GCCAAATTTACTCTTATTTTCGTGGTC 59.727 37.037 0.00 0.00 0.00 4.02
503 658 7.928873 ACAGGAGAAATCTATAAGGTGGAAAA 58.071 34.615 0.00 0.00 0.00 2.29
506 661 7.510675 AAACAGGAGAAATCTATAAGGTGGA 57.489 36.000 0.00 0.00 0.00 4.02
523 678 5.048504 CAGTACGTACTACAGGAAAACAGGA 60.049 44.000 26.95 0.00 34.13 3.86
542 697 5.593679 TGAGCTTATACCAACCTCAGTAC 57.406 43.478 0.00 0.00 0.00 2.73
543 698 7.907841 TTATGAGCTTATACCAACCTCAGTA 57.092 36.000 0.00 0.00 36.16 2.74
544 699 6.808321 TTATGAGCTTATACCAACCTCAGT 57.192 37.500 0.00 0.00 36.16 3.41
545 700 8.682936 ATTTTATGAGCTTATACCAACCTCAG 57.317 34.615 0.00 0.00 36.16 3.35
775 932 2.306847 TGGTTGAGGACTTTGAAAGGC 58.693 47.619 10.02 5.98 35.07 4.35
888 1045 3.977427 TGCTGCATAACATACTCCTACG 58.023 45.455 0.00 0.00 0.00 3.51
912 1069 2.360475 GGTGGGCAGAACAGAGGC 60.360 66.667 0.00 0.00 0.00 4.70
914 1071 0.397941 TTCAGGTGGGCAGAACAGAG 59.602 55.000 0.00 0.00 0.00 3.35
925 1086 4.026356 ACAAGATTTCCTCTTCAGGTGG 57.974 45.455 0.00 0.00 42.48 4.61
1155 1341 1.153647 CACCATCGGCGACTTGCTA 60.154 57.895 13.76 0.00 45.43 3.49
1370 1556 0.035317 GTGTGAGCATCCACTGGACA 59.965 55.000 0.00 0.00 37.89 4.02
1417 1603 1.140652 CTCCTCCAGCCTCAAGATTCC 59.859 57.143 0.00 0.00 0.00 3.01
1498 1684 8.496751 CACAAAGGAAAGTAACTACTTAAGCTC 58.503 37.037 1.29 0.00 45.17 4.09
1559 1755 2.360801 CCACAACACCAATCGGAAACTT 59.639 45.455 0.00 0.00 35.59 2.66
1579 1775 4.538746 AACTTAGAAGACCACTGCTACC 57.461 45.455 0.00 0.00 34.31 3.18
1674 1870 7.230510 AGCACAGTTGACTACAAATTATTGGAA 59.769 33.333 0.00 0.00 41.01 3.53
1680 1876 6.296026 AGGAAGCACAGTTGACTACAAATTA 58.704 36.000 0.00 0.00 37.77 1.40
1681 1877 5.133221 AGGAAGCACAGTTGACTACAAATT 58.867 37.500 0.00 0.00 37.77 1.82
1683 1879 4.127171 GAGGAAGCACAGTTGACTACAAA 58.873 43.478 0.00 0.00 37.77 2.83
1686 1882 2.037251 TGGAGGAAGCACAGTTGACTAC 59.963 50.000 0.00 0.00 0.00 2.73
1699 1899 5.535753 AAACCAGAAAAACATGGAGGAAG 57.464 39.130 0.00 0.00 39.02 3.46
1702 1902 5.427378 ACAAAAACCAGAAAAACATGGAGG 58.573 37.500 0.00 0.00 39.02 4.30
1704 1904 6.467677 TGAACAAAAACCAGAAAAACATGGA 58.532 32.000 0.00 0.00 39.02 3.41
1724 1924 8.475639 TCCTACCTAACTAAGTCATCATTGAAC 58.524 37.037 0.00 0.00 32.48 3.18
1730 1930 5.897250 TGCATCCTACCTAACTAAGTCATCA 59.103 40.000 0.00 0.00 0.00 3.07
1733 1933 5.395324 GCTTGCATCCTACCTAACTAAGTCA 60.395 44.000 0.00 0.00 0.00 3.41
1734 1934 5.051153 GCTTGCATCCTACCTAACTAAGTC 58.949 45.833 0.00 0.00 0.00 3.01
1735 1935 4.441634 CGCTTGCATCCTACCTAACTAAGT 60.442 45.833 0.00 0.00 0.00 2.24
1740 2167 1.583054 CCGCTTGCATCCTACCTAAC 58.417 55.000 0.00 0.00 0.00 2.34
1780 2224 4.508971 CAGCTAGTAATTGATGCGTTTCG 58.491 43.478 0.00 0.00 0.00 3.46
1842 2554 3.207669 CCTCAGGATGCAAGCGGC 61.208 66.667 0.00 0.00 45.13 6.53
1926 2639 5.055642 TCACGACACCTGAAGTATTACTG 57.944 43.478 0.00 0.00 0.00 2.74
1995 2708 1.150827 TCGATGCTGCTGTGTTTCAG 58.849 50.000 0.00 0.00 46.12 3.02
1996 2709 1.733912 GATCGATGCTGCTGTGTTTCA 59.266 47.619 0.54 0.00 0.00 2.69
2052 2777 2.388735 TCTTCCAGTCTGTGTGTCAGT 58.611 47.619 0.00 0.00 43.97 3.41
2079 2804 6.435591 TGTGTAATGATGCCCTTGTTTATCAA 59.564 34.615 0.00 0.00 33.71 2.57
2080 2805 5.948758 TGTGTAATGATGCCCTTGTTTATCA 59.051 36.000 0.00 0.00 34.42 2.15
2217 2946 2.250924 CCTTGAGAAAGCCATGGGTTT 58.749 47.619 35.75 35.75 46.65 3.27
2280 3015 5.416326 CCGATCGAGAGGTTTTAGGATATCT 59.584 44.000 18.66 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.