Multiple sequence alignment - TraesCS7B01G037100

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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 TraesCS7B01G037100 chr7B 100.000 2639 0 0 1 2639 36428069 36425431 0.000000e+00 4874.0
1 TraesCS7B01G037100 chr7B 80.851 188 31 5 1970 2155 316357333 316357149 2.740000e-30 143.0
2 TraesCS7B01G037100 chr6B 95.249 1810 73 7 3 1801 147950688 147948881 0.000000e+00 2854.0
3 TraesCS7B01G037100 chr6B 93.363 1808 108 7 3 1801 567118188 567116384 0.000000e+00 2663.0
4 TraesCS7B01G037100 chr6B 86.261 706 65 13 1965 2639 717732473 717733177 0.000000e+00 737.0
5 TraesCS7B01G037100 chr6B 77.011 174 34 6 1967 2137 223249641 223249811 7.780000e-16 95.3
6 TraesCS7B01G037100 chr5D 92.104 2039 124 22 3 2015 387241778 387243805 0.000000e+00 2839.0
7 TraesCS7B01G037100 chr5D 84.909 656 55 24 2016 2639 387243856 387244499 8.020000e-175 623.0
8 TraesCS7B01G037100 chr2B 92.554 2001 116 20 3 1976 664330485 664328491 0.000000e+00 2839.0
9 TraesCS7B01G037100 chr2B 90.674 697 38 9 1970 2639 664328456 664327760 0.000000e+00 902.0
10 TraesCS7B01G037100 chr2B 85.735 701 66 17 1971 2639 225323777 225323079 0.000000e+00 710.0
11 TraesCS7B01G037100 chr4D 94.868 1812 75 14 3 1808 473971222 473969423 0.000000e+00 2815.0
12 TraesCS7B01G037100 chr4D 88.575 709 42 16 1970 2639 473876103 473875395 0.000000e+00 824.0
13 TraesCS7B01G037100 chr5B 92.362 1990 123 14 3 1966 529280455 529282441 0.000000e+00 2806.0
14 TraesCS7B01G037100 chr5B 95.300 1702 71 7 271 1968 575037465 575035769 0.000000e+00 2691.0
15 TraesCS7B01G037100 chr5B 94.328 670 38 0 1970 2639 649895327 649895996 0.000000e+00 1027.0
16 TraesCS7B01G037100 chr5B 88.937 696 49 11 1970 2639 529282486 529283179 0.000000e+00 833.0
17 TraesCS7B01G037100 chr5B 95.154 454 19 1 2189 2639 575025523 575025070 0.000000e+00 713.0
18 TraesCS7B01G037100 chr5B 93.151 219 15 0 1752 1970 649895068 649895286 3.280000e-84 322.0
19 TraesCS7B01G037100 chr5B 91.866 209 17 0 1970 2178 575035726 575035518 2.570000e-75 292.0
20 TraesCS7B01G037100 chr3D 91.513 2062 123 23 3 2015 558679302 558681360 0.000000e+00 2791.0
21 TraesCS7B01G037100 chr3D 90.529 454 43 0 2184 2637 558681596 558682049 3.760000e-168 601.0
22 TraesCS7B01G037100 chr3D 85.638 188 23 4 1967 2152 558681348 558681533 7.450000e-46 195.0
23 TraesCS7B01G037100 chr4B 94.358 1808 91 6 3 1801 622503281 622501476 0.000000e+00 2763.0
24 TraesCS7B01G037100 chr1B 93.151 438 29 1 2202 2639 359218425 359217989 2.210000e-180 641.0
25 TraesCS7B01G037100 chr4A 79.885 522 95 6 3 519 695050434 695049918 8.920000e-100 374.0
26 TraesCS7B01G037100 chr7A 93.836 146 8 1 3 148 202826911 202826767 4.420000e-53 219.0
27 TraesCS7B01G037100 chr7D 84.672 137 13 8 2022 2155 536967102 536967233 2.130000e-26 130.0
28 TraesCS7B01G037100 chr1D 78.363 171 31 6 1970 2137 491069843 491069676 3.590000e-19 106.0


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 TraesCS7B01G037100 chr7B 36425431 36428069 2638 True 4874.000000 4874 100.000000 1 2639 1 chr7B.!!$R1 2638
1 TraesCS7B01G037100 chr6B 147948881 147950688 1807 True 2854.000000 2854 95.249000 3 1801 1 chr6B.!!$R1 1798
2 TraesCS7B01G037100 chr6B 567116384 567118188 1804 True 2663.000000 2663 93.363000 3 1801 1 chr6B.!!$R2 1798
3 TraesCS7B01G037100 chr6B 717732473 717733177 704 False 737.000000 737 86.261000 1965 2639 1 chr6B.!!$F2 674
4 TraesCS7B01G037100 chr5D 387241778 387244499 2721 False 1731.000000 2839 88.506500 3 2639 2 chr5D.!!$F1 2636
5 TraesCS7B01G037100 chr2B 664327760 664330485 2725 True 1870.500000 2839 91.614000 3 2639 2 chr2B.!!$R2 2636
6 TraesCS7B01G037100 chr2B 225323079 225323777 698 True 710.000000 710 85.735000 1971 2639 1 chr2B.!!$R1 668
7 TraesCS7B01G037100 chr4D 473969423 473971222 1799 True 2815.000000 2815 94.868000 3 1808 1 chr4D.!!$R2 1805
8 TraesCS7B01G037100 chr4D 473875395 473876103 708 True 824.000000 824 88.575000 1970 2639 1 chr4D.!!$R1 669
9 TraesCS7B01G037100 chr5B 529280455 529283179 2724 False 1819.500000 2806 90.649500 3 2639 2 chr5B.!!$F1 2636
10 TraesCS7B01G037100 chr5B 575035518 575037465 1947 True 1491.500000 2691 93.583000 271 2178 2 chr5B.!!$R2 1907
11 TraesCS7B01G037100 chr5B 649895068 649895996 928 False 674.500000 1027 93.739500 1752 2639 2 chr5B.!!$F2 887
12 TraesCS7B01G037100 chr3D 558679302 558682049 2747 False 1195.666667 2791 89.226667 3 2637 3 chr3D.!!$F1 2634
13 TraesCS7B01G037100 chr4B 622501476 622503281 1805 True 2763.000000 2763 94.358000 3 1801 1 chr4B.!!$R1 1798
14 TraesCS7B01G037100 chr4A 695049918 695050434 516 True 374.000000 374 79.885000 3 519 1 chr4A.!!$R1 516

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
250 251 1.040646 GTGGTGTCAGTGTGAGAGGA 58.959 55.000 0.0 0.0 0.00 3.71 F
673 677 1.547901 GCTCTAGCCAAAGGGGTGTTT 60.548 52.381 0.0 0.0 46.52 2.83 F
1549 1556 0.793250 GAAGGCTGCTCGTGAAGAAC 59.207 55.000 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1466 1473 0.098025 CTCCTTCTGACGACGCTCTC 59.902 60.000 0.00 0.0 0.00 3.20 R
1574 1581 1.134580 CCTCCTCTTGTGCATCACGAT 60.135 52.381 0.00 0.0 37.14 3.73 R
2389 2570 1.209621 TAGGGGATCCTTTTCGGGTG 58.790 55.000 12.58 0.0 41.56 4.61 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
147 148 9.778993 ATTAGATTCAACGACAAAGAAATGATG 57.221 29.630 0.00 0.00 0.00 3.07
220 221 2.354403 GGTGTTGCGTATAAGGTGGACT 60.354 50.000 0.00 0.00 0.00 3.85
250 251 1.040646 GTGGTGTCAGTGTGAGAGGA 58.959 55.000 0.00 0.00 0.00 3.71
363 364 2.229792 GAGTTCACATTGGAAGCCACA 58.770 47.619 0.00 0.00 30.78 4.17
409 410 3.394274 TCATCCTTTCCTTGACCAGTCAA 59.606 43.478 12.40 12.40 46.27 3.18
562 566 2.158957 GGTAGCGGTCATTTCATGGAGA 60.159 50.000 0.00 0.00 0.00 3.71
665 669 1.728971 CAACACGAGCTCTAGCCAAAG 59.271 52.381 12.85 0.00 43.38 2.77
673 677 1.547901 GCTCTAGCCAAAGGGGTGTTT 60.548 52.381 0.00 0.00 46.52 2.83
724 728 2.815684 TAGGACTGGTGGCCGTGGAT 62.816 60.000 0.00 0.00 0.00 3.41
1175 1181 1.740380 CGACCGCAAGAAGTCATGGAT 60.740 52.381 0.00 0.00 43.02 3.41
1292 1298 9.750125 GAGTAATCTCAAATTTTGTCCAACTTT 57.250 29.630 8.89 0.00 40.18 2.66
1464 1471 2.015587 GCATTTCAGAGAGGCTTGGAG 58.984 52.381 0.00 0.00 0.00 3.86
1466 1473 0.987294 TTTCAGAGAGGCTTGGAGGG 59.013 55.000 0.00 0.00 0.00 4.30
1549 1556 0.793250 GAAGGCTGCTCGTGAAGAAC 59.207 55.000 0.00 0.00 0.00 3.01
1719 1733 5.578336 CGGATACTTGATGATATTGCGATGT 59.422 40.000 0.00 0.00 0.00 3.06
2037 2141 2.353607 GTACTCGCGCGCATAGCT 60.354 61.111 32.61 18.35 45.59 3.32
2069 2183 4.873810 TGGTGTGCGCAACAGGCT 62.874 61.111 15.41 0.00 40.26 4.58
2199 2345 2.500098 GGTAGACTATGTTGCACAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
2210 2356 4.874966 TGTTGCACAGGGAAAAATGAAAAG 59.125 37.500 0.00 0.00 0.00 2.27
2217 2368 7.212274 CACAGGGAAAAATGAAAAGAAGTGAT 58.788 34.615 0.00 0.00 0.00 3.06
2221 2372 9.312904 AGGGAAAAATGAAAAGAAGTGATATGA 57.687 29.630 0.00 0.00 0.00 2.15
2324 2505 2.797156 GACACATGTCATGTCCGATAGC 59.203 50.000 15.73 0.00 42.70 2.97
2344 2525 7.042523 CGATAGCTCAAATGACACACATCATTA 60.043 37.037 0.00 0.00 46.35 1.90
2389 2570 1.954651 GCCCGGTAGCATCGTAAGC 60.955 63.158 0.00 0.00 37.18 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.164338 GGTGGTTTCGGAATGCCTAAA 58.836 47.619 11.44 0.00 0.00 1.85
147 148 1.407437 CCTGGCTCATCCACTTGGTAC 60.407 57.143 0.00 0.00 40.72 3.34
179 180 1.671850 CGTCGTAAGCCACACCATCTT 60.672 52.381 0.00 0.00 37.18 2.40
183 184 2.340809 CCGTCGTAAGCCACACCA 59.659 61.111 0.00 0.00 37.18 4.17
220 221 0.542333 TGACACCACCGGTTCTTGAA 59.458 50.000 2.97 0.00 31.02 2.69
250 251 1.480954 CGGCCAGTGGTACTTATGAGT 59.519 52.381 11.74 0.00 39.97 3.41
363 364 2.676471 GGCGCCCATGTCAACCTT 60.676 61.111 18.11 0.00 0.00 3.50
409 410 1.133976 GCCATCATACTCAGGCCACTT 60.134 52.381 5.01 0.00 41.25 3.16
562 566 1.134220 ACAGTTGTTGATGTCCGGTGT 60.134 47.619 0.00 0.00 0.00 4.16
665 669 1.359168 ACCTCCTCTACAAACACCCC 58.641 55.000 0.00 0.00 0.00 4.95
673 677 0.613853 CCACCGGAACCTCCTCTACA 60.614 60.000 9.46 0.00 33.30 2.74
699 703 2.368011 GCCACCAGTCCTACCTCCC 61.368 68.421 0.00 0.00 0.00 4.30
724 728 3.996921 ACCTCTAAGACTAGTCCGTCA 57.003 47.619 19.38 0.88 36.38 4.35
865 869 3.058777 TCCGGATTAAGCAAAACGTCAAC 60.059 43.478 0.00 0.00 0.00 3.18
1043 1049 2.485426 CACTTGTTCGGCATGTCTTCAT 59.515 45.455 0.00 0.00 33.82 2.57
1175 1181 4.104738 ACACAAAGAATCTTCTCCCTTCCA 59.895 41.667 0.00 0.00 36.28 3.53
1464 1471 1.137825 CTTCTGACGACGCTCTCCC 59.862 63.158 0.00 0.00 0.00 4.30
1466 1473 0.098025 CTCCTTCTGACGACGCTCTC 59.902 60.000 0.00 0.00 0.00 3.20
1574 1581 1.134580 CCTCCTCTTGTGCATCACGAT 60.135 52.381 0.00 0.00 37.14 3.73
1687 1701 4.890158 TCATCAAGTATCCGGCATATGT 57.110 40.909 4.29 0.00 0.00 2.29
2069 2183 3.000819 CTGTGGCGGTAGGGTCCA 61.001 66.667 0.00 0.00 0.00 4.02
2210 2356 6.518493 TGTACCGGGTATTTCATATCACTTC 58.482 40.000 10.62 0.00 0.00 3.01
2217 2368 7.600231 TGAACTATGTACCGGGTATTTCATA 57.400 36.000 10.62 11.93 0.00 2.15
2221 2372 7.281549 GTCATTTGAACTATGTACCGGGTATTT 59.718 37.037 10.62 3.77 0.00 1.40
2224 2375 5.187381 TGTCATTTGAACTATGTACCGGGTA 59.813 40.000 6.32 1.88 0.00 3.69
2324 2505 6.072563 TGTGGTAATGATGTGTGTCATTTGAG 60.073 38.462 7.35 0.00 44.23 3.02
2344 2525 3.766591 TGTTGGTCATTTGAACTTGTGGT 59.233 39.130 0.00 0.00 31.73 4.16
2389 2570 1.209621 TAGGGGATCCTTTTCGGGTG 58.790 55.000 12.58 0.00 41.56 4.61


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

AutoCloner maintained by Alex Coulton.