Multiple sequence alignment - TraesCS1A01G053700

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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 TraesCS1A01G053700 chr1A 100.000 2983 0 0 1 2983 35531922 35534904 0.000000e+00 5509.0
1 TraesCS1A01G053700 chr1A 97.199 1214 30 4 1 1213 35499634 35500844 0.000000e+00 2050.0
2 TraesCS1A01G053700 chr1A 93.857 586 24 4 1209 1785 35507257 35507839 0.000000e+00 872.0
3 TraesCS1A01G053700 chr1A 84.153 366 31 13 2639 2983 35513675 35514034 2.220000e-86 329.0
4 TraesCS1A01G053700 chr1A 96.296 189 5 1 2221 2409 35508277 35508463 2.890000e-80 309.0
5 TraesCS1A01G053700 chr1A 97.403 77 2 0 2437 2513 35513272 35513348 6.710000e-27 132.0
6 TraesCS1A01G053700 chr1A 98.148 54 1 0 2460 2513 35483745 35483798 8.800000e-16 95.3
7 TraesCS1A01G053700 chr1D 98.880 1786 17 3 1 1785 36311648 36313431 0.000000e+00 3184.0
8 TraesCS1A01G053700 chr1D 96.870 1214 22 7 1783 2983 36313475 36314685 0.000000e+00 2017.0
9 TraesCS1A01G053700 chr1B 94.505 1201 44 9 1 1187 56013085 56014277 0.000000e+00 1832.0
10 TraesCS1A01G053700 chr1B 93.551 1194 60 10 1 1187 55969923 55971106 0.000000e+00 1762.0
11 TraesCS1A01G053700 chr1B 93.551 1194 60 10 1 1187 55991921 55993104 0.000000e+00 1762.0
12 TraesCS1A01G053700 chr1B 93.132 597 24 9 1192 1785 56014322 56014904 0.000000e+00 859.0
13 TraesCS1A01G053700 chr1B 92.955 582 24 9 1207 1785 55971373 55971940 0.000000e+00 832.0
14 TraesCS1A01G053700 chr1B 92.220 437 32 2 1351 1785 55953601 55954037 4.220000e-173 617.0
15 TraesCS1A01G053700 chr1B 94.444 396 18 3 1791 2184 55954104 55954497 9.140000e-170 606.0
16 TraesCS1A01G053700 chr1B 94.192 396 19 3 1791 2184 55942850 55943243 4.250000e-168 601.0
17 TraesCS1A01G053700 chr1B 92.132 394 22 3 1791 2184 55972002 55972386 5.620000e-152 547.0
18 TraesCS1A01G053700 chr1B 92.132 394 22 3 1791 2184 55993727 55994111 5.620000e-152 547.0
19 TraesCS1A01G053700 chr1B 93.305 239 10 2 1192 1430 55971151 55971383 6.120000e-92 348.0
20 TraesCS1A01G053700 chr1B 95.213 188 9 0 2222 2409 55943252 55943439 6.250000e-77 298.0
21 TraesCS1A01G053700 chr1B 95.213 188 9 0 2222 2409 55954506 55954693 6.250000e-77 298.0
22 TraesCS1A01G053700 chr1B 94.652 187 6 2 2223 2409 55972396 55972578 1.350000e-73 287.0
23 TraesCS1A01G053700 chr4D 96.424 783 27 1 1004 1785 336661177 336661959 0.000000e+00 1290.0
24 TraesCS1A01G053700 chr4D 92.621 393 25 3 1793 2183 336662026 336662416 2.010000e-156 562.0
25 TraesCS1A01G053700 chr4D 97.340 188 5 0 2222 2409 336662426 336662613 1.330000e-83 320.0
26 TraesCS1A01G053700 chr4D 87.970 133 12 4 2800 2928 336663989 336664121 1.430000e-33 154.0
27 TraesCS1A01G053700 chr4D 97.403 77 2 0 2437 2513 336663339 336663415 6.710000e-27 132.0
28 TraesCS1A01G053700 chr4B 96.424 783 27 1 1004 1785 414862828 414863610 0.000000e+00 1290.0
29 TraesCS1A01G053700 chr4B 91.878 394 28 3 1793 2184 414863677 414864068 5.620000e-152 547.0
30 TraesCS1A01G053700 chr4B 96.791 187 6 0 2222 2408 414864077 414864263 2.230000e-81 313.0
31 TraesCS1A01G053700 chr4B 92.500 160 9 1 2639 2795 414865433 414865592 2.990000e-55 226.0
32 TraesCS1A01G053700 chr4B 88.976 127 9 4 2800 2921 414865632 414865758 5.150000e-33 152.0
33 TraesCS1A01G053700 chr4B 97.403 77 2 0 2437 2513 414864992 414865068 6.710000e-27 132.0
34 TraesCS1A01G053700 chr4A 96.424 783 27 1 1004 1785 136756542 136755760 0.000000e+00 1290.0
35 TraesCS1A01G053700 chr4A 92.670 382 25 2 1804 2184 136755677 136755298 5.620000e-152 547.0
36 TraesCS1A01G053700 chr4A 96.335 191 7 0 2222 2412 136755289 136755099 6.210000e-82 315.0
37 TraesCS1A01G053700 chr4A 87.970 133 12 4 2800 2928 136753712 136753580 1.430000e-33 154.0
38 TraesCS1A01G053700 chr4A 97.500 80 2 0 2437 2516 136754361 136754282 1.440000e-28 137.0
39 TraesCS1A01G053700 chr2B 83.486 763 122 4 1010 1770 64994803 64994043 0.000000e+00 708.0
40 TraesCS1A01G053700 chrUn 92.132 394 22 3 1791 2184 319316340 319316724 5.620000e-152 547.0
41 TraesCS1A01G053700 chrUn 94.652 187 6 2 2223 2409 319316734 319316916 1.350000e-73 287.0
42 TraesCS1A01G053700 chr6A 74.187 492 93 26 476 963 575562391 575561930 1.100000e-39 174.0


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 TraesCS1A01G053700 chr1A 35531922 35534904 2982 False 5509.000000 5509 100.000000 1 2983 1 chr1A.!!$F3 2982
1 TraesCS1A01G053700 chr1A 35499634 35500844 1210 False 2050.000000 2050 97.199000 1 1213 1 chr1A.!!$F2 1212
2 TraesCS1A01G053700 chr1A 35507257 35508463 1206 False 590.500000 872 95.076500 1209 2409 2 chr1A.!!$F4 1200
3 TraesCS1A01G053700 chr1A 35513272 35514034 762 False 230.500000 329 90.778000 2437 2983 2 chr1A.!!$F5 546
4 TraesCS1A01G053700 chr1D 36311648 36314685 3037 False 2600.500000 3184 97.875000 1 2983 2 chr1D.!!$F1 2982
5 TraesCS1A01G053700 chr1B 56013085 56014904 1819 False 1345.500000 1832 93.818500 1 1785 2 chr1B.!!$F5 1784
6 TraesCS1A01G053700 chr1B 55991921 55994111 2190 False 1154.500000 1762 92.841500 1 2184 2 chr1B.!!$F4 2183
7 TraesCS1A01G053700 chr1B 55969923 55972578 2655 False 755.200000 1762 93.319000 1 2409 5 chr1B.!!$F3 2408
8 TraesCS1A01G053700 chr1B 55953601 55954693 1092 False 507.000000 617 93.959000 1351 2409 3 chr1B.!!$F2 1058
9 TraesCS1A01G053700 chr1B 55942850 55943439 589 False 449.500000 601 94.702500 1791 2409 2 chr1B.!!$F1 618
10 TraesCS1A01G053700 chr4D 336661177 336664121 2944 False 491.600000 1290 94.351600 1004 2928 5 chr4D.!!$F1 1924
11 TraesCS1A01G053700 chr4B 414862828 414865758 2930 False 443.333333 1290 93.995333 1004 2921 6 chr4B.!!$F1 1917
12 TraesCS1A01G053700 chr4A 136753580 136756542 2962 True 488.600000 1290 94.179800 1004 2928 5 chr4A.!!$R1 1924
13 TraesCS1A01G053700 chr2B 64994043 64994803 760 True 708.000000 708 83.486000 1010 1770 1 chr2B.!!$R1 760
14 TraesCS1A01G053700 chrUn 319316340 319316916 576 False 417.000000 547 93.392000 1791 2409 2 chrUn.!!$F1 618

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
894 902 1.073722 TGCTCCACCTCAAAGCTGG 59.926 57.895 0.0 0.0 36.96 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2786 4161 1.283793 CCAGGCGTGCTTCAAACAG 59.716 57.895 0.0 0.0 0.0 3.16 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
226 229 2.031682 GGGCAAAGCTAGCGTGAATATG 60.032 50.000 21.41 9.69 0.00 1.78
256 259 8.407832 CAGCTAATATTTGGAATCACATCAACA 58.592 33.333 0.00 0.00 0.00 3.33
409 412 7.195646 TCTGTAGAAGTTCTGCAAAATTGTTG 58.804 34.615 21.85 9.85 38.60 3.33
517 525 5.381174 CACAAATGCTCCAGAAAGATTCA 57.619 39.130 0.00 0.00 0.00 2.57
637 645 5.936686 AGATCATCGTAATGAAGCAATGG 57.063 39.130 0.00 0.00 44.85 3.16
644 652 6.634035 CATCGTAATGAAGCAATGGTAACATG 59.366 38.462 0.00 0.00 46.37 3.21
753 761 1.234821 TCATTGTGGAAAGCGGTGAC 58.765 50.000 0.00 0.00 0.00 3.67
894 902 1.073722 TGCTCCACCTCAAAGCTGG 59.926 57.895 0.00 0.00 36.96 4.85
1083 1099 6.959639 TCTGTTTTTGGTTCTAAGCTTCAT 57.040 33.333 0.00 0.00 0.00 2.57
2025 2372 2.022754 GCATTTCCTGAGGATGCTGCT 61.023 52.381 17.56 0.00 42.12 4.24
2576 3654 3.446442 AAGATGAAATGGTCACAGGCT 57.554 42.857 0.00 0.00 39.72 4.58
2596 3674 3.490761 GCTTTGTGTGCCTTGAGCTTTAA 60.491 43.478 0.00 0.00 44.23 1.52
2610 3688 3.295973 AGCTTTAAAAGGTTCTGGCACA 58.704 40.909 0.00 0.00 35.27 4.57
2642 4014 1.153353 ACCGCAATACGTTTCACAGG 58.847 50.000 0.00 0.00 41.42 4.00
2786 4161 2.163211 GCAAAGAATTCCTGTGGAGAGC 59.837 50.000 0.65 0.00 31.21 4.09
2795 4170 2.149578 CCTGTGGAGAGCTGTTTGAAG 58.850 52.381 0.00 0.00 0.00 3.02
2845 4267 0.657840 CCCATCTCCATCGCGTTTTC 59.342 55.000 5.77 0.00 0.00 2.29
2944 4372 3.459598 ACCATAGCATGTTATCCACTGGT 59.540 43.478 6.10 6.10 0.00 4.00
2975 4403 5.118286 GGATTGATATTTTTGGGGTTGCTG 58.882 41.667 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 229 7.801716 TGTGATTCCAAATATTAGCTGTACC 57.198 36.000 0.0 0.0 0.00 3.34
309 312 6.594788 ACACTGAATGCCATACAGATTTTT 57.405 33.333 0.0 0.0 35.85 1.94
637 645 6.446318 TCATCTTTTGTTTCAGGCATGTTAC 58.554 36.000 0.0 0.0 0.00 2.50
644 652 3.256558 GCCATCATCTTTTGTTTCAGGC 58.743 45.455 0.0 0.0 0.00 4.85
894 902 4.706962 AGTACCTGAAATGAAATGGAAGGC 59.293 41.667 0.0 0.0 0.00 4.35
2557 3635 3.446442 AAGCCTGTGACCATTTCATCT 57.554 42.857 0.0 0.0 36.32 2.90
2558 3636 3.256631 ACAAAGCCTGTGACCATTTCATC 59.743 43.478 0.0 0.0 36.69 2.92
2559 3637 3.233507 ACAAAGCCTGTGACCATTTCAT 58.766 40.909 0.0 0.0 36.69 2.57
2560 3638 2.665165 ACAAAGCCTGTGACCATTTCA 58.335 42.857 0.0 0.0 36.69 2.69
2576 3654 4.727507 TTTAAAGCTCAAGGCACACAAA 57.272 36.364 0.0 0.0 44.79 2.83
2596 3674 1.750778 CAACTGTGTGCCAGAACCTTT 59.249 47.619 0.0 0.0 44.49 3.11
2610 3688 2.902705 TTGCGGTAGTCTTCAACTGT 57.097 45.000 0.0 0.0 39.11 3.55
2642 4014 3.656559 AGCCACAACATCAAAATGCTTC 58.343 40.909 0.0 0.0 36.26 3.86
2786 4161 1.283793 CCAGGCGTGCTTCAAACAG 59.716 57.895 0.0 0.0 0.00 3.16
2845 4267 2.266055 GAGCGGAAGGACCCACAG 59.734 66.667 0.0 0.0 34.64 3.66
2944 4372 7.127032 ACCCCAAAAATATCAATCCAATGCTAA 59.873 33.333 0.0 0.0 0.00 3.09


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

AutoCloner maintained by Alex Coulton.