Multiple sequence alignment - TraesCS1B01G361800

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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 TraesCS1B01G361800 chr1B 100.000 2769 0 0 1 2769 590413775 590411007 0.000000e+00 5114.0
1 TraesCS1B01G361800 chr1B 91.010 723 54 8 778 1492 191002748 191003467 0.000000e+00 965.0
2 TraesCS1B01G361800 chr1B 95.455 110 3 1 557 664 590413112 590413003 1.020000e-39 174.0
3 TraesCS1B01G361800 chr1B 95.455 110 3 1 664 773 590413219 590413112 1.020000e-39 174.0
4 TraesCS1B01G361800 chr1B 100.000 30 0 0 1804 1833 590412060 590412031 3.850000e-04 56.5
5 TraesCS1B01G361800 chr5A 99.205 2769 22 0 1 2769 473425209 473427977 0.000000e+00 4992.0
6 TraesCS1B01G361800 chr5A 96.364 110 2 1 557 664 473425872 473425981 2.190000e-41 180.0
7 TraesCS1B01G361800 chr5A 95.455 110 3 1 664 773 473425765 473425872 1.020000e-39 174.0
8 TraesCS1B01G361800 chr2D 94.763 1413 51 9 1376 2769 641347870 641349278 0.000000e+00 2178.0
9 TraesCS1B01G361800 chr2D 94.270 925 30 11 1864 2769 641360705 641361625 0.000000e+00 1393.0
10 TraesCS1B01G361800 chr2D 94.581 406 22 0 1839 2244 81963399 81963804 1.810000e-176 628.0
11 TraesCS1B01G361800 chr2D 93.842 406 25 0 1839 2244 412045808 412046213 1.820000e-171 612.0
12 TraesCS1B01G361800 chr2D 89.423 208 16 6 452 655 113498761 113498556 9.840000e-65 257.0
13 TraesCS1B01G361800 chr5B 94.173 1064 42 12 779 1840 407322316 407321271 0.000000e+00 1604.0
14 TraesCS1B01G361800 chr5B 100.000 33 0 0 1713 1745 407321310 407321278 8.280000e-06 62.1
15 TraesCS1B01G361800 chr4A 94.173 1064 42 12 779 1840 638241309 638240264 0.000000e+00 1604.0
16 TraesCS1B01G361800 chr4A 93.895 950 39 7 1839 2769 735600230 735601179 0.000000e+00 1415.0
17 TraesCS1B01G361800 chr4A 92.424 132 10 0 452 583 684031943 684031812 3.640000e-44 189.0
18 TraesCS1B01G361800 chr4A 92.424 132 10 0 452 583 684058399 684058268 3.640000e-44 189.0
19 TraesCS1B01G361800 chr4A 100.000 33 0 0 1713 1745 638240303 638240271 8.280000e-06 62.1
20 TraesCS1B01G361800 chr1D 92.944 1063 50 10 780 1840 468030621 468031660 0.000000e+00 1524.0
21 TraesCS1B01G361800 chr1D 91.010 723 55 8 778 1492 142151364 142150644 0.000000e+00 966.0
22 TraesCS1B01G361800 chr1D 96.970 33 1 0 1801 1833 468031537 468031569 3.850000e-04 56.5
23 TraesCS1B01G361800 chr7B 92.596 1067 66 7 778 1840 210629748 210628691 0.000000e+00 1520.0
24 TraesCS1B01G361800 chr7B 90.604 149 9 2 509 652 439597350 439597498 2.810000e-45 193.0
25 TraesCS1B01G361800 chr7B 100.000 33 0 0 1713 1745 210628729 210628697 8.280000e-06 62.1
26 TraesCS1B01G361800 chr7B 100.000 30 0 0 1804 1833 210628814 210628785 3.850000e-04 56.5
27 TraesCS1B01G361800 chrUn 93.684 950 41 7 1839 2769 8836870 8837819 0.000000e+00 1404.0
28 TraesCS1B01G361800 chrUn 100.000 418 0 0 806 1223 477073136 477072719 0.000000e+00 773.0
29 TraesCS1B01G361800 chr3B 93.158 950 41 8 1839 2769 73591853 73592797 0.000000e+00 1373.0
30 TraesCS1B01G361800 chr3D 93.787 853 34 2 1936 2769 424221330 424222182 0.000000e+00 1264.0
31 TraesCS1B01G361800 chr3D 88.121 926 70 17 792 1712 335212975 335213865 0.000000e+00 1064.0
32 TraesCS1B01G361800 chr7D 88.324 925 69 16 792 1712 573797799 573798688 0.000000e+00 1074.0
33 TraesCS1B01G361800 chr7D 92.672 464 30 4 1839 2300 17696853 17697314 0.000000e+00 665.0
34 TraesCS1B01G361800 chr7D 88.318 214 17 3 450 655 27253774 27253561 1.650000e-62 250.0
35 TraesCS1B01G361800 chr2A 88.229 926 71 15 792 1712 448555023 448554131 0.000000e+00 1072.0
36 TraesCS1B01G361800 chr5D 87.939 912 72 18 806 1712 69675448 69676326 0.000000e+00 1040.0
37 TraesCS1B01G361800 chr3A 94.179 670 18 10 2120 2769 472429037 472429705 0.000000e+00 1002.0
38 TraesCS1B01G361800 chr3A 93.284 670 24 8 2120 2769 202986566 202987234 0.000000e+00 968.0
39 TraesCS1B01G361800 chr1A 91.637 562 39 6 778 1333 148268089 148268648 0.000000e+00 771.0
40 TraesCS1B01G361800 chr6D 89.904 208 15 6 452 655 435994601 435994396 2.110000e-66 263.0
41 TraesCS1B01G361800 chr4D 89.904 208 15 6 452 655 416843922 416843717 2.110000e-66 263.0
42 TraesCS1B01G361800 chr7A 89.423 208 16 6 452 655 612426530 612426325 9.840000e-65 257.0


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 TraesCS1B01G361800 chr1B 590411007 590413775 2768 True 1379.625 5114 97.7275 1 2769 4 chr1B.!!$R1 2768
1 TraesCS1B01G361800 chr1B 191002748 191003467 719 False 965.000 965 91.0100 778 1492 1 chr1B.!!$F1 714
2 TraesCS1B01G361800 chr5A 473425209 473427977 2768 False 1782.000 4992 97.0080 1 2769 3 chr5A.!!$F1 2768
3 TraesCS1B01G361800 chr2D 641347870 641349278 1408 False 2178.000 2178 94.7630 1376 2769 1 chr2D.!!$F3 1393
4 TraesCS1B01G361800 chr2D 641360705 641361625 920 False 1393.000 1393 94.2700 1864 2769 1 chr2D.!!$F4 905
5 TraesCS1B01G361800 chr5B 407321271 407322316 1045 True 833.050 1604 97.0865 779 1840 2 chr5B.!!$R1 1061
6 TraesCS1B01G361800 chr4A 735600230 735601179 949 False 1415.000 1415 93.8950 1839 2769 1 chr4A.!!$F1 930
7 TraesCS1B01G361800 chr4A 638240264 638241309 1045 True 833.050 1604 97.0865 779 1840 2 chr4A.!!$R3 1061
8 TraesCS1B01G361800 chr1D 142150644 142151364 720 True 966.000 966 91.0100 778 1492 1 chr1D.!!$R1 714
9 TraesCS1B01G361800 chr1D 468030621 468031660 1039 False 790.250 1524 94.9570 780 1840 2 chr1D.!!$F1 1060
10 TraesCS1B01G361800 chr7B 210628691 210629748 1057 True 546.200 1520 97.5320 778 1840 3 chr7B.!!$R1 1062
11 TraesCS1B01G361800 chrUn 8836870 8837819 949 False 1404.000 1404 93.6840 1839 2769 1 chrUn.!!$F1 930
12 TraesCS1B01G361800 chr3B 73591853 73592797 944 False 1373.000 1373 93.1580 1839 2769 1 chr3B.!!$F1 930
13 TraesCS1B01G361800 chr3D 424221330 424222182 852 False 1264.000 1264 93.7870 1936 2769 1 chr3D.!!$F2 833
14 TraesCS1B01G361800 chr3D 335212975 335213865 890 False 1064.000 1064 88.1210 792 1712 1 chr3D.!!$F1 920
15 TraesCS1B01G361800 chr7D 573797799 573798688 889 False 1074.000 1074 88.3240 792 1712 1 chr7D.!!$F2 920
16 TraesCS1B01G361800 chr2A 448554131 448555023 892 True 1072.000 1072 88.2290 792 1712 1 chr2A.!!$R1 920
17 TraesCS1B01G361800 chr5D 69675448 69676326 878 False 1040.000 1040 87.9390 806 1712 1 chr5D.!!$F1 906
18 TraesCS1B01G361800 chr3A 472429037 472429705 668 False 1002.000 1002 94.1790 2120 2769 1 chr3A.!!$F2 649
19 TraesCS1B01G361800 chr3A 202986566 202987234 668 False 968.000 968 93.2840 2120 2769 1 chr3A.!!$F1 649
20 TraesCS1B01G361800 chr1A 148268089 148268648 559 False 771.000 771 91.6370 778 1333 1 chr1A.!!$F1 555

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
804 808 0.896923 GGGCACTTCATTTGGCATCA 59.103 50.0 0.0 0.0 41.25 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2058 3.118592 AGGTTGCTATTCTCCTTCGGAAG 60.119 47.826 10.82 10.82 0.0 3.46 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
24 25 7.591421 TTCATATTTCTGGCATGTGATTGAT 57.409 32.000 0.00 0.00 0.00 2.57
679 680 5.576895 GGAGCTTAAGATGCTGATTTTGAC 58.423 41.667 6.67 0.00 41.30 3.18
804 808 0.896923 GGGCACTTCATTTGGCATCA 59.103 50.000 0.00 0.00 41.25 3.07
1311 1323 0.037303 CTGCCACAGGGATGTGAAGT 59.963 55.000 9.86 0.00 42.02 3.01
1802 1823 4.081198 AGTGAGATTCCGAGAAAATCTGCT 60.081 41.667 3.25 0.04 42.17 4.24
1989 2010 3.963665 CACATGTTTAGTTGGTGTGTGG 58.036 45.455 0.00 0.00 36.37 4.17
2037 2058 3.743396 CAGGAGACAAAGACTGCAGTTAC 59.257 47.826 22.65 9.32 0.00 2.50
2321 2360 6.704493 ACAGTAGCTTCGACAGATTTTTGTTA 59.296 34.615 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.777910 AGTATTGCTTTGGTTATAGTAATGCCA 59.222 33.333 0.00 0.00 32.46 4.92
414 415 3.281341 TGTCAACCGTGAAATGATTGC 57.719 42.857 0.00 0.00 34.87 3.56
804 808 5.189180 GGTTAGAGCAATCACCTGAAAGAT 58.811 41.667 0.00 0.00 34.07 2.40
1802 1823 6.018262 GCATTGACCTTGCGATATACTTGTAA 60.018 38.462 0.00 0.00 0.00 2.41
1989 2010 8.524870 AGAAACATGCATTTTATCTGACAAAC 57.475 30.769 0.00 0.00 0.00 2.93
2037 2058 3.118592 AGGTTGCTATTCTCCTTCGGAAG 60.119 47.826 10.82 10.82 0.00 3.46
2062 2083 6.824305 TTTAAGTACGTACCTAGCAGAAGT 57.176 37.500 21.80 0.00 0.00 3.01
2173 2194 8.972127 AGTATATACATGCTACGGAAGATTGAT 58.028 33.333 15.18 0.00 0.00 2.57
2321 2360 9.236006 AGAAGCATACAGAAACAATCATAGTTT 57.764 29.630 0.00 0.00 41.53 2.66


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

AutoCloner maintained by Alex Coulton.