Multiple sequence alignment - TraesCS2A01G274600

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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 TraesCS2A01G274600 chr2A 100.000 2921 0 0 1 2921 450933511 450936431 0.000000e+00 5395.0
1 TraesCS2A01G274600 chr2A 97.221 1727 43 2 1 1724 450913507 450915231 0.000000e+00 2918.0
2 TraesCS2A01G274600 chr2A 91.837 1764 126 15 1172 2920 302984298 302982538 0.000000e+00 2444.0
3 TraesCS2A01G274600 chr2A 96.783 1057 30 2 1867 2920 450927243 450928298 0.000000e+00 1760.0
4 TraesCS2A01G274600 chr2A 97.426 777 20 0 1 777 384124026 384123250 0.000000e+00 1325.0
5 TraesCS2A01G274600 chr2A 97.013 770 20 3 1 768 384098681 384097913 0.000000e+00 1291.0
6 TraesCS2A01G274600 chr2A 97.013 770 19 4 1 768 388501923 388501156 0.000000e+00 1291.0
7 TraesCS2A01G274600 chr2A 97.354 756 19 1 1 756 388510035 388509281 0.000000e+00 1284.0
8 TraesCS2A01G274600 chr2A 95.385 780 30 5 1 777 217313233 217314009 0.000000e+00 1236.0
9 TraesCS2A01G274600 chr2A 93.860 684 42 0 878 1561 302964499 302963816 0.000000e+00 1031.0
10 TraesCS2A01G274600 chr2A 90.943 541 42 6 1309 1847 407205945 407205410 0.000000e+00 721.0
11 TraesCS2A01G274600 chr2A 90.779 488 36 8 1364 1848 407197538 407197057 0.000000e+00 643.0
12 TraesCS2A01G274600 chr2A 84.496 258 22 4 1272 1511 627621940 627621683 3.760000e-59 239.0
13 TraesCS2A01G274600 chr2A 92.727 110 8 0 771 880 388509212 388509103 3.010000e-35 159.0
14 TraesCS2A01G274600 chr2A 91.964 112 9 0 773 884 247135117 247135228 1.080000e-34 158.0
15 TraesCS2A01G274600 chr2A 93.814 97 6 0 771 867 139132420 139132516 2.350000e-31 147.0
16 TraesCS2A01G274600 chr3A 94.150 1846 97 8 1084 2921 403938120 403936278 0.000000e+00 2800.0
17 TraesCS2A01G274600 chr3A 93.442 1845 113 6 1084 2921 403946353 403944510 0.000000e+00 2730.0
18 TraesCS2A01G274600 chr3A 97.339 1165 31 0 1 1165 506491091 506492255 0.000000e+00 1980.0
19 TraesCS2A01G274600 chr3A 96.506 973 32 2 1 973 506485902 506486872 0.000000e+00 1607.0
20 TraesCS2A01G274600 chr3A 91.081 1166 82 17 1769 2919 207408438 207409596 0.000000e+00 1557.0
21 TraesCS2A01G274600 chr3A 84.429 1445 160 44 1517 2921 286110583 286109164 0.000000e+00 1362.0
22 TraesCS2A01G274600 chr3A 95.000 780 33 5 1 777 122648525 122649301 0.000000e+00 1219.0
23 TraesCS2A01G274600 chr3A 94.872 117 6 0 980 1096 522973627 522973743 1.790000e-42 183.0
24 TraesCS2A01G274600 chr3A 90.598 117 11 0 980 1096 522965678 522965794 3.900000e-34 156.0
25 TraesCS2A01G274600 chr7A 95.330 1242 50 3 878 2112 193678328 193677088 0.000000e+00 1965.0
26 TraesCS2A01G274600 chr6A 95.527 939 36 6 1987 2921 521586295 521585359 0.000000e+00 1496.0
27 TraesCS2A01G274600 chr6A 95.275 910 36 4 2016 2921 521578046 521577140 0.000000e+00 1435.0
28 TraesCS2A01G274600 chr6A 92.667 150 8 3 1128 1275 551829406 551829554 2.280000e-51 213.0
29 TraesCS2A01G274600 chr1A 90.766 1018 73 19 1917 2921 366580698 366579689 0.000000e+00 1339.0
30 TraesCS2A01G274600 chr1A 94.737 114 6 0 771 884 509445814 509445927 8.320000e-41 178.0
31 TraesCS2A01G274600 chr1A 94.545 110 6 0 771 880 509664540 509664649 1.390000e-38 171.0
32 TraesCS2A01G274600 chr1A 92.308 65 3 2 1084 1148 271133801 271133739 1.110000e-14 91.6
33 TraesCS2A01G274600 chr4A 83.206 1435 169 52 1519 2921 391003645 391002251 0.000000e+00 1249.0
34 TraesCS2A01G274600 chr4A 90.239 543 44 8 1309 1848 400452322 400452858 0.000000e+00 701.0
35 TraesCS2A01G274600 chr4A 91.613 155 11 2 1123 1275 460037094 460037248 2.280000e-51 213.0
36 TraesCS2A01G274600 chr4A 90.604 149 14 0 878 1026 538690813 538690665 6.390000e-47 198.0
37 TraesCS2A01G274600 chr4A 91.935 124 5 4 980 1102 527030168 527030049 5.010000e-38 169.0
38 TraesCS2A01G274600 chr5A 85.897 1170 127 34 1769 2921 599479249 599478101 0.000000e+00 1212.0
39 TraesCS2A01G274600 chr5A 91.275 149 13 0 878 1026 479311842 479311694 1.370000e-48 204.0
40 TraesCS2A01G274600 chr5A 89.933 149 15 0 878 1026 282156734 282156586 2.970000e-45 193.0
41 TraesCS2A01G274600 chr5A 90.345 145 14 0 882 1026 172439049 172438905 1.070000e-44 191.0
42 TraesCS2A01G274600 chr5A 92.982 114 8 0 771 884 441410894 441410781 1.800000e-37 167.0
43 TraesCS2A01G274600 chr5A 89.189 74 6 2 1001 1074 191350437 191350366 1.110000e-14 91.6
44 TraesCS2A01G274600 chr5A 94.444 36 1 1 1046 1081 193958948 193958982 1.000000e-03 54.7
45 TraesCS2A01G274600 chr4D 89.441 161 15 2 1123 1281 98479875 98479715 4.940000e-48 202.0
46 TraesCS2A01G274600 chr5D 92.208 77 2 4 1073 1148 148266301 148266228 3.980000e-19 106.0
47 TraesCS2A01G274600 chr4B 92.857 70 3 2 1073 1141 311421146 311421214 1.850000e-17 100.0


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 TraesCS2A01G274600 chr2A 450933511 450936431 2920 False 5395.0 5395 100.0000 1 2921 1 chr2A.!!$F6 2920
1 TraesCS2A01G274600 chr2A 450913507 450915231 1724 False 2918.0 2918 97.2210 1 1724 1 chr2A.!!$F4 1723
2 TraesCS2A01G274600 chr2A 302982538 302984298 1760 True 2444.0 2444 91.8370 1172 2920 1 chr2A.!!$R2 1748
3 TraesCS2A01G274600 chr2A 450927243 450928298 1055 False 1760.0 1760 96.7830 1867 2920 1 chr2A.!!$F5 1053
4 TraesCS2A01G274600 chr2A 384123250 384124026 776 True 1325.0 1325 97.4260 1 777 1 chr2A.!!$R4 776
5 TraesCS2A01G274600 chr2A 384097913 384098681 768 True 1291.0 1291 97.0130 1 768 1 chr2A.!!$R3 767
6 TraesCS2A01G274600 chr2A 388501156 388501923 767 True 1291.0 1291 97.0130 1 768 1 chr2A.!!$R5 767
7 TraesCS2A01G274600 chr2A 217313233 217314009 776 False 1236.0 1236 95.3850 1 777 1 chr2A.!!$F2 776
8 TraesCS2A01G274600 chr2A 302963816 302964499 683 True 1031.0 1031 93.8600 878 1561 1 chr2A.!!$R1 683
9 TraesCS2A01G274600 chr2A 388509103 388510035 932 True 721.5 1284 95.0405 1 880 2 chr2A.!!$R9 879
10 TraesCS2A01G274600 chr2A 407205410 407205945 535 True 721.0 721 90.9430 1309 1847 1 chr2A.!!$R7 538
11 TraesCS2A01G274600 chr3A 403936278 403938120 1842 True 2800.0 2800 94.1500 1084 2921 1 chr3A.!!$R2 1837
12 TraesCS2A01G274600 chr3A 403944510 403946353 1843 True 2730.0 2730 93.4420 1084 2921 1 chr3A.!!$R3 1837
13 TraesCS2A01G274600 chr3A 506491091 506492255 1164 False 1980.0 1980 97.3390 1 1165 1 chr3A.!!$F4 1164
14 TraesCS2A01G274600 chr3A 506485902 506486872 970 False 1607.0 1607 96.5060 1 973 1 chr3A.!!$F3 972
15 TraesCS2A01G274600 chr3A 207408438 207409596 1158 False 1557.0 1557 91.0810 1769 2919 1 chr3A.!!$F2 1150
16 TraesCS2A01G274600 chr3A 286109164 286110583 1419 True 1362.0 1362 84.4290 1517 2921 1 chr3A.!!$R1 1404
17 TraesCS2A01G274600 chr3A 122648525 122649301 776 False 1219.0 1219 95.0000 1 777 1 chr3A.!!$F1 776
18 TraesCS2A01G274600 chr7A 193677088 193678328 1240 True 1965.0 1965 95.3300 878 2112 1 chr7A.!!$R1 1234
19 TraesCS2A01G274600 chr6A 521585359 521586295 936 True 1496.0 1496 95.5270 1987 2921 1 chr6A.!!$R2 934
20 TraesCS2A01G274600 chr6A 521577140 521578046 906 True 1435.0 1435 95.2750 2016 2921 1 chr6A.!!$R1 905
21 TraesCS2A01G274600 chr1A 366579689 366580698 1009 True 1339.0 1339 90.7660 1917 2921 1 chr1A.!!$R2 1004
22 TraesCS2A01G274600 chr4A 391002251 391003645 1394 True 1249.0 1249 83.2060 1519 2921 1 chr4A.!!$R1 1402
23 TraesCS2A01G274600 chr4A 400452322 400452858 536 False 701.0 701 90.2390 1309 1848 1 chr4A.!!$F1 539
24 TraesCS2A01G274600 chr5A 599478101 599479249 1148 True 1212.0 1212 85.8970 1769 2921 1 chr5A.!!$R6 1152

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
777 835 0.187361 CTCCCCCTCGATTCCTCTCT 59.813 60.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 2303 1.08992 GAGCGTGTCATGCAAGGATT 58.91 50.0 19.04 0.0 31.07 3.01 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 49 0.463204 TCCGGGTTTCGTTGTGTGTA 59.537 50.000 0.00 0.00 37.11 2.90
169 172 4.142249 GGTCCATTTAAACCGAGGGAATTG 60.142 45.833 0.00 0.00 0.00 2.32
376 379 4.081752 ACATTTCTGGTGCACTTCAAAACA 60.082 37.500 17.98 3.04 0.00 2.83
468 471 4.780815 TCTAATTTTCTCGGACCATGCAT 58.219 39.130 0.00 0.00 0.00 3.96
534 537 3.007614 CCCCTACCGTCTCTTTCTTTTCA 59.992 47.826 0.00 0.00 0.00 2.69
579 582 9.504710 GTTTTAAAAAGGAAAAGAGTGAGAGAC 57.495 33.333 1.31 0.00 0.00 3.36
777 835 0.187361 CTCCCCCTCGATTCCTCTCT 59.813 60.000 0.00 0.00 0.00 3.10
1037 1095 2.494445 CCGCGCACACATAGAGGA 59.506 61.111 8.75 0.00 0.00 3.71
1755 1820 4.511246 TACCGTCGCCCCGAGGAT 62.511 66.667 8.66 0.00 43.12 3.24
1858 1924 2.874457 GCAAGTACCACTCCGAACCATT 60.874 50.000 0.00 0.00 0.00 3.16
1935 2001 0.108329 CGTGAACCGCTACTTCCCAT 60.108 55.000 0.00 0.00 0.00 4.00
2491 2651 3.648339 AAAATGCCTAGCTGTGTGTTG 57.352 42.857 0.00 0.00 0.00 3.33
2826 3008 2.484264 CCGTTTGTCTTCTTCATGGACC 59.516 50.000 0.00 0.00 0.00 4.46
2854 3036 0.695924 TTCCTTGCGGGATTTCAGGA 59.304 50.000 0.00 0.00 44.66 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 49 3.181471 TGAAATGCAACGGACCAAACAAT 60.181 39.130 0.00 0.00 0.00 2.71
376 379 5.222048 TCAAATGGTTTGAACTAGGGCTAGT 60.222 40.000 2.84 0.00 45.94 2.57
468 471 8.411991 ACAATTTTCCCGGACTCTTAAAAATA 57.588 30.769 0.73 0.00 0.00 1.40
579 582 2.437359 CTGGGCTGGCTTTCCTCG 60.437 66.667 0.00 0.00 0.00 4.63
1412 1476 2.221055 GTCTTGACGTTAACAGCCACAG 59.779 50.000 6.39 2.01 0.00 3.66
1571 1636 3.324117 GTCAACTCGAAAGGGGTACTTC 58.676 50.000 0.00 0.00 38.85 3.01
1755 1820 5.232463 GTGAGGTACTTAACGAATCCAACA 58.768 41.667 0.00 0.00 41.55 3.33
2171 2303 1.089920 GAGCGTGTCATGCAAGGATT 58.910 50.000 19.04 0.00 31.07 3.01
2261 2405 3.046870 GCCACGGCAACAATTCCA 58.953 55.556 2.36 0.00 41.49 3.53
2491 2651 3.058639 GCAAGAGGTGAAACATGAGTGAC 60.059 47.826 0.00 0.00 39.98 3.67
2854 3036 4.837093 TTTCGAGGGTATGGTCATCTTT 57.163 40.909 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.