Multiple sequence alignment - TraesCS3A01G319300

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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 TraesCS3A01G319300 chr3A 100.000 2377 0 0 1 2377 561248752 561246376 0.000000e+00 4390.0
1 TraesCS3A01G319300 chr3A 97.643 2376 51 4 1 2375 561291942 561289571 0.000000e+00 4072.0
2 TraesCS3A01G319300 chr3A 90.035 1134 89 14 1262 2377 561674901 561676028 0.000000e+00 1447.0
3 TraesCS3A01G319300 chr3A 85.640 1149 108 24 961 2096 119796547 119795443 0.000000e+00 1155.0
4 TraesCS3A01G319300 chr3A 100.000 187 0 0 2583 2769 561246170 561245984 2.040000e-91 346.0
5 TraesCS3A01G319300 chr3A 98.396 187 3 0 2583 2769 561289547 561289361 2.060000e-86 329.0
6 TraesCS3A01G319300 chr3A 94.410 161 9 0 952 1112 561670278 561670438 5.920000e-62 248.0
7 TraesCS3A01G319300 chr3A 87.166 187 10 4 2583 2769 561676049 561676221 1.680000e-47 200.0
8 TraesCS3A01G319300 chr3B 92.624 1437 78 12 952 2377 556404109 556405528 0.000000e+00 2041.0
9 TraesCS3A01G319300 chr3B 94.118 187 9 1 2583 2769 556405552 556405736 1.620000e-72 283.0
10 TraesCS3A01G319300 chr3D 90.166 1444 119 13 952 2377 425977373 425978811 0.000000e+00 1858.0
11 TraesCS3A01G319300 chr3D 85.583 1193 114 36 940 2103 425990681 425991844 0.000000e+00 1197.0
12 TraesCS3A01G319300 chr3D 94.652 187 10 0 2583 2769 425978832 425979018 9.700000e-75 291.0
13 TraesCS3A01G319300 chr3D 79.512 205 27 7 666 870 425990488 425990677 6.220000e-27 132.0
14 TraesCS3A01G319300 chr2D 92.045 88 7 0 961 1048 91786566 91786653 1.040000e-24 124.0
15 TraesCS3A01G319300 chr2D 91.209 91 8 0 961 1051 105671512 105671422 1.040000e-24 124.0
16 TraesCS3A01G319300 chr2B 90.909 88 8 0 961 1048 155819973 155820060 4.840000e-23 119.0
17 TraesCS3A01G319300 chr2A 90.110 91 9 0 961 1051 109325245 109325155 4.840000e-23 119.0
18 TraesCS3A01G319300 chr6D 79.167 96 18 2 116 209 458594160 458594065 6.400000e-07 65.8
19 TraesCS3A01G319300 chr6D 91.111 45 4 0 165 209 103729818 103729774 8.280000e-06 62.1
20 TraesCS3A01G319300 chr4D 91.111 45 4 0 165 209 443789582 443789538 8.280000e-06 62.1
21 TraesCS3A01G319300 chr4D 91.111 45 4 0 165 209 443796473 443796429 8.280000e-06 62.1
22 TraesCS3A01G319300 chr1D 91.111 45 4 0 165 209 132425826 132425870 8.280000e-06 62.1
23 TraesCS3A01G319300 chr1D 91.111 45 4 0 165 209 178388331 178388375 8.280000e-06 62.1
24 TraesCS3A01G319300 chr1D 91.111 45 4 0 165 209 178410109 178410153 8.280000e-06 62.1
25 TraesCS3A01G319300 chr1D 91.111 45 4 0 165 209 178420267 178420311 8.280000e-06 62.1


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 TraesCS3A01G319300 chr3A 561245984 561248752 2768 True 2368.0 4390 100.0000 1 2769 2 chr3A.!!$R2 2768
1 TraesCS3A01G319300 chr3A 561289361 561291942 2581 True 2200.5 4072 98.0195 1 2769 2 chr3A.!!$R3 2768
2 TraesCS3A01G319300 chr3A 119795443 119796547 1104 True 1155.0 1155 85.6400 961 2096 1 chr3A.!!$R1 1135
3 TraesCS3A01G319300 chr3A 561674901 561676221 1320 False 823.5 1447 88.6005 1262 2769 2 chr3A.!!$F2 1507
4 TraesCS3A01G319300 chr3B 556404109 556405736 1627 False 1162.0 2041 93.3710 952 2769 2 chr3B.!!$F1 1817
5 TraesCS3A01G319300 chr3D 425977373 425979018 1645 False 1074.5 1858 92.4090 952 2769 2 chr3D.!!$F1 1817
6 TraesCS3A01G319300 chr3D 425990488 425991844 1356 False 664.5 1197 82.5475 666 2103 2 chr3D.!!$F2 1437

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
28 29 1.418637 GGACTTCCTGTAACACCCACA 59.581 52.381 0.00 0.0 0.00 4.17 F
474 475 3.198853 GGCCCAGAGGGTATCTATTCATC 59.801 52.174 3.68 0.0 46.51 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1631 0.672401 GAACCGGCGTTCCATCTCAA 60.672 55.000 6.01 0.0 42.26 3.02 R
2217 2259 4.530710 ACAATGTTCTCATTTGCTGCAT 57.469 36.364 1.84 0.0 41.66 3.96 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
28 29 1.418637 GGACTTCCTGTAACACCCACA 59.581 52.381 0.00 0.00 0.00 4.17
104 105 3.337694 TTCATACACACCCCTAAACCG 57.662 47.619 0.00 0.00 0.00 4.44
287 288 4.909696 TCACAAAATGTTACACACCCTG 57.090 40.909 0.00 0.00 0.00 4.45
327 328 9.770097 AGTATCTCGTGATCAATATTTGAACAT 57.230 29.630 2.72 0.00 43.03 2.71
474 475 3.198853 GGCCCAGAGGGTATCTATTCATC 59.801 52.174 3.68 0.00 46.51 2.92
656 657 4.112634 CGAGAGATCGATTAGCAAAACCA 58.887 43.478 0.00 0.00 34.64 3.67
703 704 9.028284 CCATTCACCTAATTTTCCAGCATATAT 57.972 33.333 0.00 0.00 0.00 0.86
705 706 8.408043 TTCACCTAATTTTCCAGCATATATGG 57.592 34.615 14.51 0.00 39.33 2.74
751 752 6.183360 TGCTTGATTTTGTTTGGACACATAGT 60.183 34.615 0.00 0.00 34.98 2.12
767 768 9.607285 GGACACATAGTAAACATTGTTTTAGTG 57.393 33.333 19.15 19.18 0.00 2.74
827 828 7.618964 TCTCGACGTAAATGAAATACTATGC 57.381 36.000 0.00 0.00 0.00 3.14
882 883 6.556116 GTGTAAATTATAGTAGGAGTCCCCCA 59.444 42.308 5.25 0.00 34.66 4.96
884 885 4.845530 ATTATAGTAGGAGTCCCCCACA 57.154 45.455 5.25 0.00 34.66 4.17
1390 1403 9.092322 GCAATAGTACAAATGATCGTATTTTCG 57.908 33.333 0.00 0.00 0.00 3.46
1492 1517 4.029520 AGTCACAAGTAGCTCCAGATGAT 58.970 43.478 0.00 0.00 0.00 2.45
1605 1631 1.299165 GCATATCGCGTGACCGTCT 60.299 57.895 5.77 0.00 36.15 4.18
1692 1718 1.202758 TCTTGTGGATGGCGAGTTGTT 60.203 47.619 0.00 0.00 0.00 2.83
2217 2259 4.141135 TGGTTACTTGGATTGGTTCTTCCA 60.141 41.667 0.00 0.00 45.60 3.53
2343 2385 0.550914 GGATGTATCTTGGTGGCCCA 59.449 55.000 0.00 0.00 39.65 5.36
2733 2775 3.307242 GTGAGTCGATGGAGTTTATGCAC 59.693 47.826 0.00 0.00 28.84 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.901192 TCGGAGAATCTTGTGGGTGTTA 59.099 45.455 0.00 0.00 33.73 2.41
28 29 2.303022 TGAAAGTGCCTCGGAGAATCTT 59.697 45.455 6.58 4.87 34.09 2.40
104 105 1.933853 CTGTAGGGTCATGCGCTTAAC 59.066 52.381 9.73 0.00 40.99 2.01
287 288 6.480651 TCACGAGATACTGTCATAGTCTCTTC 59.519 42.308 0.00 0.00 41.41 2.87
382 383 7.934855 TTAAGGAGTTAGTCACGAGAATACT 57.065 36.000 0.00 0.00 0.00 2.12
474 475 5.595885 AGACTGTGATTTACTCATCCGATG 58.404 41.667 1.55 1.55 35.97 3.84
703 704 5.819901 CAGCAAAAATAAAAACCCTTCACCA 59.180 36.000 0.00 0.00 0.00 4.17
705 706 5.527214 AGCAGCAAAAATAAAAACCCTTCAC 59.473 36.000 0.00 0.00 0.00 3.18
751 752 9.509855 GTTCACATCACACTAAAACAATGTTTA 57.490 29.630 12.11 0.00 0.00 2.01
767 768 7.769272 TTTCAAGAAAATTGGTTCACATCAC 57.231 32.000 0.00 0.00 0.00 3.06
923 924 9.677567 CGTTCATTCCTTTTGATTTTCTTTCTA 57.322 29.630 0.00 0.00 0.00 2.10
945 946 6.127810 AGGGTTTGTAAGTTCTTTTCGTTC 57.872 37.500 0.00 0.00 0.00 3.95
1195 1205 5.420409 CAGTCCCTACCTGTTTATTCAGAC 58.580 45.833 0.00 0.00 37.61 3.51
1312 1324 4.092343 CCTTGCAAGGCAGAGCTT 57.908 55.556 31.70 0.00 40.61 3.74
1492 1517 3.181455 CGAGATGGGGGTGTATGATTTCA 60.181 47.826 0.00 0.00 0.00 2.69
1605 1631 0.672401 GAACCGGCGTTCCATCTCAA 60.672 55.000 6.01 0.00 42.26 3.02
1692 1718 7.050377 GGTCTGATCTGAAAATCTGGTCATTA 58.950 38.462 3.59 0.00 35.41 1.90
2217 2259 4.530710 ACAATGTTCTCATTTGCTGCAT 57.469 36.364 1.84 0.00 41.66 3.96
2343 2385 7.099764 CCCAGCGATAAGAACATGTATATTCT 58.900 38.462 0.00 0.00 36.73 2.40
2733 2775 6.823689 ACATGCTGTTATAAGACCTAACCAAG 59.176 38.462 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.