Multiple sequence alignment - TraesCS5A01G070800

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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 TraesCS5A01G070800 chr5A 100.000 2567 0 0 1 2567 79272870 79275436 0.000000e+00 4741
1 TraesCS5A01G070800 chr5A 93.648 976 55 6 1595 2567 692383105 692382134 0.000000e+00 1452
2 TraesCS5A01G070800 chr5A 92.355 981 55 15 1595 2567 608276140 608275172 0.000000e+00 1378
3 TraesCS5A01G070800 chr2A 97.180 1596 44 1 1 1595 769612685 769614280 0.000000e+00 2697
4 TraesCS5A01G070800 chr2A 96.322 1604 54 4 1 1601 596376300 596374699 0.000000e+00 2630
5 TraesCS5A01G070800 chr2A 91.549 994 61 13 1595 2567 25471339 25472330 0.000000e+00 1349
6 TraesCS5A01G070800 chr2A 91.147 994 64 14 1595 2567 25459700 25460690 0.000000e+00 1327
7 TraesCS5A01G070800 chr2A 92.108 925 66 7 1595 2516 136638746 136637826 0.000000e+00 1297
8 TraesCS5A01G070800 chr2A 94.444 198 11 0 2319 2516 44178714 44178517 3.210000e-79 305
9 TraesCS5A01G070800 chr6A 96.930 1596 48 1 1 1595 510871920 510873515 0.000000e+00 2675
10 TraesCS5A01G070800 chr2D 95.298 1595 74 1 1 1595 116761578 116763171 0.000000e+00 2529
11 TraesCS5A01G070800 chr2D 87.868 816 84 14 1595 2404 68567958 68568764 0.000000e+00 944
12 TraesCS5A01G070800 chr2D 87.653 818 83 16 1595 2404 68591579 68592386 0.000000e+00 935
13 TraesCS5A01G070800 chr2D 89.180 610 55 10 1801 2404 68659755 68660359 0.000000e+00 750
14 TraesCS5A01G070800 chr6B 92.969 1593 108 4 3 1594 218018603 218017014 0.000000e+00 2318
15 TraesCS5A01G070800 chr6B 92.216 1593 121 2 2 1594 119509680 119508091 0.000000e+00 2252
16 TraesCS5A01G070800 chr4A 91.927 1598 124 5 1 1596 660341828 660343422 0.000000e+00 2231
17 TraesCS5A01G070800 chr2B 89.675 1598 156 9 3 1595 417498186 417496593 0.000000e+00 2028
18 TraesCS5A01G070800 chr2B 91.736 121 10 0 1595 1715 128379519 128379639 4.390000e-38 169
19 TraesCS5A01G070800 chr4B 88.784 1596 175 4 7 1600 635324597 635323004 0.000000e+00 1953
20 TraesCS5A01G070800 chr4D 88.292 837 84 13 1595 2426 120834802 120835629 0.000000e+00 990


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 TraesCS5A01G070800 chr5A 79272870 79275436 2566 False 4741 4741 100.000 1 2567 1 chr5A.!!$F1 2566
1 TraesCS5A01G070800 chr5A 692382134 692383105 971 True 1452 1452 93.648 1595 2567 1 chr5A.!!$R2 972
2 TraesCS5A01G070800 chr5A 608275172 608276140 968 True 1378 1378 92.355 1595 2567 1 chr5A.!!$R1 972
3 TraesCS5A01G070800 chr2A 769612685 769614280 1595 False 2697 2697 97.180 1 1595 1 chr2A.!!$F3 1594
4 TraesCS5A01G070800 chr2A 596374699 596376300 1601 True 2630 2630 96.322 1 1601 1 chr2A.!!$R3 1600
5 TraesCS5A01G070800 chr2A 25471339 25472330 991 False 1349 1349 91.549 1595 2567 1 chr2A.!!$F2 972
6 TraesCS5A01G070800 chr2A 25459700 25460690 990 False 1327 1327 91.147 1595 2567 1 chr2A.!!$F1 972
7 TraesCS5A01G070800 chr2A 136637826 136638746 920 True 1297 1297 92.108 1595 2516 1 chr2A.!!$R2 921
8 TraesCS5A01G070800 chr6A 510871920 510873515 1595 False 2675 2675 96.930 1 1595 1 chr6A.!!$F1 1594
9 TraesCS5A01G070800 chr2D 116761578 116763171 1593 False 2529 2529 95.298 1 1595 1 chr2D.!!$F4 1594
10 TraesCS5A01G070800 chr2D 68567958 68568764 806 False 944 944 87.868 1595 2404 1 chr2D.!!$F1 809
11 TraesCS5A01G070800 chr2D 68591579 68592386 807 False 935 935 87.653 1595 2404 1 chr2D.!!$F2 809
12 TraesCS5A01G070800 chr2D 68659755 68660359 604 False 750 750 89.180 1801 2404 1 chr2D.!!$F3 603
13 TraesCS5A01G070800 chr6B 218017014 218018603 1589 True 2318 2318 92.969 3 1594 1 chr6B.!!$R2 1591
14 TraesCS5A01G070800 chr6B 119508091 119509680 1589 True 2252 2252 92.216 2 1594 1 chr6B.!!$R1 1592
15 TraesCS5A01G070800 chr4A 660341828 660343422 1594 False 2231 2231 91.927 1 1596 1 chr4A.!!$F1 1595
16 TraesCS5A01G070800 chr2B 417496593 417498186 1593 True 2028 2028 89.675 3 1595 1 chr2B.!!$R1 1592
17 TraesCS5A01G070800 chr4B 635323004 635324597 1593 True 1953 1953 88.784 7 1600 1 chr4B.!!$R1 1593
18 TraesCS5A01G070800 chr4D 120834802 120835629 827 False 990 990 88.292 1595 2426 1 chr4D.!!$F1 831

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
25 26 3.18147 GGCTGCACCAAAAGTTAAAGGAA 60.181 43.478 0.5 0.0 38.86 3.36 F
85 86 3.92563 CTCGGCAAGCATGGGTGGT 62.926 63.158 0.0 0.0 37.76 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1080 1082 1.690985 CTTGACCTCCCCCTCCTCC 60.691 68.421 0.00 0.0 0.00 4.30 R
1726 1739 2.101917 TGCGCTATCCTAGTTGGTTACC 59.898 50.000 9.73 0.0 37.07 2.85 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
25 26 3.181470 GGCTGCACCAAAAGTTAAAGGAA 60.181 43.478 0.50 0.00 38.86 3.36
45 46 5.492524 AGGAAGGATGGGATTCAAAGACTTA 59.507 40.000 0.00 0.00 0.00 2.24
85 86 3.925630 CTCGGCAAGCATGGGTGGT 62.926 63.158 0.00 0.00 37.76 4.16
311 313 5.723887 GGATCCCTGATACCAGAACTATGAT 59.276 44.000 0.00 0.00 43.02 2.45
621 623 7.175104 AGAAACAGTTATGGACCACATTATGT 58.825 34.615 0.00 0.00 41.03 2.29
627 629 9.607988 CAGTTATGGACCACATTATGTAAACTA 57.392 33.333 0.00 0.00 41.03 2.24
685 687 4.525100 GGGTTTTACAAGGTATTCTGCCAA 59.475 41.667 0.00 0.00 0.00 4.52
693 695 6.904626 ACAAGGTATTCTGCCAATAGAATCT 58.095 36.000 4.44 0.00 44.15 2.40
1080 1082 2.203252 CATGGATGGAGGCCACCG 60.203 66.667 15.06 0.00 38.44 4.94
1164 1166 0.324738 TGGGAGGAGTTGCTCGATCT 60.325 55.000 0.00 0.00 0.00 2.75
1166 1168 1.398692 GGAGGAGTTGCTCGATCTCT 58.601 55.000 0.00 0.00 0.00 3.10
1283 1285 3.244044 GCTAAGCTCAGGGGTTATGAGAG 60.244 52.174 7.13 0.00 45.80 3.20
1335 1337 2.194271 GTTAATCTCTGGAACTCGCGG 58.806 52.381 6.13 0.00 0.00 6.46
1616 1622 1.764134 ACAAACTAGAACACGTCCCCA 59.236 47.619 0.00 0.00 0.00 4.96
1651 1663 7.489239 GCCCTGGCCCATTTATTAATTTATA 57.511 36.000 0.00 0.00 34.56 0.98
1710 1723 0.834612 TCGAACACCCAACCTCTTGT 59.165 50.000 0.00 0.00 0.00 3.16
1716 1729 5.528870 GAACACCCAACCTCTTGTTTTATG 58.471 41.667 0.00 0.00 34.00 1.90
1718 1731 5.697067 ACACCCAACCTCTTGTTTTATGTA 58.303 37.500 0.00 0.00 34.00 2.29
1726 1739 8.814235 CAACCTCTTGTTTTATGTATACCTACG 58.186 37.037 0.00 0.00 34.00 3.51
1741 1754 3.986435 ACCTACGGTAACCAACTAGGAT 58.014 45.455 0.00 0.00 35.66 3.24
1751 1764 1.269831 CCAACTAGGATAGCGCACCTC 60.270 57.143 20.57 9.29 44.39 3.85
1754 1767 1.957877 ACTAGGATAGCGCACCTCTTC 59.042 52.381 20.57 3.89 44.39 2.87
1755 1768 1.271102 CTAGGATAGCGCACCTCTTCC 59.729 57.143 20.57 11.77 37.68 3.46
1791 1831 9.878599 CTTCTTTTATTCGTCTTGTTGTGTATT 57.121 29.630 0.00 0.00 0.00 1.89
1991 2033 9.935682 TCGCATACTTTTATCAATTTCAAGATC 57.064 29.630 0.00 0.00 0.00 2.75
2322 2378 9.837525 CCTTTTGAAAATTTGAAATTTCACACA 57.162 25.926 20.35 8.21 43.20 3.72
2552 2608 1.577736 ACCAGGCTGATAGCAAGTCT 58.422 50.000 17.94 0.00 44.75 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 5.779241 TGTAAGTCTTTGAATCCCATCCT 57.221 39.130 0.00 0.0 0.00 3.24
45 46 7.331193 CCGAGTAGTGCTAAATTAAAGAGTTGT 59.669 37.037 0.00 0.0 0.00 3.32
85 86 2.083774 GTTGGGATTCGTCATCAAGCA 58.916 47.619 0.00 0.0 32.79 3.91
174 175 4.016444 TCCACACAGCTGAAGAAAACTTT 58.984 39.130 23.35 0.0 0.00 2.66
311 313 0.179004 ACCAATGTGAGCAACCGGAA 60.179 50.000 9.46 0.0 0.00 4.30
587 589 4.461431 TCCATAACTGTTTCTCTGTCGCTA 59.539 41.667 0.00 0.0 0.00 4.26
621 623 6.603997 TCACTTTTGGCAGAACCTTTAGTTTA 59.396 34.615 0.00 0.0 39.40 2.01
627 629 3.631250 TCTCACTTTTGGCAGAACCTTT 58.369 40.909 0.00 0.0 40.22 3.11
693 695 9.406828 GTTGCTATATGTCGATATTTGAGTGTA 57.593 33.333 0.00 0.0 0.00 2.90
799 801 0.035458 ACCGGAGCTTGAGTCCAAAG 59.965 55.000 9.46 0.0 33.14 2.77
895 897 0.608640 AGTTTGGCTCGATCGGACTT 59.391 50.000 16.41 0.0 0.00 3.01
1080 1082 1.690985 CTTGACCTCCCCCTCCTCC 60.691 68.421 0.00 0.0 0.00 4.30
1117 1119 2.485426 CTCTTCGAGCTTCCAATGCAAA 59.515 45.455 0.00 0.0 0.00 3.68
1164 1166 2.158769 TGCAGCTCTGAAAGTGGAAAGA 60.159 45.455 0.29 0.0 33.76 2.52
1166 1168 2.346766 TGCAGCTCTGAAAGTGGAAA 57.653 45.000 0.29 0.0 33.76 3.13
1335 1337 3.562973 CCACAACAGTCCTATCATCATGC 59.437 47.826 0.00 0.0 0.00 4.06
1547 1551 4.702131 AGCTTTATTCAACAATCGAAGCCT 59.298 37.500 0.00 0.0 39.68 4.58
1606 1611 2.291043 GGATGGAGTGGGGACGTGT 61.291 63.158 0.00 0.0 0.00 4.49
1726 1739 2.101917 TGCGCTATCCTAGTTGGTTACC 59.898 50.000 9.73 0.0 37.07 2.85
1754 1767 5.163754 ACGAATAAAAGAAGAATCCAAGCGG 60.164 40.000 0.00 0.0 0.00 5.52
1755 1768 5.869350 ACGAATAAAAGAAGAATCCAAGCG 58.131 37.500 0.00 0.0 0.00 4.68
1758 1771 8.391075 ACAAGACGAATAAAAGAAGAATCCAA 57.609 30.769 0.00 0.0 0.00 3.53
2205 2261 0.383949 GCTTCCTGGCGTGACAAAAA 59.616 50.000 0.00 0.0 0.00 1.94
2322 2378 5.473504 CCAAGAATTAGGCACTACACACTTT 59.526 40.000 0.00 0.0 42.67 2.66


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

AutoCloner maintained by Alex Coulton.