Multiple sequence alignment - TraesCS4A01G300200

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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 TraesCS4A01G300200 chr4A 100.000 2614 0 0 1 2614 597972288 597969675 0.000000e+00 4828
1 TraesCS4A01G300200 chr4A 89.988 859 78 7 1760 2614 145676935 145677789 0.000000e+00 1103
2 TraesCS4A01G300200 chr4A 85.081 496 64 6 991 1481 597946190 597945700 5.020000e-137 497
3 TraesCS4A01G300200 chr4D 95.852 1760 63 7 1 1756 5570727 5572480 0.000000e+00 2837
4 TraesCS4A01G300200 chr4D 80.078 768 106 27 991 1754 5578876 5579600 6.410000e-146 527
5 TraesCS4A01G300200 chr4D 89.933 149 10 4 822 969 5578655 5578799 1.240000e-43 187
6 TraesCS4A01G300200 chr7A 92.173 856 66 1 1759 2614 501802390 501801536 0.000000e+00 1208
7 TraesCS4A01G300200 chr7A 89.988 859 78 6 1759 2614 144069818 144068965 0.000000e+00 1103
8 TraesCS4A01G300200 chr7A 89.627 858 84 5 1759 2614 223145662 223144808 0.000000e+00 1086
9 TraesCS4A01G300200 chr3A 91.715 857 69 2 1759 2614 152321642 152320787 0.000000e+00 1188
10 TraesCS4A01G300200 chr3A 88.668 856 95 1 1759 2614 101243662 101244515 0.000000e+00 1042
11 TraesCS4A01G300200 chr6A 91.725 858 60 7 1759 2614 249399848 249399000 0.000000e+00 1181
12 TraesCS4A01G300200 chr4B 92.186 819 47 3 739 1541 9693970 9694787 0.000000e+00 1142
13 TraesCS4A01G300200 chr4B 91.016 256 18 4 344 595 9693695 9693949 8.960000e-90 340
14 TraesCS4A01G300200 chr4B 96.000 125 5 0 1630 1754 9694804 9694928 1.230000e-48 204
15 TraesCS4A01G300200 chr4B 92.105 76 6 0 243 318 9693619 9693694 9.890000e-20 108
16 TraesCS4A01G300200 chr2A 89.227 854 89 1 1761 2614 441786082 441785232 0.000000e+00 1064
17 TraesCS4A01G300200 chr2A 88.304 855 95 3 1761 2614 441843337 441842487 0.000000e+00 1020
18 TraesCS4A01G300200 chr5D 82.323 198 27 4 1288 1481 356838695 356838502 5.790000e-37 165
19 TraesCS4A01G300200 chr5A 81.643 207 30 4 1279 1481 458193014 458192812 5.790000e-37 165
20 TraesCS4A01G300200 chr5A 81.463 205 32 3 1286 1487 458279110 458278909 2.080000e-36 163
21 TraesCS4A01G300200 chr5A 81.407 199 31 4 1286 1481 458273855 458273660 9.680000e-35 158
22 TraesCS4A01G300200 chr5B 79.902 204 37 3 1286 1487 421621988 421621787 2.100000e-31 147
23 TraesCS4A01G300200 chr5B 78.846 208 38 4 1286 1490 421697747 421697543 4.540000e-28 135


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 TraesCS4A01G300200 chr4A 597969675 597972288 2613 True 4828.0 4828 100.00000 1 2614 1 chr4A.!!$R2 2613
1 TraesCS4A01G300200 chr4A 145676935 145677789 854 False 1103.0 1103 89.98800 1760 2614 1 chr4A.!!$F1 854
2 TraesCS4A01G300200 chr4D 5570727 5572480 1753 False 2837.0 2837 95.85200 1 1756 1 chr4D.!!$F1 1755
3 TraesCS4A01G300200 chr4D 5578655 5579600 945 False 357.0 527 85.00550 822 1754 2 chr4D.!!$F2 932
4 TraesCS4A01G300200 chr7A 501801536 501802390 854 True 1208.0 1208 92.17300 1759 2614 1 chr7A.!!$R3 855
5 TraesCS4A01G300200 chr7A 144068965 144069818 853 True 1103.0 1103 89.98800 1759 2614 1 chr7A.!!$R1 855
6 TraesCS4A01G300200 chr7A 223144808 223145662 854 True 1086.0 1086 89.62700 1759 2614 1 chr7A.!!$R2 855
7 TraesCS4A01G300200 chr3A 152320787 152321642 855 True 1188.0 1188 91.71500 1759 2614 1 chr3A.!!$R1 855
8 TraesCS4A01G300200 chr3A 101243662 101244515 853 False 1042.0 1042 88.66800 1759 2614 1 chr3A.!!$F1 855
9 TraesCS4A01G300200 chr6A 249399000 249399848 848 True 1181.0 1181 91.72500 1759 2614 1 chr6A.!!$R1 855
10 TraesCS4A01G300200 chr4B 9693619 9694928 1309 False 448.5 1142 92.82675 243 1754 4 chr4B.!!$F1 1511
11 TraesCS4A01G300200 chr2A 441785232 441786082 850 True 1064.0 1064 89.22700 1761 2614 1 chr2A.!!$R1 853
12 TraesCS4A01G300200 chr2A 441842487 441843337 850 True 1020.0 1020 88.30400 1761 2614 1 chr2A.!!$R2 853

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
43 44 0.029834 CGCTTGCAATGGTAGCCATC 59.97 55.0 0.0 0.0 44.4 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 1964 1.176619 TCTTTGGTGAGTCGCCTCGA 61.177 55.0 22.95 13.31 40.85 4.04 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 4.406069 CTTGATGGTTGCTTGATAACACG 58.594 43.478 0.00 0.00 0.00 4.49
43 44 0.029834 CGCTTGCAATGGTAGCCATC 59.970 55.000 0.00 0.00 44.40 3.51
47 48 0.747644 TGCAATGGTAGCCATCGGTG 60.748 55.000 0.70 0.00 44.40 4.94
91 92 6.369059 AGACTTGAAAAATGTCAGTGACAG 57.631 37.500 28.54 15.84 46.04 3.51
123 124 1.243342 CGGGAAGTGATTGCCTTGCA 61.243 55.000 0.00 0.00 36.47 4.08
124 125 1.188863 GGGAAGTGATTGCCTTGCAT 58.811 50.000 0.00 0.00 38.76 3.96
189 190 6.954487 TTTTCTTCTACTTCACCTTTTCCC 57.046 37.500 0.00 0.00 0.00 3.97
194 195 2.256117 ACTTCACCTTTTCCCGAGTG 57.744 50.000 0.00 0.00 0.00 3.51
200 201 1.071857 ACCTTTTCCCGAGTGAAGTCC 59.928 52.381 0.00 0.00 0.00 3.85
286 287 3.417101 AGATCGAGCGGTATGAGATCTT 58.583 45.455 14.48 0.00 43.66 2.40
333 334 2.424956 GTCTCCAAGGAATGCAATGTCC 59.575 50.000 6.37 6.37 0.00 4.02
399 401 3.443681 ACCATTTCCTTGCTGAAATACGG 59.556 43.478 8.44 9.09 41.74 4.02
414 416 2.183478 TACGGTCGACAGGTAGTTCA 57.817 50.000 19.84 0.00 0.00 3.18
479 482 3.976793 TGAGAAGCTTTGCAAGTCTTG 57.023 42.857 16.67 8.31 0.00 3.02
485 488 2.961062 AGCTTTGCAAGTCTTGTGGAAT 59.039 40.909 14.03 0.00 0.00 3.01
630 636 6.769512 AGCTAGTTGTCAAAGGAGTCAATAA 58.230 36.000 0.00 0.00 0.00 1.40
639 645 6.096001 GTCAAAGGAGTCAATAAAGATGCCAT 59.904 38.462 0.00 0.00 0.00 4.40
730 736 1.068741 GATCCGCGACAATTAGGGAGT 59.931 52.381 8.23 0.00 0.00 3.85
849 871 6.160576 ACATTGTTTTGGTAAATGAGTGCT 57.839 33.333 1.89 0.00 35.67 4.40
972 994 3.693807 TCTTGCTCAGATGGCATCTTTT 58.306 40.909 26.87 4.45 39.54 2.27
1024 1101 9.273016 ACCTATAAAATCCATGTGAATTAGACG 57.727 33.333 0.00 0.00 0.00 4.18
1031 1108 6.160576 TCCATGTGAATTAGACGATCATCA 57.839 37.500 0.00 0.00 0.00 3.07
1102 1182 9.533831 ACTATTACTGTTGGATTCCATCTTTTT 57.466 29.630 6.15 0.00 31.53 1.94
1280 1360 0.981277 CCCCCGAACAGATGGGTACT 60.981 60.000 0.00 0.00 44.44 2.73
1282 1362 1.191535 CCCGAACAGATGGGTACTCA 58.808 55.000 0.00 0.00 40.76 3.41
1330 1410 1.355563 CGACAAGATCTCGGCGCTA 59.644 57.895 7.64 0.00 0.00 4.26
1336 1416 2.123854 ATCTCGGCGCTACCAGGA 60.124 61.111 7.64 0.00 39.03 3.86
1389 1469 1.568612 GGGTACGTGACTGTCGACGA 61.569 60.000 27.09 14.89 38.94 4.20
1414 1494 2.032860 ATGGCCGCGCACTCTTCTAT 62.033 55.000 8.75 0.00 0.00 1.98
1724 1804 3.279434 GGTGAACAGAGACAACCAAACT 58.721 45.455 0.00 0.00 0.00 2.66
1756 1836 0.609662 AACCATGCCTGGAACAATGC 59.390 50.000 15.66 0.00 46.37 3.56
1757 1837 1.259840 ACCATGCCTGGAACAATGCC 61.260 55.000 15.66 0.00 46.37 4.40
1815 1895 0.913451 AGATTGCTGCTCCTGGGACT 60.913 55.000 0.00 0.00 0.00 3.85
1854 1934 2.677337 GGTTAGCGGCGGTTTATACAAA 59.323 45.455 19.60 0.00 0.00 2.83
1883 1964 8.599792 AGAAAAAGATTCATTTGGGATGAACAT 58.400 29.630 3.79 0.00 40.37 2.71
1946 2027 1.874739 CGGTGTTTTAAGCCGGTGAGA 60.875 52.381 1.90 0.00 41.60 3.27
1949 2030 2.418976 GTGTTTTAAGCCGGTGAGATCC 59.581 50.000 1.90 0.00 0.00 3.36
2039 2120 3.922240 CCCATGTTTTTCTTTCTGCATCG 59.078 43.478 0.00 0.00 0.00 3.84
2090 2172 7.664552 AGATATGCTGAATGGGAATTTTGAA 57.335 32.000 0.00 0.00 0.00 2.69
2091 2173 8.081517 AGATATGCTGAATGGGAATTTTGAAA 57.918 30.769 0.00 0.00 0.00 2.69
2092 2174 8.542080 AGATATGCTGAATGGGAATTTTGAAAA 58.458 29.630 0.00 0.00 0.00 2.29
2120 2202 4.163427 TCTGGGTCTCAGATTCTTGACTT 58.837 43.478 0.00 0.00 46.71 3.01
2144 2226 0.392461 GCCGGGTCTTTGCATCAGTA 60.392 55.000 2.18 0.00 0.00 2.74
2276 2359 1.758122 GGCACTTGGGGGCTAATGG 60.758 63.158 0.00 0.00 0.00 3.16
2299 2384 4.558860 GCTGCCGAAAAATTCAGTCATAAC 59.441 41.667 0.00 0.00 0.00 1.89
2304 2389 6.419413 GCCGAAAAATTCAGTCATAACAAACA 59.581 34.615 0.00 0.00 0.00 2.83
2374 2459 1.148273 GGGGGCTAATGCACATCGA 59.852 57.895 0.00 0.00 46.28 3.59
2385 2470 5.633830 AATGCACATCGATTGAGTTTTCT 57.366 34.783 0.00 0.00 0.00 2.52
2479 2564 9.093970 AGCTTTCACTTTTAAACAATGGTAAAC 57.906 29.630 0.00 0.00 0.00 2.01
2499 2584 0.749454 AGAACCGGCTCATTCATGCC 60.749 55.000 7.76 0.00 45.25 4.40
2510 2595 3.536570 TCATTCATGCCGATTAAACCGA 58.463 40.909 2.68 0.00 0.00 4.69
2581 2666 4.755266 ATTCTAACTATGACAACCGGCT 57.245 40.909 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.029834 CGATGGCTACCATTGCAAGC 59.970 55.000 4.94 1.35 45.26 4.01
43 44 1.935873 CTGGCTATCAACATGACACCG 59.064 52.381 0.00 0.00 0.00 4.94
47 48 2.358957 TGCACTGGCTATCAACATGAC 58.641 47.619 0.00 0.00 41.91 3.06
189 190 0.387367 CGACCACTGGACTTCACTCG 60.387 60.000 0.71 0.00 0.00 4.18
194 195 2.818432 TCTACTTCGACCACTGGACTTC 59.182 50.000 0.71 0.00 0.00 3.01
200 201 5.068234 TGGTATTTCTACTTCGACCACTG 57.932 43.478 0.00 0.00 32.10 3.66
286 287 2.093500 ACTATGCGATCACAAAGGCTCA 60.093 45.455 0.00 0.00 0.00 4.26
359 361 2.203337 GTGTGGTTGCCTGAGCCA 60.203 61.111 0.00 0.00 38.69 4.75
399 401 6.367969 ACAAACAATATGAACTACCTGTCGAC 59.632 38.462 9.11 9.11 0.00 4.20
446 449 4.936685 AGCTTCTCATAAAGTTTCCCCT 57.063 40.909 0.00 0.00 0.00 4.79
479 482 2.793933 GCTAGACACGGTCGTATTCCAC 60.794 54.545 0.00 0.00 37.67 4.02
639 645 2.269940 CCTCCCTTCTTTCCCTGAAGA 58.730 52.381 5.21 0.00 42.37 2.87
730 736 0.906775 AAAGATAAGGGAACGGGCGA 59.093 50.000 0.00 0.00 0.00 5.54
740 746 7.920682 ACTTTTTGTAGTGTGCAAAAGATAAGG 59.079 33.333 9.58 0.00 43.70 2.69
972 994 3.395273 GGAGTTAGGTAGCTAGGGAGAGA 59.605 52.174 1.31 0.00 0.00 3.10
1024 1101 6.148315 TCAACTTGTGTGTGAGATTGATGATC 59.852 38.462 0.00 0.00 34.83 2.92
1031 1108 6.146184 CGACTATTCAACTTGTGTGTGAGATT 59.854 38.462 0.00 0.00 0.00 2.40
1102 1182 4.952071 TGCAATTGTGGGAATGAGAAAA 57.048 36.364 7.40 0.00 0.00 2.29
1280 1360 2.710902 CGATGTGGTCGGAGCCTGA 61.711 63.158 4.54 0.00 46.47 3.86
1301 1381 2.257409 ATCTTGTCGGCCGCCTTCAT 62.257 55.000 23.51 6.58 0.00 2.57
1389 1469 3.209097 GTGCGCGGCCATTATGGT 61.209 61.111 13.28 0.00 40.46 3.55
1414 1494 1.479323 CCGGGAGATTCCACGAAGTAA 59.521 52.381 0.00 0.00 41.61 2.24
1462 1542 1.599047 CTCACCTCCGTTGAGCCAT 59.401 57.895 0.00 0.00 37.29 4.40
1578 1658 8.885302 ATCGTATCAATTCATTATGCATTTCG 57.115 30.769 3.54 0.00 0.00 3.46
1615 1695 8.689061 GCATGCTCCATATCAATCCATTATTTA 58.311 33.333 11.37 0.00 0.00 1.40
1617 1697 6.666113 TGCATGCTCCATATCAATCCATTATT 59.334 34.615 20.33 0.00 0.00 1.40
1618 1698 6.192044 TGCATGCTCCATATCAATCCATTAT 58.808 36.000 20.33 0.00 0.00 1.28
1619 1699 5.572252 TGCATGCTCCATATCAATCCATTA 58.428 37.500 20.33 0.00 0.00 1.90
1724 1804 2.027192 GGCATGGTTGTTCCTAGTGAGA 60.027 50.000 0.00 0.00 37.07 3.27
1815 1895 6.620678 GCTAACCAATCTGCAATTTACTCAA 58.379 36.000 0.00 0.00 0.00 3.02
1854 1934 7.965718 TCATCCCAAATGAATCTTTTTCTTGT 58.034 30.769 0.00 0.00 0.00 3.16
1883 1964 1.176619 TCTTTGGTGAGTCGCCTCGA 61.177 55.000 22.95 13.31 40.85 4.04
1946 2027 1.276421 CTTCAAGAGGTGACCACGGAT 59.724 52.381 3.63 0.00 35.39 4.18
1949 2030 1.937108 GCTCTTCAAGAGGTGACCACG 60.937 57.143 16.46 0.00 42.54 4.94
2039 2120 3.304057 CGGAGAAACTGAAAACCAGCTTC 60.304 47.826 0.00 0.00 46.81 3.86
2079 2161 4.696877 CCAGAAGGCATTTTCAAAATTCCC 59.303 41.667 7.82 4.86 0.00 3.97
2090 2172 2.503895 CTGAGACCCAGAAGGCATTT 57.496 50.000 0.00 0.00 45.78 2.32
2120 2202 2.046314 GCAAAGACCCGGCTAGCA 60.046 61.111 18.24 0.00 0.00 3.49
2144 2226 7.809806 GCTACTGCTAAACTTGAATCACAATTT 59.190 33.333 0.00 0.00 35.62 1.82
2276 2359 2.704725 TGACTGAATTTTTCGGCAGC 57.295 45.000 0.00 0.00 39.72 5.25
2299 2384 5.856455 GGGACTTATTCACGTGAATTGTTTG 59.144 40.000 39.86 27.25 41.64 2.93
2304 2389 4.156008 GCTTGGGACTTATTCACGTGAATT 59.844 41.667 39.86 26.74 41.64 2.17
2310 2395 2.699954 AGTGCTTGGGACTTATTCACG 58.300 47.619 0.00 0.00 0.00 4.35
2385 2470 7.281324 CACAACCGGGTCATCATAAAATAGTAA 59.719 37.037 6.32 0.00 0.00 2.24
2479 2564 0.379669 GCATGAATGAGCCGGTTCTG 59.620 55.000 19.73 9.79 0.00 3.02
2482 2567 3.924507 GGCATGAATGAGCCGGTT 58.075 55.556 1.90 0.00 41.70 4.44
2499 2584 1.375551 CCCAAGGGTCGGTTTAATCG 58.624 55.000 0.00 0.00 0.00 3.34
2510 2595 0.981277 CATCCGTAGTCCCCAAGGGT 60.981 60.000 4.11 0.00 44.74 4.34
2581 2666 8.497910 AGCATCTATAGTAGAATCCTTCCAAA 57.502 34.615 0.00 0.00 38.50 3.28


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

AutoCloner maintained by Alex Coulton.