Multiple sequence alignment - TraesCS2A01G036800

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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 TraesCS2A01G036800 chr2A 100.000 2555 0 0 1 2555 15750836 15748282 0.000000e+00 4719
1 TraesCS2A01G036800 chr2A 91.711 2268 107 31 301 2555 613797 611598 0.000000e+00 3072
2 TraesCS2A01G036800 chr2A 94.278 1765 72 9 791 2555 30580899 30582634 0.000000e+00 2673
3 TraesCS2A01G036800 chr7A 93.803 1759 78 11 791 2547 10993585 10995314 0.000000e+00 2615
4 TraesCS2A01G036800 chr7A 94.348 1663 64 15 893 2555 15520954 15519322 0.000000e+00 2523
5 TraesCS2A01G036800 chr7A 93.754 1665 72 14 893 2555 41971280 41972914 0.000000e+00 2470
6 TraesCS2A01G036800 chr4A 93.654 1765 82 9 791 2555 600513507 600511773 0.000000e+00 2612
7 TraesCS2A01G036800 chr5A 92.941 1785 74 18 791 2555 153575068 153573316 0.000000e+00 2551
8 TraesCS2A01G036800 chr5A 92.861 1667 86 14 891 2555 693843665 693845300 0.000000e+00 2388
9 TraesCS2A01G036800 chr5A 85.059 937 55 33 1 888 565287066 565286166 0.000000e+00 876
10 TraesCS2A01G036800 chr6A 94.408 1663 60 13 893 2555 555103857 555102228 0.000000e+00 2525
11 TraesCS2A01G036800 chr6A 93.938 1666 70 15 891 2555 602796927 602795292 0.000000e+00 2488
12 TraesCS2A01G036800 chr6A 93.814 1665 72 15 891 2555 597466973 597465340 0.000000e+00 2475
13 TraesCS2A01G036800 chr3A 92.149 1312 57 16 1262 2555 38170700 38171983 0.000000e+00 1810
14 TraesCS2A01G036800 chr3A 83.941 741 56 33 1 699 669776109 669775390 0.000000e+00 651
15 TraesCS2A01G036800 chr2B 89.807 932 40 25 1 888 655694360 655693440 0.000000e+00 1144
16 TraesCS2A01G036800 chr3B 88.571 910 47 30 24 888 60566553 60567450 0.000000e+00 1051
17 TraesCS2A01G036800 chr2D 88.121 926 53 35 1 888 630081801 630080895 0.000000e+00 1048
18 TraesCS2A01G036800 chr2D 87.055 927 59 39 1 888 87947863 87948767 0.000000e+00 990
19 TraesCS2A01G036800 chr6D 87.987 924 53 32 1 888 257991902 257992803 0.000000e+00 1038
20 TraesCS2A01G036800 chr6D 92.632 475 22 11 414 888 305380477 305380016 0.000000e+00 671
21 TraesCS2A01G036800 chr5D 87.905 926 51 36 1 888 36561835 36562737 0.000000e+00 1033
22 TraesCS2A01G036800 chr1D 87.581 926 59 37 1 888 383359718 383358811 0.000000e+00 1022
23 TraesCS2A01G036800 chr4B 94.483 580 23 8 308 887 15516871 15517441 0.000000e+00 885
24 TraesCS2A01G036800 chr4B 91.900 321 12 3 1 307 15516519 15516839 1.090000e-118 436


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 TraesCS2A01G036800 chr2A 15748282 15750836 2554 True 4719.0 4719 100.0000 1 2555 1 chr2A.!!$R2 2554
1 TraesCS2A01G036800 chr2A 611598 613797 2199 True 3072.0 3072 91.7110 301 2555 1 chr2A.!!$R1 2254
2 TraesCS2A01G036800 chr2A 30580899 30582634 1735 False 2673.0 2673 94.2780 791 2555 1 chr2A.!!$F1 1764
3 TraesCS2A01G036800 chr7A 10993585 10995314 1729 False 2615.0 2615 93.8030 791 2547 1 chr7A.!!$F1 1756
4 TraesCS2A01G036800 chr7A 15519322 15520954 1632 True 2523.0 2523 94.3480 893 2555 1 chr7A.!!$R1 1662
5 TraesCS2A01G036800 chr7A 41971280 41972914 1634 False 2470.0 2470 93.7540 893 2555 1 chr7A.!!$F2 1662
6 TraesCS2A01G036800 chr4A 600511773 600513507 1734 True 2612.0 2612 93.6540 791 2555 1 chr4A.!!$R1 1764
7 TraesCS2A01G036800 chr5A 153573316 153575068 1752 True 2551.0 2551 92.9410 791 2555 1 chr5A.!!$R1 1764
8 TraesCS2A01G036800 chr5A 693843665 693845300 1635 False 2388.0 2388 92.8610 891 2555 1 chr5A.!!$F1 1664
9 TraesCS2A01G036800 chr5A 565286166 565287066 900 True 876.0 876 85.0590 1 888 1 chr5A.!!$R2 887
10 TraesCS2A01G036800 chr6A 555102228 555103857 1629 True 2525.0 2525 94.4080 893 2555 1 chr6A.!!$R1 1662
11 TraesCS2A01G036800 chr6A 602795292 602796927 1635 True 2488.0 2488 93.9380 891 2555 1 chr6A.!!$R3 1664
12 TraesCS2A01G036800 chr6A 597465340 597466973 1633 True 2475.0 2475 93.8140 891 2555 1 chr6A.!!$R2 1664
13 TraesCS2A01G036800 chr3A 38170700 38171983 1283 False 1810.0 1810 92.1490 1262 2555 1 chr3A.!!$F1 1293
14 TraesCS2A01G036800 chr3A 669775390 669776109 719 True 651.0 651 83.9410 1 699 1 chr3A.!!$R1 698
15 TraesCS2A01G036800 chr2B 655693440 655694360 920 True 1144.0 1144 89.8070 1 888 1 chr2B.!!$R1 887
16 TraesCS2A01G036800 chr3B 60566553 60567450 897 False 1051.0 1051 88.5710 24 888 1 chr3B.!!$F1 864
17 TraesCS2A01G036800 chr2D 630080895 630081801 906 True 1048.0 1048 88.1210 1 888 1 chr2D.!!$R1 887
18 TraesCS2A01G036800 chr2D 87947863 87948767 904 False 990.0 990 87.0550 1 888 1 chr2D.!!$F1 887
19 TraesCS2A01G036800 chr6D 257991902 257992803 901 False 1038.0 1038 87.9870 1 888 1 chr6D.!!$F1 887
20 TraesCS2A01G036800 chr5D 36561835 36562737 902 False 1033.0 1033 87.9050 1 888 1 chr5D.!!$F1 887
21 TraesCS2A01G036800 chr1D 383358811 383359718 907 True 1022.0 1022 87.5810 1 888 1 chr1D.!!$R1 887
22 TraesCS2A01G036800 chr4B 15516519 15517441 922 False 660.5 885 93.1915 1 887 2 chr4B.!!$F1 886

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
421 485 1.417517 AGAGCGATCATGCCCATAACA 59.582 47.619 2.38 0.0 34.65 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 2338 0.465097 CATAGGCAAGCTGACCCCAG 60.465 60.0 1.67 0.0 43.22 4.45 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
61 63 2.790433 TCCTCTTGGTCATTTTTCCCG 58.210 47.619 0.00 0.00 34.23 5.14
146 166 7.879070 AGAGACAGTTGTGTAGTACGATTTAA 58.121 34.615 0.00 0.00 36.88 1.52
151 171 8.758715 ACAGTTGTGTAGTACGATTTAACTTTC 58.241 33.333 0.00 0.00 34.05 2.62
185 205 4.289410 TCCTTCACCATGATCCAAGAAAGA 59.711 41.667 0.00 0.00 0.00 2.52
189 209 4.400251 TCACCATGATCCAAGAAAGATTGC 59.600 41.667 0.00 0.00 0.00 3.56
287 313 5.880054 ATACCAACAACTATCAACTGCAC 57.120 39.130 0.00 0.00 0.00 4.57
344 402 9.797556 ATGAAACCTAAAAACTGTCAACTTAAC 57.202 29.630 0.00 0.00 0.00 2.01
359 418 8.879759 TGTCAACTTAACTTCTTTCTAACACAG 58.120 33.333 0.00 0.00 0.00 3.66
375 438 8.185506 TCTAACACAGAAACATAGGTACTGAA 57.814 34.615 17.24 4.02 41.52 3.02
376 439 8.644216 TCTAACACAGAAACATAGGTACTGAAA 58.356 33.333 17.24 3.78 41.52 2.69
377 440 7.730364 AACACAGAAACATAGGTACTGAAAG 57.270 36.000 17.24 10.79 41.52 2.62
378 441 5.701290 ACACAGAAACATAGGTACTGAAAGC 59.299 40.000 17.24 0.00 41.52 3.51
379 442 5.700832 CACAGAAACATAGGTACTGAAAGCA 59.299 40.000 17.24 0.00 41.52 3.91
421 485 1.417517 AGAGCGATCATGCCCATAACA 59.582 47.619 2.38 0.00 34.65 2.41
460 524 8.911918 TTTCCTAACACTAAACATGCTCTAAA 57.088 30.769 0.00 0.00 0.00 1.85
475 541 4.195416 GCTCTAAACTCTCTGATTTGGGG 58.805 47.826 0.00 0.00 0.00 4.96
566 635 5.927689 TCAATGTTGCCTGCATTTAAGAAAG 59.072 36.000 0.00 0.00 34.68 2.62
570 639 4.771590 TGCCTGCATTTAAGAAAGACAG 57.228 40.909 0.00 0.00 0.00 3.51
571 640 4.397420 TGCCTGCATTTAAGAAAGACAGA 58.603 39.130 0.00 0.00 32.12 3.41
575 645 6.701400 GCCTGCATTTAAGAAAGACAGAAAAA 59.299 34.615 0.00 0.00 32.12 1.94
861 947 4.219944 CCTGAGTTTAGTGTGGTACTAGCA 59.780 45.833 0.00 0.00 42.57 3.49
925 1011 5.763204 GCTATTGGCTTGCCTGTATTTACTA 59.237 40.000 13.18 0.00 38.06 1.82
930 1016 4.023707 GGCTTGCCTGTATTTACTATGCTG 60.024 45.833 4.11 0.00 0.00 4.41
1132 1219 2.176045 TCCAAAGAGTCGATGGTGCTA 58.824 47.619 14.52 0.00 35.66 3.49
1133 1220 2.565391 TCCAAAGAGTCGATGGTGCTAA 59.435 45.455 14.52 0.00 35.66 3.09
1136 1223 5.070446 TCCAAAGAGTCGATGGTGCTAATAT 59.930 40.000 14.52 0.00 35.66 1.28
1476 1563 6.475402 GGGAGTTGATAAAACAACAGTTTGTG 59.525 38.462 12.78 0.00 45.69 3.33
1540 1627 5.601662 CAGAAAAGATTCCCGTGCTAGATA 58.398 41.667 0.00 0.00 36.12 1.98
1552 1639 4.870426 CCGTGCTAGATAACATTGTTGAGT 59.130 41.667 12.30 0.00 0.00 3.41
1557 1644 6.255670 TGCTAGATAACATTGTTGAGTAAGCG 59.744 38.462 12.30 0.00 0.00 4.68
1560 1647 7.849804 AGATAACATTGTTGAGTAAGCGAAT 57.150 32.000 12.30 0.00 0.00 3.34
1704 1791 3.843027 AGGTAATAGATGGCAGATGGGAG 59.157 47.826 0.00 0.00 0.00 4.30
1797 1884 2.507944 CAAGGGATCCCGCCAGAG 59.492 66.667 25.48 8.76 41.95 3.35
1809 1896 1.077445 GCCAGAGGAAAGGGCCTTT 59.923 57.895 30.88 30.88 41.90 3.11
1936 2026 5.472137 TGTTTCTTAGCCCATCAACAAGTAC 59.528 40.000 0.00 0.00 0.00 2.73
1937 2027 4.216411 TCTTAGCCCATCAACAAGTACC 57.784 45.455 0.00 0.00 0.00 3.34
2027 2118 7.148239 GCCACTAAATTGCTTACAACAGTAGAT 60.148 37.037 0.00 0.00 38.99 1.98
2042 2133 9.787435 ACAACAGTAGATAAAAGACATAACCAA 57.213 29.630 0.00 0.00 0.00 3.67
2044 2135 9.787435 AACAGTAGATAAAAGACATAACCAACA 57.213 29.630 0.00 0.00 0.00 3.33
2045 2136 9.787435 ACAGTAGATAAAAGACATAACCAACAA 57.213 29.630 0.00 0.00 0.00 2.83
2083 2192 2.557924 TGCTGGACTTGCCTAATGTTTG 59.442 45.455 0.00 0.00 37.63 2.93
2123 2232 2.887152 CAAAAGTTCCTGCTTGCCTAGT 59.113 45.455 0.00 0.00 0.00 2.57
2165 2274 1.606668 GTGTTGAATCCGAACTTGCCA 59.393 47.619 0.00 0.00 0.00 4.92
2184 2293 5.626142 TGCCAATGGTTAGTCTCTTTGTAA 58.374 37.500 0.00 0.00 0.00 2.41
2187 2296 6.206829 GCCAATGGTTAGTCTCTTTGTAACTT 59.793 38.462 0.00 0.00 0.00 2.66
2236 2347 0.178992 TTGTTTCTGGCTGGGGTCAG 60.179 55.000 0.00 0.00 45.72 3.51
2251 2362 2.421952 GGGTCAGCTTGCCTATGATTGA 60.422 50.000 3.61 0.00 0.00 2.57
2276 2388 7.510428 AAATTTGTATTGCTCACTAAATGCG 57.490 32.000 0.00 0.00 0.00 4.73
2278 2390 5.621197 TTGTATTGCTCACTAAATGCGTT 57.379 34.783 0.00 0.00 0.00 4.84
2376 2490 5.221106 GCTTGTATAGCTTCATGAATTGCCA 60.221 40.000 8.96 0.00 46.77 4.92
2392 2506 3.128852 TGCCAAAGCTTTGCATTTGAT 57.871 38.095 29.93 0.00 38.42 2.57
2414 2528 3.441496 TGCCTTGCTGAAAACAGAAAG 57.559 42.857 10.10 10.10 37.54 2.62
2415 2529 2.760092 TGCCTTGCTGAAAACAGAAAGT 59.240 40.909 14.38 0.00 36.35 2.66
2455 2569 8.190784 CACTGTTTTTGTGTAGAAGAAGGATTT 58.809 33.333 0.00 0.00 0.00 2.17
2477 2591 2.886523 ACCACCATTGTGACTTCATGTG 59.113 45.455 0.00 0.00 45.76 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 7.109501 AGAGGAATCTTTTTCTAGCTTCTTCC 58.890 38.462 0.00 0.00 30.89 3.46
146 166 6.116126 GGTGAAGGATATGCTGTAAGAAAGT 58.884 40.000 0.00 0.00 34.07 2.66
151 171 5.614308 TCATGGTGAAGGATATGCTGTAAG 58.386 41.667 0.00 0.00 0.00 2.34
189 209 2.798283 CAACTGCATCTTGGCAACTTTG 59.202 45.455 0.00 0.00 44.40 2.77
287 313 6.427150 AGCAGTATGTTTTGAAGTAACGTTG 58.573 36.000 11.99 0.00 39.31 4.10
359 418 7.435068 TTTCTGCTTTCAGTACCTATGTTTC 57.565 36.000 0.00 0.00 41.10 2.78
421 485 7.054751 AGTGTTAGGAAAAACTCAAGTTAGCT 58.945 34.615 0.00 0.00 37.25 3.32
460 524 1.912043 CTCACCCCCAAATCAGAGAGT 59.088 52.381 0.00 0.00 0.00 3.24
475 541 3.748568 GTGTCTTCAGAATGGAACTCACC 59.251 47.826 0.00 0.00 36.16 4.02
535 602 2.367894 TGCAGGCAACATTGATTTTGGA 59.632 40.909 0.00 0.00 41.41 3.53
861 947 4.447389 GCAAATTTTACGTTGTTGAGGCAT 59.553 37.500 0.00 0.00 0.00 4.40
930 1016 1.382692 GCAGAGGGATGGAAGCAAGC 61.383 60.000 0.00 0.00 0.00 4.01
1132 1219 7.166851 CCATCTGTCTCCATTGCTTCTATATT 58.833 38.462 0.00 0.00 0.00 1.28
1133 1220 6.296317 CCCATCTGTCTCCATTGCTTCTATAT 60.296 42.308 0.00 0.00 0.00 0.86
1136 1223 3.135348 CCCATCTGTCTCCATTGCTTCTA 59.865 47.826 0.00 0.00 0.00 2.10
1476 1563 1.477105 GCTTCCGAAACTTGTTGCAC 58.523 50.000 0.00 0.00 0.00 4.57
1540 1627 5.940192 TCATTCGCTTACTCAACAATGTT 57.060 34.783 0.00 0.00 0.00 2.71
1552 1639 9.148104 CTCATCTTCATTATCATCATTCGCTTA 57.852 33.333 0.00 0.00 0.00 3.09
1557 1644 7.925043 AGCCTCATCTTCATTATCATCATTC 57.075 36.000 0.00 0.00 0.00 2.67
1560 1647 8.380867 ACAATAGCCTCATCTTCATTATCATCA 58.619 33.333 0.00 0.00 0.00 3.07
1608 1695 1.620822 TCTTGCTCCTCTTTTTGCCC 58.379 50.000 0.00 0.00 0.00 5.36
1704 1791 3.552294 GCTCGCTAACAAAGTAGATCACC 59.448 47.826 0.00 0.00 0.00 4.02
1809 1896 9.453572 AAATTGCAGTTATGAAGATGAGTAAGA 57.546 29.630 0.00 0.00 0.00 2.10
1936 2026 3.258971 TGTTTCAAGCAAAAACAGGGG 57.741 42.857 7.08 0.00 40.64 4.79
1937 2027 4.190772 ACATGTTTCAAGCAAAAACAGGG 58.809 39.130 19.93 14.55 46.87 4.45
2027 2118 9.743057 CAAATCAGTTGTTGGTTATGTCTTTTA 57.257 29.630 0.00 0.00 32.08 1.52
2044 2135 4.021719 CCAGCATCCAGAAACAAATCAGTT 60.022 41.667 0.00 0.00 0.00 3.16
2045 2136 3.508793 CCAGCATCCAGAAACAAATCAGT 59.491 43.478 0.00 0.00 0.00 3.41
2083 2192 1.142474 GCATTGAGCAACAAACAGGC 58.858 50.000 0.86 0.00 44.79 4.85
2106 2215 2.959465 AAACTAGGCAAGCAGGAACT 57.041 45.000 0.00 0.00 43.88 3.01
2130 2239 8.555361 CGGATTCAACACCAAATTTGTTTTATT 58.445 29.630 16.73 1.76 34.91 1.40
2205 2314 6.653320 CCAGCCAGAAACAAGTACTATTTGTA 59.347 38.462 9.22 0.00 37.77 2.41
2206 2315 5.473504 CCAGCCAGAAACAAGTACTATTTGT 59.526 40.000 9.22 1.73 40.30 2.83
2207 2316 5.106157 CCCAGCCAGAAACAAGTACTATTTG 60.106 44.000 9.22 1.12 0.00 2.32
2208 2317 5.010282 CCCAGCCAGAAACAAGTACTATTT 58.990 41.667 0.00 0.00 0.00 1.40
2227 2338 0.465097 CATAGGCAAGCTGACCCCAG 60.465 60.000 1.67 0.00 43.22 4.45
2236 2347 6.973229 ACAAATTTTCAATCATAGGCAAGC 57.027 33.333 0.00 0.00 0.00 4.01
2251 2362 7.598493 ACGCATTTAGTGAGCAATACAAATTTT 59.402 29.630 0.00 0.00 0.00 1.82
2304 2418 5.960113 ACACACAAGCAAAATACACAGAAA 58.040 33.333 0.00 0.00 0.00 2.52
2307 2421 4.026640 GCAACACACAAGCAAAATACACAG 60.027 41.667 0.00 0.00 0.00 3.66
2376 2490 4.139038 AGGCAAATCAAATGCAAAGCTTT 58.861 34.783 5.69 5.69 45.60 3.51
2392 2506 3.883830 TTCTGTTTTCAGCAAGGCAAA 57.116 38.095 0.00 0.00 46.59 3.68
2414 2528 8.661257 ACAAAAACAGTGCCAAAAATAGTTTAC 58.339 29.630 0.00 0.00 0.00 2.01
2415 2529 8.660373 CACAAAAACAGTGCCAAAAATAGTTTA 58.340 29.630 0.00 0.00 0.00 2.01
2455 2569 4.071423 CACATGAAGTCACAATGGTGGTA 58.929 43.478 0.00 0.00 45.32 3.25
2477 2591 2.616960 TGTGCATCATACGACCTGTTC 58.383 47.619 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.